---
_id: '995'
abstract:
- lang: eng
text: Recently it was shown that an impurity exchanging orbital angular momentum
with a surrounding bath can be described in terms of the angulon quasiparticle
[Phys. Rev. Lett. 118, 095301 (2017)]. The angulon consists of a quantum rotor
dressed by a many-particle field of boson excitations, and can be formed out of,
for example, a molecule or a nonspherical atom in superfluid helium, or out of
an electron coupled to lattice phonons or a Bose condensate. Here we develop an
approach to the angulon based on the path-integral formalism, which sets the ground
for a systematic, perturbative treatment of the angulon problem. The resulting
perturbation series can be interpreted in terms of Feynman diagrams, from which,
in turn, one can derive a set of diagrammatic rules. These rules extend the machinery
of the graphical theory of angular momentum - well known from theoretical atomic
spectroscopy - to the case where an environment with an infinite number of degrees
of freedom is present. In particular, we show that each diagram can be interpreted
as a 'skeleton', which enforces angular momentum conservation, dressed by an additional
many-body contribution. This connection between the angulon theory and the graphical
theory of angular momentum is particularly important as it allows to systematically
and substantially simplify the analytical representation of each diagram. In order
to exemplify the technique, we calculate the 1- and 2-loop contributions to the
angulon self-energy, the spectral function, and the quasiparticle weight. The
diagrammatic theory we develop paves the way to investigate next-to-leading order
quantities in a more compact way compared to the variational approaches.
article_number: '085410'
article_processing_charge: No
author:
- first_name: Giacomo
full_name: Bighin, Giacomo
id: 4CA96FD4-F248-11E8-B48F-1D18A9856A87
last_name: Bighin
orcid: 0000-0001-8823-9777
- first_name: Mikhail
full_name: Lemeshko, Mikhail
id: 37CB05FA-F248-11E8-B48F-1D18A9856A87
last_name: Lemeshko
orcid: 0000-0002-6990-7802
citation:
ama: Bighin G, Lemeshko M. Diagrammatic approach to orbital quantum impurities interacting
with a many-particle environment. Physical Review B - Condensed Matter and
Materials Physics. 2017;96(8). doi:10.1103/PhysRevB.96.085410
apa: Bighin, G., & Lemeshko, M. (2017). Diagrammatic approach to orbital quantum
impurities interacting with a many-particle environment. Physical Review B
- Condensed Matter and Materials Physics. American Physical Society. https://doi.org/10.1103/PhysRevB.96.085410
chicago: Bighin, Giacomo, and Mikhail Lemeshko. “Diagrammatic Approach to Orbital
Quantum Impurities Interacting with a Many-Particle Environment.” Physical
Review B - Condensed Matter and Materials Physics. American Physical Society,
2017. https://doi.org/10.1103/PhysRevB.96.085410.
ieee: G. Bighin and M. Lemeshko, “Diagrammatic approach to orbital quantum impurities
interacting with a many-particle environment,” Physical Review B - Condensed
Matter and Materials Physics, vol. 96, no. 8. American Physical Society, 2017.
ista: Bighin G, Lemeshko M. 2017. Diagrammatic approach to orbital quantum impurities
interacting with a many-particle environment. Physical Review B - Condensed Matter
and Materials Physics. 96(8), 085410.
mla: Bighin, Giacomo, and Mikhail Lemeshko. “Diagrammatic Approach to Orbital Quantum
Impurities Interacting with a Many-Particle Environment.” Physical Review B
- Condensed Matter and Materials Physics, vol. 96, no. 8, 085410, American
Physical Society, 2017, doi:10.1103/PhysRevB.96.085410.
short: G. Bighin, M. Lemeshko, Physical Review B - Condensed Matter and Materials
Physics 96 (2017).
date_created: 2018-12-11T11:49:36Z
date_published: 2017-08-07T00:00:00Z
date_updated: 2023-09-22T09:53:17Z
day: '07'
department:
- _id: MiLe
doi: 10.1103/PhysRevB.96.085410
external_id:
isi:
- '000407017100009'
intvolume: ' 96'
isi: 1
issue: '8'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/1704.02616
month: '08'
oa: 1
oa_version: Submitted Version
project:
- _id: 26031614-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: P29902
name: Quantum rotations in the presence of a many-body environment
publication: Physical Review B - Condensed Matter and Materials Physics
publication_identifier:
issn:
- '24699950'
publication_status: published
publisher: American Physical Society
publist_id: '6404'
quality_controlled: '1'
scopus_import: '1'
status: public
title: Diagrammatic approach to orbital quantum impurities interacting with a many-particle
environment
type: journal_article
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
volume: 96
year: '2017'
...
---
_id: '996'
abstract:
- lang: eng
text: 'Iodine (I 2 ) molecules embedded in He nanodroplets are aligned by a 160
ps long laser pulse. The highest degree of alignment, occurring at the peak of
the pulse and quantified by ⟨cos 2 θ 2D ⟩ , is measured as a function of the laser
intensity. The results are well described by ⟨cos 2 θ 2D ⟩ calculated for a gas
of isolated molecules each with an effective rotational constant of 0.6 times
the gas-phase value, and at a temperature of 0.4 K. Theoretical analysis using
the angulon quasiparticle to describe rotating molecules in superfluid helium
rationalizes why the alignment mechanism is similar to that of isolated molecules
with an effective rotational constant. A major advantage of molecules in He droplets
is that their 0.4 K temperature leads to stronger alignment than what can generally
be achieved for gas phase molecules -- here demonstrated by a direct comparison
of the droplet results to measurements on a ∼ 1 K supersonic beam of isolated
molecules. This point is further illustrated for more complex system by measurements
on 1,4-diiodobenzene and 1,4-dibromobenzene. For all three molecular species studied
the highest values of ⟨cos 2 θ 2D ⟩ achieved in He droplets exceed 0.96. '
article_number: '013946'
article_processing_charge: No
author:
- first_name: Benjamin
full_name: Shepperson, Benjamin
last_name: Shepperson
- first_name: Adam
full_name: Chatterley, Adam
last_name: Chatterley
- first_name: Anders
full_name: Søndergaard, Anders
last_name: Søndergaard
- first_name: Lars
full_name: Christiansen, Lars
last_name: Christiansen
- first_name: Mikhail
full_name: Lemeshko, Mikhail
id: 37CB05FA-F248-11E8-B48F-1D18A9856A87
last_name: Lemeshko
orcid: 0000-0002-6990-7802
- first_name: Henrik
full_name: Stapelfeldt, Henrik
last_name: Stapelfeldt
citation:
ama: Shepperson B, Chatterley A, Søndergaard A, Christiansen L, Lemeshko M, Stapelfeldt
H. Strongly aligned molecules inside helium droplets in the near-adiabatic regime.
The Journal of Chemical Physics. 2017;147(1). doi:10.1063/1.4983703
apa: Shepperson, B., Chatterley, A., Søndergaard, A., Christiansen, L., Lemeshko,
M., & Stapelfeldt, H. (2017). Strongly aligned molecules inside helium droplets
in the near-adiabatic regime. The Journal of Chemical Physics. AIP Publishing.
https://doi.org/10.1063/1.4983703
chicago: Shepperson, Benjamin, Adam Chatterley, Anders Søndergaard, Lars Christiansen,
Mikhail Lemeshko, and Henrik Stapelfeldt. “Strongly Aligned Molecules inside Helium
Droplets in the Near-Adiabatic Regime.” The Journal of Chemical Physics.
AIP Publishing, 2017. https://doi.org/10.1063/1.4983703.
ieee: B. Shepperson, A. Chatterley, A. Søndergaard, L. Christiansen, M. Lemeshko,
and H. Stapelfeldt, “Strongly aligned molecules inside helium droplets in the
near-adiabatic regime,” The Journal of Chemical Physics, vol. 147, no.
1. AIP Publishing, 2017.
ista: Shepperson B, Chatterley A, Søndergaard A, Christiansen L, Lemeshko M, Stapelfeldt
H. 2017. Strongly aligned molecules inside helium droplets in the near-adiabatic
regime. The Journal of Chemical Physics. 147(1), 013946.
mla: Shepperson, Benjamin, et al. “Strongly Aligned Molecules inside Helium Droplets
in the Near-Adiabatic Regime.” The Journal of Chemical Physics, vol. 147,
no. 1, 013946, AIP Publishing, 2017, doi:10.1063/1.4983703.
short: B. Shepperson, A. Chatterley, A. Søndergaard, L. Christiansen, M. Lemeshko,
H. Stapelfeldt, The Journal of Chemical Physics 147 (2017).
date_created: 2018-12-11T11:49:36Z
date_published: 2017-06-01T00:00:00Z
date_updated: 2024-02-28T13:02:26Z
day: '01'
department:
- _id: MiLe
doi: 10.1063/1.4983703
external_id:
isi:
- '000405089400047'
intvolume: ' 147'
isi: 1
issue: '1'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/1704.03684
month: '06'
oa: 1
oa_version: Submitted Version
publication: The Journal of Chemical Physics
publication_identifier:
issn:
- '00219606'
publication_status: published
publisher: AIP Publishing
publist_id: '6403'
quality_controlled: '1'
scopus_import: '1'
status: public
title: Strongly aligned molecules inside helium droplets in the near-adiabatic regime
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 147
year: '2017'
...
---
_id: '997'
abstract:
- lang: eng
text: Recently it was shown that molecules rotating in superfluid helium can be
described in terms of the angulon quasiparticles (Phys. Rev. Lett. 118, 095301
(2017)). Here we demonstrate that in the experimentally realized regime the angulon
can be seen as a point charge on a 2-sphere interacting with a gauge field of
a non-abelian magnetic monopole. Unlike in several other settings, the gauge fields
of the angulon problem emerge in the real coordinate space, as opposed to the
momentum space or some effective parameter space. Furthermore, we find a topological
transition associated with making the monopole abelian, which takes place in the
vicinity of the previously reported angulon instabilities. These results pave
the way for studying topological phenomena in experiments on molecules trapped
in superfluid helium nanodroplets, as well as on other realizations of orbital
impurity problems.
article_number: '235301'
article_processing_charge: No
article_type: original
arxiv: 1
author:
- first_name: Enderalp
full_name: Yakaboylu, Enderalp
id: 38CB71F6-F248-11E8-B48F-1D18A9856A87
last_name: Yakaboylu
orcid: 0000-0001-5973-0874
- first_name: Andreas
full_name: Deuchert, Andreas
id: 4DA65CD0-F248-11E8-B48F-1D18A9856A87
last_name: Deuchert
orcid: 0000-0003-3146-6746
- first_name: Mikhail
full_name: Lemeshko, Mikhail
id: 37CB05FA-F248-11E8-B48F-1D18A9856A87
last_name: Lemeshko
orcid: 0000-0002-6990-7802
citation:
ama: Yakaboylu E, Deuchert A, Lemeshko M. Emergence of non-abelian magnetic monopoles
in a quantum impurity problem. Physical Review Letters. 2017;119(23). doi:10.1103/PhysRevLett.119.235301
apa: Yakaboylu, E., Deuchert, A., & Lemeshko, M. (2017). Emergence of non-abelian
magnetic monopoles in a quantum impurity problem. Physical Review Letters.
American Physical Society. https://doi.org/10.1103/PhysRevLett.119.235301
chicago: Yakaboylu, Enderalp, Andreas Deuchert, and Mikhail Lemeshko. “Emergence
of Non-Abelian Magnetic Monopoles in a Quantum Impurity Problem.” Physical
Review Letters. American Physical Society, 2017. https://doi.org/10.1103/PhysRevLett.119.235301.
ieee: E. Yakaboylu, A. Deuchert, and M. Lemeshko, “Emergence of non-abelian magnetic
monopoles in a quantum impurity problem,” Physical Review Letters, vol.
119, no. 23. American Physical Society, 2017.
ista: Yakaboylu E, Deuchert A, Lemeshko M. 2017. Emergence of non-abelian magnetic
monopoles in a quantum impurity problem. Physical Review Letters. 119(23), 235301.
mla: Yakaboylu, Enderalp, et al. “Emergence of Non-Abelian Magnetic Monopoles in
a Quantum Impurity Problem.” Physical Review Letters, vol. 119, no. 23,
235301, American Physical Society, 2017, doi:10.1103/PhysRevLett.119.235301.
short: E. Yakaboylu, A. Deuchert, M. Lemeshko, Physical Review Letters 119 (2017).
date_created: 2018-12-11T11:49:36Z
date_published: 2017-12-06T00:00:00Z
date_updated: 2023-10-10T13:31:54Z
day: '06'
department:
- _id: MiLe
- _id: RoSe
doi: 10.1103/PhysRevLett.119.235301
ec_funded: 1
external_id:
arxiv:
- '1705.05162'
isi:
- '000417132100007'
intvolume: ' 119'
isi: 1
issue: '23'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/1705.05162
month: '12'
oa: 1
oa_version: Preprint
project:
- _id: 25681D80-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '291734'
name: International IST Postdoc Fellowship Programme
- _id: 25C6DC12-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '694227'
name: Analysis of quantum many-body systems
- _id: 26031614-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: P29902
name: Quantum rotations in the presence of a many-body environment
publication: Physical Review Letters
publication_identifier:
issn:
- 0031-9007
publication_status: published
publisher: American Physical Society
publist_id: '6401'
quality_controlled: '1'
scopus_import: '1'
status: public
title: Emergence of non-abelian magnetic monopoles in a quantum impurity problem
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 119
year: '2017'
...
---
_id: '998'
abstract:
- lang: eng
text: 'A major open problem on the road to artificial intelligence is the development
of incrementally learning systems that learn about more and more concepts over
time from a stream of data. In this work, we introduce a new training strategy,
iCaRL, that allows learning in such a class-incremental way: only the training
data for a small number of classes has to be present at the same time and new
classes can be added progressively. iCaRL learns strong classifiers and a data
representation simultaneously. This distinguishes it from earlier works that were
fundamentally limited to fixed data representations and therefore incompatible
with deep learning architectures. We show by experiments on CIFAR-100 and ImageNet
ILSVRC 2012 data that iCaRL can learn many classes incrementally over a long period
of time where other strategies quickly fail. '
article_processing_charge: No
author:
- first_name: Sylvestre Alvise
full_name: Rebuffi, Sylvestre Alvise
last_name: Rebuffi
- first_name: Alexander
full_name: Kolesnikov, Alexander
id: 2D157DB6-F248-11E8-B48F-1D18A9856A87
last_name: Kolesnikov
- first_name: Georg
full_name: Sperl, Georg
id: 4DD40360-F248-11E8-B48F-1D18A9856A87
last_name: Sperl
- first_name: Christoph
full_name: Lampert, Christoph
id: 40C20FD2-F248-11E8-B48F-1D18A9856A87
last_name: Lampert
orcid: 0000-0001-8622-7887
citation:
ama: 'Rebuffi SA, Kolesnikov A, Sperl G, Lampert C. iCaRL: Incremental classifier
and representation learning. In: Vol 2017. IEEE; 2017:5533-5542. doi:10.1109/CVPR.2017.587'
apa: 'Rebuffi, S. A., Kolesnikov, A., Sperl, G., & Lampert, C. (2017). iCaRL:
Incremental classifier and representation learning (Vol. 2017, pp. 5533–5542).
Presented at the CVPR: Computer Vision and Pattern Recognition, Honolulu, HA,
United States: IEEE. https://doi.org/10.1109/CVPR.2017.587'
chicago: 'Rebuffi, Sylvestre Alvise, Alexander Kolesnikov, Georg Sperl, and Christoph
Lampert. “ICaRL: Incremental Classifier and Representation Learning,” 2017:5533–42.
IEEE, 2017. https://doi.org/10.1109/CVPR.2017.587.'
ieee: 'S. A. Rebuffi, A. Kolesnikov, G. Sperl, and C. Lampert, “iCaRL: Incremental
classifier and representation learning,” presented at the CVPR: Computer Vision
and Pattern Recognition, Honolulu, HA, United States, 2017, vol. 2017, pp. 5533–5542.'
ista: 'Rebuffi SA, Kolesnikov A, Sperl G, Lampert C. 2017. iCaRL: Incremental classifier
and representation learning. CVPR: Computer Vision and Pattern Recognition vol.
2017, 5533–5542.'
mla: 'Rebuffi, Sylvestre Alvise, et al. ICaRL: Incremental Classifier and Representation
Learning. Vol. 2017, IEEE, 2017, pp. 5533–42, doi:10.1109/CVPR.2017.587.'
short: S.A. Rebuffi, A. Kolesnikov, G. Sperl, C. Lampert, in:, IEEE, 2017, pp. 5533–5542.
conference:
end_date: 2017-07-26
location: Honolulu, HA, United States
name: 'CVPR: Computer Vision and Pattern Recognition'
start_date: 2017-07-21
date_created: 2018-12-11T11:49:37Z
date_published: 2017-04-14T00:00:00Z
date_updated: 2023-09-22T09:51:58Z
day: '14'
department:
- _id: ChLa
- _id: ChWo
doi: 10.1109/CVPR.2017.587
ec_funded: 1
external_id:
isi:
- '000418371405066'
intvolume: ' 2017'
isi: 1
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/1611.07725
month: '04'
oa: 1
oa_version: Submitted Version
page: 5533 - 5542
project:
- _id: 2532554C-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '308036'
name: Lifelong Learning of Visual Scene Understanding
publication_identifier:
isbn:
- 978-153860457-1
publication_status: published
publisher: IEEE
publist_id: '6400'
quality_controlled: '1'
scopus_import: '1'
status: public
title: 'iCaRL: Incremental classifier and representation learning'
type: conference
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
volume: 2017
year: '2017'
...
---
_id: '999'
abstract:
- lang: eng
text: 'In multi-task learning, a learner is given a collection of prediction tasks
and needs to solve all of them. In contrast to previous work, which required that
annotated training data must be available for all tasks, we consider a new setting,
in which for some tasks, potentially most of them, only unlabeled training data
is provided. Consequently, to solve all tasks, information must be transferred
between tasks with labels and tasks without labels. Focusing on an instance-based
transfer method we analyze two variants of this setting: when the set of labeled
tasks is fixed, and when it can be actively selected by the learner. We state
and prove a generalization bound that covers both scenarios and derive from it
an algorithm for making the choice of labeled tasks (in the active case) and for
transferring information between the tasks in a principled way. We also illustrate
the effectiveness of the algorithm on synthetic and real data. '
alternative_title:
- PMLR
article_processing_charge: No
author:
- first_name: Anastasia
full_name: Pentina, Anastasia
id: 42E87FC6-F248-11E8-B48F-1D18A9856A87
last_name: Pentina
- first_name: Christoph
full_name: Lampert, Christoph
id: 40C20FD2-F248-11E8-B48F-1D18A9856A87
last_name: Lampert
orcid: 0000-0001-8622-7887
citation:
ama: 'Pentina A, Lampert C. Multi-task learning with labeled and unlabeled tasks.
In: Vol 70. ML Research Press; 2017:2807-2816.'
apa: 'Pentina, A., & Lampert, C. (2017). Multi-task learning with labeled and
unlabeled tasks (Vol. 70, pp. 2807–2816). Presented at the ICML: International
Conference on Machine Learning, Sydney, Australia: ML Research Press.'
chicago: Pentina, Anastasia, and Christoph Lampert. “Multi-Task Learning with Labeled
and Unlabeled Tasks,” 70:2807–16. ML Research Press, 2017.
ieee: 'A. Pentina and C. Lampert, “Multi-task learning with labeled and unlabeled
tasks,” presented at the ICML: International Conference on Machine Learning, Sydney,
Australia, 2017, vol. 70, pp. 2807–2816.'
ista: 'Pentina A, Lampert C. 2017. Multi-task learning with labeled and unlabeled
tasks. ICML: International Conference on Machine Learning, PMLR, vol. 70, 2807–2816.'
mla: Pentina, Anastasia, and Christoph Lampert. Multi-Task Learning with Labeled
and Unlabeled Tasks. Vol. 70, ML Research Press, 2017, pp. 2807–16.
short: A. Pentina, C. Lampert, in:, ML Research Press, 2017, pp. 2807–2816.
conference:
end_date: 2017-08-11
location: Sydney, Australia
name: 'ICML: International Conference on Machine Learning'
start_date: 2017-08-06
date_created: 2018-12-11T11:49:37Z
date_published: 2017-06-08T00:00:00Z
date_updated: 2023-10-17T11:53:32Z
day: '08'
department:
- _id: ChLa
ec_funded: 1
external_id:
isi:
- '000683309502093'
intvolume: ' 70'
isi: 1
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/1602.06518
month: '06'
oa: 1
oa_version: Submitted Version
page: 2807 - 2816
project:
- _id: 2532554C-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '308036'
name: Lifelong Learning of Visual Scene Understanding
publication_identifier:
isbn:
- '9781510855144'
publication_status: published
publisher: ML Research Press
publist_id: '6399'
quality_controlled: '1'
scopus_import: '1'
status: public
title: Multi-task learning with labeled and unlabeled tasks
type: conference
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 70
year: '2017'
...
---
_id: '1084'
abstract:
- lang: eng
text: 'BceRS and PsdRS are paralogous two-component systems in Bacillus subtilis
controlling the response to antimicrobial peptides. In the presence of extracellular
bacitracin and nisin, respectively, the two response regulators (RRs) bind their
target promoters, PbceA or PpsdA, resulting in a strong up-regulation of target
gene expression and ultimately antibiotic resistance. Despite high sequence similarity
between the RRs BceR and PsdR and their known binding sites, no cross-regulation
has been observed between them. We therefore investigated the specificity determinants
of PbceA and PpsdA that ensure the insulation of these two paralogous pathways
at the RR–promoter interface. In vivo and in vitro analyses demonstrate that the
regulatory regions within these two promoters contain three important elements:
in addition to the known (main) binding site, we identified a linker region and
a secondary binding site that are crucial for functionality. Initial binding to
the high-affinity, low-specificity main binding site is a prerequisite for the
subsequent highly specific binding of a second RR dimer to the low-affinity secondary
binding site. In addition to this hierarchical cooperative binding, discrimination
requires a competition of the two RRs for their respective binding site mediated
by only slight differences in binding affinities.'
article_processing_charge: No
author:
- first_name: Chong
full_name: Fang, Chong
last_name: Fang
- first_name: Anna A
full_name: Nagy-Staron, Anna A
id: 3ABC5BA6-F248-11E8-B48F-1D18A9856A87
last_name: Nagy-Staron
orcid: 0000-0002-1391-8377
- first_name: Martin
full_name: Grafe, Martin
last_name: Grafe
- first_name: Ralf
full_name: Heermann, Ralf
last_name: Heermann
- first_name: Kirsten
full_name: Jung, Kirsten
last_name: Jung
- first_name: Susanne
full_name: Gebhard, Susanne
last_name: Gebhard
- first_name: Thorsten
full_name: Mascher, Thorsten
last_name: Mascher
citation:
ama: Fang C, Nagy-Staron AA, Grafe M, et al. Insulation and wiring specificity of
BceR like response regulators and their target promoters in Bacillus subtilis.
Molecular Microbiology. 2017;104(1):16-31. doi:10.1111/mmi.13597
apa: Fang, C., Nagy-Staron, A. A., Grafe, M., Heermann, R., Jung, K., Gebhard, S.,
& Mascher, T. (2017). Insulation and wiring specificity of BceR like response
regulators and their target promoters in Bacillus subtilis. Molecular Microbiology.
Wiley-Blackwell. https://doi.org/10.1111/mmi.13597
chicago: Fang, Chong, Anna A Nagy-Staron, Martin Grafe, Ralf Heermann, Kirsten Jung,
Susanne Gebhard, and Thorsten Mascher. “Insulation and Wiring Specificity of BceR
like Response Regulators and Their Target Promoters in Bacillus Subtilis.” Molecular
Microbiology. Wiley-Blackwell, 2017. https://doi.org/10.1111/mmi.13597.
ieee: C. Fang et al., “Insulation and wiring specificity of BceR like response
regulators and their target promoters in Bacillus subtilis,” Molecular Microbiology,
vol. 104, no. 1. Wiley-Blackwell, pp. 16–31, 2017.
ista: Fang C, Nagy-Staron AA, Grafe M, Heermann R, Jung K, Gebhard S, Mascher T.
2017. Insulation and wiring specificity of BceR like response regulators and their
target promoters in Bacillus subtilis. Molecular Microbiology. 104(1), 16–31.
mla: Fang, Chong, et al. “Insulation and Wiring Specificity of BceR like Response
Regulators and Their Target Promoters in Bacillus Subtilis.” Molecular Microbiology,
vol. 104, no. 1, Wiley-Blackwell, 2017, pp. 16–31, doi:10.1111/mmi.13597.
short: C. Fang, A.A. Nagy-Staron, M. Grafe, R. Heermann, K. Jung, S. Gebhard, T.
Mascher, Molecular Microbiology 104 (2017) 16–31.
date_created: 2018-12-11T11:50:03Z
date_published: 2017-04-01T00:00:00Z
date_updated: 2023-09-20T11:48:43Z
day: '01'
department:
- _id: CaGu
doi: 10.1111/mmi.13597
external_id:
isi:
- '000398059200002'
intvolume: ' 104'
isi: 1
issue: '1'
language:
- iso: eng
month: '04'
oa_version: None
page: 16 - 31
publication: Molecular Microbiology
publication_identifier:
issn:
- ' 0950382X'
publication_status: published
publisher: Wiley-Blackwell
publist_id: '6294'
quality_controlled: '1'
scopus_import: '1'
status: public
title: Insulation and wiring specificity of BceR like response regulators and their
target promoters in Bacillus subtilis
type: journal_article
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
volume: 104
year: '2017'
...
---
_id: '1085'
abstract:
- lang: eng
text: Sex chromosomes evolve once recombination is halted between a homologous pair
of chromosomes. The dominant model of sex chromosome evolution posits that recombination
is suppressed between emerging X and Y chromosomes in order to resolve sexual
conflict. Here we test this model using whole genome and transcriptome resequencing
data in the guppy, a model for sexual selection with many Y-linked colour traits.
We show that although the nascent Y chromosome encompasses nearly half of the
linkage group, there has been no perceptible degradation of Y chromosome gene
content or activity. Using replicate wild populations with differing levels of
sexually antagonistic selection for colour, we also show that sexual selection
leads to greater expansion of the non-recombining region and increased Y chromosome
divergence. These results provide empirical support for longstanding models of
sex chromosome catalysis, and suggest an important role for sexual selection and
sexual conflict in genome evolution.
article_number: '14251'
article_processing_charge: No
author:
- first_name: Alison
full_name: Wright, Alison
last_name: Wright
- first_name: Iulia
full_name: Darolti, Iulia
last_name: Darolti
- first_name: Natasha
full_name: Bloch, Natasha
last_name: Bloch
- first_name: Vicencio
full_name: Oostra, Vicencio
last_name: Oostra
- first_name: Benjamin
full_name: Sandkam, Benjamin
last_name: Sandkam
- first_name: Séverine
full_name: Buechel, Séverine
last_name: Buechel
- first_name: Niclas
full_name: Kolm, Niclas
last_name: Kolm
- first_name: Felix
full_name: Breden, Felix
last_name: Breden
- first_name: Beatriz
full_name: Vicoso, Beatriz
id: 49E1C5C6-F248-11E8-B48F-1D18A9856A87
last_name: Vicoso
orcid: 0000-0002-4579-8306
- first_name: Judith
full_name: Mank, Judith
last_name: Mank
citation:
ama: Wright A, Darolti I, Bloch N, et al. Convergent recombination suppression suggests
role of sexual selection in guppy sex chromosome formation. Nature Communications.
2017;8. doi:10.1038/ncomms14251
apa: Wright, A., Darolti, I., Bloch, N., Oostra, V., Sandkam, B., Buechel, S., …
Mank, J. (2017). Convergent recombination suppression suggests role of sexual
selection in guppy sex chromosome formation. Nature Communications. Nature
Publishing Group. https://doi.org/10.1038/ncomms14251
chicago: Wright, Alison, Iulia Darolti, Natasha Bloch, Vicencio Oostra, Benjamin
Sandkam, Séverine Buechel, Niclas Kolm, Felix Breden, Beatriz Vicoso, and Judith
Mank. “Convergent Recombination Suppression Suggests Role of Sexual Selection
in Guppy Sex Chromosome Formation.” Nature Communications. Nature Publishing
Group, 2017. https://doi.org/10.1038/ncomms14251.
ieee: A. Wright et al., “Convergent recombination suppression suggests role
of sexual selection in guppy sex chromosome formation,” Nature Communications,
vol. 8. Nature Publishing Group, 2017.
ista: Wright A, Darolti I, Bloch N, Oostra V, Sandkam B, Buechel S, Kolm N, Breden
F, Vicoso B, Mank J. 2017. Convergent recombination suppression suggests role
of sexual selection in guppy sex chromosome formation. Nature Communications.
8, 14251.
mla: Wright, Alison, et al. “Convergent Recombination Suppression Suggests Role
of Sexual Selection in Guppy Sex Chromosome Formation.” Nature Communications,
vol. 8, 14251, Nature Publishing Group, 2017, doi:10.1038/ncomms14251.
short: A. Wright, I. Darolti, N. Bloch, V. Oostra, B. Sandkam, S. Buechel, N. Kolm,
F. Breden, B. Vicoso, J. Mank, Nature Communications 8 (2017).
date_created: 2018-12-11T11:50:04Z
date_published: 2017-01-31T00:00:00Z
date_updated: 2023-09-20T11:48:16Z
day: '31'
ddc:
- '570'
- '576'
department:
- _id: BeVi
doi: 10.1038/ncomms14251
external_id:
isi:
- '000392953700001'
file:
- access_level: open_access
content_type: application/pdf
creator: system
date_created: 2018-12-12T10:15:22Z
date_updated: 2018-12-12T10:15:22Z
file_id: '5141'
file_name: IST-2017-791-v1+1_ncomms14251.pdf
file_size: 955256
relation: main_file
file_date_updated: 2018-12-12T10:15:22Z
has_accepted_license: '1'
intvolume: ' 8'
isi: 1
language:
- iso: eng
month: '01'
oa: 1
oa_version: Published Version
publication: Nature Communications
publication_identifier:
issn:
- '20411723'
publication_status: published
publisher: Nature Publishing Group
publist_id: '6292'
pubrep_id: '791'
quality_controlled: '1'
scopus_import: '1'
status: public
title: Convergent recombination suppression suggests role of sexual selection in guppy
sex chromosome formation
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: journal_article
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
volume: 8
year: '2017'
...
---
_id: '1086'
abstract:
- lang: eng
text: 'Characterisation of G protein-coupled receptors (GPCR) relies on the availability
of a toolbox of ligands that selectively modulate different functional states
of the receptors. To uncover such molecules, we explored a unique strategy for
ligand discovery that takes advantage of the evolutionary conservation of the
600-million-year-old oxytocin/vasopressin signalling system. We isolated the insect
oxytocin/vasopressin orthologue inotocin from the black garden ant (Lasius niger),
identified and cloned its cognate receptor and determined its pharmacological
properties on the insect and human oxytocin/vasopressin receptors. Subsequently,
we identified a functional dichotomy: inotocin activated the insect inotocin and
the human vasopressin V1b receptors, but inhibited the human V1aR. Replacement
of Arg8 of inotocin by D-Arg8 led to a potent, stable and competitive V1aR-antagonist
([D-Arg8]-inotocin) with a 3,000-fold binding selectivity for the human V1aR over
the other three subtypes, OTR, V1bR and V2R. The Arg8/D-Arg8 ligand-pair was further
investigated to gain novel insights into the oxytocin/vasopressin peptide-receptor
interaction, which led to the identification of key residues of the receptors
that are important for ligand functionality and selectivity. These observations
could play an important role for development of oxytocin/vasopressin receptor
modulators that would enable clear distinction of the physiological and pathological
responses of the individual receptor subtypes.'
article_processing_charge: No
author:
- first_name: Maria
full_name: Di Giglio, Maria
last_name: Di Giglio
- first_name: Markus
full_name: Muttenthaler, Markus
last_name: Muttenthaler
- first_name: Kasper
full_name: Harpsøe, Kasper
last_name: Harpsøe
- first_name: Zita
full_name: Liutkeviciute, Zita
last_name: Liutkeviciute
- first_name: Peter
full_name: Keov, Peter
last_name: Keov
- first_name: Thomas
full_name: Eder, Thomas
last_name: Eder
- first_name: Thomas
full_name: Rattei, Thomas
last_name: Rattei
- first_name: Sarah
full_name: Arrowsmith, Sarah
last_name: Arrowsmith
- first_name: Susan
full_name: Wray, Susan
last_name: Wray
- first_name: Ales
full_name: Marek, Ales
last_name: Marek
- first_name: Tomas
full_name: Elbert, Tomas
last_name: Elbert
- first_name: Paul
full_name: Alewood, Paul
last_name: Alewood
- first_name: David
full_name: Gloriam, David
last_name: Gloriam
- first_name: Christian
full_name: Gruber, Christian
last_name: Gruber
citation:
ama: Di Giglio M, Muttenthaler M, Harpsøe K, et al. Development of a human vasopressin
V1a-receptor antagonist from an evolutionary-related insect neuropeptide. Scientific
Reports. 2017;7:41002. doi:10.1038/srep41002
apa: Di Giglio, M., Muttenthaler, M., Harpsøe, K., Liutkeviciute, Z., Keov, P.,
Eder, T., … Gruber, C. (2017). Development of a human vasopressin V1a-receptor
antagonist from an evolutionary-related insect neuropeptide. Scientific Reports.
Nature Publishing Group. https://doi.org/10.1038/srep41002
chicago: Di Giglio, Maria, Markus Muttenthaler, Kasper Harpsøe, Zita Liutkeviciute,
Peter Keov, Thomas Eder, Thomas Rattei, et al. “Development of a Human Vasopressin
V1a-Receptor Antagonist from an Evolutionary-Related Insect Neuropeptide.” Scientific
Reports. Nature Publishing Group, 2017. https://doi.org/10.1038/srep41002.
ieee: M. Di Giglio et al., “Development of a human vasopressin V1a-receptor
antagonist from an evolutionary-related insect neuropeptide,” Scientific Reports,
vol. 7. Nature Publishing Group, p. 41002, 2017.
ista: Di Giglio M, Muttenthaler M, Harpsøe K, Liutkeviciute Z, Keov P, Eder T, Rattei
T, Arrowsmith S, Wray S, Marek A, Elbert T, Alewood P, Gloriam D, Gruber C. 2017.
Development of a human vasopressin V1a-receptor antagonist from an evolutionary-related
insect neuropeptide. Scientific Reports. 7, 41002.
mla: Di Giglio, Maria, et al. “Development of a Human Vasopressin V1a-Receptor Antagonist
from an Evolutionary-Related Insect Neuropeptide.” Scientific Reports,
vol. 7, Nature Publishing Group, 2017, p. 41002, doi:10.1038/srep41002.
short: M. Di Giglio, M. Muttenthaler, K. Harpsøe, Z. Liutkeviciute, P. Keov, T.
Eder, T. Rattei, S. Arrowsmith, S. Wray, A. Marek, T. Elbert, P. Alewood, D. Gloriam,
C. Gruber, Scientific Reports 7 (2017) 41002.
date_created: 2018-12-11T11:50:04Z
date_published: 2017-02-01T00:00:00Z
date_updated: 2023-09-20T11:47:47Z
day: '01'
ddc:
- '570'
- '590'
doi: 10.1038/srep41002
external_id:
isi:
- '000393163800001'
file:
- access_level: open_access
content_type: application/pdf
creator: system
date_created: 2018-12-12T10:14:59Z
date_updated: 2018-12-12T10:14:59Z
file_id: '5115'
file_name: IST-2017-790-v1+1_srep41002_1_.pdf
file_size: 1994139
relation: main_file
file_date_updated: 2018-12-12T10:14:59Z
has_accepted_license: '1'
intvolume: ' 7'
isi: 1
language:
- iso: eng
month: '02'
oa: 1
oa_version: Published Version
page: '41002'
publication: Scientific Reports
publication_status: published
publisher: Nature Publishing Group
publist_id: '6291'
pubrep_id: '790'
quality_controlled: '1'
scopus_import: '1'
status: public
title: Development of a human vasopressin V1a-receptor antagonist from an evolutionary-related
insect neuropeptide
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: journal_article
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
volume: 7
year: '2017'
...
---
_id: '1087'
abstract:
- lang: eng
text: Using extensive direct numerical simulations, the dynamics of laminar-turbulent
fronts in pipe flow is investigated for Reynolds numbers between and 5500. We
here investigate the physical distinction between the fronts of weak and strong
slugs both by analysing the turbulent kinetic energy budget and by comparing the
downstream front motion to the advection speed of bulk turbulent structures. Our
study shows that weak downstream fronts travel slower than turbulent structures
in the bulk and correspond to decaying turbulence at the front. At the downstream
front speed becomes faster than the advection speed, marking the onset of strong
fronts. In contrast to weak fronts, turbulent eddies are generated at strong fronts
by feeding on the downstream laminar flow. Our study also suggests that temporal
fluctuations of production and dissipation at the downstream laminar-turbulent
front drive the dynamical switches between the two types of front observed up
to.
acknowledged_ssus:
- _id: ScienComp
article_processing_charge: No
author:
- first_name: Baofang
full_name: Song, Baofang
last_name: Song
- first_name: Dwight
full_name: Barkley, Dwight
last_name: Barkley
- first_name: Björn
full_name: Hof, Björn
id: 3A374330-F248-11E8-B48F-1D18A9856A87
last_name: Hof
orcid: 0000-0003-2057-2754
- first_name: Marc
full_name: Avila, Marc
last_name: Avila
citation:
ama: Song B, Barkley D, Hof B, Avila M. Speed and structure of turbulent fronts
in pipe flow. Journal of Fluid Mechanics. 2017;813:1045-1059. doi:10.1017/jfm.2017.14
apa: Song, B., Barkley, D., Hof, B., & Avila, M. (2017). Speed and structure
of turbulent fronts in pipe flow. Journal of Fluid Mechanics. Cambridge
University Press. https://doi.org/10.1017/jfm.2017.14
chicago: Song, Baofang, Dwight Barkley, Björn Hof, and Marc Avila. “Speed and Structure
of Turbulent Fronts in Pipe Flow.” Journal of Fluid Mechanics. Cambridge
University Press, 2017. https://doi.org/10.1017/jfm.2017.14.
ieee: B. Song, D. Barkley, B. Hof, and M. Avila, “Speed and structure of turbulent
fronts in pipe flow,” Journal of Fluid Mechanics, vol. 813. Cambridge University
Press, pp. 1045–1059, 2017.
ista: Song B, Barkley D, Hof B, Avila M. 2017. Speed and structure of turbulent
fronts in pipe flow. Journal of Fluid Mechanics. 813, 1045–1059.
mla: Song, Baofang, et al. “Speed and Structure of Turbulent Fronts in Pipe Flow.”
Journal of Fluid Mechanics, vol. 813, Cambridge University Press, 2017,
pp. 1045–59, doi:10.1017/jfm.2017.14.
short: B. Song, D. Barkley, B. Hof, M. Avila, Journal of Fluid Mechanics 813 (2017)
1045–1059.
date_created: 2018-12-11T11:50:04Z
date_published: 2017-02-25T00:00:00Z
date_updated: 2023-09-20T11:47:22Z
day: '25'
department:
- _id: BjHo
doi: 10.1017/jfm.2017.14
ec_funded: 1
external_id:
isi:
- '000394376400044'
intvolume: ' 813'
isi: 1
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/1603.04077
month: '02'
oa: 1
oa_version: Submitted Version
page: 1045 - 1059
project:
- _id: 25152F3A-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '306589'
name: Decoding the complexity of turbulence at its origin
publication: Journal of Fluid Mechanics
publication_identifier:
issn:
- '00221120'
publication_status: published
publisher: Cambridge University Press
publist_id: '6290'
quality_controlled: '1'
scopus_import: '1'
status: public
title: Speed and structure of turbulent fronts in pipe flow
type: journal_article
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
volume: 813
year: '2017'
...
---
_id: '1089'
abstract:
- lang: eng
text: We discuss properties of distributions that are multivariate totally positive
of order two (MTP2) related to conditional independence. In particular, we show
that any independence model generated by an MTP2 distribution is a compositional
semigraphoid which is upward-stable and singleton-transitive. In addition, we
prove that any MTP2 distribution satisfying an appropriate support condition is
faithful to its concentration graph. Finally, we analyze factorization properties
of MTP2 distributions and discuss ways of constructing MTP2 distributions; in
particular we give conditions on the log-linear parameters of a discrete distribution
which ensure MTP2 and characterize conditional Gaussian distributions which satisfy
MTP2.
article_processing_charge: No
author:
- first_name: Shaun
full_name: Fallat, Shaun
last_name: Fallat
- first_name: Steffen
full_name: Lauritzen, Steffen
last_name: Lauritzen
- first_name: Kayvan
full_name: Sadeghi, Kayvan
last_name: Sadeghi
- first_name: Caroline
full_name: Uhler, Caroline
id: 49ADD78E-F248-11E8-B48F-1D18A9856A87
last_name: Uhler
orcid: 0000-0002-7008-0216
- first_name: Nanny
full_name: Wermuth, Nanny
last_name: Wermuth
- first_name: Piotr
full_name: Zwiernik, Piotr
last_name: Zwiernik
citation:
ama: Fallat S, Lauritzen S, Sadeghi K, Uhler C, Wermuth N, Zwiernik P. Total positivity
in Markov structures. Annals of Statistics. 2017;45(3):1152-1184. doi:10.1214/16-AOS1478
apa: Fallat, S., Lauritzen, S., Sadeghi, K., Uhler, C., Wermuth, N., & Zwiernik,
P. (2017). Total positivity in Markov structures. Annals of Statistics.
Institute of Mathematical Statistics. https://doi.org/10.1214/16-AOS1478
chicago: Fallat, Shaun, Steffen Lauritzen, Kayvan Sadeghi, Caroline Uhler, Nanny
Wermuth, and Piotr Zwiernik. “Total Positivity in Markov Structures.” Annals
of Statistics. Institute of Mathematical Statistics, 2017. https://doi.org/10.1214/16-AOS1478.
ieee: S. Fallat, S. Lauritzen, K. Sadeghi, C. Uhler, N. Wermuth, and P. Zwiernik,
“Total positivity in Markov structures,” Annals of Statistics, vol. 45,
no. 3. Institute of Mathematical Statistics, pp. 1152–1184, 2017.
ista: Fallat S, Lauritzen S, Sadeghi K, Uhler C, Wermuth N, Zwiernik P. 2017. Total
positivity in Markov structures. Annals of Statistics. 45(3), 1152–1184.
mla: Fallat, Shaun, et al. “Total Positivity in Markov Structures.” Annals of
Statistics, vol. 45, no. 3, Institute of Mathematical Statistics, 2017, pp.
1152–84, doi:10.1214/16-AOS1478.
short: S. Fallat, S. Lauritzen, K. Sadeghi, C. Uhler, N. Wermuth, P. Zwiernik, Annals
of Statistics 45 (2017) 1152–1184.
date_created: 2018-12-11T11:50:05Z
date_published: 2017-06-01T00:00:00Z
date_updated: 2023-09-20T11:46:53Z
day: '01'
department:
- _id: CaUh
doi: 10.1214/16-AOS1478
external_id:
isi:
- '000404395900008'
intvolume: ' 45'
isi: 1
issue: '3'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/1510.01290
month: '06'
oa: 1
oa_version: Submitted Version
page: 1152 - 1184
project:
- _id: 2530CA10-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: Y 903-N35
name: 'Gaussian Graphical Models: Theory and Applications'
publication: Annals of Statistics
publication_identifier:
issn:
- '00905364'
publication_status: published
publisher: Institute of Mathematical Statistics
publist_id: '6288'
quality_controlled: '1'
scopus_import: '1'
status: public
title: Total positivity in Markov structures
type: journal_article
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
volume: 45
year: '2017'
...
---
_id: '1104'
abstract:
- lang: eng
text: In the early visual system, cells of the same type perform the same computation
in different places of the visual field. How these cells code together a complex
visual scene is unclear. A common assumption is that cells of a single-type extract
a single-stimulus feature to form a feature map, but this has rarely been observed
directly. Using large-scale recordings in the rat retina, we show that a homogeneous
population of fast OFF ganglion cells simultaneously encodes two radically different
features of a visual scene. Cells close to a moving object code quasilinearly
for its position, while distant cells remain largely invariant to the object's
position and, instead, respond nonlinearly to changes in the object's speed. We
develop a quantitative model that accounts for this effect and identify a disinhibitory
circuit that mediates it. Ganglion cells of a single type thus do not code for
one, but two features simultaneously. This richer, flexible neural map might also
be present in other sensory systems.
article_number: '1964'
article_processing_charge: No
author:
- first_name: Stephane
full_name: Deny, Stephane
last_name: Deny
- first_name: Ulisse
full_name: Ferrari, Ulisse
last_name: Ferrari
- first_name: Emilie
full_name: Mace, Emilie
last_name: Mace
- first_name: Pierre
full_name: Yger, Pierre
last_name: Yger
- first_name: Romain
full_name: Caplette, Romain
last_name: Caplette
- first_name: Serge
full_name: Picaud, Serge
last_name: Picaud
- first_name: Gasper
full_name: Tkacik, Gasper
id: 3D494DCA-F248-11E8-B48F-1D18A9856A87
last_name: Tkacik
orcid: 0000-0002-6699-1455
- first_name: Olivier
full_name: Marre, Olivier
last_name: Marre
citation:
ama: Deny S, Ferrari U, Mace E, et al. Multiplexed computations in retinal ganglion
cells of a single type. Nature Communications. 2017;8(1). doi:10.1038/s41467-017-02159-y
apa: Deny, S., Ferrari, U., Mace, E., Yger, P., Caplette, R., Picaud, S., … Marre,
O. (2017). Multiplexed computations in retinal ganglion cells of a single type.
Nature Communications. Nature Publishing Group. https://doi.org/10.1038/s41467-017-02159-y
chicago: Deny, Stephane, Ulisse Ferrari, Emilie Mace, Pierre Yger, Romain Caplette,
Serge Picaud, Gašper Tkačik, and Olivier Marre. “Multiplexed Computations in Retinal
Ganglion Cells of a Single Type.” Nature Communications. Nature Publishing
Group, 2017. https://doi.org/10.1038/s41467-017-02159-y.
ieee: S. Deny et al., “Multiplexed computations in retinal ganglion cells
of a single type,” Nature Communications, vol. 8, no. 1. Nature Publishing
Group, 2017.
ista: Deny S, Ferrari U, Mace E, Yger P, Caplette R, Picaud S, Tkačik G, Marre O.
2017. Multiplexed computations in retinal ganglion cells of a single type. Nature
Communications. 8(1), 1964.
mla: Deny, Stephane, et al. “Multiplexed Computations in Retinal Ganglion Cells
of a Single Type.” Nature Communications, vol. 8, no. 1, 1964, Nature Publishing
Group, 2017, doi:10.1038/s41467-017-02159-y.
short: S. Deny, U. Ferrari, E. Mace, P. Yger, R. Caplette, S. Picaud, G. Tkačik,
O. Marre, Nature Communications 8 (2017).
date_created: 2018-12-11T11:50:10Z
date_published: 2017-12-06T00:00:00Z
date_updated: 2023-09-20T11:41:19Z
day: '06'
ddc:
- '571'
department:
- _id: GaTk
doi: 10.1038/s41467-017-02159-y
ec_funded: 1
external_id:
isi:
- '000417241200004'
file:
- access_level: open_access
content_type: application/pdf
creator: system
date_created: 2018-12-12T10:16:06Z
date_updated: 2018-12-12T10:16:06Z
file_id: '5191'
file_name: IST-2018-921-v1+1_s41467-017-02159-y.pdf
file_size: 2872887
relation: main_file
file_date_updated: 2018-12-12T10:16:06Z
has_accepted_license: '1'
intvolume: ' 8'
isi: 1
issue: '1'
language:
- iso: eng
month: '12'
oa: 1
oa_version: Published Version
project:
- _id: 25CD3DD2-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '604102'
name: Localization of ion channels and receptors by two and three-dimensional immunoelectron
microscopic approaches
- _id: 254D1A94-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: P 25651-N26
name: Sensitivity to higher-order statistics in natural scenes
publication: Nature Communications
publication_identifier:
issn:
- '20411723'
publication_status: published
publisher: Nature Publishing Group
publist_id: '6266'
pubrep_id: '921'
quality_controlled: '1'
scopus_import: '1'
status: public
title: Multiplexed computations in retinal ganglion cells of a single type
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: journal_article
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
volume: 8
year: '2017'
...
---
_id: '11065'
abstract:
- lang: eng
text: Premature aging disorders provide an opportunity to study the mechanisms that
drive aging. In Hutchinson-Gilford progeria syndrome (HGPS), a mutant form of
the nuclear scaffold protein lamin A distorts nuclei and sequesters nuclear proteins.
We sought to investigate protein homeostasis in this disease. Here, we report
a widespread increase in protein turnover in HGPS-derived cells compared to normal
cells. We determine that global protein synthesis is elevated as a consequence
of activated nucleoli and enhanced ribosome biogenesis in HGPS-derived fibroblasts.
Depleting normal lamin A or inducing mutant lamin A expression are each sufficient
to drive nucleolar expansion. We further show that nucleolar size correlates with
donor age in primary fibroblasts derived from healthy individuals and that ribosomal
RNA production increases with age, indicating that nucleolar size and activity
can serve as aging biomarkers. While limiting ribosome biogenesis extends lifespan
in several systems, we show that increased ribosome biogenesis and activity are
a hallmark of premature aging.
article_number: '328'
article_processing_charge: No
article_type: original
author:
- first_name: Abigail
full_name: Buchwalter, Abigail
last_name: Buchwalter
- first_name: Martin W
full_name: HETZER, Martin W
id: 86c0d31b-b4eb-11ec-ac5a-eae7b2e135ed
last_name: HETZER
orcid: 0000-0002-2111-992X
citation:
ama: Buchwalter A, Hetzer M. Nucleolar expansion and elevated protein translation
in premature aging. Nature Communications. 2017;8. doi:10.1038/s41467-017-00322-z
apa: Buchwalter, A., & Hetzer, M. (2017). Nucleolar expansion and elevated protein
translation in premature aging. Nature Communications. Springer Nature.
https://doi.org/10.1038/s41467-017-00322-z
chicago: Buchwalter, Abigail, and Martin Hetzer. “Nucleolar Expansion and Elevated
Protein Translation in Premature Aging.” Nature Communications. Springer
Nature, 2017. https://doi.org/10.1038/s41467-017-00322-z.
ieee: A. Buchwalter and M. Hetzer, “Nucleolar expansion and elevated protein translation
in premature aging,” Nature Communications, vol. 8. Springer Nature, 2017.
ista: Buchwalter A, Hetzer M. 2017. Nucleolar expansion and elevated protein translation
in premature aging. Nature Communications. 8, 328.
mla: Buchwalter, Abigail, and Martin Hetzer. “Nucleolar Expansion and Elevated Protein
Translation in Premature Aging.” Nature Communications, vol. 8, 328, Springer
Nature, 2017, doi:10.1038/s41467-017-00322-z.
short: A. Buchwalter, M. Hetzer, Nature Communications 8 (2017).
date_created: 2022-04-07T07:45:50Z
date_published: 2017-08-30T00:00:00Z
date_updated: 2022-07-18T08:33:03Z
day: '30'
doi: 10.1038/s41467-017-00322-z
extern: '1'
external_id:
pmid:
- '28855503'
intvolume: ' 8'
keyword:
- General Physics and Astronomy
- General Biochemistry
- Genetics and Molecular Biology
- General Chemistry
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.1038/s41467-017-00322-z
month: '08'
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: Nucleolar expansion and elevated protein translation in premature aging
type: journal_article
user_id: 72615eeb-f1f3-11ec-aa25-d4573ddc34fd
volume: 8
year: '2017'
...
---
_id: '11066'
abstract:
- lang: eng
text: Recent studies have shown that a subset of nucleoporins (Nups) can detach
from the nuclear pore complex and move into the nuclear interior to regulate transcription.
One such dynamic Nup, called Nup98, has been implicated in gene activation in
healthy cells and has been shown to drive leukemogenesis when mutated in patients
with acute myeloid leukemia (AML). Here we show that in hematopoietic cells, Nup98
binds predominantly to transcription start sites to recruit the Wdr82–Set1A/COMPASS
(complex of proteins associated with Set1) complex, which is required for deposition
of the histone 3 Lys4 trimethyl (H3K4me3)-activating mark. Depletion of Nup98
or Wdr82 abolishes Set1A recruitment to chromatin and subsequently ablates H3K4me3
at adjacent promoters. Furthermore, expression of a Nup98 fusion protein implicated
in aggressive AML causes mislocalization of H3K4me3 at abnormal regions and up-regulation
of associated genes. Our findings establish a function of Nup98 in hematopoietic
gene activation and provide mechanistic insight into which Nup98 leukemic fusion
proteins promote AML.
article_processing_charge: No
article_type: original
author:
- first_name: Tobias M.
full_name: Franks, Tobias M.
last_name: Franks
- first_name: Asako
full_name: McCloskey, Asako
last_name: McCloskey
- first_name: Maxim Nikolaievich
full_name: Shokhirev, Maxim Nikolaievich
last_name: Shokhirev
- first_name: Chris
full_name: Benner, Chris
last_name: Benner
- first_name: Annie
full_name: Rathore, Annie
last_name: Rathore
- first_name: Martin W
full_name: HETZER, Martin W
id: 86c0d31b-b4eb-11ec-ac5a-eae7b2e135ed
last_name: HETZER
orcid: 0000-0002-2111-992X
citation:
ama: Franks TM, McCloskey A, Shokhirev MN, Benner C, Rathore A, Hetzer M. Nup98
recruits the Wdr82–Set1A/COMPASS complex to promoters to regulate H3K4 trimethylation
in hematopoietic progenitor cells. Genes & Development. 2017;31(22):2222-2234.
doi:10.1101/gad.306753.117
apa: Franks, T. M., McCloskey, A., Shokhirev, M. N., Benner, C., Rathore, A., &
Hetzer, M. (2017). Nup98 recruits the Wdr82–Set1A/COMPASS complex to promoters
to regulate H3K4 trimethylation in hematopoietic progenitor cells. Genes &
Development. Cold Spring Harbor Laboratory. https://doi.org/10.1101/gad.306753.117
chicago: Franks, Tobias M., Asako McCloskey, Maxim Nikolaievich Shokhirev, Chris
Benner, Annie Rathore, and Martin Hetzer. “Nup98 Recruits the Wdr82–Set1A/COMPASS
Complex to Promoters to Regulate H3K4 Trimethylation in Hematopoietic Progenitor
Cells.” Genes & Development. Cold Spring Harbor Laboratory, 2017. https://doi.org/10.1101/gad.306753.117.
ieee: T. M. Franks, A. McCloskey, M. N. Shokhirev, C. Benner, A. Rathore, and M.
Hetzer, “Nup98 recruits the Wdr82–Set1A/COMPASS complex to promoters to regulate
H3K4 trimethylation in hematopoietic progenitor cells,” Genes & Development,
vol. 31, no. 22. Cold Spring Harbor Laboratory, pp. 2222–2234, 2017.
ista: Franks TM, McCloskey A, Shokhirev MN, Benner C, Rathore A, Hetzer M. 2017.
Nup98 recruits the Wdr82–Set1A/COMPASS complex to promoters to regulate H3K4 trimethylation
in hematopoietic progenitor cells. Genes & Development. 31(22), 2222–2234.
mla: Franks, Tobias M., et al. “Nup98 Recruits the Wdr82–Set1A/COMPASS Complex to
Promoters to Regulate H3K4 Trimethylation in Hematopoietic Progenitor Cells.”
Genes & Development, vol. 31, no. 22, Cold Spring Harbor Laboratory,
2017, pp. 2222–34, doi:10.1101/gad.306753.117.
short: T.M. Franks, A. McCloskey, M.N. Shokhirev, C. Benner, A. Rathore, M. Hetzer,
Genes & Development 31 (2017) 2222–2234.
date_created: 2022-04-07T07:45:59Z
date_published: 2017-12-21T00:00:00Z
date_updated: 2022-07-18T08:33:05Z
day: '21'
doi: 10.1101/gad.306753.117
extern: '1'
external_id:
pmid:
- '29269482'
intvolume: ' 31'
issue: '22'
keyword:
- Developmental Biology
- Genetics
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.1101/gad.306753.117
month: '12'
oa: 1
oa_version: Published Version
page: 2222-2234
pmid: 1
publication: Genes & Development
publication_identifier:
issn:
- 0890-9369
- 1549-5477
publication_status: published
publisher: Cold Spring Harbor Laboratory
quality_controlled: '1'
scopus_import: '1'
status: public
title: Nup98 recruits the Wdr82–Set1A/COMPASS complex to promoters to regulate H3K4
trimethylation in hematopoietic progenitor cells
type: journal_article
user_id: 72615eeb-f1f3-11ec-aa25-d4573ddc34fd
volume: 31
year: '2017'
...
---
_id: '11067'
abstract:
- lang: eng
text: Neural progenitor cells (NeuPCs) possess a unique nuclear architecture that
changes during differentiation. Nucleoporins are linked with cell-type-specific
gene regulation, coupling physical changes in nuclear structure to transcriptional
output; but, whether and how they coordinate with key fate-determining transcription
factors is unclear. Here we show that the nucleoporin Nup153 interacts with Sox2
in adult NeuPCs, where it is indispensable for their maintenance and controls
neuronal differentiation. Genome-wide analyses show that Nup153 and Sox2 bind
and co-regulate hundreds of genes. Binding of Nup153 to gene promoters or transcriptional
end sites correlates with increased or decreased gene expression, respectively,
and inhibiting Nup153 expression alters open chromatin configurations at its target
genes, disrupts genomic localization of Sox2, and promotes differentiation in
vitro and a gliogenic fate switch in vivo. Together, these findings reveal that
nuclear structural proteins may exert bimodal transcriptional effects to control
cell fate.
article_processing_charge: No
article_type: original
author:
- first_name: Tomohisa
full_name: Toda, Tomohisa
last_name: Toda
- first_name: Jonathan Y.
full_name: Hsu, Jonathan Y.
last_name: Hsu
- first_name: Sara B.
full_name: Linker, Sara B.
last_name: Linker
- first_name: Lauren
full_name: Hu, Lauren
last_name: Hu
- first_name: Simon T.
full_name: Schafer, Simon T.
last_name: Schafer
- first_name: Jerome
full_name: Mertens, Jerome
last_name: Mertens
- first_name: Filipe V.
full_name: Jacinto, Filipe V.
last_name: Jacinto
- first_name: Martin W
full_name: HETZER, Martin W
id: 86c0d31b-b4eb-11ec-ac5a-eae7b2e135ed
last_name: HETZER
orcid: 0000-0002-2111-992X
- first_name: Fred H.
full_name: Gage, Fred H.
last_name: Gage
citation:
ama: Toda T, Hsu JY, Linker SB, et al. Nup153 interacts with Sox2 to enable bimodal
gene regulation and maintenance of neural progenitor cells. Cell Stem Cell.
2017;21(5):618-634.e7. doi:10.1016/j.stem.2017.08.012
apa: Toda, T., Hsu, J. Y., Linker, S. B., Hu, L., Schafer, S. T., Mertens, J., …
Gage, F. H. (2017). Nup153 interacts with Sox2 to enable bimodal gene regulation
and maintenance of neural progenitor cells. Cell Stem Cell. Elsevier. https://doi.org/10.1016/j.stem.2017.08.012
chicago: Toda, Tomohisa, Jonathan Y. Hsu, Sara B. Linker, Lauren Hu, Simon T. Schafer,
Jerome Mertens, Filipe V. Jacinto, Martin Hetzer, and Fred H. Gage. “Nup153 Interacts
with Sox2 to Enable Bimodal Gene Regulation and Maintenance of Neural Progenitor
Cells.” Cell Stem Cell. Elsevier, 2017. https://doi.org/10.1016/j.stem.2017.08.012.
ieee: T. Toda et al., “Nup153 interacts with Sox2 to enable bimodal gene
regulation and maintenance of neural progenitor cells,” Cell Stem Cell,
vol. 21, no. 5. Elsevier, p. 618–634.e7, 2017.
ista: Toda T, Hsu JY, Linker SB, Hu L, Schafer ST, Mertens J, Jacinto FV, Hetzer
M, Gage FH. 2017. Nup153 interacts with Sox2 to enable bimodal gene regulation
and maintenance of neural progenitor cells. Cell Stem Cell. 21(5), 618–634.e7.
mla: Toda, Tomohisa, et al. “Nup153 Interacts with Sox2 to Enable Bimodal Gene Regulation
and Maintenance of Neural Progenitor Cells.” Cell Stem Cell, vol. 21, no.
5, Elsevier, 2017, p. 618–634.e7, doi:10.1016/j.stem.2017.08.012.
short: T. Toda, J.Y. Hsu, S.B. Linker, L. Hu, S.T. Schafer, J. Mertens, F.V. Jacinto,
M. Hetzer, F.H. Gage, Cell Stem Cell 21 (2017) 618–634.e7.
date_created: 2022-04-07T07:46:12Z
date_published: 2017-11-02T00:00:00Z
date_updated: 2022-07-18T08:33:07Z
day: '02'
doi: 10.1016/j.stem.2017.08.012
extern: '1'
external_id:
pmid:
- '28919367'
intvolume: ' 21'
issue: '5'
keyword:
- Cell Biology
- Genetics
- Molecular Medicine
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.1016/j.stem.2017.08.012
month: '11'
oa: 1
oa_version: Published Version
page: 618-634.e7
pmid: 1
publication: Cell Stem Cell
publication_identifier:
issn:
- 1934-5909
publication_status: published
publisher: Elsevier
quality_controlled: '1'
scopus_import: '1'
status: public
title: Nup153 interacts with Sox2 to enable bimodal gene regulation and maintenance
of neural progenitor cells
type: journal_article
user_id: 72615eeb-f1f3-11ec-aa25-d4573ddc34fd
volume: 21
year: '2017'
...
---
_id: '1107'
abstract:
- lang: eng
text: The generation, migration, and differentiation of neurons requires the functional
integrity of the microtubule cytoskeleton. Mutations in the tubulin gene family
are known to cause various neurological diseases including lissencephaly, ocular
motor disorders, polymicrogyria and amyotrophic lateral sclerosis. We have previously
reported that mutations in TUBB5 cause microcephaly that is accompanied by severe
intellectual impairment and motor delay. Here we present the characterization
of a Tubb5 mouse model that allows for the conditional expression of the pathogenic
E401K mutation. Homozygous knockin animals exhibit a severe reduction in brain
size and in body weight. These animals do not show any significant impairment
in general activity, anxiety, or in the acoustic startle response, however, present
with notable defects in motor coordination. When assessed on the static rod apparatus
mice took longer to orient and often lost their balance completely. Interestingly,
mutant animals also showed defects in prepulse inhibition, a phenotype associated
with sensorimotor gating and considered an endophenotype for schizophrenia. This
study provides insight into the behavioral consequences of tubulin gene mutations.
acknowledgement: Austrian Science Fund (FWF) for funding this research [I914,P21092]
article_processing_charge: No
author:
- first_name: Martin
full_name: Breuss, Martin
last_name: Breuss
- first_name: Andi H
full_name: Hansen, Andi H
id: 38853E16-F248-11E8-B48F-1D18A9856A87
last_name: Hansen
- first_name: Lukas
full_name: Landler, Lukas
last_name: Landler
- first_name: David
full_name: Keays, David
last_name: Keays
citation:
ama: Breuss M, Hansen AH, Landler L, Keays D. Brain specific knockin of the pathogenic
Tubb5 E401K allele causes defects in motor coordination and prepulse inhibition.
Behavioural Brain Research. 2017;323:47-55. doi:10.1016/j.bbr.2017.01.029
apa: Breuss, M., Hansen, A. H., Landler, L., & Keays, D. (2017). Brain specific
knockin of the pathogenic Tubb5 E401K allele causes defects in motor coordination
and prepulse inhibition. Behavioural Brain Research. Elsevier. https://doi.org/10.1016/j.bbr.2017.01.029
chicago: Breuss, Martin, Andi H Hansen, Lukas Landler, and David Keays. “Brain Specific
Knockin of the Pathogenic Tubb5 E401K Allele Causes Defects in Motor Coordination
and Prepulse Inhibition.” Behavioural Brain Research. Elsevier, 2017. https://doi.org/10.1016/j.bbr.2017.01.029.
ieee: M. Breuss, A. H. Hansen, L. Landler, and D. Keays, “Brain specific knockin
of the pathogenic Tubb5 E401K allele causes defects in motor coordination and
prepulse inhibition,” Behavioural Brain Research, vol. 323. Elsevier, pp.
47–55, 2017.
ista: Breuss M, Hansen AH, Landler L, Keays D. 2017. Brain specific knockin of the
pathogenic Tubb5 E401K allele causes defects in motor coordination and prepulse
inhibition. Behavioural Brain Research. 323, 47–55.
mla: Breuss, Martin, et al. “Brain Specific Knockin of the Pathogenic Tubb5 E401K
Allele Causes Defects in Motor Coordination and Prepulse Inhibition.” Behavioural
Brain Research, vol. 323, Elsevier, 2017, pp. 47–55, doi:10.1016/j.bbr.2017.01.029.
short: M. Breuss, A.H. Hansen, L. Landler, D. Keays, Behavioural Brain Research
323 (2017) 47–55.
date_created: 2018-12-11T11:50:11Z
date_published: 2017-04-14T00:00:00Z
date_updated: 2023-09-20T11:37:25Z
day: '14'
ddc:
- '570'
- '571'
doi: 10.1016/j.bbr.2017.01.029
extern: '1'
external_id:
isi:
- '000397369100007'
file:
- access_level: open_access
content_type: application/pdf
creator: system
date_created: 2018-12-12T10:12:03Z
date_updated: 2018-12-12T10:12:03Z
file_id: '4921'
file_name: IST-2017-868-v1+1_1-s2.0-S0166432816309160-main.pdf
file_size: 2291511
relation: main_file
file_date_updated: 2018-12-12T10:12:03Z
has_accepted_license: '1'
intvolume: ' 323'
isi: 1
language:
- iso: eng
month: '04'
oa: 1
oa_version: Published Version
page: 47 - 55
publication: Behavioural Brain Research
publication_identifier:
issn:
- '01664328'
publication_status: published
publisher: Elsevier
publist_id: '6262'
pubrep_id: '868'
quality_controlled: '1'
status: public
title: Brain specific knockin of the pathogenic Tubb5 E401K allele causes defects
in motor coordination and prepulse inhibition
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: 323
year: '2017'
...
---
_id: '1108'
abstract:
- lang: eng
text: In this work we study the learnability of stochastic processes with respect
to the conditional risk, i.e. the existence of a learning algorithm that improves
its next-step performance with the amount of observed data. We introduce a notion
of pairwise discrepancy between conditional distributions at different times steps
and show how certain properties of these discrepancies can be used to construct
a successful learning algorithm. Our main results are two theorems that establish
criteria for learnability for many classes of stochastic processes, including
all special cases studied previously in the literature.
alternative_title:
- PMLR
article_processing_charge: No
author:
- first_name: Alexander
full_name: Zimin, Alexander
id: 37099E9C-F248-11E8-B48F-1D18A9856A87
last_name: Zimin
- first_name: Christoph
full_name: Lampert, Christoph
id: 40C20FD2-F248-11E8-B48F-1D18A9856A87
last_name: Lampert
orcid: 0000-0001-8622-7887
citation:
ama: 'Zimin A, Lampert C. Learning theory for conditional risk minimization. In:
Vol 54. ML Research Press; 2017:213-222.'
apa: 'Zimin, A., & Lampert, C. (2017). Learning theory for conditional risk
minimization (Vol. 54, pp. 213–222). Presented at the AISTATS: Artificial Intelligence
and Statistics, Fort Lauderdale, FL, United States: ML Research Press.'
chicago: Zimin, Alexander, and Christoph Lampert. “Learning Theory for Conditional
Risk Minimization,” 54:213–22. ML Research Press, 2017.
ieee: 'A. Zimin and C. Lampert, “Learning theory for conditional risk minimization,”
presented at the AISTATS: Artificial Intelligence and Statistics, Fort Lauderdale,
FL, United States, 2017, vol. 54, pp. 213–222.'
ista: 'Zimin A, Lampert C. 2017. Learning theory for conditional risk minimization.
AISTATS: Artificial Intelligence and Statistics, PMLR, vol. 54, 213–222.'
mla: Zimin, Alexander, and Christoph Lampert. Learning Theory for Conditional
Risk Minimization. Vol. 54, ML Research Press, 2017, pp. 213–22.
short: A. Zimin, C. Lampert, in:, ML Research Press, 2017, pp. 213–222.
conference:
end_date: 2017-04-22
location: Fort Lauderdale, FL, United States
name: 'AISTATS: Artificial Intelligence and Statistics'
start_date: 2017-04-20
date_created: 2018-12-11T11:50:11Z
date_published: 2017-04-01T00:00:00Z
date_updated: 2023-10-17T10:01:12Z
day: '01'
department:
- _id: ChLa
ec_funded: 1
external_id:
isi:
- '000509368500024'
intvolume: ' 54'
isi: 1
language:
- iso: eng
main_file_link:
- open_access: '1'
url: http://proceedings.mlr.press/v54/zimin17a/zimin17a.pdf
month: '04'
oa: 1
oa_version: Submitted Version
page: 213 - 222
project:
- _id: 2532554C-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '308036'
name: Lifelong Learning of Visual Scene Understanding
publication_status: published
publisher: ML Research Press
publist_id: '6261'
quality_controlled: '1'
status: public
title: Learning theory for conditional risk minimization
type: conference
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 54
year: '2017'
...
---
_id: '1109'
abstract:
- lang: eng
text: 'Rotation of molecules embedded in He nanodroplets is explored by a combination
of fs laser-induced alignment experiments and angulon quasiparticle theory. We
demonstrate that at low fluence of the fs alignment pulse, the molecule and its
solvation shell can be set into coherent collective rotation lasting long enough
to form revivals. With increasing fluence, however, the revivals disappear --
instead, rotational dynamics as rapid as for an isolated molecule is observed
during the first few picoseconds. Classical calculations trace this phenomenon
to transient decoupling of the molecule from its He shell. Our results open novel
opportunities for studying non-equilibrium solute-solvent dynamics and quantum
thermalization. '
article_number: '203203'
article_processing_charge: No
author:
- first_name: Benjamin
full_name: Shepperson, Benjamin
last_name: Shepperson
- first_name: Anders
full_name: Søndergaard, Anders
last_name: Søndergaard
- first_name: Lars
full_name: Christiansen, Lars
last_name: Christiansen
- first_name: Jan
full_name: Kaczmarczyk, Jan
id: 46C405DE-F248-11E8-B48F-1D18A9856A87
last_name: Kaczmarczyk
orcid: 0000-0002-1629-3675
- first_name: Robert
full_name: Zillich, Robert
last_name: Zillich
- first_name: Mikhail
full_name: Lemeshko, Mikhail
id: 37CB05FA-F248-11E8-B48F-1D18A9856A87
last_name: Lemeshko
orcid: 0000-0002-6990-7802
- first_name: Henrik
full_name: Stapelfeldt, Henrik
last_name: Stapelfeldt
citation:
ama: 'Shepperson B, Søndergaard A, Christiansen L, et al. Laser-induced rotation
of iodine molecules in helium nanodroplets: Revivals and breaking-free. Physical
Review Letters. 2017;118(20). doi:10.1103/PhysRevLett.118.203203'
apa: 'Shepperson, B., Søndergaard, A., Christiansen, L., Kaczmarczyk, J., Zillich,
R., Lemeshko, M., & Stapelfeldt, H. (2017). Laser-induced rotation of iodine
molecules in helium nanodroplets: Revivals and breaking-free. Physical Review
Letters. American Physical Society. https://doi.org/10.1103/PhysRevLett.118.203203'
chicago: 'Shepperson, Benjamin, Anders Søndergaard, Lars Christiansen, Jan Kaczmarczyk,
Robert Zillich, Mikhail Lemeshko, and Henrik Stapelfeldt. “Laser-Induced Rotation
of Iodine Molecules in Helium Nanodroplets: Revivals and Breaking-Free.” Physical
Review Letters. American Physical Society, 2017. https://doi.org/10.1103/PhysRevLett.118.203203.'
ieee: 'B. Shepperson et al., “Laser-induced rotation of iodine molecules
in helium nanodroplets: Revivals and breaking-free,” Physical Review Letters,
vol. 118, no. 20. American Physical Society, 2017.'
ista: 'Shepperson B, Søndergaard A, Christiansen L, Kaczmarczyk J, Zillich R, Lemeshko
M, Stapelfeldt H. 2017. Laser-induced rotation of iodine molecules in helium nanodroplets:
Revivals and breaking-free. Physical Review Letters. 118(20), 203203.'
mla: 'Shepperson, Benjamin, et al. “Laser-Induced Rotation of Iodine Molecules in
Helium Nanodroplets: Revivals and Breaking-Free.” Physical Review Letters,
vol. 118, no. 20, 203203, American Physical Society, 2017, doi:10.1103/PhysRevLett.118.203203.'
short: B. Shepperson, A. Søndergaard, L. Christiansen, J. Kaczmarczyk, R. Zillich,
M. Lemeshko, H. Stapelfeldt, Physical Review Letters 118 (2017).
date_created: 2018-12-11T11:50:12Z
date_published: 2017-05-19T00:00:00Z
date_updated: 2023-09-20T11:36:17Z
day: '19'
department:
- _id: MiLe
doi: 10.1103/PhysRevLett.118.203203
external_id:
isi:
- '000401664000005'
intvolume: ' 118'
isi: 1
issue: '20'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/1702.01977
month: '05'
oa: 1
oa_version: Preprint
project:
- _id: 26031614-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: P29902
name: Quantum rotations in the presence of a many-body environment
publication: Physical Review Letters
publication_status: published
publisher: American Physical Society
publist_id: '6260'
quality_controlled: '1'
scopus_import: '1'
status: public
title: 'Laser-induced rotation of iodine molecules in helium nanodroplets: Revivals
and breaking-free'
type: journal_article
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
volume: 118
year: '2017'
...
---
_id: '1110'
abstract:
- lang: eng
text: The phytohormone auxin is a major determinant and regulatory component important
for plant development. Auxin transport between cells is mediated by a complex
system of transporters such as AUX1/LAX, PIN, and ABCB proteins, and their localization
and activity is thought to be influenced by phosphatases and kinases. Flavonols
have been shown to alter auxin transport activity and changes in flavonol accumulation
in the Arabidopsis thaliana rol1-2 mutant cause defects in auxin transport and
seedling development. A new mutation in ROOTS CURL IN NPA 1 (RCN1), encoding a
regulatory subunit of the phosphatase PP2A, was found to suppress the growth defects
of rol1-2 without changing the flavonol content. rol1-2 rcn1-3 double mutants
show wild type-like auxin transport activity while levels of free auxin are not
affected by rcn1-3. In the rol1-2 mutant, PIN2 shows a flavonol-induced basal-to-apical
shift in polar localization which is reversed in the rol1-2 rcn1-3 to basal localization.
In vivo analysis of PINOID action, a kinase known to influence PIN protein localization
in a PP2A-antagonistic manner, revealed a negative impact of flavonols on PINOID
activity. Together, these data suggest that flavonols affect auxin transport by
modifying the antagonistic kinase/phosphatase equilibrium.
acknowledgement: European Research Council (project ERC-2011-StG-20101109-PSDP), European
Social Fund (CZ.1.07/2.3.00/20.0043) and the Czech Science Foundation (GA13-40637S)
[JF].
article_number: '41906'
article_processing_charge: No
author:
- first_name: Benjamin
full_name: Kuhn, Benjamin
last_name: Kuhn
- first_name: Tomasz
full_name: Nodzyński, Tomasz
last_name: Nodzyński
- first_name: Sanae
full_name: Errafi, Sanae
last_name: Errafi
- first_name: Rahel
full_name: Bucher, Rahel
last_name: Bucher
- first_name: Shibu
full_name: Gupta, Shibu
last_name: Gupta
- first_name: Bibek
full_name: Aryal, Bibek
last_name: Aryal
- first_name: Petre
full_name: Dobrev, Petre
last_name: Dobrev
- first_name: Laurent
full_name: Bigler, Laurent
last_name: Bigler
- first_name: Markus
full_name: Geisler, Markus
last_name: Geisler
- first_name: Eva
full_name: Zažímalová, Eva
last_name: Zažímalová
- first_name: Jirí
full_name: Friml, Jirí
id: 4159519E-F248-11E8-B48F-1D18A9856A87
last_name: Friml
orcid: 0000-0002-8302-7596
- first_name: Christoph
full_name: Ringli, Christoph
last_name: Ringli
citation:
ama: Kuhn B, Nodzyński T, Errafi S, et al. Flavonol-induced changes in PIN2 polarity
and auxin transport in the Arabidopsis thaliana rol1-2 mutant require phosphatase
activity. Scientific Reports. 2017;7. doi:10.1038/srep41906
apa: Kuhn, B., Nodzyński, T., Errafi, S., Bucher, R., Gupta, S., Aryal, B., … Ringli,
C. (2017). Flavonol-induced changes in PIN2 polarity and auxin transport in the
Arabidopsis thaliana rol1-2 mutant require phosphatase activity. Scientific
Reports. Nature Publishing Group. https://doi.org/10.1038/srep41906
chicago: Kuhn, Benjamin, Tomasz Nodzyński, Sanae Errafi, Rahel Bucher, Shibu Gupta,
Bibek Aryal, Petre Dobrev, et al. “Flavonol-Induced Changes in PIN2 Polarity and
Auxin Transport in the Arabidopsis Thaliana Rol1-2 Mutant Require Phosphatase
Activity.” Scientific Reports. Nature Publishing Group, 2017. https://doi.org/10.1038/srep41906.
ieee: B. Kuhn et al., “Flavonol-induced changes in PIN2 polarity and auxin
transport in the Arabidopsis thaliana rol1-2 mutant require phosphatase activity,”
Scientific Reports, vol. 7. Nature Publishing Group, 2017.
ista: Kuhn B, Nodzyński T, Errafi S, Bucher R, Gupta S, Aryal B, Dobrev P, Bigler
L, Geisler M, Zažímalová E, Friml J, Ringli C. 2017. Flavonol-induced changes
in PIN2 polarity and auxin transport in the Arabidopsis thaliana rol1-2 mutant
require phosphatase activity. Scientific Reports. 7, 41906.
mla: Kuhn, Benjamin, et al. “Flavonol-Induced Changes in PIN2 Polarity and Auxin
Transport in the Arabidopsis Thaliana Rol1-2 Mutant Require Phosphatase Activity.”
Scientific Reports, vol. 7, 41906, Nature Publishing Group, 2017, doi:10.1038/srep41906.
short: B. Kuhn, T. Nodzyński, S. Errafi, R. Bucher, S. Gupta, B. Aryal, P. Dobrev,
L. Bigler, M. Geisler, E. Zažímalová, J. Friml, C. Ringli, Scientific Reports
7 (2017).
date_created: 2018-12-11T11:50:12Z
date_published: 2017-02-06T00:00:00Z
date_updated: 2025-05-07T11:12:29Z
day: '06'
ddc:
- '581'
department:
- _id: JiFr
doi: 10.1038/srep41906
ec_funded: 1
external_id:
isi:
- '000393367600001'
file:
- access_level: open_access
content_type: application/pdf
creator: system
date_created: 2018-12-12T10:18:09Z
date_updated: 2018-12-12T10:18:09Z
file_id: '5328'
file_name: IST-2017-803-v1+1_srep41906.pdf
file_size: 1654496
relation: main_file
file_date_updated: 2018-12-12T10:18:09Z
has_accepted_license: '1'
intvolume: ' 7'
isi: 1
language:
- iso: eng
month: '02'
oa: 1
oa_version: Published Version
project:
- _id: 25716A02-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '282300'
name: Polarity and subcellular dynamics in plants
publication: Scientific Reports
publication_identifier:
issn:
- '20452322'
publication_status: published
publisher: Nature Publishing Group
publist_id: '6258'
pubrep_id: '803'
quality_controlled: '1'
scopus_import: '1'
status: public
title: Flavonol-induced changes in PIN2 polarity and auxin transport in the Arabidopsis
thaliana rol1-2 mutant require phosphatase activity
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: journal_article
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
volume: 7
year: '2017'
...
---
_id: '1111'
abstract:
- lang: eng
text: Adaptation depends critically on the effects of new mutations and their dependency
on the genetic background in which they occur. These two factors can be summarized
by the fitness landscape. However, it would require testing all mutations in all
backgrounds, making the definition and analysis of fitness landscapes mostly inaccessible.
Instead of postulating a particular fitness landscape, we address this problem
by considering general classes of landscapes and calculating an upper limit for
the time it takes for a population to reach a fitness peak, circumventing the
need to have full knowledge about the fitness landscape. We analyze populations
in the weak-mutation regime and characterize the conditions that enable them to
quickly reach the fitness peak as a function of the number of sites under selection.
We show that for additive landscapes there is a critical selection strength enabling
populations to reach high-fitness genotypes, regardless of the distribution of
effects. This threshold scales with the number of sites under selection, effectively
setting a limit to adaptation, and results from the inevitable increase in deleterious
mutational pressure as the population adapts in a space of discrete genotypes.
Furthermore, we show that for the class of all unimodal landscapes this condition
is sufficient but not necessary for rapid adaptation, as in some highly epistatic
landscapes the critical strength does not depend on the number of sites under
selection; effectively removing this barrier to adaptation.
article_processing_charge: No
article_type: original
author:
- first_name: Jorge
full_name: Heredia, Jorge
last_name: Heredia
- first_name: Barbora
full_name: Trubenova, Barbora
id: 42302D54-F248-11E8-B48F-1D18A9856A87
last_name: Trubenova
orcid: 0000-0002-6873-2967
- first_name: Dirk
full_name: Sudholt, Dirk
last_name: Sudholt
- first_name: Tiago
full_name: Paixao, Tiago
id: 2C5658E6-F248-11E8-B48F-1D18A9856A87
last_name: Paixao
orcid: 0000-0003-2361-3953
citation:
ama: Heredia J, Trubenova B, Sudholt D, Paixao T. Selection limits to adaptive walks
on correlated landscapes. Genetics. 2017;205(2):803-825. doi:10.1534/genetics.116.189340
apa: Heredia, J., Trubenova, B., Sudholt, D., & Paixao, T. (2017). Selection
limits to adaptive walks on correlated landscapes. Genetics. Genetics Society
of America. https://doi.org/10.1534/genetics.116.189340
chicago: Heredia, Jorge, Barbora Trubenova, Dirk Sudholt, and Tiago Paixao. “Selection
Limits to Adaptive Walks on Correlated Landscapes.” Genetics. Genetics
Society of America, 2017. https://doi.org/10.1534/genetics.116.189340.
ieee: J. Heredia, B. Trubenova, D. Sudholt, and T. Paixao, “Selection limits to
adaptive walks on correlated landscapes,” Genetics, vol. 205, no. 2. Genetics
Society of America, pp. 803–825, 2017.
ista: Heredia J, Trubenova B, Sudholt D, Paixao T. 2017. Selection limits to adaptive
walks on correlated landscapes. Genetics. 205(2), 803–825.
mla: Heredia, Jorge, et al. “Selection Limits to Adaptive Walks on Correlated Landscapes.”
Genetics, vol. 205, no. 2, Genetics Society of America, 2017, pp. 803–25,
doi:10.1534/genetics.116.189340.
short: J. Heredia, B. Trubenova, D. Sudholt, T. Paixao, Genetics 205 (2017) 803–825.
date_created: 2018-12-11T11:50:12Z
date_published: 2017-02-01T00:00:00Z
date_updated: 2023-09-20T11:35:03Z
day: '01'
department:
- _id: NiBa
doi: 10.1534/genetics.116.189340
ec_funded: 1
external_id:
isi:
- '000394144900025'
pmid:
- '27881471'
intvolume: ' 205'
isi: 1
issue: '2'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.1534/genetics.116.189340
month: '02'
oa: 1
oa_version: Published Version
page: 803 - 825
pmid: 1
project:
- _id: 25B1EC9E-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '618091'
name: Speed of Adaptation in Population Genetics and Evolutionary Computation
publication: Genetics
publication_identifier:
issn:
- '00166731'
publication_status: published
publisher: Genetics Society of America
publist_id: '6256'
quality_controlled: '1'
scopus_import: '1'
status: public
title: Selection limits to adaptive walks on correlated landscapes
type: journal_article
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
volume: 205
year: '2017'
...
---
_id: '1112'
abstract:
- lang: eng
text: There has been renewed interest in modelling the behaviour of evolutionary
algorithms by more traditional mathematical objects, such as ordinary differential
equations or Markov chains. The advantage is that the analysis becomes greatly
facilitated due to the existence of well established methods. However, this typically
comes at the cost of disregarding information about the process. Here, we introduce
the use of stochastic differential equations (SDEs) for the study of EAs. SDEs
can produce simple analytical results for the dynamics of stochastic processes,
unlike Markov chains which can produce rigorous but unwieldy expressions about
the dynamics. On the other hand, unlike ordinary differential equations (ODEs),
they do not discard information about the stochasticity of the process. We show
that these are especially suitable for the analysis of fixed budget scenarios
and present analogs of the additive and multiplicative drift theorems for SDEs.
We exemplify the use of these methods for two model algorithms ((1+1) EA and RLS)
on two canonical problems(OneMax and LeadingOnes).
author:
- first_name: Tiago
full_name: Paixao, Tiago
id: 2C5658E6-F248-11E8-B48F-1D18A9856A87
last_name: Paixao
orcid: 0000-0003-2361-3953
- first_name: Jorge
full_name: Pérez Heredia, Jorge
last_name: Pérez Heredia
citation:
ama: 'Paixao T, Pérez Heredia J. An application of stochastic differential equations
to evolutionary algorithms. In: Proceedings of the 14th ACM/SIGEVO Conference
on Foundations of Genetic Algorithms. ACM; 2017:3-11. doi:10.1145/3040718.3040729'
apa: 'Paixao, T., & Pérez Heredia, J. (2017). An application of stochastic differential
equations to evolutionary algorithms. In Proceedings of the 14th ACM/SIGEVO
Conference on Foundations of Genetic Algorithms (pp. 3–11). Copenhagen, Denmark:
ACM. https://doi.org/10.1145/3040718.3040729'
chicago: Paixao, Tiago, and Jorge Pérez Heredia. “An Application of Stochastic Differential
Equations to Evolutionary Algorithms.” In Proceedings of the 14th ACM/SIGEVO
Conference on Foundations of Genetic Algorithms, 3–11. ACM, 2017. https://doi.org/10.1145/3040718.3040729.
ieee: T. Paixao and J. Pérez Heredia, “An application of stochastic differential
equations to evolutionary algorithms,” in Proceedings of the 14th ACM/SIGEVO
Conference on Foundations of Genetic Algorithms, Copenhagen, Denmark, 2017,
pp. 3–11.
ista: 'Paixao T, Pérez Heredia J. 2017. An application of stochastic differential
equations to evolutionary algorithms. Proceedings of the 14th ACM/SIGEVO Conference
on Foundations of Genetic Algorithms. FOGA: Foundations of Genetic Algorithms,
3–11.'
mla: Paixao, Tiago, and Jorge Pérez Heredia. “An Application of Stochastic Differential
Equations to Evolutionary Algorithms.” Proceedings of the 14th ACM/SIGEVO Conference
on Foundations of Genetic Algorithms, ACM, 2017, pp. 3–11, doi:10.1145/3040718.3040729.
short: T. Paixao, J. Pérez Heredia, in:, Proceedings of the 14th ACM/SIGEVO Conference
on Foundations of Genetic Algorithms, ACM, 2017, pp. 3–11.
conference:
end_date: 2017-01-15
location: Copenhagen, Denmark
name: 'FOGA: Foundations of Genetic Algorithms'
start_date: 2017-01-12
date_created: 2018-12-11T11:50:12Z
date_published: 2017-01-12T00:00:00Z
date_updated: 2021-01-12T06:48:22Z
day: '12'
department:
- _id: NiBa
doi: 10.1145/3040718.3040729
language:
- iso: eng
month: '01'
oa_version: None
page: 3 - 11
publication: Proceedings of the 14th ACM/SIGEVO Conference on Foundations of Genetic
Algorithms
publication_identifier:
isbn:
- 978-145034651-1
publication_status: published
publisher: ACM
publist_id: '6255'
quality_controlled: '1'
scopus_import: 1
status: public
title: An application of stochastic differential equations to evolutionary algorithms
type: conference
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
year: '2017'
...