---
_id: '709'
abstract:
- lang: eng
text: Adipose tissues play key roles in energy homeostasis. Brown adipocytes and
beige adipocytes in white adipose tissue (WAT) share the similar characters of
thermogenesis, both of them could be potential targets for obesity management.
Several thermo-sensitive transient receptor potential channels (thermoTRPs) are
shown to be involved in adipocyte biology. However, the expression pattern of
thermoTRPs in adipose tissues from obese mice is still unknown. The mRNA expression
of thermoTRPs in subcutaneous WAT (sWAT) and interscapular brown adipose tissue
(iBAT) from lean and obese mice were measured using reverse transcriptase-quantitative
PCRs (RT-qPCR). The results demonstrated that all 10 thermoTRPs are expressed
in both iBAT and sWAT, and without significant difference in the mRNA expression
level of thermoTRPs between these two tissues. Moreover, Trpv1 and Trpv3 mRNA
expression levels in both iBAT and sWAT were significantly decreased in high fat
diet (HFD)-induced obese mice and db/db (leptin receptor deficient) mice. Trpm2
mRNA expression level was significantly decreased only in sWAT from HFD-induced
obese mice and db/db mice. On the other hand, Trpv2 and Trpv4 mRNA expression
levels in iBAT and sWAT were significantly increased in HFD-induced obese mice
and db/db mice. Taken together, we conclude that all 10 thermoTRPs are expressed
in iBAT and sWAT. And several thermoTRPs differentially expressed in adipose tissues
from HFD-induced obese mice and db/db mice, suggesting a potential involvement
in anti-obesity regulations.
author:
- first_name: Wuping
full_name: Sun, Wuping
last_name: Sun
- first_name: Chen
full_name: Li, Chen
last_name: Li
- first_name: Yonghong
full_name: Zhang, Yonghong
last_name: Zhang
- first_name: Changyu
full_name: Jiang, Changyu
last_name: Jiang
- first_name: Ming-Zhu
full_name: Zhai, Ming-Zhu
id: 34009CFA-F248-11E8-B48F-1D18A9856A87
last_name: Zhai
- first_name: Qian
full_name: Zhou, Qian
last_name: Zhou
- first_name: Lizu
full_name: Xiao, Lizu
last_name: Xiao
- first_name: Qiwen
full_name: Deng, Qiwen
last_name: Deng
citation:
ama: Sun W, Li C, Zhang Y, et al. Gene expression changes of thermo sensitive transient
receptor potential channels in obese mice. Cell Biology International.
2017;41(8):908-913. doi:10.1002/cbin.10783
apa: Sun, W., Li, C., Zhang, Y., Jiang, C., Zhai, M.-Z., Zhou, Q., … Deng, Q. (2017).
Gene expression changes of thermo sensitive transient receptor potential channels
in obese mice. Cell Biology International. Wiley-Blackwell. https://doi.org/10.1002/cbin.10783
chicago: Sun, Wuping, Chen Li, Yonghong Zhang, Changyu Jiang, Ming-Zhu Zhai, Qian
Zhou, Lizu Xiao, and Qiwen Deng. “Gene Expression Changes of Thermo Sensitive
Transient Receptor Potential Channels in Obese Mice.” Cell Biology International.
Wiley-Blackwell, 2017. https://doi.org/10.1002/cbin.10783.
ieee: W. Sun et al., “Gene expression changes of thermo sensitive transient
receptor potential channels in obese mice,” Cell Biology International,
vol. 41, no. 8. Wiley-Blackwell, pp. 908–913, 2017.
ista: Sun W, Li C, Zhang Y, Jiang C, Zhai M-Z, Zhou Q, Xiao L, Deng Q. 2017. Gene
expression changes of thermo sensitive transient receptor potential channels in
obese mice. Cell Biology International. 41(8), 908–913.
mla: Sun, Wuping, et al. “Gene Expression Changes of Thermo Sensitive Transient
Receptor Potential Channels in Obese Mice.” Cell Biology International,
vol. 41, no. 8, Wiley-Blackwell, 2017, pp. 908–13, doi:10.1002/cbin.10783.
short: W. Sun, C. Li, Y. Zhang, C. Jiang, M.-Z. Zhai, Q. Zhou, L. Xiao, Q. Deng,
Cell Biology International 41 (2017) 908–913.
date_created: 2018-12-11T11:48:04Z
date_published: 2017-08-01T00:00:00Z
date_updated: 2021-01-12T08:11:47Z
day: '01'
department:
- _id: RySh
doi: 10.1002/cbin.10783
intvolume: ' 41'
issue: '8'
language:
- iso: eng
month: '08'
oa_version: None
page: 908 - 913
publication: Cell Biology International
publication_identifier:
issn:
- '10656995'
publication_status: published
publisher: Wiley-Blackwell
publist_id: '6981'
quality_controlled: '1'
scopus_import: 1
status: public
title: Gene expression changes of thermo sensitive transient receptor potential channels
in obese mice
type: journal_article
user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87
volume: 41
year: '2017'
...
---
_id: '710'
abstract:
- lang: eng
text: 'We revisit the problem of estimating entropy of discrete distributions from
independent samples, studied recently by Acharya, Orlitsky, Suresh and Tyagi (SODA
2015), improving their upper and lower bounds on the necessary sample size n.
For estimating Renyi entropy of order alpha, up to constant accuracy and error
probability, we show the following * Upper bounds n = O(1) 2^{(1-1/alpha)H_alpha}
for integer alpha>1, as the worst case over distributions with Renyi entropy
equal to H_alpha. * Lower bounds n = Omega(1) K^{1-1/alpha} for any real alpha>1,
with the constant being an inverse polynomial of the accuracy, as the worst case
over all distributions on K elements. Our upper bounds essentially replace the
alphabet size by a factor exponential in the entropy, which offers improvements
especially in low or medium entropy regimes (interesting for example in anomaly
detection). As for the lower bounds, our proof explicitly shows how the complexity
depends on both alphabet and accuracy, partially solving the open problem posted
in previous works. The argument for upper bounds derives a clean identity for
the variance of falling-power sum of a multinomial distribution. Our approach
for lower bounds utilizes convex optimization to find a distribution with possibly
worse estimation performance, and may be of independent interest as a tool to
work with Le Cam’s two point method. '
alternative_title:
- LIPIcs
article_number: '20'
author:
- first_name: Maciej
full_name: Obremski, Maciej
last_name: Obremski
- first_name: Maciej
full_name: Skórski, Maciej
id: EC09FA6A-02D0-11E9-8223-86B7C91467DD
last_name: Skórski
citation:
ama: 'Obremski M, Skórski M. Renyi entropy estimation revisited. In: Vol 81. Schloss
Dagstuhl - Leibniz-Zentrum für Informatik; 2017. doi:10.4230/LIPIcs.APPROX-RANDOM.2017.20'
apa: 'Obremski, M., & Skórski, M. (2017). Renyi entropy estimation revisited
(Vol. 81). Presented at the 20th International Workshop on Approximation Algorithms
for Combinatorial Optimization Problems, APPROX, Berkeley, USA: Schloss Dagstuhl
- Leibniz-Zentrum für Informatik. https://doi.org/10.4230/LIPIcs.APPROX-RANDOM.2017.20'
chicago: Obremski, Maciej, and Maciej Skórski. “Renyi Entropy Estimation Revisited,”
Vol. 81. Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2017. https://doi.org/10.4230/LIPIcs.APPROX-RANDOM.2017.20.
ieee: M. Obremski and M. Skórski, “Renyi entropy estimation revisited,” presented
at the 20th International Workshop on Approximation Algorithms for Combinatorial
Optimization Problems, APPROX, Berkeley, USA, 2017, vol. 81.
ista: Obremski M, Skórski M. 2017. Renyi entropy estimation revisited. 20th International
Workshop on Approximation Algorithms for Combinatorial Optimization Problems,
APPROX, LIPIcs, vol. 81, 20.
mla: Obremski, Maciej, and Maciej Skórski. Renyi Entropy Estimation Revisited.
Vol. 81, 20, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2017, doi:10.4230/LIPIcs.APPROX-RANDOM.2017.20.
short: M. Obremski, M. Skórski, in:, Schloss Dagstuhl - Leibniz-Zentrum für Informatik,
2017.
conference:
end_date: 2017-08-18
location: Berkeley, USA
name: 20th International Workshop on Approximation Algorithms for Combinatorial
Optimization Problems, APPROX
start_date: 2017-08-18
date_created: 2018-12-11T11:48:04Z
date_published: 2017-08-01T00:00:00Z
date_updated: 2021-01-12T08:11:50Z
day: '01'
ddc:
- '005'
- '600'
department:
- _id: KrPi
doi: 10.4230/LIPIcs.APPROX-RANDOM.2017.20
ec_funded: 1
file:
- access_level: open_access
checksum: 89225c7dcec2c93838458c9102858985
content_type: application/pdf
creator: system
date_created: 2018-12-12T10:13:10Z
date_updated: 2020-07-14T12:47:49Z
file_id: '4991'
file_name: IST-2017-888-v1+1_LIPIcs-APPROX-RANDOM-2017-20.pdf
file_size: 604813
relation: main_file
file_date_updated: 2020-07-14T12:47:49Z
has_accepted_license: '1'
intvolume: ' 81'
language:
- iso: eng
license: https://creativecommons.org/licenses/by/4.0/
month: '08'
oa: 1
oa_version: Published Version
project:
- _id: 258AA5B2-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '682815'
name: Teaching Old Crypto New Tricks
publication_identifier:
issn:
- '18688969'
publication_status: published
publisher: Schloss Dagstuhl - Leibniz-Zentrum für Informatik
publist_id: '6979'
pubrep_id: '888'
quality_controlled: '1'
scopus_import: 1
status: public
title: Renyi entropy estimation revisited
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: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87
volume: 81
year: '2017'
...
---
_id: '713'
abstract:
- lang: eng
text: To determine the dynamics of allelic-specific expression during mouse development,
we analyzed RNA-seq data from 23 F1 tissues from different developmental stages,
including 19 female tissues allowing X chromosome inactivation (XCI) escapers
to also be detected. We demonstrate that allelic expression arising from genetic
or epigenetic differences is highly tissue-specific. We find that tissue-specific
strain-biased gene expression may be regulated by tissue-specific enhancers or
by post-transcriptional differences in stability between the alleles. We also
find that escape from X-inactivation is tissue-specific, with leg muscle showing
an unexpectedly high rate of XCI escapers. By surveying a range of tissues during
development, and performing extensive validation, we are able to provide a high
confidence list of mouse imprinted genes including 18 novel genes. This shows
that cluster size varies dynamically during development and can be substantially
larger than previously thought, with the Igf2r cluster extending over 10 Mb in
placenta.
article_number: e25125
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: Dyniel
full_name: Wenzel, Dyniel
last_name: Wenzel
- first_name: Verena
full_name: Sigl, Verena
last_name: Sigl
- first_name: Philipp
full_name: Bammer, Philipp
last_name: Bammer
- first_name: Markus
full_name: Muckenhuber, Markus
last_name: Muckenhuber
- first_name: Daniela
full_name: Mayer, Daniela
last_name: Mayer
- first_name: Tomasz
full_name: Kulinski, Tomasz
last_name: Kulinski
- first_name: Hans
full_name: Theussl, Hans
last_name: Theussl
- first_name: Josef
full_name: Penninger, Josef
last_name: Penninger
- first_name: Christoph
full_name: Bock, Christoph
last_name: Bock
- first_name: Denise
full_name: Barlow, Denise
last_name: Barlow
- first_name: Florian
full_name: Pauler, Florian
id: 48EA0138-F248-11E8-B48F-1D18A9856A87
last_name: Pauler
- first_name: Quanah
full_name: Hudson, Quanah
last_name: Hudson
citation:
ama: Andergassen D, Dotter C, Wenzel D, et al. Mapping the mouse Allelome reveals
tissue specific regulation of allelic expression. eLife. 2017;6. doi:10.7554/eLife.25125
apa: Andergassen, D., Dotter, C., Wenzel, D., Sigl, V., Bammer, P., Muckenhuber,
M., … Hudson, Q. (2017). Mapping the mouse Allelome reveals tissue specific regulation
of allelic expression. ELife. eLife Sciences Publications. https://doi.org/10.7554/eLife.25125
chicago: Andergassen, Daniel, Christoph Dotter, Dyniel Wenzel, Verena Sigl, Philipp
Bammer, Markus Muckenhuber, Daniela Mayer, et al. “Mapping the Mouse Allelome
Reveals Tissue Specific Regulation of Allelic Expression.” ELife. eLife
Sciences Publications, 2017. https://doi.org/10.7554/eLife.25125.
ieee: D. Andergassen et al., “Mapping the mouse Allelome reveals tissue specific
regulation of allelic expression,” eLife, vol. 6. eLife Sciences Publications,
2017.
ista: Andergassen D, Dotter C, Wenzel D, Sigl V, Bammer P, Muckenhuber M, Mayer
D, Kulinski T, Theussl H, Penninger J, Bock C, Barlow D, Pauler F, Hudson Q. 2017.
Mapping the mouse Allelome reveals tissue specific regulation of allelic expression.
eLife. 6, e25125.
mla: Andergassen, Daniel, et al. “Mapping the Mouse Allelome Reveals Tissue Specific
Regulation of Allelic Expression.” ELife, vol. 6, e25125, eLife Sciences
Publications, 2017, doi:10.7554/eLife.25125.
short: D. Andergassen, C. Dotter, D. Wenzel, V. Sigl, P. Bammer, M. Muckenhuber,
D. Mayer, T. Kulinski, H. Theussl, J. Penninger, C. Bock, D. Barlow, F. Pauler,
Q. Hudson, ELife 6 (2017).
date_created: 2018-12-11T11:48:05Z
date_published: 2017-08-14T00:00:00Z
date_updated: 2021-01-12T08:11:57Z
day: '14'
ddc:
- '576'
department:
- _id: GaNo
- _id: SiHi
doi: 10.7554/eLife.25125
file:
- access_level: open_access
checksum: 1ace3462e64a971b9ead896091829549
content_type: application/pdf
creator: system
date_created: 2018-12-12T10:13:36Z
date_updated: 2020-07-14T12:47:50Z
file_id: '5020'
file_name: IST-2017-885-v1+1_elife-25125-figures-v2.pdf
file_size: 6399510
relation: main_file
- access_level: open_access
checksum: 6241dc31eeb87b03facadec3a53a6827
content_type: application/pdf
creator: system
date_created: 2018-12-12T10:13:36Z
date_updated: 2020-07-14T12:47:50Z
file_id: '5021'
file_name: IST-2017-885-v1+2_elife-25125-v2.pdf
file_size: 4264398
relation: main_file
file_date_updated: 2020-07-14T12:47:50Z
has_accepted_license: '1'
intvolume: ' 6'
language:
- iso: eng
month: '08'
oa: 1
oa_version: Published Version
project:
- _id: 25E9AF9E-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: P27201-B22
name: Revealing the mechanisms underlying drug interactions
publication: eLife
publication_identifier:
issn:
- 2050084X
publication_status: published
publisher: eLife Sciences Publications
publist_id: '6971'
pubrep_id: '885'
quality_controlled: '1'
scopus_import: 1
status: public
title: Mapping the mouse Allelome reveals tissue specific regulation of allelic 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: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 6
year: '2017'
...
---
_id: '711'
abstract:
- lang: eng
text: Nested weighted automata (NWA) present a robust and convenient automata-theoretic
formalism for quantitative specifications. Previous works have considered NWA
that processed input words only in the forward direction. It is natural to allow
the automata to process input words backwards as well, for example, to measure
the maximal or average time between a response and the preceding request. We therefore
introduce and study bidirectional NWA that can process input words in both directions.
First, we show that bidirectional NWA can express interesting quantitative properties
that are not expressible by forward-only NWA. Second, for the fundamental decision
problems of emptiness and universality, we establish decidability and complexity
results for the new framework which match the best-known results for the special
case of forward-only NWA. Thus, for NWA, the increased expressiveness of bidirectionality
is achieved at no additional computational complexity. This is in stark contrast
to the unweighted case, where bidirectional finite automata are no more expressive
but exponentially more succinct than their forward-only counterparts.
alternative_title:
- LIPIcs
article_number: '5'
author:
- first_name: Krishnendu
full_name: Chatterjee, Krishnendu
id: 2E5DCA20-F248-11E8-B48F-1D18A9856A87
last_name: Chatterjee
orcid: 0000-0002-4561-241X
- first_name: Thomas A
full_name: Henzinger, Thomas A
id: 40876CD8-F248-11E8-B48F-1D18A9856A87
last_name: Henzinger
orcid: 0000−0002−2985−7724
- first_name: Jan
full_name: Otop, Jan
last_name: Otop
citation:
ama: 'Chatterjee K, Henzinger TA, Otop J. Bidirectional nested weighted automata.
In: Vol 85. Schloss Dagstuhl - Leibniz-Zentrum für Informatik; 2017. doi:10.4230/LIPIcs.CONCUR.2017.5'
apa: 'Chatterjee, K., Henzinger, T. A., & Otop, J. (2017). Bidirectional nested
weighted automata (Vol. 85). Presented at the 28th International Conference on
Concurrency Theory, CONCUR, Berlin, Germany: Schloss Dagstuhl - Leibniz-Zentrum
für Informatik. https://doi.org/10.4230/LIPIcs.CONCUR.2017.5'
chicago: Chatterjee, Krishnendu, Thomas A Henzinger, and Jan Otop. “Bidirectional
Nested Weighted Automata,” Vol. 85. Schloss Dagstuhl - Leibniz-Zentrum für Informatik,
2017. https://doi.org/10.4230/LIPIcs.CONCUR.2017.5.
ieee: K. Chatterjee, T. A. Henzinger, and J. Otop, “Bidirectional nested weighted
automata,” presented at the 28th International Conference on Concurrency Theory,
CONCUR, Berlin, Germany, 2017, vol. 85.
ista: Chatterjee K, Henzinger TA, Otop J. 2017. Bidirectional nested weighted automata.
28th International Conference on Concurrency Theory, CONCUR, LIPIcs, vol. 85,
5.
mla: Chatterjee, Krishnendu, et al. Bidirectional Nested Weighted Automata.
Vol. 85, 5, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2017, doi:10.4230/LIPIcs.CONCUR.2017.5.
short: K. Chatterjee, T.A. Henzinger, J. Otop, in:, Schloss Dagstuhl - Leibniz-Zentrum
für Informatik, 2017.
conference:
end_date: 2017-09-08
location: Berlin, Germany
name: 28th International Conference on Concurrency Theory, CONCUR
start_date: 2017-09-05
date_created: 2018-12-11T11:48:04Z
date_published: 2017-08-01T00:00:00Z
date_updated: 2021-01-12T08:11:53Z
day: '01'
ddc:
- '004'
- '005'
department:
- _id: KrCh
- _id: ToHe
doi: 10.4230/LIPIcs.CONCUR.2017.5
file:
- access_level: open_access
checksum: d2bda4783821a6358333fe27f11f4737
content_type: application/pdf
creator: system
date_created: 2018-12-12T10:08:02Z
date_updated: 2020-07-14T12:47:49Z
file_id: '4661'
file_name: IST-2017-886-v1+1_LIPIcs-CONCUR-2017-5.pdf
file_size: 570294
relation: main_file
file_date_updated: 2020-07-14T12:47:49Z
has_accepted_license: '1'
intvolume: ' 85'
language:
- iso: eng
month: '08'
oa: 1
oa_version: Published Version
publication_identifier:
issn:
- '18688969'
publication_status: published
publisher: Schloss Dagstuhl - Leibniz-Zentrum für Informatik
publist_id: '6976'
pubrep_id: '886'
quality_controlled: '1'
scopus_import: 1
status: public
title: Bidirectional nested weighted automata
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: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87
volume: 85
year: '2017'
...
---
_id: '712'
abstract:
- lang: eng
text: 'We establish a weak–strong uniqueness principle for solutions to entropy-dissipating
reaction–diffusion equations: As long as a strong solution to the reaction–diffusion
equation exists, any weak solution and even any renormalized solution must coincide
with this strong solution. Our assumptions on the reaction rates are just the
entropy condition and local Lipschitz continuity; in particular, we do not impose
any growth restrictions on the reaction rates. Therefore, our result applies to
any single reversible reaction with mass-action kinetics as well as to systems
of reversible reactions with mass-action kinetics satisfying the detailed balance
condition. Renormalized solutions are known to exist globally in time for reaction–diffusion
equations with entropy-dissipating reaction rates; in contrast, the global-in-time
existence of weak solutions is in general still an open problem–even for smooth
data–, thereby motivating the study of renormalized solutions. The key ingredient
of our result is a careful adjustment of the usual relative entropy functional,
whose evolution cannot be controlled properly for weak solutions or renormalized
solutions.'
author:
- first_name: Julian L
full_name: Fischer, Julian L
id: 2C12A0B0-F248-11E8-B48F-1D18A9856A87
last_name: Fischer
orcid: 0000-0002-0479-558X
citation:
ama: 'Fischer JL. Weak–strong uniqueness of solutions to entropy dissipating reaction–diffusion
equations. Nonlinear Analysis: Theory, Methods and Applications. 2017;159:181-207.
doi:10.1016/j.na.2017.03.001'
apa: 'Fischer, J. L. (2017). Weak–strong uniqueness of solutions to entropy dissipating
reaction–diffusion equations. Nonlinear Analysis: Theory, Methods and Applications.
Elsevier. https://doi.org/10.1016/j.na.2017.03.001'
chicago: 'Fischer, Julian L. “Weak–Strong Uniqueness of Solutions to Entropy Dissipating
Reaction–Diffusion Equations.” Nonlinear Analysis: Theory, Methods and Applications.
Elsevier, 2017. https://doi.org/10.1016/j.na.2017.03.001.'
ieee: 'J. L. Fischer, “Weak–strong uniqueness of solutions to entropy dissipating
reaction–diffusion equations,” Nonlinear Analysis: Theory, Methods and Applications,
vol. 159. Elsevier, pp. 181–207, 2017.'
ista: 'Fischer JL. 2017. Weak–strong uniqueness of solutions to entropy dissipating
reaction–diffusion equations. Nonlinear Analysis: Theory, Methods and Applications.
159, 181–207.'
mla: 'Fischer, Julian L. “Weak–Strong Uniqueness of Solutions to Entropy Dissipating
Reaction–Diffusion Equations.” Nonlinear Analysis: Theory, Methods and Applications,
vol. 159, Elsevier, 2017, pp. 181–207, doi:10.1016/j.na.2017.03.001.'
short: 'J.L. Fischer, Nonlinear Analysis: Theory, Methods and Applications 159 (2017)
181–207.'
date_created: 2018-12-11T11:48:05Z
date_published: 2017-08-01T00:00:00Z
date_updated: 2021-01-12T08:11:55Z
day: '01'
department:
- _id: JuFi
doi: 10.1016/j.na.2017.03.001
intvolume: ' 159'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/1703.00730
month: '08'
oa: 1
oa_version: Submitted Version
page: 181 - 207
publication: 'Nonlinear Analysis: Theory, Methods and Applications'
publication_identifier:
issn:
- 0362546X
publication_status: published
publisher: Elsevier
publist_id: '6975'
quality_controlled: '1'
scopus_import: 1
status: public
title: Weak–strong uniqueness of solutions to entropy dissipating reaction–diffusion
equations
type: journal_article
user_id: 4435EBFC-F248-11E8-B48F-1D18A9856A87
volume: 159
year: '2017'
...
---
_id: '714'
abstract:
- lang: eng
text: Background HIV-1 infection and drug abuse are frequently co-morbid and their
association greatly increases the severity of HIV-1-induced neuropathology. While
nucleus accumbens (NAcc) function is severely perturbed by drugs of abuse, little
is known about how HIV-1 infection affects NAcc. Methods We used calcium and voltage
imaging to investigate the effect of HIV-1 trans-activator of transcription (Tat)
on rat NAcc. Based on previous neuronal studies, we hypothesized that Tat modulates
intracellular Ca2+ homeostasis of NAcc neurons. Results We provide evidence that
Tat triggers a Ca2+ signaling cascade in NAcc medium spiny neurons (MSN) expressing
D1-like dopamine receptors leading to neuronal depolarization. Firstly, Tat induced
inositol 1,4,5-trisphsophate (IP3) receptor-mediated Ca2+ release from endoplasmic
reticulum, followed by Ca2+ and Na+ influx via transient receptor potential canonical
channels. The influx of cations depolarizes the membrane promoting additional
Ca2+ entry through voltage-gated P/Q-type Ca2+ channels and opening of tetrodotoxin-sensitive
Na+ channels. By activating this mechanism, Tat elicits a feed-forward depolarization
increasing the excitability of D1-phosphatidylinositol-linked NAcc MSN. We previously
found that cocaine targets NAcc neurons directly (independent of the inhibition
of dopamine transporter) only when IP3-generating mechanisms are concomitantly
initiated. When tested here, cocaine produced a dose-dependent potentiation of
the effect of Tat on cytosolic Ca2+. Conclusion We describe for the first time
a HIV-1 Tat-triggered Ca2+ signaling in MSN of NAcc involving TRPC and depolarization
and a potentiation of the effect of Tat by cocaine, which may be relevant for
the reward axis in cocaine-abusing HIV-1-positive patients.
acknowledgement: This work was supported by the National Institutes of Health grants
DA035926 (to MEA), and P30DA013429 (to EMU).
article_processing_charge: No
article_type: original
author:
- first_name: Gabriela
full_name: Brailoiu, Gabriela
last_name: Brailoiu
- first_name: Elena
full_name: Deliu, Elena
id: 37A40D7E-F248-11E8-B48F-1D18A9856A87
last_name: Deliu
orcid: 0000-0002-7370-5293
- first_name: Jeffrey
full_name: Barr, Jeffrey
last_name: Barr
- first_name: Linda
full_name: Console Bram, Linda
last_name: Console Bram
- first_name: Alexandra
full_name: Ciuciu, Alexandra
last_name: Ciuciu
- first_name: Mary
full_name: Abood, Mary
last_name: Abood
- first_name: Ellen
full_name: Unterwald, Ellen
last_name: Unterwald
- first_name: Eugen
full_name: Brǎiloiu, Eugen
last_name: Brǎiloiu
citation:
ama: Brailoiu G, Deliu E, Barr J, et al. HIV Tat excites D1 receptor-like expressing
neurons from rat nucleus accumbens. Drug and Alcohol Dependence. 2017;178:7-14.
doi:10.1016/j.drugalcdep.2017.04.015
apa: Brailoiu, G., Deliu, E., Barr, J., Console Bram, L., Ciuciu, A., Abood, M.,
… Brǎiloiu, E. (2017). HIV Tat excites D1 receptor-like expressing neurons from
rat nucleus accumbens. Drug and Alcohol Dependence. Elsevier. https://doi.org/10.1016/j.drugalcdep.2017.04.015
chicago: Brailoiu, Gabriela, Elena Deliu, Jeffrey Barr, Linda Console Bram, Alexandra
Ciuciu, Mary Abood, Ellen Unterwald, and Eugen Brǎiloiu. “HIV Tat Excites D1 Receptor-like
Expressing Neurons from Rat Nucleus Accumbens.” Drug and Alcohol Dependence.
Elsevier, 2017. https://doi.org/10.1016/j.drugalcdep.2017.04.015.
ieee: G. Brailoiu et al., “HIV Tat excites D1 receptor-like expressing neurons
from rat nucleus accumbens,” Drug and Alcohol Dependence, vol. 178. Elsevier,
pp. 7–14, 2017.
ista: Brailoiu G, Deliu E, Barr J, Console Bram L, Ciuciu A, Abood M, Unterwald
E, Brǎiloiu E. 2017. HIV Tat excites D1 receptor-like expressing neurons from
rat nucleus accumbens. Drug and Alcohol Dependence. 178, 7–14.
mla: Brailoiu, Gabriela, et al. “HIV Tat Excites D1 Receptor-like Expressing Neurons
from Rat Nucleus Accumbens.” Drug and Alcohol Dependence, vol. 178, Elsevier,
2017, pp. 7–14, doi:10.1016/j.drugalcdep.2017.04.015.
short: G. Brailoiu, E. Deliu, J. Barr, L. Console Bram, A. Ciuciu, M. Abood, E.
Unterwald, E. Brǎiloiu, Drug and Alcohol Dependence 178 (2017) 7–14.
date_created: 2018-12-11T11:48:05Z
date_published: 2017-09-01T00:00:00Z
date_updated: 2021-01-12T08:12:00Z
day: '01'
department:
- _id: GaNo
doi: 10.1016/j.drugalcdep.2017.04.015
external_id:
pmid:
- '28623807'
intvolume: ' 178'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5797705
month: '09'
oa: 1
oa_version: Submitted Version
page: 7 - 14
pmid: 1
publication: Drug and Alcohol Dependence
publication_identifier:
issn:
- '03768716'
publication_status: published
publisher: Elsevier
publist_id: '6967'
quality_controlled: '1'
scopus_import: 1
status: public
title: HIV Tat excites D1 receptor-like expressing neurons from rat nucleus accumbens
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 178
year: '2017'
...
---
_id: '715'
abstract:
- lang: eng
text: D-cycloserine ameliorates breathing abnormalities and survival rate in a mouse
model of Rett syndrome.
article_number: aao4218
author:
- first_name: Gaia
full_name: Novarino, Gaia
id: 3E57A680-F248-11E8-B48F-1D18A9856A87
last_name: Novarino
orcid: 0000-0002-7673-7178
citation:
ama: Novarino G. More excitation for Rett syndrome. Science Translational Medicine.
2017;9(405). doi:10.1126/scitranslmed.aao4218
apa: Novarino, G. (2017). More excitation for Rett syndrome. Science Translational
Medicine. American Association for the Advancement of Science. https://doi.org/10.1126/scitranslmed.aao4218
chicago: Novarino, Gaia. “More Excitation for Rett Syndrome.” Science Translational
Medicine. American Association for the Advancement of Science, 2017. https://doi.org/10.1126/scitranslmed.aao4218.
ieee: G. Novarino, “More excitation for Rett syndrome,” Science Translational
Medicine, vol. 9, no. 405. American Association for the Advancement of Science,
2017.
ista: Novarino G. 2017. More excitation for Rett syndrome. Science Translational
Medicine. 9(405), aao4218.
mla: Novarino, Gaia. “More Excitation for Rett Syndrome.” Science Translational
Medicine, vol. 9, no. 405, aao4218, American Association for the Advancement
of Science, 2017, doi:10.1126/scitranslmed.aao4218.
short: G. Novarino, Science Translational Medicine 9 (2017).
date_created: 2018-12-11T11:48:06Z
date_published: 2017-08-30T00:00:00Z
date_updated: 2021-01-12T08:12:04Z
day: '30'
department:
- _id: GaNo
doi: 10.1126/scitranslmed.aao4218
intvolume: ' 9'
issue: '405'
language:
- iso: eng
month: '08'
oa_version: None
publication: Science Translational Medicine
publication_identifier:
issn:
- '19466234'
publication_status: published
publisher: American Association for the Advancement of Science
publist_id: '6968'
quality_controlled: '1'
scopus_import: 1
status: public
title: More excitation for Rett syndrome
type: journal_article
user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87
volume: 9
year: '2017'
...
---
_id: '716'
abstract:
- lang: eng
text: 'Two-player games on graphs are central in many problems in formal verification
and program analysis, such as synthesis and verification of open systems. In this
work, we consider solving recursive game graphs (or pushdown game graphs) that
model the control flow of sequential programs with recursion.While pushdown games
have been studied before with qualitative objectives-such as reachability and
?-regular objectives- in this work, we study for the first time such games with
the most well-studied quantitative objective, the mean-payoff objective. In pushdown
games, two types of strategies are relevant: (1) global strategies, which depend
on the entire global history; and (2) modular strategies, which have only local
memory and thus do not depend on the context of invocation but rather only on
the history of the current invocation of the module. Our main results are as follows:
(1) One-player pushdown games with mean-payoff objectives under global strategies
are decidable in polynomial time. (2) Two-player pushdown games with mean-payoff
objectives under global strategies are undecidable. (3) One-player pushdown games
with mean-payoff objectives under modular strategies are NP-hard. (4) Two-player
pushdown games with mean-payoff objectives under modular strategies can be solved
in NP (i.e., both one-player and two-player pushdown games with mean-payoff objectives
under modular strategies are NP-complete). We also establish the optimal strategy
complexity by showing that global strategies for mean-payoff objectives require
infinite memory even in one-player pushdown games and memoryless modular strategies
are sufficient in two-player pushdown games. Finally, we also show that all the
problems have the same complexity if the stack boundedness condition is added,
where along with the mean-payoff objective the player must also ensure that the
stack height is bounded.'
article_type: original
author:
- first_name: Krishnendu
full_name: Chatterjee, Krishnendu
id: 2E5DCA20-F248-11E8-B48F-1D18A9856A87
last_name: Chatterjee
orcid: 0000-0002-4561-241X
- first_name: Yaron
full_name: Velner, Yaron
last_name: Velner
citation:
ama: Chatterjee K, Velner Y. The complexity of mean-payoff pushdown games. Journal
of the ACM. 2017;64(5):34. doi:10.1145/3121408
apa: Chatterjee, K., & Velner, Y. (2017). The complexity of mean-payoff pushdown
games. Journal of the ACM. ACM. https://doi.org/10.1145/3121408
chicago: Chatterjee, Krishnendu, and Yaron Velner. “The Complexity of Mean-Payoff
Pushdown Games.” Journal of the ACM. ACM, 2017. https://doi.org/10.1145/3121408.
ieee: K. Chatterjee and Y. Velner, “The complexity of mean-payoff pushdown games,”
Journal of the ACM, vol. 64, no. 5. ACM, p. 34, 2017.
ista: Chatterjee K, Velner Y. 2017. The complexity of mean-payoff pushdown games.
Journal of the ACM. 64(5), 34.
mla: Chatterjee, Krishnendu, and Yaron Velner. “The Complexity of Mean-Payoff Pushdown
Games.” Journal of the ACM, vol. 64, no. 5, ACM, 2017, p. 34, doi:10.1145/3121408.
short: K. Chatterjee, Y. Velner, Journal of the ACM 64 (2017) 34.
date_created: 2018-12-11T11:48:06Z
date_published: 2017-09-01T00:00:00Z
date_updated: 2021-01-12T08:12:08Z
day: '01'
department:
- _id: KrCh
doi: 10.1145/3121408
ec_funded: 1
external_id:
arxiv:
- '1201.2829'
intvolume: ' 64'
issue: '5'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/1201.2829
month: '09'
oa: 1
oa_version: Preprint
page: '34'
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: Journal of the ACM
publication_identifier:
issn:
- '00045411'
publication_status: published
publisher: ACM
publist_id: '6964'
quality_controlled: '1'
scopus_import: 1
status: public
title: The complexity of mean-payoff pushdown games
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 64
year: '2017'
...
---
_id: '717'
abstract:
- lang: eng
text: 'We consider finite-state and recursive game graphs with multidimensional
mean-payoff objectives. In recursive games two types of strategies are relevant:
global strategies and modular strategies. Our contributions are: (1) We show that
finite-state multidimensional mean-payoff games can be solved in polynomial time
if the number of dimensions and the maximal absolute value of weights are fixed;
whereas for arbitrary dimensions the problem is coNP-complete. (2) We show that
one-player recursive games with multidimensional mean-payoff objectives can be
solved in polynomial time. Both above algorithms are based on hyperplane separation
technique. (3) For recursive games we show that under modular strategies the multidimensional
problem is undecidable. We show that if the number of modules, exits, and the
maximal absolute value of the weights are fixed, then one-dimensional recursive
mean-payoff games under modular strategies can be solved in polynomial time, whereas
for unbounded number of exits or modules the problem is NP-hard.'
acknowledgement: 'The research was supported by Austrian Science Fund (FWF) Grant
No. P 23499-N23, FWF NFN Grant No. S11407-N23 (RiSE), ERC Start grant (279307: Graph
Games), Microsoft faculty fellows award, the RICH Model Toolkit (ICT COST Action
IC0901), and was carried out in partial fulfillment of the requirements for the
Ph.D. degree of the second author.'
author:
- first_name: Krishnendu
full_name: Chatterjee, Krishnendu
id: 2E5DCA20-F248-11E8-B48F-1D18A9856A87
last_name: Chatterjee
orcid: 0000-0002-4561-241X
- first_name: Yaron
full_name: Velner, Yaron
last_name: Velner
citation:
ama: Chatterjee K, Velner Y. Hyperplane separation technique for multidimensional
mean-payoff games. Journal of Computer and System Sciences. 2017;88:236-259.
doi:10.1016/j.jcss.2017.04.005
apa: Chatterjee, K., & Velner, Y. (2017). Hyperplane separation technique for
multidimensional mean-payoff games. Journal of Computer and System Sciences.
Academic Press. https://doi.org/10.1016/j.jcss.2017.04.005
chicago: Chatterjee, Krishnendu, and Yaron Velner. “Hyperplane Separation Technique
for Multidimensional Mean-Payoff Games.” Journal of Computer and System Sciences.
Academic Press, 2017. https://doi.org/10.1016/j.jcss.2017.04.005.
ieee: K. Chatterjee and Y. Velner, “Hyperplane separation technique for multidimensional
mean-payoff games,” Journal of Computer and System Sciences, vol. 88. Academic
Press, pp. 236–259, 2017.
ista: Chatterjee K, Velner Y. 2017. Hyperplane separation technique for multidimensional
mean-payoff games. Journal of Computer and System Sciences. 88, 236–259.
mla: Chatterjee, Krishnendu, and Yaron Velner. “Hyperplane Separation Technique
for Multidimensional Mean-Payoff Games.” Journal of Computer and System Sciences,
vol. 88, Academic Press, 2017, pp. 236–59, doi:10.1016/j.jcss.2017.04.005.
short: K. Chatterjee, Y. Velner, Journal of Computer and System Sciences 88 (2017)
236–259.
date_created: 2018-12-11T11:48:07Z
date_published: 2017-09-01T00:00:00Z
date_updated: 2023-02-23T10:38:15Z
day: '01'
department:
- _id: KrCh
doi: 10.1016/j.jcss.2017.04.005
ec_funded: 1
intvolume: ' 88'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/1210.3141
month: '09'
oa: 1
oa_version: Preprint
page: 236 - 259
project:
- _id: 2584A770-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: P 23499-N23
name: Modern Graph Algorithmic Techniques in Formal Verification
- _id: 25863FF4-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: S11407
name: Game Theory
- _id: 2581B60A-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '279307'
name: 'Quantitative Graph Games: Theory and Applications'
- _id: 2587B514-B435-11E9-9278-68D0E5697425
name: Microsoft Research Faculty Fellowship
publication: Journal of Computer and System Sciences
publication_status: published
publisher: Academic Press
publist_id: '6963'
quality_controlled: '1'
related_material:
record:
- id: '2329'
relation: earlier_version
status: public
scopus_import: 1
status: public
title: Hyperplane separation technique for multidimensional mean-payoff games
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 88
year: '2017'
...
---
_id: '719'
abstract:
- lang: eng
text: 'The ubiquity of computation in modern machines and devices imposes a need
to assert the correctness of their behavior. Especially in the case of safety-critical
systems, their designers need to take measures that enforce their safe operation.
Formal methods has emerged as a research field that addresses this challenge:
by rigorously proving that all system executions adhere to their specifications,
the correctness of an implementation under concern can be assured. To achieve
this goal, a plethora of techniques are nowadays available, all of which are optimized
for different system types and application domains.'
author:
- first_name: Krishnendu
full_name: Chatterjee, Krishnendu
id: 2E5DCA20-F248-11E8-B48F-1D18A9856A87
last_name: Chatterjee
orcid: 0000-0002-4561-241X
- first_name: Rüdiger
full_name: Ehlers, Rüdiger
last_name: Ehlers
citation:
ama: 'Chatterjee K, Ehlers R. Special issue: Synthesis and SYNT 2014. Acta Informatica.
2017;54(6):543-544. doi:10.1007/s00236-017-0299-0'
apa: 'Chatterjee, K., & Ehlers, R. (2017). Special issue: Synthesis and SYNT
2014. Acta Informatica. Springer. https://doi.org/10.1007/s00236-017-0299-0'
chicago: 'Chatterjee, Krishnendu, and Rüdiger Ehlers. “Special Issue: Synthesis
and SYNT 2014.” Acta Informatica. Springer, 2017. https://doi.org/10.1007/s00236-017-0299-0.'
ieee: 'K. Chatterjee and R. Ehlers, “Special issue: Synthesis and SYNT 2014,” Acta
Informatica, vol. 54, no. 6. Springer, pp. 543–544, 2017.'
ista: 'Chatterjee K, Ehlers R. 2017. Special issue: Synthesis and SYNT 2014. Acta
Informatica. 54(6), 543–544.'
mla: 'Chatterjee, Krishnendu, and Rüdiger Ehlers. “Special Issue: Synthesis and
SYNT 2014.” Acta Informatica, vol. 54, no. 6, Springer, 2017, pp. 543–44,
doi:10.1007/s00236-017-0299-0.'
short: K. Chatterjee, R. Ehlers, Acta Informatica 54 (2017) 543–544.
date_created: 2018-12-11T11:48:07Z
date_published: 2017-09-01T00:00:00Z
date_updated: 2021-01-12T08:12:18Z
day: '01'
department:
- _id: KrCh
doi: 10.1007/s00236-017-0299-0
intvolume: ' 54'
issue: '6'
language:
- iso: eng
month: '09'
oa_version: None
page: 543 - 544
publication: Acta Informatica
publication_identifier:
issn:
- '00015903'
publication_status: published
publisher: Springer
publist_id: '6961'
quality_controlled: '1'
scopus_import: 1
status: public
title: 'Special issue: Synthesis and SYNT 2014'
type: journal_article
user_id: 4435EBFC-F248-11E8-B48F-1D18A9856A87
volume: 54
year: '2017'
...
---
_id: '720'
abstract:
- lang: eng
text: 'Advances in multi-unit recordings pave the way for statistical modeling of
activity patterns in large neural populations. Recent studies have shown that
the summed activity of all neurons strongly shapes the population response. A
separate recent finding has been that neural populations also exhibit criticality,
an anomalously large dynamic range for the probabilities of different population
activity patterns. Motivated by these two observations, we introduce a class of
probabilistic models which takes into account the prior knowledge that the neural
population could be globally coupled and close to critical. These models consist
of an energy function which parametrizes interactions between small groups of
neurons, and an arbitrary positive, strictly increasing, and twice differentiable
function which maps the energy of a population pattern to its probability. We
show that: 1) augmenting a pairwise Ising model with a nonlinearity yields an
accurate description of the activity of retinal ganglion cells which outperforms
previous models based on the summed activity of neurons; 2) prior knowledge that
the population is critical translates to prior expectations about the shape of
the nonlinearity; 3) the nonlinearity admits an interpretation in terms of a continuous
latent variable globally coupling the system whose distribution we can infer from
data. Our method is independent of the underlying system’s state space; hence,
it can be applied to other systems such as natural scenes or amino acid sequences
of proteins which are also known to exhibit criticality.'
article_number: e1005763
article_processing_charge: Yes
author:
- first_name: Jan
full_name: Humplik, Jan
id: 2E9627A8-F248-11E8-B48F-1D18A9856A87
last_name: Humplik
- first_name: Gasper
full_name: Tkacik, Gasper
id: 3D494DCA-F248-11E8-B48F-1D18A9856A87
last_name: Tkacik
orcid: 0000-0002-6699-1455
citation:
ama: Humplik J, Tkačik G. Probabilistic models for neural populations that naturally
capture global coupling and criticality. PLoS Computational Biology. 2017;13(9).
doi:10.1371/journal.pcbi.1005763
apa: Humplik, J., & Tkačik, G. (2017). Probabilistic models for neural populations
that naturally capture global coupling and criticality. PLoS Computational
Biology. Public Library of Science. https://doi.org/10.1371/journal.pcbi.1005763
chicago: Humplik, Jan, and Gašper Tkačik. “Probabilistic Models for Neural Populations
That Naturally Capture Global Coupling and Criticality.” PLoS Computational
Biology. Public Library of Science, 2017. https://doi.org/10.1371/journal.pcbi.1005763.
ieee: J. Humplik and G. Tkačik, “Probabilistic models for neural populations that
naturally capture global coupling and criticality,” PLoS Computational Biology,
vol. 13, no. 9. Public Library of Science, 2017.
ista: Humplik J, Tkačik G. 2017. Probabilistic models for neural populations that
naturally capture global coupling and criticality. PLoS Computational Biology.
13(9), e1005763.
mla: Humplik, Jan, and Gašper Tkačik. “Probabilistic Models for Neural Populations
That Naturally Capture Global Coupling and Criticality.” PLoS Computational
Biology, vol. 13, no. 9, e1005763, Public Library of Science, 2017, doi:10.1371/journal.pcbi.1005763.
short: J. Humplik, G. Tkačik, PLoS Computational Biology 13 (2017).
date_created: 2018-12-11T11:48:08Z
date_published: 2017-09-19T00:00:00Z
date_updated: 2021-01-12T08:12:21Z
day: '19'
ddc:
- '530'
- '571'
department:
- _id: GaTk
doi: 10.1371/journal.pcbi.1005763
file:
- access_level: open_access
checksum: 81107096c19771c36ddbe6f0282a3acb
content_type: application/pdf
creator: system
date_created: 2018-12-12T10:18:30Z
date_updated: 2020-07-14T12:47:53Z
file_id: '5352'
file_name: IST-2017-884-v1+1_journal.pcbi.1005763.pdf
file_size: 14167050
relation: main_file
file_date_updated: 2020-07-14T12:47:53Z
has_accepted_license: '1'
intvolume: ' 13'
issue: '9'
language:
- iso: eng
month: '09'
oa: 1
oa_version: Published Version
project:
- _id: 255008E4-B435-11E9-9278-68D0E5697425
grant_number: RGP0065/2012
name: Information processing and computation in fish groups
- _id: 254D1A94-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: P 25651-N26
name: Sensitivity to higher-order statistics in natural scenes
publication: PLoS Computational Biology
publication_identifier:
issn:
- 1553734X
publication_status: published
publisher: Public Library of Science
publist_id: '6960'
pubrep_id: '884'
quality_controlled: '1'
scopus_import: 1
status: public
title: Probabilistic models for neural populations that naturally capture global coupling
and criticality
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: '2017'
...
---
_id: '721'
abstract:
- lang: eng
text: 'Let S be a positivity-preserving symmetric linear operator acting on bounded
functions. The nonlinear equation -1/m=z+Sm with a parameter z in the complex
upper half-plane ℍ has a unique solution m with values in ℍ. We show that the
z-dependence of this solution can be represented as the Stieltjes transforms of
a family of probability measures v on ℝ. Under suitable conditions on S, we show
that v has a real analytic density apart from finitely many algebraic singularities
of degree at most 3. Our motivation comes from large random matrices. The solution
m determines the density of eigenvalues of two prominent matrix ensembles: (i)
matrices with centered independent entries whose variances are given by S and
(ii) matrices with correlated entries with a translation-invariant correlation
structure. Our analysis shows that the limiting eigenvalue density has only square
root singularities or cubic root cusps; no other singularities occur.'
author:
- first_name: Oskari H
full_name: Ajanki, Oskari H
id: 36F2FB7E-F248-11E8-B48F-1D18A9856A87
last_name: Ajanki
- first_name: Torben H
full_name: Krüger, Torben H
id: 3020C786-F248-11E8-B48F-1D18A9856A87
last_name: Krüger
orcid: 0000-0002-4821-3297
- first_name: László
full_name: Erdös, László
id: 4DBD5372-F248-11E8-B48F-1D18A9856A87
last_name: Erdös
orcid: 0000-0001-5366-9603
citation:
ama: Ajanki OH, Krüger TH, Erdös L. Singularities of solutions to quadratic vector
equations on the complex upper half plane. Communications on Pure and Applied
Mathematics. 2017;70(9):1672-1705. doi:10.1002/cpa.21639
apa: Ajanki, O. H., Krüger, T. H., & Erdös, L. (2017). Singularities of solutions
to quadratic vector equations on the complex upper half plane. Communications
on Pure and Applied Mathematics. Wiley-Blackwell. https://doi.org/10.1002/cpa.21639
chicago: Ajanki, Oskari H, Torben H Krüger, and László Erdös. “Singularities of
Solutions to Quadratic Vector Equations on the Complex Upper Half Plane.” Communications
on Pure and Applied Mathematics. Wiley-Blackwell, 2017. https://doi.org/10.1002/cpa.21639.
ieee: O. H. Ajanki, T. H. Krüger, and L. Erdös, “Singularities of solutions to quadratic
vector equations on the complex upper half plane,” Communications on Pure and
Applied Mathematics, vol. 70, no. 9. Wiley-Blackwell, pp. 1672–1705, 2017.
ista: Ajanki OH, Krüger TH, Erdös L. 2017. Singularities of solutions to quadratic
vector equations on the complex upper half plane. Communications on Pure and Applied
Mathematics. 70(9), 1672–1705.
mla: Ajanki, Oskari H., et al. “Singularities of Solutions to Quadratic Vector Equations
on the Complex Upper Half Plane.” Communications on Pure and Applied Mathematics,
vol. 70, no. 9, Wiley-Blackwell, 2017, pp. 1672–705, doi:10.1002/cpa.21639.
short: O.H. Ajanki, T.H. Krüger, L. Erdös, Communications on Pure and Applied Mathematics
70 (2017) 1672–1705.
date_created: 2018-12-11T11:48:08Z
date_published: 2017-09-01T00:00:00Z
date_updated: 2021-01-12T08:12:24Z
day: '01'
department:
- _id: LaEr
doi: 10.1002/cpa.21639
ec_funded: 1
intvolume: ' 70'
issue: '9'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/1512.03703
month: '09'
oa: 1
oa_version: Submitted Version
page: 1672 - 1705
project:
- _id: 258DCDE6-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '338804'
name: Random matrices, universality and disordered quantum systems
publication: Communications on Pure and Applied Mathematics
publication_identifier:
issn:
- '00103640'
publication_status: published
publisher: Wiley-Blackwell
publist_id: '6959'
quality_controlled: '1'
scopus_import: 1
status: public
title: Singularities of solutions to quadratic vector equations on the complex upper
half plane
type: journal_article
user_id: 4435EBFC-F248-11E8-B48F-1D18A9856A87
volume: 70
year: '2017'
...
---
_id: '722'
abstract:
- lang: eng
text: Plants are sessile organisms rooted in one place. The soil resources that
plants require are often distributed in a highly heterogeneous pattern. To aid
foraging, plants have evolved roots whose growth and development are highly responsive
to soil signals. As a result, 3D root architecture is shaped by myriad environmental
signals to ensure resource capture is optimised and unfavourable environments
are avoided. The first signals sensed by newly germinating seeds — gravity and
light — direct root growth into the soil to aid seedling establishment. Heterogeneous
soil resources, such as water, nitrogen and phosphate, also act as signals that
shape 3D root growth to optimise uptake. Root architecture is also modified through
biotic interactions that include soil fungi and neighbouring plants. This developmental
plasticity results in a ‘custom-made’ 3D root system that is best adapted to forage
for resources in each soil environment that a plant colonises.
author:
- first_name: Emily
full_name: Morris, Emily
last_name: Morris
- first_name: Marcus
full_name: Griffiths, Marcus
last_name: Griffiths
- first_name: Agata
full_name: Golebiowska, Agata
last_name: Golebiowska
- first_name: Stefan
full_name: Mairhofer, Stefan
last_name: Mairhofer
- first_name: Jasmine
full_name: Burr Hersey, Jasmine
last_name: Burr Hersey
- first_name: Tatsuaki
full_name: Goh, Tatsuaki
last_name: Goh
- first_name: Daniel
full_name: Von Wangenheim, Daniel
id: 49E91952-F248-11E8-B48F-1D18A9856A87
last_name: Von Wangenheim
orcid: 0000-0002-6862-1247
- first_name: Brian
full_name: Atkinson, Brian
last_name: Atkinson
- first_name: Craig
full_name: Sturrock, Craig
last_name: Sturrock
- first_name: Jonathan
full_name: Lynch, Jonathan
last_name: Lynch
- first_name: Kris
full_name: Vissenberg, Kris
last_name: Vissenberg
- first_name: Karl
full_name: Ritz, Karl
last_name: Ritz
- first_name: Darren
full_name: Wells, Darren
last_name: Wells
- first_name: Sacha
full_name: Mooney, Sacha
last_name: Mooney
- first_name: Malcolm
full_name: Bennett, Malcolm
last_name: Bennett
citation:
ama: Morris E, Griffiths M, Golebiowska A, et al. Shaping 3D root system architecture.
Current Biology. 2017;27(17):R919-R930. doi:10.1016/j.cub.2017.06.043
apa: Morris, E., Griffiths, M., Golebiowska, A., Mairhofer, S., Burr Hersey, J.,
Goh, T., … Bennett, M. (2017). Shaping 3D root system architecture. Current
Biology. Cell Press. https://doi.org/10.1016/j.cub.2017.06.043
chicago: Morris, Emily, Marcus Griffiths, Agata Golebiowska, Stefan Mairhofer, Jasmine
Burr Hersey, Tatsuaki Goh, Daniel von Wangenheim, et al. “Shaping 3D Root System
Architecture.” Current Biology. Cell Press, 2017. https://doi.org/10.1016/j.cub.2017.06.043.
ieee: E. Morris et al., “Shaping 3D root system architecture,” Current
Biology, vol. 27, no. 17. Cell Press, pp. R919–R930, 2017.
ista: Morris E, Griffiths M, Golebiowska A, Mairhofer S, Burr Hersey J, Goh T, von
Wangenheim D, Atkinson B, Sturrock C, Lynch J, Vissenberg K, Ritz K, Wells D,
Mooney S, Bennett M. 2017. Shaping 3D root system architecture. Current Biology.
27(17), R919–R930.
mla: Morris, Emily, et al. “Shaping 3D Root System Architecture.” Current Biology,
vol. 27, no. 17, Cell Press, 2017, pp. R919–30, doi:10.1016/j.cub.2017.06.043.
short: E. Morris, M. Griffiths, A. Golebiowska, S. Mairhofer, J. Burr Hersey, T.
Goh, D. von Wangenheim, B. Atkinson, C. Sturrock, J. Lynch, K. Vissenberg, K.
Ritz, D. Wells, S. Mooney, M. Bennett, Current Biology 27 (2017) R919–R930.
date_created: 2018-12-11T11:48:08Z
date_published: 2017-09-11T00:00:00Z
date_updated: 2021-01-12T08:12:29Z
day: '11'
ddc:
- '581'
department:
- _id: JiFr
doi: 10.1016/j.cub.2017.06.043
ec_funded: 1
external_id:
pmid:
- '28898665'
file:
- access_level: open_access
checksum: e45588b21097b408da6276a3e5eedb2e
content_type: application/pdf
creator: dernst
date_created: 2019-04-17T07:46:40Z
date_updated: 2020-07-14T12:47:54Z
file_id: '6332'
file_name: 2017_CurrentBiology_Morris.pdf
file_size: 1576593
relation: main_file
file_date_updated: 2020-07-14T12:47:54Z
has_accepted_license: '1'
intvolume: ' 27'
issue: '17'
language:
- iso: eng
license: https://creativecommons.org/licenses/by-nc-nd/4.0/
month: '09'
oa: 1
oa_version: Submitted Version
page: R919 - R930
pmid: 1
project:
- _id: 25681D80-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '291734'
name: International IST Postdoc Fellowship Programme
publication: Current Biology
publication_identifier:
issn:
- '09609822'
publication_status: published
publisher: Cell Press
publist_id: '6956'
pubrep_id: '982'
quality_controlled: '1'
scopus_import: 1
status: public
title: Shaping 3D root system architecture
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: 27
year: '2017'
...
---
_id: '725'
abstract:
- lang: eng
text: Individual computations and social interactions underlying collective behavior
in groups of animals are of great ethological, behavioral, and theoretical interest.
While complex individual behaviors have successfully been parsed into small dictionaries
of stereotyped behavioral modes, studies of collective behavior largely ignored
these findings; instead, their focus was on inferring single, mode-independent
social interaction rules that reproduced macroscopic and often qualitative features
of group behavior. Here, we bring these two approaches together to predict individual
swimming patterns of adult zebrafish in a group. We show that fish alternate between
an “active” mode, in which they are sensitive to the swimming patterns of conspecifics,
and a “passive” mode, where they ignore them. Using a model that accounts for
these two modes explicitly, we predict behaviors of individual fish with high
accuracy, outperforming previous approaches that assumed a single continuous computation
by individuals and simple metric or topological weighing of neighbors’ behavior.
At the group level, switching between active and passive modes is uncorrelated
among fish, but correlated directional swimming behavior still emerges. Our quantitative
approach for studying complex, multi-modal individual behavior jointly with emergent
group behavior is readily extensible to additional behavioral modes and their
neural correlates as well as to other species.
author:
- first_name: Roy
full_name: Harpaz, Roy
last_name: Harpaz
- first_name: Gasper
full_name: Tkacik, Gasper
id: 3D494DCA-F248-11E8-B48F-1D18A9856A87
last_name: Tkacik
orcid: 0000-0002-6699-1455
- first_name: Elad
full_name: Schneidman, Elad
last_name: Schneidman
citation:
ama: Harpaz R, Tkačik G, Schneidman E. Discrete modes of social information processing
predict individual behavior of fish in a group. PNAS. 2017;114(38):10149-10154.
doi:10.1073/pnas.1703817114
apa: Harpaz, R., Tkačik, G., & Schneidman, E. (2017). Discrete modes of social
information processing predict individual behavior of fish in a group. PNAS.
National Academy of Sciences. https://doi.org/10.1073/pnas.1703817114
chicago: Harpaz, Roy, Gašper Tkačik, and Elad Schneidman. “Discrete Modes of Social
Information Processing Predict Individual Behavior of Fish in a Group.” PNAS.
National Academy of Sciences, 2017. https://doi.org/10.1073/pnas.1703817114.
ieee: R. Harpaz, G. Tkačik, and E. Schneidman, “Discrete modes of social information
processing predict individual behavior of fish in a group,” PNAS, vol.
114, no. 38. National Academy of Sciences, pp. 10149–10154, 2017.
ista: Harpaz R, Tkačik G, Schneidman E. 2017. Discrete modes of social information
processing predict individual behavior of fish in a group. PNAS. 114(38), 10149–10154.
mla: Harpaz, Roy, et al. “Discrete Modes of Social Information Processing Predict
Individual Behavior of Fish in a Group.” PNAS, vol. 114, no. 38, National
Academy of Sciences, 2017, pp. 10149–54, doi:10.1073/pnas.1703817114.
short: R. Harpaz, G. Tkačik, E. Schneidman, PNAS 114 (2017) 10149–10154.
date_created: 2018-12-11T11:48:10Z
date_published: 2017-09-19T00:00:00Z
date_updated: 2021-01-12T08:12:36Z
day: '19'
department:
- _id: GaTk
doi: 10.1073/pnas.1703817114
external_id:
pmid:
- '28874581'
intvolume: ' 114'
issue: '38'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5617265/
month: '09'
oa: 1
oa_version: Submitted Version
page: 10149 - 10154
pmid: 1
publication: PNAS
publication_identifier:
issn:
- '00278424'
publication_status: published
publisher: National Academy of Sciences
publist_id: '6953'
quality_controlled: '1'
scopus_import: 1
status: public
title: Discrete modes of social information processing predict individual behavior
of fish in a group
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 114
year: '2017'
...
---
_id: '724'
abstract:
- lang: eng
text: We investigate the stationary and dynamical behavior of an Anderson localized
chain coupled to a single central bound state. Although this coupling partially
dilutes the Anderson localized peaks towards nearly resonant sites, the most weight
of the original peaks remains unchanged. This leads to multifractal wave functions
with a frozen spectrum of fractal dimensions, which is characteristic for localized
phases in models with power-law hopping. Using a perturbative approach we identify
two different dynamical regimes. At weak couplings to the central site, the transport
of particles and information is logarithmic in time, a feature usually attributed
to many-body localization. We connect such transport to the persistence of the
Poisson statistics of level spacings in parts of the spectrum. In contrast, at
stronger couplings the level repulsion is established in the entire spectrum,
the problem can be mapped to the Fano resonance, and the transport is ballistic.
acknowledgement: "We would like to thank Dmitry Abanin, Christophe De\r\nBeule,
\ Joel Moore, Romain Vasseur, and Norman Yao for\r\nmany stimulating discussions.
\ Financial support has been\r\nprovided by the Deutsche Forschungsgemeinschaft
\ (DFG)\r\nvia Grant No. TR950/8-1, SFB 1170 “ToCoTronics” and the\r\nENB Graduate
\ School on Topological Insulators. M.S. was\r\nsupported by Gordon and Betty
Moore Foundation’s EPiQS\r\nInitiative through Grant No. GBMF4307. F.P. acknowledges\r\nsupport
from the DFG Research Unit FOR 1807 through Grant\r\nNo. PO 1370/2-1."
article_number: '104203'
author:
- first_name: Daniel
full_name: Hetterich, Daniel
last_name: Hetterich
- first_name: Maksym
full_name: Serbyn, Maksym
id: 47809E7E-F248-11E8-B48F-1D18A9856A87
last_name: Serbyn
orcid: 0000-0002-2399-5827
- first_name: Fernando
full_name: Domínguez, Fernando
last_name: Domínguez
- first_name: Frank
full_name: Pollmann, Frank
last_name: Pollmann
- first_name: Björn
full_name: Trauzettel, Björn
last_name: Trauzettel
citation:
ama: Hetterich D, Serbyn M, Domínguez F, Pollmann F, Trauzettel B. Noninteracting
central site model localization and logarithmic entanglement growth. Physical
Review B. 2017;96(10). doi:10.1103/PhysRevB.96.104203
apa: Hetterich, D., Serbyn, M., Domínguez, F., Pollmann, F., & Trauzettel, B.
(2017). Noninteracting central site model localization and logarithmic entanglement
growth. Physical Review B. American Physical Society. https://doi.org/10.1103/PhysRevB.96.104203
chicago: Hetterich, Daniel, Maksym Serbyn, Fernando Domínguez, Frank Pollmann, and
Björn Trauzettel. “Noninteracting Central Site Model Localization and Logarithmic
Entanglement Growth.” Physical Review B. American Physical Society, 2017.
https://doi.org/10.1103/PhysRevB.96.104203.
ieee: D. Hetterich, M. Serbyn, F. Domínguez, F. Pollmann, and B. Trauzettel, “Noninteracting
central site model localization and logarithmic entanglement growth,” Physical
Review B, vol. 96, no. 10. American Physical Society, 2017.
ista: Hetterich D, Serbyn M, Domínguez F, Pollmann F, Trauzettel B. 2017. Noninteracting
central site model localization and logarithmic entanglement growth. Physical
Review B. 96(10), 104203.
mla: Hetterich, Daniel, et al. “Noninteracting Central Site Model Localization and
Logarithmic Entanglement Growth.” Physical Review B, vol. 96, no. 10, 104203,
American Physical Society, 2017, doi:10.1103/PhysRevB.96.104203.
short: D. Hetterich, M. Serbyn, F. Domínguez, F. Pollmann, B. Trauzettel, Physical
Review B 96 (2017).
date_created: 2018-12-11T11:48:09Z
date_published: 2017-09-13T00:00:00Z
date_updated: 2021-01-12T08:12:35Z
day: '13'
department:
- _id: MaSe
doi: 10.1103/PhysRevB.96.104203
intvolume: ' 96'
issue: '10'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/1701.02744
month: '09'
oa: 1
oa_version: Submitted Version
publication: Physical Review B
publication_identifier:
issn:
- '24699950'
publication_status: published
publisher: American Physical Society
publist_id: '6955'
quality_controlled: '1'
scopus_import: 1
status: public
title: Noninteracting central site model localization and logarithmic entanglement
growth
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 96
year: '2017'
...
---
_id: '731'
abstract:
- lang: eng
text: Genetic variations in the oxytocin receptor gene affect patients with ASD
and ADHD differently.
article_number: eaap8168
author:
- first_name: Gaia
full_name: Novarino, Gaia
id: 3E57A680-F248-11E8-B48F-1D18A9856A87
last_name: Novarino
orcid: 0000-0002-7673-7178
citation:
ama: Novarino G. The science of love in ASD and ADHD. Science Translational Medicine.
2017;9(411). doi:10.1126/scitranslmed.aap8168
apa: Novarino, G. (2017). The science of love in ASD and ADHD. Science Translational
Medicine. American Association for the Advancement of Science. https://doi.org/10.1126/scitranslmed.aap8168
chicago: Novarino, Gaia. “The Science of Love in ASD and ADHD.” Science Translational
Medicine. American Association for the Advancement of Science, 2017. https://doi.org/10.1126/scitranslmed.aap8168.
ieee: G. Novarino, “The science of love in ASD and ADHD,” Science Translational
Medicine, vol. 9, no. 411. American Association for the Advancement of Science,
2017.
ista: Novarino G. 2017. The science of love in ASD and ADHD. Science Translational
Medicine. 9(411), eaap8168.
mla: Novarino, Gaia. “The Science of Love in ASD and ADHD.” Science Translational
Medicine, vol. 9, no. 411, eaap8168, American Association for the Advancement
of Science, 2017, doi:10.1126/scitranslmed.aap8168.
short: G. Novarino, Science Translational Medicine 9 (2017).
date_created: 2018-12-11T11:48:12Z
date_published: 2017-10-11T00:00:00Z
date_updated: 2021-01-12T08:12:57Z
day: '11'
department:
- _id: GaNo
doi: 10.1126/scitranslmed.aap8168
intvolume: ' 9'
issue: '411'
language:
- iso: eng
month: '10'
oa_version: None
publication: Science Translational Medicine
publication_identifier:
issn:
- '19466234'
publication_status: published
publisher: American Association for the Advancement of Science
publist_id: '6938'
quality_controlled: '1'
scopus_import: 1
status: public
title: The science of love in ASD and ADHD
type: journal_article
user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87
volume: 9
year: '2017'
...
---
_id: '7360'
abstract:
- lang: eng
text: Inflammation, which is a highly regulated host response against danger signals,
may be harmful if it is excessive and deregulated. Ideally, anti-inflammatory
therapy should autonomously commence as soon as possible after the onset of inflammation,
should be controllable by a physician, and should not systemically block beneficial
immune response in the long term. We describe a genetically encoded anti-inflammatory
mammalian cell device based on a modular engineered genetic circuit comprising
a sensor, an amplifier, a “thresholder” to restrict activation of a positive-feedback
loop, a combination of advanced clinically used biopharmaceutical proteins, and
orthogonal regulatory elements that linked modules into the functional device.
This genetic circuit was autonomously activated by inflammatory signals, including
endogenous cecal ligation and puncture (CLP)-induced inflammation in mice and
serum from a systemic juvenile idiopathic arthritis (sIJA) patient, and could
be reset externally by a chemical signal. The microencapsulated anti-inflammatory
device significantly reduced the pathology in dextran sodium sulfate (DSS)-induced
acute murine colitis, demonstrating a synthetic immunological approach for autonomous
anti-inflammatory therapy.
article_processing_charge: No
article_type: original
author:
- first_name: Anže
full_name: Smole, Anže
last_name: Smole
- first_name: Duško
full_name: Lainšček, Duško
last_name: Lainšček
- first_name: Urban
full_name: Bezeljak, Urban
id: 2A58201A-F248-11E8-B48F-1D18A9856A87
last_name: Bezeljak
orcid: 0000-0003-1365-5631
- first_name: Simon
full_name: Horvat, Simon
last_name: Horvat
- first_name: Roman
full_name: Jerala, Roman
last_name: Jerala
citation:
ama: Smole A, Lainšček D, Bezeljak U, Horvat S, Jerala R. A synthetic mammalian
therapeutic gene circuit for sensing and suppressing inflammation. Molecular
Therapy. 2017;25(1):102-119. doi:10.1016/j.ymthe.2016.10.005
apa: Smole, A., Lainšček, D., Bezeljak, U., Horvat, S., & Jerala, R. (2017).
A synthetic mammalian therapeutic gene circuit for sensing and suppressing inflammation.
Molecular Therapy. Elsevier. https://doi.org/10.1016/j.ymthe.2016.10.005
chicago: Smole, Anže, Duško Lainšček, Urban Bezeljak, Simon Horvat, and Roman Jerala.
“A Synthetic Mammalian Therapeutic Gene Circuit for Sensing and Suppressing Inflammation.”
Molecular Therapy. Elsevier, 2017. https://doi.org/10.1016/j.ymthe.2016.10.005.
ieee: A. Smole, D. Lainšček, U. Bezeljak, S. Horvat, and R. Jerala, “A synthetic
mammalian therapeutic gene circuit for sensing and suppressing inflammation,”
Molecular Therapy, vol. 25, no. 1. Elsevier, pp. 102–119, 2017.
ista: Smole A, Lainšček D, Bezeljak U, Horvat S, Jerala R. 2017. A synthetic mammalian
therapeutic gene circuit for sensing and suppressing inflammation. Molecular Therapy.
25(1), 102–119.
mla: Smole, Anže, et al. “A Synthetic Mammalian Therapeutic Gene Circuit for Sensing
and Suppressing Inflammation.” Molecular Therapy, vol. 25, no. 1, Elsevier,
2017, pp. 102–19, doi:10.1016/j.ymthe.2016.10.005.
short: A. Smole, D. Lainšček, U. Bezeljak, S. Horvat, R. Jerala, Molecular Therapy
25 (2017) 102–119.
date_created: 2020-01-25T15:55:39Z
date_published: 2017-01-01T00:00:00Z
date_updated: 2021-01-12T08:13:14Z
day: '01'
ddc:
- '570'
department:
- _id: MaLo
doi: 10.1016/j.ymthe.2016.10.005
external_id:
pmid:
- '28129106'
file:
- access_level: open_access
checksum: ea8b1b28606dd1edab7379ba4fa3641f
content_type: application/pdf
creator: dernst
date_created: 2020-03-03T10:55:13Z
date_updated: 2020-07-14T12:47:56Z
file_id: '7561'
file_name: 2017_MolecularTherapy_Smole.pdf
file_size: 3404806
relation: main_file
file_date_updated: 2020-07-14T12:47:56Z
has_accepted_license: '1'
intvolume: ' 25'
issue: '1'
language:
- iso: eng
month: '01'
oa: 1
oa_version: Published Version
page: 102-119
pmid: 1
publication: Molecular Therapy
publication_identifier:
issn:
- 1525-0016
publication_status: published
publisher: Elsevier
quality_controlled: '1'
status: public
title: A synthetic mammalian therapeutic gene circuit for sensing and suppressing
inflammation
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: 25
year: '2017'
...
---
_id: '750'
abstract:
- lang: eng
text: Modern communication technologies allow first responders to contact thousands
of potential volunteers simultaneously for support during a crisis or disaster
event. However, such volunteer efforts must be well coordinated and monitored,
in order to offer an effective relief to the professionals. In this paper we extend
earlier work on optimally assigning volunteers to selected landmark locations.
In particular, we emphasize the aspect that obtaining good assignments requires
not only advanced computational tools, but also a realistic measure of distance
between volunteers and landmarks. Specifically, we propose the use of the Open
Street Map (OSM) driving distance instead of he previously used flight distance.
We find the OSM driving distance to be better aligned with the interests of volunteers
and first responders. Furthermore, we show that relying on the flying distance
leads to a substantial underestimation of the number of required volunteers, causing
negative side effects in case of an actual crisis situation.
author:
- first_name: Jasmin
full_name: Pielorz, Jasmin
id: 49BC895A-F248-11E8-B48F-1D18A9856A87
last_name: Pielorz
- first_name: Matthias
full_name: Prandtstetter, Matthias
last_name: Prandtstetter
- first_name: Markus
full_name: Straub, Markus
last_name: Straub
- first_name: Christoph
full_name: Lampert, Christoph
id: 40C20FD2-F248-11E8-B48F-1D18A9856A87
last_name: Lampert
orcid: 0000-0001-8622-7887
citation:
ama: 'Pielorz J, Prandtstetter M, Straub M, Lampert C. Optimal geospatial volunteer
allocation needs realistic distances. In: 2017 IEEE International Conference
on Big Data. IEEE; 2017:3760-3763. doi:10.1109/BigData.2017.8258375'
apa: 'Pielorz, J., Prandtstetter, M., Straub, M., & Lampert, C. (2017). Optimal
geospatial volunteer allocation needs realistic distances. In 2017 IEEE International
Conference on Big Data (pp. 3760–3763). Boston, MA, United States: IEEE. https://doi.org/10.1109/BigData.2017.8258375'
chicago: Pielorz, Jasmin, Matthias Prandtstetter, Markus Straub, and Christoph Lampert.
“Optimal Geospatial Volunteer Allocation Needs Realistic Distances.” In 2017
IEEE International Conference on Big Data, 3760–63. IEEE, 2017. https://doi.org/10.1109/BigData.2017.8258375.
ieee: J. Pielorz, M. Prandtstetter, M. Straub, and C. Lampert, “Optimal geospatial
volunteer allocation needs realistic distances,” in 2017 IEEE International
Conference on Big Data, Boston, MA, United States, 2017, pp. 3760–3763.
ista: Pielorz J, Prandtstetter M, Straub M, Lampert C. 2017. Optimal geospatial
volunteer allocation needs realistic distances. 2017 IEEE International Conference
on Big Data. Big Data, 3760–3763.
mla: Pielorz, Jasmin, et al. “Optimal Geospatial Volunteer Allocation Needs Realistic
Distances.” 2017 IEEE International Conference on Big Data, IEEE, 2017,
pp. 3760–63, doi:10.1109/BigData.2017.8258375.
short: J. Pielorz, M. Prandtstetter, M. Straub, C. Lampert, in:, 2017 IEEE International
Conference on Big Data, IEEE, 2017, pp. 3760–3763.
conference:
end_date: 2017-12-14
location: Boston, MA, United States
name: Big Data
start_date: 2017-12-11
date_created: 2018-12-11T11:48:18Z
date_published: 2017-12-01T00:00:00Z
date_updated: 2021-01-12T08:13:55Z
day: '01'
department:
- _id: ChLa
doi: 10.1109/BigData.2017.8258375
language:
- iso: eng
month: '12'
oa_version: None
page: 3760 - 3763
publication: 2017 IEEE International Conference on Big Data
publication_identifier:
isbn:
- 978-153862714-3
publication_status: published
publisher: IEEE
publist_id: '6906'
quality_controlled: '1'
scopus_import: 1
status: public
title: Optimal geospatial volunteer allocation needs realistic distances
type: conference
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
year: '2017'
...
---
_id: '795'
abstract:
- lang: eng
text: 'We introduce a common generalization of the strong Hanani–Tutte theorem and
the weak Hanani–Tutte theorem: if a graph G has a drawing D in the plane where
every pair of independent edges crosses an even number of times, then G has a
planar drawing preserving the rotation of each vertex whose incident edges cross
each other evenly in D. The theorem is implicit in the proof of the strong Hanani–Tutte
theorem by Pelsmajer, Schaefer and Štefankovič. We give a new, somewhat simpler
proof.'
article_number: P3.18
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: Dömötör
full_name: Pálvölgyi, Dömötör
last_name: Pálvölgyi
citation:
ama: Fulek R, Kynčl J, Pálvölgyi D. Unified Hanani Tutte theorem. Electronic
Journal of Combinatorics. 2017;24(3). doi:10.37236/6663
apa: Fulek, R., Kynčl, J., & Pálvölgyi, D. (2017). Unified Hanani Tutte theorem.
Electronic Journal of Combinatorics. International Press. https://doi.org/10.37236/6663
chicago: Fulek, Radoslav, Jan Kynčl, and Dömötör Pálvölgyi. “Unified Hanani Tutte
Theorem.” Electronic Journal of Combinatorics. International Press, 2017.
https://doi.org/10.37236/6663.
ieee: R. Fulek, J. Kynčl, and D. Pálvölgyi, “Unified Hanani Tutte theorem,” Electronic
Journal of Combinatorics, vol. 24, no. 3. International Press, 2017.
ista: Fulek R, Kynčl J, Pálvölgyi D. 2017. Unified Hanani Tutte theorem. Electronic
Journal of Combinatorics. 24(3), P3.18.
mla: Fulek, Radoslav, et al. “Unified Hanani Tutte Theorem.” Electronic Journal
of Combinatorics, vol. 24, no. 3, P3.18, International Press, 2017, doi:10.37236/6663.
short: R. Fulek, J. Kynčl, D. Pálvölgyi, Electronic Journal of Combinatorics 24
(2017).
date_created: 2018-12-11T11:48:32Z
date_published: 2017-07-28T00:00:00Z
date_updated: 2022-03-18T12:58:53Z
day: '28'
ddc:
- '000'
department:
- _id: UlWa
doi: 10.37236/6663
ec_funded: 1
file:
- access_level: open_access
checksum: ef320cff0f062051e858f929be6a3581
content_type: application/pdf
creator: dernst
date_created: 2019-01-18T14:04:08Z
date_updated: 2020-07-14T12:48:06Z
file_id: '5853'
file_name: 2017_ElectrCombi_Fulek.pdf
file_size: 236944
relation: main_file
file_date_updated: 2020-07-14T12:48:06Z
has_accepted_license: '1'
intvolume: ' 24'
issue: '3'
language:
- iso: eng
month: '07'
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:
issn:
- '10778926'
publication_status: published
publisher: International Press
publist_id: '6859'
quality_controlled: '1'
scopus_import: '1'
status: public
title: Unified Hanani Tutte theorem
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 24
year: '2017'
...
---
_id: '797'
abstract:
- lang: ger
text: Phasenübergänge helfen beim Verständnis von Vielteilchensystemen in der Festkörperphysik
und Fluiddynamik bis hin zur Teilchenphysik. Unserer internationalen Kollaboration
ist es gelungen, einen neuartigen Phasenübergang in einem Quantensystem zu beobachten
[1]. In einem Mikrowellenresonator konnte erstmals die spontane Zustandsänderung
von undurchsichtig zu transparent nachgewiesen werden.
article_processing_charge: No
article_type: original
author:
- first_name: Johannes M
full_name: Fink, Johannes M
id: 4B591CBA-F248-11E8-B48F-1D18A9856A87
last_name: Fink
orcid: 0000-0001-8112-028X
citation:
ama: Fink JM. Photonenblockade aufgelöst. Physik in unserer Zeit. 2017;48(3):111-113.
doi:10.1002/piuz.201770305
apa: Fink, J. M. (2017). Photonenblockade aufgelöst. Physik in Unserer Zeit.
Wiley. https://doi.org/10.1002/piuz.201770305
chicago: Fink, Johannes M. “Photonenblockade Aufgelöst.” Physik in Unserer Zeit.
Wiley, 2017. https://doi.org/10.1002/piuz.201770305.
ieee: J. M. Fink, “Photonenblockade aufgelöst,” Physik in unserer Zeit, vol.
48, no. 3. Wiley, pp. 111–113, 2017.
ista: Fink JM. 2017. Photonenblockade aufgelöst. Physik in unserer Zeit. 48(3),
111–113.
mla: Fink, Johannes M. “Photonenblockade Aufgelöst.” Physik in Unserer Zeit,
vol. 48, no. 3, Wiley, 2017, pp. 111–13, doi:10.1002/piuz.201770305.
short: J.M. Fink, Physik in Unserer Zeit 48 (2017) 111–113.
date_created: 2018-12-11T11:48:33Z
date_published: 2017-05-01T00:00:00Z
date_updated: 2022-03-24T09:16:20Z
day: '01'
department:
- _id: JoFi
doi: 10.1002/piuz.201770305
intvolume: ' 48'
issue: '3'
language:
- iso: eng
month: '05'
oa_version: None
page: 111 - 113
publication: Physik in unserer Zeit
publication_status: published
publisher: Wiley
publist_id: '6856'
quality_controlled: '1'
status: public
title: Photonenblockade aufgelöst
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 48
year: '2017'
...
---
_id: '807'
abstract:
- lang: eng
text: 'On January the 1st, 2016 a new agreement between 32 Austrian scientific libraries
and the publisher Springer took its effect: this deal covers accessing the licensed
content on the one hand, and publishing open access on the other hand. More than
1000 papers by Austrian authors were published open access at Springer in the
first year alone. The working group "Springer Compact Evaluierung" made
the data for these articles available via the platform OpenAPC and would like
to use this opportunity to give a short account of what this publishing agreement
actually entails and the working group intends to do.'
author:
- first_name: Magdalena
full_name: Andrae, Magdalena
last_name: Andrae
- first_name: Márton
full_name: Villányi, Márton
id: 3FFCCD3A-F248-11E8-B48F-1D18A9856A87
last_name: Villányi
orcid: 0000-0001-8126-0426
citation:
ama: Andrae M, Villányi M. Der Springer Compact-Deal – Ein erster Einblick in die
Evaluierung einer Offsetting-Vereinbarung. Mitteilungen der Vereinigung Österreichischer
Bibliothekarinnen und Bibliothekare. 2017;70(2):274-280. doi:10.31263/voebm.v70i2.1898
apa: Andrae, M., & Villányi, M. (2017). Der Springer Compact-Deal – Ein erster
Einblick in die Evaluierung einer Offsetting-Vereinbarung. Mitteilungen Der
Vereinigung Österreichischer Bibliothekarinnen Und Bibliothekare. VÖB. https://doi.org/10.31263/voebm.v70i2.1898
chicago: Andrae, Magdalena, and Márton Villányi. “Der Springer Compact-Deal – Ein
Erster Einblick in Die Evaluierung Einer Offsetting-Vereinbarung.” Mitteilungen
Der Vereinigung Österreichischer Bibliothekarinnen Und Bibliothekare. VÖB,
2017. https://doi.org/10.31263/voebm.v70i2.1898.
ieee: M. Andrae and M. Villányi, “Der Springer Compact-Deal – Ein erster Einblick
in die Evaluierung einer Offsetting-Vereinbarung,” Mitteilungen der Vereinigung
Österreichischer Bibliothekarinnen und Bibliothekare, vol. 70, no. 2. VÖB,
pp. 274–280, 2017.
ista: Andrae M, Villányi M. 2017. Der Springer Compact-Deal – Ein erster Einblick
in die Evaluierung einer Offsetting-Vereinbarung. Mitteilungen der Vereinigung
Österreichischer Bibliothekarinnen und Bibliothekare. 70(2), 274–280.
mla: Andrae, Magdalena, and Márton Villányi. “Der Springer Compact-Deal – Ein Erster
Einblick in Die Evaluierung Einer Offsetting-Vereinbarung.” Mitteilungen Der
Vereinigung Österreichischer Bibliothekarinnen Und Bibliothekare, vol. 70,
no. 2, VÖB, 2017, pp. 274–80, doi:10.31263/voebm.v70i2.1898.
short: M. Andrae, M. Villányi, Mitteilungen Der Vereinigung Österreichischer Bibliothekarinnen
Und Bibliothekare 70 (2017) 274–280.
date_created: 2018-12-11T11:48:36Z
date_published: 2017-08-01T00:00:00Z
date_updated: 2021-01-12T08:16:45Z
day: '01'
ddc:
- '020'
department:
- _id: E-Lib
doi: 10.31263/voebm.v70i2.1898
file:
- access_level: open_access
checksum: 558c18bcf5580d87dd371ec626d52075
content_type: application/pdf
creator: dernst
date_created: 2019-01-18T13:39:26Z
date_updated: 2020-07-14T12:48:09Z
file_id: '5851'
file_name: 2017_VOEB_Andrae.pdf
file_size: 125065
relation: main_file
file_date_updated: 2020-07-14T12:48:09Z
has_accepted_license: '1'
intvolume: ' 70'
issue: '2'
language:
- iso: eng
month: '08'
oa: 1
oa_version: Published Version
page: 274 - 280
popular_science: '1'
publication: Mitteilungen der Vereinigung Österreichischer Bibliothekarinnen und Bibliothekare
publication_identifier:
issn:
- '10222588'
publication_status: published
publisher: VÖB
publist_id: '6843'
scopus_import: 1
status: public
title: Der Springer Compact-Deal – Ein erster Einblick in die Evaluierung einer Offsetting-Vereinbarung
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: 70
year: '2017'
...
---
_id: '825'
abstract:
- lang: eng
text: What data is needed about data? Describing the process to answer this question
for the institutional data repository IST DataRep.
author:
- first_name: Barbara
full_name: Petritsch, Barbara
id: 406048EC-F248-11E8-B48F-1D18A9856A87
last_name: Petritsch
orcid: 0000-0003-2724-4614
citation:
ama: Petritsch B. Metadata for research data in practice. Mitteilungen der Vereinigung
Österreichischer Bibliothekarinnen & Bibliothekare. 2017;70(2):200-207.
doi:10.31263/voebm.v70i2.1678
apa: Petritsch, B. (2017). Metadata for research data in practice. Mitteilungen
Der Vereinigung Österreichischer Bibliothekarinnen & Bibliothekare. VÖB.
https://doi.org/10.31263/voebm.v70i2.1678
chicago: Petritsch, Barbara. “Metadata for Research Data in Practice.” Mitteilungen
Der Vereinigung Österreichischer Bibliothekarinnen & Bibliothekare. VÖB,
2017. https://doi.org/10.31263/voebm.v70i2.1678.
ieee: B. Petritsch, “Metadata for research data in practice,” Mitteilungen der
Vereinigung Österreichischer Bibliothekarinnen & Bibliothekare, vol. 70,
no. 2. VÖB, pp. 200–207, 2017.
ista: Petritsch B. 2017. Metadata for research data in practice. Mitteilungen der
Vereinigung Österreichischer Bibliothekarinnen & Bibliothekare. 70(2), 200–207.
mla: Petritsch, Barbara. “Metadata for Research Data in Practice.” Mitteilungen
Der Vereinigung Österreichischer Bibliothekarinnen & Bibliothekare, vol.
70, no. 2, VÖB, 2017, pp. 200–07, doi:10.31263/voebm.v70i2.1678.
short: B. Petritsch, Mitteilungen Der Vereinigung Österreichischer Bibliothekarinnen
& Bibliothekare 70 (2017) 200–207.
date_created: 2018-12-11T11:48:42Z
date_published: 2017-08-01T00:00:00Z
date_updated: 2021-01-12T08:17:44Z
day: '01'
ddc:
- '020'
department:
- _id: E-Lib
doi: 10.31263/voebm.v70i2.1678
file:
- access_level: open_access
checksum: 7c4544d07efa2c2add8612b489abb4e2
content_type: application/pdf
creator: dernst
date_created: 2019-01-18T13:32:17Z
date_updated: 2020-07-14T12:48:11Z
file_id: '5850'
file_name: 2017_VOEB_Petritsch.pdf
file_size: 7843975
relation: main_file
file_date_updated: 2020-07-14T12:48:11Z
has_accepted_license: '1'
intvolume: ' 70'
issue: '2'
language:
- iso: eng
month: '08'
oa: 1
oa_version: Published Version
page: 200 - 207
publication: Mitteilungen der Vereinigung Österreichischer Bibliothekarinnen & Bibliothekare
publication_identifier:
issn:
- '10222588'
publication_status: published
publisher: VÖB
publist_id: '6823'
scopus_import: 1
status: public
title: Metadata for research data in practice
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: 70
year: '2017'
...
---
_id: '9445'
abstract:
- lang: eng
text: Cytosine methylation regulates essential genome functions across eukaryotes,
but the fundamental question of whether nucleosomal or naked DNA is the preferred
substrate of plant and animal methyltransferases remains unresolved. Here, we
show that genetic inactivation of a single DDM1/Lsh family nucleosome remodeler
biases methylation toward inter-nucleosomal linker DNA in Arabidopsis thaliana
and mouse. We find that DDM1 enables methylation of DNA bound to the nucleosome,
suggesting that nucleosome-free DNA is the preferred substrate of eukaryotic methyltransferases
in vivo. Furthermore, we show that simultaneous mutation of DDM1 and linker histone
H1 in Arabidopsis reproduces the strong linker-specific methylation patterns of
species that diverged from flowering plants and animals over a billion years ago.
Our results indicate that in the absence of remodeling, nucleosomes are strong
barriers to DNA methyltransferases. Linker-specific methylation can evolve simply
by breaking the connection between nucleosome remodeling and DNA methylation.
article_number: e30674
article_processing_charge: No
article_type: original
author:
- first_name: David B
full_name: Lyons, David B
last_name: Lyons
- first_name: Daniel
full_name: Zilberman, Daniel
id: 6973db13-dd5f-11ea-814e-b3e5455e9ed1
last_name: Zilberman
orcid: 0000-0002-0123-8649
citation:
ama: Lyons DB, Zilberman D. DDM1 and Lsh remodelers allow methylation of DNA wrapped
in nucleosomes. eLife. 2017;6. doi:10.7554/elife.30674
apa: Lyons, D. B., & Zilberman, D. (2017). DDM1 and Lsh remodelers allow methylation
of DNA wrapped in nucleosomes. ELife. eLife Sciences Publications. https://doi.org/10.7554/elife.30674
chicago: Lyons, David B, and Daniel Zilberman. “DDM1 and Lsh Remodelers Allow Methylation
of DNA Wrapped in Nucleosomes.” ELife. eLife Sciences Publications, 2017.
https://doi.org/10.7554/elife.30674.
ieee: D. B. Lyons and D. Zilberman, “DDM1 and Lsh remodelers allow methylation of
DNA wrapped in nucleosomes,” eLife, vol. 6. eLife Sciences Publications,
2017.
ista: Lyons DB, Zilberman D. 2017. DDM1 and Lsh remodelers allow methylation of
DNA wrapped in nucleosomes. eLife. 6, e30674.
mla: Lyons, David B., and Daniel Zilberman. “DDM1 and Lsh Remodelers Allow Methylation
of DNA Wrapped in Nucleosomes.” ELife, vol. 6, e30674, eLife Sciences Publications,
2017, doi:10.7554/elife.30674.
short: D.B. Lyons, D. Zilberman, ELife 6 (2017).
date_created: 2021-06-02T14:28:58Z
date_published: 2017-11-15T00:00:00Z
date_updated: 2021-12-14T07:54:36Z
day: '15'
ddc:
- '570'
department:
- _id: DaZi
doi: 10.7554/elife.30674
extern: '1'
external_id:
pmid:
- '29140247'
file:
- access_level: open_access
checksum: 4cfcdd67511ae4aed3d993550e46e146
content_type: application/pdf
creator: cziletti
date_created: 2021-06-02T14:33:36Z
date_updated: 2021-06-02T14:33:36Z
file_id: '9446'
file_name: 2017_eLife_Lyons.pdf
file_size: 1603102
relation: main_file
success: 1
file_date_updated: 2021-06-02T14:33:36Z
has_accepted_license: '1'
intvolume: ' 6'
language:
- iso: eng
month: '11'
oa: 1
oa_version: Published Version
pmid: 1
publication: eLife
publication_identifier:
eissn:
- 2050-084X
publication_status: published
publisher: eLife Sciences Publications
quality_controlled: '1'
scopus_import: '1'
status: public
title: DDM1 and Lsh remodelers allow methylation of DNA wrapped in nucleosomes
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: 8b945eb4-e2f2-11eb-945a-df72226e66a9
volume: 6
year: '2017'
...
---
_id: '957'
abstract:
- lang: eng
text: Small molecule biosensors based on Forster resonance energy transfer (FRET)
enable small molecule signaling to be monitored with high spatial and temporal
resolution in complex cellular environments. FRET sensors can be constructed by
fusing a pair of fluorescent proteins to a suitable recognition domain, such as
a member of the solute-binding protein (SBP) superfamily. However, naturally occurring
SBPs may be unsuitable for incorporation into FRET sensors due to their low thermostability,
which may preclude imaging under physiological conditions, or because the positions
of their N- and C-termini may be suboptimal for fusion of fluorescent proteins,
which may limit the dynamic range of the resulting sensors. Here, we show how
these problems can be overcome using ancestral protein reconstruction and circular
permutation. Ancestral protein reconstruction, used as a protein engineering strategy,
leverages phylogenetic information to improve the thermostability of proteins,
while circular permutation enables the termini of an SBP to be repositioned to
maximize the dynamic range of the resulting FRET sensor. We also provide a protocol
for cloning the engineered SBPs into FRET sensor constructs using Golden Gate
assembly and discuss considerations for in situ characterization of the FRET sensors.
alternative_title:
- Methods in Molecular Biology
author:
- first_name: Ben
full_name: Clifton, Ben
last_name: Clifton
- first_name: Jason
full_name: Whitfield, Jason
last_name: Whitfield
- first_name: Inmaculada
full_name: Sanchez Romero, Inmaculada
id: 3D9C5D30-F248-11E8-B48F-1D18A9856A87
last_name: Sanchez Romero
- first_name: Michel
full_name: Herde, Michel
last_name: Herde
- first_name: Christian
full_name: Henneberger, Christian
last_name: Henneberger
- 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: Colin
full_name: Jackson, Colin
last_name: Jackson
citation:
ama: 'Clifton B, Whitfield J, Sanchez-Romero I, et al. Ancestral protein reconstruction
and circular permutation for improving the stability and dynamic range of FRET
sensors. In: Stein V, ed. Synthetic Protein Switches. Vol 1596. Synthetic
Protein Switches. Springer; 2017:71-87. doi:10.1007/978-1-4939-6940-1_5'
apa: Clifton, B., Whitfield, J., Sanchez-Romero, I., Herde, M., Henneberger, C.,
Janovjak, H. L., & Jackson, C. (2017). Ancestral protein reconstruction and
circular permutation for improving the stability and dynamic range of FRET sensors.
In V. Stein (Ed.), Synthetic Protein Switches (Vol. 1596, pp. 71–87). Springer.
https://doi.org/10.1007/978-1-4939-6940-1_5
chicago: Clifton, Ben, Jason Whitfield, Inmaculada Sanchez-Romero, Michel Herde,
Christian Henneberger, Harald L Janovjak, and Colin Jackson. “Ancestral Protein
Reconstruction and Circular Permutation for Improving the Stability and Dynamic
Range of FRET Sensors.” In Synthetic Protein Switches, edited by Viktor
Stein, 1596:71–87. Synthetic Protein Switches. Springer, 2017. https://doi.org/10.1007/978-1-4939-6940-1_5.
ieee: B. Clifton et al., “Ancestral protein reconstruction and circular permutation
for improving the stability and dynamic range of FRET sensors,” in Synthetic
Protein Switches, vol. 1596, V. Stein, Ed. Springer, 2017, pp. 71–87.
ista: 'Clifton B, Whitfield J, Sanchez-Romero I, Herde M, Henneberger C, Janovjak
HL, Jackson C. 2017.Ancestral protein reconstruction and circular permutation
for improving the stability and dynamic range of FRET sensors. In: Synthetic Protein
Switches. Methods in Molecular Biology, vol. 1596, 71–87.'
mla: Clifton, Ben, et al. “Ancestral Protein Reconstruction and Circular Permutation
for Improving the Stability and Dynamic Range of FRET Sensors.” Synthetic Protein
Switches, edited by Viktor Stein, vol. 1596, Springer, 2017, pp. 71–87, doi:10.1007/978-1-4939-6940-1_5.
short: B. Clifton, J. Whitfield, I. Sanchez-Romero, M. Herde, C. Henneberger, H.L.
Janovjak, C. Jackson, in:, V. Stein (Ed.), Synthetic Protein Switches, Springer,
2017, pp. 71–87.
date_created: 2018-12-11T11:49:24Z
date_published: 2017-03-15T00:00:00Z
date_updated: 2021-01-12T08:22:13Z
day: '15'
department:
- _id: HaJa
doi: 10.1007/978-1-4939-6940-1_5
editor:
- first_name: Viktor
full_name: Stein, Viktor
last_name: Stein
intvolume: ' 1596'
language:
- iso: eng
month: '03'
oa_version: None
page: 71 - 87
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: Synthetic Protein Switches
publication_identifier:
issn:
- '10643745'
publication_status: published
publisher: Springer
publist_id: '6451'
quality_controlled: '1'
scopus_import: 1
series_title: Synthetic Protein Switches
status: public
title: Ancestral protein reconstruction and circular permutation for improving the
stability and dynamic range of FRET sensors
type: book_chapter
user_id: 4435EBFC-F248-11E8-B48F-1D18A9856A87
volume: 1596
year: '2017'
...
---
_id: '963'
abstract:
- lang: eng
text: 'Network games are widely used as a model for selfish resource-allocation
problems. In the classical model, each player selects a path connecting her source
and target vertex. The cost of traversing an edge depends on the number of players
that traverse it. Thus, it abstracts the fact that different users may use a resource
at different times and for different durations, which plays an important role
in defining the costs of the users in reality. For example, when transmitting
packets in a communication network, routing traffic in a road network, or processing
a task in a production system, the traversal of the network involves an inherent
delay, and so sharing and congestion of resources crucially depends on time. We
study timed network games , which add a time component to network games. Each
vertex v in the network is associated with a cost function, mapping the load on
v to the price that a player pays for staying in v for one time unit with this
load. In addition, each edge has a guard, describing time intervals in which the
edge can be traversed, forcing the players to spend time on vertices. Unlike earlier
work that add a time component to network games, the time in our model is continuous
and cannot be discretized. In particular, players have uncountably many strategies,
and a game may have uncountably many pure Nash equilibria. We study properties
of timed network games with cost-sharing or congestion cost functions: their stability,
equilibrium inefficiency, and complexity. In particular, we show that the answer
to the question whether we can restrict attention to boundary strategies, namely
ones in which edges are traversed only at the boundaries of guards, is mixed. '
alternative_title:
- LIPIcs
article_number: '37'
author:
- first_name: Guy
full_name: Avni, Guy
id: 463C8BC2-F248-11E8-B48F-1D18A9856A87
last_name: Avni
orcid: 0000-0001-5588-8287
- first_name: Shibashis
full_name: Guha, Shibashis
last_name: Guha
- first_name: Orna
full_name: Kupferman, Orna
last_name: Kupferman
citation:
ama: 'Avni G, Guha S, Kupferman O. Timed network games with clocks. In: Vol 83.
Schloss Dagstuhl - Leibniz-Zentrum für Informatik; 2017. doi:10.4230/LIPIcs.MFCS.2017.37'
apa: 'Avni, G., Guha, S., & Kupferman, O. (2017). Timed network games with clocks
(Vol. 83). Presented at the MFCS: Mathematical Foundations of Computer Science
(SG), Aalborg, Denmark: Schloss Dagstuhl - Leibniz-Zentrum für Informatik. https://doi.org/10.4230/LIPIcs.MFCS.2017.37'
chicago: Avni, Guy, Shibashis Guha, and Orna Kupferman. “Timed Network Games with
Clocks,” Vol. 83. Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2017. https://doi.org/10.4230/LIPIcs.MFCS.2017.37.
ieee: 'G. Avni, S. Guha, and O. Kupferman, “Timed network games with clocks,” presented
at the MFCS: Mathematical Foundations of Computer Science (SG), Aalborg, Denmark,
2017, vol. 83.'
ista: 'Avni G, Guha S, Kupferman O. 2017. Timed network games with clocks. MFCS:
Mathematical Foundations of Computer Science (SG), LIPIcs, vol. 83, 37.'
mla: Avni, Guy, et al. Timed Network Games with Clocks. Vol. 83, 37, Schloss
Dagstuhl - Leibniz-Zentrum für Informatik, 2017, doi:10.4230/LIPIcs.MFCS.2017.37.
short: G. Avni, S. Guha, O. Kupferman, in:, Schloss Dagstuhl - Leibniz-Zentrum für
Informatik, 2017.
conference:
end_date: 2017-08-25
location: Aalborg, Denmark
name: 'MFCS: Mathematical Foundations of Computer Science (SG)'
start_date: 2017-08-21
date_created: 2018-12-11T11:49:26Z
date_published: 2017-06-01T00:00:00Z
date_updated: 2023-02-23T12:35:50Z
day: '01'
ddc:
- '004'
department:
- _id: ToHe
doi: 10.4230/LIPIcs.MFCS.2017.37
file:
- access_level: open_access
checksum: f55eaf7f3c36ea07801112acfedd17d5
content_type: application/pdf
creator: system
date_created: 2018-12-12T10:14:10Z
date_updated: 2020-07-14T12:48:18Z
file_id: '5059'
file_name: IST-2017-829-v1+1_mfcs-cr.pdf
file_size: 369730
relation: main_file
file_date_updated: 2020-07-14T12:48:18Z
has_accepted_license: '1'
intvolume: ' 83'
language:
- iso: eng
month: '06'
oa: 1
oa_version: Published Version
project:
- _id: 25F5A88A-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: S11402-N23
name: Moderne Concurrency Paradigms
publication_identifier:
issn:
- '18688969'
publication_status: published
publisher: Schloss Dagstuhl - Leibniz-Zentrum für Informatik
publist_id: '6438'
pubrep_id: '829'
quality_controlled: '1'
related_material:
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relation: later_version
status: public
scopus_import: 1
status: public
title: Timed network games with clocks
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: 83
year: '2017'
...
---
_id: '9709'
abstract:
- lang: eng
text: Across the nervous system, certain population spiking patterns are observed
far more frequently than others. A hypothesis about this structure is that these
collective activity patterns function as population codewords–collective modes–carrying
information distinct from that of any single cell. We investigate this phenomenon
in recordings of ∼150 retinal ganglion cells, the retina’s output. We develop
a novel statistical model that decomposes the population response into modes;
it predicts the distribution of spiking activity in the ganglion cell population
with high accuracy. We found that the modes represent localized features of the
visual stimulus that are distinct from the features represented by single neurons.
Modes form clusters of activity states that are readily discriminated from one
another. When we repeated the same visual stimulus, we found that the same mode
was robustly elicited. These results suggest that retinal ganglion cells’ collective
signaling is endowed with a form of error-correcting code–a principle that may
hold in brain areas beyond retina.
article_processing_charge: No
author:
- first_name: Jason
full_name: Prentice, Jason
last_name: Prentice
- first_name: Olivier
full_name: Marre, Olivier
last_name: Marre
- first_name: Mark
full_name: Ioffe, Mark
last_name: Ioffe
- first_name: Adrianna
full_name: Loback, Adrianna
last_name: Loback
- first_name: Gašper
full_name: Tkačik, Gašper
id: 3D494DCA-F248-11E8-B48F-1D18A9856A87
last_name: Tkačik
orcid: 0000-0002-6699-1455
- first_name: Michael
full_name: Berry, Michael
last_name: Berry
citation:
ama: 'Prentice J, Marre O, Ioffe M, Loback A, Tkačik G, Berry M. Data from: Error-robust
modes of the retinal population code. 2017. doi:10.5061/dryad.1f1rc'
apa: 'Prentice, J., Marre, O., Ioffe, M., Loback, A., Tkačik, G., & Berry, M.
(2017). Data from: Error-robust modes of the retinal population code. Dryad. https://doi.org/10.5061/dryad.1f1rc'
chicago: 'Prentice, Jason, Olivier Marre, Mark Ioffe, Adrianna Loback, Gašper Tkačik,
and Michael Berry. “Data from: Error-Robust Modes of the Retinal Population Code.”
Dryad, 2017. https://doi.org/10.5061/dryad.1f1rc.'
ieee: 'J. Prentice, O. Marre, M. Ioffe, A. Loback, G. Tkačik, and M. Berry, “Data
from: Error-robust modes of the retinal population code.” Dryad, 2017.'
ista: 'Prentice J, Marre O, Ioffe M, Loback A, Tkačik G, Berry M. 2017. Data from:
Error-robust modes of the retinal population code, Dryad, 10.5061/dryad.1f1rc.'
mla: 'Prentice, Jason, et al. Data from: Error-Robust Modes of the Retinal Population
Code. Dryad, 2017, doi:10.5061/dryad.1f1rc.'
short: J. Prentice, O. Marre, M. Ioffe, A. Loback, G. Tkačik, M. Berry, (2017).
date_created: 2021-07-23T11:34:34Z
date_published: 2017-10-18T00:00:00Z
date_updated: 2023-02-21T16:34:41Z
day: '18'
department:
- _id: GaTk
doi: 10.5061/dryad.1f1rc
main_file_link:
- open_access: '1'
url: https://doi.org/10.5061/dryad.1f1rc
month: '10'
oa: 1
oa_version: Published Version
publisher: Dryad
related_material:
record:
- id: '1197'
relation: used_in_publication
status: public
status: public
title: 'Data from: Error-robust modes of the retinal population code'
type: research_data_reference
user_id: 6785fbc1-c503-11eb-8a32-93094b40e1cf
year: '2017'
...
---
_id: '541'
abstract:
- lang: eng
text: 'While we have good understanding of bacterial metabolism at the population
level, we know little about the metabolic behavior of individual cells: do single
cells in clonal populations sometimes specialize on different metabolic pathways?
Such metabolic specialization could be driven by stochastic gene expression and
could provide individual cells with growth benefits of specialization. We measured
the degree of phenotypic specialization in two parallel metabolic pathways, the
assimilation of glucose and arabinose. We grew Escherichia coli in chemostats,
and used isotope-labeled sugars in combination with nanometer-scale secondary
ion mass spectrometry and mathematical modeling to quantify sugar assimilation
at the single-cell level. We found large variation in metabolic activities between
single cells, both in absolute assimilation and in the degree to which individual
cells specialize in the assimilation of different sugars. Analysis of transcriptional
reporters indicated that this variation was at least partially based on cell-to-cell
variation in gene expression. Metabolic differences between cells in clonal populations
could potentially reduce metabolic incompatibilities between different pathways,
and increase the rate at which parallel reactions can be performed.'
article_number: e1007122
author:
- first_name: Nela
full_name: Nikolic, Nela
id: 42D9CABC-F248-11E8-B48F-1D18A9856A87
last_name: Nikolic
orcid: 0000-0001-9068-6090
- first_name: Frank
full_name: Schreiber, Frank
last_name: Schreiber
- first_name: Alma
full_name: Dal Co, Alma
last_name: Dal Co
- first_name: Daniel
full_name: Kiviet, Daniel
last_name: Kiviet
- first_name: Tobias
full_name: Bergmiller, Tobias
id: 2C471CFA-F248-11E8-B48F-1D18A9856A87
last_name: Bergmiller
orcid: 0000-0001-5396-4346
- first_name: Sten
full_name: Littmann, Sten
last_name: Littmann
- first_name: Marcel
full_name: Kuypers, Marcel
last_name: Kuypers
- first_name: Martin
full_name: Ackermann, Martin
last_name: Ackermann
citation:
ama: Nikolic N, Schreiber F, Dal Co A, et al. Cell-to-cell variation and specialization
in sugar metabolism in clonal bacterial populations. PLoS Genetics. 2017;13(12).
doi:10.1371/journal.pgen.1007122
apa: Nikolic, N., Schreiber, F., Dal Co, A., Kiviet, D., Bergmiller, T., Littmann,
S., … Ackermann, M. (2017). Cell-to-cell variation and specialization in sugar
metabolism in clonal bacterial populations. PLoS Genetics. Public Library
of Science. https://doi.org/10.1371/journal.pgen.1007122
chicago: Nikolic, Nela, Frank Schreiber, Alma Dal Co, Daniel Kiviet, Tobias Bergmiller,
Sten Littmann, Marcel Kuypers, and Martin Ackermann. “Cell-to-Cell Variation and
Specialization in Sugar Metabolism in Clonal Bacterial Populations.” PLoS Genetics.
Public Library of Science, 2017. https://doi.org/10.1371/journal.pgen.1007122.
ieee: N. Nikolic et al., “Cell-to-cell variation and specialization in sugar
metabolism in clonal bacterial populations,” PLoS Genetics, vol. 13, no.
12. Public Library of Science, 2017.
ista: Nikolic N, Schreiber F, Dal Co A, Kiviet D, Bergmiller T, Littmann S, Kuypers
M, Ackermann M. 2017. Cell-to-cell variation and specialization in sugar metabolism
in clonal bacterial populations. PLoS Genetics. 13(12), e1007122.
mla: Nikolic, Nela, et al. “Cell-to-Cell Variation and Specialization in Sugar Metabolism
in Clonal Bacterial Populations.” PLoS Genetics, vol. 13, no. 12, e1007122,
Public Library of Science, 2017, doi:10.1371/journal.pgen.1007122.
short: N. Nikolic, F. Schreiber, A. Dal Co, D. Kiviet, T. Bergmiller, S. Littmann,
M. Kuypers, M. Ackermann, PLoS Genetics 13 (2017).
date_created: 2018-12-11T11:47:04Z
date_published: 2017-12-18T00:00:00Z
date_updated: 2023-02-23T14:10:34Z
day: '18'
ddc:
- '576'
- '579'
department:
- _id: CaGu
doi: 10.1371/journal.pgen.1007122
ec_funded: 1
file:
- access_level: open_access
checksum: 22426d9382f21554bad5fa5967afcfd0
content_type: application/pdf
creator: system
date_created: 2018-12-12T10:14:35Z
date_updated: 2020-07-14T12:46:46Z
file_id: '5088'
file_name: IST-2018-959-v1+1_2017_Nikolic_Cell-to-cell.pdf
file_size: 1308475
relation: main_file
file_date_updated: 2020-07-14T12:46:46Z
has_accepted_license: '1'
intvolume: ' 13'
issue: '12'
language:
- iso: eng
month: '12'
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: PLoS Genetics
publication_identifier:
issn:
- '15537390'
publication_status: published
publisher: Public Library of Science
publist_id: '7275'
pubrep_id: '959'
quality_controlled: '1'
related_material:
record:
- id: '9844'
relation: research_data
status: public
- id: '9845'
relation: research_data
status: public
- id: '9846'
relation: research_data
status: public
scopus_import: 1
status: public
title: Cell-to-cell variation and specialization in sugar metabolism in clonal bacterial
populations
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: '2017'
...
---
_id: '9847'
abstract:
- lang: eng
text: information on culture conditions, phage mutagenesis, verification and lysate
preparation; Raw data
article_processing_charge: No
author:
- first_name: Maros
full_name: Pleska, Maros
id: 4569785E-F248-11E8-B48F-1D18A9856A87
last_name: Pleska
orcid: 0000-0001-7460-7479
- first_name: Calin C
full_name: Guet, Calin C
id: 47F8433E-F248-11E8-B48F-1D18A9856A87
last_name: Guet
orcid: 0000-0001-6220-2052
citation:
ama: Pleska M, Guet CC. Supplementary materials and methods; Full data set from
effects of mutations in phage restriction sites during escape from restriction–modification.
2017. doi:10.6084/m9.figshare.5633917.v1
apa: Pleska, M., & Guet, C. C. (2017). Supplementary materials and methods;
Full data set from effects of mutations in phage restriction sites during escape
from restriction–modification. The Royal Society. https://doi.org/10.6084/m9.figshare.5633917.v1
chicago: Pleska, Maros, and Calin C Guet. “Supplementary Materials and Methods;
Full Data Set from Effects of Mutations in Phage Restriction Sites during Escape
from Restriction–Modification.” The Royal Society, 2017. https://doi.org/10.6084/m9.figshare.5633917.v1.
ieee: M. Pleska and C. C. Guet, “Supplementary materials and methods; Full data
set from effects of mutations in phage restriction sites during escape from restriction–modification.”
The Royal Society, 2017.
ista: Pleska M, Guet CC. 2017. Supplementary materials and methods; Full data set
from effects of mutations in phage restriction sites during escape from restriction–modification,
The Royal Society, 10.6084/m9.figshare.5633917.v1.
mla: Pleska, Maros, and Calin C. Guet. Supplementary Materials and Methods; Full
Data Set from Effects of Mutations in Phage Restriction Sites during Escape from
Restriction–Modification. The Royal Society, 2017, doi:10.6084/m9.figshare.5633917.v1.
short: M. Pleska, C.C. Guet, (2017).
date_created: 2021-08-09T13:54:38Z
date_published: 2017-11-27T00:00:00Z
date_updated: 2023-02-23T12:29:44Z
day: '27'
department:
- _id: CaGu
doi: 10.6084/m9.figshare.5633917.v1
main_file_link:
- open_access: '1'
url: https://doi.org/10.6084/m9.figshare.5633917.v1
month: '11'
oa: 1
oa_version: Published Version
publisher: The Royal Society
related_material:
record:
- id: '561'
relation: used_in_publication
status: public
status: public
title: Supplementary materials and methods; Full data set from effects of mutations
in phage restriction sites during escape from restriction–modification
type: research_data_reference
user_id: 6785fbc1-c503-11eb-8a32-93094b40e1cf
year: '2017'
...
---
_id: '9845'
abstract:
- lang: eng
text: "Estimates of 13 C-arabinose and 2 H-glucose uptake from the fractions of
heavy isotopes measured\tin single cells"
article_processing_charge: No
author:
- first_name: Nela
full_name: Nikolic, Nela
id: 42D9CABC-F248-11E8-B48F-1D18A9856A87
last_name: Nikolic
orcid: 0000-0001-9068-6090
- first_name: Frank
full_name: Schreiber, Frank
last_name: Schreiber
- first_name: Alma
full_name: Dal Co, Alma
last_name: Dal Co
- first_name: Daniel
full_name: Kiviet, Daniel
last_name: Kiviet
- first_name: Tobias
full_name: Bergmiller, Tobias
id: 2C471CFA-F248-11E8-B48F-1D18A9856A87
last_name: Bergmiller
orcid: 0000-0001-5396-4346
- first_name: Sten
full_name: Littmann, Sten
last_name: Littmann
- first_name: Marcel
full_name: Kuypers, Marcel
last_name: Kuypers
- first_name: Martin
full_name: Ackermann, Martin
last_name: Ackermann
citation:
ama: Nikolic N, Schreiber F, Dal Co A, et al. Mathematical model. 2017. doi:10.1371/journal.pgen.1007122.s017
apa: Nikolic, N., Schreiber, F., Dal Co, A., Kiviet, D., Bergmiller, T., Littmann,
S., … Ackermann, M. (2017). Mathematical model. Public Library of Science. https://doi.org/10.1371/journal.pgen.1007122.s017
chicago: Nikolic, Nela, Frank Schreiber, Alma Dal Co, Daniel Kiviet, Tobias Bergmiller,
Sten Littmann, Marcel Kuypers, and Martin Ackermann. “Mathematical Model.” Public
Library of Science, 2017. https://doi.org/10.1371/journal.pgen.1007122.s017.
ieee: N. Nikolic et al., “Mathematical model.” Public Library of Science,
2017.
ista: Nikolic N, Schreiber F, Dal Co A, Kiviet D, Bergmiller T, Littmann S, Kuypers
M, Ackermann M. 2017. Mathematical model, Public Library of Science, 10.1371/journal.pgen.1007122.s017.
mla: Nikolic, Nela, et al. Mathematical Model. Public Library of Science,
2017, doi:10.1371/journal.pgen.1007122.s017.
short: N. Nikolic, F. Schreiber, A. Dal Co, D. Kiviet, T. Bergmiller, S. Littmann,
M. Kuypers, M. Ackermann, (2017).
date_created: 2021-08-09T13:31:51Z
date_published: 2017-12-18T00:00:00Z
date_updated: 2023-02-23T12:25:04Z
day: '18'
department:
- _id: CaGu
doi: 10.1371/journal.pgen.1007122.s017
month: '12'
oa_version: None
publisher: Public Library of Science
related_material:
record:
- id: '541'
relation: used_in_publication
status: public
status: public
title: Mathematical model
type: research_data_reference
user_id: 6785fbc1-c503-11eb-8a32-93094b40e1cf
year: '2017'
...
---
_id: '9849'
abstract:
- lang: eng
text: This text provides additional information about the model, a derivation of
the analytic results in Eq (4), and details about simulations of an additional
parameter set.
article_processing_charge: No
author:
- first_name: Marta
full_name: Lukacisinova, Marta
id: 4342E402-F248-11E8-B48F-1D18A9856A87
last_name: Lukacisinova
orcid: 0000-0002-2519-8004
- first_name: Sebastian
full_name: Novak, Sebastian
id: 461468AE-F248-11E8-B48F-1D18A9856A87
last_name: Novak
- first_name: Tiago
full_name: Paixao, Tiago
id: 2C5658E6-F248-11E8-B48F-1D18A9856A87
last_name: Paixao
orcid: 0000-0003-2361-3953
citation:
ama: Lukacisinova M, Novak S, Paixao T. Modelling and simulation details. 2017.
doi:10.1371/journal.pcbi.1005609.s001
apa: Lukacisinova, M., Novak, S., & Paixao, T. (2017). Modelling and simulation
details. Public Library of Science. https://doi.org/10.1371/journal.pcbi.1005609.s001
chicago: Lukacisinova, Marta, Sebastian Novak, and Tiago Paixao. “Modelling and
Simulation Details.” Public Library of Science, 2017. https://doi.org/10.1371/journal.pcbi.1005609.s001.
ieee: M. Lukacisinova, S. Novak, and T. Paixao, “Modelling and simulation details.”
Public Library of Science, 2017.
ista: Lukacisinova M, Novak S, Paixao T. 2017. Modelling and simulation details,
Public Library of Science, 10.1371/journal.pcbi.1005609.s001.
mla: Lukacisinova, Marta, et al. Modelling and Simulation Details. Public
Library of Science, 2017, doi:10.1371/journal.pcbi.1005609.s001.
short: M. Lukacisinova, S. Novak, T. Paixao, (2017).
date_created: 2021-08-09T14:02:34Z
date_published: 2017-07-18T00:00:00Z
date_updated: 2023-02-23T12:55:39Z
day: '18'
department:
- _id: ToBo
- _id: NiBa
- _id: CaGu
doi: 10.1371/journal.pcbi.1005609.s001
month: '07'
oa_version: Published Version
publisher: Public Library of Science
related_material:
record:
- id: '696'
relation: used_in_publication
status: public
status: public
title: Modelling and simulation details
type: research_data_reference
user_id: 6785fbc1-c503-11eb-8a32-93094b40e1cf
year: '2017'
...
---
_id: '9850'
abstract:
- lang: eng
text: In this text, we discuss how a cost of resistance and the possibility of lethal
mutations impact our model.
article_processing_charge: No
author:
- first_name: Marta
full_name: Lukacisinova, Marta
id: 4342E402-F248-11E8-B48F-1D18A9856A87
last_name: Lukacisinova
orcid: 0000-0002-2519-8004
- first_name: Sebastian
full_name: Novak, Sebastian
id: 461468AE-F248-11E8-B48F-1D18A9856A87
last_name: Novak
- first_name: Tiago
full_name: Paixao, Tiago
id: 2C5658E6-F248-11E8-B48F-1D18A9856A87
last_name: Paixao
orcid: 0000-0003-2361-3953
citation:
ama: Lukacisinova M, Novak S, Paixao T. Extensions of the model. 2017. doi:10.1371/journal.pcbi.1005609.s002
apa: Lukacisinova, M., Novak, S., & Paixao, T. (2017). Extensions of the model.
Public Library of Science. https://doi.org/10.1371/journal.pcbi.1005609.s002
chicago: Lukacisinova, Marta, Sebastian Novak, and Tiago Paixao. “Extensions of
the Model.” Public Library of Science, 2017. https://doi.org/10.1371/journal.pcbi.1005609.s002.
ieee: M. Lukacisinova, S. Novak, and T. Paixao, “Extensions of the model.” Public
Library of Science, 2017.
ista: Lukacisinova M, Novak S, Paixao T. 2017. Extensions of the model, Public Library
of Science, 10.1371/journal.pcbi.1005609.s002.
mla: Lukacisinova, Marta, et al. Extensions of the Model. Public Library
of Science, 2017, doi:10.1371/journal.pcbi.1005609.s002.
short: M. Lukacisinova, S. Novak, T. Paixao, (2017).
date_created: 2021-08-09T14:05:24Z
date_published: 2017-07-18T00:00:00Z
date_updated: 2023-02-23T12:55:39Z
day: '18'
department:
- _id: ToBo
- _id: CaGu
- _id: NiBa
doi: 10.1371/journal.pcbi.1005609.s002
month: '07'
oa_version: Published Version
publisher: Public Library of Science
related_material:
record:
- id: '696'
relation: used_in_publication
status: public
status: public
title: Extensions of the model
type: research_data_reference
user_id: 6785fbc1-c503-11eb-8a32-93094b40e1cf
year: '2017'
...
---
_id: '9846'
article_processing_charge: No
author:
- first_name: Nela
full_name: Nikolic, Nela
id: 42D9CABC-F248-11E8-B48F-1D18A9856A87
last_name: Nikolic
orcid: 0000-0001-9068-6090
- first_name: Frank
full_name: Schreiber, Frank
last_name: Schreiber
- first_name: Alma
full_name: Dal Co, Alma
last_name: Dal Co
- first_name: Daniel
full_name: Kiviet, Daniel
last_name: Kiviet
- first_name: Tobias
full_name: Bergmiller, Tobias
id: 2C471CFA-F248-11E8-B48F-1D18A9856A87
last_name: Bergmiller
orcid: 0000-0001-5396-4346
- first_name: Sten
full_name: Littmann, Sten
last_name: Littmann
- first_name: Marcel
full_name: Kuypers, Marcel
last_name: Kuypers
- first_name: Martin
full_name: Ackermann, Martin
last_name: Ackermann
citation:
ama: Nikolic N, Schreiber F, Dal Co A, et al. Supplementary methods. 2017. doi:10.1371/journal.pgen.1007122.s016
apa: Nikolic, N., Schreiber, F., Dal Co, A., Kiviet, D., Bergmiller, T., Littmann,
S., … Ackermann, M. (2017). Supplementary methods. Public Library of Science.
https://doi.org/10.1371/journal.pgen.1007122.s016
chicago: Nikolic, Nela, Frank Schreiber, Alma Dal Co, Daniel Kiviet, Tobias Bergmiller,
Sten Littmann, Marcel Kuypers, and Martin Ackermann. “Supplementary Methods.”
Public Library of Science, 2017. https://doi.org/10.1371/journal.pgen.1007122.s016.
ieee: N. Nikolic et al., “Supplementary methods.” Public Library of Science,
2017.
ista: Nikolic N, Schreiber F, Dal Co A, Kiviet D, Bergmiller T, Littmann S, Kuypers
M, Ackermann M. 2017. Supplementary methods, Public Library of Science, 10.1371/journal.pgen.1007122.s016.
mla: Nikolic, Nela, et al. Supplementary Methods. Public Library of Science,
2017, doi:10.1371/journal.pgen.1007122.s016.
short: N. Nikolic, F. Schreiber, A. Dal Co, D. Kiviet, T. Bergmiller, S. Littmann,
M. Kuypers, M. Ackermann, (2017).
date_created: 2021-08-09T13:35:17Z
date_published: 2017-12-18T00:00:00Z
date_updated: 2023-02-23T12:25:04Z
day: '18'
department:
- _id: CaGu
doi: 10.1371/journal.pgen.1007122.s016
month: '12'
oa_version: Published Version
publisher: Public Library of Science
related_material:
record:
- id: '541'
relation: used_in_publication
status: public
status: public
title: Supplementary methods
type: research_data_reference
user_id: 6785fbc1-c503-11eb-8a32-93094b40e1cf
year: '2017'
...
---
_id: '680'
abstract:
- lang: eng
text: In order to respond reliably to specific features of their environment, sensory
neurons need to integrate multiple incoming noisy signals. Crucially, they also
need to compete for the interpretation of those signals with other neurons representing
similar features. The form that this competition should take depends critically
on the noise corrupting these signals. In this study we show that for the type
of noise commonly observed in sensory systems, whose variance scales with the
mean signal, sensory neurons should selectively divide their input signals by
their predictions, suppressing ambiguous cues while amplifying others. Any change
in the stimulus context alters which inputs are suppressed, leading to a deep
dynamic reshaping of neural receptive fields going far beyond simple surround
suppression. Paradoxically, these highly variable receptive fields go alongside
and are in fact required for an invariant representation of external sensory features.
In addition to offering a normative account of context-dependent changes in sensory
responses, perceptual inference in the presence of signal-dependent noise accounts
for ubiquitous features of sensory neurons such as divisive normalization, gain
control and contrast dependent temporal dynamics.
article_number: e1005582
author:
- first_name: Matthew J
full_name: Chalk, Matthew J
id: 2BAAC544-F248-11E8-B48F-1D18A9856A87
last_name: Chalk
orcid: 0000-0001-7782-4436
- first_name: Paul
full_name: Masset, Paul
last_name: Masset
- first_name: Boris
full_name: Gutkin, Boris
last_name: Gutkin
- first_name: Sophie
full_name: Denève, Sophie
last_name: Denève
citation:
ama: Chalk MJ, Masset P, Gutkin B, Denève S. Sensory noise predicts divisive reshaping
of receptive fields. PLoS Computational Biology. 2017;13(6). doi:10.1371/journal.pcbi.1005582
apa: Chalk, M. J., Masset, P., Gutkin, B., & Denève, S. (2017). Sensory noise
predicts divisive reshaping of receptive fields. PLoS Computational Biology.
Public Library of Science. https://doi.org/10.1371/journal.pcbi.1005582
chicago: Chalk, Matthew J, Paul Masset, Boris Gutkin, and Sophie Denève. “Sensory
Noise Predicts Divisive Reshaping of Receptive Fields.” PLoS Computational
Biology. Public Library of Science, 2017. https://doi.org/10.1371/journal.pcbi.1005582.
ieee: M. J. Chalk, P. Masset, B. Gutkin, and S. Denève, “Sensory noise predicts
divisive reshaping of receptive fields,” PLoS Computational Biology, vol.
13, no. 6. Public Library of Science, 2017.
ista: Chalk MJ, Masset P, Gutkin B, Denève S. 2017. Sensory noise predicts divisive
reshaping of receptive fields. PLoS Computational Biology. 13(6), e1005582.
mla: Chalk, Matthew J., et al. “Sensory Noise Predicts Divisive Reshaping of Receptive
Fields.” PLoS Computational Biology, vol. 13, no. 6, e1005582, Public Library
of Science, 2017, doi:10.1371/journal.pcbi.1005582.
short: M.J. Chalk, P. Masset, B. Gutkin, S. Denève, PLoS Computational Biology 13
(2017).
date_created: 2018-12-11T11:47:53Z
date_published: 2017-06-01T00:00:00Z
date_updated: 2023-02-23T14:10:54Z
day: '01'
ddc:
- '571'
department:
- _id: GaTk
doi: 10.1371/journal.pcbi.1005582
file:
- access_level: open_access
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creator: system
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file_name: IST-2017-898-v1+1_journal.pcbi.1005582.pdf
file_size: 14555676
relation: main_file
file_date_updated: 2020-07-14T12:47:40Z
has_accepted_license: '1'
intvolume: ' 13'
issue: '6'
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month: '06'
oa: 1
oa_version: Published Version
publication: PLoS Computational Biology
publication_identifier:
issn:
- 1553734X
publication_status: published
publisher: Public Library of Science
publist_id: '7035'
pubrep_id: '898'
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related_material:
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relation: research_data
status: public
scopus_import: 1
status: public
title: Sensory noise predicts divisive reshaping of receptive fields
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: '2017'
...
---
_id: '9851'
abstract:
- lang: eng
text: Based on the intuitive derivation of the dynamics of SIM allele frequency
pM in the main text, we present a heuristic prediction for the long-term SIM allele
frequencies with χ > 1 stresses and compare it to numerical simulations.
article_processing_charge: No
author:
- first_name: Marta
full_name: Lukacisinova, Marta
id: 4342E402-F248-11E8-B48F-1D18A9856A87
last_name: Lukacisinova
orcid: 0000-0002-2519-8004
- first_name: Sebastian
full_name: Novak, Sebastian
id: 461468AE-F248-11E8-B48F-1D18A9856A87
last_name: Novak
- first_name: Tiago
full_name: Paixao, Tiago
id: 2C5658E6-F248-11E8-B48F-1D18A9856A87
last_name: Paixao
orcid: 0000-0003-2361-3953
citation:
ama: Lukacisinova M, Novak S, Paixao T. Heuristic prediction for multiple stresses.
2017. doi:10.1371/journal.pcbi.1005609.s003
apa: Lukacisinova, M., Novak, S., & Paixao, T. (2017). Heuristic prediction
for multiple stresses. Public Library of Science. https://doi.org/10.1371/journal.pcbi.1005609.s003
chicago: Lukacisinova, Marta, Sebastian Novak, and Tiago Paixao. “Heuristic Prediction
for Multiple Stresses.” Public Library of Science, 2017. https://doi.org/10.1371/journal.pcbi.1005609.s003.
ieee: M. Lukacisinova, S. Novak, and T. Paixao, “Heuristic prediction for multiple
stresses.” Public Library of Science, 2017.
ista: Lukacisinova M, Novak S, Paixao T. 2017. Heuristic prediction for multiple
stresses, Public Library of Science, 10.1371/journal.pcbi.1005609.s003.
mla: Lukacisinova, Marta, et al. Heuristic Prediction for Multiple Stresses.
Public Library of Science, 2017, doi:10.1371/journal.pcbi.1005609.s003.
short: M. Lukacisinova, S. Novak, T. Paixao, (2017).
date_created: 2021-08-09T14:08:14Z
date_published: 2017-07-18T00:00:00Z
date_updated: 2023-02-23T12:55:39Z
day: '18'
department:
- _id: ToBo
- _id: CaGu
- _id: NiBa
doi: 10.1371/journal.pcbi.1005609.s003
month: '07'
oa_version: Published Version
publisher: Public Library of Science
related_material:
record:
- id: '696'
relation: used_in_publication
status: public
status: public
title: Heuristic prediction for multiple stresses
type: research_data_reference
user_id: 6785fbc1-c503-11eb-8a32-93094b40e1cf
year: '2017'
...
---
_id: '9852'
abstract:
- lang: eng
text: We show how different combination strategies affect the fraction of individuals
that are multi-resistant.
article_processing_charge: No
author:
- first_name: Marta
full_name: Lukacisinova, Marta
id: 4342E402-F248-11E8-B48F-1D18A9856A87
last_name: Lukacisinova
orcid: 0000-0002-2519-8004
- first_name: Sebastian
full_name: Novak, Sebastian
id: 461468AE-F248-11E8-B48F-1D18A9856A87
last_name: Novak
- first_name: Tiago
full_name: Paixao, Tiago
id: 2C5658E6-F248-11E8-B48F-1D18A9856A87
last_name: Paixao
orcid: 0000-0003-2361-3953
citation:
ama: Lukacisinova M, Novak S, Paixao T. Resistance frequencies for different combination
strategies. 2017. doi:10.1371/journal.pcbi.1005609.s004
apa: Lukacisinova, M., Novak, S., & Paixao, T. (2017). Resistance frequencies
for different combination strategies. Public Library of Science. https://doi.org/10.1371/journal.pcbi.1005609.s004
chicago: Lukacisinova, Marta, Sebastian Novak, and Tiago Paixao. “Resistance Frequencies
for Different Combination Strategies.” Public Library of Science, 2017. https://doi.org/10.1371/journal.pcbi.1005609.s004.
ieee: M. Lukacisinova, S. Novak, and T. Paixao, “Resistance frequencies for different
combination strategies.” Public Library of Science, 2017.
ista: Lukacisinova M, Novak S, Paixao T. 2017. Resistance frequencies for different
combination strategies, Public Library of Science, 10.1371/journal.pcbi.1005609.s004.
mla: Lukacisinova, Marta, et al. Resistance Frequencies for Different Combination
Strategies. Public Library of Science, 2017, doi:10.1371/journal.pcbi.1005609.s004.
short: M. Lukacisinova, S. Novak, T. Paixao, (2017).
date_created: 2021-08-09T14:11:40Z
date_published: 2017-07-18T00:00:00Z
date_updated: 2023-02-23T12:55:39Z
day: '18'
department:
- _id: ToBo
- _id: CaGu
- _id: NiBa
doi: 10.1371/journal.pcbi.1005609.s004
month: '07'
oa_version: Published Version
publisher: Public Library of Science
related_material:
record:
- id: '696'
relation: used_in_publication
status: public
status: public
title: Resistance frequencies for different combination strategies
type: research_data_reference
user_id: 6785fbc1-c503-11eb-8a32-93094b40e1cf
year: '2017'
...
---
_id: '9855'
abstract:
- lang: eng
text: Includes derivation of optimal estimation algorithm, generalisation to non-poisson
noise statistics, correlated input noise, and implementation of in a multi-layer
neural network.
article_processing_charge: No
author:
- first_name: Matthew J
full_name: Chalk, Matthew J
id: 2BAAC544-F248-11E8-B48F-1D18A9856A87
last_name: Chalk
orcid: 0000-0001-7782-4436
- first_name: Paul
full_name: Masset, Paul
last_name: Masset
- first_name: Boris
full_name: Gutkin, Boris
last_name: Gutkin
- first_name: Sophie
full_name: Denève, Sophie
last_name: Denève
citation:
ama: Chalk MJ, Masset P, Gutkin B, Denève S. Supplementary appendix. 2017. doi:10.1371/journal.pcbi.1005582.s001
apa: Chalk, M. J., Masset, P., Gutkin, B., & Denève, S. (2017). Supplementary
appendix. Public Library of Science. https://doi.org/10.1371/journal.pcbi.1005582.s001
chicago: Chalk, Matthew J, Paul Masset, Boris Gutkin, and Sophie Denève. “Supplementary
Appendix.” Public Library of Science, 2017. https://doi.org/10.1371/journal.pcbi.1005582.s001.
ieee: M. J. Chalk, P. Masset, B. Gutkin, and S. Denève, “Supplementary appendix.”
Public Library of Science, 2017.
ista: Chalk MJ, Masset P, Gutkin B, Denève S. 2017. Supplementary appendix, Public
Library of Science, 10.1371/journal.pcbi.1005582.s001.
mla: Chalk, Matthew J., et al. Supplementary Appendix. Public Library of
Science, 2017, doi:10.1371/journal.pcbi.1005582.s001.
short: M.J. Chalk, P. Masset, B. Gutkin, S. Denève, (2017).
date_created: 2021-08-10T07:05:10Z
date_published: 2017-06-01T00:00:00Z
date_updated: 2023-02-23T12:52:17Z
day: '01'
department:
- _id: GaTk
doi: 10.1371/journal.pcbi.1005582.s001
month: '06'
oa_version: Published Version
publisher: Public Library of Science
related_material:
record:
- id: '680'
relation: used_in_publication
status: public
status: public
title: Supplementary appendix
type: research_data_reference
user_id: 6785fbc1-c503-11eb-8a32-93094b40e1cf
year: '2017'
...
---
_id: '941'
abstract:
- lang: eng
text: 'Recently there has been a proliferation of automated program repair (APR)
techniques, targeting various programming languages. Such techniques can be generally
classified into two families: syntactic- and semantics-based. Semantics-based
APR, on which we focus, typically uses symbolic execution to infer semantic constraints
and then program synthesis to construct repairs conforming to them. While syntactic-based
APR techniques have been shown successful on bugs in real-world programs written
in both C and Java, semantics-based APR techniques mostly target C programs. This
leaves empirical comparisons of the APR families not fully explored, and developers
without a Java-based semantics APR technique. We present JFix, a semantics-based
APR framework that targets Java, and an associated Eclipse plugin. JFix is implemented
atop Symbolic PathFinder, a well-known symbolic execution engine for Java programs.
It extends one particular APR technique (Angelix), and is designed to be sufficiently
generic to support a variety of such techniques. We demonstrate that semantics-based
APR can indeed efficiently and effectively repair a variety of classes of bugs
in large real-world Java programs. This supports our claim that the framework
can both support developers seeking semantics-based repair of bugs in Java programs,
as well as enable larger scale empirical studies comparing syntactic- and semantics-based
APR targeting Java. The demonstration of our tool is available via the project
website at: https://xuanbachle.github.io/semanticsrepair/ '
author:
- first_name: Xuan
full_name: Le, Xuan
last_name: Le
- first_name: Duc Hiep
full_name: Chu, Duc Hiep
id: 3598E630-F248-11E8-B48F-1D18A9856A87
last_name: Chu
- first_name: David
full_name: Lo, David
last_name: Lo
- first_name: Claire
full_name: Le Goues, Claire
last_name: Le Goues
- first_name: Willem
full_name: Visser, Willem
last_name: Visser
citation:
ama: 'Le X, Chu DH, Lo D, Le Goues C, Visser W. JFIX: Semantics-based repair of
Java programs via symbolic PathFinder. In: Proceedings of the 26th ACM SIGSOFT
International Symposium on Software Testing and Analysis. ACM; 2017:376-379.
doi:10.1145/3092703.3098225'
apa: 'Le, X., Chu, D. H., Lo, D., Le Goues, C., & Visser, W. (2017). JFIX: Semantics-based
repair of Java programs via symbolic PathFinder. In Proceedings of the 26th
ACM SIGSOFT International Symposium on Software Testing and Analysis (pp.
376–379). Santa Barbara, CA, United States: ACM. https://doi.org/10.1145/3092703.3098225'
chicago: 'Le, Xuan, Duc Hiep Chu, David Lo, Claire Le Goues, and Willem Visser.
“JFIX: Semantics-Based Repair of Java Programs via Symbolic PathFinder.” In Proceedings
of the 26th ACM SIGSOFT International Symposium on Software Testing and Analysis,
376–79. ACM, 2017. https://doi.org/10.1145/3092703.3098225.'
ieee: 'X. Le, D. H. Chu, D. Lo, C. Le Goues, and W. Visser, “JFIX: Semantics-based
repair of Java programs via symbolic PathFinder,” in Proceedings of the 26th
ACM SIGSOFT International Symposium on Software Testing and Analysis, Santa
Barbara, CA, United States, 2017, pp. 376–379.'
ista: 'Le X, Chu DH, Lo D, Le Goues C, Visser W. 2017. JFIX: Semantics-based repair
of Java programs via symbolic PathFinder. Proceedings of the 26th ACM SIGSOFT
International Symposium on Software Testing and Analysis. ISSTA: International
Symposium on Software Testing and Analysis, 376–379.'
mla: 'Le, Xuan, et al. “JFIX: Semantics-Based Repair of Java Programs via Symbolic
PathFinder.” Proceedings of the 26th ACM SIGSOFT International Symposium on
Software Testing and Analysis, ACM, 2017, pp. 376–79, doi:10.1145/3092703.3098225.'
short: X. Le, D.H. Chu, D. Lo, C. Le Goues, W. Visser, in:, Proceedings of the 26th
ACM SIGSOFT International Symposium on Software Testing and Analysis, ACM, 2017,
pp. 376–379.
conference:
end_date: 2017-07-14
location: Santa Barbara, CA, United States
name: 'ISSTA: International Symposium on Software Testing and Analysis'
start_date: 2017-07-10
date_created: 2018-12-11T11:49:19Z
date_published: 2017-07-10T00:00:00Z
date_updated: 2021-01-12T08:22:05Z
day: '10'
department:
- _id: ToHe
doi: 10.1145/3092703.3098225
language:
- iso: eng
month: '07'
oa_version: None
page: '376 - 379 '
project:
- _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
publication: Proceedings of the 26th ACM SIGSOFT International Symposium on Software
Testing and Analysis
publication_status: published
publisher: ACM
publist_id: '6478'
quality_controlled: '1'
scopus_import: 1
status: public
title: 'JFIX: Semantics-based repair of Java programs via symbolic PathFinder'
type: conference
user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87
year: '2017'
...
---
_id: '9506'
abstract:
- lang: eng
text: Methylation in the bodies of active genes is common in animals and vascular
plants. Evolutionary patterns indicate homeostatic functions for this type of
methylation.
article_number: '87'
article_processing_charge: No
author:
- first_name: Daniel
full_name: Zilberman, Daniel
id: 6973db13-dd5f-11ea-814e-b3e5455e9ed1
last_name: Zilberman
orcid: 0000-0002-0123-8649
citation:
ama: Zilberman D. An evolutionary case for functional gene body methylation in plants
and animals. Genome Biology. 2017;18(1). doi:10.1186/s13059-017-1230-2
apa: Zilberman, D. (2017). An evolutionary case for functional gene body methylation
in plants and animals. Genome Biology. Springer Nature. https://doi.org/10.1186/s13059-017-1230-2
chicago: Zilberman, Daniel. “An Evolutionary Case for Functional Gene Body Methylation
in Plants and Animals.” Genome Biology. Springer Nature, 2017. https://doi.org/10.1186/s13059-017-1230-2.
ieee: D. Zilberman, “An evolutionary case for functional gene body methylation in
plants and animals,” Genome Biology, vol. 18, no. 1. Springer Nature, 2017.
ista: Zilberman D. 2017. An evolutionary case for functional gene body methylation
in plants and animals. Genome Biology. 18(1), 87.
mla: Zilberman, Daniel. “An Evolutionary Case for Functional Gene Body Methylation
in Plants and Animals.” Genome Biology, vol. 18, no. 1, 87, Springer Nature,
2017, doi:10.1186/s13059-017-1230-2.
short: D. Zilberman, Genome Biology 18 (2017).
date_created: 2021-06-07T12:27:39Z
date_published: 2017-05-09T00:00:00Z
date_updated: 2021-12-14T07:55:02Z
day: '09'
ddc:
- '570'
department:
- _id: DaZi
doi: 10.1186/s13059-017-1230-2
extern: '1'
external_id:
pmid:
- '28486944'
file:
- access_level: open_access
checksum: 5a455ad914e7d225b1baa4ab07fd925e
content_type: application/pdf
creator: asandaue
date_created: 2021-06-07T12:31:36Z
date_updated: 2021-06-07T12:31:36Z
file_id: '9507'
file_name: 2017_GenomeBiology_Zilberman.pdf
file_size: 278183
relation: main_file
success: 1
file_date_updated: 2021-06-07T12:31:36Z
has_accepted_license: '1'
intvolume: ' 18'
issue: '1'
language:
- iso: eng
month: '05'
oa: 1
oa_version: Published Version
pmid: 1
publication: Genome Biology
publication_identifier:
eissn:
- 1465-6906
issn:
- 1474-760X
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
scopus_import: '1'
status: public
title: An evolutionary case for functional gene body methylation in plants and animals
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: 8b945eb4-e2f2-11eb-945a-df72226e66a9
volume: 18
year: '2017'
...
---
_id: '958'
abstract:
- lang: eng
text: Biosensors that exploit Forster resonance energy transfer (FRET) can be used
to visualize biological and physiological processes and are capable of providing
detailed information in both spatial and temporal dimensions. In a FRET-based
biosensor, substrate binding is associated with a change in the relative positions
of two fluorophores, leading to a change in FRET efficiency that may be observed
in the fluorescence spectrum. As a result, their design requires a ligand-binding
protein that exhibits a conformational change upon binding. However, not all ligand-binding
proteins produce responsive sensors upon conjugation to fluorescent proteins or
dyes, and identifying the optimum locations for the fluorophores often involves
labor-intensive iterative design or high-throughput screening. Combining the genetic
fusion of a fluorescent protein to the ligand-binding protein with site-specific
covalent attachment of a fluorescent dye can allow fine control over the positions
of the two fluorophores, allowing the construction of very sensitive sensors.
This relies upon the accurate prediction of the locations of the two fluorophores
in bound and unbound states. In this chapter, we describe a method for computational
identification of dye-attachment sites that allows the use of cysteine modification
to attach synthetic dyes that can be paired with a fluorescent protein for the
purposes of creating FRET sensors.
alternative_title:
- Methods in Molecular Biology
author:
- first_name: Joshua
full_name: Mitchell, Joshua
last_name: Mitchell
- first_name: William
full_name: Zhang, William
last_name: Zhang
- first_name: Michel
full_name: Herde, Michel
last_name: Herde
- first_name: Christian
full_name: Henneberger, Christian
last_name: Henneberger
- 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: Megan
full_name: O'Mara, Megan
last_name: O'Mara
- first_name: Colin
full_name: Jackson, Colin
last_name: Jackson
citation:
ama: 'Mitchell J, Zhang W, Herde M, et al. Method for developing optical sensors
using a synthetic dye fluorescent protein FRET pair and computational modeling
and assessment. In: Stein V, ed. Synthetic Protein Switches. Vol 1596.
Synthetic Protein Switches. Springer; 2017:89-99. doi:10.1007/978-1-4939-6940-1_6'
apa: Mitchell, J., Zhang, W., Herde, M., Henneberger, C., Janovjak, H. L., O’Mara,
M., & Jackson, C. (2017). Method for developing optical sensors using a synthetic
dye fluorescent protein FRET pair and computational modeling and assessment. In
V. Stein (Ed.), Synthetic Protein Switches (Vol. 1596, pp. 89–99). Springer.
https://doi.org/10.1007/978-1-4939-6940-1_6
chicago: Mitchell, Joshua, William Zhang, Michel Herde, Christian Henneberger, Harald
L Janovjak, Megan O’Mara, and Colin Jackson. “Method for Developing Optical Sensors
Using a Synthetic Dye Fluorescent Protein FRET Pair and Computational Modeling
and Assessment.” In Synthetic Protein Switches, edited by Viktor Stein,
1596:89–99. Synthetic Protein Switches. Springer, 2017. https://doi.org/10.1007/978-1-4939-6940-1_6.
ieee: J. Mitchell et al., “Method for developing optical sensors using a
synthetic dye fluorescent protein FRET pair and computational modeling and assessment,”
in Synthetic Protein Switches, vol. 1596, V. Stein, Ed. Springer, 2017,
pp. 89–99.
ista: 'Mitchell J, Zhang W, Herde M, Henneberger C, Janovjak HL, O’Mara M, Jackson
C. 2017.Method for developing optical sensors using a synthetic dye fluorescent
protein FRET pair and computational modeling and assessment. In: Synthetic Protein
Switches. Methods in Molecular Biology, vol. 1596, 89–99.'
mla: Mitchell, Joshua, et al. “Method for Developing Optical Sensors Using a Synthetic
Dye Fluorescent Protein FRET Pair and Computational Modeling and Assessment.”
Synthetic Protein Switches, edited by Viktor Stein, vol. 1596, Springer,
2017, pp. 89–99, doi:10.1007/978-1-4939-6940-1_6.
short: J. Mitchell, W. Zhang, M. Herde, C. Henneberger, H.L. Janovjak, M. O’Mara,
C. Jackson, in:, V. Stein (Ed.), Synthetic Protein Switches, Springer, 2017, pp.
89–99.
date_created: 2018-12-11T11:49:24Z
date_published: 2017-05-15T00:00:00Z
date_updated: 2021-01-12T08:22:13Z
day: '15'
department:
- _id: HaJa
doi: 10.1007/978-1-4939-6940-1_6
editor:
- first_name: Viktor
full_name: Stein, Viktor
last_name: Stein
intvolume: ' 1596'
language:
- iso: eng
month: '05'
oa_version: None
page: 89 - 99
publication: Synthetic Protein Switches
publication_identifier:
issn:
- '10643745'
publication_status: published
publisher: Springer
publist_id: '6450'
quality_controlled: '1'
scopus_import: 1
series_title: Synthetic Protein Switches
status: public
title: Method for developing optical sensors using a synthetic dye fluorescent protein
FRET pair and computational modeling and assessment
type: book_chapter
user_id: 4435EBFC-F248-11E8-B48F-1D18A9856A87
volume: 1596
year: '2017'
...
---
_id: '9707'
abstract:
- lang: eng
text: Branching morphogenesis of the epithelial ureteric bud forms the renal collecting
duct system and is critical for normal nephron number, while low nephron number
is implicated in hypertension and renal disease. Ureteric bud growth and branching
requires GDNF signaling from the surrounding mesenchyme to cells at the ureteric
bud tips, via the Ret receptor tyrosine kinase and coreceptor Gfrα1; Ret signaling
up-regulates transcription factors Etv4 and Etv5, which are also critical for
branching. Despite extensive knowledge of the genetic control of these events,
it is not understood, at the cellular level, how renal branching morphogenesis
is achieved or how Ret signaling influences epithelial cell behaviors to promote
this process. Analysis of chimeric embryos previously suggested a role for Ret
signaling in promoting cell rearrangements in the nephric duct, but this method
was unsuited to study individual cell behaviors during ureteric bud branching.
Here, we use Mosaic Analysis with Double Markers (MADM), combined with organ culture
and time-lapse imaging, to trace the movements and divisions of individual ureteric
bud tip cells. We first examine wild-type clones and then Ret or Etv4 mutant/wild-type
clones in which the mutant and wild-type sister cells are differentially and heritably
marked by green and red fluorescent proteins. We find that, in normal kidneys,
most individual tip cells behave as self-renewing progenitors, some of whose progeny
remain at the tips while others populate the growing UB trunks. In Ret or Etv4
MADM clones, the wild-type cells generated at a UB tip are much more likely to
remain at, or move to, the new tips during branching and elongation, while their
Ret−/− or Etv4−/− sister cells tend to lag behind and contribute only to the trunks.
By tracking successive mitoses in a cell lineage, we find that Ret signaling has
little effect on proliferation, in contrast to its effects on cell movement. Our
results show that Ret/Etv4 signaling promotes directed cell movements in the ureteric
bud tips, and suggest a model in which these cell movements mediate branching
morphogenesis.
article_processing_charge: No
author:
- first_name: Paul
full_name: Riccio, Paul
last_name: Riccio
- first_name: Christina
full_name: Cebrián, Christina
last_name: Cebrián
- first_name: Hui
full_name: Zong, Hui
last_name: Zong
- first_name: Simon
full_name: Hippenmeyer, Simon
id: 37B36620-F248-11E8-B48F-1D18A9856A87
last_name: Hippenmeyer
orcid: 0000-0003-2279-1061
- first_name: Frank
full_name: Costantini, Frank
last_name: Costantini
citation:
ama: 'Riccio P, Cebrián C, Zong H, Hippenmeyer S, Costantini F. Data from: Ret and
Etv4 promote directed movements of progenitor cells during renal branching morphogenesis.
2017. doi:10.5061/dryad.pk16b'
apa: 'Riccio, P., Cebrián, C., Zong, H., Hippenmeyer, S., & Costantini, F. (2017).
Data from: Ret and Etv4 promote directed movements of progenitor cells during
renal branching morphogenesis. Dryad. https://doi.org/10.5061/dryad.pk16b'
chicago: 'Riccio, Paul, Christina Cebrián, Hui Zong, Simon Hippenmeyer, and Frank
Costantini. “Data from: Ret and Etv4 Promote Directed Movements of Progenitor
Cells during Renal Branching Morphogenesis.” Dryad, 2017. https://doi.org/10.5061/dryad.pk16b.'
ieee: 'P. Riccio, C. Cebrián, H. Zong, S. Hippenmeyer, and F. Costantini, “Data
from: Ret and Etv4 promote directed movements of progenitor cells during renal
branching morphogenesis.” Dryad, 2017.'
ista: 'Riccio P, Cebrián C, Zong H, Hippenmeyer S, Costantini F. 2017. Data from:
Ret and Etv4 promote directed movements of progenitor cells during renal branching
morphogenesis, Dryad, 10.5061/dryad.pk16b.'
mla: 'Riccio, Paul, et al. Data from: Ret and Etv4 Promote Directed Movements
of Progenitor Cells during Renal Branching Morphogenesis. Dryad, 2017, doi:10.5061/dryad.pk16b.'
short: P. Riccio, C. Cebrián, H. Zong, S. Hippenmeyer, F. Costantini, (2017).
date_created: 2021-07-23T09:39:34Z
date_published: 2017-01-14T00:00:00Z
date_updated: 2022-08-25T13:34:55Z
day: '14'
department:
- _id: SiHi
doi: 10.5061/dryad.pk16b
main_file_link:
- open_access: '1'
url: https://doi.org/10.5061/dryad.pk16b
month: '01'
oa: 1
oa_version: Published Version
publisher: Dryad
related_material:
record:
- id: '9702'
relation: used_in_publication
status: deleted
status: public
title: 'Data from: Ret and Etv4 promote directed movements of progenitor cells during
renal branching morphogenesis'
type: research_data_reference
user_id: 6785fbc1-c503-11eb-8a32-93094b40e1cf
year: '2017'
...
---
_id: '9844'
article_processing_charge: No
author:
- first_name: Nela
full_name: Nikolic, Nela
id: 42D9CABC-F248-11E8-B48F-1D18A9856A87
last_name: Nikolic
orcid: 0000-0001-9068-6090
- first_name: Frank
full_name: Schreiber, Frank
last_name: Schreiber
- first_name: Alma
full_name: Dal Co, Alma
last_name: Dal Co
- first_name: Daniel
full_name: Kiviet, Daniel
last_name: Kiviet
- first_name: Tobias
full_name: Bergmiller, Tobias
id: 2C471CFA-F248-11E8-B48F-1D18A9856A87
last_name: Bergmiller
orcid: 0000-0001-5396-4346
- first_name: Sten
full_name: Littmann, Sten
last_name: Littmann
- first_name: Marcel
full_name: Kuypers, Marcel
last_name: Kuypers
- first_name: Martin
full_name: Ackermann, Martin
last_name: Ackermann
citation:
ama: Nikolic N, Schreiber F, Dal Co A, et al. Source data for figures and tables.
2017. doi:10.1371/journal.pgen.1007122.s018
apa: Nikolic, N., Schreiber, F., Dal Co, A., Kiviet, D., Bergmiller, T., Littmann,
S., … Ackermann, M. (2017). Source data for figures and tables. Public Library
of Science. https://doi.org/10.1371/journal.pgen.1007122.s018
chicago: Nikolic, Nela, Frank Schreiber, Alma Dal Co, Daniel Kiviet, Tobias Bergmiller,
Sten Littmann, Marcel Kuypers, and Martin Ackermann. “Source Data for Figures
and Tables.” Public Library of Science, 2017. https://doi.org/10.1371/journal.pgen.1007122.s018.
ieee: N. Nikolic et al., “Source data for figures and tables.” Public Library
of Science, 2017.
ista: Nikolic N, Schreiber F, Dal Co A, Kiviet D, Bergmiller T, Littmann S, Kuypers
M, Ackermann M. 2017. Source data for figures and tables, Public Library of Science,
10.1371/journal.pgen.1007122.s018.
mla: Nikolic, Nela, et al. Source Data for Figures and Tables. Public Library
of Science, 2017, doi:10.1371/journal.pgen.1007122.s018.
short: N. Nikolic, F. Schreiber, A. Dal Co, D. Kiviet, T. Bergmiller, S. Littmann,
M. Kuypers, M. Ackermann, (2017).
date_created: 2021-08-09T13:27:16Z
date_published: 2017-12-18T00:00:00Z
date_updated: 2023-02-23T12:25:04Z
day: '18'
department:
- _id: CaGu
doi: 10.1371/journal.pgen.1007122.s018
month: '12'
oa_version: Published Version
publisher: Public Library of Science
related_material:
record:
- id: '541'
relation: used_in_publication
status: public
status: public
title: Source data for figures and tables
type: research_data_reference
user_id: 6785fbc1-c503-11eb-8a32-93094b40e1cf
year: '2017'
...
---
_id: '12905'
article_processing_charge: No
author:
- first_name: Alois
full_name: Schlögl, Alois
id: 45BF87EE-F248-11E8-B48F-1D18A9856A87
last_name: Schlögl
orcid: 0000-0002-5621-8100
- first_name: Janos
full_name: Kiss, Janos
id: 3D3A06F8-F248-11E8-B48F-1D18A9856A87
last_name: Kiss
citation:
ama: 'Schlögl A, Kiss J. Scientific Computing at IST Austria. In: AHPC17 – Austrian
HPC Meeting 2017. FSP Scientific Computing; 2017:28.'
apa: 'Schlögl, A., & Kiss, J. (2017). Scientific Computing at IST Austria. In
AHPC17 – Austrian HPC Meeting 2017 (p. 28). Grundlsee, Austria: FSP Scientific
Computing.'
chicago: Schlögl, Alois, and Janos Kiss. “Scientific Computing at IST Austria.”
In AHPC17 – Austrian HPC Meeting 2017, 28. FSP Scientific Computing, 2017.
ieee: A. Schlögl and J. Kiss, “Scientific Computing at IST Austria,” in AHPC17
– Austrian HPC Meeting 2017, Grundlsee, Austria, 2017, p. 28.
ista: 'Schlögl A, Kiss J. 2017. Scientific Computing at IST Austria. AHPC17 – Austrian
HPC Meeting 2017. AHPC: Austrian HPC Meeting, 28.'
mla: Schlögl, Alois, and Janos Kiss. “Scientific Computing at IST Austria.” AHPC17
– Austrian HPC Meeting 2017, FSP Scientific Computing, 2017, p. 28.
short: A. Schlögl, J. Kiss, in:, AHPC17 – Austrian HPC Meeting 2017, FSP Scientific
Computing, 2017, p. 28.
conference:
end_date: 2017-03-03
location: Grundlsee, Austria
name: 'AHPC: Austrian HPC Meeting'
start_date: 2017-03-01
date_created: 2023-05-05T12:58:53Z
date_published: 2017-03-03T00:00:00Z
date_updated: 2023-05-16T07:22:23Z
day: '03'
ddc:
- '000'
department:
- _id: ScienComp
file:
- access_level: open_access
checksum: 7bcc499479d4f4c5ce6c0071c24ca6c6
content_type: application/pdf
creator: dernst
date_created: 2023-05-16T07:20:50Z
date_updated: 2023-05-16T07:20:50Z
file_id: '12969'
file_name: 2017_AHPC_Schloegl.pdf
file_size: 1005486
relation: main_file
success: 1
file_date_updated: 2023-05-16T07:20:50Z
has_accepted_license: '1'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://vsc.ac.at/fileadmin/user_upload/vsc/conferences/ahpc17/BOOKLET_AHPC17.pdf
month: '03'
oa: 1
oa_version: Published Version
page: '28'
publication: AHPC17 – Austrian HPC Meeting 2017
publication_status: published
publisher: FSP Scientific Computing
status: public
title: Scientific Computing at IST Austria
type: conference_abstract
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
year: '2017'
...
---
_id: '13160'
abstract:
- lang: eng
text: "Transforming deterministic ω\r\n-automata into deterministic parity automata
is traditionally done using variants of appearance records. We present a more
efficient variant of this approach, tailored to Rabin automata, and several optimizations
applicable to all appearance records. We compare the methods experimentally and
find out that our method produces smaller automata than previous approaches. Moreover,
the experiments demonstrate the potential of our method for LTL synthesis, using
LTL-to-Rabin translators. It leads to significantly smaller parity automata when
compared to state-of-the-art approaches on complex formulae."
acknowledgement: This work is partially funded by the DFG project “Verified Model
Checkers” and by the Czech Science Foundation, grant No. P202/12/G061.
alternative_title:
- LNCS
article_processing_charge: No
author:
- first_name: Jan
full_name: Kretinsky, Jan
id: 44CEF464-F248-11E8-B48F-1D18A9856A87
last_name: Kretinsky
orcid: 0000-0002-8122-2881
- first_name: Tobias
full_name: Meggendorfer, Tobias
id: b21b0c15-30a2-11eb-80dc-f13ca25802e1
last_name: Meggendorfer
orcid: 0000-0002-1712-2165
- first_name: Clara
full_name: Waldmann, Clara
last_name: Waldmann
- first_name: Maximilian
full_name: Weininger, Maximilian
last_name: Weininger
citation:
ama: 'Kretinsky J, Meggendorfer T, Waldmann C, Weininger M. Index appearance record
for transforming Rabin automata into parity automata. In: Tools and Algorithms
for the Construction and Analysis of Systems. Vol 10205. Springer; 2017:443-460.
doi:10.1007/978-3-662-54577-5_26'
apa: 'Kretinsky, J., Meggendorfer, T., Waldmann, C., & Weininger, M. (2017).
Index appearance record for transforming Rabin automata into parity automata.
In Tools and Algorithms for the Construction and Analysis of Systems (Vol.
10205, pp. 443–460). Uppsala, Sweden: Springer. https://doi.org/10.1007/978-3-662-54577-5_26'
chicago: Kretinsky, Jan, Tobias Meggendorfer, Clara Waldmann, and Maximilian Weininger.
“Index Appearance Record for Transforming Rabin Automata into Parity Automata.”
In Tools and Algorithms for the Construction and Analysis of Systems, 10205:443–60.
Springer, 2017. https://doi.org/10.1007/978-3-662-54577-5_26.
ieee: J. Kretinsky, T. Meggendorfer, C. Waldmann, and M. Weininger, “Index appearance
record for transforming Rabin automata into parity automata,” in Tools and
Algorithms for the Construction and Analysis of Systems, Uppsala, Sweden,
2017, vol. 10205, pp. 443–460.
ista: 'Kretinsky J, Meggendorfer T, Waldmann C, Weininger M. 2017. Index appearance
record for transforming Rabin automata into parity automata. Tools and Algorithms
for the Construction and Analysis of Systems. TACAS: Tools and Algorithms for
the Construction and Analysis of Systems, LNCS, vol. 10205, 443–460.'
mla: Kretinsky, Jan, et al. “Index Appearance Record for Transforming Rabin Automata
into Parity Automata.” Tools and Algorithms for the Construction and Analysis
of Systems, vol. 10205, Springer, 2017, pp. 443–60, doi:10.1007/978-3-662-54577-5_26.
short: J. Kretinsky, T. Meggendorfer, C. Waldmann, M. Weininger, in:, Tools and
Algorithms for the Construction and Analysis of Systems, Springer, 2017, pp. 443–460.
conference:
end_date: 2017-04-29
location: Uppsala, Sweden
name: 'TACAS: Tools and Algorithms for the Construction and Analysis of Systems'
start_date: 2017-04-22
date_created: 2023-06-21T13:21:14Z
date_published: 2017-03-31T00:00:00Z
date_updated: 2023-06-21T13:29:46Z
day: '31'
department:
- _id: KrCh
doi: 10.1007/978-3-662-54577-5_26
external_id:
arxiv:
- '1701.05738'
intvolume: ' 10205'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.48550/arXiv.1701.05738
month: '03'
oa: 1
oa_version: Preprint
page: 443-460
publication: Tools and Algorithms for the Construction and Analysis of Systems
publication_identifier:
eisbn:
- '9783662545775'
eissn:
- 1611-3349
isbn:
- '9783662545768'
issn:
- 0302-9743
publication_status: published
publisher: Springer
quality_controlled: '1'
status: public
title: Index appearance record for transforming Rabin automata into parity automata
type: conference
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 10205
year: '2017'
...
---
_id: '950'
abstract:
- lang: eng
text: "Two-player games on graphs are widely studied in formal methods as they model
the interaction between a system and its environment. The game is played by moving
a token throughout a graph to produce an infinite path. There are several common
modes to determine how the players move the token through the graph; e.g., in
turn-based games the players alternate turns in moving the token. We study the
bidding mode of moving the token, which, to the best of our knowledge, has never
been studied in infinite-duration games. Both players have separate budgets, which
sum up to $1$. In each turn, a bidding takes place. Both players submit bids simultaneously,
and a bid is legal if it does not exceed the available budget. The winner of the
bidding pays his bid to the other player and moves the token. For reachability
objectives, repeated bidding games have been studied and are called Richman games.
There, a central question is the existence and computation of threshold budgets;
namely, a value t\\in [0,1] such that if\\PO's budget exceeds $t$, he can win
the game, and if\\PT's budget exceeds 1-t, he can win the game. We focus on parity
games and mean-payoff games. We show the existence of threshold budgets in these
games, and reduce the problem of finding them to Richman games. We also determine
the strategy-complexity of an optimal strategy. Our most interesting result shows
that memoryless strategies suffice for mean-payoff bidding games. \r\n"
alternative_title:
- LIPIcs
article_number: '17'
author:
- first_name: Guy
full_name: Avni, Guy
id: 463C8BC2-F248-11E8-B48F-1D18A9856A87
last_name: Avni
orcid: 0000-0001-5588-8287
- 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: Ventsislav K
full_name: Chonev, Ventsislav K
id: 36CBE2E6-F248-11E8-B48F-1D18A9856A87
last_name: Chonev
citation:
ama: 'Avni G, Henzinger TA, Chonev VK. Infinite-duration bidding games. In: Vol
85. Schloss Dagstuhl - Leibniz-Zentrum für Informatik; 2017. doi:10.4230/LIPIcs.CONCUR.2017.21'
apa: 'Avni, G., Henzinger, T. A., & Chonev, V. K. (2017). Infinite-duration
bidding games (Vol. 85). Presented at the CONCUR: Concurrency Theory, Berlin,
Germany: Schloss Dagstuhl - Leibniz-Zentrum für Informatik. https://doi.org/10.4230/LIPIcs.CONCUR.2017.21'
chicago: Avni, Guy, Thomas A Henzinger, and Ventsislav K Chonev. “Infinite-Duration
Bidding Games,” Vol. 85. Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2017.
https://doi.org/10.4230/LIPIcs.CONCUR.2017.21.
ieee: 'G. Avni, T. A. Henzinger, and V. K. Chonev, “Infinite-duration bidding games,”
presented at the CONCUR: Concurrency Theory, Berlin, Germany, 2017, vol. 85.'
ista: 'Avni G, Henzinger TA, Chonev VK. 2017. Infinite-duration bidding games. CONCUR:
Concurrency Theory, LIPIcs, vol. 85, 17.'
mla: Avni, Guy, et al. Infinite-Duration Bidding Games. Vol. 85, 17, Schloss
Dagstuhl - Leibniz-Zentrum für Informatik, 2017, doi:10.4230/LIPIcs.CONCUR.2017.21.
short: G. Avni, T.A. Henzinger, V.K. Chonev, in:, Schloss Dagstuhl - Leibniz-Zentrum
für Informatik, 2017.
conference:
end_date: 2017-09-07
location: Berlin, Germany
name: 'CONCUR: Concurrency Theory'
start_date: 2017-09-05
date_created: 2018-12-11T11:49:22Z
date_published: 2017-09-01T00:00:00Z
date_updated: 2023-08-29T07:02:13Z
day: '01'
ddc:
- '000'
department:
- _id: ToHe
- _id: KrCh
doi: 10.4230/LIPIcs.CONCUR.2017.21
external_id:
arxiv:
- '1705.01433'
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month: '09'
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oa_version: Published Version
project:
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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
publication_identifier:
issn:
- 1868-8969
publication_status: published
publisher: Schloss Dagstuhl - Leibniz-Zentrum für Informatik
publist_id: '6466'
pubrep_id: '844'
quality_controlled: '1'
related_material:
record:
- id: '6752'
relation: later_version
status: public
scopus_import: 1
status: public
title: Infinite-duration bidding games
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: 85
year: '2017'
...
---
_id: '683'
abstract:
- lang: eng
text: 'Given a triangulation of a point set in the plane, a flip deletes an edge
e whose removal leaves a convex quadrilateral, and replaces e by the opposite
diagonal of the quadrilateral. It is well known that any triangulation of a point
set can be reconfigured to any other triangulation by some sequence of flips.
We explore this question in the setting where each edge of a triangulation has
a label, and a flip transfers the label of the removed edge to the new edge. It
is not true that every labelled triangulation of a point set can be reconfigured
to every other labelled triangulation via a sequence of flips, but we characterize
when this is possible. There is an obvious necessary condition: for each label
l, if edge e has label l in the first triangulation and edge f has label l in
the second triangulation, then there must be some sequence of flips that moves
label l from e to f, ignoring all other labels. Bose, Lubiw, Pathak and Verdonschot
formulated the Orbit Conjecture, which states that this necessary condition is
also sufficient, i.e. that all labels can be simultaneously mapped to their destination
if and only if each label individually can be mapped to its destination. We prove
this conjecture. Furthermore, we give a polynomial-time algorithm to find a sequence
of flips to reconfigure one labelled triangulation to another, if such a sequence
exists, and we prove an upper bound of O(n7) on the length of the flip sequence.
Our proof uses the topological result that the sets of pairwise non-crossing edges
on a planar point set form a simplicial complex that is homeomorphic to a high-dimensional
ball (this follows from a result of Orden and Santos; we give a different proof
based on a shelling argument). The dual cell complex of this simplicial ball,
called the flip complex, has the usual flip graph as its 1-skeleton. We use properties
of the 2-skeleton of the flip complex to prove the Orbit Conjecture.'
alternative_title:
- LIPIcs
article_number: '49'
author:
- first_name: Anna
full_name: Lubiw, Anna
last_name: Lubiw
- first_name: Zuzana
full_name: Masárová, Zuzana
id: 45CFE238-F248-11E8-B48F-1D18A9856A87
last_name: Masárová
orcid: 0000-0002-6660-1322
- first_name: Uli
full_name: Wagner, Uli
id: 36690CA2-F248-11E8-B48F-1D18A9856A87
last_name: Wagner
orcid: 0000-0002-1494-0568
citation:
ama: 'Lubiw A, Masárová Z, Wagner U. A proof of the orbit conjecture for flipping
edge labelled triangulations. In: Vol 77. Schloss Dagstuhl - Leibniz-Zentrum für
Informatik; 2017. doi:10.4230/LIPIcs.SoCG.2017.49'
apa: 'Lubiw, A., Masárová, Z., & Wagner, U. (2017). A proof of the orbit conjecture
for flipping edge labelled triangulations (Vol. 77). Presented at the SoCG: Symposium
on Computational Geometry, Brisbane, Australia: Schloss Dagstuhl - Leibniz-Zentrum
für Informatik. https://doi.org/10.4230/LIPIcs.SoCG.2017.49'
chicago: Lubiw, Anna, Zuzana Masárová, and Uli Wagner. “A Proof of the Orbit Conjecture
for Flipping Edge Labelled Triangulations,” Vol. 77. Schloss Dagstuhl - Leibniz-Zentrum
für Informatik, 2017. https://doi.org/10.4230/LIPIcs.SoCG.2017.49.
ieee: 'A. Lubiw, Z. Masárová, and U. Wagner, “A proof of the orbit conjecture for
flipping edge labelled triangulations,” presented at the SoCG: Symposium on Computational
Geometry, Brisbane, Australia, 2017, vol. 77.'
ista: 'Lubiw A, Masárová Z, Wagner U. 2017. A proof of the orbit conjecture for
flipping edge labelled triangulations. SoCG: Symposium on Computational Geometry,
LIPIcs, vol. 77, 49.'
mla: Lubiw, Anna, et al. A Proof of the Orbit Conjecture for Flipping Edge Labelled
Triangulations. Vol. 77, 49, Schloss Dagstuhl - Leibniz-Zentrum für Informatik,
2017, doi:10.4230/LIPIcs.SoCG.2017.49.
short: A. Lubiw, Z. Masárová, U. Wagner, in:, Schloss Dagstuhl - Leibniz-Zentrum
für Informatik, 2017.
conference:
end_date: 2017-07-07
location: Brisbane, Australia
name: 'SoCG: Symposium on Computational Geometry'
start_date: 2017-07-04
date_created: 2018-12-11T11:47:54Z
date_published: 2017-06-01T00:00:00Z
date_updated: 2023-09-05T15:01:43Z
day: '01'
ddc:
- '514'
- '516'
department:
- _id: UlWa
doi: 10.4230/LIPIcs.SoCG.2017.49
file:
- access_level: open_access
checksum: 24fdde981cc513352a78dcf9b0660ae9
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creator: system
date_created: 2018-12-12T10:17:12Z
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file_id: '5265'
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file_size: 710007
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file_date_updated: 2020-07-14T12:47:41Z
has_accepted_license: '1'
intvolume: ' 77'
language:
- iso: eng
month: '06'
oa: 1
oa_version: Published Version
publication_status: published
publisher: Schloss Dagstuhl - Leibniz-Zentrum für Informatik
publist_id: '7033'
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related_material:
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relation: later_version
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scopus_import: 1
status: public
title: A proof of the orbit conjecture for flipping edge labelled triangulations
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: 77
year: '2017'
...
---
_id: '1155'
abstract:
- lang: eng
text: This dissertation concerns the automatic verification of probabilistic systems
and programs with arrays by statistical and logical methods. Although statistical
and logical methods are different in nature, we show that they can be successfully
combined for system analysis. In the first part of the dissertation we present
a new statistical algorithm for the verification of probabilistic systems with
respect to unbounded properties, including linear temporal logic. Our algorithm
often performs faster than the previous approaches, and at the same time requires
less information about the system. In addition, our method can be generalized
to unbounded quantitative properties such as mean-payoff bounds. In the second
part, we introduce two techniques for comparing probabilistic systems. Probabilistic
systems are typically compared using the notion of equivalence, which requires
the systems to have the equal probability of all behaviors. However, this notion
is often too strict, since probabilities are typically only empirically estimated,
and any imprecision may break the relation between processes. On the one hand,
we propose to replace the Boolean notion of equivalence by a quantitative distance
of similarity. For this purpose, we introduce a statistical framework for estimating
distances between Markov chains based on their simulation runs, and we investigate
which distances can be approximated in our framework. On the other hand, we propose
to compare systems with respect to a new qualitative logic, which expresses that
behaviors occur with probability one or a positive probability. This qualitative
analysis is robust with respect to modeling errors and applicable to many domains.
In the last part, we present a new quantifier-free logic for integer arrays, which
allows us to express counting. Counting properties are prevalent in array-manipulating
programs, however they cannot be expressed in the quantified fragments of the
theory of arrays. We present a decision procedure for our logic, and provide several
complexity results.
acknowledgement: ' First of all, I want to thank my advisor, prof. Thomas A. Henzinger,
for his guidance during my PhD program. I am grateful for the freedom I was given
to pursue my research interests, and his continuous support. Working with prof.
Henzinger was a truly inspiring experience and taught me what it means to be a scientist.
I want to express my gratitude to my collaborators: Nikola Beneš, Krishnendu Chatterjee,
Martin Chmelík, Ashutosh Gupta, Willibald Krenn, Jan Kˇretínský, Dejan Nickovic,
Andrey Kupriyanov, and Tatjana Petrov. I have learned a great deal from my collaborators,
and without their help this thesis would not be possible. In addition, I want to
thank the members of my thesis committee: Dirk Beyer, Dejan Nickovic, and Georg
Weissenbacher for their advice and reviewing this dissertation. I would especially
like to acknowledge the late Helmut Veith, who was a member of my committee. I will
remember Helmut for his kindness, enthusiasm, and wit, as well as for being an inspiring
scientist. Finally, I would like to thank my colleagues for making my stay at IST
such a pleasant experience: Guy Avni, Sergiy Bogomolov, Ventsislav Chonev, Rasmus
Ibsen-Jensen, Mirco Giacobbe, Bernhard Kragl, Hui Kong, Petr Novotný, Jan Otop,
Andreas Pavlogiannis, Tantjana Petrov, Arjun Radhakrishna, Jakob Ruess, Thorsten
Tarrach, as well as other members of groups Henzinger and Chatterjee. '
alternative_title:
- ISTA Thesis
article_processing_charge: No
author:
- first_name: Przemyslaw
full_name: Daca, Przemyslaw
id: 49351290-F248-11E8-B48F-1D18A9856A87
last_name: Daca
citation:
ama: Daca P. Statistical and logical methods for property checking. 2017. doi:10.15479/AT:ISTA:TH_730
apa: Daca, P. (2017). Statistical and logical methods for property checking.
Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:TH_730
chicago: Daca, Przemyslaw. “Statistical and Logical Methods for Property Checking.”
Institute of Science and Technology Austria, 2017. https://doi.org/10.15479/AT:ISTA:TH_730.
ieee: P. Daca, “Statistical and logical methods for property checking,” Institute
of Science and Technology Austria, 2017.
ista: Daca P. 2017. Statistical and logical methods for property checking. Institute
of Science and Technology Austria.
mla: Daca, Przemyslaw. Statistical and Logical Methods for Property Checking.
Institute of Science and Technology Austria, 2017, doi:10.15479/AT:ISTA:TH_730.
short: P. Daca, Statistical and Logical Methods for Property Checking, Institute
of Science and Technology Austria, 2017.
date_created: 2018-12-11T11:50:27Z
date_published: 2017-01-02T00:00:00Z
date_updated: 2023-09-07T11:58:34Z
day: '02'
ddc:
- '004'
- '005'
degree_awarded: PhD
department:
- _id: ToHe
doi: 10.15479/AT:ISTA:TH_730
ec_funded: 1
file:
- access_level: open_access
checksum: 1406a681cb737508234fde34766be2c2
content_type: application/pdf
creator: system
date_created: 2018-12-12T10:11:26Z
date_updated: 2020-07-14T12:44:34Z
file_id: '4880'
file_name: IST-2017-730-v1+1_Statistical_and_Logical_Methods_for_Property_Checking.pdf
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file_date_updated: 2020-07-14T12:44:34Z
has_accepted_license: '1'
language:
- iso: eng
month: '01'
oa: 1
oa_version: Published Version
page: '163'
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_identifier:
issn:
- 2663-337X
publication_status: published
publisher: Institute of Science and Technology Austria
publist_id: '6203'
pubrep_id: '730'
related_material:
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- id: '1093'
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status: public
- id: '1230'
relation: part_of_dissertation
status: public
- id: '1234'
relation: part_of_dissertation
status: public
- id: '1391'
relation: part_of_dissertation
status: public
- id: '1501'
relation: part_of_dissertation
status: public
- id: '1502'
relation: part_of_dissertation
status: public
- id: '2063'
relation: part_of_dissertation
status: public
- id: '2167'
relation: part_of_dissertation
status: public
status: public
supervisor:
- first_name: Thomas A
full_name: Henzinger, Thomas A
id: 40876CD8-F248-11E8-B48F-1D18A9856A87
last_name: Henzinger
orcid: 0000−0002−2985−7724
title: Statistical and logical methods for property checking
type: dissertation
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
year: '2017'
...
---
_id: '6291'
abstract:
- lang: eng
text: Bacteria and their pathogens – phages – are the most abundant living entities
on Earth. Throughout their coevolution, bacteria have evolved multiple immune
systems to overcome the ubiquitous threat from the phages. Although the molecu-
lar details of these immune systems’ functions are relatively well understood,
their epidemiological consequences for the phage-bacterial communities have been
largely neglected. In this thesis we employed both experimental and theoretical
methods to explore whether herd and social immunity may arise in bacterial popu-
lations. Using our experimental system consisting of Escherichia coli strains
with a CRISPR based immunity to the T7 phage we show that herd immunity arises
in phage-bacterial communities and that it is accentuated when the populations
are spatially structured. By fitting a mathematical model, we inferred expressions
for the herd immunity threshold and the velocity of spread of a phage epidemic
in partially resistant bacterial populations, which both depend on the bacterial
growth rate, phage burst size and phage latent period. We also investigated the
poten- tial for social immunity in Streptococcus thermophilus and its phage 2972
using a bioinformatic analysis of potentially coding short open reading frames
with a signalling signature, encoded within the CRISPR associated genes. Subsequently,
we tested one identified potentially signalling peptide and found that its addition
to a phage-challenged culture increases probability of survival of bacteria two
fold, although the results were only marginally significant. Together, these results
demonstrate that the ubiquitous arms races between bacteria and phages have further
consequences at the level of the population.
alternative_title:
- ISTA Thesis
article_processing_charge: No
author:
- first_name: Pavel
full_name: Payne, Pavel
id: 35F78294-F248-11E8-B48F-1D18A9856A87
last_name: Payne
orcid: 0000-0002-2711-9453
citation:
ama: Payne P. Bacterial herd and social immunity to phages. 2017.
apa: Payne, P. (2017). Bacterial herd and social immunity to phages. Institute
of Science and Technology Austria.
chicago: Payne, Pavel. “Bacterial Herd and Social Immunity to Phages.” Institute
of Science and Technology Austria, 2017.
ieee: P. Payne, “Bacterial herd and social immunity to phages,” Institute of Science
and Technology Austria, 2017.
ista: Payne P. 2017. Bacterial herd and social immunity to phages. Institute of
Science and Technology Austria.
mla: Payne, Pavel. Bacterial Herd and Social Immunity to Phages. Institute
of Science and Technology Austria, 2017.
short: P. Payne, Bacterial Herd and Social Immunity to Phages, Institute of Science
and Technology Austria, 2017.
date_created: 2019-04-09T15:16:45Z
date_published: 2017-02-01T00:00:00Z
date_updated: 2023-09-07T12:00:00Z
day: '01'
ddc:
- '570'
degree_awarded: PhD
department:
- _id: NiBa
- _id: JoBo
file:
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checksum: a0fc5c26a89c0ea759947ffba87d0d8f
content_type: application/pdf
creator: dernst
date_created: 2019-04-09T15:15:32Z
date_updated: 2020-07-14T12:47:27Z
file_id: '6292'
file_name: thesis_pavel_payne_final_w_signature_page.pdf
file_size: 3025175
relation: main_file
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checksum: af531e921a7f64a9e0af4cd8783b2226
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creator: dernst
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date_updated: 2021-02-22T13:45:59Z
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file_name: 2017_Payne_Thesis.pdf
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language:
- iso: eng
month: '02'
oa: 1
oa_version: Published Version
page: '83'
publication_identifier:
issn:
- 2663-337X
publication_status: published
publisher: Institute of Science and Technology Austria
status: public
supervisor:
- first_name: Jonathan P
full_name: Bollback, Jonathan P
id: 2C6FA9CC-F248-11E8-B48F-1D18A9856A87
last_name: Bollback
orcid: 0000-0002-4624-4612
- first_name: Nicholas H
full_name: Barton, Nicholas H
id: 4880FE40-F248-11E8-B48F-1D18A9856A87
last_name: Barton
orcid: 0000-0002-8548-5240
title: Bacterial herd and social immunity to phages
type: dissertation
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
year: '2017'
...
---
_id: '561'
abstract:
- lang: eng
text: Restriction–modification systems are widespread genetic elements that protect
bacteria from bacteriophage infections by recognizing and cleaving heterologous
DNA at short, well-defined sequences called restriction sites. Bioinformatic evidence
shows that restriction sites are significantly underrepresented in bacteriophage
genomes, presumably because bacteriophages with fewer restriction sites are more
likely to escape cleavage by restriction–modification systems. However, how mutations
in restriction sites affect the likelihood of bacteriophage escape is unknown.
Using the bacteriophage l and the restriction–modification system EcoRI, we show
that while mutation effects at different restriction sites are unequal, they are
independent. As a result, the probability of bacteriophage escape increases with
each mutated restriction site. Our results experimentally support the role of
restriction site avoidance as a response to selection imposed by restriction–modification
systems and offer an insight into the events underlying the process of bacteriophage
escape.
acknowledgement: This work was funded by an HFSP Young Investigators' grant RGY0079/2011
(C.C.G.). M.P. is a recipient of a DOC Fellowship of the Austrian Academy of Science
at the Institute of Science and Technology Austria.
article_number: '20170646'
article_processing_charge: No
article_type: original
author:
- first_name: Maros
full_name: Pleska, Maros
id: 4569785E-F248-11E8-B48F-1D18A9856A87
last_name: Pleska
orcid: 0000-0001-7460-7479
- first_name: Calin C
full_name: Guet, Calin C
id: 47F8433E-F248-11E8-B48F-1D18A9856A87
last_name: Guet
orcid: 0000-0001-6220-2052
citation:
ama: Pleska M, Guet CC. Effects of mutations in phage restriction sites during escape
from restriction–modification. Biology Letters. 2017;13(12). doi:10.1098/rsbl.2017.0646
apa: Pleska, M., & Guet, C. C. (2017). Effects of mutations in phage restriction
sites during escape from restriction–modification. Biology Letters. The
Royal Society. https://doi.org/10.1098/rsbl.2017.0646
chicago: Pleska, Maros, and Calin C Guet. “Effects of Mutations in Phage Restriction
Sites during Escape from Restriction–Modification.” Biology Letters. The
Royal Society, 2017. https://doi.org/10.1098/rsbl.2017.0646.
ieee: M. Pleska and C. C. Guet, “Effects of mutations in phage restriction sites
during escape from restriction–modification,” Biology Letters, vol. 13,
no. 12. The Royal Society, 2017.
ista: Pleska M, Guet CC. 2017. Effects of mutations in phage restriction sites during
escape from restriction–modification. Biology Letters. 13(12), 20170646.
mla: Pleska, Maros, and Calin C. Guet. “Effects of Mutations in Phage Restriction
Sites during Escape from Restriction–Modification.” Biology Letters, vol.
13, no. 12, 20170646, The Royal Society, 2017, doi:10.1098/rsbl.2017.0646.
short: M. Pleska, C.C. Guet, Biology Letters 13 (2017).
date_created: 2018-12-11T11:47:11Z
date_published: 2017-12-01T00:00:00Z
date_updated: 2023-09-07T11:59:32Z
day: '01'
department:
- _id: CaGu
doi: 10.1098/rsbl.2017.0646
external_id:
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- '29237814'
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issue: '12'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.1098/rsbl.2017.0646
month: '12'
oa: 1
oa_version: Published Version
pmid: 1
project:
- _id: 251BCBEC-B435-11E9-9278-68D0E5697425
grant_number: RGY0079/2011
name: Multi-Level Conflicts in Evolutionary Dynamics of Restriction-Modification
Systems (HFSP Young investigators' grant)
- _id: 251D65D8-B435-11E9-9278-68D0E5697425
grant_number: '24210'
name: Effects of Stochasticity on the Function of Restriction-Modi cation Systems
at the Single-Cell Level (DOC Fellowship)
publication: Biology Letters
publication_identifier:
issn:
- 1744-9561
publication_status: published
publisher: The Royal Society
publist_id: '7253'
quality_controlled: '1'
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scopus_import: '1'
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title: Effects of mutations in phage restriction sites during escape from restriction–modification
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 13
year: '2017'
...
---
_id: '818'
abstract:
- lang: eng
text: 'Antibiotics have diverse effects on bacteria, including massive changes in
bacterial gene expression. Whereas the gene expression changes under many antibiotics
have been measured, the temporal organization of these responses and their dependence
on the bacterial growth rate are unclear. As described in Chapter 1, we quantified
the temporal gene expression changes in the bacterium Escherichia coli in response
to the sudden exposure to antibiotics using a fluorescent reporter library and
a robotic system. Our data show temporally structured gene expression responses,
with response times for individual genes ranging from tens of minutes to several
hours. We observed that many stress response genes were activated in response
to antibiotics. As certain stress responses cross-protect bacteria from other
stressors, we then asked whether cellular responses to antibiotics have a similar
protective role in Chapter 2. Indeed, we found that the trimethoprim-induced acid
stress response protects bacteria from subsequent acid stress. We combined microfluidics
with time-lapse imaging to monitor survival, intracellular pH, and acid stress
response in single cells. This approach revealed that the variable expression
of the acid resistance operon gadBC strongly correlates with single-cell survival
time. Cells with higher gadBC expression following trimethoprim maintain higher
intracellular pH and survive the acid stress longer. Overall, we provide a way
to identify single-cell cross-protection between antibiotics and environmental
stressors from temporal gene expression data, and show how antibiotics can increase
bacterial fitness in changing environments. While gene expression changes to antibiotics
show a clear temporal structure at the population-level, it is unclear whether
this clear temporal order is followed by every single cell. Using dual-reporter
strains described in Chapter 3, we measured gene expression dynamics of promoter
pairs in the same cells using microfluidics and microscopy. Chapter 4 shows that
the oxidative stress response and the DNA stress response showed little timing
variability and a clear temporal order under the antibiotic nitrofurantoin. In
contrast, the acid stress response under trimethoprim ran independently from all
other activated response programs including the DNA stress response, which showed
particularly high timing variability in this stress condition. In summary, this
approach provides insight into the temporal organization of gene expression programs
at the single-cell level and suggests dependencies between response programs and
the underlying variability-introducing mechanisms. Altogether, this work advances
our understanding of the diverse effects that antibiotics have on bacteria. These
results were obtained by taking into account gene expression dynamics, which allowed
us to identify general principles, molecular mechanisms, and dependencies between
genes. Our findings may have implications for infectious disease treatments, and
microbial communities in the human body and in nature. '
acknowledgement: 'First of all, I would like to express great gratitude to my PhD
supervisor Tobias Bollenbach. Through his open and trusting attitude I had the freedom
to explore different scientific directions during this project, and follow the research
lines of my interest. I am thankful for constructive and often extensive discussions
and his support and commitment during the different stages of my PhD. I want to
thank my committee members, Călin Guet, Terry Hwa and Nassos Typas for their interest
and their valuable input to this project. Special thanks to Nassos for career guidance,
and for accepting me in his lab. A big thank you goes to the past, present and affiliated
members of the Bollenbach group: Guillaume Chevereau, Marjon de Vos, Marta Lukačišinová,
Veronika Bierbaum, Qi Qin, Marcin Zagórski, Martin Lukačišin, Andreas Angermayr,
Bor Kavčič, Julia Tischler, Dilay Ayhan, Jaroslav Ferenc, and Georg Rieckh. I enjoyed
working and discussing with you very much and I will miss our lengthy group meetings,
our inspiring journal clubs, and our common lunches. Special thanks to Bor for great
mental and professional support during the hard months of thesis writing, and to
Marta for very creative times during the beginning of our PhDs. May the ‘Bacterial
Survival Guide’ decorate the walls of IST forever! A great thanks to my friend and
collaborator Georg Rieckh for his enthusiasm and for getting so involved in these
projects, for his endurance and for his company throughout the years. Thanks to
the FriSBi crowd at IST Austria for interesting meetings and discussions. In particular
I want to thank Magdalena Steinrück, and Anna Andersson for inspiring exchange,
and enjoyable time together. Thanks to everybody who contributed to the cover for
Cell Systems: The constructive input from Tobias Bollenbach, Bor Kavčič, Georg Rieckh,
Marta Lukačišinová, and Sebastian Nozzi, and the professional implementation by
the graphic designer Martina Markus from the University of Cologne. Thanks to all
my office mates in the first floor Bertalanffy building throughout the years: for
ensuring a pleasant working atmosphere, and for your company! In general, I want
to thank all the people that make IST such a great environment, with the many possibilities
to shape our own social and research environment. I want to thank my family for
all kind of practical support during the years, and my second family in Argentina
for their enthusiasm. Thanks to my brother Bernhard and my sister Martina for being
great siblings, and to Helena and Valentin for the joy you brought to my life. My
deep gratitude goes to Sebastian Nozzi, for constant support, patience, love and
for believing in me. '
alternative_title:
- ISTA Thesis
article_processing_charge: No
author:
- first_name: Karin
full_name: Mitosch, Karin
id: 39B66846-F248-11E8-B48F-1D18A9856A87
last_name: Mitosch
citation:
ama: Mitosch K. Timing, variability and cross-protection in bacteria – insights
from dynamic gene expression responses to antibiotics. 2017. doi:10.15479/AT:ISTA:th_862
apa: Mitosch, K. (2017). Timing, variability and cross-protection in bacteria
– insights from dynamic gene expression responses to antibiotics. Institute
of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:th_862
chicago: Mitosch, Karin. “Timing, Variability and Cross-Protection in Bacteria –
Insights from Dynamic Gene Expression Responses to Antibiotics.” Institute of
Science and Technology Austria, 2017. https://doi.org/10.15479/AT:ISTA:th_862.
ieee: K. Mitosch, “Timing, variability and cross-protection in bacteria – insights
from dynamic gene expression responses to antibiotics,” Institute of Science and
Technology Austria, 2017.
ista: Mitosch K. 2017. Timing, variability and cross-protection in bacteria – insights
from dynamic gene expression responses to antibiotics. Institute of Science and
Technology Austria.
mla: Mitosch, Karin. Timing, Variability and Cross-Protection in Bacteria – Insights
from Dynamic Gene Expression Responses to Antibiotics. Institute of Science
and Technology Austria, 2017, doi:10.15479/AT:ISTA:th_862.
short: K. Mitosch, Timing, Variability and Cross-Protection in Bacteria – Insights
from Dynamic Gene Expression Responses to Antibiotics, Institute of Science and
Technology Austria, 2017.
date_created: 2018-12-11T11:48:40Z
date_published: 2017-09-27T00:00:00Z
date_updated: 2023-09-07T12:00:26Z
day: '27'
ddc:
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- '579'
degree_awarded: PhD
department:
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doi: 10.15479/AT:ISTA:th_862
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relation: part_of_dissertation
status: public
- id: '666'
relation: part_of_dissertation
status: public
status: public
supervisor:
- first_name: Mark Tobias
full_name: Bollenbach, Mark Tobias
id: 3E6DB97A-F248-11E8-B48F-1D18A9856A87
last_name: Bollenbach
orcid: 0000-0003-4398-476X
title: Timing, variability and cross-protection in bacteria – insights from dynamic
gene expression responses to antibiotics
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: dissertation
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
year: '2017'
...
---
_id: '666'
abstract:
- lang: eng
text: Antibiotics elicit drastic changes in microbial gene expression, including
the induction of stress response genes. While certain stress responses are known
to “cross-protect” bacteria from other stressors, it is unclear whether cellular
responses to antibiotics have a similar protective role. By measuring the genome-wide
transcriptional response dynamics of Escherichia coli to four antibiotics, we
found that trimethoprim induces a rapid acid stress response that protects bacteria
from subsequent exposure to acid. Combining microfluidics with time-lapse imaging
to monitor survival and acid stress response in single cells revealed that the
noisy expression of the acid resistance operon gadBC correlates with single-cell
survival. Cells with higher gadBC expression following trimethoprim maintain higher
intracellular pH and survive the acid stress longer. The seemingly random single-cell
survival under acid stress can therefore be predicted from gadBC expression and
rationalized in terms of GadB/C molecular function. Overall, we provide a roadmap
for identifying the molecular mechanisms of single-cell cross-protection between
antibiotics and other stressors.
article_processing_charge: Yes (in subscription journal)
author:
- first_name: Karin
full_name: Mitosch, Karin
id: 39B66846-F248-11E8-B48F-1D18A9856A87
last_name: Mitosch
- first_name: Georg
full_name: Rieckh, Georg
id: 34DA8BD6-F248-11E8-B48F-1D18A9856A87
last_name: Rieckh
- first_name: Tobias
full_name: Bollenbach, Tobias
id: 3E6DB97A-F248-11E8-B48F-1D18A9856A87
last_name: Bollenbach
orcid: 0000-0003-4398-476X
citation:
ama: Mitosch K, Rieckh G, Bollenbach MT. Noisy response to antibiotic stress predicts
subsequent single cell survival in an acidic environment. Cell Systems.
2017;4(4):393-403. doi:10.1016/j.cels.2017.03.001
apa: Mitosch, K., Rieckh, G., & Bollenbach, M. T. (2017). Noisy response to
antibiotic stress predicts subsequent single cell survival in an acidic environment.
Cell Systems. Cell Press. https://doi.org/10.1016/j.cels.2017.03.001
chicago: Mitosch, Karin, Georg Rieckh, and Mark Tobias Bollenbach. “Noisy Response
to Antibiotic Stress Predicts Subsequent Single Cell Survival in an Acidic Environment.”
Cell Systems. Cell Press, 2017. https://doi.org/10.1016/j.cels.2017.03.001.
ieee: K. Mitosch, G. Rieckh, and M. T. Bollenbach, “Noisy response to antibiotic
stress predicts subsequent single cell survival in an acidic environment,” Cell
Systems, vol. 4, no. 4. Cell Press, pp. 393–403, 2017.
ista: Mitosch K, Rieckh G, Bollenbach MT. 2017. Noisy response to antibiotic stress
predicts subsequent single cell survival in an acidic environment. Cell Systems.
4(4), 393–403.
mla: Mitosch, Karin, et al. “Noisy Response to Antibiotic Stress Predicts Subsequent
Single Cell Survival in an Acidic Environment.” Cell Systems, vol. 4, no.
4, Cell Press, 2017, pp. 393–403, doi:10.1016/j.cels.2017.03.001.
short: K. Mitosch, G. Rieckh, M.T. Bollenbach, Cell Systems 4 (2017) 393–403.
date_created: 2018-12-11T11:47:48Z
date_published: 2017-04-26T00:00:00Z
date_updated: 2023-09-07T12:00:25Z
day: '26'
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oa: 1
oa_version: Published Version
page: 393 - 403
project:
- _id: 25E83C2C-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '303507'
name: Optimality principles in responses to antibiotics
- _id: 25E9AF9E-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: P27201-B22
name: Revealing the mechanisms underlying drug interactions
- _id: 25EB3A80-B435-11E9-9278-68D0E5697425
grant_number: RGP0042/2013
name: Revealing the fundamental limits of cell growth
publication: Cell Systems
publication_identifier:
issn:
- '24054712'
publication_status: published
publisher: Cell Press
publist_id: '7061'
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relation: dissertation_contains
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scopus_import: 1
status: public
title: Noisy response to antibiotic stress predicts subsequent single cell survival
in an acidic environment
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: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87
volume: 4
year: '2017'
...
---
_id: '821'
abstract:
- lang: eng
text: "This dissertation focuses on algorithmic aspects of program verification,
and presents modeling and complexity advances on several problems related to the\r\nstatic
analysis of programs, the stateless model checking of concurrent programs, and
the competitive analysis of real-time scheduling algorithms.\r\nOur contributions
can be broadly grouped into five categories.\r\n\r\nOur first contribution is
a set of new algorithms and data structures for the quantitative and data-flow
analysis of programs, based on the graph-theoretic notion of treewidth.\r\nIt
has been observed that the control-flow graphs of typical programs have special
structure, and are characterized as graphs of small treewidth.\r\nWe utilize this
structural property to provide faster algorithms for the quantitative and data-flow
analysis of recursive and concurrent programs.\r\nIn most cases we make an algebraic
treatment of the considered problem,\r\nwhere several interesting analyses, such
as the reachability, shortest path, and certain kind of data-flow analysis problems
follow as special cases. \r\nWe exploit the constant-treewidth property to obtain
algorithmic improvements for on-demand versions of the problems, \r\nand provide
data structures with various tradeoffs between the resources spent in the preprocessing
and querying phase.\r\nWe also improve on the algorithmic complexity of quantitative
problems outside the algebraic path framework,\r\nnamely of the minimum mean-payoff,
minimum ratio, and minimum initial credit for energy problems.\r\n\r\n\r\nOur
second contribution is a set of algorithms for Dyck reachability with applications
to data-dependence analysis and alias analysis.\r\nIn particular, we develop an
optimal algorithm for Dyck reachability on bidirected graphs, which are ubiquitous
in context-insensitive, field-sensitive points-to analysis.\r\nAdditionally, we
develop an efficient algorithm for context-sensitive data-dependence analysis
via Dyck reachability,\r\nwhere the task is to obtain analysis summaries of library
code in the presence of callbacks.\r\nOur algorithm preprocesses libraries in
almost linear time, after which the contribution of the library in the complexity
of the client analysis is (i)~linear in the number of call sites and (ii)~only
logarithmic in the size of the whole library, as opposed to linear in the size
of the whole library.\r\nFinally, we prove that Dyck reachability is Boolean Matrix
Multiplication-hard in general, and the hardness also holds for graphs of constant
treewidth.\r\nThis hardness result strongly indicates that there exist no combinatorial
algorithms for Dyck reachability with truly subcubic complexity.\r\n\r\n\r\nOur
third contribution is the formalization and algorithmic treatment of the Quantitative
Interprocedural Analysis framework.\r\nIn this framework, the transitions of a
recursive program are annotated as good, bad or neutral, and receive a weight
which measures\r\nthe magnitude of their respective effect.\r\nThe Quantitative
Interprocedural Analysis problem asks to determine whether there exists an infinite
run of the program where the long-run ratio of the bad weights over the good weights
is above a given threshold.\r\nWe illustrate how several quantitative problems
related to static analysis of recursive programs can be instantiated in this framework,\r\nand
present some case studies to this direction.\r\n\r\n\r\nOur fourth contribution
is a new dynamic partial-order reduction for the stateless model checking of concurrent
programs. Traditional approaches rely on the standard Mazurkiewicz equivalence
between traces, by means of partitioning the trace space into equivalence classes,
and attempting to explore a few representatives from each class.\r\nWe present
a new dynamic partial-order reduction method called the Data-centric Partial
Order Reduction (DC-DPOR).\r\nOur algorithm is based on a new equivalence between
traces, called the observation equivalence.\r\nDC-DPOR explores a coarser partitioning
of the trace space than any exploration method based on the standard Mazurkiewicz
equivalence.\r\nDepending on the program, the new partitioning can be even exponentially
coarser.\r\nAdditionally, DC-DPOR spends only polynomial time in each explored
class.\r\n\r\n\r\nOur fifth contribution is the use of automata and game-theoretic
verification techniques in the competitive analysis and synthesis of real-time
scheduling algorithms for firm-deadline tasks.\r\nOn the analysis side, we leverage
automata on infinite words to compute the competitive ratio of real-time schedulers
subject to various environmental constraints.\r\nOn the synthesis side, we introduce
a new instance of two-player mean-payoff partial-information games, and show\r\nhow
the synthesis of an optimal real-time scheduler can be reduced to computing winning
strategies in this new type of games."
acknowledgement: "First, I am thankful to my advisor, Krishnendu Chatterjee, for offering
me the opportunity to\r\nmaterialize my scientific curiosity in a remarkably wide
range of interesting topics, as well as for his constant availability and continuous
support throughout my doctoral studies. I have had the privilege of collaborating
with, discussing and getting inspired by all members of my committee: Thomas A.
Henzinger, Ulrich Schmid and Martin A. Nowak. The role of the above four people
has been very instrumental both to the research carried out for this dissertation,
and to the researcher I evolved to in the process.\r\nI have greatly enjoyed my
numerous brainstorming sessions with Rasmus Ibsen-Jensen, many\r\nof which led to
results on low-treewidth graphs presented here. I thank Alex Kößler for our\r\ndiscussions
on modeling and analyzing real-time scheduling algorithms, Yaron Velner for our\r\ncollaboration
on the Quantitative Interprocedural Analysis framework, and Nishant Sinha for our
initial discussions on partial order reduction techniques in stateless model checking.
I also thank Jan Otop, Ben Adlam, Bernhard Kragl and Josef Tkadlec for our fruitful
collaborations on\r\ntopics outside the scope of this dissertation, as well as the
interns Prateesh Goyal, Amir Kafshdar Goharshady, Samarth Mishra, Bhavya Choudhary
and Marek Chalupa, with whom I have shared my excitement on various research topics.
Together with my collaborators, I thank officemates and members of the Chatterjee
and Henzinger groups throughout the years, Thorsten Tarrach, Ventsi Chonev, Roopsha
Samanta, Przemek Daca, Mirco Giacobbe, Tanja Petrov, Ashutosh\r\nGupta, Arjun Radhakrishna,
\ Petr Novontý, Christian Hilbe, Jakob Ruess, Martin Chmelik,\r\nCezara Dragoi,
Johannes Reiter, Andrey Kupriyanov, Guy Avni, Sasha Rubin, Jessica Davies, Hongfei
Fu, Thomas Ferrère, Pavol Cerný, Ali Sezgin, Jan Kretínský, Sergiy Bogomolov, Hui\r\nKong,
Benjamin Aminof, Duc-Hiep Chu, and Damien Zufferey. Besides collaborations and
office spaces, with many of the above people I have been fortunate to share numerous
whiteboard\r\ndiscussions, as well as memorable long walks and amicable meals accompanied
by stimulating\r\nconversations. I am highly indebted to Elisabeth Hacker for her
continuous assistance in matters\r\nthat often exceeded her official duties, and
who made my integration in Austria a smooth process."
alternative_title:
- ISTA Thesis
article_processing_charge: No
author:
- first_name: Andreas
full_name: Pavlogiannis, Andreas
id: 49704004-F248-11E8-B48F-1D18A9856A87
last_name: Pavlogiannis
orcid: 0000-0002-8943-0722
citation:
ama: Pavlogiannis A. Algorithmic advances in program analysis and their applications.
2017. doi:10.15479/AT:ISTA:th_854
apa: Pavlogiannis, A. (2017). Algorithmic advances in program analysis and their
applications. Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:th_854
chicago: Pavlogiannis, Andreas. “Algorithmic Advances in Program Analysis and Their
Applications.” Institute of Science and Technology Austria, 2017. https://doi.org/10.15479/AT:ISTA:th_854.
ieee: A. Pavlogiannis, “Algorithmic advances in program analysis and their applications,”
Institute of Science and Technology Austria, 2017.
ista: Pavlogiannis A. 2017. Algorithmic advances in program analysis and their applications.
Institute of Science and Technology Austria.
mla: Pavlogiannis, Andreas. Algorithmic Advances in Program Analysis and Their
Applications. Institute of Science and Technology Austria, 2017, doi:10.15479/AT:ISTA:th_854.
short: A. Pavlogiannis, Algorithmic Advances in Program Analysis and Their Applications,
Institute of Science and Technology Austria, 2017.
date_created: 2018-12-11T11:48:41Z
date_published: 2017-08-09T00:00:00Z
date_updated: 2023-09-07T12:01:59Z
day: '09'
ddc:
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degree_awarded: PhD
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month: '08'
oa: 1
oa_version: Published Version
page: '418'
project:
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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
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call_identifier: FP7
grant_number: '279307'
name: 'Quantitative Graph Games: Theory and Applications'
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publisher: Institute of Science and Technology Austria
publist_id: '6828'
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- id: '1071'
relation: part_of_dissertation
status: public
- id: '1437'
relation: part_of_dissertation
status: public
- id: '1602'
relation: part_of_dissertation
status: public
- id: '1604'
relation: part_of_dissertation
status: public
- id: '1607'
relation: part_of_dissertation
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- id: '1714'
relation: part_of_dissertation
status: public
status: public
supervisor:
- first_name: Krishnendu
full_name: Chatterjee, Krishnendu
id: 2E5DCA20-F248-11E8-B48F-1D18A9856A87
last_name: Chatterjee
orcid: 0000-0002-4561-241X
title: Algorithmic advances in program analysis and their applications
tmp:
image: /image/cc_by_nd.png
legal_code_url: https://creativecommons.org/licenses/by-nd/4.0/legalcode
name: Creative Commons Attribution-NoDerivatives 4.0 International (CC BY-ND 4.0)
short: CC BY-ND (4.0)
type: dissertation
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
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...
---
_id: '820'
abstract:
- lang: eng
text: "The lac operon is a classic model system for bacterial gene regulation, and
has been studied extensively in E. coli, a classic model organism. However, not
much is known about E. coli’s ecology and life outside the laboratory, in particular
in soil and water environments. The natural diversity of the lac operon outside
the laboratory, its role in the ecology of E. coli and the selection pressures
it is exposed to, are similarly unknown.\r\nIn Chapter Two of this thesis, I explore
the genetic diversity, phylogenetic history and signatures of selection of the
lac operon across 20 natural isolates of E. coli and divergent clades of Escherichia.
I found that complete lac operons were present in all isolates examined, which
in all but one case were functional. The lac operon phylogeny conformed to the
whole-genome phylogeny of the divergent Escherichia clades, which excludes horizontal
gene transfer as an explanation for the presence of functional lac operons in
these clades. All lac operon genes showed a signature of purifying selection;
this signature was strongest for the lacY gene. Lac operon genes of human and
environmental isolates showed similar signatures of selection, except the lacZ
gene, which showed a stronger signature of selection in environmental isolates.\r\nIn
Chapter Three, I try to identify the natural genetic variation relevant for phenotype
and fitness in the lac operon, comparing growth rate on lactose and LacZ activity
of the lac operons of these wild isolates in a common genetic background. Sequence
variation in the lac promoter region, upstream of the -10 and -35 RNA polymerase
binding motif, predicted variation in LacZ activity at full induction, using a
thermodynamic model of polymerase binding (Tugrul, 2016). However, neither variation
in LacZ activity, nor RNA polymerase binding predicted by the model correlated
with variation in growth rate. Lac operons of human and environmental isolates
did not differ systematically in either growth rate on lactose or LacZ protein
activity, suggesting that these lac operons have been exposed to similar selection
pressures. We thus have no evidence that the phenotypic variation we measured
is relevant for fitness.\r\nTo start assessing the effect of genomic background
on the growth phenotype conferred by the lac operon, I compared growth on minimal
medium with lactose between lac operon constructs and the corresponding original
isolates, I found that maximal growth rate was determined by genomic background,
with almost all backgrounds conferring higher growth rates than lab strain K12
MG1655. However, I found no evidence that the lactose concentration at which growth
was half maximal depended on genomic background."
acknowledgement: "ERC H2020 programme (grant agreement no. 648440)\r\nThanks to Jon
Bollback for giving me the chance to do this work, for sharing the ideas that lay
at the basis of this work, for his honesty and openness, showing himself to me as
a person and not just as a boss. Thanks to Nick Barton for his guidance at the last
stage, reading and commenting extensively on several versions of this manuscript,
and for his encouragement; thanks to both Jon and Nick for their kindness and patience.
Thanks to Erik van Nimwegen and Calin Guet for their time and willingness to be
in my thesis committee, and to Erik van Nimwegen especially for agreeing to enter
my thesis committee at the last moment, and for his very sharp, helpful and relevant
comments during and after the defense. Thanks to my collaborators and discussion
partners: Anne Kupczok, for her guidance, ideas and discussions during the construction
of the manuscript of Chapter Two, and her comments on the manuscript; Georg Rieckh
for making me aware of the issue of parameter identifiability, suggesting how to
solve it, and for his unfortunate idea to start the plasmid enterprise in the first
place; Murat Tugrul for sharing his model, for his enthusiasm, and his comments
on Chapter Three; Srdjan Sarikas for his collaboration on the Monod model fitting,
fast forwarding the analysis to turbo speed and making beautiful figures, and making
the discussion fun on top of it all; Vanessa Barone for her last minute comments,
especially on Chapter Three, providing a sharp and very helpful experimentalist
perspective at the last moment; Maros Pleska and Marjon de Vos for their comments
on the manuscript of Chapter Two; Gasper Tkacik for his crucial input on the relation
between growth rate and lactose concentration; Bor Kavcic for his input on growth
rate modeling and error propagation. Thanks to the Bollback, Bollenbach, Barton,
Guet and Tkacik group members for both pro- viding an inspiring and supportive scientific
environment to work in, as well as a lot of warmth and colour to everyday life.
And thanks to the friends I found here, to the people who were there for me and
to the people who changed my life, making it stranger and more beautiful than I
could have imagined, Maros, Vanessa, Tade, Suzi, Andrej, Peter, Tiago, Kristof,
Karin, Irene, Misha, Mato, Guillaume and Zanin. "
alternative_title:
- ISTA Thesis
article_processing_charge: No
author:
- first_name: Fabienne
full_name: Jesse, Fabienne
id: 4C8C26A4-F248-11E8-B48F-1D18A9856A87
last_name: Jesse
citation:
ama: Jesse F. The lac operon in the wild. 2017. doi:10.15479/AT:ISTA:th_857
apa: Jesse, F. (2017). The lac operon in the wild. Institute of Science and
Technology Austria. https://doi.org/10.15479/AT:ISTA:th_857
chicago: Jesse, Fabienne. “The Lac Operon in the Wild.” Institute of Science and
Technology Austria, 2017. https://doi.org/10.15479/AT:ISTA:th_857.
ieee: F. Jesse, “The lac operon in the wild,” Institute of Science and Technology
Austria, 2017.
ista: Jesse F. 2017. The lac operon in the wild. Institute of Science and Technology
Austria.
mla: Jesse, Fabienne. The Lac Operon in the Wild. Institute of Science and
Technology Austria, 2017, doi:10.15479/AT:ISTA:th_857.
short: F. Jesse, The Lac Operon in the Wild, Institute of Science and Technology
Austria, 2017.
date_created: 2018-12-11T11:48:41Z
date_published: 2017-08-25T00:00:00Z
date_updated: 2023-09-07T12:01:21Z
day: '25'
ddc:
- '576'
- '577'
- '579'
degree_awarded: PhD
department:
- _id: JoBo
doi: 10.15479/AT:ISTA:th_857
ec_funded: 1
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checksum: c62257a7bff0c5f39e1abffc6bfcca5c
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content_type: application/x-tex
creator: dernst
date_created: 2019-04-05T08:51:59Z
date_updated: 2020-07-14T12:48:10Z
file_id: '6212'
file_name: 2017_thesis_Jesse_source.tex
file_size: 215899
relation: source_file
file_date_updated: 2020-07-14T12:48:10Z
has_accepted_license: '1'
language:
- iso: eng
month: '08'
oa: 1
oa_version: Published Version
page: '87'
project:
- _id: 2578D616-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '648440'
name: Selective Barriers to Horizontal Gene Transfer
publication_identifier:
issn:
- 2663-337X
publication_status: published
publisher: Institute of Science and Technology Austria
publist_id: '6829'
pubrep_id: '857'
status: public
supervisor:
- first_name: Jonathan P
full_name: Bollback, Jonathan P
id: 2C6FA9CC-F248-11E8-B48F-1D18A9856A87
last_name: Bollback
orcid: 0000-0002-4624-4612
title: The lac operon in the wild
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: dissertation
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
year: '2017'
...
---
_id: '838'
abstract:
- lang: eng
text: 'In this thesis we discuss the exact security of message authentications codes
HMAC , NMAC , and PMAC . NMAC is a mode of operation which turns a fixed input-length
keyed hash function f into a variable input-length function. A practical single-key
variant of NMAC called HMAC is a very popular and widely deployed message authentication
code (MAC). PMAC is a block-cipher based mode of operation, which also happens
to be the most famous fully parallel MAC. NMAC was introduced by Bellare, Canetti
and Krawczyk Crypto’96, who proved it to be a secure pseudorandom function (PRF),
and thus also a MAC, under two assumptions. Unfortunately, for many instantiations
of HMAC one of them has been found to be wrong. To restore the provable guarantees
for NMAC , Bellare [Crypto’06] showed its security without this assumption. PMAC
was introduced by Black and Rogaway at Eurocrypt 2002. If instantiated with a
pseudorandom permutation over n -bit strings, PMAC constitutes a provably secure
variable input-length PRF. For adversaries making q queries, each of length at
most ` (in n -bit blocks), and of total length σ ≤ q` , the original paper proves
an upper bound on the distinguishing advantage of O ( σ 2 / 2 n ), while the currently
best bound is O ( qσ/ 2 n ). In this work we show that this bound is tight by
giving an attack with advantage Ω( q 2 `/ 2 n ). In the PMAC construction one
initially XORs a mask to every message block, where the mask for the i th block
is computed as τ i := γ i · L , where L is a (secret) random value, and γ i is
the i -th codeword of the Gray code. Our attack applies more generally to any
sequence of γ i ’s which contains a large coset of a subgroup of GF (2 n ). As
for NMAC , our first contribution is a simpler and uniform proof: If f is an ε
-secure PRF (against q queries) and a δ - non-adaptively secure PRF (against q
queries), then NMAC f is an ( ε + `qδ )-secure PRF against q queries of length
at most ` blocks each. We also show that this ε + `qδ bound is basically tight
by constructing an f for which an attack with advantage `qδ exists. Moreover,
we analyze the PRF-security of a modification of NMAC called NI by An and Bellare
that avoids the constant rekeying on multi-block messages in NMAC and allows for
an information-theoretic analysis. We carry out such an analysis, obtaining a
tight `q 2 / 2 c bound for this step, improving over the trivial bound of ` 2
q 2 / 2 c . Finally, we investigate, if the security of PMAC can be further improved
by using τ i ’s that are k -wise independent, for k > 1 (the original has k
= 1). We observe that the security of PMAC will not increase in general if k =
2, and then prove that the security increases to O ( q 2 / 2 n ), if the k = 4.
Due to simple extension attacks, this is the best bound one can hope for, using
any distribution on the masks. Whether k = 3 is already sufficient to get this
level of security is left as an open problem. Keywords: Message authentication
codes, Pseudorandom functions, HMAC, PMAC. '
alternative_title:
- ISTA Thesis
article_processing_charge: No
author:
- first_name: Michal
full_name: Rybar, Michal
id: 2B3E3DE8-F248-11E8-B48F-1D18A9856A87
last_name: Rybar
citation:
ama: Rybar M. (The exact security of) Message authentication codes. 2017. doi:10.15479/AT:ISTA:th_828
apa: Rybar, M. (2017). (The exact security of) Message authentication codes.
Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:th_828
chicago: Rybar, Michal. “(The Exact Security of) Message Authentication Codes.”
Institute of Science and Technology Austria, 2017. https://doi.org/10.15479/AT:ISTA:th_828.
ieee: M. Rybar, “(The exact security of) Message authentication codes,” Institute
of Science and Technology Austria, 2017.
ista: Rybar M. 2017. (The exact security of) Message authentication codes. Institute
of Science and Technology Austria.
mla: Rybar, Michal. (The Exact Security of) Message Authentication Codes.
Institute of Science and Technology Austria, 2017, doi:10.15479/AT:ISTA:th_828.
short: M. Rybar, (The Exact Security of) Message Authentication Codes, Institute
of Science and Technology Austria, 2017.
date_created: 2018-12-11T11:48:46Z
date_published: 2017-06-26T00:00:00Z
date_updated: 2023-09-07T12:02:28Z
day: '26'
ddc:
- '000'
degree_awarded: PhD
department:
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language:
- iso: eng
month: '06'
oa: 1
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publication_identifier:
issn:
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publication_status: published
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publist_id: '6810'
pubrep_id: '828'
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status: public
title: (The exact security of) Message authentication codes
type: dissertation
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
year: '2017'
...
---
_id: '6196'
abstract:
- lang: eng
text: PMAC is a simple and parallel block-cipher mode of operation, which was introduced
by Black and Rogaway at Eurocrypt 2002. If instantiated with a (pseudo)random
permutation over n-bit strings, PMAC constitutes a provably secure variable input-length
(pseudo)random function. For adversaries making q queries, each of length at most
l (in n-bit blocks), and of total length σ ≤ ql, the original paper proves an
upper bound on the distinguishing advantage of Ο(σ2/2n), while the currently
best bound is Ο (qσ/2n).In this work we show that this bound is tight by giving
an attack with advantage Ω (q2l/2n). In the PMAC construction one initially XORs
a mask to every message block, where the mask for the ith block is computed as
τi := γi·L, where L is a (secret) random value, and γi is the i-th codeword of
the Gray code. Our attack applies more generally to any sequence of γi’s which
contains a large coset of a subgroup of GF(2n). We then investigate if the security
of PMAC can be further improved by using τi’s that are k-wise independent, for
k > 1 (the original distribution is only 1-wise independent). We observe that
the security of PMAC will not increase in general, even if the masks are chosen
from a 2-wise independent distribution, and then prove that the security increases
to O(q<2/2n), if the τi are 4-wise independent. Due to simple extension attacks,
this is the best bound one can hope for, using any distribution on the masks.
Whether 3-wise independence is already sufficient to get this level of security
is left as an open problem.
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: Michal
full_name: Rybar, Michal
id: 2B3E3DE8-F248-11E8-B48F-1D18A9856A87
last_name: Rybar
citation:
ama: Gazi P, Pietrzak KZ, Rybar M. The exact security of PMAC. IACR Transactions
on Symmetric Cryptology. 2017;2016(2):145-161. doi:10.13154/TOSC.V2016.I2.145-161
apa: Gazi, P., Pietrzak, K. Z., & Rybar, M. (2017). The exact security of PMAC.
IACR Transactions on Symmetric Cryptology. Ruhr University Bochum. https://doi.org/10.13154/TOSC.V2016.I2.145-161
chicago: Gazi, Peter, Krzysztof Z Pietrzak, and Michal Rybar. “The Exact Security
of PMAC.” IACR Transactions on Symmetric Cryptology. Ruhr University Bochum,
2017. https://doi.org/10.13154/TOSC.V2016.I2.145-161.
ieee: P. Gazi, K. Z. Pietrzak, and M. Rybar, “The exact security of PMAC,” IACR
Transactions on Symmetric Cryptology, vol. 2016, no. 2. Ruhr University Bochum,
pp. 145–161, 2017.
ista: Gazi P, Pietrzak KZ, Rybar M. 2017. The exact security of PMAC. IACR Transactions
on Symmetric Cryptology. 2016(2), 145–161.
mla: Gazi, Peter, et al. “The Exact Security of PMAC.” IACR Transactions on Symmetric
Cryptology, vol. 2016, no. 2, Ruhr University Bochum, 2017, pp. 145–61, doi:10.13154/TOSC.V2016.I2.145-161.
short: P. Gazi, K.Z. Pietrzak, M. Rybar, IACR Transactions on Symmetric Cryptology
2016 (2017) 145–161.
date_created: 2019-04-04T13:48:23Z
date_published: 2017-02-03T00:00:00Z
date_updated: 2023-09-07T12:02:27Z
day: '03'
ddc:
- '000'
department:
- _id: KrPi
doi: 10.13154/TOSC.V2016.I2.145-161
ec_funded: 1
file:
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checksum: f23161d685dd957ae8d7274132999684
content_type: application/pdf
creator: dernst
date_created: 2019-04-04T13:53:58Z
date_updated: 2020-07-14T12:47:24Z
file_id: '6197'
file_name: 2017_IACR_Gazi.pdf
file_size: 597335
relation: main_file
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has_accepted_license: '1'
intvolume: ' 2016'
issue: '2'
language:
- iso: eng
month: '02'
oa: 1
oa_version: Published Version
page: 145-161
project:
- _id: 258AA5B2-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '682815'
name: Teaching Old Crypto New Tricks
publication: IACR Transactions on Symmetric Cryptology
publication_identifier:
eissn:
- 2519-173X
publication_status: published
publisher: Ruhr University Bochum
quality_controlled: '1'
related_material:
record:
- id: '838'
relation: dissertation_contains
status: public
status: public
title: The exact security of PMAC
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)
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type: journal_article
user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87
volume: 2016
year: '2017'
...
---
_id: '837'
abstract:
- lang: eng
text: 'The hippocampus is a key brain region for memory and notably for spatial
memory, and is needed for both spatial working and reference memories. Hippocampal
place cells selectively discharge in specific locations of the environment to
form mnemonic represen tations of space. Several behavioral protocols have been
designed to test spatial memory which requires the experimental subject to utilize
working memory and reference memory. However, less is known about how these memory
traces are presented in the hippo campus, especially considering tasks that require
both spatial working and long -term reference memory demand. The aim of my thesis
was to elucidate how spatial working memory, reference memory, and the combination
of both are represented in the hippocampus. In this thesis, using a radial eight
-arm maze, I examined how the combined demand on these memories influenced place
cell assemblies while reference memories were partially updated by changing some
of the reward- arms. This was contrasted with task varian ts requiring working
or reference memories only. Reference memory update led to gradual place field
shifts towards the rewards on the switched arms. Cells developed enhanced firing
in passes between newly -rewarded arms as compared to those containing an unchanged
reward. The working memory task did not show such gradual changes. Place assemblies
on occasions replayed trajectories of the maze; at decision points the next arm
choice was preferentially replayed in tasks needing reference memory while in
the pure working memory task the previously visited arm was replayed. Hence trajectory
replay only reflected the decision of the animal in tasks needing reference memory
update. At the reward locations, in all three tasks outbound trajectories of the
current arm were preferentially replayed, showing the animals’ next path to the
center. At reward locations trajectories were replayed preferentially in reverse
temporal order. Moreover, in the center reverse replay was seen in the working
memory task but in the other tasks forward replay was seen. Hence, the direction
of reactivation was determined by the goal locations so that part of the trajectory
which was closer to the goal was reactivated later in an HSE while places further
away from the goal were reactivated earlier. Altogether my work demonstrated that
reference memory update triggers several levels of reorganization of the hippocampal
cognitive map which are not seen in simpler working memory demand s. Moreover,
hippocampus is likely to be involved in spatial decisions through reactivating
planned trajectories when reference memory recall is required for such a decision. '
acknowledgement: 'I am very grateful for the opportunity I have had as a graduate
student to explore and incredibly interesting branch of neuroscience, and for the
people who made it possible. Firstly, I would like to offer my thanks to my supervisor
Professor Jozsef Csicsvari for his great support, guidance and patience offered
over the years. The door to his office was always open whenever I had questions.
I have learned a lot from him about carefully designing experiments, asking interesting
questions and how to integrate results into a broader picture. I also express my
gratitude to the remarkable post- doc , Dr. Joseph O’Neill. He is a gre at scientific
role model who is always willing to teach , and advice and talk through problems
with his full attention. Many thanks to my wonderful “office mates” over the years
and their support and encouragement, Alice Avernhe, Philipp Schönenberger, Desiree
Dickerson, Karel Blahna, Charlotte Boccara, Igor Gridchyn, Peter Baracskay, Krisztián
Kovács, Dámaris Rangel, Karola Käfer and Federico Stella. They were the ones in
the lab for the many useful discussions about science and for making the laboratory
such a nice and friendly place to work in. A special thank goes to Michael LoBianco
and Jago Wallenschus for wonderful technical support. I would also like to thank
Professor Peter Jonas and Professor David M Bannerman for being my qualifying exam
and thesi s committee members despite their busy schedule. I am also very thankful
to IST Austria for their support all throughout my PhD. '
alternative_title:
- ISTA Thesis
article_processing_charge: No
author:
- first_name: Haibing
full_name: Xu, Haibing
id: 310349D0-F248-11E8-B48F-1D18A9856A87
last_name: Xu
citation:
ama: Xu H. Reactivation of the hippocampal cognitive map in goal-directed spatial
tasks. 2017. doi:10.15479/AT:ISTA:th_858
apa: Xu, H. (2017). Reactivation of the hippocampal cognitive map in goal-directed
spatial tasks. Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:th_858
chicago: Xu, Haibing. “Reactivation of the Hippocampal Cognitive Map in Goal-Directed
Spatial Tasks.” Institute of Science and Technology Austria, 2017. https://doi.org/10.15479/AT:ISTA:th_858.
ieee: H. Xu, “Reactivation of the hippocampal cognitive map in goal-directed spatial
tasks,” Institute of Science and Technology Austria, 2017.
ista: Xu H. 2017. Reactivation of the hippocampal cognitive map in goal-directed
spatial tasks. Institute of Science and Technology Austria.
mla: Xu, Haibing. Reactivation of the Hippocampal Cognitive Map in Goal-Directed
Spatial Tasks. Institute of Science and Technology Austria, 2017, doi:10.15479/AT:ISTA:th_858.
short: H. Xu, Reactivation of the Hippocampal Cognitive Map in Goal-Directed Spatial
Tasks, Institute of Science and Technology Austria, 2017.
date_created: 2018-12-11T11:48:46Z
date_published: 2017-08-23T00:00:00Z
date_updated: 2023-09-07T12:06:38Z
day: '23'
ddc:
- '571'
degree_awarded: PhD
department:
- _id: JoCs
doi: 10.15479/AT:ISTA:th_858
file:
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checksum: f11925fbbce31e495124b6bc4f10573c
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publication_identifier:
issn:
- 2663-337X
publication_status: published
publisher: Institute of Science and Technology Austria
publist_id: '6811'
pubrep_id: '858'
related_material:
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- id: '5828'
relation: part_of_dissertation
status: public
status: public
supervisor:
- first_name: Jozsef L
full_name: Csicsvari, Jozsef L
id: 3FA14672-F248-11E8-B48F-1D18A9856A87
last_name: Csicsvari
orcid: 0000-0002-5193-4036
title: Reactivation of the hippocampal cognitive map in goal-directed spatial tasks
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: dissertation
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
year: '2017'
...
---
_id: '938'
abstract:
- lang: eng
text: The thesis encompasses several topics of plant cell biology which were studied
in the model plant Arabidopsis thaliana. Chapter 1 concerns the plant hormone
auxin and its polar transport through cells and tissues. The highly controlled,
directional transport of auxin is facilitated by plasma membrane-localized transporters.
Transporters from the PIN family direct auxin transport due to their polarized
localizations at cell membranes. Substantial effort has been put into research
on cellular trafficking of PIN proteins, which is thought to underlie their polar
distribution. I participated in a forward genetic screen aimed at identifying
novel regulators of PIN polarity. The screen yielded several genes which may be
involved in PIN polarity regulation or participate in polar auxin transport by
other means. Chapter 2 focuses on the endomembrane system, with particular attention
to clathrin-mediated endocytosis. The project started with identification of several
proteins that interact with clathrin light chains. Among them, I focused on two
putative homologues of auxilin, which in non-plant systems is an endocytotic factor
known for uncoating clathrin-coated vesicles in the final step of endocytosis.
The body of my work consisted of an in-depth characterization of transgenic A.
thaliana lines overexpressing these putative auxilins in an inducible manner.
Overexpression of these proteins leads to an inhibition of endocytosis, as documented
by imaging of cargoes and clathrin-related endocytic machinery. An extension of
this work is an investigation into a concept of homeostatic regulation acting
between distinct transport processes in the endomembrane system. With auxilin
overexpressing lines, where endocytosis is blocked specifically, I made observations
on the mutual relationship between two opposite trafficking processes of secretion
and endocytosis. In Chapter 3, I analyze cortical microtubule arrays and their
relationship to auxin signaling and polarized growth in elongating cells. In plants,
microtubules are organized into arrays just below the plasma membrane, and it
is thought that their function is to guide membrane-docked cellulose synthase
complexes. These, in turn, influence cell wall structure and cell shape by directed
deposition of cellulose fibres. In elongating cells, cortical microtubule arrays
are able to reorient in relation to long cell axis, and these reorientations have
been linked to cell growth and to signaling of growth-regulating factors such
as auxin or light. In this chapter, I am addressing the causal relationship between
microtubule array reorientation, growth, and auxin signaling. I arrive at a model
where array reorientation is not guided by auxin directly, but instead is only
controlled by growth, which, in turn, is regulated by auxin.
alternative_title:
- ISTA Thesis
article_processing_charge: No
author:
- first_name: Maciek
full_name: Adamowski, Maciek
id: 45F536D2-F248-11E8-B48F-1D18A9856A87
last_name: Adamowski
orcid: 0000-0001-6463-5257
citation:
ama: Adamowski M. Investigations into cell polarity and trafficking in the plant
model Arabidopsis thaliana . 2017. doi:10.15479/AT:ISTA:th_842
apa: Adamowski, M. (2017). Investigations into cell polarity and trafficking
in the plant model Arabidopsis thaliana . Institute of Science and Technology
Austria. https://doi.org/10.15479/AT:ISTA:th_842
chicago: Adamowski, Maciek. “Investigations into Cell Polarity and Trafficking in
the Plant Model Arabidopsis Thaliana .” Institute of Science and Technology Austria,
2017. https://doi.org/10.15479/AT:ISTA:th_842.
ieee: M. Adamowski, “Investigations into cell polarity and trafficking in the plant
model Arabidopsis thaliana ,” Institute of Science and Technology Austria, 2017.
ista: Adamowski M. 2017. Investigations into cell polarity and trafficking in the
plant model Arabidopsis thaliana . Institute of Science and Technology Austria.
mla: Adamowski, Maciek. Investigations into Cell Polarity and Trafficking in
the Plant Model Arabidopsis Thaliana . Institute of Science and Technology
Austria, 2017, doi:10.15479/AT:ISTA:th_842.
short: M. Adamowski, Investigations into Cell Polarity and Trafficking in the Plant
Model Arabidopsis Thaliana , Institute of Science and Technology Austria, 2017.
date_created: 2018-12-11T11:49:18Z
date_published: 2017-06-02T00:00:00Z
date_updated: 2023-09-07T12:06:09Z
day: '02'
ddc:
- '581'
- '583'
- '580'
degree_awarded: PhD
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page: '117'
publication_identifier:
issn:
- 2663-337X
publication_status: published
publisher: Institute of Science and Technology Austria
publist_id: '6483'
pubrep_id: '842'
related_material:
record:
- id: '1591'
relation: part_of_dissertation
status: public
status: public
supervisor:
- first_name: Jiří
full_name: Friml, Jiří
id: 4159519E-F248-11E8-B48F-1D18A9856A87
last_name: Friml
orcid: 0000-0002-8302-7596
title: 'Investigations into cell polarity and trafficking in the plant model Arabidopsis
thaliana '
type: dissertation
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
year: '2017'
...
---
_id: '992'
abstract:
- lang: eng
text: "An instance of the Constraint Satisfaction Problem (CSP) is given by a finite
set of\r\nvariables, a finite domain of labels, and a set of constraints, each
constraint acting on\r\na subset of the variables. The goal is to find an assignment
of labels to its variables\r\nthat satisfies all constraints (or decide whether
one exists). If we allow more general\r\n“soft” constraints, which come with (possibly
infinite) costs of particular assignments,\r\nwe obtain instances from a richer
class called Valued Constraint Satisfaction Problem\r\n(VCSP). There the goal
is to find an assignment with minimum total cost.\r\nIn this thesis, we focus
(assuming that P\r\n6\r\n=\r\nNP) on classifying computational com-\r\nplexity
of CSPs and VCSPs under certain restricting conditions. Two results are the core\r\ncontent
of the work. In one of them, we consider VCSPs parametrized by a constraint\r\nlanguage,
that is the set of “soft” constraints allowed to form the instances, and finish\r\nthe
complexity classification modulo (missing pieces of) complexity classification
for\r\nanalogously parametrized CSP. The other result is a generalization of Edmonds’
perfect\r\nmatching algorithm. This generalization contributes to complexity classfications
in two\r\nways. First, it gives a new (largest known) polynomial-time solvable
class of Boolean\r\nCSPs in which every variable may appear in at most two constraints
and second, it\r\nsettles full classification of Boolean CSPs with planar drawing
(again parametrized by a\r\nconstraint language)."
acknowledgement: FP7/2007-2013/ERC grant agreement no 616160
alternative_title:
- ISTA Thesis
article_processing_charge: No
author:
- first_name: Michal
full_name: Rolinek, Michal
id: 3CB3BC06-F248-11E8-B48F-1D18A9856A87
last_name: Rolinek
citation:
ama: Rolinek M. Complexity of constraint satisfaction. 2017. doi:10.15479/AT:ISTA:th_815
apa: Rolinek, M. (2017). Complexity of constraint satisfaction. Institute
of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:th_815
chicago: Rolinek, Michal. “Complexity of Constraint Satisfaction.” Institute of
Science and Technology Austria, 2017. https://doi.org/10.15479/AT:ISTA:th_815.
ieee: M. Rolinek, “Complexity of constraint satisfaction,” Institute of Science
and Technology Austria, 2017.
ista: Rolinek M. 2017. Complexity of constraint satisfaction. Institute of Science
and Technology Austria.
mla: Rolinek, Michal. Complexity of Constraint Satisfaction. Institute of
Science and Technology Austria, 2017, doi:10.15479/AT:ISTA:th_815.
short: M. Rolinek, Complexity of Constraint Satisfaction, Institute of Science and
Technology Austria, 2017.
date_created: 2018-12-11T11:49:35Z
date_published: 2017-05-01T00:00:00Z
date_updated: 2023-09-07T12:05:41Z
day: '01'
ddc:
- '004'
degree_awarded: PhD
department:
- _id: VlKo
doi: 10.15479/AT:ISTA:th_815
ec_funded: 1
file:
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checksum: 81761fb939acb7585c36629f765b4373
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language:
- iso: eng
month: '05'
oa: 1
oa_version: Published Version
page: '97'
project:
- _id: 25FBA906-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '616160'
name: 'Discrete Optimization in Computer Vision: Theory and Practice'
publication_identifier:
issn:
- 2663-337X
publication_status: published
publisher: Institute of Science and Technology Austria
publist_id: '6407'
pubrep_id: '815'
status: public
supervisor:
- first_name: Vladimir
full_name: Kolmogorov, Vladimir
id: 3D50B0BA-F248-11E8-B48F-1D18A9856A87
last_name: Kolmogorov
title: Complexity of constraint satisfaction
type: dissertation
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
year: '2017'
...
---
_id: '718'
abstract:
- lang: eng
text: Mapping every simplex in the Delaunay mosaic of a discrete point set to the
radius of the smallest empty circumsphere gives a generalized discrete Morse function.
Choosing the points from a Poisson point process in ℝ n , we study the expected
number of simplices in the Delaunay mosaic as well as the expected number of critical
simplices and nonsingular intervals in the corresponding generalized discrete
gradient. Observing connections with other probabilistic models, we obtain precise
expressions for the expected numbers in low dimensions. In particular, we obtain
the expected numbers of simplices in the Poisson–Delaunay mosaic in dimensions
n ≤ 4.
author:
- first_name: Herbert
full_name: Edelsbrunner, Herbert
id: 3FB178DA-F248-11E8-B48F-1D18A9856A87
last_name: Edelsbrunner
orcid: 0000-0002-9823-6833
- first_name: Anton
full_name: Nikitenko, Anton
id: 3E4FF1BA-F248-11E8-B48F-1D18A9856A87
last_name: Nikitenko
orcid: 0000-0002-0659-3201
- first_name: Matthias
full_name: Reitzner, Matthias
last_name: Reitzner
citation:
ama: Edelsbrunner H, Nikitenko A, Reitzner M. Expected sizes of poisson Delaunay
mosaics and their discrete Morse functions. Advances in Applied Probability.
2017;49(3):745-767. doi:10.1017/apr.2017.20
apa: Edelsbrunner, H., Nikitenko, A., & Reitzner, M. (2017). Expected sizes
of poisson Delaunay mosaics and their discrete Morse functions. Advances in
Applied Probability. Cambridge University Press. https://doi.org/10.1017/apr.2017.20
chicago: Edelsbrunner, Herbert, Anton Nikitenko, and Matthias Reitzner. “Expected
Sizes of Poisson Delaunay Mosaics and Their Discrete Morse Functions.” Advances
in Applied Probability. Cambridge University Press, 2017. https://doi.org/10.1017/apr.2017.20.
ieee: H. Edelsbrunner, A. Nikitenko, and M. Reitzner, “Expected sizes of poisson
Delaunay mosaics and their discrete Morse functions,” Advances in Applied Probability,
vol. 49, no. 3. Cambridge University Press, pp. 745–767, 2017.
ista: Edelsbrunner H, Nikitenko A, Reitzner M. 2017. Expected sizes of poisson Delaunay
mosaics and their discrete Morse functions. Advances in Applied Probability. 49(3),
745–767.
mla: Edelsbrunner, Herbert, et al. “Expected Sizes of Poisson Delaunay Mosaics and
Their Discrete Morse Functions.” Advances in Applied Probability, vol.
49, no. 3, Cambridge University Press, 2017, pp. 745–67, doi:10.1017/apr.2017.20.
short: H. Edelsbrunner, A. Nikitenko, M. Reitzner, Advances in Applied Probability
49 (2017) 745–767.
date_created: 2018-12-11T11:48:07Z
date_published: 2017-09-01T00:00:00Z
date_updated: 2023-09-07T12:07:12Z
day: '01'
department:
- _id: HeEd
doi: 10.1017/apr.2017.20
ec_funded: 1
external_id:
arxiv:
- '1607.05915'
intvolume: ' 49'
issue: '3'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/1607.05915
month: '09'
oa: 1
oa_version: Preprint
page: 745 - 767
project:
- _id: 255D761E-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '318493'
name: Topological Complex Systems
- _id: 2561EBF4-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: I02979-N35
name: Persistence and stability of geometric complexes
publication: Advances in Applied Probability
publication_identifier:
issn:
- '00018678'
publication_status: published
publisher: Cambridge University Press
publist_id: '6962'
quality_controlled: '1'
related_material:
record:
- id: '6287'
relation: dissertation_contains
status: public
scopus_import: 1
status: public
title: Expected sizes of poisson Delaunay mosaics and their discrete Morse functions
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 49
year: '2017'
...
---
_id: '559'
abstract:
- lang: eng
text: 'Proofs of space (PoS) were suggested as more ecological and economical alternative
to proofs of work, which are currently used in blockchain designs like Bitcoin.
The existing PoS are based on rather sophisticated graph pebbling lower bounds.
Much simpler and in several aspects more efficient schemes based on inverting
random functions have been suggested, but they don’t give meaningful security
guarantees due to existing time-memory trade-offs. In particular, Hellman showed
that any permutation over a domain of size N can be inverted in time T by an algorithm
that is given S bits of auxiliary information whenever (Formula presented). For
functions Hellman gives a weaker attack with S2· T≈ N2 (e.g., S= T≈ N2/3). To
prove lower bounds, one considers an adversary who has access to an oracle f:
[ N] → [N] and can make T oracle queries. The best known lower bound is S· T∈
Ω(N) and holds for random functions and permutations. We construct functions that
provably require more time and/or space to invert. Specifically, for any constant
k we construct a function [N] → [N] that cannot be inverted unless Sk· T∈ Ω(Nk)
(in particular, S= T≈ (Formula presented). Our construction does not contradict
Hellman’s time-memory trade-off, because it cannot be efficiently evaluated in
forward direction. However, its entire function table can be computed in time
quasilinear in N, which is sufficient for the PoS application. Our simplest construction
is built from a random function oracle g: [N] × [N] → [ N] and a random permutation
oracle f: [N] → N] and is defined as h(x) = g(x, x′) where f(x) = π(f(x′)) with
π being any involution without a fixed point, e.g. flipping all the bits. For
this function we prove that any adversary who gets S bits of auxiliary information,
makes at most T oracle queries, and inverts h on an ϵ fraction of outputs must
satisfy S2· T∈ Ω(ϵ2N2).'
alternative_title:
- LNCS
author:
- first_name: Hamza M
full_name: Abusalah, Hamza M
id: 40297222-F248-11E8-B48F-1D18A9856A87
last_name: Abusalah
- first_name: Joel F
full_name: Alwen, Joel F
id: 2A8DFA8C-F248-11E8-B48F-1D18A9856A87
last_name: Alwen
- first_name: Bram
full_name: Cohen, Bram
last_name: Cohen
- first_name: Danylo
full_name: Khilko, Danylo
last_name: Khilko
- 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: Leonid
full_name: Reyzin, Leonid
last_name: Reyzin
citation:
ama: 'Abusalah HM, Alwen JF, Cohen B, Khilko D, Pietrzak KZ, Reyzin L. Beyond Hellman’s
time-memory trade-offs with applications to proofs of space. In: Vol 10625. Springer;
2017:357-379. doi:10.1007/978-3-319-70697-9_13'
apa: 'Abusalah, H. M., Alwen, J. F., Cohen, B., Khilko, D., Pietrzak, K. Z., &
Reyzin, L. (2017). Beyond Hellman’s time-memory trade-offs with applications to
proofs of space (Vol. 10625, pp. 357–379). Presented at the ASIACRYPT: Theory
and Applications of Cryptology and Information Security, Hong Kong, China: Springer.
https://doi.org/10.1007/978-3-319-70697-9_13'
chicago: Abusalah, Hamza M, Joel F Alwen, Bram Cohen, Danylo Khilko, Krzysztof Z
Pietrzak, and Leonid Reyzin. “Beyond Hellman’s Time-Memory Trade-Offs with Applications
to Proofs of Space,” 10625:357–79. Springer, 2017. https://doi.org/10.1007/978-3-319-70697-9_13.
ieee: 'H. M. Abusalah, J. F. Alwen, B. Cohen, D. Khilko, K. Z. Pietrzak, and L.
Reyzin, “Beyond Hellman’s time-memory trade-offs with applications to proofs of
space,” presented at the ASIACRYPT: Theory and Applications of Cryptology and
Information Security, Hong Kong, China, 2017, vol. 10625, pp. 357–379.'
ista: 'Abusalah HM, Alwen JF, Cohen B, Khilko D, Pietrzak KZ, Reyzin L. 2017. Beyond
Hellman’s time-memory trade-offs with applications to proofs of space. ASIACRYPT:
Theory and Applications of Cryptology and Information Security, LNCS, vol. 10625,
357–379.'
mla: Abusalah, Hamza M., et al. Beyond Hellman’s Time-Memory Trade-Offs with
Applications to Proofs of Space. Vol. 10625, Springer, 2017, pp. 357–79, doi:10.1007/978-3-319-70697-9_13.
short: H.M. Abusalah, J.F. Alwen, B. Cohen, D. Khilko, K.Z. Pietrzak, L. Reyzin,
in:, Springer, 2017, pp. 357–379.
conference:
end_date: 2017-12-07
location: Hong Kong, China
name: 'ASIACRYPT: Theory and Applications of Cryptology and Information Security'
start_date: 2017-12-03
date_created: 2018-12-11T11:47:10Z
date_published: 2017-11-18T00:00:00Z
date_updated: 2023-09-07T12:30:22Z
day: '18'
department:
- _id: KrPi
doi: 10.1007/978-3-319-70697-9_13
ec_funded: 1
intvolume: ' 10625'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://eprint.iacr.org/2017/893.pdf
month: '11'
oa: 1
oa_version: Submitted Version
page: 357 - 379
project:
- _id: 258AA5B2-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '682815'
name: Teaching Old Crypto New Tricks
publication_identifier:
isbn:
- 978-331970696-2
publication_status: published
publisher: Springer
publist_id: '7257'
quality_controlled: '1'
related_material:
record:
- id: '83'
relation: dissertation_contains
status: public
scopus_import: 1
status: public
title: Beyond Hellman’s time-memory trade-offs with applications to proofs of space
type: conference
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 10625
year: '2017'
...
---
_id: '550'
abstract:
- lang: eng
text: For large random matrices X with independent, centered entries but not necessarily
identical variances, the eigenvalue density of XX* is well-approximated by a deterministic
measure on ℝ. We show that the density of this measure has only square and cubic-root
singularities away from zero. We also extend the bulk local law in [5] to the
vicinity of these singularities.
article_number: '63'
author:
- first_name: Johannes
full_name: Alt, Johannes
id: 36D3D8B6-F248-11E8-B48F-1D18A9856A87
last_name: Alt
citation:
ama: Alt J. Singularities of the density of states of random Gram matrices. Electronic
Communications in Probability. 2017;22. doi:10.1214/17-ECP97
apa: Alt, J. (2017). Singularities of the density of states of random Gram matrices.
Electronic Communications in Probability. Institute of Mathematical Statistics.
https://doi.org/10.1214/17-ECP97
chicago: Alt, Johannes. “Singularities of the Density of States of Random Gram Matrices.”
Electronic Communications in Probability. Institute of Mathematical Statistics,
2017. https://doi.org/10.1214/17-ECP97.
ieee: J. Alt, “Singularities of the density of states of random Gram matrices,”
Electronic Communications in Probability, vol. 22. Institute of Mathematical
Statistics, 2017.
ista: Alt J. 2017. Singularities of the density of states of random Gram matrices.
Electronic Communications in Probability. 22, 63.
mla: Alt, Johannes. “Singularities of the Density of States of Random Gram Matrices.”
Electronic Communications in Probability, vol. 22, 63, Institute of Mathematical
Statistics, 2017, doi:10.1214/17-ECP97.
short: J. Alt, Electronic Communications in Probability 22 (2017).
date_created: 2018-12-11T11:47:07Z
date_published: 2017-11-21T00:00:00Z
date_updated: 2023-09-07T12:38:08Z
day: '21'
ddc:
- '539'
department:
- _id: LaEr
doi: 10.1214/17-ECP97
ec_funded: 1
file:
- access_level: open_access
checksum: 0ec05303a0de190de145654237984c79
content_type: application/pdf
creator: system
date_created: 2018-12-12T10:08:04Z
date_updated: 2020-07-14T12:47:00Z
file_id: '4663'
file_name: IST-2018-926-v1+1_euclid.ecp.1511233247.pdf
file_size: 470876
relation: main_file
file_date_updated: 2020-07-14T12:47:00Z
has_accepted_license: '1'
intvolume: ' 22'
language:
- iso: eng
month: '11'
oa: 1
oa_version: Published Version
project:
- _id: 258DCDE6-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '338804'
name: Random matrices, universality and disordered quantum systems
publication: Electronic Communications in Probability
publication_identifier:
issn:
- 1083589X
publication_status: published
publisher: Institute of Mathematical Statistics
publist_id: '7265'
pubrep_id: '926'
quality_controlled: '1'
related_material:
record:
- id: '149'
relation: dissertation_contains
status: public
scopus_import: 1
status: public
title: Singularities of the density of states of random Gram matrices
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: 22
year: '2017'
...
---
_id: '647'
abstract:
- lang: eng
text: Despite researchers’ efforts in the last couple of decades, reachability analysis
is still a challenging problem even for linear hybrid systems. Among the existing
approaches, the most practical ones are mainly based on bounded-time reachable
set over-approximations. For the purpose of unbounded-time analysis, one important
strategy is to abstract the original system and find an invariant for the abstraction.
In this paper, we propose an approach to constructing a new kind of abstraction
called conic abstraction for affine hybrid systems, and to computing reachable
sets based on this abstraction. The essential feature of a conic abstraction is
that it partitions the state space of a system into a set of convex polyhedral
cones which is derived from a uniform conic partition of the derivative space.
Such a set of polyhedral cones is able to cut all trajectories of the system into
almost straight segments so that every segment of a reach pipe in a polyhedral
cone tends to be straight as well, and hence can be over-approximated tightly
by polyhedra using similar techniques as HyTech or PHAVer. In particular, for
diagonalizable affine systems, our approach can guarantee to find an invariant
for unbounded reachable sets, which is beyond the capability of bounded-time reachability
analysis tools. We implemented the approach in a tool and experiments on benchmarks
show that our approach is more powerful than SpaceEx and PHAVer in dealing with
diagonalizable systems.
alternative_title:
- LNCS
author:
- first_name: Sergiy
full_name: Bogomolov, Sergiy
id: 369D9A44-F248-11E8-B48F-1D18A9856A87
last_name: Bogomolov
orcid: 0000-0002-0686-0365
- first_name: Mirco
full_name: Giacobbe, Mirco
id: 3444EA5E-F248-11E8-B48F-1D18A9856A87
last_name: Giacobbe
orcid: 0000-0001-8180-0904
- 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: Hui
full_name: Kong, Hui
id: 3BDE25AA-F248-11E8-B48F-1D18A9856A87
last_name: Kong
orcid: 0000-0002-3066-6941
citation:
ama: 'Bogomolov S, Giacobbe M, Henzinger TA, Kong H. Conic abstractions for hybrid
systems. In: Vol 10419. Springer; 2017:116-132. doi:10.1007/978-3-319-65765-3_7'
apa: 'Bogomolov, S., Giacobbe, M., Henzinger, T. A., & Kong, H. (2017). Conic
abstractions for hybrid systems (Vol. 10419, pp. 116–132). Presented at the FORMATS:
Formal Modelling and Analysis of Timed Systems, Berlin, Germany: Springer. https://doi.org/10.1007/978-3-319-65765-3_7'
chicago: Bogomolov, Sergiy, Mirco Giacobbe, Thomas A Henzinger, and Hui Kong. “Conic
Abstractions for Hybrid Systems,” 10419:116–32. Springer, 2017. https://doi.org/10.1007/978-3-319-65765-3_7.
ieee: 'S. Bogomolov, M. Giacobbe, T. A. Henzinger, and H. Kong, “Conic abstractions
for hybrid systems,” presented at the FORMATS: Formal Modelling and Analysis of
Timed Systems, Berlin, Germany, 2017, vol. 10419, pp. 116–132.'
ista: 'Bogomolov S, Giacobbe M, Henzinger TA, Kong H. 2017. Conic abstractions for
hybrid systems. FORMATS: Formal Modelling and Analysis of Timed Systems, LNCS,
vol. 10419, 116–132.'
mla: Bogomolov, Sergiy, et al. Conic Abstractions for Hybrid Systems. Vol.
10419, Springer, 2017, pp. 116–32, doi:10.1007/978-3-319-65765-3_7.
short: S. Bogomolov, M. Giacobbe, T.A. Henzinger, H. Kong, in:, Springer, 2017,
pp. 116–132.
conference:
end_date: 2017-09-07
location: Berlin, Germany
name: 'FORMATS: Formal Modelling and Analysis of Timed Systems'
start_date: 2017-09-05
date_created: 2018-12-11T11:47:41Z
date_published: 2017-09-01T00:00:00Z
date_updated: 2023-09-07T12:53:00Z
day: '01'
ddc:
- '005'
department:
- _id: ToHe
doi: 10.1007/978-3-319-65765-3_7
file:
- access_level: open_access
checksum: faf546914ba29bcf9974ee36b6b16750
content_type: application/pdf
creator: system
date_created: 2018-12-12T10:12:38Z
date_updated: 2020-07-14T12:47:31Z
file_id: '4956'
file_name: IST-2017-831-v1+1_main.pdf
file_size: 3806864
relation: main_file
file_date_updated: 2020-07-14T12:47:31Z
has_accepted_license: '1'
language:
- iso: eng
month: '09'
oa: 1
oa_version: Submitted Version
page: 116 - 132
project:
- _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:
- 978-331965764-6
publication_status: published
publisher: Springer
publist_id: '7129'
pubrep_id: '831'
quality_controlled: '1'
related_material:
record:
- id: '6894'
relation: dissertation_contains
status: public
scopus_import: 1
status: public
title: Conic abstractions for hybrid systems
type: conference
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: '10419 '
year: '2017'
...
---
_id: '631'
abstract:
- lang: eng
text: Template polyhedra generalize intervals and octagons to polyhedra whose facets
are orthogonal to a given set of arbitrary directions. They have been employed
in the abstract interpretation of programs and, with particular success, in the
reachability analysis of hybrid automata. While previously, the choice of directions
has been left to the user or a heuristic, we present a method for the automatic
discovery of directions that generalize and eliminate spurious counterexamples.
We show that for the class of convex hybrid automata, i.e., hybrid automata with
(possibly nonlinear) convex constraints on derivatives, such directions always
exist and can be found using convex optimization. We embed our method inside a
CEGAR loop, thus enabling the time-unbounded reachability analysis of an important
and richer class of hybrid automata than was previously possible. We evaluate
our method on several benchmarks, demonstrating also its superior efficiency for
the special case of linear hybrid automata.
acknowledgement: This research was supported in part by the Austrian Science Fund
(FWF) under grants S11402-N23 (RiSE/SHiNE) and Z211-N23 (Wittgenstein Award), by
the European Commission under grant 643921 (UnCoVerCPS), and by the ARC project
DP140104219 (Robust AI Planning for Hybrid Systems).
alternative_title:
- LNCS
author:
- first_name: Sergiy
full_name: Bogomolov, Sergiy
id: 369D9A44-F248-11E8-B48F-1D18A9856A87
last_name: Bogomolov
orcid: 0000-0002-0686-0365
- first_name: Goran
full_name: Frehse, Goran
last_name: Frehse
- first_name: Mirco
full_name: Giacobbe, Mirco
id: 3444EA5E-F248-11E8-B48F-1D18A9856A87
last_name: Giacobbe
orcid: 0000-0001-8180-0904
- first_name: Thomas A
full_name: Henzinger, Thomas A
id: 40876CD8-F248-11E8-B48F-1D18A9856A87
last_name: Henzinger
orcid: 0000−0002−2985−7724
citation:
ama: 'Bogomolov S, Frehse G, Giacobbe M, Henzinger TA. Counterexample guided refinement
of template polyhedra. In: Vol 10205. Springer; 2017:589-606. doi:10.1007/978-3-662-54577-5_34'
apa: 'Bogomolov, S., Frehse, G., Giacobbe, M., & Henzinger, T. A. (2017). Counterexample
guided refinement of template polyhedra (Vol. 10205, pp. 589–606). Presented at
the TACAS: Tools and Algorithms for the Construction and Analysis of Systems,
Uppsala, Sweden: Springer. https://doi.org/10.1007/978-3-662-54577-5_34'
chicago: Bogomolov, Sergiy, Goran Frehse, Mirco Giacobbe, and Thomas A Henzinger.
“Counterexample Guided Refinement of Template Polyhedra,” 10205:589–606. Springer,
2017. https://doi.org/10.1007/978-3-662-54577-5_34.
ieee: 'S. Bogomolov, G. Frehse, M. Giacobbe, and T. A. Henzinger, “Counterexample
guided refinement of template polyhedra,” presented at the TACAS: Tools and Algorithms
for the Construction and Analysis of Systems, Uppsala, Sweden, 2017, vol. 10205,
pp. 589–606.'
ista: 'Bogomolov S, Frehse G, Giacobbe M, Henzinger TA. 2017. Counterexample guided
refinement of template polyhedra. TACAS: Tools and Algorithms for the Construction
and Analysis of Systems, LNCS, vol. 10205, 589–606.'
mla: Bogomolov, Sergiy, et al. Counterexample Guided Refinement of Template Polyhedra.
Vol. 10205, Springer, 2017, pp. 589–606, doi:10.1007/978-3-662-54577-5_34.
short: S. Bogomolov, G. Frehse, M. Giacobbe, T.A. Henzinger, in:, Springer, 2017,
pp. 589–606.
conference:
end_date: 2017-04-29
location: Uppsala, Sweden
name: 'TACAS: Tools and Algorithms for the Construction and Analysis of Systems'
start_date: 2017-04-22
date_created: 2018-12-11T11:47:36Z
date_published: 2017-03-31T00:00:00Z
date_updated: 2023-09-07T12:53:00Z
day: '31'
ddc:
- '000'
department:
- _id: ToHe
doi: 10.1007/978-3-662-54577-5_34
file:
- access_level: open_access
checksum: f395d0d20102b89aeaad8b4ef4f18f4f
content_type: application/pdf
creator: system
date_created: 2018-12-12T10:11:41Z
date_updated: 2020-07-14T12:47:27Z
file_id: '4897'
file_name: IST-2017-741-v1+1_main.pdf
file_size: 569863
relation: main_file
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checksum: f416ee1ae4497b23ecdf28b1f18bb8df
content_type: application/pdf
creator: system
date_created: 2018-12-12T10:11:42Z
date_updated: 2020-07-14T12:47:27Z
file_id: '4898'
file_name: IST-2018-741-v2+2_main.pdf
file_size: 563276
relation: main_file
file_date_updated: 2020-07-14T12:47:27Z
has_accepted_license: '1'
intvolume: ' 10205'
language:
- iso: eng
month: '03'
oa: 1
oa_version: Submitted Version
page: 589 - 606
project:
- _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:
- 978-366254576-8
publication_status: published
publisher: Springer
publist_id: '7162'
pubrep_id: '966'
quality_controlled: '1'
related_material:
record:
- id: '6894'
relation: dissertation_contains
status: public
scopus_import: 1
status: public
title: Counterexample guided refinement of template polyhedra
type: conference
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 10205
year: '2017'
...
---
_id: '1144'
abstract:
- lang: eng
text: We show that matrix elements of functions of N × N Wigner matrices fluctuate
on a scale of order N−1/2 and we identify the limiting fluctuation. Our result
holds for any function f of the matrix that has bounded variation thus considerably
relaxing the regularity requirement imposed in [7, 11].
acknowledgement: Partially supported by the IST Austria Excellence Scholarship.
article_number: '86'
author:
- first_name: László
full_name: Erdös, László
id: 4DBD5372-F248-11E8-B48F-1D18A9856A87
last_name: Erdös
orcid: 0000-0001-5366-9603
- first_name: Dominik J
full_name: Schröder, Dominik J
id: 408ED176-F248-11E8-B48F-1D18A9856A87
last_name: Schröder
orcid: 0000-0002-2904-1856
citation:
ama: Erdös L, Schröder DJ. Fluctuations of functions of Wigner matrices. Electronic
Communications in Probability. 2017;21. doi:10.1214/16-ECP38
apa: Erdös, L., & Schröder, D. J. (2017). Fluctuations of functions of Wigner
matrices. Electronic Communications in Probability. Institute of Mathematical
Statistics. https://doi.org/10.1214/16-ECP38
chicago: Erdös, László, and Dominik J Schröder. “Fluctuations of Functions of Wigner
Matrices.” Electronic Communications in Probability. Institute of Mathematical
Statistics, 2017. https://doi.org/10.1214/16-ECP38.
ieee: L. Erdös and D. J. Schröder, “Fluctuations of functions of Wigner matrices,”
Electronic Communications in Probability, vol. 21. Institute of Mathematical
Statistics, 2017.
ista: Erdös L, Schröder DJ. 2017. Fluctuations of functions of Wigner matrices.
Electronic Communications in Probability. 21, 86.
mla: Erdös, László, and Dominik J. Schröder. “Fluctuations of Functions of Wigner
Matrices.” Electronic Communications in Probability, vol. 21, 86, Institute
of Mathematical Statistics, 2017, doi:10.1214/16-ECP38.
short: L. Erdös, D.J. Schröder, Electronic Communications in Probability 21 (2017).
date_created: 2018-12-11T11:50:23Z
date_published: 2017-01-02T00:00:00Z
date_updated: 2023-09-07T12:54:12Z
day: '02'
ddc:
- '510'
department:
- _id: LaEr
doi: 10.1214/16-ECP38
ec_funded: 1
file:
- access_level: open_access
content_type: application/pdf
creator: system
date_created: 2018-12-12T10:18:10Z
date_updated: 2018-12-12T10:18:10Z
file_id: '5329'
file_name: IST-2017-747-v1+1_euclid.ecp.1483347665.pdf
file_size: 440770
relation: main_file
file_date_updated: 2018-12-12T10:18:10Z
has_accepted_license: '1'
intvolume: ' 21'
language:
- iso: eng
month: '01'
oa: 1
oa_version: Published Version
project:
- _id: 258DCDE6-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '338804'
name: Random matrices, universality and disordered quantum systems
publication: Electronic Communications in Probability
publication_status: published
publisher: Institute of Mathematical Statistics
publist_id: '6214'
pubrep_id: '747'
quality_controlled: '1'
related_material:
record:
- id: '6179'
relation: dissertation_contains
status: public
scopus_import: 1
status: public
title: Fluctuations of functions of Wigner matrices
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: 21
year: '2017'
...
---
_id: '486'
abstract:
- lang: eng
text: Color texture reproduction in 3D printing commonly ignores volumetric light
transport (cross-talk) between surface points on a 3D print. Such light diffusion
leads to significant blur of details and color bleeding, and is particularly severe
for highly translucent resin-based print materials. Given their widely varying
scattering properties, this cross-talk between surface points strongly depends
on the internal structure of the volume surrounding each surface point. Existing
scattering-aware methods use simplified models for light diffusion, and often
accept the visual blur as an immutable property of the print medium. In contrast,
our work counteracts heterogeneous scattering to obtain the impression of a crisp
albedo texture on top of the 3D print, by optimizing for a fully volumetric material
distribution that preserves the target appearance. Our method employs an efficient
numerical optimizer on top of a general Monte-Carlo simulation of heterogeneous
scattering, supported by a practical calibration procedure to obtain scattering
parameters from a given set of printer materials. Despite the inherent translucency
of the medium, we reproduce detailed surface textures on 3D prints. We evaluate
our system using a commercial, five-tone 3D print process and compare against
the printer’s native color texturing mode, demonstrating that our method preserves
high-frequency features well without having to compromise on color gamut.
article_number: '241'
article_processing_charge: No
article_type: original
author:
- first_name: Oskar
full_name: Elek, Oskar
last_name: Elek
- first_name: Denis
full_name: Sumin, Denis
last_name: Sumin
- first_name: Ran
full_name: Zhang, Ran
id: 4DDBCEB0-F248-11E8-B48F-1D18A9856A87
last_name: Zhang
orcid: 0000-0002-3808-281X
- first_name: Tim
full_name: Weyrich, Tim
last_name: Weyrich
- first_name: Karol
full_name: Myszkowski, Karol
last_name: Myszkowski
- first_name: Bernd
full_name: Bickel, Bernd
id: 49876194-F248-11E8-B48F-1D18A9856A87
last_name: Bickel
orcid: 0000-0001-6511-9385
- first_name: Alexander
full_name: Wilkie, Alexander
last_name: Wilkie
- first_name: Jaroslav
full_name: Krivanek, Jaroslav
last_name: Krivanek
citation:
ama: Elek O, Sumin D, Zhang R, et al. Scattering-aware texture reproduction for
3D printing. ACM Transactions on Graphics. 2017;36(6). doi:10.1145/3130800.3130890
apa: Elek, O., Sumin, D., Zhang, R., Weyrich, T., Myszkowski, K., Bickel, B., …
Krivanek, J. (2017). Scattering-aware texture reproduction for 3D printing. ACM
Transactions on Graphics. ACM. https://doi.org/10.1145/3130800.3130890
chicago: Elek, Oskar, Denis Sumin, Ran Zhang, Tim Weyrich, Karol Myszkowski, Bernd
Bickel, Alexander Wilkie, and Jaroslav Krivanek. “Scattering-Aware Texture Reproduction
for 3D Printing.” ACM Transactions on Graphics. ACM, 2017. https://doi.org/10.1145/3130800.3130890.
ieee: O. Elek et al., “Scattering-aware texture reproduction for 3D printing,”
ACM Transactions on Graphics, vol. 36, no. 6. ACM, 2017.
ista: Elek O, Sumin D, Zhang R, Weyrich T, Myszkowski K, Bickel B, Wilkie A, Krivanek
J. 2017. Scattering-aware texture reproduction for 3D printing. ACM Transactions
on Graphics. 36(6), 241.
mla: Elek, Oskar, et al. “Scattering-Aware Texture Reproduction for 3D Printing.”
ACM Transactions on Graphics, vol. 36, no. 6, 241, ACM, 2017, doi:10.1145/3130800.3130890.
short: O. Elek, D. Sumin, R. Zhang, T. Weyrich, K. Myszkowski, B. Bickel, A. Wilkie,
J. Krivanek, ACM Transactions on Graphics 36 (2017).
date_created: 2018-12-11T11:46:44Z
date_published: 2017-11-20T00:00:00Z
date_updated: 2023-09-07T13:11:15Z
day: '20'
ddc:
- '003'
- '000'
- '005'
department:
- _id: BeBi
doi: 10.1145/3130800.3130890
ec_funded: 1
file:
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checksum: 48386fa6956c3645fc89594dc898b147
content_type: application/pdf
creator: system
date_created: 2018-12-12T10:10:46Z
date_updated: 2020-07-14T12:46:35Z
file_id: '4836'
file_name: IST-2018-1052-v1+1_ElekSumin2017SGA.pdf
file_size: 107349827
relation: main_file
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checksum: 21c89c28fb8d70f6602f752bf997aa0f
content_type: application/pdf
creator: bbickel
date_created: 2019-12-16T14:48:57Z
date_updated: 2020-07-14T12:46:35Z
file_id: '7189'
file_name: ElekSumin2017SGA_reduced_file_size.pdf
file_size: 4683145
relation: main_file
file_date_updated: 2020-07-14T12:46:35Z
has_accepted_license: '1'
intvolume: ' 36'
issue: '6'
language:
- iso: eng
month: '11'
oa: 1
oa_version: Submitted Version
project:
- _id: 2508E324-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '642841'
name: Distributed 3D Object Design
- _id: 24F9549A-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '715767'
name: 'MATERIALIZABLE: Intelligent fabrication-oriented Computational Design and
Modeling'
- _id: 25681D80-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '291734'
name: International IST Postdoc Fellowship Programme
publication: ACM Transactions on Graphics
publication_identifier:
issn:
- '07300301'
publication_status: published
publisher: ACM
publist_id: '7334'
pubrep_id: '1052'
quality_controlled: '1'
related_material:
record:
- id: '8386'
relation: dissertation_contains
status: public
scopus_import: 1
status: public
title: Scattering-aware texture reproduction for 3D printing
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 36
year: '2017'
...
---
_id: '637'
abstract:
- lang: eng
text: For many cryptographic primitives, it is relatively easy to achieve selective
security (where the adversary commits a-priori to some of the choices to be made
later in the attack) but appears difficult to achieve the more natural notion
of adaptive security (where the adversary can make all choices on the go as the
attack progresses). A series of several recent works shows how to cleverly achieve
adaptive security in several such scenarios including generalized selective decryption
(Panjwani, TCC ’07 and Fuchsbauer et al., CRYPTO ’15), constrained PRFs (Fuchsbauer
et al., ASIACRYPT ’14), and Yao garbled circuits (Jafargholi and Wichs, TCC ’16b).
Although the above works expressed vague intuition that they share a common technique,
the connection was never made precise. In this work we present a new framework
that connects all of these works and allows us to present them in a unified and
simplified fashion. Moreover, we use the framework to derive a new result for
adaptively secure secret sharing over access structures defined via monotone circuits.
We envision that further applications will follow in the future. Underlying our
framework is the following simple idea. It is well known that selective security,
where the adversary commits to n-bits of information about his future choices,
automatically implies adaptive security at the cost of amplifying the adversary’s
advantage by a factor of up to 2n. However, in some cases the proof of selective
security proceeds via a sequence of hybrids, where each pair of adjacent hybrids
locally only requires some smaller partial information consisting of m ≪ n bits.
The partial information needed might be completely different between different
pairs of hybrids, and if we look across all the hybrids we might rely on the entire
n-bit commitment. Nevertheless, the above is sufficient to prove adaptive security,
at the cost of amplifying the adversary’s advantage by a factor of only 2m ≪ 2n.
In all of our examples using the above framework, the different hybrids are captured
by some sort of a graph pebbling game and the amount of information that the adversary
needs to commit to in each pair of hybrids is bounded by the maximum number of
pebbles in play at any point in time. Therefore, coming up with better strategies
for proving adaptive security translates to various pebbling strategies for different
types of graphs.
alternative_title:
- LNCS
author:
- first_name: Zahra
full_name: Jafargholi, Zahra
last_name: Jafargholi
- first_name: Chethan
full_name: Kamath Hosdurg, Chethan
id: 4BD3F30E-F248-11E8-B48F-1D18A9856A87
last_name: Kamath Hosdurg
- first_name: Karen
full_name: Klein, Karen
id: 3E83A2F8-F248-11E8-B48F-1D18A9856A87
last_name: Klein
- first_name: Ilan
full_name: Komargodski, Ilan
last_name: Komargodski
- 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: Daniel
full_name: Wichs, Daniel
last_name: Wichs
citation:
ama: 'Jafargholi Z, Kamath Hosdurg C, Klein K, Komargodski I, Pietrzak KZ, Wichs
D. Be adaptive avoid overcommitting. In: Katz J, Shacham H, eds. Vol 10401. Springer;
2017:133-163. doi:10.1007/978-3-319-63688-7_5'
apa: 'Jafargholi, Z., Kamath Hosdurg, C., Klein, K., Komargodski, I., Pietrzak,
K. Z., & Wichs, D. (2017). Be adaptive avoid overcommitting. In J. Katz &
H. Shacham (Eds.) (Vol. 10401, pp. 133–163). Presented at the CRYPTO: Cryptology,
Santa Barbara, CA, United States: Springer. https://doi.org/10.1007/978-3-319-63688-7_5'
chicago: Jafargholi, Zahra, Chethan Kamath Hosdurg, Karen Klein, Ilan Komargodski,
Krzysztof Z Pietrzak, and Daniel Wichs. “Be Adaptive Avoid Overcommitting.” edited
by Jonathan Katz and Hovav Shacham, 10401:133–63. Springer, 2017. https://doi.org/10.1007/978-3-319-63688-7_5.
ieee: 'Z. Jafargholi, C. Kamath Hosdurg, K. Klein, I. Komargodski, K. Z. Pietrzak,
and D. Wichs, “Be adaptive avoid overcommitting,” presented at the CRYPTO: Cryptology,
Santa Barbara, CA, United States, 2017, vol. 10401, pp. 133–163.'
ista: 'Jafargholi Z, Kamath Hosdurg C, Klein K, Komargodski I, Pietrzak KZ, Wichs
D. 2017. Be adaptive avoid overcommitting. CRYPTO: Cryptology, LNCS, vol. 10401,
133–163.'
mla: Jafargholi, Zahra, et al. Be Adaptive Avoid Overcommitting. Edited by
Jonathan Katz and Hovav Shacham, vol. 10401, Springer, 2017, pp. 133–63, doi:10.1007/978-3-319-63688-7_5.
short: Z. Jafargholi, C. Kamath Hosdurg, K. Klein, I. Komargodski, K.Z. Pietrzak,
D. Wichs, in:, J. Katz, H. Shacham (Eds.), Springer, 2017, pp. 133–163.
conference:
end_date: 2017-07-24
location: Santa Barbara, CA, United States
name: 'CRYPTO: Cryptology'
start_date: 2017-07-20
date_created: 2018-12-11T11:47:38Z
date_published: 2017-01-01T00:00:00Z
date_updated: 2023-09-07T13:32:11Z
day: '01'
department:
- _id: KrPi
doi: 10.1007/978-3-319-63688-7_5
ec_funded: 1
editor:
- first_name: Jonathan
full_name: Katz, Jonathan
last_name: Katz
- first_name: Hovav
full_name: Shacham, Hovav
last_name: Shacham
intvolume: ' 10401'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://eprint.iacr.org/2017/515
month: '01'
oa: 1
oa_version: Submitted Version
page: 133 - 163
project:
- _id: 258AA5B2-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '682815'
name: Teaching Old Crypto New Tricks
publication_identifier:
isbn:
- 978-331963687-0
publication_status: published
publisher: Springer
publist_id: '7151'
quality_controlled: '1'
related_material:
record:
- id: '10035'
relation: dissertation_contains
status: public
scopus_import: 1
status: public
title: Be adaptive avoid overcommitting
type: conference
user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87
volume: 10401
year: '2017'
...
---
_id: '9842'
abstract:
- lang: eng
text: Mathematica notebooks used to generate figures.
article_processing_charge: No
author:
- first_name: Alison
full_name: Etheridge, Alison
last_name: Etheridge
- first_name: Nicholas H
full_name: Barton, Nicholas H
id: 4880FE40-F248-11E8-B48F-1D18A9856A87
last_name: Barton
orcid: 0000-0002-8548-5240
citation:
ama: 'Etheridge A, Barton NH. Data for: Establishment in a new habitat by polygenic
adaptation. 2017. doi:10.17632/nw68fxzjpm.1'
apa: 'Etheridge, A., & Barton, N. H. (2017). Data for: Establishment in a new
habitat by polygenic adaptation. Mendeley Data. https://doi.org/10.17632/nw68fxzjpm.1'
chicago: 'Etheridge, Alison, and Nicholas H Barton. “Data for: Establishment in
a New Habitat by Polygenic Adaptation.” Mendeley Data, 2017. https://doi.org/10.17632/nw68fxzjpm.1.'
ieee: 'A. Etheridge and N. H. Barton, “Data for: Establishment in a new habitat
by polygenic adaptation.” Mendeley Data, 2017.'
ista: 'Etheridge A, Barton NH. 2017. Data for: Establishment in a new habitat by
polygenic adaptation, Mendeley Data, 10.17632/nw68fxzjpm.1.'
mla: 'Etheridge, Alison, and Nicholas H. Barton. Data for: Establishment in a
New Habitat by Polygenic Adaptation. Mendeley Data, 2017, doi:10.17632/nw68fxzjpm.1.'
short: A. Etheridge, N.H. Barton, (2017).
date_created: 2021-08-09T13:18:55Z
date_published: 2017-12-29T00:00:00Z
date_updated: 2023-09-11T13:41:21Z
day: '29'
department:
- _id: NiBa
doi: 10.17632/nw68fxzjpm.1
main_file_link:
- open_access: '1'
url: https://doi.org/10.17632/nw68fxzjpm.1
month: '12'
oa: 1
oa_version: Published Version
publisher: Mendeley Data
related_material:
record:
- id: '564'
relation: used_in_publication
status: public
status: public
title: 'Data for: Establishment in a new habitat by polygenic adaptation'
type: research_data_reference
user_id: 6785fbc1-c503-11eb-8a32-93094b40e1cf
year: '2017'
...
---
_id: '14206'
abstract:
- lang: eng
text: Greedy optimization methods such as Matching Pursuit (MP) and Frank-Wolfe
(FW) algorithms regained popularity in recent years due to their simplicity, effectiveness
and theoretical guarantees. MP and FW address optimization over the linear span
and the convex hull of a set of atoms, respectively. In this paper, we consider
the intermediate case of optimization over the convex cone, parametrized as the
conic hull of a generic atom set, leading to the first principled definitions
of non-negative MP algorithms for which we give explicit convergence rates and
demonstrate excellent empirical performance. In particular, we derive sublinear
(O(1/t)) convergence on general smooth and convex objectives, and linear convergence
(O(e−t)) on strongly convex objectives, in both cases for general sets of atoms.
Furthermore, we establish a clear correspondence of our algorithms to known algorithms
from the MP and FW literature. Our novel algorithms and analyses target general
atom sets and general objective functions, and hence are directly applicable to
a large variety of learning settings.
article_processing_charge: No
author:
- first_name: Francesco
full_name: Locatello, Francesco
id: 26cfd52f-2483-11ee-8040-88983bcc06d4
last_name: Locatello
orcid: 0000-0002-4850-0683
- first_name: Michael
full_name: Tschannen, Michael
last_name: Tschannen
- first_name: Gunnar
full_name: Rätsch, Gunnar
last_name: Rätsch
- first_name: Martin
full_name: Jaggi, Martin
last_name: Jaggi
citation:
ama: 'Locatello F, Tschannen M, Rätsch G, Jaggi M. Greedy algorithms for cone constrained
optimization with convergence guarantees. In: Advances in Neural Information
Processing Systems. ; 2017.'
apa: Locatello, F., Tschannen, M., Rätsch, G., & Jaggi, M. (2017). Greedy algorithms
for cone constrained optimization with convergence guarantees. In Advances
in Neural Information Processing Systems. Long Beach, CA, United States.
chicago: Locatello, Francesco, Michael Tschannen, Gunnar Rätsch, and Martin Jaggi.
“Greedy Algorithms for Cone Constrained Optimization with Convergence Guarantees.”
In Advances in Neural Information Processing Systems, 2017.
ieee: F. Locatello, M. Tschannen, G. Rätsch, and M. Jaggi, “Greedy algorithms for
cone constrained optimization with convergence guarantees,” in Advances in
Neural Information Processing Systems, Long Beach, CA, United States, 2017.
ista: 'Locatello F, Tschannen M, Rätsch G, Jaggi M. 2017. Greedy algorithms for
cone constrained optimization with convergence guarantees. Advances in Neural
Information Processing Systems. NeurIPS: Neural Information Processing Systems.'
mla: Locatello, Francesco, et al. “Greedy Algorithms for Cone Constrained Optimization
with Convergence Guarantees.” Advances in Neural Information Processing Systems,
2017.
short: F. Locatello, M. Tschannen, G. Rätsch, M. Jaggi, in:, Advances in Neural
Information Processing Systems, 2017.
conference:
end_date: 2017-12-09
location: Long Beach, CA, United States
name: 'NeurIPS: Neural Information Processing Systems'
start_date: 2017-12-04
date_created: 2023-08-22T14:17:38Z
date_published: 2017-05-31T00:00:00Z
date_updated: 2023-09-13T08:32:23Z
day: '31'
department:
- _id: FrLo
extern: '1'
external_id:
arxiv:
- '1705.11041'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/1705.11041
month: '05'
oa: 1
oa_version: Preprint
publication: Advances in Neural Information Processing Systems
publication_identifier:
isbn:
- '9781510860964'
publication_status: published
quality_controlled: '1'
status: public
title: Greedy algorithms for cone constrained optimization with convergence guarantees
type: conference
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
year: '2017'
...
---
_id: '14205'
abstract:
- lang: eng
text: Two of the most fundamental prototypes of greedy optimization are the matching
pursuit and Frank-Wolfe algorithms. In this paper, we take a unified view on both
classes of methods, leading to the first explicit convergence rates of matching
pursuit methods in an optimization sense, for general sets of atoms. We derive
sublinear (1/t) convergence for both classes on general smooth objectives, and
linear convergence on strongly convex objectives, as well as a clear correspondence
of algorithm variants. Our presented algorithms and rates are affine invariant,
and do not need any incoherence or sparsity assumptions.
article_processing_charge: No
author:
- first_name: Francesco
full_name: Locatello, Francesco
id: 26cfd52f-2483-11ee-8040-88983bcc06d4
last_name: Locatello
orcid: 0000-0002-4850-0683
- first_name: Rajiv
full_name: Khanna, Rajiv
last_name: Khanna
- first_name: Michael
full_name: Tschannen, Michael
last_name: Tschannen
- first_name: Martin
full_name: Jaggi, Martin
last_name: Jaggi
citation:
ama: 'Locatello F, Khanna R, Tschannen M, Jaggi M. A unified optimization view on
generalized matching pursuit and Frank-Wolfe. In: Proceedings of the 20th International
Conference on Artificial Intelligence and Statistics. Vol 54. ML Research
Press; 2017:860-868.'
apa: 'Locatello, F., Khanna, R., Tschannen, M., & Jaggi, M. (2017). A unified
optimization view on generalized matching pursuit and Frank-Wolfe. In Proceedings
of the 20th International Conference on Artificial Intelligence and Statistics
(Vol. 54, pp. 860–868). Fort Lauderdale, FL, United States: ML Research Press.'
chicago: Locatello, Francesco, Rajiv Khanna, Michael Tschannen, and Martin Jaggi.
“A Unified Optimization View on Generalized Matching Pursuit and Frank-Wolfe.”
In Proceedings of the 20th International Conference on Artificial Intelligence
and Statistics, 54:860–68. ML Research Press, 2017.
ieee: F. Locatello, R. Khanna, M. Tschannen, and M. Jaggi, “A unified optimization
view on generalized matching pursuit and Frank-Wolfe,” in Proceedings of the
20th International Conference on Artificial Intelligence and Statistics, Fort
Lauderdale, FL, United States, 2017, vol. 54, pp. 860–868.
ista: 'Locatello F, Khanna R, Tschannen M, Jaggi M. 2017. A unified optimization
view on generalized matching pursuit and Frank-Wolfe. Proceedings of the 20th
International Conference on Artificial Intelligence and Statistics. AISTATS: Conference
on Artificial Intelligence and Statistics vol. 54, 860–868.'
mla: Locatello, Francesco, et al. “A Unified Optimization View on Generalized Matching
Pursuit and Frank-Wolfe.” Proceedings of the 20th International Conference
on Artificial Intelligence and Statistics, vol. 54, ML Research Press, 2017,
pp. 860–68.
short: F. Locatello, R. Khanna, M. Tschannen, M. Jaggi, in:, Proceedings of the
20th International Conference on Artificial Intelligence and Statistics, ML Research
Press, 2017, pp. 860–868.
conference:
end_date: 2017-04-22
location: Fort Lauderdale, FL, United States
name: 'AISTATS: Conference on Artificial Intelligence and Statistics'
start_date: 2017-04-20
date_created: 2023-08-22T14:17:19Z
date_published: 2017-02-21T00:00:00Z
date_updated: 2023-09-13T09:49:10Z
day: '21'
department:
- _id: FrLo
extern: '1'
external_id:
arxiv:
- '1702.06457'
intvolume: ' 54'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.48550/arXiv.1702.06457
month: '02'
oa: 1
oa_version: Preprint
page: 860-868
publication: Proceedings of the 20th International Conference on Artificial Intelligence
and Statistics
publication_status: published
publisher: ML Research Press
quality_controlled: '1'
status: public
title: A unified optimization view on generalized matching pursuit and Frank-Wolfe
type: conference
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
volume: 54
year: '2017'
...
---
_id: '202'
abstract:
- lang: eng
text: 'Restriction-modification (RM) represents the simplest and possibly the most
widespread mechanism of self/non-self discrimination in nature. In order to provide
bacteria with immunity against bacteriophages and other parasitic genetic elements,
RM systems rely on a balance between two enzymes: the restriction enzyme, which
cleaves non-self DNA at specific restriction sites, and the modification enzyme,
which tags the host’s DNA as self and thus protects it from cleavage. In this
thesis, I use population and single-cell level experiments in combination with
mathematical modeling to study different aspects of the interplay between RM systems,
bacteria and bacteriophages. First, I analyze how mutations in phage restriction
sites affect the probability of phage escape – an inherently stochastic process,
during which phages accidently get modified instead of restricted. Next, I use
single-cell experiments to show that RM systems can, with a low probability, attack
the genome of their bacterial host and that this primitive form of autoimmunity
leads to a tradeoff between the evolutionary cost and benefit of RM systems. Finally,
I investigate the nature of interactions between bacteria, RM systems and temperate
bacteriophages to find that, as a consequence of phage escape and its impact on
population dynamics, RM systems can promote acquisition of symbiotic bacteriophages,
rather than limit it. The results presented here uncover new fundamental biological
properties of RM systems and highlight their importance in the ecology and evolution
of bacteria, bacteriophages and their interactions.'
acknowledgement: "During my PhD studies, I received help from many people, all of
which unfortunately cannot be listed here. I thank them deeply and hope that I never
made them regret their kindness.\r\nI would like to express my deepest gratitude
to Călin Guet, who went far beyond his responsibilities as an advisor and was to
me also a great mentor and a friend. Călin never questioned my potential or lacked
compassion and I cannot thank him enough for cultivating in me an independent scientist.
I was amazed by his ability to recognize the most fascinating scientific problems
in objects of study that others would find mundane. I hope I adopted at least a
fraction of this ability.\r\nI will be forever grateful to Bruce Levin for all his
support and especially for giving me the best possible example of how one can practice
excellent science with humor and style. Working with Bruce was a true privilege.\r\nI
thank Jonathan Bollback and Gašper Tkačik for serving in my PhD committee and the
Austrian Academy of Science for funding my PhD research via the DOC fellowship.\r\nI
thank all our lab members: Tobias Bergmiller for his guidance, especially in the
first years of my research, and for being a good friend throughout; Remy Chait for
staying in the lab at unreasonable hours and for the good laughs at bad jokes we
shared; Anna Staron for supportively listening to my whines whenever I had to run
a gel; Magdalena Steinrück for her pioneering work in the lab; Kathrin Tomasek for
keeping the entropic forces in check and for her FACS virtuosity; Isabella Tomanek
for always being nice to me, no matter how much bench space I took from her.\r\nI
thank all my collaborators: Reiko Okura and Yuichi Wakamoto for performing and analyzing
the microfluidic experiments; Long Qian and Edo Kussell for their bioinformatics
analysis; Dominik Refardt for the λ kan phage; Moritz for his help with the mathematical
modeling. I thank Fabienne Jesse for her tireless editorial work on all our manuscripts.\r\nFinally,
I would like to thank my family and especially my wife Edita, who sacrificed a lot
so that I can pursue my goals and dreams.\r\n"
alternative_title:
- ISTA Thesis
article_processing_charge: No
author:
- first_name: Maros
full_name: Pleska, Maros
id: 4569785E-F248-11E8-B48F-1D18A9856A87
last_name: Pleska
orcid: 0000-0001-7460-7479
citation:
ama: Pleska M. Biology of restriction-modification systems at the single-cell and
population level. 2017. doi:10.15479/AT:ISTA:th_916
apa: Pleska, M. (2017). Biology of restriction-modification systems at the single-cell
and population level. Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:th_916
chicago: Pleska, Maros. “Biology of Restriction-Modification Systems at the Single-Cell
and Population Level.” Institute of Science and Technology Austria, 2017. https://doi.org/10.15479/AT:ISTA:th_916.
ieee: M. Pleska, “Biology of restriction-modification systems at the single-cell
and population level,” Institute of Science and Technology Austria, 2017.
ista: Pleska M. 2017. Biology of restriction-modification systems at the single-cell
and population level. Institute of Science and Technology Austria.
mla: Pleska, Maros. Biology of Restriction-Modification Systems at the Single-Cell
and Population Level. Institute of Science and Technology Austria, 2017, doi:10.15479/AT:ISTA:th_916.
short: M. Pleska, Biology of Restriction-Modification Systems at the Single-Cell
and Population Level, Institute of Science and Technology Austria, 2017.
date_created: 2018-12-11T11:45:10Z
date_published: 2017-10-01T00:00:00Z
date_updated: 2023-09-15T12:04:56Z
day: '01'
ddc:
- '576'
- '579'
degree_awarded: PhD
department:
- _id: CaGu
doi: 10.15479/AT:ISTA:th_916
file:
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checksum: 33cfb59674e91f82e3738396d3fb3776
content_type: application/pdf
creator: system
date_created: 2018-12-12T10:08:48Z
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file_size: 18569590
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date_created: 2019-04-05T08:33:14Z
date_updated: 2020-07-14T12:45:24Z
file_id: '6204'
file_name: 2017_Pleska_Maros_Thesis.docx
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relation: source_file
file_date_updated: 2020-07-14T12:45:24Z
has_accepted_license: '1'
language:
- iso: eng
month: '10'
oa: 1
oa_version: Published Version
page: '126'
project:
- _id: 251D65D8-B435-11E9-9278-68D0E5697425
grant_number: '24210'
name: Effects of Stochasticity on the Function of Restriction-Modi cation Systems
at the Single-Cell Level (DOC Fellowship)
publication_identifier:
issn:
- 2663-337X
publication_status: published
publisher: Institute of Science and Technology Austria
publist_id: '7711'
pubrep_id: '916'
related_material:
record:
- id: '1243'
relation: part_of_dissertation
status: public
- id: '561'
relation: part_of_dissertation
status: public
- id: '457'
relation: part_of_dissertation
status: public
status: public
supervisor:
- first_name: Calin C
full_name: Guet, Calin C
id: 47F8433E-F248-11E8-B48F-1D18A9856A87
last_name: Guet
orcid: 0000-0001-6220-2052
title: Biology of restriction-modification systems at the single-cell and population
level
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: dissertation
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
year: '2017'
...
---
_id: '6287'
abstract:
- lang: eng
text: The main objects considered in the present work are simplicial and CW-complexes
with vertices forming a random point cloud. In particular, we consider a Poisson
point process in R^n and study Delaunay and Voronoi complexes of the first and
higher orders and weighted Delaunay complexes obtained as sections of Delaunay
complexes, as well as the Čech complex. Further, we examine theDelaunay complex
of a Poisson point process on the sphere S^n, as well as of a uniform point cloud,
which is equivalent to the convex hull, providing a connection to the theory of
random polytopes. Each of the complexes in question can be endowed with a radius
function, which maps its cells to the radii of appropriately chosen circumspheres,
called the radius of the cell. Applying and developing discrete Morse theory for
these functions, joining it together with probabilistic and sometimes analytic
machinery, and developing several integral geometric tools, we aim at getting
the distributions of circumradii of typical cells. For all considered complexes,
we are able to generalize and obtain up to constants the distribution of radii
of typical intervals of all types. In low dimensions the constants can be computed
explicitly, thus providing the explicit expressions for the expected numbers of
cells. In particular, it allows to find the expected density of simplices of every
dimension for a Poisson point process in R^4, whereas the result for R^3 was known
already in 1970's.
alternative_title:
- ISTA Thesis
article_processing_charge: No
author:
- first_name: Anton
full_name: Nikitenko, Anton
id: 3E4FF1BA-F248-11E8-B48F-1D18A9856A87
last_name: Nikitenko
orcid: 0000-0002-0659-3201
citation:
ama: Nikitenko A. Discrete Morse theory for random complexes . 2017. doi:10.15479/AT:ISTA:th_873
apa: Nikitenko, A. (2017). Discrete Morse theory for random complexes . Institute
of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:th_873
chicago: Nikitenko, Anton. “Discrete Morse Theory for Random Complexes .” Institute
of Science and Technology Austria, 2017. https://doi.org/10.15479/AT:ISTA:th_873.
ieee: A. Nikitenko, “Discrete Morse theory for random complexes ,” Institute of
Science and Technology Austria, 2017.
ista: Nikitenko A. 2017. Discrete Morse theory for random complexes . Institute
of Science and Technology Austria.
mla: Nikitenko, Anton. Discrete Morse Theory for Random Complexes . Institute
of Science and Technology Austria, 2017, doi:10.15479/AT:ISTA:th_873.
short: A. Nikitenko, Discrete Morse Theory for Random Complexes , Institute of Science
and Technology Austria, 2017.
date_created: 2019-04-09T15:04:32Z
date_published: 2017-10-27T00:00:00Z
date_updated: 2023-09-15T12:10:34Z
day: '27'
ddc:
- '514'
- '516'
- '519'
degree_awarded: PhD
department:
- _id: HeEd
doi: 10.15479/AT:ISTA:th_873
file:
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checksum: ece7e598a2f060b263c2febf7f3fe7f9
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date_created: 2019-04-09T14:54:51Z
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file_name: 2017_Thesis_Nikitenko.pdf
file_size: 2324870
relation: main_file
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date_created: 2019-04-09T14:54:51Z
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file_name: 2017_Thesis_Nikitenko_source.zip
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language:
- iso: eng
month: '10'
oa: 1
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page: '86'
publication_identifier:
issn:
- 2663-337X
publication_status: published
publisher: Institute of Science and Technology Austria
pubrep_id: '873'
related_material:
record:
- id: '718'
relation: part_of_dissertation
status: public
- id: '5678'
relation: part_of_dissertation
status: public
- id: '87'
relation: part_of_dissertation
status: public
status: public
supervisor:
- first_name: Herbert
full_name: Edelsbrunner, Herbert
id: 3FB178DA-F248-11E8-B48F-1D18A9856A87
last_name: Edelsbrunner
orcid: 0000-0002-9823-6833
title: 'Discrete Morse theory for random complexes '
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: dissertation
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
year: '2017'
...
---
_id: '1127'
abstract:
- lang: eng
text: "Plant hormone auxin and its transport between cells belong to the most important\r\nmechanisms
controlling plant development. Auxin itself could change localization of PINs
and\r\nthereby control direction of its own flow. We performed an expression profiling
experiment\r\nin Arabidopsis roots to identify potential regulators of PIN polarity
which are transcriptionally\r\nregulated by auxin signalling. We identified several
novel regulators and performed a detailed\r\ncharacterization of the transcription
factor WRKY23 (At2g47260) and its role in auxin\r\nfeedback on PIN polarity. Gain-of-function
and dominant-negative mutants revealed that\r\nWRKY23 plays a crucial role in
mediating the auxin effect on PIN polarity. In concordance,\r\ntypical polar auxin
transport processes such as gravitropism and leaf vascular pattern\r\nformation
were disturbed by interfering with WRKY23 function.\r\nIn order to identify direct
targets of WRKY23, we performed consequential expression\r\nprofiling experiments
using a WRKY23 inducible gain-of-function line and dominant-negative\r\nWRKY23
line that is defunct in PIN re-arrangement. Among several genes mostly related
to\r\nthe groups of cell wall and defense process regulators, we identified LYSINE-HISTIDINE\r\nTRANSPORTER
1 (LHT1; At5g40780), a small amino acid permease gene from the amino\r\nacid/auxin
permease family (AAAP), we present its detailed characterisation in auxin feedback\r\non
PIN repolarization, identified its transcriptional regulation, we propose a potential\r\nmechanism
of its action. Moreover, we identified also a member of receptor-like protein\r\nkinase
LRR-RLK (LEUCINE-RICH REPEAT TRANSMEMBRANE PROTEIN KINASE PROTEIN 1;\r\nLRRK1;
At1g05700), which also affects auxin-dependent PIN re-arrangement. We described\r\nits
transcriptional behaviour, subcellular localization. Based on global expression
data, we\r\ntried to identify ligand responsible for mechanism of signalling and
suggest signalling partner\r\nand interactors. Additionally, we described role
of novel phytohormone group, strigolactone,\r\nin auxin-dependent PIN re-arrangement,
that could be a fundament for future studies in this\r\nfield.\r\nOur results
provide first insights into an auxin transcriptional network targeting PIN\r\nlocalization
and thus regulating plant development. We highlighted WRKY23 transcriptional\r\nnetwork
and characterised its mediatory role in plant development. We identified direct\r\neffectors
of this network, LHT1 and LRRK1, and describe their roles in PIN re-arrangement
and\r\nPIN-dependent auxin transport processes."
acknowledgement: I would like to first acknowledge my supervisor Jiří Friml for support,
kind advice and patience. It was a pleasure to be a part of your lab, Jiří. I will
remember the atmosphere present in auxin lab at VIB in Ghent and at IST in Klosterneuburg
forever. I would like to thank all past and present lab members for the friendship
and friendly and scientific environment in the groups. It was so nice to cooperate
with you, guys. There was always someone who helped me with experiments, troubleshoot
issues coming from our work etc. At this place, I would like to thank especially
to Gergo Molnár. I’m happy (and lucky) that I have met him; he naturally became
my tutor and guide through my PhD. From no one else during my entire professional
career, I’ve learned that much.
alternative_title:
- ISTA Thesis
article_processing_charge: No
author:
- first_name: Tomas
full_name: Prat, Tomas
id: 3DA3BFEE-F248-11E8-B48F-1D18A9856A87
last_name: Prat
citation:
ama: Prat T. Identification of novel regulators of PIN polarity and development
of novel auxin sensor. 2017.
apa: Prat, T. (2017). Identification of novel regulators of PIN polarity and
development of novel auxin sensor. Institute of Science and Technology Austria.
chicago: Prat, Tomas. “Identification of Novel Regulators of PIN Polarity and Development
of Novel Auxin Sensor.” Institute of Science and Technology Austria, 2017.
ieee: T. Prat, “Identification of novel regulators of PIN polarity and development
of novel auxin sensor,” Institute of Science and Technology Austria, 2017.
ista: Prat T. 2017. Identification of novel regulators of PIN polarity and development
of novel auxin sensor. Institute of Science and Technology Austria.
mla: Prat, Tomas. Identification of Novel Regulators of PIN Polarity and Development
of Novel Auxin Sensor. Institute of Science and Technology Austria, 2017.
short: T. Prat, Identification of Novel Regulators of PIN Polarity and Development
of Novel Auxin Sensor, Institute of Science and Technology Austria, 2017.
date_created: 2018-12-11T11:50:17Z
date_published: 2017-01-12T00:00:00Z
date_updated: 2023-09-19T10:39:33Z
day: '12'
ddc:
- '580'
degree_awarded: PhD
department:
- _id: JiFr
file:
- access_level: closed
checksum: d192c7c6c5ea32c8432437286dc4909e
content_type: application/pdf
creator: dernst
date_created: 2019-04-05T08:45:14Z
date_updated: 2019-04-05T08:45:14Z
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file_name: IST_Austria_Thesis_Tomáš_Prát.pdf
file_size: 10285946
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creator: dernst
date_created: 2021-02-22T11:52:56Z
date_updated: 2021-02-22T11:52:56Z
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file_name: 2017_Thesis_Prat.pdf
file_size: 9802991
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success: 1
file_date_updated: 2021-02-22T11:52:56Z
has_accepted_license: '1'
language:
- iso: eng
month: '01'
oa: 1
oa_version: Published Version
page: '131'
publication_identifier:
issn:
- 2663-337X
publication_status: published
publisher: Institute of Science and Technology Austria
publist_id: '6233'
related_material:
record:
- id: '449'
relation: part_of_dissertation
status: public
status: public
supervisor:
- first_name: Jiří
full_name: Friml, Jiří
id: 4159519E-F248-11E8-B48F-1D18A9856A87
last_name: Friml
orcid: 0000-0002-8302-7596
title: Identification of novel regulators of PIN polarity and development of novel
auxin sensor
type: dissertation
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
year: '2017'
...
---
_id: '2016'
abstract:
- lang: eng
text: The Ising model is one of the simplest and most famous models of interacting
systems. It was originally proposed to model ferromagnetic interactions in statistical
physics and is now widely used to model spatial processes in many areas such as
ecology, sociology, and genetics, usually without testing its goodness-of-fit.
Here, we propose an exact goodness-of-fit test for the finite-lattice Ising model.
The theory of Markov bases has been developed in algebraic statistics for exact
goodness-of-fit testing using a Monte Carlo approach. However, this beautiful
theory has fallen short of its promise for applications, because finding a Markov
basis is usually computationally intractable. We develop a Monte Carlo method
for exact goodness-of-fit testing for the Ising model which avoids computing a
Markov basis and also leads to a better connectivity of the Markov chain and hence
to a faster convergence. We show how this method can be applied to analyze the
spatial organization of receptors on the cell membrane.
article_processing_charge: No
author:
- first_name: Abraham
full_name: Martin Del Campo Sanchez, Abraham
last_name: Martin Del Campo Sanchez
- first_name: Sarah A
full_name: Cepeda Humerez, Sarah A
id: 3DEE19A4-F248-11E8-B48F-1D18A9856A87
last_name: Cepeda Humerez
- first_name: Caroline
full_name: Uhler, Caroline
id: 49ADD78E-F248-11E8-B48F-1D18A9856A87
last_name: Uhler
orcid: 0000-0002-7008-0216
citation:
ama: Martin Del Campo Sanchez A, Cepeda Humerez SA, Uhler C. Exact goodness-of-fit
testing for the Ising model. Scandinavian Journal of Statistics. 2017;44(2):285-306.
doi:10.1111/sjos.12251
apa: Martin Del Campo Sanchez, A., Cepeda Humerez, S. A., & Uhler, C. (2017).
Exact goodness-of-fit testing for the Ising model. Scandinavian Journal of
Statistics. Wiley-Blackwell. https://doi.org/10.1111/sjos.12251
chicago: Martin Del Campo Sanchez, Abraham, Sarah A Cepeda Humerez, and Caroline
Uhler. “Exact Goodness-of-Fit Testing for the Ising Model.” Scandinavian Journal
of Statistics. Wiley-Blackwell, 2017. https://doi.org/10.1111/sjos.12251.
ieee: A. Martin Del Campo Sanchez, S. A. Cepeda Humerez, and C. Uhler, “Exact goodness-of-fit
testing for the Ising model,” Scandinavian Journal of Statistics, vol.
44, no. 2. Wiley-Blackwell, pp. 285–306, 2017.
ista: Martin Del Campo Sanchez A, Cepeda Humerez SA, Uhler C. 2017. Exact goodness-of-fit
testing for the Ising model. Scandinavian Journal of Statistics. 44(2), 285–306.
mla: Martin Del Campo Sanchez, Abraham, et al. “Exact Goodness-of-Fit Testing for
the Ising Model.” Scandinavian Journal of Statistics, vol. 44, no. 2, Wiley-Blackwell,
2017, pp. 285–306, doi:10.1111/sjos.12251.
short: A. Martin Del Campo Sanchez, S.A. Cepeda Humerez, C. Uhler, Scandinavian
Journal of Statistics 44 (2017) 285–306.
date_created: 2018-12-11T11:55:13Z
date_published: 2017-06-01T00:00:00Z
date_updated: 2023-09-19T15:13:27Z
day: '01'
department:
- _id: GaTk
doi: 10.1111/sjos.12251
external_id:
arxiv:
- '1410.1242'
isi:
- '000400985000001'
intvolume: ' 44'
isi: 1
issue: '2'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: http://arxiv.org/abs/1410.1242
month: '06'
oa: 1
oa_version: Preprint
page: 285 - 306
publication: Scandinavian Journal of Statistics
publication_identifier:
issn:
- '03036898'
publication_status: published
publisher: Wiley-Blackwell
publist_id: '5060'
quality_controlled: '1'
related_material:
record:
- id: '6473'
relation: part_of_dissertation
status: public
scopus_import: '1'
status: public
title: Exact goodness-of-fit testing for the Ising model
type: journal_article
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
volume: 44
year: '2017'
...
---
_id: '1528'
abstract:
- lang: eng
text: 'We consider N×N Hermitian random matrices H consisting of blocks of size
M≥N6/7. The matrix elements are i.i.d. within the blocks, close to a Gaussian
in the four moment matching sense, but their distribution varies from block to
block to form a block-band structure, with an essential band width M. We show
that the entries of the Green’s function G(z)=(H−z)−1 satisfy the local semicircle
law with spectral parameter z=E+iη down to the real axis for any η≫N−1, using
a combination of the supersymmetry method inspired by Shcherbina (J Stat Phys
155(3): 466–499, 2014) and the Green’s function comparison strategy. Previous
estimates were valid only for η≫M−1. The new estimate also implies that the eigenvectors
in the middle of the spectrum are fully delocalized.'
acknowledgement: "Z. Bao was supported by ERC Advanced Grant RANMAT No. 338804; L.
Erdős was partially supported by ERC Advanced Grant RANMAT No. 338804.\r\nOpen access
funding provided by Institute of Science and Technology (IST Austria). The authors
are very grateful to the anonymous referees for careful reading and valuable comments,
which helped to improve the organization."
article_processing_charge: Yes (via OA deal)
article_type: original
author:
- first_name: Zhigang
full_name: Bao, Zhigang
id: 442E6A6C-F248-11E8-B48F-1D18A9856A87
last_name: Bao
orcid: 0000-0003-3036-1475
- first_name: László
full_name: Erdös, László
id: 4DBD5372-F248-11E8-B48F-1D18A9856A87
last_name: Erdös
orcid: 0000-0001-5366-9603
citation:
ama: Bao Z, Erdös L. Delocalization for a class of random block band matrices. Probability
Theory and Related Fields. 2017;167(3-4):673-776. doi:10.1007/s00440-015-0692-y
apa: Bao, Z., & Erdös, L. (2017). Delocalization for a class of random block
band matrices. Probability Theory and Related Fields. Springer. https://doi.org/10.1007/s00440-015-0692-y
chicago: Bao, Zhigang, and László Erdös. “Delocalization for a Class of Random Block
Band Matrices.” Probability Theory and Related Fields. Springer, 2017.
https://doi.org/10.1007/s00440-015-0692-y.
ieee: Z. Bao and L. Erdös, “Delocalization for a class of random block band matrices,”
Probability Theory and Related Fields, vol. 167, no. 3–4. Springer, pp.
673–776, 2017.
ista: Bao Z, Erdös L. 2017. Delocalization for a class of random block band matrices.
Probability Theory and Related Fields. 167(3–4), 673–776.
mla: Bao, Zhigang, and László Erdös. “Delocalization for a Class of Random Block
Band Matrices.” Probability Theory and Related Fields, vol. 167, no. 3–4,
Springer, 2017, pp. 673–776, doi:10.1007/s00440-015-0692-y.
short: Z. Bao, L. Erdös, Probability Theory and Related Fields 167 (2017) 673–776.
date_created: 2018-12-11T11:52:32Z
date_published: 2017-04-01T00:00:00Z
date_updated: 2023-09-20T09:42:12Z
day: '01'
ddc:
- '530'
department:
- _id: LaEr
doi: 10.1007/s00440-015-0692-y
ec_funded: 1
external_id:
isi:
- '000398842700004'
file:
- access_level: open_access
checksum: 67afa85ff1e220cbc1f9f477a828513c
content_type: application/pdf
creator: system
date_created: 2018-12-12T10:08:05Z
date_updated: 2020-07-14T12:45:00Z
file_id: '4665'
file_name: IST-2016-489-v1+1_s00440-015-0692-y.pdf
file_size: 1615755
relation: main_file
file_date_updated: 2020-07-14T12:45:00Z
has_accepted_license: '1'
intvolume: ' 167'
isi: 1
issue: 3-4
language:
- iso: eng
month: '04'
oa: 1
oa_version: Published Version
page: 673 - 776
project:
- _id: 258DCDE6-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '338804'
name: Random matrices, universality and disordered quantum systems
publication: Probability Theory and Related Fields
publication_identifier:
issn:
- '01788051'
publication_status: published
publisher: Springer
publist_id: '5644'
pubrep_id: '489'
quality_controlled: '1'
scopus_import: '1'
status: public
title: Delocalization for a class of random block band matrices
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: c635000d-4b10-11ee-a964-aac5a93f6ac1
volume: 167
year: '2017'
...
---
_id: '1433'
abstract:
- lang: eng
text: Phat is an open-source C. ++ library for the computation of persistent homology
by matrix reduction, targeted towards developers of software for topological data
analysis. We aim for a simple generic design that decouples algorithms from data
structures without sacrificing efficiency or user-friendliness. We provide numerous
different reduction strategies as well as data types to store and manipulate the
boundary matrix. We compare the different combinations through extensive experimental
evaluation and identify optimization techniques that work well in practical situations.
We also compare our software with various other publicly available libraries for
persistent homology.
article_processing_charge: No
article_type: original
author:
- first_name: Ulrich
full_name: Bauer, Ulrich
last_name: Bauer
- first_name: Michael
full_name: Kerber, Michael
last_name: Kerber
- first_name: Jan
full_name: Reininghaus, Jan
last_name: Reininghaus
- first_name: Hubert
full_name: Wagner, Hubert
id: 379CA8B8-F248-11E8-B48F-1D18A9856A87
last_name: Wagner
citation:
ama: Bauer U, Kerber M, Reininghaus J, Wagner H. Phat - Persistent homology algorithms
toolbox. Journal of Symbolic Computation. 2017;78:76-90. doi:10.1016/j.jsc.2016.03.008
apa: Bauer, U., Kerber, M., Reininghaus, J., & Wagner, H. (2017). Phat - Persistent
homology algorithms toolbox. Journal of Symbolic Computation. Academic
Press. https://doi.org/10.1016/j.jsc.2016.03.008
chicago: Bauer, Ulrich, Michael Kerber, Jan Reininghaus, and Hubert Wagner. “Phat
- Persistent Homology Algorithms Toolbox.” Journal of Symbolic Computation.
Academic Press, 2017. https://doi.org/10.1016/j.jsc.2016.03.008.
ieee: U. Bauer, M. Kerber, J. Reininghaus, and H. Wagner, “Phat - Persistent homology
algorithms toolbox,” Journal of Symbolic Computation, vol. 78. Academic
Press, pp. 76–90, 2017.
ista: Bauer U, Kerber M, Reininghaus J, Wagner H. 2017. Phat - Persistent homology
algorithms toolbox. Journal of Symbolic Computation. 78, 76–90.
mla: Bauer, Ulrich, et al. “Phat - Persistent Homology Algorithms Toolbox.” Journal
of Symbolic Computation, vol. 78, Academic Press, 2017, pp. 76–90, doi:10.1016/j.jsc.2016.03.008.
short: U. Bauer, M. Kerber, J. Reininghaus, H. Wagner, Journal of Symbolic Computation
78 (2017) 76–90.
date_created: 2018-12-11T11:51:59Z
date_published: 2017-01-01T00:00:00Z
date_updated: 2023-09-20T09:42:40Z
day: '01'
department:
- _id: HeEd
doi: 10.1016/j.jsc.2016.03.008
ec_funded: 1
external_id:
isi:
- '000384396000005'
intvolume: ' 78'
isi: 1
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.1016/j.jsc.2016.03.008
month: '01'
oa: 1
oa_version: Published Version
page: 76 - 90
project:
- _id: 255D761E-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '318493'
name: Topological Complex Systems
publication: Journal of Symbolic Computation
publication_identifier:
issn:
- ' 07477171'
publication_status: published
publisher: Academic Press
publist_id: '5765'
quality_controlled: '1'
related_material:
record:
- id: '10894'
relation: earlier_version
status: public
scopus_import: '1'
status: public
title: Phat - Persistent homology algorithms toolbox
type: journal_article
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
volume: 78
year: '2017'
...
---
_id: '1407'
abstract:
- lang: eng
text: We consider the problem of computing the set of initial states of a dynamical
system such that there exists a control strategy to ensure that the trajectories
satisfy a temporal logic specification with probability 1 (almost-surely). We
focus on discrete-time, stochastic linear dynamics and specifications given as
formulas of the Generalized Reactivity(1) fragment of Linear Temporal Logic over
linear predicates in the states of the system. We propose a solution based on
iterative abstraction-refinement, and turn-based 2-player probabilistic games.
While the theoretical guarantee of our algorithm after any finite number of iterations
is only a partial solution, we show that if our algorithm terminates, then the
result is the set of all satisfying initial states. Moreover, for any (partial)
solution our algorithm synthesizes witness control strategies to ensure almost-sure
satisfaction of the temporal logic specification. While the proposed algorithm
guarantees progress and soundness in every iteration, it is computationally demanding.
We offer an alternative, more efficient solution for the reachability properties
that decomposes the problem into a series of smaller problems of the same type.
All algorithms are demonstrated on an illustrative case study.
article_processing_charge: No
author:
- first_name: Mária
full_name: Svoreňová, Mária
last_name: Svoreňová
- first_name: Jan
full_name: Kretinsky, Jan
id: 44CEF464-F248-11E8-B48F-1D18A9856A87
last_name: Kretinsky
orcid: 0000-0002-8122-2881
- first_name: Martin
full_name: Chmelik, Martin
id: 3624234E-F248-11E8-B48F-1D18A9856A87
last_name: Chmelik
- first_name: Krishnendu
full_name: Chatterjee, Krishnendu
id: 2E5DCA20-F248-11E8-B48F-1D18A9856A87
last_name: Chatterjee
orcid: 0000-0002-4561-241X
- first_name: Ivana
full_name: Cěrná, Ivana
last_name: Cěrná
- first_name: Cǎlin
full_name: Belta, Cǎlin
last_name: Belta
citation:
ama: 'Svoreňová M, Kretinsky J, Chmelik M, Chatterjee K, Cěrná I, Belta C. Temporal
logic control for stochastic linear systems using abstraction refinement of probabilistic
games. Nonlinear Analysis: Hybrid Systems. 2017;23(2):230-253. doi:10.1016/j.nahs.2016.04.006'
apa: 'Svoreňová, M., Kretinsky, J., Chmelik, M., Chatterjee, K., Cěrná, I., &
Belta, C. (2017). Temporal logic control for stochastic linear systems using abstraction
refinement of probabilistic games. Nonlinear Analysis: Hybrid Systems.
Elsevier. https://doi.org/10.1016/j.nahs.2016.04.006'
chicago: 'Svoreňová, Mária, Jan Kretinsky, Martin Chmelik, Krishnendu Chatterjee,
Ivana Cěrná, and Cǎlin Belta. “Temporal Logic Control for Stochastic Linear Systems
Using Abstraction Refinement of Probabilistic Games.” Nonlinear Analysis: Hybrid
Systems. Elsevier, 2017. https://doi.org/10.1016/j.nahs.2016.04.006.'
ieee: 'M. Svoreňová, J. Kretinsky, M. Chmelik, K. Chatterjee, I. Cěrná, and C. Belta,
“Temporal logic control for stochastic linear systems using abstraction refinement
of probabilistic games,” Nonlinear Analysis: Hybrid Systems, vol. 23, no.
2. Elsevier, pp. 230–253, 2017.'
ista: 'Svoreňová M, Kretinsky J, Chmelik M, Chatterjee K, Cěrná I, Belta C. 2017.
Temporal logic control for stochastic linear systems using abstraction refinement
of probabilistic games. Nonlinear Analysis: Hybrid Systems. 23(2), 230–253.'
mla: 'Svoreňová, Mária, et al. “Temporal Logic Control for Stochastic Linear Systems
Using Abstraction Refinement of Probabilistic Games.” Nonlinear Analysis: Hybrid
Systems, vol. 23, no. 2, Elsevier, 2017, pp. 230–53, doi:10.1016/j.nahs.2016.04.006.'
short: 'M. Svoreňová, J. Kretinsky, M. Chmelik, K. Chatterjee, I. Cěrná, C. Belta,
Nonlinear Analysis: Hybrid Systems 23 (2017) 230–253.'
date_created: 2018-12-11T11:51:50Z
date_published: 2017-02-01T00:00:00Z
date_updated: 2023-09-20T09:43:09Z
day: '01'
department:
- _id: ToHe
- _id: KrCh
doi: 10.1016/j.nahs.2016.04.006
ec_funded: 1
external_id:
arxiv:
- '1410.5387'
isi:
- '000390637000014'
intvolume: ' 23'
isi: 1
issue: '2'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: http://arxiv.org/abs/1410.5387
month: '02'
oa: 1
oa_version: Preprint
page: 230 - 253
project:
- _id: 25681D80-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '291734'
name: International IST Postdoc Fellowship Programme
- _id: 25EE3708-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '267989'
name: Quantitative Reactive Modeling
- _id: 2581B60A-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '279307'
name: 'Quantitative Graph Games: Theory and Applications'
- _id: 25832EC2-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: S 11407_N23
name: Rigorous Systems Engineering
- _id: 2584A770-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: P 23499-N23
name: Modern Graph Algorithmic Techniques in Formal Verification
- _id: 25863FF4-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: S11407
name: Game Theory
publication: 'Nonlinear Analysis: Hybrid Systems'
publication_status: published
publisher: Elsevier
publist_id: '5800'
quality_controlled: '1'
related_material:
record:
- id: '1689'
relation: earlier_version
status: public
scopus_import: '1'
status: public
title: Temporal logic control for stochastic linear systems using abstraction refinement
of probabilistic games
type: journal_article
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
volume: 23
year: '2017'
...
---
_id: '1367'
abstract:
- lang: eng
text: One of the major challenges in physically based modelling is making simulations
efficient. Adaptive models provide an essential solution to these efficiency goals.
These models are able to self-adapt in space and time, attempting to provide the
best possible compromise between accuracy and speed. This survey reviews the adaptive
solutions proposed so far in computer graphics. Models are classified according
to the strategy they use for adaptation, from time-stepping and freezing techniques
to geometric adaptivity in the form of structured grids, meshes and particles.
Applications range from fluids, through deformable bodies, to articulated solids.
acknowledgement: This work was partly supported by the starting grants ADAPT and BigSplash,
as well as the advanced grant EXPRESSIVE from the European Research Council (ERC-2012-StG_20111012,
ERC-2014-StG_638176 and ERC-2011-ADG_20110209).
article_processing_charge: No
author:
- first_name: Pierre
full_name: Manteaux, Pierre
last_name: Manteaux
- 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: Rahul
full_name: Narain, Rahul
last_name: Narain
- first_name: Stéphane
full_name: Redon, Stéphane
last_name: Redon
- first_name: François
full_name: Faure, François
last_name: Faure
- first_name: Marie
full_name: Cani, Marie
last_name: Cani
citation:
ama: Manteaux P, Wojtan C, Narain R, Redon S, Faure F, Cani M. Adaptive physically
based models in computer graphics. Computer Graphics Forum. 2017;36(6):312-337.
doi:10.1111/cgf.12941
apa: Manteaux, P., Wojtan, C., Narain, R., Redon, S., Faure, F., & Cani, M.
(2017). Adaptive physically based models in computer graphics. Computer Graphics
Forum. Wiley-Blackwell. https://doi.org/10.1111/cgf.12941
chicago: Manteaux, Pierre, Chris Wojtan, Rahul Narain, Stéphane Redon, François
Faure, and Marie Cani. “Adaptive Physically Based Models in Computer Graphics.”
Computer Graphics Forum. Wiley-Blackwell, 2017. https://doi.org/10.1111/cgf.12941.
ieee: P. Manteaux, C. Wojtan, R. Narain, S. Redon, F. Faure, and M. Cani, “Adaptive
physically based models in computer graphics,” Computer Graphics Forum,
vol. 36, no. 6. Wiley-Blackwell, pp. 312–337, 2017.
ista: Manteaux P, Wojtan C, Narain R, Redon S, Faure F, Cani M. 2017. Adaptive physically
based models in computer graphics. Computer Graphics Forum. 36(6), 312–337.
mla: Manteaux, Pierre, et al. “Adaptive Physically Based Models in Computer Graphics.”
Computer Graphics Forum, vol. 36, no. 6, Wiley-Blackwell, 2017, pp. 312–37,
doi:10.1111/cgf.12941.
short: P. Manteaux, C. Wojtan, R. Narain, S. Redon, F. Faure, M. Cani, Computer
Graphics Forum 36 (2017) 312–337.
date_created: 2018-12-11T11:51:37Z
date_published: 2017-09-01T00:00:00Z
date_updated: 2023-09-20T11:05:36Z
day: '01'
ddc:
- '000'
department:
- _id: ChWo
doi: 10.1111/cgf.12941
external_id:
isi:
- '000408634200019'
file:
- access_level: open_access
checksum: 7676e9a9ead6d58c3000988c97deb2ef
content_type: application/pdf
creator: system
date_created: 2018-12-12T10:16:21Z
date_updated: 2020-07-14T12:44:47Z
file_id: '5208'
file_name: IST-2016-634-v1+1_starAdaptivity-cgf.pdf
file_size: 1434439
relation: main_file
file_date_updated: 2020-07-14T12:44:47Z
has_accepted_license: '1'
intvolume: ' 36'
isi: 1
issue: '6'
language:
- iso: eng
month: '09'
oa: 1
oa_version: Submitted Version
page: 312 - 337
publication: Computer Graphics Forum
publication_identifier:
issn:
- '01677055'
publication_status: published
publisher: Wiley-Blackwell
publist_id: '5873'
pubrep_id: '634'
quality_controlled: '1'
scopus_import: '1'
status: public
title: Adaptive physically based models in computer graphics
type: journal_article
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
volume: 36
year: '2017'
...
---
_id: '1338'
abstract:
- lang: eng
text: We present a computer-aided programming approach to concurrency. The approach
allows programmers to program assuming a friendly, non-preemptive scheduler, and
our synthesis procedure inserts synchronization to ensure that the final program
works even with a preemptive scheduler. The correctness specification is implicit,
inferred from the non-preemptive behavior. Let us consider sequences of calls
that the program makes to an external interface. The specification requires that
any such sequence produced under a preemptive scheduler should be included in
the set of sequences produced under a non-preemptive scheduler. We guarantee that
our synthesis does not introduce deadlocks and that the synchronization inserted
is optimal w.r.t. a given objective function. The solution is based on a finitary
abstraction, an algorithm for bounded language inclusion modulo an independence
relation, and generation of a set of global constraints over synchronization placements.
Each model of the global constraints set corresponds to a correctness-ensuring
synchronization placement. The placement that is optimal w.r.t. the given objective
function is chosen as the synchronization solution. We apply the approach to device-driver
programming, where the driver threads call the software interface of the device
and the API provided by the operating system. Our experiments demonstrate that
our synthesis method is precise and efficient. The implicit specification helped
us find one concurrency bug previously missed when model-checking using an explicit,
user-provided specification. We implemented objective functions for coarse-grained
and fine-grained locking and observed that different synchronization placements
are produced for our experiments, favoring a minimal number of synchronization
operations or maximum concurrency, respectively.
article_processing_charge: No
author:
- first_name: Pavol
full_name: Cerny, Pavol
id: 4DCBEFFE-F248-11E8-B48F-1D18A9856A87
last_name: Cerny
- first_name: Edmund
full_name: Clarke, Edmund
last_name: Clarke
- 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: Arjun
full_name: Radhakrishna, Arjun
id: 3B51CAC4-F248-11E8-B48F-1D18A9856A87
last_name: Radhakrishna
- first_name: Leonid
full_name: Ryzhyk, Leonid
last_name: Ryzhyk
- first_name: Roopsha
full_name: Samanta, Roopsha
id: 3D2AAC08-F248-11E8-B48F-1D18A9856A87
last_name: Samanta
- first_name: Thorsten
full_name: Tarrach, Thorsten
id: 3D6E8F2C-F248-11E8-B48F-1D18A9856A87
last_name: Tarrach
orcid: 0000-0003-4409-8487
citation:
ama: Cerny P, Clarke E, Henzinger TA, et al. From non-preemptive to preemptive scheduling
using synchronization synthesis. Formal Methods in System Design. 2017;50(2-3):97-139.
doi:10.1007/s10703-016-0256-5
apa: Cerny, P., Clarke, E., Henzinger, T. A., Radhakrishna, A., Ryzhyk, L., Samanta,
R., & Tarrach, T. (2017). From non-preemptive to preemptive scheduling using
synchronization synthesis. Formal Methods in System Design. Springer. https://doi.org/10.1007/s10703-016-0256-5
chicago: Cerny, Pavol, Edmund Clarke, Thomas A Henzinger, Arjun Radhakrishna, Leonid
Ryzhyk, Roopsha Samanta, and Thorsten Tarrach. “From Non-Preemptive to Preemptive
Scheduling Using Synchronization Synthesis.” Formal Methods in System Design.
Springer, 2017. https://doi.org/10.1007/s10703-016-0256-5.
ieee: P. Cerny et al., “From non-preemptive to preemptive scheduling using
synchronization synthesis,” Formal Methods in System Design, vol. 50, no.
2–3. Springer, pp. 97–139, 2017.
ista: Cerny P, Clarke E, Henzinger TA, Radhakrishna A, Ryzhyk L, Samanta R, Tarrach
T. 2017. From non-preemptive to preemptive scheduling using synchronization synthesis.
Formal Methods in System Design. 50(2–3), 97–139.
mla: Cerny, Pavol, et al. “From Non-Preemptive to Preemptive Scheduling Using Synchronization
Synthesis.” Formal Methods in System Design, vol. 50, no. 2–3, Springer,
2017, pp. 97–139, doi:10.1007/s10703-016-0256-5.
short: P. Cerny, E. Clarke, T.A. Henzinger, A. Radhakrishna, L. Ryzhyk, R. Samanta,
T. Tarrach, Formal Methods in System Design 50 (2017) 97–139.
date_created: 2018-12-11T11:51:27Z
date_published: 2017-06-01T00:00:00Z
date_updated: 2023-09-20T11:13:51Z
day: '01'
ddc:
- '000'
department:
- _id: ToHe
doi: 10.1007/s10703-016-0256-5
ec_funded: 1
external_id:
isi:
- '000399888900001'
file:
- access_level: open_access
checksum: 1163dfd997e8212c789525d4178b1653
content_type: application/pdf
creator: system
date_created: 2018-12-12T10:13:05Z
date_updated: 2020-07-14T12:44:44Z
file_id: '4985'
file_name: IST-2016-656-v1+1_s10703-016-0256-5.pdf
file_size: 1416170
relation: main_file
file_date_updated: 2020-07-14T12:44:44Z
has_accepted_license: '1'
intvolume: ' 50'
isi: 1
issue: 2-3
language:
- iso: eng
month: '06'
oa: 1
oa_version: Published Version
page: 97 - 139
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: B67AFEDC-15C9-11EA-A837-991A96BB2854
name: IST Austria Open Access Fund
publication: Formal Methods in System Design
publication_status: published
publisher: Springer
publist_id: '5929'
pubrep_id: '656'
quality_controlled: '1'
related_material:
record:
- id: '1729'
relation: earlier_version
status: public
scopus_import: '1'
status: public
title: From non-preemptive to preemptive scheduling using synchronization synthesis
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: c635000d-4b10-11ee-a964-aac5a93f6ac1
volume: 50
year: '2017'
...
---
_id: '1351'
abstract:
- lang: eng
text: The behaviour of gene regulatory networks (GRNs) is typically analysed using
simulation-based statistical testing-like methods. In this paper, we demonstrate
that we can replace this approach by a formal verification-like method that gives
higher assurance and scalability. We focus on Wagner’s weighted GRN model with
varying weights, which is used in evolutionary biology. In the model, weight parameters
represent the gene interaction strength that may change due to genetic mutations.
For a property of interest, we synthesise the constraints over the parameter space
that represent the set of GRNs satisfying the property. We experimentally show
that our parameter synthesis procedure computes the mutational robustness of GRNs—an
important problem of interest in evolutionary biology—more efficiently than the
classical simulation method. We specify the property in linear temporal logic.
We employ symbolic bounded model checking and SMT solving to compute the space
of GRNs that satisfy the property, which amounts to synthesizing a set of linear
constraints on the weights.
article_processing_charge: No
author:
- first_name: Mirco
full_name: Giacobbe, Mirco
id: 3444EA5E-F248-11E8-B48F-1D18A9856A87
last_name: Giacobbe
orcid: 0000-0001-8180-0904
- first_name: Calin C
full_name: Guet, Calin C
id: 47F8433E-F248-11E8-B48F-1D18A9856A87
last_name: Guet
orcid: 0000-0001-6220-2052
- first_name: Ashutosh
full_name: Gupta, Ashutosh
id: 335E5684-F248-11E8-B48F-1D18A9856A87
last_name: Gupta
- first_name: Thomas A
full_name: Henzinger, Thomas A
id: 40876CD8-F248-11E8-B48F-1D18A9856A87
last_name: Henzinger
orcid: 0000−0002−2985−7724
- first_name: Tiago
full_name: Paixao, Tiago
id: 2C5658E6-F248-11E8-B48F-1D18A9856A87
last_name: Paixao
orcid: 0000-0003-2361-3953
- first_name: Tatjana
full_name: Petrov, Tatjana
id: 3D5811FC-F248-11E8-B48F-1D18A9856A87
last_name: Petrov
orcid: 0000-0002-9041-0905
citation:
ama: Giacobbe M, Guet CC, Gupta A, Henzinger TA, Paixao T, Petrov T. Model checking
the evolution of gene regulatory networks. Acta Informatica. 2017;54(8):765-787.
doi:10.1007/s00236-016-0278-x
apa: Giacobbe, M., Guet, C. C., Gupta, A., Henzinger, T. A., Paixao, T., & Petrov,
T. (2017). Model checking the evolution of gene regulatory networks. Acta Informatica.
Springer. https://doi.org/10.1007/s00236-016-0278-x
chicago: Giacobbe, Mirco, Calin C Guet, Ashutosh Gupta, Thomas A Henzinger, Tiago
Paixao, and Tatjana Petrov. “Model Checking the Evolution of Gene Regulatory Networks.”
Acta Informatica. Springer, 2017. https://doi.org/10.1007/s00236-016-0278-x.
ieee: M. Giacobbe, C. C. Guet, A. Gupta, T. A. Henzinger, T. Paixao, and T. Petrov,
“Model checking the evolution of gene regulatory networks,” Acta Informatica,
vol. 54, no. 8. Springer, pp. 765–787, 2017.
ista: Giacobbe M, Guet CC, Gupta A, Henzinger TA, Paixao T, Petrov T. 2017. Model
checking the evolution of gene regulatory networks. Acta Informatica. 54(8), 765–787.
mla: Giacobbe, Mirco, et al. “Model Checking the Evolution of Gene Regulatory Networks.”
Acta Informatica, vol. 54, no. 8, Springer, 2017, pp. 765–87, doi:10.1007/s00236-016-0278-x.
short: M. Giacobbe, C.C. Guet, A. Gupta, T.A. Henzinger, T. Paixao, T. Petrov, Acta
Informatica 54 (2017) 765–787.
date_created: 2018-12-11T11:51:32Z
date_published: 2017-12-01T00:00:00Z
date_updated: 2023-09-20T11:06:03Z
day: '01'
ddc:
- '006'
- '576'
department:
- _id: ToHe
- _id: CaGu
- _id: NiBa
doi: 10.1007/s00236-016-0278-x
ec_funded: 1
external_id:
isi:
- '000414343200003'
file:
- access_level: open_access
checksum: 4e661d9135d7f8c342e8e258dee76f3e
content_type: application/pdf
creator: dernst
date_created: 2019-01-17T15:57:29Z
date_updated: 2020-07-14T12:44:46Z
file_id: '5841'
file_name: 2017_ActaInformatica_Giacobbe.pdf
file_size: 755241
relation: main_file
file_date_updated: 2020-07-14T12:44:46Z
has_accepted_license: '1'
intvolume: ' 54'
isi: 1
issue: '8'
language:
- iso: eng
month: '12'
oa: 1
oa_version: Published Version
page: 765 - 787
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: 25B1EC9E-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '618091'
name: Speed of Adaptation in Population Genetics and Evolutionary Computation
- _id: 25681D80-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '291734'
name: International IST Postdoc Fellowship Programme
- _id: 25B07788-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '250152'
name: Limits to selection in biology and in evolutionary computation
publication: Acta Informatica
publication_identifier:
issn:
- '00015903'
publication_status: published
publisher: Springer
publist_id: '5898'
pubrep_id: '649'
quality_controlled: '1'
related_material:
record:
- id: '1835'
relation: earlier_version
status: public
scopus_import: '1'
status: public
title: Model checking the evolution of gene regulatory networks
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: c635000d-4b10-11ee-a964-aac5a93f6ac1
volume: 54
year: '2017'
...
---
_id: '1336'
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 the runtimes of EAs 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 occurrences of new mutations is much longer than the time it takes
for a mutated genotype to take over the population. In this situation, the population
only contains copies of one genotype and evolution can be modelled as a stochastic
process evolving one genotype by means of mutation and selection between the resident
and the mutated genotype. The probability of accepting the mutated genotype then
depends on the change in fitness. We study this process, SSWM, from an algorithmic
perspective, quantifying its expected optimisation time for various parameters
and investigating differences to a similar evolutionary algorithm, the well-known
(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.
article_processing_charge: No
author:
- first_name: Tiago
full_name: Paixao, Tiago
id: 2C5658E6-F248-11E8-B48F-1D18A9856A87
last_name: Paixao
orcid: 0000-0003-2361-3953
- first_name: Jorge
full_name: Pérez Heredia, Jorge
last_name: Pérez Heredia
- first_name: Dirk
full_name: Sudholt, Dirk
last_name: Sudholt
- 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, Pérez Heredia J, Sudholt D, Trubenova B. Towards a runtime comparison
of natural and artificial evolution. Algorithmica. 2017;78(2):681-713.
doi:10.1007/s00453-016-0212-1
apa: Paixao, T., Pérez Heredia, J., Sudholt, D., & Trubenova, B. (2017). Towards
a runtime comparison of natural and artificial evolution. Algorithmica.
Springer. https://doi.org/10.1007/s00453-016-0212-1
chicago: Paixao, Tiago, Jorge Pérez Heredia, Dirk Sudholt, and Barbora Trubenova.
“Towards a Runtime Comparison of Natural and Artificial Evolution.” Algorithmica.
Springer, 2017. https://doi.org/10.1007/s00453-016-0212-1.
ieee: T. Paixao, J. Pérez Heredia, D. Sudholt, and B. Trubenova, “Towards a runtime
comparison of natural and artificial evolution,” Algorithmica, vol. 78,
no. 2. Springer, pp. 681–713, 2017.
ista: Paixao T, Pérez Heredia J, Sudholt D, Trubenova B. 2017. Towards a runtime
comparison of natural and artificial evolution. Algorithmica. 78(2), 681–713.
mla: Paixao, Tiago, et al. “Towards a Runtime Comparison of Natural and Artificial
Evolution.” Algorithmica, vol. 78, no. 2, Springer, 2017, pp. 681–713,
doi:10.1007/s00453-016-0212-1.
short: T. Paixao, J. Pérez Heredia, D. Sudholt, B. Trubenova, Algorithmica 78 (2017)
681–713.
date_created: 2018-12-11T11:51:27Z
date_published: 2017-06-01T00:00:00Z
date_updated: 2023-09-20T11:14:42Z
day: '01'
ddc:
- '576'
department:
- _id: NiBa
- _id: CaGu
doi: 10.1007/s00453-016-0212-1
ec_funded: 1
external_id:
isi:
- '000400379500013'
file:
- access_level: open_access
checksum: 7873f665a0c598ac747c908f34cb14b9
content_type: application/pdf
creator: system
date_created: 2018-12-12T10:10:19Z
date_updated: 2020-07-14T12:44:44Z
file_id: '4805'
file_name: IST-2016-658-v1+1_s00453-016-0212-1.pdf
file_size: 710206
relation: main_file
file_date_updated: 2020-07-14T12:44:44Z
has_accepted_license: '1'
intvolume: ' 78'
isi: 1
issue: '2'
language:
- iso: eng
month: '06'
oa: 1
oa_version: Published Version
page: 681 - 713
project:
- _id: 25B1EC9E-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '618091'
name: Speed of Adaptation in Population Genetics and Evolutionary Computation
publication: Algorithmica
publication_identifier:
issn:
- '01784617'
publication_status: published
publisher: Springer
publist_id: '5931'
pubrep_id: '658'
quality_controlled: '1'
scopus_import: '1'
status: public
title: Towards a runtime comparison of natural and artificial evolution
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: journal_article
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
volume: 78
year: '2017'
...
---
_id: '1337'
abstract:
- lang: eng
text: We consider the local eigenvalue distribution of large self-adjoint N×N random
matrices H=H∗ with centered independent entries. In contrast to previous works
the matrix of variances sij=\mathbbmE|hij|2 is not assumed to be stochastic. Hence
the density of states is not the Wigner semicircle law. Its possible shapes are
described in the companion paper (Ajanki et al. in Quadratic Vector Equations
on the Complex Upper Half Plane. arXiv:1506.05095). We show that as N grows, the
resolvent, G(z)=(H−z)−1, converges to a diagonal matrix, diag(m(z)), where m(z)=(m1(z),…,mN(z))
solves the vector equation −1/mi(z)=z+∑jsijmj(z) that has been analyzed in Ajanki
et al. (Quadratic Vector Equations on the Complex Upper Half Plane. arXiv:1506.05095).
We prove a local law down to the smallest spectral resolution scale, and bulk
universality for both real symmetric and complex hermitian symmetry classes.
acknowledgement: 'Open access funding provided by Institute of Science and Technology
(IST Austria). '
article_processing_charge: Yes (via OA deal)
author:
- first_name: Oskari H
full_name: Ajanki, Oskari H
id: 36F2FB7E-F248-11E8-B48F-1D18A9856A87
last_name: Ajanki
- first_name: László
full_name: Erdös, László
id: 4DBD5372-F248-11E8-B48F-1D18A9856A87
last_name: Erdös
orcid: 0000-0001-5366-9603
- first_name: Torben H
full_name: Krüger, Torben H
id: 3020C786-F248-11E8-B48F-1D18A9856A87
last_name: Krüger
orcid: 0000-0002-4821-3297
citation:
ama: Ajanki OH, Erdös L, Krüger TH. Universality for general Wigner-type matrices.
Probability Theory and Related Fields. 2017;169(3-4):667-727. doi:10.1007/s00440-016-0740-2
apa: Ajanki, O. H., Erdös, L., & Krüger, T. H. (2017). Universality for general
Wigner-type matrices. Probability Theory and Related Fields. Springer.
https://doi.org/10.1007/s00440-016-0740-2
chicago: Ajanki, Oskari H, László Erdös, and Torben H Krüger. “Universality for
General Wigner-Type Matrices.” Probability Theory and Related Fields. Springer,
2017. https://doi.org/10.1007/s00440-016-0740-2.
ieee: O. H. Ajanki, L. Erdös, and T. H. Krüger, “Universality for general Wigner-type
matrices,” Probability Theory and Related Fields, vol. 169, no. 3–4. Springer,
pp. 667–727, 2017.
ista: Ajanki OH, Erdös L, Krüger TH. 2017. Universality for general Wigner-type
matrices. Probability Theory and Related Fields. 169(3–4), 667–727.
mla: Ajanki, Oskari H., et al. “Universality for General Wigner-Type Matrices.”
Probability Theory and Related Fields, vol. 169, no. 3–4, Springer, 2017,
pp. 667–727, doi:10.1007/s00440-016-0740-2.
short: O.H. Ajanki, L. Erdös, T.H. Krüger, Probability Theory and Related Fields
169 (2017) 667–727.
date_created: 2018-12-11T11:51:27Z
date_published: 2017-12-01T00:00:00Z
date_updated: 2023-09-20T11:14:17Z
day: '01'
ddc:
- '510'
- '530'
department:
- _id: LaEr
doi: 10.1007/s00440-016-0740-2
ec_funded: 1
external_id:
isi:
- '000414358400002'
file:
- access_level: open_access
checksum: 29f5a72c3f91e408aeb9e78344973803
content_type: application/pdf
creator: system
date_created: 2018-12-12T10:08:25Z
date_updated: 2020-07-14T12:44:44Z
file_id: '4686'
file_name: IST-2017-657-v1+2_s00440-016-0740-2.pdf
file_size: 988843
relation: main_file
file_date_updated: 2020-07-14T12:44:44Z
has_accepted_license: '1'
intvolume: ' 169'
isi: 1
issue: 3-4
language:
- iso: eng
month: '12'
oa: 1
oa_version: Published Version
page: 667 - 727
project:
- _id: 258DCDE6-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '338804'
name: Random matrices, universality and disordered quantum systems
- _id: B67AFEDC-15C9-11EA-A837-991A96BB2854
name: IST Austria Open Access Fund
publication: Probability Theory and Related Fields
publication_identifier:
issn:
- '01788051'
publication_status: published
publisher: Springer
publist_id: '5930'
pubrep_id: '657'
quality_controlled: '1'
scopus_import: '1'
status: public
title: Universality for general Wigner-type matrices
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: c635000d-4b10-11ee-a964-aac5a93f6ac1
volume: 169
year: '2017'
...
---
_id: '1294'
abstract:
- lang: eng
text: We study controller synthesis problems for finite-state Markov decision processes,
where the objective is to optimize the expected mean-payoff performance and stability
(also known as variability in the literature). We argue that the basic notion
of expressing the stability using the statistical variance of the mean payoff
is sometimes insufficient, and propose an alternative definition. We show that
a strategy ensuring both the expected mean payoff and the variance below given
bounds requires randomization and memory, under both the above definitions. We
then show that the problem of finding such a strategy can be expressed as a set
of constraints.
article_processing_charge: No
author:
- first_name: Tomáš
full_name: Brázdil, Tomáš
last_name: Brázdil
- first_name: Krishnendu
full_name: Chatterjee, Krishnendu
id: 2E5DCA20-F248-11E8-B48F-1D18A9856A87
last_name: Chatterjee
orcid: 0000-0002-4561-241X
- first_name: Vojtěch
full_name: Forejt, Vojtěch
last_name: Forejt
- first_name: Antonín
full_name: Kučera, Antonín
last_name: Kučera
citation:
ama: Brázdil T, Chatterjee K, Forejt V, Kučera A. Trading performance for stability
in Markov decision processes. Journal of Computer and System Sciences.
2017;84:144-170. doi:10.1016/j.jcss.2016.09.009
apa: Brázdil, T., Chatterjee, K., Forejt, V., & Kučera, A. (2017). Trading performance
for stability in Markov decision processes. Journal of Computer and System
Sciences. Elsevier. https://doi.org/10.1016/j.jcss.2016.09.009
chicago: Brázdil, Tomáš, Krishnendu Chatterjee, Vojtěch Forejt, and Antonín Kučera.
“Trading Performance for Stability in Markov Decision Processes.” Journal of
Computer and System Sciences. Elsevier, 2017. https://doi.org/10.1016/j.jcss.2016.09.009.
ieee: T. Brázdil, K. Chatterjee, V. Forejt, and A. Kučera, “Trading performance
for stability in Markov decision processes,” Journal of Computer and System
Sciences, vol. 84. Elsevier, pp. 144–170, 2017.
ista: Brázdil T, Chatterjee K, Forejt V, Kučera A. 2017. Trading performance for
stability in Markov decision processes. Journal of Computer and System Sciences.
84, 144–170.
mla: Brázdil, Tomáš, et al. “Trading Performance for Stability in Markov Decision
Processes.” Journal of Computer and System Sciences, vol. 84, Elsevier,
2017, pp. 144–70, doi:10.1016/j.jcss.2016.09.009.
short: T. Brázdil, K. Chatterjee, V. Forejt, A. Kučera, Journal of Computer and
System Sciences 84 (2017) 144–170.
date_created: 2018-12-11T11:51:12Z
date_published: 2017-03-01T00:00:00Z
date_updated: 2023-09-20T11:15:31Z
day: '01'
ddc:
- '004'
- '006'
department:
- _id: KrCh
doi: 10.1016/j.jcss.2016.09.009
ec_funded: 1
external_id:
isi:
- '000388430000011'
file:
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checksum: 91271b23cf884d7c06d33bef0cd623b1
content_type: application/pdf
creator: system
date_created: 2018-12-12T10:11:30Z
date_updated: 2020-07-14T12:44:42Z
file_id: '4885'
file_name: IST-2016-717-v1+1_1-s2.0-S0022000016300897-main.pdf
file_size: 708657
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isi: 1
language:
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month: '03'
oa: 1
oa_version: Published Version
page: 144 - 170
project:
- _id: 2584A770-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: P 23499-N23
name: Modern Graph Algorithmic Techniques in Formal Verification
- _id: 25863FF4-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: S11407
name: Game Theory
- _id: 2581B60A-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '279307'
name: 'Quantitative Graph Games: Theory and Applications'
- _id: 2587B514-B435-11E9-9278-68D0E5697425
name: Microsoft Research Faculty Fellowship
publication: Journal of Computer and System Sciences
publication_status: published
publisher: Elsevier
publist_id: '6009'
pubrep_id: '717'
quality_controlled: '1'
related_material:
record:
- id: '2305'
relation: earlier_version
status: public
scopus_import: '1'
status: public
title: Trading performance for stability in Markov decision processes
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: journal_article
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
volume: 84
year: '2017'
...
---
_id: '1228'
abstract:
- lang: eng
text: Since 2006, reprogrammed cells have increasingly been used as a biomedical
research technique in addition to neuro-psychiatric methods. These rapidly evolving
techniques allow for the generation of neuronal sub-populations, and have sparked
interest not only in monogenetic neuro-psychiatric diseases, but also in poly-genetic
and poly-aetiological disorders such as schizophrenia (SCZ) and bipolar disorder
(BPD). This review provides a summary of 19 publications on reprogrammed adult
somatic cells derived from patients with SCZ, and five publications using this
technique in patients with BPD. As both disorders are complex and heterogeneous,
there is a plurality of hypotheses to be tested in vitro. In SCZ, data on alterations
of dopaminergic transmission in vitro are sparse, despite the great explanatory
power of the so-called DA hypothesis of SCZ. Some findings correspond to perturbations
of cell energy metabolism, and observations in reprogrammed cells suggest neuro-developmental
alterations. Some studies also report on the efficacy of medicinal compounds to
revert alterations observed in cellular models. However, due to the paucity of
replication studies, no comprehensive conclusions can be drawn from studies using
reprogrammed cells at the present time. In the future, findings from cell culture
methods need to be integrated with clinical, epidemiological, pharmacological
and imaging data in order to generate a more comprehensive picture of SCZ and
BPD.
acknowledgement: This work was supported by grants of the Austrian Science Fund (FWF)
P23585B09 to M.W. and F3506 to H.H.S. and the “Wiener Wissenschafts-, Forschungs-
und Technologiefonds” (Vienna Science and Technology Fund; WWTF) CS15-033 to M.W.
article_processing_charge: No
article_type: review
author:
- first_name: Ulrich
full_name: Sauerzopf, Ulrich
last_name: Sauerzopf
- first_name: Roberto
full_name: Sacco, Roberto
id: 42C9F57E-F248-11E8-B48F-1D18A9856A87
last_name: Sacco
- first_name: Gaia
full_name: Novarino, Gaia
id: 3E57A680-F248-11E8-B48F-1D18A9856A87
last_name: Novarino
orcid: 0000-0002-7673-7178
- first_name: Marco
full_name: Niello, Marco
last_name: Niello
- first_name: Ana
full_name: Weidenauer, Ana
last_name: Weidenauer
- first_name: Nicole
full_name: Praschak Rieder, Nicole
last_name: Praschak Rieder
- first_name: Harald
full_name: Sitte, Harald
last_name: Sitte
- first_name: Matthaeus
full_name: Willeit, Matthaeus
last_name: Willeit
citation:
ama: Sauerzopf U, Sacco R, Novarino G, et al. Are reprogrammed cells a useful tool
for studying dopamine dysfunction in psychotic disorders? A review of the current
evidence. European Journal of Neuroscience. 2017;45(1):45-57. doi:10.1111/ejn.13418
apa: Sauerzopf, U., Sacco, R., Novarino, G., Niello, M., Weidenauer, A., Praschak
Rieder, N., … Willeit, M. (2017). Are reprogrammed cells a useful tool for studying
dopamine dysfunction in psychotic disorders? A review of the current evidence.
European Journal of Neuroscience. Wiley-Blackwell. https://doi.org/10.1111/ejn.13418
chicago: Sauerzopf, Ulrich, Roberto Sacco, Gaia Novarino, Marco Niello, Ana Weidenauer,
Nicole Praschak Rieder, Harald Sitte, and Matthaeus Willeit. “Are Reprogrammed
Cells a Useful Tool for Studying Dopamine Dysfunction in Psychotic Disorders?
A Review of the Current Evidence.” European Journal of Neuroscience. Wiley-Blackwell,
2017. https://doi.org/10.1111/ejn.13418.
ieee: U. Sauerzopf et al., “Are reprogrammed cells a useful tool for studying
dopamine dysfunction in psychotic disorders? A review of the current evidence,”
European Journal of Neuroscience, vol. 45, no. 1. Wiley-Blackwell, pp.
45–57, 2017.
ista: Sauerzopf U, Sacco R, Novarino G, Niello M, Weidenauer A, Praschak Rieder
N, Sitte H, Willeit M. 2017. Are reprogrammed cells a useful tool for studying
dopamine dysfunction in psychotic disorders? A review of the current evidence.
European Journal of Neuroscience. 45(1), 45–57.
mla: Sauerzopf, Ulrich, et al. “Are Reprogrammed Cells a Useful Tool for Studying
Dopamine Dysfunction in Psychotic Disorders? A Review of the Current Evidence.”
European Journal of Neuroscience, vol. 45, no. 1, Wiley-Blackwell, 2017,
pp. 45–57, doi:10.1111/ejn.13418.
short: U. Sauerzopf, R. Sacco, G. Novarino, M. Niello, A. Weidenauer, N. Praschak
Rieder, H. Sitte, M. Willeit, European Journal of Neuroscience 45 (2017) 45–57.
date_created: 2018-12-11T11:50:50Z
date_published: 2017-01-01T00:00:00Z
date_updated: 2023-09-20T11:16:01Z
day: '01'
ddc:
- '616'
department:
- _id: GaNo
doi: 10.1111/ejn.13418
external_id:
isi:
- '000392487100005'
pmid:
- '27690184'
file:
- access_level: open_access
checksum: c572cf02be8fbb7020cfcfb892182e4c
content_type: application/pdf
creator: system
date_created: 2018-12-12T10:10:48Z
date_updated: 2020-07-14T12:44:39Z
file_id: '4838'
file_name: IST-2017-738-v1+1_Sauerzopf_et_al-2017-European_Journal_of_Neuroscience.pdf
file_size: 169145
relation: main_file
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has_accepted_license: '1'
intvolume: ' 45'
isi: 1
issue: '1'
language:
- iso: eng
month: '01'
oa: 1
oa_version: Published Version
page: 45 - 57
pmid: 1
publication: European Journal of Neuroscience
publication_status: published
publisher: Wiley-Blackwell
publist_id: '6106'
pubrep_id: '738'
quality_controlled: '1'
scopus_import: '1'
status: public
title: Are reprogrammed cells a useful tool for studying dopamine dysfunction in psychotic
disorders? A review of the current evidence
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: c635000d-4b10-11ee-a964-aac5a93f6ac1
volume: 45
year: '2017'
...
---
_id: '1213'
abstract:
- lang: eng
text: Bacterial cytokinesis is commonly initiated by the Z-ring, a dynamic cytoskeletal
structure that assembles at the site of division. Its primary component is FtsZ,
a tubulin-like GTPase, that like its eukaryotic relative forms protein filaments
in the presence of GTP. Since the discovery of the Z-ring 25 years ago, various
models for the role of FtsZ have been suggested. However, important information
about the architecture and dynamics of FtsZ filaments during cytokinesis is still
missing. One reason for this lack of knowledge has been the small size of bacteria,
which has made it difficult to resolve the orientation and dynamics of individual
FtsZ filaments in the Z-ring. While superresolution microscopy experiments have
helped to gain more information about the organization of the Z-ring in the dividing
cell, they were not yet able to elucidate a mechanism of how FtsZ filaments reorganize
during assembly and disassembly of the Z-ring. In this chapter, we explain how
to use an in vitro reconstitution approach to investigate the self-organization
of FtsZ filaments recruited to a biomimetic lipid bilayer by its membrane anchor
FtsA. We show how to perform single-molecule experiments to study the behavior
of individual FtsZ monomers during the constant reorganization of the FtsZ-FtsA
filament network. We describe how to analyze the dynamics of single molecules
and explain why this information can help to shed light onto possible mechanism
of Z-ring constriction. We believe that similar experimental approaches will be
useful to study the mechanism of membrane-based polymerization of other cytoskeletal
systems, not only from prokaryotic but also eukaryotic origin.
acknowledged_ssus:
- _id: Bio
acknowledgement: Natalia Baranova is supported by an EMBO Long-Term Fellowship (EMBO
ALTF 1163-2015) and Martin Loose by an ERC Starting Grant (ERCStG-2015-SelfOrganiCell).
alternative_title:
- Methods in Cell Biology
article_processing_charge: No
author:
- first_name: Natalia
full_name: Baranova, Natalia
id: 38661662-F248-11E8-B48F-1D18A9856A87
last_name: Baranova
orcid: 0000-0002-3086-9124
- first_name: Martin
full_name: Loose, Martin
id: 462D4284-F248-11E8-B48F-1D18A9856A87
last_name: Loose
orcid: 0000-0001-7309-9724
citation:
ama: 'Baranova NS, Loose M. Single-molecule measurements to study polymerization
dynamics of FtsZ-FtsA copolymers. In: Echard A, ed. Cytokinesis. Vol 137.
Academic Press; 2017:355-370. doi:10.1016/bs.mcb.2016.03.036'
apa: Baranova, N. S., & Loose, M. (2017). Single-molecule measurements to study
polymerization dynamics of FtsZ-FtsA copolymers. In A. Echard (Ed.), Cytokinesis
(Vol. 137, pp. 355–370). Academic Press. https://doi.org/10.1016/bs.mcb.2016.03.036
chicago: Baranova, Natalia S., and Martin Loose. “Single-Molecule Measurements to
Study Polymerization Dynamics of FtsZ-FtsA Copolymers.” In Cytokinesis,
edited by Arnaud Echard, 137:355–70. Academic Press, 2017. https://doi.org/10.1016/bs.mcb.2016.03.036.
ieee: N. S. Baranova and M. Loose, “Single-molecule measurements to study polymerization
dynamics of FtsZ-FtsA copolymers,” in Cytokinesis, vol. 137, A. Echard,
Ed. Academic Press, 2017, pp. 355–370.
ista: 'Baranova NS, Loose M. 2017.Single-molecule measurements to study polymerization
dynamics of FtsZ-FtsA copolymers. In: Cytokinesis. Methods in Cell Biology, vol.
137, 355–370.'
mla: Baranova, Natalia S., and Martin Loose. “Single-Molecule Measurements to Study
Polymerization Dynamics of FtsZ-FtsA Copolymers.” Cytokinesis, edited by
Arnaud Echard, vol. 137, Academic Press, 2017, pp. 355–70, doi:10.1016/bs.mcb.2016.03.036.
short: N.S. Baranova, M. Loose, in:, A. Echard (Ed.), Cytokinesis, Academic Press,
2017, pp. 355–370.
date_created: 2018-12-11T11:50:45Z
date_published: 2017-12-01T00:00:00Z
date_updated: 2023-09-20T11:16:30Z
day: '01'
department:
- _id: MaLo
doi: 10.1016/bs.mcb.2016.03.036
ec_funded: 1
editor:
- first_name: 'Arnaud '
full_name: 'Echard, Arnaud '
last_name: Echard
external_id:
isi:
- '000403542900022'
intvolume: ' 137'
isi: 1
language:
- iso: eng
month: '12'
oa_version: None
page: 355 - 370
project:
- _id: 2596EAB6-B435-11E9-9278-68D0E5697425
grant_number: ALTF 2015-1163
name: Synthesis of bacterial cell wall
- _id: 25681D80-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '291734'
name: International IST Postdoc Fellowship Programme
publication: Cytokinesis
publication_identifier:
issn:
- 0091679X
publication_status: published
publisher: Academic Press
publist_id: '6134'
quality_controlled: '1'
scopus_import: '1'
status: public
title: Single-molecule measurements to study polymerization dynamics of FtsZ-FtsA
copolymers
type: book_chapter
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
volume: 137
year: '2017'
...
---
_id: '1198'
abstract:
- lang: eng
text: We consider a model of fermions interacting via point interactions, defined
via a certain weighted Dirichlet form. While for two particles the interaction
corresponds to infinite scattering length, the presence of further particles effectively
decreases the interaction strength. We show that the model becomes trivial in
the thermodynamic limit, in the sense that the free energy density at any given
particle density and temperature agrees with the corresponding expression for
non-interacting particles.
acknowledgement: 'Open access funding provided by Institute of Science and Technology
(IST Austria). '
article_processing_charge: Yes (via OA deal)
author:
- first_name: Thomas
full_name: Moser, Thomas
id: 2B5FC9A4-F248-11E8-B48F-1D18A9856A87
last_name: Moser
- first_name: Robert
full_name: Seiringer, Robert
id: 4AFD0470-F248-11E8-B48F-1D18A9856A87
last_name: Seiringer
orcid: 0000-0002-6781-0521
citation:
ama: Moser T, Seiringer R. Triviality of a model of particles with point interactions
in the thermodynamic limit. Letters in Mathematical Physics. 2017;107(3):533-552.
doi:10.1007/s11005-016-0915-x
apa: Moser, T., & Seiringer, R. (2017). Triviality of a model of particles with
point interactions in the thermodynamic limit. Letters in Mathematical Physics.
Springer. https://doi.org/10.1007/s11005-016-0915-x
chicago: Moser, Thomas, and Robert Seiringer. “Triviality of a Model of Particles
with Point Interactions in the Thermodynamic Limit.” Letters in Mathematical
Physics. Springer, 2017. https://doi.org/10.1007/s11005-016-0915-x.
ieee: T. Moser and R. Seiringer, “Triviality of a model of particles with point
interactions in the thermodynamic limit,” Letters in Mathematical Physics,
vol. 107, no. 3. Springer, pp. 533–552, 2017.
ista: Moser T, Seiringer R. 2017. Triviality of a model of particles with point
interactions in the thermodynamic limit. Letters in Mathematical Physics. 107(3),
533–552.
mla: Moser, Thomas, and Robert Seiringer. “Triviality of a Model of Particles with
Point Interactions in the Thermodynamic Limit.” Letters in Mathematical Physics,
vol. 107, no. 3, Springer, 2017, pp. 533–52, doi:10.1007/s11005-016-0915-x.
short: T. Moser, R. Seiringer, Letters in Mathematical Physics 107 (2017) 533–552.
date_created: 2018-12-11T11:50:40Z
date_published: 2017-03-01T00:00:00Z
date_updated: 2023-09-20T11:18:13Z
day: '01'
ddc:
- '510'
- '539'
department:
- _id: RoSe
doi: 10.1007/s11005-016-0915-x
external_id:
isi:
- '000394280200007'
file:
- access_level: open_access
checksum: c0c835def162c1bc52f978fad26e3c2f
content_type: application/pdf
creator: system
date_created: 2018-12-12T10:17:40Z
date_updated: 2020-07-14T12:44:38Z
file_id: '5296'
file_name: IST-2016-723-v1+1_s11005-016-0915-x.pdf
file_size: 587207
relation: main_file
file_date_updated: 2020-07-14T12:44:38Z
has_accepted_license: '1'
intvolume: ' 107'
isi: 1
issue: '3'
language:
- iso: eng
month: '03'
oa: 1
oa_version: Published Version
page: ' 533 - 552'
project:
- _id: 25C878CE-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: P27533_N27
name: Structure of the Excitation Spectrum for Many-Body Quantum Systems
- _id: B67AFEDC-15C9-11EA-A837-991A96BB2854
name: IST Austria Open Access Fund
publication: Letters in Mathematical Physics
publication_identifier:
issn:
- '03779017'
publication_status: published
publisher: Springer
publist_id: '6152'
pubrep_id: '723'
quality_controlled: '1'
related_material:
record:
- id: '52'
relation: dissertation_contains
status: public
scopus_import: '1'
status: public
title: Triviality of a model of particles with point interactions in the thermodynamic
limit
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: c635000d-4b10-11ee-a964-aac5a93f6ac1
volume: 107
year: '2017'
...
---
_id: '1207'
abstract:
- lang: eng
text: The eigenvalue distribution of the sum of two large Hermitian matrices, when
one of them is conjugated by a Haar distributed unitary matrix, is asymptotically
given by the free convolution of their spectral distributions. We prove that this
convergence also holds locally in the bulk of the spectrum, down to the optimal
scales larger than the eigenvalue spacing. The corresponding eigenvectors are
fully delocalized. Similar results hold for the sum of two real symmetric matrices,
when one is conjugated by Haar orthogonal matrix.
article_processing_charge: Yes (via OA deal)
author:
- first_name: Zhigang
full_name: Bao, Zhigang
id: 442E6A6C-F248-11E8-B48F-1D18A9856A87
last_name: Bao
orcid: 0000-0003-3036-1475
- first_name: László
full_name: Erdös, László
id: 4DBD5372-F248-11E8-B48F-1D18A9856A87
last_name: Erdös
orcid: 0000-0001-5366-9603
- first_name: Kevin
full_name: Schnelli, Kevin
id: 434AD0AE-F248-11E8-B48F-1D18A9856A87
last_name: Schnelli
orcid: 0000-0003-0954-3231
citation:
ama: Bao Z, Erdös L, Schnelli K. Local law of addition of random matrices on optimal
scale. Communications in Mathematical Physics. 2017;349(3):947-990. doi:10.1007/s00220-016-2805-6
apa: Bao, Z., Erdös, L., & Schnelli, K. (2017). Local law of addition of random
matrices on optimal scale. Communications in Mathematical Physics. Springer.
https://doi.org/10.1007/s00220-016-2805-6
chicago: Bao, Zhigang, László Erdös, and Kevin Schnelli. “Local Law of Addition
of Random Matrices on Optimal Scale.” Communications in Mathematical Physics.
Springer, 2017. https://doi.org/10.1007/s00220-016-2805-6.
ieee: Z. Bao, L. Erdös, and K. Schnelli, “Local law of addition of random matrices
on optimal scale,” Communications in Mathematical Physics, vol. 349, no.
3. Springer, pp. 947–990, 2017.
ista: Bao Z, Erdös L, Schnelli K. 2017. Local law of addition of random matrices
on optimal scale. Communications in Mathematical Physics. 349(3), 947–990.
mla: Bao, Zhigang, et al. “Local Law of Addition of Random Matrices on Optimal Scale.”
Communications in Mathematical Physics, vol. 349, no. 3, Springer, 2017,
pp. 947–90, doi:10.1007/s00220-016-2805-6.
short: Z. Bao, L. Erdös, K. Schnelli, Communications in Mathematical Physics 349
(2017) 947–990.
date_created: 2018-12-11T11:50:43Z
date_published: 2017-02-01T00:00:00Z
date_updated: 2023-09-20T11:16:57Z
day: '01'
ddc:
- '530'
department:
- _id: LaEr
doi: 10.1007/s00220-016-2805-6
ec_funded: 1
external_id:
isi:
- '000393696700005'
file:
- access_level: open_access
checksum: ddff79154c3daf27237de5383b1264a9
content_type: application/pdf
creator: system
date_created: 2018-12-12T10:14:47Z
date_updated: 2020-07-14T12:44:39Z
file_id: '5102'
file_name: IST-2016-722-v1+1_s00220-016-2805-6.pdf
file_size: 1033743
relation: main_file
file_date_updated: 2020-07-14T12:44:39Z
has_accepted_license: '1'
intvolume: ' 349'
isi: 1
issue: '3'
language:
- iso: eng
month: '02'
oa: 1
oa_version: Published Version
page: 947 - 990
project:
- _id: 258DCDE6-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '338804'
name: Random matrices, universality and disordered quantum systems
publication: Communications in Mathematical Physics
publication_identifier:
issn:
- '00103616'
publication_status: published
publisher: Springer
publist_id: '6141'
pubrep_id: '722'
quality_controlled: '1'
scopus_import: '1'
status: public
title: Local law of addition of random matrices on optimal scale
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: c635000d-4b10-11ee-a964-aac5a93f6ac1
volume: 349
year: '2017'
...
---
_id: '1196'
abstract:
- lang: eng
text: 'We define the . model-measuring problem: given a model . M and specification
. ϕ, what is the maximal distance . ρ such that all models . M'' within distance
. ρ from . M satisfy (or violate) . ϕ. The model-measuring problem presupposes
a distance function on models. We concentrate on . automatic distance functions,
which are defined by weighted automata. The model-measuring problem subsumes several
generalizations of the classical model-checking problem, in particular, quantitative
model-checking problems that measure the degree of satisfaction of a specification;
robustness problems that measure how much a model can be perturbed without violating
the specification; and parameter synthesis for hybrid systems. We show that for
automatic distance functions, and (a) . ω-regular linear-time, (b) . ω-regular
branching-time, and (c) hybrid specifications, the model-measuring problem can
be solved.We use automata-theoretic model-checking methods for model measuring,
replacing the emptiness question for word, tree, and hybrid automata by the .
optimal-value question for the weighted versions of these automata. For automata
over words and trees, we consider weighted automata that accumulate weights by
maximizing, summing, discounting, and limit averaging. For hybrid automata, we
consider monotonic (parametric) hybrid automata, a hybrid counterpart of (discrete)
weighted automata.We give several examples of using the model-measuring problem
to compute various notions of robustness and quantitative satisfaction for temporal
specifications. Further, we propose the modeling framework for model measuring
to ease the specification and reduce the likelihood of errors in modeling.Finally,
we present a variant of the model-measuring problem, called the . model-repair
problem. The model-repair problem applies to models that do not satisfy the specification;
it can be used to derive restrictions, under which the model satisfies the specification,
i.e., to repair the model.'
acknowledgement: "This research was supported in part by the European Research Council
(ERC) under grant 267989 (QUAREM), by the Austrian Science Fund1 (FWF) under grants
S11402-N23 (RiSE) and Z211-N23 (Wittgenstein Award), and by the National Science
Centre (NCN), Poland under grant 2014/15/D/ST6/04543.\r\nA Technical Report of this
article is available via: https://repository.ist.ac.at/171/"
article_processing_charge: No
author:
- first_name: Thomas A
full_name: Henzinger, Thomas A
id: 40876CD8-F248-11E8-B48F-1D18A9856A87
last_name: Henzinger
orcid: 0000−0002−2985−7724
- first_name: Jan
full_name: Otop, Jan
id: 2FC5DA74-F248-11E8-B48F-1D18A9856A87
last_name: Otop
citation:
ama: 'Henzinger TA, Otop J. Model measuring for discrete and hybrid systems. Nonlinear
Analysis: Hybrid Systems. 2017;23:166-190. doi:10.1016/j.nahs.2016.09.001'
apa: 'Henzinger, T. A., & Otop, J. (2017). Model measuring for discrete and
hybrid systems. Nonlinear Analysis: Hybrid Systems. Elsevier. https://doi.org/10.1016/j.nahs.2016.09.001'
chicago: 'Henzinger, Thomas A, and Jan Otop. “Model Measuring for Discrete and Hybrid
Systems.” Nonlinear Analysis: Hybrid Systems. Elsevier, 2017. https://doi.org/10.1016/j.nahs.2016.09.001.'
ieee: 'T. A. Henzinger and J. Otop, “Model measuring for discrete and hybrid systems,”
Nonlinear Analysis: Hybrid Systems, vol. 23. Elsevier, pp. 166–190, 2017.'
ista: 'Henzinger TA, Otop J. 2017. Model measuring for discrete and hybrid systems.
Nonlinear Analysis: Hybrid Systems. 23, 166–190.'
mla: 'Henzinger, Thomas A., and Jan Otop. “Model Measuring for Discrete and Hybrid
Systems.” Nonlinear Analysis: Hybrid Systems, vol. 23, Elsevier, 2017,
pp. 166–90, doi:10.1016/j.nahs.2016.09.001.'
short: 'T.A. Henzinger, J. Otop, Nonlinear Analysis: Hybrid Systems 23 (2017) 166–190.'
date_created: 2018-12-11T11:50:39Z
date_published: 2017-02-01T00:00:00Z
date_updated: 2023-09-20T11:18:50Z
day: '01'
department:
- _id: ToHe
doi: 10.1016/j.nahs.2016.09.001
ec_funded: 1
external_id:
isi:
- '000390637000011'
intvolume: ' 23'
isi: 1
language:
- iso: eng
month: '02'
oa_version: None
page: 166 - 190
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
publication: 'Nonlinear Analysis: Hybrid Systems'
publication_status: published
publisher: Elsevier
publist_id: '6154'
quality_controlled: '1'
scopus_import: '1'
status: public
title: Model measuring for discrete and hybrid systems
type: journal_article
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
volume: 23
year: '2017'
...
---
_id: '1199'
abstract:
- lang: eng
text: Much of quantitative genetics is based on the ‘infinitesimal model’, under
which selection has a negligible effect on the genetic variance. This is typically
justified by assuming a very large number of loci with additive effects. However,
it applies even when genes interact, provided that the number of loci is large
enough that selection on each of them is weak relative to random drift. In the
long term, directional selection will change allele frequencies, but even then,
the effects of epistasis on the ultimate change in trait mean due to selection
may be modest. Stabilising selection can maintain many traits close to their optima,
even when the underlying alleles are weakly selected. However, the number of traits
that can be optimised is apparently limited to ~4Ne by the ‘drift load’, and this
is hard to reconcile with the apparent complexity of many organisms. Just as for
the mutation load, this limit can be evaded by a particular form of negative epistasis.
A more robust limit is set by the variance in reproductive success. This suggests
that selection accumulates information most efficiently in the infinitesimal regime,
when selection on individual alleles is weak, and comparable with random drift.
A review of evidence on selection strength suggests that although most variance
in fitness may be because of alleles with large Nes, substantial amounts of adaptation
may be because of alleles in the infinitesimal regime, in which epistasis has
modest effects.
article_processing_charge: No
author:
- first_name: Nicholas H
full_name: Barton, Nicholas H
id: 4880FE40-F248-11E8-B48F-1D18A9856A87
last_name: Barton
orcid: 0000-0002-8548-5240
citation:
ama: Barton NH. How does epistasis influence the response to selection? Heredity.
2017;118:96-109. doi:10.1038/hdy.2016.109
apa: Barton, N. H. (2017). How does epistasis influence the response to selection?
Heredity. Nature Publishing Group. https://doi.org/10.1038/hdy.2016.109
chicago: Barton, Nicholas H. “How Does Epistasis Influence the Response to Selection?”
Heredity. Nature Publishing Group, 2017. https://doi.org/10.1038/hdy.2016.109.
ieee: N. H. Barton, “How does epistasis influence the response to selection?,” Heredity,
vol. 118. Nature Publishing Group, pp. 96–109, 2017.
ista: Barton NH. 2017. How does epistasis influence the response to selection? Heredity.
118, 96–109.
mla: Barton, Nicholas H. “How Does Epistasis Influence the Response to Selection?”
Heredity, vol. 118, Nature Publishing Group, 2017, pp. 96–109, doi:10.1038/hdy.2016.109.
short: N.H. Barton, Heredity 118 (2017) 96–109.
date_created: 2018-12-11T11:50:40Z
date_published: 2017-01-01T00:00:00Z
date_updated: 2023-09-20T11:17:47Z
day: '01'
department:
- _id: NiBa
doi: 10.1038/hdy.2016.109
ec_funded: 1
external_id:
isi:
- '000392229100011'
intvolume: ' 118'
isi: 1
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5176114/
month: '01'
oa: 1
oa_version: Submitted Version
page: 96 - 109
project:
- _id: 25B07788-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '250152'
name: Limits to selection in biology and in evolutionary computation
publication: Heredity
publication_status: published
publisher: Nature Publishing Group
publist_id: '6151'
quality_controlled: '1'
related_material:
record:
- id: '9710'
relation: research_data
status: public
scopus_import: '1'
status: public
title: How does epistasis influence the response to selection?
type: journal_article
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
volume: 118
year: '2017'
...
---
_id: '1208'
abstract:
- lang: eng
text: We study parameter estimation in linear Gaussian covariance models, which
are p-dimensional Gaussian models with linear constraints on the covariance matrix.
Maximum likelihood estimation for this class of models leads to a non-convex optimization
problem which typically has many local maxima. Using recent results on the asymptotic
distribution of extreme eigenvalues of the Wishart distribution, we provide sufficient
conditions for any hill climbing method to converge to the global maximum. Although
we are primarily interested in the case in which n≫p, the proofs of our results
utilize large sample asymptotic theory under the scheme n/p→γ>1. Remarkably,
our numerical simulations indicate that our results remain valid for p as small
as 2. An important consequence of this analysis is that, for sample sizes n≃14p,
maximum likelihood estimation for linear Gaussian covariance models behaves as
if it were a convex optimization problem. © 2016 The Royal Statistical Society
and Blackwell Publishing Ltd.
article_processing_charge: No
author:
- first_name: Piotr
full_name: Zwiernik, Piotr
last_name: Zwiernik
- first_name: Caroline
full_name: Uhler, Caroline
id: 49ADD78E-F248-11E8-B48F-1D18A9856A87
last_name: Uhler
orcid: 0000-0002-7008-0216
- first_name: Donald
full_name: Richards, Donald
last_name: Richards
citation:
ama: 'Zwiernik P, Uhler C, Richards D. Maximum likelihood estimation for linear
Gaussian covariance models. Journal of the Royal Statistical Society Series
B: Statistical Methodology. 2017;79(4):1269-1292. doi:10.1111/rssb.12217'
apa: 'Zwiernik, P., Uhler, C., & Richards, D. (2017). Maximum likelihood estimation
for linear Gaussian covariance models. Journal of the Royal Statistical Society.
Series B: Statistical Methodology. Wiley-Blackwell. https://doi.org/10.1111/rssb.12217'
chicago: 'Zwiernik, Piotr, Caroline Uhler, and Donald Richards. “Maximum Likelihood
Estimation for Linear Gaussian Covariance Models.” Journal of the Royal Statistical
Society. Series B: Statistical Methodology. Wiley-Blackwell, 2017. https://doi.org/10.1111/rssb.12217.'
ieee: 'P. Zwiernik, C. Uhler, and D. Richards, “Maximum likelihood estimation for
linear Gaussian covariance models,” Journal of the Royal Statistical Society.
Series B: Statistical Methodology, vol. 79, no. 4. Wiley-Blackwell, pp. 1269–1292,
2017.'
ista: 'Zwiernik P, Uhler C, Richards D. 2017. Maximum likelihood estimation for
linear Gaussian covariance models. Journal of the Royal Statistical Society. Series
B: Statistical Methodology. 79(4), 1269–1292.'
mla: 'Zwiernik, Piotr, et al. “Maximum Likelihood Estimation for Linear Gaussian
Covariance Models.” Journal of the Royal Statistical Society. Series B: Statistical
Methodology, vol. 79, no. 4, Wiley-Blackwell, 2017, pp. 1269–92, doi:10.1111/rssb.12217.'
short: 'P. Zwiernik, C. Uhler, D. Richards, Journal of the Royal Statistical Society.
Series B: Statistical Methodology 79 (2017) 1269–1292.'
date_created: 2018-12-11T11:50:43Z
date_published: 2017-09-01T00:00:00Z
date_updated: 2023-09-20T11:17:21Z
day: '01'
department:
- _id: CaUh
doi: 10.1111/rssb.12217
external_id:
isi:
- '000411712300012'
intvolume: ' 79'
isi: 1
issue: '4'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/1408.5604
month: '09'
oa: 1
oa_version: Submitted Version
page: 1269 - 1292
project:
- _id: 2530CA10-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: Y 903-N35
name: 'Gaussian Graphical Models: Theory and Applications'
publication: 'Journal of the Royal Statistical Society. Series B: Statistical Methodology'
publication_identifier:
issn:
- '13697412'
publication_status: published
publisher: Wiley-Blackwell
publist_id: '6142'
quality_controlled: '1'
scopus_import: '1'
status: public
title: Maximum likelihood estimation for linear Gaussian covariance models
type: journal_article
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
volume: 79
year: '2017'
...
---
_id: '1174'
abstract:
- lang: eng
text: Security of cryptographic applications is typically defined by security games.
The adversary, within certain resources, cannot win with probability much better
than 0 (for unpredictability applications, like one-way functions) or much better
than 1/2 (indistinguishability applications for instance encryption schemes).
In so called squared-friendly applications the winning probability of the adversary,
for different values of the application secret randomness, is not only close to
0 or 1/2 on average, but also concentrated in the sense that its second central
moment is small. The class of squared-friendly applications, which contains all
unpredictability applications and many indistinguishability applications, is particularly
important for key derivation. Barak et al. observed that for square-friendly applications
one can beat the "RT-bound", extracting secure keys with significantly
smaller entropy loss. In turn Dodis and Yu showed that in squared-friendly applications
one can directly use a "weak" key, which has only high entropy, as a
secure key. In this paper we give sharp lower bounds on square security assuming
security for "weak" keys. We show that any application which is either
(a) secure with weak keys or (b) allows for entropy savings for keys derived by
universal hashing, must be square-friendly. Quantitatively, our lower bounds match
the positive results of Dodis and Yu and Barak et al. (TCC\'13, CRYPTO\'11) Hence,
they can be understood as a general characterization of squared-friendly applications.
While the positive results on squared-friendly applications where derived by one
clever application of the Cauchy-Schwarz Inequality, for tight lower bounds we
need more machinery. In our approach we use convex optimization techniques and
some theory of circular matrices.
alternative_title:
- LIPIcs
article_number: '57'
article_processing_charge: No
author:
- first_name: Maciej
full_name: Skórski, Maciej
id: EC09FA6A-02D0-11E9-8223-86B7C91467DD
last_name: Skórski
citation:
ama: 'Skórski M. Lower bounds on key derivation for square-friendly applications.
In: Vol 66. Schloss Dagstuhl - Leibniz-Zentrum für Informatik; 2017. doi:10.4230/LIPIcs.STACS.2017.57'
apa: 'Skórski, M. (2017). Lower bounds on key derivation for square-friendly applications
(Vol. 66). Presented at the STACS: Symposium on Theoretical Aspects of Computer
Science, Hannover, Germany: Schloss Dagstuhl - Leibniz-Zentrum für Informatik.
https://doi.org/10.4230/LIPIcs.STACS.2017.57'
chicago: Skórski, Maciej. “Lower Bounds on Key Derivation for Square-Friendly Applications,”
Vol. 66. Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2017. https://doi.org/10.4230/LIPIcs.STACS.2017.57.
ieee: 'M. Skórski, “Lower bounds on key derivation for square-friendly applications,”
presented at the STACS: Symposium on Theoretical Aspects of Computer Science,
Hannover, Germany, 2017, vol. 66.'
ista: 'Skórski M. 2017. Lower bounds on key derivation for square-friendly applications.
STACS: Symposium on Theoretical Aspects of Computer Science, LIPIcs, vol. 66,
57.'
mla: Skórski, Maciej. Lower Bounds on Key Derivation for Square-Friendly Applications.
Vol. 66, 57, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2017, doi:10.4230/LIPIcs.STACS.2017.57.
short: M. Skórski, in:, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2017.
conference:
end_date: 2017-03-11
location: Hannover, Germany
name: 'STACS: Symposium on Theoretical Aspects of Computer Science'
start_date: 2017-03-08
date_created: 2018-12-11T11:50:32Z
date_published: 2017-03-01T00:00:00Z
date_updated: 2023-09-20T11:23:15Z
day: '01'
department:
- _id: KrPi
doi: 10.4230/LIPIcs.STACS.2017.57
ec_funded: 1
external_id:
isi:
- '000521077300057'
intvolume: ' 66'
isi: 1
language:
- iso: eng
main_file_link:
- open_access: '1'
url: http://drops.dagstuhl.de/opus/volltexte/2017/6976
month: '03'
oa: 1
oa_version: Submitted Version
project:
- _id: 258AA5B2-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '682815'
name: Teaching Old Crypto New Tricks
publication_identifier:
issn:
- '18688969'
publication_status: published
publisher: Schloss Dagstuhl - Leibniz-Zentrum für Informatik
publist_id: '6180'
quality_controlled: '1'
scopus_import: '1'
status: public
title: Lower bounds on key derivation for square-friendly applications
type: conference
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
volume: 66
year: '2017'
...
---
_id: '1176'
abstract:
- lang: eng
text: The algorithm Argon2i-B of Biryukov, Dinu and Khovratovich is currently being
considered by the IRTF (Internet Research Task Force) as a new de-facto standard
for password hashing. An older version (Argon2i-A) of the same algorithm was chosen
as the winner of the recent Password Hashing Competition. An important competitor
to Argon2i-B is the recently introduced Balloon Hashing (BH) algorithm of Corrigan-Gibs,
Boneh and Schechter. A key security desiderata for any such algorithm is that
evaluating it (even using a custom device) requires a large amount of memory amortized
across multiple instances. Alwen and Blocki (CRYPTO 2016) introduced a class of
theoretical attacks against Argon2i-A and BH. While these attacks yield large
asymptotic reductions in the amount of memory, it was not, a priori, clear if
(1) they can be extended to the newer Argon2i-B, (2) the attacks are effective
on any algorithm for practical parameter ranges (e.g., 1GB of memory) and (3)
if they can be effectively instantiated against any algorithm under realistic
hardware constrains. In this work we answer all three of these questions in the
affirmative for all three algorithms. This is also the first work to analyze the
security of Argon2i-B. In more detail, we extend the theoretical attacks of Alwen
and Blocki (CRYPTO 2016) to the recent Argon2i-B proposal demonstrating severe
asymptotic deficiencies in its security. Next we introduce several novel heuristics
for improving the attack's concrete memory efficiency even when on-chip memory
bandwidth is bounded. We then simulate our attacks on randomly sampled Argon2i-A,
Argon2i-B and BH instances and measure the resulting memory consumption for various
practical parameter ranges and for a variety of upperbounds on the amount of parallelism
available to the attacker. Finally we describe, implement, and test a new heuristic
for applying the Alwen-Blocki attack to functions employing a technique developed
by Corrigan-Gibs et al. for improving concrete security of memory-hard functions.
We analyze the collected data and show the effects various parameters have on
the memory consumption of the attack. In particular, we can draw several interesting
conclusions about the level of security provided by these functions. · For the
Alwen-Blocki attack to fail against practical memory parameters, Argon2i-B must
be instantiated with more than 10 passes on memory - beyond the "paranoid" parameter
setting in the current IRTF proposal. · The technique of Corrigan-Gibs for improving
security can also be overcome by the Alwen-Blocki attack under realistic hardware
constraints. · On a positive note, both the asymptotic and concrete security of
Argon2i-B seem to improve on that of Argon2i-A.
article_number: '7961977'
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: Jeremiah
full_name: Blocki, Jeremiah
last_name: Blocki
citation:
ama: 'Alwen JF, Blocki J. Towards practical attacks on Argon2i and balloon hashing.
In: IEEE; 2017. doi:10.1109/EuroSP.2017.47'
apa: 'Alwen, J. F., & Blocki, J. (2017). Towards practical attacks on Argon2i
and balloon hashing. Presented at the EuroS&P: European Symposium on Security
and Privacy, Paris, France: IEEE. https://doi.org/10.1109/EuroSP.2017.47'
chicago: Alwen, Joel F, and Jeremiah Blocki. “Towards Practical Attacks on Argon2i
and Balloon Hashing.” IEEE, 2017. https://doi.org/10.1109/EuroSP.2017.47.
ieee: 'J. F. Alwen and J. Blocki, “Towards practical attacks on Argon2i and balloon
hashing,” presented at the EuroS&P: European Symposium on Security and Privacy,
Paris, France, 2017.'
ista: 'Alwen JF, Blocki J. 2017. Towards practical attacks on Argon2i and balloon
hashing. EuroS&P: European Symposium on Security and Privacy, 7961977.'
mla: Alwen, Joel F., and Jeremiah Blocki. Towards Practical Attacks on Argon2i
and Balloon Hashing. 7961977, IEEE, 2017, doi:10.1109/EuroSP.2017.47.
short: J.F. Alwen, J. Blocki, in:, IEEE, 2017.
conference:
end_date: 2017-04-28
location: Paris, France
name: 'EuroS&P: European Symposium on Security and Privacy'
start_date: 2017-04-26
date_created: 2018-12-11T11:50:33Z
date_published: 2017-07-03T00:00:00Z
date_updated: 2023-09-20T11:22:25Z
day: '03'
department:
- _id: KrPi
doi: 10.1109/EuroSP.2017.47
external_id:
isi:
- '000424197300011'
isi: 1
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://eprint.iacr.org/2016/759
month: '07'
oa: 1
oa_version: Submitted Version
publication_identifier:
isbn:
- 978-150905761-0
publication_status: published
publisher: IEEE
publist_id: '6178'
quality_controlled: '1'
scopus_import: '1'
status: public
title: Towards practical attacks on Argon2i and balloon hashing
type: conference
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
year: '2017'
...
---
_id: '1187'
abstract:
- lang: eng
text: We construct efficient authentication protocols and message authentication
codes (MACs) whose security can be reduced to the learning parity with noise (LPN)
problem. Despite a large body of work—starting with the (Formula presented.) protocol
of Hopper and Blum in 2001—until now it was not even known how to construct an
efficient authentication protocol from LPN which is secure against man-in-the-middle
attacks. A MAC implies such a (two-round) protocol.
article_processing_charge: No
article_type: original
author:
- first_name: Eike
full_name: Kiltz, Eike
last_name: Kiltz
- 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: Daniele
full_name: Venturi, Daniele
last_name: Venturi
- first_name: David
full_name: Cash, David
last_name: Cash
- first_name: Abhishek
full_name: Jain, Abhishek
last_name: Jain
citation:
ama: Kiltz E, Pietrzak KZ, Venturi D, Cash D, Jain A. Efficient authentication from
hard learning problems. Journal of Cryptology. 2017;30(4):1238-1275. doi:10.1007/s00145-016-9247-3
apa: Kiltz, E., Pietrzak, K. Z., Venturi, D., Cash, D., & Jain, A. (2017). Efficient
authentication from hard learning problems. Journal of Cryptology. Springer.
https://doi.org/10.1007/s00145-016-9247-3
chicago: Kiltz, Eike, Krzysztof Z Pietrzak, Daniele Venturi, David Cash, and Abhishek
Jain. “Efficient Authentication from Hard Learning Problems.” Journal of Cryptology.
Springer, 2017. https://doi.org/10.1007/s00145-016-9247-3.
ieee: E. Kiltz, K. Z. Pietrzak, D. Venturi, D. Cash, and A. Jain, “Efficient authentication
from hard learning problems,” Journal of Cryptology, vol. 30, no. 4. Springer,
pp. 1238–1275, 2017.
ista: Kiltz E, Pietrzak KZ, Venturi D, Cash D, Jain A. 2017. Efficient authentication
from hard learning problems. Journal of Cryptology. 30(4), 1238–1275.
mla: Kiltz, Eike, et al. “Efficient Authentication from Hard Learning Problems.”
Journal of Cryptology, vol. 30, no. 4, Springer, 2017, pp. 1238–75, doi:10.1007/s00145-016-9247-3.
short: E. Kiltz, K.Z. Pietrzak, D. Venturi, D. Cash, A. Jain, Journal of Cryptology
30 (2017) 1238–1275.
date_created: 2018-12-11T11:50:37Z
date_published: 2017-10-01T00:00:00Z
date_updated: 2023-09-20T11:20:58Z
day: '01'
ddc:
- '000'
department:
- _id: KrPi
doi: 10.1007/s00145-016-9247-3
ec_funded: 1
external_id:
isi:
- '000410788600007'
file:
- access_level: open_access
checksum: c647520d115b772a1682fc06fa273eb1
content_type: application/pdf
creator: dernst
date_created: 2020-05-14T16:30:17Z
date_updated: 2020-07-14T12:44:37Z
file_id: '7843'
file_name: 2017_JournalCrypto_Kiltz.pdf
file_size: 516959
relation: main_file
file_date_updated: 2020-07-14T12:44:37Z
has_accepted_license: '1'
intvolume: ' 30'
isi: 1
issue: '4'
language:
- iso: eng
month: '10'
oa: 1
oa_version: Submitted Version
page: 1238 - 1275
project:
- _id: 258AA5B2-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '682815'
name: Teaching Old Crypto New Tricks
- _id: 258C570E-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '259668'
name: Provable Security for Physical Cryptography
publication: Journal of Cryptology
publication_status: published
publisher: Springer
publist_id: '6166'
quality_controlled: '1'
related_material:
record:
- id: '3238'
relation: earlier_version
status: public
scopus_import: '1'
status: public
title: Efficient authentication from hard learning problems
type: journal_article
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
volume: 30
year: '2017'
...
---
_id: '1192'
abstract:
- lang: eng
text: The main result of this paper is a generalization of the classical blossom
algorithm for finding perfect matchings. Our algorithm can efficiently solve Boolean
CSPs where each variable appears in exactly two constraints (we call it edge CSP)
and all constraints are even Δ-matroid relations (represented by lists of tuples).
As a consequence of this, we settle the complexity classification of planar Boolean
CSPs started by Dvorak and Kupec. Knowing that edge CSP is tractable for even
Δ-matroid constraints allows us to extend the tractability result to a larger
class of Δ-matroids that includes many classes that were known to be tractable
before, namely co-independent, compact, local and binary.
article_processing_charge: No
author:
- first_name: Alexandr
full_name: Kazda, Alexandr
id: 3B32BAA8-F248-11E8-B48F-1D18A9856A87
last_name: Kazda
- 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
citation:
ama: 'Kazda A, Kolmogorov V, Rolinek M. Even delta-matroids and the complexity of
planar Boolean CSPs. In: SIAM; 2017:307-326. doi:10.1137/1.9781611974782.20'
apa: 'Kazda, A., Kolmogorov, V., & Rolinek, M. (2017). Even delta-matroids and
the complexity of planar Boolean CSPs (pp. 307–326). Presented at the SODA: Symposium
on Discrete Algorithms, Barcelona, Spain: SIAM. https://doi.org/10.1137/1.9781611974782.20'
chicago: Kazda, Alexandr, Vladimir Kolmogorov, and Michal Rolinek. “Even Delta-Matroids
and the Complexity of Planar Boolean CSPs,” 307–26. SIAM, 2017. https://doi.org/10.1137/1.9781611974782.20.
ieee: 'A. Kazda, V. Kolmogorov, and M. Rolinek, “Even delta-matroids and the complexity
of planar Boolean CSPs,” presented at the SODA: Symposium on Discrete Algorithms,
Barcelona, Spain, 2017, pp. 307–326.'
ista: 'Kazda A, Kolmogorov V, Rolinek M. 2017. Even delta-matroids and the complexity
of planar Boolean CSPs. SODA: Symposium on Discrete Algorithms, 307–326.'
mla: Kazda, Alexandr, et al. Even Delta-Matroids and the Complexity of Planar
Boolean CSPs. SIAM, 2017, pp. 307–26, doi:10.1137/1.9781611974782.20.
short: A. Kazda, V. Kolmogorov, M. Rolinek, in:, SIAM, 2017, pp. 307–326.
conference:
end_date: 2017-01019
location: Barcelona, Spain
name: 'SODA: Symposium on Discrete Algorithms'
start_date: 2017-01-16
date_created: 2018-12-11T11:50:38Z
date_published: 2017-01-01T00:00:00Z
date_updated: 2023-09-20T11:20:26Z
day: '01'
department:
- _id: VlKo
doi: 10.1137/1.9781611974782.20
ec_funded: 1
external_id:
isi:
- '000426965800020'
isi: 1
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/1602.03124
month: '01'
oa: 1
oa_version: Submitted Version
page: 307 - 326
project:
- _id: 25FBA906-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '616160'
name: 'Discrete Optimization in Computer Vision: Theory and Practice'
publication_identifier:
isbn:
- 978-161197478-2
publication_status: published
publisher: SIAM
publist_id: '6159'
quality_controlled: '1'
related_material:
record:
- id: '6032'
relation: later_version
status: public
status: public
title: Even delta-matroids and the complexity of planar Boolean CSPs
type: conference
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
year: '2017'
...
---
_id: '1180'
abstract:
- lang: eng
text: In this article we define an algebraic vertex of a generalized polyhedron
and show that the set of algebraic vertices is the smallest set of points needed
to define the polyhedron. We prove that the indicator function of a generalized
polytope P is a linear combination of indicator functions of simplices whose vertices
are algebraic vertices of P. We also show that the indicator function of any generalized
polyhedron is a linear combination, with integer coefficients, of indicator functions
of cones with apices at algebraic vertices and line-cones. The concept of an algebraic
vertex is closely related to the Fourier–Laplace transform. We show that a point
v is an algebraic vertex of a generalized polyhedron P if and only if the tangent
cone of P, at v, has non-zero Fourier–Laplace transform.
article_processing_charge: No
author:
- first_name: Arseniy
full_name: Akopyan, Arseniy
id: 430D2C90-F248-11E8-B48F-1D18A9856A87
last_name: Akopyan
orcid: 0000-0002-2548-617X
- first_name: Imre
full_name: Bárány, Imre
last_name: Bárány
- first_name: Sinai
full_name: Robins, Sinai
last_name: Robins
citation:
ama: Akopyan A, Bárány I, Robins S. Algebraic vertices of non-convex polyhedra.
Advances in Mathematics. 2017;308:627-644. doi:10.1016/j.aim.2016.12.026
apa: Akopyan, A., Bárány, I., & Robins, S. (2017). Algebraic vertices of non-convex
polyhedra. Advances in Mathematics. Academic Press. https://doi.org/10.1016/j.aim.2016.12.026
chicago: Akopyan, Arseniy, Imre Bárány, and Sinai Robins. “Algebraic Vertices of
Non-Convex Polyhedra.” Advances in Mathematics. Academic Press, 2017. https://doi.org/10.1016/j.aim.2016.12.026.
ieee: A. Akopyan, I. Bárány, and S. Robins, “Algebraic vertices of non-convex polyhedra,”
Advances in Mathematics, vol. 308. Academic Press, pp. 627–644, 2017.
ista: Akopyan A, Bárány I, Robins S. 2017. Algebraic vertices of non-convex polyhedra.
Advances in Mathematics. 308, 627–644.
mla: Akopyan, Arseniy, et al. “Algebraic Vertices of Non-Convex Polyhedra.” Advances
in Mathematics, vol. 308, Academic Press, 2017, pp. 627–44, doi:10.1016/j.aim.2016.12.026.
short: A. Akopyan, I. Bárány, S. Robins, Advances in Mathematics 308 (2017) 627–644.
date_created: 2018-12-11T11:50:34Z
date_published: 2017-02-21T00:00:00Z
date_updated: 2023-09-20T11:21:27Z
day: '21'
department:
- _id: HeEd
doi: 10.1016/j.aim.2016.12.026
ec_funded: 1
external_id:
isi:
- '000409292900015'
intvolume: ' 308'
isi: 1
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/1508.07594
month: '02'
oa: 1
oa_version: Submitted Version
page: 627 - 644
project:
- _id: 25681D80-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '291734'
name: International IST Postdoc Fellowship Programme
publication: Advances in Mathematics
publication_identifier:
issn:
- '00018708'
publication_status: published
publisher: Academic Press
publist_id: '6173'
quality_controlled: '1'
scopus_import: '1'
status: public
title: Algebraic vertices of non-convex polyhedra
type: journal_article
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
volume: 308
year: '2017'
...
---
_id: '1159'
abstract:
- lang: eng
text: Auxin steers numerous physiological processes in plants, making the tight
control of its endogenous levels and spatiotemporal distribution a necessity.
This regulation is achieved by different mechanisms, including auxin biosynthesis,
metabolic conversions, degradation, and transport. Here, we introduce cis-cinnamic
acid (c-CA) as a novel and unique addition to a small group of endogenous molecules
affecting in planta auxin concentrations. c-CA is the photo-isomerization product
of the phenylpropanoid pathway intermediate trans-CA (t-CA). When grown on c-CA-containing
medium, an evolutionary diverse set of plant species were shown to exhibit phenotypes
characteristic for high auxin levels, including inhibition of primary root growth,
induction of root hairs, and promotion of adventitious and lateral rooting. By
molecular docking and receptor binding assays, we showed that c-CA itself is neither
an auxin nor an anti-auxin, and auxin profiling data revealed that c-CA does not
significantly interfere with auxin biosynthesis. Single cell-based auxin accumulation
assays showed that c-CA, and not t-CA, is a potent inhibitor of auxin efflux.
Auxin signaling reporters detected changes in spatiotemporal distribution of the
auxin response along the root of c-CA-treated plants, and long-distance auxin
transport assays showed no inhibition of rootward auxin transport. Overall, these
results suggest that the phenotypes of c-CA-treated plants are the consequence
of a local change in auxin accumulation, induced by the inhibition of auxin efflux.
This work reveals a novel mechanism how plants may regulate auxin levels and adds
a novel, naturally occurring molecule to the chemical toolbox for the studies
of auxin homeostasis.
article_processing_charge: No
article_type: original
author:
- first_name: Ward
full_name: Steenackers, Ward
last_name: Steenackers
- first_name: Petr
full_name: Klíma, Petr
last_name: Klíma
- first_name: Mussa
full_name: Quareshy, Mussa
last_name: Quareshy
- first_name: Igor
full_name: Cesarino, Igor
last_name: Cesarino
- first_name: Robert
full_name: Kumpf, Robert
last_name: Kumpf
- first_name: Sander
full_name: Corneillie, Sander
last_name: Corneillie
- first_name: Pedro
full_name: Araújo, Pedro
last_name: Araújo
- first_name: Tom
full_name: Viaene, Tom
last_name: Viaene
- first_name: Geert
full_name: Goeminne, Geert
last_name: Goeminne
- first_name: Moritz
full_name: Nowack, Moritz
last_name: Nowack
- first_name: Karin
full_name: Ljung, Karin
last_name: Ljung
- first_name: Jirí
full_name: Friml, Jirí
id: 4159519E-F248-11E8-B48F-1D18A9856A87
last_name: Friml
orcid: 0000-0002-8302-7596
- first_name: Joshua
full_name: Blakeslee, Joshua
last_name: Blakeslee
- first_name: Ondřej
full_name: Novák, Ondřej
last_name: Novák
- first_name: Eva
full_name: Zažímalová, Eva
last_name: Zažímalová
- first_name: Richard
full_name: Napier, Richard
last_name: Napier
- first_name: Wout
full_name: Boerjan, Wout
last_name: Boerjan
- first_name: Bartel
full_name: Vanholme, Bartel
last_name: Vanholme
citation:
ama: Steenackers W, Klíma P, Quareshy M, et al. Cis-cinnamic acid is a novel natural
auxin efflux inhibitor that promotes lateral root formation. Plant Physiology.
2017;173(1):552-565. doi:10.1104/pp.16.00943
apa: Steenackers, W., Klíma, P., Quareshy, M., Cesarino, I., Kumpf, R., Corneillie,
S., … Vanholme, B. (2017). Cis-cinnamic acid is a novel natural auxin efflux inhibitor
that promotes lateral root formation. Plant Physiology. American Society
of Plant Biologists. https://doi.org/10.1104/pp.16.00943
chicago: Steenackers, Ward, Petr Klíma, Mussa Quareshy, Igor Cesarino, Robert Kumpf,
Sander Corneillie, Pedro Araújo, et al. “Cis-Cinnamic Acid Is a Novel Natural
Auxin Efflux Inhibitor That Promotes Lateral Root Formation.” Plant Physiology.
American Society of Plant Biologists, 2017. https://doi.org/10.1104/pp.16.00943.
ieee: W. Steenackers et al., “Cis-cinnamic acid is a novel natural auxin
efflux inhibitor that promotes lateral root formation,” Plant Physiology,
vol. 173, no. 1. American Society of Plant Biologists, pp. 552–565, 2017.
ista: Steenackers W, Klíma P, Quareshy M, Cesarino I, Kumpf R, Corneillie S, Araújo
P, Viaene T, Goeminne G, Nowack M, Ljung K, Friml J, Blakeslee J, Novák O, Zažímalová
E, Napier R, Boerjan W, Vanholme B. 2017. Cis-cinnamic acid is a novel natural
auxin efflux inhibitor that promotes lateral root formation. Plant Physiology.
173(1), 552–565.
mla: Steenackers, Ward, et al. “Cis-Cinnamic Acid Is a Novel Natural Auxin Efflux
Inhibitor That Promotes Lateral Root Formation.” Plant Physiology, vol.
173, no. 1, American Society of Plant Biologists, 2017, pp. 552–65, doi:10.1104/pp.16.00943.
short: W. Steenackers, P. Klíma, M. Quareshy, I. Cesarino, R. Kumpf, S. Corneillie,
P. Araújo, T. Viaene, G. Goeminne, M. Nowack, K. Ljung, J. Friml, J. Blakeslee,
O. Novák, E. Zažímalová, R. Napier, W. Boerjan, B. Vanholme, Plant Physiology
173 (2017) 552–565.
date_created: 2018-12-11T11:50:28Z
date_published: 2017-01-01T00:00:00Z
date_updated: 2023-09-20T11:29:17Z
day: '01'
ddc:
- '580'
department:
- _id: JiFr
doi: 10.1104/pp.16.00943
ec_funded: 1
external_id:
isi:
- '000394135800041'
pmid:
- '27837086'
file:
- access_level: open_access
checksum: fd4d1cfe7ed70e54bb12ae3881f3fb91
content_type: application/pdf
creator: dernst
date_created: 2019-11-18T16:12:25Z
date_updated: 2020-07-14T12:44:36Z
file_id: '7040'
file_name: 2016_PlantPhysi_Steenackers.pdf
file_size: 4109142
relation: main_file
file_date_updated: 2020-07-14T12:44:36Z
has_accepted_license: '1'
intvolume: ' 173'
isi: 1
issue: '1'
language:
- iso: eng
month: '01'
oa: 1
oa_version: Submitted Version
page: 552 - 565
pmid: 1
project:
- _id: 25716A02-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '282300'
name: Polarity and subcellular dynamics in plants
publication: Plant Physiology
publication_identifier:
issn:
- 0032-0889
publication_status: published
publisher: American Society of Plant Biologists
publist_id: '6199'
quality_controlled: '1'
scopus_import: '1'
status: public
title: Cis-cinnamic acid is a novel natural auxin efflux inhibitor that promotes lateral
root formation
type: journal_article
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
volume: 173
year: '2017'
...
---
_id: '1169'
abstract:
- lang: eng
text: Dispersal is a crucial factor in natural evolution, since it determines the
habitat experienced by any population and defines the spatial scale of interactions
between individuals. There is compelling evidence for systematic differences in
dispersal characteristics within the same population, i.e., genotype-dependent
dispersal. The consequences of genotype-dependent dispersal on other evolutionary
phenomena, however, are poorly understood. In this article we investigate the
effect of genotype-dependent dispersal on spatial gene frequency patterns, using
a generalization of the classical diffusion model of selection and dispersal.
Dispersal is characterized by the variance of dispersal (diffusion coefficient)
and the mean displacement (directional advection term). We demonstrate that genotype-dependent
dispersal may change the qualitative behavior of Fisher waves, which change from
being “pulled” to being “pushed” wave fronts as the discrepancy in dispersal between
genotypes increases. The speed of any wave is partitioned into components due
to selection, genotype-dependent variance of dispersal, and genotype-dependent
mean displacement. We apply our findings to wave fronts maintained by selection
against heterozygotes. Furthermore, we identify a benefit of increased variance
of dispersal, quantify its effect on the speed of the wave, and discuss the implications
for the evolution of dispersal strategies.
article_processing_charge: No
author:
- first_name: Sebastian
full_name: Novak, Sebastian
id: 461468AE-F248-11E8-B48F-1D18A9856A87
last_name: Novak
orcid: 0000-0002-2519-824X
- first_name: Richard
full_name: Kollár, Richard
last_name: Kollár
citation:
ama: Novak S, Kollár R. Spatial gene frequency waves under genotype dependent dispersal.
Genetics. 2017;205(1):367-374. doi:10.1534/genetics.116.193946
apa: Novak, S., & Kollár, R. (2017). Spatial gene frequency waves under genotype
dependent dispersal. Genetics. Genetics Society of America. https://doi.org/10.1534/genetics.116.193946
chicago: Novak, Sebastian, and Richard Kollár. “Spatial Gene Frequency Waves under
Genotype Dependent Dispersal.” Genetics. Genetics Society of America, 2017.
https://doi.org/10.1534/genetics.116.193946.
ieee: S. Novak and R. Kollár, “Spatial gene frequency waves under genotype dependent
dispersal,” Genetics, vol. 205, no. 1. Genetics Society of America, pp.
367–374, 2017.
ista: Novak S, Kollár R. 2017. Spatial gene frequency waves under genotype dependent
dispersal. Genetics. 205(1), 367–374.
mla: Novak, Sebastian, and Richard Kollár. “Spatial Gene Frequency Waves under Genotype
Dependent Dispersal.” Genetics, vol. 205, no. 1, Genetics Society of America,
2017, pp. 367–74, doi:10.1534/genetics.116.193946.
short: S. Novak, R. Kollár, Genetics 205 (2017) 367–374.
date_created: 2018-12-11T11:50:31Z
date_published: 2017-01-01T00:00:00Z
date_updated: 2023-09-20T11:24:21Z
day: '01'
ddc:
- '576'
department:
- _id: NiBa
doi: 10.1534/genetics.116.193946
ec_funded: 1
external_id:
isi:
- '000393677300025'
file:
- access_level: open_access
checksum: 7c8ab79cda1f92760bbbbe0f53175bfc
content_type: application/pdf
creator: system
date_created: 2018-12-12T10:10:43Z
date_updated: 2020-07-14T12:44:37Z
file_id: '4833'
file_name: IST-2016-727-v1+1_SFC_Genetics_final.pdf
file_size: 361500
relation: main_file
file_date_updated: 2020-07-14T12:44:37Z
has_accepted_license: '1'
intvolume: ' 205'
isi: 1
issue: '1'
language:
- iso: eng
month: '01'
oa: 1
oa_version: Submitted Version
page: 367 - 374
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: Genetics
publication_identifier:
issn:
- '00166731'
publication_status: published
publisher: Genetics Society of America
publist_id: '6188'
pubrep_id: '727'
quality_controlled: '1'
scopus_import: '1'
status: public
title: Spatial gene frequency waves under genotype dependent dispersal
type: journal_article
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
volume: 205
year: '2017'
...
---
_id: '1160'
abstract:
- lang: eng
text: 'We investigate fundamental nonlinear dynamics of ferrofluidic Taylor-Couette
flow - flow confined be-tween two concentric independently rotating cylinders
- consider small aspect ratio by solving the ferro-hydrodynamical equations, carrying
out systematic bifurcation analysis. Without magnetic field, we find steady flow
patterns, previously observed with a simple fluid, such as those containing normal
one- or two vortex cells, as well as anomalous one-cell and twin-cell flow states.
However, when a symmetry-breaking transverse magnetic field is present, all flow
states exhibit stimulated, finite two-fold mode. Various bifurcations between
steady and unsteady states can occur, corresponding to the transitions between
the two-cell and one-cell states. While unsteady, axially oscillating flow states
can arise, we also detect the emergence of new unsteady flow states. In particular,
we uncover two new states: one contains only the azimuthally oscillating solution
in the configuration of the twin-cell flow state, and an-other a rotating flow
state. Topologically, these flow states are a limit cycle and a quasiperiodic
solution on a two-torus, respectively. Emergence of new flow states in addition
to observed ones with classical fluid, indicates that richer but potentially more
controllable dynamics in ferrofluidic flows, as such flow states depend on the
external magnetic field.'
article_number: '40012'
article_processing_charge: No
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. Dynamics of ferrofluidic flow in the Taylor-Couette
system with a small aspect ratio. Scientific Reports. 2017;7. doi:10.1038/srep40012
apa: Altmeyer, S., Do, Y., & Lai, Y. (2017). Dynamics of ferrofluidic flow in
the Taylor-Couette system with a small aspect ratio. Scientific Reports.
Nature Publishing Group. https://doi.org/10.1038/srep40012
chicago: Altmeyer, Sebastian, Younghae Do, and Ying Lai. “Dynamics of Ferrofluidic
Flow in the Taylor-Couette System with a Small Aspect Ratio.” Scientific Reports.
Nature Publishing Group, 2017. https://doi.org/10.1038/srep40012.
ieee: S. Altmeyer, Y. Do, and Y. Lai, “Dynamics of ferrofluidic flow in the Taylor-Couette
system with a small aspect ratio,” Scientific Reports, vol. 7. Nature Publishing
Group, 2017.
ista: Altmeyer S, Do Y, Lai Y. 2017. Dynamics of ferrofluidic flow in the Taylor-Couette
system with a small aspect ratio. Scientific Reports. 7, 40012.
mla: Altmeyer, Sebastian, et al. “Dynamics of Ferrofluidic Flow in the Taylor-Couette
System with a Small Aspect Ratio.” Scientific Reports, vol. 7, 40012, Nature
Publishing Group, 2017, doi:10.1038/srep40012.
short: S. Altmeyer, Y. Do, Y. Lai, Scientific Reports 7 (2017).
date_created: 2018-12-11T11:50:28Z
date_published: 2017-01-06T00:00:00Z
date_updated: 2023-09-20T11:28:49Z
day: '06'
ddc:
- '532'
department:
- _id: BjHo
doi: 10.1038/srep40012
external_id:
isi:
- '000391269700001'
file:
- access_level: open_access
checksum: 694aa70399444570825099c1a7ec91f2
content_type: application/pdf
creator: system
date_created: 2018-12-12T10:10:16Z
date_updated: 2020-07-14T12:44:36Z
file_id: '4802'
file_name: IST-2017-743-v1+1_srep40012.pdf
file_size: 4546835
relation: main_file
file_date_updated: 2020-07-14T12:44:36Z
has_accepted_license: '1'
intvolume: ' 7'
isi: 1
language:
- iso: eng
month: '01'
oa: 1
oa_version: Published Version
publication: Scientific Reports
publication_identifier:
issn:
- '20452322'
publication_status: published
publisher: Nature Publishing Group
publist_id: '6198'
pubrep_id: '743'
quality_controlled: '1'
scopus_import: '1'
status: public
title: Dynamics of ferrofluidic flow in the Taylor-Couette system with a small aspect
ratio
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: c635000d-4b10-11ee-a964-aac5a93f6ac1
volume: 7
year: '2017'
...
---
_id: '1162'
abstract:
- lang: eng
text: Selected universal experimental properties of high-temperature superconducting
(HTS) cuprates have been singled out in the last decade. One of the pivotal challenges
in this field is the designation of a consistent interpretation framework within
which we can describe quantitatively the universal features of those systems.
Here we analyze in a detailed manner the principal experimental data and compare
them quantitatively with the approach based on a single-band model of strongly
correlated electrons supplemented with strong antiferromagnetic (super)exchange
interaction (the so-called t−J−U model). The model rationale is provided by estimating
its microscopic parameters on the basis of the three-band approach for the Cu-O
plane. We use our original full Gutzwiller wave-function solution by going beyond
the renormalized mean-field theory (RMFT) in a systematic manner. Our approach
reproduces very well the observed hole doping (δ) dependence of the kinetic-energy
gain in the superconducting phase, one of the principal non-Bardeen-Cooper-Schrieffer
features of the cuprates. The calculated Fermi velocity in the nodal direction
is practically δ-independent and its universal value agrees very well with that
determined experimentally. Also, a weak doping dependence of the Fermi wave vector
leads to an almost constant value of the effective mass in a pure superconducting
phase which is both observed in experiment and reproduced within our approach.
An assessment of the currently used models (t−J, Hubbard) is carried out and the
results of the canonical RMFT as a zeroth-order solution are provided for comparison
to illustrate the necessity of the introduced higher-order contributions.
article_number: '024506'
article_processing_charge: No
author:
- first_name: Jozef
full_name: Spałek, Jozef
last_name: Spałek
- first_name: Michał
full_name: Zegrodnik, Michał
last_name: Zegrodnik
- first_name: Jan
full_name: Kaczmarczyk, Jan
id: 46C405DE-F248-11E8-B48F-1D18A9856A87
last_name: Kaczmarczyk
orcid: 0000-0002-1629-3675
citation:
ama: Spałek J, Zegrodnik M, Kaczmarczyk J. Universal properties of high temperature
superconductors from real space pairing t-J-U model and its quantitative comparison
with experiment. Physical Review B - Condensed Matter and Materials Physics.
2017;95(2). doi:10.1103/PhysRevB.95.024506
apa: Spałek, J., Zegrodnik, M., & Kaczmarczyk, J. (2017). Universal properties
of high temperature superconductors from real space pairing t-J-U model and its
quantitative comparison with experiment. Physical Review B - Condensed Matter
and Materials Physics. American Physical Society. https://doi.org/10.1103/PhysRevB.95.024506
chicago: Spałek, Jozef, Michał Zegrodnik, and Jan Kaczmarczyk. “Universal Properties
of High Temperature Superconductors from Real Space Pairing T-J-U Model and Its
Quantitative Comparison with Experiment.” Physical Review B - Condensed Matter
and Materials Physics. American Physical Society, 2017. https://doi.org/10.1103/PhysRevB.95.024506.
ieee: J. Spałek, M. Zegrodnik, and J. Kaczmarczyk, “Universal properties of high
temperature superconductors from real space pairing t-J-U model and its quantitative
comparison with experiment,” Physical Review B - Condensed Matter and Materials
Physics, vol. 95, no. 2. American Physical Society, 2017.
ista: Spałek J, Zegrodnik M, Kaczmarczyk J. 2017. Universal properties of high temperature
superconductors from real space pairing t-J-U model and its quantitative comparison
with experiment. Physical Review B - Condensed Matter and Materials Physics. 95(2),
024506.
mla: Spałek, Jozef, et al. “Universal Properties of High Temperature Superconductors
from Real Space Pairing T-J-U Model and Its Quantitative Comparison with Experiment.”
Physical Review B - Condensed Matter and Materials Physics, vol. 95, no.
2, 024506, American Physical Society, 2017, doi:10.1103/PhysRevB.95.024506.
short: J. Spałek, M. Zegrodnik, J. Kaczmarczyk, Physical Review B - Condensed Matter
and Materials Physics 95 (2017).
date_created: 2018-12-11T11:50:29Z
date_published: 2017-01-13T00:00:00Z
date_updated: 2023-09-20T11:25:56Z
day: '13'
department:
- _id: MiLe
doi: 10.1103/PhysRevB.95.024506
ec_funded: 1
external_id:
isi:
- '000391852800006'
intvolume: ' 95'
isi: 1
issue: '2'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/1606.03247
month: '01'
oa: 1
oa_version: Submitted Version
project:
- _id: 25681D80-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '291734'
name: International IST Postdoc Fellowship Programme
publication: Physical Review B - Condensed Matter and Materials Physics
publication_identifier:
issn:
- '24699950'
publication_status: published
publisher: American Physical Society
publist_id: '6195'
quality_controlled: '1'
scopus_import: '1'
status: public
title: Universal properties of high temperature superconductors from real space pairing
t-J-U model and its quantitative comparison with experiment
type: journal_article
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
volume: 95
year: '2017'
...
---
_id: '1152'
abstract:
- lang: eng
text: We propose a new memetic strategy that can solve the multi-physics, complex
inverse problems, formulated as the multi-objective optimization ones, in which
objectives are misfits between the measured and simulated states of various governing
processes. The multi-deme structure of the strategy allows for both, intensive,
relatively cheap exploration with a moderate accuracy and more accurate search
many regions of Pareto set in parallel. The special type of selection operator
prefers the coherent alternative solutions, eliminating artifacts appearing in
the particular processes. The additional accuracy increment is obtained by the
parallel convex searches applied to the local scalarizations of the misfit vector.
The strategy is dedicated for solving ill-conditioned problems, for which inverting
the single physical process can lead to the ambiguous results. The skill of the
selection in artifact elimination is shown on the benchmark problem, while the
whole strategy was applied for identification of oil deposits, where the misfits
are related to various frequencies of the magnetic and electric waves of the magnetotelluric
measurements. 2016 Elsevier B.V.
article_processing_charge: No
author:
- first_name: Ewa P
full_name: Gajda-Zagorska, Ewa P
id: 47794CF0-F248-11E8-B48F-1D18A9856A87
last_name: Gajda-Zagorska
- first_name: Robert
full_name: Schaefer, Robert
last_name: Schaefer
- first_name: Maciej
full_name: Smołka, Maciej
last_name: Smołka
- first_name: David
full_name: Pardo, David
last_name: Pardo
- first_name: Julen
full_name: Alvarez Aramberri, Julen
last_name: Alvarez Aramberri
citation:
ama: Gajda-Zagorska EP, Schaefer R, Smołka M, Pardo D, Alvarez Aramberri J. A multi
objective memetic inverse solver reinforced by local optimization methods. Journal
of Computational Science. 2017;18:85-94. doi:10.1016/j.jocs.2016.06.007
apa: Gajda-Zagorska, E. P., Schaefer, R., Smołka, M., Pardo, D., & Alvarez Aramberri,
J. (2017). A multi objective memetic inverse solver reinforced by local optimization
methods. Journal of Computational Science. Elsevier. https://doi.org/10.1016/j.jocs.2016.06.007
chicago: Gajda-Zagorska, Ewa P, Robert Schaefer, Maciej Smołka, David Pardo, and
Julen Alvarez Aramberri. “A Multi Objective Memetic Inverse Solver Reinforced
by Local Optimization Methods.” Journal of Computational Science. Elsevier,
2017. https://doi.org/10.1016/j.jocs.2016.06.007.
ieee: E. P. Gajda-Zagorska, R. Schaefer, M. Smołka, D. Pardo, and J. Alvarez Aramberri,
“A multi objective memetic inverse solver reinforced by local optimization methods,”
Journal of Computational Science, vol. 18. Elsevier, pp. 85–94, 2017.
ista: Gajda-Zagorska EP, Schaefer R, Smołka M, Pardo D, Alvarez Aramberri J. 2017.
A multi objective memetic inverse solver reinforced by local optimization methods.
Journal of Computational Science. 18, 85–94.
mla: Gajda-Zagorska, Ewa P., et al. “A Multi Objective Memetic Inverse Solver Reinforced
by Local Optimization Methods.” Journal of Computational Science, vol.
18, Elsevier, 2017, pp. 85–94, doi:10.1016/j.jocs.2016.06.007.
short: E.P. Gajda-Zagorska, R. Schaefer, M. Smołka, D. Pardo, J. Alvarez Aramberri,
Journal of Computational Science 18 (2017) 85–94.
date_created: 2018-12-11T11:50:26Z
date_published: 2017-01-01T00:00:00Z
date_updated: 2023-09-20T11:29:44Z
day: '01'
ddc:
- '000'
department:
- _id: ChWo
doi: 10.1016/j.jocs.2016.06.007
external_id:
isi:
- '000393528700009'
file:
- access_level: open_access
content_type: application/pdf
creator: dernst
date_created: 2019-01-18T08:43:16Z
date_updated: 2019-01-18T08:43:16Z
file_id: '5842'
file_name: 2016_jocs_ewa.pdf
file_size: 1083911
relation: main_file
success: 1
file_date_updated: 2019-01-18T08:43:16Z
has_accepted_license: '1'
intvolume: ' 18'
isi: 1
language:
- iso: eng
month: '01'
oa: 1
oa_version: Submitted Version
page: 85 - 94
publication: Journal of Computational Science
publication_identifier:
issn:
- '18777503'
publication_status: published
publisher: Elsevier
publist_id: '6206'
quality_controlled: '1'
scopus_import: '1'
status: public
title: A multi objective memetic inverse solver reinforced by local optimization methods
type: journal_article
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
volume: 18
year: '2017'
...
---
_id: '1168'
abstract:
- lang: eng
text: Optimum experimental design theory has recently been extended for parameter
estimation in copula models. The use of these models allows one to gain in flexibility
by considering the model parameter set split into marginal and dependence parameters.
However, this separation also leads to the natural issue of estimating only a
subset of all model parameters. In this work, we treat this problem with the application
of the (Formula presented.)-optimality to copula models. First, we provide an
extension of the corresponding equivalence theory. Then, we analyze a wide range
of flexible copula models to highlight the usefulness of (Formula presented.)-optimality
in many possible scenarios. Finally, we discuss how the usage of the introduced
design criterion also relates to the more general issue of copula selection and
optimal design for model discrimination.
acknowledgement: 'This work has been supported by the project ANR-2011-IS01-001-01
“DESIRE” and Austrian Science Fund (FWF) I833-N18. Open access funding is provided
by the Austrian Science Fund (FWF). '
article_processing_charge: No
author:
- first_name: Elisa
full_name: Perrone, Elisa
id: 2A5F8724-F248-11E8-B48F-1D18A9856A87
last_name: Perrone
orcid: 0000-0003-0370-9835
- first_name: Andreas
full_name: Rappold, Andreas
last_name: Rappold
- first_name: Werner
full_name: Müller, Werner
last_name: Müller
citation:
ama: Perrone E, Rappold A, Müller W. D inf s optimality in copula models. Statistical
Methods and Applications. 2017;26(3):403-418. doi:10.1007/s10260-016-0375-6
apa: Perrone, E., Rappold, A., & Müller, W. (2017). D inf s optimality in copula
models. Statistical Methods and Applications. Springer. https://doi.org/10.1007/s10260-016-0375-6
chicago: Perrone, Elisa, Andreas Rappold, and Werner Müller. “D Inf s Optimality
in Copula Models.” Statistical Methods and Applications. Springer, 2017.
https://doi.org/10.1007/s10260-016-0375-6.
ieee: E. Perrone, A. Rappold, and W. Müller, “D inf s optimality in copula models,”
Statistical Methods and Applications, vol. 26, no. 3. Springer, pp. 403–418,
2017.
ista: Perrone E, Rappold A, Müller W. 2017. D inf s optimality in copula models.
Statistical Methods and Applications. 26(3), 403–418.
mla: Perrone, Elisa, et al. “D Inf s Optimality in Copula Models.” Statistical
Methods and Applications, vol. 26, no. 3, Springer, 2017, pp. 403–18, doi:10.1007/s10260-016-0375-6.
short: E. Perrone, A. Rappold, W. Müller, Statistical Methods and Applications 26
(2017) 403–418.
date_created: 2018-12-11T11:50:31Z
date_published: 2017-08-01T00:00:00Z
date_updated: 2023-09-20T11:25:09Z
day: '01'
ddc:
- '519'
department:
- _id: CaUh
doi: 10.1007/s10260-016-0375-6
external_id:
isi:
- '000407973200004'
file:
- access_level: open_access
checksum: 0b2d1b647ca96e9ef13a14b8b6775e0f
content_type: application/pdf
creator: system
date_created: 2018-12-12T10:16:13Z
date_updated: 2020-07-14T12:44:37Z
file_id: '5199'
file_name: IST-2017-739-v1+2_10260_2016_375_MOESM1_ESM.pdf
file_size: 56664
relation: main_file
- access_level: open_access
checksum: 3321ef34e02e28acfc427f77cf32812a
content_type: application/pdf
creator: system
date_created: 2018-12-12T10:16:14Z
date_updated: 2020-07-14T12:44:37Z
file_id: '5200'
file_name: IST-2017-739-v1+3_s10260-016-0375-6.pdf
file_size: 688953
relation: main_file
file_date_updated: 2020-07-14T12:44:37Z
has_accepted_license: '1'
intvolume: ' 26'
isi: 1
issue: '3'
language:
- iso: eng
month: '08'
oa: 1
oa_version: Submitted Version
page: 403 - 418
publication: Statistical Methods and Applications
publication_status: published
publisher: Springer
publist_id: '6189'
pubrep_id: '739'
quality_controlled: '1'
scopus_import: '1'
status: public
title: D inf s optimality in copula models
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: c635000d-4b10-11ee-a964-aac5a93f6ac1
volume: 26
year: '2017'
...
---
_id: '1163'
abstract:
- lang: eng
text: 'We investigate the effect of the electron-hole (e-h) symmetry breaking on
d-wave superconductivity induced by non-local effects of correlations in the generalized
Hubbard model. The symmetry breaking is introduced in a two-fold manner: by the
next-to-nearest neighbor hopping of electrons and by the charge-bond interaction
- the off-diagonal term of the Coulomb potential. Both terms lead to a pronounced
asymmetry of the superconducting order parameter. The next-to-nearest neighbor
hopping enhances superconductivity for h-doping, while diminishes it for e-doping.
The charge-bond interaction alone leads to the opposite effect and, additionally,
to the kinetic-energy gain upon condensation in the underdoped regime. With both
terms included, with similar amplitudes, the height of the superconducting dome
and the critical doping remain in favor of h-doping. The influence of the charge-bond
interaction on deviations from symmetry of the shape of the gap at the Fermi surface
in the momentum space is briefly discussed.'
article_number: '085604'
article_processing_charge: No
author:
- first_name: Marcin
full_name: Wysokiński, Marcin
last_name: Wysokiński
- first_name: Jan
full_name: Kaczmarczyk, Jan
id: 46C405DE-F248-11E8-B48F-1D18A9856A87
last_name: Kaczmarczyk
orcid: 0000-0002-1629-3675
citation:
ama: 'Wysokiński M, Kaczmarczyk J. Unconventional superconductivity in generalized
Hubbard model role of electron–hole symmetry breaking terms. Journal of Physics:
Condensed Matter. 2017;29(8). doi:10.1088/1361-648X/aa532f'
apa: 'Wysokiński, M., & Kaczmarczyk, J. (2017). Unconventional superconductivity
in generalized Hubbard model role of electron–hole symmetry breaking terms. Journal
of Physics: Condensed Matter. IOP Publishing Ltd. https://doi.org/10.1088/1361-648X/aa532f'
chicago: 'Wysokiński, Marcin, and Jan Kaczmarczyk. “Unconventional Superconductivity
in Generalized Hubbard Model Role of Electron–Hole Symmetry Breaking Terms.” Journal
of Physics: Condensed Matter. IOP Publishing Ltd., 2017. https://doi.org/10.1088/1361-648X/aa532f.'
ieee: 'M. Wysokiński and J. Kaczmarczyk, “Unconventional superconductivity in generalized
Hubbard model role of electron–hole symmetry breaking terms,” Journal of Physics:
Condensed Matter, vol. 29, no. 8. IOP Publishing Ltd., 2017.'
ista: 'Wysokiński M, Kaczmarczyk J. 2017. Unconventional superconductivity in generalized
Hubbard model role of electron–hole symmetry breaking terms. Journal of Physics:
Condensed Matter. 29(8), 085604.'
mla: 'Wysokiński, Marcin, and Jan Kaczmarczyk. “Unconventional Superconductivity
in Generalized Hubbard Model Role of Electron–Hole Symmetry Breaking Terms.” Journal
of Physics: Condensed Matter, vol. 29, no. 8, 085604, IOP Publishing Ltd.,
2017, doi:10.1088/1361-648X/aa532f.'
short: 'M. Wysokiński, J. Kaczmarczyk, Journal of Physics: Condensed Matter 29 (2017).'
date_created: 2018-12-11T11:50:29Z
date_published: 2017-01-16T00:00:00Z
date_updated: 2023-09-20T11:25:32Z
day: '16'
department:
- _id: MiLe
doi: 10.1088/1361-648X/aa532f
ec_funded: 1
external_id:
isi:
- '000393955500001'
intvolume: ' 29'
isi: 1
issue: '8'
language:
- iso: eng
month: '01'
oa_version: None
project:
- _id: 25681D80-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '291734'
name: International IST Postdoc Fellowship Programme
publication: 'Journal of Physics: Condensed Matter'
publication_identifier:
issn:
- '09538984'
publication_status: published
publisher: IOP Publishing Ltd.
publist_id: '6194'
quality_controlled: '1'
scopus_import: '1'
status: public
title: Unconventional superconductivity in generalized Hubbard model role of electron–hole
symmetry breaking terms
type: journal_article
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
volume: 29
year: '2017'
...