---
_id: '7010'
abstract:
- lang: eng
text: Numerous biophysical questions require the quantification of short-range interactions
between (functionalized) surfaces and synthetic or biological objects such as
cells. Here, we present an original, custom built setup for reflection interference
contrast microscopy that can assess distances between a substrate and a flowing
object at high speed with nanometric accuracy. We demonstrate its use to decipher
the complex biochemical and mechanical interplay regulating blood cell homing
at the vessel wall in the microcirculation using an in vitro approach. We show
that in the absence of specific biochemical interactions, flowing cells are repelled
from the soft layer lining the vessel wall, contributing to red blood cell repulsion
in vivo. In contrast, this so-called glycocalyx stabilizes rolling of cells under
flow in the presence of a specific receptor naturally present on activated leucocytes
and a number of cancer cell lines.
article_number: 110760V
article_processing_charge: No
author:
- first_name: Heather S.
full_name: Davies, Heather S.
last_name: Davies
- first_name: Natalia S.
full_name: Baranova, Natalia S.
id: 38661662-F248-11E8-B48F-1D18A9856A87
last_name: Baranova
orcid: 0000-0002-3086-9124
- first_name: Nouha
full_name: El Amri, Nouha
last_name: El Amri
- first_name: Liliane
full_name: Coche-Guérente, Liliane
last_name: Coche-Guérente
- first_name: Claude
full_name: Verdier, Claude
last_name: Verdier
- first_name: Lionel
full_name: Bureau, Lionel
last_name: Bureau
- first_name: Ralf P.
full_name: Richter, Ralf P.
last_name: Richter
- first_name: Delphine
full_name: Débarre, Delphine
last_name: Débarre
citation:
ama: 'Davies HS, Baranova NS, El Amri N, et al. Blood cell-vessel wall interactions
probed by reflection interference contrast microscopy. In: Advances in Microscopic
Imaging II. Vol 11076. SPIE; 2019. doi:10.1117/12.2527058'
apa: 'Davies, H. S., Baranova, N. S., El Amri, N., Coche-Guérente, L., Verdier,
C., Bureau, L., … Débarre, D. (2019). Blood cell-vessel wall interactions probed
by reflection interference contrast microscopy. In Advances in Microscopic
Imaging II (Vol. 11076). Munich, Germany: SPIE. https://doi.org/10.1117/12.2527058'
chicago: Davies, Heather S., Natalia S. Baranova, Nouha El Amri, Liliane Coche-Guérente,
Claude Verdier, Lionel Bureau, Ralf P. Richter, and Delphine Débarre. “Blood Cell-Vessel
Wall Interactions Probed by Reflection Interference Contrast Microscopy.” In Advances
in Microscopic Imaging II, Vol. 11076. SPIE, 2019. https://doi.org/10.1117/12.2527058.
ieee: H. S. Davies et al., “Blood cell-vessel wall interactions probed by
reflection interference contrast microscopy,” in Advances in Microscopic Imaging
II, Munich, Germany, 2019, vol. 11076.
ista: Davies HS, Baranova NS, El Amri N, Coche-Guérente L, Verdier C, Bureau L,
Richter RP, Débarre D. 2019. Blood cell-vessel wall interactions probed by reflection
interference contrast microscopy. Advances in Microscopic Imaging II. European
Conferences on Biomedical Optics vol. 11076, 110760V.
mla: Davies, Heather S., et al. “Blood Cell-Vessel Wall Interactions Probed by Reflection
Interference Contrast Microscopy.” Advances in Microscopic Imaging II,
vol. 11076, 110760V, SPIE, 2019, doi:10.1117/12.2527058.
short: H.S. Davies, N.S. Baranova, N. El Amri, L. Coche-Guérente, C. Verdier, L.
Bureau, R.P. Richter, D. Débarre, in:, Advances in Microscopic Imaging II, SPIE,
2019.
conference:
end_date: 2019-06-27
location: Munich, Germany
name: European Conferences on Biomedical Optics
start_date: 2019-06-26
date_created: 2019-11-12T15:10:18Z
date_published: 2019-07-22T00:00:00Z
date_updated: 2023-08-29T06:54:38Z
day: '22'
department:
- _id: MaLo
doi: 10.1117/12.2527058
external_id:
isi:
- '000535353000023'
intvolume: ' 11076'
isi: 1
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://hal.archives-ouvertes.fr/hal-02368135/file/110760V.pdf
month: '07'
oa: 1
oa_version: Published Version
publication: Advances in Microscopic Imaging II
publication_identifier:
isbn:
- '9781510628458'
issn:
- 1605-7422
publication_status: published
publisher: SPIE
quality_controlled: '1'
scopus_import: '1'
status: public
title: Blood cell-vessel wall interactions probed by reflection interference contrast
microscopy
type: conference
user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
volume: 11076
year: '2019'
...
---
_id: '6763'
abstract:
- lang: eng
text: "When grape-sized aqueous dimers are irradiated in a microwave oven, an intense
electromagnetic hotspot forms at their point of contact, often igniting a plasma.
Here we show that this irradiation can result in the injection of mechanical energy.
By examining irradiated hydrogel dimers through high-speed imaging, we find that
they repeatedly bounce off of each other while irradiated. We determine that an
average of 1 lJ of mechanical energy is injected into the pair during each collision.
Furthermore, a characteristic high-pitched audio signal is found to accompany
each collision.\r\nWe show that both the audio signal and the energy injection
arise via an interplay between vaporization and elastic deformations in the region
of contact, the so-called ‘elastic Liedenfrost effect’. Our results establish
a novel, non-contact method of injecting mechanical energy into soft matter systems,
suggesting application in fields such as soft robotics."
article_processing_charge: No
article_type: original
author:
- first_name: Hamza K.
full_name: Khattak, Hamza K.
last_name: Khattak
- first_name: Scott R
full_name: Waitukaitis, Scott R
id: 3A1FFC16-F248-11E8-B48F-1D18A9856A87
last_name: Waitukaitis
orcid: 0000-0002-2299-3176
- first_name: Aaron D.
full_name: Slepkov, Aaron D.
last_name: Slepkov
citation:
ama: Khattak HK, Waitukaitis SR, Slepkov AD. Microwave induced mechanical activation
of hydrogel dimers. Soft Matter. 2019;15(29):5804-5809. doi:10.1039/c9sm00756c
apa: Khattak, H. K., Waitukaitis, S. R., & Slepkov, A. D. (2019). Microwave
induced mechanical activation of hydrogel dimers. Soft Matter. Royal Society
of Chemistry. https://doi.org/10.1039/c9sm00756c
chicago: Khattak, Hamza K., Scott R Waitukaitis, and Aaron D. Slepkov. “Microwave
Induced Mechanical Activation of Hydrogel Dimers.” Soft Matter. Royal Society
of Chemistry, 2019. https://doi.org/10.1039/c9sm00756c.
ieee: H. K. Khattak, S. R. Waitukaitis, and A. D. Slepkov, “Microwave induced mechanical
activation of hydrogel dimers,” Soft Matter, vol. 15, no. 29. Royal Society
of Chemistry, pp. 5804–5809, 2019.
ista: Khattak HK, Waitukaitis SR, Slepkov AD. 2019. Microwave induced mechanical
activation of hydrogel dimers. Soft Matter. 15(29), 5804–5809.
mla: Khattak, Hamza K., et al. “Microwave Induced Mechanical Activation of Hydrogel
Dimers.” Soft Matter, vol. 15, no. 29, Royal Society of Chemistry, 2019,
pp. 5804–09, doi:10.1039/c9sm00756c.
short: H.K. Khattak, S.R. Waitukaitis, A.D. Slepkov, Soft Matter 15 (2019) 5804–5809.
date_created: 2019-08-04T21:59:21Z
date_published: 2019-07-15T00:00:00Z
date_updated: 2023-08-29T06:53:34Z
day: '15'
department:
- _id: ScWa
doi: 10.1039/c9sm00756c
external_id:
isi:
- '000476909200002'
pmid:
- '31305853'
intvolume: ' 15'
isi: 1
issue: '29'
language:
- iso: eng
month: '07'
oa_version: None
page: 5804-5809
pmid: 1
publication: Soft Matter
publication_identifier:
eissn:
- '17446848'
issn:
- 1744683X
publication_status: published
publisher: Royal Society of Chemistry
quality_controlled: '1'
scopus_import: '1'
status: public
title: Microwave induced mechanical activation of hydrogel dimers
type: journal_article
user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
volume: 15
year: '2019'
...
---
_id: '6784'
abstract:
- lang: eng
text: Mathematical models have been used successfully at diverse scales of biological
organization, ranging from ecology and population dynamics to stochastic reaction
events occurring between individual molecules in single cells. Generally, many
biological processes unfold across multiple scales, with mutations being the best
studied example of how stochasticity at the molecular scale can influence outcomes
at the population scale. In many other contexts, however, an analogous link between
micro- and macro-scale remains elusive, primarily due to the challenges involved
in setting up and analyzing multi-scale models. Here, we employ such a model to
investigate how stochasticity propagates from individual biochemical reaction
events in the bacterial innate immune system to the ecology of bacteria and bacterial
viruses. We show analytically how the dynamics of bacterial populations are shaped
by the activities of immunity-conferring enzymes in single cells and how the ecological
consequences imply optimal bacterial defense strategies against viruses. Our results
suggest that bacterial populations in the presence of viruses can either optimize
their initial growth rate or their population size, with the first strategy favoring
simple immunity featuring a single restriction modification system and the second
strategy favoring complex bacterial innate immunity featuring several simultaneously
active restriction modification systems.
article_number: e1007168
article_processing_charge: No
article_type: original
author:
- first_name: Jakob
full_name: Ruess, Jakob
id: 4A245D00-F248-11E8-B48F-1D18A9856A87
last_name: Ruess
orcid: 0000-0003-1615-3282
- first_name: Maros
full_name: Pleska, Maros
id: 4569785E-F248-11E8-B48F-1D18A9856A87
last_name: Pleska
orcid: 0000-0001-7460-7479
- first_name: Calin C
full_name: Guet, Calin C
id: 47F8433E-F248-11E8-B48F-1D18A9856A87
last_name: Guet
orcid: 0000-0001-6220-2052
- first_name: Gašper
full_name: Tkačik, Gašper
id: 3D494DCA-F248-11E8-B48F-1D18A9856A87
last_name: Tkačik
orcid: 0000-0002-6699-1455
citation:
ama: Ruess J, Pleska M, Guet CC, Tkačik G. Molecular noise of innate immunity shapes
bacteria-phage ecologies. PLoS Computational Biology. 2019;15(7). doi:10.1371/journal.pcbi.1007168
apa: Ruess, J., Pleska, M., Guet, C. C., & Tkačik, G. (2019). Molecular noise
of innate immunity shapes bacteria-phage ecologies. PLoS Computational Biology.
Public Library of Science. https://doi.org/10.1371/journal.pcbi.1007168
chicago: Ruess, Jakob, Maros Pleska, Calin C Guet, and Gašper Tkačik. “Molecular
Noise of Innate Immunity Shapes Bacteria-Phage Ecologies.” PLoS Computational
Biology. Public Library of Science, 2019. https://doi.org/10.1371/journal.pcbi.1007168.
ieee: J. Ruess, M. Pleska, C. C. Guet, and G. Tkačik, “Molecular noise of innate
immunity shapes bacteria-phage ecologies,” PLoS Computational Biology,
vol. 15, no. 7. Public Library of Science, 2019.
ista: Ruess J, Pleska M, Guet CC, Tkačik G. 2019. Molecular noise of innate immunity
shapes bacteria-phage ecologies. PLoS Computational Biology. 15(7), e1007168.
mla: Ruess, Jakob, et al. “Molecular Noise of Innate Immunity Shapes Bacteria-Phage
Ecologies.” PLoS Computational Biology, vol. 15, no. 7, e1007168, Public
Library of Science, 2019, doi:10.1371/journal.pcbi.1007168.
short: J. Ruess, M. Pleska, C.C. Guet, G. Tkačik, PLoS Computational Biology 15
(2019).
date_created: 2019-08-11T21:59:19Z
date_published: 2019-07-02T00:00:00Z
date_updated: 2023-08-29T07:10:06Z
day: '02'
ddc:
- '570'
department:
- _id: CaGu
- _id: GaTk
doi: 10.1371/journal.pcbi.1007168
external_id:
isi:
- '000481577700032'
file:
- access_level: open_access
checksum: 7ded4721b41c2a0fc66a1c634540416a
content_type: application/pdf
creator: dernst
date_created: 2019-08-12T12:27:26Z
date_updated: 2020-07-14T12:47:40Z
file_id: '6803'
file_name: 2019_PlosComputBiology_Ruess.pdf
file_size: 2200003
relation: main_file
file_date_updated: 2020-07-14T12:47:40Z
has_accepted_license: '1'
intvolume: ' 15'
isi: 1
issue: '7'
language:
- iso: eng
license: https://creativecommons.org/licenses/by/4.0/
month: '07'
oa: 1
oa_version: Published Version
project:
- _id: 251D65D8-B435-11E9-9278-68D0E5697425
grant_number: '24210'
name: Effects of Stochasticity on the Function of Restriction-Modi cation Systems
at the Single-Cell Level
- _id: 251BCBEC-B435-11E9-9278-68D0E5697425
grant_number: RGY0079/2011
name: Multi-Level Conflicts in Evolutionary Dynamics of Restriction-Modification
Systems
publication: PLoS Computational Biology
publication_identifier:
eissn:
- 1553-7358
publication_status: published
publisher: Public Library of Science
quality_controlled: '1'
related_material:
record:
- id: '9786'
relation: research_data
status: public
scopus_import: '1'
status: public
title: Molecular noise of innate immunity shapes bacteria-phage ecologies
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: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
volume: 15
year: '2019'
...
---
_id: '6778'
abstract:
- lang: eng
text: "An important adaptation during colonization of land by plants is gravitropic
growth of roots, which enabled roots to reach water and nutrients, and firmly
anchor plants in the ground. Here we provide insights into the evolution of an
efficient root gravitropic mechanism in the seed plants. Architectural innovation,
with gravity perception constrained in the root tips\r\nalong with a shootward
transport route for the phytohormone auxin, appeared only upon the emergence of
seed plants. Interspecies complementation and protein domain swapping revealed
functional innovations within the PIN family of auxin transporters leading to
the evolution of gravitropism-specific PINs. The unique apical/shootward subcellular
localization of PIN proteins is the major evolutionary innovation that connected
the anatomically separated sites of gravity perception and growth response via
the mobile auxin signal. We conclude that the crucial anatomical and functional
components emerged hand-in-hand to facilitate the evolution of fast gravitropic
response, which is one of the major adaptations of seed plants to dry land."
article_number: '3480'
article_processing_charge: No
article_type: original
author:
- first_name: Yuzhou
full_name: Zhang, Yuzhou
id: 3B6137F2-F248-11E8-B48F-1D18A9856A87
last_name: Zhang
orcid: 0000-0003-2627-6956
- first_name: G
full_name: Xiao, G
last_name: Xiao
- first_name: X
full_name: Wang, X
last_name: Wang
- first_name: Xixi
full_name: Zhang, Xixi
id: 61A66458-47E9-11EA-85BA-8AEAAF14E49A
last_name: Zhang
orcid: 0000-0001-7048-4627
- first_name: Jiří
full_name: Friml, Jiří
id: 4159519E-F248-11E8-B48F-1D18A9856A87
last_name: Friml
orcid: 0000-0002-8302-7596
citation:
ama: Zhang Y, Xiao G, Wang X, Zhang X, Friml J. Evolution of fast root gravitropism
in seed plants. Nature Communications. 2019;10. doi:10.1038/s41467-019-11471-8
apa: Zhang, Y., Xiao, G., Wang, X., Zhang, X., & Friml, J. (2019). Evolution
of fast root gravitropism in seed plants. Nature Communications. Springer
Nature. https://doi.org/10.1038/s41467-019-11471-8
chicago: Zhang, Yuzhou, G Xiao, X Wang, Xixi Zhang, and Jiří Friml. “Evolution of
Fast Root Gravitropism in Seed Plants.” Nature Communications. Springer
Nature, 2019. https://doi.org/10.1038/s41467-019-11471-8.
ieee: Y. Zhang, G. Xiao, X. Wang, X. Zhang, and J. Friml, “Evolution of fast root
gravitropism in seed plants,” Nature Communications, vol. 10. Springer
Nature, 2019.
ista: Zhang Y, Xiao G, Wang X, Zhang X, Friml J. 2019. Evolution of fast root gravitropism
in seed plants. Nature Communications. 10, 3480.
mla: Zhang, Yuzhou, et al. “Evolution of Fast Root Gravitropism in Seed Plants.”
Nature Communications, vol. 10, 3480, Springer Nature, 2019, doi:10.1038/s41467-019-11471-8.
short: Y. Zhang, G. Xiao, X. Wang, X. Zhang, J. Friml, Nature Communications 10
(2019).
date_created: 2019-08-09T08:46:26Z
date_published: 2019-08-02T00:00:00Z
date_updated: 2023-08-29T07:02:44Z
day: '02'
ddc:
- '580'
department:
- _id: JiFr
doi: 10.1038/s41467-019-11471-8
ec_funded: 1
external_id:
isi:
- '000478576500012'
pmid:
- '31375675'
file:
- access_level: open_access
checksum: d2c654fdb97f33078f606fe0c298bf6e
content_type: application/pdf
creator: dernst
date_created: 2019-08-12T07:09:20Z
date_updated: 2020-07-14T12:47:40Z
file_id: '6798'
file_name: 2019_NatureComm_Zhang.pdf
file_size: 6406141
relation: main_file
file_date_updated: 2020-07-14T12:47:40Z
has_accepted_license: '1'
intvolume: ' 10'
isi: 1
language:
- iso: eng
month: '08'
oa: 1
oa_version: Published Version
pmid: 1
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
- _id: 25681D80-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '291734'
name: International IST Postdoc Fellowship Programme
publication: Nature Communications
publication_identifier:
issn:
- 2041-1723
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
related_material:
link:
- description: News on IST Homepage
relation: press_release
url: https://ist.ac.at/en/news/when-plant-roots-learned-to-follow-gravity/
scopus_import: '1'
status: public
title: Evolution of fast root gravitropism in seed plants
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: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
volume: 10
year: '2019'
...
---
_id: '6821'
abstract:
- lang: eng
text: To determine the visual sensitivities of an organism of interest, quantitative
reverse transcription–polymerase chain reaction (qRT–PCR) is often used to quantify
expression of the light‐sensitive opsins in the retina. While qRT–PCR is an affordable,
high‐throughput method for measuring expression, it comes with inherent normalization
issues that affect the interpretation of results, especially as opsin expression
can vary greatly based on developmental stage, light environment or diurnal cycles.
We tested for diurnal cycles of opsin expression over a period of 24 hr at 1‐hr
increments and examined how normalization affects a data set with fluctuating
expression levels using qRT–PCR and transcriptome data from the retinae of the
cichlid Pelmatolapia mariae. We compared five methods of normalizing opsin expression
relative to (a) the average of three stably expressed housekeeping genes (Ube2z,
EF1‐α and β‐actin), (b) total RNA concentration, (c) GNAT2, (the cone‐specific
subunit of transducin), (d) total opsin expression and (e) only opsins expressed
in the same cone type. Normalizing by proportion of cone type produced the least
variation and would be best for removing time‐of‐day variation. In contrast, normalizing
by housekeeping genes produced the highest daily variation in expression and demonstrated
that the peak of cone opsin expression was in the late afternoon. A weighted correlation
network analysis showed that the expression of different cone opsins follows a
very similar daily cycle. With the knowledge of how these normalization methods
affect opsin expression data, we make recommendations for designing sampling approaches
and quantification methods based upon the scientific question being examined.
article_processing_charge: No
article_type: original
author:
- first_name: Miranda R.
full_name: Yourick, Miranda R.
last_name: Yourick
- first_name: Benjamin A.
full_name: Sandkam, Benjamin A.
last_name: Sandkam
- first_name: William J
full_name: Gammerdinger, William J
id: 3A7E01BC-F248-11E8-B48F-1D18A9856A87
last_name: Gammerdinger
orcid: 0000-0001-9638-1220
- first_name: Daniel
full_name: Escobar-Camacho, Daniel
last_name: Escobar-Camacho
- first_name: Sri Pratima
full_name: Nandamuri, Sri Pratima
last_name: Nandamuri
- first_name: Frances E.
full_name: Clark, Frances E.
last_name: Clark
- first_name: Brendan
full_name: Joyce, Brendan
last_name: Joyce
- first_name: Matthew A.
full_name: Conte, Matthew A.
last_name: Conte
- first_name: Thomas D.
full_name: Kocher, Thomas D.
last_name: Kocher
- first_name: Karen L.
full_name: Carleton, Karen L.
last_name: Carleton
citation:
ama: Yourick MR, Sandkam BA, Gammerdinger WJ, et al. Diurnal variation in opsin
expression and common housekeeping genes necessitates comprehensive normalization
methods for quantitative real-time PCR analyses. Molecular Ecology Resources.
2019;19(6):1447-1460. doi:10.1111/1755-0998.13062
apa: Yourick, M. R., Sandkam, B. A., Gammerdinger, W. J., Escobar-Camacho, D., Nandamuri,
S. P., Clark, F. E., … Carleton, K. L. (2019). Diurnal variation in opsin expression
and common housekeeping genes necessitates comprehensive normalization methods
for quantitative real-time PCR analyses. Molecular Ecology Resources. Wiley.
https://doi.org/10.1111/1755-0998.13062
chicago: Yourick, Miranda R., Benjamin A. Sandkam, William J Gammerdinger, Daniel
Escobar-Camacho, Sri Pratima Nandamuri, Frances E. Clark, Brendan Joyce, Matthew
A. Conte, Thomas D. Kocher, and Karen L. Carleton. “Diurnal Variation in Opsin
Expression and Common Housekeeping Genes Necessitates Comprehensive Normalization
Methods for Quantitative Real-Time PCR Analyses.” Molecular Ecology Resources.
Wiley, 2019. https://doi.org/10.1111/1755-0998.13062.
ieee: M. R. Yourick et al., “Diurnal variation in opsin expression and common
housekeeping genes necessitates comprehensive normalization methods for quantitative
real-time PCR analyses,” Molecular Ecology Resources, vol. 19, no. 6. Wiley,
pp. 1447–1460, 2019.
ista: Yourick MR, Sandkam BA, Gammerdinger WJ, Escobar-Camacho D, Nandamuri SP,
Clark FE, Joyce B, Conte MA, Kocher TD, Carleton KL. 2019. Diurnal variation in
opsin expression and common housekeeping genes necessitates comprehensive normalization
methods for quantitative real-time PCR analyses. Molecular Ecology Resources.
19(6), 1447–1460.
mla: Yourick, Miranda R., et al. “Diurnal Variation in Opsin Expression and Common
Housekeeping Genes Necessitates Comprehensive Normalization Methods for Quantitative
Real-Time PCR Analyses.” Molecular Ecology Resources, vol. 19, no. 6, Wiley,
2019, pp. 1447–60, doi:10.1111/1755-0998.13062.
short: M.R. Yourick, B.A. Sandkam, W.J. Gammerdinger, D. Escobar-Camacho, S.P. Nandamuri,
F.E. Clark, B. Joyce, M.A. Conte, T.D. Kocher, K.L. Carleton, Molecular Ecology
Resources 19 (2019) 1447–1460.
date_created: 2019-08-18T22:00:41Z
date_published: 2019-11-01T00:00:00Z
date_updated: 2023-08-29T07:10:44Z
day: '01'
department:
- _id: BeVi
doi: 10.1111/1755-0998.13062
external_id:
isi:
- '000480196800001'
pmid:
- '31325910'
intvolume: ' 19'
isi: 1
issue: '6'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6995727
month: '11'
oa: 1
oa_version: Submitted Version
page: 1447-1460
pmid: 1
publication: Molecular Ecology Resources
publication_identifier:
eissn:
- 1755-0998
publication_status: published
publisher: Wiley
quality_controlled: '1'
scopus_import: '1'
status: public
title: Diurnal variation in opsin expression and common housekeeping genes necessitates
comprehensive normalization methods for quantitative real-time PCR analyses
type: journal_article
user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
volume: 19
year: '2019'
...
---
_id: '6788'
abstract:
- lang: eng
text: We consider the Nelson model with ultraviolet cutoff, which describes the
interaction between non-relativistic particles and a positive or zero mass quantized
scalar field. We take the non-relativistic particles to obey Fermi statistics
and discuss the time evolution in a mean-field limit of many fermions. In this
case, the limit is known to be also a semiclassical limit. We prove convergence
in terms of reduced density matrices of the many-body state to a tensor product
of a Slater determinant with semiclassical structure and a coherent state, which
evolve according to a fermionic version of the Schrödinger–Klein–Gordon equations.
article_processing_charge: Yes (via OA deal)
article_type: original
author:
- first_name: Nikolai K
full_name: Leopold, Nikolai K
id: 4BC40BEC-F248-11E8-B48F-1D18A9856A87
last_name: Leopold
orcid: 0000-0002-0495-6822
- first_name: Sören P
full_name: Petrat, Sören P
id: 40AC02DC-F248-11E8-B48F-1D18A9856A87
last_name: Petrat
orcid: 0000-0002-9166-5889
citation:
ama: Leopold NK, Petrat SP. Mean-field dynamics for the Nelson model with fermions.
Annales Henri Poincare. 2019;20(10):3471–3508. doi:10.1007/s00023-019-00828-w
apa: Leopold, N. K., & Petrat, S. P. (2019). Mean-field dynamics for the Nelson
model with fermions. Annales Henri Poincare. Springer Nature. https://doi.org/10.1007/s00023-019-00828-w
chicago: Leopold, Nikolai K, and Sören P Petrat. “Mean-Field Dynamics for the Nelson
Model with Fermions.” Annales Henri Poincare. Springer Nature, 2019. https://doi.org/10.1007/s00023-019-00828-w.
ieee: N. K. Leopold and S. P. Petrat, “Mean-field dynamics for the Nelson model
with fermions,” Annales Henri Poincare, vol. 20, no. 10. Springer Nature,
pp. 3471–3508, 2019.
ista: Leopold NK, Petrat SP. 2019. Mean-field dynamics for the Nelson model with
fermions. Annales Henri Poincare. 20(10), 3471–3508.
mla: Leopold, Nikolai K., and Sören P. Petrat. “Mean-Field Dynamics for the Nelson
Model with Fermions.” Annales Henri Poincare, vol. 20, no. 10, Springer
Nature, 2019, pp. 3471–3508, doi:10.1007/s00023-019-00828-w.
short: N.K. Leopold, S.P. Petrat, Annales Henri Poincare 20 (2019) 3471–3508.
date_created: 2019-08-11T21:59:21Z
date_published: 2019-10-01T00:00:00Z
date_updated: 2023-08-29T07:09:06Z
day: '01'
ddc:
- '510'
department:
- _id: RoSe
doi: 10.1007/s00023-019-00828-w
ec_funded: 1
external_id:
arxiv:
- '1807.06781'
isi:
- '000487036900008'
file:
- access_level: open_access
checksum: b6dbf0d837d809293d449adf77138904
content_type: application/pdf
creator: dernst
date_created: 2019-08-12T12:05:58Z
date_updated: 2020-07-14T12:47:40Z
file_id: '6801'
file_name: 2019_AnnalesHenriPoincare_Leopold.pdf
file_size: 681139
relation: main_file
file_date_updated: 2020-07-14T12:47:40Z
has_accepted_license: '1'
intvolume: ' 20'
isi: 1
issue: '10'
language:
- iso: eng
month: '10'
oa: 1
oa_version: Published Version
page: 3471–3508
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_identifier:
eissn:
- 1424-0661
issn:
- 1424-0637
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
scopus_import: '1'
status: public
title: Mean-field dynamics for the Nelson model with fermions
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: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
volume: 20
year: '2019'
...
---
_id: '6795'
abstract:
- lang: eng
text: The green‐beard effect is one proposed mechanism predicted to underpin the
evolu‐tion of altruistic behavior. It relies on the recognition and the selective
help of altruists to each other in order to promote and sustain altruistic behavior.
However, this mechanism has often been dismissed as unlikely or uncommon, as it
is assumed that both the signaling trait and altruistic trait need to be encoded
by the same gene or through tightly linked genes. Here, we use models of indirect
genetic effects (IGEs) to find the minimum correlation between the signaling and
altruistic trait required for the evolution of the latter. We show that this correlation
threshold depends on the strength of the interaction (influence of the green beard
on the expression of the altruistic trait), as well as the costs and benefits
of the altruistic behavior. We further show that this correlation does not necessarily
have to be high and support our analytical results by simulations.
article_processing_charge: No
article_type: original
author:
- first_name: Barbora
full_name: Trubenova, Barbora
id: 42302D54-F248-11E8-B48F-1D18A9856A87
last_name: Trubenova
orcid: 0000-0002-6873-2967
- first_name: Reinmar
full_name: Hager, Reinmar
last_name: Hager
citation:
ama: Trubenova B, Hager R. Green beards in the light of indirect genetic effects.
Ecology and Evolution. 2019;9(17):9597-9608. doi:10.1002/ece3.5484
apa: Trubenova, B., & Hager, R. (2019). Green beards in the light of indirect
genetic effects. Ecology and Evolution. Wiley. https://doi.org/10.1002/ece3.5484
chicago: Trubenova, Barbora, and Reinmar Hager. “Green Beards in the Light of Indirect
Genetic Effects.” Ecology and Evolution. Wiley, 2019. https://doi.org/10.1002/ece3.5484.
ieee: B. Trubenova and R. Hager, “Green beards in the light of indirect genetic
effects,” Ecology and Evolution, vol. 9, no. 17. Wiley, pp. 9597–9608,
2019.
ista: Trubenova B, Hager R. 2019. Green beards in the light of indirect genetic
effects. Ecology and Evolution. 9(17), 9597–9608.
mla: Trubenova, Barbora, and Reinmar Hager. “Green Beards in the Light of Indirect
Genetic Effects.” Ecology and Evolution, vol. 9, no. 17, Wiley, 2019, pp.
9597–608, doi:10.1002/ece3.5484.
short: B. Trubenova, R. Hager, Ecology and Evolution 9 (2019) 9597–9608.
date_created: 2019-08-11T21:59:24Z
date_published: 2019-09-01T00:00:00Z
date_updated: 2023-08-29T07:03:10Z
day: '01'
ddc:
- '576'
department:
- _id: NiBa
doi: 10.1002/ece3.5484
ec_funded: 1
external_id:
isi:
- '000479973400001'
file:
- access_level: open_access
checksum: adcb70af4901977d95b8747eeee01bd7
content_type: application/pdf
creator: dernst
date_created: 2019-08-12T07:30:30Z
date_updated: 2020-07-14T12:47:40Z
file_id: '6799'
file_name: 2019_EcologyEvolution_Trubenova.pdf
file_size: 2839636
relation: main_file
file_date_updated: 2020-07-14T12:47:40Z
has_accepted_license: '1'
intvolume: ' 9'
isi: 1
issue: '17'
language:
- iso: eng
month: '09'
oa: 1
oa_version: Published Version
page: 9597-9608
project:
- _id: 25AEDD42-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '704172'
name: Rate of Adaptation in Changing Environment
publication: Ecology and Evolution
publication_identifier:
eissn:
- '20457758'
publication_status: published
publisher: Wiley
quality_controlled: '1'
scopus_import: '1'
status: public
title: Green beards in the light of indirect genetic effects
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: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
volume: 9
year: '2019'
...
---
_id: '6793'
abstract:
- lang: eng
text: The Regge symmetry is a set of remarkable relations between two tetrahedra
whose edge lengths are related in a simple fashion. It was first discovered as
a consequence of an asymptotic formula in mathematical physics. Here, we give
a simple geometric proof of Regge symmetries in Euclidean, spherical, and hyperbolic
geometry.
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
- first_name: Ivan
full_name: Izmestiev, Ivan
last_name: Izmestiev
citation:
ama: Akopyan A, Izmestiev I. The Regge symmetry, confocal conics, and the Schläfli
formula. Bulletin of the London Mathematical Society. 2019;51(5):765-775.
doi:10.1112/blms.12276
apa: Akopyan, A., & Izmestiev, I. (2019). The Regge symmetry, confocal conics,
and the Schläfli formula. Bulletin of the London Mathematical Society.
London Mathematical Society. https://doi.org/10.1112/blms.12276
chicago: Akopyan, Arseniy, and Ivan Izmestiev. “The Regge Symmetry, Confocal Conics,
and the Schläfli Formula.” Bulletin of the London Mathematical Society.
London Mathematical Society, 2019. https://doi.org/10.1112/blms.12276.
ieee: A. Akopyan and I. Izmestiev, “The Regge symmetry, confocal conics, and the
Schläfli formula,” Bulletin of the London Mathematical Society, vol. 51,
no. 5. London Mathematical Society, pp. 765–775, 2019.
ista: Akopyan A, Izmestiev I. 2019. The Regge symmetry, confocal conics, and the
Schläfli formula. Bulletin of the London Mathematical Society. 51(5), 765–775.
mla: Akopyan, Arseniy, and Ivan Izmestiev. “The Regge Symmetry, Confocal Conics,
and the Schläfli Formula.” Bulletin of the London Mathematical Society,
vol. 51, no. 5, London Mathematical Society, 2019, pp. 765–75, doi:10.1112/blms.12276.
short: A. Akopyan, I. Izmestiev, Bulletin of the London Mathematical Society 51
(2019) 765–775.
date_created: 2019-08-11T21:59:23Z
date_published: 2019-10-01T00:00:00Z
date_updated: 2023-08-29T07:08:34Z
day: '01'
department:
- _id: HeEd
doi: 10.1112/blms.12276
ec_funded: 1
external_id:
arxiv:
- '1903.04929'
isi:
- '000478560200001'
intvolume: ' 51'
isi: 1
issue: '5'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/1903.04929
month: '10'
oa: 1
oa_version: Preprint
page: 765-775
project:
- _id: 266A2E9E-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '788183'
name: Alpha Shape Theory Extended
publication: Bulletin of the London Mathematical Society
publication_identifier:
eissn:
- '14692120'
issn:
- '00246093'
publication_status: published
publisher: London Mathematical Society
quality_controlled: '1'
scopus_import: '1'
status: public
title: The Regge symmetry, confocal conics, and the Schläfli formula
type: journal_article
user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
volume: 51
year: '2019'
...
---
_id: '9786'
article_processing_charge: No
author:
- first_name: Jakob
full_name: Ruess, Jakob
id: 4A245D00-F248-11E8-B48F-1D18A9856A87
last_name: Ruess
orcid: 0000-0003-1615-3282
- first_name: Maros
full_name: Pleska, Maros
id: 4569785E-F248-11E8-B48F-1D18A9856A87
last_name: Pleska
orcid: 0000-0001-7460-7479
- first_name: Calin C
full_name: Guet, Calin C
id: 47F8433E-F248-11E8-B48F-1D18A9856A87
last_name: Guet
orcid: 0000-0001-6220-2052
- first_name: Gašper
full_name: Tkačik, Gašper
id: 3D494DCA-F248-11E8-B48F-1D18A9856A87
last_name: Tkačik
orcid: 0000-0002-6699-1455
citation:
ama: Ruess J, Pleska M, Guet CC, Tkačik G. Supporting text and results. 2019. doi:10.1371/journal.pcbi.1007168.s001
apa: Ruess, J., Pleska, M., Guet, C. C., & Tkačik, G. (2019). Supporting text
and results. Public Library of Science. https://doi.org/10.1371/journal.pcbi.1007168.s001
chicago: Ruess, Jakob, Maros Pleska, Calin C Guet, and Gašper Tkačik. “Supporting
Text and Results.” Public Library of Science, 2019. https://doi.org/10.1371/journal.pcbi.1007168.s001.
ieee: J. Ruess, M. Pleska, C. C. Guet, and G. Tkačik, “Supporting text and results.”
Public Library of Science, 2019.
ista: Ruess J, Pleska M, Guet CC, Tkačik G. 2019. Supporting text and results, Public
Library of Science, 10.1371/journal.pcbi.1007168.s001.
mla: Ruess, Jakob, et al. Supporting Text and Results. Public Library of
Science, 2019, doi:10.1371/journal.pcbi.1007168.s001.
short: J. Ruess, M. Pleska, C.C. Guet, G. Tkačik, (2019).
date_created: 2021-08-06T08:23:43Z
date_published: 2019-07-02T00:00:00Z
date_updated: 2023-08-29T07:10:05Z
day: '02'
department:
- _id: CaGu
- _id: GaTk
doi: 10.1371/journal.pcbi.1007168.s001
month: '07'
oa_version: Published Version
publisher: Public Library of Science
related_material:
record:
- id: '6784'
relation: used_in_publication
status: public
status: public
title: Supporting text and results
type: research_data_reference
user_id: 6785fbc1-c503-11eb-8a32-93094b40e1cf
year: '2019'
...
---
_id: '6831'
abstract:
- lang: eng
text: "* Understanding the mechanisms causing phenotypic differences between females
and males has long fascinated evolutionary biologists. An extensive literature
exists on animal sexual dimorphism but less information is known about sex differences
in plants, particularly the extent of geographical variation in sexual dimorphism
and its life‐cycle dynamics.\r\n* Here, we investigated patterns of genetically
based sexual dimorphism in vegetative and reproductive traits of a wind‐pollinated
dioecious plant, Rumex hastatulus, across three life‐cycle stages using open‐pollinated
families from 30 populations spanning the geographic range and chromosomal variation
(XY and XY1Y2) of the species.\r\n* The direction and degree of sexual dimorphism
was highly variable among populations and life‐cycle stages. Sex‐specific differences
in reproductive function explained a significant amount of temporal change in
sexual dimorphism. For several traits, geographical variation in sexual dimorphism
was associated with bioclimatic parameters, likely due to the differential responses
of the sexes to climate. We found no systematic differences in sexual dimorphism
between chromosome races.\r\n* Sex‐specific trait differences in dioecious plants
largely result from a balance between sexual and natural selection on resource
allocation. Our results indicate that abiotic factors associated with geographical
context also play a role in modifying sexual dimorphism during the plant life‐cycle."
article_processing_charge: Yes (via OA deal)
article_type: original
author:
- first_name: Gemma
full_name: Puixeu Sala, Gemma
id: 33AB266C-F248-11E8-B48F-1D18A9856A87
last_name: Puixeu Sala
orcid: 0000-0001-8330-1754
- first_name: Melinda
full_name: Pickup, Melinda
id: 2C78037E-F248-11E8-B48F-1D18A9856A87
last_name: Pickup
orcid: 0000-0001-6118-0541
- first_name: David
full_name: Field, David
last_name: Field
orcid: 0000-0002-4014-8478
- first_name: Spencer C.H.
full_name: Barrett, Spencer C.H.
last_name: Barrett
citation:
ama: 'Puixeu Sala G, Pickup M, Field D, Barrett SCH. Variation in sexual dimorphism
in a wind-pollinated plant: The influence of geographical context and life-cycle
dynamics. New Phytologist. 2019;224(3):1108-1120. doi:10.1111/nph.16050'
apa: 'Puixeu Sala, G., Pickup, M., Field, D., & Barrett, S. C. H. (2019). Variation
in sexual dimorphism in a wind-pollinated plant: The influence of geographical
context and life-cycle dynamics. New Phytologist. Wiley. https://doi.org/10.1111/nph.16050'
chicago: 'Puixeu Sala, Gemma, Melinda Pickup, David Field, and Spencer C.H. Barrett.
“Variation in Sexual Dimorphism in a Wind-Pollinated Plant: The Influence of Geographical
Context and Life-Cycle Dynamics.” New Phytologist. Wiley, 2019. https://doi.org/10.1111/nph.16050.'
ieee: 'G. Puixeu Sala, M. Pickup, D. Field, and S. C. H. Barrett, “Variation in
sexual dimorphism in a wind-pollinated plant: The influence of geographical context
and life-cycle dynamics,” New Phytologist, vol. 224, no. 3. Wiley, pp.
1108–1120, 2019.'
ista: 'Puixeu Sala G, Pickup M, Field D, Barrett SCH. 2019. Variation in sexual
dimorphism in a wind-pollinated plant: The influence of geographical context and
life-cycle dynamics. New Phytologist. 224(3), 1108–1120.'
mla: 'Puixeu Sala, Gemma, et al. “Variation in Sexual Dimorphism in a Wind-Pollinated
Plant: The Influence of Geographical Context and Life-Cycle Dynamics.” New
Phytologist, vol. 224, no. 3, Wiley, 2019, pp. 1108–20, doi:10.1111/nph.16050.'
short: G. Puixeu Sala, M. Pickup, D. Field, S.C.H. Barrett, New Phytologist 224
(2019) 1108–1120.
date_created: 2019-08-25T22:00:51Z
date_published: 2019-11-01T00:00:00Z
date_updated: 2023-08-29T07:17:07Z
day: '01'
ddc:
- '570'
department:
- _id: NiBa
- _id: BeVi
doi: 10.1111/nph.16050
ec_funded: 1
external_id:
isi:
- '000481376500001'
file:
- access_level: open_access
checksum: 6370e7567d96b7b562e77d8b89653f80
content_type: application/pdf
creator: apreinsp
date_created: 2019-08-27T12:44:54Z
date_updated: 2020-07-14T12:47:42Z
file_id: '6833'
file_name: 2019_NewPhytologist_Puixeu.pdf
file_size: 2314016
relation: main_file
file_date_updated: 2020-07-14T12:47:42Z
has_accepted_license: '1'
intvolume: ' 224'
isi: 1
issue: '3'
language:
- iso: eng
month: '11'
oa: 1
oa_version: Published Version
page: 1108-1120
project:
- _id: 2564DBCA-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '665385'
name: International IST Doctoral Program
publication: New Phytologist
publication_identifier:
eissn:
- 1469-8137
publication_status: published
publisher: Wiley
quality_controlled: '1'
related_material:
record:
- id: '9803'
relation: research_data
status: public
- id: '14058'
relation: dissertation_contains
status: public
scopus_import: '1'
status: public
title: 'Variation in sexual dimorphism in a wind-pollinated plant: The influence of
geographical context and life-cycle dynamics'
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: journal_article
user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
volume: 224
year: '2019'
...