---
_id: '715'
abstract:
- lang: eng
text: D-cycloserine ameliorates breathing abnormalities and survival rate in a mouse
model of Rett syndrome.
article_number: aao4218
author:
- first_name: Gaia
full_name: Novarino, Gaia
id: 3E57A680-F248-11E8-B48F-1D18A9856A87
last_name: Novarino
orcid: 0000-0002-7673-7178
citation:
ama: Novarino G. More excitation for Rett syndrome. Science Translational Medicine.
2017;9(405). doi:10.1126/scitranslmed.aao4218
apa: Novarino, G. (2017). More excitation for Rett syndrome. Science Translational
Medicine. American Association for the Advancement of Science. https://doi.org/10.1126/scitranslmed.aao4218
chicago: Novarino, Gaia. “More Excitation for Rett Syndrome.” Science Translational
Medicine. American Association for the Advancement of Science, 2017. https://doi.org/10.1126/scitranslmed.aao4218.
ieee: G. Novarino, “More excitation for Rett syndrome,” Science Translational
Medicine, vol. 9, no. 405. American Association for the Advancement of Science,
2017.
ista: Novarino G. 2017. More excitation for Rett syndrome. Science Translational
Medicine. 9(405), aao4218.
mla: Novarino, Gaia. “More Excitation for Rett Syndrome.” Science Translational
Medicine, vol. 9, no. 405, aao4218, American Association for the Advancement
of Science, 2017, doi:10.1126/scitranslmed.aao4218.
short: G. Novarino, Science Translational Medicine 9 (2017).
date_created: 2018-12-11T11:48:06Z
date_published: 2017-08-30T00:00:00Z
date_updated: 2021-01-12T08:12:04Z
day: '30'
department:
- _id: GaNo
doi: 10.1126/scitranslmed.aao4218
intvolume: ' 9'
issue: '405'
language:
- iso: eng
month: '08'
oa_version: None
publication: Science Translational Medicine
publication_identifier:
issn:
- '19466234'
publication_status: published
publisher: American Association for the Advancement of Science
publist_id: '6968'
quality_controlled: '1'
scopus_import: 1
status: public
title: More excitation for Rett syndrome
type: journal_article
user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87
volume: 9
year: '2017'
...
---
_id: '716'
abstract:
- lang: eng
text: 'Two-player games on graphs are central in many problems in formal verification
and program analysis, such as synthesis and verification of open systems. In this
work, we consider solving recursive game graphs (or pushdown game graphs) that
model the control flow of sequential programs with recursion.While pushdown games
have been studied before with qualitative objectives-such as reachability and
?-regular objectives- in this work, we study for the first time such games with
the most well-studied quantitative objective, the mean-payoff objective. In pushdown
games, two types of strategies are relevant: (1) global strategies, which depend
on the entire global history; and (2) modular strategies, which have only local
memory and thus do not depend on the context of invocation but rather only on
the history of the current invocation of the module. Our main results are as follows:
(1) One-player pushdown games with mean-payoff objectives under global strategies
are decidable in polynomial time. (2) Two-player pushdown games with mean-payoff
objectives under global strategies are undecidable. (3) One-player pushdown games
with mean-payoff objectives under modular strategies are NP-hard. (4) Two-player
pushdown games with mean-payoff objectives under modular strategies can be solved
in NP (i.e., both one-player and two-player pushdown games with mean-payoff objectives
under modular strategies are NP-complete). We also establish the optimal strategy
complexity by showing that global strategies for mean-payoff objectives require
infinite memory even in one-player pushdown games and memoryless modular strategies
are sufficient in two-player pushdown games. Finally, we also show that all the
problems have the same complexity if the stack boundedness condition is added,
where along with the mean-payoff objective the player must also ensure that the
stack height is bounded.'
article_type: original
author:
- first_name: Krishnendu
full_name: Chatterjee, Krishnendu
id: 2E5DCA20-F248-11E8-B48F-1D18A9856A87
last_name: Chatterjee
orcid: 0000-0002-4561-241X
- first_name: Yaron
full_name: Velner, Yaron
last_name: Velner
citation:
ama: Chatterjee K, Velner Y. The complexity of mean-payoff pushdown games. Journal
of the ACM. 2017;64(5):34. doi:10.1145/3121408
apa: Chatterjee, K., & Velner, Y. (2017). The complexity of mean-payoff pushdown
games. Journal of the ACM. ACM. https://doi.org/10.1145/3121408
chicago: Chatterjee, Krishnendu, and Yaron Velner. “The Complexity of Mean-Payoff
Pushdown Games.” Journal of the ACM. ACM, 2017. https://doi.org/10.1145/3121408.
ieee: K. Chatterjee and Y. Velner, “The complexity of mean-payoff pushdown games,”
Journal of the ACM, vol. 64, no. 5. ACM, p. 34, 2017.
ista: Chatterjee K, Velner Y. 2017. The complexity of mean-payoff pushdown games.
Journal of the ACM. 64(5), 34.
mla: Chatterjee, Krishnendu, and Yaron Velner. “The Complexity of Mean-Payoff Pushdown
Games.” Journal of the ACM, vol. 64, no. 5, ACM, 2017, p. 34, doi:10.1145/3121408.
short: K. Chatterjee, Y. Velner, Journal of the ACM 64 (2017) 34.
date_created: 2018-12-11T11:48:06Z
date_published: 2017-09-01T00:00:00Z
date_updated: 2021-01-12T08:12:08Z
day: '01'
department:
- _id: KrCh
doi: 10.1145/3121408
ec_funded: 1
external_id:
arxiv:
- '1201.2829'
intvolume: ' 64'
issue: '5'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/1201.2829
month: '09'
oa: 1
oa_version: Preprint
page: '34'
project:
- _id: 2584A770-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: P 23499-N23
name: Modern Graph Algorithmic Techniques in Formal Verification
- _id: 25863FF4-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: S11407
name: Game Theory
- _id: 2581B60A-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '279307'
name: 'Quantitative Graph Games: Theory and Applications'
publication: Journal of the ACM
publication_identifier:
issn:
- '00045411'
publication_status: published
publisher: ACM
publist_id: '6964'
quality_controlled: '1'
scopus_import: 1
status: public
title: The complexity of mean-payoff pushdown games
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 64
year: '2017'
...
---
_id: '717'
abstract:
- lang: eng
text: 'We consider finite-state and recursive game graphs with multidimensional
mean-payoff objectives. In recursive games two types of strategies are relevant:
global strategies and modular strategies. Our contributions are: (1) We show that
finite-state multidimensional mean-payoff games can be solved in polynomial time
if the number of dimensions and the maximal absolute value of weights are fixed;
whereas for arbitrary dimensions the problem is coNP-complete. (2) We show that
one-player recursive games with multidimensional mean-payoff objectives can be
solved in polynomial time. Both above algorithms are based on hyperplane separation
technique. (3) For recursive games we show that under modular strategies the multidimensional
problem is undecidable. We show that if the number of modules, exits, and the
maximal absolute value of the weights are fixed, then one-dimensional recursive
mean-payoff games under modular strategies can be solved in polynomial time, whereas
for unbounded number of exits or modules the problem is NP-hard.'
acknowledgement: 'The research was supported by Austrian Science Fund (FWF) Grant
No. P 23499-N23, FWF NFN Grant No. S11407-N23 (RiSE), ERC Start grant (279307: Graph
Games), Microsoft faculty fellows award, the RICH Model Toolkit (ICT COST Action
IC0901), and was carried out in partial fulfillment of the requirements for the
Ph.D. degree of the second author.'
author:
- first_name: Krishnendu
full_name: Chatterjee, Krishnendu
id: 2E5DCA20-F248-11E8-B48F-1D18A9856A87
last_name: Chatterjee
orcid: 0000-0002-4561-241X
- first_name: Yaron
full_name: Velner, Yaron
last_name: Velner
citation:
ama: Chatterjee K, Velner Y. Hyperplane separation technique for multidimensional
mean-payoff games. Journal of Computer and System Sciences. 2017;88:236-259.
doi:10.1016/j.jcss.2017.04.005
apa: Chatterjee, K., & Velner, Y. (2017). Hyperplane separation technique for
multidimensional mean-payoff games. Journal of Computer and System Sciences.
Academic Press. https://doi.org/10.1016/j.jcss.2017.04.005
chicago: Chatterjee, Krishnendu, and Yaron Velner. “Hyperplane Separation Technique
for Multidimensional Mean-Payoff Games.” Journal of Computer and System Sciences.
Academic Press, 2017. https://doi.org/10.1016/j.jcss.2017.04.005.
ieee: K. Chatterjee and Y. Velner, “Hyperplane separation technique for multidimensional
mean-payoff games,” Journal of Computer and System Sciences, vol. 88. Academic
Press, pp. 236–259, 2017.
ista: Chatterjee K, Velner Y. 2017. Hyperplane separation technique for multidimensional
mean-payoff games. Journal of Computer and System Sciences. 88, 236–259.
mla: Chatterjee, Krishnendu, and Yaron Velner. “Hyperplane Separation Technique
for Multidimensional Mean-Payoff Games.” Journal of Computer and System Sciences,
vol. 88, Academic Press, 2017, pp. 236–59, doi:10.1016/j.jcss.2017.04.005.
short: K. Chatterjee, Y. Velner, Journal of Computer and System Sciences 88 (2017)
236–259.
date_created: 2018-12-11T11:48:07Z
date_published: 2017-09-01T00:00:00Z
date_updated: 2023-02-23T10:38:15Z
day: '01'
department:
- _id: KrCh
doi: 10.1016/j.jcss.2017.04.005
ec_funded: 1
intvolume: ' 88'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/1210.3141
month: '09'
oa: 1
oa_version: Preprint
page: 236 - 259
project:
- _id: 2584A770-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: P 23499-N23
name: Modern Graph Algorithmic Techniques in Formal Verification
- _id: 25863FF4-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: S11407
name: Game Theory
- _id: 2581B60A-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '279307'
name: 'Quantitative Graph Games: Theory and Applications'
- _id: 2587B514-B435-11E9-9278-68D0E5697425
name: Microsoft Research Faculty Fellowship
publication: Journal of Computer and System Sciences
publication_status: published
publisher: Academic Press
publist_id: '6963'
quality_controlled: '1'
related_material:
record:
- id: '2329'
relation: earlier_version
status: public
scopus_import: 1
status: public
title: Hyperplane separation technique for multidimensional mean-payoff games
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 88
year: '2017'
...
---
_id: '719'
abstract:
- lang: eng
text: 'The ubiquity of computation in modern machines and devices imposes a need
to assert the correctness of their behavior. Especially in the case of safety-critical
systems, their designers need to take measures that enforce their safe operation.
Formal methods has emerged as a research field that addresses this challenge:
by rigorously proving that all system executions adhere to their specifications,
the correctness of an implementation under concern can be assured. To achieve
this goal, a plethora of techniques are nowadays available, all of which are optimized
for different system types and application domains.'
author:
- first_name: Krishnendu
full_name: Chatterjee, Krishnendu
id: 2E5DCA20-F248-11E8-B48F-1D18A9856A87
last_name: Chatterjee
orcid: 0000-0002-4561-241X
- first_name: Rüdiger
full_name: Ehlers, Rüdiger
last_name: Ehlers
citation:
ama: 'Chatterjee K, Ehlers R. Special issue: Synthesis and SYNT 2014. Acta Informatica.
2017;54(6):543-544. doi:10.1007/s00236-017-0299-0'
apa: 'Chatterjee, K., & Ehlers, R. (2017). Special issue: Synthesis and SYNT
2014. Acta Informatica. Springer. https://doi.org/10.1007/s00236-017-0299-0'
chicago: 'Chatterjee, Krishnendu, and Rüdiger Ehlers. “Special Issue: Synthesis
and SYNT 2014.” Acta Informatica. Springer, 2017. https://doi.org/10.1007/s00236-017-0299-0.'
ieee: 'K. Chatterjee and R. Ehlers, “Special issue: Synthesis and SYNT 2014,” Acta
Informatica, vol. 54, no. 6. Springer, pp. 543–544, 2017.'
ista: 'Chatterjee K, Ehlers R. 2017. Special issue: Synthesis and SYNT 2014. Acta
Informatica. 54(6), 543–544.'
mla: 'Chatterjee, Krishnendu, and Rüdiger Ehlers. “Special Issue: Synthesis and
SYNT 2014.” Acta Informatica, vol. 54, no. 6, Springer, 2017, pp. 543–44,
doi:10.1007/s00236-017-0299-0.'
short: K. Chatterjee, R. Ehlers, Acta Informatica 54 (2017) 543–544.
date_created: 2018-12-11T11:48:07Z
date_published: 2017-09-01T00:00:00Z
date_updated: 2021-01-12T08:12:18Z
day: '01'
department:
- _id: KrCh
doi: 10.1007/s00236-017-0299-0
intvolume: ' 54'
issue: '6'
language:
- iso: eng
month: '09'
oa_version: None
page: 543 - 544
publication: Acta Informatica
publication_identifier:
issn:
- '00015903'
publication_status: published
publisher: Springer
publist_id: '6961'
quality_controlled: '1'
scopus_import: 1
status: public
title: 'Special issue: Synthesis and SYNT 2014'
type: journal_article
user_id: 4435EBFC-F248-11E8-B48F-1D18A9856A87
volume: 54
year: '2017'
...
---
_id: '720'
abstract:
- lang: eng
text: 'Advances in multi-unit recordings pave the way for statistical modeling of
activity patterns in large neural populations. Recent studies have shown that
the summed activity of all neurons strongly shapes the population response. A
separate recent finding has been that neural populations also exhibit criticality,
an anomalously large dynamic range for the probabilities of different population
activity patterns. Motivated by these two observations, we introduce a class of
probabilistic models which takes into account the prior knowledge that the neural
population could be globally coupled and close to critical. These models consist
of an energy function which parametrizes interactions between small groups of
neurons, and an arbitrary positive, strictly increasing, and twice differentiable
function which maps the energy of a population pattern to its probability. We
show that: 1) augmenting a pairwise Ising model with a nonlinearity yields an
accurate description of the activity of retinal ganglion cells which outperforms
previous models based on the summed activity of neurons; 2) prior knowledge that
the population is critical translates to prior expectations about the shape of
the nonlinearity; 3) the nonlinearity admits an interpretation in terms of a continuous
latent variable globally coupling the system whose distribution we can infer from
data. Our method is independent of the underlying system’s state space; hence,
it can be applied to other systems such as natural scenes or amino acid sequences
of proteins which are also known to exhibit criticality.'
article_number: e1005763
article_processing_charge: Yes
author:
- first_name: Jan
full_name: Humplik, Jan
id: 2E9627A8-F248-11E8-B48F-1D18A9856A87
last_name: Humplik
- first_name: Gasper
full_name: Tkacik, Gasper
id: 3D494DCA-F248-11E8-B48F-1D18A9856A87
last_name: Tkacik
orcid: 0000-0002-6699-1455
citation:
ama: Humplik J, Tkačik G. Probabilistic models for neural populations that naturally
capture global coupling and criticality. PLoS Computational Biology. 2017;13(9).
doi:10.1371/journal.pcbi.1005763
apa: Humplik, J., & Tkačik, G. (2017). Probabilistic models for neural populations
that naturally capture global coupling and criticality. PLoS Computational
Biology. Public Library of Science. https://doi.org/10.1371/journal.pcbi.1005763
chicago: Humplik, Jan, and Gašper Tkačik. “Probabilistic Models for Neural Populations
That Naturally Capture Global Coupling and Criticality.” PLoS Computational
Biology. Public Library of Science, 2017. https://doi.org/10.1371/journal.pcbi.1005763.
ieee: J. Humplik and G. Tkačik, “Probabilistic models for neural populations that
naturally capture global coupling and criticality,” PLoS Computational Biology,
vol. 13, no. 9. Public Library of Science, 2017.
ista: Humplik J, Tkačik G. 2017. Probabilistic models for neural populations that
naturally capture global coupling and criticality. PLoS Computational Biology.
13(9), e1005763.
mla: Humplik, Jan, and Gašper Tkačik. “Probabilistic Models for Neural Populations
That Naturally Capture Global Coupling and Criticality.” PLoS Computational
Biology, vol. 13, no. 9, e1005763, Public Library of Science, 2017, doi:10.1371/journal.pcbi.1005763.
short: J. Humplik, G. Tkačik, PLoS Computational Biology 13 (2017).
date_created: 2018-12-11T11:48:08Z
date_published: 2017-09-19T00:00:00Z
date_updated: 2021-01-12T08:12:21Z
day: '19'
ddc:
- '530'
- '571'
department:
- _id: GaTk
doi: 10.1371/journal.pcbi.1005763
file:
- access_level: open_access
checksum: 81107096c19771c36ddbe6f0282a3acb
content_type: application/pdf
creator: system
date_created: 2018-12-12T10:18:30Z
date_updated: 2020-07-14T12:47:53Z
file_id: '5352'
file_name: IST-2017-884-v1+1_journal.pcbi.1005763.pdf
file_size: 14167050
relation: main_file
file_date_updated: 2020-07-14T12:47:53Z
has_accepted_license: '1'
intvolume: ' 13'
issue: '9'
language:
- iso: eng
license: https://creativecommons.org/licenses/by/4.0/
month: '09'
oa: 1
oa_version: Published Version
project:
- _id: 255008E4-B435-11E9-9278-68D0E5697425
grant_number: RGP0065/2012
name: Information processing and computation in fish groups
- _id: 254D1A94-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: P 25651-N26
name: Sensitivity to higher-order statistics in natural scenes
publication: PLoS Computational Biology
publication_identifier:
issn:
- 1553734X
publication_status: published
publisher: Public Library of Science
publist_id: '6960'
pubrep_id: '884'
quality_controlled: '1'
scopus_import: 1
status: public
title: Probabilistic models for neural populations that naturally capture global coupling
and criticality
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: journal_article
user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87
volume: 13
year: '2017'
...
---
_id: '721'
abstract:
- lang: eng
text: 'Let S be a positivity-preserving symmetric linear operator acting on bounded
functions. The nonlinear equation -1/m=z+Sm with a parameter z in the complex
upper half-plane ℍ has a unique solution m with values in ℍ. We show that the
z-dependence of this solution can be represented as the Stieltjes transforms of
a family of probability measures v on ℝ. Under suitable conditions on S, we show
that v has a real analytic density apart from finitely many algebraic singularities
of degree at most 3. Our motivation comes from large random matrices. The solution
m determines the density of eigenvalues of two prominent matrix ensembles: (i)
matrices with centered independent entries whose variances are given by S and
(ii) matrices with correlated entries with a translation-invariant correlation
structure. Our analysis shows that the limiting eigenvalue density has only square
root singularities or cubic root cusps; no other singularities occur.'
author:
- first_name: Oskari H
full_name: Ajanki, Oskari H
id: 36F2FB7E-F248-11E8-B48F-1D18A9856A87
last_name: Ajanki
- first_name: Torben H
full_name: Krüger, Torben H
id: 3020C786-F248-11E8-B48F-1D18A9856A87
last_name: Krüger
orcid: 0000-0002-4821-3297
- first_name: László
full_name: Erdös, László
id: 4DBD5372-F248-11E8-B48F-1D18A9856A87
last_name: Erdös
orcid: 0000-0001-5366-9603
citation:
ama: Ajanki OH, Krüger TH, Erdös L. Singularities of solutions to quadratic vector
equations on the complex upper half plane. Communications on Pure and Applied
Mathematics. 2017;70(9):1672-1705. doi:10.1002/cpa.21639
apa: Ajanki, O. H., Krüger, T. H., & Erdös, L. (2017). Singularities of solutions
to quadratic vector equations on the complex upper half plane. Communications
on Pure and Applied Mathematics. Wiley-Blackwell. https://doi.org/10.1002/cpa.21639
chicago: Ajanki, Oskari H, Torben H Krüger, and László Erdös. “Singularities of
Solutions to Quadratic Vector Equations on the Complex Upper Half Plane.” Communications
on Pure and Applied Mathematics. Wiley-Blackwell, 2017. https://doi.org/10.1002/cpa.21639.
ieee: O. H. Ajanki, T. H. Krüger, and L. Erdös, “Singularities of solutions to quadratic
vector equations on the complex upper half plane,” Communications on Pure and
Applied Mathematics, vol. 70, no. 9. Wiley-Blackwell, pp. 1672–1705, 2017.
ista: Ajanki OH, Krüger TH, Erdös L. 2017. Singularities of solutions to quadratic
vector equations on the complex upper half plane. Communications on Pure and Applied
Mathematics. 70(9), 1672–1705.
mla: Ajanki, Oskari H., et al. “Singularities of Solutions to Quadratic Vector Equations
on the Complex Upper Half Plane.” Communications on Pure and Applied Mathematics,
vol. 70, no. 9, Wiley-Blackwell, 2017, pp. 1672–705, doi:10.1002/cpa.21639.
short: O.H. Ajanki, T.H. Krüger, L. Erdös, Communications on Pure and Applied Mathematics
70 (2017) 1672–1705.
date_created: 2018-12-11T11:48:08Z
date_published: 2017-09-01T00:00:00Z
date_updated: 2021-01-12T08:12:24Z
day: '01'
department:
- _id: LaEr
doi: 10.1002/cpa.21639
ec_funded: 1
intvolume: ' 70'
issue: '9'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/1512.03703
month: '09'
oa: 1
oa_version: Submitted Version
page: 1672 - 1705
project:
- _id: 258DCDE6-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '338804'
name: Random matrices, universality and disordered quantum systems
publication: Communications on Pure and Applied Mathematics
publication_identifier:
issn:
- '00103640'
publication_status: published
publisher: Wiley-Blackwell
publist_id: '6959'
quality_controlled: '1'
scopus_import: 1
status: public
title: Singularities of solutions to quadratic vector equations on the complex upper
half plane
type: journal_article
user_id: 4435EBFC-F248-11E8-B48F-1D18A9856A87
volume: 70
year: '2017'
...
---
_id: '722'
abstract:
- lang: eng
text: Plants are sessile organisms rooted in one place. The soil resources that
plants require are often distributed in a highly heterogeneous pattern. To aid
foraging, plants have evolved roots whose growth and development are highly responsive
to soil signals. As a result, 3D root architecture is shaped by myriad environmental
signals to ensure resource capture is optimised and unfavourable environments
are avoided. The first signals sensed by newly germinating seeds — gravity and
light — direct root growth into the soil to aid seedling establishment. Heterogeneous
soil resources, such as water, nitrogen and phosphate, also act as signals that
shape 3D root growth to optimise uptake. Root architecture is also modified through
biotic interactions that include soil fungi and neighbouring plants. This developmental
plasticity results in a ‘custom-made’ 3D root system that is best adapted to forage
for resources in each soil environment that a plant colonises.
author:
- first_name: Emily
full_name: Morris, Emily
last_name: Morris
- first_name: Marcus
full_name: Griffiths, Marcus
last_name: Griffiths
- first_name: Agata
full_name: Golebiowska, Agata
last_name: Golebiowska
- first_name: Stefan
full_name: Mairhofer, Stefan
last_name: Mairhofer
- first_name: Jasmine
full_name: Burr Hersey, Jasmine
last_name: Burr Hersey
- first_name: Tatsuaki
full_name: Goh, Tatsuaki
last_name: Goh
- first_name: Daniel
full_name: Von Wangenheim, Daniel
id: 49E91952-F248-11E8-B48F-1D18A9856A87
last_name: Von Wangenheim
orcid: 0000-0002-6862-1247
- first_name: Brian
full_name: Atkinson, Brian
last_name: Atkinson
- first_name: Craig
full_name: Sturrock, Craig
last_name: Sturrock
- first_name: Jonathan
full_name: Lynch, Jonathan
last_name: Lynch
- first_name: Kris
full_name: Vissenberg, Kris
last_name: Vissenberg
- first_name: Karl
full_name: Ritz, Karl
last_name: Ritz
- first_name: Darren
full_name: Wells, Darren
last_name: Wells
- first_name: Sacha
full_name: Mooney, Sacha
last_name: Mooney
- first_name: Malcolm
full_name: Bennett, Malcolm
last_name: Bennett
citation:
ama: Morris E, Griffiths M, Golebiowska A, et al. Shaping 3D root system architecture.
Current Biology. 2017;27(17):R919-R930. doi:10.1016/j.cub.2017.06.043
apa: Morris, E., Griffiths, M., Golebiowska, A., Mairhofer, S., Burr Hersey, J.,
Goh, T., … Bennett, M. (2017). Shaping 3D root system architecture. Current
Biology. Cell Press. https://doi.org/10.1016/j.cub.2017.06.043
chicago: Morris, Emily, Marcus Griffiths, Agata Golebiowska, Stefan Mairhofer, Jasmine
Burr Hersey, Tatsuaki Goh, Daniel von Wangenheim, et al. “Shaping 3D Root System
Architecture.” Current Biology. Cell Press, 2017. https://doi.org/10.1016/j.cub.2017.06.043.
ieee: E. Morris et al., “Shaping 3D root system architecture,” Current
Biology, vol. 27, no. 17. Cell Press, pp. R919–R930, 2017.
ista: Morris E, Griffiths M, Golebiowska A, Mairhofer S, Burr Hersey J, Goh T, von
Wangenheim D, Atkinson B, Sturrock C, Lynch J, Vissenberg K, Ritz K, Wells D,
Mooney S, Bennett M. 2017. Shaping 3D root system architecture. Current Biology.
27(17), R919–R930.
mla: Morris, Emily, et al. “Shaping 3D Root System Architecture.” Current Biology,
vol. 27, no. 17, Cell Press, 2017, pp. R919–30, doi:10.1016/j.cub.2017.06.043.
short: E. Morris, M. Griffiths, A. Golebiowska, S. Mairhofer, J. Burr Hersey, T.
Goh, D. von Wangenheim, B. Atkinson, C. Sturrock, J. Lynch, K. Vissenberg, K.
Ritz, D. Wells, S. Mooney, M. Bennett, Current Biology 27 (2017) R919–R930.
date_created: 2018-12-11T11:48:08Z
date_published: 2017-09-11T00:00:00Z
date_updated: 2021-01-12T08:12:29Z
day: '11'
ddc:
- '581'
department:
- _id: JiFr
doi: 10.1016/j.cub.2017.06.043
ec_funded: 1
external_id:
pmid:
- '28898665'
file:
- access_level: open_access
checksum: e45588b21097b408da6276a3e5eedb2e
content_type: application/pdf
creator: dernst
date_created: 2019-04-17T07:46:40Z
date_updated: 2020-07-14T12:47:54Z
file_id: '6332'
file_name: 2017_CurrentBiology_Morris.pdf
file_size: 1576593
relation: main_file
file_date_updated: 2020-07-14T12:47:54Z
has_accepted_license: '1'
intvolume: ' 27'
issue: '17'
language:
- iso: eng
license: https://creativecommons.org/licenses/by-nc-nd/4.0/
month: '09'
oa: 1
oa_version: Submitted Version
page: R919 - R930
pmid: 1
project:
- _id: 25681D80-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '291734'
name: International IST Postdoc Fellowship Programme
publication: Current Biology
publication_identifier:
issn:
- '09609822'
publication_status: published
publisher: Cell Press
publist_id: '6956'
pubrep_id: '982'
quality_controlled: '1'
scopus_import: 1
status: public
title: Shaping 3D root system architecture
tmp:
image: /images/cc_by_nc_nd.png
legal_code_url: https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode
name: Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International
(CC BY-NC-ND 4.0)
short: CC BY-NC-ND (4.0)
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 27
year: '2017'
...
---
_id: '725'
abstract:
- lang: eng
text: Individual computations and social interactions underlying collective behavior
in groups of animals are of great ethological, behavioral, and theoretical interest.
While complex individual behaviors have successfully been parsed into small dictionaries
of stereotyped behavioral modes, studies of collective behavior largely ignored
these findings; instead, their focus was on inferring single, mode-independent
social interaction rules that reproduced macroscopic and often qualitative features
of group behavior. Here, we bring these two approaches together to predict individual
swimming patterns of adult zebrafish in a group. We show that fish alternate between
an “active” mode, in which they are sensitive to the swimming patterns of conspecifics,
and a “passive” mode, where they ignore them. Using a model that accounts for
these two modes explicitly, we predict behaviors of individual fish with high
accuracy, outperforming previous approaches that assumed a single continuous computation
by individuals and simple metric or topological weighing of neighbors’ behavior.
At the group level, switching between active and passive modes is uncorrelated
among fish, but correlated directional swimming behavior still emerges. Our quantitative
approach for studying complex, multi-modal individual behavior jointly with emergent
group behavior is readily extensible to additional behavioral modes and their
neural correlates as well as to other species.
author:
- first_name: Roy
full_name: Harpaz, Roy
last_name: Harpaz
- first_name: Gasper
full_name: Tkacik, Gasper
id: 3D494DCA-F248-11E8-B48F-1D18A9856A87
last_name: Tkacik
orcid: 0000-0002-6699-1455
- first_name: Elad
full_name: Schneidman, Elad
last_name: Schneidman
citation:
ama: Harpaz R, Tkačik G, Schneidman E. Discrete modes of social information processing
predict individual behavior of fish in a group. PNAS. 2017;114(38):10149-10154.
doi:10.1073/pnas.1703817114
apa: Harpaz, R., Tkačik, G., & Schneidman, E. (2017). Discrete modes of social
information processing predict individual behavior of fish in a group. PNAS.
National Academy of Sciences. https://doi.org/10.1073/pnas.1703817114
chicago: Harpaz, Roy, Gašper Tkačik, and Elad Schneidman. “Discrete Modes of Social
Information Processing Predict Individual Behavior of Fish in a Group.” PNAS.
National Academy of Sciences, 2017. https://doi.org/10.1073/pnas.1703817114.
ieee: R. Harpaz, G. Tkačik, and E. Schneidman, “Discrete modes of social information
processing predict individual behavior of fish in a group,” PNAS, vol.
114, no. 38. National Academy of Sciences, pp. 10149–10154, 2017.
ista: Harpaz R, Tkačik G, Schneidman E. 2017. Discrete modes of social information
processing predict individual behavior of fish in a group. PNAS. 114(38), 10149–10154.
mla: Harpaz, Roy, et al. “Discrete Modes of Social Information Processing Predict
Individual Behavior of Fish in a Group.” PNAS, vol. 114, no. 38, National
Academy of Sciences, 2017, pp. 10149–54, doi:10.1073/pnas.1703817114.
short: R. Harpaz, G. Tkačik, E. Schneidman, PNAS 114 (2017) 10149–10154.
date_created: 2018-12-11T11:48:10Z
date_published: 2017-09-19T00:00:00Z
date_updated: 2021-01-12T08:12:36Z
day: '19'
department:
- _id: GaTk
doi: 10.1073/pnas.1703817114
external_id:
pmid:
- '28874581'
intvolume: ' 114'
issue: '38'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5617265/
month: '09'
oa: 1
oa_version: Submitted Version
page: 10149 - 10154
pmid: 1
publication: PNAS
publication_identifier:
issn:
- '00278424'
publication_status: published
publisher: National Academy of Sciences
publist_id: '6953'
quality_controlled: '1'
scopus_import: 1
status: public
title: Discrete modes of social information processing predict individual behavior
of fish in a group
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 114
year: '2017'
...
---
_id: '724'
abstract:
- lang: eng
text: We investigate the stationary and dynamical behavior of an Anderson localized
chain coupled to a single central bound state. Although this coupling partially
dilutes the Anderson localized peaks towards nearly resonant sites, the most weight
of the original peaks remains unchanged. This leads to multifractal wave functions
with a frozen spectrum of fractal dimensions, which is characteristic for localized
phases in models with power-law hopping. Using a perturbative approach we identify
two different dynamical regimes. At weak couplings to the central site, the transport
of particles and information is logarithmic in time, a feature usually attributed
to many-body localization. We connect such transport to the persistence of the
Poisson statistics of level spacings in parts of the spectrum. In contrast, at
stronger couplings the level repulsion is established in the entire spectrum,
the problem can be mapped to the Fano resonance, and the transport is ballistic.
acknowledgement: "We would like to thank Dmitry Abanin, Christophe De\r\nBeule,
\ Joel Moore, Romain Vasseur, and Norman Yao for\r\nmany stimulating discussions.
\ Financial support has been\r\nprovided by the Deutsche Forschungsgemeinschaft
\ (DFG)\r\nvia Grant No. TR950/8-1, SFB 1170 “ToCoTronics” and the\r\nENB Graduate
\ School on Topological Insulators. M.S. was\r\nsupported by Gordon and Betty
Moore Foundation’s EPiQS\r\nInitiative through Grant No. GBMF4307. F.P. acknowledges\r\nsupport
from the DFG Research Unit FOR 1807 through Grant\r\nNo. PO 1370/2-1."
article_number: '104203'
author:
- first_name: Daniel
full_name: Hetterich, Daniel
last_name: Hetterich
- first_name: Maksym
full_name: Serbyn, Maksym
id: 47809E7E-F248-11E8-B48F-1D18A9856A87
last_name: Serbyn
orcid: 0000-0002-2399-5827
- first_name: Fernando
full_name: Domínguez, Fernando
last_name: Domínguez
- first_name: Frank
full_name: Pollmann, Frank
last_name: Pollmann
- first_name: Björn
full_name: Trauzettel, Björn
last_name: Trauzettel
citation:
ama: Hetterich D, Serbyn M, Domínguez F, Pollmann F, Trauzettel B. Noninteracting
central site model localization and logarithmic entanglement growth. Physical
Review B. 2017;96(10). doi:10.1103/PhysRevB.96.104203
apa: Hetterich, D., Serbyn, M., Domínguez, F., Pollmann, F., & Trauzettel, B.
(2017). Noninteracting central site model localization and logarithmic entanglement
growth. Physical Review B. American Physical Society. https://doi.org/10.1103/PhysRevB.96.104203
chicago: Hetterich, Daniel, Maksym Serbyn, Fernando Domínguez, Frank Pollmann, and
Björn Trauzettel. “Noninteracting Central Site Model Localization and Logarithmic
Entanglement Growth.” Physical Review B. American Physical Society, 2017.
https://doi.org/10.1103/PhysRevB.96.104203.
ieee: D. Hetterich, M. Serbyn, F. Domínguez, F. Pollmann, and B. Trauzettel, “Noninteracting
central site model localization and logarithmic entanglement growth,” Physical
Review B, vol. 96, no. 10. American Physical Society, 2017.
ista: Hetterich D, Serbyn M, Domínguez F, Pollmann F, Trauzettel B. 2017. Noninteracting
central site model localization and logarithmic entanglement growth. Physical
Review B. 96(10), 104203.
mla: Hetterich, Daniel, et al. “Noninteracting Central Site Model Localization and
Logarithmic Entanglement Growth.” Physical Review B, vol. 96, no. 10, 104203,
American Physical Society, 2017, doi:10.1103/PhysRevB.96.104203.
short: D. Hetterich, M. Serbyn, F. Domínguez, F. Pollmann, B. Trauzettel, Physical
Review B 96 (2017).
date_created: 2018-12-11T11:48:09Z
date_published: 2017-09-13T00:00:00Z
date_updated: 2021-01-12T08:12:35Z
day: '13'
department:
- _id: MaSe
doi: 10.1103/PhysRevB.96.104203
intvolume: ' 96'
issue: '10'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/1701.02744
month: '09'
oa: 1
oa_version: Submitted Version
publication: Physical Review B
publication_identifier:
issn:
- '24699950'
publication_status: published
publisher: American Physical Society
publist_id: '6955'
quality_controlled: '1'
scopus_import: 1
status: public
title: Noninteracting central site model localization and logarithmic entanglement
growth
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 96
year: '2017'
...
---
_id: '7289'
abstract:
- lang: eng
text: Aprotic sodium–O2 batteries require the reversible formation/dissolution of
sodium superoxide (NaO2) on cycling. Poor cycle life has been associated with
parasitic chemistry caused by the reactivity of electrolyte and electrode with
NaO2, a strong nucleophile and base. Its reactivity can, however, not consistently
explain the side reactions and irreversibility. Herein we show that singlet oxygen
(1O2) forms at all stages of cycling and that it is a main driver for parasitic
chemistry. It was detected in‐ and ex‐situ via a 1O2 trap that selectively and
rapidly forms a stable adduct with 1O2. The 1O2 formation mechanism involves proton‐mediated
superoxide disproportionation on discharge, rest, and charge below ca. 3.3 V,
and direct electrochemical 1O2 evolution above ca. 3.3 V. Trace water, which is
needed for high capacities also drives parasitic chemistry. Controlling the highly
reactive singlet oxygen is thus crucial for achieving highly reversible cell operation.
article_processing_charge: No
article_type: original
author:
- first_name: Lukas
full_name: Schafzahl, Lukas
last_name: Schafzahl
- first_name: Nika
full_name: Mahne, Nika
last_name: Mahne
- first_name: Bettina
full_name: Schafzahl, Bettina
last_name: Schafzahl
- first_name: Martin
full_name: Wilkening, Martin
last_name: Wilkening
- first_name: Christian
full_name: Slugovc, Christian
last_name: Slugovc
- first_name: Sergey M.
full_name: Borisov, Sergey M.
last_name: Borisov
- first_name: Stefan Alexander
full_name: Freunberger, Stefan Alexander
id: A8CA28E6-CE23-11E9-AD2D-EC27E6697425
last_name: Freunberger
orcid: 0000-0003-2902-5319
citation:
ama: Schafzahl L, Mahne N, Schafzahl B, et al. Singlet oxygen during cycling of
the aprotic sodium-O2 battery. Angewandte Chemie International Edition.
2017;56(49):15728-15732. doi:10.1002/anie.201709351
apa: Schafzahl, L., Mahne, N., Schafzahl, B., Wilkening, M., Slugovc, C., Borisov,
S. M., & Freunberger, S. A. (2017). Singlet oxygen during cycling of the aprotic
sodium-O2 battery. Angewandte Chemie International Edition. Wiley. https://doi.org/10.1002/anie.201709351
chicago: Schafzahl, Lukas, Nika Mahne, Bettina Schafzahl, Martin Wilkening, Christian
Slugovc, Sergey M. Borisov, and Stefan Alexander Freunberger. “Singlet Oxygen
during Cycling of the Aprotic Sodium-O2 Battery.” Angewandte Chemie International
Edition. Wiley, 2017. https://doi.org/10.1002/anie.201709351.
ieee: L. Schafzahl et al., “Singlet oxygen during cycling of the aprotic
sodium-O2 battery,” Angewandte Chemie International Edition, vol. 56, no.
49. Wiley, pp. 15728–15732, 2017.
ista: Schafzahl L, Mahne N, Schafzahl B, Wilkening M, Slugovc C, Borisov SM, Freunberger
SA. 2017. Singlet oxygen during cycling of the aprotic sodium-O2 battery. Angewandte
Chemie International Edition. 56(49), 15728–15732.
mla: Schafzahl, Lukas, et al. “Singlet Oxygen during Cycling of the Aprotic Sodium-O2
Battery.” Angewandte Chemie International Edition, vol. 56, no. 49, Wiley,
2017, pp. 15728–32, doi:10.1002/anie.201709351.
short: L. Schafzahl, N. Mahne, B. Schafzahl, M. Wilkening, C. Slugovc, S.M. Borisov,
S.A. Freunberger, Angewandte Chemie International Edition 56 (2017) 15728–15732.
date_created: 2020-01-15T12:15:05Z
date_published: 2017-12-04T00:00:00Z
date_updated: 2021-01-12T08:12:47Z
day: '04'
ddc:
- '540'
doi: 10.1002/anie.201709351
extern: '1'
file:
- access_level: open_access
checksum: 3c5b1e51954554dffb13c7d58f69836c
content_type: application/pdf
creator: dernst
date_created: 2020-01-26T14:58:07Z
date_updated: 2020-07-14T12:47:55Z
file_id: '7362'
file_name: 2017_AngChemieInternat_Schafzahl.pdf
file_size: 1013492
relation: main_file
file_date_updated: 2020-07-14T12:47:55Z
has_accepted_license: '1'
intvolume: ' 56'
issue: '49'
language:
- iso: eng
license: https://creativecommons.org/licenses/by-nc/4.0/
month: '12'
oa: 1
oa_version: Published Version
page: 15728-15732
publication: Angewandte Chemie International Edition
publication_identifier:
issn:
- 1433-7851
publication_status: published
publisher: Wiley
quality_controlled: '1'
status: public
title: Singlet oxygen during cycling of the aprotic sodium-O2 battery
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: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 56
year: '2017'
...
---
_id: '7288'
abstract:
- lang: eng
text: Nowadays commercial supercapacitors are based on purely capacitive storage
at the porous carbons that are used for the electrodes. However, the limits that
capacitive storage imposes on energy density calls to investigate new materials
to improve the capacitance of the device. This new type of electrodes (e.g., RuO2,
MnO2…) involves pseudo-capacitive faradaic redox processes with the solid material.
Ion exchange with solid materials is, however, much slower than the adsorption
process in capacitive storage and inevitably leads to significant loss of power.
Faradaic process in the liquid state, in contrast can be similarly fast as capacitive
processes due to the fast ion transport. Designing new devices with liquid like
dynamics and improved specific capacitance is challenging. We present a new approach
to increase the specific capacitance using biredox ionic liquids, where redox
moieties are tethered to the electrolyte ions, allowing high redox concentrations
and significant pseudo-capacitive storage in the liquid state. Anions and cations
are functionalized with anthraquinone (AQ) and 2,2,6,6-tetramethylpiperidinyl-1-oxyl
(TEMPO) moieties, respectively. Glassy carbon, carbon-onion, and commercial activated
carbon electrodes that exhibit different double layer structures and thus different
diffusion dynamics were used to simultaneously study the electrochemical response
of biredox ionic liquids at the positive and negative electrode.
article_processing_charge: No
article_type: original
author:
- first_name: C.
full_name: Bodin, C.
last_name: Bodin
- first_name: E.
full_name: Mourad, E.
last_name: Mourad
- first_name: D.
full_name: Zigah, D.
last_name: Zigah
- first_name: S.
full_name: Le Vot, S.
last_name: Le Vot
- first_name: Stefan Alexander
full_name: Freunberger, Stefan Alexander
id: A8CA28E6-CE23-11E9-AD2D-EC27E6697425
last_name: Freunberger
orcid: 0000-0003-2902-5319
- first_name: F.
full_name: Favier, F.
last_name: Favier
- first_name: O.
full_name: Fontaine, O.
last_name: Fontaine
citation:
ama: 'Bodin C, Mourad E, Zigah D, et al. Biredox ionic liquids: New opportunities
toward high performance supercapacitors. Faraday Discussions. 2017;206:393-404.
doi:10.1039/c7fd00174f'
apa: 'Bodin, C., Mourad, E., Zigah, D., Le Vot, S., Freunberger, S. A., Favier,
F., & Fontaine, O. (2017). Biredox ionic liquids: New opportunities toward
high performance supercapacitors. Faraday Discussions. Royal Society of
Chemistry. https://doi.org/10.1039/c7fd00174f'
chicago: 'Bodin, C., E. Mourad, D. Zigah, S. Le Vot, Stefan Alexander Freunberger,
F. Favier, and O. Fontaine. “Biredox Ionic Liquids: New Opportunities toward High
Performance Supercapacitors.” Faraday Discussions. Royal Society of Chemistry,
2017. https://doi.org/10.1039/c7fd00174f.'
ieee: 'C. Bodin et al., “Biredox ionic liquids: New opportunities toward
high performance supercapacitors,” Faraday Discussions, vol. 206. Royal
Society of Chemistry, pp. 393–404, 2017.'
ista: 'Bodin C, Mourad E, Zigah D, Le Vot S, Freunberger SA, Favier F, Fontaine
O. 2017. Biredox ionic liquids: New opportunities toward high performance supercapacitors.
Faraday Discussions. 206, 393–404.'
mla: 'Bodin, C., et al. “Biredox Ionic Liquids: New Opportunities toward High Performance
Supercapacitors.” Faraday Discussions, vol. 206, Royal Society of Chemistry,
2017, pp. 393–404, doi:10.1039/c7fd00174f.'
short: C. Bodin, E. Mourad, D. Zigah, S. Le Vot, S.A. Freunberger, F. Favier, O.
Fontaine, Faraday Discussions 206 (2017) 393–404.
date_created: 2020-01-15T12:14:04Z
date_published: 2017-06-29T00:00:00Z
date_updated: 2021-06-10T06:17:17Z
day: '29'
doi: 10.1039/c7fd00174f
extern: '1'
intvolume: ' 206'
language:
- iso: eng
month: '06'
oa_version: None
page: 393-404
publication: Faraday Discussions
publication_identifier:
issn:
- 1359-6640
- 1364-5498
publication_status: published
publisher: Royal Society of Chemistry
quality_controlled: '1'
status: public
title: 'Biredox ionic liquids: New opportunities toward high performance supercapacitors'
type: journal_article
user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87
volume: 206
year: '2017'
...
---
_id: '7290'
abstract:
- lang: eng
text: 'We report a family of Pt and Pd benzoporphyrin dyes with versatile photophysical
properties and easy access from cheap and abundant chemicals. Attaching 4 or 8
alkylsulfone groups onto a meso-tetraphenyltetrabenzoporphyrin (TPTBP) macrocylcle
renders the dyes highly soluble in organic solvents, photostable, and electron-deficient
with the redox potential raised up to 0.65 V versus the parent porphyrin. The
new dyes intensively absorb in the blue (Soret band, 440–480 nm) and in the red
(Q-band, 620–650 nm) parts of the electromagnetic spectrum and show bright phosphorescence
at room-temperature in the NIR with quantum yields up to 30% in solution. The
small singlet–triplet energy gap yields unusually efficient thermally activated
delayed fluorescence (TADF) at elevated temperatures in solution and in polymeric
matrices with quantum yields as high as 27% at 120 °C, which is remarkable for
benzoporphyrins. Apart from oxygen sensing, these properties enable unprecedented
simultaneous, self-referenced oxygen and temperature sensing with a single indicator
dye: whereas oxygen can be determined either via the decay time of phosphorescence
or TADF, the temperature is accessed via the ratio of the two emissions. Moreover,
the dyes are efficient sensitizers for triplet–triplet annihilation (TTA)-based
upconversion making possible longer sensitization wavelength than the conventional
benzoporphyrin complexes. The Pt-octa-sulfone dye also features interesting semireversible
transformation in basic media, which generates new NIR absorbing species.'
article_processing_charge: No
article_type: original
author:
- first_name: Peter W.
full_name: Zach, Peter W.
last_name: Zach
- first_name: Stefan Alexander
full_name: Freunberger, Stefan Alexander
id: A8CA28E6-CE23-11E9-AD2D-EC27E6697425
last_name: Freunberger
orcid: 0000-0003-2902-5319
- first_name: Ingo
full_name: Klimant, Ingo
last_name: Klimant
- first_name: Sergey M.
full_name: Borisov, Sergey M.
last_name: Borisov
citation:
ama: 'Zach PW, Freunberger SA, Klimant I, Borisov SM. Electron-deficient near-infrared
Pt(II) and Pd(II) benzoporphyrins with dual phosphorescence and unusually efficient
thermally activated delayed fluorescence: First demonstration of simultaneous
oxygen and temperature sensing with a single emitter. ACS Applied Materials
& Interfaces. 2017;9(43):38008-38023. doi:10.1021/acsami.7b10669'
apa: 'Zach, P. W., Freunberger, S. A., Klimant, I., & Borisov, S. M. (2017).
Electron-deficient near-infrared Pt(II) and Pd(II) benzoporphyrins with dual phosphorescence
and unusually efficient thermally activated delayed fluorescence: First demonstration
of simultaneous oxygen and temperature sensing with a single emitter. ACS Applied
Materials & Interfaces. ACS. https://doi.org/10.1021/acsami.7b10669'
chicago: 'Zach, Peter W., Stefan Alexander Freunberger, Ingo Klimant, and Sergey
M. Borisov. “Electron-Deficient near-Infrared Pt(II) and Pd(II) Benzoporphyrins
with Dual Phosphorescence and Unusually Efficient Thermally Activated Delayed
Fluorescence: First Demonstration of Simultaneous Oxygen and Temperature Sensing
with a Single Emitter.” ACS Applied Materials & Interfaces. ACS, 2017.
https://doi.org/10.1021/acsami.7b10669.'
ieee: 'P. W. Zach, S. A. Freunberger, I. Klimant, and S. M. Borisov, “Electron-deficient
near-infrared Pt(II) and Pd(II) benzoporphyrins with dual phosphorescence and
unusually efficient thermally activated delayed fluorescence: First demonstration
of simultaneous oxygen and temperature sensing with a single emitter,” ACS
Applied Materials & Interfaces, vol. 9, no. 43. ACS, pp. 38008–38023,
2017.'
ista: 'Zach PW, Freunberger SA, Klimant I, Borisov SM. 2017. Electron-deficient
near-infrared Pt(II) and Pd(II) benzoporphyrins with dual phosphorescence and
unusually efficient thermally activated delayed fluorescence: First demonstration
of simultaneous oxygen and temperature sensing with a single emitter. ACS Applied
Materials & Interfaces. 9(43), 38008–38023.'
mla: 'Zach, Peter W., et al. “Electron-Deficient near-Infrared Pt(II) and Pd(II)
Benzoporphyrins with Dual Phosphorescence and Unusually Efficient Thermally Activated
Delayed Fluorescence: First Demonstration of Simultaneous Oxygen and Temperature
Sensing with a Single Emitter.” ACS Applied Materials & Interfaces,
vol. 9, no. 43, ACS, 2017, pp. 38008–23, doi:10.1021/acsami.7b10669.'
short: P.W. Zach, S.A. Freunberger, I. Klimant, S.M. Borisov, ACS Applied Materials
& Interfaces 9 (2017) 38008–38023.
date_created: 2020-01-15T12:15:16Z
date_published: 2017-10-10T00:00:00Z
date_updated: 2021-01-12T08:12:48Z
day: '10'
ddc:
- '540'
- '543'
doi: 10.1021/acsami.7b10669
extern: '1'
file:
- access_level: open_access
checksum: 0461c990eb910f19a70c6e5349ec35ed
content_type: application/pdf
creator: sfreunbe
date_created: 2020-06-29T14:49:32Z
date_updated: 2020-07-14T12:47:55Z
file_id: '8051'
file_name: Paper_Manuscript_submitted.pdf
file_size: 2072792
relation: main_file
file_date_updated: 2020-07-14T12:47:55Z
has_accepted_license: '1'
intvolume: ' 9'
issue: '43'
language:
- iso: eng
month: '10'
oa: 1
oa_version: Submitted Version
page: 38008-38023
publication: ACS Applied Materials & Interfaces
publication_identifier:
eissn:
- 1944-8252
issn:
- 1944-8244
publication_status: published
publisher: ACS
quality_controlled: '1'
status: public
title: 'Electron-deficient near-infrared Pt(II) and Pd(II) benzoporphyrins with dual
phosphorescence and unusually efficient thermally activated delayed fluorescence:
First demonstration of simultaneous oxygen and temperature sensing with a single
emitter'
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 9
year: '2017'
...
---
_id: '7292'
abstract:
- lang: eng
text: 'Rechargeable Li–O2 batteries have amongst the highest formal energy and could
store significantly more energy than other rechargeable batteries in practice
if at least a large part of their promise could be realized. Realization, however,
still faces many challenges than can only be overcome by fundamental understanding
of the processes taking place. Here, we review recent advances in understanding
the chemistry of the Li–O2 cathode and provide a perspective on dominant research
needs. We put particular emphasis on issues that are often grossly misunderstood:
realistic performance metrics and their reporting as well as identifying reversibility
and quantitative measures to do so. Parasitic reactions are the prime obstacle
for reversible cell operation and have recently been identified to be predominantly
caused by singlet oxygen and not by reduced oxygen species as thought before.
We discuss the far reaching implications of this finding on electrolyte and cathode
stability, electrocatalysis, and future research needs.'
article_processing_charge: No
article_type: original
author:
- first_name: Nika
full_name: Mahne, Nika
last_name: Mahne
- first_name: Olivier
full_name: Fontaine, Olivier
last_name: Fontaine
- first_name: Musthafa Ottakam
full_name: Thotiyl, Musthafa Ottakam
last_name: Thotiyl
- first_name: Martin
full_name: Wilkening, Martin
last_name: Wilkening
- first_name: Stefan Alexander
full_name: Freunberger, Stefan Alexander
id: A8CA28E6-CE23-11E9-AD2D-EC27E6697425
last_name: Freunberger
orcid: 0000-0003-2902-5319
citation:
ama: Mahne N, Fontaine O, Thotiyl MO, Wilkening M, Freunberger SA. Mechanism and
performance of lithium–oxygen batteries – a perspective. Chemical Science.
2017;8(10):6716-6729. doi:10.1039/c7sc02519j
apa: Mahne, N., Fontaine, O., Thotiyl, M. O., Wilkening, M., & Freunberger,
S. A. (2017). Mechanism and performance of lithium–oxygen batteries – a perspective.
Chemical Science. RSC. https://doi.org/10.1039/c7sc02519j
chicago: Mahne, Nika, Olivier Fontaine, Musthafa Ottakam Thotiyl, Martin Wilkening,
and Stefan Alexander Freunberger. “Mechanism and Performance of Lithium–Oxygen
Batteries – a Perspective.” Chemical Science. RSC, 2017. https://doi.org/10.1039/c7sc02519j.
ieee: N. Mahne, O. Fontaine, M. O. Thotiyl, M. Wilkening, and S. A. Freunberger,
“Mechanism and performance of lithium–oxygen batteries – a perspective,” Chemical
Science, vol. 8, no. 10. RSC, pp. 6716–6729, 2017.
ista: Mahne N, Fontaine O, Thotiyl MO, Wilkening M, Freunberger SA. 2017. Mechanism
and performance of lithium–oxygen batteries – a perspective. Chemical Science.
8(10), 6716–6729.
mla: Mahne, Nika, et al. “Mechanism and Performance of Lithium–Oxygen Batteries
– a Perspective.” Chemical Science, vol. 8, no. 10, RSC, 2017, pp. 6716–29,
doi:10.1039/c7sc02519j.
short: N. Mahne, O. Fontaine, M.O. Thotiyl, M. Wilkening, S.A. Freunberger, Chemical
Science 8 (2017) 6716–6729.
date_created: 2020-01-15T12:15:42Z
date_published: 2017-07-31T00:00:00Z
date_updated: 2021-01-12T08:12:49Z
day: '31'
ddc:
- '540'
doi: 10.1039/c7sc02519j
extern: '1'
file:
- access_level: open_access
checksum: 70c7c2ce5430b6e8605ccbf0275f1e80
content_type: application/pdf
creator: dernst
date_created: 2020-01-26T15:04:44Z
date_updated: 2020-07-14T12:47:55Z
file_id: '7363'
file_name: 2017_ChemicalScience_Mahne.pdf
file_size: 992106
relation: main_file
file_date_updated: 2020-07-14T12:47:55Z
has_accepted_license: '1'
intvolume: ' 8'
issue: '10'
language:
- iso: eng
month: '07'
oa: 1
oa_version: Published Version
page: 6716-6729
publication: Chemical Science
publication_identifier:
eissn:
- 2041-6539
issn:
- 2041-6520
publication_status: published
publisher: RSC
quality_controlled: '1'
status: public
title: Mechanism and performance of lithium–oxygen batteries – a perspective
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: 8
year: '2017'
...
---
_id: '7291'
abstract:
- lang: eng
text: Na battery chemistries show poor passivation behavior of low voltage Na storage
compounds and Na metal with organic carbonate‐based electrolytes adopted from
Li‐ion batteries. Therefore, a suitable electrolyte remains a major challenge
for establishing Na batteries. Here we report highly concentrated sodium bis(fluorosulfonyl)imide
(NaFSI) in dimethoxyethane (DME) electrolytes and investigate them for Na metal
and hard carbon anodes and intercalation cathodes. For a DME/NaFSI ratio of 2,
a stable passivation of anode materials was found owing to the formation of a
stable solid electrolyte interface, which was characterized spectroscopically.
This permitted non‐dentritic Na metal cycling with approximately 98 % coulombic
efficiency as shown for up to 300 cycles. The NaFSI/DME electrolyte may enable
Na‐metal anodes and allows for more reliable assessment of electrode materials
in Na‐ion half‐cells, as is demonstrated by comparing half‐cell cycling of hard
carbon anodes and Na3V2(PO4)3 cathodes with a widely used carbonate and the NaFSI/DME
electrolyte.
article_processing_charge: No
article_type: original
author:
- first_name: Lukas
full_name: Schafzahl, Lukas
last_name: Schafzahl
- first_name: Ilie
full_name: Hanzu, Ilie
last_name: Hanzu
- first_name: Martin
full_name: Wilkening, Martin
last_name: Wilkening
- first_name: Stefan Alexander
full_name: Freunberger, Stefan Alexander
id: A8CA28E6-CE23-11E9-AD2D-EC27E6697425
last_name: Freunberger
orcid: 0000-0003-2902-5319
citation:
ama: Schafzahl L, Hanzu I, Wilkening M, Freunberger SA. An electrolyte for reversible
cycling of sodium metal and intercalation compounds. ChemSusChem. 2017;10(2):401-408.
doi:10.1002/cssc.201601222
apa: Schafzahl, L., Hanzu, I., Wilkening, M., & Freunberger, S. A. (2017). An
electrolyte for reversible cycling of sodium metal and intercalation compounds.
ChemSusChem. Wiley. https://doi.org/10.1002/cssc.201601222
chicago: Schafzahl, Lukas, Ilie Hanzu, Martin Wilkening, and Stefan Alexander Freunberger.
“An Electrolyte for Reversible Cycling of Sodium Metal and Intercalation Compounds.”
ChemSusChem. Wiley, 2017. https://doi.org/10.1002/cssc.201601222.
ieee: L. Schafzahl, I. Hanzu, M. Wilkening, and S. A. Freunberger, “An electrolyte
for reversible cycling of sodium metal and intercalation compounds,” ChemSusChem,
vol. 10, no. 2. Wiley, pp. 401–408, 2017.
ista: Schafzahl L, Hanzu I, Wilkening M, Freunberger SA. 2017. An electrolyte for
reversible cycling of sodium metal and intercalation compounds. ChemSusChem. 10(2),
401–408.
mla: Schafzahl, Lukas, et al. “An Electrolyte for Reversible Cycling of Sodium Metal
and Intercalation Compounds.” ChemSusChem, vol. 10, no. 2, Wiley, 2017,
pp. 401–08, doi:10.1002/cssc.201601222.
short: L. Schafzahl, I. Hanzu, M. Wilkening, S.A. Freunberger, ChemSusChem 10 (2017)
401–408.
date_created: 2020-01-15T12:15:29Z
date_published: 2017-01-20T00:00:00Z
date_updated: 2021-01-12T08:12:48Z
day: '20'
doi: 10.1002/cssc.201601222
extern: '1'
intvolume: ' 10'
issue: '2'
language:
- iso: eng
month: '01'
oa_version: None
page: 401-408
publication: ChemSusChem
publication_identifier:
issn:
- 1864-5631
publication_status: published
publisher: Wiley
quality_controlled: '1'
status: public
title: An electrolyte for reversible cycling of sodium metal and intercalation compounds
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 10
year: '2017'
...
---
_id: '731'
abstract:
- lang: eng
text: Genetic variations in the oxytocin receptor gene affect patients with ASD
and ADHD differently.
article_number: eaap8168
author:
- first_name: Gaia
full_name: Novarino, Gaia
id: 3E57A680-F248-11E8-B48F-1D18A9856A87
last_name: Novarino
orcid: 0000-0002-7673-7178
citation:
ama: Novarino G. The science of love in ASD and ADHD. Science Translational Medicine.
2017;9(411). doi:10.1126/scitranslmed.aap8168
apa: Novarino, G. (2017). The science of love in ASD and ADHD. Science Translational
Medicine. American Association for the Advancement of Science. https://doi.org/10.1126/scitranslmed.aap8168
chicago: Novarino, Gaia. “The Science of Love in ASD and ADHD.” Science Translational
Medicine. American Association for the Advancement of Science, 2017. https://doi.org/10.1126/scitranslmed.aap8168.
ieee: G. Novarino, “The science of love in ASD and ADHD,” Science Translational
Medicine, vol. 9, no. 411. American Association for the Advancement of Science,
2017.
ista: Novarino G. 2017. The science of love in ASD and ADHD. Science Translational
Medicine. 9(411), eaap8168.
mla: Novarino, Gaia. “The Science of Love in ASD and ADHD.” Science Translational
Medicine, vol. 9, no. 411, eaap8168, American Association for the Advancement
of Science, 2017, doi:10.1126/scitranslmed.aap8168.
short: G. Novarino, Science Translational Medicine 9 (2017).
date_created: 2018-12-11T11:48:12Z
date_published: 2017-10-11T00:00:00Z
date_updated: 2021-01-12T08:12:57Z
day: '11'
department:
- _id: GaNo
doi: 10.1126/scitranslmed.aap8168
intvolume: ' 9'
issue: '411'
language:
- iso: eng
month: '10'
oa_version: None
publication: Science Translational Medicine
publication_identifier:
issn:
- '19466234'
publication_status: published
publisher: American Association for the Advancement of Science
publist_id: '6938'
quality_controlled: '1'
scopus_import: 1
status: public
title: The science of love in ASD and ADHD
type: journal_article
user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87
volume: 9
year: '2017'
...
---
_id: '7360'
abstract:
- lang: eng
text: Inflammation, which is a highly regulated host response against danger signals,
may be harmful if it is excessive and deregulated. Ideally, anti-inflammatory
therapy should autonomously commence as soon as possible after the onset of inflammation,
should be controllable by a physician, and should not systemically block beneficial
immune response in the long term. We describe a genetically encoded anti-inflammatory
mammalian cell device based on a modular engineered genetic circuit comprising
a sensor, an amplifier, a “thresholder” to restrict activation of a positive-feedback
loop, a combination of advanced clinically used biopharmaceutical proteins, and
orthogonal regulatory elements that linked modules into the functional device.
This genetic circuit was autonomously activated by inflammatory signals, including
endogenous cecal ligation and puncture (CLP)-induced inflammation in mice and
serum from a systemic juvenile idiopathic arthritis (sIJA) patient, and could
be reset externally by a chemical signal. The microencapsulated anti-inflammatory
device significantly reduced the pathology in dextran sodium sulfate (DSS)-induced
acute murine colitis, demonstrating a synthetic immunological approach for autonomous
anti-inflammatory therapy.
article_processing_charge: No
article_type: original
author:
- first_name: Anže
full_name: Smole, Anže
last_name: Smole
- first_name: Duško
full_name: Lainšček, Duško
last_name: Lainšček
- first_name: Urban
full_name: Bezeljak, Urban
id: 2A58201A-F248-11E8-B48F-1D18A9856A87
last_name: Bezeljak
orcid: 0000-0003-1365-5631
- first_name: Simon
full_name: Horvat, Simon
last_name: Horvat
- first_name: Roman
full_name: Jerala, Roman
last_name: Jerala
citation:
ama: Smole A, Lainšček D, Bezeljak U, Horvat S, Jerala R. A synthetic mammalian
therapeutic gene circuit for sensing and suppressing inflammation. Molecular
Therapy. 2017;25(1):102-119. doi:10.1016/j.ymthe.2016.10.005
apa: Smole, A., Lainšček, D., Bezeljak, U., Horvat, S., & Jerala, R. (2017).
A synthetic mammalian therapeutic gene circuit for sensing and suppressing inflammation.
Molecular Therapy. Elsevier. https://doi.org/10.1016/j.ymthe.2016.10.005
chicago: Smole, Anže, Duško Lainšček, Urban Bezeljak, Simon Horvat, and Roman Jerala.
“A Synthetic Mammalian Therapeutic Gene Circuit for Sensing and Suppressing Inflammation.”
Molecular Therapy. Elsevier, 2017. https://doi.org/10.1016/j.ymthe.2016.10.005.
ieee: A. Smole, D. Lainšček, U. Bezeljak, S. Horvat, and R. Jerala, “A synthetic
mammalian therapeutic gene circuit for sensing and suppressing inflammation,”
Molecular Therapy, vol. 25, no. 1. Elsevier, pp. 102–119, 2017.
ista: Smole A, Lainšček D, Bezeljak U, Horvat S, Jerala R. 2017. A synthetic mammalian
therapeutic gene circuit for sensing and suppressing inflammation. Molecular Therapy.
25(1), 102–119.
mla: Smole, Anže, et al. “A Synthetic Mammalian Therapeutic Gene Circuit for Sensing
and Suppressing Inflammation.” Molecular Therapy, vol. 25, no. 1, Elsevier,
2017, pp. 102–19, doi:10.1016/j.ymthe.2016.10.005.
short: A. Smole, D. Lainšček, U. Bezeljak, S. Horvat, R. Jerala, Molecular Therapy
25 (2017) 102–119.
date_created: 2020-01-25T15:55:39Z
date_published: 2017-01-01T00:00:00Z
date_updated: 2021-01-12T08:13:14Z
day: '01'
ddc:
- '570'
department:
- _id: MaLo
doi: 10.1016/j.ymthe.2016.10.005
external_id:
pmid:
- '28129106'
file:
- access_level: open_access
checksum: ea8b1b28606dd1edab7379ba4fa3641f
content_type: application/pdf
creator: dernst
date_created: 2020-03-03T10:55:13Z
date_updated: 2020-07-14T12:47:56Z
file_id: '7561'
file_name: 2017_MolecularTherapy_Smole.pdf
file_size: 3404806
relation: main_file
file_date_updated: 2020-07-14T12:47:56Z
has_accepted_license: '1'
intvolume: ' 25'
issue: '1'
language:
- iso: eng
month: '01'
oa: 1
oa_version: Published Version
page: 102-119
pmid: 1
publication: Molecular Therapy
publication_identifier:
issn:
- 1525-0016
publication_status: published
publisher: Elsevier
quality_controlled: '1'
status: public
title: A synthetic mammalian therapeutic gene circuit for sensing and suppressing
inflammation
tmp:
image: /images/cc_by_nc_nd.png
legal_code_url: https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode
name: Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International
(CC BY-NC-ND 4.0)
short: CC BY-NC-ND (4.0)
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 25
year: '2017'
...
---
_id: '748'
abstract:
- lang: eng
text: The essay focuses on individual and collective forms of liminality in John
Marlyn’s Under the Ribs of Death. Set in early twentieth-century Winnipeg, the
1957 immigrant novel explores liminal experiences related to ethnic identity,
male sexuality, social class, urban spaces and turbulent economic times. As the
son of a poor working-class family from Hungary, Sandor Hunyadi makes every effort
to become a true Canadian and a successful businessman, but, no matter how hard
he tries to overcome contemporary ethnic prejudices and economic hardships, his
personal and professional life remains in liminality. In other words, the protagonist
undergoes separation, fails at incorporation, and becomes stuck in transition.
alternative_title:
- Canadiana
author:
- first_name: Bernhard
full_name: Bernhard Wenzl
id: 479E9046-F248-11E8-B48F-1D18A9856A87
last_name: Wenzl
citation:
ama: 'Wenzl B. “...beyond the invisible barrier at Portage and Main”: Liminality
in John Marlyn’s Under the Ribs of Death. In: Brandt S, ed. In-Between - Liminal
Spaces in Canadian Literature and Culture. Peter Lang GmbH; 2017:91-100. doi:10.3726/b11899'
apa: 'Wenzl, B. (2017). “...beyond the invisible barrier at Portage and Main”: Liminality
in John Marlyn’s Under the Ribs of Death. In S. Brandt (Ed.), In-Between -
Liminal Spaces in Canadian Literature and Culture (pp. 91–100). Peter Lang
GmbH. https://doi.org/10.3726/b11899'
chicago: 'Wenzl, Bernhard. “‘...Beyond the Invisible Barrier at Portage and Main’:
Liminality in John Marlyn’s Under the Ribs of Death.” In In-Between - Liminal
Spaces in Canadian Literature and Culture, edited by Stefan Brandt, 91–100.
Peter Lang GmbH, 2017. https://doi.org/10.3726/b11899.'
ieee: 'B. Wenzl, “‘...beyond the invisible barrier at Portage and Main’: Liminality
in John Marlyn’s Under the Ribs of Death,” in In-Between - Liminal Spaces in
Canadian Literature and Culture, S. Brandt, Ed. Peter Lang GmbH, 2017, pp.
91–100.'
ista: 'Wenzl B. 2017.‘...beyond the invisible barrier at Portage and Main’: Liminality
in John Marlyn’s Under the Ribs of Death. In: In-Between - Liminal Spaces in Canadian
Literature and Culture. Canadiana, , 91–100.'
mla: 'Wenzl, Bernhard. “‘...Beyond the Invisible Barrier at Portage and Main’: Liminality
in John Marlyn’s Under the Ribs of Death.” In-Between - Liminal Spaces in Canadian
Literature and Culture, edited by Stefan Brandt, Peter Lang GmbH, 2017, pp.
91–100, doi:10.3726/b11899.'
short: B. Wenzl, in:, S. Brandt (Ed.), In-Between - Liminal Spaces in Canadian Literature
and Culture, Peter Lang GmbH, 2017, pp. 91–100.
date_created: 2018-12-11T11:48:18Z
date_published: 2017-12-01T00:00:00Z
date_updated: 2021-01-12T08:13:49Z
day: '01'
doi: 10.3726/b11899
editor:
- first_name: Stefan
full_name: Brandt, Stefan L.
last_name: Brandt
extern: 1
month: '12'
page: 91 - 100
publication: In-Between - Liminal Spaces in Canadian Literature and Culture
publication_status: published
publisher: Peter Lang GmbH
publist_id: '6909'
quality_controlled: 0
status: public
title: '''...beyond the invisible barrier at Portage and Main'': Liminality in John
Marlyn''s Under the Ribs of Death'
type: book_chapter
year: '2017'
...
---
_id: '750'
abstract:
- lang: eng
text: Modern communication technologies allow first responders to contact thousands
of potential volunteers simultaneously for support during a crisis or disaster
event. However, such volunteer efforts must be well coordinated and monitored,
in order to offer an effective relief to the professionals. In this paper we extend
earlier work on optimally assigning volunteers to selected landmark locations.
In particular, we emphasize the aspect that obtaining good assignments requires
not only advanced computational tools, but also a realistic measure of distance
between volunteers and landmarks. Specifically, we propose the use of the Open
Street Map (OSM) driving distance instead of he previously used flight distance.
We find the OSM driving distance to be better aligned with the interests of volunteers
and first responders. Furthermore, we show that relying on the flying distance
leads to a substantial underestimation of the number of required volunteers, causing
negative side effects in case of an actual crisis situation.
author:
- first_name: Jasmin
full_name: Pielorz, Jasmin
id: 49BC895A-F248-11E8-B48F-1D18A9856A87
last_name: Pielorz
- first_name: Matthias
full_name: Prandtstetter, Matthias
last_name: Prandtstetter
- first_name: Markus
full_name: Straub, Markus
last_name: Straub
- first_name: Christoph
full_name: Lampert, Christoph
id: 40C20FD2-F248-11E8-B48F-1D18A9856A87
last_name: Lampert
orcid: 0000-0001-8622-7887
citation:
ama: 'Pielorz J, Prandtstetter M, Straub M, Lampert C. Optimal geospatial volunteer
allocation needs realistic distances. In: 2017 IEEE International Conference
on Big Data. IEEE; 2017:3760-3763. doi:10.1109/BigData.2017.8258375'
apa: 'Pielorz, J., Prandtstetter, M., Straub, M., & Lampert, C. (2017). Optimal
geospatial volunteer allocation needs realistic distances. In 2017 IEEE International
Conference on Big Data (pp. 3760–3763). Boston, MA, United States: IEEE. https://doi.org/10.1109/BigData.2017.8258375'
chicago: Pielorz, Jasmin, Matthias Prandtstetter, Markus Straub, and Christoph Lampert.
“Optimal Geospatial Volunteer Allocation Needs Realistic Distances.” In 2017
IEEE International Conference on Big Data, 3760–63. IEEE, 2017. https://doi.org/10.1109/BigData.2017.8258375.
ieee: J. Pielorz, M. Prandtstetter, M. Straub, and C. Lampert, “Optimal geospatial
volunteer allocation needs realistic distances,” in 2017 IEEE International
Conference on Big Data, Boston, MA, United States, 2017, pp. 3760–3763.
ista: Pielorz J, Prandtstetter M, Straub M, Lampert C. 2017. Optimal geospatial
volunteer allocation needs realistic distances. 2017 IEEE International Conference
on Big Data. Big Data, 3760–3763.
mla: Pielorz, Jasmin, et al. “Optimal Geospatial Volunteer Allocation Needs Realistic
Distances.” 2017 IEEE International Conference on Big Data, IEEE, 2017,
pp. 3760–63, doi:10.1109/BigData.2017.8258375.
short: J. Pielorz, M. Prandtstetter, M. Straub, C. Lampert, in:, 2017 IEEE International
Conference on Big Data, IEEE, 2017, pp. 3760–3763.
conference:
end_date: 2017-12-14
location: Boston, MA, United States
name: Big Data
start_date: 2017-12-11
date_created: 2018-12-11T11:48:18Z
date_published: 2017-12-01T00:00:00Z
date_updated: 2021-01-12T08:13:55Z
day: '01'
department:
- _id: ChLa
doi: 10.1109/BigData.2017.8258375
language:
- iso: eng
month: '12'
oa_version: None
page: 3760 - 3763
publication: 2017 IEEE International Conference on Big Data
publication_identifier:
isbn:
- 978-153862714-3
publication_status: published
publisher: IEEE
publist_id: '6906'
quality_controlled: '1'
scopus_import: 1
status: public
title: Optimal geospatial volunteer allocation needs realistic distances
type: conference
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
year: '2017'
...
---
_id: '7728'
abstract:
- lang: eng
text: 'Meta-analyses of genome-wide association studies, which dominate genetic
discovery, are based on data from diverse historical time periods and populations.
Genetic scores derived from genome-wide association studies explain only a fraction
of the heritability estimates obtained from whole-genome studies on single populations,
known as the ‘hidden heritability’ puzzle. Using seven sampling populations (n = 35,062),
we test whether hidden heritability is attributed to heterogeneity across sampling
populations and time, showing that estimates are substantially smaller across
populations compared with within populations. We show that the hidden heritability
varies substantially: from zero for height to 20% for body mass index, 37% for
education, 40% for age at first birth and up to 75% for number of children. Simulations
demonstrate that our results are more likely to reflect heterogeneity in phenotypic
measurement or gene–environment interactions than genetic heterogeneity. These
findings have substantial implications for genetic discovery, suggesting that
large homogenous datasets are required for behavioural phenotypes and that gene–environment
interaction may be a central challenge for genetic discovery.'
article_processing_charge: No
article_type: original
author:
- first_name: Felix C.
full_name: Tropf, Felix C.
last_name: Tropf
- first_name: S. Hong
full_name: Lee, S. Hong
last_name: Lee
- first_name: Renske M.
full_name: Verweij, Renske M.
last_name: Verweij
- first_name: Gert
full_name: Stulp, Gert
last_name: Stulp
- first_name: Peter J.
full_name: van der Most, Peter J.
last_name: van der Most
- first_name: Ronald
full_name: de Vlaming, Ronald
last_name: de Vlaming
- first_name: Andrew
full_name: Bakshi, Andrew
last_name: Bakshi
- first_name: Daniel A.
full_name: Briley, Daniel A.
last_name: Briley
- first_name: Charles
full_name: Rahal, Charles
last_name: Rahal
- first_name: Robert
full_name: Hellpap, Robert
last_name: Hellpap
- first_name: Anastasia N.
full_name: Iliadou, Anastasia N.
last_name: Iliadou
- first_name: Tõnu
full_name: Esko, Tõnu
last_name: Esko
- first_name: Andres
full_name: Metspalu, Andres
last_name: Metspalu
- first_name: Sarah E.
full_name: Medland, Sarah E.
last_name: Medland
- first_name: Nicholas G.
full_name: Martin, Nicholas G.
last_name: Martin
- first_name: Nicola
full_name: Barban, Nicola
last_name: Barban
- first_name: Harold
full_name: Snieder, Harold
last_name: Snieder
- 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: Melinda C.
full_name: Mills, Melinda C.
last_name: Mills
citation:
ama: Tropf FC, Lee SH, Verweij RM, et al. Hidden heritability due to heterogeneity
across seven populations. Nature Human Behaviour. 2017;1(10):757-765. doi:10.1038/s41562-017-0195-1
apa: Tropf, F. C., Lee, S. H., Verweij, R. M., Stulp, G., van der Most, P. J., de
Vlaming, R., … Mills, M. C. (2017). Hidden heritability due to heterogeneity across
seven populations. Nature Human Behaviour. Springer Nature. https://doi.org/10.1038/s41562-017-0195-1
chicago: Tropf, Felix C., S. Hong Lee, Renske M. Verweij, Gert Stulp, Peter J. van
der Most, Ronald de Vlaming, Andrew Bakshi, et al. “Hidden Heritability Due to
Heterogeneity across Seven Populations.” Nature Human Behaviour. Springer
Nature, 2017. https://doi.org/10.1038/s41562-017-0195-1.
ieee: F. C. Tropf et al., “Hidden heritability due to heterogeneity across
seven populations,” Nature Human Behaviour, vol. 1, no. 10. Springer Nature,
pp. 757–765, 2017.
ista: Tropf FC, Lee SH, Verweij RM, Stulp G, van der Most PJ, de Vlaming R, Bakshi
A, Briley DA, Rahal C, Hellpap R, Iliadou AN, Esko T, Metspalu A, Medland SE,
Martin NG, Barban N, Snieder H, Robinson MR, Mills MC. 2017. Hidden heritability
due to heterogeneity across seven populations. Nature Human Behaviour. 1(10),
757–765.
mla: Tropf, Felix C., et al. “Hidden Heritability Due to Heterogeneity across Seven
Populations.” Nature Human Behaviour, vol. 1, no. 10, Springer Nature,
2017, pp. 757–65, doi:10.1038/s41562-017-0195-1.
short: F.C. Tropf, S.H. Lee, R.M. Verweij, G. Stulp, P.J. van der Most, R. de Vlaming,
A. Bakshi, D.A. Briley, C. Rahal, R. Hellpap, A.N. Iliadou, T. Esko, A. Metspalu,
S.E. Medland, N.G. Martin, N. Barban, H. Snieder, M.R. Robinson, M.C. Mills, Nature
Human Behaviour 1 (2017) 757–765.
date_created: 2020-04-30T10:47:02Z
date_published: 2017-09-11T00:00:00Z
date_updated: 2021-01-12T08:15:08Z
day: '11'
doi: 10.1038/s41562-017-0195-1
extern: '1'
intvolume: ' 1'
issue: '10'
language:
- iso: eng
month: '09'
oa_version: None
page: 757-765
publication: Nature Human Behaviour
publication_identifier:
issn:
- 2397-3374
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
status: public
title: Hidden heritability due to heterogeneity across seven populations
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 1
year: '2017'
...
---
_id: '7727'
abstract:
- lang: eng
text: Genes of the major histocompatibility complex (MHC) have been shown to influence
social signalling and mate preferences in many species, including humans. First
observations suggest that MHC signalling may also affect female fertility. To
test this hypothesis, we exposed 191 female horses (Equus caballus) to either
an MHC-similar or an MHC-dissimilar stimulus male around the time of ovulation
and conception. A within-subject experimental design controlled for non-MHC-linked
male characteristics, and instrumental insemination with semen of other males
(n = 106) controlled for potential confounding effects of semen or embryo characteristics.
We found that females were more likely to become pregnant if exposed to an MHC-dissimilar
than to an MHC-similar male, while overall genetic distance to the stimulus males
(based on microsatellite markers on 20 chromosomes) had no effect. Our results
demonstrate that early pregnancy failures can be due to maternal life-history
decisions (cryptic female choice) influenced by MHC-linked social signalling.
article_number: '20171824'
article_processing_charge: No
article_type: original
author:
- first_name: D.
full_name: Burger, D.
last_name: Burger
- first_name: S.
full_name: Thomas, S.
last_name: Thomas
- first_name: H.
full_name: Aepli, H.
last_name: Aepli
- first_name: M.
full_name: Dreyer, M.
last_name: Dreyer
- first_name: G.
full_name: Fabre, G.
last_name: Fabre
- first_name: E.
full_name: Marti, E.
last_name: Marti
- first_name: H.
full_name: Sieme, H.
last_name: Sieme
- 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: C.
full_name: Wedekind, C.
last_name: Wedekind
citation:
ama: 'Burger D, Thomas S, Aepli H, et al. Major histocompatibility complex-linked
social signalling affects female fertility. Proceedings of the Royal Society
B: Biological Sciences. 2017;284(1868). doi:10.1098/rspb.2017.1824'
apa: 'Burger, D., Thomas, S., Aepli, H., Dreyer, M., Fabre, G., Marti, E., … Wedekind,
C. (2017). Major histocompatibility complex-linked social signalling affects female
fertility. Proceedings of the Royal Society B: Biological Sciences. The
Royal Society. https://doi.org/10.1098/rspb.2017.1824'
chicago: 'Burger, D., S. Thomas, H. Aepli, M. Dreyer, G. Fabre, E. Marti, H. Sieme,
Matthew Richard Robinson, and C. Wedekind. “Major Histocompatibility Complex-Linked
Social Signalling Affects Female Fertility.” Proceedings of the Royal Society
B: Biological Sciences. The Royal Society, 2017. https://doi.org/10.1098/rspb.2017.1824.'
ieee: 'D. Burger et al., “Major histocompatibility complex-linked social
signalling affects female fertility,” Proceedings of the Royal Society B: Biological
Sciences, vol. 284, no. 1868. The Royal Society, 2017.'
ista: 'Burger D, Thomas S, Aepli H, Dreyer M, Fabre G, Marti E, Sieme H, Robinson
MR, Wedekind C. 2017. Major histocompatibility complex-linked social signalling
affects female fertility. Proceedings of the Royal Society B: Biological Sciences.
284(1868), 20171824.'
mla: 'Burger, D., et al. “Major Histocompatibility Complex-Linked Social Signalling
Affects Female Fertility.” Proceedings of the Royal Society B: Biological Sciences,
vol. 284, no. 1868, 20171824, The Royal Society, 2017, doi:10.1098/rspb.2017.1824.'
short: 'D. Burger, S. Thomas, H. Aepli, M. Dreyer, G. Fabre, E. Marti, H. Sieme,
M.R. Robinson, C. Wedekind, Proceedings of the Royal Society B: Biological Sciences
284 (2017).'
date_created: 2020-04-30T10:46:43Z
date_published: 2017-12-06T00:00:00Z
date_updated: 2021-01-12T08:15:08Z
day: '06'
doi: 10.1098/rspb.2017.1824
extern: '1'
external_id:
pmid:
- '29212724'
intvolume: ' 284'
issue: '1868'
language:
- iso: eng
month: '12'
oa_version: None
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: Major histocompatibility complex-linked social signalling affects female fertility
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 284
year: '2017'
...
---
_id: '7729'
abstract:
- lang: eng
text: Quantifying the effects of inbreeding is critical to characterizing the genetic
architecture of complex traits. This study highlights through theory and simulations
the strengths and shortcomings of three SNP-based inbreeding measures commonly
used to estimate inbreeding depression (ID). We demonstrate that heterogeneity
in linkage disequilibrium (LD) between causal variants and SNPs biases ID estimates,
and we develop an approach to correct this bias using LD and minor allele frequency
stratified inference (LDMS). We quantified ID in 25 traits measured in ∼140,000
participants of the UK Biobank, using LDMS, and confirmed previously published
ID for 4 traits. We find unique evidence of ID for handgrip strength, waist/hip
ratio, and visual and auditory acuity (ID between −2.3 and −5.2 phenotypic SDs
for complete inbreeding; P<0.001). Our results illustrate that a careful choice
of the measure of inbreeding combined with LDMS stratification improves both detection
and quantification of ID using SNP data.
article_processing_charge: No
article_type: original
author:
- first_name: Loic
full_name: Yengo, Loic
last_name: Yengo
- first_name: Zhihong
full_name: Zhu, Zhihong
last_name: Zhu
- first_name: Naomi R.
full_name: Wray, Naomi R.
last_name: Wray
- first_name: Bruce S.
full_name: Weir, Bruce S.
last_name: Weir
- first_name: Jian
full_name: Yang, Jian
last_name: Yang
- 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: Peter M.
full_name: Visscher, Peter M.
last_name: Visscher
citation:
ama: Yengo L, Zhu Z, Wray NR, et al. Detection and quantification of inbreeding
depression for complex traits from SNP data. Proceedings of the National Academy
of Sciences. 2017;114(32):8602-8607. doi:10.1073/pnas.1621096114
apa: Yengo, L., Zhu, Z., Wray, N. R., Weir, B. S., Yang, J., Robinson, M. R., &
Visscher, P. M. (2017). Detection and quantification of inbreeding depression
for complex traits from SNP data. Proceedings of the National Academy of Sciences.
Proceedings of the National Academy of Sciences. https://doi.org/10.1073/pnas.1621096114
chicago: Yengo, Loic, Zhihong Zhu, Naomi R. Wray, Bruce S. Weir, Jian Yang, Matthew
Richard Robinson, and Peter M. Visscher. “Detection and Quantification of Inbreeding
Depression for Complex Traits from SNP Data.” Proceedings of the National Academy
of Sciences. Proceedings of the National Academy of Sciences, 2017. https://doi.org/10.1073/pnas.1621096114.
ieee: L. Yengo et al., “Detection and quantification of inbreeding depression
for complex traits from SNP data,” Proceedings of the National Academy of Sciences,
vol. 114, no. 32. Proceedings of the National Academy of Sciences, pp. 8602–8607,
2017.
ista: Yengo L, Zhu Z, Wray NR, Weir BS, Yang J, Robinson MR, Visscher PM. 2017.
Detection and quantification of inbreeding depression for complex traits from
SNP data. Proceedings of the National Academy of Sciences. 114(32), 8602–8607.
mla: Yengo, Loic, et al. “Detection and Quantification of Inbreeding Depression
for Complex Traits from SNP Data.” Proceedings of the National Academy of Sciences,
vol. 114, no. 32, Proceedings of the National Academy of Sciences, 2017, pp. 8602–07,
doi:10.1073/pnas.1621096114.
short: L. Yengo, Z. Zhu, N.R. Wray, B.S. Weir, J. Yang, M.R. Robinson, P.M. Visscher,
Proceedings of the National Academy of Sciences 114 (2017) 8602–8607.
date_created: 2020-04-30T10:47:19Z
date_published: 2017-08-08T00:00:00Z
date_updated: 2021-01-12T08:15:09Z
day: '08'
doi: 10.1073/pnas.1621096114
extern: '1'
intvolume: ' 114'
issue: '32'
language:
- iso: eng
month: '08'
oa_version: None
page: 8602-8607
publication: Proceedings of the National Academy of Sciences
publication_identifier:
issn:
- 0027-8424
- 1091-6490
publication_status: published
publisher: Proceedings of the National Academy of Sciences
quality_controlled: '1'
related_material:
link:
- relation: other
url: https://doi.org/10.1073/pnas.1718598115
status: public
title: Detection and quantification of inbreeding depression for complex traits from
SNP data
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 114
year: '2017'
...
---
_id: '7725'
abstract:
- lang: eng
text: Phenotypic plasticity is the ability of an individual genotype to alter aspects
of its phenotype depending on the current environment. It is central to the persistence,
resistance and resilience of populations facing variation in physical or biological
factors. Genetic variation in plasticity is pervasive, which suggests its local
adaptation is plausible. Existing studies on the adaptation of plasticity typically
focus on single traits and a few populations, while theory about interactions
among genes (for example, pleiotropy) suggests that a multi-trait, landscape scale
(for example, multiple populations) perspective is required. We present data from
a landscape scale, replicated, multi-trait experiment using a classic predator–prey
system centred on the water flea Daphnia pulex. We find predator regime-driven
differences in genetic variation of multivariate plasticity. These differences
are associated with strong divergent selection linked to a predation regime. Our
findings are evidence for local adaptation of plasticity, suggesting that responses
of populations to environmental variation depend on the conditions in which they
evolved in the past.
article_processing_charge: No
article_type: original
author:
- first_name: Julia
full_name: Reger, Julia
last_name: Reger
- first_name: Martin I.
full_name: Lind, Martin I.
last_name: Lind
- 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: Andrew P.
full_name: Beckerman, Andrew P.
last_name: Beckerman
citation:
ama: Reger J, Lind MI, Robinson MR, Beckerman AP. Predation drives local adaptation
of phenotypic plasticity. Nature Ecology & Evolution. 2017;2:100-107.
doi:10.1038/s41559-017-0373-6
apa: Reger, J., Lind, M. I., Robinson, M. R., & Beckerman, A. P. (2017). Predation
drives local adaptation of phenotypic plasticity. Nature Ecology & Evolution.
Springer Nature. https://doi.org/10.1038/s41559-017-0373-6
chicago: Reger, Julia, Martin I. Lind, Matthew Richard Robinson, and Andrew P. Beckerman.
“Predation Drives Local Adaptation of Phenotypic Plasticity.” Nature Ecology
& Evolution. Springer Nature, 2017. https://doi.org/10.1038/s41559-017-0373-6.
ieee: J. Reger, M. I. Lind, M. R. Robinson, and A. P. Beckerman, “Predation drives
local adaptation of phenotypic plasticity,” Nature Ecology & Evolution,
vol. 2. Springer Nature, pp. 100–107, 2017.
ista: Reger J, Lind MI, Robinson MR, Beckerman AP. 2017. Predation drives local
adaptation of phenotypic plasticity. Nature Ecology & Evolution. 2, 100–107.
mla: Reger, Julia, et al. “Predation Drives Local Adaptation of Phenotypic Plasticity.”
Nature Ecology & Evolution, vol. 2, Springer Nature, 2017, pp. 100–07,
doi:10.1038/s41559-017-0373-6.
short: J. Reger, M.I. Lind, M.R. Robinson, A.P. Beckerman, Nature Ecology &
Evolution 2 (2017) 100–107.
date_created: 2020-04-30T10:46:02Z
date_published: 2017-11-27T00:00:00Z
date_updated: 2021-01-12T08:15:07Z
day: '27'
doi: 10.1038/s41559-017-0373-6
extern: '1'
intvolume: ' 2'
language:
- iso: eng
month: '11'
oa_version: None
page: 100-107
publication: Nature Ecology & Evolution
publication_identifier:
issn:
- 2397-334X
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
status: public
title: Predation drives local adaptation of phenotypic plasticity
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 2
year: '2017'
...
---
_id: '7733'
abstract:
- lang: eng
text: "Sections\r\nPDFPDF\r\nTools\r\nShare\r\nAbstract\r\nBackground: Gene discovery
has provided remarkable biological insights into amyotrophic lateral sclerosis
(ALS). One challenge for clinical application of genetic testing is critical evaluation
of the significance of reported variants.\r\nMethods: We use whole exome sequencing
(WES) to develop a clinically relevant approach to identify a subset of ALS patients
harboring likely pathogenic mutations. In parallel, we assess if DNA methylation
can be used to screen for pathogenicity of novel variants since a methylation
signature has been shown to associate with the pathogenic C9orf72 expansion, but
has not been explored for other ALS mutations. Australian patients identified
with ALS‐relevant variants were cross‐checked with population databases and case
reports to critically assess whether they were “likely causal,” “uncertain significance,”
or “unlikely causal.”\r\nResults: Published ALS variants were identified in >10%
of patients; however, in only 3% of patients (4/120) could these be confidently
considered pathogenic (in SOD1 and TARDBP). We found no evidence for a differential
DNA methylation signature in these mutation carriers.\r\nConclusions: The use
of WES in a typical ALS clinic demonstrates a critical approach to variant assessment
with the capability to combine cohorts to enhance the largely unknown genetic
basis of ALS."
article_processing_charge: No
article_type: original
author:
- first_name: Fleur C.
full_name: Garton, Fleur C.
last_name: Garton
- first_name: Beben
full_name: Benyamin, Beben
last_name: Benyamin
- first_name: Qiongyi
full_name: Zhao, Qiongyi
last_name: Zhao
- first_name: Zhijun
full_name: Liu, Zhijun
last_name: Liu
- first_name: Jacob
full_name: Gratten, Jacob
last_name: Gratten
- first_name: Anjali K.
full_name: Henders, Anjali K.
last_name: Henders
- first_name: Zong-Hong
full_name: Zhang, Zong-Hong
last_name: Zhang
- first_name: Janette
full_name: Edson, Janette
last_name: Edson
- first_name: Sarah
full_name: Furlong, Sarah
last_name: Furlong
- first_name: Sarah
full_name: Morgan, Sarah
last_name: Morgan
- first_name: Susan
full_name: Heggie, Susan
last_name: Heggie
- first_name: Kathryn
full_name: Thorpe, Kathryn
last_name: Thorpe
- first_name: Casey
full_name: Pfluger, Casey
last_name: Pfluger
- first_name: Karen A.
full_name: Mather, Karen A.
last_name: Mather
- first_name: Perminder S.
full_name: Sachdev, Perminder S.
last_name: Sachdev
- first_name: Allan F.
full_name: McRae, Allan F.
last_name: McRae
- 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: Sonia
full_name: Shah, Sonia
last_name: Shah
- first_name: Peter M.
full_name: Visscher, Peter M.
last_name: Visscher
- first_name: Marie
full_name: Mangelsdorf, Marie
last_name: Mangelsdorf
- first_name: Robert D.
full_name: Henderson, Robert D.
last_name: Henderson
- first_name: Naomi R.
full_name: Wray, Naomi R.
last_name: Wray
- first_name: Pamela A.
full_name: McCombe, Pamela A.
last_name: McCombe
citation:
ama: Garton FC, Benyamin B, Zhao Q, et al. Whole exome sequencing and DNA methylation
analysis in a clinical amyotrophic lateral sclerosis cohort. Molecular Genetics
& Genomic Medicine. 2017;5(4):418-428. doi:10.1002/mgg3.302
apa: Garton, F. C., Benyamin, B., Zhao, Q., Liu, Z., Gratten, J., Henders, A. K.,
… McCombe, P. A. (2017). Whole exome sequencing and DNA methylation analysis in
a clinical amyotrophic lateral sclerosis cohort. Molecular Genetics & Genomic
Medicine. Wiley. https://doi.org/10.1002/mgg3.302
chicago: Garton, Fleur C., Beben Benyamin, Qiongyi Zhao, Zhijun Liu, Jacob Gratten,
Anjali K. Henders, Zong-Hong Zhang, et al. “Whole Exome Sequencing and DNA Methylation
Analysis in a Clinical Amyotrophic Lateral Sclerosis Cohort.” Molecular Genetics
& Genomic Medicine. Wiley, 2017. https://doi.org/10.1002/mgg3.302.
ieee: F. C. Garton et al., “Whole exome sequencing and DNA methylation analysis
in a clinical amyotrophic lateral sclerosis cohort,” Molecular Genetics &
Genomic Medicine, vol. 5, no. 4. Wiley, pp. 418–428, 2017.
ista: Garton FC, Benyamin B, Zhao Q, Liu Z, Gratten J, Henders AK, Zhang Z-H, Edson
J, Furlong S, Morgan S, Heggie S, Thorpe K, Pfluger C, Mather KA, Sachdev PS,
McRae AF, Robinson MR, Shah S, Visscher PM, Mangelsdorf M, Henderson RD, Wray
NR, McCombe PA. 2017. Whole exome sequencing and DNA methylation analysis in a
clinical amyotrophic lateral sclerosis cohort. Molecular Genetics & Genomic
Medicine. 5(4), 418–428.
mla: Garton, Fleur C., et al. “Whole Exome Sequencing and DNA Methylation Analysis
in a Clinical Amyotrophic Lateral Sclerosis Cohort.” Molecular Genetics &
Genomic Medicine, vol. 5, no. 4, Wiley, 2017, pp. 418–28, doi:10.1002/mgg3.302.
short: F.C. Garton, B. Benyamin, Q. Zhao, Z. Liu, J. Gratten, A.K. Henders, Z.-H.
Zhang, J. Edson, S. Furlong, S. Morgan, S. Heggie, K. Thorpe, C. Pfluger, K.A.
Mather, P.S. Sachdev, A.F. McRae, M.R. Robinson, S. Shah, P.M. Visscher, M. Mangelsdorf,
R.D. Henderson, N.R. Wray, P.A. McCombe, Molecular Genetics & Genomic Medicine
5 (2017) 418–428.
date_created: 2020-04-30T10:48:25Z
date_published: 2017-07-01T00:00:00Z
date_updated: 2021-01-12T08:15:10Z
day: '01'
doi: 10.1002/mgg3.302
extern: '1'
intvolume: ' 5'
issue: '4'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.1002/mgg3.302
month: '07'
oa: 1
oa_version: Published Version
page: 418-428
publication: Molecular Genetics & Genomic Medicine
publication_identifier:
issn:
- 2324-9269
publication_status: published
publisher: Wiley
quality_controlled: '1'
status: public
title: Whole exome sequencing and DNA methylation analysis in a clinical amyotrophic
lateral sclerosis cohort
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 5
year: '2017'
...
---
_id: '7731'
abstract:
- lang: eng
text: 'Genetic association studies in admixed populations are underrepresented in
the genomics literature, with a key concern for researchers being the adequate
control of spurious associations due to population structure. Linear mixed models
(LMMs) are well suited for genome-wide association studies (GWAS) because they
account for both population stratification and cryptic relatedness and achieve
increased statistical power by jointly modeling all genotyped markers. Additionally,
Bayesian LMMs allow for more flexible assumptions about the underlying distribution
of genetic effects, and can concurrently estimate the proportion of phenotypic
variance explained by genetic markers. Using three recently published Bayesian
LMMs, Bayes R, BSLMM, and BOLT-LMM, we investigate an existing data set on eye
(n = 625) and skin (n = 684) color from Cape Verde, an island nation off West
Africa that is home to individuals with a broad range of phenotypic values for
eye and skin color due to the mix of West African and European ancestry. We use
simulations to demonstrate the utility of Bayesian LMMs for mapping loci and studying
the genetic architecture of quantitative traits in admixed populations. The Bayesian
LMMs provide evidence for two new pigmentation loci: one for eye color (AHRR)
and one for skin color (DDB1).'
article_processing_charge: No
article_type: original
author:
- first_name: Luke R.
full_name: Lloyd-Jones, Luke R.
last_name: Lloyd-Jones
- 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: Gerhard
full_name: Moser, Gerhard
last_name: Moser
- first_name: Jian
full_name: Zeng, Jian
last_name: Zeng
- first_name: Sandra
full_name: Beleza, Sandra
last_name: Beleza
- first_name: Gregory S.
full_name: Barsh, Gregory S.
last_name: Barsh
- first_name: Hua
full_name: Tang, Hua
last_name: Tang
- first_name: Peter M.
full_name: Visscher, Peter M.
last_name: Visscher
citation:
ama: Lloyd-Jones LR, Robinson MR, Moser G, et al. Inference on the genetic basis
of eye and skin color in an admixed population via Bayesian linear mixed models.
Genetics. 2017;206(2):1113-1126. doi:10.1534/genetics.116.193383
apa: Lloyd-Jones, L. R., Robinson, M. R., Moser, G., Zeng, J., Beleza, S., Barsh,
G. S., … Visscher, P. M. (2017). Inference on the genetic basis of eye and skin
color in an admixed population via Bayesian linear mixed models. Genetics.
Genetics Society of America. https://doi.org/10.1534/genetics.116.193383
chicago: Lloyd-Jones, Luke R., Matthew Richard Robinson, Gerhard Moser, Jian Zeng,
Sandra Beleza, Gregory S. Barsh, Hua Tang, and Peter M. Visscher. “Inference on
the Genetic Basis of Eye and Skin Color in an Admixed Population via Bayesian
Linear Mixed Models.” Genetics. Genetics Society of America, 2017. https://doi.org/10.1534/genetics.116.193383.
ieee: L. R. Lloyd-Jones et al., “Inference on the genetic basis of eye and
skin color in an admixed population via Bayesian linear mixed models,” Genetics,
vol. 206, no. 2. Genetics Society of America, pp. 1113–1126, 2017.
ista: Lloyd-Jones LR, Robinson MR, Moser G, Zeng J, Beleza S, Barsh GS, Tang H,
Visscher PM. 2017. Inference on the genetic basis of eye and skin color in an
admixed population via Bayesian linear mixed models. Genetics. 206(2), 1113–1126.
mla: Lloyd-Jones, Luke R., et al. “Inference on the Genetic Basis of Eye and Skin
Color in an Admixed Population via Bayesian Linear Mixed Models.” Genetics,
vol. 206, no. 2, Genetics Society of America, 2017, pp. 1113–26, doi:10.1534/genetics.116.193383.
short: L.R. Lloyd-Jones, M.R. Robinson, G. Moser, J. Zeng, S. Beleza, G.S. Barsh,
H. Tang, P.M. Visscher, Genetics 206 (2017) 1113–1126.
date_created: 2020-04-30T10:47:50Z
date_published: 2017-06-01T00:00:00Z
date_updated: 2021-01-12T08:15:10Z
day: '01'
doi: 10.1534/genetics.116.193383
extern: '1'
intvolume: ' 206'
issue: '2'
language:
- iso: eng
month: '06'
oa_version: None
page: 1113-1126
publication: Genetics
publication_identifier:
issn:
- 0016-6731
- 1943-2631
publication_status: published
publisher: Genetics Society of America
quality_controlled: '1'
status: public
title: Inference on the genetic basis of eye and skin color in an admixed population
via Bayesian linear mixed models
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 206
year: '2017'
...
---
_id: '7755'
abstract:
- lang: eng
text: We give a bird's-eye view of the plastic deformation of crystals aimed at
the statistical physics community, as well as a broad introduction to the statistical
theories of forced rigid systems aimed at the plasticity community. Memory effects
in magnets, spin glasses, charge density waves, and dilute colloidal suspensions
are discussed in relation to the onset of plastic yielding in crystals. Dislocation
avalanches and complex dislocation tangles are discussed via a brief introduction
to the renormalization group and scaling. Analogies to emergent scale invariance
in fracture, jamming, coarsening, and a variety of depinning transitions are explored.
Dislocation dynamics in crystals challenge nonequilibrium statistical physics.
Statistical physics provides both cautionary tales of subtle memory effects in
nonequilibrium systems and systematic tools designed to address complex scale-invariant
behavior on multiple length scales and timescales.
article_processing_charge: No
article_type: original
author:
- first_name: James P.
full_name: Sethna, James P.
last_name: Sethna
- first_name: Matthew K.
full_name: Bierbaum, Matthew K.
last_name: Bierbaum
- first_name: Karin A.
full_name: Dahmen, Karin A.
last_name: Dahmen
- 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: Julia R.
full_name: Greer, Julia R.
last_name: Greer
- first_name: Lorien X.
full_name: Hayden, Lorien X.
last_name: Hayden
- first_name: Jaron P.
full_name: Kent-Dobias, Jaron P.
last_name: Kent-Dobias
- first_name: Edward D.
full_name: Lee, Edward D.
last_name: Lee
- first_name: Danilo B.
full_name: Liarte, Danilo B.
last_name: Liarte
- first_name: Xiaoyue
full_name: Ni, Xiaoyue
last_name: Ni
- first_name: Katherine N.
full_name: Quinn, Katherine N.
last_name: Quinn
- first_name: Archishman
full_name: Raju, Archishman
last_name: Raju
- first_name: D. Zeb
full_name: Rocklin, D. Zeb
last_name: Rocklin
- first_name: Ashivni
full_name: Shekhawat, Ashivni
last_name: Shekhawat
- first_name: Stefano
full_name: Zapperi, Stefano
last_name: Zapperi
citation:
ama: 'Sethna JP, Bierbaum MK, Dahmen KA, et al. Deformation of crystals: Connections
with statistical physics. Annual Review of Materials Research. 2017;47:217-246.
doi:10.1146/annurev-matsci-070115-032036'
apa: 'Sethna, J. P., Bierbaum, M. K., Dahmen, K. A., Goodrich, C. P., Greer, J.
R., Hayden, L. X., … Zapperi, S. (2017). Deformation of crystals: Connections
with statistical physics. Annual Review of Materials Research. Annual Reviews.
https://doi.org/10.1146/annurev-matsci-070115-032036'
chicago: 'Sethna, James P., Matthew K. Bierbaum, Karin A. Dahmen, Carl Peter Goodrich,
Julia R. Greer, Lorien X. Hayden, Jaron P. Kent-Dobias, et al. “Deformation of
Crystals: Connections with Statistical Physics.” Annual Review of Materials
Research. Annual Reviews, 2017. https://doi.org/10.1146/annurev-matsci-070115-032036.'
ieee: 'J. P. Sethna et al., “Deformation of crystals: Connections with statistical
physics,” Annual Review of Materials Research, vol. 47. Annual Reviews,
pp. 217–246, 2017.'
ista: 'Sethna JP, Bierbaum MK, Dahmen KA, Goodrich CP, Greer JR, Hayden LX, Kent-Dobias
JP, Lee ED, Liarte DB, Ni X, Quinn KN, Raju A, Rocklin DZ, Shekhawat A, Zapperi
S. 2017. Deformation of crystals: Connections with statistical physics. Annual
Review of Materials Research. 47, 217–246.'
mla: 'Sethna, James P., et al. “Deformation of Crystals: Connections with Statistical
Physics.” Annual Review of Materials Research, vol. 47, Annual Reviews,
2017, pp. 217–46, doi:10.1146/annurev-matsci-070115-032036.'
short: J.P. Sethna, M.K. Bierbaum, K.A. Dahmen, C.P. Goodrich, J.R. Greer, L.X.
Hayden, J.P. Kent-Dobias, E.D. Lee, D.B. Liarte, X. Ni, K.N. Quinn, A. Raju, D.Z.
Rocklin, A. Shekhawat, S. Zapperi, Annual Review of Materials Research 47 (2017)
217–246.
date_created: 2020-04-30T11:38:24Z
date_published: 2017-07-01T00:00:00Z
date_updated: 2021-01-12T08:15:18Z
day: '01'
doi: 10.1146/annurev-matsci-070115-032036
extern: '1'
intvolume: ' 47'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.1146/annurev-matsci-070115-032036
month: '07'
oa: 1
oa_version: Published Version
page: 217-246
publication: Annual Review of Materials Research
publication_identifier:
issn:
- 1531-7331
- 1545-4118
publication_status: published
publisher: Annual Reviews
quality_controlled: '1'
status: public
title: 'Deformation of crystals: Connections with statistical physics'
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 47
year: '2017'
...
---
_id: '7757'
abstract:
- lang: eng
text: Recent advances in designing metamaterials have demonstrated that global mechanical
properties of disordered spring networks can be tuned by selectively modifying
only a small subset of bonds. Here, using a computationally efficient approach,
we extend this idea to tune more general properties of networks. With nearly complete
success, we are able to produce a strain between any two target nodes in a network
in response to an applied source strain on any other pair of nodes by removing
only ∼1% of the bonds. We are also able to control multiple pairs of target nodes,
each with a different individual response, from a single source, and to tune multiple
independent source/target responses simultaneously into a network. We have fabricated
physical networks in macroscopic 2D and 3D systems that exhibit these responses.
This work is inspired by the long-range coupled conformational changes that constitute
allosteric function in proteins. The fact that allostery is a common means for
regulation in biological molecules suggests that it is a relatively easy property
to develop through evolution. In analogy, our results show that long-range coupled
mechanical responses are similarly easy to achieve in disordered networks.
article_processing_charge: No
article_type: original
author:
- first_name: Jason W.
full_name: Rocks, Jason W.
last_name: Rocks
- first_name: Nidhi
full_name: Pashine, Nidhi
last_name: Pashine
- first_name: Irmgard
full_name: Bischofberger, Irmgard
last_name: Bischofberger
- 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: Rocks JW, Pashine N, Bischofberger I, Goodrich CP, Liu AJ, Nagel SR. Designing
allostery-inspired response in mechanical networks. Proceedings of the National
Academy of Sciences. 2017;114(10):2520-2525. doi:10.1073/pnas.1612139114
apa: Rocks, J. W., Pashine, N., Bischofberger, I., Goodrich, C. P., Liu, A. J.,
& Nagel, S. R. (2017). Designing allostery-inspired response in mechanical
networks. Proceedings of the National Academy of Sciences. Proceedings
of the National Academy of Sciences. https://doi.org/10.1073/pnas.1612139114
chicago: Rocks, Jason W., Nidhi Pashine, Irmgard Bischofberger, Carl Peter Goodrich,
Andrea J. Liu, and Sidney R. Nagel. “Designing Allostery-Inspired Response in
Mechanical Networks.” Proceedings of the National Academy of Sciences.
Proceedings of the National Academy of Sciences, 2017. https://doi.org/10.1073/pnas.1612139114.
ieee: J. W. Rocks, N. Pashine, I. Bischofberger, C. P. Goodrich, A. J. Liu, and
S. R. Nagel, “Designing allostery-inspired response in mechanical networks,” Proceedings
of the National Academy of Sciences, vol. 114, no. 10. Proceedings of the
National Academy of Sciences, pp. 2520–2525, 2017.
ista: Rocks JW, Pashine N, Bischofberger I, Goodrich CP, Liu AJ, Nagel SR. 2017.
Designing allostery-inspired response in mechanical networks. Proceedings of the
National Academy of Sciences. 114(10), 2520–2525.
mla: Rocks, Jason W., et al. “Designing Allostery-Inspired Response in Mechanical
Networks.” Proceedings of the National Academy of Sciences, vol. 114, no.
10, Proceedings of the National Academy of Sciences, 2017, pp. 2520–25, doi:10.1073/pnas.1612139114.
short: J.W. Rocks, N. Pashine, I. Bischofberger, C.P. Goodrich, A.J. Liu, S.R. Nagel,
Proceedings of the National Academy of Sciences 114 (2017) 2520–2525.
date_created: 2020-04-30T11:38:53Z
date_published: 2017-03-07T00:00:00Z
date_updated: 2021-01-12T08:15:19Z
day: '07'
doi: 10.1073/pnas.1612139114
extern: '1'
intvolume: ' 114'
issue: '10'
language:
- iso: eng
month: '03'
oa_version: None
page: 2520-2525
publication: Proceedings of the National Academy of Sciences
publication_identifier:
issn:
- 0027-8424
- 1091-6490
publication_status: published
publisher: Proceedings of the National Academy of Sciences
quality_controlled: '1'
status: public
title: Designing allostery-inspired response in mechanical networks
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 114
year: '2017'
...
---
_id: '7758'
abstract:
- lang: eng
text: Controlling motion at the microscopic scale is a fundamental goal in the development
of biologically inspired systems. We show that the motion of active, self-propelled
colloids can be sufficiently controlled for use as a tool to assemble complex
structures such as braids and weaves out of microscopic filaments. Unlike typical
self-assembly paradigms, these structures are held together by geometric constraints
rather than adhesive bonds. The out-of-equilibrium assembly that we propose involves
precisely controlling the 2D motion of active colloids so that their path has
a nontrivial topology. We demonstrate with proof-of-principle Brownian dynamics
simulations that, when the colloids are attached to long semiflexible filaments,
this motion causes the filaments to braid. The ability of the active particles
to provide sufficient force necessary to bend the filaments into a braid depends
on a number of factors, including the self-propulsion mechanism, the properties
of the filament, and the maximum curvature in the braid. Our work demonstrates
that nonequilibrium assembly pathways can be designed using active particles.
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: Michael P.
full_name: Brenner, Michael P.
last_name: Brenner
citation:
ama: Goodrich CP, Brenner MP. Using active colloids as machines to weave and braid
on the micrometer scale. Proceedings of the National Academy of Sciences.
2017;114(2):257-262. doi:10.1073/pnas.1608838114
apa: Goodrich, C. P., & Brenner, M. P. (2017). Using active colloids as machines
to weave and braid on the micrometer scale. Proceedings of the National Academy
of Sciences. Proceedings of the National Academy of Sciences. https://doi.org/10.1073/pnas.1608838114
chicago: Goodrich, Carl Peter, and Michael P. Brenner. “Using Active Colloids as
Machines to Weave and Braid on the Micrometer Scale.” Proceedings of the National
Academy of Sciences. Proceedings of the National Academy of Sciences, 2017.
https://doi.org/10.1073/pnas.1608838114.
ieee: C. P. Goodrich and M. P. Brenner, “Using active colloids as machines to weave
and braid on the micrometer scale,” Proceedings of the National Academy of
Sciences, vol. 114, no. 2. Proceedings of the National Academy of Sciences,
pp. 257–262, 2017.
ista: Goodrich CP, Brenner MP. 2017. Using active colloids as machines to weave
and braid on the micrometer scale. Proceedings of the National Academy of Sciences.
114(2), 257–262.
mla: Goodrich, Carl Peter, and Michael P. Brenner. “Using Active Colloids as Machines
to Weave and Braid on the Micrometer Scale.” Proceedings of the National Academy
of Sciences, vol. 114, no. 2, Proceedings of the National Academy of Sciences,
2017, pp. 257–62, doi:10.1073/pnas.1608838114.
short: C.P. Goodrich, M.P. Brenner, Proceedings of the National Academy of Sciences
114 (2017) 257–262.
date_created: 2020-04-30T11:39:09Z
date_published: 2017-01-10T00:00:00Z
date_updated: 2021-01-12T08:15:20Z
day: '10'
doi: 10.1073/pnas.1608838114
extern: '1'
intvolume: ' 114'
issue: '2'
language:
- iso: eng
month: '01'
oa_version: None
page: 257-262
publication: Proceedings of the National Academy of Sciences
publication_identifier:
issn:
- 0027-8424
- 1091-6490
publication_status: published
publisher: Proceedings of the National Academy of Sciences
quality_controlled: '1'
status: public
title: Using active colloids as machines to weave and braid on the micrometer scale
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 114
year: '2017'
...
---
_id: '7756'
abstract:
- lang: eng
text: We study the shear jamming of athermal frictionless soft spheres, and find
that in the thermodynamic limit, a shear-jammed state exists with different elastic
properties from the isotropically-jammed state. For example, shear-jammed states
can have a non-zero residual shear stress in the thermodynamic limit that arises
from long-range stress-stress correlations. As a result, the ratio of the shear
and bulk moduli, which in isotropically-jammed systems vanishes as the jamming
transition is approached from above, instead approaches a constant. Despite these
striking differences, we argue that in a deeper sense, the shear jamming and isotropic
jamming transitions actually have the same symmetry, and that the differences
can be fully understood by rotating the six-dimensional basis of the elastic modulus
tensor.
article_processing_charge: No
article_type: original
author:
- first_name: Marco
full_name: Baity-Jesi, Marco
last_name: Baity-Jesi
- 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
- first_name: James P.
full_name: Sethna, James P.
last_name: Sethna
citation:
ama: Baity-Jesi M, Goodrich CP, Liu AJ, Nagel SR, Sethna JP. Emergent SO(3) symmetry
of the frictionless shear jamming transition. Journal of Statistical Physics.
2017;167(3-4):735-748. doi:10.1007/s10955-016-1703-9
apa: Baity-Jesi, M., Goodrich, C. P., Liu, A. J., Nagel, S. R., & Sethna, J.
P. (2017). Emergent SO(3) symmetry of the frictionless shear jamming transition.
Journal of Statistical Physics. Springer Nature. https://doi.org/10.1007/s10955-016-1703-9
chicago: Baity-Jesi, Marco, Carl Peter Goodrich, Andrea J. Liu, Sidney R. Nagel,
and James P. Sethna. “Emergent SO(3) Symmetry of the Frictionless Shear Jamming
Transition.” Journal of Statistical Physics. Springer Nature, 2017. https://doi.org/10.1007/s10955-016-1703-9.
ieee: M. Baity-Jesi, C. P. Goodrich, A. J. Liu, S. R. Nagel, and J. P. Sethna, “Emergent
SO(3) symmetry of the frictionless shear jamming transition,” Journal of Statistical
Physics, vol. 167, no. 3–4. Springer Nature, pp. 735–748, 2017.
ista: Baity-Jesi M, Goodrich CP, Liu AJ, Nagel SR, Sethna JP. 2017. Emergent SO(3)
symmetry of the frictionless shear jamming transition. Journal of Statistical
Physics. 167(3–4), 735–748.
mla: Baity-Jesi, Marco, et al. “Emergent SO(3) Symmetry of the Frictionless Shear
Jamming Transition.” Journal of Statistical Physics, vol. 167, no. 3–4,
Springer Nature, 2017, pp. 735–48, doi:10.1007/s10955-016-1703-9.
short: M. Baity-Jesi, C.P. Goodrich, A.J. Liu, S.R. Nagel, J.P. Sethna, Journal
of Statistical Physics 167 (2017) 735–748.
date_created: 2020-04-30T11:38:38Z
date_published: 2017-01-03T00:00:00Z
date_updated: 2021-01-12T08:15:19Z
day: '03'
doi: 10.1007/s10955-016-1703-9
extern: '1'
intvolume: ' 167'
issue: 3-4
language:
- iso: eng
month: '01'
oa_version: None
page: 735-748
publication: Journal of Statistical Physics
publication_identifier:
issn:
- 0022-4715
- 1572-9613
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
status: public
title: Emergent SO(3) symmetry of the frictionless shear jamming transition
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 167
year: '2017'
...
---
_id: '788'
abstract:
- lang: eng
text: In contrast to electronic computation, chemical computation is noisy and susceptible
to a variety of sources of error, which has prevented the construction of robust
complex systems. To be effective, chemical algorithms must be designed with an
appropriate error model in mind. Here we consider the model of chemical reaction
networks that preserve molecular count (population protocols), and ask whether
computation can be made robust to a natural model of unintended “leak” reactions.
Our definition of leak is motivated by both the particular spurious behavior seen
when implementing chemical reaction networks with DNA strand displacement cascades,
as well as the unavoidable side reactions in any implementation due to the basic
laws of chemistry. We develop a new “Robust Detection” algorithm for the problem
of fast (logarithmic time) single molecule detection, and prove that it is robust
to this general model of leaks. Besides potential applications in single molecule
detection, the error-correction ideas developed here might enable a new class
of robust-by-design chemical algorithms. Our analysis is based on a non-standard
hybrid argument, combining ideas from discrete analysis of population protocols
with classic Markov chain techniques.
acknowledgement: "D. Alistarh - Supported by an SNF Ambizione Fellowship. A. Kosowski
— Supported by Inria project GANG, ANR project DESCARTES, and\r\nNCN grant 2015/17/B/ST6/01897.
D. Soloveichik — Supported by NSF grants CCF-1618895 and CCF-1652824.\r\n\r\n"
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: Bartłomiej
full_name: Dudek, Bartłomiej
last_name: Dudek
- first_name: Adrian
full_name: Kosowski, Adrian
last_name: Kosowski
- first_name: David
full_name: Soloveichik, David
last_name: Soloveichik
- first_name: Przemysław
full_name: Uznański, Przemysław
last_name: Uznański
citation:
ama: 'Alistarh D-A, Dudek B, Kosowski A, Soloveichik D, Uznański P. Robust detection
in leak-prone population protocols. In: Vol 10467 LNCS. Springer; 2017:155-171.
doi:10.1007/978-3-319-66799-7_11'
apa: Alistarh, D.-A., Dudek, B., Kosowski, A., Soloveichik, D., & Uznański,
P. (2017). Robust detection in leak-prone population protocols (Vol. 10467 LNCS,
pp. 155–171). Presented at the DNA Computing and Molecular Programming, Springer.
https://doi.org/10.1007/978-3-319-66799-7_11
chicago: Alistarh, Dan-Adrian, Bartłomiej Dudek, Adrian Kosowski, David Soloveichik,
and Przemysław Uznański. “Robust Detection in Leak-Prone Population Protocols,”
10467 LNCS:155–71. Springer, 2017. https://doi.org/10.1007/978-3-319-66799-7_11.
ieee: D.-A. Alistarh, B. Dudek, A. Kosowski, D. Soloveichik, and P. Uznański, “Robust
detection in leak-prone population protocols,” presented at the DNA Computing
and Molecular Programming, 2017, vol. 10467 LNCS, pp. 155–171.
ista: Alistarh D-A, Dudek B, Kosowski A, Soloveichik D, Uznański P. 2017. Robust
detection in leak-prone population protocols. DNA Computing and Molecular Programming,
LNCS, vol. 10467 LNCS, 155–171.
mla: Alistarh, Dan-Adrian, et al. Robust Detection in Leak-Prone Population Protocols.
Vol. 10467 LNCS, Springer, 2017, pp. 155–71, doi:10.1007/978-3-319-66799-7_11.
short: D.-A. Alistarh, B. Dudek, A. Kosowski, D. Soloveichik, P. Uznański, in:,
Springer, 2017, pp. 155–171.
conference:
name: DNA Computing and Molecular Programming
date_created: 2018-12-11T11:48:30Z
date_published: 2017-01-01T00:00:00Z
date_updated: 2022-03-18T12:48:02Z
day: '01'
doi: 10.1007/978-3-319-66799-7_11
extern: '1'
external_id:
arxiv:
- '1706.09937'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/1706.09937
month: '01'
oa: 1
oa_version: None
page: 155 - 171
publication_status: published
publisher: Springer
publist_id: '6868'
quality_controlled: '1'
scopus_import: '1'
status: public
title: Robust detection in leak-prone population protocols
type: conference
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 10467 LNCS
year: '2017'
...
---
_id: '787'
abstract:
- lang: eng
text: 'Population protocols are a popular model of distributed computing, in which
randomly-interacting agents with little computational power cooperate to jointly
perform computational tasks. Inspired by developments in molecular computation,
and in particular DNA computing, recent algorithmic work has focused on the complexity
of solving simple yet fundamental tasks in the population model, such as leader
election (which requires convergence to a single agent in a special "leader"
state), and majority (in which agents must converge to a decision as to which
of two possible initial states had higher initial count). Known results point
towards an inherent trade-off between the time complexity of such algorithms,
and the space complexity, i.e. size of the memory available to each agent. In
this paper, we explore this trade-off and provide new upper and lower bounds for
majority and leader election. First, we prove a unified lower bound, which relates
the space available per node with the time complexity achievable by a protocol:
for instance, our result implies that any protocol solving either of these tasks
for n agents using O(log log n) states must take (n=polylogn) expected time. This
is the first result to characterize time complexity for protocols which employ
super-constant number of states per node, and proves that fast, poly-logarithmic
running times require protocols to have relatively large space costs. On the positive
side, we give algorithms showing that fast, poly-logarithmic convergence time
can be achieved using O(log2 n) space per node, in the case of both tasks. Overall,
our results highlight a time complexity separation between O(log log n) and (log2
n) state space size for both majority and leader election in population protocols,
and introduce new techniques, which should be applicable more broadly.'
acknowledgement: "Dan Alistarh was supported by a Swiss National Science\r\nFoundation
Ambizione Fellowship. James Aspnes was supported by the National Science Foundation
\ under grants\r\nCCF-1637385 and CCF-1650596. Rati Gelashvili was supported by
\ the National Science Foundation under grants\r\nCCF-1217921, CCF-1301926,
and IIS-1447786, the Department of Energy under grant ER26116/DE-SC0008923, and\r\nOracle
and Intel corporations.\r\nThe authors would like to thank David Doty, David\r\nSoloveichik,
\ and Milan Vojnovic for insightful discussions\r\nand feedback during the development
of this work."
author:
- first_name: Dan-Adrian
full_name: Alistarh, Dan-Adrian
id: 4A899BFC-F248-11E8-B48F-1D18A9856A87
last_name: Alistarh
orcid: 0000-0003-3650-940X
- first_name: James
full_name: Aspnes, James
last_name: Aspnes
- first_name: David
full_name: Eisenstat, David
last_name: Eisenstat
- first_name: Ronald
full_name: Rivest, Ronald
last_name: Rivest
- first_name: Rati
full_name: Gelashvili, Rati
last_name: Gelashvili
citation:
ama: 'Alistarh D-A, Aspnes J, Eisenstat D, Rivest R, Gelashvili R. Time-space trade-offs
in population protocols. In: SIAM; 2017:2560-2579. doi:doi.org/10.1137/1.9781611974782.169'
apa: 'Alistarh, D.-A., Aspnes, J., Eisenstat, D., Rivest, R., & Gelashvili,
R. (2017). Time-space trade-offs in population protocols (pp. 2560–2579). Presented
at the SODA: Symposium on Discrete Algorithms, SIAM. https://doi.org/doi.org/10.1137/1.9781611974782.169'
chicago: Alistarh, Dan-Adrian, James Aspnes, David Eisenstat, Ronald Rivest, and
Rati Gelashvili. “Time-Space Trade-Offs in Population Protocols,” 2560–79. SIAM,
2017. https://doi.org/doi.org/10.1137/1.9781611974782.169.
ieee: 'D.-A. Alistarh, J. Aspnes, D. Eisenstat, R. Rivest, and R. Gelashvili, “Time-space
trade-offs in population protocols,” presented at the SODA: Symposium on Discrete
Algorithms, 2017, pp. 2560–2579.'
ista: 'Alistarh D-A, Aspnes J, Eisenstat D, Rivest R, Gelashvili R. 2017. Time-space
trade-offs in population protocols. SODA: Symposium on Discrete Algorithms, 2560–2579.'
mla: Alistarh, Dan-Adrian, et al. Time-Space Trade-Offs in Population Protocols.
SIAM, 2017, pp. 2560–79, doi:doi.org/10.1137/1.9781611974782.169.
short: D.-A. Alistarh, J. Aspnes, D. Eisenstat, R. Rivest, R. Gelashvili, in:, SIAM,
2017, pp. 2560–2579.
conference:
name: 'SODA: Symposium on Discrete Algorithms'
date_created: 2018-12-11T11:48:30Z
date_published: 2017-01-01T00:00:00Z
date_updated: 2023-02-23T13:19:13Z
day: '01'
doi: doi.org/10.1137/1.9781611974782.169
extern: '1'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/1602.08032
month: '01'
oa: 1
oa_version: None
page: 2560 - 2579
publication_status: published
publisher: SIAM
publist_id: '6869'
status: public
title: Time-space trade-offs in population protocols
type: conference
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
year: '2017'
...
---
_id: '789'
abstract:
- lang: eng
text: 'The problem of efficient concurrent memory reclamation in unmanaged languages
such as C or C++ is one of the major challenges facing the parallelization of
billions of lines of legacy code. Garbage collectors for C/C++ can be inefficient;
thus, programmers are often forced to use finely-crafted concurrent memory reclamation
techniques. These techniques can provide good performance, but require considerable
programming effort to deploy, and have strict requirements, allowing the programmer
very little room for error. In this work, we present Forkscan, a new conservative
concurrent memory reclamation scheme which is fully automatic and surprisingly
scalable. Forkscan''s semantics place it between automatic garbage collectors
(it requires the programmer to explicitly retire nodes before they can be reclaimed),
and concurrent memory reclamation techniques (as it does not assume that nodes
are completely unlinked from the data structure for correctness). Forkscan''s
implementation exploits these new semantics for efficiency: we leverage parallelism
and optimized implementations of signaling and copy-on-write in modern operating
systems to efficiently obtain and process consistent snapshots of memory that
can be scanned concurrently with the normal program operation. Empirical evaluation
on a range of classical concurrent data structure microbenchmarks shows that Forkscan
can preserve the scalability of the original code, while maintaining an order
of magnitude lower latency than automatic garbage collection, and demonstrating
competitive performance with finely crafted memory reclamation techniques.'
acknowledgement: William Leiserson, Alexander Matveev, and Nir Shavit were supported
by the NSF under grants IIS-1447786 and CCF-1563880, and Dan Alistarh was supported
by a Swiss National Fund Ambizione Fellowship.
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: William
full_name: Leiserson, William
last_name: Leiserson
- first_name: Alexander
full_name: Matveev, Alexander
last_name: Matveev
- first_name: Nir
full_name: Shavit, Nir
last_name: Shavit
citation:
ama: 'Alistarh D-A, Leiserson W, Matveev A, Shavit N. Forkscan: Conservative memory
reclamation for modern operating systems. In: ACM; 2017:483-498. doi:10.1145/3064176.3064214'
apa: 'Alistarh, D.-A., Leiserson, W., Matveev, A., & Shavit, N. (2017). Forkscan:
Conservative memory reclamation for modern operating systems (pp. 483–498). Presented
at the EuroSys: European Conference on Computer Systems, ACM. https://doi.org/10.1145/3064176.3064214'
chicago: 'Alistarh, Dan-Adrian, William Leiserson, Alexander Matveev, and Nir Shavit.
“Forkscan: Conservative Memory Reclamation for Modern Operating Systems,” 483–98.
ACM, 2017. https://doi.org/10.1145/3064176.3064214.'
ieee: 'D.-A. Alistarh, W. Leiserson, A. Matveev, and N. Shavit, “Forkscan: Conservative
memory reclamation for modern operating systems,” presented at the EuroSys: European
Conference on Computer Systems, 2017, pp. 483–498.'
ista: 'Alistarh D-A, Leiserson W, Matveev A, Shavit N. 2017. Forkscan: Conservative
memory reclamation for modern operating systems. EuroSys: European Conference
on Computer Systems, 483–498.'
mla: 'Alistarh, Dan-Adrian, et al. Forkscan: Conservative Memory Reclamation
for Modern Operating Systems. ACM, 2017, pp. 483–98, doi:10.1145/3064176.3064214.'
short: D.-A. Alistarh, W. Leiserson, A. Matveev, N. Shavit, in:, ACM, 2017, pp.
483–498.
conference:
name: 'EuroSys: European Conference on Computer Systems'
date_created: 2018-12-11T11:48:30Z
date_published: 2017-01-01T00:00:00Z
date_updated: 2023-02-23T13:19:44Z
day: '01'
doi: 10.1145/3064176.3064214
extern: '1'
language:
- iso: eng
month: '01'
oa_version: None
page: 483 - 498
publication_status: published
publisher: ACM
publist_id: '6867'
status: public
title: 'Forkscan: Conservative memory reclamation for modern operating systems'
type: conference
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
year: '2017'
...
---
_id: '790'
abstract:
- lang: eng
text: Stochastic gradient descent (SGD) is a commonly used algorithm for training
linear machine learning models. Based on vector algebra, it benefits from the
inherent parallelism available in an FPGA. In this paper, we first present a single-precision
floating-point SGD implementation on an FPGA that provides similar performance
as a 10-core CPU. We then adapt the design to make it capable of processing low-precision
data. The low-precision data is obtained from a novel compression scheme - called
stochastic quantization, specifically designed for machine learning applications.
We test both full-precision and low-precision designs on various regression and
classification data sets. We achieve up to an order of magnitude training speedup
when using low-precision data compared to a full-precision SGD on the same FPGA
and a state-of-the-art multi-core solution, while maintaining the quality of training.
We open source the designs presented in this paper.
article_processing_charge: No
author:
- first_name: Kaan
full_name: Kara, Kaan
last_name: Kara
- 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: Gustavo
full_name: Alonso, Gustavo
last_name: Alonso
- first_name: Onur
full_name: Mutlu, Onur
last_name: Mutlu
- first_name: Ce
full_name: Zhang, Ce
last_name: Zhang
citation:
ama: 'Kara K, Alistarh D-A, Alonso G, Mutlu O, Zhang C. FPGA-accelerated dense linear
machine learning: A precision-convergence trade-off. In: IEEE; 2017:160-167. doi:10.1109/FCCM.2017.39'
apa: 'Kara, K., Alistarh, D.-A., Alonso, G., Mutlu, O., & Zhang, C. (2017).
FPGA-accelerated dense linear machine learning: A precision-convergence trade-off
(pp. 160–167). Presented at the FCCM: Field-Programmable Custom Computing Machines,
IEEE. https://doi.org/10.1109/FCCM.2017.39'
chicago: 'Kara, Kaan, Dan-Adrian Alistarh, Gustavo Alonso, Onur Mutlu, and Ce Zhang.
“FPGA-Accelerated Dense Linear Machine Learning: A Precision-Convergence Trade-Off,”
160–67. IEEE, 2017. https://doi.org/10.1109/FCCM.2017.39.'
ieee: 'K. Kara, D.-A. Alistarh, G. Alonso, O. Mutlu, and C. Zhang, “FPGA-accelerated
dense linear machine learning: A precision-convergence trade-off,” presented at
the FCCM: Field-Programmable Custom Computing Machines, 2017, pp. 160–167.'
ista: 'Kara K, Alistarh D-A, Alonso G, Mutlu O, Zhang C. 2017. FPGA-accelerated
dense linear machine learning: A precision-convergence trade-off. FCCM: Field-Programmable
Custom Computing Machines, 160–167.'
mla: 'Kara, Kaan, et al. FPGA-Accelerated Dense Linear Machine Learning: A Precision-Convergence
Trade-Off. IEEE, 2017, pp. 160–67, doi:10.1109/FCCM.2017.39.'
short: K. Kara, D.-A. Alistarh, G. Alonso, O. Mutlu, C. Zhang, in:, IEEE, 2017,
pp. 160–167.
conference:
name: 'FCCM: Field-Programmable Custom Computing Machines'
date_created: 2018-12-11T11:48:31Z
date_published: 2017-06-30T00:00:00Z
date_updated: 2023-02-23T13:19:52Z
day: '30'
doi: 10.1109/FCCM.2017.39
extern: '1'
language:
- iso: eng
month: '06'
oa_version: None
page: 160 - 167
publication_status: published
publisher: IEEE
publist_id: '6865'
status: public
title: 'FPGA-accelerated dense linear machine learning: A precision-convergence trade-off'
type: conference
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
year: '2017'
...
---
_id: '795'
abstract:
- lang: eng
text: 'We introduce a common generalization of the strong Hanani–Tutte theorem and
the weak Hanani–Tutte theorem: if a graph G has a drawing D in the plane where
every pair of independent edges crosses an even number of times, then G has a
planar drawing preserving the rotation of each vertex whose incident edges cross
each other evenly in D. The theorem is implicit in the proof of the strong Hanani–Tutte
theorem by Pelsmajer, Schaefer and Štefankovič. We give a new, somewhat simpler
proof.'
article_number: P3.18
article_processing_charge: No
article_type: original
author:
- first_name: Radoslav
full_name: Fulek, Radoslav
id: 39F3FFE4-F248-11E8-B48F-1D18A9856A87
last_name: Fulek
orcid: 0000-0001-8485-1774
- first_name: Jan
full_name: Kynčl, Jan
last_name: Kynčl
- first_name: Dömötör
full_name: Pálvölgyi, Dömötör
last_name: Pálvölgyi
citation:
ama: Fulek R, Kynčl J, Pálvölgyi D. Unified Hanani Tutte theorem. Electronic
Journal of Combinatorics. 2017;24(3). doi:10.37236/6663
apa: Fulek, R., Kynčl, J., & Pálvölgyi, D. (2017). Unified Hanani Tutte theorem.
Electronic Journal of Combinatorics. International Press. https://doi.org/10.37236/6663
chicago: Fulek, Radoslav, Jan Kynčl, and Dömötör Pálvölgyi. “Unified Hanani Tutte
Theorem.” Electronic Journal of Combinatorics. International Press, 2017.
https://doi.org/10.37236/6663.
ieee: R. Fulek, J. Kynčl, and D. Pálvölgyi, “Unified Hanani Tutte theorem,” Electronic
Journal of Combinatorics, vol. 24, no. 3. International Press, 2017.
ista: Fulek R, Kynčl J, Pálvölgyi D. 2017. Unified Hanani Tutte theorem. Electronic
Journal of Combinatorics. 24(3), P3.18.
mla: Fulek, Radoslav, et al. “Unified Hanani Tutte Theorem.” Electronic Journal
of Combinatorics, vol. 24, no. 3, P3.18, International Press, 2017, doi:10.37236/6663.
short: R. Fulek, J. Kynčl, D. Pálvölgyi, Electronic Journal of Combinatorics 24
(2017).
date_created: 2018-12-11T11:48:32Z
date_published: 2017-07-28T00:00:00Z
date_updated: 2022-03-18T12:58:53Z
day: '28'
ddc:
- '000'
department:
- _id: UlWa
doi: 10.37236/6663
ec_funded: 1
file:
- access_level: open_access
checksum: ef320cff0f062051e858f929be6a3581
content_type: application/pdf
creator: dernst
date_created: 2019-01-18T14:04:08Z
date_updated: 2020-07-14T12:48:06Z
file_id: '5853'
file_name: 2017_ElectrCombi_Fulek.pdf
file_size: 236944
relation: main_file
file_date_updated: 2020-07-14T12:48:06Z
has_accepted_license: '1'
intvolume: ' 24'
issue: '3'
language:
- iso: eng
month: '07'
oa: 1
oa_version: Published Version
project:
- _id: 25681D80-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '291734'
name: International IST Postdoc Fellowship Programme
publication: Electronic Journal of Combinatorics
publication_identifier:
issn:
- '10778926'
publication_status: published
publisher: International Press
publist_id: '6859'
quality_controlled: '1'
scopus_import: '1'
status: public
title: Unified Hanani Tutte theorem
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 24
year: '2017'
...
---
_id: '7981'
abstract:
- lang: ger
text: Aprotische Natrium‐O2‐Batterien basieren auf der reversiblen Bildung und Auflösung
von Natriumsuperoxid (NaO2) während des Zellbetriebs. Nebenreaktionen des Elektrolyten
und der Elektrode mit dem stark nukleophilen und basischen NaO2 führen zu mangelhafter
Zyklenstabilität. Seine Reaktivität allein kann die Nebenreaktionen und schlechte
Reversibilität jedoch nicht schlüssig erklären. Hier wird gezeigt, dass Singulett‐Sauerstoff
(1O2) in allen Phasen des Betriebs entsteht und eine Hauptursache für Nebenreaktionen
ist. 1O2 wurde in situ und ex situ mit einem 1O2‐Fänger detektiert, der schnell
und selektiv ein Addukt mit 1O2 bildet. Mechanistisch betrachtet entsteht 1O2
entweder durch protonenunterstützte Disproportionierung von Superoxid während
des Entladens, Lagerns und Ladens unter ca. 3.3 V oder durch direkte elektrochemische
1O2‐Entwicklung über ca. 3.3 V. Spuren von Wasser ermöglichen hohe Kapazitäten,
beschleunigen aber auch Nebenreaktionen. Daher muss das hochreaktive 1O2 unbedingt
kontrolliert werden, um die Zelle reversibel zu betreiben.
article_processing_charge: No
article_type: original
author:
- first_name: Lukas
full_name: Schafzahl, Lukas
last_name: Schafzahl
- first_name: Nika
full_name: Mahne, Nika
last_name: Mahne
- first_name: Bettina
full_name: Schafzahl, Bettina
last_name: Schafzahl
- first_name: Martin
full_name: Wilkening, Martin
last_name: Wilkening
- first_name: Christian
full_name: Slugovc, Christian
last_name: Slugovc
- first_name: Sergey M.
full_name: Borisov, Sergey M.
last_name: Borisov
- first_name: Stefan Alexander
full_name: Freunberger, Stefan Alexander
id: A8CA28E6-CE23-11E9-AD2D-EC27E6697425
last_name: Freunberger
orcid: 0000-0003-2902-5319
citation:
ama: Schafzahl L, Mahne N, Schafzahl B, et al. Singulett-Sauerstoff in der aprotischen
Natrium-O2-Batterie. Angewandte Chemie. 2017;129(49):15934-15938. doi:10.1002/ange.201709351
apa: Schafzahl, L., Mahne, N., Schafzahl, B., Wilkening, M., Slugovc, C., Borisov,
S. M., & Freunberger, S. A. (2017). Singulett-Sauerstoff in der aprotischen
Natrium-O2-Batterie. Angewandte Chemie. Wiley. https://doi.org/10.1002/ange.201709351
chicago: Schafzahl, Lukas, Nika Mahne, Bettina Schafzahl, Martin Wilkening, Christian
Slugovc, Sergey M. Borisov, and Stefan Alexander Freunberger. “Singulett-Sauerstoff
in Der Aprotischen Natrium-O2-Batterie.” Angewandte Chemie. Wiley, 2017.
https://doi.org/10.1002/ange.201709351.
ieee: L. Schafzahl et al., “Singulett-Sauerstoff in der aprotischen Natrium-O2-Batterie,”
Angewandte Chemie, vol. 129, no. 49. Wiley, pp. 15934–15938, 2017.
ista: Schafzahl L, Mahne N, Schafzahl B, Wilkening M, Slugovc C, Borisov SM, Freunberger
SA. 2017. Singulett-Sauerstoff in der aprotischen Natrium-O2-Batterie. Angewandte
Chemie. 129(49), 15934–15938.
mla: Schafzahl, Lukas, et al. “Singulett-Sauerstoff in Der Aprotischen Natrium-O2-Batterie.”
Angewandte Chemie, vol. 129, no. 49, Wiley, 2017, pp. 15934–38, doi:10.1002/ange.201709351.
short: L. Schafzahl, N. Mahne, B. Schafzahl, M. Wilkening, C. Slugovc, S.M. Borisov,
S.A. Freunberger, Angewandte Chemie 129 (2017) 15934–15938.
date_created: 2020-06-19T08:22:06Z
date_published: 2017-12-04T00:00:00Z
date_updated: 2021-01-12T08:16:20Z
day: '04'
ddc:
- '540'
doi: 10.1002/ange.201709351
extern: '1'
file:
- access_level: open_access
checksum: 38f2c2383bc9573f6770c1dba72d7a9a
content_type: application/pdf
creator: dernst
date_created: 2020-06-19T11:39:09Z
date_updated: 2020-07-14T12:48:06Z
file_id: '7987'
file_name: 2017_AngChemieDT_Schafzahl.pdf
file_size: 988125
relation: main_file
file_date_updated: 2020-07-14T12:48:06Z
has_accepted_license: '1'
intvolume: ' 129'
issue: '49'
language:
- iso: eng
month: '12'
oa: 1
oa_version: Published Version
page: 15934-15938
publication: Angewandte Chemie
publication_identifier:
issn:
- 0044-8249
publication_status: published
publisher: Wiley
quality_controlled: '1'
status: public
title: Singulett-Sauerstoff in der aprotischen Natrium-O2-Batterie
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: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 129
year: '2017'
...
---
_id: '7980'
abstract:
- lang: eng
text: In this part, the use of polysaccharides, either directly through composite
approaches, or by carbonization will be described. In many cases, materials are
obtained which are competitive in terms of capacitance and cycle lifetime. In
this part, the use of polysaccharides, either directly through composite approaches,
or by carbonization will be described. In many cases, materials are obtained which
are competitive in terms of capacitance and cycle lifetime. The following part
will focus mainly on cellulosic composites with conductive polymers since cellulose
is most abundant and therefore has attracted much more research interest in this
field whereas in the second part also other polysaccharides, such as chitin, xylans,
alginates, pectins, dextrans and caragenaans have been used in carbonization experiments.
alternative_title:
- SpringerBriefs in Molecular Science
article_processing_charge: No
author:
- first_name: Soon
full_name: Yee Liew, Soon
last_name: Yee Liew
- first_name: Wim
full_name: Thielemans, Wim
last_name: Thielemans
- first_name: Stefan Alexander
full_name: Freunberger, Stefan Alexander
id: A8CA28E6-CE23-11E9-AD2D-EC27E6697425
last_name: Freunberger
orcid: 0000-0003-2902-5319
- first_name: Stefan
full_name: Spirk, Stefan
last_name: Spirk
citation:
ama: 'Yee Liew S, Thielemans W, Freunberger SA, Spirk S. Polysaccharides in supercapacitors.
In: Yee Liew S, Thielemans W, Freunberger SA, Spirk S, eds. Polysaccharide
Based Supercapacitors. Springer Nature; 2017:15-53. doi:10.1007/978-3-319-50754-5_2'
apa: Yee Liew, S., Thielemans, W., Freunberger, S. A., & Spirk, S. (2017). Polysaccharides
in supercapacitors. In S. Yee Liew, W. Thielemans, S. A. Freunberger, & S.
Spirk (Eds.), Polysaccharide Based Supercapacitors (pp. 15–53). Springer
Nature. https://doi.org/10.1007/978-3-319-50754-5_2
chicago: Yee Liew, Soon, Wim Thielemans, Stefan Alexander Freunberger, and Stefan
Spirk. “Polysaccharides in Supercapacitors.” In Polysaccharide Based Supercapacitors,
edited by Soon Yee Liew, Wim Thielemans, Stefan Alexander Freunberger, and Stefan
Spirk, 15–53. Springer Nature, 2017. https://doi.org/10.1007/978-3-319-50754-5_2.
ieee: S. Yee Liew, W. Thielemans, S. A. Freunberger, and S. Spirk, “Polysaccharides
in supercapacitors,” in Polysaccharide Based Supercapacitors, S. Yee Liew,
W. Thielemans, S. A. Freunberger, and S. Spirk, Eds. Springer Nature, 2017, pp.
15–53.
ista: 'Yee Liew S, Thielemans W, Freunberger SA, Spirk S. 2017.Polysaccharides in
supercapacitors. In: Polysaccharide Based Supercapacitors. SpringerBriefs in Molecular
Science, , 15–53.'
mla: Yee Liew, Soon, et al. “Polysaccharides in Supercapacitors.” Polysaccharide
Based Supercapacitors, edited by Soon Yee Liew et al., Springer Nature, 2017,
pp. 15–53, doi:10.1007/978-3-319-50754-5_2.
short: S. Yee Liew, W. Thielemans, S.A. Freunberger, S. Spirk, in:, S. Yee Liew,
W. Thielemans, S.A. Freunberger, S. Spirk (Eds.), Polysaccharide Based Supercapacitors,
Springer Nature, 2017, pp. 15–53.
date_created: 2020-06-19T08:11:08Z
date_published: 2017-03-26T00:00:00Z
date_updated: 2021-01-12T08:16:19Z
day: '26'
ddc:
- '540'
- '541'
doi: 10.1007/978-3-319-50754-5_2
editor:
- first_name: Soon
full_name: Yee Liew, Soon
last_name: Yee Liew
- first_name: Wim
full_name: Thielemans, Wim
last_name: Thielemans
- first_name: Stefan Alexander
full_name: Freunberger, Stefan Alexander
id: A8CA28E6-CE23-11E9-AD2D-EC27E6697425
last_name: Freunberger
orcid: 0000-0003-2902-5319
- first_name: Stefan
full_name: Spirk, Stefan
last_name: Spirk
extern: '1'
file:
- access_level: open_access
checksum: 4182aeee32c9263a626a7e522f1934f5
content_type: application/pdf
creator: sfreunbe
date_created: 2020-06-29T14:13:44Z
date_updated: 2020-07-14T12:48:06Z
file_id: '8048'
file_name: Final_EPNOE.pdf
file_size: 3339826
relation: main_file
file_date_updated: 2020-07-14T12:48:06Z
has_accepted_license: '1'
language:
- iso: eng
month: '03'
oa: 1
oa_version: Submitted Version
page: 15-53
publication: Polysaccharide Based Supercapacitors
publication_identifier:
isbn:
- '9783319507538'
- '9783319507545'
issn:
- 2191-5407
- 2191-5415
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
status: public
title: Polysaccharides in supercapacitors
type: book_chapter
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
year: '2017'
...
---
_id: '7982'
abstract:
- lang: eng
text: Beyond-intercalation batteries promise a step-change in energy storage compared
to intercalation-based lithium-ion and sodium-ion batteries. However, only performance
metrics that include all cell components and operation parameters can tell whether
a true advance over intercalation batteries has been achieved.
article_number: '17091'
article_processing_charge: No
article_type: original
author:
- first_name: Stefan Alexander
full_name: Freunberger, Stefan Alexander
id: A8CA28E6-CE23-11E9-AD2D-EC27E6697425
last_name: Freunberger
orcid: 0000-0003-2902-5319
citation:
ama: Freunberger SA. True performance metrics in beyond-intercalation batteries.
Nature Energy. 2017;2(7). doi:10.1038/nenergy.2017.91
apa: Freunberger, S. A. (2017). True performance metrics in beyond-intercalation
batteries. Nature Energy. Springer Nature. https://doi.org/10.1038/nenergy.2017.91
chicago: Freunberger, Stefan Alexander. “True Performance Metrics in Beyond-Intercalation
Batteries.” Nature Energy. Springer Nature, 2017. https://doi.org/10.1038/nenergy.2017.91.
ieee: S. A. Freunberger, “True performance metrics in beyond-intercalation batteries,”
Nature Energy, vol. 2, no. 7. Springer Nature, 2017.
ista: Freunberger SA. 2017. True performance metrics in beyond-intercalation batteries.
Nature Energy. 2(7), 17091.
mla: Freunberger, Stefan Alexander. “True Performance Metrics in Beyond-Intercalation
Batteries.” Nature Energy, vol. 2, no. 7, 17091, Springer Nature, 2017,
doi:10.1038/nenergy.2017.91.
short: S.A. Freunberger, Nature Energy 2 (2017).
date_created: 2020-06-19T08:23:47Z
date_published: 2017-06-05T00:00:00Z
date_updated: 2021-01-12T08:16:20Z
day: '05'
ddc:
- '540'
- '546'
- '541'
doi: 10.1038/nenergy.2017.91
extern: '1'
external_id:
arxiv:
- '2002.00712'
file:
- access_level: open_access
checksum: 2564255b76f5346a32e764dbfd17fa2f
content_type: application/pdf
creator: sfreunbe
date_created: 2020-06-29T13:26:55Z
date_updated: 2020-07-14T12:48:06Z
file_id: '8046'
file_name: NEnergy_Comment_final.pdf
file_size: 817665
relation: main_file
file_date_updated: 2020-07-14T12:48:06Z
has_accepted_license: '1'
intvolume: ' 2'
issue: '7'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/2002.00712
month: '06'
oa: 1
oa_version: Submitted Version
publication: Nature Energy
publication_identifier:
issn:
- 2058-7546
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
status: public
title: True performance metrics in beyond-intercalation batteries
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 2
year: '2017'
...
---
_id: '7986'
article_number: '17036 '
article_processing_charge: No
article_type: original
author:
- first_name: Nika
full_name: Mahne, Nika
last_name: Mahne
- first_name: Bettina
full_name: Schafzahl, Bettina
last_name: Schafzahl
- first_name: Christian
full_name: Leypold, Christian
last_name: Leypold
- first_name: Mario
full_name: Leypold, Mario
last_name: Leypold
- first_name: Sandra
full_name: Grumm, Sandra
last_name: Grumm
- first_name: Anita
full_name: Leitgeb, Anita
last_name: Leitgeb
- first_name: Gernot A.
full_name: Strohmeier, Gernot A.
last_name: Strohmeier
- first_name: Martin
full_name: Wilkening, Martin
last_name: Wilkening
- first_name: Olivier
full_name: Fontaine, Olivier
last_name: Fontaine
- first_name: Denis
full_name: Kramer, Denis
last_name: Kramer
- first_name: Christian
full_name: Slugovc, Christian
last_name: Slugovc
- first_name: Sergey M.
full_name: Borisov, Sergey M.
last_name: Borisov
- first_name: Stefan Alexander
full_name: Freunberger, Stefan Alexander
id: A8CA28E6-CE23-11E9-AD2D-EC27E6697425
last_name: Freunberger
orcid: 0000-0003-2902-5319
citation:
ama: Mahne N, Schafzahl B, Leypold C, et al. Singlet oxygen generation as a major
cause for parasitic reactions during cycling of aprotic lithium–oxygen batteries.
Nature Energy. 2017;2(5). doi:10.1038/nenergy.2017.36
apa: Mahne, N., Schafzahl, B., Leypold, C., Leypold, M., Grumm, S., Leitgeb, A.,
… Freunberger, S. A. (2017). Singlet oxygen generation as a major cause for parasitic
reactions during cycling of aprotic lithium–oxygen batteries. Nature Energy.
Springer Nature. https://doi.org/10.1038/nenergy.2017.36
chicago: Mahne, Nika, Bettina Schafzahl, Christian Leypold, Mario Leypold, Sandra
Grumm, Anita Leitgeb, Gernot A. Strohmeier, et al. “Singlet Oxygen Generation
as a Major Cause for Parasitic Reactions during Cycling of Aprotic Lithium–Oxygen
Batteries.” Nature Energy. Springer Nature, 2017. https://doi.org/10.1038/nenergy.2017.36.
ieee: N. Mahne et al., “Singlet oxygen generation as a major cause for parasitic
reactions during cycling of aprotic lithium–oxygen batteries,” Nature Energy,
vol. 2, no. 5. Springer Nature, 2017.
ista: Mahne N, Schafzahl B, Leypold C, Leypold M, Grumm S, Leitgeb A, Strohmeier
GA, Wilkening M, Fontaine O, Kramer D, Slugovc C, Borisov SM, Freunberger SA.
2017. Singlet oxygen generation as a major cause for parasitic reactions during
cycling of aprotic lithium–oxygen batteries. Nature Energy. 2(5), 17036.
mla: Mahne, Nika, et al. “Singlet Oxygen Generation as a Major Cause for Parasitic
Reactions during Cycling of Aprotic Lithium–Oxygen Batteries.” Nature Energy,
vol. 2, no. 5, 17036, Springer Nature, 2017, doi:10.1038/nenergy.2017.36.
short: N. Mahne, B. Schafzahl, C. Leypold, M. Leypold, S. Grumm, A. Leitgeb, G.A.
Strohmeier, M. Wilkening, O. Fontaine, D. Kramer, C. Slugovc, S.M. Borisov, S.A.
Freunberger, Nature Energy 2 (2017).
date_created: 2020-06-19T10:42:33Z
date_published: 2017-03-20T00:00:00Z
date_updated: 2021-01-12T08:16:21Z
day: '20'
doi: 10.1038/nenergy.2017.36
extern: '1'
external_id:
arxiv:
- '1711.10340'
intvolume: ' 2'
issue: '5'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/1711.10340
month: '03'
oa: 1
oa_version: Preprint
publication: Nature Energy
publication_identifier:
issn:
- 2058-7546
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
status: public
title: Singlet oxygen generation as a major cause for parasitic reactions during cycling
of aprotic lithium–oxygen batteries
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 2
year: '2017'
...
---
_id: '797'
abstract:
- lang: ger
text: Phasenübergänge helfen beim Verständnis von Vielteilchensystemen in der Festkörperphysik
und Fluiddynamik bis hin zur Teilchenphysik. Unserer internationalen Kollaboration
ist es gelungen, einen neuartigen Phasenübergang in einem Quantensystem zu beobachten
[1]. In einem Mikrowellenresonator konnte erstmals die spontane Zustandsänderung
von undurchsichtig zu transparent nachgewiesen werden.
article_processing_charge: No
article_type: original
author:
- first_name: Johannes M
full_name: Fink, Johannes M
id: 4B591CBA-F248-11E8-B48F-1D18A9856A87
last_name: Fink
orcid: 0000-0001-8112-028X
citation:
ama: Fink JM. Photonenblockade aufgelöst. Physik in unserer Zeit. 2017;48(3):111-113.
doi:10.1002/piuz.201770305
apa: Fink, J. M. (2017). Photonenblockade aufgelöst. Physik in Unserer Zeit.
Wiley. https://doi.org/10.1002/piuz.201770305
chicago: Fink, Johannes M. “Photonenblockade Aufgelöst.” Physik in Unserer Zeit.
Wiley, 2017. https://doi.org/10.1002/piuz.201770305.
ieee: J. M. Fink, “Photonenblockade aufgelöst,” Physik in unserer Zeit, vol.
48, no. 3. Wiley, pp. 111–113, 2017.
ista: Fink JM. 2017. Photonenblockade aufgelöst. Physik in unserer Zeit. 48(3),
111–113.
mla: Fink, Johannes M. “Photonenblockade Aufgelöst.” Physik in Unserer Zeit,
vol. 48, no. 3, Wiley, 2017, pp. 111–13, doi:10.1002/piuz.201770305.
short: J.M. Fink, Physik in Unserer Zeit 48 (2017) 111–113.
date_created: 2018-12-11T11:48:33Z
date_published: 2017-05-01T00:00:00Z
date_updated: 2022-03-24T09:16:20Z
day: '01'
department:
- _id: JoFi
doi: 10.1002/piuz.201770305
intvolume: ' 48'
issue: '3'
language:
- iso: eng
month: '05'
oa_version: None
page: 111 - 113
publication: Physik in unserer Zeit
publication_status: published
publisher: Wiley
publist_id: '6856'
quality_controlled: '1'
status: public
title: Photonenblockade aufgelöst
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 48
year: '2017'
...
---
_id: '8016'
abstract:
- lang: eng
text: Long-term modifications of neuronal connections are critical for reliable
memory storage in the brain. However, their locus of expression—pre- or postsynaptic—is
highly variable. Here we introduce a theoretical framework in which long-term
plasticity performs an optimization of the postsynaptic response statistics toward
a given mean with minimal variance. Consequently, the state of the synapse at
the time of plasticity induction determines the ratio of pre- and postsynaptic
modifications. Our theory explains the experimentally observed expression loci
of the hippocampal and neocortical synaptic potentiation studies we examined.
Moreover, the theory predicts presynaptic expression of long-term depression,
consistent with experimental observations. At inhibitory synapses, the theory
suggests a statistically efficient excitatory-inhibitory balance in which changes
in inhibitory postsynaptic response statistics specifically target the mean excitation.
Our results provide a unifying theory for understanding the expression mechanisms
and functions of long-term synaptic transmission plasticity.
article_processing_charge: No
article_type: original
author:
- first_name: Rui Ponte
full_name: Costa, Rui Ponte
last_name: Costa
- first_name: Zahid
full_name: Padamsey, Zahid
last_name: Padamsey
- first_name: James A.
full_name: D’Amour, James A.
last_name: D’Amour
- first_name: Nigel J.
full_name: Emptage, Nigel J.
last_name: Emptage
- first_name: Robert C.
full_name: Froemke, Robert C.
last_name: Froemke
- first_name: Tim P
full_name: Vogels, Tim P
id: CB6FF8D2-008F-11EA-8E08-2637E6697425
last_name: Vogels
orcid: 0000-0003-3295-6181
citation:
ama: Costa RP, Padamsey Z, D’Amour JA, Emptage NJ, Froemke RC, Vogels TP. Synaptic
transmission optimization predicts expression loci of long-term plasticity. Neuron.
2017;96(1):177-189.e7. doi:10.1016/j.neuron.2017.09.021
apa: Costa, R. P., Padamsey, Z., D’Amour, J. A., Emptage, N. J., Froemke, R. C.,
& Vogels, T. P. (2017). Synaptic transmission optimization predicts expression
loci of long-term plasticity. Neuron. Elsevier. https://doi.org/10.1016/j.neuron.2017.09.021
chicago: Costa, Rui Ponte, Zahid Padamsey, James A. D’Amour, Nigel J. Emptage, Robert
C. Froemke, and Tim P Vogels. “Synaptic Transmission Optimization Predicts Expression
Loci of Long-Term Plasticity.” Neuron. Elsevier, 2017. https://doi.org/10.1016/j.neuron.2017.09.021.
ieee: R. P. Costa, Z. Padamsey, J. A. D’Amour, N. J. Emptage, R. C. Froemke, and
T. P. Vogels, “Synaptic transmission optimization predicts expression loci of
long-term plasticity,” Neuron, vol. 96, no. 1. Elsevier, p. 177–189.e7,
2017.
ista: Costa RP, Padamsey Z, D’Amour JA, Emptage NJ, Froemke RC, Vogels TP. 2017.
Synaptic transmission optimization predicts expression loci of long-term plasticity.
Neuron. 96(1), 177–189.e7.
mla: Costa, Rui Ponte, et al. “Synaptic Transmission Optimization Predicts Expression
Loci of Long-Term Plasticity.” Neuron, vol. 96, no. 1, Elsevier, 2017,
p. 177–189.e7, doi:10.1016/j.neuron.2017.09.021.
short: R.P. Costa, Z. Padamsey, J.A. D’Amour, N.J. Emptage, R.C. Froemke, T.P. Vogels,
Neuron 96 (2017) 177–189.e7.
date_created: 2020-06-25T12:54:46Z
date_published: 2017-09-27T00:00:00Z
date_updated: 2021-01-12T08:16:32Z
day: '27'
ddc:
- '570'
doi: 10.1016/j.neuron.2017.09.021
extern: '1'
external_id:
pmid:
- '28957667'
file:
- access_level: open_access
checksum: 49fbca2821066c0965bd5678b32b6b48
content_type: application/pdf
creator: cziletti
date_created: 2020-07-09T09:42:49Z
date_updated: 2020-07-14T12:48:08Z
file_id: '8103'
file_name: 2017_Neuron_Costa.pdf
file_size: 7140149
relation: main_file
file_date_updated: 2020-07-14T12:48:08Z
has_accepted_license: '1'
intvolume: ' 96'
issue: '1'
language:
- iso: eng
month: '09'
oa: 1
oa_version: Published Version
page: 177-189.e7
pmid: 1
publication: Neuron
publication_identifier:
issn:
- 0896-6273
publication_status: published
publisher: Elsevier
quality_controlled: '1'
status: public
title: Synaptic transmission optimization predicts expression loci of long-term plasticity
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: D865714E-FA4E-11E9-B85B-F5C5E5697425
volume: 96
year: '2017'
...
---
_id: '8018'
abstract:
- lang: eng
text: 'Nervous systems use excitatory cell assemblies to encode and represent sensory
percepts. Similarly, synaptically connected cell assemblies or "engrams" are thought
to represent memories of past experience. Multiple lines of recent evidence indicate
that brain systems create and use inhibitory replicas of excitatory representations
for important cognitive functions. Such matched "inhibitory engrams" can form
through homeostatic potentiation of inhibition onto postsynaptic cells that show
increased levels of excitation. Inhibitory engrams can reduce behavioral responses
to familiar stimuli, thereby resulting in behavioral habituation. In addition,
by preventing inappropriate activation of excitatory memory engrams, inhibitory
engrams can make memories quiescent, stored in a latent form that is available
for context-relevant activation. In neural networks with balanced excitatory and
inhibitory engrams, the release of innate responses and recall of associative
memories can occur through focused disinhibition. Understanding mechanisms that
regulate the formation and expression of inhibitory engrams in vivo may help not
only to explain key features of cognition but also to provide insight into transdiagnostic
traits associated with psychiatric conditions such as autism, schizophrenia, and
posttraumatic stress disorder. '
article_processing_charge: No
article_type: original
author:
- first_name: Helen C.
full_name: Barron, Helen C.
last_name: Barron
- first_name: Tim P
full_name: Vogels, Tim P
id: CB6FF8D2-008F-11EA-8E08-2637E6697425
last_name: Vogels
orcid: 0000-0003-3295-6181
- first_name: Timothy E.
full_name: Behrens, Timothy E.
last_name: Behrens
- first_name: Mani
full_name: Ramaswami, Mani
last_name: Ramaswami
citation:
ama: Barron HC, Vogels TP, Behrens TE, Ramaswami M. Inhibitory engrams in perception
and memory. Proceedings of the National Academy of Sciences. 2017;114(26):6666-6674.
doi:10.1073/pnas.1701812114
apa: Barron, H. C., Vogels, T. P., Behrens, T. E., & Ramaswami, M. (2017). Inhibitory
engrams in perception and memory. Proceedings of the National Academy of Sciences.
Proceedings of the National Academy of Sciences. https://doi.org/10.1073/pnas.1701812114
chicago: Barron, Helen C., Tim P Vogels, Timothy E. Behrens, and Mani Ramaswami.
“Inhibitory Engrams in Perception and Memory.” Proceedings of the National
Academy of Sciences. Proceedings of the National Academy of Sciences, 2017.
https://doi.org/10.1073/pnas.1701812114.
ieee: H. C. Barron, T. P. Vogels, T. E. Behrens, and M. Ramaswami, “Inhibitory engrams
in perception and memory,” Proceedings of the National Academy of Sciences,
vol. 114, no. 26. Proceedings of the National Academy of Sciences, pp. 6666–6674,
2017.
ista: Barron HC, Vogels TP, Behrens TE, Ramaswami M. 2017. Inhibitory engrams in
perception and memory. Proceedings of the National Academy of Sciences. 114(26),
6666–6674.
mla: Barron, Helen C., et al. “Inhibitory Engrams in Perception and Memory.” Proceedings
of the National Academy of Sciences, vol. 114, no. 26, Proceedings of the
National Academy of Sciences, 2017, pp. 6666–74, doi:10.1073/pnas.1701812114.
short: H.C. Barron, T.P. Vogels, T.E. Behrens, M. Ramaswami, Proceedings of the
National Academy of Sciences 114 (2017) 6666–6674.
date_created: 2020-06-25T12:56:58Z
date_published: 2017-06-27T00:00:00Z
date_updated: 2021-01-12T08:16:33Z
day: '27'
doi: 10.1073/pnas.1701812114
extern: '1'
external_id:
pmid:
- '28611219'
intvolume: ' 114'
issue: '26'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5495250/
month: '06'
oa: 1
oa_version: Published Version
page: 6666-6674
pmid: 1
publication: Proceedings of the National Academy of Sciences
publication_identifier:
eissn:
- 1091-6490
issn:
- 0027-8424
publication_status: published
publisher: Proceedings of the National Academy of Sciences
quality_controlled: '1'
status: public
title: Inhibitory engrams in perception and memory
type: journal_article
user_id: D865714E-FA4E-11E9-B85B-F5C5E5697425
volume: 114
year: '2017'
...
---
_id: '8019'
abstract:
- lang: eng
text: Synaptic plasticity is essential for the function of neural systems. It sets
up initial circuitry and adjusts connection strengths according to the maintenance
requirements of its host networks. Like all things biological, synaptic plasticity
must rely on genetic programs to provide the molecular components of its machinery
to integrate ongoing, often multi-sensory experience without destabilising effects.
Because of its fundamental importance to healthy behaviour, understanding plasticity
is thought to hold the key to understanding the brain. There are innumerable ways
to approach this topic and a complete review of its status quo would be impossible.
In the current issue we dig into some of the finer points of synaptic plasticity,
starting small, at the level of genes, and slowly zooming out to synapses, populations
of synapses, and finally entire systems and brain regions. At each level, we tried
to represent different perspectives, different systems, and approaches to the
same questions to give a broad sampling of how synaptic plasticity is being studied.
article_processing_charge: No
article_type: letter_note
author:
- first_name: Tim P
full_name: Vogels, Tim P
id: CB6FF8D2-008F-11EA-8E08-2637E6697425
last_name: Vogels
orcid: 0000-0003-3295-6181
- first_name: Leslie C
full_name: Griffith, Leslie C
last_name: Griffith
citation:
ama: 'Vogels TP, Griffith LC. Editorial overview: Neurobiology of learning and plasticity
2017. Current Opinion in Neurobiology. 2017;43:A1-A5. doi:10.1016/j.conb.2017.04.002'
apa: 'Vogels, T. P., & Griffith, L. C. (2017). Editorial overview: Neurobiology
of learning and plasticity 2017. Current Opinion in Neurobiology. Elsevier.
https://doi.org/10.1016/j.conb.2017.04.002'
chicago: 'Vogels, Tim P, and Leslie C Griffith. “Editorial Overview: Neurobiology
of Learning and Plasticity 2017.” Current Opinion in Neurobiology. Elsevier,
2017. https://doi.org/10.1016/j.conb.2017.04.002.'
ieee: 'T. P. Vogels and L. C. Griffith, “Editorial overview: Neurobiology of learning
and plasticity 2017,” Current Opinion in Neurobiology, vol. 43. Elsevier,
pp. A1–A5, 2017.'
ista: 'Vogels TP, Griffith LC. 2017. Editorial overview: Neurobiology of learning
and plasticity 2017. Current Opinion in Neurobiology. 43, A1–A5.'
mla: 'Vogels, Tim P., and Leslie C. Griffith. “Editorial Overview: Neurobiology
of Learning and Plasticity 2017.” Current Opinion in Neurobiology, vol.
43, Elsevier, 2017, pp. A1–5, doi:10.1016/j.conb.2017.04.002.'
short: T.P. Vogels, L.C. Griffith, Current Opinion in Neurobiology 43 (2017) A1–A5.
date_created: 2020-06-25T13:03:30Z
date_published: 2017-04-17T00:00:00Z
date_updated: 2021-01-12T08:16:33Z
day: '17'
doi: 10.1016/j.conb.2017.04.002
extern: '1'
external_id:
pmid:
- '28427877'
intvolume: ' 43'
language:
- iso: eng
month: '04'
oa_version: None
page: A1-A5
pmid: 1
publication: Current Opinion in Neurobiology
publication_identifier:
issn:
- 0959-4388
publication_status: published
publisher: Elsevier
quality_controlled: '1'
status: public
title: 'Editorial overview: Neurobiology of learning and plasticity 2017'
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 43
year: '2017'
...
---
_id: '8017'
abstract:
- lang: eng
text: nhibitory neurons, although relatively few in number, exert powerful control
over brain circuits. They stabilize network activity in the face of strong feedback
excitation and actively engage in computations. Recent studies reveal the importance
of a precise balance of excitation and inhibition in neural circuits, which often
requires exquisite fine-tuning of inhibitory connections. We review inhibitory
synaptic plasticity and its roles in shaping both feedforward and feedback control.
We discuss the necessity of complex, codependent plasticity mechanisms to build
nontrivial, functioning networks, and we end by summarizing experimental evidence
of such interactions.
article_processing_charge: No
article_type: original
author:
- first_name: Guillaume
full_name: Hennequin, Guillaume
last_name: Hennequin
- first_name: Everton J.
full_name: Agnes, Everton J.
last_name: Agnes
- first_name: Tim P
full_name: Vogels, Tim P
id: CB6FF8D2-008F-11EA-8E08-2637E6697425
last_name: Vogels
orcid: 0000-0003-3295-6181
citation:
ama: 'Hennequin G, Agnes EJ, Vogels TP. Inhibitory plasticity: Balance, control,
and codependence. Annual Review of Neuroscience. 2017;40(1):557-579. doi:10.1146/annurev-neuro-072116-031005'
apa: 'Hennequin, G., Agnes, E. J., & Vogels, T. P. (2017). Inhibitory plasticity:
Balance, control, and codependence. Annual Review of Neuroscience. Annual
Reviews. https://doi.org/10.1146/annurev-neuro-072116-031005'
chicago: 'Hennequin, Guillaume, Everton J. Agnes, and Tim P Vogels. “Inhibitory
Plasticity: Balance, Control, and Codependence.” Annual Review of Neuroscience.
Annual Reviews, 2017. https://doi.org/10.1146/annurev-neuro-072116-031005.'
ieee: 'G. Hennequin, E. J. Agnes, and T. P. Vogels, “Inhibitory plasticity: Balance,
control, and codependence,” Annual Review of Neuroscience, vol. 40, no.
1. Annual Reviews, pp. 557–579, 2017.'
ista: 'Hennequin G, Agnes EJ, Vogels TP. 2017. Inhibitory plasticity: Balance, control,
and codependence. Annual Review of Neuroscience. 40(1), 557–579.'
mla: 'Hennequin, Guillaume, et al. “Inhibitory Plasticity: Balance, Control, and
Codependence.” Annual Review of Neuroscience, vol. 40, no. 1, Annual Reviews,
2017, pp. 557–79, doi:10.1146/annurev-neuro-072116-031005.'
short: G. Hennequin, E.J. Agnes, T.P. Vogels, Annual Review of Neuroscience 40 (2017)
557–579.
date_created: 2020-06-25T12:55:53Z
date_published: 2017-07-01T00:00:00Z
date_updated: 2021-01-12T08:16:32Z
day: '01'
doi: 10.1146/annurev-neuro-072116-031005
extern: '1'
external_id:
pmid:
- '28598717'
intvolume: ' 40'
issue: '1'
language:
- iso: eng
month: '07'
oa_version: None
page: 557-579
pmid: 1
publication: Annual Review of Neuroscience
publication_identifier:
issn:
- 0147-006X
- 1545-4126
publication_status: published
publisher: Annual Reviews
quality_controlled: '1'
status: public
title: 'Inhibitory plasticity: Balance, control, and codependence'
type: journal_article
user_id: D865714E-FA4E-11E9-B85B-F5C5E5697425
volume: 40
year: '2017'
...
---
_id: '8075'
abstract:
- lang: eng
text: Ion channel models are the building blocks of computational neuron models.
Their biological fidelity is therefore crucial for the interpretation of simulations.
However, the number of published models, and the lack of standardization, make
the comparison of ion channel models with one another and with experimental data
difficult. Here, we present a framework for the automated large-scale classification
of ion channel models. Using annotated metadata and responses to a set of voltage-clamp
protocols, we assigned 2378 models of voltage- and calcium-gated ion channels
coded in NEURON to 211 clusters. The IonChannelGenealogy (ICGenealogy) web interface
provides an interactive resource for the categorization of new and existing models
and experimental recordings. It enables quantitative comparisons of simulated
and/or measured ion channel kinetics, and facilitates field-wide standardization
of experimentally-constrained modeling.
article_number: e22152
article_processing_charge: No
article_type: original
author:
- first_name: William F
full_name: Podlaski, William F
last_name: Podlaski
- first_name: Alexander
full_name: Seeholzer, Alexander
last_name: Seeholzer
- first_name: Lukas N
full_name: Groschner, Lukas N
last_name: Groschner
- first_name: Gero
full_name: Miesenböck, Gero
last_name: Miesenböck
- first_name: Rajnish
full_name: Ranjan, Rajnish
last_name: Ranjan
- first_name: Tim P
full_name: Vogels, Tim P
id: CB6FF8D2-008F-11EA-8E08-2637E6697425
last_name: Vogels
orcid: 0000-0003-3295-6181
citation:
ama: Podlaski WF, Seeholzer A, Groschner LN, Miesenböck G, Ranjan R, Vogels TP.
Mapping the function of neuronal ion channels in model and experiment. eLife.
2017;6. doi:10.7554/elife.22152
apa: Podlaski, W. F., Seeholzer, A., Groschner, L. N., Miesenböck, G., Ranjan, R.,
& Vogels, T. P. (2017). Mapping the function of neuronal ion channels in model
and experiment. ELife. eLife Sciences Publications, Ltd. https://doi.org/10.7554/elife.22152
chicago: Podlaski, William F, Alexander Seeholzer, Lukas N Groschner, Gero Miesenböck,
Rajnish Ranjan, and Tim P Vogels. “Mapping the Function of Neuronal Ion Channels
in Model and Experiment.” ELife. eLife Sciences Publications, Ltd, 2017.
https://doi.org/10.7554/elife.22152.
ieee: W. F. Podlaski, A. Seeholzer, L. N. Groschner, G. Miesenböck, R. Ranjan, and
T. P. Vogels, “Mapping the function of neuronal ion channels in model and experiment,”
eLife, vol. 6. eLife Sciences Publications, Ltd, 2017.
ista: Podlaski WF, Seeholzer A, Groschner LN, Miesenböck G, Ranjan R, Vogels TP.
2017. Mapping the function of neuronal ion channels in model and experiment. eLife.
6, e22152.
mla: Podlaski, William F., et al. “Mapping the Function of Neuronal Ion Channels
in Model and Experiment.” ELife, vol. 6, e22152, eLife Sciences Publications,
Ltd, 2017, doi:10.7554/elife.22152.
short: W.F. Podlaski, A. Seeholzer, L.N. Groschner, G. Miesenböck, R. Ranjan, T.P.
Vogels, ELife 6 (2017).
date_created: 2020-06-30T13:32:18Z
date_published: 2017-03-06T00:00:00Z
date_updated: 2021-01-12T08:16:46Z
day: '06'
ddc:
- '570'
doi: 10.7554/elife.22152
extern: '1'
external_id:
pmid:
- '28267430'
file:
- access_level: open_access
checksum: e5c5a33bcb3ac38ad62df1010ab29040
content_type: application/pdf
creator: cziletti
date_created: 2020-07-16T12:08:40Z
date_updated: 2020-07-16T12:08:40Z
file_id: '8124'
file_name: 2017_elife_Podlaski.pdf
file_size: 16034505
relation: main_file
success: 1
file_date_updated: 2020-07-16T12:08:40Z
has_accepted_license: '1'
intvolume: ' 6'
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, Ltd
quality_controlled: '1'
status: public
title: Mapping the function of neuronal ion channels in model and experiment
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: D865714E-FA4E-11E9-B85B-F5C5E5697425
volume: 6
year: '2017'
...
---
_id: '807'
abstract:
- lang: eng
text: 'On January the 1st, 2016 a new agreement between 32 Austrian scientific libraries
and the publisher Springer took its effect: this deal covers accessing the licensed
content on the one hand, and publishing open access on the other hand. More than
1000 papers by Austrian authors were published open access at Springer in the
first year alone. The working group "Springer Compact Evaluierung" made
the data for these articles available via the platform OpenAPC and would like
to use this opportunity to give a short account of what this publishing agreement
actually entails and the working group intends to do.'
author:
- first_name: Magdalena
full_name: Andrae, Magdalena
last_name: Andrae
- first_name: Márton
full_name: Villányi, Márton
id: 3FFCCD3A-F248-11E8-B48F-1D18A9856A87
last_name: Villányi
orcid: 0000-0001-8126-0426
citation:
ama: Andrae M, Villányi M. Der Springer Compact-Deal – Ein erster Einblick in die
Evaluierung einer Offsetting-Vereinbarung. Mitteilungen der Vereinigung Österreichischer
Bibliothekarinnen und Bibliothekare. 2017;70(2):274-280. doi:10.31263/voebm.v70i2.1898
apa: Andrae, M., & Villányi, M. (2017). Der Springer Compact-Deal – Ein erster
Einblick in die Evaluierung einer Offsetting-Vereinbarung. Mitteilungen Der
Vereinigung Österreichischer Bibliothekarinnen Und Bibliothekare. VÖB. https://doi.org/10.31263/voebm.v70i2.1898
chicago: Andrae, Magdalena, and Márton Villányi. “Der Springer Compact-Deal – Ein
Erster Einblick in Die Evaluierung Einer Offsetting-Vereinbarung.” Mitteilungen
Der Vereinigung Österreichischer Bibliothekarinnen Und Bibliothekare. VÖB,
2017. https://doi.org/10.31263/voebm.v70i2.1898.
ieee: M. Andrae and M. Villányi, “Der Springer Compact-Deal – Ein erster Einblick
in die Evaluierung einer Offsetting-Vereinbarung,” Mitteilungen der Vereinigung
Österreichischer Bibliothekarinnen und Bibliothekare, vol. 70, no. 2. VÖB,
pp. 274–280, 2017.
ista: Andrae M, Villányi M. 2017. Der Springer Compact-Deal – Ein erster Einblick
in die Evaluierung einer Offsetting-Vereinbarung. Mitteilungen der Vereinigung
Österreichischer Bibliothekarinnen und Bibliothekare. 70(2), 274–280.
mla: Andrae, Magdalena, and Márton Villányi. “Der Springer Compact-Deal – Ein Erster
Einblick in Die Evaluierung Einer Offsetting-Vereinbarung.” Mitteilungen Der
Vereinigung Österreichischer Bibliothekarinnen Und Bibliothekare, vol. 70,
no. 2, VÖB, 2017, pp. 274–80, doi:10.31263/voebm.v70i2.1898.
short: M. Andrae, M. Villányi, Mitteilungen Der Vereinigung Österreichischer Bibliothekarinnen
Und Bibliothekare 70 (2017) 274–280.
date_created: 2018-12-11T11:48:36Z
date_published: 2017-08-01T00:00:00Z
date_updated: 2021-01-12T08:16:45Z
day: '01'
ddc:
- '020'
department:
- _id: E-Lib
doi: 10.31263/voebm.v70i2.1898
file:
- access_level: open_access
checksum: 558c18bcf5580d87dd371ec626d52075
content_type: application/pdf
creator: dernst
date_created: 2019-01-18T13:39:26Z
date_updated: 2020-07-14T12:48:09Z
file_id: '5851'
file_name: 2017_VOEB_Andrae.pdf
file_size: 125065
relation: main_file
file_date_updated: 2020-07-14T12:48:09Z
has_accepted_license: '1'
intvolume: ' 70'
issue: '2'
language:
- iso: eng
month: '08'
oa: 1
oa_version: Published Version
page: 274 - 280
popular_science: '1'
publication: Mitteilungen der Vereinigung Österreichischer Bibliothekarinnen und Bibliothekare
publication_identifier:
issn:
- '10222588'
publication_status: published
publisher: VÖB
publist_id: '6843'
scopus_import: 1
status: public
title: Der Springer Compact-Deal – Ein erster Einblick in die Evaluierung einer Offsetting-Vereinbarung
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: journal_article
user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87
volume: 70
year: '2017'
...
---
_id: '8129'
abstract:
- lang: eng
text: "Cortical circuits exhibit intricate recurrent architectures that are remarkably
similar across different brain areas. Such stereotyped structure suggests the
existence of common computational principles. However, such principles have remained
largely elusive. Inspired by gated-memory networks, namely long short-term memory
networks (LSTMs), we introduce a recurrent neural network in which information
is gated through inhibitory cells that are subtractive (subLSTM). We propose a
natural mapping of subLSTMs onto known canonical excitatory-inhibitory cortical
microcircuits. Our empirical evaluation across sequential image classification
and language modelling tasks shows that subLSTM units can achieve similar performance
to LSTM units. These results suggest that cortical circuits can be optimised to
solve complex contextual problems and proposes a novel view on their computational
function.\r\nOverall our work provides a step towards unifying recurrent networks
as used in machine learning with their biological counterparts."
article_processing_charge: No
author:
- first_name: Rui Ponte
full_name: Costa, Rui Ponte
last_name: Costa
- first_name: Yannis M.
full_name: Assael, Yannis M.
last_name: Assael
- first_name: Brendan
full_name: Shillingford, Brendan
last_name: Shillingford
- first_name: Nando de
full_name: Freitas, Nando de
last_name: Freitas
- first_name: Tim P
full_name: Vogels, Tim P
id: CB6FF8D2-008F-11EA-8E08-2637E6697425
last_name: Vogels
orcid: 0000-0003-3295-6181
citation:
ama: 'Costa RP, Assael YM, Shillingford B, Freitas N de, Vogels TP. Cortical microcircuits
as gated-recurrent neural networks. In: Advances in Neural Information Processing
Systems. Vol 30. Neural Information Processing Systems Foundation; 2017:272-283.'
apa: 'Costa, R. P., Assael, Y. M., Shillingford, B., Freitas, N. de, & Vogels,
T. P. (2017). Cortical microcircuits as gated-recurrent neural networks. In Advances
in Neural Information Processing Systems (Vol. 30, pp. 272–283). Long Beach,
CA, United States: Neural Information Processing Systems Foundation.'
chicago: Costa, Rui Ponte, Yannis M. Assael, Brendan Shillingford, Nando de Freitas,
and Tim P Vogels. “Cortical Microcircuits as Gated-Recurrent Neural Networks.”
In Advances in Neural Information Processing Systems, 30:272–83. Neural
Information Processing Systems Foundation, 2017.
ieee: R. P. Costa, Y. M. Assael, B. Shillingford, N. de Freitas, and T. P. Vogels,
“Cortical microcircuits as gated-recurrent neural networks,” in Advances in
Neural Information Processing Systems, Long Beach, CA, United States, 2017,
vol. 30, pp. 272–283.
ista: 'Costa RP, Assael YM, Shillingford B, Freitas N de, Vogels TP. 2017. Cortical
microcircuits as gated-recurrent neural networks. Advances in Neural Information
Processing Systems. NIPS: Neural Information Processing System vol. 30, 272–283.'
mla: Costa, Rui Ponte, et al. “Cortical Microcircuits as Gated-Recurrent Neural
Networks.” Advances in Neural Information Processing Systems, vol. 30,
Neural Information Processing Systems Foundation, 2017, pp. 272–83.
short: R.P. Costa, Y.M. Assael, B. Shillingford, N. de Freitas, T.P. Vogels, in:,
Advances in Neural Information Processing Systems, Neural Information Processing
Systems Foundation, 2017, pp. 272–283.
conference:
end_date: 2017-12-09
location: Long Beach, CA, United States
name: 'NIPS: Neural Information Processing System'
start_date: 2017-12-04
date_created: 2020-07-16T19:13:10Z
date_published: 2017-12-01T00:00:00Z
date_updated: 2021-01-12T08:17:03Z
day: '01'
extern: '1'
external_id:
arxiv:
- '1711.02448'
intvolume: ' 30'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/1711.02448
month: '12'
oa: 1
oa_version: Preprint
page: 272-283
publication: Advances in Neural Information Processing Systems
publication_identifier:
issn:
- '10495258'
publication_status: published
publisher: Neural Information Processing Systems Foundation
quality_controlled: '1'
status: public
title: Cortical microcircuits as gated-recurrent neural networks
type: conference
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 30
year: '2017'
...
---
_id: '817'
abstract:
- lang: eng
text: Cryo-electron tomography (cryo-ET) allows cellular ultrastructures and macromolecular
complexes to be imaged in three-dimensions in their native environments. Cryo-electron
tomograms are reconstructed from projection images taken at defined tilt-angles.
In order to recover high-resolution information from cryo-electron tomograms,
it is necessary to measure and correct for the contrast transfer function (CTF)
of the microscope. Most commonly, this is performed using protocols that approximate
the sample as a two-dimensional (2D) plane. This approximation accounts for differences
in defocus and therefore CTF across the tilted sample. It does not account for
differences in defocus of objects at different heights within the sample; instead,
a 3D approach is required. Currently available approaches for 3D-CTF correction
are computationally expensive and have not been widely implemented. Here we simulate
the benefits of 3D-CTF correction for high-resolution subtomogram averaging, and
present a user-friendly, computationally-efficient 3D-CTF correction tool, NovaCTF,
that is compatible with standard tomogram reconstruction workflows in IMOD. We
validate the approach on synthetic data and test it using subtomogram averaging
of real data. Consistent with our simulations, we find that 3D-CTF correction
allows high-resolution structures to be obtained with much smaller subtomogram
averaging datasets than are required using 2D-CTF. We also show that using equivalent
dataset sizes, 3D-CTF correction can be used to obtain higher-resolution structures.
We present a 3.4. Å resolution structure determined by subtomogram averaging.
author:
- first_name: Beata
full_name: Turoňová, Beata
last_name: Turoňová
- first_name: Florian
full_name: Schur, Florian
id: 48AD8942-F248-11E8-B48F-1D18A9856A87
last_name: Schur
orcid: 0000-0003-4790-8078
- first_name: William
full_name: Wan, William
last_name: Wan
- first_name: John
full_name: Briggs, John
last_name: Briggs
citation:
ama: Turoňová B, Schur FK, Wan W, Briggs J. Efficient 3D-CTF correction for cryo-electron
tomography using NovaCTF improves subtomogram averaging resolution to 3.4Å. Journal
of Structural Biology. 2017;199(3):187-195. doi:10.1016/j.jsb.2017.07.007
apa: Turoňová, B., Schur, F. K., Wan, W., & Briggs, J. (2017). Efficient 3D-CTF
correction for cryo-electron tomography using NovaCTF improves subtomogram averaging
resolution to 3.4Å. Journal of Structural Biology. Academic Press. https://doi.org/10.1016/j.jsb.2017.07.007
chicago: Turoňová, Beata, Florian KM Schur, William Wan, and John Briggs. “Efficient
3D-CTF Correction for Cryo-Electron Tomography Using NovaCTF Improves Subtomogram
Averaging Resolution to 3.4Å.” Journal of Structural Biology. Academic
Press, 2017. https://doi.org/10.1016/j.jsb.2017.07.007.
ieee: B. Turoňová, F. K. Schur, W. Wan, and J. Briggs, “Efficient 3D-CTF correction
for cryo-electron tomography using NovaCTF improves subtomogram averaging resolution
to 3.4Å,” Journal of Structural Biology, vol. 199, no. 3. Academic Press,
pp. 187–195, 2017.
ista: Turoňová B, Schur FK, Wan W, Briggs J. 2017. Efficient 3D-CTF correction for
cryo-electron tomography using NovaCTF improves subtomogram averaging resolution
to 3.4Å. Journal of Structural Biology. 199(3), 187–195.
mla: Turoňová, Beata, et al. “Efficient 3D-CTF Correction for Cryo-Electron Tomography
Using NovaCTF Improves Subtomogram Averaging Resolution to 3.4Å.” Journal of
Structural Biology, vol. 199, no. 3, Academic Press, 2017, pp. 187–95, doi:10.1016/j.jsb.2017.07.007.
short: B. Turoňová, F.K. Schur, W. Wan, J. Briggs, Journal of Structural Biology
199 (2017) 187–195.
date_created: 2018-12-11T11:48:40Z
date_published: 2017-09-01T00:00:00Z
date_updated: 2021-01-12T08:17:16Z
day: '01'
ddc:
- '570'
doi: 10.1016/j.jsb.2017.07.007
extern: '1'
file:
- access_level: open_access
checksum: 7f2d4bbac767f9acc254d1a4114d181a
content_type: application/pdf
creator: kschuh
date_created: 2019-03-22T09:29:44Z
date_updated: 2020-07-14T12:48:09Z
file_id: '6168'
file_name: 2017_Elsevier_Turonova.pdf
file_size: 1310009
relation: main_file
file_date_updated: 2020-07-14T12:48:09Z
has_accepted_license: '1'
intvolume: ' 199'
issue: '3'
language:
- iso: eng
month: '09'
oa: 1
oa_version: Published Version
page: 187-195
publication: Journal of Structural Biology
publication_status: published
publisher: Academic Press
publist_id: '6832'
quality_controlled: '1'
status: public
title: Efficient 3D-CTF correction for cryo-electron tomography using NovaCTF improves
subtomogram averaging resolution to 3.4Å
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: 199
year: '2017'
...
---
_id: '8237'
abstract:
- lang: eng
text: Monoclonal antibodies find broad application as therapy for various types
of cancer by employing multiple mechanisms of action against tumors. Manipulating
the Fc-mediated functions of antibodies that engage immune effector cells, such
as NK cells, represents a strategy to influence effector cell activation and to
enhance antibody potency and potentially efficacy. We developed a novel approach
to generate and ascertain the functional attributes of Fc mutant monoclonal antibodies.
This entailed coupling single expression vector (pVitro1) antibody cloning, using
polymerase incomplete primer extension (PIPE) polymerase chain reaction, together
with simultaneous Fc region point mutagenesis and high yield transient expression
in human mammalian cells. Employing this, we engineered wild type, low (N297Q,
NQ), and high (S239D/I332E, DE) FcR-binding Fc mutant monoclonal antibody panels
recognizing two cancer antigens, HER2/neu and chondroitin sulfate proteoglycan
4. Antibodies were generated with universal mutagenic primers applicable to any
IgG1 pVitro1 constructs, with high mutagenesis and transfection efficiency, in
small culture volumes, at high yields and within 12 days from design to purified
material. Antibody variants conserved their Fab-mediated recognition of target
antigens and their direct anti-proliferative effects against cancer cells. Fc
mutations had a significant impact on antibody interactions with Fc receptors
(FcRs) on human NK cells, and consequently on the potency of NK cell activation,
quantified by immune complex-mediated calcium mobilization and by antibody-dependent
cellular cytotoxicity (ADCC) of tumor cells. This strategy for manipulation and
testing of Fc region engagement with cognate FcRs can facilitate the design of
antibodies with defined effector functions and potentially enhanced efficacy against
tumor cells.
article_number: '1112'
article_processing_charge: No
article_type: original
author:
- first_name: Kristina M.
full_name: Ilieva, Kristina M.
last_name: Ilieva
- first_name: Judit
full_name: Fazekas-Singer, Judit
id: 36432834-F248-11E8-B48F-1D18A9856A87
last_name: Fazekas-Singer
orcid: 0000-0002-8777-3502
- first_name: Daniela Y.
full_name: Achkova, Daniela Y.
last_name: Achkova
- first_name: Tihomir S.
full_name: Dodev, Tihomir S.
last_name: Dodev
- first_name: Silvia
full_name: Mele, Silvia
last_name: Mele
- first_name: Silvia
full_name: Crescioli, Silvia
last_name: Crescioli
- first_name: Heather J.
full_name: Bax, Heather J.
last_name: Bax
- first_name: Anthony
full_name: Cheung, Anthony
last_name: Cheung
- first_name: Panagiotis
full_name: Karagiannis, Panagiotis
last_name: Karagiannis
- first_name: Isabel
full_name: Correa, Isabel
last_name: Correa
- first_name: Mariangela
full_name: Figini, Mariangela
last_name: Figini
- first_name: Rebecca
full_name: Marlow, Rebecca
last_name: Marlow
- first_name: Debra H.
full_name: Josephs, Debra H.
last_name: Josephs
- first_name: Andrew J.
full_name: Beavil, Andrew J.
last_name: Beavil
- first_name: John
full_name: Maher, John
last_name: Maher
- first_name: James F.
full_name: Spicer, James F.
last_name: Spicer
- first_name: Erika
full_name: Jensen-Jarolim, Erika
last_name: Jensen-Jarolim
- first_name: Andrew N.
full_name: Tutt, Andrew N.
last_name: Tutt
- first_name: Sophia N.
full_name: Karagiannis, Sophia N.
last_name: Karagiannis
citation:
ama: Ilieva KM, Singer J, Achkova DY, et al. Functionally active Fc mutant antibodies
recognizing cancer antigens generated rapidly at high yields. Frontiers in
Immunology. 2017;8. doi:10.3389/fimmu.2017.01112
apa: Ilieva, K. M., Singer, J., Achkova, D. Y., Dodev, T. S., Mele, S., Crescioli,
S., … Karagiannis, S. N. (2017). Functionally active Fc mutant antibodies recognizing
cancer antigens generated rapidly at high yields. Frontiers in Immunology.
Frontiers. https://doi.org/10.3389/fimmu.2017.01112
chicago: Ilieva, Kristina M., Judit Singer, Daniela Y. Achkova, Tihomir S. Dodev,
Silvia Mele, Silvia Crescioli, Heather J. Bax, et al. “Functionally Active Fc
Mutant Antibodies Recognizing Cancer Antigens Generated Rapidly at High Yields.”
Frontiers in Immunology. Frontiers, 2017. https://doi.org/10.3389/fimmu.2017.01112.
ieee: K. M. Ilieva et al., “Functionally active Fc mutant antibodies recognizing
cancer antigens generated rapidly at high yields,” Frontiers in Immunology,
vol. 8. Frontiers, 2017.
ista: Ilieva KM, Singer J, Achkova DY, Dodev TS, Mele S, Crescioli S, Bax HJ, Cheung
A, Karagiannis P, Correa I, Figini M, Marlow R, Josephs DH, Beavil AJ, Maher J,
Spicer JF, Jensen-Jarolim E, Tutt AN, Karagiannis SN. 2017. Functionally active
Fc mutant antibodies recognizing cancer antigens generated rapidly at high yields.
Frontiers in Immunology. 8, 1112.
mla: Ilieva, Kristina M., et al. “Functionally Active Fc Mutant Antibodies Recognizing
Cancer Antigens Generated Rapidly at High Yields.” Frontiers in Immunology,
vol. 8, 1112, Frontiers, 2017, doi:10.3389/fimmu.2017.01112.
short: K.M. Ilieva, J. Singer, D.Y. Achkova, T.S. Dodev, S. Mele, S. Crescioli,
H.J. Bax, A. Cheung, P. Karagiannis, I. Correa, M. Figini, R. Marlow, D.H. Josephs,
A.J. Beavil, J. Maher, J.F. Spicer, E. Jensen-Jarolim, A.N. Tutt, S.N. Karagiannis,
Frontiers in Immunology 8 (2017).
date_created: 2020-08-10T11:53:32Z
date_published: 2017-09-11T00:00:00Z
date_updated: 2021-01-12T08:17:39Z
day: '11'
doi: 10.3389/fimmu.2017.01112
extern: '1'
intvolume: ' 8'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.3389/fimmu.2017.01112
month: '09'
oa: 1
oa_version: Published Version
publication: Frontiers in Immunology
publication_identifier:
issn:
- 1664-3224
publication_status: published
publisher: Frontiers
quality_controlled: '1'
status: public
title: Functionally active Fc mutant antibodies recognizing cancer antigens generated
rapidly at high yields
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 8
year: '2017'
...
---
_id: '8236'
abstract:
- lang: eng
text: Th2 immunity and allergic immune surveillance play critical roles in host
responses to pathogens, parasites and allergens. Numerous studies have reported
significant links between Th2 responses and cancer, including insights into the
functions of IgE antibodies and associated effector cells in both antitumour immune
surveillance and therapy. The interdisciplinary field of AllergoOncology was given
Task Force status by the European Academy of Allergy and Clinical Immunology in
2014. Affiliated expert groups focus on the interface between allergic responses
and cancer, applied to immune surveillance, immunomodulation and the functions
of IgE‐mediated immune responses against cancer, to derive novel insights into
more effective treatments. Coincident with rapid expansion in clinical application
of cancer immunotherapies, here we review the current state‐of‐the‐art and future
translational opportunities, as well as challenges in this relatively new field.
Recent developments include improved understanding of Th2 antibodies, intratumoral
innate allergy effector cells and mediators, IgE‐mediated tumour antigen cross‐presentation
by dendritic cells, as well as immunotherapeutic strategies such as vaccines and
recombinant antibodies, and finally, the management of allergy in daily clinical
oncology. Shedding light on the crosstalk between allergic response and cancer
is paving the way for new avenues of treatment.
article_processing_charge: No
article_type: original
author:
- first_name: E.
full_name: Jensen-Jarolim, E.
last_name: Jensen-Jarolim
orcid: 0000-0003-4019-5765
- first_name: H. J.
full_name: Bax, H. J.
last_name: Bax
- first_name: R.
full_name: Bianchini, R.
last_name: Bianchini
- first_name: M.
full_name: Capron, M.
last_name: Capron
- first_name: C.
full_name: Corrigan, C.
last_name: Corrigan
- first_name: M.
full_name: Castells, M.
last_name: Castells
- first_name: D.
full_name: Dombrowicz, D.
last_name: Dombrowicz
- first_name: T. R.
full_name: Daniels-Wells, T. R.
last_name: Daniels-Wells
- first_name: Judit
full_name: Fazekas, Judit
id: 36432834-F248-11E8-B48F-1D18A9856A87
last_name: Fazekas
orcid: 0000-0002-8777-3502
- first_name: E.
full_name: Fiebiger, E.
last_name: Fiebiger
- first_name: S.
full_name: Gatault, S.
last_name: Gatault
- first_name: H. J.
full_name: Gould, H. J.
last_name: Gould
- first_name: J.
full_name: Janda, J.
last_name: Janda
- first_name: D. H.
full_name: Josephs, D. H.
last_name: Josephs
- first_name: P.
full_name: Karagiannis, P.
last_name: Karagiannis
- first_name: F.
full_name: Levi-Schaffer, F.
last_name: Levi-Schaffer
- first_name: A.
full_name: Meshcheryakova, A.
last_name: Meshcheryakova
- first_name: D.
full_name: Mechtcheriakova, D.
last_name: Mechtcheriakova
- first_name: Y.
full_name: Mekori, Y.
last_name: Mekori
- first_name: F.
full_name: Mungenast, F.
last_name: Mungenast
- first_name: E. A.
full_name: Nigro, E. A.
last_name: Nigro
- first_name: M. L.
full_name: Penichet, M. L.
last_name: Penichet
- first_name: F.
full_name: Redegeld, F.
last_name: Redegeld
- first_name: L.
full_name: Saul, L.
last_name: Saul
- first_name: J.
full_name: Singer, J.
last_name: Singer
- first_name: J. F.
full_name: Spicer, J. F.
last_name: Spicer
- first_name: A. G.
full_name: Siccardi, A. G.
last_name: Siccardi
- first_name: E.
full_name: Spillner, E.
last_name: Spillner
- first_name: M. C.
full_name: Turner, M. C.
last_name: Turner
- first_name: E.
full_name: Untersmayr, E.
last_name: Untersmayr
- first_name: L.
full_name: Vangelista, L.
last_name: Vangelista
- first_name: S. N.
full_name: Karagiannis, S. N.
last_name: Karagiannis
citation:
ama: 'Jensen-Jarolim E, Bax HJ, Bianchini R, et al. AllergoOncology - the impact
of allergy in oncology: EAACI position paper. Allergy. 2017;72(6):866-887.
doi:10.1111/all.13119'
apa: 'Jensen-Jarolim, E., Bax, H. J., Bianchini, R., Capron, M., Corrigan, C., Castells,
M., … Karagiannis, S. N. (2017). AllergoOncology - the impact of allergy in oncology:
EAACI position paper. Allergy. Wiley. https://doi.org/10.1111/all.13119'
chicago: 'Jensen-Jarolim, E., H. J. Bax, R. Bianchini, M. Capron, C. Corrigan, M.
Castells, D. Dombrowicz, et al. “AllergoOncology - the Impact of Allergy in Oncology:
EAACI Position Paper.” Allergy. Wiley, 2017. https://doi.org/10.1111/all.13119.'
ieee: 'E. Jensen-Jarolim et al., “AllergoOncology - the impact of allergy
in oncology: EAACI position paper,” Allergy, vol. 72, no. 6. Wiley, pp.
866–887, 2017.'
ista: 'Jensen-Jarolim E, Bax HJ, Bianchini R, Capron M, Corrigan C, Castells M,
Dombrowicz D, Daniels-Wells TR, Singer J, Fiebiger E, Gatault S, Gould HJ, Janda
J, Josephs DH, Karagiannis P, Levi-Schaffer F, Meshcheryakova A, Mechtcheriakova
D, Mekori Y, Mungenast F, Nigro EA, Penichet ML, Redegeld F, Saul L, Singer J,
Spicer JF, Siccardi AG, Spillner E, Turner MC, Untersmayr E, Vangelista L, Karagiannis
SN. 2017. AllergoOncology - the impact of allergy in oncology: EAACI position
paper. Allergy. 72(6), 866–887.'
mla: 'Jensen-Jarolim, E., et al. “AllergoOncology - the Impact of Allergy in Oncology:
EAACI Position Paper.” Allergy, vol. 72, no. 6, Wiley, 2017, pp. 866–87,
doi:10.1111/all.13119.'
short: E. Jensen-Jarolim, H.J. Bax, R. Bianchini, M. Capron, C. Corrigan, M. Castells,
D. Dombrowicz, T.R. Daniels-Wells, J. Singer, E. Fiebiger, S. Gatault, H.J. Gould,
J. Janda, D.H. Josephs, P. Karagiannis, F. Levi-Schaffer, A. Meshcheryakova, D.
Mechtcheriakova, Y. Mekori, F. Mungenast, E.A. Nigro, M.L. Penichet, F. Redegeld,
L. Saul, J. Singer, J.F. Spicer, A.G. Siccardi, E. Spillner, M.C. Turner, E. Untersmayr,
L. Vangelista, S.N. Karagiannis, Allergy 72 (2017) 866–887.
date_created: 2020-08-10T11:53:26Z
date_published: 2017-06-01T00:00:00Z
date_updated: 2021-01-12T08:17:39Z
day: '01'
doi: 10.1111/all.13119
extern: '1'
intvolume: ' 72'
issue: '6'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.1111/all.13119
month: '06'
oa: 1
oa_version: Published Version
page: 866-887
publication: Allergy
publication_identifier:
issn:
- 0105-4538
publication_status: published
publisher: Wiley
quality_controlled: '1'
status: public
title: 'AllergoOncology - the impact of allergy in oncology: EAACI position paper'
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 72
year: '2017'
...
---
_id: '8239'
abstract:
- lang: eng
text: Acrolein, a highly reactive unsaturated aldehyde, is generated in large amounts
during smoking and is best known for its genotoxic capacity. Here, we aimed to
assess whether acrolein at concentrations relevant for smokers may also exert
immunomodulatory effects that could be relevant in allergy or cancer. In a BALB/c
allergy model repeated nasal exposure to acrolein abrogated allergen-specific
antibody and cytokine formation, and led to a relative accumulation of regulatory
T cells in the lungs. Only the acrolein-treated mice were protected from bronchial
hyperreactivity as well as from anaphylactic reactions upon challenge with the
specific allergen. Moreover, grafted D2F2 tumor cells grew faster and intratumoral
Foxp3+ cell accumulation was observed in these mice compared to sham-treated controls.
Results from reporter cell lines suggested that acrolein acts via the aryl-hydrocarbon
receptor which could be inhibited by resveratrol and 3′-methoxy-4′-nitroflavone
Acrolein- stimulation of human PBMCs increased Foxp3+ expression by T cells which
could be antagonized by resveratrol. Our mouse and human data thus revealed that
acrolein exerts systemic immunosuppression by promoting Foxp3+ regulatory cells.
This provides a novel explanation why smokers have a lower allergy, but higher
cancer risk.
article_number: '45067'
article_processing_charge: No
article_type: original
author:
- first_name: Franziska
full_name: Roth-Walter, Franziska
last_name: Roth-Walter
- first_name: Cornelia
full_name: Bergmayr, Cornelia
last_name: Bergmayr
- first_name: Sarah
full_name: Meitz, Sarah
last_name: Meitz
- first_name: Stefan
full_name: Buchleitner, Stefan
last_name: Buchleitner
- first_name: Caroline
full_name: Stremnitzer, Caroline
last_name: Stremnitzer
- first_name: Judit
full_name: Fazekas, Judit
id: 36432834-F248-11E8-B48F-1D18A9856A87
last_name: Fazekas
orcid: 0000-0002-8777-3502
- first_name: Anna
full_name: Moskovskich, Anna
last_name: Moskovskich
- first_name: Mario A.
full_name: Müller, Mario A.
last_name: Müller
- first_name: Georg A.
full_name: Roth, Georg A.
last_name: Roth
- first_name: Krisztina
full_name: Manzano-Szalai, Krisztina
last_name: Manzano-Szalai
- first_name: Zdenek
full_name: Dvorak, Zdenek
last_name: Dvorak
- first_name: Alina
full_name: Neunkirchner, Alina
last_name: Neunkirchner
- first_name: Erika
full_name: Jensen-Jarolim, Erika
last_name: Jensen-Jarolim
citation:
ama: 'Roth-Walter F, Bergmayr C, Meitz S, et al. Janus-faced Acrolein prevents allergy
but accelerates tumor growth by promoting immunoregulatory Foxp3+ cells: Mouse
model for passive respiratory exposure. Scientific Reports. 2017;7. doi:10.1038/srep45067'
apa: 'Roth-Walter, F., Bergmayr, C., Meitz, S., Buchleitner, S., Stremnitzer, C.,
Singer, J., … Jensen-Jarolim, E. (2017). Janus-faced Acrolein prevents allergy
but accelerates tumor growth by promoting immunoregulatory Foxp3+ cells: Mouse
model for passive respiratory exposure. Scientific Reports. Springer Nature.
https://doi.org/10.1038/srep45067'
chicago: 'Roth-Walter, Franziska, Cornelia Bergmayr, Sarah Meitz, Stefan Buchleitner,
Caroline Stremnitzer, Judit Singer, Anna Moskovskich, et al. “Janus-Faced Acrolein
Prevents Allergy but Accelerates Tumor Growth by Promoting Immunoregulatory Foxp3+
Cells: Mouse Model for Passive Respiratory Exposure.” Scientific Reports.
Springer Nature, 2017. https://doi.org/10.1038/srep45067.'
ieee: 'F. Roth-Walter et al., “Janus-faced Acrolein prevents allergy but
accelerates tumor growth by promoting immunoregulatory Foxp3+ cells: Mouse model
for passive respiratory exposure,” Scientific Reports, vol. 7. Springer
Nature, 2017.'
ista: 'Roth-Walter F, Bergmayr C, Meitz S, Buchleitner S, Stremnitzer C, Singer
J, Moskovskich A, Müller MA, Roth GA, Manzano-Szalai K, Dvorak Z, Neunkirchner
A, Jensen-Jarolim E. 2017. Janus-faced Acrolein prevents allergy but accelerates
tumor growth by promoting immunoregulatory Foxp3+ cells: Mouse model for passive
respiratory exposure. Scientific Reports. 7, 45067.'
mla: 'Roth-Walter, Franziska, et al. “Janus-Faced Acrolein Prevents Allergy but
Accelerates Tumor Growth by Promoting Immunoregulatory Foxp3+ Cells: Mouse Model
for Passive Respiratory Exposure.” Scientific Reports, vol. 7, 45067, Springer
Nature, 2017, doi:10.1038/srep45067.'
short: F. Roth-Walter, C. Bergmayr, S. Meitz, S. Buchleitner, C. Stremnitzer, J.
Singer, A. Moskovskich, M.A. Müller, G.A. Roth, K. Manzano-Szalai, Z. Dvorak,
A. Neunkirchner, E. Jensen-Jarolim, Scientific Reports 7 (2017).
date_created: 2020-08-10T11:53:46Z
date_published: 2017-03-23T00:00:00Z
date_updated: 2021-01-12T08:17:40Z
day: '23'
doi: 10.1038/srep45067
extern: '1'
intvolume: ' 7'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.1038/srep45067
month: '03'
oa: 1
oa_version: Published Version
publication: Scientific Reports
publication_identifier:
issn:
- 2045-2322
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
status: public
title: 'Janus-faced Acrolein prevents allergy but accelerates tumor growth by promoting
immunoregulatory Foxp3+ cells: Mouse model for passive respiratory exposure'
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 7
year: '2017'
...
---
_id: '8240'
abstract:
- lang: eng
text: "Background/Aim: Cancer cell lines are indispensible surrogate models in cancer
research, as they can be used off-the-shelf, expanded to the desired extent, easily
modified and exchanged between research groups for affirmation, reproduction or
follow-up experiments.\r\nAs malignant cells are prone to genomic instability,
phenotypical changes may occur after certain passages in culture. Thus, cell lines
have to be regularly authenticated to ensure data quality. In between experiments
these cell lines are often stored in liquid nitrogen for extended time periods.\r\nAlthough
freezing of cells is a necessary evil, little research is performed on how long-term
storage affects cancer cell lines. Therefore, this study investigated the effects
of a 28-year long liquid nitrogen storage period on BT474 cells with regard to
phenotypical changes, differences in cell-surface receptor expression as well
as cytokine and gene expressional variations.\r\nMethods: Two batches of BT474
cells, one frozen in 1986, the other directly purchased from ATCC were investigated
by light microscopy, cell growth analysis, flow cytometry and cytokine as well
as whole-transcriptome expression profiling.\r\nResults: The cell lines were morphologically
indifferent and showed similar growth rates and similar cell-surface receptor
expression. Transcriptome analysis revealed significant differences in only 26
of 40,716 investigated RefSeq transcripts with 4 of them being up-regulated and
22 down-regulated.\r\nConclusion: This study demonstrates that even after very
long periods of storage in liquid nitrogen, cancer cell lines display only minimal
changes in their gene expression profiles. However, also such minor changes should
be carefully assessed before continuation of experiments, especially if phenotypic
alterations can be additionally observed."
article_processing_charge: No
article_type: original
author:
- first_name: Judit
full_name: Fazekas, Judit
id: 36432834-F248-11E8-B48F-1D18A9856A87
last_name: Fazekas
orcid: 0000-0002-8777-3502
- first_name: Thomas W.
full_name: Grunt, Thomas W.
last_name: Grunt
- first_name: Erika
full_name: Jensen-Jarolim, Erika
last_name: Jensen-Jarolim
- first_name: Josef
full_name: Singer, Josef
last_name: Singer
citation:
ama: Singer J, Grunt TW, Jensen-Jarolim E, Singer J. Long term storage in liquid
nitrogen leads to only minor phenotypic and gene expression changes in the mammary
carcinoma model cell line BT474. Oncotarget. 2017;8:35076-35087. doi:10.18632/oncotarget.16623
apa: Singer, J., Grunt, T. W., Jensen-Jarolim, E., & Singer, J. (2017). Long
term storage in liquid nitrogen leads to only minor phenotypic and gene expression
changes in the mammary carcinoma model cell line BT474. Oncotarget. Impact
Journals. https://doi.org/10.18632/oncotarget.16623
chicago: Singer, Judit, Thomas W. Grunt, Erika Jensen-Jarolim, and Josef Singer.
“Long Term Storage in Liquid Nitrogen Leads to Only Minor Phenotypic and Gene
Expression Changes in the Mammary Carcinoma Model Cell Line BT474.” Oncotarget.
Impact Journals, 2017. https://doi.org/10.18632/oncotarget.16623.
ieee: J. Singer, T. W. Grunt, E. Jensen-Jarolim, and J. Singer, “Long term storage
in liquid nitrogen leads to only minor phenotypic and gene expression changes
in the mammary carcinoma model cell line BT474,” Oncotarget, vol. 8. Impact
Journals, pp. 35076–35087, 2017.
ista: Singer J, Grunt TW, Jensen-Jarolim E, Singer J. 2017. Long term storage in
liquid nitrogen leads to only minor phenotypic and gene expression changes in
the mammary carcinoma model cell line BT474. Oncotarget. 8, 35076–35087.
mla: Singer, Judit, et al. “Long Term Storage in Liquid Nitrogen Leads to Only Minor
Phenotypic and Gene Expression Changes in the Mammary Carcinoma Model Cell Line
BT474.” Oncotarget, vol. 8, Impact Journals, 2017, pp. 35076–87, doi:10.18632/oncotarget.16623.
short: J. Singer, T.W. Grunt, E. Jensen-Jarolim, J. Singer, Oncotarget 8 (2017)
35076–35087.
date_created: 2020-08-10T11:53:53Z
date_published: 2017-03-28T00:00:00Z
date_updated: 2021-01-12T08:17:41Z
day: '28'
doi: 10.18632/oncotarget.16623
extern: '1'
intvolume: ' 8'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.18632/oncotarget.16623
month: '03'
oa: 1
oa_version: Published Version
page: 35076-35087
publication: Oncotarget
publication_identifier:
issn:
- 1949-2553
publication_status: published
publisher: Impact Journals
quality_controlled: '1'
status: public
title: Long term storage in liquid nitrogen leads to only minor phenotypic and gene
expression changes in the mammary carcinoma model cell line BT474
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 8
year: '2017'
...
---
_id: '8235'
abstract:
- lang: eng
text: Due to large homology of human and canine EGFR, dogs suffering from spontaneous
EGFR+ cancer can be considered as ideal translational models. Thereby, novel immunotherapeutic
compounds can be developed for both human and veterinary patients. This study
describes the radiolabeling of a canine anti-EGFR IgG antibody (can225IgG) with
potential diagnostic and therapeutic value in comparative clinical settings. Can225IgG
was functionalized with DTPA for subsequent chelation with the radionuclide 99mTc.
Successful coupling of 10 DTPA molecules per antibody on average was proven by
significant mass increase in MALDI-TOF spectroscopy, gel electrophoresis and immunoblots.
Following functionalization and radiolabeling, 99mTc-DTPA-can225IgG fully retained
its binding capacity towards human and canine EGFR in flow cytometry, immuno-
and radioblots, and autoradiography. The affinity of radiolabeled can225IgG was
determined to KD 0.8 ±0.0031 nM in a real-time kinetics assay on canine carcinoma
cells by a competition binding technique. Stability tests of the radiolabeled
compound identified TRIS buffered saline as the ideal formulation for short-term
storage with 87.11 ±6.04% intact compound being still detected 60 minutes post
radiolabeling. High stability, specificity and EGFR binding affinity pinpoint
towards 99mTc-radiolabeled can225IgG antibody as an ideal lead compound for the
first proof-of-concept diagnostic and therapeutic applications in canine cancer
patients.
article_processing_charge: No
article_type: original
author:
- first_name: Judit
full_name: Fazekas-Singer, Judit
id: 36432834-F248-11E8-B48F-1D18A9856A87
last_name: Fazekas-Singer
orcid: 0000-0002-8777-3502
- first_name: Neydher
full_name: Berroterán-Infante, Neydher
last_name: Berroterán-Infante
- first_name: Christina
full_name: Rami-Mark, Christina
last_name: Rami-Mark
- first_name: Monika
full_name: Dumanic, Monika
last_name: Dumanic
- first_name: Miroslawa
full_name: Matz, Miroslawa
last_name: Matz
- first_name: Michael
full_name: Willmann, Michael
last_name: Willmann
- first_name: Fritz
full_name: Andreae, Fritz
last_name: Andreae
- first_name: Josef
full_name: Singer, Josef
last_name: Singer
- first_name: Wolfgang
full_name: Wadsak, Wolfgang
last_name: Wadsak
- first_name: Markus
full_name: Mitterhauser, Markus
last_name: Mitterhauser
- first_name: Erika
full_name: Jensen-Jarolim, Erika
last_name: Jensen-Jarolim
citation:
ama: Singer J, Berroterán-Infante N, Rami-Mark C, et al. Development of a radiolabeled
caninized anti-EGFR antibody for comparative oncology trials. Oncotarget.
2017;8:83128-83141. doi:10.18632/oncotarget.20914
apa: Singer, J., Berroterán-Infante, N., Rami-Mark, C., Dumanic, M., Matz, M., Willmann,
M., … Jensen-Jarolim, E. (2017). Development of a radiolabeled caninized anti-EGFR
antibody for comparative oncology trials. Oncotarget. Impact Journals.
https://doi.org/10.18632/oncotarget.20914
chicago: Singer, Judit, Neydher Berroterán-Infante, Christina Rami-Mark, Monika
Dumanic, Miroslawa Matz, Michael Willmann, Fritz Andreae, et al. “Development
of a Radiolabeled Caninized Anti-EGFR Antibody for Comparative Oncology Trials.”
Oncotarget. Impact Journals, 2017. https://doi.org/10.18632/oncotarget.20914.
ieee: J. Singer et al., “Development of a radiolabeled caninized anti-EGFR
antibody for comparative oncology trials,” Oncotarget, vol. 8. Impact Journals,
pp. 83128–83141, 2017.
ista: Singer J, Berroterán-Infante N, Rami-Mark C, Dumanic M, Matz M, Willmann M,
Andreae F, Singer J, Wadsak W, Mitterhauser M, Jensen-Jarolim E. 2017. Development
of a radiolabeled caninized anti-EGFR antibody for comparative oncology trials.
Oncotarget. 8, 83128–83141.
mla: Singer, Judit, et al. “Development of a Radiolabeled Caninized Anti-EGFR Antibody
for Comparative Oncology Trials.” Oncotarget, vol. 8, Impact Journals,
2017, pp. 83128–41, doi:10.18632/oncotarget.20914.
short: J. Singer, N. Berroterán-Infante, C. Rami-Mark, M. Dumanic, M. Matz, M. Willmann,
F. Andreae, J. Singer, W. Wadsak, M. Mitterhauser, E. Jensen-Jarolim, Oncotarget
8 (2017) 83128–83141.
date_created: 2020-08-10T11:53:18Z
date_published: 2017-09-15T00:00:00Z
date_updated: 2021-01-12T08:17:39Z
day: '15'
doi: 10.18632/oncotarget.20914
extern: '1'
intvolume: ' 8'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.18632/oncotarget.20914
month: '09'
oa: 1
oa_version: Published Version
page: 83128-83141
publication: Oncotarget
publication_identifier:
issn:
- 1949-2553
publication_status: published
publisher: Impact Journals
quality_controlled: '1'
status: public
title: Development of a radiolabeled caninized anti-EGFR antibody for comparative
oncology trials
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 8
year: '2017'
...
---
_id: '825'
abstract:
- lang: eng
text: What data is needed about data? Describing the process to answer this question
for the institutional data repository IST DataRep.
author:
- first_name: Barbara
full_name: Petritsch, Barbara
id: 406048EC-F248-11E8-B48F-1D18A9856A87
last_name: Petritsch
orcid: 0000-0003-2724-4614
citation:
ama: Petritsch B. Metadata for research data in practice. Mitteilungen der Vereinigung
Österreichischer Bibliothekarinnen & Bibliothekare. 2017;70(2):200-207.
doi:10.31263/voebm.v70i2.1678
apa: Petritsch, B. (2017). Metadata for research data in practice. Mitteilungen
Der Vereinigung Österreichischer Bibliothekarinnen & Bibliothekare. VÖB.
https://doi.org/10.31263/voebm.v70i2.1678
chicago: Petritsch, Barbara. “Metadata for Research Data in Practice.” Mitteilungen
Der Vereinigung Österreichischer Bibliothekarinnen & Bibliothekare. VÖB,
2017. https://doi.org/10.31263/voebm.v70i2.1678.
ieee: B. Petritsch, “Metadata for research data in practice,” Mitteilungen der
Vereinigung Österreichischer Bibliothekarinnen & Bibliothekare, vol. 70,
no. 2. VÖB, pp. 200–207, 2017.
ista: Petritsch B. 2017. Metadata for research data in practice. Mitteilungen der
Vereinigung Österreichischer Bibliothekarinnen & Bibliothekare. 70(2), 200–207.
mla: Petritsch, Barbara. “Metadata for Research Data in Practice.” Mitteilungen
Der Vereinigung Österreichischer Bibliothekarinnen & Bibliothekare, vol.
70, no. 2, VÖB, 2017, pp. 200–07, doi:10.31263/voebm.v70i2.1678.
short: B. Petritsch, Mitteilungen Der Vereinigung Österreichischer Bibliothekarinnen
& Bibliothekare 70 (2017) 200–207.
date_created: 2018-12-11T11:48:42Z
date_published: 2017-08-01T00:00:00Z
date_updated: 2021-01-12T08:17:44Z
day: '01'
ddc:
- '020'
department:
- _id: E-Lib
doi: 10.31263/voebm.v70i2.1678
file:
- access_level: open_access
checksum: 7c4544d07efa2c2add8612b489abb4e2
content_type: application/pdf
creator: dernst
date_created: 2019-01-18T13:32:17Z
date_updated: 2020-07-14T12:48:11Z
file_id: '5850'
file_name: 2017_VOEB_Petritsch.pdf
file_size: 7843975
relation: main_file
file_date_updated: 2020-07-14T12:48:11Z
has_accepted_license: '1'
intvolume: ' 70'
issue: '2'
language:
- iso: eng
month: '08'
oa: 1
oa_version: Published Version
page: 200 - 207
publication: Mitteilungen der Vereinigung Österreichischer Bibliothekarinnen & Bibliothekare
publication_identifier:
issn:
- '10222588'
publication_status: published
publisher: VÖB
publist_id: '6823'
scopus_import: 1
status: public
title: Metadata for research data in practice
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 70
year: '2017'
...
---
_id: '8299'
abstract:
- lang: eng
text: 'Permissionless blockchain-based cryptocurrencies commonly use proof-of-work
(PoW) or proof-of-stake (PoS) to ensure their security, e.g. to prevent double
spending attacks. However, both approaches have disadvantages: PoW leads to massive
amounts of wasted electricity and re-centralization, whereas major stakeholders
in PoS might be able to create a monopoly. In this work, we propose proof-of-personhood
(PoP), a mechanism that binds physical entities to virtual identities in a way
that enables accountability while preserving anonymity. Afterwards we introduce
PoPCoin, a new cryptocurrency, whose consensus mechanism leverages PoP to eliminate
the dis-advantages of PoW and PoS while ensuring security. PoPCoin leads to a
continuously fair and democratic wealth creation process which paves the way for
an experimental basic income infrastructure.'
article_number: '7966966'
article_processing_charge: No
author:
- first_name: Maria
full_name: Borge, Maria
last_name: Borge
- first_name: Eleftherios
full_name: Kokoris Kogias, Eleftherios
id: f5983044-d7ef-11ea-ac6d-fd1430a26d30
last_name: Kokoris Kogias
- first_name: Philipp
full_name: Jovanovic, Philipp
last_name: Jovanovic
- first_name: Linus
full_name: Gasser, Linus
last_name: Gasser
- first_name: Nicolas
full_name: Gailly, Nicolas
last_name: Gailly
- first_name: Bryan
full_name: Ford, Bryan
last_name: Ford
citation:
ama: 'Borge M, Kokoris Kogias E, Jovanovic P, Gasser L, Gailly N, Ford B. Proof-of-personhood:
Redemocratizing permissionless cryptocurrencies. In: 2017 IEEE European Symposium
on Security and Privacy Workshops. IEEE; 2017. doi:10.1109/eurospw.2017.46'
apa: 'Borge, M., Kokoris Kogias, E., Jovanovic, P., Gasser, L., Gailly, N., &
Ford, B. (2017). Proof-of-personhood: Redemocratizing permissionless cryptocurrencies.
In 2017 IEEE European Symposium on Security and Privacy Workshops. Paris,
France: IEEE. https://doi.org/10.1109/eurospw.2017.46'
chicago: 'Borge, Maria, Eleftherios Kokoris Kogias, Philipp Jovanovic, Linus Gasser,
Nicolas Gailly, and Bryan Ford. “Proof-of-Personhood: Redemocratizing Permissionless
Cryptocurrencies.” In 2017 IEEE European Symposium on Security and Privacy
Workshops. IEEE, 2017. https://doi.org/10.1109/eurospw.2017.46.'
ieee: 'M. Borge, E. Kokoris Kogias, P. Jovanovic, L. Gasser, N. Gailly, and B. Ford,
“Proof-of-personhood: Redemocratizing permissionless cryptocurrencies,” in 2017
IEEE European Symposium on Security and Privacy Workshops, Paris, France,
2017.'
ista: 'Borge M, Kokoris Kogias E, Jovanovic P, Gasser L, Gailly N, Ford B. 2017.
Proof-of-personhood: Redemocratizing permissionless cryptocurrencies. 2017 IEEE
European Symposium on Security and Privacy Workshops. EuroS&PW: European Symposium
on Security and Privacy Workshops, 7966966.'
mla: 'Borge, Maria, et al. “Proof-of-Personhood: Redemocratizing Permissionless
Cryptocurrencies.” 2017 IEEE European Symposium on Security and Privacy Workshops,
7966966, IEEE, 2017, doi:10.1109/eurospw.2017.46.'
short: M. Borge, E. Kokoris Kogias, P. Jovanovic, L. Gasser, N. Gailly, B. Ford,
in:, 2017 IEEE European Symposium on Security and Privacy Workshops, IEEE, 2017.
conference:
end_date: 2017-04-28
location: Paris, France
name: 'EuroS&PW: European Symposium on Security and Privacy Workshops'
start_date: 2017-04-26
date_created: 2020-08-26T11:48:11Z
date_published: 2017-06-30T00:00:00Z
date_updated: 2021-01-12T08:17:57Z
day: '30'
doi: 10.1109/eurospw.2017.46
extern: '1'
language:
- iso: eng
month: '06'
oa_version: None
publication: 2017 IEEE European Symposium on Security and Privacy Workshops
publication_identifier:
eisbn:
- '9781538622445'
publication_status: published
publisher: IEEE
quality_controlled: '1'
status: public
title: 'Proof-of-personhood: Redemocratizing permissionless cryptocurrencies'
type: conference
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
year: '2017'
...
---
_id: '8306'
abstract:
- lang: eng
text: Bias-resistant public randomness is a critical component in many (distributed)
protocols. Generating public randomness is hard, however, because active adversaries
may behave dishonestly to bias public random choices toward their advantage. Existing
solutions do not scale to hundreds or thousands of participants, as is needed
in many decentralized systems. We propose two large-scale distributed protocols,
RandHound and RandHerd, which provide publicly-verifiable, unpredictable, and
unbiasable randomness against Byzantine adversaries. RandHound relies on an untrusted
client to divide a set of randomness servers into groups for scalability, and
it depends on the pigeonhole principle to ensure output integrity, even for non-random,
adversarial group choices. RandHerd implements an efficient, decentralized randomness
beacon. RandHerd is structurally similar to a BFT protocol, but uses RandHound
in a one-time setup to arrange participants into verifiably unbiased random secret-sharing
groups, which then repeatedly produce random output at predefined intervals. Our
prototype demonstrates that RandHound and RandHerd achieve good performance across
hundreds of participants while retaining a low failure probability by properly
selecting protocol parameters, such as a group size and secret-sharing threshold.
For example, when sharding 512 nodes into groups of 32, our experiments show that
RandHound can produce fresh random output after 240 seconds. RandHerd, after a
setup phase of 260 seconds, is able to generate fresh random output in intervals
of approximately 6 seconds. For this configuration, both protocols operate at
a failure probability of at most 0.08% against a Byzantine adversary.
article_processing_charge: No
author:
- first_name: E.
full_name: Syta, E.
last_name: Syta
- first_name: P.
full_name: Jovanovic, P.
last_name: Jovanovic
- first_name: Eleftherios
full_name: Kokoris Kogias, Eleftherios
id: f5983044-d7ef-11ea-ac6d-fd1430a26d30
last_name: Kokoris Kogias
- first_name: N.
full_name: Gailly, N.
last_name: Gailly
- first_name: L.
full_name: Gasser, L.
last_name: Gasser
- first_name: I.
full_name: Khoffi, I.
last_name: Khoffi
- first_name: M. J.
full_name: Fischer, M. J.
last_name: Fischer
- first_name: B.
full_name: Ford, B.
last_name: Ford
citation:
ama: 'Syta E, Jovanovic P, Kokoris Kogias E, et al. Scalable bias-resistant distributed
randomness. In: 2017 IEEE Symposium on Security and Privacy. IEEE; 2017:444-460.
doi:10.1109/SP.2017.45'
apa: 'Syta, E., Jovanovic, P., Kokoris Kogias, E., Gailly, N., Gasser, L., Khoffi,
I., … Ford, B. (2017). Scalable bias-resistant distributed randomness. In 2017
IEEE Symposium on Security and Privacy (pp. 444–460). San Jose, CA, United
States: IEEE. https://doi.org/10.1109/SP.2017.45'
chicago: Syta, E., P. Jovanovic, Eleftherios Kokoris Kogias, N. Gailly, L. Gasser,
I. Khoffi, M. J. Fischer, and B. Ford. “Scalable Bias-Resistant Distributed Randomness.”
In 2017 IEEE Symposium on Security and Privacy, 444–60. IEEE, 2017. https://doi.org/10.1109/SP.2017.45.
ieee: E. Syta et al., “Scalable bias-resistant distributed randomness,” in
2017 IEEE Symposium on Security and Privacy, San Jose, CA, United States,
2017, pp. 444–460.
ista: 'Syta E, Jovanovic P, Kokoris Kogias E, Gailly N, Gasser L, Khoffi I, Fischer
MJ, Ford B. 2017. Scalable bias-resistant distributed randomness. 2017 IEEE Symposium
on Security and Privacy. SP: Symposium on Security and Privacy, 444–460.'
mla: Syta, E., et al. “Scalable Bias-Resistant Distributed Randomness.” 2017
IEEE Symposium on Security and Privacy, IEEE, 2017, pp. 444–60, doi:10.1109/SP.2017.45.
short: E. Syta, P. Jovanovic, E. Kokoris Kogias, N. Gailly, L. Gasser, I. Khoffi,
M.J. Fischer, B. Ford, in:, 2017 IEEE Symposium on Security and Privacy, IEEE,
2017, pp. 444–460.
conference:
end_date: 2017-05-26
location: San Jose, CA, United States
name: 'SP: Symposium on Security and Privacy'
start_date: 2017-05-22
date_created: 2020-08-26T12:26:08Z
date_published: 2017-06-01T00:00:00Z
date_updated: 2021-01-12T08:18:02Z
day: '01'
doi: 10.1109/SP.2017.45
extern: '1'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://eprint.iacr.org/2016/1067
month: '06'
oa: 1
oa_version: Preprint
page: 444-460
publication: 2017 IEEE Symposium on Security and Privacy
publication_identifier:
isbn:
- '9781509055340'
issn:
- 2375-1207
publication_status: published
publisher: IEEE
quality_controlled: '1'
status: public
title: Scalable bias-resistant distributed randomness
type: conference
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
year: '2017'
...
---
_id: '8301'
abstract:
- lang: eng
text: Software-update mechanisms are critical to the security of modern systems,
but their typically centralized design presents a lucrative and frequently attacked
target. In this work, we propose CHAINIAC, a decentralized software-update framework
that eliminates single points of failure, enforces transparency, and provides
efficient verifiability of integrity and authenticity for software-release processes.
Independent witness servers collectively verify conformance of software updates
to release policies, build verifiers validate the source-to-binary correspondence,
and a tamper-proof release log stores collectively signed updates, thus ensuring
that no release is accepted by clients before being widely disclosed and validated.
The release log embodies a skipchain, a novel data structure, enabling arbitrarily
out-of-date clients to efficiently validate updates and signing keys. Evaluation
of our CHAINIAC prototype on reproducible Debian packages shows that the automated
update process takes the average of 5 minutes per release for individual packages,
and only 20 seconds for the aggregate timeline. We further evaluate the framework
using real-world data from the PyPI package repository and show that it offers
clients security comparable to verifying every single update themselves while
consuming only one-fifth of the bandwidth and having a minimal computational overhead.
article_processing_charge: No
author:
- first_name: Kirill
full_name: Nikitin, Kirill
last_name: Nikitin
- first_name: Eleftherios
full_name: Kokoris Kogias, Eleftherios
id: f5983044-d7ef-11ea-ac6d-fd1430a26d30
last_name: Kokoris Kogias
- first_name: Philipp
full_name: Jovanovic, Philipp
last_name: Jovanovic
- first_name: Linus
full_name: Gasser, Linus
last_name: Gasser
- first_name: Nicolas
full_name: Gailly, Nicolas
last_name: Gailly
- first_name: Ismail
full_name: Khoffi, Ismail
last_name: Khoffi
- first_name: Justin
full_name: Cappos, Justin
last_name: Cappos
- first_name: Bryan
full_name: Ford, Bryan
last_name: Ford
citation:
ama: 'Nikitin K, Kokoris Kogias E, Jovanovic P, et al. CHAINIAC: Proactive software-update
transparency via collectively signed skipchains and verified builds. In: Proceedings
of the 26th USENIX Conference on Security Symposium. USENIX Association; 2017:1271–1287.'
apa: 'Nikitin, K., Kokoris Kogias, E., Jovanovic, P., Gasser, L., Gailly, N., Khoffi,
I., … Ford, B. (2017). CHAINIAC: Proactive software-update transparency via collectively
signed skipchains and verified builds. In Proceedings of the 26th USENIX Conference
on Security Symposium (pp. 1271–1287). Vancouver, Canada: USENIX Association.'
chicago: 'Nikitin, Kirill, Eleftherios Kokoris Kogias, Philipp Jovanovic, Linus
Gasser, Nicolas Gailly, Ismail Khoffi, Justin Cappos, and Bryan Ford. “CHAINIAC:
Proactive Software-Update Transparency via Collectively Signed Skipchains and
Verified Builds.” In Proceedings of the 26th USENIX Conference on Security
Symposium, 1271–1287. USENIX Association, 2017.'
ieee: 'K. Nikitin et al., “CHAINIAC: Proactive software-update transparency
via collectively signed skipchains and verified builds,” in Proceedings of
the 26th USENIX Conference on Security Symposium, Vancouver, Canada, 2017,
pp. 1271–1287.'
ista: 'Nikitin K, Kokoris Kogias E, Jovanovic P, Gasser L, Gailly N, Khoffi I, Cappos
J, Ford B. 2017. CHAINIAC: Proactive software-update transparency via collectively
signed skipchains and verified builds. Proceedings of the 26th USENIX Conference
on Security Symposium. SEC: Security Symposium, 1271–1287.'
mla: 'Nikitin, Kirill, et al. “CHAINIAC: Proactive Software-Update Transparency
via Collectively Signed Skipchains and Verified Builds.” Proceedings of the
26th USENIX Conference on Security Symposium, USENIX Association, 2017, pp.
1271–1287.'
short: K. Nikitin, E. Kokoris Kogias, P. Jovanovic, L. Gasser, N. Gailly, I. Khoffi,
J. Cappos, B. Ford, in:, Proceedings of the 26th USENIX Conference on Security
Symposium, USENIX Association, 2017, pp. 1271–1287.
conference:
end_date: 2017-08-18
location: Vancouver, Canada
name: 'SEC: Security Symposium'
start_date: 2017-08-16
date_created: 2020-08-26T12:04:44Z
date_published: 2017-09-01T00:00:00Z
date_updated: 2021-01-12T08:18:00Z
day: '01'
extern: '1'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://www.usenix.org/system/files/conference/usenixsecurity17/sec17-nikitin.pdf
month: '09'
oa: 1
oa_version: Published Version
page: 1271–1287
publication: Proceedings of the 26th USENIX Conference on Security Symposium
publication_identifier:
isbn:
- '9781931971409'
publication_status: published
publisher: USENIX Association
quality_controlled: '1'
status: public
title: 'CHAINIAC: Proactive software-update transparency via collectively signed skipchains
and verified builds'
type: conference
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
year: '2017'
...
---
_id: '8446'
abstract:
- lang: eng
text: Solid‐state NMR spectroscopy can provide insight into protein structure and
dynamics at the atomic level without inherent protein size limitations. However,
a major hurdle to studying large proteins by solid‐state NMR spectroscopy is related
to spectral complexity and resonance overlap, which increase with molecular weight
and severely hamper the assignment process. Here the use of two sets of experiments
is shown to expand the tool kit of 1H‐detected assignment approaches, which correlate
a given amide pair either to the two adjacent CO–CA pairs (4D hCOCANH/hCOCAcoNH),
or to the amide 1H of the neighboring residue (3D HcocaNH/HcacoNH, which can be
extended to 5D). The experiments are based on efficient coherence transfers between
backbone atoms using INEPT transfers between carbons and cross‐polarization for
heteronuclear transfers. The utility of these experiments is exemplified with
application to assemblies of deuterated, fully amide‐protonated proteins from
approximately 20 to 60 kDa monomer, at magic‐angle spinning (MAS) frequencies
from approximately 40 to 55 kHz. These experiments will also be applicable to
protonated proteins at higher MAS frequencies. The resonance assignment of a domain
within the 50.4 kDa bacteriophage T5 tube protein pb6 is reported, and this is
compared to NMR assignments of the isolated domain in solution. This comparison
reveals contacts of this domain to the core of the polymeric tail tube assembly.
article_processing_charge: No
article_type: original
author:
- first_name: Hugo
full_name: Fraga, Hugo
last_name: Fraga
- first_name: Charles‐Adrien
full_name: Arnaud, Charles‐Adrien
last_name: Arnaud
- first_name: Diego F.
full_name: Gauto, Diego F.
last_name: Gauto
- first_name: Maxime
full_name: Audin, Maxime
last_name: Audin
- first_name: Vilius
full_name: Kurauskas, Vilius
last_name: Kurauskas
- first_name: Pavel
full_name: Macek, Pavel
last_name: Macek
- first_name: Carsten
full_name: Krichel, Carsten
last_name: Krichel
- first_name: Jia‐Ying
full_name: Guan, Jia‐Ying
last_name: Guan
- first_name: Jerome
full_name: Boisbouvier, Jerome
last_name: Boisbouvier
- first_name: Remco
full_name: Sprangers, Remco
last_name: Sprangers
- first_name: Cécile
full_name: Breyton, Cécile
last_name: Breyton
- first_name: Paul
full_name: Schanda, Paul
id: 7B541462-FAF6-11E9-A490-E8DFE5697425
last_name: Schanda
orcid: 0000-0002-9350-7606
citation:
ama: Fraga H, Arnaud C, Gauto DF, et al. Solid‐state NMR H–N–(C)–H and H–N–C–C 3D/4D
correlation experiments for resonance assignment of large proteins. ChemPhysChem.
2017;18(19):2697-2703. doi:10.1002/cphc.201700572
apa: Fraga, H., Arnaud, C., Gauto, D. F., Audin, M., Kurauskas, V., Macek, P., …
Schanda, P. (2017). Solid‐state NMR H–N–(C)–H and H–N–C–C 3D/4D correlation experiments
for resonance assignment of large proteins. ChemPhysChem. Wiley. https://doi.org/10.1002/cphc.201700572
chicago: Fraga, Hugo, Charles‐Adrien Arnaud, Diego F. Gauto, Maxime Audin, Vilius
Kurauskas, Pavel Macek, Carsten Krichel, et al. “Solid‐state NMR H–N–(C)–H and
H–N–C–C 3D/4D Correlation Experiments for Resonance Assignment of Large Proteins.”
ChemPhysChem. Wiley, 2017. https://doi.org/10.1002/cphc.201700572.
ieee: H. Fraga et al., “Solid‐state NMR H–N–(C)–H and H–N–C–C 3D/4D correlation
experiments for resonance assignment of large proteins,” ChemPhysChem,
vol. 18, no. 19. Wiley, pp. 2697–2703, 2017.
ista: Fraga H, Arnaud C, Gauto DF, Audin M, Kurauskas V, Macek P, Krichel C, Guan
J, Boisbouvier J, Sprangers R, Breyton C, Schanda P. 2017. Solid‐state NMR H–N–(C)–H
and H–N–C–C 3D/4D correlation experiments for resonance assignment of large proteins.
ChemPhysChem. 18(19), 2697–2703.
mla: Fraga, Hugo, et al. “Solid‐state NMR H–N–(C)–H and H–N–C–C 3D/4D Correlation
Experiments for Resonance Assignment of Large Proteins.” ChemPhysChem,
vol. 18, no. 19, Wiley, 2017, pp. 2697–703, doi:10.1002/cphc.201700572.
short: H. Fraga, C. Arnaud, D.F. Gauto, M. Audin, V. Kurauskas, P. Macek, C. Krichel,
J. Guan, J. Boisbouvier, R. Sprangers, C. Breyton, P. Schanda, ChemPhysChem 18
(2017) 2697–2703.
date_created: 2020-09-18T10:06:09Z
date_published: 2017-08-09T00:00:00Z
date_updated: 2021-01-12T08:19:19Z
day: '09'
doi: 10.1002/cphc.201700572
extern: '1'
intvolume: ' 18'
issue: '19'
keyword:
- Physical and Theoretical Chemistry
- Atomic and Molecular Physics
- and Optics
language:
- iso: eng
month: '08'
oa_version: None
page: 2697-2703
publication: ChemPhysChem
publication_identifier:
issn:
- 1439-4235
- 1439-7641
publication_status: published
publisher: Wiley
quality_controlled: '1'
status: public
title: Solid‐state NMR H–N–(C)–H and H–N–C–C 3D/4D correlation experiments for resonance
assignment of large proteins
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 18
year: '2017'
...
---
_id: '8445'
abstract:
- lang: eng
text: Proteins perform their functions in solution but their structures are most
frequently studied inside crystals. Here we probe how the crystal packing alters
microsecond dynamics, using solid-state NMR measurements and multi-microsecond
MD simulations of different crystal forms of ubiquitin. In particular, near-rotary-resonance
relaxation dispersion (NERRD) experiments probe angular backbone motion, while
Bloch–McConnell relaxation dispersion data report on fluctuations of the local
electronic environment. These experiments and simulations reveal that the packing
of the protein can significantly alter the thermodynamics and kinetics of local
conformational exchange. Moreover, we report small-amplitude reorientational motion
of protein molecules in the crystal lattice with an ~3–5° amplitude on a tens-of-microseconds
time scale in one of the crystals, but not in others. An intriguing possibility
arises that overall motion is to some extent coupled to local dynamics. Our study
highlights the importance of considering the packing when analyzing dynamics of
crystalline proteins.
article_number: '145'
article_processing_charge: No
article_type: original
author:
- first_name: Vilius
full_name: Kurauskas, Vilius
last_name: Kurauskas
- first_name: Sergei A.
full_name: Izmailov, Sergei A.
last_name: Izmailov
- first_name: Olga N.
full_name: Rogacheva, Olga N.
last_name: Rogacheva
- first_name: Audrey
full_name: Hessel, Audrey
last_name: Hessel
- first_name: Isabel
full_name: Ayala, Isabel
last_name: Ayala
- first_name: Joyce
full_name: Woodhouse, Joyce
last_name: Woodhouse
- first_name: Anastasya
full_name: Shilova, Anastasya
last_name: Shilova
- first_name: Yi
full_name: Xue, Yi
last_name: Xue
- first_name: Tairan
full_name: Yuwen, Tairan
last_name: Yuwen
- first_name: Nicolas
full_name: Coquelle, Nicolas
last_name: Coquelle
- 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: Kurauskas V, Izmailov SA, Rogacheva ON, et al. Slow conformational exchange
and overall rocking motion in ubiquitin protein crystals. Nature Communications.
2017;8. doi:10.1038/s41467-017-00165-8
apa: Kurauskas, V., Izmailov, S. A., Rogacheva, O. N., Hessel, A., Ayala, I., Woodhouse,
J., … Schanda, P. (2017). Slow conformational exchange and overall rocking motion
in ubiquitin protein crystals. Nature Communications. Springer Nature.
https://doi.org/10.1038/s41467-017-00165-8
chicago: Kurauskas, Vilius, Sergei A. Izmailov, Olga N. Rogacheva, Audrey Hessel,
Isabel Ayala, Joyce Woodhouse, Anastasya Shilova, et al. “Slow Conformational
Exchange and Overall Rocking Motion in Ubiquitin Protein Crystals.” Nature
Communications. Springer Nature, 2017. https://doi.org/10.1038/s41467-017-00165-8.
ieee: V. Kurauskas et al., “Slow conformational exchange and overall rocking
motion in ubiquitin protein crystals,” Nature Communications, vol. 8. Springer
Nature, 2017.
ista: Kurauskas V, Izmailov SA, Rogacheva ON, Hessel A, Ayala I, Woodhouse J, Shilova
A, Xue Y, Yuwen T, Coquelle N, Colletier J-P, Skrynnikov NR, Schanda P. 2017.
Slow conformational exchange and overall rocking motion in ubiquitin protein crystals.
Nature Communications. 8, 145.
mla: Kurauskas, Vilius, et al. “Slow Conformational Exchange and Overall Rocking
Motion in Ubiquitin Protein Crystals.” Nature Communications, vol. 8, 145,
Springer Nature, 2017, doi:10.1038/s41467-017-00165-8.
short: V. Kurauskas, S.A. Izmailov, O.N. Rogacheva, A. Hessel, I. Ayala, J. Woodhouse,
A. Shilova, Y. Xue, T. Yuwen, N. Coquelle, J.-P. Colletier, N.R. Skrynnikov, P.
Schanda, Nature Communications 8 (2017).
date_created: 2020-09-18T10:06:01Z
date_published: 2017-07-27T00:00:00Z
date_updated: 2021-01-12T08:19:19Z
day: '27'
doi: 10.1038/s41467-017-00165-8
extern: '1'
intvolume: ' 8'
language:
- iso: eng
month: '07'
oa_version: Published Version
publication: Nature Communications
publication_identifier:
issn:
- 2041-1723
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
status: public
title: Slow conformational exchange and overall rocking motion in ubiquitin protein
crystals
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 8
year: '2017'
...
---
_id: '8444'
abstract:
- lang: eng
text: Biophysical investigation of membrane proteins generally requires their extraction
from native sources using detergents, a step that can lead, possibly irreversibly,
to protein denaturation. The propensity of dodecylphosphocholine (DPC), a detergent
widely utilized in NMR studies of membrane proteins, to distort their structure
has been the subject of much controversy. It has been recently proposed that the
binding specificity of the yeast mitochondrial ADP/ATP carrier (yAAC3) toward
cardiolipins is preserved in DPC, thereby suggesting that DPC is a suitable environment
in which to study membrane proteins. In this communication, we used all-atom molecular
dynamics simulations to investigate the specific binding of cardiolipins to yAAC3.
Our data demonstrate that the interaction interface observed in a native-like
environment differs markedly from that inferred from an NMR investigation in DPC,
implying that in this detergent, the protein structure is distorted. We further
investigated yAAC3 solubilized in DPC and in the milder dodecylmaltoside with
thermal-shift assays. The loss of thermal transition observed in DPC confirms
that the protein is no longer properly folded in this environment.
article_processing_charge: No
article_type: original
author:
- first_name: François
full_name: Dehez, François
last_name: Dehez
- first_name: Paul
full_name: Schanda, Paul
id: 7B541462-FAF6-11E9-A490-E8DFE5697425
last_name: Schanda
orcid: 0000-0002-9350-7606
- first_name: Martin S.
full_name: King, Martin S.
last_name: King
- first_name: Edmund R.S.
full_name: Kunji, Edmund R.S.
last_name: Kunji
- first_name: Christophe
full_name: Chipot, Christophe
last_name: Chipot
citation:
ama: Dehez F, Schanda P, King MS, Kunji ERS, Chipot C. Mitochondrial ADP/ATP carrier
in dodecylphosphocholine binds cardiolipins with non-native affinity. Biophysical
Journal. 2017;113(11):2311-2315. doi:10.1016/j.bpj.2017.09.019
apa: Dehez, F., Schanda, P., King, M. S., Kunji, E. R. S., & Chipot, C. (2017).
Mitochondrial ADP/ATP carrier in dodecylphosphocholine binds cardiolipins with
non-native affinity. Biophysical Journal. Elsevier. https://doi.org/10.1016/j.bpj.2017.09.019
chicago: Dehez, François, Paul Schanda, Martin S. King, Edmund R.S. Kunji, and Christophe
Chipot. “Mitochondrial ADP/ATP Carrier in Dodecylphosphocholine Binds Cardiolipins
with Non-Native Affinity.” Biophysical Journal. Elsevier, 2017. https://doi.org/10.1016/j.bpj.2017.09.019.
ieee: F. Dehez, P. Schanda, M. S. King, E. R. S. Kunji, and C. Chipot, “Mitochondrial
ADP/ATP carrier in dodecylphosphocholine binds cardiolipins with non-native affinity,”
Biophysical Journal, vol. 113, no. 11. Elsevier, pp. 2311–2315, 2017.
ista: Dehez F, Schanda P, King MS, Kunji ERS, Chipot C. 2017. Mitochondrial ADP/ATP
carrier in dodecylphosphocholine binds cardiolipins with non-native affinity.
Biophysical Journal. 113(11), 2311–2315.
mla: Dehez, François, et al. “Mitochondrial ADP/ATP Carrier in Dodecylphosphocholine
Binds Cardiolipins with Non-Native Affinity.” Biophysical Journal, vol.
113, no. 11, Elsevier, 2017, pp. 2311–15, doi:10.1016/j.bpj.2017.09.019.
short: F. Dehez, P. Schanda, M.S. King, E.R.S. Kunji, C. Chipot, Biophysical Journal
113 (2017) 2311–2315.
date_created: 2020-09-18T10:05:54Z
date_published: 2017-12-05T00:00:00Z
date_updated: 2021-01-12T08:19:18Z
day: '05'
doi: 10.1016/j.bpj.2017.09.019
extern: '1'
intvolume: ' 113'
issue: '11'
keyword:
- Biophysics
language:
- iso: eng
month: '12'
oa_version: None
page: 2311-2315
publication: Biophysical Journal
publication_identifier:
issn:
- 0006-3495
publication_status: published
publisher: Elsevier
quality_controlled: '1'
status: public
title: Mitochondrial ADP/ATP carrier in dodecylphosphocholine binds cardiolipins with
non-native affinity
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 113
year: '2017'
...
---
_id: '9065'
abstract:
- lang: eng
text: Magnetic anisotropy in strontium iridate (Sr2IrO4) is found to be large because
of the strong spin-orbit interactions. In our work, we studied the in-plane magnetic
anisotropy of Sr2IrO4 and traced the anisotropic exchange interactions between
the isospins in the crystal. The magnetic-field-dependent torque τ(H) showed a
prominent transition from the canted antiferromagnetic state to the weak ferromagnetic
(WFM) state. A comprehensive analysis was conducted to examine the isotropic and
anisotropic regimes and probe the easy magnetization axis along the a b plane.
The angle-dependent torque τ(θ) revealed a deviation from the sinusoidal behavior,
and small differences in hysteresis were observed around 0° and 90° in the low-magnetic-field
regime. This indicates that the orientation of the easy axis of the FM component
is along the b axis, where the antiferromagnetic to WFM spin-flop transition occurs.
We compared the coefficients of the magnetic susceptibility tensors and captured
the anisotropy of the material. The in-plane τ(θ) revealed a tendency toward isotropic
behavior for fields with values above the field value of the WFM transition.
article_number: '155102'
article_processing_charge: No
article_type: original
author:
- first_name: Muhammad
full_name: Nauman, Muhammad
id: 32c21954-2022-11eb-9d5f-af9f93c24e71
last_name: Nauman
orcid: 0000-0002-2111-4846
- first_name: Yunjeong
full_name: Hong, Yunjeong
last_name: Hong
- first_name: Tayyaba
full_name: Hussain, Tayyaba
last_name: Hussain
- first_name: M. S.
full_name: Seo, M. S.
last_name: Seo
- first_name: S. Y.
full_name: Park, S. Y.
last_name: Park
- first_name: N.
full_name: Lee, N.
last_name: Lee
- first_name: Y. J.
full_name: Choi, Y. J.
last_name: Choi
- first_name: Woun
full_name: Kang, Woun
last_name: Kang
- first_name: Younjung
full_name: Jo, Younjung
last_name: Jo
citation:
ama: Nauman M, Hong Y, Hussain T, et al. In-plane magnetic anisotropy in strontium
iridate Sr2IrO4. Physical Review B. 2017;96(15). doi:10.1103/physrevb.96.155102
apa: Nauman, M., Hong, Y., Hussain, T., Seo, M. S., Park, S. Y., Lee, N., … Jo,
Y. (2017). In-plane magnetic anisotropy in strontium iridate Sr2IrO4. Physical
Review B. American Physical Society. https://doi.org/10.1103/physrevb.96.155102
chicago: Nauman, Muhammad, Yunjeong Hong, Tayyaba Hussain, M. S. Seo, S. Y. Park,
N. Lee, Y. J. Choi, Woun Kang, and Younjung Jo. “In-Plane Magnetic Anisotropy
in Strontium Iridate Sr2IrO4.” Physical Review B. American Physical Society,
2017. https://doi.org/10.1103/physrevb.96.155102.
ieee: M. Nauman et al., “In-plane magnetic anisotropy in strontium iridate
Sr2IrO4,” Physical Review B, vol. 96, no. 15. American Physical Society,
2017.
ista: Nauman M, Hong Y, Hussain T, Seo MS, Park SY, Lee N, Choi YJ, Kang W, Jo Y.
2017. In-plane magnetic anisotropy in strontium iridate Sr2IrO4. Physical Review
B. 96(15), 155102.
mla: Nauman, Muhammad, et al. “In-Plane Magnetic Anisotropy in Strontium Iridate
Sr2IrO4.” Physical Review B, vol. 96, no. 15, 155102, American Physical
Society, 2017, doi:10.1103/physrevb.96.155102.
short: M. Nauman, Y. Hong, T. Hussain, M.S. Seo, S.Y. Park, N. Lee, Y.J. Choi, W.
Kang, Y. Jo, Physical Review B 96 (2017).
date_created: 2021-02-02T15:49:21Z
date_published: 2017-10-01T00:00:00Z
date_updated: 2021-02-03T12:53:00Z
day: '01'
doi: 10.1103/physrevb.96.155102
extern: '1'
intvolume: ' 96'
issue: '15'
language:
- iso: eng
month: '10'
oa_version: None
publication: Physical Review B
publication_identifier:
issn:
- 2469-9950
- 2469-9969
publication_status: published
publisher: American Physical Society
quality_controlled: '1'
status: public
title: In-plane magnetic anisotropy in strontium iridate Sr2IrO4
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 96
year: '2017'
...
---
_id: '9165'
abstract:
- lang: eng
text: Advances in colloidal synthesis allow for the design of particles with controlled
patches. This article reviews routes towards colloidal locomotion, where energy
is consumed and converted into motion, and its implementation with active patchy
particles. A special emphasis is given to phoretic swimmers, where the self-propulsion
originates from an interfacial phenomenon, raising experimental challenges and
opening up opportunities for particles with controlled anisotropic surface chemistry
and novel behaviors.
article_processing_charge: No
article_type: original
author:
- first_name: A.
full_name: Aubret, A.
last_name: Aubret
- first_name: S.
full_name: Ramananarivo, S.
last_name: Ramananarivo
- first_name: Jérémie A
full_name: Palacci, Jérémie A
id: 8fb92548-2b22-11eb-b7c1-a3f0d08d7c7d
last_name: Palacci
orcid: 0000-0002-7253-9465
citation:
ama: 'Aubret A, Ramananarivo S, Palacci JA. Eppur si muove, and yet it moves: Patchy
(phoretic) swimmers. Current Opinion in Colloid & Interface Science.
2017;30:81-89. doi:10.1016/j.cocis.2017.05.007'
apa: 'Aubret, A., Ramananarivo, S., & Palacci, J. A. (2017). Eppur si muove,
and yet it moves: Patchy (phoretic) swimmers. Current Opinion in Colloid &
Interface Science. Elsevier. https://doi.org/10.1016/j.cocis.2017.05.007'
chicago: 'Aubret, A., S. Ramananarivo, and Jérémie A Palacci. “Eppur Si Muove, and
yet It Moves: Patchy (Phoretic) Swimmers.” Current Opinion in Colloid &
Interface Science. Elsevier, 2017. https://doi.org/10.1016/j.cocis.2017.05.007.'
ieee: 'A. Aubret, S. Ramananarivo, and J. A. Palacci, “Eppur si muove, and yet it
moves: Patchy (phoretic) swimmers,” Current Opinion in Colloid & Interface
Science, vol. 30. Elsevier, pp. 81–89, 2017.'
ista: 'Aubret A, Ramananarivo S, Palacci JA. 2017. Eppur si muove, and yet it moves:
Patchy (phoretic) swimmers. Current Opinion in Colloid & Interface Science.
30, 81–89.'
mla: 'Aubret, A., et al. “Eppur Si Muove, and yet It Moves: Patchy (Phoretic) Swimmers.”
Current Opinion in Colloid & Interface Science, vol. 30, Elsevier,
2017, pp. 81–89, doi:10.1016/j.cocis.2017.05.007.'
short: A. Aubret, S. Ramananarivo, J.A. Palacci, Current Opinion in Colloid &
Interface Science 30 (2017) 81–89.
date_created: 2021-02-18T14:29:42Z
date_published: 2017-07-01T00:00:00Z
date_updated: 2021-02-22T09:32:11Z
day: '01'
doi: 10.1016/j.cocis.2017.05.007
extern: '1'
intvolume: ' 30'
language:
- iso: eng
month: '07'
oa_version: None
page: 81-89
publication: Current Opinion in Colloid & Interface Science
publication_identifier:
issn:
- 1359-0294
publication_status: published
publisher: Elsevier
quality_controlled: '1'
scopus_import: '1'
status: public
title: 'Eppur si muove, and yet it moves: Patchy (phoretic) swimmers'
type: journal_article
user_id: D865714E-FA4E-11E9-B85B-F5C5E5697425
volume: 30
year: '2017'
...
---
_id: '9190'
abstract:
- lang: eng
text: Plant meristems carry pools of continuously active stem cells, whose
activity is controlled by developmental and environmental signals. After stem
cell division, daughter cells that exit the stem cell domain acquire transit amplifying
cell identity before they are incorporated into organs and differentiate. In this
study, we used an integrated approach to elucidate the role of HECATE (HEC) genes
in regulating developmental trajectories of shoot stem cells in Arabidopsis thaliana.
Our work reveals that HEC function stabilizes cell fate in distinct zones of the
shoot meristem thereby controlling the spatio-temporal dynamics of stem cell differentiation.
Importantly, this activity is concomitant with the local modulation of cellular
responses to cytokinin and auxin, two key phytohormones regulating cell behaviour.
Mechanistically, we show that HEC factors transcriptionally control and physically
interact with MONOPTEROS (MP), a key regulator of auxin signalling, and modulate
the autocatalytic stabilization of auxin signalling output.
article_number: e30135
article_processing_charge: No
article_type: original
author:
- first_name: Christophe
full_name: Gaillochet, Christophe
last_name: Gaillochet
- first_name: Thomas
full_name: Stiehl, Thomas
last_name: Stiehl
- first_name: Christian
full_name: Wenzl, Christian
last_name: Wenzl
- first_name: Juan-José
full_name: Ripoll, Juan-José
last_name: Ripoll
- first_name: Lindsay J
full_name: Bailey-Steinitz, Lindsay J
last_name: Bailey-Steinitz
- first_name: Lanxin
full_name: Li, Lanxin
id: 367EF8FA-F248-11E8-B48F-1D18A9856A87
last_name: Li
orcid: 0000-0002-5607-272X
- first_name: Anne
full_name: Pfeiffer, Anne
last_name: Pfeiffer
- first_name: Andrej
full_name: Miotk, Andrej
last_name: Miotk
- first_name: Jana P
full_name: Hakenjos, Jana P
last_name: Hakenjos
- first_name: Joachim
full_name: Forner, Joachim
last_name: Forner
- first_name: Martin F
full_name: Yanofsky, Martin F
last_name: Yanofsky
- first_name: Anna
full_name: Marciniak-Czochra, Anna
last_name: Marciniak-Czochra
- first_name: Jan U
full_name: Lohmann, Jan U
last_name: Lohmann
citation:
ama: Gaillochet C, Stiehl T, Wenzl C, et al. Control of plant cell fate transitions
by transcriptional and hormonal signals. eLife. 2017;6. doi:10.7554/elife.30135
apa: Gaillochet, C., Stiehl, T., Wenzl, C., Ripoll, J.-J., Bailey-Steinitz, L. J.,
Li, L., … Lohmann, J. U. (2017). Control of plant cell fate transitions by transcriptional
and hormonal signals. ELife. eLife Sciences Publications. https://doi.org/10.7554/elife.30135
chicago: Gaillochet, Christophe, Thomas Stiehl, Christian Wenzl, Juan-José Ripoll,
Lindsay J Bailey-Steinitz, Lanxin Li, Anne Pfeiffer, et al. “Control of Plant
Cell Fate Transitions by Transcriptional and Hormonal Signals.” ELife.
eLife Sciences Publications, 2017. https://doi.org/10.7554/elife.30135.
ieee: C. Gaillochet et al., “Control of plant cell fate transitions by transcriptional
and hormonal signals,” eLife, vol. 6. eLife Sciences Publications, 2017.
ista: Gaillochet C, Stiehl T, Wenzl C, Ripoll J-J, Bailey-Steinitz LJ, Li L, Pfeiffer
A, Miotk A, Hakenjos JP, Forner J, Yanofsky MF, Marciniak-Czochra A, Lohmann JU.
2017. Control of plant cell fate transitions by transcriptional and hormonal signals.
eLife. 6, e30135.
mla: Gaillochet, Christophe, et al. “Control of Plant Cell Fate Transitions by Transcriptional
and Hormonal Signals.” ELife, vol. 6, e30135, eLife Sciences Publications,
2017, doi:10.7554/elife.30135.
short: C. Gaillochet, T. Stiehl, C. Wenzl, J.-J. Ripoll, L.J. Bailey-Steinitz, L.
Li, A. Pfeiffer, A. Miotk, J.P. Hakenjos, J. Forner, M.F. Yanofsky, A. Marciniak-Czochra,
J.U. Lohmann, ELife 6 (2017).
date_created: 2021-02-24T17:06:13Z
date_published: 2017-10-23T00:00:00Z
date_updated: 2021-03-02T09:33:54Z
day: '23'
ddc:
- '580'
doi: 10.7554/elife.30135
extern: '1'
external_id:
pmid:
- '29058667'
file:
- access_level: open_access
checksum: 51c8968a845df5077643c3e3e139d34f
content_type: application/pdf
creator: dernst
date_created: 2021-03-02T09:29:56Z
date_updated: 2021-03-02T09:29:56Z
file_id: '9214'
file_name: 2017_eLife_Gaillochet.pdf
file_size: 11669407
relation: main_file
success: 1
file_date_updated: 2021-03-02T09:29:56Z
has_accepted_license: '1'
intvolume: ' 6'
language:
- iso: eng
month: '10'
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: Control of plant cell fate transitions by transcriptional and hormonal signals
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 6
year: '2017'
...
---
_id: '93'
abstract:
- lang: eng
text: An electro-optomechanical device capable of microwave-to-optics conversion
has recently been demonstrated, with the vision of enabling optical networks of
superconducting qubits. Here we present an improved converter design that uses
a three-dimensional microwave cavity for coupling between the microwave transmission
line and an integrated LC resonator on the converter chip. The new design simplifies
the optical assembly and decouples it from the microwave part of the setup. Experimental
demonstrations show that the modular device assembly allows us to flexibly tune
the microwave coupling to the converter chip while maintaining small loss. We
also find that electromechanical experiments are not impacted by the additional
microwave cavity. Our design is compatible with a high-finesse optical cavity
and will improve optical performance.
article_number: '094701'
author:
- first_name: Tim
full_name: Menke, Tim
last_name: Menke
- first_name: Peter
full_name: Burns, Peter
last_name: Burns
- 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: N S
full_name: Kampel, N S
last_name: Kampel
- first_name: Robert
full_name: Peterson, Robert
last_name: Peterson
- first_name: Katarina
full_name: Cicak, Katarina
last_name: Cicak
- first_name: Raymond
full_name: Simmonds, Raymond
last_name: Simmonds
- first_name: Cindy
full_name: Regal, Cindy
last_name: Regal
- first_name: Konrad
full_name: Lehnert, Konrad
last_name: Lehnert
citation:
ama: Menke T, Burns P, Higginbotham AP, et al. Reconfigurable re-entrant cavity
for wireless coupling to an electro-optomechanical device. Review of Scientific
Instruments. 2017;88(9). doi:10.1063/1.5000973
apa: Menke, T., Burns, P., Higginbotham, A. P., Kampel, N. S., Peterson, R., Cicak,
K., … Lehnert, K. (2017). Reconfigurable re-entrant cavity for wireless coupling
to an electro-optomechanical device. Review of Scientific Instruments.
American Institute of Physics. https://doi.org/10.1063/1.5000973
chicago: Menke, Tim, Peter Burns, Andrew P Higginbotham, N S Kampel, Robert Peterson,
Katarina Cicak, Raymond Simmonds, Cindy Regal, and Konrad Lehnert. “Reconfigurable
Re-Entrant Cavity for Wireless Coupling to an Electro-Optomechanical Device.”
Review of Scientific Instruments. American Institute of Physics, 2017.
https://doi.org/10.1063/1.5000973.
ieee: T. Menke et al., “Reconfigurable re-entrant cavity for wireless coupling
to an electro-optomechanical device,” Review of Scientific Instruments,
vol. 88, no. 9. American Institute of Physics, 2017.
ista: Menke T, Burns P, Higginbotham AP, Kampel NS, Peterson R, Cicak K, Simmonds
R, Regal C, Lehnert K. 2017. Reconfigurable re-entrant cavity for wireless coupling
to an electro-optomechanical device. Review of Scientific Instruments. 88(9),
094701.
mla: Menke, Tim, et al. “Reconfigurable Re-Entrant Cavity for Wireless Coupling
to an Electro-Optomechanical Device.” Review of Scientific Instruments,
vol. 88, no. 9, 094701, American Institute of Physics, 2017, doi:10.1063/1.5000973.
short: T. Menke, P. Burns, A.P. Higginbotham, N.S. Kampel, R. Peterson, K. Cicak,
R. Simmonds, C. Regal, K. Lehnert, Review of Scientific Instruments 88 (2017).
date_created: 2018-12-11T11:44:35Z
date_published: 2017-09-08T00:00:00Z
date_updated: 2021-01-12T08:21:59Z
day: '08'
doi: 10.1063/1.5000973
extern: '1'
external_id:
arxiv:
- '1703.06470'
pmid:
- '28964202'
intvolume: ' 88'
issue: '9'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/1703.06470
month: '09'
oa: 1
oa_version: Preprint
pmid: 1
publication: Review of Scientific Instruments
publication_status: published
publisher: American Institute of Physics
publist_id: '7961'
quality_controlled: '1'
status: public
title: Reconfigurable re-entrant cavity for wireless coupling to an electro-optomechanical
device
type: journal_article
user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87
volume: 88
year: '2017'
...
---
_id: '94'
abstract:
- lang: eng
text: We introduce a method for breaking Lorentz reciprocity based upon the noncommutation
of frequency conversion and delay. The method requires no magnetic materials or
resonant physics, allowing for the design of scalable and broadband nonreciprocal
circuits. With this approach, two types of gyrators - universal building blocks
for linear, nonreciprocal circuits - are constructed. Using one of these gyrators,
we create a circulator with >15 dB of isolation across the 5-9 GHz band. Our
designs may be readily extended to any platform with suitable frequency conversion
elements, including semiconducting devices for telecommunication or an on-chip
superconducting implementation for quantum information processing.
article_number: '147703'
author:
- first_name: Eric
full_name: Rosenthal, Eric
last_name: Rosenthal
- first_name: Benjamin
full_name: Chapman, Benjamin
last_name: Chapman
- 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: Joseph
full_name: Kerckhoff, Joseph
last_name: Kerckhoff
- first_name: Konrad
full_name: Lehnert, Konrad
last_name: Lehnert
citation:
ama: Rosenthal E, Chapman B, Higginbotham AP, Kerckhoff J, Lehnert K. Breaking Lorentz
reciprocity with frequency conversion and delay. APS Physics, Physical Review
Letters. 2017;119(14). doi:10.1103/PhysRevLett.119.147703
apa: Rosenthal, E., Chapman, B., Higginbotham, A. P., Kerckhoff, J., & Lehnert,
K. (2017). Breaking Lorentz reciprocity with frequency conversion and delay. APS
Physics, Physical Review Letters. American Physical Society. https://doi.org/10.1103/PhysRevLett.119.147703
chicago: Rosenthal, Eric, Benjamin Chapman, Andrew P Higginbotham, Joseph Kerckhoff,
and Konrad Lehnert. “Breaking Lorentz Reciprocity with Frequency Conversion and
Delay.” APS Physics, Physical Review Letters. American Physical Society,
2017. https://doi.org/10.1103/PhysRevLett.119.147703.
ieee: E. Rosenthal, B. Chapman, A. P. Higginbotham, J. Kerckhoff, and K. Lehnert,
“Breaking Lorentz reciprocity with frequency conversion and delay,” APS Physics,
Physical Review Letters, vol. 119, no. 14. American Physical Society, 2017.
ista: Rosenthal E, Chapman B, Higginbotham AP, Kerckhoff J, Lehnert K. 2017. Breaking
Lorentz reciprocity with frequency conversion and delay. APS Physics, Physical
Review Letters. 119(14), 147703.
mla: Rosenthal, Eric, et al. “Breaking Lorentz Reciprocity with Frequency Conversion
and Delay.” APS Physics, Physical Review Letters, vol. 119, no. 14, 147703,
American Physical Society, 2017, doi:10.1103/PhysRevLett.119.147703.
short: E. Rosenthal, B. Chapman, A.P. Higginbotham, J. Kerckhoff, K. Lehnert, APS
Physics, Physical Review Letters 119 (2017).
date_created: 2018-12-11T11:44:35Z
date_published: 2017-10-06T00:00:00Z
date_updated: 2021-01-12T08:22:04Z
day: '06'
doi: 10.1103/PhysRevLett.119.147703
extern: '1'
external_id:
arxiv:
- '1705.09548'
intvolume: ' 119'
issue: '14'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/1705.09548
month: '10'
oa: 1
oa_version: Submitted Version
publication: APS Physics, Physical Review Letters
publication_status: published
publisher: American Physical Society
publist_id: '7960'
quality_controlled: '1'
status: public
title: Breaking Lorentz reciprocity with frequency conversion and delay
type: journal_article
user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87
volume: 119
year: '2017'
...
---
_id: '9445'
abstract:
- lang: eng
text: Cytosine methylation regulates essential genome functions across eukaryotes,
but the fundamental question of whether nucleosomal or naked DNA is the preferred
substrate of plant and animal methyltransferases remains unresolved. Here, we
show that genetic inactivation of a single DDM1/Lsh family nucleosome remodeler
biases methylation toward inter-nucleosomal linker DNA in Arabidopsis thaliana
and mouse. We find that DDM1 enables methylation of DNA bound to the nucleosome,
suggesting that nucleosome-free DNA is the preferred substrate of eukaryotic methyltransferases
in vivo. Furthermore, we show that simultaneous mutation of DDM1 and linker histone
H1 in Arabidopsis reproduces the strong linker-specific methylation patterns of
species that diverged from flowering plants and animals over a billion years ago.
Our results indicate that in the absence of remodeling, nucleosomes are strong
barriers to DNA methyltransferases. Linker-specific methylation can evolve simply
by breaking the connection between nucleosome remodeling and DNA methylation.
article_number: e30674
article_processing_charge: No
article_type: original
author:
- first_name: David B
full_name: Lyons, David B
last_name: Lyons
- first_name: Daniel
full_name: Zilberman, Daniel
id: 6973db13-dd5f-11ea-814e-b3e5455e9ed1
last_name: Zilberman
orcid: 0000-0002-0123-8649
citation:
ama: Lyons DB, Zilberman D. DDM1 and Lsh remodelers allow methylation of DNA wrapped
in nucleosomes. eLife. 2017;6. doi:10.7554/elife.30674
apa: Lyons, D. B., & Zilberman, D. (2017). DDM1 and Lsh remodelers allow methylation
of DNA wrapped in nucleosomes. ELife. eLife Sciences Publications. https://doi.org/10.7554/elife.30674
chicago: Lyons, David B, and Daniel Zilberman. “DDM1 and Lsh Remodelers Allow Methylation
of DNA Wrapped in Nucleosomes.” ELife. eLife Sciences Publications, 2017.
https://doi.org/10.7554/elife.30674.
ieee: D. B. Lyons and D. Zilberman, “DDM1 and Lsh remodelers allow methylation of
DNA wrapped in nucleosomes,” eLife, vol. 6. eLife Sciences Publications,
2017.
ista: Lyons DB, Zilberman D. 2017. DDM1 and Lsh remodelers allow methylation of
DNA wrapped in nucleosomes. eLife. 6, e30674.
mla: Lyons, David B., and Daniel Zilberman. “DDM1 and Lsh Remodelers Allow Methylation
of DNA Wrapped in Nucleosomes.” ELife, vol. 6, e30674, eLife Sciences Publications,
2017, doi:10.7554/elife.30674.
short: D.B. Lyons, D. Zilberman, ELife 6 (2017).
date_created: 2021-06-02T14:28:58Z
date_published: 2017-11-15T00:00:00Z
date_updated: 2021-12-14T07:54:36Z
day: '15'
ddc:
- '570'
department:
- _id: DaZi
doi: 10.7554/elife.30674
extern: '1'
external_id:
pmid:
- '29140247'
file:
- access_level: open_access
checksum: 4cfcdd67511ae4aed3d993550e46e146
content_type: application/pdf
creator: cziletti
date_created: 2021-06-02T14:33:36Z
date_updated: 2021-06-02T14:33:36Z
file_id: '9446'
file_name: 2017_eLife_Lyons.pdf
file_size: 1603102
relation: main_file
success: 1
file_date_updated: 2021-06-02T14:33:36Z
has_accepted_license: '1'
intvolume: ' 6'
language:
- iso: eng
month: '11'
oa: 1
oa_version: Published Version
pmid: 1
publication: eLife
publication_identifier:
eissn:
- 2050-084X
publication_status: published
publisher: eLife Sciences Publications
quality_controlled: '1'
scopus_import: '1'
status: public
title: DDM1 and Lsh remodelers allow methylation of DNA wrapped in nucleosomes
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: journal_article
user_id: 8b945eb4-e2f2-11eb-945a-df72226e66a9
volume: 6
year: '2017'
...
---
_id: '957'
abstract:
- lang: eng
text: Small molecule biosensors based on Forster resonance energy transfer (FRET)
enable small molecule signaling to be monitored with high spatial and temporal
resolution in complex cellular environments. FRET sensors can be constructed by
fusing a pair of fluorescent proteins to a suitable recognition domain, such as
a member of the solute-binding protein (SBP) superfamily. However, naturally occurring
SBPs may be unsuitable for incorporation into FRET sensors due to their low thermostability,
which may preclude imaging under physiological conditions, or because the positions
of their N- and C-termini may be suboptimal for fusion of fluorescent proteins,
which may limit the dynamic range of the resulting sensors. Here, we show how
these problems can be overcome using ancestral protein reconstruction and circular
permutation. Ancestral protein reconstruction, used as a protein engineering strategy,
leverages phylogenetic information to improve the thermostability of proteins,
while circular permutation enables the termini of an SBP to be repositioned to
maximize the dynamic range of the resulting FRET sensor. We also provide a protocol
for cloning the engineered SBPs into FRET sensor constructs using Golden Gate
assembly and discuss considerations for in situ characterization of the FRET sensors.
alternative_title:
- Methods in Molecular Biology
author:
- first_name: Ben
full_name: Clifton, Ben
last_name: Clifton
- first_name: Jason
full_name: Whitfield, Jason
last_name: Whitfield
- first_name: Inmaculada
full_name: Sanchez Romero, Inmaculada
id: 3D9C5D30-F248-11E8-B48F-1D18A9856A87
last_name: Sanchez Romero
- first_name: Michel
full_name: Herde, Michel
last_name: Herde
- first_name: Christian
full_name: Henneberger, Christian
last_name: Henneberger
- first_name: Harald L
full_name: Janovjak, Harald L
id: 33BA6C30-F248-11E8-B48F-1D18A9856A87
last_name: Janovjak
orcid: 0000-0002-8023-9315
- first_name: Colin
full_name: Jackson, Colin
last_name: Jackson
citation:
ama: 'Clifton B, Whitfield J, Sanchez-Romero I, et al. Ancestral protein reconstruction
and circular permutation for improving the stability and dynamic range of FRET
sensors. In: Stein V, ed. Synthetic Protein Switches. Vol 1596. Synthetic
Protein Switches. Springer; 2017:71-87. doi:10.1007/978-1-4939-6940-1_5'
apa: Clifton, B., Whitfield, J., Sanchez-Romero, I., Herde, M., Henneberger, C.,
Janovjak, H. L., & Jackson, C. (2017). Ancestral protein reconstruction and
circular permutation for improving the stability and dynamic range of FRET sensors.
In V. Stein (Ed.), Synthetic Protein Switches (Vol. 1596, pp. 71–87). Springer.
https://doi.org/10.1007/978-1-4939-6940-1_5
chicago: Clifton, Ben, Jason Whitfield, Inmaculada Sanchez-Romero, Michel Herde,
Christian Henneberger, Harald L Janovjak, and Colin Jackson. “Ancestral Protein
Reconstruction and Circular Permutation for Improving the Stability and Dynamic
Range of FRET Sensors.” In Synthetic Protein Switches, edited by Viktor
Stein, 1596:71–87. Synthetic Protein Switches. Springer, 2017. https://doi.org/10.1007/978-1-4939-6940-1_5.
ieee: B. Clifton et al., “Ancestral protein reconstruction and circular permutation
for improving the stability and dynamic range of FRET sensors,” in Synthetic
Protein Switches, vol. 1596, V. Stein, Ed. Springer, 2017, pp. 71–87.
ista: 'Clifton B, Whitfield J, Sanchez-Romero I, Herde M, Henneberger C, Janovjak
HL, Jackson C. 2017.Ancestral protein reconstruction and circular permutation
for improving the stability and dynamic range of FRET sensors. In: Synthetic Protein
Switches. Methods in Molecular Biology, vol. 1596, 71–87.'
mla: Clifton, Ben, et al. “Ancestral Protein Reconstruction and Circular Permutation
for Improving the Stability and Dynamic Range of FRET Sensors.” Synthetic Protein
Switches, edited by Viktor Stein, vol. 1596, Springer, 2017, pp. 71–87, doi:10.1007/978-1-4939-6940-1_5.
short: B. Clifton, J. Whitfield, I. Sanchez-Romero, M. Herde, C. Henneberger, H.L.
Janovjak, C. Jackson, in:, V. Stein (Ed.), Synthetic Protein Switches, Springer,
2017, pp. 71–87.
date_created: 2018-12-11T11:49:24Z
date_published: 2017-03-15T00:00:00Z
date_updated: 2021-01-12T08:22:13Z
day: '15'
department:
- _id: HaJa
doi: 10.1007/978-1-4939-6940-1_5
editor:
- first_name: Viktor
full_name: Stein, Viktor
last_name: Stein
intvolume: ' 1596'
language:
- iso: eng
month: '03'
oa_version: None
page: 71 - 87
project:
- _id: 255BFFFA-B435-11E9-9278-68D0E5697425
grant_number: RGY0084/2012
name: In situ real-time imaging of neurotransmitter signaling using designer optical
sensors (HFSP Young Investigator)
publication: Synthetic Protein Switches
publication_identifier:
issn:
- '10643745'
publication_status: published
publisher: Springer
publist_id: '6451'
quality_controlled: '1'
scopus_import: 1
series_title: Synthetic Protein Switches
status: public
title: Ancestral protein reconstruction and circular permutation for improving the
stability and dynamic range of FRET sensors
type: book_chapter
user_id: 4435EBFC-F248-11E8-B48F-1D18A9856A87
volume: 1596
year: '2017'
...
---
_id: '9574'
abstract:
- lang: eng
text: 'Consider the sum X(ξ)=∑ni=1aiξi, where a=(ai)ni=1 is a sequence of non-zero
reals and ξ=(ξi)ni=1 is a sequence of i.i.d. Rademacher random variables (that
is, Pr[ξi=1]=Pr[ξi=−1]=1/2). The classical Littlewood-Offord problem asks for
the best possible upper bound on the concentration probabilities Pr[X=x]. In this
paper we study a resilience version of the Littlewood-Offord problem: how many
of the ξi is an adversary typically allowed to change without being able to force
concentration on a particular value? We solve this problem asymptotically, and
present a few interesting open problems.'
article_processing_charge: No
article_type: original
author:
- first_name: Afonso S.
full_name: Bandeira, Afonso S.
last_name: Bandeira
- first_name: Asaf
full_name: Ferber, Asaf
last_name: Ferber
- first_name: Matthew Alan
full_name: Kwan, Matthew Alan
id: 5fca0887-a1db-11eb-95d1-ca9d5e0453b3
last_name: Kwan
orcid: 0000-0002-4003-7567
citation:
ama: Bandeira AS, Ferber A, Kwan MA. Resilience for the Littlewood-Offord problem.
Electronic Notes in Discrete Mathematics. 2017;61:93-99. doi:10.1016/j.endm.2017.06.025
apa: Bandeira, A. S., Ferber, A., & Kwan, M. A. (2017). Resilience for the Littlewood-Offord
problem. Electronic Notes in Discrete Mathematics. Elsevier. https://doi.org/10.1016/j.endm.2017.06.025
chicago: Bandeira, Afonso S., Asaf Ferber, and Matthew Alan Kwan. “Resilience for
the Littlewood-Offord Problem.” Electronic Notes in Discrete Mathematics.
Elsevier, 2017. https://doi.org/10.1016/j.endm.2017.06.025.
ieee: A. S. Bandeira, A. Ferber, and M. A. Kwan, “Resilience for the Littlewood-Offord
problem,” Electronic Notes in Discrete Mathematics, vol. 61. Elsevier,
pp. 93–99, 2017.
ista: Bandeira AS, Ferber A, Kwan MA. 2017. Resilience for the Littlewood-Offord
problem. Electronic Notes in Discrete Mathematics. 61, 93–99.
mla: Bandeira, Afonso S., et al. “Resilience for the Littlewood-Offord Problem.”
Electronic Notes in Discrete Mathematics, vol. 61, Elsevier, 2017, pp.
93–99, doi:10.1016/j.endm.2017.06.025.
short: A.S. Bandeira, A. Ferber, M.A. Kwan, Electronic Notes in Discrete Mathematics
61 (2017) 93–99.
date_created: 2021-06-21T06:31:10Z
date_published: 2017-08-01T00:00:00Z
date_updated: 2023-02-23T14:01:26Z
day: '01'
doi: 10.1016/j.endm.2017.06.025
extern: '1'
external_id:
arxiv:
- '1609.08136'
intvolume: ' 61'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/1609.08136
month: '08'
oa: 1
oa_version: Preprint
page: 93-99
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: Resilience for the Littlewood-Offord problem
type: journal_article
user_id: 6785fbc1-c503-11eb-8a32-93094b40e1cf
volume: 61
year: '2017'
...
---
_id: '9590'
abstract:
- lang: eng
text: We show that for any fixed dense graph G and bounded-degree tree T on the
same number of vertices, a modest random perturbation of G will typically contain
a copy of T . This combines the viewpoints of the well-studied problems of embedding
trees into fixed dense graphs and into random graphs, and extends a sizeable body
of existing research on randomly perturbed graphs. Specifically, we show that
there is c=c(α,Δ) such that if G is an n-vertex graph with minimum degree at least
αn, and T is an n-vertex tree with maximum degree at most Δ , then if we add cn
uniformly random edges to G, the resulting graph will contain T asymptotically
almost surely (as n→∞ ). Our proof uses a lemma concerning the decomposition of
a dense graph into super-regular pairs of comparable sizes, which may be of independent
interest.
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. Bounded-degree spanning trees in randomly
perturbed graphs. SIAM Journal on Discrete Mathematics. 2017;31(1):155-171.
doi:10.1137/15m1032910
apa: Krivelevich, M., Kwan, M. A., & Sudakov, B. (2017). Bounded-degree spanning
trees in randomly perturbed graphs. SIAM Journal on Discrete Mathematics.
Society for Industrial & Applied Mathematics. https://doi.org/10.1137/15m1032910
chicago: Krivelevich, Michael, Matthew Alan Kwan, and Benny Sudakov. “Bounded-Degree
Spanning Trees in Randomly Perturbed Graphs.” SIAM Journal on Discrete Mathematics.
Society for Industrial & Applied Mathematics, 2017. https://doi.org/10.1137/15m1032910.
ieee: M. Krivelevich, M. A. Kwan, and B. Sudakov, “Bounded-degree spanning trees
in randomly perturbed graphs,” SIAM Journal on Discrete Mathematics, vol.
31, no. 1. Society for Industrial & Applied Mathematics, pp. 155–171, 2017.
ista: Krivelevich M, Kwan MA, Sudakov B. 2017. Bounded-degree spanning trees in
randomly perturbed graphs. SIAM Journal on Discrete Mathematics. 31(1), 155–171.
mla: Krivelevich, Michael, et al. “Bounded-Degree Spanning Trees in Randomly Perturbed
Graphs.” SIAM Journal on Discrete Mathematics, vol. 31, no. 1, Society
for Industrial & Applied Mathematics, 2017, pp. 155–71, doi:10.1137/15m1032910.
short: M. Krivelevich, M.A. Kwan, B. Sudakov, SIAM Journal on Discrete Mathematics
31 (2017) 155–171.
date_created: 2021-06-22T12:26:25Z
date_published: 2017-01-12T00:00:00Z
date_updated: 2023-02-23T14:02:05Z
day: '12'
doi: 10.1137/15m1032910
extern: '1'
external_id:
arxiv:
- '1507.07960'
intvolume: ' 31'
issue: '1'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/1507.07960
month: '01'
oa: 1
oa_version: Preprint
page: 155-171
publication: SIAM Journal on Discrete Mathematics
publication_identifier:
eissn:
- 1095-7146
issn:
- 0895-4801
publication_status: published
publisher: Society for Industrial & Applied Mathematics
quality_controlled: '1'
scopus_import: '1'
status: public
title: Bounded-degree spanning trees in randomly perturbed graphs
type: journal_article
user_id: 6785fbc1-c503-11eb-8a32-93094b40e1cf
volume: 31
year: '2017'
...
---
_id: '9588'
abstract:
- lang: eng
text: 'Consider the sum X(ξ)=∑ni=1aiξi , where a=(ai)ni=1 is a sequence of non-zero
reals and ξ=(ξi)ni=1 is a sequence of i.i.d. Rademacher random variables (that
is, Pr[ξi=1]=Pr[ξi=−1]=1/2 ). The classical Littlewood-Offord problem asks for
the best possible upper bound on the concentration probabilities Pr[X=x] . In
this paper we study a resilience version of the Littlewood-Offord problem: how
many of the ξi is an adversary typically allowed to change without being able
to force concentration on a particular value? We solve this problem asymptotically,
and present a few interesting open problems.'
article_processing_charge: No
article_type: original
author:
- first_name: Afonso S.
full_name: Bandeira, Afonso S.
last_name: Bandeira
- first_name: Asaf
full_name: Ferber, Asaf
last_name: Ferber
- first_name: Matthew Alan
full_name: Kwan, Matthew Alan
id: 5fca0887-a1db-11eb-95d1-ca9d5e0453b3
last_name: Kwan
orcid: 0000-0002-4003-7567
citation:
ama: Bandeira AS, Ferber A, Kwan MA. Resilience for the Littlewood–Offord problem.
Advances in Mathematics. 2017;319:292-312. doi:10.1016/j.aim.2017.08.031
apa: Bandeira, A. S., Ferber, A., & Kwan, M. A. (2017). Resilience for the Littlewood–Offord
problem. Advances in Mathematics. Elsevier. https://doi.org/10.1016/j.aim.2017.08.031
chicago: Bandeira, Afonso S., Asaf Ferber, and Matthew Alan Kwan. “Resilience for
the Littlewood–Offord Problem.” Advances in Mathematics. Elsevier, 2017.
https://doi.org/10.1016/j.aim.2017.08.031.
ieee: A. S. Bandeira, A. Ferber, and M. A. Kwan, “Resilience for the Littlewood–Offord
problem,” Advances in Mathematics, vol. 319. Elsevier, pp. 292–312, 2017.
ista: Bandeira AS, Ferber A, Kwan MA. 2017. Resilience for the Littlewood–Offord
problem. Advances in Mathematics. 319, 292–312.
mla: Bandeira, Afonso S., et al. “Resilience for the Littlewood–Offord Problem.”
Advances in Mathematics, vol. 319, Elsevier, 2017, pp. 292–312, doi:10.1016/j.aim.2017.08.031.
short: A.S. Bandeira, A. Ferber, M.A. Kwan, Advances in Mathematics 319 (2017) 292–312.
date_created: 2021-06-22T11:51:27Z
date_published: 2017-10-15T00:00:00Z
date_updated: 2023-02-23T14:01:57Z
day: '15'
doi: 10.1016/j.aim.2017.08.031
extern: '1'
external_id:
arxiv:
- '1609.08136'
intvolume: ' 319'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/1609.08136
month: '10'
oa: 1
oa_version: Preprint
page: 292-312
publication: Advances in Mathematics
publication_identifier:
issn:
- 0001-8708
publication_status: published
publisher: Elsevier
quality_controlled: '1'
scopus_import: '1'
status: public
title: Resilience for the Littlewood–Offord problem
type: journal_article
user_id: 6785fbc1-c503-11eb-8a32-93094b40e1cf
volume: 319
year: '2017'
...
---
_id: '9589'
abstract:
- lang: eng
text: We give an asymptotic expression for the expected number of spanning trees
in a random graph with a given degree sequence , provided that the number of edges
is at least , where is the maximum degree. A key part of our argument involves
establishing a concentration result for a certain family of functions over random
trees with given degrees, using Prüfer codes.
article_processing_charge: No
article_type: original
author:
- first_name: Catherine
full_name: Greenhill, Catherine
last_name: Greenhill
- first_name: Mikhail
full_name: Isaev, Mikhail
last_name: Isaev
- 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: Brendan D.
full_name: McKay, Brendan D.
last_name: McKay
citation:
ama: Greenhill C, Isaev M, Kwan MA, McKay BD. The average number of spanning trees
in sparse graphs with given degrees. European Journal of Combinatorics.
2017;63:6-25. doi:10.1016/j.ejc.2017.02.003
apa: Greenhill, C., Isaev, M., Kwan, M. A., & McKay, B. D. (2017). The average
number of spanning trees in sparse graphs with given degrees. European Journal
of Combinatorics. Elsevier. https://doi.org/10.1016/j.ejc.2017.02.003
chicago: Greenhill, Catherine, Mikhail Isaev, Matthew Alan Kwan, and Brendan D.
McKay. “The Average Number of Spanning Trees in Sparse Graphs with given Degrees.”
European Journal of Combinatorics. Elsevier, 2017. https://doi.org/10.1016/j.ejc.2017.02.003.
ieee: C. Greenhill, M. Isaev, M. A. Kwan, and B. D. McKay, “The average number of
spanning trees in sparse graphs with given degrees,” European Journal of Combinatorics,
vol. 63. Elsevier, pp. 6–25, 2017.
ista: Greenhill C, Isaev M, Kwan MA, McKay BD. 2017. The average number of spanning
trees in sparse graphs with given degrees. European Journal of Combinatorics.
63, 6–25.
mla: Greenhill, Catherine, et al. “The Average Number of Spanning Trees in Sparse
Graphs with given Degrees.” European Journal of Combinatorics, vol. 63,
Elsevier, 2017, pp. 6–25, doi:10.1016/j.ejc.2017.02.003.
short: C. Greenhill, M. Isaev, M.A. Kwan, B.D. McKay, European Journal of Combinatorics
63 (2017) 6–25.
date_created: 2021-06-22T12:18:59Z
date_published: 2017-06-01T00:00:00Z
date_updated: 2023-02-23T14:02:00Z
day: '01'
doi: 10.1016/j.ejc.2017.02.003
extern: '1'
external_id:
arxiv:
- '1606.01586'
intvolume: ' 63'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.1016/j.ejc.2017.02.003
month: '06'
oa: 1
oa_version: Published Version
page: 6-25
publication: European Journal of Combinatorics
publication_identifier:
issn:
- 0195-6698
publication_status: published
publisher: Elsevier
quality_controlled: '1'
scopus_import: '1'
status: public
title: The average number of spanning trees in sparse graphs with given degrees
type: journal_article
user_id: 6785fbc1-c503-11eb-8a32-93094b40e1cf
volume: 63
year: '2017'
...
---
_id: '963'
abstract:
- lang: eng
text: 'Network games are widely used as a model for selfish resource-allocation
problems. In the classical model, each player selects a path connecting her source
and target vertex. The cost of traversing an edge depends on the number of players
that traverse it. Thus, it abstracts the fact that different users may use a resource
at different times and for different durations, which plays an important role
in defining the costs of the users in reality. For example, when transmitting
packets in a communication network, routing traffic in a road network, or processing
a task in a production system, the traversal of the network involves an inherent
delay, and so sharing and congestion of resources crucially depends on time. We
study timed network games , which add a time component to network games. Each
vertex v in the network is associated with a cost function, mapping the load on
v to the price that a player pays for staying in v for one time unit with this
load. In addition, each edge has a guard, describing time intervals in which the
edge can be traversed, forcing the players to spend time on vertices. Unlike earlier
work that add a time component to network games, the time in our model is continuous
and cannot be discretized. In particular, players have uncountably many strategies,
and a game may have uncountably many pure Nash equilibria. We study properties
of timed network games with cost-sharing or congestion cost functions: their stability,
equilibrium inefficiency, and complexity. In particular, we show that the answer
to the question whether we can restrict attention to boundary strategies, namely
ones in which edges are traversed only at the boundaries of guards, is mixed. '
alternative_title:
- LIPIcs
article_number: '37'
author:
- first_name: Guy
full_name: Avni, Guy
id: 463C8BC2-F248-11E8-B48F-1D18A9856A87
last_name: Avni
orcid: 0000-0001-5588-8287
- first_name: Shibashis
full_name: Guha, Shibashis
last_name: Guha
- first_name: Orna
full_name: Kupferman, Orna
last_name: Kupferman
citation:
ama: 'Avni G, Guha S, Kupferman O. Timed network games with clocks. In: Vol 83.
Schloss Dagstuhl - Leibniz-Zentrum für Informatik; 2017. doi:10.4230/LIPIcs.MFCS.2017.37'
apa: 'Avni, G., Guha, S., & Kupferman, O. (2017). Timed network games with clocks
(Vol. 83). Presented at the MFCS: Mathematical Foundations of Computer Science
(SG), Aalborg, Denmark: Schloss Dagstuhl - Leibniz-Zentrum für Informatik. https://doi.org/10.4230/LIPIcs.MFCS.2017.37'
chicago: Avni, Guy, Shibashis Guha, and Orna Kupferman. “Timed Network Games with
Clocks,” Vol. 83. Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2017. https://doi.org/10.4230/LIPIcs.MFCS.2017.37.
ieee: 'G. Avni, S. Guha, and O. Kupferman, “Timed network games with clocks,” presented
at the MFCS: Mathematical Foundations of Computer Science (SG), Aalborg, Denmark,
2017, vol. 83.'
ista: 'Avni G, Guha S, Kupferman O. 2017. Timed network games with clocks. MFCS:
Mathematical Foundations of Computer Science (SG), LIPIcs, vol. 83, 37.'
mla: Avni, Guy, et al. Timed Network Games with Clocks. Vol. 83, 37, Schloss
Dagstuhl - Leibniz-Zentrum für Informatik, 2017, doi:10.4230/LIPIcs.MFCS.2017.37.
short: G. Avni, S. Guha, O. Kupferman, in:, Schloss Dagstuhl - Leibniz-Zentrum für
Informatik, 2017.
conference:
end_date: 2017-08-25
location: Aalborg, Denmark
name: 'MFCS: Mathematical Foundations of Computer Science (SG)'
start_date: 2017-08-21
date_created: 2018-12-11T11:49:26Z
date_published: 2017-06-01T00:00:00Z
date_updated: 2023-02-23T12:35:50Z
day: '01'
ddc:
- '004'
department:
- _id: ToHe
doi: 10.4230/LIPIcs.MFCS.2017.37
file:
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checksum: f55eaf7f3c36ea07801112acfedd17d5
content_type: application/pdf
creator: system
date_created: 2018-12-12T10:14:10Z
date_updated: 2020-07-14T12:48:18Z
file_id: '5059'
file_name: IST-2017-829-v1+1_mfcs-cr.pdf
file_size: 369730
relation: main_file
file_date_updated: 2020-07-14T12:48:18Z
has_accepted_license: '1'
intvolume: ' 83'
language:
- iso: eng
month: '06'
oa: 1
oa_version: Published Version
project:
- _id: 25F5A88A-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: S11402-N23
name: Moderne Concurrency Paradigms
publication_identifier:
issn:
- '18688969'
publication_status: published
publisher: Schloss Dagstuhl - Leibniz-Zentrum für Informatik
publist_id: '6438'
pubrep_id: '829'
quality_controlled: '1'
related_material:
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relation: later_version
status: public
scopus_import: 1
status: public
title: Timed network games with clocks
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: conference
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 83
year: '2017'
...
---
_id: '9709'
abstract:
- lang: eng
text: Across the nervous system, certain population spiking patterns are observed
far more frequently than others. A hypothesis about this structure is that these
collective activity patterns function as population codewords–collective modes–carrying
information distinct from that of any single cell. We investigate this phenomenon
in recordings of ∼150 retinal ganglion cells, the retina’s output. We develop
a novel statistical model that decomposes the population response into modes;
it predicts the distribution of spiking activity in the ganglion cell population
with high accuracy. We found that the modes represent localized features of the
visual stimulus that are distinct from the features represented by single neurons.
Modes form clusters of activity states that are readily discriminated from one
another. When we repeated the same visual stimulus, we found that the same mode
was robustly elicited. These results suggest that retinal ganglion cells’ collective
signaling is endowed with a form of error-correcting code–a principle that may
hold in brain areas beyond retina.
article_processing_charge: No
author:
- first_name: Jason
full_name: Prentice, Jason
last_name: Prentice
- first_name: Olivier
full_name: Marre, Olivier
last_name: Marre
- first_name: Mark
full_name: Ioffe, Mark
last_name: Ioffe
- first_name: Adrianna
full_name: Loback, Adrianna
last_name: Loback
- first_name: Gašper
full_name: Tkačik, Gašper
id: 3D494DCA-F248-11E8-B48F-1D18A9856A87
last_name: Tkačik
orcid: 0000-0002-6699-1455
- first_name: Michael
full_name: Berry, Michael
last_name: Berry
citation:
ama: 'Prentice J, Marre O, Ioffe M, Loback A, Tkačik G, Berry M. Data from: Error-robust
modes of the retinal population code. 2017. doi:10.5061/dryad.1f1rc'
apa: 'Prentice, J., Marre, O., Ioffe, M., Loback, A., Tkačik, G., & Berry, M.
(2017). Data from: Error-robust modes of the retinal population code. Dryad. https://doi.org/10.5061/dryad.1f1rc'
chicago: 'Prentice, Jason, Olivier Marre, Mark Ioffe, Adrianna Loback, Gašper Tkačik,
and Michael Berry. “Data from: Error-Robust Modes of the Retinal Population Code.”
Dryad, 2017. https://doi.org/10.5061/dryad.1f1rc.'
ieee: 'J. Prentice, O. Marre, M. Ioffe, A. Loback, G. Tkačik, and M. Berry, “Data
from: Error-robust modes of the retinal population code.” Dryad, 2017.'
ista: 'Prentice J, Marre O, Ioffe M, Loback A, Tkačik G, Berry M. 2017. Data from:
Error-robust modes of the retinal population code, Dryad, 10.5061/dryad.1f1rc.'
mla: 'Prentice, Jason, et al. Data from: Error-Robust Modes of the Retinal Population
Code. Dryad, 2017, doi:10.5061/dryad.1f1rc.'
short: J. Prentice, O. Marre, M. Ioffe, A. Loback, G. Tkačik, M. Berry, (2017).
date_created: 2021-07-23T11:34:34Z
date_published: 2017-10-18T00:00:00Z
date_updated: 2023-02-21T16:34:41Z
day: '18'
department:
- _id: GaTk
doi: 10.5061/dryad.1f1rc
main_file_link:
- open_access: '1'
url: https://doi.org/10.5061/dryad.1f1rc
month: '10'
oa: 1
oa_version: Published Version
publisher: Dryad
related_material:
record:
- id: '1197'
relation: used_in_publication
status: public
status: public
title: 'Data from: Error-robust modes of the retinal population code'
type: research_data_reference
user_id: 6785fbc1-c503-11eb-8a32-93094b40e1cf
year: '2017'
...
---
_id: '541'
abstract:
- lang: eng
text: 'While we have good understanding of bacterial metabolism at the population
level, we know little about the metabolic behavior of individual cells: do single
cells in clonal populations sometimes specialize on different metabolic pathways?
Such metabolic specialization could be driven by stochastic gene expression and
could provide individual cells with growth benefits of specialization. We measured
the degree of phenotypic specialization in two parallel metabolic pathways, the
assimilation of glucose and arabinose. We grew Escherichia coli in chemostats,
and used isotope-labeled sugars in combination with nanometer-scale secondary
ion mass spectrometry and mathematical modeling to quantify sugar assimilation
at the single-cell level. We found large variation in metabolic activities between
single cells, both in absolute assimilation and in the degree to which individual
cells specialize in the assimilation of different sugars. Analysis of transcriptional
reporters indicated that this variation was at least partially based on cell-to-cell
variation in gene expression. Metabolic differences between cells in clonal populations
could potentially reduce metabolic incompatibilities between different pathways,
and increase the rate at which parallel reactions can be performed.'
article_number: e1007122
author:
- first_name: Nela
full_name: Nikolic, Nela
id: 42D9CABC-F248-11E8-B48F-1D18A9856A87
last_name: Nikolic
orcid: 0000-0001-9068-6090
- first_name: Frank
full_name: Schreiber, Frank
last_name: Schreiber
- first_name: Alma
full_name: Dal Co, Alma
last_name: Dal Co
- first_name: Daniel
full_name: Kiviet, Daniel
last_name: Kiviet
- first_name: Tobias
full_name: Bergmiller, Tobias
id: 2C471CFA-F248-11E8-B48F-1D18A9856A87
last_name: Bergmiller
orcid: 0000-0001-5396-4346
- first_name: Sten
full_name: Littmann, Sten
last_name: Littmann
- first_name: Marcel
full_name: Kuypers, Marcel
last_name: Kuypers
- first_name: Martin
full_name: Ackermann, Martin
last_name: Ackermann
citation:
ama: Nikolic N, Schreiber F, Dal Co A, et al. Cell-to-cell variation and specialization
in sugar metabolism in clonal bacterial populations. PLoS Genetics. 2017;13(12).
doi:10.1371/journal.pgen.1007122
apa: Nikolic, N., Schreiber, F., Dal Co, A., Kiviet, D., Bergmiller, T., Littmann,
S., … Ackermann, M. (2017). Cell-to-cell variation and specialization in sugar
metabolism in clonal bacterial populations. PLoS Genetics. Public Library
of Science. https://doi.org/10.1371/journal.pgen.1007122
chicago: Nikolic, Nela, Frank Schreiber, Alma Dal Co, Daniel Kiviet, Tobias Bergmiller,
Sten Littmann, Marcel Kuypers, and Martin Ackermann. “Cell-to-Cell Variation and
Specialization in Sugar Metabolism in Clonal Bacterial Populations.” PLoS Genetics.
Public Library of Science, 2017. https://doi.org/10.1371/journal.pgen.1007122.
ieee: N. Nikolic et al., “Cell-to-cell variation and specialization in sugar
metabolism in clonal bacterial populations,” PLoS Genetics, vol. 13, no.
12. Public Library of Science, 2017.
ista: Nikolic N, Schreiber F, Dal Co A, Kiviet D, Bergmiller T, Littmann S, Kuypers
M, Ackermann M. 2017. Cell-to-cell variation and specialization in sugar metabolism
in clonal bacterial populations. PLoS Genetics. 13(12), e1007122.
mla: Nikolic, Nela, et al. “Cell-to-Cell Variation and Specialization in Sugar Metabolism
in Clonal Bacterial Populations.” PLoS Genetics, vol. 13, no. 12, e1007122,
Public Library of Science, 2017, doi:10.1371/journal.pgen.1007122.
short: N. Nikolic, F. Schreiber, A. Dal Co, D. Kiviet, T. Bergmiller, S. Littmann,
M. Kuypers, M. Ackermann, PLoS Genetics 13 (2017).
date_created: 2018-12-11T11:47:04Z
date_published: 2017-12-18T00:00:00Z
date_updated: 2023-02-23T14:10:34Z
day: '18'
ddc:
- '576'
- '579'
department:
- _id: CaGu
doi: 10.1371/journal.pgen.1007122
ec_funded: 1
file:
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checksum: 22426d9382f21554bad5fa5967afcfd0
content_type: application/pdf
creator: system
date_created: 2018-12-12T10:14:35Z
date_updated: 2020-07-14T12:46:46Z
file_id: '5088'
file_name: IST-2018-959-v1+1_2017_Nikolic_Cell-to-cell.pdf
file_size: 1308475
relation: main_file
file_date_updated: 2020-07-14T12:46:46Z
has_accepted_license: '1'
intvolume: ' 13'
issue: '12'
language:
- iso: eng
month: '12'
oa: 1
oa_version: Published Version
project:
- _id: 25681D80-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '291734'
name: International IST Postdoc Fellowship Programme
publication: PLoS Genetics
publication_identifier:
issn:
- '15537390'
publication_status: published
publisher: Public Library of Science
publist_id: '7275'
pubrep_id: '959'
quality_controlled: '1'
related_material:
record:
- id: '9844'
relation: research_data
status: public
- id: '9845'
relation: research_data
status: public
- id: '9846'
relation: research_data
status: public
scopus_import: 1
status: public
title: Cell-to-cell variation and specialization in sugar metabolism in clonal bacterial
populations
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 13
year: '2017'
...
---
_id: '9847'
abstract:
- lang: eng
text: information on culture conditions, phage mutagenesis, verification and lysate
preparation; Raw data
article_processing_charge: No
author:
- first_name: Maros
full_name: Pleska, Maros
id: 4569785E-F248-11E8-B48F-1D18A9856A87
last_name: Pleska
orcid: 0000-0001-7460-7479
- first_name: Calin C
full_name: Guet, Calin C
id: 47F8433E-F248-11E8-B48F-1D18A9856A87
last_name: Guet
orcid: 0000-0001-6220-2052
citation:
ama: Pleska M, Guet CC. Supplementary materials and methods; Full data set from
effects of mutations in phage restriction sites during escape from restriction–modification.
2017. doi:10.6084/m9.figshare.5633917.v1
apa: Pleska, M., & Guet, C. C. (2017). Supplementary materials and methods;
Full data set from effects of mutations in phage restriction sites during escape
from restriction–modification. The Royal Society. https://doi.org/10.6084/m9.figshare.5633917.v1
chicago: Pleska, Maros, and Calin C Guet. “Supplementary Materials and Methods;
Full Data Set from Effects of Mutations in Phage Restriction Sites during Escape
from Restriction–Modification.” The Royal Society, 2017. https://doi.org/10.6084/m9.figshare.5633917.v1.
ieee: M. Pleska and C. C. Guet, “Supplementary materials and methods; Full data
set from effects of mutations in phage restriction sites during escape from restriction–modification.”
The Royal Society, 2017.
ista: Pleska M, Guet CC. 2017. Supplementary materials and methods; Full data set
from effects of mutations in phage restriction sites during escape from restriction–modification,
The Royal Society, 10.6084/m9.figshare.5633917.v1.
mla: Pleska, Maros, and Calin C. Guet. Supplementary Materials and Methods; Full
Data Set from Effects of Mutations in Phage Restriction Sites during Escape from
Restriction–Modification. The Royal Society, 2017, doi:10.6084/m9.figshare.5633917.v1.
short: M. Pleska, C.C. Guet, (2017).
date_created: 2021-08-09T13:54:38Z
date_published: 2017-11-27T00:00:00Z
date_updated: 2023-02-23T12:29:44Z
day: '27'
department:
- _id: CaGu
doi: 10.6084/m9.figshare.5633917.v1
main_file_link:
- open_access: '1'
url: https://doi.org/10.6084/m9.figshare.5633917.v1
month: '11'
oa: 1
oa_version: Published Version
publisher: The Royal Society
related_material:
record:
- id: '561'
relation: used_in_publication
status: public
status: public
title: Supplementary materials and methods; Full data set from effects of mutations
in phage restriction sites during escape from restriction–modification
type: research_data_reference
user_id: 6785fbc1-c503-11eb-8a32-93094b40e1cf
year: '2017'
...
---
_id: '9845'
abstract:
- lang: eng
text: "Estimates of 13 C-arabinose and 2 H-glucose uptake from the fractions of
heavy isotopes measured\tin single cells"
article_processing_charge: No
author:
- first_name: Nela
full_name: Nikolic, Nela
id: 42D9CABC-F248-11E8-B48F-1D18A9856A87
last_name: Nikolic
orcid: 0000-0001-9068-6090
- first_name: Frank
full_name: Schreiber, Frank
last_name: Schreiber
- first_name: Alma
full_name: Dal Co, Alma
last_name: Dal Co
- first_name: Daniel
full_name: Kiviet, Daniel
last_name: Kiviet
- first_name: Tobias
full_name: Bergmiller, Tobias
id: 2C471CFA-F248-11E8-B48F-1D18A9856A87
last_name: Bergmiller
orcid: 0000-0001-5396-4346
- first_name: Sten
full_name: Littmann, Sten
last_name: Littmann
- first_name: Marcel
full_name: Kuypers, Marcel
last_name: Kuypers
- first_name: Martin
full_name: Ackermann, Martin
last_name: Ackermann
citation:
ama: Nikolic N, Schreiber F, Dal Co A, et al. Mathematical model. 2017. doi:10.1371/journal.pgen.1007122.s017
apa: Nikolic, N., Schreiber, F., Dal Co, A., Kiviet, D., Bergmiller, T., Littmann,
S., … Ackermann, M. (2017). Mathematical model. Public Library of Science. https://doi.org/10.1371/journal.pgen.1007122.s017
chicago: Nikolic, Nela, Frank Schreiber, Alma Dal Co, Daniel Kiviet, Tobias Bergmiller,
Sten Littmann, Marcel Kuypers, and Martin Ackermann. “Mathematical Model.” Public
Library of Science, 2017. https://doi.org/10.1371/journal.pgen.1007122.s017.
ieee: N. Nikolic et al., “Mathematical model.” Public Library of Science,
2017.
ista: Nikolic N, Schreiber F, Dal Co A, Kiviet D, Bergmiller T, Littmann S, Kuypers
M, Ackermann M. 2017. Mathematical model, Public Library of Science, 10.1371/journal.pgen.1007122.s017.
mla: Nikolic, Nela, et al. Mathematical Model. Public Library of Science,
2017, doi:10.1371/journal.pgen.1007122.s017.
short: N. Nikolic, F. Schreiber, A. Dal Co, D. Kiviet, T. Bergmiller, S. Littmann,
M. Kuypers, M. Ackermann, (2017).
date_created: 2021-08-09T13:31:51Z
date_published: 2017-12-18T00:00:00Z
date_updated: 2023-02-23T12:25:04Z
day: '18'
department:
- _id: CaGu
doi: 10.1371/journal.pgen.1007122.s017
month: '12'
oa_version: None
publisher: Public Library of Science
related_material:
record:
- id: '541'
relation: used_in_publication
status: public
status: public
title: Mathematical model
type: research_data_reference
user_id: 6785fbc1-c503-11eb-8a32-93094b40e1cf
year: '2017'
...
---
_id: '9849'
abstract:
- lang: eng
text: This text provides additional information about the model, a derivation of
the analytic results in Eq (4), and details about simulations of an additional
parameter set.
article_processing_charge: No
author:
- first_name: Marta
full_name: Lukacisinova, Marta
id: 4342E402-F248-11E8-B48F-1D18A9856A87
last_name: Lukacisinova
orcid: 0000-0002-2519-8004
- first_name: Sebastian
full_name: Novak, Sebastian
id: 461468AE-F248-11E8-B48F-1D18A9856A87
last_name: Novak
- first_name: Tiago
full_name: Paixao, Tiago
id: 2C5658E6-F248-11E8-B48F-1D18A9856A87
last_name: Paixao
orcid: 0000-0003-2361-3953
citation:
ama: Lukacisinova M, Novak S, Paixao T. Modelling and simulation details. 2017.
doi:10.1371/journal.pcbi.1005609.s001
apa: Lukacisinova, M., Novak, S., & Paixao, T. (2017). Modelling and simulation
details. Public Library of Science. https://doi.org/10.1371/journal.pcbi.1005609.s001
chicago: Lukacisinova, Marta, Sebastian Novak, and Tiago Paixao. “Modelling and
Simulation Details.” Public Library of Science, 2017. https://doi.org/10.1371/journal.pcbi.1005609.s001.
ieee: M. Lukacisinova, S. Novak, and T. Paixao, “Modelling and simulation details.”
Public Library of Science, 2017.
ista: Lukacisinova M, Novak S, Paixao T. 2017. Modelling and simulation details,
Public Library of Science, 10.1371/journal.pcbi.1005609.s001.
mla: Lukacisinova, Marta, et al. Modelling and Simulation Details. Public
Library of Science, 2017, doi:10.1371/journal.pcbi.1005609.s001.
short: M. Lukacisinova, S. Novak, T. Paixao, (2017).
date_created: 2021-08-09T14:02:34Z
date_published: 2017-07-18T00:00:00Z
date_updated: 2023-02-23T12:55:39Z
day: '18'
department:
- _id: ToBo
- _id: NiBa
- _id: CaGu
doi: 10.1371/journal.pcbi.1005609.s001
month: '07'
oa_version: Published Version
publisher: Public Library of Science
related_material:
record:
- id: '696'
relation: used_in_publication
status: public
status: public
title: Modelling and simulation details
type: research_data_reference
user_id: 6785fbc1-c503-11eb-8a32-93094b40e1cf
year: '2017'
...
---
_id: '9850'
abstract:
- lang: eng
text: In this text, we discuss how a cost of resistance and the possibility of lethal
mutations impact our model.
article_processing_charge: No
author:
- first_name: Marta
full_name: Lukacisinova, Marta
id: 4342E402-F248-11E8-B48F-1D18A9856A87
last_name: Lukacisinova
orcid: 0000-0002-2519-8004
- first_name: Sebastian
full_name: Novak, Sebastian
id: 461468AE-F248-11E8-B48F-1D18A9856A87
last_name: Novak
- first_name: Tiago
full_name: Paixao, Tiago
id: 2C5658E6-F248-11E8-B48F-1D18A9856A87
last_name: Paixao
orcid: 0000-0003-2361-3953
citation:
ama: Lukacisinova M, Novak S, Paixao T. Extensions of the model. 2017. doi:10.1371/journal.pcbi.1005609.s002
apa: Lukacisinova, M., Novak, S., & Paixao, T. (2017). Extensions of the model.
Public Library of Science. https://doi.org/10.1371/journal.pcbi.1005609.s002
chicago: Lukacisinova, Marta, Sebastian Novak, and Tiago Paixao. “Extensions of
the Model.” Public Library of Science, 2017. https://doi.org/10.1371/journal.pcbi.1005609.s002.
ieee: M. Lukacisinova, S. Novak, and T. Paixao, “Extensions of the model.” Public
Library of Science, 2017.
ista: Lukacisinova M, Novak S, Paixao T. 2017. Extensions of the model, Public Library
of Science, 10.1371/journal.pcbi.1005609.s002.
mla: Lukacisinova, Marta, et al. Extensions of the Model. Public Library
of Science, 2017, doi:10.1371/journal.pcbi.1005609.s002.
short: M. Lukacisinova, S. Novak, T. Paixao, (2017).
date_created: 2021-08-09T14:05:24Z
date_published: 2017-07-18T00:00:00Z
date_updated: 2023-02-23T12:55:39Z
day: '18'
department:
- _id: ToBo
- _id: CaGu
- _id: NiBa
doi: 10.1371/journal.pcbi.1005609.s002
month: '07'
oa_version: Published Version
publisher: Public Library of Science
related_material:
record:
- id: '696'
relation: used_in_publication
status: public
status: public
title: Extensions of the model
type: research_data_reference
user_id: 6785fbc1-c503-11eb-8a32-93094b40e1cf
year: '2017'
...
---
_id: '9846'
article_processing_charge: No
author:
- first_name: Nela
full_name: Nikolic, Nela
id: 42D9CABC-F248-11E8-B48F-1D18A9856A87
last_name: Nikolic
orcid: 0000-0001-9068-6090
- first_name: Frank
full_name: Schreiber, Frank
last_name: Schreiber
- first_name: Alma
full_name: Dal Co, Alma
last_name: Dal Co
- first_name: Daniel
full_name: Kiviet, Daniel
last_name: Kiviet
- first_name: Tobias
full_name: Bergmiller, Tobias
id: 2C471CFA-F248-11E8-B48F-1D18A9856A87
last_name: Bergmiller
orcid: 0000-0001-5396-4346
- first_name: Sten
full_name: Littmann, Sten
last_name: Littmann
- first_name: Marcel
full_name: Kuypers, Marcel
last_name: Kuypers
- first_name: Martin
full_name: Ackermann, Martin
last_name: Ackermann
citation:
ama: Nikolic N, Schreiber F, Dal Co A, et al. Supplementary methods. 2017. doi:10.1371/journal.pgen.1007122.s016
apa: Nikolic, N., Schreiber, F., Dal Co, A., Kiviet, D., Bergmiller, T., Littmann,
S., … Ackermann, M. (2017). Supplementary methods. Public Library of Science.
https://doi.org/10.1371/journal.pgen.1007122.s016
chicago: Nikolic, Nela, Frank Schreiber, Alma Dal Co, Daniel Kiviet, Tobias Bergmiller,
Sten Littmann, Marcel Kuypers, and Martin Ackermann. “Supplementary Methods.”
Public Library of Science, 2017. https://doi.org/10.1371/journal.pgen.1007122.s016.
ieee: N. Nikolic et al., “Supplementary methods.” Public Library of Science,
2017.
ista: Nikolic N, Schreiber F, Dal Co A, Kiviet D, Bergmiller T, Littmann S, Kuypers
M, Ackermann M. 2017. Supplementary methods, Public Library of Science, 10.1371/journal.pgen.1007122.s016.
mla: Nikolic, Nela, et al. Supplementary Methods. Public Library of Science,
2017, doi:10.1371/journal.pgen.1007122.s016.
short: N. Nikolic, F. Schreiber, A. Dal Co, D. Kiviet, T. Bergmiller, S. Littmann,
M. Kuypers, M. Ackermann, (2017).
date_created: 2021-08-09T13:35:17Z
date_published: 2017-12-18T00:00:00Z
date_updated: 2023-02-23T12:25:04Z
day: '18'
department:
- _id: CaGu
doi: 10.1371/journal.pgen.1007122.s016
month: '12'
oa_version: Published Version
publisher: Public Library of Science
related_material:
record:
- id: '541'
relation: used_in_publication
status: public
status: public
title: Supplementary methods
type: research_data_reference
user_id: 6785fbc1-c503-11eb-8a32-93094b40e1cf
year: '2017'
...
---
_id: '680'
abstract:
- lang: eng
text: In order to respond reliably to specific features of their environment, sensory
neurons need to integrate multiple incoming noisy signals. Crucially, they also
need to compete for the interpretation of those signals with other neurons representing
similar features. The form that this competition should take depends critically
on the noise corrupting these signals. In this study we show that for the type
of noise commonly observed in sensory systems, whose variance scales with the
mean signal, sensory neurons should selectively divide their input signals by
their predictions, suppressing ambiguous cues while amplifying others. Any change
in the stimulus context alters which inputs are suppressed, leading to a deep
dynamic reshaping of neural receptive fields going far beyond simple surround
suppression. Paradoxically, these highly variable receptive fields go alongside
and are in fact required for an invariant representation of external sensory features.
In addition to offering a normative account of context-dependent changes in sensory
responses, perceptual inference in the presence of signal-dependent noise accounts
for ubiquitous features of sensory neurons such as divisive normalization, gain
control and contrast dependent temporal dynamics.
article_number: e1005582
author:
- first_name: Matthew J
full_name: Chalk, Matthew J
id: 2BAAC544-F248-11E8-B48F-1D18A9856A87
last_name: Chalk
orcid: 0000-0001-7782-4436
- first_name: Paul
full_name: Masset, Paul
last_name: Masset
- first_name: Boris
full_name: Gutkin, Boris
last_name: Gutkin
- first_name: Sophie
full_name: Denève, Sophie
last_name: Denève
citation:
ama: Chalk MJ, Masset P, Gutkin B, Denève S. Sensory noise predicts divisive reshaping
of receptive fields. PLoS Computational Biology. 2017;13(6). doi:10.1371/journal.pcbi.1005582
apa: Chalk, M. J., Masset, P., Gutkin, B., & Denève, S. (2017). Sensory noise
predicts divisive reshaping of receptive fields. PLoS Computational Biology.
Public Library of Science. https://doi.org/10.1371/journal.pcbi.1005582
chicago: Chalk, Matthew J, Paul Masset, Boris Gutkin, and Sophie Denève. “Sensory
Noise Predicts Divisive Reshaping of Receptive Fields.” PLoS Computational
Biology. Public Library of Science, 2017. https://doi.org/10.1371/journal.pcbi.1005582.
ieee: M. J. Chalk, P. Masset, B. Gutkin, and S. Denève, “Sensory noise predicts
divisive reshaping of receptive fields,” PLoS Computational Biology, vol.
13, no. 6. Public Library of Science, 2017.
ista: Chalk MJ, Masset P, Gutkin B, Denève S. 2017. Sensory noise predicts divisive
reshaping of receptive fields. PLoS Computational Biology. 13(6), e1005582.
mla: Chalk, Matthew J., et al. “Sensory Noise Predicts Divisive Reshaping of Receptive
Fields.” PLoS Computational Biology, vol. 13, no. 6, e1005582, Public Library
of Science, 2017, doi:10.1371/journal.pcbi.1005582.
short: M.J. Chalk, P. Masset, B. Gutkin, S. Denève, PLoS Computational Biology 13
(2017).
date_created: 2018-12-11T11:47:53Z
date_published: 2017-06-01T00:00:00Z
date_updated: 2023-02-23T14:10:54Z
day: '01'
ddc:
- '571'
department:
- _id: GaTk
doi: 10.1371/journal.pcbi.1005582
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file_date_updated: 2020-07-14T12:47:40Z
has_accepted_license: '1'
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issue: '6'
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month: '06'
oa: 1
oa_version: Published Version
publication: PLoS Computational Biology
publication_identifier:
issn:
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publisher: Public Library of Science
publist_id: '7035'
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related_material:
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relation: research_data
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status: public
title: Sensory noise predicts divisive reshaping of receptive fields
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 13
year: '2017'
...
---
_id: '9851'
abstract:
- lang: eng
text: Based on the intuitive derivation of the dynamics of SIM allele frequency
pM in the main text, we present a heuristic prediction for the long-term SIM allele
frequencies with χ > 1 stresses and compare it to numerical simulations.
article_processing_charge: No
author:
- first_name: Marta
full_name: Lukacisinova, Marta
id: 4342E402-F248-11E8-B48F-1D18A9856A87
last_name: Lukacisinova
orcid: 0000-0002-2519-8004
- first_name: Sebastian
full_name: Novak, Sebastian
id: 461468AE-F248-11E8-B48F-1D18A9856A87
last_name: Novak
- first_name: Tiago
full_name: Paixao, Tiago
id: 2C5658E6-F248-11E8-B48F-1D18A9856A87
last_name: Paixao
orcid: 0000-0003-2361-3953
citation:
ama: Lukacisinova M, Novak S, Paixao T. Heuristic prediction for multiple stresses.
2017. doi:10.1371/journal.pcbi.1005609.s003
apa: Lukacisinova, M., Novak, S., & Paixao, T. (2017). Heuristic prediction
for multiple stresses. Public Library of Science. https://doi.org/10.1371/journal.pcbi.1005609.s003
chicago: Lukacisinova, Marta, Sebastian Novak, and Tiago Paixao. “Heuristic Prediction
for Multiple Stresses.” Public Library of Science, 2017. https://doi.org/10.1371/journal.pcbi.1005609.s003.
ieee: M. Lukacisinova, S. Novak, and T. Paixao, “Heuristic prediction for multiple
stresses.” Public Library of Science, 2017.
ista: Lukacisinova M, Novak S, Paixao T. 2017. Heuristic prediction for multiple
stresses, Public Library of Science, 10.1371/journal.pcbi.1005609.s003.
mla: Lukacisinova, Marta, et al. Heuristic Prediction for Multiple Stresses.
Public Library of Science, 2017, doi:10.1371/journal.pcbi.1005609.s003.
short: M. Lukacisinova, S. Novak, T. Paixao, (2017).
date_created: 2021-08-09T14:08:14Z
date_published: 2017-07-18T00:00:00Z
date_updated: 2023-02-23T12:55:39Z
day: '18'
department:
- _id: ToBo
- _id: CaGu
- _id: NiBa
doi: 10.1371/journal.pcbi.1005609.s003
month: '07'
oa_version: Published Version
publisher: Public Library of Science
related_material:
record:
- id: '696'
relation: used_in_publication
status: public
status: public
title: Heuristic prediction for multiple stresses
type: research_data_reference
user_id: 6785fbc1-c503-11eb-8a32-93094b40e1cf
year: '2017'
...
---
_id: '9852'
abstract:
- lang: eng
text: We show how different combination strategies affect the fraction of individuals
that are multi-resistant.
article_processing_charge: No
author:
- first_name: Marta
full_name: Lukacisinova, Marta
id: 4342E402-F248-11E8-B48F-1D18A9856A87
last_name: Lukacisinova
orcid: 0000-0002-2519-8004
- first_name: Sebastian
full_name: Novak, Sebastian
id: 461468AE-F248-11E8-B48F-1D18A9856A87
last_name: Novak
- first_name: Tiago
full_name: Paixao, Tiago
id: 2C5658E6-F248-11E8-B48F-1D18A9856A87
last_name: Paixao
orcid: 0000-0003-2361-3953
citation:
ama: Lukacisinova M, Novak S, Paixao T. Resistance frequencies for different combination
strategies. 2017. doi:10.1371/journal.pcbi.1005609.s004
apa: Lukacisinova, M., Novak, S., & Paixao, T. (2017). Resistance frequencies
for different combination strategies. Public Library of Science. https://doi.org/10.1371/journal.pcbi.1005609.s004
chicago: Lukacisinova, Marta, Sebastian Novak, and Tiago Paixao. “Resistance Frequencies
for Different Combination Strategies.” Public Library of Science, 2017. https://doi.org/10.1371/journal.pcbi.1005609.s004.
ieee: M. Lukacisinova, S. Novak, and T. Paixao, “Resistance frequencies for different
combination strategies.” Public Library of Science, 2017.
ista: Lukacisinova M, Novak S, Paixao T. 2017. Resistance frequencies for different
combination strategies, Public Library of Science, 10.1371/journal.pcbi.1005609.s004.
mla: Lukacisinova, Marta, et al. Resistance Frequencies for Different Combination
Strategies. Public Library of Science, 2017, doi:10.1371/journal.pcbi.1005609.s004.
short: M. Lukacisinova, S. Novak, T. Paixao, (2017).
date_created: 2021-08-09T14:11:40Z
date_published: 2017-07-18T00:00:00Z
date_updated: 2023-02-23T12:55:39Z
day: '18'
department:
- _id: ToBo
- _id: CaGu
- _id: NiBa
doi: 10.1371/journal.pcbi.1005609.s004
month: '07'
oa_version: Published Version
publisher: Public Library of Science
related_material:
record:
- id: '696'
relation: used_in_publication
status: public
status: public
title: Resistance frequencies for different combination strategies
type: research_data_reference
user_id: 6785fbc1-c503-11eb-8a32-93094b40e1cf
year: '2017'
...
---
_id: '9855'
abstract:
- lang: eng
text: Includes derivation of optimal estimation algorithm, generalisation to non-poisson
noise statistics, correlated input noise, and implementation of in a multi-layer
neural network.
article_processing_charge: No
author:
- first_name: Matthew J
full_name: Chalk, Matthew J
id: 2BAAC544-F248-11E8-B48F-1D18A9856A87
last_name: Chalk
orcid: 0000-0001-7782-4436
- first_name: Paul
full_name: Masset, Paul
last_name: Masset
- first_name: Boris
full_name: Gutkin, Boris
last_name: Gutkin
- first_name: Sophie
full_name: Denève, Sophie
last_name: Denève
citation:
ama: Chalk MJ, Masset P, Gutkin B, Denève S. Supplementary appendix. 2017. doi:10.1371/journal.pcbi.1005582.s001
apa: Chalk, M. J., Masset, P., Gutkin, B., & Denève, S. (2017). Supplementary
appendix. Public Library of Science. https://doi.org/10.1371/journal.pcbi.1005582.s001
chicago: Chalk, Matthew J, Paul Masset, Boris Gutkin, and Sophie Denève. “Supplementary
Appendix.” Public Library of Science, 2017. https://doi.org/10.1371/journal.pcbi.1005582.s001.
ieee: M. J. Chalk, P. Masset, B. Gutkin, and S. Denève, “Supplementary appendix.”
Public Library of Science, 2017.
ista: Chalk MJ, Masset P, Gutkin B, Denève S. 2017. Supplementary appendix, Public
Library of Science, 10.1371/journal.pcbi.1005582.s001.
mla: Chalk, Matthew J., et al. Supplementary Appendix. Public Library of
Science, 2017, doi:10.1371/journal.pcbi.1005582.s001.
short: M.J. Chalk, P. Masset, B. Gutkin, S. Denève, (2017).
date_created: 2021-08-10T07:05:10Z
date_published: 2017-06-01T00:00:00Z
date_updated: 2023-02-23T12:52:17Z
day: '01'
department:
- _id: GaTk
doi: 10.1371/journal.pcbi.1005582.s001
month: '06'
oa_version: Published Version
publisher: Public Library of Science
related_material:
record:
- id: '680'
relation: used_in_publication
status: public
status: public
title: Supplementary appendix
type: research_data_reference
user_id: 6785fbc1-c503-11eb-8a32-93094b40e1cf
year: '2017'
...
---
_id: '8423'
abstract:
- lang: eng
text: In this paper we show that for a generic strictly convex domain, one can recover
the eigendata corresponding to Aubry–Mather periodic orbits of the induced billiard
map from the (maximal) marked length spectrum of the domain.
article_processing_charge: No
article_type: original
author:
- first_name: Guan
full_name: Huang, Guan
last_name: Huang
- first_name: Vadim
full_name: Kaloshin, Vadim
id: FE553552-CDE8-11E9-B324-C0EBE5697425
last_name: Kaloshin
orcid: 0000-0002-6051-2628
- first_name: Alfonso
full_name: Sorrentino, Alfonso
last_name: Sorrentino
citation:
ama: Huang G, Kaloshin V, Sorrentino A. On the marked length spectrum of generic
strictly convex billiard tables. Duke Mathematical Journal. 2017;167(1):175-209.
doi:10.1215/00127094-2017-0038
apa: Huang, G., Kaloshin, V., & Sorrentino, A. (2017). On the marked length
spectrum of generic strictly convex billiard tables. Duke Mathematical Journal.
Duke University Press. https://doi.org/10.1215/00127094-2017-0038
chicago: Huang, Guan, Vadim Kaloshin, and Alfonso Sorrentino. “On the Marked Length
Spectrum of Generic Strictly Convex Billiard Tables.” Duke Mathematical Journal.
Duke University Press, 2017. https://doi.org/10.1215/00127094-2017-0038.
ieee: G. Huang, V. Kaloshin, and A. Sorrentino, “On the marked length spectrum of
generic strictly convex billiard tables,” Duke Mathematical Journal, vol.
167, no. 1. Duke University Press, pp. 175–209, 2017.
ista: Huang G, Kaloshin V, Sorrentino A. 2017. On the marked length spectrum of
generic strictly convex billiard tables. Duke Mathematical Journal. 167(1), 175–209.
mla: Huang, Guan, et al. “On the Marked Length Spectrum of Generic Strictly Convex
Billiard Tables.” Duke Mathematical Journal, vol. 167, no. 1, Duke University
Press, 2017, pp. 175–209, doi:10.1215/00127094-2017-0038.
short: G. Huang, V. Kaloshin, A. Sorrentino, Duke Mathematical Journal 167 (2017)
175–209.
date_created: 2020-09-17T10:42:42Z
date_published: 2017-12-08T00:00:00Z
date_updated: 2021-01-12T08:19:11Z
day: '08'
doi: 10.1215/00127094-2017-0038
extern: '1'
external_id:
arxiv:
- '1603.08838'
intvolume: ' 167'
issue: '1'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/1603.08838
month: '12'
oa: 1
oa_version: Preprint
page: 175-209
publication: Duke Mathematical Journal
publication_identifier:
issn:
- 0012-7094
publication_status: published
publisher: Duke University Press
quality_controlled: '1'
status: public
title: On the marked length spectrum of generic strictly convex billiard tables
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 167
year: '2017'
...
---
_id: '8427'
abstract:
- lang: eng
text: We show that any sufficiently (finitely) smooth ℤ₂-symmetric strictly convex
domain sufficiently close to a circle is dynamically spectrally rigid; i.e., all
deformations among domains in the same class that preserve the length of all periodic
orbits of the associated billiard flow must necessarily be isometric deformations.
This gives a partial answer to a question of P. Sarnak.
article_processing_charge: No
article_type: original
author:
- first_name: Jacopo
full_name: De Simoi, Jacopo
last_name: De Simoi
- first_name: Vadim
full_name: Kaloshin, Vadim
id: FE553552-CDE8-11E9-B324-C0EBE5697425
last_name: Kaloshin
orcid: 0000-0002-6051-2628
- first_name: Qiaoling
full_name: Wei, Qiaoling
last_name: Wei
citation:
ama: De Simoi J, Kaloshin V, Wei Q. Dynamical spectral rigidity among Z2-symmetric
strictly convex domains close to a circle. Annals of Mathematics. 2017;186(1):277-314.
doi:10.4007/annals.2017.186.1.7
apa: De Simoi, J., Kaloshin, V., & Wei, Q. (2017). Dynamical spectral rigidity
among Z2-symmetric strictly convex domains close to a circle. Annals of Mathematics.
Annals of Mathematics. https://doi.org/10.4007/annals.2017.186.1.7
chicago: De Simoi, Jacopo, Vadim Kaloshin, and Qiaoling Wei. “Dynamical Spectral
Rigidity among Z2-Symmetric Strictly Convex Domains Close to a Circle.” Annals
of Mathematics. Annals of Mathematics, 2017. https://doi.org/10.4007/annals.2017.186.1.7.
ieee: J. De Simoi, V. Kaloshin, and Q. Wei, “Dynamical spectral rigidity among Z2-symmetric
strictly convex domains close to a circle,” Annals of Mathematics, vol.
186, no. 1. Annals of Mathematics, pp. 277–314, 2017.
ista: De Simoi J, Kaloshin V, Wei Q. 2017. Dynamical spectral rigidity among Z2-symmetric
strictly convex domains close to a circle. Annals of Mathematics. 186(1), 277–314.
mla: De Simoi, Jacopo, et al. “Dynamical Spectral Rigidity among Z2-Symmetric Strictly
Convex Domains Close to a Circle.” Annals of Mathematics, vol. 186, no.
1, Annals of Mathematics, 2017, pp. 277–314, doi:10.4007/annals.2017.186.1.7.
short: J. De Simoi, V. Kaloshin, Q. Wei, Annals of Mathematics 186 (2017) 277–314.
date_created: 2020-09-17T10:46:42Z
date_published: 2017-07-01T00:00:00Z
date_updated: 2021-01-12T08:19:12Z
day: '01'
doi: 10.4007/annals.2017.186.1.7
extern: '1'
external_id:
arxiv:
- '1606.00230'
intvolume: ' 186'
issue: '1'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/1606.00230
month: '07'
oa: 1
oa_version: Preprint
page: 277-314
publication: Annals of Mathematics
publication_identifier:
issn:
- 0003-486X
publication_status: published
publisher: Annals of Mathematics
quality_controlled: '1'
status: public
title: Dynamical spectral rigidity among Z2-symmetric strictly convex domains close
to a circle
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 186
year: '2017'
...
---
_id: '8449'
abstract:
- lang: eng
text: Ensuring the correct folding of RNA molecules in the cell is of major importance
for a large variety of biological functions. Therefore, chaperone proteins that
assist RNA in adopting their functionally active states are abundant in all living
organisms. An important feature of RNA chaperone proteins is that they do not
require an external energy source to perform their activity, and that they interact
transiently and non-specifically with their RNA targets. So far, little is known
about the mechanistic details of the RNA chaperone activity of these proteins.
Prominent examples of RNA chaperones are bacterial cold shock proteins (Csp) that
have been reported to bind single-stranded RNA and DNA. Here, we have used advanced
NMR spectroscopy techniques to investigate at atomic resolution the RNA-melting
activity of CspA, the major cold shock protein of Escherichia coli, upon binding
to different RNA hairpins. Real-time NMR provides detailed information on the
folding kinetics and folding pathways. Finally, comparison of wild-type CspA with
single-point mutants and small peptides yields insights into the complementary
roles of aromatic and positively charged amino-acid side chains for the RNA chaperone
activity of the protein.
article_processing_charge: No
article_type: original
author:
- first_name: Enrico
full_name: Rennella, Enrico
last_name: Rennella
- first_name: Tomáš
full_name: Sára, Tomáš
last_name: Sára
- first_name: Michael
full_name: Juen, Michael
last_name: Juen
- first_name: Christoph
full_name: Wunderlich, Christoph
last_name: Wunderlich
- first_name: Lionel
full_name: Imbert, Lionel
last_name: Imbert
- first_name: Zsofia
full_name: Solyom, Zsofia
last_name: Solyom
- first_name: Adrien
full_name: Favier, Adrien
last_name: Favier
- first_name: Isabel
full_name: Ayala, Isabel
last_name: Ayala
- first_name: Katharina
full_name: Weinhäupl, Katharina
last_name: Weinhäupl
- first_name: Paul
full_name: Schanda, Paul
id: 7B541462-FAF6-11E9-A490-E8DFE5697425
last_name: Schanda
orcid: 0000-0002-9350-7606
- first_name: Robert
full_name: Konrat, Robert
last_name: Konrat
- first_name: Christoph
full_name: Kreutz, Christoph
last_name: Kreutz
- first_name: Bernhard
full_name: Brutscher, Bernhard
last_name: Brutscher
citation:
ama: Rennella E, Sára T, Juen M, et al. RNA binding and chaperone activity of the
E.coli cold-shock protein CspA. Nucleic Acids Research. 2017;45(7):4255-4268.
doi:10.1093/nar/gkx044
apa: Rennella, E., Sára, T., Juen, M., Wunderlich, C., Imbert, L., Solyom, Z., …
Brutscher, B. (2017). RNA binding and chaperone activity of the E.coli cold-shock
protein CspA. Nucleic Acids Research. Oxford University Press. https://doi.org/10.1093/nar/gkx044
chicago: Rennella, Enrico, Tomáš Sára, Michael Juen, Christoph Wunderlich, Lionel
Imbert, Zsofia Solyom, Adrien Favier, et al. “RNA Binding and Chaperone Activity
of the E.Coli Cold-Shock Protein CspA.” Nucleic Acids Research. Oxford
University Press, 2017. https://doi.org/10.1093/nar/gkx044.
ieee: E. Rennella et al., “RNA binding and chaperone activity of the E.coli
cold-shock protein CspA,” Nucleic Acids Research, vol. 45, no. 7. Oxford
University Press, pp. 4255–4268, 2017.
ista: Rennella E, Sára T, Juen M, Wunderlich C, Imbert L, Solyom Z, Favier A, Ayala
I, Weinhäupl K, Schanda P, Konrat R, Kreutz C, Brutscher B. 2017. RNA binding
and chaperone activity of the E.coli cold-shock protein CspA. Nucleic Acids Research.
45(7), 4255–4268.
mla: Rennella, Enrico, et al. “RNA Binding and Chaperone Activity of the E.Coli
Cold-Shock Protein CspA.” Nucleic Acids Research, vol. 45, no. 7, Oxford
University Press, 2017, pp. 4255–68, doi:10.1093/nar/gkx044.
short: E. Rennella, T. Sára, M. Juen, C. Wunderlich, L. Imbert, Z. Solyom, A. Favier,
I. Ayala, K. Weinhäupl, P. Schanda, R. Konrat, C. Kreutz, B. Brutscher, Nucleic
Acids Research 45 (2017) 4255–4268.
date_created: 2020-09-18T10:06:34Z
date_published: 2017-04-20T00:00:00Z
date_updated: 2021-01-12T08:19:20Z
day: '20'
doi: 10.1093/nar/gkx044
extern: '1'
intvolume: ' 45'
issue: '7'
language:
- iso: eng
month: '04'
oa_version: None
page: 4255-4268
publication: Nucleic Acids Research
publication_identifier:
issn:
- 0305-1048
- 1362-4962
publication_status: published
publisher: Oxford University Press
quality_controlled: '1'
status: public
title: RNA binding and chaperone activity of the E.coli cold-shock protein CspA
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 45
year: '2017'
...
---
_id: '8447'
abstract:
- lang: eng
text: 'Solid-state NMR spectroscopy can provide site-resolved information about
protein dynamics over many time scales. Here we combine protein deuteration, fast
magic-angle spinning (~45–60 kHz) and proton detection to study dynamics of ubiquitin
in microcrystals, and in particular a mutant in a region that undergoes microsecond
motions in a β-turn region in the wild-type protein. We use 15N R1ρ relaxation
measurements as a function of the radio-frequency (RF) field strength, i.e. relaxation
dispersion, to probe how the G53A mutation alters these dynamics. We report a
population-inversion of conformational states: the conformation that in the wild-type
protein is populated only sparsely becomes the predominant state. We furthermore
explore the potential to use amide-1H R1ρ relaxation to obtain insight into dynamics.
We show that while quantitative interpretation of 1H relaxation remains beyond
reach under the experimental conditions, due to coherent contributions to decay,
one may extract qualitative information about flexibility.'
article_processing_charge: No
article_type: original
author:
- first_name: Diego F.
full_name: Gauto, Diego F.
last_name: Gauto
- first_name: Audrey
full_name: Hessel, Audrey
last_name: Hessel
- first_name: Petra
full_name: Rovó, Petra
last_name: Rovó
- first_name: Vilius
full_name: Kurauskas, Vilius
last_name: Kurauskas
- first_name: Rasmus
full_name: Linser, Rasmus
last_name: Linser
- first_name: Paul
full_name: Schanda, Paul
id: 7B541462-FAF6-11E9-A490-E8DFE5697425
last_name: Schanda
orcid: 0000-0002-9350-7606
citation:
ama: 'Gauto DF, Hessel A, Rovó P, Kurauskas V, Linser R, Schanda P. Protein conformational
dynamics studied by 15N and 1HR1ρ relaxation dispersion: Application to wild-type
and G53A ubiquitin crystals. Solid State Nuclear Magnetic Resonance. 2017;87(10):86-95.
doi:10.1016/j.ssnmr.2017.04.002'
apa: 'Gauto, D. F., Hessel, A., Rovó, P., Kurauskas, V., Linser, R., & Schanda,
P. (2017). Protein conformational dynamics studied by 15N and 1HR1ρ relaxation
dispersion: Application to wild-type and G53A ubiquitin crystals. Solid State
Nuclear Magnetic Resonance. Elsevier. https://doi.org/10.1016/j.ssnmr.2017.04.002'
chicago: 'Gauto, Diego F., Audrey Hessel, Petra Rovó, Vilius Kurauskas, Rasmus Linser,
and Paul Schanda. “Protein Conformational Dynamics Studied by 15N and 1HR1ρ Relaxation
Dispersion: Application to Wild-Type and G53A Ubiquitin Crystals.” Solid State
Nuclear Magnetic Resonance. Elsevier, 2017. https://doi.org/10.1016/j.ssnmr.2017.04.002.'
ieee: 'D. F. Gauto, A. Hessel, P. Rovó, V. Kurauskas, R. Linser, and P. Schanda,
“Protein conformational dynamics studied by 15N and 1HR1ρ relaxation dispersion:
Application to wild-type and G53A ubiquitin crystals,” Solid State Nuclear
Magnetic Resonance, vol. 87, no. 10. Elsevier, pp. 86–95, 2017.'
ista: 'Gauto DF, Hessel A, Rovó P, Kurauskas V, Linser R, Schanda P. 2017. Protein
conformational dynamics studied by 15N and 1HR1ρ relaxation dispersion: Application
to wild-type and G53A ubiquitin crystals. Solid State Nuclear Magnetic Resonance.
87(10), 86–95.'
mla: 'Gauto, Diego F., et al. “Protein Conformational Dynamics Studied by 15N and
1HR1ρ Relaxation Dispersion: Application to Wild-Type and G53A Ubiquitin Crystals.”
Solid State Nuclear Magnetic Resonance, vol. 87, no. 10, Elsevier, 2017,
pp. 86–95, doi:10.1016/j.ssnmr.2017.04.002.'
short: D.F. Gauto, A. Hessel, P. Rovó, V. Kurauskas, R. Linser, P. Schanda, Solid
State Nuclear Magnetic Resonance 87 (2017) 86–95.
date_created: 2020-09-18T10:06:18Z
date_published: 2017-10-01T00:00:00Z
date_updated: 2021-01-12T08:19:20Z
day: '01'
doi: 10.1016/j.ssnmr.2017.04.002
extern: '1'
intvolume: ' 87'
issue: '10'
keyword:
- Nuclear and High Energy Physics
- Instrumentation
- General Chemistry
- Radiation
language:
- iso: eng
month: '10'
oa_version: None
page: 86-95
publication: Solid State Nuclear Magnetic Resonance
publication_identifier:
issn:
- 0926-2040
publication_status: published
publisher: Elsevier
quality_controlled: '1'
status: public
title: 'Protein conformational dynamics studied by 15N and 1HR1ρ relaxation dispersion:
Application to wild-type and G53A ubiquitin crystals'
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 87
year: '2017'
...
---
_id: '8448'
abstract:
- lang: eng
text: We present an improved fast mixing device based on the rapid mixing of two
solutions inside the NMR probe, as originally proposed by Hore and coworkers (J.
Am. Chem. Soc. 125 (2003) 12484–12492). Such a device is important for off-equilibrium
studies of molecular kinetics by multidimensional real-time NMR spectrsocopy.
The novelty of this device is that it allows removing the injector from the NMR
detection volume after mixing, and thus provides good magnetic field homogeneity
independently of the initial sample volume placed in the NMR probe. The apparatus
is simple to build, inexpensive, and can be used without any hardware modification
on any type of liquid-state NMR spectrometer. We demonstrate the performance of
our fast mixing device in terms of improved magnetic field homogeneity, and show
an application to the study of protein folding and the structural characterization
of transiently populated folding intermediates.
article_processing_charge: No
article_type: original
author:
- first_name: Rémi
full_name: Franco, Rémi
last_name: Franco
- first_name: Adrien
full_name: Favier, Adrien
last_name: Favier
- first_name: Paul
full_name: Schanda, Paul
id: 7B541462-FAF6-11E9-A490-E8DFE5697425
last_name: Schanda
orcid: 0000-0002-9350-7606
- first_name: Bernhard
full_name: Brutscher, Bernhard
last_name: Brutscher
citation:
ama: Franco R, Favier A, Schanda P, Brutscher B. Optimized fast mixing device for
real-time NMR applications. Journal of Magnetic Resonance. 2017;281(8):125-129.
doi:10.1016/j.jmr.2017.05.016
apa: Franco, R., Favier, A., Schanda, P., & Brutscher, B. (2017). Optimized
fast mixing device for real-time NMR applications. Journal of Magnetic Resonance.
Elsevier. https://doi.org/10.1016/j.jmr.2017.05.016
chicago: Franco, Rémi, Adrien Favier, Paul Schanda, and Bernhard Brutscher. “Optimized
Fast Mixing Device for Real-Time NMR Applications.” Journal of Magnetic Resonance.
Elsevier, 2017. https://doi.org/10.1016/j.jmr.2017.05.016.
ieee: R. Franco, A. Favier, P. Schanda, and B. Brutscher, “Optimized fast mixing
device for real-time NMR applications,” Journal of Magnetic Resonance,
vol. 281, no. 8. Elsevier, pp. 125–129, 2017.
ista: Franco R, Favier A, Schanda P, Brutscher B. 2017. Optimized fast mixing device
for real-time NMR applications. Journal of Magnetic Resonance. 281(8), 125–129.
mla: Franco, Rémi, et al. “Optimized Fast Mixing Device for Real-Time NMR Applications.”
Journal of Magnetic Resonance, vol. 281, no. 8, Elsevier, 2017, pp. 125–29,
doi:10.1016/j.jmr.2017.05.016.
short: R. Franco, A. Favier, P. Schanda, B. Brutscher, Journal of Magnetic Resonance
281 (2017) 125–129.
date_created: 2020-09-18T10:06:27Z
date_published: 2017-08-01T00:00:00Z
date_updated: 2021-01-12T08:19:20Z
day: '01'
doi: 10.1016/j.jmr.2017.05.016
extern: '1'
intvolume: ' 281'
issue: '8'
keyword:
- Nuclear and High Energy Physics
- Biophysics
- Biochemistry
- Condensed Matter Physics
language:
- iso: eng
month: '08'
oa_version: None
page: 125-129
publication: Journal of Magnetic Resonance
publication_identifier:
issn:
- 1090-7807
publication_status: published
publisher: Elsevier
quality_controlled: '1'
status: public
title: Optimized fast mixing device for real-time NMR applications
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 281
year: '2017'
...
---
_id: '8451'
abstract:
- lang: eng
text: The structure, dynamics, and function of membrane proteins are intimately
linked to the properties of the membrane environment in which the proteins are
embedded. For structural and biophysical characterization, membrane proteins generally
need to be extracted from the membrane and reconstituted in a suitable membrane‐mimicking
environment. Ensuring functional and structural integrity in these environments
is often a major concern. The styrene/maleic acid co‐polymer has recently been
shown to be able to extract lipid/membrane protein patches directly from native
membranes to form nanosize discoidal proteolipid particles, also referred to as
native nanodiscs. In this work, we show that high‐resolution solid‐state NMR spectra
can be obtained from an integral membrane protein in native nanodiscs, as exemplified
by the 2×34 kDa bacterial cation diffusion facilitator CzcD.
article_processing_charge: No
article_type: original
author:
- first_name: Beate
full_name: Bersch, Beate
last_name: Bersch
- first_name: Jonas M.
full_name: Dörr, Jonas M.
last_name: Dörr
- first_name: Audrey
full_name: Hessel, Audrey
last_name: Hessel
- first_name: J. Antoinette
full_name: Killian, J. Antoinette
last_name: Killian
- first_name: Paul
full_name: Schanda, Paul
id: 7B541462-FAF6-11E9-A490-E8DFE5697425
last_name: Schanda
orcid: 0000-0002-9350-7606
citation:
ama: Bersch B, Dörr JM, Hessel A, Killian JA, Schanda P. Proton-detected solid-state
NMR spectroscopy of a Zinc diffusion facilitator protein in native nanodiscs.
Angewandte Chemie International Edition. 2017;56(9):2508-2512. doi:10.1002/anie.201610441
apa: Bersch, B., Dörr, J. M., Hessel, A., Killian, J. A., & Schanda, P. (2017).
Proton-detected solid-state NMR spectroscopy of a Zinc diffusion facilitator protein
in native nanodiscs. Angewandte Chemie International Edition. Wiley. https://doi.org/10.1002/anie.201610441
chicago: Bersch, Beate, Jonas M. Dörr, Audrey Hessel, J. Antoinette Killian, and
Paul Schanda. “Proton-Detected Solid-State NMR Spectroscopy of a Zinc Diffusion
Facilitator Protein in Native Nanodiscs.” Angewandte Chemie International Edition.
Wiley, 2017. https://doi.org/10.1002/anie.201610441.
ieee: B. Bersch, J. M. Dörr, A. Hessel, J. A. Killian, and P. Schanda, “Proton-detected
solid-state NMR spectroscopy of a Zinc diffusion facilitator protein in native
nanodiscs,” Angewandte Chemie International Edition, vol. 56, no. 9. Wiley,
pp. 2508–2512, 2017.
ista: Bersch B, Dörr JM, Hessel A, Killian JA, Schanda P. 2017. Proton-detected
solid-state NMR spectroscopy of a Zinc diffusion facilitator protein in native
nanodiscs. Angewandte Chemie International Edition. 56(9), 2508–2512.
mla: Bersch, Beate, et al. “Proton-Detected Solid-State NMR Spectroscopy of a Zinc
Diffusion Facilitator Protein in Native Nanodiscs.” Angewandte Chemie International
Edition, vol. 56, no. 9, Wiley, 2017, pp. 2508–12, doi:10.1002/anie.201610441.
short: B. Bersch, J.M. Dörr, A. Hessel, J.A. Killian, P. Schanda, Angewandte Chemie
International Edition 56 (2017) 2508–2512.
date_created: 2020-09-18T10:06:50Z
date_published: 2017-01-27T00:00:00Z
date_updated: 2021-01-12T08:19:22Z
day: '27'
doi: 10.1002/anie.201610441
extern: '1'
intvolume: ' 56'
issue: '9'
language:
- iso: eng
month: '01'
oa_version: None
page: 2508-2512
publication: Angewandte Chemie International Edition
publication_identifier:
issn:
- 1433-7851
publication_status: published
publisher: Wiley
quality_controlled: '1'
status: public
title: Proton-detected solid-state NMR spectroscopy of a Zinc diffusion facilitator
protein in native nanodiscs
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 56
year: '2017'
...
---
_id: '8450'
abstract:
- lang: eng
text: Methyl groups are very useful probes of structure, dynamics, and interactions
in protein NMR spectroscopy. In particular, methyl-directed experiments provide
high sensitivity even in very large proteins, such as membrane proteins in a membrane-mimicking
environment. In this chapter, we discuss the approach for labeling methyl groups
in E. coli-based protein expression, as exemplified with the mitochondrial carrier
GGC.
alternative_title:
- Methods in Molecular Biology
article_processing_charge: No
author:
- first_name: Vilius
full_name: Kurauskas, Vilius
last_name: Kurauskas
- first_name: Paul
full_name: Schanda, Paul
id: 7B541462-FAF6-11E9-A490-E8DFE5697425
last_name: Schanda
orcid: 0000-0002-9350-7606
- first_name: Remy
full_name: Sounier, Remy
last_name: Sounier
citation:
ama: 'Kurauskas V, Schanda P, Sounier R. Methyl-specific isotope labeling strategies
for NMR studies of membrane proteins. In: Membrane Protein Structure and Function
Characterization. Vol 1635. Springer Nature; 2017:109-123. doi:10.1007/978-1-4939-7151-0_6'
apa: Kurauskas, V., Schanda, P., & Sounier, R. (2017). Methyl-specific isotope
labeling strategies for NMR studies of membrane proteins. In Membrane protein
structure and function characterization (Vol. 1635, pp. 109–123). Springer
Nature. https://doi.org/10.1007/978-1-4939-7151-0_6
chicago: Kurauskas, Vilius, Paul Schanda, and Remy Sounier. “Methyl-Specific Isotope
Labeling Strategies for NMR Studies of Membrane Proteins.” In Membrane Protein
Structure and Function Characterization, 1635:109–23. Springer Nature, 2017.
https://doi.org/10.1007/978-1-4939-7151-0_6.
ieee: V. Kurauskas, P. Schanda, and R. Sounier, “Methyl-specific isotope labeling
strategies for NMR studies of membrane proteins,” in Membrane protein structure
and function characterization, vol. 1635, Springer Nature, 2017, pp. 109–123.
ista: 'Kurauskas V, Schanda P, Sounier R. 2017.Methyl-specific isotope labeling
strategies for NMR studies of membrane proteins. In: Membrane protein structure
and function characterization. Methods in Molecular Biology, vol. 1635, 109–123.'
mla: Kurauskas, Vilius, et al. “Methyl-Specific Isotope Labeling Strategies for
NMR Studies of Membrane Proteins.” Membrane Protein Structure and Function
Characterization, vol. 1635, Springer Nature, 2017, pp. 109–23, doi:10.1007/978-1-4939-7151-0_6.
short: V. Kurauskas, P. Schanda, R. Sounier, in:, Membrane Protein Structure and
Function Characterization, Springer Nature, 2017, pp. 109–123.
date_created: 2020-09-18T10:06:44Z
date_published: 2017-07-29T00:00:00Z
date_updated: 2022-08-26T09:14:20Z
day: '29'
doi: 10.1007/978-1-4939-7151-0_6
extern: '1'
intvolume: ' 1635'
language:
- iso: eng
month: '07'
oa_version: None
page: 109-123
publication: Membrane protein structure and function characterization
publication_identifier:
isbn:
- '9781493971497'
- '9781493971510'
issn:
- 1064-3745
- 1940-6029
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
status: public
title: Methyl-specific isotope labeling strategies for NMR studies of membrane proteins
type: book_chapter
user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87
volume: 1635
year: '2017'
...
---
_id: '9137'
abstract:
- lang: eng
text: Pools of air cooled by partial rain evaporation span up to several hundreds
of kilometers in nature and typically last less than 1 day, ultimately losing
their identity to the large-scale flow. These fundamentally differ in character
from the radiatively-driven dry pools defining convective aggregation. Advancement
in remote sensing and in computer capabilities has promoted exploration of how
precipitation-induced cold pool processes modify the convective spectrum and life
cycle. This contribution surveys current understanding of such cold pools over
the tropical and subtropical oceans. In shallow convection with low rain rates,
the cold pools moisten, preserving the near-surface equivalent potential temperature
or increasing it if the surface moisture fluxes cannot ventilate beyond the new
surface layer; both conditions indicate downdraft origin air from within the boundary
layer. When rain rates exceed ∼ 2 mm h−1, convective-scale downdrafts can bring
down drier air of lower equivalent potential temperature from above the boundary
layer. The resulting density currents facilitate the lifting of locally thermodynamically
favorable air and can impose an arc-shaped mesoscale cloud organization. This
organization allows clouds capable of reaching 4–5 km within otherwise dry environments.
These are more commonly observed in the northern hemisphere trade wind regime,
where the flow to the intertropical convergence zone is unimpeded by the equator.
Their near-surface air properties share much with those shown from cold pools
sampled in the equatorial Indian Ocean. Cold pools are most effective at influencing
the mesoscale organization when the atmosphere is moist in the lower free troposphere
and dry above, suggesting an optimal range of water vapor paths. Outstanding questions
on the relationship between cold pools, their accompanying moisture distribution
and cloud cover are detailed further. Near-surface water vapor rings are documented
in one model inside but near the cold pool edge; these are not consistent with
observations, but do improve with smaller horizontal grid spacings.
article_processing_charge: No
article_type: original
author:
- first_name: Paquita
full_name: Zuidema, Paquita
last_name: Zuidema
- first_name: Giuseppe
full_name: Torri, Giuseppe
last_name: Torri
- 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: Arunchandra
full_name: Chandra, Arunchandra
last_name: Chandra
citation:
ama: Zuidema P, Torri G, Muller CJ, Chandra A. A survey of precipitation-induced
atmospheric cold pools over oceans and their interactions with the larger-scale
environment. Surveys in Geophysics. 2017;38(6):1283-1305. doi:10.1007/s10712-017-9447-x
apa: Zuidema, P., Torri, G., Muller, C. J., & Chandra, A. (2017). A survey of
precipitation-induced atmospheric cold pools over oceans and their interactions
with the larger-scale environment. Surveys in Geophysics. Springer Nature.
https://doi.org/10.1007/s10712-017-9447-x
chicago: Zuidema, Paquita, Giuseppe Torri, Caroline J Muller, and Arunchandra Chandra.
“A Survey of Precipitation-Induced Atmospheric Cold Pools over Oceans and Their
Interactions with the Larger-Scale Environment.” Surveys in Geophysics.
Springer Nature, 2017. https://doi.org/10.1007/s10712-017-9447-x.
ieee: P. Zuidema, G. Torri, C. J. Muller, and A. Chandra, “A survey of precipitation-induced
atmospheric cold pools over oceans and their interactions with the larger-scale
environment,” Surveys in Geophysics, vol. 38, no. 6. Springer Nature, pp.
1283–1305, 2017.
ista: Zuidema P, Torri G, Muller CJ, Chandra A. 2017. A survey of precipitation-induced
atmospheric cold pools over oceans and their interactions with the larger-scale
environment. Surveys in Geophysics. 38(6), 1283–1305.
mla: Zuidema, Paquita, et al. “A Survey of Precipitation-Induced Atmospheric Cold
Pools over Oceans and Their Interactions with the Larger-Scale Environment.” Surveys
in Geophysics, vol. 38, no. 6, Springer Nature, 2017, pp. 1283–305, doi:10.1007/s10712-017-9447-x.
short: P. Zuidema, G. Torri, C.J. Muller, A. Chandra, Surveys in Geophysics 38 (2017)
1283–1305.
date_created: 2021-02-15T14:20:07Z
date_published: 2017-11-14T00:00:00Z
date_updated: 2022-01-24T12:41:45Z
day: '14'
doi: 10.1007/s10712-017-9447-x
extern: '1'
intvolume: ' 38'
issue: '6'
keyword:
- Geochemistry and Petrology
- Geophysics
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.1007/s10712-017-9447-x
month: '11'
oa: 1
oa_version: Published Version
page: 1283-1305
publication: Surveys in Geophysics
publication_identifier:
issn:
- 0169-3298
- 1573-0956
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
status: public
title: A survey of precipitation-induced atmospheric cold pools over oceans and their
interactions with the larger-scale environment
type: journal_article
user_id: 8b945eb4-e2f2-11eb-945a-df72226e66a9
volume: 38
year: '2017'
...
---
_id: '9138'
abstract:
- lang: eng
text: Convective self-aggregation, the spontaneous organization of initially scattered
convection into isolated convective clusters despite spatially homogeneous boundary
conditions and forcing, was first recognized and studied in idealized numerical
simulations. While there is a rich history of observational work on convective
clustering and organization, there have been only a few studies that have analyzed
observations to look specifically for processes related to self-aggregation in
models. Here we review observational work in both of these categories and motivate
the need for more of this work. We acknowledge that self-aggregation may appear
to be far-removed from observed convective organization in terms of time scales,
initial conditions, initiation processes, and mean state extremes, but we argue
that these differences vary greatly across the diverse range of model simulations
in the literature and that these comparisons are already offering important insights
into real tropical phenomena. Some preliminary new findings are presented, including
results showing that a self-aggregation simulation with square geometry has too
broad distribution of humidity and is too dry in the driest regions when compared
with radiosonde records from Nauru, while an elongated channel simulation has
realistic representations of atmospheric humidity and its variability. We discuss
recent work increasing our understanding of how organized convection and climate
change may interact, and how model discrepancies related to this question are
prompting interest in observational comparisons. We also propose possible future
directions for observational work related to convective aggregation, including
novel satellite approaches and a ground-based observational network.
article_processing_charge: No
article_type: original
author:
- first_name: Christopher E.
full_name: Holloway, Christopher E.
last_name: Holloway
- first_name: Allison A.
full_name: Wing, Allison A.
last_name: Wing
- first_name: Sandrine
full_name: Bony, Sandrine
last_name: Bony
- 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: Hirohiko
full_name: Masunaga, Hirohiko
last_name: Masunaga
- first_name: Tristan S.
full_name: L’Ecuyer, Tristan S.
last_name: L’Ecuyer
- first_name: David D.
full_name: Turner, David D.
last_name: Turner
- first_name: Paquita
full_name: Zuidema, Paquita
last_name: Zuidema
citation:
ama: Holloway CE, Wing AA, Bony S, et al. Observing convective aggregation. Surveys
in Geophysics. 2017;38(6):1199-1236. doi:10.1007/s10712-017-9419-1
apa: Holloway, C. E., Wing, A. A., Bony, S., Muller, C. J., Masunaga, H., L’Ecuyer,
T. S., … Zuidema, P. (2017). Observing convective aggregation. Surveys in Geophysics.
Springer Nature. https://doi.org/10.1007/s10712-017-9419-1
chicago: Holloway, Christopher E., Allison A. Wing, Sandrine Bony, Caroline J Muller,
Hirohiko Masunaga, Tristan S. L’Ecuyer, David D. Turner, and Paquita Zuidema.
“Observing Convective Aggregation.” Surveys in Geophysics. Springer Nature,
2017. https://doi.org/10.1007/s10712-017-9419-1.
ieee: C. E. Holloway et al., “Observing convective aggregation,” Surveys
in Geophysics, vol. 38, no. 6. Springer Nature, pp. 1199–1236, 2017.
ista: Holloway CE, Wing AA, Bony S, Muller CJ, Masunaga H, L’Ecuyer TS, Turner DD,
Zuidema P. 2017. Observing convective aggregation. Surveys in Geophysics. 38(6),
1199–1236.
mla: Holloway, Christopher E., et al. “Observing Convective Aggregation.” Surveys
in Geophysics, vol. 38, no. 6, Springer Nature, 2017, pp. 1199–236, doi:10.1007/s10712-017-9419-1.
short: C.E. Holloway, A.A. Wing, S. Bony, C.J. Muller, H. Masunaga, T.S. L’Ecuyer,
D.D. Turner, P. Zuidema, Surveys in Geophysics 38 (2017) 1199–1236.
date_created: 2021-02-15T14:20:38Z
date_published: 2017-11-01T00:00:00Z
date_updated: 2022-01-24T12:43:13Z
day: '01'
doi: 10.1007/s10712-017-9419-1
extern: '1'
intvolume: ' 38'
issue: '6'
keyword:
- Geochemistry and Petrology
- Geophysics
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.1007/s10712-017-9419-1
month: '11'
oa: 1
oa_version: Published Version
page: 1199-1236
publication: Surveys in Geophysics
publication_identifier:
issn:
- 0169-3298
- 1573-0956
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
status: public
title: Observing convective aggregation
type: journal_article
user_id: 8b945eb4-e2f2-11eb-945a-df72226e66a9
volume: 38
year: '2017'
...
---
_id: '9139'
abstract:
- lang: eng
text: Organized convection in the tropics occurs across a range of spatial and temporal
scales and strongly influences cloud cover and humidity. One mode of organization
found is “self-aggregation,” in which moist convection spontaneously organizes
into one or several isolated clusters despite spatially homogeneous boundary conditions
and forcing. Self-aggregation is driven by interactions between clouds, moisture,
radiation, surface fluxes, and circulation, and occurs in a wide variety of idealized
simulations of radiative–convective equilibrium. Here we provide a review of convective
self-aggregation in numerical simulations, including its character, causes, and
effects. We describe the evolution of self-aggregation including its time and
length scales and the physical mechanisms leading to its triggering and maintenance,
and we also discuss possible links to climate and climate change.
article_processing_charge: No
article_type: original
author:
- first_name: Allison A.
full_name: Wing, Allison A.
last_name: Wing
- first_name: Kerry
full_name: Emanuel, Kerry
last_name: Emanuel
- first_name: Christopher E.
full_name: Holloway, Christopher E.
last_name: Holloway
- first_name: Caroline J
full_name: Muller, Caroline J
id: f978ccb0-3f7f-11eb-b193-b0e2bd13182b
last_name: Muller
orcid: 0000-0001-5836-5350
citation:
ama: 'Wing AA, Emanuel K, Holloway CE, Muller CJ. Convective self-aggregation in
numerical simulations: A review. Surveys in Geophysics. 2017;38(6):1173-1197.
doi:10.1007/s10712-017-9408-4'
apa: 'Wing, A. A., Emanuel, K., Holloway, C. E., & Muller, C. J. (2017). Convective
self-aggregation in numerical simulations: A review. Surveys in Geophysics.
Springer Nature. https://doi.org/10.1007/s10712-017-9408-4'
chicago: 'Wing, Allison A., Kerry Emanuel, Christopher E. Holloway, and Caroline
J Muller. “Convective Self-Aggregation in Numerical Simulations: A Review.” Surveys
in Geophysics. Springer Nature, 2017. https://doi.org/10.1007/s10712-017-9408-4.'
ieee: 'A. A. Wing, K. Emanuel, C. E. Holloway, and C. J. Muller, “Convective self-aggregation
in numerical simulations: A review,” Surveys in Geophysics, vol. 38, no.
6. Springer Nature, pp. 1173–1197, 2017.'
ista: 'Wing AA, Emanuel K, Holloway CE, Muller CJ. 2017. Convective self-aggregation
in numerical simulations: A review. Surveys in Geophysics. 38(6), 1173–1197.'
mla: 'Wing, Allison A., et al. “Convective Self-Aggregation in Numerical Simulations:
A Review.” Surveys in Geophysics, vol. 38, no. 6, Springer Nature, 2017,
pp. 1173–97, doi:10.1007/s10712-017-9408-4.'
short: A.A. Wing, K. Emanuel, C.E. Holloway, C.J. Muller, Surveys in Geophysics
38 (2017) 1173–1197.
date_created: 2021-02-15T14:20:56Z
date_published: 2017-11-01T00:00:00Z
date_updated: 2022-01-24T12:42:36Z
day: '01'
doi: 10.1007/s10712-017-9408-4
extern: '1'
intvolume: ' 38'
issue: '6'
keyword:
- Geochemistry and Petrology
- Geophysics
language:
- iso: eng
month: '11'
oa_version: None
page: 1173-1197
publication: Surveys in Geophysics
publication_identifier:
issn:
- 0169-3298
- 1573-0956
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
status: public
title: 'Convective self-aggregation in numerical simulations: A review'
type: journal_article
user_id: 8b945eb4-e2f2-11eb-945a-df72226e66a9
volume: 38
year: '2017'
...
---
_id: '9152'
abstract:
- lang: eng
text: Previous numerical studies of the dissipation of internal tides in idealized
settings suggest the existence of a critical latitude (~29°) where dissipation
is enhanced. But observations only indicate a modest enhancement at this latitude.
To resolve this difference between observational and numerical results, the authors
study the latitudinal dependence of internal tides’ dissipation in more realistic
conditions. In particular, the ocean is not a quiescent medium; the presence of
large-scale currents or mesoscale eddies can impact the propagation and dissipation
of internal tides. This paper investigates the impact of a weak background mean
current in numerical simulations. The authors focus on the local dissipation of
high spatial mode internal waves near their generation site. The vertical profile
of dissipation and its variation with latitude without the mean current are consistent
with earlier studies. But adding a weak mean current has a major impact on the
latitudinal distribution of dissipation. The peak at the critical latitude disappears,
and the dissipation is closer to a constant, albeit with two weak peaks at ~25°
and ~35° latitude. This disappearance results from the Doppler shift of the internal
tides’ frequency, which hinders the nonlinear transfer of energy to small-scale
secondary waves via the parametric subharmonic instability (PSI). The new two
weak peaks correspond to the Doppler-shifted critical latitudes of the left- and
right-propagating waves. The results are confirmed in simulations with simple
sinusoidal topography. Thus, although nonlinear transfers via PSI are efficient
at dissipating internal tides, the exact location of the dissipation is sensitive
to large-scale oceanic conditions.
article_processing_charge: No
article_type: original
author:
- first_name: O.
full_name: Richet, O.
last_name: Richet
- 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: J.-M.
full_name: Chomaz, J.-M.
last_name: Chomaz
citation:
ama: Richet O, Muller CJ, Chomaz J-M. Impact of a mean current on the internal tide
energy dissipation at the critical latitude. Journal of Physical Oceanography.
2017;47(6):1457-1472. doi:10.1175/jpo-d-16-0197.1
apa: Richet, O., Muller, C. J., & Chomaz, J.-M. (2017). Impact of a mean current
on the internal tide energy dissipation at the critical latitude. Journal of
Physical Oceanography. American Meteorological Society. https://doi.org/10.1175/jpo-d-16-0197.1
chicago: Richet, O., Caroline J Muller, and J.-M. Chomaz. “Impact of a Mean Current
on the Internal Tide Energy Dissipation at the Critical Latitude.” Journal
of Physical Oceanography. American Meteorological Society, 2017. https://doi.org/10.1175/jpo-d-16-0197.1.
ieee: O. Richet, C. J. Muller, and J.-M. Chomaz, “Impact of a mean current on the
internal tide energy dissipation at the critical latitude,” Journal of Physical
Oceanography, vol. 47, no. 6. American Meteorological Society, pp. 1457–1472,
2017.
ista: Richet O, Muller CJ, Chomaz J-M. 2017. Impact of a mean current on the internal
tide energy dissipation at the critical latitude. Journal of Physical Oceanography.
47(6), 1457–1472.
mla: Richet, O., et al. “Impact of a Mean Current on the Internal Tide Energy Dissipation
at the Critical Latitude.” Journal of Physical Oceanography, vol. 47, no.
6, American Meteorological Society, 2017, pp. 1457–72, doi:10.1175/jpo-d-16-0197.1.
short: O. Richet, C.J. Muller, J.-M. Chomaz, Journal of Physical Oceanography 47
(2017) 1457–1472.
date_created: 2021-02-15T15:11:04Z
date_published: 2017-06-01T00:00:00Z
date_updated: 2022-01-24T13:36:31Z
day: '01'
doi: 10.1175/jpo-d-16-0197.1
extern: '1'
intvolume: ' 47'
issue: '6'
keyword:
- Oceanography
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.1175/JPO-D-16-0197.1
month: '06'
oa: 1
oa_version: Published Version
page: 1457-1472
publication: Journal of Physical Oceanography
publication_identifier:
issn:
- 0022-3670
- 1520-0485
publication_status: published
publisher: American Meteorological Society
quality_controlled: '1'
status: public
title: Impact of a mean current on the internal tide energy dissipation at the critical
latitude
type: journal_article
user_id: 8b945eb4-e2f2-11eb-945a-df72226e66a9
volume: 47
year: '2017'
...
---
_id: '934'
abstract:
- lang: eng
text: During puberty, the mouse mammary gland develops into a highly branched epithelial
network. Owing to the absence of exclusive stem cell markers, the location, multiplicity,
dynamics and fate of mammary stem cells (MaSCs), which drive branching morphogenesis,
are unknown. Here we show that morphogenesis is driven by proliferative terminal
end buds that terminate or bifurcate with near equal probability, in a stochastic
and time-invariant manner, leading to a heterogeneous epithelial network. We show
that the majority of terminal end bud cells function as highly proliferative,
lineage-committed MaSCs that are heterogeneous in their expression profile and
short-term contribution to ductal extension. Yet, through cell rearrangements
during terminal end bud bifurcation, each MaSC is able to contribute actively
to long-term growth. Our study shows that the behaviour of MaSCs is not directly
linked to a single expression profile. Instead, morphogenesis relies upon lineage-restricted
heterogeneous MaSC populations that function as single equipotent pools in the
long term.
author:
- first_name: Colinda
full_name: Scheele, Colinda
last_name: Scheele
- 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: Mauro
full_name: Muraro, Mauro
last_name: Muraro
- first_name: Anoek
full_name: Zomer, Anoek
last_name: Zomer
- first_name: Nathalia
full_name: Langedijk, Nathalia
last_name: Langedijk
- first_name: Alexander
full_name: Van Oudenaarden, Alexander
last_name: Van Oudenaarden
- first_name: Benjamin
full_name: Simons, Benjamin
last_name: Simons
- first_name: Jacco
full_name: Van Rheenen, Jacco
last_name: Van Rheenen
citation:
ama: Scheele C, Hannezo EB, Muraro M, et al. Identity and dynamics of mammary stem
cells during branching morphogenesis. Nature. 2017;542(7641):313-317. doi:10.1038/nature21046
apa: Scheele, C., Hannezo, E. B., Muraro, M., Zomer, A., Langedijk, N., Van Oudenaarden,
A., … Van Rheenen, J. (2017). Identity and dynamics of mammary stem cells during
branching morphogenesis. Nature. Nature Publishing Group. https://doi.org/10.1038/nature21046
chicago: Scheele, Colinda, Edouard B Hannezo, Mauro Muraro, Anoek Zomer, Nathalia
Langedijk, Alexander Van Oudenaarden, Benjamin Simons, and Jacco Van Rheenen.
“Identity and Dynamics of Mammary Stem Cells during Branching Morphogenesis.”
Nature. Nature Publishing Group, 2017. https://doi.org/10.1038/nature21046.
ieee: C. Scheele et al., “Identity and dynamics of mammary stem cells during
branching morphogenesis,” Nature, vol. 542, no. 7641. Nature Publishing
Group, pp. 313–317, 2017.
ista: Scheele C, Hannezo EB, Muraro M, Zomer A, Langedijk N, Van Oudenaarden A,
Simons B, Van Rheenen J. 2017. Identity and dynamics of mammary stem cells during
branching morphogenesis. Nature. 542(7641), 313–317.
mla: Scheele, Colinda, et al. “Identity and Dynamics of Mammary Stem Cells during
Branching Morphogenesis.” Nature, vol. 542, no. 7641, Nature Publishing
Group, 2017, pp. 313–17, doi:10.1038/nature21046.
short: C. Scheele, E.B. Hannezo, M. Muraro, A. Zomer, N. Langedijk, A. Van Oudenaarden,
B. Simons, J. Van Rheenen, Nature 542 (2017) 313–317.
date_created: 2018-12-11T11:49:17Z
date_published: 2017-02-16T00:00:00Z
date_updated: 2021-01-12T08:22:01Z
day: '16'
doi: 10.1038/nature21046
extern: '1'
intvolume: ' 542'
issue: '7641'
language:
- iso: eng
month: '02'
oa_version: None
page: 313 - 317
publication: Nature
publication_identifier:
issn:
- '00280836'
publication_status: published
publisher: Nature Publishing Group
publist_id: '6505'
quality_controlled: '1'
status: public
title: Identity and dynamics of mammary stem cells during branching morphogenesis
type: journal_article
user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87
volume: 542
year: '2017'
...
---
_id: '936'
abstract:
- lang: eng
text: Homeostatic replacement of epithelial cells from basal precursors is a multistep
process involving progenitor cell specification, radial intercalation and, finally,
apical surface emergence. Recent data demonstrate that actin-based pushing under
the control of the formin protein Fmn1 drives apical emergence in nascent multiciliated
epithelial cells (MCCs), but little else is known about this actin network or
the control of Fmn1. Here, we explore the role of the small GTPase RhoA in MCC
apical emergence. Disruption of RhoA function reduced the rate of apical surface
expansion and decreased the final size of the apical domain. Analysis of cell
shapes suggests that RhoA alters the balance of forces exerted on the MCC apical
surface. Finally, quantitative time-lapse imaging and fluorescence recovery after
photobleaching studies argue that RhoA works in concert with Fmn1 to control assembly
of the specialized apical actin network in MCCs. These data provide new molecular
insights into epithelial apical surface assembly and could also shed light on
mechanisms of apical lumen formation
author:
- first_name: Jakub
full_name: Sedzinski, Jakub
last_name: Sedzinski
- 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: Fan
full_name: Tu, Fan
last_name: Tu
- first_name: Maté
full_name: Biro, Maté
last_name: Biro
- first_name: John
full_name: Wallingford, John
last_name: Wallingford
citation:
ama: Sedzinski J, Hannezo EB, Tu F, Biro M, Wallingford J. RhoA regulates actin
network dynamics during apical surface emergence in multiciliated epithelial cells
. Journal of Cell Science. 2017;130(5). doi:10.1242/jcs.202234
apa: Sedzinski, J., Hannezo, E. B., Tu, F., Biro, M., & Wallingford, J. (2017).
RhoA regulates actin network dynamics during apical surface emergence in multiciliated
epithelial cells . Journal of Cell Science. Company of Biologists. https://doi.org/10.1242/jcs.202234
chicago: Sedzinski, Jakub, Edouard B Hannezo, Fan Tu, Maté Biro, and John Wallingford.
“RhoA Regulates Actin Network Dynamics during Apical Surface Emergence in Multiciliated
Epithelial Cells .” Journal of Cell Science. Company of Biologists, 2017.
https://doi.org/10.1242/jcs.202234.
ieee: J. Sedzinski, E. B. Hannezo, F. Tu, M. Biro, and J. Wallingford, “RhoA regulates
actin network dynamics during apical surface emergence in multiciliated epithelial
cells ,” Journal of Cell Science, vol. 130, no. 5. Company of Biologists,
2017.
ista: Sedzinski J, Hannezo EB, Tu F, Biro M, Wallingford J. 2017. RhoA regulates
actin network dynamics during apical surface emergence in multiciliated epithelial
cells . Journal of Cell Science. 130(5).
mla: Sedzinski, Jakub, et al. “RhoA Regulates Actin Network Dynamics during Apical
Surface Emergence in Multiciliated Epithelial Cells .” Journal of Cell Science,
vol. 130, no. 5, Company of Biologists, 2017, doi:10.1242/jcs.202234.
short: J. Sedzinski, E.B. Hannezo, F. Tu, M. Biro, J. Wallingford, Journal of Cell
Science 130 (2017).
date_created: 2018-12-11T11:49:17Z
date_published: 2017-01-01T00:00:00Z
date_updated: 2021-01-12T08:22:02Z
day: '01'
doi: 10.1242/jcs.202234
extern: '1'
intvolume: ' 130'
issue: '5'
language:
- iso: eng
month: '01'
oa_version: None
publication: Journal of Cell Science
publication_status: published
publisher: Company of Biologists
publist_id: '6507'
quality_controlled: '1'
status: public
title: 'RhoA regulates actin network dynamics during apical surface emergence in multiciliated
epithelial cells '
type: journal_article
user_id: 4435EBFC-F248-11E8-B48F-1D18A9856A87
volume: 130
year: '2017'
...
---
_id: '937'
abstract:
- lang: eng
text: During epithelial cytokinesis, the remodelling of adhesive cell-cell contacts
between the dividing cell and its neighbours has profound implications for the
integrity, arrangement and morphogenesis of proliferative tissues. In both vertebrates
and invertebrates, this remodelling requires the activity of non-muscle myosin
II (MyoII) in the interphasic cells neighbouring the dividing cell. However, the
mechanisms that coordinate cytokinesis and MyoII activity in the neighbours are
unknown. Here we show that in the Drosophila notum epithelium, each cell division
is associated with a mechanosensing and transmission event that controls MyoII
dynamics in neighbouring cells. We find that the ring pulling forces promote local
junction elongation, which results in local E-cadherin dilution at the ingressing
adherens junction. In turn, the reduction in E-cadherin concentration and the
contractility of the neighbouring cells promote self-organized actomyosin flows,
ultimately leading to accumulation of MyoII at the base of the ingressing junction.
Although force transduction has been extensively studied in the context of adherens
junction reinforcement to stabilize adhesive cell-cell contacts, we propose an
alternative mechanosensing mechanism that coordinates actomyosin dynamics between
epithelial cells and sustains the remodelling of the adherens junction in response
to mechanical forces.
author:
- first_name: Diana
full_name: Pinheiro, Diana
last_name: Pinheiro
- 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: Sophie
full_name: Herszterg, Sophie
last_name: Herszterg
- first_name: Floris
full_name: Bosveld, Floris
last_name: Bosveld
- first_name: Isabelle
full_name: Gaugué, Isabelle
last_name: Gaugué
- first_name: Maria
full_name: Balakireva, Maria
last_name: Balakireva
- first_name: Zhimin
full_name: Wang, Zhimin
last_name: Wang
- first_name: Inês
full_name: Cristo, Inês
last_name: Cristo
- first_name: Stéphane
full_name: Rigaud, Stéphane
last_name: Rigaud
- first_name: Olga
full_name: Markova, Olga
last_name: Markova
- first_name: Yohanns
full_name: Bellaïche, Yohanns
last_name: Bellaïche
citation:
ama: Pinheiro D, Hannezo EB, Herszterg S, et al. Transmission of cytokinesis forces
via E cadherin dilution and actomyosin flows. Nature. 2017;545(7652):103-107.
doi:10.1038/nature22041
apa: Pinheiro, D., Hannezo, E. B., Herszterg, S., Bosveld, F., Gaugué, I., Balakireva,
M., … Bellaïche, Y. (2017). Transmission of cytokinesis forces via E cadherin
dilution and actomyosin flows. Nature. Nature Publishing Group. https://doi.org/10.1038/nature22041
chicago: Pinheiro, Diana, Edouard B Hannezo, Sophie Herszterg, Floris Bosveld, Isabelle
Gaugué, Maria Balakireva, Zhimin Wang, et al. “Transmission of Cytokinesis Forces
via E Cadherin Dilution and Actomyosin Flows.” Nature. Nature Publishing
Group, 2017. https://doi.org/10.1038/nature22041.
ieee: D. Pinheiro et al., “Transmission of cytokinesis forces via E cadherin
dilution and actomyosin flows,” Nature, vol. 545, no. 7652. Nature Publishing
Group, pp. 103–107, 2017.
ista: Pinheiro D, Hannezo EB, Herszterg S, Bosveld F, Gaugué I, Balakireva M, Wang
Z, Cristo I, Rigaud S, Markova O, Bellaïche Y. 2017. Transmission of cytokinesis
forces via E cadherin dilution and actomyosin flows. Nature. 545(7652), 103–107.
mla: Pinheiro, Diana, et al. “Transmission of Cytokinesis Forces via E Cadherin
Dilution and Actomyosin Flows.” Nature, vol. 545, no. 7652, Nature Publishing
Group, 2017, pp. 103–07, doi:10.1038/nature22041.
short: D. Pinheiro, E.B. Hannezo, S. Herszterg, F. Bosveld, I. Gaugué, M. Balakireva,
Z. Wang, I. Cristo, S. Rigaud, O. Markova, Y. Bellaïche, Nature 545 (2017) 103–107.
date_created: 2018-12-11T11:49:18Z
date_published: 2017-05-04T00:00:00Z
date_updated: 2021-01-12T08:22:02Z
day: '04'
doi: 10.1038/nature22041
extern: '1'
intvolume: ' 545'
issue: '7652'
language:
- iso: eng
month: '05'
oa_version: None
page: 103 - 107
publication: Nature
publication_identifier:
issn:
- '00280836'
publication_status: published
publisher: Nature Publishing Group
publist_id: '6504'
quality_controlled: '1'
status: public
title: Transmission of cytokinesis forces via E cadherin dilution and actomyosin flows
type: journal_article
user_id: 4435EBFC-F248-11E8-B48F-1D18A9856A87
volume: 545
year: '2017'
...
---
_id: '941'
abstract:
- lang: eng
text: 'Recently there has been a proliferation of automated program repair (APR)
techniques, targeting various programming languages. Such techniques can be generally
classified into two families: syntactic- and semantics-based. Semantics-based
APR, on which we focus, typically uses symbolic execution to infer semantic constraints
and then program synthesis to construct repairs conforming to them. While syntactic-based
APR techniques have been shown successful on bugs in real-world programs written
in both C and Java, semantics-based APR techniques mostly target C programs. This
leaves empirical comparisons of the APR families not fully explored, and developers
without a Java-based semantics APR technique. We present JFix, a semantics-based
APR framework that targets Java, and an associated Eclipse plugin. JFix is implemented
atop Symbolic PathFinder, a well-known symbolic execution engine for Java programs.
It extends one particular APR technique (Angelix), and is designed to be sufficiently
generic to support a variety of such techniques. We demonstrate that semantics-based
APR can indeed efficiently and effectively repair a variety of classes of bugs
in large real-world Java programs. This supports our claim that the framework
can both support developers seeking semantics-based repair of bugs in Java programs,
as well as enable larger scale empirical studies comparing syntactic- and semantics-based
APR targeting Java. The demonstration of our tool is available via the project
website at: https://xuanbachle.github.io/semanticsrepair/ '
author:
- first_name: Xuan
full_name: Le, Xuan
last_name: Le
- first_name: Duc Hiep
full_name: Chu, Duc Hiep
id: 3598E630-F248-11E8-B48F-1D18A9856A87
last_name: Chu
- first_name: David
full_name: Lo, David
last_name: Lo
- first_name: Claire
full_name: Le Goues, Claire
last_name: Le Goues
- first_name: Willem
full_name: Visser, Willem
last_name: Visser
citation:
ama: 'Le X, Chu DH, Lo D, Le Goues C, Visser W. JFIX: Semantics-based repair of
Java programs via symbolic PathFinder. In: Proceedings of the 26th ACM SIGSOFT
International Symposium on Software Testing and Analysis. ACM; 2017:376-379.
doi:10.1145/3092703.3098225'
apa: 'Le, X., Chu, D. H., Lo, D., Le Goues, C., & Visser, W. (2017). JFIX: Semantics-based
repair of Java programs via symbolic PathFinder. In Proceedings of the 26th
ACM SIGSOFT International Symposium on Software Testing and Analysis (pp.
376–379). Santa Barbara, CA, United States: ACM. https://doi.org/10.1145/3092703.3098225'
chicago: 'Le, Xuan, Duc Hiep Chu, David Lo, Claire Le Goues, and Willem Visser.
“JFIX: Semantics-Based Repair of Java Programs via Symbolic PathFinder.” In Proceedings
of the 26th ACM SIGSOFT International Symposium on Software Testing and Analysis,
376–79. ACM, 2017. https://doi.org/10.1145/3092703.3098225.'
ieee: 'X. Le, D. H. Chu, D. Lo, C. Le Goues, and W. Visser, “JFIX: Semantics-based
repair of Java programs via symbolic PathFinder,” in Proceedings of the 26th
ACM SIGSOFT International Symposium on Software Testing and Analysis, Santa
Barbara, CA, United States, 2017, pp. 376–379.'
ista: 'Le X, Chu DH, Lo D, Le Goues C, Visser W. 2017. JFIX: Semantics-based repair
of Java programs via symbolic PathFinder. Proceedings of the 26th ACM SIGSOFT
International Symposium on Software Testing and Analysis. ISSTA: International
Symposium on Software Testing and Analysis, 376–379.'
mla: 'Le, Xuan, et al. “JFIX: Semantics-Based Repair of Java Programs via Symbolic
PathFinder.” Proceedings of the 26th ACM SIGSOFT International Symposium on
Software Testing and Analysis, ACM, 2017, pp. 376–79, doi:10.1145/3092703.3098225.'
short: X. Le, D.H. Chu, D. Lo, C. Le Goues, W. Visser, in:, Proceedings of the 26th
ACM SIGSOFT International Symposium on Software Testing and Analysis, ACM, 2017,
pp. 376–379.
conference:
end_date: 2017-07-14
location: Santa Barbara, CA, United States
name: 'ISSTA: International Symposium on Software Testing and Analysis'
start_date: 2017-07-10
date_created: 2018-12-11T11:49:19Z
date_published: 2017-07-10T00:00:00Z
date_updated: 2021-01-12T08:22:05Z
day: '10'
department:
- _id: ToHe
doi: 10.1145/3092703.3098225
language:
- iso: eng
month: '07'
oa_version: None
page: '376 - 379 '
project:
- _id: 25832EC2-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: S 11407_N23
name: Rigorous Systems Engineering
- _id: 25F42A32-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: Z211
name: The Wittgenstein Prize
publication: Proceedings of the 26th ACM SIGSOFT International Symposium on Software
Testing and Analysis
publication_status: published
publisher: ACM
publist_id: '6478'
quality_controlled: '1'
scopus_import: 1
status: public
title: 'JFIX: Semantics-based repair of Java programs via symbolic PathFinder'
type: conference
user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87
year: '2017'
...
---
_id: '9506'
abstract:
- lang: eng
text: Methylation in the bodies of active genes is common in animals and vascular
plants. Evolutionary patterns indicate homeostatic functions for this type of
methylation.
article_number: '87'
article_processing_charge: No
author:
- first_name: Daniel
full_name: Zilberman, Daniel
id: 6973db13-dd5f-11ea-814e-b3e5455e9ed1
last_name: Zilberman
orcid: 0000-0002-0123-8649
citation:
ama: Zilberman D. An evolutionary case for functional gene body methylation in plants
and animals. Genome Biology. 2017;18(1). doi:10.1186/s13059-017-1230-2
apa: Zilberman, D. (2017). An evolutionary case for functional gene body methylation
in plants and animals. Genome Biology. Springer Nature. https://doi.org/10.1186/s13059-017-1230-2
chicago: Zilberman, Daniel. “An Evolutionary Case for Functional Gene Body Methylation
in Plants and Animals.” Genome Biology. Springer Nature, 2017. https://doi.org/10.1186/s13059-017-1230-2.
ieee: D. Zilberman, “An evolutionary case for functional gene body methylation in
plants and animals,” Genome Biology, vol. 18, no. 1. Springer Nature, 2017.
ista: Zilberman D. 2017. An evolutionary case for functional gene body methylation
in plants and animals. Genome Biology. 18(1), 87.
mla: Zilberman, Daniel. “An Evolutionary Case for Functional Gene Body Methylation
in Plants and Animals.” Genome Biology, vol. 18, no. 1, 87, Springer Nature,
2017, doi:10.1186/s13059-017-1230-2.
short: D. Zilberman, Genome Biology 18 (2017).
date_created: 2021-06-07T12:27:39Z
date_published: 2017-05-09T00:00:00Z
date_updated: 2021-12-14T07:55:02Z
day: '09'
ddc:
- '570'
department:
- _id: DaZi
doi: 10.1186/s13059-017-1230-2
extern: '1'
external_id:
pmid:
- '28486944'
file:
- access_level: open_access
checksum: 5a455ad914e7d225b1baa4ab07fd925e
content_type: application/pdf
creator: asandaue
date_created: 2021-06-07T12:31:36Z
date_updated: 2021-06-07T12:31:36Z
file_id: '9507'
file_name: 2017_GenomeBiology_Zilberman.pdf
file_size: 278183
relation: main_file
success: 1
file_date_updated: 2021-06-07T12:31:36Z
has_accepted_license: '1'
intvolume: ' 18'
issue: '1'
language:
- iso: eng
month: '05'
oa: 1
oa_version: Published Version
pmid: 1
publication: Genome Biology
publication_identifier:
eissn:
- 1465-6906
issn:
- 1474-760X
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
scopus_import: '1'
status: public
title: An evolutionary case for functional gene body methylation in plants and animals
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: journal_article
user_id: 8b945eb4-e2f2-11eb-945a-df72226e66a9
volume: 18
year: '2017'
...
---
_id: '958'
abstract:
- lang: eng
text: Biosensors that exploit Forster resonance energy transfer (FRET) can be used
to visualize biological and physiological processes and are capable of providing
detailed information in both spatial and temporal dimensions. In a FRET-based
biosensor, substrate binding is associated with a change in the relative positions
of two fluorophores, leading to a change in FRET efficiency that may be observed
in the fluorescence spectrum. As a result, their design requires a ligand-binding
protein that exhibits a conformational change upon binding. However, not all ligand-binding
proteins produce responsive sensors upon conjugation to fluorescent proteins or
dyes, and identifying the optimum locations for the fluorophores often involves
labor-intensive iterative design or high-throughput screening. Combining the genetic
fusion of a fluorescent protein to the ligand-binding protein with site-specific
covalent attachment of a fluorescent dye can allow fine control over the positions
of the two fluorophores, allowing the construction of very sensitive sensors.
This relies upon the accurate prediction of the locations of the two fluorophores
in bound and unbound states. In this chapter, we describe a method for computational
identification of dye-attachment sites that allows the use of cysteine modification
to attach synthetic dyes that can be paired with a fluorescent protein for the
purposes of creating FRET sensors.
alternative_title:
- Methods in Molecular Biology
author:
- first_name: Joshua
full_name: Mitchell, Joshua
last_name: Mitchell
- first_name: William
full_name: Zhang, William
last_name: Zhang
- first_name: Michel
full_name: Herde, Michel
last_name: Herde
- first_name: Christian
full_name: Henneberger, Christian
last_name: Henneberger
- first_name: Harald L
full_name: Janovjak, Harald L
id: 33BA6C30-F248-11E8-B48F-1D18A9856A87
last_name: Janovjak
orcid: 0000-0002-8023-9315
- first_name: Megan
full_name: O'Mara, Megan
last_name: O'Mara
- first_name: Colin
full_name: Jackson, Colin
last_name: Jackson
citation:
ama: 'Mitchell J, Zhang W, Herde M, et al. Method for developing optical sensors
using a synthetic dye fluorescent protein FRET pair and computational modeling
and assessment. In: Stein V, ed. Synthetic Protein Switches. Vol 1596.
Synthetic Protein Switches. Springer; 2017:89-99. doi:10.1007/978-1-4939-6940-1_6'
apa: Mitchell, J., Zhang, W., Herde, M., Henneberger, C., Janovjak, H. L., O’Mara,
M., & Jackson, C. (2017). Method for developing optical sensors using a synthetic
dye fluorescent protein FRET pair and computational modeling and assessment. In
V. Stein (Ed.), Synthetic Protein Switches (Vol. 1596, pp. 89–99). Springer.
https://doi.org/10.1007/978-1-4939-6940-1_6
chicago: Mitchell, Joshua, William Zhang, Michel Herde, Christian Henneberger, Harald
L Janovjak, Megan O’Mara, and Colin Jackson. “Method for Developing Optical Sensors
Using a Synthetic Dye Fluorescent Protein FRET Pair and Computational Modeling
and Assessment.” In Synthetic Protein Switches, edited by Viktor Stein,
1596:89–99. Synthetic Protein Switches. Springer, 2017. https://doi.org/10.1007/978-1-4939-6940-1_6.
ieee: J. Mitchell et al., “Method for developing optical sensors using a
synthetic dye fluorescent protein FRET pair and computational modeling and assessment,”
in Synthetic Protein Switches, vol. 1596, V. Stein, Ed. Springer, 2017,
pp. 89–99.
ista: 'Mitchell J, Zhang W, Herde M, Henneberger C, Janovjak HL, O’Mara M, Jackson
C. 2017.Method for developing optical sensors using a synthetic dye fluorescent
protein FRET pair and computational modeling and assessment. In: Synthetic Protein
Switches. Methods in Molecular Biology, vol. 1596, 89–99.'
mla: Mitchell, Joshua, et al. “Method for Developing Optical Sensors Using a Synthetic
Dye Fluorescent Protein FRET Pair and Computational Modeling and Assessment.”
Synthetic Protein Switches, edited by Viktor Stein, vol. 1596, Springer,
2017, pp. 89–99, doi:10.1007/978-1-4939-6940-1_6.
short: J. Mitchell, W. Zhang, M. Herde, C. Henneberger, H.L. Janovjak, M. O’Mara,
C. Jackson, in:, V. Stein (Ed.), Synthetic Protein Switches, Springer, 2017, pp.
89–99.
date_created: 2018-12-11T11:49:24Z
date_published: 2017-05-15T00:00:00Z
date_updated: 2021-01-12T08:22:13Z
day: '15'
department:
- _id: HaJa
doi: 10.1007/978-1-4939-6940-1_6
editor:
- first_name: Viktor
full_name: Stein, Viktor
last_name: Stein
intvolume: ' 1596'
language:
- iso: eng
month: '05'
oa_version: None
page: 89 - 99
publication: Synthetic Protein Switches
publication_identifier:
issn:
- '10643745'
publication_status: published
publisher: Springer
publist_id: '6450'
quality_controlled: '1'
scopus_import: 1
series_title: Synthetic Protein Switches
status: public
title: Method for developing optical sensors using a synthetic dye fluorescent protein
FRET pair and computational modeling and assessment
type: book_chapter
user_id: 4435EBFC-F248-11E8-B48F-1D18A9856A87
volume: 1596
year: '2017'
...
---
_id: '9660'
abstract:
- lang: eng
text: In this paper we discuss how the information contained in atomistic simulations
of homogeneous nucleation should be used when fitting the parameters in macroscopic
nucleation models. We show how the number of solid and liquid atoms in such simulations
can be determined unambiguously by using a Gibbs dividing surface and how the
free energy as a function of the number of solid atoms in the nucleus can thus
be extracted. We then show that the parameters (the chemical potential, the interfacial
free energy, and a Tolman correction) of a model based on classical nucleation
theory can be fitted using the information contained in these free-energy profiles
but that the parameters in such models are highly correlated. This correlation
is unfortunate as it ensures that small errors in the computed free energy surface
can give rise to large errors in the extrapolated properties of the fitted model.
To resolve this problem we thus propose a method for fitting macroscopic nucleation
models that uses simulations of planar interfaces and simulations of three-dimensional
nuclei in tandem. We show that when the chemical potentials and the interface
energy are pinned to their planar-interface values, more precise estimates for
the Tolman length are obtained. Extrapolating the free energy profile obtained
from small simulation boxes to larger nuclei is thus more reliable.
article_number: '104707'
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. The Gibbs free energy of homogeneous nucleation:
From atomistic nuclei to the planar limit. The Journal of Chemical Physics.
2017;147(10). doi:10.1063/1.4997180'
apa: 'Cheng, B., Tribello, G. A., & Ceriotti, M. (2017). The Gibbs free energy
of homogeneous nucleation: From atomistic nuclei to the planar limit. The Journal
of Chemical Physics. AIP Publishing. https://doi.org/10.1063/1.4997180'
chicago: 'Cheng, Bingqing, Gareth A. Tribello, and Michele Ceriotti. “The Gibbs
Free Energy of Homogeneous Nucleation: From Atomistic Nuclei to the Planar Limit.”
The Journal of Chemical Physics. AIP Publishing, 2017. https://doi.org/10.1063/1.4997180.'
ieee: 'B. Cheng, G. A. Tribello, and M. Ceriotti, “The Gibbs free energy of homogeneous
nucleation: From atomistic nuclei to the planar limit,” The Journal of Chemical
Physics, vol. 147, no. 10. AIP Publishing, 2017.'
ista: 'Cheng B, Tribello GA, Ceriotti M. 2017. The Gibbs free energy of homogeneous
nucleation: From atomistic nuclei to the planar limit. The Journal of Chemical
Physics. 147(10), 104707.'
mla: 'Cheng, Bingqing, et al. “The Gibbs Free Energy of Homogeneous Nucleation:
From Atomistic Nuclei to the Planar Limit.” The Journal of Chemical Physics,
vol. 147, no. 10, 104707, AIP Publishing, 2017, doi:10.1063/1.4997180.'
short: B. Cheng, G.A. Tribello, M. Ceriotti, The Journal of Chemical Physics 147
(2017).
date_created: 2021-07-15T08:13:29Z
date_published: 2017-09-14T00:00:00Z
date_updated: 2023-02-23T14:04:02Z
day: '14'
doi: 10.1063/1.4997180
extern: '1'
external_id:
arxiv:
- '1703.06062'
pmid:
- '28915742'
intvolume: ' 147'
issue: '10'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://pure.qub.ac.uk/en/publications/the-gibbs-free-energy-of-homogeneous-nucleation-from-atomistic-nuclei-to-the-planar-limit(4599cdb4-dcc4-4522-8763-7b2a165ebf12).html
month: '09'
oa: 1
oa_version: Submitted Version
pmid: 1
publication: The Journal of Chemical Physics
publication_identifier:
eissn:
- 1089-7690
issn:
- 0021-9606
publication_status: published
publisher: AIP Publishing
quality_controlled: '1'
scopus_import: '1'
status: public
title: 'The Gibbs free energy of homogeneous nucleation: From atomistic nuclei to
the planar limit'
type: journal_article
user_id: 6785fbc1-c503-11eb-8a32-93094b40e1cf
volume: 147
year: '2017'
...
---
_id: '9661'
abstract:
- lang: eng
text: Macroscopic theories of nucleation such as classical nucleation theory envision
that clusters of the bulk stable phase form inside the bulk metastable phase.
Molecular dynamics simulations are often used to elucidate nucleation mechanisms,
by capturing the microscopic configurations of all the atoms. In this paper, we
introduce a thermodynamic model that links macroscopic theories and atomic-scale
simulations and thus provide a simple and elegant framework for testing the limits
of classical nucleation theory.
article_number: '034106'
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: Michele
full_name: Ceriotti, Michele
last_name: Ceriotti
citation:
ama: Cheng B, Ceriotti M. Bridging the gap between atomistic and macroscopic models
of homogeneous nucleation. The Journal of Chemical Physics. 2017;146(3).
doi:10.1063/1.4973883
apa: Cheng, B., & Ceriotti, M. (2017). Bridging the gap between atomistic and
macroscopic models of homogeneous nucleation. The Journal of Chemical Physics.
AIP Publishing. https://doi.org/10.1063/1.4973883
chicago: Cheng, Bingqing, and Michele Ceriotti. “Bridging the Gap between Atomistic
and Macroscopic Models of Homogeneous Nucleation.” The Journal of Chemical
Physics. AIP Publishing, 2017. https://doi.org/10.1063/1.4973883.
ieee: B. Cheng and M. Ceriotti, “Bridging the gap between atomistic and macroscopic
models of homogeneous nucleation,” The Journal of Chemical Physics, vol.
146, no. 3. AIP Publishing, 2017.
ista: Cheng B, Ceriotti M. 2017. Bridging the gap between atomistic and macroscopic
models of homogeneous nucleation. The Journal of Chemical Physics. 146(3), 034106.
mla: Cheng, Bingqing, and Michele Ceriotti. “Bridging the Gap between Atomistic
and Macroscopic Models of Homogeneous Nucleation.” The Journal of Chemical
Physics, vol. 146, no. 3, 034106, AIP Publishing, 2017, doi:10.1063/1.4973883.
short: B. Cheng, M. Ceriotti, The Journal of Chemical Physics 146 (2017).
date_created: 2021-07-15T08:27:31Z
date_published: 2017-01-21T00:00:00Z
date_updated: 2021-08-09T12:31:57Z
day: '21'
doi: 10.1063/1.4973883
extern: '1'
external_id:
arxiv:
- '1610.01322'
pmid:
- '28109231'
intvolume: ' 146'
issue: '3'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/1610.01322
month: '01'
oa: 1
oa_version: Preprint
pmid: 1
publication: The Journal of Chemical Physics
publication_identifier:
eissn:
- 1089-7690
issn:
- 0021-9606
publication_status: published
publisher: AIP Publishing
quality_controlled: '1'
scopus_import: '1'
status: public
title: Bridging the gap between atomistic and macroscopic models of homogeneous nucleation
type: journal_article
user_id: 6785fbc1-c503-11eb-8a32-93094b40e1cf
volume: 146
year: '2017'
...