---
_id: '152'
abstract:
- lang: eng
text: Complex I has an essential role in ATP production by coupling electron transfer
from NADH to quinone with translocation of protons across the inner mitochondrial
membrane. Isolated complex I deficiency is a frequent cause of mitochondrial inherited
diseases. Complex I has also been implicated in cancer, ageing, and neurodegenerative
conditions. Until recently, the understanding of complex I deficiency on the molecular
level was limited due to the lack of high-resolution structures of the enzyme.
However, due to developments in single particle cryo-electron microscopy (cryo-EM),
recent studies have reported nearly atomic resolution maps and models of mitochondrial
complex I. These structures significantly add to our understanding of complex
I mechanism and assembly. The disease-causing mutations are discussed here in
their structural context.
article_processing_charge: No
article_type: original
author:
- first_name: Karol
full_name: Fiedorczuk, Karol
id: 5BFF67CE-02D1-11E9-B11A-A5A4D7DFFFD0
last_name: Fiedorczuk
- first_name: Leonid A
full_name: Sazanov, Leonid A
id: 338D39FE-F248-11E8-B48F-1D18A9856A87
last_name: Sazanov
orcid: 0000-0002-0977-7989
citation:
ama: Fiedorczuk K, Sazanov LA. Mammalian mitochondrial complex I structure and disease
causing mutations. Trends in Cell Biology. 2018;28(10):835-867. doi:10.1016/j.tcb.2018.06.006
apa: Fiedorczuk, K., & Sazanov, L. A. (2018). Mammalian mitochondrial complex
I structure and disease causing mutations. Trends in Cell Biology. Elsevier.
https://doi.org/10.1016/j.tcb.2018.06.006
chicago: Fiedorczuk, Karol, and Leonid A Sazanov. “Mammalian Mitochondrial Complex
I Structure and Disease Causing Mutations.” Trends in Cell Biology. Elsevier,
2018. https://doi.org/10.1016/j.tcb.2018.06.006.
ieee: K. Fiedorczuk and L. A. Sazanov, “Mammalian mitochondrial complex I structure
and disease causing mutations,” Trends in Cell Biology, vol. 28, no. 10.
Elsevier, pp. 835–867, 2018.
ista: Fiedorczuk K, Sazanov LA. 2018. Mammalian mitochondrial complex I structure
and disease causing mutations. Trends in Cell Biology. 28(10), 835–867.
mla: Fiedorczuk, Karol, and Leonid A. Sazanov. “Mammalian Mitochondrial Complex
I Structure and Disease Causing Mutations.” Trends in Cell Biology, vol.
28, no. 10, Elsevier, 2018, pp. 835–67, doi:10.1016/j.tcb.2018.06.006.
short: K. Fiedorczuk, L.A. Sazanov, Trends in Cell Biology 28 (2018) 835–867.
date_created: 2018-12-11T11:44:54Z
date_published: 2018-07-26T00:00:00Z
date_updated: 2023-09-13T08:51:56Z
day: '26'
ddc:
- '572'
department:
- _id: LeSa
doi: 10.1016/j.tcb.2018.06.006
external_id:
isi:
- '000445118200007'
file:
- access_level: open_access
checksum: ef6d2b4e1fd63948539639242610bfa6
content_type: application/pdf
creator: lsazanov
date_created: 2019-11-07T12:55:20Z
date_updated: 2020-07-14T12:45:00Z
file_id: '6994'
file_name: SasanovFinalMS+EdComments_LS_allacc_withFigs.pdf
file_size: 2185385
relation: main_file
file_date_updated: 2020-07-14T12:45:00Z
has_accepted_license: '1'
intvolume: ' 28'
isi: 1
issue: '10'
language:
- iso: eng
license: https://creativecommons.org/licenses/by-nc-nd/4.0/
month: '07'
oa: 1
oa_version: Submitted Version
page: 835 - 867
publication: Trends in Cell Biology
publication_status: published
publisher: Elsevier
publist_id: '7769'
quality_controlled: '1'
scopus_import: '1'
status: public
title: Mammalian mitochondrial complex I structure and disease causing mutations
tmp:
image: /images/cc_by_nc_nd.png
legal_code_url: https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode
name: Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International
(CC BY-NC-ND 4.0)
short: CC BY-NC-ND (4.0)
type: journal_article
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
volume: 28
year: '2018'
...
---
_id: '310'
abstract:
- lang: eng
text: A model of computation that is widely used in the formal analysis of reactive
systems is symbolic algorithms. In this model the access to the input graph is
restricted to consist of symbolic operations, which are expensive in comparison
to the standard RAM operations. We give lower bounds on the number of symbolic
operations for basic graph problems such as the computation of the strongly connected
components and of the approximate diameter as well as for fundamental problems
in model checking such as safety, liveness, and coliveness. Our lower bounds are
linear in the number of vertices of the graph, even for constant-diameter graphs.
For none of these problems lower bounds on the number of symbolic operations were
known before. The lower bounds show an interesting separation of these problems
from the reachability problem, which can be solved with O(D) symbolic operations,
where D is the diameter of the graph. Additionally we present an approximation
algorithm for the graph diameter which requires Õ(n/D) symbolic steps to achieve
a (1 +ϵ)-approximation for any constant > 0. This compares to O(n/D) symbolic
steps for the (naive) exact algorithm and O(D) symbolic steps for a 2-approximation.
Finally we also give a refined analysis of the strongly connected components algorithms
of [15], showing that it uses an optimal number of symbolic steps that is proportional
to the sum of the diameters of the strongly connected components.
article_processing_charge: No
author:
- first_name: Krishnendu
full_name: Chatterjee, Krishnendu
id: 2E5DCA20-F248-11E8-B48F-1D18A9856A87
last_name: Chatterjee
orcid: 0000-0002-4561-241X
- first_name: Wolfgang
full_name: Dvorák, Wolfgang
last_name: Dvorák
- first_name: Monika H
full_name: Henzinger, Monika H
id: 540c9bbd-f2de-11ec-812d-d04a5be85630
last_name: Henzinger
orcid: 0000-0002-5008-6530
- first_name: Veronika
full_name: Loitzenbauer, Veronika
last_name: Loitzenbauer
citation:
ama: 'Chatterjee K, Dvorák W, Henzinger MH, Loitzenbauer V. Lower bounds for symbolic
computation on graphs: Strongly connected components, liveness, safety, and diameter.
In: ACM; 2018:2341-2356. doi:10.1137/1.9781611975031.151'
apa: 'Chatterjee, K., Dvorák, W., Henzinger, M. H., & Loitzenbauer, V. (2018).
Lower bounds for symbolic computation on graphs: Strongly connected components,
liveness, safety, and diameter (pp. 2341–2356). Presented at the SODA: Symposium
on Discrete Algorithms, New Orleans, Louisiana, United States: ACM. https://doi.org/10.1137/1.9781611975031.151'
chicago: 'Chatterjee, Krishnendu, Wolfgang Dvorák, Monika H Henzinger, and Veronika
Loitzenbauer. “Lower Bounds for Symbolic Computation on Graphs: Strongly Connected
Components, Liveness, Safety, and Diameter,” 2341–56. ACM, 2018. https://doi.org/10.1137/1.9781611975031.151.'
ieee: 'K. Chatterjee, W. Dvorák, M. H. Henzinger, and V. Loitzenbauer, “Lower bounds
for symbolic computation on graphs: Strongly connected components, liveness, safety,
and diameter,” presented at the SODA: Symposium on Discrete Algorithms, New Orleans,
Louisiana, United States, 2018, pp. 2341–2356.'
ista: 'Chatterjee K, Dvorák W, Henzinger MH, Loitzenbauer V. 2018. Lower bounds
for symbolic computation on graphs: Strongly connected components, liveness, safety,
and diameter. SODA: Symposium on Discrete Algorithms, 2341–2356.'
mla: 'Chatterjee, Krishnendu, et al. Lower Bounds for Symbolic Computation on
Graphs: Strongly Connected Components, Liveness, Safety, and Diameter. ACM,
2018, pp. 2341–56, doi:10.1137/1.9781611975031.151.'
short: K. Chatterjee, W. Dvorák, M.H. Henzinger, V. Loitzenbauer, in:, ACM, 2018,
pp. 2341–2356.
conference:
end_date: 2018-01-10
location: New Orleans, Louisiana, United States
name: 'SODA: Symposium on Discrete Algorithms'
start_date: 2018-01-07
date_created: 2018-12-11T11:45:45Z
date_published: 2018-01-01T00:00:00Z
date_updated: 2023-09-13T08:50:16Z
day: '01'
department:
- _id: KrCh
doi: 10.1137/1.9781611975031.151
ec_funded: 1
external_id:
arxiv:
- '1711.09148'
isi:
- '000483921200152'
isi: 1
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/1711.09148
month: '01'
oa: 1
oa_version: Preprint
page: 2341 - 2356
project:
- _id: 25832EC2-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: S 11407_N23
name: Rigorous Systems Engineering
- _id: 2581B60A-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '279307'
name: 'Quantitative Graph Games: Theory and Applications'
- _id: 25892FC0-B435-11E9-9278-68D0E5697425
grant_number: ICT15-003
name: Efficient Algorithms for Computer Aided Verification
publication_status: published
publisher: ACM
publist_id: '7555'
quality_controlled: '1'
scopus_import: '1'
status: public
title: 'Lower bounds for symbolic computation on graphs: Strongly connected components,
liveness, safety, and diameter'
type: conference
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
year: '2018'
...
---
_id: '436'
abstract:
- lang: eng
text: There has been significant interest recently in using complex quantum systems
to create effective nonreciprocal dynamics. Proposals have been put forward for
the realization of artificial magnetic fields for photons and phonons; experimental
progress is fast making these proposals a reality. Much work has concentrated
on the use of such systems for controlling the flow of signals, e.g., to create
isolators or directional amplifiers for optical signals. In this Letter, we build
on this work but move in a different direction. We develop the theory of and discuss
a potential realization for the controllable flow of thermal noise in quantum
systems. We demonstrate theoretically that the unidirectional flow of thermal
noise is possible within quantum cascaded systems. Viewing an optomechanical platform
as a cascaded system we show here that one can ultimately control the direction
of the flow of thermal noise. By appropriately engineering the mechanical resonator,
which acts as an artificial reservoir, the flow of thermal noise can be constrained
to a desired direction, yielding a thermal rectifier. The proposed quantum thermal
noise rectifier could potentially be used to develop devices such as a thermal
modulator, a thermal router, and a thermal amplifier for nanoelectronic devices
and superconducting circuits.
article_number: '060601 '
article_processing_charge: No
author:
- first_name: Shabir
full_name: Barzanjeh, Shabir
id: 2D25E1F6-F248-11E8-B48F-1D18A9856A87
last_name: Barzanjeh
orcid: 0000-0003-0415-1423
- first_name: Matteo
full_name: Aquilina, Matteo
last_name: Aquilina
- first_name: André
full_name: Xuereb, André
last_name: Xuereb
citation:
ama: Barzanjeh S, Aquilina M, Xuereb A. Manipulating the flow of thermal noise in
quantum devices. Physical Review Letters. 2018;120(6). doi:10.1103/PhysRevLett.120.060601
apa: Barzanjeh, S., Aquilina, M., & Xuereb, A. (2018). Manipulating the flow
of thermal noise in quantum devices. Physical Review Letters. American
Physical Society. https://doi.org/10.1103/PhysRevLett.120.060601
chicago: Barzanjeh, Shabir, Matteo Aquilina, and André Xuereb. “Manipulating the
Flow of Thermal Noise in Quantum Devices.” Physical Review Letters. American
Physical Society, 2018. https://doi.org/10.1103/PhysRevLett.120.060601.
ieee: S. Barzanjeh, M. Aquilina, and A. Xuereb, “Manipulating the flow of thermal
noise in quantum devices,” Physical Review Letters, vol. 120, no. 6. American
Physical Society, 2018.
ista: Barzanjeh S, Aquilina M, Xuereb A. 2018. Manipulating the flow of thermal
noise in quantum devices. Physical Review Letters. 120(6), 060601.
mla: Barzanjeh, Shabir, et al. “Manipulating the Flow of Thermal Noise in Quantum
Devices.” Physical Review Letters, vol. 120, no. 6, 060601, American Physical
Society, 2018, doi:10.1103/PhysRevLett.120.060601.
short: S. Barzanjeh, M. Aquilina, A. Xuereb, Physical Review Letters 120 (2018).
date_created: 2018-12-11T11:46:28Z
date_published: 2018-02-07T00:00:00Z
date_updated: 2023-09-13T08:52:27Z
day: '07'
department:
- _id: JoFi
doi: 10.1103/PhysRevLett.120.060601
ec_funded: 1
external_id:
arxiv:
- '1706.09051'
isi:
- '000424382100004'
intvolume: ' 120'
isi: 1
issue: '6'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/1706.09051
month: '02'
oa: 1
oa_version: Preprint
project:
- _id: 257EB838-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '732894'
name: Hybrid Optomechanical Technologies
- _id: 258047B6-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '707438'
name: 'Microwave-to-Optical Quantum Link: Quantum Teleportation and Quantum Illumination
with cavity Optomechanics SUPEREOM'
publication: Physical Review Letters
publication_status: published
publisher: American Physical Society
publist_id: '7387'
quality_controlled: '1'
related_material:
link:
- description: News on IST Homepage
relation: press_release
url: https://ist.ac.at/en/news/interference-as-a-new-method-for-cooling-quantum-devices/
scopus_import: '1'
status: public
title: Manipulating the flow of thermal noise in quantum devices
type: journal_article
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
volume: 120
year: '2018'
...
---
_id: '5858'
abstract:
- lang: eng
text: Spatial patterns are ubiquitous on the subcellular, cellular and tissue level,
and can be studied using imaging techniques such as light and fluorescence microscopy.
Imaging data provide quantitative information about biological systems; however,
mechanisms causing spatial patterning often remain elusive. In recent years, spatio-temporal
mathematical modelling has helped to overcome this problem. Yet, outliers and
structured noise limit modelling of whole imaging data, and models often consider
spatial summary statistics. Here, we introduce an integrated data-driven modelling
approach that can cope with measurement artefacts and whole imaging data. Our
approach combines mechanistic models of the biological processes with robust statistical
models of the measurement process. The parameters of the integrated model are
calibrated using a maximum-likelihood approach. We used this integrated modelling
approach to study in vivo gradients of the chemokine (C-C motif) ligand 21 (CCL21).
CCL21 gradients guide dendritic cells and are important in the adaptive immune
response. Using artificial data, we verified that the integrated modelling approach
provides reliable parameter estimates in the presence of measurement noise and
that bias and variance of these estimates are reduced compared to conventional
approaches. The application to experimental data allowed the parametrization and
subsequent refinement of the model using additional mechanisms. Among other results,
model-based hypothesis testing predicted lymphatic vessel-dependent concentration
of heparan sulfate, the binding partner of CCL21. The selected model provided
an accurate description of the experimental data and was partially validated using
published data. Our findings demonstrate that integrated statistical modelling
of whole imaging data is computationally feasible and can provide novel biological
insights.
article_number: '20180600'
article_processing_charge: No
author:
- first_name: Sabrina
full_name: Hross, Sabrina
last_name: Hross
- first_name: Fabian J.
full_name: Theis, Fabian J.
last_name: Theis
- first_name: Michael K
full_name: Sixt, Michael K
id: 41E9FBEA-F248-11E8-B48F-1D18A9856A87
last_name: Sixt
orcid: 0000-0002-6620-9179
- first_name: Jan
full_name: Hasenauer, Jan
last_name: Hasenauer
citation:
ama: Hross S, Theis FJ, Sixt MK, Hasenauer J. Mechanistic description of spatial
processes using integrative modelling of noise-corrupted imaging data. Journal
of the Royal Society Interface. 2018;15(149). doi:10.1098/rsif.2018.0600
apa: Hross, S., Theis, F. J., Sixt, M. K., & Hasenauer, J. (2018). Mechanistic
description of spatial processes using integrative modelling of noise-corrupted
imaging data. Journal of the Royal Society Interface. Royal Society Publishing.
https://doi.org/10.1098/rsif.2018.0600
chicago: Hross, Sabrina, Fabian J. Theis, Michael K Sixt, and Jan Hasenauer. “Mechanistic
Description of Spatial Processes Using Integrative Modelling of Noise-Corrupted
Imaging Data.” Journal of the Royal Society Interface. Royal Society Publishing,
2018. https://doi.org/10.1098/rsif.2018.0600.
ieee: S. Hross, F. J. Theis, M. K. Sixt, and J. Hasenauer, “Mechanistic description
of spatial processes using integrative modelling of noise-corrupted imaging data,”
Journal of the Royal Society Interface, vol. 15, no. 149. Royal Society
Publishing, 2018.
ista: Hross S, Theis FJ, Sixt MK, Hasenauer J. 2018. Mechanistic description of
spatial processes using integrative modelling of noise-corrupted imaging data.
Journal of the Royal Society Interface. 15(149), 20180600.
mla: Hross, Sabrina, et al. “Mechanistic Description of Spatial Processes Using
Integrative Modelling of Noise-Corrupted Imaging Data.” Journal of the Royal
Society Interface, vol. 15, no. 149, 20180600, Royal Society Publishing, 2018,
doi:10.1098/rsif.2018.0600.
short: S. Hross, F.J. Theis, M.K. Sixt, J. Hasenauer, Journal of the Royal Society
Interface 15 (2018).
date_created: 2019-01-20T22:59:18Z
date_published: 2018-12-05T00:00:00Z
date_updated: 2023-09-13T08:55:05Z
day: '05'
ddc:
- '570'
department:
- _id: MiSi
doi: 10.1098/rsif.2018.0600
external_id:
isi:
- '000456783800011'
file:
- access_level: open_access
checksum: 56eb4308a15b7190bff938fab1f780e8
content_type: application/pdf
creator: dernst
date_created: 2019-02-05T14:46:44Z
date_updated: 2020-07-14T12:47:13Z
file_id: '5925'
file_name: 2018_Interface_Hross.pdf
file_size: 1464288
relation: main_file
file_date_updated: 2020-07-14T12:47:13Z
has_accepted_license: '1'
intvolume: ' 15'
isi: 1
issue: '149'
language:
- iso: eng
license: https://creativecommons.org/licenses/by/4.0/
month: '12'
oa: 1
oa_version: Published Version
publication: Journal of the Royal Society Interface
publication_identifier:
issn:
- '17425689'
publication_status: published
publisher: Royal Society Publishing
quality_controlled: '1'
scopus_import: '1'
status: public
title: Mechanistic description of spatial processes using integrative modelling of
noise-corrupted imaging data
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: journal_article
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
volume: 15
year: '2018'
...
---
_id: '16'
abstract:
- lang: eng
text: We report quantitative evidence of mixing-layer elastic instability in a viscoelastic
fluid flow between two widely spaced obstacles hindering a channel flow at Re
1 and Wi 1. Two mixing layers with nonuniform shear velocity profiles are formed
in the region between the obstacles. The mixing-layer instability arises in the
vicinity of an inflection point on the shear velocity profile with a steep variation
in the elastic stress. The instability results in an intermittent appearance of
small vortices in the mixing layers and an amplification of spatiotemporal averaged
vorticity in the elastic turbulence regime. The latter is characterized through
scaling of friction factor with Wi and both pressure and velocity spectra. Furthermore,
the observations reported provide improved understanding of the stability of the
mixing layer in a viscoelastic fluid at large elasticity, i.e., Wi 1 and Re 1
and oppose the current view of suppression of vorticity solely by polymer additives.
acknowledgement: This work was partially supported by the Israel Science Foundation
(ISF; Grant No. 882/15) and the Binational USA-Israel Foundation (BSF; Grant No.
2016145).
article_number: '103303'
article_processing_charge: No
article_type: original
author:
- first_name: Atul
full_name: Varshney, Atul
id: 2A2006B2-F248-11E8-B48F-1D18A9856A87
last_name: Varshney
orcid: 0000-0002-3072-5999
- first_name: Victor
full_name: Steinberg, Victor
last_name: Steinberg
citation:
ama: Varshney A, Steinberg V. Mixing layer instability and vorticity amplification
in a creeping viscoelastic flow. Physical Review Fluids. 2018;3(10). doi:10.1103/PhysRevFluids.3.103303
apa: Varshney, A., & Steinberg, V. (2018). Mixing layer instability and vorticity
amplification in a creeping viscoelastic flow. Physical Review Fluids.
American Physical Society. https://doi.org/10.1103/PhysRevFluids.3.103303
chicago: Varshney, Atul, and Victor Steinberg. “Mixing Layer Instability and Vorticity
Amplification in a Creeping Viscoelastic Flow.” Physical Review Fluids.
American Physical Society, 2018. https://doi.org/10.1103/PhysRevFluids.3.103303.
ieee: A. Varshney and V. Steinberg, “Mixing layer instability and vorticity amplification
in a creeping viscoelastic flow,” Physical Review Fluids, vol. 3, no. 10.
American Physical Society, 2018.
ista: Varshney A, Steinberg V. 2018. Mixing layer instability and vorticity amplification
in a creeping viscoelastic flow. Physical Review Fluids. 3(10), 103303.
mla: Varshney, Atul, and Victor Steinberg. “Mixing Layer Instability and Vorticity
Amplification in a Creeping Viscoelastic Flow.” Physical Review Fluids,
vol. 3, no. 10, 103303, American Physical Society, 2018, doi:10.1103/PhysRevFluids.3.103303.
short: A. Varshney, V. Steinberg, Physical Review Fluids 3 (2018).
date_created: 2018-12-11T11:44:10Z
date_published: 2018-10-16T00:00:00Z
date_updated: 2023-09-13T08:57:05Z
day: '16'
ddc:
- '532'
department:
- _id: BjHo
doi: 10.1103/PhysRevFluids.3.103303
ec_funded: 1
external_id:
isi:
- '000447469200001'
file:
- access_level: open_access
checksum: 7fc0a2322214d1c04debef36d5bf2e8a
content_type: application/pdf
creator: system
date_created: 2018-12-12T10:13:56Z
date_updated: 2020-07-14T12:45:04Z
file_id: '5043'
file_name: IST-2018-1062-v1+1_PhysRevFluids.3.103303.pdf
file_size: 1838431
relation: main_file
file_date_updated: 2020-07-14T12:45:04Z
has_accepted_license: '1'
intvolume: ' 3'
isi: 1
issue: '10'
language:
- iso: eng
month: '10'
oa: 1
oa_version: Submitted Version
project:
- _id: 260C2330-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '754411'
name: ISTplus - Postdoctoral Fellowships
publication: Physical Review Fluids
publication_status: published
publisher: American Physical Society
publist_id: '8039'
pubrep_id: '1062'
quality_controlled: '1'
scopus_import: '1'
status: public
title: Mixing layer instability and vorticity amplification in a creeping viscoelastic
flow
type: journal_article
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
volume: 3
year: '2018'
...
---
_id: '43'
abstract:
- lang: eng
text: 'The initial amount of pathogens required to start an infection within a susceptible
host is called the infective dose and is known to vary to a large extent between
different pathogen species. We investigate the hypothesis that the differences
in infective doses are explained by the mode of action in the underlying mechanism
of pathogenesis: Pathogens with locally acting mechanisms tend to have smaller
infective doses than pathogens with distantly acting mechanisms. While empirical
evidence tends to support the hypothesis, a formal theoretical explanation has
been lacking. We give simple analytical models to gain insight into this phenomenon
and also investigate a stochastic, spatially explicit, mechanistic within-host
model for toxin-dependent bacterial infections. The model shows that pathogens
secreting locally acting toxins have smaller infective doses than pathogens secreting
diffusive toxins, as hypothesized. While local pathogenetic mechanisms require
smaller infective doses, pathogens with distantly acting toxins tend to spread
faster and may cause more damage to the host. The proposed model can serve as
a basis for the spatially explicit analysis of various virulence factors also
in the context of other problems in infection dynamics.'
acknowledgement: J.R. and J.V.A. were also supported by the Academy of Finland Grants
1273253 and 267541.
article_processing_charge: No
author:
- first_name: Joel
full_name: Rybicki, Joel
id: 334EFD2E-F248-11E8-B48F-1D18A9856A87
last_name: Rybicki
orcid: 0000-0002-6432-6646
- first_name: Eva
full_name: Kisdi, Eva
last_name: Kisdi
- first_name: Jani
full_name: Anttila, Jani
last_name: Anttila
citation:
ama: Rybicki J, Kisdi E, Anttila J. Model of bacterial toxin-dependent pathogenesis
explains infective dose. PNAS. 2018;115(42):10690-10695. doi:10.1073/pnas.1721061115
apa: Rybicki, J., Kisdi, E., & Anttila, J. (2018). Model of bacterial toxin-dependent
pathogenesis explains infective dose. PNAS. National Academy of Sciences.
https://doi.org/10.1073/pnas.1721061115
chicago: Rybicki, Joel, Eva Kisdi, and Jani Anttila. “Model of Bacterial Toxin-Dependent
Pathogenesis Explains Infective Dose.” PNAS. National Academy of Sciences,
2018. https://doi.org/10.1073/pnas.1721061115.
ieee: J. Rybicki, E. Kisdi, and J. Anttila, “Model of bacterial toxin-dependent
pathogenesis explains infective dose,” PNAS, vol. 115, no. 42. National
Academy of Sciences, pp. 10690–10695, 2018.
ista: Rybicki J, Kisdi E, Anttila J. 2018. Model of bacterial toxin-dependent pathogenesis
explains infective dose. PNAS. 115(42), 10690–10695.
mla: Rybicki, Joel, et al. “Model of Bacterial Toxin-Dependent Pathogenesis Explains
Infective Dose.” PNAS, vol. 115, no. 42, National Academy of Sciences,
2018, pp. 10690–95, doi:10.1073/pnas.1721061115.
short: J. Rybicki, E. Kisdi, J. Anttila, PNAS 115 (2018) 10690–10695.
date_created: 2018-12-11T11:44:19Z
date_published: 2018-10-02T00:00:00Z
date_updated: 2023-09-13T08:57:38Z
day: '02'
ddc:
- '570'
- '577'
department:
- _id: DaAl
doi: 10.1073/pnas.1721061115
ec_funded: 1
external_id:
isi:
- '000447491300057'
file:
- access_level: open_access
checksum: df7ac544a587c06b75692653b9fabd18
content_type: application/pdf
creator: dernst
date_created: 2019-04-09T08:02:50Z
date_updated: 2020-07-14T12:46:26Z
file_id: '6258'
file_name: 2018_PNAS_Rybicki.pdf
file_size: 4070777
relation: main_file
file_date_updated: 2020-07-14T12:46:26Z
has_accepted_license: '1'
intvolume: ' 115'
isi: 1
issue: '42'
language:
- iso: eng
month: '10'
oa: 1
oa_version: Submitted Version
page: 10690 - 10695
project:
- _id: 260C2330-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '754411'
name: ISTplus - Postdoctoral Fellowships
publication: PNAS
publication_status: published
publisher: National Academy of Sciences
publist_id: '8011'
pubrep_id: '1063'
quality_controlled: '1'
scopus_import: '1'
status: public
title: Model of bacterial toxin-dependent pathogenesis explains infective dose
type: journal_article
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
volume: 115
year: '2018'
...
---
_id: '13'
abstract:
- lang: eng
text: We propose a new method for fabricating digital objects through reusable silicone
molds. Molds are generated by casting liquid silicone into custom 3D printed containers
called metamolds. Metamolds automatically define the cuts that are needed to extract
the cast object from the silicone mold. The shape of metamolds is designed through
a novel segmentation technique, which takes into account both geometric and topological
constraints involved in the process of mold casting. Our technique is simple,
does not require changing the shape or topology of the input objects, and only
requires off-the- shelf materials and technologies. We successfully tested our
method on a set of challenging examples with complex shapes and rich geometric
detail. © 2018 Association for Computing Machinery.
article_number: '136'
article_processing_charge: No
author:
- first_name: Thomas
full_name: Alderighi, Thomas
last_name: Alderighi
- first_name: Luigi
full_name: Malomo, Luigi
last_name: Malomo
- first_name: Daniela
full_name: Giorgi, Daniela
last_name: Giorgi
- first_name: Nico
full_name: Pietroni, Nico
last_name: Pietroni
- first_name: Bernd
full_name: Bickel, Bernd
id: 49876194-F248-11E8-B48F-1D18A9856A87
last_name: Bickel
orcid: 0000-0001-6511-9385
- first_name: Paolo
full_name: Cignoni, Paolo
last_name: Cignoni
citation:
ama: 'Alderighi T, Malomo L, Giorgi D, Pietroni N, Bickel B, Cignoni P. Metamolds:
Computational design of silicone molds. ACM Trans Graph. 2018;37(4). doi:10.1145/3197517.3201381'
apa: 'Alderighi, T., Malomo, L., Giorgi, D., Pietroni, N., Bickel, B., & Cignoni,
P. (2018). Metamolds: Computational design of silicone molds. ACM Trans. Graph.
ACM. https://doi.org/10.1145/3197517.3201381'
chicago: 'Alderighi, Thomas, Luigi Malomo, Daniela Giorgi, Nico Pietroni, Bernd
Bickel, and Paolo Cignoni. “Metamolds: Computational Design of Silicone Molds.”
ACM Trans. Graph. ACM, 2018. https://doi.org/10.1145/3197517.3201381.'
ieee: 'T. Alderighi, L. Malomo, D. Giorgi, N. Pietroni, B. Bickel, and P. Cignoni,
“Metamolds: Computational design of silicone molds,” ACM Trans. Graph.,
vol. 37, no. 4. ACM, 2018.'
ista: 'Alderighi T, Malomo L, Giorgi D, Pietroni N, Bickel B, Cignoni P. 2018. Metamolds:
Computational design of silicone molds. ACM Trans. Graph. 37(4), 136.'
mla: 'Alderighi, Thomas, et al. “Metamolds: Computational Design of Silicone Molds.”
ACM Trans. Graph., vol. 37, no. 4, 136, ACM, 2018, doi:10.1145/3197517.3201381.'
short: T. Alderighi, L. Malomo, D. Giorgi, N. Pietroni, B. Bickel, P. Cignoni, ACM
Trans. Graph. 37 (2018).
date_created: 2018-12-11T11:44:09Z
date_published: 2018-08-04T00:00:00Z
date_updated: 2023-09-13T08:56:07Z
day: '04'
ddc:
- '004'
department:
- _id: BeBi
doi: 10.1145/3197517.3201381
ec_funded: 1
external_id:
isi:
- '000448185000097'
file:
- access_level: open_access
checksum: 61d46273dca4de626accef1d17a0aaad
content_type: application/pdf
creator: system
date_created: 2018-12-12T10:18:52Z
date_updated: 2020-07-14T12:44:43Z
file_id: '5374'
file_name: IST-2018-1038-v1+1_metamolds_authorversion.pdf
file_size: 91939066
relation: main_file
file_date_updated: 2020-07-14T12:44:43Z
has_accepted_license: '1'
intvolume: ' 37'
isi: 1
issue: '4'
language:
- iso: eng
month: '08'
oa: 1
oa_version: Submitted Version
project:
- _id: 24F9549A-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '715767'
name: 'MATERIALIZABLE: Intelligent fabrication-oriented Computational Design and
Modeling'
publication: ACM Trans. Graph.
publication_status: published
publisher: ACM
publist_id: '8043'
pubrep_id: '1038'
quality_controlled: '1'
related_material:
link:
- description: News on IST Homepage
relation: press_release
url: https://ist.ac.at/en/news/metamolds-molding-a-mold/
scopus_import: '1'
status: public
title: 'Metamolds: Computational design of silicone molds'
type: journal_article
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
volume: 37
year: '2018'
...
---
_id: '137'
abstract:
- lang: eng
text: Fluorescent sensors are an essential part of the experimental toolbox of the
life sciences, where they are used ubiquitously to visualize intra- and extracellular
signaling. In the brain, optical neurotransmitter sensors can shed light on temporal
and spatial aspects of signal transmission by directly observing, for instance,
neurotransmitter release and spread. Here we report the development and application
of the first optical sensor for the amino acid glycine, which is both an inhibitory
neurotransmitter and a co-agonist of the N-methyl-d-aspartate receptors (NMDARs)
involved in synaptic plasticity. Computational design of a glycine-specific binding
protein allowed us to produce the optical glycine FRET sensor (GlyFS), which can
be used with single and two-photon excitation fluorescence microscopy. We took
advantage of this newly developed sensor to test predictions about the uneven
spatial distribution of glycine in extracellular space and to demonstrate that
extracellular glycine levels are controlled by plasticity-inducing stimuli.
article_processing_charge: No
article_type: original
author:
- first_name: William
full_name: Zhang, William
last_name: Zhang
- first_name: Michel
full_name: Herde, Michel
last_name: Herde
- first_name: Joshua
full_name: Mitchell, Joshua
last_name: Mitchell
- first_name: Jason
full_name: Whitfield, Jason
last_name: Whitfield
- first_name: Andreas
full_name: Wulff, Andreas
last_name: Wulff
- first_name: Vanessa
full_name: Vongsouthi, Vanessa
last_name: Vongsouthi
- first_name: Inmaculada
full_name: Sanchez Romero, Inmaculada
id: 3D9C5D30-F248-11E8-B48F-1D18A9856A87
last_name: Sanchez Romero
- first_name: Polina
full_name: Gulakova, Polina
last_name: Gulakova
- first_name: Daniel
full_name: Minge, Daniel
last_name: Minge
- first_name: Björn
full_name: Breithausen, Björn
last_name: Breithausen
- first_name: Susanne
full_name: Schoch, Susanne
last_name: Schoch
- first_name: Harald L
full_name: Janovjak, Harald L
id: 33BA6C30-F248-11E8-B48F-1D18A9856A87
last_name: Janovjak
orcid: 0000-0002-8023-9315
- first_name: Colin
full_name: Jackson, Colin
last_name: Jackson
- first_name: Christian
full_name: Henneberger, Christian
last_name: Henneberger
citation:
ama: Zhang W, Herde M, Mitchell J, et al. Monitoring hippocampal glycine with the
computationally designed optical sensor GlyFS. Nature Chemical Biology.
2018;14(9):861-869. doi:10.1038/s41589-018-0108-2
apa: Zhang, W., Herde, M., Mitchell, J., Whitfield, J., Wulff, A., Vongsouthi, V.,
… Henneberger, C. (2018). Monitoring hippocampal glycine with the computationally
designed optical sensor GlyFS. Nature Chemical Biology. Nature Publishing
Group. https://doi.org/10.1038/s41589-018-0108-2
chicago: Zhang, William, Michel Herde, Joshua Mitchell, Jason Whitfield, Andreas
Wulff, Vanessa Vongsouthi, Inmaculada Sanchez-Romero, et al. “Monitoring Hippocampal
Glycine with the Computationally Designed Optical Sensor GlyFS.” Nature Chemical
Biology. Nature Publishing Group, 2018. https://doi.org/10.1038/s41589-018-0108-2.
ieee: W. Zhang et al., “Monitoring hippocampal glycine with the computationally
designed optical sensor GlyFS,” Nature Chemical Biology, vol. 14, no. 9.
Nature Publishing Group, pp. 861–869, 2018.
ista: Zhang W, Herde M, Mitchell J, Whitfield J, Wulff A, Vongsouthi V, Sanchez-Romero
I, Gulakova P, Minge D, Breithausen B, Schoch S, Janovjak HL, Jackson C, Henneberger
C. 2018. Monitoring hippocampal glycine with the computationally designed optical
sensor GlyFS. Nature Chemical Biology. 14(9), 861–869.
mla: Zhang, William, et al. “Monitoring Hippocampal Glycine with the Computationally
Designed Optical Sensor GlyFS.” Nature Chemical Biology, vol. 14, no. 9,
Nature Publishing Group, 2018, pp. 861–69, doi:10.1038/s41589-018-0108-2.
short: W. Zhang, M. Herde, J. Mitchell, J. Whitfield, A. Wulff, V. Vongsouthi, I.
Sanchez-Romero, P. Gulakova, D. Minge, B. Breithausen, S. Schoch, H.L. Janovjak,
C. Jackson, C. Henneberger, Nature Chemical Biology 14 (2018) 861–869.
date_created: 2018-12-11T11:44:49Z
date_published: 2018-07-30T00:00:00Z
date_updated: 2023-09-13T08:58:05Z
day: '30'
department:
- _id: HaJa
doi: 10.1038/s41589-018-0108-2
external_id:
isi:
- '000442174500013'
pmid:
- '30061718 '
intvolume: ' 14'
isi: 1
issue: '9'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://www.ncbi.nlm.nih.gov/pubmed/30061718
month: '07'
oa: 1
oa_version: Submitted Version
page: 861 - 869
pmid: 1
project:
- _id: 255BFFFA-B435-11E9-9278-68D0E5697425
grant_number: RGY0084/2012
name: In situ real-time imaging of neurotransmitter signaling using designer optical
sensors (HFSP Young Investigator)
publication: Nature Chemical Biology
publication_status: published
publisher: Nature Publishing Group
publist_id: '7786'
quality_controlled: '1'
scopus_import: '1'
status: public
title: Monitoring hippocampal glycine with the computationally designed optical sensor
GlyFS
type: journal_article
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
volume: 14
year: '2018'
...
---
_id: '153'
abstract:
- lang: eng
text: Cells migrating in multicellular organisms steadily traverse complex three-dimensional
(3D) environments. To decipher the underlying cell biology, current experimental
setups either use simplified 2D, tissue-mimetic 3D (e.g., collagen matrices) or
in vivo environments. While only in vivo experiments are truly physiological,
they do not allow for precise manipulation of environmental parameters. 2D in
vitro experiments do allow mechanical and chemical manipulations, but increasing
evidence demonstrates substantial differences of migratory mechanisms in 2D and
3D. Here, we describe simple, robust, and versatile “pillar forests” to investigate
cell migration in complex but fully controllable 3D environments. Pillar forests
are polydimethylsiloxane-based setups, in which two closely adjacent surfaces
are interconnected by arrays of micrometer-sized pillars. Changing the pillar
shape, size, height and the inter-pillar distance precisely manipulates microenvironmental
parameters (e.g., pore sizes, micro-geometry, micro-topology), while being easily
combined with chemotactic cues, surface coatings, diverse cell types and advanced
imaging techniques. Thus, pillar forests combine the advantages of 2D cell migration
assays with the precise definition of 3D environmental parameters.
article_processing_charge: No
author:
- first_name: Jörg
full_name: Renkawitz, Jörg
id: 3F0587C8-F248-11E8-B48F-1D18A9856A87
last_name: Renkawitz
orcid: 0000-0003-2856-3369
- first_name: Anne
full_name: Reversat, Anne
id: 35B76592-F248-11E8-B48F-1D18A9856A87
last_name: Reversat
orcid: 0000-0003-0666-8928
- first_name: Alexander F
full_name: Leithner, Alexander F
id: 3B1B77E4-F248-11E8-B48F-1D18A9856A87
last_name: Leithner
orcid: 0000-0002-1073-744X
- first_name: Jack
full_name: Merrin, Jack
id: 4515C308-F248-11E8-B48F-1D18A9856A87
last_name: Merrin
orcid: 0000-0001-5145-4609
- first_name: Michael K
full_name: Sixt, Michael K
id: 41E9FBEA-F248-11E8-B48F-1D18A9856A87
last_name: Sixt
orcid: 0000-0002-6620-9179
citation:
ama: 'Renkawitz J, Reversat A, Leithner AF, Merrin J, Sixt MK. Micro-engineered
“pillar forests” to study cell migration in complex but controlled 3D environments.
In: Methods in Cell Biology. Vol 147. Academic Press; 2018:79-91. doi:10.1016/bs.mcb.2018.07.004'
apa: Renkawitz, J., Reversat, A., Leithner, A. F., Merrin, J., & Sixt, M. K.
(2018). Micro-engineered “pillar forests” to study cell migration in complex but
controlled 3D environments. In Methods in Cell Biology (Vol. 147, pp. 79–91).
Academic Press. https://doi.org/10.1016/bs.mcb.2018.07.004
chicago: Renkawitz, Jörg, Anne Reversat, Alexander F Leithner, Jack Merrin, and
Michael K Sixt. “Micro-Engineered ‘Pillar Forests’ to Study Cell Migration in
Complex but Controlled 3D Environments.” In Methods in Cell Biology, 147:79–91.
Academic Press, 2018. https://doi.org/10.1016/bs.mcb.2018.07.004.
ieee: J. Renkawitz, A. Reversat, A. F. Leithner, J. Merrin, and M. K. Sixt, “Micro-engineered
‘pillar forests’ to study cell migration in complex but controlled 3D environments,”
in Methods in Cell Biology, vol. 147, Academic Press, 2018, pp. 79–91.
ista: 'Renkawitz J, Reversat A, Leithner AF, Merrin J, Sixt MK. 2018.Micro-engineered
“pillar forests” to study cell migration in complex but controlled 3D environments.
In: Methods in Cell Biology. vol. 147, 79–91.'
mla: Renkawitz, Jörg, et al. “Micro-Engineered ‘Pillar Forests’ to Study Cell Migration
in Complex but Controlled 3D Environments.” Methods in Cell Biology, vol.
147, Academic Press, 2018, pp. 79–91, doi:10.1016/bs.mcb.2018.07.004.
short: J. Renkawitz, A. Reversat, A.F. Leithner, J. Merrin, M.K. Sixt, in:, Methods
in Cell Biology, Academic Press, 2018, pp. 79–91.
date_created: 2018-12-11T11:44:54Z
date_published: 2018-07-27T00:00:00Z
date_updated: 2023-09-13T08:56:35Z
day: '27'
department:
- _id: MiSi
- _id: NanoFab
doi: 10.1016/bs.mcb.2018.07.004
external_id:
isi:
- '000452412300006'
pmid:
- '30165964'
intvolume: ' 147'
isi: 1
language:
- iso: eng
month: '07'
oa_version: None
page: 79 - 91
pmid: 1
publication: Methods in Cell Biology
publication_identifier:
issn:
- 0091679X
publication_status: published
publisher: Academic Press
publist_id: '7768'
quality_controlled: '1'
scopus_import: '1'
status: public
title: Micro-engineered “pillar forests” to study cell migration in complex but controlled
3D environments
type: book_chapter
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
volume: 147
year: '2018'
...
---
_id: '54'
abstract:
- lang: eng
text: During epithelial tissue development, repair, and homeostasis, adherens junctions
(AJs) ensure intercellular adhesion and tissue integrity while allowing for cell
and tissue dynamics. Mechanical forces play critical roles in AJs’ composition
and dynamics. Recent findings highlight that beyond a well-established role in
reinforcing cell-cell adhesion, AJ mechanosensitivity promotes junctional remodeling
and polarization, thereby regulating critical processes such as cell intercalation,
division, and collective migration. Here, we provide an integrated view of mechanosensing
mechanisms that regulate cell-cell contact composition, geometry, and integrity
under tension and highlight pivotal roles for mechanosensitive AJ remodeling in
preserving epithelial integrity and sustaining tissue dynamics.
acknowledgement: Research in the Bellaïche laboratory is supported by the European
Research Council (ERC Advanced, TiMoprh, 340784), the Fondation ARC pour la Recherche
sur le Cancer (SL220130607097), the Agence Nationale de la Recherche (ANR lLabex
DEEP; 11-LBX-0044, ANR-10-IDEX-0001-02), the Centre National de la Recherche Scientifique,
the Institut National de la Santé et de la Recherche Médicale, and Institut Curie
and PSL Research University funding or grants.
article_processing_charge: No
article_type: review
author:
- first_name: Diana C
full_name: Nunes Pinheiro, Diana C
id: 2E839F16-F248-11E8-B48F-1D18A9856A87
last_name: Nunes Pinheiro
orcid: 0000-0003-4333-7503
- first_name: Yohanns
full_name: Bellaïche, Yohanns
last_name: Bellaïche
citation:
ama: Nunes Pinheiro DC, Bellaïche Y. Mechanical force-driven adherents junction
remodeling and epithelial dynamics. Developmental Cell. 2018;47(1):3-19.
doi:10.1016/j.devcel.2018.09.014
apa: Nunes Pinheiro, D. C., & Bellaïche, Y. (2018). Mechanical force-driven
adherents junction remodeling and epithelial dynamics. Developmental Cell.
Cell Press. https://doi.org/10.1016/j.devcel.2018.09.014
chicago: Nunes Pinheiro, Diana C, and Yohanns Bellaïche. “Mechanical Force-Driven
Adherents Junction Remodeling and Epithelial Dynamics.” Developmental Cell.
Cell Press, 2018. https://doi.org/10.1016/j.devcel.2018.09.014.
ieee: D. C. Nunes Pinheiro and Y. Bellaïche, “Mechanical force-driven adherents
junction remodeling and epithelial dynamics,” Developmental Cell, vol.
47, no. 1. Cell Press, pp. 3–19, 2018.
ista: Nunes Pinheiro DC, Bellaïche Y. 2018. Mechanical force-driven adherents junction
remodeling and epithelial dynamics. Developmental Cell. 47(1), 3–19.
mla: Nunes Pinheiro, Diana C., and Yohanns Bellaïche. “Mechanical Force-Driven Adherents
Junction Remodeling and Epithelial Dynamics.” Developmental Cell, vol.
47, no. 1, Cell Press, 2018, pp. 3–19, doi:10.1016/j.devcel.2018.09.014.
short: D.C. Nunes Pinheiro, Y. Bellaïche, Developmental Cell 47 (2018) 3–19.
date_created: 2018-12-11T11:44:23Z
date_published: 2018-10-08T00:00:00Z
date_updated: 2023-09-13T08:54:38Z
day: '08'
department:
- _id: CaHe
doi: 10.1016/j.devcel.2018.09.014
external_id:
isi:
- '000446579900002'
intvolume: ' 47'
isi: 1
issue: '1'
language:
- iso: eng
main_file_link:
- url: https://doi.org/10.1016/j.devcel.2018.09.014
month: '10'
oa_version: Published Version
page: 3 - 19
publication: Developmental Cell
publication_status: published
publisher: Cell Press
publist_id: '8000'
quality_controlled: '1'
scopus_import: '1'
status: public
title: Mechanical force-driven adherents junction remodeling and epithelial dynamics
type: journal_article
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
volume: 47
year: '2018'
...
---
_id: '276'
abstract:
- lang: eng
text: Directed migration of cells relies on their ability to sense directional guidance
cues and to interact with pericellular structures in order to transduce contractile
cytoskeletal- into mechanical forces. These biomechanical processes depend highly
on microenvironmental factors such as exposure to 2D surfaces or 3D matrices.
In vivo, the majority of cells are exposed to 3D environments. Data on 3D cell
migration are mostly derived from intravital microscopy or collagen-based in vitro
assays. Both approaches offer only limited controlla-bility of experimental conditions.
Here, we developed an automated microfluidic system that allows positioning of
cells in 3D microenvironments containing highly controlled diffusion-based chemokine
gradients. Tracking migration in such gradients was feasible in real time at the
single cell level. Moreover, the setup allowed on-chip immunocytochemistry and
thus linking of functional with phenotypical properties in individual cells. Spatially
defined retrieval of cells from the device allows down-stream off-chip analysis.
Using dendritic cells as a model, our setup specifically allowed us for the first
time to quantitate key migration characteristics of cells exposed to identical
gradients of the chemokine CCL19 yet placed on 2D vs in 3D environments. Migration
properties between 2D and 3D migration were distinct. Morphological features of
cells migrating in an in vitro 3D environment were similar to those of cells migrating
in animal tissues, but different from cells migrating on a surface. Our system
thus offers a highly controllable in vitro-mimic of a 3D environment that cells
traffic in vivo.
acknowledgement: This work was supported by the Swiss National Science Foundation
(MD-PhD fellowships, 323530_164221 to C.F.; and 323630_151483 to A.J.; grant PZ00P3_144863
to M.R, grant 31003A_156431 to T.S.; PZ00P3_148000 to C.T.B.; PZ00P3_154733 to M.M.),
a Novartis “FreeNovation” grant to M.M. and T.S. and an EMBO long-term fellowship
(ALTF 1396-2014) co-funded by the European Commission (LTFCOFUND2013, GA-2013-609409)
to J.R.. M.R. was supported by the Gebert Rüf Foundation (GRS 058/14). The funders
had no role in study design, data collection and analysis, decision to publish,
or preparation of the manuscript.
article_number: e0198330
article_processing_charge: No
article_type: original
author:
- first_name: Corina
full_name: Frick, Corina
last_name: Frick
- first_name: Philip
full_name: Dettinger, Philip
last_name: Dettinger
- first_name: Jörg
full_name: Renkawitz, Jörg
id: 3F0587C8-F248-11E8-B48F-1D18A9856A87
last_name: Renkawitz
orcid: 0000-0003-2856-3369
- first_name: Annaïse
full_name: Jauch, Annaïse
last_name: Jauch
- first_name: Christoph
full_name: Berger, Christoph
last_name: Berger
- first_name: Mike
full_name: Recher, Mike
last_name: Recher
- first_name: Timm
full_name: Schroeder, Timm
last_name: Schroeder
- first_name: Matthias
full_name: Mehling, Matthias
last_name: Mehling
citation:
ama: Frick C, Dettinger P, Renkawitz J, et al. Nano-scale microfluidics to study
3D chemotaxis at the single cell level. PLoS One. 2018;13(6). doi:10.1371/journal.pone.0198330
apa: Frick, C., Dettinger, P., Renkawitz, J., Jauch, A., Berger, C., Recher, M.,
… Mehling, M. (2018). Nano-scale microfluidics to study 3D chemotaxis at the single
cell level. PLoS One. Public Library of Science. https://doi.org/10.1371/journal.pone.0198330
chicago: Frick, Corina, Philip Dettinger, Jörg Renkawitz, Annaïse Jauch, Christoph
Berger, Mike Recher, Timm Schroeder, and Matthias Mehling. “Nano-Scale Microfluidics
to Study 3D Chemotaxis at the Single Cell Level.” PLoS One. Public Library
of Science, 2018. https://doi.org/10.1371/journal.pone.0198330.
ieee: C. Frick et al., “Nano-scale microfluidics to study 3D chemotaxis at
the single cell level,” PLoS One, vol. 13, no. 6. Public Library of Science,
2018.
ista: Frick C, Dettinger P, Renkawitz J, Jauch A, Berger C, Recher M, Schroeder
T, Mehling M. 2018. Nano-scale microfluidics to study 3D chemotaxis at the single
cell level. PLoS One. 13(6), e0198330.
mla: Frick, Corina, et al. “Nano-Scale Microfluidics to Study 3D Chemotaxis at the
Single Cell Level.” PLoS One, vol. 13, no. 6, e0198330, Public Library
of Science, 2018, doi:10.1371/journal.pone.0198330.
short: C. Frick, P. Dettinger, J. Renkawitz, A. Jauch, C. Berger, M. Recher, T.
Schroeder, M. Mehling, PLoS One 13 (2018).
date_created: 2018-12-11T11:45:34Z
date_published: 2018-06-07T00:00:00Z
date_updated: 2023-09-13T09:00:15Z
day: '07'
ddc:
- '570'
department:
- _id: MiSi
doi: 10.1371/journal.pone.0198330
external_id:
isi:
- '000434384900031'
file:
- access_level: open_access
checksum: 95fc5dc3938b3ad3b7697d10c83cc143
content_type: application/pdf
creator: dernst
date_created: 2018-12-17T14:10:32Z
date_updated: 2020-07-14T12:45:45Z
file_id: '5709'
file_name: 2018_Plos_Frick.pdf
file_size: 7682167
relation: main_file
file_date_updated: 2020-07-14T12:45:45Z
has_accepted_license: '1'
intvolume: ' 13'
isi: 1
issue: '6'
language:
- iso: eng
month: '06'
oa: 1
oa_version: Published Version
publication: PLoS One
publication_status: published
publisher: Public Library of Science
publist_id: '7626'
quality_controlled: '1'
scopus_import: '1'
status: public
title: Nano-scale microfluidics to study 3D chemotaxis at the single cell level
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: journal_article
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
volume: 13
year: '2018'
...
---
_id: '283'
abstract:
- lang: eng
text: Light represents the principal signal driving circadian clock entrainment.
However, how light influences the evolution of the clock remains poorly understood.
The cavefish Phreatichthys andruzzii represents a fascinating model to explore
how evolution under extreme aphotic conditions shapes the circadian clock, since
in this species the clock is unresponsive to light. We have previously demonstrated
that loss-of-function mutations targeting non-visual opsins contribute in part
to this blind clock phenotype. Here, we have compared orthologs of two core clock
genes that play a key role in photic entrainment, cry1a and per2, in both zebrafish
and P. andruzzii. We encountered aberrantly spliced variants for the P. andruzzii
per2 transcript. The most abundant transcript encodes a truncated protein lacking
the C-terminal Cry binding domain and incorporating an intronic, transposon-derived
coding sequence. We demonstrate that the transposon insertion leads to a predominantly
cytoplasmic localization of the cavefish Per2 protein in contrast to the zebrafish
ortholog which is distributed in both the nucleus and cytoplasm. Thus, it seems
that during evolution in complete darkness, the photic entrainment pathway of
the circadian clock has been subject to mutation at multiple levels, extending
from opsin photoreceptors to nuclear effectors.
article_number: '8754'
article_processing_charge: No
author:
- first_name: Rosa Maria
full_name: Ceinos, Rosa Maria
last_name: Ceinos
- first_name: Elena
full_name: Frigato, Elena
last_name: Frigato
- first_name: Cristina
full_name: Pagano, Cristina
last_name: Pagano
- first_name: Nadine
full_name: Frohlich, Nadine
last_name: Frohlich
- first_name: Pietro
full_name: Negrini, Pietro
last_name: Negrini
- first_name: Nicola
full_name: Cavallari, Nicola
id: 457160E6-F248-11E8-B48F-1D18A9856A87
last_name: Cavallari
- first_name: Daniela
full_name: Vallone, Daniela
last_name: Vallone
- first_name: Silvia
full_name: Fuselli, Silvia
last_name: Fuselli
- first_name: Cristiano
full_name: Bertolucci, Cristiano
last_name: Bertolucci
- first_name: Nicholas S
full_name: Foulkes, Nicholas S
last_name: Foulkes
citation:
ama: Ceinos RM, Frigato E, Pagano C, et al. Mutations in blind cavefish target the
light regulated circadian clock gene period 2. Scientific Reports. 2018;8(1).
doi:10.1038/s41598-018-27080-2
apa: Ceinos, R. M., Frigato, E., Pagano, C., Frohlich, N., Negrini, P., Cavallari,
N., … Foulkes, N. S. (2018). Mutations in blind cavefish target the light regulated
circadian clock gene period 2. Scientific Reports. Nature Publishing Group.
https://doi.org/10.1038/s41598-018-27080-2
chicago: Ceinos, Rosa Maria, Elena Frigato, Cristina Pagano, Nadine Frohlich, Pietro
Negrini, Nicola Cavallari, Daniela Vallone, Silvia Fuselli, Cristiano Bertolucci,
and Nicholas S Foulkes. “Mutations in Blind Cavefish Target the Light Regulated
Circadian Clock Gene Period 2.” Scientific Reports. Nature Publishing Group,
2018. https://doi.org/10.1038/s41598-018-27080-2.
ieee: R. M. Ceinos et al., “Mutations in blind cavefish target the light
regulated circadian clock gene period 2,” Scientific Reports, vol. 8, no.
1. Nature Publishing Group, 2018.
ista: Ceinos RM, Frigato E, Pagano C, Frohlich N, Negrini P, Cavallari N, Vallone
D, Fuselli S, Bertolucci C, Foulkes NS. 2018. Mutations in blind cavefish target
the light regulated circadian clock gene period 2. Scientific Reports. 8(1), 8754.
mla: Ceinos, Rosa Maria, et al. “Mutations in Blind Cavefish Target the Light Regulated
Circadian Clock Gene Period 2.” Scientific Reports, vol. 8, no. 1, 8754,
Nature Publishing Group, 2018, doi:10.1038/s41598-018-27080-2.
short: R.M. Ceinos, E. Frigato, C. Pagano, N. Frohlich, P. Negrini, N. Cavallari,
D. Vallone, S. Fuselli, C. Bertolucci, N.S. Foulkes, Scientific Reports 8 (2018).
date_created: 2018-12-11T11:45:36Z
date_published: 2018-06-08T00:00:00Z
date_updated: 2023-09-13T08:59:27Z
day: '08'
ddc:
- '570'
department:
- _id: EvBe
doi: 10.1038/s41598-018-27080-2
external_id:
isi:
- '000434640800008'
file:
- access_level: open_access
checksum: 9c3942d772f84f3df032ffde0ed9a8ea
content_type: application/pdf
creator: dernst
date_created: 2018-12-17T13:04:46Z
date_updated: 2020-07-14T12:45:49Z
file_id: '5707'
file_name: 2018_ScientificReports_Ceinos.pdf
file_size: 1855324
relation: main_file
file_date_updated: 2020-07-14T12:45:49Z
has_accepted_license: '1'
intvolume: ' 8'
isi: 1
issue: '1'
language:
- iso: eng
month: '06'
oa: 1
oa_version: Published Version
publication: Scientific Reports
publication_status: published
publisher: Nature Publishing Group
publist_id: '7616'
quality_controlled: '1'
scopus_import: '1'
status: public
title: Mutations in blind cavefish target the light regulated circadian clock gene
period 2
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: journal_article
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
volume: 8
year: '2018'
...
---
_id: '81'
abstract:
- lang: eng
text: We solve the offline monitoring problem for timed propositional temporal logic
(TPTL), interpreted over dense-time Boolean signals. The variant of TPTL we consider
extends linear temporal logic (LTL) with clock variables and reset quantifiers,
providing a mechanism to specify real-time constraints. We first describe a general
monitoring algorithm based on an exhaustive computation of the set of satisfying
clock assignments as a finite union of zones. We then propose a specialized monitoring
algorithm for the one-variable case using a partition of the time domain based
on the notion of region equivalence, whose complexity is linear in the length
of the signal, thereby generalizing a known result regarding the monitoring of
metric temporal logic (MTL). The region and zone representations of time constraints
are known from timed automata verification and can also be used in the discrete-time
case. Our prototype implementation appears to outperform previous discrete-time
implementations of TPTL monitoring,
alternative_title:
- LNCS
article_processing_charge: No
author:
- first_name: Adrian
full_name: Elgyütt, Adrian
id: 4A2E9DBA-F248-11E8-B48F-1D18A9856A87
last_name: Elgyütt
- first_name: Thomas
full_name: Ferrere, Thomas
id: 40960E6E-F248-11E8-B48F-1D18A9856A87
last_name: Ferrere
orcid: 0000-0001-5199-3143
- first_name: Thomas A
full_name: Henzinger, Thomas A
id: 40876CD8-F248-11E8-B48F-1D18A9856A87
last_name: Henzinger
orcid: 0000−0002−2985−7724
citation:
ama: 'Elgyütt A, Ferrere T, Henzinger TA. Monitoring temporal logic with clock variables.
In: Vol 11022. Springer; 2018:53-70. doi:10.1007/978-3-030-00151-3_4'
apa: 'Elgyütt, A., Ferrere, T., & Henzinger, T. A. (2018). Monitoring temporal
logic with clock variables (Vol. 11022, pp. 53–70). Presented at the FORMATS:
Formal Modeling and Analysis of Timed Systems, Beijing, China: Springer. https://doi.org/10.1007/978-3-030-00151-3_4'
chicago: Elgyütt, Adrian, Thomas Ferrere, and Thomas A Henzinger. “Monitoring Temporal
Logic with Clock Variables,” 11022:53–70. Springer, 2018. https://doi.org/10.1007/978-3-030-00151-3_4.
ieee: 'A. Elgyütt, T. Ferrere, and T. A. Henzinger, “Monitoring temporal logic with
clock variables,” presented at the FORMATS: Formal Modeling and Analysis of Timed
Systems, Beijing, China, 2018, vol. 11022, pp. 53–70.'
ista: 'Elgyütt A, Ferrere T, Henzinger TA. 2018. Monitoring temporal logic with
clock variables. FORMATS: Formal Modeling and Analysis of Timed Systems, LNCS,
vol. 11022, 53–70.'
mla: Elgyütt, Adrian, et al. Monitoring Temporal Logic with Clock Variables.
Vol. 11022, Springer, 2018, pp. 53–70, doi:10.1007/978-3-030-00151-3_4.
short: A. Elgyütt, T. Ferrere, T.A. Henzinger, in:, Springer, 2018, pp. 53–70.
conference:
end_date: 2018-09-06
location: Beijing, China
name: 'FORMATS: Formal Modeling and Analysis of Timed Systems'
start_date: 2018-09-04
date_created: 2018-12-11T11:44:31Z
date_published: 2018-08-26T00:00:00Z
date_updated: 2023-09-13T08:58:34Z
day: '26'
ddc:
- '000'
department:
- _id: ToHe
doi: 10.1007/978-3-030-00151-3_4
external_id:
isi:
- '000884993200004'
file:
- access_level: open_access
checksum: e5d81c9b50a6bd9d8a2c16953aad7e23
content_type: application/pdf
creator: dernst
date_created: 2020-10-09T06:24:21Z
date_updated: 2020-10-09T06:24:21Z
file_id: '8638'
file_name: 2018_LNCS_Elgyuett.pdf
file_size: 537219
relation: main_file
success: 1
file_date_updated: 2020-10-09T06:24:21Z
has_accepted_license: '1'
intvolume: ' 11022'
isi: 1
language:
- iso: eng
month: '08'
oa: 1
oa_version: Submitted Version
page: 53 - 70
project:
- _id: 25F5A88A-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: S11402-N23
name: Moderne Concurrency Paradigms
- _id: 25F42A32-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: Z211
name: The Wittgenstein Prize
publication_status: published
publisher: Springer
publist_id: '7973'
quality_controlled: '1'
scopus_import: '1'
status: public
title: Monitoring temporal logic with clock variables
type: conference
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
volume: 11022
year: '2018'
...
---
_id: '76'
abstract:
- lang: eng
text: 'Consider a fully-connected synchronous distributed system consisting of n
nodes, where up to f nodes may be faulty and every node starts in an arbitrary
initial state. In the synchronous C-counting problem, all nodes need to eventually
agree on a counter that is increased by one modulo C in each round for given C>1.
In the self-stabilising firing squad problem, the task is to eventually guarantee
that all non-faulty nodes have simultaneous responses to external inputs: if a
subset of the correct nodes receive an external “go” signal as input, then all
correct nodes should agree on a round (in the not-too-distant future) in which
to jointly output a “fire” signal. Moreover, no node should generate a “fire”
signal without some correct node having previously received a “go” signal as input.
We present a framework reducing both tasks to binary consensus at very small cost.
For example, we obtain a deterministic algorithm for self-stabilising Byzantine
firing squads with optimal resilience f<n/3, asymptotically optimal stabilisation
and response time O(f), and message size O(log f). As our framework does not restrict
the type of consensus routines used, we also obtain efficient randomised solutions.'
article_processing_charge: Yes (via OA deal)
author:
- first_name: Christoph
full_name: Lenzen, Christoph
last_name: Lenzen
- first_name: Joel
full_name: Rybicki, Joel
id: 334EFD2E-F248-11E8-B48F-1D18A9856A87
last_name: Rybicki
orcid: 0000-0002-6432-6646
citation:
ama: Lenzen C, Rybicki J. Near-optimal self-stabilising counting and firing squads.
Distributed Computing. 2018. doi:10.1007/s00446-018-0342-6
apa: Lenzen, C., & Rybicki, J. (2018). Near-optimal self-stabilising counting
and firing squads. Distributed Computing. Springer. https://doi.org/10.1007/s00446-018-0342-6
chicago: Lenzen, Christoph, and Joel Rybicki. “Near-Optimal Self-Stabilising Counting
and Firing Squads.” Distributed Computing. Springer, 2018. https://doi.org/10.1007/s00446-018-0342-6.
ieee: C. Lenzen and J. Rybicki, “Near-optimal self-stabilising counting and firing
squads,” Distributed Computing. Springer, 2018.
ista: Lenzen C, Rybicki J. 2018. Near-optimal self-stabilising counting and firing
squads. Distributed Computing.
mla: Lenzen, Christoph, and Joel Rybicki. “Near-Optimal Self-Stabilising Counting
and Firing Squads.” Distributed Computing, Springer, 2018, doi:10.1007/s00446-018-0342-6.
short: C. Lenzen, J. Rybicki, Distributed Computing (2018).
date_created: 2018-12-11T11:44:30Z
date_published: 2018-09-12T00:00:00Z
date_updated: 2023-09-13T09:01:06Z
day: '12'
ddc:
- '000'
department:
- _id: DaAl
doi: 10.1007/s00446-018-0342-6
external_id:
isi:
- '000475627800005'
file:
- access_level: open_access
checksum: 872db70bba9b401500abe3c6ae2f1a61
content_type: application/pdf
creator: dernst
date_created: 2018-12-17T14:21:22Z
date_updated: 2020-07-14T12:48:01Z
file_id: '5711'
file_name: 2018_DistributedComputing_Lenzen.pdf
file_size: 799337
relation: main_file
file_date_updated: 2020-07-14T12:48:01Z
has_accepted_license: '1'
isi: 1
language:
- iso: eng
month: '09'
oa: 1
oa_version: Published Version
project:
- _id: B67AFEDC-15C9-11EA-A837-991A96BB2854
name: IST Austria Open Access Fund
publication: Distributed Computing
publication_status: published
publisher: Springer
publist_id: '7978'
quality_controlled: '1'
scopus_import: '1'
status: public
title: Near-optimal self-stabilising counting and firing squads
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: journal_article
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
year: '2018'
...
---
_id: '530'
abstract:
- lang: eng
text: Inclusion–exclusion is an effective method for computing the volume of a union
of measurable sets. We extend it to multiple coverings, proving short inclusion–exclusion
formulas for the subset of Rn covered by at least k balls in a finite set. We
implement two of the formulas in dimension n=3 and report on results obtained
with our software.
article_processing_charge: No
author:
- first_name: Herbert
full_name: Edelsbrunner, Herbert
id: 3FB178DA-F248-11E8-B48F-1D18A9856A87
last_name: Edelsbrunner
orcid: 0000-0002-9823-6833
- first_name: Mabel
full_name: Iglesias Ham, Mabel
id: 41B58C0C-F248-11E8-B48F-1D18A9856A87
last_name: Iglesias Ham
citation:
ama: 'Edelsbrunner H, Iglesias Ham M. Multiple covers with balls I: Inclusion–exclusion.
Computational Geometry: Theory and Applications. 2018;68:119-133. doi:10.1016/j.comgeo.2017.06.014'
apa: 'Edelsbrunner, H., & Iglesias Ham, M. (2018). Multiple covers with balls
I: Inclusion–exclusion. Computational Geometry: Theory and Applications.
Elsevier. https://doi.org/10.1016/j.comgeo.2017.06.014'
chicago: 'Edelsbrunner, Herbert, and Mabel Iglesias Ham. “Multiple Covers with Balls
I: Inclusion–Exclusion.” Computational Geometry: Theory and Applications.
Elsevier, 2018. https://doi.org/10.1016/j.comgeo.2017.06.014.'
ieee: 'H. Edelsbrunner and M. Iglesias Ham, “Multiple covers with balls I: Inclusion–exclusion,”
Computational Geometry: Theory and Applications, vol. 68. Elsevier, pp.
119–133, 2018.'
ista: 'Edelsbrunner H, Iglesias Ham M. 2018. Multiple covers with balls I: Inclusion–exclusion.
Computational Geometry: Theory and Applications. 68, 119–133.'
mla: 'Edelsbrunner, Herbert, and Mabel Iglesias Ham. “Multiple Covers with Balls
I: Inclusion–Exclusion.” Computational Geometry: Theory and Applications,
vol. 68, Elsevier, 2018, pp. 119–33, doi:10.1016/j.comgeo.2017.06.014.'
short: 'H. Edelsbrunner, M. Iglesias Ham, Computational Geometry: Theory and Applications
68 (2018) 119–133.'
date_created: 2018-12-11T11:46:59Z
date_published: 2018-03-01T00:00:00Z
date_updated: 2023-09-13T08:59:00Z
day: '01'
ddc:
- '000'
department:
- _id: HeEd
doi: 10.1016/j.comgeo.2017.06.014
ec_funded: 1
external_id:
isi:
- '000415778300010'
file:
- access_level: open_access
checksum: 1c8d58cd489a66cd3e2064c1141c8c5e
content_type: application/pdf
creator: dernst
date_created: 2019-02-12T06:47:52Z
date_updated: 2020-07-14T12:46:38Z
file_id: '5953'
file_name: 2018_Edelsbrunner.pdf
file_size: 708357
relation: main_file
file_date_updated: 2020-07-14T12:46:38Z
has_accepted_license: '1'
intvolume: ' 68'
isi: 1
language:
- iso: eng
month: '03'
oa: 1
oa_version: Preprint
page: 119 - 133
project:
- _id: 255D761E-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '318493'
name: Topological Complex Systems
publication: 'Computational Geometry: Theory and Applications'
publication_status: published
publisher: Elsevier
publist_id: '7289'
quality_controlled: '1'
scopus_import: '1'
status: public
title: 'Multiple covers with balls I: Inclusion–exclusion'
type: journal_article
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
volume: 68
year: '2018'
...
---
_id: '307'
abstract:
- lang: eng
text: 'Spontaneous emission spectra of two initially excited closely spaced identical
atoms are very sensitive to the strength and the direction of the applied magnetic
field. We consider the relevant schemes that ensure the determination of the mutual
spatial orientation of the atoms and the distance between them by entirely optical
means. A corresponding theoretical description is given accounting for the dipole-dipole
interaction between the two atoms in the presence of a magnetic field and for
polarizations of the quantum field interacting with magnetic sublevels of the
two-atom system. '
acknowledgement: The work was partially supported by Russian Foundation for Basic
Research (Grant No. 15-02-05657a) and by the Basic research program of Higher School
of Economics (HSE).
article_number: ' 043812 '
article_processing_charge: No
article_type: original
author:
- first_name: Elena
full_name: Redchenko, Elena
id: 2C21D6E8-F248-11E8-B48F-1D18A9856A87
last_name: Redchenko
- first_name: Alexander
full_name: Makarov, Alexander
last_name: Makarov
- first_name: Vladimir
full_name: Yudson, Vladimir
last_name: Yudson
citation:
ama: Redchenko E, Makarov A, Yudson V. Nanoscopy of pairs of atoms by fluorescence
in a magnetic field. Physical Review A - Atomic, Molecular, and Optical Physics.
2018;97(4). doi:10.1103/PhysRevA.97.043812
apa: Redchenko, E., Makarov, A., & Yudson, V. (2018). Nanoscopy of pairs of
atoms by fluorescence in a magnetic field. Physical Review A - Atomic, Molecular,
and Optical Physics. American Physical Society. https://doi.org/10.1103/PhysRevA.97.043812
chicago: Redchenko, Elena, Alexander Makarov, and Vladimir Yudson. “Nanoscopy of
Pairs of Atoms by Fluorescence in a Magnetic Field.” Physical Review A - Atomic,
Molecular, and Optical Physics. American Physical Society, 2018. https://doi.org/10.1103/PhysRevA.97.043812.
ieee: E. Redchenko, A. Makarov, and V. Yudson, “Nanoscopy of pairs of atoms by fluorescence
in a magnetic field,” Physical Review A - Atomic, Molecular, and Optical Physics,
vol. 97, no. 4. American Physical Society, 2018.
ista: Redchenko E, Makarov A, Yudson V. 2018. Nanoscopy of pairs of atoms by fluorescence
in a magnetic field. Physical Review A - Atomic, Molecular, and Optical Physics.
97(4), 043812.
mla: Redchenko, Elena, et al. “Nanoscopy of Pairs of Atoms by Fluorescence in a
Magnetic Field.” Physical Review A - Atomic, Molecular, and Optical Physics,
vol. 97, no. 4, 043812, American Physical Society, 2018, doi:10.1103/PhysRevA.97.043812.
short: E. Redchenko, A. Makarov, V. Yudson, Physical Review A - Atomic, Molecular,
and Optical Physics 97 (2018).
date_created: 2018-12-11T11:45:44Z
date_published: 2018-04-09T00:00:00Z
date_updated: 2023-09-13T09:00:41Z
day: '09'
department:
- _id: JoFi
doi: 10.1103/PhysRevA.97.043812
external_id:
arxiv:
- '1712.10127'
isi:
- '000429454000015'
intvolume: ' 97'
isi: 1
issue: '4'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/1712.10127
month: '04'
oa: 1
oa_version: Submitted Version
publication: ' Physical Review A - Atomic, Molecular, and Optical Physics'
publication_status: published
publisher: American Physical Society
publist_id: '7572'
quality_controlled: '1'
scopus_import: '1'
status: public
title: Nanoscopy of pairs of atoms by fluorescence in a magnetic field
type: journal_article
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
volume: 97
year: '2018'
...
---
_id: '279'
abstract:
- lang: eng
text: 'Background: Natural selection shapes cancer genomes. Previous studies used
signatures of positive selection to identify genes driving malignant transformation.
However, the contribution of negative selection against somatic mutations that
affect essential tumor functions or specific domains remains a controversial topic.
Results: Here, we analyze 7546 individual exomes from 26 tumor types from TCGA
data to explore the portion of the cancer exome under negative selection. Although
we find most of the genes neutrally evolving in a pan-cancer framework, we identify
essential cancer genes and immune-exposed protein regions under significant negative
selection. Moreover, our simulations suggest that the amount of negative selection
is underestimated. We therefore choose an empirical approach to identify genes,
functions, and protein regions under negative selection. We find that expression
and mutation status of negatively selected genes is indicative of patient survival.
Processes that are most strongly conserved are those that play fundamental cellular
roles such as protein synthesis, glucose metabolism, and molecular transport.
Intriguingly, we observe strong signals of selection in the immunopeptidome and
proteins controlling peptide exposition, highlighting the importance of immune
surveillance evasion. Additionally, tumor type-specific immune activity correlates
with the strength of negative selection on human epitopes. Conclusions: In summary,
our results show that negative selection is a hallmark of cell essentiality and
immune response in cancer. The functional domains identified could be exploited
therapeutically, ultimately allowing for the development of novel cancer treatments.'
article_number: '67'
article_processing_charge: No
author:
- first_name: Luis
full_name: Zapata, Luis
last_name: Zapata
- first_name: Oriol
full_name: Pich, Oriol
last_name: Pich
- first_name: Luis
full_name: Serrano, Luis
last_name: Serrano
- first_name: Fyodor
full_name: Kondrashov, Fyodor
id: 44FDEF62-F248-11E8-B48F-1D18A9856A87
last_name: Kondrashov
orcid: 0000-0001-8243-4694
- first_name: Stephan
full_name: Ossowski, Stephan
last_name: Ossowski
- first_name: Martin
full_name: Schaefer, Martin
last_name: Schaefer
citation:
ama: Zapata L, Pich O, Serrano L, Kondrashov F, Ossowski S, Schaefer M. Negative
selection in tumor genome evolution acts on essential cellular functions and the
immunopeptidome. Genome Biology. 2018;19. doi:10.1186/s13059-018-1434-0
apa: Zapata, L., Pich, O., Serrano, L., Kondrashov, F., Ossowski, S., & Schaefer,
M. (2018). Negative selection in tumor genome evolution acts on essential cellular
functions and the immunopeptidome. Genome Biology. BioMed Central. https://doi.org/10.1186/s13059-018-1434-0
chicago: Zapata, Luis, Oriol Pich, Luis Serrano, Fyodor Kondrashov, Stephan Ossowski,
and Martin Schaefer. “Negative Selection in Tumor Genome Evolution Acts on Essential
Cellular Functions and the Immunopeptidome.” Genome Biology. BioMed Central,
2018. https://doi.org/10.1186/s13059-018-1434-0.
ieee: L. Zapata, O. Pich, L. Serrano, F. Kondrashov, S. Ossowski, and M. Schaefer,
“Negative selection in tumor genome evolution acts on essential cellular functions
and the immunopeptidome,” Genome Biology, vol. 19. BioMed Central, 2018.
ista: Zapata L, Pich O, Serrano L, Kondrashov F, Ossowski S, Schaefer M. 2018. Negative
selection in tumor genome evolution acts on essential cellular functions and the
immunopeptidome. Genome Biology. 19, 67.
mla: Zapata, Luis, et al. “Negative Selection in Tumor Genome Evolution Acts on
Essential Cellular Functions and the Immunopeptidome.” Genome Biology,
vol. 19, 67, BioMed Central, 2018, doi:10.1186/s13059-018-1434-0.
short: L. Zapata, O. Pich, L. Serrano, F. Kondrashov, S. Ossowski, M. Schaefer,
Genome Biology 19 (2018).
date_created: 2018-12-11T11:45:35Z
date_published: 2018-05-31T00:00:00Z
date_updated: 2023-09-13T09:01:32Z
day: '31'
ddc:
- '570'
department:
- _id: FyKo
doi: 10.1186/s13059-018-1434-0
ec_funded: 1
external_id:
isi:
- '000433986200001'
file:
- access_level: open_access
checksum: f3e4922486bd9bf1483271bdbed394a7
content_type: application/pdf
creator: dernst
date_created: 2018-12-17T14:05:01Z
date_updated: 2020-07-14T12:45:47Z
file_id: '5708'
file_name: 2018_GenomeBiology_Zapata.pdf
file_size: 1414722
relation: main_file
file_date_updated: 2020-07-14T12:45:47Z
has_accepted_license: '1'
intvolume: ' 19'
isi: 1
language:
- iso: eng
month: '05'
oa: 1
oa_version: Published Version
project:
- _id: 26120F5C-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '335980'
name: Systematic investigation of epistasis in molecular evolution
publication: Genome Biology
publication_status: published
publisher: BioMed Central
publist_id: '7620'
quality_controlled: '1'
related_material:
record:
- id: '9811'
relation: research_data
status: public
- id: '9812'
relation: research_data
status: public
scopus_import: '1'
status: public
title: Negative selection in tumor genome evolution acts on essential cellular functions
and the immunopeptidome
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: journal_article
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
volume: 19
year: '2018'
...
---
_id: '145'
abstract:
- lang: eng
text: Aged proteins can become hazardous to cellular function, by accumulating molecular
damage. This implies that cells should preferentially rely on newly produced ones.
We tested this hypothesis in cultured hippocampal neurons, focusing on synaptic
transmission. We found that newly synthesized vesicle proteins were incorporated
in the actively recycling pool of vesicles responsible for all neurotransmitter
release during physiological activity. We observed this for the calcium sensor
Synaptotagmin 1, for the neurotransmitter transporter VGAT, and for the fusion
protein VAMP2 (Synaptobrevin 2). Metabolic labeling of proteins and visualization
by secondary ion mass spectrometry enabled us to query the entire protein makeup
of the actively recycling vesicles, which we found to be younger than that of
non-recycling vesicles. The young vesicle proteins remained in use for up to ~
24 h, during which they participated in recycling a few hundred times. They were
afterward reluctant to release and were degraded after an additional ~ 24–48 h.
We suggest that the recycling pool of synaptic vesicles relies on newly synthesized
proteins, while the inactive reserve pool contains older proteins.
acknowledgement: We thank Reinhard Jahn for providing a plasmid for YFP-SNAP25. We
thank Erwin Neher for help with the development of the mathematical model of the
synaptic vesicle life cycle. We thank Martin Meschkat, Andreas Höbartner, Annedore
Punge, and Peer Hoopmann for help with the experiments. We thank Burkhard Rammner
for providing the illustrations of synaptic vesicle and protein dynamics. We thank
Manuel Maidorn, Martin Helm, and Katharina N. Richter for critically reading the
manuscript. S.T. was supported by an Excellence Stipend of the Göttingen Graduate
School for Neurosciences, Biophysics, and Molecular Biosciences (GGNB). E.F.F. is
a recipient of long-term fellowships from the European Molecular Biology Organization
(ALTF_797-2012) and from the Human Frontier Science Program (HFSP_LT000830/2013).
The work was supported by grants to S.O.R. from the European Research Council (ERC-2013-CoG
NeuroMolAnatomy) and from the Deutsche Forschungsgemeinschaft (Cluster of Excellence
Nanoscale Microscopy and Molecular Physiology of the Brain, SFB1190/P09, SFB889/A05,
and SFB1286/A03, and DFG RI 1967 7/1). The nanoSIMS instrument was funded by the
German Federal Ministry of Education and Research (03F0626A).
article_number: e98044
article_processing_charge: No
article_type: original
author:
- first_name: Sven M
full_name: Truckenbrodt, Sven M
id: 45812BD4-F248-11E8-B48F-1D18A9856A87
last_name: Truckenbrodt
- first_name: Abhiyan
full_name: Viplav, Abhiyan
last_name: Viplav
- first_name: Sebsatian
full_name: Jähne, Sebsatian
last_name: Jähne
- first_name: Angela
full_name: Vogts, Angela
last_name: Vogts
- first_name: Annette
full_name: Denker, Annette
last_name: Denker
- first_name: Hanna
full_name: Wildhagen, Hanna
last_name: Wildhagen
- first_name: Eugenio
full_name: Fornasiero, Eugenio
last_name: Fornasiero
- first_name: Silvio
full_name: Rizzoli, Silvio
last_name: Rizzoli
citation:
ama: Truckenbrodt SM, Viplav A, Jähne S, et al. Newly produced synaptic vesicle
proteins are preferentially used in synaptic transmission. The EMBO Journal.
2018;37(15). doi:10.15252/embj.201798044
apa: Truckenbrodt, S. M., Viplav, A., Jähne, S., Vogts, A., Denker, A., Wildhagen,
H., … Rizzoli, S. (2018). Newly produced synaptic vesicle proteins are preferentially
used in synaptic transmission. The EMBO Journal. Wiley. https://doi.org/10.15252/embj.201798044
chicago: Truckenbrodt, Sven M, Abhiyan Viplav, Sebsatian Jähne, Angela Vogts, Annette
Denker, Hanna Wildhagen, Eugenio Fornasiero, and Silvio Rizzoli. “Newly Produced
Synaptic Vesicle Proteins Are Preferentially Used in Synaptic Transmission.” The
EMBO Journal. Wiley, 2018. https://doi.org/10.15252/embj.201798044.
ieee: S. M. Truckenbrodt et al., “Newly produced synaptic vesicle proteins
are preferentially used in synaptic transmission,” The EMBO Journal, vol.
37, no. 15. Wiley, 2018.
ista: Truckenbrodt SM, Viplav A, Jähne S, Vogts A, Denker A, Wildhagen H, Fornasiero
E, Rizzoli S. 2018. Newly produced synaptic vesicle proteins are preferentially
used in synaptic transmission. The EMBO Journal. 37(15), e98044.
mla: Truckenbrodt, Sven M., et al. “Newly Produced Synaptic Vesicle Proteins Are
Preferentially Used in Synaptic Transmission.” The EMBO Journal, vol. 37,
no. 15, e98044, Wiley, 2018, doi:10.15252/embj.201798044.
short: S.M. Truckenbrodt, A. Viplav, S. Jähne, A. Vogts, A. Denker, H. Wildhagen,
E. Fornasiero, S. Rizzoli, The EMBO Journal 37 (2018).
date_created: 2018-12-11T11:44:52Z
date_published: 2018-08-01T00:00:00Z
date_updated: 2023-09-13T09:02:48Z
day: '01'
ddc:
- '570'
department:
- _id: JoDa
doi: 10.15252/embj.201798044
external_id:
isi:
- '000440416900005'
pmid:
- '29950309'
file:
- access_level: open_access
checksum: a540feb6c9af6aefc78de531461a8835
content_type: application/pdf
creator: dernst
date_created: 2018-12-17T14:17:29Z
date_updated: 2020-07-14T12:44:56Z
file_id: '5710'
file_name: 2018_EMBO_Truckenbrodt.pdf
file_size: 2846470
relation: main_file
file_date_updated: 2020-07-14T12:44:56Z
has_accepted_license: '1'
intvolume: ' 37'
isi: 1
issue: '15'
language:
- iso: eng
month: '08'
oa: 1
oa_version: Published Version
pmid: 1
publication: The EMBO Journal
publication_identifier:
issn:
- 0261-4189
publication_status: published
publisher: Wiley
publist_id: '7778'
quality_controlled: '1'
scopus_import: '1'
status: public
title: Newly produced synaptic vesicle proteins are preferentially used in synaptic
transmission
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: journal_article
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
volume: 37
year: '2018'
...
---
_id: '462'
abstract:
- lang: eng
text: 'AtNHX5 and AtNHX6 are endosomal Na+,K+/H+ antiporters that are critical for
growth and development in Arabidopsis, but the mechanism behind their action remains
unknown. Here, we report that AtNHX5 and AtNHX6, functioning as H+ leak, control
auxin homeostasis and auxin-mediated development. We found that nhx5 nhx6 exhibited
growth variations of auxin-related defects. We further showed that nhx5 nhx6 was
affected in auxin homeostasis. Genetic analysis showed that AtNHX5 and AtNHX6
were required for the function of the ER-localized auxin transporter PIN5. Although
AtNHX5 and AtNHX6 were co-localized with PIN5 at ER, they did not interact directly.
Instead, the conserved acidic residues in AtNHX5 and AtNHX6, which are essential
for exchange activity, were required for PIN5 function. AtNHX5 and AtNHX6 regulated
the pH in ER. Overall, AtNHX5 and AtNHX6 may regulate auxin transport across the
ER via the pH gradient created by their transport activity. H+-leak pathway provides
a fine-tuning mechanism that controls cellular auxin fluxes. '
acknowledgement: 'This work was supported by the National Natural Science Foundation
of China (31571464, 31371438 and 31070222 to Q.S.Q.), the National Basic Research
Program of China (973 project, 2013CB429904 to Q.S.Q.), the Research Fund for the
Doctoral Program of Higher Education of China (20130211110001 to Q.S.Q.), the Ministry
of Education, Youth and Sports of the Czech Republic (the National Program for Sustainability
I, LO1204), and The Czech Science Foundation GAČR (GA13–40637S) to JF. We thank
Dr. Tom J. Guilfoyle for DR5::GUS line and Dr. Jia Li for pBIB‐RFP vector and DR5::GFP
line. We thank Liping Guan and Yang Zhao for their help with the confocal microscope
assay. '
article_processing_charge: No
article_type: original
author:
- first_name: Ligang
full_name: Fan, Ligang
last_name: Fan
- first_name: Lei
full_name: Zhao, Lei
last_name: Zhao
- first_name: Wei
full_name: Hu, Wei
last_name: Hu
- first_name: Weina
full_name: Li, Weina
last_name: Li
- first_name: Ondřej
full_name: Novák, Ondřej
last_name: Novák
- first_name: Miroslav
full_name: Strnad, Miroslav
last_name: Strnad
- first_name: Sibu
full_name: Simon, Sibu
id: 4542EF9A-F248-11E8-B48F-1D18A9856A87
last_name: Simon
orcid: 0000-0002-1998-6741
- first_name: Jirí
full_name: Friml, Jirí
id: 4159519E-F248-11E8-B48F-1D18A9856A87
last_name: Friml
orcid: 0000-0002-8302-7596
- first_name: Jinbo
full_name: Shen, Jinbo
last_name: Shen
- first_name: Liwen
full_name: Jiang, Liwen
last_name: Jiang
- first_name: Quan
full_name: Qiu, Quan
last_name: Qiu
citation:
ama: Fan L, Zhao L, Hu W, et al. NHX antiporters regulate the pH of endoplasmic
reticulum and auxin-mediated development. Plant, Cell and Environment.
2018;41:850-864. doi:10.1111/pce.13153
apa: Fan, L., Zhao, L., Hu, W., Li, W., Novák, O., Strnad, M., … Qiu, Q. (2018).
NHX antiporters regulate the pH of endoplasmic reticulum and auxin-mediated development.
Plant, Cell and Environment. Wiley-Blackwell. https://doi.org/10.1111/pce.13153
chicago: Fan, Ligang, Lei Zhao, Wei Hu, Weina Li, Ondřej Novák, Miroslav Strnad,
Sibu Simon, et al. “NHX Antiporters Regulate the PH of Endoplasmic Reticulum and
Auxin-Mediated Development.” Plant, Cell and Environment. Wiley-Blackwell,
2018. https://doi.org/10.1111/pce.13153.
ieee: L. Fan et al., “NHX antiporters regulate the pH of endoplasmic reticulum
and auxin-mediated development,” Plant, Cell and Environment, vol. 41.
Wiley-Blackwell, pp. 850–864, 2018.
ista: Fan L, Zhao L, Hu W, Li W, Novák O, Strnad M, Simon S, Friml J, Shen J, Jiang
L, Qiu Q. 2018. NHX antiporters regulate the pH of endoplasmic reticulum and auxin-mediated
development. Plant, Cell and Environment. 41, 850–864.
mla: Fan, Ligang, et al. “NHX Antiporters Regulate the PH of Endoplasmic Reticulum
and Auxin-Mediated Development.” Plant, Cell and Environment, vol. 41,
Wiley-Blackwell, 2018, pp. 850–64, doi:10.1111/pce.13153.
short: L. Fan, L. Zhao, W. Hu, W. Li, O. Novák, M. Strnad, S. Simon, J. Friml, J.
Shen, L. Jiang, Q. Qiu, Plant, Cell and Environment 41 (2018) 850–864.
date_created: 2018-12-11T11:46:36Z
date_published: 2018-05-01T00:00:00Z
date_updated: 2023-09-13T09:03:18Z
day: '01'
ddc:
- '580'
department:
- _id: JiFr
doi: 10.1111/pce.13153
external_id:
isi:
- '000426870500012'
pmid:
- '29360148'
file:
- access_level: open_access
checksum: 6a20f843565f962cb20281cdf5e40914
content_type: application/pdf
creator: dernst
date_created: 2019-11-18T16:22:22Z
date_updated: 2020-07-14T12:46:32Z
file_id: '7042'
file_name: 2018_PlantCellEnv_Fan.pdf
file_size: 1937976
relation: main_file
file_date_updated: 2020-07-14T12:46:32Z
has_accepted_license: '1'
intvolume: ' 41'
isi: 1
language:
- iso: eng
license: https://creativecommons.org/licenses/by-nc/4.0/
month: '05'
oa: 1
oa_version: Submitted Version
page: 850 - 864
pmid: 1
publication: Plant, Cell and Environment
publication_status: published
publisher: Wiley-Blackwell
publist_id: '7359'
quality_controlled: '1'
scopus_import: '1'
status: public
title: NHX antiporters regulate the pH of endoplasmic reticulum and auxin-mediated
development
tmp:
image: /images/cc_by_nc.png
legal_code_url: https://creativecommons.org/licenses/by-nc/4.0/legalcode
name: Creative Commons Attribution-NonCommercial 4.0 International (CC BY-NC 4.0)
short: CC BY-NC (4.0)
type: journal_article
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
volume: 41
year: '2018'
...
---
_id: '519'
abstract:
- lang: eng
text: 'This study treats with the influence of a symmetry-breaking transversal magnetic
field on the nonlinear dynamics of ferrofluidic Taylor-Couette flow – flow confined
between two concentric independently rotating cylinders. We detected alternating
‘flip’ solutions which are flow states featuring typical characteristics of slow-fast-dynamics
in dynamical systems. The flip corresponds to a temporal change in the axial wavenumber
and we find them to appear either as pure 2-fold axisymmetric (due to the symmetry-breaking
nature of the applied transversal magnetic field) or involving non-axisymmetric,
helical modes in its interim solution. The latter ones show features of typical
ribbon solutions. In any case the flip solutions have a preferential first axial
wavenumber which corresponds to the more stable state (slow dynamics) and second
axial wavenumber, corresponding to the short appearing more unstable state (fast
dynamics). However, in both cases the flip time grows exponential with increasing
the magnetic field strength before the flip solutions, living on 2-tori invariant
manifolds, cease to exist, with lifetime going to infinity. Further we show that
ferrofluidic flow turbulence differ from the classical, ordinary (usually at high
Reynolds number) turbulence. The applied magnetic field hinders the free motion
of ferrofluid partials and therefore smoothen typical turbulent quantities and
features so that speaking of mildly chaotic dynamics seems to be a more appropriate
expression for the observed motion. '
acknowledgement: S.Altmeyer is a Serra Húnter Fellow
article_processing_charge: No
article_type: original
author:
- first_name: Sebastian
full_name: Altmeyer, Sebastian
id: 2EE67FDC-F248-11E8-B48F-1D18A9856A87
last_name: Altmeyer
orcid: 0000-0001-5964-0203
citation:
ama: Altmeyer S. Non-linear dynamics and alternating ‘flip’ solutions in ferrofluidic
Taylor-Couette flow. Journal of Magnetism and Magnetic Materials. 2018;452:427-441.
doi:10.1016/j.jmmm.2017.12.073
apa: Altmeyer, S. (2018). Non-linear dynamics and alternating ‘flip’ solutions in
ferrofluidic Taylor-Couette flow. Journal of Magnetism and Magnetic Materials.
Elsevier. https://doi.org/10.1016/j.jmmm.2017.12.073
chicago: Altmeyer, Sebastian. “Non-Linear Dynamics and Alternating ‘Flip’ Solutions
in Ferrofluidic Taylor-Couette Flow.” Journal of Magnetism and Magnetic Materials.
Elsevier, 2018. https://doi.org/10.1016/j.jmmm.2017.12.073.
ieee: S. Altmeyer, “Non-linear dynamics and alternating ‘flip’ solutions in ferrofluidic
Taylor-Couette flow,” Journal of Magnetism and Magnetic Materials, vol.
452. Elsevier, pp. 427–441, 2018.
ista: Altmeyer S. 2018. Non-linear dynamics and alternating ‘flip’ solutions in
ferrofluidic Taylor-Couette flow. Journal of Magnetism and Magnetic Materials.
452, 427–441.
mla: Altmeyer, Sebastian. “Non-Linear Dynamics and Alternating ‘Flip’ Solutions
in Ferrofluidic Taylor-Couette Flow.” Journal of Magnetism and Magnetic Materials,
vol. 452, Elsevier, 2018, pp. 427–41, doi:10.1016/j.jmmm.2017.12.073.
short: S. Altmeyer, Journal of Magnetism and Magnetic Materials 452 (2018) 427–441.
date_created: 2018-12-11T11:46:56Z
date_published: 2018-04-15T00:00:00Z
date_updated: 2023-09-13T09:03:44Z
day: '15'
ddc:
- '530'
department:
- _id: BjHo
doi: 10.1016/j.jmmm.2017.12.073
external_id:
isi:
- '000425547700061'
file:
- access_level: open_access
checksum: 431f5cd4a628d7ca21161f82b14ccb4f
content_type: application/pdf
creator: dernst
date_created: 2020-05-14T14:41:17Z
date_updated: 2020-07-14T12:46:37Z
file_id: '7838'
file_name: 2018_Magnetism_Altmeyer.pdf
file_size: 17309535
relation: main_file
file_date_updated: 2020-07-14T12:46:37Z
has_accepted_license: '1'
intvolume: ' 452'
isi: 1
language:
- iso: eng
month: '04'
oa: 1
oa_version: Submitted Version
page: 427 - 441
publication: Journal of Magnetism and Magnetic Materials
publication_status: published
publisher: Elsevier
publist_id: '7297'
quality_controlled: '1'
scopus_import: '1'
status: public
title: Non-linear dynamics and alternating ‘flip’ solutions in ferrofluidic Taylor-Couette
flow
type: journal_article
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
volume: 452
year: '2018'
...
---
_id: '5679'
abstract:
- lang: eng
text: We study the almost-sure termination problem for probabilistic programs. First,
we show that supermartingales with lower bounds on conditional absolute difference
provide a sound approach for the almost-sure termination problem. Moreover, using
this approach we can obtain explicit optimal bounds on tail probabilities of non-termination
within a given number of steps. Second, we present a new approach based on Central
Limit Theorem for the almost-sure termination problem, and show that this approach
can establish almost-sure termination of programs which none of the existing approaches
can handle. Finally, we discuss algorithmic approaches for the two above methods
that lead to automated analysis techniques for almost-sure termination of probabilistic
programs.
alternative_title:
- LNCS
article_processing_charge: No
author:
- first_name: Mingzhang
full_name: Huang, Mingzhang
last_name: Huang
- first_name: Hongfei
full_name: Fu, Hongfei
last_name: Fu
- first_name: Krishnendu
full_name: Chatterjee, Krishnendu
id: 2E5DCA20-F248-11E8-B48F-1D18A9856A87
last_name: Chatterjee
orcid: 0000-0002-4561-241X
citation:
ama: 'Huang M, Fu H, Chatterjee K. New approaches for almost-sure termination of
probabilistic programs. In: Ryu S, ed. Vol 11275. Springer; 2018:181-201. doi:10.1007/978-3-030-02768-1_11'
apa: 'Huang, M., Fu, H., & Chatterjee, K. (2018). New approaches for almost-sure
termination of probabilistic programs. In S. Ryu (Ed.) (Vol. 11275, pp. 181–201).
Presented at the 16th Asian Symposium on Programming Languages and Systems, APLAS,
Wellington, New Zealand: Springer. https://doi.org/10.1007/978-3-030-02768-1_11'
chicago: Huang, Mingzhang, Hongfei Fu, and Krishnendu Chatterjee. “New Approaches
for Almost-Sure Termination of Probabilistic Programs.” edited by Sukyoung Ryu,
11275:181–201. Springer, 2018. https://doi.org/10.1007/978-3-030-02768-1_11.
ieee: M. Huang, H. Fu, and K. Chatterjee, “New approaches for almost-sure termination
of probabilistic programs,” presented at the 16th Asian Symposium on Programming
Languages and Systems, APLAS, Wellington, New Zealand, 2018, vol. 11275, pp. 181–201.
ista: Huang M, Fu H, Chatterjee K. 2018. New approaches for almost-sure termination
of probabilistic programs. 16th Asian Symposium on Programming Languages and Systems,
APLAS, LNCS, vol. 11275, 181–201.
mla: Huang, Mingzhang, et al. New Approaches for Almost-Sure Termination of Probabilistic
Programs. Edited by Sukyoung Ryu, vol. 11275, Springer, 2018, pp. 181–201,
doi:10.1007/978-3-030-02768-1_11.
short: M. Huang, H. Fu, K. Chatterjee, in:, S. Ryu (Ed.), Springer, 2018, pp. 181–201.
conference:
end_date: 2018-12-06
location: Wellington, New Zealand
name: 16th Asian Symposium on Programming Languages and Systems, APLAS
start_date: 2018-12-02
date_created: 2018-12-16T22:59:20Z
date_published: 2018-12-01T00:00:00Z
date_updated: 2023-09-13T09:02:22Z
day: '01'
department:
- _id: KrCh
doi: 10.1007/978-3-030-02768-1_11
editor:
- first_name: Sukyoung
full_name: Ryu, Sukyoung
last_name: Ryu
external_id:
arxiv:
- '1806.06683'
isi:
- '000916310900011'
intvolume: ' 11275'
isi: 1
language:
- iso: eng
main_file_link:
- open_access: '1'
url: http://arxiv.org/abs/1806.06683
month: '12'
oa: 1
oa_version: Preprint
page: 181-201
project:
- _id: 25832EC2-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: S 11407_N23
name: Rigorous Systems Engineering
- _id: 25892FC0-B435-11E9-9278-68D0E5697425
grant_number: ICT15-003
name: Efficient Algorithms for Computer Aided Verification
publication_identifier:
isbn:
- '9783030027674'
issn:
- '03029743'
publisher: Springer
quality_controlled: '1'
scopus_import: '1'
status: public
title: New approaches for almost-sure termination of probabilistic programs
type: conference
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
volume: 11275
year: '2018'
...
---
_id: '546'
abstract:
- lang: eng
text: The precise control of neural stem cell (NSC) proliferation and differentiation
is crucial for the development and function of the human brain. Here, we review
the emerging links between the alteration of embryonic and adult neurogenesis
and the etiology of neuropsychiatric disorders (NPDs) such as autism spectrum
disorders (ASDs) and schizophrenia (SCZ), as well as the advances in stem cell-based
modeling and the novel therapeutic targets derived from these studies.
article_processing_charge: No
author:
- first_name: Roberto
full_name: Sacco, Roberto
id: 42C9F57E-F248-11E8-B48F-1D18A9856A87
last_name: Sacco
- first_name: Emanuele
full_name: Cacci, Emanuele
last_name: Cacci
- first_name: Gaia
full_name: Novarino, Gaia
id: 3E57A680-F248-11E8-B48F-1D18A9856A87
last_name: Novarino
orcid: 0000-0002-7673-7178
citation:
ama: Sacco R, Cacci E, Novarino G. Neural stem cells in neuropsychiatric disorders.
Current Opinion in Neurobiology. 2018;48(2):131-138. doi:10.1016/j.conb.2017.12.005
apa: Sacco, R., Cacci, E., & Novarino, G. (2018). Neural stem cells in neuropsychiatric
disorders. Current Opinion in Neurobiology. Elsevier. https://doi.org/10.1016/j.conb.2017.12.005
chicago: Sacco, Roberto, Emanuele Cacci, and Gaia Novarino. “Neural Stem Cells in
Neuropsychiatric Disorders.” Current Opinion in Neurobiology. Elsevier,
2018. https://doi.org/10.1016/j.conb.2017.12.005.
ieee: R. Sacco, E. Cacci, and G. Novarino, “Neural stem cells in neuropsychiatric
disorders,” Current Opinion in Neurobiology, vol. 48, no. 2. Elsevier,
pp. 131–138, 2018.
ista: Sacco R, Cacci E, Novarino G. 2018. Neural stem cells in neuropsychiatric
disorders. Current Opinion in Neurobiology. 48(2), 131–138.
mla: Sacco, Roberto, et al. “Neural Stem Cells in Neuropsychiatric Disorders.” Current
Opinion in Neurobiology, vol. 48, no. 2, Elsevier, 2018, pp. 131–38, doi:10.1016/j.conb.2017.12.005.
short: R. Sacco, E. Cacci, G. Novarino, Current Opinion in Neurobiology 48 (2018)
131–138.
date_created: 2018-12-11T11:47:06Z
date_published: 2018-02-01T00:00:00Z
date_updated: 2023-09-13T09:01:56Z
day: '01'
department:
- _id: GaNo
doi: 10.1016/j.conb.2017.12.005
external_id:
isi:
- '000427101600018'
intvolume: ' 48'
isi: 1
issue: '2'
language:
- iso: eng
month: '02'
oa_version: None
page: 131 - 138
publication: Current Opinion in Neurobiology
publication_status: published
publisher: Elsevier
publist_id: '7268'
quality_controlled: '1'
scopus_import: '1'
status: public
title: Neural stem cells in neuropsychiatric disorders
type: journal_article
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
volume: 48
year: '2018'
...
---
_id: '9812'
abstract:
- lang: eng
text: This document contains the full list of genes with their respective significance
and dN/dS values. (TXT 4499Â kb)
article_processing_charge: No
author:
- first_name: Luis
full_name: Zapata, Luis
last_name: Zapata
- first_name: Oriol
full_name: Pich, Oriol
last_name: Pich
- first_name: Luis
full_name: Serrano, Luis
last_name: Serrano
- first_name: Fyodor
full_name: Kondrashov, Fyodor
id: 44FDEF62-F248-11E8-B48F-1D18A9856A87
last_name: Kondrashov
orcid: 0000-0001-8243-4694
- first_name: Stephan
full_name: Ossowski, Stephan
last_name: Ossowski
- first_name: Martin
full_name: Schaefer, Martin
last_name: Schaefer
citation:
ama: 'Zapata L, Pich O, Serrano L, Kondrashov F, Ossowski S, Schaefer M. Additional
file 2: Of negative selection in tumor genome evolution acts on essential cellular
functions and the immunopeptidome. 2018. doi:10.6084/m9.figshare.6401414.v1'
apa: 'Zapata, L., Pich, O., Serrano, L., Kondrashov, F., Ossowski, S., & Schaefer,
M. (2018). Additional file 2: Of negative selection in tumor genome evolution
acts on essential cellular functions and the immunopeptidome. Springer Nature.
https://doi.org/10.6084/m9.figshare.6401414.v1'
chicago: 'Zapata, Luis, Oriol Pich, Luis Serrano, Fyodor Kondrashov, Stephan Ossowski,
and Martin Schaefer. “Additional File 2: Of Negative Selection in Tumor Genome
Evolution Acts on Essential Cellular Functions and the Immunopeptidome.” Springer
Nature, 2018. https://doi.org/10.6084/m9.figshare.6401414.v1.'
ieee: 'L. Zapata, O. Pich, L. Serrano, F. Kondrashov, S. Ossowski, and M. Schaefer,
“Additional file 2: Of negative selection in tumor genome evolution acts on essential
cellular functions and the immunopeptidome.” Springer Nature, 2018.'
ista: 'Zapata L, Pich O, Serrano L, Kondrashov F, Ossowski S, Schaefer M. 2018.
Additional file 2: Of negative selection in tumor genome evolution acts on essential
cellular functions and the immunopeptidome, Springer Nature, 10.6084/m9.figshare.6401414.v1.'
mla: 'Zapata, Luis, et al. Additional File 2: Of Negative Selection in Tumor
Genome Evolution Acts on Essential Cellular Functions and the Immunopeptidome.
Springer Nature, 2018, doi:10.6084/m9.figshare.6401414.v1.'
short: L. Zapata, O. Pich, L. Serrano, F. Kondrashov, S. Ossowski, M. Schaefer,
(2018).
date_created: 2021-08-06T12:58:25Z
date_published: 2018-05-31T00:00:00Z
date_updated: 2023-09-13T09:01:31Z
day: '31'
department:
- _id: FyKo
doi: 10.6084/m9.figshare.6401414.v1
main_file_link:
- open_access: '1'
url: https://doi.org/10.6084/m9.figshare.6401414.v1
month: '05'
oa: 1
oa_version: Published Version
publisher: Springer Nature
related_material:
record:
- id: '279'
relation: used_in_publication
status: public
status: public
title: 'Additional file 2: Of negative selection in tumor genome evolution acts on
essential cellular functions and the immunopeptidome'
type: research_data_reference
user_id: 6785fbc1-c503-11eb-8a32-93094b40e1cf
year: '2018'
...
---
_id: '9811'
abstract:
- lang: eng
text: This document contains additional supporting evidence presented as supplemental
tables. (XLSX 50Â kb)
article_processing_charge: No
author:
- first_name: Luis
full_name: Zapata, Luis
last_name: Zapata
- first_name: Oriol
full_name: Pich, Oriol
last_name: Pich
- first_name: Luis
full_name: Serrano, Luis
last_name: Serrano
- first_name: Fyodor
full_name: Kondrashov, Fyodor
id: 44FDEF62-F248-11E8-B48F-1D18A9856A87
last_name: Kondrashov
orcid: 0000-0001-8243-4694
- first_name: Stephan
full_name: Ossowski, Stephan
last_name: Ossowski
- first_name: Martin
full_name: Schaefer, Martin
last_name: Schaefer
citation:
ama: 'Zapata L, Pich O, Serrano L, Kondrashov F, Ossowski S, Schaefer M. Additional
file 1: Of negative selection in tumor genome evolution acts on essential cellular
functions and the immunopeptidome. 2018. doi:10.6084/m9.figshare.6401390.v1'
apa: 'Zapata, L., Pich, O., Serrano, L., Kondrashov, F., Ossowski, S., & Schaefer,
M. (2018). Additional file 1: Of negative selection in tumor genome evolution
acts on essential cellular functions and the immunopeptidome. Springer Nature.
https://doi.org/10.6084/m9.figshare.6401390.v1'
chicago: 'Zapata, Luis, Oriol Pich, Luis Serrano, Fyodor Kondrashov, Stephan Ossowski,
and Martin Schaefer. “Additional File 1: Of Negative Selection in Tumor Genome
Evolution Acts on Essential Cellular Functions and the Immunopeptidome.” Springer
Nature, 2018. https://doi.org/10.6084/m9.figshare.6401390.v1.'
ieee: 'L. Zapata, O. Pich, L. Serrano, F. Kondrashov, S. Ossowski, and M. Schaefer,
“Additional file 1: Of negative selection in tumor genome evolution acts on essential
cellular functions and the immunopeptidome.” Springer Nature, 2018.'
ista: 'Zapata L, Pich O, Serrano L, Kondrashov F, Ossowski S, Schaefer M. 2018.
Additional file 1: Of negative selection in tumor genome evolution acts on essential
cellular functions and the immunopeptidome, Springer Nature, 10.6084/m9.figshare.6401390.v1.'
mla: 'Zapata, Luis, et al. Additional File 1: Of Negative Selection in Tumor
Genome Evolution Acts on Essential Cellular Functions and the Immunopeptidome.
Springer Nature, 2018, doi:10.6084/m9.figshare.6401390.v1.'
short: L. Zapata, O. Pich, L. Serrano, F. Kondrashov, S. Ossowski, M. Schaefer,
(2018).
date_created: 2021-08-06T12:53:49Z
date_published: 2018-05-31T00:00:00Z
date_updated: 2023-09-13T09:01:31Z
day: '31'
department:
- _id: FyKo
doi: 10.6084/m9.figshare.6401390.v1
main_file_link:
- open_access: '1'
url: https://doi.org/10.6084/m9.figshare.6401390.v1
month: '05'
oa: 1
oa_version: Preprint
publisher: Springer Nature
related_material:
record:
- id: '279'
relation: used_in_publication
status: public
status: public
title: 'Additional file 1: Of negative selection in tumor genome evolution acts on
essential cellular functions and the immunopeptidome'
type: research_data_reference
user_id: 6785fbc1-c503-11eb-8a32-93094b40e1cf
year: '2018'
...
---
_id: '20'
abstract:
- lang: eng
text: 'Background: Norepinephrine (NE) signaling has a key role in white adipose
tissue (WAT) functions, including lipolysis, free fatty acid liberation and, under
certain conditions, conversion of white into brite (brown-in-white) adipocytes.
However, acute effects of NE stimulation have not been described at the transcriptional
network level. Results: We used RNA-seq to uncover a broad transcriptional response.
The inference of protein-protein and protein-DNA interaction networks allowed
us to identify a set of immediate-early genes (IEGs) with high betweenness, validating
our approach and suggesting a hierarchical control of transcriptional regulation.
In addition, we identified a transcriptional regulatory network with IEGs as master
regulators, including HSF1 and NFIL3 as novel NE-induced IEG candidates. Moreover,
a functional enrichment analysis and gene clustering into functional modules suggest
a crosstalk between metabolic, signaling, and immune responses. Conclusions: Altogether,
our network biology approach explores for the first time the immediate-early systems
level response of human adipocytes to acute sympathetic activation, thereby providing
a first network basis of early cell fate programs and crosstalks between metabolic
and transcriptional networks required for proper WAT function.'
acknowledgement: This work was funded by the German Centre for Diabetes Research (DZD)
and the Austrian Science Fund (FWF, P25729-B19).
article_processing_charge: No
article_type: original
author:
- first_name: Juan
full_name: Higareda Almaraz, Juan
last_name: Higareda Almaraz
- first_name: Michael
full_name: Karbiener, Michael
last_name: Karbiener
- first_name: Maude
full_name: Giroud, Maude
last_name: Giroud
- first_name: Florian
full_name: Pauler, Florian
id: 48EA0138-F248-11E8-B48F-1D18A9856A87
last_name: Pauler
orcid: 0000-0002-7462-0048
- first_name: Teresa
full_name: Gerhalter, Teresa
last_name: Gerhalter
- first_name: Stephan
full_name: Herzig, Stephan
last_name: Herzig
- first_name: Marcel
full_name: Scheideler, Marcel
last_name: Scheideler
citation:
ama: Higareda Almaraz J, Karbiener M, Giroud M, et al. Norepinephrine triggers an
immediate-early regulatory network response in primary human white adipocytes.
BMC Genomics. 2018;19(1). doi:10.1186/s12864-018-5173-0
apa: Higareda Almaraz, J., Karbiener, M., Giroud, M., Pauler, F., Gerhalter, T.,
Herzig, S., & Scheideler, M. (2018). Norepinephrine triggers an immediate-early
regulatory network response in primary human white adipocytes. BMC Genomics.
BioMed Central. https://doi.org/10.1186/s12864-018-5173-0
chicago: Higareda Almaraz, Juan, Michael Karbiener, Maude Giroud, Florian Pauler,
Teresa Gerhalter, Stephan Herzig, and Marcel Scheideler. “Norepinephrine Triggers
an Immediate-Early Regulatory Network Response in Primary Human White Adipocytes.”
BMC Genomics. BioMed Central, 2018. https://doi.org/10.1186/s12864-018-5173-0.
ieee: J. Higareda Almaraz et al., “Norepinephrine triggers an immediate-early
regulatory network response in primary human white adipocytes,” BMC Genomics,
vol. 19, no. 1. BioMed Central, 2018.
ista: Higareda Almaraz J, Karbiener M, Giroud M, Pauler F, Gerhalter T, Herzig S,
Scheideler M. 2018. Norepinephrine triggers an immediate-early regulatory network
response in primary human white adipocytes. BMC Genomics. 19(1).
mla: Higareda Almaraz, Juan, et al. “Norepinephrine Triggers an Immediate-Early
Regulatory Network Response in Primary Human White Adipocytes.” BMC Genomics,
vol. 19, no. 1, BioMed Central, 2018, doi:10.1186/s12864-018-5173-0.
short: J. Higareda Almaraz, M. Karbiener, M. Giroud, F. Pauler, T. Gerhalter, S.
Herzig, M. Scheideler, BMC Genomics 19 (2018).
date_created: 2018-12-11T11:44:12Z
date_published: 2018-11-03T00:00:00Z
date_updated: 2023-09-13T09:10:47Z
day: '03'
ddc:
- '570'
department:
- _id: SiHi
doi: 10.1186/s12864-018-5173-0
external_id:
isi:
- '000450976700002'
file:
- access_level: open_access
checksum: a56516e734dab589dc7f3e1915973b4d
content_type: application/pdf
creator: dernst
date_created: 2018-12-17T14:52:57Z
date_updated: 2020-07-14T12:45:23Z
file_id: '5712'
file_name: 2018_BMCGenomics_Higareda.pdf
file_size: 4629784
relation: main_file
file_date_updated: 2020-07-14T12:45:23Z
has_accepted_license: '1'
intvolume: ' 19'
isi: 1
issue: '1'
language:
- iso: eng
month: '11'
oa: 1
oa_version: Published Version
publication: BMC Genomics
publication_identifier:
issn:
- 1471-2164
publication_status: published
publisher: BioMed Central
publist_id: '8035'
quality_controlled: '1'
related_material:
record:
- id: '9807'
relation: research_data
status: public
- id: '9808'
relation: research_data
status: public
scopus_import: '1'
status: public
title: Norepinephrine triggers an immediate-early regulatory network response in primary
human white adipocytes
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: journal_article
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
volume: 19
year: '2018'
...
---
_id: '107'
abstract:
- lang: eng
text: 'We introduce the notion of “non-malleable codes” which relaxes the notion
of error correction and error detection. Informally, a code is non-malleable if
the message contained in a modified codeword is either the original message, or
a completely unrelated value. In contrast to error correction and error detection,
non-malleability can be achieved for very rich classes of modifications. We construct
an efficient code that is non-malleable with respect to modifications that affect
each bit of the codeword arbitrarily (i.e., leave it untouched, flip it, or set
it to either 0 or 1), but independently of the value of the other bits of the
codeword. Using the probabilistic method, we also show a very strong and general
statement: there exists a non-malleable code for every “small enough” family F
of functions via which codewords can be modified. Although this probabilistic
method argument does not directly yield efficient constructions, it gives us efficient
non-malleable codes in the random-oracle model for very general classes of tampering
functions—e.g., functions where every bit in the tampered codeword can depend
arbitrarily on any 99% of the bits in the original codeword. As an application
of non-malleable codes, we show that they provide an elegant algorithmic solution
to the task of protecting functionalities implemented in hardware (e.g., signature
cards) against “tampering attacks.” In such attacks, the secret state of a physical
system is tampered, in the hopes that future interaction with the modified system
will reveal some secret information. This problem was previously studied in the
work of Gennaro et al. in 2004 under the name “algorithmic tamper proof security”
(ATP). We show that non-malleable codes can be used to achieve important improvements
over the prior work. In particular, we show that any functionality can be made
secure against a large class of tampering attacks, simply by encoding the secret
state with a non-malleable code while it is stored in memory.'
article_number: '20'
article_processing_charge: No
article_type: original
author:
- first_name: Stefan
full_name: Dziembowski, Stefan
last_name: Dziembowski
- first_name: Krzysztof Z
full_name: Pietrzak, Krzysztof Z
id: 3E04A7AA-F248-11E8-B48F-1D18A9856A87
last_name: Pietrzak
orcid: 0000-0002-9139-1654
- first_name: Daniel
full_name: Wichs, Daniel
last_name: Wichs
citation:
ama: Dziembowski S, Pietrzak KZ, Wichs D. Non-malleable codes. Journal of the
ACM. 2018;65(4). doi:10.1145/3178432
apa: Dziembowski, S., Pietrzak, K. Z., & Wichs, D. (2018). Non-malleable codes.
Journal of the ACM. ACM. https://doi.org/10.1145/3178432
chicago: Dziembowski, Stefan, Krzysztof Z Pietrzak, and Daniel Wichs. “Non-Malleable
Codes.” Journal of the ACM. ACM, 2018. https://doi.org/10.1145/3178432.
ieee: S. Dziembowski, K. Z. Pietrzak, and D. Wichs, “Non-malleable codes,” Journal
of the ACM, vol. 65, no. 4. ACM, 2018.
ista: Dziembowski S, Pietrzak KZ, Wichs D. 2018. Non-malleable codes. Journal of
the ACM. 65(4), 20.
mla: Dziembowski, Stefan, et al. “Non-Malleable Codes.” Journal of the ACM,
vol. 65, no. 4, 20, ACM, 2018, doi:10.1145/3178432.
short: S. Dziembowski, K.Z. Pietrzak, D. Wichs, Journal of the ACM 65 (2018).
date_created: 2018-12-11T11:44:40Z
date_published: 2018-08-01T00:00:00Z
date_updated: 2023-09-13T09:05:17Z
day: '01'
department:
- _id: KrPi
doi: 10.1145/3178432
ec_funded: 1
external_id:
isi:
- '000442938200004'
intvolume: ' 65'
isi: 1
issue: '4'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://eprint.iacr.org/2009/608
month: '08'
oa: 1
oa_version: Preprint
project:
- _id: 258AA5B2-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '682815'
name: Teaching Old Crypto New Tricks
- _id: 258C570E-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '259668'
name: Provable Security for Physical Cryptography
publication: Journal of the ACM
publication_status: published
publisher: ACM
publist_id: '7947'
quality_controlled: '1'
scopus_import: '1'
status: public
title: Non-malleable codes
type: journal_article
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
volume: 65
year: '2018'
...
---
_id: '5676'
abstract:
- lang: eng
text: 'In epithelial tissues, cells tightly connect to each other through cell–cell
junctions, but they also present the remarkable capacity of reorganizing themselves
without compromising tissue integrity. Upon injury, simple epithelia efficiently
resolve small lesions through the action of actin cytoskeleton contractile structures
at the wound edge and cellular rearrangements. However, the underlying mechanisms
and how they cooperate are still poorly understood. In this study, we combine
live imaging and theoretical modeling to reveal a novel and indispensable role
for occluding junctions (OJs) in this process. We demonstrate that OJ loss of
function leads to defects in wound-closure dynamics: instead of contracting, wounds
dramatically increase their area. OJ mutants exhibit phenotypes in cell shape,
cellular rearrangements, and mechanical properties as well as in actin cytoskeleton
dynamics at the wound edge. We propose that OJs are essential for wound closure
by impacting on epithelial mechanics at the tissue level, which in turn is crucial
for correct regulation of the cellular events occurring at the wound edge.'
article_processing_charge: No
author:
- first_name: Lara
full_name: Carvalho, Lara
last_name: Carvalho
- first_name: Pedro
full_name: Patricio, Pedro
last_name: Patricio
- first_name: Susana
full_name: Ponte, Susana
last_name: Ponte
- first_name: Carl-Philipp J
full_name: Heisenberg, Carl-Philipp J
id: 39427864-F248-11E8-B48F-1D18A9856A87
last_name: Heisenberg
orcid: 0000-0002-0912-4566
- first_name: Luis
full_name: Almeida, Luis
last_name: Almeida
- first_name: André S.
full_name: Nunes, André S.
last_name: Nunes
- first_name: Nuno A.M.
full_name: Araújo, Nuno A.M.
last_name: Araújo
- first_name: Antonio
full_name: Jacinto, Antonio
last_name: Jacinto
citation:
ama: Carvalho L, Patricio P, Ponte S, et al. Occluding junctions as novel regulators
of tissue mechanics during wound repair. Journal of Cell Biology. 2018;217(12):4267-4283.
doi:10.1083/jcb.201804048
apa: Carvalho, L., Patricio, P., Ponte, S., Heisenberg, C.-P. J., Almeida, L., Nunes,
A. S., … Jacinto, A. (2018). Occluding junctions as novel regulators of tissue
mechanics during wound repair. Journal of Cell Biology. Rockefeller University
Press. https://doi.org/10.1083/jcb.201804048
chicago: Carvalho, Lara, Pedro Patricio, Susana Ponte, Carl-Philipp J Heisenberg,
Luis Almeida, André S. Nunes, Nuno A.M. Araújo, and Antonio Jacinto. “Occluding
Junctions as Novel Regulators of Tissue Mechanics during Wound Repair.” Journal
of Cell Biology. Rockefeller University Press, 2018. https://doi.org/10.1083/jcb.201804048.
ieee: L. Carvalho et al., “Occluding junctions as novel regulators of tissue
mechanics during wound repair,” Journal of Cell Biology, vol. 217, no.
12. Rockefeller University Press, pp. 4267–4283, 2018.
ista: Carvalho L, Patricio P, Ponte S, Heisenberg C-PJ, Almeida L, Nunes AS, Araújo
NAM, Jacinto A. 2018. Occluding junctions as novel regulators of tissue mechanics
during wound repair. Journal of Cell Biology. 217(12), 4267–4283.
mla: Carvalho, Lara, et al. “Occluding Junctions as Novel Regulators of Tissue Mechanics
during Wound Repair.” Journal of Cell Biology, vol. 217, no. 12, Rockefeller
University Press, 2018, pp. 4267–83, doi:10.1083/jcb.201804048.
short: L. Carvalho, P. Patricio, S. Ponte, C.-P.J. Heisenberg, L. Almeida, A.S.
Nunes, N.A.M. Araújo, A. Jacinto, Journal of Cell Biology 217 (2018) 4267–4283.
date_created: 2018-12-16T22:59:19Z
date_published: 2018-12-01T00:00:00Z
date_updated: 2023-09-13T09:11:17Z
day: '01'
department:
- _id: CaHe
doi: 10.1083/jcb.201804048
ec_funded: 1
external_id:
isi:
- '000451960800018'
pmid:
- '30228162 '
intvolume: ' 217'
isi: 1
issue: '12'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://www.ncbi.nlm.nih.gov/pubmed/30228162
month: '12'
oa: 1
oa_version: Submitted Version
page: 4267-4283
pmid: 1
project:
- _id: 25681D80-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '291734'
name: International IST Postdoc Fellowship Programme
publication: Journal of Cell Biology
publication_identifier:
issn:
- '00219525'
publication_status: published
publisher: Rockefeller University Press
quality_controlled: '1'
scopus_import: '1'
status: public
title: Occluding junctions as novel regulators of tissue mechanics during wound repair
type: journal_article
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
volume: 217
year: '2018'
...
---
_id: '14224'
abstract:
- lang: eng
text: Clustering is a cornerstone of unsupervised learning which can be thought
as disentangling multiple generative mechanisms underlying the data. In this paper
we introduce an algorithmic framework to train mixtures of implicit generative
models which we particularize for variational autoencoders. Relying on an additional
set of discriminators, we propose a competitive procedure in which the models
only need to approximate the portion of the data distribution from which they
can produce realistic samples. As a byproduct, each model is simpler to train,
and a clustering interpretation arises naturally from the partitioning of the
training points among the models. We empirically show that our approach splits
the training distribution in a reasonable way and increases the quality of the
generated samples.
article_processing_charge: No
author:
- first_name: Francesco
full_name: Locatello, Francesco
id: 26cfd52f-2483-11ee-8040-88983bcc06d4
last_name: Locatello
orcid: 0000-0002-4850-0683
- first_name: Damien
full_name: Vincent, Damien
last_name: Vincent
- first_name: Ilya
full_name: Tolstikhin, Ilya
last_name: Tolstikhin
- first_name: Gunnar
full_name: Ratsch, Gunnar
last_name: Ratsch
- first_name: Sylvain
full_name: Gelly, Sylvain
last_name: Gelly
- first_name: Bernhard
full_name: Scholkopf, Bernhard
last_name: Scholkopf
citation:
ama: 'Locatello F, Vincent D, Tolstikhin I, Ratsch G, Gelly S, Scholkopf B. Clustering
meets implicit generative models. In: 6th International Conference on Learning
Representations. ; 2018.'
apa: Locatello, F., Vincent, D., Tolstikhin, I., Ratsch, G., Gelly, S., & Scholkopf,
B. (2018). Clustering meets implicit generative models. In 6th International
Conference on Learning Representations. Vancouver, Canada.
chicago: Locatello, Francesco, Damien Vincent, Ilya Tolstikhin, Gunnar Ratsch, Sylvain
Gelly, and Bernhard Scholkopf. “Clustering Meets Implicit Generative Models.”
In 6th International Conference on Learning Representations, 2018.
ieee: F. Locatello, D. Vincent, I. Tolstikhin, G. Ratsch, S. Gelly, and B. Scholkopf,
“Clustering meets implicit generative models,” in 6th International Conference
on Learning Representations, Vancouver, Canada, 2018.
ista: Locatello F, Vincent D, Tolstikhin I, Ratsch G, Gelly S, Scholkopf B. 2018.
Clustering meets implicit generative models. 6th International Conference on Learning
Representations. International Conference on Machine Learning.
mla: Locatello, Francesco, et al. “Clustering Meets Implicit Generative Models.”
6th International Conference on Learning Representations, 2018.
short: F. Locatello, D. Vincent, I. Tolstikhin, G. Ratsch, S. Gelly, B. Scholkopf,
in:, 6th International Conference on Learning Representations, 2018.
conference:
end_date: 2018-05-03
location: Vancouver, Canada
name: International Conference on Machine Learning
start_date: 2018-04-30
date_created: 2023-08-22T14:25:34Z
date_published: 2018-05-01T00:00:00Z
date_updated: 2023-09-13T09:08:24Z
day: '01'
department:
- _id: FrLo
extern: '1'
external_id:
arxiv:
- '1804.11130'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/1804.11130
month: '05'
oa: 1
oa_version: Preprint
publication: 6th International Conference on Learning Representations
publication_status: published
quality_controlled: '1'
scopus_import: '1'
status: public
title: Clustering meets implicit generative models
type: conference
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
year: '2018'
...
---
_id: '9807'
abstract:
- lang: eng
text: Table S1. Genes with highest betweenness. Table S2. Local and Master regulators
up-regulated. Table S3. Local and Master regulators down-regulated (XLSX 23 kb).
article_processing_charge: No
author:
- first_name: Juan
full_name: Higareda Almaraz, Juan
last_name: Higareda Almaraz
- first_name: Michael
full_name: Karbiener, Michael
last_name: Karbiener
- first_name: Maude
full_name: Giroud, Maude
last_name: Giroud
- first_name: Florian
full_name: Pauler, Florian
id: 48EA0138-F248-11E8-B48F-1D18A9856A87
last_name: Pauler
orcid: 0000-0002-7462-0048
- first_name: Teresa
full_name: Gerhalter, Teresa
last_name: Gerhalter
- first_name: Stephan
full_name: Herzig, Stephan
last_name: Herzig
- first_name: Marcel
full_name: Scheideler, Marcel
last_name: Scheideler
citation:
ama: 'Higareda Almaraz J, Karbiener M, Giroud M, et al. Additional file 1: Of Norepinephrine
triggers an immediate-early regulatory network response in primary human white
adipocytes. 2018. doi:10.6084/m9.figshare.7295339.v1'
apa: 'Higareda Almaraz, J., Karbiener, M., Giroud, M., Pauler, F., Gerhalter, T.,
Herzig, S., & Scheideler, M. (2018). Additional file 1: Of Norepinephrine
triggers an immediate-early regulatory network response in primary human white
adipocytes. Springer Nature. https://doi.org/10.6084/m9.figshare.7295339.v1'
chicago: 'Higareda Almaraz, Juan, Michael Karbiener, Maude Giroud, Florian Pauler,
Teresa Gerhalter, Stephan Herzig, and Marcel Scheideler. “Additional File 1: Of
Norepinephrine Triggers an Immediate-Early Regulatory Network Response in Primary
Human White Adipocytes.” Springer Nature, 2018. https://doi.org/10.6084/m9.figshare.7295339.v1.'
ieee: 'J. Higareda Almaraz et al., “Additional file 1: Of Norepinephrine
triggers an immediate-early regulatory network response in primary human white
adipocytes.” Springer Nature, 2018.'
ista: 'Higareda Almaraz J, Karbiener M, Giroud M, Pauler F, Gerhalter T, Herzig
S, Scheideler M. 2018. Additional file 1: Of Norepinephrine triggers an immediate-early
regulatory network response in primary human white adipocytes, Springer Nature,
10.6084/m9.figshare.7295339.v1.'
mla: 'Higareda Almaraz, Juan, et al. Additional File 1: Of Norepinephrine Triggers
an Immediate-Early Regulatory Network Response in Primary Human White Adipocytes.
Springer Nature, 2018, doi:10.6084/m9.figshare.7295339.v1.'
short: J. Higareda Almaraz, M. Karbiener, M. Giroud, F. Pauler, T. Gerhalter, S.
Herzig, M. Scheideler, (2018).
date_created: 2021-08-06T12:26:53Z
date_published: 2018-11-03T00:00:00Z
date_updated: 2023-09-13T09:10:47Z
day: '03'
department:
- _id: SiHi
doi: 10.6084/m9.figshare.7295339.v1
main_file_link:
- open_access: '1'
url: https://doi.org/10.6084/m9.figshare.7295339.v1
month: '11'
oa: 1
oa_version: Published Version
publisher: Springer Nature
related_material:
record:
- id: '20'
relation: used_in_publication
status: public
status: public
title: 'Additional file 1: Of Norepinephrine triggers an immediate-early regulatory
network response in primary human white adipocytes'
type: research_data_reference
user_id: 6785fbc1-c503-11eb-8a32-93094b40e1cf
year: '2018'
...
---
_id: '9808'
abstract:
- lang: eng
text: Table S4. Counts per Gene per Million Reads Mapped. (XLSX 2751 kb).
article_processing_charge: No
author:
- first_name: Juan
full_name: Higareda Almaraz, Juan
last_name: Higareda Almaraz
- first_name: Michael
full_name: Karbiener, Michael
last_name: Karbiener
- first_name: Maude
full_name: Giroud, Maude
last_name: Giroud
- first_name: Florian
full_name: Pauler, Florian
id: 48EA0138-F248-11E8-B48F-1D18A9856A87
last_name: Pauler
orcid: 0000-0002-7462-0048
- first_name: Teresa
full_name: Gerhalter, Teresa
last_name: Gerhalter
- first_name: Stephan
full_name: Herzig, Stephan
last_name: Herzig
- first_name: Marcel
full_name: Scheideler, Marcel
last_name: Scheideler
citation:
ama: 'Higareda Almaraz J, Karbiener M, Giroud M, et al. Additional file 3: Of Norepinephrine
triggers an immediate-early regulatory network response in primary human white
adipocytes. 2018. doi:10.6084/m9.figshare.7295369.v1'
apa: 'Higareda Almaraz, J., Karbiener, M., Giroud, M., Pauler, F., Gerhalter, T.,
Herzig, S., & Scheideler, M. (2018). Additional file 3: Of Norepinephrine
triggers an immediate-early regulatory network response in primary human white
adipocytes. Springer Nature. https://doi.org/10.6084/m9.figshare.7295369.v1'
chicago: 'Higareda Almaraz, Juan, Michael Karbiener, Maude Giroud, Florian Pauler,
Teresa Gerhalter, Stephan Herzig, and Marcel Scheideler. “Additional File 3: Of
Norepinephrine Triggers an Immediate-Early Regulatory Network Response in Primary
Human White Adipocytes.” Springer Nature, 2018. https://doi.org/10.6084/m9.figshare.7295369.v1.'
ieee: 'J. Higareda Almaraz et al., “Additional file 3: Of Norepinephrine
triggers an immediate-early regulatory network response in primary human white
adipocytes.” Springer Nature, 2018.'
ista: 'Higareda Almaraz J, Karbiener M, Giroud M, Pauler F, Gerhalter T, Herzig
S, Scheideler M. 2018. Additional file 3: Of Norepinephrine triggers an immediate-early
regulatory network response in primary human white adipocytes, Springer Nature,
10.6084/m9.figshare.7295369.v1.'
mla: 'Higareda Almaraz, Juan, et al. Additional File 3: Of Norepinephrine Triggers
an Immediate-Early Regulatory Network Response in Primary Human White Adipocytes.
Springer Nature, 2018, doi:10.6084/m9.figshare.7295369.v1.'
short: J. Higareda Almaraz, M. Karbiener, M. Giroud, F. Pauler, T. Gerhalter, S.
Herzig, M. Scheideler, (2018).
date_created: 2021-08-06T12:31:57Z
date_published: 2018-11-03T00:00:00Z
date_updated: 2023-09-13T09:10:47Z
day: '03'
department:
- _id: SiHi
doi: 10.6084/m9.figshare.7295369.v1
main_file_link:
- open_access: '1'
url: https://doi.org/10.6084/m9.figshare.7295369.v1
month: '11'
oa: 1
oa_version: Published Version
publisher: Springer Nature
related_material:
record:
- id: '20'
relation: used_in_publication
status: public
status: public
title: 'Additional file 3: Of Norepinephrine triggers an immediate-early regulatory
network response in primary human white adipocytes'
type: research_data_reference
user_id: 6785fbc1-c503-11eb-8a32-93094b40e1cf
year: '2018'
...
---
_id: '193'
abstract:
- lang: eng
text: 'We show attacks on five data-independent memory-hard functions (iMHF) that
were submitted to the password hashing competition (PHC). Informally, an MHF is
a function which cannot be evaluated on dedicated hardware, like ASICs, at significantly
lower hardware and/or energy cost than evaluating a single instance on a standard
single-core architecture. Data-independent means the memory access pattern of
the function is independent of the input; this makes iMHFs harder to construct
than data-dependent ones, but the latter can be attacked by various side-channel
attacks. Following [Alwen-Blocki''16], we capture the evaluation of an iMHF as
a directed acyclic graph (DAG). The cumulative parallel pebbling complexity of
this DAG is a measure for the hardware cost of evaluating the iMHF on an ASIC.
Ideally, one would like the complexity of a DAG underlying an iMHF to be as close
to quadratic in the number of nodes of the graph as possible. Instead, we show
that (the DAGs underlying) the following iMHFs are far from this bound: Rig.v2,
TwoCats and Gambit each having an exponent no more than 1.75. Moreover, we show
that the complexity of the iMHF modes of the PHC finalists Pomelo and Lyra2 have
exponents at most 1.83 and 1.67 respectively. To show this we investigate a combinatorial
property of each underlying DAG (called its depth-robustness. By establishing
upper bounds on this property we are then able to apply the general technique
of [Alwen-Block''16] for analyzing the hardware costs of an iMHF.'
acknowledgement: Leonid Reyzin was supported in part by IST Austria and by US NSF
grants 1012910, 1012798, and 1422965; this research was performed while he was visiting
IST Austria.
article_processing_charge: No
author:
- first_name: Joel F
full_name: Alwen, Joel F
id: 2A8DFA8C-F248-11E8-B48F-1D18A9856A87
last_name: Alwen
- first_name: Peter
full_name: Gazi, Peter
last_name: Gazi
- first_name: Chethan
full_name: Kamath Hosdurg, Chethan
id: 4BD3F30E-F248-11E8-B48F-1D18A9856A87
last_name: Kamath Hosdurg
- first_name: Karen
full_name: Klein, Karen
id: 3E83A2F8-F248-11E8-B48F-1D18A9856A87
last_name: Klein
- first_name: Georg F
full_name: Osang, Georg F
id: 464B40D6-F248-11E8-B48F-1D18A9856A87
last_name: Osang
orcid: 0000-0002-8882-5116
- first_name: Krzysztof Z
full_name: Pietrzak, Krzysztof Z
id: 3E04A7AA-F248-11E8-B48F-1D18A9856A87
last_name: Pietrzak
orcid: 0000-0002-9139-1654
- first_name: Lenoid
full_name: Reyzin, Lenoid
last_name: Reyzin
- first_name: Michal
full_name: Rolinek, Michal
id: 3CB3BC06-F248-11E8-B48F-1D18A9856A87
last_name: Rolinek
- first_name: Michal
full_name: Rybar, Michal
id: 2B3E3DE8-F248-11E8-B48F-1D18A9856A87
last_name: Rybar
citation:
ama: 'Alwen JF, Gazi P, Kamath Hosdurg C, et al. On the memory hardness of data
independent password hashing functions. In: Proceedings of the 2018 on Asia
Conference on Computer and Communication Security. ACM; 2018:51-65. doi:10.1145/3196494.3196534'
apa: 'Alwen, J. F., Gazi, P., Kamath Hosdurg, C., Klein, K., Osang, G. F., Pietrzak,
K. Z., … Rybar, M. (2018). On the memory hardness of data independent password
hashing functions. In Proceedings of the 2018 on Asia Conference on Computer
and Communication Security (pp. 51–65). Incheon, Republic of Korea: ACM. https://doi.org/10.1145/3196494.3196534'
chicago: Alwen, Joel F, Peter Gazi, Chethan Kamath Hosdurg, Karen Klein, Georg F
Osang, Krzysztof Z Pietrzak, Lenoid Reyzin, Michal Rolinek, and Michal Rybar.
“On the Memory Hardness of Data Independent Password Hashing Functions.” In Proceedings
of the 2018 on Asia Conference on Computer and Communication Security, 51–65.
ACM, 2018. https://doi.org/10.1145/3196494.3196534.
ieee: J. F. Alwen et al., “On the memory hardness of data independent password
hashing functions,” in Proceedings of the 2018 on Asia Conference on Computer
and Communication Security, Incheon, Republic of Korea, 2018, pp. 51–65.
ista: 'Alwen JF, Gazi P, Kamath Hosdurg C, Klein K, Osang GF, Pietrzak KZ, Reyzin
L, Rolinek M, Rybar M. 2018. On the memory hardness of data independent password
hashing functions. Proceedings of the 2018 on Asia Conference on Computer and
Communication Security. ASIACCS: Asia Conference on Computer and Communications
Security , 51–65.'
mla: Alwen, Joel F., et al. “On the Memory Hardness of Data Independent Password
Hashing Functions.” Proceedings of the 2018 on Asia Conference on Computer
and Communication Security, ACM, 2018, pp. 51–65, doi:10.1145/3196494.3196534.
short: J.F. Alwen, P. Gazi, C. Kamath Hosdurg, K. Klein, G.F. Osang, K.Z. Pietrzak,
L. Reyzin, M. Rolinek, M. Rybar, in:, Proceedings of the 2018 on Asia Conference
on Computer and Communication Security, ACM, 2018, pp. 51–65.
conference:
end_date: 2018-06-08
location: Incheon, Republic of Korea
name: 'ASIACCS: Asia Conference on Computer and Communications Security '
start_date: 2018-06-04
date_created: 2018-12-11T11:45:07Z
date_published: 2018-06-01T00:00:00Z
date_updated: 2023-09-13T09:13:12Z
day: '01'
department:
- _id: KrPi
- _id: HeEd
- _id: VlKo
doi: 10.1145/3196494.3196534
ec_funded: 1
external_id:
isi:
- '000516620100005'
isi: 1
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://eprint.iacr.org/2016/783
month: '06'
oa: 1
oa_version: Submitted Version
page: 51 - 65
project:
- _id: 25FBA906-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '616160'
name: 'Discrete Optimization in Computer Vision: Theory and Practice'
- _id: 258AA5B2-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '682815'
name: Teaching Old Crypto New Tricks
publication: Proceedings of the 2018 on Asia Conference on Computer and Communication
Security
publication_status: published
publisher: ACM
publist_id: '7723'
quality_controlled: '1'
scopus_import: '1'
status: public
title: On the memory hardness of data independent password hashing functions
type: conference
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
year: '2018'
...
---
_id: '300'
abstract:
- lang: eng
text: We introduce a formal quantitative notion of “bit security” for a general
type of cryptographic games (capturing both decision and search problems), aimed
at capturing the intuition that a cryptographic primitive with k-bit security
is as hard to break as an ideal cryptographic function requiring a brute force
attack on a k-bit key space. Our new definition matches the notion of bit security
commonly used by cryptographers and cryptanalysts when studying search (e.g.,
key recovery) problems, where the use of the traditional definition is well established.
However, it produces a quantitatively different metric in the case of decision
(indistinguishability) problems, where the use of (a straightforward generalization
of) the traditional definition is more problematic and leads to a number of paradoxical
situations or mismatches between theoretical/provable security and practical/common
sense intuition. Key to our new definition is to consider adversaries that may
explicitly declare failure of the attack. We support and justify the new definition
by proving a number of technical results, including tight reductions between several
standard cryptographic problems, a new hybrid theorem that preserves bit security,
and an application to the security analysis of indistinguishability primitives
making use of (approximate) floating point numbers. This is the first result showing
that (standard precision) 53-bit floating point numbers can be used to achieve
100-bit security in the context of cryptographic primitives with general indistinguishability-based
security definitions. Previous results of this type applied only to search problems,
or special types of decision problems.
acknowledgement: Research supported in part by the Defense Advanced Research Projects
Agency (DARPA) and the U.S. Army Research Office under the SafeWare program. Opinions,
findings and conclusions or recommendations expressed in this material are those
of the author(s) and do not necessarily reflect the views, position or policy of
the Government. The second author was also supported by the European Research Council,
ERC consolidator grant (682815 - TOCNeT).
alternative_title:
- LNCS
article_processing_charge: No
author:
- first_name: Daniele
full_name: Micciancio, Daniele
last_name: Micciancio
- first_name: Michael
full_name: Walter, Michael
id: 488F98B0-F248-11E8-B48F-1D18A9856A87
last_name: Walter
orcid: 0000-0003-3186-2482
citation:
ama: 'Micciancio D, Walter M. On the bit security of cryptographic primitives. In:
Vol 10820. Springer; 2018:3-28. doi:10.1007/978-3-319-78381-9_1'
apa: 'Micciancio, D., & Walter, M. (2018). On the bit security of cryptographic
primitives (Vol. 10820, pp. 3–28). Presented at the Eurocrypt: Advances in Cryptology,
Tel Aviv, Israel: Springer. https://doi.org/10.1007/978-3-319-78381-9_1'
chicago: Micciancio, Daniele, and Michael Walter. “On the Bit Security of Cryptographic
Primitives,” 10820:3–28. Springer, 2018. https://doi.org/10.1007/978-3-319-78381-9_1.
ieee: 'D. Micciancio and M. Walter, “On the bit security of cryptographic primitives,”
presented at the Eurocrypt: Advances in Cryptology, Tel Aviv, Israel, 2018, vol.
10820, pp. 3–28.'
ista: 'Micciancio D, Walter M. 2018. On the bit security of cryptographic primitives.
Eurocrypt: Advances in Cryptology, LNCS, vol. 10820, 3–28.'
mla: Micciancio, Daniele, and Michael Walter. On the Bit Security of Cryptographic
Primitives. Vol. 10820, Springer, 2018, pp. 3–28, doi:10.1007/978-3-319-78381-9_1.
short: D. Micciancio, M. Walter, in:, Springer, 2018, pp. 3–28.
conference:
end_date: 2018-05-03
location: Tel Aviv, Israel
name: 'Eurocrypt: Advances in Cryptology'
start_date: 2018-04-29
date_created: 2018-12-11T11:45:42Z
date_published: 2018-03-31T00:00:00Z
date_updated: 2023-09-13T09:12:04Z
day: '31'
department:
- _id: KrPi
doi: 10.1007/978-3-319-78381-9_1
ec_funded: 1
external_id:
isi:
- '000517097500001'
intvolume: ' 10820'
isi: 1
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://eprint.iacr.org/2018/077
month: '03'
oa: 1
oa_version: Submitted Version
page: 3 - 28
project:
- _id: 258AA5B2-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '682815'
name: Teaching Old Crypto New Tricks
publication_status: published
publisher: Springer
publist_id: '7581'
quality_controlled: '1'
scopus_import: '1'
status: public
title: On the bit security of cryptographic primitives
type: conference
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
volume: 10820
year: '2018'
...
---
_id: '312'
abstract:
- lang: eng
text: Motivated by biological questions, we study configurations of equal spheres
that neither pack nor cover. Placing their centers on a lattice, we define the
soft density of the configuration by penalizing multiple overlaps. Considering
the 1-parameter family of diagonally distorted 3-dimensional integer lattices,
we show that the soft density is maximized at the FCC lattice.
acknowledgement: This work was partially supported by the DFG Collaborative Research
Center TRR 109, “Discretization in Geometry and Dynamics,” through grant I02979-N35
of the Austrian Science Fund (FWF).
article_processing_charge: No
article_type: original
author:
- first_name: Herbert
full_name: Edelsbrunner, Herbert
id: 3FB178DA-F248-11E8-B48F-1D18A9856A87
last_name: Edelsbrunner
orcid: 0000-0002-9823-6833
- first_name: Mabel
full_name: Iglesias Ham, Mabel
id: 41B58C0C-F248-11E8-B48F-1D18A9856A87
last_name: Iglesias Ham
citation:
ama: Edelsbrunner H, Iglesias Ham M. On the optimality of the FCC lattice for soft
sphere packing. SIAM J Discrete Math. 2018;32(1):750-782. doi:10.1137/16M1097201
apa: Edelsbrunner, H., & Iglesias Ham, M. (2018). On the optimality of the FCC
lattice for soft sphere packing. SIAM J Discrete Math. Society for Industrial
and Applied Mathematics . https://doi.org/10.1137/16M1097201
chicago: Edelsbrunner, Herbert, and Mabel Iglesias Ham. “On the Optimality of the
FCC Lattice for Soft Sphere Packing.” SIAM J Discrete Math. Society for
Industrial and Applied Mathematics , 2018. https://doi.org/10.1137/16M1097201.
ieee: H. Edelsbrunner and M. Iglesias Ham, “On the optimality of the FCC lattice
for soft sphere packing,” SIAM J Discrete Math, vol. 32, no. 1. Society
for Industrial and Applied Mathematics , pp. 750–782, 2018.
ista: Edelsbrunner H, Iglesias Ham M. 2018. On the optimality of the FCC lattice
for soft sphere packing. SIAM J Discrete Math. 32(1), 750–782.
mla: Edelsbrunner, Herbert, and Mabel Iglesias Ham. “On the Optimality of the FCC
Lattice for Soft Sphere Packing.” SIAM J Discrete Math, vol. 32, no. 1,
Society for Industrial and Applied Mathematics , 2018, pp. 750–82, doi:10.1137/16M1097201.
short: H. Edelsbrunner, M. Iglesias Ham, SIAM J Discrete Math 32 (2018) 750–782.
date_created: 2018-12-11T11:45:46Z
date_published: 2018-03-29T00:00:00Z
date_updated: 2023-09-13T09:34:38Z
day: '29'
department:
- _id: HeEd
doi: 10.1137/16M1097201
external_id:
isi:
- '000428958900038'
intvolume: ' 32'
isi: 1
issue: '1'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: http://pdfs.semanticscholar.org/d2d5/6da00fbc674e6a8b1bb9d857167e54200dc6.pdf
month: '03'
oa: 1
oa_version: Submitted Version
page: 750 - 782
project:
- _id: 2561EBF4-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: I02979-N35
name: Persistence and stability of geometric complexes
publication: SIAM J Discrete Math
publication_identifier:
issn:
- '08954801'
publication_status: published
publisher: 'Society for Industrial and Applied Mathematics '
publist_id: '7553'
quality_controlled: '1'
scopus_import: '1'
status: public
title: On the optimality of the FCC lattice for soft sphere packing
type: journal_article
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
volume: 32
year: '2018'
...
---
_id: '409'
abstract:
- lang: eng
text: We give a simple proof of T. Stehling's result [4], whereby in any normal
tiling of the plane with convex polygons with number of sides not less than six,
all tiles except a finite number are hexagons.
article_processing_charge: No
article_type: original
author:
- first_name: Arseniy
full_name: Akopyan, Arseniy
id: 430D2C90-F248-11E8-B48F-1D18A9856A87
last_name: Akopyan
orcid: 0000-0002-2548-617X
citation:
ama: Akopyan A. On the number of non-hexagons in a planar tiling. Comptes Rendus
Mathematique. 2018;356(4):412-414. doi:10.1016/j.crma.2018.03.005
apa: Akopyan, A. (2018). On the number of non-hexagons in a planar tiling. Comptes
Rendus Mathematique. Elsevier. https://doi.org/10.1016/j.crma.2018.03.005
chicago: Akopyan, Arseniy. “On the Number of Non-Hexagons in a Planar Tiling.” Comptes
Rendus Mathematique. Elsevier, 2018. https://doi.org/10.1016/j.crma.2018.03.005.
ieee: A. Akopyan, “On the number of non-hexagons in a planar tiling,” Comptes
Rendus Mathematique, vol. 356, no. 4. Elsevier, pp. 412–414, 2018.
ista: Akopyan A. 2018. On the number of non-hexagons in a planar tiling. Comptes
Rendus Mathematique. 356(4), 412–414.
mla: Akopyan, Arseniy. “On the Number of Non-Hexagons in a Planar Tiling.” Comptes
Rendus Mathematique, vol. 356, no. 4, Elsevier, 2018, pp. 412–14, doi:10.1016/j.crma.2018.03.005.
short: A. Akopyan, Comptes Rendus Mathematique 356 (2018) 412–414.
date_created: 2018-12-11T11:46:19Z
date_published: 2018-04-01T00:00:00Z
date_updated: 2023-09-13T09:34:12Z
day: '01'
department:
- _id: HeEd
doi: 10.1016/j.crma.2018.03.005
external_id:
arxiv:
- '1805.01652'
isi:
- '000430402700009'
intvolume: ' 356'
isi: 1
issue: '4'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/1805.01652
month: '04'
oa: 1
oa_version: Preprint
page: 412-414
publication: Comptes Rendus Mathematique
publication_identifier:
issn:
- 1631073X
publication_status: published
publisher: Elsevier
publist_id: '7420'
quality_controlled: '1'
scopus_import: '1'
status: public
title: On the number of non-hexagons in a planar tiling
type: journal_article
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
volume: 356
year: '2018'
...
---
_id: '419'
abstract:
- lang: eng
text: 'Reciprocity is a major factor in human social life and accounts for a large
part of cooperation in our communities. Direct reciprocity arises when repeated
interactions occur between the same individuals. The framework of iterated games
formalizes this phenomenon. Despite being introduced more than five decades ago,
the concept keeps offering beautiful surprises. Recent theoretical research driven
by new mathematical tools has proposed a remarkable dichotomy among the crucial
strategies: successful individuals either act as partners or as rivals. Rivals
strive for unilateral advantages by applying selfish or extortionate strategies.
Partners aim to share the payoff for mutual cooperation, but are ready to fight
back when being exploited. Which of these behaviours evolves depends on the environment.
Whereas small population sizes and a limited number of rounds favour rivalry,
partner strategies are selected when populations are large and relationships stable.
Only partners allow for evolution of cooperation, while the rivals’ attempt to
put themselves first leads to defection. Hilbe et al. synthesize recent theoretical
work on zero-determinant and ‘rival’ versus ‘partner’ strategies in social dilemmas.
They describe the environments under which these contrasting selfish or cooperative
strategies emerge in evolution.'
article_processing_charge: No
article_type: review
author:
- first_name: Christian
full_name: Hilbe, Christian
id: 2FDF8F3C-F248-11E8-B48F-1D18A9856A87
last_name: Hilbe
orcid: 0000-0001-5116-955X
- first_name: Krishnendu
full_name: Chatterjee, Krishnendu
id: 2E5DCA20-F248-11E8-B48F-1D18A9856A87
last_name: Chatterjee
orcid: 0000-0002-4561-241X
- first_name: Martin
full_name: Nowak, Martin
last_name: Nowak
citation:
ama: Hilbe C, Chatterjee K, Nowak M. Partners and rivals in direct reciprocity.
Nature Human Behaviour. 2018;2:469–477. doi:10.1038/s41562-018-0320-9
apa: Hilbe, C., Chatterjee, K., & Nowak, M. (2018). Partners and rivals in direct
reciprocity. Nature Human Behaviour. Nature Publishing Group. https://doi.org/10.1038/s41562-018-0320-9
chicago: Hilbe, Christian, Krishnendu Chatterjee, and Martin Nowak. “Partners and
Rivals in Direct Reciprocity.” Nature Human Behaviour. Nature Publishing
Group, 2018. https://doi.org/10.1038/s41562-018-0320-9.
ieee: C. Hilbe, K. Chatterjee, and M. Nowak, “Partners and rivals in direct reciprocity,”
Nature Human Behaviour, vol. 2. Nature Publishing Group, pp. 469–477, 2018.
ista: Hilbe C, Chatterjee K, Nowak M. 2018. Partners and rivals in direct reciprocity.
Nature Human Behaviour. 2, 469–477.
mla: Hilbe, Christian, et al. “Partners and Rivals in Direct Reciprocity.” Nature
Human Behaviour, vol. 2, Nature Publishing Group, 2018, pp. 469–477, doi:10.1038/s41562-018-0320-9.
short: C. Hilbe, K. Chatterjee, M. Nowak, Nature Human Behaviour 2 (2018) 469–477.
date_created: 2018-12-11T11:46:22Z
date_published: 2018-03-19T00:00:00Z
date_updated: 2023-09-13T09:38:54Z
day: '19'
ddc:
- '000'
department:
- _id: KrCh
doi: 10.1038/s41562-018-0320-9
ec_funded: 1
external_id:
isi:
- '000446612000016'
file:
- access_level: open_access
checksum: 571b8cc0ba14e8d5d8b18e439a9835eb
content_type: application/pdf
creator: dernst
date_created: 2019-11-19T08:19:51Z
date_updated: 2020-07-14T12:46:25Z
file_id: '7052'
file_name: 2018_NatureHumanBeh_Hilbe.pdf
file_size: 598033
relation: main_file
file_date_updated: 2020-07-14T12:46:25Z
has_accepted_license: '1'
intvolume: ' 2'
isi: 1
language:
- iso: eng
month: '03'
oa: 1
oa_version: Submitted Version
page: 469–477
project:
- _id: 2581B60A-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '279307'
name: 'Quantitative Graph Games: Theory and Applications'
- _id: 2584A770-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: P 23499-N23
name: Modern Graph Algorithmic Techniques in Formal Verification
- _id: 25832EC2-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: S 11407_N23
name: Rigorous Systems Engineering
- _id: 25681D80-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '291734'
name: International IST Postdoc Fellowship Programme
publication: Nature Human Behaviour
publication_status: published
publisher: Nature Publishing Group
publist_id: '7404'
quality_controlled: '1'
related_material:
link:
- relation: erratum
url: http://doi.org/10.1038/s41562-018-0342-3
scopus_import: '1'
status: public
title: Partners and rivals in direct reciprocity
type: journal_article
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
volume: 2
year: '2018'
...
---
_id: '78'
abstract:
- lang: eng
text: We provide a procedure for detecting the sub-segments of an incrementally
observed Boolean signal ω that match a given temporal pattern ϕ. As a pattern
specification language, we use timed regular expressions, a formalism well-suited
for expressing properties of concurrent asynchronous behaviors embedded in metric
time. We construct a timed automaton accepting the timed language denoted by ϕ
and modify it slightly for the purpose of matching. We then apply zone-based reachability
computation to this automaton while it reads ω, and retrieve all the matching
segments from the results. Since the procedure is automaton based, it can be applied
to patterns specified by other formalisms such as timed temporal logics reducible
to timed automata or directly encoded as timed automata. The procedure has been
implemented and its performance on synthetic examples is demonstrated.
alternative_title:
- LNCS
article_processing_charge: No
author:
- first_name: Alexey
full_name: Bakhirkin, Alexey
last_name: Bakhirkin
- first_name: Thomas
full_name: Ferrere, Thomas
id: 40960E6E-F248-11E8-B48F-1D18A9856A87
last_name: Ferrere
orcid: 0000-0001-5199-3143
- first_name: Dejan
full_name: Nickovic, Dejan
last_name: Nickovic
- first_name: Oded
full_name: Maler, Oded
last_name: Maler
- first_name: Eugene
full_name: Asarin, Eugene
last_name: Asarin
citation:
ama: 'Bakhirkin A, Ferrere T, Nickovic D, Maler O, Asarin E. Online timed pattern
matching using automata. In: Vol 11022. Springer; 2018:215-232. doi:10.1007/978-3-030-00151-3_13'
apa: 'Bakhirkin, A., Ferrere, T., Nickovic, D., Maler, O., & Asarin, E. (2018).
Online timed pattern matching using automata (Vol. 11022, pp. 215–232). Presented
at the FORMATS: Formal Modeling and Analysis of Timed Systems, Bejing, China:
Springer. https://doi.org/10.1007/978-3-030-00151-3_13'
chicago: Bakhirkin, Alexey, Thomas Ferrere, Dejan Nickovic, Oded Maler, and Eugene
Asarin. “Online Timed Pattern Matching Using Automata,” 11022:215–32. Springer,
2018. https://doi.org/10.1007/978-3-030-00151-3_13.
ieee: 'A. Bakhirkin, T. Ferrere, D. Nickovic, O. Maler, and E. Asarin, “Online timed
pattern matching using automata,” presented at the FORMATS: Formal Modeling and
Analysis of Timed Systems, Bejing, China, 2018, vol. 11022, pp. 215–232.'
ista: 'Bakhirkin A, Ferrere T, Nickovic D, Maler O, Asarin E. 2018. Online timed
pattern matching using automata. FORMATS: Formal Modeling and Analysis of Timed
Systems, LNCS, vol. 11022, 215–232.'
mla: Bakhirkin, Alexey, et al. Online Timed Pattern Matching Using Automata.
Vol. 11022, Springer, 2018, pp. 215–32, doi:10.1007/978-3-030-00151-3_13.
short: A. Bakhirkin, T. Ferrere, D. Nickovic, O. Maler, E. Asarin, in:, Springer,
2018, pp. 215–232.
conference:
end_date: 2018-09-06
location: Bejing, China
name: 'FORMATS: Formal Modeling and Analysis of Timed Systems'
start_date: 2018-09-04
date_created: 2018-12-11T11:44:31Z
date_published: 2018-08-26T00:00:00Z
date_updated: 2023-09-13T09:35:46Z
day: '26'
ddc:
- '000'
department:
- _id: ToHe
doi: 10.1007/978-3-030-00151-3_13
external_id:
isi:
- '000884993200013'
file:
- access_level: open_access
checksum: 436b7574934324cfa7d1d3986fddc65b
content_type: application/pdf
creator: dernst
date_created: 2020-05-14T11:34:34Z
date_updated: 2020-07-14T12:48:03Z
file_id: '7831'
file_name: 2018_LNCS_Bakhirkin.pdf
file_size: 374851
relation: main_file
file_date_updated: 2020-07-14T12:48:03Z
has_accepted_license: '1'
intvolume: ' 11022'
isi: 1
language:
- iso: eng
month: '08'
oa: 1
oa_version: Submitted Version
page: 215 - 232
project:
- _id: 25832EC2-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: S 11407_N23
name: Rigorous Systems Engineering
- _id: 25F42A32-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: Z211
name: The Wittgenstein Prize
publication_identifier:
isbn:
- 978-3-030-00150-6
publication_status: published
publisher: Springer
publist_id: '7976'
quality_controlled: '1'
scopus_import: '1'
status: public
title: Online timed pattern matching using automata
type: conference
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
volume: 11022
year: '2018'
...
---
_id: '317'
abstract:
- lang: eng
text: We replace the established aluminium gates for the formation of quantum dots
in silicon with gates made from palladium. We study the morphology of both aluminium
and palladium gates with transmission electron microscopy. The native aluminium
oxide is found to be formed all around the aluminium gates, which could lead to
the formation of unintentional dots. Therefore, we report on a novel fabrication
route that replaces aluminium and its native oxide by palladium with atomic-layer-deposition-grown
aluminium oxide. Using this approach, we show the formation of low-disorder gate-defined
quantum dots, which are reproducibly fabricated. Furthermore, palladium enables
us to further shrink the gate design, allowing us to perform electron transport
measurements in the few-electron regime in devices comprising only two gate layers,
a major technological advancement. It remains to be seen, whether the introduction
of palladium gates can improve the excellent results on electron and nuclear spin
qubits defined with an aluminium gate stack.
article_number: '5690'
article_processing_charge: No
author:
- first_name: Matthias
full_name: Brauns, Matthias
id: 33F94E3C-F248-11E8-B48F-1D18A9856A87
last_name: Brauns
- first_name: Sergey
full_name: Amitonov, Sergey
last_name: Amitonov
- first_name: Paul
full_name: Spruijtenburg, Paul
last_name: Spruijtenburg
- first_name: Floris
full_name: Zwanenburg, Floris
last_name: Zwanenburg
citation:
ama: Brauns M, Amitonov S, Spruijtenburg P, Zwanenburg F. Palladium gates for reproducible
quantum dots in silicon. Scientific Reports. 2018;8(1). doi:10.1038/s41598-018-24004-y
apa: Brauns, M., Amitonov, S., Spruijtenburg, P., & Zwanenburg, F. (2018). Palladium
gates for reproducible quantum dots in silicon. Scientific Reports. Nature
Publishing Group. https://doi.org/10.1038/s41598-018-24004-y
chicago: Brauns, Matthias, Sergey Amitonov, Paul Spruijtenburg, and Floris Zwanenburg.
“Palladium Gates for Reproducible Quantum Dots in Silicon.” Scientific Reports.
Nature Publishing Group, 2018. https://doi.org/10.1038/s41598-018-24004-y.
ieee: M. Brauns, S. Amitonov, P. Spruijtenburg, and F. Zwanenburg, “Palladium gates
for reproducible quantum dots in silicon,” Scientific Reports, vol. 8,
no. 1. Nature Publishing Group, 2018.
ista: Brauns M, Amitonov S, Spruijtenburg P, Zwanenburg F. 2018. Palladium gates
for reproducible quantum dots in silicon. Scientific Reports. 8(1), 5690.
mla: Brauns, Matthias, et al. “Palladium Gates for Reproducible Quantum Dots in
Silicon.” Scientific Reports, vol. 8, no. 1, 5690, Nature Publishing Group,
2018, doi:10.1038/s41598-018-24004-y.
short: M. Brauns, S. Amitonov, P. Spruijtenburg, F. Zwanenburg, Scientific Reports
8 (2018).
date_created: 2018-12-11T11:45:47Z
date_published: 2018-04-09T00:00:00Z
date_updated: 2023-09-13T09:38:00Z
day: '09'
ddc:
- '539'
department:
- _id: GeKa
doi: 10.1038/s41598-018-24004-y
external_id:
isi:
- '000429404300013'
file:
- access_level: open_access
checksum: 20af238ca4ba6491b77270be8d826bf5
content_type: application/pdf
creator: system
date_created: 2018-12-12T10:17:04Z
date_updated: 2020-07-14T12:46:02Z
file_id: '5256'
file_name: IST-2018-1016-v1+1_2018_Brauns_Palladium_gates.pdf
file_size: 1850530
relation: main_file
file_date_updated: 2020-07-14T12:46:02Z
has_accepted_license: '1'
intvolume: ' 8'
isi: 1
issue: '1'
language:
- iso: eng
month: '04'
oa: 1
oa_version: Published Version
publication: Scientific Reports
publication_status: published
publisher: Nature Publishing Group
publist_id: '7548'
pubrep_id: '1016'
quality_controlled: '1'
scopus_import: '1'
status: public
title: Palladium gates for reproducible quantum dots in silicon
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: journal_article
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
volume: 8
year: '2018'
...
---
_id: '194'
abstract:
- lang: eng
text: Ants are emerging model systems to study cellular signaling because distinct
castes possess different physiologic phenotypes within the same colony. Here we
studied the functionality of inotocin signaling, an insect ortholog of mammalian
oxytocin (OT), which was recently discovered in ants. In Lasius ants, we determined
that specialization within the colony, seasonal factors, and physiologic conditions
down-regulated the expression of the OT-like signaling system. Given this natural
variation, we interrogated its function using RNAi knockdowns. Next-generation
RNA sequencing of OT-like precursor knock-down ants highlighted its role in the
regulation of genes involved in metabolism. Knock-down ants exhibited higher walking
activity and increased self-grooming in the brood chamber. We propose that OT-like
signaling in ants is important for regulating metabolic processes and locomotion.
article_processing_charge: No
article_type: original
author:
- first_name: Zita
full_name: Liutkeviciute, Zita
last_name: Liutkeviciute
- first_name: Esther
full_name: Gil Mansilla, Esther
last_name: Gil Mansilla
- first_name: Thomas
full_name: Eder, Thomas
last_name: Eder
- first_name: Barbara E
full_name: Casillas Perez, Barbara E
id: 351ED2AA-F248-11E8-B48F-1D18A9856A87
last_name: Casillas Perez
- first_name: Maria
full_name: Giulia Di Giglio, Maria
last_name: Giulia Di Giglio
- first_name: Edin
full_name: Muratspahić, Edin
last_name: Muratspahić
- first_name: Florian
full_name: Grebien, Florian
last_name: Grebien
- first_name: Thomas
full_name: Rattei, Thomas
last_name: Rattei
- first_name: Markus
full_name: Muttenthaler, Markus
last_name: Muttenthaler
- first_name: Sylvia
full_name: Cremer, Sylvia
id: 2F64EC8C-F248-11E8-B48F-1D18A9856A87
last_name: Cremer
orcid: 0000-0002-2193-3868
- first_name: Christian
full_name: Gruber, Christian
last_name: Gruber
citation:
ama: Liutkeviciute Z, Gil Mansilla E, Eder T, et al. Oxytocin-like signaling in
ants influences metabolic gene expression and locomotor activity. The FASEB
Journal. 2018;32(12):6808-6821. doi:10.1096/fj.201800443
apa: Liutkeviciute, Z., Gil Mansilla, E., Eder, T., Casillas Perez, B. E., Giulia
Di Giglio, M., Muratspahić, E., … Gruber, C. (2018). Oxytocin-like signaling in
ants influences metabolic gene expression and locomotor activity. The FASEB
Journal. FASEB. https://doi.org/10.1096/fj.201800443
chicago: Liutkeviciute, Zita, Esther Gil Mansilla, Thomas Eder, Barbara E Casillas
Perez, Maria Giulia Di Giglio, Edin Muratspahić, Florian Grebien, et al. “Oxytocin-like
Signaling in Ants Influences Metabolic Gene Expression and Locomotor Activity.”
The FASEB Journal. FASEB, 2018. https://doi.org/10.1096/fj.201800443.
ieee: Z. Liutkeviciute et al., “Oxytocin-like signaling in ants influences
metabolic gene expression and locomotor activity,” The FASEB Journal, vol.
32, no. 12. FASEB, pp. 6808–6821, 2018.
ista: Liutkeviciute Z, Gil Mansilla E, Eder T, Casillas Perez BE, Giulia Di Giglio
M, Muratspahić E, Grebien F, Rattei T, Muttenthaler M, Cremer S, Gruber C. 2018.
Oxytocin-like signaling in ants influences metabolic gene expression and locomotor
activity. The FASEB Journal. 32(12), 6808–6821.
mla: Liutkeviciute, Zita, et al. “Oxytocin-like Signaling in Ants Influences Metabolic
Gene Expression and Locomotor Activity.” The FASEB Journal, vol. 32, no.
12, FASEB, 2018, pp. 6808–21, doi:10.1096/fj.201800443.
short: Z. Liutkeviciute, E. Gil Mansilla, T. Eder, B.E. Casillas Perez, M. Giulia
Di Giglio, E. Muratspahić, F. Grebien, T. Rattei, M. Muttenthaler, S. Cremer,
C. Gruber, The FASEB Journal 32 (2018) 6808–6821.
date_created: 2018-12-11T11:45:08Z
date_published: 2018-11-29T00:00:00Z
date_updated: 2023-09-13T09:37:32Z
day: '29'
department:
- _id: SyCr
doi: 10.1096/fj.201800443
external_id:
isi:
- '000449359700035'
pmid:
- '29939785'
intvolume: ' 32'
isi: 1
issue: '12'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: ' https://doi.org/10.1096/fj.201800443'
month: '11'
oa: 1
oa_version: Published Version
page: 6808-6821
pmid: 1
project:
- _id: 25E3D34E-B435-11E9-9278-68D0E5697425
name: Individual function and social role of oxytocin-like neuropeptides in ants
publication: The FASEB Journal
publication_identifier:
issn:
- '08926638'
publication_status: published
publisher: FASEB
publist_id: '7721'
quality_controlled: '1'
scopus_import: '1'
status: public
title: Oxytocin-like signaling in ants influences metabolic gene expression and locomotor
activity
type: journal_article
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
volume: 32
year: '2018'
...
---
_id: '159'
abstract:
- lang: eng
text: L-type Ca2+ channels (LTCCs) play a crucial role in excitation-contraction
coupling and release of hormones from secretory cells. They are targets of antihypertensive
and antiarrhythmic drugs such as diltiazem. Here, we present a photoswitchable
diltiazem, FHU-779, which can be used to reversibly block endogenous LTCCs by
light. FHU-779 is as potent as diltiazem and can be used to place pancreatic β-cell
function and cardiac activity under optical control.
article_processing_charge: No
article_type: original
author:
- first_name: Timm
full_name: Fehrentz, Timm
last_name: Fehrentz
- first_name: Florian
full_name: Huber, Florian
last_name: Huber
- first_name: Nina
full_name: Hartrampf, Nina
last_name: Hartrampf
- first_name: Tobias
full_name: Bruegmann, Tobias
last_name: Bruegmann
- first_name: James
full_name: Frank, James
last_name: Frank
- first_name: Nicholas
full_name: Fine, Nicholas
last_name: Fine
- first_name: Daniela
full_name: Malan, Daniela
last_name: Malan
- first_name: Johann G
full_name: Danzl, Johann G
id: 42EFD3B6-F248-11E8-B48F-1D18A9856A87
last_name: Danzl
orcid: 0000-0001-8559-3973
- first_name: Denis
full_name: Tikhonov, Denis
last_name: Tikhonov
- first_name: Maritn
full_name: Sumser, Maritn
last_name: Sumser
- first_name: Philipp
full_name: Sasse, Philipp
last_name: Sasse
- first_name: David
full_name: Hodson, David
last_name: Hodson
- first_name: Boris
full_name: Zhorov, Boris
last_name: Zhorov
- first_name: Nikolaj
full_name: Klocker, Nikolaj
last_name: Klocker
- first_name: Dirk
full_name: Trauner, Dirk
last_name: Trauner
citation:
ama: Fehrentz T, Huber F, Hartrampf N, et al. Optical control of L-type Ca2+ channels
using a diltiazem photoswitch. Nature Chemical Biology. 2018;14(8):764-767.
doi:10.1038/s41589-018-0090-8
apa: Fehrentz, T., Huber, F., Hartrampf, N., Bruegmann, T., Frank, J., Fine, N.,
… Trauner, D. (2018). Optical control of L-type Ca2+ channels using a diltiazem
photoswitch. Nature Chemical Biology. Nature Publishing Group. https://doi.org/10.1038/s41589-018-0090-8
chicago: Fehrentz, Timm, Florian Huber, Nina Hartrampf, Tobias Bruegmann, James
Frank, Nicholas Fine, Daniela Malan, et al. “Optical Control of L-Type Ca2+ Channels
Using a Diltiazem Photoswitch.” Nature Chemical Biology. Nature Publishing
Group, 2018. https://doi.org/10.1038/s41589-018-0090-8.
ieee: T. Fehrentz et al., “Optical control of L-type Ca2+ channels using
a diltiazem photoswitch,” Nature Chemical Biology, vol. 14, no. 8. Nature
Publishing Group, pp. 764–767, 2018.
ista: Fehrentz T, Huber F, Hartrampf N, Bruegmann T, Frank J, Fine N, Malan D, Danzl
JG, Tikhonov D, Sumser M, Sasse P, Hodson D, Zhorov B, Klocker N, Trauner D. 2018.
Optical control of L-type Ca2+ channels using a diltiazem photoswitch. Nature
Chemical Biology. 14(8), 764–767.
mla: Fehrentz, Timm, et al. “Optical Control of L-Type Ca2+ Channels Using a Diltiazem
Photoswitch.” Nature Chemical Biology, vol. 14, no. 8, Nature Publishing
Group, 2018, pp. 764–67, doi:10.1038/s41589-018-0090-8.
short: T. Fehrentz, F. Huber, N. Hartrampf, T. Bruegmann, J. Frank, N. Fine, D.
Malan, J.G. Danzl, D. Tikhonov, M. Sumser, P. Sasse, D. Hodson, B. Zhorov, N.
Klocker, D. Trauner, Nature Chemical Biology 14 (2018) 764–767.
date_created: 2018-12-11T11:44:56Z
date_published: 2018-07-16T00:00:00Z
date_updated: 2023-09-13T09:36:35Z
day: '16'
ddc:
- '570'
department:
- _id: JoDa
doi: 10.1038/s41589-018-0090-8
external_id:
isi:
- '000438970200010'
file:
- access_level: open_access
checksum: d42935094ec845f54a0688bf12986d62
content_type: application/pdf
creator: dernst
date_created: 2020-05-14T12:14:09Z
date_updated: 2020-07-14T12:45:03Z
file_id: '7832'
file_name: 2018_NatureChemicalBiology_Fehrentz.pdf
file_size: 6321000
relation: main_file
file_date_updated: 2020-07-14T12:45:03Z
has_accepted_license: '1'
intvolume: ' 14'
isi: 1
issue: '8'
language:
- iso: eng
month: '07'
oa: 1
oa_version: Submitted Version
page: 764 - 767
publication: Nature Chemical Biology
publication_status: published
publisher: Nature Publishing Group
publist_id: '7762'
quality_controlled: '1'
related_material:
link:
- relation: erratum
url: https://doi.org/10.1038/s41589-021-00744-3
scopus_import: '1'
status: public
title: Optical control of L-type Ca2+ channels using a diltiazem photoswitch
type: journal_article
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
volume: 14
year: '2018'
...
---
_id: '79'
abstract:
- lang: eng
text: 'Markov Decision Processes (MDPs) are a popular class of models suitable for
solving control decision problems in probabilistic reactive systems. We consider
parametric MDPs (pMDPs) that include parameters in some of the transition probabilities
to account for stochastic uncertainties of the environment such as noise or input
disturbances. We study pMDPs with reachability objectives where the parameter
values are unknown and impossible to measure directly during execution, but there
is a probability distribution known over the parameter values. We study for the
first time computing parameter-independent strategies that are expectation optimal,
i.e., optimize the expected reachability probability under the probability distribution
over the parameters. We present an encoding of our problem to partially observable
MDPs (POMDPs), i.e., a reduction of our problem to computing optimal strategies
in POMDPs. We evaluate our method experimentally on several benchmarks: a motivating
(repeated) learner model; a series of benchmarks of varying configurations of
a robot moving on a grid; and a consensus protocol.'
alternative_title:
- LNCS
article_processing_charge: No
author:
- first_name: Sebastian
full_name: Arming, Sebastian
last_name: Arming
- first_name: Ezio
full_name: Bartocci, Ezio
last_name: Bartocci
- first_name: Krishnendu
full_name: Chatterjee, Krishnendu
id: 2E5DCA20-F248-11E8-B48F-1D18A9856A87
last_name: Chatterjee
orcid: 0000-0002-4561-241X
- first_name: Joost P
full_name: Katoen, Joost P
id: 4524F760-F248-11E8-B48F-1D18A9856A87
last_name: Katoen
- first_name: Ana
full_name: Sokolova, Ana
last_name: Sokolova
citation:
ama: 'Arming S, Bartocci E, Chatterjee K, Katoen JP, Sokolova A. Parameter-independent
strategies for pMDPs via POMDPs. In: Vol 11024. Springer; 2018:53-70. doi:10.1007/978-3-319-99154-2_4'
apa: 'Arming, S., Bartocci, E., Chatterjee, K., Katoen, J. P., & Sokolova, A.
(2018). Parameter-independent strategies for pMDPs via POMDPs (Vol. 11024, pp.
53–70). Presented at the QEST: Quantitative Evaluation of Systems, Beijing, China:
Springer. https://doi.org/10.1007/978-3-319-99154-2_4'
chicago: Arming, Sebastian, Ezio Bartocci, Krishnendu Chatterjee, Joost P Katoen,
and Ana Sokolova. “Parameter-Independent Strategies for PMDPs via POMDPs,” 11024:53–70.
Springer, 2018. https://doi.org/10.1007/978-3-319-99154-2_4.
ieee: 'S. Arming, E. Bartocci, K. Chatterjee, J. P. Katoen, and A. Sokolova, “Parameter-independent
strategies for pMDPs via POMDPs,” presented at the QEST: Quantitative Evaluation
of Systems, Beijing, China, 2018, vol. 11024, pp. 53–70.'
ista: 'Arming S, Bartocci E, Chatterjee K, Katoen JP, Sokolova A. 2018. Parameter-independent
strategies for pMDPs via POMDPs. QEST: Quantitative Evaluation of Systems, LNCS,
vol. 11024, 53–70.'
mla: Arming, Sebastian, et al. Parameter-Independent Strategies for PMDPs via
POMDPs. Vol. 11024, Springer, 2018, pp. 53–70, doi:10.1007/978-3-319-99154-2_4.
short: S. Arming, E. Bartocci, K. Chatterjee, J.P. Katoen, A. Sokolova, in:, Springer,
2018, pp. 53–70.
conference:
end_date: 2018-09-07
location: Beijing, China
name: 'QEST: Quantitative Evaluation of Systems'
start_date: 2018-09-04
date_created: 2018-12-11T11:44:31Z
date_published: 2018-08-15T00:00:00Z
date_updated: 2023-09-13T09:38:28Z
day: '15'
department:
- _id: KrCh
- _id: ToHe
doi: 10.1007/978-3-319-99154-2_4
external_id:
arxiv:
- '1806.05126'
isi:
- '000548912200004'
intvolume: ' 11024'
isi: 1
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/1806.05126
month: '08'
oa: 1
oa_version: Preprint
page: 53-70
publication_status: published
publisher: Springer
publist_id: '7975'
quality_controlled: '1'
scopus_import: '1'
status: public
title: Parameter-independent strategies for pMDPs via POMDPs
type: conference
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
volume: 11024
year: '2018'
...
---
_id: '14327'
abstract:
- lang: eng
text: "A common assumption in causal modeling posits that the data is generated
by a\r\nset of independent mechanisms, and algorithms should aim to recover this\r\nstructure.
Standard unsupervised learning, however, is often concerned with\r\ntraining a
single model to capture the overall distribution or aspects thereof.\r\nInspired
by clustering approaches, we consider mixtures of implicit generative\r\nmodels
that ``disentangle'' the independent generative mechanisms underlying\r\nthe data.
Relying on an additional set of discriminators, we propose a\r\ncompetitive training
procedure in which the models only need to capture the\r\nportion of the data
distribution from which they can produce realistic samples.\r\nAs a by-product,
each model is simpler and faster to train. We empirically show\r\nthat our approach
splits the training distribution in a sensible way and\r\nincreases the quality
of the generated samples."
article_number: '1804.11130'
article_processing_charge: No
author:
- first_name: Francesco
full_name: Locatello, Francesco
id: 26cfd52f-2483-11ee-8040-88983bcc06d4
last_name: Locatello
orcid: 0000-0002-4850-0683
- first_name: Damien
full_name: Vincent, Damien
last_name: Vincent
- first_name: Ilya
full_name: Tolstikhin, Ilya
last_name: Tolstikhin
- first_name: Gunnar
full_name: Rätsch, Gunnar
last_name: Rätsch
- first_name: Sylvain
full_name: Gelly, Sylvain
last_name: Gelly
- first_name: Bernhard
full_name: Schölkopf, Bernhard
last_name: Schölkopf
citation:
ama: Locatello F, Vincent D, Tolstikhin I, Rätsch G, Gelly S, Schölkopf B. Competitive
training of mixtures of independent deep generative models. arXiv. doi:10.48550/arXiv.1804.11130
apa: Locatello, F., Vincent, D., Tolstikhin, I., Rätsch, G., Gelly, S., & Schölkopf,
B. (n.d.). Competitive training of mixtures of independent deep generative models.
arXiv. https://doi.org/10.48550/arXiv.1804.11130
chicago: Locatello, Francesco, Damien Vincent, Ilya Tolstikhin, Gunnar Rätsch, Sylvain
Gelly, and Bernhard Schölkopf. “Competitive Training of Mixtures of Independent
Deep Generative Models.” ArXiv, n.d. https://doi.org/10.48550/arXiv.1804.11130.
ieee: F. Locatello, D. Vincent, I. Tolstikhin, G. Rätsch, S. Gelly, and B. Schölkopf,
“Competitive training of mixtures of independent deep generative models,” arXiv.
.
ista: Locatello F, Vincent D, Tolstikhin I, Rätsch G, Gelly S, Schölkopf B. Competitive
training of mixtures of independent deep generative models. arXiv, 1804.11130.
mla: Locatello, Francesco, et al. “Competitive Training of Mixtures of Independent
Deep Generative Models.” ArXiv, 1804.11130, doi:10.48550/arXiv.1804.11130.
short: F. Locatello, D. Vincent, I. Tolstikhin, G. Rätsch, S. Gelly, B. Schölkopf,
ArXiv (n.d.).
date_created: 2023-09-13T12:20:49Z
date_published: 2018-04-30T00:00:00Z
date_updated: 2023-09-13T12:23:03Z
day: '30'
department:
- _id: FrLo
doi: 10.48550/arXiv.1804.11130
extern: '1'
external_id:
arxiv:
- '1804.11130'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.48550/arXiv.1804.11130
month: '04'
oa: 1
oa_version: Preprint
publication: arXiv
publication_status: submitted
status: public
title: Competitive training of mixtures of independent deep generative models
type: preprint
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
year: '2018'
...
---
_id: '400'
abstract:
- lang: eng
text: We consider the two-dimensional BCS functional with a radial pair interaction.
We show that the translational symmetry is not broken in a certain temperature
interval below the critical temperature. In the case of vanishing angular momentum,
our results carry over to the three-dimensional case.
article_processing_charge: Yes (via OA deal)
author:
- first_name: Andreas
full_name: Deuchert, Andreas
id: 4DA65CD0-F248-11E8-B48F-1D18A9856A87
last_name: Deuchert
orcid: 0000-0003-3146-6746
- first_name: Alissa
full_name: Geisinge, Alissa
last_name: Geisinge
- first_name: Christian
full_name: Hainzl, Christian
last_name: Hainzl
- first_name: Michael
full_name: Loss, Michael
last_name: Loss
citation:
ama: Deuchert A, Geisinge A, Hainzl C, Loss M. Persistence of translational symmetry
in the BCS model with radial pair interaction. Annales Henri Poincare.
2018;19(5):1507-1527. doi:10.1007/s00023-018-0665-7
apa: Deuchert, A., Geisinge, A., Hainzl, C., & Loss, M. (2018). Persistence
of translational symmetry in the BCS model with radial pair interaction. Annales
Henri Poincare. Springer. https://doi.org/10.1007/s00023-018-0665-7
chicago: Deuchert, Andreas, Alissa Geisinge, Christian Hainzl, and Michael Loss.
“Persistence of Translational Symmetry in the BCS Model with Radial Pair Interaction.”
Annales Henri Poincare. Springer, 2018. https://doi.org/10.1007/s00023-018-0665-7.
ieee: A. Deuchert, A. Geisinge, C. Hainzl, and M. Loss, “Persistence of translational
symmetry in the BCS model with radial pair interaction,” Annales Henri Poincare,
vol. 19, no. 5. Springer, pp. 1507–1527, 2018.
ista: Deuchert A, Geisinge A, Hainzl C, Loss M. 2018. Persistence of translational
symmetry in the BCS model with radial pair interaction. Annales Henri Poincare.
19(5), 1507–1527.
mla: Deuchert, Andreas, et al. “Persistence of Translational Symmetry in the BCS
Model with Radial Pair Interaction.” Annales Henri Poincare, vol. 19, no.
5, Springer, 2018, pp. 1507–27, doi:10.1007/s00023-018-0665-7.
short: A. Deuchert, A. Geisinge, C. Hainzl, M. Loss, Annales Henri Poincare 19 (2018)
1507–1527.
date_created: 2018-12-11T11:46:15Z
date_published: 2018-05-01T00:00:00Z
date_updated: 2023-09-15T12:04:15Z
day: '01'
ddc:
- '510'
department:
- _id: RoSe
doi: 10.1007/s00023-018-0665-7
ec_funded: 1
external_id:
isi:
- '000429799900008'
file:
- access_level: open_access
checksum: 04d2c9bd7cbf3ca1d7acaaf4e7dca3e5
content_type: application/pdf
creator: system
date_created: 2018-12-12T10:12:47Z
date_updated: 2020-07-14T12:46:22Z
file_id: '4966'
file_name: IST-2018-1011-v1+1_2018_Deuchert_Persistence.pdf
file_size: 582680
relation: main_file
file_date_updated: 2020-07-14T12:46:22Z
has_accepted_license: '1'
intvolume: ' 19'
isi: 1
issue: '5'
language:
- iso: eng
month: '05'
oa: 1
oa_version: Published Version
page: 1507 - 1527
project:
- _id: 25C6DC12-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '694227'
name: Analysis of quantum many-body systems
- _id: B67AFEDC-15C9-11EA-A837-991A96BB2854
name: IST Austria Open Access Fund
publication: Annales Henri Poincare
publication_status: published
publisher: Springer
publist_id: '7429'
pubrep_id: '1011'
quality_controlled: '1'
scopus_import: '1'
status: public
title: Persistence of translational symmetry in the BCS model with radial pair interaction
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: journal_article
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
volume: 19
year: '2018'
...
---
_id: '406'
abstract:
- lang: eng
text: 'Recent developments in automated tracking allow uninterrupted, high-resolution
recording of animal trajectories, sometimes coupled with the identification of
stereotyped changes of body pose or other behaviors of interest. Analysis and
interpretation of such data represents a challenge: the timing of animal behaviors
may be stochastic and modulated by kinematic variables, by the interaction with
the environment or with the conspecifics within the animal group, and dependent
on internal cognitive or behavioral state of the individual. Existing models for
collective motion typically fail to incorporate the discrete, stochastic, and
internal-state-dependent aspects of behavior, while models focusing on individual
animal behavior typically ignore the spatial aspects of the problem. Here we propose
a probabilistic modeling framework to address this gap. Each animal can switch
stochastically between different behavioral states, with each state resulting
in a possibly different law of motion through space. Switching rates for behavioral
transitions can depend in a very general way, which we seek to identify from data,
on the effects of the environment as well as the interaction between the animals.
We represent the switching dynamics as a Generalized Linear Model and show that:
(i) forward simulation of multiple interacting animals is possible using a variant
of the Gillespie’s Stochastic Simulation Algorithm; (ii) formulated properly,
the maximum likelihood inference of switching rate functions is tractably solvable
by gradient descent; (iii) model selection can be used to identify factors that
modulate behavioral state switching and to appropriately adjust model complexity
to data. To illustrate our framework, we apply it to two synthetic models of animal
motion and to real zebrafish tracking data. '
acknowledgement: This work was supported by the Human Frontier Science Program RGP0065/2012
(GT, ES).
article_processing_charge: Yes
author:
- first_name: Katarína
full_name: Bod’Ová, Katarína
last_name: Bod’Ová
- first_name: Gabriel
full_name: Mitchell, Gabriel
id: 315BCD80-F248-11E8-B48F-1D18A9856A87
last_name: Mitchell
- first_name: Roy
full_name: Harpaz, Roy
last_name: Harpaz
- first_name: Elad
full_name: Schneidman, Elad
last_name: Schneidman
- first_name: Gasper
full_name: Tkacik, Gasper
id: 3D494DCA-F248-11E8-B48F-1D18A9856A87
last_name: Tkacik
orcid: 0000-0002-6699-1455
citation:
ama: Bod’Ová K, Mitchell G, Harpaz R, Schneidman E, Tkačik G. Probabilistic models
of individual and collective animal behavior. PLoS One. 2018;13(3). doi:10.1371/journal.pone.0193049
apa: Bod’Ová, K., Mitchell, G., Harpaz, R., Schneidman, E., & Tkačik, G. (2018).
Probabilistic models of individual and collective animal behavior. PLoS One.
Public Library of Science. https://doi.org/10.1371/journal.pone.0193049
chicago: Bod’Ová, Katarína, Gabriel Mitchell, Roy Harpaz, Elad Schneidman, and Gašper
Tkačik. “Probabilistic Models of Individual and Collective Animal Behavior.” PLoS
One. Public Library of Science, 2018. https://doi.org/10.1371/journal.pone.0193049.
ieee: K. Bod’Ová, G. Mitchell, R. Harpaz, E. Schneidman, and G. Tkačik, “Probabilistic
models of individual and collective animal behavior,” PLoS One, vol. 13,
no. 3. Public Library of Science, 2018.
ista: Bod’Ová K, Mitchell G, Harpaz R, Schneidman E, Tkačik G. 2018. Probabilistic
models of individual and collective animal behavior. PLoS One. 13(3).
mla: Bod’Ová, Katarína, et al. “Probabilistic Models of Individual and Collective
Animal Behavior.” PLoS One, vol. 13, no. 3, Public Library of Science,
2018, doi:10.1371/journal.pone.0193049.
short: K. Bod’Ová, G. Mitchell, R. Harpaz, E. Schneidman, G. Tkačik, PLoS One 13
(2018).
date_created: 2018-12-11T11:46:18Z
date_published: 2018-03-07T00:00:00Z
date_updated: 2023-09-15T12:06:19Z
day: '07'
ddc:
- '530'
- '571'
department:
- _id: GaTk
doi: 10.1371/journal.pone.0193049
external_id:
isi:
- '000426896800032'
file:
- access_level: open_access
checksum: 684229493db75b43e98a46cd922da497
content_type: application/pdf
creator: system
date_created: 2018-12-12T10:15:43Z
date_updated: 2020-07-14T12:46:22Z
file_id: '5165'
file_name: IST-2018-995-v1+1_2018_Bodova_Probabilistic.pdf
file_size: 6887358
relation: main_file
file_date_updated: 2020-07-14T12:46:22Z
has_accepted_license: '1'
intvolume: ' 13'
isi: 1
issue: '3'
language:
- iso: eng
month: '03'
oa: 1
oa_version: Submitted Version
project:
- _id: 255008E4-B435-11E9-9278-68D0E5697425
grant_number: RGP0065/2012
name: Information processing and computation in fish groups
publication: PLoS One
publication_status: published
publisher: Public Library of Science
publist_id: '7423'
pubrep_id: '995'
quality_controlled: '1'
related_material:
record:
- id: '9831'
relation: research_data
status: public
scopus_import: '1'
status: public
title: Probabilistic models of individual and collective animal behavior
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: journal_article
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
volume: 13
year: '2018'
...
---
_id: '457'
abstract:
- lang: eng
text: Temperate bacteriophages integrate in bacterial genomes as prophages and represent
an important source of genetic variation for bacterial evolution, frequently transmitting
fitness-augmenting genes such as toxins responsible for virulence of major pathogens.
However, only a fraction of bacteriophage infections are lysogenic and lead to
prophage acquisition, whereas the majority are lytic and kill the infected bacteria.
Unless able to discriminate lytic from lysogenic infections, mechanisms of immunity
to bacteriophages are expected to act as a double-edged sword and increase the
odds of survival at the cost of depriving bacteria of potentially beneficial prophages.
We show that although restriction-modification systems as mechanisms of innate
immunity prevent both lytic and lysogenic infections indiscriminately in individual
bacteria, they increase the number of prophage-acquiring individuals at the population
level. We find that this counterintuitive result is a consequence of phage-host
population dynamics, in which restriction-modification systems delay infection
onset until bacteria reach densities at which the probability of lysogeny increases.
These results underscore the importance of population-level dynamics as a key
factor modulating costs and benefits of immunity to temperate bacteriophages
article_processing_charge: No
author:
- first_name: Maros
full_name: Pleska, Maros
id: 4569785E-F248-11E8-B48F-1D18A9856A87
last_name: Pleska
orcid: 0000-0001-7460-7479
- first_name: Moritz
full_name: Lang, Moritz
id: 29E0800A-F248-11E8-B48F-1D18A9856A87
last_name: Lang
- first_name: Dominik
full_name: Refardt, Dominik
last_name: Refardt
- first_name: Bruce
full_name: Levin, Bruce
last_name: Levin
- first_name: Calin C
full_name: Guet, Calin C
id: 47F8433E-F248-11E8-B48F-1D18A9856A87
last_name: Guet
orcid: 0000-0001-6220-2052
citation:
ama: Pleska M, Lang M, Refardt D, Levin B, Guet CC. Phage-host population dynamics
promotes prophage acquisition in bacteria with innate immunity. Nature Ecology
and Evolution. 2018;2(2):359-366. doi:10.1038/s41559-017-0424-z
apa: Pleska, M., Lang, M., Refardt, D., Levin, B., & Guet, C. C. (2018). Phage-host
population dynamics promotes prophage acquisition in bacteria with innate immunity.
Nature Ecology and Evolution. Springer Nature. https://doi.org/10.1038/s41559-017-0424-z
chicago: Pleska, Maros, Moritz Lang, Dominik Refardt, Bruce Levin, and Calin C Guet.
“Phage-Host Population Dynamics Promotes Prophage Acquisition in Bacteria with
Innate Immunity.” Nature Ecology and Evolution. Springer Nature, 2018.
https://doi.org/10.1038/s41559-017-0424-z.
ieee: M. Pleska, M. Lang, D. Refardt, B. Levin, and C. C. Guet, “Phage-host population
dynamics promotes prophage acquisition in bacteria with innate immunity,” Nature
Ecology and Evolution, vol. 2, no. 2. Springer Nature, pp. 359–366, 2018.
ista: Pleska M, Lang M, Refardt D, Levin B, Guet CC. 2018. Phage-host population
dynamics promotes prophage acquisition in bacteria with innate immunity. Nature
Ecology and Evolution. 2(2), 359–366.
mla: Pleska, Maros, et al. “Phage-Host Population Dynamics Promotes Prophage Acquisition
in Bacteria with Innate Immunity.” Nature Ecology and Evolution, vol. 2,
no. 2, Springer Nature, 2018, pp. 359–66, doi:10.1038/s41559-017-0424-z.
short: M. Pleska, M. Lang, D. Refardt, B. Levin, C.C. Guet, Nature Ecology and Evolution
2 (2018) 359–366.
date_created: 2018-12-11T11:46:35Z
date_published: 2018-02-01T00:00:00Z
date_updated: 2023-09-15T12:04:57Z
day: '01'
department:
- _id: CaGu
- _id: GaTk
doi: 10.1038/s41559-017-0424-z
ec_funded: 1
external_id:
isi:
- '000426516400027'
intvolume: ' 2'
isi: 1
issue: '2'
language:
- iso: eng
month: '02'
oa_version: None
page: 359 - 366
project:
- _id: 25681D80-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '291734'
name: International IST Postdoc Fellowship Programme
- _id: 251BCBEC-B435-11E9-9278-68D0E5697425
grant_number: RGY0079/2011
name: Multi-Level Conflicts in Evolutionary Dynamics of Restriction-Modification
Systems (HFSP Young investigators' grant)
- _id: 251D65D8-B435-11E9-9278-68D0E5697425
grant_number: '24210'
name: Effects of Stochasticity on the Function of Restriction-Modi cation Systems
at the Single-Cell Level (DOC Fellowship)
publication: Nature Ecology and Evolution
publication_status: published
publisher: Springer Nature
publist_id: '7364'
quality_controlled: '1'
related_material:
record:
- id: '202'
relation: dissertation_contains
status: public
scopus_import: '1'
status: public
title: Phage-host population dynamics promotes prophage acquisition in bacteria with
innate immunity
type: journal_article
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
volume: 2
year: '2018'
...
---
_id: '55'
abstract:
- lang: eng
text: Many animals use antimicrobials to prevent or cure disease [1,2]. For example,
some animals will ingest plants with medicinal properties, both prophylactically
to prevent infection and therapeutically to self-medicate when sick. Antimicrobial
substances are also used as topical disinfectants, to prevent infection, protect
offspring and to sanitise their surroundings [1,2]. Social insects (ants, bees,
wasps and termites) build nests in environments with a high abundance and diversity
of pathogenic microorganisms — such as soil and rotting wood — and colonies are
often densely crowded, creating conditions that favour disease outbreaks. Consequently,
social insects have evolved collective disease defences to protect their colonies
from epidemics. These traits can be seen as functionally analogous to the immune
system of individual organisms [3,4]. This ‘social immunity’ utilises antimicrobials
to prevent and eradicate infections, and to keep the brood and nest clean. However,
these antimicrobial compounds can be harmful to the insects themselves, and it
is unknown how colonies prevent collateral damage when using them. Here, we demonstrate
that antimicrobial acids, produced by workers to disinfect the colony, are harmful
to the delicate pupal brood stage, but that the pupae are protected from the acids
by the presence of a silk cocoon. Garden ants spray their nests with an antimicrobial
poison to sanitize contaminated nestmates and brood. Here, Pull et al show that
they also prophylactically sanitise their colonies, and that the silk cocoon serves
as a barrier to protect developing pupae, thus preventing collateral damage during
nest sanitation.
article_processing_charge: No
article_type: original
author:
- first_name: Christopher
full_name: Pull, Christopher
id: 3C7F4840-F248-11E8-B48F-1D18A9856A87
last_name: Pull
orcid: 0000-0003-1122-3982
- first_name: Sina
full_name: Metzler, Sina
id: 48204546-F248-11E8-B48F-1D18A9856A87
last_name: Metzler
orcid: 0000-0002-9547-2494
- first_name: Elisabeth
full_name: Naderlinger, Elisabeth
id: 31757262-F248-11E8-B48F-1D18A9856A87
last_name: Naderlinger
- first_name: Sylvia
full_name: Cremer, Sylvia
id: 2F64EC8C-F248-11E8-B48F-1D18A9856A87
last_name: Cremer
orcid: 0000-0002-2193-3868
citation:
ama: Pull C, Metzler S, Naderlinger E, Cremer S. Protection against the lethal side
effects of social immunity in ants. Current Biology. 2018;28(19):R1139-R1140.
doi:10.1016/j.cub.2018.08.063
apa: Pull, C., Metzler, S., Naderlinger, E., & Cremer, S. (2018). Protection
against the lethal side effects of social immunity in ants. Current Biology.
Cell Press. https://doi.org/10.1016/j.cub.2018.08.063
chicago: Pull, Christopher, Sina Metzler, Elisabeth Naderlinger, and Sylvia Cremer.
“Protection against the Lethal Side Effects of Social Immunity in Ants.” Current
Biology. Cell Press, 2018. https://doi.org/10.1016/j.cub.2018.08.063.
ieee: C. Pull, S. Metzler, E. Naderlinger, and S. Cremer, “Protection against the
lethal side effects of social immunity in ants,” Current Biology, vol.
28, no. 19. Cell Press, pp. R1139–R1140, 2018.
ista: Pull C, Metzler S, Naderlinger E, Cremer S. 2018. Protection against the lethal
side effects of social immunity in ants. Current Biology. 28(19), R1139–R1140.
mla: Pull, Christopher, et al. “Protection against the Lethal Side Effects of Social
Immunity in Ants.” Current Biology, vol. 28, no. 19, Cell Press, 2018,
pp. R1139–40, doi:10.1016/j.cub.2018.08.063.
short: C. Pull, S. Metzler, E. Naderlinger, S. Cremer, Current Biology 28 (2018)
R1139–R1140.
date_created: 2018-12-11T11:44:23Z
date_published: 2018-10-08T00:00:00Z
date_updated: 2023-09-15T12:06:46Z
day: '08'
department:
- _id: SyCr
doi: 10.1016/j.cub.2018.08.063
external_id:
isi:
- '000446693400008'
intvolume: ' 28'
isi: 1
issue: '19'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.1016/j.cub.2018.08.063
month: '10'
oa: 1
oa_version: Published Version
page: R1139 - R1140
publication: Current Biology
publication_status: published
publisher: Cell Press
publist_id: '7999'
quality_controlled: '1'
scopus_import: '1'
status: public
title: Protection against the lethal side effects of social immunity in ants
type: journal_article
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
volume: 28
year: '2018'
...
---
_id: '181'
abstract:
- lang: eng
text: We consider large random matrices X with centered, independent entries but
possibly di erent variances. We compute the normalized trace of f(X)g(X∗) for
f, g functions analytic on the spectrum of X. We use these results to compute
the long time asymptotics for systems of coupled di erential equations with random
coe cients. We show that when the coupling is critical, the norm squared of the
solution decays like t−1/2.
acknowledgement: The work of the second author was also partially supported by the
Hausdorff Center of Mathematics.
article_processing_charge: No
author:
- first_name: László
full_name: Erdös, László
id: 4DBD5372-F248-11E8-B48F-1D18A9856A87
last_name: Erdös
orcid: 0000-0001-5366-9603
- first_name: Torben H
full_name: Krüger, Torben H
id: 3020C786-F248-11E8-B48F-1D18A9856A87
last_name: Krüger
orcid: 0000-0002-4821-3297
- first_name: David T
full_name: Renfrew, David T
id: 4845BF6A-F248-11E8-B48F-1D18A9856A87
last_name: Renfrew
orcid: 0000-0003-3493-121X
citation:
ama: Erdös L, Krüger TH, Renfrew DT. Power law decay for systems of randomly coupled
differential equations. SIAM Journal on Mathematical Analysis. 2018;50(3):3271-3290.
doi:10.1137/17M1143125
apa: Erdös, L., Krüger, T. H., & Renfrew, D. T. (2018). Power law decay for
systems of randomly coupled differential equations. SIAM Journal on Mathematical
Analysis. Society for Industrial and Applied Mathematics . https://doi.org/10.1137/17M1143125
chicago: Erdös, László, Torben H Krüger, and David T Renfrew. “Power Law Decay for
Systems of Randomly Coupled Differential Equations.” SIAM Journal on Mathematical
Analysis. Society for Industrial and Applied Mathematics , 2018. https://doi.org/10.1137/17M1143125.
ieee: L. Erdös, T. H. Krüger, and D. T. Renfrew, “Power law decay for systems of
randomly coupled differential equations,” SIAM Journal on Mathematical Analysis,
vol. 50, no. 3. Society for Industrial and Applied Mathematics , pp. 3271–3290,
2018.
ista: Erdös L, Krüger TH, Renfrew DT. 2018. Power law decay for systems of randomly
coupled differential equations. SIAM Journal on Mathematical Analysis. 50(3),
3271–3290.
mla: Erdös, László, et al. “Power Law Decay for Systems of Randomly Coupled Differential
Equations.” SIAM Journal on Mathematical Analysis, vol. 50, no. 3, Society
for Industrial and Applied Mathematics , 2018, pp. 3271–90, doi:10.1137/17M1143125.
short: L. Erdös, T.H. Krüger, D.T. Renfrew, SIAM Journal on Mathematical Analysis
50 (2018) 3271–3290.
date_created: 2018-12-11T11:45:03Z
date_published: 2018-01-01T00:00:00Z
date_updated: 2023-09-15T12:05:52Z
day: '01'
department:
- _id: LaEr
doi: 10.1137/17M1143125
ec_funded: 1
external_id:
arxiv:
- '1708.01546'
isi:
- '000437018500032'
intvolume: ' 50'
isi: 1
issue: '3'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/1708.01546
month: '01'
oa: 1
oa_version: Published Version
page: 3271 - 3290
project:
- _id: 258DCDE6-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '338804'
name: Random matrices, universality and disordered quantum systems
- _id: 258F40A4-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: M02080
name: Structured Non-Hermitian Random Matrices
publication: SIAM Journal on Mathematical Analysis
publication_status: published
publisher: 'Society for Industrial and Applied Mathematics '
publist_id: '7740'
quality_controlled: '1'
scopus_import: '1'
status: public
title: Power law decay for systems of randomly coupled differential equations
type: journal_article
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
volume: 50
year: '2018'
...
---
_id: '322'
abstract:
- lang: eng
text: We construct quantizations of multiplicative hypertoric varieties using an
algebra of q-difference operators on affine space, where q is a root of unity
in C. The quantization defines a matrix bundle (i.e. Azumaya algebra) over the
multiplicative hypertoric variety and admits an explicit finite étale splitting.
The global sections of this Azumaya algebra is a hypertoric quantum group, and
we prove a localization theorem. We introduce a general framework of Frobenius
quantum moment maps and their Hamiltonian reductions; our results shed light on
an instance of this framework.
acknowledgement: "National Science Foundation: Graduate Research Fellowship and grant
No.0932078000; ERC Advanced Grant “Arithmetic and Physics of Higgs moduli spaces”
No. 320593 \r\nThe author is grateful to David Jordan for suggesting this project
and providing guidance throughout, particularly for the formulation of Frobenius
quantum moment maps and key ideas in the proofs of Theorems 3.12 and 4.8. Special
thanks to David Ben-Zvi (the author's PhD advisor) for numerous discussions and
constant encouragement, and for suggesting the term ‘hypertoric quantum group.’
Many results appearing in the current paper were proven independently by Nicholas
Cooney; the author is grateful to Nicholas for sharing his insight on various topics,
including Proposition 3.8. The author also thanks Nicholas Proudfoot for relating
the definition of multiplicative hypertoric varieties, as well as the content of
Remark 2.14. The author also benefited immensely from the close reading and detailed
comments of an anonymous referee, and from conversations with Justin Hilburn, Kobi
Kremnitzer, Michael McBreen, Tom Nevins, Travis Schedler, and Ben Webster. \r\n\r\n\r\n\r\n"
article_processing_charge: No
author:
- first_name: Iordan V
full_name: Ganev, Iordan V
id: 447491B8-F248-11E8-B48F-1D18A9856A87
last_name: Ganev
citation:
ama: Ganev IV. Quantizations of multiplicative hypertoric varieties at a root of
unity. Journal of Algebra. 2018;506:92-128. doi:10.1016/j.jalgebra.2018.03.015
apa: Ganev, I. V. (2018). Quantizations of multiplicative hypertoric varieties at
a root of unity. Journal of Algebra. World Scientific Publishing. https://doi.org/10.1016/j.jalgebra.2018.03.015
chicago: Ganev, Iordan V. “Quantizations of Multiplicative Hypertoric Varieties
at a Root of Unity.” Journal of Algebra. World Scientific Publishing, 2018.
https://doi.org/10.1016/j.jalgebra.2018.03.015.
ieee: I. V. Ganev, “Quantizations of multiplicative hypertoric varieties at a root
of unity,” Journal of Algebra, vol. 506. World Scientific Publishing, pp.
92–128, 2018.
ista: Ganev IV. 2018. Quantizations of multiplicative hypertoric varieties at a
root of unity. Journal of Algebra. 506, 92–128.
mla: Ganev, Iordan V. “Quantizations of Multiplicative Hypertoric Varieties at a
Root of Unity.” Journal of Algebra, vol. 506, World Scientific Publishing,
2018, pp. 92–128, doi:10.1016/j.jalgebra.2018.03.015.
short: I.V. Ganev, Journal of Algebra 506 (2018) 92–128.
date_created: 2018-12-11T11:45:49Z
date_published: 2018-07-15T00:00:00Z
date_updated: 2023-09-15T12:08:38Z
day: '15'
department:
- _id: TaHa
doi: 10.1016/j.jalgebra.2018.03.015
ec_funded: 1
external_id:
arxiv:
- '1412.7211'
isi:
- '000433270600005'
intvolume: ' 506'
isi: 1
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/1412.7211
month: '07'
oa: 1
oa_version: Preprint
page: 92 - 128
project:
- _id: 25E549F4-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '320593'
name: Arithmetic and physics of Higgs moduli spaces
publication: Journal of Algebra
publication_status: published
publisher: World Scientific Publishing
publist_id: '7543'
quality_controlled: '1'
scopus_import: '1'
status: public
title: Quantizations of multiplicative hypertoric varieties at a root of unity
type: journal_article
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
volume: 506
year: '2018'
...
---
_id: '9831'
abstract:
- lang: eng
text: 'Implementation of the inference method in Matlab, including three applications
of the method: The first one for the model of ant motion, the second one for bacterial
chemotaxis, and the third one for the motion of fish.'
article_processing_charge: No
author:
- first_name: Katarína
full_name: Bod’Ová, Katarína
last_name: Bod’Ová
- first_name: Gabriel
full_name: Mitchell, Gabriel
id: 315BCD80-F248-11E8-B48F-1D18A9856A87
last_name: Mitchell
- first_name: Roy
full_name: Harpaz, Roy
last_name: Harpaz
- first_name: Elad
full_name: Schneidman, Elad
last_name: Schneidman
- first_name: Gašper
full_name: Tkačik, Gašper
id: 3D494DCA-F248-11E8-B48F-1D18A9856A87
last_name: Tkačik
orcid: 0000-0002-6699-1455
citation:
ama: Bod’Ová K, Mitchell G, Harpaz R, Schneidman E, Tkačik G. Implementation of
the inference method in Matlab. 2018. doi:10.1371/journal.pone.0193049.s001
apa: Bod’Ová, K., Mitchell, G., Harpaz, R., Schneidman, E., & Tkačik, G. (2018).
Implementation of the inference method in Matlab. Public Library of Science. https://doi.org/10.1371/journal.pone.0193049.s001
chicago: Bod’Ová, Katarína, Gabriel Mitchell, Roy Harpaz, Elad Schneidman, and Gašper
Tkačik. “Implementation of the Inference Method in Matlab.” Public Library of
Science, 2018. https://doi.org/10.1371/journal.pone.0193049.s001.
ieee: K. Bod’Ová, G. Mitchell, R. Harpaz, E. Schneidman, and G. Tkačik, “Implementation
of the inference method in Matlab.” Public Library of Science, 2018.
ista: Bod’Ová K, Mitchell G, Harpaz R, Schneidman E, Tkačik G. 2018. Implementation
of the inference method in Matlab, Public Library of Science, 10.1371/journal.pone.0193049.s001.
mla: Bod’Ová, Katarína, et al. Implementation of the Inference Method in Matlab.
Public Library of Science, 2018, doi:10.1371/journal.pone.0193049.s001.
short: K. Bod’Ová, G. Mitchell, R. Harpaz, E. Schneidman, G. Tkačik, (2018).
date_created: 2021-08-09T07:01:24Z
date_published: 2018-03-07T00:00:00Z
date_updated: 2023-09-15T12:06:18Z
day: '07'
department:
- _id: GaTk
doi: 10.1371/journal.pone.0193049.s001
month: '03'
oa_version: Published Version
publisher: Public Library of Science
related_material:
record:
- id: '406'
relation: used_in_publication
status: public
status: public
title: Implementation of the inference method in Matlab
type: research_data_reference
user_id: 6785fbc1-c503-11eb-8a32-93094b40e1cf
year: '2018'
...
---
_id: '142'
abstract:
- lang: eng
text: We address the problem of analyzing the reachable set of a polynomial nonlinear
continuous system by over-approximating the flowpipe of its dynamics. The common
approach to tackle this problem is to perform a numerical integration over a given
time horizon based on Taylor expansion and interval arithmetic. However, this
method results to be very conservative when there is a large difference in speed
between trajectories as time progresses. In this paper, we propose to use combinations
of barrier functions, which we call piecewise barrier tube (PBT), to over-approximate
flowpipe. The basic idea of PBT is that for each segment of a flowpipe, a coarse
box which is big enough to contain the segment is constructed using sampled simulation
and then in the box we compute by linear programming a set of barrier functions
(called barrier tube or BT for short) which work together to form a tube surrounding
the flowpipe. The benefit of using PBT is that (1) BT is independent of time and
hence can avoid being stretched and deformed by time; and (2) a small number of
BTs can form a tight over-approximation for the flowpipe, which means that the
computation required to decide whether the BTs intersect the unsafe set can be
reduced significantly. We implemented a prototype called PBTS in C++. Experiments
on some benchmark systems show that our approach is effective.
acknowledgement: 'Austrian Science Fund FWF: S11402-N23, S11405-N23, Z211-N32'
alternative_title:
- LNCS
article_processing_charge: No
author:
- first_name: Hui
full_name: Kong, Hui
id: 3BDE25AA-F248-11E8-B48F-1D18A9856A87
last_name: Kong
orcid: 0000-0002-3066-6941
- first_name: Ezio
full_name: Bartocci, Ezio
last_name: Bartocci
- first_name: Thomas A
full_name: Henzinger, Thomas A
id: 40876CD8-F248-11E8-B48F-1D18A9856A87
last_name: Henzinger
orcid: 0000−0002−2985−7724
citation:
ama: 'Kong H, Bartocci E, Henzinger TA. Reachable set over-approximation for nonlinear
systems using piecewise barrier tubes. In: Vol 10981. Springer; 2018:449-467.
doi:10.1007/978-3-319-96145-3_24'
apa: 'Kong, H., Bartocci, E., & Henzinger, T. A. (2018). Reachable set over-approximation
for nonlinear systems using piecewise barrier tubes (Vol. 10981, pp. 449–467).
Presented at the CAV: Computer Aided Verification, Oxford, United Kingdom: Springer.
https://doi.org/10.1007/978-3-319-96145-3_24'
chicago: Kong, Hui, Ezio Bartocci, and Thomas A Henzinger. “Reachable Set Over-Approximation
for Nonlinear Systems Using Piecewise Barrier Tubes,” 10981:449–67. Springer,
2018. https://doi.org/10.1007/978-3-319-96145-3_24.
ieee: 'H. Kong, E. Bartocci, and T. A. Henzinger, “Reachable set over-approximation
for nonlinear systems using piecewise barrier tubes,” presented at the CAV: Computer
Aided Verification, Oxford, United Kingdom, 2018, vol. 10981, pp. 449–467.'
ista: 'Kong H, Bartocci E, Henzinger TA. 2018. Reachable set over-approximation
for nonlinear systems using piecewise barrier tubes. CAV: Computer Aided Verification,
LNCS, vol. 10981, 449–467.'
mla: Kong, Hui, et al. Reachable Set Over-Approximation for Nonlinear Systems
Using Piecewise Barrier Tubes. Vol. 10981, Springer, 2018, pp. 449–67, doi:10.1007/978-3-319-96145-3_24.
short: H. Kong, E. Bartocci, T.A. Henzinger, in:, Springer, 2018, pp. 449–467.
conference:
end_date: 2018-07-17
location: Oxford, United Kingdom
name: 'CAV: Computer Aided Verification'
start_date: 2018-07-14
date_created: 2018-12-11T11:44:51Z
date_published: 2018-07-18T00:00:00Z
date_updated: 2023-09-15T12:12:08Z
day: '18'
ddc:
- '000'
department:
- _id: ToHe
doi: 10.1007/978-3-319-96145-3_24
external_id:
isi:
- '000491481600024'
file:
- access_level: open_access
checksum: fd95e8026deacef3dc752a733bb9355f
content_type: application/pdf
creator: dernst
date_created: 2018-12-17T15:57:06Z
date_updated: 2020-07-14T12:44:53Z
file_id: '5718'
file_name: 2018_LNCS_Kong.pdf
file_size: 5591566
relation: main_file
file_date_updated: 2020-07-14T12:44:53Z
has_accepted_license: '1'
intvolume: ' 10981'
isi: 1
language:
- iso: eng
month: '07'
oa: 1
oa_version: Published Version
page: 449 - 467
project:
- _id: 25832EC2-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: S 11407_N23
name: Rigorous Systems Engineering
- _id: 25F42A32-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: Z211
name: The Wittgenstein Prize
publication_status: published
publisher: Springer
publist_id: '7781'
quality_controlled: '1'
scopus_import: '1'
status: public
title: Reachable set over-approximation for nonlinear systems using piecewise barrier
tubes
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: conference
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
volume: 10981
year: '2018'
...
---
_id: '427'
abstract:
- lang: eng
text: We investigate the quantum interference induced shifts between energetically
close states in highly charged ions, with the energy structure being observed
by laser spectroscopy. In this work, we focus on hyperfine states of lithiumlike
heavy-Z isotopes and quantify how much quantum interference changes the observed
transition frequencies. The process of photon excitation and subsequent photon
decay for the transition 2s→2p→2s is implemented with fully relativistic and full-multipole
frameworks, which are relevant for such relativistic atomic systems. We consider
the isotopes Pb79+207 and Bi80+209 due to experimental interest, as well as other
examples of isotopes with lower Z, namely Pr56+141 and Ho64+165. We conclude that
quantum interference can induce shifts up to 11% of the linewidth in the measurable
resonances of the considered isotopes, if interference between resonances is neglected.
The inclusion of relativity decreases the cross section by 35%, mainly due to
the complete retardation form of the electric dipole multipole. However, the contribution
of the next higher multipoles (e.g., magnetic quadrupole) to the cross section
is negligible. This makes the contribution of relativity and higher-order multipoles
to the quantum interference induced shifts a minor effect, even for heavy-Z elements.
acknowledgement: "This work was funded by the Portuguese Fundação para a Ciência e
a Tecnologia (FCT/MCTES/PIDDAC) under Grant No. UID/FIS/04559/2013 (LIBPhys). P.A.
acknowledges the support of the FCT, under Contract No. SFRH/BPD/92329/2013. L.S.
acknowledges financial support from the People Programme (Marie Curie Actions) of
the European Union's Seventh Framework Programme (FP7/2007-2013) under REA Grant
Agreement No. (291734). Laboratoire Kastler Brossel (LKB) is “Unité Mixte de Recherche
de Sorbonne Université, de ENS-PSL Research University, du Collège de France et
du CNRS No. 8552.” APPENDIX:\r\n"
article_number: '022510'
article_processing_charge: No
article_type: original
author:
- first_name: Pedro
full_name: Amaro, Pedro
last_name: Amaro
- first_name: Ulisses
full_name: Loureiro, Ulisses
last_name: Loureiro
- first_name: Laleh
full_name: Safari, Laleh
id: 3C325E5E-F248-11E8-B48F-1D18A9856A87
last_name: Safari
- first_name: Filippo
full_name: Fratini, Filippo
last_name: Fratini
- first_name: Paul
full_name: Indelicato, Paul
last_name: Indelicato
- first_name: Thomas
full_name: Stöhlker, Thomas
last_name: Stöhlker
- first_name: José
full_name: Santos, José
last_name: Santos
citation:
ama: Amaro P, Loureiro U, Safari L, et al. Quantum interference in laser spectroscopy
of highly charged lithiumlike ions. Physical Review A - Atomic, Molecular,
and Optical Physics. 2018;97(2). doi:10.1103/PhysRevA.97.022510
apa: Amaro, P., Loureiro, U., Safari, L., Fratini, F., Indelicato, P., Stöhlker,
T., & Santos, J. (2018). Quantum interference in laser spectroscopy of highly
charged lithiumlike ions. Physical Review A - Atomic, Molecular, and Optical
Physics. American Physical Society. https://doi.org/10.1103/PhysRevA.97.022510
chicago: Amaro, Pedro, Ulisses Loureiro, Laleh Safari, Filippo Fratini, Paul Indelicato,
Thomas Stöhlker, and José Santos. “Quantum Interference in Laser Spectroscopy
of Highly Charged Lithiumlike Ions.” Physical Review A - Atomic, Molecular,
and Optical Physics. American Physical Society, 2018. https://doi.org/10.1103/PhysRevA.97.022510.
ieee: P. Amaro et al., “Quantum interference in laser spectroscopy of highly
charged lithiumlike ions,” Physical Review A - Atomic, Molecular, and Optical
Physics, vol. 97, no. 2. American Physical Society, 2018.
ista: Amaro P, Loureiro U, Safari L, Fratini F, Indelicato P, Stöhlker T, Santos
J. 2018. Quantum interference in laser spectroscopy of highly charged lithiumlike
ions. Physical Review A - Atomic, Molecular, and Optical Physics. 97(2), 022510.
mla: Amaro, Pedro, et al. “Quantum Interference in Laser Spectroscopy of Highly
Charged Lithiumlike Ions.” Physical Review A - Atomic, Molecular, and Optical
Physics, vol. 97, no. 2, 022510, American Physical Society, 2018, doi:10.1103/PhysRevA.97.022510.
short: P. Amaro, U. Loureiro, L. Safari, F. Fratini, P. Indelicato, T. Stöhlker,
J. Santos, Physical Review A - Atomic, Molecular, and Optical Physics 97 (2018).
date_created: 2018-12-11T11:46:25Z
date_published: 2018-02-21T00:00:00Z
date_updated: 2023-09-15T12:09:35Z
day: '21'
department:
- _id: MiLe
doi: 10.1103/PhysRevA.97.022510
ec_funded: 1
external_id:
arxiv:
- '1802.07920'
isi:
- '000425601000004'
intvolume: ' 97'
isi: 1
issue: '2'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/1802.07920
month: '02'
oa: 1
oa_version: Preprint
project:
- _id: 25681D80-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '291734'
name: International IST Postdoc Fellowship Programme
publication: ' Physical Review A - Atomic, Molecular, and Optical Physics'
publication_status: published
publisher: American Physical Society
publist_id: '7396'
quality_controlled: '1'
scopus_import: '1'
status: public
title: Quantum interference in laser spectroscopy of highly charged lithiumlike ions
type: journal_article
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
volume: 97
year: '2018'
...