---
_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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month: '04'
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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'
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relation: research_data
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relation: research_data
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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'
...
---
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article_processing_charge: No
author:
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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'
...
---
_id: '6609'
abstract:
- lang: eng
text: Mechanical systems facilitate the development of a hybrid quantum technology
comprising electrical, optical, atomic and acoustic degrees of freedom1, and entanglement
is essential to realize quantum-enabled devices. Continuous-variable entangled
fields—known as Einstein–Podolsky–Rosen (EPR) states—are spatially separated two-mode
squeezed states that can be used for quantum teleportation and quantum communication2.
In the optical domain, EPR states are typically generated using nondegenerate
optical amplifiers3, and at microwave frequencies Josephson circuits can serve
as a nonlinear medium4,5,6. An outstanding goal is to deterministically generate
and distribute entangled states with a mechanical oscillator, which requires a
carefully arranged balance between excitation, cooling and dissipation in an ultralow
noise environment. Here we observe stationary emission of path-entangled microwave
radiation from a parametrically driven 30-micrometre-long silicon nanostring oscillator,
squeezing the joint field operators of two thermal modes by 3.40 decibels below
the vacuum level. The motion of this micromechanical system correlates up to 50
photons per second per hertz, giving rise to a quantum discord that is robust
with respect to microwave noise7. Such generalized quantum correlations of separable
states are important for quantum-enhanced detection8 and provide direct evidence
of the non-classical nature of the mechanical oscillator without directly measuring
its state9. This noninvasive measurement scheme allows to infer information about
otherwise inaccessible objects, with potential implications for sensing, open-system
dynamics and fundamental tests of quantum gravity. In the future, similar on-chip
devices could be used to entangle subsystems on very different energy scales,
such as microwave and optical photons.
acknowledged_ssus:
- _id: NanoFab
article_processing_charge: No
author:
- first_name: Shabir
full_name: Barzanjeh, Shabir
id: 2D25E1F6-F248-11E8-B48F-1D18A9856A87
last_name: Barzanjeh
orcid: 0000-0003-0415-1423
- first_name: Elena
full_name: Redchenko, Elena
id: 2C21D6E8-F248-11E8-B48F-1D18A9856A87
last_name: Redchenko
- first_name: Matilda
full_name: Peruzzo, Matilda
id: 3F920B30-F248-11E8-B48F-1D18A9856A87
last_name: Peruzzo
orcid: 0000-0002-3415-4628
- first_name: Matthias
full_name: Wulf, Matthias
id: 45598606-F248-11E8-B48F-1D18A9856A87
last_name: Wulf
orcid: 0000-0001-6613-1378
- first_name: Dylan
full_name: Lewis, Dylan
last_name: Lewis
- first_name: Georg M
full_name: Arnold, Georg M
id: 3770C838-F248-11E8-B48F-1D18A9856A87
last_name: Arnold
orcid: 0000-0003-1397-7876
- first_name: Johannes M
full_name: Fink, Johannes M
id: 4B591CBA-F248-11E8-B48F-1D18A9856A87
last_name: Fink
orcid: 0000-0001-8112-028X
citation:
ama: Barzanjeh S, Redchenko E, Peruzzo M, et al. Stationary entangled radiation
from micromechanical motion. Nature. 2019;570:480-483. doi:10.1038/s41586-019-1320-2
apa: Barzanjeh, S., Redchenko, E., Peruzzo, M., Wulf, M., Lewis, D., Arnold, G.
M., & Fink, J. M. (2019). Stationary entangled radiation from micromechanical
motion. Nature. Nature Publishing Group. https://doi.org/10.1038/s41586-019-1320-2
chicago: Barzanjeh, Shabir, Elena Redchenko, Matilda Peruzzo, Matthias Wulf, Dylan
Lewis, Georg M Arnold, and Johannes M Fink. “Stationary Entangled Radiation from
Micromechanical Motion.” Nature. Nature Publishing Group, 2019. https://doi.org/10.1038/s41586-019-1320-2.
ieee: S. Barzanjeh et al., “Stationary entangled radiation from micromechanical
motion,” Nature, vol. 570. Nature Publishing Group, pp. 480–483, 2019.
ista: Barzanjeh S, Redchenko E, Peruzzo M, Wulf M, Lewis D, Arnold GM, Fink JM.
2019. Stationary entangled radiation from micromechanical motion. Nature. 570,
480–483.
mla: Barzanjeh, Shabir, et al. “Stationary Entangled Radiation from Micromechanical
Motion.” Nature, vol. 570, Nature Publishing Group, 2019, pp. 480–83, doi:10.1038/s41586-019-1320-2.
short: S. Barzanjeh, E. Redchenko, M. Peruzzo, M. Wulf, D. Lewis, G.M. Arnold, J.M.
Fink, Nature 570 (2019) 480–483.
date_created: 2019-07-07T21:59:20Z
date_published: 2019-06-27T00:00:00Z
date_updated: 2023-08-28T12:29:56Z
day: '27'
department:
- _id: JoFi
doi: 10.1038/s41586-019-1320-2
ec_funded: 1
external_id:
arxiv:
- '1809.05865'
isi:
- '000472860000042'
intvolume: ' 570'
isi: 1
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/1809.05865
month: '06'
oa: 1
oa_version: Preprint
page: 480-483
project:
- _id: 257EB838-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '732894'
name: Hybrid Optomechanical Technologies
- _id: 26336814-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '758053'
name: A Fiber Optic Transceiver for Superconducting Qubits
- _id: 258047B6-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '707438'
name: 'Microwave-to-Optical Quantum Link: Quantum Teleportation and Quantum Illumination
with cavity Optomechanics'
- _id: 2671EB66-B435-11E9-9278-68D0E5697425
name: Coherent on-chip conversion of superconducting qubit signals from microwaves
to optical frequencies
publication: Nature
publication_status: published
publisher: Nature Publishing Group
quality_controlled: '1'
scopus_import: '1'
status: public
title: Stationary entangled radiation from micromechanical motion
type: journal_article
user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
volume: 570
year: '2019'
...
---
_id: '6596'
abstract:
- lang: eng
text: It is well known that many problems in image recovery, signal processing,
and machine learning can be modeled as finding zeros of the sum of maximal monotone
and Lipschitz continuous monotone operators. Many papers have studied forward-backward
splitting methods for finding zeros of the sum of two monotone operators in Hilbert
spaces. Most of the proposed splitting methods in the literature have been proposed
for the sum of maximal monotone and inverse-strongly monotone operators in Hilbert
spaces. In this paper, we consider splitting methods for finding zeros of the
sum of maximal monotone operators and Lipschitz continuous monotone operators
in Banach spaces. We obtain weak and strong convergence results for the zeros
of the sum of maximal monotone and Lipschitz continuous monotone operators in
Banach spaces. Many already studied problems in the literature can be considered
as special cases of this paper.
article_number: '138'
article_processing_charge: Yes (via OA deal)
article_type: original
author:
- first_name: Yekini
full_name: Shehu, Yekini
id: 3FC7CB58-F248-11E8-B48F-1D18A9856A87
last_name: Shehu
orcid: 0000-0001-9224-7139
citation:
ama: Shehu Y. Convergence results of forward-backward algorithms for sum of monotone
operators in Banach spaces. Results in Mathematics. 2019;74(4). doi:10.1007/s00025-019-1061-4
apa: Shehu, Y. (2019). Convergence results of forward-backward algorithms for sum
of monotone operators in Banach spaces. Results in Mathematics. Springer.
https://doi.org/10.1007/s00025-019-1061-4
chicago: Shehu, Yekini. “Convergence Results of Forward-Backward Algorithms for
Sum of Monotone Operators in Banach Spaces.” Results in Mathematics. Springer,
2019. https://doi.org/10.1007/s00025-019-1061-4.
ieee: Y. Shehu, “Convergence results of forward-backward algorithms for sum of monotone
operators in Banach spaces,” Results in Mathematics, vol. 74, no. 4. Springer,
2019.
ista: Shehu Y. 2019. Convergence results of forward-backward algorithms for sum
of monotone operators in Banach spaces. Results in Mathematics. 74(4), 138.
mla: Shehu, Yekini. “Convergence Results of Forward-Backward Algorithms for Sum
of Monotone Operators in Banach Spaces.” Results in Mathematics, vol. 74,
no. 4, 138, Springer, 2019, doi:10.1007/s00025-019-1061-4.
short: Y. Shehu, Results in Mathematics 74 (2019).
date_created: 2019-06-29T10:11:30Z
date_published: 2019-12-01T00:00:00Z
date_updated: 2023-08-28T12:26:22Z
day: '01'
ddc:
- '000'
department:
- _id: VlKo
doi: 10.1007/s00025-019-1061-4
ec_funded: 1
external_id:
arxiv:
- '2101.09068'
isi:
- '000473237500002'
file:
- access_level: open_access
checksum: c6d18cb1e16fc0c36a0e0f30b4ebbc2d
content_type: application/pdf
creator: kschuh
date_created: 2019-07-03T15:20:40Z
date_updated: 2020-07-14T12:47:34Z
file_id: '6605'
file_name: Springer_2019_Shehu.pdf
file_size: 466942
relation: main_file
file_date_updated: 2020-07-14T12:47:34Z
has_accepted_license: '1'
intvolume: ' 74'
isi: 1
issue: '4'
language:
- iso: eng
month: '12'
oa: 1
oa_version: Published Version
project:
- _id: 25FBA906-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '616160'
name: 'Discrete Optimization in Computer Vision: Theory and Practice'
- _id: B67AFEDC-15C9-11EA-A837-991A96BB2854
name: IST Austria Open Access Fund
publication: Results in Mathematics
publication_identifier:
eissn:
- 1420-9012
issn:
- 1422-6383
publication_status: published
publisher: Springer
quality_controlled: '1'
scopus_import: '1'
status: public
title: Convergence results of forward-backward algorithms for sum of monotone operators
in Banach spaces
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: 74
year: '2019'
...
---
_id: '6601'
abstract:
- lang: eng
text: There is increasing evidence that both mechanical and biochemical signals
play important roles in development and disease. The development of complex organisms,
in particular, has been proposed to rely on the feedback between mechanical and
biochemical patterning events. This feedback occurs at the molecular level via
mechanosensation but can also arise as an emergent property of the system at the
cellular and tissue level. In recent years, dynamic changes in tissue geometry,
flow, rheology, and cell fate specification have emerged as key platforms of mechanochemical
feedback loops in multiple processes. Here, we review recent experimental and
theoretical advances in understanding how these feedbacks function in development
and disease.
article_processing_charge: No
article_type: review
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: 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: Hannezo EB, Heisenberg C-PJ. Mechanochemical feedback loops in development
and disease. Cell. 2019;178(1):12-25. doi:10.1016/j.cell.2019.05.052
apa: Hannezo, E. B., & Heisenberg, C.-P. J. (2019). Mechanochemical feedback
loops in development and disease. Cell. Elsevier. https://doi.org/10.1016/j.cell.2019.05.052
chicago: Hannezo, Edouard B, and Carl-Philipp J Heisenberg. “Mechanochemical Feedback
Loops in Development and Disease.” Cell. Elsevier, 2019. https://doi.org/10.1016/j.cell.2019.05.052.
ieee: E. B. Hannezo and C.-P. J. Heisenberg, “Mechanochemical feedback loops in
development and disease,” Cell, vol. 178, no. 1. Elsevier, pp. 12–25, 2019.
ista: Hannezo EB, Heisenberg C-PJ. 2019. Mechanochemical feedback loops in development
and disease. Cell. 178(1), 12–25.
mla: Hannezo, Edouard B., and Carl-Philipp J. Heisenberg. “Mechanochemical Feedback
Loops in Development and Disease.” Cell, vol. 178, no. 1, Elsevier, 2019,
pp. 12–25, doi:10.1016/j.cell.2019.05.052.
short: E.B. Hannezo, C.-P.J. Heisenberg, Cell 178 (2019) 12–25.
date_created: 2019-06-30T21:59:11Z
date_published: 2019-07-27T00:00:00Z
date_updated: 2023-08-28T12:25:21Z
day: '27'
department:
- _id: CaHe
- _id: EdHa
doi: 10.1016/j.cell.2019.05.052
ec_funded: 1
external_id:
isi:
- '000473002700005'
pmid:
- '31251912'
intvolume: ' 178'
isi: 1
issue: '1'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.1016/j.cell.2019.05.052
month: '07'
oa: 1
oa_version: Published Version
page: 12-25
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
- _id: 268294B6-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: P31639
name: Active mechano-chemical description of the cell cytoskeleton
publication: Cell
publication_identifier:
issn:
- '00928674'
publication_status: published
publisher: Elsevier
quality_controlled: '1'
scopus_import: '1'
status: public
title: Mechanochemical feedback loops in development and disease
type: journal_article
user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
volume: 178
year: '2019'
...
---
_id: '6617'
abstract:
- lang: eng
text: 'The effective large-scale properties of materials with random heterogeneities
on a small scale are typically determined by the method of representative volumes:
a sample of the random material is chosen—the representative volume—and its effective
properties are computed by the cell formula. Intuitively, for a fixed sample size
it should be possible to increase the accuracy of the method by choosing a material
sample which captures the statistical properties of the material particularly
well; for example, for a composite material consisting of two constituents, one
would select a representative volume in which the volume fraction of the constituents
matches closely with their volume fraction in the overall material. Inspired by
similar attempts in materials science, Le Bris, Legoll and Minvielle have designed
a selection approach for representative volumes which performs remarkably well
in numerical examples of linear materials with moderate contrast. In the present
work, we provide a rigorous analysis of this selection approach for representative
volumes in the context of stochastic homogenization of linear elliptic equations.
In particular, we prove that the method essentially never performs worse than
a random selection of the material sample and may perform much better if the selection
criterion for the material samples is chosen suitably.'
article_processing_charge: Yes (via OA deal)
article_type: original
author:
- first_name: Julian L
full_name: Fischer, Julian L
id: 2C12A0B0-F248-11E8-B48F-1D18A9856A87
last_name: Fischer
orcid: 0000-0002-0479-558X
citation:
ama: Fischer JL. The choice of representative volumes in the approximation of effective
properties of random materials. Archive for Rational Mechanics and Analysis.
2019;234(2):635–726. doi:10.1007/s00205-019-01400-w
apa: Fischer, J. L. (2019). The choice of representative volumes in the approximation
of effective properties of random materials. Archive for Rational Mechanics
and Analysis. Springer. https://doi.org/10.1007/s00205-019-01400-w
chicago: Fischer, Julian L. “The Choice of Representative Volumes in the Approximation
of Effective Properties of Random Materials.” Archive for Rational Mechanics
and Analysis. Springer, 2019. https://doi.org/10.1007/s00205-019-01400-w.
ieee: J. L. Fischer, “The choice of representative volumes in the approximation
of effective properties of random materials,” Archive for Rational Mechanics
and Analysis, vol. 234, no. 2. Springer, pp. 635–726, 2019.
ista: Fischer JL. 2019. The choice of representative volumes in the approximation
of effective properties of random materials. Archive for Rational Mechanics and
Analysis. 234(2), 635–726.
mla: Fischer, Julian L. “The Choice of Representative Volumes in the Approximation
of Effective Properties of Random Materials.” Archive for Rational Mechanics
and Analysis, vol. 234, no. 2, Springer, 2019, pp. 635–726, doi:10.1007/s00205-019-01400-w.
short: J.L. Fischer, Archive for Rational Mechanics and Analysis 234 (2019) 635–726.
date_created: 2019-07-07T21:59:23Z
date_published: 2019-11-01T00:00:00Z
date_updated: 2023-08-28T12:31:21Z
day: '01'
ddc:
- '500'
department:
- _id: JuFi
doi: 10.1007/s00205-019-01400-w
external_id:
arxiv:
- '1807.00834'
isi:
- '000482386000006'
file:
- access_level: open_access
checksum: 4cff75fa6addb0770991ad9c474ab404
content_type: application/pdf
creator: kschuh
date_created: 2019-07-08T15:56:47Z
date_updated: 2020-07-14T12:47:34Z
file_id: '6626'
file_name: Springer_2019_Fischer.pdf
file_size: 1377659
relation: main_file
file_date_updated: 2020-07-14T12:47:34Z
has_accepted_license: '1'
intvolume: ' 234'
isi: 1
issue: '2'
language:
- iso: eng
month: '11'
oa: 1
oa_version: Published Version
page: 635–726
project:
- _id: B67AFEDC-15C9-11EA-A837-991A96BB2854
name: IST Austria Open Access Fund
publication: Archive for Rational Mechanics and Analysis
publication_identifier:
eissn:
- 1432-0673
issn:
- 0003-9527
publication_status: published
publisher: Springer
quality_controlled: '1'
scopus_import: '1'
status: public
title: The choice of representative volumes in the approximation of effective properties
of random materials
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: 234
year: '2019'
...
---
_id: '6611'
abstract:
- lang: eng
text: 'Cell polarity is crucial for the coordinated development of all multicellular
organisms. In plants, this is exemplified by the PIN-FORMED (PIN) efflux carriers
of the phytohormone auxin: The polar subcellular localization of the PINs is instructive
to the directional intercellular auxin transport, and thus to a plethora of auxin-regulated
growth and developmental processes. Despite its importance, the regulation of
PIN polar subcellular localization remains poorly understood. Here, we have employed
advanced live-cell imaging techniques to study the roles of microtubules and actin
microfilaments in the establishment of apical polar localization of PIN2 in the
epidermis of the Arabidopsis root meristem. We report that apical PIN2 polarity
requires neither intact actin microfilaments nor microtubules, suggesting that
the primary spatial cue for polar PIN distribution is likely independent of cytoskeleton-guided
endomembrane trafficking.'
acknowledged_ssus:
- _id: Bio
article_number: '222'
article_processing_charge: No
author:
- first_name: Matous
full_name: Glanc, Matous
id: 1AE1EA24-02D0-11E9-9BAA-DAF4881429F2
last_name: Glanc
orcid: 0000-0003-0619-7783
- first_name: Matyas
full_name: Fendrych, Matyas
id: 43905548-F248-11E8-B48F-1D18A9856A87
last_name: Fendrych
orcid: 0000-0002-9767-8699
- first_name: Jiří
full_name: Friml, Jiří
id: 4159519E-F248-11E8-B48F-1D18A9856A87
last_name: Friml
orcid: 0000-0002-8302-7596
citation:
ama: Glanc M, Fendrych M, Friml J. PIN2 polarity establishment in arabidopsis in
the absence of an intact cytoskeleton. Biomolecules. 2019;9(6). doi:10.3390/biom9060222
apa: Glanc, M., Fendrych, M., & Friml, J. (2019). PIN2 polarity establishment
in arabidopsis in the absence of an intact cytoskeleton. Biomolecules.
MDPI. https://doi.org/10.3390/biom9060222
chicago: Glanc, Matous, Matyas Fendrych, and Jiří Friml. “PIN2 Polarity Establishment
in Arabidopsis in the Absence of an Intact Cytoskeleton.” Biomolecules.
MDPI, 2019. https://doi.org/10.3390/biom9060222.
ieee: M. Glanc, M. Fendrych, and J. Friml, “PIN2 polarity establishment in arabidopsis
in the absence of an intact cytoskeleton,” Biomolecules, vol. 9, no. 6.
MDPI, 2019.
ista: Glanc M, Fendrych M, Friml J. 2019. PIN2 polarity establishment in arabidopsis
in the absence of an intact cytoskeleton. Biomolecules. 9(6), 222.
mla: Glanc, Matous, et al. “PIN2 Polarity Establishment in Arabidopsis in the Absence
of an Intact Cytoskeleton.” Biomolecules, vol. 9, no. 6, 222, MDPI, 2019,
doi:10.3390/biom9060222.
short: M. Glanc, M. Fendrych, J. Friml, Biomolecules 9 (2019).
date_created: 2019-07-07T21:59:21Z
date_published: 2019-06-07T00:00:00Z
date_updated: 2023-08-28T12:30:24Z
day: '07'
ddc:
- '580'
department:
- _id: JiFr
doi: 10.3390/biom9060222
ec_funded: 1
external_id:
isi:
- '000475301500018'
pmid:
- '31181636'
file:
- access_level: open_access
checksum: 1ce1bd36038fe5381057a1bcc6760083
content_type: application/pdf
creator: kschuh
date_created: 2019-07-08T15:46:32Z
date_updated: 2020-07-14T12:47:34Z
file_id: '6625'
file_name: biomolecules-2019-Matous.pdf
file_size: 1066773
relation: main_file
file_date_updated: 2020-07-14T12:47:34Z
has_accepted_license: '1'
intvolume: ' 9'
isi: 1
issue: '6'
language:
- iso: eng
month: '06'
oa: 1
oa_version: Published Version
pmid: 1
project:
- _id: 261099A6-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '742985'
name: Tracing Evolution of Auxin Transport and Polarity in Plants
publication: Biomolecules
publication_status: published
publisher: MDPI
quality_controlled: '1'
scopus_import: '1'
status: public
title: PIN2 polarity establishment in arabidopsis in the absence of an intact cytoskeleton
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: journal_article
user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
volume: 9
year: '2019'
...
---
_id: '6620'
abstract:
- lang: eng
text: "This paper establishes an asymptotic formula with a power-saving error term
for the number of rational points of bounded height on the singular cubic surface
of ℙ3ℚ given by the following equation \U0001D4650(\U0001D46521+\U0001D46522)−\U0001D46533=0
in agreement with the Manin-Peyre conjectures.\r\n"
article_processing_charge: No
article_type: original
author:
- first_name: Régis
full_name: De La Bretèche, Régis
last_name: De La Bretèche
- first_name: Kevin N
full_name: Destagnol, Kevin N
id: 44DDECBC-F248-11E8-B48F-1D18A9856A87
last_name: Destagnol
- first_name: Jianya
full_name: Liu, Jianya
last_name: Liu
- first_name: Jie
full_name: Wu, Jie
last_name: Wu
- first_name: Yongqiang
full_name: Zhao, Yongqiang
last_name: Zhao
citation:
ama: De La Bretèche R, Destagnol KN, Liu J, Wu J, Zhao Y. On a certain non-split
cubic surface. Science China Mathematics. 2019;62(12):2435–2446. doi:10.1007/s11425-018-9543-8
apa: De La Bretèche, R., Destagnol, K. N., Liu, J., Wu, J., & Zhao, Y. (2019).
On a certain non-split cubic surface. Science China Mathematics. Springer.
https://doi.org/10.1007/s11425-018-9543-8
chicago: De La Bretèche, Régis, Kevin N Destagnol, Jianya Liu, Jie Wu, and Yongqiang
Zhao. “On a Certain Non-Split Cubic Surface.” Science China Mathematics.
Springer, 2019. https://doi.org/10.1007/s11425-018-9543-8.
ieee: R. De La Bretèche, K. N. Destagnol, J. Liu, J. Wu, and Y. Zhao, “On a certain
non-split cubic surface,” Science China Mathematics, vol. 62, no. 12. Springer,
pp. 2435–2446, 2019.
ista: De La Bretèche R, Destagnol KN, Liu J, Wu J, Zhao Y. 2019. On a certain non-split
cubic surface. Science China Mathematics. 62(12), 2435–2446.
mla: De La Bretèche, Régis, et al. “On a Certain Non-Split Cubic Surface.” Science
China Mathematics, vol. 62, no. 12, Springer, 2019, pp. 2435–2446, doi:10.1007/s11425-018-9543-8.
short: R. De La Bretèche, K.N. Destagnol, J. Liu, J. Wu, Y. Zhao, Science China
Mathematics 62 (2019) 2435–2446.
date_created: 2019-07-07T21:59:25Z
date_published: 2019-12-01T00:00:00Z
date_updated: 2023-08-28T12:32:20Z
day: '01'
department:
- _id: TiBr
doi: 10.1007/s11425-018-9543-8
external_id:
arxiv:
- '1709.09476'
isi:
- '000509102200001'
intvolume: ' 62'
isi: 1
issue: '12'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/1709.09476
month: '12'
oa: 1
oa_version: Preprint
page: 2435–2446
publication: Science China Mathematics
publication_identifier:
issn:
- '16747283'
publication_status: published
publisher: Springer
quality_controlled: '1'
scopus_import: '1'
status: public
title: On a certain non-split cubic surface
type: journal_article
user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
volume: 62
year: '2019'
...
---
_id: '6637'
abstract:
- lang: eng
text: The environment changes constantly at various time scales and, in order to
survive, species need to keep adapting. Whether these species succeed in avoiding
extinction is a major evolutionary question. Using a multilocus evolutionary model
of a mutation‐limited population adapting under strong selection, we investigate
the effects of the frequency of environmental fluctuations on adaptation. Our
results rely on an “adaptive‐walk” approximation and use mathematical methods
from evolutionary computation theory to investigate the interplay between fluctuation
frequency, the similarity of environments, and the number of loci contributing
to adaptation. First, we assume a linear additive fitness function, but later
generalize our results to include several types of epistasis. We show that frequent
environmental changes prevent populations from reaching a fitness peak, but they
may also prevent the large fitness loss that occurs after a single environmental
change. Thus, the population can survive, although not thrive, in a wide range
of conditions. Furthermore, we show that in a frequently changing environment,
the similarity of threats that a population faces affects the level of adaptation
that it is able to achieve. We check and supplement our analytical results with
simulations.
acknowledgement: The authors would like to thank to Tiago Paixao and Nick Barton for
useful comments and advice.
article_processing_charge: Yes (via OA deal)
article_type: original
author:
- first_name: Barbora
full_name: Trubenova, Barbora
id: 42302D54-F248-11E8-B48F-1D18A9856A87
last_name: Trubenova
orcid: 0000-0002-6873-2967
- first_name: 'Martin '
full_name: 'Krejca, Martin '
last_name: Krejca
- first_name: Per Kristian
full_name: Lehre, Per Kristian
last_name: Lehre
- first_name: Timo
full_name: Kötzing, Timo
last_name: Kötzing
citation:
ama: 'Trubenova B, Krejca M, Lehre PK, Kötzing T. Surfing on the seascape: Adaptation
in a changing environment. Evolution. 2019;73(7):1356-1374. doi:10.1111/evo.13784'
apa: 'Trubenova, B., Krejca, M., Lehre, P. K., & Kötzing, T. (2019). Surfing
on the seascape: Adaptation in a changing environment. Evolution. Wiley.
https://doi.org/10.1111/evo.13784'
chicago: 'Trubenova, Barbora, Martin Krejca, Per Kristian Lehre, and Timo Kötzing.
“Surfing on the Seascape: Adaptation in a Changing Environment.” Evolution.
Wiley, 2019. https://doi.org/10.1111/evo.13784.'
ieee: 'B. Trubenova, M. Krejca, P. K. Lehre, and T. Kötzing, “Surfing on the seascape:
Adaptation in a changing environment,” Evolution, vol. 73, no. 7. Wiley,
pp. 1356–1374, 2019.'
ista: 'Trubenova B, Krejca M, Lehre PK, Kötzing T. 2019. Surfing on the seascape:
Adaptation in a changing environment. Evolution. 73(7), 1356–1374.'
mla: 'Trubenova, Barbora, et al. “Surfing on the Seascape: Adaptation in a Changing
Environment.” Evolution, vol. 73, no. 7, Wiley, 2019, pp. 1356–74, doi:10.1111/evo.13784.'
short: B. Trubenova, M. Krejca, P.K. Lehre, T. Kötzing, Evolution 73 (2019) 1356–1374.
date_created: 2019-07-14T21:59:20Z
date_published: 2019-07-01T00:00:00Z
date_updated: 2023-08-29T06:31:14Z
day: '01'
ddc:
- '576'
department:
- _id: NiBa
doi: 10.1111/evo.13784
ec_funded: 1
external_id:
isi:
- '000474031600001'
file:
- access_level: open_access
checksum: 9831ca65def2d62498c7b08338b6d237
content_type: application/pdf
creator: apreinsp
date_created: 2019-07-16T06:08:31Z
date_updated: 2020-07-14T12:47:34Z
file_id: '6643'
file_name: 2019_Evolution_TrubenovaBarbora.pdf
file_size: 815416
relation: main_file
file_date_updated: 2020-07-14T12:47:34Z
has_accepted_license: '1'
intvolume: ' 73'
isi: 1
issue: '7'
language:
- iso: eng
month: '07'
oa: 1
oa_version: Published Version
page: 1356-1374
project:
- _id: 25AEDD42-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '704172'
name: Rate of Adaptation in Changing Environment
- _id: 25B1EC9E-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '618091'
name: Speed of Adaptation in Population Genetics and Evolutionary Computation
publication: Evolution
publication_status: published
publisher: Wiley
quality_controlled: '1'
scopus_import: '1'
status: public
title: 'Surfing on the seascape: Adaptation in a changing environment'
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: 73
year: '2019'
...
---
_id: '6634'
abstract:
- lang: eng
text: In this paper we prove several new results around Gromov's waist theorem.
We give a simple proof of Vaaler's theorem on sections of the unit cube using
the Borsuk-Ulam-Crofton technique, consider waists of real and complex projective
spaces, flat tori, convex bodies in Euclidean space; and establish waist-type
results in terms of the Hausdorff measure.
article_processing_charge: No
author:
- first_name: Arseniy
full_name: Akopyan, Arseniy
id: 430D2C90-F248-11E8-B48F-1D18A9856A87
last_name: Akopyan
orcid: 0000-0002-2548-617X
- first_name: Alfredo
full_name: Hubard, Alfredo
last_name: Hubard
- first_name: Roman
full_name: Karasev, Roman
last_name: Karasev
citation:
ama: Akopyan A, Hubard A, Karasev R. Lower and upper bounds for the waists of different
spaces. Topological Methods in Nonlinear Analysis. 2019;53(2):457-490.
doi:10.12775/TMNA.2019.008
apa: Akopyan, A., Hubard, A., & Karasev, R. (2019). Lower and upper bounds for
the waists of different spaces. Topological Methods in Nonlinear Analysis.
Akademicka Platforma Czasopism. https://doi.org/10.12775/TMNA.2019.008
chicago: Akopyan, Arseniy, Alfredo Hubard, and Roman Karasev. “Lower and Upper Bounds
for the Waists of Different Spaces.” Topological Methods in Nonlinear Analysis.
Akademicka Platforma Czasopism, 2019. https://doi.org/10.12775/TMNA.2019.008.
ieee: A. Akopyan, A. Hubard, and R. Karasev, “Lower and upper bounds for the waists
of different spaces,” Topological Methods in Nonlinear Analysis, vol. 53,
no. 2. Akademicka Platforma Czasopism, pp. 457–490, 2019.
ista: Akopyan A, Hubard A, Karasev R. 2019. Lower and upper bounds for the waists
of different spaces. Topological Methods in Nonlinear Analysis. 53(2), 457–490.
mla: Akopyan, Arseniy, et al. “Lower and Upper Bounds for the Waists of Different
Spaces.” Topological Methods in Nonlinear Analysis, vol. 53, no. 2, Akademicka
Platforma Czasopism, 2019, pp. 457–90, doi:10.12775/TMNA.2019.008.
short: A. Akopyan, A. Hubard, R. Karasev, Topological Methods in Nonlinear Analysis
53 (2019) 457–490.
date_created: 2019-07-14T21:59:19Z
date_published: 2019-06-01T00:00:00Z
date_updated: 2023-08-29T06:32:48Z
day: '01'
department:
- _id: HeEd
doi: 10.12775/TMNA.2019.008
ec_funded: 1
external_id:
arxiv:
- '1612.06926'
isi:
- '000472541600004'
intvolume: ' 53'
isi: 1
issue: '2'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/1612.06926
month: '06'
oa: 1
oa_version: Preprint
page: 457-490
project:
- _id: 25681D80-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '291734'
name: International IST Postdoc Fellowship Programme
publication: Topological Methods in Nonlinear Analysis
publication_status: published
publisher: Akademicka Platforma Czasopism
quality_controlled: '1'
scopus_import: '1'
status: public
title: Lower and upper bounds for the waists of different spaces
type: journal_article
user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
volume: 53
year: '2019'
...
---
_id: '6638'
abstract:
- lang: eng
text: The crossing number of a graph G is the least number of crossings over all
possible drawings of G. We present a structural characterization of graphs with
crossing number one.
article_processing_charge: No
author:
- first_name: 'André '
full_name: 'Silva, André '
last_name: Silva
- first_name: Alan M
full_name: Arroyo Guevara, Alan M
id: 3207FDC6-F248-11E8-B48F-1D18A9856A87
last_name: Arroyo Guevara
orcid: 0000-0003-2401-8670
- first_name: Bruce
full_name: Richter, Bruce
last_name: Richter
- first_name: Orlando
full_name: Lee, Orlando
last_name: Lee
citation:
ama: Silva A, Arroyo Guevara AM, Richter B, Lee O. Graphs with at most one crossing.
Discrete Mathematics. 2019;342(11):3201-3207. doi:10.1016/j.disc.2019.06.031
apa: Silva, A., Arroyo Guevara, A. M., Richter, B., & Lee, O. (2019). Graphs
with at most one crossing. Discrete Mathematics. Elsevier. https://doi.org/10.1016/j.disc.2019.06.031
chicago: Silva, André , Alan M Arroyo Guevara, Bruce Richter, and Orlando Lee. “Graphs
with at Most One Crossing.” Discrete Mathematics. Elsevier, 2019. https://doi.org/10.1016/j.disc.2019.06.031.
ieee: A. Silva, A. M. Arroyo Guevara, B. Richter, and O. Lee, “Graphs with at most
one crossing,” Discrete Mathematics, vol. 342, no. 11. Elsevier, pp. 3201–3207,
2019.
ista: Silva A, Arroyo Guevara AM, Richter B, Lee O. 2019. Graphs with at most one
crossing. Discrete Mathematics. 342(11), 3201–3207.
mla: Silva, André, et al. “Graphs with at Most One Crossing.” Discrete Mathematics,
vol. 342, no. 11, Elsevier, 2019, pp. 3201–07, doi:10.1016/j.disc.2019.06.031.
short: A. Silva, A.M. Arroyo Guevara, B. Richter, O. Lee, Discrete Mathematics 342
(2019) 3201–3207.
date_created: 2019-07-14T21:59:20Z
date_published: 2019-11-01T00:00:00Z
date_updated: 2023-08-29T06:31:41Z
day: '01'
department:
- _id: UlWa
doi: 10.1016/j.disc.2019.06.031
ec_funded: 1
external_id:
arxiv:
- '1901.09955'
isi:
- '000486358100025'
intvolume: ' 342'
isi: 1
issue: '11'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/1901.09955
month: '11'
oa: 1
oa_version: Preprint
page: 3201-3207
project:
- _id: 26366136-B435-11E9-9278-68D0E5697425
name: Reglas de Conectividad funcional en el hipocampo
- _id: 260C2330-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '754411'
name: ISTplus - Postdoctoral Fellowships
publication: Discrete Mathematics
publication_identifier:
issn:
- 0012-365X
publication_status: published
publisher: Elsevier
quality_controlled: '1'
scopus_import: '1'
status: public
title: Graphs with at most one crossing
type: journal_article
user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
volume: 342
year: '2019'
...
---
_id: '6631'
abstract:
- lang: eng
text: The spatiotemporal organization of cell divisions constitutes an integral
part in the development of multicellular organisms, and mis-regulation of cell
divisions can lead to severe developmental defects. Cell divisions have an important
morphogenetic function in development by regulating growth and shape acquisition
of developing tissues, and, conversely, tissue morphogenesis is known to affect
both the rate and orientation of cell divisions. Moreover, cell divisions are
associated with an extensive reorganization of the cytoskeleton and adhesion apparatus
in the dividing cells that in turn can affect large-scale tissue rheological properties.
Thus, the interplay between cell divisions and tissue morphogenesis plays a key
role in embryo and tissue morphogenesis.
article_processing_charge: No
author:
- first_name: Benoit G
full_name: Godard, Benoit G
id: 33280250-F248-11E8-B48F-1D18A9856A87
last_name: Godard
- 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: Godard BG, Heisenberg C-PJ. Cell division and tissue mechanics. Current
Opinion in Cell Biology. 2019;60:114-120. doi:10.1016/j.ceb.2019.05.007
apa: Godard, B. G., & Heisenberg, C.-P. J. (2019). Cell division and tissue
mechanics. Current Opinion in Cell Biology. Elsevier. https://doi.org/10.1016/j.ceb.2019.05.007
chicago: Godard, Benoit G, and Carl-Philipp J Heisenberg. “Cell Division and Tissue
Mechanics.” Current Opinion in Cell Biology. Elsevier, 2019. https://doi.org/10.1016/j.ceb.2019.05.007.
ieee: B. G. Godard and C.-P. J. Heisenberg, “Cell division and tissue mechanics,”
Current Opinion in Cell Biology, vol. 60. Elsevier, pp. 114–120, 2019.
ista: Godard BG, Heisenberg C-PJ. 2019. Cell division and tissue mechanics. Current
Opinion in Cell Biology. 60, 114–120.
mla: Godard, Benoit G., and Carl-Philipp J. Heisenberg. “Cell Division and Tissue
Mechanics.” Current Opinion in Cell Biology, vol. 60, Elsevier, 2019, pp.
114–20, doi:10.1016/j.ceb.2019.05.007.
short: B.G. Godard, C.-P.J. Heisenberg, Current Opinion in Cell Biology 60 (2019)
114–120.
date_created: 2019-07-14T21:59:17Z
date_published: 2019-10-01T00:00:00Z
date_updated: 2023-08-29T06:33:14Z
day: '01'
department:
- _id: CaHe
doi: 10.1016/j.ceb.2019.05.007
external_id:
isi:
- '000486545800016'
intvolume: ' 60'
isi: 1
language:
- iso: eng
month: '10'
oa_version: None
page: 114-120
publication: Current Opinion in Cell Biology
publication_identifier:
issn:
- 0955-0674
publication_status: published
publisher: Elsevier
quality_controlled: '1'
scopus_import: '1'
status: public
title: Cell division and tissue mechanics
type: journal_article
user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
volume: 60
year: '2019'
...
---
_id: '6660'
abstract:
- lang: eng
text: "Commercially available full-color 3D printing allows for detailed control
of material deposition in a volume, but an exact reproduction of a target surface
appearance is hampered by the strong subsurface scattering that causes nontrivial
volumetric cross-talk at the print surface. Previous work showed how an iterative
optimization scheme based on accumulating absorptive materials at the surface
can be used to find a volumetric distribution of print materials that closely
approximates a given target appearance.\r\n\r\nIn this work, we first revisit
the assumption that pushing the absorptive materials to the surface results in
minimal volumetric cross-talk. We design a full-fledged optimization on a small
domain for this task and confirm this previously reported heuristic. Then, we
extend the above approach that is critically limited to color reproduction on
planar surfaces, to arbitrary 3D shapes. Our method enables high-fidelity color
texture reproduction on 3D prints by effectively compensating for internal light
scattering within arbitrarily shaped objects. In addition, we propose a content-aware
gamut mapping that significantly improves color reproduction for the pathological
case of thin geometric features. Using a wide range of sample objects with complex
textures and geometries, we demonstrate color reproduction whose fidelity is superior
to state-of-the-art drivers for color 3D printers."
article_number: '111'
article_processing_charge: No
author:
- first_name: Denis
full_name: Sumin, Denis
last_name: Sumin
- first_name: Tim
full_name: Weyrich, Tim
last_name: Weyrich
- first_name: Tobias
full_name: Rittig, Tobias
last_name: Rittig
- first_name: Vahid
full_name: Babaei, Vahid
last_name: Babaei
- first_name: Thomas
full_name: Nindel, Thomas
last_name: Nindel
- first_name: Alexander
full_name: Wilkie, Alexander
last_name: Wilkie
- first_name: Piotr
full_name: Didyk, Piotr
last_name: Didyk
- first_name: Bernd
full_name: Bickel, Bernd
id: 49876194-F248-11E8-B48F-1D18A9856A87
last_name: Bickel
orcid: 0000-0001-6511-9385
- first_name: Jaroslav
full_name: Křivánek, Jaroslav
last_name: Křivánek
- first_name: Karol
full_name: Myszkowski, Karol
last_name: Myszkowski
citation:
ama: Sumin D, Weyrich T, Rittig T, et al. Geometry-aware scattering compensation
for 3D printing. ACM Transactions on Graphics. 2019;38(4). doi:10.1145/3306346.3322992
apa: Sumin, D., Weyrich, T., Rittig, T., Babaei, V., Nindel, T., Wilkie, A., … Myszkowski,
K. (2019). Geometry-aware scattering compensation for 3D printing. ACM Transactions
on Graphics. ACM. https://doi.org/10.1145/3306346.3322992
chicago: Sumin, Denis, Tim Weyrich, Tobias Rittig, Vahid Babaei, Thomas Nindel,
Alexander Wilkie, Piotr Didyk, Bernd Bickel, Jaroslav Křivánek, and Karol Myszkowski.
“Geometry-Aware Scattering Compensation for 3D Printing.” ACM Transactions
on Graphics. ACM, 2019. https://doi.org/10.1145/3306346.3322992.
ieee: D. Sumin et al., “Geometry-aware scattering compensation for 3D printing,”
ACM Transactions on Graphics, vol. 38, no. 4. ACM, 2019.
ista: Sumin D, Weyrich T, Rittig T, Babaei V, Nindel T, Wilkie A, Didyk P, Bickel
B, Křivánek J, Myszkowski K. 2019. Geometry-aware scattering compensation for
3D printing. ACM Transactions on Graphics. 38(4), 111.
mla: Sumin, Denis, et al. “Geometry-Aware Scattering Compensation for 3D Printing.”
ACM Transactions on Graphics, vol. 38, no. 4, 111, ACM, 2019, doi:10.1145/3306346.3322992.
short: D. Sumin, T. Weyrich, T. Rittig, V. Babaei, T. Nindel, A. Wilkie, P. Didyk,
B. Bickel, J. Křivánek, K. Myszkowski, ACM Transactions on Graphics 38 (2019).
date_created: 2019-07-22T07:22:28Z
date_published: 2019-07-04T00:00:00Z
date_updated: 2023-08-29T06:40:49Z
day: '04'
ddc:
- '000'
department:
- _id: BeBi
doi: 10.1145/3306346.3322992
ec_funded: 1
external_id:
isi:
- '000475740600085'
file:
- access_level: open_access
checksum: 43c2019d6b48ed9c56e31686c4c2d1f5
content_type: application/pdf
creator: dernst
date_created: 2019-07-24T07:36:08Z
date_updated: 2020-07-14T12:47:36Z
file_id: '6669'
file_name: 2019_ACM_Sumin_AuthorVersion.pdf
file_size: 10109800
relation: main_file
- access_level: open_access
checksum: f80f365a04e35855fa467ea7ab26b16c
content_type: application/zip
creator: dernst
date_created: 2019-10-11T06:51:07Z
date_updated: 2020-07-14T12:47:36Z
file_id: '6938'
file_name: sumin19geometry-aware-suppl.zip
file_size: 11051245
relation: supplementary_material
file_date_updated: 2020-07-14T12:47:36Z
has_accepted_license: '1'
intvolume: ' 38'
isi: 1
issue: '4'
language:
- iso: eng
month: '07'
oa: 1
oa_version: Submitted Version
project:
- _id: 2508E324-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '642841'
name: Distributed 3D Object Design
- _id: 24F9549A-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '715767'
name: 'MATERIALIZABLE: Intelligent fabrication-oriented Computational Design and
Modeling'
publication: ACM Transactions on Graphics
publication_identifier:
issn:
- 0730-0301
publication_status: published
publisher: ACM
quality_controlled: '1'
scopus_import: '1'
status: public
title: Geometry-aware scattering compensation for 3D printing
type: journal_article
user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
volume: 38
year: '2019'
...
---
_id: '6658'
abstract:
- lang: eng
text: 'New genes are a major source of novelties, and a disproportionate amount
of them are known to show testis expression in later phases of male gametogenesis
in different groups such as mammals and plants. Here, we propose that this enhanced
expression is a consequence of haploid selection during the latter stages of male
gametogenesis. Because emerging adaptive mutations will be fixed faster if their
phenotypes are expressed by haploid rather than diploid genotypes, new genes with
advantageous functions arising during this unique stage of development have a
better chance to become fixed. To test this hypothesis, expression levels of genes
of differing evolutionary age were examined at various stages of Drosophila spermatogenesis.
We found, consistent with a model based on haploid selection, that new Drosophila
genes are both expressed in later haploid phases of spermatogenesis and harbor
a significant enrichment of adaptive mutations. Additionally, the observed overexpression
of new genes in the latter phases of spermatogenesis was limited to the autosomes.
Because all male cells exhibit hemizygous expression for X-linked genes (and therefore
effectively haploid), there is no expectation that selection acting on late spermatogenesis
will have a different effect on X-linked genes in comparison to initial diploid
phases. Together, our proposed hypothesis and the analyzed data suggest that natural
selection in haploid cells elucidates several aspects of the origin of new genes
by explaining the general prevalence of their testis expression, and a parsimonious
solution for new alleles to avoid being lost by genetic drift or pseudogenization. '
article_processing_charge: No
author:
- first_name: Julia
full_name: Raices, Julia
id: 3EE67F22-F248-11E8-B48F-1D18A9856A87
last_name: Raices
- first_name: Paulo
full_name: Otto, Paulo
last_name: Otto
- first_name: Maria
full_name: Vibranovski, Maria
last_name: Vibranovski
citation:
ama: Raices J, Otto P, Vibranovski M. Haploid selection drives new gene male germline
expression. Genome Research. 2019;29(7):1115-1122. doi:10.1101/gr.238824.118
apa: Raices, J., Otto, P., & Vibranovski, M. (2019). Haploid selection drives
new gene male germline expression. Genome Research. CSH Press. https://doi.org/10.1101/gr.238824.118
chicago: Raices, Julia, Paulo Otto, and Maria Vibranovski. “Haploid Selection Drives
New Gene Male Germline Expression.” Genome Research. CSH Press, 2019. https://doi.org/10.1101/gr.238824.118.
ieee: J. Raices, P. Otto, and M. Vibranovski, “Haploid selection drives new gene
male germline expression,” Genome Research, vol. 29, no. 7. CSH Press,
pp. 1115–1122, 2019.
ista: Raices J, Otto P, Vibranovski M. 2019. Haploid selection drives new gene male
germline expression. Genome Research. 29(7), 1115–1122.
mla: Raices, Julia, et al. “Haploid Selection Drives New Gene Male Germline Expression.”
Genome Research, vol. 29, no. 7, CSH Press, 2019, pp. 1115–22, doi:10.1101/gr.238824.118.
short: J. Raices, P. Otto, M. Vibranovski, Genome Research 29 (2019) 1115–1122.
date_created: 2019-07-21T21:59:15Z
date_published: 2019-07-01T00:00:00Z
date_updated: 2023-08-29T06:35:05Z
day: '01'
ddc:
- '576'
department:
- _id: BeVi
doi: 10.1101/gr.238824.118
external_id:
isi:
- '000473730600007'
file:
- access_level: open_access
checksum: 4636f03a6750f90b88bf2bc3eb9d71ae
content_type: application/pdf
creator: apreinsp
date_created: 2019-07-24T08:05:56Z
date_updated: 2020-07-14T12:47:35Z
file_id: '6670'
file_name: 2019_GenomeResearch_Raices.pdf
file_size: 2319022
relation: main_file
file_date_updated: 2020-07-14T12:47:35Z
has_accepted_license: '1'
intvolume: ' 29'
isi: 1
issue: '7'
language:
- iso: eng
license: https://creativecommons.org/licenses/by-nc/4.0/
month: '07'
oa: 1
oa_version: Published Version
page: 1115-1122
publication: Genome Research
publication_status: published
publisher: CSH Press
quality_controlled: '1'
scopus_import: '1'
status: public
title: Haploid selection drives new gene male germline expression
tmp:
image: /images/cc_by_nc.png
legal_code_url: https://creativecommons.org/licenses/by-nc/4.0/legalcode
name: Creative Commons Attribution-NonCommercial 4.0 International (CC BY-NC 4.0)
short: CC BY-NC (4.0)
type: journal_article
user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
volume: 29
year: '2019'
...
---
_id: '6650'
abstract:
- lang: eng
text: We propose a novel technique for the automatic design of molds to cast highly
complex shapes. The technique generates composite, two-piece molds. Each mold
piece is made up of a hard plastic shell and a flexible silicone part. Thanks
to the thin, soft, and smartly shaped silicone part, which is kept in place by
a hard plastic shell, we can cast objects of unprecedented complexity. An innovative
algorithm based on a volumetric analysis defines the layout of the internal cuts
in the silicone mold part. Our approach can robustly handle thin protruding features
and intertwined topologies that have caused previous methods to fail. We compare
our results with state of the art techniques, and we demonstrate the casting of
shapes with extremely complex geometry.
article_number: '110'
article_processing_charge: No
author:
- first_name: Thomas
full_name: Alderighi, Thomas
last_name: Alderighi
- first_name: Luigi
full_name: Malomo, Luigi
last_name: Malomo
- first_name: Daniela
full_name: Giorgi, Daniela
last_name: Giorgi
- first_name: Bernd
full_name: Bickel, Bernd
id: 49876194-F248-11E8-B48F-1D18A9856A87
last_name: Bickel
orcid: 0000-0001-6511-9385
- first_name: Paolo
full_name: Cignoni, Paolo
last_name: Cignoni
- first_name: Nico
full_name: Pietroni, Nico
last_name: Pietroni
citation:
ama: Alderighi T, Malomo L, Giorgi D, Bickel B, Cignoni P, Pietroni N. Volume-aware
design of composite molds. ACM Transactions on Graphics. 2019;38(4). doi:10.1145/3306346.3322981
apa: Alderighi, T., Malomo, L., Giorgi, D., Bickel, B., Cignoni, P., & Pietroni,
N. (2019). Volume-aware design of composite molds. ACM Transactions on Graphics.
ACM. https://doi.org/10.1145/3306346.3322981
chicago: Alderighi, Thomas, Luigi Malomo, Daniela Giorgi, Bernd Bickel, Paolo Cignoni,
and Nico Pietroni. “Volume-Aware Design of Composite Molds.” ACM Transactions
on Graphics. ACM, 2019. https://doi.org/10.1145/3306346.3322981.
ieee: T. Alderighi, L. Malomo, D. Giorgi, B. Bickel, P. Cignoni, and N. Pietroni,
“Volume-aware design of composite molds,” ACM Transactions on Graphics,
vol. 38, no. 4. ACM, 2019.
ista: Alderighi T, Malomo L, Giorgi D, Bickel B, Cignoni P, Pietroni N. 2019. Volume-aware
design of composite molds. ACM Transactions on Graphics. 38(4), 110.
mla: Alderighi, Thomas, et al. “Volume-Aware Design of Composite Molds.” ACM
Transactions on Graphics, vol. 38, no. 4, 110, ACM, 2019, doi:10.1145/3306346.3322981.
short: T. Alderighi, L. Malomo, D. Giorgi, B. Bickel, P. Cignoni, N. Pietroni, ACM
Transactions on Graphics 38 (2019).
date_created: 2019-07-19T06:18:15Z
date_published: 2019-07-01T00:00:00Z
date_updated: 2023-08-29T06:35:52Z
day: '01'
ddc:
- '000'
department:
- _id: BeBi
doi: 10.1145/3306346.3322981
ec_funded: 1
external_id:
isi:
- '000475740600084'
file:
- access_level: open_access
checksum: b4562af94672b44d2a501046427412af
content_type: application/pdf
creator: dernst
date_created: 2019-07-19T06:18:53Z
date_updated: 2020-07-14T12:47:35Z
file_id: '6651'
file_name: 2019_ACM_Alderighi_AuthorVersion.pdf
file_size: 74316182
relation: main_file
file_date_updated: 2020-07-14T12:47:35Z
has_accepted_license: '1'
intvolume: ' 38'
isi: 1
issue: '4'
language:
- iso: eng
month: '07'
oa: 1
oa_version: Submitted Version
project:
- _id: 24F9549A-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '715767'
name: 'MATERIALIZABLE: Intelligent fabrication-oriented Computational Design and
Modeling'
publication: ACM Transactions on Graphics
publication_identifier:
issn:
- 0730-0301
publication_status: published
publisher: ACM
quality_controlled: '1'
related_material:
link:
- description: YouTube Video
relation: supplementary_material
url: https://youtu.be/SO349S8-x_w
scopus_import: '1'
status: public
title: Volume-aware design of composite molds
type: journal_article
user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
volume: 38
year: '2019'
...
---
_id: '6717'
abstract:
- lang: eng
text: With the recent publication by Silpe and Bassler (2019), considering phage
detection of a bacterial quorum-sensing (QS) autoinducer, we now have as many
as five examples of phage-associated intercellular communication (Table 1). Each
potentially involves ecological inferences by phages as to concentrations of surrounding
phage-infected or uninfected bacteria. While the utility of phage detection of
bacterial QS molecules may at first glance appear to be straightforward, we suggest
in this commentary that the underlying ecological explanation is unlikely to be
simple.
article_number: '1171'
article_processing_charge: Yes (via OA deal)
author:
- first_name: Claudia
full_name: Igler, Claudia
id: 46613666-F248-11E8-B48F-1D18A9856A87
last_name: Igler
- first_name: Stephen T.
full_name: Abedon, Stephen T.
last_name: Abedon
citation:
ama: 'Igler C, Abedon ST. Commentary: A host-produced quorum-sensing autoinducer
controls a phage lysis-lysogeny decision. Frontiers in Microbiology. 2019;10.
doi:10.3389/fmicb.2019.01171'
apa: 'Igler, C., & Abedon, S. T. (2019). Commentary: A host-produced quorum-sensing
autoinducer controls a phage lysis-lysogeny decision. Frontiers in Microbiology.
Frontiers. https://doi.org/10.3389/fmicb.2019.01171'
chicago: 'Igler, Claudia, and Stephen T. Abedon. “Commentary: A Host-Produced Quorum-Sensing
Autoinducer Controls a Phage Lysis-Lysogeny Decision.” Frontiers in Microbiology.
Frontiers, 2019. https://doi.org/10.3389/fmicb.2019.01171.'
ieee: 'C. Igler and S. T. Abedon, “Commentary: A host-produced quorum-sensing autoinducer
controls a phage lysis-lysogeny decision,” Frontiers in Microbiology, vol.
10. Frontiers, 2019.'
ista: 'Igler C, Abedon ST. 2019. Commentary: A host-produced quorum-sensing autoinducer
controls a phage lysis-lysogeny decision. Frontiers in Microbiology. 10, 1171.'
mla: 'Igler, Claudia, and Stephen T. Abedon. “Commentary: A Host-Produced Quorum-Sensing
Autoinducer Controls a Phage Lysis-Lysogeny Decision.” Frontiers in Microbiology,
vol. 10, 1171, Frontiers, 2019, doi:10.3389/fmicb.2019.01171.'
short: C. Igler, S.T. Abedon, Frontiers in Microbiology 10 (2019).
date_created: 2019-07-28T21:59:18Z
date_published: 2019-06-03T00:00:00Z
date_updated: 2023-08-29T06:41:20Z
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publication: Frontiers in Microbiology
publication_status: published
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title: 'Commentary: A host-produced quorum-sensing autoinducer controls a phage lysis-lysogeny
decision'
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---
_id: '6680'
abstract:
- lang: eng
text: This paper analyzes how partial selfing in a large source population influences
its ability to colonize a new habitat via the introduction of a few founder individuals.
Founders experience inbreeding depression due to partially recessive deleterious
alleles as well as maladaptation to the new environment due to selection on a
large number of additive loci. I first introduce a simplified version of the Inbreeding
History Model (Kelly, 2007) in order to characterize mutation‐selection balance
in a large, partially selfing source population under selection involving multiple
non‐identical loci. I then use individual‐based simulations to study the eco‐evolutionary
dynamics of founders establishing in the new habitat under a model of hard selection.
The study explores how selfing rate shapes establishment probabilities of founders
via effects on both inbreeding depression and adaptability to the new environment,
and also distinguishes the effects of selfing on the initial fitness of founders
from its effects on the long‐term adaptive response of the populations they found.
A high rate of (but not complete) selfing is found to aid establishment over a
wide range of parameters, even in the absence of mate limitation. The sensitivity
of the results to assumptions about the nature of polygenic selection are discussed.
article_processing_charge: Yes (via OA deal)
author:
- first_name: Himani
full_name: Sachdeva, Himani
id: 42377A0A-F248-11E8-B48F-1D18A9856A87
last_name: Sachdeva
citation:
ama: Sachdeva H. Effect of partial selfing and polygenic selection on establishment
in a new habitat. Evolution. 2019;73(9):1729-1745. doi:10.1111/evo.13812
apa: Sachdeva, H. (2019). Effect of partial selfing and polygenic selection on establishment
in a new habitat. Evolution. Wiley. https://doi.org/10.1111/evo.13812
chicago: Sachdeva, Himani. “Effect of Partial Selfing and Polygenic Selection on
Establishment in a New Habitat.” Evolution. Wiley, 2019. https://doi.org/10.1111/evo.13812.
ieee: H. Sachdeva, “Effect of partial selfing and polygenic selection on establishment
in a new habitat,” Evolution, vol. 73, no. 9. Wiley, pp. 1729–1745, 2019.
ista: Sachdeva H. 2019. Effect of partial selfing and polygenic selection on establishment
in a new habitat. Evolution. 73(9), 1729–1745.
mla: Sachdeva, Himani. “Effect of Partial Selfing and Polygenic Selection on Establishment
in a New Habitat.” Evolution, vol. 73, no. 9, Wiley, 2019, pp. 1729–45,
doi:10.1111/evo.13812.
short: H. Sachdeva, Evolution 73 (2019) 1729–1745.
date_created: 2019-07-25T09:08:28Z
date_published: 2019-09-01T00:00:00Z
date_updated: 2023-08-29T06:43:58Z
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department:
- _id: NiBa
doi: 10.1111/evo.13812
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issue: '9'
language:
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month: '09'
oa: 1
oa_version: Published Version
page: 1729-1745
publication: Evolution
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issn:
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publication_status: published
publisher: Wiley
quality_controlled: '1'
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title: Effect of partial selfing and polygenic selection on establishment in a new
habitat
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short: CC BY (4.0)
type: journal_article
user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
volume: 73
year: '2019'
...