---
_id: '1360'
abstract:
- lang: eng
text: 'We apply the technique of Károly Bezdek and Daniel Bezdek to study billiard
trajectories in convex bodies, when the length is measured with a (possibly asymmetric)
norm. We prove a lower bound for the length of the shortest closed billiard trajectory,
related to the non-symmetric Mahler problem. With this technique we are able to
give short and elementary proofs to some known results. '
acknowledgement: The first and third authors were supported by the Dynasty Foundation.
The first, second and third authors were supported by the Russian Foundation for
Basic Re- search grant 15-31-20403 (mol a ved).
article_processing_charge: No
author:
- first_name: Arseniy
full_name: Akopyan, Arseniy
id: 430D2C90-F248-11E8-B48F-1D18A9856A87
last_name: Akopyan
orcid: 0000-0002-2548-617X
- first_name: Alexey
full_name: Balitskiy, Alexey
last_name: Balitskiy
- first_name: Roman
full_name: Karasev, Roman
last_name: Karasev
- first_name: Anastasia
full_name: Sharipova, Anastasia
last_name: Sharipova
citation:
ama: Akopyan A, Balitskiy A, Karasev R, Sharipova A. Elementary approach to closed
billiard trajectories in asymmetric normed spaces. Proceedings of the American
Mathematical Society. 2016;144(10):4501-4513. doi:10.1090/proc/13062
apa: Akopyan, A., Balitskiy, A., Karasev, R., & Sharipova, A. (2016). Elementary
approach to closed billiard trajectories in asymmetric normed spaces. Proceedings
of the American Mathematical Society. American Mathematical Society. https://doi.org/10.1090/proc/13062
chicago: Akopyan, Arseniy, Alexey Balitskiy, Roman Karasev, and Anastasia Sharipova.
“Elementary Approach to Closed Billiard Trajectories in Asymmetric Normed Spaces.”
Proceedings of the American Mathematical Society. American Mathematical
Society, 2016. https://doi.org/10.1090/proc/13062.
ieee: A. Akopyan, A. Balitskiy, R. Karasev, and A. Sharipova, “Elementary approach
to closed billiard trajectories in asymmetric normed spaces,” Proceedings of
the American Mathematical Society, vol. 144, no. 10. American Mathematical
Society, pp. 4501–4513, 2016.
ista: Akopyan A, Balitskiy A, Karasev R, Sharipova A. 2016. Elementary approach
to closed billiard trajectories in asymmetric normed spaces. Proceedings of the
American Mathematical Society. 144(10), 4501–4513.
mla: Akopyan, Arseniy, et al. “Elementary Approach to Closed Billiard Trajectories
in Asymmetric Normed Spaces.” Proceedings of the American Mathematical Society,
vol. 144, no. 10, American Mathematical Society, 2016, pp. 4501–13, doi:10.1090/proc/13062.
short: A. Akopyan, A. Balitskiy, R. Karasev, A. Sharipova, Proceedings of the American
Mathematical Society 144 (2016) 4501–4513.
date_created: 2018-12-11T11:51:34Z
date_published: 2016-10-01T00:00:00Z
date_updated: 2021-01-12T06:50:09Z
day: '01'
department:
- _id: HeEd
doi: 10.1090/proc/13062
ec_funded: 1
intvolume: ' 144'
issue: '10'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/1401.0442
month: '10'
oa: 1
oa_version: Preprint
page: 4501 - 4513
project:
- _id: 25681D80-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '291734'
name: International IST Postdoc Fellowship Programme
publication: Proceedings of the American Mathematical Society
publication_status: published
publisher: American Mathematical Society
publist_id: '5885'
quality_controlled: '1'
scopus_import: 1
status: public
title: Elementary approach to closed billiard trajectories in asymmetric normed spaces
type: journal_article
user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87
volume: 144
year: '2016'
...
---
_id: '1372'
abstract:
- lang: eng
text: Redirection of intercellular auxin fluxes via relocalization of the PIN-FORMED
3 (PIN3) and PIN7 auxin efflux carriers has been suggested to be necessary for
the root gravitropic response. Cytokinins have also been proposed to play a role
in controlling root gravitropism, but conclusive evidence is lacking. We present
a detailed study of the dynamics of root bending early after gravistimulation,
which revealed a delayed gravitropic response in transgenic lines with depleted
endogenous cytokinins (Pro35S:AtCKX) and cytokinin signaling mutants. Pro35S:AtCKX
lines, as well as a cytokinin receptor mutant ahk3, showed aberrations in the
auxin response distribution in columella cells consistent with defects in the
auxin transport machinery. Using in vivo real-time imaging of PIN3-GFP and PIN7-GFP
in AtCKX3 overexpression and ahk3 backgrounds, we observed wild-type-like relocalization
of PIN proteins in the columella early after gravistimulation, with gravity-induced
relocalization of PIN7 faster than that of PIN3. Nonetheless, the cellular distribution
of PIN3 and PIN7 and expression of PIN7 and the auxin influx carrier AUX1 was
affected in AtCKX overexpression lines. Based on the retained cytokinin sensitivity
in pin3 pin4 pin7 mutant, we propose the AUX1-mediated auxin transport rather
than columella-located PIN proteins as a target of endogenous cytokinins in the
control of root gravitropism.
acknowledgement: 'Funded by Ministry of Education, Youth and Sports Czech Republic.
Grant Numbers: CEITEC 2020, LQ1601, LO1204, LH14104 and The European Research Council.
Grant Number: ERC-2011-StG-20101109-PSDP and The Czech Science Foundation. Grant
Numbers: GAP501/11/1150, GA13-40637S, GP14-30004P'
author:
- first_name: Markéta
full_name: Pernisová, Markéta
last_name: Pernisová
- first_name: Tomas
full_name: Prat, Tomas
id: 3DA3BFEE-F248-11E8-B48F-1D18A9856A87
last_name: Prat
- first_name: Peter
full_name: Grones, Peter
id: 399876EC-F248-11E8-B48F-1D18A9856A87
last_name: Grones
- first_name: Danka
full_name: Haruštiaková, Danka
last_name: Haruštiaková
- first_name: Martina
full_name: Matonohova, Martina
last_name: Matonohova
- first_name: Lukáš
full_name: Spíchal, Lukáš
last_name: Spíchal
- first_name: Tomasz
full_name: Nodzyński, Tomasz
last_name: Nodzyński
- first_name: Jirí
full_name: Friml, Jirí
id: 4159519E-F248-11E8-B48F-1D18A9856A87
last_name: Friml
orcid: 0000-0002-8302-7596
- first_name: Jan
full_name: Hejátko, Jan
last_name: Hejátko
citation:
ama: Pernisová M, Prat T, Grones P, et al. Cytokinins influence root gravitropism
via differential regulation of auxin transporter expression and localization in
Arabidopsis. New Phytologist. 2016;212(2):497-509. doi:10.1111/nph.14049
apa: Pernisová, M., Prat, T., Grones, P., Haruštiaková, D., Matonohova, M., Spíchal,
L., … Hejátko, J. (2016). Cytokinins influence root gravitropism via differential
regulation of auxin transporter expression and localization in Arabidopsis. New
Phytologist. Wiley-Blackwell. https://doi.org/10.1111/nph.14049
chicago: Pernisová, Markéta, Tomas Prat, Peter Grones, Danka Haruštiaková, Martina
Matonohova, Lukáš Spíchal, Tomasz Nodzyński, Jiří Friml, and Jan Hejátko. “Cytokinins
Influence Root Gravitropism via Differential Regulation of Auxin Transporter Expression
and Localization in Arabidopsis.” New Phytologist. Wiley-Blackwell, 2016.
https://doi.org/10.1111/nph.14049.
ieee: M. Pernisová et al., “Cytokinins influence root gravitropism via differential
regulation of auxin transporter expression and localization in Arabidopsis,” New
Phytologist, vol. 212, no. 2. Wiley-Blackwell, pp. 497–509, 2016.
ista: Pernisová M, Prat T, Grones P, Haruštiaková D, Matonohova M, Spíchal L, Nodzyński
T, Friml J, Hejátko J. 2016. Cytokinins influence root gravitropism via differential
regulation of auxin transporter expression and localization in Arabidopsis. New
Phytologist. 212(2), 497–509.
mla: Pernisová, Markéta, et al. “Cytokinins Influence Root Gravitropism via Differential
Regulation of Auxin Transporter Expression and Localization in Arabidopsis.” New
Phytologist, vol. 212, no. 2, Wiley-Blackwell, 2016, pp. 497–509, doi:10.1111/nph.14049.
short: M. Pernisová, T. Prat, P. Grones, D. Haruštiaková, M. Matonohova, L. Spíchal,
T. Nodzyński, J. Friml, J. Hejátko, New Phytologist 212 (2016) 497–509.
date_created: 2018-12-11T11:51:38Z
date_published: 2016-10-01T00:00:00Z
date_updated: 2021-01-12T06:50:13Z
day: '01'
ddc:
- '581'
department:
- _id: JiFr
doi: 10.1111/nph.14049
file:
- access_level: open_access
checksum: 27fd841ceaf0403559d7048ef51500f9
content_type: application/pdf
creator: system
date_created: 2018-12-12T10:14:53Z
date_updated: 2020-07-14T12:44:47Z
file_id: '5108'
file_name: IST-2018-1006-v1+1_Pernisova_NewPhytol_2016_peer_review.pdf
file_size: 972763
relation: main_file
file_date_updated: 2020-07-14T12:44:47Z
has_accepted_license: '1'
intvolume: ' 212'
issue: '2'
language:
- iso: eng
month: '10'
oa: 1
oa_version: Submitted Version
page: 497 - 509
publication: New Phytologist
publication_status: published
publisher: Wiley-Blackwell
publist_id: '5839'
pubrep_id: '1006'
quality_controlled: '1'
scopus_import: 1
status: public
title: Cytokinins influence root gravitropism via differential regulation of auxin
transporter expression and localization in Arabidopsis
type: journal_article
user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87
volume: 212
year: '2016'
...
---
_id: '1369'
abstract:
- lang: eng
text: 'We introduce a new loss function for the weakly-supervised training of semantic
image segmentation models based on three guiding principles: to seed with weak
localization cues, to expand objects based on the information about which classes
can occur in an image, and to constrain the segmentations to coincide with object
boundaries. We show experimentally that training a deep convolutional neural network
using the proposed loss function leads to substantially better segmentations than
previous state-of-the-art methods on the challenging PASCAL VOC 2012 dataset.
We furthermore give insight into the working mechanism of our method by a detailed
experimental study that illustrates how the segmentation quality is affected by
each term of the proposed loss function as well as their combinations.'
alternative_title:
- LNCS
author:
- first_name: Alexander
full_name: Kolesnikov, Alexander
id: 2D157DB6-F248-11E8-B48F-1D18A9856A87
last_name: Kolesnikov
- first_name: Christoph
full_name: Lampert, Christoph
id: 40C20FD2-F248-11E8-B48F-1D18A9856A87
last_name: Lampert
orcid: 0000-0001-8622-7887
citation:
ama: 'Kolesnikov A, Lampert C. Seed, expand and constrain: Three principles for
weakly-supervised image segmentation. In: Vol 9908. Springer; 2016:695-711. doi:10.1007/978-3-319-46493-0_42'
apa: 'Kolesnikov, A., & Lampert, C. (2016). Seed, expand and constrain: Three
principles for weakly-supervised image segmentation (Vol. 9908, pp. 695–711).
Presented at the ECCV: European Conference on Computer Vision, Amsterdam, The
Netherlands: Springer. https://doi.org/10.1007/978-3-319-46493-0_42'
chicago: 'Kolesnikov, Alexander, and Christoph Lampert. “Seed, Expand and Constrain:
Three Principles for Weakly-Supervised Image Segmentation,” 9908:695–711. Springer,
2016. https://doi.org/10.1007/978-3-319-46493-0_42.'
ieee: 'A. Kolesnikov and C. Lampert, “Seed, expand and constrain: Three principles
for weakly-supervised image segmentation,” presented at the ECCV: European Conference
on Computer Vision, Amsterdam, The Netherlands, 2016, vol. 9908, pp. 695–711.'
ista: 'Kolesnikov A, Lampert C. 2016. Seed, expand and constrain: Three principles
for weakly-supervised image segmentation. ECCV: European Conference on Computer
Vision, LNCS, vol. 9908, 695–711.'
mla: 'Kolesnikov, Alexander, and Christoph Lampert. Seed, Expand and Constrain:
Three Principles for Weakly-Supervised Image Segmentation. Vol. 9908, Springer,
2016, pp. 695–711, doi:10.1007/978-3-319-46493-0_42.'
short: A. Kolesnikov, C. Lampert, in:, Springer, 2016, pp. 695–711.
conference:
end_date: 2016-10-14
location: Amsterdam, The Netherlands
name: 'ECCV: European Conference on Computer Vision'
start_date: 2016-10-11
date_created: 2018-12-11T11:51:37Z
date_published: 2016-09-15T00:00:00Z
date_updated: 2021-01-12T06:50:12Z
day: '15'
department:
- _id: ChLa
doi: 10.1007/978-3-319-46493-0_42
ec_funded: 1
intvolume: ' 9908'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/1603.06098
month: '09'
oa: 1
oa_version: Preprint
page: 695 - 711
project:
- _id: 2532554C-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '308036'
name: Lifelong Learning of Visual Scene Understanding
publication_status: published
publisher: Springer
publist_id: '5842'
quality_controlled: '1'
scopus_import: 1
status: public
title: 'Seed, expand and constrain: Three principles for weakly-supervised image segmentation'
type: conference
user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87
volume: 9908
year: '2016'
...
---
_id: '1368'
abstract:
- lang: eng
text: Superconductivity in heavy-fermion systems has an unconventional nature and
is considered to originate from the universal features of the electronic structure.
Here, the Anderson lattice model is studied by means of the full variational Gutzwiller
wave function incorporating nonlocal effects of the on-site interaction. We show
that the d-wave superconducting ground state can be driven solely by interelectronic
correlations. The proposed microscopic mechanism leads to a multigap superconductivity
with the dominant contribution due to f electrons and in the dx2−y2-wave channel.
Our results rationalize several important observations for CeCoIn5.
acknowledgement: "The work has been supported by the National Science Center
\ (NCN) under the Grant MAESTRO, No.\r\nDEC-2012/04/A/ST3/00342. "
article_number: '024517'
author:
- first_name: Marcin
full_name: Wysokiński, Marcin
last_name: Wysokiński
- first_name: Jan
full_name: Kaczmarczyk, Jan
id: 46C405DE-F248-11E8-B48F-1D18A9856A87
last_name: Kaczmarczyk
orcid: 0000-0002-1629-3675
- first_name: Jozef
full_name: Spałek, Jozef
last_name: Spałek
citation:
ama: 'Wysokiński M, Kaczmarczyk J, Spałek J. Correlation driven d wave superconductivity
in Anderson lattice model: Two gaps. Physical Review B - Condensed Matter and
Materials Physics. 2016;94(2). doi:10.1103/PhysRevB.94.024517'
apa: 'Wysokiński, M., Kaczmarczyk, J., & Spałek, J. (2016). Correlation driven
d wave superconductivity in Anderson lattice model: Two gaps. Physical Review
B - Condensed Matter and Materials Physics. American Physical Society. https://doi.org/10.1103/PhysRevB.94.024517'
chicago: 'Wysokiński, Marcin, Jan Kaczmarczyk, and Jozef Spałek. “Correlation Driven
d Wave Superconductivity in Anderson Lattice Model: Two Gaps.” Physical Review
B - Condensed Matter and Materials Physics. American Physical Society, 2016.
https://doi.org/10.1103/PhysRevB.94.024517.'
ieee: 'M. Wysokiński, J. Kaczmarczyk, and J. Spałek, “Correlation driven d wave
superconductivity in Anderson lattice model: Two gaps,” Physical Review B -
Condensed Matter and Materials Physics, vol. 94, no. 2. American Physical
Society, 2016.'
ista: 'Wysokiński M, Kaczmarczyk J, Spałek J. 2016. Correlation driven d wave superconductivity
in Anderson lattice model: Two gaps. Physical Review B - Condensed Matter and
Materials Physics. 94(2), 024517.'
mla: 'Wysokiński, Marcin, et al. “Correlation Driven d Wave Superconductivity in
Anderson Lattice Model: Two Gaps.” Physical Review B - Condensed Matter and
Materials Physics, vol. 94, no. 2, 024517, American Physical Society, 2016,
doi:10.1103/PhysRevB.94.024517.'
short: M. Wysokiński, J. Kaczmarczyk, J. Spałek, Physical Review B - Condensed Matter
and Materials Physics 94 (2016).
date_created: 2018-12-11T11:51:37Z
date_published: 2016-07-01T00:00:00Z
date_updated: 2021-01-12T06:50:12Z
day: '01'
department:
- _id: MiLe
doi: 10.1103/PhysRevB.94.024517
ec_funded: 1
intvolume: ' 94'
issue: '2'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/1510.00224
month: '07'
oa: 1
oa_version: Preprint
project:
- _id: 25681D80-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '291734'
name: International IST Postdoc Fellowship Programme
publication: Physical Review B - Condensed Matter and Materials Physics
publication_status: published
publisher: American Physical Society
publist_id: '5844'
quality_controlled: '1'
scopus_import: 1
status: public
title: 'Correlation driven d wave superconductivity in Anderson lattice model: Two
gaps'
type: journal_article
user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87
volume: 94
year: '2016'
...
---
_id: '1370'
abstract:
- lang: eng
text: 'We study coherent phonon oscillations and tunneling between two coupled nonlinear
nanomechanical resonators. We show that the coupling between two nanomechanical
resonators creates an effective phonon Josephson junction, which exhibits two
different dynamical behaviors: Josephson oscillation (phonon-Rabi oscillation)
and macroscopic self-trapping (phonon blockade). Self-trapping originates from
mechanical nonlinearities, meaning that when the nonlinearity exceeds its critical
value, the energy exchange between the two resonators is suppressed, and phonon
Josephson oscillations between them are completely blocked. An effective classical
Hamiltonian for the phonon Josephson junction is derived and its mean-field dynamics
is studied in phase space. Finally, we study the phonon-phonon coherence quantified
by the mean fringe visibility, and show that the interaction between the two resonators
may lead to the loss of coherence in the phononic junction.'
acknowledgement: 'The work of S.B. has been supported by the European Commission (Belgium)
via the SCALEQIT program and by the Alexander von Humboldt Foundation. '
article_number: '033846'
author:
- first_name: Shabir
full_name: Barzanjeh, Shabir
id: 2D25E1F6-F248-11E8-B48F-1D18A9856A87
last_name: Barzanjeh
orcid: 0000-0003-0415-1423
- first_name: David
full_name: Vitali, David
last_name: Vitali
citation:
ama: Barzanjeh S, Vitali D. Phonon Josephson junction with nanomechanical resonators.
Physical Review A - Atomic, Molecular, and Optical Physics. 2016;93(3).
doi:10.1103/PhysRevA.93.033846
apa: Barzanjeh, S., & Vitali, D. (2016). Phonon Josephson junction with nanomechanical
resonators. Physical Review A - Atomic, Molecular, and Optical Physics.
American Physical Society. https://doi.org/10.1103/PhysRevA.93.033846
chicago: Barzanjeh, Shabir, and David Vitali. “Phonon Josephson Junction with Nanomechanical
Resonators.” Physical Review A - Atomic, Molecular, and Optical Physics.
American Physical Society, 2016. https://doi.org/10.1103/PhysRevA.93.033846.
ieee: S. Barzanjeh and D. Vitali, “Phonon Josephson junction with nanomechanical
resonators,” Physical Review A - Atomic, Molecular, and Optical Physics,
vol. 93, no. 3. American Physical Society, 2016.
ista: Barzanjeh S, Vitali D. 2016. Phonon Josephson junction with nanomechanical
resonators. Physical Review A - Atomic, Molecular, and Optical Physics. 93(3),
033846.
mla: Barzanjeh, Shabir, and David Vitali. “Phonon Josephson Junction with Nanomechanical
Resonators.” Physical Review A - Atomic, Molecular, and Optical Physics,
vol. 93, no. 3, 033846, American Physical Society, 2016, doi:10.1103/PhysRevA.93.033846.
short: S. Barzanjeh, D. Vitali, Physical Review A - Atomic, Molecular, and Optical
Physics 93 (2016).
date_created: 2018-12-11T11:51:38Z
date_published: 2016-03-28T00:00:00Z
date_updated: 2023-02-21T10:36:32Z
day: '28'
department:
- _id: JoFi
doi: 10.1103/PhysRevA.93.033846
intvolume: ' 93'
issue: '3'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: http://arxiv.org/abs/1601.01818
month: '03'
oa: 1
oa_version: Preprint
publication: Physical Review A - Atomic, Molecular, and Optical Physics
publication_status: published
publisher: American Physical Society
publist_id: '5841'
quality_controlled: '1'
scopus_import: 1
status: public
title: Phonon Josephson junction with nanomechanical resonators
type: journal_article
user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87
volume: 93
year: '2016'
...
---
_id: '1373'
article_processing_charge: No
author:
- first_name: Olivier
full_name: Martin, Olivier
last_name: Martin
- first_name: Marcin P
full_name: Zagórski, Marcin P
id: 343DA0DC-F248-11E8-B48F-1D18A9856A87
last_name: Zagórski
orcid: 0000-0001-7896-7762
citation:
ama: 'Martin O, Zagórski MP. Network architectures and operating principles. Reply
to comments on "Drivers of structural features in gene regulatory networks:
From biophysical constraints to biological function" Physics of Life
Reviews. 2016;17:168-171. doi:10.1016/j.plrev.2016.06.006'
apa: 'Martin, O., & Zagórski, M. P. (2016). Network architectures and operating
principles. Reply to comments on "Drivers of structural features in gene
regulatory networks: From biophysical constraints to biological function"
Physics of Life Reviews. Elsevier. https://doi.org/10.1016/j.plrev.2016.06.006'
chicago: 'Martin, Olivier, and Marcin P Zagórski. “Network Architectures and Operating
Principles. Reply to Comments on "Drivers of Structural Features in Gene
Regulatory Networks: From Biophysical Constraints to Biological Function"”
Physics of Life Reviews. Elsevier, 2016. https://doi.org/10.1016/j.plrev.2016.06.006.'
ieee: 'O. Martin and M. P. Zagórski, “Network architectures and operating principles.
Reply to comments on "Drivers of structural features in gene regulatory
networks: From biophysical constraints to biological function",” Physics
of Life Reviews, vol. 17. Elsevier, pp. 168–171, 2016.'
ista: 'Martin O, Zagórski MP. 2016. Network architectures and operating principles.
Reply to comments on "Drivers of structural features in gene regulatory
networks: From biophysical constraints to biological function" Physics
of Life Reviews. 17, 168–171.'
mla: 'Martin, Olivier, and Marcin P. Zagórski. “Network Architectures and Operating
Principles. Reply to Comments on "Drivers of Structural Features in Gene
Regulatory Networks: From Biophysical Constraints to Biological Function"”
Physics of Life Reviews, vol. 17, Elsevier, 2016, pp. 168–71, doi:10.1016/j.plrev.2016.06.006.'
short: O. Martin, M.P. Zagórski, Physics of Life Reviews 17 (2016) 168–171.
date_created: 2018-12-11T11:51:39Z
date_published: 2016-07-01T00:00:00Z
date_updated: 2022-08-26T09:39:27Z
day: '01'
department:
- _id: AnKi
doi: 10.1016/j.plrev.2016.06.006
intvolume: ' 17'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://hal.archives-ouvertes.fr/hal-01531698
month: '07'
oa: 1
oa_version: Preprint
page: 168 - 171
publication: Physics of Life Reviews
publication_status: published
publisher: Elsevier
publist_id: '5838'
quality_controlled: '1'
scopus_import: '1'
status: public
title: 'Network architectures and operating principles. Reply to comments on "Drivers
of structural features in gene regulatory networks: From biophysical constraints
to biological function"'
type: journal_article
user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87
volume: 17
year: '2016'
...
---
_id: '1377'
abstract:
- lang: eng
text: We consider the problem of minimizing the continuous valued total variation
subject to different unary terms on trees and propose fast direct algorithms based
on dynamic programming to solve these problems. We treat both the convex and the
nonconvex case and derive worst-case complexities that are equal to or better
than existing methods. We show applications to total variation based two dimensional
image processing and computer vision problems based on a Lagrangian decomposition
approach. The resulting algorithms are very effcient, offer a high degree of parallelism,
and come along with memory requirements which are only in the order of the number
of image pixels.
author:
- first_name: Vladimir
full_name: Kolmogorov, Vladimir
id: 3D50B0BA-F248-11E8-B48F-1D18A9856A87
last_name: Kolmogorov
- first_name: Thomas
full_name: Pock, Thomas
last_name: Pock
- first_name: Michal
full_name: Rolinek, Michal
id: 3CB3BC06-F248-11E8-B48F-1D18A9856A87
last_name: Rolinek
citation:
ama: Kolmogorov V, Pock T, Rolinek M. Total variation on a tree. SIAM Journal
on Imaging Sciences. 2016;9(2):605-636. doi:10.1137/15M1010257
apa: Kolmogorov, V., Pock, T., & Rolinek, M. (2016). Total variation on a tree.
SIAM Journal on Imaging Sciences. Society for Industrial and Applied Mathematics
. https://doi.org/10.1137/15M1010257
chicago: Kolmogorov, Vladimir, Thomas Pock, and Michal Rolinek. “Total Variation
on a Tree.” SIAM Journal on Imaging Sciences. Society for Industrial and
Applied Mathematics , 2016. https://doi.org/10.1137/15M1010257.
ieee: V. Kolmogorov, T. Pock, and M. Rolinek, “Total variation on a tree,” SIAM
Journal on Imaging Sciences, vol. 9, no. 2. Society for Industrial and Applied
Mathematics , pp. 605–636, 2016.
ista: Kolmogorov V, Pock T, Rolinek M. 2016. Total variation on a tree. SIAM Journal
on Imaging Sciences. 9(2), 605–636.
mla: Kolmogorov, Vladimir, et al. “Total Variation on a Tree.” SIAM Journal on
Imaging Sciences, vol. 9, no. 2, Society for Industrial and Applied Mathematics
, 2016, pp. 605–36, doi:10.1137/15M1010257.
short: V. Kolmogorov, T. Pock, M. Rolinek, SIAM Journal on Imaging Sciences 9 (2016)
605–636.
date_created: 2018-12-11T11:51:40Z
date_published: 2016-05-03T00:00:00Z
date_updated: 2021-01-12T06:50:15Z
day: '03'
department:
- _id: VlKo
doi: 10.1137/15M1010257
ec_funded: 1
intvolume: ' 9'
issue: '2'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: http://arxiv.org/abs/1502.07770
month: '05'
oa: 1
oa_version: Preprint
page: 605 - 636
project:
- _id: 25FBA906-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '616160'
name: 'Discrete Optimization in Computer Vision: Theory and Practice'
publication: SIAM Journal on Imaging Sciences
publication_status: published
publisher: 'Society for Industrial and Applied Mathematics '
publist_id: '5834'
quality_controlled: '1'
scopus_import: 1
status: public
title: Total variation on a tree
type: journal_article
user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87
volume: 9
year: '2016'
...
---
_id: '1381'
abstract:
- lang: eng
text: 'Motivated by Tverberg-type problems in topological combinatorics and by classical
results about embeddings (maps without double points), we study the question whether
a finite simplicial complex K can be mapped into double-struck Rd without higher-multiplicity
intersections. We focus on conditions for the existence of almost r-embeddings,
i.e., maps f : K → double-struck Rd such that f(σ1) ∩ ⋯ ∩ f(σr) = ∅ whenever σ1,
..., σr are pairwise disjoint simplices of K. Generalizing the classical Haefliger-Weber
embeddability criterion, we show that a well-known necessary deleted product condition
for the existence of almost r-embeddings is sufficient in a suitable r-metastable
range of dimensions: If rd ≥ (r + 1) dim K + 3, then there exists an almost r-embedding
K → double-struck Rd if and only if there exists an equivariant map (K)Δ r → Sr
Sd(r-1)-1, where (K)Δ r is the deleted r-fold product of K, the target Sd(r-1)-1
is the sphere of dimension d(r - 1) - 1, and Sr is the symmetric group. This significantly
extends one of the main results of our previous paper (which treated the special
case where d = rk and dim K = (r - 1)k for some k ≥ 3), and settles an open question
raised there.'
alternative_title:
- LIPIcs
author:
- first_name: Isaac
full_name: Mabillard, Isaac
id: 32BF9DAA-F248-11E8-B48F-1D18A9856A87
last_name: Mabillard
- first_name: Uli
full_name: Wagner, Uli
id: 36690CA2-F248-11E8-B48F-1D18A9856A87
last_name: Wagner
orcid: 0000-0002-1494-0568
citation:
ama: 'Mabillard I, Wagner U. Eliminating higher-multiplicity intersections, II.
The deleted product criterion in the r-metastable range. In: Vol 51. Schloss Dagstuhl-
Leibniz-Zentrum fur Informatik GmbH; 2016:51.1-51.12. doi:10.4230/LIPIcs.SoCG.2016.51'
apa: 'Mabillard, I., & Wagner, U. (2016). Eliminating higher-multiplicity intersections,
II. The deleted product criterion in the r-metastable range (Vol. 51, p. 51.1-51.12).
Presented at the SoCG: Symposium on Computational Geometry, Medford, MA, USA:
Schloss Dagstuhl- Leibniz-Zentrum fur Informatik GmbH. https://doi.org/10.4230/LIPIcs.SoCG.2016.51'
chicago: Mabillard, Isaac, and Uli Wagner. “Eliminating Higher-Multiplicity Intersections,
II. The Deleted Product Criterion in the r-Metastable Range,” 51:51.1-51.12. Schloss
Dagstuhl- Leibniz-Zentrum fur Informatik GmbH, 2016. https://doi.org/10.4230/LIPIcs.SoCG.2016.51.
ieee: 'I. Mabillard and U. Wagner, “Eliminating higher-multiplicity intersections,
II. The deleted product criterion in the r-metastable range,” presented at the
SoCG: Symposium on Computational Geometry, Medford, MA, USA, 2016, vol. 51, p.
51.1-51.12.'
ista: 'Mabillard I, Wagner U. 2016. Eliminating higher-multiplicity intersections,
II. The deleted product criterion in the r-metastable range. SoCG: Symposium on
Computational Geometry, LIPIcs, vol. 51, 51.1-51.12.'
mla: Mabillard, Isaac, and Uli Wagner. Eliminating Higher-Multiplicity Intersections,
II. The Deleted Product Criterion in the r-Metastable Range. Vol. 51, Schloss
Dagstuhl- Leibniz-Zentrum fur Informatik GmbH, 2016, p. 51.1-51.12, doi:10.4230/LIPIcs.SoCG.2016.51.
short: I. Mabillard, U. Wagner, in:, Schloss Dagstuhl- Leibniz-Zentrum fur Informatik
GmbH, 2016, p. 51.1-51.12.
conference:
end_date: 2016-06-17
location: Medford, MA, USA
name: 'SoCG: Symposium on Computational Geometry'
start_date: 2016-06-14
date_created: 2018-12-11T11:51:41Z
date_published: 2016-06-01T00:00:00Z
date_updated: 2021-01-12T06:50:17Z
day: '01'
ddc:
- '510'
department:
- _id: UlWa
doi: 10.4230/LIPIcs.SoCG.2016.51
file:
- access_level: open_access
checksum: 92c0c3735fe908f8ded6e484005cb3b1
content_type: application/pdf
creator: system
date_created: 2018-12-12T10:10:06Z
date_updated: 2020-07-14T12:44:47Z
file_id: '4791'
file_name: IST-2016-621-v1+1_LIPIcs-SoCG-2016-51.pdf
file_size: 622969
relation: main_file
file_date_updated: 2020-07-14T12:44:47Z
has_accepted_license: '1'
intvolume: ' 51'
language:
- iso: eng
month: '06'
oa: 1
oa_version: Published Version
page: 51.1 - 51.12
project:
- _id: 25FA3206-B435-11E9-9278-68D0E5697425
grant_number: PP00P2_138948
name: 'Embeddings in Higher Dimensions: Algorithms and Combinatorics'
publication_status: published
publisher: Schloss Dagstuhl- Leibniz-Zentrum fur Informatik GmbH
publist_id: '5830'
pubrep_id: '621'
quality_controlled: '1'
scopus_import: 1
status: public
title: Eliminating higher-multiplicity intersections, II. The deleted product criterion
in the r-metastable range
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: conference
user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87
volume: 51
year: '2016'
...
---
_id: '1380'
abstract:
- lang: eng
text: We consider higher-dimensional versions of Kannan and Lipton's Orbit Problem
- determining whether a target vector space V may be reached from a starting point
x under repeated applications of a linear transformation A. Answering two questions
posed by Kannan and Lipton in the 1980s, we show that when V has dimension one,
this problem is solvable in polynomial time, and when V has dimension two or three,
the problem is in NPRP.
article_number: '23'
author:
- first_name: Ventsislav K
full_name: Chonev, Ventsislav K
id: 36CBE2E6-F248-11E8-B48F-1D18A9856A87
last_name: Chonev
- first_name: Joël
full_name: Ouaknine, Joël
last_name: Ouaknine
- first_name: James
full_name: Worrell, James
last_name: Worrell
citation:
ama: Chonev VK, Ouaknine J, Worrell J. On the complexity of the orbit problem. Journal
of the ACM. 2016;63(3). doi:10.1145/2857050
apa: Chonev, V. K., Ouaknine, J., & Worrell, J. (2016). On the complexity of
the orbit problem. Journal of the ACM. ACM. https://doi.org/10.1145/2857050
chicago: Chonev, Ventsislav K, Joël Ouaknine, and James Worrell. “On the Complexity
of the Orbit Problem.” Journal of the ACM. ACM, 2016. https://doi.org/10.1145/2857050.
ieee: V. K. Chonev, J. Ouaknine, and J. Worrell, “On the complexity of the orbit
problem,” Journal of the ACM, vol. 63, no. 3. ACM, 2016.
ista: Chonev VK, Ouaknine J, Worrell J. 2016. On the complexity of the orbit problem.
Journal of the ACM. 63(3), 23.
mla: Chonev, Ventsislav K., et al. “On the Complexity of the Orbit Problem.” Journal
of the ACM, vol. 63, no. 3, 23, ACM, 2016, doi:10.1145/2857050.
short: V.K. Chonev, J. Ouaknine, J. Worrell, Journal of the ACM 63 (2016).
date_created: 2018-12-11T11:51:41Z
date_published: 2016-06-01T00:00:00Z
date_updated: 2021-01-12T06:50:17Z
day: '01'
department:
- _id: KrCh
doi: 10.1145/2857050
intvolume: ' 63'
issue: '3'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: http://arxiv.org/abs/1303.2981
month: '06'
oa: 1
oa_version: Preprint
publication: Journal of the ACM
publication_status: published
publisher: ACM
publist_id: '5831'
quality_controlled: '1'
scopus_import: 1
status: public
title: On the complexity of the orbit problem
type: journal_article
user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87
volume: 63
year: '2016'
...
---
_id: '1389'
abstract:
- lang: eng
text: "The continuous evolution of a wide variety of systems, including continous-time
Markov chains and linear hybrid automata, can be\r\ndescribed in terms of linear
differential equations. In this paper we study the decision problem of whether
the solution x(t) of a system of linear differential equations dx/dt = Ax reaches
a target halfspace infinitely often. This recurrent reachability problem can\r\nequivalently
be formulated as the following Infinite Zeros Problem: does a real-valued function
f:R≥0 --> R satisfying a given linear\r\ndifferential equation have infinitely
many zeros? Our main decidability result is that if the differential equation
has order at most 7, then the Infinite Zeros Problem is decidable. On the other
hand, we show that a decision procedure for the Infinite Zeros Problem at order
9 (and above) would entail a major breakthrough in Diophantine Approximation,
specifically an algorithm for computing the Lagrange constants of arbitrary real
algebraic numbers to arbitrary precision."
author:
- first_name: Ventsislav K
full_name: Chonev, Ventsislav K
id: 36CBE2E6-F248-11E8-B48F-1D18A9856A87
last_name: Chonev
- first_name: Joël
full_name: Ouaknine, Joël
last_name: Ouaknine
- first_name: James
full_name: Worrell, James
last_name: Worrell
citation:
ama: 'Chonev VK, Ouaknine J, Worrell J. On recurrent reachability for continuous
linear dynamical systems. In: LICS ’16. IEEE; 2016:515-524. doi:10.1145/2933575.2934548'
apa: 'Chonev, V. K., Ouaknine, J., & Worrell, J. (2016). On recurrent reachability
for continuous linear dynamical systems. In LICS ’16 (pp. 515–524). New
York, NY, USA: IEEE. https://doi.org/10.1145/2933575.2934548'
chicago: Chonev, Ventsislav K, Joël Ouaknine, and James Worrell. “On Recurrent Reachability
for Continuous Linear Dynamical Systems.” In LICS ’16, 515–24. IEEE, 2016.
https://doi.org/10.1145/2933575.2934548.
ieee: V. K. Chonev, J. Ouaknine, and J. Worrell, “On recurrent reachability for
continuous linear dynamical systems,” in LICS ’16, New York, NY, USA, 2016,
pp. 515–524.
ista: 'Chonev VK, Ouaknine J, Worrell J. 2016. On recurrent reachability for continuous
linear dynamical systems. LICS ’16. LICS: Logic in Computer Science, 515–524.'
mla: Chonev, Ventsislav K., et al. “On Recurrent Reachability for Continuous Linear
Dynamical Systems.” LICS ’16, IEEE, 2016, pp. 515–24, doi:10.1145/2933575.2934548.
short: V.K. Chonev, J. Ouaknine, J. Worrell, in:, LICS ’16, IEEE, 2016, pp. 515–524.
conference:
end_date: 2018-07-08
location: New York, NY, USA
name: 'LICS: Logic in Computer Science'
start_date: 2018-07-05
date_created: 2018-12-11T11:51:44Z
date_published: 2016-07-05T00:00:00Z
date_updated: 2021-01-12T06:50:20Z
day: '05'
department:
- _id: KrCh
doi: 10.1145/2933575.2934548
ec_funded: 1
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/1507.03632
month: '07'
oa: 1
oa_version: Preprint
page: 515 - 524
project:
- _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
- _id: 25EE3708-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '267989'
name: Quantitative Reactive Modeling
publication: LICS '16
publication_status: published
publisher: IEEE
publist_id: '5820'
quality_controlled: '1'
scopus_import: 1
status: public
title: On recurrent reachability for continuous linear dynamical systems
type: conference
user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87
year: '2016'
...
---
_id: '1394'
abstract:
- lang: eng
text: "The solution space of genome-scale models of cellular metabolism provides
a map between physically\r\nviable flux configurations and cellular metabolic
phenotypes described, at the most basic level, by the\r\ncorresponding growth
rates. By sampling the solution space of E. coliʼs metabolic network, we show\r\nthat
empirical growth rate distributions recently obtained in experiments at single-cell
resolution can\r\nbe explained in terms of a trade-off between the higher fitness
of fast-growing phenotypes and the\r\nhigher entropy of slow-growing ones. Based
on this, we propose a minimal model for the evolution of\r\na large bacterial
population that captures this trade-off. The scaling relationships observed in\r\nexperiments
encode, in such frameworks, for the same distance from the maximum achievable
growth\r\nrate, the same degree of growth rate maximization, and/or the same rate
of phenotypic change. Being\r\ngrounded on genome-scale metabolic network reconstructions,
these results allow for multiple\r\nimplications and extensions in spite of the
underlying conceptual simplicity."
acknowledgement: "The research leading to these results has received funding from
the from the Marie\r\nCurie Action ITN NETADIS, grant agreement no. 290038."
article_number: '036005'
author:
- first_name: Daniele
full_name: De Martino, Daniele
id: 3FF5848A-F248-11E8-B48F-1D18A9856A87
last_name: De Martino
orcid: 0000-0002-5214-4706
- first_name: Fabrizio
full_name: Capuani, Fabrizio
last_name: Capuani
- first_name: Andrea
full_name: De Martino, Andrea
last_name: De Martino
citation:
ama: 'De Martino D, Capuani F, De Martino A. Growth against entropy in bacterial
metabolism: the phenotypic trade-off behind empirical growth rate distributions
in E. coli. Physical Biology. 2016;13(3). doi:10.1088/1478-3975/13/3/036005'
apa: 'De Martino, D., Capuani, F., & De Martino, A. (2016). Growth against entropy
in bacterial metabolism: the phenotypic trade-off behind empirical growth rate
distributions in E. coli. Physical Biology. IOP Publishing Ltd. https://doi.org/10.1088/1478-3975/13/3/036005'
chicago: 'De Martino, Daniele, Fabrizio Capuani, and Andrea De Martino. “Growth
against Entropy in Bacterial Metabolism: The Phenotypic Trade-off behind Empirical
Growth Rate Distributions in E. Coli.” Physical Biology. IOP Publishing
Ltd., 2016. https://doi.org/10.1088/1478-3975/13/3/036005.'
ieee: 'D. De Martino, F. Capuani, and A. De Martino, “Growth against entropy in
bacterial metabolism: the phenotypic trade-off behind empirical growth rate distributions
in E. coli,” Physical Biology, vol. 13, no. 3. IOP Publishing Ltd., 2016.'
ista: 'De Martino D, Capuani F, De Martino A. 2016. Growth against entropy in bacterial
metabolism: the phenotypic trade-off behind empirical growth rate distributions
in E. coli. Physical Biology. 13(3), 036005.'
mla: 'De Martino, Daniele, et al. “Growth against Entropy in Bacterial Metabolism:
The Phenotypic Trade-off behind Empirical Growth Rate Distributions in E. Coli.”
Physical Biology, vol. 13, no. 3, 036005, IOP Publishing Ltd., 2016, doi:10.1088/1478-3975/13/3/036005.'
short: D. De Martino, F. Capuani, A. De Martino, Physical Biology 13 (2016).
date_created: 2018-12-11T11:51:46Z
date_published: 2016-05-27T00:00:00Z
date_updated: 2021-01-12T06:50:23Z
day: '27'
department:
- _id: GaTk
doi: 10.1088/1478-3975/13/3/036005
ec_funded: 1
intvolume: ' 13'
issue: '3'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/1601.03243
month: '05'
oa: 1
oa_version: Preprint
project:
- _id: 25681D80-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '291734'
name: International IST Postdoc Fellowship Programme
publication: Physical Biology
publication_status: published
publisher: IOP Publishing Ltd.
publist_id: '5815'
quality_controlled: '1'
scopus_import: 1
status: public
title: 'Growth against entropy in bacterial metabolism: the phenotypic trade-off behind
empirical growth rate distributions in E. coli'
type: journal_article
user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87
volume: 13
year: '2016'
...
---
_id: '1412'
abstract:
- lang: eng
text: Combining high-resolution level set surface tracking with lower resolution
physics is an inexpensive method for achieving highly detailed liquid animations.
Unfortunately, the inherent resolution mismatch introduces several types of disturbing
visual artifacts. We identify the primary sources of these artifacts and present
simple, efficient, and practical solutions to address them. First, we propose
an unconditionally stable filtering method that selectively removes sub-grid surface
artifacts not seen by the fluid physics, while preserving fine detail in dynamic
splashing regions. It provides comparable results to recent error-correction techniques
at lower cost, without substepping, and with better scaling behavior. Second,
we show how a modified narrow-band scheme can ensure accurate free surface boundary
conditions in the presence of large resolution mismatches. Our scheme preserves
the efficiency of the narrow-band methodology, while eliminating objectionable
stairstep artifacts observed in prior work. Third, we demonstrate that the use
of linear interpolation of velocity during advection of the high-resolution level
set surface is responsible for visible grid-aligned kinks; we therefore advocate
higher-order velocity interpolation, and show that it dramatically reduces this
artifact. While these three contributions are orthogonal, our results demonstrate
that taken together they efficiently address the dominant sources of visual artifacts
arising with high-resolution embedded liquid surfaces; the proposed approach offers
improved visual quality, a straightforward implementation, and substantially greater
scalability than competing methods.
acknowledgement: 'This research was supported by NSERC (RGPIN-04360-2014) and IST
Austria. '
author:
- first_name: Ryan
full_name: Goldade, Ryan
last_name: Goldade
- first_name: Christopher
full_name: Batty, Christopher
last_name: Batty
- first_name: Christopher J
full_name: Wojtan, Christopher J
id: 3C61F1D2-F248-11E8-B48F-1D18A9856A87
last_name: Wojtan
orcid: 0000-0001-6646-5546
citation:
ama: Goldade R, Batty C, Wojtan C. A practical method for high-resolution embedded
liquid surfaces. Computer Graphics Forum. 2016;35(2):233-242. doi:10.1111/cgf.12826
apa: Goldade, R., Batty, C., & Wojtan, C. (2016). A practical method for high-resolution
embedded liquid surfaces. Computer Graphics Forum. Wiley-Blackwell. https://doi.org/10.1111/cgf.12826
chicago: Goldade, Ryan, Christopher Batty, and Chris Wojtan. “A Practical Method
for High-Resolution Embedded Liquid Surfaces.” Computer Graphics Forum.
Wiley-Blackwell, 2016. https://doi.org/10.1111/cgf.12826.
ieee: R. Goldade, C. Batty, and C. Wojtan, “A practical method for high-resolution
embedded liquid surfaces,” Computer Graphics Forum, vol. 35, no. 2. Wiley-Blackwell,
pp. 233–242, 2016.
ista: Goldade R, Batty C, Wojtan C. 2016. A practical method for high-resolution
embedded liquid surfaces. Computer Graphics Forum. 35(2), 233–242.
mla: Goldade, Ryan, et al. “A Practical Method for High-Resolution Embedded Liquid
Surfaces.” Computer Graphics Forum, vol. 35, no. 2, Wiley-Blackwell, 2016,
pp. 233–42, doi:10.1111/cgf.12826.
short: R. Goldade, C. Batty, C. Wojtan, Computer Graphics Forum 35 (2016) 233–242.
date_created: 2018-12-11T11:51:52Z
date_published: 2016-05-27T00:00:00Z
date_updated: 2023-02-21T10:38:30Z
day: '27'
ddc:
- '000'
department:
- _id: ChWo
doi: 10.1111/cgf.12826
ec_funded: 1
file:
- access_level: open_access
checksum: 8e61387ee2e3bd0e776fbe301629bfd9
content_type: application/pdf
creator: system
date_created: 2018-12-12T10:13:18Z
date_updated: 2020-07-14T12:44:53Z
file_id: '5000'
file_name: IST-2016-612-v1+2_Wojtan_APracticalMethod_PostPrint_2016.pdf
file_size: 15873858
relation: main_file
file_date_updated: 2020-07-14T12:44:53Z
has_accepted_license: '1'
intvolume: ' 35'
issue: '2'
language:
- iso: eng
month: '05'
oa: 1
oa_version: Submitted Version
page: 233 - 242
project:
- _id: 2533E772-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '638176'
name: Efficient Simulation of Natural Phenomena at Extremely Large Scales
publication: Computer Graphics Forum
publication_status: published
publisher: Wiley-Blackwell
publist_id: '5795'
pubrep_id: '612'
quality_controlled: '1'
scopus_import: 1
status: public
title: A practical method for high-resolution embedded liquid surfaces
type: journal_article
user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87
volume: 35
year: '2016'
...
---
_id: '1410'
abstract:
- lang: eng
text: The pollen grains arise after meiosis of pollen mother cells within the anthers.
A series of complex structural changes follows, generating mature pollen grains
capable of performing the double fertilization of the female megasporophyte. Several
signaling molecules, including hormones and lipids, have been involved in the
regulation and appropriate control of pollen development. Phosphatidylinositol
4-phophate 5-kinases (PIP5K), which catalyze the biosynthesis of the phosphoinositide
PtdIns(4,5)P2, are important for tip polar growth of root hairs and pollen tubes,
embryo development, vegetative plant growth, and responses to the environment.
Here, we report a role of PIP5Ks during microgametogenesis. PIP5K1 and PIP5K2
are expressed during early stages of pollen development and their transcriptional
activity respond to auxin in pollen grains. Early male gametophytic lethality
to certain grade was observed in both pip5k1-/- and pip5k2-/- single mutants.
The number of pip5k mutant alleles is directly related to the frequency of aborted
pollen grains suggesting the two genes are involved in the same function. Indeed
PIP5K1 and PIP5K2 are functionally redundant since homozygous double mutants did
not render viable pollen grains. The loss of function of PIP5K1 and PIP5K2results
in defects in vacuole morphology in pollen at the later stages and epidermal root
cells. Our results show that PIP5K1, PIP5K2 and phosphoinositide signaling are
important cues for early developmental stages and vacuole formation during microgametogenesis.
acknowledgement: the Odysseus Program of the Research Foundation-Flanders [G091608]
to JF.
author:
- first_name: José
full_name: Ugalde, José
last_name: Ugalde
- first_name: Cecilia
full_name: Rodríguez Furlán, Cecilia
last_name: Rodríguez Furlán
- first_name: Riet
full_name: De Rycke, Riet
last_name: De Rycke
- first_name: Lorena
full_name: Norambuena, Lorena
last_name: Norambuena
- first_name: Jirí
full_name: Friml, Jirí
id: 4159519E-F248-11E8-B48F-1D18A9856A87
last_name: Friml
orcid: 0000-0002-8302-7596
- first_name: Gabriel
full_name: León, Gabriel
last_name: León
- first_name: Ricardo
full_name: Tejos, Ricardo
last_name: Tejos
citation:
ama: Ugalde J, Rodríguez Furlán C, De Rycke R, et al. Phosphatidylinositol 4-phosphate
5-kinases 1 and 2 are involved in the regulation of vacuole morphology during
Arabidopsis thaliana pollen development. Plant Science. 2016;250:10-19.
doi:10.1016/j.plantsci.2016.05.014
apa: Ugalde, J., Rodríguez Furlán, C., De Rycke, R., Norambuena, L., Friml, J.,
León, G., & Tejos, R. (2016). Phosphatidylinositol 4-phosphate 5-kinases 1
and 2 are involved in the regulation of vacuole morphology during Arabidopsis
thaliana pollen development. Plant Science. Elsevier. https://doi.org/10.1016/j.plantsci.2016.05.014
chicago: Ugalde, José, Cecilia Rodríguez Furlán, Riet De Rycke, Lorena Norambuena,
Jiří Friml, Gabriel León, and Ricardo Tejos. “Phosphatidylinositol 4-Phosphate
5-Kinases 1 and 2 Are Involved in the Regulation of Vacuole Morphology during
Arabidopsis Thaliana Pollen Development.” Plant Science. Elsevier, 2016.
https://doi.org/10.1016/j.plantsci.2016.05.014.
ieee: J. Ugalde et al., “Phosphatidylinositol 4-phosphate 5-kinases 1 and
2 are involved in the regulation of vacuole morphology during Arabidopsis thaliana
pollen development,” Plant Science, vol. 250. Elsevier, pp. 10–19, 2016.
ista: Ugalde J, Rodríguez Furlán C, De Rycke R, Norambuena L, Friml J, León G, Tejos
R. 2016. Phosphatidylinositol 4-phosphate 5-kinases 1 and 2 are involved in the
regulation of vacuole morphology during Arabidopsis thaliana pollen development.
Plant Science. 250, 10–19.
mla: Ugalde, José, et al. “Phosphatidylinositol 4-Phosphate 5-Kinases 1 and 2 Are
Involved in the Regulation of Vacuole Morphology during Arabidopsis Thaliana Pollen
Development.” Plant Science, vol. 250, Elsevier, 2016, pp. 10–19, doi:10.1016/j.plantsci.2016.05.014.
short: J. Ugalde, C. Rodríguez Furlán, R. De Rycke, L. Norambuena, J. Friml, G.
León, R. Tejos, Plant Science 250 (2016) 10–19.
date_created: 2018-12-11T11:51:51Z
date_published: 2016-09-01T00:00:00Z
date_updated: 2021-01-12T06:50:33Z
day: '01'
ddc:
- '581'
department:
- _id: JiFr
doi: 10.1016/j.plantsci.2016.05.014
external_id:
pmid:
- '27457979'
file:
- access_level: open_access
checksum: ca08de036e6ddc81e6f760e0ccdebd3f
content_type: application/pdf
creator: dernst
date_created: 2019-04-17T07:41:57Z
date_updated: 2020-07-14T12:44:53Z
file_id: '6331'
file_name: 2016_PlantScience_Ugalde.pdf
file_size: 4338545
relation: main_file
file_date_updated: 2020-07-14T12:44:53Z
has_accepted_license: '1'
intvolume: ' 250'
language:
- iso: eng
month: '09'
oa: 1
oa_version: Submitted Version
page: 10 - 19
pmid: 1
publication: Plant Science
publication_status: published
publisher: Elsevier
publist_id: '5797'
pubrep_id: '1005'
quality_controlled: '1'
scopus_import: 1
status: public
title: Phosphatidylinositol 4-phosphate 5-kinases 1 and 2 are involved in the regulation
of vacuole morphology during Arabidopsis thaliana pollen development
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 250
year: '2016'
...
---
_id: '1409'
author:
- first_name: Richard
full_name: Abbott, Richard
last_name: Abbott
- first_name: Nicholas H
full_name: Barton, Nicholas H
id: 4880FE40-F248-11E8-B48F-1D18A9856A87
last_name: Barton
orcid: 0000-0002-8548-5240
- first_name: Jeffrey
full_name: Good, Jeffrey
last_name: Good
citation:
ama: Abbott R, Barton NH, Good J. Genomics of hybridization and its evolutionary
consequences. Molecular Ecology. 2016;25(11):2325-2332. doi:10.1111/mec.13685
apa: Abbott, R., Barton, N. H., & Good, J. (2016). Genomics of hybridization
and its evolutionary consequences. Molecular Ecology. Wiley-Blackwell.
https://doi.org/10.1111/mec.13685
chicago: Abbott, Richard, Nicholas H Barton, and Jeffrey Good. “Genomics of Hybridization
and Its Evolutionary Consequences.” Molecular Ecology. Wiley-Blackwell,
2016. https://doi.org/10.1111/mec.13685.
ieee: R. Abbott, N. H. Barton, and J. Good, “Genomics of hybridization and its evolutionary
consequences,” Molecular Ecology, vol. 25, no. 11. Wiley-Blackwell, pp.
2325–2332, 2016.
ista: Abbott R, Barton NH, Good J. 2016. Genomics of hybridization and its evolutionary
consequences. Molecular Ecology. 25(11), 2325–2332.
mla: Abbott, Richard, et al. “Genomics of Hybridization and Its Evolutionary Consequences.”
Molecular Ecology, vol. 25, no. 11, Wiley-Blackwell, 2016, pp. 2325–32,
doi:10.1111/mec.13685.
short: R. Abbott, N.H. Barton, J. Good, Molecular Ecology 25 (2016) 2325–2332.
date_created: 2018-12-11T11:51:51Z
date_published: 2016-06-08T00:00:00Z
date_updated: 2021-01-12T06:50:33Z
day: '08'
ddc:
- '576'
department:
- _id: NiBa
doi: 10.1111/mec.13685
file:
- access_level: open_access
checksum: ede7d0b8a471754f71f17e2b20f3135b
content_type: application/pdf
creator: system
date_created: 2018-12-12T10:10:12Z
date_updated: 2020-07-14T12:44:53Z
file_id: '4797'
file_name: IST-2017-772-v1+1_AbbotEtAl2016-3.pdf
file_size: 226137
relation: main_file
file_date_updated: 2020-07-14T12:44:53Z
has_accepted_license: '1'
intvolume: ' 25'
issue: '11'
language:
- iso: eng
month: '06'
oa: 1
oa_version: Submitted Version
page: 2325 - 2332
publication: Molecular Ecology
publication_status: published
publisher: Wiley-Blackwell
publist_id: '5798'
pubrep_id: '772'
quality_controlled: '1'
scopus_import: 1
status: public
title: Genomics of hybridization and its evolutionary consequences
type: journal_article
user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87
volume: 25
year: '2016'
...
---
_id: '1417'
abstract:
- lang: eng
text: Plant development mediated by the phytohormone auxin depends on tightly controlled
cellular auxin levels at its target tissue that are largely established by intercellular
and intracellular auxin transport mediated by PIN auxin transporters. Among the
eight members of the Arabidopsis PIN family, PIN6 is the least characterized candidate.
In this study we generated functional, fluorescent protein-tagged PIN6 proteins
and performed comprehensive analysis of their subcellular localization and also
performed a detailed functional characterization of PIN6 and its developmental
roles. The localization study of PIN6 revealed a dual localization at the plasma
membrane (PM) and endoplasmic reticulum (ER). Transport and metabolic profiling
assays in cultured cells and Arabidopsis strongly suggest that PIN6 mediates both
auxin transport across the PM and intracellular auxin homeostasis, including the
regulation of free auxin and auxin conjugates levels. As evidenced by the loss-
and gain-of-function analysis, the complex function of PIN6 in auxin transport
and homeostasis is required for auxin distribution during lateral and adventitious
root organogenesis and for progression of these developmental processes. These
results illustrate a unique position of PIN6 within the family of PIN auxin transporters
and further add complexity to the developmentally crucial process of auxin transport.
acknowledgement: This work was supported by the European Research Council (project
ERC-2011-StG-20101109-PSDP, project CEITEC (CZ.1.05/1.1.00/02.0068) and the Czech
Science Foundation GACR (project no. 13-4063 7S to J.F.)
author:
- first_name: Sibu
full_name: Simon, Sibu
id: 4542EF9A-F248-11E8-B48F-1D18A9856A87
last_name: Simon
orcid: 0000-0002-1998-6741
- first_name: Petr
full_name: Skůpa, Petr
last_name: Skůpa
- first_name: Tom
full_name: Viaene, Tom
last_name: Viaene
- first_name: Marta
full_name: Zwiewka, Marta
last_name: Zwiewka
- first_name: Ricardo
full_name: Tejos, Ricardo
last_name: Tejos
- first_name: Petr
full_name: Klíma, Petr
last_name: Klíma
- first_name: Mária
full_name: Čarná, Mária
last_name: Čarná
- first_name: Jakub
full_name: Rolčík, Jakub
last_name: Rolčík
- first_name: Riet
full_name: De Rycke, Riet
last_name: De Rycke
- first_name: Ignacio
full_name: Moreno, Ignacio
last_name: Moreno
- first_name: Petre
full_name: Dobrev, Petre
last_name: Dobrev
- first_name: Ariel
full_name: Orellana, Ariel
last_name: Orellana
- 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
citation:
ama: Simon S, Skůpa P, Viaene T, et al. PIN6 auxin transporter at endoplasmic reticulum
and plasma membrane mediates auxin homeostasis and organogenesis in Arabidopsis.
New Phytologist. 2016;211(1):65-74. doi:10.1111/nph.14019
apa: Simon, S., Skůpa, P., Viaene, T., Zwiewka, M., Tejos, R., Klíma, P., … Friml,
J. (2016). PIN6 auxin transporter at endoplasmic reticulum and plasma membrane
mediates auxin homeostasis and organogenesis in Arabidopsis. New Phytologist.
Wiley-Blackwell. https://doi.org/10.1111/nph.14019
chicago: Simon, Sibu, Petr Skůpa, Tom Viaene, Marta Zwiewka, Ricardo Tejos, Petr
Klíma, Mária Čarná, et al. “PIN6 Auxin Transporter at Endoplasmic Reticulum and
Plasma Membrane Mediates Auxin Homeostasis and Organogenesis in Arabidopsis.”
New Phytologist. Wiley-Blackwell, 2016. https://doi.org/10.1111/nph.14019.
ieee: S. Simon et al., “PIN6 auxin transporter at endoplasmic reticulum and
plasma membrane mediates auxin homeostasis and organogenesis in Arabidopsis,”
New Phytologist, vol. 211, no. 1. Wiley-Blackwell, pp. 65–74, 2016.
ista: Simon S, Skůpa P, Viaene T, Zwiewka M, Tejos R, Klíma P, Čarná M, Rolčík J,
De Rycke R, Moreno I, Dobrev P, Orellana A, Zažímalová E, Friml J. 2016. PIN6
auxin transporter at endoplasmic reticulum and plasma membrane mediates auxin
homeostasis and organogenesis in Arabidopsis. New Phytologist. 211(1), 65–74.
mla: Simon, Sibu, et al. “PIN6 Auxin Transporter at Endoplasmic Reticulum and Plasma
Membrane Mediates Auxin Homeostasis and Organogenesis in Arabidopsis.” New
Phytologist, vol. 211, no. 1, Wiley-Blackwell, 2016, pp. 65–74, doi:10.1111/nph.14019.
short: S. Simon, P. Skůpa, T. Viaene, M. Zwiewka, R. Tejos, P. Klíma, M. Čarná,
J. Rolčík, R. De Rycke, I. Moreno, P. Dobrev, A. Orellana, E. Zažímalová, J. Friml,
New Phytologist 211 (2016) 65–74.
date_created: 2018-12-11T11:51:54Z
date_published: 2016-07-01T00:00:00Z
date_updated: 2021-01-12T06:50:36Z
day: '01'
ddc:
- '581'
department:
- _id: JiFr
doi: 10.1111/nph.14019
file:
- access_level: open_access
checksum: 23522ced3508ffe7a4f247c4230e6493
content_type: application/pdf
creator: system
date_created: 2018-12-12T10:13:32Z
date_updated: 2020-07-14T12:44:53Z
file_id: '5016'
file_name: IST-2018-1004-v1+1_Simon_NewPhytol_2016_proof.pdf
file_size: 3828383
relation: main_file
file_date_updated: 2020-07-14T12:44:53Z
has_accepted_license: '1'
intvolume: ' 211'
issue: '1'
language:
- iso: eng
month: '07'
oa: 1
oa_version: Submitted Version
page: 65 - 74
publication: New Phytologist
publication_status: published
publisher: Wiley-Blackwell
publist_id: '5790'
pubrep_id: '1004'
quality_controlled: '1'
scopus_import: 1
status: public
title: PIN6 auxin transporter at endoplasmic reticulum and plasma membrane mediates
auxin homeostasis and organogenesis in Arabidopsis
type: journal_article
user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87
volume: 211
year: '2016'
...
---
_id: '1415'
abstract:
- lang: eng
text: The Fluid Implicit Particle method (FLIP) for liquid simulations uses particles
to reduce numerical dissipation and provide important visual cues for events like
complex splashes and small-scale features near the liquid surface. Unfortunately,
FLIP simulations can be computationally expensive, because they require a dense
sampling of particles to fill the entire liquid volume. Furthermore, the vast
majority of these FLIP particles contribute nothing to the fluid's visual appearance,
especially for larger volumes of liquid. We present a method that only uses FLIP
particles within a narrow band of the liquid surface, while efficiently representing
the remaining inner volume on a regular grid. We show that a naïve realization
of this idea introduces unstable and uncontrollable energy fluctuations, and we
propose a novel coupling scheme between FLIP particles and regular grid which
overcomes this problem. Our method drastically reduces the particle count and
simulation times while yielding results that are nearly indistinguishable from
regular FLIP simulations. Our approach is easy to integrate into any existing
FLIP implementation.
author:
- first_name: Florian
full_name: Ferstl, Florian
last_name: Ferstl
- first_name: Ryoichi
full_name: Ando, Ryoichi
last_name: Ando
- first_name: Christopher J
full_name: Wojtan, Christopher J
id: 3C61F1D2-F248-11E8-B48F-1D18A9856A87
last_name: Wojtan
orcid: 0000-0001-6646-5546
- first_name: Rüdiger
full_name: Westermann, Rüdiger
last_name: Westermann
- first_name: Nils
full_name: Thuerey, Nils
last_name: Thuerey
citation:
ama: Ferstl F, Ando R, Wojtan C, Westermann R, Thuerey N. Narrow band FLIP for liquid
simulations. Computer Graphics Forum. 2016;35(2):225-232. doi:10.1111/cgf.12825
apa: Ferstl, F., Ando, R., Wojtan, C., Westermann, R., & Thuerey, N. (2016).
Narrow band FLIP for liquid simulations. Computer Graphics Forum. Wiley-Blackwell.
https://doi.org/10.1111/cgf.12825
chicago: Ferstl, Florian, Ryoichi Ando, Chris Wojtan, Rüdiger Westermann, and Nils
Thuerey. “Narrow Band FLIP for Liquid Simulations.” Computer Graphics Forum.
Wiley-Blackwell, 2016. https://doi.org/10.1111/cgf.12825.
ieee: F. Ferstl, R. Ando, C. Wojtan, R. Westermann, and N. Thuerey, “Narrow band
FLIP for liquid simulations,” Computer Graphics Forum, vol. 35, no. 2.
Wiley-Blackwell, pp. 225–232, 2016.
ista: Ferstl F, Ando R, Wojtan C, Westermann R, Thuerey N. 2016. Narrow band FLIP
for liquid simulations. Computer Graphics Forum. 35(2), 225–232.
mla: Ferstl, Florian, et al. “Narrow Band FLIP for Liquid Simulations.” Computer
Graphics Forum, vol. 35, no. 2, Wiley-Blackwell, 2016, pp. 225–32, doi:10.1111/cgf.12825.
short: F. Ferstl, R. Ando, C. Wojtan, R. Westermann, N. Thuerey, Computer Graphics
Forum 35 (2016) 225–232.
date_created: 2018-12-11T11:51:53Z
date_published: 2016-05-01T00:00:00Z
date_updated: 2023-02-21T10:38:38Z
day: '01'
ddc:
- '000'
department:
- _id: ChWo
doi: 10.1111/cgf.12825
file:
- access_level: open_access
checksum: 984afbe510ed48019025dff1dcc7baad
content_type: application/pdf
creator: system
date_created: 2018-12-12T10:12:22Z
date_updated: 2020-07-14T12:44:53Z
file_id: '4940'
file_name: IST-2016-611-v1+3_CW_nbflip_postprint_2016.pdf
file_size: 5938324
relation: main_file
file_date_updated: 2020-07-14T12:44:53Z
has_accepted_license: '1'
intvolume: ' 35'
issue: '2'
language:
- iso: eng
month: '05'
oa: 1
oa_version: Submitted Version
page: 225 - 232
publication: Computer Graphics Forum
publication_status: published
publisher: Wiley-Blackwell
publist_id: '5793'
pubrep_id: '611'
quality_controlled: '1'
scopus_import: 1
status: public
title: Narrow band FLIP for liquid simulations
type: journal_article
user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87
volume: 35
year: '2016'
...
---
_id: '1416'
abstract:
- lang: eng
text: Anisotropic dipole-dipole interactions between ultracold dipolar fermions
break the symmetry of the Fermi surface and thereby deform it. Here we demonstrate
that such a Fermi surface deformation induces a topological phase transition -
the so-called Lifshitz transition - in the regime accessible to present-day experiments.
We describe the impact of the Lifshitz transition on observable quantities such
as the Fermi surface topology, the density-density correlation function, and the
excitation spectrum of the system. The Lifshitz transition in ultracold atoms
can be controlled by tuning the dipole orientation and, in contrast to the transition
studied in crystalline solids, is completely interaction driven.
article_number: '195145'
author:
- first_name: Erik
full_name: Van Loon, Erik
last_name: Van Loon
- first_name: Mikhail
full_name: Katsnelson, Mikhail
last_name: Katsnelson
- first_name: Lauriane
full_name: Chomaz, Lauriane
last_name: Chomaz
- first_name: Mikhail
full_name: Lemeshko, Mikhail
id: 37CB05FA-F248-11E8-B48F-1D18A9856A87
last_name: Lemeshko
orcid: 0000-0002-6990-7802
citation:
ama: Van Loon E, Katsnelson M, Chomaz L, Lemeshko M. Interaction-driven Lifshitz
transition with dipolar fermions in optical lattices. Physical Review B - Condensed
Matter and Materials Physics. 2016;93(19). doi:10.1103/PhysRevB.93.195145
apa: Van Loon, E., Katsnelson, M., Chomaz, L., & Lemeshko, M. (2016). Interaction-driven
Lifshitz transition with dipolar fermions in optical lattices. Physical Review
B - Condensed Matter and Materials Physics. American Physical Society. https://doi.org/10.1103/PhysRevB.93.195145
chicago: Van Loon, Erik, Mikhail Katsnelson, Lauriane Chomaz, and Mikhail Lemeshko.
“Interaction-Driven Lifshitz Transition with Dipolar Fermions in Optical Lattices.”
Physical Review B - Condensed Matter and Materials Physics. American Physical
Society, 2016. https://doi.org/10.1103/PhysRevB.93.195145.
ieee: E. Van Loon, M. Katsnelson, L. Chomaz, and M. Lemeshko, “Interaction-driven
Lifshitz transition with dipolar fermions in optical lattices,” Physical Review
B - Condensed Matter and Materials Physics, vol. 93, no. 19. American Physical
Society, 2016.
ista: Van Loon E, Katsnelson M, Chomaz L, Lemeshko M. 2016. Interaction-driven Lifshitz
transition with dipolar fermions in optical lattices. Physical Review B - Condensed
Matter and Materials Physics. 93(19), 195145.
mla: Van Loon, Erik, et al. “Interaction-Driven Lifshitz Transition with Dipolar
Fermions in Optical Lattices.” Physical Review B - Condensed Matter and Materials
Physics, vol. 93, no. 19, 195145, American Physical Society, 2016, doi:10.1103/PhysRevB.93.195145.
short: E. Van Loon, M. Katsnelson, L. Chomaz, M. Lemeshko, Physical Review B - Condensed
Matter and Materials Physics 93 (2016).
date_created: 2018-12-11T11:51:54Z
date_published: 2016-05-15T00:00:00Z
date_updated: 2021-01-12T06:50:36Z
day: '15'
department:
- _id: MiLe
doi: 10.1103/PhysRevB.93.195145
intvolume: ' 93'
issue: '19'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: http://arxiv.org/abs/1603.09358
month: '05'
oa: 1
oa_version: Preprint
publication: Physical Review B - Condensed Matter and Materials Physics
publication_status: published
publisher: American Physical Society
publist_id: '5791'
quality_controlled: '1'
scopus_import: 1
status: public
title: Interaction-driven Lifshitz transition with dipolar fermions in optical lattices
type: journal_article
user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87
volume: 93
year: '2016'
...
---
_id: '1427'
abstract:
- lang: eng
text: Changes in gene expression are an important mode of evolution; however, the
proximate mechanism of these changes is poorly understood. In particular, little
is known about the effects of mutations within cis binding sites for transcription
factors, or the nature of epistatic interactions between these mutations. Here,
we tested the effects of single and double mutants in two cis binding sites involved
in the transcriptional regulation of the Escherichia coli araBAD operon, a component
of arabinose metabolism, using a synthetic system. This system decouples transcriptional
control from any posttranslational effects on fitness, allowing a precise estimate
of the effect of single and double mutations, and hence epistasis, on gene expression.
We found that epistatic interactions between mutations in the araBAD cis-regulatory
element are common, and that the predominant form of epistasis is negative. The
magnitude of the interactions depended on whether the mutations are located in
the same or in different operator sites. Importantly, these epistatic interactions
were dependent on the presence of arabinose, a native inducer of the araBAD operon
in vivo, with some interactions changing in sign (e.g., from negative to positive)
in its presence. This study thus reveals that mutations in even relatively simple
cis-regulatory elements interact in complex ways such that selection on the level
of gene expression in one environment might perturb regulation in the other environment
in an unpredictable and uncorrelated manner.
author:
- first_name: Mato
full_name: Lagator, Mato
id: 345D25EC-F248-11E8-B48F-1D18A9856A87
last_name: Lagator
- first_name: Claudia
full_name: Igler, Claudia
id: 46613666-F248-11E8-B48F-1D18A9856A87
last_name: Igler
- first_name: Anaisa
full_name: Moreno, Anaisa
last_name: Moreno
- first_name: Calin C
full_name: Guet, Calin C
id: 47F8433E-F248-11E8-B48F-1D18A9856A87
last_name: Guet
orcid: 0000-0001-6220-2052
- first_name: Jonathan P
full_name: Bollback, Jonathan P
id: 2C6FA9CC-F248-11E8-B48F-1D18A9856A87
last_name: Bollback
orcid: 0000-0002-4624-4612
citation:
ama: Lagator M, Igler C, Moreno A, Guet CC, Bollback JP. Epistatic interactions
in the arabinose cis-regulatory element. Molecular Biology and Evolution.
2016;33(3):761-769. doi:10.1093/molbev/msv269
apa: Lagator, M., Igler, C., Moreno, A., Guet, C. C., & Bollback, J. P. (2016).
Epistatic interactions in the arabinose cis-regulatory element. Molecular Biology
and Evolution. Oxford University Press. https://doi.org/10.1093/molbev/msv269
chicago: Lagator, Mato, Claudia Igler, Anaisa Moreno, Calin C Guet, and Jonathan
P Bollback. “Epistatic Interactions in the Arabinose Cis-Regulatory Element.”
Molecular Biology and Evolution. Oxford University Press, 2016. https://doi.org/10.1093/molbev/msv269.
ieee: M. Lagator, C. Igler, A. Moreno, C. C. Guet, and J. P. Bollback, “Epistatic
interactions in the arabinose cis-regulatory element,” Molecular Biology and
Evolution, vol. 33, no. 3. Oxford University Press, pp. 761–769, 2016.
ista: Lagator M, Igler C, Moreno A, Guet CC, Bollback JP. 2016. Epistatic interactions
in the arabinose cis-regulatory element. Molecular Biology and Evolution. 33(3),
761–769.
mla: Lagator, Mato, et al. “Epistatic Interactions in the Arabinose Cis-Regulatory
Element.” Molecular Biology and Evolution, vol. 33, no. 3, Oxford University
Press, 2016, pp. 761–69, doi:10.1093/molbev/msv269.
short: M. Lagator, C. Igler, A. Moreno, C.C. Guet, J.P. Bollback, Molecular Biology
and Evolution 33 (2016) 761–769.
date_created: 2018-12-11T11:51:57Z
date_published: 2016-03-01T00:00:00Z
date_updated: 2021-01-12T06:50:39Z
day: '01'
ddc:
- '570'
- '576'
department:
- _id: CaGu
- _id: JoBo
doi: 10.1093/molbev/msv269
ec_funded: 1
file:
- access_level: open_access
checksum: 1f456ce1d2aa2f67176a1709f9702ecf
content_type: application/pdf
creator: system
date_created: 2018-12-12T10:09:27Z
date_updated: 2020-07-14T12:44:53Z
file_id: '4751'
file_name: IST-2016-588-v1+1_Mol_Biol_Evol-2016-Lagator-761-9.pdf
file_size: 648115
relation: main_file
file_date_updated: 2020-07-14T12:44:53Z
has_accepted_license: '1'
intvolume: ' 33'
issue: '3'
language:
- iso: eng
month: '03'
oa: 1
oa_version: Published Version
page: 761 - 769
project:
- _id: 25681D80-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '291734'
name: International IST Postdoc Fellowship Programme
publication: Molecular Biology and Evolution
publication_status: published
publisher: Oxford University Press
publist_id: '5772'
pubrep_id: '588'
quality_controlled: '1'
scopus_import: 1
status: public
title: Epistatic interactions in the arabinose cis-regulatory element
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: journal_article
user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87
volume: 33
year: '2016'
...
---
_id: '1428'
abstract:
- lang: eng
text: We report on a mathematically rigorous analysis of the superfluid properties
of a Bose- Einstein condensate in the many-body ground state of a one-dimensional
model of interacting bosons in a random potential.
article_number: '012016'
author:
- first_name: Martin
full_name: Könenberg, Martin
last_name: Könenberg
- first_name: Thomas
full_name: Moser, Thomas
id: 2B5FC9A4-F248-11E8-B48F-1D18A9856A87
last_name: Moser
- first_name: Robert
full_name: Seiringer, Robert
id: 4AFD0470-F248-11E8-B48F-1D18A9856A87
last_name: Seiringer
orcid: 0000-0002-6781-0521
- first_name: Jakob
full_name: Yngvason, Jakob
last_name: Yngvason
citation:
ama: 'Könenberg M, Moser T, Seiringer R, Yngvason J. Superfluidity and BEC in a
Model of Interacting Bosons in a Random Potential. In: Journal of Physics:
Conference Series. Vol 691. IOP Publishing Ltd.; 2016. doi:10.1088/1742-6596/691/1/012016'
apa: 'Könenberg, M., Moser, T., Seiringer, R., & Yngvason, J. (2016). Superfluidity
and BEC in a Model of Interacting Bosons in a Random Potential. In Journal
of Physics: Conference Series (Vol. 691). Shanghai, China: IOP Publishing
Ltd. https://doi.org/10.1088/1742-6596/691/1/012016'
chicago: 'Könenberg, Martin, Thomas Moser, Robert Seiringer, and Jakob Yngvason.
“Superfluidity and BEC in a Model of Interacting Bosons in a Random Potential.”
In Journal of Physics: Conference Series, Vol. 691. IOP Publishing Ltd.,
2016. https://doi.org/10.1088/1742-6596/691/1/012016.'
ieee: 'M. Könenberg, T. Moser, R. Seiringer, and J. Yngvason, “Superfluidity and
BEC in a Model of Interacting Bosons in a Random Potential,” in Journal of
Physics: Conference Series, Shanghai, China, 2016, vol. 691, no. 1.'
ista: 'Könenberg M, Moser T, Seiringer R, Yngvason J. 2016. Superfluidity and BEC
in a Model of Interacting Bosons in a Random Potential. Journal of Physics: Conference
Series. 24th International Laser Physics Workshop (LPHYS’15) vol. 691, 012016.'
mla: 'Könenberg, Martin, et al. “Superfluidity and BEC in a Model of Interacting
Bosons in a Random Potential.” Journal of Physics: Conference Series, vol.
691, no. 1, 012016, IOP Publishing Ltd., 2016, doi:10.1088/1742-6596/691/1/012016.'
short: 'M. Könenberg, T. Moser, R. Seiringer, J. Yngvason, in:, Journal of Physics:
Conference Series, IOP Publishing Ltd., 2016.'
conference:
end_date: 2015-08-25
location: Shanghai, China
name: 24th International Laser Physics Workshop (LPHYS'15)
start_date: 2015-08-21
date_created: 2018-12-11T11:51:58Z
date_published: 2016-03-07T00:00:00Z
date_updated: 2021-01-12T06:50:40Z
day: '07'
ddc:
- '510'
- '530'
department:
- _id: RoSe
doi: 10.1088/1742-6596/691/1/012016
file:
- access_level: open_access
checksum: 109db801749072c3f6c8f1a1848700fa
content_type: application/pdf
creator: system
date_created: 2018-12-12T10:10:55Z
date_updated: 2020-07-14T12:44:53Z
file_id: '4847'
file_name: IST-2016-585-v1+1_JPCS_691_1_012016.pdf
file_size: 1434688
relation: main_file
file_date_updated: 2020-07-14T12:44:53Z
has_accepted_license: '1'
intvolume: ' 691'
issue: '1'
language:
- iso: eng
month: '03'
oa: 1
oa_version: Published Version
project:
- _id: 25C878CE-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: P27533_N27
name: Structure of the Excitation Spectrum for Many-Body Quantum Systems
publication: 'Journal of Physics: Conference Series'
publication_status: published
publisher: IOP Publishing Ltd.
publist_id: '5770'
pubrep_id: '585'
quality_controlled: '1'
scopus_import: 1
status: public
title: Superfluidity and BEC in a Model of Interacting Bosons in a Random Potential
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: conference
user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87
volume: 691
year: '2016'
...
---
_id: '1426'
abstract:
- lang: eng
text: 'Brood parasites exploit their host in order to increase their own fitness.
Typically, this results in an arms race between parasite trickery and host defence.
Thus, it is puzzling to observe hosts that accept parasitism without any resistance.
The ‘mafia’ hypothesis suggests that these hosts accept parasitism to avoid retaliation.
Retaliation has been shown to evolve when the hosts condition their response to
mafia parasites, who use depredation as a targeted response to rejection. However,
it is unclear if acceptance would also emerge when ‘farming’ parasites are present
in the population. Farming parasites use depredation to synchronize the timing
with the host, destroying mature clutches to force the host to re-nest. Herein,
we develop an evolutionary model to analyse the interaction between depredatory
parasites and their hosts. We show that coevolutionary cycles between farmers
and mafia can still induce host acceptance of brood parasites. However, this equilibrium
is unstable and in the long-run the dynamics of this host–parasite interaction
exhibits strong oscillations: when farmers are the majority, accepters conditional
to mafia (the host will reject first and only accept after retaliation by the
parasite) have a higher fitness than unconditional accepters (the host always
accepts parasitism). This leads to an increase in mafia parasites’ fitness and
in turn induce an optimal environment for accepter hosts.'
acknowledgement: C.H. gratefully acknowledges funding by the Schrödinger scholarship
of the Austrian Science Fund (FWF) J3475.
article_number: '160036'
author:
- first_name: Maria
full_name: Chakra, Maria
last_name: Chakra
- first_name: Christian
full_name: Hilbe, Christian
id: 2FDF8F3C-F248-11E8-B48F-1D18A9856A87
last_name: Hilbe
orcid: 0000-0001-5116-955X
- first_name: Arne
full_name: Traulsen, Arne
last_name: Traulsen
citation:
ama: Chakra M, Hilbe C, Traulsen A. Coevolutionary interactions between farmers
and mafia induce host acceptance of avian brood parasites. Royal Society Open
Science. 2016;3(5). doi:10.1098/rsos.160036
apa: Chakra, M., Hilbe, C., & Traulsen, A. (2016). Coevolutionary interactions
between farmers and mafia induce host acceptance of avian brood parasites. Royal
Society Open Science. Royal Society, The. https://doi.org/10.1098/rsos.160036
chicago: Chakra, Maria, Christian Hilbe, and Arne Traulsen. “Coevolutionary Interactions
between Farmers and Mafia Induce Host Acceptance of Avian Brood Parasites.” Royal
Society Open Science. Royal Society, The, 2016. https://doi.org/10.1098/rsos.160036.
ieee: M. Chakra, C. Hilbe, and A. Traulsen, “Coevolutionary interactions between
farmers and mafia induce host acceptance of avian brood parasites,” Royal Society
Open Science, vol. 3, no. 5. Royal Society, The, 2016.
ista: Chakra M, Hilbe C, Traulsen A. 2016. Coevolutionary interactions between farmers
and mafia induce host acceptance of avian brood parasites. Royal Society Open
Science. 3(5), 160036.
mla: Chakra, Maria, et al. “Coevolutionary Interactions between Farmers and Mafia
Induce Host Acceptance of Avian Brood Parasites.” Royal Society Open Science,
vol. 3, no. 5, 160036, Royal Society, The, 2016, doi:10.1098/rsos.160036.
short: M. Chakra, C. Hilbe, A. Traulsen, Royal Society Open Science 3 (2016).
date_created: 2018-12-11T11:51:57Z
date_published: 2016-05-01T00:00:00Z
date_updated: 2021-01-12T06:50:39Z
day: '01'
ddc:
- '000'
department:
- _id: KrCh
doi: 10.1098/rsos.160036
file:
- access_level: open_access
checksum: bf84211b31fe87451e738ba301d729c3
content_type: application/pdf
creator: system
date_created: 2018-12-12T10:14:49Z
date_updated: 2020-07-14T12:44:53Z
file_id: '5104'
file_name: IST-2016-589-v1+1_160036.full.pdf
file_size: 937002
relation: main_file
file_date_updated: 2020-07-14T12:44:53Z
has_accepted_license: '1'
intvolume: ' 3'
issue: '5'
language:
- iso: eng
month: '05'
oa: 1
oa_version: Published Version
publication: Royal Society Open Science
publication_status: published
publisher: Royal Society, The
publist_id: '5776'
pubrep_id: '589'
quality_controlled: '1'
scopus_import: 1
status: public
title: Coevolutionary interactions between farmers and mafia induce host acceptance
of avian brood parasites
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: journal_article
user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87
volume: 3
year: '2016'
...
---
_id: '1423'
abstract:
- lang: eng
text: 'Direct reciprocity is a mechanism for the evolution of cooperation based
on repeated interactions. When individuals meet repeatedly, they can use conditional
strategies to enforce cooperative outcomes that would not be feasible in one-shot
social dilemmas. Direct reciprocity requires that individuals keep track of their
past interactions and find the right response. However, there are natural bounds
on strategic complexity: Humans find it difficult to remember past interactions
accurately, especially over long timespans. Given these limitations, it is natural
to ask how complex strategies need to be for cooperation to evolve. Here, we study
stochastic evolutionary game dynamics in finite populations to systematically
compare the evolutionary performance of reactive strategies, which only respond
to the co-player''s previous move, and memory-one strategies, which take into
account the own and the co-player''s previous move. In both cases, we compare
deterministic strategy and stochastic strategy spaces. For reactive strategies
and small costs, we find that stochasticity benefits cooperation, because it allows
for generous-tit-for-tat. For memory one strategies and small costs, we find that
stochasticity does not increase the propensity for cooperation, because the deterministic
rule of win-stay, lose-shift works best. For memory one strategies and large costs,
however, stochasticity can augment cooperation.'
acknowledgement: C.H. acknowledges generous funding from the Schrödinger scholarship
of the Austrian Science Fund (FWF), J3475.
article_number: '25676'
author:
- first_name: Seung
full_name: Baek, Seung
last_name: Baek
- first_name: Hyeongchai
full_name: Jeong, Hyeongchai
last_name: Jeong
- first_name: Christian
full_name: Hilbe, Christian
id: 2FDF8F3C-F248-11E8-B48F-1D18A9856A87
last_name: Hilbe
orcid: 0000-0001-5116-955X
- first_name: Martin
full_name: Nowak, Martin
last_name: Nowak
citation:
ama: Baek S, Jeong H, Hilbe C, Nowak M. Comparing reactive and memory-one strategies
of direct reciprocity. Scientific Reports. 2016;6. doi:10.1038/srep25676
apa: Baek, S., Jeong, H., Hilbe, C., & Nowak, M. (2016). Comparing reactive
and memory-one strategies of direct reciprocity. Scientific Reports. Nature
Publishing Group. https://doi.org/10.1038/srep25676
chicago: Baek, Seung, Hyeongchai Jeong, Christian Hilbe, and Martin Nowak. “Comparing
Reactive and Memory-One Strategies of Direct Reciprocity.” Scientific Reports.
Nature Publishing Group, 2016. https://doi.org/10.1038/srep25676.
ieee: S. Baek, H. Jeong, C. Hilbe, and M. Nowak, “Comparing reactive and memory-one
strategies of direct reciprocity,” Scientific Reports, vol. 6. Nature Publishing
Group, 2016.
ista: Baek S, Jeong H, Hilbe C, Nowak M. 2016. Comparing reactive and memory-one
strategies of direct reciprocity. Scientific Reports. 6, 25676.
mla: Baek, Seung, et al. “Comparing Reactive and Memory-One Strategies of Direct
Reciprocity.” Scientific Reports, vol. 6, 25676, Nature Publishing Group,
2016, doi:10.1038/srep25676.
short: S. Baek, H. Jeong, C. Hilbe, M. Nowak, Scientific Reports 6 (2016).
date_created: 2018-12-11T11:51:56Z
date_published: 2016-05-10T00:00:00Z
date_updated: 2021-01-12T06:50:38Z
day: '10'
ddc:
- '000'
department:
- _id: KrCh
doi: 10.1038/srep25676
file:
- access_level: open_access
checksum: ee17c482370d2e1b3add393710d3c696
content_type: application/pdf
creator: system
date_created: 2018-12-12T10:18:08Z
date_updated: 2020-07-14T12:44:53Z
file_id: '5327'
file_name: IST-2016-590-v1+1_srep25676.pdf
file_size: 1349915
relation: main_file
file_date_updated: 2020-07-14T12:44:53Z
has_accepted_license: '1'
intvolume: ' 6'
language:
- iso: eng
month: '05'
oa: 1
oa_version: Published Version
publication: Scientific Reports
publication_status: published
publisher: Nature Publishing Group
publist_id: '5784'
pubrep_id: '590'
quality_controlled: '1'
scopus_import: 1
status: public
title: Comparing reactive and memory-one strategies of direct reciprocity
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: journal_article
user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87
volume: 6
year: '2016'
...
---
_id: '1422'
abstract:
- lang: eng
text: We study the time-dependent Bogoliubov–de-Gennes equations for generic translation-invariant
fermionic many-body systems. For initial states that are close to thermal equilibrium
states at temperatures near the critical temperature, we show that the magnitude
of the order parameter stays approximately constant in time and, in particular,
does not follow a time-dependent Ginzburg–Landau equation, which is often employed
as a phenomenological description and predicts a decay of the order parameter
in time. The full non-linear structure of the equations is necessary to understand
this behavior.
acknowledgement: 'Open access funding provided by Institute of Science and Technology
(IST Austria). '
article_processing_charge: Yes (via OA deal)
author:
- first_name: Rupert
full_name: Frank, Rupert
last_name: Frank
- first_name: Christian
full_name: Hainzl, Christian
last_name: Hainzl
- first_name: Benjamin
full_name: Schlein, Benjamin
last_name: Schlein
- first_name: Robert
full_name: Seiringer, Robert
id: 4AFD0470-F248-11E8-B48F-1D18A9856A87
last_name: Seiringer
orcid: 0000-0002-6781-0521
citation:
ama: Frank R, Hainzl C, Schlein B, Seiringer R. Incompatibility of time-dependent
Bogoliubov–de-Gennes and Ginzburg–Landau equations. Letters in Mathematical
Physics. 2016;106(7):913-923. doi:10.1007/s11005-016-0847-5
apa: Frank, R., Hainzl, C., Schlein, B., & Seiringer, R. (2016). Incompatibility
of time-dependent Bogoliubov–de-Gennes and Ginzburg–Landau equations. Letters
in Mathematical Physics. Springer. https://doi.org/10.1007/s11005-016-0847-5
chicago: Frank, Rupert, Christian Hainzl, Benjamin Schlein, and Robert Seiringer.
“Incompatibility of Time-Dependent Bogoliubov–de-Gennes and Ginzburg–Landau Equations.”
Letters in Mathematical Physics. Springer, 2016. https://doi.org/10.1007/s11005-016-0847-5.
ieee: R. Frank, C. Hainzl, B. Schlein, and R. Seiringer, “Incompatibility of time-dependent
Bogoliubov–de-Gennes and Ginzburg–Landau equations,” Letters in Mathematical
Physics, vol. 106, no. 7. Springer, pp. 913–923, 2016.
ista: Frank R, Hainzl C, Schlein B, Seiringer R. 2016. Incompatibility of time-dependent
Bogoliubov–de-Gennes and Ginzburg–Landau equations. Letters in Mathematical Physics.
106(7), 913–923.
mla: Frank, Rupert, et al. “Incompatibility of Time-Dependent Bogoliubov–de-Gennes
and Ginzburg–Landau Equations.” Letters in Mathematical Physics, vol. 106,
no. 7, Springer, 2016, pp. 913–23, doi:10.1007/s11005-016-0847-5.
short: R. Frank, C. Hainzl, B. Schlein, R. Seiringer, Letters in Mathematical Physics
106 (2016) 913–923.
date_created: 2018-12-11T11:51:56Z
date_published: 2016-07-01T00:00:00Z
date_updated: 2021-01-12T06:50:38Z
day: '01'
ddc:
- '510'
- '530'
department:
- _id: RoSe
doi: 10.1007/s11005-016-0847-5
file:
- access_level: open_access
checksum: fb404923d8ca9a1faeb949561f26cbea
content_type: application/pdf
creator: system
date_created: 2018-12-12T10:15:57Z
date_updated: 2020-07-14T12:44:53Z
file_id: '5181'
file_name: IST-2016-591-v1+1_s11005-016-0847-5.pdf
file_size: 458968
relation: main_file
file_date_updated: 2020-07-14T12:44:53Z
has_accepted_license: '1'
intvolume: ' 106'
issue: '7'
language:
- iso: eng
month: '07'
oa: 1
oa_version: Published Version
page: 913 - 923
project:
- _id: 25C878CE-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: P27533_N27
name: Structure of the Excitation Spectrum for Many-Body Quantum Systems
- _id: B67AFEDC-15C9-11EA-A837-991A96BB2854
name: IST Austria Open Access Fund
publication: Letters in Mathematical Physics
publication_status: published
publisher: Springer
publist_id: '5785'
pubrep_id: '591'
quality_controlled: '1'
scopus_import: 1
status: public
title: Incompatibility of time-dependent Bogoliubov–de-Gennes and Ginzburg–Landau
equations
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: 106
year: '2016'
...
---
_id: '1420'
abstract:
- lang: eng
text: 'Selection, mutation, and random drift affect the dynamics of allele frequencies
and consequently of quantitative traits. While the macroscopic dynamics of quantitative
traits can be measured, the underlying allele frequencies are typically unobserved.
Can we understand how the macroscopic observables evolve without following these
microscopic processes? This problem has been studied previously by analogy with
statistical mechanics: the allele frequency distribution at each time point is
approximated by the stationary form, which maximizes entropy. We explore the limitations
of this method when mutation is small (4Nμ < 1) so that populations are typically
close to fixation, and we extend the theory in this regime to account for changes
in mutation strength. We consider a single diallelic locus either under directional
selection or with overdominance and then generalize to multiple unlinked biallelic
loci with unequal effects. We find that the maximum-entropy approximation is remarkably
accurate, even when mutation and selection change rapidly. '
article_processing_charge: No
author:
- first_name: Katarína
full_name: Bod'ová, Katarína
id: 2BA24EA0-F248-11E8-B48F-1D18A9856A87
last_name: Bod'ová
orcid: 0000-0002-7214-0171
- first_name: Gasper
full_name: Tkacik, Gasper
id: 3D494DCA-F248-11E8-B48F-1D18A9856A87
last_name: Tkacik
orcid: 0000-0002-6699-1455
- first_name: Nicholas H
full_name: Barton, Nicholas H
id: 4880FE40-F248-11E8-B48F-1D18A9856A87
last_name: Barton
orcid: 0000-0002-8548-5240
citation:
ama: Bodova K, Tkačik G, Barton NH. A general approximation for the dynamics of
quantitative traits. Genetics. 2016;202(4):1523-1548. doi:10.1534/genetics.115.184127
apa: Bodova, K., Tkačik, G., & Barton, N. H. (2016). A general approximation
for the dynamics of quantitative traits. Genetics. Genetics Society of
America. https://doi.org/10.1534/genetics.115.184127
chicago: Bodova, Katarina, Gašper Tkačik, and Nicholas H Barton. “A General Approximation
for the Dynamics of Quantitative Traits.” Genetics. Genetics Society of
America, 2016. https://doi.org/10.1534/genetics.115.184127.
ieee: K. Bodova, G. Tkačik, and N. H. Barton, “A general approximation for the dynamics
of quantitative traits,” Genetics, vol. 202, no. 4. Genetics Society of
America, pp. 1523–1548, 2016.
ista: Bodova K, Tkačik G, Barton NH. 2016. A general approximation for the dynamics
of quantitative traits. Genetics. 202(4), 1523–1548.
mla: Bodova, Katarina, et al. “A General Approximation for the Dynamics of Quantitative
Traits.” Genetics, vol. 202, no. 4, Genetics Society of America, 2016,
pp. 1523–48, doi:10.1534/genetics.115.184127.
short: K. Bodova, G. Tkačik, N.H. Barton, Genetics 202 (2016) 1523–1548.
date_created: 2018-12-11T11:51:55Z
date_published: 2016-04-06T00:00:00Z
date_updated: 2022-08-01T10:49:55Z
day: '06'
department:
- _id: GaTk
- _id: NiBa
doi: 10.1534/genetics.115.184127
ec_funded: 1
external_id:
arxiv:
- '1510.08344'
intvolume: ' 202'
issue: '4'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: http://arxiv.org/abs/1510.08344
month: '04'
oa: 1
oa_version: Preprint
page: 1523 - 1548
project:
- _id: 25B07788-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '250152'
name: Limits to selection in biology and in evolutionary computation
- _id: 255008E4-B435-11E9-9278-68D0E5697425
grant_number: RGP0065/2012
name: Information processing and computation in fish groups
publication: Genetics
publication_status: published
publisher: Genetics Society of America
publist_id: '5787'
quality_controlled: '1'
scopus_import: '1'
status: public
title: A general approximation for the dynamics of quantitative traits
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 202
year: '2016'
...
---
_id: '1429'
abstract:
- lang: eng
text: Solitons are localized waves formed by a balance of focusing and defocusing
effects. These nonlinear waves exist in diverse forms of matter yet exhibit similar
properties including stability, periodic recurrence and particle-like trajectories.
One important property is soliton fission, a process by which an energetic higher-order
soliton breaks apart due to dispersive or nonlinear perturbations. Here we demonstrate
through both experiment and theory that nonlinear photocarrier generation can
induce soliton fission. Using near-field measurements, we directly observe the
nonlinear spatial and temporal evolution of optical pulses in situ in a nanophotonic
semiconductor waveguide. We develop an analytic formalism describing the free-carrier
dispersion (FCD) perturbation and show the experiment exceeds the minimum threshold
by an order of magnitude. We confirm these observations with a numerical nonlinear
Schrödinger equation model. These results provide a fundamental explanation and
physical scaling of optical pulse evolution in free-carrier media and could enable
improved supercontinuum sources in gas based and integrated semiconductor waveguides.
acknowledgement: This research was supported by the Australian Research Council (ARC)
Center of Excellence CUDOS (CE110001018), ARC Laureate Fellowship (FL120100029),
ARC Discovery Early Career Researcher Award (DECRA DE120102069), the Netherlands
Foundation for Fundamental Research on Matter (FOM) and the Netherlands Organization
for Scientific Research (NWO). L.K. acknowledges funding from ERC Advanced Investigator
Grant (no. 240438-CONSTANS). A.D.R, S.C., and G.L. acknowledge financial support
from the ERC-Pharos programme lead by A. P. Mosk.
article_number: 11332 (2016)
author:
- first_name: Chad
full_name: Husko, Chad
last_name: Husko
- first_name: Matthias
full_name: Wulf, Matthias
id: 45598606-F248-11E8-B48F-1D18A9856A87
last_name: Wulf
orcid: 0000-0001-6613-1378
- first_name: Simon
full_name: Lefrançois, Simon
last_name: Lefrançois
- first_name: Sylvain
full_name: Combrié, Sylvain
last_name: Combrié
- first_name: Gaëlle
full_name: Lehoucq, Gaëlle
last_name: Lehoucq
- first_name: Alfredo
full_name: De Rossi, Alfredo
last_name: De Rossi
- first_name: Benjamin
full_name: Eggleton, Benjamin
last_name: Eggleton
- first_name: Laurens
full_name: Kuipers, Laurens
last_name: Kuipers
citation:
ama: Husko C, Wulf M, Lefrançois S, et al. Free-carrier-induced soliton fission
unveiled by in situ measurements in nanophotonic waveguides. Nature Communications.
2016;7. doi:10.1038/ncomms11332
apa: Husko, C., Wulf, M., Lefrançois, S., Combrié, S., Lehoucq, G., De Rossi, A.,
… Kuipers, L. (2016). Free-carrier-induced soliton fission unveiled by in situ
measurements in nanophotonic waveguides. Nature Communications. Nature
Publishing Group. https://doi.org/10.1038/ncomms11332
chicago: Husko, Chad, Matthias Wulf, Simon Lefrançois, Sylvain Combrié, Gaëlle Lehoucq,
Alfredo De Rossi, Benjamin Eggleton, and Laurens Kuipers. “Free-Carrier-Induced
Soliton Fission Unveiled by in Situ Measurements in Nanophotonic Waveguides.”
Nature Communications. Nature Publishing Group, 2016. https://doi.org/10.1038/ncomms11332.
ieee: C. Husko et al., “Free-carrier-induced soliton fission unveiled by
in situ measurements in nanophotonic waveguides,” Nature Communications,
vol. 7. Nature Publishing Group, 2016.
ista: Husko C, Wulf M, Lefrançois S, Combrié S, Lehoucq G, De Rossi A, Eggleton
B, Kuipers L. 2016. Free-carrier-induced soliton fission unveiled by in situ measurements
in nanophotonic waveguides. Nature Communications. 7, 11332 (2016).
mla: Husko, Chad, et al. “Free-Carrier-Induced Soliton Fission Unveiled by in Situ
Measurements in Nanophotonic Waveguides.” Nature Communications, vol. 7,
11332 (2016), Nature Publishing Group, 2016, doi:10.1038/ncomms11332.
short: C. Husko, M. Wulf, S. Lefrançois, S. Combrié, G. Lehoucq, A. De Rossi, B.
Eggleton, L. Kuipers, Nature Communications 7 (2016).
date_created: 2018-12-11T11:51:58Z
date_published: 2016-04-15T00:00:00Z
date_updated: 2021-01-12T06:50:40Z
day: '15'
ddc:
- '530'
department:
- _id: JoFi
doi: 10.1038/ncomms11332
file:
- access_level: open_access
checksum: 6484fa81a2e52e4fdd7935e1ae6091d4
content_type: application/pdf
creator: system
date_created: 2018-12-12T10:15:53Z
date_updated: 2020-07-14T12:44:53Z
file_id: '5177'
file_name: IST-2016-583-v1+1_ncomms11332.pdf
file_size: 965176
relation: main_file
file_date_updated: 2020-07-14T12:44:53Z
has_accepted_license: '1'
intvolume: ' 7'
language:
- iso: eng
month: '04'
oa: 1
oa_version: Published Version
publication: Nature Communications
publication_status: published
publisher: Nature Publishing Group
publist_id: '5769'
pubrep_id: '583'
quality_controlled: '1'
scopus_import: 1
status: public
title: Free-carrier-induced soliton fission unveiled by in situ measurements in nanophotonic
waveguides
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: journal_article
user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87
volume: 7
year: '2016'
...
---
_id: '1431'
abstract:
- lang: eng
text: The rare socially parasitic butterfly Maculinea alcon occurs in two forms,
which are characteristic of hygric or xeric habitats and which exploit different
host plants and host ants. The status of these two forms has been the subject
of considerable controversy. Populations of the two forms are usually spatially
distinct, but at Răscruci in Romania both forms occur on the same site (syntopically).
We examined the genetic differentiation between the two forms using eight microsatellite
markers, and compared with a nearby hygric site, Şardu. Our results showed that
while the two forms are strongly differentiated at Răscruci, it is the xeric form
there that is most similar to the hygric form at Şardu, and Bayesian clustering
algorithms suggest that these two populations have exchanged genes relatively
recently. We found strong evidence for population substructuring, caused by high
within host ant nest relatedness, indicating very limited dispersal of most ovipositing
females, but not association with particular host ant species. Our results are
consistent with the results of larger scale phylogeographic studies that suggest
that the two forms represent local ecotypes specialising on different host plants,
each with a distinct flowering phenology, providing a temporal rather than spatial
barrier to gene flow.
article_number: '1865'
author:
- first_name: András
full_name: Tartally, András
last_name: Tartally
- first_name: Andreas
full_name: Kelager, Andreas
last_name: Kelager
- first_name: Matthias
full_name: Fürst, Matthias
id: 393B1196-F248-11E8-B48F-1D18A9856A87
last_name: Fürst
orcid: 0000-0002-3712-925X
- first_name: David
full_name: Nash, David
last_name: Nash
citation:
ama: Tartally A, Kelager A, Fürst M, Nash D. Host plant use drives genetic differentiation
in syntopic populations of Maculinea alcon. PeerJ. 2016;2016(3). doi:10.7717/peerj.1865
apa: Tartally, A., Kelager, A., Fürst, M., & Nash, D. (2016). Host plant use
drives genetic differentiation in syntopic populations of Maculinea alcon. PeerJ.
PeerJ. https://doi.org/10.7717/peerj.1865
chicago: Tartally, András, Andreas Kelager, Matthias Fürst, and David Nash. “Host
Plant Use Drives Genetic Differentiation in Syntopic Populations of Maculinea
Alcon.” PeerJ. PeerJ, 2016. https://doi.org/10.7717/peerj.1865.
ieee: A. Tartally, A. Kelager, M. Fürst, and D. Nash, “Host plant use drives genetic
differentiation in syntopic populations of Maculinea alcon,” PeerJ, vol.
2016, no. 3. PeerJ, 2016.
ista: Tartally A, Kelager A, Fürst M, Nash D. 2016. Host plant use drives genetic
differentiation in syntopic populations of Maculinea alcon. PeerJ. 2016(3), 1865.
mla: Tartally, András, et al. “Host Plant Use Drives Genetic Differentiation in
Syntopic Populations of Maculinea Alcon.” PeerJ, vol. 2016, no. 3, 1865,
PeerJ, 2016, doi:10.7717/peerj.1865.
short: A. Tartally, A. Kelager, M. Fürst, D. Nash, PeerJ 2016 (2016).
date_created: 2018-12-11T11:51:59Z
date_published: 2016-01-01T00:00:00Z
date_updated: 2021-01-12T06:50:41Z
day: '01'
ddc:
- '570'
department:
- _id: SyCr
doi: 10.7717/peerj.1865
file:
- access_level: open_access
checksum: c27d898598a1e3d7f629607a309254e1
content_type: application/pdf
creator: system
date_created: 2018-12-12T10:17:19Z
date_updated: 2020-07-14T12:44:53Z
file_id: '5272'
file_name: IST-2016-584-v1+1_peerj-1865.pdf
file_size: 1216360
relation: main_file
file_date_updated: 2020-07-14T12:44:53Z
has_accepted_license: '1'
intvolume: ' 2016'
issue: '3'
language:
- iso: eng
month: '01'
oa: 1
oa_version: Published Version
publication: PeerJ
publication_status: published
publisher: PeerJ
publist_id: '5767'
pubrep_id: '584'
quality_controlled: '1'
scopus_import: 1
status: public
title: Host plant use drives genetic differentiation in syntopic populations of Maculinea
alcon
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: journal_article
user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87
volume: 2016
year: '2016'
...
---
_id: '1434'
abstract:
- lang: eng
text: We prove that the system of subordination equations, defining the free additive
convolution of two probability measures, is stable away from the edges of the
support and blow-up singularities by showing that the recent smoothness condition
of Kargin is always satisfied. As an application, we consider the local spectral
statistics of the random matrix ensemble A+UBU⁎A+UBU⁎, where U is a Haar distributed
random unitary or orthogonal matrix, and A and B are deterministic matrices.
In the bulk regime, we prove that the empirical spectral distribution of A+UBU⁎A+UBU⁎
concentrates around the free additive convolution of the spectral distributions
of A and B on scales down to N−2/3N−2/3.
author:
- first_name: Zhigang
full_name: Bao, Zhigang
id: 442E6A6C-F248-11E8-B48F-1D18A9856A87
last_name: Bao
orcid: 0000-0003-3036-1475
- first_name: László
full_name: Erdös, László
id: 4DBD5372-F248-11E8-B48F-1D18A9856A87
last_name: Erdös
orcid: 0000-0001-5366-9603
- first_name: Kevin
full_name: Schnelli, Kevin
id: 434AD0AE-F248-11E8-B48F-1D18A9856A87
last_name: Schnelli
orcid: 0000-0003-0954-3231
citation:
ama: Bao Z, Erdös L, Schnelli K. Local stability of the free additive convolution.
Journal of Functional Analysis. 2016;271(3):672-719. doi:10.1016/j.jfa.2016.04.006
apa: Bao, Z., Erdös, L., & Schnelli, K. (2016). Local stability of the free
additive convolution. Journal of Functional Analysis. Academic Press. https://doi.org/10.1016/j.jfa.2016.04.006
chicago: Bao, Zhigang, László Erdös, and Kevin Schnelli. “Local Stability of the
Free Additive Convolution.” Journal of Functional Analysis. Academic Press,
2016. https://doi.org/10.1016/j.jfa.2016.04.006.
ieee: Z. Bao, L. Erdös, and K. Schnelli, “Local stability of the free additive convolution,”
Journal of Functional Analysis, vol. 271, no. 3. Academic Press, pp. 672–719,
2016.
ista: Bao Z, Erdös L, Schnelli K. 2016. Local stability of the free additive convolution.
Journal of Functional Analysis. 271(3), 672–719.
mla: Bao, Zhigang, et al. “Local Stability of the Free Additive Convolution.” Journal
of Functional Analysis, vol. 271, no. 3, Academic Press, 2016, pp. 672–719,
doi:10.1016/j.jfa.2016.04.006.
short: Z. Bao, L. Erdös, K. Schnelli, Journal of Functional Analysis 271 (2016)
672–719.
date_created: 2018-12-11T11:52:00Z
date_published: 2016-08-01T00:00:00Z
date_updated: 2021-01-12T06:50:42Z
day: '01'
department:
- _id: LaEr
doi: 10.1016/j.jfa.2016.04.006
ec_funded: 1
intvolume: ' 271'
issue: '3'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: http://arxiv.org/abs/1508.05905
month: '08'
oa: 1
oa_version: Preprint
page: 672 - 719
project:
- _id: 258DCDE6-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '338804'
name: Random matrices, universality and disordered quantum systems
publication: Journal of Functional Analysis
publication_status: published
publisher: Academic Press
publist_id: '5764'
quality_controlled: '1'
scopus_import: 1
status: public
title: Local stability of the free additive convolution
type: journal_article
user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87
volume: 271
year: '2016'
...
---
_id: '1436'
abstract:
- lang: eng
text: We study the time evolution of a system of N spinless fermions in R3 which
interact through a pair potential, e.g., the Coulomb potential. We compare the
dynamics given by the solution to Schrödinger's equation with the time-dependent
Hartree-Fock approximation, and we give an estimate for the accuracy of this approximation
in terms of the kinetic energy of the system. This leads, in turn, to bounds in
terms of the initial total energy of the system.
author:
- first_name: Volker
full_name: Bach, Volker
last_name: Bach
- first_name: Sébastien
full_name: Breteaux, Sébastien
last_name: Breteaux
- first_name: Sören P
full_name: Petrat, Sören P
id: 40AC02DC-F248-11E8-B48F-1D18A9856A87
last_name: Petrat
orcid: 0000-0002-9166-5889
- first_name: Peter
full_name: Pickl, Peter
last_name: Pickl
- first_name: Tim
full_name: Tzaneteas, Tim
last_name: Tzaneteas
citation:
ama: Bach V, Breteaux S, Petrat SP, Pickl P, Tzaneteas T. Kinetic energy estimates
for the accuracy of the time-dependent Hartree-Fock approximation with Coulomb
interaction. Journal de Mathématiques Pures et Appliquées. 2016;105(1):1-30.
doi:10.1016/j.matpur.2015.09.003
apa: Bach, V., Breteaux, S., Petrat, S. P., Pickl, P., & Tzaneteas, T. (2016).
Kinetic energy estimates for the accuracy of the time-dependent Hartree-Fock approximation
with Coulomb interaction. Journal de Mathématiques Pures et Appliquées.
Elsevier. https://doi.org/10.1016/j.matpur.2015.09.003
chicago: Bach, Volker, Sébastien Breteaux, Sören P Petrat, Peter Pickl, and Tim
Tzaneteas. “Kinetic Energy Estimates for the Accuracy of the Time-Dependent Hartree-Fock
Approximation with Coulomb Interaction.” Journal de Mathématiques Pures et
Appliquées. Elsevier, 2016. https://doi.org/10.1016/j.matpur.2015.09.003.
ieee: V. Bach, S. Breteaux, S. P. Petrat, P. Pickl, and T. Tzaneteas, “Kinetic energy
estimates for the accuracy of the time-dependent Hartree-Fock approximation with
Coulomb interaction,” Journal de Mathématiques Pures et Appliquées, vol.
105, no. 1. Elsevier, pp. 1–30, 2016.
ista: Bach V, Breteaux S, Petrat SP, Pickl P, Tzaneteas T. 2016. Kinetic energy
estimates for the accuracy of the time-dependent Hartree-Fock approximation with
Coulomb interaction. Journal de Mathématiques Pures et Appliquées. 105(1), 1–30.
mla: Bach, Volker, et al. “Kinetic Energy Estimates for the Accuracy of the Time-Dependent
Hartree-Fock Approximation with Coulomb Interaction.” Journal de Mathématiques
Pures et Appliquées, vol. 105, no. 1, Elsevier, 2016, pp. 1–30, doi:10.1016/j.matpur.2015.09.003.
short: V. Bach, S. Breteaux, S.P. Petrat, P. Pickl, T. Tzaneteas, Journal de Mathématiques
Pures et Appliquées 105 (2016) 1–30.
date_created: 2018-12-11T11:52:00Z
date_published: 2016-01-01T00:00:00Z
date_updated: 2021-01-12T06:50:43Z
day: '01'
ddc:
- '510'
- '530'
department:
- _id: RoSe
doi: 10.1016/j.matpur.2015.09.003
ec_funded: 1
file:
- access_level: open_access
checksum: c5afe1f6935bc7f2b546adbde1d31a35
content_type: application/pdf
creator: system
date_created: 2018-12-12T10:10:36Z
date_updated: 2020-07-14T12:44:54Z
file_id: '4825'
file_name: IST-2016-581-v1+1_1-s2.0-S0021782415001191-main.pdf
file_size: 658491
relation: main_file
file_date_updated: 2020-07-14T12:44:54Z
has_accepted_license: '1'
intvolume: ' 105'
issue: '1'
language:
- iso: eng
month: '01'
oa: 1
oa_version: Published Version
page: 1 - 30
project:
- _id: 25681D80-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '291734'
name: International IST Postdoc Fellowship Programme
publication: Journal de Mathématiques Pures et Appliquées
publication_status: published
publisher: Elsevier
publist_id: '5763'
pubrep_id: '581'
quality_controlled: '1'
scopus_import: 1
status: public
title: Kinetic energy estimates for the accuracy of the time-dependent Hartree-Fock
approximation with Coulomb interaction
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: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87
volume: 105
year: '2016'
...
---
_id: '1435'
abstract:
- lang: eng
text: ATP released from neurons and astrocytes during neuronal activity or under
pathophysiological circumstances is able to influence information flow in neuronal
circuits by activation of ionotropic P2X and metabotropic P2Y receptors and subsequent
modulation of cellular excitability, synaptic strength, and plasticity. In the
present paper we review cellular and network effects of P2Y receptors in the brain.
We show that P2Y receptors inhibit the release of neurotransmitters, modulate
voltage- and ligand-gated ion channels, and differentially influence the induction
of synaptic plasticity in the prefrontal cortex, hippocampus, and cerebellum.
The findings discussed here may explain how P2Y1 receptor activation during brain
injury, hypoxia, inflammation, schizophrenia, or Alzheimer's disease leads to
an impairment of cognitive processes. Hence, it is suggested that the blockade
of P2Y1 receptors may have therapeutic potential against cognitive disturbances
in these states.
article_number: '1207393'
author:
- first_name: José
full_name: Guzmán, José
id: 30CC5506-F248-11E8-B48F-1D18A9856A87
last_name: Guzmán
- first_name: Zoltan
full_name: Gerevich, Zoltan
last_name: Gerevich
citation:
ama: 'Guzmán J, Gerevich Z. P2Y receptors in synaptic transmission and plasticity:
Therapeutic potential in cognitive dysfunction. Neural Plasticity. 2016;2016.
doi:10.1155/2016/1207393'
apa: 'Guzmán, J., & Gerevich, Z. (2016). P2Y receptors in synaptic transmission
and plasticity: Therapeutic potential in cognitive dysfunction. Neural Plasticity.
Hindawi Publishing Corporation. https://doi.org/10.1155/2016/1207393'
chicago: 'Guzmán, José, and Zoltan Gerevich. “P2Y Receptors in Synaptic Transmission
and Plasticity: Therapeutic Potential in Cognitive Dysfunction.” Neural Plasticity.
Hindawi Publishing Corporation, 2016. https://doi.org/10.1155/2016/1207393.'
ieee: 'J. Guzmán and Z. Gerevich, “P2Y receptors in synaptic transmission and plasticity:
Therapeutic potential in cognitive dysfunction,” Neural Plasticity, vol.
2016. Hindawi Publishing Corporation, 2016.'
ista: 'Guzmán J, Gerevich Z. 2016. P2Y receptors in synaptic transmission and plasticity:
Therapeutic potential in cognitive dysfunction. Neural Plasticity. 2016, 1207393.'
mla: 'Guzmán, José, and Zoltan Gerevich. “P2Y Receptors in Synaptic Transmission
and Plasticity: Therapeutic Potential in Cognitive Dysfunction.” Neural Plasticity,
vol. 2016, 1207393, Hindawi Publishing Corporation, 2016, doi:10.1155/2016/1207393.'
short: J. Guzmán, Z. Gerevich, Neural Plasticity 2016 (2016).
date_created: 2018-12-11T11:52:00Z
date_published: 2016-01-01T00:00:00Z
date_updated: 2021-01-12T06:50:43Z
day: '01'
ddc:
- '570'
department:
- _id: PeJo
doi: 10.1155/2016/1207393
file:
- access_level: open_access
checksum: 8dc5c2f3d44d4775a6e7e3edb0d7a0da
content_type: application/pdf
creator: system
date_created: 2018-12-12T10:09:17Z
date_updated: 2020-07-14T12:44:54Z
file_id: '4740'
file_name: IST-2016-580-v1+1_1207393.pdf
file_size: 1395180
relation: main_file
file_date_updated: 2020-07-14T12:44:54Z
has_accepted_license: '1'
intvolume: ' 2016'
language:
- iso: eng
month: '01'
oa: 1
oa_version: Published Version
publication: Neural Plasticity
publication_status: published
publisher: Hindawi Publishing Corporation
publist_id: '5762'
pubrep_id: '580'
quality_controlled: '1'
scopus_import: 1
status: public
title: 'P2Y receptors in synaptic transmission and plasticity: Therapeutic potential
in cognitive dysfunction'
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: journal_article
user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87
volume: 2016
year: '2016'
...
---
_id: '1439'
abstract:
- lang: eng
text: Fault-tolerant distributed algorithms play an important role in many critical/high-availability
applications. These algorithms are notoriously difficult to implement correctly,
due to asynchronous communication and the occurrence of faults, such as the network
dropping messages or computers crashing. We introduce PSYNC, a domain specific
language based on the Heard-Of model, which views asynchronous faulty systems
as synchronous ones with an adversarial environment that simulates asynchrony
and faults by dropping messages. We define a runtime system for PSYNC that efficiently
executes on asynchronous networks. We formalize the relation between the runtime
system and PSYNC in terms of observational refinement. The high-level lockstep
abstraction introduced by PSYNC simplifies the design and implementation of fault-tolerant
distributed algorithms and enables automated formal verification. We have implemented
an embedding of PSYNC in the SCALA programming language with a runtime system
for asynchronous networks. We show the applicability of PSYNC by implementing
several important fault-tolerant distributed algorithms and we compare the implementation
of consensus algorithms in PSYNC against implementations in other languages in
terms of code size, runtime efficiency, and verification.
acknowledgement: 'Damien Zufferey was supported by DARPA (Grants FA8650-11-C-7192
and FA8650-15-C-7564) and NSF (Grant CCF-1138967). '
alternative_title:
- ACM SIGPLAN Notices
author:
- first_name: Cezara
full_name: Dragoi, Cezara
id: 2B2B5ED0-F248-11E8-B48F-1D18A9856A87
last_name: Dragoi
- first_name: Thomas A
full_name: Henzinger, Thomas A
id: 40876CD8-F248-11E8-B48F-1D18A9856A87
last_name: Henzinger
orcid: 0000−0002−2985−7724
- first_name: Damien
full_name: Zufferey, Damien
id: 4397AC76-F248-11E8-B48F-1D18A9856A87
last_name: Zufferey
orcid: 0000-0002-3197-8736
citation:
ama: 'Dragoi C, Henzinger TA, Zufferey D. PSYNC: A partially synchronous language
for fault-tolerant distributed algorithms. In: Vol 20-22. ACM; 2016:400-415. doi:10.1145/2837614.2837650'
apa: 'Dragoi, C., Henzinger, T. A., & Zufferey, D. (2016). PSYNC: A partially
synchronous language for fault-tolerant distributed algorithms (Vol. 20–22, pp.
400–415). Presented at the POPL: Principles of Programming Languages, St. Petersburg,
FL, USA: ACM. https://doi.org/10.1145/2837614.2837650'
chicago: 'Dragoi, Cezara, Thomas A Henzinger, and Damien Zufferey. “PSYNC: A Partially
Synchronous Language for Fault-Tolerant Distributed Algorithms,” 20–22:400–415.
ACM, 2016. https://doi.org/10.1145/2837614.2837650.'
ieee: 'C. Dragoi, T. A. Henzinger, and D. Zufferey, “PSYNC: A partially synchronous
language for fault-tolerant distributed algorithms,” presented at the POPL: Principles
of Programming Languages, St. Petersburg, FL, USA, 2016, vol. 20–22, pp. 400–415.'
ista: 'Dragoi C, Henzinger TA, Zufferey D. 2016. PSYNC: A partially synchronous
language for fault-tolerant distributed algorithms. POPL: Principles of Programming
Languages, ACM SIGPLAN Notices, vol. 20–22, 400–415.'
mla: 'Dragoi, Cezara, et al. PSYNC: A Partially Synchronous Language for Fault-Tolerant
Distributed Algorithms. Vol. 20–22, ACM, 2016, pp. 400–15, doi:10.1145/2837614.2837650.'
short: C. Dragoi, T.A. Henzinger, D. Zufferey, in:, ACM, 2016, pp. 400–415.
conference:
end_date: 2016-01-22
location: St. Petersburg, FL, USA
name: 'POPL: Principles of Programming Languages'
start_date: 2016-01-20
date_created: 2018-12-11T11:52:01Z
date_published: 2016-01-11T00:00:00Z
date_updated: 2021-01-12T06:50:45Z
day: '11'
department:
- _id: ToHe
doi: 10.1145/2837614.2837650
ec_funded: 1
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://hal.inria.fr/hal-01251199/
month: '01'
oa: 1
oa_version: Preprint
page: 400 - 415
project:
- _id: 25EE3708-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '267989'
name: Quantitative Reactive Modeling
- _id: 25F42A32-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: Z211
name: The Wittgenstein Prize
- _id: 25832EC2-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: S 11407_N23
name: Rigorous Systems Engineering
publication_status: published
publisher: ACM
publist_id: '5759'
quality_controlled: '1'
scopus_import: 1
status: public
title: 'PSYNC: A partially synchronous language for fault-tolerant distributed algorithms'
type: conference
user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87
volume: 20-22
year: '2016'
...
---
_id: '1446'
abstract:
- lang: eng
text: The accuracy of interdisciplinarity measurements is directly related to the
quality of the underlying bibliographic data. Existing indicators of interdisciplinarity
are not capable of reflecting the inaccuracies introduced by incorrect and incomplete
records because correct and complete bibliographic data can rarely be obtained.
This is the case for the Rao–Stirling index, which cannot handle references that
are not categorized into disciplinary fields. We introduce a method that addresses
this problem. It extends the Rao–Stirling index to acknowledge missing data by
calculating its interval of uncertainty using computational optimization. The
evaluation of our method indicates that the uncertainty interval is not only useful
for estimating the inaccuracy of interdisciplinarity measurements, but it also
delivers slightly more accurate aggregated interdisciplinarity measurements than
the Rao–Stirling index.
article_processing_charge: No
author:
- first_name: Maria
full_name: Calatrava Moreno, Maria
last_name: Calatrava Moreno
- first_name: Thomas
full_name: Auzinger, Thomas
id: 4718F954-F248-11E8-B48F-1D18A9856A87
last_name: Auzinger
orcid: 0000-0002-1546-3265
- first_name: Hannes
full_name: Werthner, Hannes
last_name: Werthner
citation:
ama: Calatrava Moreno M, Auzinger T, Werthner H. On the uncertainty of interdisciplinarity
measurements due to incomplete bibliographic data. Scientometrics. 2016;107(1):213-232.
doi:10.1007/s11192-016-1842-4
apa: Calatrava Moreno, M., Auzinger, T., & Werthner, H. (2016). On the uncertainty
of interdisciplinarity measurements due to incomplete bibliographic data. Scientometrics.
Springer. https://doi.org/10.1007/s11192-016-1842-4
chicago: Calatrava Moreno, Maria, Thomas Auzinger, and Hannes Werthner. “On the
Uncertainty of Interdisciplinarity Measurements Due to Incomplete Bibliographic
Data.” Scientometrics. Springer, 2016. https://doi.org/10.1007/s11192-016-1842-4.
ieee: M. Calatrava Moreno, T. Auzinger, and H. Werthner, “On the uncertainty of
interdisciplinarity measurements due to incomplete bibliographic data,” Scientometrics,
vol. 107, no. 1. Springer, pp. 213–232, 2016.
ista: Calatrava Moreno M, Auzinger T, Werthner H. 2016. On the uncertainty of interdisciplinarity
measurements due to incomplete bibliographic data. Scientometrics. 107(1), 213–232.
mla: Calatrava Moreno, Maria, et al. “On the Uncertainty of Interdisciplinarity
Measurements Due to Incomplete Bibliographic Data.” Scientometrics, vol.
107, no. 1, Springer, 2016, pp. 213–32, doi:10.1007/s11192-016-1842-4.
short: M. Calatrava Moreno, T. Auzinger, H. Werthner, Scientometrics 107 (2016)
213–232.
date_created: 2018-12-11T11:52:04Z
date_published: 2016-04-01T00:00:00Z
date_updated: 2021-11-16T08:29:11Z
day: '01'
ddc:
- '000'
department:
- _id: BeBi
doi: 10.1007/s11192-016-1842-4
file:
- access_level: open_access
checksum: 32d46268588b87d9b686492018e6a2b2
content_type: application/pdf
creator: system
date_created: 2018-12-12T10:10:56Z
date_updated: 2020-07-14T12:44:55Z
file_id: '4848'
file_name: IST-2016-530-v1+1_s11192-016-1842-4.pdf
file_size: 806035
relation: main_file
file_date_updated: 2020-07-14T12:44:55Z
has_accepted_license: '1'
intvolume: ' 107'
issue: '1'
language:
- iso: eng
month: '04'
oa: 1
oa_version: Published Version
page: 213 - 232
publication: Scientometrics
publication_status: published
publisher: Springer
publist_id: '5750'
pubrep_id: '530'
quality_controlled: '1'
related_material:
link:
- relation: erratum
url: https://doi.org/10.1007/s11192-016-1902-9
scopus_import: '1'
status: public
title: On the uncertainty of interdisciplinarity measurements due to incomplete bibliographic
data
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: journal_article
user_id: 8b945eb4-e2f2-11eb-945a-df72226e66a9
volume: 107
year: '2016'
...
---
_id: '1448'
abstract:
- lang: eng
text: We develop a new and systematic method for proving entropic Ricci curvature
lower bounds for Markov chains on discrete sets. Using different methods, such
bounds have recently been obtained in several examples (e.g., 1-dimensional birth
and death chains, product chains, Bernoulli–Laplace models, and random transposition
models). However, a general method to obtain discrete Ricci bounds had been lacking.
Our method covers all of the examples above. In addition we obtain new Ricci curvature
bounds for zero-range processes on the complete graph. The method is inspired
by recent work of Caputo, Dai Pra and Posta on discrete functional inequalities.
acknowledgement: "Supported by the German Research Foundation through the Collaborative
Research Center 1060\r\nThe Mathematics of Emergent Effects and the Hausdorff Center
for Mathematics. Part of this work has been done while M. Fathi visited J. Maas
at the University of Bonn in July 2014.We would like to thank the referees for their
careful reading of the manuscript. "
author:
- first_name: Max
full_name: Fathi, Max
last_name: Fathi
- first_name: Jan
full_name: Maas, Jan
id: 4C5696CE-F248-11E8-B48F-1D18A9856A87
last_name: Maas
orcid: 0000-0002-0845-1338
citation:
ama: Fathi M, Maas J. Entropic Ricci curvature bounds for discrete interacting systems.
The Annals of Applied Probability. 2016;26(3):1774-1806. doi:10.1214/15-AAP1133
apa: Fathi, M., & Maas, J. (2016). Entropic Ricci curvature bounds for discrete
interacting systems. The Annals of Applied Probability. Institute of Mathematical
Statistics. https://doi.org/10.1214/15-AAP1133
chicago: Fathi, Max, and Jan Maas. “Entropic Ricci Curvature Bounds for Discrete
Interacting Systems.” The Annals of Applied Probability. Institute of Mathematical
Statistics, 2016. https://doi.org/10.1214/15-AAP1133.
ieee: M. Fathi and J. Maas, “Entropic Ricci curvature bounds for discrete interacting
systems,” The Annals of Applied Probability, vol. 26, no. 3. Institute
of Mathematical Statistics, pp. 1774–1806, 2016.
ista: Fathi M, Maas J. 2016. Entropic Ricci curvature bounds for discrete interacting
systems. The Annals of Applied Probability. 26(3), 1774–1806.
mla: Fathi, Max, and Jan Maas. “Entropic Ricci Curvature Bounds for Discrete Interacting
Systems.” The Annals of Applied Probability, vol. 26, no. 3, Institute
of Mathematical Statistics, 2016, pp. 1774–806, doi:10.1214/15-AAP1133.
short: M. Fathi, J. Maas, The Annals of Applied Probability 26 (2016) 1774–1806.
date_created: 2018-12-11T11:52:05Z
date_published: 2016-06-01T00:00:00Z
date_updated: 2021-01-12T06:50:49Z
day: '01'
department:
- _id: JaMa
doi: 10.1214/15-AAP1133
intvolume: ' 26'
issue: '3'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: http://arxiv.org/abs/1501.00562
month: '06'
oa: 1
oa_version: Preprint
page: 1774 - 1806
publication: The Annals of Applied Probability
publication_status: published
publisher: Institute of Mathematical Statistics
publist_id: '5748'
quality_controlled: '1'
scopus_import: 1
status: public
title: Entropic Ricci curvature bounds for discrete interacting systems
type: journal_article
user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87
volume: 26
year: '2016'
...
---
_id: '1476'
abstract:
- lang: eng
text: The dynamic assembly and disassembly of actin filaments is essential for the
formation and transport of vesicles during endocytosis. In yeast, two types of
actin structures, namely cortical patches and cytoplasmic cables, play a direct
role in endocytosis, but how their interaction is regulated remains unclear. Here,
we show that Srv2/CAP, an evolutionarily conserved actin regulator, is required
for efficient endocytosis owing to its role in the formation of the actin patches
that aid initial vesicle invagination and of the actin cables that these move
along. Deletion of the SRV2 gene resulted in the appearance of aberrant fragmented
actin cables that frequently moved past actin patches, the sites of endocytosis.
We find that the C-terminal CARP domain of Srv2p is vitally important for the
proper assembly of actin patches and cables; we also demonstrate that the N-terminal
helical folded domain of Srv2 is required for its localization to actin patches,
specifically to the ADP-actin rich region through an interaction with cofilin.
These results demonstrate the in vivo roles of Srv2p in the regulation of the
actin cytoskeleton during clathrin-mediated endocytosis
acknowledgement: We are grateful to Anthony Bretscher (Cornell University, NY) for
providing the bni1-12 bnr1Δ (Y4135) strain. J.Y.T. was supported by a Japan Society
for the Promotion of Science (JSPS) KAKENHI grant [grant number 26440067]; the Takeda
Science Foundation; and the Novartis Foundation (Japan). J.T. was supported by a
JSPS KAKENHI grant [grant number 25440054]; the Takeda Science Foundation; and the
Kurata Memorial Hitachi Science and Technology Foundation. D.E.S. was supported
by the European Union [grant number PCIG12-GA-2012-334077].
author:
- first_name: Junko
full_name: Toshima, Junko
last_name: Toshima
- first_name: Chika
full_name: Horikomi, Chika
last_name: Horikomi
- first_name: Asuka
full_name: Okada, Asuka
last_name: Okada
- first_name: Makiko
full_name: Hatori, Makiko
last_name: Hatori
- first_name: Makoto
full_name: Nagano, Makoto
last_name: Nagano
- first_name: Atsushi
full_name: Masuda, Atsushi
last_name: Masuda
- first_name: Wataru
full_name: Yamamoto, Wataru
last_name: Yamamoto
- first_name: Daria E
full_name: Siekhaus, Daria E
id: 3D224B9E-F248-11E8-B48F-1D18A9856A87
last_name: Siekhaus
orcid: 0000-0001-8323-8353
- first_name: Jiro
full_name: Toshima, Jiro
last_name: Toshima
citation:
ama: Toshima J, Horikomi C, Okada A, et al. Srv2/CAP is required for polarized actin
cable assembly and patch internalization during clathrin-mediated endocytosis.
Journal of Cell Science. 2016;129(2):367-379. doi:10.1242/jcs.176651
apa: Toshima, J., Horikomi, C., Okada, A., Hatori, M., Nagano, M., Masuda, A., …
Toshima, J. (2016). Srv2/CAP is required for polarized actin cable assembly and
patch internalization during clathrin-mediated endocytosis. Journal of Cell
Science. Company of Biologists. https://doi.org/10.1242/jcs.176651
chicago: Toshima, Junko, Chika Horikomi, Asuka Okada, Makiko Hatori, Makoto Nagano,
Atsushi Masuda, Wataru Yamamoto, Daria E Siekhaus, and Jiro Toshima. “Srv2/CAP
Is Required for Polarized Actin Cable Assembly and Patch Internalization during
Clathrin-Mediated Endocytosis.” Journal of Cell Science. Company of Biologists,
2016. https://doi.org/10.1242/jcs.176651.
ieee: J. Toshima et al., “Srv2/CAP is required for polarized actin cable
assembly and patch internalization during clathrin-mediated endocytosis,” Journal
of Cell Science, vol. 129, no. 2. Company of Biologists, pp. 367–379, 2016.
ista: Toshima J, Horikomi C, Okada A, Hatori M, Nagano M, Masuda A, Yamamoto W,
Siekhaus DE, Toshima J. 2016. Srv2/CAP is required for polarized actin cable assembly
and patch internalization during clathrin-mediated endocytosis. Journal of Cell
Science. 129(2), 367–379.
mla: Toshima, Junko, et al. “Srv2/CAP Is Required for Polarized Actin Cable Assembly
and Patch Internalization during Clathrin-Mediated Endocytosis.” Journal of
Cell Science, vol. 129, no. 2, Company of Biologists, 2016, pp. 367–79, doi:10.1242/jcs.176651.
short: J. Toshima, C. Horikomi, A. Okada, M. Hatori, M. Nagano, A. Masuda, W. Yamamoto,
D.E. Siekhaus, J. Toshima, Journal of Cell Science 129 (2016) 367–379.
date_created: 2018-12-11T11:52:14Z
date_published: 2016-01-15T00:00:00Z
date_updated: 2021-01-12T06:51:00Z
day: '15'
ddc:
- '570'
- '576'
department:
- _id: DaSi
doi: 10.1242/jcs.176651
ec_funded: 1
file:
- access_level: open_access
checksum: 2da0a09149a9ed956cdf79a95c17f08a
content_type: application/pdf
creator: system
date_created: 2018-12-12T10:11:08Z
date_updated: 2020-07-14T12:44:56Z
file_id: '4861'
file_name: IST-2017-767-v1+1_367.full.pdf
file_size: 7176912
relation: main_file
file_date_updated: 2020-07-14T12:44:56Z
has_accepted_license: '1'
intvolume: ' 129'
issue: '2'
language:
- iso: eng
month: '01'
oa: 1
oa_version: Published Version
page: 367 - 379
project:
- _id: 2536F660-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '334077'
name: Investigating the role of transporters in invasive migration through junctions
publication: Journal of Cell Science
publication_status: published
publisher: Company of Biologists
publist_id: '5720'
pubrep_id: '767'
quality_controlled: '1'
scopus_import: 1
status: public
title: Srv2/CAP is required for polarized actin cable assembly and patch internalization
during clathrin-mediated endocytosis
type: journal_article
user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87
volume: 129
year: '2016'
...
---
_id: '1475'
abstract:
- lang: eng
text: The actin cytoskeleton plays important roles in the formation and internalization
of endocytic vesicles. In yeast, endocytic vesicles move towards early endosomes
along actin cables, however, the molecular machinery regulating interaction between
endocytic vesicles and actin cables is poorly understood. The Eps15-like protein
Pan1p plays a key role in actin-mediated endocytosis and is negatively regulated
by Ark1 and Prk1 kinases. Here we show that pan1 mutated to prevent phosphorylation
at all 18 threonines, pan1-18TA, displayed almost the same endocytic defect as
ark1Δ prk1Δ cells, and contained abnormal actin concentrations including several
endocytic compartments. Early endosomes were highly localized in the actin concentrations
and displayed movement along actin cables. The dephosphorylated form of Pan1p
also caused stable associations between endocytic vesicles and actin cables, and
between endocytic vesicles and endosomes. Thus Pan1 phosphorylation is part of
a novel mechanism that regulates endocytic compartment interactions with each
other and with actin cables.
article_number: e10276
author:
- first_name: Junko
full_name: Toshima, Junko
last_name: Toshima
- first_name: Eri
full_name: Furuya, Eri
last_name: Furuya
- first_name: Makoto
full_name: Nagano, Makoto
last_name: Nagano
- first_name: Chisa
full_name: Kanno, Chisa
last_name: Kanno
- first_name: Yuta
full_name: Sakamoto, Yuta
last_name: Sakamoto
- first_name: Masashi
full_name: Ebihara, Masashi
last_name: Ebihara
- first_name: Daria E
full_name: Siekhaus, Daria E
id: 3D224B9E-F248-11E8-B48F-1D18A9856A87
last_name: Siekhaus
orcid: 0000-0001-8323-8353
- first_name: Jiro
full_name: Toshima, Jiro
last_name: Toshima
citation:
ama: Toshima J, Furuya E, Nagano M, et al. Yeast Eps15-like endocytic protein Pan1p
regulates the interaction between endocytic vesicles, endosomes and the actin
cytoskeleton. eLife. 2016;5(February 2016). doi:10.7554/eLife.10276
apa: Toshima, J., Furuya, E., Nagano, M., Kanno, C., Sakamoto, Y., Ebihara, M.,
… Toshima, J. (2016). Yeast Eps15-like endocytic protein Pan1p regulates the interaction
between endocytic vesicles, endosomes and the actin cytoskeleton. ELife.
eLife Sciences Publications. https://doi.org/10.7554/eLife.10276
chicago: Toshima, Junko, Eri Furuya, Makoto Nagano, Chisa Kanno, Yuta Sakamoto,
Masashi Ebihara, Daria E Siekhaus, and Jiro Toshima. “Yeast Eps15-like Endocytic
Protein Pan1p Regulates the Interaction between Endocytic Vesicles, Endosomes
and the Actin Cytoskeleton.” ELife. eLife Sciences Publications, 2016.
https://doi.org/10.7554/eLife.10276.
ieee: J. Toshima et al., “Yeast Eps15-like endocytic protein Pan1p regulates
the interaction between endocytic vesicles, endosomes and the actin cytoskeleton,”
eLife, vol. 5, no. February 2016. eLife Sciences Publications, 2016.
ista: Toshima J, Furuya E, Nagano M, Kanno C, Sakamoto Y, Ebihara M, Siekhaus DE,
Toshima J. 2016. Yeast Eps15-like endocytic protein Pan1p regulates the interaction
between endocytic vesicles, endosomes and the actin cytoskeleton. eLife. 5(February
2016), e10276.
mla: Toshima, Junko, et al. “Yeast Eps15-like Endocytic Protein Pan1p Regulates
the Interaction between Endocytic Vesicles, Endosomes and the Actin Cytoskeleton.”
ELife, vol. 5, no. February 2016, e10276, eLife Sciences Publications,
2016, doi:10.7554/eLife.10276.
short: J. Toshima, E. Furuya, M. Nagano, C. Kanno, Y. Sakamoto, M. Ebihara, D.E.
Siekhaus, J. Toshima, ELife 5 (2016).
date_created: 2018-12-11T11:52:14Z
date_published: 2016-02-25T00:00:00Z
date_updated: 2021-01-12T06:50:59Z
day: '25'
ddc:
- '570'
department:
- _id: DaSi
doi: 10.7554/eLife.10276
ec_funded: 1
file:
- access_level: open_access
checksum: d1cc44870580756ba8badd8e41adfdb5
content_type: application/pdf
creator: system
date_created: 2018-12-12T10:10:08Z
date_updated: 2020-07-14T12:44:56Z
file_id: '4793'
file_name: IST-2016-529-v1+1_elife-10276-v1.pdf
file_size: 5198001
relation: main_file
file_date_updated: 2020-07-14T12:44:56Z
has_accepted_license: '1'
intvolume: ' 5'
issue: February 2016
language:
- iso: eng
month: '02'
oa: 1
oa_version: Published Version
project:
- _id: 2536F660-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '334077'
name: Investigating the role of transporters in invasive migration through junctions
publication: eLife
publication_status: published
publisher: eLife Sciences Publications
publist_id: '5721'
pubrep_id: '529'
quality_controlled: '1'
scopus_import: 1
status: public
title: Yeast Eps15-like endocytic protein Pan1p regulates the interaction between
endocytic vesicles, endosomes and the actin cytoskeleton
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: journal_article
user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87
volume: 5
year: '2016'
...
---
_id: '1478'
abstract:
- lang: eng
text: We consider the Tonks-Girardeau gas subject to a random external potential.
If the disorder is such that the underlying one-particle Hamiltonian displays
localization (which is known to be generically the case), we show that there is
exponential decay of correlations in the many-body eigenstates. Moreover, there
is no Bose-Einstein condensation and no superfluidity, even at zero temperature.
article_number: '035002'
author:
- first_name: Robert
full_name: Seiringer, Robert
id: 4AFD0470-F248-11E8-B48F-1D18A9856A87
last_name: Seiringer
orcid: 0000-0002-6781-0521
- first_name: Simone
full_name: Warzel, Simone
last_name: Warzel
citation:
ama: Seiringer R, Warzel S. Decay of correlations and absence of superfluidity in
the disordered Tonks-Girardeau gas. New Journal of Physics. 2016;18(3).
doi:10.1088/1367-2630/18/3/035002
apa: Seiringer, R., & Warzel, S. (2016). Decay of correlations and absence of
superfluidity in the disordered Tonks-Girardeau gas. New Journal of Physics.
IOP Publishing Ltd. https://doi.org/10.1088/1367-2630/18/3/035002
chicago: Seiringer, Robert, and Simone Warzel. “Decay of Correlations and Absence
of Superfluidity in the Disordered Tonks-Girardeau Gas.” New Journal of Physics.
IOP Publishing Ltd., 2016. https://doi.org/10.1088/1367-2630/18/3/035002.
ieee: R. Seiringer and S. Warzel, “Decay of correlations and absence of superfluidity
in the disordered Tonks-Girardeau gas,” New Journal of Physics, vol. 18,
no. 3. IOP Publishing Ltd., 2016.
ista: Seiringer R, Warzel S. 2016. Decay of correlations and absence of superfluidity
in the disordered Tonks-Girardeau gas. New Journal of Physics. 18(3), 035002.
mla: Seiringer, Robert, and Simone Warzel. “Decay of Correlations and Absence of
Superfluidity in the Disordered Tonks-Girardeau Gas.” New Journal of Physics,
vol. 18, no. 3, 035002, IOP Publishing Ltd., 2016, doi:10.1088/1367-2630/18/3/035002.
short: R. Seiringer, S. Warzel, New Journal of Physics 18 (2016).
date_created: 2018-12-11T11:52:15Z
date_published: 2016-02-29T00:00:00Z
date_updated: 2021-01-12T06:51:01Z
day: '29'
ddc:
- '510'
- '530'
department:
- _id: RoSe
doi: 10.1088/1367-2630/18/3/035002
file:
- access_level: open_access
checksum: 4f959eabc19d2a2f518318a450a4d424
content_type: application/pdf
creator: system
date_created: 2018-12-12T10:17:22Z
date_updated: 2020-07-14T12:44:56Z
file_id: '5276'
file_name: IST-2016-579-v1+1_njp_18_3_035002.pdf
file_size: 965607
relation: main_file
file_date_updated: 2020-07-14T12:44:56Z
has_accepted_license: '1'
intvolume: ' 18'
issue: '3'
language:
- iso: eng
month: '02'
oa: 1
oa_version: Published Version
project:
- _id: 25C878CE-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: P27533_N27
name: Structure of the Excitation Spectrum for Many-Body Quantum Systems
publication: New Journal of Physics
publication_status: published
publisher: IOP Publishing Ltd.
publist_id: '5716'
pubrep_id: '579'
quality_controlled: '1'
scopus_import: 1
status: public
title: Decay of correlations and absence of superfluidity in the disordered Tonks-Girardeau
gas
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: journal_article
user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87
volume: 18
year: '2016'
...
---
_id: '1480'
abstract:
- lang: eng
text: 'Exponential varieties arise from exponential families in statistics. These
real algebraic varieties have strong positivity and convexity properties, familiar
from toric varieties and their moment maps. Among them are varieties of inverses
of symmetric matrices satisfying linear constraints. This class includes Gaussian
graphical models. We develop a general theory of exponential varieties. These
are derived from hyperbolic polynomials and their integral representations. We
compare the multidegrees and ML degrees of the gradient map for hyperbolic polynomials. '
author:
- first_name: Mateusz
full_name: Michałek, Mateusz
last_name: Michałek
- first_name: Bernd
full_name: Sturmfels, Bernd
last_name: Sturmfels
- first_name: Caroline
full_name: Uhler, Caroline
id: 49ADD78E-F248-11E8-B48F-1D18A9856A87
last_name: Uhler
orcid: 0000-0002-7008-0216
- first_name: Piotr
full_name: Zwiernik, Piotr
last_name: Zwiernik
citation:
ama: Michałek M, Sturmfels B, Uhler C, Zwiernik P. Exponential varieties. Proceedings
of the London Mathematical Society. 2016;112(1):27-56. doi:10.1112/plms/pdv066
apa: Michałek, M., Sturmfels, B., Uhler, C., & Zwiernik, P. (2016). Exponential
varieties. Proceedings of the London Mathematical Society. Oxford University
Press. https://doi.org/10.1112/plms/pdv066
chicago: Michałek, Mateusz, Bernd Sturmfels, Caroline Uhler, and Piotr Zwiernik.
“Exponential Varieties.” Proceedings of the London Mathematical Society.
Oxford University Press, 2016. https://doi.org/10.1112/plms/pdv066.
ieee: M. Michałek, B. Sturmfels, C. Uhler, and P. Zwiernik, “Exponential varieties,”
Proceedings of the London Mathematical Society, vol. 112, no. 1. Oxford
University Press, pp. 27–56, 2016.
ista: Michałek M, Sturmfels B, Uhler C, Zwiernik P. 2016. Exponential varieties.
Proceedings of the London Mathematical Society. 112(1), 27–56.
mla: Michałek, Mateusz, et al. “Exponential Varieties.” Proceedings of the London
Mathematical Society, vol. 112, no. 1, Oxford University Press, 2016, pp.
27–56, doi:10.1112/plms/pdv066.
short: M. Michałek, B. Sturmfels, C. Uhler, P. Zwiernik, Proceedings of the London
Mathematical Society 112 (2016) 27–56.
date_created: 2018-12-11T11:52:16Z
date_published: 2016-01-07T00:00:00Z
date_updated: 2021-01-12T06:51:02Z
day: '07'
department:
- _id: CaUh
doi: 10.1112/plms/pdv066
intvolume: ' 112'
issue: '1'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: http://arxiv.org/abs/1412.6185
month: '01'
oa: 1
oa_version: Preprint
page: 27 - 56
publication: Proceedings of the London Mathematical Society
publication_status: published
publisher: Oxford University Press
publist_id: '5714'
quality_controlled: '1'
scopus_import: 1
status: public
title: Exponential varieties
type: journal_article
user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87
volume: 112
year: '2016'
...
---
_id: '1487'
abstract:
- lang: eng
text: Rhythms with time scales of multiple cycles per second permeate the mammalian
brain, yet neuroscientists are not certain of their functional roles. One leading
idea is that coherent oscillation between two brain regions facilitates the exchange
of information between them. In rats, the hippocampus and the vibrissal sensorimotor
system both are characterized by rhythmic oscillation in the theta range, 5–12
Hz. Previous work has been divided as to whether the two rhythms are independent
or coherent. To resolve this question, we acquired three measures from rats—whisker
motion, hippocampal local field potential (LFP), and barrel cortex unit firing—during
a whisker-mediated texture discrimination task and during control conditions (not
engaged in a whisker-mediated memory task). Compared to control conditions, the
theta band of hippocampal LFP showed a marked increase in power as the rats approached
and then palpated the texture. Phase synchronization between whisking and hippocampal
LFP increased by almost 50% during approach and texture palpation. In addition,
a greater proportion of barrel cortex neurons showed firing that was phase-locked
to hippocampal theta while rats were engaged in the discrimination task. Consistent
with a behavioral consequence of phase synchronization, the rats identified the
texture more rapidly and with lower error likelihood on trials in which there
was an increase in theta-whisking coherence at the moment of texture palpation.
These results suggest that coherence between the whisking rhythm, barrel cortex
firing, and hippocampal LFP is augmented selectively during epochs in which the
rat collects sensory information and that such coherence enhances the efficiency
of integration of stimulus information into memory and decision-making centers.
acknowledgement: We thank Eric Maris, Demian Battaglia, and Rodrigo Quian Quiroga
for useful discussions. We are grateful to Fabrizio Manzino and Marco Gigante for
construction of the behavioral apparatus, Igor Perkon for developing custom whisker
tracking software and to Francesca Pulecchi for animal care and histological processing.
article_number: e1002384
author:
- first_name: Natalia
full_name: Grion, Natalia
last_name: Grion
- first_name: Athena
full_name: Akrami, Athena
last_name: Akrami
- first_name: Yangfang
full_name: Zuo, Yangfang
last_name: Zuo
- first_name: Federico
full_name: Stella, Federico
id: 39AF1E74-F248-11E8-B48F-1D18A9856A87
last_name: Stella
orcid: 0000-0001-9439-3148
- first_name: Mathew
full_name: Diamond, Mathew
last_name: Diamond
citation:
ama: Grion N, Akrami A, Zuo Y, Stella F, Diamond M. Coherence between rat sensorimotor
system and hippocampus is enhanced during tactile discrimination. PLoS Biology.
2016;14(2). doi:10.1371/journal.pbio.1002384
apa: Grion, N., Akrami, A., Zuo, Y., Stella, F., & Diamond, M. (2016). Coherence
between rat sensorimotor system and hippocampus is enhanced during tactile discrimination.
PLoS Biology. Public Library of Science. https://doi.org/10.1371/journal.pbio.1002384
chicago: Grion, Natalia, Athena Akrami, Yangfang Zuo, Federico Stella, and Mathew
Diamond. “Coherence between Rat Sensorimotor System and Hippocampus Is Enhanced
during Tactile Discrimination.” PLoS Biology. Public Library of Science,
2016. https://doi.org/10.1371/journal.pbio.1002384.
ieee: N. Grion, A. Akrami, Y. Zuo, F. Stella, and M. Diamond, “Coherence between
rat sensorimotor system and hippocampus is enhanced during tactile discrimination,”
PLoS Biology, vol. 14, no. 2. Public Library of Science, 2016.
ista: Grion N, Akrami A, Zuo Y, Stella F, Diamond M. 2016. Coherence between rat
sensorimotor system and hippocampus is enhanced during tactile discrimination.
PLoS Biology. 14(2), e1002384.
mla: Grion, Natalia, et al. “Coherence between Rat Sensorimotor System and Hippocampus
Is Enhanced during Tactile Discrimination.” PLoS Biology, vol. 14, no.
2, e1002384, Public Library of Science, 2016, doi:10.1371/journal.pbio.1002384.
short: N. Grion, A. Akrami, Y. Zuo, F. Stella, M. Diamond, PLoS Biology 14 (2016).
date_created: 2018-12-11T11:52:18Z
date_published: 2016-02-18T00:00:00Z
date_updated: 2021-01-12T06:51:05Z
day: '18'
ddc:
- '570'
department:
- _id: JoCs
doi: 10.1371/journal.pbio.1002384
file:
- access_level: open_access
checksum: 3a5ce0d4e4e36bd6ceb4be761f85644a
content_type: application/pdf
creator: system
date_created: 2018-12-12T10:15:11Z
date_updated: 2020-07-14T12:44:57Z
file_id: '5129'
file_name: IST-2016-518-v1+1_journal.pbio.1002384.PDF
file_size: 2879899
relation: main_file
file_date_updated: 2020-07-14T12:44:57Z
has_accepted_license: '1'
intvolume: ' 14'
issue: '2'
language:
- iso: eng
month: '02'
oa: 1
oa_version: Published Version
publication: PLoS Biology
publication_status: published
publisher: Public Library of Science
publist_id: '5700'
pubrep_id: '518'
quality_controlled: '1'
scopus_import: 1
status: public
title: Coherence between rat sensorimotor system and hippocampus is enhanced during
tactile discrimination
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: journal_article
user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87
volume: 14
year: '2016'
...
---
_id: '1482'
abstract:
- lang: eng
text: Plants have the ability to continously generate new organs by maintaining
populations of stem cells throught their lives. The shoot apical meristem (SAM)
provides a stable environment for the maintenance of stem cells. All cells inside
the SAM divide, yet boundaries and patterns are maintained. Experimental evidence
indicates that patterning is independent of cell lineage, thus a dynamic self-regulatory
mechanism is required. A pivotal role in the organization of the SAM is played
by the WUSCHEL gene (WUS). An important question in this regard is that how WUS
expression is positioned in the SAM via a cell-lineage independent signaling mechanism.
In this study we demonstrate via mathematical modeling that a combination of an
inhibitor of the Cytokinin (CK) receptor, Arabidopsis histidine kinase 4 (AHK4)
and two morphogens originating from the top cell layer, can plausibly account
for the cell lineage-independent centering of WUS expression within SAM. Furthermore,
our laser ablation and microsurgical experiments support the hypothesis that patterning
in SAM occurs at the level of CK reception and signaling. The model suggests that
the interplay between CK signaling, WUS/CLV feedback loop and boundary signals
can account for positioning of the WUS expression, and provides directions for
further experimental investigation.
acknowledgement: We thank J. Traas, B. Müller and V. Reddy for providing seed materials
and Y. Deb for advice regarding the laser ablation experiments. We specially thank
Thomas Laux for stimulating discussions and support in the initial phase of this
project.
article_number: e0147830
author:
- first_name: Milad
full_name: Adibi, Milad
last_name: Adibi
- first_name: Saiko
full_name: Yoshida, Saiko
id: 2E46069C-F248-11E8-B48F-1D18A9856A87
last_name: Yoshida
- first_name: Dolf
full_name: Weijers, Dolf
last_name: Weijers
- first_name: Christian
full_name: Fleck, Christian
last_name: Fleck
citation:
ama: Adibi M, Yoshida S, Weijers D, Fleck C. Centering the organizing center in
the Arabidopsis thaliana shoot apical meristem by a combination of cytokinin signaling
and self-organization. PLoS One. 2016;11(2). doi:10.1371/journal.pone.0147830
apa: Adibi, M., Yoshida, S., Weijers, D., & Fleck, C. (2016). Centering the
organizing center in the Arabidopsis thaliana shoot apical meristem by a combination
of cytokinin signaling and self-organization. PLoS One. Public Library
of Science. https://doi.org/10.1371/journal.pone.0147830
chicago: Adibi, Milad, Saiko Yoshida, Dolf Weijers, and Christian Fleck. “Centering
the Organizing Center in the Arabidopsis Thaliana Shoot Apical Meristem by a Combination
of Cytokinin Signaling and Self-Organization.” PLoS One. Public Library
of Science, 2016. https://doi.org/10.1371/journal.pone.0147830.
ieee: M. Adibi, S. Yoshida, D. Weijers, and C. Fleck, “Centering the organizing
center in the Arabidopsis thaliana shoot apical meristem by a combination of cytokinin
signaling and self-organization,” PLoS One, vol. 11, no. 2. Public Library
of Science, 2016.
ista: Adibi M, Yoshida S, Weijers D, Fleck C. 2016. Centering the organizing center
in the Arabidopsis thaliana shoot apical meristem by a combination of cytokinin
signaling and self-organization. PLoS One. 11(2), e0147830.
mla: Adibi, Milad, et al. “Centering the Organizing Center in the Arabidopsis Thaliana
Shoot Apical Meristem by a Combination of Cytokinin Signaling and Self-Organization.”
PLoS One, vol. 11, no. 2, e0147830, Public Library of Science, 2016, doi:10.1371/journal.pone.0147830.
short: M. Adibi, S. Yoshida, D. Weijers, C. Fleck, PLoS One 11 (2016).
date_created: 2018-12-11T11:52:17Z
date_published: 2016-02-01T00:00:00Z
date_updated: 2021-01-12T06:51:03Z
day: '01'
ddc:
- '570'
department:
- _id: JiFr
doi: 10.1371/journal.pone.0147830
file:
- access_level: open_access
checksum: 6066146e527335030f83aa5924ab72a6
content_type: application/pdf
creator: system
date_created: 2018-12-12T10:14:16Z
date_updated: 2020-07-14T12:44:57Z
file_id: '5066'
file_name: IST-2016-521-v1+1_journal.pone.0147830.PDF
file_size: 4297148
relation: main_file
file_date_updated: 2020-07-14T12:44:57Z
has_accepted_license: '1'
intvolume: ' 11'
issue: '2'
language:
- iso: eng
month: '02'
oa: 1
oa_version: Published Version
publication: PLoS One
publication_status: published
publisher: Public Library of Science
publist_id: '5711'
pubrep_id: '521'
quality_controlled: '1'
scopus_import: 1
status: public
title: Centering the organizing center in the Arabidopsis thaliana shoot apical meristem
by a combination of cytokinin signaling and self-organization
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: journal_article
user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87
volume: 11
year: '2016'
...
---
_id: '1484'
acknowledgement: We thank Maciek Adamowski for helpful discussions and Qiang Zhu and
Israel Ausin for critical reading of the manuscript. We sincerely apologize to colleagues
whose work we could not include owing to space limitations.
article_type: review
author:
- first_name: Xu
full_name: Chen, Xu
id: 4E5ADCAA-F248-11E8-B48F-1D18A9856A87
last_name: Chen
- first_name: Shuang
full_name: Wu, Shuang
last_name: Wu
- first_name: Zengyu
full_name: Liu, Zengyu
last_name: Liu
- first_name: Jiřĺ
full_name: Friml, Jiřĺ
id: 4159519E-F248-11E8-B48F-1D18A9856A87
last_name: Friml
orcid: 0000-0002-8302-7596
citation:
ama: Chen X, Wu S, Liu Z, Friml J. Environmental and endogenous control of cortical
microtubule orientation. Trends in Cell Biology. 2016;26(6):409-419. doi:10.1016/j.tcb.2016.02.003
apa: Chen, X., Wu, S., Liu, Z., & Friml, J. (2016). Environmental and endogenous
control of cortical microtubule orientation. Trends in Cell Biology. Cell
Press. https://doi.org/10.1016/j.tcb.2016.02.003
chicago: Chen, Xu, Shuang Wu, Zengyu Liu, and Jiří Friml. “Environmental and Endogenous
Control of Cortical Microtubule Orientation.” Trends in Cell Biology. Cell
Press, 2016. https://doi.org/10.1016/j.tcb.2016.02.003.
ieee: X. Chen, S. Wu, Z. Liu, and J. Friml, “Environmental and endogenous control
of cortical microtubule orientation,” Trends in Cell Biology, vol. 26,
no. 6. Cell Press, pp. 409–419, 2016.
ista: Chen X, Wu S, Liu Z, Friml J. 2016. Environmental and endogenous control of
cortical microtubule orientation. Trends in Cell Biology. 26(6), 409–419.
mla: Chen, Xu, et al. “Environmental and Endogenous Control of Cortical Microtubule
Orientation.” Trends in Cell Biology, vol. 26, no. 6, Cell Press, 2016,
pp. 409–19, doi:10.1016/j.tcb.2016.02.003.
short: X. Chen, S. Wu, Z. Liu, J. Friml, Trends in Cell Biology 26 (2016) 409–419.
date_created: 2018-12-11T11:52:17Z
date_published: 2016-06-01T00:00:00Z
date_updated: 2021-01-12T06:51:04Z
day: '01'
ddc:
- '581'
department:
- _id: JiFr
doi: 10.1016/j.tcb.2016.02.003
file:
- access_level: open_access
checksum: b229e5bb4676ec3e27b7b9ea603b3a63
content_type: application/pdf
creator: system
date_created: 2018-12-12T10:15:34Z
date_updated: 2020-07-14T12:44:57Z
file_id: '5155'
file_name: IST-2018-1002-v1+1_Chen_TICB_2016_proofs.pdf
file_size: 2329117
relation: main_file
file_date_updated: 2020-07-14T12:44:57Z
has_accepted_license: '1'
intvolume: ' 26'
issue: '6'
language:
- iso: eng
month: '06'
oa: 1
oa_version: Submitted Version
page: 409 - 419
publication: Trends in Cell Biology
publication_status: published
publisher: Cell Press
publist_id: '5704'
pubrep_id: '1002'
quality_controlled: '1'
scopus_import: 1
status: public
title: Environmental and endogenous control of cortical microtubule orientation
type: journal_article
user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87
volume: 26
year: '2016'
...
---
_id: '1485'
abstract:
- lang: eng
text: In this article the notion of metabolic turnover is revisited in the light
of recent results of out-of-equilibrium thermodynamics. By means of Monte Carlo
methods we perform an exact sampling of the enzymatic fluxes in a genome scale
metabolic network of E. Coli in stationary growth conditions from which we infer
the metabolites turnover times. However the latter are inferred from net fluxes,
and we argue that this approximation is not valid for enzymes working nearby thermodynamic
equilibrium. We recalculate turnover times from total fluxes by performing an
energy balance analysis of the network and recurring to the fluctuation theorem.
We find in many cases values one of order of magnitude lower, implying a faster
picture of intermediate metabolism.
article_number: '016003'
author:
- first_name: Daniele
full_name: De Martino, Daniele
id: 3FF5848A-F248-11E8-B48F-1D18A9856A87
last_name: De Martino
orcid: 0000-0002-5214-4706
citation:
ama: De Martino D. Genome-scale estimate of the metabolic turnover of E. Coli from
the energy balance analysis. Physical Biology. 2016;13(1). doi:10.1088/1478-3975/13/1/016003
apa: De Martino, D. (2016). Genome-scale estimate of the metabolic turnover of E.
Coli from the energy balance analysis. Physical Biology. IOP Publishing
Ltd. https://doi.org/10.1088/1478-3975/13/1/016003
chicago: De Martino, Daniele. “Genome-Scale Estimate of the Metabolic Turnover of
E. Coli from the Energy Balance Analysis.” Physical Biology. IOP Publishing
Ltd., 2016. https://doi.org/10.1088/1478-3975/13/1/016003.
ieee: D. De Martino, “Genome-scale estimate of the metabolic turnover of E. Coli
from the energy balance analysis,” Physical Biology, vol. 13, no. 1. IOP
Publishing Ltd., 2016.
ista: De Martino D. 2016. Genome-scale estimate of the metabolic turnover of E.
Coli from the energy balance analysis. Physical Biology. 13(1), 016003.
mla: De Martino, Daniele. “Genome-Scale Estimate of the Metabolic Turnover of E.
Coli from the Energy Balance Analysis.” Physical Biology, vol. 13, no.
1, 016003, IOP Publishing Ltd., 2016, doi:10.1088/1478-3975/13/1/016003.
short: D. De Martino, Physical Biology 13 (2016).
date_created: 2018-12-11T11:52:18Z
date_published: 2016-01-29T00:00:00Z
date_updated: 2021-01-12T06:51:04Z
day: '29'
department:
- _id: GaTk
doi: 10.1088/1478-3975/13/1/016003
ec_funded: 1
intvolume: ' 13'
issue: '1'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: http://arxiv.org/abs/1505.04613
month: '01'
oa: 1
oa_version: Preprint
project:
- _id: 25681D80-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '291734'
name: International IST Postdoc Fellowship Programme
publication: Physical Biology
publication_status: published
publisher: IOP Publishing Ltd.
publist_id: '5702'
quality_controlled: '1'
scopus_import: 1
status: public
title: Genome-scale estimate of the metabolic turnover of E. Coli from the energy
balance analysis
type: journal_article
user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87
volume: 13
year: '2016'
...
---
_id: '1486'
abstract:
- lang: eng
text: We review recent results concerning the mathematical properties of the Bardeen-Cooper-Schrieffer
(BCS) functional of superconductivity, which were obtained in a series of papers,
partly in collaboration with R. Frank, E. Hamza, S. Naboko, and J. P. Solovej.
Our discussion includes, in particular, an investigation of the critical temperature
for a general class of interaction potentials, as well as a study of its dependence
on external fields. We shall explain how the Ginzburg-Landau model can be derived
from the BCS theory in a suitable parameter regime.
article_number: '021101'
author:
- first_name: Christian
full_name: Hainzl, Christian
last_name: Hainzl
- first_name: Robert
full_name: Seiringer, Robert
id: 4AFD0470-F248-11E8-B48F-1D18A9856A87
last_name: Seiringer
orcid: 0000-0002-6781-0521
citation:
ama: Hainzl C, Seiringer R. The Bardeen–Cooper–Schrieffer functional of superconductivity
and its mathematical properties. Journal of Mathematical Physics. 2016;57(2).
doi:10.1063/1.4941723
apa: Hainzl, C., & Seiringer, R. (2016). The Bardeen–Cooper–Schrieffer functional
of superconductivity and its mathematical properties. Journal of Mathematical
Physics. American Institute of Physics. https://doi.org/10.1063/1.4941723
chicago: Hainzl, Christian, and Robert Seiringer. “The Bardeen–Cooper–Schrieffer
Functional of Superconductivity and Its Mathematical Properties.” Journal of
Mathematical Physics. American Institute of Physics, 2016. https://doi.org/10.1063/1.4941723.
ieee: C. Hainzl and R. Seiringer, “The Bardeen–Cooper–Schrieffer functional of superconductivity
and its mathematical properties,” Journal of Mathematical Physics, vol.
57, no. 2. American Institute of Physics, 2016.
ista: Hainzl C, Seiringer R. 2016. The Bardeen–Cooper–Schrieffer functional of superconductivity
and its mathematical properties. Journal of Mathematical Physics. 57(2), 021101.
mla: Hainzl, Christian, and Robert Seiringer. “The Bardeen–Cooper–Schrieffer Functional
of Superconductivity and Its Mathematical Properties.” Journal of Mathematical
Physics, vol. 57, no. 2, 021101, American Institute of Physics, 2016, doi:10.1063/1.4941723.
short: C. Hainzl, R. Seiringer, Journal of Mathematical Physics 57 (2016).
date_created: 2018-12-11T11:52:18Z
date_published: 2016-02-24T00:00:00Z
date_updated: 2021-01-12T06:51:04Z
day: '24'
department:
- _id: RoSe
doi: 10.1063/1.4941723
intvolume: ' 57'
issue: '2'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: http://arxiv.org/abs/1511.01995
month: '02'
oa: 1
oa_version: Preprint
publication: Journal of Mathematical Physics
publication_status: published
publisher: American Institute of Physics
publist_id: '5701'
quality_controlled: '1'
scopus_import: 1
status: public
title: The Bardeen–Cooper–Schrieffer functional of superconductivity and its mathematical
properties
type: journal_article
user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87
volume: 57
year: '2016'
...
---
_id: '1488'
abstract:
- lang: eng
text: Branching morphogenesis of the epithelial ureteric bud forms the renal collecting
duct system and is critical for normal nephron number, while low nephron number
is implicated in hypertension and renal disease. Ureteric bud growth and branching
requires GDNF signaling from the surrounding mesenchyme to cells at the ureteric
bud tips, via the Ret receptor tyrosine kinase and coreceptor Gfrα1; Ret signaling
up-regulates transcription factors Etv4 and Etv5, which are also critical for
branching. Despite extensive knowledge of the genetic control of these events,
it is not understood, at the cellular level, how renal branching morphogenesis
is achieved or how Ret signaling influences epithelial cell behaviors to promote
this process. Analysis of chimeric embryos previously suggested a role for Ret
signaling in promoting cell rearrangements in the nephric duct, but this method
was unsuited to study individual cell behaviors during ureteric bud branching.
Here, we use Mosaic Analysis with Double Markers (MADM), combined with organ culture
and time-lapse imaging, to trace the movements and divisions of individual ureteric
bud tip cells. We first examine wild-type clones and then Ret or Etv4 mutant/wild-type
clones in which the mutant and wild-type sister cells are differentially and heritably
marked by green and red fluorescent proteins. We find that, in normal kidneys,
most individual tip cells behave as self-renewing progenitors, some of whose progeny
remain at the tips while others populate the growing UB trunks. In Ret or Etv4
MADM clones, the wild-type cells generated at a UB tip are much more likely to
remain at, or move to, the new tips during branching and elongation, while their
Ret−/− or Etv4−/− sister cells tend to lag behind and contribute only to the trunks.
By tracking successive mitoses in a cell lineage, we find that Ret signaling has
little effect on proliferation, in contrast to its effects on cell movement. Our
results show that Ret/Etv4 signaling promotes directed cell movements in the ureteric
bud tips, and suggest a model in which these cell movements mediate branching
morphogenesis.
acknowledgement: We thank Silvia Arber, Thomas Jessell, Kenneth M. Murphy, Carlton
Bates, Hideki Enomoto, Liqun Luo and Andrew McMahon for mouse strains; Thomas Jessell
for antibodies; and Laura Martinez Prat for experimental assistance.
article_number: e1002382
author:
- first_name: Paul
full_name: Riccio, Paul
last_name: Riccio
- first_name: Cristina
full_name: Cebrián, Cristina
last_name: Cebrián
- first_name: Hui
full_name: Zong, Hui
last_name: Zong
- first_name: Simon
full_name: Hippenmeyer, Simon
id: 37B36620-F248-11E8-B48F-1D18A9856A87
last_name: Hippenmeyer
orcid: 0000-0003-2279-1061
- first_name: Frank
full_name: Costantini, Frank
last_name: Costantini
citation:
ama: Riccio P, Cebrián C, Zong H, Hippenmeyer S, Costantini F. Ret and Etv4 promote
directed movements of progenitor cells during renal branching morphogenesis. PLoS
Biology. 2016;14(2). doi:10.1371/journal.pbio.1002382
apa: Riccio, P., Cebrián, C., Zong, H., Hippenmeyer, S., & Costantini, F. (2016).
Ret and Etv4 promote directed movements of progenitor cells during renal branching
morphogenesis. PLoS Biology. Public Library of Science. https://doi.org/10.1371/journal.pbio.1002382
chicago: Riccio, Paul, Cristina Cebrián, Hui Zong, Simon Hippenmeyer, and Frank
Costantini. “Ret and Etv4 Promote Directed Movements of Progenitor Cells during
Renal Branching Morphogenesis.” PLoS Biology. Public Library of Science,
2016. https://doi.org/10.1371/journal.pbio.1002382.
ieee: P. Riccio, C. Cebrián, H. Zong, S. Hippenmeyer, and F. Costantini, “Ret and
Etv4 promote directed movements of progenitor cells during renal branching morphogenesis,”
PLoS Biology, vol. 14, no. 2. Public Library of Science, 2016.
ista: Riccio P, Cebrián C, Zong H, Hippenmeyer S, Costantini F. 2016. Ret and Etv4
promote directed movements of progenitor cells during renal branching morphogenesis.
PLoS Biology. 14(2), e1002382.
mla: Riccio, Paul, et al. “Ret and Etv4 Promote Directed Movements of Progenitor
Cells during Renal Branching Morphogenesis.” PLoS Biology, vol. 14, no.
2, e1002382, Public Library of Science, 2016, doi:10.1371/journal.pbio.1002382.
short: P. Riccio, C. Cebrián, H. Zong, S. Hippenmeyer, F. Costantini, PLoS Biology
14 (2016).
date_created: 2018-12-11T11:52:19Z
date_published: 2016-02-19T00:00:00Z
date_updated: 2023-02-23T10:01:08Z
day: '19'
ddc:
- '570'
department:
- _id: SiHi
doi: 10.1371/journal.pbio.1002382
file:
- access_level: open_access
checksum: 7f8fa1b3a29f94c0a14dd4465278cdbc
content_type: application/pdf
creator: system
date_created: 2018-12-12T10:13:42Z
date_updated: 2020-07-14T12:44:57Z
file_id: '5027'
file_name: IST-2016-517-v1+1_journal.pbio.1002382_1_.PDF
file_size: 5904773
relation: main_file
file_date_updated: 2020-07-14T12:44:57Z
has_accepted_license: '1'
intvolume: ' 14'
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language:
- iso: eng
month: '02'
oa: 1
oa_version: Published Version
publication: PLoS Biology
publication_status: published
publisher: Public Library of Science
publist_id: '5699'
pubrep_id: '517'
quality_controlled: '1'
related_material:
record:
- id: '9703'
relation: research_data
status: deleted
scopus_import: 1
status: public
title: Ret and Etv4 promote directed movements of progenitor cells during renal branching
morphogenesis
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: journal_article
user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87
volume: 14
year: '2016'
...
---
_id: '1489'
abstract:
- lang: eng
text: 'We prove optimal local law, bulk universality and non-trivial decay for the
off-diagonal elements of the resolvent for a class of translation invariant Gaussian
random matrix ensembles with correlated entries. '
acknowledgement: Open access funding provided by Institute of Science and Technology
(IST Austria). Oskari H. Ajanki was Partially supported by ERC Advanced Grant RANMAT
No. 338804, and SFB-TR 12 Grant of the German Research Council. László Erdős was
Partially supported by ERC Advanced Grant RANMAT No. 338804. Torben Krüger was Partially
supported by ERC Advanced Grant RANMAT No. 338804, and SFB-TR 12 Grant of the German
Research Council.
article_processing_charge: Yes (via OA deal)
author:
- first_name: Oskari H
full_name: Ajanki, Oskari H
id: 36F2FB7E-F248-11E8-B48F-1D18A9856A87
last_name: Ajanki
- first_name: László
full_name: Erdös, László
id: 4DBD5372-F248-11E8-B48F-1D18A9856A87
last_name: Erdös
orcid: 0000-0001-5366-9603
- first_name: Torben H
full_name: Krüger, Torben H
id: 3020C786-F248-11E8-B48F-1D18A9856A87
last_name: Krüger
orcid: 0000-0002-4821-3297
citation:
ama: Ajanki OH, Erdös L, Krüger TH. Local spectral statistics of Gaussian matrices
with correlated entries. Journal of Statistical Physics. 2016;163(2):280-302.
doi:10.1007/s10955-016-1479-y
apa: Ajanki, O. H., Erdös, L., & Krüger, T. H. (2016). Local spectral statistics
of Gaussian matrices with correlated entries. Journal of Statistical Physics.
Springer. https://doi.org/10.1007/s10955-016-1479-y
chicago: Ajanki, Oskari H, László Erdös, and Torben H Krüger. “Local Spectral Statistics
of Gaussian Matrices with Correlated Entries.” Journal of Statistical Physics.
Springer, 2016. https://doi.org/10.1007/s10955-016-1479-y.
ieee: O. H. Ajanki, L. Erdös, and T. H. Krüger, “Local spectral statistics of Gaussian
matrices with correlated entries,” Journal of Statistical Physics, vol.
163, no. 2. Springer, pp. 280–302, 2016.
ista: Ajanki OH, Erdös L, Krüger TH. 2016. Local spectral statistics of Gaussian
matrices with correlated entries. Journal of Statistical Physics. 163(2), 280–302.
mla: Ajanki, Oskari H., et al. “Local Spectral Statistics of Gaussian Matrices with
Correlated Entries.” Journal of Statistical Physics, vol. 163, no. 2, Springer,
2016, pp. 280–302, doi:10.1007/s10955-016-1479-y.
short: O.H. Ajanki, L. Erdös, T.H. Krüger, Journal of Statistical Physics 163 (2016)
280–302.
date_created: 2018-12-11T11:52:19Z
date_published: 2016-04-01T00:00:00Z
date_updated: 2021-01-12T06:51:05Z
day: '01'
ddc:
- '510'
department:
- _id: LaEr
doi: 10.1007/s10955-016-1479-y
ec_funded: 1
file:
- access_level: open_access
checksum: 7139598dcb1cafbe6866bd2bfd732b33
content_type: application/pdf
creator: system
date_created: 2018-12-12T10:11:16Z
date_updated: 2020-07-14T12:44:57Z
file_id: '4869'
file_name: IST-2016-516-v1+1_s10955-016-1479-y.pdf
file_size: 660602
relation: main_file
file_date_updated: 2020-07-14T12:44:57Z
has_accepted_license: '1'
intvolume: ' 163'
issue: '2'
language:
- iso: eng
month: '04'
oa: 1
oa_version: Published Version
page: 280 - 302
project:
- _id: 258DCDE6-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '338804'
name: Random matrices, universality and disordered quantum systems
- _id: B67AFEDC-15C9-11EA-A837-991A96BB2854
name: IST Austria Open Access Fund
publication: Journal of Statistical Physics
publication_status: published
publisher: Springer
publist_id: '5698'
pubrep_id: '516'
quality_controlled: '1'
scopus_import: 1
status: public
title: Local spectral statistics of Gaussian matrices with correlated entries
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: 163
year: '2016'
...
---
_id: '1490'
abstract:
- lang: eng
text: To induce adaptive immunity, dendritic cells (DCs) migrate through afferent
lymphatic vessels (LVs) to draining lymph nodes (dLNs). This process occurs in
several consecutive steps. Upon entry into lymphatic capillaries, DCs first actively
crawl into downstream collecting vessels. From there, they are next passively
and rapidly transported to the dLN by lymph flow. Here, we describe a role for
the chemokine CCL21 in intralymphatic DC crawling. Performing time-lapse imaging
in murine skin, we found that blockade of CCL21-but not the absence of lymph flow-completely
abolished DC migration from capillaries toward collecting vessels and reduced
the ability of intralymphatic DCs to emigrate from skin. Moreover, we found that
in vitro low laminar flow established a CCL21 gradient along lymphatic endothelial
monolayers, thereby inducing downstream-directed DC migration. These findings
reveal a role for intralymphatic CCL21 in promoting DC trafficking to dLNs, through
the formation of a flow-induced gradient.
author:
- first_name: Erica
full_name: Russo, Erica
last_name: Russo
- first_name: Alvaro
full_name: Teijeira, Alvaro
last_name: Teijeira
- first_name: Kari
full_name: Vaahtomeri, Kari
id: 368EE576-F248-11E8-B48F-1D18A9856A87
last_name: Vaahtomeri
orcid: 0000-0001-7829-3518
- first_name: Ann
full_name: Willrodt, Ann
last_name: Willrodt
- first_name: Joël
full_name: Bloch, Joël
last_name: Bloch
- first_name: Maximilian
full_name: Nitschké, Maximilian
last_name: Nitschké
- first_name: Laura
full_name: Santambrogio, Laura
last_name: Santambrogio
- first_name: Dontscho
full_name: Kerjaschki, Dontscho
last_name: Kerjaschki
- first_name: Michael K
full_name: Sixt, Michael K
id: 41E9FBEA-F248-11E8-B48F-1D18A9856A87
last_name: Sixt
orcid: 0000-0002-6620-9179
- first_name: Cornelia
full_name: Halin, Cornelia
last_name: Halin
citation:
ama: Russo E, Teijeira A, Vaahtomeri K, et al. Intralymphatic CCL21 promotes tissue
egress of dendritic cells through afferent lymphatic vessels. Cell Reports.
2016;14(7):1723-1734. doi:10.1016/j.celrep.2016.01.048
apa: Russo, E., Teijeira, A., Vaahtomeri, K., Willrodt, A., Bloch, J., Nitschké,
M., … Halin, C. (2016). Intralymphatic CCL21 promotes tissue egress of dendritic
cells through afferent lymphatic vessels. Cell Reports. Cell Press. https://doi.org/10.1016/j.celrep.2016.01.048
chicago: Russo, Erica, Alvaro Teijeira, Kari Vaahtomeri, Ann Willrodt, Joël Bloch,
Maximilian Nitschké, Laura Santambrogio, Dontscho Kerjaschki, Michael K Sixt,
and Cornelia Halin. “Intralymphatic CCL21 Promotes Tissue Egress of Dendritic
Cells through Afferent Lymphatic Vessels.” Cell Reports. Cell Press, 2016.
https://doi.org/10.1016/j.celrep.2016.01.048.
ieee: E. Russo et al., “Intralymphatic CCL21 promotes tissue egress of dendritic
cells through afferent lymphatic vessels,” Cell Reports, vol. 14, no. 7.
Cell Press, pp. 1723–1734, 2016.
ista: Russo E, Teijeira A, Vaahtomeri K, Willrodt A, Bloch J, Nitschké M, Santambrogio
L, Kerjaschki D, Sixt MK, Halin C. 2016. Intralymphatic CCL21 promotes tissue
egress of dendritic cells through afferent lymphatic vessels. Cell Reports. 14(7),
1723–1734.
mla: Russo, Erica, et al. “Intralymphatic CCL21 Promotes Tissue Egress of Dendritic
Cells through Afferent Lymphatic Vessels.” Cell Reports, vol. 14, no. 7,
Cell Press, 2016, pp. 1723–34, doi:10.1016/j.celrep.2016.01.048.
short: E. Russo, A. Teijeira, K. Vaahtomeri, A. Willrodt, J. Bloch, M. Nitschké,
L. Santambrogio, D. Kerjaschki, M.K. Sixt, C. Halin, Cell Reports 14 (2016) 1723–1734.
date_created: 2018-12-11T11:52:19Z
date_published: 2016-02-23T00:00:00Z
date_updated: 2021-01-12T06:51:07Z
day: '23'
ddc:
- '570'
department:
- _id: MiSi
doi: 10.1016/j.celrep.2016.01.048
file:
- access_level: open_access
checksum: c98c1151d5f1e5ce1643a83d8d7f3c29
content_type: application/pdf
creator: system
date_created: 2018-12-12T10:12:30Z
date_updated: 2020-07-14T12:44:58Z
file_id: '4948'
file_name: IST-2016-515-v1+1_1-s2.0-S2211124716300262-main.pdf
file_size: 5489897
relation: main_file
file_date_updated: 2020-07-14T12:44:58Z
has_accepted_license: '1'
intvolume: ' 14'
issue: '7'
language:
- iso: eng
month: '02'
oa: 1
oa_version: Published Version
page: 1723 - 1734
publication: Cell Reports
publication_status: published
publisher: Cell Press
publist_id: '5697'
pubrep_id: '515'
quality_controlled: '1'
scopus_import: 1
status: public
title: Intralymphatic CCL21 promotes tissue egress of dendritic cells through afferent
lymphatic vessels
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: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87
volume: 14
year: '2016'
...
---
_id: '1493'
abstract:
- lang: eng
text: We introduce a new method for deriving the time-dependent Hartree or Hartree-Fock
equations as an effective mean-field dynamics from the microscopic Schrödinger
equation for fermionic many-particle systems in quantum mechanics. The method
is an adaption of the method used in Pickl (Lett. Math. Phys. 97 (2) 151–164 2011)
for bosonic systems to fermionic systems. It is based on a Gronwall type estimate
for a suitable measure of distance between the microscopic solution and an antisymmetrized
product state. We use this method to treat a new mean-field limit for fermions
with long-range interactions in a large volume. Some of our results hold for singular
attractive or repulsive interactions. We can also treat Coulomb interaction assuming
either a mild singularity cutoff or certain regularity conditions on the solutions
to the Hartree(-Fock) equations. In the considered limit, the kinetic and interaction
energy are of the same order, while the average force is subleading. For some
interactions, we prove that the Hartree(-Fock) dynamics is a more accurate approximation
than a simpler dynamics that one would expect from the subleading force. With
our method we also treat the mean-field limit coupled to a semiclassical limit,
which was discussed in the literature before, and we recover some of the previous
results. All results hold for initial data close (but not necessarily equal) to
antisymmetrized product states and we always provide explicit rates of convergence.
acknowledgement: 'Open access funding provided by Institute of Science and Technology
(IST Austria). '
article_number: '3'
article_processing_charge: Yes (via OA deal)
author:
- first_name: Sören P
full_name: Petrat, Sören P
id: 40AC02DC-F248-11E8-B48F-1D18A9856A87
last_name: Petrat
orcid: 0000-0002-9166-5889
- first_name: Peter
full_name: Pickl, Peter
last_name: Pickl
citation:
ama: Petrat SP, Pickl P. A new method and a new scaling for deriving fermionic mean-field
dynamics. Mathematical Physics, Analysis and Geometry. 2016;19(1). doi:10.1007/s11040-016-9204-2
apa: Petrat, S. P., & Pickl, P. (2016). A new method and a new scaling for deriving
fermionic mean-field dynamics. Mathematical Physics, Analysis and Geometry.
Springer. https://doi.org/10.1007/s11040-016-9204-2
chicago: Petrat, Sören P, and Peter Pickl. “A New Method and a New Scaling for Deriving
Fermionic Mean-Field Dynamics.” Mathematical Physics, Analysis and Geometry.
Springer, 2016. https://doi.org/10.1007/s11040-016-9204-2.
ieee: S. P. Petrat and P. Pickl, “A new method and a new scaling for deriving fermionic
mean-field dynamics,” Mathematical Physics, Analysis and Geometry, vol.
19, no. 1. Springer, 2016.
ista: Petrat SP, Pickl P. 2016. A new method and a new scaling for deriving fermionic
mean-field dynamics. Mathematical Physics, Analysis and Geometry. 19(1), 3.
mla: Petrat, Sören P., and Peter Pickl. “A New Method and a New Scaling for Deriving
Fermionic Mean-Field Dynamics.” Mathematical Physics, Analysis and Geometry,
vol. 19, no. 1, 3, Springer, 2016, doi:10.1007/s11040-016-9204-2.
short: S.P. Petrat, P. Pickl, Mathematical Physics, Analysis and Geometry 19 (2016).
date_created: 2018-12-11T11:52:20Z
date_published: 2016-03-01T00:00:00Z
date_updated: 2021-01-12T06:51:08Z
day: '01'
ddc:
- '510'
- '530'
department:
- _id: RoSe
doi: 10.1007/s11040-016-9204-2
ec_funded: 1
file:
- access_level: open_access
checksum: eb5d2145ef0d377c4f78bf06e18f4529
content_type: application/pdf
creator: system
date_created: 2018-12-12T10:16:55Z
date_updated: 2020-07-14T12:44:58Z
file_id: '5246'
file_name: IST-2016-514-v1+1_s11040-016-9204-2.pdf
file_size: 911310
relation: main_file
file_date_updated: 2020-07-14T12:44:58Z
has_accepted_license: '1'
intvolume: ' 19'
issue: '1'
language:
- iso: eng
month: '03'
oa: 1
oa_version: Published Version
project:
- _id: 25681D80-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '291734'
name: International IST Postdoc Fellowship Programme
- _id: B67AFEDC-15C9-11EA-A837-991A96BB2854
name: IST Austria Open Access Fund
publication: Mathematical Physics, Analysis and Geometry
publication_status: published
publisher: Springer
publist_id: '5690'
pubrep_id: '514'
quality_controlled: '1'
scopus_import: 1
status: public
title: A new method and a new scaling for deriving fermionic mean-field dynamics
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: 19
year: '2016'
...
---
_id: '1492'
abstract:
- lang: eng
text: To sustain a lifelong ability to initiate organs, plants retain pools of undifferentiated
cells with a preserved prolif eration capacity. The root pericycle represents
a unique tissue with conditional meristematic activity, and its tight control
determines initiation of lateral organs. Here we show that the meristematic activity
of the pericycle is constrained by the interaction with the adjacent endodermis.
Release of these restraints by elimination of endo dermal cells by single-cell
ablation triggers the pericycle to re-enter the cell cycle. We found that endodermis
removal substitutes for the phytohormone auxin-dependent initiation of the pericycle
meristematic activity. However, auxin is indispensable to steer the cell division
plane orientation of new organ-defining divisions. We propose a dual, spatiotemporally
distinct role for auxin during lateral root initiation. In the endodermis, auxin
releases constraints arising from cell-to-cell interactions that compromise the
pericycle meristematic activity, whereas, in the pericycle, auxin defines the
orientation of the cell division plane to initiate lateral roots.
acknowledged_ssus:
- _id: LifeSc
acknowledgement: 'This work was supported by a European Research Council Starting
Inde-pendent Research grant (ERC-2007-Stg-207362-HCPO to J.D.), Research Foundation-Flanders
(G033711N to A.A.), and the Austrian Science Fund (FWF01_I1774S to E.B.). P.M. is
indebted to the Federation of European Biochemical Sciences for a Long-Term Fellowship. '
author:
- first_name: Peter
full_name: Marhavy, Peter
id: 3F45B078-F248-11E8-B48F-1D18A9856A87
last_name: Marhavy
orcid: 0000-0001-5227-5741
- first_name: Juan C
full_name: Montesinos López, Juan C
id: 310A8E3E-F248-11E8-B48F-1D18A9856A87
last_name: Montesinos López
orcid: 0000-0001-9179-6099
- first_name: Anas
full_name: Abuzeineh, Anas
last_name: Abuzeineh
- first_name: Daniël
full_name: Van Damme, Daniël
last_name: Van Damme
- first_name: Joop
full_name: Vermeer, Joop
last_name: Vermeer
- first_name: Jérôme
full_name: Duclercq, Jérôme
last_name: Duclercq
- first_name: Hana
full_name: Rakusova, Hana
last_name: Rakusova
- first_name: Petra
full_name: Marhavá, Petra
id: 44E59624-F248-11E8-B48F-1D18A9856A87
last_name: Marhavá
- first_name: Jirí
full_name: Friml, Jirí
id: 4159519E-F248-11E8-B48F-1D18A9856A87
last_name: Friml
orcid: 0000-0002-8302-7596
- first_name: Niko
full_name: Geldner, Niko
last_name: Geldner
- first_name: Eva
full_name: Benková, Eva
id: 38F4F166-F248-11E8-B48F-1D18A9856A87
last_name: Benková
orcid: 0000-0002-8510-9739
citation:
ama: Marhavý P, Montesinos López JC, Abuzeineh A, et al. Targeted cell elimination
reveals an auxin-guided biphasic mode of lateral root initiation. Genes and
Development. 2016;30(4):471-483. doi:10.1101/gad.276964.115
apa: Marhavý, P., Montesinos López, J. C., Abuzeineh, A., Van Damme, D., Vermeer,
J., Duclercq, J., … Benková, E. (2016). Targeted cell elimination reveals an auxin-guided
biphasic mode of lateral root initiation. Genes and Development. Cold Spring
Harbor Laboratory Press. https://doi.org/10.1101/gad.276964.115
chicago: Marhavý, Peter, Juan C Montesinos López, Anas Abuzeineh, Daniël Van Damme,
Joop Vermeer, Jérôme Duclercq, Hana Rakusova, et al. “Targeted Cell Elimination
Reveals an Auxin-Guided Biphasic Mode of Lateral Root Initiation.” Genes and
Development. Cold Spring Harbor Laboratory Press, 2016. https://doi.org/10.1101/gad.276964.115.
ieee: P. Marhavý et al., “Targeted cell elimination reveals an auxin-guided
biphasic mode of lateral root initiation,” Genes and Development, vol.
30, no. 4. Cold Spring Harbor Laboratory Press, pp. 471–483, 2016.
ista: Marhavý P, Montesinos López JC, Abuzeineh A, Van Damme D, Vermeer J, Duclercq
J, Rakusova H, Marhavá P, Friml J, Geldner N, Benková E. 2016. Targeted cell elimination
reveals an auxin-guided biphasic mode of lateral root initiation. Genes and Development.
30(4), 471–483.
mla: Marhavý, Peter, et al. “Targeted Cell Elimination Reveals an Auxin-Guided Biphasic
Mode of Lateral Root Initiation.” Genes and Development, vol. 30, no. 4,
Cold Spring Harbor Laboratory Press, 2016, pp. 471–83, doi:10.1101/gad.276964.115.
short: P. Marhavý, J.C. Montesinos López, A. Abuzeineh, D. Van Damme, J. Vermeer,
J. Duclercq, H. Rakusova, P. Marhavá, J. Friml, N. Geldner, E. Benková, Genes
and Development 30 (2016) 471–483.
date_created: 2018-12-11T11:52:20Z
date_published: 2016-03-01T00:00:00Z
date_updated: 2021-01-12T06:51:08Z
day: '01'
ddc:
- '570'
department:
- _id: EvBe
doi: 10.1101/gad.276964.115
external_id:
pmid:
- ' 26883363'
file:
- access_level: open_access
checksum: ea394498ee56270e021d1028a29358a0
content_type: application/pdf
creator: kschuh
date_created: 2019-01-25T09:56:11Z
date_updated: 2020-07-14T12:44:58Z
file_id: '5883'
file_name: 2016_GeneDev_Marhavy.pdf
file_size: 2757636
relation: main_file
file_date_updated: 2020-07-14T12:44:58Z
has_accepted_license: '1'
intvolume: ' 30'
issue: '4'
language:
- iso: eng
month: '03'
oa: 1
oa_version: Published Version
page: 471 - 483
pmid: 1
publication: Genes and Development
publication_status: published
publisher: Cold Spring Harbor Laboratory Press
publist_id: '5691'
quality_controlled: '1'
scopus_import: 1
status: public
title: Targeted cell elimination reveals an auxin-guided biphasic mode of lateral
root initiation
tmp:
image: /images/cc_by_nc.png
legal_code_url: https://creativecommons.org/licenses/by-nc/4.0/legalcode
name: Creative Commons Attribution-NonCommercial 4.0 International (CC BY-NC 4.0)
short: CC BY-NC (4.0)
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 30
year: '2016'
...
---
_id: '1496'
abstract:
- lang: eng
text: The two-photon 1s2 2s 2p 3P0 1s22s2 1S0 transition in berylliumlike ions is
theoretically investigated within a fully relativistic framework and a second-order
perturbation theory. We focus our analysis on how electron correlation, as well
as the negative-energy spectrum, can affect the forbidden E1M1 decay rate. For
this purpose, we include the electronic correlation via an effective local potential
and within a single configuration-state model. Due to its experimental interest,
evaluations of decay rates are performed for berylliumlike xenon and uranium.
We find that the negative-energy contribution can be neglected at the present
level of accuracy in the evaluation of the decay rate. On the other hand, if contributions
of electronic correlation are not carefully taken into account, it may change
the lifetime of the metastable state by up to 20%. By performing a full-relativistic
jj-coupling calculation, we found a decrease of the decay rate by two orders of
magnitude compared to non-relativistic LS-coupling calculations, for the selected
heavy ions.
acknowledgement: 'This research was supported in part by FCT, Portugal, through
Project No. PTDC/FIS/117606/2010, financed by the European Community Fund FEDER through the COMPETE. '
article_number: '032502'
author:
- first_name: Pedro
full_name: Amaro, Pedro
last_name: Amaro
- first_name: Filippo
full_name: Fratini, Filippo
last_name: Fratini
- first_name: Laleh
full_name: Safari, Laleh
id: 3C325E5E-F248-11E8-B48F-1D18A9856A87
last_name: Safari
- first_name: Jorge
full_name: Machado, Jorge
last_name: Machado
- first_name: Mauro
full_name: Guerra, Mauro
last_name: Guerra
- first_name: Paul
full_name: Indelicato, Paul
last_name: Indelicato
- first_name: José
full_name: Santos, José
last_name: Santos
citation:
ama: Amaro P, Fratini F, Safari L, et al. Relativistic evaluation of the two-photon
decay of the metastable 1s22s2p3P0 state in berylliumlike ions with an effective-potential
model. Physical Review A - Atomic, Molecular, and Optical Physics. 2016;93(3).
doi:10.1103/PhysRevA.93.032502
apa: Amaro, P., Fratini, F., Safari, L., Machado, J., Guerra, M., Indelicato, P.,
& Santos, J. (2016). Relativistic evaluation of the two-photon decay of the
metastable 1s22s2p3P0 state in berylliumlike ions with an effective-potential
model. Physical Review A - Atomic, Molecular, and Optical Physics. American
Physical Society. https://doi.org/10.1103/PhysRevA.93.032502
chicago: Amaro, Pedro, Filippo Fratini, Laleh Safari, Jorge Machado, Mauro Guerra,
Paul Indelicato, and José Santos. “Relativistic Evaluation of the Two-Photon Decay
of the Metastable 1s22s2p3P0 State in Berylliumlike Ions with an Effective-Potential
Model.” Physical Review A - Atomic, Molecular, and Optical Physics. American
Physical Society, 2016. https://doi.org/10.1103/PhysRevA.93.032502.
ieee: P. Amaro et al., “Relativistic evaluation of the two-photon decay of
the metastable 1s22s2p3P0 state in berylliumlike ions with an effective-potential
model,” Physical Review A - Atomic, Molecular, and Optical Physics, vol.
93, no. 3. American Physical Society, 2016.
ista: Amaro P, Fratini F, Safari L, Machado J, Guerra M, Indelicato P, Santos J.
2016. Relativistic evaluation of the two-photon decay of the metastable 1s22s2p3P0
state in berylliumlike ions with an effective-potential model. Physical Review
A - Atomic, Molecular, and Optical Physics. 93(3), 032502.
mla: Amaro, Pedro, et al. “Relativistic Evaluation of the Two-Photon Decay of the
Metastable 1s22s2p3P0 State in Berylliumlike Ions with an Effective-Potential
Model.” Physical Review A - Atomic, Molecular, and Optical Physics, vol.
93, no. 3, 032502, American Physical Society, 2016, doi:10.1103/PhysRevA.93.032502.
short: P. Amaro, F. Fratini, L. Safari, J. Machado, M. Guerra, P. Indelicato, J.
Santos, Physical Review A - Atomic, Molecular, and Optical Physics 93 (2016).
date_created: 2018-12-11T11:52:21Z
date_published: 2016-03-07T00:00:00Z
date_updated: 2021-01-12T06:51:09Z
day: '07'
department:
- _id: MiLe
doi: 10.1103/PhysRevA.93.032502
ec_funded: 1
intvolume: ' 93'
issue: '3'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: http://arxiv.org/abs/1508.06169
month: '03'
oa: 1
oa_version: Preprint
project:
- _id: 25681D80-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '291734'
name: International IST Postdoc Fellowship Programme
publication: Physical Review A - Atomic, Molecular, and Optical Physics
publication_status: published
publisher: American Physical Society
publist_id: '5683'
quality_controlled: '1'
scopus_import: 1
status: public
title: Relativistic evaluation of the two-photon decay of the metastable 1s22s2p3P0
state in berylliumlike ions with an effective-potential model
type: journal_article
user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87
volume: 93
year: '2016'
...
---
_id: '1491'
abstract:
- lang: eng
text: We study the ground state of a trapped Bose gas, starting from the full many-body
Schrödinger Hamiltonian, and derive the non-linear Schrödinger energy functional
in the limit of a large particle number, when the interaction potential converges
slowly to a Dirac delta function. Our method is based on quantitative estimates
on the discrepancy between the full many-body energy and its mean-field approximation
using Hartree states. These are proved using finite dimensional localization and
a quantitative version of the quantum de Finetti theorem. Our approach covers
the case of attractive interactions in the regime of stability. In particular,
our main new result is a derivation of the 2D attractive non-linear Schrödinger
ground state.
acknowledgement: The authors acknowledge financial support from the European Research
Council (FP7/2007-2013 Grant Agreement MNIQS 258023) and the ANR (Mathostaq project,
ANR-13-JS01-0005-01). The second and third authors have benefited from the hospitality
of the Institute for Mathematical Science of the National University of Singapore.
author:
- first_name: Mathieu
full_name: Lewin, Mathieu
last_name: Lewin
- first_name: Phan
full_name: Nam, Phan
id: 404092F4-F248-11E8-B48F-1D18A9856A87
last_name: Nam
- first_name: Nicolas
full_name: Rougerie, Nicolas
last_name: Rougerie
citation:
ama: Lewin M, Nam P, Rougerie N. The mean-field approximation and the non-linear
Schrödinger functional for trapped Bose gases. Transactions of the American
Mathematical Society. 2016;368(9):6131-6157. doi:10.1090/tran/6537
apa: Lewin, M., Nam, P., & Rougerie, N. (2016). The mean-field approximation
and the non-linear Schrödinger functional for trapped Bose gases. Transactions
of the American Mathematical Society. American Mathematical Society. https://doi.org/10.1090/tran/6537
chicago: Lewin, Mathieu, Phan Nam, and Nicolas Rougerie. “The Mean-Field Approximation
and the Non-Linear Schrödinger Functional for Trapped Bose Gases.” Transactions
of the American Mathematical Society. American Mathematical Society, 2016.
https://doi.org/10.1090/tran/6537.
ieee: M. Lewin, P. Nam, and N. Rougerie, “The mean-field approximation and the non-linear
Schrödinger functional for trapped Bose gases,” Transactions of the American
Mathematical Society, vol. 368, no. 9. American Mathematical Society, pp.
6131–6157, 2016.
ista: Lewin M, Nam P, Rougerie N. 2016. The mean-field approximation and the non-linear
Schrödinger functional for trapped Bose gases. Transactions of the American Mathematical
Society. 368(9), 6131–6157.
mla: Lewin, Mathieu, et al. “The Mean-Field Approximation and the Non-Linear Schrödinger
Functional for Trapped Bose Gases.” Transactions of the American Mathematical
Society, vol. 368, no. 9, American Mathematical Society, 2016, pp. 6131–57,
doi:10.1090/tran/6537.
short: M. Lewin, P. Nam, N. Rougerie, Transactions of the American Mathematical
Society 368 (2016) 6131–6157.
date_created: 2018-12-11T11:52:20Z
date_published: 2016-01-01T00:00:00Z
date_updated: 2021-01-12T06:51:07Z
day: '01'
department:
- _id: RoSe
doi: 10.1090/tran/6537
intvolume: ' 368'
issue: '9'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: http://arxiv.org/abs/1405.3220
month: '01'
oa: 1
oa_version: Submitted Version
page: 6131 - 6157
publication: Transactions of the American Mathematical Society
publication_status: published
publisher: American Mathematical Society
publist_id: '5692'
quality_controlled: '1'
scopus_import: 1
status: public
title: The mean-field approximation and the non-linear Schrödinger functional for
trapped Bose gases
type: journal_article
user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87
volume: 368
year: '2016'
...
---
_id: '1408'
abstract:
- lang: eng
text: 'The concept of well group in a special but important case captures homological
properties of the zero set of a continuous map (Formula presented.) on a compact
space K that are invariant with respect to perturbations of f. The perturbations
are arbitrary continuous maps within (Formula presented.) distance r from f for
a given (Formula presented.). The main drawback of the approach is that the computability
of well groups was shown only when (Formula presented.) or (Formula presented.).
Our contribution to the theory of well groups is twofold: on the one hand we improve
on the computability issue, but on the other hand we present a range of examples
where the well groups are incomplete invariants, that is, fail to capture certain
important robust properties of the zero set. For the first part, we identify a
computable subgroup of the well group that is obtained by cap product with the
pullback of the orientation of (Formula presented.) by f. In other words, well
groups can be algorithmically approximated from below. When f is smooth and (Formula
presented.), our approximation of the (Formula presented.)th well group is exact.
For the second part, we find examples of maps (Formula presented.) with all well
groups isomorphic but whose perturbations have different zero sets. We discuss
on a possible replacement of the well groups of vector valued maps by an invariant
of a better descriptive power and computability status.'
acknowledgement: 'Open access funding provided by Institute of Science and Technology
(IST Austria). '
article_processing_charge: Yes (via OA deal)
author:
- first_name: Peter
full_name: Franek, Peter
id: 473294AE-F248-11E8-B48F-1D18A9856A87
last_name: Franek
- first_name: Marek
full_name: Krcál, Marek
id: 33E21118-F248-11E8-B48F-1D18A9856A87
last_name: Krcál
citation:
ama: Franek P, Krcál M. On computability and triviality of well groups. Discrete
& Computational Geometry. 2016;56(1):126-164. doi:10.1007/s00454-016-9794-2
apa: Franek, P., & Krcál, M. (2016). On computability and triviality of well
groups. Discrete & Computational Geometry. Springer. https://doi.org/10.1007/s00454-016-9794-2
chicago: Franek, Peter, and Marek Krcál. “On Computability and Triviality of Well
Groups.” Discrete & Computational Geometry. Springer, 2016. https://doi.org/10.1007/s00454-016-9794-2.
ieee: P. Franek and M. Krcál, “On computability and triviality of well groups,”
Discrete & Computational Geometry, vol. 56, no. 1. Springer, pp. 126–164,
2016.
ista: Franek P, Krcál M. 2016. On computability and triviality of well groups. Discrete
& Computational Geometry. 56(1), 126–164.
mla: Franek, Peter, and Marek Krcál. “On Computability and Triviality of Well Groups.”
Discrete & Computational Geometry, vol. 56, no. 1, Springer, 2016,
pp. 126–64, doi:10.1007/s00454-016-9794-2.
short: P. Franek, M. Krcál, Discrete & Computational Geometry 56 (2016) 126–164.
date_created: 2018-12-11T11:51:51Z
date_published: 2016-07-01T00:00:00Z
date_updated: 2023-02-23T10:02:11Z
day: '01'
ddc:
- '510'
department:
- _id: UlWa
- _id: HeEd
doi: 10.1007/s00454-016-9794-2
ec_funded: 1
file:
- access_level: open_access
checksum: e0da023abf6b72abd8c6a8c76740d53c
content_type: application/pdf
creator: system
date_created: 2018-12-12T10:10:55Z
date_updated: 2020-07-14T12:44:53Z
file_id: '4846'
file_name: IST-2016-614-v1+1_s00454-016-9794-2.pdf
file_size: 905303
relation: main_file
file_date_updated: 2020-07-14T12:44:53Z
has_accepted_license: '1'
intvolume: ' 56'
issue: '1'
language:
- iso: eng
month: '07'
oa: 1
oa_version: Published Version
page: 126 - 164
project:
- _id: 25F8B9BC-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: M01980
name: Robust invariants of Nonlinear Systems
- _id: 25681D80-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '291734'
name: International IST Postdoc Fellowship Programme
- _id: B67AFEDC-15C9-11EA-A837-991A96BB2854
name: IST Austria Open Access Fund
publication: Discrete & Computational Geometry
publication_status: published
publisher: Springer
publist_id: '5799'
pubrep_id: '614'
quality_controlled: '1'
related_material:
record:
- id: '1510'
relation: earlier_version
status: public
scopus_import: 1
status: public
title: On computability and triviality of well groups
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: journal_article
user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87
volume: 56
year: '2016'
...
---
_id: '1518'
abstract:
- lang: eng
text: The inference of demographic history from genome data is hindered by a lack
of efficient computational approaches. In particular, it has proved difficult
to exploit the information contained in the distribution of genealogies across
the genome. We have previously shown that the generating function (GF) of genealogies
can be used to analytically compute likelihoods of demographic models from configurations
of mutations in short sequence blocks (Lohse et al. 2011). Although the GF has
a simple, recursive form, the size of such likelihood calculations explodes quickly
with the number of individuals and applications of this framework have so far
been mainly limited to small samples (pairs and triplets) for which the GF can
be written by hand. Here we investigate several strategies for exploiting the
inherent symmetries of the coalescent. In particular, we show that the GF of genealogies
can be decomposed into a set of equivalence classes that allows likelihood calculations
from nontrivial samples. Using this strategy, we automated blockwise likelihood
calculations for a general set of demographic scenarios in Mathematica. These
histories may involve population size changes, continuous migration, discrete
divergence, and admixture between multiple populations. To give a concrete example,
we calculate the likelihood for a model of isolation with migration (IM), assuming
two diploid samples without phase and outgroup information. We demonstrate the
new inference scheme with an analysis of two individual butterfly genomes from
the sister species Heliconius melpomene rosina and H. cydno.
acknowledgement: "We thank Lynsey Bunnefeld for discussions throughout the project
and Joshua Schraiber and one anonymous reviewer\r\nfor constructive comments on
an earlier version of this manuscript. This work was supported by funding from the\r\nUnited
Kingdom Natural Environment Research Council (to K.L.) (NE/I020288/1) and a grant
from the European\r\nResearch Council (250152) (to N.H.B.)."
article_processing_charge: No
article_type: original
author:
- first_name: Konrad
full_name: Lohse, Konrad
last_name: Lohse
- first_name: Martin
full_name: Chmelik, Martin
id: 3624234E-F248-11E8-B48F-1D18A9856A87
last_name: Chmelik
- first_name: Simon
full_name: Martin, Simon
last_name: Martin
- first_name: Nicholas H
full_name: Barton, Nicholas H
id: 4880FE40-F248-11E8-B48F-1D18A9856A87
last_name: Barton
orcid: 0000-0002-8548-5240
citation:
ama: Lohse K, Chmelik M, Martin S, Barton NH. Efficient strategies for calculating
blockwise likelihoods under the coalescent. Genetics. 2016;202(2):775-786.
doi:10.1534/genetics.115.183814
apa: Lohse, K., Chmelik, M., Martin, S., & Barton, N. H. (2016). Efficient strategies
for calculating blockwise likelihoods under the coalescent. Genetics. Genetics
Society of America. https://doi.org/10.1534/genetics.115.183814
chicago: Lohse, Konrad, Martin Chmelik, Simon Martin, and Nicholas H Barton. “Efficient
Strategies for Calculating Blockwise Likelihoods under the Coalescent.” Genetics.
Genetics Society of America, 2016. https://doi.org/10.1534/genetics.115.183814.
ieee: K. Lohse, M. Chmelik, S. Martin, and N. H. Barton, “Efficient strategies for
calculating blockwise likelihoods under the coalescent,” Genetics, vol.
202, no. 2. Genetics Society of America, pp. 775–786, 2016.
ista: Lohse K, Chmelik M, Martin S, Barton NH. 2016. Efficient strategies for calculating
blockwise likelihoods under the coalescent. Genetics. 202(2), 775–786.
mla: Lohse, Konrad, et al. “Efficient Strategies for Calculating Blockwise Likelihoods
under the Coalescent.” Genetics, vol. 202, no. 2, Genetics Society of America,
2016, pp. 775–86, doi:10.1534/genetics.115.183814.
short: K. Lohse, M. Chmelik, S. Martin, N.H. Barton, Genetics 202 (2016) 775–786.
date_created: 2018-12-11T11:52:29Z
date_published: 2016-02-01T00:00:00Z
date_updated: 2022-05-24T09:16:22Z
day: '01'
ddc:
- '570'
department:
- _id: KrCh
- _id: NiBa
doi: 10.1534/genetics.115.183814
ec_funded: 1
external_id:
pmid:
- '26715666'
file:
- access_level: open_access
checksum: 41c9b5d72e7fe4624dd22dfe622337d5
content_type: application/pdf
creator: system
date_created: 2018-12-12T10:16:51Z
date_updated: 2020-07-14T12:45:00Z
file_id: '5241'
file_name: IST-2016-561-v1+1_Lohse_et_al_Genetics_2015.pdf
file_size: 957466
relation: main_file
file_date_updated: 2020-07-14T12:45:00Z
has_accepted_license: '1'
intvolume: ' 202'
issue: '2'
language:
- iso: eng
month: '02'
oa: 1
oa_version: Preprint
page: 775 - 786
pmid: 1
project:
- _id: 25B07788-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '250152'
name: Limits to selection in biology and in evolutionary computation
publication: Genetics
publication_status: published
publisher: Genetics Society of America
publist_id: '5658'
pubrep_id: '561'
quality_controlled: '1'
scopus_import: '1'
status: public
title: Efficient strategies for calculating blockwise likelihoods under the coalescent
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 202
year: '2016'
...
---
_id: '1524'
abstract:
- lang: eng
text: "When designing genetic circuits, the typical primitives used in major existing
modelling formalisms are gene interaction graphs, where edges between genes denote
either an activation or inhibition relation. However, when designing experiments,
it is important to be precise about the low-level mechanistic details as to how
each such relation is implemented. The rule-based modelling language Kappa allows
to unambiguously specify mechanistic details such as DNA binding sites, dimerisation
of transcription factors, or co-operative interactions. Such a detailed description
comes with complexity and computationally costly executions. We propose a general
method for automatically transforming a rule-based program, by eliminating intermediate
species and adjusting the rate constants accordingly. To the best of our knowledge,
we show the first automated reduction of rule-based models based on equilibrium
approximations.\r\nOur algorithm is an adaptation of an existing algorithm, which
was designed for reducing reaction-based programs; our version of the algorithm
scans the rule-based Kappa model in search for those interaction patterns known
to be amenable to equilibrium approximations (e.g. Michaelis-Menten scheme). Additional
checks are then performed in order to verify if the reduction is meaningful in
the context of the full model. The reduced model is efficiently obtained by static
inspection over the rule-set. The tool is tested on a detailed rule-based model
of a λ-phage switch, which lists 92 rules and 13 agents. The reduced model has
11 rules and 5 agents, and provides a dramatic reduction in simulation time of
several orders of magnitude."
acknowledgement: This research was supported by the People Programme (Marie Curie
Actions) of the European Union’s Seventh Framework Programme (FP7/2007-2013) under
REA grant agreement no. 291734, and the SNSF Early Postdoc.Mobility Fellowship,
the grant number P2EZP2_148797.
alternative_title:
- LNCS
author:
- first_name: Andreea
full_name: Beica, Andreea
last_name: Beica
- first_name: Calin C
full_name: Guet, Calin C
id: 47F8433E-F248-11E8-B48F-1D18A9856A87
last_name: Guet
orcid: 0000-0001-6220-2052
- first_name: Tatjana
full_name: Petrov, Tatjana
id: 3D5811FC-F248-11E8-B48F-1D18A9856A87
last_name: Petrov
orcid: 0000-0002-9041-0905
citation:
ama: 'Beica A, Guet CC, Petrov T. Efficient reduction of kappa models by static
inspection of the rule-set. In: Vol 9271. Springer; 2016:173-191. doi:10.1007/978-3-319-26916-0_10'
apa: 'Beica, A., Guet, C. C., & Petrov, T. (2016). Efficient reduction of kappa
models by static inspection of the rule-set (Vol. 9271, pp. 173–191). Presented
at the HSB: Hybrid Systems Biology, Madrid, Spain: Springer. https://doi.org/10.1007/978-3-319-26916-0_10'
chicago: Beica, Andreea, Calin C Guet, and Tatjana Petrov. “Efficient Reduction
of Kappa Models by Static Inspection of the Rule-Set,” 9271:173–91. Springer,
2016. https://doi.org/10.1007/978-3-319-26916-0_10.
ieee: 'A. Beica, C. C. Guet, and T. Petrov, “Efficient reduction of kappa models
by static inspection of the rule-set,” presented at the HSB: Hybrid Systems Biology,
Madrid, Spain, 2016, vol. 9271, pp. 173–191.'
ista: 'Beica A, Guet CC, Petrov T. 2016. Efficient reduction of kappa models by
static inspection of the rule-set. HSB: Hybrid Systems Biology, LNCS, vol. 9271,
173–191.'
mla: Beica, Andreea, et al. Efficient Reduction of Kappa Models by Static Inspection
of the Rule-Set. Vol. 9271, Springer, 2016, pp. 173–91, doi:10.1007/978-3-319-26916-0_10.
short: A. Beica, C.C. Guet, T. Petrov, in:, Springer, 2016, pp. 173–191.
conference:
end_date: 2015-09-05
location: Madrid, Spain
name: 'HSB: Hybrid Systems Biology'
start_date: 2015-09-04
date_created: 2018-12-11T11:52:31Z
date_published: 2016-01-10T00:00:00Z
date_updated: 2021-01-12T06:51:22Z
day: '10'
department:
- _id: CaGu
- _id: ToHe
doi: 10.1007/978-3-319-26916-0_10
ec_funded: 1
intvolume: ' 9271'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: http://arxiv.org/abs/1501.00440
month: '01'
oa: 1
oa_version: Preprint
page: 173 - 191
project:
- _id: 25681D80-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '291734'
name: International IST Postdoc Fellowship Programme
publication_status: published
publisher: Springer
publist_id: '5649'
quality_controlled: '1'
scopus_import: 1
status: public
title: Efficient reduction of kappa models by static inspection of the rule-set
type: conference
user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87
volume: 9271
year: '2016'
...
---
_id: '1522'
abstract:
- lang: eng
text: 'We classify smooth Brunnian (i.e., unknotted on both components) embeddings
(S2 × S1) ⊔ S3 → ℝ6. Any Brunnian embedding (S2 × S1) ⊔ S3 → ℝ6 is isotopic to
an explicitly constructed embedding fk,m,n for some integers k, m, n such that
m ≡ n (mod 2). Two embeddings fk,m,n and fk′ ,m′,n′ are isotopic if and only if
k = k′, m ≡ m′ (mod 2k) and n ≡ n′ (mod 2k). We use Haefliger’s classification
of embeddings S3 ⊔ S3 → ℝ6 in our proof. The relation between the embeddings (S2
× S1) ⊔ S3 → ℝ6 and S3 ⊔ S3 → ℝ6 is not trivial, however. For example, we show
that there exist embeddings f: (S2 ×S1) ⊔ S3 → ℝ6 and g, g′ : S3 ⊔ S3 → ℝ6 such
that the componentwise embedded connected sum f # g is isotopic to f # g′ but
g is not isotopic to g′.'
acknowledgement: "I thank A. Skopenkov for telling me about the problem and for his
useful remarks. I also thank A. Sossinsky,\r\nA. Zhubr, M. Skopenkov, P. Akhmetiev,
and an anonymous referee for their feedback. Author was partially\r\nsupported
by Dobrushin fellowship, 2013, and by RFBR grant 15-01-06302."
article_processing_charge: No
article_type: original
author:
- first_name: Serhii
full_name: Avvakumov, Serhii
id: 3827DAC8-F248-11E8-B48F-1D18A9856A87
last_name: Avvakumov
citation:
ama: Avvakumov S. The classification of certain linked 3-manifolds in 6-space. Moscow
Mathematical Journal. 2016;16(1):1-25. doi:10.17323/1609-4514-2016-16-1-1-25
apa: Avvakumov, S. (2016). The classification of certain linked 3-manifolds in 6-space.
Moscow Mathematical Journal. Independent University of Moscow. https://doi.org/10.17323/1609-4514-2016-16-1-1-25
chicago: Avvakumov, Sergey. “The Classification of Certain Linked 3-Manifolds in
6-Space.” Moscow Mathematical Journal. Independent University of Moscow,
2016. https://doi.org/10.17323/1609-4514-2016-16-1-1-25.
ieee: S. Avvakumov, “The classification of certain linked 3-manifolds in 6-space,”
Moscow Mathematical Journal, vol. 16, no. 1. Independent University of
Moscow, pp. 1–25, 2016.
ista: Avvakumov S. 2016. The classification of certain linked 3-manifolds in 6-space.
Moscow Mathematical Journal. 16(1), 1–25.
mla: Avvakumov, Sergey. “The Classification of Certain Linked 3-Manifolds in 6-Space.”
Moscow Mathematical Journal, vol. 16, no. 1, Independent University of
Moscow, 2016, pp. 1–25, doi:10.17323/1609-4514-2016-16-1-1-25.
short: S. Avvakumov, Moscow Mathematical Journal 16 (2016) 1–25.
date_created: 2018-12-11T11:52:30Z
date_published: 2016-01-01T00:00:00Z
date_updated: 2022-02-25T10:15:57Z
day: '01'
department:
- _id: UlWa
doi: 10.17323/1609-4514-2016-16-1-1-25
external_id:
arxiv:
- '1408.3918'
intvolume: ' 16'
issue: '1'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: http://arxiv.org/abs/1408.3918
month: '01'
oa: 1
oa_version: Preprint
page: 1 - 25
publication: Moscow Mathematical Journal
publication_identifier:
eissn:
- 1609-4514
publication_status: published
publisher: Independent University of Moscow
publist_id: '5652'
quality_controlled: '1'
scopus_import: '1'
status: public
title: The classification of certain linked 3-manifolds in 6-space
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 16
year: '2016'
...
---
_id: '1523'
abstract:
- lang: eng
text: For random graphs, the containment problem considers the probability that
a binomial random graph G(n, p) contains a given graph as a substructure. When
asking for the graph as a topological minor, i.e., for a copy of a subdivision
of the given graph, it is well known that the (sharp) threshold is at p = 1/n.
We consider a natural analogue of this question for higher-dimensional random
complexes Xk(n, p), first studied by Cohen, Costa, Farber and Kappeler for k =
2. Improving previous results, we show that p = Θ(1/ √n) is the (coarse) threshold
for containing a subdivision of any fixed complete 2-complex. For higher dimensions
k > 2, we get that p = O(n−1/k) is an upper bound for the threshold probability
of containing a subdivision of a fixed k-dimensional complex.
acknowledgement: This research was supported by the Swiss National Science Foundation
(SNF Projects 200021-125309 and 200020-138230
author:
- first_name: Anna
full_name: Gundert, Anna
last_name: Gundert
- first_name: Uli
full_name: Wagner, Uli
id: 36690CA2-F248-11E8-B48F-1D18A9856A87
last_name: Wagner
orcid: 0000-0002-1494-0568
citation:
ama: Gundert A, Wagner U. On topological minors in random simplicial complexes.
Proceedings of the American Mathematical Society. 2016;144(4):1815-1828.
doi:10.1090/proc/12824
apa: Gundert, A., & Wagner, U. (2016). On topological minors in random simplicial
complexes. Proceedings of the American Mathematical Society. American Mathematical
Society. https://doi.org/10.1090/proc/12824
chicago: Gundert, Anna, and Uli Wagner. “On Topological Minors in Random Simplicial
Complexes.” Proceedings of the American Mathematical Society. American
Mathematical Society, 2016. https://doi.org/10.1090/proc/12824.
ieee: A. Gundert and U. Wagner, “On topological minors in random simplicial complexes,”
Proceedings of the American Mathematical Society, vol. 144, no. 4. American
Mathematical Society, pp. 1815–1828, 2016.
ista: Gundert A, Wagner U. 2016. On topological minors in random simplicial complexes.
Proceedings of the American Mathematical Society. 144(4), 1815–1828.
mla: Gundert, Anna, and Uli Wagner. “On Topological Minors in Random Simplicial
Complexes.” Proceedings of the American Mathematical Society, vol. 144,
no. 4, American Mathematical Society, 2016, pp. 1815–28, doi:10.1090/proc/12824.
short: A. Gundert, U. Wagner, Proceedings of the American Mathematical Society 144
(2016) 1815–1828.
date_created: 2018-12-11T11:52:30Z
date_published: 2016-04-01T00:00:00Z
date_updated: 2021-01-12T06:51:22Z
day: '01'
department:
- _id: UlWa
doi: 10.1090/proc/12824
intvolume: ' 144'
issue: '4'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: http://arxiv.org/abs/1404.2106
month: '04'
oa: 1
oa_version: Preprint
page: 1815 - 1828
publication: Proceedings of the American Mathematical Society
publication_status: published
publisher: American Mathematical Society
publist_id: '5650'
quality_controlled: '1'
scopus_import: 1
status: public
title: On topological minors in random simplicial complexes
type: journal_article
user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87
volume: 144
year: '2016'
...
---
_id: '1526'
abstract:
- lang: eng
text: 'We present the first study of robustness of systems that are both timed as
well as reactive (I/O). We study the behavior of such timed I/O systems in the
presence of uncertain inputs and formalize their robustness using the analytic
notion of Lipschitz continuity: a timed I/O system is K-(Lipschitz) robust if
the perturbation in its output is at most K times the perturbation in its input.
We quantify input and output perturbation using similarity functions over timed
words such as the timed version of the Manhattan distance and the Skorokhod distance.
We consider two models of timed I/O systems — timed transducers and asynchronous
sequential circuits. We show that K-robustness of timed transducers can be decided
in polynomial space under certain conditions. For asynchronous sequential circuits,
we reduce K-robustness w.r.t. timed Manhattan distances to K-robustness of discrete
letter-to-letter transducers and show PSpace-completeness of the problem.'
acknowledgement: This research was supported in part by the European Research Council
(ERC) under grant 267989 (QUAREM), by the Austrian Science Fund (FWF) under grants
S11402-N23 (RiSE) and Z211-N23 (Wittgenstein Award), and by the National Science
Centre (NCN), Poland under grant 2014/15/D/ST6/04543.
alternative_title:
- LNCS
author:
- first_name: Thomas A
full_name: Henzinger, Thomas A
id: 40876CD8-F248-11E8-B48F-1D18A9856A87
last_name: Henzinger
orcid: 0000−0002−2985−7724
- first_name: Jan
full_name: Otop, Jan
id: 2FC5DA74-F248-11E8-B48F-1D18A9856A87
last_name: Otop
- first_name: Roopsha
full_name: Samanta, Roopsha
id: 3D2AAC08-F248-11E8-B48F-1D18A9856A87
last_name: Samanta
citation:
ama: 'Henzinger TA, Otop J, Samanta R. Lipschitz robustness of timed I/O systems.
In: Vol 9583. Springer; 2016:250-267. doi:10.1007/978-3-662-49122-5_12'
apa: 'Henzinger, T. A., Otop, J., & Samanta, R. (2016). Lipschitz robustness
of timed I/O systems (Vol. 9583, pp. 250–267). Presented at the VMCAI: Verification,
Model Checking and Abstract Interpretation, St. Petersburg, FL, USA: Springer.
https://doi.org/10.1007/978-3-662-49122-5_12'
chicago: Henzinger, Thomas A, Jan Otop, and Roopsha Samanta. “Lipschitz Robustness
of Timed I/O Systems,” 9583:250–67. Springer, 2016. https://doi.org/10.1007/978-3-662-49122-5_12.
ieee: 'T. A. Henzinger, J. Otop, and R. Samanta, “Lipschitz robustness of timed
I/O systems,” presented at the VMCAI: Verification, Model Checking and Abstract
Interpretation, St. Petersburg, FL, USA, 2016, vol. 9583, pp. 250–267.'
ista: 'Henzinger TA, Otop J, Samanta R. 2016. Lipschitz robustness of timed I/O
systems. VMCAI: Verification, Model Checking and Abstract Interpretation, LNCS,
vol. 9583, 250–267.'
mla: Henzinger, Thomas A., et al. Lipschitz Robustness of Timed I/O Systems.
Vol. 9583, Springer, 2016, pp. 250–67, doi:10.1007/978-3-662-49122-5_12.
short: T.A. Henzinger, J. Otop, R. Samanta, in:, Springer, 2016, pp. 250–267.
conference:
end_date: 2016-01-19
location: St. Petersburg, FL, USA
name: 'VMCAI: Verification, Model Checking and Abstract Interpretation'
start_date: 2016-01-17
date_created: 2018-12-11T11:52:32Z
date_published: 2016-01-01T00:00:00Z
date_updated: 2021-01-12T06:51:23Z
day: '01'
department:
- _id: ToHe
doi: 10.1007/978-3-662-49122-5_12
ec_funded: 1
intvolume: ' 9583'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: http://arxiv.org/abs/1506.01233
month: '01'
oa: 1
oa_version: Preprint
page: 250 - 267
project:
- _id: 25EE3708-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '267989'
name: Quantitative Reactive Modeling
- _id: 25F42A32-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: Z211
name: The Wittgenstein Prize
- _id: 25832EC2-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: S 11407_N23
name: Rigorous Systems Engineering
publication_status: published
publisher: Springer
publist_id: '5647'
quality_controlled: '1'
scopus_import: 1
status: public
title: Lipschitz robustness of timed I/O systems
type: conference
user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87
volume: 9583
year: '2016'
...
---
_id: '1545'
abstract:
- lang: eng
text: We provide general conditions for which bosonic quadratic Hamiltonians on
Fock spaces can be diagonalized by Bogoliubov transformations. Our results cover
the case when quantum systems have infinite degrees of freedom and the associated
one-body kinetic and paring operators are unbounded. Our sufficient conditions
are optimal in the sense that they become necessary when the relevant one-body
operators commute.
acknowledgement: We thank Jan Dereziński for several inspiring discussions and useful
remarks. We thank the referee for helpful comments. J.P.S. thanks the Erwin Schrödinger
Institute for the hospitality during the thematic programme “Quantum many-body systems,
random matrices, and disorder”. We gratefully acknowledge the financial supports
by the European Union's Seventh Framework Programme under the ERC Advanced Grant
ERC-2012-AdG 321029 (J.P.S.) and the REA grant agreement No. 291734 (P.T.N.), as
well as the support of the National Science Center (NCN) grant No. 2012/07/N/ST1/03185
and the Austrian Science Fund (FWF) project No. P 27533-N27 (M.N.).
author:
- first_name: Phan
full_name: Nam, Phan
id: 404092F4-F248-11E8-B48F-1D18A9856A87
last_name: Nam
- first_name: Marcin M
full_name: Napiórkowski, Marcin M
id: 4197AD04-F248-11E8-B48F-1D18A9856A87
last_name: Napiórkowski
- first_name: Jan
full_name: Solovej, Jan
last_name: Solovej
citation:
ama: Nam P, Napiórkowski MM, Solovej J. Diagonalization of bosonic quadratic Hamiltonians
by Bogoliubov transformations. Journal of Functional Analysis. 2016;270(11):4340-4368.
doi:10.1016/j.jfa.2015.12.007
apa: Nam, P., Napiórkowski, M. M., & Solovej, J. (2016). Diagonalization of
bosonic quadratic Hamiltonians by Bogoliubov transformations. Journal of Functional
Analysis. Academic Press. https://doi.org/10.1016/j.jfa.2015.12.007
chicago: Nam, Phan, Marcin M Napiórkowski, and Jan Solovej. “Diagonalization of
Bosonic Quadratic Hamiltonians by Bogoliubov Transformations.” Journal of Functional
Analysis. Academic Press, 2016. https://doi.org/10.1016/j.jfa.2015.12.007.
ieee: P. Nam, M. M. Napiórkowski, and J. Solovej, “Diagonalization of bosonic quadratic
Hamiltonians by Bogoliubov transformations,” Journal of Functional Analysis,
vol. 270, no. 11. Academic Press, pp. 4340–4368, 2016.
ista: Nam P, Napiórkowski MM, Solovej J. 2016. Diagonalization of bosonic quadratic
Hamiltonians by Bogoliubov transformations. Journal of Functional Analysis. 270(11),
4340–4368.
mla: Nam, Phan, et al. “Diagonalization of Bosonic Quadratic Hamiltonians by Bogoliubov
Transformations.” Journal of Functional Analysis, vol. 270, no. 11, Academic
Press, 2016, pp. 4340–68, doi:10.1016/j.jfa.2015.12.007.
short: P. Nam, M.M. Napiórkowski, J. Solovej, Journal of Functional Analysis 270
(2016) 4340–4368.
date_created: 2018-12-11T11:52:38Z
date_published: 2016-06-01T00:00:00Z
date_updated: 2021-01-12T06:51:30Z
day: '01'
department:
- _id: RoSe
doi: 10.1016/j.jfa.2015.12.007
ec_funded: 1
intvolume: ' 270'
issue: '11'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: http://arxiv.org/abs/1508.07321
month: '06'
oa: 1
oa_version: Submitted Version
page: 4340 - 4368
project:
- _id: 25681D80-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '291734'
name: International IST Postdoc Fellowship Programme
- _id: 25C878CE-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: P27533_N27
name: Structure of the Excitation Spectrum for Many-Body Quantum Systems
publication: Journal of Functional Analysis
publication_status: published
publisher: Academic Press
publist_id: '5626'
quality_controlled: '1'
scopus_import: 1
status: public
title: Diagonalization of bosonic quadratic Hamiltonians by Bogoliubov transformations
type: journal_article
user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87
volume: 270
year: '2016'
...
---
_id: '1552'
abstract:
- lang: eng
text: Antibiotic resistance carries a fitness cost that must be overcome in order
for resistance to persist over the long term. Compensatory mutations that recover
the functional defects associated with resistance mutations have been argued to
play a key role in overcoming the cost of resistance, but compensatory mutations
are expected to be rare relative to generally beneficial mutations that increase
fitness, irrespective of antibiotic resistance. Given this asymmetry, population
genetics theory predicts that populations should adapt by compensatory mutations
when the cost of resistance is large, whereas generally beneficial mutations should
drive adaptation when the cost of resistance is small. We tested this prediction
by determining the genomic mechanisms underpinning adaptation to antibiotic-free
conditions in populations of the pathogenic bacterium Pseudomonas aeruginosa that
carry costly antibiotic resistance mutations. Whole-genome sequencing revealed
that populations founded by high-cost rifampicin-resistant mutants adapted via
compensatory mutations in three genes of the RNA polymerase core enzyme, whereas
populations founded by low-cost mutants adapted by generally beneficial mutations,
predominantly in the quorum-sensing transcriptional regulator gene lasR. Even
though the importance of compensatory evolution in maintaining resistance has
been widely recognized, our study shows that the roles of general adaptation in
maintaining resistance should not be underestimated and highlights the need to
understand how selection at other sites in the genome influences the dynamics
of resistance alleles in clinical settings.
acknowledgement: "We thank the High-Throughput Genomics Group at the Wellcome Trust
Centre for Human Genetics funded by Wellcome\r\nTrust grant reference 090532/Z/09/Z
and Medical Research Council Hub grant no. G0900747 91070 for generation of the
high-throughput sequencing data. We thank Wook Kim and two anonymous reviewers for
their constructive feedback on previous versions of our manuscript."
article_number: '20152452'
author:
- first_name: Qin
full_name: Qi, Qin
id: 3B22D412-F248-11E8-B48F-1D18A9856A87
last_name: Qi
orcid: 0000-0002-6148-2416
- first_name: Macarena
full_name: Toll Riera, Macarena
last_name: Toll Riera
- first_name: Karl
full_name: Heilbron, Karl
last_name: Heilbron
- first_name: Gail
full_name: Preston, Gail
last_name: Preston
- first_name: R Craig
full_name: Maclean, R Craig
last_name: Maclean
citation:
ama: Qi Q, Toll Riera M, Heilbron K, Preston G, Maclean RC. The genomic basis of
adaptation to the fitness cost of rifampicin resistance in Pseudomonas aeruginosa.
Proceedings of the Royal Society of London Series B Biological Sciences.
2016;283(1822). doi:10.1098/rspb.2015.2452
apa: Qi, Q., Toll Riera, M., Heilbron, K., Preston, G., & Maclean, R. C. (2016).
The genomic basis of adaptation to the fitness cost of rifampicin resistance in
Pseudomonas aeruginosa. Proceedings of the Royal Society of London Series B
Biological Sciences. Royal Society, The. https://doi.org/10.1098/rspb.2015.2452
chicago: Qi, Qin, Macarena Toll Riera, Karl Heilbron, Gail Preston, and R Craig
Maclean. “The Genomic Basis of Adaptation to the Fitness Cost of Rifampicin Resistance
in Pseudomonas Aeruginosa.” Proceedings of the Royal Society of London Series
B Biological Sciences. Royal Society, The, 2016. https://doi.org/10.1098/rspb.2015.2452.
ieee: Q. Qi, M. Toll Riera, K. Heilbron, G. Preston, and R. C. Maclean, “The genomic
basis of adaptation to the fitness cost of rifampicin resistance in Pseudomonas
aeruginosa,” Proceedings of the Royal Society of London Series B Biological
Sciences, vol. 283, no. 1822. Royal Society, The, 2016.
ista: Qi Q, Toll Riera M, Heilbron K, Preston G, Maclean RC. 2016. The genomic basis
of adaptation to the fitness cost of rifampicin resistance in Pseudomonas aeruginosa.
Proceedings of the Royal Society of London Series B Biological Sciences. 283(1822),
20152452.
mla: Qi, Qin, et al. “The Genomic Basis of Adaptation to the Fitness Cost of Rifampicin
Resistance in Pseudomonas Aeruginosa.” Proceedings of the Royal Society of
London Series B Biological Sciences, vol. 283, no. 1822, 20152452, Royal Society,
The, 2016, doi:10.1098/rspb.2015.2452.
short: Q. Qi, M. Toll Riera, K. Heilbron, G. Preston, R.C. Maclean, Proceedings
of the Royal Society of London Series B Biological Sciences 283 (2016).
date_created: 2018-12-11T11:52:40Z
date_published: 2016-01-13T00:00:00Z
date_updated: 2021-01-12T06:51:33Z
day: '13'
ddc:
- '570'
department:
- _id: ToBo
doi: 10.1098/rspb.2015.2452
file:
- access_level: open_access
checksum: 78ffe70c1c88af3856d31ca6b7195a27
content_type: application/pdf
creator: system
date_created: 2018-12-12T10:11:43Z
date_updated: 2020-07-14T12:45:02Z
file_id: '4899'
file_name: IST-2016-488-v1+1_20152452.full.pdf
file_size: 626804
relation: main_file
file_date_updated: 2020-07-14T12:45:02Z
has_accepted_license: '1'
intvolume: ' 283'
issue: '1822'
language:
- iso: eng
month: '01'
oa: 1
oa_version: Published Version
publication: Proceedings of the Royal Society of London Series B Biological Sciences
publication_status: published
publisher: Royal Society, The
publist_id: '5619'
pubrep_id: '488'
quality_controlled: '1'
scopus_import: 1
status: public
title: The genomic basis of adaptation to the fitness cost of rifampicin resistance
in Pseudomonas aeruginosa
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: journal_article
user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87
volume: 283
year: '2016'
...
---
_id: '1289'
abstract:
- lang: eng
text: 'Aiming at the automatic diagnosis of tumors using narrow band imaging (NBI)
magnifying endoscopic (ME) images of the stomach, we combine methods from image
processing, topology, geometry, and machine learning to classify patterns into
three classes: oval, tubular and irregular. Training the algorithm on a small
number of images of each type, we achieve a high rate of correct classifications.
The analysis of the learning algorithm reveals that a handful of geometric and
topological features are responsible for the overwhelming majority of decisions.'
article_processing_charge: No
author:
- first_name: Olga
full_name: Dunaeva, Olga
last_name: Dunaeva
- first_name: Herbert
full_name: Edelsbrunner, Herbert
id: 3FB178DA-F248-11E8-B48F-1D18A9856A87
last_name: Edelsbrunner
orcid: 0000-0002-9823-6833
- first_name: Anton
full_name: Lukyanov, Anton
last_name: Lukyanov
- first_name: Michael
full_name: Machin, Michael
last_name: Machin
- first_name: Daria
full_name: Malkova, Daria
last_name: Malkova
- first_name: Roman
full_name: Kuvaev, Roman
last_name: Kuvaev
- first_name: Sergey
full_name: Kashin, Sergey
last_name: Kashin
citation:
ama: Dunaeva O, Edelsbrunner H, Lukyanov A, et al. The classification of endoscopy
images with persistent homology. Pattern Recognition Letters. 2016;83(1):13-22.
doi:10.1016/j.patrec.2015.12.012
apa: Dunaeva, O., Edelsbrunner, H., Lukyanov, A., Machin, M., Malkova, D., Kuvaev,
R., & Kashin, S. (2016). The classification of endoscopy images with persistent
homology. Pattern Recognition Letters. Elsevier. https://doi.org/10.1016/j.patrec.2015.12.012
chicago: Dunaeva, Olga, Herbert Edelsbrunner, Anton Lukyanov, Michael Machin, Daria
Malkova, Roman Kuvaev, and Sergey Kashin. “The Classification of Endoscopy Images
with Persistent Homology.” Pattern Recognition Letters. Elsevier, 2016.
https://doi.org/10.1016/j.patrec.2015.12.012.
ieee: O. Dunaeva et al., “The classification of endoscopy images with persistent
homology,” Pattern Recognition Letters, vol. 83, no. 1. Elsevier, pp. 13–22,
2016.
ista: Dunaeva O, Edelsbrunner H, Lukyanov A, Machin M, Malkova D, Kuvaev R, Kashin
S. 2016. The classification of endoscopy images with persistent homology. Pattern
Recognition Letters. 83(1), 13–22.
mla: Dunaeva, Olga, et al. “The Classification of Endoscopy Images with Persistent
Homology.” Pattern Recognition Letters, vol. 83, no. 1, Elsevier, 2016,
pp. 13–22, doi:10.1016/j.patrec.2015.12.012.
short: O. Dunaeva, H. Edelsbrunner, A. Lukyanov, M. Machin, D. Malkova, R. Kuvaev,
S. Kashin, Pattern Recognition Letters 83 (2016) 13–22.
date_created: 2018-12-11T11:51:10Z
date_published: 2016-11-01T00:00:00Z
date_updated: 2023-02-23T10:04:40Z
day: '01'
ddc:
- '004'
- '514'
department:
- _id: HeEd
doi: 10.1016/j.patrec.2015.12.012
file:
- access_level: open_access
checksum: 33458bbb8c32a339e1adeca6d5a1112d
content_type: application/pdf
creator: dernst
date_created: 2019-04-17T07:55:51Z
date_updated: 2020-07-14T12:44:42Z
file_id: '6334'
file_name: 2016-Edelsbrunner_The_classification.pdf
file_size: 1921113
relation: main_file
file_date_updated: 2020-07-14T12:44:42Z
has_accepted_license: '1'
intvolume: ' 83'
issue: '1'
language:
- iso: eng
month: '11'
oa: 1
oa_version: Submitted Version
page: 13 - 22
publication: Pattern Recognition Letters
publication_status: published
publisher: Elsevier
publist_id: '6027'
pubrep_id: '975'
quality_controlled: '1'
related_material:
record:
- id: '1568'
relation: earlier_version
status: public
scopus_import: 1
status: public
title: The classification of endoscopy images with persistent homology
tmp:
image: /images/cc_by_nc_nd.png
legal_code_url: https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode
name: Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International
(CC BY-NC-ND 4.0)
short: CC BY-NC-ND (4.0)
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 83
year: '2016'
...
---
_id: '1164'
abstract:
- lang: eng
text: 'A drawing of a graph G is radial if the vertices of G are placed on concentric
circles C1, … , Ck with common center c, and edges are drawn radially: every edge
intersects every circle centered at c at most once. G is radial planar if it has
a radial embedding, that is, a crossing-free radial drawing. If the vertices of
G are ordered or partitioned into ordered levels (as they are for leveled graphs),
we require that the assignment of vertices to circles corresponds to the given
ordering or leveling. A pair of edges e and f in a graph is independent if e and
f do not share a vertex. We show that a graph G is radial planar if G has a radial
drawing in which every two independent edges cross an even number of times; the
radial embedding has the same leveling as the radial drawing. In other words,
we establish the strong Hanani-Tutte theorem for radial planarity. This characterization
yields a very simple algorithm for radial planarity testing.'
alternative_title:
- LNCS
article_processing_charge: No
author:
- first_name: Radoslav
full_name: Fulek, Radoslav
id: 39F3FFE4-F248-11E8-B48F-1D18A9856A87
last_name: Fulek
orcid: 0000-0001-8485-1774
- first_name: Michael
full_name: Pelsmajer, Michael
last_name: Pelsmajer
- first_name: Marcus
full_name: Schaefer, Marcus
last_name: Schaefer
citation:
ama: 'Fulek R, Pelsmajer M, Schaefer M. Hanani-Tutte for radial planarity II. In:
Vol 9801. Springer; 2016:468-481. doi:10.1007/978-3-319-50106-2_36'
apa: 'Fulek, R., Pelsmajer, M., & Schaefer, M. (2016). Hanani-Tutte for radial
planarity II (Vol. 9801, pp. 468–481). Presented at the GD: Graph Drawing and
Network Visualization, Athens, Greece: Springer. https://doi.org/10.1007/978-3-319-50106-2_36'
chicago: Fulek, Radoslav, Michael Pelsmajer, and Marcus Schaefer. “Hanani-Tutte
for Radial Planarity II,” 9801:468–81. Springer, 2016. https://doi.org/10.1007/978-3-319-50106-2_36.
ieee: 'R. Fulek, M. Pelsmajer, and M. Schaefer, “Hanani-Tutte for radial planarity
II,” presented at the GD: Graph Drawing and Network Visualization, Athens, Greece,
2016, vol. 9801, pp. 468–481.'
ista: 'Fulek R, Pelsmajer M, Schaefer M. 2016. Hanani-Tutte for radial planarity
II. GD: Graph Drawing and Network Visualization, LNCS, vol. 9801, 468–481.'
mla: Fulek, Radoslav, et al. Hanani-Tutte for Radial Planarity II. Vol. 9801,
Springer, 2016, pp. 468–81, doi:10.1007/978-3-319-50106-2_36.
short: R. Fulek, M. Pelsmajer, M. Schaefer, in:, Springer, 2016, pp. 468–481.
conference:
end_date: 2016-09-21
location: Athens, Greece
name: 'GD: Graph Drawing and Network Visualization'
start_date: 2016-09-19
date_created: 2018-12-11T11:50:29Z
date_published: 2016-12-08T00:00:00Z
date_updated: 2023-02-23T10:05:57Z
day: '08'
department:
- _id: UlWa
doi: 10.1007/978-3-319-50106-2_36
ec_funded: 1
external_id:
arxiv:
- '1608.08662'
intvolume: ' 9801'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/1608.08662
month: '12'
oa: 1
oa_version: Preprint
page: 468 - 481
project:
- _id: 25681D80-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '291734'
name: International IST Postdoc Fellowship Programme
publication_status: published
publisher: Springer
publist_id: '6193'
quality_controlled: '1'
related_material:
record:
- id: '1113'
relation: later_version
status: public
- id: '1595'
relation: earlier_version
status: public
scopus_import: 1
status: public
title: Hanani-Tutte for radial planarity II
type: conference
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 9801
year: '2016'
...
---
_id: '1599'
abstract:
- lang: eng
text: "The addition of polysialic acid to N- and/or O-linked glycans, referred to
as polysialylation, is a rare posttranslational modification that is mainly known
to control the developmental plasticity of the nervous system. Here we show that
CCR7, the central chemokine receptor controlling immune cell trafficking to secondary
lymphatic organs, carries polysialic acid. This modification is essential for
the recognition of the CCR7 ligand CCL21. As a consequence, dendritic cell trafficking
is abrogated in polysialyltransferase-deficient mice, manifesting as disturbed
lymph node homeostasis and unresponsiveness to inflammatory stimuli. Structure-function
analysis of chemokine-receptor interactions reveals that CCL21 adopts an autoinhibited
conformation, which is released upon interaction with polysialic acid. Thus, we
describe a glycosylation-mediated immune cell trafficking disorder and its mechanistic
basis.\r\n"
acknowledged_ssus:
- _id: SSU
acknowledgement: 'We thank S. Schüchner and E. Ogris for kindly providing the antibody
to GFP, M. Helmbrecht and A. Huber for providing Nrp2−/− mice, the IST Scientific
Support Facilities for excellent services, and J. Renkawitz and K. Vaahtomeri for
critically reading the manuscript. '
article_processing_charge: No
article_type: original
author:
- first_name: Eva
full_name: Kiermaier, Eva
id: 3EB04B78-F248-11E8-B48F-1D18A9856A87
last_name: Kiermaier
orcid: 0000-0001-6165-5738
- first_name: Christine
full_name: Moussion, Christine
id: 3356F664-F248-11E8-B48F-1D18A9856A87
last_name: Moussion
- first_name: Christopher
full_name: Veldkamp, Christopher
last_name: Veldkamp
- first_name: Rita
full_name: Gerardy Schahn, Rita
last_name: Gerardy Schahn
- first_name: Ingrid
full_name: De Vries, Ingrid
id: 4C7D837E-F248-11E8-B48F-1D18A9856A87
last_name: De Vries
- first_name: Larry
full_name: Williams, Larry
last_name: Williams
- first_name: Gary
full_name: Chaffee, Gary
last_name: Chaffee
- first_name: Andrew
full_name: Phillips, Andrew
last_name: Phillips
- first_name: Friedrich
full_name: Freiberger, Friedrich
last_name: Freiberger
- first_name: Richard
full_name: Imre, Richard
last_name: Imre
- first_name: Deni
full_name: Taleski, Deni
last_name: Taleski
- first_name: Richard
full_name: Payne, Richard
last_name: Payne
- first_name: Asolina
full_name: Braun, Asolina
last_name: Braun
- first_name: Reinhold
full_name: Förster, Reinhold
last_name: Förster
- first_name: Karl
full_name: Mechtler, Karl
last_name: Mechtler
- first_name: Martina
full_name: Mühlenhoff, Martina
last_name: Mühlenhoff
- first_name: Brian
full_name: Volkman, Brian
last_name: Volkman
- first_name: Michael K
full_name: Sixt, Michael K
id: 41E9FBEA-F248-11E8-B48F-1D18A9856A87
last_name: Sixt
orcid: 0000-0002-6620-9179
citation:
ama: Kiermaier E, Moussion C, Veldkamp C, et al. Polysialylation controls dendritic
cell trafficking by regulating chemokine recognition. Science. 2016;351(6269):186-190.
doi:10.1126/science.aad0512
apa: Kiermaier, E., Moussion, C., Veldkamp, C., Gerardy Schahn, R., de Vries, I.,
Williams, L., … Sixt, M. K. (2016). Polysialylation controls dendritic cell trafficking
by regulating chemokine recognition. Science. American Association for
the Advancement of Science. https://doi.org/10.1126/science.aad0512
chicago: Kiermaier, Eva, Christine Moussion, Christopher Veldkamp, Rita Gerardy
Schahn, Ingrid de Vries, Larry Williams, Gary Chaffee, et al. “Polysialylation
Controls Dendritic Cell Trafficking by Regulating Chemokine Recognition.” Science.
American Association for the Advancement of Science, 2016. https://doi.org/10.1126/science.aad0512.
ieee: E. Kiermaier et al., “Polysialylation controls dendritic cell trafficking
by regulating chemokine recognition,” Science, vol. 351, no. 6269. American
Association for the Advancement of Science, pp. 186–190, 2016.
ista: Kiermaier E, Moussion C, Veldkamp C, Gerardy Schahn R, de Vries I, Williams
L, Chaffee G, Phillips A, Freiberger F, Imre R, Taleski D, Payne R, Braun A, Förster
R, Mechtler K, Mühlenhoff M, Volkman B, Sixt MK. 2016. Polysialylation controls
dendritic cell trafficking by regulating chemokine recognition. Science. 351(6269),
186–190.
mla: Kiermaier, Eva, et al. “Polysialylation Controls Dendritic Cell Trafficking
by Regulating Chemokine Recognition.” Science, vol. 351, no. 6269, American
Association for the Advancement of Science, 2016, pp. 186–90, doi:10.1126/science.aad0512.
short: E. Kiermaier, C. Moussion, C. Veldkamp, R. Gerardy Schahn, I. de Vries,
L. Williams, G. Chaffee, A. Phillips, F. Freiberger, R. Imre, D. Taleski, R. Payne,
A. Braun, R. Förster, K. Mechtler, M. Mühlenhoff, B. Volkman, M.K. Sixt, Science
351 (2016) 186–190.
date_created: 2018-12-11T11:52:57Z
date_published: 2016-01-08T00:00:00Z
date_updated: 2021-01-12T06:51:52Z
day: '08'
department:
- _id: MiSi
doi: 10.1126/science.aad0512
ec_funded: 1
external_id:
pmid:
- '26657283'
intvolume: ' 351'
issue: '6269'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5583642/
month: '01'
oa: 1
oa_version: Submitted Version
page: 186 - 190
pmid: 1
project:
- _id: 25A603A2-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '281556'
name: Cytoskeletal force generation and force transduction of migrating leukocytes
(EU)
- _id: 25A76F58-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '289720'
name: Stromal Cell-immune Cell Interactions in Health and Disease
- _id: 25A8E5EA-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: Y 564-B12
name: Cytoskeletal force generation and transduction of leukocytes (FWF)
publication: Science
publication_status: published
publisher: American Association for the Advancement of Science
publist_id: '5570'
quality_controlled: '1'
scopus_import: 1
status: public
title: Polysialylation controls dendritic cell trafficking by regulating chemokine
recognition
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 351
year: '2016'
...
---
_id: '1608'
abstract:
- lang: eng
text: 'We show that the Anderson model has a transition from localization to delocalization
at exactly 2 dimensional growth rate on antitrees with normalized edge weights
which are certain discrete graphs. The kinetic part has a one-dimensional structure
allowing a description through transfer matrices which involve some Schur complement.
For such operators we introduce the notion of having one propagating channel and
extend theorems from the theory of one-dimensional Jacobi operators that relate
the behavior of transfer matrices with the spectrum. These theorems are then applied
to the considered model. In essence, in a certain energy region the kinetic part
averages the random potentials along shells and the transfer matrices behave similar
as for a one-dimensional operator with random potential of decaying variance.
At d dimensional growth for d>2 this effective decay is strong enough to obtain
absolutely continuous spectrum, whereas for some uniform d dimensional growth
with d<2 one has pure point spectrum in this energy region. At exactly uniform
2 dimensional growth also some singular continuous spectrum appears, at least
at small disorder. As a corollary we also obtain a change from singular spectrum
(d≤2) to absolutely continuous spectrum (d≥3) for random operators of the type
rΔdr+λ on ℤd, where r is an orthogonal radial projection, Δd the discrete
adjacency operator (Laplacian) on ℤd and λ a random potential. '
author:
- first_name: Christian
full_name: Sadel, Christian
id: 4760E9F8-F248-11E8-B48F-1D18A9856A87
last_name: Sadel
orcid: 0000-0001-8255-3968
citation:
ama: Sadel C. Anderson transition at 2 dimensional growth rate on antitrees and
spectral theory for operators with one propagating channel. Annales Henri Poincare.
2016;17(7):1631-1675. doi:10.1007/s00023-015-0456-3
apa: Sadel, C. (2016). Anderson transition at 2 dimensional growth rate on antitrees
and spectral theory for operators with one propagating channel. Annales Henri
Poincare. Birkhäuser. https://doi.org/10.1007/s00023-015-0456-3
chicago: Sadel, Christian. “Anderson Transition at 2 Dimensional Growth Rate on
Antitrees and Spectral Theory for Operators with One Propagating Channel.” Annales
Henri Poincare. Birkhäuser, 2016. https://doi.org/10.1007/s00023-015-0456-3.
ieee: C. Sadel, “Anderson transition at 2 dimensional growth rate on antitrees and
spectral theory for operators with one propagating channel,” Annales Henri
Poincare, vol. 17, no. 7. Birkhäuser, pp. 1631–1675, 2016.
ista: Sadel C. 2016. Anderson transition at 2 dimensional growth rate on antitrees
and spectral theory for operators with one propagating channel. Annales Henri
Poincare. 17(7), 1631–1675.
mla: Sadel, Christian. “Anderson Transition at 2 Dimensional Growth Rate on Antitrees
and Spectral Theory for Operators with One Propagating Channel.” Annales Henri
Poincare, vol. 17, no. 7, Birkhäuser, 2016, pp. 1631–75, doi:10.1007/s00023-015-0456-3.
short: C. Sadel, Annales Henri Poincare 17 (2016) 1631–1675.
date_created: 2018-12-11T11:53:00Z
date_published: 2016-07-01T00:00:00Z
date_updated: 2021-01-12T06:51:58Z
day: '01'
department:
- _id: LaEr
doi: 10.1007/s00023-015-0456-3
ec_funded: 1
intvolume: ' 17'
issue: '7'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: http://arxiv.org/abs/1501.04287
month: '07'
oa: 1
oa_version: Preprint
page: 1631 - 1675
project:
- _id: 25681D80-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '291734'
name: International IST Postdoc Fellowship Programme
publication: Annales Henri Poincare
publication_status: published
publisher: Birkhäuser
publist_id: '5558'
quality_controlled: '1'
scopus_import: 1
status: public
title: Anderson transition at 2 dimensional growth rate on antitrees and spectral
theory for operators with one propagating channel
type: journal_article
user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87
volume: 17
year: '2016'
...
---
_id: '1612'
abstract:
- lang: eng
text: We prove that whenever A is a 3-conservative relational structure with only
binary and unary relations,then the algebra of polymorphisms of A either has no
Taylor operation (i.e.,CSP(A)is NP-complete),or it generates an SD(∧) variety
(i.e.,CSP(A)has bounded width).
author:
- first_name: Alexandr
full_name: Kazda, Alexandr
id: 3B32BAA8-F248-11E8-B48F-1D18A9856A87
last_name: Kazda
citation:
ama: Kazda A. CSP for binary conservative relational structures. Algebra Universalis.
2016;75(1):75-84. doi:10.1007/s00012-015-0358-8
apa: Kazda, A. (2016). CSP for binary conservative relational structures. Algebra
Universalis. Springer. https://doi.org/10.1007/s00012-015-0358-8
chicago: Kazda, Alexandr. “CSP for Binary Conservative Relational Structures.” Algebra
Universalis. Springer, 2016. https://doi.org/10.1007/s00012-015-0358-8.
ieee: A. Kazda, “CSP for binary conservative relational structures,” Algebra
Universalis, vol. 75, no. 1. Springer, pp. 75–84, 2016.
ista: Kazda A. 2016. CSP for binary conservative relational structures. Algebra
Universalis. 75(1), 75–84.
mla: Kazda, Alexandr. “CSP for Binary Conservative Relational Structures.” Algebra
Universalis, vol. 75, no. 1, Springer, 2016, pp. 75–84, doi:10.1007/s00012-015-0358-8.
short: A. Kazda, Algebra Universalis 75 (2016) 75–84.
date_created: 2018-12-11T11:53:01Z
date_published: 2016-02-01T00:00:00Z
date_updated: 2021-01-12T06:52:00Z
day: '01'
department:
- _id: VlKo
doi: 10.1007/s00012-015-0358-8
intvolume: ' 75'
issue: '1'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: http://arxiv.org/abs/1112.1099
month: '02'
oa: 1
oa_version: Preprint
page: 75 - 84
publication: Algebra Universalis
publication_status: published
publisher: Springer
publist_id: '5554'
quality_controlled: '1'
scopus_import: 1
status: public
title: CSP for binary conservative relational structures
type: journal_article
user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87
volume: 75
year: '2016'
...
---
_id: '1617'
abstract:
- lang: eng
text: 'We study the discrepancy of jittered sampling sets: such a set P⊂ [0,1]d
is generated for fixed m∈ℕ by partitioning [0,1]d into md axis aligned cubes of
equal measure and placing a random point inside each of the N=md cubes. We prove
that, for N sufficiently large, 1/10 d/N1/2+1/2d ≤EDN∗(P)≤ √d(log N) 1/2/N1/2+1/2d,
where the upper bound with an unspecified constant Cd was proven earlier by Beck.
Our proof makes crucial use of the sharp Dvoretzky-Kiefer-Wolfowitz inequality
and a suitably taylored Bernstein inequality; we have reasons to believe that
the upper bound has the sharp scaling in N. Additional heuristics suggest that
jittered sampling should be able to improve known bounds on the inverse of the
star-discrepancy in the regime N≳dd. We also prove a partition principle showing
that every partition of [0,1]d combined with a jittered sampling construction
gives rise to a set whose expected squared L2-discrepancy is smaller than that
of purely random points.'
acknowledgement: We are grateful to the referee whose suggestions greatly improved
the quality and clarity of the exposition.
author:
- first_name: Florian
full_name: Pausinger, Florian
id: 2A77D7A2-F248-11E8-B48F-1D18A9856A87
last_name: Pausinger
orcid: 0000-0002-8379-3768
- first_name: Stefan
full_name: Steinerberger, Stefan
last_name: Steinerberger
citation:
ama: Pausinger F, Steinerberger S. On the discrepancy of jittered sampling. Journal
of Complexity. 2016;33:199-216. doi:10.1016/j.jco.2015.11.003
apa: Pausinger, F., & Steinerberger, S. (2016). On the discrepancy of jittered
sampling. Journal of Complexity. Academic Press. https://doi.org/10.1016/j.jco.2015.11.003
chicago: Pausinger, Florian, and Stefan Steinerberger. “On the Discrepancy of Jittered
Sampling.” Journal of Complexity. Academic Press, 2016. https://doi.org/10.1016/j.jco.2015.11.003.
ieee: F. Pausinger and S. Steinerberger, “On the discrepancy of jittered sampling,”
Journal of Complexity, vol. 33. Academic Press, pp. 199–216, 2016.
ista: Pausinger F, Steinerberger S. 2016. On the discrepancy of jittered sampling.
Journal of Complexity. 33, 199–216.
mla: Pausinger, Florian, and Stefan Steinerberger. “On the Discrepancy of Jittered
Sampling.” Journal of Complexity, vol. 33, Academic Press, 2016, pp. 199–216,
doi:10.1016/j.jco.2015.11.003.
short: F. Pausinger, S. Steinerberger, Journal of Complexity 33 (2016) 199–216.
date_created: 2018-12-11T11:53:03Z
date_published: 2016-04-01T00:00:00Z
date_updated: 2021-01-12T06:52:02Z
day: '01'
department:
- _id: HeEd
doi: 10.1016/j.jco.2015.11.003
intvolume: ' 33'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: http://arxiv.org/abs/1510.00251
month: '04'
oa: 1
oa_version: Submitted Version
page: 199 - 216
publication: Journal of Complexity
publication_status: published
publisher: Academic Press
publist_id: '5549'
quality_controlled: '1'
scopus_import: 1
status: public
title: On the discrepancy of jittered sampling
type: journal_article
user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87
volume: 33
year: '2016'
...
---
_id: '1620'
abstract:
- lang: eng
text: We consider the Bardeen–Cooper–Schrieffer free energy functional for particles
interacting via a two-body potential on a microscopic scale and in the presence
of weak external fields varying on a macroscopic scale. We study the influence
of the external fields on the critical temperature. We show that in the limit
where the ratio between the microscopic and macroscopic scale tends to zero, the
next to leading order of the critical temperature is determined by the lowest
eigenvalue of the linearization of the Ginzburg–Landau equation.
acknowledgement: The authors are grateful to I. M. Sigal for useful discussions. Financial
support from the US National Science Foundation through Grants PHY-1347399 and DMS-1363432
(R.L.F.), from the Danish council for independent research and from ERC Advanced
Grant 321029 (J.P.S.) is acknowledged.
author:
- first_name: Rupert
full_name: Frank, Rupert
last_name: Frank
- first_name: Christian
full_name: Hainzl, Christian
last_name: Hainzl
- first_name: Robert
full_name: Seiringer, Robert
id: 4AFD0470-F248-11E8-B48F-1D18A9856A87
last_name: Seiringer
orcid: 0000-0002-6781-0521
- first_name: Jan
full_name: Solovej, Jan
last_name: Solovej
citation:
ama: Frank R, Hainzl C, Seiringer R, Solovej J. The external field dependence of
the BCS critical temperature. Communications in Mathematical Physics. 2016;342(1):189-216.
doi:10.1007/s00220-015-2526-2
apa: Frank, R., Hainzl, C., Seiringer, R., & Solovej, J. (2016). The external
field dependence of the BCS critical temperature. Communications in Mathematical
Physics. Springer. https://doi.org/10.1007/s00220-015-2526-2
chicago: Frank, Rupert, Christian Hainzl, Robert Seiringer, and Jan Solovej. “The
External Field Dependence of the BCS Critical Temperature.” Communications
in Mathematical Physics. Springer, 2016. https://doi.org/10.1007/s00220-015-2526-2.
ieee: R. Frank, C. Hainzl, R. Seiringer, and J. Solovej, “The external field dependence
of the BCS critical temperature,” Communications in Mathematical Physics,
vol. 342, no. 1. Springer, pp. 189–216, 2016.
ista: Frank R, Hainzl C, Seiringer R, Solovej J. 2016. The external field dependence
of the BCS critical temperature. Communications in Mathematical Physics. 342(1),
189–216.
mla: Frank, Rupert, et al. “The External Field Dependence of the BCS Critical Temperature.”
Communications in Mathematical Physics, vol. 342, no. 1, Springer, 2016,
pp. 189–216, doi:10.1007/s00220-015-2526-2.
short: R. Frank, C. Hainzl, R. Seiringer, J. Solovej, Communications in Mathematical
Physics 342 (2016) 189–216.
date_created: 2018-12-11T11:53:04Z
date_published: 2016-02-01T00:00:00Z
date_updated: 2021-01-12T06:52:03Z
day: '01'
department:
- _id: RoSe
doi: 10.1007/s00220-015-2526-2
intvolume: ' 342'
issue: '1'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: http://arxiv.org/abs/1410.2352
month: '02'
oa: 1
oa_version: Submitted Version
page: 189 - 216
publication: Communications in Mathematical Physics
publication_status: published
publisher: Springer
publist_id: '5546'
quality_controlled: '1'
scopus_import: 1
status: public
title: The external field dependence of the BCS critical temperature
type: journal_article
user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87
volume: 342
year: '2016'
...
---
_id: '1622'
abstract:
- lang: eng
text: We prove analogues of the Lieb–Thirring and Hardy–Lieb–Thirring inequalities
for many-body quantum systems with fractional kinetic operators and homogeneous
interaction potentials, where no anti-symmetry on the wave functions is assumed.
These many-body inequalities imply interesting one-body interpolation inequalities,
and we show that the corresponding one- and many-body inequalities are actually
equivalent in certain cases.
acknowledgement: "We thank Jan Philip Solovej, Robert Seiringer and Vladimir Maz’ya
for helpful discussions, as well as Rupert Frank\r\nand the anonymous referee for
useful comments. Part of this work has been carried out during a visit at the Institut
Mittag-Leffler (Stockholm). D.L. acknowledges financial support by the grant KAW
2010.0063 from the Knut and Alice Wallenberg Foundation and the Swedish Research
Council grant no. 2013-4734. P.T.N. is supported by the People Programme (Marie
Curie Actions) of the European Union’s Seventh Framework Programme (FP7/2007-2013)
under REA grant agreement no. 291734. F.P. acknowledges support from the ERC project
no. 321029 “The\r\nmathematics of the structure of matter”."
author:
- first_name: Douglas
full_name: Lundholm, Douglas
last_name: Lundholm
- first_name: Phan
full_name: Nam, Phan
id: 404092F4-F248-11E8-B48F-1D18A9856A87
last_name: Nam
- first_name: Fabian
full_name: Portmann, Fabian
last_name: Portmann
citation:
ama: Lundholm D, Nam P, Portmann F. Fractional Hardy–Lieb–Thirring and related Inequalities
for interacting systems. Archive for Rational Mechanics and Analysis. 2016;219(3):1343-1382.
doi:10.1007/s00205-015-0923-5
apa: Lundholm, D., Nam, P., & Portmann, F. (2016). Fractional Hardy–Lieb–Thirring
and related Inequalities for interacting systems. Archive for Rational Mechanics
and Analysis. Springer. https://doi.org/10.1007/s00205-015-0923-5
chicago: Lundholm, Douglas, Phan Nam, and Fabian Portmann. “Fractional Hardy–Lieb–Thirring
and Related Inequalities for Interacting Systems.” Archive for Rational Mechanics
and Analysis. Springer, 2016. https://doi.org/10.1007/s00205-015-0923-5.
ieee: D. Lundholm, P. Nam, and F. Portmann, “Fractional Hardy–Lieb–Thirring and
related Inequalities for interacting systems,” Archive for Rational Mechanics
and Analysis, vol. 219, no. 3. Springer, pp. 1343–1382, 2016.
ista: Lundholm D, Nam P, Portmann F. 2016. Fractional Hardy–Lieb–Thirring and related
Inequalities for interacting systems. Archive for Rational Mechanics and Analysis.
219(3), 1343–1382.
mla: Lundholm, Douglas, et al. “Fractional Hardy–Lieb–Thirring and Related Inequalities
for Interacting Systems.” Archive for Rational Mechanics and Analysis,
vol. 219, no. 3, Springer, 2016, pp. 1343–82, doi:10.1007/s00205-015-0923-5.
short: D. Lundholm, P. Nam, F. Portmann, Archive for Rational Mechanics and Analysis
219 (2016) 1343–1382.
date_created: 2018-12-11T11:53:05Z
date_published: 2016-03-01T00:00:00Z
date_updated: 2021-01-12T06:52:04Z
day: '01'
department:
- _id: RoSe
doi: 10.1007/s00205-015-0923-5
ec_funded: 1
intvolume: ' 219'
issue: '3'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: http://arxiv.org/abs/1501.04570
month: '03'
oa: 1
oa_version: Submitted Version
page: 1343 - 1382
project:
- _id: 25681D80-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '291734'
name: International IST Postdoc Fellowship Programme
publication: Archive for Rational Mechanics and Analysis
publication_status: published
publisher: Springer
publist_id: '5542'
quality_controlled: '1'
scopus_import: 1
status: public
title: Fractional Hardy–Lieb–Thirring and related Inequalities for interacting systems
type: journal_article
user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87
volume: 219
year: '2016'
...
---
_id: '1631'
abstract:
- lang: eng
text: 'Ancestral processes are fundamental to modern population genetics and spatial
structure has been the subject of intense interest for many years. Despite this
interest, almost nothing is known about the distribution of the locations of pedigree
or genetic ancestors. Using both spatially continuous and stepping-stone models,
we show that the distribution of pedigree ancestors approaches a travelling wave,
for which we develop two alternative approximations. The speed and width of the
wave are sensitive to the local details of the model. After a short time, genetic
ancestors spread far more slowly than pedigree ancestors, ultimately diffusing
out with radius ## rather than spreading at constant speed. In contrast to the
wave of pedigree ancestors, the spread of genetic ancestry is insensitive to the
local details of the models.'
author:
- first_name: Jerome
full_name: Kelleher, Jerome
last_name: Kelleher
- first_name: Alison
full_name: Etheridge, Alison
last_name: Etheridge
- first_name: Amandine
full_name: Véber, Amandine
last_name: Véber
- first_name: Nicholas H
full_name: Barton, Nicholas H
id: 4880FE40-F248-11E8-B48F-1D18A9856A87
last_name: Barton
orcid: 0000-0002-8548-5240
citation:
ama: Kelleher J, Etheridge A, Véber A, Barton NH. Spread of pedigree versus genetic
ancestry in spatially distributed populations. Theoretical Population Biology.
2016;108:1-12. doi:10.1016/j.tpb.2015.10.008
apa: Kelleher, J., Etheridge, A., Véber, A., & Barton, N. H. (2016). Spread
of pedigree versus genetic ancestry in spatially distributed populations. Theoretical
Population Biology. Academic Press. https://doi.org/10.1016/j.tpb.2015.10.008
chicago: Kelleher, Jerome, Alison Etheridge, Amandine Véber, and Nicholas H Barton.
“Spread of Pedigree versus Genetic Ancestry in Spatially Distributed Populations.”
Theoretical Population Biology. Academic Press, 2016. https://doi.org/10.1016/j.tpb.2015.10.008.
ieee: J. Kelleher, A. Etheridge, A. Véber, and N. H. Barton, “Spread of pedigree
versus genetic ancestry in spatially distributed populations,” Theoretical
Population Biology, vol. 108. Academic Press, pp. 1–12, 2016.
ista: Kelleher J, Etheridge A, Véber A, Barton NH. 2016. Spread of pedigree versus
genetic ancestry in spatially distributed populations. Theoretical Population
Biology. 108, 1–12.
mla: Kelleher, Jerome, et al. “Spread of Pedigree versus Genetic Ancestry in Spatially
Distributed Populations.” Theoretical Population Biology, vol. 108, Academic
Press, 2016, pp. 1–12, doi:10.1016/j.tpb.2015.10.008.
short: J. Kelleher, A. Etheridge, A. Véber, N.H. Barton, Theoretical Population
Biology 108 (2016) 1–12.
date_created: 2018-12-11T11:53:08Z
date_published: 2016-04-01T00:00:00Z
date_updated: 2021-01-12T06:52:07Z
day: '01'
ddc:
- '576'
department:
- _id: NiBa
doi: 10.1016/j.tpb.2015.10.008
ec_funded: 1
file:
- access_level: open_access
checksum: 6a65ba187994d4ad86c1c509e0ff482a
content_type: application/pdf
creator: system
date_created: 2018-12-12T10:11:12Z
date_updated: 2020-07-14T12:45:07Z
file_id: '4865'
file_name: IST-2016-465-v1+1_1-s2.0-S0040580915001094-main.pdf
file_size: 1684043
relation: main_file
file_date_updated: 2020-07-14T12:45:07Z
has_accepted_license: '1'
intvolume: ' 108'
language:
- iso: eng
month: '04'
oa: 1
oa_version: Published Version
page: 1 - 12
project:
- _id: 25B07788-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '250152'
name: Limits to selection in biology and in evolutionary computation
publication: Theoretical Population Biology
publication_status: published
publisher: Academic Press
publist_id: '5524'
pubrep_id: '465'
quality_controlled: '1'
scopus_import: 1
status: public
title: Spread of pedigree versus genetic ancestry in spatially distributed populations
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: journal_article
user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87
volume: 108
year: '2016'
...
---
_id: '1641'
abstract:
- lang: eng
text: The plant hormone auxin (indole-3-acetic acid) is a major regulator of plant
growth and development including embryo and root patterning, lateral organ formation
and growth responses to environmental stimuli. Auxin is directionally transported
from cell to cell by the action of specific auxin influx [AUXIN-RESISTANT1 (AUX1)]
and efflux [PIN-FORMED (PIN)] transport regulators, whose polar, subcellular localizations
are aligned with the direction of the auxin flow. Auxin itself regulates its own
transport by modulation of the expression and subcellular localization of the
auxin transporters. Increased auxin levels promote the transcription of PIN2 and
AUX1 genes as well as stabilize PIN proteins at the plasma membrane, whereas prolonged
auxin exposure increases the turnover of PIN proteins and their degradation in
the vacuole. In this study, we applied a forward genetic approach, to identify
molecular components playing a role in the auxin-mediated degradation. We generated
EMS-mutagenized Arabidopsis PIN2::PIN2:GFP, AUX1::AUX1:YFP eir1aux1 populations
and designed a screen for mutants with persistently strong fluorescent signals
of the tagged PIN2 and AUX1 after prolonged treatment with the synthetic auxin
2,4-dichlorophenoxyacetic acid (2,4-D). This approach yielded novel auxin degradation
mutants defective in trafficking and degradation of PIN2 and AUX1 proteins and
established a role for auxin-mediated degradation in plant development.
acknowledgement: 'European Social Fund (CZ.1.07/2.3.00/20.0043) and the Czech Science
Foundation GAČR (GA13-40637S) to JF. '
author:
- first_name: Radka
full_name: Zemová, Radka
last_name: Zemová
- first_name: Marta
full_name: Zwiewka, Marta
last_name: Zwiewka
- first_name: Agnieszka
full_name: Bielach, Agnieszka
last_name: Bielach
- first_name: Hélène
full_name: Robert, Hélène
last_name: Robert
- first_name: Jirí
full_name: Friml, Jirí
id: 4159519E-F248-11E8-B48F-1D18A9856A87
last_name: Friml
orcid: 0000-0002-8302-7596
citation:
ama: Zemová R, Zwiewka M, Bielach A, Robert H, Friml J. A forward genetic screen
for new regulators of auxin mediated degradation of auxin transport proteins in
Arabidopsis thaliana. Journal of Plant Growth Regulation. 2016;35(2):465-476.
doi:10.1007/s00344-015-9553-2
apa: Zemová, R., Zwiewka, M., Bielach, A., Robert, H., & Friml, J. (2016). A
forward genetic screen for new regulators of auxin mediated degradation of auxin
transport proteins in Arabidopsis thaliana. Journal of Plant Growth Regulation.
Springer. https://doi.org/10.1007/s00344-015-9553-2
chicago: Zemová, Radka, Marta Zwiewka, Agnieszka Bielach, Hélène Robert, and Jiří
Friml. “A Forward Genetic Screen for New Regulators of Auxin Mediated Degradation
of Auxin Transport Proteins in Arabidopsis Thaliana.” Journal of Plant Growth
Regulation. Springer, 2016. https://doi.org/10.1007/s00344-015-9553-2.
ieee: R. Zemová, M. Zwiewka, A. Bielach, H. Robert, and J. Friml, “A forward genetic
screen for new regulators of auxin mediated degradation of auxin transport proteins
in Arabidopsis thaliana,” Journal of Plant Growth Regulation, vol. 35,
no. 2. Springer, pp. 465–476, 2016.
ista: Zemová R, Zwiewka M, Bielach A, Robert H, Friml J. 2016. A forward genetic
screen for new regulators of auxin mediated degradation of auxin transport proteins
in Arabidopsis thaliana. Journal of Plant Growth Regulation. 35(2), 465–476.
mla: Zemová, Radka, et al. “A Forward Genetic Screen for New Regulators of Auxin
Mediated Degradation of Auxin Transport Proteins in Arabidopsis Thaliana.” Journal
of Plant Growth Regulation, vol. 35, no. 2, Springer, 2016, pp. 465–76, doi:10.1007/s00344-015-9553-2.
short: R. Zemová, M. Zwiewka, A. Bielach, H. Robert, J. Friml, Journal of Plant
Growth Regulation 35 (2016) 465–476.
date_created: 2018-12-11T11:53:12Z
date_published: 2016-06-01T00:00:00Z
date_updated: 2021-01-12T06:52:11Z
day: '01'
ddc:
- '581'
department:
- _id: JiFr
doi: 10.1007/s00344-015-9553-2
file:
- access_level: open_access
checksum: 0dc6a300cde6536ceedd2bcdd2060efb
content_type: application/pdf
creator: system
date_created: 2018-12-12T10:08:34Z
date_updated: 2020-07-14T12:45:08Z
file_id: '4695'
file_name: IST-2018-1001-v1+1_Zemova_JPlantGrowthRegul_2016_proofs.pdf
file_size: 5637591
relation: main_file
file_date_updated: 2020-07-14T12:45:08Z
has_accepted_license: '1'
intvolume: ' 35'
issue: '2'
language:
- iso: eng
month: '06'
oa: 1
oa_version: Preprint
page: 465 - 476
publication: Journal of Plant Growth Regulation
publication_status: published
publisher: Springer
publist_id: '5512'
pubrep_id: '1001'
quality_controlled: '1'
scopus_import: 1
status: public
title: A forward genetic screen for new regulators of auxin mediated degradation of
auxin transport proteins in Arabidopsis thaliana
type: journal_article
user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87
volume: 35
year: '2016'
...
---
_id: '1225'
abstract:
- lang: eng
text: At Crypto 2015 Fuchsbauer, Hanser and Slamanig (FHS) presented the first standard-model
construction of efficient roundoptimal blind signatures that does not require
complexity leveraging. It is conceptually simple and builds on the primitive of
structure-preserving signatures on equivalence classes (SPS-EQ). FHS prove the
unforgeability of their scheme assuming EUF-CMA security of the SPS-EQ scheme
and hardness of a version of the DH inversion problem. Blindness under adversarially
chosen keys is proven under an interactive variant of the DDH assumption. We propose
a variant of their scheme whose blindness can be proven under a non-interactive
assumption, namely a variant of the bilinear DDH assumption. We moreover prove
its unforgeability assuming only unforgeability of the underlying SPS-EQ but no
additional assumptions as needed for the FHS scheme.
alternative_title:
- LNCS
author:
- first_name: Georg
full_name: Fuchsbauer, Georg
id: 46B4C3EE-F248-11E8-B48F-1D18A9856A87
last_name: Fuchsbauer
- first_name: Christian
full_name: Hanser, Christian
last_name: Hanser
- first_name: Chethan
full_name: Kamath Hosdurg, Chethan
id: 4BD3F30E-F248-11E8-B48F-1D18A9856A87
last_name: Kamath Hosdurg
- first_name: Daniel
full_name: Slamanig, Daniel
last_name: Slamanig
citation:
ama: 'Fuchsbauer G, Hanser C, Kamath Hosdurg C, Slamanig D. Practical round-optimal
blind signatures in the standard model from weaker assumptions. In: Vol 9841.
Springer; 2016:391-408. doi:10.1007/978-3-319-44618-9_21'
apa: 'Fuchsbauer, G., Hanser, C., Kamath Hosdurg, C., & Slamanig, D. (2016).
Practical round-optimal blind signatures in the standard model from weaker assumptions
(Vol. 9841, pp. 391–408). Presented at the SCN: Security and Cryptography for
Networks, Amalfi, Italy: Springer. https://doi.org/10.1007/978-3-319-44618-9_21'
chicago: Fuchsbauer, Georg, Christian Hanser, Chethan Kamath Hosdurg, and Daniel
Slamanig. “Practical Round-Optimal Blind Signatures in the Standard Model from
Weaker Assumptions,” 9841:391–408. Springer, 2016. https://doi.org/10.1007/978-3-319-44618-9_21.
ieee: 'G. Fuchsbauer, C. Hanser, C. Kamath Hosdurg, and D. Slamanig, “Practical
round-optimal blind signatures in the standard model from weaker assumptions,”
presented at the SCN: Security and Cryptography for Networks, Amalfi, Italy, 2016,
vol. 9841, pp. 391–408.'
ista: 'Fuchsbauer G, Hanser C, Kamath Hosdurg C, Slamanig D. 2016. Practical round-optimal
blind signatures in the standard model from weaker assumptions. SCN: Security
and Cryptography for Networks, LNCS, vol. 9841, 391–408.'
mla: Fuchsbauer, Georg, et al. Practical Round-Optimal Blind Signatures in the
Standard Model from Weaker Assumptions. Vol. 9841, Springer, 2016, pp. 391–408,
doi:10.1007/978-3-319-44618-9_21.
short: G. Fuchsbauer, C. Hanser, C. Kamath Hosdurg, D. Slamanig, in:, Springer,
2016, pp. 391–408.
conference:
end_date: 2016-09-02
location: Amalfi, Italy
name: 'SCN: Security and Cryptography for Networks'
start_date: 2016-08-31
date_created: 2018-12-11T11:50:49Z
date_published: 2016-08-11T00:00:00Z
date_updated: 2023-02-23T10:08:16Z
day: '11'
department:
- _id: KrPi
doi: 10.1007/978-3-319-44618-9_21
ec_funded: 1
intvolume: ' 9841'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://eprint.iacr.org/2016/662
month: '08'
oa: 1
oa_version: Submitted Version
page: 391 - 408
project:
- _id: 258C570E-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '259668'
name: Provable Security for Physical Cryptography
- _id: 258AA5B2-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '682815'
name: Teaching Old Crypto New Tricks
publication_status: published
publisher: Springer
publist_id: '6109'
quality_controlled: '1'
related_material:
record:
- id: '1647'
relation: earlier_version
status: public
scopus_import: 1
status: public
title: Practical round-optimal blind signatures in the standard model from weaker
assumptions
type: conference
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 9841
year: '2016'
...
---
_id: '1653'
abstract:
- lang: eng
text: "A somewhere statistically binding (SSB) hash, introduced by Hubáček and Wichs
(ITCS ’15), can be used to hash a long string x to a short digest y = H hk (x)
using a public hashing-key hk. Furthermore, there is a way to set up the hash
key hk to make it statistically binding on some arbitrary hidden position i, meaning
that: (1) the digest y completely determines the i’th bit (or symbol) of x so
that all pre-images of y have the same value in the i’th position, (2) it is computationally
infeasible to distinguish the position i on which hk is statistically binding
from any other position i’. Lastly, the hash should have a local opening property
analogous to Merkle-Tree hashing, meaning that given x and y = H hk (x) it should
be possible to create a short proof π that certifies the value of the i’th bit
(or symbol) of x without having to provide the entire input x. A similar primitive
called a positional accumulator, introduced by Koppula, Lewko and Waters (STOC
’15) further supports dynamic updates of the hashed value. These tools, which
are interesting in their own right, also serve as one of the main technical components
in several recent works building advanced applications from indistinguishability
obfuscation (iO).\r\n\r\nThe prior constructions of SSB hashing and positional
accumulators required fully homomorphic encryption (FHE) and iO respectively.
In this work, we give new constructions of these tools based on well studied number-theoretic
assumptions such as DDH, Phi-Hiding and DCR, as well as a general construction
from lossy/injective functions."
alternative_title:
- LNCS
author:
- first_name: Tatsuaki
full_name: Okamoto, Tatsuaki
last_name: Okamoto
- first_name: Krzysztof Z
full_name: Pietrzak, Krzysztof Z
id: 3E04A7AA-F248-11E8-B48F-1D18A9856A87
last_name: Pietrzak
orcid: 0000-0002-9139-1654
- first_name: Brent
full_name: Waters, Brent
last_name: Waters
- first_name: Daniel
full_name: Wichs, Daniel
last_name: Wichs
citation:
ama: 'Okamoto T, Pietrzak KZ, Waters B, Wichs D. New realizations of somewhere statistically
binding hashing and positional accumulators. In: Vol 9452. Springer; 2016:121-145.
doi:10.1007/978-3-662-48797-6_6'
apa: 'Okamoto, T., Pietrzak, K. Z., Waters, B., & Wichs, D. (2016). New realizations
of somewhere statistically binding hashing and positional accumulators (Vol. 9452,
pp. 121–145). Presented at the ASIACRYPT: Theory and Application of Cryptology
and Information Security, Auckland, New Zealand: Springer. https://doi.org/10.1007/978-3-662-48797-6_6'
chicago: Okamoto, Tatsuaki, Krzysztof Z Pietrzak, Brent Waters, and Daniel Wichs.
“New Realizations of Somewhere Statistically Binding Hashing and Positional Accumulators,”
9452:121–45. Springer, 2016. https://doi.org/10.1007/978-3-662-48797-6_6.
ieee: 'T. Okamoto, K. Z. Pietrzak, B. Waters, and D. Wichs, “New realizations of
somewhere statistically binding hashing and positional accumulators,” presented
at the ASIACRYPT: Theory and Application of Cryptology and Information Security,
Auckland, New Zealand, 2016, vol. 9452, pp. 121–145.'
ista: 'Okamoto T, Pietrzak KZ, Waters B, Wichs D. 2016. New realizations of somewhere
statistically binding hashing and positional accumulators. ASIACRYPT: Theory and
Application of Cryptology and Information Security, LNCS, vol. 9452, 121–145.'
mla: Okamoto, Tatsuaki, et al. New Realizations of Somewhere Statistically Binding
Hashing and Positional Accumulators. Vol. 9452, Springer, 2016, pp. 121–45,
doi:10.1007/978-3-662-48797-6_6.
short: T. Okamoto, K.Z. Pietrzak, B. Waters, D. Wichs, in:, Springer, 2016, pp.
121–145.
conference:
end_date: 2015-12-03
location: Auckland, New Zealand
name: 'ASIACRYPT: Theory and Application of Cryptology and Information Security'
start_date: 2015-11-29
date_created: 2018-12-11T11:53:16Z
date_published: 2016-01-08T00:00:00Z
date_updated: 2021-01-12T06:52:16Z
day: '08'
ddc:
- '000'
department:
- _id: KrPi
doi: 10.1007/978-3-662-48797-6_6
ec_funded: 1
file:
- access_level: open_access
checksum: a57711cb660c5b17b42bb47275a00180
content_type: application/pdf
creator: system
date_created: 2018-12-12T10:12:05Z
date_updated: 2020-07-14T12:45:08Z
file_id: '4923'
file_name: IST-2016-677-v1+1_869.pdf
file_size: 580088
relation: main_file
file_date_updated: 2020-07-14T12:45:08Z
has_accepted_license: '1'
intvolume: ' 9452'
language:
- iso: eng
month: '01'
oa: 1
oa_version: Submitted Version
page: 121 - 145
project:
- _id: 258C570E-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '259668'
name: Provable Security for Physical Cryptography
publication_status: published
publisher: Springer
publist_id: '5497'
pubrep_id: '677'
quality_controlled: '1'
scopus_import: 1
status: public
title: New realizations of somewhere statistically binding hashing and positional
accumulators
type: conference
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 9452
year: '2016'
...
---
_id: '1705'
abstract:
- lang: eng
text: Hybrid systems represent an important and powerful formalism for modeling
real-world applications such as embedded systems. A verification tool like SpaceEx
is based on the exploration of a symbolic search space (the region space). As
a verification tool, it is typically optimized towards proving the absence of
errors. In some settings, e.g., when the verification tool is employed in a feedback-directed
design cycle, one would like to have the option to call a version that is optimized
towards finding an error trajectory in the region space. A recent approach in
this direction is based on guided search. Guided search relies on a cost function
that indicates which states are promising to be explored, and preferably explores
more promising states first. In this paper, we propose an abstraction-based cost
function based on coarse-grained space abstractions for guiding the reachability
analysis. For this purpose, a suitable abstraction technique that exploits the
flexible granularity of modern reachability analysis algorithms is introduced.
The new cost function is an effective extension of pattern database approaches
that have been successfully applied in other areas. The approach has been implemented
in the SpaceEx model checker. The evaluation shows its practical potential.
article_processing_charge: Yes (via OA deal)
author:
- first_name: Sergiy
full_name: Bogomolov, Sergiy
id: 369D9A44-F248-11E8-B48F-1D18A9856A87
last_name: Bogomolov
orcid: 0000-0002-0686-0365
- first_name: Alexandre
full_name: Donzé, Alexandre
last_name: Donzé
- first_name: Goran
full_name: Frehse, Goran
last_name: Frehse
- first_name: Radu
full_name: Grosu, Radu
last_name: Grosu
- first_name: Taylor
full_name: Johnson, Taylor
last_name: Johnson
- first_name: Hamed
full_name: Ladan, Hamed
last_name: Ladan
- first_name: Andreas
full_name: Podelski, Andreas
last_name: Podelski
- first_name: Martin
full_name: Wehrle, Martin
last_name: Wehrle
citation:
ama: Bogomolov S, Donzé A, Frehse G, et al. Guided search for hybrid systems based
on coarse-grained space abstractions. International Journal on Software Tools
for Technology Transfer. 2016;18(4):449-467. doi:10.1007/s10009-015-0393-y
apa: Bogomolov, S., Donzé, A., Frehse, G., Grosu, R., Johnson, T., Ladan, H., …
Wehrle, M. (2016). Guided search for hybrid systems based on coarse-grained space
abstractions. International Journal on Software Tools for Technology Transfer.
Springer. https://doi.org/10.1007/s10009-015-0393-y
chicago: Bogomolov, Sergiy, Alexandre Donzé, Goran Frehse, Radu Grosu, Taylor Johnson,
Hamed Ladan, Andreas Podelski, and Martin Wehrle. “Guided Search for Hybrid Systems
Based on Coarse-Grained Space Abstractions.” International Journal on Software
Tools for Technology Transfer. Springer, 2016. https://doi.org/10.1007/s10009-015-0393-y.
ieee: S. Bogomolov et al., “Guided search for hybrid systems based on coarse-grained
space abstractions,” International Journal on Software Tools for Technology
Transfer, vol. 18, no. 4. Springer, pp. 449–467, 2016.
ista: Bogomolov S, Donzé A, Frehse G, Grosu R, Johnson T, Ladan H, Podelski A, Wehrle
M. 2016. Guided search for hybrid systems based on coarse-grained space abstractions.
International Journal on Software Tools for Technology Transfer. 18(4), 449–467.
mla: Bogomolov, Sergiy, et al. “Guided Search for Hybrid Systems Based on Coarse-Grained
Space Abstractions.” International Journal on Software Tools for Technology
Transfer, vol. 18, no. 4, Springer, 2016, pp. 449–67, doi:10.1007/s10009-015-0393-y.
short: S. Bogomolov, A. Donzé, G. Frehse, R. Grosu, T. Johnson, H. Ladan, A. Podelski,
M. Wehrle, International Journal on Software Tools for Technology Transfer 18
(2016) 449–467.
date_created: 2018-12-11T11:53:34Z
date_published: 2016-08-01T00:00:00Z
date_updated: 2021-01-12T06:52:38Z
day: '01'
ddc:
- '000'
department:
- _id: ToHe
doi: 10.1007/s10009-015-0393-y
ec_funded: 1
file:
- access_level: open_access
checksum: 31561d7705599a9bd4ea816accc0752e
content_type: application/pdf
creator: system
date_created: 2018-12-12T10:15:26Z
date_updated: 2020-07-14T12:45:13Z
file_id: '5146'
file_name: IST-2016-457-v1+1_s10009-015-0393-y.pdf
file_size: 2296522
relation: main_file
file_date_updated: 2020-07-14T12:45:13Z
has_accepted_license: '1'
intvolume: ' 18'
issue: '4'
language:
- iso: eng
month: '08'
oa: 1
oa_version: Published Version
page: 449 - 467
project:
- _id: 25EE3708-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '267989'
name: Quantitative Reactive Modeling
- _id: 25F42A32-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: Z211
name: The Wittgenstein Prize
- _id: 25832EC2-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: S 11407_N23
name: Rigorous Systems Engineering
publication: International Journal on Software Tools for Technology Transfer
publication_status: published
publisher: Springer
publist_id: '5431'
pubrep_id: '457'
quality_controlled: '1'
scopus_import: 1
status: public
title: Guided search for hybrid systems based on coarse-grained space abstractions
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: journal_article
user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87
volume: 18
year: '2016'
...
---
_id: '1833'
abstract:
- lang: eng
text: 'Relational models for contingency tables are generalizations of log-linear
models, allowing effects associated with arbitrary subsets of cells in the table,
and not necessarily containing the overall effect, that is, a common parameter
in every cell. Similarly to log-linear models, relational models can be extended
to non-negative distributions, but the extension requires more complex methods.
An extended relational model is defined as an algebraic variety, and it turns
out to be the closure of the original model with respect to the Bregman divergence.
In the extended relational model, the MLE of the cell parameters always exists
and is unique, but some of its properties may be different from those of the MLE
under log-linear models. The MLE can be computed using a generalized iterative
scaling procedure based on Bregman projections. '
author:
- first_name: Anna
full_name: Klimova, Anna
id: 31934120-F248-11E8-B48F-1D18A9856A87
last_name: Klimova
- first_name: Tamás
full_name: Rudas, Tamás
last_name: Rudas
citation:
ama: Klimova A, Rudas T. On the closure of relational models. Journal of Multivariate
Analysis. 2016;143:440-452. doi:10.1016/j.jmva.2015.10.005
apa: Klimova, A., & Rudas, T. (2016). On the closure of relational models. Journal
of Multivariate Analysis. Elsevier. https://doi.org/10.1016/j.jmva.2015.10.005
chicago: Klimova, Anna, and Tamás Rudas. “On the Closure of Relational Models.”
Journal of Multivariate Analysis. Elsevier, 2016. https://doi.org/10.1016/j.jmva.2015.10.005.
ieee: A. Klimova and T. Rudas, “On the closure of relational models,” Journal
of Multivariate Analysis, vol. 143. Elsevier, pp. 440–452, 2016.
ista: Klimova A, Rudas T. 2016. On the closure of relational models. Journal of
Multivariate Analysis. 143, 440–452.
mla: Klimova, Anna, and Tamás Rudas. “On the Closure of Relational Models.” Journal
of Multivariate Analysis, vol. 143, Elsevier, 2016, pp. 440–52, doi:10.1016/j.jmva.2015.10.005.
short: A. Klimova, T. Rudas, Journal of Multivariate Analysis 143 (2016) 440–452.
date_created: 2018-12-11T11:54:15Z
date_published: 2016-01-01T00:00:00Z
date_updated: 2021-01-12T06:53:30Z
day: '01'
department:
- _id: CaUh
doi: 10.1016/j.jmva.2015.10.005
intvolume: ' 143'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: http://arxiv.org/abs/1501.00600
month: '01'
oa: 1
oa_version: Preprint
page: 440 - 452
publication: Journal of Multivariate Analysis
publication_status: published
publisher: Elsevier
publist_id: '5270'
quality_controlled: '1'
scopus_import: 1
status: public
title: On the closure of relational models
type: journal_article
user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87
volume: 143
year: '2016'
...
---
_id: '1881'
abstract:
- lang: eng
text: 'We consider random matrices of the form H=W+λV, λ∈ℝ+, where W is a real symmetric
or complex Hermitian Wigner matrix of size N and V is a real bounded diagonal
random matrix of size N with i.i.d.\ entries that are independent of W. We assume
subexponential decay for the matrix entries of W and we choose λ∼1, so that the
eigenvalues of W and λV are typically of the same order. Further, we assume that
the density of the entries of V is supported on a single interval and is convex
near the edges of its support. In this paper we prove that there is λ+∈ℝ+ such
that the largest eigenvalues of H are in the limit of large N determined by the
order statistics of V for λ>λ+. In particular, the largest eigenvalue of H
has a Weibull distribution in the limit N→∞ if λ>λ+. Moreover, for N sufficiently
large, we show that the eigenvectors associated to the largest eigenvalues are
partially localized for λ>λ+, while they are completely delocalized for λ<λ+.
Similar results hold for the lowest eigenvalues. '
acknowledgement: "Most of the presented work was obtained while Kevin Schnelli was
staying at the IAS with the support of\r\nThe Fund For Math."
author:
- first_name: Jioon
full_name: Lee, Jioon
last_name: Lee
- first_name: Kevin
full_name: Schnelli, Kevin
id: 434AD0AE-F248-11E8-B48F-1D18A9856A87
last_name: Schnelli
orcid: 0000-0003-0954-3231
citation:
ama: Lee J, Schnelli K. Extremal eigenvalues and eigenvectors of deformed Wigner
matrices. Probability Theory and Related Fields. 2016;164(1-2):165-241.
doi:10.1007/s00440-014-0610-8
apa: Lee, J., & Schnelli, K. (2016). Extremal eigenvalues and eigenvectors of
deformed Wigner matrices. Probability Theory and Related Fields. Springer.
https://doi.org/10.1007/s00440-014-0610-8
chicago: Lee, Jioon, and Kevin Schnelli. “Extremal Eigenvalues and Eigenvectors
of Deformed Wigner Matrices.” Probability Theory and Related Fields. Springer,
2016. https://doi.org/10.1007/s00440-014-0610-8.
ieee: J. Lee and K. Schnelli, “Extremal eigenvalues and eigenvectors of deformed
Wigner matrices,” Probability Theory and Related Fields, vol. 164, no.
1–2. Springer, pp. 165–241, 2016.
ista: Lee J, Schnelli K. 2016. Extremal eigenvalues and eigenvectors of deformed
Wigner matrices. Probability Theory and Related Fields. 164(1–2), 165–241.
mla: Lee, Jioon, and Kevin Schnelli. “Extremal Eigenvalues and Eigenvectors of Deformed
Wigner Matrices.” Probability Theory and Related Fields, vol. 164, no.
1–2, Springer, 2016, pp. 165–241, doi:10.1007/s00440-014-0610-8.
short: J. Lee, K. Schnelli, Probability Theory and Related Fields 164 (2016) 165–241.
date_created: 2018-12-11T11:54:31Z
date_published: 2016-02-01T00:00:00Z
date_updated: 2021-01-12T06:53:49Z
day: '01'
department:
- _id: LaEr
doi: 10.1007/s00440-014-0610-8
ec_funded: 1
intvolume: ' 164'
issue: 1-2
language:
- iso: eng
main_file_link:
- open_access: '1'
url: http://arxiv.org/abs/1310.7057
month: '02'
oa: 1
oa_version: Preprint
page: 165 - 241
project:
- _id: 258DCDE6-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '338804'
name: Random matrices, universality and disordered quantum systems
publication: Probability Theory and Related Fields
publication_status: published
publisher: Springer
publist_id: '5215'
quality_controlled: '1'
scopus_import: 1
status: public
title: Extremal eigenvalues and eigenvectors of deformed Wigner matrices
type: journal_article
user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87
volume: 164
year: '2016'
...
---
_id: '1411'
abstract:
- lang: eng
text: We consider two systems (α1, …, αm) and (β1, …,βn) of simple curves drawn
on a compact two-dimensional surface M with boundary. Each αi and each βj is either
an arc meeting the boundary of M at its two endpoints, or a closed curve. The
αi are pairwise disjoint except for possibly sharing endpoints, and similarly
for the βj. We want to “untangle” the βj from the ai by a self-homeomorphism of
M; more precisely, we seek a homeomorphism φ:M→M fixing the boundary of M pointwise
such that the total number of crossings of the ai with the φ(βj) is as small as
possible. This problem is motivated by an application in the algorithmic theory
of embeddings and 3-manifolds. We prove that if M is planar, i.e., a sphere with
h ≥ 0 boundary components (“holes”), then O(mn) crossings can be achieved (independently
of h), which is asymptotically tight, as an easy lower bound shows. In general,
for an arbitrary (orientable or nonorientable) surface M with h holes and of (orientable
or nonorientable) genus g ≥ 0, we obtain an O((m + n)4) upper bound, again independent
of h and g. The proofs rely, among other things, on a result concerning simultaneous
planar drawings of graphs by Erten and Kobourov.
acknowledgement: 'Supported by the ERC Adv anced Grant No. 267165. '
author:
- first_name: Jiří
full_name: Matoušek, Jiří
last_name: Matoušek
- first_name: Eric
full_name: Sedgwick, Eric
last_name: Sedgwick
- first_name: Martin
full_name: Tancer, Martin
id: 38AC689C-F248-11E8-B48F-1D18A9856A87
last_name: Tancer
orcid: 0000-0002-1191-6714
- first_name: Uli
full_name: Wagner, Uli
id: 36690CA2-F248-11E8-B48F-1D18A9856A87
last_name: Wagner
orcid: 0000-0002-1494-0568
citation:
ama: Matoušek J, Sedgwick E, Tancer M, Wagner U. Untangling two systems of noncrossing
curves. Israel Journal of Mathematics. 2016;212(1):37-79. doi:10.1007/s11856-016-1294-9
apa: Matoušek, J., Sedgwick, E., Tancer, M., & Wagner, U. (2016). Untangling
two systems of noncrossing curves. Israel Journal of Mathematics. Springer.
https://doi.org/10.1007/s11856-016-1294-9
chicago: Matoušek, Jiří, Eric Sedgwick, Martin Tancer, and Uli Wagner. “Untangling
Two Systems of Noncrossing Curves.” Israel Journal of Mathematics. Springer,
2016. https://doi.org/10.1007/s11856-016-1294-9.
ieee: J. Matoušek, E. Sedgwick, M. Tancer, and U. Wagner, “Untangling two systems
of noncrossing curves,” Israel Journal of Mathematics, vol. 212, no. 1.
Springer, pp. 37–79, 2016.
ista: Matoušek J, Sedgwick E, Tancer M, Wagner U. 2016. Untangling two systems of
noncrossing curves. Israel Journal of Mathematics. 212(1), 37–79.
mla: Matoušek, Jiří, et al. “Untangling Two Systems of Noncrossing Curves.” Israel
Journal of Mathematics, vol. 212, no. 1, Springer, 2016, pp. 37–79, doi:10.1007/s11856-016-1294-9.
short: J. Matoušek, E. Sedgwick, M. Tancer, U. Wagner, Israel Journal of Mathematics
212 (2016) 37–79.
date_created: 2018-12-11T11:51:52Z
date_published: 2016-05-01T00:00:00Z
date_updated: 2023-02-23T10:34:31Z
day: '01'
department:
- _id: UlWa
doi: 10.1007/s11856-016-1294-9
intvolume: ' 212'
issue: '1'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: http://arxiv.org/abs/1302.6475
month: '05'
oa: 1
oa_version: Preprint
page: 37 - 79
project:
- _id: 25FA3206-B435-11E9-9278-68D0E5697425
grant_number: PP00P2_138948
name: 'Embeddings in Higher Dimensions: Algorithms and Combinatorics'
publication: Israel Journal of Mathematics
publication_status: published
publisher: Springer
publist_id: '5796'
quality_controlled: '1'
related_material:
record:
- id: '2244'
relation: earlier_version
status: public
scopus_import: 1
status: public
title: Untangling two systems of noncrossing curves
type: journal_article
user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87
volume: 212
year: '2016'
...
---
_id: '1479'
abstract:
- lang: eng
text: "Most entropy notions H(.) like Shannon or min-entropy satisfy a chain rule
stating that for random variables X,Z, and A we have H(X|Z,A)≥H(X|Z)−|A|. That
is, by conditioning on A the entropy of X can decrease by at most the bitlength
|A| of A. Such chain rules are known to hold for some computational entropy notions
like Yao’s and unpredictability-entropy. For HILL entropy, the computational analogue
of min-entropy, the chain rule is of special interest and has found many applications,
including leakage-resilient cryptography, deterministic encryption, and memory
delegation. These applications rely on restricted special cases of the chain rule.
Whether the chain rule for conditional HILL entropy holds in general was an open
problem for which we give a strong negative answer: we construct joint distributions
(X,Z,A), where A is a distribution over a single bit, such that the HILL entropy
H HILL (X|Z) is large but H HILL (X|Z,A) is basically zero.\r\n\r\nOur counterexample
just makes the minimal assumption that NP⊈P/poly. Under the stronger assumption
that injective one-way function exist, we can make all the distributions efficiently
samplable.\r\n\r\nFinally, we show that some more sophisticated cryptographic
objects like lossy functions can be used to sample a distribution constituting
a counterexample to the chain rule making only a single invocation to the underlying
object."
acknowledgement: "This work was partly funded by the European Research Council under
ERC Starting Grant 259668-PSPC and ERC Advanced Grant 321310-PERCY.\r\n"
author:
- first_name: Stephan
full_name: Krenn, Stephan
id: 329FCCF0-F248-11E8-B48F-1D18A9856A87
last_name: Krenn
orcid: 0000-0003-2835-9093
- first_name: Krzysztof Z
full_name: Pietrzak, Krzysztof Z
id: 3E04A7AA-F248-11E8-B48F-1D18A9856A87
last_name: Pietrzak
orcid: 0000-0002-9139-1654
- first_name: Akshay
full_name: Wadia, Akshay
last_name: Wadia
- first_name: Daniel
full_name: Wichs, Daniel
last_name: Wichs
citation:
ama: Krenn S, Pietrzak KZ, Wadia A, Wichs D. A counterexample to the chain rule
for conditional HILL entropy. Computational Complexity. 2016;25(3):567-605.
doi:10.1007/s00037-015-0120-9
apa: Krenn, S., Pietrzak, K. Z., Wadia, A., & Wichs, D. (2016). A counterexample
to the chain rule for conditional HILL entropy. Computational Complexity.
Springer. https://doi.org/10.1007/s00037-015-0120-9
chicago: Krenn, Stephan, Krzysztof Z Pietrzak, Akshay Wadia, and Daniel Wichs. “A
Counterexample to the Chain Rule for Conditional HILL Entropy.” Computational
Complexity. Springer, 2016. https://doi.org/10.1007/s00037-015-0120-9.
ieee: S. Krenn, K. Z. Pietrzak, A. Wadia, and D. Wichs, “A counterexample to the
chain rule for conditional HILL entropy,” Computational Complexity, vol.
25, no. 3. Springer, pp. 567–605, 2016.
ista: Krenn S, Pietrzak KZ, Wadia A, Wichs D. 2016. A counterexample to the chain
rule for conditional HILL entropy. Computational Complexity. 25(3), 567–605.
mla: Krenn, Stephan, et al. “A Counterexample to the Chain Rule for Conditional
HILL Entropy.” Computational Complexity, vol. 25, no. 3, Springer, 2016,
pp. 567–605, doi:10.1007/s00037-015-0120-9.
short: S. Krenn, K.Z. Pietrzak, A. Wadia, D. Wichs, Computational Complexity 25
(2016) 567–605.
date_created: 2018-12-11T11:52:16Z
date_published: 2016-09-01T00:00:00Z
date_updated: 2023-02-23T11:05:09Z
day: '01'
ddc:
- '004'
department:
- _id: KrPi
doi: 10.1007/s00037-015-0120-9
ec_funded: 1
file:
- access_level: open_access
checksum: 7659296174fa75f5f0364f31f46f4bcf
content_type: application/pdf
creator: system
date_created: 2018-12-12T10:13:29Z
date_updated: 2020-07-14T12:44:56Z
file_id: '5012'
file_name: IST-2017-766-v1+1_678.pdf
file_size: 483258
relation: main_file
file_date_updated: 2020-07-14T12:44:56Z
has_accepted_license: '1'
intvolume: ' 25'
issue: '3'
language:
- iso: eng
month: '09'
oa: 1
oa_version: Submitted Version
page: 567 - 605
project:
- _id: 258C570E-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '259668'
name: Provable Security for Physical Cryptography
publication: Computational Complexity
publication_status: published
publisher: Springer
publist_id: '5715'
pubrep_id: '766'
quality_controlled: '1'
related_material:
record:
- id: '2940'
relation: earlier_version
status: public
scopus_import: 1
status: public
title: A counterexample to the chain rule for conditional HILL entropy
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: journal_article
user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87
volume: 25
year: '2016'
...
---
_id: '478'
abstract:
- lang: eng
text: 'Magic: the Gathering is a game about magical combat for any number of players.
Formally it is a zero-sum, imperfect information stochastic game that consists
of a potentially unbounded number of steps. We consider the problem of deciding
if a move is legal in a given single step of Magic. We show that the problem is
(a) coNP-complete in general; and (b) in P if either of two small sets of cards
are not used. Our lower bound holds even for single-player Magic games. The significant
aspects of our results are as follows: First, in most real-life game problems,
the task of deciding whether a given move is legal in a single step is trivial,
and the computationally hard task is to find the best sequence of legal moves
in the presence of multiple players. In contrast, quite uniquely our hardness
result holds for single step and with only one-player. Second, we establish efficient
algorithms for important special cases of Magic.'
alternative_title:
- Frontiers in Artificial Intelligence and Applications
author:
- first_name: Krishnendu
full_name: Chatterjee, Krishnendu
id: 2E5DCA20-F248-11E8-B48F-1D18A9856A87
last_name: Chatterjee
orcid: 0000-0002-4561-241X
- first_name: Rasmus
full_name: Ibsen-Jensen, Rasmus
id: 3B699956-F248-11E8-B48F-1D18A9856A87
last_name: Ibsen-Jensen
orcid: 0000-0003-4783-0389
citation:
ama: 'Chatterjee K, Ibsen-Jensen R. The complexity of deciding legality of a single
step of magic: The gathering. In: Vol 285. IOS Press; 2016:1432-1439. doi:10.3233/978-1-61499-672-9-1432'
apa: 'Chatterjee, K., & Ibsen-Jensen, R. (2016). The complexity of deciding
legality of a single step of magic: The gathering (Vol. 285, pp. 1432–1439). Presented
at the ECAI: European Conference on Artificial Intelligence, The Hague, Netherlands:
IOS Press. https://doi.org/10.3233/978-1-61499-672-9-1432'
chicago: 'Chatterjee, Krishnendu, and Rasmus Ibsen-Jensen. “The Complexity of Deciding
Legality of a Single Step of Magic: The Gathering,” 285:1432–39. IOS Press, 2016.
https://doi.org/10.3233/978-1-61499-672-9-1432.'
ieee: 'K. Chatterjee and R. Ibsen-Jensen, “The complexity of deciding legality of
a single step of magic: The gathering,” presented at the ECAI: European Conference
on Artificial Intelligence, The Hague, Netherlands, 2016, vol. 285, pp. 1432–1439.'
ista: 'Chatterjee K, Ibsen-Jensen R. 2016. The complexity of deciding legality of
a single step of magic: The gathering. ECAI: European Conference on Artificial
Intelligence, Frontiers in Artificial Intelligence and Applications, vol. 285,
1432–1439.'
mla: 'Chatterjee, Krishnendu, and Rasmus Ibsen-Jensen. The Complexity of Deciding
Legality of a Single Step of Magic: The Gathering. Vol. 285, IOS Press, 2016,
pp. 1432–39, doi:10.3233/978-1-61499-672-9-1432.'
short: K. Chatterjee, R. Ibsen-Jensen, in:, IOS Press, 2016, pp. 1432–1439.
conference:
end_date: 2016-09-02
location: The Hague, Netherlands
name: 'ECAI: European Conference on Artificial Intelligence'
start_date: 2016-08-29
date_created: 2018-12-11T11:46:41Z
date_published: 2016-01-01T00:00:00Z
date_updated: 2021-01-12T08:00:54Z
day: '01'
ddc:
- '004'
department:
- _id: KrCh
doi: 10.3233/978-1-61499-672-9-1432
file:
- access_level: open_access
checksum: 848043c812ace05e459579c923f3d3cf
content_type: application/pdf
creator: system
date_created: 2018-12-12T10:07:59Z
date_updated: 2020-07-14T12:46:35Z
file_id: '4658'
file_name: IST-2018-950-v1+1_2016_Chatterjee_The_complexity.pdf
file_size: 2116225
relation: main_file
file_date_updated: 2020-07-14T12:46:35Z
has_accepted_license: '1'
intvolume: ' 285'
language:
- iso: eng
month: '01'
oa: 1
oa_version: Published Version
page: 1432 - 1439
publication_status: published
publisher: IOS Press
publist_id: '7342'
pubrep_id: '950'
quality_controlled: '1'
scopus_import: 1
status: public
title: 'The complexity of deciding legality of a single step of magic: The gathering'
tmp:
image: /images/cc_by_nc.png
legal_code_url: https://creativecommons.org/licenses/by-nc/4.0/legalcode
name: Creative Commons Attribution-NonCommercial 4.0 International (CC BY-NC 4.0)
short: CC BY-NC (4.0)
type: conference
user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87
volume: 285
year: '2016'
...
---
_id: '480'
abstract:
- lang: eng
text: Graph games provide the foundation for modeling and synthesizing reactive
processes. In the synthesis of stochastic reactive processes, the traditional
model is perfect-information stochastic games, where some transitions of the game
graph are controlled by two adversarial players, and the other transitions are
executed probabilistically. We consider such games where the objective is the
conjunction of several quantitative objectives (specified as mean-payoff conditions),
which we refer to as generalized mean-payoff objectives. The basic decision problem
asks for the existence of a finite-memory strategy for a player that ensures the
generalized mean-payoff objective be satisfied with a desired probability against
all strategies of the opponent. A special case of the decision problem is the
almost-sure problem where the desired probability is 1. Previous results presented
a semi-decision procedure for -approximations of the almost-sure problem. In this
work, we show that both the almost-sure problem as well as the general basic decision
problem are coNP-complete, significantly improving the previous results. Moreover,
we show that in the case of 1-player stochastic games, randomized memoryless strategies
are sufficient and the problem can be solved in polynomial time. In contrast,
in two-player stochastic games, we show that even with randomized strategies exponential
memory is required in general, and present a matching exponential upper bound.
We also study the basic decision problem with infinite-memory strategies and present
computational complexity results for the problem. Our results are relevant in
the synthesis of stochastic reactive systems with multiple quantitative requirements.
alternative_title:
- Proceedings Symposium on Logic in Computer Science
author:
- first_name: Krishnendu
full_name: Chatterjee, Krishnendu
id: 2E5DCA20-F248-11E8-B48F-1D18A9856A87
last_name: Chatterjee
orcid: 0000-0002-4561-241X
- first_name: Laurent
full_name: Doyen, Laurent
last_name: Doyen
citation:
ama: 'Chatterjee K, Doyen L. Perfect-information stochastic games with generalized
mean-payoff objectives. In: Vol 05-08-July-2016. IEEE; 2016:247-256. doi:10.1145/2933575.2934513'
apa: 'Chatterjee, K., & Doyen, L. (2016). Perfect-information stochastic games
with generalized mean-payoff objectives (Vol. 05-08-July-2016, pp. 247–256). Presented
at the LICS: Logic in Computer Science, New York, NY, USA: IEEE. https://doi.org/10.1145/2933575.2934513'
chicago: Chatterjee, Krishnendu, and Laurent Doyen. “Perfect-Information Stochastic
Games with Generalized Mean-Payoff Objectives,” 05-08-July-2016:247–56. IEEE,
2016. https://doi.org/10.1145/2933575.2934513.
ieee: 'K. Chatterjee and L. Doyen, “Perfect-information stochastic games with generalized
mean-payoff objectives,” presented at the LICS: Logic in Computer Science, New
York, NY, USA, 2016, vol. 05-08-July-2016, pp. 247–256.'
ista: 'Chatterjee K, Doyen L. 2016. Perfect-information stochastic games with generalized
mean-payoff objectives. LICS: Logic in Computer Science, Proceedings Symposium
on Logic in Computer Science, vol. 05-08-July-2016, 247–256.'
mla: Chatterjee, Krishnendu, and Laurent Doyen. Perfect-Information Stochastic
Games with Generalized Mean-Payoff Objectives. Vol. 05-08-July-2016, IEEE,
2016, pp. 247–56, doi:10.1145/2933575.2934513.
short: K. Chatterjee, L. Doyen, in:, IEEE, 2016, pp. 247–256.
conference:
end_date: 2016-07-08
location: New York, NY, USA
name: 'LICS: Logic in Computer Science'
start_date: 2016-07-05
date_created: 2018-12-11T11:46:42Z
date_published: 2016-07-05T00:00:00Z
date_updated: 2021-01-12T08:00:56Z
day: '05'
department:
- _id: KrCh
doi: 10.1145/2933575.2934513
ec_funded: 1
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/1604.06376
month: '07'
oa: 1
oa_version: Preprint
page: 247 - 256
project:
- _id: 25832EC2-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: S 11407_N23
name: Rigorous Systems Engineering
- _id: 2581B60A-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '279307'
name: 'Quantitative Graph Games: Theory and Applications'
- _id: 25892FC0-B435-11E9-9278-68D0E5697425
grant_number: ICT15-003
name: Efficient Algorithms for Computer Aided Verification
publication_status: published
publisher: IEEE
publist_id: '7340'
quality_controlled: '1'
scopus_import: 1
status: public
title: Perfect-information stochastic games with generalized mean-payoff objectives
type: conference
user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87
volume: 05-08-July-2016
year: '2016'
...
---
_id: '1379'
abstract:
- lang: eng
text: We investigate the complexity of finding an embedded non-orientable surface
of Euler genus g in a triangulated 3-manifold. This problem occurs both as a natural
question in low-dimensional topology, and as a first non-trivial instance of embeddability
of complexes into 3-manifolds. We prove that the problem is NP-hard, thus adding
to the relatively few hardness results that are currently known in 3-manifold
topology. In addition, we show that the problem lies in NP when the Euler genus
g is odd, and we give an explicit algorithm in this case.
alternative_title:
- LIPIcs
author:
- first_name: Benjamin
full_name: Burton, Benjamin
last_name: Burton
- first_name: Arnaud N
full_name: De Mesmay, Arnaud N
id: 3DB2F25C-F248-11E8-B48F-1D18A9856A87
last_name: De Mesmay
- first_name: Uli
full_name: Wagner, Uli
id: 36690CA2-F248-11E8-B48F-1D18A9856A87
last_name: Wagner
orcid: 0000-0002-1494-0568
citation:
ama: 'Burton B, de Mesmay AN, Wagner U. Finding non-orientable surfaces in 3-manifolds.
In: Vol 51. Schloss Dagstuhl- Leibniz-Zentrum fur Informatik GmbH, Dagstuhl Publishing;
2016:24.1-24.15. doi:10.4230/LIPIcs.SoCG.2016.24'
apa: 'Burton, B., de Mesmay, A. N., & Wagner, U. (2016). Finding non-orientable
surfaces in 3-manifolds (Vol. 51, p. 24.1-24.15). Presented at the SoCG: Symposium
on Computational Geometry, Medford, MA, USA: Schloss Dagstuhl- Leibniz-Zentrum
fur Informatik GmbH, Dagstuhl Publishing. https://doi.org/10.4230/LIPIcs.SoCG.2016.24'
chicago: Burton, Benjamin, Arnaud N de Mesmay, and Uli Wagner. “Finding Non-Orientable
Surfaces in 3-Manifolds,” 51:24.1-24.15. Schloss Dagstuhl- Leibniz-Zentrum fur
Informatik GmbH, Dagstuhl Publishing, 2016. https://doi.org/10.4230/LIPIcs.SoCG.2016.24.
ieee: 'B. Burton, A. N. de Mesmay, and U. Wagner, “Finding non-orientable surfaces
in 3-manifolds,” presented at the SoCG: Symposium on Computational Geometry, Medford,
MA, USA, 2016, vol. 51, p. 24.1-24.15.'
ista: 'Burton B, de Mesmay AN, Wagner U. 2016. Finding non-orientable surfaces in
3-manifolds. SoCG: Symposium on Computational Geometry, LIPIcs, vol. 51, 24.1-24.15.'
mla: Burton, Benjamin, et al. Finding Non-Orientable Surfaces in 3-Manifolds.
Vol. 51, Schloss Dagstuhl- Leibniz-Zentrum fur Informatik GmbH, Dagstuhl Publishing,
2016, p. 24.1-24.15, doi:10.4230/LIPIcs.SoCG.2016.24.
short: B. Burton, A.N. de Mesmay, U. Wagner, in:, Schloss Dagstuhl- Leibniz-Zentrum
fur Informatik GmbH, Dagstuhl Publishing, 2016, p. 24.1-24.15.
conference:
end_date: 2016-06-17
location: Medford, MA, USA
name: 'SoCG: Symposium on Computational Geometry'
start_date: 2016-06-14
date_created: 2018-12-11T11:51:41Z
date_published: 2016-06-01T00:00:00Z
date_updated: 2023-02-23T12:23:20Z
day: '01'
ddc:
- '510'
department:
- _id: UlWa
doi: 10.4230/LIPIcs.SoCG.2016.24
file:
- access_level: open_access
checksum: f04248a61c24297cfabd30c5f8e0deb9
content_type: application/pdf
creator: system
date_created: 2018-12-12T10:12:12Z
date_updated: 2020-07-14T12:44:47Z
file_id: '4930'
file_name: IST-2016-622-v1+1_LIPIcs-SoCG-2016-24.pdf
file_size: 574770
relation: main_file
file_date_updated: 2020-07-14T12:44:47Z
has_accepted_license: '1'
intvolume: ' 51'
language:
- iso: eng
month: '06'
oa: 1
oa_version: Published Version
page: 24.1 - 24.15
publication_status: published
publisher: Schloss Dagstuhl- Leibniz-Zentrum fur Informatik GmbH, Dagstuhl Publishing
publist_id: '5832'
pubrep_id: '622'
quality_controlled: '1'
related_material:
record:
- id: '534'
relation: later_version
status: public
scopus_import: 1
status: public
title: Finding non-orientable surfaces in 3-manifolds
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: conference
user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87
volume: 51
year: '2016'
...
---
_id: '1477'
abstract:
- lang: eng
text: We consider partially observable Markov decision processes (POMDPs) with ω-regular
conditions specified as parity objectives. The class of ω-regular languages provides
a robust specification language to express properties in verification, and parity
objectives are canonical forms to express them. The qualitative analysis problem
given a POMDP and a parity objective asks whether there is a strategy to ensure
that the objective is satisfied with probability 1 (resp. positive probability).
While the qualitative analysis problems are undecidable even for special cases
of parity objectives, we establish decidability (with optimal complexity) for
POMDPs with all parity objectives under finite-memory strategies. We establish
optimal (exponential) memory bounds and EXPTIME-completeness of the qualitative
analysis problems under finite-memory strategies for POMDPs with parity objectives.
We also present a practical approach, where we design heuristics to deal with
the exponential complexity, and have applied our implementation on a number of
POMDP examples.
author:
- first_name: Krishnendu
full_name: Chatterjee, Krishnendu
id: 2E5DCA20-F248-11E8-B48F-1D18A9856A87
last_name: Chatterjee
orcid: 0000-0002-4561-241X
- first_name: Martin
full_name: Chmelik, Martin
id: 3624234E-F248-11E8-B48F-1D18A9856A87
last_name: Chmelik
- first_name: Mathieu
full_name: Tracol, Mathieu
id: 3F54FA38-F248-11E8-B48F-1D18A9856A87
last_name: Tracol
citation:
ama: Chatterjee K, Chmelik M, Tracol M. What is decidable about partially observable
Markov decision processes with ω-regular objectives. Journal of Computer and
System Sciences. 2016;82(5):878-911. doi:10.1016/j.jcss.2016.02.009
apa: Chatterjee, K., Chmelik, M., & Tracol, M. (2016). What is decidable about
partially observable Markov decision processes with ω-regular objectives. Journal
of Computer and System Sciences. Elsevier. https://doi.org/10.1016/j.jcss.2016.02.009
chicago: Chatterjee, Krishnendu, Martin Chmelik, and Mathieu Tracol. “What Is Decidable
about Partially Observable Markov Decision Processes with ω-Regular Objectives.”
Journal of Computer and System Sciences. Elsevier, 2016. https://doi.org/10.1016/j.jcss.2016.02.009.
ieee: K. Chatterjee, M. Chmelik, and M. Tracol, “What is decidable about partially
observable Markov decision processes with ω-regular objectives,” Journal of
Computer and System Sciences, vol. 82, no. 5. Elsevier, pp. 878–911, 2016.
ista: Chatterjee K, Chmelik M, Tracol M. 2016. What is decidable about partially
observable Markov decision processes with ω-regular objectives. Journal of Computer
and System Sciences. 82(5), 878–911.
mla: Chatterjee, Krishnendu, et al. “What Is Decidable about Partially Observable
Markov Decision Processes with ω-Regular Objectives.” Journal of Computer and
System Sciences, vol. 82, no. 5, Elsevier, 2016, pp. 878–911, doi:10.1016/j.jcss.2016.02.009.
short: K. Chatterjee, M. Chmelik, M. Tracol, Journal of Computer and System Sciences
82 (2016) 878–911.
date_created: 2018-12-11T11:52:15Z
date_published: 2016-08-01T00:00:00Z
date_updated: 2023-02-23T12:24:38Z
day: '01'
department:
- _id: KrCh
doi: 10.1016/j.jcss.2016.02.009
ec_funded: 1
external_id:
arxiv:
- '1309.2802'
intvolume: ' 82'
issue: '5'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/1309.2802
month: '08'
oa: 1
oa_version: Preprint
page: 878 - 911
project:
- _id: 2584A770-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: P 23499-N23
name: Modern Graph Algorithmic Techniques in Formal Verification
- _id: 25863FF4-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: S11407
name: Game Theory
- _id: 2581B60A-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '279307'
name: 'Quantitative Graph Games: Theory and Applications'
- _id: 2587B514-B435-11E9-9278-68D0E5697425
name: Microsoft Research Faculty Fellowship
publication: Journal of Computer and System Sciences
publication_status: published
publisher: Elsevier
publist_id: '5718'
quality_controlled: '1'
related_material:
record:
- id: '2295'
relation: earlier_version
status: public
- id: '5400'
relation: earlier_version
status: public
scopus_import: 1
status: public
title: What is decidable about partially observable Markov decision processes with
ω-regular objectives
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 82
year: '2016'
...
---
_id: '1529'
abstract:
- lang: eng
text: 'We consider partially observable Markov decision processes (POMDPs) with
a set of target states and an integer cost associated with every transition. The
optimization objective we study asks to minimize the expected total cost of reaching
a state in the target set, while ensuring that the target set is reached almost
surely (with probability 1). We show that for integer costs approximating the
optimal cost is undecidable. For positive costs, our results are as follows: (i)
we establish matching lower and upper bounds for the optimal cost, both double
exponential in the POMDP state space size; (ii) we show that the problem of approximating
the optimal cost is decidable and present approximation algorithms developing
on the existing algorithms for POMDPs with finite-horizon objectives. While the
worst-case running time of our algorithm is double exponential, we also present
efficient stopping criteria for the algorithm and show experimentally that it
performs well in many examples of interest.'
acknowledgement: 'We thank Blai Bonet for helping us with RTDP-Bel. The research was
partly supported by Austrian Science Fund (FWF) Grant No P23499-N23, FWF NFN Grant
No S11407-N23 (RiSE), ERC Start grant (279307: Graph Games), and Microsoft faculty
fellows award.'
article_processing_charge: No
author:
- first_name: Krishnendu
full_name: Chatterjee, Krishnendu
id: 2E5DCA20-F248-11E8-B48F-1D18A9856A87
last_name: Chatterjee
orcid: 0000-0002-4561-241X
- first_name: Martin
full_name: Chmelik, Martin
id: 3624234E-F248-11E8-B48F-1D18A9856A87
last_name: Chmelik
- first_name: Raghav
full_name: Gupta, Raghav
last_name: Gupta
- first_name: Ayush
full_name: Kanodia, Ayush
last_name: Kanodia
citation:
ama: Chatterjee K, Chmelik M, Gupta R, Kanodia A. Optimal cost almost-sure reachability
in POMDPs. Artificial Intelligence. 2016;234:26-48. doi:10.1016/j.artint.2016.01.007
apa: Chatterjee, K., Chmelik, M., Gupta, R., & Kanodia, A. (2016). Optimal cost
almost-sure reachability in POMDPs. Artificial Intelligence. Elsevier.
https://doi.org/10.1016/j.artint.2016.01.007
chicago: Chatterjee, Krishnendu, Martin Chmelik, Raghav Gupta, and Ayush Kanodia.
“Optimal Cost Almost-Sure Reachability in POMDPs.” Artificial Intelligence.
Elsevier, 2016. https://doi.org/10.1016/j.artint.2016.01.007.
ieee: K. Chatterjee, M. Chmelik, R. Gupta, and A. Kanodia, “Optimal cost almost-sure
reachability in POMDPs,” Artificial Intelligence, vol. 234. Elsevier, pp.
26–48, 2016.
ista: Chatterjee K, Chmelik M, Gupta R, Kanodia A. 2016. Optimal cost almost-sure
reachability in POMDPs. Artificial Intelligence. 234, 26–48.
mla: Chatterjee, Krishnendu, et al. “Optimal Cost Almost-Sure Reachability in POMDPs.”
Artificial Intelligence, vol. 234, Elsevier, 2016, pp. 26–48, doi:10.1016/j.artint.2016.01.007.
short: K. Chatterjee, M. Chmelik, R. Gupta, A. Kanodia, Artificial Intelligence
234 (2016) 26–48.
date_created: 2018-12-11T11:52:33Z
date_published: 2016-05-01T00:00:00Z
date_updated: 2023-02-23T12:25:49Z
day: '01'
department:
- _id: KrCh
doi: 10.1016/j.artint.2016.01.007
ec_funded: 1
external_id:
arxiv:
- '1411.3880'
intvolume: ' 234'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: http://arxiv.org/abs/1411.3880
month: '05'
oa: 1
oa_version: Preprint
page: 26 - 48
project:
- _id: 2584A770-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: P 23499-N23
name: Modern Graph Algorithmic Techniques in Formal Verification
- _id: 25832EC2-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: S 11407_N23
name: Rigorous Systems Engineering
- _id: 2581B60A-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '279307'
name: 'Quantitative Graph Games: Theory and Applications'
publication: Artificial Intelligence
publication_status: published
publisher: Elsevier
publist_id: '5642'
quality_controlled: '1'
related_material:
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relation: earlier_version
status: public
- id: '5425'
relation: earlier_version
status: public
scopus_import: 1
status: public
title: Optimal cost almost-sure reachability in POMDPs
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 234
year: '2016'
...
---
_id: '5445'
abstract:
- lang: eng
text: 'We consider the quantitative analysis problem for interprocedural control-flow
graphs (ICFGs). The input consists of an ICFG, a positive weight function that
assigns every transition a positive integer-valued number, and a labelling of
the transitions (events) as good, bad, and neutral events. The weight function
assigns to each transition a numerical value that represents ameasure of how good
or bad an event is. The quantitative analysis problem asks whether there is a
run of the ICFG where the ratio of the sum of the numerical weights of good events
versus the sum of weights of bad events in the long-run is at least a given threshold
(or equivalently, to compute the maximal ratio among all valid paths in the ICFG).
The quantitative analysis problem for ICFGs can be solved in polynomial time,
and we present an efficient and practical algorithm for the problem. We show that
several problems relevant for static program analysis, such as estimating the
worst-case execution time of a program or the average energy consumption of a
mobile application, can be modeled in our framework. We have implemented our algorithm
as a tool in the Java Soot framework. We demonstrate the effectiveness of our
approach with two case studies. First, we show that our framework provides a sound
approach (no false positives) for the analysis of inefficiently-used containers.
Second, we show that our approach can also be used for static profiling of programs
which reasons about methods that are frequently invoked. Our experimental results
show that our tool scales to relatively large benchmarks, and discovers relevant
and useful information that can be used to optimize performance of the programs. '
alternative_title:
- IST Austria Technical Report
author:
- first_name: Krishnendu
full_name: Chatterjee, Krishnendu
id: 2E5DCA20-F248-11E8-B48F-1D18A9856A87
last_name: Chatterjee
orcid: 0000-0002-4561-241X
- first_name: Andreas
full_name: Pavlogiannis, Andreas
id: 49704004-F248-11E8-B48F-1D18A9856A87
last_name: Pavlogiannis
orcid: 0000-0002-8943-0722
- first_name: Yaron
full_name: Velner, Yaron
last_name: Velner
citation:
ama: Chatterjee K, Pavlogiannis A, Velner Y. Quantitative Interprocedural Analysis.
IST Austria; 2016. doi:10.15479/AT:IST-2016-523-v1-1
apa: Chatterjee, K., Pavlogiannis, A., & Velner, Y. (2016). Quantitative
interprocedural analysis. IST Austria. https://doi.org/10.15479/AT:IST-2016-523-v1-1
chicago: Chatterjee, Krishnendu, Andreas Pavlogiannis, and Yaron Velner. Quantitative
Interprocedural Analysis. IST Austria, 2016. https://doi.org/10.15479/AT:IST-2016-523-v1-1.
ieee: K. Chatterjee, A. Pavlogiannis, and Y. Velner, Quantitative interprocedural
analysis. IST Austria, 2016.
ista: Chatterjee K, Pavlogiannis A, Velner Y. 2016. Quantitative interprocedural
analysis, IST Austria, 33p.
mla: Chatterjee, Krishnendu, et al. Quantitative Interprocedural Analysis.
IST Austria, 2016, doi:10.15479/AT:IST-2016-523-v1-1.
short: K. Chatterjee, A. Pavlogiannis, Y. Velner, Quantitative Interprocedural Analysis,
IST Austria, 2016.
date_created: 2018-12-12T11:39:22Z
date_published: 2016-03-31T00:00:00Z
date_updated: 2023-02-23T10:06:22Z
day: '31'
ddc:
- '005'
department:
- _id: KrCh
doi: 10.15479/AT:IST-2016-523-v1-1
file:
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checksum: cef516fa091925b5868813e355268fb4
content_type: application/pdf
creator: system
date_created: 2018-12-12T11:53:52Z
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has_accepted_license: '1'
language:
- iso: eng
month: '03'
oa: 1
oa_version: Published Version
page: '33'
publication_identifier:
issn:
- 2664-1690
publication_status: published
publisher: IST Austria
pubrep_id: '523'
related_material:
record:
- id: '1604'
relation: later_version
status: public
status: public
title: Quantitative interprocedural analysis
type: technical_report
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
year: '2016'
...
---
_id: '5449'
abstract:
- lang: eng
text: "The fixation probability is the probability that a new mutant introduced
in a homogeneous population eventually takes over the entire population.\r\nThe
fixation probability is a fundamental quantity of natural selection, and known
to depend on the population structure.\r\nAmplifiers of natural selection are
population structures which increase the fixation probability of advantageous
mutants, as compared to the baseline case of well-mixed populations. In this work
we focus on symmetric population structures represented as undirected graphs.
In the regime of undirected graphs, the strongest amplifier known has been the
Star graph, and the existence of undirected graphs with stronger amplification
properties has remained open for over a decade.\r\nIn this work we present the
Comet and Comet-swarm families of undirected graphs. We show that for a range
of fitness values of the mutants, the Comet and Comet-swarm graphs have fixation
probability strictly larger than the fixation probability of the Star graph, for
fixed population size and at the limit of large populations, respectively."
alternative_title:
- IST Austria Technical Report
author:
- first_name: Andreas
full_name: Pavlogiannis, Andreas
id: 49704004-F248-11E8-B48F-1D18A9856A87
last_name: Pavlogiannis
orcid: 0000-0002-8943-0722
- first_name: Josef
full_name: Tkadlec, Josef
id: 3F24CCC8-F248-11E8-B48F-1D18A9856A87
last_name: Tkadlec
orcid: 0000-0002-1097-9684
- first_name: Krishnendu
full_name: Chatterjee, Krishnendu
id: 2E5DCA20-F248-11E8-B48F-1D18A9856A87
last_name: Chatterjee
orcid: 0000-0002-4561-241X
- first_name: Martin
full_name: Nowak, Martin
last_name: Nowak
citation:
ama: 'Pavlogiannis A, Tkadlec J, Chatterjee K, Nowak M. Amplification on Undirected
Population Structures: Comets Beat Stars. IST Austria; 2016. doi:10.15479/AT:IST-2016-648-v1-1'
apa: 'Pavlogiannis, A., Tkadlec, J., Chatterjee, K., & Nowak, M. (2016). Amplification
on undirected population structures: Comets beat stars. IST Austria. https://doi.org/10.15479/AT:IST-2016-648-v1-1'
chicago: 'Pavlogiannis, Andreas, Josef Tkadlec, Krishnendu Chatterjee, and Martin
Nowak. Amplification on Undirected Population Structures: Comets Beat Stars.
IST Austria, 2016. https://doi.org/10.15479/AT:IST-2016-648-v1-1.'
ieee: 'A. Pavlogiannis, J. Tkadlec, K. Chatterjee, and M. Nowak, Amplification
on undirected population structures: Comets beat stars. IST Austria, 2016.'
ista: 'Pavlogiannis A, Tkadlec J, Chatterjee K, Nowak M. 2016. Amplification on
undirected population structures: Comets beat stars, IST Austria, 22p.'
mla: 'Pavlogiannis, Andreas, et al. Amplification on Undirected Population Structures:
Comets Beat Stars. IST Austria, 2016, doi:10.15479/AT:IST-2016-648-v1-1.'
short: 'A. Pavlogiannis, J. Tkadlec, K. Chatterjee, M. Nowak, Amplification on Undirected
Population Structures: Comets Beat Stars, IST Austria, 2016.'
date_created: 2018-12-12T11:39:24Z
date_published: 2016-11-09T00:00:00Z
date_updated: 2023-02-23T12:22:21Z
day: '09'
ddc:
- '519'
department:
- _id: KrCh
doi: 10.15479/AT:IST-2016-648-v1-1
file:
- access_level: open_access
checksum: 8345a8c1e7d7f0cd92516d182b7fc59e
content_type: application/pdf
creator: system
date_created: 2018-12-12T11:54:07Z
date_updated: 2020-07-14T12:46:58Z
file_id: '5529'
file_name: IST-2016-648-v1+1_tr.pdf
file_size: 1264221
relation: main_file
file_date_updated: 2020-07-14T12:46:58Z
has_accepted_license: '1'
language:
- iso: eng
month: '11'
oa: 1
oa_version: Updated Version
page: '22'
publication_identifier:
issn:
- 2664-1690
publication_status: published
publisher: IST Austria
pubrep_id: '648'
related_material:
record:
- id: '512'
relation: later_version
status: public
status: public
title: 'Amplification on undirected population structures: Comets beat stars'
type: technical_report
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
year: '2016'
...
---
_id: '5446'
abstract:
- lang: eng
text: "We study the problem of developing efficient approaches for proving termination
of recursive programs with one-dimensional arrays. Ranking functions serve as
a sound and complete approach for proving termination of non-recursive programs
without array operations. First, we generalize ranking functions to the notion
of measure functions, and prove that measure functions (i) provide a sound method
to prove termination of recursive programs (with one-dimensional arrays), and
(ii) is both sound and complete over recursive programs without array operations.
Our second contribution is the synthesis of measure functions of specific forms
in polynomial time. More precisely, we prove that (i) polynomial measure functions
over recursive programs can be synthesized in polynomial time through Farkas’
Lemma and Handelman’s Theorem, and (ii) measure functions involving logarithm
and exponentiation can be synthesized in polynomial time through abstraction of
logarithmic or exponential terms and Handelman’s Theorem. A key application of
our method is the worst-case analysis of recursive programs. While previous methods
obtain worst-case polynomial bounds of the form O(n^k), where k is an integer,
our polynomial time methods can synthesize bounds of the form O(n log n), as well
as O(n^x), where x is not an integer. We show the applicability of our automated
technique to obtain worst-case complexity of classical recursive algorithms such
as (i) Merge-Sort, the divideand-\r\nconquer algorithm for the Closest-Pair problem,
where we obtain O(n log n) worst-case bound, and (ii) Karatsuba’s algorithm for
polynomial multiplication and Strassen’s algorithm for matrix multiplication,
where we obtain O(n^x) bound, where x is not an integer and close to the best-known
bounds for the respective algorithms. Finally, we present experimental results
to demonstrate the\r\neffectiveness of our approach."
alternative_title:
- IST Austria Technical Report
author:
- first_name: '1'
full_name: Anonymous, 1
last_name: Anonymous
- first_name: '2'
full_name: Anonymous, 2
last_name: Anonymous
- first_name: '3'
full_name: Anonymous, 3
last_name: Anonymous
citation:
ama: Anonymous 1, Anonymous 2, Anonymous 3. Termination and Worst-Case Analysis
of Recursive Programs. IST Austria; 2016.
apa: Anonymous, 1, Anonymous, 2, & Anonymous, 3. (2016). Termination and
worst-case analysis of recursive programs. IST Austria.
chicago: Anonymous, 1, 2 Anonymous, and 3 Anonymous. Termination and Worst-Case
Analysis of Recursive Programs. IST Austria, 2016.
ieee: 1 Anonymous, 2 Anonymous, and 3 Anonymous, Termination and worst-case analysis
of recursive programs. IST Austria, 2016.
ista: Anonymous 1, Anonymous 2, Anonymous 3. 2016. Termination and worst-case analysis
of recursive programs, IST Austria, 26p.
mla: Anonymous, 1, et al. Termination and Worst-Case Analysis of Recursive Programs.
IST Austria, 2016.
short: 1 Anonymous, 2 Anonymous, 3 Anonymous, Termination and Worst-Case Analysis
of Recursive Programs, IST Austria, 2016.
date_created: 2018-12-12T11:39:23Z
date_published: 2016-07-15T00:00:00Z
date_updated: 2020-07-14T23:05:05Z
day: '15'
ddc:
- '000'
file:
- access_level: open_access
checksum: 689069a7abbb34b21516164cbee9e0df
content_type: application/pdf
creator: dernst
date_created: 2019-05-10T13:27:24Z
date_updated: 2020-07-14T12:46:58Z
file_id: '6403'
file_name: popl2017a.pdf
file_size: 686241
relation: main_file
- access_level: closed
checksum: fc08022bfbaac07bac047a9407c0bbb3
content_type: text/plain
creator: dernst
date_created: 2019-05-10T13:27:31Z
date_updated: 2020-07-14T12:46:58Z
file_id: '6404'
file_name: author_names.txt
file_size: 258
relation: main_file
file_date_updated: 2020-07-14T12:46:58Z
has_accepted_license: '1'
language:
- iso: eng
month: '07'
oa: 1
oa_version: Published Version
page: '26'
publication_identifier:
issn:
- 2664-1690
publication_status: published
publisher: IST Austria
pubrep_id: '618'
status: public
title: Termination and worst-case analysis of recursive programs
type: technical_report
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
year: '2016'
...
---
_id: '5447'
abstract:
- lang: eng
text: "We consider the problem of developing automated techniques to aid the average-case
complexity analysis of programs. Several classical textbook algorithms have quite
efficient average-case complexity, whereas the corresponding worst-case bounds
are either inefficient (e.g., QUICK-SORT), or completely ineffective (e.g., COUPONCOLLECTOR).
Since the main focus of average-case analysis is to obtain efficient bounds, we
consider bounds that are either logarithmic,\r\nlinear, or almost-linear (O(log
n), O(n), O(n · log n),\r\nrespectively, where n represents the size of the input).
Our main contribution is a sound approach for deriving such average-case bounds
for randomized recursive programs. Our approach is efficient (a simple linear-time
algorithm), and it is based on (a) the analysis of recurrence relations induced
by randomized algorithms, and (b) a guess-and-check technique. Our approach can
infer the asymptotically optimal average-case bounds for classical randomized
algorithms, including RANDOMIZED-SEARCH, QUICKSORT, QUICK-SELECT, COUPON-COLLECTOR,
where the worstcase\r\nbounds are either inefficient (such as linear as compared
to logarithmic of average-case, or quadratic as compared to linear or almost-linear
of average-case), or ineffective. We have implemented our approach, and the experimental
results show that we obtain the bounds efficiently for various classical algorithms."
alternative_title:
- IST Austria Technical Report
author:
- first_name: '1'
full_name: Anonymous, 1
last_name: Anonymous
- first_name: '2'
full_name: Anonymous, 2
last_name: Anonymous
- first_name: '3'
full_name: Anonymous, 3
last_name: Anonymous
citation:
ama: 'Anonymous 1, Anonymous 2, Anonymous 3. Average-Case Analysis of Programs:
Automated Recurrence Analysis for Almost-Linear Bounds. IST Austria; 2016.'
apa: 'Anonymous, 1, Anonymous, 2, & Anonymous, 3. (2016). Average-case analysis
of programs: Automated recurrence analysis for almost-linear bounds. IST Austria.'
chicago: 'Anonymous, 1, 2 Anonymous, and 3 Anonymous. Average-Case Analysis of
Programs: Automated Recurrence Analysis for Almost-Linear Bounds. IST Austria,
2016.'
ieee: '1 Anonymous, 2 Anonymous, and 3 Anonymous, Average-case analysis of programs:
Automated recurrence analysis for almost-linear bounds. IST Austria, 2016.'
ista: 'Anonymous 1, Anonymous 2, Anonymous 3. 2016. Average-case analysis of programs:
Automated recurrence analysis for almost-linear bounds, IST Austria, 20p.'
mla: 'Anonymous, 1, et al. Average-Case Analysis of Programs: Automated Recurrence
Analysis for Almost-Linear Bounds. IST Austria, 2016.'
short: '1 Anonymous, 2 Anonymous, 3 Anonymous, Average-Case Analysis of Programs:
Automated Recurrence Analysis for Almost-Linear Bounds, IST Austria, 2016.'
date_created: 2018-12-12T11:39:23Z
date_published: 2016-07-15T00:00:00Z
date_updated: 2020-07-14T23:05:06Z
day: '15'
ddc:
- '000'
file:
- access_level: closed
checksum: cf53cdb6d092e68db0b4a0a1506ef8fb
content_type: text/plain
creator: dernst
date_created: 2019-05-10T13:32:16Z
date_updated: 2020-07-14T12:46:58Z
file_id: '6406'
file_name: listofauthors.txt
file_size: 281
relation: main_file
- access_level: open_access
checksum: 7bdd94ba13aa0dec9c46887fcf13870b
content_type: application/pdf
creator: dernst
date_created: 2019-05-10T13:32:16Z
date_updated: 2020-07-14T12:46:58Z
file_id: '6407'
file_name: popl2017b.pdf
file_size: 563642
relation: main_file
file_date_updated: 2020-07-14T12:46:58Z
has_accepted_license: '1'
language:
- iso: eng
month: '07'
oa: 1
oa_version: Published Version
page: '20'
publication_identifier:
issn:
- 2664-1690
publication_status: published
publisher: IST Austria
pubrep_id: '619'
status: public
title: 'Average-case analysis of programs: Automated recurrence analysis for almost-linear
bounds'
type: technical_report
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
year: '2016'
...
---
_id: '5453'
alternative_title:
- IST Austria Technical Report
author:
- first_name: Andreas
full_name: Pavlogiannis, Andreas
id: 49704004-F248-11E8-B48F-1D18A9856A87
last_name: Pavlogiannis
orcid: 0000-0002-8943-0722
- first_name: Josef
full_name: Tkadlec, Josef
id: 3F24CCC8-F248-11E8-B48F-1D18A9856A87
last_name: Tkadlec
orcid: 0000-0002-1097-9684
- first_name: Krishnendu
full_name: Chatterjee, Krishnendu
id: 2E5DCA20-F248-11E8-B48F-1D18A9856A87
last_name: Chatterjee
orcid: 0000-0002-4561-241X
- first_name: Martin
full_name: Nowak, Martin
last_name: Nowak
citation:
ama: Pavlogiannis A, Tkadlec J, Chatterjee K, Nowak M. Arbitrarily Strong Amplifiers
of Natural Selection. IST Austria; 2016. doi:10.15479/AT:IST-2017-749-v3-1
apa: Pavlogiannis, A., Tkadlec, J., Chatterjee, K., & Nowak, M. (2016). Arbitrarily
strong amplifiers of natural selection. IST Austria. https://doi.org/10.15479/AT:IST-2017-749-v3-1
chicago: Pavlogiannis, Andreas, Josef Tkadlec, Krishnendu Chatterjee, and Martin
Nowak. Arbitrarily Strong Amplifiers of Natural Selection. IST Austria,
2016. https://doi.org/10.15479/AT:IST-2017-749-v3-1.
ieee: A. Pavlogiannis, J. Tkadlec, K. Chatterjee, and M. Nowak, Arbitrarily strong
amplifiers of natural selection. IST Austria, 2016.
ista: Pavlogiannis A, Tkadlec J, Chatterjee K, Nowak M. 2016. Arbitrarily strong
amplifiers of natural selection, IST Austria, 34p.
mla: Pavlogiannis, Andreas, et al. Arbitrarily Strong Amplifiers of Natural Selection.
IST Austria, 2016, doi:10.15479/AT:IST-2017-749-v3-1.
short: A. Pavlogiannis, J. Tkadlec, K. Chatterjee, M. Nowak, Arbitrarily Strong
Amplifiers of Natural Selection, IST Austria, 2016.
date_created: 2018-12-12T11:39:25Z
date_published: 2016-12-30T00:00:00Z
date_updated: 2023-02-23T12:27:07Z
day: '30'
ddc:
- '000'
department:
- _id: KrCh
doi: 10.15479/AT:IST-2017-749-v3-1
file:
- access_level: open_access
checksum: 83b0313dab3bff4bdb6ac38695026fda
content_type: application/pdf
creator: system
date_created: 2018-12-12T11:53:13Z
date_updated: 2020-07-14T12:46:59Z
file_id: '5474'
file_name: IST-2017-749-v3+1_main.pdf
file_size: 1015647
relation: main_file
file_date_updated: 2020-07-14T12:46:59Z
has_accepted_license: '1'
language:
- iso: eng
month: '12'
oa: 1
oa_version: Published Version
page: '34'
publication_identifier:
issn:
- 2664-1690
publication_status: published
publisher: IST Austria
pubrep_id: '755'
related_material:
record:
- id: '5452'
relation: earlier_version
status: public
status: public
title: Arbitrarily strong amplifiers of natural selection
type: technical_report
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
year: '2016'
...
---
_id: '5451'
alternative_title:
- IST Austria Technical Report
author:
- first_name: Andreas
full_name: Pavlogiannis, Andreas
id: 49704004-F248-11E8-B48F-1D18A9856A87
last_name: Pavlogiannis
orcid: 0000-0002-8943-0722
- first_name: Josef
full_name: Tkadlec, Josef
id: 3F24CCC8-F248-11E8-B48F-1D18A9856A87
last_name: Tkadlec
orcid: 0000-0002-1097-9684
- first_name: Krishnendu
full_name: Chatterjee, Krishnendu
id: 2E5DCA20-F248-11E8-B48F-1D18A9856A87
last_name: Chatterjee
orcid: 0000-0002-4561-241X
- first_name: Martin
full_name: Nowak, Martin
last_name: Nowak
citation:
ama: Pavlogiannis A, Tkadlec J, Chatterjee K, Nowak M. Strong Amplifiers of Natural
Selection. IST Austria; 2016. doi:10.15479/AT:IST-2016-728-v1-1
apa: Pavlogiannis, A., Tkadlec, J., Chatterjee, K., & Nowak, M. (2016). Strong
amplifiers of natural selection. IST Austria. https://doi.org/10.15479/AT:IST-2016-728-v1-1
chicago: Pavlogiannis, Andreas, Josef Tkadlec, Krishnendu Chatterjee, and Martin
Nowak. Strong Amplifiers of Natural Selection. IST Austria, 2016. https://doi.org/10.15479/AT:IST-2016-728-v1-1.
ieee: A. Pavlogiannis, J. Tkadlec, K. Chatterjee, and M. Nowak, Strong amplifiers
of natural selection. IST Austria, 2016.
ista: Pavlogiannis A, Tkadlec J, Chatterjee K, Nowak M. 2016. Strong amplifiers
of natural selection, IST Austria, 34p.
mla: Pavlogiannis, Andreas, et al. Strong Amplifiers of Natural Selection.
IST Austria, 2016, doi:10.15479/AT:IST-2016-728-v1-1.
short: A. Pavlogiannis, J. Tkadlec, K. Chatterjee, M. Nowak, Strong Amplifiers of
Natural Selection, IST Austria, 2016.
date_created: 2018-12-12T11:39:24Z
date_published: 2016-12-30T00:00:00Z
date_updated: 2023-02-23T12:27:05Z
day: '30'
ddc:
- '000'
department:
- _id: KrCh
doi: 10.15479/AT:IST-2016-728-v1-1
file:
- access_level: open_access
checksum: 7b8bb17c322c0556acba6ac169fa71c1
content_type: application/pdf
creator: system
date_created: 2018-12-12T11:53:04Z
date_updated: 2020-07-14T12:46:59Z
file_id: '5465'
file_name: IST-2016-728-v1+1_main.pdf
file_size: 1014732
relation: main_file
file_date_updated: 2020-07-14T12:46:59Z
has_accepted_license: '1'
language:
- iso: eng
month: '12'
oa: 1
oa_version: Published Version
page: '34'
publication_identifier:
issn:
- 2664-1690
publication_status: published
publisher: IST Austria
pubrep_id: '728'
status: public
title: Strong amplifiers of natural selection
type: technical_report
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
year: '2016'
...
---
_id: '5448'
abstract:
- lang: eng
text: "We present a new dynamic partial-order reduction method for stateless model
checking of concurrent programs. A common approach for exploring program behaviors
relies on enumerating the traces of the program, without storing the visited states
(aka stateless exploration). As the number of distinct traces grows exponentially,
dynamic partial-order reduction (DPOR) techniques have been successfully used
to partition the space of traces into equivalence classes (Mazurkiewicz partitioning),
with the goal of exploring only few representative traces from each class.\r\nWe
introduce a new equivalence on traces under sequential consistency semantics,
which we call the observation equivalence. Two traces are observationally equivalent
if every read event observes the same write event in both traces. While the traditional
Mazurkiewicz equivalence is control-centric, our new definition is data-centric.
We show that our observation equivalence is coarser than the Mazurkiewicz equivalence,
and in many cases even exponentially coarser. We devise a DPOR exploration of
the trace space, called data-centric DPOR, based on the observation equivalence.\r\n1.
For acyclic architectures, our algorithm is guaranteed to explore exactly one
representative trace from each observation class, while spending polynomial time
per class. Hence, our algorithm is optimal wrt the observation equivalence, and
in several cases explores exponentially fewer traces than any enumerative method
based on the Mazurkiewicz equivalence.\r\n2. For cyclic architectures, we consider
an equivalence between traces which is finer than the observation equivalence;
but coarser than the Mazurkiewicz equivalence, and in some cases is exponentially
coarser. Our data-centric DPOR algorithm remains optimal under this trace equivalence.
\r\nFinally, we perform a basic experimental comparison between the existing Mazurkiewicz-based
DPOR and our data-centric DPOR on a set of academic benchmarks. Our results show
a significant reduction in both running time and the number of explored equivalence
classes."
alternative_title:
- IST Austria Technical Report
author:
- first_name: '1'
full_name: Anonymous, 1
last_name: Anonymous
- first_name: '2'
full_name: Anonymous, 2
last_name: Anonymous
- first_name: '3'
full_name: Anonymous, 3
last_name: Anonymous
- first_name: '4'
full_name: Anonymous, 4
last_name: Anonymous
citation:
ama: Anonymous 1, Anonymous 2, Anonymous 3, Anonymous 4. Data-Centric Dynamic
Partial Order Reduction. IST Austria; 2016.
apa: Anonymous, 1, Anonymous, 2, Anonymous, 3, & Anonymous, 4. (2016). Data-centric
dynamic partial order reduction. IST Austria.
chicago: Anonymous, 1, 2 Anonymous, 3 Anonymous, and 4 Anonymous. Data-Centric
Dynamic Partial Order Reduction. IST Austria, 2016.
ieee: 1 Anonymous, 2 Anonymous, 3 Anonymous, and 4 Anonymous, Data-centric dynamic
partial order reduction. IST Austria, 2016.
ista: Anonymous 1, Anonymous 2, Anonymous 3, Anonymous 4. 2016. Data-centric dynamic
partial order reduction, IST Austria, 20p.
mla: Anonymous, 1, et al. Data-Centric Dynamic Partial Order Reduction. IST
Austria, 2016.
short: 1 Anonymous, 2 Anonymous, 3 Anonymous, 4 Anonymous, Data-Centric Dynamic
Partial Order Reduction, IST Austria, 2016.
date_created: 2018-12-12T11:39:23Z
date_published: 2016-07-15T00:00:00Z
date_updated: 2023-02-23T12:27:16Z
day: '15'
ddc:
- '000'
external_id:
arxiv:
- '1610.01188'
file:
- access_level: open_access
checksum: 1d69252d66bcdf782615ddfb911d2957
content_type: application/pdf
creator: system
date_created: 2018-12-12T11:53:45Z
date_updated: 2020-07-14T12:46:58Z
file_id: '5506'
file_name: IST-2016-620-v1+1_main.pdf
file_size: 538881
relation: main_file
- access_level: closed
checksum: deabb0eb8f237cae4f9542b28b0b6eb2
content_type: text/plain
creator: dernst
date_created: 2019-05-10T13:30:40Z
date_updated: 2020-07-14T12:46:58Z
file_id: '6405'
file_name: authornames.txt
file_size: 121
relation: main_file
file_date_updated: 2020-07-14T12:46:58Z
has_accepted_license: '1'
language:
- iso: eng
month: '07'
oa: 1
oa_version: Published Version
page: '20'
publication_identifier:
issn:
- 2664-1690
publication_status: published
publisher: IST Austria
pubrep_id: '620'
related_material:
record:
- id: '10417'
relation: later_version
status: public
- id: '5456'
relation: later_version
status: public
status: public
title: Data-centric dynamic partial order reduction
type: technical_report
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
year: '2016'
...
---
_id: '8094'
abstract:
- lang: eng
text: 'With the accelerated development of robot technologies, optimal control becomes
one of the central themes of research. In traditional approaches, the controller,
by its internal functionality, finds appropriate actions on the basis of the history
of sensor values, guided by the goals, intentions, objectives, learning schemes,
and so forth. The idea is that the controller controls the world---the body plus
its environment---as reliably as possible. This paper focuses on new lines of
self-organization for developmental robotics. We apply the recently developed
differential extrinsic synaptic plasticity to a muscle-tendon driven arm-shoulder
system from the Myorobotics toolkit. In the experiments, we observe a vast variety
of self-organized behavior patterns: when left alone, the arm realizes pseudo-random
sequences of different poses. By applying physical forces, the system can be entrained
into definite motion patterns like wiping a table. Most interestingly, after attaching
an object, the controller gets in a functional resonance with the object''s internal
dynamics, starting to shake spontaneously bottles half-filled with water or sensitively
driving an attached pendulum into a circular mode. When attached to the crank
of a wheel the neural system independently discovers how to rotate it. In this
way, the robot discovers affordances of objects its body is interacting with.'
article_processing_charge: No
author:
- first_name: Georg S
full_name: Martius, Georg S
id: 3A276B68-F248-11E8-B48F-1D18A9856A87
last_name: Martius
- first_name: Rafael
full_name: Hostettler, Rafael
last_name: Hostettler
- first_name: Alois
full_name: Knoll, Alois
last_name: Knoll
- first_name: Ralf
full_name: Der, Ralf
last_name: Der
citation:
ama: 'Martius GS, Hostettler R, Knoll A, Der R. Self-organized control of an tendon
driven arm by differential extrinsic plasticity. In: Proceedings of the Artificial
Life Conference 2016. Vol 28. MIT Press; 2016:142-143. doi:10.7551/978-0-262-33936-0-ch029'
apa: 'Martius, G. S., Hostettler, R., Knoll, A., & Der, R. (2016). Self-organized
control of an tendon driven arm by differential extrinsic plasticity. In Proceedings
of the Artificial Life Conference 2016 (Vol. 28, pp. 142–143). Cancun, Mexico:
MIT Press. https://doi.org/10.7551/978-0-262-33936-0-ch029'
chicago: Martius, Georg S, Rafael Hostettler, Alois Knoll, and Ralf Der. “Self-Organized
Control of an Tendon Driven Arm by Differential Extrinsic Plasticity.” In Proceedings
of the Artificial Life Conference 2016, 28:142–43. MIT Press, 2016. https://doi.org/10.7551/978-0-262-33936-0-ch029.
ieee: G. S. Martius, R. Hostettler, A. Knoll, and R. Der, “Self-organized control
of an tendon driven arm by differential extrinsic plasticity,” in Proceedings
of the Artificial Life Conference 2016, Cancun, Mexico, 2016, vol. 28, pp.
142–143.
ista: 'Martius GS, Hostettler R, Knoll A, Der R. 2016. Self-organized control of
an tendon driven arm by differential extrinsic plasticity. Proceedings of the
Artificial Life Conference 2016. ALIFE 2016: 15th International Conference on
the Synthesis and Simulation of Living Systems vol. 28, 142–143.'
mla: Martius, Georg S., et al. “Self-Organized Control of an Tendon Driven Arm by
Differential Extrinsic Plasticity.” Proceedings of the Artificial Life Conference
2016, vol. 28, MIT Press, 2016, pp. 142–43, doi:10.7551/978-0-262-33936-0-ch029.
short: G.S. Martius, R. Hostettler, A. Knoll, R. Der, in:, Proceedings of the Artificial
Life Conference 2016, MIT Press, 2016, pp. 142–143.
conference:
end_date: 2016-07-08
location: Cancun, Mexico
name: 'ALIFE 2016: 15th International Conference on the Synthesis and Simulation
of Living Systems'
start_date: 2016-07-04
date_created: 2020-07-05T22:00:47Z
date_published: 2016-09-01T00:00:00Z
date_updated: 2021-01-12T08:16:53Z
day: '01'
ddc:
- '610'
department:
- _id: ChLa
- _id: GaTk
doi: 10.7551/978-0-262-33936-0-ch029
ec_funded: 1
file:
- access_level: open_access
checksum: cff63e7a4b8ac466ba51a9c84153a940
content_type: application/pdf
creator: cziletti
date_created: 2020-07-06T12:59:09Z
date_updated: 2020-07-14T12:48:09Z
file_id: '8096'
file_name: 2016_ProcALIFE_Martius.pdf
file_size: 678670
relation: main_file
file_date_updated: 2020-07-14T12:48:09Z
has_accepted_license: '1'
intvolume: ' 28'
language:
- iso: eng
month: '09'
oa: 1
oa_version: Published Version
page: 142-143
project:
- _id: 25681D80-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '291734'
name: International IST Postdoc Fellowship Programme
publication: Proceedings of the Artificial Life Conference 2016
publication_identifier:
isbn:
- '9780262339360'
publication_status: published
publisher: MIT Press
quality_controlled: '1'
scopus_import: 1
status: public
title: Self-organized control of an tendon driven arm by differential extrinsic plasticity
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: conference
user_id: D865714E-FA4E-11E9-B85B-F5C5E5697425
volume: 28
year: '2016'
...
---
_id: '1197'
abstract:
- lang: eng
text: Across the nervous system, certain population spiking patterns are observed
far more frequently than others. A hypothesis about this structure is that these
collective activity patterns function as population codewords–collective modes–carrying
information distinct from that of any single cell. We investigate this phenomenon
in recordings of ∼150 retinal ganglion cells, the retina’s output. We develop
a novel statistical model that decomposes the population response into modes;
it predicts the distribution of spiking activity in the ganglion cell population
with high accuracy. We found that the modes represent localized features of the
visual stimulus that are distinct from the features represented by single neurons.
Modes form clusters of activity states that are readily discriminated from one
another. When we repeated the same visual stimulus, we found that the same mode
was robustly elicited. These results suggest that retinal ganglion cells’ collective
signaling is endowed with a form of error-correcting code–a principle that may
hold in brain areas beyond retina.
acknowledgement: JSP was supported by a C.V. Starr Fellowship from the Starr Foundation
(http://www.starrfoundation.org/). GT was supported by Austrian Research Foundation
(https://www.fwf.ac.at/en/) grant FWF P25651. MJB received support from National
Eye Institute (https://nei.nih.gov/) grant EY 14196 and from the National Science
Foundation grant 1504977. The authors thank Cristina Savin and Vicent Botella-Soler
for helpful comments on the manuscript.
article_number: e1005855
author:
- first_name: Jason
full_name: Prentice, Jason
last_name: Prentice
- first_name: Olivier
full_name: Marre, Olivier
last_name: Marre
- first_name: Mark
full_name: Ioffe, Mark
last_name: Ioffe
- first_name: Adrianna
full_name: Loback, Adrianna
last_name: Loback
- first_name: Gasper
full_name: Tkacik, Gasper
id: 3D494DCA-F248-11E8-B48F-1D18A9856A87
last_name: Tkacik
orcid: 0000-0002-6699-1455
- first_name: Michael
full_name: Berry, Michael
last_name: Berry
citation:
ama: Prentice J, Marre O, Ioffe M, Loback A, Tkačik G, Berry M. Error-robust modes
of the retinal population code. PLoS Computational Biology. 2016;12(11).
doi:10.1371/journal.pcbi.1005148
apa: Prentice, J., Marre, O., Ioffe, M., Loback, A., Tkačik, G., & Berry, M.
(2016). Error-robust modes of the retinal population code. PLoS Computational
Biology. Public Library of Science. https://doi.org/10.1371/journal.pcbi.1005148
chicago: Prentice, Jason, Olivier Marre, Mark Ioffe, Adrianna Loback, Gašper Tkačik,
and Michael Berry. “Error-Robust Modes of the Retinal Population Code.” PLoS
Computational Biology. Public Library of Science, 2016. https://doi.org/10.1371/journal.pcbi.1005148.
ieee: J. Prentice, O. Marre, M. Ioffe, A. Loback, G. Tkačik, and M. Berry, “Error-robust
modes of the retinal population code,” PLoS Computational Biology, vol.
12, no. 11. Public Library of Science, 2016.
ista: Prentice J, Marre O, Ioffe M, Loback A, Tkačik G, Berry M. 2016. Error-robust
modes of the retinal population code. PLoS Computational Biology. 12(11), e1005855.
mla: Prentice, Jason, et al. “Error-Robust Modes of the Retinal Population Code.”
PLoS Computational Biology, vol. 12, no. 11, e1005855, Public Library of
Science, 2016, doi:10.1371/journal.pcbi.1005148.
short: J. Prentice, O. Marre, M. Ioffe, A. Loback, G. Tkačik, M. Berry, PLoS Computational
Biology 12 (2016).
date_created: 2018-12-11T11:50:40Z
date_published: 2016-11-17T00:00:00Z
date_updated: 2023-02-23T14:05:40Z
day: '17'
ddc:
- '570'
department:
- _id: GaTk
doi: 10.1371/journal.pcbi.1005148
file:
- access_level: open_access
checksum: 47b08cbd4dbf32b25ba161f5f4b262cc
content_type: application/pdf
creator: kschuh
date_created: 2019-01-25T10:35:00Z
date_updated: 2020-07-14T12:44:38Z
file_id: '5884'
file_name: 2016_PLOS_Prentice.pdf
file_size: 4492021
relation: main_file
file_date_updated: 2020-07-14T12:44:38Z
has_accepted_license: '1'
intvolume: ' 12'
issue: '11'
language:
- iso: eng
month: '11'
oa: 1
oa_version: Published Version
project:
- _id: 254D1A94-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: P 25651-N26
name: Sensitivity to higher-order statistics in natural scenes
publication: PLoS Computational Biology
publication_status: published
publisher: Public Library of Science
publist_id: '6153'
quality_controlled: '1'
related_material:
record:
- id: '9709'
relation: research_data
status: public
scopus_import: 1
status: public
title: Error-robust modes of the retinal population code
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: journal_article
user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87
volume: 12
year: '2016'
...
---
_id: '9720'
abstract:
- lang: eng
text: 'Summary: Declining populations of bee pollinators are a cause of concern,
with major repercussions for biodiversity loss and food security. RNA viruses
associated with honeybees represent a potential threat to other insect pollinators,
but the extent of this threat is poorly understood. This study aims to attain
a detailed understanding of the current and ongoing risk of emerging infectious
disease (EID) transmission between managed and wild pollinator species across
a wide range of RNA viruses. Within a structured large-scale national survey across
26 independent sites, we quantify the prevalence and pathogen loads of multiple
RNA viruses in co-occurring managed honeybee (Apis mellifera) and wild bumblebee
(Bombus spp.) populations. We then construct models that compare virus prevalence
between wild and managed pollinators. Multiple RNA viruses associated with honeybees
are widespread in sympatric wild bumblebee populations. Virus prevalence in honeybees
is a significant predictor of virus prevalence in bumblebees, but we remain cautious
in speculating over the principle direction of pathogen transmission. We demonstrate
species-specific differences in prevalence, indicating significant variation in
disease susceptibility or tolerance. Pathogen loads within individual bumblebees
may be high and in the case of at least one RNA virus, prevalence is higher in
wild bumblebees than in managed honeybee populations. Our findings indicate widespread
transmission of RNA viruses between managed and wild bee pollinators, pointing
to an interconnected network of potential disease pressures within and among pollinator
species. In the context of the biodiversity crisis, our study emphasizes the importance
of targeting a wide range of pathogens and defining host associations when considering
potential drivers of population decline.'
article_processing_charge: No
author:
- first_name: Dino
full_name: Mcmahon, Dino
last_name: Mcmahon
- first_name: Matthias
full_name: Fürst, Matthias
id: 393B1196-F248-11E8-B48F-1D18A9856A87
last_name: Fürst
orcid: 0000-0002-3712-925X
- first_name: Jesicca
full_name: Caspar, Jesicca
last_name: Caspar
- first_name: Panagiotis
full_name: Theodorou, Panagiotis
last_name: Theodorou
- first_name: Mark
full_name: Brown, Mark
last_name: Brown
- first_name: Robert
full_name: Paxton, Robert
last_name: Paxton
citation:
ama: 'Mcmahon D, Fürst M, Caspar J, Theodorou P, Brown M, Paxton R. Data from: A
sting in the spit: widespread cross-infection of multiple RNA viruses across wild
and managed bees. 2016. doi:10.5061/dryad.4b565'
apa: 'Mcmahon, D., Fürst, M., Caspar, J., Theodorou, P., Brown, M., & Paxton,
R. (2016). Data from: A sting in the spit: widespread cross-infection of multiple
RNA viruses across wild and managed bees. Dryad. https://doi.org/10.5061/dryad.4b565'
chicago: 'Mcmahon, Dino, Matthias Fürst, Jesicca Caspar, Panagiotis Theodorou, Mark
Brown, and Robert Paxton. “Data from: A Sting in the Spit: Widespread Cross-Infection
of Multiple RNA Viruses across Wild and Managed Bees.” Dryad, 2016. https://doi.org/10.5061/dryad.4b565.'
ieee: 'D. Mcmahon, M. Fürst, J. Caspar, P. Theodorou, M. Brown, and R. Paxton, “Data
from: A sting in the spit: widespread cross-infection of multiple RNA viruses
across wild and managed bees.” Dryad, 2016.'
ista: 'Mcmahon D, Fürst M, Caspar J, Theodorou P, Brown M, Paxton R. 2016. Data
from: A sting in the spit: widespread cross-infection of multiple RNA viruses
across wild and managed bees, Dryad, 10.5061/dryad.4b565.'
mla: 'Mcmahon, Dino, et al. Data from: A Sting in the Spit: Widespread Cross-Infection
of Multiple RNA Viruses across Wild and Managed Bees. Dryad, 2016, doi:10.5061/dryad.4b565.'
short: D. Mcmahon, M. Fürst, J. Caspar, P. Theodorou, M. Brown, R. Paxton, (2016).
date_created: 2021-07-26T09:14:19Z
date_published: 2016-01-22T00:00:00Z
date_updated: 2023-02-23T10:17:25Z
day: '22'
department:
- _id: SyCr
doi: 10.5061/dryad.4b565
main_file_link:
- open_access: '1'
url: https://doi.org/10.5061/dryad.4b565
month: '01'
oa: 1
oa_version: Published Version
publisher: Dryad
related_material:
record:
- id: '1855'
relation: used_in_publication
status: public
status: public
title: 'Data from: A sting in the spit: widespread cross-infection of multiple RNA
viruses across wild and managed bees'
type: research_data_reference
user_id: 6785fbc1-c503-11eb-8a32-93094b40e1cf
year: '2016'
...
---
_id: '1158'
abstract:
- lang: eng
text: Speciation results from the progressive accumulation of mutations that decrease
the probability of mating between parental populations or reduce the fitness of
hybrids—the so-called species barriers. The speciation genomic literature, however,
is mainly a collection of case studies, each with its own approach and specificities,
such that a global view of the gradual process of evolution from one to two species
is currently lacking. Of primary importance is the prevalence of gene flow between
diverging entities, which is central in most species concepts and has been widely
discussed in recent years. Here, we explore the continuum of speciation thanks
to a comparative analysis of genomic data from 61 pairs of populations/species
of animals with variable levels of divergence. Gene flow between diverging gene
pools is assessed under an approximate Bayesian computation (ABC) framework. We
show that the intermediate "grey zone" of speciation, in which taxonomy
is often controversial, spans from 0.5% to 2% of net synonymous divergence, irrespective
of species life history traits or ecology. Thanks to appropriate modeling of among-locus
variation in genetic drift and introgression rate, we clarify the status of the
majority of ambiguous cases and uncover a number of cryptic species. Our analysis
also reveals the high incidence in animals of semi-isolated species (when some
but not all loci are affected by barriers to gene flow) and highlights the intrinsic
difficulty, both statistical and conceptual, of delineating species in the grey
zone of speciation.
acknowledgement: "European Research Council (ERC) https://erc.europa.eu/ (grant number
ERC grant 232971). PopPhyl project. The funder had no role in study design, data
collection and analysis, decision to publish, or preparation of the manuscript.
French National Research Agency (ANR) http://www.agence-nationale-recherche.fr/en/project-based-funding-to-advance-french-research/
(grant number ANR-12-BSV7- 0011). HYSEA project.\r\nWe thank Aude Darracq, Vincent
Castric, Pierre-Alexandre Gagnaire, Xavier Vekemans, and John Welch for insightful
discussions. The computations were performed at the Vital-IT (http://www.vital-it.ch)
Center for high-performance computing of the SIB Swiss Institute of Bioinformatics
and the ISEM computing cluster at the platform Montpellier Bioinformatique et Biodiversité."
article_number: e2000234
author:
- first_name: Camille
full_name: Roux, Camille
last_name: Roux
- first_name: Christelle
full_name: Fraisse, Christelle
id: 32DF5794-F248-11E8-B48F-1D18A9856A87
last_name: Fraisse
orcid: 0000-0001-8441-5075
- first_name: Jonathan
full_name: Romiguier, Jonathan
last_name: Romiguier
- first_name: Youann
full_name: Anciaux, Youann
last_name: Anciaux
- first_name: Nicolas
full_name: Galtier, Nicolas
last_name: Galtier
- first_name: Nicolas
full_name: Bierne, Nicolas
last_name: Bierne
citation:
ama: Roux C, Fraisse C, Romiguier J, Anciaux Y, Galtier N, Bierne N. Shedding light
on the grey zone of speciation along a continuum of genomic divergence. PLoS
Biology. 2016;14(12). doi:10.1371/journal.pbio.2000234
apa: Roux, C., Fraisse, C., Romiguier, J., Anciaux, Y., Galtier, N., & Bierne,
N. (2016). Shedding light on the grey zone of speciation along a continuum of
genomic divergence. PLoS Biology. Public Library of Science. https://doi.org/10.1371/journal.pbio.2000234
chicago: Roux, Camille, Christelle Fraisse, Jonathan Romiguier, Youann Anciaux,
Nicolas Galtier, and Nicolas Bierne. “Shedding Light on the Grey Zone of Speciation
along a Continuum of Genomic Divergence.” PLoS Biology. Public Library
of Science, 2016. https://doi.org/10.1371/journal.pbio.2000234.
ieee: C. Roux, C. Fraisse, J. Romiguier, Y. Anciaux, N. Galtier, and N. Bierne,
“Shedding light on the grey zone of speciation along a continuum of genomic divergence,”
PLoS Biology, vol. 14, no. 12. Public Library of Science, 2016.
ista: Roux C, Fraisse C, Romiguier J, Anciaux Y, Galtier N, Bierne N. 2016. Shedding
light on the grey zone of speciation along a continuum of genomic divergence.
PLoS Biology. 14(12), e2000234.
mla: Roux, Camille, et al. “Shedding Light on the Grey Zone of Speciation along
a Continuum of Genomic Divergence.” PLoS Biology, vol. 14, no. 12, e2000234,
Public Library of Science, 2016, doi:10.1371/journal.pbio.2000234.
short: C. Roux, C. Fraisse, J. Romiguier, Y. Anciaux, N. Galtier, N. Bierne, PLoS
Biology 14 (2016).
date_created: 2018-12-11T11:50:28Z
date_published: 2016-12-27T00:00:00Z
date_updated: 2023-02-23T14:11:16Z
day: '27'
ddc:
- '576'
department:
- _id: BeVi
- _id: NiBa
doi: 10.1371/journal.pbio.2000234
file:
- access_level: open_access
checksum: 2bab63b068a9840efd532b9ae583f9bb
content_type: application/pdf
creator: system
date_created: 2018-12-12T10:15:42Z
date_updated: 2020-07-14T12:44:36Z
file_id: '5164'
file_name: IST-2017-742-v1+1_journal.pbio.2000234.pdf
file_size: 2494348
relation: main_file
file_date_updated: 2020-07-14T12:44:36Z
has_accepted_license: '1'
intvolume: ' 14'
issue: '12'
language:
- iso: eng
month: '12'
oa: 1
oa_version: Published Version
publication: PLoS Biology
publication_status: published
publisher: Public Library of Science
publist_id: '6200'
pubrep_id: '742'
quality_controlled: '1'
related_material:
record:
- id: '9862'
relation: research_data
status: public
- id: '9863'
relation: research_data
status: public
scopus_import: 1
status: public
title: Shedding light on the grey zone of speciation along a continuum of genomic
divergence
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: journal_article
user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87
volume: 14
year: '2016'
...
---
_id: '1167'
abstract:
- lang: eng
text: Evolutionary pathways describe trajectories of biological evolution in the
space of different variants of organisms (genotypes). The probability of existence
and the number of evolutionary pathways that lead from a given genotype to a better-adapted
genotype are important measures of accessibility of local fitness optima and the
reproducibility of evolution. Both quantities have been studied in simple mathematical
models where genotypes are represented as binary sequences of two types of basic
units, and the network of permitted mutations between the genotypes is a hypercube
graph. However, it is unclear how these results translate to the biologically
relevant case in which genotypes are represented by sequences of more than two
units, for example four nucleotides (DNA) or 20 amino acids (proteins), and the
mutational graph is not the hypercube. Here we investigate accessibility of the
best-adapted genotype in the general case of K > 2 units. Using computer generated
and experimental fitness landscapes we show that accessibility of the global fitness
maximum increases with K and can be much higher than for binary sequences. The
increase in accessibility comes from the increase in the number of indirect trajectories
exploited by evolution for higher K. As one of the consequences, the fraction
of genotypes that are accessible increases by three orders of magnitude when the
number of units K increases from 2 to 16 for landscapes of size N ∼ 106genotypes.
This suggests that evolution can follow many different trajectories on such landscapes
and the reconstruction of evolutionary pathways from experimental data might be
an extremely difficult task.
acknowledgement: MZ acknowledges the Polish National Science Centre grant no. DEC-2012/07/N/NZ2/00107.
BW was supported by the Scottish Government/Royal Society of Edinburgh Personal
Research Fellowship. We thank Marjon de Vos and Oliver Martin for critically reading
the manuscript.
article_number: e1005218
article_processing_charge: No
author:
- first_name: Marcin P
full_name: Zagórski, Marcin P
id: 343DA0DC-F248-11E8-B48F-1D18A9856A87
last_name: Zagórski
orcid: 0000-0001-7896-7762
- first_name: Zdzisław
full_name: Burda, Zdzisław
last_name: Burda
- first_name: Bartłomiej
full_name: Wacław, Bartłomiej
last_name: Wacław
citation:
ama: Zagórski MP, Burda Z, Wacław B. Beyond the hypercube evolutionary accessibility
of fitness landscapes with realistic mutational networks. PLoS Computational
Biology. 2016;12(12). doi:10.1371/journal.pcbi.1005218
apa: Zagórski, M. P., Burda, Z., & Wacław, B. (2016). Beyond the hypercube evolutionary
accessibility of fitness landscapes with realistic mutational networks. PLoS
Computational Biology. Public Library of Science. https://doi.org/10.1371/journal.pcbi.1005218
chicago: Zagórski, Marcin P, Zdzisław Burda, and Bartłomiej Wacław. “Beyond the
Hypercube Evolutionary Accessibility of Fitness Landscapes with Realistic Mutational
Networks.” PLoS Computational Biology. Public Library of Science, 2016.
https://doi.org/10.1371/journal.pcbi.1005218.
ieee: M. P. Zagórski, Z. Burda, and B. Wacław, “Beyond the hypercube evolutionary
accessibility of fitness landscapes with realistic mutational networks,” PLoS
Computational Biology, vol. 12, no. 12. Public Library of Science, 2016.
ista: Zagórski MP, Burda Z, Wacław B. 2016. Beyond the hypercube evolutionary accessibility
of fitness landscapes with realistic mutational networks. PLoS Computational Biology.
12(12), e1005218.
mla: Zagórski, Marcin P., et al. “Beyond the Hypercube Evolutionary Accessibility
of Fitness Landscapes with Realistic Mutational Networks.” PLoS Computational
Biology, vol. 12, no. 12, e1005218, Public Library of Science, 2016, doi:10.1371/journal.pcbi.1005218.
short: M.P. Zagórski, Z. Burda, B. Wacław, PLoS Computational Biology 12 (2016).
date_created: 2018-12-11T11:50:30Z
date_published: 2016-12-09T00:00:00Z
date_updated: 2023-02-23T14:11:22Z
day: '09'
ddc:
- '570'
department:
- _id: AnKi
doi: 10.1371/journal.pcbi.1005218
file:
- access_level: open_access
checksum: 84f44ae92866c52ff1ca8a574558dca7
content_type: application/pdf
creator: system
date_created: 2018-12-12T10:12:08Z
date_updated: 2020-07-14T12:44:37Z
file_id: '4926'
file_name: IST-2017-740-v1+1_journal.pcbi.1005218.pdf
file_size: 3822299
relation: main_file
file_date_updated: 2020-07-14T12:44:37Z
has_accepted_license: '1'
intvolume: ' 12'
issue: '12'
language:
- iso: eng
month: '12'
oa: 1
oa_version: Published Version
publication: PLoS Computational Biology
publication_status: published
publisher: Public Library of Science
publist_id: '6190'
pubrep_id: '740'
quality_controlled: '1'
related_material:
record:
- id: '9866'
relation: research_data
status: public
scopus_import: '1'
status: public
title: Beyond the hypercube evolutionary accessibility of fitness landscapes with
realistic mutational networks
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: journal_article
user_id: 6785fbc1-c503-11eb-8a32-93094b40e1cf
volume: 12
year: '2016'
...
---
_id: '1262'
abstract:
- lang: eng
text: Emerging infectious diseases (EIDs) have contributed significantly to the
current biodiversity crisis, leading to widespread epidemics and population loss.
Owing to genetic variation in pathogen virulence, a complete understanding of
species decline requires the accurate identification and characterization of EIDs.
We explore this issue in the Western honeybee, where increasing mortality of populations
in the Northern Hemisphere has caused major concern. Specifically, we investigate
the importance of genetic identity of the main suspect in mortality, deformed
wing virus (DWV), in driving honeybee loss. Using laboratory experiments and a
systematic field survey, we demonstrate that an emerging DWV genotype (DWV-B)
is more virulent than the established DWV genotype (DWV-A) and is widespread in
the landscape. Furthermore, we show in a simple model that colonies infected with
DWV-B collapse sooner than colonies infected with DWV-A. We also identify potential
for rapid DWV evolution by revealing extensive genome-wide recombination in vivo.
The emergence of DWV-B in naive honeybee populations, including via recombination
with DWV-A, could be of significant ecological and economic importance. Our findings
emphasize that knowledge of pathogen genetic identity and diversity is critical
to understanding drivers of species decline.
acknowledgement: "This work was supported by the Federal Ministry of Food, Agriculture
and Consumer Protection (Germany): Fit Bee project (grant 511-06.01-28-1-71.007-10),
the EU: BeeDoc (grant 244956), iDiv (2013 NGS-Fast Track grant W47004118) and the
Insect Pollinators Initiative (IPI grant BB/I000100/1 and BB/I000151/1). The IPI
is funded jointly by the Biotechnology and Biological Sciences Research Council,
the Department for Environment, Food and Rural Affairs, the Natural Environment
Research Council, the Scottish Government and the Wellcome Trust, under the Living
with Environmental Change Partnership. We thank A. Abrahams, M. Husemann and A.
Soro\r\nfor support in obtaining\r\nV. destructor\r\n-free honeybees; and BBKA\r\nPresident
D. Aston for access to records of colony overwinter\r\n2011–2012 mortality in the
UK. We also thank the anonymous refe-\r\nrees and Stephen Martin for comments that
led to substantial\r\nimprovement of the manuscript."
article_number: '20160811'
author:
- first_name: Dino
full_name: Mcmahon, Dino
last_name: Mcmahon
- first_name: Myrsini
full_name: Natsopoulou, Myrsini
last_name: Natsopoulou
- first_name: Vincent
full_name: Doublet, Vincent
last_name: Doublet
- first_name: Matthias
full_name: Fürst, Matthias
id: 393B1196-F248-11E8-B48F-1D18A9856A87
last_name: Fürst
orcid: 0000-0002-3712-925X
- first_name: Silvio
full_name: Weging, Silvio
last_name: Weging
- first_name: Mark
full_name: Brown, Mark
last_name: Brown
- first_name: Andreas
full_name: Gogol Döring, Andreas
last_name: Gogol Döring
- first_name: Robert
full_name: Paxton, Robert
last_name: Paxton
citation:
ama: Mcmahon D, Natsopoulou M, Doublet V, et al. Elevated virulence of an emerging
viral genotype as a driver of honeybee loss. Proceedings of the Royal Society
of London Series B Biological Sciences. 2016;283(1833). doi:10.1098/rspb.2016.0811
apa: Mcmahon, D., Natsopoulou, M., Doublet, V., Fürst, M., Weging, S., Brown, M.,
… Paxton, R. (2016). Elevated virulence of an emerging viral genotype as a driver
of honeybee loss. Proceedings of the Royal Society of London Series B Biological
Sciences. Royal Society, The. https://doi.org/10.1098/rspb.2016.0811
chicago: Mcmahon, Dino, Myrsini Natsopoulou, Vincent Doublet, Matthias Fürst, Silvio
Weging, Mark Brown, Andreas Gogol Döring, and Robert Paxton. “Elevated Virulence
of an Emerging Viral Genotype as a Driver of Honeybee Loss.” Proceedings of
the Royal Society of London Series B Biological Sciences. Royal Society, The,
2016. https://doi.org/10.1098/rspb.2016.0811.
ieee: D. Mcmahon et al., “Elevated virulence of an emerging viral genotype
as a driver of honeybee loss,” Proceedings of the Royal Society of London Series
B Biological Sciences, vol. 283, no. 1833. Royal Society, The, 2016.
ista: Mcmahon D, Natsopoulou M, Doublet V, Fürst M, Weging S, Brown M, Gogol Döring
A, Paxton R. 2016. Elevated virulence of an emerging viral genotype as a driver
of honeybee loss. Proceedings of the Royal Society of London Series B Biological
Sciences. 283(1833), 20160811.
mla: Mcmahon, Dino, et al. “Elevated Virulence of an Emerging Viral Genotype as
a Driver of Honeybee Loss.” Proceedings of the Royal Society of London Series
B Biological Sciences, vol. 283, no. 1833, 20160811, Royal Society, The, 2016,
doi:10.1098/rspb.2016.0811.
short: D. Mcmahon, M. Natsopoulou, V. Doublet, M. Fürst, S. Weging, M. Brown, A.
Gogol Döring, R. Paxton, Proceedings of the Royal Society of London Series B Biological
Sciences 283 (2016).
date_created: 2018-12-11T11:51:00Z
date_published: 2016-06-29T00:00:00Z
date_updated: 2023-02-23T14:05:30Z
day: '29'
ddc:
- '576'
- '592'
department:
- _id: SyCr
doi: 10.1098/rspb.2016.0811
file:
- access_level: open_access
checksum: 0b0d1be38b497d004064650acb3baced
content_type: application/pdf
creator: system
date_created: 2018-12-12T10:08:46Z
date_updated: 2020-07-14T12:44:42Z
file_id: '4708'
file_name: IST-2016-701-v1+1_20160811.full.pdf
file_size: 796872
relation: main_file
file_date_updated: 2020-07-14T12:44:42Z
has_accepted_license: '1'
intvolume: ' 283'
issue: '1833'
language:
- iso: eng
month: '06'
oa: 1
oa_version: Published Version
publication: Proceedings of the Royal Society of London Series B Biological Sciences
publication_status: published
publisher: Royal Society, The
publist_id: '6060'
pubrep_id: '701'
quality_controlled: '1'
related_material:
record:
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relation: research_data
status: public
scopus_import: 1
status: public
title: Elevated virulence of an emerging viral genotype as a driver of honeybee loss
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: journal_article
user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87
volume: 283
year: '2016'
...
---
_id: '9704'
abstract:
- lang: eng
text: Emerging infectious diseases (EIDs) have contributed significantly to the
current biodiversity crisis, leading to widespread epidemics and population loss.
Owing to genetic variation in pathogen virulence, a complete understanding of
species decline requires the accurate identification and characterization of EIDs.
We explore this issue in the Western honeybee, where increasing mortality of populations
in the Northern Hemisphere has caused major concern. Specifically, we investigate
the importance of genetic identity of the main suspect in mortality, deformed
wing virus (DWV), in driving honeybee loss. Using laboratory experiments and a
systematic field survey, we demonstrate that an emerging DWV genotype (DWV-B)
is more virulent than the established DWV genotype (DWV-A) and is widespread in
the landscape. Furthermore, we show in a simple model that colonies infected with
DWV-B collapse sooner than colonies infected with DWV-A. We also identify potential
for rapid DWV evolution by revealing extensive genome-wide recombination in vivo.
The emergence of DWV-B in naive honeybee populations, including via recombination
with DWV-A, could be of significant ecological and economic importance. Our findings
emphasize that knowledge of pathogen genetic identity and diversity is critical
to understanding drivers of species decline.
article_processing_charge: No
author:
- first_name: Dino
full_name: Mcmahon, Dino
last_name: Mcmahon
- first_name: Myrsini
full_name: Natsopoulou, Myrsini
last_name: Natsopoulou
- first_name: Vincent
full_name: Doublet, Vincent
last_name: Doublet
- first_name: Matthias
full_name: Fürst, Matthias
id: 393B1196-F248-11E8-B48F-1D18A9856A87
last_name: Fürst
orcid: 0000-0002-3712-925X
- first_name: Silvio
full_name: Weging, Silvio
last_name: Weging
- first_name: Mark
full_name: Brown, Mark
last_name: Brown
- first_name: Andreas
full_name: Gogol Döring, Andreas
last_name: Gogol Döring
- first_name: Robert
full_name: Paxton, Robert
last_name: Paxton
citation:
ama: 'Mcmahon D, Natsopoulou M, Doublet V, et al. Data from: Elevated virulence
of an emerging viral genotype as a driver of honeybee loss. 2016. doi:10.5061/dryad.cq7t1'
apa: 'Mcmahon, D., Natsopoulou, M., Doublet, V., Fürst, M., Weging, S., Brown, M.,
… Paxton, R. (2016). Data from: Elevated virulence of an emerging viral genotype
as a driver of honeybee loss. Dryad. https://doi.org/10.5061/dryad.cq7t1'
chicago: 'Mcmahon, Dino, Myrsini Natsopoulou, Vincent Doublet, Matthias Fürst, Silvio
Weging, Mark Brown, Andreas Gogol Döring, and Robert Paxton. “Data from: Elevated
Virulence of an Emerging Viral Genotype as a Driver of Honeybee Loss.” Dryad,
2016. https://doi.org/10.5061/dryad.cq7t1.'
ieee: 'D. Mcmahon et al., “Data from: Elevated virulence of an emerging viral
genotype as a driver of honeybee loss.” Dryad, 2016.'
ista: 'Mcmahon D, Natsopoulou M, Doublet V, Fürst M, Weging S, Brown M, Gogol Döring
A, Paxton R. 2016. Data from: Elevated virulence of an emerging viral genotype
as a driver of honeybee loss, Dryad, 10.5061/dryad.cq7t1.'
mla: 'Mcmahon, Dino, et al. Data from: Elevated Virulence of an Emerging Viral
Genotype as a Driver of Honeybee Loss. Dryad, 2016, doi:10.5061/dryad.cq7t1.'
short: D. Mcmahon, M. Natsopoulou, V. Doublet, M. Fürst, S. Weging, M. Brown, A.
Gogol Döring, R. Paxton, (2016).
date_created: 2021-07-23T08:30:38Z
date_published: 2016-05-06T00:00:00Z
date_updated: 2023-02-21T16:54:31Z
day: '06'
department:
- _id: SyCr
doi: 10.5061/dryad.cq7t1
main_file_link:
- open_access: '1'
url: https://doi.org/10.5061/dryad.cq7t1
month: '05'
oa: 1
oa_version: Published Version
publisher: Dryad
related_material:
record:
- id: '1262'
relation: used_in_publication
status: public
status: public
title: 'Data from: Elevated virulence of an emerging viral genotype as a driver of
honeybee loss'
type: research_data_reference
user_id: 6785fbc1-c503-11eb-8a32-93094b40e1cf
year: '2016'
...
---
_id: '1322'
abstract:
- lang: eng
text: Direct reciprocity is a major mechanism for the evolution of cooperation.
Several classical studies have suggested that humans should quickly learn to adopt
reciprocal strategies to establish mutual cooperation in repeated interactions.
On the other hand, the recently discovered theory of ZD strategies has found that
subjects who use extortionate strategies are able to exploit and subdue cooperators.
Although such extortioners have been predicted to succeed in any population of
adaptive opponents, theoretical follow-up studies questioned whether extortion
can evolve in reality. However, most of these studies presumed that individuals
have similar strategic possibilities and comparable outside options, whereas asymmetries
are ubiquitous in real world applications. Here we show with a model and an economic
experiment that extortionate strategies readily emerge once subjects differ in
their strategic power. Our experiment combines a repeated social dilemma with
asymmetric partner choice. In our main treatment there is one randomly chosen
group member who is unilaterally allowed to exchange one of the other group members
after every ten rounds of the social dilemma. We find that this asymmetric replacement
opportunity generally promotes cooperation, but often the resulting payoff distribution
reflects the underlying power structure. Almost half of the subjects in a better
strategic position turn into extortioners, who quickly proceed to exploit their
peers. By adapting their cooperation probabilities consistent with ZD theory,
extortioners force their co-players to cooperate without being similarly cooperative
themselves. Comparison to non-extortionate players under the same conditions indicates
a substantial net gain to extortion. Our results thus highlight how power asymmetries
can endanger mutually beneficial interactions, and transform them into exploitative
relationships. In particular, our results indicate that the extortionate strategies
predicted from ZD theory could play a more prominent role in our daily interactions
than previously thought.
acknowledgement: 'CH was funded by the Schrödinger program of the Austrian Science
Fund (FWF) J3475. '
article_number: e0163867
author:
- first_name: Christian
full_name: Hilbe, Christian
id: 2FDF8F3C-F248-11E8-B48F-1D18A9856A87
last_name: Hilbe
orcid: 0000-0001-5116-955X
- first_name: Kristin
full_name: Hagel, Kristin
last_name: Hagel
- first_name: Manfred
full_name: Milinski, Manfred
last_name: Milinski
citation:
ama: Hilbe C, Hagel K, Milinski M. Asymmetric power boosts extortion in an economic
experiment. PLoS One. 2016;11(10). doi:10.1371/journal.pone.0163867
apa: Hilbe, C., Hagel, K., & Milinski, M. (2016). Asymmetric power boosts extortion
in an economic experiment. PLoS One. Public Library of Science. https://doi.org/10.1371/journal.pone.0163867
chicago: Hilbe, Christian, Kristin Hagel, and Manfred Milinski. “Asymmetric Power
Boosts Extortion in an Economic Experiment.” PLoS One. Public Library of
Science, 2016. https://doi.org/10.1371/journal.pone.0163867.
ieee: C. Hilbe, K. Hagel, and M. Milinski, “Asymmetric power boosts extortion in
an economic experiment,” PLoS One, vol. 11, no. 10. Public Library of Science,
2016.
ista: Hilbe C, Hagel K, Milinski M. 2016. Asymmetric power boosts extortion in an
economic experiment. PLoS One. 11(10), e0163867.
mla: Hilbe, Christian, et al. “Asymmetric Power Boosts Extortion in an Economic
Experiment.” PLoS One, vol. 11, no. 10, e0163867, Public Library of Science,
2016, doi:10.1371/journal.pone.0163867.
short: C. Hilbe, K. Hagel, M. Milinski, PLoS One 11 (2016).
date_created: 2018-12-11T11:51:22Z
date_published: 2016-10-04T00:00:00Z
date_updated: 2023-02-23T14:11:27Z
day: '04'
ddc:
- '004'
- '006'
department:
- _id: KrCh
doi: 10.1371/journal.pone.0163867
file:
- access_level: open_access
checksum: 6b33e394003dfe8b4ca6be1858aaa8e3
content_type: application/pdf
creator: system
date_created: 2018-12-12T10:08:08Z
date_updated: 2020-07-14T12:44:44Z
file_id: '4668'
file_name: IST-2016-716-v1+1_journal.pone.0163867.PDF
file_size: 2077905
relation: main_file
file_date_updated: 2020-07-14T12:44:44Z
has_accepted_license: '1'
intvolume: ' 11'
issue: '10'
language:
- iso: eng
month: '10'
oa: 1
oa_version: Published Version
publication: PLoS One
publication_status: published
publisher: Public Library of Science
publist_id: '5948'
pubrep_id: '716'
quality_controlled: '1'
related_material:
record:
- id: '9867'
relation: research_data
status: public
- id: '9868'
relation: research_data
status: public
scopus_import: 1
status: public
title: Asymmetric power boosts extortion in an economic experiment
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: journal_article
user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87
volume: 11
year: '2016'
...
---
_id: '1270'
abstract:
- lang: eng
text: A crucial step in the early development of multicellular organisms involves
the establishment of spatial patterns of gene expression which later direct proliferating
cells to take on different cell fates. These patterns enable the cells to infer
their global position within a tissue or an organism by reading out local gene
expression levels. The patterning system is thus said to encode positional information,
a concept that was formalized recently in the framework of information theory.
Here we introduce a toy model of patterning in one spatial dimension, which can
be seen as an extension of Wolpert's paradigmatic "French Flag" model,
to patterning by several interacting, spatially coupled genes subject to intrinsic
and extrinsic noise. Our model, a variant of an Ising spin system, allows us to
systematically explore expression patterns that optimally encode positional information.
We find that optimal patterning systems use positional cues, as in the French
Flag model, together with gene-gene interactions to generate combinatorial codes
for position which we call "Counter" patterns. Counter patterns can
also be stabilized against noise and variations in system size or morphogen dosage
by longer-range spatial interactions of the type invoked in the Turing model.
The simple setup proposed here qualitatively captures many of the experimentally
observed properties of biological patterning systems and allows them to be studied
in a single, theoretically consistent framework.
acknowledgement: The authors would like to thank Thomas Sokolowski and Filipe Tostevin
for helpful discussions. PH and UG were funded by the German Excellence Initiative
via the program "Nanosystems Initiative Munich" (https://www.nano-initiative-munich.de)
and the German Research Foundation via the SFB 1032 "Nanoagents for Spatiotemporal
Control of Molecular and Cellular Reactions" (http://www.sfb1032.physik.uni-muenchen.de).
GT was funded by the Austrian Science Fund (FWF P 28844) (http://www.fwf.ac.at).
article_number: e0163628
author:
- first_name: Patrick
full_name: Hillenbrand, Patrick
last_name: Hillenbrand
- first_name: Ulrich
full_name: Gerland, Ulrich
last_name: Gerland
- first_name: Gasper
full_name: Tkacik, Gasper
id: 3D494DCA-F248-11E8-B48F-1D18A9856A87
last_name: Tkacik
orcid: 0000-0002-6699-1455
citation:
ama: 'Hillenbrand P, Gerland U, Tkačik G. Beyond the French flag model: Exploiting
spatial and gene regulatory interactions for positional information. PLoS One.
2016;11(9). doi:10.1371/journal.pone.0163628'
apa: 'Hillenbrand, P., Gerland, U., & Tkačik, G. (2016). Beyond the French flag
model: Exploiting spatial and gene regulatory interactions for positional information.
PLoS One. Public Library of Science. https://doi.org/10.1371/journal.pone.0163628'
chicago: 'Hillenbrand, Patrick, Ulrich Gerland, and Gašper Tkačik. “Beyond the French
Flag Model: Exploiting Spatial and Gene Regulatory Interactions for Positional
Information.” PLoS One. Public Library of Science, 2016. https://doi.org/10.1371/journal.pone.0163628.'
ieee: 'P. Hillenbrand, U. Gerland, and G. Tkačik, “Beyond the French flag model:
Exploiting spatial and gene regulatory interactions for positional information,”
PLoS One, vol. 11, no. 9. Public Library of Science, 2016.'
ista: 'Hillenbrand P, Gerland U, Tkačik G. 2016. Beyond the French flag model: Exploiting
spatial and gene regulatory interactions for positional information. PLoS One.
11(9), e0163628.'
mla: 'Hillenbrand, Patrick, et al. “Beyond the French Flag Model: Exploiting Spatial
and Gene Regulatory Interactions for Positional Information.” PLoS One,
vol. 11, no. 9, e0163628, Public Library of Science, 2016, doi:10.1371/journal.pone.0163628.'
short: P. Hillenbrand, U. Gerland, G. Tkačik, PLoS One 11 (2016).
date_created: 2018-12-11T11:51:03Z
date_published: 2016-09-27T00:00:00Z
date_updated: 2023-02-23T14:11:37Z
day: '27'
ddc:
- '571'
department:
- _id: GaTk
doi: 10.1371/journal.pone.0163628
file:
- access_level: open_access
checksum: 3d0d55d373096a033bd9cf79288c8586
content_type: application/pdf
creator: system
date_created: 2018-12-12T10:10:47Z
date_updated: 2020-07-14T12:44:42Z
file_id: '4837'
file_name: IST-2016-696-v1+1_journal.pone.0163628.PDF
file_size: 4950415
relation: main_file
file_date_updated: 2020-07-14T12:44:42Z
has_accepted_license: '1'
intvolume: ' 11'
issue: '9'
language:
- iso: eng
month: '09'
oa: 1
oa_version: Published Version
project:
- _id: 254E9036-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: P28844-B27
name: Biophysics of information processing in gene regulation
publication: PLoS One
publication_status: published
publisher: Public Library of Science
publist_id: '6050'
pubrep_id: '696'
quality_controlled: '1'
related_material:
record:
- id: '9869'
relation: research_data
status: public
- id: '9870'
relation: research_data
status: public
- id: '9871'
relation: research_data
status: public
scopus_import: 1
status: public
title: 'Beyond the French flag model: Exploiting spatial and gene regulatory interactions
for positional information'
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: journal_article
user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87
volume: 11
year: '2016'
...
---
_id: '1250'
abstract:
- lang: eng
text: In bacteria, replicative aging manifests as a difference in growth or survival
between the two cells emerging from division. One cell can be regarded as an aging
mother with a decreased potential for future survival and division, the other
as a rejuvenated daughter. Here, we aimed at investigating some of the processes
involved in aging in the bacterium Escherichia coli, where the two types of cells
can be distinguished by the age of their cell poles. We found that certain changes
in the regulation of the carbohydrate metabolism can affect aging. A mutation
in the carbon storage regulator gene, csrA, leads to a dramatically shorter replicative
lifespan; csrA mutants stop dividing once their pole exceeds an age of about five
divisions. These old-pole cells accumulate glycogen at their old cell poles; after
their last division, they do not contain a chromosome, presumably because of spatial
exclusion by the glycogen aggregates. The new-pole daughters produced by these
aging mothers are born young; they only express the deleterious phenotype once
their pole is old. These results demonstrate how manipulations of nutrient allocation
can lead to the exclusion of the chromosome and limit replicative lifespan in
E. coli, and illustrate how mutations can have phenotypic effects that are specific
for cells with old poles. This raises the question how bacteria can avoid the
accumulation of such mutations in their genomes over evolutionary times, and how
they can achieve the long replicative lifespans that have recently been reported.
acknowledgement: This manuscript is dedicated to the memory of Alex Böhm, who was
a great friend and a passionate biologist. Alex passed away after the initial submission
of this manuscript. We thank Vesna Olivera and Ursula Sauder from the Zentrum für
Mikroskopie Uni Basel for excellent service, and Olin Silander, Nikki Freed, and
Nela Nikolic for helpful discussions. This work was supported by the Swiss National
Science Foundation grants to M. Ackermann and Urs Jenal (supporting AB).
article_number: e1005974
author:
- first_name: Alex
full_name: Boehm, Alex
last_name: Boehm
- first_name: Markus
full_name: Arnoldini, Markus
last_name: Arnoldini
- first_name: Tobias
full_name: Bergmiller, Tobias
id: 2C471CFA-F248-11E8-B48F-1D18A9856A87
last_name: Bergmiller
orcid: 0000-0001-5396-4346
- first_name: Thomas
full_name: Röösli, Thomas
last_name: Röösli
- first_name: Colette
full_name: Bigosch, Colette
last_name: Bigosch
- first_name: Martin
full_name: Ackermann, Martin
last_name: Ackermann
citation:
ama: Boehm A, Arnoldini M, Bergmiller T, Röösli T, Bigosch C, Ackermann M. Genetic
manipulation of glycogen allocation affects replicative lifespan in E coli. PLoS
Genetics. 2016;12(4). doi:10.1371/journal.pgen.1005974
apa: Boehm, A., Arnoldini, M., Bergmiller, T., Röösli, T., Bigosch, C., & Ackermann,
M. (2016). Genetic manipulation of glycogen allocation affects replicative lifespan
in E coli. PLoS Genetics. Public Library of Science. https://doi.org/10.1371/journal.pgen.1005974
chicago: Boehm, Alex, Markus Arnoldini, Tobias Bergmiller, Thomas Röösli, Colette
Bigosch, and Martin Ackermann. “Genetic Manipulation of Glycogen Allocation Affects
Replicative Lifespan in E Coli.” PLoS Genetics. Public Library of Science,
2016. https://doi.org/10.1371/journal.pgen.1005974.
ieee: A. Boehm, M. Arnoldini, T. Bergmiller, T. Röösli, C. Bigosch, and M. Ackermann,
“Genetic manipulation of glycogen allocation affects replicative lifespan in E
coli,” PLoS Genetics, vol. 12, no. 4. Public Library of Science, 2016.
ista: Boehm A, Arnoldini M, Bergmiller T, Röösli T, Bigosch C, Ackermann M. 2016.
Genetic manipulation of glycogen allocation affects replicative lifespan in E
coli. PLoS Genetics. 12(4), e1005974.
mla: Boehm, Alex, et al. “Genetic Manipulation of Glycogen Allocation Affects Replicative
Lifespan in E Coli.” PLoS Genetics, vol. 12, no. 4, e1005974, Public Library
of Science, 2016, doi:10.1371/journal.pgen.1005974.
short: A. Boehm, M. Arnoldini, T. Bergmiller, T. Röösli, C. Bigosch, M. Ackermann,
PLoS Genetics 12 (2016).
date_created: 2018-12-11T11:50:56Z
date_published: 2016-04-19T00:00:00Z
date_updated: 2023-02-23T14:11:39Z
day: '19'
ddc:
- '576'
- '579'
department:
- _id: CaGu
doi: 10.1371/journal.pgen.1005974
file:
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date_updated: 2020-07-14T12:44:41Z
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month: '04'
oa: 1
oa_version: Published Version
publication: PLoS Genetics
publication_status: published
publisher: Public Library of Science
publist_id: '6077'
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record:
- id: '9873'
relation: research_data
status: public
scopus_import: 1
status: public
title: Genetic manipulation of glycogen allocation affects replicative lifespan in
E coli
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: journal_article
user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87
volume: 12
year: '2016'
...
---
_id: '12903'
article_processing_charge: No
author:
- first_name: Alois
full_name: Schlögl, Alois
id: 45BF87EE-F248-11E8-B48F-1D18A9856A87
last_name: Schlögl
orcid: 0000-0002-5621-8100
- first_name: Stephan
full_name: Stadlbauer, Stephan
id: 4D0BC184-F248-11E8-B48F-1D18A9856A87
last_name: Stadlbauer
citation:
ama: 'Schlögl A, Stadlbauer S. High performance computing at IST Austria: Modelling
the human hippocampus. In: AHPC16 - Austrian HPC Meeting 2016. VSC - Vienna
Scientific Cluster; 2016:37.'
apa: 'Schlögl, A., & Stadlbauer, S. (2016). High performance computing at IST
Austria: Modelling the human hippocampus. In AHPC16 - Austrian HPC Meeting
2016 (p. 37). Grundlsee, Austria: VSC - Vienna Scientific Cluster.'
chicago: 'Schlögl, Alois, and Stephan Stadlbauer. “High Performance Computing at
IST Austria: Modelling the Human Hippocampus.” In AHPC16 - Austrian HPC Meeting
2016, 37. VSC - Vienna Scientific Cluster, 2016.'
ieee: 'A. Schlögl and S. Stadlbauer, “High performance computing at IST Austria:
Modelling the human hippocampus,” in AHPC16 - Austrian HPC Meeting 2016,
Grundlsee, Austria, 2016, p. 37.'
ista: 'Schlögl A, Stadlbauer S. 2016. High performance computing at IST Austria:
Modelling the human hippocampus. AHPC16 - Austrian HPC Meeting 2016. AHPC: Austrian
HPC Meeting, 37.'
mla: 'Schlögl, Alois, and Stephan Stadlbauer. “High Performance Computing at IST
Austria: Modelling the Human Hippocampus.” AHPC16 - Austrian HPC Meeting 2016,
VSC - Vienna Scientific Cluster, 2016, p. 37.'
short: A. Schlögl, S. Stadlbauer, in:, AHPC16 - Austrian HPC Meeting 2016, VSC -
Vienna Scientific Cluster, 2016, p. 37.
conference:
end_date: 2016-02-24
location: Grundlsee, Austria
name: 'AHPC: Austrian HPC Meeting'
start_date: 2016-02-22
date_created: 2023-05-05T12:54:47Z
date_published: 2016-02-24T00:00:00Z
date_updated: 2023-05-16T07:15:14Z
day: '24'
ddc:
- '000'
department:
- _id: ScienComp
- _id: PeJo
file:
- access_level: open_access
checksum: 4a7b00362e81358d568f5e216fa03c3e
content_type: application/pdf
creator: dernst
date_created: 2023-05-16T07:03:56Z
date_updated: 2023-05-16T07:03:56Z
file_id: '12968'
file_name: 2016_AHPC_Schloegl.pdf
file_size: 1073523
relation: main_file
success: 1
file_date_updated: 2023-05-16T07:03:56Z
has_accepted_license: '1'
language:
- iso: eng
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url: https://vsc.ac.at/fileadmin/user_upload/vsc/conferences/ahpc16/BOOKLET_AHPC16.pdf
month: '02'
oa: 1
oa_version: Published Version
page: '37'
publication: AHPC16 - Austrian HPC Meeting 2016
publication_status: published
publisher: VSC - Vienna Scientific Cluster
quality_controlled: '1'
status: public
title: 'High performance computing at IST Austria: Modelling the human hippocampus'
type: conference_abstract
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
year: '2016'
...
---
_id: '1341'
abstract:
- lang: eng
text: In resource allocation games, selfish players share resources that are needed
in order to fulfill their objectives. The cost of using a resource depends on
the load on it. In the traditional setting, the players make their choices concurrently
and in one-shot. That is, a strategy for a player is a subset of the resources.
We introduce and study dynamic resource allocation games. In this setting, the
game proceeds in phases. In each phase each player chooses one resource. A scheduler
dictates the order in which the players proceed in a phase, possibly scheduling
several players to proceed concurrently. The game ends when each player has collected
a set of resources that fulfills his objective. The cost for each player then
depends on this set as well as on the load on the resources in it – we consider
both congestion and cost-sharing games. We argue that the dynamic setting is the
suitable setting for many applications in practice. We study the stability of
dynamic resource allocation games, where the appropriate notion of stability is
that of subgame perfect equilibrium, study the inefficiency incurred due to selfish
behavior, and also study problems that are particular to the dynamic setting,
like constraints on the order in which resources can be chosen or the problem
of finding a scheduler that achieves stability.
acknowledgement: This research was supported in part by the European Research Council
(ERC) under grants 267989 (QUAREM) and 278410 (QUALITY), and by the Austrian Science
Fund (FWF) under grants S11402-N23 (RiSE) and Z211-N23 (Wittgenstein Award).
alternative_title:
- LNCS
author:
- first_name: Guy
full_name: Avni, Guy
id: 463C8BC2-F248-11E8-B48F-1D18A9856A87
last_name: Avni
orcid: 0000-0001-5588-8287
- first_name: Thomas A
full_name: Henzinger, Thomas A
id: 40876CD8-F248-11E8-B48F-1D18A9856A87
last_name: Henzinger
orcid: 0000−0002−2985−7724
- first_name: Orna
full_name: Kupferman, Orna
last_name: Kupferman
citation:
ama: 'Avni G, Henzinger TA, Kupferman O. Dynamic resource allocation games. In:
Vol 9928. Springer; 2016:153-166. doi:10.1007/978-3-662-53354-3_13'
apa: 'Avni, G., Henzinger, T. A., & Kupferman, O. (2016). Dynamic resource allocation
games (Vol. 9928, pp. 153–166). Presented at the SAGT: Symposium on Algorithmic
Game Theory, Liverpool, United Kingdom: Springer. https://doi.org/10.1007/978-3-662-53354-3_13'
chicago: Avni, Guy, Thomas A Henzinger, and Orna Kupferman. “Dynamic Resource Allocation
Games,” 9928:153–66. Springer, 2016. https://doi.org/10.1007/978-3-662-53354-3_13.
ieee: 'G. Avni, T. A. Henzinger, and O. Kupferman, “Dynamic resource allocation
games,” presented at the SAGT: Symposium on Algorithmic Game Theory, Liverpool,
United Kingdom, 2016, vol. 9928, pp. 153–166.'
ista: 'Avni G, Henzinger TA, Kupferman O. 2016. Dynamic resource allocation games.
SAGT: Symposium on Algorithmic Game Theory, LNCS, vol. 9928, 153–166.'
mla: Avni, Guy, et al. Dynamic Resource Allocation Games. Vol. 9928, Springer,
2016, pp. 153–66, doi:10.1007/978-3-662-53354-3_13.
short: G. Avni, T.A. Henzinger, O. Kupferman, in:, Springer, 2016, pp. 153–166.
conference:
end_date: 2016-09-21
location: Liverpool, United Kingdom
name: 'SAGT: Symposium on Algorithmic Game Theory'
start_date: 2016-09-19
date_created: 2018-12-11T11:51:28Z
date_published: 2016-09-01T00:00:00Z
date_updated: 2023-08-17T13:52:49Z
day: '01'
ddc:
- '000'
department:
- _id: ToHe
doi: 10.1007/978-3-662-53354-3_13
ec_funded: 1
file:
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checksum: 0825eefd4e22774f6f62cb7d7389b05a
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creator: system
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date_updated: 2020-07-14T12:44:45Z
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intvolume: ' 9928'
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month: '09'
oa: 1
oa_version: Preprint
page: 153 - 166
project:
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call_identifier: FP7
grant_number: '267989'
name: Quantitative Reactive Modeling
- _id: 25832EC2-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: S 11407_N23
name: Rigorous Systems Engineering
- _id: 25F42A32-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: Z211
name: The Wittgenstein Prize
publication_status: published
publisher: Springer
publist_id: '5926'
pubrep_id: '645'
quality_controlled: '1'
related_material:
record:
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relation: later_version
status: public
scopus_import: 1
status: public
title: Dynamic resource allocation games
type: conference
user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87
volume: 9928
year: '2016'
...
---
_id: '5749'
abstract:
- lang: eng
text: Parasitism creates selection for resistance mechanisms in host populations
and is hypothesized to promote increased host evolvability. However, the influence
of these traits on host evolution when parasites are no longer present is unclear.
We used experimental evolution and whole-genome sequencing of Escherichia coli
to determine the effects of past and present exposure to parasitic viruses (phages)
on the spread of mutator alleles, resistance, and bacterial competitive fitness.
We found that mutator alleles spread rapidly during adaptation to any of four
different phage species, and this pattern was even more pronounced with multiple
phages present simultaneously. However, hypermutability did not detectably accelerate
adaptation in the absence of phages and recovery of fitness costs associated with
resistance. Several lineages evolved phage resistance through elevated mucoidy,
and during subsequent evolution in phage-free conditions they rapidly reverted
to nonmucoid, phage-susceptible phenotypes. Genome sequencing revealed that this
phenotypic reversion was achieved by additional genetic changes rather than by
genotypic reversion of the initial resistance mutations. Insertion sequence (IS)
elements played a key role in both the acquisition of resistance and adaptation
in the absence of parasites; unlike single nucleotide polymorphisms, IS insertions
were not more frequent in mutator lineages. Our results provide a genetic explanation
for rapid reversion of mucoidy, a phenotype observed in other bacterial species
including human pathogens. Moreover, this demonstrates that the types of genetic
change underlying adaptation to fitness costs, and consequently the impact of
evolvability mechanisms such as increased point-mutation rates, depend critically
on the mechanism of resistance.
acknowledgement: The authors thank three anonymous reviewers and the editor for helpful
comments on the manuscript, as well as Dominique Schneider for feedback on an earlier
draft, Jenna Gallie for lytic λ and Julien Capelle for T5 and T6. This work was
supported by the Swiss National Science Foundation (PZ00P3_148255 to A.H.) and an
EU Marie Curie PEOPLE Postdoctoral Fellowship for Career Development (FP7-PEOPLE-2012-IEF-331824
to S.W.).
article_processing_charge: No
author:
- first_name: Sébastien
full_name: Wielgoss, Sébastien
last_name: Wielgoss
- first_name: Tobias
full_name: Bergmiller, Tobias
id: 2C471CFA-F248-11E8-B48F-1D18A9856A87
last_name: Bergmiller
orcid: 0000-0001-5396-4346
- first_name: Anna M.
full_name: Bischofberger, Anna M.
last_name: Bischofberger
- first_name: Alex R.
full_name: Hall, Alex R.
last_name: Hall
citation:
ama: Wielgoss S, Bergmiller T, Bischofberger AM, Hall AR. Adaptation to parasites
and costs of parasite resistance in mutator and nonmutator bacteria. Molecular
Biology and Evolution. 2016;33(3):770-782. doi:10.1093/molbev/msv270
apa: Wielgoss, S., Bergmiller, T., Bischofberger, A. M., & Hall, A. R. (2016).
Adaptation to parasites and costs of parasite resistance in mutator and nonmutator
bacteria. Molecular Biology and Evolution. Oxford University Press. https://doi.org/10.1093/molbev/msv270
chicago: Wielgoss, Sébastien, Tobias Bergmiller, Anna M. Bischofberger, and Alex
R. Hall. “Adaptation to Parasites and Costs of Parasite Resistance in Mutator
and Nonmutator Bacteria.” Molecular Biology and Evolution. Oxford University
Press, 2016. https://doi.org/10.1093/molbev/msv270.
ieee: S. Wielgoss, T. Bergmiller, A. M. Bischofberger, and A. R. Hall, “Adaptation
to parasites and costs of parasite resistance in mutator and nonmutator bacteria,”
Molecular Biology and Evolution, vol. 33, no. 3. Oxford University Press,
pp. 770–782, 2016.
ista: Wielgoss S, Bergmiller T, Bischofberger AM, Hall AR. 2016. Adaptation to parasites
and costs of parasite resistance in mutator and nonmutator bacteria. Molecular
Biology and Evolution. 33(3), 770–782.
mla: Wielgoss, Sébastien, et al. “Adaptation to Parasites and Costs of Parasite
Resistance in Mutator and Nonmutator Bacteria.” Molecular Biology and Evolution,
vol. 33, no. 3, Oxford University Press, 2016, pp. 770–82, doi:10.1093/molbev/msv270.
short: S. Wielgoss, T. Bergmiller, A.M. Bischofberger, A.R. Hall, Molecular Biology
and Evolution 33 (2016) 770–782.
date_created: 2018-12-18T13:18:10Z
date_published: 2016-03-01T00:00:00Z
date_updated: 2023-09-05T13:46:05Z
day: '01'
ddc:
- '576'
department:
- _id: CaGu
doi: 10.1093/molbev/msv270
external_id:
pmid:
- '26609077'
file:
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checksum: 47d9010690b6c5c17f2ac830cc63ac5c
content_type: application/pdf
creator: dernst
date_created: 2018-12-18T13:21:45Z
date_updated: 2020-07-14T12:47:10Z
file_id: '5750'
file_name: 2016_MolBiolEvol_Wielgoss.pdf
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intvolume: ' 33'
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- iso: eng
month: '03'
oa: 1
oa_version: Published Version
page: 770-782
pmid: 1
publication: Molecular Biology and Evolution
publication_identifier:
eissn:
- 1537-1719
issn:
- 0737-4038
publication_status: published
publisher: Oxford University Press
pubrep_id: '587'
quality_controlled: '1'
related_material:
record:
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relation: research_data
status: public
scopus_import: '1'
status: public
title: Adaptation to parasites and costs of parasite resistance in mutator and nonmutator
bacteria
tmp:
image: /images/cc_by_nc.png
legal_code_url: https://creativecommons.org/licenses/by-nc/4.0/legalcode
name: Creative Commons Attribution-NonCommercial 4.0 International (CC BY-NC 4.0)
short: CC BY-NC (4.0)
type: journal_article
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
volume: 33
year: '2016'
...
---
_id: '1121'
abstract:
- lang: eng
text: "Horizontal gene transfer (HGT), the lateral acquisition of genes across existing
species\r\nboundaries, is a major evolutionary force shaping microbial genomes
that facilitates\r\nadaptation to new environments as well as resistance to antimicrobial
drugs. As such,\r\nunderstanding the mechanisms and constraints that determine
the outcomes of HGT\r\nevents is crucial to understand the dynamics of HGT and
to design better strategies to\r\novercome the challenges that originate from
it.\r\nFollowing the insertion and expression of a newly transferred gene, the
success of an\r\nHGT event will depend on the fitness effect it has on the recipient
(host) cell. Therefore,\r\npredicting the impact of HGT on the genetic composition
of a population critically\r\ndepends on the distribution of fitness effects (DFE)
of horizontally transferred genes.\r\nHowever, to date, we have little knowledge
of the DFE of newly transferred genes, and\r\nhence little is known about the
shape and scale of this distribution.\r\nIt is particularly important to better
understand the selective barriers that determine\r\nthe fitness effects of newly
transferred genes. In spite of substantial bioinformatics\r\nefforts to identify
horizontally transferred genes and selective barriers, a systematic\r\nexperimental
approach to elucidate the roles of different selective barriers in defining\r\nthe
fate of a transfer event has largely been absent. Similarly, although the fact
that\r\nenvironment might alter the fitness effect of a horizontally transferred
gene may seem\r\nobvious, little attention has been given to it in a systematic
experimental manner.\r\nIn this study, we developed a systematic experimental
approach that consists of\r\ntransferring 44 arbitrarily selected Salmonella typhimurium
orthologous genes into an\r\nEscherichia coli host, and estimating the fitness
effects of these transferred genes at a\r\nconstant expression level by performing
competition assays against the wild type.\r\nIn chapter 2, we performed one-to-one
competition assays between a mutant strain\r\ncarrying a transferred gene and
the wild type strain. By using flow cytometry we\r\nestimated selection coefficients
for the transferred genes with a precision level of 10-3,and obtained the DFE
of horizontally transferred genes. We then investigated if these\r\nfitness effects
could be predicted by any of the intrinsic properties of the genes, namely,\r\nfunctional
category, degree of complexity (protein-protein interactions), GC content,\r\ncodon
usage and length. Our analyses revealed that the functional category and length\r\nof
the genes act as potential selective barriers. Finally, using the same procedure
with\r\nthe endogenous E. coli orthologs of these 44 genes, we demonstrated that
gene dosage is\r\nthe most prominent selective barrier to HGT.\r\nIn chapter 3,
using the same set of genes we investigated the role of environment on the\r\nsuccess
of HGT events. Under six different environments with different levels of stress\r\nwe
performed more complex competition assays, where we mixed all 44 mutant strains\r\ncarrying
transferred genes with the wild type strain. To estimate the fitness effects of\r\ngenes
relative to wild type we used next generation sequencing. We found that the DFEs\r\nof
horizontally transferred genes are highly dependent on the environment, with\r\nabundant
gene–by-environment interactions. Furthermore, we demonstrated a\r\nrelationship
between average fitness effect of a gene across all environments and its\r\nenvironmental
variance, and thus its predictability. Finally, in spite of the fitness effects\r\nof
genes being highly environment-dependent, we still observed a common shape of\r\nDFEs
across all tested environments."
acknowledgement: "This study was supported by European Research Council ERC CoG 2014
– EVOLHGT,\r\nunder the grant number 648440.\r\n\r\nIt is a pleasure to thank the
many people who made this thesis possible.\r\nI would like to first thank my advisor,
Jonathan Paul Bollback for providing guidance in\r\nall aspects of my life, encouragement,
sound advice, and good teaching over the last six\r\nyears.\r\nI would also like
to thank the members of my dissertation committee – Călin C. Guet\r\nand John F.
Baines – not only for their time and guidance, but for their intellectual\r\ncontributions
to my development as a scientist.\r\nI would like to thank Flavia Gama and Rodrigo
Redondo who have taught me all the\r\nskills in the laboratory with their graciousness
and friendship. Also special thanks to\r\nBollback group for their support and for
providing a stimulating and fun environment:\r\nIsabella Tomanek, Fabienne Jesse,
Claudia Igler, and Pavel Payne.\r\nJerneja Beslagic is not only an amazing assistant,
she also has a smile brighter and\r\nwarmer than the sunshine, bringing happiness
to every moment. Always keep your light\r\nNeja, I will miss our invaluable chatters
a lot."
alternative_title:
- ISTA Thesis
article_processing_charge: No
author:
- first_name: Hande
full_name: Acar, Hande
id: 2DDF136A-F248-11E8-B48F-1D18A9856A87
last_name: Acar
orcid: 0000-0003-1986-9753
citation:
ama: Acar H. Selective barriers to horizontal gene transfer. 2016.
apa: Acar, H. (2016). Selective barriers to horizontal gene transfer. Institute
of Science and Technology Austria.
chicago: Acar, Hande. “Selective Barriers to Horizontal Gene Transfer.” Institute
of Science and Technology Austria, 2016.
ieee: H. Acar, “Selective barriers to horizontal gene transfer,” Institute of Science
and Technology Austria, 2016.
ista: Acar H. 2016. Selective barriers to horizontal gene transfer. Institute of
Science and Technology Austria.
mla: Acar, Hande. Selective Barriers to Horizontal Gene Transfer. Institute
of Science and Technology Austria, 2016.
short: H. Acar, Selective Barriers to Horizontal Gene Transfer, Institute of Science
and Technology Austria, 2016.
date_created: 2018-12-11T11:50:16Z
date_published: 2016-12-01T00:00:00Z
date_updated: 2023-09-07T11:42:26Z
day: '01'
ddc:
- '570'
degree_awarded: PhD
department:
- _id: JoBo
ec_funded: 1
file:
- access_level: closed
checksum: 94bbbc754c36115bf37f8fc11fad43c4
content_type: application/pdf
creator: dernst
date_created: 2019-08-13T11:17:50Z
date_updated: 2019-08-13T11:17:50Z
file_id: '6814'
file_name: PhDThesis_HandeAcar_1230.pdf
file_size: 3682711
relation: main_file
- access_level: open_access
checksum: 94bbbc754c36115bf37f8fc11fad43c4
content_type: application/pdf
creator: dernst
date_created: 2021-02-22T11:51:13Z
date_updated: 2021-02-22T11:51:13Z
file_id: '9184'
file_name: 2016_Thesis_HandeAcar.pdf
file_size: 3682711
relation: main_file
success: 1
file_date_updated: 2021-02-22T11:51:13Z
has_accepted_license: '1'
language:
- iso: eng
month: '12'
oa: 1
oa_version: Published Version
page: '75'
project:
- _id: 2578D616-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '648440'
name: Selective Barriers to Horizontal Gene Transfer
publication_identifier:
issn:
- 2663-337X
publication_status: published
publisher: Institute of Science and Technology Austria
publist_id: '6239'
status: public
supervisor:
- first_name: Jonathan P
full_name: Bollback, Jonathan P
id: 2C6FA9CC-F248-11E8-B48F-1D18A9856A87
last_name: Bollback
orcid: 0000-0002-4624-4612
title: Selective barriers to horizontal gene transfer
type: dissertation
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
year: '2016'
...
---
_id: '1662'
abstract:
- lang: eng
text: We introduce a modification of the classic notion of intrinsic volume using
persistence moments of height functions. Evaluating the modified first intrinsic
volume on digital approximations of a compact body with smoothly embedded boundary
in Rn, we prove convergence to the first intrinsic volume of the body as the resolution
of the approximation improves. We have weaker results for the other modified intrinsic
volumes, proving they converge to the corresponding intrinsic volumes of the n-dimensional
unit ball.
acknowledgement: "This research is partially supported by the Toposys project FP7-ICT-318493-STREP,
and by ESF under the ACAT Research Network Programme.\r\nBoth authors thank Anne
Marie Svane for her comments on an early version of this paper. The second author
wishes to thank Eva B. Vedel Jensen and Markus Kiderlen from Aarhus University for
enlightening discussions and their kind hospitality during a visit of their department
in 2014."
author:
- first_name: Herbert
full_name: Edelsbrunner, Herbert
id: 3FB178DA-F248-11E8-B48F-1D18A9856A87
last_name: Edelsbrunner
orcid: 0000-0002-9823-6833
- first_name: Florian
full_name: Pausinger, Florian
id: 2A77D7A2-F248-11E8-B48F-1D18A9856A87
last_name: Pausinger
orcid: 0000-0002-8379-3768
citation:
ama: Edelsbrunner H, Pausinger F. Approximation and convergence of the intrinsic
volume. Advances in Mathematics. 2016;287:674-703. doi:10.1016/j.aim.2015.10.004
apa: Edelsbrunner, H., & Pausinger, F. (2016). Approximation and convergence
of the intrinsic volume. Advances in Mathematics. Academic Press. https://doi.org/10.1016/j.aim.2015.10.004
chicago: Edelsbrunner, Herbert, and Florian Pausinger. “Approximation and Convergence
of the Intrinsic Volume.” Advances in Mathematics. Academic Press, 2016.
https://doi.org/10.1016/j.aim.2015.10.004.
ieee: H. Edelsbrunner and F. Pausinger, “Approximation and convergence of the intrinsic
volume,” Advances in Mathematics, vol. 287. Academic Press, pp. 674–703,
2016.
ista: Edelsbrunner H, Pausinger F. 2016. Approximation and convergence of the intrinsic
volume. Advances in Mathematics. 287, 674–703.
mla: Edelsbrunner, Herbert, and Florian Pausinger. “Approximation and Convergence
of the Intrinsic Volume.” Advances in Mathematics, vol. 287, Academic Press,
2016, pp. 674–703, doi:10.1016/j.aim.2015.10.004.
short: H. Edelsbrunner, F. Pausinger, Advances in Mathematics 287 (2016) 674–703.
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title: Approximation and convergence of the intrinsic volume
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---
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abstract:
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text: "The process of gene expression is central to the modern understanding of
how cellular systems\r\nfunction. In this process, a special kind of regulatory
proteins, called transcription factors,\r\nare important to determine how much
protein is produced from a given gene. As biological\r\ninformation is transmitted
from transcription factor concentration to mRNA levels to amounts of\r\nprotein,
various sources of noise arise and pose limits to the fidelity of intracellular
signaling.\r\nThis thesis concerns itself with several aspects of stochastic gene
expression: (i) the mathematical\r\ndescription of complex promoters responsible
for the stochastic production of biomolecules,\r\n(ii) fundamental limits to information
processing the cell faces due to the interference from multiple\r\nfluctuating
signals, (iii) how the presence of gene expression noise influences the evolution\r\nof
regulatory sequences, (iv) and tools for the experimental study of origins and
consequences\r\nof cell-cell heterogeneity, including an application to bacterial
stress response systems."
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full_name: Rieckh, Georg
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citation:
ama: Rieckh G. Studying the complexities of transcriptional regulation. 2016.
apa: Rieckh, G. (2016). Studying the complexities of transcriptional regulation.
Institute of Science and Technology Austria.
chicago: Rieckh, Georg. “Studying the Complexities of Transcriptional Regulation.”
Institute of Science and Technology Austria, 2016.
ieee: G. Rieckh, “Studying the complexities of transcriptional regulation,” Institute
of Science and Technology Austria, 2016.
ista: Rieckh G. 2016. Studying the complexities of transcriptional regulation. Institute
of Science and Technology Austria.
mla: Rieckh, Georg. Studying the Complexities of Transcriptional Regulation.
Institute of Science and Technology Austria, 2016.
short: G. Rieckh, Studying the Complexities of Transcriptional Regulation, Institute
of Science and Technology Austria, 2016.
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supervisor:
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full_name: Tkacik, Gasper
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last_name: Tkacik
orcid: 0000-0002-6699-1455
title: Studying the complexities of transcriptional regulation
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...