---
_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
arxiv: 1
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: '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
arxiv: 1
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: '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
arxiv: 1
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: 2024-10-14T12:29:40Z
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: '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
arxiv: 1
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: 2024-10-14T12:30:32Z
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: '14284'
abstract:
- lang: eng
text: Pore-forming toxins (PFT) are virulence factors that transform from soluble
to membrane-bound states. The Yersinia YaxAB system represents a family of binary
α-PFTs with orthologues in human, insect, and plant pathogens, with unknown structures.
YaxAB was shown to be cytotoxic and likely involved in pathogenesis, though the
molecular basis for its two-component lytic mechanism remains elusive. Here, we
present crystal structures of YaxA and YaxB, together with a cryo-electron microscopy
map of the YaxAB complex. Our structures reveal a pore predominantly composed
of decamers of YaxA–YaxB heterodimers. Both subunits bear membrane-active moieties,
but only YaxA is capable of binding to membranes by itself. YaxB can subsequently
be recruited to membrane-associated YaxA and induced to present its lytic transmembrane
helices. Pore formation can progress by further oligomerization of YaxA–YaxB dimers.
Our results allow for a comparison between pore assemblies belonging to the wider
ClyA-like family of α-PFTs, highlighting diverse pore architectures.
article_number: '1806'
article_processing_charge: No
article_type: original
author:
- first_name: Bastian
full_name: Bräuning, Bastian
last_name: Bräuning
- first_name: Eva
full_name: Bertosin, Eva
last_name: Bertosin
- first_name: Florian M
full_name: Praetorius, Florian M
id: dfec9381-4341-11ee-8fd8-faa02bba7d62
last_name: Praetorius
- first_name: Christian
full_name: Ihling, Christian
last_name: Ihling
- first_name: Alexandra
full_name: Schatt, Alexandra
last_name: Schatt
- first_name: Agnes
full_name: Adler, Agnes
last_name: Adler
- first_name: Klaus
full_name: Richter, Klaus
last_name: Richter
- first_name: Andrea
full_name: Sinz, Andrea
last_name: Sinz
- first_name: Hendrik
full_name: Dietz, Hendrik
last_name: Dietz
- first_name: Michael
full_name: Groll, Michael
last_name: Groll
citation:
ama: Bräuning B, Bertosin E, Praetorius FM, et al. Structure and mechanism of the
two-component α-helical pore-forming toxin YaxAB. Nature Communications.
2018;9. doi:10.1038/s41467-018-04139-2
apa: Bräuning, B., Bertosin, E., Praetorius, F. M., Ihling, C., Schatt, A., Adler,
A., … Groll, M. (2018). Structure and mechanism of the two-component α-helical
pore-forming toxin YaxAB. Nature Communications. Springer Nature. https://doi.org/10.1038/s41467-018-04139-2
chicago: Bräuning, Bastian, Eva Bertosin, Florian M Praetorius, Christian Ihling,
Alexandra Schatt, Agnes Adler, Klaus Richter, Andrea Sinz, Hendrik Dietz, and
Michael Groll. “Structure and Mechanism of the Two-Component α-Helical Pore-Forming
Toxin YaxAB.” Nature Communications. Springer Nature, 2018. https://doi.org/10.1038/s41467-018-04139-2.
ieee: B. Bräuning et al., “Structure and mechanism of the two-component α-helical
pore-forming toxin YaxAB,” Nature Communications, vol. 9. Springer Nature,
2018.
ista: Bräuning B, Bertosin E, Praetorius FM, Ihling C, Schatt A, Adler A, Richter
K, Sinz A, Dietz H, Groll M. 2018. Structure and mechanism of the two-component
α-helical pore-forming toxin YaxAB. Nature Communications. 9, 1806.
mla: Bräuning, Bastian, et al. “Structure and Mechanism of the Two-Component α-Helical
Pore-Forming Toxin YaxAB.” Nature Communications, vol. 9, 1806, Springer
Nature, 2018, doi:10.1038/s41467-018-04139-2.
short: B. Bräuning, E. Bertosin, F.M. Praetorius, C. Ihling, A. Schatt, A. Adler,
K. Richter, A. Sinz, H. Dietz, M. Groll, Nature Communications 9 (2018).
date_created: 2023-09-06T12:07:33Z
date_published: 2018-05-04T00:00:00Z
date_updated: 2023-11-07T11:46:12Z
day: '04'
doi: 10.1038/s41467-018-04139-2
extern: '1'
external_id:
pmid:
- '29728606'
intvolume: ' 9'
keyword:
- General Physics and Astronomy
- General Biochemistry
- Genetics and Molecular Biology
- General Chemistry
- Multidisciplinary
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.1038/s41467-018-04139-2
month: '05'
oa: 1
oa_version: Published Version
pmid: 1
publication: Nature Communications
publication_identifier:
issn:
- 2041-1723
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
scopus_import: '1'
status: public
title: Structure and mechanism of the two-component α-helical pore-forming toxin YaxAB
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 9
year: '2018'
...
---
_id: '143'
abstract:
- lang: eng
text: 'Vector Addition Systems with States (VASS) provide a well-known and fundamental
model for the analysis of concurrent processes, parameterized systems, and are
also used as abstract models of programs in resource bound analysis. In this paper
we study the problem of obtaining asymptotic bounds on the termination time of
a given VASS. In particular, we focus on the practically important case of obtaining
polynomial bounds on termination time. Our main contributions are as follows:
First, we present a polynomial-time algorithm for deciding whether a given VASS
has a linear asymptotic complexity. We also show that if the complexity of a VASS
is not linear, it is at least quadratic. Second, we classify VASS according to
quantitative properties of their cycles. We show that certain singularities in
these properties are the key reason for non-polynomial asymptotic complexity of
VASS. In absence of singularities, we show that the asymptotic complexity is always
polynomial and of the form Θ(nk), for some integer k d, where d is the dimension
of the VASS. We present a polynomial-time algorithm computing the optimal k. For
general VASS, the same algorithm, which is based on a complete technique for the
construction of ranking functions in VASS, produces a valid lower bound, i.e.,
a k such that the termination complexity is (nk). Our results are based on new
insights into the geometry of VASS dynamics, which hold the potential for further
applicability to VASS analysis.'
alternative_title:
- ACM/IEEE Symposium on Logic in Computer Science
article_processing_charge: No
arxiv: 1
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: Antonín
full_name: Kučera, Antonín
last_name: Kučera
- first_name: Petr
full_name: Novotny, Petr
id: 3CC3B868-F248-11E8-B48F-1D18A9856A87
last_name: Novotny
- first_name: Dominik
full_name: Velan, Dominik
last_name: Velan
- first_name: Florian
full_name: Zuleger, Florian
last_name: Zuleger
citation:
ama: 'Brázdil T, Chatterjee K, Kučera A, Novotný P, Velan D, Zuleger F. Efficient
algorithms for asymptotic bounds on termination time in VASS. In: Vol F138033.
IEEE; 2018:185-194. doi:10.1145/3209108.3209191'
apa: 'Brázdil, T., Chatterjee, K., Kučera, A., Novotný, P., Velan, D., & Zuleger,
F. (2018). Efficient algorithms for asymptotic bounds on termination time in VASS
(Vol. F138033, pp. 185–194). Presented at the LICS: Logic in Computer Science,
Oxford, United Kingdom: IEEE. https://doi.org/10.1145/3209108.3209191'
chicago: Brázdil, Tomáš, Krishnendu Chatterjee, Antonín Kučera, Petr Novotný, Dominik
Velan, and Florian Zuleger. “Efficient Algorithms for Asymptotic Bounds on Termination
Time in VASS,” F138033:185–94. IEEE, 2018. https://doi.org/10.1145/3209108.3209191.
ieee: 'T. Brázdil, K. Chatterjee, A. Kučera, P. Novotný, D. Velan, and F. Zuleger,
“Efficient algorithms for asymptotic bounds on termination time in VASS,” presented
at the LICS: Logic in Computer Science, Oxford, United Kingdom, 2018, vol. F138033,
pp. 185–194.'
ista: 'Brázdil T, Chatterjee K, Kučera A, Novotný P, Velan D, Zuleger F. 2018. Efficient
algorithms for asymptotic bounds on termination time in VASS. LICS: Logic in Computer
Science, ACM/IEEE Symposium on Logic in Computer Science, vol. F138033, 185–194.'
mla: Brázdil, Tomáš, et al. Efficient Algorithms for Asymptotic Bounds on Termination
Time in VASS. Vol. F138033, IEEE, 2018, pp. 185–94, doi:10.1145/3209108.3209191.
short: T. Brázdil, K. Chatterjee, A. Kučera, P. Novotný, D. Velan, F. Zuleger, in:,
IEEE, 2018, pp. 185–194.
conference:
end_date: 2018-07-12
location: Oxford, United Kingdom
name: 'LICS: Logic in Computer Science'
start_date: 2018-07-09
date_created: 2018-12-11T11:44:51Z
date_published: 2018-07-09T00:00:00Z
date_updated: 2025-06-04T08:04:55Z
day: '09'
department:
- _id: KrCh
doi: 10.1145/3209108.3209191
ec_funded: 1
external_id:
arxiv:
- '1804.10985'
isi:
- '000545262800020'
isi: 1
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/1804.10985
month: '07'
oa: 1
oa_version: Preprint
page: 185 - 194
project:
- _id: 25892FC0-B435-11E9-9278-68D0E5697425
grant_number: ICT15-003
name: Efficient Algorithms for Computer Aided Verification
- _id: 2581B60A-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '279307'
name: 'Quantitative Graph Games: Theory and Applications'
- _id: 25832EC2-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: S 11407_N23
name: Rigorous Systems Engineering
publication_identifier:
isbn:
- 978-1-4503-5583-4
publication_status: published
publisher: IEEE
publist_id: '7780'
quality_controlled: '1'
scopus_import: '1'
status: public
title: Efficient algorithms for asymptotic bounds on termination time in VASS
type: conference
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: F138033
year: '2018'
...
---
_id: '14306'
abstract:
- lang: eng
text: 'Function and activity of biomolecules often depend on their spatial arrangement.
The method introduced here allows genetically encoding the spatial arrangement
of proteins and DNA. The approach relies on staple proteins that fold double-stranded
DNA into user-defined shapes. This thesis describes the development of staple
proteins based on the DNA recognition of TAL effectors and presents experimentally
derived rules for designing a variety of self-assembling nanoscale shapes featuring
structural motifs such as curvature, vertices, corners, and multilayer helix packing. '
article_processing_charge: No
author:
- first_name: Florian M
full_name: Praetorius, Florian M
id: dfec9381-4341-11ee-8fd8-faa02bba7d62
last_name: Praetorius
citation:
ama: Praetorius FM. Genetically encoding the spatial arrangement of DNA and proteins
in self-assembling nanostructures. 2018.
apa: Praetorius, F. M. (2018). Genetically encoding the spatial arrangement of
DNA and proteins in self-assembling nanostructures. Technische Universität
München.
chicago: Praetorius, Florian M. “Genetically Encoding the Spatial Arrangement of
DNA and Proteins in Self-Assembling Nanostructures.” Technische Universität München,
2018.
ieee: F. M. Praetorius, “Genetically encoding the spatial arrangement of DNA and
proteins in self-assembling nanostructures,” Technische Universität München, 2018.
ista: Praetorius FM. 2018. Genetically encoding the spatial arrangement of DNA and
proteins in self-assembling nanostructures. Technische Universität München.
mla: Praetorius, Florian M. Genetically Encoding the Spatial Arrangement of DNA
and Proteins in Self-Assembling Nanostructures. Technische Universität München,
2018.
short: F.M. Praetorius, Genetically Encoding the Spatial Arrangement of DNA and
Proteins in Self-Assembling Nanostructures, Technische Universität München, 2018.
date_created: 2023-09-06T13:11:22Z
date_published: 2018-01-16T00:00:00Z
date_updated: 2024-10-14T12:31:46Z
day: '16'
degree_awarded: PhD
extern: '1'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://mediatum.ub.tum.de/1398662
month: '01'
oa: 1
oa_version: Published Version
publication_status: published
publisher: Technische Universität München
status: public
supervisor:
- first_name: Hendrik
full_name: Dietz, Hendrik
last_name: Dietz
title: Genetically encoding the spatial arrangement of DNA and proteins in self-assembling
nanostructures
type: dissertation
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
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
arxiv: 1
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: 2024-10-14T12:31:09Z
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: '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).
corr_author: '1'
date_created: 2018-12-11T11:44:52Z
date_published: 2018-08-01T00:00:00Z
date_updated: 2024-10-09T20:58:32Z
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: '146'
abstract:
- lang: eng
text: The root cap protects the stem cell niche of angiosperm roots from damage.
In Arabidopsis, lateral root cap (LRC) cells covering the meristematic zone are
regularly lost through programmed cell death, while the outermost layer of the
root cap covering the tip is repeatedly sloughed. Efficient coordination with
stem cells producing new layers is needed to maintain a constant size of the cap.
We present a signalling pair, the peptide IDA-LIKE1 (IDL1) and its receptor HAESA-LIKE2
(HSL2), mediating such communication. Live imaging over several days characterized
this process from initial fractures in LRC cell files to full separation of a
layer. Enhanced expression of IDL1 in the separating root cap layers resulted
in increased frequency of sloughing, balanced with generation of new layers in
a HSL2-dependent manner. Transcriptome analyses linked IDL1-HSL2 signalling to
the transcription factors BEARSKIN1/2 and genes associated with programmed cell
death. Mutations in either IDL1 or HSL2 slowed down cell division, maturation
and separation. Thus, IDL1-HSL2 signalling potentiates dynamic regulation of the
homeostatic balance between stem cell division and sloughing activity.
article_processing_charge: No
article_type: original
author:
- first_name: Chun Lin
full_name: Shi, Chun Lin
last_name: Shi
- first_name: Daniel
full_name: Von Wangenheim, Daniel
id: 49E91952-F248-11E8-B48F-1D18A9856A87
last_name: Von Wangenheim
orcid: 0000-0002-6862-1247
- first_name: Ullrich
full_name: Herrmann, Ullrich
last_name: Herrmann
- first_name: Mari
full_name: Wildhagen, Mari
last_name: Wildhagen
- first_name: Ivan
full_name: Kulik, Ivan
id: F0AB3FCE-02D1-11E9-BD0E-99399A5D3DEB
last_name: Kulik
- first_name: Andreas
full_name: Kopf, Andreas
last_name: Kopf
- first_name: Takashi
full_name: Ishida, Takashi
last_name: Ishida
- first_name: Vilde
full_name: Olsson, Vilde
last_name: Olsson
- first_name: Mari Kristine
full_name: Anker, Mari Kristine
last_name: Anker
- first_name: Markus
full_name: Albert, Markus
last_name: Albert
- first_name: Melinka A
full_name: Butenko, Melinka A
last_name: Butenko
- first_name: Georg
full_name: Felix, Georg
last_name: Felix
- first_name: Shinichiro
full_name: Sawa, Shinichiro
last_name: Sawa
- first_name: Manfred
full_name: Claassen, Manfred
last_name: Claassen
- first_name: Jirí
full_name: Friml, Jirí
id: 4159519E-F248-11E8-B48F-1D18A9856A87
last_name: Friml
orcid: 0000-0002-8302-7596
- first_name: Reidunn B
full_name: Aalen, Reidunn B
last_name: Aalen
citation:
ama: Shi CL, von Wangenheim D, Herrmann U, et al. The dynamics of root cap sloughing
in Arabidopsis is regulated by peptide signalling. Nature Plants. 2018;4(8):596-604.
doi:10.1038/s41477-018-0212-z
apa: Shi, C. L., von Wangenheim, D., Herrmann, U., Wildhagen, M., Kulik, I., Kopf,
A., … Aalen, R. B. (2018). The dynamics of root cap sloughing in Arabidopsis is
regulated by peptide signalling. Nature Plants. Nature Publishing Group.
https://doi.org/10.1038/s41477-018-0212-z
chicago: Shi, Chun Lin, Daniel von Wangenheim, Ullrich Herrmann, Mari Wildhagen,
Ivan Kulik, Andreas Kopf, Takashi Ishida, et al. “The Dynamics of Root Cap Sloughing
in Arabidopsis Is Regulated by Peptide Signalling.” Nature Plants. Nature
Publishing Group, 2018. https://doi.org/10.1038/s41477-018-0212-z.
ieee: C. L. Shi et al., “The dynamics of root cap sloughing in Arabidopsis
is regulated by peptide signalling,” Nature Plants, vol. 4, no. 8. Nature
Publishing Group, pp. 596–604, 2018.
ista: Shi CL, von Wangenheim D, Herrmann U, Wildhagen M, Kulik I, Kopf A, Ishida
T, Olsson V, Anker MK, Albert M, Butenko MA, Felix G, Sawa S, Claassen M, Friml
J, Aalen RB. 2018. The dynamics of root cap sloughing in Arabidopsis is regulated
by peptide signalling. Nature Plants. 4(8), 596–604.
mla: Shi, Chun Lin, et al. “The Dynamics of Root Cap Sloughing in Arabidopsis Is
Regulated by Peptide Signalling.” Nature Plants, vol. 4, no. 8, Nature
Publishing Group, 2018, pp. 596–604, doi:10.1038/s41477-018-0212-z.
short: C.L. Shi, D. von Wangenheim, U. Herrmann, M. Wildhagen, I. Kulik, A. Kopf,
T. Ishida, V. Olsson, M.K. Anker, M. Albert, M.A. Butenko, G. Felix, S. Sawa,
M. Claassen, J. Friml, R.B. Aalen, Nature Plants 4 (2018) 596–604.
date_created: 2018-12-11T11:44:52Z
date_published: 2018-07-30T00:00:00Z
date_updated: 2023-09-19T10:08:45Z
day: '30'
ddc:
- '580'
department:
- _id: JiFr
doi: 10.1038/s41477-018-0212-z
external_id:
isi:
- '000443861300016'
pmid:
- '30061750'
file:
- access_level: open_access
checksum: da33101c76ee1b2dc5ab28fd2ccba9d0
content_type: application/pdf
creator: dernst
date_created: 2019-11-18T16:24:07Z
date_updated: 2020-07-14T12:44:56Z
file_id: '7043'
file_name: 2018_NaturePlants_Shi.pdf
file_size: 226829
relation: main_file
file_date_updated: 2020-07-14T12:44:56Z
has_accepted_license: '1'
intvolume: ' 4'
isi: 1
issue: '8'
language:
- iso: eng
month: '07'
oa: 1
oa_version: Submitted Version
page: 596 - 604
pmid: 1
publication: Nature Plants
publication_status: published
publisher: Nature Publishing Group
publist_id: '7777'
quality_controlled: '1'
related_material:
link:
- description: News on IST Homepage
relation: press_release
url: https://ist.ac.at/en/news/new-process-in-root-development-discovered/
scopus_import: '1'
status: public
title: The dynamics of root cap sloughing in Arabidopsis is regulated by peptide signalling
type: journal_article
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
volume: 4
year: '2018'
...
---
_id: '147'
abstract:
- lang: eng
text: The trafficking of subcellular cargos in eukaryotic cells crucially depends
on vesicle budding, a process mediated by ARF-GEFs (ADP-ribosylation factor guanine
nucleotide exchange factors). In plants, ARF-GEFs play essential roles in endocytosis,
vacuolar trafficking, recycling, secretion, and polar trafficking. Moreover, they
are important for plant development, mainly through controlling the polar subcellular
localization of PIN-FORMED (PIN) transporters of the plant hormone auxin. Here,
using a chemical genetics screen in Arabidopsis thaliana, we identified Endosidin
4 (ES4), an inhibitor of eukaryotic ARF-GEFs. ES4 acts similarly to and synergistically
with the established ARF-GEF inhibitor Brefeldin A and has broad effects on intracellular
trafficking, including endocytosis, exocytosis, and vacuolar targeting. Additionally,
Arabidopsis and yeast (Sacharomyces cerevisiae) mutants defective in ARF-GEF show
altered sensitivity to ES4. ES4 interferes with the activation-based membrane
association of the ARF1 GTPases, but not of their mutant variants that are activated
independently of ARF-GEF activity. Biochemical approaches and docking simulations
confirmed that ES4 specifically targets the SEC7 domain-containing ARF-GEFs. These
observations collectively identify ES4 as a chemical tool enabling the study of
ARF-GEF-mediated processes, including ARF-GEF-mediated plant development.
acknowledgement: We thank Gerd Jürgens, Sandra Richter, and Sheng Yang He for providing
antibodies; Maciek Adamowski, Fernando Aniento, Sebastian Bednarek, Nico Callewaert,
Matyás Fendrych, Elena Feraru, and Mugurel I. Feraru for helpful suggestions; Siamsa
Doyle for critical reading of the manuscript and helpful comments and suggestions;
and Stephanie Smith and Martine De Cock for help in editing and language corrections.
We acknowledge the core facility Cellular Imaging of CEITEC supported by the Czech-BioImaging
large RI project (LM2015062 funded by MEYS CR) for their support with obtaining
scientific data presented in this article. Plant Sciences Core Facility of CEITEC
Masaryk University is gratefully acknowledged for obtaining part of the scientific
data presented in this article. We acknowledge support from the Fondation pour la
Recherche Médicale and from the Institut National du Cancer (J.C.). The research
leading to these results was funded by the European Research Council under the European
Union's 7th Framework Program (FP7/2007-2013)/ERC grant agreement numbers 282300
and 742985 and the Czech Science Foundation GAČR (GA18-26981S; J.F.); Ministry of
Education, Youth, and Sports/MEYS of the Czech Republic under the Project CEITEC
2020 (LQ1601; T.N.); the China Science Council for a predoctoral fellowship (Q.L.);
a joint research project within the framework of cooperation between the Research
Foundation-Flanders and the Bulgarian Academy of Sciences (VS.025.13N; K.M. and
E.R.); Vetenskapsrådet and Vinnova (Verket för Innovationssystem; S.R.), Knut och
Alice Wallenbergs Stiftelse via “Shapesystem” Grant 2012.0050 (S.R.), Kempe stiftelserna
(P.G.), Tryggers CTS410 (P.G.).
article_processing_charge: No
article_type: original
author:
- first_name: Urszula
full_name: Kania, Urszula
id: 4AE5C486-F248-11E8-B48F-1D18A9856A87
last_name: Kania
- first_name: Tomasz
full_name: Nodzyński, Tomasz
last_name: Nodzyński
- first_name: Qing
full_name: Lu, Qing
last_name: Lu
- first_name: Glenn R
full_name: Hicks, Glenn R
last_name: Hicks
- first_name: Wim
full_name: Nerinckx, Wim
last_name: Nerinckx
- first_name: Kiril
full_name: Mishev, Kiril
last_name: Mishev
- first_name: Francois
full_name: Peurois, Francois
last_name: Peurois
- first_name: Jacqueline
full_name: Cherfils, Jacqueline
last_name: Cherfils
- first_name: Rycke Riet Maria
full_name: De, Rycke Riet Maria
last_name: De
- first_name: Peter
full_name: Grones, Peter
id: 399876EC-F248-11E8-B48F-1D18A9856A87
last_name: Grones
- first_name: Stéphanie
full_name: Robert, Stéphanie
last_name: Robert
- first_name: Eugenia
full_name: Russinova, Eugenia
last_name: Russinova
- first_name: Jirí
full_name: Friml, Jirí
id: 4159519E-F248-11E8-B48F-1D18A9856A87
last_name: Friml
orcid: 0000-0002-8302-7596
citation:
ama: Kania U, Nodzyński T, Lu Q, et al. The inhibitor Endosidin 4 targets SEC7 domain-type
ARF GTPase exchange factors and interferes with sub cellular trafficking in eukaryotes.
The Plant Cell. 2018;30(10):2553-2572. doi:10.1105/tpc.18.00127
apa: Kania, U., Nodzyński, T., Lu, Q., Hicks, G. R., Nerinckx, W., Mishev, K., …
Friml, J. (2018). The inhibitor Endosidin 4 targets SEC7 domain-type ARF GTPase
exchange factors and interferes with sub cellular trafficking in eukaryotes. The
Plant Cell. Oxford University Press. https://doi.org/10.1105/tpc.18.00127
chicago: Kania, Urszula, Tomasz Nodzyński, Qing Lu, Glenn R Hicks, Wim Nerinckx,
Kiril Mishev, Francois Peurois, et al. “The Inhibitor Endosidin 4 Targets SEC7
Domain-Type ARF GTPase Exchange Factors and Interferes with Sub Cellular Trafficking
in Eukaryotes.” The Plant Cell. Oxford University Press, 2018. https://doi.org/10.1105/tpc.18.00127.
ieee: U. Kania et al., “The inhibitor Endosidin 4 targets SEC7 domain-type
ARF GTPase exchange factors and interferes with sub cellular trafficking in eukaryotes,”
The Plant Cell, vol. 30, no. 10. Oxford University Press, pp. 2553–2572,
2018.
ista: Kania U, Nodzyński T, Lu Q, Hicks GR, Nerinckx W, Mishev K, Peurois F, Cherfils
J, De RRM, Grones P, Robert S, Russinova E, Friml J. 2018. The inhibitor Endosidin
4 targets SEC7 domain-type ARF GTPase exchange factors and interferes with sub
cellular trafficking in eukaryotes. The Plant Cell. 30(10), 2553–2572.
mla: Kania, Urszula, et al. “The Inhibitor Endosidin 4 Targets SEC7 Domain-Type
ARF GTPase Exchange Factors and Interferes with Sub Cellular Trafficking in Eukaryotes.”
The Plant Cell, vol. 30, no. 10, Oxford University Press, 2018, pp. 2553–72,
doi:10.1105/tpc.18.00127.
short: U. Kania, T. Nodzyński, Q. Lu, G.R. Hicks, W. Nerinckx, K. Mishev, F. Peurois,
J. Cherfils, R.R.M. De, P. Grones, S. Robert, E. Russinova, J. Friml, The Plant
Cell 30 (2018) 2553–2572.
corr_author: '1'
date_created: 2018-12-11T11:44:52Z
date_published: 2018-11-12T00:00:00Z
date_updated: 2026-06-18T17:36:26Z
day: '12'
ddc:
- '580'
department:
- _id: JiFr
doi: 10.1105/tpc.18.00127
ec_funded: 1
external_id:
isi:
- '000450000500023'
pmid:
- '30018156'
intvolume: ' 30'
isi: 1
issue: '10'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.1105/tpc.18.00127
month: '11'
oa: 1
oa_version: Published Version
page: 2553 - 2572
pmid: 1
project:
- _id: 25716A02-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '282300'
name: Polarity and subcellular dynamics in plants
- _id: 261099A6-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '742985'
name: Tracing Evolution of Auxin Transport and Polarity in Plants
publication: The Plant Cell
publication_identifier:
issn:
- 1040-4651
publication_status: published
publisher: Oxford University Press
publist_id: '7776'
quality_controlled: '1'
scopus_import: '1'
status: public
title: The inhibitor Endosidin 4 targets SEC7 domain-type ARF GTPase exchange factors
and interferes with sub cellular trafficking in eukaryotes
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 30
year: '2018'
...
---
_id: '148'
abstract:
- lang: eng
text: 'Land plants evolved from charophytic algae, among which Charophyceae possess
the most complex body plans. We present the genome of Chara braunii; comparison
of the genome to those of land plants identified evolutionary novelties for plant
terrestrialization and land plant heritage genes. C. braunii employs unique xylan
synthases for cell wall biosynthesis, a phragmoplast (cell separation) mechanism
similar to that of land plants, and many phytohormones. C. braunii plastids are
controlled via land-plant-like retrograde signaling, and transcriptional regulation
is more elaborate than in other algae. The morphological complexity of this organism
may result from expanded gene families, with three cases of particular note: genes
effecting tolerance to reactive oxygen species (ROS), LysM receptor-like kinases,
and transcription factors (TFs). Transcriptomic analysis of sexual reproductive
structures reveals intricate control by TFs, activity of the ROS gene network,
and the ancestral use of plant-like storage and stress protection proteins in
the zygote.'
acknowledgement: In-Data-Review
article_processing_charge: No
author:
- first_name: Tomoaki
full_name: Nishiyama, Tomoaki
last_name: Nishiyama
- first_name: Hidetoshi
full_name: Sakayama, Hidetoshi
last_name: Sakayama
- first_name: Jan
full_name: De Vries, Jan
last_name: De Vries
- first_name: Henrik
full_name: Buschmann, Henrik
last_name: Buschmann
- first_name: Denis
full_name: Saint Marcoux, Denis
last_name: Saint Marcoux
- first_name: Kristian
full_name: Ullrich, Kristian
last_name: Ullrich
- first_name: Fabian
full_name: Haas, Fabian
last_name: Haas
- first_name: Lisa
full_name: Vanderstraeten, Lisa
last_name: Vanderstraeten
- first_name: Dirk
full_name: Becker, Dirk
last_name: Becker
- first_name: Daniel
full_name: Lang, Daniel
last_name: Lang
- first_name: Stanislav
full_name: Vosolsobě, Stanislav
last_name: Vosolsobě
- first_name: Stephane
full_name: Rombauts, Stephane
last_name: Rombauts
- first_name: Per
full_name: Wilhelmsson, Per
last_name: Wilhelmsson
- first_name: Philipp
full_name: Janitza, Philipp
last_name: Janitza
- first_name: Ramona
full_name: Kern, Ramona
last_name: Kern
- first_name: Alexander
full_name: Heyl, Alexander
last_name: Heyl
- first_name: Florian
full_name: Rümpler, Florian
last_name: Rümpler
- first_name: Luz
full_name: Calderón Villalobos, Luz
last_name: Calderón Villalobos
- first_name: John
full_name: Clay, John
last_name: Clay
- first_name: Roman
full_name: Skokan, Roman
last_name: Skokan
- first_name: Atsushi
full_name: Toyoda, Atsushi
last_name: Toyoda
- first_name: Yutaka
full_name: Suzuki, Yutaka
last_name: Suzuki
- first_name: Hiroshi
full_name: Kagoshima, Hiroshi
last_name: Kagoshima
- first_name: Elio
full_name: Schijlen, Elio
last_name: Schijlen
- first_name: Navindra
full_name: Tajeshwar, Navindra
last_name: Tajeshwar
- first_name: Bruno
full_name: Catarino, Bruno
last_name: Catarino
- first_name: Alexander
full_name: Hetherington, Alexander
last_name: Hetherington
- first_name: Assia
full_name: Saltykova, Assia
last_name: Saltykova
- first_name: Clemence
full_name: Bonnot, Clemence
last_name: Bonnot
- first_name: Holger
full_name: Breuninger, Holger
last_name: Breuninger
- first_name: Aikaterini
full_name: Symeonidi, Aikaterini
last_name: Symeonidi
- first_name: Guru
full_name: Radhakrishnan, Guru
last_name: Radhakrishnan
- first_name: Filip
full_name: Van Nieuwerburgh, Filip
last_name: Van Nieuwerburgh
- first_name: Dieter
full_name: Deforce, Dieter
last_name: Deforce
- first_name: Caren
full_name: Chang, Caren
last_name: Chang
- first_name: Kenneth
full_name: Karol, Kenneth
last_name: Karol
- first_name: Rainer
full_name: Hedrich, Rainer
last_name: Hedrich
- first_name: Peter
full_name: Ulvskov, Peter
last_name: Ulvskov
- first_name: Gernot
full_name: Glöckner, Gernot
last_name: Glöckner
- first_name: Charles
full_name: Delwiche, Charles
last_name: Delwiche
- first_name: Jan
full_name: Petrášek, Jan
last_name: Petrášek
- first_name: Yves
full_name: Van De Peer, Yves
last_name: Van De Peer
- first_name: Jirí
full_name: Friml, Jirí
id: 4159519E-F248-11E8-B48F-1D18A9856A87
last_name: Friml
orcid: 0000-0002-8302-7596
- first_name: Mary
full_name: Beilby, Mary
last_name: Beilby
- first_name: Liam
full_name: Dolan, Liam
last_name: Dolan
- first_name: Yuji
full_name: Kohara, Yuji
last_name: Kohara
- first_name: Sumio
full_name: Sugano, Sumio
last_name: Sugano
- first_name: Asao
full_name: Fujiyama, Asao
last_name: Fujiyama
- first_name: Pierre Marc
full_name: Delaux, Pierre Marc
last_name: Delaux
- first_name: Marcel
full_name: Quint, Marcel
last_name: Quint
- first_name: Gunter
full_name: Theissen, Gunter
last_name: Theissen
- first_name: Martin
full_name: Hagemann, Martin
last_name: Hagemann
- first_name: Jesper
full_name: Harholt, Jesper
last_name: Harholt
- first_name: Christophe
full_name: Dunand, Christophe
last_name: Dunand
- first_name: Sabine
full_name: Zachgo, Sabine
last_name: Zachgo
- first_name: Jane
full_name: Langdale, Jane
last_name: Langdale
- first_name: Florian
full_name: Maumus, Florian
last_name: Maumus
- first_name: Dominique
full_name: Van Der Straeten, Dominique
last_name: Van Der Straeten
- first_name: Sven B
full_name: Gould, Sven B
last_name: Gould
- first_name: Stefan
full_name: Rensing, Stefan
last_name: Rensing
citation:
ama: 'Nishiyama T, Sakayama H, De Vries J, et al. The Chara genome: Secondary complexity
and implications for plant terrestrialization. Cell. 2018;174(2):448-464.e24.
doi:10.1016/j.cell.2018.06.033'
apa: 'Nishiyama, T., Sakayama, H., De Vries, J., Buschmann, H., Saint Marcoux, D.,
Ullrich, K., … Rensing, S. (2018). The Chara genome: Secondary complexity and
implications for plant terrestrialization. Cell. Cell Press. https://doi.org/10.1016/j.cell.2018.06.033'
chicago: 'Nishiyama, Tomoaki, Hidetoshi Sakayama, Jan De Vries, Henrik Buschmann,
Denis Saint Marcoux, Kristian Ullrich, Fabian Haas, et al. “The Chara Genome:
Secondary Complexity and Implications for Plant Terrestrialization.” Cell.
Cell Press, 2018. https://doi.org/10.1016/j.cell.2018.06.033.'
ieee: 'T. Nishiyama et al., “The Chara genome: Secondary complexity and implications
for plant terrestrialization,” Cell, vol. 174, no. 2. Cell Press, p. 448–464.e24,
2018.'
ista: 'Nishiyama T, Sakayama H, De Vries J, Buschmann H, Saint Marcoux D, Ullrich
K, Haas F, Vanderstraeten L, Becker D, Lang D, Vosolsobě S, Rombauts S, Wilhelmsson
P, Janitza P, Kern R, Heyl A, Rümpler F, Calderón Villalobos L, Clay J, Skokan
R, Toyoda A, Suzuki Y, Kagoshima H, Schijlen E, Tajeshwar N, Catarino B, Hetherington
A, Saltykova A, Bonnot C, Breuninger H, Symeonidi A, Radhakrishnan G, Van Nieuwerburgh
F, Deforce D, Chang C, Karol K, Hedrich R, Ulvskov P, Glöckner G, Delwiche C,
Petrášek J, Van De Peer Y, Friml J, Beilby M, Dolan L, Kohara Y, Sugano S, Fujiyama
A, Delaux PM, Quint M, Theissen G, Hagemann M, Harholt J, Dunand C, Zachgo S,
Langdale J, Maumus F, Van Der Straeten D, Gould SB, Rensing S. 2018. The Chara
genome: Secondary complexity and implications for plant terrestrialization. Cell.
174(2), 448–464.e24.'
mla: 'Nishiyama, Tomoaki, et al. “The Chara Genome: Secondary Complexity and Implications
for Plant Terrestrialization.” Cell, vol. 174, no. 2, Cell Press, 2018,
p. 448–464.e24, doi:10.1016/j.cell.2018.06.033.'
short: T. Nishiyama, H. Sakayama, J. De Vries, H. Buschmann, D. Saint Marcoux, K.
Ullrich, F. Haas, L. Vanderstraeten, D. Becker, D. Lang, S. Vosolsobě, S. Rombauts,
P. Wilhelmsson, P. Janitza, R. Kern, A. Heyl, F. Rümpler, L. Calderón Villalobos,
J. Clay, R. Skokan, A. Toyoda, Y. Suzuki, H. Kagoshima, E. Schijlen, N. Tajeshwar,
B. Catarino, A. Hetherington, A. Saltykova, C. Bonnot, H. Breuninger, A. Symeonidi,
G. Radhakrishnan, F. Van Nieuwerburgh, D. Deforce, C. Chang, K. Karol, R. Hedrich,
P. Ulvskov, G. Glöckner, C. Delwiche, J. Petrášek, Y. Van De Peer, J. Friml, M.
Beilby, L. Dolan, Y. Kohara, S. Sugano, A. Fujiyama, P.M. Delaux, M. Quint, G.
Theissen, M. Hagemann, J. Harholt, C. Dunand, S. Zachgo, J. Langdale, F. Maumus,
D. Van Der Straeten, S.B. Gould, S. Rensing, Cell 174 (2018) 448–464.e24.
date_created: 2018-12-11T11:44:53Z
date_published: 2018-07-12T00:00:00Z
date_updated: 2026-06-18T17:39:09Z
day: '12'
ddc:
- '580'
department:
- _id: JiFr
doi: 10.1016/j.cell.2018.06.033
ec_funded: 1
external_id:
isi:
- '000438482800019'
pmid:
- '30007417'
intvolume: ' 174'
isi: 1
issue: '2'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://www.ncbi.nlm.nih.gov/pubmed/30007417
month: '07'
oa: 1
oa_version: Published Version
page: 448 - 464.e24
pmid: 1
project:
- _id: 261099A6-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '742985'
name: Tracing Evolution of Auxin Transport and Polarity in Plants
publication: Cell
publication_status: published
publisher: Cell Press
publist_id: '7774'
quality_controlled: '1'
scopus_import: '1'
status: public
title: 'The Chara genome: Secondary complexity and implications for plant terrestrialization'
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 174
year: '2018'
...
---
_id: '150'
abstract:
- lang: eng
text: A short, 14-amino-acid segment called SP1, located in the Gag structural protein1,
has a critical role during the formation of the HIV-1 virus particle. During virus
assembly, the SP1 peptide and seven preceding residues fold into a six-helix bundle,
which holds together the Gag hexamer and facilitates the formation of a curved
immature hexagonal lattice underneath the viral membrane2,3. Upon completion of
assembly and budding, proteolytic cleavage of Gag leads to virus maturation, in
which the immature lattice is broken down; the liberated CA domain of Gag then
re-assembles into the mature conical capsid that encloses the viral genome and
associated enzymes. Folding and proteolysis of the six-helix bundle are crucial
rate-limiting steps of both Gag assembly and disassembly, and the six-helix bundle
is an established target of HIV-1 inhibitors4,5. Here, using a combination of
structural and functional analyses, we show that inositol hexakisphosphate (InsP6,
also known as IP6) facilitates the formation of the six-helix bundle and assembly
of the immature HIV-1 Gag lattice. IP6 makes ionic contacts with two rings of
lysine residues at the centre of the Gag hexamer. Proteolytic cleavage then unmasks
an alternative binding site, where IP6 interaction promotes the assembly of the
mature capsid lattice. These studies identify IP6 as a naturally occurring small
molecule that promotes both assembly and maturation of HIV-1.
article_processing_charge: No
article_type: original
author:
- first_name: Robert
full_name: Dick, Robert
last_name: Dick
- first_name: Kaneil K
full_name: Zadrozny, Kaneil K
last_name: Zadrozny
- first_name: Chaoyi
full_name: Xu, Chaoyi
last_name: Xu
- first_name: Florian
full_name: Schur, Florian
id: 48AD8942-F248-11E8-B48F-1D18A9856A87
last_name: Schur
orcid: 0000-0003-4790-8078
- first_name: Terri D
full_name: Lyddon, Terri D
last_name: Lyddon
- first_name: Clifton L
full_name: Ricana, Clifton L
last_name: Ricana
- first_name: Jonathan M
full_name: Wagner, Jonathan M
last_name: Wagner
- first_name: Juan R
full_name: Perilla, Juan R
last_name: Perilla
- first_name: Pornillos Barbie K
full_name: Ganser, Pornillos Barbie K
last_name: Ganser
- first_name: Marc C
full_name: Johnson, Marc C
last_name: Johnson
- first_name: Owen
full_name: Pornillos, Owen
last_name: Pornillos
- first_name: Volker
full_name: Vogt, Volker
last_name: Vogt
citation:
ama: Dick R, Zadrozny KK, Xu C, et al. Inositol phosphates are assembly co-factors
for HIV-1. Nature. 2018;560(7719):509–512. doi:10.1038/s41586-018-0396-4
apa: Dick, R., Zadrozny, K. K., Xu, C., Schur, F. K., Lyddon, T. D., Ricana, C.
L., … Vogt, V. (2018). Inositol phosphates are assembly co-factors for HIV-1.
Nature. Nature Publishing Group. https://doi.org/10.1038/s41586-018-0396-4
chicago: Dick, Robert, Kaneil K Zadrozny, Chaoyi Xu, Florian KM Schur, Terri D Lyddon,
Clifton L Ricana, Jonathan M Wagner, et al. “Inositol Phosphates Are Assembly
Co-Factors for HIV-1.” Nature. Nature Publishing Group, 2018. https://doi.org/10.1038/s41586-018-0396-4.
ieee: R. Dick et al., “Inositol phosphates are assembly co-factors for HIV-1,”
Nature, vol. 560, no. 7719. Nature Publishing Group, pp. 509–512, 2018.
ista: Dick R, Zadrozny KK, Xu C, Schur FK, Lyddon TD, Ricana CL, Wagner JM, Perilla
JR, Ganser PBK, Johnson MC, Pornillos O, Vogt V. 2018. Inositol phosphates are
assembly co-factors for HIV-1. Nature. 560(7719), 509–512.
mla: Dick, Robert, et al. “Inositol Phosphates Are Assembly Co-Factors for HIV-1.”
Nature, vol. 560, no. 7719, Nature Publishing Group, 2018, pp. 509–512,
doi:10.1038/s41586-018-0396-4.
short: R. Dick, K.K. Zadrozny, C. Xu, F.K. Schur, T.D. Lyddon, C.L. Ricana, J.M.
Wagner, J.R. Perilla, P.B.K. Ganser, M.C. Johnson, O. Pornillos, V. Vogt, Nature
560 (2018) 509–512.
date_created: 2018-12-11T11:44:53Z
date_published: 2018-08-29T00:00:00Z
date_updated: 2023-09-12T07:44:37Z
day: '29'
department:
- _id: FlSc
doi: 10.1038/s41586-018-0396-4
external_id:
isi:
- '000442483400046'
pmid:
- '30158708'
intvolume: ' 560'
isi: 1
issue: '7719'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6242333/
month: '08'
oa: 1
oa_version: Submitted Version
page: 509–512
pmid: 1
publication: Nature
publication_identifier:
eissn:
- 1476-4687
publication_status: published
publisher: Nature Publishing Group
quality_controlled: '1'
related_material:
link:
- relation: erratum
url: https://doi.org/10.1038/s41586-018-0505-4
scopus_import: '1'
status: public
title: Inositol phosphates are assembly co-factors for HIV-1
type: journal_article
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
volume: 560
year: '2018'
...
---
_id: '15143'
abstract:
- lang: eng
text: To maintain genome integrity, segmented double-stranded RNA viruses of the
Reoviridae family must accurately select and package a complete set of up to a
dozen distinct genomic RNAs. It is thought that the high fidelity segmented genome
assembly involves multiple sequence-specific RNA–RNA interactions between single-stranded
RNA segment precursors. These are mediated by virus-encoded non-structural proteins
with RNA chaperone-like activities, such as rotavirus (RV) NSP2 and avian reovirus
σNS. Here, we compared the abilities of NSP2 and σNS to mediate sequence-specific
interactions between RV genomic segment precursors. Despite their similar activities,
NSP2 successfully promotes inter-segment association, while σNS fails to do so.
To understand the mechanisms underlying such selectivity in promoting inter-molecular
duplex formation, we compared RNA-binding and helix-unwinding activities of both
proteins. We demonstrate that octameric NSP2 binds structured RNAs with high affinity,
resulting in efficient intramolecular RNA helix disruption. Hexameric σNS oligomerizes
into an octamer that binds two RNAs, yet it exhibits only limited RNA-unwinding
activity compared to NSP2. Thus, the formation of intersegment RNA–RNA interactions
is governed by both helix-unwinding capacity of the chaperones and stability of
RNA structure. We propose that this protein-mediated RNA selection mechanism may
underpin the high fidelity assembly of multi-segmented RNA genomes in Reoviridae.
article_processing_charge: Yes
article_type: original
author:
- first_name: Jack Peter Kelly
full_name: Bravo, Jack Peter Kelly
id: 96aecfa5-8931-11ee-af30-aa6a5d6eee0e
last_name: Bravo
orcid: 0000-0003-0456-0753
- first_name: Alexander
full_name: Borodavka, Alexander
last_name: Borodavka
- first_name: Anders
full_name: Barth, Anders
last_name: Barth
- first_name: Antonio N
full_name: Calabrese, Antonio N
last_name: Calabrese
- first_name: Peter
full_name: Mojzes, Peter
last_name: Mojzes
- first_name: Joseph J B
full_name: Cockburn, Joseph J B
last_name: Cockburn
- first_name: Don C
full_name: Lamb, Don C
last_name: Lamb
- first_name: Roman
full_name: Tuma, Roman
last_name: Tuma
citation:
ama: Bravo JPK, Borodavka A, Barth A, et al. Stability of local secondary structure
determines selectivity of viral RNA chaperones. Nucleic Acids Research.
2018;46(15):7924-7937. doi:10.1093/nar/gky394
apa: Bravo, J. P. K., Borodavka, A., Barth, A., Calabrese, A. N., Mojzes, P., Cockburn,
J. J. B., … Tuma, R. (2018). Stability of local secondary structure determines
selectivity of viral RNA chaperones. Nucleic Acids Research. Oxford University
Press. https://doi.org/10.1093/nar/gky394
chicago: Bravo, Jack Peter Kelly, Alexander Borodavka, Anders Barth, Antonio N Calabrese,
Peter Mojzes, Joseph J B Cockburn, Don C Lamb, and Roman Tuma. “Stability of Local
Secondary Structure Determines Selectivity of Viral RNA Chaperones.” Nucleic
Acids Research. Oxford University Press, 2018. https://doi.org/10.1093/nar/gky394.
ieee: J. P. K. Bravo et al., “Stability of local secondary structure determines
selectivity of viral RNA chaperones,” Nucleic Acids Research, vol. 46,
no. 15. Oxford University Press, pp. 7924–7937, 2018.
ista: Bravo JPK, Borodavka A, Barth A, Calabrese AN, Mojzes P, Cockburn JJB, Lamb
DC, Tuma R. 2018. Stability of local secondary structure determines selectivity
of viral RNA chaperones. Nucleic Acids Research. 46(15), 7924–7937.
mla: Bravo, Jack Peter Kelly, et al. “Stability of Local Secondary Structure Determines
Selectivity of Viral RNA Chaperones.” Nucleic Acids Research, vol. 46,
no. 15, Oxford University Press, 2018, pp. 7924–37, doi:10.1093/nar/gky394.
short: J.P.K. Bravo, A. Borodavka, A. Barth, A.N. Calabrese, P. Mojzes, J.J.B. Cockburn,
D.C. Lamb, R. Tuma, Nucleic Acids Research 46 (2018) 7924–7937.
date_created: 2024-03-20T10:43:13Z
date_published: 2018-09-06T00:00:00Z
date_updated: 2024-04-09T11:07:07Z
day: '06'
doi: 10.1093/nar/gky394
extern: '1'
external_id:
pmid:
- '29796667'
intvolume: ' 46'
issue: '15'
keyword:
- Genetics
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.1093/nar/gky394
month: '09'
oa: 1
oa_version: Published Version
page: 7924-7937
pmid: 1
publication: Nucleic Acids Research
publication_identifier:
eissn:
- 1362-4962
issn:
- 0305-1048
publication_status: published
publisher: Oxford University Press
quality_controlled: '1'
scopus_import: '1'
status: public
title: Stability of local secondary structure determines selectivity of viral RNA
chaperones
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 46
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
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: '15232'
abstract:
- lang: eng
text: 'In this paper we describe the potential of the enhanced X-ray Timing and
Polarimetry (eXTP) mission for studies related to accretion flows in the strong
field gravity regime around both stellar-mass and supermassive black-holes. eXTP
has the unique capability of using advanced “spectral-timing-polarimetry” techniques
to analyze the rapid variations with three orthogonal diagnostics of the flow
and its geometry, yielding unprecedented insight into the inner accreting regions,
the effects of strong field gravity on the material within them and the powerful
outflows which are driven by the accretion process. '
article_number: '29504'
article_processing_charge: No
article_type: original
arxiv: 1
author:
- first_name: Alessandra De
full_name: Rosa, Alessandra De
last_name: Rosa
- first_name: Phil
full_name: Uttley, Phil
last_name: Uttley
- first_name: LiJun
full_name: Gou, LiJun
last_name: Gou
- first_name: Yuan
full_name: Liu, Yuan
last_name: Liu
- first_name: Cosimo
full_name: Bambi, Cosimo
last_name: Bambi
- first_name: Didier
full_name: Barret, Didier
last_name: Barret
- first_name: Tomaso
full_name: Belloni, Tomaso
last_name: Belloni
- first_name: Emanuele
full_name: Berti, Emanuele
last_name: Berti
- first_name: Stefano
full_name: Bianchi, Stefano
last_name: Bianchi
- first_name: Ilaria
full_name: Caiazzo, Ilaria
id: 8ae5b6e7-2a03-11ee-914d-b58ed7a3b47d
last_name: Caiazzo
orcid: 0000-0002-4770-5388
- first_name: Piergiorgio
full_name: Casella, Piergiorgio
last_name: Casella
- first_name: Marco
full_name: Feroci, Marco
last_name: Feroci
- first_name: Valeria
full_name: Ferrari, Valeria
last_name: Ferrari
- first_name: Leonardo
full_name: Gualtieri, Leonardo
last_name: Gualtieri
- first_name: Jeremy
full_name: Heyl, Jeremy
last_name: Heyl
- first_name: Adam
full_name: Ingram, Adam
last_name: Ingram
- first_name: Vladimir
full_name: Karas, Vladimir
last_name: Karas
- first_name: FangJun
full_name: Lu, FangJun
last_name: Lu
- first_name: Bin
full_name: Luo, Bin
last_name: Luo
- first_name: Giorgio
full_name: Matt, Giorgio
last_name: Matt
- first_name: Sara
full_name: Motta, Sara
last_name: Motta
- first_name: Joseph
full_name: Neilsen, Joseph
last_name: Neilsen
- first_name: Paolo
full_name: Pani, Paolo
last_name: Pani
- first_name: Andrea
full_name: Santangelo, Andrea
last_name: Santangelo
- first_name: XinWen
full_name: Shu, XinWen
last_name: Shu
- first_name: JunFeng
full_name: Wang, JunFeng
last_name: Wang
- first_name: Jian-Min
full_name: Wang, Jian-Min
last_name: Wang
- first_name: YongQuan
full_name: Xue, YongQuan
last_name: Xue
- first_name: YuPeng
full_name: Xu, YuPeng
last_name: Xu
- first_name: WeiMin
full_name: Yuan, WeiMin
last_name: Yuan
- first_name: YeFei
full_name: Yuan, YeFei
last_name: Yuan
- first_name: Shuang-Nan
full_name: Zhang, Shuang-Nan
last_name: Zhang
- first_name: Shu
full_name: Zhang, Shu
last_name: Zhang
- first_name: Ivan
full_name: Agudo, Ivan
last_name: Agudo
- first_name: Lorenzo
full_name: Amati, Lorenzo
last_name: Amati
- first_name: Nils
full_name: Andersson, Nils
last_name: Andersson
- first_name: Cristina
full_name: Baglio, Cristina
last_name: Baglio
- first_name: Pavel
full_name: Bakala, Pavel
last_name: Bakala
- first_name: Altan
full_name: Baykal, Altan
last_name: Baykal
- first_name: Sudip
full_name: Bhattacharyya, Sudip
last_name: Bhattacharyya
- first_name: Ignazio
full_name: Bombaci, Ignazio
last_name: Bombaci
- first_name: Niccoló
full_name: Bucciantini, Niccoló
last_name: Bucciantini
- first_name: Fiamma
full_name: Capitanio, Fiamma
last_name: Capitanio
- first_name: Riccardo
full_name: Ciolfi, Riccardo
last_name: Ciolfi
- first_name: Wei K.
full_name: Cui, Wei K.
last_name: Cui
- first_name: Filippo
full_name: D’Ammando, Filippo
last_name: D’Ammando
- first_name: Thomas
full_name: Dauser, Thomas
last_name: Dauser
- first_name: Melania
full_name: Del Santo, Melania
last_name: Del Santo
- first_name: Barbara
full_name: De Marco, Barbara
last_name: De Marco
- first_name: Tiziana
full_name: Di Salvo, Tiziana
last_name: Di Salvo
- first_name: Chris
full_name: Done, Chris
last_name: Done
- first_name: Michal
full_name: Dovčiak, Michal
last_name: Dovčiak
- first_name: Andrew C.
full_name: Fabian, Andrew C.
last_name: Fabian
- first_name: Maurizio
full_name: Falanga, Maurizio
last_name: Falanga
- first_name: Angelo Francesco
full_name: Gambino, Angelo Francesco
last_name: Gambino
- first_name: Bruce
full_name: Gendre, Bruce
last_name: Gendre
- first_name: Victoria
full_name: Grinberg, Victoria
last_name: Grinberg
- first_name: Alexander
full_name: Heger, Alexander
last_name: Heger
- first_name: Jeroen
full_name: Homan, Jeroen
last_name: Homan
- first_name: Rosario
full_name: Iaria, Rosario
last_name: Iaria
- first_name: JiaChen
full_name: Jiang, JiaChen
last_name: Jiang
- first_name: ChiChuan
full_name: Jin, ChiChuan
last_name: Jin
- first_name: Elmar
full_name: Koerding, Elmar
last_name: Koerding
- first_name: Manu
full_name: Linares, Manu
last_name: Linares
- first_name: Zhu
full_name: Liu, Zhu
last_name: Liu
- first_name: Thomas J.
full_name: Maccarone, Thomas J.
last_name: Maccarone
- first_name: Julien
full_name: Malzac, Julien
last_name: Malzac
- first_name: Antonios
full_name: Manousakis, Antonios
last_name: Manousakis
- first_name: Frédéric
full_name: Marin, Frédéric
last_name: Marin
- first_name: Andrea
full_name: Marinucci, Andrea
last_name: Marinucci
- first_name: Missagh
full_name: Mehdipour, Missagh
last_name: Mehdipour
- first_name: Mariano
full_name: Méndez, Mariano
last_name: Méndez
- first_name: Simone
full_name: Migliari, Simone
last_name: Migliari
- first_name: Cole
full_name: Miller, Cole
last_name: Miller
- first_name: Giovanni
full_name: Miniutti, Giovanni
last_name: Miniutti
- first_name: Emanuele
full_name: Nardini, Emanuele
last_name: Nardini
- first_name: Paul T.
full_name: O’Brien, Paul T.
last_name: O’Brien
- first_name: Julian P.
full_name: Osborne, Julian P.
last_name: Osborne
- first_name: Pierre Olivier
full_name: Petrucci, Pierre Olivier
last_name: Petrucci
- first_name: Andrea
full_name: Possenti, Andrea
last_name: Possenti
- first_name: Alessandro
full_name: Riggio, Alessandro
last_name: Riggio
- first_name: Jerome
full_name: Rodriguez, Jerome
last_name: Rodriguez
- first_name: Andrea
full_name: Sanna, Andrea
last_name: Sanna
- first_name: LiJing
full_name: Shao, LiJing
last_name: Shao
- first_name: Malgosia
full_name: Sobolewska, Malgosia
last_name: Sobolewska
- first_name: Eva
full_name: Sramkova, Eva
last_name: Sramkova
- first_name: Abigail L.
full_name: Stevens, Abigail L.
last_name: Stevens
- first_name: Holger
full_name: Stiele, Holger
last_name: Stiele
- first_name: Giulia
full_name: Stratta, Giulia
last_name: Stratta
- first_name: Zdenek
full_name: Stuchlik, Zdenek
last_name: Stuchlik
- first_name: Jiri
full_name: Svoboda, Jiri
last_name: Svoboda
- first_name: Fabrizio
full_name: Tamburini, Fabrizio
last_name: Tamburini
- first_name: Thomas M.
full_name: Tauris, Thomas M.
last_name: Tauris
- first_name: Francesco
full_name: Tombesi, Francesco
last_name: Tombesi
- first_name: Gabriel
full_name: Torok, Gabriel
last_name: Torok
- first_name: Martin
full_name: Urbanec, Martin
last_name: Urbanec
- first_name: Frederic
full_name: Vincent, Frederic
last_name: Vincent
- first_name: QingWen
full_name: Wu, QingWen
last_name: Wu
- first_name: Feng
full_name: Yuan, Feng
last_name: Yuan
- first_name: Jean J. M.
full_name: in’ t Zand, Jean J. M.
last_name: in’ t Zand
- first_name: Andrzej A.
full_name: Zdziarski, Andrzej A.
last_name: Zdziarski
- first_name: XinLin
full_name: Zhou, XinLin
last_name: Zhou
citation:
ama: Rosa AD, Uttley P, Gou L, et al. Accretion in strong field gravity with eXTP.
Science China Physics, Mechanics & Astronomy. 2018;62(2). doi:10.1007/s11433-018-9297-0
apa: Rosa, A. D., Uttley, P., Gou, L., Liu, Y., Bambi, C., Barret, D., … Zhou, X.
(2018). Accretion in strong field gravity with eXTP. Science China Physics,
Mechanics & Astronomy. Springer Nature. https://doi.org/10.1007/s11433-018-9297-0
chicago: Rosa, Alessandra De, Phil Uttley, LiJun Gou, Yuan Liu, Cosimo Bambi, Didier
Barret, Tomaso Belloni, et al. “Accretion in Strong Field Gravity with EXTP.”
Science China Physics, Mechanics & Astronomy. Springer Nature, 2018.
https://doi.org/10.1007/s11433-018-9297-0.
ieee: A. D. Rosa et al., “Accretion in strong field gravity with eXTP,” Science
China Physics, Mechanics & Astronomy, vol. 62, no. 2. Springer Nature,
2018.
ista: Rosa AD et al. 2018. Accretion in strong field gravity with eXTP. Science
China Physics, Mechanics & Astronomy. 62(2), 29504.
mla: Rosa, Alessandra De, et al. “Accretion in Strong Field Gravity with EXTP.”
Science China Physics, Mechanics & Astronomy, vol. 62, no. 2, 29504,
Springer Nature, 2018, doi:10.1007/s11433-018-9297-0.
short: A.D. Rosa, P. Uttley, L. Gou, Y. Liu, C. Bambi, D. Barret, T. Belloni, E.
Berti, S. Bianchi, I. Caiazzo, P. Casella, M. Feroci, V. Ferrari, L. Gualtieri,
J. Heyl, A. Ingram, V. Karas, F. Lu, B. Luo, G. Matt, S. Motta, J. Neilsen, P.
Pani, A. Santangelo, X. Shu, J. Wang, J.-M. Wang, Y. Xue, Y. Xu, W. Yuan, Y. Yuan,
S.-N. Zhang, S. Zhang, I. Agudo, L. Amati, N. Andersson, C. Baglio, P. Bakala,
A. Baykal, S. Bhattacharyya, I. Bombaci, N. Bucciantini, F. Capitanio, R. Ciolfi,
W.K. Cui, F. D’Ammando, T. Dauser, M. Del Santo, B. De Marco, T. Di Salvo, C.
Done, M. Dovčiak, A.C. Fabian, M. Falanga, A.F. Gambino, B. Gendre, V. Grinberg,
A. Heger, J. Homan, R. Iaria, J. Jiang, C. Jin, E. Koerding, M. Linares, Z. Liu,
T.J. Maccarone, J. Malzac, A. Manousakis, F. Marin, A. Marinucci, M. Mehdipour,
M. Méndez, S. Migliari, C. Miller, G. Miniutti, E. Nardini, P.T. O’Brien, J.P.
Osborne, P.O. Petrucci, A. Possenti, A. Riggio, J. Rodriguez, A. Sanna, L. Shao,
M. Sobolewska, E. Sramkova, A.L. Stevens, H. Stiele, G. Stratta, Z. Stuchlik,
J. Svoboda, F. Tamburini, T.M. Tauris, F. Tombesi, G. Torok, M. Urbanec, F. Vincent,
Q. Wu, F. Yuan, J.J.M. in’ t Zand, A.A. Zdziarski, X. Zhou, Science China Physics,
Mechanics & Astronomy 62 (2018).
date_created: 2024-03-26T10:37:41Z
date_published: 2018-12-07T00:00:00Z
date_updated: 2024-04-05T07:12:09Z
day: '07'
doi: 10.1007/s11433-018-9297-0
extern: '1'
external_id:
arxiv:
- '1812.04022'
intvolume: ' 62'
issue: '2'
keyword:
- General Physics and Astronomy
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.48550/arXiv.1812.04022
month: '12'
oa: 1
oa_version: Preprint
publication: Science China Physics, Mechanics & Astronomy
publication_identifier:
eissn:
- 1869-1927
issn:
- 1674-7348
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
scopus_import: '1'
status: public
title: Accretion in strong field gravity with eXTP
type: journal_article
user_id: 8b945eb4-e2f2-11eb-945a-df72226e66a9
volume: 62
year: '2018'
...
---
_id: '15233'
abstract:
- lang: eng
text: In this paper we present the science potential of the enhanced X-ray Timing
and Polarimetry (eXTP) mission for studies of strongly magnetized objects. We
will focus on the physics and astrophysics of strongly magnetized objects, namely
magnetars, accreting X-ray pulsars, and rotation powered pulsars. We also discuss
the science potential of eXTP for QED studies. Developed by an international Consortium
led by the Institute of High Energy Physics of the Chinese Academy of Sciences,
the eXTP mission is expected to be launched in the mid 2020s.
article_number: '29505'
article_processing_charge: No
article_type: original
arxiv: 1
author:
- first_name: Andrea
full_name: Santangelo, Andrea
last_name: Santangelo
- first_name: Silvia
full_name: Zane, Silvia
last_name: Zane
- first_name: Hua
full_name: Feng, Hua
last_name: Feng
- first_name: RenXin
full_name: Xu, RenXin
last_name: Xu
- first_name: Victor
full_name: Doroshenko, Victor
last_name: Doroshenko
- first_name: Enrico
full_name: Bozzo, Enrico
last_name: Bozzo
- first_name: Ilaria
full_name: Caiazzo, Ilaria
id: 8ae5b6e7-2a03-11ee-914d-b58ed7a3b47d
last_name: Caiazzo
orcid: 0000-0002-4770-5388
- first_name: Francesco Coti
full_name: Zelati, Francesco Coti
last_name: Zelati
- first_name: Paolo
full_name: Esposito, Paolo
last_name: Esposito
- first_name: Denis
full_name: González-Caniulef, Denis
last_name: González-Caniulef
- first_name: Jeremy
full_name: Heyl, Jeremy
last_name: Heyl
- first_name: Daniela
full_name: Huppenkothen, Daniela
last_name: Huppenkothen
- first_name: Gianluca
full_name: Israel, Gianluca
last_name: Israel
- first_name: ZhaoSheng
full_name: Li, ZhaoSheng
last_name: Li
- first_name: Lin
full_name: Lin, Lin
last_name: Lin
- first_name: Roberto
full_name: Mignani, Roberto
last_name: Mignani
- first_name: Nanda
full_name: Rea, Nanda
last_name: Rea
- first_name: Mauro
full_name: Orlandini, Mauro
last_name: Orlandini
- first_name: Roberto
full_name: Taverna, Roberto
last_name: Taverna
- first_name: Hao
full_name: Tong, Hao
last_name: Tong
- first_name: Roberto
full_name: Turolla, Roberto
last_name: Turolla
- first_name: Cristina
full_name: Baglio, Cristina
last_name: Baglio
- first_name: Federico
full_name: Bernardini, Federico
last_name: Bernardini
- first_name: Niccolo’
full_name: Bucciantini, Niccolo’
last_name: Bucciantini
- first_name: Marco
full_name: Feroci, Marco
last_name: Feroci
- first_name: Felix
full_name: Fürst, Felix
last_name: Fürst
- first_name: Ersin
full_name: Göğüş, Ersin
last_name: Göğüş
- first_name: Can
full_name: Güngör, Can
last_name: Güngör
- first_name: Long
full_name: Ji, Long
last_name: Ji
- first_name: FangJun
full_name: Lu, FangJun
last_name: Lu
- first_name: Antonios
full_name: Manousakis, Antonios
last_name: Manousakis
- first_name: Sandro
full_name: Mereghetti, Sandro
last_name: Mereghetti
- first_name: Romana
full_name: Mikusincova, Romana
last_name: Mikusincova
- first_name: Biswajit
full_name: Paul, Biswajit
last_name: Paul
- first_name: Chanda
full_name: Prescod-Weinstein, Chanda
last_name: Prescod-Weinstein
- first_name: George
full_name: Younes, George
last_name: Younes
- first_name: Andrea
full_name: Tiengo, Andrea
last_name: Tiengo
- first_name: YuPeng
full_name: Xu, YuPeng
last_name: Xu
- first_name: Anna
full_name: Watts, Anna
last_name: Watts
- first_name: Shu
full_name: Zhang, Shu
last_name: Zhang
- first_name: Shuang-Nan
full_name: Zhan, Shuang-Nan
last_name: Zhan
citation:
ama: Santangelo A, Zane S, Feng H, et al. Physics and astrophysics of strong magnetic
field systems with eXTP. Science China Physics, Mechanics & Astronomy.
2018;62(2). doi:10.1007/s11433-018-9234-3
apa: Santangelo, A., Zane, S., Feng, H., Xu, R., Doroshenko, V., Bozzo, E., … Zhan,
S.-N. (2018). Physics and astrophysics of strong magnetic field systems with eXTP.
Science China Physics, Mechanics & Astronomy. Springer Nature. https://doi.org/10.1007/s11433-018-9234-3
chicago: Santangelo, Andrea, Silvia Zane, Hua Feng, RenXin Xu, Victor Doroshenko,
Enrico Bozzo, Ilaria Caiazzo, et al. “Physics and Astrophysics of Strong Magnetic
Field Systems with EXTP.” Science China Physics, Mechanics & Astronomy.
Springer Nature, 2018. https://doi.org/10.1007/s11433-018-9234-3.
ieee: A. Santangelo et al., “Physics and astrophysics of strong magnetic
field systems with eXTP,” Science China Physics, Mechanics & Astronomy,
vol. 62, no. 2. Springer Nature, 2018.
ista: Santangelo A, Zane S, Feng H, Xu R, Doroshenko V, Bozzo E, Caiazzo I, Zelati
FC, Esposito P, González-Caniulef D, Heyl J, Huppenkothen D, Israel G, Li Z, Lin
L, Mignani R, Rea N, Orlandini M, Taverna R, Tong H, Turolla R, Baglio C, Bernardini
F, Bucciantini N, Feroci M, Fürst F, Göğüş E, Güngör C, Ji L, Lu F, Manousakis
A, Mereghetti S, Mikusincova R, Paul B, Prescod-Weinstein C, Younes G, Tiengo
A, Xu Y, Watts A, Zhang S, Zhan S-N. 2018. Physics and astrophysics of strong
magnetic field systems with eXTP. Science China Physics, Mechanics & Astronomy.
62(2), 29505.
mla: Santangelo, Andrea, et al. “Physics and Astrophysics of Strong Magnetic Field
Systems with EXTP.” Science China Physics, Mechanics & Astronomy, vol.
62, no. 2, 29505, Springer Nature, 2018, doi:10.1007/s11433-018-9234-3.
short: A. Santangelo, S. Zane, H. Feng, R. Xu, V. Doroshenko, E. Bozzo, I. Caiazzo,
F.C. Zelati, P. Esposito, D. González-Caniulef, J. Heyl, D. Huppenkothen, G. Israel,
Z. Li, L. Lin, R. Mignani, N. Rea, M. Orlandini, R. Taverna, H. Tong, R. Turolla,
C. Baglio, F. Bernardini, N. Bucciantini, M. Feroci, F. Fürst, E. Göğüş, C. Güngör,
L. Ji, F. Lu, A. Manousakis, S. Mereghetti, R. Mikusincova, B. Paul, C. Prescod-Weinstein,
G. Younes, A. Tiengo, Y. Xu, A. Watts, S. Zhang, S.-N. Zhan, Science China Physics,
Mechanics & Astronomy 62 (2018).
date_created: 2024-03-26T10:38:05Z
date_published: 2018-10-08T00:00:00Z
date_updated: 2024-04-08T07:01:20Z
day: '08'
doi: 10.1007/s11433-018-9234-3
extern: '1'
external_id:
arxiv:
- '1812.04460'
intvolume: ' 62'
issue: '2'
keyword:
- General Physics and Astronomy
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.48550/arXiv.1812.04460
month: '10'
oa: 1
oa_version: Preprint
publication: Science China Physics, Mechanics & Astronomy
publication_identifier:
eissn:
- 1869-1927
issn:
- 1674-7348
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
scopus_import: '1'
status: public
title: Physics and astrophysics of strong magnetic field systems with eXTP
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 62
year: '2018'
...
---
_id: '15234'
abstract:
- lang: eng
text: Using parallaxes from Gaia Data Release 2 (Gaia DR2), we estimate the distance
to the globular clusters 47 Tuc and NGC 362, taking advantage of the background
stars in the Small Magellanic Cloud and quasars to account for various parallax
systematics. We found the parallax to be dependent on the Gaia DR2 G-band apparent
magnitude for stars with 13 < G < 18, where brighter stars have a lower parallax
zero point than fainter stars. The distance to 47 Tuc was found to be 4.45 ± 0.01
± 0.12 kpc, and for NGC 362 8.54 ± 0.20 ± 0.44 kpc, with random and systematic
errors listed, respectively. This is the first time a precise distance measurement
directly using parallaxes has been determined for either of these two globular
clusters.
article_number: '132'
article_processing_charge: No
article_type: original
arxiv: 1
author:
- first_name: Seery
full_name: Chen, Seery
last_name: Chen
- first_name: Harvey
full_name: Richer, Harvey
last_name: Richer
- first_name: Ilaria
full_name: Caiazzo, Ilaria
id: 8ae5b6e7-2a03-11ee-914d-b58ed7a3b47d
last_name: Caiazzo
orcid: 0000-0002-4770-5388
- first_name: Jeremy
full_name: Heyl, Jeremy
last_name: Heyl
citation:
ama: Chen S, Richer H, Caiazzo I, Heyl J. Distances to the globular clusters 47
Tucanae and NGC 362 using Gaia DR2 parallaxes. The Astrophysical Journal.
2018;867(2). doi:10.3847/1538-4357/aae089
apa: Chen, S., Richer, H., Caiazzo, I., & Heyl, J. (2018). Distances to the
globular clusters 47 Tucanae and NGC 362 using Gaia DR2 parallaxes. The Astrophysical
Journal. American Astronomical Society. https://doi.org/10.3847/1538-4357/aae089
chicago: Chen, Seery, Harvey Richer, Ilaria Caiazzo, and Jeremy Heyl. “Distances
to the Globular Clusters 47 Tucanae and NGC 362 Using Gaia DR2 Parallaxes.” The
Astrophysical Journal. American Astronomical Society, 2018. https://doi.org/10.3847/1538-4357/aae089.
ieee: S. Chen, H. Richer, I. Caiazzo, and J. Heyl, “Distances to the globular clusters
47 Tucanae and NGC 362 using Gaia DR2 parallaxes,” The Astrophysical Journal,
vol. 867, no. 2. American Astronomical Society, 2018.
ista: Chen S, Richer H, Caiazzo I, Heyl J. 2018. Distances to the globular clusters
47 Tucanae and NGC 362 using Gaia DR2 parallaxes. The Astrophysical Journal. 867(2),
132.
mla: Chen, Seery, et al. “Distances to the Globular Clusters 47 Tucanae and NGC
362 Using Gaia DR2 Parallaxes.” The Astrophysical Journal, vol. 867, no.
2, 132, American Astronomical Society, 2018, doi:10.3847/1538-4357/aae089.
short: S. Chen, H. Richer, I. Caiazzo, J. Heyl, The Astrophysical Journal 867 (2018).
date_created: 2024-03-26T10:38:28Z
date_published: 2018-11-07T00:00:00Z
date_updated: 2024-04-08T07:01:51Z
day: '07'
doi: 10.3847/1538-4357/aae089
extern: '1'
external_id:
arxiv:
- '1807.07089'
intvolume: ' 867'
issue: '2'
keyword:
- Space and Planetary Science
- Astronomy and Astrophysics
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.48550/arXiv.1807.07089
month: '11'
oa: 1
oa_version: Preprint
publication: The Astrophysical Journal
publication_identifier:
eissn:
- 1538-4357
issn:
- 0004-637X
publication_status: published
publisher: American Astronomical Society
quality_controlled: '1'
scopus_import: '1'
status: public
title: Distances to the globular clusters 47 Tucanae and NGC 362 using Gaia DR2 parallaxes
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 867
year: '2018'
...
---
_id: '15235'
abstract:
- lang: eng
text: Radiative corrections of quantum electrodynamics cause a vacuum threaded by
a magnetic field to be birefringent. This means that radiation of different polarizations
travels at different speeds. Even in the strong magnetic fields of astrophysical
sources, the difference in speed is small. However, it has profound consequences
for the extent of polarization expected from strongly magnetized sources. We demonstrate
how the birefringence arises from first principles, show how birefringence affects
the polarization state of radiation and present recent calculations for the expected
polarization from magnetars and X-ray pulsars.
article_number: '76'
article_processing_charge: No
article_type: original
arxiv: 1
author:
- first_name: Jeremy
full_name: Heyl, Jeremy
last_name: Heyl
- first_name: Ilaria
full_name: Caiazzo, Ilaria
id: 8ae5b6e7-2a03-11ee-914d-b58ed7a3b47d
last_name: Caiazzo
orcid: 0000-0002-4770-5388
citation:
ama: 'Heyl J, Caiazzo I. Strongly magnetized sources: QED and X-ray polarization.
Galaxies. 2018;6(3). doi:10.3390/galaxies6030076'
apa: 'Heyl, J., & Caiazzo, I. (2018). Strongly magnetized sources: QED and X-ray
polarization. Galaxies. MDPI. https://doi.org/10.3390/galaxies6030076'
chicago: 'Heyl, Jeremy, and Ilaria Caiazzo. “Strongly Magnetized Sources: QED and
X-Ray Polarization.” Galaxies. MDPI, 2018. https://doi.org/10.3390/galaxies6030076.'
ieee: 'J. Heyl and I. Caiazzo, “Strongly magnetized sources: QED and X-ray polarization,”
Galaxies, vol. 6, no. 3. MDPI, 2018.'
ista: 'Heyl J, Caiazzo I. 2018. Strongly magnetized sources: QED and X-ray polarization.
Galaxies. 6(3), 76.'
mla: 'Heyl, Jeremy, and Ilaria Caiazzo. “Strongly Magnetized Sources: QED and X-Ray
Polarization.” Galaxies, vol. 6, no. 3, 76, MDPI, 2018, doi:10.3390/galaxies6030076.'
short: J. Heyl, I. Caiazzo, Galaxies 6 (2018).
date_created: 2024-03-26T10:38:46Z
date_published: 2018-07-21T00:00:00Z
date_updated: 2024-04-08T07:02:25Z
day: '21'
doi: 10.3390/galaxies6030076
extern: '1'
external_id:
arxiv:
- '1802.00358'
intvolume: ' 6'
issue: '3'
keyword:
- Astronomy and Astrophysics
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.3390/galaxies6030076
month: '07'
oa: 1
oa_version: Published Version
publication: Galaxies
publication_identifier:
eissn:
- 2075-4434
publication_status: published
publisher: MDPI
quality_controlled: '1'
scopus_import: '1'
status: public
title: 'Strongly magnetized sources: QED and X-ray polarization'
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 6
year: '2018'
...
---
_id: '15236'
abstract:
- lang: eng
text: 'Radio pulsars found in binary systems with short orbital periods are usually
fast spinning as a consequence of recycling via mass transfer from their companion
stars; this process is also thought to decrease the magnetic field of the neutron
star being recycled. Here, we report on timing observations of the recently discovered
binary PSR J1755−2550 and find that this pulsar is an exception: with a characteristic
age of 2.1 Myr, it is relatively young; furthermore, with a spin period of 315 ms
and a surface magnetic field strength at its poles of 0.88 × 1012 G, the pulsar
shows no sign of having been recycled. Based on its timing and orbital characteristics,
the pulsar either has a massive white dwarf (WD) or a neutron star (NS) companion.
To distinguish between these two cases, we searched radio observations for a potential
recycled pulsar companion and analysed archival optical data for a potential WD
companion. Neither work returned conclusive detections. We apply population synthesis
modelling and find that both solutions are roughly equally probable. Our population
synthesis also predicts a minimum mass of 0.90 M⊙ for the companion star to PSR
J1755−2550 and we simulate the systemic runaway velocities for the resulting WDNS
systems which may merge and possibly produce Ca-rich supernovae. Whether PSR J1755−2550
hosts a WD or a NS companion star, it is certainly a member of a rare subpopulation
of binary radio pulsars.'
article_processing_charge: No
article_type: original
arxiv: 1
author:
- first_name: C
full_name: Ng, C
last_name: Ng
- first_name: M U
full_name: Kruckow, M U
last_name: Kruckow
- first_name: T M
full_name: Tauris, T M
last_name: Tauris
- first_name: A G
full_name: Lyne, A G
last_name: Lyne
- first_name: P C C
full_name: Freire, P C C
last_name: Freire
- first_name: A
full_name: Ridolfi, A
last_name: Ridolfi
- first_name: Ilaria
full_name: Caiazzo, Ilaria
id: 8ae5b6e7-2a03-11ee-914d-b58ed7a3b47d
last_name: Caiazzo
orcid: 0000-0002-4770-5388
- first_name: J
full_name: Heyl, J
last_name: Heyl
- first_name: M
full_name: Kramer, M
last_name: Kramer
- first_name: A D
full_name: Cameron, A D
last_name: Cameron
- first_name: D J
full_name: Champion, D J
last_name: Champion
- first_name: B
full_name: Stappers, B
last_name: Stappers
citation:
ama: 'Ng C, Kruckow MU, Tauris TM, et al. PSR J1755−2550: A young radio pulsar with
a massive, compact companion. Monthly Notices of the Royal Astronomical Society.
2018;476(4):4315-4326. doi:10.1093/mnras/sty482'
apa: 'Ng, C., Kruckow, M. U., Tauris, T. M., Lyne, A. G., Freire, P. C. C., Ridolfi,
A., … Stappers, B. (2018). PSR J1755−2550: A young radio pulsar with a massive,
compact companion. Monthly Notices of the Royal Astronomical Society. Oxford
University Press. https://doi.org/10.1093/mnras/sty482'
chicago: 'Ng, C, M U Kruckow, T M Tauris, A G Lyne, P C C Freire, A Ridolfi, Ilaria
Caiazzo, et al. “PSR J1755−2550: A Young Radio Pulsar with a Massive, Compact
Companion.” Monthly Notices of the Royal Astronomical Society. Oxford University
Press, 2018. https://doi.org/10.1093/mnras/sty482.'
ieee: 'C. Ng et al., “PSR J1755−2550: A young radio pulsar with a massive,
compact companion,” Monthly Notices of the Royal Astronomical Society,
vol. 476, no. 4. Oxford University Press, pp. 4315–4326, 2018.'
ista: 'Ng C, Kruckow MU, Tauris TM, Lyne AG, Freire PCC, Ridolfi A, Caiazzo I, Heyl
J, Kramer M, Cameron AD, Champion DJ, Stappers B. 2018. PSR J1755−2550: A young
radio pulsar with a massive, compact companion. Monthly Notices of the Royal Astronomical
Society. 476(4), 4315–4326.'
mla: 'Ng, C., et al. “PSR J1755−2550: A Young Radio Pulsar with a Massive, Compact
Companion.” Monthly Notices of the Royal Astronomical Society, vol. 476,
no. 4, Oxford University Press, 2018, pp. 4315–26, doi:10.1093/mnras/sty482.'
short: C. Ng, M.U. Kruckow, T.M. Tauris, A.G. Lyne, P.C.C. Freire, A. Ridolfi, I.
Caiazzo, J. Heyl, M. Kramer, A.D. Cameron, D.J. Champion, B. Stappers, Monthly
Notices of the Royal Astronomical Society 476 (2018) 4315–4326.
date_created: 2024-03-26T10:39:05Z
date_published: 2018-02-23T00:00:00Z
date_updated: 2024-04-08T07:02:52Z
day: '23'
doi: 10.1093/mnras/sty482
extern: '1'
external_id:
arxiv:
- '1802.08248'
intvolume: ' 476'
issue: '4'
keyword:
- Space and Planetary Science
- Astronomy and Astrophysics
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.48550/arXiv.1802.08248
month: '02'
oa: 1
oa_version: Preprint
page: 4315-4326
publication: Monthly Notices of the Royal Astronomical Society
publication_identifier:
eissn:
- 1365-2966
issn:
- 0035-8711
publication_status: published
publisher: Oxford University Press
quality_controlled: '1'
scopus_import: '1'
status: public
title: 'PSR J1755−2550: A young radio pulsar with a massive, compact companion'
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 476
year: '2018'
...