---
_id: '5434'
abstract:
- lang: eng
text: DEC-POMDPs extend POMDPs to a multi-agent setting, where several agents operate
in an uncertain environment independently to achieve a joint objective. DEC-POMDPs
have been studied with finite-horizon and infinite-horizon discounted-sum objectives,
and there exist solvers both for exact and approximate solutions. In this work
we consider Goal-DEC-POMDPs, where given a set of target states, the objective
is to ensure that the target set is reached with minimal cost. We consider the
indefinite-horizon (infinite-horizon with either discounted-sum, or undiscounted-sum,
where absorbing goal states have zero-cost) problem. We present a new method to
solve the problem that extends methods for finite-horizon DEC- POMDPs and the
RTDP-Bel approach for POMDPs. We present experimental results on several examples,
and show our approach presents promising results.
alternative_title:
- IST Austria Technical Report
author:
- first_name: '1'
full_name: Anonymous, 1
last_name: Anonymous
- first_name: '2'
full_name: Anonymous, 2
last_name: Anonymous
citation:
ama: Anonymous 1, Anonymous 2. Optimal Cost Indefinite-Horizon Reachability in
Goal DEC-POMDPs. IST Austria; 2015.
apa: Anonymous, 1, & Anonymous, 2. (2015). Optimal cost indefinite-horizon
reachability in goal DEC-POMDPs. IST Austria.
chicago: Anonymous, 1, and 2 Anonymous. Optimal Cost Indefinite-Horizon Reachability
in Goal DEC-POMDPs. IST Austria, 2015.
ieee: 1 Anonymous and 2 Anonymous, Optimal cost indefinite-horizon reachability
in goal DEC-POMDPs. IST Austria, 2015.
ista: Anonymous 1, Anonymous 2. 2015. Optimal cost indefinite-horizon reachability
in goal DEC-POMDPs, IST Austria, 16p.
mla: Anonymous, 1, and 2 Anonymous. Optimal Cost Indefinite-Horizon Reachability
in Goal DEC-POMDPs. IST Austria, 2015.
short: 1 Anonymous, 2 Anonymous, Optimal Cost Indefinite-Horizon Reachability in
Goal DEC-POMDPs, IST Austria, 2015.
date_created: 2018-12-12T11:39:18Z
date_published: 2015-02-19T00:00:00Z
date_updated: 2020-07-14T23:04:59Z
day: '19'
ddc:
- '000'
file:
- access_level: open_access
checksum: 8542fd0b10aed7811cd41077b8ccb632
content_type: application/pdf
creator: system
date_created: 2018-12-12T11:53:14Z
date_updated: 2020-07-14T12:46:53Z
file_id: '5475'
file_name: IST-2015-326-v1+1_main.pdf
file_size: 378162
relation: main_file
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checksum: 84c31c537bdaf7a91909f18d25d640ab
content_type: text/plain
creator: dernst
date_created: 2019-04-16T13:00:33Z
date_updated: 2020-07-14T12:46:53Z
file_id: '6317'
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file_size: 64
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file_date_updated: 2020-07-14T12:46:53Z
has_accepted_license: '1'
language:
- iso: eng
month: '02'
oa: 1
oa_version: Published Version
page: '16'
publication_identifier:
issn:
- 2664-1690
publication_status: published
publisher: IST Austria
pubrep_id: '326'
status: public
title: Optimal cost indefinite-horizon reachability in goal DEC-POMDPs
type: technical_report
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
year: '2015'
...
---
_id: '1657'
abstract:
- lang: eng
text: 'We consider Markov decision processes (MDPs) with multiple limit-average
(or mean-payoff) objectives. There exist two different views: (i) ~the expectation
semantics, where the goal is to optimize the expected mean-payoff objective, and
(ii) ~the satisfaction semantics, where the goal is to maximize the probability
of runs such that the mean-payoff value stays above a given vector. We consider
optimization with respect to both objectives at once, thus unifying the existing
semantics. Precisely, the goal is to optimize the expectation while ensuring the
satisfaction constraint. Our problem captures the notion of optimization with
respect to strategies that are risk-averse (i.e., Ensure certain probabilistic
guarantee). Our main results are as follows: First, we present algorithms for
the decision problems, which are always polynomial in the size of the MDP. We
also show that an approximation of the Pareto curve can be computed in time polynomial
in the size of the MDP, and the approximation factor, but exponential in the number
of dimensions. Second, we present a complete characterization of the strategy
complexity (in terms of memory bounds and randomization) required to solve our
problem. '
acknowledgement: "A Technical Report of this paper is available at: https://repository.ist.ac.at/327\r\n"
alternative_title:
- LICS
author:
- first_name: Krishnendu
full_name: Chatterjee, Krishnendu
id: 2E5DCA20-F248-11E8-B48F-1D18A9856A87
last_name: Chatterjee
orcid: 0000-0002-4561-241X
- first_name: Zuzana
full_name: Komárková, Zuzana
last_name: Komárková
- first_name: Jan
full_name: Kretinsky, Jan
id: 44CEF464-F248-11E8-B48F-1D18A9856A87
last_name: Kretinsky
orcid: 0000-0002-8122-2881
citation:
ama: Chatterjee K, Komárková Z, Kretinsky J. Unifying two views on multiple mean-payoff
objectives in Markov decision processes. 2015:244-256. doi:10.1109/LICS.2015.32
apa: 'Chatterjee, K., Komárková, Z., & Kretinsky, J. (2015). Unifying two views
on multiple mean-payoff objectives in Markov decision processes. Presented at
the LICS: Logic in Computer Science, Kyoto, Japan: IEEE. https://doi.org/10.1109/LICS.2015.32'
chicago: Chatterjee, Krishnendu, Zuzana Komárková, and Jan Kretinsky. “Unifying
Two Views on Multiple Mean-Payoff Objectives in Markov Decision Processes.” LICS.
IEEE, 2015. https://doi.org/10.1109/LICS.2015.32.
ieee: K. Chatterjee, Z. Komárková, and J. Kretinsky, “Unifying two views on multiple
mean-payoff objectives in Markov decision processes.” IEEE, pp. 244–256, 2015.
ista: Chatterjee K, Komárková Z, Kretinsky J. 2015. Unifying two views on multiple
mean-payoff objectives in Markov decision processes. , 244–256.
mla: Chatterjee, Krishnendu, et al. Unifying Two Views on Multiple Mean-Payoff
Objectives in Markov Decision Processes. IEEE, 2015, pp. 244–56, doi:10.1109/LICS.2015.32.
short: K. Chatterjee, Z. Komárková, J. Kretinsky, (2015) 244–256.
conference:
end_date: 2015-07-10
location: Kyoto, Japan
name: 'LICS: Logic in Computer Science'
start_date: 2015-07-06
date_created: 2018-12-11T11:53:18Z
date_published: 2015-07-01T00:00:00Z
date_updated: 2023-02-23T12:26:16Z
day: '01'
department:
- _id: KrCh
- _id: ToHe
doi: 10.1109/LICS.2015.32
ec_funded: 1
language:
- iso: eng
month: '07'
oa_version: None
page: 244 - 256
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: 25F42A32-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: Z211
name: The Wittgenstein Prize
- _id: 2581B60A-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '279307'
name: 'Quantitative Graph Games: Theory and Applications'
- _id: 25EE3708-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '267989'
name: Quantitative Reactive Modeling
- _id: 25681D80-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '291734'
name: International IST Postdoc Fellowship Programme
publication_status: published
publisher: IEEE
publist_id: '5493'
quality_controlled: '1'
related_material:
record:
- id: '466'
relation: later_version
status: public
- id: '5429'
relation: earlier_version
status: public
- id: '5435'
relation: earlier_version
status: public
scopus_import: 1
series_title: LICS
status: public
title: Unifying two views on multiple mean-payoff objectives in Markov decision processes
type: conference
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
year: '2015'
...
---
_id: '1656'
abstract:
- lang: eng
text: Recently there has been a significant effort to handle quantitative properties
in formal verification and synthesis. While weighted automata over finite and
infinite words provide a natural and flexible framework to express quantitative
properties, perhaps surprisingly, some basic system properties such as average
response time cannot be expressed using weighted automata, nor in any other know
decidable formalism. In this work, we introduce nested weighted automata as a
natural extension of weighted automata which makes it possible to express important
quantitative properties such as average response time. In nested weighted automata,
a master automaton spins off and collects results from weighted slave automata,
each of which computes a quantity along a finite portion of an infinite word.
Nested weighted automata can be viewed as the quantitative analogue of monitor
automata, which are used in run-time verification. We establish an almost complete
decidability picture for the basic decision problems about nested weighted automata,
and illustrate their applicability in several domains. In particular, nested weighted
automata can be used to decide average response time properties.
acknowledgement: "This research was funded in part by the European Research Council
(ERC) under grant agreement 267989 (QUAREM), by the Austrian Science Fund (FWF)
projects S11402-N23 (RiSE), Z211-N23 (Wittgenstein Award), FWF Grant No P23499-
N23, FWF NFN Grant No S11407-N23 (RiSE), ERC Start grant (279307: Graph Games),
and Microsoft faculty fellows award.\r\nA Technical Report of the paper is available
at: \r\nhttps://repository.ist.ac.at/331/\r\n"
article_number: '7174926'
author:
- first_name: Krishnendu
full_name: Chatterjee, Krishnendu
id: 2E5DCA20-F248-11E8-B48F-1D18A9856A87
last_name: Chatterjee
orcid: 0000-0002-4561-241X
- first_name: Thomas A
full_name: Henzinger, Thomas A
id: 40876CD8-F248-11E8-B48F-1D18A9856A87
last_name: Henzinger
orcid: 0000−0002−2985−7724
- first_name: Jan
full_name: Otop, Jan
id: 2FC5DA74-F248-11E8-B48F-1D18A9856A87
last_name: Otop
citation:
ama: 'Chatterjee K, Henzinger TA, Otop J. Nested weighted automata. In: Proceedings
- Symposium on Logic in Computer Science. Vol 2015-July. IEEE; 2015. doi:10.1109/LICS.2015.72'
apa: 'Chatterjee, K., Henzinger, T. A., & Otop, J. (2015). Nested weighted automata.
In Proceedings - Symposium on Logic in Computer Science (Vol. 2015–July).
Kyoto, Japan: IEEE. https://doi.org/10.1109/LICS.2015.72'
chicago: Chatterjee, Krishnendu, Thomas A Henzinger, and Jan Otop. “Nested Weighted
Automata.” In Proceedings - Symposium on Logic in Computer Science, Vol.
2015–July. IEEE, 2015. https://doi.org/10.1109/LICS.2015.72.
ieee: K. Chatterjee, T. A. Henzinger, and J. Otop, “Nested weighted automata,” in
Proceedings - Symposium on Logic in Computer Science, Kyoto, Japan, 2015,
vol. 2015–July.
ista: 'Chatterjee K, Henzinger TA, Otop J. 2015. Nested weighted automata. Proceedings
- Symposium on Logic in Computer Science. LICS: Logic in Computer Science vol.
2015–July, 7174926.'
mla: Chatterjee, Krishnendu, et al. “Nested Weighted Automata.” Proceedings -
Symposium on Logic in Computer Science, vol. 2015–July, 7174926, IEEE, 2015,
doi:10.1109/LICS.2015.72.
short: K. Chatterjee, T.A. Henzinger, J. Otop, in:, Proceedings - Symposium on Logic
in Computer Science, IEEE, 2015.
conference:
end_date: 2015-07-10
location: Kyoto, Japan
name: 'LICS: Logic in Computer Science'
start_date: 2015-07-06
date_created: 2018-12-11T11:53:17Z
date_published: 2015-07-31T00:00:00Z
date_updated: 2023-02-23T12:26:19Z
day: '31'
department:
- _id: KrCh
- _id: ToHe
doi: 10.1109/LICS.2015.72
ec_funded: 1
external_id:
arxiv:
- '1606.03598'
language:
- iso: eng
month: '07'
oa_version: None
project:
- _id: 25EE3708-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '267989'
name: Quantitative Reactive Modeling
- _id: 25832EC2-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: S 11407_N23
name: Rigorous Systems Engineering
- _id: 25F42A32-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: Z211
name: The Wittgenstein Prize
- _id: 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: 2587B514-B435-11E9-9278-68D0E5697425
name: Microsoft Research Faculty Fellowship
publication: Proceedings - Symposium on Logic in Computer Science
publication_status: published
publisher: IEEE
publist_id: '5494'
quality_controlled: '1'
related_material:
record:
- id: '467'
relation: later_version
status: public
- id: '5415'
relation: earlier_version
status: public
- id: '5436'
relation: earlier_version
status: public
scopus_import: 1
status: public
title: Nested weighted automata
type: conference
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 2015-July
year: '2015'
...
---
_id: '5429'
abstract:
- lang: eng
text: "We consider Markov decision processes (MDPs) with multiple limit-average
(or mean-payoff) objectives. \r\nThere have been two different views: (i) the
expectation semantics, where the goal is to optimize the expected mean-payoff
objective, and (ii) the satisfaction semantics, where the goal is to maximize
the probability of runs such that the mean-payoff value stays above a given vector.
\ \r\nWe consider the problem where the goal is to optimize the expectation under
the constraint that the satisfaction semantics is ensured, and thus consider a
generalization that unifies the existing semantics.\r\nOur problem captures the
notion of optimization with respect to strategies that are risk-averse (i.e.,
ensures certain probabilistic guarantee).\r\nOur main results are algorithms for
the decision problem which are always polynomial in the size of the MDP. We also
show that an approximation of the Pareto-curve can be computed in time polynomial
in the size of the MDP, and the approximation factor, but exponential in the number
of dimensions.\r\nFinally, we present a complete characterization of the strategy
complexity (in terms of memory bounds and randomization) required to solve our
problem."
alternative_title:
- IST Austria Technical Report
author:
- first_name: Krishnendu
full_name: Chatterjee, Krishnendu
id: 2E5DCA20-F248-11E8-B48F-1D18A9856A87
last_name: Chatterjee
orcid: 0000-0002-4561-241X
- first_name: Zuzana
full_name: Komarkova, Zuzana
last_name: Komarkova
- first_name: Jan
full_name: Kretinsky, Jan
id: 44CEF464-F248-11E8-B48F-1D18A9856A87
last_name: Kretinsky
orcid: 0000-0002-8122-2881
citation:
ama: Chatterjee K, Komarkova Z, Kretinsky J. Unifying Two Views on Multiple Mean-Payoff
Objectives in Markov Decision Processes. IST Austria; 2015. doi:10.15479/AT:IST-2015-318-v1-1
apa: Chatterjee, K., Komarkova, Z., & Kretinsky, J. (2015). Unifying two
views on multiple mean-payoff objectives in Markov decision processes. IST
Austria. https://doi.org/10.15479/AT:IST-2015-318-v1-1
chicago: Chatterjee, Krishnendu, Zuzana Komarkova, and Jan Kretinsky. Unifying
Two Views on Multiple Mean-Payoff Objectives in Markov Decision Processes.
IST Austria, 2015. https://doi.org/10.15479/AT:IST-2015-318-v1-1.
ieee: K. Chatterjee, Z. Komarkova, and J. Kretinsky, Unifying two views on multiple
mean-payoff objectives in Markov decision processes. IST Austria, 2015.
ista: Chatterjee K, Komarkova Z, Kretinsky J. 2015. Unifying two views on multiple
mean-payoff objectives in Markov decision processes, IST Austria, 41p.
mla: Chatterjee, Krishnendu, et al. Unifying Two Views on Multiple Mean-Payoff
Objectives in Markov Decision Processes. IST Austria, 2015, doi:10.15479/AT:IST-2015-318-v1-1.
short: K. Chatterjee, Z. Komarkova, J. Kretinsky, Unifying Two Views on Multiple
Mean-Payoff Objectives in Markov Decision Processes, IST Austria, 2015.
date_created: 2018-12-12T11:39:17Z
date_published: 2015-01-12T00:00:00Z
date_updated: 2023-02-23T12:26:16Z
day: '12'
ddc:
- '004'
department:
- _id: KrCh
doi: 10.15479/AT:IST-2015-318-v1-1
file:
- access_level: open_access
checksum: e4869a584567c506349abda9c8ec7db3
content_type: application/pdf
creator: system
date_created: 2018-12-12T11:54:11Z
date_updated: 2020-07-14T12:46:52Z
file_id: '5533'
file_name: IST-2015-318-v1+1_main.pdf
file_size: 689863
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file_date_updated: 2020-07-14T12:46:52Z
has_accepted_license: '1'
language:
- iso: eng
month: '01'
oa: 1
oa_version: Published Version
page: '41'
publication_identifier:
issn:
- 2664-1690
publication_status: published
publisher: IST Austria
pubrep_id: '318'
related_material:
record:
- id: '1657'
relation: later_version
status: public
- id: '466'
relation: later_version
status: public
- id: '5435'
relation: later_version
status: public
status: public
title: Unifying two views on multiple mean-payoff objectives in Markov decision processes
type: technical_report
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
year: '2015'
...
---
_id: '5435'
abstract:
- lang: eng
text: "We consider Markov decision processes (MDPs) with multiple limit-average
(or mean-payoff) objectives. \r\nThere have been two different views: (i) the
expectation semantics, where the goal is to optimize the expected mean-payoff
objective, and (ii) the satisfaction semantics, where the goal is to maximize
the probability of runs such that the mean-payoff value stays above a given vector.
\ \r\nWe consider the problem where the goal is to optimize the expectation under
the constraint that the satisfaction semantics is ensured, and thus consider a
generalization that unifies the existing semantics. Our problem captures the notion
of optimization with respect to strategies that are risk-averse (i.e., ensures
certain probabilistic guarantee).\r\nOur main results are algorithms for the decision
problem which are always polynomial in the size of the MDP.\r\nWe also show that
an approximation of the Pareto-curve can be computed in time polynomial in the
size of the MDP, and the approximation factor, but exponential in the number of
dimensions. Finally, we present a complete characterization of the strategy complexity
(in terms of memory bounds and randomization) required to solve our problem."
alternative_title:
- IST Austria Technical Report
author:
- first_name: Krishnendu
full_name: Chatterjee, Krishnendu
id: 2E5DCA20-F248-11E8-B48F-1D18A9856A87
last_name: Chatterjee
orcid: 0000-0002-4561-241X
- first_name: Zuzana
full_name: Komarkova, Zuzana
last_name: Komarkova
- first_name: Jan
full_name: Kretinsky, Jan
id: 44CEF464-F248-11E8-B48F-1D18A9856A87
last_name: Kretinsky
orcid: 0000-0002-8122-2881
citation:
ama: Chatterjee K, Komarkova Z, Kretinsky J. Unifying Two Views on Multiple Mean-Payoff
Objectives in Markov Decision Processes. IST Austria; 2015. doi:10.15479/AT:IST-2015-318-v2-1
apa: Chatterjee, K., Komarkova, Z., & Kretinsky, J. (2015). Unifying two
views on multiple mean-payoff objectives in Markov decision processes. IST
Austria. https://doi.org/10.15479/AT:IST-2015-318-v2-1
chicago: Chatterjee, Krishnendu, Zuzana Komarkova, and Jan Kretinsky. Unifying
Two Views on Multiple Mean-Payoff Objectives in Markov Decision Processes.
IST Austria, 2015. https://doi.org/10.15479/AT:IST-2015-318-v2-1.
ieee: K. Chatterjee, Z. Komarkova, and J. Kretinsky, Unifying two views on multiple
mean-payoff objectives in Markov decision processes. IST Austria, 2015.
ista: Chatterjee K, Komarkova Z, Kretinsky J. 2015. Unifying two views on multiple
mean-payoff objectives in Markov decision processes, IST Austria, 51p.
mla: Chatterjee, Krishnendu, et al. Unifying Two Views on Multiple Mean-Payoff
Objectives in Markov Decision Processes. IST Austria, 2015, doi:10.15479/AT:IST-2015-318-v2-1.
short: K. Chatterjee, Z. Komarkova, J. Kretinsky, Unifying Two Views on Multiple
Mean-Payoff Objectives in Markov Decision Processes, IST Austria, 2015.
date_created: 2018-12-12T11:39:19Z
date_published: 2015-02-23T00:00:00Z
date_updated: 2023-02-23T12:26:00Z
day: '23'
ddc:
- '004'
department:
- _id: KrCh
doi: 10.15479/AT:IST-2015-318-v2-1
file:
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checksum: 75284adec80baabdfe71ff9ebbc27445
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publication_identifier:
issn:
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publication_status: published
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pubrep_id: '327'
related_material:
record:
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relation: later_version
status: public
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relation: later_version
status: public
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status: public
title: Unifying two views on multiple mean-payoff objectives in Markov decision processes
type: technical_report
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
year: '2015'
...
---
_id: '5436'
abstract:
- lang: eng
text: "Recently there has been a significant effort to handle quantitative properties
in formal verification and synthesis. While weighted automata over finite and
infinite words provide a natural and flexible framework to express quantitative
properties, perhaps surprisingly, some basic system properties such as average
response time cannot be expressed using weighted automata, nor in any other know
decidable formalism. In this work, we introduce nested weighted automata as a
natural extension of weighted automata which makes it possible to express important
quantitative properties such as average response time.\r\nIn nested weighted automata,
a master automaton spins off and collects results from weighted slave automata,
each of which computes a quantity along a finite portion of an infinite word.
Nested weighted automata can be viewed as the quantitative analogue of monitor
automata, which are used in run-time verification. We establish an almost complete
decidability picture for the basic decision problems about nested weighted automata,
and illustrate their applicability in several domains. In particular, nested weighted
automata can be used to decide average response time properties."
alternative_title:
- IST Austria Technical Report
author:
- first_name: Krishnendu
full_name: Chatterjee, Krishnendu
id: 2E5DCA20-F248-11E8-B48F-1D18A9856A87
last_name: Chatterjee
orcid: 0000-0002-4561-241X
- first_name: Thomas A
full_name: Henzinger, Thomas A
id: 40876CD8-F248-11E8-B48F-1D18A9856A87
last_name: Henzinger
orcid: 0000−0002−2985−7724
- first_name: Jan
full_name: Otop, Jan
id: 2FC5DA74-F248-11E8-B48F-1D18A9856A87
last_name: Otop
citation:
ama: Chatterjee K, Henzinger TA, Otop J. Nested Weighted Automata. IST Austria;
2015. doi:10.15479/AT:IST-2015-170-v2-2
apa: Chatterjee, K., Henzinger, T. A., & Otop, J. (2015). Nested weighted
automata. IST Austria. https://doi.org/10.15479/AT:IST-2015-170-v2-2
chicago: Chatterjee, Krishnendu, Thomas A Henzinger, and Jan Otop. Nested Weighted
Automata. IST Austria, 2015. https://doi.org/10.15479/AT:IST-2015-170-v2-2.
ieee: K. Chatterjee, T. A. Henzinger, and J. Otop, Nested weighted automata.
IST Austria, 2015.
ista: Chatterjee K, Henzinger TA, Otop J. 2015. Nested weighted automata, IST Austria,
29p.
mla: Chatterjee, Krishnendu, et al. Nested Weighted Automata. IST Austria,
2015, doi:10.15479/AT:IST-2015-170-v2-2.
short: K. Chatterjee, T.A. Henzinger, J. Otop, Nested Weighted Automata, IST Austria,
2015.
date_created: 2018-12-12T11:39:19Z
date_published: 2015-04-24T00:00:00Z
date_updated: 2023-02-23T12:25:21Z
day: '24'
ddc:
- '000'
department:
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- _id: ToHe
doi: 10.15479/AT:IST-2015-170-v2-2
file:
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checksum: 3c402f47d3669c28d04d1af405a08e3f
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language:
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month: '04'
oa: 1
oa_version: Published Version
page: '29'
publication_identifier:
issn:
- 2664-1690
publication_status: published
publisher: IST Austria
pubrep_id: '331'
related_material:
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status: public
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relation: later_version
status: public
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relation: earlier_version
status: public
status: public
title: Nested weighted automata
type: technical_report
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
year: '2015'
...
---
_id: '1659'
abstract:
- lang: eng
text: 'The target discounted-sum problem is the following: Given a rational discount
factor 0 < λ < 1 and three rational values a, b, and t, does there exist
a finite or an infinite sequence w ε(a, b)∗ or w ε(a, b)w, such that Σ|w| i=0
w(i)λi equals t? The problem turns out to relate to many fields of mathematics
and computer science, and its decidability question is surprisingly hard to solve.
We solve the finite version of the problem, and show the hardness of the infinite
version, linking it to various areas and open problems in mathematics and computer
science: β-expansions, discounted-sum automata, piecewise affine maps, and generalizations
of the Cantor set. We provide some partial results to the infinite version, among
which are solutions to its restriction to eventually-periodic sequences and to
the cases that λ λ 1/2 or λ = 1/n, for every n ε N. We use our results for solving
some open problems on discounted-sum automata, among which are the exact-value
problem for nondeterministic automata over finite words and the universality and
inclusion problems for functional automata.'
acknowledgement: 'A technical report of the article is available at: https://research-explorer.app.ist.ac.at/record/5439'
article_processing_charge: No
author:
- first_name: Udi
full_name: Boker, Udi
id: 31E297B6-F248-11E8-B48F-1D18A9856A87
last_name: Boker
- first_name: Thomas A
full_name: Henzinger, Thomas A
id: 40876CD8-F248-11E8-B48F-1D18A9856A87
last_name: Henzinger
orcid: 0000−0002−2985−7724
- first_name: Jan
full_name: Otop, Jan
id: 2FC5DA74-F248-11E8-B48F-1D18A9856A87
last_name: Otop
citation:
ama: 'Boker U, Henzinger TA, Otop J. The target discounted-sum problem. In: LICS.
Logic in Computer Science. IEEE; 2015:750-761. doi:10.1109/LICS.2015.74'
apa: 'Boker, U., Henzinger, T. A., & Otop, J. (2015). The target discounted-sum
problem. In LICS (pp. 750–761). Kyoto, Japan: IEEE. https://doi.org/10.1109/LICS.2015.74'
chicago: Boker, Udi, Thomas A Henzinger, and Jan Otop. “The Target Discounted-Sum
Problem.” In LICS, 750–61. Logic in Computer Science. IEEE, 2015. https://doi.org/10.1109/LICS.2015.74.
ieee: U. Boker, T. A. Henzinger, and J. Otop, “The target discounted-sum problem,”
in LICS, Kyoto, Japan, 2015, pp. 750–761.
ista: 'Boker U, Henzinger TA, Otop J. 2015. The target discounted-sum problem. LICS.
LICS: Logic in Computer ScienceLogic in Computer Science, 750–761.'
mla: Boker, Udi, et al. “The Target Discounted-Sum Problem.” LICS, IEEE,
2015, pp. 750–61, doi:10.1109/LICS.2015.74.
short: U. Boker, T.A. Henzinger, J. Otop, in:, LICS, IEEE, 2015, pp. 750–761.
conference:
end_date: 2015-07-10
location: Kyoto, Japan
name: 'LICS: Logic in Computer Science'
start_date: 2015-007-06
date_created: 2018-12-11T11:53:19Z
date_published: 2015-07-01T00:00:00Z
date_updated: 2023-02-23T12:26:27Z
day: '01'
ddc:
- '000'
department:
- _id: ToHe
doi: 10.1109/LICS.2015.74
ec_funded: 1
file:
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checksum: 6abebca9c1a620e9e103a8f9222befac
content_type: application/pdf
creator: dernst
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file_size: 340215
relation: main_file
file_date_updated: 2020-07-14T12:45:10Z
has_accepted_license: '1'
language:
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month: '07'
oa: 1
oa_version: Submitted Version
page: 750 - 761
project:
- _id: 25EE3708-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '267989'
name: Quantitative Reactive Modeling
- _id: 25832EC2-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: S 11407_N23
name: Rigorous Systems Engineering
- _id: 25F42A32-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: Z211
name: The Wittgenstein Prize
publication: LICS
publication_identifier:
eisbn:
- '978-1-4799-8875-4 '
issn:
- '1043-6871 '
publication_status: published
publisher: IEEE
publist_id: '5491'
quality_controlled: '1'
related_material:
record:
- id: '5439'
relation: earlier_version
status: public
scopus_import: 1
series_title: Logic in Computer Science
status: public
title: The target discounted-sum problem
type: conference
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
year: '2015'
...
---
_id: '1610'
abstract:
- lang: eng
text: The edit distance between two words w1, w2 is the minimal number of word operations
(letter insertions, deletions, and substitutions) necessary to transform w1 to
w2. The edit distance generalizes to languages L1,L2, where the edit distance
is the minimal number k such that for every word from L1 there exists a word in
L2 with edit distance at most k. We study the edit distance computation problem
between pushdown automata and their subclasses. The problem of computing edit
distance to pushdown automata is undecidable, and in practice, the interesting
question is to compute the edit distance from a pushdown automaton (the implementation,
a standard model for programs with recursion) to a regular language (the specification).
In this work, we present a complete picture of decidability and complexity for
deciding whether, for a given threshold k, the edit distance from a pushdown automaton
to a finite automaton is at most k.
alternative_title:
- LNCS
article_processing_charge: No
author:
- first_name: Krishnendu
full_name: Chatterjee, Krishnendu
id: 2E5DCA20-F248-11E8-B48F-1D18A9856A87
last_name: Chatterjee
orcid: 0000-0002-4561-241X
- first_name: Thomas A
full_name: Henzinger, Thomas A
id: 40876CD8-F248-11E8-B48F-1D18A9856A87
last_name: Henzinger
orcid: 0000−0002−2985−7724
- first_name: Rasmus
full_name: Ibsen-Jensen, Rasmus
id: 3B699956-F248-11E8-B48F-1D18A9856A87
last_name: Ibsen-Jensen
orcid: 0000-0003-4783-0389
- first_name: Jan
full_name: Otop, Jan
id: 2FC5DA74-F248-11E8-B48F-1D18A9856A87
last_name: Otop
citation:
ama: 'Chatterjee K, Henzinger TA, Ibsen-Jensen R, Otop J. Edit distance for pushdown
automata. In: 42nd International Colloquium. Vol 9135. Springer Nature;
2015:121-133. doi:10.1007/978-3-662-47666-6_10'
apa: 'Chatterjee, K., Henzinger, T. A., Ibsen-Jensen, R., & Otop, J. (2015).
Edit distance for pushdown automata. In 42nd International Colloquium (Vol.
9135, pp. 121–133). Kyoto, Japan: Springer Nature. https://doi.org/10.1007/978-3-662-47666-6_10'
chicago: Chatterjee, Krishnendu, Thomas A Henzinger, Rasmus Ibsen-Jensen, and Jan
Otop. “Edit Distance for Pushdown Automata.” In 42nd International Colloquium,
9135:121–33. Springer Nature, 2015. https://doi.org/10.1007/978-3-662-47666-6_10.
ieee: K. Chatterjee, T. A. Henzinger, R. Ibsen-Jensen, and J. Otop, “Edit distance
for pushdown automata,” in 42nd International Colloquium, Kyoto, Japan,
2015, vol. 9135, no. Part II, pp. 121–133.
ista: 'Chatterjee K, Henzinger TA, Ibsen-Jensen R, Otop J. 2015. Edit distance for
pushdown automata. 42nd International Colloquium. ICALP: Automata, Languages and
Programming, LNCS, vol. 9135, 121–133.'
mla: Chatterjee, Krishnendu, et al. “Edit Distance for Pushdown Automata.” 42nd
International Colloquium, vol. 9135, no. Part II, Springer Nature, 2015, pp.
121–33, doi:10.1007/978-3-662-47666-6_10.
short: K. Chatterjee, T.A. Henzinger, R. Ibsen-Jensen, J. Otop, in:, 42nd International
Colloquium, Springer Nature, 2015, pp. 121–133.
conference:
end_date: 2015-07-10
location: Kyoto, Japan
name: 'ICALP: Automata, Languages and Programming'
start_date: 2015-07-06
date_created: 2018-12-11T11:53:01Z
date_published: 2015-07-01T00:00:00Z
date_updated: 2023-02-23T12:26:24Z
day: '01'
department:
- _id: KrCh
- _id: ToHe
doi: 10.1007/978-3-662-47666-6_10
ec_funded: 1
external_id:
arxiv:
- '1504.08259'
intvolume: ' 9135'
issue: Part II
language:
- iso: eng
main_file_link:
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url: https://arxiv.org/abs/1504.08259
month: '07'
oa: 1
oa_version: None
page: 121 - 133
project:
- _id: 25EE3708-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '267989'
name: Quantitative Reactive Modeling
- _id: 25F42A32-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: Z211
name: The Wittgenstein Prize
- _id: 2584A770-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: P 23499-N23
name: Modern Graph Algorithmic Techniques in Formal Verification
- _id: 25863FF4-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: S11407
name: Game Theory
- _id: 2581B60A-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '279307'
name: 'Quantitative Graph Games: Theory and Applications'
- _id: 2587B514-B435-11E9-9278-68D0E5697425
name: Microsoft Research Faculty Fellowship
- _id: 25832EC2-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: S 11407_N23
name: Rigorous Systems Engineering
publication: 42nd International Colloquium
publication_identifier:
isbn:
- 978-3-662-47665-9
publication_status: published
publisher: Springer Nature
publist_id: '5556'
pubrep_id: '321'
quality_controlled: '1'
related_material:
record:
- id: '465'
relation: later_version
status: public
- id: '5438'
relation: earlier_version
status: public
scopus_import: '1'
status: public
title: Edit distance for pushdown automata
type: conference
user_id: 8b945eb4-e2f2-11eb-945a-df72226e66a9
volume: 9135
year: '2015'
...
---
_id: '5437'
abstract:
- lang: eng
text: "We consider the core algorithmic problems related to verification of systems
with respect to three classical quantitative properties, namely, the mean-payoff
property, the ratio property, and the minimum initial credit for energy property.
\r\nThe algorithmic problem given a graph and a quantitative property asks to
compute the optimal value (the infimum value over all traces) from every node
of the graph. We consider graphs with constant treewidth, and it is well-known
that the control-flow graphs of most programs have constant treewidth. Let $n$
denote the number of nodes of a graph, $m$ the number of edges (for constant treewidth
graphs $m=O(n)$) and $W$ the largest absolute value of the weights.\r\nOur main
theoretical results are as follows.\r\nFirst, for constant treewidth graphs we
present an algorithm that approximates the mean-payoff value within a multiplicative
factor of $\\epsilon$ in time $O(n \\cdot \\log (n/\\epsilon))$ and linear space,
as compared to the classical algorithms that require quadratic time. Second, for
the ratio property we present an algorithm that for constant treewidth graphs
works in time $O(n \\cdot \\log (|a\\cdot b|))=O(n\\cdot\\log (n\\cdot W))$, when
the output is $\\frac{a}{b}$, as compared to the previously best known algorithm
with running time $O(n^2 \\cdot \\log (n\\cdot W))$. Third, for the minimum initial
credit problem we show that (i)~for general graphs the problem can be solved in
$O(n^2\\cdot m)$ time and the associated decision problem can be solved in $O(n\\cdot
m)$ time, improving the previous known $O(n^3\\cdot m\\cdot \\log (n\\cdot W))$
and $O(n^2 \\cdot m)$ bounds, respectively; and (ii)~for constant treewidth graphs
we present an algorithm that requires $O(n\\cdot \\log n)$ time, improving the
previous known $O(n^4 \\cdot \\log (n \\cdot W))$ bound.\r\nWe have implemented
some of our algorithms and show that they present a significant speedup on standard
benchmarks. "
alternative_title:
- IST Austria Technical Report
author:
- first_name: Krishnendu
full_name: Chatterjee, Krishnendu
id: 2E5DCA20-F248-11E8-B48F-1D18A9856A87
last_name: Chatterjee
orcid: 0000-0002-4561-241X
- first_name: Rasmus
full_name: Ibsen-Jensen, Rasmus
id: 3B699956-F248-11E8-B48F-1D18A9856A87
last_name: Ibsen-Jensen
orcid: 0000-0003-4783-0389
- first_name: Andreas
full_name: Pavlogiannis, Andreas
id: 49704004-F248-11E8-B48F-1D18A9856A87
last_name: Pavlogiannis
orcid: 0000-0002-8943-0722
citation:
ama: Chatterjee K, Ibsen-Jensen R, Pavlogiannis A. Faster Algorithms for Quantitative
Verification in Constant Treewidth Graphs. IST Austria; 2015. doi:10.15479/AT:IST-2015-330-v2-1
apa: Chatterjee, K., Ibsen-Jensen, R., & Pavlogiannis, A. (2015). Faster
algorithms for quantitative verification in constant treewidth graphs. IST
Austria. https://doi.org/10.15479/AT:IST-2015-330-v2-1
chicago: Chatterjee, Krishnendu, Rasmus Ibsen-Jensen, and Andreas Pavlogiannis.
Faster Algorithms for Quantitative Verification in Constant Treewidth Graphs.
IST Austria, 2015. https://doi.org/10.15479/AT:IST-2015-330-v2-1.
ieee: K. Chatterjee, R. Ibsen-Jensen, and A. Pavlogiannis, Faster algorithms
for quantitative verification in constant treewidth graphs. IST Austria, 2015.
ista: Chatterjee K, Ibsen-Jensen R, Pavlogiannis A. 2015. Faster algorithms for
quantitative verification in constant treewidth graphs, IST Austria, 27p.
mla: Chatterjee, Krishnendu, et al. Faster Algorithms for Quantitative Verification
in Constant Treewidth Graphs. IST Austria, 2015, doi:10.15479/AT:IST-2015-330-v2-1.
short: K. Chatterjee, R. Ibsen-Jensen, A. Pavlogiannis, Faster Algorithms for Quantitative
Verification in Constant Treewidth Graphs, IST Austria, 2015.
date_created: 2018-12-12T11:39:19Z
date_published: 2015-04-27T00:00:00Z
date_updated: 2023-02-23T12:26:05Z
day: '27'
ddc:
- '000'
department:
- _id: KrCh
doi: 10.15479/AT:IST-2015-330-v2-1
file:
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checksum: f5917c20f84018b362d385c000a2e123
content_type: application/pdf
creator: system
date_created: 2018-12-12T11:53:12Z
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language:
- iso: eng
month: '04'
oa: 1
oa_version: Published Version
page: '27'
publication_identifier:
issn:
- 2664-1690
publication_status: published
publisher: IST Austria
pubrep_id: '333'
related_material:
record:
- id: '1607'
relation: later_version
status: public
- id: '5430'
relation: earlier_version
status: public
status: public
title: Faster algorithms for quantitative verification in constant treewidth graphs
type: technical_report
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
year: '2015'
...
---
_id: '5430'
abstract:
- lang: eng
text: We consider the core algorithmic problems related to verification of systems
with respect to three classical quantitative properties, namely, the mean- payoff
property, the ratio property, and the minimum initial credit for energy property.
The algorithmic problem given a graph and a quantitative property asks to compute
the optimal value (the infimum value over all traces) from every node of the graph.
We consider graphs with constant treewidth, and it is well-known that the control-flow
graphs of most programs have constant treewidth. Let n denote the number of nodes
of a graph, m the number of edges (for constant treewidth graphs m = O ( n ) )
and W the largest absolute value of the weights. Our main theoretical results
are as follows. First, for constant treewidth graphs we present an algorithm that
approximates the mean-payoff value within a mul- tiplicative factor of ∊ in time
O ( n · log( n/∊ )) and linear space, as compared to the classical algorithms
that require quadratic time. Second, for the ratio property we present an algorithm
that for constant treewidth graphs works in time O ( n · log( | a · b · n | ))
= O ( n · log( n · W )) , when the output is a b , as compared to the previously
best known algorithm with running time O ( n 2 · log( n · W )) . Third, for the
minimum initial credit problem we show that (i) for general graphs the problem
can be solved in O ( n 2 · m ) time and the associated decision problem can be
solved in O ( n · m ) time, improving the previous known O ( n 3 · m · log( n
· W )) and O ( n 2 · m ) bounds, respectively; and (ii) for constant treewidth
graphs we present an algorithm that requires O ( n · log n ) time, improving the
previous known O ( n 4 · log( n · W )) bound. We have implemented some of our
algorithms and show that they present a significant speedup on standard benchmarks.
alternative_title:
- IST Austria Technical Report
author:
- first_name: Krishnendu
full_name: Chatterjee, Krishnendu
id: 2E5DCA20-F248-11E8-B48F-1D18A9856A87
last_name: Chatterjee
orcid: 0000-0002-4561-241X
- first_name: Rasmus
full_name: Ibsen-Jensen, Rasmus
id: 3B699956-F248-11E8-B48F-1D18A9856A87
last_name: Ibsen-Jensen
orcid: 0000-0003-4783-0389
- first_name: Andreas
full_name: Pavlogiannis, Andreas
id: 49704004-F248-11E8-B48F-1D18A9856A87
last_name: Pavlogiannis
orcid: 0000-0002-8943-0722
citation:
ama: Chatterjee K, Ibsen-Jensen R, Pavlogiannis A. Faster Algorithms for Quantitative
Verification in Constant Treewidth Graphs. IST Austria; 2015. doi:10.15479/AT:IST-2015-319-v1-1
apa: Chatterjee, K., Ibsen-Jensen, R., & Pavlogiannis, A. (2015). Faster
algorithms for quantitative verification in constant treewidth graphs. IST
Austria. https://doi.org/10.15479/AT:IST-2015-319-v1-1
chicago: Chatterjee, Krishnendu, Rasmus Ibsen-Jensen, and Andreas Pavlogiannis.
Faster Algorithms for Quantitative Verification in Constant Treewidth Graphs.
IST Austria, 2015. https://doi.org/10.15479/AT:IST-2015-319-v1-1.
ieee: K. Chatterjee, R. Ibsen-Jensen, and A. Pavlogiannis, Faster algorithms
for quantitative verification in constant treewidth graphs. IST Austria, 2015.
ista: Chatterjee K, Ibsen-Jensen R, Pavlogiannis A. 2015. Faster algorithms for
quantitative verification in constant treewidth graphs, IST Austria, 31p.
mla: Chatterjee, Krishnendu, et al. Faster Algorithms for Quantitative Verification
in Constant Treewidth Graphs. IST Austria, 2015, doi:10.15479/AT:IST-2015-319-v1-1.
short: K. Chatterjee, R. Ibsen-Jensen, A. Pavlogiannis, Faster Algorithms for Quantitative
Verification in Constant Treewidth Graphs, IST Austria, 2015.
date_created: 2018-12-12T11:39:17Z
date_published: 2015-02-10T00:00:00Z
date_updated: 2023-02-23T12:26:22Z
day: '10'
ddc:
- '000'
department:
- _id: KrCh
doi: 10.15479/AT:IST-2015-319-v1-1
file:
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checksum: 62c6ea01e342553dcafb88a070fb1ad5
content_type: application/pdf
creator: system
date_created: 2018-12-12T11:53:21Z
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has_accepted_license: '1'
language:
- iso: eng
month: '02'
oa: 1
oa_version: Published Version
page: '31'
publication_identifier:
issn:
- 2664-1690
publication_status: published
publisher: IST Austria
pubrep_id: '319'
related_material:
record:
- id: '1607'
relation: later_version
status: public
- id: '5437'
relation: later_version
status: public
status: public
title: Faster algorithms for quantitative verification in constant treewidth graphs
type: technical_report
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
year: '2015'
...
---
_id: '5439'
abstract:
- lang: eng
text: 'The target discounted-sum problem is the following: Given a rational discount
factor 0 < λ < 1 and three rational values a, b, and t, does there exist a finite
or an infinite sequence w ε(a, b)∗ or w ε(a, b)w, such that Σ|w| i=0 w(i)λi equals
t? The problem turns out to relate to many fields of mathematics and computer
science, and its decidability question is surprisingly hard to solve. We solve
the finite version of the problem, and show the hardness of the infinite version,
linking it to various areas and open problems in mathematics and computer science:
β-expansions, discounted-sum automata, piecewise affine maps, and generalizations
of the Cantor set. We provide some partial results to the infinite version, among
which are solutions to its restriction to eventually-periodic sequences and to
the cases that λ λ 1/2 or λ = 1/n, for every n ε N. We use our results for solving
some open problems on discounted-sum automata, among which are the exact-value
problem for nondeterministic automata over finite words and the universality and
inclusion problems for functional automata. '
alternative_title:
- IST Austria Technical Report
author:
- first_name: Udi
full_name: Boker, Udi
id: 31E297B6-F248-11E8-B48F-1D18A9856A87
last_name: Boker
- first_name: Thomas A
full_name: Henzinger, Thomas A
id: 40876CD8-F248-11E8-B48F-1D18A9856A87
last_name: Henzinger
orcid: 0000−0002−2985−7724
- first_name: Jan
full_name: Otop, Jan
id: 2FC5DA74-F248-11E8-B48F-1D18A9856A87
last_name: Otop
citation:
ama: Boker U, Henzinger TA, Otop J. The Target Discounted-Sum Problem. IST
Austria; 2015. doi:10.15479/AT:IST-2015-335-v1-1
apa: Boker, U., Henzinger, T. A., & Otop, J. (2015). The target discounted-sum
problem. IST Austria. https://doi.org/10.15479/AT:IST-2015-335-v1-1
chicago: Boker, Udi, Thomas A Henzinger, and Jan Otop. The Target Discounted-Sum
Problem. IST Austria, 2015. https://doi.org/10.15479/AT:IST-2015-335-v1-1.
ieee: U. Boker, T. A. Henzinger, and J. Otop, The target discounted-sum problem.
IST Austria, 2015.
ista: Boker U, Henzinger TA, Otop J. 2015. The target discounted-sum problem, IST
Austria, 20p.
mla: Boker, Udi, et al. The Target Discounted-Sum Problem. IST Austria, 2015,
doi:10.15479/AT:IST-2015-335-v1-1.
short: U. Boker, T.A. Henzinger, J. Otop, The Target Discounted-Sum Problem, IST
Austria, 2015.
date_created: 2018-12-12T11:39:20Z
date_published: 2015-05-18T00:00:00Z
date_updated: 2023-02-23T10:08:48Z
day: '18'
ddc:
- '004'
- '512'
- '513'
department:
- _id: ToHe
doi: 10.15479/AT:IST-2015-335-v1-1
file:
- access_level: open_access
checksum: 40405907aa012acece1bc26cf0be554d
content_type: application/pdf
creator: system
date_created: 2018-12-12T11:53:55Z
date_updated: 2020-07-14T12:46:55Z
file_id: '5517'
file_name: IST-2015-335-v1+1_report.pdf
file_size: 589619
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file_date_updated: 2020-07-14T12:46:55Z
has_accepted_license: '1'
language:
- iso: eng
month: '05'
oa: 1
oa_version: Published Version
page: '20'
publication_identifier:
issn:
- 2664-1690
publication_status: published
publisher: IST Austria
pubrep_id: '335'
related_material:
record:
- id: '1659'
relation: later_version
status: public
status: public
title: The target discounted-sum problem
type: technical_report
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
year: '2015'
...
---
_id: '5438'
abstract:
- lang: eng
text: "The edit distance between two words w1, w2 is the minimal number of word
operations (letter insertions, deletions, and substitutions) necessary to transform
w1 to w2. The edit distance generalizes to languages L1, L2, where the edit distance
is the minimal number k such that for every word from L1 there exists a word in
L2 with edit distance at most k. We study the edit distance computation problem
between pushdown automata and their subclasses.\r\nThe problem of computing edit
distance to a pushdown automaton is undecidable, and in practice, the interesting
question is to compute the edit distance from a pushdown automaton (the implementation,
a standard model for programs with recursion) to a regular language (the specification).
In this work, we present a complete picture of decidability and complexity for
deciding whether, for a given threshold k, the edit distance from a pushdown automaton
to a finite automaton is at most k. "
alternative_title:
- IST Austria Technical Report
author:
- first_name: Krishnendu
full_name: Chatterjee, Krishnendu
id: 2E5DCA20-F248-11E8-B48F-1D18A9856A87
last_name: Chatterjee
orcid: 0000-0002-4561-241X
- first_name: Thomas A
full_name: Henzinger, Thomas A
id: 40876CD8-F248-11E8-B48F-1D18A9856A87
last_name: Henzinger
orcid: 0000−0002−2985−7724
- first_name: Rasmus
full_name: Ibsen-Jensen, Rasmus
id: 3B699956-F248-11E8-B48F-1D18A9856A87
last_name: Ibsen-Jensen
orcid: 0000-0003-4783-0389
- first_name: Jan
full_name: Otop, Jan
id: 2FC5DA74-F248-11E8-B48F-1D18A9856A87
last_name: Otop
citation:
ama: Chatterjee K, Henzinger TA, Ibsen-Jensen R, Otop J. Edit Distance for Pushdown
Automata. IST Austria; 2015. doi:10.15479/AT:IST-2015-334-v1-1
apa: Chatterjee, K., Henzinger, T. A., Ibsen-Jensen, R., & Otop, J. (2015).
Edit distance for pushdown automata. IST Austria. https://doi.org/10.15479/AT:IST-2015-334-v1-1
chicago: Chatterjee, Krishnendu, Thomas A Henzinger, Rasmus Ibsen-Jensen, and Jan
Otop. Edit Distance for Pushdown Automata. IST Austria, 2015. https://doi.org/10.15479/AT:IST-2015-334-v1-1.
ieee: K. Chatterjee, T. A. Henzinger, R. Ibsen-Jensen, and J. Otop, Edit distance
for pushdown automata. IST Austria, 2015.
ista: Chatterjee K, Henzinger TA, Ibsen-Jensen R, Otop J. 2015. Edit distance for
pushdown automata, IST Austria, 15p.
mla: Chatterjee, Krishnendu, et al. Edit Distance for Pushdown Automata.
IST Austria, 2015, doi:10.15479/AT:IST-2015-334-v1-1.
short: K. Chatterjee, T.A. Henzinger, R. Ibsen-Jensen, J. Otop, Edit Distance for
Pushdown Automata, IST Austria, 2015.
date_created: 2018-12-12T11:39:20Z
date_published: 2015-05-05T00:00:00Z
date_updated: 2023-02-23T12:20:08Z
day: '05'
ddc:
- '004'
department:
- _id: KrCh
doi: 10.15479/AT:IST-2015-334-v1-1
file:
- access_level: open_access
checksum: 8a5f2d77560e552af87eb1982437a43b
content_type: application/pdf
creator: system
date_created: 2018-12-12T11:53:56Z
date_updated: 2020-07-14T12:46:55Z
file_id: '5518'
file_name: IST-2015-334-v1+1_report.pdf
file_size: 422573
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file_date_updated: 2020-07-14T12:46:55Z
has_accepted_license: '1'
language:
- iso: eng
month: '05'
oa: 1
oa_version: Published Version
page: '15'
publication_identifier:
issn:
- 2664-1690
publication_status: published
publisher: IST Austria
pubrep_id: '334'
related_material:
record:
- id: '1610'
relation: later_version
status: public
- id: '465'
relation: later_version
status: public
status: public
title: Edit distance for pushdown automata
type: technical_report
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
year: '2015'
...
---
_id: '5440'
abstract:
- lang: eng
text: 'Evolution occurs in populations of reproducing individuals. The structure
of the population affects the outcome of the evolutionary process. Evolutionary
graph theory is a powerful approach to study this phenomenon. There are two graphs.
The interaction graph specifies who interacts with whom for payoff in the context
of evolution. The replacement graph specifies who competes with whom for reproduction.
The vertices of the two graphs are the same, and each vertex corresponds to an
individual of the population. The fitness (or the reproductive rate) is a non-negative
number, and depends on the payoff. A key quantity is the fixation probability
of a new mutant. It is defined as the probability that a newly introduced mutant
(on a single vertex) generates a lineage of offspring which eventually takes over
the entire population of resident individuals. The basic computational questions
are as follows: (i) the qualitative question asks whether the fixation probability
is positive; and (ii) the quantitative approximation question asks for an approximation
of the fixation probability. Our main results are as follows: First, we consider
a special case of the general problem, where the residents do not reproduce. We
show that the qualitative question is NP-complete, and the quantitative approximation
question is #P-complete, and the hardness results hold even in the special case
where the interaction and the replacement graphs coincide. Second, we show that
in general both the qualitative and the quantitative approximation questions are
PSPACE-complete. The PSPACE-hardness result for quantitative approximation holds
even when the fitness is always positive.'
alternative_title:
- IST Austria Technical Report
author:
- first_name: Krishnendu
full_name: Chatterjee, Krishnendu
id: 2E5DCA20-F248-11E8-B48F-1D18A9856A87
last_name: Chatterjee
orcid: 0000-0002-4561-241X
- first_name: Rasmus
full_name: Ibsen-Jensen, Rasmus
id: 3B699956-F248-11E8-B48F-1D18A9856A87
last_name: Ibsen-Jensen
orcid: 0000-0003-4783-0389
- first_name: Martin
full_name: Nowak, Martin
last_name: Nowak
citation:
ama: Chatterjee K, Ibsen-Jensen R, Nowak M. The Complexity of Evolutionary Games
on Graphs. IST Austria; 2015. doi:10.15479/AT:IST-2015-323-v2-2
apa: Chatterjee, K., Ibsen-Jensen, R., & Nowak, M. (2015). The complexity
of evolutionary games on graphs. IST Austria. https://doi.org/10.15479/AT:IST-2015-323-v2-2
chicago: Chatterjee, Krishnendu, Rasmus Ibsen-Jensen, and Martin Nowak. The Complexity
of Evolutionary Games on Graphs. IST Austria, 2015. https://doi.org/10.15479/AT:IST-2015-323-v2-2.
ieee: K. Chatterjee, R. Ibsen-Jensen, and M. Nowak, The complexity of evolutionary
games on graphs. IST Austria, 2015.
ista: Chatterjee K, Ibsen-Jensen R, Nowak M. 2015. The complexity of evolutionary
games on graphs, IST Austria, 18p.
mla: Chatterjee, Krishnendu, et al. The Complexity of Evolutionary Games on Graphs.
IST Austria, 2015, doi:10.15479/AT:IST-2015-323-v2-2.
short: K. Chatterjee, R. Ibsen-Jensen, M. Nowak, The Complexity of Evolutionary
Games on Graphs, IST Austria, 2015.
date_created: 2018-12-12T11:39:21Z
date_published: 2015-06-16T00:00:00Z
date_updated: 2023-02-23T12:26:10Z
day: '16'
ddc:
- '005'
- '576'
department:
- _id: KrCh
doi: 10.15479/AT:IST-2015-323-v2-2
file:
- access_level: open_access
checksum: 66aace7d367032af97c15e35c9be9636
content_type: application/pdf
creator: system
date_created: 2018-12-12T11:53:23Z
date_updated: 2020-07-14T12:46:56Z
file_id: '5484'
file_name: IST-2015-323-v2+2_main.pdf
file_size: 466161
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file_date_updated: 2020-07-14T12:46:56Z
has_accepted_license: '1'
language:
- iso: eng
month: '06'
oa: 1
oa_version: Published Version
page: '18'
publication_identifier:
issn:
- 2664-1690
publication_status: published
publisher: IST Austria
pubrep_id: '338'
related_material:
record:
- id: '5421'
relation: earlier_version
status: public
- id: '5432'
relation: earlier_version
status: public
status: public
title: The complexity of evolutionary games on graphs
type: technical_report
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
year: '2015'
...
---
_id: '5432'
abstract:
- lang: eng
text: "Evolution occurs in populations of reproducing individuals. The structure
of the population affects the outcome of the evolutionary process. Evolutionary
graph theory is a powerful approach to study this phenomenon. There are two graphs.
The interaction graph specifies who interacts with whom in the context of evolution.The
replacement graph specifies who competes with whom for reproduction. \r\nThe vertices
of the two graphs are the same, and each vertex corresponds to an individual of
the population. A key quantity is the fixation probability of a new mutant. It
is defined as the probability that a newly introduced mutant (on a single vertex)
generates a lineage of offspring which eventually takes over the entire population
of resident individuals. The basic computational questions are as follows: (i)
the qualitative question asks whether the fixation probability is positive; and
(ii) the quantitative approximation question asks for an approximation of the
fixation probability. \r\nOur main results are:\r\n(1) We show that the qualitative
question is NP-complete and the quantitative approximation question is #P-hard
in the special case when the interaction and the replacement graphs coincide and
even with the restriction that the resident individuals do not reproduce (which
corresponds to an invading population taking over an empty structure).\r\n(2)
We show that in general the qualitative question is PSPACE-complete and the quantitative
approximation question is PSPACE-hard and can be solved in exponential time.\r\n"
alternative_title:
- IST Austria Technical Report
author:
- first_name: Krishnendu
full_name: Chatterjee, Krishnendu
id: 2E5DCA20-F248-11E8-B48F-1D18A9856A87
last_name: Chatterjee
orcid: 0000-0002-4561-241X
- first_name: Rasmus
full_name: Ibsen-Jensen, Rasmus
id: 3B699956-F248-11E8-B48F-1D18A9856A87
last_name: Ibsen-Jensen
orcid: 0000-0003-4783-0389
- first_name: Martin
full_name: Nowak, Martin
last_name: Nowak
citation:
ama: Chatterjee K, Ibsen-Jensen R, Nowak M. The Complexity of Evolutionary Games
on Graphs. IST Austria; 2015. doi:10.15479/AT:IST-2015-323-v1-1
apa: Chatterjee, K., Ibsen-Jensen, R., & Nowak, M. (2015). The complexity
of evolutionary games on graphs. IST Austria. https://doi.org/10.15479/AT:IST-2015-323-v1-1
chicago: Chatterjee, Krishnendu, Rasmus Ibsen-Jensen, and Martin Nowak. The Complexity
of Evolutionary Games on Graphs. IST Austria, 2015. https://doi.org/10.15479/AT:IST-2015-323-v1-1.
ieee: K. Chatterjee, R. Ibsen-Jensen, and M. Nowak, The complexity of evolutionary
games on graphs. IST Austria, 2015.
ista: Chatterjee K, Ibsen-Jensen R, Nowak M. 2015. The complexity of evolutionary
games on graphs, IST Austria, 29p.
mla: Chatterjee, Krishnendu, et al. The Complexity of Evolutionary Games on Graphs.
IST Austria, 2015, doi:10.15479/AT:IST-2015-323-v1-1.
short: K. Chatterjee, R. Ibsen-Jensen, M. Nowak, The Complexity of Evolutionary
Games on Graphs, IST Austria, 2015.
date_created: 2018-12-12T11:39:18Z
date_published: 2015-02-19T00:00:00Z
date_updated: 2023-02-23T12:26:33Z
day: '19'
ddc:
- '005'
- '576'
department:
- _id: KrCh
doi: 10.15479/AT:IST-2015-323-v1-1
file:
- access_level: open_access
checksum: 546c1b291d545e7b24aaaf4199dac671
content_type: application/pdf
creator: system
date_created: 2018-12-12T11:53:57Z
date_updated: 2020-07-14T12:46:53Z
file_id: '5519'
file_name: IST-2015-323-v1+1_main.pdf
file_size: 576347
relation: main_file
file_date_updated: 2020-07-14T12:46:53Z
has_accepted_license: '1'
language:
- iso: eng
month: '02'
oa: 1
oa_version: Published Version
page: '29'
publication_identifier:
issn:
- 2664-1690
publication_status: published
publisher: IST Austria
pubrep_id: '323'
related_material:
record:
- id: '5421'
relation: earlier_version
status: public
- id: '5440'
relation: later_version
status: public
status: public
title: The complexity of evolutionary games on graphs
type: technical_report
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
year: '2015'
...
---
_id: '5444'
abstract:
- lang: eng
text: A comprehensive understanding of the clonal evolution of cancer is critical
for understanding neoplasia. Genome-wide sequencing data enables evolutionary
studies at unprecedented depth. However, classical phylogenetic methods often
struggle with noisy sequencing data of impure DNA samples and fail to detect subclones
that have different evolutionary trajectories. We have developed a tool, called
Treeomics, that allows us to reconstruct the phylogeny of a cancer with commonly
available sequencing technologies. Using Bayesian inference and Integer Linear
Programming, robust phylogenies consistent with the biological processes underlying
cancer evolution were obtained for pancreatic, ovarian, and prostate cancers.
Furthermore, Treeomics correctly identified sequencing artifacts such as those
resulting from low statistical power; nearly 7% of variants were misclassified
by conventional statistical methods. These artifacts can skew phylogenies by creating
illusory tumor heterogeneity among distinct samples. Importantly, we show that
the evolutionary trees generated with Treeomics are mathematically optimal.
alternative_title:
- IST Austria Technical Report
author:
- first_name: Johannes
full_name: Reiter, Johannes
id: 4A918E98-F248-11E8-B48F-1D18A9856A87
last_name: Reiter
orcid: 0000-0002-0170-7353
- first_name: Alvin
full_name: Makohon-Moore, Alvin
last_name: Makohon-Moore
- first_name: Jeffrey
full_name: Gerold, Jeffrey
last_name: Gerold
- first_name: Ivana
full_name: Bozic, Ivana
last_name: Bozic
- first_name: Krishnendu
full_name: Chatterjee, Krishnendu
id: 2E5DCA20-F248-11E8-B48F-1D18A9856A87
last_name: Chatterjee
orcid: 0000-0002-4561-241X
- first_name: Christine
full_name: Iacobuzio-Donahue, Christine
last_name: Iacobuzio-Donahue
- first_name: Bert
full_name: Vogelstein, Bert
last_name: Vogelstein
- first_name: Martin
full_name: Nowak, Martin
last_name: Nowak
citation:
ama: Reiter J, Makohon-Moore A, Gerold J, et al. Reconstructing Robust Phylogenies
of Metastatic Cancers. IST Austria; 2015. doi:10.15479/AT:IST-2015-399-v1-1
apa: Reiter, J., Makohon-Moore, A., Gerold, J., Bozic, I., Chatterjee, K., Iacobuzio-Donahue,
C., … Nowak, M. (2015). Reconstructing robust phylogenies of metastatic cancers.
IST Austria. https://doi.org/10.15479/AT:IST-2015-399-v1-1
chicago: Reiter, Johannes, Alvin Makohon-Moore, Jeffrey Gerold, Ivana Bozic, Krishnendu
Chatterjee, Christine Iacobuzio-Donahue, Bert Vogelstein, and Martin Nowak. Reconstructing
Robust Phylogenies of Metastatic Cancers. IST Austria, 2015. https://doi.org/10.15479/AT:IST-2015-399-v1-1.
ieee: J. Reiter et al., Reconstructing robust phylogenies of metastatic
cancers. IST Austria, 2015.
ista: Reiter J, Makohon-Moore A, Gerold J, Bozic I, Chatterjee K, Iacobuzio-Donahue
C, Vogelstein B, Nowak M. 2015. Reconstructing robust phylogenies of metastatic
cancers, IST Austria, 25p.
mla: Reiter, Johannes, et al. Reconstructing Robust Phylogenies of Metastatic
Cancers. IST Austria, 2015, doi:10.15479/AT:IST-2015-399-v1-1.
short: J. Reiter, A. Makohon-Moore, J. Gerold, I. Bozic, K. Chatterjee, C. Iacobuzio-Donahue,
B. Vogelstein, M. Nowak, Reconstructing Robust Phylogenies of Metastatic Cancers,
IST Austria, 2015.
date_created: 2018-12-12T11:39:22Z
date_published: 2015-12-30T00:00:00Z
date_updated: 2020-07-14T23:05:07Z
day: '30'
ddc:
- '000'
- '576'
department:
- _id: KrCh
doi: 10.15479/AT:IST-2015-399-v1-1
file:
- access_level: open_access
checksum: c47d33bdda06181753c0af36f16e7b5d
content_type: application/pdf
creator: system
date_created: 2018-12-12T11:53:24Z
date_updated: 2020-07-14T12:46:58Z
file_id: '5485'
file_name: IST-2015-399-v1+1_treeomics.pdf
file_size: 3533200
relation: main_file
file_date_updated: 2020-07-14T12:46:58Z
has_accepted_license: '1'
language:
- iso: eng
month: '12'
oa: 1
oa_version: Published Version
page: '25'
publication_identifier:
issn:
- 2664-1690
publication_status: published
publisher: IST Austria
pubrep_id: '399'
status: public
title: Reconstructing robust phylogenies of metastatic cancers
type: technical_report
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
year: '2015'
...
---
_id: '5443'
abstract:
- lang: eng
text: POMDPs are standard models for probabilistic planning problems, where an agent
interacts with an uncertain environment. We study the problem of almost-sure reachability,
where given a set of target states, the question is to decide whether there is
a policy to ensure that the target set is reached with probability 1 (almost-surely).
While in general the problem is EXPTIME-complete, in many practical cases policies
with a small amount of memory suffice. Moreover, the existing solution to the
problem is explicit, which first requires to construct explicitly an exponential
reduction to a belief-support MDP. In this work, we first study the existence
of observation-stationary strategies, which is NP-complete, and then small-memory
strategies. We present a symbolic algorithm by an efficient encoding to SAT and
using a SAT solver for the problem. We report experimental results demonstrating
the scalability of our symbolic (SAT-based) approach.
alternative_title:
- IST Austria Technical Report
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: Chmelik, Martin
id: 3624234E-F248-11E8-B48F-1D18A9856A87
last_name: Chmelik
- first_name: Jessica
full_name: Davies, Jessica
id: 378E0060-F248-11E8-B48F-1D18A9856A87
last_name: Davies
citation:
ama: Chatterjee K, Chmelik M, Davies J. A Symbolic SAT-Based Algorithm for Almost-Sure
Reachability with Small Strategies in POMDPs. IST Austria; 2015. doi:10.15479/AT:IST-2015-325-v2-1
apa: Chatterjee, K., Chmelik, M., & Davies, J. (2015). A symbolic SAT-based
algorithm for almost-sure reachability with small strategies in POMDPs. IST
Austria. https://doi.org/10.15479/AT:IST-2015-325-v2-1
chicago: Chatterjee, Krishnendu, Martin Chmelik, and Jessica Davies. A Symbolic
SAT-Based Algorithm for Almost-Sure Reachability with Small Strategies in POMDPs.
IST Austria, 2015. https://doi.org/10.15479/AT:IST-2015-325-v2-1.
ieee: K. Chatterjee, M. Chmelik, and J. Davies, A symbolic SAT-based algorithm
for almost-sure reachability with small strategies in POMDPs. IST Austria,
2015.
ista: Chatterjee K, Chmelik M, Davies J. 2015. A symbolic SAT-based algorithm for
almost-sure reachability with small strategies in POMDPs, IST Austria, 23p.
mla: Chatterjee, Krishnendu, et al. A Symbolic SAT-Based Algorithm for Almost-Sure
Reachability with Small Strategies in POMDPs. IST Austria, 2015, doi:10.15479/AT:IST-2015-325-v2-1.
short: K. Chatterjee, M. Chmelik, J. Davies, A Symbolic SAT-Based Algorithm for
Almost-Sure Reachability with Small Strategies in POMDPs, IST Austria, 2015.
date_created: 2018-12-12T11:39:22Z
date_published: 2015-11-06T00:00:00Z
date_updated: 2023-02-21T16:24:05Z
day: '06'
ddc:
- '000'
department:
- _id: KrCh
doi: 10.15479/AT:IST-2015-325-v2-1
file:
- access_level: open_access
checksum: f0fa31ad8161ed655137e94012123ef9
content_type: application/pdf
creator: system
date_created: 2018-12-12T11:53:05Z
date_updated: 2020-07-14T12:46:57Z
file_id: '5466'
file_name: IST-2015-325-v2+1_main.pdf
file_size: 412379
relation: main_file
file_date_updated: 2020-07-14T12:46:57Z
has_accepted_license: '1'
language:
- iso: eng
month: '11'
oa: 1
oa_version: Published Version
page: '23'
publication_identifier:
issn:
- 2664-1690
publication_status: published
publisher: IST Austria
pubrep_id: '362'
related_material:
record:
- id: '1166'
relation: later_version
status: public
status: public
title: A symbolic SAT-based algorithm for almost-sure reachability with small strategies
in POMDPs
type: technical_report
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
year: '2015'
...
---
_id: '5804'
abstract:
- lang: eng
text: We present here the first integer-based algorithm for constructing a well-defined
lattice sphere specified by integer radius and integer center. The algorithm evolves
from a unique correspondence between the lattice points comprising the sphere
and the distribution of sum of three square numbers in integer intervals. We characterize
these intervals to derive a useful set of recurrences, which, in turn, aids in
efficient computation. Each point of the lattice sphere is determined by resorting
to only a few primitive operations in the integer domain. The symmetry of its
quadraginta octants provides an added advantage by confining the computation to
its prima quadraginta octant. Detailed theoretical analysis and experimental results
have been furnished to demonstrate its simplicity and elegance.
author:
- first_name: Ranita
full_name: Biswas, Ranita
id: 3C2B033E-F248-11E8-B48F-1D18A9856A87
last_name: Biswas
orcid: 0000-0002-5372-7890
- first_name: Partha
full_name: Bhowmick, Partha
last_name: Bhowmick
citation:
ama: Biswas R, Bhowmick P. From prima quadraginta octant to lattice sphere through
primitive integer operations. Theoretical Computer Science. 2015;624(4):56-72.
doi:10.1016/j.tcs.2015.11.018
apa: Biswas, R., & Bhowmick, P. (2015). From prima quadraginta octant to lattice
sphere through primitive integer operations. Theoretical Computer Science.
Elsevier. https://doi.org/10.1016/j.tcs.2015.11.018
chicago: Biswas, Ranita, and Partha Bhowmick. “From Prima Quadraginta Octant to
Lattice Sphere through Primitive Integer Operations.” Theoretical Computer
Science. Elsevier, 2015. https://doi.org/10.1016/j.tcs.2015.11.018.
ieee: R. Biswas and P. Bhowmick, “From prima quadraginta octant to lattice sphere
through primitive integer operations,” Theoretical Computer Science, vol.
624, no. 4. Elsevier, pp. 56–72, 2015.
ista: Biswas R, Bhowmick P. 2015. From prima quadraginta octant to lattice sphere
through primitive integer operations. Theoretical Computer Science. 624(4), 56–72.
mla: Biswas, Ranita, and Partha Bhowmick. “From Prima Quadraginta Octant to Lattice
Sphere through Primitive Integer Operations.” Theoretical Computer Science,
vol. 624, no. 4, Elsevier, 2015, pp. 56–72, doi:10.1016/j.tcs.2015.11.018.
short: R. Biswas, P. Bhowmick, Theoretical Computer Science 624 (2015) 56–72.
date_created: 2019-01-08T20:44:06Z
date_published: 2015-04-18T00:00:00Z
date_updated: 2021-01-12T08:03:36Z
day: '18'
doi: 10.1016/j.tcs.2015.11.018
extern: '1'
intvolume: ' 624'
issue: '4'
language:
- iso: eng
month: '04'
oa_version: None
page: 56-72
publication: Theoretical Computer Science
publication_identifier:
issn:
- 0304-3975
publication_status: published
publisher: Elsevier
quality_controlled: '1'
status: public
title: From prima quadraginta octant to lattice sphere through primitive integer operations
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 624
year: '2015'
...
---
_id: '5807'
author:
- first_name: Ranita
full_name: Biswas, Ranita
id: 3C2B033E-F248-11E8-B48F-1D18A9856A87
last_name: Biswas
orcid: 0000-0002-5372-7890
- first_name: Partha
full_name: Bhowmick, Partha
last_name: Bhowmick
citation:
ama: Biswas R, Bhowmick P. On different topological classes of spherical geodesic
paths and circles inZ3. Theoretical Computer Science. 2015;605(11):146-163.
doi:10.1016/j.tcs.2015.09.003
apa: Biswas, R., & Bhowmick, P. (2015). On different topological classes of
spherical geodesic paths and circles inZ3. Theoretical Computer Science.
Elsevier. https://doi.org/10.1016/j.tcs.2015.09.003
chicago: Biswas, Ranita, and Partha Bhowmick. “On Different Topological Classes
of Spherical Geodesic Paths and Circles InZ3.” Theoretical Computer Science.
Elsevier, 2015. https://doi.org/10.1016/j.tcs.2015.09.003.
ieee: R. Biswas and P. Bhowmick, “On different topological classes of spherical
geodesic paths and circles inZ3,” Theoretical Computer Science, vol. 605,
no. 11. Elsevier, pp. 146–163, 2015.
ista: Biswas R, Bhowmick P. 2015. On different topological classes of spherical
geodesic paths and circles inZ3. Theoretical Computer Science. 605(11), 146–163.
mla: Biswas, Ranita, and Partha Bhowmick. “On Different Topological Classes of Spherical
Geodesic Paths and Circles InZ3.” Theoretical Computer Science, vol. 605,
no. 11, Elsevier, 2015, pp. 146–63, doi:10.1016/j.tcs.2015.09.003.
short: R. Biswas, P. Bhowmick, Theoretical Computer Science 605 (2015) 146–163.
date_created: 2019-01-08T20:44:52Z
date_published: 2015-11-09T00:00:00Z
date_updated: 2021-01-12T08:03:37Z
day: '09'
doi: 10.1016/j.tcs.2015.09.003
extern: '1'
intvolume: ' 605'
issue: '11'
language:
- iso: eng
month: '11'
oa_version: None
page: 146-163
publication: Theoretical Computer Science
publication_identifier:
issn:
- 0304-3975
publication_status: published
publisher: Elsevier
quality_controlled: '1'
status: public
title: On different topological classes of spherical geodesic paths and circles inZ3
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 605
year: '2015'
...
---
_id: '5808'
author:
- first_name: Ranita
full_name: Biswas, Ranita
id: 3C2B033E-F248-11E8-B48F-1D18A9856A87
last_name: Biswas
orcid: 0000-0002-5372-7890
- first_name: Partha
full_name: Bhowmick, Partha
last_name: Bhowmick
citation:
ama: Biswas R, Bhowmick P. Layer the sphere. The Visual Computer. 2015;31(6-8):787-797.
doi:10.1007/s00371-015-1101-3
apa: Biswas, R., & Bhowmick, P. (2015). Layer the sphere. The Visual Computer.
Springer Nature. https://doi.org/10.1007/s00371-015-1101-3
chicago: Biswas, Ranita, and Partha Bhowmick. “Layer the Sphere.” The Visual
Computer. Springer Nature, 2015. https://doi.org/10.1007/s00371-015-1101-3.
ieee: R. Biswas and P. Bhowmick, “Layer the sphere,” The Visual Computer,
vol. 31, no. 6–8. Springer Nature, pp. 787–797, 2015.
ista: Biswas R, Bhowmick P. 2015. Layer the sphere. The Visual Computer. 31(6–8),
787–797.
mla: Biswas, Ranita, and Partha Bhowmick. “Layer the Sphere.” The Visual Computer,
vol. 31, no. 6–8, Springer Nature, 2015, pp. 787–97, doi:10.1007/s00371-015-1101-3.
short: R. Biswas, P. Bhowmick, The Visual Computer 31 (2015) 787–797.
date_created: 2019-01-08T20:45:05Z
date_published: 2015-05-08T00:00:00Z
date_updated: 2021-01-12T08:03:37Z
day: '08'
doi: 10.1007/s00371-015-1101-3
extern: '1'
intvolume: ' 31'
issue: 6-8
language:
- iso: eng
month: '05'
oa_version: None
page: 787-797
publication: The Visual Computer
publication_identifier:
issn:
- 0178-2789
- 1432-2315
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
status: public
title: Layer the sphere
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 31
year: '2015'
...
---
_id: '594'
abstract:
- lang: eng
text: Transcription of eukaryotic protein-coding genes commences with the assembly
of a conserved initiation complex, which consists of RNA polymerase II (Pol II)
and the general transcription factors, at promoter DNA. After two decades of research,
the structural basis of transcription initiation is emerging. Crystal structures
of many components of the initiation complex have been resolved, and structural
information on Pol II complexes with general transcription factors has recently
been obtained. Although mechanistic details await elucidation, available data
outline how Pol II cooperates with the general transcription factors to bind to
and open promoter DNA, and how Pol II directs RNA synthesis and escapes from the
promoter.
article_processing_charge: No
author:
- first_name: Sarah
full_name: Sainsbury, Sarah
last_name: Sainsbury
- first_name: Carrie A
full_name: Bernecky, Carrie A
id: 2CB9DFE2-F248-11E8-B48F-1D18A9856A87
last_name: Bernecky
orcid: 0000-0003-0893-7036
- first_name: Patrick
full_name: Cramer, Patrick
last_name: Cramer
citation:
ama: Sainsbury S, Bernecky C, Cramer P. Structural basis of transcription initiation
by RNA polymerase II. Nature Reviews Molecular Cell Biology. 2015;16(3):129-143.
doi:10.1038/nrm3952
apa: Sainsbury, S., Bernecky, C., & Cramer, P. (2015). Structural basis of transcription
initiation by RNA polymerase II. Nature Reviews Molecular Cell Biology.
Nature Publishing Group. https://doi.org/10.1038/nrm3952
chicago: Sainsbury, Sarah, Carrie Bernecky, and Patrick Cramer. “Structural Basis
of Transcription Initiation by RNA Polymerase II.” Nature Reviews Molecular
Cell Biology. Nature Publishing Group, 2015. https://doi.org/10.1038/nrm3952.
ieee: S. Sainsbury, C. Bernecky, and P. Cramer, “Structural basis of transcription
initiation by RNA polymerase II,” Nature Reviews Molecular Cell Biology,
vol. 16, no. 3. Nature Publishing Group, pp. 129–143, 2015.
ista: Sainsbury S, Bernecky C, Cramer P. 2015. Structural basis of transcription
initiation by RNA polymerase II. Nature Reviews Molecular Cell Biology. 16(3),
129–143.
mla: Sainsbury, Sarah, et al. “Structural Basis of Transcription Initiation by RNA
Polymerase II.” Nature Reviews Molecular Cell Biology, vol. 16, no. 3,
Nature Publishing Group, 2015, pp. 129–43, doi:10.1038/nrm3952.
short: S. Sainsbury, C. Bernecky, P. Cramer, Nature Reviews Molecular Cell Biology
16 (2015) 129–143.
date_created: 2018-12-11T11:47:23Z
date_published: 2015-03-26T00:00:00Z
date_updated: 2021-01-12T08:05:16Z
day: '26'
doi: 10.1038/nrm3952
extern: '1'
intvolume: ' 16'
issue: '3'
language:
- iso: eng
month: '03'
oa_version: None
page: 129 - 143
publication: Nature Reviews Molecular Cell Biology
publication_status: published
publisher: Nature Publishing Group
publist_id: '7206'
status: public
title: Structural basis of transcription initiation by RNA polymerase II
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 16
year: '2015'
...
---
_id: '1511'
abstract:
- lang: eng
text: 'The fact that the complete graph K_5 does not embed in the plane has been
generalized in two independent directions. On the one hand, the solution of the
classical Heawood problem for graphs on surfaces established that the complete
graph K_n embeds in a closed surface M if and only if (n-3)(n-4) is at most 6b_1(M),
where b_1(M) is the first Z_2-Betti number of M. On the other hand, Van Kampen
and Flores proved that the k-skeleton of the n-dimensional simplex (the higher-dimensional
analogue of K_{n+1}) embeds in R^{2k} if and only if n is less or equal to 2k+2.
Two decades ago, Kuhnel conjectured that the k-skeleton of the n-simplex embeds
in a compact, (k-1)-connected 2k-manifold with kth Z_2-Betti number b_k only if
the following generalized Heawood inequality holds: binom{n-k-1}{k+1} is at most
binom{2k+1}{k+1} b_k. This is a common generalization of the case of graphs on
surfaces as well as the Van Kampen--Flores theorem. In the spirit of Kuhnel''s
conjecture, we prove that if the k-skeleton of the n-simplex embeds in a 2k-manifold
with kth Z_2-Betti number b_k, then n is at most 2b_k binom{2k+2}{k} + 2k + 5.
This bound is weaker than the generalized Heawood inequality, but does not require
the assumption that M is (k-1)-connected. Our proof uses a result of Volovikov
about maps that satisfy a certain homological triviality condition.'
acknowledgement: "The work by Z. P. was partially supported by the Charles University
Grant SVV-2014-260103. The\r\nwork by Z. P. and M. T. was partially supported by
the project CE-ITI (GACR P202/12/G061) of\r\nthe Czech Science Foundation and by
the ERC Advanced Grant No. 267165. Part of the research\r\nwork of M. T. was conducted
at IST Austria, supported by an IST Fellowship. The work by U.W.\r\nwas partially
supported by the Swiss National Science Foundation (grants SNSF-200020-138230 and\r\nSNSF-PP00P2-138948)."
alternative_title:
- LIPIcs
author:
- first_name: Xavier
full_name: Goaoc, Xavier
last_name: Goaoc
- first_name: Isaac
full_name: Mabillard, Isaac
id: 32BF9DAA-F248-11E8-B48F-1D18A9856A87
last_name: Mabillard
- first_name: Pavel
full_name: Paták, Pavel
last_name: Paták
- first_name: Zuzana
full_name: Patakova, Zuzana
id: 48B57058-F248-11E8-B48F-1D18A9856A87
last_name: Patakova
orcid: 0000-0002-3975-1683
- first_name: Martin
full_name: Tancer, Martin
id: 38AC689C-F248-11E8-B48F-1D18A9856A87
last_name: Tancer
orcid: 0000-0002-1191-6714
- first_name: Uli
full_name: Wagner, Uli
id: 36690CA2-F248-11E8-B48F-1D18A9856A87
last_name: Wagner
orcid: 0000-0002-1494-0568
citation:
ama: 'Goaoc X, Mabillard I, Paták P, Patakova Z, Tancer M, Wagner U. On generalized
Heawood inequalities for manifolds: A Van Kampen–Flores-type nonembeddability
result. In: Vol 34. Schloss Dagstuhl - Leibniz-Zentrum für Informatik; 2015:476-490.
doi:10.4230/LIPIcs.SOCG.2015.476'
apa: 'Goaoc, X., Mabillard, I., Paták, P., Patakova, Z., Tancer, M., & Wagner,
U. (2015). On generalized Heawood inequalities for manifolds: A Van Kampen–Flores-type
nonembeddability result (Vol. 34, pp. 476–490). Presented at the SoCG: Symposium
on Computational Geometry, Eindhoven, Netherlands: Schloss Dagstuhl - Leibniz-Zentrum
für Informatik. https://doi.org/10.4230/LIPIcs.SOCG.2015.476'
chicago: 'Goaoc, Xavier, Isaac Mabillard, Pavel Paták, Zuzana Patakova, Martin Tancer,
and Uli Wagner. “On Generalized Heawood Inequalities for Manifolds: A Van Kampen–Flores-Type
Nonembeddability Result,” 34:476–90. Schloss Dagstuhl - Leibniz-Zentrum für Informatik,
2015. https://doi.org/10.4230/LIPIcs.SOCG.2015.476.'
ieee: 'X. Goaoc, I. Mabillard, P. Paták, Z. Patakova, M. Tancer, and U. Wagner,
“On generalized Heawood inequalities for manifolds: A Van Kampen–Flores-type nonembeddability
result,” presented at the SoCG: Symposium on Computational Geometry, Eindhoven,
Netherlands, 2015, vol. 34, pp. 476–490.'
ista: 'Goaoc X, Mabillard I, Paták P, Patakova Z, Tancer M, Wagner U. 2015. On generalized
Heawood inequalities for manifolds: A Van Kampen–Flores-type nonembeddability
result. SoCG: Symposium on Computational Geometry, LIPIcs, vol. 34, 476–490.'
mla: 'Goaoc, Xavier, et al. On Generalized Heawood Inequalities for Manifolds:
A Van Kampen–Flores-Type Nonembeddability Result. Vol. 34, Schloss Dagstuhl
- Leibniz-Zentrum für Informatik, 2015, pp. 476–90, doi:10.4230/LIPIcs.SOCG.2015.476.'
short: X. Goaoc, I. Mabillard, P. Paták, Z. Patakova, M. Tancer, U. Wagner, in:,
Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2015, pp. 476–490.
conference:
end_date: 2015-06-25
location: Eindhoven, Netherlands
name: 'SoCG: Symposium on Computational Geometry'
start_date: 2015-06-22
date_created: 2018-12-11T11:52:27Z
date_published: 2015-06-11T00:00:00Z
date_updated: 2023-02-23T12:38:00Z
day: '11'
ddc:
- '510'
department:
- _id: UlWa
doi: 10.4230/LIPIcs.SOCG.2015.476
ec_funded: 1
file:
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checksum: 0945811875351796324189312ca29e9e
content_type: application/pdf
creator: system
date_created: 2018-12-12T10:11:18Z
date_updated: 2020-07-14T12:44:59Z
file_id: '4871'
file_name: IST-2016-502-v1+1_42.pdf
file_size: 636735
relation: main_file
file_date_updated: 2020-07-14T12:44:59Z
has_accepted_license: '1'
language:
- iso: eng
license: https://creativecommons.org/licenses/by/4.0/
month: '06'
oa: 1
oa_version: Published Version
page: 476 - 490
project:
- _id: 25681D80-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '291734'
name: International IST Postdoc Fellowship Programme
publication_status: published
publisher: Schloss Dagstuhl - Leibniz-Zentrum für Informatik
publist_id: '5666'
pubrep_id: '502'
quality_controlled: '1'
related_material:
record:
- id: '610'
relation: later_version
status: public
scopus_import: 1
status: public
title: 'On generalized Heawood inequalities for manifolds: A Van Kampen–Flores-type
nonembeddability result'
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: conference
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: '34 '
year: '2015'
...
---
_id: '6118'
abstract:
- lang: eng
text: 'Carbon dioxide (CO2) gradients are ubiquitous and provide animals with information
about their environment, such as the potential presence of prey or predators.
The nematode Caenorhabditis elegans avoids elevated CO2, and previous work identified
three neuron pairs called “BAG,” “AFD,” and “ASE” that respond to CO2 stimuli.
Using in vivo Ca2+ imaging and behavioral analysis, we show that C. elegans can
detect CO2 independently of these sensory pathways. Many of the C. elegans sensory
neurons we examined, including the AWC olfactory neurons, the ASJ and ASK gustatory
neurons, and the ASH and ADL nociceptors, respond to a rise in CO2 with a rise
in Ca2+. In contrast, glial sheath cells harboring the sensory endings of C. elegans’
major chemosensory neurons exhibit strong and sustained decreases in Ca2+ in response
to high CO2. Some of these CO2 responses appear to be cell intrinsic. Worms therefore
may couple detection of CO2 to that of other cues at the earliest stages of sensory
processing. We show that C. elegans persistently suppresses oviposition at high
CO2. Hermaphrodite-specific neurons (HSNs), the executive neurons driving egg-laying,
are tonically inhibited when CO2 is elevated. CO2 modulates the egg-laying system
partly through the AWC olfactory neurons: High CO2 tonically activates AWC by
a cGMP-dependent mechanism, and AWC output inhibits the HSNs. Our work shows that
CO2 is a more complex sensory cue for C. elegans than previously thought, both
in terms of behavior and neural circuitry.'
author:
- first_name: Lorenz A.
full_name: Fenk, Lorenz A.
last_name: Fenk
- first_name: Mario
full_name: de Bono, Mario
id: 4E3FF80E-F248-11E8-B48F-1D18A9856A87
last_name: de Bono
orcid: 0000-0001-8347-0443
citation:
ama: Fenk LA, de Bono M. Environmental CO2 inhibits Caenorhabditis elegans egg-laying
by modulating olfactory neurons and evokes widespread changes in neural activity.
Proceedings of the National Academy of Sciences. 2015;112(27):E3525-E3534.
doi:10.1073/pnas.1423808112
apa: Fenk, L. A., & de Bono, M. (2015). Environmental CO2 inhibits Caenorhabditis
elegans egg-laying by modulating olfactory neurons and evokes widespread changes
in neural activity. Proceedings of the National Academy of Sciences. National
Academy of Sciences. https://doi.org/10.1073/pnas.1423808112
chicago: Fenk, Lorenz A., and Mario de Bono. “Environmental CO2 Inhibits Caenorhabditis
Elegans Egg-Laying by Modulating Olfactory Neurons and Evokes Widespread Changes
in Neural Activity.” Proceedings of the National Academy of Sciences. National
Academy of Sciences, 2015. https://doi.org/10.1073/pnas.1423808112.
ieee: L. A. Fenk and M. de Bono, “Environmental CO2 inhibits Caenorhabditis elegans
egg-laying by modulating olfactory neurons and evokes widespread changes in neural
activity,” Proceedings of the National Academy of Sciences, vol. 112, no.
27. National Academy of Sciences, pp. E3525–E3534, 2015.
ista: Fenk LA, de Bono M. 2015. Environmental CO2 inhibits Caenorhabditis elegans
egg-laying by modulating olfactory neurons and evokes widespread changes in neural
activity. Proceedings of the National Academy of Sciences. 112(27), E3525–E3534.
mla: Fenk, Lorenz A., and Mario de Bono. “Environmental CO2 Inhibits Caenorhabditis
Elegans Egg-Laying by Modulating Olfactory Neurons and Evokes Widespread Changes
in Neural Activity.” Proceedings of the National Academy of Sciences, vol.
112, no. 27, National Academy of Sciences, 2015, pp. E3525–34, doi:10.1073/pnas.1423808112.
short: L.A. Fenk, M. de Bono, Proceedings of the National Academy of Sciences 112
(2015) E3525–E3534.
date_created: 2019-03-19T14:15:50Z
date_published: 2015-07-07T00:00:00Z
date_updated: 2021-01-12T08:06:12Z
day: '07'
ddc:
- '570'
doi: 10.1073/pnas.1423808112
extern: '1'
external_id:
pmid:
- '26100886'
file:
- access_level: open_access
checksum: 3d2da5af8d72467e382a565abc2e003d
content_type: application/pdf
creator: kschuh
date_created: 2019-03-19T14:21:07Z
date_updated: 2020-07-14T12:47:20Z
file_id: '6119'
file_name: 2015_PNAS_Fenk.pdf
file_size: 2822681
relation: main_file
file_date_updated: 2020-07-14T12:47:20Z
has_accepted_license: '1'
intvolume: ' 112'
issue: '27'
language:
- iso: eng
month: '07'
oa: 1
oa_version: Published Version
page: E3525-E3534
pmid: 1
publication: Proceedings of the National Academy of Sciences
publication_identifier:
issn:
- 0027-8424
- 1091-6490
publication_status: published
publisher: National Academy of Sciences
quality_controlled: '1'
status: public
title: Environmental CO2 inhibits Caenorhabditis elegans egg-laying by modulating
olfactory neurons and evokes widespread changes in neural activity
type: journal_article
user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87
volume: 112
year: '2015'
...
---
_id: '6120'
abstract:
- lang: eng
text: Brains organize behavior and physiology to optimize the response to threats
or opportunities. We dissect how 21% O2, an indicator of surface exposure, reprograms
C. elegans' global state, inducing sustained locomotory arousal and altering expression
of neuropeptides, metabolic enzymes, and other non-neural genes. The URX O2-sensing
neurons drive arousal at 21% O2 by tonically activating the RMG interneurons.
Stimulating RMG is sufficient to switch behavioral state. Ablating the ASH, ADL,
or ASK sensory neurons connected to RMG by gap junctions does not disrupt arousal.
However, disrupting cation currents in these neurons curtails RMG neurosecretion
and arousal. RMG signals high O2 by peptidergic secretion. Neuropeptide reporters
reveal neural circuit state, as neurosecretion stimulates neuropeptide expression.
Neural imaging in unrestrained animals shows that URX and RMG encode O2 concentration
rather than behavior, while the activity of downstream interneurons such as AVB
and AIY reflect both O2 levels and the behavior being executed.
article_number: e04241
author:
- first_name: Patrick
full_name: Laurent, Patrick
last_name: Laurent
- first_name: Zoltan
full_name: Soltesz, Zoltan
last_name: Soltesz
- first_name: Geoffrey M
full_name: Nelson, Geoffrey M
last_name: Nelson
- first_name: Changchun
full_name: Chen, Changchun
last_name: Chen
- first_name: Fausto
full_name: Arellano-Carbajal, Fausto
last_name: Arellano-Carbajal
- first_name: Emmanuel
full_name: Levy, Emmanuel
last_name: Levy
- first_name: Mario
full_name: de Bono, Mario
id: 4E3FF80E-F248-11E8-B48F-1D18A9856A87
last_name: de Bono
orcid: 0000-0001-8347-0443
citation:
ama: Laurent P, Soltesz Z, Nelson GM, et al. Decoding a neural circuit controlling
global animal state in C. elegans. eLife. 2015;4. doi:10.7554/elife.04241
apa: Laurent, P., Soltesz, Z., Nelson, G. M., Chen, C., Arellano-Carbajal, F., Levy,
E., & de Bono, M. (2015). Decoding a neural circuit controlling global animal
state in C. elegans. ELife. eLife Sciences Publications. https://doi.org/10.7554/elife.04241
chicago: Laurent, Patrick, Zoltan Soltesz, Geoffrey M Nelson, Changchun Chen, Fausto
Arellano-Carbajal, Emmanuel Levy, and Mario de Bono. “Decoding a Neural Circuit
Controlling Global Animal State in C. Elegans.” ELife. eLife Sciences Publications,
2015. https://doi.org/10.7554/elife.04241.
ieee: P. Laurent et al., “Decoding a neural circuit controlling global animal
state in C. elegans,” eLife, vol. 4. eLife Sciences Publications, 2015.
ista: Laurent P, Soltesz Z, Nelson GM, Chen C, Arellano-Carbajal F, Levy E, de Bono
M. 2015. Decoding a neural circuit controlling global animal state in C. elegans.
eLife. 4, e04241.
mla: Laurent, Patrick, et al. “Decoding a Neural Circuit Controlling Global Animal
State in C. Elegans.” ELife, vol. 4, e04241, eLife Sciences Publications,
2015, doi:10.7554/elife.04241.
short: P. Laurent, Z. Soltesz, G.M. Nelson, C. Chen, F. Arellano-Carbajal, E. Levy,
M. de Bono, ELife 4 (2015).
date_created: 2019-03-19T14:23:51Z
date_published: 2015-03-11T00:00:00Z
date_updated: 2021-01-12T08:06:13Z
day: '11'
ddc:
- '570'
doi: 10.7554/elife.04241
extern: '1'
external_id:
pmid:
- '25760081'
file:
- access_level: open_access
checksum: cf641b7a363aecd0a101755d23dee7e0
content_type: application/pdf
creator: kschuh
date_created: 2019-03-19T14:29:43Z
date_updated: 2020-07-14T12:47:20Z
file_id: '6121'
file_name: 2015_elife_Laurent.pdf
file_size: 6723528
relation: main_file
file_date_updated: 2020-07-14T12:47:20Z
has_accepted_license: '1'
intvolume: ' 4'
language:
- iso: eng
month: '03'
oa: 1
oa_version: Published Version
pmid: 1
publication: eLife
publication_identifier:
issn:
- 2050-084X
publication_status: published
publisher: eLife Sciences Publications
quality_controlled: '1'
status: public
title: Decoding a neural circuit controlling global animal state in C. elegans
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: journal_article
user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87
volume: 4
year: '2015'
...
---
_id: '1637'
abstract:
- lang: eng
text: An instance of the Valued Constraint Satisfaction Problem (VCSP) is given
by a finite set of variables, a finite domain of labels, and a sum of functions,
each function depending on a subset of the variables. Each function can take finite
values specifying costs of assignments of labels to its variables or the infinite
value, which indicates an infeasible assignment. The goal is to find an assignment
of labels to the variables that minimizes the sum. We study, assuming that P ≠
NP, how the complexity of this very general problem depends on the set of functions
allowed in the instances, the so-called constraint language. The case when all
allowed functions take values in {0, ∞} corresponds to ordinary CSPs, where one
deals only with the feasibility issue and there is no optimization. This case
is the subject of the Algebraic CSP Dichotomy Conjecture predicting for which
constraint languages CSPs are tractable (i.e. solvable in polynomial time) and
for which NP-hard. The case when all allowed functions take only finite values
corresponds to finite-valued CSP, where the feasibility aspect is trivial and
one deals only with the optimization issue. The complexity of finite-valued CSPs
was fully classified by Thapper and Zivny. An algebraic necessary condition for
tractability of a general-valued CSP with a fixed constraint language was recently
given by Kozik and Ochremiak. As our main result, we prove that if a constraint
language satisfies this algebraic necessary condition, and the feasibility CSP
(i.e. the problem of deciding whether a given instance has a feasible solution)
corresponding to the VCSP with this language is tractable, then the VCSP is tractable.
The algorithm is a simple combination of the assumed algorithm for the feasibility
CSP and the standard LP relaxation. As a corollary, we obtain that a dichotomy
for ordinary CSPs would imply a dichotomy for general-valued CSPs.
alternative_title:
- 56th Annual Symposium on Foundations of Computer Science
author:
- first_name: Vladimir
full_name: Kolmogorov, Vladimir
id: 3D50B0BA-F248-11E8-B48F-1D18A9856A87
last_name: Kolmogorov
- first_name: Andrei
full_name: Krokhin, Andrei
last_name: Krokhin
- first_name: Michal
full_name: Rolinek, Michal
id: 3CB3BC06-F248-11E8-B48F-1D18A9856A87
last_name: Rolinek
citation:
ama: 'Kolmogorov V, Krokhin A, Rolinek M. The complexity of general-valued CSPs.
In: IEEE; 2015:1246-1258. doi:10.1109/FOCS.2015.80'
apa: 'Kolmogorov, V., Krokhin, A., & Rolinek, M. (2015). The complexity of general-valued
CSPs (pp. 1246–1258). Presented at the FOCS: Foundations of Computer Science,
Berkeley, CA, United States: IEEE. https://doi.org/10.1109/FOCS.2015.80'
chicago: Kolmogorov, Vladimir, Andrei Krokhin, and Michal Rolinek. “The Complexity
of General-Valued CSPs,” 1246–58. IEEE, 2015. https://doi.org/10.1109/FOCS.2015.80.
ieee: 'V. Kolmogorov, A. Krokhin, and M. Rolinek, “The complexity of general-valued
CSPs,” presented at the FOCS: Foundations of Computer Science, Berkeley, CA, United
States, 2015, pp. 1246–1258.'
ista: 'Kolmogorov V, Krokhin A, Rolinek M. 2015. The complexity of general-valued
CSPs. FOCS: Foundations of Computer Science, 56th Annual Symposium on Foundations
of Computer Science, , 1246–1258.'
mla: Kolmogorov, Vladimir, et al. The Complexity of General-Valued CSPs.
IEEE, 2015, pp. 1246–58, doi:10.1109/FOCS.2015.80.
short: V. Kolmogorov, A. Krokhin, M. Rolinek, in:, IEEE, 2015, pp. 1246–1258.
conference:
end_date: 2015-10-20
location: Berkeley, CA, United States
name: 'FOCS: Foundations of Computer Science'
start_date: 2015-10-18
date_created: 2018-12-11T11:53:10Z
date_published: 2015-12-01T00:00:00Z
date_updated: 2023-02-23T12:44:26Z
day: '01'
department:
- _id: VlKo
doi: 10.1109/FOCS.2015.80
ec_funded: 1
language:
- iso: eng
main_file_link:
- open_access: '1'
url: http://arxiv.org/abs/1502.07327
month: '12'
oa: 1
oa_version: Preprint
page: 1246 - 1258
project:
- _id: 25FBA906-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '616160'
name: 'Discrete Optimization in Computer Vision: Theory and Practice'
publication_status: published
publisher: IEEE
publist_id: '5518'
quality_controlled: '1'
related_material:
record:
- id: '644'
relation: other
status: public
scopus_import: 1
status: public
title: The complexity of general-valued CSPs
type: conference
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
year: '2015'
...
---
_id: '6507'
abstract:
- lang: eng
text: The osteoclast-associated receptor (OSCAR) is a collagen-binding immune receptor
with important roles in dendritic cell maturation and activation of inflammatory
monocytes as well as in osteoclastogenesis. The crystal structure of the OSCAR
ectodomain is presented, both free and in complex with a consensus triple-helical
peptide (THP). The structures revealed a collagen-binding site in each immunoglobulin-like
domain (D1 and D2). The THP binds near a predicted collagen-binding groove in
D1, but a more extensive interaction with D2 is facilitated by the unusually wide
D1-D2 interdomain angle in OSCAR. Direct binding assays, combined with site-directed
mutagenesis, confirm that the primary collagen-binding site in OSCAR resides in
D2, in marked contrast to the related collagen receptors, glycoprotein VI (GPVI)
and leukocyte-associated immunoglobulin-like receptor-1 (LAIR-1). Monomeric OSCAR
D1D2 binds to the consensus THP with a KD of 28 µM measured in solution, but shows
a higher affinity (KD 1.5 μM) when binding to a solid-phase THP, most likely due
to an avidity effect. These data suggest a 2-stage model for the interaction of
OSCAR with a collagen fibril, with transient, low-affinity interactions initiated
by the membrane-distal D1, followed by firm adhesion to the primary binding site
in D2.
author:
- first_name: Long
full_name: Zhou, Long
id: 3E751364-F248-11E8-B48F-1D18A9856A87
last_name: Zhou
orcid: 0000-0002-1864-8951
- first_name: J. M.
full_name: Hinerman, J. M.
last_name: Hinerman
- first_name: M.
full_name: Blaszczyk, M.
last_name: Blaszczyk
- first_name: J. L. C.
full_name: Miller, J. L. C.
last_name: Miller
- first_name: D. G.
full_name: Conrady, D. G.
last_name: Conrady
- first_name: A. D.
full_name: Barrow, A. D.
last_name: Barrow
- first_name: D. Y.
full_name: Chirgadze, D. Y.
last_name: Chirgadze
- first_name: D.
full_name: Bihan, D.
last_name: Bihan
- first_name: R. W.
full_name: Farndale, R. W.
last_name: Farndale
- first_name: A. B.
full_name: Herr, A. B.
last_name: Herr
citation:
ama: Zhou L, Hinerman JM, Blaszczyk M, et al. Structural basis for collagen recognition
by the immune receptor OSCAR. Blood. 2015;127(5):529-537. doi:10.1182/blood-2015-08-667055
apa: Zhou, L., Hinerman, J. M., Blaszczyk, M., Miller, J. L. C., Conrady, D. G.,
Barrow, A. D., … Herr, A. B. (2015). Structural basis for collagen recognition
by the immune receptor OSCAR. Blood. American Society of Hematology. https://doi.org/10.1182/blood-2015-08-667055
chicago: Zhou, Long, J. M. Hinerman, M. Blaszczyk, J. L. C. Miller, D. G. Conrady,
A. D. Barrow, D. Y. Chirgadze, D. Bihan, R. W. Farndale, and A. B. Herr. “Structural
Basis for Collagen Recognition by the Immune Receptor OSCAR.” Blood. American
Society of Hematology, 2015. https://doi.org/10.1182/blood-2015-08-667055.
ieee: L. Zhou et al., “Structural basis for collagen recognition by the immune
receptor OSCAR,” Blood, vol. 127, no. 5. American Society of Hematology,
pp. 529–537, 2015.
ista: Zhou L, Hinerman JM, Blaszczyk M, Miller JLC, Conrady DG, Barrow AD, Chirgadze
DY, Bihan D, Farndale RW, Herr AB. 2015. Structural basis for collagen recognition
by the immune receptor OSCAR. Blood. 127(5), 529–537.
mla: Zhou, Long, et al. “Structural Basis for Collagen Recognition by the Immune
Receptor OSCAR.” Blood, vol. 127, no. 5, American Society of Hematology,
2015, pp. 529–37, doi:10.1182/blood-2015-08-667055.
short: L. Zhou, J.M. Hinerman, M. Blaszczyk, J.L.C. Miller, D.G. Conrady, A.D. Barrow,
D.Y. Chirgadze, D. Bihan, R.W. Farndale, A.B. Herr, Blood 127 (2015) 529–537.
date_created: 2019-05-31T09:38:50Z
date_published: 2015-11-02T00:00:00Z
date_updated: 2021-01-12T08:07:47Z
day: '02'
doi: 10.1182/blood-2015-08-667055
extern: '1'
external_id:
pmid:
- '26552697'
intvolume: ' 127'
issue: '5'
language:
- iso: eng
month: '11'
oa_version: None
page: 529-537
pmid: 1
publication: Blood
publication_identifier:
issn:
- 0006-4971
- 1528-0020
publication_status: published
publisher: American Society of Hematology
quality_controlled: '1'
status: public
title: Structural basis for collagen recognition by the immune receptor OSCAR
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 127
year: '2015'
...
---
_id: '6737'
abstract:
- lang: eng
text: This paper presents polar coding schemes for the two-user discrete memoryless
broadcast channel (DM-BC) which achieve Marton's region with both common and private
messages. This is the best achievable rate region known to date, and it is tight
for all classes of two-user DM-BCs whose capacity regions are known. To accomplish
this task, we first construct polar codes for both the superposition as well as
binning strategy. By combining these two schemes, we obtain Marton's region with
private messages only. Finally, we show how to handle the case of common information.
The proposed coding schemes possess the usual advantages of polar codes, i.e.,
they have low encoding and decoding complexity and a superpolynomial decay rate
of the error probability. We follow the lead of Goela, Abbe, and Gastpar, who
recently introduced polar codes emulating the superposition and binning schemes.
To align the polar indices, for both schemes, their solution involves some degradedness
constraints that are assumed to hold between the auxiliary random variables and
channel outputs. To remove these constraints, we consider the transmission of
k blocks and employ a chaining construction that guarantees the proper alignment
of the polarized indices. The techniques described in this paper are quite general,
and they can be adopted to many other multiterminal scenarios whenever there polar
indices need to be aligned.
author:
- first_name: Marco
full_name: Mondelli, Marco
id: 27EB676C-8706-11E9-9510-7717E6697425
last_name: Mondelli
orcid: 0000-0002-3242-7020
- first_name: Hamed
full_name: Hassani, Hamed
last_name: Hassani
- first_name: Igal
full_name: Sason, Igal
last_name: Sason
- first_name: Rudiger
full_name: Urbanke, Rudiger
last_name: Urbanke
citation:
ama: Mondelli M, Hassani H, Sason I, Urbanke R. Achieving Marton’s region for broadcast
channels using polar codes. IEEE Transactions on Information Theory. 2015;61(2):783-800.
doi:10.1109/tit.2014.2368555
apa: Mondelli, M., Hassani, H., Sason, I., & Urbanke, R. (2015). Achieving Marton’s
region for broadcast channels using polar codes. IEEE Transactions on Information
Theory. IEEE. https://doi.org/10.1109/tit.2014.2368555
chicago: Mondelli, Marco, Hamed Hassani, Igal Sason, and Rudiger Urbanke. “Achieving
Marton’s Region for Broadcast Channels Using Polar Codes.” IEEE Transactions
on Information Theory. IEEE, 2015. https://doi.org/10.1109/tit.2014.2368555.
ieee: M. Mondelli, H. Hassani, I. Sason, and R. Urbanke, “Achieving Marton’s region
for broadcast channels using polar codes,” IEEE Transactions on Information
Theory, vol. 61, no. 2. IEEE, pp. 783–800, 2015.
ista: Mondelli M, Hassani H, Sason I, Urbanke R. 2015. Achieving Marton’s region
for broadcast channels using polar codes. IEEE Transactions on Information Theory.
61(2), 783–800.
mla: Mondelli, Marco, et al. “Achieving Marton’s Region for Broadcast Channels Using
Polar Codes.” IEEE Transactions on Information Theory, vol. 61, no. 2,
IEEE, 2015, pp. 783–800, doi:10.1109/tit.2014.2368555.
short: M. Mondelli, H. Hassani, I. Sason, R. Urbanke, IEEE Transactions on Information
Theory 61 (2015) 783–800.
date_created: 2019-07-31T07:03:38Z
date_published: 2015-02-01T00:00:00Z
date_updated: 2021-01-12T08:08:46Z
day: '01'
doi: 10.1109/tit.2014.2368555
extern: '1'
external_id:
arxiv:
- '1401.6060'
intvolume: ' 61'
issue: '2'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/1401.6060
month: '02'
oa: 1
oa_version: Preprint
page: 783-800
publication: IEEE Transactions on Information Theory
publication_status: published
publisher: IEEE
quality_controlled: '1'
status: public
title: Achieving Marton’s region for broadcast channels using polar codes
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 61
year: '2015'
...
---
_id: '6736'
abstract:
- lang: eng
text: Motivated by the significant performance gains which polar codes experience
under successive cancellation list decoding, their scaling exponent is studied
as a function of the list size. In particular, the error probability is fixed,
and the tradeoff between the block length and back-off from capacity is analyzed.
A lower bound is provided on the error probability under MAP decoding with list
size L for any binary-input memoryless output-symmetric channel and for any class
of linear codes such that their minimum distance is unbounded as the block length
grows large. Then, it is shown that under MAP decoding, although the introduction
of a list can significantly improve the involved constants, the scaling exponent
itself, i.e., the speed at which capacity is approached, stays unaffected for
any finite list size. In particular, this result applies to polar codes, since
their minimum distance tends to infinity as the block length increases. A similar
result is proved for genie-aided successive cancellation decoding when transmission
takes place over the binary erasure channel, namely, the scaling exponent remains
constant for any fixed number of helps from the genie. Note that since genie-aided
successive cancellation decoding might be strictly worse than successive cancellation
list decoding, the problem of establishing the scaling exponent of the latter
remains open.
author:
- first_name: Marco
full_name: Mondelli, Marco
id: 27EB676C-8706-11E9-9510-7717E6697425
last_name: Mondelli
orcid: 0000-0002-3242-7020
- first_name: Hamed
full_name: Hassani, Hamed
last_name: Hassani
- first_name: Rudiger
full_name: Urbanke, Rudiger
last_name: Urbanke
citation:
ama: Mondelli M, Hassani H, Urbanke R. Scaling exponent of list decoders with applications
to polar codes. IEEE Transactions on Information Theory. 2015;61(9):4838-4851.
doi:10.1109/tit.2015.2453315
apa: Mondelli, M., Hassani, H., & Urbanke, R. (2015). Scaling exponent of list
decoders with applications to polar codes. IEEE Transactions on Information
Theory. IEEE. https://doi.org/10.1109/tit.2015.2453315
chicago: Mondelli, Marco, Hamed Hassani, and Rudiger Urbanke. “Scaling Exponent
of List Decoders with Applications to Polar Codes.” IEEE Transactions on Information
Theory. IEEE, 2015. https://doi.org/10.1109/tit.2015.2453315.
ieee: M. Mondelli, H. Hassani, and R. Urbanke, “Scaling exponent of list decoders
with applications to polar codes,” IEEE Transactions on Information Theory,
vol. 61, no. 9. IEEE, pp. 4838–4851, 2015.
ista: Mondelli M, Hassani H, Urbanke R. 2015. Scaling exponent of list decoders
with applications to polar codes. IEEE Transactions on Information Theory. 61(9),
4838–4851.
mla: Mondelli, Marco, et al. “Scaling Exponent of List Decoders with Applications
to Polar Codes.” IEEE Transactions on Information Theory, vol. 61, no.
9, IEEE, 2015, pp. 4838–51, doi:10.1109/tit.2015.2453315.
short: M. Mondelli, H. Hassani, R. Urbanke, IEEE Transactions on Information Theory
61 (2015) 4838–4851.
date_created: 2019-07-31T06:50:34Z
date_published: 2015-09-01T00:00:00Z
date_updated: 2021-01-12T08:08:45Z
day: '01'
doi: 10.1109/tit.2015.2453315
extern: '1'
external_id:
arxiv:
- '1304.5220'
intvolume: ' 61'
issue: '9'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/1304.5220
month: '09'
oa: 1
oa_version: Preprint
page: 4838-4851
publication: IEEE Transactions on Information Theory
publication_status: published
publisher: IEEE
quality_controlled: '1'
status: public
title: Scaling exponent of list decoders with applications to polar codes
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 61
year: '2015'
...
---
_id: '7070'
abstract:
- lang: eng
text: 'Torque magnetization measurements on YBa2Cu3Oy (YBCO) at doping y=6.67 (p=0.12),
in dc fields (B) up to 33 T and temperatures down to 4.5 K, show that weak diamagnetism
persists above the extrapolated irreversibility field Hirr(T=0)≈24 T. The differential
susceptibility dM/dB, however, is more rapidly suppressed for B≳16 T than expected
from the properties of the low field superconducting state, and saturates at a
low value for fields B≳24 T. In addition, torque measurements on a p=0.11 YBCO
crystal in pulsed field up to 65 T and temperatures down to 8 K show similar behavior,
with no additional features at higher fields. We offer two candidate scenarios
to explain these observations: (a) superconductivity survives but is heavily suppressed
at high field by competition with charge-density-wave (CDW) order; (b) static
superconductivity disappears near 24 T and is followed by a region of fluctuating
superconductivity, which causes dM/dB to saturate at high field. The diamagnetic
signal observed above 50 T for the p=0.11 crystal at 40 K and below may be caused
by changes in the normal state susceptibility rather than bulk or fluctuating
superconductivity. There will be orbital (Landau) diamagnetism from electron pockets
and possibly a reduction in spin susceptibility caused by the stronger three-dimensional
ordered CDW.'
article_number: '180509'
article_processing_charge: No
article_type: original
author:
- first_name: Jing Fei
full_name: Yu, Jing Fei
last_name: Yu
- first_name: B. J.
full_name: Ramshaw, B. J.
last_name: Ramshaw
- first_name: I.
full_name: Kokanović, I.
last_name: Kokanović
- first_name: Kimberly A
full_name: Modic, Kimberly A
id: 13C26AC0-EB69-11E9-87C6-5F3BE6697425
last_name: Modic
orcid: 0000-0001-9760-3147
- first_name: N.
full_name: Harrison, N.
last_name: Harrison
- first_name: James
full_name: Day, James
last_name: Day
- first_name: Ruixing
full_name: Liang, Ruixing
last_name: Liang
- first_name: W. N.
full_name: Hardy, W. N.
last_name: Hardy
- first_name: D. A.
full_name: Bonn, D. A.
last_name: Bonn
- first_name: A.
full_name: McCollam, A.
last_name: McCollam
- first_name: S. R.
full_name: Julian, S. R.
last_name: Julian
- first_name: J. R.
full_name: Cooper, J. R.
last_name: Cooper
citation:
ama: Yu JF, Ramshaw BJ, Kokanović I, et al. Magnetization of underdoped YBa2Cu3Oy
above the irreversibility field. Physical Review B. 2015;92(18). doi:10.1103/physrevb.92.180509
apa: Yu, J. F., Ramshaw, B. J., Kokanović, I., Modic, K. A., Harrison, N., Day,
J., … Cooper, J. R. (2015). Magnetization of underdoped YBa2Cu3Oy above the irreversibility
field. Physical Review B. APS. https://doi.org/10.1103/physrevb.92.180509
chicago: Yu, Jing Fei, B. J. Ramshaw, I. Kokanović, Kimberly A Modic, N. Harrison,
James Day, Ruixing Liang, et al. “Magnetization of Underdoped YBa2Cu3Oy above
the Irreversibility Field.” Physical Review B. APS, 2015. https://doi.org/10.1103/physrevb.92.180509.
ieee: J. F. Yu et al., “Magnetization of underdoped YBa2Cu3Oy above the irreversibility
field,” Physical Review B, vol. 92, no. 18. APS, 2015.
ista: Yu JF, Ramshaw BJ, Kokanović I, Modic KA, Harrison N, Day J, Liang R, Hardy
WN, Bonn DA, McCollam A, Julian SR, Cooper JR. 2015. Magnetization of underdoped
YBa2Cu3Oy above the irreversibility field. Physical Review B. 92(18), 180509.
mla: Yu, Jing Fei, et al. “Magnetization of Underdoped YBa2Cu3Oy above the Irreversibility
Field.” Physical Review B, vol. 92, no. 18, 180509, APS, 2015, doi:10.1103/physrevb.92.180509.
short: J.F. Yu, B.J. Ramshaw, I. Kokanović, K.A. Modic, N. Harrison, J. Day, R.
Liang, W.N. Hardy, D.A. Bonn, A. McCollam, S.R. Julian, J.R. Cooper, Physical
Review B 92 (2015).
date_created: 2019-11-19T13:22:06Z
date_published: 2015-11-23T00:00:00Z
date_updated: 2021-01-12T08:11:42Z
day: '23'
doi: 10.1103/physrevb.92.180509
extern: '1'
intvolume: ' 92'
issue: '18'
language:
- iso: eng
month: '11'
oa_version: None
publication: Physical Review B
publication_identifier:
issn:
- 1098-0121
- 1550-235X
publication_status: published
publisher: APS
quality_controlled: '1'
status: public
title: Magnetization of underdoped YBa2Cu3Oy above the irreversibility field
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 92
year: '2015'
...
---
_id: '7456'
abstract:
- lang: eng
text: The rational design of monodisperse ferroelectric nanocrystals with controlled
size and shape and their organization into hierarchical structures has been a
critical step for understanding the polar ordering in nanoscale ferroelectrics,
as well as the design of nanocrystal-based functional materials which harness
the properties of individual nanoparticles and the collective interactions between
them. We report here on the synthesis and self-assembly of aggregate-free, single-crystalline
titanium-based perovskite nanoparticles with controlled morphology and surface
composition by using a simple, easily scalable and highly versatile colloidal
route. Single-crystalline, non-aggregated BaTiO3 colloidal nanocrystals, used
as a model system, have been prepared under solvothermal conditions at temperatures
as low as 180 °C. The shape of the nanocrystals was tuned from spheroidal to cubic
upon changing the polarity of the solvent, whereas their size was varied from
16 to 30 nm for spheres and 5 to 78 nm for cubes by changing the concentration
of the precursors and the reaction time, respectively. The hydrophobic, oleic
acid-passivated nanoparticles exhibit very good solubility in non-polar solvents
and can be rendered dispersible in polar solvents by a simple process involving
the oxidative cleavage of the double bond upon treating the nanopowders with the
Lemieux–von Rudloff reagent. Lattice dynamic analysis indicated that regardless
of their size, BaTiO3 nanocrystals present local disorder within the perovskite
unit cell, associated with the existence of polar ordering. We also demonstrate
for the first time that, in addition to being used for fabricating large area,
crack-free, highly uniform films, BaTiO3 nanocubes can serve as building blocks
for the design of 2D and 3D mesoscale structures, such as superlattices and superparticles.
Interestingly, the type of superlattice structure (simple cubic or face centered
cubic) appears to be determined by the type of solvent in which the nanocrystals
were dispersed. This approach provides an excellent platform for the synthesis
of other titanium-based perovskite colloidal nanocrystals with controlled chemical
composition, surface structure and morphology and for their assembly into complex
architectures, therefore opening the door for the design of novel mesoscale functional
materials/nanocomposites with potential applications in energy conversion, data
storage and the biomedical field.
article_processing_charge: No
article_type: original
author:
- first_name: Daniela
full_name: Caruntu, Daniela
last_name: Caruntu
- first_name: Taha
full_name: Rostamzadeh, Taha
last_name: Rostamzadeh
- first_name: Tommaso
full_name: Costanzo, Tommaso
id: D93824F4-D9BA-11E9-BB12-F207E6697425
last_name: Costanzo
orcid: 0000-0001-9732-3815
- first_name: Saman
full_name: Salemizadeh Parizi, Saman
last_name: Salemizadeh Parizi
- first_name: Gabriel
full_name: Caruntu, Gabriel
last_name: Caruntu
citation:
ama: Caruntu D, Rostamzadeh T, Costanzo T, Salemizadeh Parizi S, Caruntu G. Solvothermal
synthesis and controlled self-assembly of monodisperse titanium-based perovskite
colloidal nanocrystals. Nanoscale. 2015;7(30):12955-12969. doi:10.1039/c5nr00737b
apa: Caruntu, D., Rostamzadeh, T., Costanzo, T., Salemizadeh Parizi, S., & Caruntu,
G. (2015). Solvothermal synthesis and controlled self-assembly of monodisperse
titanium-based perovskite colloidal nanocrystals. Nanoscale. RSC. https://doi.org/10.1039/c5nr00737b
chicago: Caruntu, Daniela, Taha Rostamzadeh, Tommaso Costanzo, Saman Salemizadeh
Parizi, and Gabriel Caruntu. “Solvothermal Synthesis and Controlled Self-Assembly
of Monodisperse Titanium-Based Perovskite Colloidal Nanocrystals.” Nanoscale.
RSC, 2015. https://doi.org/10.1039/c5nr00737b.
ieee: D. Caruntu, T. Rostamzadeh, T. Costanzo, S. Salemizadeh Parizi, and G. Caruntu,
“Solvothermal synthesis and controlled self-assembly of monodisperse titanium-based
perovskite colloidal nanocrystals,” Nanoscale, vol. 7, no. 30. RSC, pp.
12955–12969, 2015.
ista: Caruntu D, Rostamzadeh T, Costanzo T, Salemizadeh Parizi S, Caruntu G. 2015.
Solvothermal synthesis and controlled self-assembly of monodisperse titanium-based
perovskite colloidal nanocrystals. Nanoscale. 7(30), 12955–12969.
mla: Caruntu, Daniela, et al. “Solvothermal Synthesis and Controlled Self-Assembly
of Monodisperse Titanium-Based Perovskite Colloidal Nanocrystals.” Nanoscale,
vol. 7, no. 30, RSC, 2015, pp. 12955–69, doi:10.1039/c5nr00737b.
short: D. Caruntu, T. Rostamzadeh, T. Costanzo, S. Salemizadeh Parizi, G. Caruntu,
Nanoscale 7 (2015) 12955–12969.
date_created: 2020-02-05T14:16:37Z
date_published: 2015-08-14T00:00:00Z
date_updated: 2023-02-23T13:08:24Z
day: '14'
doi: 10.1039/c5nr00737b
extern: '1'
external_id:
pmid:
- '26168304'
intvolume: ' 7'
issue: '30'
language:
- iso: eng
month: '08'
oa_version: None
page: 12955-12969
pmid: 1
publication: Nanoscale
publication_identifier:
issn:
- 2040-3364
- 2040-3372
publication_status: published
publisher: RSC
quality_controlled: '1'
status: public
title: Solvothermal synthesis and controlled self-assembly of monodisperse titanium-based
perovskite colloidal nanocrystals
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 7
year: '2015'
...
---
_id: '7457'
abstract:
- lang: eng
text: A new organic–inorganic ferroelectric hybrid capacitor designed by uniformly
incorporating surface modified monodisperse 15 nm ferroelectric BaTiO3 nanocubes
into non-polar polymer blends of poly(methyl methacrylate) (PMMA) polymer and
acrylonitrile-butadiene-styrene (ABS) terpolymer is described. The investigation
of spatial distribution of nanofillers via a non-distractive thermal pulse method
illustrates that the surface functionalization of nanocubes plays a key role in
the uniform distribution of charge polarization within the polymer matrix. The
discharged energy density of the nanocomposite with 30 vol% BaTiO3 nanocubes is
∼44 × 10−3 J cm−3, which is almost six times higher than that of the neat polymer.
The facile processing, along with the superior mechanical and electrical properties
of the BaTiO3/PMMA–ABS nanocomposites make them suitable for implementation into
capacitive electrical energy storage devices.
article_processing_charge: No
article_type: original
author:
- first_name: Saman Salemizadeh
full_name: Parizi, Saman Salemizadeh
last_name: Parizi
- first_name: Gavin
full_name: Conley, Gavin
last_name: Conley
- first_name: Tommaso
full_name: Costanzo, Tommaso
id: D93824F4-D9BA-11E9-BB12-F207E6697425
last_name: Costanzo
orcid: 0000-0001-9732-3815
- first_name: Bob
full_name: Howell, Bob
last_name: Howell
- first_name: Axel
full_name: Mellinger, Axel
last_name: Mellinger
- first_name: Gabriel
full_name: Caruntu, Gabriel
last_name: Caruntu
citation:
ama: Parizi SS, Conley G, Costanzo T, Howell B, Mellinger A, Caruntu G. Fabrication
of barium titanate/acrylonitrile-butadiene styrene/poly(methyl methacrylate) nanocomposite
films for hybrid ferroelectric capacitors. RSC Advances. 2015;5(93):76356-76362.
doi:10.1039/c5ra11347d
apa: Parizi, S. S., Conley, G., Costanzo, T., Howell, B., Mellinger, A., & Caruntu,
G. (2015). Fabrication of barium titanate/acrylonitrile-butadiene styrene/poly(methyl
methacrylate) nanocomposite films for hybrid ferroelectric capacitors. RSC
Advances. RSC. https://doi.org/10.1039/c5ra11347d
chicago: Parizi, Saman Salemizadeh, Gavin Conley, Tommaso Costanzo, Bob Howell,
Axel Mellinger, and Gabriel Caruntu. “Fabrication of Barium Titanate/Acrylonitrile-Butadiene
Styrene/Poly(Methyl Methacrylate) Nanocomposite Films for Hybrid Ferroelectric
Capacitors.” RSC Advances. RSC, 2015. https://doi.org/10.1039/c5ra11347d.
ieee: S. S. Parizi, G. Conley, T. Costanzo, B. Howell, A. Mellinger, and G. Caruntu,
“Fabrication of barium titanate/acrylonitrile-butadiene styrene/poly(methyl methacrylate)
nanocomposite films for hybrid ferroelectric capacitors,” RSC Advances,
vol. 5, no. 93. RSC, pp. 76356–76362, 2015.
ista: Parizi SS, Conley G, Costanzo T, Howell B, Mellinger A, Caruntu G. 2015. Fabrication
of barium titanate/acrylonitrile-butadiene styrene/poly(methyl methacrylate) nanocomposite
films for hybrid ferroelectric capacitors. RSC Advances. 5(93), 76356–76362.
mla: Parizi, Saman Salemizadeh, et al. “Fabrication of Barium Titanate/Acrylonitrile-Butadiene
Styrene/Poly(Methyl Methacrylate) Nanocomposite Films for Hybrid Ferroelectric
Capacitors.” RSC Advances, vol. 5, no. 93, RSC, 2015, pp. 76356–62, doi:10.1039/c5ra11347d.
short: S.S. Parizi, G. Conley, T. Costanzo, B. Howell, A. Mellinger, G. Caruntu,
RSC Advances 5 (2015) 76356–76362.
date_created: 2020-02-05T14:17:26Z
date_published: 2015-09-01T00:00:00Z
date_updated: 2023-02-23T13:08:26Z
day: '01'
doi: 10.1039/c5ra11347d
extern: '1'
intvolume: ' 5'
issue: '93'
language:
- iso: eng
month: '09'
oa_version: Submitted Version
page: 76356-76362
publication: RSC Advances
publication_identifier:
issn:
- 2046-2069
publication_status: published
publisher: RSC
quality_controlled: '1'
status: public
title: Fabrication of barium titanate/acrylonitrile-butadiene styrene/poly(methyl
methacrylate) nanocomposite films for hybrid ferroelectric capacitors
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 5
year: '2015'
...
---
_id: '7742'
abstract:
- lang: eng
text: Across-nation differences in the mean values for complex traits are common1,2,3,4,5,6,7,8,
but the reasons for these differences are unknown. Here we find that many independent
loci contribute to population genetic differences in height and body mass index
(BMI) in 9,416 individuals across 14 European countries. Using discovery data
on over 250,000 individuals and unbiased effect size estimates from 17,500 sibling
pairs, we estimate that 24% (95% credible interval (CI) = 9%, 41%) and 8% (95%
CI = 4%, 16%) of the captured additive genetic variance for height and BMI, respectively,
reflect population genetic differences. Population genetic divergence differed
significantly from that in a null model (height, P < 3.94 × 10−8; BMI, P < 5.95
× 10−4), and we find an among-population genetic correlation for tall and slender
individuals (r = −0.80, 95% CI = −0.95, −0.60), consistent with correlated selection
for both phenotypes. Observed differences in height among populations reflected
the predicted genetic means (r = 0.51; P < 0.001), but environmental differences
across Europe masked genetic differentiation for BMI (P < 0.58).
article_processing_charge: No
article_type: original
author:
- first_name: Matthew Richard
full_name: Robinson, Matthew Richard
id: E5D42276-F5DA-11E9-8E24-6303E6697425
last_name: Robinson
orcid: 0000-0001-8982-8813
- first_name: Gibran
full_name: Hemani, Gibran
last_name: Hemani
- first_name: Carolina
full_name: Medina-Gomez, Carolina
last_name: Medina-Gomez
- first_name: Massimo
full_name: Mezzavilla, Massimo
last_name: Mezzavilla
- first_name: Tonu
full_name: Esko, Tonu
last_name: Esko
- first_name: Konstantin
full_name: Shakhbazov, Konstantin
last_name: Shakhbazov
- first_name: Joseph E
full_name: Powell, Joseph E
last_name: Powell
- first_name: Anna
full_name: Vinkhuyzen, Anna
last_name: Vinkhuyzen
- first_name: Sonja I
full_name: Berndt, Sonja I
last_name: Berndt
- first_name: Stefan
full_name: Gustafsson, Stefan
last_name: Gustafsson
- first_name: Anne E
full_name: Justice, Anne E
last_name: Justice
- first_name: Bratati
full_name: Kahali, Bratati
last_name: Kahali
- first_name: Adam E
full_name: Locke, Adam E
last_name: Locke
- first_name: Tune H
full_name: Pers, Tune H
last_name: Pers
- first_name: Sailaja
full_name: Vedantam, Sailaja
last_name: Vedantam
- first_name: Andrew R
full_name: Wood, Andrew R
last_name: Wood
- first_name: Wouter
full_name: van Rheenen, Wouter
last_name: van Rheenen
- first_name: Ole A
full_name: Andreassen, Ole A
last_name: Andreassen
- first_name: Paolo
full_name: Gasparini, Paolo
last_name: Gasparini
- first_name: Andres
full_name: Metspalu, Andres
last_name: Metspalu
- first_name: Leonard H van den
full_name: Berg, Leonard H van den
last_name: Berg
- first_name: Jan H
full_name: Veldink, Jan H
last_name: Veldink
- first_name: Fernando
full_name: Rivadeneira, Fernando
last_name: Rivadeneira
- first_name: Thomas M
full_name: Werge, Thomas M
last_name: Werge
- first_name: Goncalo R
full_name: Abecasis, Goncalo R
last_name: Abecasis
- first_name: Dorret I
full_name: Boomsma, Dorret I
last_name: Boomsma
- first_name: Daniel I
full_name: Chasman, Daniel I
last_name: Chasman
- first_name: Eco J C
full_name: de Geus, Eco J C
last_name: de Geus
- first_name: Timothy M
full_name: Frayling, Timothy M
last_name: Frayling
- first_name: Joel N
full_name: Hirschhorn, Joel N
last_name: Hirschhorn
- first_name: Jouke Jan
full_name: Hottenga, Jouke Jan
last_name: Hottenga
- first_name: Erik
full_name: Ingelsson, Erik
last_name: Ingelsson
- first_name: Ruth J F
full_name: Loos, Ruth J F
last_name: Loos
- first_name: Patrik K E
full_name: Magnusson, Patrik K E
last_name: Magnusson
- first_name: Nicholas G
full_name: Martin, Nicholas G
last_name: Martin
- first_name: Grant W
full_name: Montgomery, Grant W
last_name: Montgomery
- first_name: Kari E
full_name: North, Kari E
last_name: North
- first_name: Nancy L
full_name: Pedersen, Nancy L
last_name: Pedersen
- first_name: Timothy D
full_name: Spector, Timothy D
last_name: Spector
- first_name: Elizabeth K
full_name: Speliotes, Elizabeth K
last_name: Speliotes
- first_name: Michael E
full_name: Goddard, Michael E
last_name: Goddard
- first_name: Jian
full_name: Yang, Jian
last_name: Yang
- first_name: Peter M
full_name: Visscher, Peter M
last_name: Visscher
citation:
ama: Robinson MR, Hemani G, Medina-Gomez C, et al. Population genetic differentiation
of height and body mass index across Europe. Nature Genetics. 2015;47(11):1357-1362.
doi:10.1038/ng.3401
apa: Robinson, M. R., Hemani, G., Medina-Gomez, C., Mezzavilla, M., Esko, T., Shakhbazov,
K., … Visscher, P. M. (2015). Population genetic differentiation of height and
body mass index across Europe. Nature Genetics. Springer Nature. https://doi.org/10.1038/ng.3401
chicago: Robinson, Matthew Richard, Gibran Hemani, Carolina Medina-Gomez, Massimo
Mezzavilla, Tonu Esko, Konstantin Shakhbazov, Joseph E Powell, et al. “Population
Genetic Differentiation of Height and Body Mass Index across Europe.” Nature
Genetics. Springer Nature, 2015. https://doi.org/10.1038/ng.3401.
ieee: M. R. Robinson et al., “Population genetic differentiation of height
and body mass index across Europe,” Nature Genetics, vol. 47, no. 11. Springer
Nature, pp. 1357–1362, 2015.
ista: Robinson MR, Hemani G, Medina-Gomez C, Mezzavilla M, Esko T, Shakhbazov K,
Powell JE, Vinkhuyzen A, Berndt SI, Gustafsson S, Justice AE, Kahali B, Locke
AE, Pers TH, Vedantam S, Wood AR, van Rheenen W, Andreassen OA, Gasparini P, Metspalu
A, Berg LH van den, Veldink JH, Rivadeneira F, Werge TM, Abecasis GR, Boomsma
DI, Chasman DI, de Geus EJC, Frayling TM, Hirschhorn JN, Hottenga JJ, Ingelsson
E, Loos RJF, Magnusson PKE, Martin NG, Montgomery GW, North KE, Pedersen NL, Spector
TD, Speliotes EK, Goddard ME, Yang J, Visscher PM. 2015. Population genetic differentiation
of height and body mass index across Europe. Nature Genetics. 47(11), 1357–1362.
mla: Robinson, Matthew Richard, et al. “Population Genetic Differentiation of Height
and Body Mass Index across Europe.” Nature Genetics, vol. 47, no. 11, Springer
Nature, 2015, pp. 1357–62, doi:10.1038/ng.3401.
short: M.R. Robinson, G. Hemani, C. Medina-Gomez, M. Mezzavilla, T. Esko, K. Shakhbazov,
J.E. Powell, A. Vinkhuyzen, S.I. Berndt, S. Gustafsson, A.E. Justice, B. Kahali,
A.E. Locke, T.H. Pers, S. Vedantam, A.R. Wood, W. van Rheenen, O.A. Andreassen,
P. Gasparini, A. Metspalu, L.H. van den Berg, J.H. Veldink, F. Rivadeneira, T.M.
Werge, G.R. Abecasis, D.I. Boomsma, D.I. Chasman, E.J.C. de Geus, T.M. Frayling,
J.N. Hirschhorn, J.J. Hottenga, E. Ingelsson, R.J.F. Loos, P.K.E. Magnusson, N.G.
Martin, G.W. Montgomery, K.E. North, N.L. Pedersen, T.D. Spector, E.K. Speliotes,
M.E. Goddard, J. Yang, P.M. Visscher, Nature Genetics 47 (2015) 1357–1362.
date_created: 2020-04-30T10:58:23Z
date_published: 2015-09-14T00:00:00Z
date_updated: 2021-01-12T08:15:13Z
day: '14'
doi: 10.1038/ng.3401
extern: '1'
intvolume: ' 47'
issue: '11'
language:
- iso: eng
month: '09'
oa_version: None
page: 1357-1362
publication: Nature Genetics
publication_identifier:
issn:
- 1061-4036
- 1546-1718
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
status: public
title: Population genetic differentiation of height and body mass index across Europe
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 47
year: '2015'
...
---
_id: '7741'
abstract:
- lang: eng
text: Phenotypes expressed in a social context are not only a function of the individual,
but can also be shaped by the phenotypes of social partners. These social effects
may play a major role in the evolution of cooperative breeding if social partners
differ in the quality of care they provide and if individual carers adjust their
effort in relation to that of other carers. When applying social effects models
to wild study systems, it is also important to explore sources of individual plasticity
that could masquerade as social effects. We studied offspring provisioning rates
of parents and helpers in a wild population of long-tailed tits Aegithalos caudatus
using a quantitative genetic framework to identify these social effects and partition
them into genetic, permanent environment and current environment components. Controlling
for other effects, individuals were consistent in their provisioning effort at
a given nest, but adjusted their effort based on who was in their social group,
indicating the presence of social effects. However, these social effects differed
between years and social contexts, indicating a current environment effect, rather
than indicating a genetic or permanent environment effect. While this study reveals
the importance of examining environmental and genetic sources of social effects,
the framework we present is entirely general, enabling a greater understanding
of potentially important social effects within any ecological population.
article_number: '20150689'
article_processing_charge: No
article_type: original
author:
- first_name: Mark James
full_name: Adams, Mark James
last_name: Adams
- first_name: Matthew Richard
full_name: Robinson, Matthew Richard
id: E5D42276-F5DA-11E9-8E24-6303E6697425
last_name: Robinson
orcid: 0000-0001-8982-8813
- first_name: Maria-Elena
full_name: Mannarelli, Maria-Elena
last_name: Mannarelli
- first_name: Ben J.
full_name: Hatchwell, Ben J.
last_name: Hatchwell
citation:
ama: 'Adams MJ, Robinson MR, Mannarelli M-E, Hatchwell BJ. Social genetic and social
environment effects on parental and helper care in a cooperatively breeding bird.
Proceedings of the Royal Society B: Biological Sciences. 2015;282(1810).
doi:10.1098/rspb.2015.0689'
apa: 'Adams, M. J., Robinson, M. R., Mannarelli, M.-E., & Hatchwell, B. J. (2015).
Social genetic and social environment effects on parental and helper care in a
cooperatively breeding bird. Proceedings of the Royal Society B: Biological
Sciences. The Royal Society. https://doi.org/10.1098/rspb.2015.0689'
chicago: 'Adams, Mark James, Matthew Richard Robinson, Maria-Elena Mannarelli, and
Ben J. Hatchwell. “Social Genetic and Social Environment Effects on Parental and
Helper Care in a Cooperatively Breeding Bird.” Proceedings of the Royal Society
B: Biological Sciences. The Royal Society, 2015. https://doi.org/10.1098/rspb.2015.0689.'
ieee: 'M. J. Adams, M. R. Robinson, M.-E. Mannarelli, and B. J. Hatchwell, “Social
genetic and social environment effects on parental and helper care in a cooperatively
breeding bird,” Proceedings of the Royal Society B: Biological Sciences,
vol. 282, no. 1810. The Royal Society, 2015.'
ista: 'Adams MJ, Robinson MR, Mannarelli M-E, Hatchwell BJ. 2015. Social genetic
and social environment effects on parental and helper care in a cooperatively
breeding bird. Proceedings of the Royal Society B: Biological Sciences. 282(1810),
20150689.'
mla: 'Adams, Mark James, et al. “Social Genetic and Social Environment Effects on
Parental and Helper Care in a Cooperatively Breeding Bird.” Proceedings of
the Royal Society B: Biological Sciences, vol. 282, no. 1810, 20150689, The
Royal Society, 2015, doi:10.1098/rspb.2015.0689.'
short: 'M.J. Adams, M.R. Robinson, M.-E. Mannarelli, B.J. Hatchwell, Proceedings
of the Royal Society B: Biological Sciences 282 (2015).'
date_created: 2020-04-30T10:58:07Z
date_published: 2015-07-07T00:00:00Z
date_updated: 2021-01-12T08:15:12Z
day: '07'
doi: 10.1098/rspb.2015.0689
extern: '1'
external_id:
pmid:
- '26063846'
intvolume: ' 282'
issue: '1810'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.1098/rspb.2015.0689
month: '07'
oa: 1
oa_version: Published Version
pmid: 1
publication: 'Proceedings of the Royal Society B: Biological Sciences'
publication_identifier:
issn:
- 0962-8452
- 1471-2954
publication_status: published
publisher: The Royal Society
quality_controlled: '1'
status: public
title: Social genetic and social environment effects on parental and helper care in
a cooperatively breeding bird
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 282
year: '2015'
...
---
_id: '7739'
abstract:
- lang: eng
text: Currently, there is much debate on the genetic architecture of quantitative
traits in wild populations. Is trait variation influenced by many genes of small
effect or by a few genes of major effect? Where is additive genetic variation
located in the genome? Do the same loci cause similar phenotypic variation in
different populations? Great tits (Parus major) have been studied extensively
in long‐term studies across Europe and consequently are considered an ecological
‘model organism’. Recently, genomic resources have been developed for the great
tit, including a custom SNP chip and genetic linkage map. In this study, we used
a suite of approaches to investigate the genetic architecture of eight quantitative
traits in two long‐term study populations of great tits—one in the Netherlands
and the other in the United Kingdom. Overall, we found little evidence for the
presence of genes of large effects in either population. Instead, traits appeared
to be influenced by many genes of small effect, with conservative estimates of
the number of contributing loci ranging from 31 to 310. Despite concordance between
population‐specific heritabilities, we found no evidence for the presence of loci
having similar effects in both populations. While population‐specific genetic
architectures are possible, an undetected shared architecture cannot be rejected
because of limited power to map loci of small and moderate effects. This study
is one of few examples of genetic architecture analysis in replicated wild populations
and highlights some of the challenges and limitations researchers will face when
attempting similar molecular quantitative genetic studies in free‐living populations.
article_processing_charge: No
article_type: original
author:
- first_name: Anna W.
full_name: Santure, Anna W.
last_name: Santure
- first_name: Jocelyn
full_name: Poissant, Jocelyn
last_name: Poissant
- first_name: Isabelle
full_name: De Cauwer, Isabelle
last_name: De Cauwer
- first_name: Kees
full_name: van Oers, Kees
last_name: van Oers
- first_name: Matthew Richard
full_name: Robinson, Matthew Richard
id: E5D42276-F5DA-11E9-8E24-6303E6697425
last_name: Robinson
orcid: 0000-0001-8982-8813
- first_name: John L.
full_name: Quinn, John L.
last_name: Quinn
- first_name: Martien A. M.
full_name: Groenen, Martien A. M.
last_name: Groenen
- first_name: Marcel E.
full_name: Visser, Marcel E.
last_name: Visser
- first_name: Ben C.
full_name: Sheldon, Ben C.
last_name: Sheldon
- first_name: Jon
full_name: Slate, Jon
last_name: Slate
citation:
ama: Santure AW, Poissant J, De Cauwer I, et al. Replicated analysis of the genetic
architecture of quantitative traits in two wild great tit populations. Molecular
Ecology. 2015;24:6148-6162. doi:10.1111/mec.13452
apa: Santure, A. W., Poissant, J., De Cauwer, I., van Oers, K., Robinson, M. R.,
Quinn, J. L., … Slate, J. (2015). Replicated analysis of the genetic architecture
of quantitative traits in two wild great tit populations. Molecular Ecology.
Wiley. https://doi.org/10.1111/mec.13452
chicago: Santure, Anna W., Jocelyn Poissant, Isabelle De Cauwer, Kees van Oers,
Matthew Richard Robinson, John L. Quinn, Martien A. M. Groenen, Marcel E. Visser,
Ben C. Sheldon, and Jon Slate. “Replicated Analysis of the Genetic Architecture
of Quantitative Traits in Two Wild Great Tit Populations.” Molecular Ecology.
Wiley, 2015. https://doi.org/10.1111/mec.13452.
ieee: A. W. Santure et al., “Replicated analysis of the genetic architecture
of quantitative traits in two wild great tit populations,” Molecular Ecology,
vol. 24. Wiley, pp. 6148–6162, 2015.
ista: Santure AW, Poissant J, De Cauwer I, van Oers K, Robinson MR, Quinn JL, Groenen
MAM, Visser ME, Sheldon BC, Slate J. 2015. Replicated analysis of the genetic
architecture of quantitative traits in two wild great tit populations. Molecular
Ecology. 24, 6148–6162.
mla: Santure, Anna W., et al. “Replicated Analysis of the Genetic Architecture of
Quantitative Traits in Two Wild Great Tit Populations.” Molecular Ecology,
vol. 24, Wiley, 2015, pp. 6148–62, doi:10.1111/mec.13452.
short: A.W. Santure, J. Poissant, I. De Cauwer, K. van Oers, M.R. Robinson, J.L.
Quinn, M.A.M. Groenen, M.E. Visser, B.C. Sheldon, J. Slate, Molecular Ecology
24 (2015) 6148–6162.
date_created: 2020-04-30T10:51:01Z
date_published: 2015-12-10T00:00:00Z
date_updated: 2021-01-12T08:15:12Z
day: '10'
doi: 10.1111/mec.13452
extern: '1'
intvolume: ' 24'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.1111/mec.13452
month: '12'
oa: 1
oa_version: Published Version
page: 6148-6162
publication: Molecular Ecology
publication_identifier:
issn:
- 0962-1083
publication_status: published
publisher: Wiley
quality_controlled: '1'
status: public
title: Replicated analysis of the genetic architecture of quantitative traits in two
wild great tit populations
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 24
year: '2015'
...
---
_id: '776'
abstract:
- lang: eng
text: High-performance concurrent priority queues are essential for applications
such as task scheduling and discrete event simulation. Unfortunately, even the
best performing implementations do not scale past a number of threads in the single
digits. This is because of the sequential bottleneck in accessing the elements
at the head of the queue in order to perform a DeleteMin operation. In this paper,
we present the SprayList, a scalable priority queue with relaxed ordering semantics.
Starting from a non-blocking SkipList, the main innovation behind our design is
that the DeleteMin operations avoid a sequential bottleneck by "spraying"
themselves onto the head of the SkipList list in a coordinated fashion. The spraying
is implemented using a carefully designed random walk, so that DeleteMin returns
an element among the first O(plog3p) in the list, with high probability, where
p is the number of threads. We prove that the running time of a DeleteMin operation
is O(log3p), with high probability, independent of the size of the list. Our experiments
show that the relaxed semantics allow the data structure to scale for high thread
counts, comparable to a classic unordered SkipList. Furthermore, we observe that,
for reasonably parallel workloads, the scalability benefits of relaxation considerably
outweigh the additional work due to out-of-order execution.
acknowledgement: "Support is gratefully acknowledged from the National Science Foundation
under grants CCF-1217921, CCF-1301926, and IIS-1447786, the Department of Energy
under grant ER26116/DE-SC0008923, and the Oracle\r\nand Intel corporations."
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: Justin
full_name: Kopinsky, Justin
last_name: Kopinsky
- first_name: Jerry
full_name: Li, Jerry
last_name: Li
- first_name: Nir
full_name: Shavit, Nir
last_name: Shavit
citation:
ama: 'Alistarh D-A, Kopinsky J, Li J, Shavit N. The SprayList: A scalable relaxed
priority queue. In: Vol 2015-January. ACM; 2015:11-20. doi:10.1145/2688500.2688523'
apa: 'Alistarh, D.-A., Kopinsky, J., Li, J., & Shavit, N. (2015). The SprayList:
A scalable relaxed priority queue (Vol. 2015–January, pp. 11–20). Presented at
the PPoPP: Principles and Practice of Parallel Pogramming, ACM. https://doi.org/10.1145/2688500.2688523'
chicago: 'Alistarh, Dan-Adrian, Justin Kopinsky, Jerry Li, and Nir Shavit. “The
SprayList: A Scalable Relaxed Priority Queue,” 2015–January:11–20. ACM, 2015.
https://doi.org/10.1145/2688500.2688523.'
ieee: 'D.-A. Alistarh, J. Kopinsky, J. Li, and N. Shavit, “The SprayList: A scalable
relaxed priority queue,” presented at the PPoPP: Principles and Practice of Parallel
Pogramming, 2015, vol. 2015–January, pp. 11–20.'
ista: 'Alistarh D-A, Kopinsky J, Li J, Shavit N. 2015. The SprayList: A scalable
relaxed priority queue. PPoPP: Principles and Practice of Parallel Pogramming
vol. 2015–January, 11–20.'
mla: 'Alistarh, Dan-Adrian, et al. The SprayList: A Scalable Relaxed Priority
Queue. Vol. 2015–January, ACM, 2015, pp. 11–20, doi:10.1145/2688500.2688523.'
short: D.-A. Alistarh, J. Kopinsky, J. Li, N. Shavit, in:, ACM, 2015, pp. 11–20.
conference:
name: 'PPoPP: Principles and Practice of Parallel Pogramming'
date_created: 2018-12-11T11:48:26Z
date_published: 2015-01-24T00:00:00Z
date_updated: 2023-02-23T13:16:43Z
day: '24'
doi: 10.1145/2688500.2688523
extern: '1'
language:
- iso: eng
month: '01'
oa_version: None
page: 11 - 20
publication_status: published
publisher: ACM
publist_id: '6878'
status: public
title: 'The SprayList: A scalable relaxed priority queue'
type: conference
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 2015-January
year: '2015'
...
---
_id: '7765'
abstract:
- lang: eng
text: 'We introduce a principle unique to disordered solids wherein the contribution
of any bond to one global perturbation is uncorrelated with its contribution to
another. Coupled with sufficient variability in the contributions of different
bonds, this “independent bond-level response” paves the way for the design of
real materials with unusual and exquisitely tuned properties. To illustrate this,
we choose two global perturbations: compression and shear. By applying a bond
removal procedure that is both simple and experimentally relevant to remove a
very small fraction of bonds, we can drive disordered spring networks to both
the incompressible and completely auxetic limits of mechanical behavior.'
article_number: '225501'
article_processing_charge: No
article_type: original
author:
- first_name: Carl Peter
full_name: Goodrich, Carl Peter
id: EB352CD2-F68A-11E9-89C5-A432E6697425
last_name: Goodrich
orcid: 0000-0002-1307-5074
- first_name: Andrea J.
full_name: Liu, Andrea J.
last_name: Liu
- first_name: Sidney R.
full_name: Nagel, Sidney R.
last_name: Nagel
citation:
ama: 'Goodrich CP, Liu AJ, Nagel SR. The principle of independent bond-level response:
Tuning by pruning to exploit disorder for global behavior. Physical Review
Letters. 2015;114(22). doi:10.1103/physrevlett.114.225501'
apa: 'Goodrich, C. P., Liu, A. J., & Nagel, S. R. (2015). The principle of independent
bond-level response: Tuning by pruning to exploit disorder for global behavior.
Physical Review Letters. American Physical Society. https://doi.org/10.1103/physrevlett.114.225501'
chicago: 'Goodrich, Carl Peter, Andrea J. Liu, and Sidney R. Nagel. “The Principle
of Independent Bond-Level Response: Tuning by Pruning to Exploit Disorder for
Global Behavior.” Physical Review Letters. American Physical Society, 2015.
https://doi.org/10.1103/physrevlett.114.225501.'
ieee: 'C. P. Goodrich, A. J. Liu, and S. R. Nagel, “The principle of independent
bond-level response: Tuning by pruning to exploit disorder for global behavior,”
Physical Review Letters, vol. 114, no. 22. American Physical Society, 2015.'
ista: 'Goodrich CP, Liu AJ, Nagel SR. 2015. The principle of independent bond-level
response: Tuning by pruning to exploit disorder for global behavior. Physical
Review Letters. 114(22), 225501.'
mla: 'Goodrich, Carl Peter, et al. “The Principle of Independent Bond-Level Response:
Tuning by Pruning to Exploit Disorder for Global Behavior.” Physical Review
Letters, vol. 114, no. 22, 225501, American Physical Society, 2015, doi:10.1103/physrevlett.114.225501.'
short: C.P. Goodrich, A.J. Liu, S.R. Nagel, Physical Review Letters 114 (2015).
date_created: 2020-04-30T11:41:08Z
date_published: 2015-06-04T00:00:00Z
date_updated: 2021-01-12T08:15:23Z
day: '04'
doi: 10.1103/physrevlett.114.225501
extern: '1'
intvolume: ' 114'
issue: '22'
language:
- iso: eng
month: '06'
oa_version: None
publication: Physical Review Letters
publication_identifier:
issn:
- 0031-9007
- 1079-7114
publication_status: published
publisher: American Physical Society
quality_controlled: '1'
status: public
title: 'The principle of independent bond-level response: Tuning by pruning to exploit
disorder for global behavior'
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 114
year: '2015'
...
---
_id: '7767'
abstract:
- lang: eng
text: We present a model of soft active particles that leads to a rich array of
collective behavior found also in dense biological swarms of bacteria and other
unicellular organisms. Our model uses only local interactions, such as Vicsek-type
nearest-neighbor alignment, short-range repulsion, and a local boundary term.
Changing the relative strength of these interactions leads to migrating swarms,
rotating swarms, and jammed swarms, as well as swarms that exhibit run-and-tumble
motion, alternating between migration and either rotating or jammed states. Interestingly,
although a migrating swarm moves slower than an individual particle, the diffusion
constant can be up to three orders of magnitude larger, suggesting that collective
motion can be highly advantageous, for example, when searching for food.
article_number: '032706'
article_processing_charge: No
article_type: original
author:
- first_name: Ruben
full_name: van Drongelen, Ruben
last_name: van Drongelen
- first_name: Anshuman
full_name: Pal, Anshuman
last_name: Pal
- first_name: Carl Peter
full_name: Goodrich, Carl Peter
id: EB352CD2-F68A-11E9-89C5-A432E6697425
last_name: Goodrich
orcid: 0000-0002-1307-5074
- first_name: Timon
full_name: Idema, Timon
last_name: Idema
citation:
ama: van Drongelen R, Pal A, Goodrich CP, Idema T. Collective dynamics of soft active
particles. Physical Review E. 2015;91(3). doi:10.1103/physreve.91.032706
apa: van Drongelen, R., Pal, A., Goodrich, C. P., & Idema, T. (2015). Collective
dynamics of soft active particles. Physical Review E. American Physical
Society. https://doi.org/10.1103/physreve.91.032706
chicago: Drongelen, Ruben van, Anshuman Pal, Carl Peter Goodrich, and Timon Idema.
“Collective Dynamics of Soft Active Particles.” Physical Review E. American
Physical Society, 2015. https://doi.org/10.1103/physreve.91.032706.
ieee: R. van Drongelen, A. Pal, C. P. Goodrich, and T. Idema, “Collective dynamics
of soft active particles,” Physical Review E, vol. 91, no. 3. American
Physical Society, 2015.
ista: van Drongelen R, Pal A, Goodrich CP, Idema T. 2015. Collective dynamics of
soft active particles. Physical Review E. 91(3), 032706.
mla: van Drongelen, Ruben, et al. “Collective Dynamics of Soft Active Particles.”
Physical Review E, vol. 91, no. 3, 032706, American Physical Society, 2015,
doi:10.1103/physreve.91.032706.
short: R. van Drongelen, A. Pal, C.P. Goodrich, T. Idema, Physical Review E 91 (2015).
date_created: 2020-04-30T11:41:38Z
date_published: 2015-03-01T00:00:00Z
date_updated: 2021-01-12T08:15:24Z
day: '01'
doi: 10.1103/physreve.91.032706
extern: '1'
intvolume: ' 91'
issue: '3'
language:
- iso: eng
month: '03'
oa_version: None
publication: Physical Review E
publication_identifier:
issn:
- 1539-3755
- 1550-2376
publication_status: published
publisher: American Physical Society
quality_controlled: '1'
status: public
title: Collective dynamics of soft active particles
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 91
year: '2015'
...
---
_id: '7766'
abstract:
- lang: eng
text: We study the vibrational properties near a free surface of disordered spring
networks derived from jammed sphere packings. In bulk systems, without surfaces,
it is well understood that such systems have a plateau in the density of vibrational
modes extending down to a frequency scale ω*. This frequency is controlled by
ΔZ = 〈Z〉 − 2d, the difference between the average coordination of the spheres
and twice the spatial dimension, d, of the system, which vanishes at the jamming
transition. In the presence of a free surface we find that there is a density
of disordered vibrational modes associated with the surface that extends far below
ω*. The total number of these low-frequency surface modes is controlled by ΔZ,
and the profile of their decay into the bulk has two characteristic length scales,
which diverge as ΔZ−1/2 and ΔZ−1 as the jamming transition is approached.
article_processing_charge: No
article_type: original
author:
- first_name: Daniel M.
full_name: Sussman, Daniel M.
last_name: Sussman
- first_name: Carl Peter
full_name: Goodrich, Carl Peter
id: EB352CD2-F68A-11E9-89C5-A432E6697425
last_name: Goodrich
orcid: 0000-0002-1307-5074
- first_name: Andrea J.
full_name: Liu, Andrea J.
last_name: Liu
- first_name: Sidney R.
full_name: Nagel, Sidney R.
last_name: Nagel
citation:
ama: Sussman DM, Goodrich CP, Liu AJ, Nagel SR. Disordered surface vibrations in
jammed sphere packings. Soft Matter. 2015;11(14):2745-2751. doi:10.1039/c4sm02905d
apa: Sussman, D. M., Goodrich, C. P., Liu, A. J., & Nagel, S. R. (2015). Disordered
surface vibrations in jammed sphere packings. Soft Matter. Royal Society
of Chemistry. https://doi.org/10.1039/c4sm02905d
chicago: Sussman, Daniel M., Carl Peter Goodrich, Andrea J. Liu, and Sidney R. Nagel.
“Disordered Surface Vibrations in Jammed Sphere Packings.” Soft Matter.
Royal Society of Chemistry, 2015. https://doi.org/10.1039/c4sm02905d.
ieee: D. M. Sussman, C. P. Goodrich, A. J. Liu, and S. R. Nagel, “Disordered surface
vibrations in jammed sphere packings,” Soft Matter, vol. 11, no. 14. Royal
Society of Chemistry, pp. 2745–2751, 2015.
ista: Sussman DM, Goodrich CP, Liu AJ, Nagel SR. 2015. Disordered surface vibrations
in jammed sphere packings. Soft Matter. 11(14), 2745–2751.
mla: Sussman, Daniel M., et al. “Disordered Surface Vibrations in Jammed Sphere
Packings.” Soft Matter, vol. 11, no. 14, Royal Society of Chemistry, 2015,
pp. 2745–51, doi:10.1039/c4sm02905d.
short: D.M. Sussman, C.P. Goodrich, A.J. Liu, S.R. Nagel, Soft Matter 11 (2015)
2745–2751.
date_created: 2020-04-30T11:41:23Z
date_published: 2015-02-15T00:00:00Z
date_updated: 2021-01-12T08:15:23Z
day: '15'
doi: 10.1039/c4sm02905d
extern: '1'
intvolume: ' 11'
issue: '14'
language:
- iso: eng
month: '02'
oa_version: None
page: 2745-2751
publication: Soft Matter
publication_identifier:
issn:
- 1744-683X
- 1744-6848
publication_status: published
publisher: Royal Society of Chemistry
quality_controlled: '1'
status: public
title: Disordered surface vibrations in jammed sphere packings
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 11
year: '2015'
...
---
_id: '777'
abstract:
- lang: eng
text: 'In many applications, the data is of rich structure that can be represented
by a hypergraph, where the data items are represented by vertices and the associations
among items are represented by hyperedges. Equivalently, we are given an input
bipartite graph with two types of vertices: items, and associations (which we
refer to as topics). We consider the problem of partitioning the set of items
into a given number of components such that the maximum number of topics covered
by a component is minimized. This is a clustering problem with various applications,
e.g. partitioning of a set of information objects such as documents, images, and
videos, and load balancing in the context of modern computation platforms.Inthis
paper, we focus on the streaming computation model for this problem, in which
items arrive online one at a time and each item must be assigned irrevocably to
a component at its arrival time. Motivated by scalability requirements, we focus
on the class of streaming computation algorithms with memory limited to be at
most linear in the number of components. We show that a greedy assignment strategy
is able to recover a hidden co-clustering of items under a natural set of recovery
conditions. We also report results of an extensive empirical evaluation, which
demonstrate that this greedy strategy yields superior performance when compared
with alternative approaches.'
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: Jennifer
full_name: Iglesias, Jennifer
last_name: Iglesias
- first_name: Milan
full_name: Vojnović, Milan
last_name: Vojnović
citation:
ama: 'Alistarh D-A, Iglesias J, Vojnović M. Streaming min-max hypergraph partitioning.
In: Vol 2015-January. Neural Information Processing Systems; 2015:1900-1908.'
apa: 'Alistarh, D.-A., Iglesias, J., & Vojnović, M. (2015). Streaming min-max
hypergraph partitioning (Vol. 2015–January, pp. 1900–1908). Presented at the NIPS:
Neural Information Processing Systems, Neural Information Processing Systems.'
chicago: Alistarh, Dan-Adrian, Jennifer Iglesias, and Milan Vojnović. “Streaming
Min-Max Hypergraph Partitioning,” 2015–January:1900–1908. Neural Information Processing
Systems, 2015.
ieee: 'D.-A. Alistarh, J. Iglesias, and M. Vojnović, “Streaming min-max hypergraph
partitioning,” presented at the NIPS: Neural Information Processing Systems, 2015,
vol. 2015–January, pp. 1900–1908.'
ista: 'Alistarh D-A, Iglesias J, Vojnović M. 2015. Streaming min-max hypergraph
partitioning. NIPS: Neural Information Processing Systems vol. 2015–January, 1900–1908.'
mla: Alistarh, Dan-Adrian, et al. Streaming Min-Max Hypergraph Partitioning.
Vol. 2015–January, Neural Information Processing Systems, 2015, pp. 1900–08.
short: D.-A. Alistarh, J. Iglesias, M. Vojnović, in:, Neural Information Processing
Systems, 2015, pp. 1900–1908.
conference:
name: 'NIPS: Neural Information Processing Systems'
date_created: 2018-12-11T11:48:27Z
date_published: 2015-01-01T00:00:00Z
date_updated: 2023-02-23T13:17:09Z
day: '01'
extern: '1'
language:
- iso: eng
main_file_link:
- url: http://papers.nips.cc/paper/5897-streaming-min-max-hypergraph-partitioning
month: '01'
oa_version: None
page: 1900 - 1908
publication_status: published
publisher: Neural Information Processing Systems
publist_id: '6879'
status: public
title: Streaming min-max hypergraph partitioning
type: conference
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 2015-January
year: '2015'
...
---
_id: '778'
abstract:
- lang: eng
text: Several Hybrid Transactional Memory (HyTM) schemes have recently been proposed
to complement the fast, but best-effort nature of Hardware Transactional Memory
(HTM) with a slow, reliable software backup. However, the costs of providing concurrency
between hardware and software transactions in HyTM are still not well understood.
In this paper, we propose a general model for HyTM implementations, which captures
the ability of hardware transactions to buffer memory accesses. The model allows
us to formally quantify and analyze the amount of overhead (instrumentation) caused
by the potential presence of software transactions.We prove that (1) it is impossible
to build a strictly serializable HyTM implementation that has both uninstrumented
reads and writes, even for very weak progress guarantees, and (2) the instrumentation
cost incurred by a hardware transaction in any progressive opaque HyTM is linear
in the size of the transaction’s data set.We further describe two implementations
which exhibit optimal instrumentation costs for two different progress conditions.
In sum, this paper proposes the first formal HyTM model and captures for the first
time the trade-off between the degree of hardware-software TM concurrency and
the amount of instrumentation overhead.
acknowledgement: P. Kuznetsov-The author is supported by the Agence Nationale de la
Recherche, ANR-14-CE35-0010-01, project DISCMAT. N. Shavit-Support is gratfeully
acknowledgedfrom the National Science Foundation under grants CCF-1217921, CCF-1201926,
and IIS-1447786, the Department of Energy under grant ER26116/DE-SC0008923, and
the Oracle and Intel corporations.
alternative_title:
- LNCS
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: Justin
full_name: Kopinsky, Justin
last_name: Kopinsky
- first_name: Petr
full_name: Kuznetsov, Petr
last_name: Kuznetsov
- first_name: Srivatsan
full_name: Ravi, Srivatsan
last_name: Ravi
- first_name: Nir
full_name: Shavit, Nir
last_name: Shavit
citation:
ama: 'Alistarh D-A, Kopinsky J, Kuznetsov P, Ravi S, Shavit N. Inherent limitations
of hybrid transactional memory. In: Vol 9363. Springer; 2015:185-199. doi:10.1007/978-3-662-48653-5_13'
apa: 'Alistarh, D.-A., Kopinsky, J., Kuznetsov, P., Ravi, S., & Shavit, N. (2015).
Inherent limitations of hybrid transactional memory (Vol. 9363, pp. 185–199).
Presented at the DISC: Distributed Computing, Springer. https://doi.org/10.1007/978-3-662-48653-5_13'
chicago: Alistarh, Dan-Adrian, Justin Kopinsky, Petr Kuznetsov, Srivatsan Ravi,
and Nir Shavit. “Inherent Limitations of Hybrid Transactional Memory,” 9363:185–99.
Springer, 2015. https://doi.org/10.1007/978-3-662-48653-5_13.
ieee: 'D.-A. Alistarh, J. Kopinsky, P. Kuznetsov, S. Ravi, and N. Shavit, “Inherent
limitations of hybrid transactional memory,” presented at the DISC: Distributed
Computing, 2015, vol. 9363, pp. 185–199.'
ista: 'Alistarh D-A, Kopinsky J, Kuznetsov P, Ravi S, Shavit N. 2015. Inherent limitations
of hybrid transactional memory. DISC: Distributed Computing, LNCS, vol. 9363,
185–199.'
mla: Alistarh, Dan-Adrian, et al. Inherent Limitations of Hybrid Transactional
Memory. Vol. 9363, Springer, 2015, pp. 185–99, doi:10.1007/978-3-662-48653-5_13.
short: D.-A. Alistarh, J. Kopinsky, P. Kuznetsov, S. Ravi, N. Shavit, in:, Springer,
2015, pp. 185–199.
conference:
name: 'DISC: Distributed Computing'
date_created: 2018-12-11T11:48:27Z
date_published: 2015-01-01T00:00:00Z
date_updated: 2023-02-23T13:17:35Z
day: '01'
doi: 10.1007/978-3-662-48653-5_13
extern: '1'
external_id:
arxiv:
- '1405.5689'
intvolume: ' 9363'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/1405.5689
month: '01'
oa: 1
oa_version: None
page: 185 - 199
publication_status: published
publisher: Springer
publist_id: '6880'
quality_controlled: '1'
status: public
title: Inherent limitations of hybrid transactional memory
type: conference
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 9363
year: '2015'
...
---
_id: '7779'
abstract:
- lang: eng
text: "The fact that a disordered material is not constrained in its properties
in\r\nthe same way as a crystal presents significant and yet largely untapped\r\npotential
for novel material design. However, unlike their crystalline\r\ncounterparts,
disordered solids are not well understood. One of the primary\r\nobstacles is
the lack of a theoretical framework for thinking about disorder\r\nand its relation
to mechanical properties. To this end, we study an idealized\r\nsystem of frictionless
athermal soft spheres that, when compressed, undergoes a\r\njamming phase transition
with diverging length scales and clean power-law\r\nsignatures. This critical
point is the cornerstone of a much larger \"jamming\r\nscenario\" that has the
potential to provide the essential theoretical\r\nfoundation necessary for a unified
understanding of the mechanics of disordered\r\nsolids. We begin by showing that
jammed sphere packings have a valid linear\r\nregime despite the presence of \"contact
nonlinearities.\" We then investigate\r\nthe critical nature of the transition,
focusing on diverging length scales and\r\nfinite-size effects. Next, we argue
that jamming plays the same role for\r\ndisordered solids as the perfect crystal
plays for crystalline solids. Not only\r\ncan it be considered an idealized starting
point for understanding disordered\r\nmaterials, but it can even influence systems
that have a relatively high amount\r\nof crystalline order. The behavior of solids
can thus be thought of as existing\r\non a spectrum, with the perfect crystal
and the jamming transition at opposing\r\nends. Finally, we introduce a new principle
wherein the contribution of an\r\nindividual bond to one global property is independent
of its contribution to\r\nanother. This principle allows the different global
responses of a disordered\r\nsystem to be manipulated independently and provides
a great deal of flexibility\r\nin designing materials with unique, textured and
tunable properties."
article_processing_charge: No
author:
- first_name: Carl Peter
full_name: Goodrich, Carl Peter
id: EB352CD2-F68A-11E9-89C5-A432E6697425
last_name: Goodrich
orcid: 0000-0002-1307-5074
citation:
ama: 'Goodrich CP. Unearthing the anticrystal: Criticality in the linear response
of disordered solids. arXiv:151008820. 2015.'
apa: 'Goodrich, C. P. (2015). Unearthing the anticrystal: Criticality in the linear
response of disordered solids. arXiv:1510.08820.'
chicago: 'Goodrich, Carl Peter. “Unearthing the Anticrystal: Criticality in the
Linear Response of Disordered Solids.” ArXiv:1510.08820, 2015.'
ieee: 'C. P. Goodrich, “Unearthing the anticrystal: Criticality in the linear response
of disordered solids,” arXiv:1510.08820. 2015.'
ista: 'Goodrich CP. 2015. Unearthing the anticrystal: Criticality in the linear
response of disordered solids. arXiv:1510.08820, .'
mla: 'Goodrich, Carl Peter. “Unearthing the Anticrystal: Criticality in the Linear
Response of Disordered Solids.” ArXiv:1510.08820, 2015.'
short: C.P. Goodrich, ArXiv:1510.08820 (2015).
date_created: 2020-04-30T12:16:18Z
date_published: 2015-10-29T00:00:00Z
date_updated: 2021-01-12T08:15:28Z
day: '29'
extern: '1'
external_id:
arxiv:
- '1510.08820'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/1510.08820
month: '10'
oa: 1
oa_version: Preprint
page: '242'
publication: arXiv:1510.08820
publication_status: published
status: public
title: 'Unearthing the anticrystal: Criticality in the linear response of disordered
solids'
type: preprint
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
year: '2015'
...
---
_id: '779'
abstract:
- lang: eng
text: 'The concurrent memory reclamation problem is that of devising a way for a
deallocating thread to verify that no other concurrent threads hold references
to a memory block being deallocated. To date, in the absence of automatic garbage
collection, there is no satisfactory solution to this problem; existing tracking
methods like hazard pointers, reference counters, or epoch-based techniques like
RCU, are either prohibitively expensive or require significant programming expertise,
to the extent that implementing them efficiently can be worthy of a publication.
None of the existing techniques are automatic or even semi-automated. In this
paper, we take a new approach to concurrent memory reclamation: instead of manually
tracking access to memory locations as done in techniques like hazard pointers,
or restricting shared accesses to specific epoch boundaries as in RCU, our algorithm,
called ThreadScan, leverages operating system signaling to automatically detect
which memory locations are being accessed by concurrent threads. Initial empirical
evidence shows that ThreadScan scales surprisingly well and requires negligible
programming effort beyond the standard use of Malloc and Free.'
acknowledgement: Support is gratefully acknowledged from the National Science Foundation
under grants CCF-1217921, CCF-1301926, and IIS-1447786, the Department of Energy
under grant ER26116/DE-SC0008923, and the Oracle corporation. In particular, we
would like to thank Dave Dice, Alex Kogan, and Mark Moir from the Oracle Scalable
Synchronization Research Group for very useful feedback on earlier drafts of this
paper.
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: Alexander
full_name: Matveev, Alexander
last_name: Matveev
- first_name: William
full_name: Leiserson, William
last_name: Leiserson
- first_name: Nir
full_name: Shavit, Nir
last_name: Shavit
citation:
ama: 'Alistarh D-A, Matveev A, Leiserson W, Shavit N. ThreadScan: Automatic and
scalable memory reclamation. In: Vol 2015-June. ACM; 2015:123-132. doi:10.1145/2755573.2755600'
apa: 'Alistarh, D.-A., Matveev, A., Leiserson, W., & Shavit, N. (2015). ThreadScan:
Automatic and scalable memory reclamation (Vol. 2015–June, pp. 123–132). Presented
at the SPAA: Symposium on Parallelism in Algorithms and Architectures, ACM. https://doi.org/10.1145/2755573.2755600'
chicago: 'Alistarh, Dan-Adrian, Alexander Matveev, William Leiserson, and Nir Shavit.
“ThreadScan: Automatic and Scalable Memory Reclamation,” 2015–June:123–32. ACM,
2015. https://doi.org/10.1145/2755573.2755600.'
ieee: 'D.-A. Alistarh, A. Matveev, W. Leiserson, and N. Shavit, “ThreadScan: Automatic
and scalable memory reclamation,” presented at the SPAA: Symposium on Parallelism
in Algorithms and Architectures, 2015, vol. 2015–June, pp. 123–132.'
ista: 'Alistarh D-A, Matveev A, Leiserson W, Shavit N. 2015. ThreadScan: Automatic
and scalable memory reclamation. SPAA: Symposium on Parallelism in Algorithms
and Architectures vol. 2015–June, 123–132.'
mla: 'Alistarh, Dan-Adrian, et al. ThreadScan: Automatic and Scalable Memory
Reclamation. Vol. 2015–June, ACM, 2015, pp. 123–32, doi:10.1145/2755573.2755600.'
short: D.-A. Alistarh, A. Matveev, W. Leiserson, N. Shavit, in:, ACM, 2015, pp.
123–132.
conference:
name: 'SPAA: Symposium on Parallelism in Algorithms and Architectures'
date_created: 2018-12-11T11:48:27Z
date_published: 2015-06-13T00:00:00Z
date_updated: 2023-02-23T12:35:42Z
day: '13'
doi: 10.1145/2755573.2755600
extern: '1'
language:
- iso: eng
month: '06'
oa_version: None
page: 123 - 132
publication_status: published
publisher: ACM
publist_id: '6876'
related_material:
record:
- id: '6001'
relation: later_version
status: public
status: public
title: 'ThreadScan: Automatic and scalable memory reclamation'
type: conference
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 2015-June
year: '2015'
...
---
_id: '780'
abstract:
- lang: eng
text: 'Population protocols are networks of finite-state agents, interacting randomly,
and updating their states using simple rules. Despite their extreme simplicity,
these systems have been shown to cooperatively perform complex computational tasks,
such as simulating register machines to compute standard arithmetic functions.
The election of a unique leader agent is a key requirement in such computational
constructions. Yet, the fastest currently known population protocol for electing
a leader only has linear convergence time, and it has recently been shown that
no population protocol using a constant number of states per node may overcome
this linear bound. In this paper, we give the first population protocol for leader
election with polylogarithmic convergence time, using polylogarithmic memory states
per node. The protocol structure is quite simple: each node has an associated
value, and is either a leader (still in contention) or a minion (following some
leader). A leader keeps incrementing its value and “defeats” other leaders in
one-to-one interactions, and will drop from contention and become a minion if
it meets a leader with higher value. Importantly, a leader also drops out if it
meets a minion with higher absolute value. While these rules are quite simple,
the proof that this algorithm achieves polylogarithmic convergence time is non-trivial.
In particular, the argument combines careful use of concentration inequalities
with anti-concentration bounds, showing that the leaders’ values become spread
apart as the execution progresses, which in turn implies that straggling leaders
get quickly eliminated. We complement our analysis with empirical results, showing
that our protocol converges extremely fast, even for large network sizes.'
acknowledgement: Support is gratefully acknowledged from the National Science Foundation
under grants CCF-1217921, CCF-1301926, and IIS-1447786, the Department of Energy
under grant ER26116/DE-SC0008923, and the Oracle and Intel corporations.”
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: Rati
full_name: Gelashvili, Rati
last_name: Gelashvili
citation:
ama: 'Alistarh D-A, Gelashvili R. Polylogarithmic-time leader election in population
protocols. In: Vol 9135. Springer; 2015:479-491. doi:10.1007/978-3-662-47666-6_38'
apa: 'Alistarh, D.-A., & Gelashvili, R. (2015). Polylogarithmic-time leader
election in population protocols (Vol. 9135, pp. 479–491). Presented at the ICALP:
International Colloquium on Automota, Languages and Programming, Springer. https://doi.org/10.1007/978-3-662-47666-6_38'
chicago: Alistarh, Dan-Adrian, and Rati Gelashvili. “Polylogarithmic-Time Leader
Election in Population Protocols,” 9135:479–91. Springer, 2015. https://doi.org/10.1007/978-3-662-47666-6_38.
ieee: 'D.-A. Alistarh and R. Gelashvili, “Polylogarithmic-time leader election in
population protocols,” presented at the ICALP: International Colloquium on Automota,
Languages and Programming, 2015, vol. 9135, pp. 479–491.'
ista: 'Alistarh D-A, Gelashvili R. 2015. Polylogarithmic-time leader election in
population protocols. ICALP: International Colloquium on Automota, Languages and
Programming vol. 9135, 479–491.'
mla: Alistarh, Dan-Adrian, and Rati Gelashvili. Polylogarithmic-Time Leader Election
in Population Protocols. Vol. 9135, Springer, 2015, pp. 479–91, doi:10.1007/978-3-662-47666-6_38.
short: D.-A. Alistarh, R. Gelashvili, in:, Springer, 2015, pp. 479–491.
conference:
name: 'ICALP: International Colloquium on Automota, Languages and Programming'
date_created: 2018-12-11T11:48:28Z
date_published: 2015-01-01T00:00:00Z
date_updated: 2023-02-23T13:18:11Z
day: '01'
doi: 10.1007/978-3-662-47666-6_38
extern: '1'
external_id:
arxiv:
- '1502.05745'
intvolume: ' 9135'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/1502.05745
month: '01'
oa: 1
oa_version: Preprint
page: 479 - 491
publication_status: published
publisher: Springer
publist_id: '6877'
status: public
title: Polylogarithmic-time leader election in population protocols
type: conference
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 9135
year: '2015'
...
---
_id: '781'
abstract:
- lang: eng
text: 'Population protocols, roughly defined as systems consisting of large numbers
of simple identical agents, interacting at random and updating their state following
simple rules, are an important research topic at the intersection of distributed
computing and biology. One of the fundamental tasks that a population protocol
may solve is majority: each node starts in one of two states; the goal is for
all nodes to reach a correct consensus on which of the two states was initially
the majority. Despite considerable research effort, known protocols for this problem
are either exact but slow (taking linear parallel time to converge), or fast but
approximate (with non-zero probability of error). In this paper, we show that
this trade-off between preciasion and speed is not inherent. We present a new
protocol called Average and Conquer (AVC) that solves majority ex-actly in expected
parallel convergence time O(log n/(sε) + log n log s), where n is the number of
nodes, εn is the initial node advantage of the majority state, and s = Ω(log n
log log n) is the number of states the protocol employs. This shows that the majority
problem can be solved exactly in time poly-logarithmic in n, provided that the
memory per node is s = Ω(1/ε + lognlog1/ε). On the negative side, we establish
a lower bound of Ω(1/ε) on the expected paraallel convergence time for the case
of four memory states per node, and a lower bound of Ω(logn) parallel time for
protocols using any number of memory states per node.per node, and a lower bound
of (log n) parallel time for protocols using any number of memory states per node.'
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: Rati
full_name: Gelashvili, Rati
last_name: Gelashvili
- first_name: Milan
full_name: Vojnović, Milan
last_name: Vojnović
citation:
ama: 'Alistarh D-A, Gelashvili R, Vojnović M. Fast and exact majority in population
protocols. In: Vol 2015-July. ACM; 2015:47-56. doi:10.1145/2767386.2767429'
apa: 'Alistarh, D.-A., Gelashvili, R., & Vojnović, M. (2015). Fast and exact
majority in population protocols (Vol. 2015–July, pp. 47–56). Presented at the
PODC: Principles of Distributed Computing, ACM. https://doi.org/10.1145/2767386.2767429'
chicago: Alistarh, Dan-Adrian, Rati Gelashvili, and Milan Vojnović. “Fast and Exact
Majority in Population Protocols,” 2015–July:47–56. ACM, 2015. https://doi.org/10.1145/2767386.2767429.
ieee: 'D.-A. Alistarh, R. Gelashvili, and M. Vojnović, “Fast and exact majority
in population protocols,” presented at the PODC: Principles of Distributed Computing,
2015, vol. 2015–July, pp. 47–56.'
ista: 'Alistarh D-A, Gelashvili R, Vojnović M. 2015. Fast and exact majority in
population protocols. PODC: Principles of Distributed Computing vol. 2015–July,
47–56.'
mla: Alistarh, Dan-Adrian, et al. Fast and Exact Majority in Population Protocols.
Vol. 2015–July, ACM, 2015, pp. 47–56, doi:10.1145/2767386.2767429.
short: D.-A. Alistarh, R. Gelashvili, M. Vojnović, in:, ACM, 2015, pp. 47–56.
conference:
name: 'PODC: Principles of Distributed Computing'
date_created: 2018-12-11T11:48:28Z
date_published: 2015-07-21T00:00:00Z
date_updated: 2023-02-23T13:18:35Z
day: '21'
doi: 10.1145/2767386.2767429
extern: '1'
language:
- iso: eng
month: '07'
oa_version: None
page: 47 - 56
publication_status: published
publisher: ACM
publist_id: '6873'
status: public
title: Fast and exact majority in population protocols
type: conference
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 2015-July
year: '2015'
...
---
_id: '782'
abstract:
- lang: eng
text: 'In this work, we consider the following random process, mo- Tivated by the
analysis of lock-free concurrent algorithms under high memory contention. In each
round, a new scheduling step is allocated to one of n threads, according to a
distribution p = (p1; p2; : : : ; pn), where thread i is scheduled with probability
pi. When some thread first reaches a set threshold of executed steps, it registers
a win, completing its current operation, and resets its step count to 1. At the
same time, threads whose step count was close to the threshold also get reset
because of the win, but to 0 steps, being penalized for almost winning. We are
interested in two questions: how often does some thread complete an operation
(system latency), and how often does a specific thread complete an operation (individual
latency)? We provide asymptotically tight bounds for the system and individual
latency of this general concurrency pattern, for arbitrary scheduling distributions
p. Surprisingly, a sim- ple characterization exists: in expectation, the system
will complete a new operation every Θ(1/p 2) steps, while thread i will complete
a new operation every Θ(1/2=p i ) steps. The proof is interesting in its own right,
as it requires a careful analysis of how the higher norms of the vector p inuence
the thread step counts and latencies in this random process. Our result offers
a simple connection between the scheduling distribution and the average performance
of concurrent algorithms, which has several applications.'
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: Thomas
full_name: Sauerwald, Thomas
last_name: Sauerwald
- first_name: Milan
full_name: Vojnović, Milan
last_name: Vojnović
citation:
ama: 'Alistarh D-A, Sauerwald T, Vojnović M. Lock-Free algorithms under stochastic
schedulers. In: Vol 2015-July. ACM; 2015:251-260. doi:10.1145/2767386.2767430'
apa: 'Alistarh, D.-A., Sauerwald, T., & Vojnović, M. (2015). Lock-Free algorithms
under stochastic schedulers (Vol. 2015–July, pp. 251–260). Presented at the PODC:
Principles of Distributed Computing, ACM. https://doi.org/10.1145/2767386.2767430'
chicago: Alistarh, Dan-Adrian, Thomas Sauerwald, and Milan Vojnović. “Lock-Free
Algorithms under Stochastic Schedulers,” 2015–July:251–60. ACM, 2015. https://doi.org/10.1145/2767386.2767430.
ieee: 'D.-A. Alistarh, T. Sauerwald, and M. Vojnović, “Lock-Free algorithms under
stochastic schedulers,” presented at the PODC: Principles of Distributed Computing,
2015, vol. 2015–July, pp. 251–260.'
ista: 'Alistarh D-A, Sauerwald T, Vojnović M. 2015. Lock-Free algorithms under stochastic
schedulers. PODC: Principles of Distributed Computing vol. 2015–July, 251–260.'
mla: Alistarh, Dan-Adrian, et al. Lock-Free Algorithms under Stochastic Schedulers.
Vol. 2015–July, ACM, 2015, pp. 251–60, doi:10.1145/2767386.2767430.
short: D.-A. Alistarh, T. Sauerwald, M. Vojnović, in:, ACM, 2015, pp. 251–260.
conference:
name: 'PODC: Principles of Distributed Computing'
date_created: 2018-12-11T11:48:28Z
date_published: 2015-07-21T00:00:00Z
date_updated: 2023-02-23T13:18:50Z
day: '21'
doi: 10.1145/2767386.2767430
extern: '1'
language:
- iso: eng
month: '07'
oa_version: None
page: 251 - 260
publication_status: published
publisher: ACM
publist_id: '6874'
status: public
title: Lock-Free algorithms under stochastic schedulers
type: conference
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 2015-July
year: '2015'
...
---
_id: '783'
abstract:
- lang: eng
text: 'The problem of electing a leader from among n contenders is one of the fundamental
questions in distributed computing. In its simplest formulation, the task is as
follows: given n processors, all participants must eventually return a win or
lose indication, such that a single contender may win. Despite a considerable
amount of work on leader election, the following question is still open: can we
elect a leader in an asynchronous fault-prone system faster than just running
a Θ(log n)-time tournament, against a strong adaptive adversary? In this paper,
we answer this question in the affirmative, improving on a decades-old upper bound.
We introduce two new algorithmic ideas to reduce the time complexity of electing
a leader to O(log∗ n), using O(n2) point-to-point messages. A non-trivial application
of our algorithm is a new upper bound for the tight renaming problem, assigning
n items to the n participants in expected O(log2 n) time and O(n2) messages. We
complement our results with lower bound of Ω(n2) messages for solving these two
problems, closing the question of their message complexity.'
acknowledgement: "Support is gratefully acknowledged from the National Science Foundation
under grants CCF-1217921, CCF-1301926,\r\nand IIS-1447786, the Department of
\ Energy under grant\r\nER26116/DE-SC0008923, and the Oracle and Intel corporations.\r\nThe
authors would like to thank Prof. Nir Shavit for ad-\r\nvice and encouragement
during this work, and the anonymous reviewers for their very useful suggestions."
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: Rati
full_name: Gelashvili, Rati
last_name: Gelashvili
- first_name: Adrian
full_name: Vladu, Adrian
last_name: Vladu
citation:
ama: 'Alistarh D-A, Gelashvili R, Vladu A. How to elect a leader faster than a tournament.
In: Vol 2015-July. ACM; 2015:365-374. doi:10.1145/2767386.2767420'
apa: 'Alistarh, D.-A., Gelashvili, R., & Vladu, A. (2015). How to elect a leader
faster than a tournament (Vol. 2015–July, pp. 365–374). Presented at the PODC:
Principles of Distributed Computing, ACM. https://doi.org/10.1145/2767386.2767420'
chicago: Alistarh, Dan-Adrian, Rati Gelashvili, and Adrian Vladu. “How to Elect
a Leader Faster than a Tournament,” 2015–July:365–74. ACM, 2015. https://doi.org/10.1145/2767386.2767420.
ieee: 'D.-A. Alistarh, R. Gelashvili, and A. Vladu, “How to elect a leader faster
than a tournament,” presented at the PODC: Principles of Distributed Computing,
2015, vol. 2015–July, pp. 365–374.'
ista: 'Alistarh D-A, Gelashvili R, Vladu A. 2015. How to elect a leader faster than
a tournament. PODC: Principles of Distributed Computing vol. 2015–July, 365–374.'
mla: Alistarh, Dan-Adrian, et al. How to Elect a Leader Faster than a Tournament.
Vol. 2015–July, ACM, 2015, pp. 365–74, doi:10.1145/2767386.2767420.
short: D.-A. Alistarh, R. Gelashvili, A. Vladu, in:, ACM, 2015, pp. 365–374.
conference:
name: 'PODC: Principles of Distributed Computing'
date_created: 2018-12-11T11:48:28Z
date_published: 2015-07-21T00:00:00Z
date_updated: 2023-02-23T13:18:55Z
day: '21'
doi: 10.1145/2767386.2767420
extern: '1'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/1411.1001
month: '07'
oa: 1
oa_version: None
page: 365 - 374
publication_status: published
publisher: ACM
publist_id: '6875'
status: public
title: How to elect a leader faster than a tournament
type: conference
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 2015-July
year: '2015'
...
---
_id: '784'
abstract:
- lang: eng
text: We demonstrate an optical switch design that can scale up to a thousand ports
with high per-port bandwidth (25 Gbps+) and low switching latency (40 ns). Our
design uses a broadcast and select architecture, based on a passive star coupler
and fast tunable transceivers. In addition we employ time division multiplexing
to achieve very low switching latency. Our demo shows the feasibility of the switch
data plane using a small testbed, comprising two transmitters and a receiver,
connected through a star coupler.
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: Hitesh
full_name: Ballani, Hitesh
last_name: Ballani
- first_name: Paolo
full_name: Costa, Paolo
last_name: Costa
- first_name: Adam
full_name: Funnell, Adam
last_name: Funnell
- first_name: Joshua
full_name: Benjamin, Joshua
last_name: Benjamin
- first_name: Philip
full_name: Watts, Philip
last_name: Watts
- first_name: Benn
full_name: Thomsen, Benn
last_name: Thomsen
citation:
ama: 'Alistarh D-A, Ballani H, Costa P, et al. A high-radix, low-latency optical
switch for data centers. In: ACM; 2015:367-368. doi:10.1145/2785956.2790035'
apa: 'Alistarh, D.-A., Ballani, H., Costa, P., Funnell, A., Benjamin, J., Watts,
P., & Thomsen, B. (2015). A high-radix, low-latency optical switch for data
centers (pp. 367–368). Presented at the SIGCOMM: Special Interest Group on Data
Communication, London, United Kindgdom: ACM. https://doi.org/10.1145/2785956.2790035'
chicago: Alistarh, Dan-Adrian, Hitesh Ballani, Paolo Costa, Adam Funnell, Joshua
Benjamin, Philip Watts, and Benn Thomsen. “A High-Radix, Low-Latency Optical Switch
for Data Centers,” 367–68. ACM, 2015. https://doi.org/10.1145/2785956.2790035.
ieee: 'D.-A. Alistarh et al., “A high-radix, low-latency optical switch for
data centers,” presented at the SIGCOMM: Special Interest Group on Data Communication,
London, United Kindgdom, 2015, pp. 367–368.'
ista: 'Alistarh D-A, Ballani H, Costa P, Funnell A, Benjamin J, Watts P, Thomsen
B. 2015. A high-radix, low-latency optical switch for data centers. SIGCOMM: Special
Interest Group on Data Communication, 367–368.'
mla: Alistarh, Dan-Adrian, et al. A High-Radix, Low-Latency Optical Switch for
Data Centers. ACM, 2015, pp. 367–68, doi:10.1145/2785956.2790035.
short: D.-A. Alistarh, H. Ballani, P. Costa, A. Funnell, J. Benjamin, P. Watts,
B. Thomsen, in:, ACM, 2015, pp. 367–368.
conference:
end_date: 2015-08-21
location: London, United Kindgdom
name: 'SIGCOMM: Special Interest Group on Data Communication'
start_date: 2015-08-17
date_created: 2018-12-11T11:48:29Z
date_published: 2015-01-01T00:00:00Z
date_updated: 2023-02-23T13:18:57Z
day: '01'
doi: 10.1145/2785956.2790035
extern: '1'
language:
- iso: eng
month: '01'
oa_version: None
page: 367 - 368
publication_identifier:
isbn:
- 978-1-4503-3542-3
publication_status: published
publisher: ACM
publist_id: '6872'
quality_controlled: '1'
status: public
title: A high-radix, low-latency optical switch for data centers
type: conference
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
year: '2015'
...
---
_id: '802'
abstract:
- lang: eng
text: Glycoinositolphosphoceramides (GIPCs) are complex sphingolipids present at
the plasma membrane of various eukaryotes with the important exception of mammals.
In fungi, these glycosphingolipids commonly contain an alpha-mannose residue (Man)
linked at position 2 of the inositol. However, several pathogenic fungi additionally
synthesize zwitterionic GIPCs carrying an alpha-glucosamine residue (GlcN) at
this position. In the human pathogen Aspergillus fumigatus, the GlcNalpha1,2IPC
core (where IPC is inositolphosphoceramide) is elongated to Manalpha1,3Manalpha1,6GlcNalpha1,2IPC,
which is the most abundant GIPC synthesized by this fungus. In this study, we
identified an A. fumigatus N-acetylglucosaminyltransferase, named GntA, and demonstrate
its involvement in the initiation of zwitterionic GIPC biosynthesis. Targeted
deletion of the gene encoding GntA in A. fumigatus resulted in complete absence
of zwitterionic GIPC; a phenotype that could be reverted by episomal expression
of GntA in the mutant. The N-acetylhexosaminyltransferase activity of GntA was
substantiated by production of N-acetylhexosamine-IPC in the yeast Saccharomyces
cerevisiae upon GntA expression. Using an in vitro assay, GntA was furthermore
shown to use UDP-N-acetylglucosamine as donor substrate to generate a glycolipid
product resistant to saponification and to digestion by phosphatidylinositol-phospholipase
C as expected for GlcNAcalpha1,2IPC. Finally, as the enzymes involved in mannosylation
of IPC, GntA was localized to the Golgi apparatus, the site of IPC synthesis.
author:
- first_name: Jakob
full_name: Engel, Jakob
last_name: Engel
- first_name: Philipp S
full_name: Schmalhorst, Philipp S
id: 309D50DA-F248-11E8-B48F-1D18A9856A87
last_name: Schmalhorst
orcid: 0000-0002-5795-0133
- first_name: Anke
full_name: Kruger, Anke
last_name: Kruger
- first_name: Christina
full_name: Muller, Christina
last_name: Muller
- first_name: Falk
full_name: Buettner, Falk
last_name: Buettner
- first_name: Françoise
full_name: Routier, Françoise
last_name: Routier
citation:
ama: Engel J, Schmalhorst PS, Kruger A, Muller C, Buettner F, Routier F. Characterization
of an N-acetylglucosaminyltransferase involved in Aspergillus fumigatus zwitterionic
glycoinositolphosphoceramide biosynthesis. Glycobiology. 2015;25(12):1423-1430.
doi:10.1093/glycob/cwv059
apa: Engel, J., Schmalhorst, P. S., Kruger, A., Muller, C., Buettner, F., &
Routier, F. (2015). Characterization of an N-acetylglucosaminyltransferase involved
in Aspergillus fumigatus zwitterionic glycoinositolphosphoceramide biosynthesis.
Glycobiology. Oxford University Press. https://doi.org/10.1093/glycob/cwv059
chicago: Engel, Jakob, Philipp S Schmalhorst, Anke Kruger, Christina Muller, Falk
Buettner, and Françoise Routier. “Characterization of an N-Acetylglucosaminyltransferase
Involved in Aspergillus Fumigatus Zwitterionic Glycoinositolphosphoceramide Biosynthesis.”
Glycobiology. Oxford University Press, 2015. https://doi.org/10.1093/glycob/cwv059.
ieee: J. Engel, P. S. Schmalhorst, A. Kruger, C. Muller, F. Buettner, and F. Routier,
“Characterization of an N-acetylglucosaminyltransferase involved in Aspergillus
fumigatus zwitterionic glycoinositolphosphoceramide biosynthesis,” Glycobiology,
vol. 25, no. 12. Oxford University Press, pp. 1423–1430, 2015.
ista: Engel J, Schmalhorst PS, Kruger A, Muller C, Buettner F, Routier F. 2015.
Characterization of an N-acetylglucosaminyltransferase involved in Aspergillus
fumigatus zwitterionic glycoinositolphosphoceramide biosynthesis. Glycobiology.
25(12), 1423–1430.
mla: Engel, Jakob, et al. “Characterization of an N-Acetylglucosaminyltransferase
Involved in Aspergillus Fumigatus Zwitterionic Glycoinositolphosphoceramide Biosynthesis.”
Glycobiology, vol. 25, no. 12, Oxford University Press, 2015, pp. 1423–30,
doi:10.1093/glycob/cwv059.
short: J. Engel, P.S. Schmalhorst, A. Kruger, C. Muller, F. Buettner, F. Routier,
Glycobiology 25 (2015) 1423–1430.
date_created: 2018-12-11T11:48:35Z
date_published: 2015-12-01T00:00:00Z
date_updated: 2021-01-12T08:16:33Z
day: '01'
department:
- _id: CaHe
doi: 10.1093/glycob/cwv059
external_id:
pmid:
- '26306635'
intvolume: ' 25'
issue: '12'
language:
- iso: eng
month: '12'
oa_version: None
page: 1423 - 1430
pmid: 1
publication: Glycobiology
publication_status: published
publisher: Oxford University Press
publist_id: '6851'
quality_controlled: '1'
scopus_import: 1
status: public
title: Characterization of an N-acetylglucosaminyltransferase involved in Aspergillus
fumigatus zwitterionic glycoinositolphosphoceramide biosynthesis
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 25
year: '2015'
...
---
_id: '815'
abstract:
- lang: eng
text: "The polyprotein Gag is the primary structural component of retroviruses.
Gag consists of independently folded domains connected by flexible linkers. Interactions
between the conserved capsid (CA) domains of Gag mediate formation of hexameric
protein lattices that drive assembly of immature virus particles. Proteolytic
cleavage of Gag by the viral protease (PR) is required for maturation of retroviruses
from an immature form into an infectious form. Within the assembled Gag lattices
of HIV-1 and Mason- Pfizer monkey virus (M-PMV), the C-terminal domain of CA adopts
similar quaternary arrangements, while the N-terminal domain of CA is packed in
very different manners. Here, we have used cryo-electron tomography and subtomogram
averaging to study in vitro-assembled, immature virus-like Rous sarcoma virus
(RSV) Gag particles and have determined the structure of CA and the surrounding
regions to a resolution of ~8 Å. We found that the C-terminal domain of RSV CA
is arranged similarly to HIV-1 and M-PMV, whereas the N-terminal domain of CA
adopts a novel arrangement in which the upstream p10 domain folds back into the
CA lattice. In this position the cleavage site between CA and p10 appears to be
inaccessible to PR. Below CA, an extended density is consistent with the presence
of a six-helix bundle formed by the spacer-peptide region. We have also assessed
the affect of lattice assembly on proteolytic processing by exogenous PR. The
cleavage between p10 and CA is indeed inhibited in the assembled lattice, a finding
consistent with structural regulation of proteolytic maturation.\r\n"
author:
- first_name: Florian
full_name: Schur, Florian
id: 48AD8942-F248-11E8-B48F-1D18A9856A87
last_name: Schur
orcid: 0000-0003-4790-8078
- first_name: Robert
full_name: Dick, Robert
last_name: Dick
- first_name: Wim
full_name: Hagen, Wim
last_name: Hagen
- first_name: Volker
full_name: Vogt, Volker
last_name: Vogt
- first_name: John
full_name: Briggs, John
last_name: Briggs
citation:
ama: Schur FK, Dick R, Hagen W, Vogt V, Briggs J. The structure of immature virus
like Rous sarcoma virus gag particles reveals a structural role for the p10 domain
in assembly. Journal of Virology. 2015;89(20):10294-10302. doi:10.1128/JVI.01502-15
apa: Schur, F. K., Dick, R., Hagen, W., Vogt, V., & Briggs, J. (2015). The structure
of immature virus like Rous sarcoma virus gag particles reveals a structural role
for the p10 domain in assembly. Journal of Virology. ASM. https://doi.org/10.1128/JVI.01502-15
chicago: Schur, Florian KM, Robert Dick, Wim Hagen, Volker Vogt, and John Briggs.
“The Structure of Immature Virus like Rous Sarcoma Virus Gag Particles Reveals
a Structural Role for the P10 Domain in Assembly.” Journal of Virology.
ASM, 2015. https://doi.org/10.1128/JVI.01502-15.
ieee: F. K. Schur, R. Dick, W. Hagen, V. Vogt, and J. Briggs, “The structure of
immature virus like Rous sarcoma virus gag particles reveals a structural role
for the p10 domain in assembly,” Journal of Virology, vol. 89, no. 20.
ASM, pp. 10294–10302, 2015.
ista: Schur FK, Dick R, Hagen W, Vogt V, Briggs J. 2015. The structure of immature
virus like Rous sarcoma virus gag particles reveals a structural role for the
p10 domain in assembly. Journal of Virology. 89(20), 10294–10302.
mla: Schur, Florian KM, et al. “The Structure of Immature Virus like Rous Sarcoma
Virus Gag Particles Reveals a Structural Role for the P10 Domain in Assembly.”
Journal of Virology, vol. 89, no. 20, ASM, 2015, pp. 10294–302, doi:10.1128/JVI.01502-15.
short: F.K. Schur, R. Dick, W. Hagen, V. Vogt, J. Briggs, Journal of Virology 89
(2015) 10294–10302.
date_created: 2018-12-11T11:48:39Z
date_published: 2015-09-22T00:00:00Z
date_updated: 2021-01-12T08:17:09Z
day: '22'
doi: 10.1128/JVI.01502-15
extern: '1'
external_id:
pmid:
- '26223638'
intvolume: ' 89'
issue: '20'
language:
- iso: eng
month: '09'
oa_version: None
page: 10294 - 10302
pmid: 1
publication: Journal of Virology
publication_status: published
publisher: ASM
publist_id: '6837'
quality_controlled: '1'
status: public
title: The structure of immature virus like Rous sarcoma virus gag particles reveals
a structural role for the p10 domain in assembly
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 89
year: '2015'
...
---
_id: '814'
abstract:
- lang: eng
text: Human immunodeficiency virus type 1 (HIV-1) assembly proceeds in two stages.
First, the 55 kilodalton viral Gag polyprotein assembles into a hexameric protein
lattice at the plasma membrane of the infected cell, inducing budding and release
of an immature particle. Second, Gag is cleaved by the viral protease, leading
to internal rearrangement of the virus into the mature, infectious form. Immature
and mature HIV-1 particles are heterogeneous in size and morphology, preventing
high-resolution analysis of their protein arrangement in situ by conventional
structural biology methods. Here we apply cryo-electron tomography and sub-tomogram
averaging methods to resolve the structure of the capsid lattice within intact
immature HIV-1 particles at subnanometre resolution, allowing unambiguous positioning
of all α-helices. The resulting model reveals tertiary and quaternary structural
interactions that mediate HIV-1 assembly. Strikingly, these interactions differ
from those predicted by the current model based on in vitro-assembled arrays of
Gag-derived proteins from Mason-Pfizer monkey virus. To validate this difference,
we solve the structure of the capsid lattice within intact immature Mason-Pfizer
monkey virus particles. Comparison with the immature HIV-1 structure reveals that
retroviral capsid proteins, while having conserved tertiary structures, adopt
different quaternary arrangements during virus assembly. The approach demonstrated
here should be applicable to determine structures of other proteins at subnanometre
resolution within heterogeneous environments.
acknowledgement: This study was supported by Deutsche Forschungsgemeinschaft grants
BR 3635/2-1 to J.A.G.B., KR 906/7-1 to H.-G.K. and by Grant Agency of the Czech
Republic 14-15326S to M.R. The Briggs laboratory acknowledges financial support
from the European Molecular Biology Laboratory and from the Chica und Heinz Schaller
Stiftung. We thank B. Glass, M. Anders and S. Mattei for preparation of samples,
and R. Hadravova, K. H. Bui, F. Thommen, M. Schorb, S. Dodonova, S. Glatt, P. Ulbrich
and T. Bharat for technical support and/or discussion. This study was technically
supported by the European Molecular Biology Laboratory IT services unit.
author:
- first_name: Florian
full_name: Florian Schur
id: 48AD8942-F248-11E8-B48F-1D18A9856A87
last_name: Schur
orcid: 0000-0003-4790-8078
- first_name: Wim
full_name: Hagen, Wim J
last_name: Hagen
- first_name: Michaela
full_name: Rumlová, Michaela
last_name: Rumlová
- first_name: Tomáš
full_name: Ruml, Tomáš
last_name: Ruml
- first_name: B
full_name: Müller B
last_name: Müller
- first_name: Hans
full_name: Kraüsslich, Hans Georg
last_name: Kraüsslich
- first_name: John
full_name: Briggs, John A
last_name: Briggs
citation:
ama: Schur FK, Hagen W, Rumlová M, et al. Structure of the immature HIV-1 capsid
in intact virus particles at 8.8 Å resolution. Nature. 2015;517(7535):505-508.
doi:10.1038/nature13838
apa: Schur, F. K., Hagen, W., Rumlová, M., Ruml, T., Müller, B., Kraüsslich, H.,
& Briggs, J. (2015). Structure of the immature HIV-1 capsid in intact virus
particles at 8.8 Å resolution. Nature. Nature Publishing Group. https://doi.org/10.1038/nature13838
chicago: Schur, Florian KM, Wim Hagen, Michaela Rumlová, Tomáš Ruml, B Müller, Hans
Kraüsslich, and John Briggs. “Structure of the Immature HIV-1 Capsid in Intact
Virus Particles at 8.8 Å Resolution.” Nature. Nature Publishing Group,
2015. https://doi.org/10.1038/nature13838.
ieee: F. K. Schur et al., “Structure of the immature HIV-1 capsid in intact
virus particles at 8.8 Å resolution,” Nature, vol. 517, no. 7535. Nature
Publishing Group, pp. 505–508, 2015.
ista: Schur FK, Hagen W, Rumlová M, Ruml T, Müller B, Kraüsslich H, Briggs J. 2015.
Structure of the immature HIV-1 capsid in intact virus particles at 8.8 Å resolution.
Nature. 517(7535), 505–508.
mla: Schur, Florian KM, et al. “Structure of the Immature HIV-1 Capsid in Intact
Virus Particles at 8.8 Å Resolution.” Nature, vol. 517, no. 7535, Nature
Publishing Group, 2015, pp. 505–08, doi:10.1038/nature13838.
short: F.K. Schur, W. Hagen, M. Rumlová, T. Ruml, B. Müller, H. Kraüsslich, J. Briggs,
Nature 517 (2015) 505–508.
date_created: 2018-12-11T11:48:39Z
date_published: 2015-01-22T00:00:00Z
date_updated: 2021-01-12T08:17:08Z
day: '22'
doi: 10.1038/nature13838
extern: 1
intvolume: ' 517'
issue: '7535'
month: '01'
page: 505 - 508
publication: Nature
publication_status: published
publisher: Nature Publishing Group
publist_id: '6836'
quality_controlled: 0
status: public
title: Structure of the immature HIV-1 capsid in intact virus particles at 8.8 Å resolution
type: journal_article
volume: 517
year: '2015'
...
---
_id: '8242'
article_number: AB101
article_processing_charge: No
article_type: original
author:
- first_name: Lukas
full_name: Einhorn, Lukas
last_name: Einhorn
- first_name: Judit
full_name: Fazekas, Judit
id: 36432834-F248-11E8-B48F-1D18A9856A87
last_name: Fazekas
orcid: 0000-0002-8777-3502
- first_name: Martina
full_name: Muhr, Martina
last_name: Muhr
- first_name: Alexandra
full_name: Schoos, Alexandra
last_name: Schoos
- first_name: Kumiko
full_name: Oida, Kumiko
last_name: Oida
- first_name: Josef
full_name: Singer, Josef
last_name: Singer
- first_name: Lucia
full_name: Panakova, Lucia
last_name: Panakova
- first_name: Krisztina
full_name: Manzano-Szalai, Krisztina
last_name: Manzano-Szalai
- first_name: Erika
full_name: Jensen-Jarolim, Erika
last_name: Jensen-Jarolim
citation:
ama: Einhorn L, Singer J, Muhr M, et al. Generation of recombinant FcεRIα of dog,
cat and horse for component-resolved allergy diagnosis in veterinary patients.
Journal of Allergy and Clinical Immunology. 2015;135(2). doi:10.1016/j.jaci.2014.12.1263
apa: Einhorn, L., Singer, J., Muhr, M., Schoos, A., Oida, K., Singer, J., … Jensen-Jarolim,
E. (2015). Generation of recombinant FcεRIα of dog, cat and horse for component-resolved
allergy diagnosis in veterinary patients. Journal of Allergy and Clinical Immunology.
Elsevier. https://doi.org/10.1016/j.jaci.2014.12.1263
chicago: Einhorn, Lukas, Judit Singer, Martina Muhr, Alexandra Schoos, Kumiko Oida,
Josef Singer, Lucia Panakova, Krisztina Manzano-Szalai, and Erika Jensen-Jarolim.
“Generation of Recombinant FcεRIα of Dog, Cat and Horse for Component-Resolved
Allergy Diagnosis in Veterinary Patients.” Journal of Allergy and Clinical
Immunology. Elsevier, 2015. https://doi.org/10.1016/j.jaci.2014.12.1263.
ieee: L. Einhorn et al., “Generation of recombinant FcεRIα of dog, cat and
horse for component-resolved allergy diagnosis in veterinary patients,” Journal
of Allergy and Clinical Immunology, vol. 135, no. 2. Elsevier, 2015.
ista: Einhorn L, Singer J, Muhr M, Schoos A, Oida K, Singer J, Panakova L, Manzano-Szalai
K, Jensen-Jarolim E. 2015. Generation of recombinant FcεRIα of dog, cat and horse
for component-resolved allergy diagnosis in veterinary patients. Journal of Allergy
and Clinical Immunology. 135(2), AB101.
mla: Einhorn, Lukas, et al. “Generation of Recombinant FcεRIα of Dog, Cat and Horse
for Component-Resolved Allergy Diagnosis in Veterinary Patients.” Journal of
Allergy and Clinical Immunology, vol. 135, no. 2, AB101, Elsevier, 2015, doi:10.1016/j.jaci.2014.12.1263.
short: L. Einhorn, J. Singer, M. Muhr, A. Schoos, K. Oida, J. Singer, L. Panakova,
K. Manzano-Szalai, E. Jensen-Jarolim, Journal of Allergy and Clinical Immunology
135 (2015).
date_created: 2020-08-10T11:54:09Z
date_published: 2015-02-01T00:00:00Z
date_updated: 2021-01-12T08:17:42Z
day: '01'
doi: 10.1016/j.jaci.2014.12.1263
extern: '1'
intvolume: ' 135'
issue: '2'
language:
- iso: eng
month: '02'
oa_version: None
publication: Journal of Allergy and Clinical Immunology
publication_identifier:
issn:
- 0091-6749
publication_status: published
publisher: Elsevier
quality_controlled: '1'
status: public
title: Generation of recombinant FcεRIα of dog, cat and horse for component-resolved
allergy diagnosis in veterinary patients
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 135
year: '2015'
...
---
_id: '832'
abstract:
- lang: eng
text: Plants maintain capacity to form new organs such as leaves, flowers, lateral
shoots and roots throughout their postembryonic lifetime. Lateral roots (LRs)
originate from a few pericycle cells that acquire attributes of founder cells
(FCs), undergo series of anticlinal divisions, and give rise to a few short initial
cells. After initiation, coordinated cell division and differentiation occur,
giving rise to lateral root primordia (LRP). Primordia continue to grow, emerge
through the cortex and epidermal layers of the primary root, and finally a new
apical meristem is established taking over the responsibility for growth of mature
lateral roots [for detailed description of the individual stages of lateral root
organogenesis see Malamy and Benfey (1997)]. To examine this highly dynamic developmental
process and to investigate a role of various hormonal, genetic and environmental
factors in the regulation of lateral root organogenesis, the real time imaging
based analyses represent extremely powerful tools (Laskowski et al., 2008; De
Smet et al., 2012; Marhavy et al., 2013 and 2014). Herein, we describe a protocol
for real time lateral root primordia (LRP) analysis, which enables the monitoring
of an onset of the specific gene expression and subcellular protein localization
during primordia organogenesis, as well as the evaluation of the impact of genetic
and environmental perturbations on LRP organogenesis.
acknowledgement: "European Research Council with a Starting Independent Research grant:
ERC-2007-Stg-207362-HCPO, Czech Science Foundation: GA13-39982S\nWe thank Matyas
Fendrych for critical reading and comments. The protocol was developed based on
previously published work of De Rybel et al. (2010) and Laskowski et al. (2008). "
author:
- first_name: Peter
full_name: Peter Marhavy
id: 3F45B078-F248-11E8-B48F-1D18A9856A87
last_name: Marhavy
orcid: 0000-0001-5227-5741
- first_name: Eva
full_name: Eva Benková
id: 38F4F166-F248-11E8-B48F-1D18A9856A87
last_name: Benková
orcid: 0000-0002-8510-9739
citation:
ama: Marhavý P, Benková E. Real time analysis of lateral root organogenesis in arabidopsis.
Bio-protocol. 2015;5(8). doi:10.21769/BioProtoc.1446
apa: Marhavý, P., & Benková, E. (2015). Real time analysis of lateral root organogenesis
in arabidopsis. Bio-Protocol. Bio-protocol LLC. https://doi.org/10.21769/BioProtoc.1446
chicago: Marhavý, Peter, and Eva Benková. “Real Time Analysis of Lateral Root Organogenesis
in Arabidopsis.” Bio-Protocol. Bio-protocol LLC, 2015. https://doi.org/10.21769/BioProtoc.1446.
ieee: P. Marhavý and E. Benková, “Real time analysis of lateral root organogenesis
in arabidopsis,” Bio-protocol, vol. 5, no. 8. Bio-protocol LLC, 2015.
ista: Marhavý P, Benková E. 2015. Real time analysis of lateral root organogenesis
in arabidopsis. Bio-protocol. 5(8).
mla: Marhavý, Peter, and Eva Benková. “Real Time Analysis of Lateral Root Organogenesis
in Arabidopsis.” Bio-Protocol, vol. 5, no. 8, Bio-protocol LLC, 2015, doi:10.21769/BioProtoc.1446.
short: P. Marhavý, E. Benková, Bio-Protocol 5 (2015).
date_created: 2018-12-11T11:48:44Z
date_published: 2015-04-20T00:00:00Z
date_updated: 2021-01-12T08:18:07Z
day: '20'
doi: 10.21769/BioProtoc.1446
extern: 1
intvolume: ' 5'
issue: '8'
month: '04'
publication: Bio-protocol
publication_status: published
publisher: Bio-protocol LLC
publist_id: '6816'
quality_controlled: 0
status: public
title: Real time analysis of lateral root organogenesis in arabidopsis
type: journal_article
volume: 5
year: '2015'
...
---
_id: '8456'
abstract:
- lang: eng
text: The large majority of three-dimensional structures of biological macromolecules
have been determined by X-ray diffraction of crystalline samples. High-resolution
structure determination crucially depends on the homogeneity of the protein crystal.
Overall ‘rocking’ motion of molecules in the crystal is expected to influence
diffraction quality, and such motion may therefore affect the process of solving
crystal structures. Yet, so far overall molecular motion has not directly been
observed in protein crystals, and the timescale of such dynamics remains unclear.
Here we use solid-state NMR, X-ray diffraction methods and μs-long molecular dynamics
simulations to directly characterize the rigid-body motion of a protein in different
crystal forms. For ubiquitin crystals investigated in this study we determine
the range of possible correlation times of rocking motion, 0.1–100 μs. The amplitude
of rocking varies from one crystal form to another and is correlated with the
resolution obtainable in X-ray diffraction experiments.
article_number: '8361'
article_processing_charge: No
article_type: original
author:
- first_name: Peixiang
full_name: Ma, Peixiang
last_name: Ma
- first_name: Yi
full_name: Xue, Yi
last_name: Xue
- first_name: Nicolas
full_name: Coquelle, Nicolas
last_name: Coquelle
- first_name: Jens D.
full_name: Haller, Jens D.
last_name: Haller
- first_name: Tairan
full_name: Yuwen, Tairan
last_name: Yuwen
- first_name: Isabel
full_name: Ayala, Isabel
last_name: Ayala
- first_name: Oleg
full_name: Mikhailovskii, Oleg
last_name: Mikhailovskii
- first_name: Dieter
full_name: Willbold, Dieter
last_name: Willbold
- first_name: Jacques-Philippe
full_name: Colletier, Jacques-Philippe
last_name: Colletier
- first_name: Nikolai R.
full_name: Skrynnikov, Nikolai R.
last_name: Skrynnikov
- first_name: Paul
full_name: Schanda, Paul
id: 7B541462-FAF6-11E9-A490-E8DFE5697425
last_name: Schanda
orcid: 0000-0002-9350-7606
citation:
ama: Ma P, Xue Y, Coquelle N, et al. Observing the overall rocking motion of a protein
in a crystal. Nature Communications. 2015;6. doi:10.1038/ncomms9361
apa: Ma, P., Xue, Y., Coquelle, N., Haller, J. D., Yuwen, T., Ayala, I., … Schanda,
P. (2015). Observing the overall rocking motion of a protein in a crystal. Nature
Communications. Springer Nature. https://doi.org/10.1038/ncomms9361
chicago: Ma, Peixiang, Yi Xue, Nicolas Coquelle, Jens D. Haller, Tairan Yuwen, Isabel
Ayala, Oleg Mikhailovskii, et al. “Observing the Overall Rocking Motion of a Protein
in a Crystal.” Nature Communications. Springer Nature, 2015. https://doi.org/10.1038/ncomms9361.
ieee: P. Ma et al., “Observing the overall rocking motion of a protein in
a crystal,” Nature Communications, vol. 6. Springer Nature, 2015.
ista: Ma P, Xue Y, Coquelle N, Haller JD, Yuwen T, Ayala I, Mikhailovskii O, Willbold
D, Colletier J-P, Skrynnikov NR, Schanda P. 2015. Observing the overall rocking
motion of a protein in a crystal. Nature Communications. 6, 8361.
mla: Ma, Peixiang, et al. “Observing the Overall Rocking Motion of a Protein in
a Crystal.” Nature Communications, vol. 6, 8361, Springer Nature, 2015,
doi:10.1038/ncomms9361.
short: P. Ma, Y. Xue, N. Coquelle, J.D. Haller, T. Yuwen, I. Ayala, O. Mikhailovskii,
D. Willbold, J.-P. Colletier, N.R. Skrynnikov, P. Schanda, Nature Communications
6 (2015).
date_created: 2020-09-18T10:07:36Z
date_published: 2015-10-05T00:00:00Z
date_updated: 2021-01-12T08:19:24Z
day: '05'
doi: 10.1038/ncomms9361
extern: '1'
intvolume: ' 6'
keyword:
- General Biochemistry
- Genetics and Molecular Biology
- General Physics and Astronomy
- General Chemistry
language:
- iso: eng
month: '10'
oa_version: Published Version
publication: Nature Communications
publication_identifier:
issn:
- 2041-1723
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
status: public
title: Observing the overall rocking motion of a protein in a crystal
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 6
year: '2015'
...
---
_id: '8457'
abstract:
- lang: eng
text: We review recent advances in methodologies to study microseconds‐to‐milliseconds
exchange processes in biological molecules using magic‐angle spinning solid‐state
nuclear magnetic resonance (MAS ssNMR) spectroscopy. The particularities of MAS
ssNMR, as compared to solution‐state NMR, are elucidated using numerical simulations
and experimental data. These simulations reveal the potential of MAS NMR to provide
detailed insight into short‐lived conformations of biological molecules. Recent
studies of conformational exchange dynamics in microcrystalline ubiquitin are
discussed.
article_processing_charge: No
article_type: original
author:
- first_name: Peixiang
full_name: Ma, Peixiang
last_name: Ma
- first_name: Paul
full_name: Schanda, Paul
id: 7B541462-FAF6-11E9-A490-E8DFE5697425
last_name: Schanda
orcid: 0000-0002-9350-7606
citation:
ama: 'Ma P, Schanda P. Conformational exchange processes in biological systems:
Detection by solid-state NMR. eMagRes. 2015;4(3):699-708. doi:10.1002/9780470034590.emrstm1418'
apa: 'Ma, P., & Schanda, P. (2015). Conformational exchange processes in biological
systems: Detection by solid-state NMR. EMagRes. Wiley. https://doi.org/10.1002/9780470034590.emrstm1418'
chicago: 'Ma, Peixiang, and Paul Schanda. “Conformational Exchange Processes in
Biological Systems: Detection by Solid-State NMR.” EMagRes. Wiley, 2015.
https://doi.org/10.1002/9780470034590.emrstm1418.'
ieee: 'P. Ma and P. Schanda, “Conformational exchange processes in biological systems:
Detection by solid-state NMR,” eMagRes, vol. 4, no. 3. Wiley, pp. 699–708,
2015.'
ista: 'Ma P, Schanda P. 2015. Conformational exchange processes in biological systems:
Detection by solid-state NMR. eMagRes. 4(3), 699–708.'
mla: 'Ma, Peixiang, and Paul Schanda. “Conformational Exchange Processes in Biological
Systems: Detection by Solid-State NMR.” EMagRes, vol. 4, no. 3, Wiley,
2015, pp. 699–708, doi:10.1002/9780470034590.emrstm1418.'
short: P. Ma, P. Schanda, EMagRes 4 (2015) 699–708.
date_created: 2020-09-18T10:07:45Z
date_published: 2015-09-10T00:00:00Z
date_updated: 2021-01-12T08:19:24Z
day: '10'
doi: 10.1002/9780470034590.emrstm1418
extern: '1'
intvolume: ' 4'
issue: '3'
language:
- iso: eng
month: '09'
oa_version: None
page: 699-708
publication: eMagRes
publication_identifier:
isbn:
- '9780470034590'
- '9780470058213'
publication_status: published
publisher: Wiley
quality_controlled: '1'
status: public
title: 'Conformational exchange processes in biological systems: Detection by solid-state
NMR'
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 4
year: '2015'
...
---
_id: '848'
abstract:
- lang: eng
text: The nature of factors governing the tempo and mode of protein evolution is
a fundamental issue in evolutionary biology. Specifically, whether or not interactions
between different sites, or epistasis, are important in directing the course of
evolution became one of the central questions. Several recent reports have scrutinized
patterns of long-term protein evolution claiming them to be compatible only with
an epistatic fitness landscape. However, these claims have not yet been substantiated
with a formal model of protein evolution. Here, we formulate a simple covarion-like
model of protein evolution focusing on the rate at which the fitness impact of
amino acids at a site changes with time. We then apply the model to the data on
convergent and divergent protein evolution to test whether or not the incorporation
of epistatic interactions is necessary to explain the data. We find that convergent
evolution cannot be explained without the incorporation of epistasis and the rate
at which an amino acid state switches from being acceptable at a site to being
deleterious is faster than the rate of amino acid substitution. Specifically,
for proteins that have persisted in modern prokaryotic organisms since the last
universal common ancestor for one amino acid substitution approximately ten amino
acid states switch from being accessible to being deleterious, or vice versa.
Thus, molecular evolution can only be perceived in the context of rapid turnover
of which amino acids are available for evolution.
author:
- first_name: Dinara
full_name: Usmanova, Dinara
last_name: Usmanova
- first_name: Luca
full_name: Ferretti, Luca
last_name: Ferretti
- first_name: Inna
full_name: Povolotskaya, Inna
last_name: Povolotskaya
- first_name: Peter
full_name: Vlasov, Peter
last_name: Vlasov
- first_name: Fyodor
full_name: Kondrashov, Fyodor
id: 44FDEF62-F248-11E8-B48F-1D18A9856A87
last_name: Kondrashov
orcid: 0000-0001-8243-4694
citation:
ama: Usmanova D, Ferretti L, Povolotskaya I, Vlasov P, Kondrashov F. A model of
substitution trajectories in sequence space and long-term protein evolution. Molecular
Biology and Evolution. 2015;32(2):542-554. doi:10.1093/molbev/msu318
apa: Usmanova, D., Ferretti, L., Povolotskaya, I., Vlasov, P., & Kondrashov,
F. (2015). A model of substitution trajectories in sequence space and long-term
protein evolution. Molecular Biology and Evolution. Oxford University Press.
https://doi.org/10.1093/molbev/msu318
chicago: Usmanova, Dinara, Luca Ferretti, Inna Povolotskaya, Peter Vlasov, and Fyodor
Kondrashov. “A Model of Substitution Trajectories in Sequence Space and Long-Term
Protein Evolution.” Molecular Biology and Evolution. Oxford University
Press, 2015. https://doi.org/10.1093/molbev/msu318.
ieee: D. Usmanova, L. Ferretti, I. Povolotskaya, P. Vlasov, and F. Kondrashov, “A
model of substitution trajectories in sequence space and long-term protein evolution,”
Molecular Biology and Evolution, vol. 32, no. 2. Oxford University Press,
pp. 542–554, 2015.
ista: Usmanova D, Ferretti L, Povolotskaya I, Vlasov P, Kondrashov F. 2015. A model
of substitution trajectories in sequence space and long-term protein evolution.
Molecular Biology and Evolution. 32(2), 542–554.
mla: Usmanova, Dinara, et al. “A Model of Substitution Trajectories in Sequence
Space and Long-Term Protein Evolution.” Molecular Biology and Evolution,
vol. 32, no. 2, Oxford University Press, 2015, pp. 542–54, doi:10.1093/molbev/msu318.
short: D. Usmanova, L. Ferretti, I. Povolotskaya, P. Vlasov, F. Kondrashov, Molecular
Biology and Evolution 32 (2015) 542–554.
date_created: 2018-12-11T11:48:49Z
date_published: 2015-02-01T00:00:00Z
date_updated: 2021-01-12T08:19:33Z
day: '01'
doi: 10.1093/molbev/msu318
extern: '1'
intvolume: ' 32'
issue: '2'
language:
- iso: eng
month: '02'
oa_version: None
page: 542 - 554
publication: Molecular Biology and Evolution
publication_status: published
publisher: Oxford University Press
publist_id: '6804'
quality_controlled: '1'
status: public
title: A model of substitution trajectories in sequence space and long-term protein
evolution
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 32
year: '2015'
...
---
_id: '8498'
abstract:
- lang: eng
text: "In the present note we announce a proof of a strong form of Arnold diffusion
for smooth convex Hamiltonian systems. Let ${\\mathbb T}^2$ be a 2-dimensional
torus and B2 be the unit ball around the origin in ${\\mathbb R}^2$ . Fix ρ >
0. Our main result says that for a 'generic' time-periodic perturbation of an
integrable system of two degrees of freedom $H_0(p)+\\varepsilon H_1(\\theta,p,t),\\quad
\\ \\theta\\in {\\mathbb T}^2,\\ p\\in B^2,\\ t\\in {\\mathbb T}={\\mathbb R}/{\\mathbb
Z}$ , with a strictly convex H0, there exists a ρ-dense orbit (θε, pε, t)(t) in
${\\mathbb T}^2 \\times B^2 \\times {\\mathbb T}$ , namely, a ρ-neighborhood of
the orbit contains ${\\mathbb T}^2 \\times B^2 \\times {\\mathbb T}$ .\r\n\r\nOur
proof is a combination of geometric and variational methods. The fundamental elements
of the construction are the usage of crumpled normally hyperbolic invariant cylinders
from [9], flower and simple normally hyperbolic invariant manifolds from [36]
as well as their kissing property at a strong double resonance. This allows us
to build a 'connected' net of three-dimensional normally hyperbolic invariant
manifolds. To construct diffusing orbits along this net we employ a version of
the Mather variational method [41] equipped with weak KAM theory [28], proposed
by Bernard in [7]."
article_processing_charge: No
article_type: original
author:
- first_name: Vadim
full_name: Kaloshin, Vadim
id: FE553552-CDE8-11E9-B324-C0EBE5697425
last_name: Kaloshin
orcid: 0000-0002-6051-2628
- first_name: K
full_name: Zhang, K
last_name: Zhang
citation:
ama: Kaloshin V, Zhang K. Arnold diffusion for smooth convex systems of two and
a half degrees of freedom. Nonlinearity. 2015;28(8):2699-2720. doi:10.1088/0951-7715/28/8/2699
apa: Kaloshin, V., & Zhang, K. (2015). Arnold diffusion for smooth convex systems
of two and a half degrees of freedom. Nonlinearity. IOP Publishing. https://doi.org/10.1088/0951-7715/28/8/2699
chicago: Kaloshin, Vadim, and K Zhang. “Arnold Diffusion for Smooth Convex Systems
of Two and a Half Degrees of Freedom.” Nonlinearity. IOP Publishing, 2015.
https://doi.org/10.1088/0951-7715/28/8/2699.
ieee: V. Kaloshin and K. Zhang, “Arnold diffusion for smooth convex systems of two
and a half degrees of freedom,” Nonlinearity, vol. 28, no. 8. IOP Publishing,
pp. 2699–2720, 2015.
ista: Kaloshin V, Zhang K. 2015. Arnold diffusion for smooth convex systems of two
and a half degrees of freedom. Nonlinearity. 28(8), 2699–2720.
mla: Kaloshin, Vadim, and K. Zhang. “Arnold Diffusion for Smooth Convex Systems
of Two and a Half Degrees of Freedom.” Nonlinearity, vol. 28, no. 8, IOP
Publishing, 2015, pp. 2699–720, doi:10.1088/0951-7715/28/8/2699.
short: V. Kaloshin, K. Zhang, Nonlinearity 28 (2015) 2699–2720.
date_created: 2020-09-18T10:46:43Z
date_published: 2015-06-30T00:00:00Z
date_updated: 2021-01-12T08:19:41Z
day: '30'
doi: 10.1088/0951-7715/28/8/2699
extern: '1'
intvolume: ' 28'
issue: '8'
keyword:
- Mathematical Physics
- General Physics and Astronomy
- Applied Mathematics
- Statistical and Nonlinear Physics
language:
- iso: eng
month: '06'
oa_version: None
page: 2699-2720
publication: Nonlinearity
publication_identifier:
issn:
- 0951-7715
- 1361-6544
publication_status: published
publisher: IOP Publishing
quality_controlled: '1'
status: public
title: Arnold diffusion for smooth convex systems of two and a half degrees of freedom
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 28
year: '2015'
...
---
_id: '8499'
abstract:
- lang: eng
text: "We consider the cubic defocusing nonlinear Schrödinger equation in the two
dimensional torus. Fix s>1. Recently Colliander, Keel, Staffilani, Tao and Takaoka
proved the existence of solutions with s-Sobolev norm growing in time.\r\n\r\nWe
establish the existence of solutions with polynomial time estimates. More exactly,
there is c>0 such that for any K≫1 we find a solution u and a time T such that
∥u(T)∥Hs≥K∥u(0)∥Hs. Moreover, the time T satisfies the polynomial bound 0Journal of the European Mathematical Society. 2015;17(1):71-149.
doi:10.4171/jems/499
apa: Guardia, M., & Kaloshin, V. (2015). Growth of Sobolev norms in the cubic
defocusing nonlinear Schrödinger equation. Journal of the European Mathematical
Society. European Mathematical Society Publishing House. https://doi.org/10.4171/jems/499
chicago: Guardia, Marcel, and Vadim Kaloshin. “Growth of Sobolev Norms in the Cubic
Defocusing Nonlinear Schrödinger Equation.” Journal of the European Mathematical
Society. European Mathematical Society Publishing House, 2015. https://doi.org/10.4171/jems/499.
ieee: M. Guardia and V. Kaloshin, “Growth of Sobolev norms in the cubic defocusing
nonlinear Schrödinger equation,” Journal of the European Mathematical Society,
vol. 17, no. 1. European Mathematical Society Publishing House, pp. 71–149, 2015.
ista: Guardia M, Kaloshin V. 2015. Growth of Sobolev norms in the cubic defocusing
nonlinear Schrödinger equation. Journal of the European Mathematical Society.
17(1), 71–149.
mla: Guardia, Marcel, and Vadim Kaloshin. “Growth of Sobolev Norms in the Cubic
Defocusing Nonlinear Schrödinger Equation.” Journal of the European Mathematical
Society, vol. 17, no. 1, European Mathematical Society Publishing House, 2015,
pp. 71–149, doi:10.4171/jems/499.
short: M. Guardia, V. Kaloshin, Journal of the European Mathematical Society 17
(2015) 71–149.
date_created: 2020-09-18T10:46:50Z
date_published: 2015-02-05T00:00:00Z
date_updated: 2021-01-12T08:19:41Z
day: '05'
doi: 10.4171/jems/499
extern: '1'
intvolume: ' 17'
issue: '1'
language:
- iso: eng
month: '02'
oa_version: None
page: 71-149
publication: Journal of the European Mathematical Society
publication_identifier:
issn:
- 1435-9855
publication_status: published
publisher: European Mathematical Society Publishing House
quality_controlled: '1'
status: public
title: Growth of Sobolev norms in the cubic defocusing nonlinear Schrödinger equation
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 17
year: '2015'
...
---
_id: '9057'
abstract:
- lang: eng
text: Motility is a basic feature of living microorganisms, and how it works is
often determined by environmental cues. Recent efforts have focused on developing
artificial systems that can mimic microorganisms, in particular their self-propulsion.
We report on the design and characterization of synthetic self-propelled particles
that migrate upstream, known as positive rheotaxis. This phenomenon results from
a purely physical mechanism involving the interplay between the polarity of the
particles and their alignment by a viscous torque. We show quantitative agreement
between experimental data and a simple model of an overdamped Brownian pendulum.
The model notably predicts the existence of a stagnation point in a diverging
flow. We take advantage of this property to demonstrate that our active particles
can sense and predictably organize in an imposed flow. Our colloidal system represents
an important step toward the realization of biomimetic microsystems with the ability
to sense and respond to environmental changes.
article_number: e1400214
article_processing_charge: No
article_type: original
author:
- first_name: Jérémie A
full_name: Palacci, Jérémie A
id: 8fb92548-2b22-11eb-b7c1-a3f0d08d7c7d
last_name: Palacci
orcid: 0000-0002-7253-9465
- first_name: Stefano
full_name: Sacanna, Stefano
last_name: Sacanna
- first_name: Anaïs
full_name: Abramian, Anaïs
last_name: Abramian
- first_name: Jérémie
full_name: Barral, Jérémie
last_name: Barral
- first_name: Kasey
full_name: Hanson, Kasey
last_name: Hanson
- first_name: Alexander Y.
full_name: Grosberg, Alexander Y.
last_name: Grosberg
- first_name: David J.
full_name: Pine, David J.
last_name: Pine
- first_name: Paul M.
full_name: Chaikin, Paul M.
last_name: Chaikin
citation:
ama: Palacci JA, Sacanna S, Abramian A, et al. Artificial rheotaxis. Science
Advances. 2015;1(4). doi:10.1126/sciadv.1400214
apa: Palacci, J. A., Sacanna, S., Abramian, A., Barral, J., Hanson, K., Grosberg,
A. Y., … Chaikin, P. M. (2015). Artificial rheotaxis. Science Advances.
American Association for the Advancement of Science . https://doi.org/10.1126/sciadv.1400214
chicago: Palacci, Jérémie A, Stefano Sacanna, Anaïs Abramian, Jérémie Barral, Kasey
Hanson, Alexander Y. Grosberg, David J. Pine, and Paul M. Chaikin. “Artificial
Rheotaxis.” Science Advances. American Association for the Advancement
of Science , 2015. https://doi.org/10.1126/sciadv.1400214.
ieee: J. A. Palacci et al., “Artificial rheotaxis,” Science Advances,
vol. 1, no. 4. American Association for the Advancement of Science , 2015.
ista: Palacci JA, Sacanna S, Abramian A, Barral J, Hanson K, Grosberg AY, Pine DJ,
Chaikin PM. 2015. Artificial rheotaxis. Science Advances. 1(4), e1400214.
mla: Palacci, Jérémie A., et al. “Artificial Rheotaxis.” Science Advances,
vol. 1, no. 4, e1400214, American Association for the Advancement of Science ,
2015, doi:10.1126/sciadv.1400214.
short: J.A. Palacci, S. Sacanna, A. Abramian, J. Barral, K. Hanson, A.Y. Grosberg,
D.J. Pine, P.M. Chaikin, Science Advances 1 (2015).
date_created: 2021-02-02T13:15:02Z
date_published: 2015-05-01T00:00:00Z
date_updated: 2023-02-23T13:47:52Z
day: '01'
ddc:
- '530'
doi: 10.1126/sciadv.1400214
extern: '1'
external_id:
arxiv:
- '1505.05111'
pmid:
- '26601175'
file:
- access_level: open_access
checksum: b97d62433581875c1b85210c5f6ae370
content_type: application/pdf
creator: cziletti
date_created: 2021-02-02T13:22:19Z
date_updated: 2021-02-02T13:22:19Z
file_id: '9058'
file_name: 2015_ScienceAdvances_Palacci.pdf
file_size: 2416780
relation: main_file
success: 1
file_date_updated: 2021-02-02T13:22:19Z
has_accepted_license: '1'
intvolume: ' 1'
issue: '4'
language:
- iso: eng
license: https://creativecommons.org/licenses/by-nc/4.0/
month: '05'
oa: 1
oa_version: Published Version
pmid: 1
publication: Science Advances
publication_identifier:
issn:
- 2375-2548
publication_status: published
publisher: 'American Association for the Advancement of Science '
quality_controlled: '1'
scopus_import: '1'
status: public
title: Artificial rheotaxis
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: D865714E-FA4E-11E9-B85B-F5C5E5697425
volume: 1
year: '2015'
...
---
_id: '906'
abstract:
- lang: eng
text: The origin and evolution of novel biochemical functions remains one of the
key questions in molecular evolution. We study recently emerged methacrylate reductase
function that is thought to have emerged in the last century and reported in Geobacter
sulfurreducens strain AM-1. We report the sequence and study the evolution of
the operon coding for the flavin-containing methacrylate reductase (Mrd) and tetraheme
cytochrome (Mcc) in the genome of G. sulfurreducens AM-1. Different types of signal
peptides in functionally interlinked proteins Mrd and Mcc suggest a possible complex
mechanism of biogenesis for chromoproteids of the methacrylate redox system. The
homologs of the Mrd and Mcc sequence found in δ-Proteobacteria and Deferribacteres
are also organized into an operon and their phylogenetic distribution suggested
that these two genes tend to be horizontally transferred together. Specifically,
the mrd and mcc genes from G. sulfurreducens AM-1 are not monophyletic with any
of the homologs found in other Geobacter genomes. The acquisition of methacrylate
reductase function by G. sulfurreducens AM-1 appears linked to a horizontal gene
transfer event. However, the new function of the products of mrd and mcc may have
evolved either prior or subsequent to their acquisition by G. sulfurreducens AM-1.
acknowledgement: 'Funding: The work has been supported by a grant of the HHMI International
Early Career Scientist Program (55007424), the Spanish Ministry of Economy and Competitiveness
(EUI-EURYIP-2011-4320) as part of the EMBO YIP program, two grants from the Spanish
Ministry of Economy and Competitiveness, "Centro de Excelencia Severo Ochoa 2013–2017
(Sev-2012-0208)" and (BFU2012-31329), the European Union and the European Research
Council under grant agreement 335980_EinME. The funders had no role in study design,
data collection and analysis, decision to publish, or preparation of the manuscript.Our
author Dr., Prof. Akimenko Vasilii K. (1942–2013) passed away during work on the
article. Prof. Akimenko was a leading biochemist in IBPM RAS and active researcher
until last days. A number of his work remains unfinished. We mourn premature care
of Prof. Akimenko Vasilii. We thank Heinz Himmelbauer and the CRG Genomic Unit for
the sequencing.'
author:
- first_name: Oksana
full_name: Arkhipova, Oksana V
last_name: Arkhipova
- first_name: Margarita
full_name: Meer, Margarita V
last_name: Meer
- first_name: Galina
full_name: Mikoulinskaia, Galina V
last_name: Mikoulinskaia
- first_name: Marina
full_name: Zakharova, Marina V
last_name: Zakharova
- first_name: Alexander
full_name: Galushko, Alexander S
last_name: Galushko
- first_name: Vasilii
full_name: Akimenko, Vasilii K
last_name: Akimenko
- first_name: Fyodor
full_name: Fyodor Kondrashov
id: 44FDEF62-F248-11E8-B48F-1D18A9856A87
last_name: Kondrashov
orcid: 0000-0001-8243-4694
citation:
ama: Arkhipova O, Meer M, Mikoulinskaia G, et al. Recent origin of the methacrylate
redox system in Geobacter sulfurreducens AM-1 through horizontal gene transfer.
PLoS One. 2015;10(5). doi:10.1371/journal.pone.0125888
apa: Arkhipova, O., Meer, M., Mikoulinskaia, G., Zakharova, M., Galushko, A., Akimenko,
V., & Kondrashov, F. (2015). Recent origin of the methacrylate redox system
in Geobacter sulfurreducens AM-1 through horizontal gene transfer. PLoS One.
Public Library of Science. https://doi.org/10.1371/journal.pone.0125888
chicago: Arkhipova, Oksana, Margarita Meer, Galina Mikoulinskaia, Marina Zakharova,
Alexander Galushko, Vasilii Akimenko, and Fyodor Kondrashov. “Recent Origin of
the Methacrylate Redox System in Geobacter Sulfurreducens AM-1 through Horizontal
Gene Transfer.” PLoS One. Public Library of Science, 2015. https://doi.org/10.1371/journal.pone.0125888.
ieee: O. Arkhipova et al., “Recent origin of the methacrylate redox system
in Geobacter sulfurreducens AM-1 through horizontal gene transfer,” PLoS One,
vol. 10, no. 5. Public Library of Science, 2015.
ista: Arkhipova O, Meer M, Mikoulinskaia G, Zakharova M, Galushko A, Akimenko V,
Kondrashov F. 2015. Recent origin of the methacrylate redox system in Geobacter
sulfurreducens AM-1 through horizontal gene transfer. PLoS One. 10(5).
mla: Arkhipova, Oksana, et al. “Recent Origin of the Methacrylate Redox System in
Geobacter Sulfurreducens AM-1 through Horizontal Gene Transfer.” PLoS One,
vol. 10, no. 5, Public Library of Science, 2015, doi:10.1371/journal.pone.0125888.
short: O. Arkhipova, M. Meer, G. Mikoulinskaia, M. Zakharova, A. Galushko, V. Akimenko,
F. Kondrashov, PLoS One 10 (2015).
date_created: 2018-12-11T11:49:08Z
date_published: 2015-05-11T00:00:00Z
date_updated: 2021-01-12T08:21:48Z
day: '11'
doi: 10.1371/journal.pone.0125888
extern: 1
intvolume: ' 10'
issue: '5'
month: '05'
publication: PLoS One
publication_status: published
publisher: Public Library of Science
publist_id: '6742'
quality_controlled: 0
status: public
title: Recent origin of the methacrylate redox system in Geobacter sulfurreducens
AM-1 through horizontal gene transfer
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
volume: 10
year: '2015'
...
---
_id: '9141'
abstract:
- lang: eng
text: The breaking of internal tides is believed to provide a large part of the
power needed to mix the abyssal ocean and sustain the meridional overturning circulation.
Both the fraction of internal tide energy that is dissipated locally and the resulting
vertical mixing distribution are crucial for the ocean state, but remain poorly
quantified. Here we present a first worldwide estimate of mixing due to internal
tides generated at small‐scale abyssal hills. Our estimate is based on linear
wave theory, a nonlinear parameterization for wave breaking and uses quasi‐global
small‐scale abyssal hill bathymetry, stratification, and tidal data. We show that
a large fraction of abyssal‐hill generated internal tide energy is locally dissipated
over mid‐ocean ridges in the Southern Hemisphere. Significant dissipation occurs
above ridge crests, and, upon rescaling by the local stratification, follows a
monotonic exponential decay with height off the bottom, with a nonuniform decay
scale. We however show that a substantial part of the dissipation occurs over
the smoother flanks of mid‐ocean ridges, and exhibits a middepth maximum due to
the interplay of wave amplitude with stratification. We link the three‐dimensional
map of dissipation to abyssal hills characteristics, ocean stratification, and
tidal forcing, and discuss its potential implementation in time‐evolving parameterizations
for global climate models. Current tidal parameterizations only account for waves
generated at large‐scale satellite‐resolved bathymetry. Our results suggest that
the presence of small‐scale, mostly unresolved abyssal hills could significantly
enhance the spatial inhomogeneity of tidal mixing, particularly above mid‐ocean
ridges in the Southern Hemisphere.
article_processing_charge: No
article_type: original
author:
- first_name: Adrien
full_name: Lefauve, Adrien
last_name: Lefauve
- first_name: Caroline J
full_name: Muller, Caroline J
id: f978ccb0-3f7f-11eb-b193-b0e2bd13182b
last_name: Muller
orcid: 0000-0001-5836-5350
- first_name: Angélique
full_name: Melet, Angélique
last_name: Melet
citation:
ama: 'Lefauve A, Muller CJ, Melet A. A three-dimensional map of tidal dissipation
over abyssal hills. Journal of Geophysical Research: Oceans. 2015;120(7):4760-4777.
doi:10.1002/2014jc010598'
apa: 'Lefauve, A., Muller, C. J., & Melet, A. (2015). A three-dimensional map
of tidal dissipation over abyssal hills. Journal of Geophysical Research: Oceans.
American Geophysical Union. https://doi.org/10.1002/2014jc010598'
chicago: 'Lefauve, Adrien, Caroline J Muller, and Angélique Melet. “A Three-Dimensional
Map of Tidal Dissipation over Abyssal Hills.” Journal of Geophysical Research:
Oceans. American Geophysical Union, 2015. https://doi.org/10.1002/2014jc010598.'
ieee: 'A. Lefauve, C. J. Muller, and A. Melet, “A three-dimensional map of tidal
dissipation over abyssal hills,” Journal of Geophysical Research: Oceans,
vol. 120, no. 7. American Geophysical Union, pp. 4760–4777, 2015.'
ista: 'Lefauve A, Muller CJ, Melet A. 2015. A three-dimensional map of tidal dissipation
over abyssal hills. Journal of Geophysical Research: Oceans. 120(7), 4760–4777.'
mla: 'Lefauve, Adrien, et al. “A Three-Dimensional Map of Tidal Dissipation over
Abyssal Hills.” Journal of Geophysical Research: Oceans, vol. 120, no.
7, American Geophysical Union, 2015, pp. 4760–77, doi:10.1002/2014jc010598.'
short: 'A. Lefauve, C.J. Muller, A. Melet, Journal of Geophysical Research: Oceans
120 (2015) 4760–4777.'
date_created: 2021-02-15T14:21:49Z
date_published: 2015-06-08T00:00:00Z
date_updated: 2022-01-24T13:45:41Z
day: '08'
doi: 10.1002/2014jc010598
extern: '1'
intvolume: ' 120'
issue: '7'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.1002/2014JC010598
month: '06'
oa: 1
oa_version: Published Version
page: 4760-4777
publication: 'Journal of Geophysical Research: Oceans'
publication_identifier:
issn:
- 2169-9275
publication_status: published
publisher: American Geophysical Union
quality_controlled: '1'
status: public
title: A three-dimensional map of tidal dissipation over abyssal hills
type: journal_article
user_id: 8b945eb4-e2f2-11eb-945a-df72226e66a9
volume: 120
year: '2015'
...
---
_id: '928'
abstract:
- lang: eng
text: The actomyosin cytoskeleton is a primary force-generating mechanism in morphogenesis,
thus a robust spatial control of cytoskeletal positioning is essential. In this
report, we demonstrate that actomyosin contractility and planar cell polarity
(PCP) interact in post-mitotic Ciona notochord cells to self-assemble and reposition
actomyosin rings, which play an essential role for cell elongation. Intriguingly,
rings always form at the cells′ anterior edge before migrating towards the center
as contractility increases, reflecting a novel dynamical property of the cortex.
Our drug and genetic manipulations uncover a tug-of-war between contractility,
which localizes cortical flows toward the equator and PCP, which tries to reposition
them. We develop a simple model of the physical forces underlying this tug-of-war,
which quantitatively reproduces our results. We thus propose a quantitative framework
for dissecting the relative contribution of contractility and PCP to the self-assembly
and repositioning of cytoskeletal structures, which should be applicable to other
morphogenetic events.
article_number: e09206
author:
- first_name: Ivonne
full_name: Sehring, Ivonne
last_name: Sehring
- first_name: Pierre
full_name: Recho, Pierre
last_name: Recho
- first_name: Elsa
full_name: Denker, Elsa
last_name: Denker
- first_name: Matthew
full_name: Kourakis, Matthew
last_name: Kourakis
- first_name: Birthe
full_name: Mathiesen, Birthe
last_name: Mathiesen
- first_name: Edouard B
full_name: Hannezo, Edouard B
id: 3A9DB764-F248-11E8-B48F-1D18A9856A87
last_name: Hannezo
orcid: 0000-0001-6005-1561
- first_name: Bo
full_name: Dong, Bo
last_name: Dong
- first_name: Di
full_name: Jiang, Di
last_name: Jiang
citation:
ama: Sehring I, Recho P, Denker E, et al. Assembly and positioning of actomyosin
rings by contractility and planar cell polarity. eLife. 2015;4. doi:10.7554/eLife.09206
apa: Sehring, I., Recho, P., Denker, E., Kourakis, M., Mathiesen, B., Hannezo, E.
B., … Jiang, D. (2015). Assembly and positioning of actomyosin rings by contractility
and planar cell polarity. ELife. eLife Sciences Publications. https://doi.org/10.7554/eLife.09206
chicago: Sehring, Ivonne, Pierre Recho, Elsa Denker, Matthew Kourakis, Birthe Mathiesen,
Edouard B Hannezo, Bo Dong, and Di Jiang. “Assembly and Positioning of Actomyosin
Rings by Contractility and Planar Cell Polarity.” ELife. eLife Sciences
Publications, 2015. https://doi.org/10.7554/eLife.09206.
ieee: I. Sehring et al., “Assembly and positioning of actomyosin rings by
contractility and planar cell polarity,” eLife, vol. 4. eLife Sciences
Publications, 2015.
ista: Sehring I, Recho P, Denker E, Kourakis M, Mathiesen B, Hannezo EB, Dong B,
Jiang D. 2015. Assembly and positioning of actomyosin rings by contractility and
planar cell polarity. eLife. 4, e09206.
mla: Sehring, Ivonne, et al. “Assembly and Positioning of Actomyosin Rings by Contractility
and Planar Cell Polarity.” ELife, vol. 4, e09206, eLife Sciences Publications,
2015, doi:10.7554/eLife.09206.
short: I. Sehring, P. Recho, E. Denker, M. Kourakis, B. Mathiesen, E.B. Hannezo,
B. Dong, D. Jiang, ELife 4 (2015).
date_created: 2018-12-11T11:49:15Z
date_published: 2015-10-21T00:00:00Z
date_updated: 2021-01-12T08:21:58Z
day: '21'
ddc:
- '539'
- '570'
doi: 10.7554/eLife.09206
extern: '1'
file:
- access_level: open_access
checksum: 1e4024b3161adcae4a53a0b3dc8a946e
content_type: application/pdf
creator: dernst
date_created: 2018-12-20T15:50:56Z
date_updated: 2020-07-14T12:48:15Z
file_id: '5769'
file_name: 2015_eLife_Sehring.pdf
file_size: 7202224
relation: main_file
file_date_updated: 2020-07-14T12:48:15Z
has_accepted_license: '1'
intvolume: ' 4'
language:
- iso: eng
month: '10'
oa: 1
oa_version: Published Version
publication: eLife
publication_status: published
publisher: eLife Sciences Publications
publist_id: '6512'
quality_controlled: '1'
status: public
title: Assembly and positioning of actomyosin rings by contractility and planar cell
polarity
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 4
year: '2015'
...
---
_id: '9575'
abstract:
- lang: eng
text: We give several results showing that different discrete structures typically
gain certain spanning substructures (in particular, Hamilton cycles) after a modest
random perturbation. First, we prove that adding linearly many random edges to
a dense k-uniform hypergraph ensures the (asymptotically almost sure) existence
of a perfect matching or a loose Hamilton cycle. The proof involves an interesting
application of Szemerédi's Regularity Lemma, which might be independently useful.
We next prove that digraphs with certain strong expansion properties are pancyclic,
and use this to show that adding a linear number of random edges typically makes
a dense digraph pancyclic. Finally, we prove that perturbing a certain (minimum-degree-dependent)
number of random edges in a tournament typically ensures the existence of multiple
edge-disjoint Hamilton cycles. All our results are tight.
article_processing_charge: No
article_type: original
author:
- first_name: Michael
full_name: Krivelevich, Michael
last_name: Krivelevich
- first_name: Matthew Alan
full_name: Kwan, Matthew Alan
id: 5fca0887-a1db-11eb-95d1-ca9d5e0453b3
last_name: Kwan
orcid: 0000-0002-4003-7567
- first_name: Benny
full_name: Sudakov, Benny
last_name: Sudakov
citation:
ama: Krivelevich M, Kwan MA, Sudakov B. Cycles and matchings in randomly perturbed
digraphs and hypergraphs. Electronic Notes in Discrete Mathematics. 2015;49:181-187.
doi:10.1016/j.endm.2015.06.027
apa: Krivelevich, M., Kwan, M. A., & Sudakov, B. (2015). Cycles and matchings
in randomly perturbed digraphs and hypergraphs. Electronic Notes in Discrete
Mathematics. Elsevier. https://doi.org/10.1016/j.endm.2015.06.027
chicago: Krivelevich, Michael, Matthew Alan Kwan, and Benny Sudakov. “Cycles and
Matchings in Randomly Perturbed Digraphs and Hypergraphs.” Electronic Notes
in Discrete Mathematics. Elsevier, 2015. https://doi.org/10.1016/j.endm.2015.06.027.
ieee: M. Krivelevich, M. A. Kwan, and B. Sudakov, “Cycles and matchings in randomly
perturbed digraphs and hypergraphs,” Electronic Notes in Discrete Mathematics,
vol. 49. Elsevier, pp. 181–187, 2015.
ista: Krivelevich M, Kwan MA, Sudakov B. 2015. Cycles and matchings in randomly
perturbed digraphs and hypergraphs. Electronic Notes in Discrete Mathematics.
49, 181–187.
mla: Krivelevich, Michael, et al. “Cycles and Matchings in Randomly Perturbed Digraphs
and Hypergraphs.” Electronic Notes in Discrete Mathematics, vol. 49, Elsevier,
2015, pp. 181–87, doi:10.1016/j.endm.2015.06.027.
short: M. Krivelevich, M.A. Kwan, B. Sudakov, Electronic Notes in Discrete Mathematics
49 (2015) 181–187.
date_created: 2021-06-21T06:40:34Z
date_published: 2015-11-01T00:00:00Z
date_updated: 2023-02-23T14:01:28Z
day: '01'
doi: 10.1016/j.endm.2015.06.027
extern: '1'
external_id:
arxiv:
- '1501.04816'
intvolume: ' 49'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/1501.04816
month: '11'
oa: 1
oa_version: Preprint
page: 181-187
publication: Electronic Notes in Discrete Mathematics
publication_identifier:
issn:
- 1571-0653
publication_status: published
publisher: Elsevier
quality_controlled: '1'
scopus_import: '1'
status: public
title: Cycles and matchings in randomly perturbed digraphs and hypergraphs
type: journal_article
user_id: 6785fbc1-c503-11eb-8a32-93094b40e1cf
volume: 49
year: '2015'
...
---
_id: '9673'
abstract:
- lang: eng
text: Current strategies of computational crystal plasticity that focus on individual
atoms or dislocations are impractical for real-scale, large-strain problems even
with today’s computing power. Dislocation-density based approaches are a way forward
but a critical issue to address is a realistic description of the interactions
between dislocations. In this paper, a new scheme for computational dynamics of
dislocation-density functions is proposed, which takes full consideration of the
mutual elastic interactions between dislocations based on the Hirth–Lothe formulation.
Other features considered include (i) the continuity nature of the movements of
dislocation densities, (ii) forest hardening, (iii) generation according to high
spatial gradients in dislocation densities, and (iv) annihilation. Numerical implementation
by the finite-volume method, which is well suited for flow problems with high
gradients, is discussed. Numerical examples performed for a single-crystal aluminum
model show typical strength anisotropy behavior comparable to experimental observations.
Furthermore, a detailed case study on small-scale crystal plasticity successfully
captures a number of key experimental features, including power-law relation between
strength and size, low dislocation storage and jerky deformation.
article_processing_charge: No
article_type: original
author:
- first_name: H.S.
full_name: Leung, H.S.
last_name: Leung
- first_name: P.S.S.
full_name: Leung, P.S.S.
last_name: Leung
- first_name: Bingqing
full_name: Cheng, Bingqing
id: cbe3cda4-d82c-11eb-8dc7-8ff94289fcc9
last_name: Cheng
orcid: 0000-0002-3584-9632
- first_name: A.H.W.
full_name: Ngan, A.H.W.
last_name: Ngan
citation:
ama: Leung HS, Leung PSS, Cheng B, Ngan AHW. A new dislocation-density-function
dynamics scheme for computational crystal plasticity by explicit consideration
of dislocation elastic interactions. International Journal of Plasticity.
2015;67:1-25. doi:10.1016/j.ijplas.2014.09.009
apa: Leung, H. S., Leung, P. S. S., Cheng, B., & Ngan, A. H. W. (2015). A new
dislocation-density-function dynamics scheme for computational crystal plasticity
by explicit consideration of dislocation elastic interactions. International
Journal of Plasticity. Elsevier. https://doi.org/10.1016/j.ijplas.2014.09.009
chicago: Leung, H.S., P.S.S. Leung, Bingqing Cheng, and A.H.W. Ngan. “A New Dislocation-Density-Function
Dynamics Scheme for Computational Crystal Plasticity by Explicit Consideration
of Dislocation Elastic Interactions.” International Journal of Plasticity.
Elsevier, 2015. https://doi.org/10.1016/j.ijplas.2014.09.009.
ieee: H. S. Leung, P. S. S. Leung, B. Cheng, and A. H. W. Ngan, “A new dislocation-density-function
dynamics scheme for computational crystal plasticity by explicit consideration
of dislocation elastic interactions,” International Journal of Plasticity,
vol. 67. Elsevier, pp. 1–25, 2015.
ista: Leung HS, Leung PSS, Cheng B, Ngan AHW. 2015. A new dislocation-density-function
dynamics scheme for computational crystal plasticity by explicit consideration
of dislocation elastic interactions. International Journal of Plasticity. 67,
1–25.
mla: Leung, H. S., et al. “A New Dislocation-Density-Function Dynamics Scheme for
Computational Crystal Plasticity by Explicit Consideration of Dislocation Elastic
Interactions.” International Journal of Plasticity, vol. 67, Elsevier,
2015, pp. 1–25, doi:10.1016/j.ijplas.2014.09.009.
short: H.S. Leung, P.S.S. Leung, B. Cheng, A.H.W. Ngan, International Journal of
Plasticity 67 (2015) 1–25.
date_created: 2021-07-15T14:09:32Z
date_published: 2015-04-01T00:00:00Z
date_updated: 2023-02-23T14:04:28Z
day: '01'
doi: 10.1016/j.ijplas.2014.09.009
extern: '1'
intvolume: ' 67'
language:
- iso: eng
month: '04'
oa_version: None
page: 1-25
publication: International Journal of Plasticity
publication_identifier:
issn:
- 0749-6419
publication_status: published
publisher: Elsevier
scopus_import: '1'
status: public
title: A new dislocation-density-function dynamics scheme for computational crystal
plasticity by explicit consideration of dislocation elastic interactions
type: journal_article
user_id: 6785fbc1-c503-11eb-8a32-93094b40e1cf
volume: 67
year: '2015'
...
---
_id: '9688'
abstract:
- lang: eng
text: The properties of the interface between solid and melt are key to solidification
and melting, as the interfacial free energy introduces a kinetic barrier to phase
transitions. This makes solidification happen below the melting temperature, in
out-of-equilibrium conditions at which the interfacial free energy is ill defined.
Here we draw a connection between the atomistic description of a diffuse solid-liquid
interface and its thermodynamic characterization. This framework resolves the
ambiguities in defining the solid-liquid interfacial free energy above and below
the melting temperature. In addition, we introduce a simulation protocol that
allows solid-liquid interfaces to be reversibly created and destroyed at conditions
relevant for experiments. We directly evaluate the value of the interfacial free
energy away from the melting point for a simple but realistic atomic potential,
and find a more complex temperature dependence than the constant positive slope
that has been generally assumed based on phenomenological considerations and that
has been used to interpret experiments. This methodology could be easily extended
to the study of other phase transitions, from condensation to precipitation. Our
analysis can help reconcile the textbook picture of classical nucleation theory
with the growing body of atomistic studies and mesoscale models of solidification.
article_number: '180102'
article_processing_charge: No
article_type: original
author:
- first_name: Bingqing
full_name: Cheng, Bingqing
id: cbe3cda4-d82c-11eb-8dc7-8ff94289fcc9
last_name: Cheng
orcid: 0000-0002-3584-9632
- first_name: Gareth A.
full_name: Tribello, Gareth A.
last_name: Tribello
- first_name: Michele
full_name: Ceriotti, Michele
last_name: Ceriotti
citation:
ama: Cheng B, Tribello GA, Ceriotti M. Solid-liquid interfacial free energy out
of equilibrium. Physical Review B - Condensed Matter and Materials Physics.
2015;92(18). doi:10.1103/physrevb.92.180102
apa: Cheng, B., Tribello, G. A., & Ceriotti, M. (2015). Solid-liquid interfacial
free energy out of equilibrium. Physical Review B - Condensed Matter and Materials
Physics. American Physical Society. https://doi.org/10.1103/physrevb.92.180102
chicago: Cheng, Bingqing, Gareth A. Tribello, and Michele Ceriotti. “Solid-Liquid
Interfacial Free Energy out of Equilibrium.” Physical Review B - Condensed
Matter and Materials Physics. American Physical Society, 2015. https://doi.org/10.1103/physrevb.92.180102.
ieee: B. Cheng, G. A. Tribello, and M. Ceriotti, “Solid-liquid interfacial free
energy out of equilibrium,” Physical Review B - Condensed Matter and Materials
Physics, vol. 92, no. 18. American Physical Society, 2015.
ista: Cheng B, Tribello GA, Ceriotti M. 2015. Solid-liquid interfacial free energy
out of equilibrium. Physical Review B - Condensed Matter and Materials Physics.
92(18), 180102.
mla: Cheng, Bingqing, et al. “Solid-Liquid Interfacial Free Energy out of Equilibrium.”
Physical Review B - Condensed Matter and Materials Physics, vol. 92, no.
18, 180102, American Physical Society, 2015, doi:10.1103/physrevb.92.180102.
short: B. Cheng, G.A. Tribello, M. Ceriotti, Physical Review B - Condensed Matter
and Materials Physics 92 (2015).
date_created: 2021-07-19T10:07:22Z
date_published: 2015-11-01T00:00:00Z
date_updated: 2021-08-09T12:38:49Z
day: '01'
doi: 10.1103/physrevb.92.180102
extern: '1'
external_id:
arxiv:
- '1511.08668'
intvolume: ' 92'
issue: '18'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/1511.08668
month: '11'
oa: 1
oa_version: Preprint
publication: Physical Review B - Condensed Matter and Materials Physics
publication_identifier:
eissn:
- 1550-235X
issn:
- 1098-0121
publication_status: published
publisher: American Physical Society
quality_controlled: '1'
scopus_import: '1'
status: public
title: Solid-liquid interfacial free energy out of equilibrium
type: journal_article
user_id: 6785fbc1-c503-11eb-8a32-93094b40e1cf
volume: 92
year: '2015'
...
---
_id: '9711'
article_processing_charge: No
author:
- first_name: Guillaume
full_name: Chevereau, Guillaume
id: 424D78A0-F248-11E8-B48F-1D18A9856A87
last_name: Chevereau
- first_name: Marta
full_name: Lukacisinova, Marta
id: 4342E402-F248-11E8-B48F-1D18A9856A87
last_name: Lukacisinova
orcid: 0000-0002-2519-8004
- first_name: Tugce
full_name: Batur, Tugce
last_name: Batur
- first_name: Aysegul
full_name: Guvenek, Aysegul
last_name: Guvenek
- first_name: Dilay Hazal
full_name: Ayhan, Dilay Hazal
last_name: Ayhan
- first_name: Erdal
full_name: Toprak, Erdal
last_name: Toprak
- first_name: Mark Tobias
full_name: Bollenbach, Mark Tobias
id: 3E6DB97A-F248-11E8-B48F-1D18A9856A87
last_name: Bollenbach
orcid: 0000-0003-4398-476X
citation:
ama: Chevereau G, Lukacisinova M, Batur T, et al. Excel file containing the raw
data for all figures. 2015. doi:10.1371/journal.pbio.1002299.s001
apa: Chevereau, G., Lukacisinova, M., Batur, T., Guvenek, A., Ayhan, D. H., Toprak,
E., & Bollenbach, M. T. (2015). Excel file containing the raw data for all
figures. Public Library of Science. https://doi.org/10.1371/journal.pbio.1002299.s001
chicago: Chevereau, Guillaume, Marta Lukacisinova, Tugce Batur, Aysegul Guvenek,
Dilay Hazal Ayhan, Erdal Toprak, and Mark Tobias Bollenbach. “Excel File Containing
the Raw Data for All Figures.” Public Library of Science, 2015. https://doi.org/10.1371/journal.pbio.1002299.s001.
ieee: G. Chevereau et al., “Excel file containing the raw data for all figures.”
Public Library of Science, 2015.
ista: Chevereau G, Lukacisinova M, Batur T, Guvenek A, Ayhan DH, Toprak E, Bollenbach
MT. 2015. Excel file containing the raw data for all figures, Public Library of
Science, 10.1371/journal.pbio.1002299.s001.
mla: Chevereau, Guillaume, et al. Excel File Containing the Raw Data for All
Figures. Public Library of Science, 2015, doi:10.1371/journal.pbio.1002299.s001.
short: G. Chevereau, M. Lukacisinova, T. Batur, A. Guvenek, D.H. Ayhan, E. Toprak,
M.T. Bollenbach, (2015).
date_created: 2021-07-23T11:53:50Z
date_published: 2015-11-18T00:00:00Z
date_updated: 2023-02-23T10:07:02Z
day: '18'
department:
- _id: ToBo
doi: 10.1371/journal.pbio.1002299.s001
month: '11'
oa_version: Published Version
publisher: Public Library of Science
related_material:
record:
- id: '1619'
relation: used_in_publication
status: public
status: public
title: Excel file containing the raw data for all figures
type: research_data_reference
user_id: 6785fbc1-c503-11eb-8a32-93094b40e1cf
year: '2015'
...
---
_id: '1855'
abstract:
- lang: eng
text: 'Summary: Declining populations of bee pollinators are a cause of concern,
with major repercussions for biodiversity loss and food security. RNA viruses
associated with honeybees represent a potential threat to other insect pollinators,
but the extent of this threat is poorly understood. This study aims to attain
a detailed understanding of the current and ongoing risk of emerging infectious
disease (EID) transmission between managed and wild pollinator species across
a wide range of RNA viruses. Within a structured large-scale national survey across
26 independent sites, we quantify the prevalence and pathogen loads of multiple
RNA viruses in co-occurring managed honeybee (Apis mellifera) and wild bumblebee
(Bombus spp.) populations. We then construct models that compare virus prevalence
between wild and managed pollinators. Multiple RNA viruses associated with honeybees
are widespread in sympatric wild bumblebee populations. Virus prevalence in honeybees
is a significant predictor of virus prevalence in bumblebees, but we remain cautious
in speculating over the principle direction of pathogen transmission. We demonstrate
species-specific differences in prevalence, indicating significant variation in
disease susceptibility or tolerance. Pathogen loads within individual bumblebees
may be high and in the case of at least one RNA virus, prevalence is higher in
wild bumblebees than in managed honeybee populations. Our findings indicate widespread
transmission of RNA viruses between managed and wild bee pollinators, pointing
to an interconnected network of potential disease pressures within and among pollinator
species. In the context of the biodiversity crisis, our study emphasizes the importance
of targeting a wide range of pathogens and defining host associations when considering
potential drivers of population decline.'
acknowledgement: We thank J.R. de Miranda, L. De Smet and D. de Graaf for supplying
qRT-PCR and MLPA positive controls, respectively, in the form of plasmids. This
work was supported by the Insect Pollinators Initiative (IPI grants BB/1000100/1
and BB/I000151/1). The IPI is funded jointly by the Biotechnology and Biological
Sciences Research Council, the Department for Environment, Food and Rural Affairs,
the Natural Environment Research Council, The Scottish Government and The Wellcome
Trust, under the Living with Environmental Change Partnership.
article_processing_charge: No
article_type: original
author:
- first_name: Dino
full_name: Mcmahon, Dino
last_name: Mcmahon
- first_name: Matthias
full_name: Fürst, Matthias
id: 393B1196-F248-11E8-B48F-1D18A9856A87
last_name: Fürst
orcid: 0000-0002-3712-925X
- first_name: Jesicca
full_name: Caspar, Jesicca
last_name: Caspar
- first_name: Panagiotis
full_name: Theodorou, Panagiotis
last_name: Theodorou
- first_name: Mark
full_name: Brown, Mark
last_name: Brown
- first_name: Robert
full_name: Paxton, Robert
last_name: Paxton
citation:
ama: 'Mcmahon D, Fürst M, Caspar J, Theodorou P, Brown M, Paxton R. A sting in the
spit: Widespread cross-infection of multiple RNA viruses across wild and managed
bees. Journal of Animal Ecology. 2015;84(3):615-624. doi:10.1111/1365-2656.12345'
apa: 'Mcmahon, D., Fürst, M., Caspar, J., Theodorou, P., Brown, M., & Paxton,
R. (2015). A sting in the spit: Widespread cross-infection of multiple RNA viruses
across wild and managed bees. Journal of Animal Ecology. Wiley. https://doi.org/10.1111/1365-2656.12345'
chicago: 'Mcmahon, Dino, Matthias Fürst, Jesicca Caspar, Panagiotis Theodorou, Mark
Brown, and Robert Paxton. “A Sting in the Spit: Widespread Cross-Infection of
Multiple RNA Viruses across Wild and Managed Bees.” Journal of Animal Ecology.
Wiley, 2015. https://doi.org/10.1111/1365-2656.12345.'
ieee: 'D. Mcmahon, M. Fürst, J. Caspar, P. Theodorou, M. Brown, and R. Paxton, “A
sting in the spit: Widespread cross-infection of multiple RNA viruses across wild
and managed bees,” Journal of Animal Ecology, vol. 84, no. 3. Wiley, pp.
615–624, 2015.'
ista: 'Mcmahon D, Fürst M, Caspar J, Theodorou P, Brown M, Paxton R. 2015. A sting
in the spit: Widespread cross-infection of multiple RNA viruses across wild and
managed bees. Journal of Animal Ecology. 84(3), 615–624.'
mla: 'Mcmahon, Dino, et al. “A Sting in the Spit: Widespread Cross-Infection of
Multiple RNA Viruses across Wild and Managed Bees.” Journal of Animal Ecology,
vol. 84, no. 3, Wiley, 2015, pp. 615–24, doi:10.1111/1365-2656.12345.'
short: D. Mcmahon, M. Fürst, J. Caspar, P. Theodorou, M. Brown, R. Paxton, Journal
of Animal Ecology 84 (2015) 615–624.
date_created: 2018-12-11T11:54:23Z
date_published: 2015-03-03T00:00:00Z
date_updated: 2023-02-23T14:06:09Z
day: '03'
ddc:
- '570'
department:
- _id: SyCr
doi: 10.1111/1365-2656.12345
external_id:
pmid:
- '25646973'
file:
- access_level: open_access
checksum: 542a0b9b07e78050a81b35f26f0b82da
content_type: application/pdf
creator: system
date_created: 2018-12-12T10:18:29Z
date_updated: 2020-07-14T12:45:19Z
file_id: '5350'
file_name: IST-2016-460-v1+1_McMahon_et_al-2015-Journal_of_Animal_Ecology.pdf
file_size: 1823045
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intvolume: ' 84'
issue: '3'
language:
- iso: eng
month: '03'
oa: 1
oa_version: Published Version
page: 615 - 624
pmid: 1
publication: Journal of Animal Ecology
publication_status: published
publisher: Wiley
publist_id: '5245'
pubrep_id: '460'
quality_controlled: '1'
related_material:
record:
- id: '9720'
relation: research_data
status: public
scopus_import: '1'
status: public
title: 'A sting in the spit: Widespread cross-infection of multiple RNA viruses across
wild and managed bees'
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: 6785fbc1-c503-11eb-8a32-93094b40e1cf
volume: 84
year: '2015'
...
---
_id: '1830'
abstract:
- lang: eng
text: To prevent epidemics, insect societies have evolved collective disease defences
that are highly effective at curing exposed individuals and limiting disease transmission
to healthy group members. Grooming is an important sanitary behaviour—either performed
towards oneself (self-grooming) or towards others (allogrooming)—to remove infectious
agents from the body surface of exposed individuals, but at the risk of disease
contraction by the groomer. We use garden ants (Lasius neglectus) and the fungal
pathogen Metarhizium as a model system to study how pathogen presence affects
self-grooming and allogrooming between exposed and healthy individuals. We develop
an epidemiological SIS model to explore how experimentally observed grooming patterns
affect disease spread within the colony, thereby providing a direct link between
the expression and direction of sanitary behaviours, and their effects on colony-level
epidemiology. We find that fungus-exposed ants increase self-grooming, while simultaneously
decreasing allogrooming. This behavioural modulation seems universally adaptive
and is predicted to contain disease spread in a great variety of host–pathogen
systems. In contrast, allogrooming directed towards pathogen-exposed individuals
might both increase and decrease disease risk. Our model reveals that the effect
of allogrooming depends on the balance between pathogen infectiousness and efficiency
of social host defences, which are likely to vary across host–pathogen systems.
acknowledgement: We thank Meghan L. Vyleta for the genetical fungal strain characterization
and Eva Sixt for ant drawings, Matthias Konrad for discussion and Christopher D.
Pull, Barbara Casillas-Peréz, Sebastian Novak, as well as three anonymous reviewers
and the theme issue editors Peter Kappeler and Charlie Nunn for valuable comments
on the manuscript.
article_processing_charge: No
article_type: original
author:
- first_name: Fabian
full_name: Theis, Fabian
last_name: Theis
- first_name: Line V
full_name: Ugelvig, Line V
id: 3DC97C8E-F248-11E8-B48F-1D18A9856A87
last_name: Ugelvig
orcid: 0000-0003-1832-8883
- first_name: Carsten
full_name: Marr, Carsten
last_name: Marr
- first_name: Sylvia
full_name: Cremer, Sylvia
id: 2F64EC8C-F248-11E8-B48F-1D18A9856A87
last_name: Cremer
orcid: 0000-0002-2193-3868
citation:
ama: Theis F, Ugelvig LV, Marr C, Cremer S. Opposing effects of allogrooming on
disease transmission in ant societies. Philosophical Transactions of the Royal
Society of London Series B, Biological Sciences. 2015;370(1669). doi:10.1098/rstb.2014.0108
apa: Theis, F., Ugelvig, L. V., Marr, C., & Cremer, S. (2015). Opposing effects
of allogrooming on disease transmission in ant societies. Philosophical Transactions
of the Royal Society of London. Series B, Biological Sciences. Royal Society,
The. https://doi.org/10.1098/rstb.2014.0108
chicago: Theis, Fabian, Line V Ugelvig, Carsten Marr, and Sylvia Cremer. “Opposing
Effects of Allogrooming on Disease Transmission in Ant Societies.” Philosophical
Transactions of the Royal Society of London. Series B, Biological Sciences.
Royal Society, The, 2015. https://doi.org/10.1098/rstb.2014.0108.
ieee: F. Theis, L. V. Ugelvig, C. Marr, and S. Cremer, “Opposing effects of allogrooming
on disease transmission in ant societies,” Philosophical Transactions of the
Royal Society of London. Series B, Biological Sciences, vol. 370, no. 1669.
Royal Society, The, 2015.
ista: Theis F, Ugelvig LV, Marr C, Cremer S. 2015. Opposing effects of allogrooming
on disease transmission in ant societies. Philosophical Transactions of the Royal
Society of London. Series B, Biological Sciences. 370(1669).
mla: Theis, Fabian, et al. “Opposing Effects of Allogrooming on Disease Transmission
in Ant Societies.” Philosophical Transactions of the Royal Society of London.
Series B, Biological Sciences, vol. 370, no. 1669, Royal Society, The, 2015,
doi:10.1098/rstb.2014.0108.
short: F. Theis, L.V. Ugelvig, C. Marr, S. Cremer, Philosophical Transactions of
the Royal Society of London. Series B, Biological Sciences 370 (2015).
date_created: 2018-12-11T11:54:15Z
date_published: 2015-05-26T00:00:00Z
date_updated: 2023-02-23T14:06:12Z
day: '26'
department:
- _id: SyCr
doi: 10.1098/rstb.2014.0108
ec_funded: 1
external_id:
pmid:
- '25870394'
intvolume: ' 370'
issue: '1669'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4410374/
month: '05'
oa: 1
oa_version: Submitted Version
pmid: 1
project:
- _id: 25DC711C-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '243071'
name: 'Social Vaccination in Ant Colonies: from Individual Mechanisms to Society
Effects'
- _id: 25DDF0F0-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '302004'
name: 'Pathogen Detectors Collective disease defence and pathogen detection abilities
in ant societies: a chemo-neuro-immunological approach'
- _id: 25E0E184-B435-11E9-9278-68D0E5697425
name: Antnet
- _id: 25E24DB2-B435-11E9-9278-68D0E5697425
name: Fellowship of Wissenschaftskolleg zu Berlin
publication: Philosophical Transactions of the Royal Society of London. Series B,
Biological Sciences
publication_identifier:
eissn:
- 1471-2970
issn:
- 0962-8436
publication_status: published
publisher: Royal Society, The
publist_id: '5273'
quality_controlled: '1'
related_material:
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relation: research_data
status: public
scopus_import: '1'
status: public
title: Opposing effects of allogrooming on disease transmission in ant societies
type: journal_article
user_id: 6785fbc1-c503-11eb-8a32-93094b40e1cf
volume: 370
year: '2015'
...
---
_id: '9721'
abstract:
- lang: eng
text: To prevent epidemics, insect societies have evolved collective disease defences
that are highly effective at curing exposed individuals and limiting disease transmission
to healthy group members. Grooming is an important sanitary behaviour—either performed
towards oneself (self-grooming) or towards others (allogrooming)—to remove infectious
agents from the body surface of exposed individuals, but at the risk of disease
contraction by the groomer. We use garden ants (Lasius neglectus) and the fungal
pathogen Metarhizium as a model system to study how pathogen presence affects
self-grooming and allogrooming between exposed and healthy individuals. We develop
an epidemiological SIS model to explore how experimentally observed grooming patterns
affect disease spread within the colony, thereby providing a direct link between
the expression and direction of sanitary behaviours, and their effects on colony-level
epidemiology. We find that fungus-exposed ants increase self-grooming, while simultaneously
decreasing allogrooming. This behavioural modulation seems universally adaptive
and is predicted to contain disease spread in a great variety of host–pathogen
systems. In contrast, allogrooming directed towards pathogen-exposed individuals
might both increase and decrease disease risk. Our model reveals that the effect
of allogrooming depends on the balance between pathogen infectiousness and efficiency
of social host defences, which are likely to vary across host–pathogen systems.
article_processing_charge: No
author:
- first_name: Fabian
full_name: Theis, Fabian
last_name: Theis
- first_name: Line V
full_name: Ugelvig, Line V
id: 3DC97C8E-F248-11E8-B48F-1D18A9856A87
last_name: Ugelvig
orcid: 0000-0003-1832-8883
- first_name: Carsten
full_name: Marr, Carsten
last_name: Marr
- first_name: Sylvia
full_name: Cremer, Sylvia
id: 2F64EC8C-F248-11E8-B48F-1D18A9856A87
last_name: Cremer
orcid: 0000-0002-2193-3868
citation:
ama: 'Theis F, Ugelvig LV, Marr C, Cremer S. Data from: Opposing effects of allogrooming
on disease transmission in ant societies. 2015. doi:10.5061/dryad.dj2bf'
apa: 'Theis, F., Ugelvig, L. V., Marr, C., & Cremer, S. (2015). Data from: Opposing
effects of allogrooming on disease transmission in ant societies. Dryad. https://doi.org/10.5061/dryad.dj2bf'
chicago: 'Theis, Fabian, Line V Ugelvig, Carsten Marr, and Sylvia Cremer. “Data
from: Opposing Effects of Allogrooming on Disease Transmission in Ant Societies.”
Dryad, 2015. https://doi.org/10.5061/dryad.dj2bf.'
ieee: 'F. Theis, L. V. Ugelvig, C. Marr, and S. Cremer, “Data from: Opposing effects
of allogrooming on disease transmission in ant societies.” Dryad, 2015.'
ista: 'Theis F, Ugelvig LV, Marr C, Cremer S. 2015. Data from: Opposing effects
of allogrooming on disease transmission in ant societies, Dryad, 10.5061/dryad.dj2bf.'
mla: 'Theis, Fabian, et al. Data from: Opposing Effects of Allogrooming on Disease
Transmission in Ant Societies. Dryad, 2015, doi:10.5061/dryad.dj2bf.'
short: F. Theis, L.V. Ugelvig, C. Marr, S. Cremer, (2015).
date_created: 2021-07-26T09:38:36Z
date_published: 2015-12-29T00:00:00Z
date_updated: 2023-02-23T10:16:22Z
day: '29'
department:
- _id: SyCr
doi: 10.5061/dryad.dj2bf
main_file_link:
- open_access: '1'
url: https://doi.org/10.5061/dryad.dj2bf
month: '12'
oa: 1
oa_version: Published Version
publisher: Dryad
related_material:
record:
- id: '1830'
relation: used_in_publication
status: public
status: public
title: 'Data from: Opposing effects of allogrooming on disease transmission in ant
societies'
type: research_data_reference
user_id: 6785fbc1-c503-11eb-8a32-93094b40e1cf
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...
---
_id: '9718'
article_processing_charge: No
author:
- first_name: Tamar
full_name: Friedlander, Tamar
id: 36A5845C-F248-11E8-B48F-1D18A9856A87
last_name: Friedlander
- first_name: Avraham E.
full_name: Mayo, Avraham E.
last_name: Mayo
- first_name: Tsvi
full_name: Tlusty, Tsvi
last_name: Tlusty
- first_name: Uri
full_name: Alon, Uri
last_name: Alon
citation:
ama: Friedlander T, Mayo AE, Tlusty T, Alon U. Supporting information text. 2015.
doi:10.1371/journal.pcbi.1004055.s001
apa: Friedlander, T., Mayo, A. E., Tlusty, T., & Alon, U. (2015). Supporting
information text. Public Library of Science. https://doi.org/10.1371/journal.pcbi.1004055.s001
chicago: Friedlander, Tamar, Avraham E. Mayo, Tsvi Tlusty, and Uri Alon. “Supporting
Information Text.” Public Library of Science, 2015. https://doi.org/10.1371/journal.pcbi.1004055.s001.
ieee: T. Friedlander, A. E. Mayo, T. Tlusty, and U. Alon, “Supporting information
text.” Public Library of Science, 2015.
ista: Friedlander T, Mayo AE, Tlusty T, Alon U. 2015. Supporting information text,
Public Library of Science, 10.1371/journal.pcbi.1004055.s001.
mla: Friedlander, Tamar, et al. Supporting Information Text. Public Library
of Science, 2015, doi:10.1371/journal.pcbi.1004055.s001.
short: T. Friedlander, A.E. Mayo, T. Tlusty, U. Alon, (2015).
date_created: 2021-07-26T08:35:23Z
date_published: 2015-03-23T00:00:00Z
date_updated: 2023-02-23T10:16:13Z
day: '23'
department:
- _id: GaTk
doi: 10.1371/journal.pcbi.1004055.s001
month: '03'
oa_version: Published Version
publisher: Public Library of Science
related_material:
record:
- id: '1827'
relation: used_in_publication
status: public
status: public
title: Supporting information text
type: research_data_reference
user_id: 6785fbc1-c503-11eb-8a32-93094b40e1cf
year: '2015'
...
---
_id: '1793'
abstract:
- lang: eng
text: We present a software platform for reconstructing and analyzing the growth
of a plant root system from a time-series of 3D voxelized shapes. It aligns the
shapes with each other, constructs a geometric graph representation together with
the function that records the time of growth, and organizes the branches into
a hierarchy that reflects the order of creation. The software includes the automatic
computation of structural and dynamic traits for each root in the system enabling
the quantification of growth on fine-scale. These are important advances in plant
phenotyping with applications to the study of genetic and environmental influences
on growth.
article_number: e0127657
author:
- first_name: Olga
full_name: Symonova, Olga
id: 3C0C7BC6-F248-11E8-B48F-1D18A9856A87
last_name: Symonova
- first_name: Christopher
full_name: Topp, Christopher
last_name: Topp
- first_name: Herbert
full_name: Edelsbrunner, Herbert
id: 3FB178DA-F248-11E8-B48F-1D18A9856A87
last_name: Edelsbrunner
orcid: 0000-0002-9823-6833
citation:
ama: 'Symonova O, Topp C, Edelsbrunner H. DynamicRoots: A software platform for
the reconstruction and analysis of growing plant roots. PLoS One. 2015;10(6).
doi:10.1371/journal.pone.0127657'
apa: 'Symonova, O., Topp, C., & Edelsbrunner, H. (2015). DynamicRoots: A software
platform for the reconstruction and analysis of growing plant roots. PLoS One.
Public Library of Science. https://doi.org/10.1371/journal.pone.0127657'
chicago: 'Symonova, Olga, Christopher Topp, and Herbert Edelsbrunner. “DynamicRoots:
A Software Platform for the Reconstruction and Analysis of Growing Plant Roots.”
PLoS One. Public Library of Science, 2015. https://doi.org/10.1371/journal.pone.0127657.'
ieee: 'O. Symonova, C. Topp, and H. Edelsbrunner, “DynamicRoots: A software platform
for the reconstruction and analysis of growing plant roots,” PLoS One,
vol. 10, no. 6. Public Library of Science, 2015.'
ista: 'Symonova O, Topp C, Edelsbrunner H. 2015. DynamicRoots: A software platform
for the reconstruction and analysis of growing plant roots. PLoS One. 10(6), e0127657.'
mla: 'Symonova, Olga, et al. “DynamicRoots: A Software Platform for the Reconstruction
and Analysis of Growing Plant Roots.” PLoS One, vol. 10, no. 6, e0127657,
Public Library of Science, 2015, doi:10.1371/journal.pone.0127657.'
short: O. Symonova, C. Topp, H. Edelsbrunner, PLoS One 10 (2015).
date_created: 2018-12-11T11:54:02Z
date_published: 2015-06-01T00:00:00Z
date_updated: 2023-02-23T14:06:33Z
day: '01'
ddc:
- '000'
department:
- _id: MaJö
- _id: HeEd
doi: 10.1371/journal.pone.0127657
file:
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checksum: d20f26461ca575276ad3ed9ce4bfc787
content_type: application/pdf
creator: system
date_created: 2018-12-12T10:15:30Z
date_updated: 2020-07-14T12:45:16Z
file_id: '5150'
file_name: IST-2016-454-v1+1_journal.pone.0127657.pdf
file_size: 1850825
relation: main_file
file_date_updated: 2020-07-14T12:45:16Z
has_accepted_license: '1'
intvolume: ' 10'
issue: '6'
language:
- iso: eng
month: '06'
oa: 1
oa_version: Published Version
publication: PLoS One
publication_status: published
publisher: Public Library of Science
publist_id: '5318'
pubrep_id: '454'
quality_controlled: '1'
related_material:
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relation: research_data
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scopus_import: 1
status: public
title: 'DynamicRoots: A software platform for the reconstruction and analysis of growing
plant roots'
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 10
year: '2015'
...
---
_id: '9737'
article_processing_charge: No
author:
- first_name: Olga
full_name: Symonova, Olga
id: 3C0C7BC6-F248-11E8-B48F-1D18A9856A87
last_name: Symonova
- first_name: Christopher
full_name: Topp, Christopher
last_name: Topp
- first_name: Herbert
full_name: Edelsbrunner, Herbert
id: 3FB178DA-F248-11E8-B48F-1D18A9856A87
last_name: Edelsbrunner
orcid: 0000-0002-9823-6833
citation:
ama: Symonova O, Topp C, Edelsbrunner H. Root traits computed by DynamicRoots for
the maize root shown in fig 2. 2015. doi:10.1371/journal.pone.0127657.s001
apa: Symonova, O., Topp, C., & Edelsbrunner, H. (2015). Root traits computed
by DynamicRoots for the maize root shown in fig 2. Public Library of Science.
https://doi.org/10.1371/journal.pone.0127657.s001
chicago: Symonova, Olga, Christopher Topp, and Herbert Edelsbrunner. “Root Traits
Computed by DynamicRoots for the Maize Root Shown in Fig 2.” Public Library of
Science, 2015. https://doi.org/10.1371/journal.pone.0127657.s001.
ieee: O. Symonova, C. Topp, and H. Edelsbrunner, “Root traits computed by DynamicRoots
for the maize root shown in fig 2.” Public Library of Science, 2015.
ista: Symonova O, Topp C, Edelsbrunner H. 2015. Root traits computed by DynamicRoots
for the maize root shown in fig 2, Public Library of Science, 10.1371/journal.pone.0127657.s001.
mla: Symonova, Olga, et al. Root Traits Computed by DynamicRoots for the Maize
Root Shown in Fig 2. Public Library of Science, 2015, doi:10.1371/journal.pone.0127657.s001.
short: O. Symonova, C. Topp, H. Edelsbrunner, (2015).
date_created: 2021-07-28T06:20:13Z
date_published: 2015-06-01T00:00:00Z
date_updated: 2023-02-23T10:14:42Z
day: '01'
department:
- _id: MaJö
- _id: HeEd
doi: 10.1371/journal.pone.0127657.s001
month: '06'
oa_version: Published Version
publisher: Public Library of Science
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status: public
title: Root traits computed by DynamicRoots for the maize root shown in fig 2
type: research_data_reference
user_id: 6785fbc1-c503-11eb-8a32-93094b40e1cf
year: '2015'
...
---
_id: '1827'
abstract:
- lang: eng
text: Bow-tie or hourglass structure is a common architectural feature found in
many biological systems. A bow-tie in a multi-layered structure occurs when intermediate
layers have much fewer components than the input and output layers. Examples include
metabolism where a handful of building blocks mediate between multiple input nutrients
and multiple output biomass components, and signaling networks where information
from numerous receptor types passes through a small set of signaling pathways
to regulate multiple output genes. Little is known, however, about how bow-tie
architectures evolve. Here, we address the evolution of bow-tie architectures
using simulations of multi-layered systems evolving to fulfill a given input-output
goal. We find that bow-ties spontaneously evolve when the information in the evolutionary
goal can be compressed. Mathematically speaking, bow-ties evolve when the rank
of the input-output matrix describing the evolutionary goal is deficient. The
maximal compression possible (the rank of the goal) determines the size of the
narrowest part of the network—that is the bow-tie. A further requirement is that
a process is active to reduce the number of links in the network, such as product-rule
mutations, otherwise a non-bow-tie solution is found in the evolutionary simulations.
This offers a mechanism to understand a common architectural principle of biological
systems, and a way to quantitate the effective rank of the goals under which they
evolved.
article_processing_charge: No
author:
- first_name: Tamar
full_name: Friedlander, Tamar
id: 36A5845C-F248-11E8-B48F-1D18A9856A87
last_name: Friedlander
- first_name: Avraham
full_name: Mayo, Avraham
last_name: Mayo
- first_name: Tsvi
full_name: Tlusty, Tsvi
last_name: Tlusty
- first_name: Uri
full_name: Alon, Uri
last_name: Alon
citation:
ama: Friedlander T, Mayo A, Tlusty T, Alon U. Evolution of bow-tie architectures
in biology. PLoS Computational Biology. 2015;11(3). doi:10.1371/journal.pcbi.1004055
apa: Friedlander, T., Mayo, A., Tlusty, T., & Alon, U. (2015). Evolution of
bow-tie architectures in biology. PLoS Computational Biology. Public Library
of Science. https://doi.org/10.1371/journal.pcbi.1004055
chicago: Friedlander, Tamar, Avraham Mayo, Tsvi Tlusty, and Uri Alon. “Evolution
of Bow-Tie Architectures in Biology.” PLoS Computational Biology. Public
Library of Science, 2015. https://doi.org/10.1371/journal.pcbi.1004055.
ieee: T. Friedlander, A. Mayo, T. Tlusty, and U. Alon, “Evolution of bow-tie architectures
in biology,” PLoS Computational Biology, vol. 11, no. 3. Public Library
of Science, 2015.
ista: Friedlander T, Mayo A, Tlusty T, Alon U. 2015. Evolution of bow-tie architectures
in biology. PLoS Computational Biology. 11(3).
mla: Friedlander, Tamar, et al. “Evolution of Bow-Tie Architectures in Biology.”
PLoS Computational Biology, vol. 11, no. 3, Public Library of Science,
2015, doi:10.1371/journal.pcbi.1004055.
short: T. Friedlander, A. Mayo, T. Tlusty, U. Alon, PLoS Computational Biology 11
(2015).
date_created: 2018-12-11T11:54:14Z
date_published: 2015-03-23T00:00:00Z
date_updated: 2023-02-23T14:07:51Z
day: '23'
ddc:
- '576'
department:
- _id: GaTk
doi: 10.1371/journal.pcbi.1004055
ec_funded: 1
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oa_version: Published Version
project:
- _id: 25681D80-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '291734'
name: International IST Postdoc Fellowship Programme
publication: PLoS Computational Biology
publication_status: published
publisher: Public Library of Science
publist_id: '5278'
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title: Evolution of bow-tie architectures in biology
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
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volume: 11
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...
---
_id: '1809'
abstract:
- lang: eng
text: 'Background: Indirect genetic effects (IGEs) occur when genes expressed in
one individual alter the expression of traits in social partners. Previous studies
focused on the evolutionary consequences and evolutionary dynamics of IGEs, using
equilibrium solutions to predict phenotypes in subsequent generations. However,
whether or not such steady states may be reached may depend on the dynamics of
interactions themselves. Results: In our study, we focus on the dynamics of social
interactions and indirect genetic effects and investigate how they modify phenotypes
over time. Unlike previous IGE studies, we do not analyse evolutionary dynamics;
rather we consider within-individual phenotypic changes, also referred to as phenotypic
plasticity. We analyse iterative interactions, when individuals interact in a
series of discontinuous events, and investigate the stability of steady state
solutions and the dependence on model parameters, such as population size, strength,
and the nature of interactions. We show that for interactions where a feedback
loop occurs, the possible parameter space of interaction strength is fairly limited,
affecting the evolutionary consequences of IGEs. We discuss the implications of
our results for current IGE model predictions and their limitations.'
author:
- first_name: Barbora
full_name: Trubenova, Barbora
id: 42302D54-F248-11E8-B48F-1D18A9856A87
last_name: Trubenova
orcid: 0000-0002-6873-2967
- first_name: Sebastian
full_name: Novak, Sebastian
id: 461468AE-F248-11E8-B48F-1D18A9856A87
last_name: Novak
- first_name: Reinmar
full_name: Hager, Reinmar
last_name: Hager
citation:
ama: Trubenova B, Novak S, Hager R. Indirect genetic effects and the dynamics of
social interactions. PLoS One. 2015;10(5). doi:10.1371/journal.pone.0126907
apa: Trubenova, B., Novak, S., & Hager, R. (2015). Indirect genetic effects
and the dynamics of social interactions. PLoS One. Public Library of Science.
https://doi.org/10.1371/journal.pone.0126907
chicago: Trubenova, Barbora, Sebastian Novak, and Reinmar Hager. “Indirect Genetic
Effects and the Dynamics of Social Interactions.” PLoS One. Public Library
of Science, 2015. https://doi.org/10.1371/journal.pone.0126907.
ieee: B. Trubenova, S. Novak, and R. Hager, “Indirect genetic effects and the dynamics
of social interactions,” PLoS One, vol. 10, no. 5. Public Library of Science,
2015.
ista: Trubenova B, Novak S, Hager R. 2015. Indirect genetic effects and the dynamics
of social interactions. PLoS One. 10(5).
mla: Trubenova, Barbora, et al. “Indirect Genetic Effects and the Dynamics of Social
Interactions.” PLoS One, vol. 10, no. 5, Public Library of Science, 2015,
doi:10.1371/journal.pone.0126907.
short: B. Trubenova, S. Novak, R. Hager, PLoS One 10 (2015).
date_created: 2018-12-11T11:54:07Z
date_published: 2015-05-18T00:00:00Z
date_updated: 2023-02-23T14:07:48Z
day: '18'
ddc:
- '570'
- '576'
department:
- _id: NiBa
doi: 10.1371/journal.pone.0126907
file:
- access_level: open_access
checksum: d3a4a58ef4bd3b3e2f32b7fd7af4a743
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creator: system
date_created: 2018-12-12T10:09:07Z
date_updated: 2020-07-14T12:45:17Z
file_id: '4730'
file_name: IST-2016-453-v1+1_journal.pone.0126907.pdf
file_size: 2748982
relation: main_file
file_date_updated: 2020-07-14T12:45:17Z
has_accepted_license: '1'
intvolume: ' 10'
issue: '5'
language:
- iso: eng
month: '05'
oa: 1
oa_version: Published Version
publication: PLoS One
publication_status: published
publisher: Public Library of Science
publist_id: '5299'
pubrep_id: '453'
quality_controlled: '1'
related_material:
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- id: '9715'
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relation: research_data
status: public
scopus_import: 1
status: public
title: Indirect genetic effects and the dynamics of social interactions
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 10
year: '2015'
...
---
_id: '9772'
article_processing_charge: No
author:
- first_name: Barbora
full_name: Trubenova, Barbora
id: 42302D54-F248-11E8-B48F-1D18A9856A87
last_name: Trubenova
orcid: 0000-0002-6873-2967
- first_name: Sebastian
full_name: Novak, Sebastian
id: 461468AE-F248-11E8-B48F-1D18A9856A87
last_name: Novak
- first_name: Reinmar
full_name: Hager, Reinmar
last_name: Hager
citation:
ama: Trubenova B, Novak S, Hager R. Description of the agent based simulations.
2015. doi:10.1371/journal.pone.0126907.s003
apa: Trubenova, B., Novak, S., & Hager, R. (2015). Description of the agent
based simulations. Public Library of Science. https://doi.org/10.1371/journal.pone.0126907.s003
chicago: Trubenova, Barbora, Sebastian Novak, and Reinmar Hager. “Description of
the Agent Based Simulations.” Public Library of Science, 2015. https://doi.org/10.1371/journal.pone.0126907.s003.
ieee: B. Trubenova, S. Novak, and R. Hager, “Description of the agent based simulations.”
Public Library of Science, 2015.
ista: Trubenova B, Novak S, Hager R. 2015. Description of the agent based simulations,
Public Library of Science, 10.1371/journal.pone.0126907.s003.
mla: Trubenova, Barbora, et al. Description of the Agent Based Simulations.
Public Library of Science, 2015, doi:10.1371/journal.pone.0126907.s003.
short: B. Trubenova, S. Novak, R. Hager, (2015).
date_created: 2021-08-05T12:55:20Z
date_published: 2015-05-18T00:00:00Z
date_updated: 2023-02-23T10:15:25Z
day: '18'
department:
- _id: NiBa
doi: 10.1371/journal.pone.0126907.s003
month: '05'
oa_version: Published Version
publisher: Public Library of Science
related_material:
record:
- id: '1809'
relation: used_in_publication
status: public
status: public
title: Description of the agent based simulations
type: research_data_reference
user_id: 6785fbc1-c503-11eb-8a32-93094b40e1cf
year: '2015'
...
---
_id: '9773'
article_processing_charge: No
author:
- first_name: Tamar
full_name: Friedlander, Tamar
id: 36A5845C-F248-11E8-B48F-1D18A9856A87
last_name: Friedlander
- first_name: Avraham E.
full_name: Mayo, Avraham E.
last_name: Mayo
- first_name: Tsvi
full_name: Tlusty, Tsvi
last_name: Tlusty
- first_name: Uri
full_name: Alon, Uri
last_name: Alon
citation:
ama: Friedlander T, Mayo AE, Tlusty T, Alon U. Evolutionary simulation code. 2015.
doi:10.1371/journal.pcbi.1004055.s002
apa: Friedlander, T., Mayo, A. E., Tlusty, T., & Alon, U. (2015). Evolutionary
simulation code. Public Library of Science. https://doi.org/10.1371/journal.pcbi.1004055.s002
chicago: Friedlander, Tamar, Avraham E. Mayo, Tsvi Tlusty, and Uri Alon. “Evolutionary
Simulation Code.” Public Library of Science, 2015. https://doi.org/10.1371/journal.pcbi.1004055.s002.
ieee: T. Friedlander, A. E. Mayo, T. Tlusty, and U. Alon, “Evolutionary simulation
code.” Public Library of Science, 2015.
ista: Friedlander T, Mayo AE, Tlusty T, Alon U. 2015. Evolutionary simulation code,
Public Library of Science, 10.1371/journal.pcbi.1004055.s002.
mla: Friedlander, Tamar, et al. Evolutionary Simulation Code. Public Library
of Science, 2015, doi:10.1371/journal.pcbi.1004055.s002.
short: T. Friedlander, A.E. Mayo, T. Tlusty, U. Alon, (2015).
date_created: 2021-08-05T12:58:07Z
date_published: 2015-03-23T00:00:00Z
date_updated: 2023-02-23T10:16:13Z
day: '23'
department:
- _id: GaTk
doi: 10.1371/journal.pcbi.1004055.s002
month: '03'
oa_version: Published Version
publisher: Public Library of Science
related_material:
record:
- id: '1827'
relation: used_in_publication
status: public
status: public
title: Evolutionary simulation code
type: research_data_reference
user_id: 6785fbc1-c503-11eb-8a32-93094b40e1cf
year: '2015'
...
---
_id: '981'
abstract:
- lang: eng
text: The tunability of topological surface states and controllable opening of the
Dirac gap are of fundamental and practical interest in the field of topological
materials. In the newly discovered topological crystalline insulators (TCIs),
theory predicts that the Dirac node is protected by a crystalline symmetry and
that the surface state electrons can acquire a mass if this symmetry is broken.
Recent studies have detected signatures of a spontaneously generated Dirac gap
in TCIs; however, the mechanism of mass formation remains elusive. In this work,
we present scanning tunnelling microscopy (STM) measurements of the TCI Pb 1â'x
Sn x Se for a wide range of alloy compositions spanning the topological and non-topological
regimes. The STM topographies reveal a symmetry-breaking distortion on the surface,
which imparts mass to the otherwise massless Dirac electrons-a mechanism analogous
to the long sought-after Higgs mechanism in particle physics. Interestingly, the
measured Dirac gap decreases on approaching the trivial phase, whereas the magnitude
of the distortion remains nearly constant. Our data and calculations reveal that
the penetration depth of Dirac surface states controls the magnitude of the Dirac
mass. At the limit of the critical composition, the penetration depth is predicted
to go to infinity, resulting in zero mass, consistent with our measurements. Finally,
we discover the existence of surface states in the non-topological regime, which
have the characteristics of gapped, double-branched Dirac fermions and could be
exploited in realizing superconductivity in these materials.
acknowledgement: We thank R. Buczko, C. Chamon, J. C. Seamus Davis, M. El-Batanouny,
A. Mesaros, Y. Ran and A. Soumyanarayanan for useful conversations and G. McMahon
for help with EDS measurements. V.M. gratefully acknowledges funding from the US
Department of Energy, Scanned Probe Division under Award Number DE-FG02-12ER46880
for the support of I.Z., Y.O., W.Z. and D.W. for this project. Work at Massachusetts
Institute of Technology is supported by US Department of Energy, Office of Basic
Energy Sciences, Division of Materials Sciences and Engineering under Award DE-SC0010526
(L.F.), and NSF-DMR-1104498 (M.S.). H.L. acknowledges the Singapore National Research
Foundation for support under NRF Award No. NRF-NRFF2013-03. Y.O. was partly supported
by JSPS KAKENHI Grant Numbers 26707016 and 00707656. The work at Northeastern University
is supported by the US Department of Energy grant number DE-FG02-07ER46352, and
benefited from Northeastern University’s Advanced Scientific Computation Center
(ASCC), theory support at the Advanced Light Source, Berkeley and the allocation
of supercomputer time at the NERSC through DOE grant number DE-AC02-05CH11231. Work
at Princeton University is supported by the US National Science Foundation Grant,
NSF-DMR-1006492. F.C. acknowledges the support provided by MOST-Taiwan under project
number NSC-102-2119-M-002-004.
author:
- first_name: Ilija
full_name: Zeljkovic, Ilija
last_name: Zeljkovic
- first_name: Yoshinori
full_name: Okada, Yoshinori
last_name: Okada
- first_name: Maksym
full_name: Maksym Serbyn
id: 47809E7E-F248-11E8-B48F-1D18A9856A87
last_name: Serbyn
orcid: 0000-0002-2399-5827
- first_name: Raman
full_name: Sankar, Raman
last_name: Sankar
- first_name: Daniel
full_name: Walkup, Daniel
last_name: Walkup
- first_name: Wenwen
full_name: Zhou, Wenwen
last_name: Zhou
- first_name: Junwei
full_name: Liu, Junwei
last_name: Liu
- first_name: Guoqing
full_name: Chang, Guoqing
last_name: Chang
- first_name: Yungjui
full_name: Wang, Yungjui
last_name: Wang
- first_name: Md
full_name: Hasan, Md Z
last_name: Hasan
- first_name: Fangcheng
full_name: Chou, Fangcheng
last_name: Chou
- first_name: Hsin
full_name: Lin, Hsin
last_name: Lin
- first_name: Arun
full_name: Bansil, Arun
last_name: Bansil
- first_name: Liang
full_name: Fu, Liang
last_name: Fu
- first_name: Vidya
full_name: Madhavan, Vidya
last_name: Madhavan
citation:
ama: Zeljkovic I, Okada Y, Serbyn M, et al. Dirac mass generation from crystal symmetry
breaking on the surfaces of topological crystalline insulators. Nature Materials.
2015;14(3):318-324. doi:10.1038/nmat4215
apa: Zeljkovic, I., Okada, Y., Serbyn, M., Sankar, R., Walkup, D., Zhou, W., … Madhavan,
V. (2015). Dirac mass generation from crystal symmetry breaking on the surfaces
of topological crystalline insulators. Nature Materials. Nature Publishing
Group. https://doi.org/10.1038/nmat4215
chicago: Zeljkovic, Ilija, Yoshinori Okada, Maksym Serbyn, Raman Sankar, Daniel
Walkup, Wenwen Zhou, Junwei Liu, et al. “Dirac Mass Generation from Crystal Symmetry
Breaking on the Surfaces of Topological Crystalline Insulators.” Nature Materials.
Nature Publishing Group, 2015. https://doi.org/10.1038/nmat4215.
ieee: I. Zeljkovic et al., “Dirac mass generation from crystal symmetry breaking
on the surfaces of topological crystalline insulators,” Nature Materials,
vol. 14, no. 3. Nature Publishing Group, pp. 318–324, 2015.
ista: Zeljkovic I, Okada Y, Serbyn M, Sankar R, Walkup D, Zhou W, Liu J, Chang G,
Wang Y, Hasan M, Chou F, Lin H, Bansil A, Fu L, Madhavan V. 2015. Dirac mass generation
from crystal symmetry breaking on the surfaces of topological crystalline insulators.
Nature Materials. 14(3), 318–324.
mla: Zeljkovic, Ilija, et al. “Dirac Mass Generation from Crystal Symmetry Breaking
on the Surfaces of Topological Crystalline Insulators.” Nature Materials,
vol. 14, no. 3, Nature Publishing Group, 2015, pp. 318–24, doi:10.1038/nmat4215.
short: I. Zeljkovic, Y. Okada, M. Serbyn, R. Sankar, D. Walkup, W. Zhou, J. Liu,
G. Chang, Y. Wang, M. Hasan, F. Chou, H. Lin, A. Bansil, L. Fu, V. Madhavan, Nature
Materials 14 (2015) 318–324.
date_created: 2018-12-11T11:49:31Z
date_published: 2015-03-01T00:00:00Z
date_updated: 2021-01-12T08:22:24Z
day: '01'
doi: 10.1038/nmat4215
extern: 1
intvolume: ' 14'
issue: '3'
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/1403.4906
month: '03'
oa: 1
page: 318 - 324
publication: Nature Materials
publication_status: published
publisher: Nature Publishing Group
publist_id: '6419'
quality_controlled: 0
status: public
title: Dirac mass generation from crystal symmetry breaking on the surfaces of topological
crystalline insulators
type: journal_article
volume: 14
year: '2015'
...
---
_id: '982'
abstract:
- lang: eng
text: We propose a new approach to probing ergodicity and its breakdown in one-dimensional
quantum manybody systems based on their response to a local perturbation. We study
the distribution of matrix elements of a local operator between the system's eigenstates,
finding a qualitatively different behavior in the manybody localized (MBL) and
ergodic phases. To characterize how strongly a local perturbation modifies the
eigenstates, we introduce the parameter g(L) = (In (Vnm/δ)) which represents the
disorder-averaged ratio of a typical matrix element of a local operator V to energy
level spacing δ this parameter is reminiscent of the Thouless conductance in the
single-particle localization. We show that the parameter g(L) decreases with system
size L in the MBL phase and grows in the ergodic phase. We surmise that the delocalization
transition occurs when g(L) is independent of system size, g(L)=gc ~ 1. We illustrate
our approach by studying the many-body localization transition and resolving the
many-body mobility edge in a disordered one-dimensional XXZ spin-1=2 chain using
exact diagonalization and time-evolving block-decimation methods. Our criterion
for the MBL transition gives insights into microscopic details of transition.
Its direct physical consequences, in particular, logarithmically slow transport
at the transition and extensive entanglement entropy of the eigenstates, are consistent
with recent renormalization-group predictions.
acknowledgement: We acknowledge helpful discussions with Sid Parameswaran, Andrew
Potter, Antonello Scardicchio, Romain Vasseur, and especially with Ehud Altman and
David Huse. We would like to thank Miles Stoudenmire for the assistance with ITensor
library. Research at Perimeter Institute is supported by the Government of Canada
through Industry Canada and by the Province of Ontario through the Ministry of Economic
Development & Innovation. This research was supported by Gordon and Betty Moore
Foundation EPiQS Initiative through Grant No. GBMF4307 (M. S.), Sloan Foundation,
NSERC, and Early Researcher Award of Ontario (D. A.). This work made use of the
facilities of N8 HPC Centre of Excellence, provided and funded by the N8 consortium
and EPSRC (Grant No. EP/K000225/1). The Centre is coordinated by the Universities
of Leeds and Manchester.
author:
- first_name: Maksym
full_name: Maksym Serbyn
id: 47809E7E-F248-11E8-B48F-1D18A9856A87
last_name: Serbyn
orcid: 0000-0002-2399-5827
- first_name: Zlatko
full_name: Papić, Zlatko
last_name: Papić
- first_name: Dmitry
full_name: Abanin, Dmitry A
last_name: Abanin
citation:
ama: Serbyn M, Papić Z, Abanin D. Criterion for many-body localization-delocalization
phase transition. Physical Review X. 2015;5(4). doi:10.1103/PhysRevX.5.041047
apa: Serbyn, M., Papić, Z., & Abanin, D. (2015). Criterion for many-body localization-delocalization
phase transition. Physical Review X. American Physical Society. https://doi.org/10.1103/PhysRevX.5.041047
chicago: Serbyn, Maksym, Zlatko Papić, and Dmitry Abanin. “Criterion for Many-Body
Localization-Delocalization Phase Transition.” Physical Review X. American
Physical Society, 2015. https://doi.org/10.1103/PhysRevX.5.041047.
ieee: M. Serbyn, Z. Papić, and D. Abanin, “Criterion for many-body localization-delocalization
phase transition,” Physical Review X, vol. 5, no. 4. American Physical
Society, 2015.
ista: Serbyn M, Papić Z, Abanin D. 2015. Criterion for many-body localization-delocalization
phase transition. Physical Review X. 5(4).
mla: Serbyn, Maksym, et al. “Criterion for Many-Body Localization-Delocalization
Phase Transition.” Physical Review X, vol. 5, no. 4, American Physical
Society, 2015, doi:10.1103/PhysRevX.5.041047.
short: M. Serbyn, Z. Papić, D. Abanin, Physical Review X 5 (2015).
date_created: 2018-12-11T11:49:32Z
date_published: 2015-01-01T00:00:00Z
date_updated: 2021-01-12T08:22:25Z
day: '01'
doi: 10.1103/PhysRevX.5.041047
extern: 1
intvolume: ' 5'
issue: '4'
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/1507.01635
month: '01'
oa: 1
publication: Physical Review X
publication_status: published
publisher: American Physical Society
publist_id: '6418'
quality_controlled: 0
status: public
title: Criterion for many-body localization-delocalization phase transition
type: journal_article
volume: 5
year: '2015'
...
---
_id: '99'
abstract:
- lang: eng
text: Quasiparticle excitations can compromise the performance of superconducting
devices, causing high-frequency dissipation, decoherence in Josephson qubits,
and braiding errors in proposed Majorana-based topological quantum computers.
Quasiparticle dynamics have been studied in detail in metallic superconductors
but remain relatively unexplored in semiconductor-superconductor structures, which
are now being intensely pursued in the context of topological superconductivity.
To this end, we use a system comprising a gate-confined semiconductor nanowire
with an epitaxially grown superconductor layer, yielding an isolated, proximitized
nanowire segment. We identify bound states in the semiconductor by means of bias
spectroscopy, determine the characteristic temperatures and magnetic fields for
quasiparticle excitations, and extract a parity lifetime (poisoning time) of the
bound state in the semiconductor exceeding 10 ms.
acknowledgement: Research support by Microsoft Project Q, the Danish National Research
Foundation, the Lundbeck Foundation, the Carlsberg Foundation, and the European
Commission. A.P.H. acknowledges support from the US Department of Energy, C.M.M.
acknowledges support from the Villum Foundation.
author:
- first_name: Andrew P
full_name: Higginbotham, Andrew P
id: 4AD6785A-F248-11E8-B48F-1D18A9856A87
last_name: Higginbotham
orcid: 0000-0003-2607-2363
- first_name: S M
full_name: Albrecht, S M
last_name: Albrecht
- first_name: Gediminas
full_name: Kiršanskas, Gediminas
last_name: Kiršanskas
- first_name: W
full_name: Chang, W
last_name: Chang
- first_name: Ferdinand
full_name: Kuemmeth, Ferdinand
last_name: Kuemmeth
- first_name: Peter
full_name: Krogstrup, Peter
last_name: Krogstrup
- first_name: Thomas
full_name: Jespersen, Thomas
last_name: Jespersen
- first_name: Jesper
full_name: Nygård, Jesper
last_name: Nygård
- first_name: Karsten
full_name: Flensberg, Karsten
last_name: Flensberg
- first_name: Charles
full_name: Marcus, Charles
last_name: Marcus
citation:
ama: Higginbotham AP, Albrecht SM, Kiršanskas G, et al. Parity lifetime of bound
states in a proximitized semiconductor nanowire. Nature Physics. 2015;11(12):1017-1021.
doi:10.1038/nphys3461
apa: Higginbotham, A. P., Albrecht, S. M., Kiršanskas, G., Chang, W., Kuemmeth,
F., Krogstrup, P., … Marcus, C. (2015). Parity lifetime of bound states in a proximitized
semiconductor nanowire. Nature Physics. Nature Publishing Group. https://doi.org/10.1038/nphys3461
chicago: Higginbotham, Andrew P, S M Albrecht, Gediminas Kiršanskas, W Chang, Ferdinand
Kuemmeth, Peter Krogstrup, Thomas Jespersen, Jesper Nygård, Karsten Flensberg,
and Charles Marcus. “Parity Lifetime of Bound States in a Proximitized Semiconductor
Nanowire.” Nature Physics. Nature Publishing Group, 2015. https://doi.org/10.1038/nphys3461.
ieee: A. P. Higginbotham et al., “Parity lifetime of bound states in a proximitized
semiconductor nanowire,” Nature Physics, vol. 11, no. 12. Nature Publishing
Group, pp. 1017–1021, 2015.
ista: Higginbotham AP, Albrecht SM, Kiršanskas G, Chang W, Kuemmeth F, Krogstrup
P, Jespersen T, Nygård J, Flensberg K, Marcus C. 2015. Parity lifetime of bound
states in a proximitized semiconductor nanowire. Nature Physics. 11(12), 1017–1021.
mla: Higginbotham, Andrew P., et al. “Parity Lifetime of Bound States in a Proximitized
Semiconductor Nanowire.” Nature Physics, vol. 11, no. 12, Nature Publishing
Group, 2015, pp. 1017–21, doi:10.1038/nphys3461.
short: A.P. Higginbotham, S.M. Albrecht, G. Kiršanskas, W. Chang, F. Kuemmeth, P.
Krogstrup, T. Jespersen, J. Nygård, K. Flensberg, C. Marcus, Nature Physics 11
(2015) 1017–1021.
date_created: 2018-12-11T11:44:37Z
date_published: 2015-09-14T00:00:00Z
date_updated: 2021-01-12T08:22:28Z
day: '14'
doi: 10.1038/nphys3461
extern: '1'
external_id:
arxiv:
- '1501.05155'
intvolume: ' 11'
issue: '12'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/1501.05155
month: '09'
oa: 1
oa_version: Preprint
page: 1017 - 1021
publication: Nature Physics
publication_status: published
publisher: Nature Publishing Group
publist_id: '7955'
quality_controlled: '1'
status: public
title: Parity lifetime of bound states in a proximitized semiconductor nanowire
type: journal_article
user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87
volume: 11
year: '2015'
...
---
_id: '8495'
abstract:
- lang: eng
text: 'In this note, we consider the dynamics associated to a perturbation of an
integrable Hamiltonian system in action-angle coordinates in any number of degrees
of freedom and we prove the following result of ``micro-diffusion'''': under generic
assumptions on $ h$ and $ f$, there exists an orbit of the system for which the
drift of its action variables is at least of order $ \sqrt {\varepsilon }$, after
a time of order $ \sqrt {\varepsilon }^{-1}$. The assumptions, which are essentially
minimal, are that there exists a resonant point for $ h$ and that the corresponding
averaged perturbation is non-constant. The conclusions, although very weak when
compared to usual instability phenomena, are also essentially optimal within this
setting.'
article_processing_charge: No
article_type: letter_note
author:
- first_name: Abed
full_name: Bounemoura, Abed
last_name: Bounemoura
- first_name: Vadim
full_name: Kaloshin, Vadim
id: FE553552-CDE8-11E9-B324-C0EBE5697425
last_name: Kaloshin
orcid: 0000-0002-6051-2628
citation:
ama: Bounemoura A, Kaloshin V. A note on micro-instability for Hamiltonian systems
close to integrable. Proceedings of the American Mathematical Society.
2015;144(4):1553-1560. doi:10.1090/proc/12796
apa: Bounemoura, A., & Kaloshin, V. (2015). A note on micro-instability for
Hamiltonian systems close to integrable. Proceedings of the American Mathematical
Society. American Mathematical Society. https://doi.org/10.1090/proc/12796
chicago: Bounemoura, Abed, and Vadim Kaloshin. “A Note on Micro-Instability for
Hamiltonian Systems Close to Integrable.” Proceedings of the American Mathematical
Society. American Mathematical Society, 2015. https://doi.org/10.1090/proc/12796.
ieee: A. Bounemoura and V. Kaloshin, “A note on micro-instability for Hamiltonian
systems close to integrable,” Proceedings of the American Mathematical Society,
vol. 144, no. 4. American Mathematical Society, pp. 1553–1560, 2015.
ista: Bounemoura A, Kaloshin V. 2015. A note on micro-instability for Hamiltonian
systems close to integrable. Proceedings of the American Mathematical Society.
144(4), 1553–1560.
mla: Bounemoura, Abed, and Vadim Kaloshin. “A Note on Micro-Instability for Hamiltonian
Systems Close to Integrable.” Proceedings of the American Mathematical Society,
vol. 144, no. 4, American Mathematical Society, 2015, pp. 1553–60, doi:10.1090/proc/12796.
short: A. Bounemoura, V. Kaloshin, Proceedings of the American Mathematical Society
144 (2015) 1553–1560.
date_created: 2020-09-18T10:46:14Z
date_published: 2015-12-21T00:00:00Z
date_updated: 2021-01-12T08:19:40Z
day: '21'
doi: 10.1090/proc/12796
extern: '1'
intvolume: ' 144'
issue: '4'
language:
- iso: eng
month: '12'
oa_version: None
page: 1553-1560
publication: Proceedings of the American Mathematical Society
publication_identifier:
issn:
- 0002-9939
- 1088-6826
publication_status: published
publisher: American Mathematical Society
quality_controlled: '1'
status: public
title: A note on micro-instability for Hamiltonian systems close to integrable
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 144
year: '2015'
...
---
_id: '866'
abstract:
- lang: eng
text: Proteases play important roles in many biologic processes and are key mediators
of cancer, inflammation, and thrombosis. However, comprehensive and quantitative
techniques to define the substrate specificity profile of proteases are lacking.
The metalloprotease ADAMTS13 regulates blood coagulation by cleaving von Willebrand
factor (VWF), reducing its procoagulant activity. A mutagenized substrate phage
display library based on a 73-amino acid fragment of VWF was constructed, and
the ADAMTS13-dependent change in library complexity was evaluated over reaction
time points, using high-throughput sequencing. Reaction rate constants (kcat/KM)
were calculated for nearly every possible single amino acid substitution within
this fragment. This massively parallel enzyme kinetics analysis detailed the specificity
of ADAMTS13 and demonstrated the critical importance of the P1-P1' substrate residues
while defining exosite binding domains. These data provided empirical evidence
for the propensity for epistasis within VWF and showed strong correlation to conservation
across orthologs, highlighting evolutionary selective pressures for VWF.
acknowledgement: |
We thank Isabel Wang and Vivian Cheung from the Life Sciences Institute, University of Michigan, for assistance with high- throughput sequencing experiments and valuable discussions. We also thank J. Evan Sadler (Washington University) and Sriram Krishnaswamy (Children’s Hospital of Philadelphia) for helpful discussions. We thank Jeff Weitz (McMaster University), Jim Fredenburgh (McMaster University), and Steve Weiss (University of Michigan) for critical review of the manuscript. C.A.K. was awarded the Judith Graham Pool Fellowship from National Hemophilia Foundation. This work was supported by the National Institutes of Health (R01 HL039693), the National Heart, Lung, and Blood Institute (P01- HL057346), Ministerio de Economía y Competitividad Grants BFU2012- 31329 and Sev-2012-0208, and European Research Council Starting Grant 335980_EinME. D.G. is an investigator of the Howard Hughes Medical In- stitute, and F.A.K. is a Howard Hughes Medical Institute International Early Career Scientist.
author:
- first_name: Colin
full_name: Kretz, Colin A
last_name: Kretz
- first_name: Manhong
full_name: Dai, Manhong
last_name: Dai
- first_name: Onuralp
full_name: Soylemez, Onuralp
last_name: Soylemez
- first_name: Andrew
full_name: Yee, Andrew
last_name: Yee
- first_name: Karl
full_name: Desch, Karl C
last_name: Desch
- first_name: David
full_name: Siemieniak, David R
last_name: Siemieniak
- first_name: Kärt
full_name: Tomberg, Kärt
last_name: Tomberg
- first_name: Fyodor
full_name: Fyodor Kondrashov
id: 44FDEF62-F248-11E8-B48F-1D18A9856A87
last_name: Kondrashov
orcid: 0000-0001-8243-4694
- first_name: Fan
full_name: Meng, Fan
last_name: Meng
- first_name: David
full_name: Ginsburg, David B
last_name: Ginsburg
citation:
ama: Kretz C, Dai M, Soylemez O, et al. Massively parallel enzyme kinetics reveals
the substrate recognition landscape of the metalloprotease ADAMTS13. PNAS.
2015;112(30):9328-9333. doi:10.1073/pnas.1511328112
apa: Kretz, C., Dai, M., Soylemez, O., Yee, A., Desch, K., Siemieniak, D., … Ginsburg,
D. (2015). Massively parallel enzyme kinetics reveals the substrate recognition
landscape of the metalloprotease ADAMTS13. PNAS. National Academy of Sciences.
https://doi.org/10.1073/pnas.1511328112
chicago: Kretz, Colin, Manhong Dai, Onuralp Soylemez, Andrew Yee, Karl Desch, David
Siemieniak, Kärt Tomberg, Fyodor Kondrashov, Fan Meng, and David Ginsburg. “Massively
Parallel Enzyme Kinetics Reveals the Substrate Recognition Landscape of the Metalloprotease
ADAMTS13.” PNAS. National Academy of Sciences, 2015. https://doi.org/10.1073/pnas.1511328112.
ieee: C. Kretz et al., “Massively parallel enzyme kinetics reveals the substrate
recognition landscape of the metalloprotease ADAMTS13,” PNAS, vol. 112,
no. 30. National Academy of Sciences, pp. 9328–9333, 2015.
ista: Kretz C, Dai M, Soylemez O, Yee A, Desch K, Siemieniak D, Tomberg K, Kondrashov
F, Meng F, Ginsburg D. 2015. Massively parallel enzyme kinetics reveals the substrate
recognition landscape of the metalloprotease ADAMTS13. PNAS. 112(30), 9328–9333.
mla: Kretz, Colin, et al. “Massively Parallel Enzyme Kinetics Reveals the Substrate
Recognition Landscape of the Metalloprotease ADAMTS13.” PNAS, vol. 112,
no. 30, National Academy of Sciences, 2015, pp. 9328–33, doi:10.1073/pnas.1511328112.
short: C. Kretz, M. Dai, O. Soylemez, A. Yee, K. Desch, D. Siemieniak, K. Tomberg,
F. Kondrashov, F. Meng, D. Ginsburg, PNAS 112 (2015) 9328–9333.
date_created: 2018-12-11T11:48:55Z
date_published: 2015-07-28T00:00:00Z
date_updated: 2021-01-12T08:20:26Z
day: '28'
doi: 10.1073/pnas.1511328112
extern: 1
intvolume: ' 112'
issue: '30'
month: '07'
page: 9328 - 9333
publication: PNAS
publication_status: published
publisher: National Academy of Sciences
publist_id: '6783'
quality_controlled: 0
status: public
title: Massively parallel enzyme kinetics reveals the substrate recognition landscape
of the metalloprotease ADAMTS13
type: journal_article
volume: 112
year: '2015'
...
---
_id: '886'
abstract:
- lang: eng
text: The factors that determine the tempo and mode of protein evolution continue
to be a central question in molecular evolution. Traditionally, studies of protein
evolution focused on the rates of amino acid substitutions. More recently, with
the availability of sequence data and advanced experimental techniques, the focus
of attention has shifted toward the study of evolutionary trajectories and the
overall layout of protein fitness landscapes. In this review we describe the effect
of epistasis on the topology of evolutionary pathways that are likely to be found
in fitness landscapes and develop a simple theory to connect the number of maladapted
genotypes to the topology of fitness landscapes with epistatic interactions. Finally,
we review recent studies that have probed the extent of epistatic interactions
and have begun to chart the fitness landscapes in protein sequence space.
acknowledgement: 'This work has been supported by a grant from the HHMI International
Early Career Scientist Program (#55007424), the Spanish Ministry of Economy and
Competitiveness (grant #BFU2012-31329) as part of the EMBO YIP program, two grants
from the Spanish Ministry of Economy and Competitiveness, Centro de Excelencia Severo
Ochoa 2013–2017 (#Sev-2012-0208) and BES-2013-064004 funded by the European Regional
Development Fund (ERDF), the European Union, and the European Research Council under
grant agreement no 335980_EinME.'
author:
- first_name: Dmitry
full_name: Kondrashov, Dmitry A
last_name: Kondrashov
- first_name: Fyodor
full_name: Fyodor Kondrashov
id: 44FDEF62-F248-11E8-B48F-1D18A9856A87
last_name: Kondrashov
orcid: 0000-0001-8243-4694
citation:
ama: Kondrashov D, Kondrashov F. Topological features of rugged fitness landscapes
in sequence space. Trends in Genetics. 2015;31(1):24-33. doi:10.1016/j.tig.2014.09.009
apa: Kondrashov, D., & Kondrashov, F. (2015). Topological features of rugged
fitness landscapes in sequence space. Trends in Genetics. Elsevier. https://doi.org/10.1016/j.tig.2014.09.009
chicago: Kondrashov, Dmitry, and Fyodor Kondrashov. “Topological Features of Rugged
Fitness Landscapes in Sequence Space.” Trends in Genetics. Elsevier, 2015.
https://doi.org/10.1016/j.tig.2014.09.009.
ieee: D. Kondrashov and F. Kondrashov, “Topological features of rugged fitness landscapes
in sequence space,” Trends in Genetics, vol. 31, no. 1. Elsevier, pp. 24–33,
2015.
ista: Kondrashov D, Kondrashov F. 2015. Topological features of rugged fitness landscapes
in sequence space. Trends in Genetics. 31(1), 24–33.
mla: Kondrashov, Dmitry, and Fyodor Kondrashov. “Topological Features of Rugged
Fitness Landscapes in Sequence Space.” Trends in Genetics, vol. 31, no.
1, Elsevier, 2015, pp. 24–33, doi:10.1016/j.tig.2014.09.009.
short: D. Kondrashov, F. Kondrashov, Trends in Genetics 31 (2015) 24–33.
date_created: 2018-12-11T11:49:01Z
date_published: 2015-01-01T00:00:00Z
date_updated: 2021-01-12T08:21:16Z
day: '01'
doi: 10.1016/j.tig.2014.09.009
extern: 1
intvolume: ' 31'
issue: '1'
month: '01'
page: 24 - 33
publication: Trends in Genetics
publication_status: published
publisher: Elsevier
publist_id: '6764'
quality_controlled: 0
status: public
title: Topological features of rugged fitness landscapes in sequence space
type: journal_article
volume: 31
year: '2015'
...
---
_id: '9017'
abstract:
- lang: eng
text: MCM2 is a subunit of the replicative helicase machinery shown to interact
with histones H3 and H4 during the replication process through its N-terminal
domain. During replication, this interaction has been proposed to assist disassembly
and assembly of nucleosomes on DNA. However, how this interaction participates
in crosstalk with histone chaperones at the replication fork remains to be elucidated.
Here, we solved the crystal structure of the ternary complex between the histone-binding
domain of Mcm2 and the histones H3-H4 at 2.9 Å resolution. Histones H3 and H4
assemble as a tetramer in the crystal structure, but MCM2 interacts only with
a single molecule of H3-H4. The latter interaction exploits binding surfaces that
contact either DNA or H2B when H3-H4 dimers are incorporated in the nucleosome
core particle. Upon binding of the ternary complex with the histone chaperone
ASF1, the histone tetramer dissociates and both MCM2 and ASF1 interact simultaneously
with the histones forming a 1:1:1:1 heteromeric complex. Thermodynamic analysis
of the quaternary complex together with structural modeling support that ASF1
and MCM2 could form a chaperoning module for histones H3 and H4 protecting them
from promiscuous interactions. This suggests an additional function for MCM2 outside
its helicase function as a proper histone chaperone connected to the replication
pathway.
article_processing_charge: No
article_type: original
author:
- first_name: Nicolas
full_name: Richet, Nicolas
last_name: Richet
- first_name: Danni
full_name: Liu, Danni
last_name: Liu
- first_name: Pierre
full_name: Legrand, Pierre
last_name: Legrand
- first_name: Christophe
full_name: Velours, Christophe
last_name: Velours
- first_name: Armelle
full_name: Corpet, Armelle
last_name: Corpet
- first_name: Albane
full_name: Gaubert, Albane
last_name: Gaubert
- first_name: May M
full_name: Bakail, May M
id: FB3C3F8E-522F-11EA-B186-22963DDC885E
last_name: Bakail
orcid: 0000-0002-9592-1587
- first_name: Gwenaelle
full_name: Moal-Raisin, Gwenaelle
last_name: Moal-Raisin
- first_name: Raphael
full_name: Guerois, Raphael
last_name: Guerois
- first_name: Christel
full_name: Compper, Christel
last_name: Compper
- first_name: Arthur
full_name: Besle, Arthur
last_name: Besle
- first_name: Berengère
full_name: Guichard, Berengère
last_name: Guichard
- first_name: Genevieve
full_name: Almouzni, Genevieve
last_name: Almouzni
- first_name: Françoise
full_name: Ochsenbein, Françoise
last_name: Ochsenbein
citation:
ama: Richet N, Liu D, Legrand P, et al. Structural insight into how the human helicase
subunit MCM2 may act as a histone chaperone together with ASF1 at the replication
fork. Nucleic Acids Research. 2015;43(3):1905-1917. doi:10.1093/nar/gkv021
apa: Richet, N., Liu, D., Legrand, P., Velours, C., Corpet, A., Gaubert, A., … Ochsenbein,
F. (2015). Structural insight into how the human helicase subunit MCM2 may act
as a histone chaperone together with ASF1 at the replication fork. Nucleic
Acids Research. Oxford University Press. https://doi.org/10.1093/nar/gkv021
chicago: Richet, Nicolas, Danni Liu, Pierre Legrand, Christophe Velours, Armelle
Corpet, Albane Gaubert, May M Bakail, et al. “Structural Insight into How the
Human Helicase Subunit MCM2 May Act as a Histone Chaperone Together with ASF1
at the Replication Fork.” Nucleic Acids Research. Oxford University Press,
2015. https://doi.org/10.1093/nar/gkv021.
ieee: N. Richet et al., “Structural insight into how the human helicase subunit
MCM2 may act as a histone chaperone together with ASF1 at the replication fork,”
Nucleic Acids Research, vol. 43, no. 3. Oxford University Press, pp. 1905–1917,
2015.
ista: Richet N, Liu D, Legrand P, Velours C, Corpet A, Gaubert A, Bakail MM, Moal-Raisin
G, Guerois R, Compper C, Besle A, Guichard B, Almouzni G, Ochsenbein F. 2015.
Structural insight into how the human helicase subunit MCM2 may act as a histone
chaperone together with ASF1 at the replication fork. Nucleic Acids Research.
43(3), 1905–1917.
mla: Richet, Nicolas, et al. “Structural Insight into How the Human Helicase Subunit
MCM2 May Act as a Histone Chaperone Together with ASF1 at the Replication Fork.”
Nucleic Acids Research, vol. 43, no. 3, Oxford University Press, 2015,
pp. 1905–17, doi:10.1093/nar/gkv021.
short: N. Richet, D. Liu, P. Legrand, C. Velours, A. Corpet, A. Gaubert, M.M. Bakail,
G. Moal-Raisin, R. Guerois, C. Compper, A. Besle, B. Guichard, G. Almouzni, F.
Ochsenbein, Nucleic Acids Research 43 (2015) 1905–1917.
date_created: 2021-01-19T11:01:01Z
date_published: 2015-02-18T00:00:00Z
date_updated: 2023-02-23T13:46:50Z
day: '18'
doi: 10.1093/nar/gkv021
extern: '1'
external_id:
pmid:
- '25618846'
intvolume: ' 43'
issue: '3'
language:
- iso: eng
month: '02'
oa_version: Published Version
page: 1905-1917
pmid: 1
publication: Nucleic Acids Research
publication_identifier:
issn:
- 1362-4962
- 0305-1048
publication_status: published
publisher: Oxford University Press
quality_controlled: '1'
status: public
title: Structural insight into how the human helicase subunit MCM2 may act as a histone
chaperone together with ASF1 at the replication fork
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 43
year: '2015'
...
---
_id: '924'
abstract:
- lang: eng
text: This paper presents a numerical study of a Capillary Pumped Loop evaporator.
A two-dimensional unsteady mathematical model of a flat evaporator is developed
to simulate heat and mass transfer in unsaturated porous wick with phase change.
The liquid-vapor phase change inside the porous wick is described by Langmuir's
law. The governing equations are solved by the Finite Element Method. The results
are presented then for a sintered nickel wick and methanol as a working fluid.
The heat flux required to the transition from the all-liquid wick to the vapor-liquid
wick is calculated. The dynamic and thermodynamic behavior of the working fluid
in the capillary structure are discussed in this paper.
acknowledgement: The work presented in this paper is supported by Alstom Transport,
site de Tarbes (Contract number is 11099).
article_processing_charge: No
author:
- first_name: Riadh
full_name: Boubaker, Riadh
last_name: Boubaker
- first_name: Vincent
full_name: Platel, Vincent
last_name: Platel
- first_name: Alexis
full_name: Bergès, Alexis
last_name: Bergès
- first_name: Mathieu
full_name: Bancelin, Mathieu
last_name: Bancelin
- first_name: Edouard B
full_name: Hannezo, Edouard B
id: 3A9DB764-F248-11E8-B48F-1D18A9856A87
last_name: Hannezo
orcid: 0000-0001-6005-1561
citation:
ama: Boubaker R, Platel V, Bergès A, Bancelin M, Hannezo EB. Dynamic model of heat
and mass transfer in an unsaturated porous wick of capillary pumped loop. Applied
Thermal Engineering. 2015;76:1-8. doi:10.1016/j.applthermaleng.2014.10.009
apa: Boubaker, R., Platel, V., Bergès, A., Bancelin, M., & Hannezo, E. B. (2015).
Dynamic model of heat and mass transfer in an unsaturated porous wick of capillary
pumped loop. Applied Thermal Engineering. Elsevier. https://doi.org/10.1016/j.applthermaleng.2014.10.009
chicago: Boubaker, Riadh, Vincent Platel, Alexis Bergès, Mathieu Bancelin, and Edouard
B Hannezo. “Dynamic Model of Heat and Mass Transfer in an Unsaturated Porous Wick
of Capillary Pumped Loop.” Applied Thermal Engineering. Elsevier, 2015.
https://doi.org/10.1016/j.applthermaleng.2014.10.009.
ieee: R. Boubaker, V. Platel, A. Bergès, M. Bancelin, and E. B. Hannezo, “Dynamic
model of heat and mass transfer in an unsaturated porous wick of capillary pumped
loop,” Applied Thermal Engineering, vol. 76. Elsevier, pp. 1–8, 2015.
ista: Boubaker R, Platel V, Bergès A, Bancelin M, Hannezo EB. 2015. Dynamic model
of heat and mass transfer in an unsaturated porous wick of capillary pumped loop.
Applied Thermal Engineering. 76, 1–8.
mla: Boubaker, Riadh, et al. “Dynamic Model of Heat and Mass Transfer in an Unsaturated
Porous Wick of Capillary Pumped Loop.” Applied Thermal Engineering, vol.
76, Elsevier, 2015, pp. 1–8, doi:10.1016/j.applthermaleng.2014.10.009.
short: R. Boubaker, V. Platel, A. Bergès, M. Bancelin, E.B. Hannezo, Applied Thermal
Engineering 76 (2015) 1–8.
date_created: 2018-12-11T11:49:13Z
date_published: 2015-02-05T00:00:00Z
date_updated: 2021-01-12T08:21:56Z
day: '05'
doi: 10.1016/j.applthermaleng.2014.10.009
extern: '1'
intvolume: ' 76'
language:
- iso: eng
month: '02'
oa_version: None
page: 1 - 8
publication: Applied Thermal Engineering
publication_status: published
publisher: Elsevier
publist_id: '6514'
status: public
title: Dynamic model of heat and mass transfer in an unsaturated porous wick of capillary
pumped loop
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 76
year: '2015'
...
---
_id: '929'
abstract:
- lang: eng
text: 'An essential question of morphogenesis is how patterns arise without preexisting
positional information, as inspired by Turing. In the past few years, cytoskeletal
flows in the cell cortex have been identified as a key mechanism of molecular
patterning at the subcellular level. Theoretical and in vitro studies have suggested
that biological polymers such as actomyosin gels have the property to self-organize,
but the applicability of this concept in an in vivo setting remains unclear. Here,
we report that the regular spacing pattern of supracellular actin rings in the
Drosophila tracheal tubule is governed by a self-organizing principle. We propose
a simple biophysical model where pattern formation arises from the interplay of
myosin contractility and actin turnover. We validate the hypotheses of the model
using photobleaching experiments and report that the formation of actin rings
is contractility dependent. Moreover, genetic and pharmacological perturbations
of the physical properties of the actomyosin gel modify the spacing of the pattern,
as the model predicted. In addition, our model posited a role of cortical friction
in stabilizing the spacing pattern of actin rings. Consistently, genetic depletion
of apical extracellular matrix caused strikingly dynamic movements of actin rings,
mirroring our model prediction of a transition from steady to chaotic actin patterns
at low cortical friction. Our results therefore demonstrate quantitatively that
a hydrodynamical instability of the actin cortex can trigger regular pattern formation
and drive morphogenesis in an in vivo setting. '
acknowledgement: We thank H. Oda, R. E. Ward, K. Saigo, T. Nishimura, D. Pinheiro,
Y. Bellaiche, the Bloomington Stock Center, Drosophila Genetic Resource Center (Kyoto),
and the Developmental Studies Hybridoma Bank for generously providing antibodies
and fly stocks; A. Hayashi for sharing phalloidin staining samples; Y. H. Zhang
for plasmid and protocol for CBP preparation; and T. Kondo and J. Prost for suggestions
and discussion. This work was supported by the Taishan Scholar Program of Shandong
and the Fundamental Research Funds for the Central Universities in China (3005000-841412019)
(to B.D.) and a Grant-in-Aid for Scientific Research on Innovative Areas from Ministry
of Education, Culture, Sports, Science and Technology of Japan (to S.H.). E.H. acknowledges
support from the Young Researcher Prize of the Bettencourt-Schueller Foundation.
article_processing_charge: No
author:
- first_name: Edouard B
full_name: Hannezo, Edouard B
id: 3A9DB764-F248-11E8-B48F-1D18A9856A87
last_name: Hannezo
orcid: 0000-0001-6005-1561
- first_name: Bo
full_name: Dong, Bo
last_name: Dong
- first_name: Pierre
full_name: Recho, Pierre
last_name: Recho
- first_name: Jean
full_name: Joanny, Jean
last_name: Joanny
- first_name: Shigeo
full_name: Hayashi, Shigeo
last_name: Hayashi
citation:
ama: Hannezo EB, Dong B, Recho P, Joanny J, Hayashi S. Cortical instability drives
periodic supracellular actin pattern formation in epithelial tubes. PNAS.
2015;112(28):8620-8625. doi:10.1073/pnas.1504762112
apa: Hannezo, E. B., Dong, B., Recho, P., Joanny, J., & Hayashi, S. (2015).
Cortical instability drives periodic supracellular actin pattern formation in
epithelial tubes. PNAS. National Academy of Sciences. https://doi.org/10.1073/pnas.1504762112
chicago: Hannezo, Edouard B, Bo Dong, Pierre Recho, Jean Joanny, and Shigeo Hayashi.
“Cortical Instability Drives Periodic Supracellular Actin Pattern Formation in
Epithelial Tubes.” PNAS. National Academy of Sciences, 2015. https://doi.org/10.1073/pnas.1504762112.
ieee: E. B. Hannezo, B. Dong, P. Recho, J. Joanny, and S. Hayashi, “Cortical instability
drives periodic supracellular actin pattern formation in epithelial tubes,” PNAS,
vol. 112, no. 28. National Academy of Sciences, pp. 8620–8625, 2015.
ista: Hannezo EB, Dong B, Recho P, Joanny J, Hayashi S. 2015. Cortical instability
drives periodic supracellular actin pattern formation in epithelial tubes. PNAS.
112(28), 8620–8625.
mla: Hannezo, Edouard B., et al. “Cortical Instability Drives Periodic Supracellular
Actin Pattern Formation in Epithelial Tubes.” PNAS, vol. 112, no. 28, National
Academy of Sciences, 2015, pp. 8620–25, doi:10.1073/pnas.1504762112.
short: E.B. Hannezo, B. Dong, P. Recho, J. Joanny, S. Hayashi, PNAS 112 (2015) 8620–8625.
date_created: 2018-12-11T11:49:15Z
date_published: 2015-07-14T00:00:00Z
date_updated: 2021-01-12T08:21:59Z
day: '14'
doi: 10.1073/pnas.1504762112
extern: '1'
intvolume: ' 112'
issue: '28'
language:
- iso: eng
month: '07'
oa_version: None
page: 8620 - 8625
publication: PNAS
publication_status: published
publisher: National Academy of Sciences
publist_id: '6513'
status: public
title: Cortical instability drives periodic supracellular actin pattern formation
in epithelial tubes
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 112
year: '2015'
...
---
_id: '933'
abstract:
- lang: eng
text: Although collective cell motion plays an important role, for example during
wound healing, embryogenesis, or cancer progression, the fundamental rules governing
this motion are still not well understood, in particular at high cell density.
We study here the motion of human bronchial epithelial cells within a monolayer,
over long times. We observe that, as the monolayer ages, the cells slow down monotonously,
while the velocity correlation length first increases as the cells slow down but
eventually decreases at the slowest motions. By comparing experiments, analytic
model, and detailed particle-based simulations, we shed light on this biological
amorphous solidification process, demonstrating that the observed dynamics can
be explained as a consequence of the combined maturation and strengthening of
cell-cell and cell-substrate adhesions. Surprisingly, the increase of cell surface
density due to proliferation is only secondary in this process. This analysis
is confirmed with two other cell types. The very general relations between the
mean cell velocity and velocity correlation lengths, which apply for aggregates
of self-propelled particles, as well as motile cells, can possibly be used to
discriminate between various parameter changes in vivo, from noninvasive microscopy
data.
author:
- first_name: Simón
full_name: García, Simón
last_name: García
- first_name: Edouard B
full_name: Hannezo, Edouard B
id: 3A9DB764-F248-11E8-B48F-1D18A9856A87
last_name: Hannezo
orcid: 0000-0001-6005-1561
- first_name: Jens
full_name: Elgeti, Jens
last_name: Elgeti
- first_name: Jean
full_name: Joanny, Jean
last_name: Joanny
- first_name: Pascal
full_name: Silberzan, Pascal
last_name: Silberzan
- first_name: Nir
full_name: Gov, Nir
last_name: Gov
citation:
ama: García S, Hannezo EB, Elgeti J, Joanny J, Silberzan P, Gov N. Physics of active
jamming during collective cellular motion in a monolayer. PNAS. 2015;112(50):15314-15319.
doi:10.1073/pnas.1510973112
apa: García, S., Hannezo, E. B., Elgeti, J., Joanny, J., Silberzan, P., & Gov,
N. (2015). Physics of active jamming during collective cellular motion in a monolayer.
PNAS. National Academy of Sciences. https://doi.org/10.1073/pnas.1510973112
chicago: García, Simón, Edouard B Hannezo, Jens Elgeti, Jean Joanny, Pascal Silberzan,
and Nir Gov. “Physics of Active Jamming during Collective Cellular Motion in a
Monolayer.” PNAS. National Academy of Sciences, 2015. https://doi.org/10.1073/pnas.1510973112.
ieee: S. García, E. B. Hannezo, J. Elgeti, J. Joanny, P. Silberzan, and N. Gov,
“Physics of active jamming during collective cellular motion in a monolayer,”
PNAS, vol. 112, no. 50. National Academy of Sciences, pp. 15314–15319,
2015.
ista: García S, Hannezo EB, Elgeti J, Joanny J, Silberzan P, Gov N. 2015. Physics
of active jamming during collective cellular motion in a monolayer. PNAS. 112(50),
15314–15319.
mla: García, Simón, et al. “Physics of Active Jamming during Collective Cellular
Motion in a Monolayer.” PNAS, vol. 112, no. 50, National Academy of Sciences,
2015, pp. 15314–19, doi:10.1073/pnas.1510973112.
short: S. García, E.B. Hannezo, J. Elgeti, J. Joanny, P. Silberzan, N. Gov, PNAS
112 (2015) 15314–15319.
date_created: 2018-12-11T11:49:16Z
date_published: 2015-12-15T00:00:00Z
date_updated: 2021-01-12T08:22:01Z
day: '15'
doi: 10.1073/pnas.1510973112
extern: '1'
external_id:
pmid:
- '26627719'
intvolume: ' 112'
issue: '50'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://www.pnas.org/content/pnas/112/50/15314.full.pdf
month: '12'
oa: 1
oa_version: None
page: 15314 - 15319
pmid: 1
publication: PNAS
publication_status: published
publisher: National Academy of Sciences
publist_id: '6511'
quality_controlled: '1'
status: public
title: Physics of active jamming during collective cellular motion in a monolayer
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 112
year: '2015'
...
---
_id: '9532'
abstract:
- lang: eng
text: Genomic imprinting, an inherently epigenetic phenomenon defined by parent
of origin-dependent gene expression, is observed in mammals and flowering plants.
Genome-scale surveys of imprinted expression and the underlying differential epigenetic
marks have led to the discovery of hundreds of imprinted plant genes and confirmed
DNA and histone methylation as key regulators of plant imprinting. However, the
biological roles of the vast majority of imprinted plant genes are unknown, and
the evolutionary forces shaping plant imprinting remain rather opaque. Here, we
review the mechanisms of plant genomic imprinting and discuss theories of imprinting
evolution and biological significance in light of recent findings.
article_processing_charge: No
article_type: review
author:
- first_name: Jessica A.
full_name: Rodrigues, Jessica A.
last_name: Rodrigues
- first_name: Daniel
full_name: Zilberman, Daniel
id: 6973db13-dd5f-11ea-814e-b3e5455e9ed1
last_name: Zilberman
orcid: 0000-0002-0123-8649
citation:
ama: Rodrigues JA, Zilberman D. Evolution and function of genomic imprinting in
plants. Genes and Development. 2015;29(24):2517–2531. doi:10.1101/gad.269902.115
apa: Rodrigues, J. A., & Zilberman, D. (2015). Evolution and function of genomic
imprinting in plants. Genes and Development. Cold Spring Harbor Laboratory
Press. https://doi.org/10.1101/gad.269902.115
chicago: Rodrigues, Jessica A., and Daniel Zilberman. “Evolution and Function of
Genomic Imprinting in Plants.” Genes and Development. Cold Spring Harbor
Laboratory Press, 2015. https://doi.org/10.1101/gad.269902.115.
ieee: J. A. Rodrigues and D. Zilberman, “Evolution and function of genomic imprinting
in plants,” Genes and Development, vol. 29, no. 24. Cold Spring Harbor
Laboratory Press, pp. 2517–2531, 2015.
ista: Rodrigues JA, Zilberman D. 2015. Evolution and function of genomic imprinting
in plants. Genes and Development. 29(24), 2517–2531.
mla: Rodrigues, Jessica A., and Daniel Zilberman. “Evolution and Function of Genomic
Imprinting in Plants.” Genes and Development, vol. 29, no. 24, Cold Spring
Harbor Laboratory Press, 2015, pp. 2517–2531, doi:10.1101/gad.269902.115.
short: J.A. Rodrigues, D. Zilberman, Genes and Development 29 (2015) 2517–2531.
date_created: 2021-06-08T09:56:24Z
date_published: 2015-12-15T00:00:00Z
date_updated: 2021-12-14T07:58:15Z
day: '15'
ddc:
- '570'
department:
- _id: DaZi
doi: 10.1101/gad.269902.115
extern: '1'
external_id:
pmid:
- '26680300'
file:
- access_level: open_access
checksum: 086a88cfca4677646da26ed960cb02e9
content_type: application/pdf
creator: asandaue
date_created: 2021-06-08T09:55:10Z
date_updated: 2021-06-08T09:55:10Z
file_id: '9533'
file_name: 2015_GenesAndDevelopment_Rodrigues.pdf
file_size: 1116846
relation: main_file
success: 1
file_date_updated: 2021-06-08T09:55:10Z
has_accepted_license: '1'
intvolume: ' 29'
issue: '24'
language:
- iso: eng
month: '12'
oa: 1
oa_version: Published Version
page: 2517–2531
pmid: 1
publication: Genes and Development
publication_identifier:
eissn:
- 1549-5477
issn:
- 0890-9369
publication_status: published
publisher: Cold Spring Harbor Laboratory Press
quality_controlled: '1'
scopus_import: '1'
status: public
title: Evolution and function of genomic imprinting in plants
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: 8b945eb4-e2f2-11eb-945a-df72226e66a9
volume: 29
year: '2015'
...
---
_id: '9684'
abstract:
- lang: eng
text: The size dependence of the strength of nano- and micron-sized crystals is
studied using a new simulation approach in which the dynamics of the density functions
of dislocations are modeled. Since any quantity of dislocations can be represented
by a density, this approach can handle large systems containing large quantities
of dislocations, which may handicap discrete dislocation dynamics schemes due
to the excessive computation time involved. For this reason, pillar sizes spanning
a large range, from the sub-micron to micron regimes, can be simulated. The simulation
results reveal the power-law relationship between strength and specimen size up
to a certain size, beyond which the strength varies much more slowly with size.
For specimens smaller than ~4000b, their strength is found to be controlled by
the dislocation depletion condition, in which the total dislocation density remains
almost constant throughout the loading process. In specimens larger than ~4000b,
the initial dislocation distribution is of critical importance since the presence
of dislocation entanglements is found to obstruct deformation in the neighboring
regions within a distance of ~2000b. This length scale suggests that the effects
of dense dislocation clusters are greater in intermediate-sized specimens (e.g.
4000b and 8000b) than in larger specimens (e.g. 16 000b), according to the weakest-link
concept.
article_number: '035001'
article_processing_charge: No
article_type: original
author:
- first_name: P S S
full_name: Leung, P S S
last_name: Leung
- first_name: H S
full_name: Leung, H S
last_name: Leung
- first_name: Bingqing
full_name: Cheng, Bingqing
id: cbe3cda4-d82c-11eb-8dc7-8ff94289fcc9
last_name: Cheng
orcid: 0000-0002-3584-9632
- first_name: A H W
full_name: Ngan, A H W
last_name: Ngan
citation:
ama: Leung PSS, Leung HS, Cheng B, Ngan AHW. Size dependence of yield strength simulated
by a dislocation-density function dynamics approach. Modelling and Simulation
in Materials Science and Engineering. 2015;23(3). doi:10.1088/0965-0393/23/3/035001
apa: Leung, P. S. S., Leung, H. S., Cheng, B., & Ngan, A. H. W. (2015). Size
dependence of yield strength simulated by a dislocation-density function dynamics
approach. Modelling and Simulation in Materials Science and Engineering.
IOP Publishing. https://doi.org/10.1088/0965-0393/23/3/035001
chicago: Leung, P S S, H S Leung, Bingqing Cheng, and A H W Ngan. “Size Dependence
of Yield Strength Simulated by a Dislocation-Density Function Dynamics Approach.”
Modelling and Simulation in Materials Science and Engineering. IOP Publishing,
2015. https://doi.org/10.1088/0965-0393/23/3/035001.
ieee: P. S. S. Leung, H. S. Leung, B. Cheng, and A. H. W. Ngan, “Size dependence
of yield strength simulated by a dislocation-density function dynamics approach,”
Modelling and Simulation in Materials Science and Engineering, vol. 23,
no. 3. IOP Publishing, 2015.
ista: Leung PSS, Leung HS, Cheng B, Ngan AHW. 2015. Size dependence of yield strength
simulated by a dislocation-density function dynamics approach. Modelling and Simulation
in Materials Science and Engineering. 23(3), 035001.
mla: Leung, P. S. S., et al. “Size Dependence of Yield Strength Simulated by a Dislocation-Density
Function Dynamics Approach.” Modelling and Simulation in Materials Science
and Engineering, vol. 23, no. 3, 035001, IOP Publishing, 2015, doi:10.1088/0965-0393/23/3/035001.
short: P.S.S. Leung, H.S. Leung, B. Cheng, A.H.W. Ngan, Modelling and Simulation
in Materials Science and Engineering 23 (2015).
date_created: 2021-07-19T09:11:12Z
date_published: 2015-04-01T00:00:00Z
date_updated: 2023-02-23T14:04:54Z
day: '01'
doi: 10.1088/0965-0393/23/3/035001
extern: '1'
intvolume: ' 23'
issue: '3'
language:
- iso: eng
month: '04'
oa_version: None
publication: Modelling and Simulation in Materials Science and Engineering
publication_identifier:
eissn:
- 1361-651X
issn:
- 0965-0393
publication_status: published
publisher: IOP Publishing
quality_controlled: '1'
scopus_import: '1'
status: public
title: Size dependence of yield strength simulated by a dislocation-density function
dynamics approach
type: journal_article
user_id: 6785fbc1-c503-11eb-8a32-93094b40e1cf
volume: 23
year: '2015'
...
---
_id: '1566'
abstract:
- lang: eng
text: Deposits of misfolded proteins in the human brain are associated with the
development of many neurodegenerative diseases. Recent studies show that these
proteins have common traits even at the monomer level. Among them, a polyglutamine
region that is present in huntingtin is known to exhibit a correlation between
the length of the chain and the severity as well as the earliness of the onset
of Huntington disease. Here, we apply bias exchange molecular dynamics to generate
structures of polyglutamine expansions of several lengths and characterize the
resulting independent conformations. We compare the properties of these conformations
to those of the standard proteins, as well as to other homopolymeric tracts. We
find that, similar to the previously studied polyvaline chains, the set of possible
transient folds is much broader than the set of known-to-date folds, although
the conformations have different structures. We show that the mechanical stability
is not related to any simple geometrical characteristics of the structures. We
demonstrate that long polyglutamine expansions result in higher mechanical stability
than the shorter ones. They also have a longer life span and are substantially
more prone to form knotted structures. The knotted region has an average length
of 35 residues, similar to the typical threshold for most polyglutamine-related
diseases. Similarly, changes in shape and mechanical stability appear once the
total length of the peptide exceeds this threshold of 35 glutamine residues. We
suggest that knotted conformers may also harm the cellular machinery and thus
lead to disease.
acknowledgement: 'We acknowledge the support by the EU Joint Programme in Neurodegenerative
Diseases (JPND AC14/00037) project. The project is supported through the following
funding organisations under the aegis of JPND—www.jpnd.eu: Ireland, HRB; Poland,
National Science Centre; and Spain, ISCIII. '
article_number: e1004541
author:
- first_name: Àngel
full_name: Gómez Sicilia, Àngel
last_name: Gómez Sicilia
- first_name: Mateusz K
full_name: Sikora, Mateusz K
id: 2F74BCDE-F248-11E8-B48F-1D18A9856A87
last_name: Sikora
- first_name: Marek
full_name: Cieplak, Marek
last_name: Cieplak
- first_name: Mariano
full_name: Carrión Vázquez, Mariano
last_name: Carrión Vázquez
citation:
ama: Gómez Sicilia À, Sikora MK, Cieplak M, Carrión Vázquez M. An exploration of
the universe of polyglutamine structures. PLoS Computational Biology. 2015;11(10).
doi:10.1371/journal.pcbi.1004541
apa: Gómez Sicilia, À., Sikora, M. K., Cieplak, M., & Carrión Vázquez, M. (2015).
An exploration of the universe of polyglutamine structures. PLoS Computational
Biology. Public Library of Science. https://doi.org/10.1371/journal.pcbi.1004541
chicago: Gómez Sicilia, Àngel, Mateusz K Sikora, Marek Cieplak, and Mariano Carrión
Vázquez. “An Exploration of the Universe of Polyglutamine Structures.” PLoS
Computational Biology. Public Library of Science, 2015. https://doi.org/10.1371/journal.pcbi.1004541.
ieee: À. Gómez Sicilia, M. K. Sikora, M. Cieplak, and M. Carrión Vázquez, “An exploration
of the universe of polyglutamine structures,” PLoS Computational Biology,
vol. 11, no. 10. Public Library of Science, 2015.
ista: Gómez Sicilia À, Sikora MK, Cieplak M, Carrión Vázquez M. 2015. An exploration
of the universe of polyglutamine structures. PLoS Computational Biology. 11(10),
e1004541.
mla: Gómez Sicilia, Àngel, et al. “An Exploration of the Universe of Polyglutamine
Structures.” PLoS Computational Biology, vol. 11, no. 10, e1004541, Public
Library of Science, 2015, doi:10.1371/journal.pcbi.1004541.
short: À. Gómez Sicilia, M.K. Sikora, M. Cieplak, M. Carrión Vázquez, PLoS Computational
Biology 11 (2015).
date_created: 2018-12-11T11:52:45Z
date_published: 2015-10-23T00:00:00Z
date_updated: 2023-02-23T14:05:55Z
day: '23'
ddc:
- '570'
department:
- _id: CaHe
doi: 10.1371/journal.pcbi.1004541
file:
- access_level: open_access
checksum: 8b67d729be663bfc9af04bfd94459655
content_type: application/pdf
creator: system
date_created: 2018-12-12T10:16:21Z
date_updated: 2020-07-14T12:45:02Z
file_id: '5207'
file_name: IST-2016-478-v1+1_journal.pcbi.1004541.pdf
file_size: 1412511
relation: main_file
file_date_updated: 2020-07-14T12:45:02Z
has_accepted_license: '1'
intvolume: ' 11'
issue: '10'
language:
- iso: eng
month: '10'
oa: 1
oa_version: Published Version
publication: PLoS Computational Biology
publication_status: published
publisher: Public Library of Science
publist_id: '5605'
pubrep_id: '478'
quality_controlled: '1'
related_material:
record:
- id: '9714'
relation: research_data
status: public
scopus_import: 1
status: public
title: An exploration of the universe of polyglutamine structures
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 11
year: '2015'
...
---
_id: '9712'
article_processing_charge: No
author:
- first_name: Murat
full_name: Tugrul, Murat
id: 37C323C6-F248-11E8-B48F-1D18A9856A87
last_name: Tugrul
orcid: 0000-0002-8523-0758
- first_name: Tiago
full_name: Paixao, Tiago
id: 2C5658E6-F248-11E8-B48F-1D18A9856A87
last_name: Paixao
orcid: 0000-0003-2361-3953
- first_name: Nicholas H
full_name: Barton, Nicholas H
id: 4880FE40-F248-11E8-B48F-1D18A9856A87
last_name: Barton
orcid: 0000-0002-8548-5240
- first_name: Gašper
full_name: Tkačik, Gašper
id: 3D494DCA-F248-11E8-B48F-1D18A9856A87
last_name: Tkačik
orcid: 0000-0002-6699-1455
citation:
ama: Tugrul M, Paixao T, Barton NH, Tkačik G. Other fitness models for comparison
& for interacting TFBSs. 2015. doi:10.1371/journal.pgen.1005639.s001
apa: Tugrul, M., Paixao, T., Barton, N. H., & Tkačik, G. (2015). Other fitness
models for comparison & for interacting TFBSs. Public Library of Science.
https://doi.org/10.1371/journal.pgen.1005639.s001
chicago: Tugrul, Murat, Tiago Paixao, Nicholas H Barton, and Gašper Tkačik. “Other
Fitness Models for Comparison & for Interacting TFBSs.” Public Library of
Science, 2015. https://doi.org/10.1371/journal.pgen.1005639.s001.
ieee: M. Tugrul, T. Paixao, N. H. Barton, and G. Tkačik, “Other fitness models for
comparison & for interacting TFBSs.” Public Library of Science, 2015.
ista: Tugrul M, Paixao T, Barton NH, Tkačik G. 2015. Other fitness models for comparison
& for interacting TFBSs, Public Library of Science, 10.1371/journal.pgen.1005639.s001.
mla: Tugrul, Murat, et al. Other Fitness Models for Comparison & for Interacting
TFBSs. Public Library of Science, 2015, doi:10.1371/journal.pgen.1005639.s001.
short: M. Tugrul, T. Paixao, N.H. Barton, G. Tkačik, (2015).
date_created: 2021-07-23T12:00:37Z
date_published: 2015-11-06T00:00:00Z
date_updated: 2023-02-23T10:09:08Z
day: '06'
department:
- _id: NiBa
- _id: CaGu
- _id: GaTk
doi: 10.1371/journal.pgen.1005639.s001
month: '11'
oa_version: Published Version
publisher: Public Library of Science
related_material:
record:
- id: '1666'
relation: used_in_publication
status: public
status: public
title: Other fitness models for comparison & for interacting TFBSs
type: research_data_reference
user_id: 6785fbc1-c503-11eb-8a32-93094b40e1cf
year: '2015'
...
---
_id: '9714'
article_processing_charge: No
author:
- first_name: Àngel
full_name: Gómez Sicilia, Àngel
last_name: Gómez Sicilia
- first_name: Mateusz K
full_name: Sikora, Mateusz K
id: 2F74BCDE-F248-11E8-B48F-1D18A9856A87
last_name: Sikora
- first_name: Marek
full_name: Cieplak, Marek
last_name: Cieplak
- first_name: Mariano
full_name: Carrión Vázquez, Mariano
last_name: Carrión Vázquez
citation:
ama: Gómez Sicilia À, Sikora MK, Cieplak M, Carrión Vázquez M. An exploration of
the universe of polyglutamine structures - submission to PLOS journals. 2015.
doi:10.1371/journal.pcbi.1004541.s001
apa: Gómez Sicilia, À., Sikora, M. K., Cieplak, M., & Carrión Vázquez, M. (2015).
An exploration of the universe of polyglutamine structures - submission to PLOS
journals. Public Library of Science . https://doi.org/10.1371/journal.pcbi.1004541.s001
chicago: Gómez Sicilia, Àngel, Mateusz K Sikora, Marek Cieplak, and Mariano Carrión
Vázquez. “An Exploration of the Universe of Polyglutamine Structures - Submission
to PLOS Journals.” Public Library of Science , 2015. https://doi.org/10.1371/journal.pcbi.1004541.s001.
ieee: À. Gómez Sicilia, M. K. Sikora, M. Cieplak, and M. Carrión Vázquez, “An exploration
of the universe of polyglutamine structures - submission to PLOS journals.” Public
Library of Science , 2015.
ista: Gómez Sicilia À, Sikora MK, Cieplak M, Carrión Vázquez M. 2015. An exploration
of the universe of polyglutamine structures - submission to PLOS journals, Public
Library of Science , 10.1371/journal.pcbi.1004541.s001.
mla: Gómez Sicilia, Àngel, et al. An Exploration of the Universe of Polyglutamine
Structures - Submission to PLOS Journals. Public Library of Science , 2015,
doi:10.1371/journal.pcbi.1004541.s001.
short: À. Gómez Sicilia, M.K. Sikora, M. Cieplak, M. Carrión Vázquez, (2015).
date_created: 2021-07-23T12:05:28Z
date_published: 2015-10-23T00:00:00Z
date_updated: 2023-02-23T10:04:35Z
day: '23'
department:
- _id: CaHe
doi: 10.1371/journal.pcbi.1004541.s001
month: '10'
oa_version: Published Version
publisher: 'Public Library of Science '
related_material:
record:
- id: '1566'
relation: used_in_publication
status: public
status: public
title: An exploration of the universe of polyglutamine structures - submission to
PLOS journals
type: research_data_reference
user_id: 6785fbc1-c503-11eb-8a32-93094b40e1cf
year: '2015'
...
---
_id: '9715'
article_processing_charge: No
author:
- first_name: Barbora
full_name: Trubenova, Barbora
id: 42302D54-F248-11E8-B48F-1D18A9856A87
last_name: Trubenova
orcid: 0000-0002-6873-2967
- first_name: Sebastian
full_name: Novak, Sebastian
id: 461468AE-F248-11E8-B48F-1D18A9856A87
last_name: Novak
- first_name: Reinmar
full_name: Hager, Reinmar
last_name: Hager
citation:
ama: Trubenova B, Novak S, Hager R. Mathematical inference of the results. 2015.
doi:10.1371/journal.pone.0126907.s001
apa: Trubenova, B., Novak, S., & Hager, R. (2015). Mathematical inference of
the results. Public Library of Science. https://doi.org/10.1371/journal.pone.0126907.s001
chicago: Trubenova, Barbora, Sebastian Novak, and Reinmar Hager. “Mathematical Inference
of the Results.” Public Library of Science, 2015. https://doi.org/10.1371/journal.pone.0126907.s001.
ieee: B. Trubenova, S. Novak, and R. Hager, “Mathematical inference of the results.”
Public Library of Science, 2015.
ista: Trubenova B, Novak S, Hager R. 2015. Mathematical inference of the results,
Public Library of Science, 10.1371/journal.pone.0126907.s001.
mla: Trubenova, Barbora, et al. Mathematical Inference of the Results. Public
Library of Science, 2015, doi:10.1371/journal.pone.0126907.s001.
short: B. Trubenova, S. Novak, R. Hager, (2015).
date_created: 2021-07-23T12:11:30Z
date_published: 2015-05-18T00:00:00Z
date_updated: 2023-02-23T10:15:25Z
day: '18'
department:
- _id: NiBa
doi: 10.1371/journal.pone.0126907.s001
month: '05'
oa_version: Published Version
publisher: Public Library of Science
related_material:
record:
- id: '1809'
relation: used_in_publication
status: public
status: public
title: Mathematical inference of the results
type: research_data_reference
user_id: 6785fbc1-c503-11eb-8a32-93094b40e1cf
year: '2015'
...
---
_id: '1993'
abstract:
- lang: eng
text: 'The fitness effects of symbionts on their hosts can be context-dependent,
with usually benign symbionts causing detrimental effects when their hosts are
stressed, or typically parasitic symbionts providing protection towards their
hosts (e.g. against pathogen infection). Here, we studied the novel association
between the invasive garden ant Lasius neglectus and its fungal ectosymbiont Laboulbenia
formicarum for potential costs and benefits. We tested ants with different Laboulbenia
levels for their survival and immunity under resource limitation and exposure
to the obligate killing entomopathogen Metarhizium brunneum. While survival of
L. neglectus workers under starvation was significantly decreased with increasing
Laboulbenia levels, host survival under Metarhizium exposure increased with higher
levels of the ectosymbiont, suggesting a symbiont-mediated anti-pathogen protection,
which seems to be driven mechanistically by both improved sanitary behaviours
and an upregulated immune system. Ants with high Laboulbenia levels showed significantly
longer self-grooming and elevated expression of immune genes relevant for wound
repair and antifungal responses (β-1,3-glucan binding protein, Prophenoloxidase),
compared with ants carrying low Laboulbenia levels. This suggests that the ectosymbiont
Laboulbenia formicarum weakens its ant host by either direct resource exploitation
or the costs of an upregulated behavioural and immunological response, which,
however, provides a prophylactic protection upon later exposure to pathogens. '
acknowledged_ssus:
- _id: EM-Fac
acknowledgement: "Funding was obtained by the German Research Foundation (CR 118–2)
and an ERC StG (243071) by the European Research Council (both to S.C.).\r\nWe thank
Line V. Ugelvig for help with ant collection and statistical discussion, Xavier
Espadaler for detailed information on the ant collection site, Birgit Lautenschläger
for the electron microscopy images and Eva Sixt for ant drawings. We further thank
Jørgen Eilenberg for the fungal strain, Meghan L. Vyleta for genetic strain characterization
and immune gene primer development, Paul Schmid-Hempel for discussion, and Line
V. Ugelvig, Xavier Espadaler and Christopher D. Pull for comments on the manuscript.
S.C., M.K. and S.T. conceived the study; M.K. and A.V.G. performed the experiments;
M.K. performed the statistical analysis; S.C. and M.K. wrote the manuscript with
intense contributions of A.V.G. and S.T.; all authors approved the manuscript."
article_number: '20141976'
article_processing_charge: No
article_type: original
author:
- first_name: Matthias
full_name: Konrad, Matthias
id: 46528076-F248-11E8-B48F-1D18A9856A87
last_name: Konrad
- first_name: Anna V
full_name: Grasse, Anna V
id: 406F989C-F248-11E8-B48F-1D18A9856A87
last_name: Grasse
- first_name: Simon
full_name: Tragust, Simon
id: 35A7A418-F248-11E8-B48F-1D18A9856A87
last_name: Tragust
- first_name: Sylvia
full_name: Cremer, Sylvia
id: 2F64EC8C-F248-11E8-B48F-1D18A9856A87
last_name: Cremer
orcid: 0000-0002-2193-3868
citation:
ama: Konrad M, Grasse AV, Tragust S, Cremer S. Anti-pathogen protection versus survival
costs mediated by an ectosymbiont in an ant host. Proceedings of the Royal
Society of London Series B Biological Sciences. 2015;282(1799). doi:10.1098/rspb.2014.1976
apa: Konrad, M., Grasse, A. V., Tragust, S., & Cremer, S. (2015). Anti-pathogen
protection versus survival costs mediated by an ectosymbiont in an ant host. Proceedings
of the Royal Society of London Series B Biological Sciences. The Royal Society.
https://doi.org/10.1098/rspb.2014.1976
chicago: Konrad, Matthias, Anna V Grasse, Simon Tragust, and Sylvia Cremer. “Anti-Pathogen
Protection versus Survival Costs Mediated by an Ectosymbiont in an Ant Host.”
Proceedings of the Royal Society of London Series B Biological Sciences.
The Royal Society, 2015. https://doi.org/10.1098/rspb.2014.1976.
ieee: M. Konrad, A. V. Grasse, S. Tragust, and S. Cremer, “Anti-pathogen protection
versus survival costs mediated by an ectosymbiont in an ant host,” Proceedings
of the Royal Society of London Series B Biological Sciences, vol. 282, no.
1799. The Royal Society, 2015.
ista: Konrad M, Grasse AV, Tragust S, Cremer S. 2015. Anti-pathogen protection versus
survival costs mediated by an ectosymbiont in an ant host. Proceedings of the
Royal Society of London Series B Biological Sciences. 282(1799), 20141976.
mla: Konrad, Matthias, et al. “Anti-Pathogen Protection versus Survival Costs Mediated
by an Ectosymbiont in an Ant Host.” Proceedings of the Royal Society of London
Series B Biological Sciences, vol. 282, no. 1799, 20141976, The Royal Society,
2015, doi:10.1098/rspb.2014.1976.
short: M. Konrad, A.V. Grasse, S. Tragust, S. Cremer, Proceedings of the Royal Society
of London Series B Biological Sciences 282 (2015).
date_created: 2018-12-11T11:55:06Z
date_published: 2015-01-22T00:00:00Z
date_updated: 2023-02-23T14:06:41Z
day: '22'
department:
- _id: SyCr
doi: 10.1098/rspb.2014.1976
ec_funded: 1
external_id:
pmid:
- '25473011'
intvolume: ' 282'
issue: '1799'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4286035/
month: '01'
oa: 1
oa_version: Submitted Version
pmid: 1
project:
- _id: 25DC711C-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '243071'
name: 'Social Vaccination in Ant Colonies: from Individual Mechanisms to Society
Effects'
- _id: 25DAF0B2-B435-11E9-9278-68D0E5697425
grant_number: CR-118/3-1
name: Host-Parasite Coevolution
publication: Proceedings of the Royal Society of London Series B Biological Sciences
publication_identifier:
eissn:
- 1471-2954
issn:
- 0962-8452
publication_status: published
publisher: The Royal Society
publist_id: '5090'
quality_controlled: '1'
related_material:
record:
- id: '9740'
relation: research_data
status: public
scopus_import: '1'
status: public
title: Anti-pathogen protection versus survival costs mediated by an ectosymbiont
in an ant host
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 282
year: '2015'
...
---
_id: '9742'
abstract:
- lang: eng
text: 'Repeated pathogen exposure is a common threat in colonies of social insects,
posing selection pressures on colony members to respond with improved disease-defense
performance. We here tested whether experience gained by repeated tending of low-level
fungus-exposed (Metarhizium robertsii) larvae may alter the performance of sanitary
brood care in the clonal ant, Platythyrea punctata. We trained ants individually
over nine consecutive trials to either sham-treated or fungus-exposed larvae.
We then compared the larval grooming behavior of naive and trained ants and measured
how effectively they removed infectious fungal conidiospores from the fungus-exposed
larvae. We found that the ants changed the duration of larval grooming in response
to both, larval treatment and their level of experience: (1) sham-treated larvae
received longer grooming than the fungus-exposed larvae and (2) trained ants performed
less self-grooming but longer larval grooming than naive ants, which was true
for both, ants trained to fungus-exposed and also to sham-treated larvae. Ants
that groomed the fungus-exposed larvae for longer periods removed a higher number
of fungal conidiospores from the surface of the fungus-exposed larvae. As experienced
ants performed longer larval grooming, they were more effective in fungal removal,
thus making them better caretakers under pathogen attack of the colony. By studying
this clonal ant, we can thus conclude that even in the absence of genetic variation
between colony members, differences in experience levels of brood care may affect
performance of sanitary brood care in social insects.'
article_processing_charge: No
author:
- first_name: Claudia
full_name: Westhus, Claudia
last_name: Westhus
- first_name: Line V
full_name: Ugelvig, Line V
id: 3DC97C8E-F248-11E8-B48F-1D18A9856A87
last_name: Ugelvig
orcid: 0000-0003-1832-8883
- first_name: Edouard
full_name: Tourdot, Edouard
last_name: Tourdot
- first_name: Jürgen
full_name: Heinze, Jürgen
last_name: Heinze
- first_name: Claudie
full_name: Doums, Claudie
last_name: Doums
- first_name: Sylvia
full_name: Cremer, Sylvia
id: 2F64EC8C-F248-11E8-B48F-1D18A9856A87
last_name: Cremer
orcid: 0000-0002-2193-3868
citation:
ama: 'Westhus C, Ugelvig LV, Tourdot E, Heinze J, Doums C, Cremer S. Data from:
Increased grooming after repeated brood care provides sanitary benefits in a clonal
ant. 2015. doi:10.5061/dryad.7kc79'
apa: 'Westhus, C., Ugelvig, L. V., Tourdot, E., Heinze, J., Doums, C., & Cremer,
S. (2015). Data from: Increased grooming after repeated brood care provides sanitary
benefits in a clonal ant. Dryad. https://doi.org/10.5061/dryad.7kc79'
chicago: 'Westhus, Claudia, Line V Ugelvig, Edouard Tourdot, Jürgen Heinze, Claudie
Doums, and Sylvia Cremer. “Data from: Increased Grooming after Repeated Brood
Care Provides Sanitary Benefits in a Clonal Ant.” Dryad, 2015. https://doi.org/10.5061/dryad.7kc79.'
ieee: 'C. Westhus, L. V. Ugelvig, E. Tourdot, J. Heinze, C. Doums, and S. Cremer,
“Data from: Increased grooming after repeated brood care provides sanitary benefits
in a clonal ant.” Dryad, 2015.'
ista: 'Westhus C, Ugelvig LV, Tourdot E, Heinze J, Doums C, Cremer S. 2015. Data
from: Increased grooming after repeated brood care provides sanitary benefits
in a clonal ant, Dryad, 10.5061/dryad.7kc79.'
mla: 'Westhus, Claudia, et al. Data from: Increased Grooming after Repeated Brood
Care Provides Sanitary Benefits in a Clonal Ant. Dryad, 2015, doi:10.5061/dryad.7kc79.'
short: C. Westhus, L.V. Ugelvig, E. Tourdot, J. Heinze, C. Doums, S. Cremer, (2015).
date_created: 2021-07-28T08:52:53Z
date_published: 2015-07-09T00:00:00Z
date_updated: 2023-02-23T10:30:52Z
day: '09'
department:
- _id: SyCr
doi: 10.5061/dryad.7kc79
main_file_link:
- open_access: '1'
url: https://doi.org/10.5061/dryad.7kc79
month: '07'
oa: 1
oa_version: Published Version
publisher: Dryad
related_material:
record:
- id: '2161'
relation: used_in_publication
status: public
status: public
title: 'Data from: Increased grooming after repeated brood care provides sanitary
benefits in a clonal ant'
type: research_data_reference
user_id: 6785fbc1-c503-11eb-8a32-93094b40e1cf
year: '2015'
...
---
_id: '9765'
article_processing_charge: No
author:
- first_name: Guillaume
full_name: Chevereau, Guillaume
id: 424D78A0-F248-11E8-B48F-1D18A9856A87
last_name: Chevereau
- first_name: Marta
full_name: Lukacisinova, Marta
id: 4342E402-F248-11E8-B48F-1D18A9856A87
last_name: Lukacisinova
orcid: 0000-0002-2519-8004
- first_name: Tugce
full_name: Batur, Tugce
last_name: Batur
- first_name: Aysegul
full_name: Guvenek, Aysegul
last_name: Guvenek
- first_name: Dilay Hazal
full_name: Ayhan, Dilay Hazal
last_name: Ayhan
- first_name: Erdal
full_name: Toprak, Erdal
last_name: Toprak
- first_name: Mark Tobias
full_name: Bollenbach, Mark Tobias
id: 3E6DB97A-F248-11E8-B48F-1D18A9856A87
last_name: Bollenbach
orcid: 0000-0003-4398-476X
citation:
ama: Chevereau G, Lukacisinova M, Batur T, et al. Gene ontology enrichment analysis
for the most sensitive gene deletion strains for all drugs. 2015. doi:10.1371/journal.pbio.1002299.s008
apa: Chevereau, G., Lukacisinova, M., Batur, T., Guvenek, A., Ayhan, D. H., Toprak,
E., & Bollenbach, M. T. (2015). Gene ontology enrichment analysis for the
most sensitive gene deletion strains for all drugs. Public Library of Science.
https://doi.org/10.1371/journal.pbio.1002299.s008
chicago: Chevereau, Guillaume, Marta Lukacisinova, Tugce Batur, Aysegul Guvenek,
Dilay Hazal Ayhan, Erdal Toprak, and Mark Tobias Bollenbach. “Gene Ontology Enrichment
Analysis for the Most Sensitive Gene Deletion Strains for All Drugs.” Public Library
of Science, 2015. https://doi.org/10.1371/journal.pbio.1002299.s008.
ieee: G. Chevereau et al., “Gene ontology enrichment analysis for the most
sensitive gene deletion strains for all drugs.” Public Library of Science, 2015.
ista: Chevereau G, Lukacisinova M, Batur T, Guvenek A, Ayhan DH, Toprak E, Bollenbach
MT. 2015. Gene ontology enrichment analysis for the most sensitive gene deletion
strains for all drugs, Public Library of Science, 10.1371/journal.pbio.1002299.s008.
mla: Chevereau, Guillaume, et al. Gene Ontology Enrichment Analysis for the Most
Sensitive Gene Deletion Strains for All Drugs. Public Library of Science,
2015, doi:10.1371/journal.pbio.1002299.s008.
short: G. Chevereau, M. Lukacisinova, T. Batur, A. Guvenek, D.H. Ayhan, E. Toprak,
M.T. Bollenbach, (2015).
date_created: 2021-08-03T07:05:16Z
date_published: 2015-11-18T00:00:00Z
date_updated: 2023-02-23T10:07:02Z
day: '18'
department:
- _id: ToBo
doi: 10.1371/journal.pbio.1002299.s008
month: '11'
oa_version: Published Version
publisher: Public Library of Science
related_material:
record:
- id: '1619'
relation: used_in_publication
status: public
status: public
title: Gene ontology enrichment analysis for the most sensitive gene deletion strains
for all drugs
type: research_data_reference
user_id: 6785fbc1-c503-11eb-8a32-93094b40e1cf
year: '2015'
...
---
_id: '12630'
abstract:
- lang: eng
text: "The hydrology of high-elevation watersheds of the Hindu Kush-Himalaya region
(HKH) is poorly known. The correct representation of internal states and process
dynamics in glacio-hydrological models can often not be verified due to missing
in situ measurements. We use a new set of detailed ground data from the upper
Langtang valley in Nepal to systematically guide a state-of-the art glacio-hydrological
model through a parameter assigning process with the aim to understand the hydrology
of the catchment and contribution of snow and ice processes to runoff. 14 parameters
are directly calculated on the basis of local data, and 13 parameters are calibrated
against 5 different datasets of in situ or remote sensing data. Spatial fields
of debris thickness are reconstructed through a novel approach that employs data
from an Unmanned Aerial Vehicle (UAV), energy balance modeling and statistical
techniques. The model is validated against measured catchment runoff (Nash–Sutcliffe
efficiency 0.87) and modeled snow cover is compared to Landsat snow cover. The
advanced representation of processes allowed assessing the role played by avalanching
for runoff for the first time for a Himalayan catchment (5% of annual water inputs
to the hydrological system are due to snow redistribution) and to quantify the
hydrological significance of sub-debris ice melt (9% of annual water inputs).
Snowmelt is the most important contributor to total runoff during the hydrological
year 2012/2013 (representing 40% of all sources), followed by rainfall (34%) and
ice melt (26%). A sensitivity analysis is used to assess the efficiency of the
monitoring network and identify the timing and location of field measurements
that constrain model uncertainty. The methodology to set up a glacio-hydrological
model in high-elevation regions presented in this study can be regarded as a benchmark
for modelers in the HKH seeking to evaluate their calibration approach, their
experimental setup and thus to reduce the predictive model uncertainty.\r\n\r\n"
article_processing_charge: No
article_type: original
author:
- first_name: S.
full_name: Ragettli, S.
last_name: Ragettli
- first_name: Francesca
full_name: Pellicciotti, Francesca
id: b28f055a-81ea-11ed-b70c-a9fe7f7b0e70
last_name: Pellicciotti
- first_name: W.W.
full_name: Immerzeel, W.W.
last_name: Immerzeel
- first_name: E.S.
full_name: Miles, E.S.
last_name: Miles
- first_name: L.
full_name: Petersen, L.
last_name: Petersen
- first_name: M.
full_name: Heynen, M.
last_name: Heynen
- first_name: J.M.
full_name: Shea, J.M.
last_name: Shea
- first_name: D.
full_name: Stumm, D.
last_name: Stumm
- first_name: S.
full_name: Joshi, S.
last_name: Joshi
- first_name: A.
full_name: Shrestha, A.
last_name: Shrestha
citation:
ama: Ragettli S, Pellicciotti F, Immerzeel WW, et al. Unraveling the hydrology of
a Himalayan catchment through integration of high resolution in situ data and
remote sensing with an advanced simulation model. Advances in Water Resources.
2015;78(4):94-111. doi:10.1016/j.advwatres.2015.01.013
apa: Ragettli, S., Pellicciotti, F., Immerzeel, W. W., Miles, E. S., Petersen, L.,
Heynen, M., … Shrestha, A. (2015). Unraveling the hydrology of a Himalayan catchment
through integration of high resolution in situ data and remote sensing with an
advanced simulation model. Advances in Water Resources. Elsevier. https://doi.org/10.1016/j.advwatres.2015.01.013
chicago: Ragettli, S., Francesca Pellicciotti, W.W. Immerzeel, E.S. Miles, L. Petersen,
M. Heynen, J.M. Shea, D. Stumm, S. Joshi, and A. Shrestha. “Unraveling the Hydrology
of a Himalayan Catchment through Integration of High Resolution in Situ Data and
Remote Sensing with an Advanced Simulation Model.” Advances in Water Resources.
Elsevier, 2015. https://doi.org/10.1016/j.advwatres.2015.01.013.
ieee: S. Ragettli et al., “Unraveling the hydrology of a Himalayan catchment
through integration of high resolution in situ data and remote sensing with an
advanced simulation model,” Advances in Water Resources, vol. 78, no. 4.
Elsevier, pp. 94–111, 2015.
ista: Ragettli S, Pellicciotti F, Immerzeel WW, Miles ES, Petersen L, Heynen M,
Shea JM, Stumm D, Joshi S, Shrestha A. 2015. Unraveling the hydrology of a Himalayan
catchment through integration of high resolution in situ data and remote sensing
with an advanced simulation model. Advances in Water Resources. 78(4), 94–111.
mla: Ragettli, S., et al. “Unraveling the Hydrology of a Himalayan Catchment through
Integration of High Resolution in Situ Data and Remote Sensing with an Advanced
Simulation Model.” Advances in Water Resources, vol. 78, no. 4, Elsevier,
2015, pp. 94–111, doi:10.1016/j.advwatres.2015.01.013.
short: S. Ragettli, F. Pellicciotti, W.W. Immerzeel, E.S. Miles, L. Petersen, M.
Heynen, J.M. Shea, D. Stumm, S. Joshi, A. Shrestha, Advances in Water Resources
78 (2015) 94–111.
date_created: 2023-02-20T08:16:21Z
date_published: 2015-04-01T00:00:00Z
date_updated: 2023-02-24T09:28:04Z
day: '01'
doi: 10.1016/j.advwatres.2015.01.013
extern: '1'
intvolume: ' 78'
issue: '4'
keyword:
- Water Science and Technology
language:
- iso: eng
month: '04'
oa_version: None
page: 94-111
publication: Advances in Water Resources
publication_identifier:
issn:
- 0309-1708
publication_status: published
publisher: Elsevier
quality_controlled: '1'
scopus_import: '1'
status: public
title: Unraveling the hydrology of a Himalayan catchment through integration of high
resolution in situ data and remote sensing with an advanced simulation model
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 78
year: '2015'
...
---
_id: '12628'
abstract:
- lang: eng
text: Thick debris cover on glaciers can significantly reduce ice melt. However,
several studies have suggested that debris-covered glaciers in the Himalaya might
have lost mass at a rate similar to debris-free glaciers. We reconstruct elevation
and mass changes for the debris-covered glaciers of the upper Langtang valley,
Nepalese Himalaya, using a digital elevation model (DEM) from 1974 stereo Hexagon
satellite data and the 2000 SRTM (Shuttle Radar Topography Mission) DEM. Uncertainties
are high in the accumulation areas, due to data gaps in the SRTM and difficulties
with delineation of the glacier borders. Even with these uncertainties, we obtain
thinning rates comparable to those of several other studies in the Himalaya. In
particular, we obtain a total mass balance for the investigated debris-covered
glaciers of the basin of –0.32 ± 0.18 m w.e. a−1. However,
there are major spatial differences both between glaciers and within any single
glacier, exhibiting a very distinct nonlinear mass-balance profile with elevation.
Through analysis of surface velocities derived from Landsat ETM+ imagery, we show
that thinning occurs in areas of low velocity and low slope. These areas are prone
to a general, dynamic decay of surface features and to the development of supraglacial
lakes and ice cliffs, which may be responsible for a considerable increase in
overall glacier ablation.
article_processing_charge: No
article_type: original
author:
- first_name: Francesca
full_name: Pellicciotti, Francesca
id: b28f055a-81ea-11ed-b70c-a9fe7f7b0e70
last_name: Pellicciotti
- first_name: Christa
full_name: Stephan, Christa
last_name: Stephan
- first_name: Evan
full_name: Miles, Evan
last_name: Miles
- first_name: Sam
full_name: Herreid, Sam
last_name: Herreid
- first_name: Walter W.
full_name: Immerzeel, Walter W.
last_name: Immerzeel
- first_name: Tobias
full_name: Bolch, Tobias
last_name: Bolch
citation:
ama: Pellicciotti F, Stephan C, Miles E, Herreid S, Immerzeel WW, Bolch T. Mass-balance
changes of the debris-covered glaciers in the Langtang Himal, Nepal, from 1974
to 1999. Journal of Glaciology. 2015;61(226):373-386. doi:10.3189/2015jog13j237
apa: Pellicciotti, F., Stephan, C., Miles, E., Herreid, S., Immerzeel, W. W., &
Bolch, T. (2015). Mass-balance changes of the debris-covered glaciers in the Langtang
Himal, Nepal, from 1974 to 1999. Journal of Glaciology. International Glaciological
Society. https://doi.org/10.3189/2015jog13j237
chicago: Pellicciotti, Francesca, Christa Stephan, Evan Miles, Sam Herreid, Walter
W. Immerzeel, and Tobias Bolch. “Mass-Balance Changes of the Debris-Covered Glaciers
in the Langtang Himal, Nepal, from 1974 to 1999.” Journal of Glaciology.
International Glaciological Society, 2015. https://doi.org/10.3189/2015jog13j237.
ieee: F. Pellicciotti, C. Stephan, E. Miles, S. Herreid, W. W. Immerzeel, and T.
Bolch, “Mass-balance changes of the debris-covered glaciers in the Langtang Himal,
Nepal, from 1974 to 1999,” Journal of Glaciology, vol. 61, no. 226. International
Glaciological Society, pp. 373–386, 2015.
ista: Pellicciotti F, Stephan C, Miles E, Herreid S, Immerzeel WW, Bolch T. 2015.
Mass-balance changes of the debris-covered glaciers in the Langtang Himal, Nepal,
from 1974 to 1999. Journal of Glaciology. 61(226), 373–386.
mla: Pellicciotti, Francesca, et al. “Mass-Balance Changes of the Debris-Covered
Glaciers in the Langtang Himal, Nepal, from 1974 to 1999.” Journal of Glaciology,
vol. 61, no. 226, International Glaciological Society, 2015, pp. 373–86, doi:10.3189/2015jog13j237.
short: F. Pellicciotti, C. Stephan, E. Miles, S. Herreid, W.W. Immerzeel, T. Bolch,
Journal of Glaciology 61 (2015) 373–386.
date_created: 2023-02-20T08:16:11Z
date_published: 2015-03-01T00:00:00Z
date_updated: 2023-02-24T09:35:21Z
day: '01'
doi: 10.3189/2015jog13j237
extern: '1'
intvolume: ' 61'
issue: '226'
keyword:
- Earth-Surface Processes
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.3189/2015JoG13J237
month: '03'
oa: 1
oa_version: Published Version
page: 373-386
publication: Journal of Glaciology
publication_identifier:
eissn:
- 1727-5652
issn:
- 0022-1430
publication_status: published
publisher: International Glaciological Society
quality_controlled: '1'
scopus_import: '1'
status: public
title: Mass-balance changes of the debris-covered glaciers in the Langtang Himal,
Nepal, from 1974 to 1999
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 61
year: '2015'
...
---
_id: '12631'
abstract:
- lang: eng
text: Air temperature is one of the most relevant input variables for snow and ice
melt calculations. However, local meteorological conditions, complex topography,
and logistical concerns in glacierized regions make the measuring and modeling
of air temperature a difficult task. In this study, we investigate the spatial
distribution of 2 m air temperature over mountain glaciers and propose a modification
to an existing model to improve its representation. Spatially distributed meteorological
data from Haut Glacier d'Arolla (Switzerland), Place (Canada), and Juncal Norte
(Chile) Glaciers are used to examine approximate flow line temperatures during
their respective ablation seasons. During warm conditions (off-glacier temperatures
well above 0°C), observed air temperatures in the upper reaches of Place Glacier
and Haut Glacier d'Arolla decrease down glacier along the approximate flow line.
At Juncal Norte and Haut Glacier d'Arolla, an increase in air temperature is observed
over the glacier tongue. While the temperature behavior over the upper part can
be explained by the cooling effect of the glacier surface, the temperature increase
over the glacier tongue may be caused by several processes induced by the surrounding
warm atmosphere. In order to capture the latter effect, we add an additional term
to the Greuell and Böhm (GB) thermodynamic glacier wind model. For high off-glacier
temperatures, the modified GB model reduces root-mean-square error up to 32% and
provides a new approach for distributing air temperature over mountain glaciers
as a function of off-glacier temperatures and approximate glacier flow lines.
article_processing_charge: No
article_type: original
author:
- first_name: A.
full_name: Ayala, A.
last_name: Ayala
- first_name: Francesca
full_name: Pellicciotti, Francesca
id: b28f055a-81ea-11ed-b70c-a9fe7f7b0e70
last_name: Pellicciotti
- first_name: J. M.
full_name: Shea, J. M.
last_name: Shea
citation:
ama: 'Ayala A, Pellicciotti F, Shea JM. Modeling 2 m air temperatures over mountain
glaciers: Exploring the influence of katabatic cooling and external warming. Journal
of Geophysical Research: Atmospheres. 2015;120(8):3139-3157. doi:10.1002/2015jd023137'
apa: 'Ayala, A., Pellicciotti, F., & Shea, J. M. (2015). Modeling 2 m air temperatures
over mountain glaciers: Exploring the influence of katabatic cooling and external
warming. Journal of Geophysical Research: Atmospheres. American Geophysical
Union. https://doi.org/10.1002/2015jd023137'
chicago: 'Ayala, A., Francesca Pellicciotti, and J. M. Shea. “Modeling 2 m Air Temperatures
over Mountain Glaciers: Exploring the Influence of Katabatic Cooling and External
Warming.” Journal of Geophysical Research: Atmospheres. American Geophysical
Union, 2015. https://doi.org/10.1002/2015jd023137.'
ieee: 'A. Ayala, F. Pellicciotti, and J. M. Shea, “Modeling 2 m air temperatures
over mountain glaciers: Exploring the influence of katabatic cooling and external
warming,” Journal of Geophysical Research: Atmospheres, vol. 120, no. 8.
American Geophysical Union, pp. 3139–3157, 2015.'
ista: 'Ayala A, Pellicciotti F, Shea JM. 2015. Modeling 2 m air temperatures over
mountain glaciers: Exploring the influence of katabatic cooling and external warming.
Journal of Geophysical Research: Atmospheres. 120(8), 3139–3157.'
mla: 'Ayala, A., et al. “Modeling 2 m Air Temperatures over Mountain Glaciers: Exploring
the Influence of Katabatic Cooling and External Warming.” Journal of Geophysical
Research: Atmospheres, vol. 120, no. 8, American Geophysical Union, 2015,
pp. 3139–57, doi:10.1002/2015jd023137.'
short: 'A. Ayala, F. Pellicciotti, J.M. Shea, Journal of Geophysical Research: Atmospheres
120 (2015) 3139–3157.'
date_created: 2023-02-20T08:16:28Z
date_published: 2015-04-18T00:00:00Z
date_updated: 2023-02-24T09:16:26Z
day: '18'
doi: 10.1002/2015jd023137
extern: '1'
intvolume: ' 120'
issue: '8'
keyword:
- Space and Planetary Science
- Earth and Planetary Sciences (miscellaneous)
- Atmospheric Science
- Geophysics
language:
- iso: eng
month: '04'
oa_version: Published Version
page: 3139-3157
publication: 'Journal of Geophysical Research: Atmospheres'
publication_identifier:
eissn:
- 2169-8996
issn:
- 2169-897X
publication_status: published
publisher: American Geophysical Union
quality_controlled: '1'
scopus_import: '1'
status: public
title: 'Modeling 2 m air temperatures over mountain glaciers: Exploring the influence
of katabatic cooling and external warming'
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 120
year: '2015'
...
---
_id: '12629'
abstract:
- lang: eng
text: Meteorological studies in high-mountain environments form the basis of our
understanding of catchment hydrology and glacier accumulation and melt processes,
yet high-altitude (>4000 m above sea level, asl) observatories are rare. This
research presents meteorological data recorded between December 2012 and November
2013 at seven stations in Nepal, ranging in elevation from 3860 to 5360 m asl.
Seasonal and diurnal cycles in air temperature, vapour pressure, incoming short-wave
and long-wave radiation, atmospheric transmissivity, wind speed, and precipitation
are compared between sites. Solar radiation strongly affects diurnal temperature
and vapour pressure cycles, but local topography and valley-scale circulations
alter wind speed and precipitation cycles. The observed diurnal variability in
vertical temperature gradients in all seasons highlights the importance of in
situ measurements for melt modelling. The monsoon signal (progressive onset and
sharp end) is visible in all data-sets, and the passage of the remnants of Typhoon
Phailin in mid-October 2013 provides an interesting case study on the possible
effects of such storms on glaciers in the region.
article_processing_charge: No
article_type: original
author:
- first_name: J.M.
full_name: Shea, J.M.
last_name: Shea
- first_name: P.
full_name: Wagnon, P.
last_name: Wagnon
- first_name: W.W.
full_name: Immerzeel, W.W.
last_name: Immerzeel
- first_name: R.
full_name: Biron, R.
last_name: Biron
- first_name: F.
full_name: Brun, F.
last_name: Brun
- first_name: Francesca
full_name: Pellicciotti, Francesca
id: b28f055a-81ea-11ed-b70c-a9fe7f7b0e70
last_name: Pellicciotti
citation:
ama: Shea JM, Wagnon P, Immerzeel WW, Biron R, Brun F, Pellicciotti F. A comparative
high-altitude meteorological analysis from three catchments in the Nepalese Himalaya.
International Journal of Water Resources Development. 2015;31(2):174-200.
doi:10.1080/07900627.2015.1020417
apa: Shea, J. M., Wagnon, P., Immerzeel, W. W., Biron, R., Brun, F., & Pellicciotti,
F. (2015). A comparative high-altitude meteorological analysis from three catchments
in the Nepalese Himalaya. International Journal of Water Resources Development.
Taylor & Francis. https://doi.org/10.1080/07900627.2015.1020417
chicago: Shea, J.M., P. Wagnon, W.W. Immerzeel, R. Biron, F. Brun, and Francesca
Pellicciotti. “A Comparative High-Altitude Meteorological Analysis from Three
Catchments in the Nepalese Himalaya.” International Journal of Water Resources
Development. Taylor & Francis, 2015. https://doi.org/10.1080/07900627.2015.1020417.
ieee: J. M. Shea, P. Wagnon, W. W. Immerzeel, R. Biron, F. Brun, and F. Pellicciotti,
“A comparative high-altitude meteorological analysis from three catchments in
the Nepalese Himalaya,” International Journal of Water Resources Development,
vol. 31, no. 2. Taylor & Francis, pp. 174–200, 2015.
ista: Shea JM, Wagnon P, Immerzeel WW, Biron R, Brun F, Pellicciotti F. 2015. A
comparative high-altitude meteorological analysis from three catchments in the
Nepalese Himalaya. International Journal of Water Resources Development. 31(2),
174–200.
mla: Shea, J. M., et al. “A Comparative High-Altitude Meteorological Analysis from
Three Catchments in the Nepalese Himalaya.” International Journal of Water
Resources Development, vol. 31, no. 2, Taylor & Francis, 2015, pp. 174–200,
doi:10.1080/07900627.2015.1020417.
short: J.M. Shea, P. Wagnon, W.W. Immerzeel, R. Biron, F. Brun, F. Pellicciotti,
International Journal of Water Resources Development 31 (2015) 174–200.
date_created: 2023-02-20T08:16:17Z
date_published: 2015-04-18T00:00:00Z
date_updated: 2023-02-24T09:30:42Z
day: '18'
doi: 10.1080/07900627.2015.1020417
extern: '1'
intvolume: ' 31'
issue: '2'
keyword:
- Water Science and Technology
- Development
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.1080/07900627.2015.1020417
month: '04'
oa: 1
oa_version: Published Version
page: 174-200
publication: International Journal of Water Resources Development
publication_identifier:
eissn:
- 1360-0648
issn:
- 0790-0627
publication_status: published
publisher: Taylor & Francis
quality_controlled: '1'
scopus_import: '1'
status: public
title: A comparative high-altitude meteorological analysis from three catchments in
the Nepalese Himalaya
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 31
year: '2015'
...
---
_id: '12626'
abstract:
- lang: eng
text: Ice cliffs have been identified as a reason for higher ablation rates on debris-covered
glaciers than are implied by the insulation effects of the debris. This study
aims to improve our understanding of cliff backwasting, and the role of radiative
fluxes in particular. An energy-balance model is forced with new data gathered
in May and October 2013 on Lirung Glacier, Nepalese Himalaya. Observations show
substantial variability in melt between cliffs, between locations on any cliff
and between seasons. Using a high-resolution digital elevation model we calculate
longwave fluxes incident to the cliff from surrounding terrain and include the
effect of local shading on shortwave radiation. This is an advance over previous
studies, that made simplified assumptions on cliff geometry and radiative fluxes.
Measured melt rates varied between 3.25 and 8.6 cm d−1 in May and 0.18 and 1.34
cm d−1 in October. Model results reproduce the strong variability in space and
time, suggesting considerable differences in radiative fluxes over one cliff.
In October the model fails to reproduce stake readings, probably due to the lack
of a refreezing component. Disregarding local topography can lead to overestimation
of melt at the point scale by up to ∼9%.
article_processing_charge: No
article_type: original
author:
- first_name: Jakob F.
full_name: Steiner, Jakob F.
last_name: Steiner
- first_name: Francesca
full_name: Pellicciotti, Francesca
id: b28f055a-81ea-11ed-b70c-a9fe7f7b0e70
last_name: Pellicciotti
- first_name: Pascal
full_name: Buri, Pascal
last_name: Buri
- first_name: Evan S.
full_name: Miles, Evan S.
last_name: Miles
- first_name: Walter W.
full_name: Immerzeel, Walter W.
last_name: Immerzeel
- first_name: Tim D.
full_name: Reid, Tim D.
last_name: Reid
citation:
ama: Steiner JF, Pellicciotti F, Buri P, Miles ES, Immerzeel WW, Reid TD. Modelling
ice-cliff backwasting on a debris-covered glacier in the Nepalese Himalaya. Journal
of Glaciology. 2015;61(229):889-907. doi:10.3189/2015jog14j194
apa: Steiner, J. F., Pellicciotti, F., Buri, P., Miles, E. S., Immerzeel, W. W.,
& Reid, T. D. (2015). Modelling ice-cliff backwasting on a debris-covered
glacier in the Nepalese Himalaya. Journal of Glaciology. International
Glaciological Society. https://doi.org/10.3189/2015jog14j194
chicago: Steiner, Jakob F., Francesca Pellicciotti, Pascal Buri, Evan S. Miles,
Walter W. Immerzeel, and Tim D. Reid. “Modelling Ice-Cliff Backwasting on a Debris-Covered
Glacier in the Nepalese Himalaya.” Journal of Glaciology. International
Glaciological Society, 2015. https://doi.org/10.3189/2015jog14j194.
ieee: J. F. Steiner, F. Pellicciotti, P. Buri, E. S. Miles, W. W. Immerzeel, and
T. D. Reid, “Modelling ice-cliff backwasting on a debris-covered glacier in the
Nepalese Himalaya,” Journal of Glaciology, vol. 61, no. 229. International
Glaciological Society, pp. 889–907, 2015.
ista: Steiner JF, Pellicciotti F, Buri P, Miles ES, Immerzeel WW, Reid TD. 2015.
Modelling ice-cliff backwasting on a debris-covered glacier in the Nepalese Himalaya.
Journal of Glaciology. 61(229), 889–907.
mla: Steiner, Jakob F., et al. “Modelling Ice-Cliff Backwasting on a Debris-Covered
Glacier in the Nepalese Himalaya.” Journal of Glaciology, vol. 61, no.
229, International Glaciological Society, 2015, pp. 889–907, doi:10.3189/2015jog14j194.
short: J.F. Steiner, F. Pellicciotti, P. Buri, E.S. Miles, W.W. Immerzeel, T.D.
Reid, Journal of Glaciology 61 (2015) 889–907.
date_created: 2023-02-20T08:16:01Z
date_published: 2015-07-01T00:00:00Z
date_updated: 2023-02-24T09:43:14Z
day: '01'
doi: 10.3189/2015jog14j194
extern: '1'
intvolume: ' 61'
issue: '229'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.3189/2015JoG14J194
month: '07'
oa: 1
oa_version: Published Version
page: 889-907
publication: Journal of Glaciology
publication_identifier:
eissn:
- 1727-5652
issn:
- 0022-1430
publication_status: published
publisher: International Glaciological Society
quality_controlled: '1'
scopus_import: '1'
status: public
title: Modelling ice-cliff backwasting on a debris-covered glacier in the Nepalese
Himalaya
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 61
year: '2015'
...
---
_id: '12627'
abstract:
- lang: eng
text: Spatial evolution of supraglacial debris cover on mountain glaciers is a largely
unmonitored and poorly understood phenomenon that directly affects glacier melt.
Supraglacial debris cover for 93 glaciers in the Karakoram, northern Pakistan,
was mapped from Landsat imagery acquired in 1977, 1998, 2009 and 2014. Surge-type
glaciers occupy 41% of the study area and were considered separately. The time
series of debris-covered surface area change shows a mean value of zero or near-zero
change for both surging and non-surging glaciers. An increase in debris-covered
area is often associated with negative regional mass balances. We extend this
logic to suggest that the stable regional mass balances in the Karakoram explain
the zero or near-zero change in debris-covered area. This coupling of trends combined
with our 37 year time series of data suggests the Karakoram anomaly extends further
back in time than previously known.
article_processing_charge: No
article_type: original
author:
- first_name: Sam
full_name: Herreid, Sam
last_name: Herreid
- first_name: Francesca
full_name: Pellicciotti, Francesca
id: b28f055a-81ea-11ed-b70c-a9fe7f7b0e70
last_name: Pellicciotti
- first_name: Alvaro
full_name: Ayala, Alvaro
last_name: Ayala
- first_name: Anna
full_name: Chesnokova, Anna
last_name: Chesnokova
- first_name: Christian
full_name: Kienholz, Christian
last_name: Kienholz
- first_name: Joseph
full_name: Shea, Joseph
last_name: Shea
- first_name: Arun
full_name: Shrestha, Arun
last_name: Shrestha
citation:
ama: Herreid S, Pellicciotti F, Ayala A, et al. Satellite observations show no net
change in the percentage of supraglacial debris-covered area in northern Pakistan
from 1977 to 2014. Journal of Glaciology. 2015;61(227):524-536. doi:10.3189/2015jog14j227
apa: Herreid, S., Pellicciotti, F., Ayala, A., Chesnokova, A., Kienholz, C., Shea,
J., & Shrestha, A. (2015). Satellite observations show no net change in the
percentage of supraglacial debris-covered area in northern Pakistan from 1977
to 2014. Journal of Glaciology. International Glaciological Society. https://doi.org/10.3189/2015jog14j227
chicago: Herreid, Sam, Francesca Pellicciotti, Alvaro Ayala, Anna Chesnokova, Christian
Kienholz, Joseph Shea, and Arun Shrestha. “Satellite Observations Show No Net
Change in the Percentage of Supraglacial Debris-Covered Area in Northern Pakistan
from 1977 to 2014.” Journal of Glaciology. International Glaciological
Society, 2015. https://doi.org/10.3189/2015jog14j227.
ieee: S. Herreid et al., “Satellite observations show no net change in the
percentage of supraglacial debris-covered area in northern Pakistan from 1977
to 2014,” Journal of Glaciology, vol. 61, no. 227. International Glaciological
Society, pp. 524–536, 2015.
ista: Herreid S, Pellicciotti F, Ayala A, Chesnokova A, Kienholz C, Shea J, Shrestha
A. 2015. Satellite observations show no net change in the percentage of supraglacial
debris-covered area in northern Pakistan from 1977 to 2014. Journal of Glaciology.
61(227), 524–536.
mla: Herreid, Sam, et al. “Satellite Observations Show No Net Change in the Percentage
of Supraglacial Debris-Covered Area in Northern Pakistan from 1977 to 2014.” Journal
of Glaciology, vol. 61, no. 227, International Glaciological Society, 2015,
pp. 524–36, doi:10.3189/2015jog14j227.
short: S. Herreid, F. Pellicciotti, A. Ayala, A. Chesnokova, C. Kienholz, J. Shea,
A. Shrestha, Journal of Glaciology 61 (2015) 524–536.
date_created: 2023-02-20T08:16:06Z
date_published: 2015-05-01T00:00:00Z
date_updated: 2023-02-24T09:40:30Z
day: '01'
doi: 10.3189/2015jog14j227
extern: '1'
intvolume: ' 61'
issue: '227'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.3189/2015JoG14J227
month: '05'
oa: 1
oa_version: Published Version
page: 524-536
publication: Journal of Glaciology
publication_identifier:
eissn:
- 1727-5652
issn:
- 0022-1430
publication_status: published
publisher: International Glaciological Society
quality_controlled: '1'
scopus_import: '1'
status: public
title: Satellite observations show no net change in the percentage of supraglacial
debris-covered area in northern Pakistan from 1977 to 2014
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 61
year: '2015'
...
---
_id: '1618'
abstract:
- lang: eng
text: CCL19 and CCL21 are chemokines involved in the trafficking of immune cells,
particularly within the lymphatic system, through activation of CCR7. Concurrent
expression of PSGL-1 and CCR7 in naive T-cells enhances recruitment of these cells
to secondary lymphoid organs by CCL19 and CCL21. Here the solution structure of
CCL19 is reported. It contains a canonical chemokine domain. Chemical shift mapping
shows the N-termini of PSGL-1 and CCR7 have overlapping binding sites for CCL19
and binding is competitive. Implications for the mechanism of PSGL-1's enhancement
of resting T-cell recruitment are discussed.
article_processing_charge: No
author:
- first_name: Christopher
full_name: Veldkamp, Christopher
last_name: Veldkamp
- first_name: Eva
full_name: Kiermaier, Eva
id: 3EB04B78-F248-11E8-B48F-1D18A9856A87
last_name: Kiermaier
orcid: 0000-0001-6165-5738
- first_name: Skylar
full_name: Gabel Eissens, Skylar
last_name: Gabel Eissens
- first_name: Miranda
full_name: Gillitzer, Miranda
last_name: Gillitzer
- first_name: David
full_name: Lippner, David
last_name: Lippner
- first_name: Frank
full_name: Disilvio, Frank
last_name: Disilvio
- first_name: Casey
full_name: Mueller, Casey
last_name: Mueller
- first_name: Paeton
full_name: Wantuch, Paeton
last_name: Wantuch
- first_name: Gary
full_name: Chaffee, Gary
last_name: Chaffee
- first_name: Michael
full_name: Famiglietti, Michael
last_name: Famiglietti
- first_name: Danielle
full_name: Zgoba, Danielle
last_name: Zgoba
- first_name: Asha
full_name: Bailey, Asha
last_name: Bailey
- first_name: Yaya
full_name: Bah, Yaya
last_name: Bah
- first_name: Samantha
full_name: Engebretson, Samantha
last_name: Engebretson
- first_name: David
full_name: Graupner, David
last_name: Graupner
- first_name: Emily
full_name: Lackner, Emily
last_name: Lackner
- first_name: Vincent
full_name: Larosa, Vincent
last_name: Larosa
- first_name: Tysha
full_name: Medeiros, Tysha
last_name: Medeiros
- first_name: Michael
full_name: Olson, Michael
last_name: Olson
- first_name: Andrew
full_name: Phillips, Andrew
last_name: Phillips
- first_name: Harley
full_name: Pyles, Harley
last_name: Pyles
- first_name: Amanda
full_name: Richard, Amanda
last_name: Richard
- first_name: Scott
full_name: Schoeller, Scott
last_name: Schoeller
- first_name: Boris
full_name: Touzeau, Boris
last_name: Touzeau
- first_name: Larry
full_name: Williams, Larry
last_name: Williams
- 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: Francis
full_name: Peterson, Francis
last_name: Peterson
citation:
ama: Veldkamp C, Kiermaier E, Gabel Eissens S, et al. Solution structure of CCL19
and identification of overlapping CCR7 and PSGL-1 binding sites. Biochemistry.
2015;54(27):4163-4166. doi:10.1021/acs.biochem.5b00560
apa: Veldkamp, C., Kiermaier, E., Gabel Eissens, S., Gillitzer, M., Lippner, D.,
Disilvio, F., … Peterson, F. (2015). Solution structure of CCL19 and identification
of overlapping CCR7 and PSGL-1 binding sites. Biochemistry. American Chemical
Society. https://doi.org/10.1021/acs.biochem.5b00560
chicago: Veldkamp, Christopher, Eva Kiermaier, Skylar Gabel Eissens, Miranda Gillitzer,
David Lippner, Frank Disilvio, Casey Mueller, et al. “Solution Structure of CCL19
and Identification of Overlapping CCR7 and PSGL-1 Binding Sites.” Biochemistry.
American Chemical Society, 2015. https://doi.org/10.1021/acs.biochem.5b00560.
ieee: C. Veldkamp et al., “Solution structure of CCL19 and identification
of overlapping CCR7 and PSGL-1 binding sites,” Biochemistry, vol. 54, no.
27. American Chemical Society, pp. 4163–4166, 2015.
ista: Veldkamp C, Kiermaier E, Gabel Eissens S, Gillitzer M, Lippner D, Disilvio
F, Mueller C, Wantuch P, Chaffee G, Famiglietti M, Zgoba D, Bailey A, Bah Y, Engebretson
S, Graupner D, Lackner E, Larosa V, Medeiros T, Olson M, Phillips A, Pyles H,
Richard A, Schoeller S, Touzeau B, Williams L, Sixt MK, Peterson F. 2015. Solution
structure of CCL19 and identification of overlapping CCR7 and PSGL-1 binding sites.
Biochemistry. 54(27), 4163–4166.
mla: Veldkamp, Christopher, et al. “Solution Structure of CCL19 and Identification
of Overlapping CCR7 and PSGL-1 Binding Sites.” Biochemistry, vol. 54, no.
27, American Chemical Society, 2015, pp. 4163–66, doi:10.1021/acs.biochem.5b00560.
short: C. Veldkamp, E. Kiermaier, S. Gabel Eissens, M. Gillitzer, D. Lippner, F.
Disilvio, C. Mueller, P. Wantuch, G. Chaffee, M. Famiglietti, D. Zgoba, A. Bailey,
Y. Bah, S. Engebretson, D. Graupner, E. Lackner, V. Larosa, T. Medeiros, M. Olson,
A. Phillips, H. Pyles, A. Richard, S. Schoeller, B. Touzeau, L. Williams, M.K.
Sixt, F. Peterson, Biochemistry 54 (2015) 4163–4166.
date_created: 2018-12-11T11:53:03Z
date_published: 2015-06-26T00:00:00Z
date_updated: 2023-03-30T11:32:57Z
day: '26'
department:
- _id: MiSi
doi: 10.1021/acs.biochem.5b00560
ec_funded: 1
external_id:
pmid:
- '26115234'
intvolume: ' 54'
issue: '27'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4809050/
month: '06'
oa: 1
oa_version: Submitted Version
page: 4163 - 4166
pmid: 1
project:
- _id: 25A603A2-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '281556'
name: Cytoskeletal force generation and force transduction of migrating leukocytes
(EU)
publication: Biochemistry
publication_status: published
publisher: American Chemical Society
publist_id: '5548'
quality_controlled: '1'
scopus_import: '1'
status: public
title: Solution structure of CCL19 and identification of overlapping CCR7 and PSGL-1
binding sites
type: journal_article
user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87
volume: 54
year: '2015'
...