---
_id: '6049'
abstract:
- lang: eng
text: 'In this article it is shown that large systems with many interacting units
endowing multiple phases display self-oscillations in the presence of linear feedback
between the control and order parameters, where an Andronov–Hopf bifurcation takes
over the phase transition. This is simply illustrated through the mean field Landau
theory whose feedback dynamics turn out to be described by the Van der Pol equation
and it is then validated for the fully connected Ising model following heat bath
dynamics. Despite its simplicity, this theory accounts potentially for a rich
range of phenomena: here it is applied to describe in a stylized way (i) excess
demand-price cycles due to strong herding in a simple agent-based market model;
(ii) congestion waves in queuing networks triggered by user feedback to delays
in overloaded conditions; and (iii) metabolic network oscillations resulting from
cell growth control in a bistable phenotypic landscape.'
article_number: '045002'
article_processing_charge: Yes (in subscription journal)
author:
- first_name: Daniele
full_name: De Martino, Daniele
id: 3FF5848A-F248-11E8-B48F-1D18A9856A87
last_name: De Martino
orcid: 0000-0002-5214-4706
citation:
ama: 'De Martino D. Feedback-induced self-oscillations in large interacting systems
subjected to phase transitions. Journal of Physics A: Mathematical and Theoretical.
2019;52(4). doi:10.1088/1751-8121/aaf2dd'
apa: 'De Martino, D. (2019). Feedback-induced self-oscillations in large interacting
systems subjected to phase transitions. Journal of Physics A: Mathematical
and Theoretical. IOP Publishing. https://doi.org/10.1088/1751-8121/aaf2dd'
chicago: 'De Martino, Daniele. “Feedback-Induced Self-Oscillations in Large Interacting
Systems Subjected to Phase Transitions.” Journal of Physics A: Mathematical
and Theoretical. IOP Publishing, 2019. https://doi.org/10.1088/1751-8121/aaf2dd.'
ieee: 'D. De Martino, “Feedback-induced self-oscillations in large interacting systems
subjected to phase transitions,” Journal of Physics A: Mathematical and Theoretical,
vol. 52, no. 4. IOP Publishing, 2019.'
ista: 'De Martino D. 2019. Feedback-induced self-oscillations in large interacting
systems subjected to phase transitions. Journal of Physics A: Mathematical and
Theoretical. 52(4), 045002.'
mla: 'De Martino, Daniele. “Feedback-Induced Self-Oscillations in Large Interacting
Systems Subjected to Phase Transitions.” Journal of Physics A: Mathematical
and Theoretical, vol. 52, no. 4, 045002, IOP Publishing, 2019, doi:10.1088/1751-8121/aaf2dd.'
short: 'D. De Martino, Journal of Physics A: Mathematical and Theoretical 52 (2019).'
date_created: 2019-02-24T22:59:19Z
date_published: 2019-01-07T00:00:00Z
date_updated: 2023-08-24T14:49:23Z
day: '07'
ddc:
- '570'
department:
- _id: GaTk
doi: 10.1088/1751-8121/aaf2dd
ec_funded: 1
external_id:
isi:
- '000455379500001'
file:
- access_level: open_access
checksum: 1112304ad363a6d8afaeccece36473cf
content_type: application/pdf
creator: kschuh
date_created: 2019-04-19T12:18:57Z
date_updated: 2020-07-14T12:47:17Z
file_id: '6344'
file_name: 2019_IOP_DeMartino.pdf
file_size: 1804557
relation: main_file
file_date_updated: 2020-07-14T12:47:17Z
has_accepted_license: '1'
intvolume: ' 52'
isi: 1
issue: '4'
language:
- iso: eng
month: '01'
oa: 1
oa_version: Published Version
project:
- _id: 25681D80-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '291734'
name: International IST Postdoc Fellowship Programme
publication: 'Journal of Physics A: Mathematical and Theoretical'
publication_status: published
publisher: IOP Publishing
quality_controlled: '1'
scopus_import: '1'
status: public
title: Feedback-induced self-oscillations in large interacting systems subjected to
phase transitions
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: 52
year: '2019'
...
---
_id: '6091'
abstract:
- lang: eng
text: Cortical networks are characterized by sparse connectivity, with synapses
found at only a subset of axo-dendritic contacts. Yet within these networks, neurons
can exhibit high connection probabilities, suggesting that cell-intrinsic factors,
not proximity, determine connectivity. Here, we identify ephrin-B3 (eB3) as a
factor that determines synapse density by mediating a cell-cell competition that
requires ephrin-B-EphB signaling. In a microisland culture system designed to
isolate cell-cell competition, we find that eB3 determines winning and losing
neurons in a contest for synapses. In a Mosaic Analysis with Double Markers (MADM)
genetic mouse model system in vivo the relative levels of eB3 control spine density
in layer 5 and 6 neurons. MADM cortical neurons in vitro reveal that eB3 controls
synapse density independently of action potential-driven activity. Our findings
illustrate a new class of competitive mechanism mediated by trans-synaptic organizing
proteins which control the number of synapses neurons receive relative to neighboring
neurons.
article_number: e41563
article_processing_charge: No
author:
- first_name: Nathan T.
full_name: Henderson, Nathan T.
last_name: Henderson
- first_name: Sylvain J.
full_name: Le Marchand, Sylvain J.
last_name: Le Marchand
- first_name: Martin
full_name: Hruska, Martin
last_name: Hruska
- first_name: Simon
full_name: Hippenmeyer, Simon
id: 37B36620-F248-11E8-B48F-1D18A9856A87
last_name: Hippenmeyer
orcid: 0000-0003-2279-1061
- first_name: Liqun
full_name: Luo, Liqun
last_name: Luo
- first_name: Matthew B.
full_name: Dalva, Matthew B.
last_name: Dalva
citation:
ama: Henderson NT, Le Marchand SJ, Hruska M, Hippenmeyer S, Luo L, Dalva MB. Ephrin-B3
controls excitatory synapse density through cell-cell competition for EphBs. eLife.
2019;8. doi:10.7554/eLife.41563
apa: Henderson, N. T., Le Marchand, S. J., Hruska, M., Hippenmeyer, S., Luo, L.,
& Dalva, M. B. (2019). Ephrin-B3 controls excitatory synapse density through
cell-cell competition for EphBs. ELife. eLife Sciences Publications. https://doi.org/10.7554/eLife.41563
chicago: Henderson, Nathan T., Sylvain J. Le Marchand, Martin Hruska, Simon Hippenmeyer,
Liqun Luo, and Matthew B. Dalva. “Ephrin-B3 Controls Excitatory Synapse Density
through Cell-Cell Competition for EphBs.” ELife. eLife Sciences Publications,
2019. https://doi.org/10.7554/eLife.41563.
ieee: N. T. Henderson, S. J. Le Marchand, M. Hruska, S. Hippenmeyer, L. Luo, and
M. B. Dalva, “Ephrin-B3 controls excitatory synapse density through cell-cell
competition for EphBs,” eLife, vol. 8. eLife Sciences Publications, 2019.
ista: Henderson NT, Le Marchand SJ, Hruska M, Hippenmeyer S, Luo L, Dalva MB. 2019.
Ephrin-B3 controls excitatory synapse density through cell-cell competition for
EphBs. eLife. 8, e41563.
mla: Henderson, Nathan T., et al. “Ephrin-B3 Controls Excitatory Synapse Density
through Cell-Cell Competition for EphBs.” ELife, vol. 8, e41563, eLife
Sciences Publications, 2019, doi:10.7554/eLife.41563.
short: N.T. Henderson, S.J. Le Marchand, M. Hruska, S. Hippenmeyer, L. Luo, M.B.
Dalva, ELife 8 (2019).
date_created: 2019-03-10T22:59:20Z
date_published: 2019-02-21T00:00:00Z
date_updated: 2023-08-24T14:50:50Z
day: '21'
ddc:
- '570'
department:
- _id: SiHi
doi: 10.7554/eLife.41563
external_id:
isi:
- '000459380600001'
pmid:
- '30789343'
file:
- access_level: open_access
checksum: 7b0800d003f14cd06b1802dea0c52941
content_type: application/pdf
creator: dernst
date_created: 2019-03-11T16:15:37Z
date_updated: 2020-07-14T12:47:19Z
file_id: '6098'
file_name: 2019_eLife_Henderson.pdf
file_size: 7260753
relation: main_file
file_date_updated: 2020-07-14T12:47:19Z
has_accepted_license: '1'
intvolume: ' 8'
isi: 1
language:
- iso: eng
month: '02'
oa: 1
oa_version: Published Version
pmid: 1
publication: eLife
publication_status: published
publisher: eLife Sciences Publications
quality_controlled: '1'
scopus_import: '1'
status: public
title: Ephrin-B3 controls excitatory synapse density through cell-cell competition
for EphBs
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: 8
year: '2019'
...
---
_id: '6046'
abstract:
- lang: eng
text: Sudden stress often triggers diverse, temporally structured gene expression
responses in microbes, but it is largely unknown how variable in time such responses
are and if genes respond in the same temporal order in every single cell. Here,
we quantified timing variability of individual promoters responding to sublethal
antibiotic stress using fluorescent reporters, microfluidics, and time‐lapse microscopy.
We identified lower and upper bounds that put definite constraints on timing variability,
which varies strongly among promoters and conditions. Timing variability can be
interpreted using results from statistical kinetics, which enable us to estimate
the number of rate‐limiting molecular steps underlying different responses. We
found that just a few critical steps control some responses while others rely
on dozens of steps. To probe connections between different stress responses, we
then tracked the temporal order and response time correlations of promoter pairs
in individual cells. Our results support that, when bacteria are exposed to the
antibiotic nitrofurantoin, the ensuing oxidative stress and SOS responses are
part of the same causal chain of molecular events. In contrast, under trimethoprim,
the acid stress response and the SOS response are part of different chains of
events running in parallel. Our approach reveals fundamental constraints on gene
expression timing and provides new insights into the molecular events that underlie
the timing of stress responses.
acknowledged_ssus:
- _id: Bio
article_number: e8470
article_processing_charge: No
author:
- first_name: Karin
full_name: Mitosch, Karin
id: 39B66846-F248-11E8-B48F-1D18A9856A87
last_name: Mitosch
- first_name: Georg
full_name: Rieckh, Georg
id: 34DA8BD6-F248-11E8-B48F-1D18A9856A87
last_name: Rieckh
- first_name: Mark Tobias
full_name: Bollenbach, Mark Tobias
id: 3E6DB97A-F248-11E8-B48F-1D18A9856A87
last_name: Bollenbach
orcid: 0000-0003-4398-476X
citation:
ama: Mitosch K, Rieckh G, Bollenbach MT. Temporal order and precision of complex
stress responses in individual bacteria. Molecular systems biology. 2019;15(2).
doi:10.15252/msb.20188470
apa: Mitosch, K., Rieckh, G., & Bollenbach, M. T. (2019). Temporal order and
precision of complex stress responses in individual bacteria. Molecular Systems
Biology. Embo Press. https://doi.org/10.15252/msb.20188470
chicago: Mitosch, Karin, Georg Rieckh, and Mark Tobias Bollenbach. “Temporal Order
and Precision of Complex Stress Responses in Individual Bacteria.” Molecular
Systems Biology. Embo Press, 2019. https://doi.org/10.15252/msb.20188470.
ieee: K. Mitosch, G. Rieckh, and M. T. Bollenbach, “Temporal order and precision
of complex stress responses in individual bacteria,” Molecular systems biology,
vol. 15, no. 2. Embo Press, 2019.
ista: Mitosch K, Rieckh G, Bollenbach MT. 2019. Temporal order and precision of
complex stress responses in individual bacteria. Molecular systems biology. 15(2),
e8470.
mla: Mitosch, Karin, et al. “Temporal Order and Precision of Complex Stress Responses
in Individual Bacteria.” Molecular Systems Biology, vol. 15, no. 2, e8470,
Embo Press, 2019, doi:10.15252/msb.20188470.
short: K. Mitosch, G. Rieckh, M.T. Bollenbach, Molecular Systems Biology 15 (2019).
date_created: 2019-02-24T22:59:18Z
date_published: 2019-02-14T00:00:00Z
date_updated: 2023-08-24T14:49:53Z
day: '14'
department:
- _id: GaTk
doi: 10.15252/msb.20188470
external_id:
isi:
- '000459628300003'
pmid:
- '30765425'
intvolume: ' 15'
isi: 1
issue: '2'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://www.ncbi.nlm.nih.gov/pubmed/30765425
month: '02'
oa: 1
oa_version: Submitted Version
pmid: 1
project:
- _id: 25E9AF9E-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: P27201-B22
name: Revealing the mechanisms underlying drug interactions
- _id: 25EB3A80-B435-11E9-9278-68D0E5697425
grant_number: RGP0042/2013
name: Revealing the fundamental limits of cell growth
publication: Molecular systems biology
publication_status: published
publisher: Embo Press
quality_controlled: '1'
scopus_import: '1'
status: public
title: Temporal order and precision of complex stress responses in individual bacteria
type: journal_article
user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
volume: 15
year: '2019'
...
---
_id: '6105'
abstract:
- lang: eng
text: " Hosts can alter their strategy towards pathogens during their lifetime;
that is, they can show phenotypic plasticity in immunity or life history. Immune
priming is one such example, where a previous encounter with a pathogen confers
enhanced protection upon secondary challenge, resulting in reduced pathogen load
(i.e., resistance) and improved host survival. However, an initial encounter might
also enhance tolerance, particularly to less virulent opportunistic pathogens
that establish persistent infections. In this scenario, individuals are better
able to reduce the negative fecundity consequences that result from a high pathogen
burden. Finally, previous exposure may also lead to life‐history adjustments,
such as terminal investment into reproduction.\r\n Using different Drosophila
melanogaster host genotypes and two bacterial pathogens, Lactococcus lactis and
Pseudomonas entomophila, we tested whether previous exposure results in resistance
or tolerance and whether it modifies immune gene expression during an acute‐phase
infection (one day post‐challenge). We then asked whether previous pathogen exposure
affects chronic‐phase pathogen persistence and longer‐term survival (28 days post‐challenge).\r\n
\ We predicted that previous exposure would increase host resistance to an early
stage bacterial infection while it might come at a cost to host fecundity tolerance.
We reasoned that resistance would be due in part to stronger immune gene expression
after challenge. We expected that previous exposure would improve long‐term survival,
that it would reduce infection persistence, and we expected to find genetic variation
in these responses.\r\n We found that previous exposure to P. entomophila weakened
host resistance to a second infection independent of genotype and had no effect
on immune gene expression. Fecundity tolerance showed genotypic variation but
was not influenced by previous exposure. However, L. lactis persisted as a chronic
infection, whereas survivors cleared the more pathogenic P. entomophila infection.\r\n
\ To our knowledge, this is the first study that addresses host tolerance to
bacteria in relation to previous exposure, taking a multi‐faceted approach to
address the topic. Our results suggest that previous exposure comes with transient
costs to resistance during the early stage of infection in this host–pathogen
system and that infection persistence may be bacterium‐specific.\r\n"
article_processing_charge: No
article_type: original
author:
- first_name: Megan
full_name: Kutzer, Megan
id: 29D0B332-F248-11E8-B48F-1D18A9856A87
last_name: Kutzer
orcid: 0000-0002-8696-6978
- first_name: Joachim
full_name: Kurtz, Joachim
last_name: Kurtz
- first_name: Sophie A.O.
full_name: Armitage, Sophie A.O.
last_name: Armitage
citation:
ama: Kutzer M, Kurtz J, Armitage SAO. A multi-faceted approach testing the effects
of previous bacterial exposure on resistance and tolerance. Journal of Animal
Ecology. 2019;88(4):566-578. doi:10.1111/1365-2656.12953
apa: Kutzer, M., Kurtz, J., & Armitage, S. A. O. (2019). A multi-faceted approach
testing the effects of previous bacterial exposure on resistance and tolerance.
Journal of Animal Ecology. Wiley. https://doi.org/10.1111/1365-2656.12953
chicago: Kutzer, Megan, Joachim Kurtz, and Sophie A.O. Armitage. “A Multi-Faceted
Approach Testing the Effects of Previous Bacterial Exposure on Resistance and
Tolerance.” Journal of Animal Ecology. Wiley, 2019. https://doi.org/10.1111/1365-2656.12953.
ieee: M. Kutzer, J. Kurtz, and S. A. O. Armitage, “A multi-faceted approach testing
the effects of previous bacterial exposure on resistance and tolerance,” Journal
of Animal Ecology, vol. 88, no. 4. Wiley, pp. 566–578, 2019.
ista: Kutzer M, Kurtz J, Armitage SAO. 2019. A multi-faceted approach testing the
effects of previous bacterial exposure on resistance and tolerance. Journal of
Animal Ecology. 88(4), 566–578.
mla: Kutzer, Megan, et al. “A Multi-Faceted Approach Testing the Effects of Previous
Bacterial Exposure on Resistance and Tolerance.” Journal of Animal Ecology,
vol. 88, no. 4, Wiley, 2019, pp. 566–78, doi:10.1111/1365-2656.12953.
short: M. Kutzer, J. Kurtz, S.A.O. Armitage, Journal of Animal Ecology 88 (2019)
566–578.
date_created: 2019-03-17T22:59:15Z
date_published: 2019-04-01T00:00:00Z
date_updated: 2023-08-25T08:04:53Z
day: '01'
ddc:
- '570'
department:
- _id: SyCr
doi: 10.1111/1365-2656.12953
ec_funded: 1
external_id:
isi:
- '000467994800007'
file:
- access_level: open_access
checksum: 405cde15120de26018b3bd0dfa29986c
content_type: application/pdf
creator: dernst
date_created: 2019-03-18T07:43:06Z
date_updated: 2020-07-14T12:47:19Z
file_id: '6107'
file_name: 2019_JournalAnimalEcology_Kutzer.pdf
file_size: 1460662
relation: main_file
file_date_updated: 2020-07-14T12:47:19Z
has_accepted_license: '1'
intvolume: ' 88'
isi: 1
issue: '4'
language:
- iso: eng
month: '04'
oa: 1
oa_version: Published Version
page: 566-578
project:
- _id: 25681D80-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '291734'
name: International IST Postdoc Fellowship Programme
publication: Journal of Animal Ecology
publication_identifier:
eissn:
- '13652656'
issn:
- '00218790'
publication_status: published
publisher: Wiley
quality_controlled: '1'
related_material:
record:
- id: '9806'
relation: research_data
status: public
scopus_import: '1'
status: public
title: A multi-faceted approach testing the effects of previous bacterial exposure
on resistance and tolerance
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: 88
year: '2019'
...
---
_id: '6088'
abstract:
- lang: eng
text: P-Glycoprotein (ABCB1) and breast cancer resistance protein (ABCG2) are two
efflux transporters at the blood–brain barrier (BBB), which effectively restrict
brain distribution of diverse drugs, such as tyrosine kinase inhibitors. There
is a crucial need for pharmacological ABCB1 and ABCG2 inhibition protocols for
a more effective treatment of brain diseases. In the present study, seven marketed
drugs (osimertinib, erlotinib, nilotinib, imatinib, lapatinib, pazopanib, and
cyclosporine A) and one nonmarketed drug (tariquidar), with known in vitro ABCB1/ABCG2
inhibitory properties, were screened for their inhibitory potency at the BBB in
vivo. Positron emission tomography (PET) using the model ABCB1/ABCG2 substrate
[11C]erlotinib was performed in mice. Tested inhibitors were administered as i.v.
bolus injections at 30 min before the start of the PET scan, followed by a continuous
i.v. infusion for the duration of the PET scan. Five of the tested drugs increased
total distribution volume of [11C]erlotinib in the brain (VT,brain) compared to
vehicle-treated animals (tariquidar, + 69%; erlotinib, + 19% and +23% for the
21.5 mg/kg and the 43 mg/kg dose, respectively; imatinib, + 22%; lapatinib, +
25%; and cyclosporine A, + 49%). For all drugs, increases in [11C]erlotinib brain
distribution were lower than in Abcb1a/b(−/−)Abcg2(−/−) mice (+149%), which suggested
that only partial ABCB1/ABCG2 inhibition was reached at the mouse BBB. The plasma
concentrations of the tested drugs at the time of the PET scan were higher than
clinically achievable plasma concentrations. Some of the tested drugs led to significant
increases in blood radioactivity concentrations measured at the end of the PET
scan (erlotinib, + 103% and +113% for the 21.5 mg/kg and the 43 mg/kg dose, respectively;
imatinib, + 125%; and cyclosporine A, + 101%), which was most likely caused by
decreased hepatobiliary excretion of radioactivity. Taken together, our data suggest
that some marketed tyrosine kinase inhibitors may be repurposed to inhibit ABCB1
and ABCG2 at the BBB. From a clinical perspective, moderate increases in brain
delivery despite the administration of high i.v. doses as well as peripheral drug–drug
interactions due to transporter inhibition in clearance organs question the translatability
of this concept.
article_processing_charge: No
author:
- first_name: Alexander
full_name: Traxl, Alexander
last_name: Traxl
- first_name: Severin
full_name: Mairinger, Severin
last_name: Mairinger
- first_name: Thomas
full_name: Filip, Thomas
last_name: Filip
- first_name: Michael
full_name: Sauberer, Michael
last_name: Sauberer
- first_name: Johann
full_name: Stanek, Johann
last_name: Stanek
- first_name: Stefan
full_name: Poschner, Stefan
last_name: Poschner
- first_name: Walter
full_name: Jäger, Walter
last_name: Jäger
- first_name: Viktoria
full_name: Zoufal, Viktoria
last_name: Zoufal
- first_name: Gaia
full_name: Novarino, Gaia
id: 3E57A680-F248-11E8-B48F-1D18A9856A87
last_name: Novarino
orcid: 0000-0002-7673-7178
- first_name: Nicolas
full_name: Tournier, Nicolas
last_name: Tournier
- first_name: Martin
full_name: Bauer, Martin
last_name: Bauer
- first_name: Thomas
full_name: Wanek, Thomas
last_name: Wanek
- first_name: Oliver
full_name: Langer, Oliver
last_name: Langer
citation:
ama: Traxl A, Mairinger S, Filip T, et al. Inhibition of ABCB1 and ABCG2 at the
mouse blood-brain barrier with marketed drugs to improve brain delivery of the
model ABCB1/ABCG2 substrate [11C]erlotinib. Molecular Pharmaceutics. 2019;16(3):1282-1293.
doi:10.1021/acs.molpharmaceut.8b01217
apa: Traxl, A., Mairinger, S., Filip, T., Sauberer, M., Stanek, J., Poschner, S.,
… Langer, O. (2019). Inhibition of ABCB1 and ABCG2 at the mouse blood-brain barrier
with marketed drugs to improve brain delivery of the model ABCB1/ABCG2 substrate
[11C]erlotinib. Molecular Pharmaceutics. American Chemical Society. https://doi.org/10.1021/acs.molpharmaceut.8b01217
chicago: Traxl, Alexander, Severin Mairinger, Thomas Filip, Michael Sauberer, Johann
Stanek, Stefan Poschner, Walter Jäger, et al. “Inhibition of ABCB1 and ABCG2 at
the Mouse Blood-Brain Barrier with Marketed Drugs to Improve Brain Delivery of
the Model ABCB1/ABCG2 Substrate [11C]Erlotinib.” Molecular Pharmaceutics.
American Chemical Society, 2019. https://doi.org/10.1021/acs.molpharmaceut.8b01217.
ieee: A. Traxl et al., “Inhibition of ABCB1 and ABCG2 at the mouse blood-brain
barrier with marketed drugs to improve brain delivery of the model ABCB1/ABCG2
substrate [11C]erlotinib,” Molecular Pharmaceutics, vol. 16, no. 3. American
Chemical Society, pp. 1282–1293, 2019.
ista: Traxl A, Mairinger S, Filip T, Sauberer M, Stanek J, Poschner S, Jäger W,
Zoufal V, Novarino G, Tournier N, Bauer M, Wanek T, Langer O. 2019. Inhibition
of ABCB1 and ABCG2 at the mouse blood-brain barrier with marketed drugs to improve
brain delivery of the model ABCB1/ABCG2 substrate [11C]erlotinib. Molecular Pharmaceutics.
16(3), 1282–1293.
mla: Traxl, Alexander, et al. “Inhibition of ABCB1 and ABCG2 at the Mouse Blood-Brain
Barrier with Marketed Drugs to Improve Brain Delivery of the Model ABCB1/ABCG2
Substrate [11C]Erlotinib.” Molecular Pharmaceutics, vol. 16, no. 3, American
Chemical Society, 2019, pp. 1282–93, doi:10.1021/acs.molpharmaceut.8b01217.
short: A. Traxl, S. Mairinger, T. Filip, M. Sauberer, J. Stanek, S. Poschner, W.
Jäger, V. Zoufal, G. Novarino, N. Tournier, M. Bauer, T. Wanek, O. Langer, Molecular
Pharmaceutics 16 (2019) 1282–1293.
date_created: 2019-03-10T22:59:19Z
date_published: 2019-03-04T00:00:00Z
date_updated: 2023-08-25T08:02:51Z
day: '04'
department:
- _id: GaNo
doi: 10.1021/acs.molpharmaceut.8b01217
external_id:
isi:
- '000460600400031'
pmid:
- '30694684'
intvolume: ' 16'
isi: 1
issue: '3'
language:
- iso: eng
month: '03'
oa_version: None
page: 1282-1293
pmid: 1
publication: Molecular Pharmaceutics
publication_status: published
publisher: American Chemical Society
quality_controlled: '1'
scopus_import: '1'
status: public
title: Inhibition of ABCB1 and ABCG2 at the mouse blood-brain barrier with marketed
drugs to improve brain delivery of the model ABCB1/ABCG2 substrate [11C]erlotinib
type: journal_article
user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
volume: 16
year: '2019'
...
---
_id: '6087'
abstract:
- lang: eng
text: Cell fate specification by lateral inhibition typically involves contact signaling
through the Delta-Notch signaling pathway. However, whether this is the only signaling
mode mediating lateral inhibition remains unclear. Here we show that in zebrafish
oogenesis, a group of cells within the granulosa cell layer at the oocyte animal
pole acquire elevated levels of the transcriptional coactivator TAZ in their nuclei.
One of these cells, the future micropyle precursor cell (MPC), accumulates increasingly
high levels of nuclear TAZ and grows faster than its surrounding cells, mechanically
compressing those cells, which ultimately lose TAZ from their nuclei. Strikingly,
relieving neighbor-cell compression by MPC ablation or aspiration restores nuclear
TAZ accumulation in neighboring cells, eventually leading to MPC re-specification
from these cells. Conversely, MPC specification is defective in taz−/− follicles.
These findings uncover a novel mode of lateral inhibition in cell fate specification
based on mechanical signals controlling TAZ activity.
acknowledged_ssus:
- _id: Bio
- _id: EM-Fac
- _id: LifeSc
acknowledgement: We thank Roland Dosch, Makoto Furutani-Seiki, Brian Link, Mary Mullins,
and Masazumi Tada for providing transgenic and/or mutant zebrafish lines; Alexandra
Schauer, Shayan Shami-Pour, and the rest of the Heisenberg lab for technical assistance
and feedback on the manuscript; and the Bioimaging, Electron Microscopy, and Zebrafish
facilities of IST Austria for continuous support. This work was supported by an
ERC advanced grant ( MECSPEC to C.-P.H.).
article_processing_charge: No
article_type: original
author:
- first_name: Peng
full_name: Xia, Peng
id: 4AB6C7D0-F248-11E8-B48F-1D18A9856A87
last_name: Xia
orcid: 0000-0002-5419-7756
- first_name: Daniel J
full_name: Gütl, Daniel J
id: 381929CE-F248-11E8-B48F-1D18A9856A87
last_name: Gütl
- first_name: Vanessa
full_name: Zheden, Vanessa
id: 39C5A68A-F248-11E8-B48F-1D18A9856A87
last_name: Zheden
orcid: 0000-0002-9438-4783
- first_name: Carl-Philipp J
full_name: Heisenberg, Carl-Philipp J
id: 39427864-F248-11E8-B48F-1D18A9856A87
last_name: Heisenberg
orcid: 0000-0002-0912-4566
citation:
ama: Xia P, Gütl DJ, Zheden V, Heisenberg C-PJ. Lateral inhibition in cell specification
mediated by mechanical signals modulating TAZ activity. Cell. 2019;176(6):1379-1392.e14.
doi:10.1016/j.cell.2019.01.019
apa: Xia, P., Gütl, D. J., Zheden, V., & Heisenberg, C.-P. J. (2019). Lateral
inhibition in cell specification mediated by mechanical signals modulating TAZ
activity. Cell. Elsevier. https://doi.org/10.1016/j.cell.2019.01.019
chicago: Xia, Peng, Daniel J Gütl, Vanessa Zheden, and Carl-Philipp J Heisenberg.
“Lateral Inhibition in Cell Specification Mediated by Mechanical Signals Modulating
TAZ Activity.” Cell. Elsevier, 2019. https://doi.org/10.1016/j.cell.2019.01.019.
ieee: P. Xia, D. J. Gütl, V. Zheden, and C.-P. J. Heisenberg, “Lateral inhibition
in cell specification mediated by mechanical signals modulating TAZ activity,”
Cell, vol. 176, no. 6. Elsevier, p. 1379–1392.e14, 2019.
ista: Xia P, Gütl DJ, Zheden V, Heisenberg C-PJ. 2019. Lateral inhibition in cell
specification mediated by mechanical signals modulating TAZ activity. Cell. 176(6),
1379–1392.e14.
mla: Xia, Peng, et al. “Lateral Inhibition in Cell Specification Mediated by Mechanical
Signals Modulating TAZ Activity.” Cell, vol. 176, no. 6, Elsevier, 2019,
p. 1379–1392.e14, doi:10.1016/j.cell.2019.01.019.
short: P. Xia, D.J. Gütl, V. Zheden, C.-P.J. Heisenberg, Cell 176 (2019) 1379–1392.e14.
date_created: 2019-03-10T22:59:19Z
date_published: 2019-03-07T00:00:00Z
date_updated: 2023-08-25T08:02:23Z
day: '07'
department:
- _id: CaHe
- _id: EM-Fac
doi: 10.1016/j.cell.2019.01.019
ec_funded: 1
external_id:
isi:
- '000460509600013'
pmid:
- '30773315'
intvolume: ' 176'
isi: 1
issue: '6'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.1016/j.cell.2019.01.019
month: '03'
oa: 1
oa_version: Published Version
page: 1379-1392.e14
pmid: 1
project:
- _id: 260F1432-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '742573'
name: Interaction and feedback between cell mechanics and fate specification in
vertebrate gastrulation
publication: Cell
publication_status: published
publisher: Elsevier
quality_controlled: '1'
related_material:
link:
- description: News on IST Homepage
relation: press_release
url: https://ist.ac.at/en/news/in-zebrafish-eggs-most-rapidly-growing-cell-inhibits-its-neighbours-through-mechanical-signals/
scopus_import: '1'
status: public
title: Lateral inhibition in cell specification mediated by mechanical signals modulating
TAZ activity
type: journal_article
user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
volume: 176
year: '2019'
...
---
_id: '9806'
abstract:
- lang: eng
text: 1. Hosts can alter their strategy towards pathogens during their lifetime,
i.e., they can show phenotypic plasticity in immunity or life history. Immune
priming is one such example, where a previous encounter with a pathogen confers
enhanced protection upon secondary challenge, resulting in reduced pathogen load
(i.e. resistance) and improved host survival. However, an initial encounter might
also enhance tolerance, particularly to less virulent opportunistic pathogens
that establish persistent infections. In this scenario, individuals are better
able to reduce the negative fitness consequences that result from a high pathogen
load. Finally, previous exposure may also lead to life history adjustments, such
as terminal investment into reproduction. 2. Using different Drosophila melanogaster
host genotypes and two bacterial pathogens, Lactococcus lactis and Pseudomonas
entomophila, we tested if previous exposure results in resistance or tolerance
and whether it modifies immune gene expression during an acute-phase infection
(one day post-challenge). We then asked if previous pathogen exposure affects
chronic-phase pathogen persistence and longer-term survival (28 days post-challenge).
3. We predicted that previous exposure would increase host resistance to an early
stage bacterial infection while it might come at a cost to host fecundity tolerance.
We reasoned that resistance would be due in part to stronger immune gene expression
after challenge. We expected that previous exposure would improve long-term survival,
that it would reduce infection persistence, and we expected to find genetic variation
in these responses. 4. We found that previous exposure to P. entomophila weakened
host resistance to a second infection independent of genotype and had no effect
on immune gene expression. Fecundity tolerance showed genotypic variation but
was not influenced by previous exposure. However, L. lactis persisted as a chronic
infection, whereas survivors cleared the more pathogenic P. entomophila infection.
5. To our knowledge, this is the first study that addresses host tolerance to
bacteria in relation to previous exposure, taking a multi-faceted approach to
address the topic. Our results suggest that previous exposure comes with transient
costs to resistance during the early stage of infection in this host-pathogen
system and that infection persistence may be bacterium-specific.
article_processing_charge: No
author:
- first_name: Megan
full_name: Kutzer, Megan
id: 29D0B332-F248-11E8-B48F-1D18A9856A87
last_name: Kutzer
orcid: 0000-0002-8696-6978
- first_name: Joachim
full_name: Kurtz, Joachim
last_name: Kurtz
- first_name: Sophie A.O.
full_name: Armitage, Sophie A.O.
last_name: Armitage
citation:
ama: 'Kutzer M, Kurtz J, Armitage SAO. Data from: A multi-faceted approach testing
the effects of previous bacterial exposure on resistance and tolerance. 2019.
doi:10.5061/dryad.9kj41f0'
apa: 'Kutzer, M., Kurtz, J., & Armitage, S. A. O. (2019). Data from: A multi-faceted
approach testing the effects of previous bacterial exposure on resistance and
tolerance. Dryad. https://doi.org/10.5061/dryad.9kj41f0'
chicago: 'Kutzer, Megan, Joachim Kurtz, and Sophie A.O. Armitage. “Data from: A
Multi-Faceted Approach Testing the Effects of Previous Bacterial Exposure on Resistance
and Tolerance.” Dryad, 2019. https://doi.org/10.5061/dryad.9kj41f0.'
ieee: 'M. Kutzer, J. Kurtz, and S. A. O. Armitage, “Data from: A multi-faceted approach
testing the effects of previous bacterial exposure on resistance and tolerance.”
Dryad, 2019.'
ista: 'Kutzer M, Kurtz J, Armitage SAO. 2019. Data from: A multi-faceted approach
testing the effects of previous bacterial exposure on resistance and tolerance,
Dryad, 10.5061/dryad.9kj41f0.'
mla: 'Kutzer, Megan, et al. Data from: A Multi-Faceted Approach Testing the Effects
of Previous Bacterial Exposure on Resistance and Tolerance. Dryad, 2019, doi:10.5061/dryad.9kj41f0.'
short: M. Kutzer, J. Kurtz, S.A.O. Armitage, (2019).
date_created: 2021-08-06T12:06:40Z
date_published: 2019-02-05T00:00:00Z
date_updated: 2023-08-25T08:04:52Z
day: '05'
department:
- _id: SyCr
doi: 10.5061/dryad.9kj41f0
main_file_link:
- open_access: '1'
url: https://doi.org/10.5061/dryad.9kj41f0
month: '02'
oa: 1
oa_version: Published Version
publisher: Dryad
related_material:
record:
- id: '6105'
relation: used_in_publication
status: public
status: public
title: 'Data from: A multi-faceted approach testing the effects of previous bacterial
exposure on resistance and tolerance'
type: research_data_reference
user_id: 6785fbc1-c503-11eb-8a32-93094b40e1cf
year: '2019'
...
---
_id: '6086'
abstract:
- lang: eng
text: We show that linear analytic cocycles where all Lyapunov exponents are negative
infinite are nilpotent. For such one-frequency cocycles we show that they can
be analytically conjugated to an upper triangular cocycle or a Jordan normal form.
As a consequence, an arbitrarily small analytic perturbation leads to distinct
Lyapunov exponents. Moreover, in the one-frequency case where the th Lyapunov
exponent is finite and the st negative infinite, we obtain a simple criterion
for domination in which case there is a splitting into a nilpotent part and an
invertible part.
article_processing_charge: No
author:
- first_name: Christian
full_name: Sadel, Christian
id: 4760E9F8-F248-11E8-B48F-1D18A9856A87
last_name: Sadel
orcid: 0000-0001-8255-3968
- first_name: Disheng
full_name: Xu, Disheng
last_name: Xu
citation:
ama: Sadel C, Xu D. Singular analytic linear cocycles with negative infinite Lyapunov
exponents. Ergodic Theory and Dynamical Systems. 2019;39(4):1082-1098.
doi:10.1017/etds.2017.52
apa: Sadel, C., & Xu, D. (2019). Singular analytic linear cocycles with negative
infinite Lyapunov exponents. Ergodic Theory and Dynamical Systems. Cambridge
University Press. https://doi.org/10.1017/etds.2017.52
chicago: Sadel, Christian, and Disheng Xu. “Singular Analytic Linear Cocycles with
Negative Infinite Lyapunov Exponents.” Ergodic Theory and Dynamical Systems.
Cambridge University Press, 2019. https://doi.org/10.1017/etds.2017.52.
ieee: C. Sadel and D. Xu, “Singular analytic linear cocycles with negative infinite
Lyapunov exponents,” Ergodic Theory and Dynamical Systems, vol. 39, no.
4. Cambridge University Press, pp. 1082–1098, 2019.
ista: Sadel C, Xu D. 2019. Singular analytic linear cocycles with negative infinite
Lyapunov exponents. Ergodic Theory and Dynamical Systems. 39(4), 1082–1098.
mla: Sadel, Christian, and Disheng Xu. “Singular Analytic Linear Cocycles with Negative
Infinite Lyapunov Exponents.” Ergodic Theory and Dynamical Systems, vol.
39, no. 4, Cambridge University Press, 2019, pp. 1082–98, doi:10.1017/etds.2017.52.
short: C. Sadel, D. Xu, Ergodic Theory and Dynamical Systems 39 (2019) 1082–1098.
date_created: 2019-03-10T22:59:18Z
date_published: 2019-04-01T00:00:00Z
date_updated: 2023-08-25T08:03:30Z
day: '01'
department:
- _id: LaEr
doi: 10.1017/etds.2017.52
ec_funded: 1
external_id:
arxiv:
- '1601.06118'
isi:
- '000459725600012'
intvolume: ' 39'
isi: 1
issue: '4'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/1601.06118
month: '04'
oa: 1
oa_version: Preprint
page: 1082-1098
project:
- _id: 25681D80-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '291734'
name: International IST Postdoc Fellowship Programme
publication: Ergodic Theory and Dynamical Systems
publication_status: published
publisher: Cambridge University Press
quality_controlled: '1'
scopus_import: '1'
status: public
title: Singular analytic linear cocycles with negative infinite Lyapunov exponents
type: journal_article
user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
volume: 39
year: '2019'
...
---
_id: '6102'
abstract:
- lang: eng
text: 'Light is a union of electric and magnetic fields, and nowhere is the complex
relationship between these fields more evident than in the near fields of nanophotonic
structures. There, complicated electric and magnetic fields varying over subwavelength
scales are generally present, which results in photonic phenomena such as extraordinary
optical momentum, superchiral fields, and a complex spatial evolution of optical
singularities. An understanding of such phenomena requires nanoscale measurements
of the complete optical field vector. Although the sensitivity of near- field
scanning optical microscopy to the complete electromagnetic field was recently
demonstrated, a separation of different components required a priori knowledge
of the sample. Here, we introduce a robust algorithm that can disentangle all
six electric and magnetic field components from a single near-field measurement
without any numerical modeling of the structure. As examples, we unravel the fields
of two prototypical nanophotonic structures: a photonic crystal waveguide and
a plasmonic nanowire. These results pave the way for new studies of complex photonic
phenomena at the nanoscale and for the design of structures that optimize their
optical behavior.'
article_number: '28'
article_processing_charge: No
author:
- first_name: B.
full_name: Le Feber, B.
last_name: Le Feber
- first_name: J. E.
full_name: Sipe, J. E.
last_name: Sipe
- first_name: Matthias
full_name: Wulf, Matthias
id: 45598606-F248-11E8-B48F-1D18A9856A87
last_name: Wulf
orcid: 0000-0001-6613-1378
- first_name: L.
full_name: Kuipers, L.
last_name: Kuipers
- first_name: N.
full_name: Rotenberg, N.
last_name: Rotenberg
citation:
ama: 'Le Feber B, Sipe JE, Wulf M, Kuipers L, Rotenberg N. A full vectorial mapping
of nanophotonic light fields. Light: Science and Applications. 2019;8(1).
doi:10.1038/s41377-019-0124-3'
apa: 'Le Feber, B., Sipe, J. E., Wulf, M., Kuipers, L., & Rotenberg, N. (2019).
A full vectorial mapping of nanophotonic light fields. Light: Science and Applications.
Springer Nature. https://doi.org/10.1038/s41377-019-0124-3'
chicago: 'Le Feber, B., J. E. Sipe, Matthias Wulf, L. Kuipers, and N. Rotenberg.
“A Full Vectorial Mapping of Nanophotonic Light Fields.” Light: Science and
Applications. Springer Nature, 2019. https://doi.org/10.1038/s41377-019-0124-3.'
ieee: 'B. Le Feber, J. E. Sipe, M. Wulf, L. Kuipers, and N. Rotenberg, “A full vectorial
mapping of nanophotonic light fields,” Light: Science and Applications,
vol. 8, no. 1. Springer Nature, 2019.'
ista: 'Le Feber B, Sipe JE, Wulf M, Kuipers L, Rotenberg N. 2019. A full vectorial
mapping of nanophotonic light fields. Light: Science and Applications. 8(1), 28.'
mla: 'Le Feber, B., et al. “A Full Vectorial Mapping of Nanophotonic Light Fields.”
Light: Science and Applications, vol. 8, no. 1, 28, Springer Nature, 2019,
doi:10.1038/s41377-019-0124-3.'
short: 'B. Le Feber, J.E. Sipe, M. Wulf, L. Kuipers, N. Rotenberg, Light: Science
and Applications 8 (2019).'
date_created: 2019-03-17T22:59:13Z
date_published: 2019-03-06T00:00:00Z
date_updated: 2023-08-25T08:06:10Z
day: '06'
ddc:
- '530'
department:
- _id: JoFi
doi: 10.1038/s41377-019-0124-3
external_id:
arxiv:
- '1803.10145'
isi:
- '000460470700004'
file:
- access_level: open_access
checksum: d71e528cff9c56f70ccc29dd7005257f
content_type: application/pdf
creator: dernst
date_created: 2019-03-18T08:08:22Z
date_updated: 2020-07-14T12:47:19Z
file_id: '6108'
file_name: 2019_Light_LeFeber.pdf
file_size: 1119947
relation: main_file
file_date_updated: 2020-07-14T12:47:19Z
has_accepted_license: '1'
intvolume: ' 8'
isi: 1
issue: '1'
language:
- iso: eng
month: '03'
oa: 1
oa_version: Published Version
publication: 'Light: Science and Applications'
publication_identifier:
eissn:
- '20477538'
issn:
- '20955545'
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
scopus_import: '1'
status: public
title: A full vectorial mapping of nanophotonic light fields
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: 8
year: '2019'
...
---
_id: '6104'
abstract:
- lang: eng
text: Abiotic stress poses constant challenges for plant survival and is a serious
problem for global agricultural productivity. On a molecular level, stress conditions
result in elevation of reactive oxygen species (ROS) production causing oxidative
stress associated with oxidation of proteins and nucleic acids as well as impairment
of membrane functions. Adaptation of root growth to ROS accumulation is facilitated
through modification of auxin and cytokinin hormone homeostasis. Here, we report
that in Arabidopsis root meristem, ROS-induced changes of auxin levels correspond
to decreased abundance of PIN auxin efflux carriers at the plasma membrane (PM).
Specifically, increase in H2O2 levels affects PIN2 endocytic recycling. We show
that the PIN2 intracellular trafficking during adaptation to oxidative stress
requires the function of the ADP-ribosylation factor (ARF)-guanine-nucleotide
exchange factor (GEF) BEN1, an actin-associated regulator of the trafficking from
the PM to early endosomes and, presumably, indirectly, trafficking to the vacuoles.
We propose that H2O2 levels affect the actin dynamics thus modulating ARF-GEF-dependent
trafficking of PIN2. This mechanism provides a way how root growth acclimates
to stress and adapts to a changing environment.
article_processing_charge: No
author:
- first_name: Marta
full_name: Zwiewka, Marta
last_name: Zwiewka
- first_name: Agnieszka
full_name: Bielach, Agnieszka
last_name: Bielach
- first_name: Prashanth
full_name: Tamizhselvan, Prashanth
last_name: Tamizhselvan
- first_name: Sharmila
full_name: Madhavan, Sharmila
last_name: Madhavan
- first_name: Eman Elrefaay
full_name: Ryad, Eman Elrefaay
last_name: Ryad
- first_name: Shutang
full_name: Tan, Shutang
id: 2DE75584-F248-11E8-B48F-1D18A9856A87
last_name: Tan
orcid: 0000-0002-0471-8285
- first_name: Mónika
full_name: Hrtyan, Mónika
id: 45A71A74-F248-11E8-B48F-1D18A9856A87
last_name: Hrtyan
- first_name: Petre
full_name: Dobrev, Petre
last_name: Dobrev
- first_name: Radomira
full_name: Vanková, Radomira
last_name: Vanková
- first_name: Jiří
full_name: Friml, Jiří
id: 4159519E-F248-11E8-B48F-1D18A9856A87
last_name: Friml
orcid: 0000-0002-8302-7596
- first_name: Vanesa B.
full_name: Tognetti, Vanesa B.
last_name: Tognetti
citation:
ama: Zwiewka M, Bielach A, Tamizhselvan P, et al. Root adaptation to H2O2-induced
oxidative stress by ARF-GEF BEN1- and cytoskeleton-mediated PIN2 trafficking.
Plant and Cell Physiology. 2019;60(2):255-273. doi:10.1093/pcp/pcz001
apa: Zwiewka, M., Bielach, A., Tamizhselvan, P., Madhavan, S., Ryad, E. E., Tan,
S., … Tognetti, V. B. (2019). Root adaptation to H2O2-induced oxidative stress
by ARF-GEF BEN1- and cytoskeleton-mediated PIN2 trafficking. Plant and Cell
Physiology. Oxford University Press. https://doi.org/10.1093/pcp/pcz001
chicago: Zwiewka, Marta, Agnieszka Bielach, Prashanth Tamizhselvan, Sharmila Madhavan,
Eman Elrefaay Ryad, Shutang Tan, Mónika Hrtyan, et al. “Root Adaptation to H2O2-Induced
Oxidative Stress by ARF-GEF BEN1- and Cytoskeleton-Mediated PIN2 Trafficking.”
Plant and Cell Physiology. Oxford University Press, 2019. https://doi.org/10.1093/pcp/pcz001.
ieee: M. Zwiewka et al., “Root adaptation to H2O2-induced oxidative stress
by ARF-GEF BEN1- and cytoskeleton-mediated PIN2 trafficking,” Plant and Cell
Physiology, vol. 60, no. 2. Oxford University Press, pp. 255–273, 2019.
ista: Zwiewka M, Bielach A, Tamizhselvan P, Madhavan S, Ryad EE, Tan S, Hrtyan M,
Dobrev P, Vanková R, Friml J, Tognetti VB. 2019. Root adaptation to H2O2-induced
oxidative stress by ARF-GEF BEN1- and cytoskeleton-mediated PIN2 trafficking.
Plant and Cell Physiology. 60(2), 255–273.
mla: Zwiewka, Marta, et al. “Root Adaptation to H2O2-Induced Oxidative Stress by
ARF-GEF BEN1- and Cytoskeleton-Mediated PIN2 Trafficking.” Plant and Cell Physiology,
vol. 60, no. 2, Oxford University Press, 2019, pp. 255–73, doi:10.1093/pcp/pcz001.
short: M. Zwiewka, A. Bielach, P. Tamizhselvan, S. Madhavan, E.E. Ryad, S. Tan,
M. Hrtyan, P. Dobrev, R. Vanková, J. Friml, V.B. Tognetti, Plant and Cell Physiology
60 (2019) 255–273.
date_created: 2019-03-17T22:59:14Z
date_published: 2019-02-01T00:00:00Z
date_updated: 2023-08-25T08:05:28Z
day: '01'
department:
- _id: JiFr
doi: 10.1093/pcp/pcz001
external_id:
isi:
- '000459634300002'
pmid:
- '30668780'
intvolume: ' 60'
isi: 1
issue: '2'
language:
- iso: eng
month: '02'
oa_version: None
page: 255-273
pmid: 1
publication: Plant and Cell Physiology
publication_identifier:
eissn:
- 1471-9053
issn:
- 0032-0781
publication_status: published
publisher: Oxford University Press
quality_controlled: '1'
scopus_import: '1'
status: public
title: Root adaptation to H2O2-induced oxidative stress by ARF-GEF BEN1- and cytoskeleton-mediated
PIN2 trafficking
type: journal_article
user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
volume: 60
year: '2019'
...
---
_id: '6191'
abstract:
- lang: eng
text: The formation of self-organized patterns is key to the morphogenesis of multicellular
organisms, although a comprehensive theory of biological pattern formation is
still lacking. Here, we propose a minimal model combining tissue mechanics with
morphogen turnover and transport to explore routes to patterning. Our active description
couples morphogen reaction and diffusion, which impact cell differentiation and
tissue mechanics, to a two-phase poroelastic rheology, where one tissue phase
consists of a poroelastic cell network and the other one of a permeating extracellular
fluid, which provides a feedback by actively transporting morphogens. While this
model encompasses previous theories approximating tissues to inert monophasic
media, such as Turing’s reaction–diffusion model, it overcomes some of their key
limitations permitting pattern formation via any two-species biochemical kinetics
due to mechanically induced cross-diffusion flows. Moreover, we describe a qualitatively
different advection-driven Keller–Segel instability which allows for the formation
of patterns with a single morphogen and whose fundamental mode pattern robustly
scales with tissue size. We discuss the potential relevance of these findings
for tissue morphogenesis.
article_processing_charge: No
author:
- first_name: Pierre
full_name: Recho, Pierre
last_name: Recho
- first_name: Adrien
full_name: Hallou, Adrien
last_name: Hallou
- first_name: Edouard B
full_name: Hannezo, Edouard B
id: 3A9DB764-F248-11E8-B48F-1D18A9856A87
last_name: Hannezo
orcid: 0000-0001-6005-1561
citation:
ama: Recho P, Hallou A, Hannezo EB. Theory of mechanochemical patterning in biphasic
biological tissues. Proceedings of the National Academy of Sciences of the
United States of America. 2019;116(12):5344-5349. doi:10.1073/pnas.1813255116
apa: Recho, P., Hallou, A., & Hannezo, E. B. (2019). Theory of mechanochemical
patterning in biphasic biological tissues. Proceedings of the National Academy
of Sciences of the United States of America. National Academy of Sciences.
https://doi.org/10.1073/pnas.1813255116
chicago: Recho, Pierre, Adrien Hallou, and Edouard B Hannezo. “Theory of Mechanochemical
Patterning in Biphasic Biological Tissues.” Proceedings of the National Academy
of Sciences of the United States of America. National Academy of Sciences,
2019. https://doi.org/10.1073/pnas.1813255116.
ieee: P. Recho, A. Hallou, and E. B. Hannezo, “Theory of mechanochemical patterning
in biphasic biological tissues,” Proceedings of the National Academy of Sciences
of the United States of America, vol. 116, no. 12. National Academy of Sciences,
pp. 5344–5349, 2019.
ista: Recho P, Hallou A, Hannezo EB. 2019. Theory of mechanochemical patterning
in biphasic biological tissues. Proceedings of the National Academy of Sciences
of the United States of America. 116(12), 5344–5349.
mla: Recho, Pierre, et al. “Theory of Mechanochemical Patterning in Biphasic Biological
Tissues.” Proceedings of the National Academy of Sciences of the United States
of America, vol. 116, no. 12, National Academy of Sciences, 2019, pp. 5344–49,
doi:10.1073/pnas.1813255116.
short: P. Recho, A. Hallou, E.B. Hannezo, Proceedings of the National Academy of
Sciences of the United States of America 116 (2019) 5344–5349.
date_created: 2019-03-31T21:59:13Z
date_published: 2019-03-19T00:00:00Z
date_updated: 2023-08-25T08:57:30Z
day: '19'
ddc:
- '570'
department:
- _id: EdHa
doi: 10.1073/pnas.1813255116
external_id:
isi:
- '000461679000027'
pmid:
- '30819884'
file:
- access_level: open_access
checksum: 8b67eee0ea8e5db61583e4d485215258
content_type: application/pdf
creator: dernst
date_created: 2019-04-03T14:10:30Z
date_updated: 2020-07-14T12:47:23Z
file_id: '6193'
file_name: 2019_PNAS_Recho.pdf
file_size: 3456045
relation: main_file
file_date_updated: 2020-07-14T12:47:23Z
has_accepted_license: '1'
intvolume: ' 116'
isi: 1
issue: '12'
language:
- iso: eng
month: '03'
oa: 1
oa_version: Published Version
page: 5344-5349
pmid: 1
project:
- _id: 268294B6-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: P31639
name: Active mechano-chemical description of the cell cytoskeleton
publication: Proceedings of the National Academy of Sciences of the United States
of America
publication_identifier:
eissn:
- '10916490'
issn:
- '00278424'
publication_status: published
publisher: National Academy of Sciences
quality_controlled: '1'
related_material:
link:
- relation: supplementary_material
url: www.pnas.org/lookup/suppl/doi:10.1073/pnas.1813255116/-/DCSupplemental
scopus_import: '1'
status: public
title: Theory of mechanochemical patterning in biphasic biological tissues
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: 116
year: '2019'
...
---
_id: '6190'
abstract:
- lang: eng
text: "Increased levels of the chemokine CCL2 in cancer patients are associated
with poor prognosis. Experimental evidence suggests that CCL2 correlates with
inflammatory monocyte recruitment and induction of vascular activation, but the
functionality remains open. Here, we show that endothelial Ccr2 facilitates pulmonary
metastasis using an endothelial-specific Ccr2-deficient mouse model (Ccr2ecKO).
Similar levels of circulating monocytes and equal leukocyte recruitment to metastatic
lesions of Ccr2ecKO and Ccr2fl/fl littermates were observed. The absence of endothelial
Ccr2 strongly reduced pulmonary metastasis, while the primary tumor growth was
unaffected. Despite a comparable cytokine milieu in Ccr2ecKO and Ccr2fl/fl littermates
the absence of vascular permeability induction was observed only in Ccr2ecKO mice.
CCL2 stimulation of pulmonary endothelial cells resulted in increased phosphorylation
of MLC2, endothelial cell retraction, and vascular leakiness that was blocked
by an addition of a CCR2 inhibitor. These data demonstrate that endothelial CCR2
expression is required for tumor cell extravasation and pulmonary metastasis.\r\n\r\nImplications:
The findings provide mechanistic insight into how CCL2–CCR2 signaling in endothelial
cells promotes their activation through myosin light chain phosphorylation, resulting
in endothelial retraction and enhanced tumor cell migration and metastasis."
article_processing_charge: No
article_type: original
author:
- first_name: Marko
full_name: Roblek, Marko
id: 3047D808-F248-11E8-B48F-1D18A9856A87
last_name: Roblek
orcid: 0000-0001-9588-1389
- first_name: Darya
full_name: Protsyuk, Darya
last_name: Protsyuk
- first_name: Paul F.
full_name: Becker, Paul F.
last_name: Becker
- first_name: Cristina
full_name: Stefanescu, Cristina
last_name: Stefanescu
- first_name: Christian
full_name: Gorzelanny, Christian
last_name: Gorzelanny
- first_name: Jesus F.
full_name: Glaus Garzon, Jesus F.
last_name: Glaus Garzon
- first_name: Lucia
full_name: Knopfova, Lucia
last_name: Knopfova
- first_name: Mathias
full_name: Heikenwalder, Mathias
last_name: Heikenwalder
- first_name: Bruno
full_name: Luckow, Bruno
last_name: Luckow
- first_name: Stefan W.
full_name: Schneider, Stefan W.
last_name: Schneider
- first_name: Lubor
full_name: Borsig, Lubor
last_name: Borsig
citation:
ama: Roblek M, Protsyuk D, Becker PF, et al. CCL2 is a vascular permeability factor
inducing CCR2-dependent endothelial retraction during lung metastasis. Molecular
Cancer Research. 2019;17(3):783-793. doi:10.1158/1541-7786.MCR-18-0530
apa: Roblek, M., Protsyuk, D., Becker, P. F., Stefanescu, C., Gorzelanny, C., Glaus
Garzon, J. F., … Borsig, L. (2019). CCL2 is a vascular permeability factor inducing
CCR2-dependent endothelial retraction during lung metastasis. Molecular Cancer
Research. AACR. https://doi.org/10.1158/1541-7786.MCR-18-0530
chicago: Roblek, Marko, Darya Protsyuk, Paul F. Becker, Cristina Stefanescu, Christian
Gorzelanny, Jesus F. Glaus Garzon, Lucia Knopfova, et al. “CCL2 Is a Vascular
Permeability Factor Inducing CCR2-Dependent Endothelial Retraction during Lung
Metastasis.” Molecular Cancer Research. AACR, 2019. https://doi.org/10.1158/1541-7786.MCR-18-0530.
ieee: M. Roblek et al., “CCL2 is a vascular permeability factor inducing
CCR2-dependent endothelial retraction during lung metastasis,” Molecular Cancer
Research, vol. 17, no. 3. AACR, pp. 783–793, 2019.
ista: Roblek M, Protsyuk D, Becker PF, Stefanescu C, Gorzelanny C, Glaus Garzon
JF, Knopfova L, Heikenwalder M, Luckow B, Schneider SW, Borsig L. 2019. CCL2 is
a vascular permeability factor inducing CCR2-dependent endothelial retraction
during lung metastasis. Molecular Cancer Research. 17(3), 783–793.
mla: Roblek, Marko, et al. “CCL2 Is a Vascular Permeability Factor Inducing CCR2-Dependent
Endothelial Retraction during Lung Metastasis.” Molecular Cancer Research,
vol. 17, no. 3, AACR, 2019, pp. 783–93, doi:10.1158/1541-7786.MCR-18-0530.
short: M. Roblek, D. Protsyuk, P.F. Becker, C. Stefanescu, C. Gorzelanny, J.F. Glaus
Garzon, L. Knopfova, M. Heikenwalder, B. Luckow, S.W. Schneider, L. Borsig, Molecular
Cancer Research 17 (2019) 783–793.
date_created: 2019-03-31T21:59:12Z
date_published: 2019-03-01T00:00:00Z
date_updated: 2023-08-25T08:57:01Z
day: '01'
department:
- _id: DaSi
doi: 10.1158/1541-7786.MCR-18-0530
external_id:
isi:
- '000460099800012'
pmid:
- '30552233'
intvolume: ' 17'
isi: 1
issue: '3'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.1158/1541-7786.MCR-18-0530
month: '03'
oa: 1
oa_version: Published Version
page: 783-793
pmid: 1
publication: Molecular Cancer Research
publication_identifier:
eissn:
- '15573125'
issn:
- '15417786'
publication_status: published
publisher: AACR
quality_controlled: '1'
scopus_import: '1'
status: public
title: CCL2 is a vascular permeability factor inducing CCR2-dependent endothelial
retraction during lung metastasis
type: journal_article
user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
volume: 17
year: '2019'
...
---
_id: '6230'
abstract:
- lang: eng
text: Great care is needed when interpreting claims about the genetic basis of human
variation based on data from genome-wide association studies.
article_number: e45380
article_processing_charge: No
author:
- first_name: Nicholas H
full_name: Barton, Nicholas H
id: 4880FE40-F248-11E8-B48F-1D18A9856A87
last_name: Barton
orcid: 0000-0002-8548-5240
- first_name: Joachim
full_name: Hermisson, Joachim
last_name: Hermisson
- first_name: Magnus
full_name: Nordborg, Magnus
last_name: Nordborg
citation:
ama: Barton NH, Hermisson J, Nordborg M. Why structure matters. eLife. 2019;8.
doi:10.7554/eLife.45380
apa: Barton, N. H., Hermisson, J., & Nordborg, M. (2019). Why structure matters.
ELife. eLife Sciences Publications. https://doi.org/10.7554/eLife.45380
chicago: Barton, Nicholas H, Joachim Hermisson, and Magnus Nordborg. “Why Structure
Matters.” ELife. eLife Sciences Publications, 2019. https://doi.org/10.7554/eLife.45380.
ieee: N. H. Barton, J. Hermisson, and M. Nordborg, “Why structure matters,” eLife,
vol. 8. eLife Sciences Publications, 2019.
ista: Barton NH, Hermisson J, Nordborg M. 2019. Why structure matters. eLife. 8,
e45380.
mla: Barton, Nicholas H., et al. “Why Structure Matters.” ELife, vol. 8,
e45380, eLife Sciences Publications, 2019, doi:10.7554/eLife.45380.
short: N.H. Barton, J. Hermisson, M. Nordborg, ELife 8 (2019).
date_created: 2019-04-07T21:59:15Z
date_published: 2019-03-21T00:00:00Z
date_updated: 2023-08-25T08:59:38Z
day: '21'
ddc:
- '570'
department:
- _id: NiBa
doi: 10.7554/eLife.45380
external_id:
isi:
- '000461988300001'
file:
- access_level: open_access
checksum: 130d7544b57df4a6787e1263c2d7ea43
content_type: application/pdf
creator: dernst
date_created: 2019-04-11T11:43:38Z
date_updated: 2020-07-14T12:47:24Z
file_id: '6293'
file_name: 2019_eLife_Barton.pdf
file_size: 298466
relation: main_file
file_date_updated: 2020-07-14T12:47:24Z
has_accepted_license: '1'
intvolume: ' 8'
isi: 1
language:
- iso: eng
month: '03'
oa: 1
oa_version: Published Version
publication: eLife
publication_identifier:
eissn:
- 2050084X
publication_status: published
publisher: eLife Sciences Publications
quality_controlled: '1'
related_material:
link:
- description: News on IST Homepage
relation: press_release
url: https://ist.ac.at/en/news/body-height-bmi-disease-risk-co/
scopus_import: '1'
status: public
title: Why structure matters
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: 8
year: '2019'
...
---
_id: '6232'
abstract:
- lang: eng
text: 'The boundary behaviour of solutions of stochastic PDEs with Dirichlet boundary
conditions can be surprisingly—and in a sense, arbitrarily—bad: as shown by Krylov[
SIAM J. Math. Anal.34(2003) 1167–1182], for any α>0 one can find a simple 1-dimensional
constant coefficient linear equation whose solution at the boundary is not α-Hölder
continuous.We obtain a positive counterpart of this: under some mild regularity
assumptions on the coefficients, solutions of semilinear SPDEs on C1 domains are
proved to be α-Hölder continuous up to the boundary with some α>0.'
article_processing_charge: No
author:
- first_name: Mate
full_name: Gerencser, Mate
id: 44ECEDF2-F248-11E8-B48F-1D18A9856A87
last_name: Gerencser
citation:
ama: Gerencser M. Boundary regularity of stochastic PDEs. Annals of Probability.
2019;47(2):804-834. doi:10.1214/18-AOP1272
apa: Gerencser, M. (2019). Boundary regularity of stochastic PDEs. Annals of
Probability. Institute of Mathematical Statistics. https://doi.org/10.1214/18-AOP1272
chicago: Gerencser, Mate. “Boundary Regularity of Stochastic PDEs.” Annals of
Probability. Institute of Mathematical Statistics, 2019. https://doi.org/10.1214/18-AOP1272.
ieee: M. Gerencser, “Boundary regularity of stochastic PDEs,” Annals of Probability,
vol. 47, no. 2. Institute of Mathematical Statistics, pp. 804–834, 2019.
ista: Gerencser M. 2019. Boundary regularity of stochastic PDEs. Annals of Probability.
47(2), 804–834.
mla: Gerencser, Mate. “Boundary Regularity of Stochastic PDEs.” Annals of Probability,
vol. 47, no. 2, Institute of Mathematical Statistics, 2019, pp. 804–34, doi:10.1214/18-AOP1272.
short: M. Gerencser, Annals of Probability 47 (2019) 804–834.
date_created: 2019-04-07T21:59:15Z
date_published: 2019-03-01T00:00:00Z
date_updated: 2023-08-25T08:59:11Z
day: '01'
department:
- _id: JaMa
doi: 10.1214/18-AOP1272
external_id:
arxiv:
- '1705.05364'
isi:
- '000459681900005'
intvolume: ' 47'
isi: 1
issue: '2'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/1705.05364
month: '03'
oa: 1
oa_version: Preprint
page: 804-834
publication: Annals of Probability
publication_identifier:
issn:
- '00911798'
publication_status: published
publisher: Institute of Mathematical Statistics
quality_controlled: '1'
scopus_import: '1'
status: public
title: Boundary regularity of stochastic PDEs
type: journal_article
user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
volume: 47
year: '2019'
...
---
_id: '6262'
abstract:
- lang: eng
text: "Gravitropism is an adaptive response that orients plant growth parallel to
the gravity vector. Asymmetric\r\ndistribution of the phytohormone auxin is a
necessary prerequisite to the tropic bending both in roots and\r\nshoots. During
hypocotyl gravitropic response, the PIN3 auxin transporter polarizes within gravity-sensing\r\ncells
to redirect intercellular auxin fluxes. First gravity-induced PIN3 polarization
to the bottom cell mem-\r\nbranes leads to the auxin accumulation at the lower
side of the organ, initiating bending and, later, auxin\r\nfeedback-mediated repolarization
restores symmetric auxin distribution to terminate bending. Here, we per-\r\nformed
a forward genetic screen to identify regulators of both PIN3 polarization events
during gravitropic\r\nresponse. We searched for mutants with defective PIN3 polarizations
based on easy-to-score morphological\r\noutputs of decreased or increased gravity-induced
hypocotyl bending. We identified the number of\r\nhypocotyl reduced bending (hrb)
and hypocotyl hyperbending (hhb) mutants, revealing that reduced bending corre-\r\nlated
typically with defective gravity-induced PIN3 relocation whereas all analyzed
hhb mutants showed\r\ndefects in the second, auxin-mediated PIN3 relocation. Next-generation
sequencing-aided mutation map-\r\nping identified several candidate genes, including
SCARECROW and ACTIN2, revealing roles of endodermis\r\nspecification and actin
cytoskeleton in the respective gravity- and auxin-induced PIN polarization events.\r\nThe
hypocotyl gravitropism screen thus promises to provide novel insights into mechanisms
underlying cell\r\npolarity and plant adaptive development."
article_processing_charge: Yes (via OA deal)
article_type: original
author:
- first_name: Hana
full_name: Rakusová, Hana
last_name: Rakusová
- first_name: Huibin
full_name: Han, Huibin
id: 31435098-F248-11E8-B48F-1D18A9856A87
last_name: Han
- first_name: Petr
full_name: Valošek, Petr
id: 3CDB6F94-F248-11E8-B48F-1D18A9856A87
last_name: Valošek
- first_name: Jiří
full_name: Friml, Jiří
id: 4159519E-F248-11E8-B48F-1D18A9856A87
last_name: Friml
orcid: 0000-0002-8302-7596
citation:
ama: Rakusová H, Han H, Valošek P, Friml J. Genetic screen for factors mediating
PIN polarization in gravistimulated Arabidopsis thaliana hypocotyls. The Plant
Journal. 2019;98(6):1048-1059. doi:10.1111/tpj.14301
apa: Rakusová, H., Han, H., Valošek, P., & Friml, J. (2019). Genetic screen
for factors mediating PIN polarization in gravistimulated Arabidopsis thaliana
hypocotyls. The Plant Journal. Wiley. https://doi.org/10.1111/tpj.14301
chicago: Rakusová, Hana, Huibin Han, Petr Valošek, and Jiří Friml. “Genetic Screen
for Factors Mediating PIN Polarization in Gravistimulated Arabidopsis Thaliana
Hypocotyls.” The Plant Journal. Wiley, 2019. https://doi.org/10.1111/tpj.14301.
ieee: H. Rakusová, H. Han, P. Valošek, and J. Friml, “Genetic screen for factors
mediating PIN polarization in gravistimulated Arabidopsis thaliana hypocotyls,”
The Plant Journal, vol. 98, no. 6. Wiley, pp. 1048–1059, 2019.
ista: Rakusová H, Han H, Valošek P, Friml J. 2019. Genetic screen for factors mediating
PIN polarization in gravistimulated Arabidopsis thaliana hypocotyls. The Plant
Journal. 98(6), 1048–1059.
mla: Rakusová, Hana, et al. “Genetic Screen for Factors Mediating PIN Polarization
in Gravistimulated Arabidopsis Thaliana Hypocotyls.” The Plant Journal,
vol. 98, no. 6, Wiley, 2019, pp. 1048–59, doi:10.1111/tpj.14301.
short: H. Rakusová, H. Han, P. Valošek, J. Friml, The Plant Journal 98 (2019) 1048–1059.
date_created: 2019-04-09T08:46:44Z
date_published: 2019-06-01T00:00:00Z
date_updated: 2023-08-25T10:11:03Z
day: '01'
ddc:
- '580'
department:
- _id: JiFr
doi: 10.1111/tpj.14301
ec_funded: 1
external_id:
isi:
- '000473644100008'
pmid:
- '30821050'
file:
- access_level: open_access
checksum: ad3b5e270b67ba2a45f894ce3be27920
content_type: application/pdf
creator: dernst
date_created: 2019-04-15T09:38:43Z
date_updated: 2020-07-14T12:47:25Z
file_id: '6304'
file_name: 2019_PlantJournal_Rakusov.pdf
file_size: 1383100
relation: main_file
file_date_updated: 2020-07-14T12:47:25Z
has_accepted_license: '1'
intvolume: ' 98'
isi: 1
issue: '6'
language:
- iso: eng
month: '06'
oa: 1
oa_version: Published Version
page: 1048-1059
pmid: 1
project:
- _id: 25716A02-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '282300'
name: Polarity and subcellular dynamics in plants
publication: The Plant Journal
publication_identifier:
eissn:
- 1365-313x
issn:
- 0960-7412
publication_status: published
publisher: Wiley
quality_controlled: '1'
scopus_import: '1'
status: public
title: Genetic screen for factors mediating PIN polarization in gravistimulated Arabidopsis
thaliana hypocotyls
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: 98
year: '2019'
...
---
_id: '6297'
abstract:
- lang: eng
text: Cell-cell and cell-glycocalyx interactions under flow are important for the
behaviour of circulating cells in blood and lymphatic vessels. However, such interactions
are not well understood due in part to a lack of tools to study them in defined
environments. Here, we develop a versatile in vitro platform for the study of
cell-glycocalyx interactions in well-defined physical and chemical settings under
flow. Our approach is demonstrated with the interaction between hyaluronan (HA,
a key component of the endothelial glycocalyx) and its cell receptor CD44. We
generate HA brushes in situ within a microfluidic device, and demonstrate the
tuning of their physical (thickness and softness) and chemical (density of CD44
binding sites) properties using characterisation with reflection interference
contrast microscopy (RICM) and application of polymer theory. We highlight the
interactions of HA brushes with CD44-displaying beads and cells under flow. Observations
of CD44+ beads on a HA brush with RICM enabled the 3-dimensional trajectories
to be generated, and revealed interactions in the form of stop and go phases with
reduced rolling velocity and reduced distance between the bead and the HA brush,
compared to uncoated beads. Combined RICM and bright-field microscopy of CD44+
AKR1 T-lymphocytes revealed complementary information about the dynamics of cell
rolling and cell morphology, and highlighted the formation of tethers and slings,
as they interacted with a HA brush under flow. This platform can readily incorporate
more complex models of the glycocalyx, and should permit the study of how mechanical
and biochemical factors are orchestrated to enable highly selective blood cell-vessel
wall interactions under flow.
article_processing_charge: No
article_type: original
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. An integrated assay to probe endothelial
glycocalyx-blood cell interactions under flow in mechanically and biochemically
well-defined environments. Matrix Biology. 2019;78-79:47-59. doi:10.1016/j.matbio.2018.12.002
apa: Davies, H. S., Baranova, N. S., El Amri, N., Coche-Guérente, L., Verdier, C.,
Bureau, L., … Débarre, D. (2019). An integrated assay to probe endothelial glycocalyx-blood
cell interactions under flow in mechanically and biochemically well-defined environments.
Matrix Biology. Elsevier. https://doi.org/10.1016/j.matbio.2018.12.002
chicago: Davies, Heather S., Natalia S. Baranova, Nouha El Amri, Liliane Coche-Guérente,
Claude Verdier, Lionel Bureau, Ralf P. Richter, and Delphine Débarre. “An Integrated
Assay to Probe Endothelial Glycocalyx-Blood Cell Interactions under Flow in Mechanically
and Biochemically Well-Defined Environments.” Matrix Biology. Elsevier,
2019. https://doi.org/10.1016/j.matbio.2018.12.002.
ieee: H. S. Davies et al., “An integrated assay to probe endothelial glycocalyx-blood
cell interactions under flow in mechanically and biochemically well-defined environments,”
Matrix Biology, vol. 78–79. Elsevier, pp. 47–59, 2019.
ista: Davies HS, Baranova NS, El Amri N, Coche-Guérente L, Verdier C, Bureau L,
Richter RP, Débarre D. 2019. An integrated assay to probe endothelial glycocalyx-blood
cell interactions under flow in mechanically and biochemically well-defined environments.
Matrix Biology. 78–79, 47–59.
mla: Davies, Heather S., et al. “An Integrated Assay to Probe Endothelial Glycocalyx-Blood
Cell Interactions under Flow in Mechanically and Biochemically Well-Defined Environments.”
Matrix Biology, vol. 78–79, Elsevier, 2019, pp. 47–59, doi:10.1016/j.matbio.2018.12.002.
short: H.S. Davies, N.S. Baranova, N. El Amri, L. Coche-Guérente, C. Verdier, L.
Bureau, R.P. Richter, D. Débarre, Matrix Biology 78–79 (2019) 47–59.
date_created: 2019-04-11T20:55:01Z
date_published: 2019-05-01T00:00:00Z
date_updated: 2023-08-25T10:11:28Z
day: '01'
ddc:
- '570'
department:
- _id: MaLo
doi: 10.1016/j.matbio.2018.12.002
external_id:
isi:
- '000468707600005'
file:
- access_level: open_access
checksum: 790878cd78bfc54a147ddcc7c8f286a0
content_type: application/pdf
creator: dernst
date_created: 2020-05-14T09:02:07Z
date_updated: 2020-07-14T12:47:27Z
file_id: '7825'
file_name: 2018_MatrixBiology_Davies.pdf
file_size: 4444339
relation: main_file
file_date_updated: 2020-07-14T12:47:27Z
has_accepted_license: '1'
isi: 1
language:
- iso: eng
license: https://creativecommons.org/licenses/by-nc-nd/4.0/
month: '05'
oa: 1
oa_version: Submitted Version
page: 47-59
publication: Matrix Biology
publication_identifier:
issn:
- 0945-053X
publication_status: published
publisher: Elsevier
quality_controlled: '1'
status: public
title: An integrated assay to probe endothelial glycocalyx-blood cell interactions
under flow in mechanically and biochemically well-defined environments
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: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
volume: 78-79
year: '2019'
...
---
_id: '6310'
abstract:
- lang: eng
text: An asymptotic formula is established for the number of rational points of
bounded anticanonical height which lie on a certain Zariskiopen subset of an arbitrary
smooth biquadratic hypersurface in sufficiently many variables. The proof uses
the Hardy–Littlewood circle method.
article_processing_charge: No
author:
- first_name: Timothy D
full_name: Browning, Timothy D
id: 35827D50-F248-11E8-B48F-1D18A9856A87
last_name: Browning
orcid: 0000-0002-8314-0177
- first_name: L.Q.
full_name: Hu, L.Q.
last_name: Hu
citation:
ama: Browning TD, Hu LQ. Counting rational points on biquadratic hypersurfaces.
Advances in Mathematics. 2019;349:920-940. doi:10.1016/j.aim.2019.04.031
apa: Browning, T. D., & Hu, L. Q. (2019). Counting rational points on biquadratic
hypersurfaces. Advances in Mathematics. Elsevier. https://doi.org/10.1016/j.aim.2019.04.031
chicago: Browning, Timothy D, and L.Q. Hu. “Counting Rational Points on Biquadratic
Hypersurfaces.” Advances in Mathematics. Elsevier, 2019. https://doi.org/10.1016/j.aim.2019.04.031.
ieee: T. D. Browning and L. Q. Hu, “Counting rational points on biquadratic hypersurfaces,”
Advances in Mathematics, vol. 349. Elsevier, pp. 920–940, 2019.
ista: Browning TD, Hu LQ. 2019. Counting rational points on biquadratic hypersurfaces.
Advances in Mathematics. 349, 920–940.
mla: Browning, Timothy D., and L. Q. Hu. “Counting Rational Points on Biquadratic
Hypersurfaces.” Advances in Mathematics, vol. 349, Elsevier, 2019, pp.
920–40, doi:10.1016/j.aim.2019.04.031.
short: T.D. Browning, L.Q. Hu, Advances in Mathematics 349 (2019) 920–940.
date_created: 2019-04-16T09:13:25Z
date_published: 2019-06-20T00:00:00Z
date_updated: 2023-08-25T10:11:55Z
day: '20'
ddc:
- '512'
department:
- _id: TiBr
doi: 10.1016/j.aim.2019.04.031
external_id:
arxiv:
- '1810.08426'
isi:
- '000468857300025'
file:
- access_level: open_access
checksum: a63594a3a91b4ba6e2a1b78b0720b3d0
content_type: application/pdf
creator: tbrownin
date_created: 2019-04-16T09:12:20Z
date_updated: 2020-07-14T12:47:27Z
file_id: '6311'
file_name: wliqun.pdf
file_size: 379158
relation: main_file
file_date_updated: 2020-07-14T12:47:27Z
has_accepted_license: '1'
intvolume: ' 349'
isi: 1
language:
- iso: eng
month: '06'
oa: 1
oa_version: Submitted Version
page: 920-940
publication: Advances in Mathematics
publication_identifier:
eissn:
- '10902082'
issn:
- '00018708'
publication_status: published
publisher: Elsevier
quality_controlled: '1'
scopus_import: '1'
status: public
title: Counting rational points on biquadratic hypersurfaces
type: journal_article
user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
volume: 349
year: '2019'
...
---
_id: '6261'
abstract:
- lang: eng
text: Nitrate regulation of root stem cell activity is auxin-dependent.
article_processing_charge: No
article_type: letter_note
author:
- first_name: Y
full_name: Wang, Y
last_name: Wang
- first_name: Z
full_name: Gong, Z
last_name: Gong
- first_name: Jiří
full_name: Friml, Jiří
id: 4159519E-F248-11E8-B48F-1D18A9856A87
last_name: Friml
orcid: 0000-0002-8302-7596
- first_name: J
full_name: Zhang, J
last_name: Zhang
citation:
ama: Wang Y, Gong Z, Friml J, Zhang J. Nitrate modulates the differentiation of
root distal stem cells. Plant Physiology. 2019;180(1):22-25. doi:10.1104/pp.18.01305
apa: Wang, Y., Gong, Z., Friml, J., & Zhang, J. (2019). Nitrate modulates the
differentiation of root distal stem cells. Plant Physiology. ASPB. https://doi.org/10.1104/pp.18.01305
chicago: Wang, Y, Z Gong, Jiří Friml, and J Zhang. “Nitrate Modulates the Differentiation
of Root Distal Stem Cells.” Plant Physiology. ASPB, 2019. https://doi.org/10.1104/pp.18.01305.
ieee: Y. Wang, Z. Gong, J. Friml, and J. Zhang, “Nitrate modulates the differentiation
of root distal stem cells,” Plant Physiology, vol. 180, no. 1. ASPB, pp.
22–25, 2019.
ista: Wang Y, Gong Z, Friml J, Zhang J. 2019. Nitrate modulates the differentiation
of root distal stem cells. Plant Physiology. 180(1), 22–25.
mla: Wang, Y., et al. “Nitrate Modulates the Differentiation of Root Distal Stem
Cells.” Plant Physiology, vol. 180, no. 1, ASPB, 2019, pp. 22–25, doi:10.1104/pp.18.01305.
short: Y. Wang, Z. Gong, J. Friml, J. Zhang, Plant Physiology 180 (2019) 22–25.
date_created: 2019-04-09T08:46:17Z
date_published: 2019-05-01T00:00:00Z
date_updated: 2023-08-25T10:10:23Z
day: '01'
department:
- _id: JiFr
doi: 10.1104/pp.18.01305
external_id:
isi:
- '000466860800010'
pmid:
- '30787134'
intvolume: ' 180'
isi: 1
issue: '1'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.1104/pp.18.01305
month: '05'
oa: 1
oa_version: Published Version
page: 22-25
pmid: 1
publication: Plant Physiology
publication_identifier:
eissn:
- 1532-2548
issn:
- 0032-0889
publication_status: published
publisher: ASPB
quality_controlled: '1'
scopus_import: '1'
status: public
title: Nitrate modulates the differentiation of root distal stem cells
type: journal_article
user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
volume: 180
year: '2019'
...
---
_id: '6352'
abstract:
- lang: eng
text: Chronic overuse of common pharmaceuticals, e.g. acetaminophen (paracetamol),
often leads to the development of acute liver failure (ALF). This study aimed
to elucidate the effect of cultured mesenchymal stem cells (MSCs) proteome on
the onset of liver damage and regeneration dynamics in animals with ALF induced
by acetaminophen, to test the liver protective efficacy of MSCs proteome depending
on the oxygen tension in cell culture, and to blueprint protein components responsible
for the effect. Protein compositions prepared from MSCs cultured in mild hypoxic
(5% and 10% O2) and normal (21% O2) conditions were used to treat ALF induced
in mice by injection of acetaminophen. To test the effect of reduced oxygen tension
in cell culture on resulting MSCs proteome content we applied a combination of
high performance liquid chromatography and mass-spectrometry (LC–MS/MS) for the
identification of proteins in lysates of MSCs cultured at different O2 levels.
The treatment of acetaminophen-administered animals with proteins released from
cultured MSCs resulted in the inhibition of inflammatory reactions in damaged
liver; the area of hepatocyte necrosis being reduced in the first 24 h. Compositions
obtained from MSCs cultured at lower O2 level were shown to be more potent than
a composition prepared from normoxic cells. A comparative characterization of
protein pattern and identification of individual components done by a cytokine
assay and proteomics analysis of protein compositions revealed that even moderate
hypoxia produces discrete changes in the expression of various subsets of proteins
responsible for intracellular respiration and cell signaling. The application
of proteins prepared from MSCs grown in vitro at reduced oxygen tension significantly
accelerates healing process in damaged liver tissue. The proteomics data obtained
for different preparations offer new information about the potential candidates
in the MSCs protein repertoire sensitive to oxygen tension in culture medium,
which can be involved in the generalized mechanisms the cells use to respond to
acute liver failure.
acknowledgement: The studies were supported by the Austrian Federal Ministry of Economy,
Family and Youth through the initiative “Laura Bassi Centres of Expertise” funding
the Center of Optimized Structural Stud-ies, grant No. 253275
article_processing_charge: Yes (via OA deal)
author:
- first_name: Andrey Alexandrovich
full_name: Temnov, Andrey Alexandrovich
last_name: Temnov
- first_name: Konstantin Arkadevich
full_name: Rogov, Konstantin Arkadevich
last_name: Rogov
- first_name: Alla Nikolaevna
full_name: Sklifas, Alla Nikolaevna
last_name: Sklifas
- first_name: Elena Valerievna
full_name: Klychnikova, Elena Valerievna
last_name: Klychnikova
- first_name: Markus
full_name: Hartl, Markus
last_name: Hartl
- first_name: Kristina
full_name: Djinovic-Carugo, Kristina
last_name: Djinovic-Carugo
- first_name: Alexej
full_name: Charnagalov, Alexej
id: 49F06DBA-F248-11E8-B48F-1D18A9856A87
last_name: Charnagalov
citation:
ama: Temnov AA, Rogov KA, Sklifas AN, et al. Protective properties of the cultured
stem cell proteome studied in an animal model of acetaminophen-induced acute liver
failure. Molecular Biology Reports. 2019. doi:10.1007/s11033-019-04765-z
apa: Temnov, A. A., Rogov, K. A., Sklifas, A. N., Klychnikova, E. V., Hartl, M.,
Djinovic-Carugo, K., & Charnagalov, A. (2019). Protective properties of the
cultured stem cell proteome studied in an animal model of acetaminophen-induced
acute liver failure. Molecular Biology Reports. Springer. https://doi.org/10.1007/s11033-019-04765-z
chicago: Temnov, Andrey Alexandrovich, Konstantin Arkadevich Rogov, Alla Nikolaevna
Sklifas, Elena Valerievna Klychnikova, Markus Hartl, Kristina Djinovic-Carugo,
and Alexej Charnagalov. “Protective Properties of the Cultured Stem Cell Proteome
Studied in an Animal Model of Acetaminophen-Induced Acute Liver Failure.” Molecular
Biology Reports. Springer, 2019. https://doi.org/10.1007/s11033-019-04765-z.
ieee: A. A. Temnov et al., “Protective properties of the cultured stem cell
proteome studied in an animal model of acetaminophen-induced acute liver failure,”
Molecular Biology Reports. Springer, 2019.
ista: Temnov AA, Rogov KA, Sklifas AN, Klychnikova EV, Hartl M, Djinovic-Carugo
K, Charnagalov A. 2019. Protective properties of the cultured stem cell proteome
studied in an animal model of acetaminophen-induced acute liver failure. Molecular
Biology Reports.
mla: Temnov, Andrey Alexandrovich, et al. “Protective Properties of the Cultured
Stem Cell Proteome Studied in an Animal Model of Acetaminophen-Induced Acute Liver
Failure.” Molecular Biology Reports, Springer, 2019, doi:10.1007/s11033-019-04765-z.
short: A.A. Temnov, K.A. Rogov, A.N. Sklifas, E.V. Klychnikova, M. Hartl, K. Djinovic-Carugo,
A. Charnagalov, Molecular Biology Reports (2019).
date_created: 2019-04-28T21:59:14Z
date_published: 2019-04-12T00:00:00Z
date_updated: 2023-08-25T10:14:26Z
day: '12'
ddc:
- '570'
department:
- _id: LeSa
doi: 10.1007/s11033-019-04765-z
external_id:
isi:
- '000470332600049'
file:
- access_level: open_access
checksum: 45bf040bbce1cea274f6013fa18ba21b
content_type: application/pdf
creator: dernst
date_created: 2019-04-30T09:52:36Z
date_updated: 2020-07-14T12:47:28Z
file_id: '6362'
file_name: 2019_MolecularBioReport_Temnov.pdf
file_size: 1948014
relation: main_file
file_date_updated: 2020-07-14T12:47:28Z
has_accepted_license: '1'
isi: 1
language:
- iso: eng
month: '04'
oa: 1
oa_version: Published Version
publication: Molecular Biology Reports
publication_identifier:
eissn:
- '15734978'
issn:
- '03014851'
publication_status: published
publisher: Springer
quality_controlled: '1'
scopus_import: '1'
status: public
title: Protective properties of the cultured stem cell proteome studied in an animal
model of acetaminophen-induced acute liver failure
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
year: '2019'
...
---
_id: '6348'
abstract:
- lang: eng
text: 'High-speed optical telecommunication is enabled by wavelength-division multiplexing,
whereby hundreds of individually stabilized lasers encode information within a
single-mode optical fibre. Higher bandwidths require higher total optical power,
but the power sent into the fibre is limited by optical nonlinearities within
the fibre, and energy consumption by the light sources starts to become a substantial
cost factor1. Optical frequency combs have been suggested to remedy this problem
by generating numerous discrete, equidistant laser lines within a monolithic device;
however, at present their stability and coherence allow them to operate only within
small parameter ranges2,3,4. Here we show that a broadband frequency comb realized
through the electro-optic effect within a high-quality whispering-gallery-mode
resonator can operate at low microwave and optical powers. Unlike the usual third-order
Kerr nonlinear optical frequency combs, our combs rely on the second-order nonlinear
effect, which is much more efficient. Our result uses a fixed microwave signal
that is mixed with an optical-pump signal to generate a coherent frequency comb
with a precisely determined carrier separation. The resonant enhancement enables
us to work with microwave powers that are three orders of magnitude lower than
those in commercially available devices. We emphasize the practical relevance
of our results to high rates of data communication. To circumvent the limitations
imposed by nonlinear effects in optical communication fibres, one has to solve
two problems: to provide a compact and fully integrated, yet high-quality and
coherent, frequency comb generator; and to calculate nonlinear signal propagation
in real time5. We report a solution to the first problem.'
article_processing_charge: No
author:
- first_name: Alfredo R
full_name: Rueda Sanchez, Alfredo R
id: 3B82B0F8-F248-11E8-B48F-1D18A9856A87
last_name: Rueda Sanchez
orcid: 0000-0001-6249-5860
- first_name: Florian
full_name: Sedlmeir, Florian
last_name: Sedlmeir
- first_name: Madhuri
full_name: Kumari, Madhuri
last_name: Kumari
- first_name: Gerd
full_name: Leuchs, Gerd
last_name: Leuchs
- first_name: Harald G.L.
full_name: Schwefel, Harald G.L.
last_name: Schwefel
citation:
ama: Rueda Sanchez AR, Sedlmeir F, Kumari M, Leuchs G, Schwefel HGL. Resonant electro-optic
frequency comb. Nature. 2019;568(7752):378-381. doi:10.1038/s41586-019-1110-x
apa: Rueda Sanchez, A. R., Sedlmeir, F., Kumari, M., Leuchs, G., & Schwefel,
H. G. L. (2019). Resonant electro-optic frequency comb. Nature. Springer
Nature. https://doi.org/10.1038/s41586-019-1110-x
chicago: Rueda Sanchez, Alfredo R, Florian Sedlmeir, Madhuri Kumari, Gerd Leuchs,
and Harald G.L. Schwefel. “Resonant Electro-Optic Frequency Comb.” Nature.
Springer Nature, 2019. https://doi.org/10.1038/s41586-019-1110-x.
ieee: A. R. Rueda Sanchez, F. Sedlmeir, M. Kumari, G. Leuchs, and H. G. L. Schwefel,
“Resonant electro-optic frequency comb,” Nature, vol. 568, no. 7752. Springer
Nature, pp. 378–381, 2019.
ista: Rueda Sanchez AR, Sedlmeir F, Kumari M, Leuchs G, Schwefel HGL. 2019. Resonant
electro-optic frequency comb. Nature. 568(7752), 378–381.
mla: Rueda Sanchez, Alfredo R., et al. “Resonant Electro-Optic Frequency Comb.”
Nature, vol. 568, no. 7752, Springer Nature, 2019, pp. 378–81, doi:10.1038/s41586-019-1110-x.
short: A.R. Rueda Sanchez, F. Sedlmeir, M. Kumari, G. Leuchs, H.G.L. Schwefel, Nature
568 (2019) 378–381.
date_created: 2019-04-28T21:59:13Z
date_published: 2019-04-18T00:00:00Z
date_updated: 2023-08-25T10:15:25Z
day: '18'
department:
- _id: JoFi
doi: 10.1038/s41586-019-1110-x
external_id:
arxiv:
- '1808.10608'
isi:
- '000464950700053'
intvolume: ' 568'
isi: 1
issue: '7752'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/1808.10608
month: '04'
oa: 1
oa_version: Preprint
page: 378-381
publication: Nature
publication_identifier:
eissn:
- '14764687'
issn:
- '00280836'
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
related_material:
link:
- relation: erratum
url: https://doi.org/10.1038/s41586-019-1220-5
scopus_import: '1'
status: public
title: Resonant electro-optic frequency comb
type: journal_article
user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
volume: 568
year: '2019'
...
---
_id: '6338'
abstract:
- lang: eng
text: Hippocampal activity patterns representing movement trajectories are reactivated
in immobility and sleep periods, a process associated with memory recall, consolidation,
and decision making. It is thought that only fixed, behaviorally relevant patterns
can be reactivated, which are stored across hippocampal synaptic connections.
To test whether some generalized rules govern reactivation, we examined trajectory
reactivation following non-stereotypical exploration of familiar open-field environments.
We found that random trajectories of varying lengths and timescales were reactivated,
resembling that of Brownian motion of particles. The animals’ behavioral trajectory
did not follow Brownian diffusion demonstrating that the exact behavioral experience
is not reactivated. Therefore, hippocampal circuits are able to generate random
trajectories of any recently active map by following diffusion dynamics. This
ability of hippocampal circuits to generate representations of all behavioral
outcome combinations, experienced or not, may underlie a wide variety of hippocampal-dependent
cognitive functions such as learning, generalization, and planning.
article_processing_charge: No
article_type: original
author:
- first_name: Federico
full_name: Stella, Federico
id: 39AF1E74-F248-11E8-B48F-1D18A9856A87
last_name: Stella
orcid: 0000-0001-9439-3148
- first_name: Peter
full_name: Baracskay, Peter
id: 361CC00E-F248-11E8-B48F-1D18A9856A87
last_name: Baracskay
- first_name: Joseph
full_name: O'Neill, Joseph
id: 426376DC-F248-11E8-B48F-1D18A9856A87
last_name: O'Neill
- first_name: Jozsef L
full_name: Csicsvari, Jozsef L
id: 3FA14672-F248-11E8-B48F-1D18A9856A87
last_name: Csicsvari
orcid: 0000-0002-5193-4036
citation:
ama: Stella F, Baracskay P, O’Neill J, Csicsvari JL. Hippocampal reactivation of
random trajectories resembling Brownian diffusion. Neuron. 2019;102:450-461.
doi:10.1016/j.neuron.2019.01.052
apa: Stella, F., Baracskay, P., O’Neill, J., & Csicsvari, J. L. (2019). Hippocampal
reactivation of random trajectories resembling Brownian diffusion. Neuron.
Elsevier. https://doi.org/10.1016/j.neuron.2019.01.052
chicago: Stella, Federico, Peter Baracskay, Joseph O’Neill, and Jozsef L Csicsvari.
“Hippocampal Reactivation of Random Trajectories Resembling Brownian Diffusion.”
Neuron. Elsevier, 2019. https://doi.org/10.1016/j.neuron.2019.01.052.
ieee: F. Stella, P. Baracskay, J. O’Neill, and J. L. Csicsvari, “Hippocampal reactivation
of random trajectories resembling Brownian diffusion,” Neuron, vol. 102.
Elsevier, pp. 450–461, 2019.
ista: Stella F, Baracskay P, O’Neill J, Csicsvari JL. 2019. Hippocampal reactivation
of random trajectories resembling Brownian diffusion. Neuron. 102, 450–461.
mla: Stella, Federico, et al. “Hippocampal Reactivation of Random Trajectories Resembling
Brownian Diffusion.” Neuron, vol. 102, Elsevier, 2019, pp. 450–61, doi:10.1016/j.neuron.2019.01.052.
short: F. Stella, P. Baracskay, J. O’Neill, J.L. Csicsvari, Neuron 102 (2019) 450–461.
date_created: 2019-04-17T08:28:59Z
date_published: 2019-04-17T00:00:00Z
date_updated: 2023-08-25T10:13:07Z
day: '17'
department:
- _id: JoCs
doi: 10.1016/j.neuron.2019.01.052
ec_funded: 1
external_id:
isi:
- '000465169700017'
pmid:
- '30819547'
intvolume: ' 102'
isi: 1
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.1016/j.neuron.2019.01.052
month: '04'
oa: 1
oa_version: Published Version
page: 450-461
pmid: 1
project:
- _id: 257A4776-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '281511'
name: Memory-related information processing in neuronal circuits of the hippocampus
and entorhinal cortex
- _id: 2654F984-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: I03713
name: Interneuro Plasticity During Spatial Learning
publication: Neuron
publication_status: published
publisher: Elsevier
quality_controlled: '1'
related_material:
link:
- description: News on IST Homepage
relation: press_release
url: https://ist.ac.at/en/news/memories-of-movement-are-replayed-randomly-during-sleep/
scopus_import: '1'
status: public
title: Hippocampal reactivation of random trajectories resembling Brownian diffusion
type: journal_article
user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
volume: 102
year: '2019'
...
---
_id: '5878'
abstract:
- lang: eng
text: We consider the motion of a droplet bouncing on a vibrating bath of the same
fluid in the presence of a central potential. We formulate a rotation symmetry-reduced
description of this system, which allows for the straightforward application of
dynamical systems theory tools. As an illustration of the utility of the symmetry
reduction, we apply it to a model of the pilot-wave system with a central harmonic
force. We begin our analysis by identifying local bifurcations and the onset of
chaos. We then describe the emergence of chaotic regions and their merging bifurcations,
which lead to the formation of a global attractor. In this final regime, the droplet’s
angular momentum spontaneously changes its sign as observed in the experiments
of Perrard et al.
article_number: '013122'
article_processing_charge: No
article_type: original
author:
- first_name: Nazmi B
full_name: Budanur, Nazmi B
id: 3EA1010E-F248-11E8-B48F-1D18A9856A87
last_name: Budanur
orcid: 0000-0003-0423-5010
- first_name: Marc
full_name: Fleury, Marc
last_name: Fleury
citation:
ama: 'Budanur NB, Fleury M. State space geometry of the chaotic pilot-wave hydrodynamics.
Chaos: An Interdisciplinary Journal of Nonlinear Science. 2019;29(1). doi:10.1063/1.5058279'
apa: 'Budanur, N. B., & Fleury, M. (2019). State space geometry of the chaotic
pilot-wave hydrodynamics. Chaos: An Interdisciplinary Journal of Nonlinear
Science. AIP Publishing. https://doi.org/10.1063/1.5058279'
chicago: 'Budanur, Nazmi B, and Marc Fleury. “State Space Geometry of the Chaotic
Pilot-Wave Hydrodynamics.” Chaos: An Interdisciplinary Journal of Nonlinear
Science. AIP Publishing, 2019. https://doi.org/10.1063/1.5058279.'
ieee: 'N. B. Budanur and M. Fleury, “State space geometry of the chaotic pilot-wave
hydrodynamics,” Chaos: An Interdisciplinary Journal of Nonlinear Science,
vol. 29, no. 1. AIP Publishing, 2019.'
ista: 'Budanur NB, Fleury M. 2019. State space geometry of the chaotic pilot-wave
hydrodynamics. Chaos: An Interdisciplinary Journal of Nonlinear Science. 29(1),
013122.'
mla: 'Budanur, Nazmi B., and Marc Fleury. “State Space Geometry of the Chaotic Pilot-Wave
Hydrodynamics.” Chaos: An Interdisciplinary Journal of Nonlinear Science,
vol. 29, no. 1, 013122, AIP Publishing, 2019, doi:10.1063/1.5058279.'
short: 'N.B. Budanur, M. Fleury, Chaos: An Interdisciplinary Journal of Nonlinear
Science 29 (2019).'
date_created: 2019-01-23T08:35:09Z
date_published: 2019-01-22T00:00:00Z
date_updated: 2023-08-25T10:16:11Z
day: '22'
department:
- _id: BjHo
doi: 10.1063/1.5058279
external_id:
arxiv:
- '1812.09011'
isi:
- '000457409100028'
intvolume: ' 29'
isi: 1
issue: '1'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/1812.09011
month: '01'
oa: 1
oa_version: Preprint
publication: 'Chaos: An Interdisciplinary Journal of Nonlinear Science'
publication_identifier:
eissn:
- 1089-7682
issn:
- 1054-1500
publication_status: published
publisher: AIP Publishing
quality_controlled: '1'
related_material:
link:
- relation: erratum
url: https://aip.scitation.org/doi/abs/10.1063/1.5097157
scopus_import: '1'
status: public
title: State space geometry of the chaotic pilot-wave hydrodynamics
type: journal_article
user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
volume: 29
year: '2019'
...
---
_id: '6343'
abstract:
- lang: eng
text: Cryo-electron tomography (cryo-ET) provides unprecedented insights into the
molecular constituents of biological environments. In combination with an image
processing method called subtomogram averaging (STA), detailed 3D structures of
biological molecules can be obtained in large, irregular macromolecular assemblies
or in situ, without the need for purification. The contextual meta-information
these methods also provide, such as a protein’s location within its native environment,
can then be combined with functional data. This allows the derivation of a detailed
view on the physiological or pathological roles of proteins from the molecular
to cellular level. Despite their tremendous potential in in situ structural biology,
cryo-ET and STA have been restricted by methodological limitations, such as the
low obtainable resolution. Exciting progress now allows one to reach unprecedented
resolutions in situ, ranging in optimal cases beyond the nanometer barrier. Here,
I review current frontiers and future challenges in routinely determining high-resolution
structures in in situ environments using cryo-ET and STA.
acknowledgement: The author acknowledges support from IST Austria and the Austrian
Science Fund (FWF).
article_processing_charge: No
article_type: original
author:
- first_name: Florian KM
full_name: Schur, Florian KM
id: 48AD8942-F248-11E8-B48F-1D18A9856A87
last_name: Schur
orcid: 0000-0003-4790-8078
citation:
ama: Schur FK. Toward high-resolution in situ structural biology with cryo-electron
tomography and subtomogram averaging. Current Opinion in Structural Biology.
2019;58(10):1-9. doi:10.1016/j.sbi.2019.03.018
apa: Schur, F. K. (2019). Toward high-resolution in situ structural biology with
cryo-electron tomography and subtomogram averaging. Current Opinion in Structural
Biology. Elsevier. https://doi.org/10.1016/j.sbi.2019.03.018
chicago: Schur, Florian KM. “Toward High-Resolution in Situ Structural Biology with
Cryo-Electron Tomography and Subtomogram Averaging.” Current Opinion in Structural
Biology. Elsevier, 2019. https://doi.org/10.1016/j.sbi.2019.03.018.
ieee: F. K. Schur, “Toward high-resolution in situ structural biology with cryo-electron
tomography and subtomogram averaging,” Current Opinion in Structural Biology,
vol. 58, no. 10. Elsevier, pp. 1–9, 2019.
ista: Schur FK. 2019. Toward high-resolution in situ structural biology with cryo-electron
tomography and subtomogram averaging. Current Opinion in Structural Biology. 58(10),
1–9.
mla: Schur, Florian KM. “Toward High-Resolution in Situ Structural Biology with
Cryo-Electron Tomography and Subtomogram Averaging.” Current Opinion in Structural
Biology, vol. 58, no. 10, Elsevier, 2019, pp. 1–9, doi:10.1016/j.sbi.2019.03.018.
short: F.K. Schur, Current Opinion in Structural Biology 58 (2019) 1–9.
date_created: 2019-04-19T11:19:13Z
date_published: 2019-10-01T00:00:00Z
date_updated: 2023-08-25T10:13:31Z
day: '01'
department:
- _id: FlSc
doi: 10.1016/j.sbi.2019.03.018
external_id:
isi:
- '000494891800004'
intvolume: ' 58'
isi: 1
issue: '10'
language:
- iso: eng
month: '10'
oa_version: None
page: 1-9
publication: Current Opinion in Structural Biology
publication_identifier:
issn:
- 0959-440X
publication_status: published
publisher: Elsevier
quality_controlled: '1'
scopus_import: '1'
status: public
title: Toward high-resolution in situ structural biology with cryo-electron tomography
and subtomogram averaging
type: journal_article
user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
volume: 58
year: '2019'
...
---
_id: '6428'
abstract:
- lang: eng
text: 'Safety and security are major concerns in the development of Cyber-Physical
Systems (CPS). Signal temporal logic (STL) was proposedas a language to specify
and monitor the correctness of CPS relativeto formalized requirements. Incorporating
STL into a developmentprocess enables designers to automatically monitor and diagnosetraces,
compute robustness estimates based on requirements, andperform requirement falsification,
leading to productivity gains inverification and validation activities; however,
in its current formSTL is agnostic to the input/output classification of signals,
andthis negatively impacts the relevance of the analysis results.In this paper
we propose to make the interface explicit in theSTL language by introducing input/output
signal declarations. Wethen define new measures of input vacuity and output robustnessthat
better reflect the nature of the system and the specification in-tent. The resulting
framework, which we call interface-aware signaltemporal logic (IA-STL), aids verification
and validation activities.We demonstrate the benefits of IA-STL on several CPS
analysisactivities: (1) robustness-driven sensitivity analysis, (2) falsificationand
(3) fault localization. We describe an implementation of our en-hancement to STL
and associated notions of robustness and vacuityin a prototype extension of Breach,
a MATLAB®/Simulink®toolboxfor CPS verification and validation. We explore these
methodologi-cal improvements and evaluate our results on two examples fromthe
automotive domain: a benchmark powertrain control systemand a hydrogen fuel cell
system.'
article_processing_charge: No
author:
- first_name: Thomas
full_name: Ferrere, Thomas
id: 40960E6E-F248-11E8-B48F-1D18A9856A87
last_name: Ferrere
orcid: 0000-0001-5199-3143
- first_name: Dejan
full_name: Nickovic, Dejan
id: 41BCEE5C-F248-11E8-B48F-1D18A9856A87
last_name: Nickovic
- first_name: Alexandre
full_name: Donzé, Alexandre
last_name: Donzé
- first_name: Hisahiro
full_name: Ito, Hisahiro
last_name: Ito
- first_name: James
full_name: Kapinski, James
last_name: Kapinski
citation:
ama: 'Ferrere T, Nickovic D, Donzé A, Ito H, Kapinski J. Interface-aware signal
temporal logic. In: Proceedings of the 2019 22nd ACM International Conference
on Hybrid Systems: Computation and Control. ACM; 2019:57-66. doi:10.1145/3302504.3311800'
apa: 'Ferrere, T., Nickovic, D., Donzé, A., Ito, H., & Kapinski, J. (2019).
Interface-aware signal temporal logic. In Proceedings of the 2019 22nd ACM
International Conference on Hybrid Systems: Computation and Control (pp. 57–66).
Montreal, Canada: ACM. https://doi.org/10.1145/3302504.3311800'
chicago: 'Ferrere, Thomas, Dejan Nickovic, Alexandre Donzé, Hisahiro Ito, and James
Kapinski. “Interface-Aware Signal Temporal Logic.” In Proceedings of the 2019
22nd ACM International Conference on Hybrid Systems: Computation and Control,
57–66. ACM, 2019. https://doi.org/10.1145/3302504.3311800.'
ieee: 'T. Ferrere, D. Nickovic, A. Donzé, H. Ito, and J. Kapinski, “Interface-aware
signal temporal logic,” in Proceedings of the 2019 22nd ACM International Conference
on Hybrid Systems: Computation and Control, Montreal, Canada, 2019, pp. 57–66.'
ista: 'Ferrere T, Nickovic D, Donzé A, Ito H, Kapinski J. 2019. Interface-aware
signal temporal logic. Proceedings of the 2019 22nd ACM International Conference
on Hybrid Systems: Computation and Control. HSCC: Hybrid Systems Computation and
Control, 57–66.'
mla: 'Ferrere, Thomas, et al. “Interface-Aware Signal Temporal Logic.” Proceedings
of the 2019 22nd ACM International Conference on Hybrid Systems: Computation and
Control, ACM, 2019, pp. 57–66, doi:10.1145/3302504.3311800.'
short: 'T. Ferrere, D. Nickovic, A. Donzé, H. Ito, J. Kapinski, in:, Proceedings
of the 2019 22nd ACM International Conference on Hybrid Systems: Computation and
Control, ACM, 2019, pp. 57–66.'
conference:
end_date: 2019-04-18
location: Montreal, Canada
name: 'HSCC: Hybrid Systems Computation and Control'
start_date: 2019-04-16
date_created: 2019-05-13T08:13:46Z
date_published: 2019-04-16T00:00:00Z
date_updated: 2023-08-25T10:19:23Z
day: '16'
ddc:
- '000'
department:
- _id: ToHe
doi: 10.1145/3302504.3311800
external_id:
isi:
- '000516713900007'
file:
- access_level: open_access
checksum: b8e967081e051d1c55ca5d18fb187890
content_type: application/pdf
creator: dernst
date_created: 2020-10-08T17:25:45Z
date_updated: 2020-10-08T17:25:45Z
file_id: '8633'
file_name: 2019_ACM_Ferrere.pdf
file_size: 1055421
relation: main_file
success: 1
file_date_updated: 2020-10-08T17:25:45Z
has_accepted_license: '1'
isi: 1
language:
- iso: eng
month: '04'
oa: 1
oa_version: Submitted Version
page: 57-66
project:
- _id: 25832EC2-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: S 11407_N23
name: Rigorous Systems Engineering
- _id: 25F42A32-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: Z211
name: The Wittgenstein Prize
publication: 'Proceedings of the 2019 22nd ACM International Conference on Hybrid
Systems: Computation and Control'
publication_identifier:
isbn:
- '9781450362825'
publication_status: published
publisher: ACM
quality_controlled: '1'
scopus_import: '1'
status: public
title: Interface-aware signal temporal logic
type: conference
user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
year: '2019'
...
---
_id: '6442'
abstract:
- lang: eng
text: This paper investigates the use of fundamental solutions for animating detailed
linear water surface waves. We first propose an analytical solution for efficiently
animating circular ripples in closed form. We then show how to adapt the method
of fundamental solutions (MFS) to create ambient waves interacting with complex
obstacles. Subsequently, we present a novel wavelet-based discretization which
outperforms the state of the art MFS approach for simulating time-varying water
surface waves with moving obstacles. Our results feature high-resolution spatial
details, interactions with complex boundaries, and large open ocean domains. Our
method compares favorably with previous work as well as known analytical solutions.
We also present comparisons between our method and real world examples.
acknowledged_ssus:
- _id: ScienComp
article_number: '130'
article_processing_charge: No
author:
- first_name: Camille
full_name: Schreck, Camille
id: 2B14B676-F248-11E8-B48F-1D18A9856A87
last_name: Schreck
- first_name: Christian
full_name: Hafner, Christian
id: 400429CC-F248-11E8-B48F-1D18A9856A87
last_name: Hafner
- first_name: Christopher J
full_name: Wojtan, Christopher J
id: 3C61F1D2-F248-11E8-B48F-1D18A9856A87
last_name: Wojtan
orcid: 0000-0001-6646-5546
citation:
ama: Schreck C, Hafner C, Wojtan C. Fundamental solutions for water wave animation.
ACM Transactions on Graphics. 2019;38(4). doi:10.1145/3306346.3323002
apa: Schreck, C., Hafner, C., & Wojtan, C. (2019). Fundamental solutions for
water wave animation. ACM Transactions on Graphics. ACM. https://doi.org/10.1145/3306346.3323002
chicago: Schreck, Camille, Christian Hafner, and Chris Wojtan. “Fundamental Solutions
for Water Wave Animation.” ACM Transactions on Graphics. ACM, 2019. https://doi.org/10.1145/3306346.3323002.
ieee: C. Schreck, C. Hafner, and C. Wojtan, “Fundamental solutions for water wave
animation,” ACM Transactions on Graphics, vol. 38, no. 4. ACM, 2019.
ista: Schreck C, Hafner C, Wojtan C. 2019. Fundamental solutions for water wave
animation. ACM Transactions on Graphics. 38(4), 130.
mla: Schreck, Camille, et al. “Fundamental Solutions for Water Wave Animation.”
ACM Transactions on Graphics, vol. 38, no. 4, 130, ACM, 2019, doi:10.1145/3306346.3323002.
short: C. Schreck, C. Hafner, C. Wojtan, ACM Transactions on Graphics 38 (2019).
date_created: 2019-05-14T07:04:06Z
date_published: 2019-07-01T00:00:00Z
date_updated: 2023-08-25T10:18:46Z
day: '01'
ddc:
- '000'
- '005'
department:
- _id: ChWo
doi: 10.1145/3306346.3323002
ec_funded: 1
external_id:
isi:
- '000475740600104'
file:
- access_level: open_access
checksum: 1b737dfe3e051aba8f3f4ab1dceda673
content_type: application/pdf
creator: dernst
date_created: 2019-05-14T07:03:55Z
date_updated: 2020-07-14T12:47:30Z
file_id: '6443'
file_name: 2019_ACM_Schreck.pdf
file_size: 44328918
relation: main_file
file_date_updated: 2020-07-14T12:47:30Z
has_accepted_license: '1'
intvolume: ' 38'
isi: 1
issue: '4'
language:
- iso: eng
month: '07'
oa: 1
oa_version: Submitted Version
project:
- _id: 2533E772-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '638176'
name: Efficient Simulation of Natural Phenomena at Extremely Large Scales
- _id: 24F9549A-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '715767'
name: 'MATERIALIZABLE: Intelligent fabrication-oriented Computational Design and
Modeling'
- _id: 2564DBCA-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '665385'
name: International IST Doctoral Program
publication: ACM Transactions on Graphics
publication_status: published
publisher: ACM
quality_controlled: '1'
related_material:
link:
- description: News on IST Homepage
relation: press_release
url: https://ist.ac.at/en/news/new-method-makes-realistic-water-wave-animations-more-efficient/
scopus_import: '1'
status: public
title: Fundamental solutions for water wave animation
type: journal_article
user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
volume: 38
year: '2019'
...
---
_id: '6413'
abstract:
- lang: eng
text: Phase-field methods have long been used to model the flow of immiscible fluids.
Their ability to naturally capture interface topological changes is widely recognized,
but their accuracy in simulating flows of real fluids in practical geometries
is not established. We here quantitatively investigate the convergence of the
phase-field method to the sharp-interface limit with simulations of two-phase
pipe flow. We focus on core-annular flows, in which a highly viscous fluid is
lubricated by a less viscous fluid, and validate our simulations with an analytic
laminar solution, a formal linear stability analysis and also in the fully nonlinear
regime. We demonstrate the ability of the phase-field method to accurately deal
with non-rectangular geometry, strong advection, unsteady fluctuations and large
viscosity contrast. We argue that phase-field methods are very promising for quantitatively
studying moderately turbulent flows, especially at high concentrations of the
disperse phase.
article_processing_charge: No
article_type: original
author:
- first_name: Baofang
full_name: Song, Baofang
last_name: Song
- first_name: Carlos
full_name: Plana, Carlos
last_name: Plana
- first_name: Jose M
full_name: Lopez Alonso, Jose M
id: 40770848-F248-11E8-B48F-1D18A9856A87
last_name: Lopez Alonso
orcid: 0000-0002-0384-2022
- first_name: Marc
full_name: Avila, Marc
last_name: Avila
citation:
ama: Song B, Plana C, Lopez Alonso JM, Avila M. Phase-field simulation of core-annular
pipe flow. International Journal of Multiphase Flow. 2019;117:14-24. doi:10.1016/j.ijmultiphaseflow.2019.04.027
apa: Song, B., Plana, C., Lopez Alonso, J. M., & Avila, M. (2019). Phase-field
simulation of core-annular pipe flow. International Journal of Multiphase Flow.
Elsevier. https://doi.org/10.1016/j.ijmultiphaseflow.2019.04.027
chicago: Song, Baofang, Carlos Plana, Jose M Lopez Alonso, and Marc Avila. “Phase-Field
Simulation of Core-Annular Pipe Flow.” International Journal of Multiphase
Flow. Elsevier, 2019. https://doi.org/10.1016/j.ijmultiphaseflow.2019.04.027.
ieee: B. Song, C. Plana, J. M. Lopez Alonso, and M. Avila, “Phase-field simulation
of core-annular pipe flow,” International Journal of Multiphase Flow, vol.
117. Elsevier, pp. 14–24, 2019.
ista: Song B, Plana C, Lopez Alonso JM, Avila M. 2019. Phase-field simulation of
core-annular pipe flow. International Journal of Multiphase Flow. 117, 14–24.
mla: Song, Baofang, et al. “Phase-Field Simulation of Core-Annular Pipe Flow.” International
Journal of Multiphase Flow, vol. 117, Elsevier, 2019, pp. 14–24, doi:10.1016/j.ijmultiphaseflow.2019.04.027.
short: B. Song, C. Plana, J.M. Lopez Alonso, M. Avila, International Journal of
Multiphase Flow 117 (2019) 14–24.
date_created: 2019-05-13T07:58:35Z
date_published: 2019-08-01T00:00:00Z
date_updated: 2023-08-25T10:19:55Z
day: '01'
department:
- _id: BjHo
doi: 10.1016/j.ijmultiphaseflow.2019.04.027
external_id:
arxiv:
- '1902.07351'
isi:
- '000474496000002'
intvolume: ' 117'
isi: 1
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/1902.07351
month: '08'
oa: 1
oa_version: Preprint
page: 14-24
publication: International Journal of Multiphase Flow
publication_identifier:
issn:
- '03019322'
publication_status: published
publisher: Elsevier
quality_controlled: '1'
scopus_import: '1'
status: public
title: Phase-field simulation of core-annular pipe flow
type: journal_article
user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
volume: 117
year: '2019'
...
---
_id: '6419'
abstract:
- lang: eng
text: Characterizing the fitness landscape, a representation of fitness for a large
set of genotypes, is key to understanding how genetic information is interpreted
to create functional organisms. Here we determined the evolutionarily-relevant
segment of the fitness landscape of His3, a gene coding for an enzyme in the histidine
synthesis pathway, focusing on combinations of amino acid states found at orthologous
sites of extant species. Just 15% of amino acids found in yeast His3 orthologues
were always neutral while the impact on fitness of the remaining 85% depended
on the genetic background. Furthermore, at 67% of sites, amino acid replacements
were under sign epistasis, having both strongly positive and negative effect in
different genetic backgrounds. 46% of sites were under reciprocal sign epistasis.
The fitness impact of amino acid replacements was influenced by only a few genetic
backgrounds but involved interaction of multiple sites, shaping a rugged fitness
landscape in which many of the shortest paths between highly fit genotypes are
inaccessible.
article_number: e1008079
article_processing_charge: No
author:
- first_name: Victoria
full_name: Pokusaeva, Victoria
id: 3184041C-F248-11E8-B48F-1D18A9856A87
last_name: Pokusaeva
orcid: 0000-0001-7660-444X
- first_name: Dinara R.
full_name: Usmanova, Dinara R.
last_name: Usmanova
- first_name: Ekaterina V.
full_name: Putintseva, Ekaterina V.
last_name: Putintseva
- first_name: Lorena
full_name: Espinar, Lorena
last_name: Espinar
- first_name: Karen
full_name: Sarkisyan, Karen
id: 39A7BF80-F248-11E8-B48F-1D18A9856A87
last_name: Sarkisyan
orcid: 0000-0002-5375-6341
- first_name: Alexander S.
full_name: Mishin, Alexander S.
last_name: Mishin
- first_name: Natalya S.
full_name: Bogatyreva, Natalya S.
last_name: Bogatyreva
- first_name: Dmitry
full_name: Ivankov, Dmitry
id: 49FF1036-F248-11E8-B48F-1D18A9856A87
last_name: Ivankov
- first_name: Arseniy
full_name: Akopyan, Arseniy
id: 430D2C90-F248-11E8-B48F-1D18A9856A87
last_name: Akopyan
orcid: 0000-0002-2548-617X
- first_name: Sergey
full_name: Avvakumov, Sergey
id: 3827DAC8-F248-11E8-B48F-1D18A9856A87
last_name: Avvakumov
- first_name: Inna S.
full_name: Povolotskaya, Inna S.
last_name: Povolotskaya
- first_name: Guillaume J.
full_name: Filion, Guillaume J.
last_name: Filion
- first_name: Lucas B.
full_name: Carey, Lucas B.
last_name: Carey
- first_name: Fyodor
full_name: Kondrashov, Fyodor
id: 44FDEF62-F248-11E8-B48F-1D18A9856A87
last_name: Kondrashov
orcid: 0000-0001-8243-4694
citation:
ama: Pokusaeva V, Usmanova DR, Putintseva EV, et al. An experimental assay of the
interactions of amino acids from orthologous sequences shaping a complex fitness
landscape. PLoS Genetics. 2019;15(4). doi:10.1371/journal.pgen.1008079
apa: Pokusaeva, V., Usmanova, D. R., Putintseva, E. V., Espinar, L., Sarkisyan,
K., Mishin, A. S., … Kondrashov, F. (2019). An experimental assay of the interactions
of amino acids from orthologous sequences shaping a complex fitness landscape.
PLoS Genetics. Public Library of Science. https://doi.org/10.1371/journal.pgen.1008079
chicago: Pokusaeva, Victoria, Dinara R. Usmanova, Ekaterina V. Putintseva, Lorena
Espinar, Karen Sarkisyan, Alexander S. Mishin, Natalya S. Bogatyreva, et al. “An
Experimental Assay of the Interactions of Amino Acids from Orthologous Sequences
Shaping a Complex Fitness Landscape.” PLoS Genetics. Public Library of
Science, 2019. https://doi.org/10.1371/journal.pgen.1008079.
ieee: V. Pokusaeva et al., “An experimental assay of the interactions of
amino acids from orthologous sequences shaping a complex fitness landscape,” PLoS
Genetics, vol. 15, no. 4. Public Library of Science, 2019.
ista: Pokusaeva V, Usmanova DR, Putintseva EV, Espinar L, Sarkisyan K, Mishin AS,
Bogatyreva NS, Ivankov D, Akopyan A, Avvakumov S, Povolotskaya IS, Filion GJ,
Carey LB, Kondrashov F. 2019. An experimental assay of the interactions of amino
acids from orthologous sequences shaping a complex fitness landscape. PLoS Genetics.
15(4), e1008079.
mla: Pokusaeva, Victoria, et al. “An Experimental Assay of the Interactions of Amino
Acids from Orthologous Sequences Shaping a Complex Fitness Landscape.” PLoS
Genetics, vol. 15, no. 4, e1008079, Public Library of Science, 2019, doi:10.1371/journal.pgen.1008079.
short: V. Pokusaeva, D.R. Usmanova, E.V. Putintseva, L. Espinar, K. Sarkisyan, A.S.
Mishin, N.S. Bogatyreva, D. Ivankov, A. Akopyan, S. Avvakumov, I.S. Povolotskaya,
G.J. Filion, L.B. Carey, F. Kondrashov, PLoS Genetics 15 (2019).
date_created: 2019-05-13T07:58:38Z
date_published: 2019-04-10T00:00:00Z
date_updated: 2023-08-25T10:30:37Z
day: '10'
ddc:
- '570'
department:
- _id: FyKo
doi: 10.1371/journal.pgen.1008079
ec_funded: 1
external_id:
isi:
- '000466866000029'
file:
- access_level: open_access
checksum: cf3889c8a8a16053dacf9c3776cbe217
content_type: application/pdf
creator: dernst
date_created: 2019-05-14T08:26:08Z
date_updated: 2020-07-14T12:47:30Z
file_id: '6445'
file_name: 2019_PLOSGenetics_Pokusaeva.pdf
file_size: 3726017
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file_date_updated: 2020-07-14T12:47:30Z
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language:
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month: '04'
oa: 1
oa_version: Published Version
project:
- _id: 2564DBCA-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '665385'
name: International IST Doctoral Program
publication: PLoS Genetics
publication_identifier:
eissn:
- '15537404'
publication_status: published
publisher: Public Library of Science
quality_controlled: '1'
related_material:
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relation: research_data
status: public
- id: '9790'
relation: research_data
status: public
- id: '9797'
relation: research_data
status: public
scopus_import: '1'
status: public
title: An experimental assay of the interactions of amino acids from orthologous sequences
shaping a complex fitness landscape
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: '6412'
abstract:
- lang: eng
text: Polycomb group (PcG) proteins play critical roles in the epigenetic inheritance
of cell fate. The Polycomb Repressive Complexes PRC1 and PRC2 catalyse distinct
chromatin modifications to enforce gene silencing, but how transcriptional repression
is propagated through mitotic cell divisions remains a key unresolved question.
Using reversible tethering of PcG proteins to ectopic sites in mouse embryonic
stem cells, here we show that PRC1 can trigger transcriptional repression and
Polycomb-dependent chromatin modifications. We find that canonical PRC1 (cPRC1),
but not variant PRC1, maintains gene silencing through cell division upon reversal
of tethering. Propagation of gene repression is sustained by cis-acting histone
modifications, PRC2-mediated H3K27me3 and cPRC1-mediated H2AK119ub1, promoting
a sequence-independent feedback mechanism for PcG protein recruitment. Thus, the
distinct PRC1 complexes present in vertebrates can differentially regulate epigenetic
maintenance of gene silencing, potentially enabling dynamic heritable responses
to complex stimuli. Our findings reveal how PcG repression is potentially inherited
in vertebrates.
article_number: '1931'
article_processing_charge: No
author:
- first_name: Hagar F.
full_name: Moussa, Hagar F.
last_name: Moussa
- first_name: Daniel
full_name: Bsteh, Daniel
last_name: Bsteh
- first_name: Ramesh
full_name: Yelagandula, Ramesh
last_name: Yelagandula
- first_name: Carina
full_name: Pribitzer, Carina
last_name: Pribitzer
- first_name: Karin
full_name: Stecher, Karin
last_name: Stecher
- first_name: Katarina
full_name: Bartalska, Katarina
id: 4D883232-F248-11E8-B48F-1D18A9856A87
last_name: Bartalska
- first_name: Luca
full_name: Michetti, Luca
last_name: Michetti
- first_name: Jingkui
full_name: Wang, Jingkui
last_name: Wang
- first_name: Jorge A.
full_name: Zepeda-Martinez, Jorge A.
last_name: Zepeda-Martinez
- first_name: Ulrich
full_name: Elling, Ulrich
last_name: Elling
- first_name: Jacob I.
full_name: Stuckey, Jacob I.
last_name: Stuckey
- first_name: Lindsey I.
full_name: James, Lindsey I.
last_name: James
- first_name: Stephen V.
full_name: Frye, Stephen V.
last_name: Frye
- first_name: Oliver
full_name: Bell, Oliver
last_name: Bell
citation:
ama: Moussa HF, Bsteh D, Yelagandula R, et al. Canonical PRC1 controls sequence-independent
propagation of Polycomb-mediated gene silencing. Nature Communications.
2019;10(1). doi:10.1038/s41467-019-09628-6
apa: Moussa, H. F., Bsteh, D., Yelagandula, R., Pribitzer, C., Stecher, K., Bartalska,
K., … Bell, O. (2019). Canonical PRC1 controls sequence-independent propagation
of Polycomb-mediated gene silencing. Nature Communications. Springer Nature.
https://doi.org/10.1038/s41467-019-09628-6
chicago: Moussa, Hagar F., Daniel Bsteh, Ramesh Yelagandula, Carina Pribitzer, Karin
Stecher, Katarina Bartalska, Luca Michetti, et al. “Canonical PRC1 Controls Sequence-Independent
Propagation of Polycomb-Mediated Gene Silencing.” Nature Communications.
Springer Nature, 2019. https://doi.org/10.1038/s41467-019-09628-6.
ieee: H. F. Moussa et al., “Canonical PRC1 controls sequence-independent
propagation of Polycomb-mediated gene silencing,” Nature Communications,
vol. 10, no. 1. Springer Nature, 2019.
ista: Moussa HF, Bsteh D, Yelagandula R, Pribitzer C, Stecher K, Bartalska K, Michetti
L, Wang J, Zepeda-Martinez JA, Elling U, Stuckey JI, James LI, Frye SV, Bell O.
2019. Canonical PRC1 controls sequence-independent propagation of Polycomb-mediated
gene silencing. Nature Communications. 10(1), 1931.
mla: Moussa, Hagar F., et al. “Canonical PRC1 Controls Sequence-Independent Propagation
of Polycomb-Mediated Gene Silencing.” Nature Communications, vol. 10, no.
1, 1931, Springer Nature, 2019, doi:10.1038/s41467-019-09628-6.
short: H.F. Moussa, D. Bsteh, R. Yelagandula, C. Pribitzer, K. Stecher, K. Bartalska,
L. Michetti, J. Wang, J.A. Zepeda-Martinez, U. Elling, J.I. Stuckey, L.I. James,
S.V. Frye, O. Bell, Nature Communications 10 (2019).
date_created: 2019-05-13T07:58:35Z
date_published: 2019-04-29T00:00:00Z
date_updated: 2023-08-25T10:31:56Z
day: '29'
ddc:
- '570'
department:
- _id: SaSi
doi: 10.1038/s41467-019-09628-6
external_id:
isi:
- '000466118700002'
file:
- access_level: open_access
checksum: 6550a328335396c856db4cbdda7d2994
content_type: application/pdf
creator: dernst
date_created: 2019-05-14T08:45:51Z
date_updated: 2020-07-14T12:47:29Z
file_id: '6448'
file_name: 2019_NatureComm_Moussa.pdf
file_size: 1223647
relation: main_file
file_date_updated: 2020-07-14T12:47:29Z
has_accepted_license: '1'
intvolume: ' 10'
isi: 1
issue: '1'
language:
- iso: eng
month: '04'
oa: 1
oa_version: Published Version
publication: Nature Communications
publication_identifier:
eissn:
- '20411723'
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
scopus_import: '1'
status: public
title: Canonical PRC1 controls sequence-independent propagation of Polycomb-mediated
gene silencing
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: '6415'
abstract:
- lang: eng
text: Ant invasions are often harmful to native species communities. Their pathogens
and host disease defense mechanisms may be one component of their devastating
success. First, they can introduce harmful diseases to their competitors in the
introduced range, to which they themselves are tolerant. Second, their supercolonial
social structure of huge multi-queen nest networks means that they will harbor
a broad pathogen spectrum and high pathogen load while remaining resilient, unlike
the smaller, territorial colonies of the native species. Thus, it is likely that
invasive ants act as a disease reservoir, promoting their competitive advantage
and invasive success.
article_processing_charge: No
author:
- first_name: Sylvia
full_name: Cremer, Sylvia
id: 2F64EC8C-F248-11E8-B48F-1D18A9856A87
last_name: Cremer
orcid: 0000-0002-2193-3868
citation:
ama: Cremer S. Pathogens and disease defense of invasive ants. Current Opinion
in Insect Science. 2019;33:63-68. doi:10.1016/j.cois.2019.03.011
apa: Cremer, S. (2019). Pathogens and disease defense of invasive ants. Current
Opinion in Insect Science. Elsevier. https://doi.org/10.1016/j.cois.2019.03.011
chicago: Cremer, Sylvia. “Pathogens and Disease Defense of Invasive Ants.” Current
Opinion in Insect Science. Elsevier, 2019. https://doi.org/10.1016/j.cois.2019.03.011.
ieee: S. Cremer, “Pathogens and disease defense of invasive ants,” Current Opinion
in Insect Science, vol. 33. Elsevier, pp. 63–68, 2019.
ista: Cremer S. 2019. Pathogens and disease defense of invasive ants. Current Opinion
in Insect Science. 33, 63–68.
mla: Cremer, Sylvia. “Pathogens and Disease Defense of Invasive Ants.” Current
Opinion in Insect Science, vol. 33, Elsevier, 2019, pp. 63–68, doi:10.1016/j.cois.2019.03.011.
short: S. Cremer, Current Opinion in Insect Science 33 (2019) 63–68.
date_created: 2019-05-13T07:58:36Z
date_published: 2019-06-01T00:00:00Z
date_updated: 2023-08-25T10:31:31Z
day: '01'
department:
- _id: SyCr
doi: 10.1016/j.cois.2019.03.011
external_id:
isi:
- '000477666000012'
intvolume: ' 33'
isi: 1
language:
- iso: eng
month: '06'
oa_version: None
page: 63-68
publication: Current Opinion in Insect Science
publication_identifier:
eissn:
- '22145753'
issn:
- '22145745'
publication_status: published
publisher: Elsevier
quality_controlled: '1'
scopus_import: '1'
status: public
title: Pathogens and disease defense of invasive ants
type: journal_article
user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
volume: 33
year: '2019'
...
---
_id: '9790'
article_processing_charge: No
author:
- first_name: Victoria
full_name: Pokusaeva, Victoria
id: 3184041C-F248-11E8-B48F-1D18A9856A87
last_name: Pokusaeva
orcid: 0000-0001-7660-444X
- first_name: Dinara R.
full_name: Usmanova, Dinara R.
last_name: Usmanova
- first_name: Ekaterina V.
full_name: Putintseva, Ekaterina V.
last_name: Putintseva
- first_name: Lorena
full_name: Espinar, Lorena
last_name: Espinar
- first_name: Karen
full_name: Sarkisyan, Karen
id: 39A7BF80-F248-11E8-B48F-1D18A9856A87
last_name: Sarkisyan
orcid: 0000-0002-5375-6341
- first_name: Alexander S.
full_name: Mishin, Alexander S.
last_name: Mishin
- first_name: Natalya S.
full_name: Bogatyreva, Natalya S.
last_name: Bogatyreva
- first_name: Dmitry
full_name: Ivankov, Dmitry
id: 49FF1036-F248-11E8-B48F-1D18A9856A87
last_name: Ivankov
- first_name: Arseniy
full_name: Akopyan, Arseniy
id: 430D2C90-F248-11E8-B48F-1D18A9856A87
last_name: Akopyan
orcid: 0000-0002-2548-617X
- first_name: Sergey
full_name: Avvakumov, Sergey
id: 3827DAC8-F248-11E8-B48F-1D18A9856A87
last_name: Avvakumov
- first_name: Inna S.
full_name: Povolotskaya, Inna S.
last_name: Povolotskaya
- first_name: Guillaume J.
full_name: Filion, Guillaume J.
last_name: Filion
- first_name: Lucas B.
full_name: Carey, Lucas B.
last_name: Carey
- first_name: Fyodor
full_name: Kondrashov, Fyodor
id: 44FDEF62-F248-11E8-B48F-1D18A9856A87
last_name: Kondrashov
orcid: 0000-0001-8243-4694
citation:
ama: Pokusaeva V, Usmanova DR, Putintseva EV, et al. A statistical summary of segment
libraries and sequencing results. 2019. doi:10.1371/journal.pgen.1008079.s011
apa: Pokusaeva, V., Usmanova, D. R., Putintseva, E. V., Espinar, L., Sarkisyan,
K., Mishin, A. S., … Kondrashov, F. (2019). A statistical summary of segment libraries
and sequencing results. Public Library of Science. https://doi.org/10.1371/journal.pgen.1008079.s011
chicago: Pokusaeva, Victoria, Dinara R. Usmanova, Ekaterina V. Putintseva, Lorena
Espinar, Karen Sarkisyan, Alexander S. Mishin, Natalya S. Bogatyreva, et al. “A
Statistical Summary of Segment Libraries and Sequencing Results.” Public Library
of Science, 2019. https://doi.org/10.1371/journal.pgen.1008079.s011.
ieee: V. Pokusaeva et al., “A statistical summary of segment libraries and
sequencing results.” Public Library of Science, 2019.
ista: Pokusaeva V, Usmanova DR, Putintseva EV, Espinar L, Sarkisyan K, Mishin AS,
Bogatyreva NS, Ivankov D, Akopyan A, Avvakumov S, Povolotskaya IS, Filion GJ,
Carey LB, Kondrashov F. 2019. A statistical summary of segment libraries and sequencing
results, Public Library of Science, 10.1371/journal.pgen.1008079.s011.
mla: Pokusaeva, Victoria, et al. A Statistical Summary of Segment Libraries and
Sequencing Results. Public Library of Science, 2019, doi:10.1371/journal.pgen.1008079.s011.
short: V. Pokusaeva, D.R. Usmanova, E.V. Putintseva, L. Espinar, K. Sarkisyan, A.S.
Mishin, N.S. Bogatyreva, D. Ivankov, A. Akopyan, S. Avvakumov, I.S. Povolotskaya,
G.J. Filion, L.B. Carey, F. Kondrashov, (2019).
date_created: 2021-08-06T08:50:15Z
date_published: 2019-04-10T00:00:00Z
date_updated: 2023-08-25T10:30:36Z
day: '10'
department:
- _id: FyKo
doi: 10.1371/journal.pgen.1008079.s011
month: '04'
oa_version: Published Version
publisher: Public Library of Science
related_material:
record:
- id: '6419'
relation: used_in_publication
status: public
status: public
title: A statistical summary of segment libraries and sequencing results
type: research_data_reference
user_id: 6785fbc1-c503-11eb-8a32-93094b40e1cf
year: '2019'
...
---
_id: '9797'
article_processing_charge: No
author:
- first_name: Victoria
full_name: Pokusaeva, Victoria
id: 3184041C-F248-11E8-B48F-1D18A9856A87
last_name: Pokusaeva
orcid: 0000-0001-7660-444X
- first_name: Dinara R.
full_name: Usmanova, Dinara R.
last_name: Usmanova
- first_name: Ekaterina V.
full_name: Putintseva, Ekaterina V.
last_name: Putintseva
- first_name: Lorena
full_name: Espinar, Lorena
last_name: Espinar
- first_name: Karen
full_name: Sarkisyan, Karen
id: 39A7BF80-F248-11E8-B48F-1D18A9856A87
last_name: Sarkisyan
orcid: 0000-0002-5375-6341
- first_name: Alexander S.
full_name: Mishin, Alexander S.
last_name: Mishin
- first_name: Natalya S.
full_name: Bogatyreva, Natalya S.
last_name: Bogatyreva
- first_name: Dmitry
full_name: Ivankov, Dmitry
id: 49FF1036-F248-11E8-B48F-1D18A9856A87
last_name: Ivankov
- first_name: Arseniy
full_name: Akopyan, Arseniy
id: 430D2C90-F248-11E8-B48F-1D18A9856A87
last_name: Akopyan
orcid: 0000-0002-2548-617X
- first_name: Inna S.
full_name: Povolotskaya, Inna S.
last_name: Povolotskaya
- first_name: Guillaume J.
full_name: Filion, Guillaume J.
last_name: Filion
- first_name: Lucas B.
full_name: Carey, Lucas B.
last_name: Carey
- first_name: Fyodor
full_name: Kondrashov, Fyodor
id: 44FDEF62-F248-11E8-B48F-1D18A9856A87
last_name: Kondrashov
orcid: 0000-0001-8243-4694
citation:
ama: Pokusaeva V, Usmanova DR, Putintseva EV, et al. A statistical summary of segment
libraries and sequencing results. 2019. doi:10.1371/journal.pgen.1008079.s011
apa: Pokusaeva, V., Usmanova, D. R., Putintseva, E. V., Espinar, L., Sarkisyan,
K., Mishin, A. S., … Kondrashov, F. (2019). A statistical summary of segment libraries
and sequencing results. Public Library of Science. https://doi.org/10.1371/journal.pgen.1008079.s011
chicago: Pokusaeva, Victoria, Dinara R. Usmanova, Ekaterina V. Putintseva, Lorena
Espinar, Karen Sarkisyan, Alexander S. Mishin, Natalya S. Bogatyreva, et al. “A
Statistical Summary of Segment Libraries and Sequencing Results.” Public Library
of Science, 2019. https://doi.org/10.1371/journal.pgen.1008079.s011.
ieee: V. Pokusaeva et al., “A statistical summary of segment libraries and
sequencing results.” Public Library of Science, 2019.
ista: Pokusaeva V, Usmanova DR, Putintseva EV, Espinar L, Sarkisyan K, Mishin AS,
Bogatyreva NS, Ivankov D, Akopyan A, Povolotskaya IS, Filion GJ, Carey LB, Kondrashov
F. 2019. A statistical summary of segment libraries and sequencing results, Public
Library of Science, 10.1371/journal.pgen.1008079.s011.
mla: Pokusaeva, Victoria, et al. A Statistical Summary of Segment Libraries and
Sequencing Results. Public Library of Science, 2019, doi:10.1371/journal.pgen.1008079.s011.
short: V. Pokusaeva, D.R. Usmanova, E.V. Putintseva, L. Espinar, K. Sarkisyan, A.S.
Mishin, N.S. Bogatyreva, D. Ivankov, A. Akopyan, I.S. Povolotskaya, G.J. Filion,
L.B. Carey, F. Kondrashov, (2019).
date_created: 2021-08-06T11:08:20Z
date_published: 2019-04-10T00:00:00Z
date_updated: 2023-08-25T10:30:36Z
day: '10'
department:
- _id: FyKo
doi: 10.1371/journal.pgen.1008079.s011
month: '04'
oa_version: Published Version
publisher: Public Library of Science
related_material:
record:
- id: '6419'
relation: used_in_publication
status: public
status: public
title: A statistical summary of segment libraries and sequencing results
type: research_data_reference
user_id: 6785fbc1-c503-11eb-8a32-93094b40e1cf
year: '2019'
...
---
_id: '9789'
article_processing_charge: No
author:
- first_name: Victoria
full_name: Pokusaeva, Victoria
id: 3184041C-F248-11E8-B48F-1D18A9856A87
last_name: Pokusaeva
orcid: 0000-0001-7660-444X
- first_name: Dinara R.
full_name: Usmanova, Dinara R.
last_name: Usmanova
- first_name: Ekaterina V.
full_name: Putintseva, Ekaterina V.
last_name: Putintseva
- first_name: Lorena
full_name: Espinar, Lorena
last_name: Espinar
- first_name: Karen
full_name: Sarkisyan, Karen
id: 39A7BF80-F248-11E8-B48F-1D18A9856A87
last_name: Sarkisyan
orcid: 0000-0002-5375-6341
- first_name: Alexander S.
full_name: Mishin, Alexander S.
last_name: Mishin
- first_name: Natalya S.
full_name: Bogatyreva, Natalya S.
last_name: Bogatyreva
- first_name: Dmitry
full_name: Ivankov, Dmitry
id: 49FF1036-F248-11E8-B48F-1D18A9856A87
last_name: Ivankov
- first_name: Arseniy
full_name: Akopyan, Arseniy
id: 430D2C90-F248-11E8-B48F-1D18A9856A87
last_name: Akopyan
orcid: 0000-0002-2548-617X
- first_name: Sergey
full_name: Avvakumov, Sergey
id: 3827DAC8-F248-11E8-B48F-1D18A9856A87
last_name: Avvakumov
- first_name: Inna S.
full_name: Povolotskaya, Inna S.
last_name: Povolotskaya
- first_name: Guillaume J.
full_name: Filion, Guillaume J.
last_name: Filion
- first_name: Lucas B.
full_name: Carey, Lucas B.
last_name: Carey
- first_name: Fyodor
full_name: Kondrashov, Fyodor
id: 44FDEF62-F248-11E8-B48F-1D18A9856A87
last_name: Kondrashov
orcid: 0000-0001-8243-4694
citation:
ama: Pokusaeva V, Usmanova DR, Putintseva EV, et al. Multiple alignment of His3
orthologues. 2019. doi:10.1371/journal.pgen.1008079.s010
apa: Pokusaeva, V., Usmanova, D. R., Putintseva, E. V., Espinar, L., Sarkisyan,
K., Mishin, A. S., … Kondrashov, F. (2019). Multiple alignment of His3 orthologues.
Public Library of Science. https://doi.org/10.1371/journal.pgen.1008079.s010
chicago: Pokusaeva, Victoria, Dinara R. Usmanova, Ekaterina V. Putintseva, Lorena
Espinar, Karen Sarkisyan, Alexander S. Mishin, Natalya S. Bogatyreva, et al. “Multiple
Alignment of His3 Orthologues.” Public Library of Science, 2019. https://doi.org/10.1371/journal.pgen.1008079.s010.
ieee: V. Pokusaeva et al., “Multiple alignment of His3 orthologues.” Public
Library of Science, 2019.
ista: Pokusaeva V, Usmanova DR, Putintseva EV, Espinar L, Sarkisyan K, Mishin AS,
Bogatyreva NS, Ivankov D, Akopyan A, Avvakumov S, Povolotskaya IS, Filion GJ,
Carey LB, Kondrashov F. 2019. Multiple alignment of His3 orthologues, Public Library
of Science, 10.1371/journal.pgen.1008079.s010.
mla: Pokusaeva, Victoria, et al. Multiple Alignment of His3 Orthologues.
Public Library of Science, 2019, doi:10.1371/journal.pgen.1008079.s010.
short: V. Pokusaeva, D.R. Usmanova, E.V. Putintseva, L. Espinar, K. Sarkisyan, A.S.
Mishin, N.S. Bogatyreva, D. Ivankov, A. Akopyan, S. Avvakumov, I.S. Povolotskaya,
G.J. Filion, L.B. Carey, F. Kondrashov, (2019).
date_created: 2021-08-06T08:38:50Z
date_published: 2019-04-10T00:00:00Z
date_updated: 2023-08-25T10:30:36Z
day: '10'
department:
- _id: FyKo
doi: 10.1371/journal.pgen.1008079.s010
month: '04'
oa_version: Published Version
publisher: Public Library of Science
related_material:
record:
- id: '6419'
relation: used_in_publication
status: public
status: public
title: Multiple alignment of His3 orthologues
type: research_data_reference
user_id: 6785fbc1-c503-11eb-8a32-93094b40e1cf
year: '2019'
...
---
_id: '6462'
abstract:
- lang: eng
text: A controller is a device that interacts with a plant. At each time point,it
reads the plant’s state and issues commands with the goal that the plant oper-ates
optimally. Constructing optimal controllers is a fundamental and challengingproblem.
Machine learning techniques have recently been successfully applied totrain controllers,
yet they have limitations. Learned controllers are monolithic andhard to reason
about. In particular, it is difficult to add features without retraining,to guarantee
any level of performance, and to achieve acceptable performancewhen encountering
untrained scenarios. These limitations can be addressed bydeploying quantitative
run-timeshieldsthat serve as a proxy for the controller.At each time point, the
shield reads the command issued by the controller andmay choose to alter it before
passing it on to the plant. We show how optimalshields that interfere as little
as possible while guaranteeing a desired level ofcontroller performance, can be
generated systematically and automatically usingreactive synthesis. First, we abstract the plant by building a stochastic model.Second,
we consider the learned controller to be a black box. Third, we mea-surecontroller
performanceandshield interferenceby two quantitative run-timemeasures that are
formally defined using weighted automata. Then, the problemof constructing a shield
that guarantees maximal performance with minimal inter-ference is the problem
of finding an optimal strategy in a stochastic2-player game“controller versus
shield” played on the abstract state space of the plant with aquantitative objective
obtained from combining the performance and interferencemeasures. We illustrate
the effectiveness of our approach by automatically con-structing lightweight shields
for learned traffic-light controllers in various roadnetworks. The shields we
generate avoid liveness bugs, improve controller per-formance in untrained and
changing traffic situations, and add features to learnedcontrollers, such as giving
priority to emergency vehicles.
alternative_title:
- LNCS
article_processing_charge: No
author:
- first_name: Guy
full_name: Avni, Guy
id: 463C8BC2-F248-11E8-B48F-1D18A9856A87
last_name: Avni
orcid: 0000-0001-5588-8287
- first_name: Roderick
full_name: Bloem, Roderick
last_name: Bloem
- first_name: Krishnendu
full_name: Chatterjee, Krishnendu
id: 2E5DCA20-F248-11E8-B48F-1D18A9856A87
last_name: Chatterjee
orcid: 0000-0002-4561-241X
- first_name: Thomas A
full_name: Henzinger, Thomas A
id: 40876CD8-F248-11E8-B48F-1D18A9856A87
last_name: Henzinger
orcid: 0000−0002−2985−7724
- first_name: Bettina
full_name: Konighofer, Bettina
last_name: Konighofer
- first_name: Stefan
full_name: Pranger, Stefan
last_name: Pranger
citation:
ama: 'Avni G, Bloem R, Chatterjee K, Henzinger TA, Konighofer B, Pranger S. Run-time
optimization for learned controllers through quantitative games. In: 31st International
Conference on Computer-Aided Verification. Vol 11561. Springer; 2019:630-649.
doi:10.1007/978-3-030-25540-4_36'
apa: 'Avni, G., Bloem, R., Chatterjee, K., Henzinger, T. A., Konighofer, B., &
Pranger, S. (2019). Run-time optimization for learned controllers through quantitative
games. In 31st International Conference on Computer-Aided Verification
(Vol. 11561, pp. 630–649). New York, NY, United States: Springer. https://doi.org/10.1007/978-3-030-25540-4_36'
chicago: Avni, Guy, Roderick Bloem, Krishnendu Chatterjee, Thomas A Henzinger, Bettina
Konighofer, and Stefan Pranger. “Run-Time Optimization for Learned Controllers
through Quantitative Games.” In 31st International Conference on Computer-Aided
Verification, 11561:630–49. Springer, 2019. https://doi.org/10.1007/978-3-030-25540-4_36.
ieee: G. Avni, R. Bloem, K. Chatterjee, T. A. Henzinger, B. Konighofer, and S. Pranger,
“Run-time optimization for learned controllers through quantitative games,” in
31st International Conference on Computer-Aided Verification, New York,
NY, United States, 2019, vol. 11561, pp. 630–649.
ista: 'Avni G, Bloem R, Chatterjee K, Henzinger TA, Konighofer B, Pranger S. 2019.
Run-time optimization for learned controllers through quantitative games. 31st
International Conference on Computer-Aided Verification. CAV: Computer Aided Verification,
LNCS, vol. 11561, 630–649.'
mla: Avni, Guy, et al. “Run-Time Optimization for Learned Controllers through Quantitative
Games.” 31st International Conference on Computer-Aided Verification, vol.
11561, Springer, 2019, pp. 630–49, doi:10.1007/978-3-030-25540-4_36.
short: G. Avni, R. Bloem, K. Chatterjee, T.A. Henzinger, B. Konighofer, S. Pranger,
in:, 31st International Conference on Computer-Aided Verification, Springer, 2019,
pp. 630–649.
conference:
end_date: 2019-07-18
location: New York, NY, United States
name: 'CAV: Computer Aided Verification'
start_date: 2019-07-13
date_created: 2019-05-16T11:22:30Z
date_published: 2019-07-12T00:00:00Z
date_updated: 2023-08-25T10:33:27Z
day: '12'
ddc:
- '000'
department:
- _id: ToHe
- _id: KrCh
doi: 10.1007/978-3-030-25540-4_36
external_id:
isi:
- '000491468000036'
file:
- access_level: open_access
checksum: c231579f2485c6fd4df17c9443a4d80b
content_type: application/pdf
creator: dernst
date_created: 2019-08-14T09:35:24Z
date_updated: 2020-07-14T12:47:31Z
file_id: '6816'
file_name: 2019_CAV_Avni.pdf
file_size: 659766
relation: main_file
file_date_updated: 2020-07-14T12:47:31Z
has_accepted_license: '1'
intvolume: ' 11561'
isi: 1
language:
- iso: eng
month: '07'
oa: 1
oa_version: Published Version
page: 630-649
project:
- _id: 264B3912-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: M02369
name: Formal Methods meets Algorithmic Game Theory
- _id: 25F42A32-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: Z211
name: The Wittgenstein Prize
- _id: 25832EC2-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: S 11407_N23
name: Rigorous Systems Engineering
publication: 31st International Conference on Computer-Aided Verification
publication_identifier:
isbn:
- '9783030255398'
issn:
- 0302-9743
publication_status: published
publisher: Springer
quality_controlled: '1'
scopus_import: '1'
status: public
title: Run-time optimization for learned controllers through quantitative games
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: conference
user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
volume: 11561
year: '2019'
...
---
_id: '6477'
abstract:
- lang: eng
text: 'Thermalizing quantum systems are conventionallydescribed by statistical mechanics
at equilib-rium. However, not all systems fall into this category, with many-body
localization providinga generic mechanism for thermalization to fail in strongly
disordered systems. Many-bodylocalized (MBL) systems remain perfect insulators
at nonzero temperature, which do notthermalize and therefore cannot be describedusing
statistical mechanics. This Colloquiumreviews recent theoretical and experimental
advances in studies of MBL systems, focusing onthe new perspective provided by
entanglement and nonequilibrium experimental probes suchas quantum quenches. Theoretically,
MBL systems exhibit a new kind of robust integrability: anextensive set of quasilocal
integrals of motion emerges, which provides an intuitive explanationof the breakdown
of thermalization. A description based on quasilocal integrals of motion isused
to predict dynamical properties of MBL systems, such as the spreading of quantumentanglement,
the behavior of local observables, and the response to external dissipativeprocesses.
Furthermore, MBL systems can exhibit eigenstate transitions and quantum ordersforbidden
in thermodynamic equilibrium. An outline isgiven of the current theoretical under-standing
of the quantum-to-classical transitionbetween many-body localized and ergodic
phasesand anomalous transport in the vicinity of that transition. Experimentally,
synthetic quantumsystems, which are well isolated from an external thermal reservoir,
provide natural platforms forrealizing the MBL phase. Recent experiments with
ultracold atoms, trapped ions, superconductingqubits, and quantum materials, in
which different signatures of many-body localization have beenobserved, are reviewed.
This Colloquium concludes by listing outstanding challenges andpromising future
research directions.'
article_number: '021001'
article_processing_charge: No
article_type: original
author:
- first_name: Dmitry A.
full_name: Abanin, Dmitry A.
last_name: Abanin
- first_name: Ehud
full_name: Altman, Ehud
last_name: Altman
- first_name: Immanuel
full_name: Bloch, Immanuel
last_name: Bloch
- first_name: Maksym
full_name: Serbyn, Maksym
id: 47809E7E-F248-11E8-B48F-1D18A9856A87
last_name: Serbyn
orcid: 0000-0002-2399-5827
citation:
ama: 'Abanin DA, Altman E, Bloch I, Serbyn M. Colloquium: Many-body localization,
thermalization, and entanglement. Reviews of Modern Physics. 2019;91(2).
doi:10.1103/revmodphys.91.021001'
apa: 'Abanin, D. A., Altman, E., Bloch, I., & Serbyn, M. (2019). Colloquium:
Many-body localization, thermalization, and entanglement. Reviews of Modern
Physics. American Physical Society. https://doi.org/10.1103/revmodphys.91.021001'
chicago: 'Abanin, Dmitry A., Ehud Altman, Immanuel Bloch, and Maksym Serbyn. “Colloquium:
Many-Body Localization, Thermalization, and Entanglement.” Reviews of Modern
Physics. American Physical Society, 2019. https://doi.org/10.1103/revmodphys.91.021001.'
ieee: 'D. A. Abanin, E. Altman, I. Bloch, and M. Serbyn, “Colloquium: Many-body
localization, thermalization, and entanglement,” Reviews of Modern Physics,
vol. 91, no. 2. American Physical Society, 2019.'
ista: 'Abanin DA, Altman E, Bloch I, Serbyn M. 2019. Colloquium: Many-body localization,
thermalization, and entanglement. Reviews of Modern Physics. 91(2), 021001.'
mla: 'Abanin, Dmitry A., et al. “Colloquium: Many-Body Localization, Thermalization,
and Entanglement.” Reviews of Modern Physics, vol. 91, no. 2, 021001, American
Physical Society, 2019, doi:10.1103/revmodphys.91.021001.'
short: D.A. Abanin, E. Altman, I. Bloch, M. Serbyn, Reviews of Modern Physics 91
(2019).
date_created: 2019-05-23T07:38:43Z
date_published: 2019-05-22T00:00:00Z
date_updated: 2023-08-25T10:37:56Z
day: '22'
ddc:
- '530'
department:
- _id: MaSe
doi: 10.1103/revmodphys.91.021001
external_id:
arxiv:
- '1804.11065'
isi:
- '000469046900001'
file:
- access_level: open_access
checksum: 4aec0e6662b09f6e0f828cd30ff2c3a6
content_type: application/pdf
creator: mserbyn
date_created: 2019-05-23T07:39:05Z
date_updated: 2020-07-14T12:47:31Z
file_id: '6478'
file_name: RevModPhys.91.021001.pdf
file_size: 1695677
relation: main_file
file_date_updated: 2020-07-14T12:47:31Z
has_accepted_license: '1'
intvolume: ' 91'
isi: 1
issue: '2'
language:
- iso: eng
month: '05'
oa: 1
oa_version: Published Version
publication: Reviews of Modern Physics
publication_identifier:
eissn:
- 0034-6861
issn:
- 1539-0756
publication_status: published
publisher: American Physical Society
quality_controlled: '1'
scopus_import: '1'
status: public
title: 'Colloquium: Many-body localization, thermalization, and entanglement'
type: journal_article
user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
volume: 91
year: '2019'
...
---
_id: '6466'
abstract:
- lang: eng
text: "One of the most striking and consistent results in speciation genomics is
the heterogeneous divergence observed across the genomes of closely related species.
This pattern was initially attributed to different levels of gene exchange—with
divergence preserved at loci generating a barrier to gene flow but homogenized
at unlinked neutral loci. Although there is evidence to support this model, it
is now recognized that interpreting patterns of divergence across genomes is not
so straightforward. One \r\nproblem is that heterogenous divergence between populations
can also be generated by other processes (e.g. recurrent selective sweeps or background
selection) without any involvement of differential gene flow. Thus, integrated
studies that identify which loci are likely subject to divergent selection are
required to shed light on the interplay between selection and gene flow during
the early phases of speciation. In this issue of Molecular Ecology, Rifkin et
al. (2019) confront this challenge using a pair of sister morning glory species.
They wisely design their sampling to take the geographic context of individuals
into account, including geographically isolated (allopatric) and co‐occurring
(sympatric) populations. This enabled them to show that individuals are phenotypically
less differentiated in sympatry. They also found that the loci that resist introgression
are enriched for those most differentiated in allopatry and loci that exhibit
signals of divergent selection. One great strength of the \r\nstudy is the combination
of methods from population genetics and molecular evolution, including the development
of a model to simultaneously infer admixture proportions and selfing rates."
article_processing_charge: No
author:
- first_name: David
full_name: Field, David
id: 419049E2-F248-11E8-B48F-1D18A9856A87
last_name: Field
orcid: 0000-0002-4014-8478
- first_name: Christelle
full_name: Fraisse, Christelle
id: 32DF5794-F248-11E8-B48F-1D18A9856A87
last_name: Fraisse
orcid: 0000-0001-8441-5075
citation:
ama: Field D, Fraisse C. Breaking down barriers in morning glories. Molecular
ecology. 2019;28(7):1579-1581. doi:10.1111/mec.15048
apa: Field, D., & Fraisse, C. (2019). Breaking down barriers in morning glories.
Molecular Ecology. Wiley. https://doi.org/10.1111/mec.15048
chicago: Field, David, and Christelle Fraisse. “Breaking down Barriers in Morning
Glories.” Molecular Ecology. Wiley, 2019. https://doi.org/10.1111/mec.15048.
ieee: D. Field and C. Fraisse, “Breaking down barriers in morning glories,” Molecular
ecology, vol. 28, no. 7. Wiley, pp. 1579–1581, 2019.
ista: Field D, Fraisse C. 2019. Breaking down barriers in morning glories. Molecular
ecology. 28(7), 1579–1581.
mla: Field, David, and Christelle Fraisse. “Breaking down Barriers in Morning Glories.”
Molecular Ecology, vol. 28, no. 7, Wiley, 2019, pp. 1579–81, doi:10.1111/mec.15048.
short: D. Field, C. Fraisse, Molecular Ecology 28 (2019) 1579–1581.
date_created: 2019-05-19T21:59:15Z
date_published: 2019-04-01T00:00:00Z
date_updated: 2023-08-25T10:37:30Z
day: '01'
ddc:
- '580'
- '576'
department:
- _id: NiBa
doi: 10.1111/mec.15048
external_id:
isi:
- '000474808300001'
file:
- access_level: open_access
checksum: 521e3aff3e9263ddf2ffbfe0b6157715
content_type: application/pdf
creator: dernst
date_created: 2019-05-20T11:49:06Z
date_updated: 2020-07-14T12:47:31Z
file_id: '6472'
file_name: 2019_MolecularEcology_Field.pdf
file_size: 367711
relation: main_file
file_date_updated: 2020-07-14T12:47:31Z
has_accepted_license: '1'
intvolume: ' 28'
isi: 1
issue: '7'
language:
- iso: eng
month: '04'
oa: 1
oa_version: Published Version
page: 1579-1581
publication: Molecular ecology
publication_identifier:
eissn:
- 1365294X
publication_status: published
publisher: Wiley
quality_controlled: '1'
scopus_import: '1'
status: public
title: Breaking down barriers in morning glories
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: 28
year: '2019'
...
---
_id: '6465'
abstract:
- lang: eng
text: Tight control over protein degradation is a fundamental requirement for cells
to respond rapidly to various stimuli and adapt to a fluctuating environment.
Here we develop a versatile, easy-to-handle library of destabilizing tags (degrons)
for the precise regulation of protein expression profiles in mammalian cells by
modulating target protein half-lives in a predictable manner. Using the well-established
tetracycline gene-regulation system as a model, we show that the dynamics of protein
expression can be tuned by fusing appropriate degron tags to gene regulators.
Next, we apply this degron library to tune a synthetic pulse-generating circuit
in mammalian cells. With this toolbox we establish a set of pulse generators with
tailored pulse lengths and magnitudes of protein expression. This methodology
will prove useful in the functional roles of essential proteins, fine-tuning of
gene-expression systems, and enabling a higher complexity in the design of synthetic
biological systems in mammalian cells.
article_number: '2013'
article_processing_charge: No
author:
- first_name: Hélène
full_name: Chassin, Hélène
last_name: Chassin
- first_name: Marius
full_name: Müller, Marius
last_name: Müller
- first_name: Marcel
full_name: Tigges, Marcel
last_name: Tigges
- first_name: Leo
full_name: Scheller, Leo
last_name: Scheller
- first_name: Moritz
full_name: Lang, Moritz
id: 29E0800A-F248-11E8-B48F-1D18A9856A87
last_name: Lang
- first_name: Martin
full_name: Fussenegger, Martin
last_name: Fussenegger
citation:
ama: Chassin H, Müller M, Tigges M, Scheller L, Lang M, Fussenegger M. A modular
degron library for synthetic circuits in mammalian cells. Nature Communications.
2019;10(1). doi:10.1038/s41467-019-09974-5
apa: Chassin, H., Müller, M., Tigges, M., Scheller, L., Lang, M., & Fussenegger,
M. (2019). A modular degron library for synthetic circuits in mammalian cells.
Nature Communications. Springer Nature. https://doi.org/10.1038/s41467-019-09974-5
chicago: Chassin, Hélène, Marius Müller, Marcel Tigges, Leo Scheller, Moritz Lang,
and Martin Fussenegger. “A Modular Degron Library for Synthetic Circuits in Mammalian
Cells.” Nature Communications. Springer Nature, 2019. https://doi.org/10.1038/s41467-019-09974-5.
ieee: H. Chassin, M. Müller, M. Tigges, L. Scheller, M. Lang, and M. Fussenegger,
“A modular degron library for synthetic circuits in mammalian cells,” Nature
Communications, vol. 10, no. 1. Springer Nature, 2019.
ista: Chassin H, Müller M, Tigges M, Scheller L, Lang M, Fussenegger M. 2019. A
modular degron library for synthetic circuits in mammalian cells. Nature Communications.
10(1), 2013.
mla: Chassin, Hélène, et al. “A Modular Degron Library for Synthetic Circuits in
Mammalian Cells.” Nature Communications, vol. 10, no. 1, 2013, Springer
Nature, 2019, doi:10.1038/s41467-019-09974-5.
short: H. Chassin, M. Müller, M. Tigges, L. Scheller, M. Lang, M. Fussenegger, Nature
Communications 10 (2019).
date_created: 2019-05-19T21:59:14Z
date_published: 2019-05-01T00:00:00Z
date_updated: 2023-08-25T10:33:51Z
day: '01'
ddc:
- '570'
department:
- _id: CaGu
doi: 10.1038/s41467-019-09974-5
external_id:
isi:
- '000466338600006'
file:
- access_level: open_access
checksum: e214d3e4f8c81e35981583c4569b51b8
content_type: application/pdf
creator: dernst
date_created: 2019-05-20T07:33:54Z
date_updated: 2020-07-14T12:47:31Z
file_id: '6471'
file_name: 2019_NatureComm_Chassin.pdf
file_size: 1191827
relation: main_file
file_date_updated: 2020-07-14T12:47:31Z
has_accepted_license: '1'
intvolume: ' 10'
isi: 1
issue: '1'
language:
- iso: eng
month: '05'
oa: 1
oa_version: Published Version
publication: Nature Communications
publication_identifier:
eissn:
- '20411723'
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
related_material:
link:
- relation: erratum
url: https://doi.org/10.1038/s41467-023-36111-0
scopus_import: '1'
status: public
title: A modular degron library for synthetic circuits in mammalian cells
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: journal_article
user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
volume: 10
year: '2019'
...
---
_id: '6467'
abstract:
- lang: eng
text: Fitness interactions between mutations can influence a population’s evolution
in many different ways. While epistatic effects are difficult to measure precisely,
important information is captured by the mean and variance of log fitnesses for
individuals carrying different numbers of mutations. We derive predictions for
these quantities from a class of simple fitness landscapes, based on models of
optimizing selection on quantitative traits. We also explore extensions to the
models, including modular pleiotropy, variable effect sizes, mutational bias and
maladaptation of the wild type. We illustrate our approach by reanalysing a large
dataset of mutant effects in a yeast snoRNA (small nucleolar RNA). Though characterized
by some large epistatic effects, these data give a good overall fit to the non-epistatic
null model, suggesting that epistasis might have limited influence on the evolutionary
dynamics in this system. We also show how the amount of epistasis depends on both
the underlying fitness landscape and the distribution of mutations, and so is
expected to vary in consistent ways between new mutations, standing variation
and fixed mutations.
article_number: '0881'
article_processing_charge: No
article_type: original
author:
- first_name: Christelle
full_name: Fraisse, Christelle
id: 32DF5794-F248-11E8-B48F-1D18A9856A87
last_name: Fraisse
orcid: 0000-0001-8441-5075
- first_name: John J.
full_name: Welch, John J.
last_name: Welch
citation:
ama: Fraisse C, Welch JJ. The distribution of epistasis on simple fitness landscapes.
Biology Letters. 2019;15(4). doi:10.1098/rsbl.2018.0881
apa: Fraisse, C., & Welch, J. J. (2019). The distribution of epistasis on simple
fitness landscapes. Biology Letters. Royal Society of London. https://doi.org/10.1098/rsbl.2018.0881
chicago: Fraisse, Christelle, and John J. Welch. “The Distribution of Epistasis
on Simple Fitness Landscapes.” Biology Letters. Royal Society of London,
2019. https://doi.org/10.1098/rsbl.2018.0881.
ieee: C. Fraisse and J. J. Welch, “The distribution of epistasis on simple fitness
landscapes,” Biology Letters, vol. 15, no. 4. Royal Society of London,
2019.
ista: Fraisse C, Welch JJ. 2019. The distribution of epistasis on simple fitness
landscapes. Biology Letters. 15(4), 0881.
mla: Fraisse, Christelle, and John J. Welch. “The Distribution of Epistasis on Simple
Fitness Landscapes.” Biology Letters, vol. 15, no. 4, 0881, Royal Society
of London, 2019, doi:10.1098/rsbl.2018.0881.
short: C. Fraisse, J.J. Welch, Biology Letters 15 (2019).
date_created: 2019-05-19T21:59:15Z
date_published: 2019-04-03T00:00:00Z
date_updated: 2023-08-25T10:34:41Z
day: '03'
department:
- _id: BeVi
- _id: NiBa
doi: 10.1098/rsbl.2018.0881
ec_funded: 1
external_id:
isi:
- '000465405300010'
pmid:
- '31014191'
intvolume: ' 15'
isi: 1
issue: '4'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.1098/rsbl.2018.0881
month: '04'
oa: 1
oa_version: Published Version
pmid: 1
project:
- _id: 25681D80-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '291734'
name: International IST Postdoc Fellowship Programme
publication: Biology Letters
publication_identifier:
eissn:
- 1744957X
issn:
- '17449561'
publication_status: published
publisher: Royal Society of London
quality_controlled: '1'
related_material:
link:
- relation: supplementary_material
url: https://dx.doi.org/10.6084/m9.figshare.c.4461008
record:
- id: '9798'
relation: research_data
status: public
- id: '9799'
relation: research_data
status: public
scopus_import: '1'
status: public
title: The distribution of epistasis on simple fitness landscapes
type: journal_article
user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
volume: 15
year: '2019'
...
---
_id: '6470'
abstract:
- lang: eng
text: 'Investigating neuronal activity using genetically encoded Ca2+ indicators
in behaving animals is hampered by inaccuracies in spike inference from fluorescent
tracers. Here we combine two‐photon [Ca2+] imaging with cell‐attached recordings,
followed by post hoc determination of the expression level of GCaMP6f, to explore
how it affects the amplitude, kinetics and temporal summation of somatic [Ca2+]
transients in mouse hippocampal pyramidal cells (PCs). The amplitude of unitary
[Ca2+] transients (evoked by a single action potential) negatively correlates
with GCaMP6f expression, but displays large variability even among PCs with similarly
low expression levels. The summation of fluorescence signals is frequency‐dependent,
supralinear and also shows remarkable cell‐to‐cell variability. We performed experimental
data‐based simulations and found that spike inference error rates using MLspike
depend strongly on unitary peak amplitudes and GCaMP6f expression levels. We provide
simple methods for estimating the unitary [Ca2+] transients in individual weakly
GCaMP6f‐expressing PCs, with which we achieve spike inference error rates of ∼5%. '
article_processing_charge: No
article_type: original
author:
- first_name: Tímea
full_name: Éltes, Tímea
last_name: Éltes
- first_name: Miklos
full_name: Szoboszlay, Miklos
last_name: Szoboszlay
- first_name: Margit Katalin
full_name: Szigeti, Margit Katalin
id: 44F4BDC0-F248-11E8-B48F-1D18A9856A87
last_name: Szigeti
orcid: 0000-0001-9500-8758
- first_name: Zoltan
full_name: Nusser, Zoltan
last_name: Nusser
citation:
ama: Éltes T, Szoboszlay M, Szigeti MK, Nusser Z. Improved spike inference accuracy
by estimating the peak amplitude of unitary [Ca2+] transients in weakly GCaMP6f-expressing
hippocampal pyramidal cells. Journal of Physiology. 2019;597(11):2925–2947.
doi:10.1113/JP277681
apa: Éltes, T., Szoboszlay, M., Szigeti, M. K., & Nusser, Z. (2019). Improved
spike inference accuracy by estimating the peak amplitude of unitary [Ca2+] transients
in weakly GCaMP6f-expressing hippocampal pyramidal cells. Journal of Physiology.
Wiley. https://doi.org/10.1113/JP277681
chicago: Éltes, Tímea, Miklos Szoboszlay, Margit Katalin Szigeti, and Zoltan Nusser.
“Improved Spike Inference Accuracy by Estimating the Peak Amplitude of Unitary
[Ca2+] Transients in Weakly GCaMP6f-Expressing Hippocampal Pyramidal Cells.” Journal
of Physiology. Wiley, 2019. https://doi.org/10.1113/JP277681.
ieee: T. Éltes, M. Szoboszlay, M. K. Szigeti, and Z. Nusser, “Improved spike inference
accuracy by estimating the peak amplitude of unitary [Ca2+] transients in weakly
GCaMP6f-expressing hippocampal pyramidal cells,” Journal of Physiology,
vol. 597, no. 11. Wiley, pp. 2925–2947, 2019.
ista: Éltes T, Szoboszlay M, Szigeti MK, Nusser Z. 2019. Improved spike inference
accuracy by estimating the peak amplitude of unitary [Ca2+] transients in weakly
GCaMP6f-expressing hippocampal pyramidal cells. Journal of Physiology. 597(11),
2925–2947.
mla: Éltes, Tímea, et al. “Improved Spike Inference Accuracy by Estimating the Peak
Amplitude of Unitary [Ca2+] Transients in Weakly GCaMP6f-Expressing Hippocampal
Pyramidal Cells.” Journal of Physiology, vol. 597, no. 11, Wiley, 2019,
pp. 2925–2947, doi:10.1113/JP277681.
short: T. Éltes, M. Szoboszlay, M.K. Szigeti, Z. Nusser, Journal of Physiology 597
(2019) 2925–2947.
date_created: 2019-05-19T21:59:17Z
date_published: 2019-06-01T00:00:00Z
date_updated: 2023-08-25T10:34:15Z
day: '01'
department:
- _id: GaNo
doi: 10.1113/JP277681
external_id:
isi:
- '000470780400013'
pmid:
- '31006863'
intvolume: ' 597'
isi: 1
issue: '11'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.1113/JP277681
month: '06'
oa: 1
oa_version: Published Version
page: 2925–2947
pmid: 1
publication: Journal of Physiology
publication_identifier:
eissn:
- '14697793'
issn:
- '00223751'
publication_status: published
publisher: Wiley
quality_controlled: '1'
scopus_import: '1'
status: public
title: Improved spike inference accuracy by estimating the peak amplitude of unitary
[Ca2+] transients in weakly GCaMP6f-expressing hippocampal pyramidal cells
type: journal_article
user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
volume: 597
year: '2019'
...
---
_id: '6493'
abstract:
- lang: eng
text: We present two algorithmic approaches for synthesizing linear hybrid automata
from experimental data. Unlike previous approaches, our algorithms work without
a template and generate an automaton with nondeterministic guards and invariants,
and with an arbitrary number and topology of modes. They thus construct a succinct
model from the data and provide formal guarantees. In particular, (1) the generated
automaton can reproduce the data up to a specified tolerance and (2) the automaton
is tight, given the first guarantee. Our first approach encodes the synthesis
problem as a logical formula in the theory of linear arithmetic, which can then
be solved by an SMT solver. This approach minimizes the number of modes in the
resulting model but is only feasible for limited data sets. To address scalability,
we propose a second approach that does not enforce to find a minimal model. The
algorithm constructs an initial automaton and then iteratively extends the automaton
based on processing new data. Therefore the algorithm is well-suited for online
and synthesis-in-the-loop applications. The core of the algorithm is a membership
query that checks whether, within the specified tolerance, a given data set can
result from the execution of a given automaton. We solve this membership problem
for linear hybrid automata by repeated reachability computations. We demonstrate
the effectiveness of the algorithm on synthetic data sets and on cardiac-cell
measurements.
alternative_title:
- LNCS
article_processing_charge: No
author:
- first_name: Miriam
full_name: Garcia Soto, Miriam
id: 4B3207F6-F248-11E8-B48F-1D18A9856A87
last_name: Garcia Soto
orcid: 0000−0003−2936−5719
- first_name: Thomas A
full_name: Henzinger, Thomas A
id: 40876CD8-F248-11E8-B48F-1D18A9856A87
last_name: Henzinger
orcid: 0000−0002−2985−7724
- first_name: Christian
full_name: Schilling, Christian
id: 3A2F4DCE-F248-11E8-B48F-1D18A9856A87
last_name: Schilling
orcid: 0000-0003-3658-1065
- first_name: Luka
full_name: Zeleznik, Luka
id: 3ADCA2E4-F248-11E8-B48F-1D18A9856A87
last_name: Zeleznik
citation:
ama: 'Garcia Soto M, Henzinger TA, Schilling C, Zeleznik L. Membership-based synthesis
of linear hybrid automata. In: 31st International Conference on Computer-Aided
Verification. Vol 11561. Springer; 2019:297-314. doi:10.1007/978-3-030-25540-4_16'
apa: 'Garcia Soto, M., Henzinger, T. A., Schilling, C., & Zeleznik, L. (2019).
Membership-based synthesis of linear hybrid automata. In 31st International
Conference on Computer-Aided Verification (Vol. 11561, pp. 297–314). New York
City, NY, USA: Springer. https://doi.org/10.1007/978-3-030-25540-4_16'
chicago: Garcia Soto, Miriam, Thomas A Henzinger, Christian Schilling, and Luka
Zeleznik. “Membership-Based Synthesis of Linear Hybrid Automata.” In 31st International
Conference on Computer-Aided Verification, 11561:297–314. Springer, 2019.
https://doi.org/10.1007/978-3-030-25540-4_16.
ieee: M. Garcia Soto, T. A. Henzinger, C. Schilling, and L. Zeleznik, “Membership-based
synthesis of linear hybrid automata,” in 31st International Conference on Computer-Aided
Verification, New York City, NY, USA, 2019, vol. 11561, pp. 297–314.
ista: 'Garcia Soto M, Henzinger TA, Schilling C, Zeleznik L. 2019. Membership-based
synthesis of linear hybrid automata. 31st International Conference on Computer-Aided
Verification. CAV: Computer-Aided Verification, LNCS, vol. 11561, 297–314.'
mla: Garcia Soto, Miriam, et al. “Membership-Based Synthesis of Linear Hybrid Automata.”
31st International Conference on Computer-Aided Verification, vol. 11561,
Springer, 2019, pp. 297–314, doi:10.1007/978-3-030-25540-4_16.
short: M. Garcia Soto, T.A. Henzinger, C. Schilling, L. Zeleznik, in:, 31st International
Conference on Computer-Aided Verification, Springer, 2019, pp. 297–314.
conference:
end_date: 2019-07-18
location: New York City, NY, USA
name: 'CAV: Computer-Aided Verification'
start_date: 2019-07-15
date_created: 2019-05-27T07:09:53Z
date_published: 2019-07-12T00:00:00Z
date_updated: 2023-08-25T10:40:41Z
day: '12'
ddc:
- '000'
department:
- _id: ToHe
doi: 10.1007/978-3-030-25540-4_16
ec_funded: 1
external_id:
isi:
- '000491468000016'
file:
- access_level: open_access
checksum: 1f1d61b83a151031745ef70a501da3d6
content_type: application/pdf
creator: dernst
date_created: 2019-08-14T11:05:30Z
date_updated: 2020-07-14T12:47:32Z
file_id: '6817'
file_name: 2019_CAV_GarciaSoto.pdf
file_size: 674795
relation: main_file
file_date_updated: 2020-07-14T12:47:32Z
has_accepted_license: '1'
intvolume: ' 11561'
isi: 1
keyword:
- Synthesis
- Linear hybrid automaton
- Membership
language:
- iso: eng
month: '07'
oa: 1
oa_version: Published Version
page: 297-314
project:
- _id: 260C2330-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '754411'
name: ISTplus - Postdoctoral Fellowships
- _id: 25832EC2-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: S 11407_N23
name: Rigorous Systems Engineering
- _id: 25F42A32-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: Z211
name: The Wittgenstein Prize
publication: 31st International Conference on Computer-Aided Verification
publication_identifier:
isbn:
- '9783030255398'
issn:
- 0302-9743
publication_status: published
publisher: Springer
quality_controlled: '1'
scopus_import: '1'
status: public
title: Membership-based synthesis of linear hybrid automata
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: conference
user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
volume: 11561
year: '2019'
...
---
_id: '6485'
abstract:
- lang: eng
text: Traditional concurrent programming involves manipulating shared mutable state.
Alternatives to this programming style are communicating sequential processes
(CSP) [1] and actor [2] models, which share data via explicit communication. Rendezvous
channelis the common abstraction for communication between several processes,
where senders and receivers perform a rendezvous handshake as a part of their
protocol (senders wait for receivers and vice versa). Additionally to this, channels
support the select expression. In this work, we present the first efficient lock-free
channel algorithm, and compare it against Go [3] and Kotlin [4] baseline implementations.
article_processing_charge: No
author:
- first_name: Nikita
full_name: Koval, Nikita
id: 2F4DB10C-F248-11E8-B48F-1D18A9856A87
last_name: Koval
- first_name: Dan-Adrian
full_name: Alistarh, Dan-Adrian
id: 4A899BFC-F248-11E8-B48F-1D18A9856A87
last_name: Alistarh
orcid: 0000-0003-3650-940X
- first_name: Roman
full_name: Elizarov, Roman
last_name: Elizarov
citation:
ama: Koval N, Alistarh D-A, Elizarov R. Lock-Free Channels for Programming via
Communicating Sequential Processes. ACM Press; 2019:417-418. doi:10.1145/3293883.3297000
apa: 'Koval, N., Alistarh, D.-A., & Elizarov, R. (2019). Lock-free channels
for programming via communicating sequential processes. Proceedings of
the 24th Symposium on Principles and Practice of Parallel Programming (pp.
417–418). Washington, NY, United States: ACM Press. https://doi.org/10.1145/3293883.3297000'
chicago: Koval, Nikita, Dan-Adrian Alistarh, and Roman Elizarov. Lock-Free Channels
for Programming via Communicating Sequential Processes. Proceedings of
the 24th Symposium on Principles and Practice of Parallel Programming. ACM
Press, 2019. https://doi.org/10.1145/3293883.3297000.
ieee: N. Koval, D.-A. Alistarh, and R. Elizarov, Lock-free channels for programming
via communicating sequential processes. ACM Press, 2019, pp. 417–418.
ista: Koval N, Alistarh D-A, Elizarov R. 2019. Lock-free channels for programming
via communicating sequential processes, ACM Press,p.
mla: Koval, Nikita, et al. “Lock-Free Channels for Programming via Communicating
Sequential Processes.” Proceedings of the 24th Symposium on Principles and
Practice of Parallel Programming, ACM Press, 2019, pp. 417–18, doi:10.1145/3293883.3297000.
short: N. Koval, D.-A. Alistarh, R. Elizarov, Lock-Free Channels for Programming
via Communicating Sequential Processes, ACM Press, 2019.
conference:
end_date: 2019-02-20
location: Washington, NY, United States
name: 'PPoPP: Principles and Practice of Parallel Programming'
start_date: 2019-02-16
date_created: 2019-05-24T10:09:12Z
date_published: 2019-02-01T00:00:00Z
date_updated: 2023-08-25T10:41:20Z
day: '01'
department:
- _id: DaAl
doi: 10.1145/3293883.3297000
external_id:
isi:
- '000587604600044'
isi: 1
language:
- iso: eng
month: '02'
oa_version: None
page: 417-418
publication: Proceedings of the 24th Symposium on Principles and Practice of Parallel
Programming
publication_identifier:
isbn:
- '9781450362252'
publication_status: published
publisher: ACM Press
quality_controlled: '1'
status: public
title: Lock-free channels for programming via communicating sequential processes
type: conference_poster
user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
year: '2019'
...
---
_id: '6504'
abstract:
- lang: eng
text: "Root gravitropism is one of the most important processes allowing plant adaptation
to the land environment. Auxin plays a central role in mediating root gravitropism,
but how auxin contributes to gravitational perception and the subsequent response
is still unclear.\r\n\r\nHere, we showed that the local auxin maximum/gradient
within the root apex, which is generated by the PIN directional auxin transporters,
regulates the expression of three key starch granule synthesis genes, SS4, PGM
and ADG1, which in turn influence the accumulation of starch granules that serve
as a statolith perceiving gravity.\r\n\r\nMoreover, using the cvxIAA‐ccvTIR1 system,
we also showed that TIR1‐mediated auxin signaling is required for starch granule
formation and gravitropic response within root tips. In addition, axr3 mutants
showed reduced auxin‐mediated starch granule accumulation and disruption of gravitropism
within the root apex.\r\n\r\nOur results indicate that auxin‐mediated statolith
production relies on the TIR1/AFB‐AXR3‐mediated auxin signaling pathway. In summary,
we propose a dual role for auxin in gravitropism: the regulation of both gravity
perception and response."
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: P
full_name: He, P
last_name: He
- first_name: X
full_name: Ma, X
last_name: Ma
- first_name: Z
full_name: Yang, Z
last_name: Yang
- first_name: C
full_name: Pang, C
last_name: Pang
- first_name: J
full_name: Yu, J
last_name: Yu
- first_name: G
full_name: Wang, G
last_name: Wang
- first_name: Jiří
full_name: Friml, Jiří
id: 4159519E-F248-11E8-B48F-1D18A9856A87
last_name: Friml
orcid: 0000-0002-8302-7596
- first_name: G
full_name: Xiao, G
last_name: Xiao
citation:
ama: Zhang Y, He P, Ma X, et al. Auxin-mediated statolith production for root gravitropism.
New Phytologist. 2019;224(2):761-774. doi:10.1111/nph.15932
apa: Zhang, Y., He, P., Ma, X., Yang, Z., Pang, C., Yu, J., … Xiao, G. (2019). Auxin-mediated
statolith production for root gravitropism. New Phytologist. Wiley. https://doi.org/10.1111/nph.15932
chicago: Zhang, Yuzhou, P He, X Ma, Z Yang, C Pang, J Yu, G Wang, Jiří Friml, and
G Xiao. “Auxin-Mediated Statolith Production for Root Gravitropism.” New Phytologist.
Wiley, 2019. https://doi.org/10.1111/nph.15932.
ieee: Y. Zhang et al., “Auxin-mediated statolith production for root gravitropism,”
New Phytologist, vol. 224, no. 2. Wiley, pp. 761–774, 2019.
ista: Zhang Y, He P, Ma X, Yang Z, Pang C, Yu J, Wang G, Friml J, Xiao G. 2019.
Auxin-mediated statolith production for root gravitropism. New Phytologist. 224(2),
761–774.
mla: Zhang, Yuzhou, et al. “Auxin-Mediated Statolith Production for Root Gravitropism.”
New Phytologist, vol. 224, no. 2, Wiley, 2019, pp. 761–74, doi:10.1111/nph.15932.
short: Y. Zhang, P. He, X. Ma, Z. Yang, C. Pang, J. Yu, G. Wang, J. Friml, G. Xiao,
New Phytologist 224 (2019) 761–774.
date_created: 2019-05-28T14:33:26Z
date_published: 2019-10-01T00:00:00Z
date_updated: 2023-08-28T08:40:13Z
day: '01'
ddc:
- '580'
department:
- _id: JiFr
doi: 10.1111/nph.15932
external_id:
isi:
- '000487184200024'
pmid:
- '31111487'
file:
- access_level: open_access
checksum: 6488243334538f5c39099a701cbf76b9
content_type: application/pdf
creator: dernst
date_created: 2020-10-14T08:59:33Z
date_updated: 2020-10-14T08:59:33Z
file_id: '8661'
file_name: 2019_NewPhytologist_Zhang_accepted.pdf
file_size: 1099061
relation: main_file
success: 1
file_date_updated: 2020-10-14T08:59:33Z
has_accepted_license: '1'
intvolume: ' 224'
isi: 1
issue: '2'
language:
- iso: eng
month: '10'
oa: 1
oa_version: Submitted Version
page: 761-774
pmid: 1
publication: New Phytologist
publication_identifier:
eissn:
- 1469-8137
issn:
- 0028-646x
publication_status: published
publisher: Wiley
quality_controlled: '1'
scopus_import: '1'
status: public
title: Auxin-mediated statolith production for root gravitropism
type: journal_article
user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
volume: 224
year: '2019'
...
---
_id: '6506'
abstract:
- lang: eng
text: How does environmental complexity affect the evolution of single genes? Here,
we measured the effects of a set of Bacillus subtilis glutamate dehydrogenase
mutants across 19 different environments—from phenotypically homogeneous single-cell
populations in liquid media to heterogeneous biofilms, plant roots and soil populations.
The effects of individual gene mutations on organismal fitness were highly reproducible
in liquid cultures. However, 84% of the tested alleles showed opposing fitness
effects under different growth conditions (sign environmental pleiotropy). In
colony biofilms and soil samples, different alleles dominated in parallel replica
experiments. Accordingly, we found that in these heterogeneous cell populations
the fate of mutations was dictated by a combination of selection and drift. The
latter relates to programmed prophage excisions that occurred during biofilm development.
Overall, for each condition, a wide range of glutamate dehydrogenase mutations
persisted and sometimes fixated as a result of the combined action of selection,
pleiotropy and chance. However, over longer periods and in multiple environments,
nearly all of this diversity would be lost—across all the environments and conditions
that we tested, the wild type was the fittest allele.
article_processing_charge: No
article_type: original
author:
- first_name: Lianet
full_name: Noda-García, Lianet
last_name: Noda-García
- first_name: Dan
full_name: Davidi, Dan
last_name: Davidi
- first_name: Elisa
full_name: Korenblum, Elisa
last_name: Korenblum
- first_name: Assaf
full_name: Elazar, Assaf
last_name: Elazar
- first_name: Ekaterina
full_name: Putintseva, Ekaterina
id: 2EF67C84-F248-11E8-B48F-1D18A9856A87
last_name: Putintseva
- first_name: Asaph
full_name: Aharoni, Asaph
last_name: Aharoni
- first_name: Dan S.
full_name: Tawfik, Dan S.
last_name: Tawfik
citation:
ama: Noda-García L, Davidi D, Korenblum E, et al. Chance and pleiotropy dominate
genetic diversity in complex bacterial environments. Nature Microbiology.
2019;4(7):1221–1230. doi:10.1038/s41564-019-0412-y
apa: Noda-García, L., Davidi, D., Korenblum, E., Elazar, A., Putintseva, E., Aharoni,
A., & Tawfik, D. S. (2019). Chance and pleiotropy dominate genetic diversity
in complex bacterial environments. Nature Microbiology. Springer Nature.
https://doi.org/10.1038/s41564-019-0412-y
chicago: Noda-García, Lianet, Dan Davidi, Elisa Korenblum, Assaf Elazar, Ekaterina
Putintseva, Asaph Aharoni, and Dan S. Tawfik. “Chance and Pleiotropy Dominate
Genetic Diversity in Complex Bacterial Environments.” Nature Microbiology.
Springer Nature, 2019. https://doi.org/10.1038/s41564-019-0412-y.
ieee: L. Noda-García et al., “Chance and pleiotropy dominate genetic diversity
in complex bacterial environments,” Nature Microbiology, vol. 4, no. 7.
Springer Nature, pp. 1221–1230, 2019.
ista: Noda-García L, Davidi D, Korenblum E, Elazar A, Putintseva E, Aharoni A, Tawfik
DS. 2019. Chance and pleiotropy dominate genetic diversity in complex bacterial
environments. Nature Microbiology. 4(7), 1221–1230.
mla: Noda-García, Lianet, et al. “Chance and Pleiotropy Dominate Genetic Diversity
in Complex Bacterial Environments.” Nature Microbiology, vol. 4, no. 7,
Springer Nature, 2019, pp. 1221–1230, doi:10.1038/s41564-019-0412-y.
short: L. Noda-García, D. Davidi, E. Korenblum, A. Elazar, E. Putintseva, A. Aharoni,
D.S. Tawfik, Nature Microbiology 4 (2019) 1221–1230.
date_created: 2019-05-29T13:03:30Z
date_published: 2019-07-01T00:00:00Z
date_updated: 2023-08-28T08:39:47Z
day: '01'
department:
- _id: FyKo
doi: 10.1038/s41564-019-0412-y
external_id:
isi:
- '000480348200017'
intvolume: ' 4'
isi: 1
issue: '7'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://www.biorxiv.org/content/10.1101/340828v2
month: '07'
oa: 1
oa_version: Preprint
page: 1221–1230
publication: Nature Microbiology
publication_identifier:
issn:
- 2058-5276
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
scopus_import: '1'
status: public
title: Chance and pleiotropy dominate genetic diversity in complex bacterial environments
type: journal_article
user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
volume: 4
year: '2019'
...
---
_id: '6521'
abstract:
- lang: eng
text: Microglia have emerged as a critical component of neurodegenerative diseases.
Genetic manipulation of microglia can elucidate their functional impact in disease.
In neuroscience, recombinant viruses such as lentiviruses and adeno-associated
viruses (AAVs) have been successfully used to target various cell types in the
brain, although effective transduction of microglia is rare. In this review, we
provide a short background of lentiviruses and AAVs, and strategies for designing
recombinant viral vectors. Then, we will summarize recent literature on successful
microglial transductions in vitro and in vivo, and discuss the current challenges.
Finally, we provide guidelines for reporting the efficiency and specificity of
viral targeting in microglia, which will enable the microglial research community
to assess and improve methodologies for future studies.
article_number: '134310'
article_processing_charge: No
article_type: original
author:
- first_name: Margaret E
full_name: Maes, Margaret E
id: 3838F452-F248-11E8-B48F-1D18A9856A87
last_name: Maes
orcid: 0000-0001-9642-1085
- first_name: Gloria
full_name: Colombo, Gloria
id: 3483CF6C-F248-11E8-B48F-1D18A9856A87
last_name: Colombo
orcid: 0000-0001-9434-8902
- first_name: Rouven
full_name: Schulz, Rouven
id: 4C5E7B96-F248-11E8-B48F-1D18A9856A87
last_name: Schulz
orcid: 0000-0001-5297-733X
- first_name: Sandra
full_name: Siegert, Sandra
id: 36ACD32E-F248-11E8-B48F-1D18A9856A87
last_name: Siegert
orcid: 0000-0001-8635-0877
citation:
ama: 'Maes ME, Colombo G, Schulz R, Siegert S. Targeting microglia with lentivirus
and AAV: Recent advances and remaining challenges. Neuroscience Letters.
2019;707. doi:10.1016/j.neulet.2019.134310'
apa: 'Maes, M. E., Colombo, G., Schulz, R., & Siegert, S. (2019). Targeting
microglia with lentivirus and AAV: Recent advances and remaining challenges. Neuroscience
Letters. Elsevier. https://doi.org/10.1016/j.neulet.2019.134310'
chicago: 'Maes, Margaret E, Gloria Colombo, Rouven Schulz, and Sandra Siegert. “Targeting
Microglia with Lentivirus and AAV: Recent Advances and Remaining Challenges.”
Neuroscience Letters. Elsevier, 2019. https://doi.org/10.1016/j.neulet.2019.134310.'
ieee: 'M. E. Maes, G. Colombo, R. Schulz, and S. Siegert, “Targeting microglia with
lentivirus and AAV: Recent advances and remaining challenges,” Neuroscience
Letters, vol. 707. Elsevier, 2019.'
ista: 'Maes ME, Colombo G, Schulz R, Siegert S. 2019. Targeting microglia with lentivirus
and AAV: Recent advances and remaining challenges. Neuroscience Letters. 707,
134310.'
mla: 'Maes, Margaret E., et al. “Targeting Microglia with Lentivirus and AAV: Recent
Advances and Remaining Challenges.” Neuroscience Letters, vol. 707, 134310,
Elsevier, 2019, doi:10.1016/j.neulet.2019.134310.'
short: M.E. Maes, G. Colombo, R. Schulz, S. Siegert, Neuroscience Letters 707 (2019).
date_created: 2019-06-05T13:16:24Z
date_published: 2019-08-10T00:00:00Z
date_updated: 2023-08-28T09:30:57Z
day: '10'
ddc:
- '570'
department:
- _id: SaSi
doi: 10.1016/j.neulet.2019.134310
ec_funded: 1
external_id:
isi:
- '000486094600037'
pmid:
- '31158432'
file:
- access_level: open_access
checksum: 553c9dbd39727fbed55ee991c51ca4d1
content_type: application/pdf
creator: dernst
date_created: 2019-06-08T11:44:20Z
date_updated: 2020-07-14T12:47:33Z
file_id: '6551'
file_name: 2019_Neuroscience_Maes.pdf
file_size: 1779287
relation: main_file
file_date_updated: 2020-07-14T12:47:33Z
has_accepted_license: '1'
intvolume: ' 707'
isi: 1
language:
- iso: eng
month: '08'
oa: 1
oa_version: Published Version
pmid: 1
project:
- _id: 2564DBCA-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '665385'
name: International IST Doctoral Program
- _id: 25D4A630-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '715571'
name: Microglia action towards neuronal circuit formation and function in health
and disease
- _id: 267F75D8-B435-11E9-9278-68D0E5697425
name: Modulating microglia through G protein-coupled receptor (GPCR) signaling
publication: Neuroscience Letters
publication_identifier:
issn:
- 0304-3940
publication_status: published
publisher: Elsevier
quality_controlled: '1'
scopus_import: '1'
status: public
title: 'Targeting microglia with lentivirus and AAV: Recent advances and remaining
challenges'
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: 707
year: '2019'
...
---
_id: '6513'
abstract:
- lang: eng
text: Adult intestinal stem cells are located at the bottom of crypts of Lieberkühn,
where they express markers such as LGR5 1,2 and fuel the constant replenishment
of the intestinal epithelium1. Although fetal LGR5-expressing cells can give rise
to adult intestinal stem cells3,4, it remains unclear whether this population
in the patterned epithelium represents unique intestinal stem-cell precursors.
Here we show, using unbiased quantitative lineage-tracing approaches, biophysical
modelling and intestinal transplantation, that all cells of the mouse intestinal
epithelium—irrespective of their location and pattern of LGR5 expression in the
fetal gut tube—contribute actively to the adult intestinal stem cell pool. Using
3D imaging, we find that during fetal development the villus undergoes gross remodelling
and fission. This brings epithelial cells from the non-proliferative villus into
the proliferative intervillus region, which enables them to contribute to the
adult stem-cell niche. Our results demonstrate that large-scale remodelling of
the intestinal wall and cell-fate specification are closely linked. Moreover,
these findings provide a direct link between the observed plasticity and cellular
reprogramming of differentiating cells in adult tissues following damage5,6,7,8,9,
revealing that stem-cell identity is an induced rather than a hardwired property.
article_processing_charge: No
article_type: original
author:
- first_name: Jordi
full_name: Guiu, Jordi
last_name: Guiu
- first_name: Edouard B
full_name: Hannezo, Edouard B
id: 3A9DB764-F248-11E8-B48F-1D18A9856A87
last_name: Hannezo
orcid: 0000-0001-6005-1561
- first_name: Shiro
full_name: Yui, Shiro
last_name: Yui
- first_name: Samuel
full_name: Demharter, Samuel
last_name: Demharter
- first_name: Svetlana
full_name: Ulyanchenko, Svetlana
last_name: Ulyanchenko
- first_name: Martti
full_name: Maimets, Martti
last_name: Maimets
- first_name: Anne
full_name: Jørgensen, Anne
last_name: Jørgensen
- first_name: Signe
full_name: Perlman, Signe
last_name: Perlman
- first_name: Lene
full_name: Lundvall, Lene
last_name: Lundvall
- first_name: Linn Salto
full_name: Mamsen, Linn Salto
last_name: Mamsen
- first_name: Agnete
full_name: Larsen, Agnete
last_name: Larsen
- first_name: Rasmus H.
full_name: Olesen, Rasmus H.
last_name: Olesen
- first_name: Claus Yding
full_name: Andersen, Claus Yding
last_name: Andersen
- first_name: Lea Langhoff
full_name: Thuesen, Lea Langhoff
last_name: Thuesen
- first_name: Kristine Juul
full_name: Hare, Kristine Juul
last_name: Hare
- first_name: Tune H.
full_name: Pers, Tune H.
last_name: Pers
- first_name: Konstantin
full_name: Khodosevich, Konstantin
last_name: Khodosevich
- first_name: Benjamin D.
full_name: Simons, Benjamin D.
last_name: Simons
- first_name: Kim B.
full_name: Jensen, Kim B.
last_name: Jensen
citation:
ama: Guiu J, Hannezo EB, Yui S, et al. Tracing the origin of adult intestinal stem
cells. Nature. 2019;570:107-111. doi:10.1038/s41586-019-1212-5
apa: Guiu, J., Hannezo, E. B., Yui, S., Demharter, S., Ulyanchenko, S., Maimets,
M., … Jensen, K. B. (2019). Tracing the origin of adult intestinal stem cells.
Nature. Springer Nature. https://doi.org/10.1038/s41586-019-1212-5
chicago: Guiu, Jordi, Edouard B Hannezo, Shiro Yui, Samuel Demharter, Svetlana Ulyanchenko,
Martti Maimets, Anne Jørgensen, et al. “Tracing the Origin of Adult Intestinal
Stem Cells.” Nature. Springer Nature, 2019. https://doi.org/10.1038/s41586-019-1212-5.
ieee: J. Guiu et al., “Tracing the origin of adult intestinal stem cells,”
Nature, vol. 570. Springer Nature, pp. 107–111, 2019.
ista: Guiu J, Hannezo EB, Yui S, Demharter S, Ulyanchenko S, Maimets M, Jørgensen
A, Perlman S, Lundvall L, Mamsen LS, Larsen A, Olesen RH, Andersen CY, Thuesen
LL, Hare KJ, Pers TH, Khodosevich K, Simons BD, Jensen KB. 2019. Tracing the origin
of adult intestinal stem cells. Nature. 570, 107–111.
mla: Guiu, Jordi, et al. “Tracing the Origin of Adult Intestinal Stem Cells.” Nature,
vol. 570, Springer Nature, 2019, pp. 107–11, doi:10.1038/s41586-019-1212-5.
short: J. Guiu, E.B. Hannezo, S. Yui, S. Demharter, S. Ulyanchenko, M. Maimets,
A. Jørgensen, S. Perlman, L. Lundvall, L.S. Mamsen, A. Larsen, R.H. Olesen, C.Y.
Andersen, L.L. Thuesen, K.J. Hare, T.H. Pers, K. Khodosevich, B.D. Simons, K.B.
Jensen, Nature 570 (2019) 107–111.
date_created: 2019-06-02T21:59:14Z
date_published: 2019-06-06T00:00:00Z
date_updated: 2023-08-28T09:30:23Z
day: '06'
department:
- _id: EdHa
doi: 10.1038/s41586-019-1212-5
external_id:
isi:
- '000470149000048'
pmid:
- '31092921'
intvolume: ' 570'
isi: 1
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6986928
month: '06'
oa: 1
oa_version: Submitted Version
page: 107-111
pmid: 1
publication: Nature
publication_identifier:
eissn:
- '14764687'
issn:
- '00280836'
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
scopus_import: '1'
status: public
title: Tracing the origin of adult intestinal stem cells
type: journal_article
user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
volume: 570
year: '2019'
...
---
_id: '6564'
abstract:
- lang: eng
text: Optogenetics enables the spatio-temporally precise control of cell and animal
behavior. Many optogenetic tools are driven by light-controlled protein–protein
interactions (PPIs) that are repurposed from natural light-sensitive domains (LSDs).
Applying light-controlled PPIs to new target proteins is challenging because it
is difficult to predict which of the many available LSDs, if any, will yield robust
light regulation. As a consequence, fusion protein libraries need to be prepared
and tested, but methods and platforms to facilitate this process are currently
not available. Here, we developed a genetic engineering strategy and vector library
for the rapid generation of light-controlled PPIs. The strategy permits fusing
a target protein to multiple LSDs efficiently and in two orientations. The public
and expandable library contains 29 vectors with blue, green or red light-responsive
LSDs, many of which have been previously applied ex vivo and in vivo. We demonstrate
the versatility of the approach and the necessity for sampling LSDs by generating
light-activated caspase-9 (casp9) enzymes. Collectively, this work provides a
new resource for optical regulation of a broad range of target proteins in cell
and developmental biology.
article_processing_charge: No
article_type: original
author:
- first_name: Alexandra-Madelaine
full_name: Tichy, Alexandra-Madelaine
id: 29D8BB2C-F248-11E8-B48F-1D18A9856A87
last_name: Tichy
- first_name: Elliot J.
full_name: Gerrard, Elliot J.
last_name: Gerrard
- first_name: Julien M.D.
full_name: Legrand, Julien M.D.
last_name: Legrand
- first_name: Robin M.
full_name: Hobbs, Robin M.
last_name: Hobbs
- first_name: Harald L
full_name: Janovjak, Harald L
id: 33BA6C30-F248-11E8-B48F-1D18A9856A87
last_name: Janovjak
orcid: 0000-0002-8023-9315
citation:
ama: Tichy A-M, Gerrard EJ, Legrand JMD, Hobbs RM, Janovjak HL. Engineering strategy
and vector library for the rapid generation of modular light-controlled protein–protein
interactions. Journal of Molecular Biology. 2019;431(17):3046-3055. doi:10.1016/j.jmb.2019.05.033
apa: Tichy, A.-M., Gerrard, E. J., Legrand, J. M. D., Hobbs, R. M., & Janovjak,
H. L. (2019). Engineering strategy and vector library for the rapid generation
of modular light-controlled protein–protein interactions. Journal of Molecular
Biology. Elsevier. https://doi.org/10.1016/j.jmb.2019.05.033
chicago: Tichy, Alexandra-Madelaine, Elliot J. Gerrard, Julien M.D. Legrand, Robin
M. Hobbs, and Harald L Janovjak. “Engineering Strategy and Vector Library for
the Rapid Generation of Modular Light-Controlled Protein–Protein Interactions.”
Journal of Molecular Biology. Elsevier, 2019. https://doi.org/10.1016/j.jmb.2019.05.033.
ieee: A.-M. Tichy, E. J. Gerrard, J. M. D. Legrand, R. M. Hobbs, and H. L. Janovjak,
“Engineering strategy and vector library for the rapid generation of modular light-controlled
protein–protein interactions,” Journal of Molecular Biology, vol. 431,
no. 17. Elsevier, pp. 3046–3055, 2019.
ista: Tichy A-M, Gerrard EJ, Legrand JMD, Hobbs RM, Janovjak HL. 2019. Engineering
strategy and vector library for the rapid generation of modular light-controlled
protein–protein interactions. Journal of Molecular Biology. 431(17), 3046–3055.
mla: Tichy, Alexandra-Madelaine, et al. “Engineering Strategy and Vector Library
for the Rapid Generation of Modular Light-Controlled Protein–Protein Interactions.”
Journal of Molecular Biology, vol. 431, no. 17, Elsevier, 2019, pp. 3046–55,
doi:10.1016/j.jmb.2019.05.033.
short: A.-M. Tichy, E.J. Gerrard, J.M.D. Legrand, R.M. Hobbs, H.L. Janovjak, Journal
of Molecular Biology 431 (2019) 3046–3055.
date_created: 2019-06-16T21:59:14Z
date_published: 2019-08-09T00:00:00Z
date_updated: 2023-08-28T09:39:22Z
day: '09'
department:
- _id: HaJa
doi: 10.1016/j.jmb.2019.05.033
external_id:
isi:
- '000482872100002'
intvolume: ' 431'
isi: 1
issue: '17'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: http://www.biorxiv.org/content/10.1101/583369v1
month: '08'
oa: 1
oa_version: Preprint
page: 3046-3055
publication: Journal of Molecular Biology
publication_identifier:
eissn:
- '10898638'
issn:
- '00222836'
publication_status: published
publisher: Elsevier
quality_controlled: '1'
scopus_import: '1'
status: public
title: Engineering strategy and vector library for the rapid generation of modular
light-controlled protein–protein interactions
type: journal_article
user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
volume: 431
year: '2019'
...
---
_id: '6552'
abstract:
- lang: eng
text: 'When animals become sick, infected cells and an armada of activated immune
cells attempt to eliminate the pathogen from the body. Once infectious particles
have breached the body''s physical barriers of the skin or gut lining, an initially
local response quickly escalates into a systemic response, attracting mobile immune
cells to the site of infection. These cells complement the initial, unspecific
defense with a more specialized, targeted response. This can also provide long-term
immune memory and protection against future infection. The cell-autonomous defenses
of the infected cells are thus aided by the actions of recruited immune cells.
These specialized cells are the most mobile cells in the body, constantly patrolling
through the otherwise static tissue to detect incoming pathogens. Such constant
immune surveillance means infections are noticed immediately and can be rapidly
cleared from the body. Some immune cells also remove infected cells that have
succumbed to infection. All this prevents pathogen replication and spread to healthy
tissues. Although this may involve the sacrifice of some somatic tissue, this
is typically replaced quickly. Particular care is, however, given to the reproductive
organs, which should always remain disease free (immune privilege). '
article_processing_charge: No
article_type: original
author:
- first_name: Sylvia
full_name: Cremer, Sylvia
id: 2F64EC8C-F248-11E8-B48F-1D18A9856A87
last_name: Cremer
orcid: 0000-0002-2193-3868
citation:
ama: Cremer S. Social immunity in insects. Current Biology. 2019;29(11):R458-R463.
doi:10.1016/j.cub.2019.03.035
apa: Cremer, S. (2019). Social immunity in insects. Current Biology. Elsevier.
https://doi.org/10.1016/j.cub.2019.03.035
chicago: Cremer, Sylvia. “Social Immunity in Insects.” Current Biology. Elsevier,
2019. https://doi.org/10.1016/j.cub.2019.03.035.
ieee: S. Cremer, “Social immunity in insects,” Current Biology, vol. 29,
no. 11. Elsevier, pp. R458–R463, 2019.
ista: Cremer S. 2019. Social immunity in insects. Current Biology. 29(11), R458–R463.
mla: Cremer, Sylvia. “Social Immunity in Insects.” Current Biology, vol.
29, no. 11, Elsevier, 2019, pp. R458–63, doi:10.1016/j.cub.2019.03.035.
short: S. Cremer, Current Biology 29 (2019) R458–R463.
date_created: 2019-06-09T21:59:10Z
date_published: 2019-06-03T00:00:00Z
date_updated: 2023-08-28T09:38:00Z
day: '03'
department:
- _id: SyCr
doi: 10.1016/j.cub.2019.03.035
external_id:
isi:
- '000470902000023'
pmid:
- '31163158'
intvolume: ' 29'
isi: 1
issue: '11'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.1016/j.cub.2019.03.035
month: '06'
oa: 1
oa_version: Published Version
page: R458-R463
pmid: 1
publication: Current Biology
publication_identifier:
issn:
- '09609822'
publication_status: published
publisher: Elsevier
quality_controlled: '1'
scopus_import: '1'
status: public
title: Social immunity in insects
type: journal_article
user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
volume: 29
year: '2019'
...
---
_id: '6511'
abstract:
- lang: eng
text: Let U and V be two independent N by N random matrices that are distributed
according to Haar measure on U(N). Let Σ be a nonnegative deterministic N by N
matrix. The single ring theorem [Ann. of Math. (2) 174 (2011) 1189–1217] asserts
that the empirical eigenvalue distribution of the matrix X:=UΣV∗ converges weakly,
in the limit of large N, to a deterministic measure which is supported on a single
ring centered at the origin in ℂ. Within the bulk regime, that is, in the interior
of the single ring, we establish the convergence of the empirical eigenvalue distribution
on the optimal local scale of order N−1/2+ε and establish the optimal convergence
rate. The same results hold true when U and V are Haar distributed on O(N).
article_processing_charge: No
author:
- first_name: Zhigang
full_name: Bao, Zhigang
id: 442E6A6C-F248-11E8-B48F-1D18A9856A87
last_name: Bao
orcid: 0000-0003-3036-1475
- first_name: László
full_name: Erdös, László
id: 4DBD5372-F248-11E8-B48F-1D18A9856A87
last_name: Erdös
orcid: 0000-0001-5366-9603
- first_name: Kevin
full_name: Schnelli, Kevin
id: 434AD0AE-F248-11E8-B48F-1D18A9856A87
last_name: Schnelli
orcid: 0000-0003-0954-3231
citation:
ama: Bao Z, Erdös L, Schnelli K. Local single ring theorem on optimal scale. Annals
of Probability. 2019;47(3):1270-1334. doi:10.1214/18-AOP1284
apa: Bao, Z., Erdös, L., & Schnelli, K. (2019). Local single ring theorem on
optimal scale. Annals of Probability. Institute of Mathematical Statistics.
https://doi.org/10.1214/18-AOP1284
chicago: Bao, Zhigang, László Erdös, and Kevin Schnelli. “Local Single Ring Theorem
on Optimal Scale.” Annals of Probability. Institute of Mathematical Statistics,
2019. https://doi.org/10.1214/18-AOP1284.
ieee: Z. Bao, L. Erdös, and K. Schnelli, “Local single ring theorem on optimal scale,”
Annals of Probability, vol. 47, no. 3. Institute of Mathematical Statistics,
pp. 1270–1334, 2019.
ista: Bao Z, Erdös L, Schnelli K. 2019. Local single ring theorem on optimal scale.
Annals of Probability. 47(3), 1270–1334.
mla: Bao, Zhigang, et al. “Local Single Ring Theorem on Optimal Scale.” Annals
of Probability, vol. 47, no. 3, Institute of Mathematical Statistics, 2019,
pp. 1270–334, doi:10.1214/18-AOP1284.
short: Z. Bao, L. Erdös, K. Schnelli, Annals of Probability 47 (2019) 1270–1334.
date_created: 2019-06-02T21:59:13Z
date_published: 2019-05-01T00:00:00Z
date_updated: 2023-08-28T09:32:29Z
day: '01'
department:
- _id: LaEr
doi: 10.1214/18-AOP1284
ec_funded: 1
external_id:
arxiv:
- '1612.05920'
isi:
- '000466616100003'
intvolume: ' 47'
isi: 1
issue: '3'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/1612.05920
month: '05'
oa: 1
oa_version: Preprint
page: 1270-1334
project:
- _id: 258DCDE6-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '338804'
name: Random matrices, universality and disordered quantum systems
publication: Annals of Probability
publication_identifier:
issn:
- '00911798'
publication_status: published
publisher: Institute of Mathematical Statistics
quality_controlled: '1'
scopus_import: '1'
status: public
title: Local single ring theorem on optimal scale
type: journal_article
user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
volume: 47
year: '2019'
...
---
_id: '6559'
abstract:
- lang: eng
text: Branching morphogenesis is a prototypical example of complex three-dimensional
organ sculpting, required in multiple developmental settings to maximize the area
of exchange surfaces. It requires, in particular, the coordinated growth of different
cell types together with complex patterning to lead to robust macroscopic outputs.
In recent years, novel multiscale quantitative biology approaches, together with
biophysical modelling, have begun to shed new light of this topic. Here, we wish
to review some of these recent developments, highlighting the generic design principles
that can be abstracted across different branched organs, as well as the implications
for the broader fields of stem cell, developmental and systems biology.
article_processing_charge: No
article_type: original
author:
- first_name: Edouard B
full_name: Hannezo, Edouard B
id: 3A9DB764-F248-11E8-B48F-1D18A9856A87
last_name: Hannezo
orcid: 0000-0001-6005-1561
- first_name: Benjamin D.
full_name: Simons, Benjamin D.
last_name: Simons
citation:
ama: Hannezo EB, Simons BD. Multiscale dynamics of branching morphogenesis. Current
Opinion in Cell Biology. 2019;60:99-105. doi:10.1016/j.ceb.2019.04.008
apa: Hannezo, E. B., & Simons, B. D. (2019). Multiscale dynamics of branching
morphogenesis. Current Opinion in Cell Biology. Elsevier. https://doi.org/10.1016/j.ceb.2019.04.008
chicago: Hannezo, Edouard B, and Benjamin D. Simons. “Multiscale Dynamics of Branching
Morphogenesis.” Current Opinion in Cell Biology. Elsevier, 2019. https://doi.org/10.1016/j.ceb.2019.04.008.
ieee: E. B. Hannezo and B. D. Simons, “Multiscale dynamics of branching morphogenesis,”
Current Opinion in Cell Biology, vol. 60. Elsevier, pp. 99–105, 2019.
ista: Hannezo EB, Simons BD. 2019. Multiscale dynamics of branching morphogenesis.
Current Opinion in Cell Biology. 60, 99–105.
mla: Hannezo, Edouard B., and Benjamin D. Simons. “Multiscale Dynamics of Branching
Morphogenesis.” Current Opinion in Cell Biology, vol. 60, Elsevier, 2019,
pp. 99–105, doi:10.1016/j.ceb.2019.04.008.
short: E.B. Hannezo, B.D. Simons, Current Opinion in Cell Biology 60 (2019) 99–105.
date_created: 2019-06-16T21:59:12Z
date_published: 2019-10-01T00:00:00Z
date_updated: 2023-08-28T09:38:57Z
day: '01'
department:
- _id: EdHa
doi: 10.1016/j.ceb.2019.04.008
external_id:
isi:
- '000486545800014'
pmid:
- '31181348'
intvolume: ' 60'
isi: 1
language:
- iso: eng
month: '10'
oa_version: None
page: 99-105
pmid: 1
publication: Current Opinion in Cell Biology
publication_identifier:
eissn:
- '18790410'
issn:
- '09550674'
publication_status: published
publisher: Elsevier
quality_controlled: '1'
scopus_import: '1'
status: public
title: Multiscale dynamics of branching morphogenesis
type: journal_article
user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
volume: 60
year: '2019'
...
---
_id: '6566'
abstract:
- lang: eng
text: Methodologies that involve the use of nanoparticles as “artificial atoms”
to rationally build materials in a bottom-up fashion are particularly well-suited
to control the matter at the nanoscale. Colloidal synthetic routes allow for an
exquisite control over such “artificial atoms” in terms of size, shape, and crystal
phase as well as core and surface compositions. We present here a bottom-up approach
to produce Pb–Ag–K–S–Te nanocomposites, which is a highly promising system for
thermoelectric energy conversion. First, we developed a high-yield and scalable
colloidal synthesis route to uniform lead sulfide (PbS) nanorods, whose tips are
made of silver sulfide (Ag2S). We then took advantage of the large surface-to-volume
ratio to introduce a p-type dopant (K) by replacing native organic ligands with
K2Te. Upon thermal consolidation, K2Te-surface modified PbS–Ag2S nanorods yield
p-type doped nanocomposites with PbTe and PbS as major phases and Ag2S and Ag2Te
as embedded nanoinclusions. Thermoelectric characterization of such consolidated
nanosolids showed a high thermoelectric figure-of-merit of 1 at 620 K.
article_processing_charge: Yes (in subscription journal)
article_type: original
author:
- first_name: Maria
full_name: Ibáñez, Maria
id: 43C61214-F248-11E8-B48F-1D18A9856A87
last_name: Ibáñez
orcid: 0000-0001-5013-2843
- first_name: Aziz
full_name: Genç, Aziz
last_name: Genç
- first_name: Roger
full_name: Hasler, Roger
last_name: Hasler
- first_name: Yu
full_name: Liu, Yu
id: 2A70014E-F248-11E8-B48F-1D18A9856A87
last_name: Liu
orcid: 0000-0001-7313-6740
- first_name: Oleksandr
full_name: Dobrozhan, Oleksandr
last_name: Dobrozhan
- first_name: Olga
full_name: Nazarenko, Olga
last_name: Nazarenko
- first_name: María de la
full_name: Mata, María de la
last_name: Mata
- first_name: Jordi
full_name: Arbiol, Jordi
last_name: Arbiol
- first_name: Andreu
full_name: Cabot, Andreu
last_name: Cabot
- first_name: Maksym V.
full_name: Kovalenko, Maksym V.
last_name: Kovalenko
citation:
ama: Ibáñez M, Genç A, Hasler R, et al. Tuning transport properties in thermoelectric
nanocomposites through inorganic ligands and heterostructured building blocks.
ACS Nano. 2019;13(6):6572-6580. doi:10.1021/acsnano.9b00346
apa: Ibáñez, M., Genç, A., Hasler, R., Liu, Y., Dobrozhan, O., Nazarenko, O., …
Kovalenko, M. V. (2019). Tuning transport properties in thermoelectric nanocomposites
through inorganic ligands and heterostructured building blocks. ACS Nano.
American Chemical Society. https://doi.org/10.1021/acsnano.9b00346
chicago: Ibáñez, Maria, Aziz Genç, Roger Hasler, Yu Liu, Oleksandr Dobrozhan, Olga
Nazarenko, María de la Mata, Jordi Arbiol, Andreu Cabot, and Maksym V. Kovalenko.
“Tuning Transport Properties in Thermoelectric Nanocomposites through Inorganic
Ligands and Heterostructured Building Blocks.” ACS Nano. American Chemical
Society, 2019. https://doi.org/10.1021/acsnano.9b00346.
ieee: M. Ibáñez et al., “Tuning transport properties in thermoelectric nanocomposites
through inorganic ligands and heterostructured building blocks,” ACS Nano,
vol. 13, no. 6. American Chemical Society, pp. 6572–6580, 2019.
ista: Ibáñez M, Genç A, Hasler R, Liu Y, Dobrozhan O, Nazarenko O, Mata M de la,
Arbiol J, Cabot A, Kovalenko MV. 2019. Tuning transport properties in thermoelectric
nanocomposites through inorganic ligands and heterostructured building blocks.
ACS Nano. 13(6), 6572–6580.
mla: Ibáñez, Maria, et al. “Tuning Transport Properties in Thermoelectric Nanocomposites
through Inorganic Ligands and Heterostructured Building Blocks.” ACS Nano,
vol. 13, no. 6, American Chemical Society, 2019, pp. 6572–80, doi:10.1021/acsnano.9b00346.
short: M. Ibáñez, A. Genç, R. Hasler, Y. Liu, O. Dobrozhan, O. Nazarenko, M. de
la Mata, J. Arbiol, A. Cabot, M.V. Kovalenko, ACS Nano 13 (2019) 6572–6580.
date_created: 2019-06-18T13:54:34Z
date_published: 2019-06-25T00:00:00Z
date_updated: 2023-08-28T12:20:53Z
day: '25'
ddc:
- '540'
department:
- _id: MaIb
doi: 10.1021/acsnano.9b00346
ec_funded: 1
external_id:
isi:
- '000473248300043'
pmid:
- '31185159'
file:
- access_level: open_access
content_type: application/pdf
creator: dernst
date_created: 2019-07-16T14:17:09Z
date_updated: 2020-07-14T12:47:33Z
file_id: '6644'
file_name: 2019_ACSNano_Ibanez.pdf
file_size: 8628690
relation: main_file
file_date_updated: 2020-07-14T12:47:33Z
has_accepted_license: '1'
intvolume: ' 13'
isi: 1
issue: '6'
keyword:
- colloidal nanoparticles
- asymmetric nanoparticles
- inorganic ligands
- heterostructures
- catalyst assisted growth
- nanocomposites
- thermoelectrics
language:
- iso: eng
month: '06'
oa: 1
oa_version: Published Version
page: 6572-6580
pmid: 1
project:
- _id: 260C2330-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '754411'
name: ISTplus - Postdoctoral Fellowships
publication: ACS Nano
publication_identifier:
eissn:
- 1936-086X
issn:
- 1936-0851
publication_status: published
publisher: American Chemical Society
quality_controlled: '1'
scopus_import: '1'
status: public
title: Tuning transport properties in thermoelectric nanocomposites through inorganic
ligands and heterostructured building blocks
type: journal_article
user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
volume: 13
year: '2019'
...
---
_id: '6607'
abstract:
- lang: eng
text: Acute myeloid leukemia (AML) is a heterogeneous disease with respect to its
genetic and molecular basis and to patients´ outcome. Clinical, cytogenetic, and
mutational data are used to classify patients into risk groups with different
survival, however, within-group heterogeneity is still an issue. Here, we used
a robust likelihood-based survival modeling approach and publicly available gene
expression data to identify a minimal number of genes whose combined expression
values were prognostic of overall survival. The resulting gene expression signature
(4-GES) consisted of 4 genes (SOCS2, IL2RA, NPDC1, PHGDH), predicted patient survival
as an independent prognostic parameter in several cohorts of AML patients (total,
1272 patients), and further refined prognostication based on the European Leukemia
Net classification. An oncogenic role of the top scoring gene in this signature,
SOCS2, was investigated using MLL-AF9 and Flt3-ITD/NPM1c driven mouse models of
AML. SOCS2 promoted leukemogenesis as well as the abundance, quiescence, and activity
of AML stem cells. Overall, the 4-GES represents a highly discriminating prognostic
parameter in AML, whose clinical applicability is greatly enhanced by its small
number of genes. The newly established role of SOCS2 in leukemia aggressiveness
and stemness raises the possibility that the signature might even be exploitable
therapeutically.
article_number: '9139'
article_processing_charge: No
author:
- first_name: Chi Huu
full_name: Nguyen, Chi Huu
last_name: Nguyen
- first_name: Tobias
full_name: Glüxam, Tobias
last_name: Glüxam
- first_name: Angela
full_name: Schlerka, Angela
last_name: Schlerka
- first_name: Katharina
full_name: Bauer, Katharina
id: 2ED6B14C-F248-11E8-B48F-1D18A9856A87
last_name: Bauer
- first_name: Alexander M.
full_name: Grandits, Alexander M.
last_name: Grandits
- first_name: Hubert
full_name: Hackl, Hubert
last_name: Hackl
- first_name: Oliver
full_name: Dovey, Oliver
last_name: Dovey
- first_name: Sabine
full_name: Zöchbauer-Müller, Sabine
last_name: Zöchbauer-Müller
- first_name: Jonathan L.
full_name: Cooper, Jonathan L.
last_name: Cooper
- first_name: George S.
full_name: Vassiliou, George S.
last_name: Vassiliou
- first_name: Dagmar
full_name: Stoiber, Dagmar
last_name: Stoiber
- first_name: Rotraud
full_name: Wieser, Rotraud
last_name: Wieser
- first_name: Gerwin
full_name: Heller, Gerwin
last_name: Heller
citation:
ama: Nguyen CH, Glüxam T, Schlerka A, et al. SOCS2 is part of a highly prognostic
4-gene signature in AML and promotes disease aggressiveness. Scientific Reports.
2019;9(1). doi:10.1038/s41598-019-45579-0
apa: Nguyen, C. H., Glüxam, T., Schlerka, A., Bauer, K., Grandits, A. M., Hackl,
H., … Heller, G. (2019). SOCS2 is part of a highly prognostic 4-gene signature
in AML and promotes disease aggressiveness. Scientific Reports. Nature
Publishing Group. https://doi.org/10.1038/s41598-019-45579-0
chicago: Nguyen, Chi Huu, Tobias Glüxam, Angela Schlerka, Katharina Bauer, Alexander
M. Grandits, Hubert Hackl, Oliver Dovey, et al. “SOCS2 Is Part of a Highly Prognostic
4-Gene Signature in AML and Promotes Disease Aggressiveness.” Scientific Reports.
Nature Publishing Group, 2019. https://doi.org/10.1038/s41598-019-45579-0.
ieee: C. H. Nguyen et al., “SOCS2 is part of a highly prognostic 4-gene signature
in AML and promotes disease aggressiveness,” Scientific Reports, vol. 9,
no. 1. Nature Publishing Group, 2019.
ista: Nguyen CH, Glüxam T, Schlerka A, Bauer K, Grandits AM, Hackl H, Dovey O, Zöchbauer-Müller
S, Cooper JL, Vassiliou GS, Stoiber D, Wieser R, Heller G. 2019. SOCS2 is part
of a highly prognostic 4-gene signature in AML and promotes disease aggressiveness.
Scientific Reports. 9(1), 9139.
mla: Nguyen, Chi Huu, et al. “SOCS2 Is Part of a Highly Prognostic 4-Gene Signature
in AML and Promotes Disease Aggressiveness.” Scientific Reports, vol. 9,
no. 1, 9139, Nature Publishing Group, 2019, doi:10.1038/s41598-019-45579-0.
short: C.H. Nguyen, T. Glüxam, A. Schlerka, K. Bauer, A.M. Grandits, H. Hackl, O.
Dovey, S. Zöchbauer-Müller, J.L. Cooper, G.S. Vassiliou, D. Stoiber, R. Wieser,
G. Heller, Scientific Reports 9 (2019).
date_created: 2019-07-07T21:59:19Z
date_published: 2019-06-24T00:00:00Z
date_updated: 2023-08-28T12:26:51Z
day: '24'
ddc:
- '576'
department:
- _id: PreCl
doi: 10.1038/s41598-019-45579-0
external_id:
isi:
- '000472597400042'
file:
- access_level: open_access
checksum: 3283522fffadf4b5fc8c7adfe3ba4564
content_type: application/pdf
creator: kschuh
date_created: 2019-07-08T15:15:28Z
date_updated: 2020-07-14T12:47:34Z
file_id: '6623'
file_name: nature_2019_Nguyen.pdf
file_size: 2017352
relation: main_file
file_date_updated: 2020-07-14T12:47:34Z
has_accepted_license: '1'
intvolume: ' 9'
isi: 1
issue: '1'
language:
- iso: eng
month: '06'
oa: 1
oa_version: Published Version
publication: Scientific Reports
publication_status: published
publisher: Nature Publishing Group
quality_controlled: '1'
scopus_import: '1'
status: public
title: SOCS2 is part of a highly prognostic 4-gene signature in AML and promotes disease
aggressiveness
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'
...