---
_id: '5996'
abstract:
- lang: eng
text: 'In pipes, turbulence sets in despite the linear stability of the laminar
Hagen–Poiseuille flow. The Reynolds number ( ) for which turbulence first appears
in a given experiment – the ‘natural transition point’ – depends on imperfections
of the set-up, or, more precisely, on the magnitude of finite amplitude perturbations.
At onset, turbulence typically only occupies a certain fraction of the flow, and
this fraction equally is found to differ from experiment to experiment. Despite
these findings, Reynolds proposed that after sufficiently long times, flows may
settle to steady conditions: below a critical velocity, flows should (regardless
of initial conditions) always return to laminar, while above this velocity, eddying
motion should persist. As will be shown, even in pipes several thousand diameters
long, the spatio-temporal intermittent flow patterns observed at the end of the
pipe strongly depend on the initial conditions, and there is no indication that
different flow patterns would eventually settle to a (statistical) steady state.
Exploiting the fact that turbulent puffs do not age (i.e. they are memoryless),
we continuously recreate the puff sequence exiting the pipe at the pipe entrance,
and in doing so introduce periodic boundary conditions for the puff pattern. This
procedure allows us to study the evolution of the flow patterns for arbitrary
long times, and we find that after times in excess of advective time units, indeed
a statistical steady state is reached. Although the resulting flows remain spatio-temporally
intermittent, puff splitting and decay rates eventually reach a balance, so that
the turbulent fraction fluctuates around a well-defined level which only depends
on . In accordance with Reynolds’ proposition, we find that at lower (here 2020),
flows eventually always resume to laminar, while for higher ( ), turbulence persists.
The critical point for pipe flow hence falls in the interval of $2020 , which
is in very good agreement with the recently proposed value of . The latter estimate
was based on single-puff statistics and entirely neglected puff interactions.
Unlike in typical contact processes where such interactions strongly affect the
percolation threshold, in pipe flow, the critical point is only marginally influenced.
Interactions, on the other hand, are responsible for the approach to the statistical
steady state. As shown, they strongly affect the resulting flow patterns, where
they cause ‘puff clustering’, and these regions of large puff densities are observed
to travel across the puff pattern in a wave-like fashion.'
acknowledgement: ' We also thank Philipp Maier and the IST Austria workshop for theirdedicated
technical support'
article_processing_charge: No
article_type: original
author:
- first_name: Mukund
full_name: Vasudevan, Mukund
id: 3C5A959A-F248-11E8-B48F-1D18A9856A87
last_name: Vasudevan
- first_name: Björn
full_name: Hof, Björn
id: 3A374330-F248-11E8-B48F-1D18A9856A87
last_name: Hof
orcid: 0000-0003-2057-2754
citation:
ama: Vasudevan M, Hof B. The critical point of the transition to turbulence in pipe
flow. Journal of Fluid Mechanics. 2018;839:76-94. doi:10.1017/jfm.2017.923
apa: Vasudevan, M., & Hof, B. (2018). The critical point of the transition to
turbulence in pipe flow. Journal of Fluid Mechanics. Cambridge University
Press. https://doi.org/10.1017/jfm.2017.923
chicago: Vasudevan, Mukund, and Björn Hof. “The Critical Point of the Transition
to Turbulence in Pipe Flow.” Journal of Fluid Mechanics. Cambridge University
Press, 2018. https://doi.org/10.1017/jfm.2017.923.
ieee: M. Vasudevan and B. Hof, “The critical point of the transition to turbulence
in pipe flow,” Journal of Fluid Mechanics, vol. 839. Cambridge University
Press, pp. 76–94, 2018.
ista: Vasudevan M, Hof B. 2018. The critical point of the transition to turbulence
in pipe flow. Journal of Fluid Mechanics. 839, 76–94.
mla: Vasudevan, Mukund, and Björn Hof. “The Critical Point of the Transition to
Turbulence in Pipe Flow.” Journal of Fluid Mechanics, vol. 839, Cambridge
University Press, 2018, pp. 76–94, doi:10.1017/jfm.2017.923.
short: M. Vasudevan, B. Hof, Journal of Fluid Mechanics 839 (2018) 76–94.
date_created: 2019-02-14T12:50:50Z
date_published: 2018-03-25T00:00:00Z
date_updated: 2023-09-19T14:37:49Z
day: '25'
department:
- _id: BjHo
doi: 10.1017/jfm.2017.923
ec_funded: 1
external_id:
arxiv:
- '1709.06372'
isi:
- '000437858300003'
intvolume: ' 839'
isi: 1
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/1709.06372
month: '03'
oa: 1
oa_version: Preprint
page: 76-94
project:
- _id: 25152F3A-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '306589'
name: Decoding the complexity of turbulence at its origin
publication: Journal of Fluid Mechanics
publication_identifier:
eissn:
- 1469-7645
issn:
- 0022-1120
publication_status: published
publisher: Cambridge University Press
quality_controlled: '1'
scopus_import: '1'
status: public
title: The critical point of the transition to turbulence in pipe flow
type: journal_article
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
volume: 839
year: '2018'
...
---
_id: '5993'
abstract:
- lang: eng
text: 'In this article, we consider the termination problem of probabilistic programs
with real-valued variables. Thequestions concerned are: qualitative ones that
ask (i) whether the program terminates with probability 1(almost-sure termination)
and (ii) whether the expected termination time is finite (finite termination);
andquantitative ones that ask (i) to approximate the expected termination time
(expectation problem) and (ii) tocompute a boundBsuch that the probability not
to terminate afterBsteps decreases exponentially (con-centration problem). To
solve these questions, we utilize the notion of ranking supermartingales, which
isa powerful approach for proving termination of probabilistic programs. In detail,
we focus on algorithmicsynthesis of linear ranking-supermartingales over affine
probabilistic programs (Apps) with both angelic anddemonic non-determinism. An
important subclass of Apps is LRApp which is defined as the class of all Appsover
which a linear ranking-supermartingale exists.Our main contributions are as follows.
Firstly, we show that the membership problem of LRApp (i) canbe decided in polynomial
time for Apps with at most demonic non-determinism, and (ii) isNP-hard and inPSPACEfor
Apps with angelic non-determinism. Moreover, theNP-hardness result holds already
for Appswithout probability and demonic non-determinism. Secondly, we show that
the concentration problem overLRApp can be solved in the same complexity as for
the membership problem of LRApp. Finally, we show thatthe expectation problem
over LRApp can be solved in2EXPTIMEand isPSPACE-hard even for Apps withoutprobability
and non-determinism (i.e., deterministic programs). Our experimental results demonstrate
theeffectiveness of our approach to answer the qualitative and quantitative questions
over Apps with at mostdemonic non-determinism.'
article_number: '7'
article_processing_charge: No
author:
- first_name: Krishnendu
full_name: Chatterjee, Krishnendu
id: 2E5DCA20-F248-11E8-B48F-1D18A9856A87
last_name: Chatterjee
orcid: 0000-0002-4561-241X
- first_name: Hongfei
full_name: Fu, Hongfei
id: 3AAD03D6-F248-11E8-B48F-1D18A9856A87
last_name: Fu
- first_name: Petr
full_name: Novotný, Petr
id: 3CC3B868-F248-11E8-B48F-1D18A9856A87
last_name: Novotný
- first_name: Rouzbeh
full_name: Hasheminezhad, Rouzbeh
last_name: Hasheminezhad
citation:
ama: Chatterjee K, Fu H, Novotný P, Hasheminezhad R. Algorithmic analysis of qualitative
and quantitative termination problems for affine probabilistic programs. ACM
Transactions on Programming Languages and Systems. 2018;40(2). doi:10.1145/3174800
apa: Chatterjee, K., Fu, H., Novotný, P., & Hasheminezhad, R. (2018). Algorithmic
analysis of qualitative and quantitative termination problems for affine probabilistic
programs. ACM Transactions on Programming Languages and Systems. Association
for Computing Machinery (ACM). https://doi.org/10.1145/3174800
chicago: Chatterjee, Krishnendu, Hongfei Fu, Petr Novotný, and Rouzbeh Hasheminezhad.
“Algorithmic Analysis of Qualitative and Quantitative Termination Problems for
Affine Probabilistic Programs.” ACM Transactions on Programming Languages and
Systems. Association for Computing Machinery (ACM), 2018. https://doi.org/10.1145/3174800.
ieee: K. Chatterjee, H. Fu, P. Novotný, and R. Hasheminezhad, “Algorithmic analysis
of qualitative and quantitative termination problems for affine probabilistic
programs,” ACM Transactions on Programming Languages and Systems, vol.
40, no. 2. Association for Computing Machinery (ACM), 2018.
ista: Chatterjee K, Fu H, Novotný P, Hasheminezhad R. 2018. Algorithmic analysis
of qualitative and quantitative termination problems for affine probabilistic
programs. ACM Transactions on Programming Languages and Systems. 40(2), 7.
mla: Chatterjee, Krishnendu, et al. “Algorithmic Analysis of Qualitative and Quantitative
Termination Problems for Affine Probabilistic Programs.” ACM Transactions on
Programming Languages and Systems, vol. 40, no. 2, 7, Association for Computing
Machinery (ACM), 2018, doi:10.1145/3174800.
short: K. Chatterjee, H. Fu, P. Novotný, R. Hasheminezhad, ACM Transactions on Programming
Languages and Systems 40 (2018).
date_created: 2019-02-14T12:29:10Z
date_published: 2018-06-01T00:00:00Z
date_updated: 2023-09-19T14:38:42Z
day: '01'
department:
- _id: KrCh
doi: 10.1145/3174800
ec_funded: 1
external_id:
arxiv:
- '1510.08517'
isi:
- '000434634500003'
intvolume: ' 40'
isi: 1
issue: '2'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/1510.08517
month: '06'
oa: 1
oa_version: Submitted Version
project:
- _id: 2584A770-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: P 23499-N23
name: Modern Graph Algorithmic Techniques in Formal Verification
- _id: 25832EC2-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: S 11407_N23
name: Rigorous Systems Engineering
- _id: 2581B60A-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '279307'
name: 'Quantitative Graph Games: Theory and Applications'
- _id: 25681D80-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '291734'
name: International IST Postdoc Fellowship Programme
publication: ACM Transactions on Programming Languages and Systems
publication_identifier:
issn:
- 0164-0925
publication_status: published
publisher: Association for Computing Machinery (ACM)
quality_controlled: '1'
related_material:
record:
- id: '1438'
relation: earlier_version
status: public
scopus_import: '1'
status: public
title: Algorithmic analysis of qualitative and quantitative termination problems for
affine probabilistic programs
type: journal_article
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
volume: 40
year: '2018'
...
---
_id: '5999'
abstract:
- lang: eng
text: "We introduce for each quiver Q and each algebraic oriented cohomology theory
A, the cohomological Hall algebra (CoHA) of Q, as the A-homology of the moduli
of representations of the preprojective algebra of Q. This generalizes the K-theoretic
Hall algebra of commuting varieties defined by Schiffmann-Vasserot. When A is
the Morava K-theory, we show evidence that this algebra is a candidate for Lusztig's
reformulated conjecture on modular representations of algebraic groups.\r\nWe
construct an action of the preprojective CoHA on the A-homology of Nakajima quiver
varieties. We compare this with the action of the Borel subalgebra of Yangian
when A is the intersection theory. We also give a shuffle algebra description
of this CoHA in terms of the underlying formal group law of A. As applications,
we obtain a shuffle description of the Yangian. "
article_processing_charge: No
author:
- first_name: Yaping
full_name: Yang, Yaping
last_name: Yang
- first_name: Gufang
full_name: Zhao, Gufang
id: 2BC2AC5E-F248-11E8-B48F-1D18A9856A87
last_name: Zhao
citation:
ama: Yang Y, Zhao G. The cohomological Hall algebra of a preprojective algebra.
Proceedings of the London Mathematical Society. 2018;116(5):1029-1074.
doi:10.1112/plms.12111
apa: Yang, Y., & Zhao, G. (2018). The cohomological Hall algebra of a preprojective
algebra. Proceedings of the London Mathematical Society. Oxford University
Press. https://doi.org/10.1112/plms.12111
chicago: Yang, Yaping, and Gufang Zhao. “The Cohomological Hall Algebra of a Preprojective
Algebra.” Proceedings of the London Mathematical Society. Oxford University
Press, 2018. https://doi.org/10.1112/plms.12111.
ieee: Y. Yang and G. Zhao, “The cohomological Hall algebra of a preprojective algebra,”
Proceedings of the London Mathematical Society, vol. 116, no. 5. Oxford
University Press, pp. 1029–1074, 2018.
ista: Yang Y, Zhao G. 2018. The cohomological Hall algebra of a preprojective algebra.
Proceedings of the London Mathematical Society. 116(5), 1029–1074.
mla: Yang, Yaping, and Gufang Zhao. “The Cohomological Hall Algebra of a Preprojective
Algebra.” Proceedings of the London Mathematical Society, vol. 116, no.
5, Oxford University Press, 2018, pp. 1029–74, doi:10.1112/plms.12111.
short: Y. Yang, G. Zhao, Proceedings of the London Mathematical Society 116 (2018)
1029–1074.
date_created: 2019-02-14T13:14:22Z
date_published: 2018-05-01T00:00:00Z
date_updated: 2023-09-19T14:37:19Z
day: '01'
department:
- _id: TaHa
doi: 10.1112/plms.12111
external_id:
arxiv:
- '1407.7994'
isi:
- '000431506400001'
intvolume: ' 116'
isi: 1
issue: '5'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/1407.7994
month: '05'
oa: 1
oa_version: Preprint
page: 1029-1074
publication: Proceedings of the London Mathematical Society
publication_identifier:
issn:
- 0024-6115
publication_status: published
publisher: Oxford University Press
quality_controlled: '1'
scopus_import: '1'
status: public
title: The cohomological Hall algebra of a preprojective algebra
type: journal_article
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
volume: 116
year: '2018'
...
---
_id: '5989'
abstract:
- lang: eng
text: Schistosomes are the causative agents of schistosomiasis, a neglected tropical
disease affecting over 230 million people worldwide.Additionally to their major
impact on human health, they are also models of choice in evolutionary biology.
These parasitic flatwormsare unique among the common hermaphroditic trematodes
as they have separate sexes. This so-called “evolutionary scandal”displays a female
heterogametic genetic sex-determination system (ZZ males and ZW females), as well
as a pronounced adult sexualdimorphism. These phenotypic differences are determined
by a shared set of genes in both sexes, potentially leading to intralocussexual
conflicts. To resolve these conflicts in sexually selected traits, molecular mechanisms
such as sex-biased gene expression couldoccur, but parent-of-origin gene expression
also provides an alternative. In this work we investigated the latter mechanism,
that is,genes expressed preferentially from either the maternal or the paternal
allele, inSchistosoma mansonispecies. To this end, tran-scriptomes from male and
female hybrid adults obtained by strain crosses were sequenced. Strain-specific
single nucleotide poly-morphism (SNP) markers allowed us to discriminate the parental
origin, while reciprocal crosses helped to differentiate parentalexpression from
strain-specific expression. We identified genes containing SNPs expressed in a
parent-of-origin manner consistentwith paternal and maternal imprints. Although
the majority of the SNPs was identified in mitochondrial and Z-specific loci,
theremaining SNPs found in male and female transcriptomes were situated in genes
that have the potential to explain sexual differencesin schistosome parasites.
Furthermore, we identified and validated four new Z-specific scaffolds.
article_processing_charge: No
author:
- first_name: Julien
full_name: Kincaid-Smith, Julien
last_name: Kincaid-Smith
- first_name: Marion A L
full_name: Picard, Marion A L
id: 2C921A7A-F248-11E8-B48F-1D18A9856A87
last_name: Picard
orcid: 0000-0002-8101-2518
- first_name: Céline
full_name: Cosseau, Céline
last_name: Cosseau
- first_name: Jérôme
full_name: Boissier, Jérôme
last_name: Boissier
- first_name: Dany
full_name: Severac, Dany
last_name: Severac
- first_name: Christoph
full_name: Grunau, Christoph
last_name: Grunau
- first_name: Eve
full_name: Toulza, Eve
last_name: Toulza
citation:
ama: Kincaid-Smith J, Picard MAL, Cosseau C, et al. Parent-of-Origin-Dependent Gene
Expression in Male and Female Schistosome Parasites. Genome Biology and Evolution.
2018;10(3):840-856. doi:10.1093/gbe/evy037
apa: Kincaid-Smith, J., Picard, M. A. L., Cosseau, C., Boissier, J., Severac, D.,
Grunau, C., & Toulza, E. (2018). Parent-of-Origin-Dependent Gene Expression
in Male and Female Schistosome Parasites. Genome Biology and Evolution.
Oxford University Press. https://doi.org/10.1093/gbe/evy037
chicago: Kincaid-Smith, Julien, Marion A L Picard, Céline Cosseau, Jérôme Boissier,
Dany Severac, Christoph Grunau, and Eve Toulza. “Parent-of-Origin-Dependent Gene
Expression in Male and Female Schistosome Parasites.” Genome Biology and Evolution.
Oxford University Press, 2018. https://doi.org/10.1093/gbe/evy037.
ieee: J. Kincaid-Smith et al., “Parent-of-Origin-Dependent Gene Expression
in Male and Female Schistosome Parasites,” Genome Biology and Evolution,
vol. 10, no. 3. Oxford University Press, pp. 840–856, 2018.
ista: Kincaid-Smith J, Picard MAL, Cosseau C, Boissier J, Severac D, Grunau C, Toulza
E. 2018. Parent-of-Origin-Dependent Gene Expression in Male and Female Schistosome
Parasites. Genome Biology and Evolution. 10(3), 840–856.
mla: Kincaid-Smith, Julien, et al. “Parent-of-Origin-Dependent Gene Expression in
Male and Female Schistosome Parasites.” Genome Biology and Evolution, vol.
10, no. 3, Oxford University Press, 2018, pp. 840–56, doi:10.1093/gbe/evy037.
short: J. Kincaid-Smith, M.A.L. Picard, C. Cosseau, J. Boissier, D. Severac, C.
Grunau, E. Toulza, Genome Biology and Evolution 10 (2018) 840–856.
date_created: 2019-02-14T12:13:52Z
date_published: 2018-03-01T00:00:00Z
date_updated: 2023-09-19T14:39:08Z
day: '01'
ddc:
- '570'
department:
- _id: BeVi
doi: 10.1093/gbe/evy037
external_id:
isi:
- '000429483700013'
file:
- access_level: open_access
checksum: 736a459cb77de5824354466bb0331caf
content_type: application/pdf
creator: dernst
date_created: 2019-02-14T12:20:01Z
date_updated: 2020-07-14T12:47:15Z
file_id: '5991'
file_name: 2018_GBE_Kincaid_Smith.pdf
file_size: 529755
relation: main_file
file_date_updated: 2020-07-14T12:47:15Z
has_accepted_license: '1'
intvolume: ' 10'
isi: 1
issue: '3'
language:
- iso: eng
license: https://creativecommons.org/licenses/by-nc/4.0/
month: '03'
oa: 1
oa_version: Published Version
page: 840-856
publication: Genome Biology and Evolution
publication_identifier:
issn:
- 1759-6653
publication_status: published
publisher: Oxford University Press
quality_controlled: '1'
scopus_import: '1'
status: public
title: Parent-of-Origin-Dependent Gene Expression in Male and Female Schistosome Parasites
tmp:
image: /images/cc_by_nc.png
legal_code_url: https://creativecommons.org/licenses/by-nc/4.0/legalcode
name: Creative Commons Attribution-NonCommercial 4.0 International (CC BY-NC 4.0)
short: CC BY-NC (4.0)
type: journal_article
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
volume: 10
year: '2018'
...
---
_id: '6031'
abstract:
- lang: eng
text: We introduce Clover, a new library for efficient computation using low-precision
data, providing mathematical routines required by fundamental methods in optimization
and sparse recovery. Our library faithfully implements variants of stochastic
quantization that guarantee convergence at low precision, and supports data formats
from 4-bit quantized to 32-bit IEEE-754 on current Intel processors. In particular,
we show that 4-bit can be implemented efficiently using Intel AVX despite the
lack of native support for this data format. Experimental results with dot product,
matrix-vector multiplication (MVM), gradient descent (GD), and iterative hard
thresholding (IHT) demonstrate that the attainable speedups are in many cases
close to linear with respect to the reduction of precision due to reduced data
movement. Finally, for GD and IHT, we show examples of absolute speedup achieved
by 4-bit versus 32-bit, by iterating until a given target error is achieved.
article_number: '8598402'
article_processing_charge: No
author:
- first_name: Alen
full_name: Stojanov, Alen
last_name: Stojanov
- first_name: Tyler Michael
full_name: Smith, Tyler Michael
last_name: Smith
- first_name: Dan-Adrian
full_name: Alistarh, Dan-Adrian
id: 4A899BFC-F248-11E8-B48F-1D18A9856A87
last_name: Alistarh
orcid: 0000-0003-3650-940X
- first_name: Markus
full_name: Puschel, Markus
last_name: Puschel
citation:
ama: 'Stojanov A, Smith TM, Alistarh D-A, Puschel M. Fast quantized arithmetic on
x86: Trading compute for data movement. In: 2018 IEEE International Workshop
on Signal Processing Systems. Vol 2018-October. IEEE; 2018. doi:10.1109/SiPS.2018.8598402'
apa: 'Stojanov, A., Smith, T. M., Alistarh, D.-A., & Puschel, M. (2018). Fast
quantized arithmetic on x86: Trading compute for data movement. In 2018 IEEE
International Workshop on Signal Processing Systems (Vol. 2018–October). Cape
Town, South Africa: IEEE. https://doi.org/10.1109/SiPS.2018.8598402'
chicago: 'Stojanov, Alen, Tyler Michael Smith, Dan-Adrian Alistarh, and Markus Puschel.
“Fast Quantized Arithmetic on X86: Trading Compute for Data Movement.” In 2018
IEEE International Workshop on Signal Processing Systems, Vol. 2018–October.
IEEE, 2018. https://doi.org/10.1109/SiPS.2018.8598402.'
ieee: 'A. Stojanov, T. M. Smith, D.-A. Alistarh, and M. Puschel, “Fast quantized
arithmetic on x86: Trading compute for data movement,” in 2018 IEEE International
Workshop on Signal Processing Systems, Cape Town, South Africa, 2018, vol.
2018–October.'
ista: 'Stojanov A, Smith TM, Alistarh D-A, Puschel M. 2018. Fast quantized arithmetic
on x86: Trading compute for data movement. 2018 IEEE International Workshop on
Signal Processing Systems. SiPS: Workshop on Signal Processing Systems vol. 2018–October,
8598402.'
mla: 'Stojanov, Alen, et al. “Fast Quantized Arithmetic on X86: Trading Compute
for Data Movement.” 2018 IEEE International Workshop on Signal Processing Systems,
vol. 2018–October, 8598402, IEEE, 2018, doi:10.1109/SiPS.2018.8598402.'
short: A. Stojanov, T.M. Smith, D.-A. Alistarh, M. Puschel, in:, 2018 IEEE International
Workshop on Signal Processing Systems, IEEE, 2018.
conference:
end_date: 2018-10-24
location: Cape Town, South Africa
name: 'SiPS: Workshop on Signal Processing Systems'
start_date: 2018-10-21
date_created: 2019-02-17T22:59:25Z
date_published: 2018-12-31T00:00:00Z
date_updated: 2023-09-19T14:41:51Z
day: '31'
department:
- _id: DaAl
doi: 10.1109/SiPS.2018.8598402
external_id:
isi:
- '000465106800060'
isi: 1
language:
- iso: eng
month: '12'
oa_version: None
publication: 2018 IEEE International Workshop on Signal Processing Systems
publication_status: published
publisher: IEEE
quality_controlled: '1'
scopus_import: '1'
status: public
title: 'Fast quantized arithmetic on x86: Trading compute for data movement'
type: conference
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
volume: 2018-October
year: '2018'
...
---
_id: '25'
abstract:
- lang: eng
text: 'Partially observable Markov decision processes (POMDPs) are the standard
models for planning under uncertainty with both finite and infinite horizon. Besides
the well-known discounted-sum objective, indefinite-horizon objective (aka Goal-POMDPs)
is another classical objective for POMDPs. In this case, given a set of target
states and a positive cost for each transition, the optimization objective is
to minimize the expected total cost until a target state is reached. In the literature,
RTDP-Bel or heuristic search value iteration (HSVI) have been used for solving
Goal-POMDPs. Neither of these algorithms has theoretical convergence guarantees,
and HSVI may even fail to terminate its trials. We give the following contributions:
(1) We discuss the challenges introduced in Goal-POMDPs and illustrate how they
prevent the original HSVI from converging. (2) We present a novel algorithm inspired
by HSVI, termed Goal-HSVI, and show that our algorithm has convergence guarantees.
(3) We show that Goal-HSVI outperforms RTDP-Bel on a set of well-known examples.'
acknowledgement: '∗This work has been supported by Vienna Science and Technology Fund
(WWTF) Project ICT15-003, Austrian Science Fund (FWF) NFN Grant No S11407-N23 (RiSE/SHiNE),
and ERC Starting grant (279307: Graph Games). This research was sponsored by the
Army Research Laboratory and was accomplished under Cooperative Agreement Number
W911NF-13-2-0045 (ARL Cyber Security CRA). '
article_processing_charge: No
author:
- first_name: Karel
full_name: Horák, Karel
last_name: Horák
- first_name: Branislav
full_name: Bošanský, Branislav
last_name: Bošanský
- first_name: Krishnendu
full_name: Chatterjee, Krishnendu
id: 2E5DCA20-F248-11E8-B48F-1D18A9856A87
last_name: Chatterjee
orcid: 0000-0002-4561-241X
citation:
ama: 'Horák K, Bošanský B, Chatterjee K. Goal-HSVI: Heuristic search value iteration
for goal-POMDPs. In: Proceedings of the Twenty-Seventh International Joint
Conference on Artificial Intelligence. Vol 2018-July. IJCAI; 2018:4764-4770.
doi:10.24963/ijcai.2018/662'
apa: 'Horák, K., Bošanský, B., & Chatterjee, K. (2018). Goal-HSVI: Heuristic
search value iteration for goal-POMDPs. In Proceedings of the Twenty-Seventh
International Joint Conference on Artificial Intelligence (Vol. 2018–July,
pp. 4764–4770). Stockholm, Sweden: IJCAI. https://doi.org/10.24963/ijcai.2018/662'
chicago: 'Horák, Karel, Branislav Bošanský, and Krishnendu Chatterjee. “Goal-HSVI:
Heuristic Search Value Iteration for Goal-POMDPs.” In Proceedings of the Twenty-Seventh
International Joint Conference on Artificial Intelligence, 2018–July:4764–70.
IJCAI, 2018. https://doi.org/10.24963/ijcai.2018/662.'
ieee: 'K. Horák, B. Bošanský, and K. Chatterjee, “Goal-HSVI: Heuristic search value
iteration for goal-POMDPs,” in Proceedings of the Twenty-Seventh International
Joint Conference on Artificial Intelligence, Stockholm, Sweden, 2018, vol.
2018–July, pp. 4764–4770.'
ista: 'Horák K, Bošanský B, Chatterjee K. 2018. Goal-HSVI: Heuristic search value
iteration for goal-POMDPs. Proceedings of the Twenty-Seventh International Joint
Conference on Artificial Intelligence. IJCAI: International Joint Conference on
Artificial Intelligence vol. 2018–July, 4764–4770.'
mla: 'Horák, Karel, et al. “Goal-HSVI: Heuristic Search Value Iteration for Goal-POMDPs.”
Proceedings of the Twenty-Seventh International Joint Conference on Artificial
Intelligence, vol. 2018–July, IJCAI, 2018, pp. 4764–70, doi:10.24963/ijcai.2018/662.'
short: K. Horák, B. Bošanský, K. Chatterjee, in:, Proceedings of the Twenty-Seventh
International Joint Conference on Artificial Intelligence, IJCAI, 2018, pp. 4764–4770.
conference:
end_date: 2018-07-19
location: Stockholm, Sweden
name: 'IJCAI: International Joint Conference on Artificial Intelligence'
start_date: 2018-07-13
date_created: 2018-12-11T11:44:13Z
date_published: 2018-07-01T00:00:00Z
date_updated: 2023-09-19T14:44:59Z
day: '01'
department:
- _id: KrCh
doi: 10.24963/ijcai.2018/662
ec_funded: 1
external_id:
isi:
- '000764175404127'
isi: 1
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.24963/ijcai.2018/662
month: '07'
oa: 1
oa_version: Published Version
page: 4764 - 4770
project:
- _id: 25892FC0-B435-11E9-9278-68D0E5697425
grant_number: ICT15-003
name: Efficient Algorithms for Computer Aided Verification
- _id: 25832EC2-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: S 11407_N23
name: Rigorous Systems Engineering
- _id: 2581B60A-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '279307'
name: 'Quantitative Graph Games: Theory and Applications'
publication: Proceedings of the Twenty-Seventh International Joint Conference on Artificial
Intelligence
publication_status: published
publisher: IJCAI
publist_id: '8030'
quality_controlled: '1'
scopus_import: '1'
status: public
title: 'Goal-HSVI: Heuristic search value iteration for goal-POMDPs'
type: conference
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
volume: 2018-July
year: '2018'
...
---
_id: '24'
abstract:
- lang: eng
text: Partially-observable Markov decision processes (POMDPs) with discounted-sum
payoff are a standard framework to model a wide range of problems related to decision
making under uncertainty. Traditionally, the goal has been to obtain policies
that optimize the expectation of the discounted-sum payoff. A key drawback of
the expectation measure is that even low probability events with extreme payoff
can significantly affect the expectation, and thus the obtained policies are not
necessarily risk-averse. An alternate approach is to optimize the probability
that the payoff is above a certain threshold, which allows obtaining risk-averse
policies, but ignores optimization of the expectation. We consider the expectation
optimization with probabilistic guarantee (EOPG) problem, where the goal is to
optimize the expectation ensuring that the payoff is above a given threshold with
at least a specified probability. We present several results on the EOPG problem,
including the first algorithm to solve it.
acknowledgement: "This research was supported by the Vienna Science and Technology
Fund (WWTF) grant ICT15-003; Austrian Science Fund (FWF): S11407-N23(RiSE/SHiNE);and
an ERC Start Grant (279307:Graph Games).\r\n"
article_processing_charge: No
author:
- first_name: Krishnendu
full_name: Chatterjee, Krishnendu
id: 2E5DCA20-F248-11E8-B48F-1D18A9856A87
last_name: Chatterjee
orcid: 0000-0002-4561-241X
- first_name: Adrian
full_name: Elgyütt, Adrian
id: 4A2E9DBA-F248-11E8-B48F-1D18A9856A87
last_name: Elgyütt
- first_name: Petr
full_name: Novotny, Petr
id: 3CC3B868-F248-11E8-B48F-1D18A9856A87
last_name: Novotny
- first_name: Owen
full_name: Rouillé, Owen
last_name: Rouillé
citation:
ama: 'Chatterjee K, Elgyütt A, Novotný P, Rouillé O. Expectation optimization with
probabilistic guarantees in POMDPs with discounted-sum objectives. In: Vol 2018.
IJCAI; 2018:4692-4699. doi:10.24963/ijcai.2018/652'
apa: 'Chatterjee, K., Elgyütt, A., Novotný, P., & Rouillé, O. (2018). Expectation
optimization with probabilistic guarantees in POMDPs with discounted-sum objectives
(Vol. 2018, pp. 4692–4699). Presented at the IJCAI: International Joint Conference
on Artificial Intelligence, Stockholm, Sweden: IJCAI. https://doi.org/10.24963/ijcai.2018/652'
chicago: Chatterjee, Krishnendu, Adrian Elgyütt, Petr Novotný, and Owen Rouillé.
“Expectation Optimization with Probabilistic Guarantees in POMDPs with Discounted-Sum
Objectives,” 2018:4692–99. IJCAI, 2018. https://doi.org/10.24963/ijcai.2018/652.
ieee: 'K. Chatterjee, A. Elgyütt, P. Novotný, and O. Rouillé, “Expectation optimization
with probabilistic guarantees in POMDPs with discounted-sum objectives,” presented
at the IJCAI: International Joint Conference on Artificial Intelligence, Stockholm,
Sweden, 2018, vol. 2018, pp. 4692–4699.'
ista: 'Chatterjee K, Elgyütt A, Novotný P, Rouillé O. 2018. Expectation optimization
with probabilistic guarantees in POMDPs with discounted-sum objectives. IJCAI:
International Joint Conference on Artificial Intelligence vol. 2018, 4692–4699.'
mla: Chatterjee, Krishnendu, et al. Expectation Optimization with Probabilistic
Guarantees in POMDPs with Discounted-Sum Objectives. Vol. 2018, IJCAI, 2018,
pp. 4692–99, doi:10.24963/ijcai.2018/652.
short: K. Chatterjee, A. Elgyütt, P. Novotný, O. Rouillé, in:, IJCAI, 2018, pp.
4692–4699.
conference:
end_date: 2018-07-19
location: Stockholm, Sweden
name: 'IJCAI: International Joint Conference on Artificial Intelligence'
start_date: 2018-07-13
date_created: 2018-12-11T11:44:13Z
date_published: 2018-07-01T00:00:00Z
date_updated: 2023-09-19T14:45:48Z
day: '01'
department:
- _id: KrCh
- _id: ToHe
doi: 10.24963/ijcai.2018/652
ec_funded: 1
external_id:
arxiv:
- '1804.10601'
isi:
- '000764175404117'
intvolume: ' 2018'
isi: 1
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/1804.10601
month: '07'
oa: 1
oa_version: Preprint
page: 4692 - 4699
project:
- _id: 25892FC0-B435-11E9-9278-68D0E5697425
grant_number: ICT15-003
name: Efficient Algorithms for Computer Aided Verification
- _id: 25832EC2-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: S 11407_N23
name: Rigorous Systems Engineering
- _id: 2581B60A-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '279307'
name: 'Quantitative Graph Games: Theory and Applications'
publication_status: published
publisher: IJCAI
publist_id: '8031'
quality_controlled: '1'
scopus_import: '1'
status: public
title: Expectation optimization with probabilistic guarantees in POMDPs with discounted-sum
objectives
type: conference
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
volume: 2018
year: '2018'
...
---
_id: '34'
abstract:
- lang: eng
text: Partially observable Markov decision processes (POMDPs) are widely used in
probabilistic planning problems in which an agent interacts with an environment
using noisy and imprecise sensors. We study a setting in which the sensors are
only partially defined and the goal is to synthesize “weakest” additional sensors,
such that in the resulting POMDP, there is a small-memory policy for the agent
that almost-surely (with probability 1) satisfies a reachability objective. We
show that the problem is NP-complete, and present a symbolic algorithm by encoding
the problem into SAT instances. We illustrate trade-offs between the amount of
memory of the policy and the number of additional sensors on a simple example.
We have implemented our approach and consider three classical POMDP examples from
the literature, and show that in all the examples the number of sensors can be
significantly decreased (as compared to the existing solutions in the literature)
without increasing the complexity of the policies.
alternative_title:
- ICAPS
article_processing_charge: No
author:
- first_name: Krishnendu
full_name: Chatterjee, Krishnendu
id: 2E5DCA20-F248-11E8-B48F-1D18A9856A87
last_name: Chatterjee
orcid: 0000-0002-4561-241X
- first_name: Martin
full_name: Chemlík, Martin
last_name: Chemlík
- first_name: Ufuk
full_name: Topcu, Ufuk
last_name: Topcu
citation:
ama: 'Chatterjee K, Chemlík M, Topcu U. Sensor synthesis for POMDPs with reachability
objectives. In: Vol 2018. AAAI Press; 2018:47-55.'
apa: 'Chatterjee, K., Chemlík, M., & Topcu, U. (2018). Sensor synthesis for
POMDPs with reachability objectives (Vol. 2018, pp. 47–55). Presented at the ICAPS:
International Conference on Automated Planning and Scheduling, Delft, Netherlands:
AAAI Press.'
chicago: Chatterjee, Krishnendu, Martin Chemlík, and Ufuk Topcu. “Sensor Synthesis
for POMDPs with Reachability Objectives,” 2018:47–55. AAAI Press, 2018.
ieee: 'K. Chatterjee, M. Chemlík, and U. Topcu, “Sensor synthesis for POMDPs with
reachability objectives,” presented at the ICAPS: International Conference on
Automated Planning and Scheduling, Delft, Netherlands, 2018, vol. 2018, pp. 47–55.'
ista: 'Chatterjee K, Chemlík M, Topcu U. 2018. Sensor synthesis for POMDPs with
reachability objectives. ICAPS: International Conference on Automated Planning
and Scheduling, ICAPS, vol. 2018, 47–55.'
mla: Chatterjee, Krishnendu, et al. Sensor Synthesis for POMDPs with Reachability
Objectives. Vol. 2018, AAAI Press, 2018, pp. 47–55.
short: K. Chatterjee, M. Chemlík, U. Topcu, in:, AAAI Press, 2018, pp. 47–55.
conference:
end_date: 2018-06-29
location: Delft, Netherlands
name: 'ICAPS: International Conference on Automated Planning and Scheduling'
start_date: 2018-06-24
date_created: 2018-12-11T11:44:16Z
date_published: 2018-06-01T00:00:00Z
date_updated: 2023-09-19T14:44:14Z
day: '01'
department:
- _id: KrCh
ec_funded: 1
external_id:
arxiv:
- '1710.00675'
isi:
- '000492986200006'
intvolume: ' 2018'
isi: 1
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/1710.00675
month: '06'
oa: 1
oa_version: Preprint
page: 47 - 55
project:
- _id: 2584A770-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: P 23499-N23
name: Modern Graph Algorithmic Techniques in Formal Verification
- _id: 2581B60A-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '279307'
name: 'Quantitative Graph Games: Theory and Applications'
- _id: 25832EC2-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: S 11407_N23
name: Rigorous Systems Engineering
- _id: 2587B514-B435-11E9-9278-68D0E5697425
name: Microsoft Research Faculty Fellowship
publication_status: published
publisher: AAAI Press
publist_id: '8021'
quality_controlled: '1'
scopus_import: '1'
status: public
title: Sensor synthesis for POMDPs with reachability objectives
type: conference
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
volume: 2018
year: '2018'
...
---
_id: '18'
abstract:
- lang: eng
text: An N-superconcentrator is a directed, acyclic graph with N input nodes and
N output nodes such that every subset of the inputs and every subset of the outputs
of same cardinality can be connected by node-disjoint paths. It is known that
linear-size and bounded-degree superconcentrators exist. We prove the existence
of such superconcentrators with asymptotic density 25.3 (where the density is
the number of edges divided by N). The previously best known densities were 28
[12] and 27.4136 [17].
article_processing_charge: No
author:
- first_name: Vladimir
full_name: Kolmogorov, Vladimir
id: 3D50B0BA-F248-11E8-B48F-1D18A9856A87
last_name: Kolmogorov
- first_name: Michal
full_name: Rolinek, Michal
id: 3CB3BC06-F248-11E8-B48F-1D18A9856A87
last_name: Rolinek
citation:
ama: Kolmogorov V, Rolinek M. Superconcentrators of density 25.3. Ars Combinatoria.
2018;141(10):269-304.
apa: Kolmogorov, V., & Rolinek, M. (2018). Superconcentrators of density 25.3.
Ars Combinatoria. Charles Babbage Research Centre.
chicago: Kolmogorov, Vladimir, and Michal Rolinek. “Superconcentrators of Density
25.3.” Ars Combinatoria. Charles Babbage Research Centre, 2018.
ieee: V. Kolmogorov and M. Rolinek, “Superconcentrators of density 25.3,” Ars
Combinatoria, vol. 141, no. 10. Charles Babbage Research Centre, pp. 269–304,
2018.
ista: Kolmogorov V, Rolinek M. 2018. Superconcentrators of density 25.3. Ars Combinatoria.
141(10), 269–304.
mla: Kolmogorov, Vladimir, and Michal Rolinek. “Superconcentrators of Density 25.3.”
Ars Combinatoria, vol. 141, no. 10, Charles Babbage Research Centre, 2018,
pp. 269–304.
short: V. Kolmogorov, M. Rolinek, Ars Combinatoria 141 (2018) 269–304.
date_created: 2018-12-11T11:44:11Z
date_published: 2018-10-01T00:00:00Z
date_updated: 2023-09-19T14:46:18Z
day: '01'
department:
- _id: VlKo
external_id:
arxiv:
- '1405.7828'
isi:
- '000446809500022'
intvolume: ' 141'
isi: 1
issue: '10'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/1405.7828
month: '10'
oa: 1
oa_version: Preprint
page: 269 - 304
publication: Ars Combinatoria
publication_identifier:
issn:
- 0381-7032
publication_status: published
publisher: Charles Babbage Research Centre
publist_id: '8037'
quality_controlled: '1'
scopus_import: '1'
status: public
title: Superconcentrators of density 25.3
type: journal_article
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
volume: 141
year: '2018'
...
---
_id: '6355'
abstract:
- lang: eng
text: We prove that any cyclic quadrilateral can be inscribed in any closed convex
C1-curve. The smoothness condition is not required if the quadrilateral is a
rectangle.
article_number: e7
article_processing_charge: No
author:
- first_name: Arseniy
full_name: Akopyan, Arseniy
id: 430D2C90-F248-11E8-B48F-1D18A9856A87
last_name: Akopyan
orcid: 0000-0002-2548-617X
- first_name: Sergey
full_name: Avvakumov, Sergey
id: 3827DAC8-F248-11E8-B48F-1D18A9856A87
last_name: Avvakumov
citation:
ama: Akopyan A, Avvakumov S. Any cyclic quadrilateral can be inscribed in any closed
convex smooth curve. Forum of Mathematics, Sigma. 2018;6. doi:10.1017/fms.2018.7
apa: Akopyan, A., & Avvakumov, S. (2018). Any cyclic quadrilateral can be inscribed
in any closed convex smooth curve. Forum of Mathematics, Sigma. Cambridge
University Press. https://doi.org/10.1017/fms.2018.7
chicago: Akopyan, Arseniy, and Sergey Avvakumov. “Any Cyclic Quadrilateral Can Be
Inscribed in Any Closed Convex Smooth Curve.” Forum of Mathematics, Sigma.
Cambridge University Press, 2018. https://doi.org/10.1017/fms.2018.7.
ieee: A. Akopyan and S. Avvakumov, “Any cyclic quadrilateral can be inscribed in
any closed convex smooth curve,” Forum of Mathematics, Sigma, vol. 6. Cambridge
University Press, 2018.
ista: Akopyan A, Avvakumov S. 2018. Any cyclic quadrilateral can be inscribed in
any closed convex smooth curve. Forum of Mathematics, Sigma. 6, e7.
mla: Akopyan, Arseniy, and Sergey Avvakumov. “Any Cyclic Quadrilateral Can Be Inscribed
in Any Closed Convex Smooth Curve.” Forum of Mathematics, Sigma, vol. 6,
e7, Cambridge University Press, 2018, doi:10.1017/fms.2018.7.
short: A. Akopyan, S. Avvakumov, Forum of Mathematics, Sigma 6 (2018).
date_created: 2019-04-30T06:09:57Z
date_published: 2018-05-31T00:00:00Z
date_updated: 2023-09-19T14:50:12Z
day: '31'
ddc:
- '510'
department:
- _id: UlWa
- _id: HeEd
- _id: JaMa
doi: 10.1017/fms.2018.7
ec_funded: 1
external_id:
arxiv:
- '1712.10205'
isi:
- '000433915500001'
file:
- access_level: open_access
checksum: 5a71b24ba712a3eb2e46165a38fbc30a
content_type: application/pdf
creator: dernst
date_created: 2019-04-30T06:14:58Z
date_updated: 2020-07-14T12:47:28Z
file_id: '6356'
file_name: 2018_ForumMahtematics_Akopyan.pdf
file_size: 249246
relation: main_file
file_date_updated: 2020-07-14T12:47:28Z
has_accepted_license: '1'
intvolume: ' 6'
isi: 1
language:
- iso: eng
license: https://creativecommons.org/licenses/by/4.0/
month: '05'
oa: 1
oa_version: Published Version
project:
- _id: 256E75B8-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '716117'
name: Optimal Transport and Stochastic Dynamics
publication: Forum of Mathematics, Sigma
publication_identifier:
issn:
- 2050-5094
publication_status: published
publisher: Cambridge University Press
quality_controlled: '1'
related_material:
record:
- id: '8156'
relation: dissertation_contains
status: public
status: public
title: Any cyclic quadrilateral can be inscribed in any closed convex smooth curve
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: 6
year: '2018'
...
---
_id: '6195'
abstract:
- lang: eng
text: In the context of robotic manipulation and grasping, the shift from a view
that is static (force closure of a single posture) and contact-deprived (only
contact for force closure is allowed, everything else is obstacle) towards a view
that is dynamic and contact-rich (soft manipulation) has led to an increased interest
in soft hands. These hands can easily exploit environmental constraints and object
surfaces without risk, and safely interact with humans, but present also some
challenges. Designing them is difficult, as well as predicting, modelling, and
“programming” their interactions with the objects and the environment. This paper
tackles the problem of simulating them in a fast and effective way, leveraging
on novel and existing simulation technologies. We present a triple-layered simulation
framework where dynamic properties such as stiffness are determined from slow
but accurate FEM simulation data once, and then condensed into a lumped parameter
model that can be used to fast simulate soft fingers and soft hands. We apply
our approach to the simulation of soft pneumatic fingers.
article_number: '8461106'
article_processing_charge: No
author:
- first_name: Maria
full_name: Pozzi, Maria
last_name: Pozzi
- first_name: Eder
full_name: Miguel Villalba, Eder
id: 3FB91342-F248-11E8-B48F-1D18A9856A87
last_name: Miguel Villalba
orcid: 0000-0001-5665-0430
- first_name: Raphael
full_name: Deimel, Raphael
last_name: Deimel
- first_name: Monica
full_name: Malvezzi, Monica
last_name: Malvezzi
- first_name: Bernd
full_name: Bickel, Bernd
id: 49876194-F248-11E8-B48F-1D18A9856A87
last_name: Bickel
orcid: 0000-0001-6511-9385
- first_name: Oliver
full_name: Brock, Oliver
last_name: Brock
- first_name: Domenico
full_name: Prattichizzo, Domenico
last_name: Prattichizzo
citation:
ama: 'Pozzi M, Miguel Villalba E, Deimel R, et al. Efficient FEM-based simulation
of soft robots modeled as kinematic chains. In: IEEE; 2018. doi:10.1109/icra.2018.8461106'
apa: 'Pozzi, M., Miguel Villalba, E., Deimel, R., Malvezzi, M., Bickel, B., Brock,
O., & Prattichizzo, D. (2018). Efficient FEM-based simulation of soft robots
modeled as kinematic chains. Presented at the ICRA: International Conference on
Robotics and Automation, Brisbane, Australia: IEEE. https://doi.org/10.1109/icra.2018.8461106'
chicago: Pozzi, Maria, Eder Miguel Villalba, Raphael Deimel, Monica Malvezzi, Bernd
Bickel, Oliver Brock, and Domenico Prattichizzo. “Efficient FEM-Based Simulation
of Soft Robots Modeled as Kinematic Chains.” IEEE, 2018. https://doi.org/10.1109/icra.2018.8461106.
ieee: 'M. Pozzi et al., “Efficient FEM-based simulation of soft robots modeled
as kinematic chains,” presented at the ICRA: International Conference on Robotics
and Automation, Brisbane, Australia, 2018.'
ista: 'Pozzi M, Miguel Villalba E, Deimel R, Malvezzi M, Bickel B, Brock O, Prattichizzo
D. 2018. Efficient FEM-based simulation of soft robots modeled as kinematic chains.
ICRA: International Conference on Robotics and Automation, 8461106.'
mla: Pozzi, Maria, et al. Efficient FEM-Based Simulation of Soft Robots Modeled
as Kinematic Chains. 8461106, IEEE, 2018, doi:10.1109/icra.2018.8461106.
short: M. Pozzi, E. Miguel Villalba, R. Deimel, M. Malvezzi, B. Bickel, O. Brock,
D. Prattichizzo, in:, IEEE, 2018.
conference:
end_date: 2018-05-25
location: Brisbane, Australia
name: 'ICRA: International Conference on Robotics and Automation'
start_date: 2018-05-21
date_created: 2019-04-04T09:50:38Z
date_published: 2018-09-10T00:00:00Z
date_updated: 2023-09-19T14:49:03Z
day: '10'
department:
- _id: BeBi
doi: 10.1109/icra.2018.8461106
external_id:
isi:
- '000446394503031'
isi: 1
language:
- iso: eng
month: '09'
oa_version: None
publication_identifier:
isbn:
- '9781538630815'
publication_status: published
publisher: IEEE
quality_controlled: '1'
scopus_import: '1'
status: public
title: Efficient FEM-based simulation of soft robots modeled as kinematic chains
type: conference
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
year: '2018'
...
---
_id: '6941'
abstract:
- lang: eng
text: "Bitcoin has become the most successful cryptocurrency ever deployed, and
its most distinctive feature is that it is decentralized. Its underlying protocol
(Nakamoto consensus) achieves this by using proof of work, which has the drawback
that it causes the consumption of vast amounts of energy to maintain the ledger.
Moreover, Bitcoin mining dynamics have become less distributed over time.\r\n\r\nTowards
addressing these issues, we propose SpaceMint, a cryptocurrency based on proofs
of space instead of proofs of work. Miners in SpaceMint dedicate disk space rather
than computation. We argue that SpaceMint’s design solves or alleviates several
of Bitcoin’s issues: most notably, its large energy consumption. SpaceMint also
rewards smaller miners fairly according to their contribution to the network,
thus incentivizing more distributed participation.\r\n\r\nThis paper adapts proof
of space to enable its use in cryptocurrency, studies the attacks that can arise
against a Bitcoin-like blockchain that uses proof of space, and proposes a new
blockchain format and transaction types to address these attacks. Our prototype
shows that initializing 1 TB for mining takes about a day (a one-off setup cost),
and miners spend on average just a fraction of a second per block mined. Finally,
we provide a game-theoretic analysis modeling SpaceMint as an extensive game (the
canonical game-theoretic notion for games that take place over time) and show
that this stylized game satisfies a strong equilibrium notion, thereby arguing
for SpaceMint ’s stability and consensus."
alternative_title:
- LNCS
article_processing_charge: No
author:
- first_name: Sunoo
full_name: Park, Sunoo
last_name: Park
- first_name: Albert
full_name: Kwon, Albert
last_name: Kwon
- first_name: Georg
full_name: Fuchsbauer, Georg
id: 46B4C3EE-F248-11E8-B48F-1D18A9856A87
last_name: Fuchsbauer
- first_name: Peter
full_name: Gazi, Peter
id: 3E0BFE38-F248-11E8-B48F-1D18A9856A87
last_name: Gazi
- first_name: Joel F
full_name: Alwen, Joel F
id: 2A8DFA8C-F248-11E8-B48F-1D18A9856A87
last_name: Alwen
- first_name: Krzysztof Z
full_name: Pietrzak, Krzysztof Z
id: 3E04A7AA-F248-11E8-B48F-1D18A9856A87
last_name: Pietrzak
orcid: 0000-0002-9139-1654
citation:
ama: 'Park S, Kwon A, Fuchsbauer G, Gazi P, Alwen JF, Pietrzak KZ. SpaceMint: A
cryptocurrency based on proofs of space. In: 22nd International Conference
on Financial Cryptography and Data Security. Vol 10957. Springer Nature; 2018:480-499.
doi:10.1007/978-3-662-58387-6_26'
apa: 'Park, S., Kwon, A., Fuchsbauer, G., Gazi, P., Alwen, J. F., & Pietrzak,
K. Z. (2018). SpaceMint: A cryptocurrency based on proofs of space. In 22nd
International Conference on Financial Cryptography and Data Security (Vol.
10957, pp. 480–499). Nieuwpoort, Curacao: Springer Nature. https://doi.org/10.1007/978-3-662-58387-6_26'
chicago: 'Park, Sunoo, Albert Kwon, Georg Fuchsbauer, Peter Gazi, Joel F Alwen,
and Krzysztof Z Pietrzak. “SpaceMint: A Cryptocurrency Based on Proofs of Space.”
In 22nd International Conference on Financial Cryptography and Data Security,
10957:480–99. Springer Nature, 2018. https://doi.org/10.1007/978-3-662-58387-6_26.'
ieee: 'S. Park, A. Kwon, G. Fuchsbauer, P. Gazi, J. F. Alwen, and K. Z. Pietrzak,
“SpaceMint: A cryptocurrency based on proofs of space,” in 22nd International
Conference on Financial Cryptography and Data Security, Nieuwpoort, Curacao,
2018, vol. 10957, pp. 480–499.'
ista: 'Park S, Kwon A, Fuchsbauer G, Gazi P, Alwen JF, Pietrzak KZ. 2018. SpaceMint:
A cryptocurrency based on proofs of space. 22nd International Conference on Financial
Cryptography and Data Security. FC: Financial Cryptography and Data Security,
LNCS, vol. 10957, 480–499.'
mla: 'Park, Sunoo, et al. “SpaceMint: A Cryptocurrency Based on Proofs of Space.”
22nd International Conference on Financial Cryptography and Data Security,
vol. 10957, Springer Nature, 2018, pp. 480–99, doi:10.1007/978-3-662-58387-6_26.'
short: S. Park, A. Kwon, G. Fuchsbauer, P. Gazi, J.F. Alwen, K.Z. Pietrzak, in:,
22nd International Conference on Financial Cryptography and Data Security, Springer
Nature, 2018, pp. 480–499.
conference:
end_date: 2018-03-02
location: Nieuwpoort, Curacao
name: 'FC: Financial Cryptography and Data Security'
start_date: 2018-02-26
date_created: 2019-10-14T06:35:38Z
date_published: 2018-12-07T00:00:00Z
date_updated: 2023-09-19T15:02:13Z
day: '07'
department:
- _id: KrPi
doi: 10.1007/978-3-662-58387-6_26
ec_funded: 1
external_id:
isi:
- '000540656400026'
intvolume: ' 10957'
isi: 1
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://eprint.iacr.org/2015/528
month: '12'
oa: 1
oa_version: Submitted Version
page: 480-499
project:
- _id: 258AA5B2-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '682815'
name: Teaching Old Crypto New Tricks
publication: 22nd International Conference on Financial Cryptography and Data Security
publication_identifier:
eissn:
- 1611-3349
isbn:
- '9783662583869'
- '9783662583876'
issn:
- 0302-9743
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
scopus_import: '1'
status: public
title: 'SpaceMint: A cryptocurrency based on proofs of space'
type: conference
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
volume: 10957
year: '2018'
...
---
_id: '6497'
abstract:
- lang: eng
text: T cells are actively scanning pMHC-presenting cells in lymphoid organs and
nonlymphoid tissues (NLTs) with divergent topologies and confinement. How the
T cell actomyosin cytoskeleton facilitates this task in distinct environments
is incompletely understood. Here, we show that lack of Myosin IXb (Myo9b), a negative
regulator of the small GTPase Rho, led to increased Rho-GTP levels and cell surface
stiffness in primary T cells. Nonetheless, intravital imaging revealed robust
motility of Myo9b−/− CD8+ T cells in lymphoid tissue and similar expansion and
differentiation during immune responses. In contrast, accumulation of Myo9b−/−
CD8+ T cells in NLTs was strongly impaired. Specifically, Myo9b was required for
T cell crossing of basement membranes, such as those which are present between
dermis and epidermis. As consequence, Myo9b−/− CD8+ T cells showed impaired control
of skin infections. In sum, we show that Myo9b is critical for the CD8+ T cell
adaptation from lymphoid to NLT surveillance and the establishment of protective
tissue–resident T cell populations.
article_processing_charge: No
author:
- first_name: Federica
full_name: Moalli, Federica
last_name: Moalli
- first_name: Xenia
full_name: Ficht, Xenia
last_name: Ficht
- first_name: Philipp
full_name: Germann, Philipp
last_name: Germann
- first_name: Mykhailo
full_name: Vladymyrov, Mykhailo
last_name: Vladymyrov
- first_name: Bettina
full_name: Stolp, Bettina
last_name: Stolp
- first_name: Ingrid
full_name: de Vries, Ingrid
id: 4C7D837E-F248-11E8-B48F-1D18A9856A87
last_name: de Vries
- first_name: Ruth
full_name: Lyck, Ruth
last_name: Lyck
- first_name: Jasmin
full_name: Balmer, Jasmin
last_name: Balmer
- first_name: Amleto
full_name: Fiocchi, Amleto
last_name: Fiocchi
- first_name: Mario
full_name: Kreutzfeldt, Mario
last_name: Kreutzfeldt
- first_name: Doron
full_name: Merkler, Doron
last_name: Merkler
- first_name: Matteo
full_name: Iannacone, Matteo
last_name: Iannacone
- first_name: Akitaka
full_name: Ariga, Akitaka
last_name: Ariga
- first_name: Michael H.
full_name: Stoffel, Michael H.
last_name: Stoffel
- first_name: James
full_name: Sharpe, James
last_name: Sharpe
- first_name: Martin
full_name: Bähler, Martin
last_name: Bähler
- first_name: Michael K
full_name: Sixt, Michael K
id: 41E9FBEA-F248-11E8-B48F-1D18A9856A87
last_name: Sixt
orcid: 0000-0002-6620-9179
- first_name: Alba
full_name: Diz-Muñoz, Alba
last_name: Diz-Muñoz
- first_name: Jens V.
full_name: Stein, Jens V.
last_name: Stein
citation:
ama: Moalli F, Ficht X, Germann P, et al. The Rho regulator Myosin IXb enables nonlymphoid
tissue seeding of protective CD8+T cells. The Journal of Experimental Medicine.
2018;2015(7):1869–1890. doi:10.1084/jem.20170896
apa: Moalli, F., Ficht, X., Germann, P., Vladymyrov, M., Stolp, B., de Vries, I.,
… Stein, J. V. (2018). The Rho regulator Myosin IXb enables nonlymphoid tissue
seeding of protective CD8+T cells. The Journal of Experimental Medicine.
Rockefeller University Press. https://doi.org/10.1084/jem.20170896
chicago: Moalli, Federica, Xenia Ficht, Philipp Germann, Mykhailo Vladymyrov, Bettina
Stolp, Ingrid de Vries, Ruth Lyck, et al. “The Rho Regulator Myosin IXb Enables
Nonlymphoid Tissue Seeding of Protective CD8+T Cells.” The Journal of Experimental
Medicine. Rockefeller University Press, 2018. https://doi.org/10.1084/jem.20170896.
ieee: F. Moalli et al., “The Rho regulator Myosin IXb enables nonlymphoid
tissue seeding of protective CD8+T cells,” The Journal of Experimental Medicine,
vol. 2015, no. 7. Rockefeller University Press, pp. 1869–1890, 2018.
ista: Moalli F, Ficht X, Germann P, Vladymyrov M, Stolp B, de Vries I, Lyck R, Balmer
J, Fiocchi A, Kreutzfeldt M, Merkler D, Iannacone M, Ariga A, Stoffel MH, Sharpe
J, Bähler M, Sixt MK, Diz-Muñoz A, Stein JV. 2018. The Rho regulator Myosin IXb
enables nonlymphoid tissue seeding of protective CD8+T cells. The Journal of Experimental
Medicine. 2015(7), 1869–1890.
mla: Moalli, Federica, et al. “The Rho Regulator Myosin IXb Enables Nonlymphoid
Tissue Seeding of Protective CD8+T Cells.” The Journal of Experimental Medicine,
vol. 2015, no. 7, Rockefeller University Press, 2018, pp. 1869–1890, doi:10.1084/jem.20170896.
short: F. Moalli, X. Ficht, P. Germann, M. Vladymyrov, B. Stolp, I. de Vries, R.
Lyck, J. Balmer, A. Fiocchi, M. Kreutzfeldt, D. Merkler, M. Iannacone, A. Ariga,
M.H. Stoffel, J. Sharpe, M. Bähler, M.K. Sixt, A. Diz-Muñoz, J.V. Stein, The Journal
of Experimental Medicine 2015 (2018) 1869–1890.
date_created: 2019-05-28T12:36:47Z
date_published: 2018-06-06T00:00:00Z
date_updated: 2023-09-19T14:52:08Z
day: '06'
ddc:
- '570'
department:
- _id: MiSi
doi: 10.1084/jem.20170896
external_id:
isi:
- '000440822900011'
file:
- access_level: open_access
checksum: 86ae5331f9bfced9a6358a790a04bef4
content_type: application/pdf
creator: kschuh
date_created: 2019-05-28T12:40:05Z
date_updated: 2020-07-14T12:47:32Z
file_id: '6498'
file_name: 2018_rupress_Moalli.pdf
file_size: 3841660
relation: main_file
file_date_updated: 2020-07-14T12:47:32Z
has_accepted_license: '1'
intvolume: ' 2015'
isi: 1
issue: '7'
language:
- iso: eng
license: https://creativecommons.org/licenses/by-nc-sa/4.0/
month: '06'
oa: 1
oa_version: Published Version
page: 1869–1890
publication: The Journal of Experimental Medicine
publication_identifier:
eissn:
- 1540-9538
issn:
- 0022-1007
publication_status: published
publisher: Rockefeller University Press
quality_controlled: '1'
scopus_import: '1'
status: public
title: The Rho regulator Myosin IXb enables nonlymphoid tissue seeding of protective
CD8+T cells
tmp:
image: /images/cc_by_nc_sa.png
legal_code_url: https://creativecommons.org/licenses/by-nc-sa/4.0/legalcode
name: Creative Commons Attribution-NonCommercial-ShareAlike 4.0 International (CC
BY-NC-SA 4.0)
short: CC BY-NC-SA (4.0)
type: journal_article
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
volume: 2015
year: '2018'
...
---
_id: '6499'
abstract:
- lang: eng
text: Expansion microscopy is a recently introduced imaging technique that achieves
super‐resolution through physically expanding the specimen by ~4×, after embedding
into a swellable gel. The resolution attained is, correspondingly, approximately
fourfold better than the diffraction limit, or ~70 nm. This is a major improvement
over conventional microscopy, but still lags behind modern STED or STORM setups,
whose resolution can reach 20–30 nm. We addressed this issue here by introducing
an improved gel recipe that enables an expansion factor of ~10× in each dimension,
which corresponds to an expansion of the sample volume by more than 1,000‐fold.
Our protocol, which we termed X10 microscopy, achieves a resolution of 25–30 nm
on conventional epifluorescence microscopes. X10 provides multi‐color images similar
or even superior to those produced with more challenging methods, such as STED,
STORM, and iterative expansion microscopy (iExM). X10 is therefore the cheapest
and easiest option for high‐quality super‐resolution imaging currently available.
X10 should be usable in any laboratory, irrespective of the machinery owned or
of the technical knowledge.
article_number: e45836
article_processing_charge: No
author:
- first_name: Sven M
full_name: Truckenbrodt, Sven M
id: 45812BD4-F248-11E8-B48F-1D18A9856A87
last_name: Truckenbrodt
- first_name: Manuel
full_name: Maidorn, Manuel
last_name: Maidorn
- first_name: Dagmar
full_name: Crzan, Dagmar
last_name: Crzan
- first_name: Hanna
full_name: Wildhagen, Hanna
last_name: Wildhagen
- first_name: Selda
full_name: Kabatas, Selda
last_name: Kabatas
- first_name: Silvio O
full_name: Rizzoli, Silvio O
last_name: Rizzoli
citation:
ama: Truckenbrodt SM, Maidorn M, Crzan D, Wildhagen H, Kabatas S, Rizzoli SO. X10
expansion microscopy enables 25‐nm resolution on conventional microscopes. EMBO
reports. 2018;19(9). doi:10.15252/embr.201845836
apa: Truckenbrodt, S. M., Maidorn, M., Crzan, D., Wildhagen, H., Kabatas, S., &
Rizzoli, S. O. (2018). X10 expansion microscopy enables 25‐nm resolution on conventional
microscopes. EMBO Reports. EMBO. https://doi.org/10.15252/embr.201845836
chicago: Truckenbrodt, Sven M, Manuel Maidorn, Dagmar Crzan, Hanna Wildhagen, Selda
Kabatas, and Silvio O Rizzoli. “X10 Expansion Microscopy Enables 25‐nm Resolution
on Conventional Microscopes.” EMBO Reports. EMBO, 2018. https://doi.org/10.15252/embr.201845836.
ieee: S. M. Truckenbrodt, M. Maidorn, D. Crzan, H. Wildhagen, S. Kabatas, and S.
O. Rizzoli, “X10 expansion microscopy enables 25‐nm resolution on conventional
microscopes,” EMBO reports, vol. 19, no. 9. EMBO, 2018.
ista: Truckenbrodt SM, Maidorn M, Crzan D, Wildhagen H, Kabatas S, Rizzoli SO. 2018.
X10 expansion microscopy enables 25‐nm resolution on conventional microscopes.
EMBO reports. 19(9), e45836.
mla: Truckenbrodt, Sven M., et al. “X10 Expansion Microscopy Enables 25‐nm Resolution
on Conventional Microscopes.” EMBO Reports, vol. 19, no. 9, e45836, EMBO,
2018, doi:10.15252/embr.201845836.
short: S.M. Truckenbrodt, M. Maidorn, D. Crzan, H. Wildhagen, S. Kabatas, S.O. Rizzoli,
EMBO Reports 19 (2018).
date_created: 2019-05-28T13:16:08Z
date_published: 2018-09-01T00:00:00Z
date_updated: 2023-09-19T14:52:32Z
day: '01'
ddc:
- '580'
department:
- _id: JoDa
doi: 10.15252/embr.201845836
external_id:
isi:
- '000443682200009'
file:
- access_level: open_access
checksum: 6ec90abc637f09cca3a7b6424d7e7a26
content_type: application/pdf
creator: kschuh
date_created: 2019-05-28T13:17:19Z
date_updated: 2020-07-14T12:47:32Z
file_id: '6500'
file_name: 2018_embo_Truckenbrodt.pdf
file_size: 2005572
relation: main_file
file_date_updated: 2020-07-14T12:47:32Z
has_accepted_license: '1'
intvolume: ' 19'
isi: 1
issue: '9'
language:
- iso: eng
month: '09'
oa: 1
oa_version: Published Version
publication: EMBO reports
publication_identifier:
eissn:
- 1469-3178
issn:
- 1469-221X
publication_status: published
publisher: EMBO
quality_controlled: '1'
scopus_import: '1'
status: public
title: X10 expansion microscopy enables 25‐nm resolution on conventional microscopes
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: 19
year: '2018'
...
---
_id: '7123'
abstract:
- lang: eng
text: "Population protocols are a popular model of distributed computing, in which
n agents with limited local state interact randomly, and cooperate to collectively
compute global predicates. Inspired by recent developments in DNA programming,
an extensive series of papers, across different communities, has examined the
computability and complexity characteristics of this model. Majority, or consensus,
is a central task in this model, in which agents need to collectively reach a
decision as to which one of two states A or B had a higher initial count. Two
metrics are important: the time that a protocol requires to stabilize to an output
decision, and the state space size that each agent requires to do so. It is known
that majority requires Ω(log log n) states per agent to allow for fast (poly-logarithmic
time) stabilization, and that O(log2 n) states are sufficient. Thus, there is
an exponential gap between the space upper and lower bounds for this problem.
This paper addresses this question.\r\n\r\nOn the negative side, we provide a
new lower bound of Ω(log n) states for any protocol which stabilizes in O(n1–c)
expected time, for any constant c > 0. This result is conditional on monotonicity
and output assumptions, satisfied by all known protocols. Technically, it represents
a departure from previous lower bounds, in that it does not rely on the existence
of dense configurations. Instead, we introduce a new generalized surgery technique
to prove the existence of incorrect executions for any algorithm which would contradict
the lower bound. Subsequently, our lower bound also applies to general initial
configurations, including ones with a leader. On the positive side, we give a
new algorithm for majority which uses O(log n) states, and stabilizes in O(log2
n) expected time. Central to the algorithm is a new leaderless phase clock technique,
which allows agents to synchronize in phases of Θ(n log n) consecutive interactions
using O(log n) states per agent, exploiting a new connection between population
protocols and power-of-two-choices load balancing mechanisms. We also employ our
phase clock to build a leader election algorithm with a state space of size O(log
n), which stabilizes in O(log2 n) expected time."
article_processing_charge: No
author:
- first_name: Dan-Adrian
full_name: Alistarh, Dan-Adrian
id: 4A899BFC-F248-11E8-B48F-1D18A9856A87
last_name: Alistarh
orcid: 0000-0003-3650-940X
- first_name: James
full_name: Aspnes, James
last_name: Aspnes
- first_name: Rati
full_name: Gelashvili, Rati
last_name: Gelashvili
citation:
ama: 'Alistarh D-A, Aspnes J, Gelashvili R. Space-optimal majority in population
protocols. In: Proceedings of the 29th Annual ACM-SIAM Symposium on Discrete
Algorithms. ACM; 2018:2221-2239. doi:10.1137/1.9781611975031.144'
apa: 'Alistarh, D.-A., Aspnes, J., & Gelashvili, R. (2018). Space-optimal majority
in population protocols. In Proceedings of the 29th Annual ACM-SIAM Symposium
on Discrete Algorithms (pp. 2221–2239). New Orleans, LA, United States: ACM.
https://doi.org/10.1137/1.9781611975031.144'
chicago: Alistarh, Dan-Adrian, James Aspnes, and Rati Gelashvili. “Space-Optimal
Majority in Population Protocols.” In Proceedings of the 29th Annual ACM-SIAM
Symposium on Discrete Algorithms, 2221–39. ACM, 2018. https://doi.org/10.1137/1.9781611975031.144.
ieee: D.-A. Alistarh, J. Aspnes, and R. Gelashvili, “Space-optimal majority in population
protocols,” in Proceedings of the 29th Annual ACM-SIAM Symposium on Discrete
Algorithms, New Orleans, LA, United States, 2018, pp. 2221–2239.
ista: 'Alistarh D-A, Aspnes J, Gelashvili R. 2018. Space-optimal majority in population
protocols. Proceedings of the 29th Annual ACM-SIAM Symposium on Discrete Algorithms.
SODA: Symposium on Discrete Algorithms, 2221–2239.'
mla: Alistarh, Dan-Adrian, et al. “Space-Optimal Majority in Population Protocols.”
Proceedings of the 29th Annual ACM-SIAM Symposium on Discrete Algorithms,
ACM, 2018, pp. 2221–39, doi:10.1137/1.9781611975031.144.
short: D.-A. Alistarh, J. Aspnes, R. Gelashvili, in:, Proceedings of the 29th Annual
ACM-SIAM Symposium on Discrete Algorithms, ACM, 2018, pp. 2221–2239.
conference:
end_date: 2018-01-10
location: New Orleans, LA, United States
name: 'SODA: Symposium on Discrete Algorithms'
start_date: 2018-01-07
date_created: 2019-11-26T15:10:55Z
date_published: 2018-01-30T00:00:00Z
date_updated: 2023-09-19T15:03:16Z
day: '30'
department:
- _id: DaAl
doi: 10.1137/1.9781611975031.144
external_id:
arxiv:
- '1704.04947'
isi:
- '000483921200145'
isi: 1
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/1704.04947
month: '01'
oa: 1
oa_version: Preprint
page: 2221-2239
publication: Proceedings of the 29th Annual ACM-SIAM Symposium on Discrete Algorithms
publication_identifier:
isbn:
- '9781611975031'
publication_status: published
publisher: ACM
quality_controlled: '1'
status: public
title: Space-optimal majority in population protocols
type: conference
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
year: '2018'
...
---
_id: '9917'
abstract:
- lang: eng
text: Adaptive divergence and speciation may happen despite opposition by gene flow.
Identifying the genomic basis underlying divergence with gene flow is a major
task in evolutionary genomics. Most approaches (e.g., outlier scans) focus on
genomic regions of high differentiation. However, not all genomic architectures
potentially underlying divergence are expected to show extreme differentiation.
Here, we develop an approach that combines hybrid zone analysis (i.e., focuses
on spatial patterns of allele frequency change) with system-specific simulations
to identify loci inconsistent with neutral evolution. We apply this to a genome-wide
SNP set from an ideally suited study organism, the intertidal snail Littorina
saxatilis, which shows primary divergence between ecotypes associated with different
shore habitats. We detect many SNPs with clinal patterns, most of which are consistent
with neutrality. Among non-neutral SNPs, most are located within three large putative
inversions differentiating ecotypes. Many non-neutral SNPs show relatively low
levels of differentiation. We discuss potential reasons for this pattern, including
loose linkage to selected variants, polygenic adaptation and a component of balancing
selection within populations (which may be expected for inversions). Our work
is in line with theory predicting a role for inversions in divergence, and emphasizes
that genomic regions contributing to divergence may not always be accessible with
methods purely based on allele frequency differences. These conclusions call for
approaches that take spatial patterns of allele frequency change into account
in other systems.
acknowledgement: We are very grateful to people who helped with fieldwork, snail processing,
and DNA extractions, particularly Laura Brettell, Mårten Duvetorp, Juan Galindo,
Anne-Lise Liabot and Irena Senčić. We would also like to thank Magnus Alm Rosenblad
and Mats Töpel for their contribution to assembling the Littorina saxatilis genome,
Carl André, Pasi Rastas, and Romain Villoutreix for discussion, and two anonymous
reviewers for their helpful comments on the manuscript. We are grateful to RapidGenomics
for library preparation and sequencing. We thank the Natural Environment Research
Council, the European Research Council and the Swedish Research Councils VR and
Formas (Linnaeus grant to the Centre for Marine Evolutionary Biology and Tage Erlander
Guest Professorship) for funding. P.C. was funded by the University of Sheffield
Vice-chancellor's India scholarship. R.F. is funded by the European Union's Horizon
2020 research and innovation programme under the Marie Sklodowska-Curie grant agreement
no. 706376. M. Raf. was supported by the Adlerbert Research Foundation.
article_processing_charge: Yes
article_type: letter_note
author:
- first_name: Anja M
full_name: Westram, Anja M
id: 3C147470-F248-11E8-B48F-1D18A9856A87
last_name: Westram
orcid: 0000-0003-1050-4969
- first_name: Marina
full_name: Rafajlović, Marina
last_name: Rafajlović
- first_name: Pragya
full_name: Chaube, Pragya
last_name: Chaube
- first_name: Rui
full_name: Faria, Rui
last_name: Faria
- first_name: Tomas
full_name: Larsson, Tomas
last_name: Larsson
- first_name: Marina
full_name: Panova, Marina
last_name: Panova
- first_name: Mark
full_name: Ravinet, Mark
last_name: Ravinet
- first_name: Anders
full_name: Blomberg, Anders
last_name: Blomberg
- first_name: Bernhard
full_name: Mehlig, Bernhard
last_name: Mehlig
- first_name: Kerstin
full_name: Johannesson, Kerstin
last_name: Johannesson
- first_name: Roger
full_name: Butlin, Roger
last_name: Butlin
citation:
ama: 'Westram AM, Rafajlović M, Chaube P, et al. Clines on the seashore: The genomic
architecture underlying rapid divergence in the face of gene flow. Evolution
Letters. 2018;2(4):297-309. doi:10.1002/evl3.74'
apa: 'Westram, A. M., Rafajlović, M., Chaube, P., Faria, R., Larsson, T., Panova,
M., … Butlin, R. (2018). Clines on the seashore: The genomic architecture underlying
rapid divergence in the face of gene flow. Evolution Letters. Wiley. https://doi.org/10.1002/evl3.74'
chicago: 'Westram, Anja M, Marina Rafajlović, Pragya Chaube, Rui Faria, Tomas Larsson,
Marina Panova, Mark Ravinet, et al. “Clines on the Seashore: The Genomic Architecture
Underlying Rapid Divergence in the Face of Gene Flow.” Evolution Letters.
Wiley, 2018. https://doi.org/10.1002/evl3.74.'
ieee: 'A. M. Westram et al., “Clines on the seashore: The genomic architecture
underlying rapid divergence in the face of gene flow,” Evolution Letters,
vol. 2, no. 4. Wiley, pp. 297–309, 2018.'
ista: 'Westram AM, Rafajlović M, Chaube P, Faria R, Larsson T, Panova M, Ravinet
M, Blomberg A, Mehlig B, Johannesson K, Butlin R. 2018. Clines on the seashore:
The genomic architecture underlying rapid divergence in the face of gene flow.
Evolution Letters. 2(4), 297–309.'
mla: 'Westram, Anja M., et al. “Clines on the Seashore: The Genomic Architecture
Underlying Rapid Divergence in the Face of Gene Flow.” Evolution Letters,
vol. 2, no. 4, Wiley, 2018, pp. 297–309, doi:10.1002/evl3.74.'
short: A.M. Westram, M. Rafajlović, P. Chaube, R. Faria, T. Larsson, M. Panova,
M. Ravinet, A. Blomberg, B. Mehlig, K. Johannesson, R. Butlin, Evolution Letters
2 (2018) 297–309.
date_created: 2021-08-16T07:45:38Z
date_published: 2018-08-20T00:00:00Z
date_updated: 2023-09-19T15:08:25Z
day: '20'
ddc:
- '570'
department:
- _id: BeVi
doi: 10.1002/evl3.74
external_id:
isi:
- '000446774400004'
pmid:
- '30283683'
file:
- access_level: open_access
checksum: 8524e72507d521416be3f8ccfcd5e3f5
content_type: application/pdf
creator: asandaue
date_created: 2021-08-16T07:48:03Z
date_updated: 2021-08-16T07:48:03Z
file_id: '9918'
file_name: 2018_EvolutionLetters_Westram.pdf
file_size: 764299
relation: main_file
success: 1
file_date_updated: 2021-08-16T07:48:03Z
has_accepted_license: '1'
intvolume: ' 2'
isi: 1
issue: '4'
language:
- iso: eng
month: '08'
oa: 1
oa_version: Published Version
page: 297-309
pmid: 1
publication: Evolution Letters
publication_identifier:
eissn:
- 2056-3744
issn:
- 2056-3744
publication_status: published
publisher: Wiley
quality_controlled: '1'
related_material:
record:
- id: '9930'
relation: research_data
status: public
status: public
title: 'Clines on the seashore: The genomic architecture underlying rapid divergence
in the face of gene flow'
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: 2
year: '2018'
...
---
_id: '9915'
abstract:
- lang: eng
text: 'The evolution of assortative mating is a key part of the speciation process.
Stronger assortment, or greater divergence in mating traits, between species pairs
with overlapping ranges is commonly observed, but possible causes of this pattern
of reproductive character displacement are difficult to distinguish. We use a
multidisciplinary approach to provide a rare example where it is possible to distinguish
among hypotheses concerning the evolution of reproductive character displacement.
We build on an earlier comparative analysis that illustrated a strong pattern
of greater divergence in penis form between pairs of sister species with overlapping
ranges than between allopatric sister-species pairs, in a large clade of marine
gastropods (Littorinidae). We investigate both assortative mating and divergence
in male genitalia in one of the sister-species pairs, discriminating among three
contrasting processes each of which can generate a pattern of reproductive character
displacement: reinforcement, reproductive interference and the Templeton effect.
We demonstrate reproductive character displacement in assortative mating, but
not in genital form between this pair of sister species and use demographic models
to distinguish among the different processes. Our results support a model with
no gene flow since secondary contact and thus favor reproductive interference
as the cause of reproductive character displacement for mate choice, rather than
reinforcement. High gene flow within species argues against the Templeton effect.
Secondary contact appears to have had little impact on genital divergence.'
acknowledgement: The authors express a special thanks to Dr Richard Willan at the
Museum and Art Gallery of the Northern Territory for guidance and support in the
field, and to Carole Smadja for reading and commenting on the manuscript. The authors
thank the Government of Western Australia Department of Parks and Wildlife (license
no. 009254) and Fishery Research Division (exemption no. 2262) for assistance with
permits. Khalid Belkhir modified the coalescent sampler msnsam for the specific
needs of this project and Martin Hirsch helped to set up the ABC pipeline and to
modify the summary statistic calculator mscalc. The authors are grateful to the
Crafoord Foundation for supporting this project. R.K.B., A.M.W., and L.D. were supported
by grants from the Natural Environment Research Council, R.K.B. and A.M.W. were
also supported by the European Research Council and R.K.B. and L.D. by the Leverhulme
Trust. M.M.R. was supported by Consejo Nacional de Ciencia y Tecnología and Secretaría
de Educación Pública, Mexico. G.B. was supported by the Centre for Animal Movement
Research (CAnMove) financed by a Linnaeus grant (No. 349-2007-8690) from the Swedish
Research Council and Lund University.
article_processing_charge: Yes
article_type: letter_note
author:
- first_name: Johan
full_name: Hollander, Johan
last_name: Hollander
- first_name: Mauricio
full_name: Montaño-Rendón, Mauricio
last_name: Montaño-Rendón
- first_name: Giuseppe
full_name: Bianco, Giuseppe
last_name: Bianco
- first_name: Xi
full_name: Yang, Xi
last_name: Yang
- first_name: Anja M
full_name: Westram, Anja M
id: 3C147470-F248-11E8-B48F-1D18A9856A87
last_name: Westram
orcid: 0000-0003-1050-4969
- first_name: Ludovic
full_name: Duvaux, Ludovic
last_name: Duvaux
- first_name: David G.
full_name: Reid, David G.
last_name: Reid
- first_name: Roger K.
full_name: Butlin, Roger K.
last_name: Butlin
citation:
ama: Hollander J, Montaño-Rendón M, Bianco G, et al. Are assortative mating and
genital divergence driven by reinforcement? Evolution Letters. 2018;2(6):557-566.
doi:10.1002/evl3.85
apa: Hollander, J., Montaño-Rendón, M., Bianco, G., Yang, X., Westram, A. M., Duvaux,
L., … Butlin, R. K. (2018). Are assortative mating and genital divergence driven
by reinforcement? Evolution Letters. Wiley. https://doi.org/10.1002/evl3.85
chicago: Hollander, Johan, Mauricio Montaño-Rendón, Giuseppe Bianco, Xi Yang, Anja
M Westram, Ludovic Duvaux, David G. Reid, and Roger K. Butlin. “Are Assortative
Mating and Genital Divergence Driven by Reinforcement?” Evolution Letters.
Wiley, 2018. https://doi.org/10.1002/evl3.85.
ieee: J. Hollander et al., “Are assortative mating and genital divergence
driven by reinforcement?,” Evolution Letters, vol. 2, no. 6. Wiley, pp.
557–566, 2018.
ista: Hollander J, Montaño-Rendón M, Bianco G, Yang X, Westram AM, Duvaux L, Reid
DG, Butlin RK. 2018. Are assortative mating and genital divergence driven by reinforcement?
Evolution Letters. 2(6), 557–566.
mla: Hollander, Johan, et al. “Are Assortative Mating and Genital Divergence Driven
by Reinforcement?” Evolution Letters, vol. 2, no. 6, Wiley, 2018, pp. 557–66,
doi:10.1002/evl3.85.
short: J. Hollander, M. Montaño-Rendón, G. Bianco, X. Yang, A.M. Westram, L. Duvaux,
D.G. Reid, R.K. Butlin, Evolution Letters 2 (2018) 557–566.
date_created: 2021-08-16T07:30:00Z
date_published: 2018-12-13T00:00:00Z
date_updated: 2023-09-19T15:08:53Z
day: '13'
ddc:
- '570'
department:
- _id: BeVi
doi: 10.1002/evl3.85
external_id:
isi:
- '000452990000002'
pmid:
- '30564439'
file:
- access_level: open_access
checksum: 997a78ac41c809975ca69cbdea441f88
content_type: application/pdf
creator: asandaue
date_created: 2021-08-16T07:37:28Z
date_updated: 2021-08-16T07:37:28Z
file_id: '9916'
file_name: 2018_EvolutionLetters_Hollander.pdf
file_size: 584606
relation: main_file
success: 1
file_date_updated: 2021-08-16T07:37:28Z
has_accepted_license: '1'
intvolume: ' 2'
isi: 1
issue: '6'
language:
- iso: eng
month: '12'
oa: 1
oa_version: Published Version
page: 557-566
pmid: 1
publication: Evolution Letters
publication_identifier:
eissn:
- 2056-3744
issn:
- ' 2056-3744'
publication_status: published
publisher: Wiley
quality_controlled: '1'
related_material:
record:
- id: '9929'
relation: research_data
status: public
status: public
title: Are assortative mating and genital divergence driven by reinforcement?
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: 2
year: '2018'
...
---
_id: '8618'
abstract:
- lang: eng
text: The reversibly switchable fluorescent proteins (RSFPs) commonly used for RESOLFT
nanoscopy have been developed from fluorescent proteins of the GFP superfamily.
These proteins are bright, but exhibit several drawbacks such as relatively large
size, oxygen-dependence, sensitivity to low pH, and limited switching speed. Therefore,
RSFPs from other origins with improved properties need to be explored. Here, we
report the development of two RSFPs based on the LOV domain of the photoreceptor
protein YtvA from Bacillus subtilis. LOV domains obtain their fluorescence by
association with the abundant cellular cofactor flavin mononucleotide (FMN). Under
illumination with blue and ultraviolet light, they undergo a photocycle, making
these proteins inherently photoswitchable. Our first improved variant, rsLOV1,
can be used for RESOLFT imaging, whereas rsLOV2 proved useful for STED nanoscopy
of living cells with a resolution of down to 50 nm. In addition to their smaller
size compared to GFP-related proteins (17 kDa instead of 27 kDa) and their usability
at low pH, rsLOV1 and rsLOV2 exhibit faster switching kinetics, switching on and
off 3 times faster than rsEGFP2, the fastest-switching RSFP reported to date.
Therefore, LOV-domain-based RSFPs have potential for applications where the switching
speed of GFP-based proteins is limiting.
article_number: '2724'
article_processing_charge: No
article_type: original
author:
- first_name: Carola
full_name: Gregor, Carola
last_name: Gregor
- first_name: Sven C.
full_name: Sidenstein, Sven C.
last_name: Sidenstein
- first_name: Martin
full_name: Andresen, Martin
last_name: Andresen
- first_name: Steffen J.
full_name: Sahl, Steffen J.
last_name: Sahl
- first_name: Johann G
full_name: Danzl, Johann G
id: 42EFD3B6-F248-11E8-B48F-1D18A9856A87
last_name: Danzl
orcid: 0000-0001-8559-3973
- first_name: Stefan W.
full_name: Hell, Stefan W.
last_name: Hell
citation:
ama: Gregor C, Sidenstein SC, Andresen M, Sahl SJ, Danzl JG, Hell SW. Novel reversibly
switchable fluorescent proteins for RESOLFT and STED nanoscopy engineered from
the bacterial photoreceptor YtvA. Scientific Reports. 2018;8. doi:10.1038/s41598-018-19947-1
apa: Gregor, C., Sidenstein, S. C., Andresen, M., Sahl, S. J., Danzl, J. G., &
Hell, S. W. (2018). Novel reversibly switchable fluorescent proteins for RESOLFT
and STED nanoscopy engineered from the bacterial photoreceptor YtvA. Scientific
Reports. Springer Nature. https://doi.org/10.1038/s41598-018-19947-1
chicago: Gregor, Carola, Sven C. Sidenstein, Martin Andresen, Steffen J. Sahl, Johann
G Danzl, and Stefan W. Hell. “Novel Reversibly Switchable Fluorescent Proteins
for RESOLFT and STED Nanoscopy Engineered from the Bacterial Photoreceptor YtvA.”
Scientific Reports. Springer Nature, 2018. https://doi.org/10.1038/s41598-018-19947-1.
ieee: C. Gregor, S. C. Sidenstein, M. Andresen, S. J. Sahl, J. G. Danzl, and S.
W. Hell, “Novel reversibly switchable fluorescent proteins for RESOLFT and STED
nanoscopy engineered from the bacterial photoreceptor YtvA,” Scientific Reports,
vol. 8. Springer Nature, 2018.
ista: Gregor C, Sidenstein SC, Andresen M, Sahl SJ, Danzl JG, Hell SW. 2018. Novel
reversibly switchable fluorescent proteins for RESOLFT and STED nanoscopy engineered
from the bacterial photoreceptor YtvA. Scientific Reports. 8, 2724.
mla: Gregor, Carola, et al. “Novel Reversibly Switchable Fluorescent Proteins for
RESOLFT and STED Nanoscopy Engineered from the Bacterial Photoreceptor YtvA.”
Scientific Reports, vol. 8, 2724, Springer Nature, 2018, doi:10.1038/s41598-018-19947-1.
short: C. Gregor, S.C. Sidenstein, M. Andresen, S.J. Sahl, J.G. Danzl, S.W. Hell,
Scientific Reports 8 (2018).
date_created: 2020-10-06T16:33:37Z
date_published: 2018-02-09T00:00:00Z
date_updated: 2023-09-19T15:04:49Z
day: '09'
ddc:
- '570'
department:
- _id: JoDa
doi: 10.1038/s41598-018-19947-1
external_id:
isi:
- '000424630400037'
pmid:
- '29426833'
file:
- access_level: open_access
checksum: e642080fcbde9584c63544f587c74f03
content_type: application/pdf
creator: dernst
date_created: 2020-10-06T16:35:16Z
date_updated: 2020-10-06T16:35:16Z
file_id: '8619'
file_name: 2018_ScientificReports_Gregor.pdf
file_size: 2818077
relation: main_file
success: 1
file_date_updated: 2020-10-06T16:35:16Z
has_accepted_license: '1'
intvolume: ' 8'
isi: 1
keyword:
- Multidisciplinary
language:
- iso: eng
month: '02'
oa: 1
oa_version: Published Version
pmid: 1
publication: Scientific Reports
publication_identifier:
issn:
- 2045-2322
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
status: public
title: Novel reversibly switchable fluorescent proteins for RESOLFT and STED nanoscopy
engineered from the bacterial photoreceptor YtvA
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: 8
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: 2023-09-19T15:10:43Z
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: '10880'
abstract:
- lang: eng
text: Acquisition of evolutionary novelties is a fundamental process for adapting
to the external environment and invading new niches and results in the diversification
of life, which we can see in the world today. How such novel phenotypic traits
are acquired in the course of evolution and are built up in developing embryos
has been a central question in biology. Whole-genome duplication (WGD) is a process
of genome doubling that supplies raw genetic materials and increases genome complexity.
Recently, it has been gradually revealed that WGD and subsequent fate changes
of duplicated genes can facilitate phenotypic evolution. Here, we review the current
understanding of the relationship between WGD and the acquisition of evolutionary
novelties. We show some examples of this link and discuss how WGD and subsequent
duplicated genes can facilitate phenotypic evolution as well as when such genomic
doubling can be advantageous for adaptation.
acknowledgement: This work was supported by JSPS overseas research fellowships (Y.M.)
and SENSHIN Medical Research Foundation (K.K.T.).
article_processing_charge: No
article_type: original
author:
- first_name: Moriyama
full_name: Yuuta, Moriyama
id: 4968E7C8-F248-11E8-B48F-1D18A9856A87
last_name: Yuuta
orcid: 0000-0002-2853-8051
- first_name: Kazuko
full_name: Koshiba-Takeuchi, Kazuko
last_name: Koshiba-Takeuchi
citation:
ama: Yuuta M, Koshiba-Takeuchi K. Significance of whole-genome duplications on the
emergence of evolutionary novelties. Briefings in Functional Genomics.
2018;17(5):329-338. doi:10.1093/bfgp/ely007
apa: Yuuta, M., & Koshiba-Takeuchi, K. (2018). Significance of whole-genome
duplications on the emergence of evolutionary novelties. Briefings in Functional
Genomics. Oxford University Press. https://doi.org/10.1093/bfgp/ely007
chicago: Yuuta, Moriyama, and Kazuko Koshiba-Takeuchi. “Significance of Whole-Genome
Duplications on the Emergence of Evolutionary Novelties.” Briefings in Functional
Genomics. Oxford University Press, 2018. https://doi.org/10.1093/bfgp/ely007.
ieee: M. Yuuta and K. Koshiba-Takeuchi, “Significance of whole-genome duplications
on the emergence of evolutionary novelties,” Briefings in Functional Genomics,
vol. 17, no. 5. Oxford University Press, pp. 329–338, 2018.
ista: Yuuta M, Koshiba-Takeuchi K. 2018. Significance of whole-genome duplications
on the emergence of evolutionary novelties. Briefings in Functional Genomics.
17(5), 329–338.
mla: Yuuta, Moriyama, and Kazuko Koshiba-Takeuchi. “Significance of Whole-Genome
Duplications on the Emergence of Evolutionary Novelties.” Briefings in Functional
Genomics, vol. 17, no. 5, Oxford University Press, 2018, pp. 329–38, doi:10.1093/bfgp/ely007.
short: M. Yuuta, K. Koshiba-Takeuchi, Briefings in Functional Genomics 17 (2018)
329–338.
date_created: 2022-03-18T12:40:35Z
date_published: 2018-09-01T00:00:00Z
date_updated: 2023-09-19T15:11:22Z
day: '01'
department:
- _id: CaHe
doi: 10.1093/bfgp/ely007
external_id:
isi:
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pmid:
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intvolume: ' 17'
isi: 1
issue: '5'
keyword:
- Genetics
- Molecular Biology
- Biochemistry
- General Medicine
language:
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main_file_link:
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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:
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issn:
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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'
...