---
_id: '6262'
abstract:
- lang: eng
text: "Gravitropism is an adaptive response that orients plant growth parallel to
the gravity vector. Asymmetric\r\ndistribution of the phytohormone auxin is a
necessary prerequisite to the tropic bending both in roots and\r\nshoots. During
hypocotyl gravitropic response, the PIN3 auxin transporter polarizes within gravity-sensing\r\ncells
to redirect intercellular auxin fluxes. First gravity-induced PIN3 polarization
to the bottom cell mem-\r\nbranes leads to the auxin accumulation at the lower
side of the organ, initiating bending and, later, auxin\r\nfeedback-mediated repolarization
restores symmetric auxin distribution to terminate bending. Here, we per-\r\nformed
a forward genetic screen to identify regulators of both PIN3 polarization events
during gravitropic\r\nresponse. We searched for mutants with defective PIN3 polarizations
based on easy-to-score morphological\r\noutputs of decreased or increased gravity-induced
hypocotyl bending. We identified the number of\r\nhypocotyl reduced bending (hrb)
and hypocotyl hyperbending (hhb) mutants, revealing that reduced bending corre-\r\nlated
typically with defective gravity-induced PIN3 relocation whereas all analyzed
hhb mutants showed\r\ndefects in the second, auxin-mediated PIN3 relocation. Next-generation
sequencing-aided mutation map-\r\nping identified several candidate genes, including
SCARECROW and ACTIN2, revealing roles of endodermis\r\nspecification and actin
cytoskeleton in the respective gravity- and auxin-induced PIN polarization events.\r\nThe
hypocotyl gravitropism screen thus promises to provide novel insights into mechanisms
underlying cell\r\npolarity and plant adaptive development."
article_processing_charge: Yes (via OA deal)
article_type: original
author:
- first_name: Hana
full_name: Rakusová, Hana
last_name: Rakusová
- first_name: Huibin
full_name: Han, Huibin
id: 31435098-F248-11E8-B48F-1D18A9856A87
last_name: Han
- first_name: Petr
full_name: Valošek, Petr
id: 3CDB6F94-F248-11E8-B48F-1D18A9856A87
last_name: Valošek
- first_name: Jiří
full_name: Friml, Jiří
id: 4159519E-F248-11E8-B48F-1D18A9856A87
last_name: Friml
orcid: 0000-0002-8302-7596
citation:
ama: Rakusová H, Han H, Valošek P, Friml J. Genetic screen for factors mediating
PIN polarization in gravistimulated Arabidopsis thaliana hypocotyls. The Plant
Journal. 2019;98(6):1048-1059. doi:10.1111/tpj.14301
apa: Rakusová, H., Han, H., Valošek, P., & Friml, J. (2019). Genetic screen
for factors mediating PIN polarization in gravistimulated Arabidopsis thaliana
hypocotyls. The Plant Journal. Wiley. https://doi.org/10.1111/tpj.14301
chicago: Rakusová, Hana, Huibin Han, Petr Valošek, and Jiří Friml. “Genetic Screen
for Factors Mediating PIN Polarization in Gravistimulated Arabidopsis Thaliana
Hypocotyls.” The Plant Journal. Wiley, 2019. https://doi.org/10.1111/tpj.14301.
ieee: H. Rakusová, H. Han, P. Valošek, and J. Friml, “Genetic screen for factors
mediating PIN polarization in gravistimulated Arabidopsis thaliana hypocotyls,”
The Plant Journal, vol. 98, no. 6. Wiley, pp. 1048–1059, 2019.
ista: Rakusová H, Han H, Valošek P, Friml J. 2019. Genetic screen for factors mediating
PIN polarization in gravistimulated Arabidopsis thaliana hypocotyls. The Plant
Journal. 98(6), 1048–1059.
mla: Rakusová, Hana, et al. “Genetic Screen for Factors Mediating PIN Polarization
in Gravistimulated Arabidopsis Thaliana Hypocotyls.” The Plant Journal,
vol. 98, no. 6, Wiley, 2019, pp. 1048–59, doi:10.1111/tpj.14301.
short: H. Rakusová, H. Han, P. Valošek, J. Friml, The Plant Journal 98 (2019) 1048–1059.
date_created: 2019-04-09T08:46:44Z
date_published: 2019-06-01T00:00:00Z
date_updated: 2023-08-25T10:11:03Z
day: '01'
ddc:
- '580'
department:
- _id: JiFr
doi: 10.1111/tpj.14301
ec_funded: 1
external_id:
isi:
- '000473644100008'
pmid:
- '30821050'
file:
- access_level: open_access
checksum: ad3b5e270b67ba2a45f894ce3be27920
content_type: application/pdf
creator: dernst
date_created: 2019-04-15T09:38:43Z
date_updated: 2020-07-14T12:47:25Z
file_id: '6304'
file_name: 2019_PlantJournal_Rakusov.pdf
file_size: 1383100
relation: main_file
file_date_updated: 2020-07-14T12:47:25Z
has_accepted_license: '1'
intvolume: ' 98'
isi: 1
issue: '6'
language:
- iso: eng
license: https://creativecommons.org/licenses/by/4.0/
month: '06'
oa: 1
oa_version: Published Version
page: 1048-1059
pmid: 1
project:
- _id: 25716A02-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '282300'
name: Polarity and subcellular dynamics in plants
publication: The Plant Journal
publication_identifier:
eissn:
- 1365-313x
issn:
- 0960-7412
publication_status: published
publisher: Wiley
quality_controlled: '1'
scopus_import: '1'
status: public
title: Genetic screen for factors mediating PIN polarization in gravistimulated Arabidopsis
thaliana hypocotyls
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: journal_article
user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
volume: 98
year: '2019'
...
---
_id: '6297'
abstract:
- lang: eng
text: Cell-cell and cell-glycocalyx interactions under flow are important for the
behaviour of circulating cells in blood and lymphatic vessels. However, such interactions
are not well understood due in part to a lack of tools to study them in defined
environments. Here, we develop a versatile in vitro platform for the study of
cell-glycocalyx interactions in well-defined physical and chemical settings under
flow. Our approach is demonstrated with the interaction between hyaluronan (HA,
a key component of the endothelial glycocalyx) and its cell receptor CD44. We
generate HA brushes in situ within a microfluidic device, and demonstrate the
tuning of their physical (thickness and softness) and chemical (density of CD44
binding sites) properties using characterisation with reflection interference
contrast microscopy (RICM) and application of polymer theory. We highlight the
interactions of HA brushes with CD44-displaying beads and cells under flow. Observations
of CD44+ beads on a HA brush with RICM enabled the 3-dimensional trajectories
to be generated, and revealed interactions in the form of stop and go phases with
reduced rolling velocity and reduced distance between the bead and the HA brush,
compared to uncoated beads. Combined RICM and bright-field microscopy of CD44+
AKR1 T-lymphocytes revealed complementary information about the dynamics of cell
rolling and cell morphology, and highlighted the formation of tethers and slings,
as they interacted with a HA brush under flow. This platform can readily incorporate
more complex models of the glycocalyx, and should permit the study of how mechanical
and biochemical factors are orchestrated to enable highly selective blood cell-vessel
wall interactions under flow.
article_processing_charge: No
article_type: original
author:
- first_name: Heather S.
full_name: Davies, Heather S.
last_name: Davies
- first_name: Natalia S.
full_name: Baranova, Natalia S.
id: 38661662-F248-11E8-B48F-1D18A9856A87
last_name: Baranova
orcid: 0000-0002-3086-9124
- first_name: Nouha
full_name: El Amri, Nouha
last_name: El Amri
- first_name: Liliane
full_name: Coche-Guérente, Liliane
last_name: Coche-Guérente
- first_name: Claude
full_name: Verdier, Claude
last_name: Verdier
- first_name: Lionel
full_name: Bureau, Lionel
last_name: Bureau
- first_name: Ralf P.
full_name: Richter, Ralf P.
last_name: Richter
- first_name: Delphine
full_name: Débarre, Delphine
last_name: Débarre
citation:
ama: Davies HS, Baranova NS, El Amri N, et al. An integrated assay to probe endothelial
glycocalyx-blood cell interactions under flow in mechanically and biochemically
well-defined environments. Matrix Biology. 2019;78-79:47-59. doi:10.1016/j.matbio.2018.12.002
apa: Davies, H. S., Baranova, N. S., El Amri, N., Coche-Guérente, L., Verdier, C.,
Bureau, L., … Débarre, D. (2019). An integrated assay to probe endothelial glycocalyx-blood
cell interactions under flow in mechanically and biochemically well-defined environments.
Matrix Biology. Elsevier. https://doi.org/10.1016/j.matbio.2018.12.002
chicago: Davies, Heather S., Natalia S. Baranova, Nouha El Amri, Liliane Coche-Guérente,
Claude Verdier, Lionel Bureau, Ralf P. Richter, and Delphine Débarre. “An Integrated
Assay to Probe Endothelial Glycocalyx-Blood Cell Interactions under Flow in Mechanically
and Biochemically Well-Defined Environments.” Matrix Biology. Elsevier,
2019. https://doi.org/10.1016/j.matbio.2018.12.002.
ieee: H. S. Davies et al., “An integrated assay to probe endothelial glycocalyx-blood
cell interactions under flow in mechanically and biochemically well-defined environments,”
Matrix Biology, vol. 78–79. Elsevier, pp. 47–59, 2019.
ista: Davies HS, Baranova NS, El Amri N, Coche-Guérente L, Verdier C, Bureau L,
Richter RP, Débarre D. 2019. An integrated assay to probe endothelial glycocalyx-blood
cell interactions under flow in mechanically and biochemically well-defined environments.
Matrix Biology. 78–79, 47–59.
mla: Davies, Heather S., et al. “An Integrated Assay to Probe Endothelial Glycocalyx-Blood
Cell Interactions under Flow in Mechanically and Biochemically Well-Defined Environments.”
Matrix Biology, vol. 78–79, Elsevier, 2019, pp. 47–59, doi:10.1016/j.matbio.2018.12.002.
short: H.S. Davies, N.S. Baranova, N. El Amri, L. Coche-Guérente, C. Verdier, L.
Bureau, R.P. Richter, D. Débarre, Matrix Biology 78–79 (2019) 47–59.
date_created: 2019-04-11T20:55:01Z
date_published: 2019-05-01T00:00:00Z
date_updated: 2023-08-25T10:11:28Z
day: '01'
ddc:
- '570'
department:
- _id: MaLo
doi: 10.1016/j.matbio.2018.12.002
external_id:
isi:
- '000468707600005'
file:
- access_level: open_access
checksum: 790878cd78bfc54a147ddcc7c8f286a0
content_type: application/pdf
creator: dernst
date_created: 2020-05-14T09:02:07Z
date_updated: 2020-07-14T12:47:27Z
file_id: '7825'
file_name: 2018_MatrixBiology_Davies.pdf
file_size: 4444339
relation: main_file
file_date_updated: 2020-07-14T12:47:27Z
has_accepted_license: '1'
isi: 1
language:
- iso: eng
license: https://creativecommons.org/licenses/by-nc-nd/4.0/
month: '05'
oa: 1
oa_version: Submitted Version
page: 47-59
publication: Matrix Biology
publication_identifier:
issn:
- 0945-053X
publication_status: published
publisher: Elsevier
quality_controlled: '1'
status: public
title: An integrated assay to probe endothelial glycocalyx-blood cell interactions
under flow in mechanically and biochemically well-defined environments
tmp:
image: /images/cc_by_nc_nd.png
legal_code_url: https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode
name: Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International
(CC BY-NC-ND 4.0)
short: CC BY-NC-ND (4.0)
type: journal_article
user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
volume: 78-79
year: '2019'
...
---
_id: '6310'
abstract:
- lang: eng
text: An asymptotic formula is established for the number of rational points of
bounded anticanonical height which lie on a certain Zariskiopen subset of an arbitrary
smooth biquadratic hypersurface in sufficiently many variables. The proof uses
the Hardy–Littlewood circle method.
article_processing_charge: No
author:
- first_name: Timothy D
full_name: Browning, Timothy D
id: 35827D50-F248-11E8-B48F-1D18A9856A87
last_name: Browning
orcid: 0000-0002-8314-0177
- first_name: L.Q.
full_name: Hu, L.Q.
last_name: Hu
citation:
ama: Browning TD, Hu LQ. Counting rational points on biquadratic hypersurfaces.
Advances in Mathematics. 2019;349:920-940. doi:10.1016/j.aim.2019.04.031
apa: Browning, T. D., & Hu, L. Q. (2019). Counting rational points on biquadratic
hypersurfaces. Advances in Mathematics. Elsevier. https://doi.org/10.1016/j.aim.2019.04.031
chicago: Browning, Timothy D, and L.Q. Hu. “Counting Rational Points on Biquadratic
Hypersurfaces.” Advances in Mathematics. Elsevier, 2019. https://doi.org/10.1016/j.aim.2019.04.031.
ieee: T. D. Browning and L. Q. Hu, “Counting rational points on biquadratic hypersurfaces,”
Advances in Mathematics, vol. 349. Elsevier, pp. 920–940, 2019.
ista: Browning TD, Hu LQ. 2019. Counting rational points on biquadratic hypersurfaces.
Advances in Mathematics. 349, 920–940.
mla: Browning, Timothy D., and L. Q. Hu. “Counting Rational Points on Biquadratic
Hypersurfaces.” Advances in Mathematics, vol. 349, Elsevier, 2019, pp.
920–40, doi:10.1016/j.aim.2019.04.031.
short: T.D. Browning, L.Q. Hu, Advances in Mathematics 349 (2019) 920–940.
date_created: 2019-04-16T09:13:25Z
date_published: 2019-06-20T00:00:00Z
date_updated: 2023-08-25T10:11:55Z
day: '20'
ddc:
- '512'
department:
- _id: TiBr
doi: 10.1016/j.aim.2019.04.031
external_id:
arxiv:
- '1810.08426'
isi:
- '000468857300025'
file:
- access_level: open_access
checksum: a63594a3a91b4ba6e2a1b78b0720b3d0
content_type: application/pdf
creator: tbrownin
date_created: 2019-04-16T09:12:20Z
date_updated: 2020-07-14T12:47:27Z
file_id: '6311'
file_name: wliqun.pdf
file_size: 379158
relation: main_file
file_date_updated: 2020-07-14T12:47:27Z
has_accepted_license: '1'
intvolume: ' 349'
isi: 1
language:
- iso: eng
month: '06'
oa: 1
oa_version: Submitted Version
page: 920-940
publication: Advances in Mathematics
publication_identifier:
eissn:
- '10902082'
issn:
- '00018708'
publication_status: published
publisher: Elsevier
quality_controlled: '1'
scopus_import: '1'
status: public
title: Counting rational points on biquadratic hypersurfaces
type: journal_article
user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
volume: 349
year: '2019'
...
---
_id: '6261'
abstract:
- lang: eng
text: Nitrate regulation of root stem cell activity is auxin-dependent.
article_processing_charge: No
article_type: letter_note
author:
- first_name: Y
full_name: Wang, Y
last_name: Wang
- first_name: Z
full_name: Gong, Z
last_name: Gong
- first_name: Jiří
full_name: Friml, Jiří
id: 4159519E-F248-11E8-B48F-1D18A9856A87
last_name: Friml
orcid: 0000-0002-8302-7596
- first_name: J
full_name: Zhang, J
last_name: Zhang
citation:
ama: Wang Y, Gong Z, Friml J, Zhang J. Nitrate modulates the differentiation of
root distal stem cells. Plant Physiology. 2019;180(1):22-25. doi:10.1104/pp.18.01305
apa: Wang, Y., Gong, Z., Friml, J., & Zhang, J. (2019). Nitrate modulates the
differentiation of root distal stem cells. Plant Physiology. ASPB. https://doi.org/10.1104/pp.18.01305
chicago: Wang, Y, Z Gong, Jiří Friml, and J Zhang. “Nitrate Modulates the Differentiation
of Root Distal Stem Cells.” Plant Physiology. ASPB, 2019. https://doi.org/10.1104/pp.18.01305.
ieee: Y. Wang, Z. Gong, J. Friml, and J. Zhang, “Nitrate modulates the differentiation
of root distal stem cells,” Plant Physiology, vol. 180, no. 1. ASPB, pp.
22–25, 2019.
ista: Wang Y, Gong Z, Friml J, Zhang J. 2019. Nitrate modulates the differentiation
of root distal stem cells. Plant Physiology. 180(1), 22–25.
mla: Wang, Y., et al. “Nitrate Modulates the Differentiation of Root Distal Stem
Cells.” Plant Physiology, vol. 180, no. 1, ASPB, 2019, pp. 22–25, doi:10.1104/pp.18.01305.
short: Y. Wang, Z. Gong, J. Friml, J. Zhang, Plant Physiology 180 (2019) 22–25.
date_created: 2019-04-09T08:46:17Z
date_published: 2019-05-01T00:00:00Z
date_updated: 2023-08-25T10:10:23Z
day: '01'
department:
- _id: JiFr
doi: 10.1104/pp.18.01305
external_id:
isi:
- '000466860800010'
pmid:
- '30787134'
intvolume: ' 180'
isi: 1
issue: '1'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.1104/pp.18.01305
month: '05'
oa: 1
oa_version: Published Version
page: 22-25
pmid: 1
publication: Plant Physiology
publication_identifier:
eissn:
- 1532-2548
issn:
- 0032-0889
publication_status: published
publisher: ASPB
quality_controlled: '1'
scopus_import: '1'
status: public
title: Nitrate modulates the differentiation of root distal stem cells
type: journal_article
user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
volume: 180
year: '2019'
...
---
_id: '6352'
abstract:
- lang: eng
text: Chronic overuse of common pharmaceuticals, e.g. acetaminophen (paracetamol),
often leads to the development of acute liver failure (ALF). This study aimed
to elucidate the effect of cultured mesenchymal stem cells (MSCs) proteome on
the onset of liver damage and regeneration dynamics in animals with ALF induced
by acetaminophen, to test the liver protective efficacy of MSCs proteome depending
on the oxygen tension in cell culture, and to blueprint protein components responsible
for the effect. Protein compositions prepared from MSCs cultured in mild hypoxic
(5% and 10% O2) and normal (21% O2) conditions were used to treat ALF induced
in mice by injection of acetaminophen. To test the effect of reduced oxygen tension
in cell culture on resulting MSCs proteome content we applied a combination of
high performance liquid chromatography and mass-spectrometry (LC–MS/MS) for the
identification of proteins in lysates of MSCs cultured at different O2 levels.
The treatment of acetaminophen-administered animals with proteins released from
cultured MSCs resulted in the inhibition of inflammatory reactions in damaged
liver; the area of hepatocyte necrosis being reduced in the first 24 h. Compositions
obtained from MSCs cultured at lower O2 level were shown to be more potent than
a composition prepared from normoxic cells. A comparative characterization of
protein pattern and identification of individual components done by a cytokine
assay and proteomics analysis of protein compositions revealed that even moderate
hypoxia produces discrete changes in the expression of various subsets of proteins
responsible for intracellular respiration and cell signaling. The application
of proteins prepared from MSCs grown in vitro at reduced oxygen tension significantly
accelerates healing process in damaged liver tissue. The proteomics data obtained
for different preparations offer new information about the potential candidates
in the MSCs protein repertoire sensitive to oxygen tension in culture medium,
which can be involved in the generalized mechanisms the cells use to respond to
acute liver failure.
acknowledgement: The studies were supported by the Austrian Federal Ministry of Economy,
Family and Youth through the initiative “Laura Bassi Centres of Expertise” funding
the Center of Optimized Structural Stud-ies, grant No. 253275
article_processing_charge: Yes (via OA deal)
author:
- first_name: Andrey Alexandrovich
full_name: Temnov, Andrey Alexandrovich
last_name: Temnov
- first_name: Konstantin Arkadevich
full_name: Rogov, Konstantin Arkadevich
last_name: Rogov
- first_name: Alla Nikolaevna
full_name: Sklifas, Alla Nikolaevna
last_name: Sklifas
- first_name: Elena Valerievna
full_name: Klychnikova, Elena Valerievna
last_name: Klychnikova
- first_name: Markus
full_name: Hartl, Markus
last_name: Hartl
- first_name: Kristina
full_name: Djinovic-Carugo, Kristina
last_name: Djinovic-Carugo
- first_name: Alexej
full_name: Charnagalov, Alexej
id: 49F06DBA-F248-11E8-B48F-1D18A9856A87
last_name: Charnagalov
citation:
ama: Temnov AA, Rogov KA, Sklifas AN, et al. Protective properties of the cultured
stem cell proteome studied in an animal model of acetaminophen-induced acute liver
failure. Molecular Biology Reports. 2019. doi:10.1007/s11033-019-04765-z
apa: Temnov, A. A., Rogov, K. A., Sklifas, A. N., Klychnikova, E. V., Hartl, M.,
Djinovic-Carugo, K., & Charnagalov, A. (2019). Protective properties of the
cultured stem cell proteome studied in an animal model of acetaminophen-induced
acute liver failure. Molecular Biology Reports. Springer. https://doi.org/10.1007/s11033-019-04765-z
chicago: Temnov, Andrey Alexandrovich, Konstantin Arkadevich Rogov, Alla Nikolaevna
Sklifas, Elena Valerievna Klychnikova, Markus Hartl, Kristina Djinovic-Carugo,
and Alexej Charnagalov. “Protective Properties of the Cultured Stem Cell Proteome
Studied in an Animal Model of Acetaminophen-Induced Acute Liver Failure.” Molecular
Biology Reports. Springer, 2019. https://doi.org/10.1007/s11033-019-04765-z.
ieee: A. A. Temnov et al., “Protective properties of the cultured stem cell
proteome studied in an animal model of acetaminophen-induced acute liver failure,”
Molecular Biology Reports. Springer, 2019.
ista: Temnov AA, Rogov KA, Sklifas AN, Klychnikova EV, Hartl M, Djinovic-Carugo
K, Charnagalov A. 2019. Protective properties of the cultured stem cell proteome
studied in an animal model of acetaminophen-induced acute liver failure. Molecular
Biology Reports.
mla: Temnov, Andrey Alexandrovich, et al. “Protective Properties of the Cultured
Stem Cell Proteome Studied in an Animal Model of Acetaminophen-Induced Acute Liver
Failure.” Molecular Biology Reports, Springer, 2019, doi:10.1007/s11033-019-04765-z.
short: A.A. Temnov, K.A. Rogov, A.N. Sklifas, E.V. Klychnikova, M. Hartl, K. Djinovic-Carugo,
A. Charnagalov, Molecular Biology Reports (2019).
date_created: 2019-04-28T21:59:14Z
date_published: 2019-04-12T00:00:00Z
date_updated: 2023-08-25T10:14:26Z
day: '12'
ddc:
- '570'
department:
- _id: LeSa
doi: 10.1007/s11033-019-04765-z
external_id:
isi:
- '000470332600049'
file:
- access_level: open_access
checksum: 45bf040bbce1cea274f6013fa18ba21b
content_type: application/pdf
creator: dernst
date_created: 2019-04-30T09:52:36Z
date_updated: 2020-07-14T12:47:28Z
file_id: '6362'
file_name: 2019_MolecularBioReport_Temnov.pdf
file_size: 1948014
relation: main_file
file_date_updated: 2020-07-14T12:47:28Z
has_accepted_license: '1'
isi: 1
language:
- iso: eng
month: '04'
oa: 1
oa_version: Published Version
publication: Molecular Biology Reports
publication_identifier:
eissn:
- '15734978'
issn:
- '03014851'
publication_status: published
publisher: Springer
quality_controlled: '1'
scopus_import: '1'
status: public
title: Protective properties of the cultured stem cell proteome studied in an animal
model of acetaminophen-induced acute liver failure
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: journal_article
user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
year: '2019'
...
---
_id: '6348'
abstract:
- lang: eng
text: 'High-speed optical telecommunication is enabled by wavelength-division multiplexing,
whereby hundreds of individually stabilized lasers encode information within a
single-mode optical fibre. Higher bandwidths require higher total optical power,
but the power sent into the fibre is limited by optical nonlinearities within
the fibre, and energy consumption by the light sources starts to become a substantial
cost factor1. Optical frequency combs have been suggested to remedy this problem
by generating numerous discrete, equidistant laser lines within a monolithic device;
however, at present their stability and coherence allow them to operate only within
small parameter ranges2,3,4. Here we show that a broadband frequency comb realized
through the electro-optic effect within a high-quality whispering-gallery-mode
resonator can operate at low microwave and optical powers. Unlike the usual third-order
Kerr nonlinear optical frequency combs, our combs rely on the second-order nonlinear
effect, which is much more efficient. Our result uses a fixed microwave signal
that is mixed with an optical-pump signal to generate a coherent frequency comb
with a precisely determined carrier separation. The resonant enhancement enables
us to work with microwave powers that are three orders of magnitude lower than
those in commercially available devices. We emphasize the practical relevance
of our results to high rates of data communication. To circumvent the limitations
imposed by nonlinear effects in optical communication fibres, one has to solve
two problems: to provide a compact and fully integrated, yet high-quality and
coherent, frequency comb generator; and to calculate nonlinear signal propagation
in real time5. We report a solution to the first problem.'
article_processing_charge: No
author:
- first_name: Alfredo R
full_name: Rueda Sanchez, Alfredo R
id: 3B82B0F8-F248-11E8-B48F-1D18A9856A87
last_name: Rueda Sanchez
orcid: 0000-0001-6249-5860
- first_name: Florian
full_name: Sedlmeir, Florian
last_name: Sedlmeir
- first_name: Madhuri
full_name: Kumari, Madhuri
last_name: Kumari
- first_name: Gerd
full_name: Leuchs, Gerd
last_name: Leuchs
- first_name: Harald G.L.
full_name: Schwefel, Harald G.L.
last_name: Schwefel
citation:
ama: Rueda Sanchez AR, Sedlmeir F, Kumari M, Leuchs G, Schwefel HGL. Resonant electro-optic
frequency comb. Nature. 2019;568(7752):378-381. doi:10.1038/s41586-019-1110-x
apa: Rueda Sanchez, A. R., Sedlmeir, F., Kumari, M., Leuchs, G., & Schwefel,
H. G. L. (2019). Resonant electro-optic frequency comb. Nature. Springer
Nature. https://doi.org/10.1038/s41586-019-1110-x
chicago: Rueda Sanchez, Alfredo R, Florian Sedlmeir, Madhuri Kumari, Gerd Leuchs,
and Harald G.L. Schwefel. “Resonant Electro-Optic Frequency Comb.” Nature.
Springer Nature, 2019. https://doi.org/10.1038/s41586-019-1110-x.
ieee: A. R. Rueda Sanchez, F. Sedlmeir, M. Kumari, G. Leuchs, and H. G. L. Schwefel,
“Resonant electro-optic frequency comb,” Nature, vol. 568, no. 7752. Springer
Nature, pp. 378–381, 2019.
ista: Rueda Sanchez AR, Sedlmeir F, Kumari M, Leuchs G, Schwefel HGL. 2019. Resonant
electro-optic frequency comb. Nature. 568(7752), 378–381.
mla: Rueda Sanchez, Alfredo R., et al. “Resonant Electro-Optic Frequency Comb.”
Nature, vol. 568, no. 7752, Springer Nature, 2019, pp. 378–81, doi:10.1038/s41586-019-1110-x.
short: A.R. Rueda Sanchez, F. Sedlmeir, M. Kumari, G. Leuchs, H.G.L. Schwefel, Nature
568 (2019) 378–381.
date_created: 2019-04-28T21:59:13Z
date_published: 2019-04-18T00:00:00Z
date_updated: 2023-08-25T10:15:25Z
day: '18'
department:
- _id: JoFi
doi: 10.1038/s41586-019-1110-x
external_id:
arxiv:
- '1808.10608'
isi:
- '000464950700053'
intvolume: ' 568'
isi: 1
issue: '7752'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/1808.10608
month: '04'
oa: 1
oa_version: Preprint
page: 378-381
publication: Nature
publication_identifier:
eissn:
- '14764687'
issn:
- '00280836'
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
related_material:
link:
- relation: erratum
url: https://doi.org/10.1038/s41586-019-1220-5
scopus_import: '1'
status: public
title: Resonant electro-optic frequency comb
type: journal_article
user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
volume: 568
year: '2019'
...
---
_id: '6338'
abstract:
- lang: eng
text: Hippocampal activity patterns representing movement trajectories are reactivated
in immobility and sleep periods, a process associated with memory recall, consolidation,
and decision making. It is thought that only fixed, behaviorally relevant patterns
can be reactivated, which are stored across hippocampal synaptic connections.
To test whether some generalized rules govern reactivation, we examined trajectory
reactivation following non-stereotypical exploration of familiar open-field environments.
We found that random trajectories of varying lengths and timescales were reactivated,
resembling that of Brownian motion of particles. The animals’ behavioral trajectory
did not follow Brownian diffusion demonstrating that the exact behavioral experience
is not reactivated. Therefore, hippocampal circuits are able to generate random
trajectories of any recently active map by following diffusion dynamics. This
ability of hippocampal circuits to generate representations of all behavioral
outcome combinations, experienced or not, may underlie a wide variety of hippocampal-dependent
cognitive functions such as learning, generalization, and planning.
article_processing_charge: No
article_type: original
author:
- first_name: Federico
full_name: Stella, Federico
id: 39AF1E74-F248-11E8-B48F-1D18A9856A87
last_name: Stella
orcid: 0000-0001-9439-3148
- first_name: Peter
full_name: Baracskay, Peter
id: 361CC00E-F248-11E8-B48F-1D18A9856A87
last_name: Baracskay
- first_name: Joseph
full_name: O'Neill, Joseph
id: 426376DC-F248-11E8-B48F-1D18A9856A87
last_name: O'Neill
- first_name: Jozsef L
full_name: Csicsvari, Jozsef L
id: 3FA14672-F248-11E8-B48F-1D18A9856A87
last_name: Csicsvari
orcid: 0000-0002-5193-4036
citation:
ama: Stella F, Baracskay P, O’Neill J, Csicsvari JL. Hippocampal reactivation of
random trajectories resembling Brownian diffusion. Neuron. 2019;102:450-461.
doi:10.1016/j.neuron.2019.01.052
apa: Stella, F., Baracskay, P., O’Neill, J., & Csicsvari, J. L. (2019). Hippocampal
reactivation of random trajectories resembling Brownian diffusion. Neuron.
Elsevier. https://doi.org/10.1016/j.neuron.2019.01.052
chicago: Stella, Federico, Peter Baracskay, Joseph O’Neill, and Jozsef L Csicsvari.
“Hippocampal Reactivation of Random Trajectories Resembling Brownian Diffusion.”
Neuron. Elsevier, 2019. https://doi.org/10.1016/j.neuron.2019.01.052.
ieee: F. Stella, P. Baracskay, J. O’Neill, and J. L. Csicsvari, “Hippocampal reactivation
of random trajectories resembling Brownian diffusion,” Neuron, vol. 102.
Elsevier, pp. 450–461, 2019.
ista: Stella F, Baracskay P, O’Neill J, Csicsvari JL. 2019. Hippocampal reactivation
of random trajectories resembling Brownian diffusion. Neuron. 102, 450–461.
mla: Stella, Federico, et al. “Hippocampal Reactivation of Random Trajectories Resembling
Brownian Diffusion.” Neuron, vol. 102, Elsevier, 2019, pp. 450–61, doi:10.1016/j.neuron.2019.01.052.
short: F. Stella, P. Baracskay, J. O’Neill, J.L. Csicsvari, Neuron 102 (2019) 450–461.
date_created: 2019-04-17T08:28:59Z
date_published: 2019-04-17T00:00:00Z
date_updated: 2023-08-25T10:13:07Z
day: '17'
department:
- _id: JoCs
doi: 10.1016/j.neuron.2019.01.052
ec_funded: 1
external_id:
isi:
- '000465169700017'
pmid:
- '30819547'
intvolume: ' 102'
isi: 1
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.1016/j.neuron.2019.01.052
month: '04'
oa: 1
oa_version: Published Version
page: 450-461
pmid: 1
project:
- _id: 257A4776-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '281511'
name: Memory-related information processing in neuronal circuits of the hippocampus
and entorhinal cortex
- _id: 2654F984-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: I03713
name: Interneuro Plasticity During Spatial Learning
publication: Neuron
publication_status: published
publisher: Elsevier
quality_controlled: '1'
related_material:
link:
- description: News on IST Homepage
relation: press_release
url: https://ist.ac.at/en/news/memories-of-movement-are-replayed-randomly-during-sleep/
scopus_import: '1'
status: public
title: Hippocampal reactivation of random trajectories resembling Brownian diffusion
type: journal_article
user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
volume: 102
year: '2019'
...
---
_id: '5878'
abstract:
- lang: eng
text: We consider the motion of a droplet bouncing on a vibrating bath of the same
fluid in the presence of a central potential. We formulate a rotation symmetry-reduced
description of this system, which allows for the straightforward application of
dynamical systems theory tools. As an illustration of the utility of the symmetry
reduction, we apply it to a model of the pilot-wave system with a central harmonic
force. We begin our analysis by identifying local bifurcations and the onset of
chaos. We then describe the emergence of chaotic regions and their merging bifurcations,
which lead to the formation of a global attractor. In this final regime, the droplet’s
angular momentum spontaneously changes its sign as observed in the experiments
of Perrard et al.
article_number: '013122'
article_processing_charge: No
article_type: original
author:
- first_name: Nazmi B
full_name: Budanur, Nazmi B
id: 3EA1010E-F248-11E8-B48F-1D18A9856A87
last_name: Budanur
orcid: 0000-0003-0423-5010
- first_name: Marc
full_name: Fleury, Marc
last_name: Fleury
citation:
ama: 'Budanur NB, Fleury M. State space geometry of the chaotic pilot-wave hydrodynamics.
Chaos: An Interdisciplinary Journal of Nonlinear Science. 2019;29(1). doi:10.1063/1.5058279'
apa: 'Budanur, N. B., & Fleury, M. (2019). State space geometry of the chaotic
pilot-wave hydrodynamics. Chaos: An Interdisciplinary Journal of Nonlinear
Science. AIP Publishing. https://doi.org/10.1063/1.5058279'
chicago: 'Budanur, Nazmi B, and Marc Fleury. “State Space Geometry of the Chaotic
Pilot-Wave Hydrodynamics.” Chaos: An Interdisciplinary Journal of Nonlinear
Science. AIP Publishing, 2019. https://doi.org/10.1063/1.5058279.'
ieee: 'N. B. Budanur and M. Fleury, “State space geometry of the chaotic pilot-wave
hydrodynamics,” Chaos: An Interdisciplinary Journal of Nonlinear Science,
vol. 29, no. 1. AIP Publishing, 2019.'
ista: 'Budanur NB, Fleury M. 2019. State space geometry of the chaotic pilot-wave
hydrodynamics. Chaos: An Interdisciplinary Journal of Nonlinear Science. 29(1),
013122.'
mla: 'Budanur, Nazmi B., and Marc Fleury. “State Space Geometry of the Chaotic Pilot-Wave
Hydrodynamics.” Chaos: An Interdisciplinary Journal of Nonlinear Science,
vol. 29, no. 1, 013122, AIP Publishing, 2019, doi:10.1063/1.5058279.'
short: 'N.B. Budanur, M. Fleury, Chaos: An Interdisciplinary Journal of Nonlinear
Science 29 (2019).'
date_created: 2019-01-23T08:35:09Z
date_published: 2019-01-22T00:00:00Z
date_updated: 2023-08-25T10:16:11Z
day: '22'
department:
- _id: BjHo
doi: 10.1063/1.5058279
external_id:
arxiv:
- '1812.09011'
isi:
- '000457409100028'
intvolume: ' 29'
isi: 1
issue: '1'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/1812.09011
month: '01'
oa: 1
oa_version: Preprint
publication: 'Chaos: An Interdisciplinary Journal of Nonlinear Science'
publication_identifier:
eissn:
- 1089-7682
issn:
- 1054-1500
publication_status: published
publisher: AIP Publishing
quality_controlled: '1'
related_material:
link:
- relation: erratum
url: https://aip.scitation.org/doi/abs/10.1063/1.5097157
scopus_import: '1'
status: public
title: State space geometry of the chaotic pilot-wave hydrodynamics
type: journal_article
user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
volume: 29
year: '2019'
...
---
_id: '6343'
abstract:
- lang: eng
text: Cryo-electron tomography (cryo-ET) provides unprecedented insights into the
molecular constituents of biological environments. In combination with an image
processing method called subtomogram averaging (STA), detailed 3D structures of
biological molecules can be obtained in large, irregular macromolecular assemblies
or in situ, without the need for purification. The contextual meta-information
these methods also provide, such as a protein’s location within its native environment,
can then be combined with functional data. This allows the derivation of a detailed
view on the physiological or pathological roles of proteins from the molecular
to cellular level. Despite their tremendous potential in in situ structural biology,
cryo-ET and STA have been restricted by methodological limitations, such as the
low obtainable resolution. Exciting progress now allows one to reach unprecedented
resolutions in situ, ranging in optimal cases beyond the nanometer barrier. Here,
I review current frontiers and future challenges in routinely determining high-resolution
structures in in situ environments using cryo-ET and STA.
acknowledgement: The author acknowledges support from IST Austria and the Austrian
Science Fund (FWF).
article_processing_charge: No
article_type: original
author:
- first_name: Florian KM
full_name: Schur, Florian KM
id: 48AD8942-F248-11E8-B48F-1D18A9856A87
last_name: Schur
orcid: 0000-0003-4790-8078
citation:
ama: Schur FK. Toward high-resolution in situ structural biology with cryo-electron
tomography and subtomogram averaging. Current Opinion in Structural Biology.
2019;58(10):1-9. doi:10.1016/j.sbi.2019.03.018
apa: Schur, F. K. (2019). Toward high-resolution in situ structural biology with
cryo-electron tomography and subtomogram averaging. Current Opinion in Structural
Biology. Elsevier. https://doi.org/10.1016/j.sbi.2019.03.018
chicago: Schur, Florian KM. “Toward High-Resolution in Situ Structural Biology with
Cryo-Electron Tomography and Subtomogram Averaging.” Current Opinion in Structural
Biology. Elsevier, 2019. https://doi.org/10.1016/j.sbi.2019.03.018.
ieee: F. K. Schur, “Toward high-resolution in situ structural biology with cryo-electron
tomography and subtomogram averaging,” Current Opinion in Structural Biology,
vol. 58, no. 10. Elsevier, pp. 1–9, 2019.
ista: Schur FK. 2019. Toward high-resolution in situ structural biology with cryo-electron
tomography and subtomogram averaging. Current Opinion in Structural Biology. 58(10),
1–9.
mla: Schur, Florian KM. “Toward High-Resolution in Situ Structural Biology with
Cryo-Electron Tomography and Subtomogram Averaging.” Current Opinion in Structural
Biology, vol. 58, no. 10, Elsevier, 2019, pp. 1–9, doi:10.1016/j.sbi.2019.03.018.
short: F.K. Schur, Current Opinion in Structural Biology 58 (2019) 1–9.
date_created: 2019-04-19T11:19:13Z
date_published: 2019-10-01T00:00:00Z
date_updated: 2023-08-25T10:13:31Z
day: '01'
department:
- _id: FlSc
doi: 10.1016/j.sbi.2019.03.018
external_id:
isi:
- '000494891800004'
intvolume: ' 58'
isi: 1
issue: '10'
language:
- iso: eng
month: '10'
oa_version: None
page: 1-9
publication: Current Opinion in Structural Biology
publication_identifier:
issn:
- 0959-440X
publication_status: published
publisher: Elsevier
quality_controlled: '1'
scopus_import: '1'
status: public
title: Toward high-resolution in situ structural biology with cryo-electron tomography
and subtomogram averaging
type: journal_article
user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
volume: 58
year: '2019'
...
---
_id: '6428'
abstract:
- lang: eng
text: 'Safety and security are major concerns in the development of Cyber-Physical
Systems (CPS). Signal temporal logic (STL) was proposedas a language to specify
and monitor the correctness of CPS relativeto formalized requirements. Incorporating
STL into a developmentprocess enables designers to automatically monitor and diagnosetraces,
compute robustness estimates based on requirements, andperform requirement falsification,
leading to productivity gains inverification and validation activities; however,
in its current formSTL is agnostic to the input/output classification of signals,
andthis negatively impacts the relevance of the analysis results.In this paper
we propose to make the interface explicit in theSTL language by introducing input/output
signal declarations. Wethen define new measures of input vacuity and output robustnessthat
better reflect the nature of the system and the specification in-tent. The resulting
framework, which we call interface-aware signaltemporal logic (IA-STL), aids verification
and validation activities.We demonstrate the benefits of IA-STL on several CPS
analysisactivities: (1) robustness-driven sensitivity analysis, (2) falsificationand
(3) fault localization. We describe an implementation of our en-hancement to STL
and associated notions of robustness and vacuityin a prototype extension of Breach,
a MATLAB®/Simulink®toolboxfor CPS verification and validation. We explore these
methodologi-cal improvements and evaluate our results on two examples fromthe
automotive domain: a benchmark powertrain control systemand a hydrogen fuel cell
system.'
article_processing_charge: No
author:
- first_name: Thomas
full_name: Ferrere, Thomas
id: 40960E6E-F248-11E8-B48F-1D18A9856A87
last_name: Ferrere
orcid: 0000-0001-5199-3143
- first_name: Dejan
full_name: Nickovic, Dejan
id: 41BCEE5C-F248-11E8-B48F-1D18A9856A87
last_name: Nickovic
- first_name: Alexandre
full_name: Donzé, Alexandre
last_name: Donzé
- first_name: Hisahiro
full_name: Ito, Hisahiro
last_name: Ito
- first_name: James
full_name: Kapinski, James
last_name: Kapinski
citation:
ama: 'Ferrere T, Nickovic D, Donzé A, Ito H, Kapinski J. Interface-aware signal
temporal logic. In: Proceedings of the 2019 22nd ACM International Conference
on Hybrid Systems: Computation and Control. ACM; 2019:57-66. doi:10.1145/3302504.3311800'
apa: 'Ferrere, T., Nickovic, D., Donzé, A., Ito, H., & Kapinski, J. (2019).
Interface-aware signal temporal logic. In Proceedings of the 2019 22nd ACM
International Conference on Hybrid Systems: Computation and Control (pp. 57–66).
Montreal, Canada: ACM. https://doi.org/10.1145/3302504.3311800'
chicago: 'Ferrere, Thomas, Dejan Nickovic, Alexandre Donzé, Hisahiro Ito, and James
Kapinski. “Interface-Aware Signal Temporal Logic.” In Proceedings of the 2019
22nd ACM International Conference on Hybrid Systems: Computation and Control,
57–66. ACM, 2019. https://doi.org/10.1145/3302504.3311800.'
ieee: 'T. Ferrere, D. Nickovic, A. Donzé, H. Ito, and J. Kapinski, “Interface-aware
signal temporal logic,” in Proceedings of the 2019 22nd ACM International Conference
on Hybrid Systems: Computation and Control, Montreal, Canada, 2019, pp. 57–66.'
ista: 'Ferrere T, Nickovic D, Donzé A, Ito H, Kapinski J. 2019. Interface-aware
signal temporal logic. Proceedings of the 2019 22nd ACM International Conference
on Hybrid Systems: Computation and Control. HSCC: Hybrid Systems Computation and
Control, 57–66.'
mla: 'Ferrere, Thomas, et al. “Interface-Aware Signal Temporal Logic.” Proceedings
of the 2019 22nd ACM International Conference on Hybrid Systems: Computation and
Control, ACM, 2019, pp. 57–66, doi:10.1145/3302504.3311800.'
short: 'T. Ferrere, D. Nickovic, A. Donzé, H. Ito, J. Kapinski, in:, Proceedings
of the 2019 22nd ACM International Conference on Hybrid Systems: Computation and
Control, ACM, 2019, pp. 57–66.'
conference:
end_date: 2019-04-18
location: Montreal, Canada
name: 'HSCC: Hybrid Systems Computation and Control'
start_date: 2019-04-16
date_created: 2019-05-13T08:13:46Z
date_published: 2019-04-16T00:00:00Z
date_updated: 2023-08-25T10:19:23Z
day: '16'
ddc:
- '000'
department:
- _id: ToHe
doi: 10.1145/3302504.3311800
external_id:
isi:
- '000516713900007'
file:
- access_level: open_access
checksum: b8e967081e051d1c55ca5d18fb187890
content_type: application/pdf
creator: dernst
date_created: 2020-10-08T17:25:45Z
date_updated: 2020-10-08T17:25:45Z
file_id: '8633'
file_name: 2019_ACM_Ferrere.pdf
file_size: 1055421
relation: main_file
success: 1
file_date_updated: 2020-10-08T17:25:45Z
has_accepted_license: '1'
isi: 1
language:
- iso: eng
month: '04'
oa: 1
oa_version: Submitted Version
page: 57-66
project:
- _id: 25832EC2-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: S 11407_N23
name: Rigorous Systems Engineering
- _id: 25F42A32-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: Z211
name: The Wittgenstein Prize
publication: 'Proceedings of the 2019 22nd ACM International Conference on Hybrid
Systems: Computation and Control'
publication_identifier:
isbn:
- '9781450362825'
publication_status: published
publisher: ACM
quality_controlled: '1'
scopus_import: '1'
status: public
title: Interface-aware signal temporal logic
type: conference
user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
year: '2019'
...
---
_id: '6442'
abstract:
- lang: eng
text: This paper investigates the use of fundamental solutions for animating detailed
linear water surface waves. We first propose an analytical solution for efficiently
animating circular ripples in closed form. We then show how to adapt the method
of fundamental solutions (MFS) to create ambient waves interacting with complex
obstacles. Subsequently, we present a novel wavelet-based discretization which
outperforms the state of the art MFS approach for simulating time-varying water
surface waves with moving obstacles. Our results feature high-resolution spatial
details, interactions with complex boundaries, and large open ocean domains. Our
method compares favorably with previous work as well as known analytical solutions.
We also present comparisons between our method and real world examples.
acknowledged_ssus:
- _id: ScienComp
article_number: '130'
article_processing_charge: No
author:
- first_name: Camille
full_name: Schreck, Camille
id: 2B14B676-F248-11E8-B48F-1D18A9856A87
last_name: Schreck
- first_name: Christian
full_name: Hafner, Christian
id: 400429CC-F248-11E8-B48F-1D18A9856A87
last_name: Hafner
- first_name: Christopher J
full_name: Wojtan, Christopher J
id: 3C61F1D2-F248-11E8-B48F-1D18A9856A87
last_name: Wojtan
orcid: 0000-0001-6646-5546
citation:
ama: Schreck C, Hafner C, Wojtan C. Fundamental solutions for water wave animation.
ACM Transactions on Graphics. 2019;38(4). doi:10.1145/3306346.3323002
apa: Schreck, C., Hafner, C., & Wojtan, C. (2019). Fundamental solutions for
water wave animation. ACM Transactions on Graphics. ACM. https://doi.org/10.1145/3306346.3323002
chicago: Schreck, Camille, Christian Hafner, and Chris Wojtan. “Fundamental Solutions
for Water Wave Animation.” ACM Transactions on Graphics. ACM, 2019. https://doi.org/10.1145/3306346.3323002.
ieee: C. Schreck, C. Hafner, and C. Wojtan, “Fundamental solutions for water wave
animation,” ACM Transactions on Graphics, vol. 38, no. 4. ACM, 2019.
ista: Schreck C, Hafner C, Wojtan C. 2019. Fundamental solutions for water wave
animation. ACM Transactions on Graphics. 38(4), 130.
mla: Schreck, Camille, et al. “Fundamental Solutions for Water Wave Animation.”
ACM Transactions on Graphics, vol. 38, no. 4, 130, ACM, 2019, doi:10.1145/3306346.3323002.
short: C. Schreck, C. Hafner, C. Wojtan, ACM Transactions on Graphics 38 (2019).
date_created: 2019-05-14T07:04:06Z
date_published: 2019-07-01T00:00:00Z
date_updated: 2023-08-25T10:18:46Z
day: '01'
ddc:
- '000'
- '005'
department:
- _id: ChWo
doi: 10.1145/3306346.3323002
ec_funded: 1
external_id:
isi:
- '000475740600104'
file:
- access_level: open_access
checksum: 1b737dfe3e051aba8f3f4ab1dceda673
content_type: application/pdf
creator: dernst
date_created: 2019-05-14T07:03:55Z
date_updated: 2020-07-14T12:47:30Z
file_id: '6443'
file_name: 2019_ACM_Schreck.pdf
file_size: 44328918
relation: main_file
file_date_updated: 2020-07-14T12:47:30Z
has_accepted_license: '1'
intvolume: ' 38'
isi: 1
issue: '4'
language:
- iso: eng
month: '07'
oa: 1
oa_version: Submitted Version
project:
- _id: 2533E772-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '638176'
name: Efficient Simulation of Natural Phenomena at Extremely Large Scales
- _id: 24F9549A-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '715767'
name: 'MATERIALIZABLE: Intelligent fabrication-oriented Computational Design and
Modeling'
- _id: 2564DBCA-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '665385'
name: International IST Doctoral Program
publication: ACM Transactions on Graphics
publication_status: published
publisher: ACM
quality_controlled: '1'
related_material:
link:
- description: News on IST Homepage
relation: press_release
url: https://ist.ac.at/en/news/new-method-makes-realistic-water-wave-animations-more-efficient/
scopus_import: '1'
status: public
title: Fundamental solutions for water wave animation
type: journal_article
user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
volume: 38
year: '2019'
...
---
_id: '6413'
abstract:
- lang: eng
text: Phase-field methods have long been used to model the flow of immiscible fluids.
Their ability to naturally capture interface topological changes is widely recognized,
but their accuracy in simulating flows of real fluids in practical geometries
is not established. We here quantitatively investigate the convergence of the
phase-field method to the sharp-interface limit with simulations of two-phase
pipe flow. We focus on core-annular flows, in which a highly viscous fluid is
lubricated by a less viscous fluid, and validate our simulations with an analytic
laminar solution, a formal linear stability analysis and also in the fully nonlinear
regime. We demonstrate the ability of the phase-field method to accurately deal
with non-rectangular geometry, strong advection, unsteady fluctuations and large
viscosity contrast. We argue that phase-field methods are very promising for quantitatively
studying moderately turbulent flows, especially at high concentrations of the
disperse phase.
article_processing_charge: No
article_type: original
author:
- first_name: Baofang
full_name: Song, Baofang
last_name: Song
- first_name: Carlos
full_name: Plana, Carlos
last_name: Plana
- first_name: Jose M
full_name: Lopez Alonso, Jose M
id: 40770848-F248-11E8-B48F-1D18A9856A87
last_name: Lopez Alonso
orcid: 0000-0002-0384-2022
- first_name: Marc
full_name: Avila, Marc
last_name: Avila
citation:
ama: Song B, Plana C, Lopez Alonso JM, Avila M. Phase-field simulation of core-annular
pipe flow. International Journal of Multiphase Flow. 2019;117:14-24. doi:10.1016/j.ijmultiphaseflow.2019.04.027
apa: Song, B., Plana, C., Lopez Alonso, J. M., & Avila, M. (2019). Phase-field
simulation of core-annular pipe flow. International Journal of Multiphase Flow.
Elsevier. https://doi.org/10.1016/j.ijmultiphaseflow.2019.04.027
chicago: Song, Baofang, Carlos Plana, Jose M Lopez Alonso, and Marc Avila. “Phase-Field
Simulation of Core-Annular Pipe Flow.” International Journal of Multiphase
Flow. Elsevier, 2019. https://doi.org/10.1016/j.ijmultiphaseflow.2019.04.027.
ieee: B. Song, C. Plana, J. M. Lopez Alonso, and M. Avila, “Phase-field simulation
of core-annular pipe flow,” International Journal of Multiphase Flow, vol.
117. Elsevier, pp. 14–24, 2019.
ista: Song B, Plana C, Lopez Alonso JM, Avila M. 2019. Phase-field simulation of
core-annular pipe flow. International Journal of Multiphase Flow. 117, 14–24.
mla: Song, Baofang, et al. “Phase-Field Simulation of Core-Annular Pipe Flow.” International
Journal of Multiphase Flow, vol. 117, Elsevier, 2019, pp. 14–24, doi:10.1016/j.ijmultiphaseflow.2019.04.027.
short: B. Song, C. Plana, J.M. Lopez Alonso, M. Avila, International Journal of
Multiphase Flow 117 (2019) 14–24.
date_created: 2019-05-13T07:58:35Z
date_published: 2019-08-01T00:00:00Z
date_updated: 2023-08-25T10:19:55Z
day: '01'
department:
- _id: BjHo
doi: 10.1016/j.ijmultiphaseflow.2019.04.027
external_id:
arxiv:
- '1902.07351'
isi:
- '000474496000002'
intvolume: ' 117'
isi: 1
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/1902.07351
month: '08'
oa: 1
oa_version: Preprint
page: 14-24
publication: International Journal of Multiphase Flow
publication_identifier:
issn:
- '03019322'
publication_status: published
publisher: Elsevier
quality_controlled: '1'
scopus_import: '1'
status: public
title: Phase-field simulation of core-annular pipe flow
type: journal_article
user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
volume: 117
year: '2019'
...
---
_id: '6419'
abstract:
- lang: eng
text: Characterizing the fitness landscape, a representation of fitness for a large
set of genotypes, is key to understanding how genetic information is interpreted
to create functional organisms. Here we determined the evolutionarily-relevant
segment of the fitness landscape of His3, a gene coding for an enzyme in the histidine
synthesis pathway, focusing on combinations of amino acid states found at orthologous
sites of extant species. Just 15% of amino acids found in yeast His3 orthologues
were always neutral while the impact on fitness of the remaining 85% depended
on the genetic background. Furthermore, at 67% of sites, amino acid replacements
were under sign epistasis, having both strongly positive and negative effect in
different genetic backgrounds. 46% of sites were under reciprocal sign epistasis.
The fitness impact of amino acid replacements was influenced by only a few genetic
backgrounds but involved interaction of multiple sites, shaping a rugged fitness
landscape in which many of the shortest paths between highly fit genotypes are
inaccessible.
article_number: e1008079
article_processing_charge: No
author:
- first_name: Victoria
full_name: Pokusaeva, Victoria
id: 3184041C-F248-11E8-B48F-1D18A9856A87
last_name: Pokusaeva
orcid: 0000-0001-7660-444X
- first_name: Dinara R.
full_name: Usmanova, Dinara R.
last_name: Usmanova
- first_name: Ekaterina V.
full_name: Putintseva, Ekaterina V.
last_name: Putintseva
- first_name: Lorena
full_name: Espinar, Lorena
last_name: Espinar
- first_name: Karen
full_name: Sarkisyan, Karen
id: 39A7BF80-F248-11E8-B48F-1D18A9856A87
last_name: Sarkisyan
orcid: 0000-0002-5375-6341
- first_name: Alexander S.
full_name: Mishin, Alexander S.
last_name: Mishin
- first_name: Natalya S.
full_name: Bogatyreva, Natalya S.
last_name: Bogatyreva
- first_name: Dmitry
full_name: Ivankov, Dmitry
id: 49FF1036-F248-11E8-B48F-1D18A9856A87
last_name: Ivankov
- first_name: Arseniy
full_name: Akopyan, Arseniy
id: 430D2C90-F248-11E8-B48F-1D18A9856A87
last_name: Akopyan
orcid: 0000-0002-2548-617X
- first_name: Sergey
full_name: Avvakumov, Sergey
id: 3827DAC8-F248-11E8-B48F-1D18A9856A87
last_name: Avvakumov
- first_name: Inna S.
full_name: Povolotskaya, Inna S.
last_name: Povolotskaya
- first_name: Guillaume J.
full_name: Filion, Guillaume J.
last_name: Filion
- first_name: Lucas B.
full_name: Carey, Lucas B.
last_name: Carey
- first_name: Fyodor
full_name: Kondrashov, Fyodor
id: 44FDEF62-F248-11E8-B48F-1D18A9856A87
last_name: Kondrashov
orcid: 0000-0001-8243-4694
citation:
ama: Pokusaeva V, Usmanova DR, Putintseva EV, et al. An experimental assay of the
interactions of amino acids from orthologous sequences shaping a complex fitness
landscape. PLoS Genetics. 2019;15(4). doi:10.1371/journal.pgen.1008079
apa: Pokusaeva, V., Usmanova, D. R., Putintseva, E. V., Espinar, L., Sarkisyan,
K., Mishin, A. S., … Kondrashov, F. (2019). An experimental assay of the interactions
of amino acids from orthologous sequences shaping a complex fitness landscape.
PLoS Genetics. Public Library of Science. https://doi.org/10.1371/journal.pgen.1008079
chicago: Pokusaeva, Victoria, Dinara R. Usmanova, Ekaterina V. Putintseva, Lorena
Espinar, Karen Sarkisyan, Alexander S. Mishin, Natalya S. Bogatyreva, et al. “An
Experimental Assay of the Interactions of Amino Acids from Orthologous Sequences
Shaping a Complex Fitness Landscape.” PLoS Genetics. Public Library of
Science, 2019. https://doi.org/10.1371/journal.pgen.1008079.
ieee: V. Pokusaeva et al., “An experimental assay of the interactions of
amino acids from orthologous sequences shaping a complex fitness landscape,” PLoS
Genetics, vol. 15, no. 4. Public Library of Science, 2019.
ista: Pokusaeva V, Usmanova DR, Putintseva EV, Espinar L, Sarkisyan K, Mishin AS,
Bogatyreva NS, Ivankov D, Akopyan A, Avvakumov S, Povolotskaya IS, Filion GJ,
Carey LB, Kondrashov F. 2019. An experimental assay of the interactions of amino
acids from orthologous sequences shaping a complex fitness landscape. PLoS Genetics.
15(4), e1008079.
mla: Pokusaeva, Victoria, et al. “An Experimental Assay of the Interactions of Amino
Acids from Orthologous Sequences Shaping a Complex Fitness Landscape.” PLoS
Genetics, vol. 15, no. 4, e1008079, Public Library of Science, 2019, doi:10.1371/journal.pgen.1008079.
short: V. Pokusaeva, D.R. Usmanova, E.V. Putintseva, L. Espinar, K. Sarkisyan, A.S.
Mishin, N.S. Bogatyreva, D. Ivankov, A. Akopyan, S. Avvakumov, I.S. Povolotskaya,
G.J. Filion, L.B. Carey, F. Kondrashov, PLoS Genetics 15 (2019).
date_created: 2019-05-13T07:58:38Z
date_published: 2019-04-10T00:00:00Z
date_updated: 2023-08-25T10:30:37Z
day: '10'
ddc:
- '570'
department:
- _id: FyKo
doi: 10.1371/journal.pgen.1008079
ec_funded: 1
external_id:
isi:
- '000466866000029'
file:
- access_level: open_access
checksum: cf3889c8a8a16053dacf9c3776cbe217
content_type: application/pdf
creator: dernst
date_created: 2019-05-14T08:26:08Z
date_updated: 2020-07-14T12:47:30Z
file_id: '6445'
file_name: 2019_PLOSGenetics_Pokusaeva.pdf
file_size: 3726017
relation: main_file
file_date_updated: 2020-07-14T12:47:30Z
has_accepted_license: '1'
intvolume: ' 15'
isi: 1
issue: '4'
language:
- iso: eng
month: '04'
oa: 1
oa_version: Published Version
project:
- _id: 2564DBCA-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '665385'
name: International IST Doctoral Program
publication: PLoS Genetics
publication_identifier:
eissn:
- '15537404'
publication_status: published
publisher: Public Library of Science
quality_controlled: '1'
related_material:
record:
- id: '9789'
relation: research_data
status: public
- id: '9790'
relation: research_data
status: public
- id: '9797'
relation: research_data
status: public
scopus_import: '1'
status: public
title: An experimental assay of the interactions of amino acids from orthologous sequences
shaping a complex fitness landscape
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: journal_article
user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
volume: 15
year: '2019'
...
---
_id: '6412'
abstract:
- lang: eng
text: Polycomb group (PcG) proteins play critical roles in the epigenetic inheritance
of cell fate. The Polycomb Repressive Complexes PRC1 and PRC2 catalyse distinct
chromatin modifications to enforce gene silencing, but how transcriptional repression
is propagated through mitotic cell divisions remains a key unresolved question.
Using reversible tethering of PcG proteins to ectopic sites in mouse embryonic
stem cells, here we show that PRC1 can trigger transcriptional repression and
Polycomb-dependent chromatin modifications. We find that canonical PRC1 (cPRC1),
but not variant PRC1, maintains gene silencing through cell division upon reversal
of tethering. Propagation of gene repression is sustained by cis-acting histone
modifications, PRC2-mediated H3K27me3 and cPRC1-mediated H2AK119ub1, promoting
a sequence-independent feedback mechanism for PcG protein recruitment. Thus, the
distinct PRC1 complexes present in vertebrates can differentially regulate epigenetic
maintenance of gene silencing, potentially enabling dynamic heritable responses
to complex stimuli. Our findings reveal how PcG repression is potentially inherited
in vertebrates.
article_number: '1931'
article_processing_charge: No
author:
- first_name: Hagar F.
full_name: Moussa, Hagar F.
last_name: Moussa
- first_name: Daniel
full_name: Bsteh, Daniel
last_name: Bsteh
- first_name: Ramesh
full_name: Yelagandula, Ramesh
last_name: Yelagandula
- first_name: Carina
full_name: Pribitzer, Carina
last_name: Pribitzer
- first_name: Karin
full_name: Stecher, Karin
last_name: Stecher
- first_name: Katarina
full_name: Bartalska, Katarina
id: 4D883232-F248-11E8-B48F-1D18A9856A87
last_name: Bartalska
- first_name: Luca
full_name: Michetti, Luca
last_name: Michetti
- first_name: Jingkui
full_name: Wang, Jingkui
last_name: Wang
- first_name: Jorge A.
full_name: Zepeda-Martinez, Jorge A.
last_name: Zepeda-Martinez
- first_name: Ulrich
full_name: Elling, Ulrich
last_name: Elling
- first_name: Jacob I.
full_name: Stuckey, Jacob I.
last_name: Stuckey
- first_name: Lindsey I.
full_name: James, Lindsey I.
last_name: James
- first_name: Stephen V.
full_name: Frye, Stephen V.
last_name: Frye
- first_name: Oliver
full_name: Bell, Oliver
last_name: Bell
citation:
ama: Moussa HF, Bsteh D, Yelagandula R, et al. Canonical PRC1 controls sequence-independent
propagation of Polycomb-mediated gene silencing. Nature Communications.
2019;10(1). doi:10.1038/s41467-019-09628-6
apa: Moussa, H. F., Bsteh, D., Yelagandula, R., Pribitzer, C., Stecher, K., Bartalska,
K., … Bell, O. (2019). Canonical PRC1 controls sequence-independent propagation
of Polycomb-mediated gene silencing. Nature Communications. Springer Nature.
https://doi.org/10.1038/s41467-019-09628-6
chicago: Moussa, Hagar F., Daniel Bsteh, Ramesh Yelagandula, Carina Pribitzer, Karin
Stecher, Katarina Bartalska, Luca Michetti, et al. “Canonical PRC1 Controls Sequence-Independent
Propagation of Polycomb-Mediated Gene Silencing.” Nature Communications.
Springer Nature, 2019. https://doi.org/10.1038/s41467-019-09628-6.
ieee: H. F. Moussa et al., “Canonical PRC1 controls sequence-independent
propagation of Polycomb-mediated gene silencing,” Nature Communications,
vol. 10, no. 1. Springer Nature, 2019.
ista: Moussa HF, Bsteh D, Yelagandula R, Pribitzer C, Stecher K, Bartalska K, Michetti
L, Wang J, Zepeda-Martinez JA, Elling U, Stuckey JI, James LI, Frye SV, Bell O.
2019. Canonical PRC1 controls sequence-independent propagation of Polycomb-mediated
gene silencing. Nature Communications. 10(1), 1931.
mla: Moussa, Hagar F., et al. “Canonical PRC1 Controls Sequence-Independent Propagation
of Polycomb-Mediated Gene Silencing.” Nature Communications, vol. 10, no.
1, 1931, Springer Nature, 2019, doi:10.1038/s41467-019-09628-6.
short: H.F. Moussa, D. Bsteh, R. Yelagandula, C. Pribitzer, K. Stecher, K. Bartalska,
L. Michetti, J. Wang, J.A. Zepeda-Martinez, U. Elling, J.I. Stuckey, L.I. James,
S.V. Frye, O. Bell, Nature Communications 10 (2019).
date_created: 2019-05-13T07:58:35Z
date_published: 2019-04-29T00:00:00Z
date_updated: 2023-08-25T10:31:56Z
day: '29'
ddc:
- '570'
department:
- _id: SaSi
doi: 10.1038/s41467-019-09628-6
external_id:
isi:
- '000466118700002'
file:
- access_level: open_access
checksum: 6550a328335396c856db4cbdda7d2994
content_type: application/pdf
creator: dernst
date_created: 2019-05-14T08:45:51Z
date_updated: 2020-07-14T12:47:29Z
file_id: '6448'
file_name: 2019_NatureComm_Moussa.pdf
file_size: 1223647
relation: main_file
file_date_updated: 2020-07-14T12:47:29Z
has_accepted_license: '1'
intvolume: ' 10'
isi: 1
issue: '1'
language:
- iso: eng
month: '04'
oa: 1
oa_version: Published Version
publication: Nature Communications
publication_identifier:
eissn:
- '20411723'
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
scopus_import: '1'
status: public
title: Canonical PRC1 controls sequence-independent propagation of Polycomb-mediated
gene silencing
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: journal_article
user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
volume: 10
year: '2019'
...
---
_id: '6415'
abstract:
- lang: eng
text: Ant invasions are often harmful to native species communities. Their pathogens
and host disease defense mechanisms may be one component of their devastating
success. First, they can introduce harmful diseases to their competitors in the
introduced range, to which they themselves are tolerant. Second, their supercolonial
social structure of huge multi-queen nest networks means that they will harbor
a broad pathogen spectrum and high pathogen load while remaining resilient, unlike
the smaller, territorial colonies of the native species. Thus, it is likely that
invasive ants act as a disease reservoir, promoting their competitive advantage
and invasive success.
article_processing_charge: No
author:
- first_name: Sylvia
full_name: Cremer, Sylvia
id: 2F64EC8C-F248-11E8-B48F-1D18A9856A87
last_name: Cremer
orcid: 0000-0002-2193-3868
citation:
ama: Cremer S. Pathogens and disease defense of invasive ants. Current Opinion
in Insect Science. 2019;33:63-68. doi:10.1016/j.cois.2019.03.011
apa: Cremer, S. (2019). Pathogens and disease defense of invasive ants. Current
Opinion in Insect Science. Elsevier. https://doi.org/10.1016/j.cois.2019.03.011
chicago: Cremer, Sylvia. “Pathogens and Disease Defense of Invasive Ants.” Current
Opinion in Insect Science. Elsevier, 2019. https://doi.org/10.1016/j.cois.2019.03.011.
ieee: S. Cremer, “Pathogens and disease defense of invasive ants,” Current Opinion
in Insect Science, vol. 33. Elsevier, pp. 63–68, 2019.
ista: Cremer S. 2019. Pathogens and disease defense of invasive ants. Current Opinion
in Insect Science. 33, 63–68.
mla: Cremer, Sylvia. “Pathogens and Disease Defense of Invasive Ants.” Current
Opinion in Insect Science, vol. 33, Elsevier, 2019, pp. 63–68, doi:10.1016/j.cois.2019.03.011.
short: S. Cremer, Current Opinion in Insect Science 33 (2019) 63–68.
date_created: 2019-05-13T07:58:36Z
date_published: 2019-06-01T00:00:00Z
date_updated: 2023-08-25T10:31:31Z
day: '01'
department:
- _id: SyCr
doi: 10.1016/j.cois.2019.03.011
external_id:
isi:
- '000477666000012'
intvolume: ' 33'
isi: 1
language:
- iso: eng
month: '06'
oa_version: None
page: 63-68
publication: Current Opinion in Insect Science
publication_identifier:
eissn:
- '22145753'
issn:
- '22145745'
publication_status: published
publisher: Elsevier
quality_controlled: '1'
scopus_import: '1'
status: public
title: Pathogens and disease defense of invasive ants
type: journal_article
user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
volume: 33
year: '2019'
...
---
_id: '9790'
article_processing_charge: No
author:
- first_name: Victoria
full_name: Pokusaeva, Victoria
id: 3184041C-F248-11E8-B48F-1D18A9856A87
last_name: Pokusaeva
orcid: 0000-0001-7660-444X
- first_name: Dinara R.
full_name: Usmanova, Dinara R.
last_name: Usmanova
- first_name: Ekaterina V.
full_name: Putintseva, Ekaterina V.
last_name: Putintseva
- first_name: Lorena
full_name: Espinar, Lorena
last_name: Espinar
- first_name: Karen
full_name: Sarkisyan, Karen
id: 39A7BF80-F248-11E8-B48F-1D18A9856A87
last_name: Sarkisyan
orcid: 0000-0002-5375-6341
- first_name: Alexander S.
full_name: Mishin, Alexander S.
last_name: Mishin
- first_name: Natalya S.
full_name: Bogatyreva, Natalya S.
last_name: Bogatyreva
- first_name: Dmitry
full_name: Ivankov, Dmitry
id: 49FF1036-F248-11E8-B48F-1D18A9856A87
last_name: Ivankov
- first_name: Arseniy
full_name: Akopyan, Arseniy
id: 430D2C90-F248-11E8-B48F-1D18A9856A87
last_name: Akopyan
orcid: 0000-0002-2548-617X
- first_name: Sergey
full_name: Avvakumov, Sergey
id: 3827DAC8-F248-11E8-B48F-1D18A9856A87
last_name: Avvakumov
- first_name: Inna S.
full_name: Povolotskaya, Inna S.
last_name: Povolotskaya
- first_name: Guillaume J.
full_name: Filion, Guillaume J.
last_name: Filion
- first_name: Lucas B.
full_name: Carey, Lucas B.
last_name: Carey
- first_name: Fyodor
full_name: Kondrashov, Fyodor
id: 44FDEF62-F248-11E8-B48F-1D18A9856A87
last_name: Kondrashov
orcid: 0000-0001-8243-4694
citation:
ama: Pokusaeva V, Usmanova DR, Putintseva EV, et al. A statistical summary of segment
libraries and sequencing results. 2019. doi:10.1371/journal.pgen.1008079.s011
apa: Pokusaeva, V., Usmanova, D. R., Putintseva, E. V., Espinar, L., Sarkisyan,
K., Mishin, A. S., … Kondrashov, F. (2019). A statistical summary of segment libraries
and sequencing results. Public Library of Science. https://doi.org/10.1371/journal.pgen.1008079.s011
chicago: Pokusaeva, Victoria, Dinara R. Usmanova, Ekaterina V. Putintseva, Lorena
Espinar, Karen Sarkisyan, Alexander S. Mishin, Natalya S. Bogatyreva, et al. “A
Statistical Summary of Segment Libraries and Sequencing Results.” Public Library
of Science, 2019. https://doi.org/10.1371/journal.pgen.1008079.s011.
ieee: V. Pokusaeva et al., “A statistical summary of segment libraries and
sequencing results.” Public Library of Science, 2019.
ista: Pokusaeva V, Usmanova DR, Putintseva EV, Espinar L, Sarkisyan K, Mishin AS,
Bogatyreva NS, Ivankov D, Akopyan A, Avvakumov S, Povolotskaya IS, Filion GJ,
Carey LB, Kondrashov F. 2019. A statistical summary of segment libraries and sequencing
results, Public Library of Science, 10.1371/journal.pgen.1008079.s011.
mla: Pokusaeva, Victoria, et al. A Statistical Summary of Segment Libraries and
Sequencing Results. Public Library of Science, 2019, doi:10.1371/journal.pgen.1008079.s011.
short: V. Pokusaeva, D.R. Usmanova, E.V. Putintseva, L. Espinar, K. Sarkisyan, A.S.
Mishin, N.S. Bogatyreva, D. Ivankov, A. Akopyan, S. Avvakumov, I.S. Povolotskaya,
G.J. Filion, L.B. Carey, F. Kondrashov, (2019).
date_created: 2021-08-06T08:50:15Z
date_published: 2019-04-10T00:00:00Z
date_updated: 2023-08-25T10:30:36Z
day: '10'
department:
- _id: FyKo
doi: 10.1371/journal.pgen.1008079.s011
month: '04'
oa_version: Published Version
publisher: Public Library of Science
related_material:
record:
- id: '6419'
relation: used_in_publication
status: public
status: public
title: A statistical summary of segment libraries and sequencing results
type: research_data_reference
user_id: 6785fbc1-c503-11eb-8a32-93094b40e1cf
year: '2019'
...
---
_id: '9797'
article_processing_charge: No
author:
- first_name: Victoria
full_name: Pokusaeva, Victoria
id: 3184041C-F248-11E8-B48F-1D18A9856A87
last_name: Pokusaeva
orcid: 0000-0001-7660-444X
- first_name: Dinara R.
full_name: Usmanova, Dinara R.
last_name: Usmanova
- first_name: Ekaterina V.
full_name: Putintseva, Ekaterina V.
last_name: Putintseva
- first_name: Lorena
full_name: Espinar, Lorena
last_name: Espinar
- first_name: Karen
full_name: Sarkisyan, Karen
id: 39A7BF80-F248-11E8-B48F-1D18A9856A87
last_name: Sarkisyan
orcid: 0000-0002-5375-6341
- first_name: Alexander S.
full_name: Mishin, Alexander S.
last_name: Mishin
- first_name: Natalya S.
full_name: Bogatyreva, Natalya S.
last_name: Bogatyreva
- first_name: Dmitry
full_name: Ivankov, Dmitry
id: 49FF1036-F248-11E8-B48F-1D18A9856A87
last_name: Ivankov
- first_name: Arseniy
full_name: Akopyan, Arseniy
id: 430D2C90-F248-11E8-B48F-1D18A9856A87
last_name: Akopyan
orcid: 0000-0002-2548-617X
- first_name: Inna S.
full_name: Povolotskaya, Inna S.
last_name: Povolotskaya
- first_name: Guillaume J.
full_name: Filion, Guillaume J.
last_name: Filion
- first_name: Lucas B.
full_name: Carey, Lucas B.
last_name: Carey
- first_name: Fyodor
full_name: Kondrashov, Fyodor
id: 44FDEF62-F248-11E8-B48F-1D18A9856A87
last_name: Kondrashov
orcid: 0000-0001-8243-4694
citation:
ama: Pokusaeva V, Usmanova DR, Putintseva EV, et al. A statistical summary of segment
libraries and sequencing results. 2019. doi:10.1371/journal.pgen.1008079.s011
apa: Pokusaeva, V., Usmanova, D. R., Putintseva, E. V., Espinar, L., Sarkisyan,
K., Mishin, A. S., … Kondrashov, F. (2019). A statistical summary of segment libraries
and sequencing results. Public Library of Science. https://doi.org/10.1371/journal.pgen.1008079.s011
chicago: Pokusaeva, Victoria, Dinara R. Usmanova, Ekaterina V. Putintseva, Lorena
Espinar, Karen Sarkisyan, Alexander S. Mishin, Natalya S. Bogatyreva, et al. “A
Statistical Summary of Segment Libraries and Sequencing Results.” Public Library
of Science, 2019. https://doi.org/10.1371/journal.pgen.1008079.s011.
ieee: V. Pokusaeva et al., “A statistical summary of segment libraries and
sequencing results.” Public Library of Science, 2019.
ista: Pokusaeva V, Usmanova DR, Putintseva EV, Espinar L, Sarkisyan K, Mishin AS,
Bogatyreva NS, Ivankov D, Akopyan A, Povolotskaya IS, Filion GJ, Carey LB, Kondrashov
F. 2019. A statistical summary of segment libraries and sequencing results, Public
Library of Science, 10.1371/journal.pgen.1008079.s011.
mla: Pokusaeva, Victoria, et al. A Statistical Summary of Segment Libraries and
Sequencing Results. Public Library of Science, 2019, doi:10.1371/journal.pgen.1008079.s011.
short: V. Pokusaeva, D.R. Usmanova, E.V. Putintseva, L. Espinar, K. Sarkisyan, A.S.
Mishin, N.S. Bogatyreva, D. Ivankov, A. Akopyan, I.S. Povolotskaya, G.J. Filion,
L.B. Carey, F. Kondrashov, (2019).
date_created: 2021-08-06T11:08:20Z
date_published: 2019-04-10T00:00:00Z
date_updated: 2023-08-25T10:30:36Z
day: '10'
department:
- _id: FyKo
doi: 10.1371/journal.pgen.1008079.s011
month: '04'
oa_version: Published Version
publisher: Public Library of Science
related_material:
record:
- id: '6419'
relation: used_in_publication
status: public
status: public
title: A statistical summary of segment libraries and sequencing results
type: research_data_reference
user_id: 6785fbc1-c503-11eb-8a32-93094b40e1cf
year: '2019'
...
---
_id: '9789'
article_processing_charge: No
author:
- first_name: Victoria
full_name: Pokusaeva, Victoria
id: 3184041C-F248-11E8-B48F-1D18A9856A87
last_name: Pokusaeva
orcid: 0000-0001-7660-444X
- first_name: Dinara R.
full_name: Usmanova, Dinara R.
last_name: Usmanova
- first_name: Ekaterina V.
full_name: Putintseva, Ekaterina V.
last_name: Putintseva
- first_name: Lorena
full_name: Espinar, Lorena
last_name: Espinar
- first_name: Karen
full_name: Sarkisyan, Karen
id: 39A7BF80-F248-11E8-B48F-1D18A9856A87
last_name: Sarkisyan
orcid: 0000-0002-5375-6341
- first_name: Alexander S.
full_name: Mishin, Alexander S.
last_name: Mishin
- first_name: Natalya S.
full_name: Bogatyreva, Natalya S.
last_name: Bogatyreva
- first_name: Dmitry
full_name: Ivankov, Dmitry
id: 49FF1036-F248-11E8-B48F-1D18A9856A87
last_name: Ivankov
- first_name: Arseniy
full_name: Akopyan, Arseniy
id: 430D2C90-F248-11E8-B48F-1D18A9856A87
last_name: Akopyan
orcid: 0000-0002-2548-617X
- first_name: Sergey
full_name: Avvakumov, Sergey
id: 3827DAC8-F248-11E8-B48F-1D18A9856A87
last_name: Avvakumov
- first_name: Inna S.
full_name: Povolotskaya, Inna S.
last_name: Povolotskaya
- first_name: Guillaume J.
full_name: Filion, Guillaume J.
last_name: Filion
- first_name: Lucas B.
full_name: Carey, Lucas B.
last_name: Carey
- first_name: Fyodor
full_name: Kondrashov, Fyodor
id: 44FDEF62-F248-11E8-B48F-1D18A9856A87
last_name: Kondrashov
orcid: 0000-0001-8243-4694
citation:
ama: Pokusaeva V, Usmanova DR, Putintseva EV, et al. Multiple alignment of His3
orthologues. 2019. doi:10.1371/journal.pgen.1008079.s010
apa: Pokusaeva, V., Usmanova, D. R., Putintseva, E. V., Espinar, L., Sarkisyan,
K., Mishin, A. S., … Kondrashov, F. (2019). Multiple alignment of His3 orthologues.
Public Library of Science. https://doi.org/10.1371/journal.pgen.1008079.s010
chicago: Pokusaeva, Victoria, Dinara R. Usmanova, Ekaterina V. Putintseva, Lorena
Espinar, Karen Sarkisyan, Alexander S. Mishin, Natalya S. Bogatyreva, et al. “Multiple
Alignment of His3 Orthologues.” Public Library of Science, 2019. https://doi.org/10.1371/journal.pgen.1008079.s010.
ieee: V. Pokusaeva et al., “Multiple alignment of His3 orthologues.” Public
Library of Science, 2019.
ista: Pokusaeva V, Usmanova DR, Putintseva EV, Espinar L, Sarkisyan K, Mishin AS,
Bogatyreva NS, Ivankov D, Akopyan A, Avvakumov S, Povolotskaya IS, Filion GJ,
Carey LB, Kondrashov F. 2019. Multiple alignment of His3 orthologues, Public Library
of Science, 10.1371/journal.pgen.1008079.s010.
mla: Pokusaeva, Victoria, et al. Multiple Alignment of His3 Orthologues.
Public Library of Science, 2019, doi:10.1371/journal.pgen.1008079.s010.
short: V. Pokusaeva, D.R. Usmanova, E.V. Putintseva, L. Espinar, K. Sarkisyan, A.S.
Mishin, N.S. Bogatyreva, D. Ivankov, A. Akopyan, S. Avvakumov, I.S. Povolotskaya,
G.J. Filion, L.B. Carey, F. Kondrashov, (2019).
date_created: 2021-08-06T08:38:50Z
date_published: 2019-04-10T00:00:00Z
date_updated: 2023-08-25T10:30:36Z
day: '10'
department:
- _id: FyKo
doi: 10.1371/journal.pgen.1008079.s010
month: '04'
oa_version: Published Version
publisher: Public Library of Science
related_material:
record:
- id: '6419'
relation: used_in_publication
status: public
status: public
title: Multiple alignment of His3 orthologues
type: research_data_reference
user_id: 6785fbc1-c503-11eb-8a32-93094b40e1cf
year: '2019'
...
---
_id: '6462'
abstract:
- lang: eng
text: A controller is a device that interacts with a plant. At each time point,it
reads the plant’s state and issues commands with the goal that the plant oper-ates
optimally. Constructing optimal controllers is a fundamental and challengingproblem.
Machine learning techniques have recently been successfully applied totrain controllers,
yet they have limitations. Learned controllers are monolithic andhard to reason
about. In particular, it is difficult to add features without retraining,to guarantee
any level of performance, and to achieve acceptable performancewhen encountering
untrained scenarios. These limitations can be addressed bydeploying quantitative
run-timeshieldsthat serve as a proxy for the controller.At each time point, the
shield reads the command issued by the controller andmay choose to alter it before
passing it on to the plant. We show how optimalshields that interfere as little
as possible while guaranteeing a desired level ofcontroller performance, can be
generated systematically and automatically usingreactive synthesis. First, we abstract the plant by building a stochastic model.Second,
we consider the learned controller to be a black box. Third, we mea-surecontroller
performanceandshield interferenceby two quantitative run-timemeasures that are
formally defined using weighted automata. Then, the problemof constructing a shield
that guarantees maximal performance with minimal inter-ference is the problem
of finding an optimal strategy in a stochastic2-player game“controller versus
shield” played on the abstract state space of the plant with aquantitative objective
obtained from combining the performance and interferencemeasures. We illustrate
the effectiveness of our approach by automatically con-structing lightweight shields
for learned traffic-light controllers in various roadnetworks. The shields we
generate avoid liveness bugs, improve controller per-formance in untrained and
changing traffic situations, and add features to learnedcontrollers, such as giving
priority to emergency vehicles.
alternative_title:
- LNCS
article_processing_charge: No
author:
- first_name: Guy
full_name: Avni, Guy
id: 463C8BC2-F248-11E8-B48F-1D18A9856A87
last_name: Avni
orcid: 0000-0001-5588-8287
- first_name: Roderick
full_name: Bloem, Roderick
last_name: Bloem
- first_name: Krishnendu
full_name: Chatterjee, Krishnendu
id: 2E5DCA20-F248-11E8-B48F-1D18A9856A87
last_name: Chatterjee
orcid: 0000-0002-4561-241X
- first_name: Thomas A
full_name: Henzinger, Thomas A
id: 40876CD8-F248-11E8-B48F-1D18A9856A87
last_name: Henzinger
orcid: 0000−0002−2985−7724
- first_name: Bettina
full_name: Konighofer, Bettina
last_name: Konighofer
- first_name: Stefan
full_name: Pranger, Stefan
last_name: Pranger
citation:
ama: 'Avni G, Bloem R, Chatterjee K, Henzinger TA, Konighofer B, Pranger S. Run-time
optimization for learned controllers through quantitative games. In: 31st International
Conference on Computer-Aided Verification. Vol 11561. Springer; 2019:630-649.
doi:10.1007/978-3-030-25540-4_36'
apa: 'Avni, G., Bloem, R., Chatterjee, K., Henzinger, T. A., Konighofer, B., &
Pranger, S. (2019). Run-time optimization for learned controllers through quantitative
games. In 31st International Conference on Computer-Aided Verification
(Vol. 11561, pp. 630–649). New York, NY, United States: Springer. https://doi.org/10.1007/978-3-030-25540-4_36'
chicago: Avni, Guy, Roderick Bloem, Krishnendu Chatterjee, Thomas A Henzinger, Bettina
Konighofer, and Stefan Pranger. “Run-Time Optimization for Learned Controllers
through Quantitative Games.” In 31st International Conference on Computer-Aided
Verification, 11561:630–49. Springer, 2019. https://doi.org/10.1007/978-3-030-25540-4_36.
ieee: G. Avni, R. Bloem, K. Chatterjee, T. A. Henzinger, B. Konighofer, and S. Pranger,
“Run-time optimization for learned controllers through quantitative games,” in
31st International Conference on Computer-Aided Verification, New York,
NY, United States, 2019, vol. 11561, pp. 630–649.
ista: 'Avni G, Bloem R, Chatterjee K, Henzinger TA, Konighofer B, Pranger S. 2019.
Run-time optimization for learned controllers through quantitative games. 31st
International Conference on Computer-Aided Verification. CAV: Computer Aided Verification,
LNCS, vol. 11561, 630–649.'
mla: Avni, Guy, et al. “Run-Time Optimization for Learned Controllers through Quantitative
Games.” 31st International Conference on Computer-Aided Verification, vol.
11561, Springer, 2019, pp. 630–49, doi:10.1007/978-3-030-25540-4_36.
short: G. Avni, R. Bloem, K. Chatterjee, T.A. Henzinger, B. Konighofer, S. Pranger,
in:, 31st International Conference on Computer-Aided Verification, Springer, 2019,
pp. 630–649.
conference:
end_date: 2019-07-18
location: New York, NY, United States
name: 'CAV: Computer Aided Verification'
start_date: 2019-07-13
date_created: 2019-05-16T11:22:30Z
date_published: 2019-07-12T00:00:00Z
date_updated: 2023-08-25T10:33:27Z
day: '12'
ddc:
- '000'
department:
- _id: ToHe
- _id: KrCh
doi: 10.1007/978-3-030-25540-4_36
external_id:
isi:
- '000491468000036'
file:
- access_level: open_access
checksum: c231579f2485c6fd4df17c9443a4d80b
content_type: application/pdf
creator: dernst
date_created: 2019-08-14T09:35:24Z
date_updated: 2020-07-14T12:47:31Z
file_id: '6816'
file_name: 2019_CAV_Avni.pdf
file_size: 659766
relation: main_file
file_date_updated: 2020-07-14T12:47:31Z
has_accepted_license: '1'
intvolume: ' 11561'
isi: 1
language:
- iso: eng
month: '07'
oa: 1
oa_version: Published Version
page: 630-649
project:
- _id: 264B3912-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: M02369
name: Formal Methods meets Algorithmic Game Theory
- _id: 25F42A32-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: Z211
name: The Wittgenstein Prize
- _id: 25832EC2-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: S 11407_N23
name: Rigorous Systems Engineering
publication: 31st International Conference on Computer-Aided Verification
publication_identifier:
isbn:
- '9783030255398'
issn:
- 0302-9743
publication_status: published
publisher: Springer
quality_controlled: '1'
scopus_import: '1'
status: public
title: Run-time optimization for learned controllers through quantitative games
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: conference
user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
volume: 11561
year: '2019'
...
---
_id: '6477'
abstract:
- lang: eng
text: 'Thermalizing quantum systems are conventionallydescribed by statistical mechanics
at equilib-rium. However, not all systems fall into this category, with many-body
localization providinga generic mechanism for thermalization to fail in strongly
disordered systems. Many-bodylocalized (MBL) systems remain perfect insulators
at nonzero temperature, which do notthermalize and therefore cannot be describedusing
statistical mechanics. This Colloquiumreviews recent theoretical and experimental
advances in studies of MBL systems, focusing onthe new perspective provided by
entanglement and nonequilibrium experimental probes suchas quantum quenches. Theoretically,
MBL systems exhibit a new kind of robust integrability: anextensive set of quasilocal
integrals of motion emerges, which provides an intuitive explanationof the breakdown
of thermalization. A description based on quasilocal integrals of motion isused
to predict dynamical properties of MBL systems, such as the spreading of quantumentanglement,
the behavior of local observables, and the response to external dissipativeprocesses.
Furthermore, MBL systems can exhibit eigenstate transitions and quantum ordersforbidden
in thermodynamic equilibrium. An outline isgiven of the current theoretical under-standing
of the quantum-to-classical transitionbetween many-body localized and ergodic
phasesand anomalous transport in the vicinity of that transition. Experimentally,
synthetic quantumsystems, which are well isolated from an external thermal reservoir,
provide natural platforms forrealizing the MBL phase. Recent experiments with
ultracold atoms, trapped ions, superconductingqubits, and quantum materials, in
which different signatures of many-body localization have beenobserved, are reviewed.
This Colloquium concludes by listing outstanding challenges andpromising future
research directions.'
article_number: '021001'
article_processing_charge: No
article_type: original
author:
- first_name: Dmitry A.
full_name: Abanin, Dmitry A.
last_name: Abanin
- first_name: Ehud
full_name: Altman, Ehud
last_name: Altman
- first_name: Immanuel
full_name: Bloch, Immanuel
last_name: Bloch
- first_name: Maksym
full_name: Serbyn, Maksym
id: 47809E7E-F248-11E8-B48F-1D18A9856A87
last_name: Serbyn
orcid: 0000-0002-2399-5827
citation:
ama: 'Abanin DA, Altman E, Bloch I, Serbyn M. Colloquium: Many-body localization,
thermalization, and entanglement. Reviews of Modern Physics. 2019;91(2).
doi:10.1103/revmodphys.91.021001'
apa: 'Abanin, D. A., Altman, E., Bloch, I., & Serbyn, M. (2019). Colloquium:
Many-body localization, thermalization, and entanglement. Reviews of Modern
Physics. American Physical Society. https://doi.org/10.1103/revmodphys.91.021001'
chicago: 'Abanin, Dmitry A., Ehud Altman, Immanuel Bloch, and Maksym Serbyn. “Colloquium:
Many-Body Localization, Thermalization, and Entanglement.” Reviews of Modern
Physics. American Physical Society, 2019. https://doi.org/10.1103/revmodphys.91.021001.'
ieee: 'D. A. Abanin, E. Altman, I. Bloch, and M. Serbyn, “Colloquium: Many-body
localization, thermalization, and entanglement,” Reviews of Modern Physics,
vol. 91, no. 2. American Physical Society, 2019.'
ista: 'Abanin DA, Altman E, Bloch I, Serbyn M. 2019. Colloquium: Many-body localization,
thermalization, and entanglement. Reviews of Modern Physics. 91(2), 021001.'
mla: 'Abanin, Dmitry A., et al. “Colloquium: Many-Body Localization, Thermalization,
and Entanglement.” Reviews of Modern Physics, vol. 91, no. 2, 021001, American
Physical Society, 2019, doi:10.1103/revmodphys.91.021001.'
short: D.A. Abanin, E. Altman, I. Bloch, M. Serbyn, Reviews of Modern Physics 91
(2019).
date_created: 2019-05-23T07:38:43Z
date_published: 2019-05-22T00:00:00Z
date_updated: 2023-08-25T10:37:56Z
day: '22'
ddc:
- '530'
department:
- _id: MaSe
doi: 10.1103/revmodphys.91.021001
external_id:
arxiv:
- '1804.11065'
isi:
- '000469046900001'
file:
- access_level: open_access
checksum: 4aec0e6662b09f6e0f828cd30ff2c3a6
content_type: application/pdf
creator: mserbyn
date_created: 2019-05-23T07:39:05Z
date_updated: 2020-07-14T12:47:31Z
file_id: '6478'
file_name: RevModPhys.91.021001.pdf
file_size: 1695677
relation: main_file
file_date_updated: 2020-07-14T12:47:31Z
has_accepted_license: '1'
intvolume: ' 91'
isi: 1
issue: '2'
language:
- iso: eng
month: '05'
oa: 1
oa_version: Published Version
publication: Reviews of Modern Physics
publication_identifier:
eissn:
- 0034-6861
issn:
- 1539-0756
publication_status: published
publisher: American Physical Society
quality_controlled: '1'
scopus_import: '1'
status: public
title: 'Colloquium: Many-body localization, thermalization, and entanglement'
type: journal_article
user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
volume: 91
year: '2019'
...