---
_id: '159'
abstract:
- lang: eng
text: L-type Ca2+ channels (LTCCs) play a crucial role in excitation-contraction
coupling and release of hormones from secretory cells. They are targets of antihypertensive
and antiarrhythmic drugs such as diltiazem. Here, we present a photoswitchable
diltiazem, FHU-779, which can be used to reversibly block endogenous LTCCs by
light. FHU-779 is as potent as diltiazem and can be used to place pancreatic β-cell
function and cardiac activity under optical control.
article_processing_charge: No
article_type: original
author:
- first_name: Timm
full_name: Fehrentz, Timm
last_name: Fehrentz
- first_name: Florian
full_name: Huber, Florian
last_name: Huber
- first_name: Nina
full_name: Hartrampf, Nina
last_name: Hartrampf
- first_name: Tobias
full_name: Bruegmann, Tobias
last_name: Bruegmann
- first_name: James
full_name: Frank, James
last_name: Frank
- first_name: Nicholas
full_name: Fine, Nicholas
last_name: Fine
- first_name: Daniela
full_name: Malan, Daniela
last_name: Malan
- first_name: Johann G
full_name: Danzl, Johann G
id: 42EFD3B6-F248-11E8-B48F-1D18A9856A87
last_name: Danzl
orcid: 0000-0001-8559-3973
- first_name: Denis
full_name: Tikhonov, Denis
last_name: Tikhonov
- first_name: Maritn
full_name: Sumser, Maritn
last_name: Sumser
- first_name: Philipp
full_name: Sasse, Philipp
last_name: Sasse
- first_name: David
full_name: Hodson, David
last_name: Hodson
- first_name: Boris
full_name: Zhorov, Boris
last_name: Zhorov
- first_name: Nikolaj
full_name: Klocker, Nikolaj
last_name: Klocker
- first_name: Dirk
full_name: Trauner, Dirk
last_name: Trauner
citation:
ama: Fehrentz T, Huber F, Hartrampf N, et al. Optical control of L-type Ca2+ channels
using a diltiazem photoswitch. Nature Chemical Biology. 2018;14(8):764-767.
doi:10.1038/s41589-018-0090-8
apa: Fehrentz, T., Huber, F., Hartrampf, N., Bruegmann, T., Frank, J., Fine, N.,
… Trauner, D. (2018). Optical control of L-type Ca2+ channels using a diltiazem
photoswitch. Nature Chemical Biology. Nature Publishing Group. https://doi.org/10.1038/s41589-018-0090-8
chicago: Fehrentz, Timm, Florian Huber, Nina Hartrampf, Tobias Bruegmann, James
Frank, Nicholas Fine, Daniela Malan, et al. “Optical Control of L-Type Ca2+ Channels
Using a Diltiazem Photoswitch.” Nature Chemical Biology. Nature Publishing
Group, 2018. https://doi.org/10.1038/s41589-018-0090-8.
ieee: T. Fehrentz et al., “Optical control of L-type Ca2+ channels using
a diltiazem photoswitch,” Nature Chemical Biology, vol. 14, no. 8. Nature
Publishing Group, pp. 764–767, 2018.
ista: Fehrentz T, Huber F, Hartrampf N, Bruegmann T, Frank J, Fine N, Malan D, Danzl
JG, Tikhonov D, Sumser M, Sasse P, Hodson D, Zhorov B, Klocker N, Trauner D. 2018.
Optical control of L-type Ca2+ channels using a diltiazem photoswitch. Nature
Chemical Biology. 14(8), 764–767.
mla: Fehrentz, Timm, et al. “Optical Control of L-Type Ca2+ Channels Using a Diltiazem
Photoswitch.” Nature Chemical Biology, vol. 14, no. 8, Nature Publishing
Group, 2018, pp. 764–67, doi:10.1038/s41589-018-0090-8.
short: T. Fehrentz, F. Huber, N. Hartrampf, T. Bruegmann, J. Frank, N. Fine, D.
Malan, J.G. Danzl, D. Tikhonov, M. Sumser, P. Sasse, D. Hodson, B. Zhorov, N.
Klocker, D. Trauner, Nature Chemical Biology 14 (2018) 764–767.
date_created: 2018-12-11T11:44:56Z
date_published: 2018-07-16T00:00:00Z
date_updated: 2023-09-13T09:36:35Z
day: '16'
ddc:
- '570'
department:
- _id: JoDa
doi: 10.1038/s41589-018-0090-8
external_id:
isi:
- '000438970200010'
file:
- access_level: open_access
checksum: d42935094ec845f54a0688bf12986d62
content_type: application/pdf
creator: dernst
date_created: 2020-05-14T12:14:09Z
date_updated: 2020-07-14T12:45:03Z
file_id: '7832'
file_name: 2018_NatureChemicalBiology_Fehrentz.pdf
file_size: 6321000
relation: main_file
file_date_updated: 2020-07-14T12:45:03Z
has_accepted_license: '1'
intvolume: ' 14'
isi: 1
issue: '8'
language:
- iso: eng
month: '07'
oa: 1
oa_version: Submitted Version
page: 764 - 767
publication: Nature Chemical Biology
publication_status: published
publisher: Nature Publishing Group
publist_id: '7762'
quality_controlled: '1'
related_material:
link:
- relation: erratum
url: https://doi.org/10.1038/s41589-021-00744-3
scopus_import: '1'
status: public
title: Optical control of L-type Ca2+ channels using a diltiazem photoswitch
type: journal_article
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
volume: 14
year: '2018'
...
---
_id: '16'
abstract:
- lang: eng
text: We report quantitative evidence of mixing-layer elastic instability in a viscoelastic
fluid flow between two widely spaced obstacles hindering a channel flow at Re
1 and Wi 1. Two mixing layers with nonuniform shear velocity profiles are formed
in the region between the obstacles. The mixing-layer instability arises in the
vicinity of an inflection point on the shear velocity profile with a steep variation
in the elastic stress. The instability results in an intermittent appearance of
small vortices in the mixing layers and an amplification of spatiotemporal averaged
vorticity in the elastic turbulence regime. The latter is characterized through
scaling of friction factor with Wi and both pressure and velocity spectra. Furthermore,
the observations reported provide improved understanding of the stability of the
mixing layer in a viscoelastic fluid at large elasticity, i.e., Wi 1 and Re 1
and oppose the current view of suppression of vorticity solely by polymer additives.
acknowledgement: This work was partially supported by the Israel Science Foundation
(ISF; Grant No. 882/15) and the Binational USA-Israel Foundation (BSF; Grant No.
2016145).
article_number: '103303'
article_processing_charge: No
article_type: original
author:
- first_name: Atul
full_name: Varshney, Atul
id: 2A2006B2-F248-11E8-B48F-1D18A9856A87
last_name: Varshney
orcid: 0000-0002-3072-5999
- first_name: Victor
full_name: Steinberg, Victor
last_name: Steinberg
citation:
ama: Varshney A, Steinberg V. Mixing layer instability and vorticity amplification
in a creeping viscoelastic flow. Physical Review Fluids. 2018;3(10). doi:10.1103/PhysRevFluids.3.103303
apa: Varshney, A., & Steinberg, V. (2018). Mixing layer instability and vorticity
amplification in a creeping viscoelastic flow. Physical Review Fluids.
American Physical Society. https://doi.org/10.1103/PhysRevFluids.3.103303
chicago: Varshney, Atul, and Victor Steinberg. “Mixing Layer Instability and Vorticity
Amplification in a Creeping Viscoelastic Flow.” Physical Review Fluids.
American Physical Society, 2018. https://doi.org/10.1103/PhysRevFluids.3.103303.
ieee: A. Varshney and V. Steinberg, “Mixing layer instability and vorticity amplification
in a creeping viscoelastic flow,” Physical Review Fluids, vol. 3, no. 10.
American Physical Society, 2018.
ista: Varshney A, Steinberg V. 2018. Mixing layer instability and vorticity amplification
in a creeping viscoelastic flow. Physical Review Fluids. 3(10), 103303.
mla: Varshney, Atul, and Victor Steinberg. “Mixing Layer Instability and Vorticity
Amplification in a Creeping Viscoelastic Flow.” Physical Review Fluids,
vol. 3, no. 10, 103303, American Physical Society, 2018, doi:10.1103/PhysRevFluids.3.103303.
short: A. Varshney, V. Steinberg, Physical Review Fluids 3 (2018).
date_created: 2018-12-11T11:44:10Z
date_published: 2018-10-16T00:00:00Z
date_updated: 2025-04-14T07:44:02Z
day: '16'
ddc:
- '532'
department:
- _id: BjHo
doi: 10.1103/PhysRevFluids.3.103303
ec_funded: 1
external_id:
isi:
- '000447469200001'
file:
- access_level: open_access
checksum: 7fc0a2322214d1c04debef36d5bf2e8a
content_type: application/pdf
creator: system
date_created: 2018-12-12T10:13:56Z
date_updated: 2020-07-14T12:45:04Z
file_id: '5043'
file_name: IST-2018-1062-v1+1_PhysRevFluids.3.103303.pdf
file_size: 1838431
relation: main_file
file_date_updated: 2020-07-14T12:45:04Z
has_accepted_license: '1'
intvolume: ' 3'
isi: 1
issue: '10'
language:
- iso: eng
month: '10'
oa: 1
oa_version: Submitted Version
project:
- _id: 260C2330-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '754411'
name: ISTplus - Postdoctoral Fellowships
publication: Physical Review Fluids
publication_status: published
publisher: American Physical Society
publist_id: '8039'
pubrep_id: '1062'
quality_controlled: '1'
scopus_import: '1'
status: public
title: Mixing layer instability and vorticity amplification in a creeping viscoelastic
flow
type: journal_article
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
volume: 3
year: '2018'
...
---
_id: '161'
abstract:
- lang: eng
text: 'Which properties of metabolic networks can be derived solely from stoichiometry?
Predictive results have been obtained by flux balance analysis (FBA), by postulating
that cells set metabolic fluxes to maximize growth rate. Here we consider a generalization
of FBA to single-cell level using maximum entropy modeling, which we extend and
test experimentally. Specifically, we define for Escherichia coli metabolism a
flux distribution that yields the experimental growth rate: the model, containing
FBA as a limit, provides a better match to measured fluxes and it makes a wide
range of predictions: on flux variability, regulation, and correlations; on the
relative importance of stoichiometry vs. optimization; on scaling relations for
growth rate distributions. We validate the latter here with single-cell data at
different sub-inhibitory antibiotic concentrations. The model quantifies growth
optimization as emerging from the interplay of competitive dynamics in the population
and regulation of metabolism at the level of single cells.'
article_number: '2988'
article_processing_charge: No
author:
- first_name: Daniele
full_name: De Martino, Daniele
id: 3FF5848A-F248-11E8-B48F-1D18A9856A87
last_name: De Martino
orcid: 0000-0002-5214-4706
- first_name: Andersson Anna
full_name: Mc, Andersson Anna
last_name: Mc
- first_name: Tobias
full_name: Bergmiller, Tobias
id: 2C471CFA-F248-11E8-B48F-1D18A9856A87
last_name: Bergmiller
orcid: 0000-0001-5396-4346
- first_name: Calin C
full_name: Guet, Calin C
id: 47F8433E-F248-11E8-B48F-1D18A9856A87
last_name: Guet
orcid: 0000-0001-6220-2052
- first_name: Gasper
full_name: Tkacik, Gasper
id: 3D494DCA-F248-11E8-B48F-1D18A9856A87
last_name: Tkacik
orcid: 0000-0002-6699-1455
citation:
ama: De Martino D, Mc AA, Bergmiller T, Guet CC, Tkačik G. Statistical mechanics
for metabolic networks during steady state growth. Nature Communications.
2018;9(1). doi:10.1038/s41467-018-05417-9
apa: De Martino, D., Mc, A. A., Bergmiller, T., Guet, C. C., & Tkačik, G. (2018).
Statistical mechanics for metabolic networks during steady state growth. Nature
Communications. Springer Nature. https://doi.org/10.1038/s41467-018-05417-9
chicago: De Martino, Daniele, Andersson Anna Mc, Tobias Bergmiller, Calin C Guet,
and Gašper Tkačik. “Statistical Mechanics for Metabolic Networks during Steady
State Growth.” Nature Communications. Springer Nature, 2018. https://doi.org/10.1038/s41467-018-05417-9.
ieee: D. De Martino, A. A. Mc, T. Bergmiller, C. C. Guet, and G. Tkačik, “Statistical
mechanics for metabolic networks during steady state growth,” Nature Communications,
vol. 9, no. 1. Springer Nature, 2018.
ista: De Martino D, Mc AA, Bergmiller T, Guet CC, Tkačik G. 2018. Statistical mechanics
for metabolic networks during steady state growth. Nature Communications. 9(1),
2988.
mla: De Martino, Daniele, et al. “Statistical Mechanics for Metabolic Networks during
Steady State Growth.” Nature Communications, vol. 9, no. 1, 2988, Springer
Nature, 2018, doi:10.1038/s41467-018-05417-9.
short: D. De Martino, A.A. Mc, T. Bergmiller, C.C. Guet, G. Tkačik, Nature Communications
9 (2018).
date_created: 2018-12-11T11:44:57Z
date_published: 2018-07-30T00:00:00Z
date_updated: 2025-04-15T06:50:08Z
day: '30'
ddc:
- '570'
department:
- _id: GaTk
- _id: CaGu
doi: 10.1038/s41467-018-05417-9
ec_funded: 1
external_id:
isi:
- '000440149300021'
file:
- access_level: open_access
checksum: 3ba7ab27b27723c7dcf633e8fc1f8f18
content_type: application/pdf
creator: dernst
date_created: 2018-12-17T16:44:28Z
date_updated: 2020-07-14T12:45:06Z
file_id: '5728'
file_name: 2018_NatureComm_DeMartino.pdf
file_size: 1043205
relation: main_file
file_date_updated: 2020-07-14T12:45:06Z
has_accepted_license: '1'
intvolume: ' 9'
isi: 1
issue: '1'
language:
- iso: eng
license: https://creativecommons.org/licenses/by/4.0/
month: '07'
oa: 1
oa_version: Published Version
project:
- _id: 254E9036-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: P28844-B27
name: Biophysics of information processing in gene regulation
- _id: 25681D80-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '291734'
name: International IST Postdoc Fellowship Programme
publication: Nature Communications
publication_status: published
publisher: Springer Nature
publist_id: '7760'
quality_controlled: '1'
related_material:
record:
- id: '5587'
relation: popular_science
status: public
scopus_import: '1'
status: public
title: Statistical mechanics for metabolic networks during steady state growth
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: journal_article
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
volume: 9
year: '2018'
...
---
_id: '162'
abstract:
- lang: eng
text: 'Facial shape is the basis for facial recognition and categorization. Facial
features reflect the underlying geometry of the skeletal structures. Here, we
reveal that cartilaginous nasal capsule (corresponding to upper jaw and face)
is shaped by signals generated by neural structures: brain and olfactory epithelium.
Brain-derived Sonic Hedgehog (SHH) enables the induction of nasal septum and posterior
nasal capsule, whereas the formation of a capsule roof is controlled by signals
from the olfactory epithelium. Unexpectedly, the cartilage of the nasal capsule
turned out to be important for shaping membranous facial bones during development.
This suggests that conserved neurosensory structures could benefit from protection
and have evolved signals inducing cranial cartilages encasing them. Experiments
with mutant mice revealed that the genomic regulatory regions controlling production
of SHH in the nervous system contribute to facial cartilage morphogenesis, which
might be a mechanism responsible for the adaptive evolution of animal faces and
snouts.'
article_number: e34465
article_processing_charge: No
author:
- first_name: Marketa
full_name: Kaucka, Marketa
last_name: Kaucka
- first_name: Julian
full_name: Petersen, Julian
last_name: Petersen
- first_name: Marketa
full_name: Tesarova, Marketa
last_name: Tesarova
- first_name: Bara
full_name: Szarowska, Bara
last_name: Szarowska
- first_name: Maria
full_name: Kastriti, Maria
last_name: Kastriti
- first_name: Meng
full_name: Xie, Meng
last_name: Xie
- first_name: Anna
full_name: Kicheva, Anna
id: 3959A2A0-F248-11E8-B48F-1D18A9856A87
last_name: Kicheva
orcid: 0000-0003-4509-4998
- first_name: Karl
full_name: Annusver, Karl
last_name: Annusver
- first_name: Maria
full_name: Kasper, Maria
last_name: Kasper
- first_name: Orsolya
full_name: Symmons, Orsolya
last_name: Symmons
- first_name: Leslie
full_name: Pan, Leslie
last_name: Pan
- first_name: Francois
full_name: Spitz, Francois
last_name: Spitz
- first_name: Jozef
full_name: Kaiser, Jozef
last_name: Kaiser
- first_name: Maria
full_name: Hovorakova, Maria
last_name: Hovorakova
- first_name: Tomas
full_name: Zikmund, Tomas
last_name: Zikmund
- first_name: Kazunori
full_name: Sunadome, Kazunori
last_name: Sunadome
- first_name: Michael P
full_name: Matise, Michael P
last_name: Matise
- first_name: Hui
full_name: Wang, Hui
last_name: Wang
- first_name: Ulrika
full_name: Marklund, Ulrika
last_name: Marklund
- first_name: Hind
full_name: Abdo, Hind
last_name: Abdo
- first_name: Patrik
full_name: Ernfors, Patrik
last_name: Ernfors
- first_name: Pascal
full_name: Maire, Pascal
last_name: Maire
- first_name: Maud
full_name: Wurmser, Maud
last_name: Wurmser
- first_name: Andrei S
full_name: Chagin, Andrei S
last_name: Chagin
- first_name: Kaj
full_name: Fried, Kaj
last_name: Fried
- first_name: Igor
full_name: Adameyko, Igor
last_name: Adameyko
citation:
ama: Kaucka M, Petersen J, Tesarova M, et al. Signals from the brain and olfactory
epithelium control shaping of the mammalian nasal capsule cartilage. eLife.
2018;7. doi:10.7554/eLife.34465
apa: Kaucka, M., Petersen, J., Tesarova, M., Szarowska, B., Kastriti, M., Xie, M.,
… Adameyko, I. (2018). Signals from the brain and olfactory epithelium control
shaping of the mammalian nasal capsule cartilage. ELife. eLife Sciences
Publications. https://doi.org/10.7554/eLife.34465
chicago: Kaucka, Marketa, Julian Petersen, Marketa Tesarova, Bara Szarowska, Maria
Kastriti, Meng Xie, Anna Kicheva, et al. “Signals from the Brain and Olfactory
Epithelium Control Shaping of the Mammalian Nasal Capsule Cartilage.” ELife.
eLife Sciences Publications, 2018. https://doi.org/10.7554/eLife.34465.
ieee: M. Kaucka et al., “Signals from the brain and olfactory epithelium
control shaping of the mammalian nasal capsule cartilage,” eLife, vol.
7. eLife Sciences Publications, 2018.
ista: Kaucka M, Petersen J, Tesarova M, Szarowska B, Kastriti M, Xie M, Kicheva
A, Annusver K, Kasper M, Symmons O, Pan L, Spitz F, Kaiser J, Hovorakova M, Zikmund
T, Sunadome K, Matise MP, Wang H, Marklund U, Abdo H, Ernfors P, Maire P, Wurmser
M, Chagin AS, Fried K, Adameyko I. 2018. Signals from the brain and olfactory
epithelium control shaping of the mammalian nasal capsule cartilage. eLife. 7,
e34465.
mla: Kaucka, Marketa, et al. “Signals from the Brain and Olfactory Epithelium Control
Shaping of the Mammalian Nasal Capsule Cartilage.” ELife, vol. 7, e34465,
eLife Sciences Publications, 2018, doi:10.7554/eLife.34465.
short: M. Kaucka, J. Petersen, M. Tesarova, B. Szarowska, M. Kastriti, M. Xie, A.
Kicheva, K. Annusver, M. Kasper, O. Symmons, L. Pan, F. Spitz, J. Kaiser, M. Hovorakova,
T. Zikmund, K. Sunadome, M.P. Matise, H. Wang, U. Marklund, H. Abdo, P. Ernfors,
P. Maire, M. Wurmser, A.S. Chagin, K. Fried, I. Adameyko, ELife 7 (2018).
date_created: 2018-12-11T11:44:57Z
date_published: 2018-06-13T00:00:00Z
date_updated: 2025-04-14T07:27:30Z
day: '13'
ddc:
- '571'
department:
- _id: AnKi
doi: 10.7554/eLife.34465
ec_funded: 1
external_id:
isi:
- '000436227500001'
file:
- access_level: open_access
checksum: da2378cdcf6b5461dcde194e4d608343
content_type: application/pdf
creator: dernst
date_created: 2018-12-17T16:41:58Z
date_updated: 2020-07-14T12:45:07Z
file_id: '5727'
file_name: 2018_eLife_Kaucka.pdf
file_size: 9816484
relation: main_file
file_date_updated: 2020-07-14T12:45:07Z
has_accepted_license: '1'
intvolume: ' 7'
isi: 1
language:
- iso: eng
month: '06'
oa: 1
oa_version: Published Version
project:
- _id: B6FC0238-B512-11E9-945C-1524E6697425
call_identifier: H2020
grant_number: '680037'
name: Coordination of Patterning And Growth In the Spinal Cord
publication: eLife
publication_status: published
publisher: eLife Sciences Publications
publist_id: '7759'
quality_controlled: '1'
related_material:
record:
- id: '9838'
relation: research_data
status: public
scopus_import: '1'
status: public
title: Signals from the brain and olfactory epithelium control shaping of the mammalian
nasal capsule cartilage
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: journal_article
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
volume: 7
year: '2018'
...
---
_id: '163'
abstract:
- lang: eng
text: For ultrafast fixation of biological samples to avoid artifacts, high-pressure
freezing (HPF) followed by freeze substitution (FS) is preferred over chemical
fixation at room temperature. After HPF, samples are maintained at low temperature
during dehydration and fixation, while avoiding damaging recrystallization. This
is a notoriously slow process. McDonald and Webb demonstrated, in 2011, that sample
agitation during FS dramatically reduces the necessary time. Then, in 2015, we
(H.G. and S.R.) introduced an agitation module into the cryochamber of an automated
FS unit and demonstrated that the preparation of algae could be shortened from
days to a couple of hours. We argued that variability in the processing, reproducibility,
and safety issues are better addressed using automated FS units. For dissemination,
we started low-cost manufacturing of agitation modules for two of the most widely
used FS units, the Automatic Freeze Substitution Systems, AFS(1) and AFS2, from
Leica Microsystems, using three dimensional (3D)-printing of the major components.
To test them, several labs independently used the modules on a wide variety of
specimens that had previously been processed by manual agitation, or without agitation.
We demonstrate that automated processing with sample agitation saves time, increases
flexibility with respect to sample requirements and protocols, and produces data
of at least as good quality as other approaches.
article_processing_charge: No
article_type: original
author:
- first_name: Siegfried
full_name: Reipert, Siegfried
last_name: Reipert
- first_name: Helmuth
full_name: Goldammer, Helmuth
last_name: Goldammer
- first_name: Christine
full_name: Richardson, Christine
last_name: Richardson
- first_name: Martin
full_name: Goldberg, Martin
last_name: Goldberg
- first_name: Timothy
full_name: Hawkins, Timothy
last_name: Hawkins
- first_name: Elena
full_name: Hollergschwandtner, Elena
id: 3C054040-F248-11E8-B48F-1D18A9856A87
last_name: Hollergschwandtner
- first_name: Walter
full_name: Kaufmann, Walter
id: 3F99E422-F248-11E8-B48F-1D18A9856A87
last_name: Kaufmann
orcid: 0000-0001-9735-5315
- first_name: Sebastian
full_name: Antreich, Sebastian
last_name: Antreich
- first_name: York
full_name: Stierhof, York
last_name: Stierhof
citation:
ama: 'Reipert S, Goldammer H, Richardson C, et al. Agitation modules: Flexible means
to accelerate automated freeze substitution. Journal of Histochemistry and
Cytochemistry. 2018;66(12):903-921. doi:10.1369/0022155418786698'
apa: 'Reipert, S., Goldammer, H., Richardson, C., Goldberg, M., Hawkins, T., Saeckl,
E., … Stierhof, Y. (2018). Agitation modules: Flexible means to accelerate automated
freeze substitution. Journal of Histochemistry and Cytochemistry. SAGE
Publications. https://doi.org/10.1369/0022155418786698'
chicago: 'Reipert, Siegfried, Helmuth Goldammer, Christine Richardson, Martin Goldberg,
Timothy Hawkins, Elena Saeckl, Walter Kaufmann, Sebastian Antreich, and York Stierhof.
“Agitation Modules: Flexible Means to Accelerate Automated Freeze Substitution.”
Journal of Histochemistry and Cytochemistry. SAGE Publications, 2018. https://doi.org/10.1369/0022155418786698.'
ieee: 'S. Reipert et al., “Agitation modules: Flexible means to accelerate
automated freeze substitution,” Journal of Histochemistry and Cytochemistry,
vol. 66, no. 12. SAGE Publications, pp. 903–921, 2018.'
ista: 'Reipert S, Goldammer H, Richardson C, Goldberg M, Hawkins T, Saeckl E, Kaufmann
W, Antreich S, Stierhof Y. 2018. Agitation modules: Flexible means to accelerate
automated freeze substitution. Journal of Histochemistry and Cytochemistry. 66(12),
903–921.'
mla: 'Reipert, Siegfried, et al. “Agitation Modules: Flexible Means to Accelerate
Automated Freeze Substitution.” Journal of Histochemistry and Cytochemistry,
vol. 66, no. 12, SAGE Publications, 2018, pp. 903–21, doi:10.1369/0022155418786698.'
short: S. Reipert, H. Goldammer, C. Richardson, M. Goldberg, T. Hawkins, E. Saeckl,
W. Kaufmann, S. Antreich, Y. Stierhof, Journal of Histochemistry and Cytochemistry
66 (2018) 903–921.
date_created: 2018-12-11T11:44:57Z
date_published: 2018-12-01T00:00:00Z
date_updated: 2023-10-17T08:42:24Z
day: '01'
department:
- _id: RySh
- _id: EM-Fac
doi: 10.1369/0022155418786698
external_id:
isi:
- '000452277700005'
pmid:
- '29969056'
intvolume: ' 66'
isi: 1
issue: '12'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.1369/0022155418786698
month: '12'
oa: 1
oa_version: Published Version
page: 903-921
pmid: 1
publication: Journal of Histochemistry and Cytochemistry
publication_identifier:
issn:
- 0022-1554
publication_status: published
publisher: SAGE Publications
quality_controlled: '1'
scopus_import: '1'
status: public
title: 'Agitation modules: Flexible means to accelerate automated freeze substitution'
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 66
year: '2018'
...
---
_id: '17'
abstract:
- lang: eng
text: Creeping flow of polymeric fluid without inertia exhibits elastic instabilities
and elastic turbulence accompanied by drag enhancement due to elastic stress produced
by flow-stretched polymers. However, in inertia-dominated flow at high Re and
low fluid elasticity El, a reduction in turbulent frictional drag is caused by
an intricate competition between inertial and elastic stresses. Here we explore
the effect of inertia on the stability of viscoelastic flow in a broad range of
control parameters El and (Re,Wi). We present the stability diagram of observed
flow regimes in Wi-Re coordinates and find that the instabilities' onsets show
an unexpectedly nonmonotonic dependence on El. Further, three distinct regions
in the diagram are identified based on El. Strikingly, for high-elasticity fluids
we discover a complete relaminarization of flow at Reynolds number in the range
of 1 to 10, different from a well-known turbulent drag reduction. These counterintuitive
effects may be explained by a finite polymer extensibility and a suppression of
vorticity at high Wi. Our results call for further theoretical and numerical development
to uncover the role of inertial effect on elastic turbulence in a viscoelastic
flow.
article_number: '103302 '
article_processing_charge: No
author:
- first_name: Atul
full_name: Varshney, Atul
id: 2A2006B2-F248-11E8-B48F-1D18A9856A87
last_name: Varshney
orcid: 0000-0002-3072-5999
- first_name: Victor
full_name: Steinberg, Victor
last_name: Steinberg
citation:
ama: Varshney A, Steinberg V. Drag enhancement and drag reduction in viscoelastic
flow. Physical Review Fluids. 2018;3(10). doi:10.1103/PhysRevFluids.3.103302
apa: Varshney, A., & Steinberg, V. (2018). Drag enhancement and drag reduction
in viscoelastic flow. Physical Review Fluids. American Physical Society.
https://doi.org/10.1103/PhysRevFluids.3.103302
chicago: Varshney, Atul, and Victor Steinberg. “Drag Enhancement and Drag Reduction
in Viscoelastic Flow.” Physical Review Fluids. American Physical Society,
2018. https://doi.org/10.1103/PhysRevFluids.3.103302.
ieee: A. Varshney and V. Steinberg, “Drag enhancement and drag reduction in viscoelastic
flow,” Physical Review Fluids, vol. 3, no. 10. American Physical Society,
2018.
ista: Varshney A, Steinberg V. 2018. Drag enhancement and drag reduction in viscoelastic
flow. Physical Review Fluids. 3(10), 103302.
mla: Varshney, Atul, and Victor Steinberg. “Drag Enhancement and Drag Reduction
in Viscoelastic Flow.” Physical Review Fluids, vol. 3, no. 10, 103302,
American Physical Society, 2018, doi:10.1103/PhysRevFluids.3.103302.
short: A. Varshney, V. Steinberg, Physical Review Fluids 3 (2018).
date_created: 2018-12-11T11:44:11Z
date_published: 2018-10-15T00:00:00Z
date_updated: 2025-04-14T07:43:59Z
day: '15'
ddc:
- '532'
department:
- _id: BjHo
doi: 10.1103/PhysRevFluids.3.103302
ec_funded: 1
external_id:
isi:
- '000447311500001'
file:
- access_level: open_access
checksum: e1445be33e8165114e96246275600750
content_type: application/pdf
creator: system
date_created: 2018-12-12T10:10:14Z
date_updated: 2020-07-14T12:45:12Z
file_id: '4800'
file_name: IST-2018-1061-v1+1_PhysRevFluids.3.103302.pdf
file_size: 1409040
relation: main_file
file_date_updated: 2020-07-14T12:45:12Z
has_accepted_license: '1'
intvolume: ' 3'
isi: 1
issue: '10'
language:
- iso: eng
month: '10'
oa: 1
oa_version: Published Version
project:
- _id: 260C2330-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '754411'
name: ISTplus - Postdoctoral Fellowships
publication: Physical Review Fluids
publication_status: published
publisher: American Physical Society
publist_id: '8038'
pubrep_id: '1061'
quality_controlled: '1'
scopus_import: '1'
status: public
title: Drag enhancement and drag reduction in viscoelastic flow
type: journal_article
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
volume: 3
year: '2018'
...
---
_id: '78'
abstract:
- lang: eng
text: We provide a procedure for detecting the sub-segments of an incrementally
observed Boolean signal ω that match a given temporal pattern ϕ. As a pattern
specification language, we use timed regular expressions, a formalism well-suited
for expressing properties of concurrent asynchronous behaviors embedded in metric
time. We construct a timed automaton accepting the timed language denoted by ϕ
and modify it slightly for the purpose of matching. We then apply zone-based reachability
computation to this automaton while it reads ω, and retrieve all the matching
segments from the results. Since the procedure is automaton based, it can be applied
to patterns specified by other formalisms such as timed temporal logics reducible
to timed automata or directly encoded as timed automata. The procedure has been
implemented and its performance on synthetic examples is demonstrated.
alternative_title:
- LNCS
article_processing_charge: No
author:
- first_name: Alexey
full_name: Bakhirkin, Alexey
last_name: Bakhirkin
- 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
last_name: Nickovic
- first_name: Oded
full_name: Maler, Oded
last_name: Maler
- first_name: Eugene
full_name: Asarin, Eugene
last_name: Asarin
citation:
ama: 'Bakhirkin A, Ferrere T, Nickovic D, Maler O, Asarin E. Online timed pattern
matching using automata. In: Vol 11022. Springer; 2018:215-232. doi:10.1007/978-3-030-00151-3_13'
apa: 'Bakhirkin, A., Ferrere, T., Nickovic, D., Maler, O., & Asarin, E. (2018).
Online timed pattern matching using automata (Vol. 11022, pp. 215–232). Presented
at the FORMATS: Formal Modeling and Analysis of Timed Systems, Bejing, China:
Springer. https://doi.org/10.1007/978-3-030-00151-3_13'
chicago: Bakhirkin, Alexey, Thomas Ferrere, Dejan Nickovic, Oded Maler, and Eugene
Asarin. “Online Timed Pattern Matching Using Automata,” 11022:215–32. Springer,
2018. https://doi.org/10.1007/978-3-030-00151-3_13.
ieee: 'A. Bakhirkin, T. Ferrere, D. Nickovic, O. Maler, and E. Asarin, “Online timed
pattern matching using automata,” presented at the FORMATS: Formal Modeling and
Analysis of Timed Systems, Bejing, China, 2018, vol. 11022, pp. 215–232.'
ista: 'Bakhirkin A, Ferrere T, Nickovic D, Maler O, Asarin E. 2018. Online timed
pattern matching using automata. FORMATS: Formal Modeling and Analysis of Timed
Systems, LNCS, vol. 11022, 215–232.'
mla: Bakhirkin, Alexey, et al. Online Timed Pattern Matching Using Automata.
Vol. 11022, Springer, 2018, pp. 215–32, doi:10.1007/978-3-030-00151-3_13.
short: A. Bakhirkin, T. Ferrere, D. Nickovic, O. Maler, E. Asarin, in:, Springer,
2018, pp. 215–232.
conference:
end_date: 2018-09-06
location: Bejing, China
name: 'FORMATS: Formal Modeling and Analysis of Timed Systems'
start_date: 2018-09-04
date_created: 2018-12-11T11:44:31Z
date_published: 2018-08-26T00:00:00Z
date_updated: 2025-04-15T06:26:03Z
day: '26'
ddc:
- '000'
department:
- _id: ToHe
doi: 10.1007/978-3-030-00151-3_13
external_id:
isi:
- '000884993200013'
file:
- access_level: open_access
checksum: 436b7574934324cfa7d1d3986fddc65b
content_type: application/pdf
creator: dernst
date_created: 2020-05-14T11:34:34Z
date_updated: 2020-07-14T12:48:03Z
file_id: '7831'
file_name: 2018_LNCS_Bakhirkin.pdf
file_size: 374851
relation: main_file
file_date_updated: 2020-07-14T12:48:03Z
has_accepted_license: '1'
intvolume: ' 11022'
isi: 1
language:
- iso: eng
month: '08'
oa: 1
oa_version: Submitted Version
page: 215 - 232
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: Formal methods for the design and analysis of complex systems
publication_identifier:
isbn:
- 978-3-030-00150-6
publication_status: published
publisher: Springer
publist_id: '7976'
quality_controlled: '1'
scopus_import: '1'
status: public
title: Online timed pattern matching using automata
type: conference
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
volume: 11022
year: '2018'
...
---
_id: '7812'
abstract:
- lang: eng
text: Deep neural networks (DNNs) continue to make significant advances, solving
tasks from image classification to translation or reinforcement learning. One
aspect of the field receiving considerable attention is efficiently executing
deep models in resource-constrained environments, such as mobile or embedded devices.
This paper focuses on this problem, and proposes two new compression methods,
which jointly leverage weight quantization and distillation of larger teacher
networks into smaller student networks. The first method we propose is called
quantized distillation and leverages distillation during the training process,
by incorporating distillation loss, expressed with respect to the teacher, into
the training of a student network whose weights are quantized to a limited set
of levels. The second method, differentiable quantization, optimizes the location
of quantization points through stochastic gradient descent, to better fit the
behavior of the teacher model. We validate both methods through experiments on
convolutional and recurrent architectures. We show that quantized shallow students
can reach similar accuracy levels to full-precision teacher models, while providing
order of magnitude compression, and inference speedup that is linear in the depth
reduction. In sum, our results enable DNNs for resource-constrained environments
to leverage architecture and accuracy advances developed on more powerful devices.
acknowledgement: "We would like to thank Ce Zhang (ETH Zurich), Hantian Zhang (ETH
Zurich) and Martin Jaggi ´\r\n(EPFL) for their support with experiments and valuable
feedback.\r\n"
article_processing_charge: No
arxiv: 1
author:
- first_name: Antonio
full_name: Polino, Antonio
last_name: Polino
- first_name: Razvan
full_name: Pascanu, Razvan
last_name: Pascanu
- first_name: Dan-Adrian
full_name: Alistarh, Dan-Adrian
id: 4A899BFC-F248-11E8-B48F-1D18A9856A87
last_name: Alistarh
orcid: 0000-0003-3650-940X
citation:
ama: 'Polino A, Pascanu R, Alistarh D-A. Model compression via distillation and
quantization. In: 6th International Conference on Learning Representations.
; 2018.'
apa: Polino, A., Pascanu, R., & Alistarh, D.-A. (2018). Model compression via
distillation and quantization. In 6th International Conference on Learning
Representations. Vancouver, Canada.
chicago: Polino, Antonio, Razvan Pascanu, and Dan-Adrian Alistarh. “Model Compression
via Distillation and Quantization.” In 6th International Conference on Learning
Representations, 2018.
ieee: A. Polino, R. Pascanu, and D.-A. Alistarh, “Model compression via distillation
and quantization,” in 6th International Conference on Learning Representations,
Vancouver, Canada, 2018.
ista: 'Polino A, Pascanu R, Alistarh D-A. 2018. Model compression via distillation
and quantization. 6th International Conference on Learning Representations. ICLR:
International Conference on Learning Representations.'
mla: Polino, Antonio, et al. “Model Compression via Distillation and Quantization.”
6th International Conference on Learning Representations, 2018.
short: A. Polino, R. Pascanu, D.-A. Alistarh, in:, 6th International Conference
on Learning Representations, 2018.
conference:
end_date: 2018-05-03
location: Vancouver, Canada
name: 'ICLR: International Conference on Learning Representations'
start_date: 2018-04-30
date_created: 2020-05-10T22:00:51Z
date_published: 2018-05-01T00:00:00Z
date_updated: 2025-06-30T10:04:44Z
day: '01'
ddc:
- '000'
department:
- _id: DaAl
external_id:
arxiv:
- '1802.05668'
file:
- access_level: open_access
checksum: a4336c167978e81891970e4e4517a8c3
content_type: application/pdf
creator: dernst
date_created: 2020-05-26T13:02:00Z
date_updated: 2020-07-14T12:48:03Z
file_id: '7894'
file_name: 2018_ICLR_Polino.pdf
file_size: 308339
relation: main_file
file_date_updated: 2020-07-14T12:48:03Z
has_accepted_license: '1'
language:
- iso: eng
month: '05'
oa: 1
oa_version: Published Version
publication: 6th International Conference on Learning Representations
publication_status: published
quality_controlled: '1'
scopus_import: '1'
status: public
title: Model compression via distillation and quantization
type: conference
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
year: '2018'
...
---
_id: '79'
abstract:
- lang: eng
text: 'Markov Decision Processes (MDPs) are a popular class of models suitable for
solving control decision problems in probabilistic reactive systems. We consider
parametric MDPs (pMDPs) that include parameters in some of the transition probabilities
to account for stochastic uncertainties of the environment such as noise or input
disturbances. We study pMDPs with reachability objectives where the parameter
values are unknown and impossible to measure directly during execution, but there
is a probability distribution known over the parameter values. We study for the
first time computing parameter-independent strategies that are expectation optimal,
i.e., optimize the expected reachability probability under the probability distribution
over the parameters. We present an encoding of our problem to partially observable
MDPs (POMDPs), i.e., a reduction of our problem to computing optimal strategies
in POMDPs. We evaluate our method experimentally on several benchmarks: a motivating
(repeated) learner model; a series of benchmarks of varying configurations of
a robot moving on a grid; and a consensus protocol.'
alternative_title:
- LNCS
article_processing_charge: No
arxiv: 1
author:
- first_name: Sebastian
full_name: Arming, Sebastian
last_name: Arming
- first_name: Ezio
full_name: Bartocci, Ezio
last_name: Bartocci
- first_name: Krishnendu
full_name: Chatterjee, Krishnendu
id: 2E5DCA20-F248-11E8-B48F-1D18A9856A87
last_name: Chatterjee
orcid: 0000-0002-4561-241X
- first_name: Joost P
full_name: Katoen, Joost P
id: 4524F760-F248-11E8-B48F-1D18A9856A87
last_name: Katoen
- first_name: Ana
full_name: Sokolova, Ana
last_name: Sokolova
citation:
ama: 'Arming S, Bartocci E, Chatterjee K, Katoen JP, Sokolova A. Parameter-independent
strategies for pMDPs via POMDPs. In: Vol 11024. Springer; 2018:53-70. doi:10.1007/978-3-319-99154-2_4'
apa: 'Arming, S., Bartocci, E., Chatterjee, K., Katoen, J. P., & Sokolova, A.
(2018). Parameter-independent strategies for pMDPs via POMDPs (Vol. 11024, pp.
53–70). Presented at the QEST: Quantitative Evaluation of Systems, Beijing, China:
Springer. https://doi.org/10.1007/978-3-319-99154-2_4'
chicago: Arming, Sebastian, Ezio Bartocci, Krishnendu Chatterjee, Joost P Katoen,
and Ana Sokolova. “Parameter-Independent Strategies for PMDPs via POMDPs,” 11024:53–70.
Springer, 2018. https://doi.org/10.1007/978-3-319-99154-2_4.
ieee: 'S. Arming, E. Bartocci, K. Chatterjee, J. P. Katoen, and A. Sokolova, “Parameter-independent
strategies for pMDPs via POMDPs,” presented at the QEST: Quantitative Evaluation
of Systems, Beijing, China, 2018, vol. 11024, pp. 53–70.'
ista: 'Arming S, Bartocci E, Chatterjee K, Katoen JP, Sokolova A. 2018. Parameter-independent
strategies for pMDPs via POMDPs. QEST: Quantitative Evaluation of Systems, LNCS,
vol. 11024, 53–70.'
mla: Arming, Sebastian, et al. Parameter-Independent Strategies for PMDPs via
POMDPs. Vol. 11024, Springer, 2018, pp. 53–70, doi:10.1007/978-3-319-99154-2_4.
short: S. Arming, E. Bartocci, K. Chatterjee, J.P. Katoen, A. Sokolova, in:, Springer,
2018, pp. 53–70.
conference:
end_date: 2018-09-07
location: Beijing, China
name: 'QEST: Quantitative Evaluation of Systems'
start_date: 2018-09-04
date_created: 2018-12-11T11:44:31Z
date_published: 2018-08-15T00:00:00Z
date_updated: 2023-09-13T09:38:28Z
day: '15'
department:
- _id: KrCh
- _id: ToHe
doi: 10.1007/978-3-319-99154-2_4
external_id:
arxiv:
- '1806.05126'
isi:
- '000548912200004'
intvolume: ' 11024'
isi: 1
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/1806.05126
month: '08'
oa: 1
oa_version: Preprint
page: 53-70
publication_status: published
publisher: Springer
publist_id: '7975'
quality_controlled: '1'
scopus_import: '1'
status: public
title: Parameter-independent strategies for pMDPs via POMDPs
type: conference
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
volume: 11024
year: '2018'
...
---
_id: '81'
abstract:
- lang: eng
text: We solve the offline monitoring problem for timed propositional temporal logic
(TPTL), interpreted over dense-time Boolean signals. The variant of TPTL we consider
extends linear temporal logic (LTL) with clock variables and reset quantifiers,
providing a mechanism to specify real-time constraints. We first describe a general
monitoring algorithm based on an exhaustive computation of the set of satisfying
clock assignments as a finite union of zones. We then propose a specialized monitoring
algorithm for the one-variable case using a partition of the time domain based
on the notion of region equivalence, whose complexity is linear in the length
of the signal, thereby generalizing a known result regarding the monitoring of
metric temporal logic (MTL). The region and zone representations of time constraints
are known from timed automata verification and can also be used in the discrete-time
case. Our prototype implementation appears to outperform previous discrete-time
implementations of TPTL monitoring,
alternative_title:
- LNCS
article_processing_charge: No
author:
- first_name: Adrian
full_name: Elgyütt, Adrian
id: 4A2E9DBA-F248-11E8-B48F-1D18A9856A87
last_name: Elgyütt
- first_name: Thomas
full_name: Ferrere, Thomas
id: 40960E6E-F248-11E8-B48F-1D18A9856A87
last_name: Ferrere
orcid: 0000-0001-5199-3143
- first_name: Thomas A
full_name: Henzinger, Thomas A
id: 40876CD8-F248-11E8-B48F-1D18A9856A87
last_name: Henzinger
orcid: 0000−0002−2985−7724
citation:
ama: 'Elgyütt A, Ferrere T, Henzinger TA. Monitoring temporal logic with clock variables.
In: Vol 11022. Springer; 2018:53-70. doi:10.1007/978-3-030-00151-3_4'
apa: 'Elgyütt, A., Ferrere, T., & Henzinger, T. A. (2018). Monitoring temporal
logic with clock variables (Vol. 11022, pp. 53–70). Presented at the FORMATS:
Formal Modeling and Analysis of Timed Systems, Beijing, China: Springer. https://doi.org/10.1007/978-3-030-00151-3_4'
chicago: Elgyütt, Adrian, Thomas Ferrere, and Thomas A Henzinger. “Monitoring Temporal
Logic with Clock Variables,” 11022:53–70. Springer, 2018. https://doi.org/10.1007/978-3-030-00151-3_4.
ieee: 'A. Elgyütt, T. Ferrere, and T. A. Henzinger, “Monitoring temporal logic with
clock variables,” presented at the FORMATS: Formal Modeling and Analysis of Timed
Systems, Beijing, China, 2018, vol. 11022, pp. 53–70.'
ista: 'Elgyütt A, Ferrere T, Henzinger TA. 2018. Monitoring temporal logic with
clock variables. FORMATS: Formal Modeling and Analysis of Timed Systems, LNCS,
vol. 11022, 53–70.'
mla: Elgyütt, Adrian, et al. Monitoring Temporal Logic with Clock Variables.
Vol. 11022, Springer, 2018, pp. 53–70, doi:10.1007/978-3-030-00151-3_4.
short: A. Elgyütt, T. Ferrere, T.A. Henzinger, in:, Springer, 2018, pp. 53–70.
conference:
end_date: 2018-09-06
location: Beijing, China
name: 'FORMATS: Formal Modeling and Analysis of Timed Systems'
start_date: 2018-09-04
date_created: 2018-12-11T11:44:31Z
date_published: 2018-08-26T00:00:00Z
date_updated: 2025-04-15T06:26:03Z
day: '26'
ddc:
- '000'
department:
- _id: ToHe
doi: 10.1007/978-3-030-00151-3_4
external_id:
isi:
- '000884993200004'
file:
- access_level: open_access
checksum: e5d81c9b50a6bd9d8a2c16953aad7e23
content_type: application/pdf
creator: dernst
date_created: 2020-10-09T06:24:21Z
date_updated: 2020-10-09T06:24:21Z
file_id: '8638'
file_name: 2018_LNCS_Elgyuett.pdf
file_size: 537219
relation: main_file
success: 1
file_date_updated: 2020-10-09T06:24:21Z
has_accepted_license: '1'
intvolume: ' 11022'
isi: 1
language:
- iso: eng
month: '08'
oa: 1
oa_version: Submitted Version
page: 53 - 70
project:
- _id: 25F5A88A-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: S11402-N23
name: Moderne Concurrency Paradigms
- _id: 25F42A32-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: Z211
name: Formal methods for the design and analysis of complex systems
publication_status: published
publisher: Springer
publist_id: '7973'
quality_controlled: '1'
scopus_import: '1'
status: public
title: Monitoring temporal logic with clock variables
type: conference
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
volume: 11022
year: '2018'
...
---
_id: '82'
abstract:
- lang: eng
text: In experimental cultures, when bacteria are mixed with lytic (virulent) bacteriophage,
bacterial cells resistant to the phage commonly emerge and become the dominant
population of bacteria. Following the ascent of resistant mutants, the densities
of bacteria in these simple communities become limited by resources rather than
the phage. Despite the evolution of resistant hosts, upon which the phage cannot
replicate, the lytic phage population is most commonly maintained in an apparently
stable state with the resistant bacteria. Several mechanisms have been put forward
to account for this result. Here we report the results of population dynamic/evolution
experiments with a virulent mutant of phage Lambda, λVIR, and Escherichia coli
in serial transfer cultures. We show that, following the ascent of λVIR-resistant
bacteria, λVIRis maintained in the majority of cases in maltose-limited minimal
media and in all cases in nutrient-rich broth. Using mathematical models and experiments,
we show that the dominant mechanism responsible for maintenance of λVIRin these
resource-limited populations dominated by resistant E. coli is a high rate of
either phenotypic or genetic transition from resistance to susceptibility—a hitherto
undemonstrated mechanism we term "leaky resistance." We discuss the
implications of leaky resistance to our understanding of the conditions for the
maintenance of phage in populations of bacteria—their “existence conditions.”.
article_number: '2005971'
article_processing_charge: Yes
author:
- first_name: Waqas
full_name: Chaudhry, Waqas
last_name: Chaudhry
- first_name: Maros
full_name: Pleska, Maros
id: 4569785E-F248-11E8-B48F-1D18A9856A87
last_name: Pleska
orcid: 0000-0001-7460-7479
- first_name: Nilang
full_name: Shah, Nilang
last_name: Shah
- first_name: Howard
full_name: Weiss, Howard
last_name: Weiss
- first_name: Ingrid
full_name: Mccall, Ingrid
last_name: Mccall
- first_name: Justin
full_name: Meyer, Justin
last_name: Meyer
- first_name: Animesh
full_name: Gupta, Animesh
last_name: Gupta
- first_name: Calin C
full_name: Guet, Calin C
id: 47F8433E-F248-11E8-B48F-1D18A9856A87
last_name: Guet
orcid: 0000-0001-6220-2052
- first_name: Bruce
full_name: Levin, Bruce
last_name: Levin
citation:
ama: Chaudhry W, Pleska M, Shah N, et al. Leaky resistance and the conditions for
the existence of lytic bacteriophage. PLoS Biology. 2018;16(8). doi:10.1371/journal.pbio.2005971
apa: Chaudhry, W., Pleska, M., Shah, N., Weiss, H., Mccall, I., Meyer, J., … Levin,
B. (2018). Leaky resistance and the conditions for the existence of lytic bacteriophage.
PLoS Biology. Public Library of Science. https://doi.org/10.1371/journal.pbio.2005971
chicago: Chaudhry, Waqas, Maros Pleska, Nilang Shah, Howard Weiss, Ingrid Mccall,
Justin Meyer, Animesh Gupta, Calin C Guet, and Bruce Levin. “Leaky Resistance
and the Conditions for the Existence of Lytic Bacteriophage.” PLoS Biology.
Public Library of Science, 2018. https://doi.org/10.1371/journal.pbio.2005971.
ieee: W. Chaudhry et al., “Leaky resistance and the conditions for the existence
of lytic bacteriophage,” PLoS Biology, vol. 16, no. 8. Public Library of
Science, 2018.
ista: Chaudhry W, Pleska M, Shah N, Weiss H, Mccall I, Meyer J, Gupta A, Guet CC,
Levin B. 2018. Leaky resistance and the conditions for the existence of lytic
bacteriophage. PLoS Biology. 16(8), 2005971.
mla: Chaudhry, Waqas, et al. “Leaky Resistance and the Conditions for the Existence
of Lytic Bacteriophage.” PLoS Biology, vol. 16, no. 8, 2005971, Public
Library of Science, 2018, doi:10.1371/journal.pbio.2005971.
short: W. Chaudhry, M. Pleska, N. Shah, H. Weiss, I. Mccall, J. Meyer, A. Gupta,
C.C. Guet, B. Levin, PLoS Biology 16 (2018).
date_created: 2018-12-11T11:44:32Z
date_published: 2018-08-16T00:00:00Z
date_updated: 2023-09-13T08:45:41Z
day: '16'
ddc:
- '570'
department:
- _id: CaGu
doi: 10.1371/journal.pbio.2005971
external_id:
isi:
- '000443383300024'
file:
- access_level: open_access
checksum: 527076f78265cd4ea192cd1569851587
content_type: application/pdf
creator: dernst
date_created: 2018-12-17T12:55:31Z
date_updated: 2020-07-14T12:48:10Z
file_id: '5706'
file_name: 2018_Plos_Chaudhry.pdf
file_size: 4007095
relation: main_file
file_date_updated: 2020-07-14T12:48:10Z
has_accepted_license: '1'
intvolume: ' 16'
isi: 1
issue: '8'
language:
- iso: eng
month: '08'
oa: 1
oa_version: Published Version
publication: PLoS Biology
publication_status: published
publisher: Public Library of Science
publist_id: '7972'
quality_controlled: '1'
related_material:
record:
- id: '9810'
relation: research_data
status: public
scopus_import: '1'
status: public
title: Leaky resistance and the conditions for the existence of lytic bacteriophage
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: journal_article
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
volume: 16
year: '2018'
...
---
_id: '8547'
abstract:
- lang: eng
text: The cerebral cortex contains multiple hierarchically organized areas with
distinctive cytoarchitectonical patterns, but the cellular mechanisms underlying
the emergence of this diversity remain unclear. Here, we have quantitatively investigated
the neuronal output of individual progenitor cells in the ventricular zone of
the developing mouse neocortex using a combination of methods that together circumvent
the biases and limitations of individual approaches. We found that individual
cortical progenitor cells show a high degree of stochasticity and generate pyramidal
cell lineages that adopt a wide range of laminar configurations. Mathematical
modelling these lineage data suggests that a small number of progenitor cell populations,
each generating pyramidal cells following different stochastic developmental programs,
suffice to generate the heterogenous complement of pyramidal cell lineages that
collectively build the complex cytoarchitecture of the neocortex.
acknowledgement: We thank I. Andrew and S.E. Bae for excellent technical assistance,
F. Gage for plasmids, and K. Nave (Nex-Cre) for mouse colonies. We thank members
of the Marín and Rico laboratories for stimulating discussions and ideas. Our research
on this topic is supported by grants from the European Research Council (ERC-2017-AdG
787355 to O.M and ERC2016-CoG 725780 to S.H.) and Wellcome Trust (103714MA) to O.M.
L.L. was the recipient of an EMBO long-term postdoctoral fellowship, R.B. received
support from FWF Lise-Meitner program (M 2416) and F.K.W. was supported by an EMBO
postdoctoral fellowship and is currently a Marie Skłodowska-Curie Fellow from the
European Commission under the H2020 Programme.
article_processing_charge: No
author:
- first_name: Alfredo
full_name: Llorca, Alfredo
last_name: Llorca
- first_name: Gabriele
full_name: Ciceri, Gabriele
last_name: Ciceri
- first_name: Robert J
full_name: Beattie, Robert J
id: 2E26DF60-F248-11E8-B48F-1D18A9856A87
last_name: Beattie
orcid: 0000-0002-8483-8753
- first_name: Fong K.
full_name: Wong, Fong K.
last_name: Wong
- first_name: Giovanni
full_name: Diana, Giovanni
last_name: Diana
- first_name: Eleni
full_name: Serafeimidou, Eleni
last_name: Serafeimidou
- first_name: Marian
full_name: Fernández-Otero, Marian
last_name: Fernández-Otero
- first_name: Carmen
full_name: Streicher, Carmen
id: 36BCB99C-F248-11E8-B48F-1D18A9856A87
last_name: Streicher
- first_name: Sebastian J.
full_name: Arnold, Sebastian J.
last_name: Arnold
- first_name: Martin
full_name: Meyer, Martin
last_name: Meyer
- first_name: Simon
full_name: Hippenmeyer, Simon
id: 37B36620-F248-11E8-B48F-1D18A9856A87
last_name: Hippenmeyer
orcid: 0000-0003-2279-1061
- first_name: Miguel
full_name: Maravall, Miguel
last_name: Maravall
- first_name: Oscar
full_name: Marín, Oscar
last_name: Marín
citation:
ama: Llorca A, Ciceri G, Beattie RJ, et al. Heterogeneous progenitor cell behaviors
underlie the assembly of neocortical cytoarchitecture. bioRxiv. doi:10.1101/494088
apa: Llorca, A., Ciceri, G., Beattie, R. J., Wong, F. K., Diana, G., Serafeimidou,
E., … Marín, O. (n.d.). Heterogeneous progenitor cell behaviors underlie the assembly
of neocortical cytoarchitecture. bioRxiv. Cold Spring Harbor Laboratory.
https://doi.org/10.1101/494088
chicago: Llorca, Alfredo, Gabriele Ciceri, Robert J Beattie, Fong K. Wong, Giovanni
Diana, Eleni Serafeimidou, Marian Fernández-Otero, et al. “Heterogeneous Progenitor
Cell Behaviors Underlie the Assembly of Neocortical Cytoarchitecture.” BioRxiv.
Cold Spring Harbor Laboratory, n.d. https://doi.org/10.1101/494088.
ieee: A. Llorca et al., “Heterogeneous progenitor cell behaviors underlie
the assembly of neocortical cytoarchitecture,” bioRxiv. Cold Spring Harbor
Laboratory.
ista: Llorca A, Ciceri G, Beattie RJ, Wong FK, Diana G, Serafeimidou E, Fernández-Otero
M, Streicher C, Arnold SJ, Meyer M, Hippenmeyer S, Maravall M, Marín O. Heterogeneous
progenitor cell behaviors underlie the assembly of neocortical cytoarchitecture.
bioRxiv, 10.1101/494088.
mla: Llorca, Alfredo, et al. “Heterogeneous Progenitor Cell Behaviors Underlie the
Assembly of Neocortical Cytoarchitecture.” BioRxiv, Cold Spring Harbor
Laboratory, doi:10.1101/494088.
short: A. Llorca, G. Ciceri, R.J. Beattie, F.K. Wong, G. Diana, E. Serafeimidou,
M. Fernández-Otero, C. Streicher, S.J. Arnold, M. Meyer, S. Hippenmeyer, M. Maravall,
O. Marín, BioRxiv (n.d.).
date_created: 2020-09-21T12:01:50Z
date_published: 2018-12-13T00:00:00Z
date_updated: 2024-10-22T10:46:39Z
day: '13'
department:
- _id: SiHi
doi: 10.1101/494088
ec_funded: 1
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.1101/494088
month: '12'
oa: 1
oa_version: Preprint
project:
- _id: 260018B0-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '725780'
name: Principles of Neural Stem Cell Lineage Progression in Cerebral Cortex Development
- _id: 264E56E2-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: M02416
name: Molecular Mechanisms Regulating Gliogenesis in the Neocortex
publication: bioRxiv
publication_status: submitted
publisher: Cold Spring Harbor Laboratory
status: public
title: Heterogeneous progenitor cell behaviors underlie the assembly of neocortical
cytoarchitecture
type: preprint
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
year: '2018'
...
---
_id: '86'
abstract:
- lang: eng
text: Responsiveness—the requirement that every request to a system be eventually
handled—is one of the fundamental liveness properties of a reactive system. Average
response time is a quantitative measure for the responsiveness requirement used
commonly in performance evaluation. We show how average response time can be computed
on state-transition graphs, on Markov chains, and on game graphs. In all three
cases, we give polynomial-time algorithms.
acknowledgement: 'This research was supported in part by the Austrian Science Fund
(FWF) under grants S11402-N23, S11407-N23 (RiSE/SHiNE) and Z211-N23 (Wittgenstein
Award), ERC Start grant (279307: Graph Games), Vienna Science and Technology Fund
(WWTF) through project ICT15-003 and by the National Science Centre (NCN), Poland
under grant 2014/15/D/ST6/04543.'
alternative_title:
- LNCS
author:
- 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: Jan
full_name: Otop, Jan
id: 2FC5DA74-F248-11E8-B48F-1D18A9856A87
last_name: Otop
citation:
ama: 'Chatterjee K, Henzinger TA, Otop J. Computing average response time. In: Lohstroh
M, Derler P, Sirjani M, eds. Principles of Modeling. Vol 10760. Springer;
2018:143-161. doi:10.1007/978-3-319-95246-8_9'
apa: Chatterjee, K., Henzinger, T. A., & Otop, J. (2018). Computing average
response time. In M. Lohstroh, P. Derler, & M. Sirjani (Eds.), Principles
of Modeling (Vol. 10760, pp. 143–161). Springer. https://doi.org/10.1007/978-3-319-95246-8_9
chicago: Chatterjee, Krishnendu, Thomas A Henzinger, and Jan Otop. “Computing Average
Response Time.” In Principles of Modeling, edited by Marten Lohstroh, Patricia
Derler, and Marjan Sirjani, 10760:143–61. Springer, 2018. https://doi.org/10.1007/978-3-319-95246-8_9.
ieee: K. Chatterjee, T. A. Henzinger, and J. Otop, “Computing average response time,”
in Principles of Modeling, vol. 10760, M. Lohstroh, P. Derler, and M. Sirjani,
Eds. Springer, 2018, pp. 143–161.
ista: 'Chatterjee K, Henzinger TA, Otop J. 2018.Computing average response time.
In: Principles of Modeling. LNCS, vol. 10760, 143–161.'
mla: Chatterjee, Krishnendu, et al. “Computing Average Response Time.” Principles
of Modeling, edited by Marten Lohstroh et al., vol. 10760, Springer, 2018,
pp. 143–61, doi:10.1007/978-3-319-95246-8_9.
short: K. Chatterjee, T.A. Henzinger, J. Otop, in:, M. Lohstroh, P. Derler, M. Sirjani
(Eds.), Principles of Modeling, Springer, 2018, pp. 143–161.
date_created: 2018-12-11T11:44:33Z
date_published: 2018-07-20T00:00:00Z
date_updated: 2025-04-15T06:26:15Z
day: '20'
ddc:
- '000'
department:
- _id: KrCh
- _id: ToHe
doi: 10.1007/978-3-319-95246-8_9
ec_funded: 1
editor:
- first_name: Marten
full_name: Lohstroh, Marten
last_name: Lohstroh
- first_name: Patricia
full_name: Derler, Patricia
last_name: Derler
- first_name: Marjan
full_name: Sirjani, Marjan
last_name: Sirjani
file:
- access_level: open_access
checksum: 9995c6ce6957333baf616fc4f20be597
content_type: application/pdf
creator: dernst
date_created: 2019-11-19T08:22:18Z
date_updated: 2020-07-14T12:48:14Z
file_id: '7053'
file_name: 2018_PrinciplesModeling_Chatterjee.pdf
file_size: 516307
relation: main_file
file_date_updated: 2020-07-14T12:48:14Z
has_accepted_license: '1'
intvolume: ' 10760'
language:
- iso: eng
month: '07'
oa: 1
oa_version: Submitted Version
page: 143 - 161
project:
- _id: 25832EC2-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: S 11407_N23
name: Rigorous Systems Engineering
- _id: 25863FF4-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: S11407
name: Game Theory
- _id: 25F42A32-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: Z211
name: Formal methods for the design and analysis of complex systems
- _id: 2581B60A-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '279307'
name: 'Quantitative Graph Games: Theory and Applications'
- _id: 25892FC0-B435-11E9-9278-68D0E5697425
grant_number: ICT15-003
name: Efficient Algorithms for Computer Aided Verification
publication: Principles of Modeling
publication_status: published
publisher: Springer
publist_id: '7968'
quality_controlled: '1'
scopus_import: 1
status: public
title: Computing average response time
type: book_chapter
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 10760
year: '2018'
...
---
_id: '8618'
abstract:
- lang: eng
text: The reversibly switchable fluorescent proteins (RSFPs) commonly used for RESOLFT
nanoscopy have been developed from fluorescent proteins of the GFP superfamily.
These proteins are bright, but exhibit several drawbacks such as relatively large
size, oxygen-dependence, sensitivity to low pH, and limited switching speed. Therefore,
RSFPs from other origins with improved properties need to be explored. Here, we
report the development of two RSFPs based on the LOV domain of the photoreceptor
protein YtvA from Bacillus subtilis. LOV domains obtain their fluorescence by
association with the abundant cellular cofactor flavin mononucleotide (FMN). Under
illumination with blue and ultraviolet light, they undergo a photocycle, making
these proteins inherently photoswitchable. Our first improved variant, rsLOV1,
can be used for RESOLFT imaging, whereas rsLOV2 proved useful for STED nanoscopy
of living cells with a resolution of down to 50 nm. In addition to their smaller
size compared to GFP-related proteins (17 kDa instead of 27 kDa) and their usability
at low pH, rsLOV1 and rsLOV2 exhibit faster switching kinetics, switching on and
off 3 times faster than rsEGFP2, the fastest-switching RSFP reported to date.
Therefore, LOV-domain-based RSFPs have potential for applications where the switching
speed of GFP-based proteins is limiting.
article_number: '2724'
article_processing_charge: No
article_type: original
author:
- first_name: Carola
full_name: Gregor, Carola
last_name: Gregor
- first_name: Sven C.
full_name: Sidenstein, Sven C.
last_name: Sidenstein
- first_name: Martin
full_name: Andresen, Martin
last_name: Andresen
- first_name: Steffen J.
full_name: Sahl, Steffen J.
last_name: Sahl
- first_name: Johann G
full_name: Danzl, Johann G
id: 42EFD3B6-F248-11E8-B48F-1D18A9856A87
last_name: Danzl
orcid: 0000-0001-8559-3973
- first_name: Stefan W.
full_name: Hell, Stefan W.
last_name: Hell
citation:
ama: Gregor C, Sidenstein SC, Andresen M, Sahl SJ, Danzl JG, Hell SW. Novel reversibly
switchable fluorescent proteins for RESOLFT and STED nanoscopy engineered from
the bacterial photoreceptor YtvA. Scientific Reports. 2018;8. doi:10.1038/s41598-018-19947-1
apa: Gregor, C., Sidenstein, S. C., Andresen, M., Sahl, S. J., Danzl, J. G., &
Hell, S. W. (2018). Novel reversibly switchable fluorescent proteins for RESOLFT
and STED nanoscopy engineered from the bacterial photoreceptor YtvA. Scientific
Reports. Springer Nature. https://doi.org/10.1038/s41598-018-19947-1
chicago: Gregor, Carola, Sven C. Sidenstein, Martin Andresen, Steffen J. Sahl, Johann
G Danzl, and Stefan W. Hell. “Novel Reversibly Switchable Fluorescent Proteins
for RESOLFT and STED Nanoscopy Engineered from the Bacterial Photoreceptor YtvA.”
Scientific Reports. Springer Nature, 2018. https://doi.org/10.1038/s41598-018-19947-1.
ieee: C. Gregor, S. C. Sidenstein, M. Andresen, S. J. Sahl, J. G. Danzl, and S.
W. Hell, “Novel reversibly switchable fluorescent proteins for RESOLFT and STED
nanoscopy engineered from the bacterial photoreceptor YtvA,” Scientific Reports,
vol. 8. Springer Nature, 2018.
ista: Gregor C, Sidenstein SC, Andresen M, Sahl SJ, Danzl JG, Hell SW. 2018. Novel
reversibly switchable fluorescent proteins for RESOLFT and STED nanoscopy engineered
from the bacterial photoreceptor YtvA. Scientific Reports. 8, 2724.
mla: Gregor, Carola, et al. “Novel Reversibly Switchable Fluorescent Proteins for
RESOLFT and STED Nanoscopy Engineered from the Bacterial Photoreceptor YtvA.”
Scientific Reports, vol. 8, 2724, Springer Nature, 2018, doi:10.1038/s41598-018-19947-1.
short: C. Gregor, S.C. Sidenstein, M. Andresen, S.J. Sahl, J.G. Danzl, S.W. Hell,
Scientific Reports 8 (2018).
date_created: 2020-10-06T16:33:37Z
date_published: 2018-02-09T00:00:00Z
date_updated: 2024-10-21T06:02:43Z
day: '09'
ddc:
- '570'
department:
- _id: JoDa
doi: 10.1038/s41598-018-19947-1
external_id:
isi:
- '000424630400037'
pmid:
- '29426833'
file:
- access_level: open_access
checksum: e642080fcbde9584c63544f587c74f03
content_type: application/pdf
creator: dernst
date_created: 2020-10-06T16:35:16Z
date_updated: 2020-10-06T16:35:16Z
file_id: '8619'
file_name: 2018_ScientificReports_Gregor.pdf
file_size: 2818077
relation: main_file
success: 1
file_date_updated: 2020-10-06T16:35:16Z
has_accepted_license: '1'
intvolume: ' 8'
isi: 1
keyword:
- Multidisciplinary
language:
- iso: eng
month: '02'
oa: 1
oa_version: Published Version
pmid: 1
publication: Scientific Reports
publication_identifier:
issn:
- 2045-2322
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
scopus_import: '1'
status: public
title: Novel reversibly switchable fluorescent proteins for RESOLFT and STED nanoscopy
engineered from the bacterial photoreceptor YtvA
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: journal_article
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
volume: 8
year: '2018'
...
---
_id: '913'
abstract:
- lang: eng
text: Coordinated cell polarization in developing tissues is a recurrent theme in
multicellular organisms. In plants, a directional distribution of the plant hormone
auxin is at the core of many developmental programs. A feedback regulation of
auxin on the polarized localization of PIN auxin transporters in individual cells
has been proposed as a self-organizing mechanism for coordinated tissue polarization,
but the molecular mechanisms linking auxin signalling to PIN-dependent auxin transport
remain unknown. We performed a microarray-based approach to find regulators of
the auxin-induced PIN relocation in the Arabidopsis thaliana root. We identified
a subset of a family of phosphatidylinositol transfer proteins (PITP), the PATELLINs
(PATL). Here, we show that PATLs are expressed in partially overlapping cells
types in different tissues going through mitosis or initiating differentiation
programs. PATLs are plasma membrane-associated proteins accumulated in Arabidopsis
embryos, primary roots, lateral root primordia, and developing stomata. Higher
order patl mutants display reduced PIN1 repolarization in response to auxin, shorter
root apical meristem, and drastic defects in embryo and seedling development.
This suggests PATLs redundantly play a crucial role in polarity and patterning
in Arabidopsis.
article_number: jcs.204198
article_processing_charge: No
author:
- first_name: Ricardo
full_name: Tejos, Ricardo
last_name: Tejos
- first_name: Cecilia
full_name: Rodríguez Furlán, Cecilia
last_name: Rodríguez Furlán
- first_name: Maciek
full_name: Adamowski, Maciek
id: 45F536D2-F248-11E8-B48F-1D18A9856A87
last_name: Adamowski
orcid: 0000-0001-6463-5257
- first_name: Michael
full_name: Sauer, Michael
last_name: Sauer
- first_name: Lorena
full_name: Norambuena, Lorena
last_name: Norambuena
- first_name: Jirí
full_name: Friml, Jirí
id: 4159519E-F248-11E8-B48F-1D18A9856A87
last_name: Friml
orcid: 0000-0002-8302-7596
citation:
ama: Tejos R, Rodríguez Furlán C, Adamowski M, Sauer M, Norambuena L, Friml J. PATELLINS
are regulators of auxin mediated PIN1 relocation and plant development in Arabidopsis
thaliana. Journal of Cell Science. 2018;131(2). doi:10.1242/jcs.204198
apa: Tejos, R., Rodríguez Furlán, C., Adamowski, M., Sauer, M., Norambuena, L.,
& Friml, J. (2018). PATELLINS are regulators of auxin mediated PIN1 relocation
and plant development in Arabidopsis thaliana. Journal of Cell Science.
Company of Biologists. https://doi.org/10.1242/jcs.204198
chicago: Tejos, Ricardo, Cecilia Rodríguez Furlán, Maciek Adamowski, Michael Sauer,
Lorena Norambuena, and Jiří Friml. “PATELLINS Are Regulators of Auxin Mediated
PIN1 Relocation and Plant Development in Arabidopsis Thaliana.” Journal of
Cell Science. Company of Biologists, 2018. https://doi.org/10.1242/jcs.204198.
ieee: R. Tejos, C. Rodríguez Furlán, M. Adamowski, M. Sauer, L. Norambuena, and
J. Friml, “PATELLINS are regulators of auxin mediated PIN1 relocation and plant
development in Arabidopsis thaliana,” Journal of Cell Science, vol. 131,
no. 2. Company of Biologists, 2018.
ista: Tejos R, Rodríguez Furlán C, Adamowski M, Sauer M, Norambuena L, Friml J.
2018. PATELLINS are regulators of auxin mediated PIN1 relocation and plant development
in Arabidopsis thaliana. Journal of Cell Science. 131(2), jcs. 204198.
mla: Tejos, Ricardo, et al. “PATELLINS Are Regulators of Auxin Mediated PIN1 Relocation
and Plant Development in Arabidopsis Thaliana.” Journal of Cell Science,
vol. 131, no. 2, jcs. 204198, Company of Biologists, 2018, doi:10.1242/jcs.204198.
short: R. Tejos, C. Rodríguez Furlán, M. Adamowski, M. Sauer, L. Norambuena, J.
Friml, Journal of Cell Science 131 (2018).
corr_author: '1'
date_created: 2018-12-11T11:49:10Z
date_published: 2018-01-29T00:00:00Z
date_updated: 2025-07-10T12:01:38Z
day: '29'
ddc:
- '581'
department:
- _id: JiFr
doi: 10.1242/jcs.204198
ec_funded: 1
external_id:
isi:
- '000424842400019'
file:
- access_level: open_access
checksum: bf156c20a4f117b4b932370d54cbac8c
content_type: application/pdf
creator: dernst
date_created: 2019-04-12T08:46:32Z
date_updated: 2020-07-14T12:48:15Z
file_id: '6299'
file_name: 2017_adamowski_PATELLINS_are.pdf
file_size: 14925985
relation: main_file
file_date_updated: 2020-07-14T12:48:15Z
has_accepted_license: '1'
intvolume: ' 131'
isi: 1
issue: '2'
language:
- iso: eng
month: '01'
oa: 1
oa_version: Published Version
project:
- _id: 25716A02-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '282300'
name: Polarity and subcellular dynamics in plants
publication: Journal of Cell Science
publication_identifier:
issn:
- 0021-9533
publication_status: published
publisher: Company of Biologists
publist_id: '6530'
pubrep_id: '988'
quality_controlled: '1'
scopus_import: '1'
status: public
title: PATELLINS are regulators of auxin mediated PIN1 relocation and plant development
in Arabidopsis thaliana
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 131
year: '2018'
...
---
_id: '9229'
alternative_title:
- Molecular and cellular neuroscience
article_processing_charge: No
article_type: letter_note
author:
- first_name: Johann G
full_name: Danzl, Johann G
id: 42EFD3B6-F248-11E8-B48F-1D18A9856A87
last_name: Danzl
orcid: 0000-0001-8559-3973
citation:
ama: Danzl JG. Diffraction-unlimited optical imaging for synaptic physiology. Opera
Medica et Physiologica. 2018;4(S1):11. doi:10.20388/omp2018.00s1.001
apa: Danzl, J. G. (2018). Diffraction-unlimited optical imaging for synaptic physiology.
Opera Medica et Physiologica. Lobachevsky State University of Nizhny Novgorod.
https://doi.org/10.20388/omp2018.00s1.001
chicago: Danzl, Johann G. “Diffraction-Unlimited Optical Imaging for Synaptic Physiology.”
Opera Medica et Physiologica. Lobachevsky State University of Nizhny Novgorod,
2018. https://doi.org/10.20388/omp2018.00s1.001.
ieee: J. G. Danzl, “Diffraction-unlimited optical imaging for synaptic physiology,”
Opera Medica et Physiologica, vol. 4, no. S1. Lobachevsky State University
of Nizhny Novgorod, p. 11, 2018.
ista: Danzl JG. 2018. Diffraction-unlimited optical imaging for synaptic physiology.
Opera Medica et Physiologica. 4(S1), 11.
mla: Danzl, Johann G. “Diffraction-Unlimited Optical Imaging for Synaptic Physiology.”
Opera Medica et Physiologica, vol. 4, no. S1, Lobachevsky State University
of Nizhny Novgorod, 2018, p. 11, doi:10.20388/omp2018.00s1.001.
short: J.G. Danzl, Opera Medica et Physiologica 4 (2018) 11.
date_created: 2021-03-07T23:01:25Z
date_published: 2018-06-30T00:00:00Z
date_updated: 2021-12-03T07:31:05Z
day: '30'
department:
- _id: JoDa
doi: 10.20388/omp2018.00s1.001
intvolume: ' 4'
issue: S1
language:
- iso: eng
main_file_link:
- open_access: '1'
url: http://operamedphys.org/content/molecular-and-cellular-neuroscience
month: '06'
oa: 1
oa_version: Published Version
page: '11'
publication: Opera Medica et Physiologica
publication_identifier:
eissn:
- 2500-2295
issn:
- 2500-2287
publication_status: published
publisher: Lobachevsky State University of Nizhny Novgorod
quality_controlled: '1'
scopus_import: '1'
status: public
title: Diffraction-unlimited optical imaging for synaptic physiology
type: journal_article
user_id: 8b945eb4-e2f2-11eb-945a-df72226e66a9
volume: 4
year: '2018'
...
---
_id: '9471'
abstract:
- lang: eng
text: The DEMETER (DME) DNA glycosylase catalyzes genome-wide DNA demethylation
and is required for endosperm genomic imprinting and embryo viability. Targets
of DME-mediated DNA demethylation reside in small, euchromatic, AT-rich transposons
and at the boundaries of large transposons, but how DME interacts with these diverse
chromatin states is unknown. The STRUCTURE SPECIFIC RECOGNITION PROTEIN 1 (SSRP1)
subunit of the chromatin remodeler FACT (facilitates chromatin transactions),
was previously shown to be involved in the DME-dependent regulation of genomic
imprinting in Arabidopsis endosperm. Therefore, to investigate the interaction
between DME and chromatin, we focused on the activity of the two FACT subunits,
SSRP1 and SUPPRESSOR of TY16 (SPT16), during reproduction in Arabidopsis. We found
that FACT colocalizes with nuclear DME in vivo, and that DME has two classes of
target sites, the first being euchromatic and accessible to DME, but the second,
representing over half of DME targets, requiring the action of FACT for DME-mediated
DNA demethylation genome-wide. Our results show that the FACT-dependent DME targets
are GC-rich heterochromatin domains with high nucleosome occupancy enriched with
H3K9me2 and H3K27me1. Further, we demonstrate that heterochromatin-associated
linker histone H1 specifically mediates the requirement for FACT at a subset of
DME-target loci. Overall, our results demonstrate that FACT is required for DME
targeting by facilitating its access to heterochromatin.
article_processing_charge: No
article_type: original
author:
- first_name: Jennifer M.
full_name: Frost, Jennifer M.
last_name: Frost
- first_name: M. Yvonne
full_name: Kim, M. Yvonne
last_name: Kim
- first_name: Guen Tae
full_name: Park, Guen Tae
last_name: Park
- first_name: Ping-Hung
full_name: Hsieh, Ping-Hung
last_name: Hsieh
- first_name: Miyuki
full_name: Nakamura, Miyuki
last_name: Nakamura
- first_name: Samuel J. H.
full_name: Lin, Samuel J. H.
last_name: Lin
- first_name: Hyunjin
full_name: Yoo, Hyunjin
last_name: Yoo
- first_name: Jaemyung
full_name: Choi, Jaemyung
last_name: Choi
- first_name: Yoko
full_name: Ikeda, Yoko
last_name: Ikeda
- first_name: Tetsu
full_name: Kinoshita, Tetsu
last_name: Kinoshita
- first_name: Yeonhee
full_name: Choi, Yeonhee
last_name: Choi
- first_name: Daniel
full_name: Zilberman, Daniel
id: 6973db13-dd5f-11ea-814e-b3e5455e9ed1
last_name: Zilberman
orcid: 0000-0002-0123-8649
- first_name: Robert L.
full_name: Fischer, Robert L.
last_name: Fischer
citation:
ama: Frost JM, Kim MY, Park GT, et al. FACT complex is required for DNA demethylation
at heterochromatin during reproduction in Arabidopsis. Proceedings of the National
Academy of Sciences. 2018;115(20):E4720-E4729. doi:10.1073/pnas.1713333115
apa: Frost, J. M., Kim, M. Y., Park, G. T., Hsieh, P.-H., Nakamura, M., Lin, S.
J. H., … Fischer, R. L. (2018). FACT complex is required for DNA demethylation
at heterochromatin during reproduction in Arabidopsis. Proceedings of the National
Academy of Sciences. National Academy of Sciences. https://doi.org/10.1073/pnas.1713333115
chicago: Frost, Jennifer M., M. Yvonne Kim, Guen Tae Park, Ping-Hung Hsieh, Miyuki
Nakamura, Samuel J. H. Lin, Hyunjin Yoo, et al. “FACT Complex Is Required for
DNA Demethylation at Heterochromatin during Reproduction in Arabidopsis.” Proceedings
of the National Academy of Sciences. National Academy of Sciences, 2018. https://doi.org/10.1073/pnas.1713333115.
ieee: J. M. Frost et al., “FACT complex is required for DNA demethylation
at heterochromatin during reproduction in Arabidopsis,” Proceedings of the
National Academy of Sciences, vol. 115, no. 20. National Academy of Sciences,
pp. E4720–E4729, 2018.
ista: Frost JM, Kim MY, Park GT, Hsieh P-H, Nakamura M, Lin SJH, Yoo H, Choi J,
Ikeda Y, Kinoshita T, Choi Y, Zilberman D, Fischer RL. 2018. FACT complex is required
for DNA demethylation at heterochromatin during reproduction in Arabidopsis. Proceedings
of the National Academy of Sciences. 115(20), E4720–E4729.
mla: Frost, Jennifer M., et al. “FACT Complex Is Required for DNA Demethylation
at Heterochromatin during Reproduction in Arabidopsis.” Proceedings of the
National Academy of Sciences, vol. 115, no. 20, National Academy of Sciences,
2018, pp. E4720–29, doi:10.1073/pnas.1713333115.
short: J.M. Frost, M.Y. Kim, G.T. Park, P.-H. Hsieh, M. Nakamura, S.J.H. Lin, H.
Yoo, J. Choi, Y. Ikeda, T. Kinoshita, Y. Choi, D. Zilberman, R.L. Fischer, Proceedings
of the National Academy of Sciences 115 (2018) E4720–E4729.
date_created: 2021-06-07T06:11:28Z
date_published: 2018-05-15T00:00:00Z
date_updated: 2021-12-14T07:53:40Z
day: '15'
ddc:
- '580'
department:
- _id: DaZi
doi: 10.1073/pnas.1713333115
extern: '1'
external_id:
pmid:
- '29712855'
file:
- access_level: open_access
checksum: 810260dc0e3cc3033e15c19ad0dc123e
content_type: application/pdf
creator: asandaue
date_created: 2021-06-07T06:16:38Z
date_updated: 2021-06-07T06:16:38Z
file_id: '9472'
file_name: 2018_PNAS_Frost.pdf
file_size: 3045260
relation: main_file
success: 1
file_date_updated: 2021-06-07T06:16:38Z
has_accepted_license: '1'
intvolume: ' 115'
issue: '20'
keyword:
- Multidisciplinary
language:
- iso: eng
license: https://creativecommons.org/licenses/by-nc-nd/4.0/
month: '05'
oa: 1
oa_version: Published Version
page: E4720-E4729
pmid: 1
publication: Proceedings of the National Academy of Sciences
publication_identifier:
eissn:
- 1091-6490
issn:
- 0027-8424
publication_status: published
publisher: National Academy of Sciences
quality_controlled: '1'
related_material:
link:
- relation: earlier_version
url: 'https://doi.org/10.1101/187674 '
scopus_import: '1'
status: public
title: FACT complex is required for DNA demethylation at heterochromatin during reproduction
in Arabidopsis
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: 8b945eb4-e2f2-11eb-945a-df72226e66a9
volume: 115
year: '2018'
...
---
_id: '9807'
abstract:
- lang: eng
text: Table S1. Genes with highest betweenness. Table S2. Local and Master regulators
up-regulated. Table S3. Local and Master regulators down-regulated (XLSX 23 kb).
article_processing_charge: No
author:
- first_name: Juan
full_name: Higareda Almaraz, Juan
last_name: Higareda Almaraz
- first_name: Michael
full_name: Karbiener, Michael
last_name: Karbiener
- first_name: Maude
full_name: Giroud, Maude
last_name: Giroud
- first_name: Florian
full_name: Pauler, Florian
id: 48EA0138-F248-11E8-B48F-1D18A9856A87
last_name: Pauler
orcid: 0000-0002-7462-0048
- first_name: Teresa
full_name: Gerhalter, Teresa
last_name: Gerhalter
- first_name: Stephan
full_name: Herzig, Stephan
last_name: Herzig
- first_name: Marcel
full_name: Scheideler, Marcel
last_name: Scheideler
citation:
ama: 'Higareda Almaraz J, Karbiener M, Giroud M, et al. Additional file 1: Of Norepinephrine
triggers an immediate-early regulatory network response in primary human white
adipocytes. 2018. doi:10.6084/m9.figshare.7295339.v1'
apa: 'Higareda Almaraz, J., Karbiener, M., Giroud, M., Pauler, F., Gerhalter, T.,
Herzig, S., & Scheideler, M. (2018). Additional file 1: Of Norepinephrine
triggers an immediate-early regulatory network response in primary human white
adipocytes. Springer Nature. https://doi.org/10.6084/m9.figshare.7295339.v1'
chicago: 'Higareda Almaraz, Juan, Michael Karbiener, Maude Giroud, Florian Pauler,
Teresa Gerhalter, Stephan Herzig, and Marcel Scheideler. “Additional File 1: Of
Norepinephrine Triggers an Immediate-Early Regulatory Network Response in Primary
Human White Adipocytes.” Springer Nature, 2018. https://doi.org/10.6084/m9.figshare.7295339.v1.'
ieee: 'J. Higareda Almaraz et al., “Additional file 1: Of Norepinephrine
triggers an immediate-early regulatory network response in primary human white
adipocytes.” Springer Nature, 2018.'
ista: 'Higareda Almaraz J, Karbiener M, Giroud M, Pauler F, Gerhalter T, Herzig
S, Scheideler M. 2018. Additional file 1: Of Norepinephrine triggers an immediate-early
regulatory network response in primary human white adipocytes, Springer Nature,
10.6084/m9.figshare.7295339.v1.'
mla: 'Higareda Almaraz, Juan, et al. Additional File 1: Of Norepinephrine Triggers
an Immediate-Early Regulatory Network Response in Primary Human White Adipocytes.
Springer Nature, 2018, doi:10.6084/m9.figshare.7295339.v1.'
short: J. Higareda Almaraz, M. Karbiener, M. Giroud, F. Pauler, T. Gerhalter, S.
Herzig, M. Scheideler, (2018).
date_created: 2021-08-06T12:26:53Z
date_published: 2018-11-03T00:00:00Z
date_updated: 2023-09-13T09:10:47Z
day: '03'
department:
- _id: SiHi
doi: 10.6084/m9.figshare.7295339.v1
main_file_link:
- open_access: '1'
url: https://doi.org/10.6084/m9.figshare.7295339.v1
month: '11'
oa: 1
oa_version: Published Version
publisher: Springer Nature
related_material:
record:
- id: '20'
relation: used_in_publication
status: public
status: public
title: 'Additional file 1: Of Norepinephrine triggers an immediate-early regulatory
network response in primary human white adipocytes'
type: research_data_reference
user_id: 6785fbc1-c503-11eb-8a32-93094b40e1cf
year: '2018'
...
---
_id: '9808'
abstract:
- lang: eng
text: Table S4. Counts per Gene per Million Reads Mapped. (XLSX 2751 kb).
article_processing_charge: No
author:
- first_name: Juan
full_name: Higareda Almaraz, Juan
last_name: Higareda Almaraz
- first_name: Michael
full_name: Karbiener, Michael
last_name: Karbiener
- first_name: Maude
full_name: Giroud, Maude
last_name: Giroud
- first_name: Florian
full_name: Pauler, Florian
id: 48EA0138-F248-11E8-B48F-1D18A9856A87
last_name: Pauler
orcid: 0000-0002-7462-0048
- first_name: Teresa
full_name: Gerhalter, Teresa
last_name: Gerhalter
- first_name: Stephan
full_name: Herzig, Stephan
last_name: Herzig
- first_name: Marcel
full_name: Scheideler, Marcel
last_name: Scheideler
citation:
ama: 'Higareda Almaraz J, Karbiener M, Giroud M, et al. Additional file 3: Of Norepinephrine
triggers an immediate-early regulatory network response in primary human white
adipocytes. 2018. doi:10.6084/m9.figshare.7295369.v1'
apa: 'Higareda Almaraz, J., Karbiener, M., Giroud, M., Pauler, F., Gerhalter, T.,
Herzig, S., & Scheideler, M. (2018). Additional file 3: Of Norepinephrine
triggers an immediate-early regulatory network response in primary human white
adipocytes. Springer Nature. https://doi.org/10.6084/m9.figshare.7295369.v1'
chicago: 'Higareda Almaraz, Juan, Michael Karbiener, Maude Giroud, Florian Pauler,
Teresa Gerhalter, Stephan Herzig, and Marcel Scheideler. “Additional File 3: Of
Norepinephrine Triggers an Immediate-Early Regulatory Network Response in Primary
Human White Adipocytes.” Springer Nature, 2018. https://doi.org/10.6084/m9.figshare.7295369.v1.'
ieee: 'J. Higareda Almaraz et al., “Additional file 3: Of Norepinephrine
triggers an immediate-early regulatory network response in primary human white
adipocytes.” Springer Nature, 2018.'
ista: 'Higareda Almaraz J, Karbiener M, Giroud M, Pauler F, Gerhalter T, Herzig
S, Scheideler M. 2018. Additional file 3: Of Norepinephrine triggers an immediate-early
regulatory network response in primary human white adipocytes, Springer Nature,
10.6084/m9.figshare.7295369.v1.'
mla: 'Higareda Almaraz, Juan, et al. Additional File 3: Of Norepinephrine Triggers
an Immediate-Early Regulatory Network Response in Primary Human White Adipocytes.
Springer Nature, 2018, doi:10.6084/m9.figshare.7295369.v1.'
short: J. Higareda Almaraz, M. Karbiener, M. Giroud, F. Pauler, T. Gerhalter, S.
Herzig, M. Scheideler, (2018).
date_created: 2021-08-06T12:31:57Z
date_published: 2018-11-03T00:00:00Z
date_updated: 2023-09-13T09:10:47Z
day: '03'
department:
- _id: SiHi
doi: 10.6084/m9.figshare.7295369.v1
main_file_link:
- open_access: '1'
url: https://doi.org/10.6084/m9.figshare.7295369.v1
month: '11'
oa: 1
oa_version: Published Version
publisher: Springer Nature
related_material:
record:
- id: '20'
relation: used_in_publication
status: public
status: public
title: 'Additional file 3: Of Norepinephrine triggers an immediate-early regulatory
network response in primary human white adipocytes'
type: research_data_reference
user_id: 6785fbc1-c503-11eb-8a32-93094b40e1cf
year: '2018'
...
---
_id: '9810'
article_processing_charge: No
author:
- first_name: Waqas
full_name: Chaudhry, Waqas
last_name: Chaudhry
- first_name: Maros
full_name: Pleska, Maros
id: 4569785E-F248-11E8-B48F-1D18A9856A87
last_name: Pleska
orcid: 0000-0001-7460-7479
- first_name: Nilang
full_name: Shah, Nilang
last_name: Shah
- first_name: Howard
full_name: Weiss, Howard
last_name: Weiss
- first_name: Ingrid
full_name: Mccall, Ingrid
last_name: Mccall
- first_name: Justin
full_name: Meyer, Justin
last_name: Meyer
- first_name: Animesh
full_name: Gupta, Animesh
last_name: Gupta
- first_name: Calin C
full_name: Guet, Calin C
id: 47F8433E-F248-11E8-B48F-1D18A9856A87
last_name: Guet
orcid: 0000-0001-6220-2052
- first_name: Bruce
full_name: Levin, Bruce
last_name: Levin
citation:
ama: Chaudhry W, Pleska M, Shah N, et al. Numerical data used in figures. 2018.
doi:10.1371/journal.pbio.2005971.s008
apa: Chaudhry, W., Pleska, M., Shah, N., Weiss, H., Mccall, I., Meyer, J., … Levin,
B. (2018). Numerical data used in figures. Public Library of Science. https://doi.org/10.1371/journal.pbio.2005971.s008
chicago: Chaudhry, Waqas, Maros Pleska, Nilang Shah, Howard Weiss, Ingrid Mccall,
Justin Meyer, Animesh Gupta, Calin C Guet, and Bruce Levin. “Numerical Data Used
in Figures.” Public Library of Science, 2018. https://doi.org/10.1371/journal.pbio.2005971.s008.
ieee: W. Chaudhry et al., “Numerical data used in figures.” Public Library
of Science, 2018.
ista: Chaudhry W, Pleska M, Shah N, Weiss H, Mccall I, Meyer J, Gupta A, Guet CC,
Levin B. 2018. Numerical data used in figures, Public Library of Science, 10.1371/journal.pbio.2005971.s008.
mla: Chaudhry, Waqas, et al. Numerical Data Used in Figures. Public Library
of Science, 2018, doi:10.1371/journal.pbio.2005971.s008.
short: W. Chaudhry, M. Pleska, N. Shah, H. Weiss, I. Mccall, J. Meyer, A. Gupta,
C.C. Guet, B. Levin, (2018).
date_created: 2021-08-06T12:43:44Z
date_published: 2018-08-16T00:00:00Z
date_updated: 2023-09-13T08:45:41Z
day: '16'
department:
- _id: CaGu
doi: 10.1371/journal.pbio.2005971.s008
month: '08'
oa_version: Published Version
publisher: Public Library of Science
related_material:
record:
- id: '82'
relation: used_in_publication
status: public
status: public
title: Numerical data used in figures
type: research_data_reference
user_id: 6785fbc1-c503-11eb-8a32-93094b40e1cf
year: '2018'
...