---
_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
license: https://creativecommons.org/licenses/by/4.0/
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: '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: '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: '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: '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: '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'
...
---
_id: '309'
abstract:
- lang: eng
text: 'We present an efficient algorithm for a problem in the interface between
clustering and graph embeddings. An embedding '' : G ! M of a graph G into a 2manifold
M maps the vertices in V (G) to distinct points and the edges in E(G) to interior-disjoint
Jordan arcs between the corresponding vertices. In applications in clustering,
cartography, and visualization, nearby vertices and edges are often bundled to
a common node or arc, due to data compression or low resolution. This raises the
computational problem of deciding whether a given map '' : G ! M comes from an
embedding. A map '' : G ! M is a weak embedding if it can be perturbed into an
embedding ψ: G ! M with k'' "k < " for every " > 0. A polynomial-time
algorithm for recognizing weak embeddings was recently found by Fulek and Kyncl
[14], which reduces to solving a system of linear equations over Z2. It runs in
O(n2!) O(n4:75) time, where 2:373 is the matrix multiplication exponent and n
is the number of vertices and edges of G. We improve the running time to O(n log
n). Our algorithm is also conceptually simpler than [14]: We perform a sequence
of local operations that gradually "untangles" the image ''(G) into
an embedding (G), or reports that '' is not a weak embedding. It generalizes a
recent technique developed for the case that G is a cycle and the embedding is
a simple polygon [1], and combines local constraints on the orientation of subgraphs
directly, thereby eliminating the need for solving large systems of linear equations.'
acknowledgement: '∗Research supported in part by the NSF awards CCF-1422311 and CCF-1423615,
and the Science Without Borders program. The second author gratefully acknowledges
support from Austrian Science Fund (FWF): M2281-N35.'
article_processing_charge: No
author:
- first_name: Hugo
full_name: Akitaya, Hugo
last_name: Akitaya
- first_name: Radoslav
full_name: Fulek, Radoslav
id: 39F3FFE4-F248-11E8-B48F-1D18A9856A87
last_name: Fulek
orcid: 0000-0001-8485-1774
- first_name: Csaba
full_name: Tóth, Csaba
last_name: Tóth
citation:
ama: 'Akitaya H, Fulek R, Tóth C. Recognizing weak embeddings of graphs. In: ACM;
2018:274-292. doi:10.1137/1.9781611975031.20'
apa: 'Akitaya, H., Fulek, R., & Tóth, C. (2018). Recognizing weak embeddings
of graphs (pp. 274–292). Presented at the SODA: Symposium on Discrete Algorithms,
New Orleans, LA, USA: ACM. https://doi.org/10.1137/1.9781611975031.20'
chicago: Akitaya, Hugo, Radoslav Fulek, and Csaba Tóth. “Recognizing Weak Embeddings
of Graphs,” 274–92. ACM, 2018. https://doi.org/10.1137/1.9781611975031.20.
ieee: 'H. Akitaya, R. Fulek, and C. Tóth, “Recognizing weak embeddings of graphs,”
presented at the SODA: Symposium on Discrete Algorithms, New Orleans, LA, USA,
2018, pp. 274–292.'
ista: 'Akitaya H, Fulek R, Tóth C. 2018. Recognizing weak embeddings of graphs.
SODA: Symposium on Discrete Algorithms, 274–292.'
mla: Akitaya, Hugo, et al. Recognizing Weak Embeddings of Graphs. ACM, 2018,
pp. 274–92, doi:10.1137/1.9781611975031.20.
short: H. Akitaya, R. Fulek, C. Tóth, in:, ACM, 2018, pp. 274–292.
conference:
end_date: 2018-01-10
location: New Orleans, LA, USA
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: 2023-09-15T12:19:32Z
day: '01'
department:
- _id: UlWa
doi: 10.1137/1.9781611975031.20
external_id:
arxiv:
- '1709.09209'
isi:
- '000483921200021'
isi: 1
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/1709.09209
month: '01'
oa: 1
oa_version: Preprint
page: 274 - 292
project:
- _id: 261FA626-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: M02281
name: Eliminating intersections in drawings of graphs
publication_status: published
publisher: ACM
publist_id: '7556'
quality_controlled: '1'
related_material:
record:
- id: '6982'
relation: later_version
status: public
scopus_import: '1'
status: public
title: Recognizing weak embeddings of graphs
type: conference
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
year: '2018'
...
---
_id: '5794'
abstract:
- lang: eng
text: We present an approach to interacting quantum many-body systems based on the
notion of quantum groups, also known as q-deformed Lie algebras. In particular,
we show that, if the symmetry of a free quantum particle corresponds to a Lie
group G, in the presence of a many-body environment this particle can be described
by a deformed group, Gq. Crucially, the single deformation parameter, q, contains
all the information about the many-particle interactions in the system. We exemplify
our approach by considering a quantum rotor interacting with a bath of bosons,
and demonstrate that extracting the value of q from closed-form solutions in the
perturbative regime allows one to predict the behavior of the system for arbitrary
values of the impurity-bath coupling strength, in good agreement with nonperturbative
calculations. Furthermore, the value of the deformation parameter allows one to
predict at which coupling strengths rotor-bath interactions result in a formation
of a stable quasiparticle. The approach based on quantum groups does not only
allow for a drastic simplification of impurity problems, but also provides valuable
insights into hidden symmetries of interacting many-particle systems.
article_number: '255302'
article_processing_charge: No
article_type: original
author:
- first_name: Enderalp
full_name: Yakaboylu, Enderalp
id: 38CB71F6-F248-11E8-B48F-1D18A9856A87
last_name: Yakaboylu
orcid: 0000-0001-5973-0874
- first_name: Mikhail
full_name: Shkolnikov, Mikhail
id: 35084A62-F248-11E8-B48F-1D18A9856A87
last_name: Shkolnikov
orcid: 0000-0002-4310-178X
- first_name: Mikhail
full_name: Lemeshko, Mikhail
id: 37CB05FA-F248-11E8-B48F-1D18A9856A87
last_name: Lemeshko
orcid: 0000-0002-6990-7802
citation:
ama: Yakaboylu E, Shkolnikov M, Lemeshko M. Quantum groups as hidden symmetries
of quantum impurities. Physical Review Letters. 2018;121(25). doi:10.1103/PhysRevLett.121.255302
apa: Yakaboylu, E., Shkolnikov, M., & Lemeshko, M. (2018). Quantum groups as
hidden symmetries of quantum impurities. Physical Review Letters. American
Physical Society. https://doi.org/10.1103/PhysRevLett.121.255302
chicago: Yakaboylu, Enderalp, Mikhail Shkolnikov, and Mikhail Lemeshko. “Quantum
Groups as Hidden Symmetries of Quantum Impurities.” Physical Review Letters.
American Physical Society, 2018. https://doi.org/10.1103/PhysRevLett.121.255302.
ieee: E. Yakaboylu, M. Shkolnikov, and M. Lemeshko, “Quantum groups as hidden symmetries
of quantum impurities,” Physical Review Letters, vol. 121, no. 25. American
Physical Society, 2018.
ista: Yakaboylu E, Shkolnikov M, Lemeshko M. 2018. Quantum groups as hidden symmetries
of quantum impurities. Physical Review Letters. 121(25), 255302.
mla: Yakaboylu, Enderalp, et al. “Quantum Groups as Hidden Symmetries of Quantum
Impurities.” Physical Review Letters, vol. 121, no. 25, 255302, American
Physical Society, 2018, doi:10.1103/PhysRevLett.121.255302.
short: E. Yakaboylu, M. Shkolnikov, M. Lemeshko, Physical Review Letters 121 (2018).
date_created: 2019-01-06T22:59:12Z
date_published: 2018-12-17T00:00:00Z
date_updated: 2023-09-15T12:09:06Z
day: '17'
department:
- _id: MiLe
doi: 10.1103/PhysRevLett.121.255302
ec_funded: 1
external_id:
arxiv:
- '1809.00222'
isi:
- '000454178600009'
intvolume: ' 121'
isi: 1
issue: '25'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/1809.00222
month: '12'
oa: 1
oa_version: Preprint
project:
- _id: 25681D80-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '291734'
name: International IST Postdoc Fellowship Programme
- _id: 26031614-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: P29902
name: Quantum rotations in the presence of a many-body environment
publication: Physical Review Letters
publication_identifier:
issn:
- '00319007'
publication_status: published
publisher: American Physical Society
quality_controlled: '1'
scopus_import: '1'
status: public
title: Quantum groups as hidden symmetries of quantum impurities
type: journal_article
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
volume: 121
year: '2018'
...
---
_id: '87'
abstract:
- lang: eng
text: Using the geodesic distance on the n-dimensional sphere, we study the expected
radius function of the Delaunay mosaic of a random set of points. Specifically,
we consider the partition of the mosaic into intervals of the radius function
and determine the expected number of intervals whose radii are less than or equal
to a given threshold. We find that the expectations are essentially the same as
for the Poisson–Delaunay mosaic in n-dimensional Euclidean space. Assuming the
points are not contained in a hemisphere, the Delaunay mosaic is isomorphic to
the boundary complex of the convex hull in Rn+1, so we also get the expected number
of faces of a random inscribed polytope. As proved in Antonelli et al. [Adv. in
Appl. Probab. 9–12 (1977–1980)], an orthant section of the n-sphere is isometric
to the standard n-simplex equipped with the Fisher information metric. It follows
that the latter space has similar stochastic properties as the n-dimensional Euclidean
space. Our results are therefore relevant in information geometry and in population
genetics.
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: Anton
full_name: Nikitenko, Anton
id: 3E4FF1BA-F248-11E8-B48F-1D18A9856A87
last_name: Nikitenko
orcid: 0000-0002-0659-3201
citation:
ama: Edelsbrunner H, Nikitenko A. Random inscribed polytopes have similar radius
functions as Poisson-Delaunay mosaics. Annals of Applied Probability. 2018;28(5):3215-3238.
doi:10.1214/18-AAP1389
apa: Edelsbrunner, H., & Nikitenko, A. (2018). Random inscribed polytopes have
similar radius functions as Poisson-Delaunay mosaics. Annals of Applied Probability.
Institute of Mathematical Statistics. https://doi.org/10.1214/18-AAP1389
chicago: Edelsbrunner, Herbert, and Anton Nikitenko. “Random Inscribed Polytopes
Have Similar Radius Functions as Poisson-Delaunay Mosaics.” Annals of Applied
Probability. Institute of Mathematical Statistics, 2018. https://doi.org/10.1214/18-AAP1389.
ieee: H. Edelsbrunner and A. Nikitenko, “Random inscribed polytopes have similar
radius functions as Poisson-Delaunay mosaics,” Annals of Applied Probability,
vol. 28, no. 5. Institute of Mathematical Statistics, pp. 3215–3238, 2018.
ista: Edelsbrunner H, Nikitenko A. 2018. Random inscribed polytopes have similar
radius functions as Poisson-Delaunay mosaics. Annals of Applied Probability. 28(5),
3215–3238.
mla: Edelsbrunner, Herbert, and Anton Nikitenko. “Random Inscribed Polytopes Have
Similar Radius Functions as Poisson-Delaunay Mosaics.” Annals of Applied Probability,
vol. 28, no. 5, Institute of Mathematical Statistics, 2018, pp. 3215–38, doi:10.1214/18-AAP1389.
short: H. Edelsbrunner, A. Nikitenko, Annals of Applied Probability 28 (2018) 3215–3238.
date_created: 2018-12-11T11:44:33Z
date_published: 2018-10-01T00:00:00Z
date_updated: 2023-09-15T12:10:35Z
day: '01'
department:
- _id: HeEd
doi: 10.1214/18-AAP1389
external_id:
arxiv:
- '1705.02870'
isi:
- '000442893500018'
intvolume: ' 28'
isi: 1
issue: '5'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/1705.02870
month: '10'
oa: 1
oa_version: Preprint
page: 3215 - 3238
project:
- _id: 2561EBF4-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: I02979-N35
name: Persistence and stability of geometric complexes
publication: Annals of Applied Probability
publication_status: published
publisher: Institute of Mathematical Statistics
publist_id: '7967'
quality_controlled: '1'
related_material:
record:
- id: '6287'
relation: dissertation_contains
status: public
scopus_import: '1'
status: public
title: Random inscribed polytopes have similar radius functions as Poisson-Delaunay
mosaics
type: journal_article
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
volume: 28
year: '2018'
...
---
_id: '192'
abstract:
- lang: eng
text: The phytohormone auxin is the information carrier in a plethora of developmental
and physiological processes in plants(1). It has been firmly established that
canonical, nuclear auxin signalling acts through regulation of gene transcription(2).
Here, we combined microfluidics, live imaging, genetic engineering and computational
modelling to reanalyse the classical case of root growth inhibition(3) by auxin.
We show that Arabidopsis roots react to addition and removal of auxin by extremely
rapid adaptation of growth rate. This process requires intracellular auxin perception
but not transcriptional reprogramming. The formation of the canonical TIR1/AFB-Aux/IAA
co-receptor complex is required for the growth regulation, hinting to a novel,
non-transcriptional branch of this signalling pathway. Our results challenge the
current understanding of root growth regulation by auxin and suggest another,
presumably non-transcriptional, signalling output of the canonical auxin pathway.
article_processing_charge: No
article_type: original
author:
- first_name: Matyas
full_name: Fendrych, Matyas
id: 43905548-F248-11E8-B48F-1D18A9856A87
last_name: Fendrych
orcid: 0000-0002-9767-8699
- first_name: Maria
full_name: Akhmanova, Maria
id: 3425EC26-F248-11E8-B48F-1D18A9856A87
last_name: Akhmanova
orcid: 0000-0003-1522-3162
- first_name: Jack
full_name: Merrin, Jack
id: 4515C308-F248-11E8-B48F-1D18A9856A87
last_name: Merrin
orcid: 0000-0001-5145-4609
- first_name: Matous
full_name: Glanc, Matous
last_name: Glanc
- first_name: Shinya
full_name: Hagihara, Shinya
last_name: Hagihara
- first_name: Koji
full_name: Takahashi, Koji
last_name: Takahashi
- first_name: Naoyuki
full_name: Uchida, Naoyuki
last_name: Uchida
- first_name: Keiko U
full_name: Torii, Keiko U
last_name: Torii
- first_name: Jirí
full_name: Friml, Jirí
id: 4159519E-F248-11E8-B48F-1D18A9856A87
last_name: Friml
orcid: 0000-0002-8302-7596
citation:
ama: Fendrych M, Akhmanova M, Merrin J, et al. Rapid and reversible root growth
inhibition by TIR1 auxin signalling. Nature Plants. 2018;4(7):453-459.
doi:10.1038/s41477-018-0190-1
apa: Fendrych, M., Akhmanova, M., Merrin, J., Glanc, M., Hagihara, S., Takahashi,
K., … Friml, J. (2018). Rapid and reversible root growth inhibition by TIR1 auxin
signalling. Nature Plants. Springer Nature. https://doi.org/10.1038/s41477-018-0190-1
chicago: Fendrych, Matyas, Maria Akhmanova, Jack Merrin, Matous Glanc, Shinya Hagihara,
Koji Takahashi, Naoyuki Uchida, Keiko U Torii, and Jiří Friml. “Rapid and Reversible
Root Growth Inhibition by TIR1 Auxin Signalling.” Nature Plants. Springer
Nature, 2018. https://doi.org/10.1038/s41477-018-0190-1.
ieee: M. Fendrych et al., “Rapid and reversible root growth inhibition by
TIR1 auxin signalling,” Nature Plants, vol. 4, no. 7. Springer Nature,
pp. 453–459, 2018.
ista: Fendrych M, Akhmanova M, Merrin J, Glanc M, Hagihara S, Takahashi K, Uchida
N, Torii KU, Friml J. 2018. Rapid and reversible root growth inhibition by TIR1
auxin signalling. Nature Plants. 4(7), 453–459.
mla: Fendrych, Matyas, et al. “Rapid and Reversible Root Growth Inhibition by TIR1
Auxin Signalling.” Nature Plants, vol. 4, no. 7, Springer Nature, 2018,
pp. 453–59, doi:10.1038/s41477-018-0190-1.
short: M. Fendrych, M. Akhmanova, J. Merrin, M. Glanc, S. Hagihara, K. Takahashi,
N. Uchida, K.U. Torii, J. Friml, Nature Plants 4 (2018) 453–459.
date_created: 2018-12-11T11:45:07Z
date_published: 2018-06-25T00:00:00Z
date_updated: 2023-09-15T12:11:03Z
day: '25'
department:
- _id: JiFr
- _id: DaSi
- _id: NanoFab
doi: 10.1038/s41477-018-0190-1
external_id:
isi:
- '000443221200017'
pmid:
- '29942048'
intvolume: ' 4'
isi: 1
issue: '7'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://www.ncbi.nlm.nih.gov/pubmed/29942048
month: '06'
oa: 1
oa_version: Submitted Version
page: 453 - 459
pmid: 1
publication: Nature Plants
publication_status: published
publisher: Springer Nature
publist_id: '7728'
quality_controlled: '1'
related_material:
link:
- description: News on IST Homepage
relation: press_release
url: https://ist.ac.at/en/news/new-mechanism-for-the-plant-hormone-auxin-discovered/
scopus_import: '1'
status: public
title: Rapid and reversible root growth inhibition by TIR1 auxin signalling
type: journal_article
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
volume: 4
year: '2018'
...
---
_id: '14'
abstract:
- lang: eng
text: The intercellular transport of auxin is driven by PIN-formed (PIN) auxin efflux
carriers. PINs are localized at the plasma membrane (PM) and on constitutively
recycling endomembrane vesicles. Therefore, PINs can mediate auxin transport either
by direct translocation across the PM or by pumping auxin into secretory vesicles
(SVs), leading to its secretory release upon fusion with the PM. Which of these
two mechanisms dominates is a matter of debate. Here, we addressed the issue with
a mathematical modeling approach. We demonstrate that the efficiency of secretory
transport depends on SV size, half-life of PINs on the PM, pH, exocytosis frequency
and PIN density. 3D structured illumination microscopy (SIM) was used to determine
PIN density on the PM. Combining this data with published values of the other
parameters, we show that the transport activity of PINs in SVs would have to be
at least 1000× greater than on the PM in order to produce a comparable macroscopic
auxin transport. If both transport mechanisms operated simultaneously and PINs
were equally active on SVs and PM, the contribution of secretion to the total
auxin flux would be negligible. In conclusion, while secretory vesicle-mediated
transport of auxin is an intriguing and theoretically possible model, it is unlikely
to be a major mechanism of auxin transport inplanta.
acknowledgement: 'European Research Council (ERC): 742985 to Jiri Friml; M.A. was
supported by the Austrian Science Fund (FWF) (M2379-B28); AJ was supported by the
Austria Science Fund (FWF): I03630 to Jiri Friml.'
article_processing_charge: No
article_type: original
author:
- first_name: Sander
full_name: Hille, Sander
last_name: Hille
- first_name: Maria
full_name: Akhmanova, Maria
id: 3425EC26-F248-11E8-B48F-1D18A9856A87
last_name: Akhmanova
orcid: 0000-0003-1522-3162
- first_name: Matous
full_name: Glanc, Matous
id: 1AE1EA24-02D0-11E9-9BAA-DAF4881429F2
last_name: Glanc
orcid: 0000-0003-0619-7783
- first_name: Alexander J
full_name: Johnson, Alexander J
id: 46A62C3A-F248-11E8-B48F-1D18A9856A87
last_name: Johnson
orcid: 0000-0002-2739-8843
- first_name: Jirí
full_name: Friml, Jirí
id: 4159519E-F248-11E8-B48F-1D18A9856A87
last_name: Friml
orcid: 0000-0002-8302-7596
citation:
ama: 'Hille S, Akhmanova M, Glanc M, Johnson AJ, Friml J. Relative contribution
of PIN-containing secretory vesicles and plasma membrane PINs to the directed
auxin transport: Theoretical estimation. International Journal of Molecular
Sciences. 2018;19(11). doi:10.3390/ijms19113566'
apa: 'Hille, S., Akhmanova, M., Glanc, M., Johnson, A. J., & Friml, J. (2018).
Relative contribution of PIN-containing secretory vesicles and plasma membrane
PINs to the directed auxin transport: Theoretical estimation. International
Journal of Molecular Sciences. MDPI. https://doi.org/10.3390/ijms19113566'
chicago: 'Hille, Sander, Maria Akhmanova, Matous Glanc, Alexander J Johnson, and
Jiří Friml. “Relative Contribution of PIN-Containing Secretory Vesicles and Plasma
Membrane PINs to the Directed Auxin Transport: Theoretical Estimation.” International
Journal of Molecular Sciences. MDPI, 2018. https://doi.org/10.3390/ijms19113566.'
ieee: 'S. Hille, M. Akhmanova, M. Glanc, A. J. Johnson, and J. Friml, “Relative
contribution of PIN-containing secretory vesicles and plasma membrane PINs to
the directed auxin transport: Theoretical estimation,” International Journal
of Molecular Sciences, vol. 19, no. 11. MDPI, 2018.'
ista: 'Hille S, Akhmanova M, Glanc M, Johnson AJ, Friml J. 2018. Relative contribution
of PIN-containing secretory vesicles and plasma membrane PINs to the directed
auxin transport: Theoretical estimation. International Journal of Molecular Sciences.
19(11).'
mla: 'Hille, Sander, et al. “Relative Contribution of PIN-Containing Secretory Vesicles
and Plasma Membrane PINs to the Directed Auxin Transport: Theoretical Estimation.”
International Journal of Molecular Sciences, vol. 19, no. 11, MDPI, 2018,
doi:10.3390/ijms19113566.'
short: S. Hille, M. Akhmanova, M. Glanc, A.J. Johnson, J. Friml, International Journal
of Molecular Sciences 19 (2018).
date_created: 2018-12-11T11:44:09Z
date_published: 2018-11-12T00:00:00Z
date_updated: 2023-09-18T08:09:32Z
day: '12'
ddc:
- '580'
department:
- _id: DaSi
- _id: JiFr
doi: 10.3390/ijms19113566
ec_funded: 1
external_id:
isi:
- '000451528500282'
file:
- access_level: open_access
checksum: e4b59c2599b0ca26ebf5b8434bcde94a
content_type: application/pdf
creator: dernst
date_created: 2018-12-17T16:04:11Z
date_updated: 2020-07-14T12:44:50Z
file_id: '5719'
file_name: 2018_IJMS_Hille.pdf
file_size: 2200593
relation: main_file
file_date_updated: 2020-07-14T12:44:50Z
has_accepted_license: '1'
intvolume: ' 19'
isi: 1
issue: '11'
language:
- iso: eng
month: '11'
oa: 1
oa_version: Published Version
project:
- _id: 261099A6-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '742985'
name: Tracing Evolution of Auxin Transport and Polarity in Plants
- _id: 26538374-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: I03630
name: Molecular mechanisms of endocytic cargo recognition in plants
publication: International Journal of Molecular Sciences
publication_identifier:
eissn:
- 1422-0067
publication_status: published
publisher: MDPI
publist_id: '8042'
quality_controlled: '1'
scopus_import: '1'
status: public
title: 'Relative contribution of PIN-containing secretory vesicles and plasma membrane
PINs to the directed auxin transport: Theoretical estimation'
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: '39'
abstract:
- lang: eng
text: We study how a block of genome with a large number of weakly selected loci
introgresses under directional selection into a genetically homogeneous population.
We derive exact expressions for the expected rate of growth of any fragment of
the introduced block during the initial phase of introgression, and show that
the growth rate of a single-locus variant is largely insensitive to its own additive
effect, but depends instead on the combined effect of all loci within a characteristic
linkage scale. The expected growth rate of a fragment is highly correlated with
its long-term introgression probability in populations of moderate size, and can
hence identify variants that are likely to introgress across replicate populations.
We clarify how the introgression probability of an individual variant is determined
by the interplay between hitchhiking with relatively large fragments during the
early phase of introgression and selection on fine-scale variation within these,
which at longer times results in differential introgression probabilities for
beneficial and deleterious loci within successful fragments. By simulating individuals,
we also investigate how introgression probabilities at individual loci depend
on the variance of fitness effects, the net fitness of the introduced block, and
the size of the recipient population, and how this shapes the net advance under
selection. Our work suggests that even highly replicable substitutions may be
associated with a range of selective effects, which makes it challenging to fine
map the causal loci that underlie polygenic adaptation.
article_processing_charge: No
article_type: original
author:
- first_name: Himani
full_name: Sachdeva, Himani
id: 42377A0A-F248-11E8-B48F-1D18A9856A87
last_name: Sachdeva
- first_name: Nicholas H
full_name: Barton, Nicholas H
id: 4880FE40-F248-11E8-B48F-1D18A9856A87
last_name: Barton
orcid: 0000-0002-8548-5240
citation:
ama: Sachdeva H, Barton NH. Replicability of introgression under linked, polygenic
selection. Genetics. 2018;210(4):1411-1427. doi:10.1534/genetics.118.301429
apa: Sachdeva, H., & Barton, N. H. (2018). Replicability of introgression under
linked, polygenic selection. Genetics. Genetics Society of America. https://doi.org/10.1534/genetics.118.301429
chicago: Sachdeva, Himani, and Nicholas H Barton. “Replicability of Introgression
under Linked, Polygenic Selection.” Genetics. Genetics Society of America,
2018. https://doi.org/10.1534/genetics.118.301429.
ieee: H. Sachdeva and N. H. Barton, “Replicability of introgression under linked,
polygenic selection,” Genetics, vol. 210, no. 4. Genetics Society of America,
pp. 1411–1427, 2018.
ista: Sachdeva H, Barton NH. 2018. Replicability of introgression under linked,
polygenic selection. Genetics. 210(4), 1411–1427.
mla: Sachdeva, Himani, and Nicholas H. Barton. “Replicability of Introgression under
Linked, Polygenic Selection.” Genetics, vol. 210, no. 4, Genetics Society
of America, 2018, pp. 1411–27, doi:10.1534/genetics.118.301429.
short: H. Sachdeva, N.H. Barton, Genetics 210 (2018) 1411–1427.
date_created: 2018-12-11T11:44:18Z
date_published: 2018-12-04T00:00:00Z
date_updated: 2023-09-18T08:10:29Z
day: '04'
department:
- _id: NiBa
doi: 10.1534/genetics.118.301429
external_id:
isi:
- '000452315900021'
intvolume: ' 210'
isi: 1
issue: '4'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://www.biorxiv.org/content/10.1101/379578v1
month: '12'
oa: 1
oa_version: Preprint
page: 1411-1427
publication: Genetics
publication_identifier:
issn:
- '00166731'
publication_status: published
publisher: Genetics Society of America
quality_controlled: '1'
scopus_import: '1'
status: public
title: Replicability of introgression under linked, polygenic selection
type: journal_article
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
volume: 210
year: '2018'
...
---
_id: '420'
abstract:
- lang: eng
text: We analyze the theoretical derivation of the beyond-mean-field equation of
state for two-dimensional gas of dilute, ultracold alkali-metal atoms in the Bardeen–Cooper–Schrieffer
(BCS) to Bose–Einstein condensate (BEC) crossover. We show that at zero temperature
our theory — considering Gaussian fluctuations on top of the mean-field equation
of state — is in very good agreement with experimental data. Subsequently, we
investigate the superfluid density at finite temperature and its renormalization
due to the proliferation of vortex–antivortex pairs. By doing so, we determine
the Berezinskii–Kosterlitz–Thouless (BKT) critical temperature — at which the
renormalized superfluid density jumps to zero — as a function of the inter-atomic
potential strength. We find that the Nelson–Kosterlitz criterion overestimates
the BKT temperature with respect to the renormalization group equations, this
effect being particularly relevant in the intermediate regime of the crossover.
article_processing_charge: No
author:
- first_name: Giacomo
full_name: Bighin, Giacomo
id: 4CA96FD4-F248-11E8-B48F-1D18A9856A87
last_name: Bighin
orcid: 0000-0001-8823-9777
- first_name: Luca
full_name: Salasnich, Luca
last_name: Salasnich
citation:
ama: Bighin G, Salasnich L. Renormalization of the superfluid density in the two-dimensional
BCS-BEC crossover. International Journal of Modern Physics B. 2018;32(17):1840022.
doi:10.1142/S0217979218400222
apa: Bighin, G., & Salasnich, L. (2018). Renormalization of the superfluid density
in the two-dimensional BCS-BEC crossover. International Journal of Modern Physics
B. World Scientific Publishing. https://doi.org/10.1142/S0217979218400222
chicago: Bighin, Giacomo, and Luca Salasnich. “Renormalization of the Superfluid
Density in the Two-Dimensional BCS-BEC Crossover.” International Journal of
Modern Physics B. World Scientific Publishing, 2018. https://doi.org/10.1142/S0217979218400222.
ieee: G. Bighin and L. Salasnich, “Renormalization of the superfluid density in
the two-dimensional BCS-BEC crossover,” International Journal of Modern Physics
B, vol. 32, no. 17. World Scientific Publishing, p. 1840022, 2018.
ista: Bighin G, Salasnich L. 2018. Renormalization of the superfluid density in
the two-dimensional BCS-BEC crossover. International Journal of Modern Physics
B. 32(17), 1840022.
mla: Bighin, Giacomo, and Luca Salasnich. “Renormalization of the Superfluid Density
in the Two-Dimensional BCS-BEC Crossover.” International Journal of Modern
Physics B, vol. 32, no. 17, World Scientific Publishing, 2018, p. 1840022,
doi:10.1142/S0217979218400222.
short: G. Bighin, L. Salasnich, International Journal of Modern Physics B 32 (2018)
1840022.
date_created: 2018-12-11T11:46:22Z
date_published: 2018-07-10T00:00:00Z
date_updated: 2023-09-18T08:09:59Z
day: '10'
department:
- _id: MiLe
doi: 10.1142/S0217979218400222
external_id:
isi:
- '000438217300007'
intvolume: ' 32'
isi: 1
issue: '17'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/1710.11171
month: '07'
oa: 1
oa_version: Preprint
page: '1840022'
publication: International Journal of Modern Physics B
publication_status: published
publisher: World Scientific Publishing
publist_id: '7402'
quality_controlled: '1'
scopus_import: '1'
status: public
title: Renormalization of the superfluid density in the two-dimensional BCS-BEC crossover
type: journal_article
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
volume: 32
year: '2018'
...
---
_id: '38'
abstract:
- lang: eng
text: 'Genomes of closely-related species or populations often display localized
regions of enhanced relative sequence divergence, termed genomic islands. It has
been proposed that these islands arise through selective sweeps and/or barriers
to gene flow. Here, we genetically dissect a genomic island that controls flower
color pattern differences between two subspecies of Antirrhinum majus, A.m.striatum
and A.m.pseudomajus, and relate it to clinal variation across a natural hybrid
zone. We show that selective sweeps likely raised relative divergence at two tightly-linked
MYB-like transcription factors, leading to distinct flower patterns in the two
subspecies. The two patterns provide alternate floral guides and create a strong
barrier to gene flow where populations come into contact. This barrier affects
the selected flower color genes and tightlylinked loci, but does not extend outside
of this domain, allowing gene flow to lower relative divergence for the rest of
the chromosome. Thus, both selective sweeps and barriers to gene flow play a role
in shaping genomic islands: sweeps cause elevation in relative divergence, while
heterogeneous gene flow flattens the surrounding "sea," making the island of divergence
stand out. By showing how selective sweeps establish alternative adaptive phenotypes
that lead to barriers to gene flow, our study sheds light on possible mechanisms
leading to reproductive isolation and speciation.'
acknowledgement: ' ERC Grant 201252 (to N.H.B.)'
article_processing_charge: No
author:
- first_name: Hugo
full_name: Tavares, Hugo
last_name: Tavares
- first_name: Annabel
full_name: Whitley, Annabel
last_name: Whitley
- first_name: David
full_name: Field, David
id: 419049E2-F248-11E8-B48F-1D18A9856A87
last_name: Field
orcid: 0000-0002-4014-8478
- first_name: Desmond
full_name: Bradley, Desmond
last_name: Bradley
- first_name: Matthew
full_name: Couchman, Matthew
last_name: Couchman
- first_name: Lucy
full_name: Copsey, Lucy
last_name: Copsey
- first_name: Joane
full_name: Elleouet, Joane
last_name: Elleouet
- first_name: Monique
full_name: Burrus, Monique
last_name: Burrus
- first_name: Christophe
full_name: Andalo, Christophe
last_name: Andalo
- first_name: Miaomiao
full_name: Li, Miaomiao
last_name: Li
- first_name: Qun
full_name: Li, Qun
last_name: Li
- first_name: Yongbiao
full_name: Xue, Yongbiao
last_name: Xue
- first_name: Alexandra B
full_name: Rebocho, Alexandra B
last_name: Rebocho
- first_name: Nicholas H
full_name: Barton, Nicholas H
id: 4880FE40-F248-11E8-B48F-1D18A9856A87
last_name: Barton
orcid: 0000-0002-8548-5240
- first_name: Enrico
full_name: Coen, Enrico
last_name: Coen
citation:
ama: Tavares H, Whitley A, Field D, et al. Selection and gene flow shape genomic
islands that control floral guides. PNAS. 2018;115(43):11006-11011. doi:10.1073/pnas.1801832115
apa: Tavares, H., Whitley, A., Field, D., Bradley, D., Couchman, M., Copsey, L.,
… Coen, E. (2018). Selection and gene flow shape genomic islands that control
floral guides. PNAS. National Academy of Sciences. https://doi.org/10.1073/pnas.1801832115
chicago: Tavares, Hugo, Annabel Whitley, David Field, Desmond Bradley, Matthew Couchman,
Lucy Copsey, Joane Elleouet, et al. “Selection and Gene Flow Shape Genomic Islands
That Control Floral Guides.” PNAS. National Academy of Sciences, 2018.
https://doi.org/10.1073/pnas.1801832115.
ieee: H. Tavares et al., “Selection and gene flow shape genomic islands that
control floral guides,” PNAS, vol. 115, no. 43. National Academy of Sciences,
pp. 11006–11011, 2018.
ista: Tavares H, Whitley A, Field D, Bradley D, Couchman M, Copsey L, Elleouet J,
Burrus M, Andalo C, Li M, Li Q, Xue Y, Rebocho AB, Barton NH, Coen E. 2018. Selection
and gene flow shape genomic islands that control floral guides. PNAS. 115(43),
11006–11011.
mla: Tavares, Hugo, et al. “Selection and Gene Flow Shape Genomic Islands That Control
Floral Guides.” PNAS, vol. 115, no. 43, National Academy of Sciences, 2018,
pp. 11006–11, doi:10.1073/pnas.1801832115.
short: H. Tavares, A. Whitley, D. Field, D. Bradley, M. Couchman, L. Copsey, J.
Elleouet, M. Burrus, C. Andalo, M. Li, Q. Li, Y. Xue, A.B. Rebocho, N.H. Barton,
E. Coen, PNAS 115 (2018) 11006–11011.
date_created: 2018-12-11T11:44:18Z
date_published: 2018-10-23T00:00:00Z
date_updated: 2023-09-18T08:36:49Z
day: '23'
ddc:
- '570'
department:
- _id: NiBa
doi: 10.1073/pnas.1801832115
external_id:
isi:
- '000448040500065'
pmid:
- '30297406'
file:
- access_level: open_access
checksum: d2305d0cc81dbbe4c1c677d64ad6f6d1
content_type: application/pdf
creator: dernst
date_created: 2018-12-17T08:44:03Z
date_updated: 2020-07-14T12:46:16Z
file_id: '5683'
file_name: 11006.full.pdf
file_size: 1911302
relation: main_file
file_date_updated: 2020-07-14T12:46:16Z
has_accepted_license: '1'
intvolume: ' 115'
isi: 1
issue: '43'
language:
- iso: eng
license: https://creativecommons.org/licenses/by-nc-nd/4.0/
month: '10'
oa: 1
oa_version: Published Version
page: 11006 - 11011
pmid: 1
publication: PNAS
publication_identifier:
issn:
- '00278424'
publication_status: published
publisher: National Academy of Sciences
publist_id: '8017'
quality_controlled: '1'
scopus_import: '1'
status: public
title: Selection and gene flow shape genomic islands that control floral guides
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: 115
year: '2018'
...
---
_id: '155'
abstract:
- lang: eng
text: There is currently significant interest in operating devices in the quantum
regime, where their behaviour cannot be explained through classical mechanics.
Quantum states, including entangled states, are fragile and easily disturbed by
excessive thermal noise. Here we address the question of whether it is possible
to create non-reciprocal devices that encourage the flow of thermal noise towards
or away from a particular quantum device in a network. Our work makes use of the
cascaded systems formalism to answer this question in the affirmative, showing
how a three-port device can be used as an effective thermal transistor, and illustrates
how this formalism maps onto an experimentally-realisable optomechanical system.
Our results pave the way to more resilient quantum devices and to the use of thermal
noise as a resource.
alternative_title:
- Proceedings of SPIE
article_number: 106721N
article_processing_charge: No
author:
- first_name: André
full_name: Xuereb, André
last_name: Xuereb
- first_name: Matteo
full_name: Aquilina, Matteo
last_name: Aquilina
- first_name: Shabir
full_name: Barzanjeh, Shabir
id: 2D25E1F6-F248-11E8-B48F-1D18A9856A87
last_name: Barzanjeh
orcid: 0000-0003-0415-1423
citation:
ama: 'Xuereb A, Aquilina M, Barzanjeh S. Routing thermal noise through quantum networks.
In: Andrews DL, Ostendorf A, Bain AJ, Nunzi JM, eds. Vol 10672. SPIE; 2018. doi:10.1117/12.2309928'
apa: 'Xuereb, A., Aquilina, M., & Barzanjeh, S. (2018). Routing thermal noise
through quantum networks. In D. L. Andrews, A. Ostendorf, A. J. Bain, & J.
M. Nunzi (Eds.) (Vol. 10672). Presented at the SPIE: The international society
for optical engineering, Strasbourg, France: SPIE. https://doi.org/10.1117/12.2309928'
chicago: Xuereb, André, Matteo Aquilina, and Shabir Barzanjeh. “Routing Thermal
Noise through Quantum Networks.” edited by D L Andrews, A Ostendorf, A J Bain,
and J M Nunzi, Vol. 10672. SPIE, 2018. https://doi.org/10.1117/12.2309928.
ieee: 'A. Xuereb, M. Aquilina, and S. Barzanjeh, “Routing thermal noise through
quantum networks,” presented at the SPIE: The international society for optical
engineering, Strasbourg, France, 2018, vol. 10672.'
ista: 'Xuereb A, Aquilina M, Barzanjeh S. 2018. Routing thermal noise through quantum
networks. SPIE: The international society for optical engineering, Proceedings
of SPIE, vol. 10672, 106721N.'
mla: Xuereb, André, et al. Routing Thermal Noise through Quantum Networks.
Edited by D L Andrews et al., vol. 10672, 106721N, SPIE, 2018, doi:10.1117/12.2309928.
short: A. Xuereb, M. Aquilina, S. Barzanjeh, in:, D.L. Andrews, A. Ostendorf, A.J.
Bain, J.M. Nunzi (Eds.), SPIE, 2018.
conference:
end_date: 2018-04-26
location: Strasbourg, France
name: 'SPIE: The international society for optical engineering'
start_date: 2018-04-22
date_created: 2018-12-11T11:44:55Z
date_published: 2018-05-04T00:00:00Z
date_updated: 2023-09-18T08:12:24Z
day: '04'
department:
- _id: JoFi
doi: 10.1117/12.2309928
editor:
- first_name: D L
full_name: Andrews, D L
last_name: Andrews
- first_name: A
full_name: Ostendorf, A
last_name: Ostendorf
- first_name: A J
full_name: Bain, A J
last_name: Bain
- first_name: J M
full_name: Nunzi, J M
last_name: Nunzi
external_id:
arxiv:
- '1806.01000'
isi:
- '000453298500019'
intvolume: ' 10672'
isi: 1
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/1806.01000
month: '05'
oa: 1
oa_version: Preprint
publication_status: published
publisher: SPIE
publist_id: '7766'
quality_controlled: '1'
scopus_import: '1'
status: public
title: Routing thermal noise through quantum networks
type: conference
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
volume: 10672
year: '2018'
...
---
_id: '5767'
abstract:
- lang: eng
text: 'Cuprate superconductors have long been thought of as having strong electronic
correlations but negligible spin-orbit coupling. Using spin- and angle-resolved
photoemission spectroscopy, we discovered that one of the most studied cuprate
superconductors, Bi2212, has a nontrivial spin texture with a spin-momentum locking
that circles the Brillouin zone center and a spin-layer locking that allows states
of opposite spin to be localized in different parts of the unit cell. Our findings
pose challenges for the vast majority of models of cuprates, such as the Hubbard
model and its variants, where spin-orbit interaction has been mostly neglected,
and open the intriguing question of how the high-temperature superconducting state
emerges in the presence of this nontrivial spin texture. '
acknowledgement: ' M.S. was supported by the Gordon and Betty Moore Foundation s EPiQS
Initiative through grant GBMF4307'
article_processing_charge: No
article_type: original
author:
- first_name: Kenneth
full_name: Gotlieb, Kenneth
last_name: Gotlieb
- first_name: Chiu-Yun
full_name: Lin, Chiu-Yun
last_name: Lin
- first_name: Maksym
full_name: Serbyn, Maksym
id: 47809E7E-F248-11E8-B48F-1D18A9856A87
last_name: Serbyn
orcid: 0000-0002-2399-5827
- first_name: Wentao
full_name: Zhang, Wentao
last_name: Zhang
- first_name: Christopher L.
full_name: Smallwood, Christopher L.
last_name: Smallwood
- first_name: Christopher
full_name: Jozwiak, Christopher
last_name: Jozwiak
- first_name: Hiroshi
full_name: Eisaki, Hiroshi
last_name: Eisaki
- first_name: Zahid
full_name: Hussain, Zahid
last_name: Hussain
- first_name: Ashvin
full_name: Vishwanath, Ashvin
last_name: Vishwanath
- first_name: Alessandra
full_name: Lanzara, Alessandra
last_name: Lanzara
citation:
ama: Gotlieb K, Lin C-Y, Serbyn M, et al. Revealing hidden spin-momentum locking
in a high-temperature cuprate superconductor. Science. 2018;362(6420):1271-1275.
doi:10.1126/science.aao0980
apa: Gotlieb, K., Lin, C.-Y., Serbyn, M., Zhang, W., Smallwood, C. L., Jozwiak,
C., … Lanzara, A. (2018). Revealing hidden spin-momentum locking in a high-temperature
cuprate superconductor. Science. American Association for the Advancement
of Science. https://doi.org/10.1126/science.aao0980
chicago: Gotlieb, Kenneth, Chiu-Yun Lin, Maksym Serbyn, Wentao Zhang, Christopher
L. Smallwood, Christopher Jozwiak, Hiroshi Eisaki, Zahid Hussain, Ashvin Vishwanath,
and Alessandra Lanzara. “Revealing Hidden Spin-Momentum Locking in a High-Temperature
Cuprate Superconductor.” Science. American Association for the Advancement
of Science, 2018. https://doi.org/10.1126/science.aao0980.
ieee: K. Gotlieb et al., “Revealing hidden spin-momentum locking in a high-temperature
cuprate superconductor,” Science, vol. 362, no. 6420. American Association
for the Advancement of Science, pp. 1271–1275, 2018.
ista: Gotlieb K, Lin C-Y, Serbyn M, Zhang W, Smallwood CL, Jozwiak C, Eisaki H,
Hussain Z, Vishwanath A, Lanzara A. 2018. Revealing hidden spin-momentum locking
in a high-temperature cuprate superconductor. Science. 362(6420), 1271–1275.
mla: Gotlieb, Kenneth, et al. “Revealing Hidden Spin-Momentum Locking in a High-Temperature
Cuprate Superconductor.” Science, vol. 362, no. 6420, American Association
for the Advancement of Science, 2018, pp. 1271–75, doi:10.1126/science.aao0980.
short: K. Gotlieb, C.-Y. Lin, M. Serbyn, W. Zhang, C.L. Smallwood, C. Jozwiak, H.
Eisaki, Z. Hussain, A. Vishwanath, A. Lanzara, Science 362 (2018) 1271–1275.
date_created: 2018-12-19T14:53:50Z
date_published: 2018-12-14T00:00:00Z
date_updated: 2023-09-18T08:11:56Z
day: '14'
department:
- _id: MaSe
doi: 10.1126/science.aao0980
external_id:
isi:
- '000452994400048'
intvolume: ' 362'
isi: 1
issue: '6420'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.1126/science.aao0980
month: '12'
oa: 1
oa_version: Published Version
page: 1271-1275
publication: Science
publication_identifier:
eissn:
- 1095-9203
issn:
- 0036-8075
publication_status: published
publisher: American Association for the Advancement of Science
quality_controlled: '1'
scopus_import: '1'
status: public
title: Revealing hidden spin-momentum locking in a high-temperature cuprate superconductor
type: journal_article
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
volume: 362
year: '2018'
...
---
_id: '162'
abstract:
- lang: eng
text: 'Facial shape is the basis for facial recognition and categorization. Facial
features reflect the underlying geometry of the skeletal structures. Here, we
reveal that cartilaginous nasal capsule (corresponding to upper jaw and face)
is shaped by signals generated by neural structures: brain and olfactory epithelium.
Brain-derived Sonic Hedgehog (SHH) enables the induction of nasal septum and posterior
nasal capsule, whereas the formation of a capsule roof is controlled by signals
from the olfactory epithelium. Unexpectedly, the cartilage of the nasal capsule
turned out to be important for shaping membranous facial bones during development.
This suggests that conserved neurosensory structures could benefit from protection
and have evolved signals inducing cranial cartilages encasing them. Experiments
with mutant mice revealed that the genomic regulatory regions controlling production
of SHH in the nervous system contribute to facial cartilage morphogenesis, which
might be a mechanism responsible for the adaptive evolution of animal faces and
snouts.'
article_number: e34465
article_processing_charge: No
author:
- first_name: Marketa
full_name: Kaucka, Marketa
last_name: Kaucka
- first_name: Julian
full_name: Petersen, Julian
last_name: Petersen
- first_name: Marketa
full_name: Tesarova, Marketa
last_name: Tesarova
- first_name: Bara
full_name: Szarowska, Bara
last_name: Szarowska
- first_name: Maria
full_name: Kastriti, Maria
last_name: Kastriti
- first_name: Meng
full_name: Xie, Meng
last_name: Xie
- first_name: Anna
full_name: Kicheva, Anna
id: 3959A2A0-F248-11E8-B48F-1D18A9856A87
last_name: Kicheva
orcid: 0000-0003-4509-4998
- first_name: Karl
full_name: Annusver, Karl
last_name: Annusver
- first_name: Maria
full_name: Kasper, Maria
last_name: Kasper
- first_name: Orsolya
full_name: Symmons, Orsolya
last_name: Symmons
- first_name: Leslie
full_name: Pan, Leslie
last_name: Pan
- first_name: Francois
full_name: Spitz, Francois
last_name: Spitz
- first_name: Jozef
full_name: Kaiser, Jozef
last_name: Kaiser
- first_name: Maria
full_name: Hovorakova, Maria
last_name: Hovorakova
- first_name: Tomas
full_name: Zikmund, Tomas
last_name: Zikmund
- first_name: Kazunori
full_name: Sunadome, Kazunori
last_name: Sunadome
- first_name: Michael P
full_name: Matise, Michael P
last_name: Matise
- first_name: Hui
full_name: Wang, Hui
last_name: Wang
- first_name: Ulrika
full_name: Marklund, Ulrika
last_name: Marklund
- first_name: Hind
full_name: Abdo, Hind
last_name: Abdo
- first_name: Patrik
full_name: Ernfors, Patrik
last_name: Ernfors
- first_name: Pascal
full_name: Maire, Pascal
last_name: Maire
- first_name: Maud
full_name: Wurmser, Maud
last_name: Wurmser
- first_name: Andrei S
full_name: Chagin, Andrei S
last_name: Chagin
- first_name: Kaj
full_name: Fried, Kaj
last_name: Fried
- first_name: Igor
full_name: Adameyko, Igor
last_name: Adameyko
citation:
ama: Kaucka M, Petersen J, Tesarova M, et al. Signals from the brain and olfactory
epithelium control shaping of the mammalian nasal capsule cartilage. eLife.
2018;7. doi:10.7554/eLife.34465
apa: Kaucka, M., Petersen, J., Tesarova, M., Szarowska, B., Kastriti, M., Xie, M.,
… Adameyko, I. (2018). Signals from the brain and olfactory epithelium control
shaping of the mammalian nasal capsule cartilage. ELife. eLife Sciences
Publications. https://doi.org/10.7554/eLife.34465
chicago: Kaucka, Marketa, Julian Petersen, Marketa Tesarova, Bara Szarowska, Maria
Kastriti, Meng Xie, Anna Kicheva, et al. “Signals from the Brain and Olfactory
Epithelium Control Shaping of the Mammalian Nasal Capsule Cartilage.” ELife.
eLife Sciences Publications, 2018. https://doi.org/10.7554/eLife.34465.
ieee: M. Kaucka et al., “Signals from the brain and olfactory epithelium
control shaping of the mammalian nasal capsule cartilage,” eLife, vol.
7. eLife Sciences Publications, 2018.
ista: Kaucka M, Petersen J, Tesarova M, Szarowska B, Kastriti M, Xie M, Kicheva
A, Annusver K, Kasper M, Symmons O, Pan L, Spitz F, Kaiser J, Hovorakova M, Zikmund
T, Sunadome K, Matise MP, Wang H, Marklund U, Abdo H, Ernfors P, Maire P, Wurmser
M, Chagin AS, Fried K, Adameyko I. 2018. Signals from the brain and olfactory
epithelium control shaping of the mammalian nasal capsule cartilage. eLife. 7,
e34465.
mla: Kaucka, Marketa, et al. “Signals from the Brain and Olfactory Epithelium Control
Shaping of the Mammalian Nasal Capsule Cartilage.” ELife, vol. 7, e34465,
eLife Sciences Publications, 2018, doi:10.7554/eLife.34465.
short: M. Kaucka, J. Petersen, M. Tesarova, B. Szarowska, M. Kastriti, M. Xie, A.
Kicheva, K. Annusver, M. Kasper, O. Symmons, L. Pan, F. Spitz, J. Kaiser, M. Hovorakova,
T. Zikmund, K. Sunadome, M.P. Matise, H. Wang, U. Marklund, H. Abdo, P. Ernfors,
P. Maire, M. Wurmser, A.S. Chagin, K. Fried, I. Adameyko, ELife 7 (2018).
date_created: 2018-12-11T11:44:57Z
date_published: 2018-06-13T00:00:00Z
date_updated: 2023-09-18T09:29:07Z
day: '13'
ddc:
- '571'
department:
- _id: AnKi
doi: 10.7554/eLife.34465
ec_funded: 1
external_id:
isi:
- '000436227500001'
file:
- access_level: open_access
checksum: da2378cdcf6b5461dcde194e4d608343
content_type: application/pdf
creator: dernst
date_created: 2018-12-17T16:41:58Z
date_updated: 2020-07-14T12:45:07Z
file_id: '5727'
file_name: 2018_eLife_Kaucka.pdf
file_size: 9816484
relation: main_file
file_date_updated: 2020-07-14T12:45:07Z
has_accepted_license: '1'
intvolume: ' 7'
isi: 1
language:
- iso: eng
month: '06'
oa: 1
oa_version: Published Version
project:
- _id: B6FC0238-B512-11E9-945C-1524E6697425
call_identifier: H2020
grant_number: '680037'
name: Coordination of Patterning And Growth In the Spinal Cord
publication: eLife
publication_status: published
publisher: eLife Sciences Publications
publist_id: '7759'
quality_controlled: '1'
related_material:
record:
- id: '9838'
relation: research_data
status: public
scopus_import: '1'
status: public
title: Signals from the brain and olfactory epithelium control shaping of the mammalian
nasal capsule cartilage
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: journal_article
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
volume: 7
year: '2018'
...
---
_id: '302'
abstract:
- lang: eng
text: At ITCS 2013, Mahmoody, Moran and Vadhan [MMV13] introduce and construct publicly
verifiable proofs of sequential work, which is a protocol for proving that one
spent sequential computational work related to some statement. The original motivation
for such proofs included non-interactive time-stamping and universally verifiable
CPU benchmarks. A more recent application, and our main motivation, are blockchain
designs, where proofs of sequential work can be used – in combination with proofs
of space – as a more ecological and economical substitute for proofs of work which
are currently used to secure Bitcoin and other cryptocurrencies. The construction
proposed by [MMV13] is based on a hash function and can be proven secure in the
random oracle model, or assuming inherently sequential hash-functions, which is
a new standard model assumption introduced in their work. In a proof of sequential
work, a prover gets a “statement” χ, a time parameter N and access to a hash-function
H, which for the security proof is modelled as a random oracle. Correctness requires
that an honest prover can make a verifier accept making only N queries to H, while
soundness requires that any prover who makes the verifier accept must have made
(almost) N sequential queries to H. Thus a solution constitutes a proof that N
time passed since χ was received. Solutions must be publicly verifiable in time
at most polylogarithmic in N. The construction of [MMV13] is based on “depth-robust”
graphs, and as a consequence has rather poor concrete parameters. But the major
drawback is that the prover needs not just N time, but also N space to compute
a proof. In this work we propose a proof of sequential work which is much simpler,
more efficient and achieves much better concrete bounds. Most importantly, the
space required can be as small as log (N) (but we get better soundness using slightly
more memory than that). An open problem stated by [MMV13] that our construction
does not solve either is achieving a “unique” proof, where even a cheating prover
can only generate a single accepting proof. This property would be extremely useful
for applications to blockchains.
alternative_title:
- LNCS
article_processing_charge: No
author:
- first_name: Bram
full_name: Cohen, Bram
last_name: Cohen
- first_name: Krzysztof Z
full_name: Pietrzak, Krzysztof Z
id: 3E04A7AA-F248-11E8-B48F-1D18A9856A87
last_name: Pietrzak
orcid: 0000-0002-9139-1654
citation:
ama: 'Cohen B, Pietrzak KZ. Simple proofs of sequential work. In: Vol 10821. Springer;
2018:451-467. doi:10.1007/978-3-319-78375-8_15'
apa: 'Cohen, B., & Pietrzak, K. Z. (2018). Simple proofs of sequential work
(Vol. 10821, pp. 451–467). Presented at the Eurocrypt: Advances in Cryptology,
Tel Aviv, Israel: Springer. https://doi.org/10.1007/978-3-319-78375-8_15'
chicago: Cohen, Bram, and Krzysztof Z Pietrzak. “Simple Proofs of Sequential Work,”
10821:451–67. Springer, 2018. https://doi.org/10.1007/978-3-319-78375-8_15.
ieee: 'B. Cohen and K. Z. Pietrzak, “Simple proofs of sequential work,” presented
at the Eurocrypt: Advances in Cryptology, Tel Aviv, Israel, 2018, vol. 10821,
pp. 451–467.'
ista: 'Cohen B, Pietrzak KZ. 2018. Simple proofs of sequential work. Eurocrypt:
Advances in Cryptology, LNCS, vol. 10821, 451–467.'
mla: Cohen, Bram, and Krzysztof Z. Pietrzak. Simple Proofs of Sequential Work.
Vol. 10821, Springer, 2018, pp. 451–67, doi:10.1007/978-3-319-78375-8_15.
short: B. Cohen, K.Z. Pietrzak, in:, Springer, 2018, pp. 451–467.
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: 2018-05-29T00:00:00Z
date_updated: 2023-09-18T09:29:33Z
day: '29'
department:
- _id: KrPi
doi: 10.1007/978-3-319-78375-8_15
ec_funded: 1
external_id:
isi:
- '000517098700015'
intvolume: ' 10821'
isi: 1
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://eprint.iacr.org/2018/183.pdf
month: '05'
oa: 1
oa_version: Submitted Version
page: 451 - 467
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: '7579'
quality_controlled: '1'
scopus_import: '1'
status: public
title: Simple proofs of sequential work
type: conference
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
volume: 10821
year: '2018'
...
---
_id: '31'
abstract:
- lang: eng
text: Correlations in sensory neural networks have both extrinsic and intrinsic
origins. Extrinsic or stimulus correlations arise from shared inputs to the network
and, thus, depend strongly on the stimulus ensemble. Intrinsic or noise correlations
reflect biophysical mechanisms of interactions between neurons, which are expected
to be robust to changes in the stimulus ensemble. Despite the importance of this
distinction for understanding how sensory networks encode information collectively,
no method exists to reliably separate intrinsic interactions from extrinsic correlations
in neural activity data, limiting our ability to build predictive models of the
network response. In this paper we introduce a general strategy to infer population
models of interacting neurons that collectively encode stimulus information. The
key to disentangling intrinsic from extrinsic correlations is to infer the couplings
between neurons separately from the encoding model and to combine the two using
corrections calculated in a mean-field approximation. We demonstrate the effectiveness
of this approach in retinal recordings. The same coupling network is inferred
from responses to radically different stimulus ensembles, showing that these couplings
indeed reflect stimulus-independent interactions between neurons. The inferred
model predicts accurately the collective response of retinal ganglion cell populations
as a function of the stimulus.
acknowledgement: This work was supported by ANR Trajectory, the French State program
Investissements d’Avenir managed by the Agence Nationale de la Recherche (LIFESENSES;
ANR-10-LABX-65), EC Grant No. H2020-785907 from the Human Brain Project, NIH Grant
No. U01NS090501, and an AVIESAN-UNADEV grant to O.M. M.C. was supported by the Agence
Nationale de la Recherche Jeune Chercheur/Jeune Chercheuse grant (ANR-17-CE37-0013).
article_number: '042410'
article_processing_charge: No
article_type: original
author:
- first_name: Ulisse
full_name: Ferrari, Ulisse
last_name: Ferrari
- first_name: Stephane
full_name: Deny, Stephane
last_name: Deny
- first_name: Matthew J
full_name: Chalk, Matthew J
last_name: Chalk
- first_name: Gasper
full_name: Tkacik, Gasper
id: 3D494DCA-F248-11E8-B48F-1D18A9856A87
last_name: Tkacik
orcid: 0000-0002-6699-1455
- first_name: Olivier
full_name: Marre, Olivier
last_name: Marre
- first_name: Thierry
full_name: Mora, Thierry
last_name: Mora
citation:
ama: Ferrari U, Deny S, Chalk MJ, Tkačik G, Marre O, Mora T. Separating intrinsic
interactions from extrinsic correlations in a network of sensory neurons. Physical
Review E. 2018;98(4). doi:10.1103/PhysRevE.98.042410
apa: Ferrari, U., Deny, S., Chalk, M. J., Tkačik, G., Marre, O., & Mora, T.
(2018). Separating intrinsic interactions from extrinsic correlations in a network
of sensory neurons. Physical Review E. American Physical Society. https://doi.org/10.1103/PhysRevE.98.042410
chicago: Ferrari, Ulisse, Stephane Deny, Matthew J Chalk, Gašper Tkačik, Olivier
Marre, and Thierry Mora. “Separating Intrinsic Interactions from Extrinsic Correlations
in a Network of Sensory Neurons.” Physical Review E. American Physical
Society, 2018. https://doi.org/10.1103/PhysRevE.98.042410.
ieee: U. Ferrari, S. Deny, M. J. Chalk, G. Tkačik, O. Marre, and T. Mora, “Separating
intrinsic interactions from extrinsic correlations in a network of sensory neurons,”
Physical Review E, vol. 98, no. 4. American Physical Society, 2018.
ista: Ferrari U, Deny S, Chalk MJ, Tkačik G, Marre O, Mora T. 2018. Separating intrinsic
interactions from extrinsic correlations in a network of sensory neurons. Physical
Review E. 98(4), 042410.
mla: Ferrari, Ulisse, et al. “Separating Intrinsic Interactions from Extrinsic Correlations
in a Network of Sensory Neurons.” Physical Review E, vol. 98, no. 4, 042410,
American Physical Society, 2018, doi:10.1103/PhysRevE.98.042410.
short: U. Ferrari, S. Deny, M.J. Chalk, G. Tkačik, O. Marre, T. Mora, Physical Review
E 98 (2018).
date_created: 2018-12-11T11:44:15Z
date_published: 2018-10-17T00:00:00Z
date_updated: 2023-09-18T09:18:44Z
day: '17'
department:
- _id: GaTk
doi: 10.1103/PhysRevE.98.042410
ec_funded: 1
external_id:
isi:
- '000447486100004'
intvolume: ' 98'
isi: 1
issue: '4'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://www.biorxiv.org/content/10.1101/243816v2.full
month: '10'
oa: 1
oa_version: Preprint
project:
- _id: 26436750-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '785907'
name: Human Brain Project Specific Grant Agreement 2 (HBP SGA 2)
publication: Physical Review E
publication_identifier:
issn:
- '24700045'
publication_status: published
publisher: American Physical Society
publist_id: '8024'
quality_controlled: '1'
scopus_import: '1'
status: public
title: Separating intrinsic interactions from extrinsic correlations in a network
of sensory neurons
type: journal_article
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
volume: 98
year: '2018'
...
---
_id: '64'
abstract:
- lang: eng
text: Tropical geometry, an established field in pure mathematics, is a place where
string theory, mirror symmetry, computational algebra, auction theory, and so
forth meet and influence one another. In this paper, we report on our discovery
of a tropical model with self-organized criticality (SOC) behavior. Our model
is continuous, in contrast to all known models of SOC, and is a certain scaling
limit of the sandpile model, the first and archetypical model of SOC. We describe
how our model is related to pattern formation and proportional growth phenomena
and discuss the dichotomy between continuous and discrete models in several contexts.
Our aim in this context is to present an idealized tropical toy model (cf. Turing
reaction-diffusion model), requiring further investigation.
article_processing_charge: No
article_type: original
author:
- first_name: Nikita
full_name: Kalinin, Nikita
last_name: Kalinin
- first_name: Aldo
full_name: Guzmán Sáenz, Aldo
last_name: Guzmán Sáenz
- first_name: Y
full_name: Prieto, Y
last_name: Prieto
- first_name: Mikhail
full_name: Shkolnikov, Mikhail
id: 35084A62-F248-11E8-B48F-1D18A9856A87
last_name: Shkolnikov
orcid: 0000-0002-4310-178X
- first_name: V
full_name: Kalinina, V
last_name: Kalinina
- first_name: Ernesto
full_name: Lupercio, Ernesto
last_name: Lupercio
citation:
ama: 'Kalinin N, Guzmán Sáenz A, Prieto Y, Shkolnikov M, Kalinina V, Lupercio E.
Self-organized criticality and pattern emergence through the lens of tropical
geometry. PNAS: Proceedings of the National Academy of Sciences of the United
States of America. 2018;115(35):E8135-E8142. doi:10.1073/pnas.1805847115'
apa: 'Kalinin, N., Guzmán Sáenz, A., Prieto, Y., Shkolnikov, M., Kalinina, V., &
Lupercio, E. (2018). Self-organized criticality and pattern emergence through
the lens of tropical geometry. PNAS: Proceedings of the National Academy of
Sciences of the United States of America. National Academy of Sciences. https://doi.org/10.1073/pnas.1805847115'
chicago: 'Kalinin, Nikita, Aldo Guzmán Sáenz, Y Prieto, Mikhail Shkolnikov, V Kalinina,
and Ernesto Lupercio. “Self-Organized Criticality and Pattern Emergence through
the Lens of Tropical Geometry.” PNAS: Proceedings of the National Academy of
Sciences of the United States of America. National Academy of Sciences, 2018.
https://doi.org/10.1073/pnas.1805847115.'
ieee: 'N. Kalinin, A. Guzmán Sáenz, Y. Prieto, M. Shkolnikov, V. Kalinina, and E.
Lupercio, “Self-organized criticality and pattern emergence through the lens of
tropical geometry,” PNAS: Proceedings of the National Academy of Sciences of
the United States of America, vol. 115, no. 35. National Academy of Sciences,
pp. E8135–E8142, 2018.'
ista: 'Kalinin N, Guzmán Sáenz A, Prieto Y, Shkolnikov M, Kalinina V, Lupercio E.
2018. Self-organized criticality and pattern emergence through the lens of tropical
geometry. PNAS: Proceedings of the National Academy of Sciences of the United
States of America. 115(35), E8135–E8142.'
mla: 'Kalinin, Nikita, et al. “Self-Organized Criticality and Pattern Emergence
through the Lens of Tropical Geometry.” PNAS: Proceedings of the National Academy
of Sciences of the United States of America, vol. 115, no. 35, National Academy
of Sciences, 2018, pp. E8135–42, doi:10.1073/pnas.1805847115.'
short: 'N. Kalinin, A. Guzmán Sáenz, Y. Prieto, M. Shkolnikov, V. Kalinina, E. Lupercio,
PNAS: Proceedings of the National Academy of Sciences of the United States of
America 115 (2018) E8135–E8142.'
date_created: 2018-12-11T11:44:26Z
date_published: 2018-08-28T00:00:00Z
date_updated: 2023-09-18T08:41:16Z
day: '28'
department:
- _id: TaHa
doi: 10.1073/pnas.1805847115
ec_funded: 1
external_id:
arxiv:
- '1806.09153'
isi:
- '000442861600009'
intvolume: ' 115'
isi: 1
issue: '35'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/1806.09153
month: '08'
oa: 1
oa_version: Preprint
page: E8135 - E8142
project:
- _id: 25681D80-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '291734'
name: International IST Postdoc Fellowship Programme
publication: 'PNAS: Proceedings of the National Academy of Sciences of the United
States of America'
publication_identifier:
issn:
- '00278424'
publication_status: published
publisher: National Academy of Sciences
publist_id: '7990'
quality_controlled: '1'
scopus_import: '1'
status: public
title: Self-organized criticality and pattern emergence through the lens of tropical
geometry
type: journal_article
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
volume: 115
year: '2018'
...
---
_id: '9838'
abstract:
- lang: eng
text: 'Facial shape is the basis for facial recognition and categorization. Facial
features reflect the underlying geometry of the skeletal structures. Here we reveal
that cartilaginous nasal capsule (corresponding to upper jaw and face) is shaped
by signals generated by neural structures: brain and olfactory epithelium. Brain-derived
Sonic Hedgehog (SHH) enables the induction of nasal septum and posterior nasal
capsule, whereas the formation of a capsule roof is controlled by signals from
the olfactory epithelium. Unexpectedly, the cartilage of the nasal capsule turned
out to be important for shaping membranous facial bones during development. This
suggests that conserved neurosensory structures could benefit from protection
and have evolved signals inducing cranial cartilages encasing them. Experiments
with mutant mice revealed that the genomic regulatory regions controlling production
of SHH in the nervous system contribute to facial cartilage morphogenesis, which
might be a mechanism responsible for the adaptive evolution of animal faces and
snouts.'
article_processing_charge: No
author:
- first_name: Marketa
full_name: Kaucka, Marketa
last_name: Kaucka
- first_name: Julian
full_name: Petersen, Julian
last_name: Petersen
- first_name: Marketa
full_name: Tesarova, Marketa
last_name: Tesarova
- first_name: Bara
full_name: Szarowska, Bara
last_name: Szarowska
- first_name: Maria Eleni
full_name: Kastriti, Maria Eleni
last_name: Kastriti
- first_name: Meng
full_name: Xie, Meng
last_name: Xie
- first_name: Anna
full_name: Kicheva, Anna
id: 3959A2A0-F248-11E8-B48F-1D18A9856A87
last_name: Kicheva
orcid: 0000-0003-4509-4998
- first_name: Karl
full_name: Annusver, Karl
last_name: Annusver
- first_name: Maria
full_name: Kasper, Maria
last_name: Kasper
- first_name: Orsolya
full_name: Symmons, Orsolya
last_name: Symmons
- first_name: Leslie
full_name: Pan, Leslie
last_name: Pan
- first_name: Francois
full_name: Spitz, Francois
last_name: Spitz
- first_name: Jozef
full_name: Kaiser, Jozef
last_name: Kaiser
- first_name: Maria
full_name: Hovorakova, Maria
last_name: Hovorakova
- first_name: Tomas
full_name: Zikmund, Tomas
last_name: Zikmund
- first_name: Kazunori
full_name: Sunadome, Kazunori
last_name: Sunadome
- first_name: Michael P
full_name: Matise, Michael P
last_name: Matise
- first_name: Hui
full_name: Wang, Hui
last_name: Wang
- first_name: Ulrika
full_name: Marklund, Ulrika
last_name: Marklund
- first_name: Hind
full_name: Abdo, Hind
last_name: Abdo
- first_name: Patrik
full_name: Ernfors, Patrik
last_name: Ernfors
- first_name: Pascal
full_name: Maire, Pascal
last_name: Maire
- first_name: Maud
full_name: Wurmser, Maud
last_name: Wurmser
- first_name: Andrei S
full_name: Chagin, Andrei S
last_name: Chagin
- first_name: Kaj
full_name: Fried, Kaj
last_name: Fried
- first_name: Igor
full_name: Adameyko, Igor
last_name: Adameyko
citation:
ama: 'Kaucka M, Petersen J, Tesarova M, et al. Data from: Signals from the brain
and olfactory epithelium control shaping of the mammalian nasal capsule cartilage.
2018. doi:10.5061/dryad.f1s76f2'
apa: 'Kaucka, M., Petersen, J., Tesarova, M., Szarowska, B., Kastriti, M. E., Xie,
M., … Adameyko, I. (2018). Data from: Signals from the brain and olfactory epithelium
control shaping of the mammalian nasal capsule cartilage. Dryad. https://doi.org/10.5061/dryad.f1s76f2'
chicago: 'Kaucka, Marketa, Julian Petersen, Marketa Tesarova, Bara Szarowska, Maria
Eleni Kastriti, Meng Xie, Anna Kicheva, et al. “Data from: Signals from the Brain
and Olfactory Epithelium Control Shaping of the Mammalian Nasal Capsule Cartilage.”
Dryad, 2018. https://doi.org/10.5061/dryad.f1s76f2.'
ieee: 'M. Kaucka et al., “Data from: Signals from the brain and olfactory
epithelium control shaping of the mammalian nasal capsule cartilage.” Dryad, 2018.'
ista: 'Kaucka M, Petersen J, Tesarova M, Szarowska B, Kastriti ME, Xie M, Kicheva
A, Annusver K, Kasper M, Symmons O, Pan L, Spitz F, Kaiser J, Hovorakova M, Zikmund
T, Sunadome K, Matise MP, Wang H, Marklund U, Abdo H, Ernfors P, Maire P, Wurmser
M, Chagin AS, Fried K, Adameyko I. 2018. Data from: Signals from the brain and
olfactory epithelium control shaping of the mammalian nasal capsule cartilage,
Dryad, 10.5061/dryad.f1s76f2.'
mla: 'Kaucka, Marketa, et al. Data from: Signals from the Brain and Olfactory
Epithelium Control Shaping of the Mammalian Nasal Capsule Cartilage. Dryad,
2018, doi:10.5061/dryad.f1s76f2.'
short: M. Kaucka, J. Petersen, M. Tesarova, B. Szarowska, M.E. Kastriti, M. Xie,
A. Kicheva, K. Annusver, M. Kasper, O. Symmons, L. Pan, F. Spitz, J. Kaiser, M.
Hovorakova, T. Zikmund, K. Sunadome, M.P. Matise, H. Wang, U. Marklund, H. Abdo,
P. Ernfors, P. Maire, M. Wurmser, A.S. Chagin, K. Fried, I. Adameyko, (2018).
date_created: 2021-08-09T12:54:35Z
date_published: 2018-06-14T00:00:00Z
date_updated: 2023-09-18T09:29:07Z
day: '14'
department:
- _id: AnKi
doi: 10.5061/dryad.f1s76f2
main_file_link:
- open_access: '1'
url: https://doi.org/10.5061/dryad.f1s76f2
month: '06'
oa: 1
oa_version: Published Version
publisher: Dryad
related_material:
record:
- id: '162'
relation: used_in_publication
status: public
status: public
title: 'Data from: Signals from the brain and olfactory epithelium control shaping
of the mammalian nasal capsule cartilage'
type: research_data_reference
user_id: 6785fbc1-c503-11eb-8a32-93094b40e1cf
year: '2018'
...
---
_id: '41'
abstract:
- lang: eng
text: 'The small-conductance, Ca2+-activated K+ (SK) channel subtype SK2 regulates
the spike rate and firing frequency, as well as Ca2+ transients in Purkinje cells
(PCs). To understand the molecular basis by which SK2 channels mediate these functions,
we analyzed the exact location and densities of SK2 channels along the neuronal
surface of the mouse cerebellar PCs using SDS-digested freeze-fracture replica
labeling (SDS-FRL) of high sensitivity combined with quantitative analyses. Immunogold
particles for SK2 were observed on post- and pre-synaptic compartments showing
both scattered and clustered distribution patterns. We found an axo-somato-dendritic
gradient of the SK2 particle density increasing 12-fold from soma to dendritic
spines. Using two different immunogold approaches, we also found that SK2 immunoparticles
were frequently adjacent to, but never overlap with, the postsynaptic density
of excitatory synapses in PC spines. Co-immunoprecipitation analysis demonstrated
that SK2 channels form macromolecular complexes with two types of proteins that
mobilize Ca2+: CaV2.1 channels and mGlu1α receptors in the cerebellum. Freeze-fracture
replica double-labeling showed significant co-clustering of particles for SK2
with those for CaV2.1 channels and mGlu1α receptors. SK2 channels were also detected
at presynaptic sites, mostly at the presynaptic active zone (AZ), where they are
close to CaV2.1 channels, though they are not significantly co-clustered. These
data demonstrate that SK2 channels located in different neuronal compartments
can associate with distinct proteins mobilizing Ca2+, and suggest that the ultrastructural
association of SK2 with CaV2.1 and mGlu1α provides the mechanism that ensures
voltage (excitability) regulation by distinct intracellular Ca2+ transients in
PCs.'
article_number: '311'
article_processing_charge: No
article_type: original
author:
- first_name: Rafæl
full_name: Luján, Rafæl
last_name: Luján
- first_name: Carolina
full_name: Aguado, Carolina
last_name: Aguado
- first_name: Francisco
full_name: Ciruela, Francisco
last_name: Ciruela
- first_name: Xavier
full_name: Arus, Xavier
last_name: Arus
- first_name: Alejandro
full_name: Martín Belmonte, Alejandro
last_name: Martín Belmonte
- first_name: Rocío
full_name: Alfaro Ruiz, Rocío
last_name: Alfaro Ruiz
- first_name: Jesus
full_name: Martinez Gomez, Jesus
last_name: Martinez Gomez
- first_name: Luis
full_name: De La Ossa, Luis
last_name: De La Ossa
- first_name: Masahiko
full_name: Watanabe, Masahiko
last_name: Watanabe
- first_name: John
full_name: Adelman, John
last_name: Adelman
- first_name: Ryuichi
full_name: Shigemoto, Ryuichi
id: 499F3ABC-F248-11E8-B48F-1D18A9856A87
last_name: Shigemoto
orcid: 0000-0001-8761-9444
- first_name: Yugo
full_name: Fukazawa, Yugo
last_name: Fukazawa
citation:
ama: Luján R, Aguado C, Ciruela F, et al. Sk2 channels associate with mGlu1α receptors
and CaV2.1 channels in Purkinje cells. Frontiers in Cellular Neuroscience.
2018;12. doi:10.3389/fncel.2018.00311
apa: Luján, R., Aguado, C., Ciruela, F., Arus, X., Martín Belmonte, A., Alfaro Ruiz,
R., … Fukazawa, Y. (2018). Sk2 channels associate with mGlu1α receptors and CaV2.1
channels in Purkinje cells. Frontiers in Cellular Neuroscience. Frontiers
Media. https://doi.org/10.3389/fncel.2018.00311
chicago: Luján, Rafæl, Carolina Aguado, Francisco Ciruela, Xavier Arus, Alejandro
Martín Belmonte, Rocío Alfaro Ruiz, Jesus Martinez Gomez, et al. “Sk2 Channels
Associate with MGlu1α Receptors and CaV2.1 Channels in Purkinje Cells.” Frontiers
in Cellular Neuroscience. Frontiers Media, 2018. https://doi.org/10.3389/fncel.2018.00311.
ieee: R. Luján et al., “Sk2 channels associate with mGlu1α receptors and
CaV2.1 channels in Purkinje cells,” Frontiers in Cellular Neuroscience,
vol. 12. Frontiers Media, 2018.
ista: Luján R, Aguado C, Ciruela F, Arus X, Martín Belmonte A, Alfaro Ruiz R, Martinez
Gomez J, De La Ossa L, Watanabe M, Adelman J, Shigemoto R, Fukazawa Y. 2018. Sk2
channels associate with mGlu1α receptors and CaV2.1 channels in Purkinje cells.
Frontiers in Cellular Neuroscience. 12, 311.
mla: Luján, Rafæl, et al. “Sk2 Channels Associate with MGlu1α Receptors and CaV2.1
Channels in Purkinje Cells.” Frontiers in Cellular Neuroscience, vol. 12,
311, Frontiers Media, 2018, doi:10.3389/fncel.2018.00311.
short: R. Luján, C. Aguado, F. Ciruela, X. Arus, A. Martín Belmonte, R. Alfaro Ruiz,
J. Martinez Gomez, L. De La Ossa, M. Watanabe, J. Adelman, R. Shigemoto, Y. Fukazawa,
Frontiers in Cellular Neuroscience 12 (2018).
date_created: 2018-12-11T11:44:19Z
date_published: 2018-09-19T00:00:00Z
date_updated: 2023-09-18T09:31:18Z
day: '19'
ddc:
- '570'
department:
- _id: RySh
doi: 10.3389/fncel.2018.00311
ec_funded: 1
external_id:
isi:
- '000445090100002'
file:
- access_level: open_access
checksum: 0bcaec8d596162af0b7fe3f31325d480
content_type: application/pdf
creator: dernst
date_created: 2018-12-17T08:49:03Z
date_updated: 2020-07-14T12:46:23Z
file_id: '5684'
file_name: fncel-12-00311.pdf
file_size: 6834251
relation: main_file
file_date_updated: 2020-07-14T12:46:23Z
has_accepted_license: '1'
intvolume: ' 12'
isi: 1
language:
- iso: eng
month: '09'
oa: 1
oa_version: Published Version
project:
- _id: 25CBA828-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '720270'
name: Human Brain Project Specific Grant Agreement 1 (HBP SGA 1)
publication: Frontiers in Cellular Neuroscience
publication_identifier:
issn:
- '16625102'
publication_status: published
publisher: Frontiers Media
publist_id: '8013'
quality_controlled: '1'
scopus_import: '1'
status: public
title: Sk2 channels associate with mGlu1α receptors and CaV2.1 channels in Purkinje
cells
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: journal_article
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
volume: 12
year: '2018'
...
---
_id: '23'
abstract:
- lang: eng
text: The strong atomistic spin–orbit coupling of holes makes single-shot spin readout
measurements difficult because it reduces the spin lifetimes. By integrating the
charge sensor into a high bandwidth radio frequency reflectometry setup, we were
able to demonstrate single-shot readout of a germanium quantum dot hole spin and
measure the spin lifetime. Hole spin relaxation times of about 90 μs at 500 mT
are reported, with a total readout visibility of about 70%. By analyzing separately
the spin-to-charge conversion and charge readout fidelities, we have obtained
insight into the processes limiting the visibilities of hole spins. The analyses
suggest that high hole visibilities are feasible at realistic experimental conditions,
underlying the potential of hole spins for the realization of viable qubit devices.
acknowledged_ssus:
- _id: M-Shop
- _id: NanoFab
article_processing_charge: No
author:
- first_name: Lada
full_name: Vukušić, Lada
id: 31E9F056-F248-11E8-B48F-1D18A9856A87
last_name: Vukušić
orcid: 0000-0003-2424-8636
- first_name: Josip
full_name: Kukucka, Josip
id: 3F5D8856-F248-11E8-B48F-1D18A9856A87
last_name: Kukucka
- first_name: Hannes
full_name: Watzinger, Hannes
id: 35DF8E50-F248-11E8-B48F-1D18A9856A87
last_name: Watzinger
- first_name: Joshua M
full_name: Milem, Joshua M
id: 4CDE0A96-F248-11E8-B48F-1D18A9856A87
last_name: Milem
- first_name: Friedrich
full_name: Schäffler, Friedrich
last_name: Schäffler
- first_name: Georgios
full_name: Katsaros, Georgios
id: 38DB5788-F248-11E8-B48F-1D18A9856A87
last_name: Katsaros
orcid: 0000-0001-8342-202X
citation:
ama: Vukušić L, Kukucka J, Watzinger H, Milem JM, Schäffler F, Katsaros G. Single-shot
readout of hole spins in Ge. Nano Letters. 2018;18(11):7141-7145. doi:10.1021/acs.nanolett.8b03217
apa: Vukušić, L., Kukucka, J., Watzinger, H., Milem, J. M., Schäffler, F., &
Katsaros, G. (2018). Single-shot readout of hole spins in Ge. Nano Letters.
American Chemical Society. https://doi.org/10.1021/acs.nanolett.8b03217
chicago: Vukušić, Lada, Josip Kukucka, Hannes Watzinger, Joshua M Milem, Friedrich
Schäffler, and Georgios Katsaros. “Single-Shot Readout of Hole Spins in Ge.” Nano
Letters. American Chemical Society, 2018. https://doi.org/10.1021/acs.nanolett.8b03217.
ieee: L. Vukušić, J. Kukucka, H. Watzinger, J. M. Milem, F. Schäffler, and G. Katsaros,
“Single-shot readout of hole spins in Ge,” Nano Letters, vol. 18, no. 11.
American Chemical Society, pp. 7141–7145, 2018.
ista: Vukušić L, Kukucka J, Watzinger H, Milem JM, Schäffler F, Katsaros G. 2018.
Single-shot readout of hole spins in Ge. Nano Letters. 18(11), 7141–7145.
mla: Vukušić, Lada, et al. “Single-Shot Readout of Hole Spins in Ge.” Nano Letters,
vol. 18, no. 11, American Chemical Society, 2018, pp. 7141–45, doi:10.1021/acs.nanolett.8b03217.
short: L. Vukušić, J. Kukucka, H. Watzinger, J.M. Milem, F. Schäffler, G. Katsaros,
Nano Letters 18 (2018) 7141–7145.
date_created: 2018-12-11T11:44:13Z
date_published: 2018-10-25T00:00:00Z
date_updated: 2023-09-18T09:30:37Z
day: '25'
ddc:
- '530'
department:
- _id: GeKa
doi: 10.1021/acs.nanolett.8b03217
ec_funded: 1
external_id:
isi:
- '000451102100064'
pmid:
- '30359041'
file:
- access_level: open_access
checksum: 3e6034a94c6b5335e939145d88bdb371
content_type: application/pdf
creator: system
date_created: 2018-12-12T10:16:08Z
date_updated: 2020-07-14T12:45:37Z
file_id: '5194'
file_name: IST-2018-1065-v1+1_ACS_nanoletters_8b03217.pdf
file_size: 1361441
relation: main_file
file_date_updated: 2020-07-14T12:45:37Z
has_accepted_license: '1'
intvolume: ' 18'
isi: 1
issue: '11'
language:
- iso: eng
month: '10'
oa: 1
oa_version: Published Version
page: 7141 - 7145
pmid: 1
project:
- _id: 25517E86-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '335497'
name: Towards Spin qubits and Majorana fermions in Germanium selfassembled hut-wires
publication: Nano Letters
publication_identifier:
issn:
- '15306984'
publication_status: published
publisher: American Chemical Society
publist_id: '8032'
pubrep_id: '1065'
quality_controlled: '1'
related_material:
record:
- id: '7977'
relation: popular_science
- id: '69'
relation: dissertation_contains
status: public
- id: '7996'
relation: dissertation_contains
status: public
scopus_import: '1'
status: public
title: Single-shot readout of hole spins in Ge
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: 18
year: '2018'
...