---
_id: '481'
abstract:
- lang: eng
text: We introduce planar matchings on directed pseudo-line arrangements, which
yield a planar set of pseudo-line segments such that only matching-partners are
adjacent. By translating the planar matching problem into a corresponding stable
roommates problem we show that such matchings always exist. Using our new framework,
we establish, for the first time, a complete, rigorous definition of weighted
straight skeletons, which are based on a so-called wavefront propagation process.
We present a generalized and unified approach to treat structural changes in the
wavefront that focuses on the restoration of weak planarity by finding planar
matchings.
acknowledgement: 'Supported by NSERC and the Ross and Muriel Cheriton Fellowship.
Research supported by Austrian Science Fund (FWF): P25816-N15.'
author:
- first_name: Therese
full_name: Biedl, Therese
last_name: Biedl
- first_name: Stefan
full_name: Huber, Stefan
id: 4700A070-F248-11E8-B48F-1D18A9856A87
last_name: Huber
orcid: 0000-0002-8871-5814
- first_name: Peter
full_name: Palfrader, Peter
last_name: Palfrader
citation:
ama: Biedl T, Huber S, Palfrader P. Planar matchings for weighted straight skeletons.
International Journal of Computational Geometry and Applications. 2017;26(3-4):211-229.
doi:10.1142/S0218195916600050
apa: Biedl, T., Huber, S., & Palfrader, P. (2017). Planar matchings for weighted
straight skeletons. International Journal of Computational Geometry and Applications.
World Scientific Publishing. https://doi.org/10.1142/S0218195916600050
chicago: Biedl, Therese, Stefan Huber, and Peter Palfrader. “Planar Matchings for
Weighted Straight Skeletons.” International Journal of Computational Geometry
and Applications. World Scientific Publishing, 2017. https://doi.org/10.1142/S0218195916600050.
ieee: T. Biedl, S. Huber, and P. Palfrader, “Planar matchings for weighted straight
skeletons,” International Journal of Computational Geometry and Applications,
vol. 26, no. 3–4. World Scientific Publishing, pp. 211–229, 2017.
ista: Biedl T, Huber S, Palfrader P. 2017. Planar matchings for weighted straight
skeletons. International Journal of Computational Geometry and Applications. 26(3–4),
211–229.
mla: Biedl, Therese, et al. “Planar Matchings for Weighted Straight Skeletons.”
International Journal of Computational Geometry and Applications, vol.
26, no. 3–4, World Scientific Publishing, 2017, pp. 211–29, doi:10.1142/S0218195916600050.
short: T. Biedl, S. Huber, P. Palfrader, International Journal of Computational
Geometry and Applications 26 (2017) 211–229.
date_created: 2018-12-11T11:46:43Z
date_published: 2017-04-13T00:00:00Z
date_updated: 2023-02-21T16:06:22Z
day: '13'
ddc:
- '004'
- '514'
- '516'
department:
- _id: HeEd
doi: 10.1142/S0218195916600050
file:
- access_level: open_access
checksum: f79e8558bfe4b368dfefeb8eec2e3a5e
content_type: application/pdf
creator: system
date_created: 2018-12-12T10:09:34Z
date_updated: 2020-07-14T12:46:35Z
file_id: '4758'
file_name: IST-2018-949-v1+1_2016_huber_PLanar_matchings.pdf
file_size: 769296
relation: main_file
file_date_updated: 2020-07-14T12:46:35Z
has_accepted_license: '1'
intvolume: ' 26'
issue: 3-4
language:
- iso: eng
license: https://creativecommons.org/licenses/by/4.0/
month: '04'
oa: 1
oa_version: Published Version
page: 211 - 229
publication: International Journal of Computational Geometry and Applications
publication_status: published
publisher: World Scientific Publishing
publist_id: '7338'
pubrep_id: '949'
quality_controlled: '1'
related_material:
record:
- id: '10892'
relation: earlier_version
status: public
scopus_import: 1
status: public
title: Planar matchings for weighted straight skeletons
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: 26
year: '2017'
...
---
_id: '484'
abstract:
- lang: eng
text: We consider the dynamics of a large quantum system of N identical bosons in
3D interacting via a two-body potential of the form N3β-1w(Nβ(x - y)). For fixed
0 = β < 1/3 and large N, we obtain a norm approximation to the many-body evolution
in the Nparticle Hilbert space. The leading order behaviour of the dynamics is
determined by Hartree theory while the second order is given by Bogoliubov theory.
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
citation:
ama: Nam P, Napiórkowski MM. Bogoliubov correction to the mean-field dynamics of
interacting bosons. Advances in Theoretical and Mathematical Physics. 2017;21(3):683-738.
doi:10.4310/ATMP.2017.v21.n3.a4
apa: Nam, P., & Napiórkowski, M. M. (2017). Bogoliubov correction to the mean-field
dynamics of interacting bosons. Advances in Theoretical and Mathematical Physics.
International Press. https://doi.org/10.4310/ATMP.2017.v21.n3.a4
chicago: Nam, Phan, and Marcin M Napiórkowski. “Bogoliubov Correction to the Mean-Field
Dynamics of Interacting Bosons.” Advances in Theoretical and Mathematical Physics.
International Press, 2017. https://doi.org/10.4310/ATMP.2017.v21.n3.a4.
ieee: P. Nam and M. M. Napiórkowski, “Bogoliubov correction to the mean-field dynamics
of interacting bosons,” Advances in Theoretical and Mathematical Physics,
vol. 21, no. 3. International Press, pp. 683–738, 2017.
ista: Nam P, Napiórkowski MM. 2017. Bogoliubov correction to the mean-field dynamics
of interacting bosons. Advances in Theoretical and Mathematical Physics. 21(3),
683–738.
mla: Nam, Phan, and Marcin M. Napiórkowski. “Bogoliubov Correction to the Mean-Field
Dynamics of Interacting Bosons.” Advances in Theoretical and Mathematical Physics,
vol. 21, no. 3, International Press, 2017, pp. 683–738, doi:10.4310/ATMP.2017.v21.n3.a4.
short: P. Nam, M.M. Napiórkowski, Advances in Theoretical and Mathematical Physics
21 (2017) 683–738.
date_created: 2018-12-11T11:46:43Z
date_published: 2017-01-01T00:00:00Z
date_updated: 2021-01-12T08:00:58Z
day: '01'
department:
- _id: RoSe
doi: 10.4310/ATMP.2017.v21.n3.a4
ec_funded: 1
intvolume: ' 21'
issue: '3'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/1509.04631
month: '01'
oa: 1
oa_version: Submitted Version
page: 683 - 738
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: Advances in Theoretical and Mathematical Physics
publication_identifier:
issn:
- '10950761'
publication_status: published
publisher: International Press
publist_id: '7336'
quality_controlled: '1'
scopus_import: 1
status: public
title: Bogoliubov correction to the mean-field dynamics of interacting bosons
type: journal_article
user_id: 4435EBFC-F248-11E8-B48F-1D18A9856A87
volume: 21
year: '2017'
...
---
_id: '483'
abstract:
- lang: eng
text: We prove the universality for the eigenvalue gap statistics in the bulk of
the spectrum for band matrices, in the regime where the band width is comparable
with the dimension of the matrix, W ~ N. All previous results concerning universality
of non-Gaussian random matrices are for mean-field models. By relying on a new
mean-field reduction technique, we deduce universality from quantum unique ergodicity
for band matrices.
author:
- first_name: Paul
full_name: Bourgade, Paul
last_name: Bourgade
- first_name: László
full_name: Erdös, László
id: 4DBD5372-F248-11E8-B48F-1D18A9856A87
last_name: Erdös
orcid: 0000-0001-5366-9603
- first_name: Horng
full_name: Yau, Horng
last_name: Yau
- first_name: Jun
full_name: Yin, Jun
last_name: Yin
citation:
ama: Bourgade P, Erdös L, Yau H, Yin J. Universality for a class of random band
matrices. Advances in Theoretical and Mathematical Physics. 2017;21(3):739-800.
doi:10.4310/ATMP.2017.v21.n3.a5
apa: Bourgade, P., Erdös, L., Yau, H., & Yin, J. (2017). Universality for a
class of random band matrices. Advances in Theoretical and Mathematical Physics.
International Press. https://doi.org/10.4310/ATMP.2017.v21.n3.a5
chicago: Bourgade, Paul, László Erdös, Horng Yau, and Jun Yin. “Universality for
a Class of Random Band Matrices.” Advances in Theoretical and Mathematical
Physics. International Press, 2017. https://doi.org/10.4310/ATMP.2017.v21.n3.a5.
ieee: P. Bourgade, L. Erdös, H. Yau, and J. Yin, “Universality for a class of random
band matrices,” Advances in Theoretical and Mathematical Physics, vol.
21, no. 3. International Press, pp. 739–800, 2017.
ista: Bourgade P, Erdös L, Yau H, Yin J. 2017. Universality for a class of random
band matrices. Advances in Theoretical and Mathematical Physics. 21(3), 739–800.
mla: Bourgade, Paul, et al. “Universality for a Class of Random Band Matrices.”
Advances in Theoretical and Mathematical Physics, vol. 21, no. 3, International
Press, 2017, pp. 739–800, doi:10.4310/ATMP.2017.v21.n3.a5.
short: P. Bourgade, L. Erdös, H. Yau, J. Yin, Advances in Theoretical and Mathematical
Physics 21 (2017) 739–800.
date_created: 2018-12-11T11:46:43Z
date_published: 2017-08-25T00:00:00Z
date_updated: 2021-01-12T08:00:57Z
day: '25'
department:
- _id: LaEr
doi: 10.4310/ATMP.2017.v21.n3.a5
ec_funded: 1
intvolume: ' 21'
issue: '3'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/1602.02312
month: '08'
oa: 1
oa_version: Submitted Version
page: 739 - 800
project:
- _id: 258DCDE6-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '338804'
name: Random matrices, universality and disordered quantum systems
publication: Advances in Theoretical and Mathematical Physics
publication_identifier:
issn:
- '10950761'
publication_status: published
publisher: International Press
publist_id: '7337'
quality_controlled: '1'
scopus_import: 1
status: public
title: Universality for a class of random band matrices
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 21
year: '2017'
...
---
_id: '487'
abstract:
- lang: eng
text: In this paper we study network architecture for unlicensed cellular networking
for outdoor coverage in TV white spaces. The main technology proposed for TV white
spaces is 802.11af, a Wi-Fi variant adapted for TV frequencies. However, 802.11af
is originally designed for improved indoor propagation. We show that long links,
typical for outdoor use, exacerbate known Wi-Fi issues, such as hidden and exposed
terminal, and significantly reduce its efficiency. Instead, we propose CellFi,
an alternative architecture based on LTE. LTE is designed for long-range coverage
and throughput efficiency, but it is also designed to operate in tightly controlled
and centrally managed networks. CellFi overcomes these problems by designing an
LTE-compatible spectrum database component, mandatory for TV white space networking,
and introducing an interference management component for distributed coordination.
CellFi interference management is compatible with existing LTE mechanisms, requires
no explicit communication between base stations, and is more efficient than CSMA
for long links. We evaluate our design through extensive real world evaluation
on of-the-shelf LTE equipment and simulations. We show that, compared to 802.11af,
it increases coverage by 40% and reduces median flow completion times by 2.3x.
author:
- first_name: Ghufran
full_name: Baig, Ghufran
last_name: Baig
- first_name: Bozidar
full_name: Radunovic, Bozidar
last_name: Radunovic
- first_name: Dan-Adrian
full_name: Alistarh, Dan-Adrian
id: 4A899BFC-F248-11E8-B48F-1D18A9856A87
last_name: Alistarh
orcid: 0000-0003-3650-940X
- first_name: Matthew
full_name: Balkwill, Matthew
last_name: Balkwill
- first_name: Thomas
full_name: Karagiannis, Thomas
last_name: Karagiannis
- first_name: Lili
full_name: Qiu, Lili
last_name: Qiu
citation:
ama: 'Baig G, Radunovic B, Alistarh D-A, Balkwill M, Karagiannis T, Qiu L. Towards
unlicensed cellular networks in TV white spaces. In: Proceedings of the 2017
13th International Conference on Emerging Networking EXperiments and Technologies.
ACM; 2017:2-14. doi:10.1145/3143361.3143367'
apa: 'Baig, G., Radunovic, B., Alistarh, D.-A., Balkwill, M., Karagiannis, T., &
Qiu, L. (2017). Towards unlicensed cellular networks in TV white spaces. In Proceedings
of the 2017 13th International Conference on emerging Networking EXperiments and
Technologies (pp. 2–14). Incheon, South Korea: ACM. https://doi.org/10.1145/3143361.3143367'
chicago: Baig, Ghufran, Bozidar Radunovic, Dan-Adrian Alistarh, Matthew Balkwill,
Thomas Karagiannis, and Lili Qiu. “Towards Unlicensed Cellular Networks in TV
White Spaces.” In Proceedings of the 2017 13th International Conference on
Emerging Networking EXperiments and Technologies, 2–14. ACM, 2017. https://doi.org/10.1145/3143361.3143367.
ieee: G. Baig, B. Radunovic, D.-A. Alistarh, M. Balkwill, T. Karagiannis, and L.
Qiu, “Towards unlicensed cellular networks in TV white spaces,” in Proceedings
of the 2017 13th International Conference on emerging Networking EXperiments and
Technologies, Incheon, South Korea, 2017, pp. 2–14.
ista: 'Baig G, Radunovic B, Alistarh D-A, Balkwill M, Karagiannis T, Qiu L. 2017.
Towards unlicensed cellular networks in TV white spaces. Proceedings of the 2017
13th International Conference on emerging Networking EXperiments and Technologies.
CoNEXT: Conference on emerging Networking EXperiments and Technologies, 2–14.'
mla: Baig, Ghufran, et al. “Towards Unlicensed Cellular Networks in TV White Spaces.”
Proceedings of the 2017 13th International Conference on Emerging Networking
EXperiments and Technologies, ACM, 2017, pp. 2–14, doi:10.1145/3143361.3143367.
short: G. Baig, B. Radunovic, D.-A. Alistarh, M. Balkwill, T. Karagiannis, L. Qiu,
in:, Proceedings of the 2017 13th International Conference on Emerging Networking
EXperiments and Technologies, ACM, 2017, pp. 2–14.
conference:
end_date: 2017-12-15
location: Incheon, South Korea
name: 'CoNEXT: Conference on emerging Networking EXperiments and Technologies'
start_date: 2017-12-12
date_created: 2018-12-11T11:46:45Z
date_published: 2017-11-28T00:00:00Z
date_updated: 2023-02-23T12:21:11Z
day: '28'
department:
- _id: DaAl
doi: 10.1145/3143361.3143367
language:
- iso: eng
month: '11'
oa_version: None
page: 2 - 14
publication: Proceedings of the 2017 13th International Conference on emerging Networking
EXperiments and Technologies
publication_identifier:
isbn:
- 978-145035422-6
publication_status: published
publisher: ACM
publist_id: '7333'
quality_controlled: '1'
scopus_import: 1
status: public
title: Towards unlicensed cellular networks in TV white spaces
type: conference
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
year: '2017'
...
---
_id: '514'
abstract:
- lang: eng
text: 'Orientation in space is represented in specialized brain circuits. Persistent
head direction signals are transmitted from anterior thalamus to the presubiculum,
but the identity of the presubicular target neurons, their connectivity and function
in local microcircuits are unknown. Here, we examine how thalamic afferents recruit
presubicular principal neurons and Martinotti interneurons, and the ensuing synaptic
interactions between these cells. Pyramidal neuron activation of Martinotti cells
in superficial layers is strongly facilitating such that high-frequency head directional
stimulation efficiently unmutes synaptic excitation. Martinotti-cell feedback
plays a dual role: precisely timed spikes may not inhibit the firing of in-tune
head direction cells, while exerting lateral inhibition. Autonomous attractor
dynamics emerge from a modelled network implementing wiring motifs and timing
sensitive synaptic interactions in the pyramidal - Martinotti-cell feedback loop.
This inhibitory microcircuit is therefore tuned to refine and maintain head direction
information in the presubiculum.'
article_number: '16032'
author:
- first_name: Jean
full_name: Simonnet, Jean
last_name: Simonnet
- first_name: Mérie
full_name: Nassar, Mérie
last_name: Nassar
- first_name: Federico
full_name: Stella, Federico
id: 39AF1E74-F248-11E8-B48F-1D18A9856A87
last_name: Stella
orcid: 0000-0001-9439-3148
- first_name: Ivan
full_name: Cohen, Ivan
last_name: Cohen
- first_name: Bertrand
full_name: Mathon, Bertrand
last_name: Mathon
- first_name: Charlotte
full_name: Boccara, Charlotte
id: 3FC06552-F248-11E8-B48F-1D18A9856A87
last_name: Boccara
orcid: 0000-0001-7237-5109
- first_name: Richard
full_name: Miles, Richard
last_name: Miles
- first_name: Desdemona
full_name: Fricker, Desdemona
last_name: Fricker
citation:
ama: Simonnet J, Nassar M, Stella F, et al. Activity dependent feedback inhibition
may maintain head direction signals in mouse presubiculum. Nature Communications.
2017;8. doi:10.1038/ncomms16032
apa: Simonnet, J., Nassar, M., Stella, F., Cohen, I., Mathon, B., Boccara, C. N.,
… Fricker, D. (2017). Activity dependent feedback inhibition may maintain head
direction signals in mouse presubiculum. Nature Communications. Nature
Publishing Group. https://doi.org/10.1038/ncomms16032
chicago: Simonnet, Jean, Mérie Nassar, Federico Stella, Ivan Cohen, Bertrand Mathon,
Charlotte N. Boccara, Richard Miles, and Desdemona Fricker. “Activity Dependent
Feedback Inhibition May Maintain Head Direction Signals in Mouse Presubiculum.”
Nature Communications. Nature Publishing Group, 2017. https://doi.org/10.1038/ncomms16032.
ieee: J. Simonnet et al., “Activity dependent feedback inhibition may maintain
head direction signals in mouse presubiculum,” Nature Communications, vol.
8. Nature Publishing Group, 2017.
ista: Simonnet J, Nassar M, Stella F, Cohen I, Mathon B, Boccara CN, Miles R, Fricker
D. 2017. Activity dependent feedback inhibition may maintain head direction signals
in mouse presubiculum. Nature Communications. 8, 16032.
mla: Simonnet, Jean, et al. “Activity Dependent Feedback Inhibition May Maintain
Head Direction Signals in Mouse Presubiculum.” Nature Communications, vol.
8, 16032, Nature Publishing Group, 2017, doi:10.1038/ncomms16032.
short: J. Simonnet, M. Nassar, F. Stella, I. Cohen, B. Mathon, C.N. Boccara, R.
Miles, D. Fricker, Nature Communications 8 (2017).
date_created: 2018-12-11T11:46:54Z
date_published: 2017-07-01T00:00:00Z
date_updated: 2021-01-12T08:01:16Z
day: '01'
ddc:
- '571'
department:
- _id: JoCs
doi: 10.1038/ncomms16032
file:
- access_level: open_access
checksum: 76d8a2b72a58e56adb410ec37dfa7eee
content_type: application/pdf
creator: system
date_created: 2018-12-12T10:14:31Z
date_updated: 2020-07-14T12:46:36Z
file_id: '5083'
file_name: IST-2018-937-v1+1_2017_Stella_Activity_dependent.pdf
file_size: 2948357
relation: main_file
file_date_updated: 2020-07-14T12:46:36Z
has_accepted_license: '1'
intvolume: ' 8'
language:
- iso: eng
month: '07'
oa: 1
oa_version: Published Version
publication: Nature Communications
publication_identifier:
issn:
- '20411723'
publication_status: published
publisher: Nature Publishing Group
publist_id: '7305'
pubrep_id: '937'
quality_controlled: '1'
scopus_import: 1
status: public
title: Activity dependent feedback inhibition may maintain head direction signals
in mouse presubiculum
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 8
year: '2017'
...
---
_id: '515'
abstract:
- lang: eng
text: 'The oxidative phosphorylation electron transport chain (OXPHOS-ETC) of the
inner mitochondrial membrane is composed of five large protein complexes, named
CI-CV. These complexes convert energy from the food we eat into ATP, a small molecule
used to power a multitude of essential reactions throughout the cell. OXPHOS-ETC
complexes are organized into supercomplexes (SCs) of defined stoichiometry: CI
forms a supercomplex with CIII2 and CIV (SC I+III2+IV, known as the respirasome),
as well as with CIII2 alone (SC I+III2). CIII2 forms a supercomplex with CIV (SC
III2+IV) and CV forms dimers (CV2). Recent cryo-EM studies have revealed the structures
of SC I+III2+IV and SC I+III2. Furthermore, recent work has shed light on the
assembly and function of the SCs. Here we review and compare these recent studies
and discuss how they have advanced our understanding of mitochondrial electron
transport.'
article_type: original
author:
- first_name: James A
full_name: Letts, James A
id: 322DA418-F248-11E8-B48F-1D18A9856A87
last_name: Letts
orcid: 0000-0002-9864-3586
- first_name: Leonid A
full_name: Sazanov, Leonid A
id: 338D39FE-F248-11E8-B48F-1D18A9856A87
last_name: Sazanov
orcid: 0000-0002-0977-7989
citation:
ama: 'Letts JA, Sazanov LA. Clarifying the supercomplex: The higher-order organization
of the mitochondrial electron transport chain. Nature Structural and Molecular
Biology. 2017;24(10):800-808. doi:10.1038/nsmb.3460'
apa: 'Letts, J. A., & Sazanov, L. A. (2017). Clarifying the supercomplex: The
higher-order organization of the mitochondrial electron transport chain. Nature
Structural and Molecular Biology. Nature Publishing Group. https://doi.org/10.1038/nsmb.3460'
chicago: 'Letts, James A, and Leonid A Sazanov. “Clarifying the Supercomplex: The
Higher-Order Organization of the Mitochondrial Electron Transport Chain.” Nature
Structural and Molecular Biology. Nature Publishing Group, 2017. https://doi.org/10.1038/nsmb.3460.'
ieee: 'J. A. Letts and L. A. Sazanov, “Clarifying the supercomplex: The higher-order
organization of the mitochondrial electron transport chain,” Nature Structural
and Molecular Biology, vol. 24, no. 10. Nature Publishing Group, pp. 800–808,
2017.'
ista: 'Letts JA, Sazanov LA. 2017. Clarifying the supercomplex: The higher-order
organization of the mitochondrial electron transport chain. Nature Structural
and Molecular Biology. 24(10), 800–808.'
mla: 'Letts, James A., and Leonid A. Sazanov. “Clarifying the Supercomplex: The
Higher-Order Organization of the Mitochondrial Electron Transport Chain.” Nature
Structural and Molecular Biology, vol. 24, no. 10, Nature Publishing Group,
2017, pp. 800–08, doi:10.1038/nsmb.3460.'
short: J.A. Letts, L.A. Sazanov, Nature Structural and Molecular Biology 24 (2017)
800–808.
date_created: 2018-12-11T11:46:54Z
date_published: 2017-10-05T00:00:00Z
date_updated: 2021-01-12T08:01:17Z
day: '05'
ddc:
- '572'
department:
- _id: LeSa
doi: 10.1038/nsmb.3460
ec_funded: 1
file:
- access_level: open_access
checksum: 9bc7e8c41b43636dd7566289e511f096
content_type: application/pdf
creator: lsazanov
date_created: 2019-11-07T12:51:07Z
date_updated: 2020-07-14T12:46:36Z
file_id: '6993'
file_name: 29893_2_merged_1501257589_red.pdf
file_size: 4118385
relation: main_file
file_date_updated: 2020-07-14T12:46:36Z
has_accepted_license: '1'
intvolume: ' 24'
issue: '10'
language:
- iso: eng
month: '10'
oa: 1
oa_version: Submitted Version
page: 800 - 808
project:
- _id: 2590DB08-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '701309'
name: Atomic-Resolution Structures of Mitochondrial Respiratory Chain Supercomplexes
(H2020)
publication: Nature Structural and Molecular Biology
publication_identifier:
issn:
- '15459993'
publication_status: published
publisher: Nature Publishing Group
publist_id: '7304'
quality_controlled: '1'
scopus_import: 1
status: public
title: 'Clarifying the supercomplex: The higher-order organization of the mitochondrial
electron transport chain'
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 24
year: '2017'
...
---
_id: '513'
abstract:
- lang: eng
text: 'We present an experimental setup that creates a shear flow with zero mean
advection velocity achieved by counterbalancing the nonzero streamwise pressure
gradient by moving boundaries, which generates plane Couette-Poiseuille flow.
We obtain experimental results in the transitional regime for this flow. Using
flow visualization, we characterize the subcritical transition to turbulence in
Couette-Poiseuille flow and show the existence of turbulent spots generated by
a permanent perturbation. Due to the zero mean advection velocity of the base
profile, these turbulent structures are nearly stationary. We distinguish two
regions of the turbulent spot: the active turbulent core, which is characterized
by waviness of the streaks similar to traveling waves, and the surrounding region,
which includes in addition the weak undisturbed streaks and oblique waves at the
laminar-turbulent interface. We also study the dependence of the size of these
two regions on Reynolds number. Finally, we show that the traveling waves move
in the downstream (Poiseuille) direction.'
article_number: '043904'
author:
- first_name: Lukasz
full_name: Klotz, Lukasz
id: 2C9AF1C2-F248-11E8-B48F-1D18A9856A87
last_name: Klotz
orcid: 0000-0003-1740-7635
- first_name: Grégoire M
full_name: Lemoult, Grégoire M
id: 4787FE80-F248-11E8-B48F-1D18A9856A87
last_name: Lemoult
- first_name: Idalia
full_name: Frontczak, Idalia
last_name: Frontczak
- first_name: Laurette
full_name: Tuckerman, Laurette
last_name: Tuckerman
- first_name: José
full_name: Wesfreid, José
last_name: Wesfreid
citation:
ama: 'Klotz L, Lemoult GM, Frontczak I, Tuckerman L, Wesfreid J. Couette-Poiseuille
flow experiment with zero mean advection velocity: Subcritical transition to turbulence.
Physical Review Fluids. 2017;2(4). doi:10.1103/PhysRevFluids.2.043904'
apa: 'Klotz, L., Lemoult, G. M., Frontczak, I., Tuckerman, L., & Wesfreid, J.
(2017). Couette-Poiseuille flow experiment with zero mean advection velocity:
Subcritical transition to turbulence. Physical Review Fluids. American
Physical Society. https://doi.org/10.1103/PhysRevFluids.2.043904'
chicago: 'Klotz, Lukasz, Grégoire M Lemoult, Idalia Frontczak, Laurette Tuckerman,
and José Wesfreid. “Couette-Poiseuille Flow Experiment with Zero Mean Advection
Velocity: Subcritical Transition to Turbulence.” Physical Review Fluids.
American Physical Society, 2017. https://doi.org/10.1103/PhysRevFluids.2.043904.'
ieee: 'L. Klotz, G. M. Lemoult, I. Frontczak, L. Tuckerman, and J. Wesfreid, “Couette-Poiseuille
flow experiment with zero mean advection velocity: Subcritical transition to turbulence,”
Physical Review Fluids, vol. 2, no. 4. American Physical Society, 2017.'
ista: 'Klotz L, Lemoult GM, Frontczak I, Tuckerman L, Wesfreid J. 2017. Couette-Poiseuille
flow experiment with zero mean advection velocity: Subcritical transition to turbulence.
Physical Review Fluids. 2(4), 043904.'
mla: 'Klotz, Lukasz, et al. “Couette-Poiseuille Flow Experiment with Zero Mean Advection
Velocity: Subcritical Transition to Turbulence.” Physical Review Fluids,
vol. 2, no. 4, 043904, American Physical Society, 2017, doi:10.1103/PhysRevFluids.2.043904.'
short: L. Klotz, G.M. Lemoult, I. Frontczak, L. Tuckerman, J. Wesfreid, Physical
Review Fluids 2 (2017).
date_created: 2018-12-11T11:46:54Z
date_published: 2017-04-01T00:00:00Z
date_updated: 2021-01-12T08:01:16Z
day: '01'
department:
- _id: BjHo
doi: 10.1103/PhysRevFluids.2.043904
intvolume: ' 2'
issue: '4'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/1704.02619
month: '04'
oa: 1
oa_version: Preprint
publication: Physical Review Fluids
publication_status: published
publisher: American Physical Society
publist_id: '7306'
quality_controlled: '1'
scopus_import: 1
status: public
title: 'Couette-Poiseuille flow experiment with zero mean advection velocity: Subcritical
transition to turbulence'
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 2
year: '2017'
...
---
_id: '520'
abstract:
- lang: eng
text: Cyanobacteria are mostly engineered to be sustainable cell-factories by genetic
manipulations alone. Here, by modulating the concentration of allosteric effectors,
we focus on increasing product formation without further burdening the cells with
increased expression of enzymes. Resorting to a novel 96-well microplate cultivation
system for cyanobacteria, and using lactate-producing strains of Synechocystis
PCC6803 expressing different l-lactate dehydrogenases (LDH), we titrated the effect
of 2,5-anhydro-mannitol supplementation. The latter acts in cells as a nonmetabolizable
analogue of fructose 1,6-bisphosphate, a known allosteric regulator of one of
the tested LDHs. In this strain (SAA023), we achieved over 2-fold increase of
lactate productivity. Furthermore, we observed that as carbon is increasingly
deviated during growth toward product formation, there is an increased fixation
rate in the population of spontaneous mutants harboring an impaired production
pathway. This is a challenge in the development of green cell factories, which
may be countered by the incorporation in biotechnological processes of strategies
such as the one pioneered here.
article_type: letter_note
author:
- first_name: Wei
full_name: Du, Wei
last_name: Du
- first_name: Andreas
full_name: Angermayr, Andreas
id: 4677C796-F248-11E8-B48F-1D18A9856A87
last_name: Angermayr
orcid: 0000-0001-8619-2223
- first_name: Joeri
full_name: Jongbloets, Joeri
last_name: Jongbloets
- first_name: Douwe
full_name: Molenaar, Douwe
last_name: Molenaar
- first_name: Herwig
full_name: Bachmann, Herwig
last_name: Bachmann
- first_name: Klaas
full_name: Hellingwerf, Klaas
last_name: Hellingwerf
- first_name: Filipe
full_name: Branco Dos Santos, Filipe
last_name: Branco Dos Santos
citation:
ama: Du W, Angermayr A, Jongbloets J, et al. Nonhierarchical flux regulation exposes
the fitness burden associated with lactate production in Synechocystis sp. PCC6803.
ACS Synthetic Biology. 2017;6(3):395-401. doi:10.1021/acssynbio.6b00235
apa: Du, W., Angermayr, A., Jongbloets, J., Molenaar, D., Bachmann, H., Hellingwerf,
K., & Branco Dos Santos, F. (2017). Nonhierarchical flux regulation exposes
the fitness burden associated with lactate production in Synechocystis sp. PCC6803.
ACS Synthetic Biology. American Chemical Society. https://doi.org/10.1021/acssynbio.6b00235
chicago: Du, Wei, Andreas Angermayr, Joeri Jongbloets, Douwe Molenaar, Herwig Bachmann,
Klaas Hellingwerf, and Filipe Branco Dos Santos. “Nonhierarchical Flux Regulation
Exposes the Fitness Burden Associated with Lactate Production in Synechocystis
Sp. PCC6803.” ACS Synthetic Biology. American Chemical Society, 2017. https://doi.org/10.1021/acssynbio.6b00235.
ieee: W. Du et al., “Nonhierarchical flux regulation exposes the fitness
burden associated with lactate production in Synechocystis sp. PCC6803,” ACS
Synthetic Biology, vol. 6, no. 3. American Chemical Society, pp. 395–401,
2017.
ista: Du W, Angermayr A, Jongbloets J, Molenaar D, Bachmann H, Hellingwerf K, Branco
Dos Santos F. 2017. Nonhierarchical flux regulation exposes the fitness burden
associated with lactate production in Synechocystis sp. PCC6803. ACS Synthetic
Biology. 6(3), 395–401.
mla: Du, Wei, et al. “Nonhierarchical Flux Regulation Exposes the Fitness Burden
Associated with Lactate Production in Synechocystis Sp. PCC6803.” ACS Synthetic
Biology, vol. 6, no. 3, American Chemical Society, 2017, pp. 395–401, doi:10.1021/acssynbio.6b00235.
short: W. Du, A. Angermayr, J. Jongbloets, D. Molenaar, H. Bachmann, K. Hellingwerf,
F. Branco Dos Santos, ACS Synthetic Biology 6 (2017) 395–401.
date_created: 2018-12-11T11:46:56Z
date_published: 2017-03-17T00:00:00Z
date_updated: 2021-01-12T08:01:21Z
day: '17'
department:
- _id: ToBo
doi: 10.1021/acssynbio.6b00235
external_id:
pmid:
- '27936615'
intvolume: ' 6'
issue: '3'
language:
- iso: eng
month: '03'
oa_version: None
page: 395 - 401
pmid: 1
publication: ACS Synthetic Biology
publication_identifier:
issn:
- '21615063'
publication_status: published
publisher: American Chemical Society
publist_id: '7298'
quality_controlled: '1'
scopus_import: 1
status: public
title: Nonhierarchical flux regulation exposes the fitness burden associated with
lactate production in Synechocystis sp. PCC6803
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 6
year: '2017'
...
---
_id: '521'
abstract:
- lang: eng
text: Let X and Y be proper metric spaces. We show that a coarsely n-to-1 map f:X→Y
induces an n-to-1 map of Higson coronas. This viewpoint turns out to be successful
in showing that the classical dimension raising theorems hold in large scale;
that is, if f:X→Y is a coarsely n-to-1 map between proper metric spaces X and
Y then asdim(Y)≤asdim(X)+n−1. Furthermore we introduce coarsely open coarsely
n-to-1 maps, which include the natural quotient maps via a finite group action,
and prove that they preserve the asymptotic dimension.
author:
- first_name: Kyle
full_name: Austin, Kyle
last_name: Austin
- first_name: Ziga
full_name: Virk, Ziga
id: 2E36B656-F248-11E8-B48F-1D18A9856A87
last_name: Virk
citation:
ama: Austin K, Virk Z. Higson compactification and dimension raising. Topology
and its Applications. 2017;215:45-57. doi:10.1016/j.topol.2016.10.005
apa: Austin, K., & Virk, Z. (2017). Higson compactification and dimension raising.
Topology and Its Applications. Elsevier. https://doi.org/10.1016/j.topol.2016.10.005
chicago: Austin, Kyle, and Ziga Virk. “Higson Compactification and Dimension Raising.”
Topology and Its Applications. Elsevier, 2017. https://doi.org/10.1016/j.topol.2016.10.005.
ieee: K. Austin and Z. Virk, “Higson compactification and dimension raising,” Topology
and its Applications, vol. 215. Elsevier, pp. 45–57, 2017.
ista: Austin K, Virk Z. 2017. Higson compactification and dimension raising. Topology
and its Applications. 215, 45–57.
mla: Austin, Kyle, and Ziga Virk. “Higson Compactification and Dimension Raising.”
Topology and Its Applications, vol. 215, Elsevier, 2017, pp. 45–57, doi:10.1016/j.topol.2016.10.005.
short: K. Austin, Z. Virk, Topology and Its Applications 215 (2017) 45–57.
date_created: 2018-12-11T11:46:56Z
date_published: 2017-01-01T00:00:00Z
date_updated: 2021-01-12T08:01:21Z
day: '01'
department:
- _id: HeEd
doi: 10.1016/j.topol.2016.10.005
intvolume: ' 215'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/1608.03954v1
month: '01'
oa: 1
oa_version: Submitted Version
page: 45 - 57
publication: Topology and its Applications
publication_identifier:
issn:
- '01668641'
publication_status: published
publisher: Elsevier
publist_id: '7299'
quality_controlled: '1'
status: public
title: Higson compactification and dimension raising
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 215
year: '2017'
...
---
_id: '525'
abstract:
- lang: eng
text: 'The Casparian strip is an important barrier regulating water and nutrient
uptake into root tissues. New research reveals two peptide signals and their co-receptors
play critical roles patterning and maintaining barrier integrity. '
acknowledgement: "Biotechnology and Biological Sciences Research Council:\tBBSRC BB/M001806/1
and BB/H020314/1\t"
author:
- first_name: Daniel
full_name: Daniel von Wangenheim
id: 49E91952-F248-11E8-B48F-1D18A9856A87
last_name: Von Wangenheim
orcid: 0000-0002-6862-1247
- first_name: Tatsuaki
full_name: Goh, Tatsuaki
last_name: Goh
- first_name: Daniela
full_name: Dietrich, Daniela
last_name: Dietrich
- first_name: Malcolm
full_name: Bennett, Malcolm J
last_name: Bennett
citation:
ama: 'von Wangenheim D, Goh T, Dietrich D, Bennett M. Plant biology: Building barriers…
in roots. Current Biology. 2017;27(5):R172-R174. doi:10.1016/j.cub.2017.01.060'
apa: 'von Wangenheim, D., Goh, T., Dietrich, D., & Bennett, M. (2017). Plant
biology: Building barriers… in roots. Current Biology. Cell Press. https://doi.org/10.1016/j.cub.2017.01.060'
chicago: 'Wangenheim, Daniel von, Tatsuaki Goh, Daniela Dietrich, and Malcolm Bennett.
“Plant Biology: Building Barriers… in Roots.” Current Biology. Cell Press,
2017. https://doi.org/10.1016/j.cub.2017.01.060.'
ieee: 'D. von Wangenheim, T. Goh, D. Dietrich, and M. Bennett, “Plant biology: Building
barriers… in roots,” Current Biology, vol. 27, no. 5. Cell Press, pp. R172–R174,
2017.'
ista: 'von Wangenheim D, Goh T, Dietrich D, Bennett M. 2017. Plant biology: Building
barriers… in roots. Current Biology. 27(5), R172–R174.'
mla: 'von Wangenheim, Daniel, et al. “Plant Biology: Building Barriers… in Roots.”
Current Biology, vol. 27, no. 5, Cell Press, 2017, pp. R172–74, doi:10.1016/j.cub.2017.01.060.'
short: D. von Wangenheim, T. Goh, D. Dietrich, M. Bennett, Current Biology 27 (2017)
R172–R174.
date_created: 2018-12-11T11:46:58Z
date_published: 2017-03-06T00:00:00Z
date_updated: 2021-01-12T08:01:23Z
day: '06'
doi: 10.1016/j.cub.2017.01.060
extern: 1
file:
- access_level: open_access
checksum: 81fd4475c5a2a2c6f4313beeab215ed9
content_type: application/pdf
creator: system
date_created: 2018-12-12T10:18:11Z
date_updated: 2020-07-14T12:46:38Z
file_id: '5330'
file_name: IST-2018-983-v1+1_Plant_biology_Building_barriers__in_roots.pdf
file_size: 2840413
relation: main_file
file_date_updated: 2020-07-14T12:46:38Z
intvolume: ' 27'
issue: '5'
main_file_link:
- open_access: '1'
url: https://repository.ist.ac.at/id/eprint/983
month: '03'
oa: 1
page: R172 - R174
publication: Current Biology
publication_status: published
publisher: Cell Press
publist_id: '7294'
pubrep_id: '983'
quality_controlled: 0
status: public
title: 'Plant biology: Building barriers… in roots'
type: journal_article
volume: 27
year: '2017'
...
---
_id: '529'
abstract:
- lang: eng
text: The pituitary adenylyl cyclase-activating polypeptide (PACAP) and its G protein-coupled
receptors, PAC1, VPAC1 and VPAC2 form a system involved in a variety of biological
processes. Although some sympathetic stimulatory effects of this system have been
reported, its central cardiovascular regulatory properties are poorly characterized.
VPAC1 receptors are expressed in the nucleus ambiguus (nAmb), a key center controlling
cardiac parasympathetic tone. In this study, we report that selective VPAC1 activation
in rhodamine-labeled cardiac vagal preganglionic neurons of the rat nAmb produces
inositol 1,4,5-trisphosphate receptor-mediated Ca2+ mobilization, membrane depolarization
and activation of P/Q-type Ca2+ channels. In vivo, this pathway converges onto
transient reduction in heart rate of conscious rats. Therefore we demonstrate
a VPAC1-dependent mechanism in the central parasympathetic regulation of the heart
rate, adding to the complexity of PACAP-mediated cardiovascular modulation.
acknowledgement: This study was supported by startup funds from the Jefferson College
of Pharmacy, and by the National Institutes of Health DA023204 (to M.E.A) and P30
DA 013429 to Center for Substance Abuse Research, Temple University.
author:
- first_name: Florin
full_name: Gherghina, Florin L
last_name: Gherghina
- first_name: Andrei
full_name: Tica, Andrei A
last_name: Tica
- first_name: Elena
full_name: Elena Deliu
id: 37A40D7E-F248-11E8-B48F-1D18A9856A87
last_name: Deliu
orcid: 0000-0002-7370-5293
- first_name: Mary
full_name: Abood, Mary E
last_name: Abood
- first_name: G.
full_name: Brailoiu, G. Christina
last_name: Brailoiu
- first_name: Eugen
full_name: Brǎiloiu, Eugen
last_name: Brǎiloiu
citation:
ama: Gherghina F, Tica A, Deliu E, Abood M, Brailoiu G, Brǎiloiu E. Effects of VPAC1
activation in nucleus ambiguus neurons. Brain Research. 2017;1657:297-303.
doi:10.1016/j.brainres.2016.12.026
apa: Gherghina, F., Tica, A., Deliu, E., Abood, M., Brailoiu, G., & Brǎiloiu,
E. (2017). Effects of VPAC1 activation in nucleus ambiguus neurons. Brain Research.
Elsevier. https://doi.org/10.1016/j.brainres.2016.12.026
chicago: Gherghina, Florin, Andrei Tica, Elena Deliu, Mary Abood, G. Brailoiu, and
Eugen Brǎiloiu. “Effects of VPAC1 Activation in Nucleus Ambiguus Neurons.” Brain
Research. Elsevier, 2017. https://doi.org/10.1016/j.brainres.2016.12.026.
ieee: F. Gherghina, A. Tica, E. Deliu, M. Abood, G. Brailoiu, and E. Brǎiloiu, “Effects
of VPAC1 activation in nucleus ambiguus neurons,” Brain Research, vol.
1657. Elsevier, pp. 297–303, 2017.
ista: Gherghina F, Tica A, Deliu E, Abood M, Brailoiu G, Brǎiloiu E. 2017. Effects
of VPAC1 activation in nucleus ambiguus neurons. Brain Research. 1657, 297–303.
mla: Gherghina, Florin, et al. “Effects of VPAC1 Activation in Nucleus Ambiguus
Neurons.” Brain Research, vol. 1657, Elsevier, 2017, pp. 297–303, doi:10.1016/j.brainres.2016.12.026.
short: F. Gherghina, A. Tica, E. Deliu, M. Abood, G. Brailoiu, E. Brǎiloiu, Brain
Research 1657 (2017) 297–303.
date_created: 2018-12-11T11:46:59Z
date_published: 2017-02-15T00:00:00Z
date_updated: 2021-01-12T08:01:26Z
day: '15'
doi: 10.1016/j.brainres.2016.12.026
extern: 1
intvolume: ' 1657'
month: '02'
page: 297 - 303
publication: Brain Research
publication_status: published
publisher: Elsevier
publist_id: '7290'
quality_controlled: 0
status: public
title: Effects of VPAC1 activation in nucleus ambiguus neurons
type: journal_article
volume: 1657
year: '2017'
...
---
_id: '534'
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.
article_processing_charge: No
article_type: original
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.
Discrete & Computational Geometry. 2017;58(4):871-888. doi:10.1007/s00454-017-9900-0
apa: Burton, B., de Mesmay, A. N., & Wagner, U. (2017). Finding non-orientable
surfaces in 3-Manifolds. Discrete & Computational Geometry. Springer.
https://doi.org/10.1007/s00454-017-9900-0
chicago: Burton, Benjamin, Arnaud N de Mesmay, and Uli Wagner. “Finding Non-Orientable
Surfaces in 3-Manifolds.” Discrete & Computational Geometry. Springer,
2017. https://doi.org/10.1007/s00454-017-9900-0.
ieee: B. Burton, A. N. de Mesmay, and U. Wagner, “Finding non-orientable surfaces
in 3-Manifolds,” Discrete & Computational Geometry, vol. 58, no. 4.
Springer, pp. 871–888, 2017.
ista: Burton B, de Mesmay AN, Wagner U. 2017. Finding non-orientable surfaces in
3-Manifolds. Discrete & Computational Geometry. 58(4), 871–888.
mla: Burton, Benjamin, et al. “Finding Non-Orientable Surfaces in 3-Manifolds.”
Discrete & Computational Geometry, vol. 58, no. 4, Springer, 2017,
pp. 871–88, doi:10.1007/s00454-017-9900-0.
short: B. Burton, A.N. de Mesmay, U. Wagner, Discrete & Computational Geometry
58 (2017) 871–888.
date_created: 2018-12-11T11:47:01Z
date_published: 2017-06-09T00:00:00Z
date_updated: 2023-02-21T17:01:34Z
day: '09'
department:
- _id: UlWa
doi: 10.1007/s00454-017-9900-0
external_id:
arxiv:
- '1602.07907'
intvolume: ' 58'
issue: '4'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/1602.07907
month: '06'
oa: 1
oa_version: Preprint
page: 871 - 888
publication: Discrete & Computational Geometry
publication_identifier:
issn:
- '01795376'
publication_status: published
publisher: Springer
publist_id: '7283'
quality_controlled: '1'
related_material:
record:
- id: '1379'
relation: earlier_version
status: public
scopus_import: 1
status: public
title: Finding non-orientable surfaces in 3-Manifolds
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 58
year: '2017'
...
---
_id: '538'
abstract:
- lang: ger
text: 'Optogenetik und Photopharmakologie ermöglichen präzise räumliche und zeitliche
Kontrolle von Proteinwechselwirkung und -funktion in Zellen und Tieren. Optogenetische
Methoden, die auf grünes Licht ansprechen und zum Trennen von Proteinkomplexen
geeignet sind, sind nichtweitläufig verfügbar, würden jedoch mehrfarbige Experimente
zur Beantwortung von biologischen Fragestellungen ermöglichen. Hier demonstrieren
wir die Verwendung von Cobalamin(Vitamin B12)-bindenden Domänen von bakteriellen
CarH-Transkriptionsfaktoren zur Grünlicht-induzierten Dissoziation von Rezeptoren.
Fusioniert mit dem Fibroblasten-W achstumsfaktor-Rezeptor 1 führten diese im Dunkeln
in kultivierten Zellen zu Signalaktivität durch Oligomerisierung, welche durch
Beleuchten umgehend aufgehoben wurde. In Zebrafischembryonen, die einen derartigen
Rezeptor exprimieren, ermöglichte grünes Licht die Kontrolle über abnormale Signalaktivität
während der Embryonalentwicklung. '
author:
- first_name: Stephanie
full_name: Kainrath, Stephanie
id: 32CFBA64-F248-11E8-B48F-1D18A9856A87
last_name: Kainrath
- first_name: Manuela
full_name: Stadler, Manuela
last_name: Stadler
- first_name: Eva
full_name: Gschaider-Reichhart, Eva
id: 3FEE232A-F248-11E8-B48F-1D18A9856A87
last_name: Gschaider-Reichhart
orcid: 0000-0002-7218-7738
- first_name: Martin
full_name: Distel, Martin
last_name: Distel
- first_name: Harald L
full_name: Janovjak, Harald L
id: 33BA6C30-F248-11E8-B48F-1D18A9856A87
last_name: Janovjak
orcid: 0000-0002-8023-9315
citation:
ama: Kainrath S, Stadler M, Gschaider-Reichhart E, Distel M, Janovjak HL. Grünlicht-induzierte
Rezeptorinaktivierung durch Cobalamin-bindende Domänen. Angewandte Chemie.
2017;129(16):4679-4682. doi:10.1002/ange.201611998
apa: Kainrath, S., Stadler, M., Gschaider-Reichhart, E., Distel, M., & Janovjak,
H. L. (2017). Grünlicht-induzierte Rezeptorinaktivierung durch Cobalamin-bindende
Domänen. Angewandte Chemie. Wiley. https://doi.org/10.1002/ange.201611998
chicago: Kainrath, Stephanie, Manuela Stadler, Eva Gschaider-Reichhart, Martin Distel,
and Harald L Janovjak. “Grünlicht-Induzierte Rezeptorinaktivierung Durch Cobalamin-Bindende
Domänen.” Angewandte Chemie. Wiley, 2017. https://doi.org/10.1002/ange.201611998.
ieee: S. Kainrath, M. Stadler, E. Gschaider-Reichhart, M. Distel, and H. L. Janovjak,
“Grünlicht-induzierte Rezeptorinaktivierung durch Cobalamin-bindende Domänen,”
Angewandte Chemie, vol. 129, no. 16. Wiley, pp. 4679–4682, 2017.
ista: Kainrath S, Stadler M, Gschaider-Reichhart E, Distel M, Janovjak HL. 2017.
Grünlicht-induzierte Rezeptorinaktivierung durch Cobalamin-bindende Domänen. Angewandte
Chemie. 129(16), 4679–4682.
mla: Kainrath, Stephanie, et al. “Grünlicht-Induzierte Rezeptorinaktivierung Durch
Cobalamin-Bindende Domänen.” Angewandte Chemie, vol. 129, no. 16, Wiley,
2017, pp. 4679–82, doi:10.1002/ange.201611998.
short: S. Kainrath, M. Stadler, E. Gschaider-Reichhart, M. Distel, H.L. Janovjak,
Angewandte Chemie 129 (2017) 4679–4682.
date_created: 2018-12-11T11:47:02Z
date_published: 2017-05-20T00:00:00Z
date_updated: 2021-01-12T08:01:33Z
day: '20'
ddc:
- '571'
department:
- _id: CaGu
- _id: HaJa
doi: 10.1002/ange.201611998
ec_funded: 1
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month: '05'
oa: 1
oa_version: Published Version
page: 4679 - 4682
project:
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call_identifier: FP7
grant_number: '303564'
name: Microbial Ion Channels for Synthetic Neurobiology
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call_identifier: FWF
grant_number: W1232-B24
name: Molecular Drug Targets
publication: Angewandte Chemie
publication_status: published
publisher: Wiley
publist_id: '7279'
pubrep_id: '932'
quality_controlled: '1'
status: public
title: Grünlicht-induzierte Rezeptorinaktivierung durch Cobalamin-bindende Domänen
tmp:
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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: 129
year: '2017'
...
---
_id: '540'
abstract:
- lang: eng
text: RNA-dependent RNA polymerases (RdRps) play a key role in the life cycle of
RNA viruses and impact their immunobiology. The arenavirus lymphocytic choriomeningitis
virus (LCMV) strain Clone 13 provides a benchmark model for studying chronic infection.
A major genetic determinant for its ability to persist maps to a single amino
acid exchange in the viral L protein, which exhibits RdRp activity, yet its functional
consequences remain elusive. To unravel the L protein interactions with the host
proteome, we engineered infectious L protein-tagged LCMV virions by reverse genetics.
A subsequent mass-spectrometric analysis of L protein pulldowns from infected
human cells revealed a comprehensive network of interacting host proteins. The
obtained LCMV L protein interactome was bioinformatically integrated with known
host protein interactors of RdRps from other RNA viruses, emphasizing interconnected
modules of human proteins. Functional characterization of selected interactors
highlighted proviral (DDX3X) as well as antiviral (NKRF, TRIM21) host factors.
To corroborate these findings, we infected Trim21-/-mice with LCMV and found impaired
virus control in chronic infection. These results provide insights into the complex
interactions of the arenavirus LCMV and other viral RdRps with the host proteome
and contribute to a better molecular understanding of how chronic viruses interact
with their host.
article_number: e1006758
author:
- first_name: Kseniya
full_name: Khamina, Kseniya
last_name: Khamina
- first_name: Alexander
full_name: Lercher, Alexander
last_name: Lercher
- first_name: Michael
full_name: Caldera, Michael
last_name: Caldera
- first_name: Christopher
full_name: Schliehe, Christopher
last_name: Schliehe
- first_name: Bojan
full_name: Vilagos, Bojan
last_name: Vilagos
- first_name: Mehmet
full_name: Sahin, Mehmet
last_name: Sahin
- first_name: Lindsay
full_name: Kosack, Lindsay
last_name: Kosack
- first_name: Anannya
full_name: Bhattacharya, Anannya
last_name: Bhattacharya
- first_name: Peter
full_name: Májek, Peter
last_name: Májek
- first_name: Alexey
full_name: Stukalov, Alexey
last_name: Stukalov
- first_name: Roberto
full_name: Sacco, Roberto
id: 42C9F57E-F248-11E8-B48F-1D18A9856A87
last_name: Sacco
- first_name: Leo
full_name: James, Leo
last_name: James
- first_name: Daniel
full_name: Pinschewer, Daniel
last_name: Pinschewer
- first_name: Keiryn
full_name: Bennett, Keiryn
last_name: Bennett
- first_name: Jörg
full_name: Menche, Jörg
last_name: Menche
- first_name: Andreas
full_name: Bergthaler, Andreas
last_name: Bergthaler
citation:
ama: Khamina K, Lercher A, Caldera M, et al. Characterization of host proteins interacting
with the lymphocytic choriomeningitis virus L protein. PLoS Pathogens.
2017;13(12). doi:10.1371/journal.ppat.1006758
apa: Khamina, K., Lercher, A., Caldera, M., Schliehe, C., Vilagos, B., Sahin, M.,
… Bergthaler, A. (2017). Characterization of host proteins interacting with the
lymphocytic choriomeningitis virus L protein. PLoS Pathogens. Public Library
of Science. https://doi.org/10.1371/journal.ppat.1006758
chicago: Khamina, Kseniya, Alexander Lercher, Michael Caldera, Christopher Schliehe,
Bojan Vilagos, Mehmet Sahin, Lindsay Kosack, et al. “Characterization of Host
Proteins Interacting with the Lymphocytic Choriomeningitis Virus L Protein.” PLoS
Pathogens. Public Library of Science, 2017. https://doi.org/10.1371/journal.ppat.1006758.
ieee: K. Khamina et al., “Characterization of host proteins interacting with
the lymphocytic choriomeningitis virus L protein,” PLoS Pathogens, vol.
13, no. 12. Public Library of Science, 2017.
ista: Khamina K, Lercher A, Caldera M, Schliehe C, Vilagos B, Sahin M, Kosack L,
Bhattacharya A, Májek P, Stukalov A, Sacco R, James L, Pinschewer D, Bennett K,
Menche J, Bergthaler A. 2017. Characterization of host proteins interacting with
the lymphocytic choriomeningitis virus L protein. PLoS Pathogens. 13(12), e1006758.
mla: Khamina, Kseniya, et al. “Characterization of Host Proteins Interacting with
the Lymphocytic Choriomeningitis Virus L Protein.” PLoS Pathogens, vol.
13, no. 12, e1006758, Public Library of Science, 2017, doi:10.1371/journal.ppat.1006758.
short: K. Khamina, A. Lercher, M. Caldera, C. Schliehe, B. Vilagos, M. Sahin, L.
Kosack, A. Bhattacharya, P. Májek, A. Stukalov, R. Sacco, L. James, D. Pinschewer,
K. Bennett, J. Menche, A. Bergthaler, PLoS Pathogens 13 (2017).
date_created: 2018-12-11T11:47:03Z
date_published: 2017-12-01T00:00:00Z
date_updated: 2021-01-12T08:01:48Z
day: '01'
ddc:
- '576'
- '616'
department:
- _id: GaNo
doi: 10.1371/journal.ppat.1006758
file:
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checksum: 1aa20f19a1e90664fadce6e7d5284fdc
content_type: application/pdf
creator: system
date_created: 2018-12-12T10:12:26Z
date_updated: 2020-07-14T12:46:44Z
file_id: '4944'
file_name: IST-2018-931-v1+1_journal.ppat.1006758.pdf
file_size: 4106772
relation: main_file
file_date_updated: 2020-07-14T12:46:44Z
has_accepted_license: '1'
intvolume: ' 13'
issue: '12'
language:
- iso: eng
month: '12'
oa: 1
oa_version: Published Version
publication: PLoS Pathogens
publication_identifier:
issn:
- '15537366'
publication_status: published
publisher: Public Library of Science
publist_id: '7276'
pubrep_id: '931'
quality_controlled: '1'
scopus_import: 1
status: public
title: Characterization of host proteins interacting with the lymphocytic choriomeningitis
virus L protein
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 13
year: '2017'
...
---
_id: '466'
abstract:
- lang: eng
text: 'We consider Markov decision processes (MDPs) with multiple limit-average
(or mean-payoff) objectives. There exist two different views: (i) the expectation
semantics, where the goal is to optimize the expected mean-payoff objective, and
(ii) the satisfaction semantics, where the goal is to maximize the probability
of runs such that the mean-payoff value stays above a given vector. We consider
optimization with respect to both objectives at once, thus unifying the existing
semantics. Precisely, the goal is to optimize the expectation while ensuring the
satisfaction constraint. Our problem captures the notion of optimization with
respect to strategies that are risk-averse (i.e., ensure certain probabilistic
guarantee). Our main results are as follows: First, we present algorithms for
the decision problems which are always polynomial in the size of the MDP. We also
show that an approximation of the Pareto-curve can be computed in time polynomial
in the size of the MDP, and the approximation factor, but exponential in the number
of dimensions. Second, we present a complete characterization of the strategy
complexity (in terms of memory bounds and randomization) required to solve our
problem. '
article_number: '15'
author:
- first_name: Krishnendu
full_name: Chatterjee, Krishnendu
id: 2E5DCA20-F248-11E8-B48F-1D18A9856A87
last_name: Chatterjee
orcid: 0000-0002-4561-241X
- first_name: Zuzana
full_name: Křetínská, Zuzana
last_name: Křetínská
- first_name: Jan
full_name: Kretinsky, Jan
id: 44CEF464-F248-11E8-B48F-1D18A9856A87
last_name: Kretinsky
orcid: 0000-0002-8122-2881
citation:
ama: Chatterjee K, Křetínská Z, Kretinsky J. Unifying two views on multiple mean-payoff
objectives in Markov decision processes. Logical Methods in Computer Science.
2017;13(2). doi:10.23638/LMCS-13(2:15)2017
apa: Chatterjee, K., Křetínská, Z., & Kretinsky, J. (2017). Unifying two views
on multiple mean-payoff objectives in Markov decision processes. Logical Methods
in Computer Science. International Federation of Computational Logic. https://doi.org/10.23638/LMCS-13(2:15)2017
chicago: Chatterjee, Krishnendu, Zuzana Křetínská, and Jan Kretinsky. “Unifying
Two Views on Multiple Mean-Payoff Objectives in Markov Decision Processes.” Logical
Methods in Computer Science. International Federation of Computational Logic,
2017. https://doi.org/10.23638/LMCS-13(2:15)2017.
ieee: K. Chatterjee, Z. Křetínská, and J. Kretinsky, “Unifying two views on multiple
mean-payoff objectives in Markov decision processes,” Logical Methods in Computer
Science, vol. 13, no. 2. International Federation of Computational Logic,
2017.
ista: Chatterjee K, Křetínská Z, Kretinsky J. 2017. Unifying two views on multiple
mean-payoff objectives in Markov decision processes. Logical Methods in Computer
Science. 13(2), 15.
mla: Chatterjee, Krishnendu, et al. “Unifying Two Views on Multiple Mean-Payoff
Objectives in Markov Decision Processes.” Logical Methods in Computer Science,
vol. 13, no. 2, 15, International Federation of Computational Logic, 2017, doi:10.23638/LMCS-13(2:15)2017.
short: K. Chatterjee, Z. Křetínská, J. Kretinsky, Logical Methods in Computer Science
13 (2017).
date_created: 2018-12-11T11:46:38Z
date_published: 2017-07-03T00:00:00Z
date_updated: 2023-02-23T12:26:16Z
day: '03'
ddc:
- '004'
department:
- _id: KrCh
doi: 10.23638/LMCS-13(2:15)2017
ec_funded: 1
file:
- access_level: open_access
checksum: bfa405385ec6229ad5ead89ab5751639
content_type: application/pdf
creator: system
date_created: 2018-12-12T10:18:32Z
date_updated: 2020-07-14T12:46:33Z
file_id: '5354'
file_name: IST-2018-957-v1+1_2017_Chatterjee_Unifying_two.pdf
file_size: 511832
relation: main_file
file_date_updated: 2020-07-14T12:46:33Z
has_accepted_license: '1'
intvolume: ' 13'
issue: '2'
language:
- iso: eng
license: https://creativecommons.org/licenses/by-nd/4.0/
month: '07'
oa: 1
oa_version: Published Version
project:
- _id: 25681D80-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '291734'
name: International IST Postdoc Fellowship Programme
- _id: 2584A770-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: P 23499-N23
name: Modern Graph Algorithmic Techniques in Formal Verification
- _id: 2581B60A-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '279307'
name: 'Quantitative Graph Games: Theory and Applications'
- _id: 2590DB08-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '701309'
name: Atomic-Resolution Structures of Mitochondrial Respiratory Chain Supercomplexes
(H2020)
publication: Logical Methods in Computer Science
publication_identifier:
issn:
- '18605974'
publication_status: published
publisher: International Federation of Computational Logic
publist_id: '7355'
pubrep_id: '957'
quality_controlled: '1'
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relation: earlier_version
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relation: earlier_version
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relation: earlier_version
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scopus_import: 1
status: public
title: Unifying two views on multiple mean-payoff objectives in Markov decision processes
tmp:
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legal_code_url: https://creativecommons.org/licenses/by-nd/4.0/legalcode
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short: CC BY-ND (4.0)
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 13
year: '2017'
...
---
_id: '467'
abstract:
- lang: eng
text: Recently there has been a significant effort to handle quantitative properties
in formal verification and synthesis. While weighted automata over finite and
infinite words provide a natural and flexible framework to express quantitative
properties, perhaps surprisingly, some basic system properties such as average
response time cannot be expressed using weighted automata or in any other known
decidable formalism. In this work, we introduce nested weighted automata as a
natural extension of weighted automata, which makes it possible to express important
quantitative properties such as average response time. In nested weighted automata,
a master automaton spins off and collects results from weighted slave automata,
each of which computes a quantity along a finite portion of an infinite word.
Nested weighted automata can be viewed as the quantitative analogue of monitor
automata, which are used in runtime verification. We establish an almost-complete
decidability picture for the basic decision problems about nested weighted automata
and illustrate their applicability in several domains. In particular, nested weighted
automata can be used to decide average response time properties.
article_number: '31'
author:
- first_name: Krishnendu
full_name: Chatterjee, Krishnendu
id: 2E5DCA20-F248-11E8-B48F-1D18A9856A87
last_name: Chatterjee
orcid: 0000-0002-4561-241X
- 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
citation:
ama: Chatterjee K, Henzinger TA, Otop J. Nested weighted automata. ACM Transactions
on Computational Logic (TOCL). 2017;18(4). doi:10.1145/3152769
apa: Chatterjee, K., Henzinger, T. A., & Otop, J. (2017). Nested weighted automata.
ACM Transactions on Computational Logic (TOCL). ACM. https://doi.org/10.1145/3152769
chicago: Chatterjee, Krishnendu, Thomas A Henzinger, and Jan Otop. “Nested Weighted
Automata.” ACM Transactions on Computational Logic (TOCL). ACM, 2017. https://doi.org/10.1145/3152769.
ieee: K. Chatterjee, T. A. Henzinger, and J. Otop, “Nested weighted automata,” ACM
Transactions on Computational Logic (TOCL), vol. 18, no. 4. ACM, 2017.
ista: Chatterjee K, Henzinger TA, Otop J. 2017. Nested weighted automata. ACM Transactions
on Computational Logic (TOCL). 18(4), 31.
mla: Chatterjee, Krishnendu, et al. “Nested Weighted Automata.” ACM Transactions
on Computational Logic (TOCL), vol. 18, no. 4, 31, ACM, 2017, doi:10.1145/3152769.
short: K. Chatterjee, T.A. Henzinger, J. Otop, ACM Transactions on Computational
Logic (TOCL) 18 (2017).
date_created: 2018-12-11T11:46:38Z
date_published: 2017-12-01T00:00:00Z
date_updated: 2023-02-23T12:26:19Z
day: '01'
department:
- _id: KrCh
- _id: ToHe
doi: 10.1145/3152769
ec_funded: 1
external_id:
arxiv:
- '1606.03598'
intvolume: ' 18'
issue: '4'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/1606.03598
month: '12'
oa: 1
oa_version: Preprint
project:
- _id: 25832EC2-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: S 11407_N23
name: Rigorous Systems Engineering
- _id: 25F42A32-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: Z211
name: The Wittgenstein Prize
- _id: 2584A770-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: P 23499-N23
name: Modern Graph Algorithmic Techniques in Formal Verification
- _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: ACM Transactions on Computational Logic (TOCL)
publication_identifier:
issn:
- '15293785'
publication_status: published
publisher: ACM
publist_id: '7354'
quality_controlled: '1'
related_material:
record:
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relation: earlier_version
status: public
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relation: earlier_version
status: public
scopus_import: 1
status: public
title: Nested weighted automata
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 18
year: '2017'
...
---
_id: '465'
abstract:
- lang: eng
text: 'The edit distance between two words w 1 , w 2 is the minimal number of word
operations (letter insertions, deletions, and substitutions) necessary to transform
w 1 to w 2 . The edit distance generalizes to languages L 1 , L 2 , where the
edit distance from L 1 to L 2 is the minimal number k such that for every word
from L 1 there exists a word in L 2 with edit distance at most k . We study the
edit distance computation problem between pushdown automata and their subclasses.
The problem of computing edit distance to a pushdown automaton is undecidable,
and in practice, the interesting question is to compute the edit distance from
a pushdown automaton (the implementation, a standard model for programs with recursion)
to a regular language (the specification). In this work, we present a complete
picture of decidability and complexity for the following problems: (1) deciding
whether, for a given threshold k , the edit distance from a pushdown automaton
to a finite automaton is at most k , and (2) deciding whether the edit distance
from a pushdown automaton to a finite automaton is finite. '
author:
- first_name: Krishnendu
full_name: Chatterjee, Krishnendu
id: 2E5DCA20-F248-11E8-B48F-1D18A9856A87
last_name: Chatterjee
orcid: 0000-0002-4561-241X
- first_name: Thomas A
full_name: Henzinger, Thomas A
id: 40876CD8-F248-11E8-B48F-1D18A9856A87
last_name: Henzinger
orcid: 0000−0002−2985−7724
- first_name: Rasmus
full_name: Ibsen-Jensen, Rasmus
id: 3B699956-F248-11E8-B48F-1D18A9856A87
last_name: Ibsen-Jensen
orcid: 0000-0003-4783-0389
- first_name: Jan
full_name: Otop, Jan
last_name: Otop
citation:
ama: Chatterjee K, Henzinger TA, Ibsen-Jensen R, Otop J. Edit distance for pushdown
automata. Logical Methods in Computer Science. 2017;13(3). doi:10.23638/LMCS-13(3:23)2017
apa: Chatterjee, K., Henzinger, T. A., Ibsen-Jensen, R., & Otop, J. (2017).
Edit distance for pushdown automata. Logical Methods in Computer Science.
International Federation of Computational Logic. https://doi.org/10.23638/LMCS-13(3:23)2017
chicago: Chatterjee, Krishnendu, Thomas A Henzinger, Rasmus Ibsen-Jensen, and Jan
Otop. “Edit Distance for Pushdown Automata.” Logical Methods in Computer Science.
International Federation of Computational Logic, 2017. https://doi.org/10.23638/LMCS-13(3:23)2017.
ieee: K. Chatterjee, T. A. Henzinger, R. Ibsen-Jensen, and J. Otop, “Edit distance
for pushdown automata,” Logical Methods in Computer Science, vol. 13, no.
3. International Federation of Computational Logic, 2017.
ista: Chatterjee K, Henzinger TA, Ibsen-Jensen R, Otop J. 2017. Edit distance for
pushdown automata. Logical Methods in Computer Science. 13(3).
mla: Chatterjee, Krishnendu, et al. “Edit Distance for Pushdown Automata.” Logical
Methods in Computer Science, vol. 13, no. 3, International Federation of Computational
Logic, 2017, doi:10.23638/LMCS-13(3:23)2017.
short: K. Chatterjee, T.A. Henzinger, R. Ibsen-Jensen, J. Otop, Logical Methods
in Computer Science 13 (2017).
date_created: 2018-12-11T11:46:37Z
date_published: 2017-09-13T00:00:00Z
date_updated: 2023-02-23T12:26:25Z
day: '13'
ddc:
- '004'
department:
- _id: KrCh
- _id: ToHe
doi: 10.23638/LMCS-13(3:23)2017
ec_funded: 1
file:
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name: Moderne Concurrency Paradigms
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call_identifier: FWF
grant_number: P 23499-N23
name: Modern Graph Algorithmic Techniques in Formal Verification
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call_identifier: FWF
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name: The Wittgenstein Prize
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name: 'Quantitative Graph Games: Theory and Applications'
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call_identifier: FWF
grant_number: S11407
name: Game Theory
publication: Logical Methods in Computer Science
publication_identifier:
issn:
- '18605974'
publication_status: published
publisher: International Federation of Computational Logic
publist_id: '7356'
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quality_controlled: '1'
related_material:
record:
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relation: earlier_version
status: public
- id: '5438'
relation: earlier_version
status: public
scopus_import: 1
status: public
title: Edit distance for pushdown automata
tmp:
image: /image/cc_by_nd.png
legal_code_url: https://creativecommons.org/licenses/by-nd/4.0/legalcode
name: Creative Commons Attribution-NoDerivatives 4.0 International (CC BY-ND 4.0)
short: CC BY-ND (4.0)
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 13
year: '2017'
...
---
_id: '512'
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. The fixation
probability is a fundamental quantity of natural selection, and known to depend
on the population structure. Amplifiers 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. In 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 Cometswarm 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. '
article_number: '82'
article_processing_charge: No
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. Scientific Reports. 2017;7(1).
doi:10.1038/s41598-017-00107-w'
apa: 'Pavlogiannis, A., Tkadlec, J., Chatterjee, K., & Nowak, M. (2017). Amplification
on undirected population structures: Comets beat stars. Scientific Reports.
Nature Publishing Group. https://doi.org/10.1038/s41598-017-00107-w'
chicago: 'Pavlogiannis, Andreas, Josef Tkadlec, Krishnendu Chatterjee, and Martin
Nowak. “Amplification on Undirected Population Structures: Comets Beat Stars.”
Scientific Reports. Nature Publishing Group, 2017. https://doi.org/10.1038/s41598-017-00107-w.'
ieee: 'A. Pavlogiannis, J. Tkadlec, K. Chatterjee, and M. Nowak, “Amplification
on undirected population structures: Comets beat stars,” Scientific Reports,
vol. 7, no. 1. Nature Publishing Group, 2017.'
ista: 'Pavlogiannis A, Tkadlec J, Chatterjee K, Nowak M. 2017. Amplification on
undirected population structures: Comets beat stars. Scientific Reports. 7(1),
82.'
mla: 'Pavlogiannis, Andreas, et al. “Amplification on Undirected Population Structures:
Comets Beat Stars.” Scientific Reports, vol. 7, no. 1, 82, Nature Publishing
Group, 2017, doi:10.1038/s41598-017-00107-w.'
short: A. Pavlogiannis, J. Tkadlec, K. Chatterjee, M. Nowak, Scientific Reports
7 (2017).
date_created: 2018-12-11T11:46:53Z
date_published: 2017-03-06T00:00:00Z
date_updated: 2023-02-23T12:26:57Z
day: '06'
ddc:
- '004'
department:
- _id: KrCh
doi: 10.1038/s41598-017-00107-w
ec_funded: 1
file:
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checksum: 7d05cbdd914e194a019c0f91fb64e9a8
content_type: application/pdf
creator: system
date_created: 2018-12-12T10:18:35Z
date_updated: 2020-07-14T12:46:36Z
file_id: '5357'
file_name: IST-2018-938-v1+1_2017_Pavlogiannis_Amplification_on.pdf
file_size: 1536783
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file_date_updated: 2020-07-14T12:46:36Z
has_accepted_license: '1'
intvolume: ' 7'
issue: '1'
language:
- iso: eng
month: '03'
oa: 1
oa_version: Published Version
project:
- _id: 2584A770-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: P 23499-N23
name: Modern Graph Algorithmic Techniques in Formal Verification
- _id: 25863FF4-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: S11407
name: Game Theory
- _id: 2581B60A-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '279307'
name: 'Quantitative Graph Games: Theory and Applications'
publication: Scientific Reports
publication_identifier:
issn:
- '20452322'
publication_status: published
publisher: Nature Publishing Group
publist_id: '7307'
pubrep_id: '938'
quality_controlled: '1'
related_material:
record:
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status: public
scopus_import: 1
status: public
title: 'Amplification on undirected population structures: Comets beat stars'
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: 7
year: '2017'
...
---
_id: '10416'
abstract:
- lang: eng
text: 'A fundamental algorithmic problem at the heart of static analysis is Dyck
reachability. The input is a graph where the edges are labeled with different
types of opening and closing parentheses, and the reachability information is
computed via paths whose parentheses are properly matched. We present new results
for Dyck reachability problems with applications to alias analysis and data-dependence
analysis. Our main contributions, that include improved upper bounds as well as
lower bounds that establish optimality guarantees, are as follows: First, we consider
Dyck reachability on bidirected graphs, which is the standard way of performing
field-sensitive points-to analysis. Given a bidirected graph with n nodes and
m edges, we present: (i) an algorithm with worst-case running time O(m + n · α(n)),
where α(n) is the inverse Ackermann function, improving the previously known O(n2)
time bound; (ii) a matching lower bound that shows that our algorithm is optimal
wrt to worst-case complexity; and (iii) an optimal average-case upper bound of
O(m) time, improving the previously known O(m · logn) bound. Second, we consider
the problem of context-sensitive data-dependence analysis, where the task is to
obtain analysis summaries of library code in the presence of callbacks. Our algorithm
preprocesses libraries in almost linear time, after which the contribution of
the library in the complexity of the client analysis is only linear, and only
wrt the number of call sites. Third, we prove that combinatorial algorithms for
Dyck reachability on general graphs with truly sub-cubic bounds cannot be obtained
without obtaining sub-cubic combinatorial algorithms for Boolean Matrix Multiplication,
which is a long-standing open problem. Thus we establish that the existing combinatorial
algorithms for Dyck reachability are (conditionally) optimal for general graphs.
We also show that the same hardness holds for graphs of constant treewidth. Finally,
we provide a prototype implementation of our algorithms for both alias analysis
and data-dependence analysis. Our experimental evaluation demonstrates that the
new algorithms significantly outperform all existing methods on the two problems,
over real-world benchmarks.'
acknowledgement: "The research was partly supported by Austrian Science Fund (FWF)
Grant No P23499-N23, FWF NFN Grant No S11407-N23 (RiSE/SHiNE), and ERC Start grant
(279307: Graph Games).\r\n"
article_number: '30'
article_processing_charge: No
article_type: original
author:
- first_name: Krishnendu
full_name: Chatterjee, Krishnendu
id: 2E5DCA20-F248-11E8-B48F-1D18A9856A87
last_name: Chatterjee
orcid: 0000-0002-4561-241X
- first_name: Bhavya
full_name: Choudhary, Bhavya
last_name: Choudhary
- first_name: Andreas
full_name: Pavlogiannis, Andreas
id: 49704004-F248-11E8-B48F-1D18A9856A87
last_name: Pavlogiannis
orcid: 0000-0002-8943-0722
citation:
ama: Chatterjee K, Choudhary B, Pavlogiannis A. Optimal Dyck reachability for data-dependence
and Alias analysis. Proceedings of the ACM on Programming Languages. 2017;2(POPL).
doi:10.1145/3158118
apa: 'Chatterjee, K., Choudhary, B., & Pavlogiannis, A. (2017). Optimal Dyck
reachability for data-dependence and Alias analysis. Proceedings of the ACM
on Programming Languages. Los Angeles, CA, United States: Association for
Computing Machinery. https://doi.org/10.1145/3158118'
chicago: Chatterjee, Krishnendu, Bhavya Choudhary, and Andreas Pavlogiannis. “Optimal
Dyck Reachability for Data-Dependence and Alias Analysis.” Proceedings of the
ACM on Programming Languages. Association for Computing Machinery, 2017. https://doi.org/10.1145/3158118.
ieee: K. Chatterjee, B. Choudhary, and A. Pavlogiannis, “Optimal Dyck reachability
for data-dependence and Alias analysis,” Proceedings of the ACM on Programming
Languages, vol. 2, no. POPL. Association for Computing Machinery, 2017.
ista: Chatterjee K, Choudhary B, Pavlogiannis A. 2017. Optimal Dyck reachability
for data-dependence and Alias analysis. Proceedings of the ACM on Programming
Languages. 2(POPL), 30.
mla: Chatterjee, Krishnendu, et al. “Optimal Dyck Reachability for Data-Dependence
and Alias Analysis.” Proceedings of the ACM on Programming Languages, vol.
2, no. POPL, 30, Association for Computing Machinery, 2017, doi:10.1145/3158118.
short: K. Chatterjee, B. Choudhary, A. Pavlogiannis, Proceedings of the ACM on Programming
Languages 2 (2017).
conference:
end_date: 2018-01-13
location: Los Angeles, CA, United States
name: 'POPL: Programming Languages'
start_date: 2018-01-07
date_created: 2021-12-05T23:01:48Z
date_published: 2017-12-27T00:00:00Z
date_updated: 2023-02-23T12:27:13Z
day: '27'
ddc:
- '000'
department:
- _id: KrCh
doi: 10.1145/3158118
ec_funded: 1
external_id:
arxiv:
- '1910.00241'
file:
- access_level: open_access
checksum: faa3f7b3fe8aab84b50ed805c26a0ee5
content_type: application/pdf
creator: cchlebak
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date_updated: 2021-12-07T08:06:28Z
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file_name: 2017_ACMProgLang_Chatterjee.pdf
file_size: 460188
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success: 1
file_date_updated: 2021-12-07T08:06:28Z
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language:
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month: '12'
oa: 1
oa_version: Published Version
project:
- _id: 2581B60A-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '279307'
name: 'Quantitative Graph Games: Theory and Applications'
- _id: 2584A770-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: P 23499-N23
name: Modern Graph Algorithmic Techniques in Formal Verification
- _id: 25832EC2-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: S 11407_N23
name: Rigorous Systems Engineering
publication: Proceedings of the ACM on Programming Languages
publication_identifier:
eissn:
- 2475-1421
publication_status: published
publisher: Association for Computing Machinery
quality_controlled: '1'
related_material:
record:
- id: '5455'
relation: earlier_version
status: public
scopus_import: '1'
status: public
title: Optimal Dyck reachability for data-dependence and Alias analysis
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: 2
year: '2017'
...
---
_id: '5455'
abstract:
- lang: eng
text: 'A fundamental algorithmic problem at the heart of static analysis is Dyck
reachability. The input is a graphwhere the edges are labeled with different types
of opening and closing parentheses, and the reachabilityinformation is computed
via paths whose parentheses are properly matched. We present new results for Dyckreachability
problems with applications to alias analysis and data-dependence analysis. Our
main contributions,that include improved upper bounds as well as lower bounds
that establish optimality guarantees, are asfollows:First, we consider Dyck reachability
on bidirected graphs, which is the standard way of performing field-sensitive
points-to analysis. Given a bidirected graph withnnodes andmedges, we present:
(i) an algorithmwith worst-case running timeO(m+n·α(n)), whereα(n)is the inverse
Ackermann function, improving thepreviously knownO(n2)time bound; (ii) a matching
lower bound that shows that our algorithm is optimalwrt to worst-case complexity;
and (iii) an optimal average-case upper bound ofO(m)time, improving thepreviously
knownO(m·logn)bound.Second, we consider the problem of context-sensitive data-dependence
analysis, where the task is to obtainanalysis summaries of library code in the
presence of callbacks. Our algorithm preprocesses libraries in almostlinear time,
after which the contribution of the library in the complexity of the client analysis
is only linear,and only wrt the number of call sites.Third, we prove that combinatorial
algorithms for Dyck reachability on general graphs with truly sub-cubic bounds
cannot be obtained without obtaining sub-cubic combinatorial algorithms for Boolean
MatrixMultiplication, which is a long-standing open problem. Thus we establish
that the existing combinatorialalgorithms for Dyck reachability are (conditionally)
optimal for general graphs. We also show that the samehardness holds for graphs
of constant treewidth.Finally, we provide a prototype implementation of our algorithms
for both alias analysis and data-dependenceanalysis. Our experimental evaluation
demonstrates that the new algorithms significantly outperform allexisting methods
on the two problems, over real-world benchmarks.'
alternative_title:
- IST Austria Technical Report
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: Bhavya
full_name: Choudhary, Bhavya
last_name: Choudhary
- first_name: Andreas
full_name: Pavlogiannis, Andreas
id: 49704004-F248-11E8-B48F-1D18A9856A87
last_name: Pavlogiannis
orcid: 0000-0002-8943-0722
citation:
ama: Chatterjee K, Choudhary B, Pavlogiannis A. Optimal Dyck Reachability for
Data-Dependence and Alias Analysis. IST Austria; 2017. doi:10.15479/AT:IST-2017-870-v1-1
apa: Chatterjee, K., Choudhary, B., & Pavlogiannis, A. (2017). Optimal Dyck
reachability for data-dependence and alias analysis. IST Austria. https://doi.org/10.15479/AT:IST-2017-870-v1-1
chicago: Chatterjee, Krishnendu, Bhavya Choudhary, and Andreas Pavlogiannis. Optimal
Dyck Reachability for Data-Dependence and Alias Analysis. IST Austria, 2017.
https://doi.org/10.15479/AT:IST-2017-870-v1-1.
ieee: K. Chatterjee, B. Choudhary, and A. Pavlogiannis, Optimal Dyck reachability
for data-dependence and alias analysis. IST Austria, 2017.
ista: Chatterjee K, Choudhary B, Pavlogiannis A. 2017. Optimal Dyck reachability
for data-dependence and alias analysis, IST Austria, 37p.
mla: Chatterjee, Krishnendu, et al. Optimal Dyck Reachability for Data-Dependence
and Alias Analysis. IST Austria, 2017, doi:10.15479/AT:IST-2017-870-v1-1.
short: K. Chatterjee, B. Choudhary, A. Pavlogiannis, Optimal Dyck Reachability for
Data-Dependence and Alias Analysis, IST Austria, 2017.
date_created: 2018-12-12T11:39:26Z
date_published: 2017-10-23T00:00:00Z
date_updated: 2023-02-21T15:54:10Z
day: '23'
ddc:
- '000'
department:
- _id: KrCh
doi: 10.15479/AT:IST-2017-870-v1-1
file:
- access_level: open_access
checksum: 177a84a46e3ac17e87b31534ad16a4c9
content_type: application/pdf
creator: system
date_created: 2018-12-12T11:54:02Z
date_updated: 2020-07-14T12:46:59Z
file_id: '5524'
file_name: IST-2017-870-v1+1_main.pdf
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relation: main_file
file_date_updated: 2020-07-14T12:46:59Z
has_accepted_license: '1'
language:
- iso: eng
month: '10'
oa: 1
oa_version: Published Version
page: '37'
publication_identifier:
issn:
- 2664-1690
publication_status: published
publisher: IST Austria
pubrep_id: '870'
related_material:
record:
- id: '10416'
relation: later_version
status: public
status: public
title: Optimal Dyck reachability for data-dependence and alias analysis
type: technical_report
user_id: 8b945eb4-e2f2-11eb-945a-df72226e66a9
year: '2017'
...
---
_id: '5450'
abstract:
- lang: eng
text: 'In this report the implementation of the institutional data repository IST
DataRep at IST Austria will be covered: Starting with the research phase when
requirements for a repository were established, the procedure of choosing a repository-software
and its customization based on the results of user-testings will be discussed.
Followed by reflections on the marketing strategies in regard of impact, and at
the end sharing some experiences of one year operating IST DataRep.'
author:
- first_name: Barbara
full_name: Barbara Petritsch
id: 406048EC-F248-11E8-B48F-1D18A9856A87
last_name: Petritsch
orcid: 0000-0003-2724-4614
citation:
ama: Petritsch B. Implementing the Institutional Data Repository IST DataRep.
IST Austria; 2017.
apa: Petritsch, B. (2017). Implementing the institutional data repository IST
DataRep. IST Austria.
chicago: Petritsch, Barbara. Implementing the Institutional Data Repository IST
DataRep. IST Austria, 2017.
ieee: B. Petritsch, Implementing the institutional data repository IST DataRep.
IST Austria, 2017.
ista: Petritsch B. 2017. Implementing the institutional data repository IST DataRep,
IST Austria,p.
mla: Petritsch, Barbara. Implementing the Institutional Data Repository IST DataRep.
IST Austria, 2017.
short: B. Petritsch, Implementing the Institutional Data Repository IST DataRep,
IST Austria, 2017.
date_created: 2018-12-12T11:39:24Z
date_published: 2017-06-26T00:00:00Z
date_updated: 2020-07-14T23:05:03Z
day: '26'
department:
- _id: E-Lib
extern: 0
file:
- access_level: open_access
checksum: 6321792dcfa82bf490f17615a9b22355
content_type: application/pdf
creator: system
date_created: 2018-12-12T11:53:22Z
date_updated: 2020-07-14T12:46:59Z
file_id: '5483'
file_name: IST-2017-724-v1+1_DataRep_Project_Report_2017.pdf
file_size: 3460985
relation: main_file
file_date_updated: 2020-07-14T12:46:59Z
main_file_link:
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url: https://repository.ist.ac.at/id/eprint/724.
month: '06'
oa: 1
publication_date: 2017-06-26
publisher: IST Austria
pubrep_id: '724'
status: public
title: Implementing the institutional data repository IST DataRep
type: report
year: '2017'
...
---
_id: '10417'
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\n\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."
acknowledgement: "The research was partly supported by Austrian Science Fund (FWF)
Grant No P23499- N23, FWF\r\nNFN Grant No S11407-N23 (RiSE/SHiNE), ERC Start grant
(279307: Graph Games), and Czech\r\nScience Foundation grant GBP202/12/G061."
article_number: '31'
article_processing_charge: No
article_type: original
author:
- first_name: Marek
full_name: Chalupa, Marek
last_name: Chalupa
- 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: Nishant
full_name: Sinha, Nishant
last_name: Sinha
- first_name: Kapil
full_name: Vaidya, Kapil
last_name: Vaidya
citation:
ama: Chalupa M, Chatterjee K, Pavlogiannis A, Sinha N, Vaidya K. Data-centric dynamic
partial order reduction. Proceedings of the ACM on Programming Languages.
2017;2(POPL). doi:10.1145/3158119
apa: 'Chalupa, M., Chatterjee, K., Pavlogiannis, A., Sinha, N., & Vaidya, K.
(2017). Data-centric dynamic partial order reduction. Proceedings of the ACM
on Programming Languages. Los Angeles, CA, United States: Association for
Computing Machinery. https://doi.org/10.1145/3158119'
chicago: Chalupa, Marek, Krishnendu Chatterjee, Andreas Pavlogiannis, Nishant Sinha,
and Kapil Vaidya. “Data-Centric Dynamic Partial Order Reduction.” Proceedings
of the ACM on Programming Languages. Association for Computing Machinery,
2017. https://doi.org/10.1145/3158119.
ieee: M. Chalupa, K. Chatterjee, A. Pavlogiannis, N. Sinha, and K. Vaidya, “Data-centric
dynamic partial order reduction,” Proceedings of the ACM on Programming Languages,
vol. 2, no. POPL. Association for Computing Machinery, 2017.
ista: Chalupa M, Chatterjee K, Pavlogiannis A, Sinha N, Vaidya K. 2017. Data-centric
dynamic partial order reduction. Proceedings of the ACM on Programming Languages.
2(POPL), 31.
mla: Chalupa, Marek, et al. “Data-Centric Dynamic Partial Order Reduction.” Proceedings
of the ACM on Programming Languages, vol. 2, no. POPL, 31, Association for
Computing Machinery, 2017, doi:10.1145/3158119.
short: M. Chalupa, K. Chatterjee, A. Pavlogiannis, N. Sinha, K. Vaidya, Proceedings
of the ACM on Programming Languages 2 (2017).
conference:
end_date: 2018-01-13
location: Los Angeles, CA, United States
name: 'POPL: Programming Languages'
start_date: 2018-01-07
date_created: 2021-12-05T23:01:49Z
date_published: 2017-12-27T00:00:00Z
date_updated: 2023-02-23T12:27:16Z
day: '27'
department:
- _id: KrCh
doi: 10.1145/3158119
ec_funded: 1
external_id:
arxiv:
- '1610.01188'
intvolume: ' 2'
issue: POPL
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://dl.acm.org/doi/10.1145/3158119
month: '12'
oa: 1
oa_version: Published Version
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: Proceedings of the ACM on Programming Languages
publication_identifier:
eissn:
- 2475-1421
publication_status: published
publisher: Association for Computing Machinery
quality_controlled: '1'
related_material:
record:
- id: '5448'
relation: earlier_version
status: public
- id: '5456'
relation: earlier_version
status: public
scopus_import: '1'
status: public
title: Data-centric dynamic partial order reduction
type: journal_article
user_id: 8b945eb4-e2f2-11eb-945a-df72226e66a9
volume: 2
year: '2017'
...
---
_id: '5456'
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: Marek
full_name: Chalupa, Marek
last_name: Chalupa
- 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: Nishant
full_name: Sinha, Nishant
last_name: Sinha
- first_name: Kapil
full_name: Vaidya, Kapil
last_name: Vaidya
citation:
ama: Chalupa M, Chatterjee K, Pavlogiannis A, Sinha N, Vaidya K. Data-Centric
Dynamic Partial Order Reduction. IST Austria; 2017. doi:10.15479/AT:IST-2017-872-v1-1
apa: Chalupa, M., Chatterjee, K., Pavlogiannis, A., Sinha, N., & Vaidya, K.
(2017). Data-centric dynamic partial order reduction. IST Austria. https://doi.org/10.15479/AT:IST-2017-872-v1-1
chicago: Chalupa, Marek, Krishnendu Chatterjee, Andreas Pavlogiannis, Nishant Sinha,
and Kapil Vaidya. Data-Centric Dynamic Partial Order Reduction. IST Austria,
2017. https://doi.org/10.15479/AT:IST-2017-872-v1-1.
ieee: M. Chalupa, K. Chatterjee, A. Pavlogiannis, N. Sinha, and K. Vaidya, Data-centric
dynamic partial order reduction. IST Austria, 2017.
ista: Chalupa M, Chatterjee K, Pavlogiannis A, Sinha N, Vaidya K. 2017. Data-centric
dynamic partial order reduction, IST Austria, 36p.
mla: Chalupa, Marek, et al. Data-Centric Dynamic Partial Order Reduction.
IST Austria, 2017, doi:10.15479/AT:IST-2017-872-v1-1.
short: M. Chalupa, K. Chatterjee, A. Pavlogiannis, N. Sinha, K. Vaidya, Data-Centric
Dynamic Partial Order Reduction, IST Austria, 2017.
date_created: 2018-12-12T11:39:26Z
date_published: 2017-10-23T00:00:00Z
date_updated: 2023-02-23T12:26:54Z
day: '23'
ddc:
- '000'
department:
- _id: KrCh
doi: 10.15479/AT:IST-2017-872-v1-1
file:
- access_level: open_access
checksum: d2635c4cf013000f0a1b09e80f9e4ab7
content_type: application/pdf
creator: system
date_created: 2018-12-12T11:53:26Z
date_updated: 2020-07-14T12:46:59Z
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file_date_updated: 2020-07-14T12:46:59Z
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language:
- iso: eng
month: '10'
oa: 1
oa_version: Published Version
page: '36'
publication_identifier:
issn:
- 2664-1690
publication_status: published
publisher: IST Austria
pubrep_id: '872'
related_material:
record:
- id: '10417'
relation: later_version
status: public
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relation: earlier_version
status: public
status: public
title: Data-centric dynamic partial order reduction
type: technical_report
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
year: '2017'
...
---
_id: '551'
abstract:
- lang: eng
text: 'Evolutionary graph theory studies the evolutionary dynamics in a population
structure given as a connected graph. Each node of the graph represents an individual
of the population, and edges determine how offspring are placed. We consider the
classical birth-death Moran process where there are two types of individuals,
namely, the residents with fitness 1 and mutants with fitness r. The fitness indicates
the reproductive strength. The evolutionary dynamics happens as follows: in the
initial step, in a population of all resident individuals a mutant is introduced,
and then at each step, an individual is chosen proportional to the fitness of
its type to reproduce, and the offspring replaces a neighbor uniformly at random.
The process stops when all individuals are either residents or mutants. The probability
that all individuals in the end are mutants is called the fixation probability,
which is a key factor in the rate of evolution. We consider the problem of approximating
the fixation probability. The class of algorithms that is extremely relevant for
approximation of the fixation probabilities is the Monte-Carlo simulation of the
process. Previous results present a polynomial-time Monte-Carlo algorithm for
undirected graphs when r is given in unary. First, we present a simple modification:
instead of simulating each step, we discard ineffective steps, where no node changes
type (i.e., either residents replace residents, or mutants replace mutants). Using
the above simple modification and our result that the number of effective steps
is concentrated around the expected number of effective steps, we present faster
polynomial-time Monte-Carlo algorithms for undirected graphs. Our algorithms are
always at least a factor O(n2/ log n) faster as compared to the previous algorithms,
where n is the number of nodes, and is polynomial even if r is given in binary.
We also present lower bounds showing that the upper bound on the expected number
of effective steps we present is asymptotically tight for undirected graphs. '
alternative_title:
- LIPIcs
article_number: '61'
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
- first_name: Martin
full_name: Nowak, Martin
last_name: Nowak
citation:
ama: 'Chatterjee K, Ibsen-Jensen R, Nowak M. Faster Monte Carlo algorithms for fixation
probability of the Moran process on undirected graphs. In: Leibniz International
Proceedings in Informatics. Vol 83. Schloss Dagstuhl - Leibniz-Zentrum für
Informatik; 2017. doi:10.4230/LIPIcs.MFCS.2017.61'
apa: 'Chatterjee, K., Ibsen-Jensen, R., & Nowak, M. (2017). Faster Monte Carlo
algorithms for fixation probability of the Moran process on undirected graphs.
In Leibniz International Proceedings in Informatics (Vol. 83). Aalborg,
Denmark: Schloss Dagstuhl - Leibniz-Zentrum für Informatik. https://doi.org/10.4230/LIPIcs.MFCS.2017.61'
chicago: Chatterjee, Krishnendu, Rasmus Ibsen-Jensen, and Martin Nowak. “Faster
Monte Carlo Algorithms for Fixation Probability of the Moran Process on Undirected
Graphs.” In Leibniz International Proceedings in Informatics, Vol. 83.
Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2017. https://doi.org/10.4230/LIPIcs.MFCS.2017.61.
ieee: K. Chatterjee, R. Ibsen-Jensen, and M. Nowak, “Faster Monte Carlo algorithms
for fixation probability of the Moran process on undirected graphs,” in Leibniz
International Proceedings in Informatics, Aalborg, Denmark, 2017, vol. 83.
ista: 'Chatterjee K, Ibsen-Jensen R, Nowak M. 2017. Faster Monte Carlo algorithms
for fixation probability of the Moran process on undirected graphs. Leibniz International
Proceedings in Informatics. MFCS: Mathematical Foundations of Computer Science
(SG), LIPIcs, vol. 83, 61.'
mla: Chatterjee, Krishnendu, et al. “Faster Monte Carlo Algorithms for Fixation
Probability of the Moran Process on Undirected Graphs.” Leibniz International
Proceedings in Informatics, vol. 83, 61, Schloss Dagstuhl - Leibniz-Zentrum
für Informatik, 2017, doi:10.4230/LIPIcs.MFCS.2017.61.
short: K. Chatterjee, R. Ibsen-Jensen, M. Nowak, in:, Leibniz International Proceedings
in Informatics, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2017.
conference:
end_date: 2017-08-25
location: Aalborg, Denmark
name: 'MFCS: Mathematical Foundations of Computer Science (SG)'
start_date: 2017-08-21
date_created: 2018-12-11T11:47:08Z
date_published: 2017-11-01T00:00:00Z
date_updated: 2021-01-12T08:02:34Z
day: '01'
ddc:
- '004'
department:
- _id: KrCh
doi: 10.4230/LIPIcs.MFCS.2017.61
file:
- access_level: open_access
checksum: 2eed5224c0e4e259484a1d71acb8ba6a
content_type: application/pdf
creator: system
date_created: 2018-12-12T10:18:04Z
date_updated: 2020-07-14T12:47:00Z
file_id: '5322'
file_name: IST-2018-924-v1+1_LIPIcs-MFCS-2017-61.pdf
file_size: 535077
relation: main_file
file_date_updated: 2020-07-14T12:47:00Z
has_accepted_license: '1'
intvolume: ' 83'
language:
- iso: eng
month: '11'
oa: 1
oa_version: Published Version
publication: Leibniz International Proceedings in Informatics
publication_identifier:
isbn:
- 978-395977046-0
publication_status: published
publisher: Schloss Dagstuhl - Leibniz-Zentrum für Informatik
publist_id: '7263'
pubrep_id: '924'
quality_controlled: '1'
scopus_import: 1
status: public
title: Faster Monte Carlo algorithms for fixation probability of the Moran process
on undirected graphs
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: 83
year: '2017'
...
---
_id: '552'
abstract:
- lang: eng
text: 'Graph games provide the foundation for modeling and synthesis of reactive
processes. Such games are played over graphs where the vertices are controlled
by two adversarial players. We consider graph games where the objective of the
first player is the conjunction of a qualitative objective (specified as a parity
condition) and a quantitative objective (specified as a meanpayoff condition).
There are two variants of the problem, namely, the threshold problem where the
quantitative goal is to ensure that the mean-payoff value is above a threshold,
and the value problem where the quantitative goal is to ensure the optimal mean-payoff
value; in both cases ensuring the qualitative parity objective. The previous best-known
algorithms for game graphs with n vertices, m edges, parity objectives with d
priorities, and maximal absolute reward value W for mean-payoff objectives, are
as follows: O(nd+1 . m . w) for the threshold problem, and O(nd+2 · m · W) for
the value problem. Our main contributions are faster algorithms, and the running
times of our algorithms are as follows: O(nd-1 · m ·W) for the threshold problem,
and O(nd · m · W · log(n · W)) for the value problem. For mean-payoff parity objectives
with two priorities, our algorithms match the best-known bounds of the algorithms
for mean-payoff games (without conjunction with parity objectives). Our results
are relevant in synthesis of reactive systems with both functional requirement
(given as a qualitative objective) and performance requirement (given as a quantitative
objective).'
alternative_title:
- LIPIcs
article_number: '39'
article_processing_charge: No
author:
- first_name: Krishnendu
full_name: Chatterjee, Krishnendu
id: 2E5DCA20-F248-11E8-B48F-1D18A9856A87
last_name: Chatterjee
orcid: 0000-0002-4561-241X
- first_name: Monika H
full_name: Henzinger, Monika H
id: 540c9bbd-f2de-11ec-812d-d04a5be85630
last_name: Henzinger
orcid: 0000-0002-5008-6530
- first_name: Alexander
full_name: Svozil, Alexander
last_name: Svozil
citation:
ama: 'Chatterjee K, Henzinger MH, Svozil A. Faster algorithms for mean-payoff parity
games. In: Leibniz International Proceedings in Informatics. Vol 83. Schloss
Dagstuhl - Leibniz-Zentrum für Informatik; 2017. doi:10.4230/LIPIcs.MFCS.2017.39'
apa: 'Chatterjee, K., Henzinger, M. H., & Svozil, A. (2017). Faster algorithms
for mean-payoff parity games. In Leibniz International Proceedings in Informatics
(Vol. 83). Aalborg, Denmark: Schloss Dagstuhl - Leibniz-Zentrum für Informatik.
https://doi.org/10.4230/LIPIcs.MFCS.2017.39'
chicago: Chatterjee, Krishnendu, Monika H Henzinger, and Alexander Svozil. “Faster
Algorithms for Mean-Payoff Parity Games.” In Leibniz International Proceedings
in Informatics, Vol. 83. Schloss Dagstuhl - Leibniz-Zentrum für Informatik,
2017. https://doi.org/10.4230/LIPIcs.MFCS.2017.39.
ieee: K. Chatterjee, M. H. Henzinger, and A. Svozil, “Faster algorithms for mean-payoff
parity games,” in Leibniz International Proceedings in Informatics, Aalborg,
Denmark, 2017, vol. 83.
ista: 'Chatterjee K, Henzinger MH, Svozil A. 2017. Faster algorithms for mean-payoff
parity games. Leibniz International Proceedings in Informatics. MFCS: Mathematical
Foundations of Computer Science (SG), LIPIcs, vol. 83, 39.'
mla: Chatterjee, Krishnendu, et al. “Faster Algorithms for Mean-Payoff Parity Games.”
Leibniz International Proceedings in Informatics, vol. 83, 39, Schloss
Dagstuhl - Leibniz-Zentrum für Informatik, 2017, doi:10.4230/LIPIcs.MFCS.2017.39.
short: K. Chatterjee, M.H. Henzinger, A. Svozil, in:, Leibniz International Proceedings
in Informatics, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2017.
conference:
end_date: 2017-08-25
location: Aalborg, Denmark
name: 'MFCS: Mathematical Foundations of Computer Science (SG)'
start_date: 2017-08-21
date_created: 2018-12-11T11:47:08Z
date_published: 2017-11-01T00:00:00Z
date_updated: 2023-02-14T10:06:46Z
day: '01'
ddc:
- '004'
department:
- _id: KrCh
doi: 10.4230/LIPIcs.MFCS.2017.39
ec_funded: 1
file:
- access_level: open_access
checksum: c67f4866ddbfd555afef1f63ae9a8fc7
content_type: application/pdf
creator: system
date_created: 2018-12-12T10:16:57Z
date_updated: 2020-07-14T12:47:00Z
file_id: '5248'
file_name: IST-2018-923-v1+1_LIPIcs-MFCS-2017-39.pdf
file_size: 610339
relation: main_file
file_date_updated: 2020-07-14T12:47:00Z
has_accepted_license: '1'
intvolume: ' 83'
language:
- iso: eng
license: https://creativecommons.org/licenses/by/3.0/
month: '11'
oa: 1
oa_version: Published Version
project:
- _id: 25863FF4-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: S11407
name: Game Theory
- _id: 2581B60A-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '279307'
name: 'Quantitative Graph Games: Theory and Applications'
publication: Leibniz International Proceedings in Informatics
publication_identifier:
isbn:
- 978-395977046-0
publication_status: published
publisher: Schloss Dagstuhl - Leibniz-Zentrum für Informatik
publist_id: '7262'
pubrep_id: '923'
quality_controlled: '1'
scopus_import: '1'
status: public
title: Faster algorithms for mean-payoff parity games
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/3.0/legalcode
name: Creative Commons Attribution 3.0 Unported (CC BY 3.0)
short: CC BY (3.0)
type: conference
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 83
year: '2017'
...
---
_id: '553'
abstract:
- lang: eng
text: 'We consider two player, zero-sum, finite-state concurrent reachability games,
played for an infinite number of rounds, where in every round, each player simultaneously
and independently of the other players chooses an action, whereafter the successor
state is determined by a probability distribution given by the current state and
the chosen actions. Player 1 wins iff a designated goal state is eventually visited.
We are interested in the complexity of stationary strategies measured by their
patience, which is defined as the inverse of the smallest non-zero probability
employed. Our main results are as follows: We show that: (i) the optimal bound
on the patience of optimal and -optimal strategies, for both players is doubly
exponential; and (ii) even in games with a single non-absorbing state exponential
(in the number of actions) patience is necessary. '
alternative_title:
- LIPIcs
article_number: '55'
author:
- first_name: Krishnendu
full_name: Chatterjee, Krishnendu
id: 2E5DCA20-F248-11E8-B48F-1D18A9856A87
last_name: Chatterjee
orcid: 0000-0002-4561-241X
- first_name: Kristofer
full_name: Hansen, Kristofer
last_name: Hansen
- 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, Hansen K, Ibsen-Jensen R. Strategy complexity of concurrent
safety games. In: Leibniz International Proceedings in Informatics. Vol
83. Schloss Dagstuhl - Leibniz-Zentrum für Informatik; 2017. doi:10.4230/LIPIcs.MFCS.2017.55'
apa: 'Chatterjee, K., Hansen, K., & Ibsen-Jensen, R. (2017). Strategy complexity
of concurrent safety games. In Leibniz International Proceedings in Informatics
(Vol. 83). Aalborg, Denmark: Schloss Dagstuhl - Leibniz-Zentrum für Informatik.
https://doi.org/10.4230/LIPIcs.MFCS.2017.55'
chicago: Chatterjee, Krishnendu, Kristofer Hansen, and Rasmus Ibsen-Jensen. “Strategy
Complexity of Concurrent Safety Games.” In Leibniz International Proceedings
in Informatics, Vol. 83. Schloss Dagstuhl - Leibniz-Zentrum für Informatik,
2017. https://doi.org/10.4230/LIPIcs.MFCS.2017.55.
ieee: K. Chatterjee, K. Hansen, and R. Ibsen-Jensen, “Strategy complexity of concurrent
safety games,” in Leibniz International Proceedings in Informatics, Aalborg,
Denmark, 2017, vol. 83.
ista: 'Chatterjee K, Hansen K, Ibsen-Jensen R. 2017. Strategy complexity of concurrent
safety games. Leibniz International Proceedings in Informatics. MFCS: Mathematical
Foundations of Computer Science (SG), LIPIcs, vol. 83, 55.'
mla: Chatterjee, Krishnendu, et al. “Strategy Complexity of Concurrent Safety Games.”
Leibniz International Proceedings in Informatics, vol. 83, 55, Schloss
Dagstuhl - Leibniz-Zentrum für Informatik, 2017, doi:10.4230/LIPIcs.MFCS.2017.55.
short: K. Chatterjee, K. Hansen, R. Ibsen-Jensen, in:, Leibniz International Proceedings
in Informatics, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2017.
conference:
end_date: 2017-08-25
location: Aalborg, Denmark
name: 'MFCS: Mathematical Foundations of Computer Science (SG)'
start_date: 2017-08-21
date_created: 2018-12-11T11:47:08Z
date_published: 2017-11-01T00:00:00Z
date_updated: 2021-01-12T08:02:35Z
day: '01'
ddc:
- '004'
department:
- _id: KrCh
doi: 10.4230/LIPIcs.MFCS.2017.55
file:
- access_level: open_access
checksum: 7101facb56ade363205c695d72dbd173
content_type: application/pdf
creator: system
date_created: 2018-12-12T10:09:29Z
date_updated: 2020-07-14T12:47:00Z
file_id: '4753'
file_name: IST-2018-922-v1+1_LIPIcs-MFCS-2017-55.pdf
file_size: 549967
relation: main_file
file_date_updated: 2020-07-14T12:47:00Z
has_accepted_license: '1'
intvolume: ' 83'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/1506.02434
month: '11'
oa: 1
oa_version: Published Version
publication: Leibniz International Proceedings in Informatics
publication_identifier:
isbn:
- 978-395977046-0
publication_status: published
publisher: Schloss Dagstuhl - Leibniz-Zentrum für Informatik
publist_id: '7261'
pubrep_id: '922'
quality_controlled: '1'
scopus_import: 1
status: public
title: Strategy complexity of concurrent safety games
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: 83
year: '2017'
...
---
_id: '560'
abstract:
- lang: eng
text: In a recent article (Jentzen et al. 2016 Commun. Math. Sci. 14, 1477–1500
(doi:10.4310/CMS.2016.v14. n6.a1)), it has been established that, for every arbitrarily
slow convergence speed and every natural number d ? {4, 5, . . .}, there exist
d-dimensional stochastic differential equations with infinitely often differentiable
and globally bounded coefficients such that no approximation method based on finitely
many observations of the driving Brownian motion can converge in absolute mean
to the solution faster than the given speed of convergence. In this paper, we
strengthen the above result by proving that this slow convergence phenomenon also
arises in two (d = 2) and three (d = 3) space dimensions.
article_number: '0104'
author:
- first_name: Mate
full_name: Gerencser, Mate
id: 44ECEDF2-F248-11E8-B48F-1D18A9856A87
last_name: Gerencser
- first_name: Arnulf
full_name: Jentzen, Arnulf
last_name: Jentzen
- first_name: Diyora
full_name: Salimova, Diyora
last_name: Salimova
citation:
ama: 'Gerencser M, Jentzen A, Salimova D. On stochastic differential equations with
arbitrarily slow convergence rates for strong approximation in two space dimensions.
Proceedings of the Royal Society A: Mathematical, Physical and Engineering
Sciences. 2017;473(2207). doi:10.1098/rspa.2017.0104'
apa: 'Gerencser, M., Jentzen, A., & Salimova, D. (2017). On stochastic differential
equations with arbitrarily slow convergence rates for strong approximation in
two space dimensions. Proceedings of the Royal Society A: Mathematical, Physical
and Engineering Sciences. Royal Society of London. https://doi.org/10.1098/rspa.2017.0104'
chicago: 'Gerencser, Mate, Arnulf Jentzen, and Diyora Salimova. “On Stochastic Differential
Equations with Arbitrarily Slow Convergence Rates for Strong Approximation in
Two Space Dimensions.” Proceedings of the Royal Society A: Mathematical, Physical
and Engineering Sciences. Royal Society of London, 2017. https://doi.org/10.1098/rspa.2017.0104.'
ieee: 'M. Gerencser, A. Jentzen, and D. Salimova, “On stochastic differential equations
with arbitrarily slow convergence rates for strong approximation in two space
dimensions,” Proceedings of the Royal Society A: Mathematical, Physical and
Engineering Sciences, vol. 473, no. 2207. Royal Society of London, 2017.'
ista: 'Gerencser M, Jentzen A, Salimova D. 2017. On stochastic differential equations
with arbitrarily slow convergence rates for strong approximation in two space
dimensions. Proceedings of the Royal Society A: Mathematical, Physical and Engineering
Sciences. 473(2207), 0104.'
mla: 'Gerencser, Mate, et al. “On Stochastic Differential Equations with Arbitrarily
Slow Convergence Rates for Strong Approximation in Two Space Dimensions.” Proceedings
of the Royal Society A: Mathematical, Physical and Engineering Sciences, vol.
473, no. 2207, 0104, Royal Society of London, 2017, doi:10.1098/rspa.2017.0104.'
short: 'M. Gerencser, A. Jentzen, D. Salimova, Proceedings of the Royal Society
A: Mathematical, Physical and Engineering Sciences 473 (2017).'
date_created: 2018-12-11T11:47:11Z
date_published: 2017-11-01T00:00:00Z
date_updated: 2021-01-12T08:03:04Z
day: '01'
department:
- _id: JaMa
doi: 10.1098/rspa.2017.0104
ec_funded: 1
intvolume: ' 473'
issue: '2207'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/1702.03229
month: '11'
oa: 1
oa_version: Submitted Version
project:
- _id: 25681D80-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '291734'
name: International IST Postdoc Fellowship Programme
publication: 'Proceedings of the Royal Society A: Mathematical, Physical and Engineering
Sciences'
publication_identifier:
issn:
- '13645021'
publication_status: published
publisher: Royal Society of London
publist_id: '7256'
quality_controlled: '1'
scopus_import: 1
status: public
title: On stochastic differential equations with arbitrarily slow convergence rates
for strong approximation in two space dimensions
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 473
year: '2017'
...
---
_id: '567'
abstract:
- lang: eng
text: "This book is a concise and self-contained introduction of recent techniques
to prove local spectral universality for large random matrices. Random matrix
theory is a fast expanding research area, and this book mainly focuses on the
methods that the authors participated in developing over the past few years. Many
other interesting topics are not included, and neither are several new developments
within the framework of these methods. The authors have chosen instead to present
key concepts that they believe are the core of these methods and should be relevant
for future applications. They keep technicalities to a minimum to make the book
accessible to graduate students. With this in mind, they include in this book
the basic notions and tools for high-dimensional analysis, such as large deviation,
entropy, Dirichlet form, and the logarithmic Sobolev inequality.\r\n"
alternative_title:
- Courant Lecture Notes
article_processing_charge: No
author:
- first_name: László
full_name: Erdös, László
id: 4DBD5372-F248-11E8-B48F-1D18A9856A87
last_name: Erdös
orcid: 0000-0001-5366-9603
- first_name: Horng
full_name: Yau, Horng
last_name: Yau
citation:
ama: Erdös L, Yau H. A Dynamical Approach to Random Matrix Theory. Vol 28.
American Mathematical Society; 2017. doi:10.1090/cln/028
apa: Erdös, L., & Yau, H. (2017). A Dynamical Approach to Random Matrix Theory
(Vol. 28). American Mathematical Society. https://doi.org/10.1090/cln/028
chicago: Erdös, László, and Horng Yau. A Dynamical Approach to Random Matrix
Theory. Vol. 28. Courant Lecture Notes. American Mathematical Society, 2017.
https://doi.org/10.1090/cln/028.
ieee: L. Erdös and H. Yau, A Dynamical Approach to Random Matrix Theory,
vol. 28. American Mathematical Society, 2017.
ista: Erdös L, Yau H. 2017. A Dynamical Approach to Random Matrix Theory, American
Mathematical Society, 226p.
mla: Erdös, László, and Horng Yau. A Dynamical Approach to Random Matrix Theory.
Vol. 28, American Mathematical Society, 2017, doi:10.1090/cln/028.
short: L. Erdös, H. Yau, A Dynamical Approach to Random Matrix Theory, American
Mathematical Society, 2017.
date_created: 2018-12-11T11:47:13Z
date_published: 2017-01-01T00:00:00Z
date_updated: 2022-05-24T06:57:28Z
day: '01'
department:
- _id: LaEr
doi: 10.1090/cln/028
ec_funded: 1
intvolume: ' 28'
language:
- iso: eng
month: '01'
oa_version: None
page: '226'
project:
- _id: 258DCDE6-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '338804'
name: Random matrices, universality and disordered quantum systems
publication_identifier:
eisbn:
- 978-1-4704-4194-4
isbn:
- 9-781-4704-3648-3
publication_status: published
publisher: American Mathematical Society
publist_id: '7247'
quality_controlled: '1'
series_title: Courant Lecture Notes
status: public
title: A Dynamical Approach to Random Matrix Theory
type: book
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 28
year: '2017'
...
---
_id: '568'
abstract:
- lang: eng
text: 'We study robust properties of zero sets of continuous maps f: X → ℝn. Formally,
we analyze the family Z< r(f) := (g-1(0): ||g - f|| < r) of all zero sets
of all continuous maps g closer to f than r in the max-norm. All of these sets
are outside A := (x: |f(x)| ≥ r) and we claim that Z< r(f) is fully determined
by A and an element of a certain cohomotopy group which (by a recent result) is
computable whenever the dimension of X is at most 2n - 3. By considering all r
> 0 simultaneously, the pointed cohomotopy groups form a persistence module-a
structure leading to persistence diagrams as in the case of persistent homology
or well groups. Eventually, we get a descriptor of persistent robust properties
of zero sets that has better descriptive power (Theorem A) and better computability
status (Theorem B) than the established well diagrams. Moreover, if we endow every
point of each zero set with gradients of the perturbation, the robust description
of the zero sets by elements of cohomotopy groups is in some sense the best possible
(Theorem C).'
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. Persistence of zero sets. Homology, Homotopy and Applications.
2017;19(2):313-342. doi:10.4310/HHA.2017.v19.n2.a16
apa: Franek, P., & Krcál, M. (2017). Persistence of zero sets. Homology,
Homotopy and Applications. International Press. https://doi.org/10.4310/HHA.2017.v19.n2.a16
chicago: Franek, Peter, and Marek Krcál. “Persistence of Zero Sets.” Homology,
Homotopy and Applications. International Press, 2017. https://doi.org/10.4310/HHA.2017.v19.n2.a16.
ieee: P. Franek and M. Krcál, “Persistence of zero sets,” Homology, Homotopy
and Applications, vol. 19, no. 2. International Press, pp. 313–342, 2017.
ista: Franek P, Krcál M. 2017. Persistence of zero sets. Homology, Homotopy and
Applications. 19(2), 313–342.
mla: Franek, Peter, and Marek Krcál. “Persistence of Zero Sets.” Homology, Homotopy
and Applications, vol. 19, no. 2, International Press, 2017, pp. 313–42, doi:10.4310/HHA.2017.v19.n2.a16.
short: P. Franek, M. Krcál, Homology, Homotopy and Applications 19 (2017) 313–342.
date_created: 2018-12-11T11:47:14Z
date_published: 2017-01-01T00:00:00Z
date_updated: 2021-01-12T08:03:12Z
day: '01'
department:
- _id: UlWa
- _id: HeEd
doi: 10.4310/HHA.2017.v19.n2.a16
ec_funded: 1
intvolume: ' 19'
issue: '2'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/1507.04310
month: '01'
oa: 1
oa_version: Submitted Version
page: 313 - 342
project:
- _id: 25681D80-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '291734'
name: International IST Postdoc Fellowship Programme
- _id: 2590DB08-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '701309'
name: Atomic-Resolution Structures of Mitochondrial Respiratory Chain Supercomplexes
(H2020)
publication: Homology, Homotopy and Applications
publication_identifier:
issn:
- '15320073'
publication_status: published
publisher: International Press
publist_id: '7246'
quality_controlled: '1'
scopus_import: 1
status: public
title: Persistence of zero sets
type: journal_article
user_id: 4435EBFC-F248-11E8-B48F-1D18A9856A87
volume: 19
year: '2017'
...
---
_id: '570'
abstract:
- lang: eng
text: 'Most phenotypes are determined by molecular systems composed of specifically
interacting molecules. However, unlike for individual components, little is known
about the distributions of mutational effects of molecular systems as a whole.
We ask how the distribution of mutational effects of a transcriptional regulatory
system differs from the distributions of its components, by first independently,
and then simultaneously, mutating a transcription factor and the associated promoter
it represses. We find that the system distribution exhibits increased phenotypic
variation compared to individual component distributions - an effect arising from
intermolecular epistasis between the transcription factor and its DNA-binding
site. In large part, this epistasis can be qualitatively attributed to the structure
of the transcriptional regulatory system and could therefore be a common feature
in prokaryotes. Counter-intuitively, intermolecular epistasis can alleviate the
constraints of individual components, thereby increasing phenotypic variation
that selection could act on and facilitating adaptive evolution. '
article_number: e28921
author:
- first_name: Mato
full_name: Lagator, Mato
id: 345D25EC-F248-11E8-B48F-1D18A9856A87
last_name: Lagator
- first_name: Srdjan
full_name: Sarikas, Srdjan
id: 35F0286E-F248-11E8-B48F-1D18A9856A87
last_name: Sarikas
- first_name: Hande
full_name: Acar, Hande
id: 2DDF136A-F248-11E8-B48F-1D18A9856A87
last_name: Acar
orcid: 0000-0003-1986-9753
- first_name: Jonathan P
full_name: Bollback, Jonathan P
id: 2C6FA9CC-F248-11E8-B48F-1D18A9856A87
last_name: Bollback
orcid: 0000-0002-4624-4612
- first_name: Calin C
full_name: Guet, Calin C
id: 47F8433E-F248-11E8-B48F-1D18A9856A87
last_name: Guet
orcid: 0000-0001-6220-2052
citation:
ama: Lagator M, Sarikas S, Acar H, Bollback JP, Guet CC. Regulatory network structure
determines patterns of intermolecular epistasis. eLife. 2017;6. doi:10.7554/eLife.28921
apa: Lagator, M., Sarikas, S., Acar, H., Bollback, J. P., & Guet, C. C. (2017).
Regulatory network structure determines patterns of intermolecular epistasis.
ELife. eLife Sciences Publications. https://doi.org/10.7554/eLife.28921
chicago: Lagator, Mato, Srdjan Sarikas, Hande Acar, Jonathan P Bollback, and Calin
C Guet. “Regulatory Network Structure Determines Patterns of Intermolecular Epistasis.”
ELife. eLife Sciences Publications, 2017. https://doi.org/10.7554/eLife.28921.
ieee: M. Lagator, S. Sarikas, H. Acar, J. P. Bollback, and C. C. Guet, “Regulatory
network structure determines patterns of intermolecular epistasis,” eLife,
vol. 6. eLife Sciences Publications, 2017.
ista: Lagator M, Sarikas S, Acar H, Bollback JP, Guet CC. 2017. Regulatory network
structure determines patterns of intermolecular epistasis. eLife. 6, e28921.
mla: Lagator, Mato, et al. “Regulatory Network Structure Determines Patterns of
Intermolecular Epistasis.” ELife, vol. 6, e28921, eLife Sciences Publications,
2017, doi:10.7554/eLife.28921.
short: M. Lagator, S. Sarikas, H. Acar, J.P. Bollback, C.C. Guet, ELife 6 (2017).
date_created: 2018-12-11T11:47:14Z
date_published: 2017-11-13T00:00:00Z
date_updated: 2021-01-12T08:03:15Z
day: '13'
ddc:
- '576'
department:
- _id: CaGu
- _id: JoBo
- _id: NiBa
doi: 10.7554/eLife.28921
ec_funded: 1
file:
- access_level: open_access
checksum: 273ab17f33305e4eaafd911ff88e7c5b
content_type: application/pdf
creator: system
date_created: 2018-12-12T10:14:42Z
date_updated: 2020-07-14T12:47:10Z
file_id: '5096'
file_name: IST-2017-918-v1+1_elife-28921-figures-v3.pdf
file_size: 8453470
relation: main_file
- access_level: open_access
checksum: b433f90576c7be597cd43367946f8e7f
content_type: application/pdf
creator: system
date_created: 2018-12-12T10:14:43Z
date_updated: 2020-07-14T12:47:10Z
file_id: '5097'
file_name: IST-2017-918-v1+2_elife-28921-v3.pdf
file_size: 1953221
relation: main_file
file_date_updated: 2020-07-14T12:47:10Z
has_accepted_license: '1'
intvolume: ' 6'
language:
- iso: eng
month: '11'
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: 2578D616-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '648440'
name: Selective Barriers to Horizontal Gene Transfer
publication: eLife
publication_identifier:
issn:
- 2050084X
publication_status: published
publisher: eLife Sciences Publications
publist_id: '7244'
pubrep_id: '918'
quality_controlled: '1'
scopus_import: 1
status: public
title: Regulatory network structure determines patterns of intermolecular epistasis
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 6
year: '2017'
...
---
_id: '569'
abstract:
- lang: eng
text: The actomyosin ring generates force to ingress the cytokinetic cleavage furrow
in animal cells, yet its filament organization and the mechanism of contractility
is not well understood. We quantified actin filament order in human cells using
fluorescence polarization microscopy and found that cleavage furrow ingression
initiates by contraction of an equatorial actin network with randomly oriented
filaments. The network subsequently gradually reoriented actin filaments along
the cell equator. This strictly depended on myosin II activity, suggesting local
network reorganization by mechanical forces. Cortical laser microsurgery revealed
that during cytokinesis progression, mechanical tension increased substantially
along the direction of the cell equator, while the network contracted laterally
along the pole-to-pole axis without a detectable increase in tension. Our data
suggest that an asymmetric increase in cortical tension promotes filament reorientation
along the cytokinetic cleavage furrow, which might have implications for diverse
other biological processes involving actomyosin rings.
article_number: e30867
author:
- first_name: Felix
full_name: Spira, Felix
last_name: Spira
- first_name: Sara
full_name: Cuylen Haering, Sara
last_name: Cuylen Haering
- first_name: Shalin
full_name: Mehta, Shalin
last_name: Mehta
- first_name: Matthias
full_name: Samwer, Matthias
last_name: Samwer
- first_name: Anne
full_name: Reversat, Anne
id: 35B76592-F248-11E8-B48F-1D18A9856A87
last_name: Reversat
orcid: 0000-0003-0666-8928
- first_name: Amitabh
full_name: Verma, Amitabh
last_name: Verma
- first_name: Rudolf
full_name: Oldenbourg, Rudolf
last_name: Oldenbourg
- 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: Daniel
full_name: Gerlich, Daniel
last_name: Gerlich
citation:
ama: Spira F, Cuylen Haering S, Mehta S, et al. Cytokinesis in vertebrate cells
initiates by contraction of an equatorial actomyosin network composed of randomly
oriented filaments. eLife. 2017;6. doi:10.7554/eLife.30867
apa: Spira, F., Cuylen Haering, S., Mehta, S., Samwer, M., Reversat, A., Verma,
A., … Gerlich, D. (2017). Cytokinesis in vertebrate cells initiates by contraction
of an equatorial actomyosin network composed of randomly oriented filaments. ELife.
eLife Sciences Publications. https://doi.org/10.7554/eLife.30867
chicago: Spira, Felix, Sara Cuylen Haering, Shalin Mehta, Matthias Samwer, Anne
Reversat, Amitabh Verma, Rudolf Oldenbourg, Michael K Sixt, and Daniel Gerlich.
“Cytokinesis in Vertebrate Cells Initiates by Contraction of an Equatorial Actomyosin
Network Composed of Randomly Oriented Filaments.” ELife. eLife Sciences
Publications, 2017. https://doi.org/10.7554/eLife.30867.
ieee: F. Spira et al., “Cytokinesis in vertebrate cells initiates by contraction
of an equatorial actomyosin network composed of randomly oriented filaments,”
eLife, vol. 6. eLife Sciences Publications, 2017.
ista: Spira F, Cuylen Haering S, Mehta S, Samwer M, Reversat A, Verma A, Oldenbourg
R, Sixt MK, Gerlich D. 2017. Cytokinesis in vertebrate cells initiates by contraction
of an equatorial actomyosin network composed of randomly oriented filaments. eLife.
6, e30867.
mla: Spira, Felix, et al. “Cytokinesis in Vertebrate Cells Initiates by Contraction
of an Equatorial Actomyosin Network Composed of Randomly Oriented Filaments.”
ELife, vol. 6, e30867, eLife Sciences Publications, 2017, doi:10.7554/eLife.30867.
short: F. Spira, S. Cuylen Haering, S. Mehta, M. Samwer, A. Reversat, A. Verma,
R. Oldenbourg, M.K. Sixt, D. Gerlich, ELife 6 (2017).
date_created: 2018-12-11T11:47:14Z
date_published: 2017-11-06T00:00:00Z
date_updated: 2023-02-23T12:30:29Z
day: '06'
ddc:
- '570'
department:
- _id: MiSi
doi: 10.7554/eLife.30867
file:
- access_level: open_access
checksum: ba09c1451153d39e4f4b7cee013e314c
content_type: application/pdf
creator: system
date_created: 2018-12-12T10:10:40Z
date_updated: 2020-07-14T12:47:10Z
file_id: '4829'
file_name: IST-2017-919-v1+1_elife-30867-figures-v1.pdf
file_size: 9666973
relation: main_file
- access_level: open_access
checksum: 01eb51f1d6ad679947415a51c988e137
content_type: application/pdf
creator: system
date_created: 2018-12-12T10:10:41Z
date_updated: 2020-07-14T12:47:10Z
file_id: '4830'
file_name: IST-2017-919-v1+2_elife-30867-v1.pdf
file_size: 5951246
relation: main_file
file_date_updated: 2020-07-14T12:47:10Z
has_accepted_license: '1'
intvolume: ' 6'
language:
- iso: eng
month: '11'
oa: 1
oa_version: Published Version
publication: eLife
publication_identifier:
issn:
- 2050084X
publication_status: published
publisher: eLife Sciences Publications
publist_id: '7245'
pubrep_id: '919'
quality_controlled: '1'
scopus_import: 1
status: public
title: Cytokinesis in vertebrate cells initiates by contraction of an equatorial actomyosin
network composed of randomly oriented filaments
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 6
year: '2017'
...
---
_id: '571'
abstract:
- lang: eng
text: Blood platelets are critical for hemostasis and thrombosis and play diverse
roles during immune responses. Despite these versatile tasks in mammalian biology,
their skills on a cellular level are deemed limited, mainly consisting in rolling,
adhesion, and aggregate formation. Here, we identify an unappreciated asset of
platelets and show that adherent platelets use adhesion receptors to mechanically
probe the adhesive substrate in their local microenvironment. When actomyosin-dependent
traction forces overcome substrate resistance, platelets migrate and pile up the
adhesive substrate together with any bound particulate material. They use this
ability to act as cellular scavengers, scanning the vascular surface for potential
invaders and collecting deposited bacteria. Microbe collection by migrating platelets
boosts the activity of professional phagocytes, exacerbating inflammatory tissue
injury in sepsis. This assigns platelets a central role in innate immune responses
and identifies them as potential targets to dampen inflammatory tissue damage
in clinical scenarios of severe systemic infection. In addition to their role
in thrombosis and hemostasis, platelets can also migrate to sites of infection
to help trap bacteria and clear the vascular surface.
author:
- first_name: Florian R
full_name: Gärtner, Florian R
id: 397A88EE-F248-11E8-B48F-1D18A9856A87
last_name: Gärtner
orcid: 0000-0001-6120-3723
- first_name: Zerkah
full_name: Ahmad, Zerkah
last_name: Ahmad
- first_name: Gerhild
full_name: Rosenberger, Gerhild
last_name: Rosenberger
- first_name: Shuxia
full_name: Fan, Shuxia
last_name: Fan
- first_name: Leo
full_name: Nicolai, Leo
last_name: Nicolai
- first_name: Benjamin
full_name: Busch, Benjamin
last_name: Busch
- first_name: Gökce
full_name: Yavuz, Gökce
last_name: Yavuz
- first_name: Manja
full_name: Luckner, Manja
last_name: Luckner
- first_name: Hellen
full_name: Ishikawa Ankerhold, Hellen
last_name: Ishikawa Ankerhold
- first_name: Roman
full_name: Hennel, Roman
last_name: Hennel
- first_name: Alexandre
full_name: Benechet, Alexandre
last_name: Benechet
- first_name: Michael
full_name: Lorenz, Michael
last_name: Lorenz
- first_name: Sue
full_name: Chandraratne, Sue
last_name: Chandraratne
- first_name: Irene
full_name: Schubert, Irene
last_name: Schubert
- first_name: Sebastian
full_name: Helmer, Sebastian
last_name: Helmer
- first_name: Bianca
full_name: Striednig, Bianca
last_name: Striednig
- first_name: Konstantin
full_name: Stark, Konstantin
last_name: Stark
- first_name: Marek
full_name: Janko, Marek
last_name: Janko
- first_name: Ralph
full_name: Böttcher, Ralph
last_name: Böttcher
- first_name: Admar
full_name: Verschoor, Admar
last_name: Verschoor
- first_name: Catherine
full_name: Leon, Catherine
last_name: Leon
- first_name: Christian
full_name: Gachet, Christian
last_name: Gachet
- first_name: Thomas
full_name: Gudermann, Thomas
last_name: Gudermann
- first_name: Michael
full_name: Mederos Y Schnitzler, Michael
last_name: Mederos Y Schnitzler
- first_name: Zachary
full_name: Pincus, Zachary
last_name: Pincus
- first_name: Matteo
full_name: Iannacone, Matteo
last_name: Iannacone
- first_name: Rainer
full_name: Haas, Rainer
last_name: Haas
- first_name: Gerhard
full_name: Wanner, Gerhard
last_name: Wanner
- first_name: Kirsten
full_name: Lauber, Kirsten
last_name: Lauber
- 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: Steffen
full_name: Massberg, Steffen
last_name: Massberg
citation:
ama: Gärtner FR, Ahmad Z, Rosenberger G, et al. Migrating platelets are mechano
scavengers that collect and bundle bacteria. Cell Press. 2017;171(6):1368-1382.
doi:10.1016/j.cell.2017.11.001
apa: Gärtner, F. R., Ahmad, Z., Rosenberger, G., Fan, S., Nicolai, L., Busch, B.,
… Massberg, S. (2017). Migrating platelets are mechano scavengers that collect
and bundle bacteria. Cell Press. Cell Press. https://doi.org/10.1016/j.cell.2017.11.001
chicago: Gärtner, Florian R, Zerkah Ahmad, Gerhild Rosenberger, Shuxia Fan, Leo
Nicolai, Benjamin Busch, Gökce Yavuz, et al. “Migrating Platelets Are Mechano
Scavengers That Collect and Bundle Bacteria.” Cell Press. Cell Press, 2017.
https://doi.org/10.1016/j.cell.2017.11.001.
ieee: F. R. Gärtner et al., “Migrating platelets are mechano scavengers that
collect and bundle bacteria,” Cell Press, vol. 171, no. 6. Cell Press,
pp. 1368–1382, 2017.
ista: Gärtner FR, Ahmad Z, Rosenberger G, Fan S, Nicolai L, Busch B, Yavuz G, Luckner
M, Ishikawa Ankerhold H, Hennel R, Benechet A, Lorenz M, Chandraratne S, Schubert
I, Helmer S, Striednig B, Stark K, Janko M, Böttcher R, Verschoor A, Leon C, Gachet
C, Gudermann T, Mederos Y Schnitzler M, Pincus Z, Iannacone M, Haas R, Wanner
G, Lauber K, Sixt MK, Massberg S. 2017. Migrating platelets are mechano scavengers
that collect and bundle bacteria. Cell Press. 171(6), 1368–1382.
mla: Gärtner, Florian R., et al. “Migrating Platelets Are Mechano Scavengers That
Collect and Bundle Bacteria.” Cell Press, vol. 171, no. 6, Cell Press,
2017, pp. 1368–82, doi:10.1016/j.cell.2017.11.001.
short: F.R. Gärtner, Z. Ahmad, G. Rosenberger, S. Fan, L. Nicolai, B. Busch, G.
Yavuz, M. Luckner, H. Ishikawa Ankerhold, R. Hennel, A. Benechet, M. Lorenz, S.
Chandraratne, I. Schubert, S. Helmer, B. Striednig, K. Stark, M. Janko, R. Böttcher,
A. Verschoor, C. Leon, C. Gachet, T. Gudermann, M. Mederos Y Schnitzler, Z. Pincus,
M. Iannacone, R. Haas, G. Wanner, K. Lauber, M.K. Sixt, S. Massberg, Cell Press
171 (2017) 1368–1382.
date_created: 2018-12-11T11:47:15Z
date_published: 2017-11-30T00:00:00Z
date_updated: 2021-01-12T08:03:15Z
day: '30'
department:
- _id: MiSi
doi: 10.1016/j.cell.2017.11.001
ec_funded: 1
intvolume: ' 171'
issue: '6'
language:
- iso: eng
month: '11'
oa_version: None
page: 1368 - 1382
project:
- _id: 260AA4E2-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '747687'
name: Mechanical Adaptation of Lamellipodial Actin Networks in Migrating Cells
publication: Cell Press
publication_identifier:
issn:
- '00928674'
publication_status: published
publisher: Cell Press
publist_id: '7243'
quality_controlled: '1'
scopus_import: 1
status: public
title: Migrating platelets are mechano scavengers that collect and bundle bacteria
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 171
year: '2017'
...
---
_id: '572'
abstract:
- lang: eng
text: In this review, we summarize the different biosynthesis-related pathways that
contribute to the regulation of endogenous auxin in plants. We demonstrate that
all known genes involved in auxin biosynthesis also have a role in root formation,
from the initiation of a root meristem during embryogenesis to the generation
of a functional root system with a primary root, secondary lateral root branches
and adventitious roots. Furthermore, the versatile adaptation of root development
in response to environmental challenges is mediated by both local and distant
control of auxin biosynthesis. In conclusion, auxin homeostasis mediated by spatial
and temporal regulation of auxin biosynthesis plays a central role in determining
root architecture.
article_number: '2587'
article_processing_charge: No
author:
- first_name: Damilola
full_name: Olatunji, Damilola
last_name: Olatunji
- first_name: Danny
full_name: Geelen, Danny
last_name: Geelen
- first_name: Inge
full_name: Verstraeten, Inge
id: 362BF7FE-F248-11E8-B48F-1D18A9856A87
last_name: Verstraeten
orcid: 0000-0001-7241-2328
citation:
ama: Olatunji D, Geelen D, Verstraeten I. Control of endogenous auxin levels in
plant root development. International Journal of Molecular Sciences. 2017;18(12).
doi:10.3390/ijms18122587
apa: Olatunji, D., Geelen, D., & Verstraeten, I. (2017). Control of endogenous
auxin levels in plant root development. International Journal of Molecular
Sciences. MDPI. https://doi.org/10.3390/ijms18122587
chicago: Olatunji, Damilola, Danny Geelen, and Inge Verstraeten. “Control of Endogenous
Auxin Levels in Plant Root Development.” International Journal of Molecular
Sciences. MDPI, 2017. https://doi.org/10.3390/ijms18122587.
ieee: D. Olatunji, D. Geelen, and I. Verstraeten, “Control of endogenous auxin levels
in plant root development,” International Journal of Molecular Sciences,
vol. 18, no. 12. MDPI, 2017.
ista: Olatunji D, Geelen D, Verstraeten I. 2017. Control of endogenous auxin levels
in plant root development. International Journal of Molecular Sciences. 18(12),
2587.
mla: Olatunji, Damilola, et al. “Control of Endogenous Auxin Levels in Plant Root
Development.” International Journal of Molecular Sciences, vol. 18, no.
12, 2587, MDPI, 2017, doi:10.3390/ijms18122587.
short: D. Olatunji, D. Geelen, I. Verstraeten, International Journal of Molecular
Sciences 18 (2017).
date_created: 2018-12-11T11:47:15Z
date_published: 2017-12-01T00:00:00Z
date_updated: 2021-01-12T08:03:16Z
day: '01'
ddc:
- '580'
department:
- _id: JiFr
doi: 10.3390/ijms18122587
file:
- access_level: open_access
checksum: 82d51f11e493f7eec02976d9a9a9805e
content_type: application/pdf
creator: system
date_created: 2018-12-12T10:08:55Z
date_updated: 2020-07-14T12:47:10Z
file_id: '4718'
file_name: IST-2017-917-v1+1_ijms-18-02587.pdf
file_size: 920962
relation: main_file
file_date_updated: 2020-07-14T12:47:10Z
has_accepted_license: '1'
intvolume: ' 18'
issue: '12'
language:
- iso: eng
month: '12'
oa: 1
oa_version: Published Version
publication: International Journal of Molecular Sciences
publication_status: published
publisher: MDPI
publist_id: '7242'
pubrep_id: '917'
quality_controlled: '1'
scopus_import: '1'
status: public
title: Control of endogenous auxin levels in plant root development
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: '2017'
...
---
_id: '5800'
abstract:
- lang: eng
text: This paper presents a novel study on the functional gradation of coordinate
planes in connection with the thinnest and tunnel-free (i.e., naive) discretization
of sphere in the integer space. For each of the 48-symmetric quadraginta octants
of naive sphere with integer radius and integer center, we show that the corresponding
voxel set forms a bijection with its projected pixel set on a unique coordinate
plane, which thereby serves as its functional plane. We use this fundamental property
to prove several other theoretical results for naive sphere. First, the quadraginta
octants form symmetry groups and subgroups with certain equivalent topological
properties. Second, a naive sphere is always unique and consists of fewest voxels.
Third, it is efficiently constructible from its functional-plane projection. And
finally, a special class of 4-symmetric discrete 3D circles can be constructed
on a naive sphere based on back projection from the functional plane.
author:
- first_name: Ranita
full_name: Biswas, Ranita
id: 3C2B033E-F248-11E8-B48F-1D18A9856A87
last_name: Biswas
orcid: 0000-0002-5372-7890
- first_name: Partha
full_name: Bhowmick, Partha
last_name: Bhowmick
citation:
ama: Biswas R, Bhowmick P. On the functionality and usefulness of Quadraginta octants
of naive sphere. Journal of Mathematical Imaging and Vision. 2017;59(1):69-83.
doi:10.1007/s10851-017-0718-4
apa: Biswas, R., & Bhowmick, P. (2017). On the functionality and usefulness
of Quadraginta octants of naive sphere. Journal of Mathematical Imaging and
Vision. Springer Nature. https://doi.org/10.1007/s10851-017-0718-4
chicago: Biswas, Ranita, and Partha Bhowmick. “On the Functionality and Usefulness
of Quadraginta Octants of Naive Sphere.” Journal of Mathematical Imaging and
Vision. Springer Nature, 2017. https://doi.org/10.1007/s10851-017-0718-4.
ieee: R. Biswas and P. Bhowmick, “On the functionality and usefulness of Quadraginta
octants of naive sphere,” Journal of Mathematical Imaging and Vision, vol.
59, no. 1. Springer Nature, pp. 69–83, 2017.
ista: Biswas R, Bhowmick P. 2017. On the functionality and usefulness of Quadraginta
octants of naive sphere. Journal of Mathematical Imaging and Vision. 59(1), 69–83.
mla: Biswas, Ranita, and Partha Bhowmick. “On the Functionality and Usefulness of
Quadraginta Octants of Naive Sphere.” Journal of Mathematical Imaging and Vision,
vol. 59, no. 1, Springer Nature, 2017, pp. 69–83, doi:10.1007/s10851-017-0718-4.
short: R. Biswas, P. Bhowmick, Journal of Mathematical Imaging and Vision 59 (2017)
69–83.
date_created: 2019-01-08T20:42:08Z
date_published: 2017-09-01T00:00:00Z
date_updated: 2021-01-12T08:03:34Z
day: '01'
doi: 10.1007/s10851-017-0718-4
extern: '1'
intvolume: ' 59'
issue: '1'
language:
- iso: eng
month: '09'
oa_version: None
page: 69-83
publication: Journal of Mathematical Imaging and Vision
publication_identifier:
issn:
- '09249907'
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
status: public
title: On the functionality and usefulness of Quadraginta octants of naive sphere
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 59
year: '2017'
...
---
_id: '5799'
abstract:
- lang: eng
text: We construct a polyhedral surface called a graceful surface, which provides
best possible approximation to a given sphere regarding certain criteria. In digital
geometry terms, the graceful surface is uniquely characterized by its minimality
while guaranteeing the connectivity of certain discrete (polyhedral) curves defined
on it. The notion of “gracefulness” was first proposed in Brimkov and Barneva
(1999) and shown to be useful for triangular mesh discretization through graceful
planes and graceful lines. In this paper we extend the considerations to a nonlinear
object such as a sphere. In particular, we investigate the properties of a discrete
geodesic path between two voxels and show that discrete 3D circles, circular arcs,
and Mobius triangles are all constructible on a graceful sphere, with guaranteed
minimum thickness and the desired connectivity in the discrete topological space.
author:
- first_name: Ranita
full_name: Biswas, Ranita
id: 3C2B033E-F248-11E8-B48F-1D18A9856A87
last_name: Biswas
orcid: 0000-0002-5372-7890
- first_name: Partha
full_name: Bhowmick, Partha
last_name: Bhowmick
- first_name: Valentin E.
full_name: Brimkov, Valentin E.
last_name: Brimkov
citation:
ama: Biswas R, Bhowmick P, Brimkov VE. On the polyhedra of graceful spheres and
circular geodesics. Discrete Applied Mathematics. 2017;216:362-375. doi:10.1016/j.dam.2015.11.017
apa: Biswas, R., Bhowmick, P., & Brimkov, V. E. (2017). On the polyhedra of
graceful spheres and circular geodesics. Discrete Applied Mathematics.
Elsevier. https://doi.org/10.1016/j.dam.2015.11.017
chicago: Biswas, Ranita, Partha Bhowmick, and Valentin E. Brimkov. “On the Polyhedra
of Graceful Spheres and Circular Geodesics.” Discrete Applied Mathematics.
Elsevier, 2017. https://doi.org/10.1016/j.dam.2015.11.017.
ieee: R. Biswas, P. Bhowmick, and V. E. Brimkov, “On the polyhedra of graceful spheres
and circular geodesics,” Discrete Applied Mathematics, vol. 216. Elsevier,
pp. 362–375, 2017.
ista: Biswas R, Bhowmick P, Brimkov VE. 2017. On the polyhedra of graceful spheres
and circular geodesics. Discrete Applied Mathematics. 216, 362–375.
mla: Biswas, Ranita, et al. “On the Polyhedra of Graceful Spheres and Circular Geodesics.”
Discrete Applied Mathematics, vol. 216, Elsevier, 2017, pp. 362–75, doi:10.1016/j.dam.2015.11.017.
short: R. Biswas, P. Bhowmick, V.E. Brimkov, Discrete Applied Mathematics 216 (2017)
362–375.
date_created: 2019-01-08T20:41:12Z
date_published: 2017-01-10T00:00:00Z
date_updated: 2021-01-12T08:03:33Z
day: '10'
doi: 10.1016/j.dam.2015.11.017
extern: '1'
intvolume: ' 216'
language:
- iso: eng
month: '01'
oa_version: None
page: 362-375
publication: Discrete Applied Mathematics
publication_identifier:
issn:
- 0166-218X
publication_status: published
publisher: Elsevier
quality_controlled: '1'
status: public
title: On the polyhedra of graceful spheres and circular geodesics
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 216
year: '2017'
...
---
_id: '5801'
abstract:
- lang: eng
text: Space filling circles and spheres have various applications in mathematical
imaging and physical modeling. In this paper, we first show how the thinnest (i.e.,
2-minimal) model of digital sphere can be augmented to a space filling model by
fixing certain “simple voxels” and “filler voxels” associated with it. Based on
elementary number-theoretic properties of such voxels, we design an efficient
incremental algorithm for generation of these space filling spheres with successively
increasing radius. The novelty of the proposed technique is established further
through circular space filling on 3D digital plane. As evident from a preliminary
set of experimental result, this can particularly be useful for parallel computing
of 3D Voronoi diagrams in the digital space.
alternative_title:
- LNCS
article_processing_charge: No
author:
- first_name: Shivam
full_name: Dwivedi, Shivam
last_name: Dwivedi
- first_name: Aniket
full_name: Gupta, Aniket
last_name: Gupta
- first_name: Siddhant
full_name: Roy, Siddhant
last_name: Roy
- first_name: Ranita
full_name: Biswas, Ranita
id: 3C2B033E-F248-11E8-B48F-1D18A9856A87
last_name: Biswas
orcid: 0000-0002-5372-7890
- first_name: Partha
full_name: Bhowmick, Partha
last_name: Bhowmick
citation:
ama: 'Dwivedi S, Gupta A, Roy S, Biswas R, Bhowmick P. Fast and Efficient Incremental
Algorithms for Circular and Spherical Propagation in Integer Space. In: 20th
IAPR International Conference. Vol 10502. Cham: Springer Nature; 2017:347-359.
doi:10.1007/978-3-319-66272-5_28'
apa: 'Dwivedi, S., Gupta, A., Roy, S., Biswas, R., & Bhowmick, P. (2017). Fast
and Efficient Incremental Algorithms for Circular and Spherical Propagation in
Integer Space. In 20th IAPR International Conference (Vol. 10502, pp. 347–359).
Cham: Springer Nature. https://doi.org/10.1007/978-3-319-66272-5_28'
chicago: 'Dwivedi, Shivam, Aniket Gupta, Siddhant Roy, Ranita Biswas, and Partha
Bhowmick. “Fast and Efficient Incremental Algorithms for Circular and Spherical
Propagation in Integer Space.” In 20th IAPR International Conference, 10502:347–59.
Cham: Springer Nature, 2017. https://doi.org/10.1007/978-3-319-66272-5_28.'
ieee: S. Dwivedi, A. Gupta, S. Roy, R. Biswas, and P. Bhowmick, “Fast and Efficient
Incremental Algorithms for Circular and Spherical Propagation in Integer Space,”
in 20th IAPR International Conference, Vienna, Austria, 2017, vol. 10502,
pp. 347–359.
ista: 'Dwivedi S, Gupta A, Roy S, Biswas R, Bhowmick P. 2017. Fast and Efficient
Incremental Algorithms for Circular and Spherical Propagation in Integer Space.
20th IAPR International Conference. DGCI: International Conference on Discrete
Geometry for Computer Imagery, LNCS, vol. 10502, 347–359.'
mla: Dwivedi, Shivam, et al. “Fast and Efficient Incremental Algorithms for Circular
and Spherical Propagation in Integer Space.” 20th IAPR International Conference,
vol. 10502, Springer Nature, 2017, pp. 347–59, doi:10.1007/978-3-319-66272-5_28.
short: S. Dwivedi, A. Gupta, S. Roy, R. Biswas, P. Bhowmick, in:, 20th IAPR International
Conference, Springer Nature, Cham, 2017, pp. 347–359.
conference:
end_date: 2017-09-21
location: Vienna, Austria
name: 'DGCI: International Conference on Discrete Geometry for Computer Imagery'
start_date: 2017-09-19
date_created: 2019-01-08T20:42:22Z
date_published: 2017-08-22T00:00:00Z
date_updated: 2022-01-27T15:34:25Z
day: '22'
doi: 10.1007/978-3-319-66272-5_28
extern: '1'
intvolume: ' 10502'
language:
- iso: eng
month: '08'
oa_version: None
page: 347-359
place: Cham
publication: 20th IAPR International Conference
publication_identifier:
eisbn:
- 978-3-319-66272-5
eissn:
- 1611-3349
isbn:
- 978-3-319-66271-8
issn:
- 0302-9743
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
status: public
title: Fast and Efficient Incremental Algorithms for Circular and Spherical Propagation
in Integer Space
type: conference
user_id: 8b945eb4-e2f2-11eb-945a-df72226e66a9
volume: 10502
year: '2017'
...
---
_id: '5803'
abstract:
- lang: eng
text: Different distance metrics produce Voronoi diagrams with different properties.
It is a well-known that on the (real) 2D plane or even on any 3D plane, a Voronoi
diagram (VD) based on the Euclidean distance metric produces convex Voronoi regions.
In this paper, we first show that this metric produces a persistent VD on the
2D digital plane, as it comprises digitally convex Voronoi regions and hence correctly
approximates the corresponding VD on the 2D real plane. Next, we show that on
a 3D digital plane D, the Euclidean metric spanning over its voxel set does not
guarantee a digital VD which is persistent with the real-space VD. As a solution,
we introduce a novel concept of functional-plane-convexity, which is ensured by
the Euclidean metric spanning over the pedal set of D. Necessary proofs and some
visual result have been provided to adjudge the merit and usefulness of the proposed
concept.
alternative_title:
- LNCS
article_processing_charge: No
author:
- first_name: Ranita
full_name: Biswas, Ranita
id: 3C2B033E-F248-11E8-B48F-1D18A9856A87
last_name: Biswas
orcid: 0000-0002-5372-7890
- first_name: Partha
full_name: Bhowmick, Partha
last_name: Bhowmick
citation:
ama: 'Biswas R, Bhowmick P. Construction of persistent Voronoi diagram on 3D digital
plane. In: Combinatorial Image Analysis. Vol 10256. Cham: Springer Nature;
2017:93-104. doi:10.1007/978-3-319-59108-7_8'
apa: 'Biswas, R., & Bhowmick, P. (2017). Construction of persistent Voronoi
diagram on 3D digital plane. In Combinatorial image analysis (Vol. 10256,
pp. 93–104). Cham: Springer Nature. https://doi.org/10.1007/978-3-319-59108-7_8'
chicago: 'Biswas, Ranita, and Partha Bhowmick. “Construction of Persistent Voronoi
Diagram on 3D Digital Plane.” In Combinatorial Image Analysis, 10256:93–104.
Cham: Springer Nature, 2017. https://doi.org/10.1007/978-3-319-59108-7_8.'
ieee: 'R. Biswas and P. Bhowmick, “Construction of persistent Voronoi diagram on
3D digital plane,” in Combinatorial image analysis, vol. 10256, Cham: Springer
Nature, 2017, pp. 93–104.'
ista: 'Biswas R, Bhowmick P. 2017.Construction of persistent Voronoi diagram on
3D digital plane. In: Combinatorial image analysis. LNCS, vol. 10256, 93–104.'
mla: Biswas, Ranita, and Partha Bhowmick. “Construction of Persistent Voronoi Diagram
on 3D Digital Plane.” Combinatorial Image Analysis, vol. 10256, Springer
Nature, 2017, pp. 93–104, doi:10.1007/978-3-319-59108-7_8.
short: R. Biswas, P. Bhowmick, in:, Combinatorial Image Analysis, Springer Nature,
Cham, 2017, pp. 93–104.
conference:
end_date: 2017-06-21
location: Plovdiv, Bulgaria
name: 'IWCIA: International Workshop on Combinatorial Image Analysis'
start_date: 2017-06-19
date_created: 2019-01-08T20:42:56Z
date_published: 2017-05-17T00:00:00Z
date_updated: 2022-01-28T07:48:24Z
day: '17'
department:
- _id: HeEd
doi: 10.1007/978-3-319-59108-7_8
extern: '1'
intvolume: ' 10256'
language:
- iso: eng
month: '05'
oa_version: None
page: 93-104
place: Cham
publication: Combinatorial image analysis
publication_identifier:
isbn:
- 978-3-319-59107-0
- 978-3-319-59108-7
issn:
- 0302-9743
- 1611-3349
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
status: public
title: Construction of persistent Voronoi diagram on 3D digital plane
type: book_chapter
user_id: 8b945eb4-e2f2-11eb-945a-df72226e66a9
volume: 10256
year: '2017'
...
---
_id: '5802'
abstract:
- lang: eng
text: This papers introduces a definition of digital primitives based on focal points
and weighted distances (with positive weights). The proposed definition is applicable
to general dimensions and covers in its gamut various regular curves and surfaces
like circles, ellipses, digital spheres and hyperspheres, ellipsoids and k-ellipsoids,
Cartesian k-ovals, etc. Several interesting properties are presented for this
class of digital primitives such as space partitioning, topological separation,
and connectivity properties. To demonstrate further the potential of this new
way of defining digital primitives, we propose, as extension, another class of
digital conics defined by focus-directrix combination.
alternative_title:
- LNCS
article_processing_charge: No
author:
- first_name: Eric
full_name: Andres, Eric
last_name: Andres
- first_name: Ranita
full_name: Biswas, Ranita
id: 3C2B033E-F248-11E8-B48F-1D18A9856A87
last_name: Biswas
orcid: 0000-0002-5372-7890
- first_name: Partha
full_name: Bhowmick, Partha
last_name: Bhowmick
citation:
ama: 'Andres E, Biswas R, Bhowmick P. Digital primitives defined by weighted focal
set. In: 20th IAPR International Conference. Vol 10502. Cham: Springer
Nature; 2017:388-398. doi:10.1007/978-3-319-66272-5_31'
apa: 'Andres, E., Biswas, R., & Bhowmick, P. (2017). Digital primitives defined
by weighted focal set. In 20th IAPR International Conference (Vol. 10502,
pp. 388–398). Cham: Springer Nature. https://doi.org/10.1007/978-3-319-66272-5_31'
chicago: 'Andres, Eric, Ranita Biswas, and Partha Bhowmick. “Digital Primitives
Defined by Weighted Focal Set.” In 20th IAPR International Conference,
10502:388–98. Cham: Springer Nature, 2017. https://doi.org/10.1007/978-3-319-66272-5_31.'
ieee: E. Andres, R. Biswas, and P. Bhowmick, “Digital primitives defined by weighted
focal set,” in 20th IAPR International Conference, Vienna, Austria, 2017,
vol. 10502, pp. 388–398.
ista: 'Andres E, Biswas R, Bhowmick P. 2017. Digital primitives defined by weighted
focal set. 20th IAPR International Conference. DGCI: International Conference
on Discrete Geometry for Computer Imagery, LNCS, vol. 10502, 388–398.'
mla: Andres, Eric, et al. “Digital Primitives Defined by Weighted Focal Set.” 20th
IAPR International Conference, vol. 10502, Springer Nature, 2017, pp. 388–98,
doi:10.1007/978-3-319-66272-5_31.
short: E. Andres, R. Biswas, P. Bhowmick, in:, 20th IAPR International Conference,
Springer Nature, Cham, 2017, pp. 388–398.
conference:
end_date: 2017-09-21
location: Vienna, Austria
name: 'DGCI: International Conference on Discrete Geometry for Computer Imagery'
start_date: 2017-09-19
date_created: 2019-01-08T20:42:39Z
date_published: 2017-08-22T00:00:00Z
date_updated: 2022-01-27T15:38:35Z
day: '22'
doi: 10.1007/978-3-319-66272-5_31
extern: '1'
intvolume: ' 10502'
language:
- iso: eng
month: '08'
oa_version: None
page: 388-398
place: Cham
publication: 20th IAPR International Conference
publication_identifier:
eisbn:
- 978-3-319-66272-5
eissn:
- 1611-3349
isbn:
- 978-3-319-66271-8
issn:
- 0302-9743
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
status: public
title: Digital primitives defined by weighted focal set
type: conference
user_id: 8b945eb4-e2f2-11eb-945a-df72226e66a9
volume: 10502
year: '2017'
...
---
_id: '593'
abstract:
- lang: eng
text: Bell correlations, indicating nonlocality in composite quantum systems, were
until recently only seen in small systems. Here, we demonstrate Bell correlations
in squeezed states of 5×105 Rb87 atoms. The correlations are inferred using collective
measurements as witnesses and are statistically significant to 124 standard deviations.
The states are both generated and characterized using optical-cavity aided measurements.
author:
- first_name: Nils
full_name: Engelsen, Nils
last_name: Engelsen
- first_name: Rajiv
full_name: Krishnakumar, Rajiv
last_name: Krishnakumar
- first_name: Onur
full_name: Hosten, Onur
id: 4C02D85E-F248-11E8-B48F-1D18A9856A87
last_name: Hosten
orcid: 0000-0002-2031-204X
- first_name: Mark
full_name: Kasevich, Mark
last_name: Kasevich
citation:
ama: Engelsen N, Krishnakumar R, Hosten O, Kasevich M. Bell correlations in spin-squeezed
states of 500 000 atoms. Physical Review Letters. 2017;118(14). doi:10.1103/PhysRevLett.118.140401
apa: Engelsen, N., Krishnakumar, R., Hosten, O., & Kasevich, M. (2017). Bell
correlations in spin-squeezed states of 500 000 atoms. Physical Review Letters.
American Physical Society. https://doi.org/10.1103/PhysRevLett.118.140401
chicago: Engelsen, Nils, Rajiv Krishnakumar, Onur Hosten, and Mark Kasevich. “Bell
Correlations in Spin-Squeezed States of 500 000 Atoms.” Physical Review Letters.
American Physical Society, 2017. https://doi.org/10.1103/PhysRevLett.118.140401.
ieee: N. Engelsen, R. Krishnakumar, O. Hosten, and M. Kasevich, “Bell correlations
in spin-squeezed states of 500 000 atoms,” Physical Review Letters, vol.
118, no. 14. American Physical Society, 2017.
ista: Engelsen N, Krishnakumar R, Hosten O, Kasevich M. 2017. Bell correlations
in spin-squeezed states of 500 000 atoms. Physical Review Letters. 118(14).
mla: Engelsen, Nils, et al. “Bell Correlations in Spin-Squeezed States of 500 000
Atoms.” Physical Review Letters, vol. 118, no. 14, American Physical Society,
2017, doi:10.1103/PhysRevLett.118.140401.
short: N. Engelsen, R. Krishnakumar, O. Hosten, M. Kasevich, Physical Review Letters
118 (2017).
date_created: 2018-12-11T11:47:23Z
date_published: 2017-04-03T00:00:00Z
date_updated: 2021-01-12T08:05:16Z
day: '03'
doi: 10.1103/PhysRevLett.118.140401
extern: '1'
intvolume: ' 118'
issue: '14'
language:
- iso: eng
month: '04'
oa_version: None
publication: Physical Review Letters
publication_status: published
publisher: American Physical Society
publist_id: '7212'
status: public
title: Bell correlations in spin-squeezed states of 500 000 atoms
type: journal_article
user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87
volume: 118
year: '2017'
...
---
_id: '600'
abstract:
- lang: eng
text: Transcription initiation at the ribosomal RNA promoter requires RNA polymerase
(Pol) I and the initiation factors Rrn3 and core factor (CF). Here, we combine
X-ray crystallography and cryo-electron microscopy (cryo-EM) to obtain a molecular
model for basal Pol I initiation. The three-subunit CF binds upstream promoter
DNA, docks to the Pol I-Rrn3 complex, and loads DNA into the expanded active center
cleft of the polymerase. DNA unwinding between the Pol I protrusion and clamp
domains enables cleft contraction, resulting in an active Pol I conformation and
RNA synthesis. Comparison with the Pol II system suggests that promoter specificity
relies on a distinct “bendability” and “meltability” of the promoter sequence
that enables contacts between initiation factors, DNA, and polymerase.
article_processing_charge: No
author:
- first_name: Christoph
full_name: Engel, Christoph
last_name: Engel
- first_name: Tobias
full_name: Gubbey, Tobias
last_name: Gubbey
- first_name: Simon
full_name: Neyer, Simon
last_name: Neyer
- first_name: Sarah
full_name: Sainsbury, Sarah
last_name: Sainsbury
- first_name: Christiane
full_name: Oberthuer, Christiane
last_name: Oberthuer
- first_name: Carlo
full_name: Baejen, Carlo
last_name: Baejen
- first_name: Carrie A
full_name: Bernecky, Carrie A
id: 2CB9DFE2-F248-11E8-B48F-1D18A9856A87
last_name: Bernecky
orcid: 0000-0003-0893-7036
- first_name: Patrick
full_name: Cramer, Patrick
last_name: Cramer
citation:
ama: Engel C, Gubbey T, Neyer S, et al. Structural basis of RNA polymerase I transcription
initiation. Cell. 2017;169(1):120-131.e22. doi:10.1016/j.cell.2017.03.003
apa: Engel, C., Gubbey, T., Neyer, S., Sainsbury, S., Oberthuer, C., Baejen, C.,
… Cramer, P. (2017). Structural basis of RNA polymerase I transcription initiation.
Cell. Cell Press. https://doi.org/10.1016/j.cell.2017.03.003
chicago: Engel, Christoph, Tobias Gubbey, Simon Neyer, Sarah Sainsbury, Christiane
Oberthuer, Carlo Baejen, Carrie Bernecky, and Patrick Cramer. “Structural Basis
of RNA Polymerase I Transcription Initiation.” Cell. Cell Press, 2017.
https://doi.org/10.1016/j.cell.2017.03.003.
ieee: C. Engel et al., “Structural basis of RNA polymerase I transcription
initiation,” Cell, vol. 169, no. 1. Cell Press, p. 120–131.e22, 2017.
ista: Engel C, Gubbey T, Neyer S, Sainsbury S, Oberthuer C, Baejen C, Bernecky C,
Cramer P. 2017. Structural basis of RNA polymerase I transcription initiation.
Cell. 169(1), 120–131.e22.
mla: Engel, Christoph, et al. “Structural Basis of RNA Polymerase I Transcription
Initiation.” Cell, vol. 169, no. 1, Cell Press, 2017, p. 120–131.e22, doi:10.1016/j.cell.2017.03.003.
short: C. Engel, T. Gubbey, S. Neyer, S. Sainsbury, C. Oberthuer, C. Baejen, C.
Bernecky, P. Cramer, Cell 169 (2017) 120–131.e22.
date_created: 2018-12-11T11:47:25Z
date_published: 2017-03-23T00:00:00Z
date_updated: 2021-01-12T08:05:36Z
day: '23'
doi: 10.1016/j.cell.2017.03.003
extern: '1'
intvolume: ' 169'
issue: '1'
language:
- iso: eng
month: '03'
oa_version: None
page: 120 - 131.e22
publication: Cell
publication_identifier:
issn:
- '00928674'
publication_status: published
publisher: Cell Press
publist_id: '7204'
quality_controlled: '1'
status: public
title: Structural basis of RNA polymerase I transcription initiation
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 169
year: '2017'
...
---
_id: '313'
abstract:
- lang: eng
text: 'Tunneling of a particle through a potential barrier remains one of the most
remarkable quantum phenomena. Owing to advances in laser technology, electric
fields comparable to those electrons experience in atoms are readily generated
and open opportunities to dynamically investigate the process of electron tunneling
through the potential barrier formed by the superposition of both laser and atomic
fields. Attosecond-time and angstrom-space resolution of the strong laser-field
technique allow to address fundamental questions related to tunneling, which are
still open and debated: Which time is spent under the barrier and what momentum
is picked up by the particle in the meantime? In this combined experimental and
theoretical study we demonstrate that for strong-field ionization the leading
quantum mechanical Wigner treatment for the time resolved description of tunneling
is valid. We achieve a high sensitivity on the tunneling barrier and unambiguously
isolate its effects by performing a differential study of two systems with almost
identical tunneling geometry. Moreover, working with a low frequency laser, we
essentially limit the non-adiabaticity of the process as a major source of uncertainty.
The agreement between experiment and theory implies two substantial corrections
with respect to the widely employed quasiclassical treatment: In addition to a
non-vanishing longitudinal momentum along the laser field-direction we provide
clear evidence for a non-zero tunneling time delay. This addresses also the fundamental
question how the transition occurs from the tunnel barrier to free space classical
evolution of the ejected electron.'
alternative_title:
- 'Journal of Physics: Conference Series'
article_number: '012004'
author:
- first_name: Nicolas
full_name: Camus, Nicolas
last_name: Camus
- first_name: Enderalp
full_name: Yakaboylu, Enderalp
id: 38CB71F6-F248-11E8-B48F-1D18A9856A87
last_name: Yakaboylu
orcid: 0000-0001-5973-0874
- first_name: Lutz
full_name: Fechner, Lutz
last_name: Fechner
- first_name: Michael
full_name: Klaiber, Michael
last_name: Klaiber
- first_name: Martin
full_name: Laux, Martin
last_name: Laux
- first_name: Yonghao
full_name: Mi, Yonghao
last_name: Mi
- first_name: Karen
full_name: Hatsagortsyan, Karen
last_name: Hatsagortsyan
- first_name: Thomas
full_name: Pfeifer, Thomas
last_name: Pfeifer
- first_name: Cristoph
full_name: Keitel, Cristoph
last_name: Keitel
- first_name: Robert
full_name: Moshammer, Robert
last_name: Moshammer
citation:
ama: 'Camus N, Yakaboylu E, Fechner L, et al. Experimental evidence for Wigner’s
tunneling time. In: Vol 999. American Physical Society; 2017. doi:10.1088/1742-6596/999/1/012004'
apa: 'Camus, N., Yakaboylu, E., Fechner, L., Klaiber, M., Laux, M., Mi, Y., … Moshammer,
R. (2017). Experimental evidence for Wigner’s tunneling time (Vol. 999). Presented
at the Annual International Laser Physics Workshop LPHYS, Kazan, Russian Federation:
American Physical Society. https://doi.org/10.1088/1742-6596/999/1/012004'
chicago: Camus, Nicolas, Enderalp Yakaboylu, Lutz Fechner, Michael Klaiber, Martin
Laux, Yonghao Mi, Karen Hatsagortsyan, Thomas Pfeifer, Cristoph Keitel, and Robert
Moshammer. “Experimental Evidence for Wigner’s Tunneling Time,” Vol. 999. American
Physical Society, 2017. https://doi.org/10.1088/1742-6596/999/1/012004.
ieee: N. Camus et al., “Experimental evidence for Wigner’s tunneling time,”
presented at the Annual International Laser Physics Workshop LPHYS, Kazan, Russian
Federation, 2017, vol. 999, no. 1.
ista: 'Camus N, Yakaboylu E, Fechner L, Klaiber M, Laux M, Mi Y, Hatsagortsyan K,
Pfeifer T, Keitel C, Moshammer R. 2017. Experimental evidence for Wigner’s tunneling
time. Annual International Laser Physics Workshop LPHYS, Journal of Physics: Conference
Series, vol. 999, 012004.'
mla: Camus, Nicolas, et al. Experimental Evidence for Wigner’s Tunneling Time.
Vol. 999, no. 1, 012004, American Physical Society, 2017, doi:10.1088/1742-6596/999/1/012004.
short: N. Camus, E. Yakaboylu, L. Fechner, M. Klaiber, M. Laux, Y. Mi, K. Hatsagortsyan,
T. Pfeifer, C. Keitel, R. Moshammer, in:, American Physical Society, 2017.
conference:
end_date: 2017-08-21
location: Kazan, Russian Federation
name: Annual International Laser Physics Workshop LPHYS
start_date: 2017-08-17
date_created: 2018-12-11T11:45:46Z
date_published: 2017-07-14T00:00:00Z
date_updated: 2023-02-23T12:36:07Z
day: '14'
ddc:
- '530'
department:
- _id: MiLe
doi: 10.1088/1742-6596/999/1/012004
external_id:
arxiv:
- '1611.03701'
file:
- access_level: open_access
checksum: 6e70b525a84f6d5fb175c48e9f5cb59a
content_type: application/pdf
creator: dernst
date_created: 2019-01-22T08:34:10Z
date_updated: 2020-07-14T12:46:00Z
file_id: '5871'
file_name: 2017_Physics_Camus.pdf
file_size: 949321
relation: main_file
file_date_updated: 2020-07-14T12:46:00Z
has_accepted_license: '1'
intvolume: ' 999'
issue: '1'
language:
- iso: eng
month: '07'
oa: 1
oa_version: Published Version
publication_identifier:
issn:
- '17426588'
publication_status: published
publisher: American Physical Society
publist_id: '7552'
quality_controlled: '1'
related_material:
record:
- id: '6013'
relation: later_version
status: public
scopus_import: 1
status: public
title: Experimental evidence for Wigner's tunneling time
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: conference
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 999
year: '2017'
...
---
_id: '601'
abstract:
- lang: eng
text: 'The conserved polymerase-Associated factor 1 complex (Paf1C) plays multiple
roles in chromatin transcription and genomic regulation. Paf1C comprises the five
subunits Paf1, Leo1, Ctr9, Cdc73 and Rtf1, and binds to the RNA polymerase II
(Pol II) transcription elongation complex (EC). Here we report the reconstitution
of Paf1C from Saccharomyces cerevisiae, and a structural analysis of Paf1C bound
to a Pol II EC containing the elongation factor TFIIS. Cryo-electron microscopy
and crosslinking data reveal that Paf1C is highly mobile and extends over the
outer Pol II surface from the Rpb2 to the Rpb3 subunit. The Paf1-Leo1 heterodimer
and Cdc73 form opposite ends of Paf1C, whereas Ctr9 bridges between them. Consistent
with the structural observations, the initiation factor TFIIF impairs Paf1C binding
to Pol II, whereas the elongation factor TFIIS enhances it. We further show that
Paf1C is globally required for normal mRNA transcription in yeast. These results
provide a three-dimensional framework for further analysis of Paf1C function in
transcription through chromatin. '
article_number: '15741'
article_processing_charge: No
author:
- first_name: Youwei
full_name: Xu, Youwei
last_name: Xu
- first_name: Carrie A
full_name: Bernecky, Carrie A
id: 2CB9DFE2-F248-11E8-B48F-1D18A9856A87
last_name: Bernecky
orcid: 0000-0003-0893-7036
- first_name: Chung
full_name: Lee, Chung
last_name: Lee
- first_name: Kerstin
full_name: Maier, Kerstin
last_name: Maier
- first_name: Björn
full_name: Schwalb, Björn
last_name: Schwalb
- first_name: Dimitri
full_name: Tegunov, Dimitri
last_name: Tegunov
- first_name: Jürgen
full_name: Plitzko, Jürgen
last_name: Plitzko
- first_name: Henning
full_name: Urlaub, Henning
last_name: Urlaub
- first_name: Patrick
full_name: Cramer, Patrick
last_name: Cramer
citation:
ama: Xu Y, Bernecky C, Lee C, et al. Architecture of the RNA polymerase II-Paf1C-TFIIS
transcription elongation complex. Nature Communications. 2017;8. doi:10.1038/ncomms15741
apa: Xu, Y., Bernecky, C., Lee, C., Maier, K., Schwalb, B., Tegunov, D., … Cramer,
P. (2017). Architecture of the RNA polymerase II-Paf1C-TFIIS transcription elongation
complex. Nature Communications. Nature Publishing Group. https://doi.org/10.1038/ncomms15741
chicago: Xu, Youwei, Carrie Bernecky, Chung Lee, Kerstin Maier, Björn Schwalb, Dimitri
Tegunov, Jürgen Plitzko, Henning Urlaub, and Patrick Cramer. “Architecture of
the RNA Polymerase II-Paf1C-TFIIS Transcription Elongation Complex.” Nature
Communications. Nature Publishing Group, 2017. https://doi.org/10.1038/ncomms15741.
ieee: Y. Xu et al., “Architecture of the RNA polymerase II-Paf1C-TFIIS transcription
elongation complex,” Nature Communications, vol. 8. Nature Publishing Group,
2017.
ista: Xu Y, Bernecky C, Lee C, Maier K, Schwalb B, Tegunov D, Plitzko J, Urlaub
H, Cramer P. 2017. Architecture of the RNA polymerase II-Paf1C-TFIIS transcription
elongation complex. Nature Communications. 8, 15741.
mla: Xu, Youwei, et al. “Architecture of the RNA Polymerase II-Paf1C-TFIIS Transcription
Elongation Complex.” Nature Communications, vol. 8, 15741, Nature Publishing
Group, 2017, doi:10.1038/ncomms15741.
short: Y. Xu, C. Bernecky, C. Lee, K. Maier, B. Schwalb, D. Tegunov, J. Plitzko,
H. Urlaub, P. Cramer, Nature Communications 8 (2017).
date_created: 2018-12-11T11:47:25Z
date_published: 2017-06-06T00:00:00Z
date_updated: 2021-01-12T08:05:40Z
day: '06'
ddc:
- '570'
doi: 10.1038/ncomms15741
extern: '1'
file:
- access_level: open_access
checksum: 940742282a9a285dc4aeae0c2b5ebe96
content_type: application/pdf
creator: dernst
date_created: 2019-01-21T14:48:10Z
date_updated: 2020-07-14T12:47:16Z
file_id: '5865'
file_name: 2017_NatureComm_Xu.pdf
file_size: 3018075
relation: main_file
file_date_updated: 2020-07-14T12:47:16Z
has_accepted_license: '1'
intvolume: ' 8'
language:
- iso: eng
month: '06'
oa: 1
oa_version: Published Version
publication: Nature Communications
publication_identifier:
issn:
- '20411723'
publication_status: published
publisher: Nature Publishing Group
publist_id: '7203'
quality_controlled: '1'
status: public
title: Architecture of the RNA polymerase II-Paf1C-TFIIS transcription elongation
complex
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 8
year: '2017'
...
---
_id: '6013'
abstract:
- lang: eng
text: The first hundred attoseconds of the electron dynamics during strong field
tunneling ionization are investigated. We quantify theoretically how the electron’s
classical trajectories in the continuum emerge from the tunneling process and
test the results with those achieved in parallel from attoclock measurements.
An especially high sensitivity on the tunneling barrier is accomplished here by
comparing the momentum distributions of two atomic species of slightly deviating
atomic potentials (argon and krypton) being ionized under absolutely identical
conditions with near-infrared laser pulses (1300 nm). The agreement between experiment
and theory provides clear evidence for a nonzero tunneling time delay and a nonvanishing
longitudinal momentum of the electron at the “tunnel exit.”
article_number: '023201'
author:
- first_name: Nicolas
full_name: Camus, Nicolas
last_name: Camus
- first_name: Enderalp
full_name: Yakaboylu, Enderalp
id: 38CB71F6-F248-11E8-B48F-1D18A9856A87
last_name: Yakaboylu
orcid: 0000-0001-5973-0874
- first_name: Lutz
full_name: Fechner, Lutz
last_name: Fechner
- first_name: Michael
full_name: Klaiber, Michael
last_name: Klaiber
- first_name: Martin
full_name: Laux, Martin
last_name: Laux
- first_name: Yonghao
full_name: Mi, Yonghao
last_name: Mi
- first_name: Karen Z.
full_name: Hatsagortsyan, Karen Z.
last_name: Hatsagortsyan
- first_name: Thomas
full_name: Pfeifer, Thomas
last_name: Pfeifer
- first_name: Christoph H.
full_name: Keitel, Christoph H.
last_name: Keitel
- first_name: Robert
full_name: Moshammer, Robert
last_name: Moshammer
citation:
ama: Camus N, Yakaboylu E, Fechner L, et al. Experimental evidence for quantum tunneling
time. Physical Review Letters. 2017;119(2). doi:10.1103/PhysRevLett.119.023201
apa: Camus, N., Yakaboylu, E., Fechner, L., Klaiber, M., Laux, M., Mi, Y., … Moshammer,
R. (2017). Experimental evidence for quantum tunneling time. Physical Review
Letters. American Physical Society. https://doi.org/10.1103/PhysRevLett.119.023201
chicago: Camus, Nicolas, Enderalp Yakaboylu, Lutz Fechner, Michael Klaiber, Martin
Laux, Yonghao Mi, Karen Z. Hatsagortsyan, Thomas Pfeifer, Christoph H. Keitel,
and Robert Moshammer. “Experimental Evidence for Quantum Tunneling Time.” Physical
Review Letters. American Physical Society, 2017. https://doi.org/10.1103/PhysRevLett.119.023201.
ieee: N. Camus et al., “Experimental evidence for quantum tunneling time,”
Physical Review Letters, vol. 119, no. 2. American Physical Society, 2017.
ista: Camus N, Yakaboylu E, Fechner L, Klaiber M, Laux M, Mi Y, Hatsagortsyan KZ,
Pfeifer T, Keitel CH, Moshammer R. 2017. Experimental evidence for quantum tunneling
time. Physical Review Letters. 119(2), 023201.
mla: Camus, Nicolas, et al. “Experimental Evidence for Quantum Tunneling Time.”
Physical Review Letters, vol. 119, no. 2, 023201, American Physical Society,
2017, doi:10.1103/PhysRevLett.119.023201.
short: N. Camus, E. Yakaboylu, L. Fechner, M. Klaiber, M. Laux, Y. Mi, K.Z. Hatsagortsyan,
T. Pfeifer, C.H. Keitel, R. Moshammer, Physical Review Letters 119 (2017).
date_created: 2019-02-14T15:24:13Z
date_published: 2017-07-14T00:00:00Z
date_updated: 2023-02-23T11:13:36Z
day: '14'
department:
- _id: MiLe
doi: 10.1103/PhysRevLett.119.023201
external_id:
arxiv:
- '1611.03701'
intvolume: ' 119'
issue: '2'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/1611.03701
month: '07'
oa: 1
oa_version: Preprint
publication: Physical Review Letters
publication_identifier:
eissn:
- 1079-7114
issn:
- 0031-9007
publication_status: published
publisher: American Physical Society
quality_controlled: '1'
related_material:
record:
- id: '313'
relation: earlier_version
status: public
scopus_import: 1
status: public
title: Experimental evidence for quantum tunneling time
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 119
year: '2017'
...
---
_id: '603'
abstract:
- lang: eng
text: During transcription, RNA polymerase II (Pol II) associates with the conserved
elongation factor DSIF. DSIF renders the elongation complex stable and functions
during Pol II pausing and RNA processing. We combined cryo-EM and X-ray crystallography
to determine the structure of the mammalian Pol II-DSIF elongation complex at
a nominal resolution of 3.4. Human DSIF has a modular structure with two domains
forming a DNA clamp, two domains forming an RNA clamp, and one domain buttressing
the RNA clamp. The clamps maintain the transcription bubble, position upstream
DNA, and retain the RNA transcript in the exit tunnel. The mobile C-terminal region
of DSIF is located near exiting RNA, where it can recruit factors for RNA processing.
The structure provides insight into the roles of DSIF during mRNA synthesis.
article_processing_charge: No
author:
- first_name: Carrie A
full_name: Bernecky, Carrie A
id: 2CB9DFE2-F248-11E8-B48F-1D18A9856A87
last_name: Bernecky
orcid: 0000-0003-0893-7036
- first_name: Jürgen
full_name: Plitzko, Jürgen
last_name: Plitzko
- first_name: Patrick
full_name: Cramer, Patrick
last_name: Cramer
citation:
ama: Bernecky C, Plitzko J, Cramer P. Structure of a transcribing RNA polymerase
II-DSIF complex reveals a multidentate DNA-RNA clamp. Nature Structural and
Molecular Biology. 2017;24(10):809-815. doi:10.1038/nsmb.3465
apa: Bernecky, C., Plitzko, J., & Cramer, P. (2017). Structure of a transcribing
RNA polymerase II-DSIF complex reveals a multidentate DNA-RNA clamp. Nature
Structural and Molecular Biology. Nature Publishing Group. https://doi.org/10.1038/nsmb.3465
chicago: Bernecky, Carrie, Jürgen Plitzko, and Patrick Cramer. “Structure of a Transcribing
RNA Polymerase II-DSIF Complex Reveals a Multidentate DNA-RNA Clamp.” Nature
Structural and Molecular Biology. Nature Publishing Group, 2017. https://doi.org/10.1038/nsmb.3465.
ieee: C. Bernecky, J. Plitzko, and P. Cramer, “Structure of a transcribing RNA polymerase
II-DSIF complex reveals a multidentate DNA-RNA clamp,” Nature Structural and
Molecular Biology, vol. 24, no. 10. Nature Publishing Group, pp. 809–815,
2017.
ista: Bernecky C, Plitzko J, Cramer P. 2017. Structure of a transcribing RNA polymerase
II-DSIF complex reveals a multidentate DNA-RNA clamp. Nature Structural and Molecular
Biology. 24(10), 809–815.
mla: Bernecky, Carrie, et al. “Structure of a Transcribing RNA Polymerase II-DSIF
Complex Reveals a Multidentate DNA-RNA Clamp.” Nature Structural and Molecular
Biology, vol. 24, no. 10, Nature Publishing Group, 2017, pp. 809–15, doi:10.1038/nsmb.3465.
short: C. Bernecky, J. Plitzko, P. Cramer, Nature Structural and Molecular Biology
24 (2017) 809–815.
date_created: 2018-12-11T11:47:26Z
date_published: 2017-10-05T00:00:00Z
date_updated: 2021-01-12T08:05:47Z
day: '05'
doi: 10.1038/nsmb.3465
extern: '1'
intvolume: ' 24'
issue: '10'
language:
- iso: eng
month: '10'
oa_version: None
page: 809 - 815
publication: Nature Structural and Molecular Biology
publication_identifier:
issn:
- '15459993'
publication_status: published
publisher: Nature Publishing Group
publist_id: '7202'
quality_controlled: '1'
status: public
title: Structure of a transcribing RNA polymerase II-DSIF complex reveals a multidentate
DNA-RNA clamp
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 24
year: '2017'
...
---
_id: '605'
abstract:
- lang: eng
text: 'Position based cryptography (PBC), proposed in the seminal work of Chandran,
Goyal, Moriarty, and Ostrovsky (SIAM J. Computing, 2014), aims at constructing
cryptographic schemes in which the identity of the user is his geographic position.
Chandran et al. construct PBC schemes for secure positioning and position-based
key agreement in the bounded-storage model (Maurer, J. Cryptology, 1992). Apart
from bounded memory, their security proofs need a strong additional restriction
on the power of the adversary: he cannot compute joint functions of his inputs.
Removing this assumption is left as an open problem. We show that an answer to
this question would resolve a long standing open problem in multiparty communication
complexity: finding a function that is hard to compute with low communication
complexity in the simultaneous message model, but easy to compute in the fully
adaptive model. On a more positive side: we also show some implications in the
other direction, i.e.: we prove that lower bounds on the communication complexity
of certain multiparty problems imply existence of PBC primitives. Using this result
we then show two attractive ways to “bypass” our hardness result: the first uses
the random oracle model, the second weakens the locality requirement in the bounded-storage
model to online computability. The random oracle construction is arguably one
of the simplest proposed so far in this area. Our results indicate that constructing
improved provably secure protocols for PBC requires a better understanding of
multiparty communication complexity. This is yet another example where negative
results in one area (in our case: lower bounds in multiparty communication complexity)
can be used to construct secure cryptographic schemes.'
alternative_title:
- LNCS
author:
- first_name: Joshua
full_name: Brody, Joshua
last_name: Brody
- first_name: Stefan
full_name: Dziembowski, Stefan
last_name: Dziembowski
- first_name: Sebastian
full_name: Faust, Sebastian
last_name: Faust
- first_name: Krzysztof Z
full_name: Pietrzak, Krzysztof Z
id: 3E04A7AA-F248-11E8-B48F-1D18A9856A87
last_name: Pietrzak
orcid: 0000-0002-9139-1654
citation:
ama: 'Brody J, Dziembowski S, Faust S, Pietrzak KZ. Position based cryptography
and multiparty communication complexity. In: Kalai Y, Reyzin L, eds. Vol 10677.
Springer; 2017:56-81. doi:10.1007/978-3-319-70500-2_3'
apa: 'Brody, J., Dziembowski, S., Faust, S., & Pietrzak, K. Z. (2017). Position
based cryptography and multiparty communication complexity. In Y. Kalai &
L. Reyzin (Eds.) (Vol. 10677, pp. 56–81). Presented at the TCC: Theory of Cryptography
Conference, Baltimore, MD, United States: Springer. https://doi.org/10.1007/978-3-319-70500-2_3'
chicago: Brody, Joshua, Stefan Dziembowski, Sebastian Faust, and Krzysztof Z Pietrzak.
“Position Based Cryptography and Multiparty Communication Complexity.” edited
by Yael Kalai and Leonid Reyzin, 10677:56–81. Springer, 2017. https://doi.org/10.1007/978-3-319-70500-2_3.
ieee: 'J. Brody, S. Dziembowski, S. Faust, and K. Z. Pietrzak, “Position based cryptography
and multiparty communication complexity,” presented at the TCC: Theory of Cryptography
Conference, Baltimore, MD, United States, 2017, vol. 10677, pp. 56–81.'
ista: 'Brody J, Dziembowski S, Faust S, Pietrzak KZ. 2017. Position based cryptography
and multiparty communication complexity. TCC: Theory of Cryptography Conference,
LNCS, vol. 10677, 56–81.'
mla: Brody, Joshua, et al. Position Based Cryptography and Multiparty Communication
Complexity. Edited by Yael Kalai and Leonid Reyzin, vol. 10677, Springer,
2017, pp. 56–81, doi:10.1007/978-3-319-70500-2_3.
short: J. Brody, S. Dziembowski, S. Faust, K.Z. Pietrzak, in:, Y. Kalai, L. Reyzin
(Eds.), Springer, 2017, pp. 56–81.
conference:
end_date: 2017-11-15
location: Baltimore, MD, United States
name: 'TCC: Theory of Cryptography Conference'
start_date: 2017-11-12
date_created: 2018-12-11T11:47:27Z
date_published: 2017-11-05T00:00:00Z
date_updated: 2021-01-12T08:05:53Z
day: '05'
department:
- _id: KrPi
doi: 10.1007/978-3-319-70500-2_3
ec_funded: 1
editor:
- first_name: Yael
full_name: Kalai, Yael
last_name: Kalai
- first_name: Leonid
full_name: Reyzin, Leonid
last_name: Reyzin
intvolume: ' 10677'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://eprint.iacr.org/2016/536
month: '11'
oa: 1
oa_version: Submitted Version
page: 56 - 81
project:
- _id: 258AA5B2-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '682815'
name: Teaching Old Crypto New Tricks
publication_identifier:
isbn:
- 978-331970499-9
publication_status: published
publisher: Springer
publist_id: '7200'
quality_controlled: '1'
scopus_import: 1
status: public
title: Position based cryptography and multiparty communication complexity
type: conference
user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87
volume: 10677
year: '2017'
...
---
_id: '604'
abstract:
- lang: eng
text: In several settings of physics and chemistry one has to deal with molecules
interacting with some kind of an external environment, be it a gas, a solution,
or a crystal surface. Understanding molecular processes in the presence of such
a many-particle bath is inherently challenging, and usually requires large-scale
numerical computations. Here, we present an alternative approach to the problem,
based on the notion of the angulon quasiparticle. We show that molecules rotating
inside superfluid helium nanodroplets and Bose–Einstein condensates form angulons,
and therefore can be described by straightforward solutions of a simple microscopic
Hamiltonian. Casting the problem in the language of angulons allows us not only
to greatly simplify it, but also to gain insights into the origins of the observed
phenomena and to make predictions for future experimental studies.
alternative_title:
- Theoretical and Computational Chemistry Series
author:
- first_name: Mikhail
full_name: Lemeshko, Mikhail
id: 37CB05FA-F248-11E8-B48F-1D18A9856A87
last_name: Lemeshko
orcid: 0000-0002-6990-7802
- first_name: Richard
full_name: Schmidt, Richard
last_name: Schmidt
citation:
ama: 'Lemeshko M, Schmidt R. Molecular impurities interacting with a many-particle
environment: From ultracold gases to helium nanodroplets. In: Dulieu O, Osterwalder
A, eds. Cold Chemistry: Molecular Scattering and Reactivity Near Absolute Zero
. Vol 11. Theoretical and Computational Chemistry Series. The Royal Society
of Chemistry; 2017:444-495. doi:10.1039/9781782626800-00444'
apa: 'Lemeshko, M., & Schmidt, R. (2017). Molecular impurities interacting with
a many-particle environment: From ultracold gases to helium nanodroplets. In O.
Dulieu & A. Osterwalder (Eds.), Cold Chemistry: Molecular Scattering and
Reactivity Near Absolute Zero (Vol. 11, pp. 444–495). The Royal Society of
Chemistry. https://doi.org/10.1039/9781782626800-00444'
chicago: 'Lemeshko, Mikhail, and Richard Schmidt. “Molecular Impurities Interacting
with a Many-Particle Environment: From Ultracold Gases to Helium Nanodroplets.”
In Cold Chemistry: Molecular Scattering and Reactivity Near Absolute Zero ,
edited by Oliver Dulieu and Andreas Osterwalder, 11:444–95. Theoretical and Computational
Chemistry Series. The Royal Society of Chemistry, 2017. https://doi.org/10.1039/9781782626800-00444.'
ieee: 'M. Lemeshko and R. Schmidt, “Molecular impurities interacting with a many-particle
environment: From ultracold gases to helium nanodroplets,” in Cold Chemistry:
Molecular Scattering and Reactivity Near Absolute Zero , vol. 11, O. Dulieu
and A. Osterwalder, Eds. The Royal Society of Chemistry, 2017, pp. 444–495.'
ista: 'Lemeshko M, Schmidt R. 2017.Molecular impurities interacting with a many-particle
environment: From ultracold gases to helium nanodroplets. In: Cold Chemistry:
Molecular Scattering and Reactivity Near Absolute Zero . Theoretical and Computational
Chemistry Series, vol. 11, 444–495.'
mla: 'Lemeshko, Mikhail, and Richard Schmidt. “Molecular Impurities Interacting
with a Many-Particle Environment: From Ultracold Gases to Helium Nanodroplets.”
Cold Chemistry: Molecular Scattering and Reactivity Near Absolute Zero ,
edited by Oliver Dulieu and Andreas Osterwalder, vol. 11, The Royal Society of
Chemistry, 2017, pp. 444–95, doi:10.1039/9781782626800-00444.'
short: 'M. Lemeshko, R. Schmidt, in:, O. Dulieu, A. Osterwalder (Eds.), Cold Chemistry:
Molecular Scattering and Reactivity Near Absolute Zero , The Royal Society of
Chemistry, 2017, pp. 444–495.'
date_created: 2018-12-11T11:47:27Z
date_published: 2017-12-14T00:00:00Z
date_updated: 2021-01-12T08:05:50Z
day: '14'
department:
- _id: MiLe
doi: 10.1039/9781782626800-00444
editor:
- first_name: Oliver
full_name: Dulieu, Oliver
last_name: Dulieu
- first_name: Andreas
full_name: Osterwalder, Andreas
last_name: Osterwalder
intvolume: ' 11'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/1703.06753
month: '12'
oa: 1
oa_version: Submitted Version
page: 444 - 495
publication: 'Cold Chemistry: Molecular Scattering and Reactivity Near Absolute Zero '
publication_identifier:
issn:
- '20413181'
publication_status: published
publisher: The Royal Society of Chemistry
publist_id: '7201'
quality_controlled: '1'
scopus_import: 1
series_title: Theoretical and Computational Chemistry Series
status: public
title: 'Molecular impurities interacting with a many-particle environment: From ultracold
gases to helium nanodroplets'
type: book_chapter
user_id: 4435EBFC-F248-11E8-B48F-1D18A9856A87
volume: 11
year: '2017'
...
---
_id: '6059'
abstract:
- lang: eng
text: Neutrophils or polymorphonuclear cells (PMN) eliminate bacteria via phagocytosis
and/or NETosis. Apartfrom these conventional roles, PMN also have immune-regulatory
functions. They can transdifferentiateand upregulate MHCII as well as ligands
for costimulatory receptors which enables them to behave asantigen presenting
cells (APC). The initial step for activating T-cells is the formation of an immunesynapse
between T-cells and antigen-presenting cells. However, the immune synapse that
develops atthe PMN/T-cell contact zone is as yet hardly investigated due to the
non-availability of methods foranalysis of large number of PMN interactions. In
order to overcome these obstacles, we introduce herea workflow to analyse the
immune synapse of primary human PMN and T-cells using multispectral imag-ing flow
cytometry (InFlow microscopy) and super-resolution microscopy. For that purpose,
we used CD3and CD66b as the lineage markers for T-cells and PMN, respectively.
Thereafter, we applied and criticallydiscussed various ‘‘masks” for identification
of T-cell PMN interactions. Using this approach, we foundthat a small fraction
of transdifferentiated PMN (CD66b+CD86high) formed stable PMN/T-cell conjugates.Interestingly,
while both CD3 and CD66b accumulation in the immune synapse was dependent on thematuration
state of the PMN, only CD3 accumulation was greatly enhanced by the presence of
superanti-gen. The actin cytoskeleton was weakly rearranged at the PMN side on
the immune synapse upon contactwith a T-cell in the presence of superantigen.
A more detailed analysis using super-resolution microscopy(structured-illumination
microscopy, SIM) confirmed this finding. Together, we present an InFlow micro-scopy
based approach for the large scale analysis of PMN/T-cell interactions and – combined
with SIM – apossibility for an in-depth analysis of protein translocation at the
site of interactions.
author:
- first_name: Emre
full_name: Balta, Emre
last_name: Balta
- first_name: Julian A
full_name: Stopp, Julian A
id: 489E3F00-F248-11E8-B48F-1D18A9856A87
last_name: Stopp
- first_name: Laura
full_name: Castelletti, Laura
last_name: Castelletti
- first_name: Henning
full_name: Kirchgessner, Henning
last_name: Kirchgessner
- first_name: Yvonne
full_name: Samstag, Yvonne
last_name: Samstag
- first_name: Guido H.
full_name: Wabnitz, Guido H.
last_name: Wabnitz
citation:
ama: Balta E, Stopp JA, Castelletti L, Kirchgessner H, Samstag Y, Wabnitz GH. Qualitative
and quantitative analysis of PMN/T-cell interactions by InFlow and super-resolution
microscopy. Methods. 2017;112(1):25-38. doi:10.1016/j.ymeth.2016.09.013
apa: Balta, E., Stopp, J. A., Castelletti, L., Kirchgessner, H., Samstag, Y., &
Wabnitz, G. H. (2017). Qualitative and quantitative analysis of PMN/T-cell interactions
by InFlow and super-resolution microscopy. Methods. Elsevier. https://doi.org/10.1016/j.ymeth.2016.09.013
chicago: Balta, Emre, Julian A Stopp, Laura Castelletti, Henning Kirchgessner, Yvonne
Samstag, and Guido H. Wabnitz. “Qualitative and Quantitative Analysis of PMN/T-Cell
Interactions by InFlow and Super-Resolution Microscopy.” Methods. Elsevier,
2017. https://doi.org/10.1016/j.ymeth.2016.09.013.
ieee: E. Balta, J. A. Stopp, L. Castelletti, H. Kirchgessner, Y. Samstag, and G.
H. Wabnitz, “Qualitative and quantitative analysis of PMN/T-cell interactions
by InFlow and super-resolution microscopy,” Methods, vol. 112, no. 1. Elsevier,
pp. 25–38, 2017.
ista: Balta E, Stopp JA, Castelletti L, Kirchgessner H, Samstag Y, Wabnitz GH. 2017.
Qualitative and quantitative analysis of PMN/T-cell interactions by InFlow and
super-resolution microscopy. Methods. 112(1), 25–38.
mla: Balta, Emre, et al. “Qualitative and Quantitative Analysis of PMN/T-Cell Interactions
by InFlow and Super-Resolution Microscopy.” Methods, vol. 112, no. 1, Elsevier,
2017, pp. 25–38, doi:10.1016/j.ymeth.2016.09.013.
short: E. Balta, J.A. Stopp, L. Castelletti, H. Kirchgessner, Y. Samstag, G.H. Wabnitz,
Methods 112 (2017) 25–38.
date_created: 2019-02-26T13:45:17Z
date_published: 2017-01-01T00:00:00Z
date_updated: 2021-01-12T08:05:57Z
day: '01'
doi: 10.1016/j.ymeth.2016.09.013
extern: '1'
external_id:
pmid:
- '27693880'
intvolume: ' 112'
issue: '1'
language:
- iso: eng
month: '01'
oa_version: None
page: 25-38
pmid: 1
publication: Methods
publication_identifier:
issn:
- 1046-2023
publication_status: published
publisher: Elsevier
quality_controlled: '1'
related_material:
link:
- relation: supplementary_material
url: http://dx.doi.org/10.1016/j.ymeth.2016.09.013
status: public
title: Qualitative and quantitative analysis of PMN/T-cell interactions by InFlow
and super-resolution microscopy
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 112
year: '2017'
...
---
_id: '609'
abstract:
- lang: eng
text: Several cryptographic schemes and applications are based on functions that
are both reasonably efficient to compute and moderately hard to invert, including
client puzzles for Denial-of-Service protection, password protection via salted
hashes, or recent proof-of-work blockchain systems. Despite their wide use, a
definition of this concept has not yet been distilled and formalized explicitly.
Instead, either the applications are proven directly based on the assumptions
underlying the function, or some property of the function is proven, but the security
of the application is argued only informally. The goal of this work is to provide
a (universal) definition that decouples the efforts of designing new moderately
hard functions and of building protocols based on them, serving as an interface
between the two. On a technical level, beyond the mentioned definitions, we instantiate
the model for four different notions of hardness. We extend the work of Alwen
and Serbinenko (STOC 2015) by providing a general tool for proving security for
the first notion of memory-hard functions that allows for provably secure applications.
The tool allows us to recover all of the graph-theoretic techniques developed
for proving security under the older, non-composable, notion of security used
by Alwen and Serbinenko. As an application of our definition of moderately hard
functions, we prove the security of two different schemes for proofs of effort
(PoE). We also formalize and instantiate the concept of a non-interactive proof
of effort (niPoE), in which the proof is not bound to a particular communication
context but rather any bit-string chosen by the prover.
alternative_title:
- LNCS
author:
- first_name: Joel F
full_name: Alwen, Joel F
id: 2A8DFA8C-F248-11E8-B48F-1D18A9856A87
last_name: Alwen
- first_name: Björn
full_name: Tackmann, Björn
last_name: Tackmann
citation:
ama: 'Alwen JF, Tackmann B. Moderately hard functions: Definition, instantiations,
and applications. In: Kalai Y, Reyzin L, eds. Vol 10677. Springer; 2017:493-526.
doi:10.1007/978-3-319-70500-2_17'
apa: 'Alwen, J. F., & Tackmann, B. (2017). Moderately hard functions: Definition,
instantiations, and applications. In Y. Kalai & L. Reyzin (Eds.) (Vol. 10677,
pp. 493–526). Presented at the TCC: Theory of Cryptography, Baltimore, MD, United
States: Springer. https://doi.org/10.1007/978-3-319-70500-2_17'
chicago: 'Alwen, Joel F, and Björn Tackmann. “Moderately Hard Functions: Definition,
Instantiations, and Applications.” edited by Yael Kalai and Leonid Reyzin, 10677:493–526.
Springer, 2017. https://doi.org/10.1007/978-3-319-70500-2_17.'
ieee: 'J. F. Alwen and B. Tackmann, “Moderately hard functions: Definition, instantiations,
and applications,” presented at the TCC: Theory of Cryptography, Baltimore, MD,
United States, 2017, vol. 10677, pp. 493–526.'
ista: 'Alwen JF, Tackmann B. 2017. Moderately hard functions: Definition, instantiations,
and applications. TCC: Theory of Cryptography, LNCS, vol. 10677, 493–526.'
mla: 'Alwen, Joel F., and Björn Tackmann. Moderately Hard Functions: Definition,
Instantiations, and Applications. Edited by Yael Kalai and Leonid Reyzin,
vol. 10677, Springer, 2017, pp. 493–526, doi:10.1007/978-3-319-70500-2_17.'
short: J.F. Alwen, B. Tackmann, in:, Y. Kalai, L. Reyzin (Eds.), Springer, 2017,
pp. 493–526.
conference:
end_date: 2017-11-15
location: Baltimore, MD, United States
name: 'TCC: Theory of Cryptography'
start_date: 2017-11-12
date_created: 2018-12-11T11:47:28Z
date_published: 2017-11-05T00:00:00Z
date_updated: 2021-01-12T08:06:04Z
day: '05'
department:
- _id: KrPi
doi: 10.1007/978-3-319-70500-2_17
editor:
- first_name: Yael
full_name: Kalai, Yael
last_name: Kalai
- first_name: Leonid
full_name: Reyzin, Leonid
last_name: Reyzin
intvolume: ' 10677'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://eprint.iacr.org/2017/945
month: '11'
oa: 1
oa_version: Submitted Version
page: 493 - 526
publication_identifier:
isbn:
- 978-331970499-9
publication_status: published
publisher: Springer
publist_id: '7196'
quality_controlled: '1'
scopus_import: 1
status: public
title: 'Moderately hard functions: Definition, instantiations, and applications'
type: conference
user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87
volume: 10677
year: '2017'
...
---
_id: '610'
abstract:
- lang: eng
text: 'The fact that the complete graph K5 does not embed in the plane has been
generalized in two independent directions. On the one hand, the solution of the
classical Heawood problem for graphs on surfaces established that the complete
graph Kn embeds in a closed surface M (other than the Klein bottle) if and only
if (n−3)(n−4) ≤ 6b1(M), where b1(M) is the first Z2-Betti number of M. On the
other hand, van Kampen and Flores proved that the k-skeleton of the n-dimensional
simplex (the higher-dimensional analogue of Kn+1) embeds in R2k if and only if
n ≤ 2k + 1. Two decades ago, Kühnel conjectured that the k-skeleton of the n-simplex
embeds in a compact, (k − 1)-connected 2k-manifold with kth Z2-Betti number bk
only if the following generalized Heawood inequality holds: (k+1 n−k−1) ≤ (k+1
2k+1)bk. This is a common generalization of the case of graphs on surfaces as
well as the van Kampen–Flores theorem. In the spirit of Kühnel’s conjecture, we
prove that if the k-skeleton of the n-simplex embeds in a compact 2k-manifold
with kth Z2-Betti number bk, then n ≤ 2bk(k 2k+2)+2k+4. This bound is weaker than
the generalized Heawood inequality, but does not require the assumption that M
is (k−1)-connected. Our results generalize to maps without q-covered points, in
the spirit of Tverberg’s theorem, for q a prime power. Our proof uses a result
of Volovikov about maps that satisfy a certain homological triviality condition.'
acknowledgement: The work by Z. P. was partially supported by the Israel Science Foundation
grant ISF-768/12. The work by Z. P. and M. T. was partially supported by the project
CE-ITI (GACR P202/12/G061) of the Czech Science Foundation and by the ERC Advanced
Grant No. 267165. Part of the research work of M.T. was conducted at IST Austria,
supported by an IST Fellowship. The research of P. P. was supported by the ERC Advanced
grant no. 320924. The work by I. M. and U. W. was supported by the Swiss National
Science Foundation (grants SNSF-200020-138230 and SNSF-PP00P2-138948). The collaboration
between U. W. and X. G. was partially supported by the LabEx Bézout (ANR-10-LABX-58).
author:
- first_name: Xavier
full_name: Goaoc, Xavier
last_name: Goaoc
- first_name: Isaac
full_name: Mabillard, Isaac
id: 32BF9DAA-F248-11E8-B48F-1D18A9856A87
last_name: Mabillard
- first_name: Pavel
full_name: Paták, Pavel
last_name: Paták
- first_name: Zuzana
full_name: Patakova, Zuzana
id: 48B57058-F248-11E8-B48F-1D18A9856A87
last_name: Patakova
orcid: 0000-0002-3975-1683
- 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: 'Goaoc X, Mabillard I, Paták P, Patakova Z, Tancer M, Wagner U. On generalized
Heawood inequalities for manifolds: A van Kampen–Flores type nonembeddability
result. Israel Journal of Mathematics. 2017;222(2):841-866. doi:10.1007/s11856-017-1607-7'
apa: 'Goaoc, X., Mabillard, I., Paták, P., Patakova, Z., Tancer, M., & Wagner,
U. (2017). On generalized Heawood inequalities for manifolds: A van Kampen–Flores
type nonembeddability result. Israel Journal of Mathematics. Springer.
https://doi.org/10.1007/s11856-017-1607-7'
chicago: 'Goaoc, Xavier, Isaac Mabillard, Pavel Paták, Zuzana Patakova, Martin Tancer,
and Uli Wagner. “On Generalized Heawood Inequalities for Manifolds: A van Kampen–Flores
Type Nonembeddability Result.” Israel Journal of Mathematics. Springer,
2017. https://doi.org/10.1007/s11856-017-1607-7.'
ieee: 'X. Goaoc, I. Mabillard, P. Paták, Z. Patakova, M. Tancer, and U. Wagner,
“On generalized Heawood inequalities for manifolds: A van Kampen–Flores type nonembeddability
result,” Israel Journal of Mathematics, vol. 222, no. 2. Springer, pp.
841–866, 2017.'
ista: 'Goaoc X, Mabillard I, Paták P, Patakova Z, Tancer M, Wagner U. 2017. On generalized
Heawood inequalities for manifolds: A van Kampen–Flores type nonembeddability
result. Israel Journal of Mathematics. 222(2), 841–866.'
mla: 'Goaoc, Xavier, et al. “On Generalized Heawood Inequalities for Manifolds:
A van Kampen–Flores Type Nonembeddability Result.” Israel Journal of Mathematics,
vol. 222, no. 2, Springer, 2017, pp. 841–66, doi:10.1007/s11856-017-1607-7.'
short: X. Goaoc, I. Mabillard, P. Paták, Z. Patakova, M. Tancer, U. Wagner, Israel
Journal of Mathematics 222 (2017) 841–866.
date_created: 2018-12-11T11:47:29Z
date_published: 2017-10-01T00:00:00Z
date_updated: 2023-02-23T10:02:13Z
day: '01'
department:
- _id: UlWa
doi: 10.1007/s11856-017-1607-7
ec_funded: 1
intvolume: ' 222'
issue: '2'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/1610.09063
month: '10'
oa: 1
oa_version: Preprint
page: 841 - 866
project:
- _id: 25681D80-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '291734'
name: International IST Postdoc Fellowship Programme
publication: Israel Journal of Mathematics
publication_status: published
publisher: Springer
publist_id: '7194'
quality_controlled: '1'
related_material:
record:
- id: '1511'
relation: earlier_version
status: public
scopus_import: 1
status: public
title: 'On generalized Heawood inequalities for manifolds: A van Kampen–Flores type
nonembeddability result'
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 222
year: '2017'
...
---
_id: '6115'
abstract:
- lang: eng
text: Animals adjust their behavioral priorities according to momentary needs and
prior experience. We show that Caenorhabditis elegans changes how it processes
sensory information according to the oxygen environment it experienced recently.
C. elegans acclimated to 7% O2 are aroused by CO2 and repelled by pheromones that
attract animals acclimated to 21% O2. This behavioral plasticity arises from prolonged
activity differences in a circuit that continuously signals O2 levels. A sustained
change in the activity of O2-sensing neurons reprograms the properties of their
postsynaptic partners, the RMG hub interneurons. RMG is gap-junctionally coupled
to the ASK and ADL pheromone sensors that respectively drive pheromone attraction
and repulsion. Prior O2 experience has opposite effects on the pheromone responsiveness
of these neurons. These circuit changes provide a physiological correlate of altered
pheromone valence. Our results suggest C. elegans stores a memory of recent O2
experience in the RMG circuit and illustrate how a circuit is flexibly sculpted
to guide behavioral decisions in a context-dependent manner.
author:
- first_name: Lorenz A.
full_name: Fenk, Lorenz A.
last_name: Fenk
- first_name: Mario
full_name: de Bono, Mario
id: 4E3FF80E-F248-11E8-B48F-1D18A9856A87
last_name: de Bono
orcid: 0000-0001-8347-0443
citation:
ama: Fenk LA, de Bono M. Memory of recent oxygen experience switches pheromone valence
inCaenorhabditis elegans. Proceedings of the National Academy of Sciences.
2017;114(16):4195-4200. doi:10.1073/pnas.1618934114
apa: Fenk, L. A., & de Bono, M. (2017). Memory of recent oxygen experience switches
pheromone valence inCaenorhabditis elegans. Proceedings of the National Academy
of Sciences. National Academy of Sciences. https://doi.org/10.1073/pnas.1618934114
chicago: Fenk, Lorenz A., and Mario de Bono. “Memory of Recent Oxygen Experience
Switches Pheromone Valence InCaenorhabditis Elegans.” Proceedings of the National
Academy of Sciences. National Academy of Sciences, 2017. https://doi.org/10.1073/pnas.1618934114.
ieee: L. A. Fenk and M. de Bono, “Memory of recent oxygen experience switches pheromone
valence inCaenorhabditis elegans,” Proceedings of the National Academy of Sciences,
vol. 114, no. 16. National Academy of Sciences, pp. 4195–4200, 2017.
ista: Fenk LA, de Bono M. 2017. Memory of recent oxygen experience switches pheromone
valence inCaenorhabditis elegans. Proceedings of the National Academy of Sciences.
114(16), 4195–4200.
mla: Fenk, Lorenz A., and Mario de Bono. “Memory of Recent Oxygen Experience Switches
Pheromone Valence InCaenorhabditis Elegans.” Proceedings of the National Academy
of Sciences, vol. 114, no. 16, National Academy of Sciences, 2017, pp. 4195–200,
doi:10.1073/pnas.1618934114.
short: L.A. Fenk, M. de Bono, Proceedings of the National Academy of Sciences 114
(2017) 4195–4200.
date_created: 2019-03-19T13:46:36Z
date_published: 2017-04-18T00:00:00Z
date_updated: 2021-01-12T08:06:11Z
day: '18'
ddc:
- '570'
doi: 10.1073/pnas.1618934114
extern: '1'
external_id:
pmid:
- '28373553'
file:
- access_level: open_access
checksum: 1801bc8319b752fa17598004ec375279
content_type: application/pdf
creator: kschuh
date_created: 2019-03-19T14:00:42Z
date_updated: 2020-07-14T12:47:20Z
file_id: '6116'
file_name: 2017_PNAS_Fenk.pdf
file_size: 1217696
relation: main_file
file_date_updated: 2020-07-14T12:47:20Z
has_accepted_license: '1'
intvolume: ' 114'
issue: '16'
language:
- iso: eng
month: '04'
oa: 1
oa_version: Published Version
page: 4195-4200
pmid: 1
publication: Proceedings of the National Academy of Sciences
publication_identifier:
issn:
- 0027-8424
- 1091-6490
publication_status: published
publisher: National Academy of Sciences
quality_controlled: '1'
status: public
title: Memory of recent oxygen experience switches pheromone valence inCaenorhabditis
elegans
type: journal_article
user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87
volume: 114
year: '2017'
...
---
_id: '6117'
abstract:
- lang: eng
text: 'Interleukin-17 (IL-17) is a major pro-inflammatory cytokine: it mediates
responses to pathogens or tissue damage, and drives autoimmune diseases. Little
is known about its role in the nervous system. Here we show that IL-17 has neuromodulator-like
properties in Caenorhabditis elegans. IL-17 can act directly on neurons to alter
their response properties and contribution to behaviour. Using unbiased genetic
screens, we delineate an IL-17 signalling pathway and show that it acts in the
RMG hub interneurons. Disrupting IL-17 signalling reduces RMG responsiveness to
input from oxygen sensors, and renders sustained escape from 21% oxygen transient
and contingent on additional stimuli. Over-activating IL-17 receptors abnormally
heightens responses to 21% oxygen in RMG neurons and whole animals. IL-17 deficiency
can be bypassed by optogenetic stimulation of RMG. Inducing IL-17 expression in
adults can rescue mutant defects within 6 h. These findings reveal a non-immunological
role of IL-17 modulating circuit function and behaviour.'
author:
- first_name: Changchun
full_name: Chen, Changchun
last_name: Chen
- first_name: Eisuke
full_name: Itakura, Eisuke
last_name: Itakura
- first_name: Geoffrey M.
full_name: Nelson, Geoffrey M.
last_name: Nelson
- first_name: Ming
full_name: Sheng, Ming
last_name: Sheng
- first_name: Patrick
full_name: Laurent, Patrick
last_name: Laurent
- first_name: Lorenz A.
full_name: Fenk, Lorenz A.
last_name: Fenk
- first_name: Rebecca A.
full_name: Butcher, Rebecca A.
last_name: Butcher
- first_name: Ramanujan S.
full_name: Hegde, Ramanujan S.
last_name: Hegde
- first_name: Mario
full_name: de Bono, Mario
id: 4E3FF80E-F248-11E8-B48F-1D18A9856A87
last_name: de Bono
orcid: 0000-0001-8347-0443
citation:
ama: Chen C, Itakura E, Nelson GM, et al. IL-17 is a neuromodulator of Caenorhabditis
elegans sensory responses. Nature. 2017;542(7639):43-48. doi:10.1038/nature20818
apa: Chen, C., Itakura, E., Nelson, G. M., Sheng, M., Laurent, P., Fenk, L. A.,
… de Bono, M. (2017). IL-17 is a neuromodulator of Caenorhabditis elegans sensory
responses. Nature. Springer Nature. https://doi.org/10.1038/nature20818
chicago: Chen, Changchun, Eisuke Itakura, Geoffrey M. Nelson, Ming Sheng, Patrick
Laurent, Lorenz A. Fenk, Rebecca A. Butcher, Ramanujan S. Hegde, and Mario de
Bono. “IL-17 Is a Neuromodulator of Caenorhabditis Elegans Sensory Responses.”
Nature. Springer Nature, 2017. https://doi.org/10.1038/nature20818.
ieee: C. Chen et al., “IL-17 is a neuromodulator of Caenorhabditis elegans
sensory responses,” Nature, vol. 542, no. 7639. Springer Nature, pp. 43–48,
2017.
ista: Chen C, Itakura E, Nelson GM, Sheng M, Laurent P, Fenk LA, Butcher RA, Hegde
RS, de Bono M. 2017. IL-17 is a neuromodulator of Caenorhabditis elegans sensory
responses. Nature. 542(7639), 43–48.
mla: Chen, Changchun, et al. “IL-17 Is a Neuromodulator of Caenorhabditis Elegans
Sensory Responses.” Nature, vol. 542, no. 7639, Springer Nature, 2017,
pp. 43–48, doi:10.1038/nature20818.
short: C. Chen, E. Itakura, G.M. Nelson, M. Sheng, P. Laurent, L.A. Fenk, R.A. Butcher,
R.S. Hegde, M. de Bono, Nature 542 (2017) 43–48.
date_created: 2019-03-19T14:06:41Z
date_published: 2017-02-02T00:00:00Z
date_updated: 2021-01-12T08:06:12Z
day: '02'
doi: 10.1038/nature20818
extern: '1'
external_id:
pmid:
- ' 28099418'
intvolume: ' 542'
issue: '7639'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://www.ncbi.nlm.nih.gov/pubmed/28099418
month: '02'
oa: 1
oa_version: Submitted Version
page: 43-48
pmid: 1
publication: Nature
publication_identifier:
issn:
- 0028-0836
- 1476-4687
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
status: public
title: IL-17 is a neuromodulator of Caenorhabditis elegans sensory responses
type: journal_article
user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87
volume: 542
year: '2017'
...
---
_id: '611'
abstract:
- lang: eng
text: Small RNAs (sRNAs) regulate genes in plants and animals. Here, we show that
population-wide differences in color patterns in snapdragon flowers are caused
by an inverted duplication that generates sRNAs. The complexity and size of the
transcripts indicate that the duplication represents an intermediate on the pathway
to microRNA evolution. The sRNAs repress a pigment biosynthesis gene, creating
a yellow highlight at the site of pollinator entry. The inverted duplication exhibits
steep clines in allele frequency in a natural hybrid zone, showing that the allele
is under selection. Thus, regulatory interactions of evolutionarily recent sRNAs
can be acted upon by selection and contribute to the evolution of phenotypic diversity.
author:
- first_name: Desmond
full_name: Bradley, Desmond
last_name: Bradley
- first_name: Ping
full_name: Xu, Ping
last_name: Xu
- first_name: Irina
full_name: Mohorianu, Irina
last_name: Mohorianu
- first_name: Annabel
full_name: Whibley, Annabel
last_name: Whibley
- first_name: David
full_name: Field, David
id: 419049E2-F248-11E8-B48F-1D18A9856A87
last_name: Field
orcid: 0000-0002-4014-8478
- first_name: Hugo
full_name: Tavares, Hugo
last_name: Tavares
- first_name: Matthew
full_name: Couchman, Matthew
last_name: Couchman
- first_name: Lucy
full_name: Copsey, Lucy
last_name: Copsey
- first_name: Rosemary
full_name: Carpenter, Rosemary
last_name: Carpenter
- first_name: Miaomiao
full_name: Li, Miaomiao
last_name: Li
- first_name: Qun
full_name: Li, Qun
last_name: Li
- first_name: Yongbiao
full_name: Xue, Yongbiao
last_name: Xue
- first_name: Tamas
full_name: Dalmay, Tamas
last_name: Dalmay
- first_name: Enrico
full_name: Coen, Enrico
last_name: Coen
citation:
ama: Bradley D, Xu P, Mohorianu I, et al. Evolution of flower color pattern through
selection on regulatory small RNAs. Science. 2017;358(6365):925-928. doi:10.1126/science.aao3526
apa: Bradley, D., Xu, P., Mohorianu, I., Whibley, A., Field, D., Tavares, H., …
Coen, E. (2017). Evolution of flower color pattern through selection on regulatory
small RNAs. Science. American Association for the Advancement of Science.
https://doi.org/10.1126/science.aao3526
chicago: Bradley, Desmond, Ping Xu, Irina Mohorianu, Annabel Whibley, David Field,
Hugo Tavares, Matthew Couchman, et al. “Evolution of Flower Color Pattern through
Selection on Regulatory Small RNAs.” Science. American Association for
the Advancement of Science, 2017. https://doi.org/10.1126/science.aao3526.
ieee: D. Bradley et al., “Evolution of flower color pattern through selection
on regulatory small RNAs,” Science, vol. 358, no. 6365. American Association
for the Advancement of Science, pp. 925–928, 2017.
ista: Bradley D, Xu P, Mohorianu I, Whibley A, Field D, Tavares H, Couchman M, Copsey
L, Carpenter R, Li M, Li Q, Xue Y, Dalmay T, Coen E. 2017. Evolution of flower
color pattern through selection on regulatory small RNAs. Science. 358(6365),
925–928.
mla: Bradley, Desmond, et al. “Evolution of Flower Color Pattern through Selection
on Regulatory Small RNAs.” Science, vol. 358, no. 6365, American Association
for the Advancement of Science, 2017, pp. 925–28, doi:10.1126/science.aao3526.
short: D. Bradley, P. Xu, I. Mohorianu, A. Whibley, D. Field, H. Tavares, M. Couchman,
L. Copsey, R. Carpenter, M. Li, Q. Li, Y. Xue, T. Dalmay, E. Coen, Science 358
(2017) 925–928.
date_created: 2018-12-11T11:47:29Z
date_published: 2017-11-17T00:00:00Z
date_updated: 2021-01-12T08:06:10Z
day: '17'
department:
- _id: NiBa
doi: 10.1126/science.aao3526
intvolume: ' 358'
issue: '6365'
language:
- iso: eng
month: '11'
oa_version: None
page: 925 - 928
publication: Science
publication_identifier:
issn:
- '00368075'
publication_status: published
publisher: American Association for the Advancement of Science
publist_id: '7193'
quality_controlled: '1'
scopus_import: 1
status: public
title: Evolution of flower color pattern through selection on regulatory small RNAs
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 358
year: '2017'
...
---
_id: '6113'
author:
- first_name: Shigekazu
full_name: Oda, Shigekazu
last_name: Oda
- first_name: Yu
full_name: Toyoshima, Yu
last_name: Toyoshima
- first_name: Mario
full_name: de Bono, Mario
id: 4E3FF80E-F248-11E8-B48F-1D18A9856A87
last_name: de Bono
orcid: 0000-0001-8347-0443
citation:
ama: Oda S, Toyoshima Y, de Bono M. Modulation of sensory information processing
by a neuroglobin in Caenorhabditis elegans. Proceedings of the National Academy
of Sciences. 2017;114(23):E4658-E4665. doi:10.1073/pnas.1614596114
apa: Oda, S., Toyoshima, Y., & de Bono, M. (2017). Modulation of sensory information
processing by a neuroglobin in Caenorhabditis elegans. Proceedings of the National
Academy of Sciences. National Academy of Sciences. https://doi.org/10.1073/pnas.1614596114
chicago: Oda, Shigekazu, Yu Toyoshima, and Mario de Bono. “Modulation of Sensory
Information Processing by a Neuroglobin in Caenorhabditis Elegans.” Proceedings
of the National Academy of Sciences. National Academy of Sciences, 2017. https://doi.org/10.1073/pnas.1614596114.
ieee: S. Oda, Y. Toyoshima, and M. de Bono, “Modulation of sensory information processing
by a neuroglobin in Caenorhabditis elegans,” Proceedings of the National Academy
of Sciences, vol. 114, no. 23. National Academy of Sciences, pp. E4658–E4665,
2017.
ista: Oda S, Toyoshima Y, de Bono M. 2017. Modulation of sensory information processing
by a neuroglobin in Caenorhabditis elegans. Proceedings of the National Academy
of Sciences. 114(23), E4658–E4665.
mla: Oda, Shigekazu, et al. “Modulation of Sensory Information Processing by a Neuroglobin
in Caenorhabditis Elegans.” Proceedings of the National Academy of Sciences,
vol. 114, no. 23, National Academy of Sciences, 2017, pp. E4658–65, doi:10.1073/pnas.1614596114.
short: S. Oda, Y. Toyoshima, M. de Bono, Proceedings of the National Academy of
Sciences 114 (2017) E4658–E4665.
date_created: 2019-03-19T13:29:51Z
date_published: 2017-06-06T00:00:00Z
date_updated: 2021-01-12T08:06:11Z
day: '06'
ddc:
- '570'
doi: 10.1073/pnas.1614596114
extern: '1'
external_id:
pmid:
- '28536200'
file:
- access_level: open_access
checksum: 9e42ce47090ecdad7d76f2dbdebb924e
content_type: application/pdf
creator: kschuh
date_created: 2019-03-19T13:42:58Z
date_updated: 2020-07-14T12:47:19Z
file_id: '6114'
file_name: 2017_PNAS_Oda.pdf
file_size: 1469622
relation: main_file
file_date_updated: 2020-07-14T12:47:19Z
has_accepted_license: '1'
intvolume: ' 114'
issue: '23'
language:
- iso: eng
month: '06'
oa: 1
oa_version: Published Version
page: E4658-E4665
pmid: 1
publication: Proceedings of the National Academy of Sciences
publication_identifier:
issn:
- 0027-8424
- 1091-6490
publication_status: published
publisher: National Academy of Sciences
quality_controlled: '1'
status: public
title: Modulation of sensory information processing by a neuroglobin in Caenorhabditis
elegans
type: journal_article
user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87
volume: 114
year: '2017'
...
---
_id: '613'
abstract:
- lang: eng
text: 'Bacteria in groups vary individually, and interact with other bacteria and
the environment to produce population-level patterns of gene expression. Investigating
such behavior in detail requires measuring and controlling populations at the
single-cell level alongside precisely specified interactions and environmental
characteristics. Here we present an automated, programmable platform that combines
image-based gene expression and growth measurements with on-line optogenetic expression
control for hundreds of individual Escherichia coli cells over days, in a dynamically
adjustable environment. This integrated platform broadly enables experiments that
bridge individual and population behaviors. We demonstrate: (i) population structuring
by independent closed-loop control of gene expression in many individual cells,
(ii) cell-cell variation control during antibiotic perturbation, (iii) hybrid
bio-digital circuits in single cells, and freely specifiable digital communication
between individual bacteria. These examples showcase the potential for real-time
integration of theoretical models with measurement and control of many individual
cells to investigate and engineer microbial population behavior.'
acknowledgement: We are grateful to M. Lang, H. Janovjak, M. Khammash, A. Milias-Argeitis,
M. Rullan, G. Batt, A. Bosma-Moody, Aryan, S. Leibler, and members of the Guet and
Tkačik groups for helpful discussion, comments, and suggestions. We thank A. Moglich,
T. Mathes, J. Tabor, and S. Schmidl for kind gifts of strains, and R. Hauschild,
B. Knep, M. Lang, T. Asenov, E. Papusheva, T. Menner, T. Adletzberger, and J. Merrin
for technical assistance. The research leading to these results has received funding
from the People Programme (Marie Curie Actions) of the European Union’s Seventh
Framework Programme (FP7/2007–2013) under REA grant agreement no. [291734]. (to
R.C. and J.R.), Austrian Science Fund grant FWF P28844 (to G.T.), and internal IST
Austria Interdisciplinary Project Support. J.R. acknowledges support from the Agence
Nationale de la Recherche (ANR) under Grant Nos. ANR-16-CE33-0018 (MEMIP), ANR-16-CE12-0025
(COGEX) and ANR-10-BINF-06-01 (ICEBERG).
article_number: '1535'
article_processing_charge: Yes (in subscription journal)
author:
- first_name: Remy P
full_name: Chait, Remy P
id: 3464AE84-F248-11E8-B48F-1D18A9856A87
last_name: Chait
orcid: 0000-0003-0876-3187
- first_name: Jakob
full_name: Ruess, Jakob
id: 4A245D00-F248-11E8-B48F-1D18A9856A87
last_name: Ruess
orcid: 0000-0003-1615-3282
- first_name: Tobias
full_name: Bergmiller, Tobias
id: 2C471CFA-F248-11E8-B48F-1D18A9856A87
last_name: Bergmiller
orcid: 0000-0001-5396-4346
- first_name: Gasper
full_name: Tkacik, Gasper
id: 3D494DCA-F248-11E8-B48F-1D18A9856A87
last_name: Tkacik
orcid: 0000-0002-6699-1455
- first_name: Calin C
full_name: Guet, Calin C
id: 47F8433E-F248-11E8-B48F-1D18A9856A87
last_name: Guet
orcid: 0000-0001-6220-2052
citation:
ama: Chait RP, Ruess J, Bergmiller T, Tkačik G, Guet CC. Shaping bacterial population
behavior through computer interfaced control of individual cells. Nature Communications.
2017;8(1). doi:10.1038/s41467-017-01683-1
apa: Chait, R. P., Ruess, J., Bergmiller, T., Tkačik, G., & Guet, C. C. (2017).
Shaping bacterial population behavior through computer interfaced control of individual
cells. Nature Communications. Nature Publishing Group. https://doi.org/10.1038/s41467-017-01683-1
chicago: Chait, Remy P, Jakob Ruess, Tobias Bergmiller, Gašper Tkačik, and Calin
C Guet. “Shaping Bacterial Population Behavior through Computer Interfaced Control
of Individual Cells.” Nature Communications. Nature Publishing Group, 2017.
https://doi.org/10.1038/s41467-017-01683-1.
ieee: R. P. Chait, J. Ruess, T. Bergmiller, G. Tkačik, and C. C. Guet, “Shaping
bacterial population behavior through computer interfaced control of individual
cells,” Nature Communications, vol. 8, no. 1. Nature Publishing Group,
2017.
ista: Chait RP, Ruess J, Bergmiller T, Tkačik G, Guet CC. 2017. Shaping bacterial
population behavior through computer interfaced control of individual cells. Nature
Communications. 8(1), 1535.
mla: Chait, Remy P., et al. “Shaping Bacterial Population Behavior through Computer
Interfaced Control of Individual Cells.” Nature Communications, vol. 8,
no. 1, 1535, Nature Publishing Group, 2017, doi:10.1038/s41467-017-01683-1.
short: R.P. Chait, J. Ruess, T. Bergmiller, G. Tkačik, C.C. Guet, Nature Communications
8 (2017).
date_created: 2018-12-11T11:47:30Z
date_published: 2017-12-01T00:00:00Z
date_updated: 2021-01-12T08:06:15Z
day: '01'
ddc:
- '576'
- '579'
department:
- _id: CaGu
- _id: GaTk
doi: 10.1038/s41467-017-01683-1
ec_funded: 1
file:
- access_level: open_access
checksum: 44bb5d0229926c23a9955d9fe0f9723f
content_type: application/pdf
creator: system
date_created: 2018-12-12T10:16:05Z
date_updated: 2020-07-14T12:47:20Z
file_id: '5190'
file_name: IST-2017-911-v1+1_s41467-017-01683-1.pdf
file_size: 1951699
relation: main_file
file_date_updated: 2020-07-14T12:47:20Z
has_accepted_license: '1'
intvolume: ' 8'
issue: '1'
language:
- iso: eng
month: '12'
oa: 1
oa_version: Published Version
project:
- _id: 25681D80-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '291734'
name: International IST Postdoc Fellowship Programme
- _id: 254E9036-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: P28844-B27
name: Biophysics of information processing in gene regulation
publication: Nature Communications
publication_identifier:
issn:
- '20411723'
publication_status: published
publisher: Nature Publishing Group
publist_id: '7191'
pubrep_id: '911'
quality_controlled: '1'
scopus_import: 1
status: public
title: Shaping bacterial population behavior through computer interfaced control of
individual cells
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: journal_article
user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87
volume: 8
year: '2017'
...
---
_id: '615'
abstract:
- lang: eng
text: We show that the Dyson Brownian Motion exhibits local universality after a
very short time assuming that local rigidity and level repulsion of the eigenvalues
hold. These conditions are verified, hence bulk spectral universality is proven,
for a large class of Wigner-like matrices, including deformed Wigner ensembles
and ensembles with non-stochastic variance matrices whose limiting densities differ
from Wigner's semicircle law.
author:
- 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: Erdös L, Schnelli K. Universality for random matrix flows with time dependent
density. Annales de l’institut Henri Poincare (B) Probability and Statistics.
2017;53(4):1606-1656. doi:10.1214/16-AIHP765
apa: Erdös, L., & Schnelli, K. (2017). Universality for random matrix flows
with time dependent density. Annales de l’institut Henri Poincare (B) Probability
and Statistics. Institute of Mathematical Statistics. https://doi.org/10.1214/16-AIHP765
chicago: Erdös, László, and Kevin Schnelli. “Universality for Random Matrix Flows
with Time Dependent Density.” Annales de l’institut Henri Poincare (B) Probability
and Statistics. Institute of Mathematical Statistics, 2017. https://doi.org/10.1214/16-AIHP765.
ieee: L. Erdös and K. Schnelli, “Universality for random matrix flows with time
dependent density,” Annales de l’institut Henri Poincare (B) Probability and
Statistics, vol. 53, no. 4. Institute of Mathematical Statistics, pp. 1606–1656,
2017.
ista: Erdös L, Schnelli K. 2017. Universality for random matrix flows with time
dependent density. Annales de l’institut Henri Poincare (B) Probability and Statistics.
53(4), 1606–1656.
mla: Erdös, László, and Kevin Schnelli. “Universality for Random Matrix Flows with
Time Dependent Density.” Annales de l’institut Henri Poincare (B) Probability
and Statistics, vol. 53, no. 4, Institute of Mathematical Statistics, 2017,
pp. 1606–56, doi:10.1214/16-AIHP765.
short: L. Erdös, K. Schnelli, Annales de l’institut Henri Poincare (B) Probability
and Statistics 53 (2017) 1606–1656.
date_created: 2018-12-11T11:47:30Z
date_published: 2017-11-01T00:00:00Z
date_updated: 2021-01-12T08:06:22Z
day: '01'
department:
- _id: LaEr
doi: 10.1214/16-AIHP765
ec_funded: 1
intvolume: ' 53'
issue: '4'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/1504.00650
month: '11'
oa: 1
oa_version: Submitted Version
page: 1606 - 1656
project:
- _id: 258DCDE6-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '338804'
name: Random matrices, universality and disordered quantum systems
publication: Annales de l'institut Henri Poincare (B) Probability and Statistics
publication_identifier:
issn:
- '02460203'
publication_status: published
publisher: Institute of Mathematical Statistics
publist_id: '7189'
quality_controlled: '1'
scopus_import: 1
status: public
title: Universality for random matrix flows with time dependent density
type: journal_article
user_id: 4435EBFC-F248-11E8-B48F-1D18A9856A87
volume: 53
year: '2017'
...
---
_id: '618'
abstract:
- lang: eng
text: 'Background: Increasing temperatures are predicted to strongly impact host-parasite
interactions, but empirical tests are rare. Host species that are naturally exposed
to a broad temperature spectrum offer the possibility to investigate the effects
of elevated temperatures on hosts and parasites. Using three-spined sticklebacks,
Gasterosteus aculeatus L., and tapeworms, Schistocephalus solidus (Müller, 1776),
originating from a cold and a warm water site of a volcanic lake, we subjected
sympatric and allopatric host-parasite combinations to cold and warm conditions
in a fully crossed design. We predicted that warm temperatures would promote the
development of the parasites, while the hosts might benefit from cooler temperatures.
We further expected adaptations to the local temperature and mutual adaptations
of local host-parasite pairs. Results: Overall, S. solidus parasites grew faster
at warm temperatures and stickleback hosts at cold temperatures. On a finer scale,
we observed that parasites were able to exploit their hosts more efficiently at
the parasite’s temperature of origin. In contrast, host tolerance towards parasite
infection was higher when sticklebacks were infected with parasites at the parasite’s
‘foreign’ temperature. Cold-origin sticklebacks tended to grow faster and parasite
infection induced a stronger immune response. Conclusions: Our results suggest
that increasing environmental temperatures promote the parasite rather than the
host and that host tolerance is dependent on the interaction between parasite
infection and temperature. Sticklebacks might use tolerance mechanisms towards
parasite infection in combination with their high plasticity towards temperature
changes to cope with increasing parasite infection pressures and rising temperatures.'
article_number: '52'
author:
- first_name: Frederik
full_name: Franke, Frederik
last_name: Franke
- first_name: Sophie
full_name: Armitage, Sophie
last_name: Armitage
- first_name: Megan
full_name: Kutzer, Megan
id: 29D0B332-F248-11E8-B48F-1D18A9856A87
last_name: Kutzer
orcid: 0000-0002-8696-6978
- first_name: Joachim
full_name: Kurtz, Joachim
last_name: Kurtz
- first_name: Jörn
full_name: Scharsack, Jörn
last_name: Scharsack
citation:
ama: Franke F, Armitage S, Kutzer M, Kurtz J, Scharsack J. Environmental temperature
variation influences fitness trade-offs in a fish-tapeworm association . Parasites
& Vectors. 2017;10(252). doi:10.1186/s13071-017-2192-7
apa: Franke, F., Armitage, S., Kutzer, M., Kurtz, J., & Scharsack, J. (2017).
Environmental temperature variation influences fitness trade-offs in a fish-tapeworm
association . Parasites & Vectors. BioMed Central. https://doi.org/10.1186/s13071-017-2192-7
chicago: Franke, Frederik, Sophie Armitage, Megan Kutzer, Joachim Kurtz, and Jörn
Scharsack. “Environmental Temperature Variation Influences Fitness Trade-Offs
in a Fish-Tapeworm Association .” Parasites & Vectors. BioMed Central,
2017. https://doi.org/10.1186/s13071-017-2192-7.
ieee: F. Franke, S. Armitage, M. Kutzer, J. Kurtz, and J. Scharsack, “Environmental
temperature variation influences fitness trade-offs in a fish-tapeworm association
,” Parasites & Vectors, vol. 10, no. 252. BioMed Central, 2017.
ista: Franke F, Armitage S, Kutzer M, Kurtz J, Scharsack J. 2017. Environmental
temperature variation influences fitness trade-offs in a fish-tapeworm association
. Parasites & Vectors. 10(252), 52.
mla: Franke, Frederik, et al. “Environmental Temperature Variation Influences Fitness
Trade-Offs in a Fish-Tapeworm Association .” Parasites & Vectors, vol.
10, no. 252, 52, BioMed Central, 2017, doi:10.1186/s13071-017-2192-7.
short: F. Franke, S. Armitage, M. Kutzer, J. Kurtz, J. Scharsack, Parasites &
Vectors 10 (2017).
date_created: 2018-12-11T11:47:31Z
date_published: 2017-06-02T00:00:00Z
date_updated: 2021-01-12T08:06:35Z
day: '02'
ddc:
- '570'
doi: 10.1186/s13071-017-2192-7
extern: '1'
file:
- access_level: open_access
checksum: 742943377a38ee208108705b8e2f4dbf
content_type: application/pdf
creator: dernst
date_created: 2019-01-21T13:45:36Z
date_updated: 2020-07-14T12:47:22Z
file_id: '5864'
file_name: 2017_Parasites_Franke.pdf
file_size: 671807
relation: main_file
file_date_updated: 2020-07-14T12:47:22Z
has_accepted_license: '1'
intvolume: ' 10'
issue: '252'
language:
- iso: eng
month: '06'
oa: 1
oa_version: Published Version
publication: Parasites & Vectors
publication_identifier:
issn:
- '17563305'
publication_status: published
publisher: BioMed Central
publist_id: '7186'
quality_controlled: '1'
status: public
title: 'Environmental temperature variation influences fitness trade-offs in a fish-tapeworm
association '
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: 10
year: '2017'
...
---
_id: '623'
abstract:
- lang: eng
text: Genetic factors might be largely responsible for the development of autism
spectrum disorder (ASD) that alone or in combination with specific environmental
risk factors trigger the pathology. Multiple mutations identified in ASD patients
that impair synaptic function in the central nervous system are well studied in
animal models. How these mutations might interact with other risk factors is not
fully understood though. Additionally, how systems outside of the brain are altered
in the context of ASD is an emerging area of research. Extracerebral influences
on the physiology could begin in utero and contribute to changes in the brain
and in the development of other body systems and further lead to epigenetic changes.
Therefore, multiple recent studies have aimed at elucidating the role of gene-environment
interactions in ASD. Here we provide an overview on the extracerebral systems
that might play an important associative role in ASD and review evidence regarding
the potential roles of inflammation, trace metals, metabolism, genetic susceptibility,
enteric nervous system function and the microbiota of the gastrointestinal (GI)
tract on the development of endophenotypes in animal models of ASD. By influencing
environmental conditions, it might be possible to reduce or limit the severity
of ASD pathology.
alternative_title:
- ADVSANAT
author:
- first_name: Elisa
full_name: Hill Yardin, Elisa
last_name: Hill Yardin
- first_name: Sonja
full_name: Mckeown, Sonja
last_name: Mckeown
- first_name: Gaia
full_name: Novarino, Gaia
id: 3E57A680-F248-11E8-B48F-1D18A9856A87
last_name: Novarino
orcid: 0000-0002-7673-7178
- first_name: Andreas
full_name: Grabrucker, Andreas
last_name: Grabrucker
citation:
ama: 'Hill Yardin E, Mckeown S, Novarino G, Grabrucker A. Extracerebral dysfunction
in animal models of autism spectrum disorder. In: Schmeisser M, Boekers T, eds.
Translational Anatomy and Cell Biology of Autism Spectrum Disorder. Vol
224. Advances in Anatomy Embryology and Cell Biology. Springer; 2017:159-187.
doi:10.1007/978-3-319-52498-6_9'
apa: Hill Yardin, E., Mckeown, S., Novarino, G., & Grabrucker, A. (2017). Extracerebral
dysfunction in animal models of autism spectrum disorder. In M. Schmeisser &
T. Boekers (Eds.), Translational Anatomy and Cell Biology of Autism Spectrum
Disorder (Vol. 224, pp. 159–187). Springer. https://doi.org/10.1007/978-3-319-52498-6_9
chicago: Hill Yardin, Elisa, Sonja Mckeown, Gaia Novarino, and Andreas Grabrucker.
“Extracerebral Dysfunction in Animal Models of Autism Spectrum Disorder.” In Translational
Anatomy and Cell Biology of Autism Spectrum Disorder, edited by Michael Schmeisser
and Tobias Boekers, 224:159–87. Advances in Anatomy Embryology and Cell Biology.
Springer, 2017. https://doi.org/10.1007/978-3-319-52498-6_9.
ieee: E. Hill Yardin, S. Mckeown, G. Novarino, and A. Grabrucker, “Extracerebral
dysfunction in animal models of autism spectrum disorder,” in Translational
Anatomy and Cell Biology of Autism Spectrum Disorder, vol. 224, M. Schmeisser
and T. Boekers, Eds. Springer, 2017, pp. 159–187.
ista: 'Hill Yardin E, Mckeown S, Novarino G, Grabrucker A. 2017.Extracerebral dysfunction
in animal models of autism spectrum disorder. In: Translational Anatomy and Cell
Biology of Autism Spectrum Disorder. ADVSANAT, vol. 224, 159–187.'
mla: Hill Yardin, Elisa, et al. “Extracerebral Dysfunction in Animal Models of Autism
Spectrum Disorder.” Translational Anatomy and Cell Biology of Autism Spectrum
Disorder, edited by Michael Schmeisser and Tobias Boekers, vol. 224, Springer,
2017, pp. 159–87, doi:10.1007/978-3-319-52498-6_9.
short: E. Hill Yardin, S. Mckeown, G. Novarino, A. Grabrucker, in:, M. Schmeisser,
T. Boekers (Eds.), Translational Anatomy and Cell Biology of Autism Spectrum Disorder,
Springer, 2017, pp. 159–187.
date_created: 2018-12-11T11:47:33Z
date_published: 2017-05-28T00:00:00Z
date_updated: 2021-01-12T08:06:46Z
day: '28'
department:
- _id: GaNo
doi: 10.1007/978-3-319-52498-6_9
editor:
- first_name: Michael
full_name: Schmeisser, Michael
last_name: Schmeisser
- first_name: Tobias
full_name: Boekers, Tobias
last_name: Boekers
intvolume: ' 224'
language:
- iso: eng
month: '05'
oa_version: None
page: 159 - 187
publication: Translational Anatomy and Cell Biology of Autism Spectrum Disorder
publication_identifier:
isbn:
- 978-3-319-52496-2
issn:
- '03015556'
publication_status: published
publisher: Springer
publist_id: '7177'
quality_controlled: '1'
scopus_import: 1
series_title: Advances in Anatomy Embryology and Cell Biology
status: public
title: Extracerebral dysfunction in animal models of autism spectrum disorder
type: book_chapter
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 224
year: '2017'
...
---
_id: '626'
abstract:
- lang: eng
text: 'Our focus here is on the infinitesimal model. In this model, one or several
quantitative traits are described as the sum of a genetic and a non-genetic component,
the first being distributed within families as a normal random variable centred
at the average of the parental genetic components, and with a variance independent
of the parental traits. Thus, the variance that segregates within families is
not perturbed by selection, and can be predicted from the variance components.
This does not necessarily imply that the trait distribution across the whole population
should be Gaussian, and indeed selection or population structure may have a substantial
effect on the overall trait distribution. One of our main aims is to identify
some general conditions on the allelic effects for the infinitesimal model to
be accurate. We first review the long history of the infinitesimal model in quantitative
genetics. Then we formulate the model at the phenotypic level in terms of individual
trait values and relationships between individuals, but including different evolutionary
processes: genetic drift, recombination, selection, mutation, population structure,
…. We give a range of examples of its application to evolutionary questions related
to stabilising selection, assortative mating, effective population size and response
to selection, habitat preference and speciation. We provide a mathematical justification
of the model as the limit as the number M of underlying loci tends to infinity
of a model with Mendelian inheritance, mutation and environmental noise, when
the genetic component of the trait is purely additive. We also show how the model
generalises to include epistatic effects. We prove in particular that, within
each family, the genetic components of the individual trait values in the current
generation are indeed normally distributed with a variance independent of ancestral
traits, up to an error of order 1∕M. Simulations suggest that in some cases the
convergence may be as fast as 1∕M.'
author:
- 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: Alison
full_name: Etheridge, Alison
last_name: Etheridge
- first_name: Amandine
full_name: Véber, Amandine
last_name: Véber
citation:
ama: 'Barton NH, Etheridge A, Véber A. The infinitesimal model: Definition derivation
and implications. Theoretical Population Biology. 2017;118:50-73. doi:10.1016/j.tpb.2017.06.001'
apa: 'Barton, N. H., Etheridge, A., & Véber, A. (2017). The infinitesimal model:
Definition derivation and implications. Theoretical Population Biology.
Academic Press. https://doi.org/10.1016/j.tpb.2017.06.001'
chicago: 'Barton, Nicholas H, Alison Etheridge, and Amandine Véber. “The Infinitesimal
Model: Definition Derivation and Implications.” Theoretical Population Biology.
Academic Press, 2017. https://doi.org/10.1016/j.tpb.2017.06.001.'
ieee: 'N. H. Barton, A. Etheridge, and A. Véber, “The infinitesimal model: Definition
derivation and implications,” Theoretical Population Biology, vol. 118.
Academic Press, pp. 50–73, 2017.'
ista: 'Barton NH, Etheridge A, Véber A. 2017. The infinitesimal model: Definition
derivation and implications. Theoretical Population Biology. 118, 50–73.'
mla: 'Barton, Nicholas H., et al. “The Infinitesimal Model: Definition Derivation
and Implications.” Theoretical Population Biology, vol. 118, Academic Press,
2017, pp. 50–73, doi:10.1016/j.tpb.2017.06.001.'
short: N.H. Barton, A. Etheridge, A. Véber, Theoretical Population Biology 118 (2017)
50–73.
date_created: 2018-12-11T11:47:34Z
date_published: 2017-12-01T00:00:00Z
date_updated: 2021-01-12T08:06:50Z
day: '01'
ddc:
- '576'
department:
- _id: NiBa
doi: 10.1016/j.tpb.2017.06.001
ec_funded: 1
file:
- access_level: open_access
checksum: 7dd02bfcfe8f244f4a6c19091aedf2c8
content_type: application/pdf
creator: system
date_created: 2018-12-12T10:12:45Z
date_updated: 2020-07-14T12:47:25Z
file_id: '4964'
file_name: IST-2017-908-v1+1_1-s2.0-S0040580917300886-main_1_.pdf
file_size: 1133924
relation: main_file
file_date_updated: 2020-07-14T12:47:25Z
has_accepted_license: '1'
intvolume: ' 118'
language:
- iso: eng
month: '12'
oa: 1
oa_version: Published Version
page: 50 - 73
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_identifier:
issn:
- '00405809'
publication_status: published
publisher: Academic Press
publist_id: '7169'
pubrep_id: '908'
quality_controlled: '1'
scopus_import: 1
status: public
title: 'The infinitesimal model: Definition derivation and implications'
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: 118
year: '2017'
...
---
_id: '625'
abstract:
- lang: eng
text: In the analysis of reactive systems a quantitative objective assigns a real
value to every trace of the system. The value decision problem for a quantitative
objective requires a trace whose value is at least a given threshold, and the
exact value decision problem requires a trace whose value is exactly the threshold.
We compare the computational complexity of the value and exact value decision
problems for classical quantitative objectives, such as sum, discounted sum, energy,
and mean-payoff for two standard models of reactive systems, namely, graphs and
graph games.
acknowledgement: 'This research was supported in part by the Austrian Science Fund
(FWF) under grants S11402-N23 and S11407-N23 (RiSE/SHiNE), and Z211-N23 (Wittgenstein
Award), ERC Start grant (279307: Graph Games), Vienna Science and Technology Fund
(WWTF) through project ICT15-003.'
alternative_title:
- LNCS
article_processing_charge: No
author:
- first_name: Krishnendu
full_name: Chatterjee, Krishnendu
id: 2E5DCA20-F248-11E8-B48F-1D18A9856A87
last_name: Chatterjee
orcid: 0000-0002-4561-241X
- first_name: Laurent
full_name: Doyen, Laurent
last_name: Doyen
- first_name: Thomas A
full_name: Henzinger, Thomas A
id: 40876CD8-F248-11E8-B48F-1D18A9856A87
last_name: Henzinger
orcid: 0000−0002−2985−7724
citation:
ama: 'Chatterjee K, Doyen L, Henzinger TA. The cost of exactness in quantitative
reachability. In: Aceto L, Bacci G, Ingólfsdóttir A, Legay A, Mardare R, eds.
Models, Algorithms, Logics and Tools. Vol 10460. Theoretical Computer Science
and General Issues. Springer; 2017:367-381. doi:10.1007/978-3-319-63121-9_18'
apa: Chatterjee, K., Doyen, L., & Henzinger, T. A. (2017). The cost of exactness
in quantitative reachability. In L. Aceto, G. Bacci, A. Ingólfsdóttir, A. Legay,
& R. Mardare (Eds.), Models, Algorithms, Logics and Tools (Vol. 10460,
pp. 367–381). Springer. https://doi.org/10.1007/978-3-319-63121-9_18
chicago: Chatterjee, Krishnendu, Laurent Doyen, and Thomas A Henzinger. “The Cost
of Exactness in Quantitative Reachability.” In Models, Algorithms, Logics and
Tools, edited by Luca Aceto, Giorgio Bacci, Anna Ingólfsdóttir, Axel Legay,
and Radu Mardare, 10460:367–81. Theoretical Computer Science and General Issues.
Springer, 2017. https://doi.org/10.1007/978-3-319-63121-9_18.
ieee: K. Chatterjee, L. Doyen, and T. A. Henzinger, “The cost of exactness in quantitative
reachability,” in Models, Algorithms, Logics and Tools, vol. 10460, L.
Aceto, G. Bacci, A. Ingólfsdóttir, A. Legay, and R. Mardare, Eds. Springer, 2017,
pp. 367–381.
ista: 'Chatterjee K, Doyen L, Henzinger TA. 2017.The cost of exactness in quantitative
reachability. In: Models, Algorithms, Logics and Tools. LNCS, vol. 10460, 367–381.'
mla: Chatterjee, Krishnendu, et al. “The Cost of Exactness in Quantitative Reachability.”
Models, Algorithms, Logics and Tools, edited by Luca Aceto et al., vol.
10460, Springer, 2017, pp. 367–81, doi:10.1007/978-3-319-63121-9_18.
short: K. Chatterjee, L. Doyen, T.A. Henzinger, in:, L. Aceto, G. Bacci, A. Ingólfsdóttir,
A. Legay, R. Mardare (Eds.), Models, Algorithms, Logics and Tools, Springer, 2017,
pp. 367–381.
date_created: 2018-12-11T11:47:34Z
date_published: 2017-07-25T00:00:00Z
date_updated: 2022-05-23T08:54:02Z
day: '25'
ddc:
- '000'
department:
- _id: KrCh
- _id: ToHe
doi: 10.1007/978-3-319-63121-9_18
ec_funded: 1
editor:
- first_name: Luca
full_name: Aceto, Luca
last_name: Aceto
- first_name: Giorgio
full_name: Bacci, Giorgio
last_name: Bacci
- first_name: Anna
full_name: Ingólfsdóttir, Anna
last_name: Ingólfsdóttir
- first_name: Axel
full_name: Legay, Axel
last_name: Legay
- first_name: Radu
full_name: Mardare, Radu
last_name: Mardare
file:
- access_level: open_access
checksum: b2402766ec02c79801aac634bd8f9f6c
content_type: application/pdf
creator: dernst
date_created: 2019-11-19T08:06:50Z
date_updated: 2020-07-14T12:47:25Z
file_id: '7048'
file_name: 2017_ModelsAlgorithms_Chatterjee.pdf
file_size: 192826
relation: main_file
file_date_updated: 2020-07-14T12:47:25Z
has_accepted_license: '1'
intvolume: ' 10460'
language:
- iso: eng
month: '07'
oa: 1
oa_version: Submitted Version
page: 367 - 381
project:
- _id: 25F5A88A-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: S11402-N23
name: Moderne Concurrency Paradigms
- _id: 25863FF4-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: S11407
name: Game Theory
- _id: 25F42A32-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: Z211
name: The Wittgenstein Prize
- _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: Models, Algorithms, Logics and Tools
publication_identifier:
isbn:
- 978-3-319-63120-2
issn:
- 0302-9743
publication_status: published
publisher: Springer
publist_id: '7170'
quality_controlled: '1'
scopus_import: '1'
series_title: Theoretical Computer Science and General Issues
status: public
title: The cost of exactness in quantitative reachability
type: book_chapter
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 10460
year: '2017'
...
---
_id: '624'
abstract:
- lang: eng
text: Bacteria adapt to adverse environmental conditions by altering gene expression
patterns. Recently, a novel stress adaptation mechanism has been described that
allows Escherichia coli to alter gene expression at the post-transcriptional level.
The key player in this regulatory pathway is the endoribonuclease MazF, the toxin
component of the toxin-antitoxin module mazEF that is triggered by various stressful
conditions. In general, MazF degrades the majority of transcripts by cleaving
at ACA sites, which results in the retardation of bacterial growth. Furthermore,
MazF can process a small subset of mRNAs and render them leaderless by removing
their ribosome binding site. MazF concomitantly modifies ribosomes, making them
selective for the translation of leaderless mRNAs. In this study, we employed
fluorescent reporter-systems to investigate mazEF expression during stressful
conditions, and to infer consequences of the mRNA processing mediated by MazF
on gene expression at the single-cell level. Our results suggest that mazEF transcription
is maintained at low levels in single cells encountering adverse conditions, such
as antibiotic stress or amino acid starvation. Moreover, using the grcA mRNA as
a model for MazF-mediated mRNA processing, we found that MazF activation promotes
heterogeneity in the grcA reporter expression, resulting in a subpopulation of
cells with increased levels of GrcA reporter protein.
acknowledgement: 'Austrian Science Fund (FWF): M1697, P22249; Swiss National Science
Foundation (SNF): 145706; European Commission;FWF Special Research Program: RNA-REG
F43'
article_number: '3830'
author:
- first_name: Nela
full_name: Nikolic, Nela
id: 42D9CABC-F248-11E8-B48F-1D18A9856A87
last_name: Nikolic
orcid: 0000-0001-9068-6090
- first_name: Zrinka
full_name: Didara, Zrinka
last_name: Didara
- first_name: Isabella
full_name: Moll, Isabella
last_name: Moll
citation:
ama: Nikolic N, Didara Z, Moll I. MazF activation promotes translational heterogeneity
of the grcA mRNA in Escherichia coli populations. PeerJ. 2017;2017(9).
doi:10.7717/peerj.3830
apa: Nikolic, N., Didara, Z., & Moll, I. (2017). MazF activation promotes translational
heterogeneity of the grcA mRNA in Escherichia coli populations. PeerJ.
PeerJ. https://doi.org/10.7717/peerj.3830
chicago: Nikolic, Nela, Zrinka Didara, and Isabella Moll. “MazF Activation Promotes
Translational Heterogeneity of the GrcA MRNA in Escherichia Coli Populations.”
PeerJ. PeerJ, 2017. https://doi.org/10.7717/peerj.3830.
ieee: N. Nikolic, Z. Didara, and I. Moll, “MazF activation promotes translational
heterogeneity of the grcA mRNA in Escherichia coli populations,” PeerJ,
vol. 2017, no. 9. PeerJ, 2017.
ista: Nikolic N, Didara Z, Moll I. 2017. MazF activation promotes translational
heterogeneity of the grcA mRNA in Escherichia coli populations. PeerJ. 2017(9),
3830.
mla: Nikolic, Nela, et al. “MazF Activation Promotes Translational Heterogeneity
of the GrcA MRNA in Escherichia Coli Populations.” PeerJ, vol. 2017, no.
9, 3830, PeerJ, 2017, doi:10.7717/peerj.3830.
short: N. Nikolic, Z. Didara, I. Moll, PeerJ 2017 (2017).
date_created: 2018-12-11T11:47:33Z
date_published: 2017-09-21T00:00:00Z
date_updated: 2021-01-12T08:06:48Z
day: '21'
ddc:
- '579'
department:
- _id: CaGu
doi: 10.7717/peerj.3830
file:
- access_level: open_access
checksum: 3d79ae6b6eabc90b0eaaed82ff3493b0
content_type: application/pdf
creator: system
date_created: 2018-12-12T10:11:51Z
date_updated: 2020-07-14T12:47:24Z
file_id: '4908'
file_name: IST-2017-909-v1+1_peerj-3830.pdf
file_size: 682064
relation: main_file
file_date_updated: 2020-07-14T12:47:24Z
has_accepted_license: '1'
intvolume: ' 2017'
issue: '9'
language:
- iso: eng
month: '09'
oa: 1
oa_version: Published Version
publication: PeerJ
publication_identifier:
issn:
- '21678359'
publication_status: published
publisher: PeerJ
publist_id: '7172'
pubrep_id: '909'
quality_controlled: '1'
scopus_import: 1
status: public
title: MazF activation promotes translational heterogeneity of the grcA mRNA in Escherichia
coli populations
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 2017
year: '2017'
...
---
_id: '628'
abstract:
- lang: eng
text: We consider the problem of developing automated techniques for solving recurrence
relations to aid the expected-runtime analysis of programs. The motivation is
that several classical textbook algorithms have quite efficient expected-runtime
complexity, whereas the corresponding worst-case bounds are either inefficient
(e.g., Quick-Sort), or completely ineffective (e.g., Coupon-Collector). Since
the main focus of expected-runtime analysis is to obtain efficient bounds, we
consider bounds that are either logarithmic, linear or almost-linear (O(log n),
O(n), O(n · log n), respectively, where n represents the input size). Our main
contribution is an efficient (simple linear-time algorithm) sound approach for
deriving such expected-runtime bounds for the analysis of recurrence relations
induced by randomized algorithms. The experimental results show that our approach
can efficiently derive asymptotically optimal expected-runtime bounds for recurrences
of classical randomized algorithms, including Randomized-Search, Quick-Sort, Quick-Select,
Coupon-Collector, where the worst-case bounds are either inefficient (such as
linear as compared to logarithmic expected-runtime complexity, or quadratic as
compared to linear or almost-linear expected-runtime complexity), or ineffective.
alternative_title:
- LNCS
author:
- first_name: Krishnendu
full_name: Chatterjee, Krishnendu
id: 2E5DCA20-F248-11E8-B48F-1D18A9856A87
last_name: Chatterjee
orcid: 0000-0002-4561-241X
- first_name: Hongfei
full_name: Fu, Hongfei
last_name: Fu
- first_name: Aniket
full_name: Murhekar, Aniket
last_name: Murhekar
citation:
ama: 'Chatterjee K, Fu H, Murhekar A. Automated recurrence analysis for almost linear
expected runtime bounds. In: Majumdar R, Kunčak V, eds. Vol 10426. Springer; 2017:118-139.
doi:10.1007/978-3-319-63387-9_6'
apa: 'Chatterjee, K., Fu, H., & Murhekar, A. (2017). Automated recurrence analysis
for almost linear expected runtime bounds. In R. Majumdar & V. Kunčak (Eds.)
(Vol. 10426, pp. 118–139). Presented at the CAV: Computer Aided Verification,
Heidelberg, Germany: Springer. https://doi.org/10.1007/978-3-319-63387-9_6'
chicago: Chatterjee, Krishnendu, Hongfei Fu, and Aniket Murhekar. “Automated Recurrence
Analysis for Almost Linear Expected Runtime Bounds.” edited by Rupak Majumdar
and Viktor Kunčak, 10426:118–39. Springer, 2017. https://doi.org/10.1007/978-3-319-63387-9_6.
ieee: 'K. Chatterjee, H. Fu, and A. Murhekar, “Automated recurrence analysis for
almost linear expected runtime bounds,” presented at the CAV: Computer Aided Verification,
Heidelberg, Germany, 2017, vol. 10426, pp. 118–139.'
ista: 'Chatterjee K, Fu H, Murhekar A. 2017. Automated recurrence analysis for almost
linear expected runtime bounds. CAV: Computer Aided Verification, LNCS, vol. 10426,
118–139.'
mla: Chatterjee, Krishnendu, et al. Automated Recurrence Analysis for Almost
Linear Expected Runtime Bounds. Edited by Rupak Majumdar and Viktor Kunčak,
vol. 10426, Springer, 2017, pp. 118–39, doi:10.1007/978-3-319-63387-9_6.
short: K. Chatterjee, H. Fu, A. Murhekar, in:, R. Majumdar, V. Kunčak (Eds.), Springer,
2017, pp. 118–139.
conference:
end_date: 2017-07-28
location: Heidelberg, Germany
name: 'CAV: Computer Aided Verification'
start_date: 2017-07-24
date_created: 2018-12-11T11:47:35Z
date_published: 2017-01-01T00:00:00Z
date_updated: 2021-01-12T08:06:55Z
day: '01'
department:
- _id: KrCh
doi: 10.1007/978-3-319-63387-9_6
ec_funded: 1
editor:
- first_name: Rupak
full_name: Majumdar, Rupak
last_name: Majumdar
- first_name: Viktor
full_name: Kunčak, Viktor
last_name: Kunčak
intvolume: ' 10426'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/1705.00314
month: '01'
oa: 1
oa_version: Submitted Version
page: 118 - 139
project:
- _id: 25892FC0-B435-11E9-9278-68D0E5697425
grant_number: ICT15-003
name: Efficient Algorithms for Computer Aided Verification
- _id: 25863FF4-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: S11407
name: Game Theory
- _id: 2581B60A-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '279307'
name: 'Quantitative Graph Games: Theory and Applications'
publication_identifier:
isbn:
- 978-331963386-2
publication_status: published
publisher: Springer
publist_id: '7166'
quality_controlled: '1'
scopus_import: 1
status: public
title: Automated recurrence analysis for almost linear expected runtime bounds
type: conference
user_id: 4435EBFC-F248-11E8-B48F-1D18A9856A87
volume: 10426
year: '2017'
...
---
_id: '629'
abstract:
- lang: eng
text: Even simple cells like bacteria have precisely regulated cellular anatomies,
which allow them to grow, divide and to respond to internal or external cues with
high fidelity. How spatial and temporal intracellular organization in prokaryotic
cells is achieved and maintained on the basis of locally interacting proteins
still remains largely a mystery. Bulk biochemical assays with purified components
and in vivo experiments help us to approach key cellular processes from two opposite
ends, in terms of minimal and maximal complexity. However, to understand how cellular
phenomena emerge, that are more than the sum of their parts, we have to assemble
cellular subsystems step by step from the bottom up. Here, we review recent in
vitro reconstitution experiments with proteins of the bacterial cell division
machinery and illustrate how they help to shed light on fundamental cellular mechanisms
that constitute spatiotemporal order and regulate cell division.
author:
- first_name: Martin
full_name: Loose, Martin
id: 462D4284-F248-11E8-B48F-1D18A9856A87
last_name: Loose
orcid: 0000-0001-7309-9724
- first_name: Katja
full_name: Zieske, Katja
last_name: Zieske
- first_name: Petra
full_name: Schwille, Petra
last_name: Schwille
citation:
ama: 'Loose M, Zieske K, Schwille P. Reconstitution of protein dynamics involved
in bacterial cell division. In: Prokaryotic Cytoskeletons. Vol 84. Sub-Cellular
Biochemistry. Springer; 2017:419-444. doi:10.1007/978-3-319-53047-5_15'
apa: Loose, M., Zieske, K., & Schwille, P. (2017). Reconstitution of protein
dynamics involved in bacterial cell division. In Prokaryotic Cytoskeletons
(Vol. 84, pp. 419–444). Springer. https://doi.org/10.1007/978-3-319-53047-5_15
chicago: Loose, Martin, Katja Zieske, and Petra Schwille. “Reconstitution of Protein
Dynamics Involved in Bacterial Cell Division.” In Prokaryotic Cytoskeletons,
84:419–44. Sub-Cellular Biochemistry. Springer, 2017. https://doi.org/10.1007/978-3-319-53047-5_15.
ieee: M. Loose, K. Zieske, and P. Schwille, “Reconstitution of protein dynamics
involved in bacterial cell division,” in Prokaryotic Cytoskeletons, vol.
84, Springer, 2017, pp. 419–444.
ista: 'Loose M, Zieske K, Schwille P. 2017.Reconstitution of protein dynamics involved
in bacterial cell division. In: Prokaryotic Cytoskeletons. vol. 84, 419–444.'
mla: Loose, Martin, et al. “Reconstitution of Protein Dynamics Involved in Bacterial
Cell Division.” Prokaryotic Cytoskeletons, vol. 84, Springer, 2017, pp.
419–44, doi:10.1007/978-3-319-53047-5_15.
short: M. Loose, K. Zieske, P. Schwille, in:, Prokaryotic Cytoskeletons, Springer,
2017, pp. 419–444.
date_created: 2018-12-11T11:47:35Z
date_published: 2017-05-13T00:00:00Z
date_updated: 2021-01-12T08:06:57Z
day: '13'
department:
- _id: MaLo
doi: 10.1007/978-3-319-53047-5_15
external_id:
pmid:
- '28500535'
intvolume: ' 84'
language:
- iso: eng
month: '05'
oa_version: None
page: 419 - 444
pmid: 1
publication: Prokaryotic Cytoskeletons
publication_identifier:
eisbn:
- 978-3-319-53047-5
publication_status: published
publisher: Springer
publist_id: '7165'
quality_controlled: '1'
scopus_import: 1
series_title: Sub-Cellular Biochemistry
status: public
title: Reconstitution of protein dynamics involved in bacterial cell division
type: book_chapter
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 84
year: '2017'
...
---
_id: '630'
abstract:
- lang: eng
text: 'Background: Standards have become available to share semantically encoded
vital parameters from medical devices, as required for example by personal healthcare
records. Standardised sharing of biosignal data largely remains open. Objectives:
The goal of this work is to explore available biosignal file format and data exchange
standards and profiles, and to conceptualise end-To-end solutions. Methods: The
authors reviewed and discussed available biosignal file format standards with
other members of international standards development organisations (SDOs). Results:
A raw concept for standards based acquisition, storage, archiving and sharing
of biosignals was developed. The GDF format may serve for storing biosignals.
Signals can then be shared using FHIR resources and may be stored on FHIR servers
or in DICOM archives, with DICOM waveforms as one possible format. Conclusion:
Currently a group of international SDOs (e.g. HL7, IHE, DICOM, IEEE) is engaged
in intensive discussions. This discussion extends existing work that already was
adopted by large implementer communities. The concept presented here only reports
the current status of the discussion in Austria. The discussion will continue
internationally, with results to be expected over the coming years.'
alternative_title:
- Studies in Health Technology and Informatics
author:
- first_name: Stefan
full_name: Sauermann, Stefan
last_name: Sauermann
- first_name: Veronika
full_name: David, Veronika
last_name: David
- first_name: Alois
full_name: Schlögl, Alois
id: 45BF87EE-F248-11E8-B48F-1D18A9856A87
last_name: Schlögl
orcid: 0000-0002-5621-8100
- first_name: Reinhard
full_name: Egelkraut, Reinhard
last_name: Egelkraut
- first_name: Matthias
full_name: Frohner, Matthias
last_name: Frohner
- first_name: Birgit
full_name: Pohn, Birgit
last_name: Pohn
- first_name: Philipp
full_name: Urbauer, Philipp
last_name: Urbauer
- first_name: Alexander
full_name: Mense, Alexander
last_name: Mense
citation:
ama: 'Sauermann S, David V, Schlögl A, et al. Biosignals standards and FHIR: The
way to go. In: Vol 236. IOS Press; 2017:356-362. doi:10.3233/978-1-61499-759-7-356'
apa: 'Sauermann, S., David, V., Schlögl, A., Egelkraut, R., Frohner, M., Pohn, B.,
… Mense, A. (2017). Biosignals standards and FHIR: The way to go (Vol. 236, pp.
356–362). Presented at the eHealth: Health Informatics Meets eHealth, Vienna,
Austria: IOS Press. https://doi.org/10.3233/978-1-61499-759-7-356'
chicago: 'Sauermann, Stefan, Veronika David, Alois Schlögl, Reinhard Egelkraut,
Matthias Frohner, Birgit Pohn, Philipp Urbauer, and Alexander Mense. “Biosignals
Standards and FHIR: The Way to Go,” 236:356–62. IOS Press, 2017. https://doi.org/10.3233/978-1-61499-759-7-356.'
ieee: 'S. Sauermann et al., “Biosignals standards and FHIR: The way to go,”
presented at the eHealth: Health Informatics Meets eHealth, Vienna, Austria, 2017,
vol. 236, pp. 356–362.'
ista: 'Sauermann S, David V, Schlögl A, Egelkraut R, Frohner M, Pohn B, Urbauer
P, Mense A. 2017. Biosignals standards and FHIR: The way to go. eHealth: Health
Informatics Meets eHealth, Studies in Health Technology and Informatics, vol.
236, 356–362.'
mla: 'Sauermann, Stefan, et al. Biosignals Standards and FHIR: The Way to Go.
Vol. 236, IOS Press, 2017, pp. 356–62, doi:10.3233/978-1-61499-759-7-356.'
short: S. Sauermann, V. David, A. Schlögl, R. Egelkraut, M. Frohner, B. Pohn, P.
Urbauer, A. Mense, in:, IOS Press, 2017, pp. 356–362.
conference:
end_date: 2017-05-24
location: Vienna, Austria
name: 'eHealth: Health Informatics Meets eHealth'
start_date: 2017-05-23
date_created: 2018-12-11T11:47:36Z
date_published: 2017-01-01T00:00:00Z
date_updated: 2021-01-12T08:06:59Z
day: '01'
ddc:
- '005'
department:
- _id: ScienComp
- _id: PeJo
doi: 10.3233/978-1-61499-759-7-356
file:
- access_level: open_access
checksum: 1254dcc5b04a996d97fad9a726b42727
content_type: application/pdf
creator: system
date_created: 2018-12-12T10:11:56Z
date_updated: 2020-07-14T12:47:27Z
file_id: '4913'
file_name: IST-2017-906-v1+1_SHTI236-0356.pdf
file_size: 443635
relation: main_file
file_date_updated: 2020-07-14T12:47:27Z
has_accepted_license: '1'
intvolume: ' 236'
language:
- iso: eng
license: https://creativecommons.org/licenses/by-nc/4.0/
month: '01'
oa: 1
oa_version: Published Version
page: 356 - 362
publication_identifier:
isbn:
- 978-161499758-0
publication_status: published
publisher: IOS Press
publist_id: '7164'
pubrep_id: '906'
quality_controlled: '1'
scopus_import: 1
status: public
title: 'Biosignals standards and FHIR: The way to go'
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: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 236
year: '2017'
...
---
_id: '632'
abstract:
- lang: eng
text: 'We consider a 2D quantum system of N bosons in a trapping potential |x|s,
interacting via a pair potential of the form N2β−1 w(Nβ x). We show that for all
0 < β < (s + 1)/(s + 2), the leading order behavior of ground states of
the many-body system is described in the large N limit by the corresponding cubic
nonlinear Schrödinger energy functional. Our result covers the focusing case (w
< 0) where even the stability of the many-body system is not obvious. This
answers an open question mentioned by X. Chen and J. Holmer for harmonic traps
(s = 2). Together with the BBGKY hierarchy approach used by these authors, our
result implies the convergence of the many-body quantum dynamics to the focusing
NLS equation with harmonic trap for all 0 < β < 3/4. '
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. A note on 2D focusing many boson systems. Proceedings
of the American Mathematical Society. 2017;145(6):2441-2454. doi:10.1090/proc/13468
apa: Lewin, M., Nam, P., & Rougerie, N. (2017). A note on 2D focusing many boson
systems. Proceedings of the American Mathematical Society. American Mathematical
Society. https://doi.org/10.1090/proc/13468
chicago: Lewin, Mathieu, Phan Nam, and Nicolas Rougerie. “A Note on 2D Focusing
Many Boson Systems.” Proceedings of the American Mathematical Society.
American Mathematical Society, 2017. https://doi.org/10.1090/proc/13468.
ieee: M. Lewin, P. Nam, and N. Rougerie, “A note on 2D focusing many boson systems,”
Proceedings of the American Mathematical Society, vol. 145, no. 6. American
Mathematical Society, pp. 2441–2454, 2017.
ista: Lewin M, Nam P, Rougerie N. 2017. A note on 2D focusing many boson systems.
Proceedings of the American Mathematical Society. 145(6), 2441–2454.
mla: Lewin, Mathieu, et al. “A Note on 2D Focusing Many Boson Systems.” Proceedings
of the American Mathematical Society, vol. 145, no. 6, American Mathematical
Society, 2017, pp. 2441–54, doi:10.1090/proc/13468.
short: M. Lewin, P. Nam, N. Rougerie, Proceedings of the American Mathematical Society
145 (2017) 2441–2454.
date_created: 2018-12-11T11:47:36Z
date_published: 2017-01-01T00:00:00Z
date_updated: 2021-01-12T08:07:03Z
day: '01'
department:
- _id: RoSe
doi: 10.1090/proc/13468
ec_funded: 1
intvolume: ' 145'
issue: '6'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/1509.09045
month: '01'
oa: 1
oa_version: Submitted Version
page: 2441 - 2454
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: '7160'
quality_controlled: '1'
scopus_import: 1
status: public
title: A note on 2D focusing many boson systems
type: journal_article
user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87
volume: 145
year: '2017'
...
---
_id: '634'
abstract:
- lang: eng
text: As autism spectrum disorder (ASD) is largely regarded as a neurodevelopmental
condition, long-time consensus was that its hallmark features are irreversible.
However, several studies from recent years using defined mouse models of ASD have
provided clear evidence that in mice neurobiological and behavioural alterations
can be ameliorated or even reversed by genetic restoration or pharmacological
treatment either before or after symptom onset. Here, we review findings on genetic
and pharmacological reversibility of phenotypes in mouse models of ASD. Our review
should give a comprehensive overview on both aspects and encourage future studies
to better understand the underlying molecular mechanisms that might be translatable
from animals to humans.
alternative_title:
- ADVSANAT
author:
- first_name: Jan
full_name: Schroeder, Jan
last_name: Schroeder
- first_name: Elena
full_name: Deliu, Elena
id: 37A40D7E-F248-11E8-B48F-1D18A9856A87
last_name: Deliu
orcid: 0000-0002-7370-5293
- first_name: Gaia
full_name: Novarino, Gaia
id: 3E57A680-F248-11E8-B48F-1D18A9856A87
last_name: Novarino
orcid: 0000-0002-7673-7178
- first_name: Michael
full_name: Schmeisser, Michael
last_name: Schmeisser
citation:
ama: 'Schroeder J, Deliu E, Novarino G, Schmeisser M. Genetic and pharmacological
reversibility of phenotypes in mouse models of autism spectrum disorder. In: Schmeisser
M, Boekers T, eds. Translational Anatomy and Cell Biology of Autism Spectrum
Disorder. Vol 224. Advances in Anatomy Embryology and Cell Biology. Springer;
2017:189-211. doi:10.1007/978-3-319-52498-6_10'
apa: Schroeder, J., Deliu, E., Novarino, G., & Schmeisser, M. (2017). Genetic
and pharmacological reversibility of phenotypes in mouse models of autism spectrum
disorder. In M. Schmeisser & T. Boekers (Eds.), Translational Anatomy and
Cell Biology of Autism Spectrum Disorder (Vol. 224, pp. 189–211). Springer.
https://doi.org/10.1007/978-3-319-52498-6_10
chicago: Schroeder, Jan, Elena Deliu, Gaia Novarino, and Michael Schmeisser. “Genetic
and Pharmacological Reversibility of Phenotypes in Mouse Models of Autism Spectrum
Disorder.” In Translational Anatomy and Cell Biology of Autism Spectrum Disorder,
edited by Michael Schmeisser and Tobias Boekers, 224:189–211. Advances in Anatomy
Embryology and Cell Biology. Springer, 2017. https://doi.org/10.1007/978-3-319-52498-6_10.
ieee: J. Schroeder, E. Deliu, G. Novarino, and M. Schmeisser, “Genetic and pharmacological
reversibility of phenotypes in mouse models of autism spectrum disorder,” in Translational
Anatomy and Cell Biology of Autism Spectrum Disorder, vol. 224, M. Schmeisser
and T. Boekers, Eds. Springer, 2017, pp. 189–211.
ista: 'Schroeder J, Deliu E, Novarino G, Schmeisser M. 2017.Genetic and pharmacological
reversibility of phenotypes in mouse models of autism spectrum disorder. In: Translational
Anatomy and Cell Biology of Autism Spectrum Disorder. ADVSANAT, vol. 224, 189–211.'
mla: Schroeder, Jan, et al. “Genetic and Pharmacological Reversibility of Phenotypes
in Mouse Models of Autism Spectrum Disorder.” Translational Anatomy and Cell
Biology of Autism Spectrum Disorder, edited by Michael Schmeisser and Tobias
Boekers, vol. 224, Springer, 2017, pp. 189–211, doi:10.1007/978-3-319-52498-6_10.
short: J. Schroeder, E. Deliu, G. Novarino, M. Schmeisser, in:, M. Schmeisser, T.
Boekers (Eds.), Translational Anatomy and Cell Biology of Autism Spectrum Disorder,
Springer, 2017, pp. 189–211.
date_created: 2018-12-11T11:47:37Z
date_published: 2017-05-28T00:00:00Z
date_updated: 2021-01-12T08:07:08Z
day: '28'
department:
- _id: GaNo
doi: 10.1007/978-3-319-52498-6_10
editor:
- first_name: Michael
full_name: Schmeisser, Michael
last_name: Schmeisser
- first_name: Tobias
full_name: Boekers, Tobias
last_name: Boekers
intvolume: ' 224'
language:
- iso: eng
month: '05'
oa_version: None
page: 189 - 211
project:
- _id: 25473368-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: F03523
name: Transmembrane Transporters in Health and Disease
publication: Translational Anatomy and Cell Biology of Autism Spectrum Disorder
publication_identifier:
eisbn:
- 978-3-319-52498-6
publication_status: published
publisher: Springer
publist_id: '7156'
quality_controlled: '1'
scopus_import: 1
series_title: Advances in Anatomy Embryology and Cell Biology
status: public
title: Genetic and pharmacological reversibility of phenotypes in mouse models of
autism spectrum disorder
type: book_chapter
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 224
year: '2017'
...
---
_id: '633'
abstract:
- lang: eng
text: A Rapidly-exploring Random Tree (RRT) is an algorithm which can search a non-convex
region of space by incrementally building a space-filling tree. The tree is constructed
from random points drawn from system’s state space and is biased to grow towards
large unexplored areas in the system. RRT can provide better coverage of a system’s
possible behaviors compared with random simulations, but is more lightweight than
full reachability analysis. In this paper, we explore some of the design decisions
encountered while implementing a hybrid extension of the RRT algorithm, which
have not been elaborated on before. In particular, we focus on handling non-determinism,
which arises due to discrete transitions. We introduce the notion of important
points to account for this phenomena. We showcase our ideas using heater and navigation
benchmarks.
alternative_title:
- LNCS
author:
- first_name: Stanley
full_name: Bak, Stanley
last_name: Bak
- first_name: Sergiy
full_name: Bogomolov, Sergiy
id: 369D9A44-F248-11E8-B48F-1D18A9856A87
last_name: Bogomolov
orcid: 0000-0002-0686-0365
- 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: Aviral
full_name: Kumar, Aviral
last_name: Kumar
citation:
ama: 'Bak S, Bogomolov S, Henzinger TA, Kumar A. Challenges and tool implementation
of hybrid rapidly exploring random trees. In: Abate A, Bodo S, eds. Vol 10381.
Springer; 2017:83-89. doi:10.1007/978-3-319-63501-9_6'
apa: 'Bak, S., Bogomolov, S., Henzinger, T. A., & Kumar, A. (2017). Challenges
and tool implementation of hybrid rapidly exploring random trees. In A. Abate
& S. Bodo (Eds.) (Vol. 10381, pp. 83–89). Presented at the NSV: Numerical
Software Verification, Heidelberg, Germany: Springer. https://doi.org/10.1007/978-3-319-63501-9_6'
chicago: Bak, Stanley, Sergiy Bogomolov, Thomas A Henzinger, and Aviral Kumar. “Challenges
and Tool Implementation of Hybrid Rapidly Exploring Random Trees.” edited by Alessandro
Abate and Sylvie Bodo, 10381:83–89. Springer, 2017. https://doi.org/10.1007/978-3-319-63501-9_6.
ieee: 'S. Bak, S. Bogomolov, T. A. Henzinger, and A. Kumar, “Challenges and tool
implementation of hybrid rapidly exploring random trees,” presented at the NSV:
Numerical Software Verification, Heidelberg, Germany, 2017, vol. 10381, pp. 83–89.'
ista: 'Bak S, Bogomolov S, Henzinger TA, Kumar A. 2017. Challenges and tool implementation
of hybrid rapidly exploring random trees. NSV: Numerical Software Verification,
LNCS, vol. 10381, 83–89.'
mla: Bak, Stanley, et al. Challenges and Tool Implementation of Hybrid Rapidly
Exploring Random Trees. Edited by Alessandro Abate and Sylvie Bodo, vol. 10381,
Springer, 2017, pp. 83–89, doi:10.1007/978-3-319-63501-9_6.
short: S. Bak, S. Bogomolov, T.A. Henzinger, A. Kumar, in:, A. Abate, S. Bodo (Eds.),
Springer, 2017, pp. 83–89.
conference:
end_date: 2017-07-23
location: Heidelberg, Germany
name: 'NSV: Numerical Software Verification'
start_date: 2017-07-22
date_created: 2018-12-11T11:47:37Z
date_published: 2017-01-01T00:00:00Z
date_updated: 2021-01-12T08:07:06Z
day: '01'
department:
- _id: ToHe
doi: 10.1007/978-3-319-63501-9_6
editor:
- first_name: Alessandro
full_name: Abate, Alessandro
last_name: Abate
- first_name: Sylvie
full_name: Bodo, Sylvie
last_name: Bodo
intvolume: ' 10381'
language:
- iso: eng
month: '01'
oa_version: None
page: 83 - 89
project:
- _id: 25F5A88A-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: S11402-N23
name: Moderne Concurrency Paradigms
- _id: 25F42A32-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: Z211
name: The Wittgenstein Prize
publication_identifier:
isbn:
- 978-331963500-2
publication_status: published
publisher: Springer
publist_id: '7159'
quality_controlled: '1'
scopus_import: 1
status: public
title: Challenges and tool implementation of hybrid rapidly exploring random trees
type: conference
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 10381
year: '2017'
...
---
_id: '635'
abstract:
- lang: eng
text: Memory-hard functions (MHFs) are hash algorithms whose evaluation cost is
dominated by memory cost. As memory, unlike computation, costs about the same
across different platforms, MHFs cannot be evaluated at significantly lower cost
on dedicated hardware like ASICs. MHFs have found widespread applications including
password hashing, key derivation, and proofs-of-work. This paper focuses on scrypt,
a simple candidate MHF designed by Percival, and described in RFC 7914. It has
been used within a number of cryptocurrencies (e.g., Litecoin and Dogecoin) and
has been an inspiration for Argon2d, one of the winners of the recent password-hashing
competition. Despite its popularity, no rigorous lower bounds on its memory complexity
are known. We prove that scrypt is optimally memory-hard, i.e., its cumulative
memory complexity (cmc) in the parallel random oracle model is Ω(n2w), where w
and n are the output length and number of invocations of the underlying hash function,
respectively. High cmc is a strong security target for MHFs introduced by Alwen
and Serbinenko (STOC’15) which implies high memory cost even for adversaries who
can amortize the cost over many evaluations and evaluate the underlying hash functions
many times in parallel. Our proof is the first showing optimal memory-hardness
for any MHF. Our result improves both quantitatively and qualitatively upon the
recent work by Alwen et al. (EUROCRYPT’16) who proved a weaker lower bound of
Ω(n2w/ log2 n) for a restricted class of adversaries.
alternative_title:
- LNCS
author:
- first_name: Joel F
full_name: Alwen, Joel F
id: 2A8DFA8C-F248-11E8-B48F-1D18A9856A87
last_name: Alwen
- first_name: Binchi
full_name: Chen, Binchi
last_name: Chen
- 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: Leonid
full_name: Reyzin, Leonid
last_name: Reyzin
- first_name: Stefano
full_name: Tessaro, Stefano
last_name: Tessaro
citation:
ama: 'Alwen JF, Chen B, Pietrzak KZ, Reyzin L, Tessaro S. Scrypt is maximally memory
hard. In: Coron J-S, Buus Nielsen J, eds. Vol 10212. Springer; 2017:33-62. doi:10.1007/978-3-319-56617-7_2'
apa: 'Alwen, J. F., Chen, B., Pietrzak, K. Z., Reyzin, L., & Tessaro, S. (2017).
Scrypt is maximally memory hard. In J.-S. Coron & J. Buus Nielsen (Eds.) (Vol.
10212, pp. 33–62). Presented at the EUROCRYPT: Theory and Applications of Cryptographic
Techniques, Paris, France: Springer. https://doi.org/10.1007/978-3-319-56617-7_2'
chicago: Alwen, Joel F, Binchi Chen, Krzysztof Z Pietrzak, Leonid Reyzin, and Stefano
Tessaro. “Scrypt Is Maximally Memory Hard.” edited by Jean-Sébastien Coron and
Jesper Buus Nielsen, 10212:33–62. Springer, 2017. https://doi.org/10.1007/978-3-319-56617-7_2.
ieee: 'J. F. Alwen, B. Chen, K. Z. Pietrzak, L. Reyzin, and S. Tessaro, “Scrypt
is maximally memory hard,” presented at the EUROCRYPT: Theory and Applications
of Cryptographic Techniques, Paris, France, 2017, vol. 10212, pp. 33–62.'
ista: 'Alwen JF, Chen B, Pietrzak KZ, Reyzin L, Tessaro S. 2017. Scrypt is maximally
memory hard. EUROCRYPT: Theory and Applications of Cryptographic Techniques, LNCS,
vol. 10212, 33–62.'
mla: Alwen, Joel F., et al. Scrypt Is Maximally Memory Hard. Edited by Jean-Sébastien
Coron and Jesper Buus Nielsen, vol. 10212, Springer, 2017, pp. 33–62, doi:10.1007/978-3-319-56617-7_2.
short: J.F. Alwen, B. Chen, K.Z. Pietrzak, L. Reyzin, S. Tessaro, in:, J.-S. Coron,
J. Buus Nielsen (Eds.), Springer, 2017, pp. 33–62.
conference:
end_date: 2017-05-04
location: Paris, France
name: 'EUROCRYPT: Theory and Applications of Cryptographic Techniques'
start_date: 2017-04-30
date_created: 2018-12-11T11:47:37Z
date_published: 2017-01-01T00:00:00Z
date_updated: 2021-01-12T08:07:10Z
day: '01'
department:
- _id: KrPi
doi: 10.1007/978-3-319-56617-7_2
ec_funded: 1
editor:
- first_name: Jean-Sébastien
full_name: Coron, Jean-Sébastien
last_name: Coron
- first_name: Jesper
full_name: Buus Nielsen, Jesper
last_name: Buus Nielsen
intvolume: ' 10212'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://eprint.iacr.org/2016/989
month: '01'
oa: 1
oa_version: Submitted Version
page: 33 - 62
project:
- _id: 258AA5B2-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '682815'
name: Teaching Old Crypto New Tricks
publication_identifier:
isbn:
- 978-331956616-0
publication_status: published
publisher: Springer
publist_id: '7154'
quality_controlled: '1'
scopus_import: 1
status: public
title: Scrypt is maximally memory hard
type: conference
user_id: 4435EBFC-F248-11E8-B48F-1D18A9856A87
volume: 10212
year: '2017'
...
---
_id: '636'
abstract:
- lang: eng
text: Signal regular expressions can specify sequential properties of real-valued
signals based on threshold conditions, regular operations, and duration constraints.
In this paper we endow them with a quantitative semantics which indicates how
robustly a signal matches or does not match a given expression. First, we show
that this semantics is a safe approximation of a distance between the signal and
the language defined by the expression. Then, we consider the robust matching
problem, that is, computing the quantitative semantics of every segment of a given
signal relative to an expression. We present an algorithm that solves this problem
for piecewise-constant and piecewise-linear signals and show that for such signals
the robustness map is a piecewise-linear function. The availability of an indicator
describing how robustly a signal segment matches some regular pattern provides
a general framework for quantitative monitoring of cyber-physical systems.
alternative_title:
- LNCS
author:
- first_name: Alexey
full_name: Bakhirkin, Alexey
last_name: Bakhirkin
- first_name: Thomas
full_name: Ferrere, Thomas
id: 40960E6E-F248-11E8-B48F-1D18A9856A87
last_name: Ferrere
orcid: 0000-0001-5199-3143
- first_name: Oded
full_name: Maler, Oded
last_name: Maler
- first_name: Dogan
full_name: Ulus, Dogan
last_name: Ulus
citation:
ama: 'Bakhirkin A, Ferrere T, Maler O, Ulus D. On the quantitative semantics of
regular expressions over real-valued signals. In: Abate A, Geeraerts G, eds. Vol
10419. Springer; 2017:189-206. doi:10.1007/978-3-319-65765-3_11'
apa: 'Bakhirkin, A., Ferrere, T., Maler, O., & Ulus, D. (2017). On the quantitative
semantics of regular expressions over real-valued signals. In A. Abate & G.
Geeraerts (Eds.) (Vol. 10419, pp. 189–206). Presented at the FORMATS: Formal Modelling
and Analysis of Timed Systems, Berlin, Germany: Springer. https://doi.org/10.1007/978-3-319-65765-3_11'
chicago: Bakhirkin, Alexey, Thomas Ferrere, Oded Maler, and Dogan Ulus. “On the
Quantitative Semantics of Regular Expressions over Real-Valued Signals.” edited
by Alessandro Abate and Gilles Geeraerts, 10419:189–206. Springer, 2017. https://doi.org/10.1007/978-3-319-65765-3_11.
ieee: 'A. Bakhirkin, T. Ferrere, O. Maler, and D. Ulus, “On the quantitative semantics
of regular expressions over real-valued signals,” presented at the FORMATS: Formal
Modelling and Analysis of Timed Systems, Berlin, Germany, 2017, vol. 10419, pp.
189–206.'
ista: 'Bakhirkin A, Ferrere T, Maler O, Ulus D. 2017. On the quantitative semantics
of regular expressions over real-valued signals. FORMATS: Formal Modelling and
Analysis of Timed Systems, LNCS, vol. 10419, 189–206.'
mla: Bakhirkin, Alexey, et al. On the Quantitative Semantics of Regular Expressions
over Real-Valued Signals. Edited by Alessandro Abate and Gilles Geeraerts,
vol. 10419, Springer, 2017, pp. 189–206, doi:10.1007/978-3-319-65765-3_11.
short: A. Bakhirkin, T. Ferrere, O. Maler, D. Ulus, in:, A. Abate, G. Geeraerts
(Eds.), Springer, 2017, pp. 189–206.
conference:
end_date: 2017-09-07
location: Berlin, Germany
name: 'FORMATS: Formal Modelling and Analysis of Timed Systems'
start_date: 2017-09-05
date_created: 2018-12-11T11:47:38Z
date_published: 2017-08-03T00:00:00Z
date_updated: 2021-01-12T08:07:14Z
day: '03'
department:
- _id: ToHe
doi: 10.1007/978-3-319-65765-3_11
editor:
- first_name: Alessandro
full_name: Abate, Alessandro
last_name: Abate
- first_name: Gilles
full_name: Geeraerts, Gilles
last_name: Geeraerts
intvolume: ' 10419'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://hal.archives-ouvertes.fr/hal-01552132
month: '08'
oa: 1
oa_version: Submitted Version
page: 189 - 206
project:
- _id: 25F5A88A-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: S11402-N23
name: Moderne Concurrency Paradigms
- _id: 25F42A32-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: Z211
name: The Wittgenstein Prize
publication_identifier:
isbn:
- 978-331965764-6
publication_status: published
publisher: Springer
publist_id: '7152'
quality_controlled: '1'
scopus_import: 1
status: public
title: On the quantitative semantics of regular expressions over real-valued signals
type: conference
user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87
volume: 10419
year: '2017'
...
---
_id: '638'
abstract:
- lang: eng
text: "This book constitutes the refereed proceedings of the 9th InternationalWorkshop
on Numerical Software Verification, NSV 2016, held in Toronto, ON, Canada in July
2011 - colocated with CAV 2016, the 28th International Conference on Computer
Aided Verification.\r\nThe NSV workshop is dedicated to the development of logical
and mathematical techniques for the reasoning about programmability and reliability."
article_processing_charge: No
citation:
ama: Bogomolov S, Martel M, Prabhakar P, eds. Numerical Software Verification.
Vol 10152. Springer; 2017. doi:10.1007/978-3-319-54292-8
apa: 'Bogomolov, S., Martel, M., & Prabhakar, P. (Eds.). (2017). Numerical
Software Verification (Vol. 10152). Presented at the NSV: Numerical Software
Verification, Toronto, ON, Canada: Springer. https://doi.org/10.1007/978-3-319-54292-8'
chicago: Bogomolov, Sergiy, Matthieu Martel, and Pavithra Prabhakar, eds. Numerical
Software Verification. Vol. 10152. LNCS. Springer, 2017. https://doi.org/10.1007/978-3-319-54292-8.
ieee: S. Bogomolov, M. Martel, and P. Prabhakar, Eds., Numerical Software Verification,
vol. 10152. Springer, 2017.
ista: Bogomolov S, Martel M, Prabhakar P eds. 2017. Numerical Software Verification,
Springer,p.
mla: Bogomolov, Sergiy, et al., editors. Numerical Software Verification.
Vol. 10152, Springer, 2017, doi:10.1007/978-3-319-54292-8.
short: S. Bogomolov, M. Martel, P. Prabhakar, eds., Numerical Software Verification,
Springer, 2017.
conference:
end_date: 2016-07-18
location: Toronto, ON, Canada
name: 'NSV: Numerical Software Verification'
start_date: 2016-07-17
date_created: 2018-12-11T11:47:38Z
date_published: 2017-01-01T00:00:00Z
date_updated: 2022-05-24T07:09:52Z
day: '01'
department:
- _id: ToHe
doi: 10.1007/978-3-319-54292-8
editor:
- first_name: Sergiy
full_name: Bogomolov, Sergiy
id: 369D9A44-F248-11E8-B48F-1D18A9856A87
last_name: Bogomolov
orcid: 0000-0002-0686-0365
- first_name: Matthieu
full_name: Martel, Matthieu
last_name: Martel
- first_name: Pavithra
full_name: Prabhakar, Pavithra
last_name: Prabhakar
intvolume: ' 10152'
language:
- iso: eng
month: '01'
oa_version: None
publication_identifier:
eisbn:
- 978-3-319-54292-8
issn:
- 0302-9743
publication_status: published
publisher: Springer
publist_id: '7150'
quality_controlled: '1'
series_title: LNCS
status: public
title: Numerical Software Verification
type: conference_editor
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 10152
year: '2017'
...
---
_id: '640'
abstract:
- lang: eng
text: 'Data-independent Memory Hard Functions (iMHFS) are finding a growing number
of applications in security; especially in the domain of password hashing. An
important property of a concrete iMHF is specified by fixing a directed acyclic
graph (DAG) Gn on n nodes. The quality of that iMHF is then captured by the following
two pebbling complexities of Gn: – The parallel cumulative pebbling complexity
Π∥cc(Gn) must be as high as possible (to ensure that the amortized cost of computing
the function on dedicated hardware is dominated by the cost of memory). – The
sequential space-time pebbling complexity Πst(Gn) should be as close as possible
to Π∥cc(Gn) (to ensure that using many cores in parallel and amortizing over many
instances does not give much of an advantage). In this paper we construct a family
of DAGs with best possible parameters in an asymptotic sense, i.e., where Π∥cc(Gn)
= Ω(n2/ log(n)) (which matches a known upper bound) and Πst(Gn) is within a constant
factor of Π∥cc(Gn). Our analysis relies on a new connection between the pebbling
complexity of a DAG and its depth-robustness (DR) – a well studied combinatorial
property. We show that high DR is sufficient for high Π∥cc. Alwen and Blocki (CRYPTO’16)
showed that high DR is necessary and so, together, these results fully characterize
DAGs with high Π∥cc in terms of DR. Complementing these results, we provide new
upper and lower bounds on the Π∥cc of several important candidate iMHFs from the
literature. We give the first lower bounds on the memory hardness of the Catena
and Balloon Hashing functions in a parallel model of computation and we give the
first lower bounds of any kind for (a version) of Argon2i. Finally we describe
a new class of pebbling attacks improving on those of Alwen and Blocki (CRYPTO’16).
By instantiating these attacks we upperbound the Π∥cc of the Password Hashing
Competition winner Argon2i and one of the Balloon Hashing functions by O (n1.71).
We also show an upper bound of O(n1.625) for the Catena functions and the two
remaining Balloon Hashing functions.'
alternative_title:
- LNCS
author:
- first_name: Joel F
full_name: Alwen, Joel F
id: 2A8DFA8C-F248-11E8-B48F-1D18A9856A87
last_name: Alwen
- first_name: Jeremiah
full_name: Blocki, Jeremiah
last_name: Blocki
- first_name: Krzysztof Z
full_name: Pietrzak, Krzysztof Z
id: 3E04A7AA-F248-11E8-B48F-1D18A9856A87
last_name: Pietrzak
orcid: 0000-0002-9139-1654
citation:
ama: 'Alwen JF, Blocki J, Pietrzak KZ. Depth-robust graphs and their cumulative
memory complexity. In: Coron J-S, Buus Nielsen J, eds. Vol 10212. Springer; 2017:3-32.
doi:10.1007/978-3-319-56617-7_1'
apa: 'Alwen, J. F., Blocki, J., & Pietrzak, K. Z. (2017). Depth-robust graphs
and their cumulative memory complexity. In J.-S. Coron & J. Buus Nielsen (Eds.)
(Vol. 10212, pp. 3–32). Presented at the EUROCRYPT: Theory and Applications of
Cryptographic Techniques, Paris, France: Springer. https://doi.org/10.1007/978-3-319-56617-7_1'
chicago: Alwen, Joel F, Jeremiah Blocki, and Krzysztof Z Pietrzak. “Depth-Robust
Graphs and Their Cumulative Memory Complexity.” edited by Jean-Sébastien Coron
and Jesper Buus Nielsen, 10212:3–32. Springer, 2017. https://doi.org/10.1007/978-3-319-56617-7_1.
ieee: 'J. F. Alwen, J. Blocki, and K. Z. Pietrzak, “Depth-robust graphs and their
cumulative memory complexity,” presented at the EUROCRYPT: Theory and Applications
of Cryptographic Techniques, Paris, France, 2017, vol. 10212, pp. 3–32.'
ista: 'Alwen JF, Blocki J, Pietrzak KZ. 2017. Depth-robust graphs and their cumulative
memory complexity. EUROCRYPT: Theory and Applications of Cryptographic Techniques,
LNCS, vol. 10212, 3–32.'
mla: Alwen, Joel F., et al. Depth-Robust Graphs and Their Cumulative Memory Complexity.
Edited by Jean-Sébastien Coron and Jesper Buus Nielsen, vol. 10212, Springer,
2017, pp. 3–32, doi:10.1007/978-3-319-56617-7_1.
short: J.F. Alwen, J. Blocki, K.Z. Pietrzak, in:, J.-S. Coron, J. Buus Nielsen (Eds.),
Springer, 2017, pp. 3–32.
conference:
end_date: 2017-05-04
location: Paris, France
name: 'EUROCRYPT: Theory and Applications of Cryptographic Techniques'
start_date: 2017-04-30
date_created: 2018-12-11T11:47:39Z
date_published: 2017-04-01T00:00:00Z
date_updated: 2021-01-12T08:07:22Z
day: '01'
department:
- _id: KrPi
doi: 10.1007/978-3-319-56617-7_1
ec_funded: 1
editor:
- first_name: Jean-Sébastien
full_name: Coron, Jean-Sébastien
last_name: Coron
- first_name: Jesper
full_name: Buus Nielsen, Jesper
last_name: Buus Nielsen
intvolume: ' 10212'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://eprint.iacr.org/2016/875
month: '04'
oa: 1
oa_version: Submitted Version
page: 3 - 32
project:
- _id: 258AA5B2-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '682815'
name: Teaching Old Crypto New Tricks
publication_identifier:
isbn:
- 978-331956616-0
publication_status: published
publisher: Springer
publist_id: '7148'
quality_controlled: '1'
scopus_import: 1
status: public
title: Depth-robust graphs and their cumulative memory complexity
type: conference
user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87
volume: 10212
year: '2017'
...
---
_id: '641'
abstract:
- lang: eng
text: 'We introduce two novel methods for learning parameters of graphical models
for image labelling. The following two tasks underline both methods: (i) perturb
model parameters based on given features and ground truth labelings, so as to
exactly reproduce these labelings as optima of the local polytope relaxation of
the labelling problem; (ii) train a predictor for the perturbed model parameters
so that improved model parameters can be applied to the labelling of novel data.
Our first method implements task (i) by inverse linear programming and task (ii)
using a regressor e.g. a Gaussian process. Our second approach simultaneously
solves tasks (i) and (ii) in a joint manner, while being restricted to linearly
parameterised predictors. Experiments demonstrate the merits of both approaches.'
alternative_title:
- LNCS
author:
- first_name: Vera
full_name: Trajkovska, Vera
last_name: Trajkovska
- first_name: Paul
full_name: Swoboda, Paul
id: 446560C6-F248-11E8-B48F-1D18A9856A87
last_name: Swoboda
- first_name: Freddie
full_name: Åström, Freddie
last_name: Åström
- first_name: Stefanie
full_name: Petra, Stefanie
last_name: Petra
citation:
ama: 'Trajkovska V, Swoboda P, Åström F, Petra S. Graphical model parameter learning
by inverse linear programming. In: Lauze F, Dong Y, Bjorholm Dahl A, eds. Vol
10302. Springer; 2017:323-334. doi:10.1007/978-3-319-58771-4_26'
apa: 'Trajkovska, V., Swoboda, P., Åström, F., & Petra, S. (2017). Graphical
model parameter learning by inverse linear programming. In F. Lauze, Y. Dong,
& A. Bjorholm Dahl (Eds.) (Vol. 10302, pp. 323–334). Presented at the SSVM:
Scale Space and Variational Methods in Computer Vision, Kolding, Denmark: Springer.
https://doi.org/10.1007/978-3-319-58771-4_26'
chicago: Trajkovska, Vera, Paul Swoboda, Freddie Åström, and Stefanie Petra. “Graphical
Model Parameter Learning by Inverse Linear Programming.” edited by François Lauze,
Yiqiu Dong, and Anders Bjorholm Dahl, 10302:323–34. Springer, 2017. https://doi.org/10.1007/978-3-319-58771-4_26.
ieee: 'V. Trajkovska, P. Swoboda, F. Åström, and S. Petra, “Graphical model parameter
learning by inverse linear programming,” presented at the SSVM: Scale Space and
Variational Methods in Computer Vision, Kolding, Denmark, 2017, vol. 10302, pp.
323–334.'
ista: 'Trajkovska V, Swoboda P, Åström F, Petra S. 2017. Graphical model parameter
learning by inverse linear programming. SSVM: Scale Space and Variational Methods
in Computer Vision, LNCS, vol. 10302, 323–334.'
mla: Trajkovska, Vera, et al. Graphical Model Parameter Learning by Inverse Linear
Programming. Edited by François Lauze et al., vol. 10302, Springer, 2017,
pp. 323–34, doi:10.1007/978-3-319-58771-4_26.
short: V. Trajkovska, P. Swoboda, F. Åström, S. Petra, in:, F. Lauze, Y. Dong, A.
Bjorholm Dahl (Eds.), Springer, 2017, pp. 323–334.
conference:
end_date: 2017-06-08
location: Kolding, Denmark
name: 'SSVM: Scale Space and Variational Methods in Computer Vision'
start_date: 2017-06-04
date_created: 2018-12-11T11:47:39Z
date_published: 2017-01-01T00:00:00Z
date_updated: 2021-01-12T08:07:23Z
day: '01'
department:
- _id: VlKo
doi: 10.1007/978-3-319-58771-4_26
editor:
- first_name: François
full_name: Lauze, François
last_name: Lauze
- first_name: Yiqiu
full_name: Dong, Yiqiu
last_name: Dong
- first_name: Anders
full_name: Bjorholm Dahl, Anders
last_name: Bjorholm Dahl
intvolume: ' 10302'
language:
- iso: eng
month: '01'
oa_version: None
page: 323 - 334
publication_identifier:
isbn:
- 978-331958770-7
publication_status: published
publisher: Springer
publist_id: '7147'
quality_controlled: '1'
scopus_import: 1
status: public
title: Graphical model parameter learning by inverse linear programming
type: conference
user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87
volume: 10302
year: '2017'
...
---
_id: '6426'
abstract:
- lang: eng
text: Synchronous programs are easy to specify because the side effects of an operation
are finished by the time the invocation of the operation returns to the caller.
Asynchronous programs, on the other hand, are difficult to specify because there
are side effects due to pending computation scheduled as a result of the invocation
of an operation. They are also difficult to verify because of the large number
of possible interleavings of concurrent asynchronous computation threads. We show
that specifications and correctness proofs for asynchronous programs can be structured
by introducing the fiction, for proof purposes, that intermediate, non-quiescent
states of asynchronous operations can be ignored. Then, the task of specification
becomes relatively simple and the task of verification can be naturally decomposed
into smaller sub-tasks. The sub-tasks iteratively summarize, guided by the structure
of an asynchronous program, the atomic effect of non-atomic operations and the
synchronous effect of asynchronous operations. This structuring of specifications
and proofs corresponds to the introduction of multiple layers of stepwise refinement
for asynchronous programs. We present the first proof rule, called synchronization,
to reduce asynchronous invocations on a lower layer to synchronous invocations
on a higher layer. We implemented our proof method in CIVL and evaluated it on
a collection of benchmark programs.
alternative_title:
- IST Austria Technical Report
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: Bernhard
full_name: Kragl, Bernhard
id: 320FC952-F248-11E8-B48F-1D18A9856A87
last_name: Kragl
orcid: 0000-0001-7745-9117
- first_name: Shaz
full_name: Qadeer, Shaz
last_name: Qadeer
citation:
ama: Henzinger TA, Kragl B, Qadeer S. Synchronizing the Asynchronous. IST
Austria; 2017. doi:10.15479/AT:IST-2018-853-v2-2
apa: Henzinger, T. A., Kragl, B., & Qadeer, S. (2017). Synchronizing the
asynchronous. IST Austria. https://doi.org/10.15479/AT:IST-2018-853-v2-2
chicago: Henzinger, Thomas A, Bernhard Kragl, and Shaz Qadeer. Synchronizing
the Asynchronous. IST Austria, 2017. https://doi.org/10.15479/AT:IST-2018-853-v2-2.
ieee: T. A. Henzinger, B. Kragl, and S. Qadeer, Synchronizing the asynchronous.
IST Austria, 2017.
ista: Henzinger TA, Kragl B, Qadeer S. 2017. Synchronizing the asynchronous, IST
Austria, 28p.
mla: Henzinger, Thomas A., et al. Synchronizing the Asynchronous. IST Austria,
2017, doi:10.15479/AT:IST-2018-853-v2-2.
short: T.A. Henzinger, B. Kragl, S. Qadeer, Synchronizing the Asynchronous, IST
Austria, 2017.
date_created: 2019-05-13T08:15:55Z
date_published: 2017-08-04T00:00:00Z
date_updated: 2023-02-21T16:59:21Z
day: '04'
ddc:
- '000'
department:
- _id: ToHe
doi: 10.15479/AT:IST-2018-853-v2-2
file:
- access_level: open_access
checksum: b48d42725182d7ca10107a118815f4cf
content_type: application/pdf
creator: dernst
date_created: 2019-05-13T08:14:44Z
date_updated: 2020-07-14T12:47:30Z
file_id: '6431'
file_name: main(1).pdf
file_size: 971347
relation: main_file
file_date_updated: 2020-07-14T12:47:30Z
has_accepted_license: '1'
language:
- iso: eng
month: '08'
oa: 1
oa_version: Published Version
page: '28'
publication_identifier:
issn:
- 2664-1690
publication_status: published
publisher: IST Austria
related_material:
record:
- id: '133'
relation: later_version
status: public
status: public
title: Synchronizing the asynchronous
type: technical_report
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
year: '2017'
...
---
_id: '643'
abstract:
- lang: eng
text: It has been reported that nicotinamide-overload induces oxidative stress associated
with insulin resistance, the key feature of type 2 diabetes mellitus (T2DM). This
study aimed to investigate the effects of B vitamins in T2DM. Glucose tolerance
tests (GTT) were carried out in adult Sprague-Dawley rats treated with or without
cumulative doses of B vitamins. More specifically, insulin tolerance tests (ITT)
were also carried out in adult Sprague-Dawley rats treated with or without cumulative
doses of Vitamin B3. We found that cumulative Vitamin B1 and Vitamin B3 administration
significantly increased the plasma H2O2 levels associated with high insulin levels.
Only Vitamin B3 reduced muscular and hepatic glycogen contents. Cumulative administration
of nicotinic acid, another form of Vitamin B3, also significantly increased plasma
insulin level and H2O2 generation. Moreover, cumulative administration of nicotinic
acid or nicotinamide impaired glucose metabolism. This study suggested that excess
Vitamin B1 and Vitamin B3 caused oxidative stress and insulin resistance.
article_processing_charge: No
article_type: original
author:
- first_name: Wuping
full_name: Sun, Wuping
last_name: Sun
- first_name: Ming-Zhu
full_name: Zhai, Ming-Zhu
id: 34009CFA-F248-11E8-B48F-1D18A9856A87
last_name: Zhai
- first_name: Qian
full_name: Zhou, Qian
last_name: Zhou
- first_name: Chengrui
full_name: Qian, Chengrui
last_name: Qian
- first_name: Changyu
full_name: Jiang, Changyu
last_name: Jiang
citation:
ama: Sun W, Zhai M-Z, Zhou Q, Qian C, Jiang C. Effects of B vitamins overload on
plasma insulin level and hydrogen peroxide generation in rats. Chinese Journal
of Physiology. 2017;60(4):207-214. doi:10.4077/CJP.2017.BAF469
apa: Sun, W., Zhai, M.-Z., Zhou, Q., Qian, C., & Jiang, C. (2017). Effects of
B vitamins overload on plasma insulin level and hydrogen peroxide generation in
rats. Chinese Journal of Physiology. Chinese Physiological Society. https://doi.org/10.4077/CJP.2017.BAF469
chicago: Sun, Wuping, Ming-Zhu Zhai, Qian Zhou, Chengrui Qian, and Changyu Jiang.
“Effects of B Vitamins Overload on Plasma Insulin Level and Hydrogen Peroxide
Generation in Rats.” Chinese Journal of Physiology. Chinese Physiological
Society, 2017. https://doi.org/10.4077/CJP.2017.BAF469.
ieee: W. Sun, M.-Z. Zhai, Q. Zhou, C. Qian, and C. Jiang, “Effects of B vitamins
overload on plasma insulin level and hydrogen peroxide generation in rats,” Chinese
Journal of Physiology, vol. 60, no. 4. Chinese Physiological Society, pp.
207–214, 2017.
ista: Sun W, Zhai M-Z, Zhou Q, Qian C, Jiang C. 2017. Effects of B vitamins overload
on plasma insulin level and hydrogen peroxide generation in rats. Chinese Journal
of Physiology. 60(4), 207–214.
mla: Sun, Wuping, et al. “Effects of B Vitamins Overload on Plasma Insulin Level
and Hydrogen Peroxide Generation in Rats.” Chinese Journal of Physiology,
vol. 60, no. 4, Chinese Physiological Society, 2017, pp. 207–14, doi:10.4077/CJP.2017.BAF469.
short: W. Sun, M.-Z. Zhai, Q. Zhou, C. Qian, C. Jiang, Chinese Journal of Physiology
60 (2017) 207–214.
date_created: 2018-12-11T11:47:40Z
date_published: 2017-08-31T00:00:00Z
date_updated: 2021-01-12T08:07:28Z
day: '31'
ddc:
- '570'
department:
- _id: RySh
doi: 10.4077/CJP.2017.BAF469
external_id:
pmid:
- '28847140'
intvolume: ' 60'
issue: '4'
language:
- iso: eng
month: '08'
oa_version: Published Version
page: 207 - 214
pmid: 1
publication: Chinese Journal of Physiology
publication_identifier:
issn:
- '03044920'
publication_status: published
publisher: Chinese Physiological Society
publist_id: '7142'
quality_controlled: '1'
scopus_import: 1
status: public
title: Effects of B vitamins overload on plasma insulin level and hydrogen peroxide
generation in rats
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 60
year: '2017'
...
---
_id: '642'
abstract:
- lang: eng
text: Cauchy problems with SPDEs on the whole space are localized to Cauchy problems
on a ball of radius R. This localization reduces various kinds of spatial approximation
schemes to finite dimensional problems. The error is shown to be exponentially
small. As an application, a numerical scheme is presented which combines the localization
and the space and time discretization, and thus is fully implementable.
author:
- first_name: Mate
full_name: Gerencser, Mate
id: 44ECEDF2-F248-11E8-B48F-1D18A9856A87
last_name: Gerencser
- first_name: István
full_name: Gyöngy, István
last_name: Gyöngy
citation:
ama: Gerencser M, Gyöngy I. Localization errors in solving stochastic partial differential
equations in the whole space. Mathematics of Computation. 2017;86(307):2373-2397.
doi:10.1090/mcom/3201
apa: Gerencser, M., & Gyöngy, I. (2017). Localization errors in solving stochastic
partial differential equations in the whole space. Mathematics of Computation.
American Mathematical Society. https://doi.org/10.1090/mcom/3201
chicago: Gerencser, Mate, and István Gyöngy. “Localization Errors in Solving Stochastic
Partial Differential Equations in the Whole Space.” Mathematics of Computation.
American Mathematical Society, 2017. https://doi.org/10.1090/mcom/3201.
ieee: M. Gerencser and I. Gyöngy, “Localization errors in solving stochastic partial
differential equations in the whole space,” Mathematics of Computation,
vol. 86, no. 307. American Mathematical Society, pp. 2373–2397, 2017.
ista: Gerencser M, Gyöngy I. 2017. Localization errors in solving stochastic partial
differential equations in the whole space. Mathematics of Computation. 86(307),
2373–2397.
mla: Gerencser, Mate, and István Gyöngy. “Localization Errors in Solving Stochastic
Partial Differential Equations in the Whole Space.” Mathematics of Computation,
vol. 86, no. 307, American Mathematical Society, 2017, pp. 2373–97, doi:10.1090/mcom/3201.
short: M. Gerencser, I. Gyöngy, Mathematics of Computation 86 (2017) 2373–2397.
date_created: 2018-12-11T11:47:40Z
date_published: 2017-01-01T00:00:00Z
date_updated: 2021-01-12T08:07:26Z
day: '01'
department:
- _id: JaMa
doi: 10.1090/mcom/3201
intvolume: ' 86'
issue: '307'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/1508.05535
month: '01'
oa: 1
oa_version: Submitted Version
page: 2373 - 2397
publication: Mathematics of Computation
publication_identifier:
issn:
- '00255718'
publication_status: published
publisher: American Mathematical Society
publist_id: '7144'
quality_controlled: '1'
scopus_import: 1
status: public
title: Localization errors in solving stochastic partial differential equations in
the whole space
type: journal_article
user_id: 4435EBFC-F248-11E8-B48F-1D18A9856A87
volume: 86
year: '2017'
...
---
_id: '645'
abstract:
- lang: eng
text: Markov decision processes (MDPs) are standard models for probabilistic systems
with non-deterministic behaviours. Long-run average rewards provide a mathematically
elegant formalism for expressing long term performance. Value iteration (VI) is
one of the simplest and most efficient algorithmic approaches to MDPs with other
properties, such as reachability objectives. Unfortunately, a naive extension
of VI does not work for MDPs with long-run average rewards, as there is no known
stopping criterion. In this work our contributions are threefold. (1) We refute
a conjecture related to stopping criteria for MDPs with long-run average rewards.
(2) We present two practical algorithms for MDPs with long-run average rewards
based on VI. First, we show that a combination of applying VI locally for each
maximal end-component (MEC) and VI for reachability objectives can provide approximation
guarantees. Second, extending the above approach with a simulation-guided on-demand
variant of VI, we present an anytime algorithm that is able to deal with very
large models. (3) Finally, we present experimental results showing that our methods
significantly outperform the standard approaches on several benchmarks.
alternative_title:
- LNCS
author:
- first_name: Pranav
full_name: Ashok, Pranav
last_name: Ashok
- first_name: Krishnendu
full_name: Chatterjee, Krishnendu
id: 2E5DCA20-F248-11E8-B48F-1D18A9856A87
last_name: Chatterjee
orcid: 0000-0002-4561-241X
- first_name: Przemyslaw
full_name: Daca, Przemyslaw
id: 49351290-F248-11E8-B48F-1D18A9856A87
last_name: Daca
- first_name: Jan
full_name: Kretinsky, Jan
id: 44CEF464-F248-11E8-B48F-1D18A9856A87
last_name: Kretinsky
orcid: 0000-0002-8122-2881
- first_name: Tobias
full_name: Meggendorfer, Tobias
last_name: Meggendorfer
citation:
ama: 'Ashok P, Chatterjee K, Daca P, Kretinsky J, Meggendorfer T. Value iteration
for long run average reward in markov decision processes. In: Majumdar R, Kunčak
V, eds. Vol 10426. Springer; 2017:201-221. doi:10.1007/978-3-319-63387-9_10'
apa: 'Ashok, P., Chatterjee, K., Daca, P., Kretinsky, J., & Meggendorfer, T.
(2017). Value iteration for long run average reward in markov decision processes.
In R. Majumdar & V. Kunčak (Eds.) (Vol. 10426, pp. 201–221). Presented at
the CAV: Computer Aided Verification, Heidelberg, Germany: Springer. https://doi.org/10.1007/978-3-319-63387-9_10'
chicago: Ashok, Pranav, Krishnendu Chatterjee, Przemyslaw Daca, Jan Kretinsky, and
Tobias Meggendorfer. “Value Iteration for Long Run Average Reward in Markov Decision
Processes.” edited by Rupak Majumdar and Viktor Kunčak, 10426:201–21. Springer,
2017. https://doi.org/10.1007/978-3-319-63387-9_10.
ieee: 'P. Ashok, K. Chatterjee, P. Daca, J. Kretinsky, and T. Meggendorfer, “Value
iteration for long run average reward in markov decision processes,” presented
at the CAV: Computer Aided Verification, Heidelberg, Germany, 2017, vol. 10426,
pp. 201–221.'
ista: 'Ashok P, Chatterjee K, Daca P, Kretinsky J, Meggendorfer T. 2017. Value iteration
for long run average reward in markov decision processes. CAV: Computer Aided
Verification, LNCS, vol. 10426, 201–221.'
mla: Ashok, Pranav, et al. Value Iteration for Long Run Average Reward in Markov
Decision Processes. Edited by Rupak Majumdar and Viktor Kunčak, vol. 10426,
Springer, 2017, pp. 201–21, doi:10.1007/978-3-319-63387-9_10.
short: P. Ashok, K. Chatterjee, P. Daca, J. Kretinsky, T. Meggendorfer, in:, R.
Majumdar, V. Kunčak (Eds.), Springer, 2017, pp. 201–221.
conference:
end_date: 2017-07-28
location: Heidelberg, Germany
name: 'CAV: Computer Aided Verification'
start_date: 2017-07-24
date_created: 2018-12-11T11:47:41Z
date_published: 2017-07-13T00:00:00Z
date_updated: 2021-01-12T08:07:32Z
day: '13'
department:
- _id: KrCh
doi: 10.1007/978-3-319-63387-9_10
ec_funded: 1
editor:
- first_name: Rupak
full_name: Majumdar, Rupak
last_name: Majumdar
- first_name: Viktor
full_name: Kunčak, Viktor
last_name: Kunčak
intvolume: ' 10426'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/1705.02326
month: '07'
oa: 1
oa_version: Submitted Version
page: 201 - 221
project:
- _id: 25892FC0-B435-11E9-9278-68D0E5697425
grant_number: ICT15-003
name: Efficient Algorithms for Computer Aided Verification
- _id: 25863FF4-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: S11407
name: Game Theory
- _id: 2581B60A-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '279307'
name: 'Quantitative Graph Games: Theory and Applications'
publication_identifier:
isbn:
- 978-331963386-2
publication_status: published
publisher: Springer
publist_id: '7135'
quality_controlled: '1'
scopus_import: 1
status: public
title: Value iteration for long run average reward in markov decision processes
type: conference
user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87
volume: 10426
year: '2017'
...
---
_id: '644'
abstract:
- lang: eng
text: An instance of the valued constraint satisfaction problem (VCSP) is given
by a finite set of variables, a finite domain of labels, and a sum of functions,
each function depending on a subset of the variables. Each function can take finite
values specifying costs of assignments of labels to its variables or the infinite
value, which indicates an infeasible assignment. The goal is to find an assignment
of labels to the variables that minimizes the sum. We study, assuming that P 6=
NP, how the complexity of this very general problem depends on the set of functions
allowed in the instances, the so-called constraint language. The case when all
allowed functions take values in f0;1g corresponds to ordinary CSPs, where one
deals only with the feasibility issue, and there is no optimization. This case
is the subject of the algebraic CSP dichotomy conjecture predicting for which
constraint languages CSPs are tractable (i.e., solvable in polynomial time) and
for which they are NP-hard. The case when all allowed functions take only finite
values corresponds to a finitevalued CSP, where the feasibility aspect is trivial
and one deals only with the optimization issue. The complexity of finite-valued
CSPs was fully classified by Thapper and Živný. An algebraic necessary condition
for tractability of a general-valued CSP with a fixed constraint language was
recently given by Kozik and Ochremiak. As our main result, we prove that if a
constraint language satisfies this algebraic necessary condition, and the feasibility
CSP (i.e., the problem of deciding whether a given instance has a feasible solution)
corresponding to the VCSP with this language is tractable, then the VCSP is tractable.
The algorithm is a simple combination of the assumed algorithm for the feasibility
CSP and the standard LP relaxation. As a corollary, we obtain that a dichotomy
for ordinary CSPs would imply a dichotomy for general-valued CSPs.
author:
- first_name: Vladimir
full_name: Kolmogorov, Vladimir
id: 3D50B0BA-F248-11E8-B48F-1D18A9856A87
last_name: Kolmogorov
- first_name: Andrei
full_name: Krokhin, Andrei
last_name: Krokhin
- first_name: Michal
full_name: Rolinek, Michal
id: 3CB3BC06-F248-11E8-B48F-1D18A9856A87
last_name: Rolinek
citation:
ama: Kolmogorov V, Krokhin A, Rolinek M. The complexity of general-valued CSPs.
SIAM Journal on Computing. 2017;46(3):1087-1110. doi:10.1137/16M1091836
apa: Kolmogorov, V., Krokhin, A., & Rolinek, M. (2017). The complexity of general-valued
CSPs. SIAM Journal on Computing. SIAM. https://doi.org/10.1137/16M1091836
chicago: Kolmogorov, Vladimir, Andrei Krokhin, and Michal Rolinek. “The Complexity
of General-Valued CSPs.” SIAM Journal on Computing. SIAM, 2017. https://doi.org/10.1137/16M1091836.
ieee: V. Kolmogorov, A. Krokhin, and M. Rolinek, “The complexity of general-valued
CSPs,” SIAM Journal on Computing, vol. 46, no. 3. SIAM, pp. 1087–1110,
2017.
ista: Kolmogorov V, Krokhin A, Rolinek M. 2017. The complexity of general-valued
CSPs. SIAM Journal on Computing. 46(3), 1087–1110.
mla: Kolmogorov, Vladimir, et al. “The Complexity of General-Valued CSPs.” SIAM
Journal on Computing, vol. 46, no. 3, SIAM, 2017, pp. 1087–110, doi:10.1137/16M1091836.
short: V. Kolmogorov, A. Krokhin, M. Rolinek, SIAM Journal on Computing 46 (2017)
1087–1110.
date_created: 2018-12-11T11:47:40Z
date_published: 2017-06-29T00:00:00Z
date_updated: 2023-02-23T10:07:49Z
day: '29'
department:
- _id: VlKo
doi: 10.1137/16M1091836
ec_funded: 1
intvolume: ' 46'
issue: '3'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/1502.07327
month: '06'
oa: 1
oa_version: Preprint
page: 1087 - 1110
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 Computing
publication_status: published
publisher: SIAM
publist_id: '7138'
quality_controlled: '1'
related_material:
record:
- id: '1637'
relation: other
status: public
scopus_import: 1
status: public
title: The complexity of general-valued CSPs
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 46
year: '2017'
...
---
_id: '646'
abstract:
- lang: eng
text: We present a novel convex relaxation and a corresponding inference algorithm
for the non-binary discrete tomography problem, that is, reconstructing discrete-valued
images from few linear measurements. In contrast to state of the art approaches
that split the problem into a continuous reconstruction problem for the linear
measurement constraints and a discrete labeling problem to enforce discrete-valued
reconstructions, we propose a joint formulation that addresses both problems simultaneously,
resulting in a tighter convex relaxation. For this purpose a constrained graphical
model is set up and evaluated using a novel relaxation optimized by dual decomposition.
We evaluate our approach experimentally and show superior solutions both mathematically
(tighter relaxation) and experimentally in comparison to previously proposed relaxations.
alternative_title:
- LNCS
author:
- first_name: Jan
full_name: Kuske, Jan
last_name: Kuske
- first_name: Paul
full_name: Swoboda, Paul
id: 446560C6-F248-11E8-B48F-1D18A9856A87
last_name: Swoboda
- first_name: Stefanie
full_name: Petra, Stefanie
last_name: Petra
citation:
ama: 'Kuske J, Swoboda P, Petra S. A novel convex relaxation for non binary discrete
tomography. In: Lauze F, Dong Y, Bjorholm Dahl A, eds. Vol 10302. Springer; 2017:235-246.
doi:10.1007/978-3-319-58771-4_19'
apa: 'Kuske, J., Swoboda, P., & Petra, S. (2017). A novel convex relaxation
for non binary discrete tomography. In F. Lauze, Y. Dong, & A. Bjorholm Dahl
(Eds.) (Vol. 10302, pp. 235–246). Presented at the SSVM: Scale Space and Variational
Methods in Computer Vision, Kolding, Denmark: Springer. https://doi.org/10.1007/978-3-319-58771-4_19'
chicago: Kuske, Jan, Paul Swoboda, and Stefanie Petra. “A Novel Convex Relaxation
for Non Binary Discrete Tomography.” edited by François Lauze, Yiqiu Dong, and
Anders Bjorholm Dahl, 10302:235–46. Springer, 2017. https://doi.org/10.1007/978-3-319-58771-4_19.
ieee: 'J. Kuske, P. Swoboda, and S. Petra, “A novel convex relaxation for non binary
discrete tomography,” presented at the SSVM: Scale Space and Variational Methods
in Computer Vision, Kolding, Denmark, 2017, vol. 10302, pp. 235–246.'
ista: 'Kuske J, Swoboda P, Petra S. 2017. A novel convex relaxation for non binary
discrete tomography. SSVM: Scale Space and Variational Methods in Computer Vision,
LNCS, vol. 10302, 235–246.'
mla: Kuske, Jan, et al. A Novel Convex Relaxation for Non Binary Discrete Tomography.
Edited by François Lauze et al., vol. 10302, Springer, 2017, pp. 235–46, doi:10.1007/978-3-319-58771-4_19.
short: J. Kuske, P. Swoboda, S. Petra, in:, F. Lauze, Y. Dong, A. Bjorholm Dahl
(Eds.), Springer, 2017, pp. 235–246.
conference:
end_date: 2017-06-08
location: Kolding, Denmark
name: 'SSVM: Scale Space and Variational Methods in Computer Vision'
start_date: 2017-06-04
date_created: 2018-12-11T11:47:41Z
date_published: 2017-06-01T00:00:00Z
date_updated: 2021-01-12T08:07:34Z
day: '01'
department:
- _id: VlKo
doi: 10.1007/978-3-319-58771-4_19
ec_funded: 1
editor:
- first_name: François
full_name: Lauze, François
last_name: Lauze
- first_name: Yiqiu
full_name: Dong, Yiqiu
last_name: Dong
- first_name: Anders
full_name: Bjorholm Dahl, Anders
last_name: Bjorholm Dahl
intvolume: ' 10302'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/1703.03769
month: '06'
oa: 1
oa_version: Submitted Version
page: 235 - 246
project:
- _id: 25FBA906-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '616160'
name: 'Discrete Optimization in Computer Vision: Theory and Practice'
publication_identifier:
isbn:
- 978-331958770-7
publication_status: published
publisher: Springer
publist_id: '7132'
quality_controlled: '1'
scopus_import: 1
status: public
title: A novel convex relaxation for non binary discrete tomography
type: conference
user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87
volume: 10302
year: '2017'
...
---
_id: '648'
abstract:
- lang: eng
text: 'Pseudoentropy has found a lot of important applications to cryptography and
complexity theory. In this paper we focus on the foundational problem that has
not been investigated so far, namely by how much pseudoentropy (the amount seen
by computationally bounded attackers) differs from its information-theoretic counterpart
(seen by unbounded observers), given certain limits on attacker’s computational
power? We provide the following answer for HILL pseudoentropy, which exhibits
a threshold behavior around the size exponential in the entropy amount:– If the
attacker size (s) and advantage () satisfy s (formula presented) where k is the
claimed amount of pseudoentropy, then the pseudoentropy boils down to the information-theoretic
smooth entropy. – If s (formula presented) then pseudoentropy could be arbitrarily
bigger than the information-theoretic smooth entropy. Besides answering the posted
question, we show an elegant application of our result to the complexity theory,
namely that it implies the clas-sical result on the existence of functions hard
to approximate (due to Pippenger). In our approach we utilize non-constructive
techniques: the duality of linear programming and the probabilistic method.'
alternative_title:
- LNCS
author:
- first_name: Maciej
full_name: Skórski, Maciej
id: EC09FA6A-02D0-11E9-8223-86B7C91467DD
last_name: Skórski
citation:
ama: 'Skórski M. On the complexity of breaking pseudoentropy. In: Jäger G, Steila
S, eds. Vol 10185. Springer; 2017:600-613. doi:10.1007/978-3-319-55911-7_43'
apa: 'Skórski, M. (2017). On the complexity of breaking pseudoentropy. In G. Jäger
& S. Steila (Eds.) (Vol. 10185, pp. 600–613). Presented at the TAMC: Theory
and Applications of Models of Computation, Bern, Switzerland: Springer. https://doi.org/10.1007/978-3-319-55911-7_43'
chicago: Skórski, Maciej. “On the Complexity of Breaking Pseudoentropy.” edited
by Gerhard Jäger and Silvia Steila, 10185:600–613. Springer, 2017. https://doi.org/10.1007/978-3-319-55911-7_43.
ieee: 'M. Skórski, “On the complexity of breaking pseudoentropy,” presented at the
TAMC: Theory and Applications of Models of Computation, Bern, Switzerland, 2017,
vol. 10185, pp. 600–613.'
ista: 'Skórski M. 2017. On the complexity of breaking pseudoentropy. TAMC: Theory
and Applications of Models of Computation, LNCS, vol. 10185, 600–613.'
mla: Skórski, Maciej. On the Complexity of Breaking Pseudoentropy. Edited
by Gerhard Jäger and Silvia Steila, vol. 10185, Springer, 2017, pp. 600–13, doi:10.1007/978-3-319-55911-7_43.
short: M. Skórski, in:, G. Jäger, S. Steila (Eds.), Springer, 2017, pp. 600–613.
conference:
end_date: 2017-04-22
location: Bern, Switzerland
name: 'TAMC: Theory and Applications of Models of Computation'
start_date: 2017-04-20
date_created: 2018-12-11T11:47:42Z
date_published: 2017-04-01T00:00:00Z
date_updated: 2021-01-12T08:07:39Z
day: '01'
department:
- _id: KrPi
doi: 10.1007/978-3-319-55911-7_43
editor:
- first_name: Gerhard
full_name: Jäger, Gerhard
last_name: Jäger
- first_name: Silvia
full_name: Steila, Silvia
last_name: Steila
intvolume: ' 10185'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://eprint.iacr.org/2016/1186.pdf
month: '04'
oa: 1
oa_version: Submitted Version
page: 600 - 613
publication_identifier:
isbn:
- 978-331955910-0
publication_status: published
publisher: Springer
publist_id: '7125'
quality_controlled: '1'
scopus_import: 1
status: public
title: On the complexity of breaking pseudoentropy
type: conference
user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87
volume: 10185
year: '2017'
...
---
_id: '649'
abstract:
- lang: eng
text: We give a short overview on a recently developed notion of Ricci curvature
for discrete spaces. This notion relies on geodesic convexity properties of the
relative entropy along geodesics in the space of probability densities, for a
metric which is similar to (but different from) the 2-Wasserstein metric. The
theory can be considered as a discrete counterpart to the theory of Ricci curvature
for geodesic measure spaces developed by Lott–Sturm–Villani.
article_processing_charge: No
author:
- first_name: Jan
full_name: Maas, Jan
id: 4C5696CE-F248-11E8-B48F-1D18A9856A87
last_name: Maas
orcid: 0000-0002-0845-1338
citation:
ama: 'Maas J. Entropic Ricci curvature for discrete spaces. In: Najman L, Romon
P, eds. Modern Approaches to Discrete Curvature. Vol 2184. Lecture Notes
in Mathematics. Springer; 2017:159-174. doi:10.1007/978-3-319-58002-9_5'
apa: Maas, J. (2017). Entropic Ricci curvature for discrete spaces. In L. Najman
& P. Romon (Eds.), Modern Approaches to Discrete Curvature (Vol. 2184,
pp. 159–174). Springer. https://doi.org/10.1007/978-3-319-58002-9_5
chicago: Maas, Jan. “Entropic Ricci Curvature for Discrete Spaces.” In Modern
Approaches to Discrete Curvature, edited by Laurent Najman and Pascal Romon,
2184:159–74. Lecture Notes in Mathematics. Springer, 2017. https://doi.org/10.1007/978-3-319-58002-9_5.
ieee: J. Maas, “Entropic Ricci curvature for discrete spaces,” in Modern Approaches
to Discrete Curvature, vol. 2184, L. Najman and P. Romon, Eds. Springer, 2017,
pp. 159–174.
ista: 'Maas J. 2017.Entropic Ricci curvature for discrete spaces. In: Modern Approaches
to Discrete Curvature. vol. 2184, 159–174.'
mla: Maas, Jan. “Entropic Ricci Curvature for Discrete Spaces.” Modern Approaches
to Discrete Curvature, edited by Laurent Najman and Pascal Romon, vol. 2184,
Springer, 2017, pp. 159–74, doi:10.1007/978-3-319-58002-9_5.
short: J. Maas, in:, L. Najman, P. Romon (Eds.), Modern Approaches to Discrete Curvature,
Springer, 2017, pp. 159–174.
date_created: 2018-12-11T11:47:42Z
date_published: 2017-10-05T00:00:00Z
date_updated: 2022-05-24T07:01:33Z
day: '05'
department:
- _id: JaMa
doi: 10.1007/978-3-319-58002-9_5
editor:
- first_name: Laurent
full_name: Najman, Laurent
last_name: Najman
- first_name: Pascal
full_name: Romon, Pascal
last_name: Romon
intvolume: ' 2184'
language:
- iso: eng
month: '10'
oa_version: None
page: 159 - 174
publication: Modern Approaches to Discrete Curvature
publication_identifier:
eissn:
- 978-3-319-58002-9
isbn:
- 978-3-319-58001-2
publication_status: published
publisher: Springer
publist_id: '7123'
quality_controlled: '1'
scopus_import: '1'
series_title: Lecture Notes in Mathematics
status: public
title: Entropic Ricci curvature for discrete spaces
type: book_chapter
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 2184
year: '2017'
...
---
_id: '650'
abstract:
- lang: eng
text: 'In this work we present a short and unified proof for the Strong and Weak
Regularity Lemma, based on the cryptographic tech-nique called low-complexity
approximations. In short, both problems reduce to a task of finding constructively
an approximation for a certain target function under a class of distinguishers
(test functions), where dis-tinguishers are combinations of simple rectangle-indicators.
In our case these approximations can be learned by a simple iterative procedure,
which yields a unified and simple proof, achieving for any graph with density
d and any approximation parameter the partition size. The novelty in our proof
is: (a) a simple approach which yields both strong and weaker variant, and (b)
improvements when d = o(1). At an abstract level, our proof can be seen a refinement
and simplification of the “analytic” proof given by Lovasz and Szegedy.'
alternative_title:
- LNCS
author:
- first_name: Maciej
full_name: Skórski, Maciej
id: EC09FA6A-02D0-11E9-8223-86B7C91467DD
last_name: Skórski
citation:
ama: 'Skórski M. A cryptographic view of regularity lemmas: Simpler unified proofs
and refined bounds. In: Jäger G, Steila S, eds. Vol 10185. Springer; 2017:586-599.
doi:10.1007/978-3-319-55911-7_42'
apa: 'Skórski, M. (2017). A cryptographic view of regularity lemmas: Simpler unified
proofs and refined bounds. In G. Jäger & S. Steila (Eds.) (Vol. 10185, pp.
586–599). Presented at the TAMC: Theory and Applications of Models of Computation,
Bern, Switzerland: Springer. https://doi.org/10.1007/978-3-319-55911-7_42'
chicago: 'Skórski, Maciej. “A Cryptographic View of Regularity Lemmas: Simpler Unified
Proofs and Refined Bounds.” edited by Gerhard Jäger and Silvia Steila, 10185:586–99.
Springer, 2017. https://doi.org/10.1007/978-3-319-55911-7_42.'
ieee: 'M. Skórski, “A cryptographic view of regularity lemmas: Simpler unified proofs
and refined bounds,” presented at the TAMC: Theory and Applications of Models
of Computation, Bern, Switzerland, 2017, vol. 10185, pp. 586–599.'
ista: 'Skórski M. 2017. A cryptographic view of regularity lemmas: Simpler unified
proofs and refined bounds. TAMC: Theory and Applications of Models of Computation,
LNCS, vol. 10185, 586–599.'
mla: 'Skórski, Maciej. A Cryptographic View of Regularity Lemmas: Simpler Unified
Proofs and Refined Bounds. Edited by Gerhard Jäger and Silvia Steila, vol.
10185, Springer, 2017, pp. 586–99, doi:10.1007/978-3-319-55911-7_42.'
short: M. Skórski, in:, G. Jäger, S. Steila (Eds.), Springer, 2017, pp. 586–599.
conference:
end_date: 2017-04-22
location: Bern, Switzerland
name: 'TAMC: Theory and Applications of Models of Computation'
start_date: 2017-04-20
date_created: 2018-12-11T11:47:42Z
date_published: 2017-01-01T00:00:00Z
date_updated: 2021-01-12T08:07:46Z
day: '01'
department:
- _id: KrPi
doi: 10.1007/978-3-319-55911-7_42
editor:
- first_name: Gerhard
full_name: Jäger, Gerhard
last_name: Jäger
- first_name: Silvia
full_name: Steila, Silvia
last_name: Steila
intvolume: ' 10185'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://eprint.iacr.org/2016/965.pdf
month: '01'
oa: 1
oa_version: Submitted Version
page: 586 - 599
publication_identifier:
issn:
- '03029743'
publication_status: published
publisher: Springer
publist_id: '7119'
quality_controlled: '1'
scopus_import: 1
status: public
title: 'A cryptographic view of regularity lemmas: Simpler unified proofs and refined
bounds'
type: conference
user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87
volume: 10185
year: '2017'
...
---
_id: '6519'
abstract:
- lang: eng
text: 'Graph games with omega-regular winning conditions provide a mathematical
framework to analyze a wide range of problems in the analysis of reactive systems
and programs (such as the synthesis of reactive systems, program repair, and the
verification of branching time properties). Parity conditions are canonical forms
to specify omega-regular winning conditions. Graph games with parity conditions
are equivalent to mu-calculus model checking, and thus a very important algorithmic
problem. Symbolic algorithms are of great significance because they provide scalable
algorithms for the analysis of large finite-state systems, as well as algorithms
for the analysis of infinite-state systems with finite quotient. A set-based symbolic
algorithm uses the basic set operations and the one-step predecessor operators.
We consider graph games with n vertices and parity conditions with c priorities
(equivalently, a mu-calculus formula with c alternations of least and greatest
fixed points). While many explicit algorithms exist for graph games with parity
conditions, for set-based symbolic algorithms there are only two algorithms (notice
that we use space to refer to the number of sets stored by a symbolic algorithm):
(a) the basic algorithm that requires O(n^c) symbolic operations and linear space;
and (b) an improved algorithm that requires O(n^{c/2+1}) symbolic operations but
also O(n^{c/2+1}) space (i.e., exponential space). In this work we present two
set-based symbolic algorithms for parity games: (a) our first algorithm requires
O(n^{c/2+1}) symbolic operations and only requires linear space; and (b) developing
on our first algorithm, we present an algorithm that requires O(n^{c/3+1}) symbolic
operations and only linear space. We also present the first linear space set-based
symbolic algorithm for parity games that requires at most a sub-exponential number
of symbolic operations. '
article_number: '18'
article_processing_charge: No
author:
- first_name: Krishnendu
full_name: Chatterjee, Krishnendu
id: 2E5DCA20-F248-11E8-B48F-1D18A9856A87
last_name: Chatterjee
orcid: 0000-0002-4561-241X
- first_name: Wolfgang
full_name: Dvorák, Wolfgang
last_name: Dvorák
- first_name: Monika H
full_name: Henzinger, Monika H
id: 540c9bbd-f2de-11ec-812d-d04a5be85630
last_name: Henzinger
orcid: 0000-0002-5008-6530
- first_name: Veronika
full_name: Loitzenbauer, Veronika
last_name: Loitzenbauer
citation:
ama: 'Chatterjee K, Dvorák W, Henzinger MH, Loitzenbauer V. Improved set-based symbolic
algorithms for parity games. In: Vol 82. Schloss Dagstuhl -Leibniz-Zentrum fuer
Informatik; 2017. doi:10.4230/LIPICS.CSL.2017.18'
apa: 'Chatterjee, K., Dvorák, W., Henzinger, M. H., & Loitzenbauer, V. (2017).
Improved set-based symbolic algorithms for parity games (Vol. 82). Presented at
the CSL: Conference on Computer Science Logic, Stockholm, Sweden: Schloss Dagstuhl
-Leibniz-Zentrum fuer Informatik. https://doi.org/10.4230/LIPICS.CSL.2017.18'
chicago: Chatterjee, Krishnendu, Wolfgang Dvorák, Monika H Henzinger, and Veronika
Loitzenbauer. “Improved Set-Based Symbolic Algorithms for Parity Games,” Vol.
82. Schloss Dagstuhl -Leibniz-Zentrum fuer Informatik, 2017. https://doi.org/10.4230/LIPICS.CSL.2017.18.
ieee: 'K. Chatterjee, W. Dvorák, M. H. Henzinger, and V. Loitzenbauer, “Improved
set-based symbolic algorithms for parity games,” presented at the CSL: Conference
on Computer Science Logic, Stockholm, Sweden, 2017, vol. 82.'
ista: 'Chatterjee K, Dvorák W, Henzinger MH, Loitzenbauer V. 2017. Improved set-based
symbolic algorithms for parity games. CSL: Conference on Computer Science Logic
vol. 82, 18.'
mla: Chatterjee, Krishnendu, et al. Improved Set-Based Symbolic Algorithms for
Parity Games. Vol. 82, 18, Schloss Dagstuhl -Leibniz-Zentrum fuer Informatik,
2017, doi:10.4230/LIPICS.CSL.2017.18.
short: K. Chatterjee, W. Dvorák, M.H. Henzinger, V. Loitzenbauer, in:, Schloss Dagstuhl
-Leibniz-Zentrum fuer Informatik, 2017.
conference:
end_date: 2017-08-24
location: Stockholm, Sweden
name: 'CSL: Conference on Computer Science Logic'
start_date: 2017-08-20
date_created: 2019-06-04T12:42:43Z
date_published: 2017-08-01T00:00:00Z
date_updated: 2023-02-14T10:08:25Z
day: '01'
ddc:
- '004'
department:
- _id: KrCh
doi: 10.4230/LIPICS.CSL.2017.18
ec_funded: 1
file:
- access_level: open_access
checksum: 7c2c9d09970af79026d7e37d9b632ef8
content_type: application/pdf
creator: kschuh
date_created: 2019-06-04T12:56:52Z
date_updated: 2020-07-14T12:47:33Z
file_id: '6520'
file_name: 2017_LIPIcs-Chatterjee.pdf
file_size: 710185
relation: main_file
file_date_updated: 2020-07-14T12:47:33Z
has_accepted_license: '1'
intvolume: ' 82'
language:
- iso: eng
month: '08'
oa: 1
oa_version: Published Version
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: Schloss Dagstuhl -Leibniz-Zentrum fuer Informatik
quality_controlled: '1'
scopus_import: '1'
status: public
title: Improved set-based symbolic algorithms for parity games
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/3.0/legalcode
name: Creative Commons Attribution 3.0 Unported (CC BY 3.0)
short: CC BY (3.0)
type: conference
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 82
year: '2017'
...
---
_id: '6517'
abstract:
- lang: eng
text: A (possibly degenerate) drawing of a graph G in the plane is approximable
by an embedding if it can be turned into an embedding by an arbitrarily small
perturbation. We show that testing, whether a drawing of a planar graph G in the
plane is approximable by an embedding, can be carried out in polynomial time,
if a desired embedding of G belongs to a fixed isotopy class, i.e., the rotation
system (or equivalently the faces) of the embedding of G and the choice of outer
face are fixed. In other words, we show that c-planarity with embedded pipes is
tractable for graphs with fixed embeddings. To the best of our knowledge an analogous
result was previously known essentially only when G is a cycle.
article_number: '34'
author:
- first_name: Radoslav
full_name: Fulek, Radoslav
id: 39F3FFE4-F248-11E8-B48F-1D18A9856A87
last_name: Fulek
orcid: 0000-0001-8485-1774
citation:
ama: 'Fulek R. Embedding graphs into embedded graphs. In: Vol 92. Schloss Dagstuhl
- Leibniz-Zentrum für Informatik; 2017. doi:10.4230/LIPICS.ISAAC.2017.34'
apa: 'Fulek, R. (2017). Embedding graphs into embedded graphs (Vol. 92). Presented
at the ISAAC: International Symposium on Algorithms and Computation, Phuket, Thailand:
Schloss Dagstuhl - Leibniz-Zentrum für Informatik. https://doi.org/10.4230/LIPICS.ISAAC.2017.34'
chicago: Fulek, Radoslav. “Embedding Graphs into Embedded Graphs,” Vol. 92. Schloss
Dagstuhl - Leibniz-Zentrum für Informatik, 2017. https://doi.org/10.4230/LIPICS.ISAAC.2017.34.
ieee: 'R. Fulek, “Embedding graphs into embedded graphs,” presented at the ISAAC:
International Symposium on Algorithms and Computation, Phuket, Thailand, 2017,
vol. 92.'
ista: 'Fulek R. 2017. Embedding graphs into embedded graphs. ISAAC: International
Symposium on Algorithms and Computation vol. 92, 34.'
mla: Fulek, Radoslav. Embedding Graphs into Embedded Graphs. Vol. 92, 34,
Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2017, doi:10.4230/LIPICS.ISAAC.2017.34.
short: R. Fulek, in:, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2017.
conference:
end_date: 2017-12-22
location: Phuket, Thailand
name: 'ISAAC: International Symposium on Algorithms and Computation'
start_date: 2017-12-09
date_created: 2019-06-04T12:11:52Z
date_published: 2017-12-01T00:00:00Z
date_updated: 2021-01-12T08:07:51Z
day: '01'
ddc:
- '510'
department:
- _id: UlWa
doi: 10.4230/LIPICS.ISAAC.2017.34
ec_funded: 1
file:
- access_level: open_access
checksum: fc7a643e29621c8bbe49d36b39081f31
content_type: application/pdf
creator: kschuh
date_created: 2019-06-04T12:20:35Z
date_updated: 2020-07-14T12:47:33Z
file_id: '6518'
file_name: 2017_LIPIcs-Fulek.pdf
file_size: 588982
relation: main_file
file_date_updated: 2020-07-14T12:47:33Z
has_accepted_license: '1'
intvolume: ' 92'
language:
- iso: eng
month: '12'
oa: 1
oa_version: Published Version
project:
- _id: 25681D80-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '291734'
name: International IST Postdoc Fellowship Programme
- _id: 261FA626-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: M02281
name: Eliminating intersections in drawings of graphs
publication_status: published
publisher: Schloss Dagstuhl - Leibniz-Zentrum für Informatik
quality_controlled: '1'
scopus_import: 1
status: public
title: Embedding graphs into embedded graphs
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: 92
year: '2017'
...
---
_id: '652'
abstract:
- lang: eng
text: 'We present an approach that enables robots to self-organize their sensorimotor
behavior from scratch without providing specific information about neither the
robot nor its environment. This is achieved by a simple neural control law that
increases the consistency between external sensor dynamics and internal neural
dynamics of the utterly simple controller. In this way, the embodiment and the
agent-environment coupling are the only source of individual development. We show
how an anthropomorphic tendon driven arm-shoulder system develops different behaviors
depending on that coupling. For instance: Given a bottle half-filled with water,
the arm starts to shake it, driven by the physical response of the water. When
attaching a brush, the arm can be manipulated into wiping a table, and when connected
to a revolvable wheel it finds out how to rotate it. Thus, the robot may be said
to discover the affordances of the world. When allowing two (simulated) humanoid
robots to interact physically, they engage into a joint behavior development leading
to, for instance, spontaneous cooperation. More social effects are observed if
the robots can visually perceive each other. Although, as an observer, it is tempting
to attribute an apparent intentionality, there is nothing of the kind put in.
As a conclusion, we argue that emergent behavior may be much less rooted in explicit
intentions, internal motivations, or specific reward systems than is commonly
believed.'
article_number: '7846789'
author:
- first_name: Ralf
full_name: Der, Ralf
last_name: Der
- first_name: Georg S
full_name: Martius, Georg S
id: 3A276B68-F248-11E8-B48F-1D18A9856A87
last_name: Martius
citation:
ama: 'Der R, Martius GS. Dynamical self consistency leads to behavioral development
and emergent social interactions in robots. In: IEEE; 2017. doi:10.1109/DEVLRN.2016.7846789'
apa: 'Der, R., & Martius, G. S. (2017). Dynamical self consistency leads to
behavioral development and emergent social interactions in robots. Presented at
the ICDL EpiRob: International Conference on Development and Learning and Epigenetic
Robotics , Cergy-Pontoise, France: IEEE. https://doi.org/10.1109/DEVLRN.2016.7846789'
chicago: Der, Ralf, and Georg S Martius. “Dynamical Self Consistency Leads to Behavioral
Development and Emergent Social Interactions in Robots.” IEEE, 2017. https://doi.org/10.1109/DEVLRN.2016.7846789.
ieee: 'R. Der and G. S. Martius, “Dynamical self consistency leads to behavioral
development and emergent social interactions in robots,” presented at the ICDL
EpiRob: International Conference on Development and Learning and Epigenetic Robotics
, Cergy-Pontoise, France, 2017.'
ista: 'Der R, Martius GS. 2017. Dynamical self consistency leads to behavioral development
and emergent social interactions in robots. ICDL EpiRob: International Conference
on Development and Learning and Epigenetic Robotics , 7846789.'
mla: Der, Ralf, and Georg S. Martius. Dynamical Self Consistency Leads to Behavioral
Development and Emergent Social Interactions in Robots. 7846789, IEEE, 2017,
doi:10.1109/DEVLRN.2016.7846789.
short: R. Der, G.S. Martius, in:, IEEE, 2017.
conference:
end_date: 2016-09-22
location: Cergy-Pontoise, France
name: 'ICDL EpiRob: International Conference on Development and Learning and Epigenetic
Robotics '
start_date: 2016-09-19
date_created: 2018-12-11T11:47:43Z
date_published: 2017-02-07T00:00:00Z
date_updated: 2021-01-12T08:07:51Z
day: '07'
department:
- _id: ChLa
- _id: GaTk
doi: 10.1109/DEVLRN.2016.7846789
language:
- iso: eng
month: '02'
oa_version: None
publication_identifier:
isbn:
- 978-150905069-7
publication_status: published
publisher: IEEE
publist_id: '7100'
quality_controlled: '1'
scopus_import: 1
status: public
title: Dynamical self consistency leads to behavioral development and emergent social
interactions in robots
type: conference
user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87
year: '2017'
...
---
_id: '651'
abstract:
- lang: eng
text: "Superhydrophobic surfaces reduce the frictional drag between water and solid
materials, but this effect is often temporary. The realization of sustained drag
reduction has applications for water vehicles and pipeline flows.\r\n\r\n"
author:
- first_name: Björn
full_name: Hof, Björn
id: 3A374330-F248-11E8-B48F-1D18A9856A87
last_name: Hof
orcid: 0000-0003-2057-2754
citation:
ama: 'Hof B. Fluid dynamics: Water flows out of touch. Nature. 2017;541(7636):161-162.
doi:10.1038/541161a'
apa: 'Hof, B. (2017). Fluid dynamics: Water flows out of touch. Nature. Nature
Publishing Group. https://doi.org/10.1038/541161a'
chicago: 'Hof, Björn. “Fluid Dynamics: Water Flows out of Touch.” Nature.
Nature Publishing Group, 2017. https://doi.org/10.1038/541161a.'
ieee: 'B. Hof, “Fluid dynamics: Water flows out of touch,” Nature, vol. 541,
no. 7636. Nature Publishing Group, pp. 161–162, 2017.'
ista: 'Hof B. 2017. Fluid dynamics: Water flows out of touch. Nature. 541(7636),
161–162.'
mla: 'Hof, Björn. “Fluid Dynamics: Water Flows out of Touch.” Nature, vol.
541, no. 7636, Nature Publishing Group, 2017, pp. 161–62, doi:10.1038/541161a.'
short: B. Hof, Nature 541 (2017) 161–162.
date_created: 2018-12-11T11:47:43Z
date_published: 2017-01-11T00:00:00Z
date_updated: 2021-01-12T08:07:49Z
day: '11'
department:
- _id: BjHo
doi: 10.1038/541161a
intvolume: ' 541'
issue: '7636'
language:
- iso: eng
month: '01'
oa_version: None
page: 161 - 162
publication: Nature
publication_identifier:
issn:
- '00280836'
publication_status: published
publisher: Nature Publishing Group
publist_id: '7116'
quality_controlled: '1'
scopus_import: 1
status: public
title: 'Fluid dynamics: Water flows out of touch'
type: journal_article
user_id: 4435EBFC-F248-11E8-B48F-1D18A9856A87
volume: 541
year: '2017'
...
---
_id: '653'
abstract:
- lang: eng
text: The extent of heterogeneity among driver gene mutations present in naturally
occurring metastases - that is, treatment-naive metastatic disease - is largely
unknown. To address this issue, we carried out 60× whole-genome sequencing of
26 metastases from four patients with pancreatic cancer. We found that identical
mutations in known driver genes were present in every metastatic lesion for each
patient studied. Passenger gene mutations, which do not have known or predicted
functional consequences, accounted for all intratumoral heterogeneity. Even with
respect to these passenger mutations, our analysis suggests that the genetic similarity
among the founding cells of metastases was higher than that expected for any two
cells randomly taken from a normal tissue. The uniformity of known driver gene
mutations among metastases in the same patient has critical and encouraging implications
for the success of future targeted therapies in advanced-stage disease.
acknowledgement: 'We thank the Memorial Sloan Kettering Cancer Center Molecular Cytology
core facility for immunohistochemistry staining. This work was supported by Office
of Naval Research grant N00014-16-1-2914, the Bill and Melinda Gates Foundation
(OPP1148627), and a gift from B. Wu and E. Larson (M.A.N.), National Institutes
of Health grants CA179991 (C.A.I.-D. and I.B.), F31 CA180682 (A.P.M.-M.), CA43460
(B.V.), and P50 CA62924, the Monastra Foundation, the Virginia and D.K. Ludwig Fund
for Cancer Research, the Lustgarten Foundation for Pancreatic Cancer Research, the
Sol Goldman Center for Pancreatic Cancer Research, the Sol Goldman Sequencing Center,
ERC Start grant 279307: Graph Games (J.G.R., D.K., and C.K.), Austrian Science Fund
(FWF) grant P23499-N23 (J.G.R., D.K., and C.K.), and FWF NFN grant S11407-N23 RiSE/SHiNE
(J.G.R., D.K., and C.K.).'
article_processing_charge: No
article_type: original
author:
- first_name: Alvin
full_name: Makohon Moore, Alvin
last_name: Makohon Moore
- first_name: Ming
full_name: Zhang, Ming
last_name: Zhang
- first_name: Johannes
full_name: Reiter, Johannes
id: 4A918E98-F248-11E8-B48F-1D18A9856A87
last_name: Reiter
orcid: 0000-0002-0170-7353
- first_name: Ivana
full_name: Božić, Ivana
last_name: Božić
- first_name: Benjamin
full_name: Allen, Benjamin
last_name: Allen
- first_name: Deepanjan
full_name: Kundu, Deepanjan
id: 1d4c0f4f-e8a3-11ec-a351-e36772758c45
last_name: Kundu
- first_name: Krishnendu
full_name: Chatterjee, Krishnendu
id: 2E5DCA20-F248-11E8-B48F-1D18A9856A87
last_name: Chatterjee
orcid: 0000-0002-4561-241X
- first_name: Fay
full_name: Wong, Fay
last_name: Wong
- first_name: Yuchen
full_name: Jiao, Yuchen
last_name: Jiao
- first_name: Zachary
full_name: Kohutek, Zachary
last_name: Kohutek
- first_name: Jungeui
full_name: Hong, Jungeui
last_name: Hong
- first_name: Marc
full_name: Attiyeh, Marc
last_name: Attiyeh
- first_name: Breanna
full_name: Javier, Breanna
last_name: Javier
- first_name: Laura
full_name: Wood, Laura
last_name: Wood
- first_name: Ralph
full_name: Hruban, Ralph
last_name: Hruban
- first_name: Martin
full_name: Nowak, Martin
last_name: Nowak
- first_name: Nickolas
full_name: Papadopoulos, Nickolas
last_name: Papadopoulos
- first_name: Kenneth
full_name: Kinzler, Kenneth
last_name: Kinzler
- first_name: Bert
full_name: Vogelstein, Bert
last_name: Vogelstein
- first_name: Christine
full_name: Iacobuzio Donahue, Christine
last_name: Iacobuzio Donahue
citation:
ama: Makohon Moore A, Zhang M, Reiter J, et al. Limited heterogeneity of known driver
gene mutations among the metastases of individual patients with pancreatic cancer.
Nature Genetics. 2017;49(3):358-366. doi:10.1038/ng.3764
apa: Makohon Moore, A., Zhang, M., Reiter, J., Božić, I., Allen, B., Kundu, D.,
… Iacobuzio Donahue, C. (2017). Limited heterogeneity of known driver gene mutations
among the metastases of individual patients with pancreatic cancer. Nature
Genetics. Nature Publishing Group. https://doi.org/10.1038/ng.3764
chicago: Makohon Moore, Alvin, Ming Zhang, Johannes Reiter, Ivana Božić, Benjamin
Allen, Deepanjan Kundu, Krishnendu Chatterjee, et al. “Limited Heterogeneity of
Known Driver Gene Mutations among the Metastases of Individual Patients with Pancreatic
Cancer.” Nature Genetics. Nature Publishing Group, 2017. https://doi.org/10.1038/ng.3764.
ieee: A. Makohon Moore et al., “Limited heterogeneity of known driver gene
mutations among the metastases of individual patients with pancreatic cancer,”
Nature Genetics, vol. 49, no. 3. Nature Publishing Group, pp. 358–366,
2017.
ista: Makohon Moore A, Zhang M, Reiter J, Božić I, Allen B, Kundu D, Chatterjee
K, Wong F, Jiao Y, Kohutek Z, Hong J, Attiyeh M, Javier B, Wood L, Hruban R, Nowak
M, Papadopoulos N, Kinzler K, Vogelstein B, Iacobuzio Donahue C. 2017. Limited
heterogeneity of known driver gene mutations among the metastases of individual
patients with pancreatic cancer. Nature Genetics. 49(3), 358–366.
mla: Makohon Moore, Alvin, et al. “Limited Heterogeneity of Known Driver Gene Mutations
among the Metastases of Individual Patients with Pancreatic Cancer.” Nature
Genetics, vol. 49, no. 3, Nature Publishing Group, 2017, pp. 358–66, doi:10.1038/ng.3764.
short: A. Makohon Moore, M. Zhang, J. Reiter, I. Božić, B. Allen, D. Kundu, K. Chatterjee,
F. Wong, Y. Jiao, Z. Kohutek, J. Hong, M. Attiyeh, B. Javier, L. Wood, R. Hruban,
M. Nowak, N. Papadopoulos, K. Kinzler, B. Vogelstein, C. Iacobuzio Donahue, Nature
Genetics 49 (2017) 358–366.
date_created: 2018-12-11T11:47:43Z
date_published: 2017-03-01T00:00:00Z
date_updated: 2022-06-10T09:55:08Z
day: '01'
ddc:
- '000'
department:
- _id: KrCh
doi: 10.1038/ng.3764
ec_funded: 1
external_id:
pmid:
- '28092682'
file:
- access_level: open_access
checksum: e442dc3b7420a36ec805e9bb45cc1a2e
content_type: application/pdf
creator: dernst
date_created: 2019-11-19T08:13:50Z
date_updated: 2020-07-14T12:47:33Z
file_id: '7050'
file_name: 2017_NatureGenetics_Makohon.pdf
file_size: 908099
relation: main_file
file_date_updated: 2020-07-14T12:47:33Z
has_accepted_license: '1'
intvolume: ' 49'
issue: '3'
language:
- iso: eng
month: '03'
oa: 1
oa_version: Submitted Version
page: 358 - 366
pmid: 1
project:
- _id: 2581B60A-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '279307'
name: 'Quantitative Graph Games: Theory and Applications'
- _id: 2584A770-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: P 23499-N23
name: Modern Graph Algorithmic Techniques in Formal Verification
- _id: 25863FF4-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: S11407
name: Game Theory
publication: Nature Genetics
publication_identifier:
issn:
- '10614036'
publication_status: published
publisher: Nature Publishing Group
publist_id: '7092'
quality_controlled: '1'
scopus_import: '1'
status: public
title: Limited heterogeneity of known driver gene mutations among the metastases of
individual patients with pancreatic cancer
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 49
year: '2017'
...
---
_id: '6527'
abstract:
- lang: eng
text: "A memory-hard function (MHF) ƒn with parameter n can be computed in sequential
time and space n. Simultaneously, a high amortized parallel area-time complexity
(aAT) is incurred per evaluation. In practice, MHFs are used to limit the rate
at which an adversary (using a custom computational device) can evaluate a security
sensitive function that still occasionally needs to be evaluated by honest users
(using an off-the-shelf general purpose device). The most prevalent examples of
such sensitive functions are Key Derivation Functions (KDFs) and password hashing
algorithms where rate limits help mitigate off-line dictionary attacks. As the
honest users' inputs to these functions are often (low-entropy) passwords special
attention is given to a class of side-channel resistant MHFs called iMHFs.\r\n\r\nEssentially
all iMHFs can be viewed as some mode of operation (making n calls to some round
function) given by a directed acyclic graph (DAG) with very low indegree. Recently,
a combinatorial property of a DAG has been identified (called \"depth-robustness\")
which results in good provable security for an iMHF based on that DAG. Depth-robust
DAGs have also proven useful in other cryptographic applications. Unfortunately,
up till now, all known very depth-robust DAGs are impractically complicated and
little is known about their exact (i.e. non-asymptotic) depth-robustness both
in theory and in practice.\r\n\r\nIn this work we build and analyze (both formally
and empirically) several exceedingly simple and efficient to navigate practical
DAGs for use in iMHFs and other applications. For each DAG we:\r\n*Prove that
their depth-robustness is asymptotically maximal.\r\n*Prove bounds of at least
3 orders of magnitude better on their exact depth-robustness compared to known
bounds for other practical iMHF.\r\n*Implement and empirically evaluate their
depth-robustness and aAT against a variety of state-of-the art (and several new)
depth-reduction and low aAT attacks. \r\nWe find that, against all attacks, the
new DAGs perform significantly better in practice than Argon2i, the most widely
deployed iMHF in practice.\r\n\r\nAlong the way we also improve the best known
empirical attacks on the aAT of Argon2i by implementing and testing several heuristic
versions of a (hitherto purely theoretical) depth-reduction attack. Finally, we
demonstrate practicality of our constructions by modifying the Argon2i code base
to use one of the new high aAT DAGs. Experimental benchmarks on a standard off-the-shelf
CPU show that the new modifications do not adversely affect the impressive throughput
of Argon2i (despite seemingly enjoying significantly higher aAT).\r\n"
author:
- first_name: Joel F
full_name: Alwen, Joel F
id: 2A8DFA8C-F248-11E8-B48F-1D18A9856A87
last_name: Alwen
- first_name: Jeremiah
full_name: Blocki, Jeremiah
last_name: Blocki
- first_name: Ben
full_name: Harsha, Ben
last_name: Harsha
citation:
ama: 'Alwen JF, Blocki J, Harsha B. Practical graphs for optimal side-channel resistant
memory-hard functions. In: Proceedings of the 2017 ACM SIGSAC Conference on
Computer and Communications Security. ACM Press; 2017:1001-1017. doi:10.1145/3133956.3134031'
apa: 'Alwen, J. F., Blocki, J., & Harsha, B. (2017). Practical graphs for optimal
side-channel resistant memory-hard functions. In Proceedings of the 2017 ACM
SIGSAC Conference on Computer and Communications Security (pp. 1001–1017).
Dallas, TX, USA: ACM Press. https://doi.org/10.1145/3133956.3134031'
chicago: Alwen, Joel F, Jeremiah Blocki, and Ben Harsha. “Practical Graphs for Optimal
Side-Channel Resistant Memory-Hard Functions.” In Proceedings of the 2017 ACM
SIGSAC Conference on Computer and Communications Security, 1001–17. ACM Press,
2017. https://doi.org/10.1145/3133956.3134031.
ieee: J. F. Alwen, J. Blocki, and B. Harsha, “Practical graphs for optimal side-channel
resistant memory-hard functions,” in Proceedings of the 2017 ACM SIGSAC Conference
on Computer and Communications Security, Dallas, TX, USA, 2017, pp. 1001–1017.
ista: 'Alwen JF, Blocki J, Harsha B. 2017. Practical graphs for optimal side-channel
resistant memory-hard functions. Proceedings of the 2017 ACM SIGSAC Conference
on Computer and Communications Security. CCS: Conference on Computer and Communications
Security, 1001–1017.'
mla: Alwen, Joel F., et al. “Practical Graphs for Optimal Side-Channel Resistant
Memory-Hard Functions.” Proceedings of the 2017 ACM SIGSAC Conference on Computer
and Communications Security, ACM Press, 2017, pp. 1001–17, doi:10.1145/3133956.3134031.
short: J.F. Alwen, J. Blocki, B. Harsha, in:, Proceedings of the 2017 ACM SIGSAC
Conference on Computer and Communications Security, ACM Press, 2017, pp. 1001–1017.
conference:
end_date: 2017-11-03
location: Dallas, TX, USA
name: 'CCS: Conference on Computer and Communications Security'
start_date: 2017-10-30
date_created: 2019-06-06T13:21:29Z
date_published: 2017-10-30T00:00:00Z
date_updated: 2021-01-12T08:07:53Z
day: '30'
department:
- _id: KrPi
doi: 10.1145/3133956.3134031
ec_funded: 1
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://eprint.iacr.org/2017/443
month: '10'
oa: 1
oa_version: Submitted Version
page: 1001-1017
project:
- _id: 258AA5B2-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '682815'
name: Teaching Old Crypto New Tricks
publication: Proceedings of the 2017 ACM SIGSAC Conference on Computer and Communications
Security
publication_identifier:
isbn:
- '9781450349468'
publication_status: published
publisher: ACM Press
quality_controlled: '1'
scopus_import: 1
status: public
title: Practical graphs for optimal side-channel resistant memory-hard functions
type: conference
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
year: '2017'
...
---
_id: '654'
abstract:
- lang: eng
text: In November 2016, developmental biologists, synthetic biologists and engineers
gathered in Paris for a meeting called ‘Engineering the embryo’. The participants
shared an interest in exploring how synthetic systems can reveal new principles
of embryonic development, and how the in vitro manipulation and modeling of development
using stem cells can be used to integrate ideas and expertise from physics, developmental
biology and tissue engineering. As we review here, the conference pinpointed some
of the challenges arising at the intersection of these fields, along with great
enthusiasm for finding new approaches and collaborations.
author:
- first_name: Anna
full_name: Kicheva, Anna
id: 3959A2A0-F248-11E8-B48F-1D18A9856A87
last_name: Kicheva
orcid: 0000-0003-4509-4998
- first_name: Nicolas
full_name: Rivron, Nicolas
last_name: Rivron
citation:
ama: Kicheva A, Rivron N. Creating to understand – developmental biology meets engineering
in Paris. Development. 2017;144(5):733-736. doi:10.1242/dev.144915
apa: Kicheva, A., & Rivron, N. (2017). Creating to understand – developmental
biology meets engineering in Paris. Development. Company of Biologists.
https://doi.org/10.1242/dev.144915
chicago: Kicheva, Anna, and Nicolas Rivron. “Creating to Understand – Developmental
Biology Meets Engineering in Paris.” Development. Company of Biologists,
2017. https://doi.org/10.1242/dev.144915.
ieee: A. Kicheva and N. Rivron, “Creating to understand – developmental biology
meets engineering in Paris,” Development, vol. 144, no. 5. Company of Biologists,
pp. 733–736, 2017.
ista: Kicheva A, Rivron N. 2017. Creating to understand – developmental biology
meets engineering in Paris. Development. 144(5), 733–736.
mla: Kicheva, Anna, and Nicolas Rivron. “Creating to Understand – Developmental
Biology Meets Engineering in Paris.” Development, vol. 144, no. 5, Company
of Biologists, 2017, pp. 733–36, doi:10.1242/dev.144915.
short: A. Kicheva, N. Rivron, Development 144 (2017) 733–736.
date_created: 2018-12-11T11:47:44Z
date_published: 2017-03-01T00:00:00Z
date_updated: 2021-01-12T08:07:54Z
day: '01'
ddc:
- '571'
department:
- _id: AnKi
doi: 10.1242/dev.144915
ec_funded: 1
file:
- access_level: open_access
checksum: eef22a0f42a55b232cb2d1188a2322cb
content_type: application/pdf
creator: system
date_created: 2018-12-12T10:15:20Z
date_updated: 2020-07-14T12:47:33Z
file_id: '5139'
file_name: IST-2018-987-v1+1_2017_KichevaRivron__Creating_to.pdf
file_size: 228206
relation: main_file
file_date_updated: 2020-07-14T12:47:33Z
has_accepted_license: '1'
intvolume: ' 144'
issue: '5'
language:
- iso: eng
month: '03'
oa: 1
oa_version: Submitted Version
page: 733 - 736
project:
- _id: B6FC0238-B512-11E9-945C-1524E6697425
call_identifier: H2020
grant_number: '680037'
name: Coordination of Patterning And Growth In the Spinal Cord
publication: Development
publication_identifier:
issn:
- '09501991'
publication_status: published
publisher: Company of Biologists
publist_id: '7089'
pubrep_id: '987'
quality_controlled: '1'
scopus_import: 1
status: public
title: Creating to understand – developmental biology meets engineering in Paris
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 144
year: '2017'
...
---
_id: '6526'
abstract:
- lang: eng
text: 'This paper studies the complexity of estimating Rényi divergences of discrete
distributions: p observed from samples and the baseline distribution q known a
priori. Extending the results of Acharya et al. (SODA''15) on estimating Rényi
entropy, we present improved estimation techniques together with upper and lower
bounds on the sample complexity. We show that, contrarily to estimating Rényi
entropy where a sublinear (in the alphabet size) number of samples suffices, the
sample complexity is heavily dependent on events occurring unlikely in q, and
is unbounded in general (no matter what an estimation technique is used). For
any divergence of integer order bigger than 1, we provide upper and lower bounds
on the number of samples dependent on probabilities of p and q (the lower bounds
hold for non-integer orders as well). We conclude that the worst-case sample complexity
is polynomial in the alphabet size if and only if the probabilities of q are non-negligible.
This gives theoretical insights into heuristics used in the applied literature
to handle numerical instability, which occurs for small probabilities of q. Our
result shows that they should be handled with care not only because of numerical
issues, but also because of a blow up in the sample complexity.'
article_number: '8006529'
author:
- first_name: Maciej
full_name: Skórski, Maciej
id: EC09FA6A-02D0-11E9-8223-86B7C91467DD
last_name: Skórski
citation:
ama: 'Skórski M. On the complexity of estimating Rènyi divergences. In: 2017
IEEE International Symposium on Information Theory (ISIT). IEEE; 2017. doi:10.1109/isit.2017.8006529'
apa: 'Skórski, M. (2017). On the complexity of estimating Rènyi divergences. In
2017 IEEE International Symposium on Information Theory (ISIT). Aachen,
Germany: IEEE. https://doi.org/10.1109/isit.2017.8006529'
chicago: Skórski, Maciej. “On the Complexity of Estimating Rènyi Divergences.” In
2017 IEEE International Symposium on Information Theory (ISIT). IEEE, 2017.
https://doi.org/10.1109/isit.2017.8006529.
ieee: M. Skórski, “On the complexity of estimating Rènyi divergences,” in 2017
IEEE International Symposium on Information Theory (ISIT), Aachen, Germany,
2017.
ista: 'Skórski M. 2017. On the complexity of estimating Rènyi divergences. 2017
IEEE International Symposium on Information Theory (ISIT). ISIT: International
Symposium on Information Theory, 8006529.'
mla: Skórski, Maciej. “On the Complexity of Estimating Rènyi Divergences.” 2017
IEEE International Symposium on Information Theory (ISIT), 8006529, IEEE,
2017, doi:10.1109/isit.2017.8006529.
short: M. Skórski, in:, 2017 IEEE International Symposium on Information Theory
(ISIT), IEEE, 2017.
conference:
end_date: 2017-06-30
location: Aachen, Germany
name: 'ISIT: International Symposium on Information Theory'
start_date: 2017-06-25
date_created: 2019-06-06T12:53:09Z
date_published: 2017-08-09T00:00:00Z
date_updated: 2021-01-12T08:07:53Z
day: '09'
department:
- _id: KrPi
doi: 10.1109/isit.2017.8006529
ec_funded: 1
external_id:
arxiv:
- '1702.01666'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/1702.01666
month: '08'
oa: 1
oa_version: Preprint
project:
- _id: 258AA5B2-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '682815'
name: Teaching Old Crypto New Tricks
publication: 2017 IEEE International Symposium on Information Theory (ISIT)
publication_identifier:
isbn:
- '9781509040964'
publication_status: published
publisher: IEEE
quality_controlled: '1'
scopus_import: 1
status: public
title: On the complexity of estimating Rènyi divergences
type: conference
user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87
year: '2017'
...
---
_id: '655'
abstract:
- lang: eng
text: 'The bacterial flagellum is a self-assembling nanomachine. The external flagellar
filament, several times longer than a bacterial cell body, is made of a few tens
of thousands subunits of a single protein: flagellin. A fundamental problem concerns
the molecular mechanism of how the flagellum grows outside the cell, where no
discernible energy source is available. Here, we monitored the dynamic assembly
of individual flagella using in situ labelling and real-time immunostaining of
elongating flagellar filaments. We report that the rate of flagellum growth, initially
~1,700 amino acids per second, decreases with length and that the previously proposed
chain mechanism does not contribute to the filament elongation dynamics. Inhibition
of the proton motive force-dependent export apparatus revealed a major contribution
of substrate injection in driving filament elongation. The combination of experimental
and mathematical evidence demonstrates that a simple, injection-diffusion mechanism
controls bacterial flagella growth outside the cell.'
article_number: e23136
author:
- first_name: Thibaud
full_name: Renault, Thibaud
last_name: Renault
- first_name: Anthony
full_name: Abraham, Anthony
last_name: Abraham
- first_name: Tobias
full_name: Bergmiller, Tobias
id: 2C471CFA-F248-11E8-B48F-1D18A9856A87
last_name: Bergmiller
orcid: 0000-0001-5396-4346
- first_name: Guillaume
full_name: Paradis, Guillaume
last_name: Paradis
- first_name: Simon
full_name: Rainville, Simon
last_name: Rainville
- first_name: Emmanuelle
full_name: Charpentier, Emmanuelle
last_name: Charpentier
- 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: Yuhai
full_name: Tu, Yuhai
last_name: Tu
- first_name: Keiichi
full_name: Namba, Keiichi
last_name: Namba
- first_name: James
full_name: Keener, James
last_name: Keener
- first_name: Tohru
full_name: Minamino, Tohru
last_name: Minamino
- first_name: Marc
full_name: Erhardt, Marc
last_name: Erhardt
citation:
ama: Renault T, Abraham A, Bergmiller T, et al. Bacterial flagella grow through
an injection diffusion mechanism. eLife. 2017;6. doi:10.7554/eLife.23136
apa: Renault, T., Abraham, A., Bergmiller, T., Paradis, G., Rainville, S., Charpentier,
E., … Erhardt, M. (2017). Bacterial flagella grow through an injection diffusion
mechanism. ELife. eLife Sciences Publications. https://doi.org/10.7554/eLife.23136
chicago: Renault, Thibaud, Anthony Abraham, Tobias Bergmiller, Guillaume Paradis,
Simon Rainville, Emmanuelle Charpentier, Calin C Guet, et al. “Bacterial Flagella
Grow through an Injection Diffusion Mechanism.” ELife. eLife Sciences Publications,
2017. https://doi.org/10.7554/eLife.23136.
ieee: T. Renault et al., “Bacterial flagella grow through an injection diffusion
mechanism,” eLife, vol. 6. eLife Sciences Publications, 2017.
ista: Renault T, Abraham A, Bergmiller T, Paradis G, Rainville S, Charpentier E,
Guet CC, Tu Y, Namba K, Keener J, Minamino T, Erhardt M. 2017. Bacterial flagella
grow through an injection diffusion mechanism. eLife. 6, e23136.
mla: Renault, Thibaud, et al. “Bacterial Flagella Grow through an Injection Diffusion
Mechanism.” ELife, vol. 6, e23136, eLife Sciences Publications, 2017, doi:10.7554/eLife.23136.
short: T. Renault, A. Abraham, T. Bergmiller, G. Paradis, S. Rainville, E. Charpentier,
C.C. Guet, Y. Tu, K. Namba, J. Keener, T. Minamino, M. Erhardt, ELife 6 (2017).
date_created: 2018-12-11T11:47:44Z
date_published: 2017-03-06T00:00:00Z
date_updated: 2021-01-12T08:07:55Z
day: '06'
ddc:
- '579'
department:
- _id: CaGu
doi: 10.7554/eLife.23136
file:
- access_level: open_access
checksum: 39e1c3e82ddac83a30422fa72fa1a383
content_type: application/pdf
creator: system
date_created: 2018-12-12T10:08:53Z
date_updated: 2020-07-14T12:47:33Z
file_id: '4716'
file_name: IST-2017-904-v1+1_elife-23136-v2.pdf
file_size: 5520359
relation: main_file
- access_level: open_access
checksum: a6d542253028f52e00aa29739ddffe8f
content_type: application/pdf
creator: system
date_created: 2018-12-12T10:08:54Z
date_updated: 2020-07-14T12:47:33Z
file_id: '4717'
file_name: IST-2017-904-v1+2_elife-23136-figures-v2.pdf
file_size: 11242920
relation: main_file
file_date_updated: 2020-07-14T12:47:33Z
has_accepted_license: '1'
intvolume: ' 6'
language:
- iso: eng
month: '03'
oa: 1
oa_version: Published Version
publication: eLife
publication_identifier:
issn:
- 2050084X
publication_status: published
publisher: eLife Sciences Publications
publist_id: '7082'
pubrep_id: '904'
quality_controlled: '1'
scopus_import: 1
status: public
title: Bacterial flagella grow through an injection diffusion mechanism
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 6
year: '2017'
...
---
_id: '657'
abstract:
- lang: eng
text: Plant organs are typically organized into three main tissue layers. The middle
ground tissue layer comprises the majority of the plant body and serves a wide
range of functions, including photosynthesis, selective nutrient uptake and storage,
and gravity sensing. Ground tissue patterning and maintenance in Arabidopsis are
controlled by a well-established gene network revolving around the key regulator
SHORT-ROOT (SHR). In contrast, it is completely unknown how ground tissue identity
is first specified from totipotent precursor cells in the embryo. The plant signaling
molecule auxin, acting through AUXIN RESPONSE FACTOR (ARF) transcription factors,
is critical for embryo patterning. The auxin effector ARF5/MONOPTEROS (MP) acts
both cell-autonomously and noncell-autonomously to control embryonic vascular
tissue formation and root initiation, respectively. Here we show that auxin response
and ARF activity cell-autonomously control the asymmetric division of the first
ground tissue cells. By identifying embryonic target genes, we show that MP transcriptionally
initiates the ground tissue lineage and acts upstream of the regulatory network
that controls ground tissue patterning and maintenance. Strikingly, whereas the
SHR network depends on MP, this MP function is, at least in part, SHR independent.
Our study therefore identifies auxin response as a regulator of ground tissue
specification in the embryonic root, and reveals that ground tissue initiation
and maintenance use different regulators and mechanisms. Moreover, our data provide
a framework for the simultaneous formation of multiple cell types by the same
transcriptional regulator.
author:
- first_name: Barbara
full_name: Möller, Barbara
last_name: Möller
- first_name: Colette
full_name: Ten Hove, Colette
last_name: Ten Hove
- first_name: Daoquan
full_name: Xiang, Daoquan
last_name: Xiang
- first_name: Nerys
full_name: Williams, Nerys
last_name: Williams
- first_name: Lorena
full_name: López, Lorena
last_name: López
- first_name: Saiko
full_name: Yoshida, Saiko
id: 2E46069C-F248-11E8-B48F-1D18A9856A87
last_name: Yoshida
- first_name: Margot
full_name: Smit, Margot
last_name: Smit
- first_name: Raju
full_name: Datla, Raju
last_name: Datla
- first_name: Dolf
full_name: Weijers, Dolf
last_name: Weijers
citation:
ama: Möller B, Ten Hove C, Xiang D, et al. Auxin response cell autonomously controls
ground tissue initiation in the early arabidopsis embryo. PNAS. 2017;114(12):E2533-E2539.
doi:10.1073/pnas.1616493114
apa: Möller, B., Ten Hove, C., Xiang, D., Williams, N., López, L., Yoshida, S.,
… Weijers, D. (2017). Auxin response cell autonomously controls ground tissue
initiation in the early arabidopsis embryo. PNAS. National Academy of Sciences.
https://doi.org/10.1073/pnas.1616493114
chicago: Möller, Barbara, Colette Ten Hove, Daoquan Xiang, Nerys Williams, Lorena
López, Saiko Yoshida, Margot Smit, Raju Datla, and Dolf Weijers. “Auxin Response
Cell Autonomously Controls Ground Tissue Initiation in the Early Arabidopsis Embryo.”
PNAS. National Academy of Sciences, 2017. https://doi.org/10.1073/pnas.1616493114.
ieee: B. Möller et al., “Auxin response cell autonomously controls ground
tissue initiation in the early arabidopsis embryo,” PNAS, vol. 114, no.
12. National Academy of Sciences, pp. E2533–E2539, 2017.
ista: Möller B, Ten Hove C, Xiang D, Williams N, López L, Yoshida S, Smit M, Datla
R, Weijers D. 2017. Auxin response cell autonomously controls ground tissue initiation
in the early arabidopsis embryo. PNAS. 114(12), E2533–E2539.
mla: Möller, Barbara, et al. “Auxin Response Cell Autonomously Controls Ground Tissue
Initiation in the Early Arabidopsis Embryo.” PNAS, vol. 114, no. 12, National
Academy of Sciences, 2017, pp. E2533–39, doi:10.1073/pnas.1616493114.
short: B. Möller, C. Ten Hove, D. Xiang, N. Williams, L. López, S. Yoshida, M. Smit,
R. Datla, D. Weijers, PNAS 114 (2017) E2533–E2539.
date_created: 2018-12-11T11:47:45Z
date_published: 2017-03-21T00:00:00Z
date_updated: 2021-01-12T08:08:02Z
day: '21'
department:
- _id: JiFr
doi: 10.1073/pnas.1616493114
external_id:
pmid:
- '28265057'
intvolume: ' 114'
issue: '12'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5373392/
month: '03'
oa: 1
oa_version: Submitted Version
page: E2533 - E2539
pmid: 1
publication: PNAS
publication_identifier:
issn:
- '00278424'
publication_status: published
publisher: National Academy of Sciences
publist_id: '7076'
quality_controlled: '1'
scopus_import: 1
status: public
title: Auxin response cell autonomously controls ground tissue initiation in the early
arabidopsis embryo
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 114
year: '2017'
...
---
_id: '656'
abstract:
- lang: eng
text: Human neurons transplanted into a mouse model for Alzheimer’s disease show
human-specific vulnerability to β-amyloid plaques and may help to identify new
therapeutic targets.
article_number: eaam9867
author:
- first_name: Gaia
full_name: Novarino, Gaia
id: 3E57A680-F248-11E8-B48F-1D18A9856A87
last_name: Novarino
orcid: 0000-0002-7673-7178
citation:
ama: Novarino G. Modeling Alzheimer’s disease in mice with human neurons. Science
Translational Medicine. 2017;9(381). doi:10.1126/scitranslmed.aam9867
apa: Novarino, G. (2017). Modeling Alzheimer’s disease in mice with human neurons.
Science Translational Medicine. American Association for the Advancement
of Science. https://doi.org/10.1126/scitranslmed.aam9867
chicago: Novarino, Gaia. “Modeling Alzheimer’s Disease in Mice with Human Neurons.”
Science Translational Medicine. American Association for the Advancement
of Science, 2017. https://doi.org/10.1126/scitranslmed.aam9867.
ieee: G. Novarino, “Modeling Alzheimer’s disease in mice with human neurons,” Science
Translational Medicine, vol. 9, no. 381. American Association for the Advancement
of Science, 2017.
ista: Novarino G. 2017. Modeling Alzheimer’s disease in mice with human neurons.
Science Translational Medicine. 9(381), eaam9867.
mla: Novarino, Gaia. “Modeling Alzheimer’s Disease in Mice with Human Neurons.”
Science Translational Medicine, vol. 9, no. 381, eaam9867, American Association
for the Advancement of Science, 2017, doi:10.1126/scitranslmed.aam9867.
short: G. Novarino, Science Translational Medicine 9 (2017).
date_created: 2018-12-11T11:47:45Z
date_published: 2017-03-15T00:00:00Z
date_updated: 2021-01-12T08:07:59Z
day: '15'
department:
- _id: GaNo
doi: 10.1126/scitranslmed.aam9867
intvolume: ' 9'
issue: '381'
language:
- iso: eng
month: '03'
oa_version: None
publication: Science Translational Medicine
publication_identifier:
issn:
- '19466234'
publication_status: published
publisher: American Association for the Advancement of Science
publist_id: '7079'
quality_controlled: '1'
scopus_import: 1
status: public
title: Modeling Alzheimer's disease in mice with human neurons
type: journal_article
user_id: 4435EBFC-F248-11E8-B48F-1D18A9856A87
volume: 9
year: '2017'
...
---
_id: '658'
abstract:
- lang: eng
text: 'With the accelerated development of robot technologies, 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 specific
objectives for the task at hand. While very successful in many applications, self-organized
control schemes seem to be favored in large complex systems with unknown dynamics
or which are difficult to model. Reasons are the expected scalability, robustness,
and resilience of self-organizing systems. The paper presents a self-learning
neurocontroller based on extrinsic differential plasticity introduced recently,
applying it to an anthropomorphic musculoskeletal robot arm with attached objects
of unknown physical dynamics. The central finding of the paper is the following
effect: by the mere feedback through the internal dynamics of the object, the
robot is learning to relate each of the objects with a very specific sensorimotor
pattern. Specifically, an attached pendulum pilots the arm into a circular motion,
a half-filled bottle produces axis oriented shaking behavior, a wheel is getting
rotated, and wiping patterns emerge automatically in a table-plus-brush setting.
By these object-specific dynamical patterns, the robot may be said to recognize
the object''s identity, or in other words, it discovers dynamical affordances
of objects. Furthermore, when including hand coordinates obtained from a camera,
a dedicated hand-eye coordination self-organizes spontaneously. These phenomena
are discussed from a specific dynamical system perspective. Central is the dedicated
working regime at the border to instability with its potentially infinite reservoir
of (limit cycle) attractors "waiting" to be excited. Besides converging
toward one of these attractors, variate behavior is also arising from a self-induced
attractor morphing driven by the learning rule. We claim that experimental investigations
with this anthropomorphic, self-learning robot not only generate interesting and
potentially useful behaviors, but may also help to better understand what subjective
human muscle feelings are, how they can be rooted in sensorimotor patterns, and
how these concepts may feed back on robotics.'
article_number: '00008'
article_processing_charge: Yes
author:
- first_name: Ralf
full_name: Der, Ralf
last_name: Der
- first_name: Georg S
full_name: Martius, Georg S
id: 3A276B68-F248-11E8-B48F-1D18A9856A87
last_name: Martius
citation:
ama: Der R, Martius GS. Self organized behavior generation for musculoskeletal robots.
Frontiers in Neurorobotics. 2017;11(MAR). doi:10.3389/fnbot.2017.00008
apa: Der, R., & Martius, G. S. (2017). Self organized behavior generation for
musculoskeletal robots. Frontiers in Neurorobotics. Frontiers Research
Foundation. https://doi.org/10.3389/fnbot.2017.00008
chicago: Der, Ralf, and Georg S Martius. “Self Organized Behavior Generation for
Musculoskeletal Robots.” Frontiers in Neurorobotics. Frontiers Research
Foundation, 2017. https://doi.org/10.3389/fnbot.2017.00008.
ieee: R. Der and G. S. Martius, “Self organized behavior generation for musculoskeletal
robots,” Frontiers in Neurorobotics, vol. 11, no. MAR. Frontiers Research
Foundation, 2017.
ista: Der R, Martius GS. 2017. Self organized behavior generation for musculoskeletal
robots. Frontiers in Neurorobotics. 11(MAR), 00008.
mla: Der, Ralf, and Georg S. Martius. “Self Organized Behavior Generation for Musculoskeletal
Robots.” Frontiers in Neurorobotics, vol. 11, no. MAR, 00008, Frontiers
Research Foundation, 2017, doi:10.3389/fnbot.2017.00008.
short: R. Der, G.S. Martius, Frontiers in Neurorobotics 11 (2017).
date_created: 2018-12-11T11:47:45Z
date_published: 2017-03-16T00:00:00Z
date_updated: 2021-01-12T08:08:04Z
day: '16'
ddc:
- '006'
department:
- _id: ChLa
- _id: GaTk
doi: 10.3389/fnbot.2017.00008
ec_funded: 1
file:
- access_level: open_access
checksum: b1bc43f96d1df3313c03032c2a46388d
content_type: application/pdf
creator: system
date_created: 2018-12-12T10:18:49Z
date_updated: 2020-07-14T12:47:33Z
file_id: '5371'
file_name: IST-2017-903-v1+1_fnbot-11-00008.pdf
file_size: 8439566
relation: main_file
file_date_updated: 2020-07-14T12:47:33Z
has_accepted_license: '1'
intvolume: ' 11'
issue: MAR
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
publication: Frontiers in Neurorobotics
publication_identifier:
issn:
- '16625218'
publication_status: published
publisher: Frontiers Research Foundation
publist_id: '7078'
pubrep_id: '903'
quality_controlled: '1'
scopus_import: 1
status: public
title: Self organized behavior generation for musculoskeletal robots
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: 2EBD1598-F248-11E8-B48F-1D18A9856A87
volume: 11
year: '2017'
...
---
_id: '659'
abstract:
- lang: eng
text: Migration frequently involves Rac-mediated protrusion of lamellipodia, formed
by Arp2/3 complex-dependent branching thought to be crucial for force generation
and stability of these networks. The formins FMNL2 and FMNL3 are Cdc42 effectors
targeting to the lamellipodium tip and shown here to nucleate and elongate actin
filaments with complementary activities in vitro. In migrating B16-F1 melanoma
cells, both formins contribute to the velocity of lamellipodium protrusion. Loss
of FMNL2/3 function in melanoma cells and fibroblasts reduces lamellipodial width,
actin filament density and -bundling, without changing patterns of Arp2/3 complex
incorporation. Strikingly, in melanoma cells, FMNL2/3 gene inactivation almost
completely abolishes protrusion forces exerted by lamellipodia and modifies their
ultrastructural organization. Consistently, CRISPR/Cas-mediated depletion of FMNL2/3
in fibroblasts reduces both migration and capability of cells to move against
viscous media. Together, we conclude that force generation in lamellipodia strongly
depends on FMNL formin activity, operating in addition to Arp2/3 complex-dependent
filament branching.
article_number: '14832'
article_processing_charge: No
author:
- first_name: Frieda
full_name: Kage, Frieda
last_name: Kage
- first_name: Moritz
full_name: Winterhoff, Moritz
last_name: Winterhoff
- first_name: Vanessa
full_name: Dimchev, Vanessa
last_name: Dimchev
- first_name: Jan
full_name: Müller, Jan
id: AD07FDB4-0F61-11EA-8158-C4CC64CEAA8D
last_name: Müller
- first_name: Tobias
full_name: Thalheim, Tobias
last_name: Thalheim
- first_name: Anika
full_name: Freise, Anika
last_name: Freise
- first_name: Stefan
full_name: Brühmann, Stefan
last_name: Brühmann
- first_name: Jana
full_name: Kollasser, Jana
last_name: Kollasser
- first_name: Jennifer
full_name: Block, Jennifer
last_name: Block
- first_name: Georgi A
full_name: Dimchev, Georgi A
last_name: Dimchev
- first_name: Matthias
full_name: Geyer, Matthias
last_name: Geyer
- first_name: Hams
full_name: Schnittler, Hams
last_name: Schnittler
- first_name: Cord
full_name: Brakebusch, Cord
last_name: Brakebusch
- first_name: Theresia
full_name: Stradal, Theresia
last_name: Stradal
- first_name: Marie
full_name: Carlier, Marie
last_name: Carlier
- 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: Josef
full_name: Käs, Josef
last_name: Käs
- first_name: Jan
full_name: Faix, Jan
last_name: Faix
- first_name: Klemens
full_name: Rottner, Klemens
last_name: Rottner
citation:
ama: Kage F, Winterhoff M, Dimchev V, et al. FMNL formins boost lamellipodial force
generation. Nature Communications. 2017;8. doi:10.1038/ncomms14832
apa: Kage, F., Winterhoff, M., Dimchev, V., Müller, J., Thalheim, T., Freise, A.,
… Rottner, K. (2017). FMNL formins boost lamellipodial force generation. Nature
Communications. Nature Publishing Group. https://doi.org/10.1038/ncomms14832
chicago: Kage, Frieda, Moritz Winterhoff, Vanessa Dimchev, Jan Müller, Tobias Thalheim,
Anika Freise, Stefan Brühmann, et al. “FMNL Formins Boost Lamellipodial Force
Generation.” Nature Communications. Nature Publishing Group, 2017. https://doi.org/10.1038/ncomms14832.
ieee: F. Kage et al., “FMNL formins boost lamellipodial force generation,”
Nature Communications, vol. 8. Nature Publishing Group, 2017.
ista: Kage F, Winterhoff M, Dimchev V, Müller J, Thalheim T, Freise A, Brühmann
S, Kollasser J, Block J, Dimchev GA, Geyer M, Schnittler H, Brakebusch C, Stradal
T, Carlier M, Sixt MK, Käs J, Faix J, Rottner K. 2017. FMNL formins boost lamellipodial
force generation. Nature Communications. 8, 14832.
mla: Kage, Frieda, et al. “FMNL Formins Boost Lamellipodial Force Generation.” Nature
Communications, vol. 8, 14832, Nature Publishing Group, 2017, doi:10.1038/ncomms14832.
short: F. Kage, M. Winterhoff, V. Dimchev, J. Müller, T. Thalheim, A. Freise, S.
Brühmann, J. Kollasser, J. Block, G.A. Dimchev, M. Geyer, H. Schnittler, C. Brakebusch,
T. Stradal, M. Carlier, M.K. Sixt, J. Käs, J. Faix, K. Rottner, Nature Communications
8 (2017).
date_created: 2018-12-11T11:47:46Z
date_published: 2017-03-22T00:00:00Z
date_updated: 2021-01-12T08:08:06Z
day: '22'
ddc:
- '570'
department:
- _id: MiSi
doi: 10.1038/ncomms14832
file:
- access_level: open_access
checksum: dae30190291c3630e8102d8714a8d23e
content_type: application/pdf
creator: system
date_created: 2018-12-12T10:14:21Z
date_updated: 2020-07-14T12:47:34Z
file_id: '5072'
file_name: IST-2017-902-v1+1_Kage_et_al-2017-Nature_Communications.pdf
file_size: 9523746
relation: main_file
file_date_updated: 2020-07-14T12:47:34Z
has_accepted_license: '1'
intvolume: ' 8'
language:
- iso: eng
month: '03'
oa: 1
oa_version: Published Version
publication: Nature Communications
publication_identifier:
issn:
- '20411723'
publication_status: published
publisher: Nature Publishing Group
publist_id: '7075'
pubrep_id: '902'
quality_controlled: '1'
scopus_import: 1
status: public
title: FMNL formins boost lamellipodial force generation
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: 8
year: '2017'
...
---
_id: '660'
abstract:
- lang: eng
text: Growing microtubules are protected from depolymerization by the presence of
a GTP or GDP/Pi cap. End-binding proteins of the EB1 family bind to the stabilizing
cap, allowing monitoring of its size in real time. The cap size has been shown
to correlate with instantaneous microtubule stability. Here we have quantitatively
characterized the properties of cap size fluctuations during steadystate growth
and have developed a theory predicting their timescale and amplitude from the
kinetics of microtubule growth and cap maturation. In contrast to growth speed
fluctuations, cap size fluctuations show a characteristic timescale, which is
defined by the lifetime of the cap sites. Growth fluctuations affect the amplitude
of cap size fluctuations; however, cap size does not affect growth speed, indicating
that microtubules are far from instability during most of their time of growth.
Our theory provides the basis for a quantitative understanding of microtubule
stability fluctuations during steady-state growth.
acknowledgement: We thank Philippe Cluzel for helpful discussions and Gunnar Pruessner
for data analysis advice. This work was supported by the Francis Crick Institute,
which receives its core funding from Cancer Research UK Grant FC001163, Medical
Research Council Grant FC001163, and Wellcome Trust Grant FC001163. This work was
also supported by European Research Council Advanced Grant Project 323042 (to C.D.
and T.S.).
author:
- first_name: Jamie
full_name: Rickman, Jamie
last_name: Rickman
- first_name: Christian F
full_name: Düllberg, Christian F
id: 459064DC-F248-11E8-B48F-1D18A9856A87
last_name: Düllberg
orcid: 0000-0001-6335-9748
- first_name: Nicholas
full_name: Cade, Nicholas
last_name: Cade
- first_name: Lewis
full_name: Griffin, Lewis
last_name: Griffin
- first_name: Thomas
full_name: Surrey, Thomas
last_name: Surrey
citation:
ama: Rickman J, Düllberg CF, Cade N, Griffin L, Surrey T. Steady state EB cap size
fluctuations are determined by stochastic microtubule growth and maturation. PNAS.
2017;114(13):3427-3432. doi:10.1073/pnas.1620274114
apa: Rickman, J., Düllberg, C. F., Cade, N., Griffin, L., & Surrey, T. (2017).
Steady state EB cap size fluctuations are determined by stochastic microtubule
growth and maturation. PNAS. National Academy of Sciences. https://doi.org/10.1073/pnas.1620274114
chicago: Rickman, Jamie, Christian F Düllberg, Nicholas Cade, Lewis Griffin, and
Thomas Surrey. “Steady State EB Cap Size Fluctuations Are Determined by Stochastic
Microtubule Growth and Maturation.” PNAS. National Academy of Sciences,
2017. https://doi.org/10.1073/pnas.1620274114.
ieee: J. Rickman, C. F. Düllberg, N. Cade, L. Griffin, and T. Surrey, “Steady state
EB cap size fluctuations are determined by stochastic microtubule growth and maturation,”
PNAS, vol. 114, no. 13. National Academy of Sciences, pp. 3427–3432, 2017.
ista: Rickman J, Düllberg CF, Cade N, Griffin L, Surrey T. 2017. Steady state EB
cap size fluctuations are determined by stochastic microtubule growth and maturation.
PNAS. 114(13), 3427–3432.
mla: Rickman, Jamie, et al. “Steady State EB Cap Size Fluctuations Are Determined
by Stochastic Microtubule Growth and Maturation.” PNAS, vol. 114, no. 13,
National Academy of Sciences, 2017, pp. 3427–32, doi:10.1073/pnas.1620274114.
short: J. Rickman, C.F. Düllberg, N. Cade, L. Griffin, T. Surrey, PNAS 114 (2017)
3427–3432.
date_created: 2018-12-11T11:47:46Z
date_published: 2017-03-28T00:00:00Z
date_updated: 2021-01-12T08:08:09Z
day: '28'
department:
- _id: MaLo
doi: 10.1073/pnas.1620274114
external_id:
pmid:
- '28280102'
intvolume: ' 114'
issue: '13'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5380103/
month: '03'
oa: 1
oa_version: Submitted Version
page: 3427 - 3432
pmid: 1
publication: PNAS
publication_identifier:
issn:
- '00278424'
publication_status: published
publisher: National Academy of Sciences
publist_id: '7073'
quality_controlled: '1'
scopus_import: 1
status: public
title: Steady state EB cap size fluctuations are determined by stochastic microtubule
growth and maturation
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 114
year: '2017'
...
---
_id: '662'
abstract:
- lang: eng
text: 'We report a direct-numerical-simulation study of the Taylor-Couette flow
in the quasi-Keplerian regime at shear Reynolds numbers up to (105). Quasi-Keplerian
rotating flow has been investigated for decades as a simplified model system to
study the origin of turbulence in accretion disks that is not fully understood.
The flow in this study is axially periodic and thus the experimental end-wall
effects on the stability of the flow are avoided. Using optimal linear perturbations
as initial conditions, our simulations find no sustained turbulence: the strong
initial perturbations distort the velocity profile and trigger turbulence that
eventually decays.'
article_number: '044107'
author:
- first_name: Liang
full_name: Shi, Liang
last_name: Shi
- first_name: Björn
full_name: Hof, Björn
id: 3A374330-F248-11E8-B48F-1D18A9856A87
last_name: Hof
orcid: 0000-0003-2057-2754
- first_name: Markus
full_name: Rampp, Markus
last_name: Rampp
- first_name: Marc
full_name: Avila, Marc
last_name: Avila
citation:
ama: Shi L, Hof B, Rampp M, Avila M. Hydrodynamic turbulence in quasi Keplerian
rotating flows. Physics of Fluids. 2017;29(4). doi:10.1063/1.4981525
apa: Shi, L., Hof, B., Rampp, M., & Avila, M. (2017). Hydrodynamic turbulence
in quasi Keplerian rotating flows. Physics of Fluids. American Institute
of Physics. https://doi.org/10.1063/1.4981525
chicago: Shi, Liang, Björn Hof, Markus Rampp, and Marc Avila. “Hydrodynamic Turbulence
in Quasi Keplerian Rotating Flows.” Physics of Fluids. American Institute
of Physics, 2017. https://doi.org/10.1063/1.4981525.
ieee: L. Shi, B. Hof, M. Rampp, and M. Avila, “Hydrodynamic turbulence in quasi
Keplerian rotating flows,” Physics of Fluids, vol. 29, no. 4. American
Institute of Physics, 2017.
ista: Shi L, Hof B, Rampp M, Avila M. 2017. Hydrodynamic turbulence in quasi Keplerian
rotating flows. Physics of Fluids. 29(4), 044107.
mla: Shi, Liang, et al. “Hydrodynamic Turbulence in Quasi Keplerian Rotating Flows.”
Physics of Fluids, vol. 29, no. 4, 044107, American Institute of Physics,
2017, doi:10.1063/1.4981525.
short: L. Shi, B. Hof, M. Rampp, M. Avila, Physics of Fluids 29 (2017).
date_created: 2018-12-11T11:47:47Z
date_published: 2017-04-01T00:00:00Z
date_updated: 2021-01-12T08:08:15Z
day: '01'
department:
- _id: BjHo
doi: 10.1063/1.4981525
intvolume: ' 29'
issue: '4'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/1703.01714
month: '04'
oa: 1
oa_version: Submitted Version
project:
- _id: 2511D90C-B435-11E9-9278-68D0E5697425
grant_number: SFB 963 TP A8
name: Astrophysical instability of currents and turbulences
publication: Physics of Fluids
publication_identifier:
issn:
- '10706631'
publication_status: published
publisher: American Institute of Physics
publist_id: '7072'
quality_controlled: '1'
scopus_import: 1
status: public
title: Hydrodynamic turbulence in quasi Keplerian rotating flows
type: journal_article
user_id: 4435EBFC-F248-11E8-B48F-1D18A9856A87
volume: 29
year: '2017'
...
---
_id: '663'
abstract:
- lang: eng
text: 'In this paper, we propose an approach to automatically compute invariant
clusters for nonlinear semialgebraic hybrid systems. An invariant cluster for
an ordinary differential equation (ODE) is a multivariate polynomial invariant
g(u→, x→) = 0, parametric in u→, which can yield an infinite number of concrete
invariants by assigning different values to u→ so that every trajectory of the
system can be overapproximated precisely by the intersection of a group of concrete
invariants. For semialgebraic systems, which involve ODEs with multivariate polynomial
right-hand sides, given a template multivariate polynomial g(u→, x→), an invariant
cluster can be obtained by first computing the remainder of the Lie derivative
of g(u→, x→) divided by g(u→, x→) and then solving the system of polynomial equations
obtained from the coefficients of the remainder. Based on invariant clusters and
sum-of-squares (SOS) programming, we present a new method for the safety verification
of hybrid systems. Experiments on nonlinear benchmark systems from biology and
control theory show that our approach is efficient. '
author:
- first_name: Hui
full_name: Kong, Hui
id: 3BDE25AA-F248-11E8-B48F-1D18A9856A87
last_name: Kong
orcid: 0000-0002-3066-6941
- first_name: Sergiy
full_name: Bogomolov, Sergiy
last_name: Bogomolov
orcid: 0000-0002-0686-0365
- first_name: Christian
full_name: Schilling, Christian
last_name: Schilling
- first_name: Yu
full_name: Jiang, Yu
last_name: Jiang
- first_name: Thomas A
full_name: Henzinger, Thomas A
id: 40876CD8-F248-11E8-B48F-1D18A9856A87
last_name: Henzinger
orcid: 0000−0002−2985−7724
citation:
ama: 'Kong H, Bogomolov S, Schilling C, Jiang Y, Henzinger TA. Safety verification
of nonlinear hybrid systems based on invariant clusters. In: Proceedings of
the 20th International Conference on Hybrid Systems. ACM; 2017:163-172. doi:10.1145/3049797.3049814'
apa: 'Kong, H., Bogomolov, S., Schilling, C., Jiang, Y., & Henzinger, T. A.
(2017). Safety verification of nonlinear hybrid systems based on invariant clusters.
In Proceedings of the 20th International Conference on Hybrid Systems (pp.
163–172). Pittsburgh, PA, United States: ACM. https://doi.org/10.1145/3049797.3049814'
chicago: Kong, Hui, Sergiy Bogomolov, Christian Schilling, Yu Jiang, and Thomas
A Henzinger. “Safety Verification of Nonlinear Hybrid Systems Based on Invariant
Clusters.” In Proceedings of the 20th International Conference on Hybrid Systems,
163–72. ACM, 2017. https://doi.org/10.1145/3049797.3049814.
ieee: H. Kong, S. Bogomolov, C. Schilling, Y. Jiang, and T. A. Henzinger, “Safety
verification of nonlinear hybrid systems based on invariant clusters,” in Proceedings
of the 20th International Conference on Hybrid Systems, Pittsburgh, PA, United
States, 2017, pp. 163–172.
ista: 'Kong H, Bogomolov S, Schilling C, Jiang Y, Henzinger TA. 2017. Safety verification
of nonlinear hybrid systems based on invariant clusters. Proceedings of the 20th
International Conference on Hybrid Systems. HSCC: Hybrid Systems Computation and
Control , 163–172.'
mla: Kong, Hui, et al. “Safety Verification of Nonlinear Hybrid Systems Based on
Invariant Clusters.” Proceedings of the 20th International Conference on Hybrid
Systems, ACM, 2017, pp. 163–72, doi:10.1145/3049797.3049814.
short: H. Kong, S. Bogomolov, C. Schilling, Y. Jiang, T.A. Henzinger, in:, Proceedings
of the 20th International Conference on Hybrid Systems, ACM, 2017, pp. 163–172.
conference:
end_date: 2017-04-20
location: Pittsburgh, PA, United States
name: 'HSCC: Hybrid Systems Computation and Control '
start_date: 2017-04-18
date_created: 2018-12-11T11:47:47Z
date_published: 2017-04-01T00:00:00Z
date_updated: 2021-01-12T08:08:17Z
day: '01'
ddc:
- '000'
department:
- _id: ToHe
doi: 10.1145/3049797.3049814
file:
- access_level: open_access
checksum: b7667434cbf5b5f0ade3bea1dbe5bf63
content_type: application/pdf
creator: system
date_created: 2018-12-12T10:11:20Z
date_updated: 2020-07-14T12:47:34Z
file_id: '4873'
file_name: IST-2017-817-v1+1_p163-kong.pdf
file_size: 1650530
relation: main_file
file_date_updated: 2020-07-14T12:47:34Z
has_accepted_license: '1'
language:
- iso: eng
month: '04'
oa: 1
oa_version: Submitted Version
page: 163 - 172
publication: Proceedings of the 20th International Conference on Hybrid Systems
publication_identifier:
isbn:
- 978-145034590-3
publication_status: published
publisher: ACM
publist_id: '7067'
pubrep_id: '817'
quality_controlled: '1'
scopus_import: 1
status: public
title: Safety verification of nonlinear hybrid systems based on invariant clusters
type: conference
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
year: '2017'
...
---
_id: '667'
abstract:
- lang: eng
text: Perinatal exposure to penicillin may result in longlasting gut and behavioral
changes.
article_number: '2786'
author:
- first_name: Gaia
full_name: Novarino, Gaia
id: 3E57A680-F248-11E8-B48F-1D18A9856A87
last_name: Novarino
orcid: 0000-0002-7673-7178
citation:
ama: Novarino G. The antisocial side of antibiotics. Science Translational Medicine.
2017;9(387). doi:10.1126/scitranslmed.aan2786
apa: Novarino, G. (2017). The antisocial side of antibiotics. Science Translational
Medicine. American Association for the Advancement of Science. https://doi.org/10.1126/scitranslmed.aan2786
chicago: Novarino, Gaia. “The Antisocial Side of Antibiotics.” Science Translational
Medicine. American Association for the Advancement of Science, 2017. https://doi.org/10.1126/scitranslmed.aan2786.
ieee: G. Novarino, “The antisocial side of antibiotics,” Science Translational
Medicine, vol. 9, no. 387. American Association for the Advancement of Science,
2017.
ista: Novarino G. 2017. The antisocial side of antibiotics. Science Translational
Medicine. 9(387), 2786.
mla: Novarino, Gaia. “The Antisocial Side of Antibiotics.” Science Translational
Medicine, vol. 9, no. 387, 2786, American Association for the Advancement
of Science, 2017, doi:10.1126/scitranslmed.aan2786.
short: G. Novarino, Science Translational Medicine 9 (2017).
date_created: 2018-12-11T11:47:48Z
date_published: 2017-04-26T00:00:00Z
date_updated: 2021-01-12T08:08:30Z
day: '26'
department:
- _id: GaNo
doi: 10.1126/scitranslmed.aan2786
intvolume: ' 9'
issue: '387'
language:
- iso: eng
month: '04'
oa_version: None
publication: Science Translational Medicine
publication_identifier:
issn:
- '19466234'
publication_status: published
publisher: American Association for the Advancement of Science
publist_id: '7060'
quality_controlled: '1'
scopus_import: 1
status: public
title: The antisocial side of antibiotics
type: journal_article
user_id: 4435EBFC-F248-11E8-B48F-1D18A9856A87
volume: 9
year: '2017'
...
---
_id: '668'
abstract:
- lang: eng
text: Macrophage filopodia, finger-like membrane protrusions, were first implicated
in phagocytosis more than 100 years ago, but little is still known about the involvement
of these actin-dependent structures in particle clearance. Using spinning disk
confocal microscopy to image filopodial dynamics in mouse resident Lifeact-EGFP
macrophages, we show that filopodia, or filopodia-like structures, support pathogen
clearance by multiple means. Filopodia supported the phagocytic uptake of bacterial
(Escherichia coli) particles by (i) capturing along the filopodial shaft and surfing
toward the cell body, the most common mode of capture; (ii) capturing via the
tip followed by retraction; (iii) combinations of surfing and retraction; or (iv)
sweeping actions. In addition, filopodia supported the uptake of zymosan (Saccharomyces
cerevisiae) particles by (i) providing fixation, (ii) capturing at the tip and
filopodia-guided actin anterograde flow with phagocytic cup formation, and (iii)
the rapid growth of new protrusions. To explore the role of filopodia-inducing
Cdc42, we generated myeloid-restricted Cdc42 knock-out mice. Cdc42-deficient macrophages
exhibited rapid phagocytic cup kinetics, but reduced particle clearance, which
could be explained by the marked rounded-up morphology of these cells. Macrophages
lacking Myo10, thought to act downstream of Cdc42, had normal morphology, motility,
and phagocytic cup formation, but displayed markedly reduced filopodia formation.
In conclusion, live-cell imaging revealed multiple mechanisms involving macrophage
filopodia in particle capture and engulfment. Cdc42 is not critical for filopodia
or phagocytic cup formation, but plays a key role in driving macrophage lamellipodial
spreading.
article_type: original
author:
- first_name: Markus
full_name: Horsthemke, Markus
last_name: Horsthemke
- first_name: Anne
full_name: Bachg, Anne
last_name: Bachg
- first_name: Katharina
full_name: Groll, Katharina
last_name: Groll
- first_name: Sven
full_name: Moyzio, Sven
last_name: Moyzio
- first_name: Barbara
full_name: Müther, Barbara
last_name: Müther
- first_name: Sandra
full_name: Hemkemeyer, Sandra
last_name: Hemkemeyer
- first_name: Roland
full_name: Wedlich Söldner, Roland
last_name: Wedlich Söldner
- 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: Sebastian
full_name: Tacke, Sebastian
last_name: Tacke
- first_name: Martin
full_name: Bähler, Martin
last_name: Bähler
- first_name: Peter
full_name: Hanley, Peter
last_name: Hanley
citation:
ama: Horsthemke M, Bachg A, Groll K, et al. Multiple roles of filopodial dynamics
in particle capture and phagocytosis and phenotypes of Cdc42 and Myo10 deletion.
Journal of Biological Chemistry. 2017;292(17):7258-7273. doi:10.1074/jbc.M116.766923
apa: Horsthemke, M., Bachg, A., Groll, K., Moyzio, S., Müther, B., Hemkemeyer, S.,
… Hanley, P. (2017). Multiple roles of filopodial dynamics in particle capture
and phagocytosis and phenotypes of Cdc42 and Myo10 deletion. Journal of Biological
Chemistry. American Society for Biochemistry and Molecular Biology. https://doi.org/10.1074/jbc.M116.766923
chicago: Horsthemke, Markus, Anne Bachg, Katharina Groll, Sven Moyzio, Barbara Müther,
Sandra Hemkemeyer, Roland Wedlich Söldner, et al. “Multiple Roles of Filopodial
Dynamics in Particle Capture and Phagocytosis and Phenotypes of Cdc42 and Myo10
Deletion.” Journal of Biological Chemistry. American Society for Biochemistry
and Molecular Biology, 2017. https://doi.org/10.1074/jbc.M116.766923.
ieee: M. Horsthemke et al., “Multiple roles of filopodial dynamics in particle
capture and phagocytosis and phenotypes of Cdc42 and Myo10 deletion,” Journal
of Biological Chemistry, vol. 292, no. 17. American Society for Biochemistry
and Molecular Biology, pp. 7258–7273, 2017.
ista: Horsthemke M, Bachg A, Groll K, Moyzio S, Müther B, Hemkemeyer S, Wedlich
Söldner R, Sixt MK, Tacke S, Bähler M, Hanley P. 2017. Multiple roles of filopodial
dynamics in particle capture and phagocytosis and phenotypes of Cdc42 and Myo10
deletion. Journal of Biological Chemistry. 292(17), 7258–7273.
mla: Horsthemke, Markus, et al. “Multiple Roles of Filopodial Dynamics in Particle
Capture and Phagocytosis and Phenotypes of Cdc42 and Myo10 Deletion.” Journal
of Biological Chemistry, vol. 292, no. 17, American Society for Biochemistry
and Molecular Biology, 2017, pp. 7258–73, doi:10.1074/jbc.M116.766923.
short: M. Horsthemke, A. Bachg, K. Groll, S. Moyzio, B. Müther, S. Hemkemeyer, R.
Wedlich Söldner, M.K. Sixt, S. Tacke, M. Bähler, P. Hanley, Journal of Biological
Chemistry 292 (2017) 7258–7273.
date_created: 2018-12-11T11:47:49Z
date_published: 2017-04-28T00:00:00Z
date_updated: 2021-01-12T08:08:34Z
day: '28'
ddc:
- '570'
department:
- _id: MiSi
doi: 10.1074/jbc.M116.766923
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creator: dernst
date_created: 2019-10-24T15:25:42Z
date_updated: 2020-07-14T12:47:37Z
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has_accepted_license: '1'
intvolume: ' 292'
issue: '17'
language:
- iso: eng
month: '04'
oa: 1
oa_version: Published Version
page: 7258 - 7273
publication: Journal of Biological Chemistry
publication_identifier:
issn:
- '00219258'
publication_status: published
publisher: American Society for Biochemistry and Molecular Biology
publist_id: '7059'
quality_controlled: '1'
scopus_import: 1
status: public
title: Multiple roles of filopodial dynamics in particle capture and phagocytosis
and phenotypes of Cdc42 and Myo10 deletion
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 292
year: '2017'
...
---
_id: '669'
abstract:
- lang: eng
text: 'The exocyst, a eukaryotic tethering complex, coregulates targeted exocytosis
as an effector of small GTPases in polarized cell growth. In land plants, several
exocyst subunits are encoded by double or triple paralogs, culminating in tens
of EXO70 paralogs. Out of 23 Arabidopsis thaliana EXO70 isoforms, we analyzed
seven isoforms expressed in pollen. Genetic and microscopic analyses of single
mutants in EXO70A2, EXO70C1, EXO70C2, EXO70F1, EXO70H3, EXO70H5, and EXO70H6 genes
revealed that only a loss-of-function EXO70C2 allele resulted in a significant
male-specific transmission defect (segregation 40%:51%:9%) due to aberrant pollen
tube growth. Mutant pollen tubes grown in vitro exhibited an enhanced growth rate
and a decreased thickness of the tip cell wall, causing tip bursts. However, exo70C2
pollen tubes could frequently recover and restart their speedy elongation, resulting
in a repetitive stop-and-go growth dynamics. A pollenspecific depletion of the
closest paralog, EXO70C1, using artificial microRNA in the exo70C2 mutant background,
resulted in a complete pollen-specific transmission defect, suggesting redundant
functions of EXO70C1 and EXO70C2. Both EXO70C1 and EXO70C2, GFP tagged and expressed
under the control of their native promoters, localized in the cytoplasm of pollen
grains, pollen tubes, and also root trichoblast cells. The expression of EXO70C2-GFP
complemented the aberrant growth of exo70C2 pollen tubes. The absent EXO70C2 interactions
with core exocyst subunits in the yeast two-hybrid assay, cytoplasmic localization,
and genetic effect suggest an unconventional EXO70 function possibly as a regulator
of exocytosis outside the exocyst complex. In conclusion, EXO70C2 is a novel factor
contributing to the regulation of optimal tip growth of Arabidopsis pollen tubes. '
article_processing_charge: No
article_type: original
author:
- first_name: Lukáš
full_name: Synek, Lukáš
last_name: Synek
- first_name: Nemanja
full_name: Vukašinović, Nemanja
last_name: Vukašinović
- first_name: Ivan
full_name: Kulich, Ivan
last_name: Kulich
- first_name: Michal
full_name: Hála, Michal
last_name: Hála
- first_name: Klára
full_name: Aldorfová, Klára
last_name: Aldorfová
- first_name: Matyas
full_name: Fendrych, Matyas
id: 43905548-F248-11E8-B48F-1D18A9856A87
last_name: Fendrych
orcid: 0000-0002-9767-8699
- first_name: Viktor
full_name: Žárský, Viktor
last_name: Žárský
citation:
ama: Synek L, Vukašinović N, Kulich I, et al. EXO70C2 is a key regulatory factor
for optimal tip growth of pollen. Plant Physiology. 2017;174(1):223-240.
doi:10.1104/pp.16.01282
apa: Synek, L., Vukašinović, N., Kulich, I., Hála, M., Aldorfová, K., Fendrych,
M., & Žárský, V. (2017). EXO70C2 is a key regulatory factor for optimal tip
growth of pollen. Plant Physiology. American Society of Plant Biologists.
https://doi.org/10.1104/pp.16.01282
chicago: Synek, Lukáš, Nemanja Vukašinović, Ivan Kulich, Michal Hála, Klára Aldorfová,
Matyas Fendrych, and Viktor Žárský. “EXO70C2 Is a Key Regulatory Factor for Optimal
Tip Growth of Pollen.” Plant Physiology. American Society of Plant Biologists,
2017. https://doi.org/10.1104/pp.16.01282.
ieee: L. Synek et al., “EXO70C2 is a key regulatory factor for optimal tip
growth of pollen,” Plant Physiology, vol. 174, no. 1. American Society
of Plant Biologists, pp. 223–240, 2017.
ista: Synek L, Vukašinović N, Kulich I, Hála M, Aldorfová K, Fendrych M, Žárský
V. 2017. EXO70C2 is a key regulatory factor for optimal tip growth of pollen.
Plant Physiology. 174(1), 223–240.
mla: Synek, Lukáš, et al. “EXO70C2 Is a Key Regulatory Factor for Optimal Tip Growth
of Pollen.” Plant Physiology, vol. 174, no. 1, American Society of Plant
Biologists, 2017, pp. 223–40, doi:10.1104/pp.16.01282.
short: L. Synek, N. Vukašinović, I. Kulich, M. Hála, K. Aldorfová, M. Fendrych,
V. Žárský, Plant Physiology 174 (2017) 223–240.
date_created: 2018-12-11T11:47:49Z
date_published: 2017-05-01T00:00:00Z
date_updated: 2021-01-12T08:08:35Z
day: '01'
ddc:
- '580'
department:
- _id: JiFr
doi: 10.1104/pp.16.01282
external_id:
pmid:
- '28356503'
file:
- access_level: open_access
checksum: 97155acc6aa5f0d0a78e0589a932fe02
content_type: application/pdf
creator: dernst
date_created: 2019-11-18T16:16:18Z
date_updated: 2020-07-14T12:47:37Z
file_id: '7041'
file_name: 2017_PlantPhysio_Synek.pdf
file_size: 2176903
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file_date_updated: 2020-07-14T12:47:37Z
has_accepted_license: '1'
intvolume: ' 174'
issue: '1'
language:
- iso: eng
month: '05'
oa: 1
oa_version: Submitted Version
page: 223 - 240
pmid: 1
publication: Plant Physiology
publication_identifier:
issn:
- '00320889'
publication_status: published
publisher: American Society of Plant Biologists
publist_id: '7058'
quality_controlled: '1'
scopus_import: 1
status: public
title: EXO70C2 is a key regulatory factor for optimal tip growth of pollen
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 174
year: '2017'
...
---
_id: '6679'
abstract:
- lang: eng
text: 'Polar codes represent one of the major recent breakthroughs in coding theory
and, because of their attractive features, they have been selected for the incoming
5G standard. As such, a lot of attention has been devoted to the development of
decoding algorithms with good error performance and efficient hardware implementation.
One of the leading candidates in this regard is represented by successive-cancellation
list (SCL) decoding. However, its hardware implementation requires a large amount
of memory. Recently, a partitioned SCL (PSCL) decoder has been proposed to significantly
reduce the memory consumption [1]. In this paper, we examine the paradigm of PSCL
decoding from both theoretical and practical standpoints: (i) by changing the
construction of the code, we are able to improve the performance at no additional
computational, latency or memory cost, (ii) we present an optimal scheme to allocate
cyclic redundancy checks (CRCs), and (iii) we provide an upper bound on the list
size that allows MAP performance.'
author:
- first_name: Seyyed Ali
full_name: Hashemi, Seyyed Ali
last_name: Hashemi
- first_name: Marco
full_name: Mondelli, Marco
id: 27EB676C-8706-11E9-9510-7717E6697425
last_name: Mondelli
orcid: 0000-0002-3242-7020
- first_name: Hamed
full_name: Hassani, Hamed
last_name: Hassani
- first_name: Ruediger
full_name: Urbanke, Ruediger
last_name: Urbanke
- first_name: Warren
full_name: Gross, Warren
last_name: Gross
citation:
ama: 'Hashemi SA, Mondelli M, Hassani H, Urbanke R, Gross W. Partitioned list decoding
of polar codes: Analysis and improvement of finite length performance. In: 2017
IEEE Global Communications Conference. IEEE; 2017:1-7. doi:10.1109/glocom.2017.8254940'
apa: 'Hashemi, S. A., Mondelli, M., Hassani, H., Urbanke, R., & Gross, W. (2017).
Partitioned list decoding of polar codes: Analysis and improvement of finite length
performance. In 2017 IEEE Global Communications Conference (pp. 1–7). Singapore,
Singapore: IEEE. https://doi.org/10.1109/glocom.2017.8254940'
chicago: 'Hashemi, Seyyed Ali, Marco Mondelli, Hamed Hassani, Ruediger Urbanke,
and Warren Gross. “Partitioned List Decoding of Polar Codes: Analysis and Improvement
of Finite Length Performance.” In 2017 IEEE Global Communications Conference,
1–7. IEEE, 2017. https://doi.org/10.1109/glocom.2017.8254940.'
ieee: 'S. A. Hashemi, M. Mondelli, H. Hassani, R. Urbanke, and W. Gross, “Partitioned
list decoding of polar codes: Analysis and improvement of finite length performance,”
in 2017 IEEE Global Communications Conference, Singapore, Singapore, 2017,
pp. 1–7.'
ista: 'Hashemi SA, Mondelli M, Hassani H, Urbanke R, Gross W. 2017. Partitioned
list decoding of polar codes: Analysis and improvement of finite length performance.
2017 IEEE Global Communications Conference. GLOBECOM: Global Communications Conference,
1–7.'
mla: 'Hashemi, Seyyed Ali, et al. “Partitioned List Decoding of Polar Codes: Analysis
and Improvement of Finite Length Performance.” 2017 IEEE Global Communications
Conference, IEEE, 2017, pp. 1–7, doi:10.1109/glocom.2017.8254940.'
short: S.A. Hashemi, M. Mondelli, H. Hassani, R. Urbanke, W. Gross, in:, 2017 IEEE
Global Communications Conference, IEEE, 2017, pp. 1–7.
conference:
end_date: 2017-12-08
location: Singapore, Singapore
name: 'GLOBECOM: Global Communications Conference'
start_date: 2017-12-04
date_created: 2019-07-24T13:55:25Z
date_published: 2017-12-01T00:00:00Z
date_updated: 2021-01-12T08:08:34Z
day: '01'
doi: 10.1109/glocom.2017.8254940
extern: '1'
external_id:
arxiv:
- '1705.05497'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/1705.05497
month: '12'
oa: 1
oa_version: Preprint
page: 1-7
publication: 2017 IEEE Global Communications Conference
publication_status: published
publisher: IEEE
quality_controlled: '1'
status: public
title: 'Partitioned list decoding of polar codes: Analysis and improvement of finite
length performance'
type: conference
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
year: '2017'
...