---
_id: '19'
abstract:
- lang: eng
text: Bacteria regulate genes to survive antibiotic stress, but regulation can be
far from perfect. When regulation is not optimal, mutations that change gene expression
can contribute to antibiotic resistance. It is not systematically understood to
what extent natural gene regulation is or is not optimal for distinct antibiotics,
and how changes in expression of specific genes quantitatively affect antibiotic
resistance. Here we discover a simple quantitative relation between fitness, gene
expression, and antibiotic potency, which rationalizes our observation that a
multitude of genes and even innate antibiotic defense mechanisms have expression
that is critically nonoptimal under antibiotic treatment. First, we developed
a pooled-strain drug-diffusion assay and screened Escherichia coli overexpression
and knockout libraries, finding that resistance to a range of 31 antibiotics could
result from changing expression of a large and functionally diverse set of genes,
in a primarily but not exclusively drug-specific manner. Second, by synthetically
controlling the expression of single-drug and multidrug resistance genes, we observed
that their fitness-expression functions changed dramatically under antibiotic
treatment in accordance with a log-sensitivity relation. Thus, because many genes
are nonoptimally expressed under antibiotic treatment, many regulatory mutations
can contribute to resistance by altering expression and by activating latent defenses.
article_processing_charge: No
article_type: original
author:
- first_name: Adam
full_name: Palmer, Adam
last_name: Palmer
- first_name: Remy P
full_name: Chait, Remy P
id: 3464AE84-F248-11E8-B48F-1D18A9856A87
last_name: Chait
orcid: 0000-0003-0876-3187
- first_name: Roy
full_name: Kishony, Roy
last_name: Kishony
citation:
ama: Palmer A, Chait RP, Kishony R. Nonoptimal gene expression creates latent potential
for antibiotic resistance. Molecular Biology and Evolution. 2018;35(11):2669-2684.
doi:10.1093/molbev/msy163
apa: Palmer, A., Chait, R. P., & Kishony, R. (2018). Nonoptimal gene expression
creates latent potential for antibiotic resistance. Molecular Biology and Evolution.
Oxford University Press. https://doi.org/10.1093/molbev/msy163
chicago: Palmer, Adam, Remy P Chait, and Roy Kishony. “Nonoptimal Gene Expression
Creates Latent Potential for Antibiotic Resistance.” Molecular Biology and
Evolution. Oxford University Press, 2018. https://doi.org/10.1093/molbev/msy163.
ieee: A. Palmer, R. P. Chait, and R. Kishony, “Nonoptimal gene expression creates
latent potential for antibiotic resistance,” Molecular Biology and Evolution,
vol. 35, no. 11. Oxford University Press, pp. 2669–2684, 2018.
ista: Palmer A, Chait RP, Kishony R. 2018. Nonoptimal gene expression creates latent
potential for antibiotic resistance. Molecular Biology and Evolution. 35(11),
2669–2684.
mla: Palmer, Adam, et al. “Nonoptimal Gene Expression Creates Latent Potential for
Antibiotic Resistance.” Molecular Biology and Evolution, vol. 35, no. 11,
Oxford University Press, 2018, pp. 2669–84, doi:10.1093/molbev/msy163.
short: A. Palmer, R.P. Chait, R. Kishony, Molecular Biology and Evolution 35 (2018)
2669–2684.
date_created: 2018-12-11T11:44:11Z
date_published: 2018-08-28T00:00:00Z
date_updated: 2023-10-17T11:51:06Z
day: '28'
department:
- _id: CaGu
- _id: GaTk
doi: 10.1093/molbev/msy163
external_id:
isi:
- '000452567200006'
pmid:
- '30169679'
intvolume: ' 35'
isi: 1
issue: '11'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://www.ncbi.nlm.nih.gov/pubmed/30169679
month: '08'
oa: 1
oa_version: Submitted Version
page: 2669 - 2684
pmid: 1
publication: Molecular Biology and Evolution
publication_identifier:
issn:
- 0737-4038
publication_status: published
publisher: Oxford University Press
publist_id: '8036'
quality_controlled: '1'
scopus_import: '1'
status: public
title: Nonoptimal gene expression creates latent potential for antibiotic resistance
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 35
year: '2018'
...
---
_id: '190'
abstract:
- lang: eng
text: The German cockroach, Blattella germanica, is a worldwide pest that infests
buildings, including homes, restaurants, and hospitals, often living in unsanitary
conditions. As a disease vector and producer of allergens, this species has major
health and economic impacts on humans. Factors contributing to the success of
the German cockroach include its resistance to a broad range of insecticides,
immunity to many pathogens, and its ability, as an extreme generalist omnivore,
to survive on most food sources. The recently published genome shows that B. germanica
has an exceptionally high number of protein coding genes. In this study, we investigate
the functions of the 93 significantly expanded gene families with the aim to better
understand the success of B. germanica as a major pest despite such inhospitable
conditions. We find major expansions in gene families with functions related to
the detoxification of insecticides and allelochemicals, defense against pathogens,
digestion, sensory perception, and gene regulation. These expansions might have
allowed B. germanica to develop multiple resistance mechanisms to insecticides
and pathogens, and enabled a broad, flexible diet, thus explaining its success
in unsanitary conditions and under recurrent chemical control. The findings and
resources presented here provide insights for better understanding molecular mechanisms
that will facilitate more effective cockroach control.
article_processing_charge: No
article_type: original
author:
- first_name: Mark
full_name: Harrison, Mark
last_name: Harrison
- first_name: Nicolas
full_name: Arning, Nicolas
last_name: Arning
- first_name: Lucas
full_name: Kremer, Lucas
last_name: Kremer
- first_name: Guillem
full_name: Ylla, Guillem
last_name: Ylla
- first_name: Xavier
full_name: Belles, Xavier
last_name: Belles
- first_name: Erich
full_name: Bornberg Bauer, Erich
last_name: Bornberg Bauer
- first_name: Ann K
full_name: Huylmans, Ann K
id: 4C0A3874-F248-11E8-B48F-1D18A9856A87
last_name: Huylmans
orcid: 0000-0001-8871-4961
- first_name: Evelien
full_name: Jongepier, Evelien
last_name: Jongepier
- first_name: Maria
full_name: Puilachs, Maria
last_name: Puilachs
- first_name: Stephen
full_name: Richards, Stephen
last_name: Richards
- first_name: Coby
full_name: Schal, Coby
last_name: Schal
citation:
ama: 'Harrison M, Arning N, Kremer L, et al. Expansions of key protein families
in the German cockroach highlight the molecular basis of its remarkable success
as a global indoor pest. Journal of Experimental Zoology Part B: Molecular
and Developmental Evolution. 2018;330:254-264. doi:10.1002/jez.b.22824'
apa: 'Harrison, M., Arning, N., Kremer, L., Ylla, G., Belles, X., Bornberg Bauer,
E., … Schal, C. (2018). Expansions of key protein families in the German cockroach
highlight the molecular basis of its remarkable success as a global indoor pest.
Journal of Experimental Zoology Part B: Molecular and Developmental Evolution.
Wiley. https://doi.org/10.1002/jez.b.22824'
chicago: 'Harrison, Mark, Nicolas Arning, Lucas Kremer, Guillem Ylla, Xavier Belles,
Erich Bornberg Bauer, Ann K Huylmans, et al. “Expansions of Key Protein Families
in the German Cockroach Highlight the Molecular Basis of Its Remarkable Success
as a Global Indoor Pest.” Journal of Experimental Zoology Part B: Molecular
and Developmental Evolution. Wiley, 2018. https://doi.org/10.1002/jez.b.22824.'
ieee: 'M. Harrison et al., “Expansions of key protein families in the German
cockroach highlight the molecular basis of its remarkable success as a global
indoor pest,” Journal of Experimental Zoology Part B: Molecular and Developmental
Evolution, vol. 330. Wiley, pp. 254–264, 2018.'
ista: 'Harrison M, Arning N, Kremer L, Ylla G, Belles X, Bornberg Bauer E, Huylmans
AK, Jongepier E, Puilachs M, Richards S, Schal C. 2018. Expansions of key protein
families in the German cockroach highlight the molecular basis of its remarkable
success as a global indoor pest. Journal of Experimental Zoology Part B: Molecular
and Developmental Evolution. 330, 254–264.'
mla: 'Harrison, Mark, et al. “Expansions of Key Protein Families in the German Cockroach
Highlight the Molecular Basis of Its Remarkable Success as a Global Indoor Pest.”
Journal of Experimental Zoology Part B: Molecular and Developmental Evolution,
vol. 330, Wiley, 2018, pp. 254–64, doi:10.1002/jez.b.22824.'
short: 'M. Harrison, N. Arning, L. Kremer, G. Ylla, X. Belles, E. Bornberg Bauer,
A.K. Huylmans, E. Jongepier, M. Puilachs, S. Richards, C. Schal, Journal of Experimental
Zoology Part B: Molecular and Developmental Evolution 330 (2018) 254–264.'
date_created: 2018-12-11T11:45:06Z
date_published: 2018-07-11T00:00:00Z
date_updated: 2023-09-11T13:59:54Z
day: '11'
department:
- _id: BeVi
doi: 10.1002/jez.b.22824
external_id:
isi:
- '000443231000002'
pmid:
- '29998472'
intvolume: ' 330'
isi: 1
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://onlinelibrary.wiley.com/doi/am-pdf/10.1002/jez.b.22824
month: '07'
oa: 1
oa_version: Submitted Version
page: 254-264
pmid: 1
publication: 'Journal of Experimental Zoology Part B: Molecular and Developmental
Evolution'
publication_status: published
publisher: Wiley
publist_id: '7730'
quality_controlled: '1'
scopus_import: '1'
status: public
title: Expansions of key protein families in the German cockroach highlight the molecular
basis of its remarkable success as a global indoor pest
type: journal_article
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
volume: 330
year: '2018'
...
---
_id: '192'
abstract:
- lang: eng
text: The phytohormone auxin is the information carrier in a plethora of developmental
and physiological processes in plants(1). It has been firmly established that
canonical, nuclear auxin signalling acts through regulation of gene transcription(2).
Here, we combined microfluidics, live imaging, genetic engineering and computational
modelling to reanalyse the classical case of root growth inhibition(3) by auxin.
We show that Arabidopsis roots react to addition and removal of auxin by extremely
rapid adaptation of growth rate. This process requires intracellular auxin perception
but not transcriptional reprogramming. The formation of the canonical TIR1/AFB-Aux/IAA
co-receptor complex is required for the growth regulation, hinting to a novel,
non-transcriptional branch of this signalling pathway. Our results challenge the
current understanding of root growth regulation by auxin and suggest another,
presumably non-transcriptional, signalling output of the canonical auxin pathway.
article_processing_charge: No
article_type: original
author:
- first_name: Matyas
full_name: Fendrych, Matyas
id: 43905548-F248-11E8-B48F-1D18A9856A87
last_name: Fendrych
orcid: 0000-0002-9767-8699
- first_name: Maria
full_name: Akhmanova, Maria
id: 3425EC26-F248-11E8-B48F-1D18A9856A87
last_name: Akhmanova
orcid: 0000-0003-1522-3162
- first_name: Jack
full_name: Merrin, Jack
id: 4515C308-F248-11E8-B48F-1D18A9856A87
last_name: Merrin
orcid: 0000-0001-5145-4609
- first_name: Matous
full_name: Glanc, Matous
last_name: Glanc
- first_name: Shinya
full_name: Hagihara, Shinya
last_name: Hagihara
- first_name: Koji
full_name: Takahashi, Koji
last_name: Takahashi
- first_name: Naoyuki
full_name: Uchida, Naoyuki
last_name: Uchida
- first_name: Keiko U
full_name: Torii, Keiko U
last_name: Torii
- first_name: Jirí
full_name: Friml, Jirí
id: 4159519E-F248-11E8-B48F-1D18A9856A87
last_name: Friml
orcid: 0000-0002-8302-7596
citation:
ama: Fendrych M, Akhmanova M, Merrin J, et al. Rapid and reversible root growth
inhibition by TIR1 auxin signalling. Nature Plants. 2018;4(7):453-459.
doi:10.1038/s41477-018-0190-1
apa: Fendrych, M., Akhmanova, M., Merrin, J., Glanc, M., Hagihara, S., Takahashi,
K., … Friml, J. (2018). Rapid and reversible root growth inhibition by TIR1 auxin
signalling. Nature Plants. Springer Nature. https://doi.org/10.1038/s41477-018-0190-1
chicago: Fendrych, Matyas, Maria Akhmanova, Jack Merrin, Matous Glanc, Shinya Hagihara,
Koji Takahashi, Naoyuki Uchida, Keiko U Torii, and Jiří Friml. “Rapid and Reversible
Root Growth Inhibition by TIR1 Auxin Signalling.” Nature Plants. Springer
Nature, 2018. https://doi.org/10.1038/s41477-018-0190-1.
ieee: M. Fendrych et al., “Rapid and reversible root growth inhibition by
TIR1 auxin signalling,” Nature Plants, vol. 4, no. 7. Springer Nature,
pp. 453–459, 2018.
ista: Fendrych M, Akhmanova M, Merrin J, Glanc M, Hagihara S, Takahashi K, Uchida
N, Torii KU, Friml J. 2018. Rapid and reversible root growth inhibition by TIR1
auxin signalling. Nature Plants. 4(7), 453–459.
mla: Fendrych, Matyas, et al. “Rapid and Reversible Root Growth Inhibition by TIR1
Auxin Signalling.” Nature Plants, vol. 4, no. 7, Springer Nature, 2018,
pp. 453–59, doi:10.1038/s41477-018-0190-1.
short: M. Fendrych, M. Akhmanova, J. Merrin, M. Glanc, S. Hagihara, K. Takahashi,
N. Uchida, K.U. Torii, J. Friml, Nature Plants 4 (2018) 453–459.
date_created: 2018-12-11T11:45:07Z
date_published: 2018-06-25T00:00:00Z
date_updated: 2023-09-15T12:11:03Z
day: '25'
department:
- _id: JiFr
- _id: DaSi
- _id: NanoFab
doi: 10.1038/s41477-018-0190-1
external_id:
isi:
- '000443221200017'
pmid:
- '29942048'
intvolume: ' 4'
isi: 1
issue: '7'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://www.ncbi.nlm.nih.gov/pubmed/29942048
month: '06'
oa: 1
oa_version: Submitted Version
page: 453 - 459
pmid: 1
publication: Nature Plants
publication_status: published
publisher: Springer Nature
publist_id: '7728'
quality_controlled: '1'
related_material:
link:
- description: News on IST Homepage
relation: press_release
url: https://ist.ac.at/en/news/new-mechanism-for-the-plant-hormone-auxin-discovered/
scopus_import: '1'
status: public
title: Rapid and reversible root growth inhibition by TIR1 auxin signalling
type: journal_article
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
volume: 4
year: '2018'
...
---
_id: '193'
abstract:
- lang: eng
text: 'We show attacks on five data-independent memory-hard functions (iMHF) that
were submitted to the password hashing competition (PHC). Informally, an MHF is
a function which cannot be evaluated on dedicated hardware, like ASICs, at significantly
lower hardware and/or energy cost than evaluating a single instance on a standard
single-core architecture. Data-independent means the memory access pattern of
the function is independent of the input; this makes iMHFs harder to construct
than data-dependent ones, but the latter can be attacked by various side-channel
attacks. Following [Alwen-Blocki''16], we capture the evaluation of an iMHF as
a directed acyclic graph (DAG). The cumulative parallel pebbling complexity of
this DAG is a measure for the hardware cost of evaluating the iMHF on an ASIC.
Ideally, one would like the complexity of a DAG underlying an iMHF to be as close
to quadratic in the number of nodes of the graph as possible. Instead, we show
that (the DAGs underlying) the following iMHFs are far from this bound: Rig.v2,
TwoCats and Gambit each having an exponent no more than 1.75. Moreover, we show
that the complexity of the iMHF modes of the PHC finalists Pomelo and Lyra2 have
exponents at most 1.83 and 1.67 respectively. To show this we investigate a combinatorial
property of each underlying DAG (called its depth-robustness. By establishing
upper bounds on this property we are then able to apply the general technique
of [Alwen-Block''16] for analyzing the hardware costs of an iMHF.'
acknowledgement: Leonid Reyzin was supported in part by IST Austria and by US NSF
grants 1012910, 1012798, and 1422965; this research was performed while he was visiting
IST Austria.
article_processing_charge: No
author:
- first_name: Joel F
full_name: Alwen, Joel F
id: 2A8DFA8C-F248-11E8-B48F-1D18A9856A87
last_name: Alwen
- first_name: Peter
full_name: Gazi, Peter
last_name: Gazi
- first_name: Chethan
full_name: Kamath Hosdurg, Chethan
id: 4BD3F30E-F248-11E8-B48F-1D18A9856A87
last_name: Kamath Hosdurg
- first_name: Karen
full_name: Klein, Karen
id: 3E83A2F8-F248-11E8-B48F-1D18A9856A87
last_name: Klein
- first_name: Georg F
full_name: Osang, Georg F
id: 464B40D6-F248-11E8-B48F-1D18A9856A87
last_name: Osang
orcid: 0000-0002-8882-5116
- first_name: Krzysztof Z
full_name: Pietrzak, Krzysztof Z
id: 3E04A7AA-F248-11E8-B48F-1D18A9856A87
last_name: Pietrzak
orcid: 0000-0002-9139-1654
- first_name: Lenoid
full_name: Reyzin, Lenoid
last_name: Reyzin
- first_name: Michal
full_name: Rolinek, Michal
id: 3CB3BC06-F248-11E8-B48F-1D18A9856A87
last_name: Rolinek
- first_name: Michal
full_name: Rybar, Michal
id: 2B3E3DE8-F248-11E8-B48F-1D18A9856A87
last_name: Rybar
citation:
ama: 'Alwen JF, Gazi P, Kamath Hosdurg C, et al. On the memory hardness of data
independent password hashing functions. In: Proceedings of the 2018 on Asia
Conference on Computer and Communication Security. ACM; 2018:51-65. doi:10.1145/3196494.3196534'
apa: 'Alwen, J. F., Gazi, P., Kamath Hosdurg, C., Klein, K., Osang, G. F., Pietrzak,
K. Z., … Rybar, M. (2018). On the memory hardness of data independent password
hashing functions. In Proceedings of the 2018 on Asia Conference on Computer
and Communication Security (pp. 51–65). Incheon, Republic of Korea: ACM. https://doi.org/10.1145/3196494.3196534'
chicago: Alwen, Joel F, Peter Gazi, Chethan Kamath Hosdurg, Karen Klein, Georg F
Osang, Krzysztof Z Pietrzak, Lenoid Reyzin, Michal Rolinek, and Michal Rybar.
“On the Memory Hardness of Data Independent Password Hashing Functions.” In Proceedings
of the 2018 on Asia Conference on Computer and Communication Security, 51–65.
ACM, 2018. https://doi.org/10.1145/3196494.3196534.
ieee: J. F. Alwen et al., “On the memory hardness of data independent password
hashing functions,” in Proceedings of the 2018 on Asia Conference on Computer
and Communication Security, Incheon, Republic of Korea, 2018, pp. 51–65.
ista: 'Alwen JF, Gazi P, Kamath Hosdurg C, Klein K, Osang GF, Pietrzak KZ, Reyzin
L, Rolinek M, Rybar M. 2018. On the memory hardness of data independent password
hashing functions. Proceedings of the 2018 on Asia Conference on Computer and
Communication Security. ASIACCS: Asia Conference on Computer and Communications
Security , 51–65.'
mla: Alwen, Joel F., et al. “On the Memory Hardness of Data Independent Password
Hashing Functions.” Proceedings of the 2018 on Asia Conference on Computer
and Communication Security, ACM, 2018, pp. 51–65, doi:10.1145/3196494.3196534.
short: J.F. Alwen, P. Gazi, C. Kamath Hosdurg, K. Klein, G.F. Osang, K.Z. Pietrzak,
L. Reyzin, M. Rolinek, M. Rybar, in:, Proceedings of the 2018 on Asia Conference
on Computer and Communication Security, ACM, 2018, pp. 51–65.
conference:
end_date: 2018-06-08
location: Incheon, Republic of Korea
name: 'ASIACCS: Asia Conference on Computer and Communications Security '
start_date: 2018-06-04
date_created: 2018-12-11T11:45:07Z
date_published: 2018-06-01T00:00:00Z
date_updated: 2024-11-04T13:52:29Z
day: '01'
department:
- _id: KrPi
- _id: HeEd
- _id: VlKo
doi: 10.1145/3196494.3196534
ec_funded: 1
external_id:
isi:
- '000516620100005'
isi: 1
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://eprint.iacr.org/2016/783
month: '06'
oa: 1
oa_version: Submitted Version
page: 51 - 65
project:
- _id: 25FBA906-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '616160'
name: 'Discrete Optimization in Computer Vision: Theory and Practice'
- _id: 258AA5B2-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '682815'
name: Teaching Old Crypto New Tricks
publication: Proceedings of the 2018 on Asia Conference on Computer and Communication
Security
publication_status: published
publisher: ACM
publist_id: '7723'
quality_controlled: '1'
scopus_import: '1'
status: public
title: On the memory hardness of data independent password hashing functions
type: conference
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
year: '2018'
...
---
_id: '195'
abstract:
- lang: eng
text: We demonstrate that identical impurities immersed in a two-dimensional many-particle
bath can be viewed as flux-tube-charged-particle composites described by fractional
statistics. In particular, we find that the bath manifests itself as an external
magnetic flux tube with respect to the impurities, and hence the time-reversal
symmetry is broken for the effective Hamiltonian describing the impurities. The
emerging flux tube acts as a statistical gauge field after a certain critical
coupling. This critical coupling corresponds to the intersection point between
the quasiparticle state and the phonon wing, where the angular momentum is transferred
from the impurity to the bath. This amounts to a novel configuration with emerging
anyons. The proposed setup paves the way to realizing anyons using electrons interacting
with superfluid helium or lattice phonons, as well as using atomic impurities
in ultracold gases.
article_number: '045402'
article_processing_charge: No
arxiv: 1
author:
- first_name: Enderalp
full_name: Yakaboylu, Enderalp
id: 38CB71F6-F248-11E8-B48F-1D18A9856A87
last_name: Yakaboylu
orcid: 0000-0001-5973-0874
- first_name: Mikhail
full_name: Lemeshko, Mikhail
id: 37CB05FA-F248-11E8-B48F-1D18A9856A87
last_name: Lemeshko
orcid: 0000-0002-6990-7802
citation:
ama: Yakaboylu E, Lemeshko M. Anyonic statistics of quantum impurities in two dimensions.
Physical Review B - Condensed Matter and Materials Physics. 2018;98(4).
doi:10.1103/PhysRevB.98.045402
apa: Yakaboylu, E., & Lemeshko, M. (2018). Anyonic statistics of quantum impurities
in two dimensions. Physical Review B - Condensed Matter and Materials Physics.
American Physical Society. https://doi.org/10.1103/PhysRevB.98.045402
chicago: Yakaboylu, Enderalp, and Mikhail Lemeshko. “Anyonic Statistics of Quantum
Impurities in Two Dimensions.” Physical Review B - Condensed Matter and Materials
Physics. American Physical Society, 2018. https://doi.org/10.1103/PhysRevB.98.045402.
ieee: E. Yakaboylu and M. Lemeshko, “Anyonic statistics of quantum impurities in
two dimensions,” Physical Review B - Condensed Matter and Materials Physics,
vol. 98, no. 4. American Physical Society, 2018.
ista: Yakaboylu E, Lemeshko M. 2018. Anyonic statistics of quantum impurities in
two dimensions. Physical Review B - Condensed Matter and Materials Physics. 98(4),
045402.
mla: Yakaboylu, Enderalp, and Mikhail Lemeshko. “Anyonic Statistics of Quantum Impurities
in Two Dimensions.” Physical Review B - Condensed Matter and Materials Physics,
vol. 98, no. 4, 045402, American Physical Society, 2018, doi:10.1103/PhysRevB.98.045402.
short: E. Yakaboylu, M. Lemeshko, Physical Review B - Condensed Matter and Materials
Physics 98 (2018).
corr_author: '1'
date_created: 2018-12-11T11:45:08Z
date_published: 2018-07-15T00:00:00Z
date_updated: 2025-04-15T06:50:28Z
day: '15'
department:
- _id: MiLe
doi: 10.1103/PhysRevB.98.045402
ec_funded: 1
external_id:
arxiv:
- '1712.00308'
isi:
- '000436939100007'
intvolume: ' 98'
isi: 1
issue: '4'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/1712.00308
month: '07'
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
- _id: 26031614-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: P29902
name: Quantum rotations in the presence of a many-body environment
publication: Physical Review B - Condensed Matter and Materials Physics
publication_status: published
publisher: American Physical Society
quality_controlled: '1'
scopus_import: '1'
status: public
title: Anyonic statistics of quantum impurities in two dimensions
type: journal_article
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
volume: 98
year: '2018'
...
---
DOAJ_listed: '1'
OA_place: publisher
OA_type: gold
_id: '19544'
abstract:
- lang: eng
text: Medicinal bioinorganic chemistry is a thriving field of drug research for
cancer treatment. Transition metal complexes coordinated to essential biological
scaffolds represent a highly promising class of compounds for design of novel
target-specific therapeutics. We report here the biological evaluation of a novel
Isatin-Schiff base derivative and its Cu(II) complex in several tumor cell lines
by assessing their effects on cellular metabolism, real-time cell proliferation
and induction of apoptosis. Further, the impact of compounds on the p53 protein
and expression of its target genes, including MDM2, p21/CDKN1A, and PUMA was evaluated.
Results obtained in this study provide further evidence in support of our prior
data suggesting the p53-mediated mechanism of action for Isatin-Schiff base derivatives
and their complexes and also shed light on potential use of these compounds for
stimulation of apoptosis in breast cancer cells via activation of the pro-apoptotic
PUMA gene.
article_number: '103'
article_processing_charge: Yes
article_type: original
author:
- first_name: Emil
full_name: Bulatov, Emil
last_name: Bulatov
- first_name: Regina
full_name: Sayarova, Regina
last_name: Sayarova
- first_name: Rimma
full_name: Mingaleeva, Rimma
last_name: Mingaleeva
- first_name: Regina
full_name: Miftakhova, Regina
last_name: Miftakhova
- first_name: Marina
full_name: Gomzikova, Marina
last_name: Gomzikova
- first_name: Iurii
full_name: Ignatev, Iurii
id: 2ac71786-dc7d-11ea-9b2f-c5ad4b9faff6
last_name: Ignatev
- first_name: Alexey
full_name: Petukhov, Alexey
last_name: Petukhov
- first_name: Pavel
full_name: Davidovich, Pavel
last_name: Davidovich
- first_name: Albert
full_name: Rizvanov, Albert
last_name: Rizvanov
- first_name: Nickolai A.
full_name: Barlev, Nickolai A.
last_name: Barlev
citation:
ama: Bulatov E, Sayarova R, Mingaleeva R, et al. Isatin-Schiff base-copper (II)
complex induces cell death in p53-positive tumors. Cell Death Discovery.
2018;4. doi:10.1038/s41420-018-0120-z
apa: Bulatov, E., Sayarova, R., Mingaleeva, R., Miftakhova, R., Gomzikova, M., Ignatev,
I., … Barlev, N. A. (2018). Isatin-Schiff base-copper (II) complex induces cell
death in p53-positive tumors. Cell Death Discovery. Springer Nature. https://doi.org/10.1038/s41420-018-0120-z
chicago: Bulatov, Emil, Regina Sayarova, Rimma Mingaleeva, Regina Miftakhova, Marina
Gomzikova, Iurii Ignatev, Alexey Petukhov, Pavel Davidovich, Albert Rizvanov,
and Nickolai A. Barlev. “Isatin-Schiff Base-Copper (II) Complex Induces Cell Death
in P53-Positive Tumors.” Cell Death Discovery. Springer Nature, 2018. https://doi.org/10.1038/s41420-018-0120-z.
ieee: E. Bulatov et al., “Isatin-Schiff base-copper (II) complex induces
cell death in p53-positive tumors,” Cell Death Discovery, vol. 4. Springer
Nature, 2018.
ista: Bulatov E, Sayarova R, Mingaleeva R, Miftakhova R, Gomzikova M, Ignatev I,
Petukhov A, Davidovich P, Rizvanov A, Barlev NA. 2018. Isatin-Schiff base-copper
(II) complex induces cell death in p53-positive tumors. Cell Death Discovery.
4, 103.
mla: Bulatov, Emil, et al. “Isatin-Schiff Base-Copper (II) Complex Induces Cell
Death in P53-Positive Tumors.” Cell Death Discovery, vol. 4, 103, Springer
Nature, 2018, doi:10.1038/s41420-018-0120-z.
short: E. Bulatov, R. Sayarova, R. Mingaleeva, R. Miftakhova, M. Gomzikova, I. Ignatev,
A. Petukhov, P. Davidovich, A. Rizvanov, N.A. Barlev, Cell Death Discovery 4 (2018).
date_created: 2025-04-11T01:31:42Z
date_published: 2018-11-13T00:00:00Z
date_updated: 2025-07-10T11:51:52Z
day: '13'
ddc:
- '570'
department:
- _id: GradSch
- _id: LoSw
doi: 10.1038/s41420-018-0120-z
extern: '1'
external_id:
pmid:
- '30455989 '
has_accepted_license: '1'
intvolume: ' 4'
language:
- iso: eng
license: https://creativecommons.org/licenses/by/4.0/
main_file_link:
- open_access: '1'
url: https://doi.org/10.1038/s41420-018-0120-z
month: '11'
oa: 1
oa_version: Published Version
pmid: 1
publication: Cell Death Discovery
publication_identifier:
issn:
- 2058-7716
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
status: public
title: Isatin-Schiff base-copper (II) complex induces cell death in p53-positive tumors
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 4
year: '2018'
...
---
DOAJ_listed: '1'
OA_place: publisher
OA_type: gold
_id: '19706'
abstract:
- lang: eng
text: 'The importance of astrocytic l-lactate (LL) for normal functioning of neural
circuits such as those regulating learning/memory, sleep/wake state, autonomic
homeostasis, or emotional behaviour is being increasingly recognised. l-Lactate
can act on neurones as a metabolic or redox substrate, but transmembrane receptor
targets are also emerging. A comparative review of the hydroxy-carboxylic acid
receptor (HCA1, formerly known as GPR81), Olfactory Receptor Family 51 Subfamily
E Member 2 (OR51E2), and orphan receptor GPR4 highlights differences in their
LL sensitivity, pharmacology, intracellular coupling, and localisation in the
brain. In addition, a putative Gs-coupled receptor on noradrenergic neurones,
LLRx, which we previously postulated, remains to be identified. Next-generation
sequencing revealed several orphan receptors expressed in locus coeruleus neurones.
Screening of a selection of these suggests additional LL-sensitive receptors:
GPR180 which inhibits and GPR137 which activates intracellular cyclic AMP signalling
in response to LL in a heterologous expression system. To further characterise
binding of LL at LLRx, we carried out a structure–activity relationship study
which demonstrates that carboxyl and 2-hydroxyl moieties of LL are essential for
triggering d-lactate-sensitive noradrenaline release in locus coeruleus, and that
the size of the LL binding pocket is limited towards the methyl group position.
The evidence accumulating to date suggests that LL acts via multiple receptor
targets to modulate distinct brain functions.'
acknowledgement: This work was supported by grants from BBSRC BB/L019396/1, and MRC
MR/L020661/1. David Kleinfeld for his gift of CNiFER cells, Lesley Arberry for expert
technical support, Andrew Herman for support with FACS sorting.
article_processing_charge: Yes
article_type: original
author:
- first_name: Valentina
full_name: Mosienko, Valentina
last_name: Mosienko
- first_name: Seyed
full_name: Rasooli-Nejad, Seyed
last_name: Rasooli-Nejad
- first_name: Kasumi
full_name: Kishi, Kasumi
id: 3065DFC4-F248-11E8-B48F-1D18A9856A87
last_name: Kishi
- first_name: Matt
full_name: De Both, Matt
last_name: De Both
- first_name: David
full_name: Jane, David
last_name: Jane
- first_name: Matt J.
full_name: Huentelman, Matt J.
last_name: Huentelman
- first_name: Sergey
full_name: Kasparov, Sergey
last_name: Kasparov
- first_name: Anja G.
full_name: Teschemacher, Anja G.
last_name: Teschemacher
citation:
ama: Mosienko V, Rasooli-Nejad S, Kishi K, et al. Putative receptors underpinning
L-Lactate signalling in locus coeruleus. Neuroglia. 2018;1(2):365-380.
doi:10.3390/neuroglia1020025
apa: Mosienko, V., Rasooli-Nejad, S., Kishi, K., De Both, M., Jane, D., Huentelman,
M. J., … Teschemacher, A. G. (2018). Putative receptors underpinning L-Lactate
signalling in locus coeruleus. Neuroglia. MDPI. https://doi.org/10.3390/neuroglia1020025
chicago: Mosienko, Valentina, Seyed Rasooli-Nejad, Kasumi Kishi, Matt De Both, David
Jane, Matt J. Huentelman, Sergey Kasparov, and Anja G. Teschemacher. “Putative
Receptors Underpinning L-Lactate Signalling in Locus Coeruleus.” Neuroglia.
MDPI, 2018. https://doi.org/10.3390/neuroglia1020025.
ieee: V. Mosienko et al., “Putative receptors underpinning L-Lactate signalling
in locus coeruleus,” Neuroglia, vol. 1, no. 2. MDPI, pp. 365–380, 2018.
ista: Mosienko V, Rasooli-Nejad S, Kishi K, De Both M, Jane D, Huentelman MJ, Kasparov
S, Teschemacher AG. 2018. Putative receptors underpinning L-Lactate signalling
in locus coeruleus. Neuroglia. 1(2), 365–380.
mla: Mosienko, Valentina, et al. “Putative Receptors Underpinning L-Lactate Signalling
in Locus Coeruleus.” Neuroglia, vol. 1, no. 2, MDPI, 2018, pp. 365–80,
doi:10.3390/neuroglia1020025.
short: V. Mosienko, S. Rasooli-Nejad, K. Kishi, M. De Both, D. Jane, M.J. Huentelman,
S. Kasparov, A.G. Teschemacher, Neuroglia 1 (2018) 365–380.
date_created: 2025-05-18T22:02:51Z
date_published: 2018-12-01T00:00:00Z
date_updated: 2025-05-19T08:28:40Z
day: '01'
ddc:
- '570'
department:
- _id: AnKi
doi: 10.3390/neuroglia1020025
file:
- access_level: open_access
checksum: cadb56618f72edf4703b6a9855e84baa
content_type: application/pdf
creator: dernst
date_created: 2025-05-19T08:20:19Z
date_updated: 2025-05-19T08:20:19Z
file_id: '19711'
file_name: 2018_Neuroglia_Mosienko.pdf
file_size: 1909402
relation: main_file
success: 1
file_date_updated: 2025-05-19T08:20:19Z
has_accepted_license: '1'
intvolume: ' 1'
issue: '2'
language:
- iso: eng
month: '12'
oa: 1
oa_version: Published Version
page: 365-380
publication: Neuroglia
publication_identifier:
eissn:
- 2571-6980
publication_status: published
publisher: MDPI
quality_controlled: '1'
scopus_import: '1'
status: public
title: Putative receptors underpinning L-Lactate signalling in locus coeruleus
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 1
year: '2018'
...
---
_id: '148'
abstract:
- lang: eng
text: 'Land plants evolved from charophytic algae, among which Charophyceae possess
the most complex body plans. We present the genome of Chara braunii; comparison
of the genome to those of land plants identified evolutionary novelties for plant
terrestrialization and land plant heritage genes. C. braunii employs unique xylan
synthases for cell wall biosynthesis, a phragmoplast (cell separation) mechanism
similar to that of land plants, and many phytohormones. C. braunii plastids are
controlled via land-plant-like retrograde signaling, and transcriptional regulation
is more elaborate than in other algae. The morphological complexity of this organism
may result from expanded gene families, with three cases of particular note: genes
effecting tolerance to reactive oxygen species (ROS), LysM receptor-like kinases,
and transcription factors (TFs). Transcriptomic analysis of sexual reproductive
structures reveals intricate control by TFs, activity of the ROS gene network,
and the ancestral use of plant-like storage and stress protection proteins in
the zygote.'
acknowledgement: In-Data-Review
article_processing_charge: No
author:
- first_name: Tomoaki
full_name: Nishiyama, Tomoaki
last_name: Nishiyama
- first_name: Hidetoshi
full_name: Sakayama, Hidetoshi
last_name: Sakayama
- first_name: Jan
full_name: De Vries, Jan
last_name: De Vries
- first_name: Henrik
full_name: Buschmann, Henrik
last_name: Buschmann
- first_name: Denis
full_name: Saint Marcoux, Denis
last_name: Saint Marcoux
- first_name: Kristian
full_name: Ullrich, Kristian
last_name: Ullrich
- first_name: Fabian
full_name: Haas, Fabian
last_name: Haas
- first_name: Lisa
full_name: Vanderstraeten, Lisa
last_name: Vanderstraeten
- first_name: Dirk
full_name: Becker, Dirk
last_name: Becker
- first_name: Daniel
full_name: Lang, Daniel
last_name: Lang
- first_name: Stanislav
full_name: Vosolsobě, Stanislav
last_name: Vosolsobě
- first_name: Stephane
full_name: Rombauts, Stephane
last_name: Rombauts
- first_name: Per
full_name: Wilhelmsson, Per
last_name: Wilhelmsson
- first_name: Philipp
full_name: Janitza, Philipp
last_name: Janitza
- first_name: Ramona
full_name: Kern, Ramona
last_name: Kern
- first_name: Alexander
full_name: Heyl, Alexander
last_name: Heyl
- first_name: Florian
full_name: Rümpler, Florian
last_name: Rümpler
- first_name: Luz
full_name: Calderón Villalobos, Luz
last_name: Calderón Villalobos
- first_name: John
full_name: Clay, John
last_name: Clay
- first_name: Roman
full_name: Skokan, Roman
last_name: Skokan
- first_name: Atsushi
full_name: Toyoda, Atsushi
last_name: Toyoda
- first_name: Yutaka
full_name: Suzuki, Yutaka
last_name: Suzuki
- first_name: Hiroshi
full_name: Kagoshima, Hiroshi
last_name: Kagoshima
- first_name: Elio
full_name: Schijlen, Elio
last_name: Schijlen
- first_name: Navindra
full_name: Tajeshwar, Navindra
last_name: Tajeshwar
- first_name: Bruno
full_name: Catarino, Bruno
last_name: Catarino
- first_name: Alexander
full_name: Hetherington, Alexander
last_name: Hetherington
- first_name: Assia
full_name: Saltykova, Assia
last_name: Saltykova
- first_name: Clemence
full_name: Bonnot, Clemence
last_name: Bonnot
- first_name: Holger
full_name: Breuninger, Holger
last_name: Breuninger
- first_name: Aikaterini
full_name: Symeonidi, Aikaterini
last_name: Symeonidi
- first_name: Guru
full_name: Radhakrishnan, Guru
last_name: Radhakrishnan
- first_name: Filip
full_name: Van Nieuwerburgh, Filip
last_name: Van Nieuwerburgh
- first_name: Dieter
full_name: Deforce, Dieter
last_name: Deforce
- first_name: Caren
full_name: Chang, Caren
last_name: Chang
- first_name: Kenneth
full_name: Karol, Kenneth
last_name: Karol
- first_name: Rainer
full_name: Hedrich, Rainer
last_name: Hedrich
- first_name: Peter
full_name: Ulvskov, Peter
last_name: Ulvskov
- first_name: Gernot
full_name: Glöckner, Gernot
last_name: Glöckner
- first_name: Charles
full_name: Delwiche, Charles
last_name: Delwiche
- first_name: Jan
full_name: Petrášek, Jan
last_name: Petrášek
- first_name: Yves
full_name: Van De Peer, Yves
last_name: Van De Peer
- first_name: Jirí
full_name: Friml, Jirí
id: 4159519E-F248-11E8-B48F-1D18A9856A87
last_name: Friml
orcid: 0000-0002-8302-7596
- first_name: Mary
full_name: Beilby, Mary
last_name: Beilby
- first_name: Liam
full_name: Dolan, Liam
last_name: Dolan
- first_name: Yuji
full_name: Kohara, Yuji
last_name: Kohara
- first_name: Sumio
full_name: Sugano, Sumio
last_name: Sugano
- first_name: Asao
full_name: Fujiyama, Asao
last_name: Fujiyama
- first_name: Pierre Marc
full_name: Delaux, Pierre Marc
last_name: Delaux
- first_name: Marcel
full_name: Quint, Marcel
last_name: Quint
- first_name: Gunter
full_name: Theissen, Gunter
last_name: Theissen
- first_name: Martin
full_name: Hagemann, Martin
last_name: Hagemann
- first_name: Jesper
full_name: Harholt, Jesper
last_name: Harholt
- first_name: Christophe
full_name: Dunand, Christophe
last_name: Dunand
- first_name: Sabine
full_name: Zachgo, Sabine
last_name: Zachgo
- first_name: Jane
full_name: Langdale, Jane
last_name: Langdale
- first_name: Florian
full_name: Maumus, Florian
last_name: Maumus
- first_name: Dominique
full_name: Van Der Straeten, Dominique
last_name: Van Der Straeten
- first_name: Sven B
full_name: Gould, Sven B
last_name: Gould
- first_name: Stefan
full_name: Rensing, Stefan
last_name: Rensing
citation:
ama: 'Nishiyama T, Sakayama H, De Vries J, et al. The Chara genome: Secondary complexity
and implications for plant terrestrialization. Cell. 2018;174(2):448-464.e24.
doi:10.1016/j.cell.2018.06.033'
apa: 'Nishiyama, T., Sakayama, H., De Vries, J., Buschmann, H., Saint Marcoux, D.,
Ullrich, K., … Rensing, S. (2018). The Chara genome: Secondary complexity and
implications for plant terrestrialization. Cell. Cell Press. https://doi.org/10.1016/j.cell.2018.06.033'
chicago: 'Nishiyama, Tomoaki, Hidetoshi Sakayama, Jan De Vries, Henrik Buschmann,
Denis Saint Marcoux, Kristian Ullrich, Fabian Haas, et al. “The Chara Genome:
Secondary Complexity and Implications for Plant Terrestrialization.” Cell.
Cell Press, 2018. https://doi.org/10.1016/j.cell.2018.06.033.'
ieee: 'T. Nishiyama et al., “The Chara genome: Secondary complexity and implications
for plant terrestrialization,” Cell, vol. 174, no. 2. Cell Press, p. 448–464.e24,
2018.'
ista: 'Nishiyama T, Sakayama H, De Vries J, Buschmann H, Saint Marcoux D, Ullrich
K, Haas F, Vanderstraeten L, Becker D, Lang D, Vosolsobě S, Rombauts S, Wilhelmsson
P, Janitza P, Kern R, Heyl A, Rümpler F, Calderón Villalobos L, Clay J, Skokan
R, Toyoda A, Suzuki Y, Kagoshima H, Schijlen E, Tajeshwar N, Catarino B, Hetherington
A, Saltykova A, Bonnot C, Breuninger H, Symeonidi A, Radhakrishnan G, Van Nieuwerburgh
F, Deforce D, Chang C, Karol K, Hedrich R, Ulvskov P, Glöckner G, Delwiche C,
Petrášek J, Van De Peer Y, Friml J, Beilby M, Dolan L, Kohara Y, Sugano S, Fujiyama
A, Delaux PM, Quint M, Theissen G, Hagemann M, Harholt J, Dunand C, Zachgo S,
Langdale J, Maumus F, Van Der Straeten D, Gould SB, Rensing S. 2018. The Chara
genome: Secondary complexity and implications for plant terrestrialization. Cell.
174(2), 448–464.e24.'
mla: 'Nishiyama, Tomoaki, et al. “The Chara Genome: Secondary Complexity and Implications
for Plant Terrestrialization.” Cell, vol. 174, no. 2, Cell Press, 2018,
p. 448–464.e24, doi:10.1016/j.cell.2018.06.033.'
short: T. Nishiyama, H. Sakayama, J. De Vries, H. Buschmann, D. Saint Marcoux, K.
Ullrich, F. Haas, L. Vanderstraeten, D. Becker, D. Lang, S. Vosolsobě, S. Rombauts,
P. Wilhelmsson, P. Janitza, R. Kern, A. Heyl, F. Rümpler, L. Calderón Villalobos,
J. Clay, R. Skokan, A. Toyoda, Y. Suzuki, H. Kagoshima, E. Schijlen, N. Tajeshwar,
B. Catarino, A. Hetherington, A. Saltykova, C. Bonnot, H. Breuninger, A. Symeonidi,
G. Radhakrishnan, F. Van Nieuwerburgh, D. Deforce, C. Chang, K. Karol, R. Hedrich,
P. Ulvskov, G. Glöckner, C. Delwiche, J. Petrášek, Y. Van De Peer, J. Friml, M.
Beilby, L. Dolan, Y. Kohara, S. Sugano, A. Fujiyama, P.M. Delaux, M. Quint, G.
Theissen, M. Hagemann, J. Harholt, C. Dunand, S. Zachgo, J. Langdale, F. Maumus,
D. Van Der Straeten, S.B. Gould, S. Rensing, Cell 174 (2018) 448–464.e24.
date_created: 2018-12-11T11:44:53Z
date_published: 2018-07-12T00:00:00Z
date_updated: 2025-04-14T07:45:02Z
day: '12'
department:
- _id: JiFr
doi: 10.1016/j.cell.2018.06.033
ec_funded: 1
external_id:
isi:
- '000438482800019'
pmid:
- '30007417'
intvolume: ' 174'
isi: 1
issue: '2'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://www.ncbi.nlm.nih.gov/pubmed/30007417
month: '07'
oa: 1
oa_version: Published Version
page: 448 - 464.e24
pmid: 1
project:
- _id: 261099A6-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '742985'
name: Tracing Evolution of Auxin Transport and Polarity in Plants
publication: Cell
publication_status: published
publisher: Cell Press
publist_id: '7774'
quality_controlled: '1'
scopus_import: '1'
status: public
title: 'The Chara genome: Secondary complexity and implications for plant terrestrialization'
type: journal_article
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
volume: 174
year: '2018'
...
---
_id: '150'
abstract:
- lang: eng
text: A short, 14-amino-acid segment called SP1, located in the Gag structural protein1,
has a critical role during the formation of the HIV-1 virus particle. During virus
assembly, the SP1 peptide and seven preceding residues fold into a six-helix bundle,
which holds together the Gag hexamer and facilitates the formation of a curved
immature hexagonal lattice underneath the viral membrane2,3. Upon completion of
assembly and budding, proteolytic cleavage of Gag leads to virus maturation, in
which the immature lattice is broken down; the liberated CA domain of Gag then
re-assembles into the mature conical capsid that encloses the viral genome and
associated enzymes. Folding and proteolysis of the six-helix bundle are crucial
rate-limiting steps of both Gag assembly and disassembly, and the six-helix bundle
is an established target of HIV-1 inhibitors4,5. Here, using a combination of
structural and functional analyses, we show that inositol hexakisphosphate (InsP6,
also known as IP6) facilitates the formation of the six-helix bundle and assembly
of the immature HIV-1 Gag lattice. IP6 makes ionic contacts with two rings of
lysine residues at the centre of the Gag hexamer. Proteolytic cleavage then unmasks
an alternative binding site, where IP6 interaction promotes the assembly of the
mature capsid lattice. These studies identify IP6 as a naturally occurring small
molecule that promotes both assembly and maturation of HIV-1.
article_processing_charge: No
article_type: original
author:
- first_name: Robert
full_name: Dick, Robert
last_name: Dick
- first_name: Kaneil K
full_name: Zadrozny, Kaneil K
last_name: Zadrozny
- first_name: Chaoyi
full_name: Xu, Chaoyi
last_name: Xu
- first_name: Florian
full_name: Schur, Florian
id: 48AD8942-F248-11E8-B48F-1D18A9856A87
last_name: Schur
orcid: 0000-0003-4790-8078
- first_name: Terri D
full_name: Lyddon, Terri D
last_name: Lyddon
- first_name: Clifton L
full_name: Ricana, Clifton L
last_name: Ricana
- first_name: Jonathan M
full_name: Wagner, Jonathan M
last_name: Wagner
- first_name: Juan R
full_name: Perilla, Juan R
last_name: Perilla
- first_name: Pornillos Barbie K
full_name: Ganser, Pornillos Barbie K
last_name: Ganser
- first_name: Marc C
full_name: Johnson, Marc C
last_name: Johnson
- first_name: Owen
full_name: Pornillos, Owen
last_name: Pornillos
- first_name: Volker
full_name: Vogt, Volker
last_name: Vogt
citation:
ama: Dick R, Zadrozny KK, Xu C, et al. Inositol phosphates are assembly co-factors
for HIV-1. Nature. 2018;560(7719):509–512. doi:10.1038/s41586-018-0396-4
apa: Dick, R., Zadrozny, K. K., Xu, C., Schur, F. K., Lyddon, T. D., Ricana, C.
L., … Vogt, V. (2018). Inositol phosphates are assembly co-factors for HIV-1.
Nature. Nature Publishing Group. https://doi.org/10.1038/s41586-018-0396-4
chicago: Dick, Robert, Kaneil K Zadrozny, Chaoyi Xu, Florian KM Schur, Terri D Lyddon,
Clifton L Ricana, Jonathan M Wagner, et al. “Inositol Phosphates Are Assembly
Co-Factors for HIV-1.” Nature. Nature Publishing Group, 2018. https://doi.org/10.1038/s41586-018-0396-4.
ieee: R. Dick et al., “Inositol phosphates are assembly co-factors for HIV-1,”
Nature, vol. 560, no. 7719. Nature Publishing Group, pp. 509–512, 2018.
ista: Dick R, Zadrozny KK, Xu C, Schur FK, Lyddon TD, Ricana CL, Wagner JM, Perilla
JR, Ganser PBK, Johnson MC, Pornillos O, Vogt V. 2018. Inositol phosphates are
assembly co-factors for HIV-1. Nature. 560(7719), 509–512.
mla: Dick, Robert, et al. “Inositol Phosphates Are Assembly Co-Factors for HIV-1.”
Nature, vol. 560, no. 7719, Nature Publishing Group, 2018, pp. 509–512,
doi:10.1038/s41586-018-0396-4.
short: R. Dick, K.K. Zadrozny, C. Xu, F.K. Schur, T.D. Lyddon, C.L. Ricana, J.M.
Wagner, J.R. Perilla, P.B.K. Ganser, M.C. Johnson, O. Pornillos, V. Vogt, Nature
560 (2018) 509–512.
date_created: 2018-12-11T11:44:53Z
date_published: 2018-08-29T00:00:00Z
date_updated: 2023-09-12T07:44:37Z
day: '29'
department:
- _id: FlSc
doi: 10.1038/s41586-018-0396-4
external_id:
isi:
- '000442483400046'
pmid:
- '30158708'
intvolume: ' 560'
isi: 1
issue: '7719'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6242333/
month: '08'
oa: 1
oa_version: Submitted Version
page: 509–512
pmid: 1
publication: Nature
publication_identifier:
eissn:
- 1476-4687
publication_status: published
publisher: Nature Publishing Group
quality_controlled: '1'
related_material:
link:
- relation: erratum
url: https://doi.org/10.1038/s41586-018-0505-4
scopus_import: '1'
status: public
title: Inositol phosphates are assembly co-factors for HIV-1
type: journal_article
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
volume: 560
year: '2018'
...
---
_id: '152'
abstract:
- lang: eng
text: Complex I has an essential role in ATP production by coupling electron transfer
from NADH to quinone with translocation of protons across the inner mitochondrial
membrane. Isolated complex I deficiency is a frequent cause of mitochondrial inherited
diseases. Complex I has also been implicated in cancer, ageing, and neurodegenerative
conditions. Until recently, the understanding of complex I deficiency on the molecular
level was limited due to the lack of high-resolution structures of the enzyme.
However, due to developments in single particle cryo-electron microscopy (cryo-EM),
recent studies have reported nearly atomic resolution maps and models of mitochondrial
complex I. These structures significantly add to our understanding of complex
I mechanism and assembly. The disease-causing mutations are discussed here in
their structural context.
article_processing_charge: No
article_type: original
author:
- first_name: Karol
full_name: Fiedorczuk, Karol
id: 5BFF67CE-02D1-11E9-B11A-A5A4D7DFFFD0
last_name: Fiedorczuk
- first_name: Leonid A
full_name: Sazanov, Leonid A
id: 338D39FE-F248-11E8-B48F-1D18A9856A87
last_name: Sazanov
orcid: 0000-0002-0977-7989
citation:
ama: Fiedorczuk K, Sazanov LA. Mammalian mitochondrial complex I structure and disease
causing mutations. Trends in Cell Biology. 2018;28(10):835-867. doi:10.1016/j.tcb.2018.06.006
apa: Fiedorczuk, K., & Sazanov, L. A. (2018). Mammalian mitochondrial complex
I structure and disease causing mutations. Trends in Cell Biology. Elsevier.
https://doi.org/10.1016/j.tcb.2018.06.006
chicago: Fiedorczuk, Karol, and Leonid A Sazanov. “Mammalian Mitochondrial Complex
I Structure and Disease Causing Mutations.” Trends in Cell Biology. Elsevier,
2018. https://doi.org/10.1016/j.tcb.2018.06.006.
ieee: K. Fiedorczuk and L. A. Sazanov, “Mammalian mitochondrial complex I structure
and disease causing mutations,” Trends in Cell Biology, vol. 28, no. 10.
Elsevier, pp. 835–867, 2018.
ista: Fiedorczuk K, Sazanov LA. 2018. Mammalian mitochondrial complex I structure
and disease causing mutations. Trends in Cell Biology. 28(10), 835–867.
mla: Fiedorczuk, Karol, and Leonid A. Sazanov. “Mammalian Mitochondrial Complex
I Structure and Disease Causing Mutations.” Trends in Cell Biology, vol.
28, no. 10, Elsevier, 2018, pp. 835–67, doi:10.1016/j.tcb.2018.06.006.
short: K. Fiedorczuk, L.A. Sazanov, Trends in Cell Biology 28 (2018) 835–867.
date_created: 2018-12-11T11:44:54Z
date_published: 2018-07-26T00:00:00Z
date_updated: 2023-09-13T08:51:56Z
day: '26'
ddc:
- '572'
department:
- _id: LeSa
doi: 10.1016/j.tcb.2018.06.006
external_id:
isi:
- '000445118200007'
file:
- access_level: open_access
checksum: ef6d2b4e1fd63948539639242610bfa6
content_type: application/pdf
creator: lsazanov
date_created: 2019-11-07T12:55:20Z
date_updated: 2020-07-14T12:45:00Z
file_id: '6994'
file_name: SasanovFinalMS+EdComments_LS_allacc_withFigs.pdf
file_size: 2185385
relation: main_file
file_date_updated: 2020-07-14T12:45:00Z
has_accepted_license: '1'
intvolume: ' 28'
isi: 1
issue: '10'
language:
- iso: eng
license: https://creativecommons.org/licenses/by-nc-nd/4.0/
month: '07'
oa: 1
oa_version: Submitted Version
page: 835 - 867
publication: Trends in Cell Biology
publication_status: published
publisher: Elsevier
publist_id: '7769'
quality_controlled: '1'
scopus_import: '1'
status: public
title: Mammalian mitochondrial complex I structure and disease causing mutations
tmp:
image: /images/cc_by_nc_nd.png
legal_code_url: https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode
name: Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International
(CC BY-NC-ND 4.0)
short: CC BY-NC-ND (4.0)
type: journal_article
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
volume: 28
year: '2018'
...
---
_id: '153'
abstract:
- lang: eng
text: Cells migrating in multicellular organisms steadily traverse complex three-dimensional
(3D) environments. To decipher the underlying cell biology, current experimental
setups either use simplified 2D, tissue-mimetic 3D (e.g., collagen matrices) or
in vivo environments. While only in vivo experiments are truly physiological,
they do not allow for precise manipulation of environmental parameters. 2D in
vitro experiments do allow mechanical and chemical manipulations, but increasing
evidence demonstrates substantial differences of migratory mechanisms in 2D and
3D. Here, we describe simple, robust, and versatile “pillar forests” to investigate
cell migration in complex but fully controllable 3D environments. Pillar forests
are polydimethylsiloxane-based setups, in which two closely adjacent surfaces
are interconnected by arrays of micrometer-sized pillars. Changing the pillar
shape, size, height and the inter-pillar distance precisely manipulates microenvironmental
parameters (e.g., pore sizes, micro-geometry, micro-topology), while being easily
combined with chemotactic cues, surface coatings, diverse cell types and advanced
imaging techniques. Thus, pillar forests combine the advantages of 2D cell migration
assays with the precise definition of 3D environmental parameters.
article_processing_charge: No
author:
- first_name: Jörg
full_name: Renkawitz, Jörg
id: 3F0587C8-F248-11E8-B48F-1D18A9856A87
last_name: Renkawitz
orcid: 0000-0003-2856-3369
- first_name: Anne
full_name: Reversat, Anne
id: 35B76592-F248-11E8-B48F-1D18A9856A87
last_name: Reversat
orcid: 0000-0003-0666-8928
- first_name: Alexander F
full_name: Leithner, Alexander F
id: 3B1B77E4-F248-11E8-B48F-1D18A9856A87
last_name: Leithner
orcid: 0000-0002-1073-744X
- first_name: Jack
full_name: Merrin, Jack
id: 4515C308-F248-11E8-B48F-1D18A9856A87
last_name: Merrin
orcid: 0000-0001-5145-4609
- first_name: Michael K
full_name: Sixt, Michael K
id: 41E9FBEA-F248-11E8-B48F-1D18A9856A87
last_name: Sixt
orcid: 0000-0002-6620-9179
citation:
ama: 'Renkawitz J, Reversat A, Leithner AF, Merrin J, Sixt MK. Micro-engineered
“pillar forests” to study cell migration in complex but controlled 3D environments.
In: Methods in Cell Biology. Vol 147. Academic Press; 2018:79-91. doi:10.1016/bs.mcb.2018.07.004'
apa: Renkawitz, J., Reversat, A., Leithner, A. F., Merrin, J., & Sixt, M. K.
(2018). Micro-engineered “pillar forests” to study cell migration in complex but
controlled 3D environments. In Methods in Cell Biology (Vol. 147, pp. 79–91).
Academic Press. https://doi.org/10.1016/bs.mcb.2018.07.004
chicago: Renkawitz, Jörg, Anne Reversat, Alexander F Leithner, Jack Merrin, and
Michael K Sixt. “Micro-Engineered ‘Pillar Forests’ to Study Cell Migration in
Complex but Controlled 3D Environments.” In Methods in Cell Biology, 147:79–91.
Academic Press, 2018. https://doi.org/10.1016/bs.mcb.2018.07.004.
ieee: J. Renkawitz, A. Reversat, A. F. Leithner, J. Merrin, and M. K. Sixt, “Micro-engineered
‘pillar forests’ to study cell migration in complex but controlled 3D environments,”
in Methods in Cell Biology, vol. 147, Academic Press, 2018, pp. 79–91.
ista: 'Renkawitz J, Reversat A, Leithner AF, Merrin J, Sixt MK. 2018.Micro-engineered
“pillar forests” to study cell migration in complex but controlled 3D environments.
In: Methods in Cell Biology. vol. 147, 79–91.'
mla: Renkawitz, Jörg, et al. “Micro-Engineered ‘Pillar Forests’ to Study Cell Migration
in Complex but Controlled 3D Environments.” Methods in Cell Biology, vol.
147, Academic Press, 2018, pp. 79–91, doi:10.1016/bs.mcb.2018.07.004.
short: J. Renkawitz, A. Reversat, A.F. Leithner, J. Merrin, M.K. Sixt, in:, Methods
in Cell Biology, Academic Press, 2018, pp. 79–91.
date_created: 2018-12-11T11:44:54Z
date_published: 2018-07-27T00:00:00Z
date_updated: 2025-07-10T11:51:09Z
day: '27'
department:
- _id: MiSi
- _id: NanoFab
doi: 10.1016/bs.mcb.2018.07.004
external_id:
isi:
- '000452412300006'
pmid:
- '30165964'
intvolume: ' 147'
isi: 1
language:
- iso: eng
month: '07'
oa_version: None
page: 79 - 91
pmid: 1
publication: Methods in Cell Biology
publication_identifier:
issn:
- 0091-679X
publication_status: published
publisher: Academic Press
publist_id: '7768'
quality_controlled: '1'
scopus_import: '1'
status: public
title: Micro-engineered “pillar forests” to study cell migration in complex but controlled
3D environments
type: book_chapter
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 147
year: '2018'
...
---
_id: '106'
abstract:
- lang: eng
text: The goal of this article is to introduce the reader to the theory of intrinsic
geometry of convex surfaces. We illustrate the power of the tools by proving a
theorem on convex surfaces containing an arbitrarily long closed simple geodesic.
Let us remind ourselves that a curve in a surface is called geodesic if every
sufficiently short arc of the curve is length minimizing; if, in addition, it
has no self-intersections, we call it simple geodesic. A tetrahedron with equal
opposite edges is called isosceles. The axiomatic method of Alexandrov geometry
allows us to work with the metrics of convex surfaces directly, without approximating
it first by a smooth or polyhedral metric. Such approximations destroy the closed
geodesics on the surface; therefore it is difficult (if at all possible) to apply
approximations in the proof of our theorem. On the other hand, a proof in the
smooth or polyhedral case usually admits a translation into Alexandrov’s language;
such translation makes the result more general. In fact, our proof resembles a
translation of the proof given by Protasov. Note that the main theorem implies
in particular that a smooth convex surface does not have arbitrarily long simple
closed geodesics. However we do not know a proof of this corollary that is essentially
simpler than the one presented below.
article_processing_charge: No
arxiv: 1
author:
- first_name: Arseniy
full_name: Akopyan, Arseniy
id: 430D2C90-F248-11E8-B48F-1D18A9856A87
last_name: Akopyan
orcid: 0000-0002-2548-617X
- first_name: Anton
full_name: Petrunin, Anton
last_name: Petrunin
citation:
ama: Akopyan A, Petrunin A. Long geodesics on convex surfaces. Mathematical Intelligencer.
2018;40(3):26-31. doi:10.1007/s00283-018-9795-5
apa: Akopyan, A., & Petrunin, A. (2018). Long geodesics on convex surfaces.
Mathematical Intelligencer. Springer. https://doi.org/10.1007/s00283-018-9795-5
chicago: Akopyan, Arseniy, and Anton Petrunin. “Long Geodesics on Convex Surfaces.”
Mathematical Intelligencer. Springer, 2018. https://doi.org/10.1007/s00283-018-9795-5.
ieee: A. Akopyan and A. Petrunin, “Long geodesics on convex surfaces,” Mathematical
Intelligencer, vol. 40, no. 3. Springer, pp. 26–31, 2018.
ista: Akopyan A, Petrunin A. 2018. Long geodesics on convex surfaces. Mathematical
Intelligencer. 40(3), 26–31.
mla: Akopyan, Arseniy, and Anton Petrunin. “Long Geodesics on Convex Surfaces.”
Mathematical Intelligencer, vol. 40, no. 3, Springer, 2018, pp. 26–31,
doi:10.1007/s00283-018-9795-5.
short: A. Akopyan, A. Petrunin, Mathematical Intelligencer 40 (2018) 26–31.
date_created: 2018-12-11T11:44:40Z
date_published: 2018-09-01T00:00:00Z
date_updated: 2023-09-13T08:49:16Z
day: '01'
department:
- _id: HeEd
doi: 10.1007/s00283-018-9795-5
external_id:
arxiv:
- '1702.05172'
isi:
- '000444141200005'
intvolume: ' 40'
isi: 1
issue: '3'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/1702.05172
month: '09'
oa: 1
oa_version: Preprint
page: 26 - 31
publication: Mathematical Intelligencer
publication_status: published
publisher: Springer
publist_id: '7948'
quality_controlled: '1'
scopus_import: '1'
status: public
title: Long geodesics on convex surfaces
type: journal_article
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
volume: 40
year: '2018'
...
---
_id: '1064'
abstract:
- lang: eng
text: 'In 1945, A.W. Goodman and R.E. Goodman proved the following conjecture by
P. Erdős: Given a family of (round) disks of radii r1, … , rn in the plane, it
is always possible to cover them by a disk of radius R= ∑ ri, provided they cannot
be separated into two subfamilies by a straight line disjoint from the disks.
In this note we show that essentially the same idea may work for different analogues
and generalizations of their result. In particular, we prove the following: Given
a family of positive homothetic copies of a fixed convex body K⊂ Rd with homothety
coefficients τ1, … , τn> 0 , it is always possible to cover them by a translate
of d+12(∑τi)K, provided they cannot be separated into two subfamilies by a hyperplane
disjoint from the homothets.'
article_processing_charge: Yes (via OA deal)
article_type: original
author:
- first_name: Arseniy
full_name: Akopyan, Arseniy
id: 430D2C90-F248-11E8-B48F-1D18A9856A87
last_name: Akopyan
orcid: 0000-0002-2548-617X
- first_name: Alexey
full_name: Balitskiy, Alexey
last_name: Balitskiy
- first_name: Mikhail
full_name: Grigorev, Mikhail
last_name: Grigorev
citation:
ama: Akopyan A, Balitskiy A, Grigorev M. On the circle covering theorem by A.W.
Goodman and R.E. Goodman. Discrete & Computational Geometry. 2018;59(4):1001-1009.
doi:10.1007/s00454-017-9883-x
apa: Akopyan, A., Balitskiy, A., & Grigorev, M. (2018). On the circle covering
theorem by A.W. Goodman and R.E. Goodman. Discrete & Computational Geometry.
Springer. https://doi.org/10.1007/s00454-017-9883-x
chicago: Akopyan, Arseniy, Alexey Balitskiy, and Mikhail Grigorev. “On the Circle
Covering Theorem by A.W. Goodman and R.E. Goodman.” Discrete & Computational
Geometry. Springer, 2018. https://doi.org/10.1007/s00454-017-9883-x.
ieee: A. Akopyan, A. Balitskiy, and M. Grigorev, “On the circle covering theorem
by A.W. Goodman and R.E. Goodman,” Discrete & Computational Geometry,
vol. 59, no. 4. Springer, pp. 1001–1009, 2018.
ista: Akopyan A, Balitskiy A, Grigorev M. 2018. On the circle covering theorem by
A.W. Goodman and R.E. Goodman. Discrete & Computational Geometry. 59(4), 1001–1009.
mla: Akopyan, Arseniy, et al. “On the Circle Covering Theorem by A.W. Goodman and
R.E. Goodman.” Discrete & Computational Geometry, vol. 59, no. 4, Springer,
2018, pp. 1001–09, doi:10.1007/s00454-017-9883-x.
short: A. Akopyan, A. Balitskiy, M. Grigorev, Discrete & Computational Geometry
59 (2018) 1001–1009.
corr_author: '1'
date_created: 2018-12-11T11:49:57Z
date_published: 2018-06-01T00:00:00Z
date_updated: 2025-04-15T06:50:01Z
day: '01'
ddc:
- '516'
- '000'
department:
- _id: HeEd
doi: 10.1007/s00454-017-9883-x
ec_funded: 1
external_id:
isi:
- '000432205500011'
file:
- access_level: open_access
content_type: application/pdf
creator: dernst
date_created: 2019-01-18T09:27:36Z
date_updated: 2019-01-18T09:27:36Z
file_id: '5844'
file_name: 2018_DiscreteComp_Akopyan.pdf
file_size: 482518
relation: main_file
success: 1
file_date_updated: 2019-01-18T09:27:36Z
has_accepted_license: '1'
intvolume: ' 59'
isi: 1
issue: '4'
language:
- iso: eng
month: '06'
oa: 1
oa_version: Published Version
page: 1001-1009
project:
- _id: 25681D80-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '291734'
name: International IST Postdoc Fellowship Programme
publication: Discrete & Computational Geometry
publication_identifier:
eissn:
- '14320444'
issn:
- '01795376'
publication_status: published
publisher: Springer
publist_id: '6324'
quality_controlled: '1'
scopus_import: '1'
status: public
title: On the circle covering theorem by A.W. Goodman and R.E. Goodman
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: 59
year: '2018'
...
---
_id: '107'
abstract:
- lang: eng
text: 'We introduce the notion of “non-malleable codes” which relaxes the notion
of error correction and error detection. Informally, a code is non-malleable if
the message contained in a modified codeword is either the original message, or
a completely unrelated value. In contrast to error correction and error detection,
non-malleability can be achieved for very rich classes of modifications. We construct
an efficient code that is non-malleable with respect to modifications that affect
each bit of the codeword arbitrarily (i.e., leave it untouched, flip it, or set
it to either 0 or 1), but independently of the value of the other bits of the
codeword. Using the probabilistic method, we also show a very strong and general
statement: there exists a non-malleable code for every “small enough” family F
of functions via which codewords can be modified. Although this probabilistic
method argument does not directly yield efficient constructions, it gives us efficient
non-malleable codes in the random-oracle model for very general classes of tampering
functions—e.g., functions where every bit in the tampered codeword can depend
arbitrarily on any 99% of the bits in the original codeword. As an application
of non-malleable codes, we show that they provide an elegant algorithmic solution
to the task of protecting functionalities implemented in hardware (e.g., signature
cards) against “tampering attacks.” In such attacks, the secret state of a physical
system is tampered, in the hopes that future interaction with the modified system
will reveal some secret information. This problem was previously studied in the
work of Gennaro et al. in 2004 under the name “algorithmic tamper proof security”
(ATP). We show that non-malleable codes can be used to achieve important improvements
over the prior work. In particular, we show that any functionality can be made
secure against a large class of tampering attacks, simply by encoding the secret
state with a non-malleable code while it is stored in memory.'
article_number: '20'
article_processing_charge: No
article_type: original
author:
- first_name: Stefan
full_name: Dziembowski, Stefan
last_name: Dziembowski
- first_name: Krzysztof Z
full_name: Pietrzak, Krzysztof Z
id: 3E04A7AA-F248-11E8-B48F-1D18A9856A87
last_name: Pietrzak
orcid: 0000-0002-9139-1654
- first_name: Daniel
full_name: Wichs, Daniel
last_name: Wichs
citation:
ama: Dziembowski S, Pietrzak KZ, Wichs D. Non-malleable codes. Journal of the
ACM. 2018;65(4). doi:10.1145/3178432
apa: Dziembowski, S., Pietrzak, K. Z., & Wichs, D. (2018). Non-malleable codes.
Journal of the ACM. ACM. https://doi.org/10.1145/3178432
chicago: Dziembowski, Stefan, Krzysztof Z Pietrzak, and Daniel Wichs. “Non-Malleable
Codes.” Journal of the ACM. ACM, 2018. https://doi.org/10.1145/3178432.
ieee: S. Dziembowski, K. Z. Pietrzak, and D. Wichs, “Non-malleable codes,” Journal
of the ACM, vol. 65, no. 4. ACM, 2018.
ista: Dziembowski S, Pietrzak KZ, Wichs D. 2018. Non-malleable codes. Journal of
the ACM. 65(4), 20.
mla: Dziembowski, Stefan, et al. “Non-Malleable Codes.” Journal of the ACM,
vol. 65, no. 4, 20, ACM, 2018, doi:10.1145/3178432.
short: S. Dziembowski, K.Z. Pietrzak, D. Wichs, Journal of the ACM 65 (2018).
date_created: 2018-12-11T11:44:40Z
date_published: 2018-08-01T00:00:00Z
date_updated: 2025-04-14T07:22:06Z
day: '01'
department:
- _id: KrPi
doi: 10.1145/3178432
ec_funded: 1
external_id:
isi:
- '000442938200004'
intvolume: ' 65'
isi: 1
issue: '4'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://eprint.iacr.org/2009/608
month: '08'
oa: 1
oa_version: Preprint
project:
- _id: 258AA5B2-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '682815'
name: Teaching Old Crypto New Tricks
- _id: 258C570E-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '259668'
name: Provable Security for Physical Cryptography
publication: Journal of the ACM
publication_status: published
publisher: ACM
publist_id: '7947'
quality_controlled: '1'
scopus_import: '1'
status: public
title: Non-malleable codes
type: journal_article
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
volume: 65
year: '2018'
...
---
_id: '108'
abstract:
- lang: eng
text: Universal hashing found a lot of applications in computer science. In cryptography
the most important fact about universal families is the so called Leftover Hash
Lemma, proved by Impagliazzo, Levin and Luby. In the language of modern cryptography
it states that almost universal families are good extractors. In this work we
provide a somewhat surprising characterization in the opposite direction. Namely,
every extractor with sufficiently good parameters yields a universal family on
a noticeable fraction of its inputs. Our proof technique is based on tools from
extremal graph theory applied to the \'collision graph\' induced by the extractor,
and may be of independent interest. We discuss possible applications to the theory
of randomness extractors and non-malleable codes.
alternative_title:
- ISIT Proceedings
article_processing_charge: No
author:
- first_name: Marciej
full_name: Obremski, Marciej
last_name: Obremski
- first_name: Maciej
full_name: Skorski, Maciej
id: EC09FA6A-02D0-11E9-8223-86B7C91467DD
last_name: Skorski
citation:
ama: 'Obremski M, Skórski M. Inverted leftover hash lemma. In: Vol 2018. IEEE; 2018.
doi:10.1109/ISIT.2018.8437654'
apa: 'Obremski, M., & Skórski, M. (2018). Inverted leftover hash lemma (Vol.
2018). Presented at the ISIT: International Symposium on Information Theory, Vail,
CO, USA: IEEE. https://doi.org/10.1109/ISIT.2018.8437654'
chicago: Obremski, Marciej, and Maciej Skórski. “Inverted Leftover Hash Lemma,”
Vol. 2018. IEEE, 2018. https://doi.org/10.1109/ISIT.2018.8437654.
ieee: 'M. Obremski and M. Skórski, “Inverted leftover hash lemma,” presented at
the ISIT: International Symposium on Information Theory, Vail, CO, USA, 2018,
vol. 2018.'
ista: 'Obremski M, Skórski M. 2018. Inverted leftover hash lemma. ISIT: International
Symposium on Information Theory, ISIT Proceedings, vol. 2018.'
mla: Obremski, Marciej, and Maciej Skórski. Inverted Leftover Hash Lemma.
Vol. 2018, IEEE, 2018, doi:10.1109/ISIT.2018.8437654.
short: M. Obremski, M. Skórski, in:, IEEE, 2018.
conference:
end_date: 2018-06-22
location: Vail, CO, USA
name: 'ISIT: International Symposium on Information Theory'
start_date: '2018-06-17 '
date_created: 2018-12-11T11:44:40Z
date_published: 2018-08-16T00:00:00Z
date_updated: 2023-09-13T08:23:18Z
day: '16'
department:
- _id: KrPi
doi: 10.1109/ISIT.2018.8437654
external_id:
isi:
- '000448139300368'
intvolume: ' 2018'
isi: 1
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://eprint.iacr.org/2017/507
month: '08'
oa: 1
oa_version: Submitted Version
publication_status: published
publisher: IEEE
publist_id: '7946'
quality_controlled: '1'
scopus_import: '1'
status: public
title: Inverted leftover hash lemma
type: conference
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
volume: 2018
year: '2018'
...
---
_id: '10864'
abstract:
- lang: eng
text: We prove that every congruence distributive variety has directed Jónsson terms,
and every congruence modular variety has directed Gumm terms. The directed terms
we construct witness every case of absorption witnessed by the original Jónsson
or Gumm terms. This result is equivalent to a pair of claims about absorption
for admissible preorders in congruence distributive and congruence modular varieties,
respectively. For finite algebras, these absorption theorems have already seen
significant applications, but until now, it was not clear if the theorems hold
for general algebras as well. Our method also yields a novel proof of a result
by P. Lipparini about the existence of a chain of terms (which we call Pixley
terms) in varieties that are at the same time congruence distributive and k-permutable
for some k.
acknowledgement: The second author was supported by National Science Center grant
DEC-2011-/01/B/ST6/01006.
article_processing_charge: No
arxiv: 1
author:
- first_name: Alexandr
full_name: Kazda, Alexandr
id: 3B32BAA8-F248-11E8-B48F-1D18A9856A87
last_name: Kazda
- first_name: Marcin
full_name: Kozik, Marcin
last_name: Kozik
- first_name: Ralph
full_name: McKenzie, Ralph
last_name: McKenzie
- first_name: Matthew
full_name: Moore, Matthew
last_name: Moore
citation:
ama: 'Kazda A, Kozik M, McKenzie R, Moore M. Absorption and directed Jónsson terms.
In: Czelakowski J, ed. Don Pigozzi on Abstract Algebraic Logic, Universal Algebra,
and Computer Science. Vol 16. OCTR. Cham: Springer Nature; 2018:203-220. doi:10.1007/978-3-319-74772-9_7'
apa: 'Kazda, A., Kozik, M., McKenzie, R., & Moore, M. (2018). Absorption and
directed Jónsson terms. In J. Czelakowski (Ed.), Don Pigozzi on Abstract Algebraic
Logic, Universal Algebra, and Computer Science (Vol. 16, pp. 203–220). Cham:
Springer Nature. https://doi.org/10.1007/978-3-319-74772-9_7'
chicago: 'Kazda, Alexandr, Marcin Kozik, Ralph McKenzie, and Matthew Moore. “Absorption
and Directed Jónsson Terms.” In Don Pigozzi on Abstract Algebraic Logic, Universal
Algebra, and Computer Science, edited by J Czelakowski, 16:203–20. OCTR. Cham:
Springer Nature, 2018. https://doi.org/10.1007/978-3-319-74772-9_7.'
ieee: 'A. Kazda, M. Kozik, R. McKenzie, and M. Moore, “Absorption and directed Jónsson
terms,” in Don Pigozzi on Abstract Algebraic Logic, Universal Algebra, and
Computer Science, vol. 16, J. Czelakowski, Ed. Cham: Springer Nature, 2018,
pp. 203–220.'
ista: 'Kazda A, Kozik M, McKenzie R, Moore M. 2018.Absorption and directed Jónsson
terms. In: Don Pigozzi on Abstract Algebraic Logic, Universal Algebra, and Computer
Science. vol. 16, 203–220.'
mla: Kazda, Alexandr, et al. “Absorption and Directed Jónsson Terms.” Don Pigozzi
on Abstract Algebraic Logic, Universal Algebra, and Computer Science, edited
by J Czelakowski, vol. 16, Springer Nature, 2018, pp. 203–20, doi:10.1007/978-3-319-74772-9_7.
short: A. Kazda, M. Kozik, R. McKenzie, M. Moore, in:, J. Czelakowski (Ed.), Don
Pigozzi on Abstract Algebraic Logic, Universal Algebra, and Computer Science,
Springer Nature, Cham, 2018, pp. 203–220.
corr_author: '1'
date_created: 2022-03-18T10:30:32Z
date_published: 2018-03-21T00:00:00Z
date_updated: 2024-10-09T21:01:50Z
day: '21'
department:
- _id: VlKo
doi: 10.1007/978-3-319-74772-9_7
editor:
- first_name: J
full_name: Czelakowski, J
last_name: Czelakowski
external_id:
arxiv:
- '1502.01072'
intvolume: ' 16'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/1502.01072
month: '03'
oa: 1
oa_version: Preprint
page: 203-220
place: Cham
publication: Don Pigozzi on Abstract Algebraic Logic, Universal Algebra, and Computer
Science
publication_identifier:
eisbn:
- '9783319747729'
eissn:
- 2211-2766
isbn:
- '9783319747712'
issn:
- 2211-2758
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
scopus_import: '1'
series_title: OCTR
status: public
title: Absorption and directed Jónsson terms
type: book_chapter
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
volume: 16
year: '2018'
...
---
_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.
corr_author: '1'
date_created: 2022-03-18T12:40:35Z
date_published: 2018-09-01T00:00:00Z
date_updated: 2024-10-09T21:01:52Z
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: 2025-04-15T07:48:01Z
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
corr_author: '1'
date_created: 2022-03-18T12:45:09Z
date_published: 2018-12-17T00:00:00Z
date_updated: 2024-10-09T21:02:26Z
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 M, 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., & 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 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. 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 M, Svozil A. 2018. Quasipolynomial set-based
symbolic algorithms for parity games. 22nd International Conference on Logic for
Programming, Artificial Intelligence and Reasoning. LPAR: 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. Henzinger, A. Svozil, in:, 22nd International
Conference on Logic for Programming, Artificial Intelligence and Reasoning, EasyChair,
2018, pp. 233–253.
conference:
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title: Quasipolynomial set-based symbolic algorithms for parity games
type: conference
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...