---
_id: '10880'
abstract:
- lang: eng
text: Acquisition of evolutionary novelties is a fundamental process for adapting
to the external environment and invading new niches and results in the diversification
of life, which we can see in the world today. How such novel phenotypic traits
are acquired in the course of evolution and are built up in developing embryos
has been a central question in biology. Whole-genome duplication (WGD) is a process
of genome doubling that supplies raw genetic materials and increases genome complexity.
Recently, it has been gradually revealed that WGD and subsequent fate changes
of duplicated genes can facilitate phenotypic evolution. Here, we review the current
understanding of the relationship between WGD and the acquisition of evolutionary
novelties. We show some examples of this link and discuss how WGD and subsequent
duplicated genes can facilitate phenotypic evolution as well as when such genomic
doubling can be advantageous for adaptation.
acknowledgement: This work was supported by JSPS overseas research fellowships (Y.M.)
and SENSHIN Medical Research Foundation (K.K.T.).
article_processing_charge: No
article_type: original
author:
- first_name: Moriyama
full_name: Yuuta, Moriyama
id: 4968E7C8-F248-11E8-B48F-1D18A9856A87
last_name: Yuuta
orcid: 0000-0002-2853-8051
- first_name: Kazuko
full_name: Koshiba-Takeuchi, Kazuko
last_name: Koshiba-Takeuchi
citation:
ama: Yuuta M, Koshiba-Takeuchi K. Significance of whole-genome duplications on the
emergence of evolutionary novelties. Briefings in Functional Genomics.
2018;17(5):329-338. doi:10.1093/bfgp/ely007
apa: Yuuta, M., & Koshiba-Takeuchi, K. (2018). Significance of whole-genome
duplications on the emergence of evolutionary novelties. Briefings in Functional
Genomics. Oxford University Press. https://doi.org/10.1093/bfgp/ely007
chicago: Yuuta, Moriyama, and Kazuko Koshiba-Takeuchi. “Significance of Whole-Genome
Duplications on the Emergence of Evolutionary Novelties.” Briefings in Functional
Genomics. Oxford University Press, 2018. https://doi.org/10.1093/bfgp/ely007.
ieee: M. Yuuta and K. Koshiba-Takeuchi, “Significance of whole-genome duplications
on the emergence of evolutionary novelties,” Briefings in Functional Genomics,
vol. 17, no. 5. Oxford University Press, pp. 329–338, 2018.
ista: Yuuta M, Koshiba-Takeuchi K. 2018. Significance of whole-genome duplications
on the emergence of evolutionary novelties. Briefings in Functional Genomics.
17(5), 329–338.
mla: Yuuta, Moriyama, and Kazuko Koshiba-Takeuchi. “Significance of Whole-Genome
Duplications on the Emergence of Evolutionary Novelties.” Briefings in Functional
Genomics, vol. 17, no. 5, Oxford University Press, 2018, pp. 329–38, doi:10.1093/bfgp/ely007.
short: M. Yuuta, K. Koshiba-Takeuchi, Briefings in Functional Genomics 17 (2018)
329–338.
date_created: 2022-03-18T12:40:35Z
date_published: 2018-09-01T00:00:00Z
date_updated: 2023-09-19T15:11:22Z
day: '01'
department:
- _id: CaHe
doi: 10.1093/bfgp/ely007
external_id:
isi:
- '000456054400004'
pmid:
- '29579140'
intvolume: ' 17'
isi: 1
issue: '5'
keyword:
- Genetics
- Molecular Biology
- Biochemistry
- General Medicine
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.1093/bfgp/ely007
month: '09'
oa: 1
oa_version: Published Version
page: 329-338
pmid: 1
publication: Briefings in Functional Genomics
publication_identifier:
eissn:
- 2041-2657
issn:
- 2041-2649
publication_status: published
publisher: Oxford University Press
quality_controlled: '1'
scopus_import: '1'
status: public
title: Significance of whole-genome duplications on the emergence of evolutionary
novelties
type: journal_article
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
volume: 17
year: '2018'
...
---
_id: '10881'
abstract:
- lang: eng
text: Strigolactones (SLs) are a relatively recent addition to the list of plant
hormones that control different aspects of plant development. SL signalling is
perceived by an α/β hydrolase, DWARF 14 (D14). A close homolog of D14, KARRIKIN
INSENSTIVE2 (KAI2), is involved in perception of an uncharacterized molecule called
karrikin (KAR). Recent studies in Arabidopsis identified the SUPPRESSOR OF MAX2
1 (SMAX1) and SMAX1-LIKE 7 (SMXL7) to be potential SCF–MAX2 complex-mediated proteasome
targets of KAI2 and D14, respectively. Genetic studies on SMXL7 and SMAX1 demonstrated
distinct developmental roles for each, but very little is known about these repressors
in terms of their sequence features. In this study, we performed an extensive
comparative analysis of SMXLs and determined their phylogenetic and evolutionary
history in the plant lineage. Our results show that SMXL family members can be
sub-divided into four distinct phylogenetic clades/classes, with an ancient SMAX1.
Further, we identified the clade-specific motifs that have evolved and that might
act as determinants of SL-KAR signalling specificity. These specificities resulted
from functional diversities among the clades. Our results suggest that a gradual
co-evolution of SMXL members with their upstream receptors D14/KAI2 provided an
increased specificity to both the SL perception and response in land plants.
acknowledgement: "This project received funding from the European Union’s Horizon
2020 research and innovation programme under the Marie Skłodowska-Curie Actions
and it is co-financed by the South Moravian Region under grant agreement No. 665860
(SS). Access to computing and storage facilities owned by parties and projects contributing
to the national grid infrastructure, MetaCentrum, provided under the program ‘Projects
of Large Infrastructure for Research, Development, and Innovations’ (LM2010005)
was greatly appreciated (RSV). The project was funded by The Ministry of Education,
Youth and Sports/MES of the Czech Republic under the project CEITEC 2020 (LQ1601)
(TN, TRM). JF was supported by the European Research Council (project ERC-2011-StG
20101109-PSDP) and the Czech Science Foundation GAČR (GA13-40637S). We thank Dr
Kamel Chibani for active discussions on the evolutionary analysis and Nandan Mysore
Vardarajan for his critical comments on the manuscript. This article reflects\r\nonly
the authors’ views, and the EU is not responsible for any use that may be made of
the information it contains. "
article_processing_charge: No
article_type: original
author:
- first_name: Taraka Ramji
full_name: Moturu, Taraka Ramji
last_name: Moturu
- first_name: Sravankumar
full_name: Thula, Sravankumar
last_name: Thula
- first_name: Ravi Kumar
full_name: Singh, Ravi Kumar
last_name: Singh
- first_name: Tomasz
full_name: Nodzyński, Tomasz
last_name: Nodzyński
- first_name: Radka Svobodová
full_name: Vařeková, Radka Svobodová
last_name: Vařeková
- first_name: Jiří
full_name: Friml, Jiří
id: 4159519E-F248-11E8-B48F-1D18A9856A87
last_name: Friml
orcid: 0000-0002-8302-7596
- first_name: Sibu
full_name: Simon, Sibu
last_name: Simon
citation:
ama: Moturu TR, Thula S, Singh RK, et al. Molecular evolution and diversification
of the SMXL gene family. Journal of Experimental Botany. 2018;69(9):2367-2378.
doi:10.1093/jxb/ery097
apa: Moturu, T. R., Thula, S., Singh, R. K., Nodzyński, T., Vařeková, R. S., Friml,
J., & Simon, S. (2018). Molecular evolution and diversification of the SMXL
gene family. Journal of Experimental Botany. Oxford University Press. https://doi.org/10.1093/jxb/ery097
chicago: Moturu, Taraka Ramji, Sravankumar Thula, Ravi Kumar Singh, Tomasz Nodzyński,
Radka Svobodová Vařeková, Jiří Friml, and Sibu Simon. “Molecular Evolution and
Diversification of the SMXL Gene Family.” Journal of Experimental Botany.
Oxford University Press, 2018. https://doi.org/10.1093/jxb/ery097.
ieee: T. R. Moturu et al., “Molecular evolution and diversification of the
SMXL gene family,” Journal of Experimental Botany, vol. 69, no. 9. Oxford
University Press, pp. 2367–2378, 2018.
ista: Moturu TR, Thula S, Singh RK, Nodzyński T, Vařeková RS, Friml J, Simon S.
2018. Molecular evolution and diversification of the SMXL gene family. Journal
of Experimental Botany. 69(9), 2367–2378.
mla: Moturu, Taraka Ramji, et al. “Molecular Evolution and Diversification of the
SMXL Gene Family.” Journal of Experimental Botany, vol. 69, no. 9, Oxford
University Press, 2018, pp. 2367–78, doi:10.1093/jxb/ery097.
short: T.R. Moturu, S. Thula, R.K. Singh, T. Nodzyński, R.S. Vařeková, J. Friml,
S. Simon, Journal of Experimental Botany 69 (2018) 2367–2378.
date_created: 2022-03-18T12:43:22Z
date_published: 2018-04-13T00:00:00Z
date_updated: 2025-05-07T11:12:33Z
day: '13'
department:
- _id: JiFr
doi: 10.1093/jxb/ery097
ec_funded: 1
external_id:
isi:
- '000430727000016'
pmid:
- '29538714'
intvolume: ' 69'
isi: 1
issue: '9'
keyword:
- Plant Science
- Physiology
language:
- iso: eng
month: '04'
oa_version: None
page: 2367-2378
pmid: 1
project:
- _id: 25716A02-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '282300'
name: Polarity and subcellular dynamics in plants
publication: Journal of Experimental Botany
publication_identifier:
eissn:
- 1460-2431
issn:
- 0022-0957
publication_status: published
publisher: Oxford University Press
quality_controlled: '1'
scopus_import: '1'
status: public
title: Molecular evolution and diversification of the SMXL gene family
type: journal_article
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
volume: 69
year: '2018'
...
---
_id: '10882'
abstract:
- lang: eng
text: 'We introduce Intelligent Annotation Dialogs for bounding box annotation.
We train an agent to automatically choose a sequence of actions for a human annotator
to produce a bounding box in a minimal amount of time. Specifically, we consider
two actions: box verification [34], where the annotator verifies a box generated
by an object detector, and manual box drawing. We explore two kinds of agents,
one based on predicting the probability that a box will be positively verified,
and the other based on reinforcement learning. We demonstrate that (1) our agents
are able to learn efficient annotation strategies in several scenarios, automatically
adapting to the image difficulty, the desired quality of the boxes, and the detector
strength; (2) in all scenarios the resulting annotation dialogs speed up annotation
compared to manual box drawing alone and box verification alone, while also outperforming
any fixed combination of verification and drawing in most scenarios; (3) in a
realistic scenario where the detector is iteratively re-trained, our agents evolve
a series of strategies that reflect the shifting trade-off between verification
and drawing as the detector grows stronger.'
article_processing_charge: No
arxiv: 1
author:
- first_name: Jasper
full_name: Uijlings, Jasper
last_name: Uijlings
- first_name: Ksenia
full_name: Konyushkova, Ksenia
last_name: Konyushkova
- first_name: Christoph
full_name: Lampert, Christoph
id: 40C20FD2-F248-11E8-B48F-1D18A9856A87
last_name: Lampert
orcid: 0000-0001-8622-7887
- first_name: Vittorio
full_name: Ferrari, Vittorio
last_name: Ferrari
citation:
ama: 'Uijlings J, Konyushkova K, Lampert C, Ferrari V. Learning intelligent dialogs
for bounding box annotation. In: 2018 IEEE/CVF Conference on Computer Vision
and Pattern Recognition. IEEE; 2018:9175-9184. doi:10.1109/cvpr.2018.00956'
apa: 'Uijlings, J., Konyushkova, K., Lampert, C., & Ferrari, V. (2018). Learning
intelligent dialogs for bounding box annotation. In 2018 IEEE/CVF Conference
on Computer Vision and Pattern Recognition (pp. 9175–9184). Salt Lake City,
UT, United States: IEEE. https://doi.org/10.1109/cvpr.2018.00956'
chicago: Uijlings, Jasper, Ksenia Konyushkova, Christoph Lampert, and Vittorio Ferrari.
“Learning Intelligent Dialogs for Bounding Box Annotation.” In 2018 IEEE/CVF
Conference on Computer Vision and Pattern Recognition, 9175–84. IEEE, 2018.
https://doi.org/10.1109/cvpr.2018.00956.
ieee: J. Uijlings, K. Konyushkova, C. Lampert, and V. Ferrari, “Learning intelligent
dialogs for bounding box annotation,” in 2018 IEEE/CVF Conference on Computer
Vision and Pattern Recognition, Salt Lake City, UT, United States, 2018, pp.
9175–9184.
ista: 'Uijlings J, Konyushkova K, Lampert C, Ferrari V. 2018. Learning intelligent
dialogs for bounding box annotation. 2018 IEEE/CVF Conference on Computer Vision
and Pattern Recognition. CVF: Conference on Computer Vision and Pattern Recognition,
9175–9184.'
mla: Uijlings, Jasper, et al. “Learning Intelligent Dialogs for Bounding Box Annotation.”
2018 IEEE/CVF Conference on Computer Vision and Pattern Recognition, IEEE,
2018, pp. 9175–84, doi:10.1109/cvpr.2018.00956.
short: J. Uijlings, K. Konyushkova, C. Lampert, V. Ferrari, in:, 2018 IEEE/CVF Conference
on Computer Vision and Pattern Recognition, IEEE, 2018, pp. 9175–9184.
conference:
end_date: 2018-06-23
location: Salt Lake City, UT, United States
name: 'CVF: Conference on Computer Vision and Pattern Recognition'
start_date: 2018-06-18
date_created: 2022-03-18T12:45:09Z
date_published: 2018-12-17T00:00:00Z
date_updated: 2023-09-19T15:11:49Z
day: '17'
department:
- _id: ChLa
doi: 10.1109/cvpr.2018.00956
external_id:
arxiv:
- '1712.08087'
isi:
- '000457843609036'
isi: 1
language:
- iso: eng
main_file_link:
- open_access: '1'
url: ' https://doi.org/10.48550/arXiv.1712.08087'
month: '12'
oa: 1
oa_version: Preprint
page: 9175-9184
publication: 2018 IEEE/CVF Conference on Computer Vision and Pattern Recognition
publication_identifier:
eissn:
- 2575-7075
isbn:
- '9781538664209'
publication_status: published
publisher: IEEE
quality_controlled: '1'
scopus_import: '1'
status: public
title: Learning intelligent dialogs for bounding box annotation
type: conference
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
year: '2018'
...
---
_id: '10883'
abstract:
- lang: eng
text: 'Solving parity games, which are equivalent to modal μ-calculus model checking,
is a central algorithmic problem in formal methods, with applications in reactive
synthesis, program repair, verification of branching-time properties, etc. Besides
the standard compu- tation model with the explicit representation of games, another
important theoretical model of computation is that of set-based symbolic algorithms.
Set-based symbolic algorithms use basic set operations and one-step predecessor
operations on the implicit description of games, rather than the explicit representation.
The significance of symbolic algorithms is that they provide scalable algorithms
for large finite-state systems, as well as for infinite-state systems with finite
quotient. Consider parity games on graphs with n vertices and parity conditions
with d priorities. While there is a rich literature of explicit algorithms for
parity games, the main results for set-based symbolic algorithms are as follows:
(a) the basic algorithm that requires O(nd) symbolic operations and O(d) symbolic
space; and (b) an improved algorithm that requires O(nd/3+1) symbolic operations
and O(n) symbolic space. In this work, our contributions are as follows: (1) We
present a black-box set-based symbolic algorithm based on the explicit progress
measure algorithm. Two important consequences of our algorithm are as follows:
(a) a set-based symbolic algorithm for parity games that requires quasi-polynomially
many symbolic operations and O(n) symbolic space; and (b) any future improvement
in progress measure based explicit algorithms immediately imply an efficiency
improvement in our set-based symbolic algorithm for parity games. (2) We present
a set-based symbolic algorithm that requires quasi-polynomially many symbolic
operations and O(d · log n) symbolic space. Moreover, for the important special
case of d ≤ log n, our algorithm requires only polynomially many symbolic operations
and poly-logarithmic symbolic space.'
acknowledgement: 'A. S. is fully supported by the Vienna Science and Technology Fund
(WWTF) through project ICT15-003. K.C. is supported by the Austrian Science Fund
(FWF) NFN Grant No S11407-N23 (RiSE/SHiNE) and an ERC Starting grant (279307: Graph
Games). For M.H the research leading to these results has received funding from
the European Research Council under the European Union’s Seventh Framework Programme
(FP/2007-2013) /ERC Grant Agreement no. 340506.'
alternative_title:
- EPiC Series in Computing
article_processing_charge: No
arxiv: 1
author:
- first_name: Krishnendu
full_name: Chatterjee, Krishnendu
id: 2E5DCA20-F248-11E8-B48F-1D18A9856A87
last_name: Chatterjee
orcid: 0000-0002-4561-241X
- first_name: Wolfgang
full_name: Dvořák, Wolfgang
last_name: Dvořák
- first_name: Monika H
full_name: Henzinger, Monika H
id: 540c9bbd-f2de-11ec-812d-d04a5be85630
last_name: Henzinger
orcid: 0000-0002-5008-6530
- first_name: Alexander
full_name: Svozil, Alexander
last_name: Svozil
citation:
ama: 'Chatterjee K, Dvořák W, Henzinger MH, Svozil A. Quasipolynomial set-based
symbolic algorithms for parity games. In: 22nd International Conference on
Logic for Programming, Artificial Intelligence and Reasoning. Vol 57. EasyChair;
2018:233-253. doi:10.29007/5z5k'
apa: 'Chatterjee, K., Dvořák, W., Henzinger, M. H., & Svozil, A. (2018). Quasipolynomial
set-based symbolic algorithms for parity games. In 22nd International Conference
on Logic for Programming, Artificial Intelligence and Reasoning (Vol. 57,
pp. 233–253). Awassa, Ethiopia: EasyChair. https://doi.org/10.29007/5z5k'
chicago: Chatterjee, Krishnendu, Wolfgang Dvořák, Monika H Henzinger, and Alexander
Svozil. “Quasipolynomial Set-Based Symbolic Algorithms for Parity Games.” In 22nd
International Conference on Logic for Programming, Artificial Intelligence and
Reasoning, 57:233–53. EasyChair, 2018. https://doi.org/10.29007/5z5k.
ieee: K. Chatterjee, W. Dvořák, M. H. Henzinger, and A. Svozil, “Quasipolynomial
set-based symbolic algorithms for parity games,” in 22nd International Conference
on Logic for Programming, Artificial Intelligence and Reasoning, Awassa, Ethiopia,
2018, vol. 57, pp. 233–253.
ista: 'Chatterjee K, Dvořák W, Henzinger MH, Svozil A. 2018. Quasipolynomial set-based
symbolic algorithms for parity games. 22nd International Conference on Logic for
Programming, Artificial Intelligence and Reasoning. LPAR: Conference on Logic
for Programming, Artificial Intelligence and Reasoning, EPiC Series in Computing,
vol. 57, 233–253.'
mla: Chatterjee, Krishnendu, et al. “Quasipolynomial Set-Based Symbolic Algorithms
for Parity Games.” 22nd International Conference on Logic for Programming,
Artificial Intelligence and Reasoning, vol. 57, EasyChair, 2018, pp. 233–53,
doi:10.29007/5z5k.
short: K. Chatterjee, W. Dvořák, M.H. Henzinger, A. Svozil, in:, 22nd International
Conference on Logic for Programming, Artificial Intelligence and Reasoning, EasyChair,
2018, pp. 233–253.
conference:
end_date: 2018-11-21
location: Awassa, Ethiopia
name: 'LPAR: Conference on Logic for Programming, Artificial Intelligence and Reasoning'
start_date: 2018-11-17
date_created: 2022-03-18T12:46:32Z
date_published: 2018-10-23T00:00:00Z
date_updated: 2022-07-29T09:24:31Z
day: '23'
ddc:
- '000'
department:
- _id: KrCh
doi: 10.29007/5z5k
ec_funded: 1
external_id:
arxiv:
- '1909.04983'
file:
- access_level: open_access
checksum: 1229aa8640bd6db610c85decf2265480
content_type: application/pdf
creator: dernst
date_created: 2022-05-17T07:51:08Z
date_updated: 2022-05-17T07:51:08Z
file_id: '11392'
file_name: 2018_EPiCs_Chatterjee.pdf
file_size: 720893
relation: main_file
success: 1
file_date_updated: 2022-05-17T07:51:08Z
has_accepted_license: '1'
intvolume: ' 57'
language:
- iso: eng
month: '10'
oa: 1
oa_version: Published Version
page: 233-253
project:
- _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: 22nd International Conference on Logic for Programming, Artificial Intelligence
and Reasoning
publication_identifier:
issn:
- 2398-7340
publication_status: published
publisher: EasyChair
quality_controlled: '1'
scopus_import: '1'
status: public
title: Quasipolynomial set-based symbolic algorithms for parity games
type: conference
user_id: 72615eeb-f1f3-11ec-aa25-d4573ddc34fd
volume: 57
year: '2018'
...
---
_id: '11'
abstract:
- lang: eng
text: We report on a novel strategy to derive mean-field limits of quantum mechanical
systems in which a large number of particles weakly couple to a second-quantized
radiation field. The technique combines the method of counting and the coherent
state approach to study the growth of the correlations among the particles and
in the radiation field. As an instructional example, we derive the Schrödinger–Klein–Gordon
system of equations from the Nelson model with ultraviolet cutoff and possibly
massless scalar field. In particular, we prove the convergence of the reduced
density matrices (of the nonrelativistic particles and the field bosons) associated
with the exact time evolution to the projectors onto the solutions of the Schrödinger–Klein–Gordon
equations in trace norm. Furthermore, we derive explicit bounds on the rate of
convergence of the one-particle reduced density matrix of the nonrelativistic
particles in Sobolev norm.
arxiv: 1
author:
- first_name: Nikolai K
full_name: Leopold, Nikolai K
id: 4BC40BEC-F248-11E8-B48F-1D18A9856A87
last_name: Leopold
orcid: 0000-0002-0495-6822
- first_name: Peter
full_name: Pickl, Peter
last_name: Pickl
citation:
ama: 'Leopold NK, Pickl P. Mean-field limits of particles in interaction with quantised
radiation fields. In: Vol 270. Springer; 2018:185-214. doi:10.1007/978-3-030-01602-9_9'
apa: 'Leopold, N. K., & Pickl, P. (2018). Mean-field limits of particles in
interaction with quantised radiation fields (Vol. 270, pp. 185–214). Presented
at the MaLiQS: Macroscopic Limits of Quantum Systems, Munich, Germany: Springer.
https://doi.org/10.1007/978-3-030-01602-9_9'
chicago: Leopold, Nikolai K, and Peter Pickl. “Mean-Field Limits of Particles in
Interaction with Quantised Radiation Fields,” 270:185–214. Springer, 2018. https://doi.org/10.1007/978-3-030-01602-9_9.
ieee: 'N. K. Leopold and P. Pickl, “Mean-field limits of particles in interaction
with quantised radiation fields,” presented at the MaLiQS: Macroscopic Limits
of Quantum Systems, Munich, Germany, 2018, vol. 270, pp. 185–214.'
ista: 'Leopold NK, Pickl P. 2018. Mean-field limits of particles in interaction
with quantised radiation fields. MaLiQS: Macroscopic Limits of Quantum Systems
vol. 270, 185–214.'
mla: Leopold, Nikolai K., and Peter Pickl. Mean-Field Limits of Particles in
Interaction with Quantised Radiation Fields. Vol. 270, Springer, 2018, pp.
185–214, doi:10.1007/978-3-030-01602-9_9.
short: N.K. Leopold, P. Pickl, in:, Springer, 2018, pp. 185–214.
conference:
end_date: 2017-04-01
location: Munich, Germany
name: 'MaLiQS: Macroscopic Limits of Quantum Systems'
start_date: 2017-03-30
date_created: 2018-12-11T11:44:08Z
date_published: 2018-10-27T00:00:00Z
date_updated: 2021-01-12T06:48:16Z
day: '27'
department:
- _id: RoSe
doi: 10.1007/978-3-030-01602-9_9
ec_funded: 1
external_id:
arxiv:
- '1806.10843'
intvolume: ' 270'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/1806.10843
month: '10'
oa: 1
oa_version: Preprint
page: 185 - 214
project:
- _id: 25C6DC12-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '694227'
name: Analysis of quantum many-body systems
publication_status: published
publisher: Springer
publist_id: '8045'
quality_controlled: '1'
scopus_import: 1
status: public
title: Mean-field limits of particles in interaction with quantised radiation fields
type: conference
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 270
year: '2018'
...
---
_id: '12'
abstract:
- lang: eng
text: Molding is a popular mass production method, in which the initial expenses
for the mold are offset by the low per-unit production cost. However, the physical
fabrication constraints of the molding technique commonly restrict the shape of
moldable objects. For a complex shape, a decomposition of the object into moldable
parts is a common strategy to address these constraints, with plastic model kits
being a popular and illustrative example. However, conducting such a decomposition
requires considerable expertise, and it depends on the technical aspects of the
fabrication technique, as well as aesthetic considerations. We present an interactive
technique to create such decompositions for two-piece molding, in which each part
of the object is cast between two rigid mold pieces. Given the surface description
of an object, we decompose its thin-shell equivalent into moldable parts by first
performing a coarse decomposition and then utilizing an active contour model for
the boundaries between individual parts. Formulated as an optimization problem,
the movement of the contours is guided by an energy reflecting fabrication constraints
to ensure the moldability of each part. Simultaneously, the user is provided with
editing capabilities to enforce aesthetic guidelines. Our interactive interface
provides control of the contour positions by allowing, for example, the alignment
of part boundaries with object features. Our technique enables a novel workflow,
as it empowers novice users to explore the design space, and it generates fabrication-ready
two-piece molds that can be used either for casting or industrial injection molding
of free-form objects.
article_number: '135'
article_processing_charge: No
author:
- first_name: Kazutaka
full_name: Nakashima, Kazutaka
last_name: Nakashima
- first_name: Thomas
full_name: Auzinger, Thomas
id: 4718F954-F248-11E8-B48F-1D18A9856A87
last_name: Auzinger
orcid: 0000-0002-1546-3265
- first_name: Emmanuel
full_name: Iarussi, Emmanuel
id: 33F19F16-F248-11E8-B48F-1D18A9856A87
last_name: Iarussi
- first_name: Ran
full_name: Zhang, Ran
id: 4DDBCEB0-F248-11E8-B48F-1D18A9856A87
last_name: Zhang
orcid: 0000-0002-3808-281X
- first_name: Takeo
full_name: Igarashi, Takeo
last_name: Igarashi
- first_name: Bernd
full_name: Bickel, Bernd
id: 49876194-F248-11E8-B48F-1D18A9856A87
last_name: Bickel
orcid: 0000-0001-6511-9385
citation:
ama: 'Nakashima K, Auzinger T, Iarussi E, Zhang R, Igarashi T, Bickel B. CoreCavity:
Interactive shell decomposition for fabrication with two-piece rigid molds. ACM
Transaction on Graphics. 2018;37(4). doi:10.1145/3197517.3201341'
apa: 'Nakashima, K., Auzinger, T., Iarussi, E., Zhang, R., Igarashi, T., & Bickel,
B. (2018). CoreCavity: Interactive shell decomposition for fabrication with two-piece
rigid molds. ACM Transaction on Graphics. ACM. https://doi.org/10.1145/3197517.3201341'
chicago: 'Nakashima, Kazutaka, Thomas Auzinger, Emmanuel Iarussi, Ran Zhang, Takeo
Igarashi, and Bernd Bickel. “CoreCavity: Interactive Shell Decomposition for Fabrication
with Two-Piece Rigid Molds.” ACM Transaction on Graphics. ACM, 2018. https://doi.org/10.1145/3197517.3201341.'
ieee: 'K. Nakashima, T. Auzinger, E. Iarussi, R. Zhang, T. Igarashi, and B. Bickel,
“CoreCavity: Interactive shell decomposition for fabrication with two-piece rigid
molds,” ACM Transaction on Graphics, vol. 37, no. 4. ACM, 2018.'
ista: 'Nakashima K, Auzinger T, Iarussi E, Zhang R, Igarashi T, Bickel B. 2018.
CoreCavity: Interactive shell decomposition for fabrication with two-piece rigid
molds. ACM Transaction on Graphics. 37(4), 135.'
mla: 'Nakashima, Kazutaka, et al. “CoreCavity: Interactive Shell Decomposition for
Fabrication with Two-Piece Rigid Molds.” ACM Transaction on Graphics, vol.
37, no. 4, 135, ACM, 2018, doi:10.1145/3197517.3201341.'
short: K. Nakashima, T. Auzinger, E. Iarussi, R. Zhang, T. Igarashi, B. Bickel,
ACM Transaction on Graphics 37 (2018).
date_created: 2018-12-11T11:44:09Z
date_published: 2018-08-04T00:00:00Z
date_updated: 2023-09-11T12:48:09Z
day: '04'
ddc:
- '004'
- '516'
- '670'
department:
- _id: BeBi
doi: 10.1145/3197517.3201341
ec_funded: 1
external_id:
isi:
- '000448185000096'
file:
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creator: system
date_created: 2018-12-12T10:18:38Z
date_updated: 2020-07-14T12:44:38Z
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creator: system
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date_updated: 2020-07-14T12:44:38Z
file_id: '5361'
file_name: IST-2018-1037-v1+2_CoreCavity-Supplemental.zip
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date_updated: 2020-07-14T12:44:38Z
file_id: '5363'
file_name: IST-2018-1037-v1+4_CoreCavity-RepresentativeImage.jpg
file_size: 527972
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has_accepted_license: '1'
intvolume: ' 37'
isi: 1
issue: '4'
language:
- iso: eng
month: '08'
oa: 1
oa_version: Submitted Version
project:
- _id: 24F9549A-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '715767'
name: 'MATERIALIZABLE: Intelligent fabrication-oriented Computational Design and
Modeling'
- _id: 2508E324-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '642841'
name: Distributed 3D Object Design
publication: ACM Transaction on Graphics
publication_status: published
publisher: ACM
publist_id: '8044'
pubrep_id: '1037'
quality_controlled: '1'
related_material:
link:
- description: News on IST Homepage
relation: press_release
url: https://ist.ac.at/en/news/interactive-software-tool-makes-complex-mold-design-simple/
scopus_import: '1'
status: public
title: 'CoreCavity: Interactive shell decomposition for fabrication with two-piece
rigid molds'
type: journal_article
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
volume: 37
year: '2018'
...
---
_id: '12193'
abstract:
- lang: eng
text: DNA methylation regulates eukaryotic gene expression and is extensively reprogrammed
during animal development. However, whether developmental methylation reprogramming
during the sporophytic life cycle of flowering plants regulates genes is presently
unknown. Here we report a distinctive gene-targeted RNA-directed DNA methylation
(RdDM) activity in the Arabidopsis thaliana male sexual lineage that regulates
gene expression in meiocytes. Loss of sexual-lineage-specific RdDM causes mis-splicing
of the MPS1 gene (also known as PRD2), thereby disrupting meiosis. Our results
establish a regulatory paradigm in which de novo methylation creates a cell-lineage-specific
epigenetic signature that controls gene expression and contributes to cellular
function in flowering plants.
acknowledgement: We thank Daniel Zilberman for intellectual contributions to this
work and assistance with manuscript preparation. We also thank Caroline Dean, Kirsten
Bomblies, Vinod Kumar, Siobhan Brady and Sophien Kamoun for comments on the manuscript,
Hugh Dickinson and Josephine Hellberg for developing the meiocyte isolation method,
Giles Oldroyd for the pGWB13-Bar vector, Elisa Fiume for the pMDC107-NTF vector,
Matthew Hartley, Matthew Couchman and Tjelvar Sten Gunnar Olsson for bioinformatics
support, and the John Innes Centre Bioimaging Facility (Elaine Barclay and Grant
Calder) for their assistance with microscopy. This work was funded by a Biotechnology
and Biological Sciences Research Council (BBSRC) David Phillips Fellowship (BBL0250431)
to X.F., a BBSRC grant (BBM01973X1) to J.H., and a Sainsbury PhD Studentship to
J.W.
article_processing_charge: No
article_type: original
author:
- first_name: James
full_name: Walker, James
last_name: Walker
- first_name: Hongbo
full_name: Gao, Hongbo
last_name: Gao
- first_name: Jingyi
full_name: Zhang, Jingyi
last_name: Zhang
- first_name: Billy
full_name: Aldridge, Billy
last_name: Aldridge
- first_name: Martin
full_name: Vickers, Martin
last_name: Vickers
- first_name: James D.
full_name: Higgins, James D.
last_name: Higgins
- first_name: Xiaoqi
full_name: Feng, Xiaoqi
id: e0164712-22ee-11ed-b12a-d80fcdf35958
last_name: Feng
orcid: 0000-0002-4008-1234
citation:
ama: Walker J, Gao H, Zhang J, et al. Sexual-lineage-specific DNA methylation regulates
meiosis in Arabidopsis. Nature Genetics. 2017;50(1):130-137. doi:10.1038/s41588-017-0008-5
apa: Walker, J., Gao, H., Zhang, J., Aldridge, B., Vickers, M., Higgins, J. D.,
& Feng, X. (2017). Sexual-lineage-specific DNA methylation regulates meiosis
in Arabidopsis. Nature Genetics. Nature Research. https://doi.org/10.1038/s41588-017-0008-5
chicago: Walker, James, Hongbo Gao, Jingyi Zhang, Billy Aldridge, Martin Vickers,
James D. Higgins, and Xiaoqi Feng. “Sexual-Lineage-Specific DNA Methylation Regulates
Meiosis in Arabidopsis.” Nature Genetics. Nature Research, 2017. https://doi.org/10.1038/s41588-017-0008-5.
ieee: J. Walker et al., “Sexual-lineage-specific DNA methylation regulates
meiosis in Arabidopsis,” Nature Genetics, vol. 50, no. 1. Nature Research,
pp. 130–137, 2017.
ista: Walker J, Gao H, Zhang J, Aldridge B, Vickers M, Higgins JD, Feng X. 2017.
Sexual-lineage-specific DNA methylation regulates meiosis in Arabidopsis. Nature
Genetics. 50(1), 130–137.
mla: Walker, James, et al. “Sexual-Lineage-Specific DNA Methylation Regulates Meiosis
in Arabidopsis.” Nature Genetics, vol. 50, no. 1, Nature Research, 2017,
pp. 130–37, doi:10.1038/s41588-017-0008-5.
short: J. Walker, H. Gao, J. Zhang, B. Aldridge, M. Vickers, J.D. Higgins, X. Feng,
Nature Genetics 50 (2017) 130–137.
date_created: 2023-01-16T09:18:05Z
date_published: 2017-12-18T00:00:00Z
date_updated: 2023-10-18T07:21:53Z
day: '18'
department:
- _id: XiFe
doi: 10.1038/s41588-017-0008-5
external_id:
pmid:
- '29255257'
intvolume: ' 50'
issue: '1'
keyword:
- Genetics
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7611288/
month: '12'
oa: 1
oa_version: None
page: 130-137
pmid: 1
publication: Nature Genetics
publication_identifier:
eissn:
- 1546-1718
issn:
- 1061-4036
publication_status: published
publisher: Nature Research
quality_controlled: '1'
scopus_import: '1'
status: public
title: Sexual-lineage-specific DNA methylation regulates meiosis in Arabidopsis
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 50
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
file_date_updated: 2020-07-14T12:44:39Z
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: '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:
- access_level: open_access
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
relation: main_file
file_date_updated: 2020-07-14T12:44:42Z
has_accepted_license: '1'
intvolume: ' 84'
isi: 1
language:
- iso: eng
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: '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
arxiv: 1
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: '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
file:
- access_level: open_access
checksum: c62257a7bff0c5f39e1abffc6bfcca5c
content_type: application/pdf
creator: system
date_created: 2018-12-12T10:17:00Z
date_updated: 2020-07-14T12:48:10Z
file_id: '5252'
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file_size: 3417773
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checksum: fc87d7d72fce52824a3ae7dcad0413a8
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: '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:
- '000'
degree_awarded: PhD
department:
- _id: KrCh
doi: 10.15479/AT:ISTA:th_854
ec_funded: 1
file:
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checksum: 3a3ec003f6ee73f41f82a544d63dfc77
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creator: system
date_created: 2018-12-12T10:11:44Z
date_updated: 2020-07-14T12:48:10Z
file_id: '4900'
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oa: 1
oa_version: Published Version
page: '418'
project:
- _id: 2584A770-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: P 23499-N23
name: Modern Graph Algorithmic Techniques in Formal Verification
- _id: 25832EC2-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: S 11407_N23
name: Rigorous Systems Engineering
- _id: 2581B60A-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '279307'
name: 'Quantitative Graph Games: Theory and Applications'
publication_identifier:
issn:
- 2663-337X
publication_status: published
publisher: Institute of Science and Technology Austria
publist_id: '6828'
pubrep_id: '854'
related_material:
record:
- 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
status: public
- 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
year: '2017'
...
---
_id: '822'
abstract:
- lang: eng
text: 'Polymicrobial infections constitute small ecosystems that accommodate several
bacterial species. Commonly, these bacteria are investigated in isolation. However,
it is unknown to what extent the isolates interact and whether their interactions
alter bacterial growth and ecosystem resilience in the presence and absence of
antibiotics. We quantified the complete ecological interaction network for 72
bacterial isolates collected from 23 individuals diagnosed with polymicrobial
urinary tract infections and found that most interactions cluster based on evolutionary
relatedness. Statistical network analysis revealed that competitive and cooperative
reciprocal interactions are enriched in the global network, while cooperative
interactions are depleted in the individual host community networks. A population
dynamics model parameterized by our measurements suggests that interactions restrict
community stability, explaining the observed species diversity of these communities.
We further show that the clinical isolates frequently protect each other from
clinically relevant antibiotics. Together, these results highlight that ecological
interactions are crucial for the growth and survival of bacteria in polymicrobial
infection communities and affect their assembly and resilience. '
article_processing_charge: No
author:
- first_name: Marjon
full_name: De Vos, Marjon
id: 3111FFAC-F248-11E8-B48F-1D18A9856A87
last_name: De Vos
- first_name: Marcin P
full_name: Zagórski, Marcin P
id: 343DA0DC-F248-11E8-B48F-1D18A9856A87
last_name: Zagórski
orcid: 0000-0001-7896-7762
- first_name: Alan
full_name: Mcnally, Alan
last_name: Mcnally
- first_name: Mark Tobias
full_name: Bollenbach, Mark Tobias
id: 3E6DB97A-F248-11E8-B48F-1D18A9856A87
last_name: Bollenbach
orcid: 0000-0003-4398-476X
citation:
ama: de Vos M, Zagórski MP, Mcnally A, Bollenbach MT. Interaction networks, ecological
stability, and collective antibiotic tolerance in polymicrobial infections. PNAS.
2017;114(40):10666-10671. doi:10.1073/pnas.1713372114
apa: de Vos, M., Zagórski, M. P., Mcnally, A., & Bollenbach, M. T. (2017). Interaction
networks, ecological stability, and collective antibiotic tolerance in polymicrobial
infections. PNAS. National Academy of Sciences. https://doi.org/10.1073/pnas.1713372114
chicago: Vos, Marjon de, Marcin P Zagórski, Alan Mcnally, and Mark Tobias Bollenbach.
“Interaction Networks, Ecological Stability, and Collective Antibiotic Tolerance
in Polymicrobial Infections.” PNAS. National Academy of Sciences, 2017.
https://doi.org/10.1073/pnas.1713372114.
ieee: M. de Vos, M. P. Zagórski, A. Mcnally, and M. T. Bollenbach, “Interaction
networks, ecological stability, and collective antibiotic tolerance in polymicrobial
infections,” PNAS, vol. 114, no. 40. National Academy of Sciences, pp.
10666–10671, 2017.
ista: de Vos M, Zagórski MP, Mcnally A, Bollenbach MT. 2017. Interaction networks,
ecological stability, and collective antibiotic tolerance in polymicrobial infections.
PNAS. 114(40), 10666–10671.
mla: de Vos, Marjon, et al. “Interaction Networks, Ecological Stability, and Collective
Antibiotic Tolerance in Polymicrobial Infections.” PNAS, vol. 114, no.
40, National Academy of Sciences, 2017, pp. 10666–71, doi:10.1073/pnas.1713372114.
short: M. de Vos, M.P. Zagórski, A. Mcnally, M.T. Bollenbach, PNAS 114 (2017) 10666–10671.
date_created: 2018-12-11T11:48:41Z
date_published: 2017-10-03T00:00:00Z
date_updated: 2023-09-26T16:18:48Z
day: '03'
department:
- _id: ToBo
doi: 10.1073/pnas.1713372114
ec_funded: 1
external_id:
isi:
- '000412130500061'
pmid:
- '28923953'
intvolume: ' 114'
isi: 1
issue: '40'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5635929/
month: '10'
oa: 1
oa_version: Submitted Version
page: 10666 - 10671
pmid: 1
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
publication: PNAS
publication_identifier:
issn:
- '00278424'
publication_status: published
publisher: National Academy of Sciences
publist_id: '6827'
quality_controlled: '1'
scopus_import: '1'
status: public
title: Interaction networks, ecological stability, and collective antibiotic tolerance
in polymicrobial infections
type: journal_article
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
volume: 114
year: '2017'
...
---
_id: '823'
abstract:
- lang: eng
text: The resolution of a linear system with positive integer variables is a basic
yet difficult computational problem with many applications. We consider sparse
uncorrelated random systems parametrised by the density c and the ratio α=N/M
between number of variables N and number of constraints M. By means of ensemble
calculations we show that the space of feasible solutions endows a Van-Der-Waals
phase diagram in the plane (c, α). We give numerical evidence that the associated
computational problems become more difficult across the critical point and in
particular in the coexistence region.
article_number: '093404'
article_processing_charge: No
author:
- first_name: Simona
full_name: Colabrese, Simona
last_name: Colabrese
- first_name: Daniele
full_name: De Martino, Daniele
id: 3FF5848A-F248-11E8-B48F-1D18A9856A87
last_name: De Martino
orcid: 0000-0002-5214-4706
- first_name: Luca
full_name: Leuzzi, Luca
last_name: Leuzzi
- first_name: Enzo
full_name: Marinari, Enzo
last_name: Marinari
citation:
ama: 'Colabrese S, De Martino D, Leuzzi L, Marinari E. Phase transitions in integer
linear problems. Journal of Statistical Mechanics: Theory and Experiment.
2017;2017(9). doi:10.1088/1742-5468/aa85c3'
apa: 'Colabrese, S., De Martino, D., Leuzzi, L., & Marinari, E. (2017). Phase
transitions in integer linear problems. Journal of Statistical Mechanics:
Theory and Experiment. IOPscience. https://doi.org/10.1088/1742-5468/aa85c3'
chicago: 'Colabrese, Simona, Daniele De Martino, Luca Leuzzi, and Enzo Marinari.
“Phase Transitions in Integer Linear Problems.” Journal of Statistical Mechanics:
Theory and Experiment. IOPscience, 2017. https://doi.org/10.1088/1742-5468/aa85c3.'
ieee: 'S. Colabrese, D. De Martino, L. Leuzzi, and E. Marinari, “Phase transitions
in integer linear problems,” Journal of Statistical Mechanics: Theory and
Experiment, vol. 2017, no. 9. IOPscience, 2017.'
ista: 'Colabrese S, De Martino D, Leuzzi L, Marinari E. 2017. Phase transitions
in integer linear problems. Journal of Statistical Mechanics: Theory and Experiment.
2017(9), 093404.'
mla: 'Colabrese, Simona, et al. “Phase Transitions in Integer Linear Problems.”
Journal of Statistical Mechanics: Theory and Experiment, vol. 2017, no.
9, 093404, IOPscience, 2017, doi:10.1088/1742-5468/aa85c3.'
short: 'S. Colabrese, D. De Martino, L. Leuzzi, E. Marinari, Journal of Statistical
Mechanics: Theory and Experiment 2017 (2017).'
date_created: 2018-12-11T11:48:41Z
date_published: 2017-09-26T00:00:00Z
date_updated: 2023-09-26T16:18:12Z
day: '26'
department:
- _id: GaTk
doi: 10.1088/1742-5468/aa85c3
ec_funded: 1
external_id:
isi:
- '000411842900001'
intvolume: ' 2017'
isi: 1
issue: '9'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/1705.06303
month: '09'
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: ' Journal of Statistical Mechanics: Theory and Experiment'
publication_identifier:
issn:
- '17425468'
publication_status: published
publisher: IOPscience
publist_id: '6826'
quality_controlled: '1'
scopus_import: '1'
status: public
title: Phase transitions in integer linear problems
type: journal_article
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
volume: 2017
year: '2017'
...
---
_id: '824'
abstract:
- lang: eng
text: 'In shear flows at transitional Reynolds numbers, localized patches of turbulence,
known as puffs, coexist with the laminar flow. Recently, Avila et al. (Phys. Rev.
Lett., vol. 110, 2013, 224502) discovered two spatially localized relative periodic
solutions for pipe flow, which appeared in a saddle-node bifurcation at low Reynolds
number. Combining slicing methods for continuous symmetry reduction with Poincaré
sections for the first time in a shear flow setting, we compute and visualize
the unstable manifold of the lower-branch solution and show that it extends towards
the neighbourhood of the upper-branch solution. Surprisingly, this connection
even persists far above the bifurcation point and appears to mediate the first
stage of the puff generation: amplification of streamwise localized fluctuations.
When the state-space trajectories on the unstable manifold reach the vicinity
of the upper branch, corresponding fluctuations expand in space and eventually
take the usual shape of a puff.'
article_number: R1
article_processing_charge: No
author:
- first_name: Nazmi B
full_name: Budanur, Nazmi B
id: 3EA1010E-F248-11E8-B48F-1D18A9856A87
last_name: Budanur
orcid: 0000-0003-0423-5010
- first_name: Björn
full_name: Hof, Björn
id: 3A374330-F248-11E8-B48F-1D18A9856A87
last_name: Hof
orcid: 0000-0003-2057-2754
citation:
ama: Budanur NB, Hof B. Heteroclinic path to spatially localized chaos in pipe flow.
Journal of Fluid Mechanics. 2017;827. doi:10.1017/jfm.2017.516
apa: Budanur, N. B., & Hof, B. (2017). Heteroclinic path to spatially localized
chaos in pipe flow. Journal of Fluid Mechanics. Cambridge University Press.
https://doi.org/10.1017/jfm.2017.516
chicago: Budanur, Nazmi B, and Björn Hof. “Heteroclinic Path to Spatially Localized
Chaos in Pipe Flow.” Journal of Fluid Mechanics. Cambridge University Press,
2017. https://doi.org/10.1017/jfm.2017.516.
ieee: N. B. Budanur and B. Hof, “Heteroclinic path to spatially localized chaos
in pipe flow,” Journal of Fluid Mechanics, vol. 827. Cambridge University
Press, 2017.
ista: Budanur NB, Hof B. 2017. Heteroclinic path to spatially localized chaos in
pipe flow. Journal of Fluid Mechanics. 827, R1.
mla: Budanur, Nazmi B., and Björn Hof. “Heteroclinic Path to Spatially Localized
Chaos in Pipe Flow.” Journal of Fluid Mechanics, vol. 827, R1, Cambridge
University Press, 2017, doi:10.1017/jfm.2017.516.
short: N.B. Budanur, B. Hof, Journal of Fluid Mechanics 827 (2017).
date_created: 2018-12-11T11:48:42Z
date_published: 2017-08-18T00:00:00Z
date_updated: 2023-09-26T16:17:43Z
day: '18'
department:
- _id: BjHo
doi: 10.1017/jfm.2017.516
external_id:
isi:
- '000408326300001'
intvolume: ' 827'
isi: 1
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/1703.10484
month: '08'
oa: 1
oa_version: Submitted Version
publication: Journal of Fluid Mechanics
publication_identifier:
issn:
- '00221120'
publication_status: published
publisher: Cambridge University Press
publist_id: '6824'
quality_controlled: '1'
scopus_import: '1'
status: public
title: Heteroclinic path to spatially localized chaos in pipe flow
type: journal_article
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
volume: 827
year: '2017'
...
---
_id: '833'
abstract:
- lang: eng
text: We present an efficient algorithm to compute Euler characteristic curves of
gray scale images of arbitrary dimension. In various applications the Euler characteristic
curve is used as a descriptor of an image. Our algorithm is the first streaming
algorithm for Euler characteristic curves. The usage of streaming removes the
necessity to store the entire image in RAM. Experiments show that our implementation
handles terabyte scale images on commodity hardware. Due to lock-free parallelism,
it scales well with the number of processor cores. Additionally, we put the concept
of the Euler characteristic curve in the wider context of computational topology.
In particular, we explain the connection with persistence diagrams.
alternative_title:
- LNCS
article_processing_charge: No
author:
- first_name: Teresa
full_name: Heiss, Teresa
id: 4879BB4E-F248-11E8-B48F-1D18A9856A87
last_name: Heiss
orcid: 0000-0002-1780-2689
- first_name: Hubert
full_name: Wagner, Hubert
id: 379CA8B8-F248-11E8-B48F-1D18A9856A87
last_name: Wagner
citation:
ama: 'Heiss T, Wagner H. Streaming algorithm for Euler characteristic curves of
multidimensional images. In: Felsberg M, Heyden A, Krüger N, eds. Vol 10424. Springer;
2017:397-409. doi:10.1007/978-3-319-64689-3_32'
apa: 'Heiss, T., & Wagner, H. (2017). Streaming algorithm for Euler characteristic
curves of multidimensional images. In M. Felsberg, A. Heyden, & N. Krüger
(Eds.) (Vol. 10424, pp. 397–409). Presented at the CAIP: Computer Analysis of
Images and Patterns, Ystad, Sweden: Springer. https://doi.org/10.1007/978-3-319-64689-3_32'
chicago: Heiss, Teresa, and Hubert Wagner. “Streaming Algorithm for Euler Characteristic
Curves of Multidimensional Images.” edited by Michael Felsberg, Anders Heyden,
and Norbert Krüger, 10424:397–409. Springer, 2017. https://doi.org/10.1007/978-3-319-64689-3_32.
ieee: 'T. Heiss and H. Wagner, “Streaming algorithm for Euler characteristic curves
of multidimensional images,” presented at the CAIP: Computer Analysis of Images
and Patterns, Ystad, Sweden, 2017, vol. 10424, pp. 397–409.'
ista: 'Heiss T, Wagner H. 2017. Streaming algorithm for Euler characteristic curves
of multidimensional images. CAIP: Computer Analysis of Images and Patterns, LNCS,
vol. 10424, 397–409.'
mla: Heiss, Teresa, and Hubert Wagner. Streaming Algorithm for Euler Characteristic
Curves of Multidimensional Images. Edited by Michael Felsberg et al., vol.
10424, Springer, 2017, pp. 397–409, doi:10.1007/978-3-319-64689-3_32.
short: T. Heiss, H. Wagner, in:, M. Felsberg, A. Heyden, N. Krüger (Eds.), Springer,
2017, pp. 397–409.
conference:
end_date: 2017-08-24
location: Ystad, Sweden
name: 'CAIP: Computer Analysis of Images and Patterns'
start_date: 2017-08-22
date_created: 2018-12-11T11:48:45Z
date_published: 2017-07-28T00:00:00Z
date_updated: 2023-09-26T16:10:03Z
day: '28'
department:
- _id: HeEd
doi: 10.1007/978-3-319-64689-3_32
editor:
- first_name: Michael
full_name: Felsberg, Michael
last_name: Felsberg
- first_name: Anders
full_name: Heyden, Anders
last_name: Heyden
- first_name: Norbert
full_name: Krüger, Norbert
last_name: Krüger
external_id:
isi:
- '000432085900032'
intvolume: ' 10424'
isi: 1
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/1705.02045
month: '07'
oa: 1
oa_version: Submitted Version
page: 397 - 409
publication_identifier:
issn:
- '03029743'
publication_status: published
publisher: Springer
publist_id: '6815'
quality_controlled: '1'
scopus_import: '1'
status: public
title: Streaming algorithm for Euler characteristic curves of multidimensional images
type: conference
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
volume: 10424
year: '2017'
...
---
_id: '834'
abstract:
- lang: eng
text: 'Thermal and many-body localized phases are separated by a dynamical phase
transition of a new kind. We analyze the distribution of off-diagonal matrix elements
of local operators across this transition in two different models of disordered
spin chains. We show that the behavior of matrix elements can be used to characterize
the breakdown of thermalization and to extract the many-body Thouless energy.
We find that upon increasing the disorder strength the system enters a critical
region around the many-body localization transition. The properties of the system
in this region are: (i) the Thouless energy becomes smaller than the level spacing,
(ii) the matrix elements show critical dependence on the energy difference, and
(iii) the matrix elements, viewed as amplitudes of a fictitious wave function,
exhibit strong multifractality. This critical region decreases with the system
size, which we interpret as evidence for a diverging correlation length at the
many-body localization transition. Our findings show that the correlation length
becomes larger than the accessible system sizes in a broad range of disorder strength
values and shed light on the critical behavior near the many-body localization
transition.'
acknowledgement: We acknowledge useful discussions with V. Kravtsov, T. Grover,
and R. Vasseur. M.S. was supported by Gordon and Betty Moore Foundation’s EPiQS
Initiative through Grant GBMF4307. M.S. and D.A. acknowledge hospitality of KITP, where parts of
this work were completed (supported in part by the National Science Foundation under
Grant No. NSF PHY11-25915)
article_number: '104201'
article_processing_charge: No
author:
- first_name: Maksym
full_name: Serbyn, Maksym
id: 47809E7E-F248-11E8-B48F-1D18A9856A87
last_name: Serbyn
orcid: 0000-0002-2399-5827
- first_name: Papic
full_name: Zlatko, Papic
last_name: Zlatko
- first_name: Dmitry
full_name: Abanin, Dmitry
last_name: Abanin
citation:
ama: Serbyn M, Zlatko P, Abanin D. Thouless energy and multifractality across the
many-body localization transition. Physical Review B - Condensed Matter and
Materials Physics. 2017;96(10). doi:10.1103/PhysRevB.96.104201
apa: Serbyn, M., Zlatko, P., & Abanin, D. (2017). Thouless energy and multifractality
across the many-body localization transition. Physical Review B - Condensed
Matter and Materials Physics. American Physical Society. https://doi.org/10.1103/PhysRevB.96.104201
chicago: Serbyn, Maksym, Papic Zlatko, and Dmitry Abanin. “Thouless Energy and Multifractality
across the Many-Body Localization Transition.” Physical Review B - Condensed
Matter and Materials Physics. American Physical Society, 2017. https://doi.org/10.1103/PhysRevB.96.104201.
ieee: M. Serbyn, P. Zlatko, and D. Abanin, “Thouless energy and multifractality
across the many-body localization transition,” Physical Review B - Condensed
Matter and Materials Physics, vol. 96, no. 10. American Physical Society,
2017.
ista: Serbyn M, Zlatko P, Abanin D. 2017. Thouless energy and multifractality across
the many-body localization transition. Physical Review B - Condensed Matter and
Materials Physics. 96(10), 104201.
mla: Serbyn, Maksym, et al. “Thouless Energy and Multifractality across the Many-Body
Localization Transition.” Physical Review B - Condensed Matter and Materials
Physics, vol. 96, no. 10, 104201, American Physical Society, 2017, doi:10.1103/PhysRevB.96.104201.
short: M. Serbyn, P. Zlatko, D. Abanin, Physical Review B - Condensed Matter and
Materials Physics 96 (2017).
date_created: 2018-12-11T11:48:45Z
date_published: 2017-09-06T00:00:00Z
date_updated: 2023-09-26T15:51:54Z
day: '06'
department:
- _id: MaSe
doi: 10.1103/PhysRevB.96.104201
external_id:
isi:
- '000409429300004'
intvolume: ' 96'
isi: 1
issue: '10'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/1610.02389
month: '09'
oa: 1
oa_version: Submitted Version
publication: Physical Review B - Condensed Matter and Materials Physics
publication_identifier:
issn:
- '24699950'
publication_status: published
publisher: American Physical Society
publist_id: '6814'
quality_controlled: '1'
scopus_import: '1'
status: public
title: Thouless energy and multifractality across the many-body localization transition
type: journal_article
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
volume: 96
year: '2017'
...
---
_id: '836'
abstract:
- lang: eng
text: Recent research has examined how to study the topological features of a continuous
self-map by means of the persistence of the eigenspaces, for given eigenvalues,
of the endomorphism induced in homology over a field. This raised the question
of how to select dynamically significant eigenvalues. The present paper aims to
answer this question, giving an algorithm that computes the persistence of eigenspaces
for every eigenvalue simultaneously, also expressing said eigenspaces as direct
sums of “finite” and “singular” subspaces.
alternative_title:
- PROMS
article_processing_charge: No
author:
- first_name: Marc
full_name: Ethier, Marc
last_name: Ethier
- first_name: Grzegorz
full_name: Jablonski, Grzegorz
id: 4483EF78-F248-11E8-B48F-1D18A9856A87
last_name: Jablonski
orcid: 0000-0002-3536-9866
- first_name: Marian
full_name: Mrozek, Marian
last_name: Mrozek
citation:
ama: 'Ethier M, Jablonski G, Mrozek M. Finding eigenvalues of self-maps with the
Kronecker canonical form. In: Special Sessions in Applications of Computer
Algebra. Vol 198. Springer; 2017:119-136. doi:10.1007/978-3-319-56932-1_8'
apa: 'Ethier, M., Jablonski, G., & Mrozek, M. (2017). Finding eigenvalues of
self-maps with the Kronecker canonical form. In Special Sessions in Applications
of Computer Algebra (Vol. 198, pp. 119–136). Kalamata, Greece: Springer. https://doi.org/10.1007/978-3-319-56932-1_8'
chicago: Ethier, Marc, Grzegorz Jablonski, and Marian Mrozek. “Finding Eigenvalues
of Self-Maps with the Kronecker Canonical Form.” In Special Sessions in Applications
of Computer Algebra, 198:119–36. Springer, 2017. https://doi.org/10.1007/978-3-319-56932-1_8.
ieee: M. Ethier, G. Jablonski, and M. Mrozek, “Finding eigenvalues of self-maps
with the Kronecker canonical form,” in Special Sessions in Applications of
Computer Algebra, Kalamata, Greece, 2017, vol. 198, pp. 119–136.
ista: 'Ethier M, Jablonski G, Mrozek M. 2017. Finding eigenvalues of self-maps with
the Kronecker canonical form. Special Sessions in Applications of Computer Algebra.
ACA: Applications of Computer Algebra, PROMS, vol. 198, 119–136.'
mla: Ethier, Marc, et al. “Finding Eigenvalues of Self-Maps with the Kronecker Canonical
Form.” Special Sessions in Applications of Computer Algebra, vol. 198,
Springer, 2017, pp. 119–36, doi:10.1007/978-3-319-56932-1_8.
short: M. Ethier, G. Jablonski, M. Mrozek, in:, Special Sessions in Applications
of Computer Algebra, Springer, 2017, pp. 119–136.
conference:
end_date: 2015-07-23
location: Kalamata, Greece
name: 'ACA: Applications of Computer Algebra'
start_date: 2015-07-20
date_created: 2018-12-11T11:48:46Z
date_published: 2017-07-27T00:00:00Z
date_updated: 2023-09-26T15:50:52Z
day: '27'
department:
- _id: HeEd
doi: 10.1007/978-3-319-56932-1_8
ec_funded: 1
external_id:
isi:
- '000434088200008'
intvolume: ' 198'
isi: 1
language:
- iso: eng
month: '07'
oa_version: None
page: 119 - 136
project:
- _id: 255D761E-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '318493'
name: Topological Complex Systems
publication: Special Sessions in Applications of Computer Algebra
publication_identifier:
isbn:
- 978-331956930-7
publication_status: published
publisher: Springer
publist_id: '6812'
quality_controlled: '1'
scopus_import: '1'
status: public
title: Finding eigenvalues of self-maps with the Kronecker canonical form
type: conference
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
volume: 198
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
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language:
- iso: eng
month: '08'
oa: 1
oa_version: Published Version
page: '93'
publication_identifier:
issn:
- 2663-337X
publication_status: published
publisher: Institute of Science and Technology Austria
publist_id: '6811'
pubrep_id: '858'
related_material:
record:
- 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: '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:
- _id: KrPi
doi: 10.15479/AT:ISTA:th_828
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language:
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month: '06'
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page: '86'
publication_identifier:
issn:
- 2663-337X
publication_status: published
publisher: Institute of Science and Technology Austria
publist_id: '6810'
pubrep_id: '828'
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relation: part_of_dissertation
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title: (The exact security of) Message authentication codes
type: dissertation
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
year: '2017'
...