---
_id: '417'
abstract:
- lang: eng
text: 'We introduce a Diagrammatic Monte Carlo (DiagMC) approach to complex molecular
impurities with rotational degrees of freedom interacting with a many-particle
environment. The treatment is based on the diagrammatic expansion that merges
the usual Feynman diagrams with the angular momentum diagrams known from atomic
and nuclear structure theory, thereby incorporating the non-Abelian algebra inherent
to quantum rotations. Our approach works at arbitrary coupling, is free of systematic
errors and of finite size effects, and naturally provides access to the impurity
Green function. We exemplify the technique by obtaining an all-coupling solution
of the angulon model, however, the method is quite general and can be applied
to a broad variety of quantum impurities possessing angular momentum degrees of
freedom. '
article_number: '165301'
article_processing_charge: No
arxiv: 1
author:
- first_name: Giacomo
full_name: Bighin, Giacomo
id: 4CA96FD4-F248-11E8-B48F-1D18A9856A87
last_name: Bighin
orcid: 0000-0001-8823-9777
- first_name: Timur
full_name: Tscherbul, Timur
last_name: Tscherbul
- first_name: Mikhail
full_name: Lemeshko, Mikhail
id: 37CB05FA-F248-11E8-B48F-1D18A9856A87
last_name: Lemeshko
orcid: 0000-0002-6990-7802
citation:
ama: Bighin G, Tscherbul T, Lemeshko M. Diagrammatic Monte Carlo approach to rotating
molecular impurities. Physical Review Letters. 2018;121(16). doi:10.1103/PhysRevLett.121.165301
apa: Bighin, G., Tscherbul, T., & Lemeshko, M. (2018). Diagrammatic Monte Carlo
approach to rotating molecular impurities. Physical Review Letters. American
Physical Society. https://doi.org/10.1103/PhysRevLett.121.165301
chicago: Bighin, Giacomo, Timur Tscherbul, and Mikhail Lemeshko. “Diagrammatic Monte
Carlo Approach to Rotating Molecular Impurities.” Physical Review Letters.
American Physical Society, 2018. https://doi.org/10.1103/PhysRevLett.121.165301.
ieee: G. Bighin, T. Tscherbul, and M. Lemeshko, “Diagrammatic Monte Carlo approach
to rotating molecular impurities,” Physical Review Letters, vol. 121, no.
16. American Physical Society, 2018.
ista: Bighin G, Tscherbul T, Lemeshko M. 2018. Diagrammatic Monte Carlo approach
to rotating molecular impurities. Physical Review Letters. 121(16), 165301.
mla: Bighin, Giacomo, et al. “Diagrammatic Monte Carlo Approach to Rotating Molecular
Impurities.” Physical Review Letters, vol. 121, no. 16, 165301, American
Physical Society, 2018, doi:10.1103/PhysRevLett.121.165301.
short: G. Bighin, T. Tscherbul, M. Lemeshko, Physical Review Letters 121 (2018).
date_created: 2018-12-11T11:46:22Z
date_published: 2018-10-16T00:00:00Z
date_updated: 2024-02-28T13:14:53Z
day: '16'
department:
- _id: MiLe
doi: 10.1103/PhysRevLett.121.165301
external_id:
arxiv:
- '1803.07990'
intvolume: ' 121'
issue: '16'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/1803.07990
month: '10'
oa: 1
oa_version: Preprint
project:
- _id: 26031614-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: P29902
name: Quantum rotations in the presence of a many-body environment
publication: Physical Review Letters
publication_status: published
publisher: American Physical Society
publist_id: '8025'
quality_controlled: '1'
scopus_import: '1'
status: public
title: Diagrammatic Monte Carlo approach to rotating molecular impurities
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 121
year: '2018'
...
---
_id: '418'
abstract:
- lang: eng
text: "The aim of this thesis was the development of new strategies for optical
and optogenetic control of proliferative and pro-survival signaling, and characterizing
them from the molecular mechanism up to cellular effects. These new light-based
methods have unique features, such as red light as an activator, or the avoidance
of gene delivery, which enable to overcome current limitations, such as light
delivery to target tissues and feasibility as therapeutic approach. A special
focus was placed on implementing these new light-based approaches in pancreatic
β-cells, as β-cells are the key players in diabetes and especially their loss
in number negatively affects disease progression. Currently no treatment options
are available to compensate the lack of functional β-cells in diabetic patients.\r\nIn
a first approach, red-light-activated growth factor receptors, in particular receptor
tyrosine kinases were engineered and characterized. Receptor activation with light
allows spatio-temporal control compared to ligand-based activation, and especially
red light exhibits deeper tissue penetration than other wavelengths of the visible
spectrum. Red-light-activated receptor tyrosine kinases robustly activated major
growth factor related signaling pathways with a high temporal resolution. Moreover,
the remote activation of the proliferative MAPK/Erk pathway by red-light-activated
receptor tyrosine kinases in a pancreatic β-cell line was also achieved, through
one centimeter thick mouse tissue. Although red-light-activated receptor tyrosine
kinases are particularly attractive for applications in animal models due to the
deep tissue penetration of red light, a drawback, especially with regard to translation
into humans, is the requirement of gene therapy.\r\nIn a second approach an endogenous
light-sensitive mechanism was identified and its potential to promote proliferative
and pro-survival signals was explored, towards light-based tissue regeneration
without the need for gene transfer. Blue-green light illumination was found to
be sufficient for the activation of proliferation and survival promoting signaling
pathways in primary pancreatic murine and human islets. Blue-green light also
led to an increase in proliferation of primary islet cells, an effect which was
shown to be mostly β-cell specific in human islets. Moreover, it was demonstrated
that this approach of pancreatic β-cell expansion did not have any negative effect
on the β-cell function, in particular on their insulin secretion capacity. In
contrast, a trend for enhanced insulin secretion under high glucose conditions
after illumination was detected. In order to unravel the detailed characteristics
of this endogenous light-sensitive mechanism, the precise light requirements were
determined. In addition, the expression of light sensing proteins, OPN3 and rhodopsin,
was detected. The observed effects were found to be independent of handling effects
such as temperature differences and cytochrome c oxidase dependent ATP increase,
but they were found to be enhanced through the knockout of OPN3. The exact mechanism
of how islets cells sense light and the identity of the photoreceptor remains
unknown.\r\nSummarized two new light-based systems with unique features were established
that enable the activation of proliferative and pro-survival signaling pathways.
While red-light-activated receptor tyrosine kinases open a new avenue for optogenetics
research, by allowing non-invasive control of signaling in vivo, the identified
endogenous light-sensitive mechanism has the potential to be the basis of a gene
therapy-free therapeutical approach for light-based β-cell expansion."
alternative_title:
- ISTA Thesis
article_processing_charge: No
author:
- first_name: Eva
full_name: Gschaider-Reichhart, Eva
id: 3FEE232A-F248-11E8-B48F-1D18A9856A87
last_name: Gschaider-Reichhart
orcid: 0000-0002-7218-7738
citation:
ama: Gschaider-Reichhart E. Optical and optogenetic control of proliferation and
survival . 2018. doi:10.15479/AT:ISTA:th_913
apa: Gschaider-Reichhart, E. (2018). Optical and optogenetic control of proliferation
and survival . Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:th_913
chicago: Gschaider-Reichhart, Eva. “Optical and Optogenetic Control of Proliferation
and Survival .” Institute of Science and Technology Austria, 2018. https://doi.org/10.15479/AT:ISTA:th_913.
ieee: E. Gschaider-Reichhart, “Optical and optogenetic control of proliferation
and survival ,” Institute of Science and Technology Austria, 2018.
ista: Gschaider-Reichhart E. 2018. Optical and optogenetic control of proliferation
and survival . Institute of Science and Technology Austria.
mla: Gschaider-Reichhart, Eva. Optical and Optogenetic Control of Proliferation
and Survival . Institute of Science and Technology Austria, 2018, doi:10.15479/AT:ISTA:th_913.
short: E. Gschaider-Reichhart, Optical and Optogenetic Control of Proliferation
and Survival , Institute of Science and Technology Austria, 2018.
date_created: 2018-12-11T11:46:22Z
date_published: 2018-01-08T00:00:00Z
date_updated: 2023-09-22T09:20:10Z
day: '08'
ddc:
- '571'
- '570'
degree_awarded: PhD
department:
- _id: HaJa
doi: 10.15479/AT:ISTA:th_913
file:
- access_level: closed
checksum: 697fa72ca36fb1b8ceabc133d58a73e5
content_type: application/vnd.openxmlformats-officedocument.wordprocessingml.document
creator: dernst
date_created: 2019-04-05T09:28:03Z
date_updated: 2020-07-14T12:46:24Z
file_id: '6222'
file_name: 2018_THESIS_Gschaider-Reichhart_source.docx
file_size: 7012495
relation: source_file
- access_level: open_access
checksum: 58d7d1e9e58aeb7f061ab686b1d8a48c
content_type: application/pdf
creator: dernst
date_created: 2019-04-05T09:28:03Z
date_updated: 2020-07-14T12:46:24Z
file_id: '6223'
file_name: 2018_THESIS_Gschaider-Reichhart.pdf
file_size: 6355280
relation: main_file
file_date_updated: 2020-07-14T12:46:24Z
has_accepted_license: '1'
language:
- iso: eng
month: '01'
oa: 1
oa_version: Published Version
page: '107'
publication_identifier:
issn:
- 2663-337X
publication_status: published
publisher: Institute of Science and Technology Austria
publist_id: '7405'
pubrep_id: '913'
related_material:
record:
- id: '1441'
relation: part_of_dissertation
status: public
- id: '1678'
relation: part_of_dissertation
status: public
- id: '2084'
relation: part_of_dissertation
status: public
- id: '1028'
relation: part_of_dissertation
status: public
status: public
supervisor:
- first_name: Harald L
full_name: Janovjak, Harald L
id: 33BA6C30-F248-11E8-B48F-1D18A9856A87
last_name: Janovjak
orcid: 0000-0002-8023-9315
title: 'Optical and optogenetic control of proliferation and survival '
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: dissertation
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
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: '42'
abstract:
- lang: eng
text: Seeds derive from ovules upon fertilization and therefore the total number
of ovules determines the final seed yield, a fundamental trait in crop plants.
Among the factors that co-ordinate the process of ovule formation, the transcription
factors CUP-SHAPED COTYLEDON 1 (CUC1) and CUC2 and the hormone cytokinin (CK)
have a particularly prominent role. Indeed, the absence of both CUC1 and CUC2
causes a severe reduction in ovule number, a phenotype that can be rescued by
CK treatment. In this study, we combined CK quantification with an integrative
genome-wide target identification approach to select Arabidopsis genes regulated
by CUCs that are also involved in CK metabolism. We focused our attention on the
functional characterization of UDP-GLUCOSYL TRANSFERASE 85A3 (UGT85A3) and UGT73C1,
which are up-regulated in the absence of CUC1 and CUC2 and encode enzymes able
to catalyse CK inactivation by O-glucosylation. Our results demonstrate a role
for these UGTs as a link between CUCs and CK homeostasis, and highlight the importance
of CUCs and CKs in the determination of seed yield.
acknowledgement: This work was funded by the Ministry of Education, Youth and Sports
of the Czech Republic through the National Program of Sustainability (grant no.
LO1204).
article_processing_charge: No
author:
- first_name: Mara
full_name: Cucinotta, Mara
last_name: Cucinotta
- first_name: Silvia
full_name: Manrique, Silvia
last_name: Manrique
- first_name: Candela
full_name: Cuesta, Candela
id: 33A3C818-F248-11E8-B48F-1D18A9856A87
last_name: Cuesta
orcid: 0000-0003-1923-2410
- first_name: Eva
full_name: Benková, Eva
id: 38F4F166-F248-11E8-B48F-1D18A9856A87
last_name: Benková
orcid: 0000-0002-8510-9739
- first_name: Ondřej
full_name: Novák, Ondřej
last_name: Novák
- first_name: Lucia
full_name: Colombo, Lucia
last_name: Colombo
citation:
ama: Cucinotta M, Manrique S, Cuesta C, Benková E, Novák O, Colombo L. Cup-shaped
Cotyledon1 (CUC1) and CU2 regulate cytokinin homeostasis to determine ovule number
in arabidopsis. Journal of Experimental Botany. 2018;69(21):5169-5176.
doi:10.1093/jxb/ery281
apa: Cucinotta, M., Manrique, S., Cuesta, C., Benková, E., Novák, O., & Colombo,
L. (2018). Cup-shaped Cotyledon1 (CUC1) and CU2 regulate cytokinin homeostasis
to determine ovule number in arabidopsis. Journal of Experimental Botany.
Oxford University Press. https://doi.org/10.1093/jxb/ery281
chicago: Cucinotta, Mara, Silvia Manrique, Candela Cuesta, Eva Benková, Ondřej Novák,
and Lucia Colombo. “Cup-Shaped Cotyledon1 (CUC1) and CU2 Regulate Cytokinin Homeostasis
to Determine Ovule Number in Arabidopsis.” Journal of Experimental Botany.
Oxford University Press, 2018. https://doi.org/10.1093/jxb/ery281.
ieee: M. Cucinotta, S. Manrique, C. Cuesta, E. Benková, O. Novák, and L. Colombo,
“Cup-shaped Cotyledon1 (CUC1) and CU2 regulate cytokinin homeostasis to determine
ovule number in arabidopsis,” Journal of Experimental Botany, vol. 69,
no. 21. Oxford University Press, pp. 5169–5176, 2018.
ista: Cucinotta M, Manrique S, Cuesta C, Benková E, Novák O, Colombo L. 2018. Cup-shaped
Cotyledon1 (CUC1) and CU2 regulate cytokinin homeostasis to determine ovule number
in arabidopsis. Journal of Experimental Botany. 69(21), 5169–5176.
mla: Cucinotta, Mara, et al. “Cup-Shaped Cotyledon1 (CUC1) and CU2 Regulate Cytokinin
Homeostasis to Determine Ovule Number in Arabidopsis.” Journal of Experimental
Botany, vol. 69, no. 21, Oxford University Press, 2018, pp. 5169–76, doi:10.1093/jxb/ery281.
short: M. Cucinotta, S. Manrique, C. Cuesta, E. Benková, O. Novák, L. Colombo, Journal
of Experimental Botany 69 (2018) 5169–5176.
date_created: 2018-12-11T11:44:19Z
date_published: 2018-07-26T00:00:00Z
date_updated: 2023-09-11T12:52:03Z
day: '26'
ddc:
- '575'
department:
- _id: EvBe
doi: 10.1093/jxb/ery281
external_id:
isi:
- '000448163900015'
file:
- access_level: open_access
checksum: ca3b6711040b1662488aeb3d1f961f13
content_type: application/pdf
creator: dernst
date_created: 2018-12-17T10:44:16Z
date_updated: 2020-07-14T12:46:25Z
file_id: '5691'
file_name: 2018_JournalExperimBotany_Cucinotta.pdf
file_size: 1292128
relation: main_file
file_date_updated: 2020-07-14T12:46:25Z
has_accepted_license: '1'
intvolume: ' 69'
isi: 1
issue: '21'
language:
- iso: eng
month: '07'
oa: 1
oa_version: Published Version
page: 5169 - 5176
publication: Journal of Experimental Botany
publication_status: published
publisher: Oxford University Press
publist_id: '8012'
quality_controlled: '1'
scopus_import: '1'
status: public
title: Cup-shaped Cotyledon1 (CUC1) and CU2 regulate cytokinin homeostasis to determine
ovule number in arabidopsis
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: 69
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: '421'
abstract:
- lang: eng
text: Cell shape is determined by a balance of intrinsic properties of the cell
as well as its mechanochemical environment. Inhomogeneous shape changes underlie
many morphogenetic events and involve spatial gradients in active cellular forces
induced by complex chemical signaling. Here, we introduce a mechanochemical model
based on the notion that cell shape changes may be induced by external diffusible
biomolecules that influence cellular contractility (or equivalently, adhesions)
in a concentration-dependent manner—and whose spatial profile in turn is affected
by cell shape. We map out theoretically the possible interplay between chemical
concentration and cellular structure. Besides providing a direct route to spatial
gradients in cell shape profiles in tissues, we show that the dependence on cell
shape helps create robust mechanochemical gradients.
article_processing_charge: No
arxiv: 1
author:
- first_name: Kinjal
full_name: Dasbiswas, Kinjal
last_name: Dasbiswas
- first_name: Claude-Edouard B
full_name: Hannezo, Claude-Edouard B
id: 3A9DB764-F248-11E8-B48F-1D18A9856A87
last_name: Hannezo
orcid: 0000-0001-6005-1561
- first_name: Nir
full_name: Gov, Nir
last_name: Gov
citation:
ama: Dasbiswas K, Hannezo EB, Gov N. Theory of eppithelial cell shape transitions
induced by mechanoactive chemical gradients. Biophysical Journal. 2018;114(4):968-977.
doi:10.1016/j.bpj.2017.12.022
apa: Dasbiswas, K., Hannezo, E. B., & Gov, N. (2018). Theory of eppithelial
cell shape transitions induced by mechanoactive chemical gradients. Biophysical
Journal. Biophysical Society. https://doi.org/10.1016/j.bpj.2017.12.022
chicago: Dasbiswas, Kinjal, Edouard B Hannezo, and Nir Gov. “Theory of Eppithelial
Cell Shape Transitions Induced by Mechanoactive Chemical Gradients.” Biophysical
Journal. Biophysical Society, 2018. https://doi.org/10.1016/j.bpj.2017.12.022.
ieee: K. Dasbiswas, E. B. Hannezo, and N. Gov, “Theory of eppithelial cell shape
transitions induced by mechanoactive chemical gradients,” Biophysical Journal,
vol. 114, no. 4. Biophysical Society, pp. 968–977, 2018.
ista: Dasbiswas K, Hannezo EB, Gov N. 2018. Theory of eppithelial cell shape transitions
induced by mechanoactive chemical gradients. Biophysical Journal. 114(4), 968–977.
mla: Dasbiswas, Kinjal, et al. “Theory of Eppithelial Cell Shape Transitions Induced
by Mechanoactive Chemical Gradients.” Biophysical Journal, vol. 114, no.
4, Biophysical Society, 2018, pp. 968–77, doi:10.1016/j.bpj.2017.12.022.
short: K. Dasbiswas, E.B. Hannezo, N. Gov, Biophysical Journal 114 (2018) 968–977.
date_created: 2018-12-11T11:46:23Z
date_published: 2018-02-27T00:00:00Z
date_updated: 2023-09-19T10:13:55Z
day: '27'
department:
- _id: EdHa
doi: 10.1016/j.bpj.2017.12.022
external_id:
arxiv:
- '1709.01486'
isi:
- '000428016700021'
intvolume: ' 114'
isi: 1
issue: '4'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/1709.01486
month: '02'
oa: 1
oa_version: Submitted Version
page: 968 - 977
publication: Biophysical Journal
publication_status: published
publisher: Biophysical Society
publist_id: '7403'
quality_controlled: '1'
scopus_import: '1'
status: public
title: Theory of eppithelial cell shape transitions induced by mechanoactive chemical
gradients
type: journal_article
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
volume: 114
year: '2018'
...
---
_id: '422'
abstract:
- lang: eng
text: We show that a rather simple, steady modification of the streamwise velocity
profile in a pipe can lead to a complete collapse of turbulence and the flow fully
relaminarizes. Two different devices, a stationary obstacle (inset) and a device
which injects fluid through an annular gap close to the wall, are used to control
the flow. Both devices modify the streamwise velocity profile such that the flow
in the center of the pipe is decelerated and the flow in the near wall region
is accelerated. We present measurements with stereoscopic particle image velocimetry
to investigate and capture the development of the relaminarizing flow downstream
these devices and the specific circumstances responsible for relaminarization.
We find total relaminarization up to Reynolds numbers of 6000, where the skin
friction in the far downstream distance is reduced by a factor of 3.4 due to relaminarization.
In a smooth straight pipe the flow remains completely laminar downstream of the
control. Furthermore, we show that transient (temporary) relaminarization in a
spatially confined region right downstream the devices occurs also at much higher
Reynolds numbers, accompanied by a significant local skin friction drag reduction.
The underlying physical mechanism of relaminarization is attributed to a weakening
of the near-wall turbulence production cycle.
article_processing_charge: Yes (via OA deal)
author:
- first_name: Jakob
full_name: Kühnen, Jakob
id: 3A47AE32-F248-11E8-B48F-1D18A9856A87
last_name: Kühnen
orcid: 0000-0003-4312-0179
- first_name: Davide
full_name: Scarselli, Davide
id: 40315C30-F248-11E8-B48F-1D18A9856A87
last_name: Scarselli
orcid: 0000-0001-5227-4271
- first_name: Markus
full_name: Schaner, Markus
id: 316CE034-F248-11E8-B48F-1D18A9856A87
last_name: Schaner
- first_name: Björn
full_name: Hof, Björn
id: 3A374330-F248-11E8-B48F-1D18A9856A87
last_name: Hof
orcid: 0000-0003-2057-2754
citation:
ama: Kühnen J, Scarselli D, Schaner M, Hof B. Relaminarization by steady modification
of the streamwise velocity profile in a pipe. Flow Turbulence and Combustion.
2018;100(4):919-942. doi:10.1007/s10494-018-9896-4
apa: Kühnen, J., Scarselli, D., Schaner, M., & Hof, B. (2018). Relaminarization
by steady modification of the streamwise velocity profile in a pipe. Flow Turbulence
and Combustion. Springer. https://doi.org/10.1007/s10494-018-9896-4
chicago: Kühnen, Jakob, Davide Scarselli, Markus Schaner, and Björn Hof. “Relaminarization
by Steady Modification of the Streamwise Velocity Profile in a Pipe.” Flow
Turbulence and Combustion. Springer, 2018. https://doi.org/10.1007/s10494-018-9896-4.
ieee: J. Kühnen, D. Scarselli, M. Schaner, and B. Hof, “Relaminarization by steady
modification of the streamwise velocity profile in a pipe,” Flow Turbulence
and Combustion, vol. 100, no. 4. Springer, pp. 919–942, 2018.
ista: Kühnen J, Scarselli D, Schaner M, Hof B. 2018. Relaminarization by steady
modification of the streamwise velocity profile in a pipe. Flow Turbulence and
Combustion. 100(4), 919–942.
mla: Kühnen, Jakob, et al. “Relaminarization by Steady Modification of the Streamwise
Velocity Profile in a Pipe.” Flow Turbulence and Combustion, vol. 100,
no. 4, Springer, 2018, pp. 919–42, doi:10.1007/s10494-018-9896-4.
short: J. Kühnen, D. Scarselli, M. Schaner, B. Hof, Flow Turbulence and Combustion
100 (2018) 919–942.
date_created: 2018-12-11T11:46:23Z
date_published: 2018-01-01T00:00:00Z
date_updated: 2024-03-25T23:30:20Z
day: '01'
ddc:
- '530'
department:
- _id: BjHo
doi: 10.1007/s10494-018-9896-4
ec_funded: 1
external_id:
isi:
- '000433113900004'
file:
- access_level: open_access
checksum: d7c0bade150faabca150b0a9986e60ca
content_type: application/pdf
creator: dernst
date_created: 2018-12-17T15:52:37Z
date_updated: 2020-07-14T12:46:25Z
file_id: '5717'
file_name: 2018_FlowTurbulenceCombust_Kuehnen.pdf
file_size: 2210020
relation: main_file
file_date_updated: 2020-07-14T12:46:25Z
has_accepted_license: '1'
intvolume: ' 100'
isi: 1
issue: '4'
language:
- iso: eng
month: '01'
oa: 1
oa_version: Published Version
page: 919 - 942
project:
- _id: 25152F3A-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '306589'
name: Decoding the complexity of turbulence at its origin
publication: Flow Turbulence and Combustion
publication_status: published
publisher: Springer
publist_id: '7401'
quality_controlled: '1'
related_material:
record:
- id: '7258'
relation: dissertation_contains
status: public
scopus_import: '1'
status: public
title: Relaminarization by steady modification of the streamwise velocity profile
in a pipe
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: 100
year: '2018'
...
---
_id: '423'
abstract:
- lang: eng
text: Herd immunity, a process in which resistant individuals limit the spread of
a pathogen among susceptible hosts has been extensively studied in eukaryotes.
Even though bacteria have evolved multiple immune systems against their phage
pathogens, herd immunity in bacteria remains unexplored. Here we experimentally
demonstrate that herd immunity arises during phage epidemics in structured and
unstructured Escherichia coli populations consisting of differing frequencies
of susceptible and resistant cells harboring CRISPR immunity. In addition, we
develop a mathematical model that quantifies how herd immunity is affected by
spatial population structure, bacterial growth rate, and phage replication rate.
Using our model we infer a general epidemiological rule describing the relative
speed of an epidemic in partially resistant spatially structured populations.
Our experimental and theoretical findings indicate that herd immunity may be important
in bacterial communities, allowing for stable coexistence of bacteria and their
phages and the maintenance of polymorphism in bacterial immunity.
acknowledgement: "We are grateful to Remy Chait for his help and assistance with establishing
our experimental setups and to Tobias Bergmiller for valuable insights into some
specific experimental details. We thank Luciano Marraffini for donating us the pCas9
plasmid used in this study. We also want to express our gratitude to Seth Barribeau,
Andrea Betancourt, Călin Guet, Mato Lagator, Tiago Paixão and Maroš Pleška for valuable
discussions on the manuscript. Finally, we would like to thank the \r\neditors and
reviewers for their helpful comments and suggestions."
article_number: e32035
article_processing_charge: No
author:
- first_name: Pavel
full_name: Payne, Pavel
id: 35F78294-F248-11E8-B48F-1D18A9856A87
last_name: Payne
orcid: 0000-0002-2711-9453
- first_name: Lukas
full_name: Geyrhofer, Lukas
last_name: Geyrhofer
- 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: Jonathan P
full_name: Bollback, Jonathan P
id: 2C6FA9CC-F248-11E8-B48F-1D18A9856A87
last_name: Bollback
orcid: 0000-0002-4624-4612
citation:
ama: Payne P, Geyrhofer L, Barton NH, Bollback JP. CRISPR-based herd immunity can
limit phage epidemics in bacterial populations. eLife. 2018;7. doi:10.7554/eLife.32035
apa: Payne, P., Geyrhofer, L., Barton, N. H., & Bollback, J. P. (2018). CRISPR-based
herd immunity can limit phage epidemics in bacterial populations. ELife.
eLife Sciences Publications. https://doi.org/10.7554/eLife.32035
chicago: Payne, Pavel, Lukas Geyrhofer, Nicholas H Barton, and Jonathan P Bollback.
“CRISPR-Based Herd Immunity Can Limit Phage Epidemics in Bacterial Populations.”
ELife. eLife Sciences Publications, 2018. https://doi.org/10.7554/eLife.32035.
ieee: P. Payne, L. Geyrhofer, N. H. Barton, and J. P. Bollback, “CRISPR-based herd
immunity can limit phage epidemics in bacterial populations,” eLife, vol.
7. eLife Sciences Publications, 2018.
ista: Payne P, Geyrhofer L, Barton NH, Bollback JP. 2018. CRISPR-based herd immunity
can limit phage epidemics in bacterial populations. eLife. 7, e32035.
mla: Payne, Pavel, et al. “CRISPR-Based Herd Immunity Can Limit Phage Epidemics
in Bacterial Populations.” ELife, vol. 7, e32035, eLife Sciences Publications,
2018, doi:10.7554/eLife.32035.
short: P. Payne, L. Geyrhofer, N.H. Barton, J.P. Bollback, ELife 7 (2018).
date_created: 2018-12-11T11:46:23Z
date_published: 2018-03-09T00:00:00Z
date_updated: 2023-09-11T12:49:17Z
day: '09'
ddc:
- '576'
department:
- _id: NiBa
- _id: JoBo
doi: 10.7554/eLife.32035
ec_funded: 1
external_id:
isi:
- '000431035800001'
file:
- access_level: open_access
checksum: 447cf6e680bdc3c01062a8737d876569
content_type: application/pdf
creator: dernst
date_created: 2018-12-17T10:36:07Z
date_updated: 2020-07-14T12:46:25Z
file_id: '5689'
file_name: 2018_eLife_Payne.pdf
file_size: 3533881
relation: main_file
file_date_updated: 2020-07-14T12:46:25Z
has_accepted_license: '1'
intvolume: ' 7'
isi: 1
language:
- iso: eng
month: '03'
oa: 1
oa_version: Published Version
project:
- _id: 2578D616-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '648440'
name: Selective Barriers to Horizontal Gene Transfer
publication: eLife
publication_status: published
publisher: eLife Sciences Publications
publist_id: '7400'
quality_controlled: '1'
related_material:
record:
- id: '9840'
relation: research_data
status: public
scopus_import: '1'
status: public
title: CRISPR-based herd immunity can limit phage epidemics in bacterial populations
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: journal_article
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
volume: 7
year: '2018'
...
---
_id: '425'
abstract:
- lang: eng
text: 'We show that the following algorithmic problem is decidable: given a 2-dimensional
simplicial complex, can it be embedded (topologically, or equivalently, piecewise
linearly) in R3? By a known reduction, it suffices to decide the embeddability
of a given triangulated 3-manifold X into the 3-sphere S3. The main step, which
allows us to simplify X and recurse, is in proving that if X can be embedded in
S3, then there is also an embedding in which X has a short meridian, that is,
an essential curve in the boundary of X bounding a disk in S3 \ X with length
bounded by a computable function of the number of tetrahedra of X.'
article_number: '5'
article_processing_charge: No
article_type: original
arxiv: 1
author:
- first_name: Jiří
full_name: Matoušek, Jiří
last_name: Matoušek
- first_name: Eric
full_name: Sedgwick, Eric
last_name: Sedgwick
- first_name: Martin
full_name: Tancer, Martin
id: 38AC689C-F248-11E8-B48F-1D18A9856A87
last_name: Tancer
orcid: 0000-0002-1191-6714
- first_name: Uli
full_name: Wagner, Uli
id: 36690CA2-F248-11E8-B48F-1D18A9856A87
last_name: Wagner
orcid: 0000-0002-1494-0568
citation:
ama: Matoušek J, Sedgwick E, Tancer M, Wagner U. Embeddability in the 3-Sphere is
decidable. Journal of the ACM. 2018;65(1). doi:10.1145/3078632
apa: Matoušek, J., Sedgwick, E., Tancer, M., & Wagner, U. (2018). Embeddability
in the 3-Sphere is decidable. Journal of the ACM. ACM. https://doi.org/10.1145/3078632
chicago: Matoušek, Jiří, Eric Sedgwick, Martin Tancer, and Uli Wagner. “Embeddability
in the 3-Sphere Is Decidable.” Journal of the ACM. ACM, 2018. https://doi.org/10.1145/3078632.
ieee: J. Matoušek, E. Sedgwick, M. Tancer, and U. Wagner, “Embeddability in the
3-Sphere is decidable,” Journal of the ACM, vol. 65, no. 1. ACM, 2018.
ista: Matoušek J, Sedgwick E, Tancer M, Wagner U. 2018. Embeddability in the 3-Sphere
is decidable. Journal of the ACM. 65(1), 5.
mla: Matoušek, Jiří, et al. “Embeddability in the 3-Sphere Is Decidable.” Journal
of the ACM, vol. 65, no. 1, 5, ACM, 2018, doi:10.1145/3078632.
short: J. Matoušek, E. Sedgwick, M. Tancer, U. Wagner, Journal of the ACM 65 (2018).
date_created: 2018-12-11T11:46:24Z
date_published: 2018-01-01T00:00:00Z
date_updated: 2023-09-11T13:38:49Z
day: '01'
department:
- _id: UlWa
doi: 10.1145/3078632
ec_funded: 1
external_id:
arxiv:
- '1402.0815'
isi:
- '000425685900006'
intvolume: ' 65'
isi: 1
issue: '1'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/1402.0815
month: '01'
oa: 1
oa_version: Preprint
project:
- _id: 25681D80-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '291734'
name: International IST Postdoc Fellowship Programme
publication: Journal of the ACM
publication_status: published
publisher: ACM
publist_id: '7398'
quality_controlled: '1'
related_material:
record:
- id: '2157'
relation: earlier_version
status: public
scopus_import: '1'
status: public
title: Embeddability in the 3-Sphere is decidable
type: journal_article
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
volume: 65
year: '2018'
...
---
_id: '426'
abstract:
- lang: eng
text: Sperm cells are the most morphologically diverse cells across animal taxa.
Within species, sperm and ejaculate traits have been suggested to vary with the
male's competitive environment, e.g., level of sperm competition, female mating
status and quality, and also with male age, body mass, physiological condition,
and resource availability. Most previous studies have based their conclusions
on the analysis of only one or a few ejaculates per male without investigating
differences among the ejaculates of the same individual. This masks potential
ejaculate-specific traits. Here, we provide data on the length, quantity, and
viability of sperm ejaculated by wingless males of the ant Cardiocondyla obscurior.
Males of this ant species are relatively long-lived and can mate with large numbers
of female sexuals throughout their lives. We analyzed all ejaculates across the
individuals' lifespan and manipulated the availability of mating partners. Our
study shows that both the number and size of sperm cells transferred during copulations
differ among individuals and also among ejaculates of the same male. Sperm quality
does not decrease with male age, but the variation in sperm number between ejaculates
indicates that males need considerable time to replenish their sperm supplies.
Producing many ejaculates in a short time appears to be traded-off against male
longevity rather than sperm quality.
acknowledgement: "Research with C. obscurior from Brazil was permitted by Instituto
Brasileiro do Meio Ambiente e dos Recursos Naturais Renováveis, IBAMA (permit no.
20324-1). We thank the German Science Foundation ( DFG ) for funding ( Schr1135/2-1
), T. Suckert for help with sperm length measurements and A.K. Huylmans for advice
concerning graphs. One referee made helpful comments on the manuscript.\r\n"
article_processing_charge: No
author:
- first_name: Sina
full_name: Metzler, Sina
id: 48204546-F248-11E8-B48F-1D18A9856A87
last_name: Metzler
orcid: 0000-0002-9547-2494
- first_name: Alexandra
full_name: Schrempf, Alexandra
last_name: Schrempf
- first_name: Jürgen
full_name: Heinze, Jürgen
last_name: Heinze
citation:
ama: Metzler S, Schrempf A, Heinze J. Individual- and ejaculate-specific sperm traits
in ant males. Journal of Insect Physiology. 2018;107:284-290. doi:10.1016/j.jinsphys.2017.12.003
apa: Metzler, S., Schrempf, A., & Heinze, J. (2018). Individual- and ejaculate-specific
sperm traits in ant males. Journal of Insect Physiology. Elsevier. https://doi.org/10.1016/j.jinsphys.2017.12.003
chicago: Metzler, Sina, Alexandra Schrempf, and Jürgen Heinze. “Individual- and
Ejaculate-Specific Sperm Traits in Ant Males.” Journal of Insect Physiology.
Elsevier, 2018. https://doi.org/10.1016/j.jinsphys.2017.12.003.
ieee: S. Metzler, A. Schrempf, and J. Heinze, “Individual- and ejaculate-specific
sperm traits in ant males,” Journal of Insect Physiology, vol. 107. Elsevier,
pp. 284–290, 2018.
ista: Metzler S, Schrempf A, Heinze J. 2018. Individual- and ejaculate-specific
sperm traits in ant males. Journal of Insect Physiology. 107, 284–290.
mla: Metzler, Sina, et al. “Individual- and Ejaculate-Specific Sperm Traits in Ant
Males.” Journal of Insect Physiology, vol. 107, Elsevier, 2018, pp. 284–90,
doi:10.1016/j.jinsphys.2017.12.003.
short: S. Metzler, A. Schrempf, J. Heinze, Journal of Insect Physiology 107 (2018)
284–290.
date_created: 2018-12-11T11:46:25Z
date_published: 2018-05-01T00:00:00Z
date_updated: 2023-09-12T07:43:26Z
day: '01'
department:
- _id: SyCr
doi: 10.1016/j.jinsphys.2017.12.003
external_id:
isi:
- '000434751100034'
intvolume: ' 107'
isi: 1
language:
- iso: eng
month: '05'
oa_version: None
page: 284-290
publication: Journal of Insect Physiology
publication_status: published
publisher: Elsevier
publist_id: '7397'
quality_controlled: '1'
scopus_import: '1'
status: public
title: Individual- and ejaculate-specific sperm traits in ant males
type: journal_article
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
volume: 107
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
arxiv: 1
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: '428'
abstract:
- lang: eng
text: The plant hormone gibberellic acid (GA) is a crucial regulator of growth and
development. The main paradigm of GA signaling puts forward transcriptional regulation
via the degradation of DELLA transcriptional repressors. GA has also been shown
to regulate tropic responses by modulation of the plasma membrane incidence of
PIN auxin transporters by an unclear mechanism. Here we uncovered the cellular
and molecular mechanisms by which GA redirects protein trafficking and thus regulates
cell surface functionality. Photoconvertible reporters revealed that GA balances
the protein traffic between the vacuole degradation route and recycling back to
the cell surface. Low GA levels promote vacuolar delivery and degradation of multiple
cargos, including PIN proteins, whereas high GA levels promote their recycling
to the plasma membrane. This GA effect requires components of the retromer complex,
such as Sorting Nexin 1 (SNX1) and its interacting, microtubule (MT)-associated
protein, the Cytoplasmic Linker-Associated Protein (CLASP1). Accordingly, GA regulates
the subcellular distribution of SNX1 and CLASP1, and the intact MT cytoskeleton
is essential for the GA effect on trafficking. This GA cellular action occurs
through DELLA proteins that regulate the MT and retromer presumably via their
interaction partners Prefoldins (PFDs). Our study identified a branching of the
GA signaling pathway at the level of DELLA proteins, which, in parallel to regulating
transcription, also target by a nontranscriptional mechanism the retromer complex
acting at the intersection of the degradation and recycling trafficking routes.
By this mechanism, GA can redirect receptors and transporters to the cell surface,
thus coregulating multiple processes, including PIN-dependent auxin fluxes during
tropic responses.
acknowledgement: "We gratefully acknowledge M. Blázquez (Instituto de Biología Molecular
y Celular de Plantas), M. Fendrych, C. Cuesta Moliner (Institute of Science and
Technology Austria), M. Vanstraelen, M. Nowack (Center for Plant Systems Biology,
Ghent), C. Luschnig (Universitat fur Bodenkultur Wien, Vienna), S. Simon (Central
European Institute of Technology, Brno), C. Sommerville (Carnegie Institution for
Science), and Y. Gu (Penn State University) for making available the materials used
in this study;\r\n...funding from the European Research Council (ERC) under the
European Union’s Seventh Framework Programme (FP7/2007-2013)/ERC Grant Agreement
282300.\r\nCC BY NC ND"
article_processing_charge: No
author:
- first_name: Yuliya
full_name: Salanenka, Yuliya
id: 46DAAE7E-F248-11E8-B48F-1D18A9856A87
last_name: Salanenka
- first_name: Inge
full_name: Verstraeten, Inge
id: 362BF7FE-F248-11E8-B48F-1D18A9856A87
last_name: Verstraeten
orcid: 0000-0001-7241-2328
- first_name: Christian
full_name: Löfke, Christian
last_name: Löfke
- first_name: Kaori
full_name: Tabata, Kaori
id: 7DAAEDA4-02D0-11E9-B11A-A5A4D7DFFFD0
last_name: Tabata
- first_name: Satoshi
full_name: Naramoto, Satoshi
last_name: Naramoto
- first_name: Matous
full_name: Glanc, Matous
id: 1AE1EA24-02D0-11E9-9BAA-DAF4881429F2
last_name: Glanc
orcid: 0000-0003-0619-7783
- first_name: Jirí
full_name: Friml, Jirí
id: 4159519E-F248-11E8-B48F-1D18A9856A87
last_name: Friml
orcid: 0000-0002-8302-7596
citation:
ama: Salanenka Y, Verstraeten I, Löfke C, et al. Gibberellin DELLA signaling targets
the retromer complex to redirect protein trafficking to the plasma membrane. PNAS.
2018;115(14):3716-3721. doi:10.1073/pnas.1721760115
apa: Salanenka, Y., Verstraeten, I., Löfke, C., Tabata, K., Naramoto, S., Glanc,
M., & Friml, J. (2018). Gibberellin DELLA signaling targets the retromer complex
to redirect protein trafficking to the plasma membrane. PNAS. National
Academy of Sciences. https://doi.org/10.1073/pnas.1721760115
chicago: Salanenka, Yuliya, Inge Verstraeten, Christian Löfke, Kaori Tabata, Satoshi
Naramoto, Matous Glanc, and Jiří Friml. “Gibberellin DELLA Signaling Targets the
Retromer Complex to Redirect Protein Trafficking to the Plasma Membrane.” PNAS.
National Academy of Sciences, 2018. https://doi.org/10.1073/pnas.1721760115.
ieee: Y. Salanenka et al., “Gibberellin DELLA signaling targets the retromer
complex to redirect protein trafficking to the plasma membrane,” PNAS,
vol. 115, no. 14. National Academy of Sciences, pp. 3716–3721, 2018.
ista: Salanenka Y, Verstraeten I, Löfke C, Tabata K, Naramoto S, Glanc M, Friml
J. 2018. Gibberellin DELLA signaling targets the retromer complex to redirect
protein trafficking to the plasma membrane. PNAS. 115(14), 3716–3721.
mla: Salanenka, Yuliya, et al. “Gibberellin DELLA Signaling Targets the Retromer
Complex to Redirect Protein Trafficking to the Plasma Membrane.” PNAS,
vol. 115, no. 14, National Academy of Sciences, 2018, pp. 3716–21, doi:10.1073/pnas.1721760115.
short: Y. Salanenka, I. Verstraeten, C. Löfke, K. Tabata, S. Naramoto, M. Glanc,
J. Friml, PNAS 115 (2018) 3716–3721.
date_created: 2018-12-11T11:46:25Z
date_published: 2018-04-03T00:00:00Z
date_updated: 2025-05-07T11:12:27Z
day: '03'
ddc:
- '580'
department:
- _id: JiFr
doi: 10.1073/pnas.1721760115
ec_funded: 1
external_id:
isi:
- '000429012500073'
file:
- access_level: open_access
checksum: 1fcf7223fb8f99559cfa80bd6f24ce44
content_type: application/pdf
creator: dernst
date_created: 2018-12-17T12:30:14Z
date_updated: 2020-07-14T12:46:26Z
file_id: '5700'
file_name: 2018_PNAS_Salanenka.pdf
file_size: 1924101
relation: main_file
file_date_updated: 2020-07-14T12:46:26Z
has_accepted_license: '1'
intvolume: ' 115'
isi: 1
issue: '14'
language:
- iso: eng
month: '04'
oa: 1
oa_version: Published Version
page: ' 3716 - 3721'
project:
- _id: 25716A02-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '282300'
name: Polarity and subcellular dynamics in plants
publication: PNAS
publication_status: published
publisher: National Academy of Sciences
publist_id: '7395'
quality_controlled: '1'
scopus_import: '1'
status: public
title: Gibberellin DELLA signaling targets the retromer complex to redirect protein
trafficking to the plasma membrane
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: '43'
abstract:
- lang: eng
text: 'The initial amount of pathogens required to start an infection within a susceptible
host is called the infective dose and is known to vary to a large extent between
different pathogen species. We investigate the hypothesis that the differences
in infective doses are explained by the mode of action in the underlying mechanism
of pathogenesis: Pathogens with locally acting mechanisms tend to have smaller
infective doses than pathogens with distantly acting mechanisms. While empirical
evidence tends to support the hypothesis, a formal theoretical explanation has
been lacking. We give simple analytical models to gain insight into this phenomenon
and also investigate a stochastic, spatially explicit, mechanistic within-host
model for toxin-dependent bacterial infections. The model shows that pathogens
secreting locally acting toxins have smaller infective doses than pathogens secreting
diffusive toxins, as hypothesized. While local pathogenetic mechanisms require
smaller infective doses, pathogens with distantly acting toxins tend to spread
faster and may cause more damage to the host. The proposed model can serve as
a basis for the spatially explicit analysis of various virulence factors also
in the context of other problems in infection dynamics.'
acknowledgement: J.R. and J.V.A. were also supported by the Academy of Finland Grants
1273253 and 267541.
article_processing_charge: No
author:
- first_name: Joel
full_name: Rybicki, Joel
id: 334EFD2E-F248-11E8-B48F-1D18A9856A87
last_name: Rybicki
orcid: 0000-0002-6432-6646
- first_name: Eva
full_name: Kisdi, Eva
last_name: Kisdi
- first_name: Jani
full_name: Anttila, Jani
last_name: Anttila
citation:
ama: Rybicki J, Kisdi E, Anttila J. Model of bacterial toxin-dependent pathogenesis
explains infective dose. PNAS. 2018;115(42):10690-10695. doi:10.1073/pnas.1721061115
apa: Rybicki, J., Kisdi, E., & Anttila, J. (2018). Model of bacterial toxin-dependent
pathogenesis explains infective dose. PNAS. National Academy of Sciences.
https://doi.org/10.1073/pnas.1721061115
chicago: Rybicki, Joel, Eva Kisdi, and Jani Anttila. “Model of Bacterial Toxin-Dependent
Pathogenesis Explains Infective Dose.” PNAS. National Academy of Sciences,
2018. https://doi.org/10.1073/pnas.1721061115.
ieee: J. Rybicki, E. Kisdi, and J. Anttila, “Model of bacterial toxin-dependent
pathogenesis explains infective dose,” PNAS, vol. 115, no. 42. National
Academy of Sciences, pp. 10690–10695, 2018.
ista: Rybicki J, Kisdi E, Anttila J. 2018. Model of bacterial toxin-dependent pathogenesis
explains infective dose. PNAS. 115(42), 10690–10695.
mla: Rybicki, Joel, et al. “Model of Bacterial Toxin-Dependent Pathogenesis Explains
Infective Dose.” PNAS, vol. 115, no. 42, National Academy of Sciences,
2018, pp. 10690–95, doi:10.1073/pnas.1721061115.
short: J. Rybicki, E. Kisdi, J. Anttila, PNAS 115 (2018) 10690–10695.
date_created: 2018-12-11T11:44:19Z
date_published: 2018-10-02T00:00:00Z
date_updated: 2023-09-13T08:57:38Z
day: '02'
ddc:
- '570'
- '577'
department:
- _id: DaAl
doi: 10.1073/pnas.1721061115
ec_funded: 1
external_id:
isi:
- '000447491300057'
file:
- access_level: open_access
checksum: df7ac544a587c06b75692653b9fabd18
content_type: application/pdf
creator: dernst
date_created: 2019-04-09T08:02:50Z
date_updated: 2020-07-14T12:46:26Z
file_id: '6258'
file_name: 2018_PNAS_Rybicki.pdf
file_size: 4070777
relation: main_file
file_date_updated: 2020-07-14T12:46:26Z
has_accepted_license: '1'
intvolume: ' 115'
isi: 1
issue: '42'
language:
- iso: eng
month: '10'
oa: 1
oa_version: Submitted Version
page: 10690 - 10695
project:
- _id: 260C2330-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '754411'
name: ISTplus - Postdoctoral Fellowships
publication: PNAS
publication_status: published
publisher: National Academy of Sciences
publist_id: '8011'
pubrep_id: '1063'
quality_controlled: '1'
scopus_import: '1'
status: public
title: Model of bacterial toxin-dependent pathogenesis explains infective dose
type: journal_article
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
volume: 115
year: '2018'
...
---
_id: '430'
abstract:
- lang: eng
text: In this issue of GENETICS, a new method for detecting natural selection on
polygenic traits is developed and applied to sev- eral human examples ( Racimo
et al. 2018 ). By de fi nition, many loci contribute to variation in polygenic
traits, and a challenge for evolutionary ge neticists has been that these traits
can evolve by small, nearly undetectable shifts in allele frequencies across each
of many, typically unknown, loci. Recently, a helpful remedy has arisen. Genome-wide
associ- ation studies (GWAS) have been illuminating sets of loci that can be interrogated
jointly for c hanges in allele frequencies. By aggregating small signal s of change
across many such loci, directional natural selection is now in principle detect-
able using genetic data, even for highly polygenic traits. This is an exciting
arena of progress – with these methods, tests can be made for selection associated
with traits, and we can now study selection in what may be its most prevalent
mode. The continuing fast pace of GWAS publications suggest there will be many
more polygenic tests of selection in the near future, as every new GWAS is an
opportunity for an accom- panying test of polygenic selection. However, it is
important to be aware of complications th at arise in interpretation, especially
given that these studies may easily be misinter- preted both in and outside the
evolutionary genetics commu- nity. Here, we provide context for understanding
polygenic tests and urge caution regarding how these results are inter- preted
and reported upon more broadly.
article_processing_charge: No
author:
- first_name: John
full_name: Novembre, John
last_name: Novembre
- 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: Novembre J, Barton NH. Tread lightly interpreting polygenic tests of selection.
Genetics. 2018;208(4):1351-1355. doi:10.1534/genetics.118.300786
apa: Novembre, J., & Barton, N. H. (2018). Tread lightly interpreting polygenic
tests of selection. Genetics. Genetics Society of America. https://doi.org/10.1534/genetics.118.300786
chicago: Novembre, John, and Nicholas H Barton. “Tread Lightly Interpreting Polygenic
Tests of Selection.” Genetics. Genetics Society of America, 2018. https://doi.org/10.1534/genetics.118.300786.
ieee: J. Novembre and N. H. Barton, “Tread lightly interpreting polygenic tests
of selection,” Genetics, vol. 208, no. 4. Genetics Society of America,
pp. 1351–1355, 2018.
ista: Novembre J, Barton NH. 2018. Tread lightly interpreting polygenic tests of
selection. Genetics. 208(4), 1351–1355.
mla: Novembre, John, and Nicholas H. Barton. “Tread Lightly Interpreting Polygenic
Tests of Selection.” Genetics, vol. 208, no. 4, Genetics Society of America,
2018, pp. 1351–55, doi:10.1534/genetics.118.300786.
short: J. Novembre, N.H. Barton, Genetics 208 (2018) 1351–1355.
date_created: 2018-12-11T11:46:26Z
date_published: 2018-04-01T00:00:00Z
date_updated: 2023-09-19T10:17:30Z
day: '01'
ddc:
- '576'
department:
- _id: NiBa
doi: 10.1534/genetics.118.300786
external_id:
isi:
- '000429094400005'
file:
- access_level: open_access
checksum: 3d838dc285df394376555b794b6a5ad1
content_type: application/pdf
creator: system
date_created: 2018-12-12T10:12:40Z
date_updated: 2020-07-14T12:46:26Z
file_id: '4958'
file_name: IST-2018-1012-v1+1_2018_Barton_Tread.pdf
file_size: 500129
relation: main_file
file_date_updated: 2020-07-14T12:46:26Z
has_accepted_license: '1'
intvolume: ' 208'
isi: 1
issue: '4'
language:
- iso: eng
month: '04'
oa: 1
oa_version: Published Version
page: 1351 - 1355
publication: Genetics
publication_status: published
publisher: Genetics Society of America
publist_id: '7393'
pubrep_id: '1012'
quality_controlled: '1'
scopus_import: '1'
status: public
title: Tread lightly interpreting polygenic tests of selection
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: 208
year: '2018'
...
---
_id: '433'
abstract:
- lang: eng
text: 'A thrackle is a graph drawn in the plane so that every pair of its edges
meet exactly once: either at a common end vertex or in a proper crossing. We prove
that any thrackle of n vertices has at most 1.3984n edges. Quasi-thrackles are
defined similarly, except that every pair of edges that do not share a vertex
are allowed to cross an odd number of times. It is also shown that the maximum
number of edges of a quasi-thrackle on n vertices is 3/2(n-1), and that this bound
is best possible for infinitely many values of n.'
alternative_title:
- LNCS
arxiv: 1
author:
- first_name: Radoslav
full_name: Fulek, Radoslav
id: 39F3FFE4-F248-11E8-B48F-1D18A9856A87
last_name: Fulek
orcid: 0000-0001-8485-1774
- first_name: János
full_name: Pach, János
last_name: Pach
citation:
ama: 'Fulek R, Pach J. Thrackles: An improved upper bound. In: Vol 10692. Springer;
2018:160-166. doi:10.1007/978-3-319-73915-1_14'
apa: 'Fulek, R., & Pach, J. (2018). Thrackles: An improved upper bound (Vol.
10692, pp. 160–166). Presented at the GD 2017: Graph Drawing and Network Visualization,
Boston, MA, United States: Springer. https://doi.org/10.1007/978-3-319-73915-1_14'
chicago: 'Fulek, Radoslav, and János Pach. “Thrackles: An Improved Upper Bound,”
10692:160–66. Springer, 2018. https://doi.org/10.1007/978-3-319-73915-1_14.'
ieee: 'R. Fulek and J. Pach, “Thrackles: An improved upper bound,” presented at
the GD 2017: Graph Drawing and Network Visualization, Boston, MA, United States,
2018, vol. 10692, pp. 160–166.'
ista: 'Fulek R, Pach J. 2018. Thrackles: An improved upper bound. GD 2017: Graph
Drawing and Network Visualization, LNCS, vol. 10692, 160–166.'
mla: 'Fulek, Radoslav, and János Pach. Thrackles: An Improved Upper Bound.
Vol. 10692, Springer, 2018, pp. 160–66, doi:10.1007/978-3-319-73915-1_14.'
short: R. Fulek, J. Pach, in:, Springer, 2018, pp. 160–166.
conference:
end_date: 2017-09-27
location: Boston, MA, United States
name: 'GD 2017: Graph Drawing and Network Visualization'
start_date: 201-09-25
date_created: 2018-12-11T11:46:27Z
date_published: 2018-01-21T00:00:00Z
date_updated: 2023-08-24T14:39:32Z
day: '21'
department:
- _id: UlWa
doi: 10.1007/978-3-319-73915-1_14
external_id:
arxiv:
- '1708.08037'
intvolume: ' 10692'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/1708.08037
month: '01'
oa: 1
oa_version: Submitted Version
page: 160 - 166
publication_status: published
publisher: Springer
publist_id: '7390'
quality_controlled: '1'
related_material:
record:
- id: '5857'
relation: later_version
status: public
scopus_import: 1
status: public
title: 'Thrackles: An improved upper bound'
type: conference
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 10692
year: '2018'
...
---
_id: '434'
abstract:
- lang: eng
text: In this paper, we present a formal model-driven design approach to establish
a safety-assured implementation of multifunction vehicle bus controller (MVBC),
which controls the data transmission among the devices of the vehicle. First,
the generic models and safety requirements described in International Electrotechnical
Commission Standard 61375 are formalized as time automata and timed computation
tree logic formulas, respectively. With model checking tool Uppaal, we verify
whether or not the constructed timed automata satisfy the formulas and several
logic inconsistencies in the original standard are detected and corrected. Then,
we apply the code generation tool Times to generate C code from the verified model,
which is later synthesized into a real MVBC chip, with some handwriting glue code.
Furthermore, the runtime verification tool RMOR is applied on the integrated code,
to verify some safety requirements that cannot be formalized on the timed automata.
For evaluation, we compare the proposed approach with existing MVBC design methods,
such as BeagleBone, Galsblock, and Simulink. Experiments show that more ambiguousness
or bugs in the standard are detected during Uppaal verification, and the generated
code of Times outperforms the C code generated by others in terms of the synthesized
binary code size. The errors in the standard have been confirmed and the resulting
MVBC has been deployed in the real train communication network.
article_processing_charge: No
author:
- first_name: Yu
full_name: Jiang, Yu
last_name: Jiang
- first_name: Han
full_name: Liu, Han
last_name: Liu
- first_name: Huobing
full_name: Song, Huobing
last_name: Song
- first_name: Hui
full_name: Kong, Hui
id: 3BDE25AA-F248-11E8-B48F-1D18A9856A87
last_name: Kong
orcid: 0000-0002-3066-6941
- first_name: Rui
full_name: Wang, Rui
last_name: Wang
- first_name: Yong
full_name: Guan, Yong
last_name: Guan
- first_name: Lui
full_name: Sha, Lui
last_name: Sha
citation:
ama: Jiang Y, Liu H, Song H, et al. Safety-assured model-driven design of the multifunction
vehicle bus controller. IEEE Transactions on Intelligent Transportation Systems.
2018;19(10):3320-3333. doi:10.1109/TITS.2017.2778077
apa: Jiang, Y., Liu, H., Song, H., Kong, H., Wang, R., Guan, Y., & Sha, L. (2018).
Safety-assured model-driven design of the multifunction vehicle bus controller.
IEEE Transactions on Intelligent Transportation Systems. IEEE. https://doi.org/10.1109/TITS.2017.2778077
chicago: Jiang, Yu, Han Liu, Huobing Song, Hui Kong, Rui Wang, Yong Guan, and Lui
Sha. “Safety-Assured Model-Driven Design of the Multifunction Vehicle Bus Controller.”
IEEE Transactions on Intelligent Transportation Systems. IEEE, 2018. https://doi.org/10.1109/TITS.2017.2778077.
ieee: Y. Jiang et al., “Safety-assured model-driven design of the multifunction
vehicle bus controller,” IEEE Transactions on Intelligent Transportation Systems,
vol. 19, no. 10. IEEE, pp. 3320–3333, 2018.
ista: Jiang Y, Liu H, Song H, Kong H, Wang R, Guan Y, Sha L. 2018. Safety-assured
model-driven design of the multifunction vehicle bus controller. IEEE Transactions
on Intelligent Transportation Systems. 19(10), 3320–3333.
mla: Jiang, Yu, et al. “Safety-Assured Model-Driven Design of the Multifunction
Vehicle Bus Controller.” IEEE Transactions on Intelligent Transportation Systems,
vol. 19, no. 10, IEEE, 2018, pp. 3320–33, doi:10.1109/TITS.2017.2778077.
short: Y. Jiang, H. Liu, H. Song, H. Kong, R. Wang, Y. Guan, L. Sha, IEEE Transactions
on Intelligent Transportation Systems 19 (2018) 3320–3333.
date_created: 2018-12-11T11:46:27Z
date_published: 2018-01-01T00:00:00Z
date_updated: 2023-09-18T08:12:49Z
day: '01'
department:
- _id: ToHe
doi: 10.1109/TITS.2017.2778077
external_id:
isi:
- '000446651100020'
intvolume: ' 19'
isi: 1
issue: '10'
language:
- iso: eng
month: '01'
oa_version: None
page: 3320 - 3333
publication: IEEE Transactions on Intelligent Transportation Systems
publication_status: published
publisher: IEEE
publist_id: '7389'
quality_controlled: '1'
related_material:
record:
- id: '1205'
relation: earlier_version
status: public
scopus_import: '1'
status: public
title: Safety-assured model-driven design of the multifunction vehicle bus controller
type: journal_article
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
volume: 19
year: '2018'
...
---
_id: '435'
abstract:
- lang: eng
text: It is shown that two fundamentally different phenomena, the bound states in
continuum and the spectral singularity (or time-reversed spectral singularity),
can occur simultaneously. This can be achieved in a rectangular core dielectric
waveguide with an embedded active (or absorbing) layer. In such a system a two-dimensional
bound state in a continuum is created in the plane of a waveguide cross section,
and it is emitted or absorbed along the waveguide core. The idea can be used for
experimental implementation of a laser or a coherent-perfect-absorber for a photonic
bound state that resides in a continuous spectrum.
acknowledgement: 'Seventh Framework Programme (FP7) People: Marie-Curie Actions (PEOPLE)
(291734). B. M. acknowledges the financial support by the People Programme (Marie
Curie Actions) of the European Union’s Seventh Framework Programme (FP7/ 2007-2013)
under REA.'
article_processing_charge: No
arxiv: 1
author:
- first_name: Bikashkali
full_name: Midya, Bikashkali
id: 456187FC-F248-11E8-B48F-1D18A9856A87
last_name: Midya
- first_name: Vladimir
full_name: Konotop, Vladimir
last_name: Konotop
citation:
ama: Midya B, Konotop V. Coherent-perfect-absorber and laser for bound states in
a continuum. Optics Letters. 2018;43(3):607-610. doi:10.1364/OL.43.000607
apa: Midya, B., & Konotop, V. (2018). Coherent-perfect-absorber and laser for
bound states in a continuum. Optics Letters. Optica Publishing Group.
https://doi.org/10.1364/OL.43.000607
chicago: Midya, Bikashkali, and Vladimir Konotop. “Coherent-Perfect-Absorber and
Laser for Bound States in a Continuum.” Optics Letters. Optica Publishing
Group, 2018. https://doi.org/10.1364/OL.43.000607.
ieee: B. Midya and V. Konotop, “Coherent-perfect-absorber and laser for bound states
in a continuum,” Optics Letters, vol. 43, no. 3. Optica Publishing Group,
pp. 607–610, 2018.
ista: Midya B, Konotop V. 2018. Coherent-perfect-absorber and laser for bound states
in a continuum. Optics Letters. 43(3), 607–610.
mla: Midya, Bikashkali, and Vladimir Konotop. “Coherent-Perfect-Absorber and Laser
for Bound States in a Continuum.” Optics Letters, vol. 43, no. 3, Optica
Publishing Group, 2018, pp. 607–10, doi:10.1364/OL.43.000607.
short: B. Midya, V. Konotop, Optics Letters 43 (2018) 607–610.
date_created: 2018-12-11T11:46:27Z
date_published: 2018-02-01T00:00:00Z
date_updated: 2023-10-17T12:15:06Z
day: '01'
department:
- _id: MiLe
doi: 10.1364/OL.43.000607
ec_funded: 1
external_id:
arxiv:
- '1711.01986'
isi:
- '000423776600066'
intvolume: ' 43'
isi: 1
issue: '3'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/1711.01986
month: '02'
oa: 1
oa_version: Preprint
page: 607 - 610
project:
- _id: 25681D80-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '291734'
name: International IST Postdoc Fellowship Programme
publication: Optics Letters
publication_status: published
publisher: Optica Publishing Group
publist_id: '7388'
quality_controlled: '1'
scopus_import: '1'
status: public
title: Coherent-perfect-absorber and laser for bound states in a continuum
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 43
year: '2018'
...
---
_id: '436'
abstract:
- lang: eng
text: There has been significant interest recently in using complex quantum systems
to create effective nonreciprocal dynamics. Proposals have been put forward for
the realization of artificial magnetic fields for photons and phonons; experimental
progress is fast making these proposals a reality. Much work has concentrated
on the use of such systems for controlling the flow of signals, e.g., to create
isolators or directional amplifiers for optical signals. In this Letter, we build
on this work but move in a different direction. We develop the theory of and discuss
a potential realization for the controllable flow of thermal noise in quantum
systems. We demonstrate theoretically that the unidirectional flow of thermal
noise is possible within quantum cascaded systems. Viewing an optomechanical platform
as a cascaded system we show here that one can ultimately control the direction
of the flow of thermal noise. By appropriately engineering the mechanical resonator,
which acts as an artificial reservoir, the flow of thermal noise can be constrained
to a desired direction, yielding a thermal rectifier. The proposed quantum thermal
noise rectifier could potentially be used to develop devices such as a thermal
modulator, a thermal router, and a thermal amplifier for nanoelectronic devices
and superconducting circuits.
article_number: '060601 '
article_processing_charge: No
arxiv: 1
author:
- first_name: Shabir
full_name: Barzanjeh, Shabir
id: 2D25E1F6-F248-11E8-B48F-1D18A9856A87
last_name: Barzanjeh
orcid: 0000-0003-0415-1423
- first_name: Matteo
full_name: Aquilina, Matteo
last_name: Aquilina
- first_name: André
full_name: Xuereb, André
last_name: Xuereb
citation:
ama: Barzanjeh S, Aquilina M, Xuereb A. Manipulating the flow of thermal noise in
quantum devices. Physical Review Letters. 2018;120(6). doi:10.1103/PhysRevLett.120.060601
apa: Barzanjeh, S., Aquilina, M., & Xuereb, A. (2018). Manipulating the flow
of thermal noise in quantum devices. Physical Review Letters. American
Physical Society. https://doi.org/10.1103/PhysRevLett.120.060601
chicago: Barzanjeh, Shabir, Matteo Aquilina, and André Xuereb. “Manipulating the
Flow of Thermal Noise in Quantum Devices.” Physical Review Letters. American
Physical Society, 2018. https://doi.org/10.1103/PhysRevLett.120.060601.
ieee: S. Barzanjeh, M. Aquilina, and A. Xuereb, “Manipulating the flow of thermal
noise in quantum devices,” Physical Review Letters, vol. 120, no. 6. American
Physical Society, 2018.
ista: Barzanjeh S, Aquilina M, Xuereb A. 2018. Manipulating the flow of thermal
noise in quantum devices. Physical Review Letters. 120(6), 060601.
mla: Barzanjeh, Shabir, et al. “Manipulating the Flow of Thermal Noise in Quantum
Devices.” Physical Review Letters, vol. 120, no. 6, 060601, American Physical
Society, 2018, doi:10.1103/PhysRevLett.120.060601.
short: S. Barzanjeh, M. Aquilina, A. Xuereb, Physical Review Letters 120 (2018).
date_created: 2018-12-11T11:46:28Z
date_published: 2018-02-07T00:00:00Z
date_updated: 2023-09-13T08:52:27Z
day: '07'
department:
- _id: JoFi
doi: 10.1103/PhysRevLett.120.060601
ec_funded: 1
external_id:
arxiv:
- '1706.09051'
isi:
- '000424382100004'
intvolume: ' 120'
isi: 1
issue: '6'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/1706.09051
month: '02'
oa: 1
oa_version: Preprint
project:
- _id: 257EB838-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '732894'
name: Hybrid Optomechanical Technologies
- _id: 258047B6-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '707438'
name: 'Microwave-to-Optical Quantum Link: Quantum Teleportation and Quantum Illumination
with cavity Optomechanics SUPEREOM'
publication: Physical Review Letters
publication_status: published
publisher: American Physical Society
publist_id: '7387'
quality_controlled: '1'
related_material:
link:
- description: News on IST Homepage
relation: press_release
url: https://ist.ac.at/en/news/interference-as-a-new-method-for-cooling-quantum-devices/
scopus_import: '1'
status: public
title: Manipulating the flow of thermal noise in quantum devices
type: journal_article
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
volume: 120
year: '2018'
...
---
_id: '437'
abstract:
- lang: eng
text: Dendritic cells (DCs) are sentinels of the adaptive immune system that reside
in peripheral organs of mammals. Upon pathogen encounter, they undergo maturation
and up-regulate the chemokine receptor CCR7 that guides them along gradients of
its chemokine ligands CCL19 and 21 to the next draining lymph node. There, DCs
present peripherally acquired antigen to naïve T cells, thereby triggering adaptive
immunity.
acknowledged_ssus:
- _id: SSU
acknowledgement: "This work was supported by grants of the European Research Council
(ERC CoG 724373) and the Austrian Science Fund (FWF) to M.S. We thank the scientific
support units at IST Austria for excellent technical support.\r\nWe thank the scientific
\ support units at IST Austria for excellent technical support. "
article_processing_charge: Yes (via OA deal)
author:
- first_name: Alexander F
full_name: Leithner, Alexander F
id: 3B1B77E4-F248-11E8-B48F-1D18A9856A87
last_name: Leithner
orcid: 0000-0002-1073-744X
- first_name: Jörg
full_name: Renkawitz, Jörg
id: 3F0587C8-F248-11E8-B48F-1D18A9856A87
last_name: Renkawitz
orcid: 0000-0003-2856-3369
- first_name: Ingrid
full_name: De Vries, Ingrid
id: 4C7D837E-F248-11E8-B48F-1D18A9856A87
last_name: De Vries
- first_name: Robert
full_name: Hauschild, Robert
id: 4E01D6B4-F248-11E8-B48F-1D18A9856A87
last_name: Hauschild
orcid: 0000-0001-9843-3522
- first_name: Hans
full_name: Haecker, Hans
last_name: Haecker
- first_name: Michael K
full_name: Sixt, Michael K
id: 41E9FBEA-F248-11E8-B48F-1D18A9856A87
last_name: Sixt
orcid: 0000-0002-6620-9179
citation:
ama: Leithner AF, Renkawitz J, de Vries I, Hauschild R, Haecker H, Sixt MK. Fast
and efficient genetic engineering of hematopoietic precursor cells for the study
of dendritic cell migration. European Journal of Immunology. 2018;48(6):1074-1077.
doi:10.1002/eji.201747358
apa: Leithner, A. F., Renkawitz, J., de Vries, I., Hauschild, R., Haecker, H., &
Sixt, M. K. (2018). Fast and efficient genetic engineering of hematopoietic precursor
cells for the study of dendritic cell migration. European Journal of Immunology.
Wiley-Blackwell. https://doi.org/10.1002/eji.201747358
chicago: Leithner, Alexander F, Jörg Renkawitz, Ingrid de Vries, Robert Hauschild,
Hans Haecker, and Michael K Sixt. “Fast and Efficient Genetic Engineering of Hematopoietic
Precursor Cells for the Study of Dendritic Cell Migration.” European Journal
of Immunology. Wiley-Blackwell, 2018. https://doi.org/10.1002/eji.201747358.
ieee: A. F. Leithner, J. Renkawitz, I. de Vries, R. Hauschild, H. Haecker, and M.
K. Sixt, “Fast and efficient genetic engineering of hematopoietic precursor cells
for the study of dendritic cell migration,” European Journal of Immunology,
vol. 48, no. 6. Wiley-Blackwell, pp. 1074–1077, 2018.
ista: Leithner AF, Renkawitz J, de Vries I, Hauschild R, Haecker H, Sixt MK. 2018.
Fast and efficient genetic engineering of hematopoietic precursor cells for the
study of dendritic cell migration. European Journal of Immunology. 48(6), 1074–1077.
mla: Leithner, Alexander F., et al. “Fast and Efficient Genetic Engineering of Hematopoietic
Precursor Cells for the Study of Dendritic Cell Migration.” European Journal
of Immunology, vol. 48, no. 6, Wiley-Blackwell, 2018, pp. 1074–77, doi:10.1002/eji.201747358.
short: A.F. Leithner, J. Renkawitz, I. de Vries, R. Hauschild, H. Haecker, M.K.
Sixt, European Journal of Immunology 48 (2018) 1074–1077.
date_created: 2018-12-11T11:46:28Z
date_published: 2018-02-13T00:00:00Z
date_updated: 2023-09-11T14:01:18Z
day: '13'
ddc:
- '570'
department:
- _id: MiSi
- _id: Bio
doi: 10.1002/eji.201747358
ec_funded: 1
external_id:
isi:
- '000434963700016'
file:
- access_level: open_access
checksum: 9d5b74cd016505aeb9a4c2d33bbedaeb
content_type: application/pdf
creator: system
date_created: 2018-12-12T10:13:56Z
date_updated: 2020-07-14T12:46:27Z
file_id: '5044'
file_name: IST-2018-1067-v1+2_Leithner_et_al-2018-European_Journal_of_Immunology.pdf
file_size: 590106
relation: main_file
file_date_updated: 2020-07-14T12:46:27Z
has_accepted_license: '1'
intvolume: ' 48'
isi: 1
issue: '6'
language:
- iso: eng
month: '02'
oa: 1
oa_version: Published Version
page: 1074 - 1077
project:
- _id: 25FE9508-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '724373'
name: Cellular navigation along spatial gradients
publication: European Journal of Immunology
publication_status: published
publisher: Wiley-Blackwell
publist_id: '7386'
pubrep_id: '1067'
quality_controlled: '1'
scopus_import: '1'
status: public
title: Fast and efficient genetic engineering of hematopoietic precursor cells for
the study of dendritic cell migration
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: 48
year: '2018'
...
---
_id: '438'
abstract:
- lang: eng
text: The MazF toxin sequence-specifically cleaves single-stranded RNA upon various
stressful conditions, and it is activated as a part of the mazEF toxin–antitoxin
module in Escherichia coli. Although autoregulation of mazEF expression through
the MazE antitoxin-dependent transcriptional repression has been biochemically
characterized, less is known about post-transcriptional autoregulation, as well
as how both of these autoregulatory features affect growth of single cells during
conditions that promote MazF production. Here, we demonstrate post-transcriptional
autoregulation of mazF expression dynamics by MazF cleaving its own transcript.
Single-cell analyses of bacterial populations during ectopic MazF production indicated
that two-level autoregulation of mazEF expression influences cell-to-cell growth
rate heterogeneity. The increase in growth rate heterogeneity is governed by the
MazE antitoxin, and tuned by the MazF-dependent mazF mRNA cleavage. Also, both
autoregulatory features grant rapid exit from the stress caused by mazF overexpression.
Time-lapse microscopy revealed that MazF-mediated cleavage of mazF mRNA leads
to increased temporal variability in length of individual cells during ectopic
mazF overexpression, as explained by a stochastic model indicating that mazEF
mRNA cleavage underlies temporal fluctuations in MazF levels during stress.
article_processing_charge: Yes (in subscription journal)
author:
- first_name: Nela
full_name: Nikolic, Nela
id: 42D9CABC-F248-11E8-B48F-1D18A9856A87
last_name: Nikolic
orcid: 0000-0001-9068-6090
- first_name: Tobias
full_name: Bergmiller, Tobias
id: 2C471CFA-F248-11E8-B48F-1D18A9856A87
last_name: Bergmiller
orcid: 0000-0001-5396-4346
- first_name: Alexandra
full_name: Vandervelde, Alexandra
last_name: Vandervelde
- first_name: Tanino
full_name: Albanese, Tanino
last_name: Albanese
- first_name: Lendert
full_name: Gelens, Lendert
last_name: Gelens
- first_name: Isabella
full_name: Moll, Isabella
last_name: Moll
citation:
ama: Nikolic N, Bergmiller T, Vandervelde A, Albanese T, Gelens L, Moll I. Autoregulation
of mazEF expression underlies growth heterogeneity in bacterial populations. Nucleic
Acids Research. 2018;46(6):2918-2931. doi:10.1093/nar/gky079
apa: Nikolic, N., Bergmiller, T., Vandervelde, A., Albanese, T., Gelens, L., &
Moll, I. (2018). Autoregulation of mazEF expression underlies growth heterogeneity
in bacterial populations. Nucleic Acids Research. Oxford University Press.
https://doi.org/10.1093/nar/gky079
chicago: Nikolic, Nela, Tobias Bergmiller, Alexandra Vandervelde, Tanino Albanese,
Lendert Gelens, and Isabella Moll. “Autoregulation of MazEF Expression Underlies
Growth Heterogeneity in Bacterial Populations.” Nucleic Acids Research.
Oxford University Press, 2018. https://doi.org/10.1093/nar/gky079.
ieee: N. Nikolic, T. Bergmiller, A. Vandervelde, T. Albanese, L. Gelens, and I.
Moll, “Autoregulation of mazEF expression underlies growth heterogeneity in bacterial
populations,” Nucleic Acids Research, vol. 46, no. 6. Oxford University
Press, pp. 2918–2931, 2018.
ista: Nikolic N, Bergmiller T, Vandervelde A, Albanese T, Gelens L, Moll I. 2018.
Autoregulation of mazEF expression underlies growth heterogeneity in bacterial
populations. Nucleic Acids Research. 46(6), 2918–2931.
mla: Nikolic, Nela, et al. “Autoregulation of MazEF Expression Underlies Growth
Heterogeneity in Bacterial Populations.” Nucleic Acids Research, vol. 46,
no. 6, Oxford University Press, 2018, pp. 2918–31, doi:10.1093/nar/gky079.
short: N. Nikolic, T. Bergmiller, A. Vandervelde, T. Albanese, L. Gelens, I. Moll,
Nucleic Acids Research 46 (2018) 2918–2931.
date_created: 2018-12-11T11:46:29Z
date_published: 2018-04-06T00:00:00Z
date_updated: 2024-02-21T13:44:45Z
day: '06'
ddc:
- '576'
department:
- _id: CaGu
doi: 10.1093/nar/gky079
external_id:
isi:
- '000429009500021'
file:
- access_level: open_access
checksum: 3ff4f545c27e11a4cd20ccb30778793e
content_type: application/pdf
creator: system
date_created: 2018-12-12T10:15:30Z
date_updated: 2020-07-14T12:46:27Z
file_id: '5151'
file_name: IST-2018-971-v1+1_2018_Nikoloc_Autoregulation_of.pdf
file_size: 5027978
relation: main_file
file_date_updated: 2020-07-14T12:46:27Z
has_accepted_license: '1'
intvolume: ' 46'
isi: 1
issue: '6'
language:
- iso: eng
month: '04'
oa: 1
oa_version: Published Version
page: 2918-2931
project:
- _id: 3AC91DDA-15DF-11EA-824D-93A3E7B544D1
call_identifier: FWF
name: FWF Open Access Fund
publication: Nucleic Acids Research
publication_status: published
publisher: Oxford University Press
pubrep_id: '971'
quality_controlled: '1'
related_material:
record:
- id: '5569'
relation: popular_science
status: public
scopus_import: '1'
status: public
title: Autoregulation of mazEF expression underlies growth heterogeneity in bacterial
populations
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: journal_article
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
volume: 46
year: '2018'
...