---
_id: '5788'
abstract:
- lang: eng
text: In two-player games on graphs, the players move a token through a graph to
produce an infinite path, which determines the winner or payoff of the game. Such
games are central in formal verification since they model the interaction between
a non-terminating system and its environment. We study bidding games in which
the players bid for the right to move the token. Two bidding rules have been defined.
In Richman bidding, in each round, the players simultaneously submit bids, and
the higher bidder moves the token and pays the other player. Poorman bidding is
similar except that the winner of the bidding pays the “bank” rather than the
other player. While poorman reachability games have been studied before, we present,
for the first time, results on infinite-duration poorman games. A central quantity
in these games is the ratio between the two players’ initial budgets. The questions
we study concern a necessary and sufficient ratio with which a player can achieve
a goal. For reachability objectives, such threshold ratios are known to exist
for both bidding rules. We show that the properties of poorman reachability games
extend to complex qualitative objectives such as parity, similarly to the Richman
case. Our most interesting results concern quantitative poorman games, namely
poorman mean-payoff games, where we construct optimal strategies depending on
the initial ratio, by showing a connection with random-turn based games. The connection
in itself is interesting, because it does not hold for reachability poorman games.
We also solve the complexity problems that arise in poorman bidding games.
alternative_title:
- LNCS
article_processing_charge: No
author:
- first_name: Guy
full_name: Avni, Guy
id: 463C8BC2-F248-11E8-B48F-1D18A9856A87
last_name: Avni
orcid: 0000-0001-5588-8287
- first_name: Thomas A
full_name: Henzinger, Thomas A
id: 40876CD8-F248-11E8-B48F-1D18A9856A87
last_name: Henzinger
orcid: 0000−0002−2985−7724
- first_name: Rasmus
full_name: Ibsen-Jensen, Rasmus
id: 3B699956-F248-11E8-B48F-1D18A9856A87
last_name: Ibsen-Jensen
orcid: 0000-0003-4783-0389
citation:
ama: 'Avni G, Henzinger TA, Ibsen-Jensen R. Infinite-duration poorman-bidding games.
In: Vol 11316. Springer; 2018:21-36. doi:10.1007/978-3-030-04612-5_2'
apa: 'Avni, G., Henzinger, T. A., & Ibsen-Jensen, R. (2018). Infinite-duration
poorman-bidding games (Vol. 11316, pp. 21–36). Presented at the 14th International
Conference on Web and Internet Economics, WINE, Oxford, UK: Springer. https://doi.org/10.1007/978-3-030-04612-5_2'
chicago: Avni, Guy, Thomas A Henzinger, and Rasmus Ibsen-Jensen. “Infinite-Duration
Poorman-Bidding Games,” 11316:21–36. Springer, 2018. https://doi.org/10.1007/978-3-030-04612-5_2.
ieee: G. Avni, T. A. Henzinger, and R. Ibsen-Jensen, “Infinite-duration poorman-bidding
games,” presented at the 14th International Conference on Web and Internet Economics,
WINE, Oxford, UK, 2018, vol. 11316, pp. 21–36.
ista: Avni G, Henzinger TA, Ibsen-Jensen R. 2018. Infinite-duration poorman-bidding
games. 14th International Conference on Web and Internet Economics, WINE, LNCS,
vol. 11316, 21–36.
mla: Avni, Guy, et al. Infinite-Duration Poorman-Bidding Games. Vol. 11316,
Springer, 2018, pp. 21–36, doi:10.1007/978-3-030-04612-5_2.
short: G. Avni, T.A. Henzinger, R. Ibsen-Jensen, in:, Springer, 2018, pp. 21–36.
conference:
end_date: 2018-12-17
location: Oxford, UK
name: 14th International Conference on Web and Internet Economics, WINE
start_date: 2018-12-15
date_created: 2018-12-30T22:59:14Z
date_published: 2018-11-21T00:00:00Z
date_updated: 2023-09-12T07:44:01Z
day: '21'
department:
- _id: ToHe
doi: 10.1007/978-3-030-04612-5_2
external_id:
arxiv:
- '1804.04372'
isi:
- '000865933000002'
intvolume: ' 11316'
isi: 1
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/1804.04372
month: '11'
oa: 1
oa_version: Preprint
page: 21-36
project:
- _id: 25F42A32-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: Z211
name: The Wittgenstein Prize
- _id: 25832EC2-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: S 11407_N23
name: Rigorous Systems Engineering
- _id: 264B3912-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: M02369
name: Formal Methods meets Algorithmic Game Theory
publication_identifier:
isbn:
- '9783030046118'
issn:
- '03029743'
publisher: Springer
quality_controlled: '1'
scopus_import: '1'
status: public
title: Infinite-duration poorman-bidding games
type: conference
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
volume: 11316
year: '2018'
...
---
_id: '150'
abstract:
- lang: eng
text: A short, 14-amino-acid segment called SP1, located in the Gag structural protein1,
has a critical role during the formation of the HIV-1 virus particle. During virus
assembly, the SP1 peptide and seven preceding residues fold into a six-helix bundle,
which holds together the Gag hexamer and facilitates the formation of a curved
immature hexagonal lattice underneath the viral membrane2,3. Upon completion of
assembly and budding, proteolytic cleavage of Gag leads to virus maturation, in
which the immature lattice is broken down; the liberated CA domain of Gag then
re-assembles into the mature conical capsid that encloses the viral genome and
associated enzymes. Folding and proteolysis of the six-helix bundle are crucial
rate-limiting steps of both Gag assembly and disassembly, and the six-helix bundle
is an established target of HIV-1 inhibitors4,5. Here, using a combination of
structural and functional analyses, we show that inositol hexakisphosphate (InsP6,
also known as IP6) facilitates the formation of the six-helix bundle and assembly
of the immature HIV-1 Gag lattice. IP6 makes ionic contacts with two rings of
lysine residues at the centre of the Gag hexamer. Proteolytic cleavage then unmasks
an alternative binding site, where IP6 interaction promotes the assembly of the
mature capsid lattice. These studies identify IP6 as a naturally occurring small
molecule that promotes both assembly and maturation of HIV-1.
article_processing_charge: No
article_type: original
author:
- first_name: Robert
full_name: Dick, Robert
last_name: Dick
- first_name: Kaneil K
full_name: Zadrozny, Kaneil K
last_name: Zadrozny
- first_name: Chaoyi
full_name: Xu, Chaoyi
last_name: Xu
- first_name: Florian
full_name: Schur, Florian
id: 48AD8942-F248-11E8-B48F-1D18A9856A87
last_name: Schur
orcid: 0000-0003-4790-8078
- first_name: Terri D
full_name: Lyddon, Terri D
last_name: Lyddon
- first_name: Clifton L
full_name: Ricana, Clifton L
last_name: Ricana
- first_name: Jonathan M
full_name: Wagner, Jonathan M
last_name: Wagner
- first_name: Juan R
full_name: Perilla, Juan R
last_name: Perilla
- first_name: Pornillos Barbie K
full_name: Ganser, Pornillos Barbie K
last_name: Ganser
- first_name: Marc C
full_name: Johnson, Marc C
last_name: Johnson
- first_name: Owen
full_name: Pornillos, Owen
last_name: Pornillos
- first_name: Volker
full_name: Vogt, Volker
last_name: Vogt
citation:
ama: Dick R, Zadrozny KK, Xu C, et al. Inositol phosphates are assembly co-factors
for HIV-1. Nature. 2018;560(7719):509–512. doi:10.1038/s41586-018-0396-4
apa: Dick, R., Zadrozny, K. K., Xu, C., Schur, F. K., Lyddon, T. D., Ricana, C.
L., … Vogt, V. (2018). Inositol phosphates are assembly co-factors for HIV-1.
Nature. Nature Publishing Group. https://doi.org/10.1038/s41586-018-0396-4
chicago: Dick, Robert, Kaneil K Zadrozny, Chaoyi Xu, Florian KM Schur, Terri D Lyddon,
Clifton L Ricana, Jonathan M Wagner, et al. “Inositol Phosphates Are Assembly
Co-Factors for HIV-1.” Nature. Nature Publishing Group, 2018. https://doi.org/10.1038/s41586-018-0396-4.
ieee: R. Dick et al., “Inositol phosphates are assembly co-factors for HIV-1,”
Nature, vol. 560, no. 7719. Nature Publishing Group, pp. 509–512, 2018.
ista: Dick R, Zadrozny KK, Xu C, Schur FK, Lyddon TD, Ricana CL, Wagner JM, Perilla
JR, Ganser PBK, Johnson MC, Pornillos O, Vogt V. 2018. Inositol phosphates are
assembly co-factors for HIV-1. Nature. 560(7719), 509–512.
mla: Dick, Robert, et al. “Inositol Phosphates Are Assembly Co-Factors for HIV-1.”
Nature, vol. 560, no. 7719, Nature Publishing Group, 2018, pp. 509–512,
doi:10.1038/s41586-018-0396-4.
short: R. Dick, K.K. Zadrozny, C. Xu, F.K. Schur, T.D. Lyddon, C.L. Ricana, J.M.
Wagner, J.R. Perilla, P.B.K. Ganser, M.C. Johnson, O. Pornillos, V. Vogt, Nature
560 (2018) 509–512.
date_created: 2018-12-11T11:44:53Z
date_published: 2018-08-29T00:00:00Z
date_updated: 2023-09-12T07:44:37Z
day: '29'
department:
- _id: FlSc
doi: 10.1038/s41586-018-0396-4
external_id:
isi:
- '000442483400046'
pmid:
- '30158708'
intvolume: ' 560'
isi: 1
issue: '7719'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6242333/
month: '08'
oa: 1
oa_version: Submitted Version
page: 509–512
pmid: 1
publication: Nature
publication_identifier:
eissn:
- 1476-4687
publication_status: published
publisher: Nature Publishing Group
quality_controlled: '1'
related_material:
link:
- relation: erratum
url: https://doi.org/10.1038/s41586-018-0505-4
scopus_import: '1'
status: public
title: Inositol phosphates are assembly co-factors for HIV-1
type: journal_article
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
volume: 560
year: '2018'
...
---
_id: '303'
abstract:
- lang: eng
text: The theory of tropical series, that we develop here, firstly appeared in the
study of the growth of pluriharmonic functions. Motivated by waves in sandpile
models we introduce a dynamic on the set of tropical series, and it is experimentally
observed that this dynamic obeys a power law. So, this paper serves as a compilation
of results we need for other articles and also introduces several objects interesting
by themselves.
acknowledgement: The first author, Nikita Kalinin, is funded by SNCF PostDoc.Mobility
grant 168647. Support from the Basic Research Program of the National Research University
Higher School of Economics is gratefully acknowledged. The second author, Mikhail
Shkolnikov, is supported in part by the grant 159240 of the Swiss National Science
Foundation as well as by the National Center of Competence in Research SwissMAP
of the Swiss National Science Foundation.
article_processing_charge: No
author:
- first_name: Nikita
full_name: Kalinin, Nikita
last_name: Kalinin
- first_name: Mikhail
full_name: Shkolnikov, Mikhail
id: 35084A62-F248-11E8-B48F-1D18A9856A87
last_name: Shkolnikov
orcid: 0000-0002-4310-178X
citation:
ama: Kalinin N, Shkolnikov M. Introduction to tropical series and wave dynamic on
them. Discrete and Continuous Dynamical Systems- Series A. 2018;38(6):2827-2849.
doi:10.3934/dcds.2018120
apa: Kalinin, N., & Shkolnikov, M. (2018). Introduction to tropical series and
wave dynamic on them. Discrete and Continuous Dynamical Systems- Series A.
AIMS. https://doi.org/10.3934/dcds.2018120
chicago: Kalinin, Nikita, and Mikhail Shkolnikov. “Introduction to Tropical Series
and Wave Dynamic on Them.” Discrete and Continuous Dynamical Systems- Series
A. AIMS, 2018. https://doi.org/10.3934/dcds.2018120.
ieee: N. Kalinin and M. Shkolnikov, “Introduction to tropical series and wave dynamic
on them,” Discrete and Continuous Dynamical Systems- Series A, vol. 38,
no. 6. AIMS, pp. 2827–2849, 2018.
ista: Kalinin N, Shkolnikov M. 2018. Introduction to tropical series and wave dynamic
on them. Discrete and Continuous Dynamical Systems- Series A. 38(6), 2827–2849.
mla: Kalinin, Nikita, and Mikhail Shkolnikov. “Introduction to Tropical Series and
Wave Dynamic on Them.” Discrete and Continuous Dynamical Systems- Series A,
vol. 38, no. 6, AIMS, 2018, pp. 2827–49, doi:10.3934/dcds.2018120.
short: N. Kalinin, M. Shkolnikov, Discrete and Continuous Dynamical Systems- Series
A 38 (2018) 2827–2849.
date_created: 2018-12-11T11:45:43Z
date_published: 2018-06-01T00:00:00Z
date_updated: 2023-09-12T07:45:37Z
day: '01'
department:
- _id: TaHa
doi: 10.3934/dcds.2018120
external_id:
arxiv:
- '1706.03062'
isi:
- '000438818400007'
intvolume: ' 38'
isi: 1
issue: '6'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/1706.03062
month: '06'
oa: 1
oa_version: Submitted Version
page: 2827 - 2849
publication: Discrete and Continuous Dynamical Systems- Series A
publication_status: published
publisher: AIMS
publist_id: '7576'
quality_controlled: '1'
scopus_import: '1'
status: public
title: Introduction to tropical series and wave dynamic on them
type: journal_article
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
volume: 38
year: '2018'
...
---
_id: '14202'
abstract:
- lang: eng
text: "Approximating a probability density in a tractable manner is a central task\r\nin
Bayesian statistics. Variational Inference (VI) is a popular technique that\r\nachieves
tractability by choosing a relatively simple variational family.\r\nBorrowing
ideas from the classic boosting framework, recent approaches attempt\r\nto \\emph{boost}
VI by replacing the selection of a single density with a\r\ngreedily constructed
mixture of densities. In order to guarantee convergence,\r\nprevious works impose
stringent assumptions that require significant effort for\r\npractitioners. Specifically,
they require a custom implementation of the greedy\r\nstep (called the LMO) for
every probabilistic model with respect to an\r\nunnatural variational family of
truncated distributions. Our work fixes these\r\nissues with novel theoretical
and algorithmic insights. On the theoretical\r\nside, we show that boosting VI
satisfies a relaxed smoothness assumption which\r\nis sufficient for the convergence
of the functional Frank-Wolfe (FW) algorithm.\r\nFurthermore, we rephrase the
LMO problem and propose to maximize the Residual\r\nELBO (RELBO) which replaces
the standard ELBO optimization in VI. These\r\ntheoretical enhancements allow
for black box implementation of the boosting\r\nsubroutine. Finally, we present
a stopping criterion drawn from the duality gap\r\nin the classic FW analyses
and exhaustive experiments to illustrate the\r\nusefulness of our theoretical
and algorithmic contributions."
article_processing_charge: No
author:
- first_name: Francesco
full_name: Locatello, Francesco
id: 26cfd52f-2483-11ee-8040-88983bcc06d4
last_name: Locatello
orcid: 0000-0002-4850-0683
- first_name: Gideon
full_name: Dresdner, Gideon
last_name: Dresdner
- first_name: Rajiv
full_name: Khanna, Rajiv
last_name: Khanna
- first_name: Isabel
full_name: Valera, Isabel
last_name: Valera
- first_name: Gunnar
full_name: Rätsch, Gunnar
last_name: Rätsch
citation:
ama: 'Locatello F, Dresdner G, Khanna R, Valera I, Rätsch G. Boosting black box
variational inference. In: Advances in Neural Information Processing Systems.
Vol 31. Neural Information Processing Systems Foundation; 2018.'
apa: 'Locatello, F., Dresdner, G., Khanna, R., Valera, I., & Rätsch, G. (2018).
Boosting black box variational inference. In Advances in Neural Information
Processing Systems (Vol. 31). Montreal, Canada: Neural Information Processing
Systems Foundation.'
chicago: Locatello, Francesco, Gideon Dresdner, Rajiv Khanna, Isabel Valera, and
Gunnar Rätsch. “Boosting Black Box Variational Inference.” In Advances in Neural
Information Processing Systems, Vol. 31. Neural Information Processing Systems
Foundation, 2018.
ieee: F. Locatello, G. Dresdner, R. Khanna, I. Valera, and G. Rätsch, “Boosting
black box variational inference,” in Advances in Neural Information Processing
Systems, Montreal, Canada, 2018, vol. 31.
ista: 'Locatello F, Dresdner G, Khanna R, Valera I, Rätsch G. 2018. Boosting black
box variational inference. Advances in Neural Information Processing Systems.
NeurIPS: Neural Information Processing Systems vol. 31.'
mla: Locatello, Francesco, et al. “Boosting Black Box Variational Inference.” Advances
in Neural Information Processing Systems, vol. 31, Neural Information Processing
Systems Foundation, 2018.
short: F. Locatello, G. Dresdner, R. Khanna, I. Valera, G. Rätsch, in:, Advances
in Neural Information Processing Systems, Neural Information Processing Systems
Foundation, 2018.
conference:
end_date: 2018-12-08
location: Montreal, Canada
name: 'NeurIPS: Neural Information Processing Systems'
start_date: 2018-12-03
date_created: 2023-08-22T14:15:40Z
date_published: 2018-06-06T00:00:00Z
date_updated: 2023-09-13T07:38:24Z
day: '06'
department:
- _id: FrLo
extern: '1'
external_id:
arxiv:
- '1806.02185'
intvolume: ' 31'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/1806.02185
month: '06'
oa: 1
oa_version: Preprint
publication: Advances in Neural Information Processing Systems
publication_identifier:
eissn:
- 1049-5258
isbn:
- '9781510884472'
publication_status: published
publisher: Neural Information Processing Systems Foundation
quality_controlled: '1'
scopus_import: '1'
status: public
title: Boosting black box variational inference
type: conference
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 31
year: '2018'
...
---
_id: '14201'
abstract:
- lang: eng
text: "Variational inference is a popular technique to approximate a possibly\r\nintractable
Bayesian posterior with a more tractable one. Recently, boosting\r\nvariational
inference has been proposed as a new paradigm to approximate the\r\nposterior
by a mixture of densities by greedily adding components to the\r\nmixture. However,
as is the case with many other variational inference\r\nalgorithms, its theoretical
properties have not been studied. In the present\r\nwork, we study the convergence
properties of this approach from a modern\r\noptimization viewpoint by establishing
connections to the classic Frank-Wolfe\r\nalgorithm. Our analyses yields novel
theoretical insights regarding the\r\nsufficient conditions for convergence, explicit
rates, and algorithmic\r\nsimplifications. Since a lot of focus in previous works
for variational\r\ninference has been on tractability, our work is especially
important as a much\r\nneeded attempt to bridge the gap between probabilistic
models and their\r\ncorresponding theoretical properties."
alternative_title:
- PMLR
article_processing_charge: No
author:
- first_name: Francesco
full_name: Locatello, Francesco
id: 26cfd52f-2483-11ee-8040-88983bcc06d4
last_name: Locatello
orcid: 0000-0002-4850-0683
- first_name: Rajiv
full_name: Khanna, Rajiv
last_name: Khanna
- first_name: Joydeep
full_name: Ghosh, Joydeep
last_name: Ghosh
- first_name: Gunnar
full_name: Rätsch, Gunnar
last_name: Rätsch
citation:
ama: 'Locatello F, Khanna R, Ghosh J, Rätsch G. Boosting variational inference:
An optimization perspective. In: Proceedings of the 21st International Conference
on Artificial Intelligence and Statistics. Vol 84. ML Research Press; 2018:464-472.'
apa: 'Locatello, F., Khanna, R., Ghosh, J., & Rätsch, G. (2018). Boosting variational
inference: An optimization perspective. In Proceedings of the 21st International
Conference on Artificial Intelligence and Statistics (Vol. 84, pp. 464–472).
Playa Blanca, Lanzarote: ML Research Press.'
chicago: 'Locatello, Francesco, Rajiv Khanna, Joydeep Ghosh, and Gunnar Rätsch.
“Boosting Variational Inference: An Optimization Perspective.” In Proceedings
of the 21st International Conference on Artificial Intelligence and Statistics,
84:464–72. ML Research Press, 2018.'
ieee: 'F. Locatello, R. Khanna, J. Ghosh, and G. Rätsch, “Boosting variational inference:
An optimization perspective,” in Proceedings of the 21st International Conference
on Artificial Intelligence and Statistics, Playa Blanca, Lanzarote, 2018,
vol. 84, pp. 464–472.'
ista: 'Locatello F, Khanna R, Ghosh J, Rätsch G. 2018. Boosting variational inference:
An optimization perspective. Proceedings of the 21st International Conference
on Artificial Intelligence and Statistics. AISTATS: Conference on Artificial Intelligence
and Statistics, PMLR, vol. 84, 464–472.'
mla: 'Locatello, Francesco, et al. “Boosting Variational Inference: An Optimization
Perspective.” Proceedings of the 21st International Conference on Artificial
Intelligence and Statistics, vol. 84, ML Research Press, 2018, pp. 464–72.'
short: F. Locatello, R. Khanna, J. Ghosh, G. Rätsch, in:, Proceedings of the 21st
International Conference on Artificial Intelligence and Statistics, ML Research
Press, 2018, pp. 464–472.
conference:
end_date: 2018-04-11
location: Playa Blanca, Lanzarote
name: 'AISTATS: Conference on Artificial Intelligence and Statistics'
start_date: 2018-04-09
date_created: 2023-08-22T14:15:20Z
date_published: 2018-04-15T00:00:00Z
date_updated: 2023-09-13T07:52:40Z
day: '15'
department:
- _id: FrLo
extern: '1'
external_id:
arxiv:
- '1708.01733'
intvolume: ' 84'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/1708.01733
month: '04'
oa: 1
oa_version: Preprint
page: 464-472
publication: Proceedings of the 21st International Conference on Artificial Intelligence
and Statistics
publication_status: published
publisher: ML Research Press
quality_controlled: '1'
scopus_import: '1'
status: public
title: 'Boosting variational inference: An optimization perspective'
type: conference
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 84
year: '2018'
...
---
_id: '14198'
abstract:
- lang: eng
text: "High-dimensional time series are common in many domains. Since human\r\ncognition
is not optimized to work well in high-dimensional spaces, these areas\r\ncould
benefit from interpretable low-dimensional representations. However, most\r\nrepresentation
learning algorithms for time series data are difficult to\r\ninterpret. This is
due to non-intuitive mappings from data features to salient\r\nproperties of the
representation and non-smoothness over time. To address this\r\nproblem, we propose
a new representation learning framework building on ideas\r\nfrom interpretable
discrete dimensionality reduction and deep generative\r\nmodeling. This framework
allows us to learn discrete representations of time\r\nseries, which give rise
to smooth and interpretable embeddings with superior\r\nclustering performance.
We introduce a new way to overcome the\r\nnon-differentiability in discrete representation
learning and present a\r\ngradient-based version of the traditional self-organizing
map algorithm that is\r\nmore performant than the original. Furthermore, to allow
for a probabilistic\r\ninterpretation of our method, we integrate a Markov model
in the representation\r\nspace. This model uncovers the temporal transition structure,
improves\r\nclustering performance even further and provides additional explanatory\r\ninsights
as well as a natural representation of uncertainty. We evaluate our\r\nmodel in
terms of clustering performance and interpretability on static\r\n(Fashion-)MNIST
data, a time series of linearly interpolated (Fashion-)MNIST\r\nimages, a chaotic
Lorenz attractor system with two macro states, as well as on\r\na challenging
real world medical time series application on the eICU data set.\r\nOur learned
representations compare favorably with competitor methods and\r\nfacilitate downstream
tasks on the real world data."
article_processing_charge: No
author:
- first_name: Vincent
full_name: Fortuin, Vincent
last_name: Fortuin
- first_name: Matthias
full_name: Hüser, Matthias
last_name: Hüser
- first_name: Francesco
full_name: Locatello, Francesco
id: 26cfd52f-2483-11ee-8040-88983bcc06d4
last_name: Locatello
orcid: 0000-0002-4850-0683
- first_name: Heiko
full_name: Strathmann, Heiko
last_name: Strathmann
- first_name: Gunnar
full_name: Rätsch, Gunnar
last_name: Rätsch
citation:
ama: 'Fortuin V, Hüser M, Locatello F, Strathmann H, Rätsch G. SOM-VAE: Interpretable
discrete representation learning on time series. In: International Conference
on Learning Representations. ; 2018.'
apa: 'Fortuin, V., Hüser, M., Locatello, F., Strathmann, H., & Rätsch, G. (2018).
SOM-VAE: Interpretable discrete representation learning on time series. In International
Conference on Learning Representations. New Orleans, LA, United States.'
chicago: 'Fortuin, Vincent, Matthias Hüser, Francesco Locatello, Heiko Strathmann,
and Gunnar Rätsch. “SOM-VAE: Interpretable Discrete Representation Learning on
Time Series.” In International Conference on Learning Representations,
2018.'
ieee: 'V. Fortuin, M. Hüser, F. Locatello, H. Strathmann, and G. Rätsch, “SOM-VAE:
Interpretable discrete representation learning on time series,” in International
Conference on Learning Representations, New Orleans, LA, United States, 2018.'
ista: 'Fortuin V, Hüser M, Locatello F, Strathmann H, Rätsch G. 2018. SOM-VAE: Interpretable
discrete representation learning on time series. International Conference on Learning
Representations. ICLR: International Conference on Learning Representations.'
mla: 'Fortuin, Vincent, et al. “SOM-VAE: Interpretable Discrete Representation Learning
on Time Series.” International Conference on Learning Representations,
2018.'
short: V. Fortuin, M. Hüser, F. Locatello, H. Strathmann, G. Rätsch, in:, International
Conference on Learning Representations, 2018.
conference:
end_date: 2019-05-09
location: New Orleans, LA, United States
name: 'ICLR: International Conference on Learning Representations'
start_date: 2019-05-06
date_created: 2023-08-22T14:12:48Z
date_published: 2018-06-06T00:00:00Z
date_updated: 2023-09-13T06:35:12Z
day: '06'
department:
- _id: FrLo
extern: '1'
external_id:
arxiv:
- '1806.02199'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/1806.02199
month: '06'
oa: 1
oa_version: Preprint
publication: International Conference on Learning Representations
publication_status: published
quality_controlled: '1'
status: public
title: 'SOM-VAE: Interpretable discrete representation learning on time series'
type: conference
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
year: '2018'
...
---
_id: '14203'
abstract:
- lang: eng
text: We propose a conditional gradient framework for a composite convex minimization
template with broad applications. Our approach combines smoothing and homotopy
techniques under the CGM framework, and provably achieves the optimal O(1/k−−√)
convergence rate. We demonstrate that the same rate holds if the linear subproblems
are solved approximately with additive or multiplicative error. In contrast with
the relevant work, we are able to characterize the convergence when the non-smooth
term is an indicator function. Specific applications of our framework include
the non-smooth minimization, semidefinite programming, and minimization with linear
inclusion constraints over a compact domain. Numerical evidence demonstrates the
benefits of our framework.
alternative_title:
- PMLR
article_processing_charge: No
author:
- first_name: Alp
full_name: Yurtsever, Alp
last_name: Yurtsever
- first_name: Olivier
full_name: Fercoq, Olivier
last_name: Fercoq
- first_name: Francesco
full_name: Locatello, Francesco
id: 26cfd52f-2483-11ee-8040-88983bcc06d4
last_name: Locatello
orcid: 0000-0002-4850-0683
- first_name: Volkan
full_name: Cevher, Volkan
last_name: Cevher
citation:
ama: 'Yurtsever A, Fercoq O, Locatello F, Cevher V. A conditional gradient framework
for composite convex minimization with applications to semidefinite programming.
In: Proceedings of the 35th International Conference on Machine Learning.
Vol 80. ML Research Press; 2018:5727-5736.'
apa: 'Yurtsever, A., Fercoq, O., Locatello, F., & Cevher, V. (2018). A conditional
gradient framework for composite convex minimization with applications to semidefinite
programming. In Proceedings of the 35th International Conference on Machine
Learning (Vol. 80, pp. 5727–5736). Stockholm, Sweden: ML Research Press.'
chicago: Yurtsever, Alp, Olivier Fercoq, Francesco Locatello, and Volkan Cevher.
“A Conditional Gradient Framework for Composite Convex Minimization with Applications
to Semidefinite Programming.” In Proceedings of the 35th International Conference
on Machine Learning, 80:5727–36. ML Research Press, 2018.
ieee: A. Yurtsever, O. Fercoq, F. Locatello, and V. Cevher, “A conditional gradient
framework for composite convex minimization with applications to semidefinite
programming,” in Proceedings of the 35th International Conference on Machine
Learning, Stockholm, Sweden, 2018, vol. 80, pp. 5727–5736.
ista: 'Yurtsever A, Fercoq O, Locatello F, Cevher V. 2018. A conditional gradient
framework for composite convex minimization with applications to semidefinite
programming. Proceedings of the 35th International Conference on Machine Learning.
ICML: International Conference on Machine Learning, PMLR, vol. 80, 5727–5736.'
mla: Yurtsever, Alp, et al. “A Conditional Gradient Framework for Composite Convex
Minimization with Applications to Semidefinite Programming.” Proceedings of
the 35th International Conference on Machine Learning, vol. 80, ML Research
Press, 2018, pp. 5727–36.
short: A. Yurtsever, O. Fercoq, F. Locatello, V. Cevher, in:, Proceedings of the
35th International Conference on Machine Learning, ML Research Press, 2018, pp.
5727–5736.
conference:
end_date: 2018-07-15
location: Stockholm, Sweden
name: 'ICML: International Conference on Machine Learning'
start_date: 2018-07-10
date_created: 2023-08-22T14:16:01Z
date_published: 2018-07-15T00:00:00Z
date_updated: 2023-09-13T08:13:39Z
day: '15'
department:
- _id: FrLo
extern: '1'
external_id:
arxiv:
- '1804.08544'
intvolume: ' 80'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/1804.08544
month: '07'
oa: 1
oa_version: Preprint
page: 5727-5736
publication: Proceedings of the 35th International Conference on Machine Learning
publication_status: published
publisher: ML Research Press
quality_controlled: '1'
status: public
title: A conditional gradient framework for composite convex minimization with applications
to semidefinite programming
type: conference
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 80
year: '2018'
...
---
_id: '282'
abstract:
- lang: eng
text: Adaptive introgression is common in nature and can be driven by selection
acting on multiple, linked genes. We explore the effects of polygenic selection
on introgression under the infinitesimal model with linkage. This model assumes
that the introgressing block has an effectively infinite number of genes, each
with an infinitesimal effect on the trait under selection. The block is assumed
to introgress under directional selection within a native population that is genetically
homogeneous. We use individual-based simulations and a branching process approximation
to compute various statistics of the introgressing block, and explore how these
depend on parameters such as the map length and initial trait value associated
with the introgressing block, the genetic variability along the block, and the
strength of selection. Our results show that the introgression dynamics of a block
under infinitesimal selection is qualitatively different from the dynamics of
neutral introgression. We also find that in the long run, surviving descendant
blocks are likely to have intermediate lengths, and clarify how the length is
shaped by the interplay between linkage and infinitesimal selection. Our results
suggest that it may be difficult to distinguish introgression of single loci from
that of genomic blocks with multiple, tightly linked and weakly selected loci.
article_processing_charge: No
author:
- first_name: Himani
full_name: Sachdeva, Himani
id: 42377A0A-F248-11E8-B48F-1D18A9856A87
last_name: Sachdeva
- first_name: Nicholas H
full_name: Barton, Nicholas H
id: 4880FE40-F248-11E8-B48F-1D18A9856A87
last_name: Barton
orcid: 0000-0002-8548-5240
citation:
ama: Sachdeva H, Barton NH. Introgression of a block of genome under infinitesimal
selection. Genetics. 2018;209(4):1279-1303. doi:10.1534/genetics.118.301018
apa: Sachdeva, H., & Barton, N. H. (2018). Introgression of a block of genome
under infinitesimal selection. Genetics. Genetics Society of America. https://doi.org/10.1534/genetics.118.301018
chicago: Sachdeva, Himani, and Nicholas H Barton. “Introgression of a Block of Genome
under Infinitesimal Selection.” Genetics. Genetics Society of America,
2018. https://doi.org/10.1534/genetics.118.301018.
ieee: H. Sachdeva and N. H. Barton, “Introgression of a block of genome under infinitesimal
selection,” Genetics, vol. 209, no. 4. Genetics Society of America, pp.
1279–1303, 2018.
ista: Sachdeva H, Barton NH. 2018. Introgression of a block of genome under infinitesimal
selection. Genetics. 209(4), 1279–1303.
mla: Sachdeva, Himani, and Nicholas H. Barton. “Introgression of a Block of Genome
under Infinitesimal Selection.” Genetics, vol. 209, no. 4, Genetics Society
of America, 2018, pp. 1279–303, doi:10.1534/genetics.118.301018.
short: H. Sachdeva, N.H. Barton, Genetics 209 (2018) 1279–1303.
date_created: 2018-12-11T11:45:36Z
date_published: 2018-08-01T00:00:00Z
date_updated: 2023-09-13T08:22:32Z
day: '01'
department:
- _id: NiBa
doi: 10.1534/genetics.118.301018
external_id:
isi:
- '000440014100020'
intvolume: ' 209'
isi: 1
issue: '4'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://www.biorxiv.org/content/early/2017/11/30/227082
month: '08'
oa: 1
oa_version: Submitted Version
page: 1279 - 1303
publication: Genetics
publication_status: published
publisher: Genetics Society of America
publist_id: '7617'
quality_controlled: '1'
scopus_import: '1'
status: public
title: Introgression of a block of genome under infinitesimal selection
type: journal_article
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
volume: 209
year: '2018'
...
---
_id: '108'
abstract:
- lang: eng
text: Universal hashing found a lot of applications in computer science. In cryptography
the most important fact about universal families is the so called Leftover Hash
Lemma, proved by Impagliazzo, Levin and Luby. In the language of modern cryptography
it states that almost universal families are good extractors. In this work we
provide a somewhat surprising characterization in the opposite direction. Namely,
every extractor with sufficiently good parameters yields a universal family on
a noticeable fraction of its inputs. Our proof technique is based on tools from
extremal graph theory applied to the \'collision graph\' induced by the extractor,
and may be of independent interest. We discuss possible applications to the theory
of randomness extractors and non-malleable codes.
alternative_title:
- ISIT Proceedings
article_processing_charge: No
author:
- first_name: Marciej
full_name: Obremski, Marciej
last_name: Obremski
- first_name: Maciej
full_name: Skorski, Maciej
id: EC09FA6A-02D0-11E9-8223-86B7C91467DD
last_name: Skorski
citation:
ama: 'Obremski M, Skórski M. Inverted leftover hash lemma. In: Vol 2018. IEEE; 2018.
doi:10.1109/ISIT.2018.8437654'
apa: 'Obremski, M., & Skórski, M. (2018). Inverted leftover hash lemma (Vol.
2018). Presented at the ISIT: International Symposium on Information Theory, Vail,
CO, USA: IEEE. https://doi.org/10.1109/ISIT.2018.8437654'
chicago: Obremski, Marciej, and Maciej Skórski. “Inverted Leftover Hash Lemma,”
Vol. 2018. IEEE, 2018. https://doi.org/10.1109/ISIT.2018.8437654.
ieee: 'M. Obremski and M. Skórski, “Inverted leftover hash lemma,” presented at
the ISIT: International Symposium on Information Theory, Vail, CO, USA, 2018,
vol. 2018.'
ista: 'Obremski M, Skórski M. 2018. Inverted leftover hash lemma. ISIT: International
Symposium on Information Theory, ISIT Proceedings, vol. 2018.'
mla: Obremski, Marciej, and Maciej Skórski. Inverted Leftover Hash Lemma.
Vol. 2018, IEEE, 2018, doi:10.1109/ISIT.2018.8437654.
short: M. Obremski, M. Skórski, in:, IEEE, 2018.
conference:
end_date: 2018-06-22
location: Vail, CO, USA
name: 'ISIT: International Symposium on Information Theory'
start_date: '2018-06-17 '
date_created: 2018-12-11T11:44:40Z
date_published: 2018-08-16T00:00:00Z
date_updated: 2023-09-13T08:23:18Z
day: '16'
department:
- _id: KrPi
doi: 10.1109/ISIT.2018.8437654
external_id:
isi:
- '000448139300368'
intvolume: ' 2018'
isi: 1
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://eprint.iacr.org/2017/507
month: '08'
oa: 1
oa_version: Submitted Version
publication_status: published
publisher: IEEE
publist_id: '7946'
quality_controlled: '1'
scopus_import: '1'
status: public
title: Inverted leftover hash lemma
type: conference
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
volume: 2018
year: '2018'
...
---
_id: '14204'
abstract:
- lang: eng
text: Two popular examples of first-order optimization methods over linear spaces
are coordinate descent and matching pursuit algorithms, with their randomized
variants. While the former targets the optimization by moving along coordinates,
the latter considers a generalized notion of directions. Exploiting the connection
between the two algorithms, we present a unified analysis of both, providing affine
invariant sublinear O(1/t) rates on smooth objectives and linear convergence on
strongly convex objectives. As a byproduct of our affine invariant analysis of
matching pursuit, our rates for steepest coordinate descent are the tightest known.
Furthermore, we show the first accelerated convergence rate O(1/t2) for matching
pursuit and steepest coordinate descent on convex objectives.
alternative_title:
- PMLR
article_processing_charge: No
author:
- first_name: Francesco
full_name: Locatello, Francesco
id: 26cfd52f-2483-11ee-8040-88983bcc06d4
last_name: Locatello
orcid: 0000-0002-4850-0683
- first_name: Anant
full_name: Raj, Anant
last_name: Raj
- first_name: Sai Praneeth
full_name: Karimireddy, Sai Praneeth
last_name: Karimireddy
- first_name: Gunnar
full_name: Rätsch, Gunnar
last_name: Rätsch
- first_name: Bernhard
full_name: Schölkopf, Bernhard
last_name: Schölkopf
- first_name: Sebastian U.
full_name: Stich, Sebastian U.
last_name: Stich
- first_name: Martin
full_name: Jaggi, Martin
last_name: Jaggi
citation:
ama: 'Locatello F, Raj A, Karimireddy SP, et al. On matching pursuit and coordinate
descent. In: Proceedings of the 35th International Conference on Machine Learning.
Vol 80. ML Research Press; 2018:3198-3207.'
apa: Locatello, F., Raj, A., Karimireddy, S. P., Rätsch, G., Schölkopf, B., Stich,
S. U., & Jaggi, M. (2018). On matching pursuit and coordinate descent. In
Proceedings of the 35th International Conference on Machine Learning (Vol.
80, pp. 3198–3207). ML Research Press.
chicago: Locatello, Francesco, Anant Raj, Sai Praneeth Karimireddy, Gunnar Rätsch,
Bernhard Schölkopf, Sebastian U. Stich, and Martin Jaggi. “On Matching Pursuit
and Coordinate Descent.” In Proceedings of the 35th International Conference
on Machine Learning, 80:3198–3207. ML Research Press, 2018.
ieee: F. Locatello et al., “On matching pursuit and coordinate descent,”
in Proceedings of the 35th International Conference on Machine Learning,
2018, vol. 80, pp. 3198–3207.
ista: Locatello F, Raj A, Karimireddy SP, Rätsch G, Schölkopf B, Stich SU, Jaggi
M. 2018. On matching pursuit and coordinate descent. Proceedings of the 35th International
Conference on Machine Learning. , PMLR, vol. 80, 3198–3207.
mla: Locatello, Francesco, et al. “On Matching Pursuit and Coordinate Descent.”
Proceedings of the 35th International Conference on Machine Learning, vol.
80, ML Research Press, 2018, pp. 3198–207.
short: F. Locatello, A. Raj, S.P. Karimireddy, G. Rätsch, B. Schölkopf, S.U. Stich,
M. Jaggi, in:, Proceedings of the 35th International Conference on Machine Learning,
ML Research Press, 2018, pp. 3198–3207.
date_created: 2023-08-22T14:16:25Z
date_published: 2018-07-01T00:00:00Z
date_updated: 2023-09-13T08:19:05Z
day: '01'
department:
- _id: FrLo
extern: '1'
external_id:
arxiv:
- '1803.09539'
intvolume: ' 80'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/1803.09539
month: '07'
oa: 1
oa_version: Preprint
page: 3198-3207
publication: Proceedings of the 35th International Conference on Machine Learning
publication_status: published
publisher: ML Research Press
quality_controlled: '1'
scopus_import: '1'
status: public
title: On matching pursuit and coordinate descent
type: conference
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 80
year: '2018'
...
---
_id: '160'
abstract:
- lang: eng
text: We present layered concurrent programs, a compact and expressive notation
for specifying refinement proofs of concurrent programs. A layered concurrent
program specifies a sequence of connected concurrent programs, from most concrete
to most abstract, such that common parts of different programs are written exactly
once. These programs are expressed in the ordinary syntax of imperative concurrent
programs using gated atomic actions, sequencing, choice, and (recursive) procedure
calls. Each concurrent program is automatically extracted from the layered program.
We reduce refinement to the safety of a sequence of concurrent checker programs,
one each to justify the connection between every two consecutive concurrent programs.
These checker programs are also automatically extracted from the layered program.
Layered concurrent programs have been implemented in the CIVL verifier which has
been successfully used for the verification of several complex concurrent programs.
alternative_title:
- LNCS
article_processing_charge: No
author:
- first_name: Bernhard
full_name: Kragl, Bernhard
id: 320FC952-F248-11E8-B48F-1D18A9856A87
last_name: Kragl
orcid: 0000-0001-7745-9117
- first_name: Shaz
full_name: Qadeer, Shaz
last_name: Qadeer
citation:
ama: 'Kragl B, Qadeer S. Layered Concurrent Programs. In: Vol 10981. Springer; 2018:79-102.
doi:10.1007/978-3-319-96145-3_5'
apa: 'Kragl, B., & Qadeer, S. (2018). Layered Concurrent Programs (Vol. 10981,
pp. 79–102). Presented at the CAV: Computer Aided Verification, Oxford, UK: Springer.
https://doi.org/10.1007/978-3-319-96145-3_5'
chicago: Kragl, Bernhard, and Shaz Qadeer. “Layered Concurrent Programs,” 10981:79–102.
Springer, 2018. https://doi.org/10.1007/978-3-319-96145-3_5.
ieee: 'B. Kragl and S. Qadeer, “Layered Concurrent Programs,” presented at the CAV:
Computer Aided Verification, Oxford, UK, 2018, vol. 10981, pp. 79–102.'
ista: 'Kragl B, Qadeer S. 2018. Layered Concurrent Programs. CAV: Computer Aided
Verification, LNCS, vol. 10981, 79–102.'
mla: Kragl, Bernhard, and Shaz Qadeer. Layered Concurrent Programs. Vol.
10981, Springer, 2018, pp. 79–102, doi:10.1007/978-3-319-96145-3_5.
short: B. Kragl, S. Qadeer, in:, Springer, 2018, pp. 79–102.
conference:
end_date: 2018-07-17
location: Oxford, UK
name: 'CAV: Computer Aided Verification'
start_date: 2018-07-14
date_created: 2018-12-11T11:44:57Z
date_published: 2018-07-18T00:00:00Z
date_updated: 2023-09-13T08:45:09Z
day: '18'
ddc:
- '000'
department:
- _id: ToHe
doi: 10.1007/978-3-319-96145-3_5
external_id:
isi:
- '000491481600005'
file:
- access_level: open_access
checksum: c64fff560fe5a7532ec10626ad1c215e
content_type: application/pdf
creator: dernst
date_created: 2018-12-17T12:52:12Z
date_updated: 2020-07-14T12:45:04Z
file_id: '5705'
file_name: 2018_LNCS_Kragl.pdf
file_size: 1603844
relation: main_file
file_date_updated: 2020-07-14T12:45:04Z
has_accepted_license: '1'
intvolume: ' 10981'
isi: 1
language:
- iso: eng
license: https://creativecommons.org/licenses/by/4.0/
month: '07'
oa: 1
oa_version: Published Version
page: 79 - 102
project:
- _id: 25F42A32-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: Z211
name: The Wittgenstein Prize
- _id: 25832EC2-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: S 11407_N23
name: Rigorous Systems Engineering
publication_status: published
publisher: Springer
publist_id: '7761'
quality_controlled: '1'
related_material:
record:
- id: '8332'
relation: dissertation_contains
status: public
scopus_import: '1'
status: public
title: Layered Concurrent Programs
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: c635000d-4b10-11ee-a964-aac5a93f6ac1
volume: 10981
year: '2018'
...
---
_id: '280'
abstract:
- lang: eng
text: Flowers have a species-specific functional life span that determines the time
window in which pollination, fertilization and seed set can occur. The stigma
tissue plays a key role in flower receptivity by intercepting pollen and initiating
pollen tube growth toward the ovary. In this article, we show that a developmentally
controlled cell death programme terminates the functional life span of stigma
cells in Arabidopsis. We identified the leaf senescence regulator ORESARA1 (also
known as ANAC092) and the previously uncharacterized KIRA1 (also known as ANAC074)
as partially redundant transcription factors that modulate stigma longevity by
controlling the expression of programmed cell death-associated genes. KIRA1 expression
is sufficient to induce cell death and terminate floral receptivity, whereas lack
of both KIRA1 and ORESARA1 substantially increases stigma life span. Surprisingly,
the extension of stigma longevity is accompanied by only a moderate extension
of flower receptivity, suggesting that additional processes participate in the
control of the flower's receptive life span.
acknowledgement: We gratefully acknowledge funding from the Chinese Scholarship Council
(CSC; project number 201206910025 to Z.G.), the Fonds Wetenschappelijk Onderzoek
(FWO; project number G005112N to A.D.; fellowship number 12I7417N to Z.L.), the
Belgian Federal Science Policy Office (BELSPO; to Y.S.), the Agency for Innovation
by Science and Technology of Belgium (IWT; fellowship number 121110 to M.V.D.),
the Hercules foundation (grant AUGE-09-029 to K.D.), and the ERC StG PROCELLDEATH
(project number 639234 to M.K.N.).
article_processing_charge: No
author:
- first_name: Zhen
full_name: Gao, Zhen
last_name: Gao
- first_name: Anna
full_name: Daneva, Anna
last_name: Daneva
- first_name: Yuliya
full_name: Salanenka, Yuliya
id: 46DAAE7E-F248-11E8-B48F-1D18A9856A87
last_name: Salanenka
- first_name: Matthias
full_name: Van Durme, Matthias
last_name: Van Durme
- first_name: Marlies
full_name: Huysmans, Marlies
last_name: Huysmans
- first_name: Zongcheng
full_name: Lin, Zongcheng
last_name: Lin
- first_name: Freya
full_name: De Winter, Freya
last_name: De Winter
- first_name: Steffen
full_name: Vanneste, Steffen
last_name: Vanneste
- first_name: Mansour
full_name: Karimi, Mansour
last_name: Karimi
- first_name: Jan
full_name: Van De Velde, Jan
last_name: Van De Velde
- first_name: Klaas
full_name: Vandepoele, Klaas
last_name: Vandepoele
- first_name: Davy
full_name: Van De Walle, Davy
last_name: Van De Walle
- first_name: Koen
full_name: Dewettinck, Koen
last_name: Dewettinck
- first_name: Bart
full_name: Lambrecht, Bart
last_name: Lambrecht
- first_name: Moritz
full_name: Nowack, Moritz
last_name: Nowack
citation:
ama: Gao Z, Daneva A, Salanenka Y, et al. KIRA1 and ORESARA1 terminate flower receptivity
by promoting cell death in the stigma of Arabidopsis. Nature Plants. 2018;4(6):365-375.
doi:10.1038/s41477-018-0160-7
apa: Gao, Z., Daneva, A., Salanenka, Y., Van Durme, M., Huysmans, M., Lin, Z., …
Nowack, M. (2018). KIRA1 and ORESARA1 terminate flower receptivity by promoting
cell death in the stigma of Arabidopsis. Nature Plants. Nature Publishing
Group. https://doi.org/10.1038/s41477-018-0160-7
chicago: Gao, Zhen, Anna Daneva, Yuliya Salanenka, Matthias Van Durme, Marlies Huysmans,
Zongcheng Lin, Freya De Winter, et al. “KIRA1 and ORESARA1 Terminate Flower Receptivity
by Promoting Cell Death in the Stigma of Arabidopsis.” Nature Plants. Nature
Publishing Group, 2018. https://doi.org/10.1038/s41477-018-0160-7.
ieee: Z. Gao et al., “KIRA1 and ORESARA1 terminate flower receptivity by
promoting cell death in the stigma of Arabidopsis,” Nature Plants, vol.
4, no. 6. Nature Publishing Group, pp. 365–375, 2018.
ista: Gao Z, Daneva A, Salanenka Y, Van Durme M, Huysmans M, Lin Z, De Winter F,
Vanneste S, Karimi M, Van De Velde J, Vandepoele K, Van De Walle D, Dewettinck
K, Lambrecht B, Nowack M. 2018. KIRA1 and ORESARA1 terminate flower receptivity
by promoting cell death in the stigma of Arabidopsis. Nature Plants. 4(6), 365–375.
mla: Gao, Zhen, et al. “KIRA1 and ORESARA1 Terminate Flower Receptivity by Promoting
Cell Death in the Stigma of Arabidopsis.” Nature Plants, vol. 4, no. 6,
Nature Publishing Group, 2018, pp. 365–75, doi:10.1038/s41477-018-0160-7.
short: Z. Gao, A. Daneva, Y. Salanenka, M. Van Durme, M. Huysmans, Z. Lin, F. De
Winter, S. Vanneste, M. Karimi, J. Van De Velde, K. Vandepoele, D. Van De Walle,
K. Dewettinck, B. Lambrecht, M. Nowack, Nature Plants 4 (2018) 365–375.
date_created: 2018-12-11T11:45:35Z
date_published: 2018-05-28T00:00:00Z
date_updated: 2023-09-13T08:24:17Z
day: '28'
department:
- _id: JiFr
doi: 10.1038/s41477-018-0160-7
external_id:
isi:
- '000435571000017'
intvolume: ' 4'
isi: 1
issue: '6'
language:
- iso: eng
month: '05'
oa_version: None
page: 365 - 375
publication: Nature Plants
publication_status: published
publisher: Nature Publishing Group
publist_id: '7619'
quality_controlled: '1'
scopus_import: '1'
status: public
title: KIRA1 and ORESARA1 terminate flower receptivity by promoting cell death in
the stigma of Arabidopsis
type: journal_article
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
volume: 4
year: '2018'
...
---
_id: '503'
abstract:
- lang: eng
text: Buffers are essential for diluting bacterial cultures for flow cytometry analysis
in order to study bacterial physiology and gene expression parameters based on
fluorescence signals. Using a variety of constitutively expressed fluorescent
proteins in Escherichia coli K-12 strain MG1655, we found strong artifactual changes
in fluorescence levels after dilution into the commonly used flow cytometry buffer
phosphate-buffered saline (PBS) and two other buffer solutions, Tris-HCl and M9
salts. These changes appeared very rapidly after dilution, and were linked to
increased membrane permeability and loss in cell viability. We observed buffer-related
effects in several different E. coli strains, K-12, C and W, but not E. coli B,
which can be partially explained by differences in lipopolysaccharide (LPS) and
outer membrane composition. Supplementing the buffers with divalent cations responsible
for outer membrane stability, Mg2+ and Ca2+, preserved fluorescence signals, membrane
integrity and viability of E. coli. Thus, stabilizing the bacterial outer membrane
is essential for precise and unbiased measurements of fluorescence parameters
using flow cytometry.
acknowledged_ssus:
- _id: Bio
acknowledgement: "We thank R Chait and M Lagator for sharing Bacillus subtilis CR_Y1
and pZS*_2R-cIPtet-Venus-Prm, respectively. We are grateful to T Pilizota and all
members of the Guet lab for critically reading the manuscript. We also thank the
Bioimaging facility at IST Austria for assistance using the FACSAria III system.\r\n\r\n"
article_processing_charge: No
author:
- first_name: Kathrin
full_name: Tomasek, Kathrin
id: 3AEC8556-F248-11E8-B48F-1D18A9856A87
last_name: Tomasek
orcid: 0000-0003-3768-877X
- first_name: Tobias
full_name: Bergmiller, Tobias
id: 2C471CFA-F248-11E8-B48F-1D18A9856A87
last_name: Bergmiller
orcid: 0000-0001-5396-4346
- 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: Tomasek K, Bergmiller T, Guet CC. Lack of cations in flow cytometry buffers
affect fluorescence signals by reducing membrane stability and viability of Escherichia
coli strains. Journal of Biotechnology. 2018;268:40-52. doi:10.1016/j.jbiotec.2018.01.008
apa: Tomasek, K., Bergmiller, T., & Guet, C. C. (2018). Lack of cations in flow
cytometry buffers affect fluorescence signals by reducing membrane stability and
viability of Escherichia coli strains. Journal of Biotechnology. Elsevier.
https://doi.org/10.1016/j.jbiotec.2018.01.008
chicago: Tomasek, Kathrin, Tobias Bergmiller, and Calin C Guet. “Lack of Cations
in Flow Cytometry Buffers Affect Fluorescence Signals by Reducing Membrane Stability
and Viability of Escherichia Coli Strains.” Journal of Biotechnology. Elsevier,
2018. https://doi.org/10.1016/j.jbiotec.2018.01.008.
ieee: K. Tomasek, T. Bergmiller, and C. C. Guet, “Lack of cations in flow cytometry
buffers affect fluorescence signals by reducing membrane stability and viability
of Escherichia coli strains,” Journal of Biotechnology, vol. 268. Elsevier,
pp. 40–52, 2018.
ista: Tomasek K, Bergmiller T, Guet CC. 2018. Lack of cations in flow cytometry
buffers affect fluorescence signals by reducing membrane stability and viability
of Escherichia coli strains. Journal of Biotechnology. 268, 40–52.
mla: Tomasek, Kathrin, et al. “Lack of Cations in Flow Cytometry Buffers Affect
Fluorescence Signals by Reducing Membrane Stability and Viability of Escherichia
Coli Strains.” Journal of Biotechnology, vol. 268, Elsevier, 2018, pp.
40–52, doi:10.1016/j.jbiotec.2018.01.008.
short: K. Tomasek, T. Bergmiller, C.C. Guet, Journal of Biotechnology 268 (2018)
40–52.
date_created: 2018-12-11T11:46:50Z
date_published: 2018-02-20T00:00:00Z
date_updated: 2023-09-13T08:24:51Z
day: '20'
department:
- _id: CaGu
doi: 10.1016/j.jbiotec.2018.01.008
external_id:
isi:
- '000425715100006'
intvolume: ' 268'
isi: 1
language:
- iso: eng
month: '02'
oa_version: None
page: 40 - 52
publication: Journal of Biotechnology
publication_status: published
publisher: Elsevier
publist_id: '7317'
quality_controlled: '1'
scopus_import: '1'
status: public
title: Lack of cations in flow cytometry buffers affect fluorescence signals by reducing
membrane stability and viability of Escherichia coli strains
type: journal_article
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
volume: 268
year: '2018'
...
---
_id: '82'
abstract:
- lang: eng
text: In experimental cultures, when bacteria are mixed with lytic (virulent) bacteriophage,
bacterial cells resistant to the phage commonly emerge and become the dominant
population of bacteria. Following the ascent of resistant mutants, the densities
of bacteria in these simple communities become limited by resources rather than
the phage. Despite the evolution of resistant hosts, upon which the phage cannot
replicate, the lytic phage population is most commonly maintained in an apparently
stable state with the resistant bacteria. Several mechanisms have been put forward
to account for this result. Here we report the results of population dynamic/evolution
experiments with a virulent mutant of phage Lambda, λVIR, and Escherichia coli
in serial transfer cultures. We show that, following the ascent of λVIR-resistant
bacteria, λVIRis maintained in the majority of cases in maltose-limited minimal
media and in all cases in nutrient-rich broth. Using mathematical models and experiments,
we show that the dominant mechanism responsible for maintenance of λVIRin these
resource-limited populations dominated by resistant E. coli is a high rate of
either phenotypic or genetic transition from resistance to susceptibility—a hitherto
undemonstrated mechanism we term "leaky resistance." We discuss the
implications of leaky resistance to our understanding of the conditions for the
maintenance of phage in populations of bacteria—their “existence conditions.”.
article_number: '2005971'
article_processing_charge: Yes
author:
- first_name: Waqas
full_name: Chaudhry, Waqas
last_name: Chaudhry
- first_name: Maros
full_name: Pleska, Maros
id: 4569785E-F248-11E8-B48F-1D18A9856A87
last_name: Pleska
orcid: 0000-0001-7460-7479
- first_name: Nilang
full_name: Shah, Nilang
last_name: Shah
- first_name: Howard
full_name: Weiss, Howard
last_name: Weiss
- first_name: Ingrid
full_name: Mccall, Ingrid
last_name: Mccall
- first_name: Justin
full_name: Meyer, Justin
last_name: Meyer
- first_name: Animesh
full_name: Gupta, Animesh
last_name: Gupta
- first_name: Calin C
full_name: Guet, Calin C
id: 47F8433E-F248-11E8-B48F-1D18A9856A87
last_name: Guet
orcid: 0000-0001-6220-2052
- first_name: Bruce
full_name: Levin, Bruce
last_name: Levin
citation:
ama: Chaudhry W, Pleska M, Shah N, et al. Leaky resistance and the conditions for
the existence of lytic bacteriophage. PLoS Biology. 2018;16(8). doi:10.1371/journal.pbio.2005971
apa: Chaudhry, W., Pleska, M., Shah, N., Weiss, H., Mccall, I., Meyer, J., … Levin,
B. (2018). Leaky resistance and the conditions for the existence of lytic bacteriophage.
PLoS Biology. Public Library of Science. https://doi.org/10.1371/journal.pbio.2005971
chicago: Chaudhry, Waqas, Maros Pleska, Nilang Shah, Howard Weiss, Ingrid Mccall,
Justin Meyer, Animesh Gupta, Calin C Guet, and Bruce Levin. “Leaky Resistance
and the Conditions for the Existence of Lytic Bacteriophage.” PLoS Biology.
Public Library of Science, 2018. https://doi.org/10.1371/journal.pbio.2005971.
ieee: W. Chaudhry et al., “Leaky resistance and the conditions for the existence
of lytic bacteriophage,” PLoS Biology, vol. 16, no. 8. Public Library of
Science, 2018.
ista: Chaudhry W, Pleska M, Shah N, Weiss H, Mccall I, Meyer J, Gupta A, Guet CC,
Levin B. 2018. Leaky resistance and the conditions for the existence of lytic
bacteriophage. PLoS Biology. 16(8), 2005971.
mla: Chaudhry, Waqas, et al. “Leaky Resistance and the Conditions for the Existence
of Lytic Bacteriophage.” PLoS Biology, vol. 16, no. 8, 2005971, Public
Library of Science, 2018, doi:10.1371/journal.pbio.2005971.
short: W. Chaudhry, M. Pleska, N. Shah, H. Weiss, I. Mccall, J. Meyer, A. Gupta,
C.C. Guet, B. Levin, PLoS Biology 16 (2018).
date_created: 2018-12-11T11:44:32Z
date_published: 2018-08-16T00:00:00Z
date_updated: 2023-09-13T08:45:41Z
day: '16'
ddc:
- '570'
department:
- _id: CaGu
doi: 10.1371/journal.pbio.2005971
external_id:
isi:
- '000443383300024'
file:
- access_level: open_access
checksum: 527076f78265cd4ea192cd1569851587
content_type: application/pdf
creator: dernst
date_created: 2018-12-17T12:55:31Z
date_updated: 2020-07-14T12:48:10Z
file_id: '5706'
file_name: 2018_Plos_Chaudhry.pdf
file_size: 4007095
relation: main_file
file_date_updated: 2020-07-14T12:48:10Z
has_accepted_license: '1'
intvolume: ' 16'
isi: 1
issue: '8'
language:
- iso: eng
month: '08'
oa: 1
oa_version: Published Version
publication: PLoS Biology
publication_status: published
publisher: Public Library of Science
publist_id: '7972'
quality_controlled: '1'
related_material:
record:
- id: '9810'
relation: research_data
status: public
scopus_import: '1'
status: public
title: Leaky resistance and the conditions for the existence of lytic bacteriophage
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: journal_article
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
volume: 16
year: '2018'
...
---
_id: '4'
abstract:
- lang: eng
text: We present a data-driven technique to instantly predict how fluid flows around
various three-dimensional objects. Such simulation is useful for computational
fabrication and engineering, but is usually computationally expensive since it
requires solving the Navier-Stokes equation for many time steps. To accelerate
the process, we propose a machine learning framework which predicts aerodynamic
forces and velocity and pressure fields given a threedimensional shape input.
Handling detailed free-form three-dimensional shapes in a data-driven framework
is challenging because machine learning approaches usually require a consistent
parametrization of input and output. We present a novel PolyCube maps-based parametrization
that can be computed for three-dimensional shapes at interactive rates. This allows
us to efficiently learn the nonlinear response of the flow using a Gaussian process
regression. We demonstrate the effectiveness of our approach for the interactive
design and optimization of a car body.
article_number: '89'
article_processing_charge: No
author:
- first_name: Nobuyuki
full_name: Umetani, Nobuyuki
last_name: Umetani
- first_name: Bernd
full_name: Bickel, Bernd
id: 49876194-F248-11E8-B48F-1D18A9856A87
last_name: Bickel
orcid: 0000-0001-6511-9385
citation:
ama: Umetani N, Bickel B. Learning three-dimensional flow for interactive aerodynamic
design. ACM Trans Graph. 2018;37(4). doi:10.1145/3197517.3201325
apa: Umetani, N., & Bickel, B. (2018). Learning three-dimensional flow for interactive
aerodynamic design. ACM Trans. Graph. ACM. https://doi.org/10.1145/3197517.3201325
chicago: Umetani, Nobuyuki, and Bernd Bickel. “Learning Three-Dimensional Flow for
Interactive Aerodynamic Design.” ACM Trans. Graph. ACM, 2018. https://doi.org/10.1145/3197517.3201325.
ieee: N. Umetani and B. Bickel, “Learning three-dimensional flow for interactive
aerodynamic design,” ACM Trans. Graph., vol. 37, no. 4. ACM, 2018.
ista: Umetani N, Bickel B. 2018. Learning three-dimensional flow for interactive
aerodynamic design. ACM Trans. Graph. 37(4), 89.
mla: Umetani, Nobuyuki, and Bernd Bickel. “Learning Three-Dimensional Flow for Interactive
Aerodynamic Design.” ACM Trans. Graph., vol. 37, no. 4, 89, ACM, 2018,
doi:10.1145/3197517.3201325.
short: N. Umetani, B. Bickel, ACM Trans. Graph. 37 (2018).
date_created: 2018-12-11T11:44:06Z
date_published: 2018-08-04T00:00:00Z
date_updated: 2023-09-13T08:46:15Z
day: '04'
ddc:
- '003'
- '004'
department:
- _id: BeBi
doi: 10.1145/3197517.3201325
ec_funded: 1
external_id:
isi:
- '000448185000050'
file:
- access_level: open_access
checksum: 7a2243668f215821bc6aecad0320079a
content_type: application/pdf
creator: system
date_created: 2018-12-12T10:16:28Z
date_updated: 2020-07-14T12:46:22Z
file_id: '5216'
file_name: IST-2018-1049-v1+1_2018_sigg_Learning3DAerodynamics.pdf
file_size: 22803163
relation: main_file
file_date_updated: 2020-07-14T12:46:22Z
has_accepted_license: '1'
intvolume: ' 37'
isi: 1
issue: '4'
language:
- iso: eng
month: '08'
oa: 1
oa_version: Submitted Version
project:
- _id: 24F9549A-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '715767'
name: 'MATERIALIZABLE: Intelligent fabrication-oriented Computational Design and
Modeling'
publication: ACM Trans. Graph.
publication_status: published
publisher: ACM
publist_id: '8053'
pubrep_id: '1049'
quality_controlled: '1'
related_material:
link:
- description: News on IST Homepage
relation: press_release
url: https://ist.ac.at/en/news/new-interactive-machine-learning-tool-makes-car-designs-more-aerodynamic/
scopus_import: '1'
status: public
title: Learning three-dimensional flow for interactive aerodynamic design
type: journal_article
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
volume: 37
year: '2018'
...
---
_id: '183'
abstract:
- lang: eng
text: 'Fault-localization is considered to be a very tedious and time-consuming
activity in the design of complex Cyber-Physical Systems (CPS). This laborious
task essentially requires expert knowledge of the system in order to discover
the cause of the fault. In this context, we propose a new procedure that AIDS
designers in debugging Simulink/Stateflow hybrid system models, guided by Signal
Temporal Logic (STL) specifications. The proposed method relies on three main
ingredients: (1) a monitoring and a trace diagnostics procedure that checks whether
a tested behavior satisfies or violates an STL specification, localizes time segments
and interfaces variables contributing to the property violations; (2) a slicing
procedure that maps these observable behavior segments to the internal states
and transitions of the Simulink model; and (3) a spectrum-based fault-localization
method that combines the previous analysis from multiple tests to identify the
internal states and/or transitions that are the most likely to explain the fault.
We demonstrate the applicability of our approach on two Simulink models from the
automotive and the avionics domain.'
acknowledgement: This work was partially supported by the Austrian Science Fund (FWF)
under grants S11402-N23 and S11405-N23 (RiSE/SHiNE), the CPS/IoT project (HRSM),
the EU ICT COST Action IC1402 on Run-time Verification beyond Monitoring (ARVI),
the AMASS project (ECSEL 692474), and the ENABLE-S3 project (ECSEL 692455). The
CPS/IoT project receives support from the Austrian government through the Federal
Ministry of Science, Research and Economy (BMWFW) in the funding program Hochschulraum-Strukturmittel
(HRSM) 2016. The ECSEL Joint Undertaking receives support from the European Union’s
Horizon 2020 research and innovation programme and Austria, Denmark, Germany, Finland,
Czech Republic, Italy, Spain, Portugal, Poland, Ireland, Belgium, France, Netherlands,
United Kingdom, Slovakia, Norway.
alternative_title:
- HSCC Proceedings
article_processing_charge: No
author:
- first_name: Ezio
full_name: Bartocci, Ezio
last_name: Bartocci
- first_name: Thomas
full_name: Ferrere, Thomas
id: 40960E6E-F248-11E8-B48F-1D18A9856A87
last_name: Ferrere
orcid: 0000-0001-5199-3143
- first_name: Niveditha
full_name: Manjunath, Niveditha
last_name: Manjunath
- first_name: Dejan
full_name: Nickovic, Dejan
last_name: Nickovic
citation:
ama: 'Bartocci E, Ferrere T, Manjunath N, Nickovic D. Localizing faults in simulink/stateflow
models with STL. In: Association for Computing Machinery, Inc; 2018:197-206. doi:10.1145/3178126.3178131'
apa: 'Bartocci, E., Ferrere, T., Manjunath, N., & Nickovic, D. (2018). Localizing
faults in simulink/stateflow models with STL (pp. 197–206). Presented at the HSCC:
Hybrid Systems: Computation and Control, Porto, Portugal: Association for Computing
Machinery, Inc. https://doi.org/10.1145/3178126.3178131'
chicago: Bartocci, Ezio, Thomas Ferrere, Niveditha Manjunath, and Dejan Nickovic.
“Localizing Faults in Simulink/Stateflow Models with STL,” 197–206. Association
for Computing Machinery, Inc, 2018. https://doi.org/10.1145/3178126.3178131.
ieee: 'E. Bartocci, T. Ferrere, N. Manjunath, and D. Nickovic, “Localizing faults
in simulink/stateflow models with STL,” presented at the HSCC: Hybrid Systems:
Computation and Control, Porto, Portugal, 2018, pp. 197–206.'
ista: 'Bartocci E, Ferrere T, Manjunath N, Nickovic D. 2018. Localizing faults in
simulink/stateflow models with STL. HSCC: Hybrid Systems: Computation and Control,
HSCC Proceedings, , 197–206.'
mla: Bartocci, Ezio, et al. Localizing Faults in Simulink/Stateflow Models with
STL. Association for Computing Machinery, Inc, 2018, pp. 197–206, doi:10.1145/3178126.3178131.
short: E. Bartocci, T. Ferrere, N. Manjunath, D. Nickovic, in:, Association for
Computing Machinery, Inc, 2018, pp. 197–206.
conference:
end_date: 2018-04-13
location: Porto, Portugal
name: 'HSCC: Hybrid Systems: Computation and Control'
start_date: 2018-04-11
date_created: 2018-12-11T11:45:04Z
date_published: 2018-04-11T00:00:00Z
date_updated: 2023-09-13T08:48:46Z
day: '11'
department:
- _id: ToHe
doi: 10.1145/3178126.3178131
external_id:
isi:
- '000474781600022'
isi: 1
language:
- iso: eng
month: '04'
oa_version: None
page: 197 - 206
project:
- _id: 25832EC2-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: S 11407_N23
name: Rigorous Systems Engineering
publication_status: published
publisher: Association for Computing Machinery, Inc
publist_id: '7738'
quality_controlled: '1'
scopus_import: '1'
status: public
title: Localizing faults in simulink/stateflow models with STL
type: conference
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
year: '2018'
...
---
_id: '566'
abstract:
- lang: eng
text: "We consider large random matrices X with centered, independent entries which
have comparable but not necessarily identical variances. Girko's circular law
asserts that the spectrum is supported in a disk and in case of identical variances,
the limiting density is uniform. In this special case, the local circular law
by Bourgade et. al. [11,12] shows that the empirical density converges even locally
on scales slightly above the typical eigenvalue spacing. In the general case,
the limiting density is typically inhomogeneous and it is obtained via solving
a system of deterministic equations. Our main result is the local inhomogeneous
circular law in the bulk spectrum on the optimal scale for a general variance
profile of the entries of X. \r\n\r\n"
article_processing_charge: No
article_type: original
author:
- first_name: Johannes
full_name: Alt, Johannes
id: 36D3D8B6-F248-11E8-B48F-1D18A9856A87
last_name: Alt
- first_name: László
full_name: Erdös, László
id: 4DBD5372-F248-11E8-B48F-1D18A9856A87
last_name: Erdös
orcid: 0000-0001-5366-9603
- first_name: Torben H
full_name: Krüger, Torben H
id: 3020C786-F248-11E8-B48F-1D18A9856A87
last_name: Krüger
orcid: 0000-0002-4821-3297
citation:
ama: Alt J, Erdös L, Krüger TH. Local inhomogeneous circular law. Annals Applied
Probability . 2018;28(1):148-203. doi:10.1214/17-AAP1302
apa: Alt, J., Erdös, L., & Krüger, T. H. (2018). Local inhomogeneous circular
law. Annals Applied Probability . Institute of Mathematical Statistics.
https://doi.org/10.1214/17-AAP1302
chicago: Alt, Johannes, László Erdös, and Torben H Krüger. “Local Inhomogeneous
Circular Law.” Annals Applied Probability . Institute of Mathematical Statistics,
2018. https://doi.org/10.1214/17-AAP1302.
ieee: J. Alt, L. Erdös, and T. H. Krüger, “Local inhomogeneous circular law,” Annals
Applied Probability , vol. 28, no. 1. Institute of Mathematical Statistics,
pp. 148–203, 2018.
ista: Alt J, Erdös L, Krüger TH. 2018. Local inhomogeneous circular law. Annals
Applied Probability . 28(1), 148–203.
mla: Alt, Johannes, et al. “Local Inhomogeneous Circular Law.” Annals Applied
Probability , vol. 28, no. 1, Institute of Mathematical Statistics, 2018,
pp. 148–203, doi:10.1214/17-AAP1302.
short: J. Alt, L. Erdös, T.H. Krüger, Annals Applied Probability 28 (2018) 148–203.
date_created: 2018-12-11T11:47:13Z
date_published: 2018-03-03T00:00:00Z
date_updated: 2023-09-13T08:47:52Z
day: '03'
department:
- _id: LaEr
doi: 10.1214/17-AAP1302
ec_funded: 1
external_id:
arxiv:
- '1612.07776 '
isi:
- '000431721800005'
intvolume: ' 28'
isi: 1
issue: '1'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: 'https://arxiv.org/abs/1612.07776 '
month: '03'
oa: 1
oa_version: Preprint
page: 148-203
project:
- _id: 258DCDE6-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '338804'
name: Random matrices, universality and disordered quantum systems
publication: 'Annals Applied Probability '
publication_status: published
publisher: Institute of Mathematical Statistics
quality_controlled: '1'
related_material:
record:
- id: '149'
relation: dissertation_contains
status: public
scopus_import: '1'
status: public
title: Local inhomogeneous circular law
type: journal_article
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
volume: 28
year: '2018'
...
---
_id: '106'
abstract:
- lang: eng
text: The goal of this article is to introduce the reader to the theory of intrinsic
geometry of convex surfaces. We illustrate the power of the tools by proving a
theorem on convex surfaces containing an arbitrarily long closed simple geodesic.
Let us remind ourselves that a curve in a surface is called geodesic if every
sufficiently short arc of the curve is length minimizing; if, in addition, it
has no self-intersections, we call it simple geodesic. A tetrahedron with equal
opposite edges is called isosceles. The axiomatic method of Alexandrov geometry
allows us to work with the metrics of convex surfaces directly, without approximating
it first by a smooth or polyhedral metric. Such approximations destroy the closed
geodesics on the surface; therefore it is difficult (if at all possible) to apply
approximations in the proof of our theorem. On the other hand, a proof in the
smooth or polyhedral case usually admits a translation into Alexandrov’s language;
such translation makes the result more general. In fact, our proof resembles a
translation of the proof given by Protasov. Note that the main theorem implies
in particular that a smooth convex surface does not have arbitrarily long simple
closed geodesics. However we do not know a proof of this corollary that is essentially
simpler than the one presented below.
article_processing_charge: No
author:
- first_name: Arseniy
full_name: Akopyan, Arseniy
id: 430D2C90-F248-11E8-B48F-1D18A9856A87
last_name: Akopyan
orcid: 0000-0002-2548-617X
- first_name: Anton
full_name: Petrunin, Anton
last_name: Petrunin
citation:
ama: Akopyan A, Petrunin A. Long geodesics on convex surfaces. Mathematical Intelligencer.
2018;40(3):26-31. doi:10.1007/s00283-018-9795-5
apa: Akopyan, A., & Petrunin, A. (2018). Long geodesics on convex surfaces.
Mathematical Intelligencer. Springer. https://doi.org/10.1007/s00283-018-9795-5
chicago: Akopyan, Arseniy, and Anton Petrunin. “Long Geodesics on Convex Surfaces.”
Mathematical Intelligencer. Springer, 2018. https://doi.org/10.1007/s00283-018-9795-5.
ieee: A. Akopyan and A. Petrunin, “Long geodesics on convex surfaces,” Mathematical
Intelligencer, vol. 40, no. 3. Springer, pp. 26–31, 2018.
ista: Akopyan A, Petrunin A. 2018. Long geodesics on convex surfaces. Mathematical
Intelligencer. 40(3), 26–31.
mla: Akopyan, Arseniy, and Anton Petrunin. “Long Geodesics on Convex Surfaces.”
Mathematical Intelligencer, vol. 40, no. 3, Springer, 2018, pp. 26–31,
doi:10.1007/s00283-018-9795-5.
short: A. Akopyan, A. Petrunin, Mathematical Intelligencer 40 (2018) 26–31.
date_created: 2018-12-11T11:44:40Z
date_published: 2018-09-01T00:00:00Z
date_updated: 2023-09-13T08:49:16Z
day: '01'
department:
- _id: HeEd
doi: 10.1007/s00283-018-9795-5
external_id:
arxiv:
- '1702.05172'
isi:
- '000444141200005'
intvolume: ' 40'
isi: 1
issue: '3'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/1702.05172
month: '09'
oa: 1
oa_version: Preprint
page: 26 - 31
publication: Mathematical Intelligencer
publication_status: published
publisher: Springer
publist_id: '7948'
quality_controlled: '1'
scopus_import: '1'
status: public
title: Long geodesics on convex surfaces
type: journal_article
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
volume: 40
year: '2018'
...
---
_id: '9810'
article_processing_charge: No
author:
- first_name: Waqas
full_name: Chaudhry, Waqas
last_name: Chaudhry
- first_name: Maros
full_name: Pleska, Maros
id: 4569785E-F248-11E8-B48F-1D18A9856A87
last_name: Pleska
orcid: 0000-0001-7460-7479
- first_name: Nilang
full_name: Shah, Nilang
last_name: Shah
- first_name: Howard
full_name: Weiss, Howard
last_name: Weiss
- first_name: Ingrid
full_name: Mccall, Ingrid
last_name: Mccall
- first_name: Justin
full_name: Meyer, Justin
last_name: Meyer
- first_name: Animesh
full_name: Gupta, Animesh
last_name: Gupta
- first_name: Calin C
full_name: Guet, Calin C
id: 47F8433E-F248-11E8-B48F-1D18A9856A87
last_name: Guet
orcid: 0000-0001-6220-2052
- first_name: Bruce
full_name: Levin, Bruce
last_name: Levin
citation:
ama: Chaudhry W, Pleska M, Shah N, et al. Numerical data used in figures. 2018.
doi:10.1371/journal.pbio.2005971.s008
apa: Chaudhry, W., Pleska, M., Shah, N., Weiss, H., Mccall, I., Meyer, J., … Levin,
B. (2018). Numerical data used in figures. Public Library of Science. https://doi.org/10.1371/journal.pbio.2005971.s008
chicago: Chaudhry, Waqas, Maros Pleska, Nilang Shah, Howard Weiss, Ingrid Mccall,
Justin Meyer, Animesh Gupta, Calin C Guet, and Bruce Levin. “Numerical Data Used
in Figures.” Public Library of Science, 2018. https://doi.org/10.1371/journal.pbio.2005971.s008.
ieee: W. Chaudhry et al., “Numerical data used in figures.” Public Library
of Science, 2018.
ista: Chaudhry W, Pleska M, Shah N, Weiss H, Mccall I, Meyer J, Gupta A, Guet CC,
Levin B. 2018. Numerical data used in figures, Public Library of Science, 10.1371/journal.pbio.2005971.s008.
mla: Chaudhry, Waqas, et al. Numerical Data Used in Figures. Public Library
of Science, 2018, doi:10.1371/journal.pbio.2005971.s008.
short: W. Chaudhry, M. Pleska, N. Shah, H. Weiss, I. Mccall, J. Meyer, A. Gupta,
C.C. Guet, B. Levin, (2018).
date_created: 2021-08-06T12:43:44Z
date_published: 2018-08-16T00:00:00Z
date_updated: 2023-09-13T08:45:41Z
day: '16'
department:
- _id: CaGu
doi: 10.1371/journal.pbio.2005971.s008
month: '08'
oa_version: Published Version
publisher: Public Library of Science
related_material:
record:
- id: '82'
relation: used_in_publication
status: public
status: public
title: Numerical data used in figures
type: research_data_reference
user_id: 6785fbc1-c503-11eb-8a32-93094b40e1cf
year: '2018'
...
---
_id: '275'
abstract:
- lang: eng
text: Lymphatic endothelial cells (LECs) release extracellular chemokines to guide
the migration of dendritic cells. In this study, we report that LECs also release
basolateral exosome-rich endothelial vesicles (EEVs) that are secreted in greater
numbers in the presence of inflammatory cytokines and accumulate in the perivascular
stroma of small lymphatic vessels in human chronic inflammatory diseases. Proteomic
analyses of EEV fractions identified > 1,700 cargo proteins and revealed a
dominant motility-promoting protein signature. In vitro and ex vivo EEV fractions
augmented cellular protrusion formation in a CX3CL1/fractalkine-dependent fashion
and enhanced the directional migratory response of human dendritic cells along
guidance cues. We conclude that perilymphatic LEC exosomes enhance exploratory
behavior and thus promote directional migration of CX3CR1-expressing cells in
complex tissue environments.
acknowledgement: M. Brown was supported by the Cell Communication in Health and Disease
Graduate Study Program of the Austrian Science Fund and Medizinische Universität
Wien, M. Sixt by the European Research Council (ERC GA 281556) and an Austrian Science
Fund START award, K.L. Bennett by the Austrian Academy of Sciences, D.G. Jackson
and L.A. Johnson by Unit Funding (MC_UU_12010/2) and project grants from the Medical
Research Council (G1100134 and MR/L008610/1), and M. Detmar by the Schweizerischer
Nationalfonds zur Förderung der Wissenschaftlichen Forschung and Advanced European
Research Council grant LYVICAM. K. Vaahtomeri was supported by an Academy of Finland
postdoctoral research grant (287853). This project has received funding from the
European Union’s Horizon 2020 research and innovation program under grant agreement
No. 668036 (RELENT).
article_processing_charge: No
author:
- first_name: Markus
full_name: Brown, Markus
id: 3DAB9AFC-F248-11E8-B48F-1D18A9856A87
last_name: Brown
- first_name: Louise
full_name: Johnson, Louise
last_name: Johnson
- first_name: Dario
full_name: Leone, Dario
last_name: Leone
- first_name: Peter
full_name: Májek, Peter
last_name: Májek
- first_name: Kari
full_name: Vaahtomeri, Kari
id: 368EE576-F248-11E8-B48F-1D18A9856A87
last_name: Vaahtomeri
orcid: 0000-0001-7829-3518
- first_name: Daniel
full_name: Senfter, Daniel
last_name: Senfter
- first_name: Nora
full_name: Bukosza, Nora
last_name: Bukosza
- first_name: Helga
full_name: Schachner, Helga
last_name: Schachner
- first_name: Gabriele
full_name: Asfour, Gabriele
last_name: Asfour
- first_name: Brigitte
full_name: Langer, Brigitte
last_name: Langer
- first_name: Robert
full_name: Hauschild, Robert
id: 4E01D6B4-F248-11E8-B48F-1D18A9856A87
last_name: Hauschild
orcid: 0000-0001-9843-3522
- first_name: Katja
full_name: Parapatics, Katja
last_name: Parapatics
- first_name: Young
full_name: Hong, Young
last_name: Hong
- first_name: Keiryn
full_name: Bennett, Keiryn
last_name: Bennett
- first_name: Renate
full_name: Kain, Renate
last_name: Kain
- first_name: Michael
full_name: Detmar, Michael
last_name: Detmar
- first_name: Michael K
full_name: Sixt, Michael K
id: 41E9FBEA-F248-11E8-B48F-1D18A9856A87
last_name: Sixt
orcid: 0000-0002-6620-9179
- first_name: David
full_name: Jackson, David
last_name: Jackson
- first_name: Dontscho
full_name: Kerjaschki, Dontscho
last_name: Kerjaschki
citation:
ama: Brown M, Johnson L, Leone D, et al. Lymphatic exosomes promote dendritic cell
migration along guidance cues. Journal of Cell Biology. 2018;217(6):2205-2221.
doi:10.1083/jcb.201612051
apa: Brown, M., Johnson, L., Leone, D., Májek, P., Vaahtomeri, K., Senfter, D.,
… Kerjaschki, D. (2018). Lymphatic exosomes promote dendritic cell migration along
guidance cues. Journal of Cell Biology. Rockefeller University Press. https://doi.org/10.1083/jcb.201612051
chicago: Brown, Markus, Louise Johnson, Dario Leone, Peter Májek, Kari Vaahtomeri,
Daniel Senfter, Nora Bukosza, et al. “Lymphatic Exosomes Promote Dendritic Cell
Migration along Guidance Cues.” Journal of Cell Biology. Rockefeller University
Press, 2018. https://doi.org/10.1083/jcb.201612051.
ieee: M. Brown et al., “Lymphatic exosomes promote dendritic cell migration
along guidance cues,” Journal of Cell Biology, vol. 217, no. 6. Rockefeller
University Press, pp. 2205–2221, 2018.
ista: Brown M, Johnson L, Leone D, Májek P, Vaahtomeri K, Senfter D, Bukosza N,
Schachner H, Asfour G, Langer B, Hauschild R, Parapatics K, Hong Y, Bennett K,
Kain R, Detmar M, Sixt MK, Jackson D, Kerjaschki D. 2018. Lymphatic exosomes promote
dendritic cell migration along guidance cues. Journal of Cell Biology. 217(6),
2205–2221.
mla: Brown, Markus, et al. “Lymphatic Exosomes Promote Dendritic Cell Migration
along Guidance Cues.” Journal of Cell Biology, vol. 217, no. 6, Rockefeller
University Press, 2018, pp. 2205–21, doi:10.1083/jcb.201612051.
short: M. Brown, L. Johnson, D. Leone, P. Májek, K. Vaahtomeri, D. Senfter, N. Bukosza,
H. Schachner, G. Asfour, B. Langer, R. Hauschild, K. Parapatics, Y. Hong, K. Bennett,
R. Kain, M. Detmar, M.K. Sixt, D. Jackson, D. Kerjaschki, Journal of Cell Biology
217 (2018) 2205–2221.
date_created: 2018-12-11T11:45:33Z
date_published: 2018-04-12T00:00:00Z
date_updated: 2023-09-13T08:51:29Z
day: '12'
ddc:
- '570'
department:
- _id: MiSi
- _id: Bio
doi: 10.1083/jcb.201612051
ec_funded: 1
external_id:
isi:
- '000438077800026'
pmid:
- '29650776'
file:
- access_level: open_access
checksum: 9c7eba51a35c62da8c13f98120b64df4
content_type: application/pdf
creator: dernst
date_created: 2018-12-17T12:50:07Z
date_updated: 2020-07-14T12:45:45Z
file_id: '5704'
file_name: 2018_JournalCellBiology_Brown.pdf
file_size: 2252043
relation: main_file
file_date_updated: 2020-07-14T12:45:45Z
has_accepted_license: '1'
intvolume: ' 217'
isi: 1
issue: '6'
language:
- iso: eng
month: '04'
oa: 1
oa_version: Published Version
page: 2205 - 2221
pmid: 1
project:
- _id: 25A8E5EA-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: Y 564-B12
name: Cytoskeletal force generation and transduction of leukocytes (FWF)
- _id: 25A603A2-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '281556'
name: Cytoskeletal force generation and force transduction of migrating leukocytes
(EU)
publication: Journal of Cell Biology
publication_status: published
publisher: Rockefeller University Press
publist_id: '7627'
quality_controlled: '1'
scopus_import: '1'
status: public
title: Lymphatic exosomes promote dendritic cell migration along guidance cues
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: journal_article
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
volume: 217
year: '2018'
...
---
_id: '158'
abstract:
- lang: eng
text: 'The angiosperm seed is composed of three genetically distinct tissues: the
diploid embryo that originates from the fertilized egg cell, the triploid endosperm
that is produced from the fertilized central cell, and the maternal sporophytic
integuments that develop into the seed coat1. At the onset of embryo development
in Arabidopsis thaliana, the zygote divides asymmetrically, producing a small
apical embryonic cell and a larger basal cell that connects the embryo to the
maternal tissue2. The coordinated and synchronous development of the embryo and
the surrounding integuments, and the alignment of their growth axes, suggest communication
between maternal tissues and the embryo. In contrast to animals, however, where
a network of maternal factors that direct embryo patterning have been identified3,4,
only a few maternal mutations have been described to affect embryo development
in plants5–7. Early embryo patterning in Arabidopsis requires accumulation of
the phytohormone auxin in the apical cell by directed transport from the suspensor8–10.
However, the origin of this auxin has remained obscure. Here we investigate the
source of auxin for early embryogenesis and provide evidence that the mother plant
coordinates seed development by supplying auxin to the early embryo from the integuments
of the ovule. We show that auxin response increases in ovules after fertilization,
due to upregulated auxin biosynthesis in the integuments, and this maternally
produced auxin is required for correct embryo development.'
acknowledgement: This work was further supported by the Czech Science Foundation GACR
(GA13-40637S) to J.F.;
article_processing_charge: No
author:
- first_name: Hélène
full_name: Robert, Hélène
last_name: Robert
- first_name: Chulmin
full_name: Park, Chulmin
last_name: Park
- first_name: Carla
full_name: Gutièrrez, Carla
last_name: Gutièrrez
- first_name: Barbara
full_name: Wójcikowska, Barbara
last_name: Wójcikowska
- first_name: Aleš
full_name: Pěnčík, Aleš
last_name: Pěnčík
- first_name: Ondřej
full_name: Novák, Ondřej
last_name: Novák
- first_name: Junyi
full_name: Chen, Junyi
last_name: Chen
- first_name: Wim
full_name: Grunewald, Wim
last_name: Grunewald
- first_name: Thomas
full_name: Dresselhaus, Thomas
last_name: Dresselhaus
- first_name: Jirí
full_name: Friml, Jirí
id: 4159519E-F248-11E8-B48F-1D18A9856A87
last_name: Friml
orcid: 0000-0002-8302-7596
- first_name: Thomas
full_name: Laux, Thomas
last_name: Laux
citation:
ama: Robert H, Park C, Gutièrrez C, et al. Maternal auxin supply contributes to
early embryo patterning in Arabidopsis. Nature Plants. 2018;4(8):548-553.
doi:10.1038/s41477-018-0204-z
apa: Robert, H., Park, C., Gutièrrez, C., Wójcikowska, B., Pěnčík, A., Novák, O.,
… Laux, T. (2018). Maternal auxin supply contributes to early embryo patterning
in Arabidopsis. Nature Plants. Nature Publishing Group. https://doi.org/10.1038/s41477-018-0204-z
chicago: Robert, Hélène, Chulmin Park, Carla Gutièrrez, Barbara Wójcikowska, Aleš
Pěnčík, Ondřej Novák, Junyi Chen, et al. “Maternal Auxin Supply Contributes to
Early Embryo Patterning in Arabidopsis.” Nature Plants. Nature Publishing
Group, 2018. https://doi.org/10.1038/s41477-018-0204-z.
ieee: H. Robert et al., “Maternal auxin supply contributes to early embryo
patterning in Arabidopsis,” Nature Plants, vol. 4, no. 8. Nature Publishing
Group, pp. 548–553, 2018.
ista: Robert H, Park C, Gutièrrez C, Wójcikowska B, Pěnčík A, Novák O, Chen J, Grunewald
W, Dresselhaus T, Friml J, Laux T. 2018. Maternal auxin supply contributes to
early embryo patterning in Arabidopsis. Nature Plants. 4(8), 548–553.
mla: Robert, Hélène, et al. “Maternal Auxin Supply Contributes to Early Embryo Patterning
in Arabidopsis.” Nature Plants, vol. 4, no. 8, Nature Publishing Group,
2018, pp. 548–53, doi:10.1038/s41477-018-0204-z.
short: H. Robert, C. Park, C. Gutièrrez, B. Wójcikowska, A. Pěnčík, O. Novák, J.
Chen, W. Grunewald, T. Dresselhaus, J. Friml, T. Laux, Nature Plants 4 (2018)
548–553.
date_created: 2018-12-11T11:44:56Z
date_published: 2018-07-16T00:00:00Z
date_updated: 2023-09-13T08:53:28Z
day: '16'
department:
- _id: JiFr
doi: 10.1038/s41477-018-0204-z
ec_funded: 1
external_id:
isi:
- '000443861300011'
pmid:
- '30013211'
intvolume: ' 4'
isi: 1
issue: '8'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://www.ncbi.nlm.nih.gov/pubmed/30013211
month: '07'
oa: 1
oa_version: Submitted Version
page: 548 - 553
pmid: 1
project:
- _id: 25716A02-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '282300'
name: Polarity and subcellular dynamics in plants
publication: Nature Plants
publication_status: published
publisher: Nature Publishing Group
publist_id: '7763'
quality_controlled: '1'
related_material:
link:
- description: News on IST Homepage
relation: press_release
url: https://ist.ac.at/en/news/plant-mothers-talk-to-their-embryos-via-the-hormone-auxin/
scopus_import: '1'
status: public
title: Maternal auxin supply contributes to early embryo patterning in Arabidopsis
type: journal_article
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
volume: 4
year: '2018'
...
---
_id: '152'
abstract:
- lang: eng
text: Complex I has an essential role in ATP production by coupling electron transfer
from NADH to quinone with translocation of protons across the inner mitochondrial
membrane. Isolated complex I deficiency is a frequent cause of mitochondrial inherited
diseases. Complex I has also been implicated in cancer, ageing, and neurodegenerative
conditions. Until recently, the understanding of complex I deficiency on the molecular
level was limited due to the lack of high-resolution structures of the enzyme.
However, due to developments in single particle cryo-electron microscopy (cryo-EM),
recent studies have reported nearly atomic resolution maps and models of mitochondrial
complex I. These structures significantly add to our understanding of complex
I mechanism and assembly. The disease-causing mutations are discussed here in
their structural context.
article_processing_charge: No
article_type: original
author:
- first_name: Karol
full_name: Fiedorczuk, Karol
id: 5BFF67CE-02D1-11E9-B11A-A5A4D7DFFFD0
last_name: Fiedorczuk
- first_name: Leonid A
full_name: Sazanov, Leonid A
id: 338D39FE-F248-11E8-B48F-1D18A9856A87
last_name: Sazanov
orcid: 0000-0002-0977-7989
citation:
ama: Fiedorczuk K, Sazanov LA. Mammalian mitochondrial complex I structure and disease
causing mutations. Trends in Cell Biology. 2018;28(10):835-867. doi:10.1016/j.tcb.2018.06.006
apa: Fiedorczuk, K., & Sazanov, L. A. (2018). Mammalian mitochondrial complex
I structure and disease causing mutations. Trends in Cell Biology. Elsevier.
https://doi.org/10.1016/j.tcb.2018.06.006
chicago: Fiedorczuk, Karol, and Leonid A Sazanov. “Mammalian Mitochondrial Complex
I Structure and Disease Causing Mutations.” Trends in Cell Biology. Elsevier,
2018. https://doi.org/10.1016/j.tcb.2018.06.006.
ieee: K. Fiedorczuk and L. A. Sazanov, “Mammalian mitochondrial complex I structure
and disease causing mutations,” Trends in Cell Biology, vol. 28, no. 10.
Elsevier, pp. 835–867, 2018.
ista: Fiedorczuk K, Sazanov LA. 2018. Mammalian mitochondrial complex I structure
and disease causing mutations. Trends in Cell Biology. 28(10), 835–867.
mla: Fiedorczuk, Karol, and Leonid A. Sazanov. “Mammalian Mitochondrial Complex
I Structure and Disease Causing Mutations.” Trends in Cell Biology, vol.
28, no. 10, Elsevier, 2018, pp. 835–67, doi:10.1016/j.tcb.2018.06.006.
short: K. Fiedorczuk, L.A. Sazanov, Trends in Cell Biology 28 (2018) 835–867.
date_created: 2018-12-11T11:44:54Z
date_published: 2018-07-26T00:00:00Z
date_updated: 2023-09-13T08:51:56Z
day: '26'
ddc:
- '572'
department:
- _id: LeSa
doi: 10.1016/j.tcb.2018.06.006
external_id:
isi:
- '000445118200007'
file:
- access_level: open_access
checksum: ef6d2b4e1fd63948539639242610bfa6
content_type: application/pdf
creator: lsazanov
date_created: 2019-11-07T12:55:20Z
date_updated: 2020-07-14T12:45:00Z
file_id: '6994'
file_name: SasanovFinalMS+EdComments_LS_allacc_withFigs.pdf
file_size: 2185385
relation: main_file
file_date_updated: 2020-07-14T12:45:00Z
has_accepted_license: '1'
intvolume: ' 28'
isi: 1
issue: '10'
language:
- iso: eng
license: https://creativecommons.org/licenses/by-nc-nd/4.0/
month: '07'
oa: 1
oa_version: Submitted Version
page: 835 - 867
publication: Trends in Cell Biology
publication_status: published
publisher: Elsevier
publist_id: '7769'
quality_controlled: '1'
scopus_import: '1'
status: public
title: Mammalian mitochondrial complex I structure and disease causing mutations
tmp:
image: /images/cc_by_nc_nd.png
legal_code_url: https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode
name: Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International
(CC BY-NC-ND 4.0)
short: CC BY-NC-ND (4.0)
type: journal_article
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
volume: 28
year: '2018'
...
---
_id: '310'
abstract:
- lang: eng
text: A model of computation that is widely used in the formal analysis of reactive
systems is symbolic algorithms. In this model the access to the input graph is
restricted to consist of symbolic operations, which are expensive in comparison
to the standard RAM operations. We give lower bounds on the number of symbolic
operations for basic graph problems such as the computation of the strongly connected
components and of the approximate diameter as well as for fundamental problems
in model checking such as safety, liveness, and coliveness. Our lower bounds are
linear in the number of vertices of the graph, even for constant-diameter graphs.
For none of these problems lower bounds on the number of symbolic operations were
known before. The lower bounds show an interesting separation of these problems
from the reachability problem, which can be solved with O(D) symbolic operations,
where D is the diameter of the graph. Additionally we present an approximation
algorithm for the graph diameter which requires Õ(n/D) symbolic steps to achieve
a (1 +ϵ)-approximation for any constant > 0. This compares to O(n/D) symbolic
steps for the (naive) exact algorithm and O(D) symbolic steps for a 2-approximation.
Finally we also give a refined analysis of the strongly connected components algorithms
of [15], showing that it uses an optimal number of symbolic steps that is proportional
to the sum of the diameters of the strongly connected components.
article_processing_charge: No
author:
- first_name: Krishnendu
full_name: Chatterjee, Krishnendu
id: 2E5DCA20-F248-11E8-B48F-1D18A9856A87
last_name: Chatterjee
orcid: 0000-0002-4561-241X
- first_name: Wolfgang
full_name: Dvorák, Wolfgang
last_name: Dvorák
- first_name: Monika H
full_name: Henzinger, Monika H
id: 540c9bbd-f2de-11ec-812d-d04a5be85630
last_name: Henzinger
orcid: 0000-0002-5008-6530
- first_name: Veronika
full_name: Loitzenbauer, Veronika
last_name: Loitzenbauer
citation:
ama: 'Chatterjee K, Dvorák W, Henzinger MH, Loitzenbauer V. Lower bounds for symbolic
computation on graphs: Strongly connected components, liveness, safety, and diameter.
In: ACM; 2018:2341-2356. doi:10.1137/1.9781611975031.151'
apa: 'Chatterjee, K., Dvorák, W., Henzinger, M. H., & Loitzenbauer, V. (2018).
Lower bounds for symbolic computation on graphs: Strongly connected components,
liveness, safety, and diameter (pp. 2341–2356). Presented at the SODA: Symposium
on Discrete Algorithms, New Orleans, Louisiana, United States: ACM. https://doi.org/10.1137/1.9781611975031.151'
chicago: 'Chatterjee, Krishnendu, Wolfgang Dvorák, Monika H Henzinger, and Veronika
Loitzenbauer. “Lower Bounds for Symbolic Computation on Graphs: Strongly Connected
Components, Liveness, Safety, and Diameter,” 2341–56. ACM, 2018. https://doi.org/10.1137/1.9781611975031.151.'
ieee: 'K. Chatterjee, W. Dvorák, M. H. Henzinger, and V. Loitzenbauer, “Lower bounds
for symbolic computation on graphs: Strongly connected components, liveness, safety,
and diameter,” presented at the SODA: Symposium on Discrete Algorithms, New Orleans,
Louisiana, United States, 2018, pp. 2341–2356.'
ista: 'Chatterjee K, Dvorák W, Henzinger MH, Loitzenbauer V. 2018. Lower bounds
for symbolic computation on graphs: Strongly connected components, liveness, safety,
and diameter. SODA: Symposium on Discrete Algorithms, 2341–2356.'
mla: 'Chatterjee, Krishnendu, et al. Lower Bounds for Symbolic Computation on
Graphs: Strongly Connected Components, Liveness, Safety, and Diameter. ACM,
2018, pp. 2341–56, doi:10.1137/1.9781611975031.151.'
short: K. Chatterjee, W. Dvorák, M.H. Henzinger, V. Loitzenbauer, in:, ACM, 2018,
pp. 2341–2356.
conference:
end_date: 2018-01-10
location: New Orleans, Louisiana, United States
name: 'SODA: Symposium on Discrete Algorithms'
start_date: 2018-01-07
date_created: 2018-12-11T11:45:45Z
date_published: 2018-01-01T00:00:00Z
date_updated: 2023-09-13T08:50:16Z
day: '01'
department:
- _id: KrCh
doi: 10.1137/1.9781611975031.151
ec_funded: 1
external_id:
arxiv:
- '1711.09148'
isi:
- '000483921200152'
isi: 1
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/1711.09148
month: '01'
oa: 1
oa_version: Preprint
page: 2341 - 2356
project:
- _id: 25832EC2-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: S 11407_N23
name: Rigorous Systems Engineering
- _id: 2581B60A-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '279307'
name: 'Quantitative Graph Games: Theory and Applications'
- _id: 25892FC0-B435-11E9-9278-68D0E5697425
grant_number: ICT15-003
name: Efficient Algorithms for Computer Aided Verification
publication_status: published
publisher: ACM
publist_id: '7555'
quality_controlled: '1'
scopus_import: '1'
status: public
title: 'Lower bounds for symbolic computation on graphs: Strongly connected components,
liveness, safety, and diameter'
type: conference
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
year: '2018'
...
---
_id: '436'
abstract:
- lang: eng
text: There has been significant interest recently in using complex quantum systems
to create effective nonreciprocal dynamics. Proposals have been put forward for
the realization of artificial magnetic fields for photons and phonons; experimental
progress is fast making these proposals a reality. Much work has concentrated
on the use of such systems for controlling the flow of signals, e.g., to create
isolators or directional amplifiers for optical signals. In this Letter, we build
on this work but move in a different direction. We develop the theory of and discuss
a potential realization for the controllable flow of thermal noise in quantum
systems. We demonstrate theoretically that the unidirectional flow of thermal
noise is possible within quantum cascaded systems. Viewing an optomechanical platform
as a cascaded system we show here that one can ultimately control the direction
of the flow of thermal noise. By appropriately engineering the mechanical resonator,
which acts as an artificial reservoir, the flow of thermal noise can be constrained
to a desired direction, yielding a thermal rectifier. The proposed quantum thermal
noise rectifier could potentially be used to develop devices such as a thermal
modulator, a thermal router, and a thermal amplifier for nanoelectronic devices
and superconducting circuits.
article_number: '060601 '
article_processing_charge: No
author:
- first_name: Shabir
full_name: Barzanjeh, Shabir
id: 2D25E1F6-F248-11E8-B48F-1D18A9856A87
last_name: Barzanjeh
orcid: 0000-0003-0415-1423
- first_name: Matteo
full_name: Aquilina, Matteo
last_name: Aquilina
- first_name: André
full_name: Xuereb, André
last_name: Xuereb
citation:
ama: Barzanjeh S, Aquilina M, Xuereb A. Manipulating the flow of thermal noise in
quantum devices. Physical Review Letters. 2018;120(6). doi:10.1103/PhysRevLett.120.060601
apa: Barzanjeh, S., Aquilina, M., & Xuereb, A. (2018). Manipulating the flow
of thermal noise in quantum devices. Physical Review Letters. American
Physical Society. https://doi.org/10.1103/PhysRevLett.120.060601
chicago: Barzanjeh, Shabir, Matteo Aquilina, and André Xuereb. “Manipulating the
Flow of Thermal Noise in Quantum Devices.” Physical Review Letters. American
Physical Society, 2018. https://doi.org/10.1103/PhysRevLett.120.060601.
ieee: S. Barzanjeh, M. Aquilina, and A. Xuereb, “Manipulating the flow of thermal
noise in quantum devices,” Physical Review Letters, vol. 120, no. 6. American
Physical Society, 2018.
ista: Barzanjeh S, Aquilina M, Xuereb A. 2018. Manipulating the flow of thermal
noise in quantum devices. Physical Review Letters. 120(6), 060601.
mla: Barzanjeh, Shabir, et al. “Manipulating the Flow of Thermal Noise in Quantum
Devices.” Physical Review Letters, vol. 120, no. 6, 060601, American Physical
Society, 2018, doi:10.1103/PhysRevLett.120.060601.
short: S. Barzanjeh, M. Aquilina, A. Xuereb, Physical Review Letters 120 (2018).
date_created: 2018-12-11T11:46:28Z
date_published: 2018-02-07T00:00:00Z
date_updated: 2023-09-13T08:52:27Z
day: '07'
department:
- _id: JoFi
doi: 10.1103/PhysRevLett.120.060601
ec_funded: 1
external_id:
arxiv:
- '1706.09051'
isi:
- '000424382100004'
intvolume: ' 120'
isi: 1
issue: '6'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/1706.09051
month: '02'
oa: 1
oa_version: Preprint
project:
- _id: 257EB838-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '732894'
name: Hybrid Optomechanical Technologies
- _id: 258047B6-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '707438'
name: 'Microwave-to-Optical Quantum Link: Quantum Teleportation and Quantum Illumination
with cavity Optomechanics SUPEREOM'
publication: Physical Review Letters
publication_status: published
publisher: American Physical Society
publist_id: '7387'
quality_controlled: '1'
related_material:
link:
- description: News on IST Homepage
relation: press_release
url: https://ist.ac.at/en/news/interference-as-a-new-method-for-cooling-quantum-devices/
scopus_import: '1'
status: public
title: Manipulating the flow of thermal noise in quantum devices
type: journal_article
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
volume: 120
year: '2018'
...
---
_id: '5858'
abstract:
- lang: eng
text: Spatial patterns are ubiquitous on the subcellular, cellular and tissue level,
and can be studied using imaging techniques such as light and fluorescence microscopy.
Imaging data provide quantitative information about biological systems; however,
mechanisms causing spatial patterning often remain elusive. In recent years, spatio-temporal
mathematical modelling has helped to overcome this problem. Yet, outliers and
structured noise limit modelling of whole imaging data, and models often consider
spatial summary statistics. Here, we introduce an integrated data-driven modelling
approach that can cope with measurement artefacts and whole imaging data. Our
approach combines mechanistic models of the biological processes with robust statistical
models of the measurement process. The parameters of the integrated model are
calibrated using a maximum-likelihood approach. We used this integrated modelling
approach to study in vivo gradients of the chemokine (C-C motif) ligand 21 (CCL21).
CCL21 gradients guide dendritic cells and are important in the adaptive immune
response. Using artificial data, we verified that the integrated modelling approach
provides reliable parameter estimates in the presence of measurement noise and
that bias and variance of these estimates are reduced compared to conventional
approaches. The application to experimental data allowed the parametrization and
subsequent refinement of the model using additional mechanisms. Among other results,
model-based hypothesis testing predicted lymphatic vessel-dependent concentration
of heparan sulfate, the binding partner of CCL21. The selected model provided
an accurate description of the experimental data and was partially validated using
published data. Our findings demonstrate that integrated statistical modelling
of whole imaging data is computationally feasible and can provide novel biological
insights.
article_number: '20180600'
article_processing_charge: No
author:
- first_name: Sabrina
full_name: Hross, Sabrina
last_name: Hross
- first_name: Fabian J.
full_name: Theis, Fabian J.
last_name: Theis
- first_name: Michael K
full_name: Sixt, Michael K
id: 41E9FBEA-F248-11E8-B48F-1D18A9856A87
last_name: Sixt
orcid: 0000-0002-6620-9179
- first_name: Jan
full_name: Hasenauer, Jan
last_name: Hasenauer
citation:
ama: Hross S, Theis FJ, Sixt MK, Hasenauer J. Mechanistic description of spatial
processes using integrative modelling of noise-corrupted imaging data. Journal
of the Royal Society Interface. 2018;15(149). doi:10.1098/rsif.2018.0600
apa: Hross, S., Theis, F. J., Sixt, M. K., & Hasenauer, J. (2018). Mechanistic
description of spatial processes using integrative modelling of noise-corrupted
imaging data. Journal of the Royal Society Interface. Royal Society Publishing.
https://doi.org/10.1098/rsif.2018.0600
chicago: Hross, Sabrina, Fabian J. Theis, Michael K Sixt, and Jan Hasenauer. “Mechanistic
Description of Spatial Processes Using Integrative Modelling of Noise-Corrupted
Imaging Data.” Journal of the Royal Society Interface. Royal Society Publishing,
2018. https://doi.org/10.1098/rsif.2018.0600.
ieee: S. Hross, F. J. Theis, M. K. Sixt, and J. Hasenauer, “Mechanistic description
of spatial processes using integrative modelling of noise-corrupted imaging data,”
Journal of the Royal Society Interface, vol. 15, no. 149. Royal Society
Publishing, 2018.
ista: Hross S, Theis FJ, Sixt MK, Hasenauer J. 2018. Mechanistic description of
spatial processes using integrative modelling of noise-corrupted imaging data.
Journal of the Royal Society Interface. 15(149), 20180600.
mla: Hross, Sabrina, et al. “Mechanistic Description of Spatial Processes Using
Integrative Modelling of Noise-Corrupted Imaging Data.” Journal of the Royal
Society Interface, vol. 15, no. 149, 20180600, Royal Society Publishing, 2018,
doi:10.1098/rsif.2018.0600.
short: S. Hross, F.J. Theis, M.K. Sixt, J. Hasenauer, Journal of the Royal Society
Interface 15 (2018).
date_created: 2019-01-20T22:59:18Z
date_published: 2018-12-05T00:00:00Z
date_updated: 2023-09-13T08:55:05Z
day: '05'
ddc:
- '570'
department:
- _id: MiSi
doi: 10.1098/rsif.2018.0600
external_id:
isi:
- '000456783800011'
file:
- access_level: open_access
checksum: 56eb4308a15b7190bff938fab1f780e8
content_type: application/pdf
creator: dernst
date_created: 2019-02-05T14:46:44Z
date_updated: 2020-07-14T12:47:13Z
file_id: '5925'
file_name: 2018_Interface_Hross.pdf
file_size: 1464288
relation: main_file
file_date_updated: 2020-07-14T12:47:13Z
has_accepted_license: '1'
intvolume: ' 15'
isi: 1
issue: '149'
language:
- iso: eng
month: '12'
oa: 1
oa_version: Published Version
publication: Journal of the Royal Society Interface
publication_identifier:
issn:
- '17425689'
publication_status: published
publisher: Royal Society Publishing
quality_controlled: '1'
scopus_import: '1'
status: public
title: Mechanistic description of spatial processes using integrative modelling of
noise-corrupted imaging data
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: journal_article
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
volume: 15
year: '2018'
...
---
_id: '16'
abstract:
- lang: eng
text: We report quantitative evidence of mixing-layer elastic instability in a viscoelastic
fluid flow between two widely spaced obstacles hindering a channel flow at Re
1 and Wi 1. Two mixing layers with nonuniform shear velocity profiles are formed
in the region between the obstacles. The mixing-layer instability arises in the
vicinity of an inflection point on the shear velocity profile with a steep variation
in the elastic stress. The instability results in an intermittent appearance of
small vortices in the mixing layers and an amplification of spatiotemporal averaged
vorticity in the elastic turbulence regime. The latter is characterized through
scaling of friction factor with Wi and both pressure and velocity spectra. Furthermore,
the observations reported provide improved understanding of the stability of the
mixing layer in a viscoelastic fluid at large elasticity, i.e., Wi 1 and Re 1
and oppose the current view of suppression of vorticity solely by polymer additives.
acknowledgement: This work was partially supported by the Israel Science Foundation
(ISF; Grant No. 882/15) and the Binational USA-Israel Foundation (BSF; Grant No.
2016145).
article_number: '103303'
article_processing_charge: No
article_type: original
author:
- first_name: Atul
full_name: Varshney, Atul
id: 2A2006B2-F248-11E8-B48F-1D18A9856A87
last_name: Varshney
orcid: 0000-0002-3072-5999
- first_name: Victor
full_name: Steinberg, Victor
last_name: Steinberg
citation:
ama: Varshney A, Steinberg V. Mixing layer instability and vorticity amplification
in a creeping viscoelastic flow. Physical Review Fluids. 2018;3(10). doi:10.1103/PhysRevFluids.3.103303
apa: Varshney, A., & Steinberg, V. (2018). Mixing layer instability and vorticity
amplification in a creeping viscoelastic flow. Physical Review Fluids.
American Physical Society. https://doi.org/10.1103/PhysRevFluids.3.103303
chicago: Varshney, Atul, and Victor Steinberg. “Mixing Layer Instability and Vorticity
Amplification in a Creeping Viscoelastic Flow.” Physical Review Fluids.
American Physical Society, 2018. https://doi.org/10.1103/PhysRevFluids.3.103303.
ieee: A. Varshney and V. Steinberg, “Mixing layer instability and vorticity amplification
in a creeping viscoelastic flow,” Physical Review Fluids, vol. 3, no. 10.
American Physical Society, 2018.
ista: Varshney A, Steinberg V. 2018. Mixing layer instability and vorticity amplification
in a creeping viscoelastic flow. Physical Review Fluids. 3(10), 103303.
mla: Varshney, Atul, and Victor Steinberg. “Mixing Layer Instability and Vorticity
Amplification in a Creeping Viscoelastic Flow.” Physical Review Fluids,
vol. 3, no. 10, 103303, American Physical Society, 2018, doi:10.1103/PhysRevFluids.3.103303.
short: A. Varshney, V. Steinberg, Physical Review Fluids 3 (2018).
date_created: 2018-12-11T11:44:10Z
date_published: 2018-10-16T00:00:00Z
date_updated: 2023-09-13T08:57:05Z
day: '16'
ddc:
- '532'
department:
- _id: BjHo
doi: 10.1103/PhysRevFluids.3.103303
ec_funded: 1
external_id:
isi:
- '000447469200001'
file:
- access_level: open_access
checksum: 7fc0a2322214d1c04debef36d5bf2e8a
content_type: application/pdf
creator: system
date_created: 2018-12-12T10:13:56Z
date_updated: 2020-07-14T12:45:04Z
file_id: '5043'
file_name: IST-2018-1062-v1+1_PhysRevFluids.3.103303.pdf
file_size: 1838431
relation: main_file
file_date_updated: 2020-07-14T12:45:04Z
has_accepted_license: '1'
intvolume: ' 3'
isi: 1
issue: '10'
language:
- iso: eng
month: '10'
oa: 1
oa_version: Submitted Version
project:
- _id: 260C2330-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '754411'
name: ISTplus - Postdoctoral Fellowships
publication: Physical Review Fluids
publication_status: published
publisher: American Physical Society
publist_id: '8039'
pubrep_id: '1062'
quality_controlled: '1'
scopus_import: '1'
status: public
title: Mixing layer instability and vorticity amplification in a creeping viscoelastic
flow
type: journal_article
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
volume: 3
year: '2018'
...
---
_id: '43'
abstract:
- lang: eng
text: 'The initial amount of pathogens required to start an infection within a susceptible
host is called the infective dose and is known to vary to a large extent between
different pathogen species. We investigate the hypothesis that the differences
in infective doses are explained by the mode of action in the underlying mechanism
of pathogenesis: Pathogens with locally acting mechanisms tend to have smaller
infective doses than pathogens with distantly acting mechanisms. While empirical
evidence tends to support the hypothesis, a formal theoretical explanation has
been lacking. We give simple analytical models to gain insight into this phenomenon
and also investigate a stochastic, spatially explicit, mechanistic within-host
model for toxin-dependent bacterial infections. The model shows that pathogens
secreting locally acting toxins have smaller infective doses than pathogens secreting
diffusive toxins, as hypothesized. While local pathogenetic mechanisms require
smaller infective doses, pathogens with distantly acting toxins tend to spread
faster and may cause more damage to the host. The proposed model can serve as
a basis for the spatially explicit analysis of various virulence factors also
in the context of other problems in infection dynamics.'
acknowledgement: J.R. and J.V.A. were also supported by the Academy of Finland Grants
1273253 and 267541.
article_processing_charge: No
author:
- first_name: Joel
full_name: Rybicki, Joel
id: 334EFD2E-F248-11E8-B48F-1D18A9856A87
last_name: Rybicki
orcid: 0000-0002-6432-6646
- first_name: Eva
full_name: Kisdi, Eva
last_name: Kisdi
- first_name: Jani
full_name: Anttila, Jani
last_name: Anttila
citation:
ama: Rybicki J, Kisdi E, Anttila J. Model of bacterial toxin-dependent pathogenesis
explains infective dose. PNAS. 2018;115(42):10690-10695. doi:10.1073/pnas.1721061115
apa: Rybicki, J., Kisdi, E., & Anttila, J. (2018). Model of bacterial toxin-dependent
pathogenesis explains infective dose. PNAS. National Academy of Sciences.
https://doi.org/10.1073/pnas.1721061115
chicago: Rybicki, Joel, Eva Kisdi, and Jani Anttila. “Model of Bacterial Toxin-Dependent
Pathogenesis Explains Infective Dose.” PNAS. National Academy of Sciences,
2018. https://doi.org/10.1073/pnas.1721061115.
ieee: J. Rybicki, E. Kisdi, and J. Anttila, “Model of bacterial toxin-dependent
pathogenesis explains infective dose,” PNAS, vol. 115, no. 42. National
Academy of Sciences, pp. 10690–10695, 2018.
ista: Rybicki J, Kisdi E, Anttila J. 2018. Model of bacterial toxin-dependent pathogenesis
explains infective dose. PNAS. 115(42), 10690–10695.
mla: Rybicki, Joel, et al. “Model of Bacterial Toxin-Dependent Pathogenesis Explains
Infective Dose.” PNAS, vol. 115, no. 42, National Academy of Sciences,
2018, pp. 10690–95, doi:10.1073/pnas.1721061115.
short: J. Rybicki, E. Kisdi, J. Anttila, PNAS 115 (2018) 10690–10695.
date_created: 2018-12-11T11:44:19Z
date_published: 2018-10-02T00:00:00Z
date_updated: 2023-09-13T08:57:38Z
day: '02'
ddc:
- '570'
- '577'
department:
- _id: DaAl
doi: 10.1073/pnas.1721061115
ec_funded: 1
external_id:
isi:
- '000447491300057'
file:
- access_level: open_access
checksum: df7ac544a587c06b75692653b9fabd18
content_type: application/pdf
creator: dernst
date_created: 2019-04-09T08:02:50Z
date_updated: 2020-07-14T12:46:26Z
file_id: '6258'
file_name: 2018_PNAS_Rybicki.pdf
file_size: 4070777
relation: main_file
file_date_updated: 2020-07-14T12:46:26Z
has_accepted_license: '1'
intvolume: ' 115'
isi: 1
issue: '42'
language:
- iso: eng
month: '10'
oa: 1
oa_version: Submitted Version
page: 10690 - 10695
project:
- _id: 260C2330-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '754411'
name: ISTplus - Postdoctoral Fellowships
publication: PNAS
publication_status: published
publisher: National Academy of Sciences
publist_id: '8011'
pubrep_id: '1063'
quality_controlled: '1'
scopus_import: '1'
status: public
title: Model of bacterial toxin-dependent pathogenesis explains infective dose
type: journal_article
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
volume: 115
year: '2018'
...
---
_id: '13'
abstract:
- lang: eng
text: We propose a new method for fabricating digital objects through reusable silicone
molds. Molds are generated by casting liquid silicone into custom 3D printed containers
called metamolds. Metamolds automatically define the cuts that are needed to extract
the cast object from the silicone mold. The shape of metamolds is designed through
a novel segmentation technique, which takes into account both geometric and topological
constraints involved in the process of mold casting. Our technique is simple,
does not require changing the shape or topology of the input objects, and only
requires off-the- shelf materials and technologies. We successfully tested our
method on a set of challenging examples with complex shapes and rich geometric
detail. © 2018 Association for Computing Machinery.
article_number: '136'
article_processing_charge: No
author:
- first_name: Thomas
full_name: Alderighi, Thomas
last_name: Alderighi
- first_name: Luigi
full_name: Malomo, Luigi
last_name: Malomo
- first_name: Daniela
full_name: Giorgi, Daniela
last_name: Giorgi
- first_name: Nico
full_name: Pietroni, Nico
last_name: Pietroni
- first_name: Bernd
full_name: Bickel, Bernd
id: 49876194-F248-11E8-B48F-1D18A9856A87
last_name: Bickel
orcid: 0000-0001-6511-9385
- first_name: Paolo
full_name: Cignoni, Paolo
last_name: Cignoni
citation:
ama: 'Alderighi T, Malomo L, Giorgi D, Pietroni N, Bickel B, Cignoni P. Metamolds:
Computational design of silicone molds. ACM Trans Graph. 2018;37(4). doi:10.1145/3197517.3201381'
apa: 'Alderighi, T., Malomo, L., Giorgi, D., Pietroni, N., Bickel, B., & Cignoni,
P. (2018). Metamolds: Computational design of silicone molds. ACM Trans. Graph.
ACM. https://doi.org/10.1145/3197517.3201381'
chicago: 'Alderighi, Thomas, Luigi Malomo, Daniela Giorgi, Nico Pietroni, Bernd
Bickel, and Paolo Cignoni. “Metamolds: Computational Design of Silicone Molds.”
ACM Trans. Graph. ACM, 2018. https://doi.org/10.1145/3197517.3201381.'
ieee: 'T. Alderighi, L. Malomo, D. Giorgi, N. Pietroni, B. Bickel, and P. Cignoni,
“Metamolds: Computational design of silicone molds,” ACM Trans. Graph.,
vol. 37, no. 4. ACM, 2018.'
ista: 'Alderighi T, Malomo L, Giorgi D, Pietroni N, Bickel B, Cignoni P. 2018. Metamolds:
Computational design of silicone molds. ACM Trans. Graph. 37(4), 136.'
mla: 'Alderighi, Thomas, et al. “Metamolds: Computational Design of Silicone Molds.”
ACM Trans. Graph., vol. 37, no. 4, 136, ACM, 2018, doi:10.1145/3197517.3201381.'
short: T. Alderighi, L. Malomo, D. Giorgi, N. Pietroni, B. Bickel, P. Cignoni, ACM
Trans. Graph. 37 (2018).
date_created: 2018-12-11T11:44:09Z
date_published: 2018-08-04T00:00:00Z
date_updated: 2023-09-13T08:56:07Z
day: '04'
ddc:
- '004'
department:
- _id: BeBi
doi: 10.1145/3197517.3201381
ec_funded: 1
external_id:
isi:
- '000448185000097'
file:
- access_level: open_access
checksum: 61d46273dca4de626accef1d17a0aaad
content_type: application/pdf
creator: system
date_created: 2018-12-12T10:18:52Z
date_updated: 2020-07-14T12:44:43Z
file_id: '5374'
file_name: IST-2018-1038-v1+1_metamolds_authorversion.pdf
file_size: 91939066
relation: main_file
file_date_updated: 2020-07-14T12:44:43Z
has_accepted_license: '1'
intvolume: ' 37'
isi: 1
issue: '4'
language:
- iso: eng
month: '08'
oa: 1
oa_version: Submitted Version
project:
- _id: 24F9549A-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '715767'
name: 'MATERIALIZABLE: Intelligent fabrication-oriented Computational Design and
Modeling'
publication: ACM Trans. Graph.
publication_status: published
publisher: ACM
publist_id: '8043'
pubrep_id: '1038'
quality_controlled: '1'
related_material:
link:
- description: News on IST Homepage
relation: press_release
url: https://ist.ac.at/en/news/metamolds-molding-a-mold/
scopus_import: '1'
status: public
title: 'Metamolds: Computational design of silicone molds'
type: journal_article
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
volume: 37
year: '2018'
...
---
_id: '137'
abstract:
- lang: eng
text: Fluorescent sensors are an essential part of the experimental toolbox of the
life sciences, where they are used ubiquitously to visualize intra- and extracellular
signaling. In the brain, optical neurotransmitter sensors can shed light on temporal
and spatial aspects of signal transmission by directly observing, for instance,
neurotransmitter release and spread. Here we report the development and application
of the first optical sensor for the amino acid glycine, which is both an inhibitory
neurotransmitter and a co-agonist of the N-methyl-d-aspartate receptors (NMDARs)
involved in synaptic plasticity. Computational design of a glycine-specific binding
protein allowed us to produce the optical glycine FRET sensor (GlyFS), which can
be used with single and two-photon excitation fluorescence microscopy. We took
advantage of this newly developed sensor to test predictions about the uneven
spatial distribution of glycine in extracellular space and to demonstrate that
extracellular glycine levels are controlled by plasticity-inducing stimuli.
article_processing_charge: No
article_type: original
author:
- first_name: William
full_name: Zhang, William
last_name: Zhang
- first_name: Michel
full_name: Herde, Michel
last_name: Herde
- first_name: Joshua
full_name: Mitchell, Joshua
last_name: Mitchell
- first_name: Jason
full_name: Whitfield, Jason
last_name: Whitfield
- first_name: Andreas
full_name: Wulff, Andreas
last_name: Wulff
- first_name: Vanessa
full_name: Vongsouthi, Vanessa
last_name: Vongsouthi
- first_name: Inmaculada
full_name: Sanchez Romero, Inmaculada
id: 3D9C5D30-F248-11E8-B48F-1D18A9856A87
last_name: Sanchez Romero
- first_name: Polina
full_name: Gulakova, Polina
last_name: Gulakova
- first_name: Daniel
full_name: Minge, Daniel
last_name: Minge
- first_name: Björn
full_name: Breithausen, Björn
last_name: Breithausen
- first_name: Susanne
full_name: Schoch, Susanne
last_name: Schoch
- 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
- first_name: Christian
full_name: Henneberger, Christian
last_name: Henneberger
citation:
ama: Zhang W, Herde M, Mitchell J, et al. Monitoring hippocampal glycine with the
computationally designed optical sensor GlyFS. Nature Chemical Biology.
2018;14(9):861-869. doi:10.1038/s41589-018-0108-2
apa: Zhang, W., Herde, M., Mitchell, J., Whitfield, J., Wulff, A., Vongsouthi, V.,
… Henneberger, C. (2018). Monitoring hippocampal glycine with the computationally
designed optical sensor GlyFS. Nature Chemical Biology. Nature Publishing
Group. https://doi.org/10.1038/s41589-018-0108-2
chicago: Zhang, William, Michel Herde, Joshua Mitchell, Jason Whitfield, Andreas
Wulff, Vanessa Vongsouthi, Inmaculada Sanchez-Romero, et al. “Monitoring Hippocampal
Glycine with the Computationally Designed Optical Sensor GlyFS.” Nature Chemical
Biology. Nature Publishing Group, 2018. https://doi.org/10.1038/s41589-018-0108-2.
ieee: W. Zhang et al., “Monitoring hippocampal glycine with the computationally
designed optical sensor GlyFS,” Nature Chemical Biology, vol. 14, no. 9.
Nature Publishing Group, pp. 861–869, 2018.
ista: Zhang W, Herde M, Mitchell J, Whitfield J, Wulff A, Vongsouthi V, Sanchez-Romero
I, Gulakova P, Minge D, Breithausen B, Schoch S, Janovjak HL, Jackson C, Henneberger
C. 2018. Monitoring hippocampal glycine with the computationally designed optical
sensor GlyFS. Nature Chemical Biology. 14(9), 861–869.
mla: Zhang, William, et al. “Monitoring Hippocampal Glycine with the Computationally
Designed Optical Sensor GlyFS.” Nature Chemical Biology, vol. 14, no. 9,
Nature Publishing Group, 2018, pp. 861–69, doi:10.1038/s41589-018-0108-2.
short: W. Zhang, M. Herde, J. Mitchell, J. Whitfield, A. Wulff, V. Vongsouthi, I.
Sanchez-Romero, P. Gulakova, D. Minge, B. Breithausen, S. Schoch, H.L. Janovjak,
C. Jackson, C. Henneberger, Nature Chemical Biology 14 (2018) 861–869.
date_created: 2018-12-11T11:44:49Z
date_published: 2018-07-30T00:00:00Z
date_updated: 2023-09-13T08:58:05Z
day: '30'
department:
- _id: HaJa
doi: 10.1038/s41589-018-0108-2
external_id:
isi:
- '000442174500013'
pmid:
- '30061718 '
intvolume: ' 14'
isi: 1
issue: '9'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://www.ncbi.nlm.nih.gov/pubmed/30061718
month: '07'
oa: 1
oa_version: Submitted Version
page: 861 - 869
pmid: 1
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: Nature Chemical Biology
publication_status: published
publisher: Nature Publishing Group
publist_id: '7786'
quality_controlled: '1'
scopus_import: '1'
status: public
title: Monitoring hippocampal glycine with the computationally designed optical sensor
GlyFS
type: journal_article
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
volume: 14
year: '2018'
...
---
_id: '153'
abstract:
- lang: eng
text: Cells migrating in multicellular organisms steadily traverse complex three-dimensional
(3D) environments. To decipher the underlying cell biology, current experimental
setups either use simplified 2D, tissue-mimetic 3D (e.g., collagen matrices) or
in vivo environments. While only in vivo experiments are truly physiological,
they do not allow for precise manipulation of environmental parameters. 2D in
vitro experiments do allow mechanical and chemical manipulations, but increasing
evidence demonstrates substantial differences of migratory mechanisms in 2D and
3D. Here, we describe simple, robust, and versatile “pillar forests” to investigate
cell migration in complex but fully controllable 3D environments. Pillar forests
are polydimethylsiloxane-based setups, in which two closely adjacent surfaces
are interconnected by arrays of micrometer-sized pillars. Changing the pillar
shape, size, height and the inter-pillar distance precisely manipulates microenvironmental
parameters (e.g., pore sizes, micro-geometry, micro-topology), while being easily
combined with chemotactic cues, surface coatings, diverse cell types and advanced
imaging techniques. Thus, pillar forests combine the advantages of 2D cell migration
assays with the precise definition of 3D environmental parameters.
article_processing_charge: No
author:
- first_name: Jörg
full_name: Renkawitz, Jörg
id: 3F0587C8-F248-11E8-B48F-1D18A9856A87
last_name: Renkawitz
orcid: 0000-0003-2856-3369
- first_name: Anne
full_name: Reversat, Anne
id: 35B76592-F248-11E8-B48F-1D18A9856A87
last_name: Reversat
orcid: 0000-0003-0666-8928
- first_name: Alexander F
full_name: Leithner, Alexander F
id: 3B1B77E4-F248-11E8-B48F-1D18A9856A87
last_name: Leithner
orcid: 0000-0002-1073-744X
- first_name: Jack
full_name: Merrin, Jack
id: 4515C308-F248-11E8-B48F-1D18A9856A87
last_name: Merrin
orcid: 0000-0001-5145-4609
- first_name: Michael K
full_name: Sixt, Michael K
id: 41E9FBEA-F248-11E8-B48F-1D18A9856A87
last_name: Sixt
orcid: 0000-0002-6620-9179
citation:
ama: 'Renkawitz J, Reversat A, Leithner AF, Merrin J, Sixt MK. Micro-engineered
“pillar forests” to study cell migration in complex but controlled 3D environments.
In: Methods in Cell Biology. Vol 147. Academic Press; 2018:79-91. doi:10.1016/bs.mcb.2018.07.004'
apa: Renkawitz, J., Reversat, A., Leithner, A. F., Merrin, J., & Sixt, M. K.
(2018). Micro-engineered “pillar forests” to study cell migration in complex but
controlled 3D environments. In Methods in Cell Biology (Vol. 147, pp. 79–91).
Academic Press. https://doi.org/10.1016/bs.mcb.2018.07.004
chicago: Renkawitz, Jörg, Anne Reversat, Alexander F Leithner, Jack Merrin, and
Michael K Sixt. “Micro-Engineered ‘Pillar Forests’ to Study Cell Migration in
Complex but Controlled 3D Environments.” In Methods in Cell Biology, 147:79–91.
Academic Press, 2018. https://doi.org/10.1016/bs.mcb.2018.07.004.
ieee: J. Renkawitz, A. Reversat, A. F. Leithner, J. Merrin, and M. K. Sixt, “Micro-engineered
‘pillar forests’ to study cell migration in complex but controlled 3D environments,”
in Methods in Cell Biology, vol. 147, Academic Press, 2018, pp. 79–91.
ista: 'Renkawitz J, Reversat A, Leithner AF, Merrin J, Sixt MK. 2018.Micro-engineered
“pillar forests” to study cell migration in complex but controlled 3D environments.
In: Methods in Cell Biology. vol. 147, 79–91.'
mla: Renkawitz, Jörg, et al. “Micro-Engineered ‘Pillar Forests’ to Study Cell Migration
in Complex but Controlled 3D Environments.” Methods in Cell Biology, vol.
147, Academic Press, 2018, pp. 79–91, doi:10.1016/bs.mcb.2018.07.004.
short: J. Renkawitz, A. Reversat, A.F. Leithner, J. Merrin, M.K. Sixt, in:, Methods
in Cell Biology, Academic Press, 2018, pp. 79–91.
date_created: 2018-12-11T11:44:54Z
date_published: 2018-07-27T00:00:00Z
date_updated: 2023-09-13T08:56:35Z
day: '27'
department:
- _id: MiSi
- _id: NanoFab
doi: 10.1016/bs.mcb.2018.07.004
external_id:
isi:
- '000452412300006'
pmid:
- '30165964'
intvolume: ' 147'
isi: 1
language:
- iso: eng
month: '07'
oa_version: None
page: 79 - 91
pmid: 1
publication: Methods in Cell Biology
publication_identifier:
issn:
- 0091679X
publication_status: published
publisher: Academic Press
publist_id: '7768'
quality_controlled: '1'
scopus_import: '1'
status: public
title: Micro-engineered “pillar forests” to study cell migration in complex but controlled
3D environments
type: book_chapter
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
volume: 147
year: '2018'
...
---
_id: '54'
abstract:
- lang: eng
text: During epithelial tissue development, repair, and homeostasis, adherens junctions
(AJs) ensure intercellular adhesion and tissue integrity while allowing for cell
and tissue dynamics. Mechanical forces play critical roles in AJs’ composition
and dynamics. Recent findings highlight that beyond a well-established role in
reinforcing cell-cell adhesion, AJ mechanosensitivity promotes junctional remodeling
and polarization, thereby regulating critical processes such as cell intercalation,
division, and collective migration. Here, we provide an integrated view of mechanosensing
mechanisms that regulate cell-cell contact composition, geometry, and integrity
under tension and highlight pivotal roles for mechanosensitive AJ remodeling in
preserving epithelial integrity and sustaining tissue dynamics.
acknowledgement: Research in the Bellaïche laboratory is supported by the European
Research Council (ERC Advanced, TiMoprh, 340784), the Fondation ARC pour la Recherche
sur le Cancer (SL220130607097), the Agence Nationale de la Recherche (ANR lLabex
DEEP; 11-LBX-0044, ANR-10-IDEX-0001-02), the Centre National de la Recherche Scientifique,
the Institut National de la Santé et de la Recherche Médicale, and Institut Curie
and PSL Research University funding or grants.
article_processing_charge: No
article_type: review
author:
- first_name: Diana C
full_name: Nunes Pinheiro, Diana C
id: 2E839F16-F248-11E8-B48F-1D18A9856A87
last_name: Nunes Pinheiro
orcid: 0000-0003-4333-7503
- first_name: Yohanns
full_name: Bellaïche, Yohanns
last_name: Bellaïche
citation:
ama: Nunes Pinheiro DC, Bellaïche Y. Mechanical force-driven adherents junction
remodeling and epithelial dynamics. Developmental Cell. 2018;47(1):3-19.
doi:10.1016/j.devcel.2018.09.014
apa: Nunes Pinheiro, D. C., & Bellaïche, Y. (2018). Mechanical force-driven
adherents junction remodeling and epithelial dynamics. Developmental Cell.
Cell Press. https://doi.org/10.1016/j.devcel.2018.09.014
chicago: Nunes Pinheiro, Diana C, and Yohanns Bellaïche. “Mechanical Force-Driven
Adherents Junction Remodeling and Epithelial Dynamics.” Developmental Cell.
Cell Press, 2018. https://doi.org/10.1016/j.devcel.2018.09.014.
ieee: D. C. Nunes Pinheiro and Y. Bellaïche, “Mechanical force-driven adherents
junction remodeling and epithelial dynamics,” Developmental Cell, vol.
47, no. 1. Cell Press, pp. 3–19, 2018.
ista: Nunes Pinheiro DC, Bellaïche Y. 2018. Mechanical force-driven adherents junction
remodeling and epithelial dynamics. Developmental Cell. 47(1), 3–19.
mla: Nunes Pinheiro, Diana C., and Yohanns Bellaïche. “Mechanical Force-Driven Adherents
Junction Remodeling and Epithelial Dynamics.” Developmental Cell, vol.
47, no. 1, Cell Press, 2018, pp. 3–19, doi:10.1016/j.devcel.2018.09.014.
short: D.C. Nunes Pinheiro, Y. Bellaïche, Developmental Cell 47 (2018) 3–19.
date_created: 2018-12-11T11:44:23Z
date_published: 2018-10-08T00:00:00Z
date_updated: 2023-09-13T08:54:38Z
day: '08'
department:
- _id: CaHe
doi: 10.1016/j.devcel.2018.09.014
external_id:
isi:
- '000446579900002'
intvolume: ' 47'
isi: 1
issue: '1'
language:
- iso: eng
main_file_link:
- url: https://doi.org/10.1016/j.devcel.2018.09.014
month: '10'
oa_version: Published Version
page: 3 - 19
publication: Developmental Cell
publication_status: published
publisher: Cell Press
publist_id: '8000'
quality_controlled: '1'
scopus_import: '1'
status: public
title: Mechanical force-driven adherents junction remodeling and epithelial dynamics
type: journal_article
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
volume: 47
year: '2018'
...
---
_id: '276'
abstract:
- lang: eng
text: Directed migration of cells relies on their ability to sense directional guidance
cues and to interact with pericellular structures in order to transduce contractile
cytoskeletal- into mechanical forces. These biomechanical processes depend highly
on microenvironmental factors such as exposure to 2D surfaces or 3D matrices.
In vivo, the majority of cells are exposed to 3D environments. Data on 3D cell
migration are mostly derived from intravital microscopy or collagen-based in vitro
assays. Both approaches offer only limited controlla-bility of experimental conditions.
Here, we developed an automated microfluidic system that allows positioning of
cells in 3D microenvironments containing highly controlled diffusion-based chemokine
gradients. Tracking migration in such gradients was feasible in real time at the
single cell level. Moreover, the setup allowed on-chip immunocytochemistry and
thus linking of functional with phenotypical properties in individual cells. Spatially
defined retrieval of cells from the device allows down-stream off-chip analysis.
Using dendritic cells as a model, our setup specifically allowed us for the first
time to quantitate key migration characteristics of cells exposed to identical
gradients of the chemokine CCL19 yet placed on 2D vs in 3D environments. Migration
properties between 2D and 3D migration were distinct. Morphological features of
cells migrating in an in vitro 3D environment were similar to those of cells migrating
in animal tissues, but different from cells migrating on a surface. Our system
thus offers a highly controllable in vitro-mimic of a 3D environment that cells
traffic in vivo.
acknowledgement: This work was supported by the Swiss National Science Foundation
(MD-PhD fellowships, 323530_164221 to C.F.; and 323630_151483 to A.J.; grant PZ00P3_144863
to M.R, grant 31003A_156431 to T.S.; PZ00P3_148000 to C.T.B.; PZ00P3_154733 to M.M.),
a Novartis “FreeNovation” grant to M.M. and T.S. and an EMBO long-term fellowship
(ALTF 1396-2014) co-funded by the European Commission (LTFCOFUND2013, GA-2013-609409)
to J.R.. M.R. was supported by the Gebert Rüf Foundation (GRS 058/14). The funders
had no role in study design, data collection and analysis, decision to publish,
or preparation of the manuscript.
article_number: e0198330
article_processing_charge: No
article_type: original
author:
- first_name: Corina
full_name: Frick, Corina
last_name: Frick
- first_name: Philip
full_name: Dettinger, Philip
last_name: Dettinger
- first_name: Jörg
full_name: Renkawitz, Jörg
id: 3F0587C8-F248-11E8-B48F-1D18A9856A87
last_name: Renkawitz
orcid: 0000-0003-2856-3369
- first_name: Annaïse
full_name: Jauch, Annaïse
last_name: Jauch
- first_name: Christoph
full_name: Berger, Christoph
last_name: Berger
- first_name: Mike
full_name: Recher, Mike
last_name: Recher
- first_name: Timm
full_name: Schroeder, Timm
last_name: Schroeder
- first_name: Matthias
full_name: Mehling, Matthias
last_name: Mehling
citation:
ama: Frick C, Dettinger P, Renkawitz J, et al. Nano-scale microfluidics to study
3D chemotaxis at the single cell level. PLoS One. 2018;13(6). doi:10.1371/journal.pone.0198330
apa: Frick, C., Dettinger, P., Renkawitz, J., Jauch, A., Berger, C., Recher, M.,
… Mehling, M. (2018). Nano-scale microfluidics to study 3D chemotaxis at the single
cell level. PLoS One. Public Library of Science. https://doi.org/10.1371/journal.pone.0198330
chicago: Frick, Corina, Philip Dettinger, Jörg Renkawitz, Annaïse Jauch, Christoph
Berger, Mike Recher, Timm Schroeder, and Matthias Mehling. “Nano-Scale Microfluidics
to Study 3D Chemotaxis at the Single Cell Level.” PLoS One. Public Library
of Science, 2018. https://doi.org/10.1371/journal.pone.0198330.
ieee: C. Frick et al., “Nano-scale microfluidics to study 3D chemotaxis at
the single cell level,” PLoS One, vol. 13, no. 6. Public Library of Science,
2018.
ista: Frick C, Dettinger P, Renkawitz J, Jauch A, Berger C, Recher M, Schroeder
T, Mehling M. 2018. Nano-scale microfluidics to study 3D chemotaxis at the single
cell level. PLoS One. 13(6), e0198330.
mla: Frick, Corina, et al. “Nano-Scale Microfluidics to Study 3D Chemotaxis at the
Single Cell Level.” PLoS One, vol. 13, no. 6, e0198330, Public Library
of Science, 2018, doi:10.1371/journal.pone.0198330.
short: C. Frick, P. Dettinger, J. Renkawitz, A. Jauch, C. Berger, M. Recher, T.
Schroeder, M. Mehling, PLoS One 13 (2018).
date_created: 2018-12-11T11:45:34Z
date_published: 2018-06-07T00:00:00Z
date_updated: 2023-09-13T09:00:15Z
day: '07'
ddc:
- '570'
department:
- _id: MiSi
doi: 10.1371/journal.pone.0198330
external_id:
isi:
- '000434384900031'
file:
- access_level: open_access
checksum: 95fc5dc3938b3ad3b7697d10c83cc143
content_type: application/pdf
creator: dernst
date_created: 2018-12-17T14:10:32Z
date_updated: 2020-07-14T12:45:45Z
file_id: '5709'
file_name: 2018_Plos_Frick.pdf
file_size: 7682167
relation: main_file
file_date_updated: 2020-07-14T12:45:45Z
has_accepted_license: '1'
intvolume: ' 13'
isi: 1
issue: '6'
language:
- iso: eng
month: '06'
oa: 1
oa_version: Published Version
publication: PLoS One
publication_status: published
publisher: Public Library of Science
publist_id: '7626'
quality_controlled: '1'
scopus_import: '1'
status: public
title: Nano-scale microfluidics to study 3D chemotaxis at the single cell level
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: journal_article
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
volume: 13
year: '2018'
...
---
_id: '283'
abstract:
- lang: eng
text: Light represents the principal signal driving circadian clock entrainment.
However, how light influences the evolution of the clock remains poorly understood.
The cavefish Phreatichthys andruzzii represents a fascinating model to explore
how evolution under extreme aphotic conditions shapes the circadian clock, since
in this species the clock is unresponsive to light. We have previously demonstrated
that loss-of-function mutations targeting non-visual opsins contribute in part
to this blind clock phenotype. Here, we have compared orthologs of two core clock
genes that play a key role in photic entrainment, cry1a and per2, in both zebrafish
and P. andruzzii. We encountered aberrantly spliced variants for the P. andruzzii
per2 transcript. The most abundant transcript encodes a truncated protein lacking
the C-terminal Cry binding domain and incorporating an intronic, transposon-derived
coding sequence. We demonstrate that the transposon insertion leads to a predominantly
cytoplasmic localization of the cavefish Per2 protein in contrast to the zebrafish
ortholog which is distributed in both the nucleus and cytoplasm. Thus, it seems
that during evolution in complete darkness, the photic entrainment pathway of
the circadian clock has been subject to mutation at multiple levels, extending
from opsin photoreceptors to nuclear effectors.
article_number: '8754'
article_processing_charge: No
author:
- first_name: Rosa Maria
full_name: Ceinos, Rosa Maria
last_name: Ceinos
- first_name: Elena
full_name: Frigato, Elena
last_name: Frigato
- first_name: Cristina
full_name: Pagano, Cristina
last_name: Pagano
- first_name: Nadine
full_name: Frohlich, Nadine
last_name: Frohlich
- first_name: Pietro
full_name: Negrini, Pietro
last_name: Negrini
- first_name: Nicola
full_name: Cavallari, Nicola
id: 457160E6-F248-11E8-B48F-1D18A9856A87
last_name: Cavallari
- first_name: Daniela
full_name: Vallone, Daniela
last_name: Vallone
- first_name: Silvia
full_name: Fuselli, Silvia
last_name: Fuselli
- first_name: Cristiano
full_name: Bertolucci, Cristiano
last_name: Bertolucci
- first_name: Nicholas S
full_name: Foulkes, Nicholas S
last_name: Foulkes
citation:
ama: Ceinos RM, Frigato E, Pagano C, et al. Mutations in blind cavefish target the
light regulated circadian clock gene period 2. Scientific Reports. 2018;8(1).
doi:10.1038/s41598-018-27080-2
apa: Ceinos, R. M., Frigato, E., Pagano, C., Frohlich, N., Negrini, P., Cavallari,
N., … Foulkes, N. S. (2018). Mutations in blind cavefish target the light regulated
circadian clock gene period 2. Scientific Reports. Nature Publishing Group.
https://doi.org/10.1038/s41598-018-27080-2
chicago: Ceinos, Rosa Maria, Elena Frigato, Cristina Pagano, Nadine Frohlich, Pietro
Negrini, Nicola Cavallari, Daniela Vallone, Silvia Fuselli, Cristiano Bertolucci,
and Nicholas S Foulkes. “Mutations in Blind Cavefish Target the Light Regulated
Circadian Clock Gene Period 2.” Scientific Reports. Nature Publishing Group,
2018. https://doi.org/10.1038/s41598-018-27080-2.
ieee: R. M. Ceinos et al., “Mutations in blind cavefish target the light
regulated circadian clock gene period 2,” Scientific Reports, vol. 8, no.
1. Nature Publishing Group, 2018.
ista: Ceinos RM, Frigato E, Pagano C, Frohlich N, Negrini P, Cavallari N, Vallone
D, Fuselli S, Bertolucci C, Foulkes NS. 2018. Mutations in blind cavefish target
the light regulated circadian clock gene period 2. Scientific Reports. 8(1), 8754.
mla: Ceinos, Rosa Maria, et al. “Mutations in Blind Cavefish Target the Light Regulated
Circadian Clock Gene Period 2.” Scientific Reports, vol. 8, no. 1, 8754,
Nature Publishing Group, 2018, doi:10.1038/s41598-018-27080-2.
short: R.M. Ceinos, E. Frigato, C. Pagano, N. Frohlich, P. Negrini, N. Cavallari,
D. Vallone, S. Fuselli, C. Bertolucci, N.S. Foulkes, Scientific Reports 8 (2018).
date_created: 2018-12-11T11:45:36Z
date_published: 2018-06-08T00:00:00Z
date_updated: 2023-09-13T08:59:27Z
day: '08'
ddc:
- '570'
department:
- _id: EvBe
doi: 10.1038/s41598-018-27080-2
external_id:
isi:
- '000434640800008'
file:
- access_level: open_access
checksum: 9c3942d772f84f3df032ffde0ed9a8ea
content_type: application/pdf
creator: dernst
date_created: 2018-12-17T13:04:46Z
date_updated: 2020-07-14T12:45:49Z
file_id: '5707'
file_name: 2018_ScientificReports_Ceinos.pdf
file_size: 1855324
relation: main_file
file_date_updated: 2020-07-14T12:45:49Z
has_accepted_license: '1'
intvolume: ' 8'
isi: 1
issue: '1'
language:
- iso: eng
month: '06'
oa: 1
oa_version: Published Version
publication: Scientific Reports
publication_status: published
publisher: Nature Publishing Group
publist_id: '7616'
quality_controlled: '1'
scopus_import: '1'
status: public
title: Mutations in blind cavefish target the light regulated circadian clock gene
period 2
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: journal_article
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
volume: 8
year: '2018'
...
---
_id: '81'
abstract:
- lang: eng
text: We solve the offline monitoring problem for timed propositional temporal logic
(TPTL), interpreted over dense-time Boolean signals. The variant of TPTL we consider
extends linear temporal logic (LTL) with clock variables and reset quantifiers,
providing a mechanism to specify real-time constraints. We first describe a general
monitoring algorithm based on an exhaustive computation of the set of satisfying
clock assignments as a finite union of zones. We then propose a specialized monitoring
algorithm for the one-variable case using a partition of the time domain based
on the notion of region equivalence, whose complexity is linear in the length
of the signal, thereby generalizing a known result regarding the monitoring of
metric temporal logic (MTL). The region and zone representations of time constraints
are known from timed automata verification and can also be used in the discrete-time
case. Our prototype implementation appears to outperform previous discrete-time
implementations of TPTL monitoring,
alternative_title:
- LNCS
article_processing_charge: No
author:
- first_name: Adrian
full_name: Elgyütt, Adrian
id: 4A2E9DBA-F248-11E8-B48F-1D18A9856A87
last_name: Elgyütt
- first_name: Thomas
full_name: Ferrere, Thomas
id: 40960E6E-F248-11E8-B48F-1D18A9856A87
last_name: Ferrere
orcid: 0000-0001-5199-3143
- first_name: Thomas A
full_name: Henzinger, Thomas A
id: 40876CD8-F248-11E8-B48F-1D18A9856A87
last_name: Henzinger
orcid: 0000−0002−2985−7724
citation:
ama: 'Elgyütt A, Ferrere T, Henzinger TA. Monitoring temporal logic with clock variables.
In: Vol 11022. Springer; 2018:53-70. doi:10.1007/978-3-030-00151-3_4'
apa: 'Elgyütt, A., Ferrere, T., & Henzinger, T. A. (2018). Monitoring temporal
logic with clock variables (Vol. 11022, pp. 53–70). Presented at the FORMATS:
Formal Modeling and Analysis of Timed Systems, Beijing, China: Springer. https://doi.org/10.1007/978-3-030-00151-3_4'
chicago: Elgyütt, Adrian, Thomas Ferrere, and Thomas A Henzinger. “Monitoring Temporal
Logic with Clock Variables,” 11022:53–70. Springer, 2018. https://doi.org/10.1007/978-3-030-00151-3_4.
ieee: 'A. Elgyütt, T. Ferrere, and T. A. Henzinger, “Monitoring temporal logic with
clock variables,” presented at the FORMATS: Formal Modeling and Analysis of Timed
Systems, Beijing, China, 2018, vol. 11022, pp. 53–70.'
ista: 'Elgyütt A, Ferrere T, Henzinger TA. 2018. Monitoring temporal logic with
clock variables. FORMATS: Formal Modeling and Analysis of Timed Systems, LNCS,
vol. 11022, 53–70.'
mla: Elgyütt, Adrian, et al. Monitoring Temporal Logic with Clock Variables.
Vol. 11022, Springer, 2018, pp. 53–70, doi:10.1007/978-3-030-00151-3_4.
short: A. Elgyütt, T. Ferrere, T.A. Henzinger, in:, Springer, 2018, pp. 53–70.
conference:
end_date: 2018-09-06
location: Beijing, China
name: 'FORMATS: Formal Modeling and Analysis of Timed Systems'
start_date: 2018-09-04
date_created: 2018-12-11T11:44:31Z
date_published: 2018-08-26T00:00:00Z
date_updated: 2023-09-13T08:58:34Z
day: '26'
ddc:
- '000'
department:
- _id: ToHe
doi: 10.1007/978-3-030-00151-3_4
external_id:
isi:
- '000884993200004'
file:
- access_level: open_access
checksum: e5d81c9b50a6bd9d8a2c16953aad7e23
content_type: application/pdf
creator: dernst
date_created: 2020-10-09T06:24:21Z
date_updated: 2020-10-09T06:24:21Z
file_id: '8638'
file_name: 2018_LNCS_Elgyuett.pdf
file_size: 537219
relation: main_file
success: 1
file_date_updated: 2020-10-09T06:24:21Z
has_accepted_license: '1'
intvolume: ' 11022'
isi: 1
language:
- iso: eng
month: '08'
oa: 1
oa_version: Submitted Version
page: 53 - 70
project:
- _id: 25F5A88A-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: S11402-N23
name: Moderne Concurrency Paradigms
- _id: 25F42A32-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: Z211
name: The Wittgenstein Prize
publication_status: published
publisher: Springer
publist_id: '7973'
quality_controlled: '1'
scopus_import: '1'
status: public
title: Monitoring temporal logic with clock variables
type: conference
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
volume: 11022
year: '2018'
...
---
_id: '76'
abstract:
- lang: eng
text: 'Consider a fully-connected synchronous distributed system consisting of n
nodes, where up to f nodes may be faulty and every node starts in an arbitrary
initial state. In the synchronous C-counting problem, all nodes need to eventually
agree on a counter that is increased by one modulo C in each round for given C>1.
In the self-stabilising firing squad problem, the task is to eventually guarantee
that all non-faulty nodes have simultaneous responses to external inputs: if a
subset of the correct nodes receive an external “go” signal as input, then all
correct nodes should agree on a round (in the not-too-distant future) in which
to jointly output a “fire” signal. Moreover, no node should generate a “fire”
signal without some correct node having previously received a “go” signal as input.
We present a framework reducing both tasks to binary consensus at very small cost.
For example, we obtain a deterministic algorithm for self-stabilising Byzantine
firing squads with optimal resilience f<n/3, asymptotically optimal stabilisation
and response time O(f), and message size O(log f). As our framework does not restrict
the type of consensus routines used, we also obtain efficient randomised solutions.'
article_processing_charge: Yes (via OA deal)
author:
- first_name: Christoph
full_name: Lenzen, Christoph
last_name: Lenzen
- first_name: Joel
full_name: Rybicki, Joel
id: 334EFD2E-F248-11E8-B48F-1D18A9856A87
last_name: Rybicki
orcid: 0000-0002-6432-6646
citation:
ama: Lenzen C, Rybicki J. Near-optimal self-stabilising counting and firing squads.
Distributed Computing. 2018. doi:10.1007/s00446-018-0342-6
apa: Lenzen, C., & Rybicki, J. (2018). Near-optimal self-stabilising counting
and firing squads. Distributed Computing. Springer. https://doi.org/10.1007/s00446-018-0342-6
chicago: Lenzen, Christoph, and Joel Rybicki. “Near-Optimal Self-Stabilising Counting
and Firing Squads.” Distributed Computing. Springer, 2018. https://doi.org/10.1007/s00446-018-0342-6.
ieee: C. Lenzen and J. Rybicki, “Near-optimal self-stabilising counting and firing
squads,” Distributed Computing. Springer, 2018.
ista: Lenzen C, Rybicki J. 2018. Near-optimal self-stabilising counting and firing
squads. Distributed Computing.
mla: Lenzen, Christoph, and Joel Rybicki. “Near-Optimal Self-Stabilising Counting
and Firing Squads.” Distributed Computing, Springer, 2018, doi:10.1007/s00446-018-0342-6.
short: C. Lenzen, J. Rybicki, Distributed Computing (2018).
date_created: 2018-12-11T11:44:30Z
date_published: 2018-09-12T00:00:00Z
date_updated: 2023-09-13T09:01:06Z
day: '12'
ddc:
- '000'
department:
- _id: DaAl
doi: 10.1007/s00446-018-0342-6
external_id:
isi:
- '000475627800005'
file:
- access_level: open_access
checksum: 872db70bba9b401500abe3c6ae2f1a61
content_type: application/pdf
creator: dernst
date_created: 2018-12-17T14:21:22Z
date_updated: 2020-07-14T12:48:01Z
file_id: '5711'
file_name: 2018_DistributedComputing_Lenzen.pdf
file_size: 799337
relation: main_file
file_date_updated: 2020-07-14T12:48:01Z
has_accepted_license: '1'
isi: 1
language:
- iso: eng
month: '09'
oa: 1
oa_version: Published Version
project:
- _id: B67AFEDC-15C9-11EA-A837-991A96BB2854
name: IST Austria Open Access Fund
publication: Distributed Computing
publication_status: published
publisher: Springer
publist_id: '7978'
quality_controlled: '1'
scopus_import: '1'
status: public
title: Near-optimal self-stabilising counting and firing squads
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: journal_article
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
year: '2018'
...
---
_id: '530'
abstract:
- lang: eng
text: Inclusion–exclusion is an effective method for computing the volume of a union
of measurable sets. We extend it to multiple coverings, proving short inclusion–exclusion
formulas for the subset of Rn covered by at least k balls in a finite set. We
implement two of the formulas in dimension n=3 and report on results obtained
with our software.
article_processing_charge: No
author:
- first_name: Herbert
full_name: Edelsbrunner, Herbert
id: 3FB178DA-F248-11E8-B48F-1D18A9856A87
last_name: Edelsbrunner
orcid: 0000-0002-9823-6833
- first_name: Mabel
full_name: Iglesias Ham, Mabel
id: 41B58C0C-F248-11E8-B48F-1D18A9856A87
last_name: Iglesias Ham
citation:
ama: 'Edelsbrunner H, Iglesias Ham M. Multiple covers with balls I: Inclusion–exclusion.
Computational Geometry: Theory and Applications. 2018;68:119-133. doi:10.1016/j.comgeo.2017.06.014'
apa: 'Edelsbrunner, H., & Iglesias Ham, M. (2018). Multiple covers with balls
I: Inclusion–exclusion. Computational Geometry: Theory and Applications.
Elsevier. https://doi.org/10.1016/j.comgeo.2017.06.014'
chicago: 'Edelsbrunner, Herbert, and Mabel Iglesias Ham. “Multiple Covers with Balls
I: Inclusion–Exclusion.” Computational Geometry: Theory and Applications.
Elsevier, 2018. https://doi.org/10.1016/j.comgeo.2017.06.014.'
ieee: 'H. Edelsbrunner and M. Iglesias Ham, “Multiple covers with balls I: Inclusion–exclusion,”
Computational Geometry: Theory and Applications, vol. 68. Elsevier, pp.
119–133, 2018.'
ista: 'Edelsbrunner H, Iglesias Ham M. 2018. Multiple covers with balls I: Inclusion–exclusion.
Computational Geometry: Theory and Applications. 68, 119–133.'
mla: 'Edelsbrunner, Herbert, and Mabel Iglesias Ham. “Multiple Covers with Balls
I: Inclusion–Exclusion.” Computational Geometry: Theory and Applications,
vol. 68, Elsevier, 2018, pp. 119–33, doi:10.1016/j.comgeo.2017.06.014.'
short: 'H. Edelsbrunner, M. Iglesias Ham, Computational Geometry: Theory and Applications
68 (2018) 119–133.'
date_created: 2018-12-11T11:46:59Z
date_published: 2018-03-01T00:00:00Z
date_updated: 2023-09-13T08:59:00Z
day: '01'
ddc:
- '000'
department:
- _id: HeEd
doi: 10.1016/j.comgeo.2017.06.014
ec_funded: 1
external_id:
isi:
- '000415778300010'
file:
- access_level: open_access
checksum: 1c8d58cd489a66cd3e2064c1141c8c5e
content_type: application/pdf
creator: dernst
date_created: 2019-02-12T06:47:52Z
date_updated: 2020-07-14T12:46:38Z
file_id: '5953'
file_name: 2018_Edelsbrunner.pdf
file_size: 708357
relation: main_file
file_date_updated: 2020-07-14T12:46:38Z
has_accepted_license: '1'
intvolume: ' 68'
isi: 1
language:
- iso: eng
month: '03'
oa: 1
oa_version: Preprint
page: 119 - 133
project:
- _id: 255D761E-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '318493'
name: Topological Complex Systems
publication: 'Computational Geometry: Theory and Applications'
publication_status: published
publisher: Elsevier
publist_id: '7289'
quality_controlled: '1'
scopus_import: '1'
status: public
title: 'Multiple covers with balls I: Inclusion–exclusion'
type: journal_article
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
volume: 68
year: '2018'
...
---
_id: '307'
abstract:
- lang: eng
text: 'Spontaneous emission spectra of two initially excited closely spaced identical
atoms are very sensitive to the strength and the direction of the applied magnetic
field. We consider the relevant schemes that ensure the determination of the mutual
spatial orientation of the atoms and the distance between them by entirely optical
means. A corresponding theoretical description is given accounting for the dipole-dipole
interaction between the two atoms in the presence of a magnetic field and for
polarizations of the quantum field interacting with magnetic sublevels of the
two-atom system. '
acknowledgement: The work was partially supported by Russian Foundation for Basic
Research (Grant No. 15-02-05657a) and by the Basic research program of Higher School
of Economics (HSE).
article_number: ' 043812 '
article_processing_charge: No
article_type: original
author:
- first_name: Elena
full_name: Redchenko, Elena
id: 2C21D6E8-F248-11E8-B48F-1D18A9856A87
last_name: Redchenko
- first_name: Alexander
full_name: Makarov, Alexander
last_name: Makarov
- first_name: Vladimir
full_name: Yudson, Vladimir
last_name: Yudson
citation:
ama: Redchenko E, Makarov A, Yudson V. Nanoscopy of pairs of atoms by fluorescence
in a magnetic field. Physical Review A - Atomic, Molecular, and Optical Physics.
2018;97(4). doi:10.1103/PhysRevA.97.043812
apa: Redchenko, E., Makarov, A., & Yudson, V. (2018). Nanoscopy of pairs of
atoms by fluorescence in a magnetic field. Physical Review A - Atomic, Molecular,
and Optical Physics. American Physical Society. https://doi.org/10.1103/PhysRevA.97.043812
chicago: Redchenko, Elena, Alexander Makarov, and Vladimir Yudson. “Nanoscopy of
Pairs of Atoms by Fluorescence in a Magnetic Field.” Physical Review A - Atomic,
Molecular, and Optical Physics. American Physical Society, 2018. https://doi.org/10.1103/PhysRevA.97.043812.
ieee: E. Redchenko, A. Makarov, and V. Yudson, “Nanoscopy of pairs of atoms by fluorescence
in a magnetic field,” Physical Review A - Atomic, Molecular, and Optical Physics,
vol. 97, no. 4. American Physical Society, 2018.
ista: Redchenko E, Makarov A, Yudson V. 2018. Nanoscopy of pairs of atoms by fluorescence
in a magnetic field. Physical Review A - Atomic, Molecular, and Optical Physics.
97(4), 043812.
mla: Redchenko, Elena, et al. “Nanoscopy of Pairs of Atoms by Fluorescence in a
Magnetic Field.” Physical Review A - Atomic, Molecular, and Optical Physics,
vol. 97, no. 4, 043812, American Physical Society, 2018, doi:10.1103/PhysRevA.97.043812.
short: E. Redchenko, A. Makarov, V. Yudson, Physical Review A - Atomic, Molecular,
and Optical Physics 97 (2018).
date_created: 2018-12-11T11:45:44Z
date_published: 2018-04-09T00:00:00Z
date_updated: 2023-09-13T09:00:41Z
day: '09'
department:
- _id: JoFi
doi: 10.1103/PhysRevA.97.043812
external_id:
arxiv:
- '1712.10127'
isi:
- '000429454000015'
intvolume: ' 97'
isi: 1
issue: '4'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/1712.10127
month: '04'
oa: 1
oa_version: Submitted Version
publication: ' Physical Review A - Atomic, Molecular, and Optical Physics'
publication_status: published
publisher: American Physical Society
publist_id: '7572'
quality_controlled: '1'
scopus_import: '1'
status: public
title: Nanoscopy of pairs of atoms by fluorescence in a magnetic field
type: journal_article
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
volume: 97
year: '2018'
...
---
_id: '279'
abstract:
- lang: eng
text: 'Background: Natural selection shapes cancer genomes. Previous studies used
signatures of positive selection to identify genes driving malignant transformation.
However, the contribution of negative selection against somatic mutations that
affect essential tumor functions or specific domains remains a controversial topic.
Results: Here, we analyze 7546 individual exomes from 26 tumor types from TCGA
data to explore the portion of the cancer exome under negative selection. Although
we find most of the genes neutrally evolving in a pan-cancer framework, we identify
essential cancer genes and immune-exposed protein regions under significant negative
selection. Moreover, our simulations suggest that the amount of negative selection
is underestimated. We therefore choose an empirical approach to identify genes,
functions, and protein regions under negative selection. We find that expression
and mutation status of negatively selected genes is indicative of patient survival.
Processes that are most strongly conserved are those that play fundamental cellular
roles such as protein synthesis, glucose metabolism, and molecular transport.
Intriguingly, we observe strong signals of selection in the immunopeptidome and
proteins controlling peptide exposition, highlighting the importance of immune
surveillance evasion. Additionally, tumor type-specific immune activity correlates
with the strength of negative selection on human epitopes. Conclusions: In summary,
our results show that negative selection is a hallmark of cell essentiality and
immune response in cancer. The functional domains identified could be exploited
therapeutically, ultimately allowing for the development of novel cancer treatments.'
article_number: '67'
article_processing_charge: No
author:
- first_name: Luis
full_name: Zapata, Luis
last_name: Zapata
- first_name: Oriol
full_name: Pich, Oriol
last_name: Pich
- first_name: Luis
full_name: Serrano, Luis
last_name: Serrano
- first_name: Fyodor
full_name: Kondrashov, Fyodor
id: 44FDEF62-F248-11E8-B48F-1D18A9856A87
last_name: Kondrashov
orcid: 0000-0001-8243-4694
- first_name: Stephan
full_name: Ossowski, Stephan
last_name: Ossowski
- first_name: Martin
full_name: Schaefer, Martin
last_name: Schaefer
citation:
ama: Zapata L, Pich O, Serrano L, Kondrashov F, Ossowski S, Schaefer M. Negative
selection in tumor genome evolution acts on essential cellular functions and the
immunopeptidome. Genome Biology. 2018;19. doi:10.1186/s13059-018-1434-0
apa: Zapata, L., Pich, O., Serrano, L., Kondrashov, F., Ossowski, S., & Schaefer,
M. (2018). Negative selection in tumor genome evolution acts on essential cellular
functions and the immunopeptidome. Genome Biology. BioMed Central. https://doi.org/10.1186/s13059-018-1434-0
chicago: Zapata, Luis, Oriol Pich, Luis Serrano, Fyodor Kondrashov, Stephan Ossowski,
and Martin Schaefer. “Negative Selection in Tumor Genome Evolution Acts on Essential
Cellular Functions and the Immunopeptidome.” Genome Biology. BioMed Central,
2018. https://doi.org/10.1186/s13059-018-1434-0.
ieee: L. Zapata, O. Pich, L. Serrano, F. Kondrashov, S. Ossowski, and M. Schaefer,
“Negative selection in tumor genome evolution acts on essential cellular functions
and the immunopeptidome,” Genome Biology, vol. 19. BioMed Central, 2018.
ista: Zapata L, Pich O, Serrano L, Kondrashov F, Ossowski S, Schaefer M. 2018. Negative
selection in tumor genome evolution acts on essential cellular functions and the
immunopeptidome. Genome Biology. 19, 67.
mla: Zapata, Luis, et al. “Negative Selection in Tumor Genome Evolution Acts on
Essential Cellular Functions and the Immunopeptidome.” Genome Biology,
vol. 19, 67, BioMed Central, 2018, doi:10.1186/s13059-018-1434-0.
short: L. Zapata, O. Pich, L. Serrano, F. Kondrashov, S. Ossowski, M. Schaefer,
Genome Biology 19 (2018).
date_created: 2018-12-11T11:45:35Z
date_published: 2018-05-31T00:00:00Z
date_updated: 2023-09-13T09:01:32Z
day: '31'
ddc:
- '570'
department:
- _id: FyKo
doi: 10.1186/s13059-018-1434-0
ec_funded: 1
external_id:
isi:
- '000433986200001'
file:
- access_level: open_access
checksum: f3e4922486bd9bf1483271bdbed394a7
content_type: application/pdf
creator: dernst
date_created: 2018-12-17T14:05:01Z
date_updated: 2020-07-14T12:45:47Z
file_id: '5708'
file_name: 2018_GenomeBiology_Zapata.pdf
file_size: 1414722
relation: main_file
file_date_updated: 2020-07-14T12:45:47Z
has_accepted_license: '1'
intvolume: ' 19'
isi: 1
language:
- iso: eng
month: '05'
oa: 1
oa_version: Published Version
project:
- _id: 26120F5C-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '335980'
name: Systematic investigation of epistasis in molecular evolution
publication: Genome Biology
publication_status: published
publisher: BioMed Central
publist_id: '7620'
quality_controlled: '1'
related_material:
record:
- id: '9811'
relation: research_data
status: public
- id: '9812'
relation: research_data
status: public
scopus_import: '1'
status: public
title: Negative selection in tumor genome evolution acts on essential cellular functions
and the immunopeptidome
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: journal_article
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
volume: 19
year: '2018'
...
---
_id: '145'
abstract:
- lang: eng
text: Aged proteins can become hazardous to cellular function, by accumulating molecular
damage. This implies that cells should preferentially rely on newly produced ones.
We tested this hypothesis in cultured hippocampal neurons, focusing on synaptic
transmission. We found that newly synthesized vesicle proteins were incorporated
in the actively recycling pool of vesicles responsible for all neurotransmitter
release during physiological activity. We observed this for the calcium sensor
Synaptotagmin 1, for the neurotransmitter transporter VGAT, and for the fusion
protein VAMP2 (Synaptobrevin 2). Metabolic labeling of proteins and visualization
by secondary ion mass spectrometry enabled us to query the entire protein makeup
of the actively recycling vesicles, which we found to be younger than that of
non-recycling vesicles. The young vesicle proteins remained in use for up to ~
24 h, during which they participated in recycling a few hundred times. They were
afterward reluctant to release and were degraded after an additional ~ 24–48 h.
We suggest that the recycling pool of synaptic vesicles relies on newly synthesized
proteins, while the inactive reserve pool contains older proteins.
acknowledgement: We thank Reinhard Jahn for providing a plasmid for YFP-SNAP25. We
thank Erwin Neher for help with the development of the mathematical model of the
synaptic vesicle life cycle. We thank Martin Meschkat, Andreas Höbartner, Annedore
Punge, and Peer Hoopmann for help with the experiments. We thank Burkhard Rammner
for providing the illustrations of synaptic vesicle and protein dynamics. We thank
Manuel Maidorn, Martin Helm, and Katharina N. Richter for critically reading the
manuscript. S.T. was supported by an Excellence Stipend of the Göttingen Graduate
School for Neurosciences, Biophysics, and Molecular Biosciences (GGNB). E.F.F. is
a recipient of long-term fellowships from the European Molecular Biology Organization
(ALTF_797-2012) and from the Human Frontier Science Program (HFSP_LT000830/2013).
The work was supported by grants to S.O.R. from the European Research Council (ERC-2013-CoG
NeuroMolAnatomy) and from the Deutsche Forschungsgemeinschaft (Cluster of Excellence
Nanoscale Microscopy and Molecular Physiology of the Brain, SFB1190/P09, SFB889/A05,
and SFB1286/A03, and DFG RI 1967 7/1). The nanoSIMS instrument was funded by the
German Federal Ministry of Education and Research (03F0626A).
article_number: e98044
article_processing_charge: No
article_type: original
author:
- first_name: Sven M
full_name: Truckenbrodt, Sven M
id: 45812BD4-F248-11E8-B48F-1D18A9856A87
last_name: Truckenbrodt
- first_name: Abhiyan
full_name: Viplav, Abhiyan
last_name: Viplav
- first_name: Sebsatian
full_name: Jähne, Sebsatian
last_name: Jähne
- first_name: Angela
full_name: Vogts, Angela
last_name: Vogts
- first_name: Annette
full_name: Denker, Annette
last_name: Denker
- first_name: Hanna
full_name: Wildhagen, Hanna
last_name: Wildhagen
- first_name: Eugenio
full_name: Fornasiero, Eugenio
last_name: Fornasiero
- first_name: Silvio
full_name: Rizzoli, Silvio
last_name: Rizzoli
citation:
ama: Truckenbrodt SM, Viplav A, Jähne S, et al. Newly produced synaptic vesicle
proteins are preferentially used in synaptic transmission. The EMBO Journal.
2018;37(15). doi:10.15252/embj.201798044
apa: Truckenbrodt, S. M., Viplav, A., Jähne, S., Vogts, A., Denker, A., Wildhagen,
H., … Rizzoli, S. (2018). Newly produced synaptic vesicle proteins are preferentially
used in synaptic transmission. The EMBO Journal. Wiley. https://doi.org/10.15252/embj.201798044
chicago: Truckenbrodt, Sven M, Abhiyan Viplav, Sebsatian Jähne, Angela Vogts, Annette
Denker, Hanna Wildhagen, Eugenio Fornasiero, and Silvio Rizzoli. “Newly Produced
Synaptic Vesicle Proteins Are Preferentially Used in Synaptic Transmission.” The
EMBO Journal. Wiley, 2018. https://doi.org/10.15252/embj.201798044.
ieee: S. M. Truckenbrodt et al., “Newly produced synaptic vesicle proteins
are preferentially used in synaptic transmission,” The EMBO Journal, vol.
37, no. 15. Wiley, 2018.
ista: Truckenbrodt SM, Viplav A, Jähne S, Vogts A, Denker A, Wildhagen H, Fornasiero
E, Rizzoli S. 2018. Newly produced synaptic vesicle proteins are preferentially
used in synaptic transmission. The EMBO Journal. 37(15), e98044.
mla: Truckenbrodt, Sven M., et al. “Newly Produced Synaptic Vesicle Proteins Are
Preferentially Used in Synaptic Transmission.” The EMBO Journal, vol. 37,
no. 15, e98044, Wiley, 2018, doi:10.15252/embj.201798044.
short: S.M. Truckenbrodt, A. Viplav, S. Jähne, A. Vogts, A. Denker, H. Wildhagen,
E. Fornasiero, S. Rizzoli, The EMBO Journal 37 (2018).
date_created: 2018-12-11T11:44:52Z
date_published: 2018-08-01T00:00:00Z
date_updated: 2023-09-13T09:02:48Z
day: '01'
ddc:
- '570'
department:
- _id: JoDa
doi: 10.15252/embj.201798044
external_id:
isi:
- '000440416900005'
pmid:
- '29950309'
file:
- access_level: open_access
checksum: a540feb6c9af6aefc78de531461a8835
content_type: application/pdf
creator: dernst
date_created: 2018-12-17T14:17:29Z
date_updated: 2020-07-14T12:44:56Z
file_id: '5710'
file_name: 2018_EMBO_Truckenbrodt.pdf
file_size: 2846470
relation: main_file
file_date_updated: 2020-07-14T12:44:56Z
has_accepted_license: '1'
intvolume: ' 37'
isi: 1
issue: '15'
language:
- iso: eng
month: '08'
oa: 1
oa_version: Published Version
pmid: 1
publication: The EMBO Journal
publication_identifier:
issn:
- 0261-4189
publication_status: published
publisher: Wiley
publist_id: '7778'
quality_controlled: '1'
scopus_import: '1'
status: public
title: Newly produced synaptic vesicle proteins are preferentially used in synaptic
transmission
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: journal_article
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
volume: 37
year: '2018'
...
---
_id: '462'
abstract:
- lang: eng
text: 'AtNHX5 and AtNHX6 are endosomal Na+,K+/H+ antiporters that are critical for
growth and development in Arabidopsis, but the mechanism behind their action remains
unknown. Here, we report that AtNHX5 and AtNHX6, functioning as H+ leak, control
auxin homeostasis and auxin-mediated development. We found that nhx5 nhx6 exhibited
growth variations of auxin-related defects. We further showed that nhx5 nhx6 was
affected in auxin homeostasis. Genetic analysis showed that AtNHX5 and AtNHX6
were required for the function of the ER-localized auxin transporter PIN5. Although
AtNHX5 and AtNHX6 were co-localized with PIN5 at ER, they did not interact directly.
Instead, the conserved acidic residues in AtNHX5 and AtNHX6, which are essential
for exchange activity, were required for PIN5 function. AtNHX5 and AtNHX6 regulated
the pH in ER. Overall, AtNHX5 and AtNHX6 may regulate auxin transport across the
ER via the pH gradient created by their transport activity. H+-leak pathway provides
a fine-tuning mechanism that controls cellular auxin fluxes. '
acknowledgement: 'This work was supported by the National Natural Science Foundation
of China (31571464, 31371438 and 31070222 to Q.S.Q.), the National Basic Research
Program of China (973 project, 2013CB429904 to Q.S.Q.), the Research Fund for the
Doctoral Program of Higher Education of China (20130211110001 to Q.S.Q.), the Ministry
of Education, Youth and Sports of the Czech Republic (the National Program for Sustainability
I, LO1204), and The Czech Science Foundation GAČR (GA13–40637S) to JF. We thank
Dr. Tom J. Guilfoyle for DR5::GUS line and Dr. Jia Li for pBIB‐RFP vector and DR5::GFP
line. We thank Liping Guan and Yang Zhao for their help with the confocal microscope
assay. '
article_processing_charge: No
article_type: original
author:
- first_name: Ligang
full_name: Fan, Ligang
last_name: Fan
- first_name: Lei
full_name: Zhao, Lei
last_name: Zhao
- first_name: Wei
full_name: Hu, Wei
last_name: Hu
- first_name: Weina
full_name: Li, Weina
last_name: Li
- first_name: Ondřej
full_name: Novák, Ondřej
last_name: Novák
- first_name: Miroslav
full_name: Strnad, Miroslav
last_name: Strnad
- first_name: Sibu
full_name: Simon, Sibu
id: 4542EF9A-F248-11E8-B48F-1D18A9856A87
last_name: Simon
orcid: 0000-0002-1998-6741
- first_name: Jirí
full_name: Friml, Jirí
id: 4159519E-F248-11E8-B48F-1D18A9856A87
last_name: Friml
orcid: 0000-0002-8302-7596
- first_name: Jinbo
full_name: Shen, Jinbo
last_name: Shen
- first_name: Liwen
full_name: Jiang, Liwen
last_name: Jiang
- first_name: Quan
full_name: Qiu, Quan
last_name: Qiu
citation:
ama: Fan L, Zhao L, Hu W, et al. NHX antiporters regulate the pH of endoplasmic
reticulum and auxin-mediated development. Plant, Cell and Environment.
2018;41:850-864. doi:10.1111/pce.13153
apa: Fan, L., Zhao, L., Hu, W., Li, W., Novák, O., Strnad, M., … Qiu, Q. (2018).
NHX antiporters regulate the pH of endoplasmic reticulum and auxin-mediated development.
Plant, Cell and Environment. Wiley-Blackwell. https://doi.org/10.1111/pce.13153
chicago: Fan, Ligang, Lei Zhao, Wei Hu, Weina Li, Ondřej Novák, Miroslav Strnad,
Sibu Simon, et al. “NHX Antiporters Regulate the PH of Endoplasmic Reticulum and
Auxin-Mediated Development.” Plant, Cell and Environment. Wiley-Blackwell,
2018. https://doi.org/10.1111/pce.13153.
ieee: L. Fan et al., “NHX antiporters regulate the pH of endoplasmic reticulum
and auxin-mediated development,” Plant, Cell and Environment, vol. 41.
Wiley-Blackwell, pp. 850–864, 2018.
ista: Fan L, Zhao L, Hu W, Li W, Novák O, Strnad M, Simon S, Friml J, Shen J, Jiang
L, Qiu Q. 2018. NHX antiporters regulate the pH of endoplasmic reticulum and auxin-mediated
development. Plant, Cell and Environment. 41, 850–864.
mla: Fan, Ligang, et al. “NHX Antiporters Regulate the PH of Endoplasmic Reticulum
and Auxin-Mediated Development.” Plant, Cell and Environment, vol. 41,
Wiley-Blackwell, 2018, pp. 850–64, doi:10.1111/pce.13153.
short: L. Fan, L. Zhao, W. Hu, W. Li, O. Novák, M. Strnad, S. Simon, J. Friml, J.
Shen, L. Jiang, Q. Qiu, Plant, Cell and Environment 41 (2018) 850–864.
date_created: 2018-12-11T11:46:36Z
date_published: 2018-05-01T00:00:00Z
date_updated: 2023-09-13T09:03:18Z
day: '01'
ddc:
- '580'
department:
- _id: JiFr
doi: 10.1111/pce.13153
external_id:
isi:
- '000426870500012'
pmid:
- '29360148'
file:
- access_level: open_access
checksum: 6a20f843565f962cb20281cdf5e40914
content_type: application/pdf
creator: dernst
date_created: 2019-11-18T16:22:22Z
date_updated: 2020-07-14T12:46:32Z
file_id: '7042'
file_name: 2018_PlantCellEnv_Fan.pdf
file_size: 1937976
relation: main_file
file_date_updated: 2020-07-14T12:46:32Z
has_accepted_license: '1'
intvolume: ' 41'
isi: 1
language:
- iso: eng
license: https://creativecommons.org/licenses/by-nc/4.0/
month: '05'
oa: 1
oa_version: Submitted Version
page: 850 - 864
pmid: 1
publication: Plant, Cell and Environment
publication_status: published
publisher: Wiley-Blackwell
publist_id: '7359'
quality_controlled: '1'
scopus_import: '1'
status: public
title: NHX antiporters regulate the pH of endoplasmic reticulum and auxin-mediated
development
tmp:
image: /images/cc_by_nc.png
legal_code_url: https://creativecommons.org/licenses/by-nc/4.0/legalcode
name: Creative Commons Attribution-NonCommercial 4.0 International (CC BY-NC 4.0)
short: CC BY-NC (4.0)
type: journal_article
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
volume: 41
year: '2018'
...
---
_id: '519'
abstract:
- lang: eng
text: 'This study treats with the influence of a symmetry-breaking transversal magnetic
field on the nonlinear dynamics of ferrofluidic Taylor-Couette flow – flow confined
between two concentric independently rotating cylinders. We detected alternating
‘flip’ solutions which are flow states featuring typical characteristics of slow-fast-dynamics
in dynamical systems. The flip corresponds to a temporal change in the axial wavenumber
and we find them to appear either as pure 2-fold axisymmetric (due to the symmetry-breaking
nature of the applied transversal magnetic field) or involving non-axisymmetric,
helical modes in its interim solution. The latter ones show features of typical
ribbon solutions. In any case the flip solutions have a preferential first axial
wavenumber which corresponds to the more stable state (slow dynamics) and second
axial wavenumber, corresponding to the short appearing more unstable state (fast
dynamics). However, in both cases the flip time grows exponential with increasing
the magnetic field strength before the flip solutions, living on 2-tori invariant
manifolds, cease to exist, with lifetime going to infinity. Further we show that
ferrofluidic flow turbulence differ from the classical, ordinary (usually at high
Reynolds number) turbulence. The applied magnetic field hinders the free motion
of ferrofluid partials and therefore smoothen typical turbulent quantities and
features so that speaking of mildly chaotic dynamics seems to be a more appropriate
expression for the observed motion. '
acknowledgement: S.Altmeyer is a Serra Húnter Fellow
article_processing_charge: No
article_type: original
author:
- first_name: Sebastian
full_name: Altmeyer, Sebastian
id: 2EE67FDC-F248-11E8-B48F-1D18A9856A87
last_name: Altmeyer
orcid: 0000-0001-5964-0203
citation:
ama: Altmeyer S. Non-linear dynamics and alternating ‘flip’ solutions in ferrofluidic
Taylor-Couette flow. Journal of Magnetism and Magnetic Materials. 2018;452:427-441.
doi:10.1016/j.jmmm.2017.12.073
apa: Altmeyer, S. (2018). Non-linear dynamics and alternating ‘flip’ solutions in
ferrofluidic Taylor-Couette flow. Journal of Magnetism and Magnetic Materials.
Elsevier. https://doi.org/10.1016/j.jmmm.2017.12.073
chicago: Altmeyer, Sebastian. “Non-Linear Dynamics and Alternating ‘Flip’ Solutions
in Ferrofluidic Taylor-Couette Flow.” Journal of Magnetism and Magnetic Materials.
Elsevier, 2018. https://doi.org/10.1016/j.jmmm.2017.12.073.
ieee: S. Altmeyer, “Non-linear dynamics and alternating ‘flip’ solutions in ferrofluidic
Taylor-Couette flow,” Journal of Magnetism and Magnetic Materials, vol.
452. Elsevier, pp. 427–441, 2018.
ista: Altmeyer S. 2018. Non-linear dynamics and alternating ‘flip’ solutions in
ferrofluidic Taylor-Couette flow. Journal of Magnetism and Magnetic Materials.
452, 427–441.
mla: Altmeyer, Sebastian. “Non-Linear Dynamics and Alternating ‘Flip’ Solutions
in Ferrofluidic Taylor-Couette Flow.” Journal of Magnetism and Magnetic Materials,
vol. 452, Elsevier, 2018, pp. 427–41, doi:10.1016/j.jmmm.2017.12.073.
short: S. Altmeyer, Journal of Magnetism and Magnetic Materials 452 (2018) 427–441.
date_created: 2018-12-11T11:46:56Z
date_published: 2018-04-15T00:00:00Z
date_updated: 2023-09-13T09:03:44Z
day: '15'
ddc:
- '530'
department:
- _id: BjHo
doi: 10.1016/j.jmmm.2017.12.073
external_id:
isi:
- '000425547700061'
file:
- access_level: open_access
checksum: 431f5cd4a628d7ca21161f82b14ccb4f
content_type: application/pdf
creator: dernst
date_created: 2020-05-14T14:41:17Z
date_updated: 2020-07-14T12:46:37Z
file_id: '7838'
file_name: 2018_Magnetism_Altmeyer.pdf
file_size: 17309535
relation: main_file
file_date_updated: 2020-07-14T12:46:37Z
has_accepted_license: '1'
intvolume: ' 452'
isi: 1
language:
- iso: eng
month: '04'
oa: 1
oa_version: Submitted Version
page: 427 - 441
publication: Journal of Magnetism and Magnetic Materials
publication_status: published
publisher: Elsevier
publist_id: '7297'
quality_controlled: '1'
scopus_import: '1'
status: public
title: Non-linear dynamics and alternating ‘flip’ solutions in ferrofluidic Taylor-Couette
flow
type: journal_article
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
volume: 452
year: '2018'
...
---
_id: '5679'
abstract:
- lang: eng
text: We study the almost-sure termination problem for probabilistic programs. First,
we show that supermartingales with lower bounds on conditional absolute difference
provide a sound approach for the almost-sure termination problem. Moreover, using
this approach we can obtain explicit optimal bounds on tail probabilities of non-termination
within a given number of steps. Second, we present a new approach based on Central
Limit Theorem for the almost-sure termination problem, and show that this approach
can establish almost-sure termination of programs which none of the existing approaches
can handle. Finally, we discuss algorithmic approaches for the two above methods
that lead to automated analysis techniques for almost-sure termination of probabilistic
programs.
alternative_title:
- LNCS
article_processing_charge: No
author:
- first_name: Mingzhang
full_name: Huang, Mingzhang
last_name: Huang
- first_name: Hongfei
full_name: Fu, Hongfei
last_name: Fu
- first_name: Krishnendu
full_name: Chatterjee, Krishnendu
id: 2E5DCA20-F248-11E8-B48F-1D18A9856A87
last_name: Chatterjee
orcid: 0000-0002-4561-241X
citation:
ama: 'Huang M, Fu H, Chatterjee K. New approaches for almost-sure termination of
probabilistic programs. In: Ryu S, ed. Vol 11275. Springer; 2018:181-201. doi:10.1007/978-3-030-02768-1_11'
apa: 'Huang, M., Fu, H., & Chatterjee, K. (2018). New approaches for almost-sure
termination of probabilistic programs. In S. Ryu (Ed.) (Vol. 11275, pp. 181–201).
Presented at the 16th Asian Symposium on Programming Languages and Systems, APLAS,
Wellington, New Zealand: Springer. https://doi.org/10.1007/978-3-030-02768-1_11'
chicago: Huang, Mingzhang, Hongfei Fu, and Krishnendu Chatterjee. “New Approaches
for Almost-Sure Termination of Probabilistic Programs.” edited by Sukyoung Ryu,
11275:181–201. Springer, 2018. https://doi.org/10.1007/978-3-030-02768-1_11.
ieee: M. Huang, H. Fu, and K. Chatterjee, “New approaches for almost-sure termination
of probabilistic programs,” presented at the 16th Asian Symposium on Programming
Languages and Systems, APLAS, Wellington, New Zealand, 2018, vol. 11275, pp. 181–201.
ista: Huang M, Fu H, Chatterjee K. 2018. New approaches for almost-sure termination
of probabilistic programs. 16th Asian Symposium on Programming Languages and Systems,
APLAS, LNCS, vol. 11275, 181–201.
mla: Huang, Mingzhang, et al. New Approaches for Almost-Sure Termination of Probabilistic
Programs. Edited by Sukyoung Ryu, vol. 11275, Springer, 2018, pp. 181–201,
doi:10.1007/978-3-030-02768-1_11.
short: M. Huang, H. Fu, K. Chatterjee, in:, S. Ryu (Ed.), Springer, 2018, pp. 181–201.
conference:
end_date: 2018-12-06
location: Wellington, New Zealand
name: 16th Asian Symposium on Programming Languages and Systems, APLAS
start_date: 2018-12-02
date_created: 2018-12-16T22:59:20Z
date_published: 2018-12-01T00:00:00Z
date_updated: 2023-09-13T09:02:22Z
day: '01'
department:
- _id: KrCh
doi: 10.1007/978-3-030-02768-1_11
editor:
- first_name: Sukyoung
full_name: Ryu, Sukyoung
last_name: Ryu
external_id:
arxiv:
- '1806.06683'
isi:
- '000916310900011'
intvolume: ' 11275'
isi: 1
language:
- iso: eng
main_file_link:
- open_access: '1'
url: http://arxiv.org/abs/1806.06683
month: '12'
oa: 1
oa_version: Preprint
page: 181-201
project:
- _id: 25832EC2-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: S 11407_N23
name: Rigorous Systems Engineering
- _id: 25892FC0-B435-11E9-9278-68D0E5697425
grant_number: ICT15-003
name: Efficient Algorithms for Computer Aided Verification
publication_identifier:
isbn:
- '9783030027674'
issn:
- '03029743'
publisher: Springer
quality_controlled: '1'
scopus_import: '1'
status: public
title: New approaches for almost-sure termination of probabilistic programs
type: conference
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
volume: 11275
year: '2018'
...
---
_id: '546'
abstract:
- lang: eng
text: The precise control of neural stem cell (NSC) proliferation and differentiation
is crucial for the development and function of the human brain. Here, we review
the emerging links between the alteration of embryonic and adult neurogenesis
and the etiology of neuropsychiatric disorders (NPDs) such as autism spectrum
disorders (ASDs) and schizophrenia (SCZ), as well as the advances in stem cell-based
modeling and the novel therapeutic targets derived from these studies.
article_processing_charge: No
author:
- first_name: Roberto
full_name: Sacco, Roberto
id: 42C9F57E-F248-11E8-B48F-1D18A9856A87
last_name: Sacco
- first_name: Emanuele
full_name: Cacci, Emanuele
last_name: Cacci
- first_name: Gaia
full_name: Novarino, Gaia
id: 3E57A680-F248-11E8-B48F-1D18A9856A87
last_name: Novarino
orcid: 0000-0002-7673-7178
citation:
ama: Sacco R, Cacci E, Novarino G. Neural stem cells in neuropsychiatric disorders.
Current Opinion in Neurobiology. 2018;48(2):131-138. doi:10.1016/j.conb.2017.12.005
apa: Sacco, R., Cacci, E., & Novarino, G. (2018). Neural stem cells in neuropsychiatric
disorders. Current Opinion in Neurobiology. Elsevier. https://doi.org/10.1016/j.conb.2017.12.005
chicago: Sacco, Roberto, Emanuele Cacci, and Gaia Novarino. “Neural Stem Cells in
Neuropsychiatric Disorders.” Current Opinion in Neurobiology. Elsevier,
2018. https://doi.org/10.1016/j.conb.2017.12.005.
ieee: R. Sacco, E. Cacci, and G. Novarino, “Neural stem cells in neuropsychiatric
disorders,” Current Opinion in Neurobiology, vol. 48, no. 2. Elsevier,
pp. 131–138, 2018.
ista: Sacco R, Cacci E, Novarino G. 2018. Neural stem cells in neuropsychiatric
disorders. Current Opinion in Neurobiology. 48(2), 131–138.
mla: Sacco, Roberto, et al. “Neural Stem Cells in Neuropsychiatric Disorders.” Current
Opinion in Neurobiology, vol. 48, no. 2, Elsevier, 2018, pp. 131–38, doi:10.1016/j.conb.2017.12.005.
short: R. Sacco, E. Cacci, G. Novarino, Current Opinion in Neurobiology 48 (2018)
131–138.
date_created: 2018-12-11T11:47:06Z
date_published: 2018-02-01T00:00:00Z
date_updated: 2023-09-13T09:01:56Z
day: '01'
department:
- _id: GaNo
doi: 10.1016/j.conb.2017.12.005
external_id:
isi:
- '000427101600018'
intvolume: ' 48'
isi: 1
issue: '2'
language:
- iso: eng
month: '02'
oa_version: None
page: 131 - 138
publication: Current Opinion in Neurobiology
publication_status: published
publisher: Elsevier
publist_id: '7268'
quality_controlled: '1'
scopus_import: '1'
status: public
title: Neural stem cells in neuropsychiatric disorders
type: journal_article
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
volume: 48
year: '2018'
...
---
_id: '9812'
abstract:
- lang: eng
text: This document contains the full list of genes with their respective significance
and dN/dS values. (TXT 4499Â kb)
article_processing_charge: No
author:
- first_name: Luis
full_name: Zapata, Luis
last_name: Zapata
- first_name: Oriol
full_name: Pich, Oriol
last_name: Pich
- first_name: Luis
full_name: Serrano, Luis
last_name: Serrano
- first_name: Fyodor
full_name: Kondrashov, Fyodor
id: 44FDEF62-F248-11E8-B48F-1D18A9856A87
last_name: Kondrashov
orcid: 0000-0001-8243-4694
- first_name: Stephan
full_name: Ossowski, Stephan
last_name: Ossowski
- first_name: Martin
full_name: Schaefer, Martin
last_name: Schaefer
citation:
ama: 'Zapata L, Pich O, Serrano L, Kondrashov F, Ossowski S, Schaefer M. Additional
file 2: Of negative selection in tumor genome evolution acts on essential cellular
functions and the immunopeptidome. 2018. doi:10.6084/m9.figshare.6401414.v1'
apa: 'Zapata, L., Pich, O., Serrano, L., Kondrashov, F., Ossowski, S., & Schaefer,
M. (2018). Additional file 2: Of negative selection in tumor genome evolution
acts on essential cellular functions and the immunopeptidome. Springer Nature.
https://doi.org/10.6084/m9.figshare.6401414.v1'
chicago: 'Zapata, Luis, Oriol Pich, Luis Serrano, Fyodor Kondrashov, Stephan Ossowski,
and Martin Schaefer. “Additional File 2: Of Negative Selection in Tumor Genome
Evolution Acts on Essential Cellular Functions and the Immunopeptidome.” Springer
Nature, 2018. https://doi.org/10.6084/m9.figshare.6401414.v1.'
ieee: 'L. Zapata, O. Pich, L. Serrano, F. Kondrashov, S. Ossowski, and M. Schaefer,
“Additional file 2: Of negative selection in tumor genome evolution acts on essential
cellular functions and the immunopeptidome.” Springer Nature, 2018.'
ista: 'Zapata L, Pich O, Serrano L, Kondrashov F, Ossowski S, Schaefer M. 2018.
Additional file 2: Of negative selection in tumor genome evolution acts on essential
cellular functions and the immunopeptidome, Springer Nature, 10.6084/m9.figshare.6401414.v1.'
mla: 'Zapata, Luis, et al. Additional File 2: Of Negative Selection in Tumor
Genome Evolution Acts on Essential Cellular Functions and the Immunopeptidome.
Springer Nature, 2018, doi:10.6084/m9.figshare.6401414.v1.'
short: L. Zapata, O. Pich, L. Serrano, F. Kondrashov, S. Ossowski, M. Schaefer,
(2018).
date_created: 2021-08-06T12:58:25Z
date_published: 2018-05-31T00:00:00Z
date_updated: 2023-09-13T09:01:31Z
day: '31'
department:
- _id: FyKo
doi: 10.6084/m9.figshare.6401414.v1
main_file_link:
- open_access: '1'
url: https://doi.org/10.6084/m9.figshare.6401414.v1
month: '05'
oa: 1
oa_version: Published Version
publisher: Springer Nature
related_material:
record:
- id: '279'
relation: used_in_publication
status: public
status: public
title: 'Additional file 2: Of negative selection in tumor genome evolution acts on
essential cellular functions and the immunopeptidome'
type: research_data_reference
user_id: 6785fbc1-c503-11eb-8a32-93094b40e1cf
year: '2018'
...
---
_id: '9811'
abstract:
- lang: eng
text: This document contains additional supporting evidence presented as supplemental
tables. (XLSX 50Â kb)
article_processing_charge: No
author:
- first_name: Luis
full_name: Zapata, Luis
last_name: Zapata
- first_name: Oriol
full_name: Pich, Oriol
last_name: Pich
- first_name: Luis
full_name: Serrano, Luis
last_name: Serrano
- first_name: Fyodor
full_name: Kondrashov, Fyodor
id: 44FDEF62-F248-11E8-B48F-1D18A9856A87
last_name: Kondrashov
orcid: 0000-0001-8243-4694
- first_name: Stephan
full_name: Ossowski, Stephan
last_name: Ossowski
- first_name: Martin
full_name: Schaefer, Martin
last_name: Schaefer
citation:
ama: 'Zapata L, Pich O, Serrano L, Kondrashov F, Ossowski S, Schaefer M. Additional
file 1: Of negative selection in tumor genome evolution acts on essential cellular
functions and the immunopeptidome. 2018. doi:10.6084/m9.figshare.6401390.v1'
apa: 'Zapata, L., Pich, O., Serrano, L., Kondrashov, F., Ossowski, S., & Schaefer,
M. (2018). Additional file 1: Of negative selection in tumor genome evolution
acts on essential cellular functions and the immunopeptidome. Springer Nature.
https://doi.org/10.6084/m9.figshare.6401390.v1'
chicago: 'Zapata, Luis, Oriol Pich, Luis Serrano, Fyodor Kondrashov, Stephan Ossowski,
and Martin Schaefer. “Additional File 1: Of Negative Selection in Tumor Genome
Evolution Acts on Essential Cellular Functions and the Immunopeptidome.” Springer
Nature, 2018. https://doi.org/10.6084/m9.figshare.6401390.v1.'
ieee: 'L. Zapata, O. Pich, L. Serrano, F. Kondrashov, S. Ossowski, and M. Schaefer,
“Additional file 1: Of negative selection in tumor genome evolution acts on essential
cellular functions and the immunopeptidome.” Springer Nature, 2018.'
ista: 'Zapata L, Pich O, Serrano L, Kondrashov F, Ossowski S, Schaefer M. 2018.
Additional file 1: Of negative selection in tumor genome evolution acts on essential
cellular functions and the immunopeptidome, Springer Nature, 10.6084/m9.figshare.6401390.v1.'
mla: 'Zapata, Luis, et al. Additional File 1: Of Negative Selection in Tumor
Genome Evolution Acts on Essential Cellular Functions and the Immunopeptidome.
Springer Nature, 2018, doi:10.6084/m9.figshare.6401390.v1.'
short: L. Zapata, O. Pich, L. Serrano, F. Kondrashov, S. Ossowski, M. Schaefer,
(2018).
date_created: 2021-08-06T12:53:49Z
date_published: 2018-05-31T00:00:00Z
date_updated: 2023-09-13T09:01:31Z
day: '31'
department:
- _id: FyKo
doi: 10.6084/m9.figshare.6401390.v1
main_file_link:
- open_access: '1'
url: https://doi.org/10.6084/m9.figshare.6401390.v1
month: '05'
oa: 1
oa_version: Preprint
publisher: Springer Nature
related_material:
record:
- id: '279'
relation: used_in_publication
status: public
status: public
title: 'Additional file 1: Of negative selection in tumor genome evolution acts on
essential cellular functions and the immunopeptidome'
type: research_data_reference
user_id: 6785fbc1-c503-11eb-8a32-93094b40e1cf
year: '2018'
...
---
_id: '20'
abstract:
- lang: eng
text: 'Background: Norepinephrine (NE) signaling has a key role in white adipose
tissue (WAT) functions, including lipolysis, free fatty acid liberation and, under
certain conditions, conversion of white into brite (brown-in-white) adipocytes.
However, acute effects of NE stimulation have not been described at the transcriptional
network level. Results: We used RNA-seq to uncover a broad transcriptional response.
The inference of protein-protein and protein-DNA interaction networks allowed
us to identify a set of immediate-early genes (IEGs) with high betweenness, validating
our approach and suggesting a hierarchical control of transcriptional regulation.
In addition, we identified a transcriptional regulatory network with IEGs as master
regulators, including HSF1 and NFIL3 as novel NE-induced IEG candidates. Moreover,
a functional enrichment analysis and gene clustering into functional modules suggest
a crosstalk between metabolic, signaling, and immune responses. Conclusions: Altogether,
our network biology approach explores for the first time the immediate-early systems
level response of human adipocytes to acute sympathetic activation, thereby providing
a first network basis of early cell fate programs and crosstalks between metabolic
and transcriptional networks required for proper WAT function.'
acknowledgement: This work was funded by the German Centre for Diabetes Research (DZD)
and the Austrian Science Fund (FWF, P25729-B19).
article_processing_charge: No
article_type: original
author:
- first_name: Juan
full_name: Higareda Almaraz, Juan
last_name: Higareda Almaraz
- first_name: Michael
full_name: Karbiener, Michael
last_name: Karbiener
- first_name: Maude
full_name: Giroud, Maude
last_name: Giroud
- first_name: Florian
full_name: Pauler, Florian
id: 48EA0138-F248-11E8-B48F-1D18A9856A87
last_name: Pauler
orcid: 0000-0002-7462-0048
- first_name: Teresa
full_name: Gerhalter, Teresa
last_name: Gerhalter
- first_name: Stephan
full_name: Herzig, Stephan
last_name: Herzig
- first_name: Marcel
full_name: Scheideler, Marcel
last_name: Scheideler
citation:
ama: Higareda Almaraz J, Karbiener M, Giroud M, et al. Norepinephrine triggers an
immediate-early regulatory network response in primary human white adipocytes.
BMC Genomics. 2018;19(1). doi:10.1186/s12864-018-5173-0
apa: Higareda Almaraz, J., Karbiener, M., Giroud, M., Pauler, F., Gerhalter, T.,
Herzig, S., & Scheideler, M. (2018). Norepinephrine triggers an immediate-early
regulatory network response in primary human white adipocytes. BMC Genomics.
BioMed Central. https://doi.org/10.1186/s12864-018-5173-0
chicago: Higareda Almaraz, Juan, Michael Karbiener, Maude Giroud, Florian Pauler,
Teresa Gerhalter, Stephan Herzig, and Marcel Scheideler. “Norepinephrine Triggers
an Immediate-Early Regulatory Network Response in Primary Human White Adipocytes.”
BMC Genomics. BioMed Central, 2018. https://doi.org/10.1186/s12864-018-5173-0.
ieee: J. Higareda Almaraz et al., “Norepinephrine triggers an immediate-early
regulatory network response in primary human white adipocytes,” BMC Genomics,
vol. 19, no. 1. BioMed Central, 2018.
ista: Higareda Almaraz J, Karbiener M, Giroud M, Pauler F, Gerhalter T, Herzig S,
Scheideler M. 2018. Norepinephrine triggers an immediate-early regulatory network
response in primary human white adipocytes. BMC Genomics. 19(1).
mla: Higareda Almaraz, Juan, et al. “Norepinephrine Triggers an Immediate-Early
Regulatory Network Response in Primary Human White Adipocytes.” BMC Genomics,
vol. 19, no. 1, BioMed Central, 2018, doi:10.1186/s12864-018-5173-0.
short: J. Higareda Almaraz, M. Karbiener, M. Giroud, F. Pauler, T. Gerhalter, S.
Herzig, M. Scheideler, BMC Genomics 19 (2018).
date_created: 2018-12-11T11:44:12Z
date_published: 2018-11-03T00:00:00Z
date_updated: 2023-09-13T09:10:47Z
day: '03'
ddc:
- '570'
department:
- _id: SiHi
doi: 10.1186/s12864-018-5173-0
external_id:
isi:
- '000450976700002'
file:
- access_level: open_access
checksum: a56516e734dab589dc7f3e1915973b4d
content_type: application/pdf
creator: dernst
date_created: 2018-12-17T14:52:57Z
date_updated: 2020-07-14T12:45:23Z
file_id: '5712'
file_name: 2018_BMCGenomics_Higareda.pdf
file_size: 4629784
relation: main_file
file_date_updated: 2020-07-14T12:45:23Z
has_accepted_license: '1'
intvolume: ' 19'
isi: 1
issue: '1'
language:
- iso: eng
month: '11'
oa: 1
oa_version: Published Version
publication: BMC Genomics
publication_identifier:
issn:
- 1471-2164
publication_status: published
publisher: BioMed Central
publist_id: '8035'
quality_controlled: '1'
related_material:
record:
- id: '9807'
relation: research_data
status: public
- id: '9808'
relation: research_data
status: public
scopus_import: '1'
status: public
title: Norepinephrine triggers an immediate-early regulatory network response in primary
human white adipocytes
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: journal_article
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
volume: 19
year: '2018'
...
---
_id: '107'
abstract:
- lang: eng
text: 'We introduce the notion of “non-malleable codes” which relaxes the notion
of error correction and error detection. Informally, a code is non-malleable if
the message contained in a modified codeword is either the original message, or
a completely unrelated value. In contrast to error correction and error detection,
non-malleability can be achieved for very rich classes of modifications. We construct
an efficient code that is non-malleable with respect to modifications that affect
each bit of the codeword arbitrarily (i.e., leave it untouched, flip it, or set
it to either 0 or 1), but independently of the value of the other bits of the
codeword. Using the probabilistic method, we also show a very strong and general
statement: there exists a non-malleable code for every “small enough” family F
of functions via which codewords can be modified. Although this probabilistic
method argument does not directly yield efficient constructions, it gives us efficient
non-malleable codes in the random-oracle model for very general classes of tampering
functions—e.g., functions where every bit in the tampered codeword can depend
arbitrarily on any 99% of the bits in the original codeword. As an application
of non-malleable codes, we show that they provide an elegant algorithmic solution
to the task of protecting functionalities implemented in hardware (e.g., signature
cards) against “tampering attacks.” In such attacks, the secret state of a physical
system is tampered, in the hopes that future interaction with the modified system
will reveal some secret information. This problem was previously studied in the
work of Gennaro et al. in 2004 under the name “algorithmic tamper proof security”
(ATP). We show that non-malleable codes can be used to achieve important improvements
over the prior work. In particular, we show that any functionality can be made
secure against a large class of tampering attacks, simply by encoding the secret
state with a non-malleable code while it is stored in memory.'
article_number: '20'
article_processing_charge: No
article_type: original
author:
- first_name: Stefan
full_name: Dziembowski, Stefan
last_name: Dziembowski
- first_name: Krzysztof Z
full_name: Pietrzak, Krzysztof Z
id: 3E04A7AA-F248-11E8-B48F-1D18A9856A87
last_name: Pietrzak
orcid: 0000-0002-9139-1654
- first_name: Daniel
full_name: Wichs, Daniel
last_name: Wichs
citation:
ama: Dziembowski S, Pietrzak KZ, Wichs D. Non-malleable codes. Journal of the
ACM. 2018;65(4). doi:10.1145/3178432
apa: Dziembowski, S., Pietrzak, K. Z., & Wichs, D. (2018). Non-malleable codes.
Journal of the ACM. ACM. https://doi.org/10.1145/3178432
chicago: Dziembowski, Stefan, Krzysztof Z Pietrzak, and Daniel Wichs. “Non-Malleable
Codes.” Journal of the ACM. ACM, 2018. https://doi.org/10.1145/3178432.
ieee: S. Dziembowski, K. Z. Pietrzak, and D. Wichs, “Non-malleable codes,” Journal
of the ACM, vol. 65, no. 4. ACM, 2018.
ista: Dziembowski S, Pietrzak KZ, Wichs D. 2018. Non-malleable codes. Journal of
the ACM. 65(4), 20.
mla: Dziembowski, Stefan, et al. “Non-Malleable Codes.” Journal of the ACM,
vol. 65, no. 4, 20, ACM, 2018, doi:10.1145/3178432.
short: S. Dziembowski, K.Z. Pietrzak, D. Wichs, Journal of the ACM 65 (2018).
date_created: 2018-12-11T11:44:40Z
date_published: 2018-08-01T00:00:00Z
date_updated: 2023-09-13T09:05:17Z
day: '01'
department:
- _id: KrPi
doi: 10.1145/3178432
ec_funded: 1
external_id:
isi:
- '000442938200004'
intvolume: ' 65'
isi: 1
issue: '4'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://eprint.iacr.org/2009/608
month: '08'
oa: 1
oa_version: Preprint
project:
- _id: 258AA5B2-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '682815'
name: Teaching Old Crypto New Tricks
- _id: 258C570E-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '259668'
name: Provable Security for Physical Cryptography
publication: Journal of the ACM
publication_status: published
publisher: ACM
publist_id: '7947'
quality_controlled: '1'
scopus_import: '1'
status: public
title: Non-malleable codes
type: journal_article
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
volume: 65
year: '2018'
...
---
_id: '5676'
abstract:
- lang: eng
text: 'In epithelial tissues, cells tightly connect to each other through cell–cell
junctions, but they also present the remarkable capacity of reorganizing themselves
without compromising tissue integrity. Upon injury, simple epithelia efficiently
resolve small lesions through the action of actin cytoskeleton contractile structures
at the wound edge and cellular rearrangements. However, the underlying mechanisms
and how they cooperate are still poorly understood. In this study, we combine
live imaging and theoretical modeling to reveal a novel and indispensable role
for occluding junctions (OJs) in this process. We demonstrate that OJ loss of
function leads to defects in wound-closure dynamics: instead of contracting, wounds
dramatically increase their area. OJ mutants exhibit phenotypes in cell shape,
cellular rearrangements, and mechanical properties as well as in actin cytoskeleton
dynamics at the wound edge. We propose that OJs are essential for wound closure
by impacting on epithelial mechanics at the tissue level, which in turn is crucial
for correct regulation of the cellular events occurring at the wound edge.'
article_processing_charge: No
author:
- first_name: Lara
full_name: Carvalho, Lara
last_name: Carvalho
- first_name: Pedro
full_name: Patricio, Pedro
last_name: Patricio
- first_name: Susana
full_name: Ponte, Susana
last_name: Ponte
- first_name: Carl-Philipp J
full_name: Heisenberg, Carl-Philipp J
id: 39427864-F248-11E8-B48F-1D18A9856A87
last_name: Heisenberg
orcid: 0000-0002-0912-4566
- first_name: Luis
full_name: Almeida, Luis
last_name: Almeida
- first_name: André S.
full_name: Nunes, André S.
last_name: Nunes
- first_name: Nuno A.M.
full_name: Araújo, Nuno A.M.
last_name: Araújo
- first_name: Antonio
full_name: Jacinto, Antonio
last_name: Jacinto
citation:
ama: Carvalho L, Patricio P, Ponte S, et al. Occluding junctions as novel regulators
of tissue mechanics during wound repair. Journal of Cell Biology. 2018;217(12):4267-4283.
doi:10.1083/jcb.201804048
apa: Carvalho, L., Patricio, P., Ponte, S., Heisenberg, C.-P. J., Almeida, L., Nunes,
A. S., … Jacinto, A. (2018). Occluding junctions as novel regulators of tissue
mechanics during wound repair. Journal of Cell Biology. Rockefeller University
Press. https://doi.org/10.1083/jcb.201804048
chicago: Carvalho, Lara, Pedro Patricio, Susana Ponte, Carl-Philipp J Heisenberg,
Luis Almeida, André S. Nunes, Nuno A.M. Araújo, and Antonio Jacinto. “Occluding
Junctions as Novel Regulators of Tissue Mechanics during Wound Repair.” Journal
of Cell Biology. Rockefeller University Press, 2018. https://doi.org/10.1083/jcb.201804048.
ieee: L. Carvalho et al., “Occluding junctions as novel regulators of tissue
mechanics during wound repair,” Journal of Cell Biology, vol. 217, no.
12. Rockefeller University Press, pp. 4267–4283, 2018.
ista: Carvalho L, Patricio P, Ponte S, Heisenberg C-PJ, Almeida L, Nunes AS, Araújo
NAM, Jacinto A. 2018. Occluding junctions as novel regulators of tissue mechanics
during wound repair. Journal of Cell Biology. 217(12), 4267–4283.
mla: Carvalho, Lara, et al. “Occluding Junctions as Novel Regulators of Tissue Mechanics
during Wound Repair.” Journal of Cell Biology, vol. 217, no. 12, Rockefeller
University Press, 2018, pp. 4267–83, doi:10.1083/jcb.201804048.
short: L. Carvalho, P. Patricio, S. Ponte, C.-P.J. Heisenberg, L. Almeida, A.S.
Nunes, N.A.M. Araújo, A. Jacinto, Journal of Cell Biology 217 (2018) 4267–4283.
date_created: 2018-12-16T22:59:19Z
date_published: 2018-12-01T00:00:00Z
date_updated: 2023-09-13T09:11:17Z
day: '01'
department:
- _id: CaHe
doi: 10.1083/jcb.201804048
ec_funded: 1
external_id:
isi:
- '000451960800018'
pmid:
- '30228162 '
intvolume: ' 217'
isi: 1
issue: '12'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://www.ncbi.nlm.nih.gov/pubmed/30228162
month: '12'
oa: 1
oa_version: Submitted Version
page: 4267-4283
pmid: 1
project:
- _id: 25681D80-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '291734'
name: International IST Postdoc Fellowship Programme
publication: Journal of Cell Biology
publication_identifier:
issn:
- '00219525'
publication_status: published
publisher: Rockefeller University Press
quality_controlled: '1'
scopus_import: '1'
status: public
title: Occluding junctions as novel regulators of tissue mechanics during wound repair
type: journal_article
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
volume: 217
year: '2018'
...
---
_id: '14224'
abstract:
- lang: eng
text: Clustering is a cornerstone of unsupervised learning which can be thought
as disentangling multiple generative mechanisms underlying the data. In this paper
we introduce an algorithmic framework to train mixtures of implicit generative
models which we particularize for variational autoencoders. Relying on an additional
set of discriminators, we propose a competitive procedure in which the models
only need to approximate the portion of the data distribution from which they
can produce realistic samples. As a byproduct, each model is simpler to train,
and a clustering interpretation arises naturally from the partitioning of the
training points among the models. We empirically show that our approach splits
the training distribution in a reasonable way and increases the quality of the
generated samples.
article_processing_charge: No
author:
- first_name: Francesco
full_name: Locatello, Francesco
id: 26cfd52f-2483-11ee-8040-88983bcc06d4
last_name: Locatello
orcid: 0000-0002-4850-0683
- first_name: Damien
full_name: Vincent, Damien
last_name: Vincent
- first_name: Ilya
full_name: Tolstikhin, Ilya
last_name: Tolstikhin
- first_name: Gunnar
full_name: Ratsch, Gunnar
last_name: Ratsch
- first_name: Sylvain
full_name: Gelly, Sylvain
last_name: Gelly
- first_name: Bernhard
full_name: Scholkopf, Bernhard
last_name: Scholkopf
citation:
ama: 'Locatello F, Vincent D, Tolstikhin I, Ratsch G, Gelly S, Scholkopf B. Clustering
meets implicit generative models. In: 6th International Conference on Learning
Representations. ; 2018.'
apa: Locatello, F., Vincent, D., Tolstikhin, I., Ratsch, G., Gelly, S., & Scholkopf,
B. (2018). Clustering meets implicit generative models. In 6th International
Conference on Learning Representations. Vancouver, Canada.
chicago: Locatello, Francesco, Damien Vincent, Ilya Tolstikhin, Gunnar Ratsch, Sylvain
Gelly, and Bernhard Scholkopf. “Clustering Meets Implicit Generative Models.”
In 6th International Conference on Learning Representations, 2018.
ieee: F. Locatello, D. Vincent, I. Tolstikhin, G. Ratsch, S. Gelly, and B. Scholkopf,
“Clustering meets implicit generative models,” in 6th International Conference
on Learning Representations, Vancouver, Canada, 2018.
ista: Locatello F, Vincent D, Tolstikhin I, Ratsch G, Gelly S, Scholkopf B. 2018.
Clustering meets implicit generative models. 6th International Conference on Learning
Representations. International Conference on Machine Learning.
mla: Locatello, Francesco, et al. “Clustering Meets Implicit Generative Models.”
6th International Conference on Learning Representations, 2018.
short: F. Locatello, D. Vincent, I. Tolstikhin, G. Ratsch, S. Gelly, B. Scholkopf,
in:, 6th International Conference on Learning Representations, 2018.
conference:
end_date: 2018-05-03
location: Vancouver, Canada
name: International Conference on Machine Learning
start_date: 2018-04-30
date_created: 2023-08-22T14:25:34Z
date_published: 2018-05-01T00:00:00Z
date_updated: 2023-09-13T09:08:24Z
day: '01'
department:
- _id: FrLo
extern: '1'
external_id:
arxiv:
- '1804.11130'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/1804.11130
month: '05'
oa: 1
oa_version: Preprint
publication: 6th International Conference on Learning Representations
publication_status: published
quality_controlled: '1'
scopus_import: '1'
status: public
title: Clustering meets implicit generative models
type: conference
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
year: '2018'
...
---
_id: '9807'
abstract:
- lang: eng
text: Table S1. Genes with highest betweenness. Table S2. Local and Master regulators
up-regulated. Table S3. Local and Master regulators down-regulated (XLSX 23 kb).
article_processing_charge: No
author:
- first_name: Juan
full_name: Higareda Almaraz, Juan
last_name: Higareda Almaraz
- first_name: Michael
full_name: Karbiener, Michael
last_name: Karbiener
- first_name: Maude
full_name: Giroud, Maude
last_name: Giroud
- first_name: Florian
full_name: Pauler, Florian
id: 48EA0138-F248-11E8-B48F-1D18A9856A87
last_name: Pauler
orcid: 0000-0002-7462-0048
- first_name: Teresa
full_name: Gerhalter, Teresa
last_name: Gerhalter
- first_name: Stephan
full_name: Herzig, Stephan
last_name: Herzig
- first_name: Marcel
full_name: Scheideler, Marcel
last_name: Scheideler
citation:
ama: 'Higareda Almaraz J, Karbiener M, Giroud M, et al. Additional file 1: Of Norepinephrine
triggers an immediate-early regulatory network response in primary human white
adipocytes. 2018. doi:10.6084/m9.figshare.7295339.v1'
apa: 'Higareda Almaraz, J., Karbiener, M., Giroud, M., Pauler, F., Gerhalter, T.,
Herzig, S., & Scheideler, M. (2018). Additional file 1: Of Norepinephrine
triggers an immediate-early regulatory network response in primary human white
adipocytes. Springer Nature. https://doi.org/10.6084/m9.figshare.7295339.v1'
chicago: 'Higareda Almaraz, Juan, Michael Karbiener, Maude Giroud, Florian Pauler,
Teresa Gerhalter, Stephan Herzig, and Marcel Scheideler. “Additional File 1: Of
Norepinephrine Triggers an Immediate-Early Regulatory Network Response in Primary
Human White Adipocytes.” Springer Nature, 2018. https://doi.org/10.6084/m9.figshare.7295339.v1.'
ieee: 'J. Higareda Almaraz et al., “Additional file 1: Of Norepinephrine
triggers an immediate-early regulatory network response in primary human white
adipocytes.” Springer Nature, 2018.'
ista: 'Higareda Almaraz J, Karbiener M, Giroud M, Pauler F, Gerhalter T, Herzig
S, Scheideler M. 2018. Additional file 1: Of Norepinephrine triggers an immediate-early
regulatory network response in primary human white adipocytes, Springer Nature,
10.6084/m9.figshare.7295339.v1.'
mla: 'Higareda Almaraz, Juan, et al. Additional File 1: Of Norepinephrine Triggers
an Immediate-Early Regulatory Network Response in Primary Human White Adipocytes.
Springer Nature, 2018, doi:10.6084/m9.figshare.7295339.v1.'
short: J. Higareda Almaraz, M. Karbiener, M. Giroud, F. Pauler, T. Gerhalter, S.
Herzig, M. Scheideler, (2018).
date_created: 2021-08-06T12:26:53Z
date_published: 2018-11-03T00:00:00Z
date_updated: 2023-09-13T09:10:47Z
day: '03'
department:
- _id: SiHi
doi: 10.6084/m9.figshare.7295339.v1
main_file_link:
- open_access: '1'
url: https://doi.org/10.6084/m9.figshare.7295339.v1
month: '11'
oa: 1
oa_version: Published Version
publisher: Springer Nature
related_material:
record:
- id: '20'
relation: used_in_publication
status: public
status: public
title: 'Additional file 1: Of Norepinephrine triggers an immediate-early regulatory
network response in primary human white adipocytes'
type: research_data_reference
user_id: 6785fbc1-c503-11eb-8a32-93094b40e1cf
year: '2018'
...
---
_id: '9808'
abstract:
- lang: eng
text: Table S4. Counts per Gene per Million Reads Mapped. (XLSX 2751 kb).
article_processing_charge: No
author:
- first_name: Juan
full_name: Higareda Almaraz, Juan
last_name: Higareda Almaraz
- first_name: Michael
full_name: Karbiener, Michael
last_name: Karbiener
- first_name: Maude
full_name: Giroud, Maude
last_name: Giroud
- first_name: Florian
full_name: Pauler, Florian
id: 48EA0138-F248-11E8-B48F-1D18A9856A87
last_name: Pauler
orcid: 0000-0002-7462-0048
- first_name: Teresa
full_name: Gerhalter, Teresa
last_name: Gerhalter
- first_name: Stephan
full_name: Herzig, Stephan
last_name: Herzig
- first_name: Marcel
full_name: Scheideler, Marcel
last_name: Scheideler
citation:
ama: 'Higareda Almaraz J, Karbiener M, Giroud M, et al. Additional file 3: Of Norepinephrine
triggers an immediate-early regulatory network response in primary human white
adipocytes. 2018. doi:10.6084/m9.figshare.7295369.v1'
apa: 'Higareda Almaraz, J., Karbiener, M., Giroud, M., Pauler, F., Gerhalter, T.,
Herzig, S., & Scheideler, M. (2018). Additional file 3: Of Norepinephrine
triggers an immediate-early regulatory network response in primary human white
adipocytes. Springer Nature. https://doi.org/10.6084/m9.figshare.7295369.v1'
chicago: 'Higareda Almaraz, Juan, Michael Karbiener, Maude Giroud, Florian Pauler,
Teresa Gerhalter, Stephan Herzig, and Marcel Scheideler. “Additional File 3: Of
Norepinephrine Triggers an Immediate-Early Regulatory Network Response in Primary
Human White Adipocytes.” Springer Nature, 2018. https://doi.org/10.6084/m9.figshare.7295369.v1.'
ieee: 'J. Higareda Almaraz et al., “Additional file 3: Of Norepinephrine
triggers an immediate-early regulatory network response in primary human white
adipocytes.” Springer Nature, 2018.'
ista: 'Higareda Almaraz J, Karbiener M, Giroud M, Pauler F, Gerhalter T, Herzig
S, Scheideler M. 2018. Additional file 3: Of Norepinephrine triggers an immediate-early
regulatory network response in primary human white adipocytes, Springer Nature,
10.6084/m9.figshare.7295369.v1.'
mla: 'Higareda Almaraz, Juan, et al. Additional File 3: Of Norepinephrine Triggers
an Immediate-Early Regulatory Network Response in Primary Human White Adipocytes.
Springer Nature, 2018, doi:10.6084/m9.figshare.7295369.v1.'
short: J. Higareda Almaraz, M. Karbiener, M. Giroud, F. Pauler, T. Gerhalter, S.
Herzig, M. Scheideler, (2018).
date_created: 2021-08-06T12:31:57Z
date_published: 2018-11-03T00:00:00Z
date_updated: 2023-09-13T09:10:47Z
day: '03'
department:
- _id: SiHi
doi: 10.6084/m9.figshare.7295369.v1
main_file_link:
- open_access: '1'
url: https://doi.org/10.6084/m9.figshare.7295369.v1
month: '11'
oa: 1
oa_version: Published Version
publisher: Springer Nature
related_material:
record:
- id: '20'
relation: used_in_publication
status: public
status: public
title: 'Additional file 3: Of Norepinephrine triggers an immediate-early regulatory
network response in primary human white adipocytes'
type: research_data_reference
user_id: 6785fbc1-c503-11eb-8a32-93094b40e1cf
year: '2018'
...
---
_id: '193'
abstract:
- lang: eng
text: 'We show attacks on five data-independent memory-hard functions (iMHF) that
were submitted to the password hashing competition (PHC). Informally, an MHF is
a function which cannot be evaluated on dedicated hardware, like ASICs, at significantly
lower hardware and/or energy cost than evaluating a single instance on a standard
single-core architecture. Data-independent means the memory access pattern of
the function is independent of the input; this makes iMHFs harder to construct
than data-dependent ones, but the latter can be attacked by various side-channel
attacks. Following [Alwen-Blocki''16], we capture the evaluation of an iMHF as
a directed acyclic graph (DAG). The cumulative parallel pebbling complexity of
this DAG is a measure for the hardware cost of evaluating the iMHF on an ASIC.
Ideally, one would like the complexity of a DAG underlying an iMHF to be as close
to quadratic in the number of nodes of the graph as possible. Instead, we show
that (the DAGs underlying) the following iMHFs are far from this bound: Rig.v2,
TwoCats and Gambit each having an exponent no more than 1.75. Moreover, we show
that the complexity of the iMHF modes of the PHC finalists Pomelo and Lyra2 have
exponents at most 1.83 and 1.67 respectively. To show this we investigate a combinatorial
property of each underlying DAG (called its depth-robustness. By establishing
upper bounds on this property we are then able to apply the general technique
of [Alwen-Block''16] for analyzing the hardware costs of an iMHF.'
acknowledgement: Leonid Reyzin was supported in part by IST Austria and by US NSF
grants 1012910, 1012798, and 1422965; this research was performed while he was visiting
IST Austria.
article_processing_charge: No
author:
- first_name: Joel F
full_name: Alwen, Joel F
id: 2A8DFA8C-F248-11E8-B48F-1D18A9856A87
last_name: Alwen
- first_name: Peter
full_name: Gazi, Peter
last_name: Gazi
- first_name: Chethan
full_name: Kamath Hosdurg, Chethan
id: 4BD3F30E-F248-11E8-B48F-1D18A9856A87
last_name: Kamath Hosdurg
- first_name: Karen
full_name: Klein, Karen
id: 3E83A2F8-F248-11E8-B48F-1D18A9856A87
last_name: Klein
- first_name: Georg F
full_name: Osang, Georg F
id: 464B40D6-F248-11E8-B48F-1D18A9856A87
last_name: Osang
orcid: 0000-0002-8882-5116
- first_name: Krzysztof Z
full_name: Pietrzak, Krzysztof Z
id: 3E04A7AA-F248-11E8-B48F-1D18A9856A87
last_name: Pietrzak
orcid: 0000-0002-9139-1654
- first_name: Lenoid
full_name: Reyzin, Lenoid
last_name: Reyzin
- first_name: Michal
full_name: Rolinek, Michal
id: 3CB3BC06-F248-11E8-B48F-1D18A9856A87
last_name: Rolinek
- first_name: Michal
full_name: Rybar, Michal
id: 2B3E3DE8-F248-11E8-B48F-1D18A9856A87
last_name: Rybar
citation:
ama: 'Alwen JF, Gazi P, Kamath Hosdurg C, et al. On the memory hardness of data
independent password hashing functions. In: Proceedings of the 2018 on Asia
Conference on Computer and Communication Security. ACM; 2018:51-65. doi:10.1145/3196494.3196534'
apa: 'Alwen, J. F., Gazi, P., Kamath Hosdurg, C., Klein, K., Osang, G. F., Pietrzak,
K. Z., … Rybar, M. (2018). On the memory hardness of data independent password
hashing functions. In Proceedings of the 2018 on Asia Conference on Computer
and Communication Security (pp. 51–65). Incheon, Republic of Korea: ACM. https://doi.org/10.1145/3196494.3196534'
chicago: Alwen, Joel F, Peter Gazi, Chethan Kamath Hosdurg, Karen Klein, Georg F
Osang, Krzysztof Z Pietrzak, Lenoid Reyzin, Michal Rolinek, and Michal Rybar.
“On the Memory Hardness of Data Independent Password Hashing Functions.” In Proceedings
of the 2018 on Asia Conference on Computer and Communication Security, 51–65.
ACM, 2018. https://doi.org/10.1145/3196494.3196534.
ieee: J. F. Alwen et al., “On the memory hardness of data independent password
hashing functions,” in Proceedings of the 2018 on Asia Conference on Computer
and Communication Security, Incheon, Republic of Korea, 2018, pp. 51–65.
ista: 'Alwen JF, Gazi P, Kamath Hosdurg C, Klein K, Osang GF, Pietrzak KZ, Reyzin
L, Rolinek M, Rybar M. 2018. On the memory hardness of data independent password
hashing functions. Proceedings of the 2018 on Asia Conference on Computer and
Communication Security. ASIACCS: Asia Conference on Computer and Communications
Security , 51–65.'
mla: Alwen, Joel F., et al. “On the Memory Hardness of Data Independent Password
Hashing Functions.” Proceedings of the 2018 on Asia Conference on Computer
and Communication Security, ACM, 2018, pp. 51–65, doi:10.1145/3196494.3196534.
short: J.F. Alwen, P. Gazi, C. Kamath Hosdurg, K. Klein, G.F. Osang, K.Z. Pietrzak,
L. Reyzin, M. Rolinek, M. Rybar, in:, Proceedings of the 2018 on Asia Conference
on Computer and Communication Security, ACM, 2018, pp. 51–65.
conference:
end_date: 2018-06-08
location: Incheon, Republic of Korea
name: 'ASIACCS: Asia Conference on Computer and Communications Security '
start_date: 2018-06-04
date_created: 2018-12-11T11:45:07Z
date_published: 2018-06-01T00:00:00Z
date_updated: 2023-09-13T09:13:12Z
day: '01'
department:
- _id: KrPi
- _id: HeEd
- _id: VlKo
doi: 10.1145/3196494.3196534
ec_funded: 1
external_id:
isi:
- '000516620100005'
isi: 1
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://eprint.iacr.org/2016/783
month: '06'
oa: 1
oa_version: Submitted Version
page: 51 - 65
project:
- _id: 25FBA906-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '616160'
name: 'Discrete Optimization in Computer Vision: Theory and Practice'
- _id: 258AA5B2-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '682815'
name: Teaching Old Crypto New Tricks
publication: Proceedings of the 2018 on Asia Conference on Computer and Communication
Security
publication_status: published
publisher: ACM
publist_id: '7723'
quality_controlled: '1'
scopus_import: '1'
status: public
title: On the memory hardness of data independent password hashing functions
type: conference
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
year: '2018'
...
---
_id: '300'
abstract:
- lang: eng
text: We introduce a formal quantitative notion of “bit security” for a general
type of cryptographic games (capturing both decision and search problems), aimed
at capturing the intuition that a cryptographic primitive with k-bit security
is as hard to break as an ideal cryptographic function requiring a brute force
attack on a k-bit key space. Our new definition matches the notion of bit security
commonly used by cryptographers and cryptanalysts when studying search (e.g.,
key recovery) problems, where the use of the traditional definition is well established.
However, it produces a quantitatively different metric in the case of decision
(indistinguishability) problems, where the use of (a straightforward generalization
of) the traditional definition is more problematic and leads to a number of paradoxical
situations or mismatches between theoretical/provable security and practical/common
sense intuition. Key to our new definition is to consider adversaries that may
explicitly declare failure of the attack. We support and justify the new definition
by proving a number of technical results, including tight reductions between several
standard cryptographic problems, a new hybrid theorem that preserves bit security,
and an application to the security analysis of indistinguishability primitives
making use of (approximate) floating point numbers. This is the first result showing
that (standard precision) 53-bit floating point numbers can be used to achieve
100-bit security in the context of cryptographic primitives with general indistinguishability-based
security definitions. Previous results of this type applied only to search problems,
or special types of decision problems.
acknowledgement: Research supported in part by the Defense Advanced Research Projects
Agency (DARPA) and the U.S. Army Research Office under the SafeWare program. Opinions,
findings and conclusions or recommendations expressed in this material are those
of the author(s) and do not necessarily reflect the views, position or policy of
the Government. The second author was also supported by the European Research Council,
ERC consolidator grant (682815 - TOCNeT).
alternative_title:
- LNCS
article_processing_charge: No
author:
- first_name: Daniele
full_name: Micciancio, Daniele
last_name: Micciancio
- first_name: Michael
full_name: Walter, Michael
id: 488F98B0-F248-11E8-B48F-1D18A9856A87
last_name: Walter
orcid: 0000-0003-3186-2482
citation:
ama: 'Micciancio D, Walter M. On the bit security of cryptographic primitives. In:
Vol 10820. Springer; 2018:3-28. doi:10.1007/978-3-319-78381-9_1'
apa: 'Micciancio, D., & Walter, M. (2018). On the bit security of cryptographic
primitives (Vol. 10820, pp. 3–28). Presented at the Eurocrypt: Advances in Cryptology,
Tel Aviv, Israel: Springer. https://doi.org/10.1007/978-3-319-78381-9_1'
chicago: Micciancio, Daniele, and Michael Walter. “On the Bit Security of Cryptographic
Primitives,” 10820:3–28. Springer, 2018. https://doi.org/10.1007/978-3-319-78381-9_1.
ieee: 'D. Micciancio and M. Walter, “On the bit security of cryptographic primitives,”
presented at the Eurocrypt: Advances in Cryptology, Tel Aviv, Israel, 2018, vol.
10820, pp. 3–28.'
ista: 'Micciancio D, Walter M. 2018. On the bit security of cryptographic primitives.
Eurocrypt: Advances in Cryptology, LNCS, vol. 10820, 3–28.'
mla: Micciancio, Daniele, and Michael Walter. On the Bit Security of Cryptographic
Primitives. Vol. 10820, Springer, 2018, pp. 3–28, doi:10.1007/978-3-319-78381-9_1.
short: D. Micciancio, M. Walter, in:, Springer, 2018, pp. 3–28.
conference:
end_date: 2018-05-03
location: Tel Aviv, Israel
name: 'Eurocrypt: Advances in Cryptology'
start_date: 2018-04-29
date_created: 2018-12-11T11:45:42Z
date_published: 2018-03-31T00:00:00Z
date_updated: 2023-09-13T09:12:04Z
day: '31'
department:
- _id: KrPi
doi: 10.1007/978-3-319-78381-9_1
ec_funded: 1
external_id:
isi:
- '000517097500001'
intvolume: ' 10820'
isi: 1
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://eprint.iacr.org/2018/077
month: '03'
oa: 1
oa_version: Submitted Version
page: 3 - 28
project:
- _id: 258AA5B2-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '682815'
name: Teaching Old Crypto New Tricks
publication_status: published
publisher: Springer
publist_id: '7581'
quality_controlled: '1'
scopus_import: '1'
status: public
title: On the bit security of cryptographic primitives
type: conference
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
volume: 10820
year: '2018'
...
---
_id: '312'
abstract:
- lang: eng
text: Motivated by biological questions, we study configurations of equal spheres
that neither pack nor cover. Placing their centers on a lattice, we define the
soft density of the configuration by penalizing multiple overlaps. Considering
the 1-parameter family of diagonally distorted 3-dimensional integer lattices,
we show that the soft density is maximized at the FCC lattice.
acknowledgement: This work was partially supported by the DFG Collaborative Research
Center TRR 109, “Discretization in Geometry and Dynamics,” through grant I02979-N35
of the Austrian Science Fund (FWF).
article_processing_charge: No
article_type: original
author:
- first_name: Herbert
full_name: Edelsbrunner, Herbert
id: 3FB178DA-F248-11E8-B48F-1D18A9856A87
last_name: Edelsbrunner
orcid: 0000-0002-9823-6833
- first_name: Mabel
full_name: Iglesias Ham, Mabel
id: 41B58C0C-F248-11E8-B48F-1D18A9856A87
last_name: Iglesias Ham
citation:
ama: Edelsbrunner H, Iglesias Ham M. On the optimality of the FCC lattice for soft
sphere packing. SIAM J Discrete Math. 2018;32(1):750-782. doi:10.1137/16M1097201
apa: Edelsbrunner, H., & Iglesias Ham, M. (2018). On the optimality of the FCC
lattice for soft sphere packing. SIAM J Discrete Math. Society for Industrial
and Applied Mathematics . https://doi.org/10.1137/16M1097201
chicago: Edelsbrunner, Herbert, and Mabel Iglesias Ham. “On the Optimality of the
FCC Lattice for Soft Sphere Packing.” SIAM J Discrete Math. Society for
Industrial and Applied Mathematics , 2018. https://doi.org/10.1137/16M1097201.
ieee: H. Edelsbrunner and M. Iglesias Ham, “On the optimality of the FCC lattice
for soft sphere packing,” SIAM J Discrete Math, vol. 32, no. 1. Society
for Industrial and Applied Mathematics , pp. 750–782, 2018.
ista: Edelsbrunner H, Iglesias Ham M. 2018. On the optimality of the FCC lattice
for soft sphere packing. SIAM J Discrete Math. 32(1), 750–782.
mla: Edelsbrunner, Herbert, and Mabel Iglesias Ham. “On the Optimality of the FCC
Lattice for Soft Sphere Packing.” SIAM J Discrete Math, vol. 32, no. 1,
Society for Industrial and Applied Mathematics , 2018, pp. 750–82, doi:10.1137/16M1097201.
short: H. Edelsbrunner, M. Iglesias Ham, SIAM J Discrete Math 32 (2018) 750–782.
date_created: 2018-12-11T11:45:46Z
date_published: 2018-03-29T00:00:00Z
date_updated: 2023-09-13T09:34:38Z
day: '29'
department:
- _id: HeEd
doi: 10.1137/16M1097201
external_id:
isi:
- '000428958900038'
intvolume: ' 32'
isi: 1
issue: '1'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: http://pdfs.semanticscholar.org/d2d5/6da00fbc674e6a8b1bb9d857167e54200dc6.pdf
month: '03'
oa: 1
oa_version: Submitted Version
page: 750 - 782
project:
- _id: 2561EBF4-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: I02979-N35
name: Persistence and stability of geometric complexes
publication: SIAM J Discrete Math
publication_identifier:
issn:
- '08954801'
publication_status: published
publisher: 'Society for Industrial and Applied Mathematics '
publist_id: '7553'
quality_controlled: '1'
scopus_import: '1'
status: public
title: On the optimality of the FCC lattice for soft sphere packing
type: journal_article
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
volume: 32
year: '2018'
...
---
_id: '409'
abstract:
- lang: eng
text: We give a simple proof of T. Stehling's result [4], whereby in any normal
tiling of the plane with convex polygons with number of sides not less than six,
all tiles except a finite number are hexagons.
article_processing_charge: No
article_type: original
author:
- first_name: Arseniy
full_name: Akopyan, Arseniy
id: 430D2C90-F248-11E8-B48F-1D18A9856A87
last_name: Akopyan
orcid: 0000-0002-2548-617X
citation:
ama: Akopyan A. On the number of non-hexagons in a planar tiling. Comptes Rendus
Mathematique. 2018;356(4):412-414. doi:10.1016/j.crma.2018.03.005
apa: Akopyan, A. (2018). On the number of non-hexagons in a planar tiling. Comptes
Rendus Mathematique. Elsevier. https://doi.org/10.1016/j.crma.2018.03.005
chicago: Akopyan, Arseniy. “On the Number of Non-Hexagons in a Planar Tiling.” Comptes
Rendus Mathematique. Elsevier, 2018. https://doi.org/10.1016/j.crma.2018.03.005.
ieee: A. Akopyan, “On the number of non-hexagons in a planar tiling,” Comptes
Rendus Mathematique, vol. 356, no. 4. Elsevier, pp. 412–414, 2018.
ista: Akopyan A. 2018. On the number of non-hexagons in a planar tiling. Comptes
Rendus Mathematique. 356(4), 412–414.
mla: Akopyan, Arseniy. “On the Number of Non-Hexagons in a Planar Tiling.” Comptes
Rendus Mathematique, vol. 356, no. 4, Elsevier, 2018, pp. 412–14, doi:10.1016/j.crma.2018.03.005.
short: A. Akopyan, Comptes Rendus Mathematique 356 (2018) 412–414.
date_created: 2018-12-11T11:46:19Z
date_published: 2018-04-01T00:00:00Z
date_updated: 2023-09-13T09:34:12Z
day: '01'
department:
- _id: HeEd
doi: 10.1016/j.crma.2018.03.005
external_id:
arxiv:
- '1805.01652'
isi:
- '000430402700009'
intvolume: ' 356'
isi: 1
issue: '4'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/1805.01652
month: '04'
oa: 1
oa_version: Preprint
page: 412-414
publication: Comptes Rendus Mathematique
publication_identifier:
issn:
- 1631073X
publication_status: published
publisher: Elsevier
publist_id: '7420'
quality_controlled: '1'
scopus_import: '1'
status: public
title: On the number of non-hexagons in a planar tiling
type: journal_article
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
volume: 356
year: '2018'
...
---
_id: '419'
abstract:
- lang: eng
text: 'Reciprocity is a major factor in human social life and accounts for a large
part of cooperation in our communities. Direct reciprocity arises when repeated
interactions occur between the same individuals. The framework of iterated games
formalizes this phenomenon. Despite being introduced more than five decades ago,
the concept keeps offering beautiful surprises. Recent theoretical research driven
by new mathematical tools has proposed a remarkable dichotomy among the crucial
strategies: successful individuals either act as partners or as rivals. Rivals
strive for unilateral advantages by applying selfish or extortionate strategies.
Partners aim to share the payoff for mutual cooperation, but are ready to fight
back when being exploited. Which of these behaviours evolves depends on the environment.
Whereas small population sizes and a limited number of rounds favour rivalry,
partner strategies are selected when populations are large and relationships stable.
Only partners allow for evolution of cooperation, while the rivals’ attempt to
put themselves first leads to defection. Hilbe et al. synthesize recent theoretical
work on zero-determinant and ‘rival’ versus ‘partner’ strategies in social dilemmas.
They describe the environments under which these contrasting selfish or cooperative
strategies emerge in evolution.'
article_processing_charge: No
article_type: review
author:
- first_name: Christian
full_name: Hilbe, Christian
id: 2FDF8F3C-F248-11E8-B48F-1D18A9856A87
last_name: Hilbe
orcid: 0000-0001-5116-955X
- first_name: Krishnendu
full_name: Chatterjee, Krishnendu
id: 2E5DCA20-F248-11E8-B48F-1D18A9856A87
last_name: Chatterjee
orcid: 0000-0002-4561-241X
- first_name: Martin
full_name: Nowak, Martin
last_name: Nowak
citation:
ama: Hilbe C, Chatterjee K, Nowak M. Partners and rivals in direct reciprocity.
Nature Human Behaviour. 2018;2:469–477. doi:10.1038/s41562-018-0320-9
apa: Hilbe, C., Chatterjee, K., & Nowak, M. (2018). Partners and rivals in direct
reciprocity. Nature Human Behaviour. Nature Publishing Group. https://doi.org/10.1038/s41562-018-0320-9
chicago: Hilbe, Christian, Krishnendu Chatterjee, and Martin Nowak. “Partners and
Rivals in Direct Reciprocity.” Nature Human Behaviour. Nature Publishing
Group, 2018. https://doi.org/10.1038/s41562-018-0320-9.
ieee: C. Hilbe, K. Chatterjee, and M. Nowak, “Partners and rivals in direct reciprocity,”
Nature Human Behaviour, vol. 2. Nature Publishing Group, pp. 469–477, 2018.
ista: Hilbe C, Chatterjee K, Nowak M. 2018. Partners and rivals in direct reciprocity.
Nature Human Behaviour. 2, 469–477.
mla: Hilbe, Christian, et al. “Partners and Rivals in Direct Reciprocity.” Nature
Human Behaviour, vol. 2, Nature Publishing Group, 2018, pp. 469–477, doi:10.1038/s41562-018-0320-9.
short: C. Hilbe, K. Chatterjee, M. Nowak, Nature Human Behaviour 2 (2018) 469–477.
date_created: 2018-12-11T11:46:22Z
date_published: 2018-03-19T00:00:00Z
date_updated: 2023-09-13T09:38:54Z
day: '19'
ddc:
- '000'
department:
- _id: KrCh
doi: 10.1038/s41562-018-0320-9
ec_funded: 1
external_id:
isi:
- '000446612000016'
file:
- access_level: open_access
checksum: 571b8cc0ba14e8d5d8b18e439a9835eb
content_type: application/pdf
creator: dernst
date_created: 2019-11-19T08:19:51Z
date_updated: 2020-07-14T12:46:25Z
file_id: '7052'
file_name: 2018_NatureHumanBeh_Hilbe.pdf
file_size: 598033
relation: main_file
file_date_updated: 2020-07-14T12:46:25Z
has_accepted_license: '1'
intvolume: ' 2'
isi: 1
language:
- iso: eng
month: '03'
oa: 1
oa_version: Submitted Version
page: 469–477
project:
- _id: 2581B60A-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '279307'
name: 'Quantitative Graph Games: Theory and Applications'
- _id: 2584A770-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: P 23499-N23
name: Modern Graph Algorithmic Techniques in Formal Verification
- _id: 25832EC2-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: S 11407_N23
name: Rigorous Systems Engineering
- _id: 25681D80-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '291734'
name: International IST Postdoc Fellowship Programme
publication: Nature Human Behaviour
publication_status: published
publisher: Nature Publishing Group
publist_id: '7404'
quality_controlled: '1'
related_material:
link:
- relation: erratum
url: http://doi.org/10.1038/s41562-018-0342-3
scopus_import: '1'
status: public
title: Partners and rivals in direct reciprocity
type: journal_article
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
volume: 2
year: '2018'
...
---
_id: '78'
abstract:
- lang: eng
text: We provide a procedure for detecting the sub-segments of an incrementally
observed Boolean signal ω that match a given temporal pattern ϕ. As a pattern
specification language, we use timed regular expressions, a formalism well-suited
for expressing properties of concurrent asynchronous behaviors embedded in metric
time. We construct a timed automaton accepting the timed language denoted by ϕ
and modify it slightly for the purpose of matching. We then apply zone-based reachability
computation to this automaton while it reads ω, and retrieve all the matching
segments from the results. Since the procedure is automaton based, it can be applied
to patterns specified by other formalisms such as timed temporal logics reducible
to timed automata or directly encoded as timed automata. The procedure has been
implemented and its performance on synthetic examples is demonstrated.
alternative_title:
- LNCS
article_processing_charge: No
author:
- first_name: Alexey
full_name: Bakhirkin, Alexey
last_name: Bakhirkin
- first_name: Thomas
full_name: Ferrere, Thomas
id: 40960E6E-F248-11E8-B48F-1D18A9856A87
last_name: Ferrere
orcid: 0000-0001-5199-3143
- first_name: Dejan
full_name: Nickovic, Dejan
last_name: Nickovic
- first_name: Oded
full_name: Maler, Oded
last_name: Maler
- first_name: Eugene
full_name: Asarin, Eugene
last_name: Asarin
citation:
ama: 'Bakhirkin A, Ferrere T, Nickovic D, Maler O, Asarin E. Online timed pattern
matching using automata. In: Vol 11022. Springer; 2018:215-232. doi:10.1007/978-3-030-00151-3_13'
apa: 'Bakhirkin, A., Ferrere, T., Nickovic, D., Maler, O., & Asarin, E. (2018).
Online timed pattern matching using automata (Vol. 11022, pp. 215–232). Presented
at the FORMATS: Formal Modeling and Analysis of Timed Systems, Bejing, China:
Springer. https://doi.org/10.1007/978-3-030-00151-3_13'
chicago: Bakhirkin, Alexey, Thomas Ferrere, Dejan Nickovic, Oded Maler, and Eugene
Asarin. “Online Timed Pattern Matching Using Automata,” 11022:215–32. Springer,
2018. https://doi.org/10.1007/978-3-030-00151-3_13.
ieee: 'A. Bakhirkin, T. Ferrere, D. Nickovic, O. Maler, and E. Asarin, “Online timed
pattern matching using automata,” presented at the FORMATS: Formal Modeling and
Analysis of Timed Systems, Bejing, China, 2018, vol. 11022, pp. 215–232.'
ista: 'Bakhirkin A, Ferrere T, Nickovic D, Maler O, Asarin E. 2018. Online timed
pattern matching using automata. FORMATS: Formal Modeling and Analysis of Timed
Systems, LNCS, vol. 11022, 215–232.'
mla: Bakhirkin, Alexey, et al. Online Timed Pattern Matching Using Automata.
Vol. 11022, Springer, 2018, pp. 215–32, doi:10.1007/978-3-030-00151-3_13.
short: A. Bakhirkin, T. Ferrere, D. Nickovic, O. Maler, E. Asarin, in:, Springer,
2018, pp. 215–232.
conference:
end_date: 2018-09-06
location: Bejing, China
name: 'FORMATS: Formal Modeling and Analysis of Timed Systems'
start_date: 2018-09-04
date_created: 2018-12-11T11:44:31Z
date_published: 2018-08-26T00:00:00Z
date_updated: 2023-09-13T09:35:46Z
day: '26'
ddc:
- '000'
department:
- _id: ToHe
doi: 10.1007/978-3-030-00151-3_13
external_id:
isi:
- '000884993200013'
file:
- access_level: open_access
checksum: 436b7574934324cfa7d1d3986fddc65b
content_type: application/pdf
creator: dernst
date_created: 2020-05-14T11:34:34Z
date_updated: 2020-07-14T12:48:03Z
file_id: '7831'
file_name: 2018_LNCS_Bakhirkin.pdf
file_size: 374851
relation: main_file
file_date_updated: 2020-07-14T12:48:03Z
has_accepted_license: '1'
intvolume: ' 11022'
isi: 1
language:
- iso: eng
month: '08'
oa: 1
oa_version: Submitted Version
page: 215 - 232
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_identifier:
isbn:
- 978-3-030-00150-6
publication_status: published
publisher: Springer
publist_id: '7976'
quality_controlled: '1'
scopus_import: '1'
status: public
title: Online timed pattern matching using automata
type: conference
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
volume: 11022
year: '2018'
...
---
_id: '317'
abstract:
- lang: eng
text: We replace the established aluminium gates for the formation of quantum dots
in silicon with gates made from palladium. We study the morphology of both aluminium
and palladium gates with transmission electron microscopy. The native aluminium
oxide is found to be formed all around the aluminium gates, which could lead to
the formation of unintentional dots. Therefore, we report on a novel fabrication
route that replaces aluminium and its native oxide by palladium with atomic-layer-deposition-grown
aluminium oxide. Using this approach, we show the formation of low-disorder gate-defined
quantum dots, which are reproducibly fabricated. Furthermore, palladium enables
us to further shrink the gate design, allowing us to perform electron transport
measurements in the few-electron regime in devices comprising only two gate layers,
a major technological advancement. It remains to be seen, whether the introduction
of palladium gates can improve the excellent results on electron and nuclear spin
qubits defined with an aluminium gate stack.
article_number: '5690'
article_processing_charge: No
author:
- first_name: Matthias
full_name: Brauns, Matthias
id: 33F94E3C-F248-11E8-B48F-1D18A9856A87
last_name: Brauns
- first_name: Sergey
full_name: Amitonov, Sergey
last_name: Amitonov
- first_name: Paul
full_name: Spruijtenburg, Paul
last_name: Spruijtenburg
- first_name: Floris
full_name: Zwanenburg, Floris
last_name: Zwanenburg
citation:
ama: Brauns M, Amitonov S, Spruijtenburg P, Zwanenburg F. Palladium gates for reproducible
quantum dots in silicon. Scientific Reports. 2018;8(1). doi:10.1038/s41598-018-24004-y
apa: Brauns, M., Amitonov, S., Spruijtenburg, P., & Zwanenburg, F. (2018). Palladium
gates for reproducible quantum dots in silicon. Scientific Reports. Nature
Publishing Group. https://doi.org/10.1038/s41598-018-24004-y
chicago: Brauns, Matthias, Sergey Amitonov, Paul Spruijtenburg, and Floris Zwanenburg.
“Palladium Gates for Reproducible Quantum Dots in Silicon.” Scientific Reports.
Nature Publishing Group, 2018. https://doi.org/10.1038/s41598-018-24004-y.
ieee: M. Brauns, S. Amitonov, P. Spruijtenburg, and F. Zwanenburg, “Palladium gates
for reproducible quantum dots in silicon,” Scientific Reports, vol. 8,
no. 1. Nature Publishing Group, 2018.
ista: Brauns M, Amitonov S, Spruijtenburg P, Zwanenburg F. 2018. Palladium gates
for reproducible quantum dots in silicon. Scientific Reports. 8(1), 5690.
mla: Brauns, Matthias, et al. “Palladium Gates for Reproducible Quantum Dots in
Silicon.” Scientific Reports, vol. 8, no. 1, 5690, Nature Publishing Group,
2018, doi:10.1038/s41598-018-24004-y.
short: M. Brauns, S. Amitonov, P. Spruijtenburg, F. Zwanenburg, Scientific Reports
8 (2018).
date_created: 2018-12-11T11:45:47Z
date_published: 2018-04-09T00:00:00Z
date_updated: 2023-09-13T09:38:00Z
day: '09'
ddc:
- '539'
department:
- _id: GeKa
doi: 10.1038/s41598-018-24004-y
external_id:
isi:
- '000429404300013'
file:
- access_level: open_access
checksum: 20af238ca4ba6491b77270be8d826bf5
content_type: application/pdf
creator: system
date_created: 2018-12-12T10:17:04Z
date_updated: 2020-07-14T12:46:02Z
file_id: '5256'
file_name: IST-2018-1016-v1+1_2018_Brauns_Palladium_gates.pdf
file_size: 1850530
relation: main_file
file_date_updated: 2020-07-14T12:46:02Z
has_accepted_license: '1'
intvolume: ' 8'
isi: 1
issue: '1'
language:
- iso: eng
month: '04'
oa: 1
oa_version: Published Version
publication: Scientific Reports
publication_status: published
publisher: Nature Publishing Group
publist_id: '7548'
pubrep_id: '1016'
quality_controlled: '1'
scopus_import: '1'
status: public
title: Palladium gates for reproducible quantum dots in silicon
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: journal_article
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
volume: 8
year: '2018'
...
---
_id: '194'
abstract:
- lang: eng
text: Ants are emerging model systems to study cellular signaling because distinct
castes possess different physiologic phenotypes within the same colony. Here we
studied the functionality of inotocin signaling, an insect ortholog of mammalian
oxytocin (OT), which was recently discovered in ants. In Lasius ants, we determined
that specialization within the colony, seasonal factors, and physiologic conditions
down-regulated the expression of the OT-like signaling system. Given this natural
variation, we interrogated its function using RNAi knockdowns. Next-generation
RNA sequencing of OT-like precursor knock-down ants highlighted its role in the
regulation of genes involved in metabolism. Knock-down ants exhibited higher walking
activity and increased self-grooming in the brood chamber. We propose that OT-like
signaling in ants is important for regulating metabolic processes and locomotion.
article_processing_charge: No
article_type: original
author:
- first_name: Zita
full_name: Liutkeviciute, Zita
last_name: Liutkeviciute
- first_name: Esther
full_name: Gil Mansilla, Esther
last_name: Gil Mansilla
- first_name: Thomas
full_name: Eder, Thomas
last_name: Eder
- first_name: Barbara E
full_name: Casillas Perez, Barbara E
id: 351ED2AA-F248-11E8-B48F-1D18A9856A87
last_name: Casillas Perez
- first_name: Maria
full_name: Giulia Di Giglio, Maria
last_name: Giulia Di Giglio
- first_name: Edin
full_name: Muratspahić, Edin
last_name: Muratspahić
- first_name: Florian
full_name: Grebien, Florian
last_name: Grebien
- first_name: Thomas
full_name: Rattei, Thomas
last_name: Rattei
- first_name: Markus
full_name: Muttenthaler, Markus
last_name: Muttenthaler
- first_name: Sylvia
full_name: Cremer, Sylvia
id: 2F64EC8C-F248-11E8-B48F-1D18A9856A87
last_name: Cremer
orcid: 0000-0002-2193-3868
- first_name: Christian
full_name: Gruber, Christian
last_name: Gruber
citation:
ama: Liutkeviciute Z, Gil Mansilla E, Eder T, et al. Oxytocin-like signaling in
ants influences metabolic gene expression and locomotor activity. The FASEB
Journal. 2018;32(12):6808-6821. doi:10.1096/fj.201800443
apa: Liutkeviciute, Z., Gil Mansilla, E., Eder, T., Casillas Perez, B. E., Giulia
Di Giglio, M., Muratspahić, E., … Gruber, C. (2018). Oxytocin-like signaling in
ants influences metabolic gene expression and locomotor activity. The FASEB
Journal. FASEB. https://doi.org/10.1096/fj.201800443
chicago: Liutkeviciute, Zita, Esther Gil Mansilla, Thomas Eder, Barbara E Casillas
Perez, Maria Giulia Di Giglio, Edin Muratspahić, Florian Grebien, et al. “Oxytocin-like
Signaling in Ants Influences Metabolic Gene Expression and Locomotor Activity.”
The FASEB Journal. FASEB, 2018. https://doi.org/10.1096/fj.201800443.
ieee: Z. Liutkeviciute et al., “Oxytocin-like signaling in ants influences
metabolic gene expression and locomotor activity,” The FASEB Journal, vol.
32, no. 12. FASEB, pp. 6808–6821, 2018.
ista: Liutkeviciute Z, Gil Mansilla E, Eder T, Casillas Perez BE, Giulia Di Giglio
M, Muratspahić E, Grebien F, Rattei T, Muttenthaler M, Cremer S, Gruber C. 2018.
Oxytocin-like signaling in ants influences metabolic gene expression and locomotor
activity. The FASEB Journal. 32(12), 6808–6821.
mla: Liutkeviciute, Zita, et al. “Oxytocin-like Signaling in Ants Influences Metabolic
Gene Expression and Locomotor Activity.” The FASEB Journal, vol. 32, no.
12, FASEB, 2018, pp. 6808–21, doi:10.1096/fj.201800443.
short: Z. Liutkeviciute, E. Gil Mansilla, T. Eder, B.E. Casillas Perez, M. Giulia
Di Giglio, E. Muratspahić, F. Grebien, T. Rattei, M. Muttenthaler, S. Cremer,
C. Gruber, The FASEB Journal 32 (2018) 6808–6821.
date_created: 2018-12-11T11:45:08Z
date_published: 2018-11-29T00:00:00Z
date_updated: 2023-09-13T09:37:32Z
day: '29'
department:
- _id: SyCr
doi: 10.1096/fj.201800443
external_id:
isi:
- '000449359700035'
pmid:
- '29939785'
intvolume: ' 32'
isi: 1
issue: '12'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: ' https://doi.org/10.1096/fj.201800443'
month: '11'
oa: 1
oa_version: Published Version
page: 6808-6821
pmid: 1
project:
- _id: 25E3D34E-B435-11E9-9278-68D0E5697425
name: Individual function and social role of oxytocin-like neuropeptides in ants
publication: The FASEB Journal
publication_identifier:
issn:
- '08926638'
publication_status: published
publisher: FASEB
publist_id: '7721'
quality_controlled: '1'
scopus_import: '1'
status: public
title: Oxytocin-like signaling in ants influences metabolic gene expression and locomotor
activity
type: journal_article
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
volume: 32
year: '2018'
...
---
_id: '159'
abstract:
- lang: eng
text: L-type Ca2+ channels (LTCCs) play a crucial role in excitation-contraction
coupling and release of hormones from secretory cells. They are targets of antihypertensive
and antiarrhythmic drugs such as diltiazem. Here, we present a photoswitchable
diltiazem, FHU-779, which can be used to reversibly block endogenous LTCCs by
light. FHU-779 is as potent as diltiazem and can be used to place pancreatic β-cell
function and cardiac activity under optical control.
article_processing_charge: No
article_type: original
author:
- first_name: Timm
full_name: Fehrentz, Timm
last_name: Fehrentz
- first_name: Florian
full_name: Huber, Florian
last_name: Huber
- first_name: Nina
full_name: Hartrampf, Nina
last_name: Hartrampf
- first_name: Tobias
full_name: Bruegmann, Tobias
last_name: Bruegmann
- first_name: James
full_name: Frank, James
last_name: Frank
- first_name: Nicholas
full_name: Fine, Nicholas
last_name: Fine
- first_name: Daniela
full_name: Malan, Daniela
last_name: Malan
- first_name: Johann G
full_name: Danzl, Johann G
id: 42EFD3B6-F248-11E8-B48F-1D18A9856A87
last_name: Danzl
orcid: 0000-0001-8559-3973
- first_name: Denis
full_name: Tikhonov, Denis
last_name: Tikhonov
- first_name: Maritn
full_name: Sumser, Maritn
last_name: Sumser
- first_name: Philipp
full_name: Sasse, Philipp
last_name: Sasse
- first_name: David
full_name: Hodson, David
last_name: Hodson
- first_name: Boris
full_name: Zhorov, Boris
last_name: Zhorov
- first_name: Nikolaj
full_name: Klocker, Nikolaj
last_name: Klocker
- first_name: Dirk
full_name: Trauner, Dirk
last_name: Trauner
citation:
ama: Fehrentz T, Huber F, Hartrampf N, et al. Optical control of L-type Ca2+ channels
using a diltiazem photoswitch. Nature Chemical Biology. 2018;14(8):764-767.
doi:10.1038/s41589-018-0090-8
apa: Fehrentz, T., Huber, F., Hartrampf, N., Bruegmann, T., Frank, J., Fine, N.,
… Trauner, D. (2018). Optical control of L-type Ca2+ channels using a diltiazem
photoswitch. Nature Chemical Biology. Nature Publishing Group. https://doi.org/10.1038/s41589-018-0090-8
chicago: Fehrentz, Timm, Florian Huber, Nina Hartrampf, Tobias Bruegmann, James
Frank, Nicholas Fine, Daniela Malan, et al. “Optical Control of L-Type Ca2+ Channels
Using a Diltiazem Photoswitch.” Nature Chemical Biology. Nature Publishing
Group, 2018. https://doi.org/10.1038/s41589-018-0090-8.
ieee: T. Fehrentz et al., “Optical control of L-type Ca2+ channels using
a diltiazem photoswitch,” Nature Chemical Biology, vol. 14, no. 8. Nature
Publishing Group, pp. 764–767, 2018.
ista: Fehrentz T, Huber F, Hartrampf N, Bruegmann T, Frank J, Fine N, Malan D, Danzl
JG, Tikhonov D, Sumser M, Sasse P, Hodson D, Zhorov B, Klocker N, Trauner D. 2018.
Optical control of L-type Ca2+ channels using a diltiazem photoswitch. Nature
Chemical Biology. 14(8), 764–767.
mla: Fehrentz, Timm, et al. “Optical Control of L-Type Ca2+ Channels Using a Diltiazem
Photoswitch.” Nature Chemical Biology, vol. 14, no. 8, Nature Publishing
Group, 2018, pp. 764–67, doi:10.1038/s41589-018-0090-8.
short: T. Fehrentz, F. Huber, N. Hartrampf, T. Bruegmann, J. Frank, N. Fine, D.
Malan, J.G. Danzl, D. Tikhonov, M. Sumser, P. Sasse, D. Hodson, B. Zhorov, N.
Klocker, D. Trauner, Nature Chemical Biology 14 (2018) 764–767.
date_created: 2018-12-11T11:44:56Z
date_published: 2018-07-16T00:00:00Z
date_updated: 2023-09-13T09:36:35Z
day: '16'
ddc:
- '570'
department:
- _id: JoDa
doi: 10.1038/s41589-018-0090-8
external_id:
isi:
- '000438970200010'
file:
- access_level: open_access
checksum: d42935094ec845f54a0688bf12986d62
content_type: application/pdf
creator: dernst
date_created: 2020-05-14T12:14:09Z
date_updated: 2020-07-14T12:45:03Z
file_id: '7832'
file_name: 2018_NatureChemicalBiology_Fehrentz.pdf
file_size: 6321000
relation: main_file
file_date_updated: 2020-07-14T12:45:03Z
has_accepted_license: '1'
intvolume: ' 14'
isi: 1
issue: '8'
language:
- iso: eng
month: '07'
oa: 1
oa_version: Submitted Version
page: 764 - 767
publication: Nature Chemical Biology
publication_status: published
publisher: Nature Publishing Group
publist_id: '7762'
quality_controlled: '1'
related_material:
link:
- relation: erratum
url: https://doi.org/10.1038/s41589-021-00744-3
scopus_import: '1'
status: public
title: Optical control of L-type Ca2+ channels using a diltiazem photoswitch
type: journal_article
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
volume: 14
year: '2018'
...
---
_id: '79'
abstract:
- lang: eng
text: 'Markov Decision Processes (MDPs) are a popular class of models suitable for
solving control decision problems in probabilistic reactive systems. We consider
parametric MDPs (pMDPs) that include parameters in some of the transition probabilities
to account for stochastic uncertainties of the environment such as noise or input
disturbances. We study pMDPs with reachability objectives where the parameter
values are unknown and impossible to measure directly during execution, but there
is a probability distribution known over the parameter values. We study for the
first time computing parameter-independent strategies that are expectation optimal,
i.e., optimize the expected reachability probability under the probability distribution
over the parameters. We present an encoding of our problem to partially observable
MDPs (POMDPs), i.e., a reduction of our problem to computing optimal strategies
in POMDPs. We evaluate our method experimentally on several benchmarks: a motivating
(repeated) learner model; a series of benchmarks of varying configurations of
a robot moving on a grid; and a consensus protocol.'
alternative_title:
- LNCS
article_processing_charge: No
author:
- first_name: Sebastian
full_name: Arming, Sebastian
last_name: Arming
- first_name: Ezio
full_name: Bartocci, Ezio
last_name: Bartocci
- first_name: Krishnendu
full_name: Chatterjee, Krishnendu
id: 2E5DCA20-F248-11E8-B48F-1D18A9856A87
last_name: Chatterjee
orcid: 0000-0002-4561-241X
- first_name: Joost P
full_name: Katoen, Joost P
id: 4524F760-F248-11E8-B48F-1D18A9856A87
last_name: Katoen
- first_name: Ana
full_name: Sokolova, Ana
last_name: Sokolova
citation:
ama: 'Arming S, Bartocci E, Chatterjee K, Katoen JP, Sokolova A. Parameter-independent
strategies for pMDPs via POMDPs. In: Vol 11024. Springer; 2018:53-70. doi:10.1007/978-3-319-99154-2_4'
apa: 'Arming, S., Bartocci, E., Chatterjee, K., Katoen, J. P., & Sokolova, A.
(2018). Parameter-independent strategies for pMDPs via POMDPs (Vol. 11024, pp.
53–70). Presented at the QEST: Quantitative Evaluation of Systems, Beijing, China:
Springer. https://doi.org/10.1007/978-3-319-99154-2_4'
chicago: Arming, Sebastian, Ezio Bartocci, Krishnendu Chatterjee, Joost P Katoen,
and Ana Sokolova. “Parameter-Independent Strategies for PMDPs via POMDPs,” 11024:53–70.
Springer, 2018. https://doi.org/10.1007/978-3-319-99154-2_4.
ieee: 'S. Arming, E. Bartocci, K. Chatterjee, J. P. Katoen, and A. Sokolova, “Parameter-independent
strategies for pMDPs via POMDPs,” presented at the QEST: Quantitative Evaluation
of Systems, Beijing, China, 2018, vol. 11024, pp. 53–70.'
ista: 'Arming S, Bartocci E, Chatterjee K, Katoen JP, Sokolova A. 2018. Parameter-independent
strategies for pMDPs via POMDPs. QEST: Quantitative Evaluation of Systems, LNCS,
vol. 11024, 53–70.'
mla: Arming, Sebastian, et al. Parameter-Independent Strategies for PMDPs via
POMDPs. Vol. 11024, Springer, 2018, pp. 53–70, doi:10.1007/978-3-319-99154-2_4.
short: S. Arming, E. Bartocci, K. Chatterjee, J.P. Katoen, A. Sokolova, in:, Springer,
2018, pp. 53–70.
conference:
end_date: 2018-09-07
location: Beijing, China
name: 'QEST: Quantitative Evaluation of Systems'
start_date: 2018-09-04
date_created: 2018-12-11T11:44:31Z
date_published: 2018-08-15T00:00:00Z
date_updated: 2023-09-13T09:38:28Z
day: '15'
department:
- _id: KrCh
- _id: ToHe
doi: 10.1007/978-3-319-99154-2_4
external_id:
arxiv:
- '1806.05126'
isi:
- '000548912200004'
intvolume: ' 11024'
isi: 1
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/1806.05126
month: '08'
oa: 1
oa_version: Preprint
page: 53-70
publication_status: published
publisher: Springer
publist_id: '7975'
quality_controlled: '1'
scopus_import: '1'
status: public
title: Parameter-independent strategies for pMDPs via POMDPs
type: conference
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
volume: 11024
year: '2018'
...
---
_id: '14327'
abstract:
- lang: eng
text: "A common assumption in causal modeling posits that the data is generated
by a\r\nset of independent mechanisms, and algorithms should aim to recover this\r\nstructure.
Standard unsupervised learning, however, is often concerned with\r\ntraining a
single model to capture the overall distribution or aspects thereof.\r\nInspired
by clustering approaches, we consider mixtures of implicit generative\r\nmodels
that ``disentangle'' the independent generative mechanisms underlying\r\nthe data.
Relying on an additional set of discriminators, we propose a\r\ncompetitive training
procedure in which the models only need to capture the\r\nportion of the data
distribution from which they can produce realistic samples.\r\nAs a by-product,
each model is simpler and faster to train. We empirically show\r\nthat our approach
splits the training distribution in a sensible way and\r\nincreases the quality
of the generated samples."
article_number: '1804.11130'
article_processing_charge: No
author:
- first_name: Francesco
full_name: Locatello, Francesco
id: 26cfd52f-2483-11ee-8040-88983bcc06d4
last_name: Locatello
orcid: 0000-0002-4850-0683
- first_name: Damien
full_name: Vincent, Damien
last_name: Vincent
- first_name: Ilya
full_name: Tolstikhin, Ilya
last_name: Tolstikhin
- first_name: Gunnar
full_name: Rätsch, Gunnar
last_name: Rätsch
- first_name: Sylvain
full_name: Gelly, Sylvain
last_name: Gelly
- first_name: Bernhard
full_name: Schölkopf, Bernhard
last_name: Schölkopf
citation:
ama: Locatello F, Vincent D, Tolstikhin I, Rätsch G, Gelly S, Schölkopf B. Competitive
training of mixtures of independent deep generative models. arXiv. doi:10.48550/arXiv.1804.11130
apa: Locatello, F., Vincent, D., Tolstikhin, I., Rätsch, G., Gelly, S., & Schölkopf,
B. (n.d.). Competitive training of mixtures of independent deep generative models.
arXiv. https://doi.org/10.48550/arXiv.1804.11130
chicago: Locatello, Francesco, Damien Vincent, Ilya Tolstikhin, Gunnar Rätsch, Sylvain
Gelly, and Bernhard Schölkopf. “Competitive Training of Mixtures of Independent
Deep Generative Models.” ArXiv, n.d. https://doi.org/10.48550/arXiv.1804.11130.
ieee: F. Locatello, D. Vincent, I. Tolstikhin, G. Rätsch, S. Gelly, and B. Schölkopf,
“Competitive training of mixtures of independent deep generative models,” arXiv.
.
ista: Locatello F, Vincent D, Tolstikhin I, Rätsch G, Gelly S, Schölkopf B. Competitive
training of mixtures of independent deep generative models. arXiv, 1804.11130.
mla: Locatello, Francesco, et al. “Competitive Training of Mixtures of Independent
Deep Generative Models.” ArXiv, 1804.11130, doi:10.48550/arXiv.1804.11130.
short: F. Locatello, D. Vincent, I. Tolstikhin, G. Rätsch, S. Gelly, B. Schölkopf,
ArXiv (n.d.).
date_created: 2023-09-13T12:20:49Z
date_published: 2018-04-30T00:00:00Z
date_updated: 2023-09-13T12:23:03Z
day: '30'
department:
- _id: FrLo
doi: 10.48550/arXiv.1804.11130
extern: '1'
external_id:
arxiv:
- '1804.11130'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.48550/arXiv.1804.11130
month: '04'
oa: 1
oa_version: Preprint
publication: arXiv
publication_status: submitted
status: public
title: Competitive training of mixtures of independent deep generative models
type: preprint
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
year: '2018'
...
---
_id: '400'
abstract:
- lang: eng
text: We consider the two-dimensional BCS functional with a radial pair interaction.
We show that the translational symmetry is not broken in a certain temperature
interval below the critical temperature. In the case of vanishing angular momentum,
our results carry over to the three-dimensional case.
article_processing_charge: Yes (via OA deal)
author:
- first_name: Andreas
full_name: Deuchert, Andreas
id: 4DA65CD0-F248-11E8-B48F-1D18A9856A87
last_name: Deuchert
orcid: 0000-0003-3146-6746
- first_name: Alissa
full_name: Geisinge, Alissa
last_name: Geisinge
- first_name: Christian
full_name: Hainzl, Christian
last_name: Hainzl
- first_name: Michael
full_name: Loss, Michael
last_name: Loss
citation:
ama: Deuchert A, Geisinge A, Hainzl C, Loss M. Persistence of translational symmetry
in the BCS model with radial pair interaction. Annales Henri Poincare.
2018;19(5):1507-1527. doi:10.1007/s00023-018-0665-7
apa: Deuchert, A., Geisinge, A., Hainzl, C., & Loss, M. (2018). Persistence
of translational symmetry in the BCS model with radial pair interaction. Annales
Henri Poincare. Springer. https://doi.org/10.1007/s00023-018-0665-7
chicago: Deuchert, Andreas, Alissa Geisinge, Christian Hainzl, and Michael Loss.
“Persistence of Translational Symmetry in the BCS Model with Radial Pair Interaction.”
Annales Henri Poincare. Springer, 2018. https://doi.org/10.1007/s00023-018-0665-7.
ieee: A. Deuchert, A. Geisinge, C. Hainzl, and M. Loss, “Persistence of translational
symmetry in the BCS model with radial pair interaction,” Annales Henri Poincare,
vol. 19, no. 5. Springer, pp. 1507–1527, 2018.
ista: Deuchert A, Geisinge A, Hainzl C, Loss M. 2018. Persistence of translational
symmetry in the BCS model with radial pair interaction. Annales Henri Poincare.
19(5), 1507–1527.
mla: Deuchert, Andreas, et al. “Persistence of Translational Symmetry in the BCS
Model with Radial Pair Interaction.” Annales Henri Poincare, vol. 19, no.
5, Springer, 2018, pp. 1507–27, doi:10.1007/s00023-018-0665-7.
short: A. Deuchert, A. Geisinge, C. Hainzl, M. Loss, Annales Henri Poincare 19 (2018)
1507–1527.
date_created: 2018-12-11T11:46:15Z
date_published: 2018-05-01T00:00:00Z
date_updated: 2023-09-15T12:04:15Z
day: '01'
ddc:
- '510'
department:
- _id: RoSe
doi: 10.1007/s00023-018-0665-7
ec_funded: 1
external_id:
isi:
- '000429799900008'
file:
- access_level: open_access
checksum: 04d2c9bd7cbf3ca1d7acaaf4e7dca3e5
content_type: application/pdf
creator: system
date_created: 2018-12-12T10:12:47Z
date_updated: 2020-07-14T12:46:22Z
file_id: '4966'
file_name: IST-2018-1011-v1+1_2018_Deuchert_Persistence.pdf
file_size: 582680
relation: main_file
file_date_updated: 2020-07-14T12:46:22Z
has_accepted_license: '1'
intvolume: ' 19'
isi: 1
issue: '5'
language:
- iso: eng
month: '05'
oa: 1
oa_version: Published Version
page: 1507 - 1527
project:
- _id: 25C6DC12-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '694227'
name: Analysis of quantum many-body systems
- _id: B67AFEDC-15C9-11EA-A837-991A96BB2854
name: IST Austria Open Access Fund
publication: Annales Henri Poincare
publication_status: published
publisher: Springer
publist_id: '7429'
pubrep_id: '1011'
quality_controlled: '1'
scopus_import: '1'
status: public
title: Persistence of translational symmetry in the BCS model with radial pair interaction
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: journal_article
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
volume: 19
year: '2018'
...
---
_id: '406'
abstract:
- lang: eng
text: 'Recent developments in automated tracking allow uninterrupted, high-resolution
recording of animal trajectories, sometimes coupled with the identification of
stereotyped changes of body pose or other behaviors of interest. Analysis and
interpretation of such data represents a challenge: the timing of animal behaviors
may be stochastic and modulated by kinematic variables, by the interaction with
the environment or with the conspecifics within the animal group, and dependent
on internal cognitive or behavioral state of the individual. Existing models for
collective motion typically fail to incorporate the discrete, stochastic, and
internal-state-dependent aspects of behavior, while models focusing on individual
animal behavior typically ignore the spatial aspects of the problem. Here we propose
a probabilistic modeling framework to address this gap. Each animal can switch
stochastically between different behavioral states, with each state resulting
in a possibly different law of motion through space. Switching rates for behavioral
transitions can depend in a very general way, which we seek to identify from data,
on the effects of the environment as well as the interaction between the animals.
We represent the switching dynamics as a Generalized Linear Model and show that:
(i) forward simulation of multiple interacting animals is possible using a variant
of the Gillespie’s Stochastic Simulation Algorithm; (ii) formulated properly,
the maximum likelihood inference of switching rate functions is tractably solvable
by gradient descent; (iii) model selection can be used to identify factors that
modulate behavioral state switching and to appropriately adjust model complexity
to data. To illustrate our framework, we apply it to two synthetic models of animal
motion and to real zebrafish tracking data. '
acknowledgement: This work was supported by the Human Frontier Science Program RGP0065/2012
(GT, ES).
article_processing_charge: Yes
author:
- first_name: Katarína
full_name: Bod’Ová, Katarína
last_name: Bod’Ová
- first_name: Gabriel
full_name: Mitchell, Gabriel
id: 315BCD80-F248-11E8-B48F-1D18A9856A87
last_name: Mitchell
- first_name: Roy
full_name: Harpaz, Roy
last_name: Harpaz
- first_name: Elad
full_name: Schneidman, Elad
last_name: Schneidman
- first_name: Gasper
full_name: Tkacik, Gasper
id: 3D494DCA-F248-11E8-B48F-1D18A9856A87
last_name: Tkacik
orcid: 0000-0002-6699-1455
citation:
ama: Bod’Ová K, Mitchell G, Harpaz R, Schneidman E, Tkačik G. Probabilistic models
of individual and collective animal behavior. PLoS One. 2018;13(3). doi:10.1371/journal.pone.0193049
apa: Bod’Ová, K., Mitchell, G., Harpaz, R., Schneidman, E., & Tkačik, G. (2018).
Probabilistic models of individual and collective animal behavior. PLoS One.
Public Library of Science. https://doi.org/10.1371/journal.pone.0193049
chicago: Bod’Ová, Katarína, Gabriel Mitchell, Roy Harpaz, Elad Schneidman, and Gašper
Tkačik. “Probabilistic Models of Individual and Collective Animal Behavior.” PLoS
One. Public Library of Science, 2018. https://doi.org/10.1371/journal.pone.0193049.
ieee: K. Bod’Ová, G. Mitchell, R. Harpaz, E. Schneidman, and G. Tkačik, “Probabilistic
models of individual and collective animal behavior,” PLoS One, vol. 13,
no. 3. Public Library of Science, 2018.
ista: Bod’Ová K, Mitchell G, Harpaz R, Schneidman E, Tkačik G. 2018. Probabilistic
models of individual and collective animal behavior. PLoS One. 13(3).
mla: Bod’Ová, Katarína, et al. “Probabilistic Models of Individual and Collective
Animal Behavior.” PLoS One, vol. 13, no. 3, Public Library of Science,
2018, doi:10.1371/journal.pone.0193049.
short: K. Bod’Ová, G. Mitchell, R. Harpaz, E. Schneidman, G. Tkačik, PLoS One 13
(2018).
date_created: 2018-12-11T11:46:18Z
date_published: 2018-03-07T00:00:00Z
date_updated: 2023-09-15T12:06:19Z
day: '07'
ddc:
- '530'
- '571'
department:
- _id: GaTk
doi: 10.1371/journal.pone.0193049
external_id:
isi:
- '000426896800032'
file:
- access_level: open_access
checksum: 684229493db75b43e98a46cd922da497
content_type: application/pdf
creator: system
date_created: 2018-12-12T10:15:43Z
date_updated: 2020-07-14T12:46:22Z
file_id: '5165'
file_name: IST-2018-995-v1+1_2018_Bodova_Probabilistic.pdf
file_size: 6887358
relation: main_file
file_date_updated: 2020-07-14T12:46:22Z
has_accepted_license: '1'
intvolume: ' 13'
isi: 1
issue: '3'
language:
- iso: eng
month: '03'
oa: 1
oa_version: Submitted Version
project:
- _id: 255008E4-B435-11E9-9278-68D0E5697425
grant_number: RGP0065/2012
name: Information processing and computation in fish groups
publication: PLoS One
publication_status: published
publisher: Public Library of Science
publist_id: '7423'
pubrep_id: '995'
quality_controlled: '1'
related_material:
record:
- id: '9831'
relation: research_data
status: public
scopus_import: '1'
status: public
title: Probabilistic models of individual and collective animal behavior
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: journal_article
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
volume: 13
year: '2018'
...
---
_id: '457'
abstract:
- lang: eng
text: Temperate bacteriophages integrate in bacterial genomes as prophages and represent
an important source of genetic variation for bacterial evolution, frequently transmitting
fitness-augmenting genes such as toxins responsible for virulence of major pathogens.
However, only a fraction of bacteriophage infections are lysogenic and lead to
prophage acquisition, whereas the majority are lytic and kill the infected bacteria.
Unless able to discriminate lytic from lysogenic infections, mechanisms of immunity
to bacteriophages are expected to act as a double-edged sword and increase the
odds of survival at the cost of depriving bacteria of potentially beneficial prophages.
We show that although restriction-modification systems as mechanisms of innate
immunity prevent both lytic and lysogenic infections indiscriminately in individual
bacteria, they increase the number of prophage-acquiring individuals at the population
level. We find that this counterintuitive result is a consequence of phage-host
population dynamics, in which restriction-modification systems delay infection
onset until bacteria reach densities at which the probability of lysogeny increases.
These results underscore the importance of population-level dynamics as a key
factor modulating costs and benefits of immunity to temperate bacteriophages
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: Moritz
full_name: Lang, Moritz
id: 29E0800A-F248-11E8-B48F-1D18A9856A87
last_name: Lang
- first_name: Dominik
full_name: Refardt, Dominik
last_name: Refardt
- first_name: Bruce
full_name: Levin, Bruce
last_name: Levin
- 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, Lang M, Refardt D, Levin B, Guet CC. Phage-host population dynamics
promotes prophage acquisition in bacteria with innate immunity. Nature Ecology
and Evolution. 2018;2(2):359-366. doi:10.1038/s41559-017-0424-z
apa: Pleska, M., Lang, M., Refardt, D., Levin, B., & Guet, C. C. (2018). Phage-host
population dynamics promotes prophage acquisition in bacteria with innate immunity.
Nature Ecology and Evolution. Springer Nature. https://doi.org/10.1038/s41559-017-0424-z
chicago: Pleska, Maros, Moritz Lang, Dominik Refardt, Bruce Levin, and Calin C Guet.
“Phage-Host Population Dynamics Promotes Prophage Acquisition in Bacteria with
Innate Immunity.” Nature Ecology and Evolution. Springer Nature, 2018.
https://doi.org/10.1038/s41559-017-0424-z.
ieee: M. Pleska, M. Lang, D. Refardt, B. Levin, and C. C. Guet, “Phage-host population
dynamics promotes prophage acquisition in bacteria with innate immunity,” Nature
Ecology and Evolution, vol. 2, no. 2. Springer Nature, pp. 359–366, 2018.
ista: Pleska M, Lang M, Refardt D, Levin B, Guet CC. 2018. Phage-host population
dynamics promotes prophage acquisition in bacteria with innate immunity. Nature
Ecology and Evolution. 2(2), 359–366.
mla: Pleska, Maros, et al. “Phage-Host Population Dynamics Promotes Prophage Acquisition
in Bacteria with Innate Immunity.” Nature Ecology and Evolution, vol. 2,
no. 2, Springer Nature, 2018, pp. 359–66, doi:10.1038/s41559-017-0424-z.
short: M. Pleska, M. Lang, D. Refardt, B. Levin, C.C. Guet, Nature Ecology and Evolution
2 (2018) 359–366.
date_created: 2018-12-11T11:46:35Z
date_published: 2018-02-01T00:00:00Z
date_updated: 2023-09-15T12:04:57Z
day: '01'
department:
- _id: CaGu
- _id: GaTk
doi: 10.1038/s41559-017-0424-z
ec_funded: 1
external_id:
isi:
- '000426516400027'
intvolume: ' 2'
isi: 1
issue: '2'
language:
- iso: eng
month: '02'
oa_version: None
page: 359 - 366
project:
- _id: 25681D80-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '291734'
name: International IST Postdoc Fellowship Programme
- _id: 251BCBEC-B435-11E9-9278-68D0E5697425
grant_number: RGY0079/2011
name: Multi-Level Conflicts in Evolutionary Dynamics of Restriction-Modification
Systems (HFSP Young investigators' grant)
- _id: 251D65D8-B435-11E9-9278-68D0E5697425
grant_number: '24210'
name: Effects of Stochasticity on the Function of Restriction-Modi cation Systems
at the Single-Cell Level (DOC Fellowship)
publication: Nature Ecology and Evolution
publication_status: published
publisher: Springer Nature
publist_id: '7364'
quality_controlled: '1'
related_material:
record:
- id: '202'
relation: dissertation_contains
status: public
scopus_import: '1'
status: public
title: Phage-host population dynamics promotes prophage acquisition in bacteria with
innate immunity
type: journal_article
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
volume: 2
year: '2018'
...
---
_id: '55'
abstract:
- lang: eng
text: Many animals use antimicrobials to prevent or cure disease [1,2]. For example,
some animals will ingest plants with medicinal properties, both prophylactically
to prevent infection and therapeutically to self-medicate when sick. Antimicrobial
substances are also used as topical disinfectants, to prevent infection, protect
offspring and to sanitise their surroundings [1,2]. Social insects (ants, bees,
wasps and termites) build nests in environments with a high abundance and diversity
of pathogenic microorganisms — such as soil and rotting wood — and colonies are
often densely crowded, creating conditions that favour disease outbreaks. Consequently,
social insects have evolved collective disease defences to protect their colonies
from epidemics. These traits can be seen as functionally analogous to the immune
system of individual organisms [3,4]. This ‘social immunity’ utilises antimicrobials
to prevent and eradicate infections, and to keep the brood and nest clean. However,
these antimicrobial compounds can be harmful to the insects themselves, and it
is unknown how colonies prevent collateral damage when using them. Here, we demonstrate
that antimicrobial acids, produced by workers to disinfect the colony, are harmful
to the delicate pupal brood stage, but that the pupae are protected from the acids
by the presence of a silk cocoon. Garden ants spray their nests with an antimicrobial
poison to sanitize contaminated nestmates and brood. Here, Pull et al show that
they also prophylactically sanitise their colonies, and that the silk cocoon serves
as a barrier to protect developing pupae, thus preventing collateral damage during
nest sanitation.
article_processing_charge: No
article_type: original
author:
- first_name: Christopher
full_name: Pull, Christopher
id: 3C7F4840-F248-11E8-B48F-1D18A9856A87
last_name: Pull
orcid: 0000-0003-1122-3982
- first_name: Sina
full_name: Metzler, Sina
id: 48204546-F248-11E8-B48F-1D18A9856A87
last_name: Metzler
orcid: 0000-0002-9547-2494
- first_name: Elisabeth
full_name: Naderlinger, Elisabeth
id: 31757262-F248-11E8-B48F-1D18A9856A87
last_name: Naderlinger
- first_name: Sylvia
full_name: Cremer, Sylvia
id: 2F64EC8C-F248-11E8-B48F-1D18A9856A87
last_name: Cremer
orcid: 0000-0002-2193-3868
citation:
ama: Pull C, Metzler S, Naderlinger E, Cremer S. Protection against the lethal side
effects of social immunity in ants. Current Biology. 2018;28(19):R1139-R1140.
doi:10.1016/j.cub.2018.08.063
apa: Pull, C., Metzler, S., Naderlinger, E., & Cremer, S. (2018). Protection
against the lethal side effects of social immunity in ants. Current Biology.
Cell Press. https://doi.org/10.1016/j.cub.2018.08.063
chicago: Pull, Christopher, Sina Metzler, Elisabeth Naderlinger, and Sylvia Cremer.
“Protection against the Lethal Side Effects of Social Immunity in Ants.” Current
Biology. Cell Press, 2018. https://doi.org/10.1016/j.cub.2018.08.063.
ieee: C. Pull, S. Metzler, E. Naderlinger, and S. Cremer, “Protection against the
lethal side effects of social immunity in ants,” Current Biology, vol.
28, no. 19. Cell Press, pp. R1139–R1140, 2018.
ista: Pull C, Metzler S, Naderlinger E, Cremer S. 2018. Protection against the lethal
side effects of social immunity in ants. Current Biology. 28(19), R1139–R1140.
mla: Pull, Christopher, et al. “Protection against the Lethal Side Effects of Social
Immunity in Ants.” Current Biology, vol. 28, no. 19, Cell Press, 2018,
pp. R1139–40, doi:10.1016/j.cub.2018.08.063.
short: C. Pull, S. Metzler, E. Naderlinger, S. Cremer, Current Biology 28 (2018)
R1139–R1140.
date_created: 2018-12-11T11:44:23Z
date_published: 2018-10-08T00:00:00Z
date_updated: 2023-09-15T12:06:46Z
day: '08'
department:
- _id: SyCr
doi: 10.1016/j.cub.2018.08.063
external_id:
isi:
- '000446693400008'
intvolume: ' 28'
isi: 1
issue: '19'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.1016/j.cub.2018.08.063
month: '10'
oa: 1
oa_version: Published Version
page: R1139 - R1140
publication: Current Biology
publication_status: published
publisher: Cell Press
publist_id: '7999'
quality_controlled: '1'
scopus_import: '1'
status: public
title: Protection against the lethal side effects of social immunity in ants
type: journal_article
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
volume: 28
year: '2018'
...
---
_id: '181'
abstract:
- lang: eng
text: We consider large random matrices X with centered, independent entries but
possibly di erent variances. We compute the normalized trace of f(X)g(X∗) for
f, g functions analytic on the spectrum of X. We use these results to compute
the long time asymptotics for systems of coupled di erential equations with random
coe cients. We show that when the coupling is critical, the norm squared of the
solution decays like t−1/2.
acknowledgement: The work of the second author was also partially supported by the
Hausdorff Center of Mathematics.
article_processing_charge: No
author:
- first_name: László
full_name: Erdös, László
id: 4DBD5372-F248-11E8-B48F-1D18A9856A87
last_name: Erdös
orcid: 0000-0001-5366-9603
- 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: David T
full_name: Renfrew, David T
id: 4845BF6A-F248-11E8-B48F-1D18A9856A87
last_name: Renfrew
orcid: 0000-0003-3493-121X
citation:
ama: Erdös L, Krüger TH, Renfrew DT. Power law decay for systems of randomly coupled
differential equations. SIAM Journal on Mathematical Analysis. 2018;50(3):3271-3290.
doi:10.1137/17M1143125
apa: Erdös, L., Krüger, T. H., & Renfrew, D. T. (2018). Power law decay for
systems of randomly coupled differential equations. SIAM Journal on Mathematical
Analysis. Society for Industrial and Applied Mathematics . https://doi.org/10.1137/17M1143125
chicago: Erdös, László, Torben H Krüger, and David T Renfrew. “Power Law Decay for
Systems of Randomly Coupled Differential Equations.” SIAM Journal on Mathematical
Analysis. Society for Industrial and Applied Mathematics , 2018. https://doi.org/10.1137/17M1143125.
ieee: L. Erdös, T. H. Krüger, and D. T. Renfrew, “Power law decay for systems of
randomly coupled differential equations,” SIAM Journal on Mathematical Analysis,
vol. 50, no. 3. Society for Industrial and Applied Mathematics , pp. 3271–3290,
2018.
ista: Erdös L, Krüger TH, Renfrew DT. 2018. Power law decay for systems of randomly
coupled differential equations. SIAM Journal on Mathematical Analysis. 50(3),
3271–3290.
mla: Erdös, László, et al. “Power Law Decay for Systems of Randomly Coupled Differential
Equations.” SIAM Journal on Mathematical Analysis, vol. 50, no. 3, Society
for Industrial and Applied Mathematics , 2018, pp. 3271–90, doi:10.1137/17M1143125.
short: L. Erdös, T.H. Krüger, D.T. Renfrew, SIAM Journal on Mathematical Analysis
50 (2018) 3271–3290.
date_created: 2018-12-11T11:45:03Z
date_published: 2018-01-01T00:00:00Z
date_updated: 2023-09-15T12:05:52Z
day: '01'
department:
- _id: LaEr
doi: 10.1137/17M1143125
ec_funded: 1
external_id:
arxiv:
- '1708.01546'
isi:
- '000437018500032'
intvolume: ' 50'
isi: 1
issue: '3'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/1708.01546
month: '01'
oa: 1
oa_version: Published Version
page: 3271 - 3290
project:
- _id: 258DCDE6-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '338804'
name: Random matrices, universality and disordered quantum systems
- _id: 258F40A4-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: M02080
name: Structured Non-Hermitian Random Matrices
publication: SIAM Journal on Mathematical Analysis
publication_status: published
publisher: 'Society for Industrial and Applied Mathematics '
publist_id: '7740'
quality_controlled: '1'
scopus_import: '1'
status: public
title: Power law decay for systems of randomly coupled differential equations
type: journal_article
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
volume: 50
year: '2018'
...
---
_id: '322'
abstract:
- lang: eng
text: We construct quantizations of multiplicative hypertoric varieties using an
algebra of q-difference operators on affine space, where q is a root of unity
in C. The quantization defines a matrix bundle (i.e. Azumaya algebra) over the
multiplicative hypertoric variety and admits an explicit finite étale splitting.
The global sections of this Azumaya algebra is a hypertoric quantum group, and
we prove a localization theorem. We introduce a general framework of Frobenius
quantum moment maps and their Hamiltonian reductions; our results shed light on
an instance of this framework.
acknowledgement: "National Science Foundation: Graduate Research Fellowship and grant
No.0932078000; ERC Advanced Grant “Arithmetic and Physics of Higgs moduli spaces”
No. 320593 \r\nThe author is grateful to David Jordan for suggesting this project
and providing guidance throughout, particularly for the formulation of Frobenius
quantum moment maps and key ideas in the proofs of Theorems 3.12 and 4.8. Special
thanks to David Ben-Zvi (the author's PhD advisor) for numerous discussions and
constant encouragement, and for suggesting the term ‘hypertoric quantum group.’
Many results appearing in the current paper were proven independently by Nicholas
Cooney; the author is grateful to Nicholas for sharing his insight on various topics,
including Proposition 3.8. The author also thanks Nicholas Proudfoot for relating
the definition of multiplicative hypertoric varieties, as well as the content of
Remark 2.14. The author also benefited immensely from the close reading and detailed
comments of an anonymous referee, and from conversations with Justin Hilburn, Kobi
Kremnitzer, Michael McBreen, Tom Nevins, Travis Schedler, and Ben Webster. \r\n\r\n\r\n\r\n"
article_processing_charge: No
author:
- first_name: Iordan V
full_name: Ganev, Iordan V
id: 447491B8-F248-11E8-B48F-1D18A9856A87
last_name: Ganev
citation:
ama: Ganev IV. Quantizations of multiplicative hypertoric varieties at a root of
unity. Journal of Algebra. 2018;506:92-128. doi:10.1016/j.jalgebra.2018.03.015
apa: Ganev, I. V. (2018). Quantizations of multiplicative hypertoric varieties at
a root of unity. Journal of Algebra. World Scientific Publishing. https://doi.org/10.1016/j.jalgebra.2018.03.015
chicago: Ganev, Iordan V. “Quantizations of Multiplicative Hypertoric Varieties
at a Root of Unity.” Journal of Algebra. World Scientific Publishing, 2018.
https://doi.org/10.1016/j.jalgebra.2018.03.015.
ieee: I. V. Ganev, “Quantizations of multiplicative hypertoric varieties at a root
of unity,” Journal of Algebra, vol. 506. World Scientific Publishing, pp.
92–128, 2018.
ista: Ganev IV. 2018. Quantizations of multiplicative hypertoric varieties at a
root of unity. Journal of Algebra. 506, 92–128.
mla: Ganev, Iordan V. “Quantizations of Multiplicative Hypertoric Varieties at a
Root of Unity.” Journal of Algebra, vol. 506, World Scientific Publishing,
2018, pp. 92–128, doi:10.1016/j.jalgebra.2018.03.015.
short: I.V. Ganev, Journal of Algebra 506 (2018) 92–128.
date_created: 2018-12-11T11:45:49Z
date_published: 2018-07-15T00:00:00Z
date_updated: 2023-09-15T12:08:38Z
day: '15'
department:
- _id: TaHa
doi: 10.1016/j.jalgebra.2018.03.015
ec_funded: 1
external_id:
arxiv:
- '1412.7211'
isi:
- '000433270600005'
intvolume: ' 506'
isi: 1
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/1412.7211
month: '07'
oa: 1
oa_version: Preprint
page: 92 - 128
project:
- _id: 25E549F4-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '320593'
name: Arithmetic and physics of Higgs moduli spaces
publication: Journal of Algebra
publication_status: published
publisher: World Scientific Publishing
publist_id: '7543'
quality_controlled: '1'
scopus_import: '1'
status: public
title: Quantizations of multiplicative hypertoric varieties at a root of unity
type: journal_article
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
volume: 506
year: '2018'
...
---
_id: '9831'
abstract:
- lang: eng
text: 'Implementation of the inference method in Matlab, including three applications
of the method: The first one for the model of ant motion, the second one for bacterial
chemotaxis, and the third one for the motion of fish.'
article_processing_charge: No
author:
- first_name: Katarína
full_name: Bod’Ová, Katarína
last_name: Bod’Ová
- first_name: Gabriel
full_name: Mitchell, Gabriel
id: 315BCD80-F248-11E8-B48F-1D18A9856A87
last_name: Mitchell
- first_name: Roy
full_name: Harpaz, Roy
last_name: Harpaz
- first_name: Elad
full_name: Schneidman, Elad
last_name: Schneidman
- first_name: Gašper
full_name: Tkačik, Gašper
id: 3D494DCA-F248-11E8-B48F-1D18A9856A87
last_name: Tkačik
orcid: 0000-0002-6699-1455
citation:
ama: Bod’Ová K, Mitchell G, Harpaz R, Schneidman E, Tkačik G. Implementation of
the inference method in Matlab. 2018. doi:10.1371/journal.pone.0193049.s001
apa: Bod’Ová, K., Mitchell, G., Harpaz, R., Schneidman, E., & Tkačik, G. (2018).
Implementation of the inference method in Matlab. Public Library of Science. https://doi.org/10.1371/journal.pone.0193049.s001
chicago: Bod’Ová, Katarína, Gabriel Mitchell, Roy Harpaz, Elad Schneidman, and Gašper
Tkačik. “Implementation of the Inference Method in Matlab.” Public Library of
Science, 2018. https://doi.org/10.1371/journal.pone.0193049.s001.
ieee: K. Bod’Ová, G. Mitchell, R. Harpaz, E. Schneidman, and G. Tkačik, “Implementation
of the inference method in Matlab.” Public Library of Science, 2018.
ista: Bod’Ová K, Mitchell G, Harpaz R, Schneidman E, Tkačik G. 2018. Implementation
of the inference method in Matlab, Public Library of Science, 10.1371/journal.pone.0193049.s001.
mla: Bod’Ová, Katarína, et al. Implementation of the Inference Method in Matlab.
Public Library of Science, 2018, doi:10.1371/journal.pone.0193049.s001.
short: K. Bod’Ová, G. Mitchell, R. Harpaz, E. Schneidman, G. Tkačik, (2018).
date_created: 2021-08-09T07:01:24Z
date_published: 2018-03-07T00:00:00Z
date_updated: 2023-09-15T12:06:18Z
day: '07'
department:
- _id: GaTk
doi: 10.1371/journal.pone.0193049.s001
month: '03'
oa_version: Published Version
publisher: Public Library of Science
related_material:
record:
- id: '406'
relation: used_in_publication
status: public
status: public
title: Implementation of the inference method in Matlab
type: research_data_reference
user_id: 6785fbc1-c503-11eb-8a32-93094b40e1cf
year: '2018'
...
---
_id: '142'
abstract:
- lang: eng
text: We address the problem of analyzing the reachable set of a polynomial nonlinear
continuous system by over-approximating the flowpipe of its dynamics. The common
approach to tackle this problem is to perform a numerical integration over a given
time horizon based on Taylor expansion and interval arithmetic. However, this
method results to be very conservative when there is a large difference in speed
between trajectories as time progresses. In this paper, we propose to use combinations
of barrier functions, which we call piecewise barrier tube (PBT), to over-approximate
flowpipe. The basic idea of PBT is that for each segment of a flowpipe, a coarse
box which is big enough to contain the segment is constructed using sampled simulation
and then in the box we compute by linear programming a set of barrier functions
(called barrier tube or BT for short) which work together to form a tube surrounding
the flowpipe. The benefit of using PBT is that (1) BT is independent of time and
hence can avoid being stretched and deformed by time; and (2) a small number of
BTs can form a tight over-approximation for the flowpipe, which means that the
computation required to decide whether the BTs intersect the unsafe set can be
reduced significantly. We implemented a prototype called PBTS in C++. Experiments
on some benchmark systems show that our approach is effective.
acknowledgement: 'Austrian Science Fund FWF: S11402-N23, S11405-N23, Z211-N32'
alternative_title:
- LNCS
article_processing_charge: No
author:
- first_name: Hui
full_name: Kong, Hui
id: 3BDE25AA-F248-11E8-B48F-1D18A9856A87
last_name: Kong
orcid: 0000-0002-3066-6941
- first_name: Ezio
full_name: Bartocci, Ezio
last_name: Bartocci
- first_name: Thomas A
full_name: Henzinger, Thomas A
id: 40876CD8-F248-11E8-B48F-1D18A9856A87
last_name: Henzinger
orcid: 0000−0002−2985−7724
citation:
ama: 'Kong H, Bartocci E, Henzinger TA. Reachable set over-approximation for nonlinear
systems using piecewise barrier tubes. In: Vol 10981. Springer; 2018:449-467.
doi:10.1007/978-3-319-96145-3_24'
apa: 'Kong, H., Bartocci, E., & Henzinger, T. A. (2018). Reachable set over-approximation
for nonlinear systems using piecewise barrier tubes (Vol. 10981, pp. 449–467).
Presented at the CAV: Computer Aided Verification, Oxford, United Kingdom: Springer.
https://doi.org/10.1007/978-3-319-96145-3_24'
chicago: Kong, Hui, Ezio Bartocci, and Thomas A Henzinger. “Reachable Set Over-Approximation
for Nonlinear Systems Using Piecewise Barrier Tubes,” 10981:449–67. Springer,
2018. https://doi.org/10.1007/978-3-319-96145-3_24.
ieee: 'H. Kong, E. Bartocci, and T. A. Henzinger, “Reachable set over-approximation
for nonlinear systems using piecewise barrier tubes,” presented at the CAV: Computer
Aided Verification, Oxford, United Kingdom, 2018, vol. 10981, pp. 449–467.'
ista: 'Kong H, Bartocci E, Henzinger TA. 2018. Reachable set over-approximation
for nonlinear systems using piecewise barrier tubes. CAV: Computer Aided Verification,
LNCS, vol. 10981, 449–467.'
mla: Kong, Hui, et al. Reachable Set Over-Approximation for Nonlinear Systems
Using Piecewise Barrier Tubes. Vol. 10981, Springer, 2018, pp. 449–67, doi:10.1007/978-3-319-96145-3_24.
short: H. Kong, E. Bartocci, T.A. Henzinger, in:, Springer, 2018, pp. 449–467.
conference:
end_date: 2018-07-17
location: Oxford, United Kingdom
name: 'CAV: Computer Aided Verification'
start_date: 2018-07-14
date_created: 2018-12-11T11:44:51Z
date_published: 2018-07-18T00:00:00Z
date_updated: 2023-09-15T12:12:08Z
day: '18'
ddc:
- '000'
department:
- _id: ToHe
doi: 10.1007/978-3-319-96145-3_24
external_id:
isi:
- '000491481600024'
file:
- access_level: open_access
checksum: fd95e8026deacef3dc752a733bb9355f
content_type: application/pdf
creator: dernst
date_created: 2018-12-17T15:57:06Z
date_updated: 2020-07-14T12:44:53Z
file_id: '5718'
file_name: 2018_LNCS_Kong.pdf
file_size: 5591566
relation: main_file
file_date_updated: 2020-07-14T12:44:53Z
has_accepted_license: '1'
intvolume: ' 10981'
isi: 1
language:
- iso: eng
month: '07'
oa: 1
oa_version: Published Version
page: 449 - 467
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_status: published
publisher: Springer
publist_id: '7781'
quality_controlled: '1'
scopus_import: '1'
status: public
title: Reachable set over-approximation for nonlinear systems using piecewise barrier
tubes
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: c635000d-4b10-11ee-a964-aac5a93f6ac1
volume: 10981
year: '2018'
...
---
_id: '427'
abstract:
- lang: eng
text: We investigate the quantum interference induced shifts between energetically
close states in highly charged ions, with the energy structure being observed
by laser spectroscopy. In this work, we focus on hyperfine states of lithiumlike
heavy-Z isotopes and quantify how much quantum interference changes the observed
transition frequencies. The process of photon excitation and subsequent photon
decay for the transition 2s→2p→2s is implemented with fully relativistic and full-multipole
frameworks, which are relevant for such relativistic atomic systems. We consider
the isotopes Pb79+207 and Bi80+209 due to experimental interest, as well as other
examples of isotopes with lower Z, namely Pr56+141 and Ho64+165. We conclude that
quantum interference can induce shifts up to 11% of the linewidth in the measurable
resonances of the considered isotopes, if interference between resonances is neglected.
The inclusion of relativity decreases the cross section by 35%, mainly due to
the complete retardation form of the electric dipole multipole. However, the contribution
of the next higher multipoles (e.g., magnetic quadrupole) to the cross section
is negligible. This makes the contribution of relativity and higher-order multipoles
to the quantum interference induced shifts a minor effect, even for heavy-Z elements.
acknowledgement: "This work was funded by the Portuguese Fundação para a Ciência e
a Tecnologia (FCT/MCTES/PIDDAC) under Grant No. UID/FIS/04559/2013 (LIBPhys). P.A.
acknowledges the support of the FCT, under Contract No. SFRH/BPD/92329/2013. L.S.
acknowledges financial support from the People Programme (Marie Curie Actions) of
the European Union's Seventh Framework Programme (FP7/2007-2013) under REA Grant
Agreement No. (291734). Laboratoire Kastler Brossel (LKB) is “Unité Mixte de Recherche
de Sorbonne Université, de ENS-PSL Research University, du Collège de France et
du CNRS No. 8552.” APPENDIX:\r\n"
article_number: '022510'
article_processing_charge: No
article_type: original
author:
- first_name: Pedro
full_name: Amaro, Pedro
last_name: Amaro
- first_name: Ulisses
full_name: Loureiro, Ulisses
last_name: Loureiro
- first_name: Laleh
full_name: Safari, Laleh
id: 3C325E5E-F248-11E8-B48F-1D18A9856A87
last_name: Safari
- first_name: Filippo
full_name: Fratini, Filippo
last_name: Fratini
- first_name: Paul
full_name: Indelicato, Paul
last_name: Indelicato
- first_name: Thomas
full_name: Stöhlker, Thomas
last_name: Stöhlker
- first_name: José
full_name: Santos, José
last_name: Santos
citation:
ama: Amaro P, Loureiro U, Safari L, et al. Quantum interference in laser spectroscopy
of highly charged lithiumlike ions. Physical Review A - Atomic, Molecular,
and Optical Physics. 2018;97(2). doi:10.1103/PhysRevA.97.022510
apa: Amaro, P., Loureiro, U., Safari, L., Fratini, F., Indelicato, P., Stöhlker,
T., & Santos, J. (2018). Quantum interference in laser spectroscopy of highly
charged lithiumlike ions. Physical Review A - Atomic, Molecular, and Optical
Physics. American Physical Society. https://doi.org/10.1103/PhysRevA.97.022510
chicago: Amaro, Pedro, Ulisses Loureiro, Laleh Safari, Filippo Fratini, Paul Indelicato,
Thomas Stöhlker, and José Santos. “Quantum Interference in Laser Spectroscopy
of Highly Charged Lithiumlike Ions.” Physical Review A - Atomic, Molecular,
and Optical Physics. American Physical Society, 2018. https://doi.org/10.1103/PhysRevA.97.022510.
ieee: P. Amaro et al., “Quantum interference in laser spectroscopy of highly
charged lithiumlike ions,” Physical Review A - Atomic, Molecular, and Optical
Physics, vol. 97, no. 2. American Physical Society, 2018.
ista: Amaro P, Loureiro U, Safari L, Fratini F, Indelicato P, Stöhlker T, Santos
J. 2018. Quantum interference in laser spectroscopy of highly charged lithiumlike
ions. Physical Review A - Atomic, Molecular, and Optical Physics. 97(2), 022510.
mla: Amaro, Pedro, et al. “Quantum Interference in Laser Spectroscopy of Highly
Charged Lithiumlike Ions.” Physical Review A - Atomic, Molecular, and Optical
Physics, vol. 97, no. 2, 022510, American Physical Society, 2018, doi:10.1103/PhysRevA.97.022510.
short: P. Amaro, U. Loureiro, L. Safari, F. Fratini, P. Indelicato, T. Stöhlker,
J. Santos, Physical Review A - Atomic, Molecular, and Optical Physics 97 (2018).
date_created: 2018-12-11T11:46:25Z
date_published: 2018-02-21T00:00:00Z
date_updated: 2023-09-15T12:09:35Z
day: '21'
department:
- _id: MiLe
doi: 10.1103/PhysRevA.97.022510
ec_funded: 1
external_id:
arxiv:
- '1802.07920'
isi:
- '000425601000004'
intvolume: ' 97'
isi: 1
issue: '2'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/1802.07920
month: '02'
oa: 1
oa_version: Preprint
project:
- _id: 25681D80-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '291734'
name: International IST Postdoc Fellowship Programme
publication: ' Physical Review A - Atomic, Molecular, and Optical Physics'
publication_status: published
publisher: American Physical Society
publist_id: '7396'
quality_controlled: '1'
scopus_import: '1'
status: public
title: Quantum interference in laser spectroscopy of highly charged lithiumlike ions
type: journal_article
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
volume: 97
year: '2018'
...
---
_id: '309'
abstract:
- lang: eng
text: 'We present an efficient algorithm for a problem in the interface between
clustering and graph embeddings. An embedding '' : G ! M of a graph G into a 2manifold
M maps the vertices in V (G) to distinct points and the edges in E(G) to interior-disjoint
Jordan arcs between the corresponding vertices. In applications in clustering,
cartography, and visualization, nearby vertices and edges are often bundled to
a common node or arc, due to data compression or low resolution. This raises the
computational problem of deciding whether a given map '' : G ! M comes from an
embedding. A map '' : G ! M is a weak embedding if it can be perturbed into an
embedding ψ: G ! M with k'' "k < " for every " > 0. A polynomial-time
algorithm for recognizing weak embeddings was recently found by Fulek and Kyncl
[14], which reduces to solving a system of linear equations over Z2. It runs in
O(n2!) O(n4:75) time, where 2:373 is the matrix multiplication exponent and n
is the number of vertices and edges of G. We improve the running time to O(n log
n). Our algorithm is also conceptually simpler than [14]: We perform a sequence
of local operations that gradually "untangles" the image ''(G) into
an embedding (G), or reports that '' is not a weak embedding. It generalizes a
recent technique developed for the case that G is a cycle and the embedding is
a simple polygon [1], and combines local constraints on the orientation of subgraphs
directly, thereby eliminating the need for solving large systems of linear equations.'
acknowledgement: '∗Research supported in part by the NSF awards CCF-1422311 and CCF-1423615,
and the Science Without Borders program. The second author gratefully acknowledges
support from Austrian Science Fund (FWF): M2281-N35.'
article_processing_charge: No
author:
- first_name: Hugo
full_name: Akitaya, Hugo
last_name: Akitaya
- first_name: Radoslav
full_name: Fulek, Radoslav
id: 39F3FFE4-F248-11E8-B48F-1D18A9856A87
last_name: Fulek
orcid: 0000-0001-8485-1774
- first_name: Csaba
full_name: Tóth, Csaba
last_name: Tóth
citation:
ama: 'Akitaya H, Fulek R, Tóth C. Recognizing weak embeddings of graphs. In: ACM;
2018:274-292. doi:10.1137/1.9781611975031.20'
apa: 'Akitaya, H., Fulek, R., & Tóth, C. (2018). Recognizing weak embeddings
of graphs (pp. 274–292). Presented at the SODA: Symposium on Discrete Algorithms,
New Orleans, LA, USA: ACM. https://doi.org/10.1137/1.9781611975031.20'
chicago: Akitaya, Hugo, Radoslav Fulek, and Csaba Tóth. “Recognizing Weak Embeddings
of Graphs,” 274–92. ACM, 2018. https://doi.org/10.1137/1.9781611975031.20.
ieee: 'H. Akitaya, R. Fulek, and C. Tóth, “Recognizing weak embeddings of graphs,”
presented at the SODA: Symposium on Discrete Algorithms, New Orleans, LA, USA,
2018, pp. 274–292.'
ista: 'Akitaya H, Fulek R, Tóth C. 2018. Recognizing weak embeddings of graphs.
SODA: Symposium on Discrete Algorithms, 274–292.'
mla: Akitaya, Hugo, et al. Recognizing Weak Embeddings of Graphs. ACM, 2018,
pp. 274–92, doi:10.1137/1.9781611975031.20.
short: H. Akitaya, R. Fulek, C. Tóth, in:, ACM, 2018, pp. 274–292.
conference:
end_date: 2018-01-10
location: New Orleans, LA, USA
name: 'SODA: Symposium on Discrete Algorithms'
start_date: 2018-01-07
date_created: 2018-12-11T11:45:45Z
date_published: 2018-01-01T00:00:00Z
date_updated: 2023-09-15T12:19:32Z
day: '01'
department:
- _id: UlWa
doi: 10.1137/1.9781611975031.20
external_id:
arxiv:
- '1709.09209'
isi:
- '000483921200021'
isi: 1
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/1709.09209
month: '01'
oa: 1
oa_version: Preprint
page: 274 - 292
project:
- _id: 261FA626-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: M02281
name: Eliminating intersections in drawings of graphs
publication_status: published
publisher: ACM
publist_id: '7556'
quality_controlled: '1'
related_material:
record:
- id: '6982'
relation: later_version
status: public
scopus_import: '1'
status: public
title: Recognizing weak embeddings of graphs
type: conference
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
year: '2018'
...
---
_id: '5794'
abstract:
- lang: eng
text: We present an approach to interacting quantum many-body systems based on the
notion of quantum groups, also known as q-deformed Lie algebras. In particular,
we show that, if the symmetry of a free quantum particle corresponds to a Lie
group G, in the presence of a many-body environment this particle can be described
by a deformed group, Gq. Crucially, the single deformation parameter, q, contains
all the information about the many-particle interactions in the system. We exemplify
our approach by considering a quantum rotor interacting with a bath of bosons,
and demonstrate that extracting the value of q from closed-form solutions in the
perturbative regime allows one to predict the behavior of the system for arbitrary
values of the impurity-bath coupling strength, in good agreement with nonperturbative
calculations. Furthermore, the value of the deformation parameter allows one to
predict at which coupling strengths rotor-bath interactions result in a formation
of a stable quasiparticle. The approach based on quantum groups does not only
allow for a drastic simplification of impurity problems, but also provides valuable
insights into hidden symmetries of interacting many-particle systems.
article_number: '255302'
article_processing_charge: No
article_type: original
author:
- first_name: Enderalp
full_name: Yakaboylu, Enderalp
id: 38CB71F6-F248-11E8-B48F-1D18A9856A87
last_name: Yakaboylu
orcid: 0000-0001-5973-0874
- first_name: Mikhail
full_name: Shkolnikov, Mikhail
id: 35084A62-F248-11E8-B48F-1D18A9856A87
last_name: Shkolnikov
orcid: 0000-0002-4310-178X
- first_name: Mikhail
full_name: Lemeshko, Mikhail
id: 37CB05FA-F248-11E8-B48F-1D18A9856A87
last_name: Lemeshko
orcid: 0000-0002-6990-7802
citation:
ama: Yakaboylu E, Shkolnikov M, Lemeshko M. Quantum groups as hidden symmetries
of quantum impurities. Physical Review Letters. 2018;121(25). doi:10.1103/PhysRevLett.121.255302
apa: Yakaboylu, E., Shkolnikov, M., & Lemeshko, M. (2018). Quantum groups as
hidden symmetries of quantum impurities. Physical Review Letters. American
Physical Society. https://doi.org/10.1103/PhysRevLett.121.255302
chicago: Yakaboylu, Enderalp, Mikhail Shkolnikov, and Mikhail Lemeshko. “Quantum
Groups as Hidden Symmetries of Quantum Impurities.” Physical Review Letters.
American Physical Society, 2018. https://doi.org/10.1103/PhysRevLett.121.255302.
ieee: E. Yakaboylu, M. Shkolnikov, and M. Lemeshko, “Quantum groups as hidden symmetries
of quantum impurities,” Physical Review Letters, vol. 121, no. 25. American
Physical Society, 2018.
ista: Yakaboylu E, Shkolnikov M, Lemeshko M. 2018. Quantum groups as hidden symmetries
of quantum impurities. Physical Review Letters. 121(25), 255302.
mla: Yakaboylu, Enderalp, et al. “Quantum Groups as Hidden Symmetries of Quantum
Impurities.” Physical Review Letters, vol. 121, no. 25, 255302, American
Physical Society, 2018, doi:10.1103/PhysRevLett.121.255302.
short: E. Yakaboylu, M. Shkolnikov, M. Lemeshko, Physical Review Letters 121 (2018).
date_created: 2019-01-06T22:59:12Z
date_published: 2018-12-17T00:00:00Z
date_updated: 2023-09-15T12:09:06Z
day: '17'
department:
- _id: MiLe
doi: 10.1103/PhysRevLett.121.255302
ec_funded: 1
external_id:
arxiv:
- '1809.00222'
isi:
- '000454178600009'
intvolume: ' 121'
isi: 1
issue: '25'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/1809.00222
month: '12'
oa: 1
oa_version: Preprint
project:
- _id: 25681D80-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '291734'
name: International IST Postdoc Fellowship Programme
- _id: 26031614-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: P29902
name: Quantum rotations in the presence of a many-body environment
publication: Physical Review Letters
publication_identifier:
issn:
- '00319007'
publication_status: published
publisher: American Physical Society
quality_controlled: '1'
scopus_import: '1'
status: public
title: Quantum groups as hidden symmetries of quantum impurities
type: journal_article
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
volume: 121
year: '2018'
...
---
_id: '87'
abstract:
- lang: eng
text: Using the geodesic distance on the n-dimensional sphere, we study the expected
radius function of the Delaunay mosaic of a random set of points. Specifically,
we consider the partition of the mosaic into intervals of the radius function
and determine the expected number of intervals whose radii are less than or equal
to a given threshold. We find that the expectations are essentially the same as
for the Poisson–Delaunay mosaic in n-dimensional Euclidean space. Assuming the
points are not contained in a hemisphere, the Delaunay mosaic is isomorphic to
the boundary complex of the convex hull in Rn+1, so we also get the expected number
of faces of a random inscribed polytope. As proved in Antonelli et al. [Adv. in
Appl. Probab. 9–12 (1977–1980)], an orthant section of the n-sphere is isometric
to the standard n-simplex equipped with the Fisher information metric. It follows
that the latter space has similar stochastic properties as the n-dimensional Euclidean
space. Our results are therefore relevant in information geometry and in population
genetics.
article_processing_charge: No
article_type: original
author:
- first_name: Herbert
full_name: Edelsbrunner, Herbert
id: 3FB178DA-F248-11E8-B48F-1D18A9856A87
last_name: Edelsbrunner
orcid: 0000-0002-9823-6833
- first_name: Anton
full_name: Nikitenko, Anton
id: 3E4FF1BA-F248-11E8-B48F-1D18A9856A87
last_name: Nikitenko
orcid: 0000-0002-0659-3201
citation:
ama: Edelsbrunner H, Nikitenko A. Random inscribed polytopes have similar radius
functions as Poisson-Delaunay mosaics. Annals of Applied Probability. 2018;28(5):3215-3238.
doi:10.1214/18-AAP1389
apa: Edelsbrunner, H., & Nikitenko, A. (2018). Random inscribed polytopes have
similar radius functions as Poisson-Delaunay mosaics. Annals of Applied Probability.
Institute of Mathematical Statistics. https://doi.org/10.1214/18-AAP1389
chicago: Edelsbrunner, Herbert, and Anton Nikitenko. “Random Inscribed Polytopes
Have Similar Radius Functions as Poisson-Delaunay Mosaics.” Annals of Applied
Probability. Institute of Mathematical Statistics, 2018. https://doi.org/10.1214/18-AAP1389.
ieee: H. Edelsbrunner and A. Nikitenko, “Random inscribed polytopes have similar
radius functions as Poisson-Delaunay mosaics,” Annals of Applied Probability,
vol. 28, no. 5. Institute of Mathematical Statistics, pp. 3215–3238, 2018.
ista: Edelsbrunner H, Nikitenko A. 2018. Random inscribed polytopes have similar
radius functions as Poisson-Delaunay mosaics. Annals of Applied Probability. 28(5),
3215–3238.
mla: Edelsbrunner, Herbert, and Anton Nikitenko. “Random Inscribed Polytopes Have
Similar Radius Functions as Poisson-Delaunay Mosaics.” Annals of Applied Probability,
vol. 28, no. 5, Institute of Mathematical Statistics, 2018, pp. 3215–38, doi:10.1214/18-AAP1389.
short: H. Edelsbrunner, A. Nikitenko, Annals of Applied Probability 28 (2018) 3215–3238.
date_created: 2018-12-11T11:44:33Z
date_published: 2018-10-01T00:00:00Z
date_updated: 2023-09-15T12:10:35Z
day: '01'
department:
- _id: HeEd
doi: 10.1214/18-AAP1389
external_id:
arxiv:
- '1705.02870'
isi:
- '000442893500018'
intvolume: ' 28'
isi: 1
issue: '5'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/1705.02870
month: '10'
oa: 1
oa_version: Preprint
page: 3215 - 3238
project:
- _id: 2561EBF4-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: I02979-N35
name: Persistence and stability of geometric complexes
publication: Annals of Applied Probability
publication_status: published
publisher: Institute of Mathematical Statistics
publist_id: '7967'
quality_controlled: '1'
related_material:
record:
- id: '6287'
relation: dissertation_contains
status: public
scopus_import: '1'
status: public
title: Random inscribed polytopes have similar radius functions as Poisson-Delaunay
mosaics
type: journal_article
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
volume: 28
year: '2018'
...
---
_id: '192'
abstract:
- lang: eng
text: The phytohormone auxin is the information carrier in a plethora of developmental
and physiological processes in plants(1). It has been firmly established that
canonical, nuclear auxin signalling acts through regulation of gene transcription(2).
Here, we combined microfluidics, live imaging, genetic engineering and computational
modelling to reanalyse the classical case of root growth inhibition(3) by auxin.
We show that Arabidopsis roots react to addition and removal of auxin by extremely
rapid adaptation of growth rate. This process requires intracellular auxin perception
but not transcriptional reprogramming. The formation of the canonical TIR1/AFB-Aux/IAA
co-receptor complex is required for the growth regulation, hinting to a novel,
non-transcriptional branch of this signalling pathway. Our results challenge the
current understanding of root growth regulation by auxin and suggest another,
presumably non-transcriptional, signalling output of the canonical auxin pathway.
article_processing_charge: No
article_type: original
author:
- first_name: Matyas
full_name: Fendrych, Matyas
id: 43905548-F248-11E8-B48F-1D18A9856A87
last_name: Fendrych
orcid: 0000-0002-9767-8699
- first_name: Maria
full_name: Akhmanova, Maria
id: 3425EC26-F248-11E8-B48F-1D18A9856A87
last_name: Akhmanova
orcid: 0000-0003-1522-3162
- first_name: Jack
full_name: Merrin, Jack
id: 4515C308-F248-11E8-B48F-1D18A9856A87
last_name: Merrin
orcid: 0000-0001-5145-4609
- first_name: Matous
full_name: Glanc, Matous
last_name: Glanc
- first_name: Shinya
full_name: Hagihara, Shinya
last_name: Hagihara
- first_name: Koji
full_name: Takahashi, Koji
last_name: Takahashi
- first_name: Naoyuki
full_name: Uchida, Naoyuki
last_name: Uchida
- first_name: Keiko U
full_name: Torii, Keiko U
last_name: Torii
- first_name: Jirí
full_name: Friml, Jirí
id: 4159519E-F248-11E8-B48F-1D18A9856A87
last_name: Friml
orcid: 0000-0002-8302-7596
citation:
ama: Fendrych M, Akhmanova M, Merrin J, et al. Rapid and reversible root growth
inhibition by TIR1 auxin signalling. Nature Plants. 2018;4(7):453-459.
doi:10.1038/s41477-018-0190-1
apa: Fendrych, M., Akhmanova, M., Merrin, J., Glanc, M., Hagihara, S., Takahashi,
K., … Friml, J. (2018). Rapid and reversible root growth inhibition by TIR1 auxin
signalling. Nature Plants. Springer Nature. https://doi.org/10.1038/s41477-018-0190-1
chicago: Fendrych, Matyas, Maria Akhmanova, Jack Merrin, Matous Glanc, Shinya Hagihara,
Koji Takahashi, Naoyuki Uchida, Keiko U Torii, and Jiří Friml. “Rapid and Reversible
Root Growth Inhibition by TIR1 Auxin Signalling.” Nature Plants. Springer
Nature, 2018. https://doi.org/10.1038/s41477-018-0190-1.
ieee: M. Fendrych et al., “Rapid and reversible root growth inhibition by
TIR1 auxin signalling,” Nature Plants, vol. 4, no. 7. Springer Nature,
pp. 453–459, 2018.
ista: Fendrych M, Akhmanova M, Merrin J, Glanc M, Hagihara S, Takahashi K, Uchida
N, Torii KU, Friml J. 2018. Rapid and reversible root growth inhibition by TIR1
auxin signalling. Nature Plants. 4(7), 453–459.
mla: Fendrych, Matyas, et al. “Rapid and Reversible Root Growth Inhibition by TIR1
Auxin Signalling.” Nature Plants, vol. 4, no. 7, Springer Nature, 2018,
pp. 453–59, doi:10.1038/s41477-018-0190-1.
short: M. Fendrych, M. Akhmanova, J. Merrin, M. Glanc, S. Hagihara, K. Takahashi,
N. Uchida, K.U. Torii, J. Friml, Nature Plants 4 (2018) 453–459.
date_created: 2018-12-11T11:45:07Z
date_published: 2018-06-25T00:00:00Z
date_updated: 2023-09-15T12:11:03Z
day: '25'
department:
- _id: JiFr
- _id: DaSi
- _id: NanoFab
doi: 10.1038/s41477-018-0190-1
external_id:
isi:
- '000443221200017'
pmid:
- '29942048'
intvolume: ' 4'
isi: 1
issue: '7'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://www.ncbi.nlm.nih.gov/pubmed/29942048
month: '06'
oa: 1
oa_version: Submitted Version
page: 453 - 459
pmid: 1
publication: Nature Plants
publication_status: published
publisher: Springer Nature
publist_id: '7728'
quality_controlled: '1'
related_material:
link:
- description: News on IST Homepage
relation: press_release
url: https://ist.ac.at/en/news/new-mechanism-for-the-plant-hormone-auxin-discovered/
scopus_import: '1'
status: public
title: Rapid and reversible root growth inhibition by TIR1 auxin signalling
type: journal_article
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
volume: 4
year: '2018'
...
---
_id: '14'
abstract:
- lang: eng
text: The intercellular transport of auxin is driven by PIN-formed (PIN) auxin efflux
carriers. PINs are localized at the plasma membrane (PM) and on constitutively
recycling endomembrane vesicles. Therefore, PINs can mediate auxin transport either
by direct translocation across the PM or by pumping auxin into secretory vesicles
(SVs), leading to its secretory release upon fusion with the PM. Which of these
two mechanisms dominates is a matter of debate. Here, we addressed the issue with
a mathematical modeling approach. We demonstrate that the efficiency of secretory
transport depends on SV size, half-life of PINs on the PM, pH, exocytosis frequency
and PIN density. 3D structured illumination microscopy (SIM) was used to determine
PIN density on the PM. Combining this data with published values of the other
parameters, we show that the transport activity of PINs in SVs would have to be
at least 1000× greater than on the PM in order to produce a comparable macroscopic
auxin transport. If both transport mechanisms operated simultaneously and PINs
were equally active on SVs and PM, the contribution of secretion to the total
auxin flux would be negligible. In conclusion, while secretory vesicle-mediated
transport of auxin is an intriguing and theoretically possible model, it is unlikely
to be a major mechanism of auxin transport inplanta.
acknowledgement: 'European Research Council (ERC): 742985 to Jiri Friml; M.A. was
supported by the Austrian Science Fund (FWF) (M2379-B28); AJ was supported by the
Austria Science Fund (FWF): I03630 to Jiri Friml.'
article_processing_charge: No
article_type: original
author:
- first_name: Sander
full_name: Hille, Sander
last_name: Hille
- first_name: Maria
full_name: Akhmanova, Maria
id: 3425EC26-F248-11E8-B48F-1D18A9856A87
last_name: Akhmanova
orcid: 0000-0003-1522-3162
- first_name: Matous
full_name: Glanc, Matous
id: 1AE1EA24-02D0-11E9-9BAA-DAF4881429F2
last_name: Glanc
orcid: 0000-0003-0619-7783
- first_name: Alexander J
full_name: Johnson, Alexander J
id: 46A62C3A-F248-11E8-B48F-1D18A9856A87
last_name: Johnson
orcid: 0000-0002-2739-8843
- first_name: Jirí
full_name: Friml, Jirí
id: 4159519E-F248-11E8-B48F-1D18A9856A87
last_name: Friml
orcid: 0000-0002-8302-7596
citation:
ama: 'Hille S, Akhmanova M, Glanc M, Johnson AJ, Friml J. Relative contribution
of PIN-containing secretory vesicles and plasma membrane PINs to the directed
auxin transport: Theoretical estimation. International Journal of Molecular
Sciences. 2018;19(11). doi:10.3390/ijms19113566'
apa: 'Hille, S., Akhmanova, M., Glanc, M., Johnson, A. J., & Friml, J. (2018).
Relative contribution of PIN-containing secretory vesicles and plasma membrane
PINs to the directed auxin transport: Theoretical estimation. International
Journal of Molecular Sciences. MDPI. https://doi.org/10.3390/ijms19113566'
chicago: 'Hille, Sander, Maria Akhmanova, Matous Glanc, Alexander J Johnson, and
Jiří Friml. “Relative Contribution of PIN-Containing Secretory Vesicles and Plasma
Membrane PINs to the Directed Auxin Transport: Theoretical Estimation.” International
Journal of Molecular Sciences. MDPI, 2018. https://doi.org/10.3390/ijms19113566.'
ieee: 'S. Hille, M. Akhmanova, M. Glanc, A. J. Johnson, and J. Friml, “Relative
contribution of PIN-containing secretory vesicles and plasma membrane PINs to
the directed auxin transport: Theoretical estimation,” International Journal
of Molecular Sciences, vol. 19, no. 11. MDPI, 2018.'
ista: 'Hille S, Akhmanova M, Glanc M, Johnson AJ, Friml J. 2018. Relative contribution
of PIN-containing secretory vesicles and plasma membrane PINs to the directed
auxin transport: Theoretical estimation. International Journal of Molecular Sciences.
19(11).'
mla: 'Hille, Sander, et al. “Relative Contribution of PIN-Containing Secretory Vesicles
and Plasma Membrane PINs to the Directed Auxin Transport: Theoretical Estimation.”
International Journal of Molecular Sciences, vol. 19, no. 11, MDPI, 2018,
doi:10.3390/ijms19113566.'
short: S. Hille, M. Akhmanova, M. Glanc, A.J. Johnson, J. Friml, International Journal
of Molecular Sciences 19 (2018).
date_created: 2018-12-11T11:44:09Z
date_published: 2018-11-12T00:00:00Z
date_updated: 2023-09-18T08:09:32Z
day: '12'
ddc:
- '580'
department:
- _id: DaSi
- _id: JiFr
doi: 10.3390/ijms19113566
ec_funded: 1
external_id:
isi:
- '000451528500282'
file:
- access_level: open_access
checksum: e4b59c2599b0ca26ebf5b8434bcde94a
content_type: application/pdf
creator: dernst
date_created: 2018-12-17T16:04:11Z
date_updated: 2020-07-14T12:44:50Z
file_id: '5719'
file_name: 2018_IJMS_Hille.pdf
file_size: 2200593
relation: main_file
file_date_updated: 2020-07-14T12:44:50Z
has_accepted_license: '1'
intvolume: ' 19'
isi: 1
issue: '11'
language:
- iso: eng
month: '11'
oa: 1
oa_version: Published Version
project:
- _id: 261099A6-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '742985'
name: Tracing Evolution of Auxin Transport and Polarity in Plants
- _id: 26538374-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: I03630
name: Molecular mechanisms of endocytic cargo recognition in plants
publication: International Journal of Molecular Sciences
publication_identifier:
eissn:
- 1422-0067
publication_status: published
publisher: MDPI
publist_id: '8042'
quality_controlled: '1'
scopus_import: '1'
status: public
title: 'Relative contribution of PIN-containing secretory vesicles and plasma membrane
PINs to the directed auxin transport: Theoretical estimation'
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: journal_article
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
volume: 19
year: '2018'
...
---
_id: '39'
abstract:
- lang: eng
text: We study how a block of genome with a large number of weakly selected loci
introgresses under directional selection into a genetically homogeneous population.
We derive exact expressions for the expected rate of growth of any fragment of
the introduced block during the initial phase of introgression, and show that
the growth rate of a single-locus variant is largely insensitive to its own additive
effect, but depends instead on the combined effect of all loci within a characteristic
linkage scale. The expected growth rate of a fragment is highly correlated with
its long-term introgression probability in populations of moderate size, and can
hence identify variants that are likely to introgress across replicate populations.
We clarify how the introgression probability of an individual variant is determined
by the interplay between hitchhiking with relatively large fragments during the
early phase of introgression and selection on fine-scale variation within these,
which at longer times results in differential introgression probabilities for
beneficial and deleterious loci within successful fragments. By simulating individuals,
we also investigate how introgression probabilities at individual loci depend
on the variance of fitness effects, the net fitness of the introduced block, and
the size of the recipient population, and how this shapes the net advance under
selection. Our work suggests that even highly replicable substitutions may be
associated with a range of selective effects, which makes it challenging to fine
map the causal loci that underlie polygenic adaptation.
article_processing_charge: No
article_type: original
author:
- first_name: Himani
full_name: Sachdeva, Himani
id: 42377A0A-F248-11E8-B48F-1D18A9856A87
last_name: Sachdeva
- first_name: Nicholas H
full_name: Barton, Nicholas H
id: 4880FE40-F248-11E8-B48F-1D18A9856A87
last_name: Barton
orcid: 0000-0002-8548-5240
citation:
ama: Sachdeva H, Barton NH. Replicability of introgression under linked, polygenic
selection. Genetics. 2018;210(4):1411-1427. doi:10.1534/genetics.118.301429
apa: Sachdeva, H., & Barton, N. H. (2018). Replicability of introgression under
linked, polygenic selection. Genetics. Genetics Society of America. https://doi.org/10.1534/genetics.118.301429
chicago: Sachdeva, Himani, and Nicholas H Barton. “Replicability of Introgression
under Linked, Polygenic Selection.” Genetics. Genetics Society of America,
2018. https://doi.org/10.1534/genetics.118.301429.
ieee: H. Sachdeva and N. H. Barton, “Replicability of introgression under linked,
polygenic selection,” Genetics, vol. 210, no. 4. Genetics Society of America,
pp. 1411–1427, 2018.
ista: Sachdeva H, Barton NH. 2018. Replicability of introgression under linked,
polygenic selection. Genetics. 210(4), 1411–1427.
mla: Sachdeva, Himani, and Nicholas H. Barton. “Replicability of Introgression under
Linked, Polygenic Selection.” Genetics, vol. 210, no. 4, Genetics Society
of America, 2018, pp. 1411–27, doi:10.1534/genetics.118.301429.
short: H. Sachdeva, N.H. Barton, Genetics 210 (2018) 1411–1427.
date_created: 2018-12-11T11:44:18Z
date_published: 2018-12-04T00:00:00Z
date_updated: 2023-09-18T08:10:29Z
day: '04'
department:
- _id: NiBa
doi: 10.1534/genetics.118.301429
external_id:
isi:
- '000452315900021'
intvolume: ' 210'
isi: 1
issue: '4'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://www.biorxiv.org/content/10.1101/379578v1
month: '12'
oa: 1
oa_version: Preprint
page: 1411-1427
publication: Genetics
publication_identifier:
issn:
- '00166731'
publication_status: published
publisher: Genetics Society of America
quality_controlled: '1'
scopus_import: '1'
status: public
title: Replicability of introgression under linked, polygenic selection
type: journal_article
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
volume: 210
year: '2018'
...
---
_id: '420'
abstract:
- lang: eng
text: We analyze the theoretical derivation of the beyond-mean-field equation of
state for two-dimensional gas of dilute, ultracold alkali-metal atoms in the Bardeen–Cooper–Schrieffer
(BCS) to Bose–Einstein condensate (BEC) crossover. We show that at zero temperature
our theory — considering Gaussian fluctuations on top of the mean-field equation
of state — is in very good agreement with experimental data. Subsequently, we
investigate the superfluid density at finite temperature and its renormalization
due to the proliferation of vortex–antivortex pairs. By doing so, we determine
the Berezinskii–Kosterlitz–Thouless (BKT) critical temperature — at which the
renormalized superfluid density jumps to zero — as a function of the inter-atomic
potential strength. We find that the Nelson–Kosterlitz criterion overestimates
the BKT temperature with respect to the renormalization group equations, this
effect being particularly relevant in the intermediate regime of the crossover.
article_processing_charge: No
author:
- first_name: Giacomo
full_name: Bighin, Giacomo
id: 4CA96FD4-F248-11E8-B48F-1D18A9856A87
last_name: Bighin
orcid: 0000-0001-8823-9777
- first_name: Luca
full_name: Salasnich, Luca
last_name: Salasnich
citation:
ama: Bighin G, Salasnich L. Renormalization of the superfluid density in the two-dimensional
BCS-BEC crossover. International Journal of Modern Physics B. 2018;32(17):1840022.
doi:10.1142/S0217979218400222
apa: Bighin, G., & Salasnich, L. (2018). Renormalization of the superfluid density
in the two-dimensional BCS-BEC crossover. International Journal of Modern Physics
B. World Scientific Publishing. https://doi.org/10.1142/S0217979218400222
chicago: Bighin, Giacomo, and Luca Salasnich. “Renormalization of the Superfluid
Density in the Two-Dimensional BCS-BEC Crossover.” International Journal of
Modern Physics B. World Scientific Publishing, 2018. https://doi.org/10.1142/S0217979218400222.
ieee: G. Bighin and L. Salasnich, “Renormalization of the superfluid density in
the two-dimensional BCS-BEC crossover,” International Journal of Modern Physics
B, vol. 32, no. 17. World Scientific Publishing, p. 1840022, 2018.
ista: Bighin G, Salasnich L. 2018. Renormalization of the superfluid density in
the two-dimensional BCS-BEC crossover. International Journal of Modern Physics
B. 32(17), 1840022.
mla: Bighin, Giacomo, and Luca Salasnich. “Renormalization of the Superfluid Density
in the Two-Dimensional BCS-BEC Crossover.” International Journal of Modern
Physics B, vol. 32, no. 17, World Scientific Publishing, 2018, p. 1840022,
doi:10.1142/S0217979218400222.
short: G. Bighin, L. Salasnich, International Journal of Modern Physics B 32 (2018)
1840022.
date_created: 2018-12-11T11:46:22Z
date_published: 2018-07-10T00:00:00Z
date_updated: 2023-09-18T08:09:59Z
day: '10'
department:
- _id: MiLe
doi: 10.1142/S0217979218400222
external_id:
isi:
- '000438217300007'
intvolume: ' 32'
isi: 1
issue: '17'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/1710.11171
month: '07'
oa: 1
oa_version: Preprint
page: '1840022'
publication: International Journal of Modern Physics B
publication_status: published
publisher: World Scientific Publishing
publist_id: '7402'
quality_controlled: '1'
scopus_import: '1'
status: public
title: Renormalization of the superfluid density in the two-dimensional BCS-BEC crossover
type: journal_article
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
volume: 32
year: '2018'
...
---
_id: '38'
abstract:
- lang: eng
text: 'Genomes of closely-related species or populations often display localized
regions of enhanced relative sequence divergence, termed genomic islands. It has
been proposed that these islands arise through selective sweeps and/or barriers
to gene flow. Here, we genetically dissect a genomic island that controls flower
color pattern differences between two subspecies of Antirrhinum majus, A.m.striatum
and A.m.pseudomajus, and relate it to clinal variation across a natural hybrid
zone. We show that selective sweeps likely raised relative divergence at two tightly-linked
MYB-like transcription factors, leading to distinct flower patterns in the two
subspecies. The two patterns provide alternate floral guides and create a strong
barrier to gene flow where populations come into contact. This barrier affects
the selected flower color genes and tightlylinked loci, but does not extend outside
of this domain, allowing gene flow to lower relative divergence for the rest of
the chromosome. Thus, both selective sweeps and barriers to gene flow play a role
in shaping genomic islands: sweeps cause elevation in relative divergence, while
heterogeneous gene flow flattens the surrounding "sea," making the island of divergence
stand out. By showing how selective sweeps establish alternative adaptive phenotypes
that lead to barriers to gene flow, our study sheds light on possible mechanisms
leading to reproductive isolation and speciation.'
acknowledgement: ' ERC Grant 201252 (to N.H.B.)'
article_processing_charge: No
author:
- first_name: Hugo
full_name: Tavares, Hugo
last_name: Tavares
- first_name: Annabel
full_name: Whitley, Annabel
last_name: Whitley
- first_name: David
full_name: Field, David
id: 419049E2-F248-11E8-B48F-1D18A9856A87
last_name: Field
orcid: 0000-0002-4014-8478
- first_name: Desmond
full_name: Bradley, Desmond
last_name: Bradley
- first_name: Matthew
full_name: Couchman, Matthew
last_name: Couchman
- first_name: Lucy
full_name: Copsey, Lucy
last_name: Copsey
- first_name: Joane
full_name: Elleouet, Joane
last_name: Elleouet
- first_name: Monique
full_name: Burrus, Monique
last_name: Burrus
- first_name: Christophe
full_name: Andalo, Christophe
last_name: Andalo
- first_name: Miaomiao
full_name: Li, Miaomiao
last_name: Li
- first_name: Qun
full_name: Li, Qun
last_name: Li
- first_name: Yongbiao
full_name: Xue, Yongbiao
last_name: Xue
- first_name: Alexandra B
full_name: Rebocho, Alexandra B
last_name: Rebocho
- first_name: Nicholas H
full_name: Barton, Nicholas H
id: 4880FE40-F248-11E8-B48F-1D18A9856A87
last_name: Barton
orcid: 0000-0002-8548-5240
- first_name: Enrico
full_name: Coen, Enrico
last_name: Coen
citation:
ama: Tavares H, Whitley A, Field D, et al. Selection and gene flow shape genomic
islands that control floral guides. PNAS. 2018;115(43):11006-11011. doi:10.1073/pnas.1801832115
apa: Tavares, H., Whitley, A., Field, D., Bradley, D., Couchman, M., Copsey, L.,
… Coen, E. (2018). Selection and gene flow shape genomic islands that control
floral guides. PNAS. National Academy of Sciences. https://doi.org/10.1073/pnas.1801832115
chicago: Tavares, Hugo, Annabel Whitley, David Field, Desmond Bradley, Matthew Couchman,
Lucy Copsey, Joane Elleouet, et al. “Selection and Gene Flow Shape Genomic Islands
That Control Floral Guides.” PNAS. National Academy of Sciences, 2018.
https://doi.org/10.1073/pnas.1801832115.
ieee: H. Tavares et al., “Selection and gene flow shape genomic islands that
control floral guides,” PNAS, vol. 115, no. 43. National Academy of Sciences,
pp. 11006–11011, 2018.
ista: Tavares H, Whitley A, Field D, Bradley D, Couchman M, Copsey L, Elleouet J,
Burrus M, Andalo C, Li M, Li Q, Xue Y, Rebocho AB, Barton NH, Coen E. 2018. Selection
and gene flow shape genomic islands that control floral guides. PNAS. 115(43),
11006–11011.
mla: Tavares, Hugo, et al. “Selection and Gene Flow Shape Genomic Islands That Control
Floral Guides.” PNAS, vol. 115, no. 43, National Academy of Sciences, 2018,
pp. 11006–11, doi:10.1073/pnas.1801832115.
short: H. Tavares, A. Whitley, D. Field, D. Bradley, M. Couchman, L. Copsey, J.
Elleouet, M. Burrus, C. Andalo, M. Li, Q. Li, Y. Xue, A.B. Rebocho, N.H. Barton,
E. Coen, PNAS 115 (2018) 11006–11011.
date_created: 2018-12-11T11:44:18Z
date_published: 2018-10-23T00:00:00Z
date_updated: 2023-09-18T08:36:49Z
day: '23'
ddc:
- '570'
department:
- _id: NiBa
doi: 10.1073/pnas.1801832115
external_id:
isi:
- '000448040500065'
pmid:
- '30297406'
file:
- access_level: open_access
checksum: d2305d0cc81dbbe4c1c677d64ad6f6d1
content_type: application/pdf
creator: dernst
date_created: 2018-12-17T08:44:03Z
date_updated: 2020-07-14T12:46:16Z
file_id: '5683'
file_name: 11006.full.pdf
file_size: 1911302
relation: main_file
file_date_updated: 2020-07-14T12:46:16Z
has_accepted_license: '1'
intvolume: ' 115'
isi: 1
issue: '43'
language:
- iso: eng
month: '10'
oa: 1
oa_version: Published Version
page: 11006 - 11011
pmid: 1
publication: PNAS
publication_identifier:
issn:
- '00278424'
publication_status: published
publisher: National Academy of Sciences
publist_id: '8017'
quality_controlled: '1'
scopus_import: '1'
status: public
title: Selection and gene flow shape genomic islands that control floral guides
tmp:
image: /images/cc_by_nc_nd.png
legal_code_url: https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode
name: Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International
(CC BY-NC-ND 4.0)
short: CC BY-NC-ND (4.0)
type: journal_article
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
volume: 115
year: '2018'
...
---
_id: '155'
abstract:
- lang: eng
text: There is currently significant interest in operating devices in the quantum
regime, where their behaviour cannot be explained through classical mechanics.
Quantum states, including entangled states, are fragile and easily disturbed by
excessive thermal noise. Here we address the question of whether it is possible
to create non-reciprocal devices that encourage the flow of thermal noise towards
or away from a particular quantum device in a network. Our work makes use of the
cascaded systems formalism to answer this question in the affirmative, showing
how a three-port device can be used as an effective thermal transistor, and illustrates
how this formalism maps onto an experimentally-realisable optomechanical system.
Our results pave the way to more resilient quantum devices and to the use of thermal
noise as a resource.
alternative_title:
- Proceedings of SPIE
article_number: 106721N
article_processing_charge: No
author:
- first_name: André
full_name: Xuereb, André
last_name: Xuereb
- first_name: Matteo
full_name: Aquilina, Matteo
last_name: Aquilina
- first_name: Shabir
full_name: Barzanjeh, Shabir
id: 2D25E1F6-F248-11E8-B48F-1D18A9856A87
last_name: Barzanjeh
orcid: 0000-0003-0415-1423
citation:
ama: 'Xuereb A, Aquilina M, Barzanjeh S. Routing thermal noise through quantum networks.
In: Andrews DL, Ostendorf A, Bain AJ, Nunzi JM, eds. Vol 10672. SPIE; 2018. doi:10.1117/12.2309928'
apa: 'Xuereb, A., Aquilina, M., & Barzanjeh, S. (2018). Routing thermal noise
through quantum networks. In D. L. Andrews, A. Ostendorf, A. J. Bain, & J.
M. Nunzi (Eds.) (Vol. 10672). Presented at the SPIE: The international society
for optical engineering, Strasbourg, France: SPIE. https://doi.org/10.1117/12.2309928'
chicago: Xuereb, André, Matteo Aquilina, and Shabir Barzanjeh. “Routing Thermal
Noise through Quantum Networks.” edited by D L Andrews, A Ostendorf, A J Bain,
and J M Nunzi, Vol. 10672. SPIE, 2018. https://doi.org/10.1117/12.2309928.
ieee: 'A. Xuereb, M. Aquilina, and S. Barzanjeh, “Routing thermal noise through
quantum networks,” presented at the SPIE: The international society for optical
engineering, Strasbourg, France, 2018, vol. 10672.'
ista: 'Xuereb A, Aquilina M, Barzanjeh S. 2018. Routing thermal noise through quantum
networks. SPIE: The international society for optical engineering, Proceedings
of SPIE, vol. 10672, 106721N.'
mla: Xuereb, André, et al. Routing Thermal Noise through Quantum Networks.
Edited by D L Andrews et al., vol. 10672, 106721N, SPIE, 2018, doi:10.1117/12.2309928.
short: A. Xuereb, M. Aquilina, S. Barzanjeh, in:, D.L. Andrews, A. Ostendorf, A.J.
Bain, J.M. Nunzi (Eds.), SPIE, 2018.
conference:
end_date: 2018-04-26
location: Strasbourg, France
name: 'SPIE: The international society for optical engineering'
start_date: 2018-04-22
date_created: 2018-12-11T11:44:55Z
date_published: 2018-05-04T00:00:00Z
date_updated: 2023-09-18T08:12:24Z
day: '04'
department:
- _id: JoFi
doi: 10.1117/12.2309928
editor:
- first_name: D L
full_name: Andrews, D L
last_name: Andrews
- first_name: A
full_name: Ostendorf, A
last_name: Ostendorf
- first_name: A J
full_name: Bain, A J
last_name: Bain
- first_name: J M
full_name: Nunzi, J M
last_name: Nunzi
external_id:
arxiv:
- '1806.01000'
isi:
- '000453298500019'
intvolume: ' 10672'
isi: 1
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/1806.01000
month: '05'
oa: 1
oa_version: Preprint
publication_status: published
publisher: SPIE
publist_id: '7766'
quality_controlled: '1'
scopus_import: '1'
status: public
title: Routing thermal noise through quantum networks
type: conference
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
volume: 10672
year: '2018'
...
---
_id: '5767'
abstract:
- lang: eng
text: 'Cuprate superconductors have long been thought of as having strong electronic
correlations but negligible spin-orbit coupling. Using spin- and angle-resolved
photoemission spectroscopy, we discovered that one of the most studied cuprate
superconductors, Bi2212, has a nontrivial spin texture with a spin-momentum locking
that circles the Brillouin zone center and a spin-layer locking that allows states
of opposite spin to be localized in different parts of the unit cell. Our findings
pose challenges for the vast majority of models of cuprates, such as the Hubbard
model and its variants, where spin-orbit interaction has been mostly neglected,
and open the intriguing question of how the high-temperature superconducting state
emerges in the presence of this nontrivial spin texture. '
acknowledgement: ' M.S. was supported by the Gordon and Betty Moore Foundation s EPiQS
Initiative through grant GBMF4307'
article_processing_charge: No
article_type: original
author:
- first_name: Kenneth
full_name: Gotlieb, Kenneth
last_name: Gotlieb
- first_name: Chiu-Yun
full_name: Lin, Chiu-Yun
last_name: Lin
- first_name: Maksym
full_name: Serbyn, Maksym
id: 47809E7E-F248-11E8-B48F-1D18A9856A87
last_name: Serbyn
orcid: 0000-0002-2399-5827
- first_name: Wentao
full_name: Zhang, Wentao
last_name: Zhang
- first_name: Christopher L.
full_name: Smallwood, Christopher L.
last_name: Smallwood
- first_name: Christopher
full_name: Jozwiak, Christopher
last_name: Jozwiak
- first_name: Hiroshi
full_name: Eisaki, Hiroshi
last_name: Eisaki
- first_name: Zahid
full_name: Hussain, Zahid
last_name: Hussain
- first_name: Ashvin
full_name: Vishwanath, Ashvin
last_name: Vishwanath
- first_name: Alessandra
full_name: Lanzara, Alessandra
last_name: Lanzara
citation:
ama: Gotlieb K, Lin C-Y, Serbyn M, et al. Revealing hidden spin-momentum locking
in a high-temperature cuprate superconductor. Science. 2018;362(6420):1271-1275.
doi:10.1126/science.aao0980
apa: Gotlieb, K., Lin, C.-Y., Serbyn, M., Zhang, W., Smallwood, C. L., Jozwiak,
C., … Lanzara, A. (2018). Revealing hidden spin-momentum locking in a high-temperature
cuprate superconductor. Science. American Association for the Advancement
of Science. https://doi.org/10.1126/science.aao0980
chicago: Gotlieb, Kenneth, Chiu-Yun Lin, Maksym Serbyn, Wentao Zhang, Christopher
L. Smallwood, Christopher Jozwiak, Hiroshi Eisaki, Zahid Hussain, Ashvin Vishwanath,
and Alessandra Lanzara. “Revealing Hidden Spin-Momentum Locking in a High-Temperature
Cuprate Superconductor.” Science. American Association for the Advancement
of Science, 2018. https://doi.org/10.1126/science.aao0980.
ieee: K. Gotlieb et al., “Revealing hidden spin-momentum locking in a high-temperature
cuprate superconductor,” Science, vol. 362, no. 6420. American Association
for the Advancement of Science, pp. 1271–1275, 2018.
ista: Gotlieb K, Lin C-Y, Serbyn M, Zhang W, Smallwood CL, Jozwiak C, Eisaki H,
Hussain Z, Vishwanath A, Lanzara A. 2018. Revealing hidden spin-momentum locking
in a high-temperature cuprate superconductor. Science. 362(6420), 1271–1275.
mla: Gotlieb, Kenneth, et al. “Revealing Hidden Spin-Momentum Locking in a High-Temperature
Cuprate Superconductor.” Science, vol. 362, no. 6420, American Association
for the Advancement of Science, 2018, pp. 1271–75, doi:10.1126/science.aao0980.
short: K. Gotlieb, C.-Y. Lin, M. Serbyn, W. Zhang, C.L. Smallwood, C. Jozwiak, H.
Eisaki, Z. Hussain, A. Vishwanath, A. Lanzara, Science 362 (2018) 1271–1275.
date_created: 2018-12-19T14:53:50Z
date_published: 2018-12-14T00:00:00Z
date_updated: 2023-09-18T08:11:56Z
day: '14'
department:
- _id: MaSe
doi: 10.1126/science.aao0980
external_id:
isi:
- '000452994400048'
intvolume: ' 362'
isi: 1
issue: '6420'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.1126/science.aao0980
month: '12'
oa: 1
oa_version: Published Version
page: 1271-1275
publication: Science
publication_identifier:
eissn:
- 1095-9203
issn:
- 0036-8075
publication_status: published
publisher: American Association for the Advancement of Science
quality_controlled: '1'
scopus_import: '1'
status: public
title: Revealing hidden spin-momentum locking in a high-temperature cuprate superconductor
type: journal_article
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
volume: 362
year: '2018'
...
---
_id: '434'
abstract:
- lang: eng
text: In this paper, we present a formal model-driven design approach to establish
a safety-assured implementation of multifunction vehicle bus controller (MVBC),
which controls the data transmission among the devices of the vehicle. First,
the generic models and safety requirements described in International Electrotechnical
Commission Standard 61375 are formalized as time automata and timed computation
tree logic formulas, respectively. With model checking tool Uppaal, we verify
whether or not the constructed timed automata satisfy the formulas and several
logic inconsistencies in the original standard are detected and corrected. Then,
we apply the code generation tool Times to generate C code from the verified model,
which is later synthesized into a real MVBC chip, with some handwriting glue code.
Furthermore, the runtime verification tool RMOR is applied on the integrated code,
to verify some safety requirements that cannot be formalized on the timed automata.
For evaluation, we compare the proposed approach with existing MVBC design methods,
such as BeagleBone, Galsblock, and Simulink. Experiments show that more ambiguousness
or bugs in the standard are detected during Uppaal verification, and the generated
code of Times outperforms the C code generated by others in terms of the synthesized
binary code size. The errors in the standard have been confirmed and the resulting
MVBC has been deployed in the real train communication network.
article_processing_charge: No
author:
- first_name: Yu
full_name: Jiang, Yu
last_name: Jiang
- first_name: Han
full_name: Liu, Han
last_name: Liu
- first_name: Huobing
full_name: Song, Huobing
last_name: Song
- first_name: Hui
full_name: Kong, Hui
id: 3BDE25AA-F248-11E8-B48F-1D18A9856A87
last_name: Kong
orcid: 0000-0002-3066-6941
- first_name: Rui
full_name: Wang, Rui
last_name: Wang
- first_name: Yong
full_name: Guan, Yong
last_name: Guan
- first_name: Lui
full_name: Sha, Lui
last_name: Sha
citation:
ama: Jiang Y, Liu H, Song H, et al. Safety-assured model-driven design of the multifunction
vehicle bus controller. IEEE Transactions on Intelligent Transportation Systems.
2018;19(10):3320-3333. doi:10.1109/TITS.2017.2778077
apa: Jiang, Y., Liu, H., Song, H., Kong, H., Wang, R., Guan, Y., & Sha, L. (2018).
Safety-assured model-driven design of the multifunction vehicle bus controller.
IEEE Transactions on Intelligent Transportation Systems. IEEE. https://doi.org/10.1109/TITS.2017.2778077
chicago: Jiang, Yu, Han Liu, Huobing Song, Hui Kong, Rui Wang, Yong Guan, and Lui
Sha. “Safety-Assured Model-Driven Design of the Multifunction Vehicle Bus Controller.”
IEEE Transactions on Intelligent Transportation Systems. IEEE, 2018. https://doi.org/10.1109/TITS.2017.2778077.
ieee: Y. Jiang et al., “Safety-assured model-driven design of the multifunction
vehicle bus controller,” IEEE Transactions on Intelligent Transportation Systems,
vol. 19, no. 10. IEEE, pp. 3320–3333, 2018.
ista: Jiang Y, Liu H, Song H, Kong H, Wang R, Guan Y, Sha L. 2018. Safety-assured
model-driven design of the multifunction vehicle bus controller. IEEE Transactions
on Intelligent Transportation Systems. 19(10), 3320–3333.
mla: Jiang, Yu, et al. “Safety-Assured Model-Driven Design of the Multifunction
Vehicle Bus Controller.” IEEE Transactions on Intelligent Transportation Systems,
vol. 19, no. 10, IEEE, 2018, pp. 3320–33, doi:10.1109/TITS.2017.2778077.
short: Y. Jiang, H. Liu, H. Song, H. Kong, R. Wang, Y. Guan, L. Sha, IEEE Transactions
on Intelligent Transportation Systems 19 (2018) 3320–3333.
date_created: 2018-12-11T11:46:27Z
date_published: 2018-01-01T00:00:00Z
date_updated: 2023-09-18T08:12:49Z
day: '01'
department:
- _id: ToHe
doi: 10.1109/TITS.2017.2778077
external_id:
isi:
- '000446651100020'
intvolume: ' 19'
isi: 1
issue: '10'
language:
- iso: eng
month: '01'
oa_version: None
page: 3320 - 3333
publication: IEEE Transactions on Intelligent Transportation Systems
publication_status: published
publisher: IEEE
publist_id: '7389'
quality_controlled: '1'
related_material:
record:
- id: '1205'
relation: earlier_version
status: public
scopus_import: '1'
status: public
title: Safety-assured model-driven design of the multifunction vehicle bus controller
type: journal_article
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
volume: 19
year: '2018'
...
---
_id: '162'
abstract:
- lang: eng
text: 'Facial shape is the basis for facial recognition and categorization. Facial
features reflect the underlying geometry of the skeletal structures. Here, we
reveal that cartilaginous nasal capsule (corresponding to upper jaw and face)
is shaped by signals generated by neural structures: brain and olfactory epithelium.
Brain-derived Sonic Hedgehog (SHH) enables the induction of nasal septum and posterior
nasal capsule, whereas the formation of a capsule roof is controlled by signals
from the olfactory epithelium. Unexpectedly, the cartilage of the nasal capsule
turned out to be important for shaping membranous facial bones during development.
This suggests that conserved neurosensory structures could benefit from protection
and have evolved signals inducing cranial cartilages encasing them. Experiments
with mutant mice revealed that the genomic regulatory regions controlling production
of SHH in the nervous system contribute to facial cartilage morphogenesis, which
might be a mechanism responsible for the adaptive evolution of animal faces and
snouts.'
article_number: e34465
article_processing_charge: No
author:
- first_name: Marketa
full_name: Kaucka, Marketa
last_name: Kaucka
- first_name: Julian
full_name: Petersen, Julian
last_name: Petersen
- first_name: Marketa
full_name: Tesarova, Marketa
last_name: Tesarova
- first_name: Bara
full_name: Szarowska, Bara
last_name: Szarowska
- first_name: Maria
full_name: Kastriti, Maria
last_name: Kastriti
- first_name: Meng
full_name: Xie, Meng
last_name: Xie
- first_name: Anna
full_name: Kicheva, Anna
id: 3959A2A0-F248-11E8-B48F-1D18A9856A87
last_name: Kicheva
orcid: 0000-0003-4509-4998
- first_name: Karl
full_name: Annusver, Karl
last_name: Annusver
- first_name: Maria
full_name: Kasper, Maria
last_name: Kasper
- first_name: Orsolya
full_name: Symmons, Orsolya
last_name: Symmons
- first_name: Leslie
full_name: Pan, Leslie
last_name: Pan
- first_name: Francois
full_name: Spitz, Francois
last_name: Spitz
- first_name: Jozef
full_name: Kaiser, Jozef
last_name: Kaiser
- first_name: Maria
full_name: Hovorakova, Maria
last_name: Hovorakova
- first_name: Tomas
full_name: Zikmund, Tomas
last_name: Zikmund
- first_name: Kazunori
full_name: Sunadome, Kazunori
last_name: Sunadome
- first_name: Michael P
full_name: Matise, Michael P
last_name: Matise
- first_name: Hui
full_name: Wang, Hui
last_name: Wang
- first_name: Ulrika
full_name: Marklund, Ulrika
last_name: Marklund
- first_name: Hind
full_name: Abdo, Hind
last_name: Abdo
- first_name: Patrik
full_name: Ernfors, Patrik
last_name: Ernfors
- first_name: Pascal
full_name: Maire, Pascal
last_name: Maire
- first_name: Maud
full_name: Wurmser, Maud
last_name: Wurmser
- first_name: Andrei S
full_name: Chagin, Andrei S
last_name: Chagin
- first_name: Kaj
full_name: Fried, Kaj
last_name: Fried
- first_name: Igor
full_name: Adameyko, Igor
last_name: Adameyko
citation:
ama: Kaucka M, Petersen J, Tesarova M, et al. Signals from the brain and olfactory
epithelium control shaping of the mammalian nasal capsule cartilage. eLife.
2018;7. doi:10.7554/eLife.34465
apa: Kaucka, M., Petersen, J., Tesarova, M., Szarowska, B., Kastriti, M., Xie, M.,
… Adameyko, I. (2018). Signals from the brain and olfactory epithelium control
shaping of the mammalian nasal capsule cartilage. ELife. eLife Sciences
Publications. https://doi.org/10.7554/eLife.34465
chicago: Kaucka, Marketa, Julian Petersen, Marketa Tesarova, Bara Szarowska, Maria
Kastriti, Meng Xie, Anna Kicheva, et al. “Signals from the Brain and Olfactory
Epithelium Control Shaping of the Mammalian Nasal Capsule Cartilage.” ELife.
eLife Sciences Publications, 2018. https://doi.org/10.7554/eLife.34465.
ieee: M. Kaucka et al., “Signals from the brain and olfactory epithelium
control shaping of the mammalian nasal capsule cartilage,” eLife, vol.
7. eLife Sciences Publications, 2018.
ista: Kaucka M, Petersen J, Tesarova M, Szarowska B, Kastriti M, Xie M, Kicheva
A, Annusver K, Kasper M, Symmons O, Pan L, Spitz F, Kaiser J, Hovorakova M, Zikmund
T, Sunadome K, Matise MP, Wang H, Marklund U, Abdo H, Ernfors P, Maire P, Wurmser
M, Chagin AS, Fried K, Adameyko I. 2018. Signals from the brain and olfactory
epithelium control shaping of the mammalian nasal capsule cartilage. eLife. 7,
e34465.
mla: Kaucka, Marketa, et al. “Signals from the Brain and Olfactory Epithelium Control
Shaping of the Mammalian Nasal Capsule Cartilage.” ELife, vol. 7, e34465,
eLife Sciences Publications, 2018, doi:10.7554/eLife.34465.
short: M. Kaucka, J. Petersen, M. Tesarova, B. Szarowska, M. Kastriti, M. Xie, A.
Kicheva, K. Annusver, M. Kasper, O. Symmons, L. Pan, F. Spitz, J. Kaiser, M. Hovorakova,
T. Zikmund, K. Sunadome, M.P. Matise, H. Wang, U. Marklund, H. Abdo, P. Ernfors,
P. Maire, M. Wurmser, A.S. Chagin, K. Fried, I. Adameyko, ELife 7 (2018).
date_created: 2018-12-11T11:44:57Z
date_published: 2018-06-13T00:00:00Z
date_updated: 2023-09-18T09:29:07Z
day: '13'
ddc:
- '571'
department:
- _id: AnKi
doi: 10.7554/eLife.34465
ec_funded: 1
external_id:
isi:
- '000436227500001'
file:
- access_level: open_access
checksum: da2378cdcf6b5461dcde194e4d608343
content_type: application/pdf
creator: dernst
date_created: 2018-12-17T16:41:58Z
date_updated: 2020-07-14T12:45:07Z
file_id: '5727'
file_name: 2018_eLife_Kaucka.pdf
file_size: 9816484
relation: main_file
file_date_updated: 2020-07-14T12:45:07Z
has_accepted_license: '1'
intvolume: ' 7'
isi: 1
language:
- iso: eng
month: '06'
oa: 1
oa_version: Published Version
project:
- _id: B6FC0238-B512-11E9-945C-1524E6697425
call_identifier: H2020
grant_number: '680037'
name: Coordination of Patterning And Growth In the Spinal Cord
publication: eLife
publication_status: published
publisher: eLife Sciences Publications
publist_id: '7759'
quality_controlled: '1'
related_material:
record:
- id: '9838'
relation: research_data
status: public
scopus_import: '1'
status: public
title: Signals from the brain and olfactory epithelium control shaping of the mammalian
nasal capsule cartilage
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: journal_article
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
volume: 7
year: '2018'
...
---
_id: '302'
abstract:
- lang: eng
text: At ITCS 2013, Mahmoody, Moran and Vadhan [MMV13] introduce and construct publicly
verifiable proofs of sequential work, which is a protocol for proving that one
spent sequential computational work related to some statement. The original motivation
for such proofs included non-interactive time-stamping and universally verifiable
CPU benchmarks. A more recent application, and our main motivation, are blockchain
designs, where proofs of sequential work can be used – in combination with proofs
of space – as a more ecological and economical substitute for proofs of work which
are currently used to secure Bitcoin and other cryptocurrencies. The construction
proposed by [MMV13] is based on a hash function and can be proven secure in the
random oracle model, or assuming inherently sequential hash-functions, which is
a new standard model assumption introduced in their work. In a proof of sequential
work, a prover gets a “statement” χ, a time parameter N and access to a hash-function
H, which for the security proof is modelled as a random oracle. Correctness requires
that an honest prover can make a verifier accept making only N queries to H, while
soundness requires that any prover who makes the verifier accept must have made
(almost) N sequential queries to H. Thus a solution constitutes a proof that N
time passed since χ was received. Solutions must be publicly verifiable in time
at most polylogarithmic in N. The construction of [MMV13] is based on “depth-robust”
graphs, and as a consequence has rather poor concrete parameters. But the major
drawback is that the prover needs not just N time, but also N space to compute
a proof. In this work we propose a proof of sequential work which is much simpler,
more efficient and achieves much better concrete bounds. Most importantly, the
space required can be as small as log (N) (but we get better soundness using slightly
more memory than that). An open problem stated by [MMV13] that our construction
does not solve either is achieving a “unique” proof, where even a cheating prover
can only generate a single accepting proof. This property would be extremely useful
for applications to blockchains.
alternative_title:
- LNCS
article_processing_charge: No
author:
- first_name: Bram
full_name: Cohen, Bram
last_name: Cohen
- first_name: Krzysztof Z
full_name: Pietrzak, Krzysztof Z
id: 3E04A7AA-F248-11E8-B48F-1D18A9856A87
last_name: Pietrzak
orcid: 0000-0002-9139-1654
citation:
ama: 'Cohen B, Pietrzak KZ. Simple proofs of sequential work. In: Vol 10821. Springer;
2018:451-467. doi:10.1007/978-3-319-78375-8_15'
apa: 'Cohen, B., & Pietrzak, K. Z. (2018). Simple proofs of sequential work
(Vol. 10821, pp. 451–467). Presented at the Eurocrypt: Advances in Cryptology,
Tel Aviv, Israel: Springer. https://doi.org/10.1007/978-3-319-78375-8_15'
chicago: Cohen, Bram, and Krzysztof Z Pietrzak. “Simple Proofs of Sequential Work,”
10821:451–67. Springer, 2018. https://doi.org/10.1007/978-3-319-78375-8_15.
ieee: 'B. Cohen and K. Z. Pietrzak, “Simple proofs of sequential work,” presented
at the Eurocrypt: Advances in Cryptology, Tel Aviv, Israel, 2018, vol. 10821,
pp. 451–467.'
ista: 'Cohen B, Pietrzak KZ. 2018. Simple proofs of sequential work. Eurocrypt:
Advances in Cryptology, LNCS, vol. 10821, 451–467.'
mla: Cohen, Bram, and Krzysztof Z. Pietrzak. Simple Proofs of Sequential Work.
Vol. 10821, Springer, 2018, pp. 451–67, doi:10.1007/978-3-319-78375-8_15.
short: B. Cohen, K.Z. Pietrzak, in:, Springer, 2018, pp. 451–467.
conference:
end_date: 2018-05-03
location: Tel Aviv, Israel
name: 'Eurocrypt: Advances in Cryptology'
start_date: 2018-04-29
date_created: 2018-12-11T11:45:42Z
date_published: 2018-05-29T00:00:00Z
date_updated: 2023-09-18T09:29:33Z
day: '29'
department:
- _id: KrPi
doi: 10.1007/978-3-319-78375-8_15
ec_funded: 1
external_id:
isi:
- '000517098700015'
intvolume: ' 10821'
isi: 1
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://eprint.iacr.org/2018/183.pdf
month: '05'
oa: 1
oa_version: Submitted Version
page: 451 - 467
project:
- _id: 258AA5B2-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '682815'
name: Teaching Old Crypto New Tricks
publication_status: published
publisher: Springer
publist_id: '7579'
quality_controlled: '1'
scopus_import: '1'
status: public
title: Simple proofs of sequential work
type: conference
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
volume: 10821
year: '2018'
...
---
_id: '31'
abstract:
- lang: eng
text: Correlations in sensory neural networks have both extrinsic and intrinsic
origins. Extrinsic or stimulus correlations arise from shared inputs to the network
and, thus, depend strongly on the stimulus ensemble. Intrinsic or noise correlations
reflect biophysical mechanisms of interactions between neurons, which are expected
to be robust to changes in the stimulus ensemble. Despite the importance of this
distinction for understanding how sensory networks encode information collectively,
no method exists to reliably separate intrinsic interactions from extrinsic correlations
in neural activity data, limiting our ability to build predictive models of the
network response. In this paper we introduce a general strategy to infer population
models of interacting neurons that collectively encode stimulus information. The
key to disentangling intrinsic from extrinsic correlations is to infer the couplings
between neurons separately from the encoding model and to combine the two using
corrections calculated in a mean-field approximation. We demonstrate the effectiveness
of this approach in retinal recordings. The same coupling network is inferred
from responses to radically different stimulus ensembles, showing that these couplings
indeed reflect stimulus-independent interactions between neurons. The inferred
model predicts accurately the collective response of retinal ganglion cell populations
as a function of the stimulus.
acknowledgement: This work was supported by ANR Trajectory, the French State program
Investissements d’Avenir managed by the Agence Nationale de la Recherche (LIFESENSES;
ANR-10-LABX-65), EC Grant No. H2020-785907 from the Human Brain Project, NIH Grant
No. U01NS090501, and an AVIESAN-UNADEV grant to O.M. M.C. was supported by the Agence
Nationale de la Recherche Jeune Chercheur/Jeune Chercheuse grant (ANR-17-CE37-0013).
article_number: '042410'
article_processing_charge: No
article_type: original
author:
- first_name: Ulisse
full_name: Ferrari, Ulisse
last_name: Ferrari
- first_name: Stephane
full_name: Deny, Stephane
last_name: Deny
- first_name: Matthew J
full_name: Chalk, Matthew J
last_name: Chalk
- first_name: Gasper
full_name: Tkacik, Gasper
id: 3D494DCA-F248-11E8-B48F-1D18A9856A87
last_name: Tkacik
orcid: 0000-0002-6699-1455
- first_name: Olivier
full_name: Marre, Olivier
last_name: Marre
- first_name: Thierry
full_name: Mora, Thierry
last_name: Mora
citation:
ama: Ferrari U, Deny S, Chalk MJ, Tkačik G, Marre O, Mora T. Separating intrinsic
interactions from extrinsic correlations in a network of sensory neurons. Physical
Review E. 2018;98(4). doi:10.1103/PhysRevE.98.042410
apa: Ferrari, U., Deny, S., Chalk, M. J., Tkačik, G., Marre, O., & Mora, T.
(2018). Separating intrinsic interactions from extrinsic correlations in a network
of sensory neurons. Physical Review E. American Physical Society. https://doi.org/10.1103/PhysRevE.98.042410
chicago: Ferrari, Ulisse, Stephane Deny, Matthew J Chalk, Gašper Tkačik, Olivier
Marre, and Thierry Mora. “Separating Intrinsic Interactions from Extrinsic Correlations
in a Network of Sensory Neurons.” Physical Review E. American Physical
Society, 2018. https://doi.org/10.1103/PhysRevE.98.042410.
ieee: U. Ferrari, S. Deny, M. J. Chalk, G. Tkačik, O. Marre, and T. Mora, “Separating
intrinsic interactions from extrinsic correlations in a network of sensory neurons,”
Physical Review E, vol. 98, no. 4. American Physical Society, 2018.
ista: Ferrari U, Deny S, Chalk MJ, Tkačik G, Marre O, Mora T. 2018. Separating intrinsic
interactions from extrinsic correlations in a network of sensory neurons. Physical
Review E. 98(4), 042410.
mla: Ferrari, Ulisse, et al. “Separating Intrinsic Interactions from Extrinsic Correlations
in a Network of Sensory Neurons.” Physical Review E, vol. 98, no. 4, 042410,
American Physical Society, 2018, doi:10.1103/PhysRevE.98.042410.
short: U. Ferrari, S. Deny, M.J. Chalk, G. Tkačik, O. Marre, T. Mora, Physical Review
E 98 (2018).
date_created: 2018-12-11T11:44:15Z
date_published: 2018-10-17T00:00:00Z
date_updated: 2023-09-18T09:18:44Z
day: '17'
department:
- _id: GaTk
doi: 10.1103/PhysRevE.98.042410
ec_funded: 1
external_id:
isi:
- '000447486100004'
intvolume: ' 98'
isi: 1
issue: '4'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://www.biorxiv.org/content/10.1101/243816v2.full
month: '10'
oa: 1
oa_version: Preprint
project:
- _id: 26436750-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '785907'
name: Human Brain Project Specific Grant Agreement 2 (HBP SGA 2)
publication: Physical Review E
publication_identifier:
issn:
- '24700045'
publication_status: published
publisher: American Physical Society
publist_id: '8024'
quality_controlled: '1'
scopus_import: '1'
status: public
title: Separating intrinsic interactions from extrinsic correlations in a network
of sensory neurons
type: journal_article
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
volume: 98
year: '2018'
...
---
_id: '64'
abstract:
- lang: eng
text: Tropical geometry, an established field in pure mathematics, is a place where
string theory, mirror symmetry, computational algebra, auction theory, and so
forth meet and influence one another. In this paper, we report on our discovery
of a tropical model with self-organized criticality (SOC) behavior. Our model
is continuous, in contrast to all known models of SOC, and is a certain scaling
limit of the sandpile model, the first and archetypical model of SOC. We describe
how our model is related to pattern formation and proportional growth phenomena
and discuss the dichotomy between continuous and discrete models in several contexts.
Our aim in this context is to present an idealized tropical toy model (cf. Turing
reaction-diffusion model), requiring further investigation.
article_processing_charge: No
article_type: original
author:
- first_name: Nikita
full_name: Kalinin, Nikita
last_name: Kalinin
- first_name: Aldo
full_name: Guzmán Sáenz, Aldo
last_name: Guzmán Sáenz
- first_name: Y
full_name: Prieto, Y
last_name: Prieto
- first_name: Mikhail
full_name: Shkolnikov, Mikhail
id: 35084A62-F248-11E8-B48F-1D18A9856A87
last_name: Shkolnikov
orcid: 0000-0002-4310-178X
- first_name: V
full_name: Kalinina, V
last_name: Kalinina
- first_name: Ernesto
full_name: Lupercio, Ernesto
last_name: Lupercio
citation:
ama: 'Kalinin N, Guzmán Sáenz A, Prieto Y, Shkolnikov M, Kalinina V, Lupercio E.
Self-organized criticality and pattern emergence through the lens of tropical
geometry. PNAS: Proceedings of the National Academy of Sciences of the United
States of America. 2018;115(35):E8135-E8142. doi:10.1073/pnas.1805847115'
apa: 'Kalinin, N., Guzmán Sáenz, A., Prieto, Y., Shkolnikov, M., Kalinina, V., &
Lupercio, E. (2018). Self-organized criticality and pattern emergence through
the lens of tropical geometry. PNAS: Proceedings of the National Academy of
Sciences of the United States of America. National Academy of Sciences. https://doi.org/10.1073/pnas.1805847115'
chicago: 'Kalinin, Nikita, Aldo Guzmán Sáenz, Y Prieto, Mikhail Shkolnikov, V Kalinina,
and Ernesto Lupercio. “Self-Organized Criticality and Pattern Emergence through
the Lens of Tropical Geometry.” PNAS: Proceedings of the National Academy of
Sciences of the United States of America. National Academy of Sciences, 2018.
https://doi.org/10.1073/pnas.1805847115.'
ieee: 'N. Kalinin, A. Guzmán Sáenz, Y. Prieto, M. Shkolnikov, V. Kalinina, and E.
Lupercio, “Self-organized criticality and pattern emergence through the lens of
tropical geometry,” PNAS: Proceedings of the National Academy of Sciences of
the United States of America, vol. 115, no. 35. National Academy of Sciences,
pp. E8135–E8142, 2018.'
ista: 'Kalinin N, Guzmán Sáenz A, Prieto Y, Shkolnikov M, Kalinina V, Lupercio E.
2018. Self-organized criticality and pattern emergence through the lens of tropical
geometry. PNAS: Proceedings of the National Academy of Sciences of the United
States of America. 115(35), E8135–E8142.'
mla: 'Kalinin, Nikita, et al. “Self-Organized Criticality and Pattern Emergence
through the Lens of Tropical Geometry.” PNAS: Proceedings of the National Academy
of Sciences of the United States of America, vol. 115, no. 35, National Academy
of Sciences, 2018, pp. E8135–42, doi:10.1073/pnas.1805847115.'
short: 'N. Kalinin, A. Guzmán Sáenz, Y. Prieto, M. Shkolnikov, V. Kalinina, E. Lupercio,
PNAS: Proceedings of the National Academy of Sciences of the United States of
America 115 (2018) E8135–E8142.'
date_created: 2018-12-11T11:44:26Z
date_published: 2018-08-28T00:00:00Z
date_updated: 2023-09-18T08:41:16Z
day: '28'
department:
- _id: TaHa
doi: 10.1073/pnas.1805847115
ec_funded: 1
external_id:
arxiv:
- '1806.09153'
isi:
- '000442861600009'
intvolume: ' 115'
isi: 1
issue: '35'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/1806.09153
month: '08'
oa: 1
oa_version: Preprint
page: E8135 - E8142
project:
- _id: 25681D80-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '291734'
name: International IST Postdoc Fellowship Programme
publication: 'PNAS: Proceedings of the National Academy of Sciences of the United
States of America'
publication_identifier:
issn:
- '00278424'
publication_status: published
publisher: National Academy of Sciences
publist_id: '7990'
quality_controlled: '1'
scopus_import: '1'
status: public
title: Self-organized criticality and pattern emergence through the lens of tropical
geometry
type: journal_article
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
volume: 115
year: '2018'
...
---
_id: '9838'
abstract:
- lang: eng
text: 'Facial shape is the basis for facial recognition and categorization. Facial
features reflect the underlying geometry of the skeletal structures. Here we reveal
that cartilaginous nasal capsule (corresponding to upper jaw and face) is shaped
by signals generated by neural structures: brain and olfactory epithelium. Brain-derived
Sonic Hedgehog (SHH) enables the induction of nasal septum and posterior nasal
capsule, whereas the formation of a capsule roof is controlled by signals from
the olfactory epithelium. Unexpectedly, the cartilage of the nasal capsule turned
out to be important for shaping membranous facial bones during development. This
suggests that conserved neurosensory structures could benefit from protection
and have evolved signals inducing cranial cartilages encasing them. Experiments
with mutant mice revealed that the genomic regulatory regions controlling production
of SHH in the nervous system contribute to facial cartilage morphogenesis, which
might be a mechanism responsible for the adaptive evolution of animal faces and
snouts.'
article_processing_charge: No
author:
- first_name: Marketa
full_name: Kaucka, Marketa
last_name: Kaucka
- first_name: Julian
full_name: Petersen, Julian
last_name: Petersen
- first_name: Marketa
full_name: Tesarova, Marketa
last_name: Tesarova
- first_name: Bara
full_name: Szarowska, Bara
last_name: Szarowska
- first_name: Maria Eleni
full_name: Kastriti, Maria Eleni
last_name: Kastriti
- first_name: Meng
full_name: Xie, Meng
last_name: Xie
- first_name: Anna
full_name: Kicheva, Anna
id: 3959A2A0-F248-11E8-B48F-1D18A9856A87
last_name: Kicheva
orcid: 0000-0003-4509-4998
- first_name: Karl
full_name: Annusver, Karl
last_name: Annusver
- first_name: Maria
full_name: Kasper, Maria
last_name: Kasper
- first_name: Orsolya
full_name: Symmons, Orsolya
last_name: Symmons
- first_name: Leslie
full_name: Pan, Leslie
last_name: Pan
- first_name: Francois
full_name: Spitz, Francois
last_name: Spitz
- first_name: Jozef
full_name: Kaiser, Jozef
last_name: Kaiser
- first_name: Maria
full_name: Hovorakova, Maria
last_name: Hovorakova
- first_name: Tomas
full_name: Zikmund, Tomas
last_name: Zikmund
- first_name: Kazunori
full_name: Sunadome, Kazunori
last_name: Sunadome
- first_name: Michael P
full_name: Matise, Michael P
last_name: Matise
- first_name: Hui
full_name: Wang, Hui
last_name: Wang
- first_name: Ulrika
full_name: Marklund, Ulrika
last_name: Marklund
- first_name: Hind
full_name: Abdo, Hind
last_name: Abdo
- first_name: Patrik
full_name: Ernfors, Patrik
last_name: Ernfors
- first_name: Pascal
full_name: Maire, Pascal
last_name: Maire
- first_name: Maud
full_name: Wurmser, Maud
last_name: Wurmser
- first_name: Andrei S
full_name: Chagin, Andrei S
last_name: Chagin
- first_name: Kaj
full_name: Fried, Kaj
last_name: Fried
- first_name: Igor
full_name: Adameyko, Igor
last_name: Adameyko
citation:
ama: 'Kaucka M, Petersen J, Tesarova M, et al. Data from: Signals from the brain
and olfactory epithelium control shaping of the mammalian nasal capsule cartilage.
2018. doi:10.5061/dryad.f1s76f2'
apa: 'Kaucka, M., Petersen, J., Tesarova, M., Szarowska, B., Kastriti, M. E., Xie,
M., … Adameyko, I. (2018). Data from: Signals from the brain and olfactory epithelium
control shaping of the mammalian nasal capsule cartilage. Dryad. https://doi.org/10.5061/dryad.f1s76f2'
chicago: 'Kaucka, Marketa, Julian Petersen, Marketa Tesarova, Bara Szarowska, Maria
Eleni Kastriti, Meng Xie, Anna Kicheva, et al. “Data from: Signals from the Brain
and Olfactory Epithelium Control Shaping of the Mammalian Nasal Capsule Cartilage.”
Dryad, 2018. https://doi.org/10.5061/dryad.f1s76f2.'
ieee: 'M. Kaucka et al., “Data from: Signals from the brain and olfactory
epithelium control shaping of the mammalian nasal capsule cartilage.” Dryad, 2018.'
ista: 'Kaucka M, Petersen J, Tesarova M, Szarowska B, Kastriti ME, Xie M, Kicheva
A, Annusver K, Kasper M, Symmons O, Pan L, Spitz F, Kaiser J, Hovorakova M, Zikmund
T, Sunadome K, Matise MP, Wang H, Marklund U, Abdo H, Ernfors P, Maire P, Wurmser
M, Chagin AS, Fried K, Adameyko I. 2018. Data from: Signals from the brain and
olfactory epithelium control shaping of the mammalian nasal capsule cartilage,
Dryad, 10.5061/dryad.f1s76f2.'
mla: 'Kaucka, Marketa, et al. Data from: Signals from the Brain and Olfactory
Epithelium Control Shaping of the Mammalian Nasal Capsule Cartilage. Dryad,
2018, doi:10.5061/dryad.f1s76f2.'
short: M. Kaucka, J. Petersen, M. Tesarova, B. Szarowska, M.E. Kastriti, M. Xie,
A. Kicheva, K. Annusver, M. Kasper, O. Symmons, L. Pan, F. Spitz, J. Kaiser, M.
Hovorakova, T. Zikmund, K. Sunadome, M.P. Matise, H. Wang, U. Marklund, H. Abdo,
P. Ernfors, P. Maire, M. Wurmser, A.S. Chagin, K. Fried, I. Adameyko, (2018).
date_created: 2021-08-09T12:54:35Z
date_published: 2018-06-14T00:00:00Z
date_updated: 2023-09-18T09:29:07Z
day: '14'
department:
- _id: AnKi
doi: 10.5061/dryad.f1s76f2
main_file_link:
- open_access: '1'
url: https://doi.org/10.5061/dryad.f1s76f2
month: '06'
oa: 1
oa_version: Published Version
publisher: Dryad
related_material:
record:
- id: '162'
relation: used_in_publication
status: public
status: public
title: 'Data from: Signals from the brain and olfactory epithelium control shaping
of the mammalian nasal capsule cartilage'
type: research_data_reference
user_id: 6785fbc1-c503-11eb-8a32-93094b40e1cf
year: '2018'
...
---
_id: '41'
abstract:
- lang: eng
text: 'The small-conductance, Ca2+-activated K+ (SK) channel subtype SK2 regulates
the spike rate and firing frequency, as well as Ca2+ transients in Purkinje cells
(PCs). To understand the molecular basis by which SK2 channels mediate these functions,
we analyzed the exact location and densities of SK2 channels along the neuronal
surface of the mouse cerebellar PCs using SDS-digested freeze-fracture replica
labeling (SDS-FRL) of high sensitivity combined with quantitative analyses. Immunogold
particles for SK2 were observed on post- and pre-synaptic compartments showing
both scattered and clustered distribution patterns. We found an axo-somato-dendritic
gradient of the SK2 particle density increasing 12-fold from soma to dendritic
spines. Using two different immunogold approaches, we also found that SK2 immunoparticles
were frequently adjacent to, but never overlap with, the postsynaptic density
of excitatory synapses in PC spines. Co-immunoprecipitation analysis demonstrated
that SK2 channels form macromolecular complexes with two types of proteins that
mobilize Ca2+: CaV2.1 channels and mGlu1α receptors in the cerebellum. Freeze-fracture
replica double-labeling showed significant co-clustering of particles for SK2
with those for CaV2.1 channels and mGlu1α receptors. SK2 channels were also detected
at presynaptic sites, mostly at the presynaptic active zone (AZ), where they are
close to CaV2.1 channels, though they are not significantly co-clustered. These
data demonstrate that SK2 channels located in different neuronal compartments
can associate with distinct proteins mobilizing Ca2+, and suggest that the ultrastructural
association of SK2 with CaV2.1 and mGlu1α provides the mechanism that ensures
voltage (excitability) regulation by distinct intracellular Ca2+ transients in
PCs.'
article_number: '311'
article_processing_charge: No
article_type: original
author:
- first_name: Rafæl
full_name: Luján, Rafæl
last_name: Luján
- first_name: Carolina
full_name: Aguado, Carolina
last_name: Aguado
- first_name: Francisco
full_name: Ciruela, Francisco
last_name: Ciruela
- first_name: Xavier
full_name: Arus, Xavier
last_name: Arus
- first_name: Alejandro
full_name: Martín Belmonte, Alejandro
last_name: Martín Belmonte
- first_name: Rocío
full_name: Alfaro Ruiz, Rocío
last_name: Alfaro Ruiz
- first_name: Jesus
full_name: Martinez Gomez, Jesus
last_name: Martinez Gomez
- first_name: Luis
full_name: De La Ossa, Luis
last_name: De La Ossa
- first_name: Masahiko
full_name: Watanabe, Masahiko
last_name: Watanabe
- first_name: John
full_name: Adelman, John
last_name: Adelman
- first_name: Ryuichi
full_name: Shigemoto, Ryuichi
id: 499F3ABC-F248-11E8-B48F-1D18A9856A87
last_name: Shigemoto
orcid: 0000-0001-8761-9444
- first_name: Yugo
full_name: Fukazawa, Yugo
last_name: Fukazawa
citation:
ama: Luján R, Aguado C, Ciruela F, et al. Sk2 channels associate with mGlu1α receptors
and CaV2.1 channels in Purkinje cells. Frontiers in Cellular Neuroscience.
2018;12. doi:10.3389/fncel.2018.00311
apa: Luján, R., Aguado, C., Ciruela, F., Arus, X., Martín Belmonte, A., Alfaro Ruiz,
R., … Fukazawa, Y. (2018). Sk2 channels associate with mGlu1α receptors and CaV2.1
channels in Purkinje cells. Frontiers in Cellular Neuroscience. Frontiers
Media. https://doi.org/10.3389/fncel.2018.00311
chicago: Luján, Rafæl, Carolina Aguado, Francisco Ciruela, Xavier Arus, Alejandro
Martín Belmonte, Rocío Alfaro Ruiz, Jesus Martinez Gomez, et al. “Sk2 Channels
Associate with MGlu1α Receptors and CaV2.1 Channels in Purkinje Cells.” Frontiers
in Cellular Neuroscience. Frontiers Media, 2018. https://doi.org/10.3389/fncel.2018.00311.
ieee: R. Luján et al., “Sk2 channels associate with mGlu1α receptors and
CaV2.1 channels in Purkinje cells,” Frontiers in Cellular Neuroscience,
vol. 12. Frontiers Media, 2018.
ista: Luján R, Aguado C, Ciruela F, Arus X, Martín Belmonte A, Alfaro Ruiz R, Martinez
Gomez J, De La Ossa L, Watanabe M, Adelman J, Shigemoto R, Fukazawa Y. 2018. Sk2
channels associate with mGlu1α receptors and CaV2.1 channels in Purkinje cells.
Frontiers in Cellular Neuroscience. 12, 311.
mla: Luján, Rafæl, et al. “Sk2 Channels Associate with MGlu1α Receptors and CaV2.1
Channels in Purkinje Cells.” Frontiers in Cellular Neuroscience, vol. 12,
311, Frontiers Media, 2018, doi:10.3389/fncel.2018.00311.
short: R. Luján, C. Aguado, F. Ciruela, X. Arus, A. Martín Belmonte, R. Alfaro Ruiz,
J. Martinez Gomez, L. De La Ossa, M. Watanabe, J. Adelman, R. Shigemoto, Y. Fukazawa,
Frontiers in Cellular Neuroscience 12 (2018).
date_created: 2018-12-11T11:44:19Z
date_published: 2018-09-19T00:00:00Z
date_updated: 2023-09-18T09:31:18Z
day: '19'
ddc:
- '570'
department:
- _id: RySh
doi: 10.3389/fncel.2018.00311
ec_funded: 1
external_id:
isi:
- '000445090100002'
file:
- access_level: open_access
checksum: 0bcaec8d596162af0b7fe3f31325d480
content_type: application/pdf
creator: dernst
date_created: 2018-12-17T08:49:03Z
date_updated: 2020-07-14T12:46:23Z
file_id: '5684'
file_name: fncel-12-00311.pdf
file_size: 6834251
relation: main_file
file_date_updated: 2020-07-14T12:46:23Z
has_accepted_license: '1'
intvolume: ' 12'
isi: 1
language:
- iso: eng
month: '09'
oa: 1
oa_version: Published Version
project:
- _id: 25CBA828-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '720270'
name: Human Brain Project Specific Grant Agreement 1 (HBP SGA 1)
publication: Frontiers in Cellular Neuroscience
publication_identifier:
issn:
- '16625102'
publication_status: published
publisher: Frontiers Media
publist_id: '8013'
quality_controlled: '1'
scopus_import: '1'
status: public
title: Sk2 channels associate with mGlu1α receptors and CaV2.1 channels in Purkinje
cells
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: journal_article
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
volume: 12
year: '2018'
...
---
_id: '23'
abstract:
- lang: eng
text: The strong atomistic spin–orbit coupling of holes makes single-shot spin readout
measurements difficult because it reduces the spin lifetimes. By integrating the
charge sensor into a high bandwidth radio frequency reflectometry setup, we were
able to demonstrate single-shot readout of a germanium quantum dot hole spin and
measure the spin lifetime. Hole spin relaxation times of about 90 μs at 500 mT
are reported, with a total readout visibility of about 70%. By analyzing separately
the spin-to-charge conversion and charge readout fidelities, we have obtained
insight into the processes limiting the visibilities of hole spins. The analyses
suggest that high hole visibilities are feasible at realistic experimental conditions,
underlying the potential of hole spins for the realization of viable qubit devices.
acknowledged_ssus:
- _id: M-Shop
- _id: NanoFab
article_processing_charge: No
author:
- first_name: Lada
full_name: Vukušić, Lada
id: 31E9F056-F248-11E8-B48F-1D18A9856A87
last_name: Vukušić
orcid: 0000-0003-2424-8636
- first_name: Josip
full_name: Kukucka, Josip
id: 3F5D8856-F248-11E8-B48F-1D18A9856A87
last_name: Kukucka
- first_name: Hannes
full_name: Watzinger, Hannes
id: 35DF8E50-F248-11E8-B48F-1D18A9856A87
last_name: Watzinger
- first_name: Joshua M
full_name: Milem, Joshua M
id: 4CDE0A96-F248-11E8-B48F-1D18A9856A87
last_name: Milem
- first_name: Friedrich
full_name: Schäffler, Friedrich
last_name: Schäffler
- first_name: Georgios
full_name: Katsaros, Georgios
id: 38DB5788-F248-11E8-B48F-1D18A9856A87
last_name: Katsaros
orcid: 0000-0001-8342-202X
citation:
ama: Vukušić L, Kukucka J, Watzinger H, Milem JM, Schäffler F, Katsaros G. Single-shot
readout of hole spins in Ge. Nano Letters. 2018;18(11):7141-7145. doi:10.1021/acs.nanolett.8b03217
apa: Vukušić, L., Kukucka, J., Watzinger, H., Milem, J. M., Schäffler, F., &
Katsaros, G. (2018). Single-shot readout of hole spins in Ge. Nano Letters.
American Chemical Society. https://doi.org/10.1021/acs.nanolett.8b03217
chicago: Vukušić, Lada, Josip Kukucka, Hannes Watzinger, Joshua M Milem, Friedrich
Schäffler, and Georgios Katsaros. “Single-Shot Readout of Hole Spins in Ge.” Nano
Letters. American Chemical Society, 2018. https://doi.org/10.1021/acs.nanolett.8b03217.
ieee: L. Vukušić, J. Kukucka, H. Watzinger, J. M. Milem, F. Schäffler, and G. Katsaros,
“Single-shot readout of hole spins in Ge,” Nano Letters, vol. 18, no. 11.
American Chemical Society, pp. 7141–7145, 2018.
ista: Vukušić L, Kukucka J, Watzinger H, Milem JM, Schäffler F, Katsaros G. 2018.
Single-shot readout of hole spins in Ge. Nano Letters. 18(11), 7141–7145.
mla: Vukušić, Lada, et al. “Single-Shot Readout of Hole Spins in Ge.” Nano Letters,
vol. 18, no. 11, American Chemical Society, 2018, pp. 7141–45, doi:10.1021/acs.nanolett.8b03217.
short: L. Vukušić, J. Kukucka, H. Watzinger, J.M. Milem, F. Schäffler, G. Katsaros,
Nano Letters 18 (2018) 7141–7145.
date_created: 2018-12-11T11:44:13Z
date_published: 2018-10-25T00:00:00Z
date_updated: 2023-09-18T09:30:37Z
day: '25'
ddc:
- '530'
department:
- _id: GeKa
doi: 10.1021/acs.nanolett.8b03217
ec_funded: 1
external_id:
isi:
- '000451102100064'
pmid:
- '30359041'
file:
- access_level: open_access
checksum: 3e6034a94c6b5335e939145d88bdb371
content_type: application/pdf
creator: system
date_created: 2018-12-12T10:16:08Z
date_updated: 2020-07-14T12:45:37Z
file_id: '5194'
file_name: IST-2018-1065-v1+1_ACS_nanoletters_8b03217.pdf
file_size: 1361441
relation: main_file
file_date_updated: 2020-07-14T12:45:37Z
has_accepted_license: '1'
intvolume: ' 18'
isi: 1
issue: '11'
language:
- iso: eng
month: '10'
oa: 1
oa_version: Published Version
page: 7141 - 7145
pmid: 1
project:
- _id: 25517E86-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '335497'
name: Towards Spin qubits and Majorana fermions in Germanium selfassembled hut-wires
publication: Nano Letters
publication_identifier:
issn:
- '15306984'
publication_status: published
publisher: American Chemical Society
publist_id: '8032'
pubrep_id: '1065'
quality_controlled: '1'
related_material:
record:
- id: '7977'
relation: popular_science
- id: '69'
relation: dissertation_contains
status: public
- id: '7996'
relation: dissertation_contains
status: public
scopus_import: '1'
status: public
title: Single-shot readout of hole spins in Ge
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: journal_article
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
volume: 18
year: '2018'
...
---
_id: '85'
abstract:
- lang: eng
text: Concurrent accesses to shared data structures must be synchronized to avoid
data races. Coarse-grained synchronization, which locks the entire data structure,
is easy to implement but does not scale. Fine-grained synchronization can scale
well, but can be hard to reason about. Hand-over-hand locking, in which operations
are pipelined as they traverse the data structure, combines fine-grained synchronization
with ease of use. However, the traditional implementation suffers from inherent
overheads. This paper introduces snapshot-based synchronization (SBS), a novel
hand-over-hand locking mechanism. SBS decouples the synchronization state from
the data, significantly improving cache utilization. Further, it relies on guarantees
provided by pipelining to minimize synchronization that requires cross-thread
communication. Snapshot-based synchronization thus scales much better than traditional
hand-over-hand locking, while maintaining the same ease of use.
acknowledgement: Trevor Brown was supported in part by the ISF (grants 2005/17 & 1749/14)
and by a NSERC post-doctoral fellowship.
alternative_title:
- LNCS
article_processing_charge: No
author:
- first_name: Eran
full_name: Gilad, Eran
last_name: Gilad
- first_name: Trevor A
full_name: Brown, Trevor A
id: 3569F0A0-F248-11E8-B48F-1D18A9856A87
last_name: Brown
- first_name: Mark
full_name: Oskin, Mark
last_name: Oskin
- first_name: Yoav
full_name: Etsion, Yoav
last_name: Etsion
citation:
ama: 'Gilad E, Brown TA, Oskin M, Etsion Y. Snapshot based synchronization: A fast
replacement for Hand-over-Hand locking. In: Vol 11014. Springer; 2018:465-479.
doi:10.1007/978-3-319-96983-1_33'
apa: 'Gilad, E., Brown, T. A., Oskin, M., & Etsion, Y. (2018). Snapshot based
synchronization: A fast replacement for Hand-over-Hand locking (Vol. 11014, pp.
465–479). Presented at the Euro-Par: European Conference on Parallel Processing,
Turin, Italy: Springer. https://doi.org/10.1007/978-3-319-96983-1_33'
chicago: 'Gilad, Eran, Trevor A Brown, Mark Oskin, and Yoav Etsion. “Snapshot Based
Synchronization: A Fast Replacement for Hand-over-Hand Locking,” 11014:465–79.
Springer, 2018. https://doi.org/10.1007/978-3-319-96983-1_33.'
ieee: 'E. Gilad, T. A. Brown, M. Oskin, and Y. Etsion, “Snapshot based synchronization:
A fast replacement for Hand-over-Hand locking,” presented at the Euro-Par: European
Conference on Parallel Processing, Turin, Italy, 2018, vol. 11014, pp. 465–479.'
ista: 'Gilad E, Brown TA, Oskin M, Etsion Y. 2018. Snapshot based synchronization:
A fast replacement for Hand-over-Hand locking. Euro-Par: European Conference on
Parallel Processing, LNCS, vol. 11014, 465–479.'
mla: 'Gilad, Eran, et al. Snapshot Based Synchronization: A Fast Replacement
for Hand-over-Hand Locking. Vol. 11014, Springer, 2018, pp. 465–79, doi:10.1007/978-3-319-96983-1_33.'
short: E. Gilad, T.A. Brown, M. Oskin, Y. Etsion, in:, Springer, 2018, pp. 465–479.
conference:
end_date: 2018-08-31
location: Turin, Italy
name: 'Euro-Par: European Conference on Parallel Processing'
start_date: 2018-08-27
date_created: 2018-12-11T11:44:33Z
date_published: 2018-08-01T00:00:00Z
date_updated: 2023-09-18T09:32:36Z
day: '01'
ddc:
- '000'
department:
- _id: DaAl
doi: 10.1007/978-3-319-96983-1_33
external_id:
isi:
- '000851042300031'
file:
- access_level: open_access
checksum: 13a3f250be8878405e791b53c19722ad
content_type: application/pdf
creator: dernst
date_created: 2019-02-12T07:40:40Z
date_updated: 2020-07-14T12:48:14Z
file_id: '5954'
file_name: 2018_Brown.pdf
file_size: 665372
relation: main_file
file_date_updated: 2020-07-14T12:48:14Z
has_accepted_license: '1'
intvolume: ' 11014'
isi: 1
language:
- iso: eng
month: '08'
oa: 1
oa_version: Preprint
page: 465 - 479
project:
- _id: 26450934-B435-11E9-9278-68D0E5697425
name: NSERC Postdoctoral fellowship
publication_identifier:
issn:
- '03029743'
publication_status: published
publisher: Springer
publist_id: '7969'
quality_controlled: '1'
scopus_import: '1'
status: public
title: 'Snapshot based synchronization: A fast replacement for Hand-over-Hand locking'
type: conference
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
volume: 11014
year: '2018'
...
---
_id: '327'
abstract:
- lang: eng
text: Many-body quantum systems typically display fast dynamics and ballistic spreading
of information. Here we address the open problem of how slow the dynamics can
be after a generic breaking of integrability by local interactions. We develop
a method based on degenerate perturbation theory that reveals slow dynamical regimes
and delocalization processes in general translation invariant models, along with
accurate estimates of their delocalization time scales. Our results shed light
on the fundamental questions of the robustness of quantum integrable systems and
the possibility of many-body localization without disorder. As an example, we
construct a large class of one-dimensional lattice models where, despite the absence
of asymptotic localization, the transient dynamics is exceptionally slow, i.e.,
the dynamics is indistinguishable from that of many-body localized systems for
the system sizes and time scales accessible in experiments and numerical simulations.
acknowledgement: 'We thank F. Huveneers for useful discussions. Z.P. and A.M. acknowledge
support by EPSRC Grant No. EP/P009409/1 and and the Royal Society Research Grant
No. RG160635. Statement of compliance with EPSRC policy framework on research data:
This publication is theoretical work that does not require supporting research data.
D.A. acknowledges support by the Swiss National Science Foundation. M.Z., M.M. and
T.P. acknowledge Grants J1-7279 (M.Z.) and N1-0025 (M.M. and T.P.) of Slovenian
Research Agency, and Advanced Grant of European Research Council, Grant No. 694544
- OMNES (T.P.).'
article_number: '104307'
article_processing_charge: No
author:
- first_name: Alexios
full_name: Michailidis, Alexios
id: 36EBAD38-F248-11E8-B48F-1D18A9856A87
last_name: Michailidis
orcid: 0000-0002-8443-1064
- first_name: Marko
full_name: Žnidarič, Marko
last_name: Žnidarič
- first_name: Mariya
full_name: Medvedyeva, Mariya
last_name: Medvedyeva
- first_name: Dmitry
full_name: Abanin, Dmitry
last_name: Abanin
- first_name: Tomaž
full_name: Prosen, Tomaž
last_name: Prosen
- first_name: Zlatko
full_name: Papić, Zlatko
last_name: Papić
citation:
ama: Michailidis A, Žnidarič M, Medvedyeva M, Abanin D, Prosen T, Papić Z. Slow
dynamics in translation-invariant quantum lattice models. Physical Review B.
2018;97(10). doi:10.1103/PhysRevB.97.104307
apa: Michailidis, A., Žnidarič, M., Medvedyeva, M., Abanin, D., Prosen, T., &
Papić, Z. (2018). Slow dynamics in translation-invariant quantum lattice models.
Physical Review B. American Physical Society. https://doi.org/10.1103/PhysRevB.97.104307
chicago: Michailidis, Alexios, Marko Žnidarič, Mariya Medvedyeva, Dmitry Abanin,
Tomaž Prosen, and Zlatko Papić. “Slow Dynamics in Translation-Invariant Quantum
Lattice Models.” Physical Review B. American Physical Society, 2018. https://doi.org/10.1103/PhysRevB.97.104307.
ieee: A. Michailidis, M. Žnidarič, M. Medvedyeva, D. Abanin, T. Prosen, and Z. Papić,
“Slow dynamics in translation-invariant quantum lattice models,” Physical Review
B, vol. 97, no. 10. American Physical Society, 2018.
ista: Michailidis A, Žnidarič M, Medvedyeva M, Abanin D, Prosen T, Papić Z. 2018.
Slow dynamics in translation-invariant quantum lattice models. Physical Review
B. 97(10), 104307.
mla: Michailidis, Alexios, et al. “Slow Dynamics in Translation-Invariant Quantum
Lattice Models.” Physical Review B, vol. 97, no. 10, 104307, American Physical
Society, 2018, doi:10.1103/PhysRevB.97.104307.
short: A. Michailidis, M. Žnidarič, M. Medvedyeva, D. Abanin, T. Prosen, Z. Papić,
Physical Review B 97 (2018).
date_created: 2018-12-11T11:45:50Z
date_published: 2018-03-19T00:00:00Z
date_updated: 2023-09-18T09:31:46Z
day: '19'
department:
- _id: MaSe
doi: 10.1103/PhysRevB.97.104307
external_id:
isi:
- '000427798800005'
intvolume: ' 97'
isi: 1
issue: '10'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/1706.05026
month: '03'
oa: 1
oa_version: Preprint
publication: Physical Review B
publication_status: published
publisher: American Physical Society
publist_id: '7538'
quality_controlled: '1'
scopus_import: '1'
status: public
title: Slow dynamics in translation-invariant quantum lattice models
type: journal_article
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
volume: 97
year: '2018'
...
---
_id: '29'
abstract:
- lang: eng
text: Social insects have evolved enormous capacities to collectively build nests
and defend their colonies against both predators and pathogens. The latter is
achieved by a combination of individual immune responses and sophisticated collective
behavioral and organizational disease defenses, that is, social immunity. We investigated
how the presence or absence of these social defense lines affects individual-level
immunity in ant queens after bacterial infection. To this end, we injected queens
of the ant Linepithema humile with a mix of gram+ and gram− bacteria or a control
solution, reared them either with workers or alone and analyzed their gene expression
patterns at 2, 4, 8, and 12 hr post-injection, using RNA-seq. This allowed us
to test for the effect of bacterial infection, social context, as well as the
interaction between the two over the course of infection and raising of an immune
response. We found that social isolation per se affected queen gene expression
for metabolism genes, but not for immune genes. When infected, queens reared with
and without workers up-regulated similar numbers of innate immune genes revealing
activation of Toll and Imd signaling pathways and melanization. Interestingly,
however, they mostly regulated different genes along the pathways and showed a
different pattern of overall gene up-regulation or down-regulation. Hence, we
can conclude that the absence of workers does not compromise the onset of an individual
immune response by the queens, but that the social environment impacts the route
of the individual innate immune responses.
article_processing_charge: No
author:
- first_name: Lumi
full_name: Viljakainen, Lumi
last_name: Viljakainen
- first_name: Jaana
full_name: Jurvansuu, Jaana
last_name: Jurvansuu
- first_name: Ida
full_name: Holmberg, Ida
last_name: Holmberg
- first_name: Tobias
full_name: Pamminger, Tobias
last_name: Pamminger
- first_name: Silvio
full_name: Erler, Silvio
last_name: Erler
- first_name: Sylvia
full_name: Cremer, Sylvia
id: 2F64EC8C-F248-11E8-B48F-1D18A9856A87
last_name: Cremer
orcid: 0000-0002-2193-3868
citation:
ama: Viljakainen L, Jurvansuu J, Holmberg I, Pamminger T, Erler S, Cremer S. Social
environment affects the transcriptomic response to bacteria in ant queens. Ecology
and Evolution. 2018;8(22):11031-11070. doi:10.1002/ece3.4573
apa: Viljakainen, L., Jurvansuu, J., Holmberg, I., Pamminger, T., Erler, S., &
Cremer, S. (2018). Social environment affects the transcriptomic response to bacteria
in ant queens. Ecology and Evolution. Wiley. https://doi.org/10.1002/ece3.4573
chicago: Viljakainen, Lumi, Jaana Jurvansuu, Ida Holmberg, Tobias Pamminger, Silvio
Erler, and Sylvia Cremer. “Social Environment Affects the Transcriptomic Response
to Bacteria in Ant Queens.” Ecology and Evolution. Wiley, 2018. https://doi.org/10.1002/ece3.4573.
ieee: L. Viljakainen, J. Jurvansuu, I. Holmberg, T. Pamminger, S. Erler, and S.
Cremer, “Social environment affects the transcriptomic response to bacteria in
ant queens,” Ecology and Evolution, vol. 8, no. 22. Wiley, pp. 11031–11070,
2018.
ista: Viljakainen L, Jurvansuu J, Holmberg I, Pamminger T, Erler S, Cremer S. 2018.
Social environment affects the transcriptomic response to bacteria in ant queens.
Ecology and Evolution. 8(22), 11031–11070.
mla: Viljakainen, Lumi, et al. “Social Environment Affects the Transcriptomic Response
to Bacteria in Ant Queens.” Ecology and Evolution, vol. 8, no. 22, Wiley,
2018, pp. 11031–70, doi:10.1002/ece3.4573.
short: L. Viljakainen, J. Jurvansuu, I. Holmberg, T. Pamminger, S. Erler, S. Cremer,
Ecology and Evolution 8 (2018) 11031–11070.
date_created: 2018-12-11T11:44:15Z
date_published: 2018-11-01T00:00:00Z
date_updated: 2023-09-19T09:29:12Z
day: '01'
ddc:
- '576'
- '591'
department:
- _id: SyCr
doi: 10.1002/ece3.4573
external_id:
isi:
- '000451611000032'
file:
- access_level: open_access
checksum: 0d1355c78627ca7210aadd9a17a01915
content_type: application/pdf
creator: dernst
date_created: 2018-12-17T08:27:04Z
date_updated: 2020-07-14T12:45:52Z
file_id: '5682'
file_name: Viljakainen_et_al-2018-Ecology_and_Evolution.pdf
file_size: 1272096
relation: main_file
file_date_updated: 2020-07-14T12:45:52Z
has_accepted_license: '1'
intvolume: ' 8'
isi: 1
issue: '22'
language:
- iso: eng
month: '11'
oa: 1
oa_version: Published Version
page: 11031-11070
publication: Ecology and Evolution
publication_identifier:
issn:
- '20457758'
publication_status: published
publisher: Wiley
publist_id: '8026'
quality_controlled: '1'
scopus_import: '1'
status: public
title: Social environment affects the transcriptomic response to bacteria in ant queens
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: journal_article
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
volume: 8
year: '2018'
...
---
_id: '806'
abstract:
- lang: eng
text: Social insect colonies have evolved many collectively performed adaptations
that reduce the impact of infectious disease and that are expected to maximize
their fitness. This colony-level protection is termed social immunity, and it
enhances the health and survival of the colony. In this review, we address how
social immunity emerges from its mechanistic components to produce colony-level
disease avoidance, resistance, and tolerance. To understand the evolutionary causes
and consequences of social immunity, we highlight the need for studies that evaluate
the effects of social immunity on colony fitness. We discuss the role that host
life history and ecology have on predicted eco-evolutionary dynamics, which differ
among the social insect lineages. Throughout the review, we highlight current
gaps in our knowledge and promising avenues for future research, which we hope
will bring us closer to an integrated understanding of socio-eco-evo-immunology.
article_processing_charge: No
author:
- first_name: Sylvia
full_name: Cremer, Sylvia
id: 2F64EC8C-F248-11E8-B48F-1D18A9856A87
last_name: Cremer
orcid: 0000-0002-2193-3868
- first_name: Christopher
full_name: Pull, Christopher
id: 3C7F4840-F248-11E8-B48F-1D18A9856A87
last_name: Pull
orcid: 0000-0003-1122-3982
- first_name: Matthias
full_name: Fürst, Matthias
id: 393B1196-F248-11E8-B48F-1D18A9856A87
last_name: Fürst
orcid: 0000-0002-3712-925X
citation:
ama: 'Cremer S, Pull C, Fürst M. Social immunity: Emergence and evolution of colony-level
disease protection. Annual Review of Entomology. 2018;63:105-123. doi:10.1146/annurev-ento-020117-043110'
apa: 'Cremer, S., Pull, C., & Fürst, M. (2018). Social immunity: Emergence and
evolution of colony-level disease protection. Annual Review of Entomology.
Annual Reviews. https://doi.org/10.1146/annurev-ento-020117-043110'
chicago: 'Cremer, Sylvia, Christopher Pull, and Matthias Fürst. “Social Immunity:
Emergence and Evolution of Colony-Level Disease Protection.” Annual Review
of Entomology. Annual Reviews, 2018. https://doi.org/10.1146/annurev-ento-020117-043110.'
ieee: 'S. Cremer, C. Pull, and M. Fürst, “Social immunity: Emergence and evolution
of colony-level disease protection,” Annual Review of Entomology, vol.
63. Annual Reviews, pp. 105–123, 2018.'
ista: 'Cremer S, Pull C, Fürst M. 2018. Social immunity: Emergence and evolution
of colony-level disease protection. Annual Review of Entomology. 63, 105–123.'
mla: 'Cremer, Sylvia, et al. “Social Immunity: Emergence and Evolution of Colony-Level
Disease Protection.” Annual Review of Entomology, vol. 63, Annual Reviews,
2018, pp. 105–23, doi:10.1146/annurev-ento-020117-043110.'
short: S. Cremer, C. Pull, M. Fürst, Annual Review of Entomology 63 (2018) 105–123.
date_created: 2018-12-11T11:48:36Z
date_published: 2018-01-07T00:00:00Z
date_updated: 2023-09-19T09:29:45Z
day: '07'
department:
- _id: SyCr
doi: 10.1146/annurev-ento-020117-043110
external_id:
isi:
- '000424633700008'
intvolume: ' 63'
isi: 1
language:
- iso: eng
month: '01'
oa_version: None
page: 105 - 123
publication: Annual Review of Entomology
publication_identifier:
issn:
- 1545-4487
publication_status: published
publisher: Annual Reviews
publist_id: '6844'
quality_controlled: '1'
related_material:
record:
- id: '819'
relation: dissertation_contains
status: public
scopus_import: '1'
status: public
title: 'Social immunity: Emergence and evolution of colony-level disease protection'
type: journal_article
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
volume: 63
year: '2018'
...
---
_id: '140'
abstract:
- lang: eng
text: Reachability analysis is difficult for hybrid automata with affine differential
equations, because the reach set needs to be approximated. Promising abstraction
techniques usually employ interval methods or template polyhedra. Interval methods
account for dense time and guarantee soundness, and there are interval-based tools
that overapproximate affine flowpipes. But interval methods impose bounded and
rigid shapes, which make refinement expensive and fixpoint detection difficult.
Template polyhedra, on the other hand, can be adapted flexibly and can be unbounded,
but sound template refinement for unbounded reachability analysis has been implemented
only for systems with piecewise constant dynamics. We capitalize on the advantages
of both techniques, combining interval arithmetic and template polyhedra, using
the former to abstract time and the latter to abstract space. During a CEGAR loop,
whenever a spurious error trajectory is found, we compute additional space constraints
and split time intervals, and use these space-time interpolants to eliminate the
counterexample. Space-time interpolation offers a lazy, flexible framework for
increasing precision while guaranteeing soundness, both for error avoidance and
fixpoint detection. To the best of out knowledge, this is the first abstraction
refinement scheme for the reachability analysis over unbounded and dense time
of affine hybrid systems, which is both sound and automatic. We demonstrate the
effectiveness of our algorithm with several benchmark examples, which cannot be
handled by other tools.
alternative_title:
- LNCS
article_processing_charge: No
author:
- first_name: Goran
full_name: Frehse, Goran
last_name: Frehse
- first_name: Mirco
full_name: Giacobbe, Mirco
id: 3444EA5E-F248-11E8-B48F-1D18A9856A87
last_name: Giacobbe
orcid: 0000-0001-8180-0904
- first_name: Thomas A
full_name: Henzinger, Thomas A
id: 40876CD8-F248-11E8-B48F-1D18A9856A87
last_name: Henzinger
orcid: 0000−0002−2985−7724
citation:
ama: 'Frehse G, Giacobbe M, Henzinger TA. Space-time interpolants. In: Vol 10981.
Springer; 2018:468-486. doi:10.1007/978-3-319-96145-3_25'
apa: 'Frehse, G., Giacobbe, M., & Henzinger, T. A. (2018). Space-time interpolants
(Vol. 10981, pp. 468–486). Presented at the CAV: Computer Aided Verification,
Oxford, United Kingdom: Springer. https://doi.org/10.1007/978-3-319-96145-3_25'
chicago: Frehse, Goran, Mirco Giacobbe, and Thomas A Henzinger. “Space-Time Interpolants,”
10981:468–86. Springer, 2018. https://doi.org/10.1007/978-3-319-96145-3_25.
ieee: 'G. Frehse, M. Giacobbe, and T. A. Henzinger, “Space-time interpolants,” presented
at the CAV: Computer Aided Verification, Oxford, United Kingdom, 2018, vol. 10981,
pp. 468–486.'
ista: 'Frehse G, Giacobbe M, Henzinger TA. 2018. Space-time interpolants. CAV: Computer
Aided Verification, LNCS, vol. 10981, 468–486.'
mla: Frehse, Goran, et al. Space-Time Interpolants. Vol. 10981, Springer,
2018, pp. 468–86, doi:10.1007/978-3-319-96145-3_25.
short: G. Frehse, M. Giacobbe, T.A. Henzinger, in:, Springer, 2018, pp. 468–486.
conference:
end_date: 2018-07-17
location: Oxford, United Kingdom
name: 'CAV: Computer Aided Verification'
start_date: 2018-07-14
date_created: 2018-12-11T11:44:50Z
date_published: 2018-07-18T00:00:00Z
date_updated: 2023-09-19T09:30:43Z
day: '18'
ddc:
- '005'
department:
- _id: ToHe
doi: 10.1007/978-3-319-96145-3_25
external_id:
isi:
- '000491481600025'
file:
- access_level: open_access
checksum: 6dca832f575d6b3f0ea9dff56f579142
content_type: application/pdf
creator: system
date_created: 2018-12-12T10:17:53Z
date_updated: 2020-07-14T12:44:50Z
file_id: '5310'
file_name: IST-2018-1010-v1+1_space-time_interpolants.pdf
file_size: 563710
relation: main_file
file_date_updated: 2020-07-14T12:44:50Z
has_accepted_license: '1'
intvolume: ' 10981'
isi: 1
language:
- iso: eng
month: '07'
oa: 1
oa_version: Published Version
page: 468 - 486
project:
- _id: 25832EC2-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: S 11407_N23
name: Rigorous Systems Engineering
- _id: 25F5A88A-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: S11402-N23
name: Moderne Concurrency Paradigms
publication_identifier:
issn:
- '03029743'
publication_status: published
publisher: Springer
publist_id: '7783'
pubrep_id: '1010'
quality_controlled: '1'
related_material:
record:
- id: '6894'
relation: dissertation_contains
status: public
scopus_import: '1'
status: public
title: Space-time interpolants
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: c635000d-4b10-11ee-a964-aac5a93f6ac1
volume: 10981
year: '2018'
...
---
_id: '154'
abstract:
- lang: eng
text: We give a lower bound on the ground state energy of a system of two fermions
of one species interacting with two fermions of another species via point interactions.
We show that there is a critical mass ratio m2 ≈ 0.58 such that the system is
stable, i.e., the energy is bounded from below, for m∈[m2,m2−1]. So far it was
not known whether this 2 + 2 system exhibits a stable region at all or whether
the formation of four-body bound states causes an unbounded spectrum for all mass
ratios, similar to the Thomas effect. Our result gives further evidence for the
stability of the more general N + M system.
acknowledgement: Open access funding provided by Austrian Science Fund (FWF).
article_number: '19'
article_processing_charge: No
article_type: original
author:
- first_name: Thomas
full_name: Moser, Thomas
id: 2B5FC9A4-F248-11E8-B48F-1D18A9856A87
last_name: Moser
- first_name: Robert
full_name: Seiringer, Robert
id: 4AFD0470-F248-11E8-B48F-1D18A9856A87
last_name: Seiringer
orcid: 0000-0002-6781-0521
citation:
ama: Moser T, Seiringer R. Stability of the 2+2 fermionic system with point interactions.
Mathematical Physics Analysis and Geometry. 2018;21(3). doi:10.1007/s11040-018-9275-3
apa: Moser, T., & Seiringer, R. (2018). Stability of the 2+2 fermionic system
with point interactions. Mathematical Physics Analysis and Geometry. Springer.
https://doi.org/10.1007/s11040-018-9275-3
chicago: Moser, Thomas, and Robert Seiringer. “Stability of the 2+2 Fermionic System
with Point Interactions.” Mathematical Physics Analysis and Geometry. Springer,
2018. https://doi.org/10.1007/s11040-018-9275-3.
ieee: T. Moser and R. Seiringer, “Stability of the 2+2 fermionic system with point
interactions,” Mathematical Physics Analysis and Geometry, vol. 21, no.
3. Springer, 2018.
ista: Moser T, Seiringer R. 2018. Stability of the 2+2 fermionic system with point
interactions. Mathematical Physics Analysis and Geometry. 21(3), 19.
mla: Moser, Thomas, and Robert Seiringer. “Stability of the 2+2 Fermionic System
with Point Interactions.” Mathematical Physics Analysis and Geometry, vol.
21, no. 3, 19, Springer, 2018, doi:10.1007/s11040-018-9275-3.
short: T. Moser, R. Seiringer, Mathematical Physics Analysis and Geometry 21 (2018).
date_created: 2018-12-11T11:44:55Z
date_published: 2018-09-01T00:00:00Z
date_updated: 2023-09-19T09:31:15Z
day: '01'
ddc:
- '530'
department:
- _id: RoSe
doi: 10.1007/s11040-018-9275-3
ec_funded: 1
external_id:
isi:
- '000439639700001'
file:
- access_level: open_access
checksum: 411c4db5700d7297c9cd8ebc5dd29091
content_type: application/pdf
creator: dernst
date_created: 2018-12-17T16:49:02Z
date_updated: 2020-07-14T12:45:01Z
file_id: '5729'
file_name: 2018_MathPhysics_Moser.pdf
file_size: 496973
relation: main_file
file_date_updated: 2020-07-14T12:45:01Z
has_accepted_license: '1'
intvolume: ' 21'
isi: 1
issue: '3'
language:
- iso: eng
month: '09'
oa: 1
oa_version: Published Version
project:
- _id: 25C6DC12-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '694227'
name: Analysis of quantum many-body systems
- _id: 25C878CE-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: P27533_N27
name: Structure of the Excitation Spectrum for Many-Body Quantum Systems
- _id: 3AC91DDA-15DF-11EA-824D-93A3E7B544D1
call_identifier: FWF
name: FWF Open Access Fund
publication: Mathematical Physics Analysis and Geometry
publication_identifier:
eissn:
- '15729656'
issn:
- '13850172'
publication_status: published
publisher: Springer
publist_id: '7767'
quality_controlled: '1'
related_material:
record:
- id: '52'
relation: dissertation_contains
status: public
scopus_import: '1'
status: public
title: Stability of the 2+2 fermionic system with point interactions
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: journal_article
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
volume: 21
year: '2018'
...
---
_id: '5787'
abstract:
- lang: eng
text: "Branching morphogenesis remains a subject of abiding interest. Although
\ much is \r\nknown about the gene regulatory programs and signaling pathways
that operate at \r\nthe cellular scale, it has remained unclear how the macroscopic
features of branched \r\norgans, including their size, network topology and
\ spatial patterning, are encoded. \r\nLately, it has been proposed that,
these features can be explained quantitatively in \r\nseveral organs within a
single unifying framework. Based on large-\r\nscale organ recon\r\n-\r\nstructions
\ and cell lineage tracing, it has been argued that morphogenesis follows
\ \r\nfrom the collective dynamics of sublineage- \r\nrestricted self- \r\nrenewing
progenitor cells, \r\nlocalized at ductal tips, that act cooperatively to drive
a serial process of ductal elon\r\n-\r\ngation and stochastic tip bifurcation.
By correlating differentiation or cell cycle exit \r\nwith proximity to maturing
ducts, this dynamic results in the specification of a com-\r\nplex network of
\ defined density and statistical organization. These results suggest \r\nthat,
for several mammalian tissues, branched epithelial structures develop as a self-
\r\norganized process, reliant upon a strikingly simple, but generic,
\ set of local rules, \r\nwithout recourse to a rigid and deterministic
\ sequence of genetically programmed \r\nevents. Here, we review the basis
of these findings and discuss their implications."
article_processing_charge: No
author:
- first_name: Edouard B
full_name: Hannezo, Edouard B
id: 3A9DB764-F248-11E8-B48F-1D18A9856A87
last_name: Hannezo
orcid: 0000-0001-6005-1561
- first_name: Benjamin D.
full_name: Simons, Benjamin D.
last_name: Simons
citation:
ama: Hannezo EB, Simons BD. Statistical theory of branching morphogenesis. Development
Growth and Differentiation. 2018;60(9):512-521. doi:10.1111/dgd.12570
apa: Hannezo, E. B., & Simons, B. D. (2018). Statistical theory of branching
morphogenesis. Development Growth and Differentiation. Wiley. https://doi.org/10.1111/dgd.12570
chicago: Hannezo, Edouard B, and Benjamin D. Simons. “Statistical Theory of Branching
Morphogenesis.” Development Growth and Differentiation. Wiley, 2018. https://doi.org/10.1111/dgd.12570.
ieee: E. B. Hannezo and B. D. Simons, “Statistical theory of branching morphogenesis,”
Development Growth and Differentiation, vol. 60, no. 9. Wiley, pp. 512–521,
2018.
ista: Hannezo EB, Simons BD. 2018. Statistical theory of branching morphogenesis.
Development Growth and Differentiation. 60(9), 512–521.
mla: Hannezo, Edouard B., and Benjamin D. Simons. “Statistical Theory of Branching
Morphogenesis.” Development Growth and Differentiation, vol. 60, no. 9,
Wiley, 2018, pp. 512–21, doi:10.1111/dgd.12570.
short: E.B. Hannezo, B.D. Simons, Development Growth and Differentiation 60 (2018)
512–521.
date_created: 2018-12-30T22:59:14Z
date_published: 2018-12-09T00:00:00Z
date_updated: 2023-09-19T09:32:49Z
day: '09'
ddc:
- '570'
department:
- _id: EdHa
doi: 10.1111/dgd.12570
external_id:
isi:
- '000453555100002'
file:
- access_level: open_access
checksum: a6d30b0785db902c734a84fecb2eadd9
content_type: application/pdf
creator: dernst
date_created: 2019-02-06T10:40:46Z
date_updated: 2020-07-14T12:47:11Z
file_id: '5933'
file_name: 2018_DevGrowh_Hannezo.pdf
file_size: 1313606
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file_date_updated: 2020-07-14T12:47:11Z
has_accepted_license: '1'
intvolume: ' 60'
isi: 1
issue: '9'
language:
- iso: eng
month: '12'
oa: 1
oa_version: Published Version
page: 512-521
publication: Development Growth and Differentiation
publication_identifier:
issn:
- '00121592'
publisher: Wiley
quality_controlled: '1'
scopus_import: '1'
status: public
title: Statistical theory of branching morphogenesis
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: journal_article
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
volume: 60
year: '2018'
...
---
_id: '297'
abstract:
- lang: eng
text: Graph games played by two players over finite-state graphs are central in
many problems in computer science. In particular, graph games with ω -regular
winning conditions, specified as parity objectives, which can express properties
such as safety, liveness, fairness, are the basic framework for verification and
synthesis of reactive systems. The decisions for a player at various states of
the graph game are represented as strategies. While the algorithmic problem for
solving graph games with parity objectives has been widely studied, the most prominent
data-structure for strategy representation in graph games has been binary decision
diagrams (BDDs). However, due to the bit-level representation, BDDs do not retain
the inherent flavor of the decisions of strategies, and are notoriously hard to
minimize to obtain succinct representation. In this work we propose decision trees
for strategy representation in graph games. Decision trees retain the flavor of
decisions of strategies and allow entropy-based minimization to obtain succinct
trees. However, decision trees work in settings (e.g., probabilistic models) where
errors are allowed, and overfitting of data is typically avoided. In contrast,
for strategies in graph games no error is allowed, and the decision tree must
represent the entire strategy. We develop new techniques to extend decision trees
to overcome the above obstacles, while retaining the entropy-based techniques
to obtain succinct trees. We have implemented our techniques to extend the existing
decision tree solvers. We present experimental results for problems in reactive
synthesis to show that decision trees provide a much more efficient data-structure
for strategy representation as compared to BDDs.
alternative_title:
- LNCS
article_processing_charge: No
author:
- first_name: Tomáš
full_name: Brázdil, Tomáš
last_name: Brázdil
- first_name: Krishnendu
full_name: Chatterjee, Krishnendu
id: 2E5DCA20-F248-11E8-B48F-1D18A9856A87
last_name: Chatterjee
orcid: 0000-0002-4561-241X
- first_name: Jan
full_name: Kretinsky, Jan
id: 44CEF464-F248-11E8-B48F-1D18A9856A87
last_name: Kretinsky
orcid: 0000-0002-8122-2881
- first_name: Viktor
full_name: Toman, Viktor
id: 3AF3DA7C-F248-11E8-B48F-1D18A9856A87
last_name: Toman
orcid: 0000-0001-9036-063X
citation:
ama: 'Brázdil T, Chatterjee K, Kretinsky J, Toman V. Strategy representation by
decision trees in reactive synthesis. In: Vol 10805. Springer; 2018:385-407. doi:10.1007/978-3-319-89960-2_21'
apa: 'Brázdil, T., Chatterjee, K., Kretinsky, J., & Toman, V. (2018). Strategy
representation by decision trees in reactive synthesis (Vol. 10805, pp. 385–407).
Presented at the TACAS 2018: Tools and Algorithms for the Construction and Analysis
of Systems, Thessaloniki, Greece: Springer. https://doi.org/10.1007/978-3-319-89960-2_21'
chicago: Brázdil, Tomáš, Krishnendu Chatterjee, Jan Kretinsky, and Viktor Toman.
“Strategy Representation by Decision Trees in Reactive Synthesis,” 10805:385–407.
Springer, 2018. https://doi.org/10.1007/978-3-319-89960-2_21.
ieee: 'T. Brázdil, K. Chatterjee, J. Kretinsky, and V. Toman, “Strategy representation
by decision trees in reactive synthesis,” presented at the TACAS 2018: Tools and
Algorithms for the Construction and Analysis of Systems, Thessaloniki, Greece,
2018, vol. 10805, pp. 385–407.'
ista: 'Brázdil T, Chatterjee K, Kretinsky J, Toman V. 2018. Strategy representation
by decision trees in reactive synthesis. TACAS 2018: Tools and Algorithms for
the Construction and Analysis of Systems, LNCS, vol. 10805, 385–407.'
mla: Brázdil, Tomáš, et al. Strategy Representation by Decision Trees in Reactive
Synthesis. Vol. 10805, Springer, 2018, pp. 385–407, doi:10.1007/978-3-319-89960-2_21.
short: T. Brázdil, K. Chatterjee, J. Kretinsky, V. Toman, in:, Springer, 2018, pp.
385–407.
conference:
end_date: 2018-04-20
location: Thessaloniki, Greece
name: 'TACAS 2018: Tools and Algorithms for the Construction and Analysis of Systems'
start_date: 2018-04-14
date_created: 2018-12-11T11:45:41Z
date_published: 2018-04-12T00:00:00Z
date_updated: 2023-09-19T09:57:08Z
day: '12'
ddc:
- '000'
department:
- _id: KrCh
- _id: ToHe
doi: 10.1007/978-3-319-89960-2_21
ec_funded: 1
external_id:
isi:
- '000546326300021'
file:
- access_level: open_access
checksum: b13874ffb114932ad9cc2586b7469db4
content_type: application/pdf
creator: dernst
date_created: 2018-12-17T16:29:08Z
date_updated: 2020-07-14T12:45:57Z
file_id: '5723'
file_name: 2018_LNCS_Brazdil.pdf
file_size: 1829940
relation: main_file
file_date_updated: 2020-07-14T12:45:57Z
has_accepted_license: '1'
intvolume: ' 10805'
isi: 1
language:
- iso: eng
month: '04'
oa: 1
oa_version: Published Version
page: 385 - 407
project:
- _id: 25892FC0-B435-11E9-9278-68D0E5697425
grant_number: ICT15-003
name: Efficient Algorithms for Computer Aided Verification
- _id: 25832EC2-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: S 11407_N23
name: Rigorous Systems Engineering
- _id: 2581B60A-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '279307'
name: 'Quantitative Graph Games: Theory and Applications'
- _id: 2564DBCA-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '665385'
name: International IST Doctoral Program
publication_status: published
publisher: Springer
publist_id: '7584'
quality_controlled: '1'
scopus_import: '1'
status: public
title: Strategy representation by decision trees in reactive synthesis
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: c635000d-4b10-11ee-a964-aac5a93f6ac1
volume: 10805
year: '2018'
...
---
_id: '141'
abstract:
- lang: eng
text: 'Given a model and a specification, the fundamental model-checking problem
asks for algorithmic verification of whether the model satisfies the specification.
We consider graphs and Markov decision processes (MDPs), which are fundamental
models for reactive systems. One of the very basic specifications that arise in
verification of reactive systems is the strong fairness (aka Streett) objective.
Given different types of requests and corresponding grants, the objective requires
that for each type, if the request event happens infinitely often, then the corresponding
grant event must also happen infinitely often. All ω -regular objectives can be
expressed as Streett objectives and hence they are canonical in verification.
To handle the state-space explosion, symbolic algorithms are required that operate
on a succinct implicit representation of the system rather than explicitly accessing
the system. While explicit algorithms for graphs and MDPs with Streett objectives
have been widely studied, there has been no improvement of the basic symbolic
algorithms. The worst-case numbers of symbolic steps required for the basic symbolic
algorithms are as follows: quadratic for graphs and cubic for MDPs. In this work
we present the first sub-quadratic symbolic algorithm for graphs with Streett
objectives, and our algorithm is sub-quadratic even for MDPs. Based on our algorithmic
insights we present an implementation of the new symbolic approach and show that
it improves the existing approach on several academic benchmark examples.'
acknowledgement: 'Acknowledgements. K. C. and M. H. are partially supported by the
Vienna Science and Technology Fund (WWTF) grant ICT15-003. K. C. is partially supported
by the Austrian Science Fund (FWF): S11407-N23 (RiSE/SHiNE), and an ERC Start Grant
(279307: Graph Games). V. T. is partially supported by the European Union’s Horizon
2020 research and innovation programme under the Marie Sk lodowska-Curie Grant Agreement
No. 665385.'
alternative_title:
- LNCS
article_processing_charge: No
author:
- first_name: Krishnendu
full_name: Chatterjee, Krishnendu
id: 2E5DCA20-F248-11E8-B48F-1D18A9856A87
last_name: Chatterjee
orcid: 0000-0002-4561-241X
- first_name: Monika H
full_name: Henzinger, Monika H
id: 540c9bbd-f2de-11ec-812d-d04a5be85630
last_name: Henzinger
orcid: 0000-0002-5008-6530
- first_name: Veronika
full_name: Loitzenbauer, Veronika
last_name: Loitzenbauer
- first_name: Simin
full_name: Oraee, Simin
last_name: Oraee
- first_name: Viktor
full_name: Toman, Viktor
id: 3AF3DA7C-F248-11E8-B48F-1D18A9856A87
last_name: Toman
orcid: 0000-0001-9036-063X
citation:
ama: 'Chatterjee K, Henzinger MH, Loitzenbauer V, Oraee S, Toman V. Symbolic algorithms
for graphs and Markov decision processes with fairness objectives. In: Vol 10982.
Springer; 2018:178-197. doi:10.1007/978-3-319-96142-2_13'
apa: 'Chatterjee, K., Henzinger, M. H., Loitzenbauer, V., Oraee, S., & Toman,
V. (2018). Symbolic algorithms for graphs and Markov decision processes with fairness
objectives (Vol. 10982, pp. 178–197). Presented at the CAV: Computer Aided Verification,
Oxford, United Kingdom: Springer. https://doi.org/10.1007/978-3-319-96142-2_13'
chicago: Chatterjee, Krishnendu, Monika H Henzinger, Veronika Loitzenbauer, Simin
Oraee, and Viktor Toman. “Symbolic Algorithms for Graphs and Markov Decision Processes
with Fairness Objectives,” 10982:178–97. Springer, 2018. https://doi.org/10.1007/978-3-319-96142-2_13.
ieee: 'K. Chatterjee, M. H. Henzinger, V. Loitzenbauer, S. Oraee, and V. Toman,
“Symbolic algorithms for graphs and Markov decision processes with fairness objectives,”
presented at the CAV: Computer Aided Verification, Oxford, United Kingdom, 2018,
vol. 10982, pp. 178–197.'
ista: 'Chatterjee K, Henzinger MH, Loitzenbauer V, Oraee S, Toman V. 2018. Symbolic
algorithms for graphs and Markov decision processes with fairness objectives.
CAV: Computer Aided Verification, LNCS, vol. 10982, 178–197.'
mla: Chatterjee, Krishnendu, et al. Symbolic Algorithms for Graphs and Markov
Decision Processes with Fairness Objectives. Vol. 10982, Springer, 2018, pp.
178–97, doi:10.1007/978-3-319-96142-2_13.
short: K. Chatterjee, M.H. Henzinger, V. Loitzenbauer, S. Oraee, V. Toman, in:,
Springer, 2018, pp. 178–197.
conference:
end_date: 2018-07-17
location: Oxford, United Kingdom
name: 'CAV: Computer Aided Verification'
start_date: 2018-07-14
date_created: 2018-12-11T11:44:51Z
date_published: 2018-07-18T00:00:00Z
date_updated: 2023-09-19T09:59:55Z
day: '18'
ddc:
- '000'
department:
- _id: KrCh
doi: 10.1007/978-3-319-96142-2_13
ec_funded: 1
external_id:
isi:
- '000491469700013'
file:
- access_level: open_access
checksum: 1a6ffa4febe8bb8ac28be3adb3eafebc
content_type: application/pdf
creator: dernst
date_created: 2018-12-18T08:52:38Z
date_updated: 2020-07-14T12:44:53Z
file_id: '5737'
file_name: 2018_LNCS_Chatterjee.pdf
file_size: 675606
relation: main_file
file_date_updated: 2020-07-14T12:44:53Z
has_accepted_license: '1'
intvolume: ' 10982'
isi: 1
language:
- iso: eng
month: '07'
oa: 1
oa_version: Published Version
page: 178-197
project:
- _id: 2581B60A-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '279307'
name: 'Quantitative Graph Games: Theory and Applications'
- _id: 25892FC0-B435-11E9-9278-68D0E5697425
grant_number: ICT15-003
name: Efficient Algorithms for Computer Aided Verification
- _id: 25832EC2-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: S 11407_N23
name: Rigorous Systems Engineering
- _id: 2564DBCA-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '665385'
name: International IST Doctoral Program
publication_status: published
publisher: Springer
publist_id: '7782'
quality_controlled: '1'
related_material:
record:
- id: '10199'
relation: dissertation_contains
status: public
scopus_import: '1'
status: public
title: Symbolic algorithms for graphs and Markov decision processes with fairness
objectives
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: c635000d-4b10-11ee-a964-aac5a93f6ac1
volume: 10982
year: '2018'
...
---
_id: '298'
abstract:
- lang: eng
text: "Memory-hard functions (MHF) are functions whose evaluation cost is dominated
by memory cost. MHFs are egalitarian, in the sense that evaluating them on dedicated
hardware (like FPGAs or ASICs) is not much cheaper than on off-the-shelf hardware
(like x86 CPUs). MHFs have interesting cryptographic applications, most notably
to password hashing and securing blockchains.\r\n\r\nAlwen and Serbinenko [STOC’15]
define the cumulative memory complexity (cmc) of a function as the sum (over all
time-steps) of the amount of memory required to compute the function. They advocate
that a good MHF must have high cmc. Unlike previous notions, cmc takes into account
that dedicated hardware might exploit amortization and parallelism. Still, cmc
has been critizised as insufficient, as it fails to capture possible time-memory
trade-offs; as memory cost doesn’t scale linearly, functions with the same cmc
could still have very different actual hardware cost.\r\n\r\nIn this work we address
this problem, and introduce the notion of sustained-memory complexity, which requires
that any algorithm evaluating the function must use a large amount of memory for
many steps. We construct functions (in the parallel random oracle model) whose
sustained-memory complexity is almost optimal: our function can be evaluated using
n steps and O(n/log(n)) memory, in each step making one query to the (fixed-input
length) random oracle, while any algorithm that can make arbitrary many parallel
queries to the random oracle, still needs Ω(n/log(n)) memory for Ω(n) steps.\r\n\r\nAs
has been done for various notions (including cmc) before, we reduce the task of
constructing an MHFs with high sustained-memory complexity to proving pebbling
lower bounds on DAGs. Our main technical contribution is the construction is a
family of DAGs on n nodes with constant indegree with high “sustained-space complexity”,
meaning that any parallel black-pebbling strategy requires Ω(n/log(n)) pebbles
for at least Ω(n) steps.\r\n\r\nAlong the way we construct a family of maximally
“depth-robust” DAGs with maximum indegree O(logn) , improving upon the construction
of Mahmoody et al. [ITCS’13] which had maximum indegree O(log2n⋅"
alternative_title:
- LNCS
article_processing_charge: No
author:
- first_name: Joel F
full_name: Alwen, Joel F
id: 2A8DFA8C-F248-11E8-B48F-1D18A9856A87
last_name: Alwen
- first_name: Jeremiah
full_name: Blocki, Jeremiah
last_name: Blocki
- first_name: Krzysztof Z
full_name: Pietrzak, Krzysztof Z
id: 3E04A7AA-F248-11E8-B48F-1D18A9856A87
last_name: Pietrzak
orcid: 0000-0002-9139-1654
citation:
ama: 'Alwen JF, Blocki J, Pietrzak KZ. Sustained space complexity. In: Vol 10821.
Springer; 2018:99-130. doi:10.1007/978-3-319-78375-8_4'
apa: 'Alwen, J. F., Blocki, J., & Pietrzak, K. Z. (2018). Sustained space complexity
(Vol. 10821, pp. 99–130). Presented at the Eurocrypt 2018: Advances in Cryptology,
Tel Aviv, Israel: Springer. https://doi.org/10.1007/978-3-319-78375-8_4'
chicago: Alwen, Joel F, Jeremiah Blocki, and Krzysztof Z Pietrzak. “Sustained Space
Complexity,” 10821:99–130. Springer, 2018. https://doi.org/10.1007/978-3-319-78375-8_4.
ieee: 'J. F. Alwen, J. Blocki, and K. Z. Pietrzak, “Sustained space complexity,”
presented at the Eurocrypt 2018: Advances in Cryptology, Tel Aviv, Israel, 2018,
vol. 10821, pp. 99–130.'
ista: 'Alwen JF, Blocki J, Pietrzak KZ. 2018. Sustained space complexity. Eurocrypt
2018: Advances in Cryptology, LNCS, vol. 10821, 99–130.'
mla: Alwen, Joel F., et al. Sustained Space Complexity. Vol. 10821, Springer,
2018, pp. 99–130, doi:10.1007/978-3-319-78375-8_4.
short: J.F. Alwen, J. Blocki, K.Z. Pietrzak, in:, Springer, 2018, pp. 99–130.
conference:
end_date: 2018-05-03
location: Tel Aviv, Israel
name: 'Eurocrypt 2018: Advances in Cryptology'
start_date: 2018-04-29
date_created: 2018-12-11T11:45:41Z
date_published: 2018-03-31T00:00:00Z
date_updated: 2023-09-19T09:59:30Z
day: '31'
department:
- _id: KrPi
doi: 10.1007/978-3-319-78375-8_4
ec_funded: 1
external_id:
arxiv:
- '1705.05313'
isi:
- '000517098700004'
intvolume: ' 10821'
isi: 1
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/1705.05313
month: '03'
oa: 1
oa_version: Preprint
page: 99 - 130
project:
- _id: 258AA5B2-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '682815'
name: Teaching Old Crypto New Tricks
publication_status: published
publisher: Springer
publist_id: '7583'
quality_controlled: '1'
scopus_import: '1'
status: public
title: Sustained space complexity
type: conference
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
volume: 10821
year: '2018'
...
---
_id: '36'
abstract:
- lang: eng
text: Wheat (Triticum ssp.) is one of the most important human food sources. However,
this crop is very sensitive to temperature changes. Specifically, processes during
wheat leaf, flower, and seed development and photosynthesis, which all contribute
to the yield of this crop, are affected by high temperature. While this has to
some extent been investigated on physiological, developmental, and molecular levels,
very little is known about early signalling events associated with an increase
in temperature. Phosphorylation-mediated signalling mechanisms, which are quick
and dynamic, are associated with plant growth and development, also under abiotic
stress conditions. Therefore, we probed the impact of a short-term and mild increase
in temperature on the wheat leaf and spikelet phosphoproteome. In total, 3822
(containing 5178 phosphosites) and 5581 phosphopeptides (containing 7023 phosphosites)
were identified in leaf and spikelet samples, respectively. Following statistical
analysis, the resulting data set provides the scientific community with a first
large-scale plant phosphoproteome under the control of higher ambient temperature.
This community resource on the high temperature-mediated wheat phosphoproteome
will be valuable for future studies. Our analyses also revealed a core set of
common proteins between leaf and spikelet, suggesting some level of conserved
regulatory mechanisms. Furthermore, we observed temperature-regulated interconversion
of phosphoforms, which probably impacts protein activity.
acknowledgement: TZ is supported by a grant from the Chinese Scholarship Council.
article_processing_charge: No
author:
- first_name: Lam
full_name: Vu, Lam
last_name: Vu
- first_name: Tingting
full_name: Zhu, Tingting
last_name: Zhu
- first_name: Inge
full_name: Verstraeten, Inge
id: 362BF7FE-F248-11E8-B48F-1D18A9856A87
last_name: Verstraeten
orcid: 0000-0001-7241-2328
- first_name: Brigitte
full_name: Van De Cotte, Brigitte
last_name: Van De Cotte
- first_name: Kris
full_name: Gevaert, Kris
last_name: Gevaert
- first_name: Ive
full_name: De Smet, Ive
last_name: De Smet
citation:
ama: Vu L, Zhu T, Verstraeten I, Van De Cotte B, Gevaert K, De Smet I. Temperature-induced
changes in the wheat phosphoproteome reveal temperature-regulated interconversion
of phosphoforms. Journal of Experimental Botany. 2018;69(19):4609-4624.
doi:10.1093/jxb/ery204
apa: Vu, L., Zhu, T., Verstraeten, I., Van De Cotte, B., Gevaert, K., & De Smet,
I. (2018). Temperature-induced changes in the wheat phosphoproteome reveal temperature-regulated
interconversion of phosphoforms. Journal of Experimental Botany. Oxford
University Press. https://doi.org/10.1093/jxb/ery204
chicago: Vu, Lam, Tingting Zhu, Inge Verstraeten, Brigitte Van De Cotte, Kris Gevaert,
and Ive De Smet. “Temperature-Induced Changes in the Wheat Phosphoproteome Reveal
Temperature-Regulated Interconversion of Phosphoforms.” Journal of Experimental
Botany. Oxford University Press, 2018. https://doi.org/10.1093/jxb/ery204.
ieee: L. Vu, T. Zhu, I. Verstraeten, B. Van De Cotte, K. Gevaert, and I. De Smet,
“Temperature-induced changes in the wheat phosphoproteome reveal temperature-regulated
interconversion of phosphoforms,” Journal of Experimental Botany, vol.
69, no. 19. Oxford University Press, pp. 4609–4624, 2018.
ista: Vu L, Zhu T, Verstraeten I, Van De Cotte B, Gevaert K, De Smet I. 2018. Temperature-induced
changes in the wheat phosphoproteome reveal temperature-regulated interconversion
of phosphoforms. Journal of Experimental Botany. 69(19), 4609–4624.
mla: Vu, Lam, et al. “Temperature-Induced Changes in the Wheat Phosphoproteome Reveal
Temperature-Regulated Interconversion of Phosphoforms.” Journal of Experimental
Botany, vol. 69, no. 19, Oxford University Press, 2018, pp. 4609–24, doi:10.1093/jxb/ery204.
short: L. Vu, T. Zhu, I. Verstraeten, B. Van De Cotte, K. Gevaert, I. De Smet, Journal
of Experimental Botany 69 (2018) 4609–4624.
date_created: 2018-12-11T11:44:17Z
date_published: 2018-08-31T00:00:00Z
date_updated: 2023-09-19T10:00:46Z
day: '31'
ddc:
- '581'
department:
- _id: JiFr
doi: 10.1093/jxb/ery204
external_id:
isi:
- '000443568700010'
file:
- access_level: open_access
checksum: 34cb0a1611588b75bd6f4913fb4e30f1
content_type: application/pdf
creator: dernst
date_created: 2018-12-18T09:47:51Z
date_updated: 2020-07-14T12:46:13Z
file_id: '5741'
file_name: 2018_JournalExperimBotany_Vu.pdf
file_size: 3359316
relation: main_file
file_date_updated: 2020-07-14T12:46:13Z
has_accepted_license: '1'
intvolume: ' 69'
isi: 1
issue: '19'
language:
- iso: eng
month: '08'
oa: 1
oa_version: Published Version
page: 4609 - 4624
publication: Journal of Experimental Botany
publication_status: published
publisher: Oxford University Press
publist_id: '8019'
quality_controlled: '1'
scopus_import: '1'
status: public
title: Temperature-induced changes in the wheat phosphoproteome reveal temperature-regulated
interconversion of phosphoforms
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: journal_article
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
volume: 69
year: '2018'
...