---
OA_type: closed access
_id: '21819'
abstract:
- lang: eng
text: The ability of molecular photoswitches to convert on/off responses into large
macroscale property change is fundamental to light-responsive materials. However,
moving beyond simple binary responses necessitates the introduction of new elements
that control the chemistry of the photoswitching process at the molecular scale.
To achieve this goal, we designed, synthesized and developed a single photochrome,
based on a modified donor–acceptor Stenhouse adduct (DASA), capable of independently
addressing multiple molecular states. The multi-stage photoswitch enables complex
switching phenomena. To demonstrate this, we show spatial control of the transformation
of a three-stage photoswitch by tuning the population of intermediates along the
multi-step reaction pathway of the DASAs without interfering with either the first
or final stage. This allows for a photonic three-stage logic gate where the secondary
wavelength solely negates the input of the primary wavelength. These results provide
a new strategy to move beyond traditional on/off binary photochromic systems and
enable the design of future molecular logic systems.
article_processing_charge: No
article_type: original
author:
- first_name: Friedrich J
full_name: Stricker, Friedrich J
id: 7aca2cfc-46cf-11f0-abd3-8c96b5186745
last_name: Stricker
- first_name: David M.
full_name: Sanchez, David M.
last_name: Sanchez
- first_name: Umberto
full_name: Raucci, Umberto
last_name: Raucci
- first_name: Neil D.
full_name: Dolinski, Neil D.
last_name: Dolinski
- first_name: Manuel S.
full_name: Zayas, Manuel S.
last_name: Zayas
- first_name: Jan
full_name: Meisner, Jan
last_name: Meisner
- first_name: Craig. J.
full_name: Hawker, Craig. J.
last_name: Hawker
- first_name: Todd. J.
full_name: Martínez, Todd. J.
last_name: Martínez
- first_name: Javier
full_name: Read de Alaniz, Javier
last_name: Read de Alaniz
citation:
ama: Stricker FJ, Sanchez DM, Raucci U, et al. A multi-stage single photochrome
system for controlled photoswitching responses. Nature Chemistry. 2022;14:942-948.
doi:10.1038/s41557-022-00947-8
apa: Stricker, F. J., Sanchez, D. M., Raucci, U., Dolinski, N. D., Zayas, M. S.,
Meisner, J., … Read de Alaniz, J. (2022). A multi-stage single photochrome system
for controlled photoswitching responses. Nature Chemistry. Springer Nature.
https://doi.org/10.1038/s41557-022-00947-8
chicago: Stricker, Friedrich J, David M. Sanchez, Umberto Raucci, Neil D. Dolinski,
Manuel S. Zayas, Jan Meisner, Craig. J. Hawker, Todd. J. Martínez, and Javier
Read de Alaniz. “A Multi-Stage Single Photochrome System for Controlled Photoswitching
Responses.” Nature Chemistry. Springer Nature, 2022. https://doi.org/10.1038/s41557-022-00947-8.
ieee: F. J. Stricker et al., “A multi-stage single photochrome system for
controlled photoswitching responses,” Nature Chemistry, vol. 14. Springer
Nature, pp. 942–948, 2022.
ista: Stricker FJ, Sanchez DM, Raucci U, Dolinski ND, Zayas MS, Meisner J, Hawker
CJ, Martínez TJ, Read de Alaniz J. 2022. A multi-stage single photochrome system
for controlled photoswitching responses. Nature Chemistry. 14, 942–948.
mla: Stricker, Friedrich J., et al. “A Multi-Stage Single Photochrome System for
Controlled Photoswitching Responses.” Nature Chemistry, vol. 14, Springer
Nature, 2022, pp. 942–48, doi:10.1038/s41557-022-00947-8.
short: F.J. Stricker, D.M. Sanchez, U. Raucci, N.D. Dolinski, M.S. Zayas, J. Meisner,
C.J. Hawker, T.J. Martínez, J. Read de Alaniz, Nature Chemistry 14 (2022) 942–948.
date_created: 2026-05-06T10:56:14Z
date_published: 2022-06-09T00:00:00Z
date_updated: 2026-05-18T09:13:44Z
day: '09'
ddc:
- '540'
doi: 10.1038/s41557-022-00947-8
extern: '1'
external_id:
pmid:
- '35681046'
intvolume: ' 14'
language:
- iso: eng
month: '06'
oa_version: None
page: 942-948
pmid: 1
publication: Nature Chemistry
publication_identifier:
eissn:
- 1755-4349
issn:
- 1755-4330
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
scopus_import: '1'
status: public
title: A multi-stage single photochrome system for controlled photoswitching responses
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 14
year: '2022'
...
---
OA_type: green
_id: '21823'
abstract:
- lang: eng
text: DFT calculations were used to find an optimal substitution site on the triene
backbone of a donor–acceptor Stenhouse adduct photoswitch to tune the equillibrium
and switching kinetics of DASA without modifying the donor and acceptor groups.
Using this approach we demonstrate a new means to tuning DASA based photoswitches
by increasing the energy of the closed form relative to the open form. To highlight
the potential of this approach a new DASA derivative bearing a methyl substituent
on the 5-position of the triene was synthesized and the effect of this substitution
was studied using 1H NMR spectroscopy, time-dependent UV-Vis and solvatochromic
analysis. The new DASA derivative shows a higher dark equillibrium, favoring the
open form, and drastically faster thermal recovery than the unsubstituted derivative
with the same donor and acceptor.
article_processing_charge: No
article_type: original
author:
- first_name: Julie A.
full_name: Peterson, Julie A.
last_name: Peterson
- first_name: Friedrich J
full_name: Stricker, Friedrich J
id: 7aca2cfc-46cf-11f0-abd3-8c96b5186745
last_name: Stricker
- first_name: Javier
full_name: Read de Alaniz, Javier
last_name: Read de Alaniz
citation:
ama: Peterson JA, Stricker FJ, Read de Alaniz J. Improving the kinetics and dark
equilibrium of donor-acceptor Stenhouse adduct by triene backbone design. Chemical
Communications. 2022;58(14):2303-2306. doi:10.1039/d1cc06235b
apa: Peterson, J. A., Stricker, F. J., & Read de Alaniz, J. (2022). Improving
the kinetics and dark equilibrium of donor-acceptor Stenhouse adduct by triene
backbone design. Chemical Communications. Royal Society of Chemistry. https://doi.org/10.1039/d1cc06235b
chicago: Peterson, Julie A., Friedrich J Stricker, and Javier Read de Alaniz. “Improving
the Kinetics and Dark Equilibrium of Donor-Acceptor Stenhouse Adduct by Triene
Backbone Design.” Chemical Communications. Royal Society of Chemistry,
2022. https://doi.org/10.1039/d1cc06235b.
ieee: J. A. Peterson, F. J. Stricker, and J. Read de Alaniz, “Improving the kinetics
and dark equilibrium of donor-acceptor Stenhouse adduct by triene backbone design,”
Chemical Communications, vol. 58, no. 14. Royal Society of Chemistry, pp.
2303–2306, 2022.
ista: Peterson JA, Stricker FJ, Read de Alaniz J. 2022. Improving the kinetics and
dark equilibrium of donor-acceptor Stenhouse adduct by triene backbone design.
Chemical Communications. 58(14), 2303–2306.
mla: Peterson, Julie A., et al. “Improving the Kinetics and Dark Equilibrium of
Donor-Acceptor Stenhouse Adduct by Triene Backbone Design.” Chemical Communications,
vol. 58, no. 14, Royal Society of Chemistry, 2022, pp. 2303–06, doi:10.1039/d1cc06235b.
short: J.A. Peterson, F.J. Stricker, J. Read de Alaniz, Chemical Communications
58 (2022) 2303–2306.
date_created: 2026-05-06T10:59:03Z
date_published: 2022-01-17T00:00:00Z
date_updated: 2026-05-18T09:46:30Z
day: '17'
ddc:
- '540'
doi: 10.1039/d1cc06235b
extern: '1'
external_id:
pmid:
- '35075464'
intvolume: ' 58'
issue: '14'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.1039/D1CC06235B
month: '01'
oa: 1
oa_version: Accepted Version
page: 2303-2306
pmid: 1
publication: Chemical Communications
publication_identifier:
eissn:
- 1364-548X
issn:
- 1359-7345
publication_status: published
publisher: Royal Society of Chemistry
quality_controlled: '1'
scopus_import: '1'
status: public
title: Improving the kinetics and dark equilibrium of donor-acceptor Stenhouse adduct
by triene backbone design
type: journal_article
user_id: ba8df636-2132-11f1-aed0-ed93e2281fdd
volume: 58
year: '2022'
...
---
_id: '14520'
abstract:
- lang: eng
text: 'This dataset comprises all data shown in the figures of the submitted article
"Compact vacuum gap transmon qubits: Selective and sensitive probes for superconductor
surface losses" at arxiv.org/abs/2206.14104. Additional raw data are available
from the corresponding author on reasonable request.'
article_processing_charge: No
author:
- first_name: Martin
full_name: Zemlicka, Martin
id: 2DCF8DE6-F248-11E8-B48F-1D18A9856A87
last_name: Zemlicka
orcid: 0009-0005-0878-3032
- first_name: Elena
full_name: Redchenko, Elena
id: 2C21D6E8-F248-11E8-B48F-1D18A9856A87
last_name: Redchenko
- first_name: Matilda
full_name: Peruzzo, Matilda
id: 3F920B30-F248-11E8-B48F-1D18A9856A87
last_name: Peruzzo
orcid: 0000-0002-3415-4628
- first_name: Farid
full_name: Hassani, Farid
id: 2AED110C-F248-11E8-B48F-1D18A9856A87
last_name: Hassani
orcid: 0000-0001-6937-5773
- first_name: Andrea
full_name: Trioni, Andrea
id: 42F71B44-F248-11E8-B48F-1D18A9856A87
last_name: Trioni
- first_name: Shabir
full_name: Barzanjeh, Shabir
id: 2D25E1F6-F248-11E8-B48F-1D18A9856A87
last_name: Barzanjeh
orcid: 0000-0003-0415-1423
- first_name: Johannes M
full_name: Fink, Johannes M
id: 4B591CBA-F248-11E8-B48F-1D18A9856A87
last_name: Fink
orcid: 0000-0001-8112-028X
citation:
ama: 'Zemlicka M, Redchenko E, Peruzzo M, et al. Compact vacuum gap transmon qubits:
Selective and sensitive probes for superconductor surface losses. 2022. doi:10.5281/ZENODO.8408897'
apa: 'Zemlicka, M., Redchenko, E., Peruzzo, M., Hassani, F., Trioni, A., Barzanjeh,
S., & Fink, J. M. (2022). Compact vacuum gap transmon qubits: Selective and
sensitive probes for superconductor surface losses. Zenodo. https://doi.org/10.5281/ZENODO.8408897'
chicago: 'Zemlicka, Martin, Elena Redchenko, Matilda Peruzzo, Farid Hassani, Andrea
Trioni, Shabir Barzanjeh, and Johannes M Fink. “Compact Vacuum Gap Transmon Qubits:
Selective and Sensitive Probes for Superconductor Surface Losses.” Zenodo, 2022.
https://doi.org/10.5281/ZENODO.8408897.'
ieee: 'M. Zemlicka et al., “Compact vacuum gap transmon qubits: Selective
and sensitive probes for superconductor surface losses.” Zenodo, 2022.'
ista: 'Zemlicka M, Redchenko E, Peruzzo M, Hassani F, Trioni A, Barzanjeh S, Fink
JM. 2022. Compact vacuum gap transmon qubits: Selective and sensitive probes for
superconductor surface losses, Zenodo, 10.5281/ZENODO.8408897.'
mla: 'Zemlicka, Martin, et al. Compact Vacuum Gap Transmon Qubits: Selective
and Sensitive Probes for Superconductor Surface Losses. Zenodo, 2022, doi:10.5281/ZENODO.8408897.'
short: M. Zemlicka, E. Redchenko, M. Peruzzo, F. Hassani, A. Trioni, S. Barzanjeh,
J.M. Fink, (2022).
corr_author: '1'
date_created: 2023-11-13T08:09:10Z
date_published: 2022-06-28T00:00:00Z
date_updated: 2026-06-03T07:16:02Z
day: '28'
ddc:
- '530'
department:
- _id: JoFi
doi: 10.5281/ZENODO.8408897
has_accepted_license: '1'
license: https://creativecommons.org/publicdomain/zero/1.0/
main_file_link:
- open_access: '1'
url: https://doi.org/10.5281/ZENODO.8408897
month: '06'
oa: 1
oa_version: Published Version
publisher: Zenodo
related_material:
record:
- id: '14517'
relation: used_in_publication
status: public
status: public
title: 'Compact vacuum gap transmon qubits: Selective and sensitive probes for superconductor
surface losses'
tmp:
image: /images/cc_0.png
legal_code_url: https://creativecommons.org/publicdomain/zero/1.0/legalcode
name: Creative Commons Public Domain Dedication (CC0 1.0)
short: CC0 (1.0)
type: research_data_reference
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
year: '2022'
...
---
_id: '11447'
abstract:
- lang: eng
text: Empirical essays of fitness landscapes suggest that they may be rugged, that
is having multiple fitness peaks. Such fitness landscapes, those that have multiple
peaks, necessarily have special local structures, called reciprocal sign epistasis
(Poelwijk et al. in J Theor Biol 272:141–144, 2011). Here, we investigate the
quantitative relationship between the number of fitness peaks and the number of
reciprocal sign epistatic interactions. Previously, it has been shown (Poelwijk
et al. in J Theor Biol 272:141–144, 2011) that pairwise reciprocal sign epistasis
is a necessary but not sufficient condition for the existence of multiple peaks.
Applying discrete Morse theory, which to our knowledge has never been used in
this context, we extend this result by giving the minimal number of reciprocal
sign epistatic interactions required to create a given number of peaks.
acknowledgement: We are grateful to Herbert Edelsbrunner and Jeferson Zapata for helpful
discussions. Open access funding provided by Austrian Science Fund (FWF). Partially
supported by the ERC Consolidator (771209–CharFL) and the FWF Austrian Science Fund
(I5127-B) grants to FAK.
article_number: '74'
article_processing_charge: Yes (via OA deal)
article_type: original
author:
- first_name: Raimundo J
full_name: Saona Urmeneta, Raimundo J
id: BD1DF4C4-D767-11E9-B658-BC13E6697425
last_name: Saona Urmeneta
orcid: 0000-0001-5103-038X
- first_name: Fyodor
full_name: Kondrashov, Fyodor
id: 44FDEF62-F248-11E8-B48F-1D18A9856A87
last_name: Kondrashov
orcid: 0000-0001-8243-4694
- first_name: Kseniia
full_name: Khudiakova, Kseniia
id: 4E6DC800-AE37-11E9-AC72-31CAE5697425
last_name: Khudiakova
orcid: 0000-0002-6246-1465
citation:
ama: Saona Urmeneta RJ, Kondrashov F, Khudiakova K. Relation between the number
of peaks and the number of reciprocal sign epistatic interactions. Bulletin
of Mathematical Biology. 2022;84(8). doi:10.1007/s11538-022-01029-z
apa: Saona Urmeneta, R. J., Kondrashov, F., & Khudiakova, K. (2022). Relation
between the number of peaks and the number of reciprocal sign epistatic interactions.
Bulletin of Mathematical Biology. Springer Nature. https://doi.org/10.1007/s11538-022-01029-z
chicago: Saona Urmeneta, Raimundo J, Fyodor Kondrashov, and Kseniia Khudiakova.
“Relation between the Number of Peaks and the Number of Reciprocal Sign Epistatic
Interactions.” Bulletin of Mathematical Biology. Springer Nature, 2022.
https://doi.org/10.1007/s11538-022-01029-z.
ieee: R. J. Saona Urmeneta, F. Kondrashov, and K. Khudiakova, “Relation between
the number of peaks and the number of reciprocal sign epistatic interactions,”
Bulletin of Mathematical Biology, vol. 84, no. 8. Springer Nature, 2022.
ista: Saona Urmeneta RJ, Kondrashov F, Khudiakova K. 2022. Relation between the
number of peaks and the number of reciprocal sign epistatic interactions. Bulletin
of Mathematical Biology. 84(8), 74.
mla: Saona Urmeneta, Raimundo J., et al. “Relation between the Number of Peaks and
the Number of Reciprocal Sign Epistatic Interactions.” Bulletin of Mathematical
Biology, vol. 84, no. 8, 74, Springer Nature, 2022, doi:10.1007/s11538-022-01029-z.
short: R.J. Saona Urmeneta, F. Kondrashov, K. Khudiakova, Bulletin of Mathematical
Biology 84 (2022).
corr_author: '1'
date_created: 2022-06-17T16:16:15Z
date_published: 2022-06-17T00:00:00Z
date_updated: 2026-06-12T12:43:34Z
day: '17'
ddc:
- '510'
- '570'
department:
- _id: GradSch
- _id: NiBa
- _id: JaMa
doi: 10.1007/s11538-022-01029-z
ec_funded: 1
external_id:
isi:
- '000812509800001'
pmid:
- '35713756'
file:
- access_level: open_access
checksum: 05a1fe7d10914a00c2bca9b447993a65
content_type: application/pdf
creator: dernst
date_created: 2022-06-20T07:51:32Z
date_updated: 2022-06-20T07:51:32Z
file_id: '11455'
file_name: 2022_BulletinMathBiology_Saona.pdf
file_size: 463025
relation: main_file
success: 1
file_date_updated: 2022-06-20T07:51:32Z
has_accepted_license: '1'
intvolume: ' 84'
isi: 1
issue: '8'
keyword:
- Computational Theory and Mathematics
- General Agricultural and Biological Sciences
- Pharmacology
- General Environmental Science
- General Biochemistry
- Genetics and Molecular Biology
- General Mathematics
- Immunology
- General Neuroscience
language:
- iso: eng
month: '06'
oa: 1
oa_version: Published Version
pmid: 1
project:
- _id: 26580278-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '771209'
name: Characterizing the fitness landscape on population and global scales
- _id: 34e076d6-11ca-11ed-8bc3-aec76c41a181
grant_number: I05127
name: Evolutionary analysis of gene regulation
publication: Bulletin of Mathematical Biology
publication_identifier:
eissn:
- 1522-9602
issn:
- 0092-8240
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
related_material:
link:
- relation: erratum
url: https://doi.org/10.1007/s11538-022-01118-z
record:
- id: '21918'
relation: dissertation_contains
status: public
scopus_import: '1'
status: public
title: Relation between the number of peaks and the number of reciprocal sign epistatic
interactions
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: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 84
year: '2022'
...
---
_id: '10016'
abstract:
- lang: eng
text: 'Auxin has always been at the forefront of research in plant physiology and
development. Since the earliest contemplations by Julius von Sachs and Charles
Darwin, more than a century-long struggle has been waged to understand its function.
This largely reflects the failures, successes, and inevitable progress in the
entire field of plant signaling and development. Here I present 14 stations on
our long and sometimes mystical journey to understand auxin. These highlights
were selected to give a flavor of the field and to show the scope and limits of
our current knowledge. A special focus is put on features that make auxin unique
among phytohormones, such as its dynamic, directional transport network, which
integrates external and internal signals, including self-organizing feedback.
Accented are persistent mysteries and controversies. The unexpected discoveries
related to rapid auxin responses and growth regulation recently disturbed our
contentment regarding understanding of the auxin signaling mechanism. These new
revelations, along with advances in technology, usher us into a new, exciting
era in auxin research. '
acknowledgement: "The author thanks the whole community of researchers consciously
or unconsciously working on questions related to auxin, whose hard work and enthusiasm
contributed to development of this exciting story. Particular thanks go to many\r\nbrilliant
present and past members of the Friml group and our numerous excellent collaborators,
without whom my own personal journey would not be possible. The way of the cross
with its 14 stations is a popular devotion among Roman Catholics and inspires them
to make a spiritual pilgrimage through contemplation of Christ on his last day.
Its aspects of gradual progress, struggle, passion, and revelation served as an
inspiration for the formal depiction of our journey to understanding auxin as described
in this review. It is in no way intended to reflect the personal beliefs of the
author and readers. I am grateful to Nick Barton, Eva Benková, Lenka Caisová, Matyáš
Fendrych, Lukáš Fiedler, Monika Frátriková, Jarmila Frimlová, Michelle Gallei, Jakub
Hajný, Lukas Hoermayer, Alexandra Mally, Ondrˇej Novák, Jan Petrášek, Aleš Pěnčík,
Steffen Vanneste, Tongda Xu, and Zhenbiao Yang for their valuable comments. Special
thanks go to Michelle Gallei for her invaluable assistance with the figures."
article_number: a039859
article_processing_charge: No
article_type: review
author:
- first_name: Jiří
full_name: Friml, Jiří
id: 4159519E-F248-11E8-B48F-1D18A9856A87
last_name: Friml
orcid: 0000-0002-8302-7596
citation:
ama: Friml J. Fourteen stations of auxin. Cold Spring Harbor Perspectives in
Biology. 2022;14(5). doi:10.1101/cshperspect.a039859
apa: Friml, J. (2022). Fourteen stations of auxin. Cold Spring Harbor Perspectives
in Biology. Cold Spring Harbor Laboratory Press. https://doi.org/10.1101/cshperspect.a039859
chicago: Friml, Jiří. “Fourteen Stations of Auxin.” Cold Spring Harbor Perspectives
in Biology. Cold Spring Harbor Laboratory Press, 2022. https://doi.org/10.1101/cshperspect.a039859.
ieee: J. Friml, “Fourteen stations of auxin,” Cold Spring Harbor Perspectives
in Biology, vol. 14, no. 5. Cold Spring Harbor Laboratory Press, 2022.
ista: Friml J. 2022. Fourteen stations of auxin. Cold Spring Harbor Perspectives
in Biology. 14(5), a039859.
mla: Friml, Jiří. “Fourteen Stations of Auxin.” Cold Spring Harbor Perspectives
in Biology, vol. 14, no. 5, a039859, Cold Spring Harbor Laboratory Press,
2022, doi:10.1101/cshperspect.a039859.
short: J. Friml, Cold Spring Harbor Perspectives in Biology 14 (2022).
corr_author: '1'
date_created: 2021-09-14T11:36:53Z
date_published: 2022-05-27T00:00:00Z
date_updated: 2026-06-18T08:35:48Z
day: '27'
ddc:
- '580'
department:
- _id: JiFr
doi: 10.1101/cshperspect.a039859
external_id:
isi:
- '000806563000003'
pmid:
- '34400554'
intvolume: ' 14'
isi: 1
issue: '5'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: 'https://doi.org/10.1101/cshperspect.a039859 '
month: '05'
oa: 1
oa_version: Published Version
pmid: 1
publication: Cold Spring Harbor Perspectives in Biology
publication_identifier:
issn:
- 1943-0264
publication_status: published
publisher: Cold Spring Harbor Laboratory Press
quality_controlled: '1'
scopus_import: '1'
status: public
title: Fourteen stations of auxin
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 14
year: '2022'
...
---
_id: '10181'
abstract:
- lang: eng
text: In this article we study some geometric properties of proximally smooth sets.
First, we introduce a modification of the metric projection and prove its existence.
Then we provide an algorithm for constructing a rectifiable curve between two
sufficiently close points of a proximally smooth set in a uniformly convex and
uniformly smooth Banach space, with the moduli of smoothness and convexity of
power type. Our algorithm returns a reasonably short curve between two sufficiently
close points of a proximally smooth set, is iterative and uses our modification
of the metric projection. We estimate the length of the constructed curve and
its deviation from the segment with the same endpoints. These estimates coincide
up to a constant factor with those for the geodesics in a proximally smooth set
in a Hilbert space.
acknowledgement: Theorem 2 was obtained at Steklov Mathematical Institute RAS and
supported by Russian Science Foundation, grant N 19-11-00087.
article_processing_charge: No
article_type: original
arxiv: 1
author:
- first_name: Grigory
full_name: Ivanov, Grigory
id: 87744F66-5C6F-11EA-AFE0-D16B3DDC885E
last_name: Ivanov
orcid: 0000-0002-5021-3982
- first_name: Mariana S.
full_name: Lopushanski, Mariana S.
last_name: Lopushanski
citation:
ama: Ivanov G, Lopushanski MS. Rectifiable curves in proximally smooth sets. Set-Valued
and Variational Analysis. 2022;30(2):657-675. doi:10.1007/s11228-021-00612-1
apa: Ivanov, G., & Lopushanski, M. S. (2022). Rectifiable curves in proximally
smooth sets. Set-Valued and Variational Analysis. Springer Nature. https://doi.org/10.1007/s11228-021-00612-1
chicago: Ivanov, Grigory, and Mariana S. Lopushanski. “Rectifiable Curves in Proximally
Smooth Sets.” Set-Valued and Variational Analysis. Springer Nature, 2022.
https://doi.org/10.1007/s11228-021-00612-1.
ieee: G. Ivanov and M. S. Lopushanski, “Rectifiable curves in proximally smooth
sets,” Set-Valued and Variational Analysis, vol. 30, no. 2. Springer Nature,
pp. 657–675, 2022.
ista: Ivanov G, Lopushanski MS. 2022. Rectifiable curves in proximally smooth sets.
Set-Valued and Variational Analysis. 30(2), 657–675.
mla: Ivanov, Grigory, and Mariana S. Lopushanski. “Rectifiable Curves in Proximally
Smooth Sets.” Set-Valued and Variational Analysis, vol. 30, no. 2, Springer
Nature, 2022, pp. 657–75, doi:10.1007/s11228-021-00612-1.
short: G. Ivanov, M.S. Lopushanski, Set-Valued and Variational Analysis 30 (2022)
657–675.
date_created: 2021-10-24T22:01:35Z
date_published: 2022-06-01T00:00:00Z
date_updated: 2026-06-18T08:36:30Z
day: '01'
ddc:
- '500'
department:
- _id: UlWa
doi: 10.1007/s11228-021-00612-1
external_id:
arxiv:
- '2012.10691'
isi:
- '000705774800001'
intvolume: ' 30'
isi: 1
issue: '2'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/2012.10691
month: '06'
oa: 1
oa_version: Published Version
page: 657-675
publication: Set-Valued and Variational Analysis
publication_identifier:
eissn:
- 1877-0541
issn:
- 0927-6947
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
scopus_import: '1'
status: public
title: Rectifiable curves in proximally smooth sets
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 30
year: '2022'
...
---
_id: '10639'
abstract:
- lang: eng
text: With more than 80 members worldwide, the Orthobunyavirus genus in the Peribunyaviridae
family is a large genus of enveloped RNA viruses, many of which are emerging pathogens
in humans and livestock. How orthobunyaviruses (OBVs) penetrate and infect mammalian
host cells remains poorly characterized. Here, we investigated the entry mechanisms
of the OBV Germiston (GERV). Viral particles were visualized by cryo-electron
microscopy and appeared roughly spherical with an average diameter of 98 nm. Labeling
of the virus with fluorescent dyes did not adversely affect its infectivity and
allowed the monitoring of single particles in fixed and live cells. Using this
approach, we found that endocytic internalization of bound viruses was asynchronous
and occurred within 30-40 min. The virus entered Rab5a+ early endosomes and, subsequently,
late endosomal vacuoles containing Rab7a but not LAMP-1. Infectious entry did
not require proteolytic cleavage, and endosomal acidification was sufficient and
necessary for viral fusion. Acid-activated penetration began 15-25 min after initiation
of virus internalization and relied on maturation of early endosomes to late endosomes.
The optimal pH for viral membrane fusion was slightly below 6.0, and penetration
was hampered when the potassium influx was abolished. Overall, our study provides
real-time visualization of GERV entry into host cells and demonstrates the importance
of late endosomal maturation in facilitating OBV penetration.
acknowledged_ssus:
- _id: EM-Fac
acknowledgement: This work was supported by INRAE starter funds, Project IDEXLYON (University of Lyon)
within the Programme Investissements d’Avenir (ANR-16-IDEX-0005), and FINOVIAO14
(Fondation pour l’Université de Lyon), all to P.Y.L. This work was also supported by
CellNetworks Research Group funds and Deutsche Forschungsgemeinschaft (DFG) funding
(grant numbers LO-2338/1-1 and LO-2338/3-1) awarded to P.Y.L., Austrian Science Fund
(FWF) grant P31445 to F.K.M.S., a Chinese Scholarship Council (CSC;no. 201904910701)
fellowship to Q.X., and a ministére de l’enseignement supérieur, de la recherche et de
l’innovation (MESRI) doctoral thesis grant to M.D.
article_number: e02146-21
article_processing_charge: No
article_type: original
author:
- first_name: Stefan
full_name: Windhaber, Stefan
last_name: Windhaber
- first_name: Qilin
full_name: Xin, Qilin
last_name: Xin
- first_name: Zina M.
full_name: Uckeley, Zina M.
last_name: Uckeley
- first_name: Jana
full_name: Koch, Jana
last_name: Koch
- first_name: Martin
full_name: Obr, Martin
id: 4741CA5A-F248-11E8-B48F-1D18A9856A87
last_name: Obr
orcid: 0000-0003-1756-6564
- first_name: Céline
full_name: Garnier, Céline
last_name: Garnier
- first_name: Catherine
full_name: Luengo-Guyonnot, Catherine
last_name: Luengo-Guyonnot
- first_name: Maëva
full_name: Duboeuf, Maëva
last_name: Duboeuf
- first_name: Florian KM
full_name: Schur, Florian KM
id: 48AD8942-F248-11E8-B48F-1D18A9856A87
last_name: Schur
orcid: 0000-0003-4790-8078
- first_name: Pierre-Yves
full_name: Lozach, Pierre-Yves
last_name: Lozach
citation:
ama: Windhaber S, Xin Q, Uckeley ZM, et al. The Orthobunyavirus Germiston enters
host cells from late endosomes. Journal of Virology. 2022;96(5). doi:10.1128/jvi.02146-21
apa: Windhaber, S., Xin, Q., Uckeley, Z. M., Koch, J., Obr, M., Garnier, C., … Lozach,
P.-Y. (2022). The Orthobunyavirus Germiston enters host cells from late endosomes.
Journal of Virology. American Society for Microbiology. https://doi.org/10.1128/jvi.02146-21
chicago: Windhaber, Stefan, Qilin Xin, Zina M. Uckeley, Jana Koch, Martin Obr, Céline
Garnier, Catherine Luengo-Guyonnot, Maëva Duboeuf, Florian KM Schur, and Pierre-Yves
Lozach. “The Orthobunyavirus Germiston Enters Host Cells from Late Endosomes.”
Journal of Virology. American Society for Microbiology, 2022. https://doi.org/10.1128/jvi.02146-21.
ieee: S. Windhaber et al., “The Orthobunyavirus Germiston enters host cells
from late endosomes,” Journal of Virology, vol. 96, no. 5. American Society
for Microbiology, 2022.
ista: Windhaber S, Xin Q, Uckeley ZM, Koch J, Obr M, Garnier C, Luengo-Guyonnot
C, Duboeuf M, Schur FK, Lozach P-Y. 2022. The Orthobunyavirus Germiston enters
host cells from late endosomes. Journal of Virology. 96(5), e02146-21.
mla: Windhaber, Stefan, et al. “The Orthobunyavirus Germiston Enters Host Cells
from Late Endosomes.” Journal of Virology, vol. 96, no. 5, e02146-21, American
Society for Microbiology, 2022, doi:10.1128/jvi.02146-21.
short: S. Windhaber, Q. Xin, Z.M. Uckeley, J. Koch, M. Obr, C. Garnier, C. Luengo-Guyonnot,
M. Duboeuf, F.K. Schur, P.-Y. Lozach, Journal of Virology 96 (2022).
date_created: 2022-01-18T10:04:18Z
date_published: 2022-03-01T00:00:00Z
date_updated: 2026-06-18T08:44:25Z
day: '01'
ddc:
- '570'
department:
- _id: FlSc
doi: 10.1128/jvi.02146-21
external_id:
isi:
- '000779305000033'
pmid:
- '35019710'
intvolume: ' 96'
isi: 1
issue: '5'
keyword:
- virology
- insect science
- immunology
- microbiology
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8906410
month: '03'
oa: 1
oa_version: Published Version
pmid: 1
project:
- _id: 26736D6A-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: P31445
name: Structural conservation and diversity in retroviral capsid
publication: Journal of Virology
publication_identifier:
eissn:
- 1098-5514
issn:
- 0022-538X
publication_status: published
publisher: American Society for Microbiology
quality_controlled: '1'
scopus_import: '1'
status: public
title: The Orthobunyavirus Germiston enters host cells from late endosomes
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 96
year: '2022'
...
---
_id: '10583'
abstract:
- lang: eng
text: The synthetic strigolactone (SL) analog, rac-GR24, has been instrumental in
studying the role of SLs as well as karrikins because it activates the receptors
DWARF14 (D14) and KARRIKIN INSENSITIVE 2 (KAI2) of their signaling pathways, respectively.
Treatment with rac-GR24 modifies the root architecture at different levels, such
as decreasing the lateral root density (LRD), while promoting root hair elongation
or flavonol accumulation. Previously, we have shown that the flavonol biosynthesis
is transcriptionally activated in the root by rac-GR24 treatment, but, thus far,
the molecular players involved in that response have remained unknown. To get
an in-depth insight into the changes that occur after the compound is perceived
by the roots, we compared the root transcriptomes of the wild type and the more
axillary growth2 (max2) mutant, affected in both SL and karrikin signaling pathways,
with and without rac-GR24 treatment. Quantitative reverse transcription (qRT)-PCR,
reporter line analysis and mutant phenotyping indicated that the flavonol response
and the root hair elongation are controlled by the ELONGATED HYPOCOTYL 5 (HY5)
and MYB12 transcription factors, but HY5, in contrast to MYB12, affects the LRD
as well. Furthermore, we identified the transcription factors TARGET OF MONOPTEROS
5 (TMO5) and TMO5 LIKE1 as negative and the Mediator complex as positive regulators
of the rac-GR24 effect on LRD. Altogether, hereby, we get closer toward understanding
the molecular mechanisms that underlay the rac-GR24 responses in the root.
acknowledgement: The authors thank Ralf Stracke (Bielefeld University, Bielefeld,
Germany) for providing the myb mutants and their colleagues Bert De Rybel for the
tmo5t;mo5l1 double mutant, Boris Parizot for tips on the RNA-seq analysis, Veronique
Storme for statistical help on both the RNA-seq and lateral root density, and Martine
De Cock for help in preparing the manuscript.
article_processing_charge: No
article_type: original
author:
- first_name: Sylwia
full_name: Struk, Sylwia
last_name: Struk
- first_name: Lukas
full_name: Braem, Lukas
last_name: Braem
- first_name: Cedrick
full_name: Matthys, Cedrick
last_name: Matthys
- first_name: Alan
full_name: Walton, Alan
last_name: Walton
- first_name: Nick
full_name: Vangheluwe, Nick
last_name: Vangheluwe
- first_name: Stan
full_name: Van Praet, Stan
last_name: Van Praet
- first_name: Lingxiang
full_name: Jiang, Lingxiang
last_name: Jiang
- first_name: Pawel
full_name: Baster, Pawel
id: 3028BD74-F248-11E8-B48F-1D18A9856A87
last_name: Baster
- first_name: Carolien
full_name: De Cuyper, Carolien
last_name: De Cuyper
- first_name: Francois-Didier
full_name: Boyer, Francois-Didier
last_name: Boyer
- first_name: Elisabeth
full_name: Stes, Elisabeth
last_name: Stes
- first_name: Tom
full_name: Beeckman, Tom
last_name: Beeckman
- first_name: Jiří
full_name: Friml, Jiří
id: 4159519E-F248-11E8-B48F-1D18A9856A87
last_name: Friml
orcid: 0000-0002-8302-7596
- first_name: Kris
full_name: Gevaert, Kris
last_name: Gevaert
- first_name: Sofie
full_name: Goormachtig, Sofie
last_name: Goormachtig
citation:
ama: Struk S, Braem L, Matthys C, et al. Transcriptional analysis in the Arabidopsis
roots reveals new regulators that link rac-GR24 treatment with changes in flavonol
accumulation, root hair elongation and lateral root density. Plant & Cell
Physiology. 2022;63(1):104-119. doi:10.1093/pcp/pcab149
apa: Struk, S., Braem, L., Matthys, C., Walton, A., Vangheluwe, N., Van Praet, S.,
… Goormachtig, S. (2022). Transcriptional analysis in the Arabidopsis roots reveals
new regulators that link rac-GR24 treatment with changes in flavonol accumulation,
root hair elongation and lateral root density. Plant & Cell Physiology.
Oxford University Press. https://doi.org/10.1093/pcp/pcab149
chicago: Struk, Sylwia, Lukas Braem, Cedrick Matthys, Alan Walton, Nick Vangheluwe,
Stan Van Praet, Lingxiang Jiang, et al. “Transcriptional Analysis in the Arabidopsis
Roots Reveals New Regulators That Link Rac-GR24 Treatment with Changes in Flavonol
Accumulation, Root Hair Elongation and Lateral Root Density.” Plant & Cell
Physiology. Oxford University Press, 2022. https://doi.org/10.1093/pcp/pcab149.
ieee: S. Struk et al., “Transcriptional analysis in the Arabidopsis roots
reveals new regulators that link rac-GR24 treatment with changes in flavonol accumulation,
root hair elongation and lateral root density,” Plant & Cell Physiology,
vol. 63, no. 1. Oxford University Press, pp. 104–119, 2022.
ista: Struk S, Braem L, Matthys C, Walton A, Vangheluwe N, Van Praet S, Jiang L,
Baster P, De Cuyper C, Boyer F-D, Stes E, Beeckman T, Friml J, Gevaert K, Goormachtig
S. 2022. Transcriptional analysis in the Arabidopsis roots reveals new regulators
that link rac-GR24 treatment with changes in flavonol accumulation, root hair
elongation and lateral root density. Plant & Cell Physiology. 63(1), 104–119.
mla: Struk, Sylwia, et al. “Transcriptional Analysis in the Arabidopsis Roots Reveals
New Regulators That Link Rac-GR24 Treatment with Changes in Flavonol Accumulation,
Root Hair Elongation and Lateral Root Density.” Plant & Cell Physiology,
vol. 63, no. 1, Oxford University Press, 2022, pp. 104–19, doi:10.1093/pcp/pcab149.
short: S. Struk, L. Braem, C. Matthys, A. Walton, N. Vangheluwe, S. Van Praet, L.
Jiang, P. Baster, C. De Cuyper, F.-D. Boyer, E. Stes, T. Beeckman, J. Friml, K.
Gevaert, S. Goormachtig, Plant & Cell Physiology 63 (2022) 104–119.
date_created: 2021-12-28T11:44:18Z
date_published: 2022-01-21T00:00:00Z
date_updated: 2026-06-18T08:43:19Z
day: '21'
ddc:
- '580'
department:
- _id: JiFr
doi: 10.1093/pcp/pcab149
external_id:
isi:
- '000877899400009'
pmid:
- '34791413'
intvolume: ' 63'
isi: 1
issue: '1'
keyword:
- flavonols
- MAX2
- rac-Gr24
- RNA-seq
- root development
- transcriptional regulation
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.1093/pcp/pcab149
month: '01'
oa: 1
oa_version: Published Version
page: 104-119
pmid: 1
publication: Plant & Cell Physiology
publication_identifier:
eissn:
- 1471-9053
issn:
- 0032-0781
publication_status: published
publisher: Oxford University Press
quality_controlled: '1'
scopus_import: '1'
status: public
title: Transcriptional analysis in the Arabidopsis roots reveals new regulators that
link rac-GR24 treatment with changes in flavonol accumulation, root hair elongation
and lateral root density
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 63
year: '2022'
...
---
_id: '10656'
abstract:
- lang: eng
text: Idealized simulations of the tropical atmosphere have predicted that clouds
can spontaneously clump together in space, despite perfectly homogeneous settings.
This phenomenon has been called self-aggregation, and it results in a state where
a moist cloudy region with intense deep convective storms is surrounded by extremely
dry subsiding air devoid of deep clouds. We review here the main findings from
theoretical work and idealized models of this phenomenon, highlighting the physical
processes believed to play a key role in convective self-aggregation. We also
review the growing literature on the importance and implications of this phenomenon
for the tropical atmosphere, notably, for the hydrological cycle and for precipitation
extremes, in our current and in a warming climate.
acknowledgement: C.M. gratefully acknowledges funding from the European Research Council
(ERC) under the European Union's Horizon 2020 research and innovation program (Project
CLUSTER, grant agreement 805041). She also thanks Grand Équipement National de Calcul
Intensif (GENCI), France, for providing access to their computing platforms at Très
Grand Centre de Calcul (TGCC). J.O.H. gratefully acknowledges funding from the Villum
Foundation (grant 13168), the ERC under the Horizon 2020 research and innovation
program (grant 771859), and the Novo Nordisk Foundation's Interdisciplinary Synergy
Program (grant NNF19OC0057374). G.C. gratefully acknowledges the support of the
transregional collaborative research center (SFB/TRR 165) “Waves to Weather” (http://www.wavestoweather.de)
funded by the German Research Foundation (DFG). D.Y. is supported by a Packard Fellowship
in Science and Engineering, the France–Berkeley Fund, Laboratory Directed Research
and Development (LDRD) funding from the Lawrence Berkeley National Laboratory, and
the US Department of Energy, Office of Science, Office of Biological and Environmental
Research, Climate and Environmental Sciences Division, Regional and Global Climate
Modeling Program under award DE-AC02-05CH11231.
article_processing_charge: No
article_type: original
author:
- first_name: Caroline J
full_name: Muller, Caroline J
id: f978ccb0-3f7f-11eb-b193-b0e2bd13182b
last_name: Muller
orcid: 0000-0001-5836-5350
- first_name: Da
full_name: Yang, Da
last_name: Yang
- first_name: George
full_name: Craig, George
last_name: Craig
- first_name: Timothy
full_name: Cronin, Timothy
last_name: Cronin
- first_name: Benjamin
full_name: Fildier, Benjamin
last_name: Fildier
- first_name: Jan O.
full_name: Haerter, Jan O.
last_name: Haerter
- first_name: Cathy
full_name: Hohenegger, Cathy
last_name: Hohenegger
- first_name: Brian
full_name: Mapes, Brian
last_name: Mapes
- first_name: David
full_name: Randall, David
last_name: Randall
- first_name: Sara
full_name: Shamekh, Sara
last_name: Shamekh
- first_name: Steven C.
full_name: Sherwood, Steven C.
last_name: Sherwood
citation:
ama: Muller CJ, Yang D, Craig G, et al. Spontaneous aggregation of convective storms.
Annual Review of Fluid Mechanics. 2022;54:133-157. doi:10.1146/annurev-fluid-022421-011319
apa: Muller, C. J., Yang, D., Craig, G., Cronin, T., Fildier, B., Haerter, J. O.,
… Sherwood, S. C. (2022). Spontaneous aggregation of convective storms. Annual
Review of Fluid Mechanics. Annual Reviews. https://doi.org/10.1146/annurev-fluid-022421-011319
chicago: Muller, Caroline J, Da Yang, George Craig, Timothy Cronin, Benjamin Fildier,
Jan O. Haerter, Cathy Hohenegger, et al. “Spontaneous Aggregation of Convective
Storms.” Annual Review of Fluid Mechanics. Annual Reviews, 2022. https://doi.org/10.1146/annurev-fluid-022421-011319.
ieee: C. J. Muller et al., “Spontaneous aggregation of convective storms,”
Annual Review of Fluid Mechanics, vol. 54. Annual Reviews, pp. 133–157,
2022.
ista: Muller CJ, Yang D, Craig G, Cronin T, Fildier B, Haerter JO, Hohenegger C,
Mapes B, Randall D, Shamekh S, Sherwood SC. 2022. Spontaneous aggregation of convective
storms. Annual Review of Fluid Mechanics. 54, 133–157.
mla: Muller, Caroline J., et al. “Spontaneous Aggregation of Convective Storms.”
Annual Review of Fluid Mechanics, vol. 54, Annual Reviews, 2022, pp. 133–57,
doi:10.1146/annurev-fluid-022421-011319.
short: C.J. Muller, D. Yang, G. Craig, T. Cronin, B. Fildier, J.O. Haerter, C. Hohenegger,
B. Mapes, D. Randall, S. Shamekh, S.C. Sherwood, Annual Review of Fluid Mechanics
54 (2022) 133–157.
corr_author: '1'
date_created: 2022-01-23T23:01:29Z
date_published: 2022-01-01T00:00:00Z
date_updated: 2026-06-18T08:46:40Z
day: '01'
ddc:
- '550'
department:
- _id: CaMu
doi: 10.1146/annurev-fluid-022421-011319
ec_funded: 1
external_id:
isi:
- '000794152800006'
intvolume: ' 54'
isi: 1
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.1146/annurev-fluid-022421-011319
month: '01'
oa: 1
oa_version: Published Version
page: 133-157
project:
- _id: 629205d8-2b32-11ec-9570-e1356ff73576
call_identifier: H2020
grant_number: '805041'
name: Organization of CLoUdS, and implications of Tropical cyclones and for the
Energetics of the tropics, in current and waRming climate
publication: Annual Review of Fluid Mechanics
publication_identifier:
eissn:
- 1545-4479
issn:
- 0066-4189
publication_status: published
publisher: Annual Reviews
quality_controlled: '1'
scopus_import: '1'
status: public
title: Spontaneous aggregation of convective storms
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 54
year: '2022'
...
---
_id: '10719'
abstract:
- lang: eng
text: Auxin, one of the first identified and most widely studied phytohormones,
has been and will remain a hot topic in plant biology. After more than a century
of passionate exploration, the mysteries of its synthesis, transport, signaling,
and metabolism have largely been unlocked. Due to the rapid development of new
technologies, new methods, and new genetic materials, the study of auxin has entered
the fast lane over the past 30 years. Here, we highlight advances in understanding
auxin signaling, including auxin perception, rapid auxin responses, TRANSPORT
INHIBITOR RESPONSE 1 and AUXIN SIGNALING F-boxes (TIR1/AFBs)-mediated transcriptional
and non-transcriptional branches, and the epigenetic regulation of auxin signaling.
We also focus on feedback inhibition mechanisms that prevent the over-amplification
of auxin signals. In addition, we cover the TRANSMEMBRANE KINASEs (TMKs)-mediated
non-canonical signaling, which converges with TIR1/AFBs-mediated transcriptional
regulation to coordinate plant growth and development. The identification of additional
auxin signaling components and their regulation will continue to open new avenues
of research in this field, leading to an increasingly deeper, more comprehensive
understanding of how auxin signals are interpreted at the cellular level to regulate
plant growth and development.
acknowledgement: "This research was financially supported by the National Natural
Science Foundation of China and the Israel Science Foundation (NSFC-ISF; 32061143005),
National Natural Science Foundation of China (32000225), Natural Science Foundation
of Shandong Province (ZR2020QC036), and China Postdoctoral Science Foundation (2020M682165).\r\n"
article_processing_charge: No
article_type: review
author:
- first_name: Z
full_name: Yu, Z
last_name: Yu
- first_name: F
full_name: Zhang, F
last_name: Zhang
- first_name: Jiří
full_name: Friml, Jiří
id: 4159519E-F248-11E8-B48F-1D18A9856A87
last_name: Friml
orcid: 0000-0002-8302-7596
- first_name: Z
full_name: Ding, Z
last_name: Ding
citation:
ama: 'Yu Z, Zhang F, Friml J, Ding Z. Auxin signaling: Research advances over the
past 30 years. Journal of Integrative Plant Biology. 2022;64(2):371-392.
doi:10.1111/jipb.13225'
apa: 'Yu, Z., Zhang, F., Friml, J., & Ding, Z. (2022). Auxin signaling: Research
advances over the past 30 years. Journal of Integrative Plant Biology.
Wiley. https://doi.org/10.1111/jipb.13225'
chicago: 'Yu, Z, F Zhang, Jiří Friml, and Z Ding. “Auxin Signaling: Research Advances
over the Past 30 Years.” Journal of Integrative Plant Biology. Wiley, 2022.
https://doi.org/10.1111/jipb.13225.'
ieee: 'Z. Yu, F. Zhang, J. Friml, and Z. Ding, “Auxin signaling: Research advances
over the past 30 years,” Journal of Integrative Plant Biology, vol. 64,
no. 2. Wiley, pp. 371–392, 2022.'
ista: 'Yu Z, Zhang F, Friml J, Ding Z. 2022. Auxin signaling: Research advances
over the past 30 years. Journal of Integrative Plant Biology. 64(2), 371–392.'
mla: 'Yu, Z., et al. “Auxin Signaling: Research Advances over the Past 30 Years.”
Journal of Integrative Plant Biology, vol. 64, no. 2, Wiley, 2022, pp.
371–92, doi:10.1111/jipb.13225.'
short: Z. Yu, F. Zhang, J. Friml, Z. Ding, Journal of Integrative Plant Biology
64 (2022) 371–392.
corr_author: '1'
date_created: 2022-02-03T09:52:59Z
date_published: 2022-02-01T00:00:00Z
date_updated: 2026-06-18T08:47:21Z
day: '01'
ddc:
- '580'
department:
- _id: JiFr
doi: 10.1111/jipb.13225
external_id:
isi:
- '000761281200011'
pmid:
- '35018726'
intvolume: ' 64'
isi: 1
issue: '2'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.1111/jipb.13225
month: '02'
oa: 1
oa_version: Published Version
page: 371-392
pmid: 1
publication: Journal of Integrative Plant Biology
publication_identifier:
eissn:
- 1744-7909
issn:
- 1672-9072
publication_status: published
publisher: Wiley
quality_controlled: '1'
scopus_import: '1'
status: public
title: 'Auxin signaling: Research advances over the past 30 years'
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 64
year: '2022'
...
---
_id: '10753'
abstract:
- lang: eng
text: This is a comment on "Meta-learning synaptic plasticity and memory addressing
for continual familiarity detection." Neuron. 2022 Feb 2;110(3):544-557.e8.
article_processing_charge: No
article_type: letter_note
author:
- first_name: Basile J
full_name: Confavreux, Basile J
id: C7610134-B532-11EA-BD9F-F5753DDC885E
last_name: Confavreux
- first_name: Tim P
full_name: Vogels, Tim P
id: CB6FF8D2-008F-11EA-8E08-2637E6697425
last_name: Vogels
orcid: 0000-0003-3295-6181
citation:
ama: 'Confavreux BJ, Vogels TP. A familiar thought: Machines that replace us? Neuron.
2022;110(3):361-362. doi:10.1016/j.neuron.2022.01.014'
apa: 'Confavreux, B. J., & Vogels, T. P. (2022). A familiar thought: Machines
that replace us? Neuron. Elsevier. https://doi.org/10.1016/j.neuron.2022.01.014'
chicago: 'Confavreux, Basile J, and Tim P Vogels. “A Familiar Thought: Machines
That Replace Us?” Neuron. Elsevier, 2022. https://doi.org/10.1016/j.neuron.2022.01.014.'
ieee: 'B. J. Confavreux and T. P. Vogels, “A familiar thought: Machines that replace
us?,” Neuron, vol. 110, no. 3. Elsevier, pp. 361–362, 2022.'
ista: 'Confavreux BJ, Vogels TP. 2022. A familiar thought: Machines that replace
us? Neuron. 110(3), 361–362.'
mla: 'Confavreux, Basile J., and Tim P. Vogels. “A Familiar Thought: Machines That
Replace Us?” Neuron, vol. 110, no. 3, Elsevier, 2022, pp. 361–62, doi:10.1016/j.neuron.2022.01.014.'
short: B.J. Confavreux, T.P. Vogels, Neuron 110 (2022) 361–362.
corr_author: '1'
date_created: 2022-02-13T23:01:34Z
date_published: 2022-02-02T00:00:00Z
date_updated: 2026-06-18T08:47:45Z
day: '02'
ddc:
- '570'
department:
- _id: TiVo
doi: 10.1016/j.neuron.2022.01.014
external_id:
isi:
- '000751819100005'
pmid:
- '35114107'
intvolume: ' 110'
isi: 1
issue: '3'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.1016/j.neuron.2022.01.014
month: '02'
oa: 1
oa_version: Published Version
page: 361-362
pmid: 1
publication: Neuron
publication_identifier:
eissn:
- 1097-4199
publication_status: published
publisher: Elsevier
quality_controlled: '1'
scopus_import: '1'
status: public
title: 'A familiar thought: Machines that replace us?'
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 110
year: '2022'
...
---
_id: '10889'
abstract:
- lang: eng
text: Genetically encoded tags have introduced extensive lines of application from
purification of tagged proteins to their visualization at the single molecular,
cellular, histological and whole-body levels. Combined with other rapidly developing
technologies such as clustered regularly interspaced palindromic repeats (CRISPR)/CRISPR-associated
protein 9 (Cas9) system, proteomics, super-resolution microscopy and proximity
labeling, a large variety of genetically encoded tags have been developed in the
last two decades. In this review, I focus on the current status of tag development
for electron microscopic (EM) visualization of proteins with metal particle labeling.
Compared with conventional immunoelectron microscopy using gold particles, tag-mediated
metal particle labeling has several advantages that could potentially improve
the sensitivity, spatial and temporal resolution, and applicability to a wide
range of proteins of interest (POIs). It may enable researchers to detect single
molecules in situ, allowing the quantitative measurement of absolute numbers and
exact localization patterns of POI in the ultrastructural context. Thus, genetically
encoded tags for EM could revolutionize the field as green fluorescence protein
did for light microscopy, although we still have many challenges to overcome before
reaching this goal.
acknowledgement: European Research Council Advanced Grant (694539 to R.S.).
article_processing_charge: No
article_type: original
author:
- first_name: Ryuichi
full_name: Shigemoto, Ryuichi
id: 499F3ABC-F248-11E8-B48F-1D18A9856A87
last_name: Shigemoto
orcid: 0000-0001-8761-9444
citation:
ama: Shigemoto R. Electron microscopic visualization of single molecules by tag-mediated
metal particle labeling. Microscopy. 2022;71(Supplement_1):i72-i80. doi:10.1093/jmicro/dfab048
apa: Shigemoto, R. (2022). Electron microscopic visualization of single molecules
by tag-mediated metal particle labeling. Microscopy. Oxford University
Press. https://doi.org/10.1093/jmicro/dfab048
chicago: Shigemoto, Ryuichi. “Electron Microscopic Visualization of Single Molecules
by Tag-Mediated Metal Particle Labeling.” Microscopy. Oxford University
Press, 2022. https://doi.org/10.1093/jmicro/dfab048.
ieee: R. Shigemoto, “Electron microscopic visualization of single molecules by tag-mediated
metal particle labeling,” Microscopy, vol. 71, no. Supplement_1. Oxford
University Press, pp. i72–i80, 2022.
ista: Shigemoto R. 2022. Electron microscopic visualization of single molecules
by tag-mediated metal particle labeling. Microscopy. 71(Supplement_1), i72–i80.
mla: Shigemoto, Ryuichi. “Electron Microscopic Visualization of Single Molecules
by Tag-Mediated Metal Particle Labeling.” Microscopy, vol. 71, no. Supplement_1,
Oxford University Press, 2022, pp. i72–80, doi:10.1093/jmicro/dfab048.
short: R. Shigemoto, Microscopy 71 (2022) i72–i80.
corr_author: '1'
date_created: 2022-03-20T23:01:39Z
date_published: 2022-03-01T00:00:00Z
date_updated: 2026-06-18T10:44:57Z
day: '01'
ddc:
- '570'
department:
- _id: RySh
doi: 10.1093/jmicro/dfab048
ec_funded: 1
external_id:
isi:
- '000768384100011'
pmid:
- '35275179'
intvolume: ' 71'
isi: 1
issue: Supplement_1
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.1093/jmicro/dfab048
month: '03'
oa: 1
oa_version: Published Version
page: i72-i80
pmid: 1
project:
- _id: 25CA28EA-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '694539'
name: 'In situ analysis of single channel subunit composition in neurons: physiological
implication in synaptic plasticity and behaviour'
publication: Microscopy
publication_identifier:
eissn:
- 2050-5701
issn:
- 2050-5698
publication_status: published
publisher: Oxford University Press
quality_controlled: '1'
scopus_import: '1'
status: public
title: Electron microscopic visualization of single molecules by tag-mediated metal
particle labeling
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 71
year: '2022'
...
---
_id: '10846'
abstract:
- lang: eng
text: The Golgi apparatus regulates the process of modification and subcellular
localization of macromolecules, including proteins and lipids. Aberrant protein
sorting caused by defects in the Golgi leads to various diseases in mammals. However,
the role of the Golgi apparatus in organismal longevity remained largely unknown.
By employing a quantitative proteomic approach, we demonstrated that MON-2, an
evolutionarily conserved Arf-GEF protein implicated in Golgi-to-endosome trafficking,
promotes longevity via upregulating macroautophagy/autophagy in C. elegans. Our
data using cultured mammalian cells indicate that MON2 translocates from the Golgi
to the endosome under starvation conditions, subsequently increasing autophagic
flux by binding LGG-1/GABARAPL2. Thus, Golgi-to-endosome trafficking appears to
be an evolutionarily conserved process for the upregulation of autophagy, which
contributes to organismal longevity.
acknowledgement: This work is funded by National Research Foundation of Korea (NRF)
grants NRF-2019R1A3B2067745 from the Korean Government (Ministry of Science and
Information and Communications Technology (S-J.V.L.). NRF-2017R1A5A1015366 (S.Y.P,
S-J.V.L). Korea Institute of Science and Technology (KIST) intramural grant (C.L).
article_processing_charge: No
article_type: original
author:
- first_name: Murat
full_name: Artan, Murat
id: C407B586-6052-11E9-B3AE-7006E6697425
last_name: Artan
orcid: 0000-0001-8945-6992
- first_name: Jooyeon
full_name: Sohn, Jooyeon
last_name: Sohn
- first_name: Cheolju
full_name: Lee, Cheolju
last_name: Lee
- first_name: Seung Yeol
full_name: Park, Seung Yeol
last_name: Park
- first_name: Seung Jae V.
full_name: Lee, Seung Jae V.
last_name: Lee
citation:
ama: Artan M, Sohn J, Lee C, Park SY, Lee SJV. MON-2, a Golgi protein, promotes
longevity by upregulating autophagy through mediating inter-organelle communications.
Autophagy. 2022;18(5):1208-1210. doi:10.1080/15548627.2022.2039523
apa: Artan, M., Sohn, J., Lee, C., Park, S. Y., & Lee, S. J. V. (2022). MON-2,
a Golgi protein, promotes longevity by upregulating autophagy through mediating
inter-organelle communications. Autophagy. Taylor & Francis. https://doi.org/10.1080/15548627.2022.2039523
chicago: Artan, Murat, Jooyeon Sohn, Cheolju Lee, Seung Yeol Park, and Seung Jae
V. Lee. “MON-2, a Golgi Protein, Promotes Longevity by Upregulating Autophagy
through Mediating Inter-Organelle Communications.” Autophagy. Taylor &
Francis, 2022. https://doi.org/10.1080/15548627.2022.2039523.
ieee: M. Artan, J. Sohn, C. Lee, S. Y. Park, and S. J. V. Lee, “MON-2, a Golgi protein,
promotes longevity by upregulating autophagy through mediating inter-organelle
communications,” Autophagy, vol. 18, no. 5. Taylor & Francis, pp. 1208–1210,
2022.
ista: Artan M, Sohn J, Lee C, Park SY, Lee SJV. 2022. MON-2, a Golgi protein, promotes
longevity by upregulating autophagy through mediating inter-organelle communications.
Autophagy. 18(5), 1208–1210.
mla: Artan, Murat, et al. “MON-2, a Golgi Protein, Promotes Longevity by Upregulating
Autophagy through Mediating Inter-Organelle Communications.” Autophagy,
vol. 18, no. 5, Taylor & Francis, 2022, pp. 1208–10, doi:10.1080/15548627.2022.2039523.
short: M. Artan, J. Sohn, C. Lee, S.Y. Park, S.J.V. Lee, Autophagy 18 (2022) 1208–1210.
date_created: 2022-03-13T23:01:47Z
date_published: 2022-02-19T00:00:00Z
date_updated: 2026-06-18T10:40:40Z
day: '19'
ddc:
- '570'
department:
- _id: MaDe
doi: 10.1080/15548627.2022.2039523
external_id:
isi:
- '000758859600001'
pmid:
- '35188063'
intvolume: ' 18'
isi: 1
issue: '5'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.1080/15548627.2022.2039523
month: '02'
oa: 1
oa_version: Published Version
page: 1208-1210
pmid: 1
publication: Autophagy
publication_identifier:
eissn:
- 1554-8635
issn:
- 1554-8627
publication_status: published
publisher: Taylor & Francis
quality_controlled: '1'
scopus_import: '1'
status: public
title: MON-2, a Golgi protein, promotes longevity by upregulating autophagy through
mediating inter-organelle communications
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 18
year: '2022'
...
---
_id: '11187'
abstract:
- lang: eng
text: During the COVID-19 pandemic, genomics and bioinformatics have emerged as
essential public health tools. The genomic data acquired using these methods have
supported the global health response, facilitated the development of testing methods
and allowed the timely tracking of novel SARS-CoV-2 variants. Yet the virtually
unlimited potential for rapid generation and analysis of genomic data is also
coupled with unique technical, scientific and organizational challenges. Here,
we discuss the application of genomic and computational methods for efficient
data-driven COVID-19 response, the advantages of the democratization of viral
sequencing around the world and the challenges associated with viral genome data
collection and processing.
acknowledgement: 'Our paper is dedicated to all freedom-loving people around the world,
and to the people of Ukraine who fight for our freedom. We thank William M. Switzer
and Ellsworth M. Campbell from the Division of HIV/AIDS Prevention, Centers for
Disease Control and Prevention (CDC), Atlanta, GA, USA, for discussions and suggestions.
We thank Jason Ladner from the Pathogen and Microbiome Institute, Northern Arizona
University, Flagstaff, AZ, for providing suggestions and feedback. S.M. was partially
supported by National Science Foundation grants 2041984. T.L. is supported by the
NSFC Excellent Young Scientists Fund (Hong Kong and Macau; 31922087), Research Grants
Council (RGC) Collaborative Research Fund (C7144-20GF), RGC Research Impact Fund
(R7021-20), Innovation and Technology Commission’s InnoHK funding (D24H) and Health
and Medical Research Fund (COVID190223). P.S. was supported by US National Institutes
of Health (NIH) grant 1R01EB025022 and National Science Foundation (NSF) grant 2047828.
M.A. acknowledges King Abdulaziz City for Science and Technology and the Saudi Human
Genome Project for technical and financial support (https://shgp.kacst.edu.sa) N.W.
was supported by US NIH grants R00 AI139445, DP2 AT011966 and R01 AI167910. A.S.
acknowledge funding from NSF grant no. 2029025. A.Z. has been partially supported
by NIH grants 1R01EB025022-01 and 1R21CA241044-01A1. S. Knyazev has been partly
supported by Molecular Basis of Disease at Georgia State University and NIH awards
R01 HG009120, R01 MH115676, R01 AI153827 and U01 HG011715. A.W. has been supported
by the CAMS Innovation Fund for Medical Sciences (2021-I2M-1-061). R.K. was supported
by NSF project 2038509, RAPID: Improving QIIME 2 and UniFrac for Viruses to Respond
to COVID-19, CDC project 30055281 with Scripps led by Kristian Andersen, Genomic
sequencing of SARS-CoV-2 to investigate local and cross-border emergence and spread.
J.O.W. was supported by NIH–National Institute of Allergy and Infectious Diseases
(NIAID) R01 AI135992 and receives funding from the CDC unrelated to this work. T.I.V.
is supported by the Branco Weiss Fellowship. Y.P. was supported by the Ministry
of Science and Higher Education of the Russian Federation within the framework of
state support for the creation and development of World-Class Research Centers “Digital
biodesign and personalized healthcare” N◦075-15-2020-926. E.B. was supported by
a US National Institute of General Medical Sciences IDeA Alaska INBRE (P20GM103395)
and NIAID CEIRR (75N93019R00028). C.E.M. thanks Testing for America (501c3), OpenCovidScreen
Foundation, Igor Tulchinsky and the WorldQuant Foundation, Bill Ackman and Olivia
Flatto and the Pershing Square Foundation, Ken Griffin and Citadel, the US National
Institutes of Health (R01AI125416, R01AI151059, R21AI129851, U01DA053941), and the
Alfred P. Sloan Foundation (G-2015-13964). C.Y.C. is supported by US CDC Epidemiology
and Laboratory Capacity (ELC) for Infectious Diseases grant 6NU50CK000539 to the
California Department of Public Health, the Innovative Genomics Institute (IGI)
at the University of California, Berkeley, and University of California, San Francisco,
NIH grant R33AI12945 and US CDC contract 75D30121C10991. A.K. was partly supported
by RFBR grant 20-515-80017. P.L. acknowledges support from the European Research
Council (ERC) under the European Union’s Horizon 2020 research and innovation program
(grant agreement no. ~725422 - ReservoirDOCS), the Wellcome Trust through project
206298/Z/17/Z (Artic Network) and NIH grants R01 AI153044 and U19 AI135995. K.C.
acknowledges support from the US NSF award EEID-IOS-2109688. F.K.’s work was supported
by an ERC Consolidator grant to F.K. (771209–CharFL).'
article_processing_charge: No
article_type: letter_note
author:
- first_name: Sergey
full_name: Knyazev, Sergey
last_name: Knyazev
- first_name: Karishma
full_name: Chhugani, Karishma
last_name: Chhugani
- first_name: Varuni
full_name: Sarwal, Varuni
last_name: Sarwal
- first_name: Ram
full_name: Ayyala, Ram
last_name: Ayyala
- first_name: Harman
full_name: Singh, Harman
last_name: Singh
- first_name: Smruthi
full_name: Karthikeyan, Smruthi
last_name: Karthikeyan
- first_name: Dhrithi
full_name: Deshpande, Dhrithi
last_name: Deshpande
- first_name: Pelin Icer
full_name: Baykal, Pelin Icer
last_name: Baykal
- first_name: Zoia
full_name: Comarova, Zoia
last_name: Comarova
- first_name: Angela
full_name: Lu, Angela
last_name: Lu
- first_name: Yuri
full_name: Porozov, Yuri
last_name: Porozov
- first_name: Tetyana I.
full_name: Vasylyeva, Tetyana I.
last_name: Vasylyeva
- first_name: Joel O.
full_name: Wertheim, Joel O.
last_name: Wertheim
- first_name: Braden T.
full_name: Tierney, Braden T.
last_name: Tierney
- first_name: Charles Y.
full_name: Chiu, Charles Y.
last_name: Chiu
- first_name: Ren
full_name: Sun, Ren
last_name: Sun
- first_name: Aiping
full_name: Wu, Aiping
last_name: Wu
- first_name: Malak S.
full_name: Abedalthagafi, Malak S.
last_name: Abedalthagafi
- first_name: Victoria M.
full_name: Pak, Victoria M.
last_name: Pak
- first_name: Shivashankar H.
full_name: Nagaraj, Shivashankar H.
last_name: Nagaraj
- first_name: Adam L.
full_name: Smith, Adam L.
last_name: Smith
- first_name: Pavel
full_name: Skums, Pavel
last_name: Skums
- first_name: Bogdan
full_name: Pasaniuc, Bogdan
last_name: Pasaniuc
- first_name: Andrey
full_name: Komissarov, Andrey
last_name: Komissarov
- first_name: Christopher E.
full_name: Mason, Christopher E.
last_name: Mason
- first_name: Eric
full_name: Bortz, Eric
last_name: Bortz
- first_name: Philippe
full_name: Lemey, Philippe
last_name: Lemey
- first_name: Fyodor
full_name: Kondrashov, Fyodor
id: 44FDEF62-F248-11E8-B48F-1D18A9856A87
last_name: Kondrashov
orcid: 0000-0001-8243-4694
- first_name: Niko
full_name: Beerenwinkel, Niko
last_name: Beerenwinkel
- first_name: Tommy Tsan Yuk
full_name: Lam, Tommy Tsan Yuk
last_name: Lam
- first_name: Nicholas C.
full_name: Wu, Nicholas C.
last_name: Wu
- first_name: Alex
full_name: Zelikovsky, Alex
last_name: Zelikovsky
- first_name: Rob
full_name: Knight, Rob
last_name: Knight
- first_name: Keith A.
full_name: Crandall, Keith A.
last_name: Crandall
- first_name: Serghei
full_name: Mangul, Serghei
last_name: Mangul
citation:
ama: Knyazev S, Chhugani K, Sarwal V, et al. Unlocking capacities of genomics for
the COVID-19 response and future pandemics. Nature Methods. 2022;19(4):374-380.
doi:10.1038/s41592-022-01444-z
apa: Knyazev, S., Chhugani, K., Sarwal, V., Ayyala, R., Singh, H., Karthikeyan,
S., … Mangul, S. (2022). Unlocking capacities of genomics for the COVID-19 response
and future pandemics. Nature Methods. Springer Nature. https://doi.org/10.1038/s41592-022-01444-z
chicago: Knyazev, Sergey, Karishma Chhugani, Varuni Sarwal, Ram Ayyala, Harman Singh,
Smruthi Karthikeyan, Dhrithi Deshpande, et al. “Unlocking Capacities of Genomics
for the COVID-19 Response and Future Pandemics.” Nature Methods. Springer
Nature, 2022. https://doi.org/10.1038/s41592-022-01444-z.
ieee: S. Knyazev et al., “Unlocking capacities of genomics for the COVID-19
response and future pandemics,” Nature Methods, vol. 19, no. 4. Springer
Nature, pp. 374–380, 2022.
ista: Knyazev S, Chhugani K, Sarwal V, Ayyala R, Singh H, Karthikeyan S, Deshpande
D, Baykal PI, Comarova Z, Lu A, Porozov Y, Vasylyeva TI, Wertheim JO, Tierney
BT, Chiu CY, Sun R, Wu A, Abedalthagafi MS, Pak VM, Nagaraj SH, Smith AL, Skums
P, Pasaniuc B, Komissarov A, Mason CE, Bortz E, Lemey P, Kondrashov F, Beerenwinkel
N, Lam TTY, Wu NC, Zelikovsky A, Knight R, Crandall KA, Mangul S. 2022. Unlocking
capacities of genomics for the COVID-19 response and future pandemics. Nature
Methods. 19(4), 374–380.
mla: Knyazev, Sergey, et al. “Unlocking Capacities of Genomics for the COVID-19
Response and Future Pandemics.” Nature Methods, vol. 19, no. 4, Springer
Nature, 2022, pp. 374–80, doi:10.1038/s41592-022-01444-z.
short: S. Knyazev, K. Chhugani, V. Sarwal, R. Ayyala, H. Singh, S. Karthikeyan,
D. Deshpande, P.I. Baykal, Z. Comarova, A. Lu, Y. Porozov, T.I. Vasylyeva, J.O.
Wertheim, B.T. Tierney, C.Y. Chiu, R. Sun, A. Wu, M.S. Abedalthagafi, V.M. Pak,
S.H. Nagaraj, A.L. Smith, P. Skums, B. Pasaniuc, A. Komissarov, C.E. Mason, E.
Bortz, P. Lemey, F. Kondrashov, N. Beerenwinkel, T.T.Y. Lam, N.C. Wu, A. Zelikovsky,
R. Knight, K.A. Crandall, S. Mangul, Nature Methods 19 (2022) 374–380.
date_created: 2022-04-17T22:01:48Z
date_published: 2022-04-08T00:00:00Z
date_updated: 2026-06-18T10:47:32Z
day: '08'
ddc:
- '570'
department:
- _id: FyKo
doi: 10.1038/s41592-022-01444-z
ec_funded: 1
external_id:
isi:
- '000781199600011'
pmid:
- '35396471'
intvolume: ' 19'
isi: 1
issue: '4'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.1038/s41592-022-01444-z
month: '04'
oa: 1
oa_version: Published Version
page: 374-380
pmid: 1
project:
- _id: 26580278-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '771209'
name: Characterizing the fitness landscape on population and global scales
publication: Nature Methods
publication_identifier:
eissn:
- 1548-7105
issn:
- 1548-7091
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
scopus_import: '1'
status: public
title: Unlocking capacities of genomics for the COVID-19 response and future pandemics
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 19
year: '2022'
...
---
_id: '10925'
abstract:
- lang: eng
text: Direct numerical simulations (DNS) of turbulent channel flows up to Reτ≈1000 are
conducted to investigate the three-dimensional (consisting of streamwise wavenumber,
spanwise wavenumber and frequency) spectrum of wall pressure fluctuations. To
develop a predictive model of the wavenumber–frequency spectrum from the wavenumber
spectrum, the time decorrelation mechanisms of wall pressure fluctuations are
investigated. It is discovered that the energy-containing part of the wavenumber–frequency
spectrum of wall pressure fluctuations can be well predicted using a similar random
sweeping model for streamwise velocity fluctuations. To refine the investigation,
we further decompose the spectrum of the total wall pressure fluctuations into
the autospectra of rapid and slow pressure fluctuations, and the cross-spectrum
between them. We focus on evaluating the assumption applied in many predictive
models, that is, the magnitude of the cross-spectrum is negligibly small. The
present DNS shows that neglecting the cross-spectrum causes a maximum error up
to 4.7 dB in the subconvective region for all Reynolds numbers under test. Our
analyses indicate that the approximation of neglecting the cross-spectrum needs
to be applied carefully in the investigations of acoustics at low Mach numbers,
in which the subconvective components of wall pressure fluctuations make important
contributions to the radiated acoustic power.
acknowledgement: This research is supported by the NSFC Basic Science Center Program
for ‘Multiscale Problems in Nonlinear Mechanics’ (no. 11988102), National Key Project
(GJXM92579) and the Strategic Priority Research Program (XDB22040104).
article_number: A39
article_processing_charge: No
article_type: original
arxiv: 1
author:
- first_name: Bowen
full_name: Yang, Bowen
id: 71b6ff4b-15b2-11ec-abd3-aef6b028cf7e
last_name: Yang
orcid: 0000-0002-4843-6853
- first_name: Zixuan
full_name: Yang, Zixuan
last_name: Yang
citation:
ama: Yang B, Yang Z. On the wavenumber-frequency spectrum of the wall pressure fluctuations
in turbulent channel flow. Journal of Fluid Mechanics. 2022;937. doi:10.1017/jfm.2022.137
apa: Yang, B., & Yang, Z. (2022). On the wavenumber-frequency spectrum of the
wall pressure fluctuations in turbulent channel flow. Journal of Fluid Mechanics.
Cambridge University Press. https://doi.org/10.1017/jfm.2022.137
chicago: Yang, Bowen, and Zixuan Yang. “On the Wavenumber-Frequency Spectrum of
the Wall Pressure Fluctuations in Turbulent Channel Flow.” Journal of Fluid
Mechanics. Cambridge University Press, 2022. https://doi.org/10.1017/jfm.2022.137.
ieee: B. Yang and Z. Yang, “On the wavenumber-frequency spectrum of the wall pressure
fluctuations in turbulent channel flow,” Journal of Fluid Mechanics, vol.
937. Cambridge University Press, 2022.
ista: Yang B, Yang Z. 2022. On the wavenumber-frequency spectrum of the wall pressure
fluctuations in turbulent channel flow. Journal of Fluid Mechanics. 937, A39.
mla: Yang, Bowen, and Zixuan Yang. “On the Wavenumber-Frequency Spectrum of the
Wall Pressure Fluctuations in Turbulent Channel Flow.” Journal of Fluid Mechanics,
vol. 937, A39, Cambridge University Press, 2022, doi:10.1017/jfm.2022.137.
short: B. Yang, Z. Yang, Journal of Fluid Mechanics 937 (2022).
date_created: 2022-03-27T22:01:45Z
date_published: 2022-04-25T00:00:00Z
date_updated: 2026-06-18T10:46:00Z
day: '25'
ddc:
- '530'
department:
- _id: GradSch
doi: 10.1017/jfm.2022.137
external_id:
arxiv:
- '2201.04702'
isi:
- '000763547000001'
intvolume: ' 937'
isi: 1
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.1017/jfm.2022.137
month: '04'
oa: 1
oa_version: Published Version
publication: Journal of Fluid Mechanics
publication_identifier:
eissn:
- 1469-7645
issn:
- 0022-1120
publication_status: published
publisher: Cambridge University Press
quality_controlled: '1'
scopus_import: '1'
status: public
title: On the wavenumber-frequency spectrum of the wall pressure fluctuations in turbulent
channel flow
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 937
year: '2022'
...
---
_id: '11333'
abstract:
- lang: eng
text: Adenosine triphosphate (ATP) is the energy source for various biochemical
processes and biomolecular motors in living things. Development of ATP antagonists
and their stimuli-controlled actions offer a novel approach to regulate biological
processes. Herein, we developed azobenzene-based photoswitchable ATP antagonists
for controlling the activity of motor proteins; cytoplasmic and axonemal dyneins.
The new ATP antagonists showed reversible photoswitching of cytoplasmic dynein
activity in an in vitro dynein-microtubule system due to the trans and cis photoisomerization
of their azobenzene segment. Importantly, our ATP antagonists reversibly regulated
the axonemal dynein motor activity for the force generation in a demembranated
model of Chlamydomonas reinhardtii. We found that the trans and cis isomers of
ATP antagonists significantly differ in their affinity to the ATP binding site.
article_number: e202200807
article_processing_charge: No
article_type: original
author:
- first_name: Sampreeth
full_name: Thayyil, Sampreeth
last_name: Thayyil
- first_name: Yukinori
full_name: Nishigami, Yukinori
last_name: Nishigami
- first_name: Muhammad J
full_name: Islam, Muhammad J
id: C94881D2-008F-11EA-8E08-2637E6697425
last_name: Islam
- first_name: P. K.
full_name: Hashim, P. K.
last_name: Hashim
- first_name: Ken'Ya
full_name: Furuta, Ken'Ya
last_name: Furuta
- first_name: Kazuhiro
full_name: Oiwa, Kazuhiro
last_name: Oiwa
- first_name: Jian
full_name: Yu, Jian
last_name: Yu
- first_name: Min
full_name: Yao, Min
last_name: Yao
- first_name: Toshiyuki
full_name: Nakagaki, Toshiyuki
last_name: Nakagaki
- first_name: Nobuyuki
full_name: Tamaoki, Nobuyuki
last_name: Tamaoki
citation:
ama: Thayyil S, Nishigami Y, Islam MJ, et al. Dynamic control of microbial movement
by photoswitchable ATP antagonists. Chemistry - A European Journal. 2022;28(30).
doi:10.1002/chem.202200807
apa: Thayyil, S., Nishigami, Y., Islam, M. J., Hashim, P. K., Furuta, K., Oiwa,
K., … Tamaoki, N. (2022). Dynamic control of microbial movement by photoswitchable
ATP antagonists. Chemistry - A European Journal. Wiley. https://doi.org/10.1002/chem.202200807
chicago: Thayyil, Sampreeth, Yukinori Nishigami, Muhammad J Islam, P. K. Hashim,
Ken’Ya Furuta, Kazuhiro Oiwa, Jian Yu, Min Yao, Toshiyuki Nakagaki, and Nobuyuki
Tamaoki. “Dynamic Control of Microbial Movement by Photoswitchable ATP Antagonists.”
Chemistry - A European Journal. Wiley, 2022. https://doi.org/10.1002/chem.202200807.
ieee: S. Thayyil et al., “Dynamic control of microbial movement by photoswitchable
ATP antagonists,” Chemistry - A European Journal, vol. 28, no. 30. Wiley,
2022.
ista: Thayyil S, Nishigami Y, Islam MJ, Hashim PK, Furuta K, Oiwa K, Yu J, Yao M,
Nakagaki T, Tamaoki N. 2022. Dynamic control of microbial movement by photoswitchable
ATP antagonists. Chemistry - A European Journal. 28(30), e202200807.
mla: Thayyil, Sampreeth, et al. “Dynamic Control of Microbial Movement by Photoswitchable
ATP Antagonists.” Chemistry - A European Journal, vol. 28, no. 30, e202200807,
Wiley, 2022, doi:10.1002/chem.202200807.
short: S. Thayyil, Y. Nishigami, M.J. Islam, P.K. Hashim, K. Furuta, K. Oiwa, J.
Yu, M. Yao, T. Nakagaki, N. Tamaoki, Chemistry - A European Journal 28 (2022).
date_created: 2022-04-24T22:01:44Z
date_published: 2022-05-25T00:00:00Z
date_updated: 2026-06-18T10:49:46Z
day: '25'
ddc:
- '570'
department:
- _id: RySh
doi: 10.1002/chem.202200807
external_id:
isi:
- '000781658800001'
pmid:
- '35332959'
intvolume: ' 28'
isi: 1
issue: '30'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.1002/chem.202200807
month: '05'
oa: 1
oa_version: Published Version
pmid: 1
publication: Chemistry - A European Journal
publication_identifier:
eissn:
- 1521-3765
issn:
- 0947-6539
publication_status: published
publisher: Wiley
quality_controlled: '1'
scopus_import: '1'
status: public
title: Dynamic control of microbial movement by photoswitchable ATP antagonists
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 28
year: '2022'
...
---
_id: '11449'
abstract:
- lang: eng
text: Mutations are acquired frequently, such that each cell's genome inscribes
its history of cell divisions. Common genomic alterations involve loss of heterozygosity
(LOH). LOH accumulates throughout the genome, offering large encoding capacity
for inferring cell lineage. Using only single-cell RNA sequencing (scRNA-seq)
of mouse brain cells, we found that LOH events spanning multiple genes are revealed
as tracts of monoallelically expressed, constitutionally heterozygous single-nucleotide
variants (SNVs). We simultaneously inferred cell lineage and marked developmental
time points based on X chromosome inactivation and the total number of LOH events
while identifying cell types from gene expression patterns. Our results are consistent
with progenitor cells giving rise to multiple cortical cell types through stereotyped
expansion and distinct waves of neurogenesis. This type of retrospective analysis
could be incorporated into scRNA-seq pipelines and, compared with experimental
approaches for determining lineage in model organisms, is applicable where genetic
engineering is prohibited, such as humans.
acknowledgement: D.J.A. thanks Wayne K. Potts, Alan R. Rogers, Kristen Hawkes, Ryk
Ward, and Jon Seger for inspiring a young undergraduate to apply evolutionary theory
to intraorganism development. Supported by the Paul G. Allen Frontiers Group (University
of Washington); NIH R00HG010152 (Dartmouth); and NÖ Forschung und Bildung n[f+b]
life science call grant (C13-002) and the European Research Council (ERC) under
the European Union’s Horizon 2020 research and innovation program 725780 LinPro
to S.H.
article_processing_charge: No
article_type: original
author:
- first_name: Donovan J.
full_name: Anderson, Donovan J.
last_name: Anderson
- first_name: Florian
full_name: Pauler, Florian
id: 48EA0138-F248-11E8-B48F-1D18A9856A87
last_name: Pauler
orcid: 0000-0002-7462-0048
- first_name: Aaron
full_name: Mckenna, Aaron
last_name: Mckenna
- first_name: Jay
full_name: Shendure, Jay
last_name: Shendure
- first_name: Simon
full_name: Hippenmeyer, Simon
id: 37B36620-F248-11E8-B48F-1D18A9856A87
last_name: Hippenmeyer
orcid: 0000-0003-2279-1061
- first_name: Marshall S.
full_name: Horwitz, Marshall S.
last_name: Horwitz
citation:
ama: Anderson DJ, Pauler F, Mckenna A, Shendure J, Hippenmeyer S, Horwitz MS. Simultaneous
brain cell type and lineage determined by scRNA-seq reveals stereotyped cortical
development. Cell Systems. 2022;13(6):438-453.e5. doi:10.1016/j.cels.2022.03.006
apa: Anderson, D. J., Pauler, F., Mckenna, A., Shendure, J., Hippenmeyer, S., &
Horwitz, M. S. (2022). Simultaneous brain cell type and lineage determined by
scRNA-seq reveals stereotyped cortical development. Cell Systems. Elsevier.
https://doi.org/10.1016/j.cels.2022.03.006
chicago: Anderson, Donovan J., Florian Pauler, Aaron Mckenna, Jay Shendure, Simon
Hippenmeyer, and Marshall S. Horwitz. “Simultaneous Brain Cell Type and Lineage
Determined by ScRNA-Seq Reveals Stereotyped Cortical Development.” Cell Systems.
Elsevier, 2022. https://doi.org/10.1016/j.cels.2022.03.006.
ieee: D. J. Anderson, F. Pauler, A. Mckenna, J. Shendure, S. Hippenmeyer, and M.
S. Horwitz, “Simultaneous brain cell type and lineage determined by scRNA-seq
reveals stereotyped cortical development,” Cell Systems, vol. 13, no. 6.
Elsevier, p. 438–453.e5, 2022.
ista: Anderson DJ, Pauler F, Mckenna A, Shendure J, Hippenmeyer S, Horwitz MS. 2022.
Simultaneous brain cell type and lineage determined by scRNA-seq reveals stereotyped
cortical development. Cell Systems. 13(6), 438–453.e5.
mla: Anderson, Donovan J., et al. “Simultaneous Brain Cell Type and Lineage Determined
by ScRNA-Seq Reveals Stereotyped Cortical Development.” Cell Systems, vol.
13, no. 6, Elsevier, 2022, p. 438–453.e5, doi:10.1016/j.cels.2022.03.006.
short: D.J. Anderson, F. Pauler, A. Mckenna, J. Shendure, S. Hippenmeyer, M.S. Horwitz,
Cell Systems 13 (2022) 438–453.e5.
date_created: 2022-06-19T22:01:57Z
date_published: 2022-06-15T00:00:00Z
date_updated: 2026-06-18T17:15:22Z
day: '15'
ddc:
- '570'
department:
- _id: SiHi
doi: 10.1016/j.cels.2022.03.006
ec_funded: 1
external_id:
isi:
- '000814124400002'
pmid:
- '35452605'
intvolume: ' 13'
isi: 1
issue: '6'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.1016/j.cels.2022.03.006
month: '06'
oa: 1
oa_version: Published Version
page: 438-453.e5
pmid: 1
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: 25D92700-B435-11E9-9278-68D0E5697425
grant_number: LS13-002
name: Mapping Cell-Type Specificity of the Genomic Imprintome in the Brain
publication: Cell Systems
publication_identifier:
eissn:
- 2405-4720
issn:
- 2405-4712
publication_status: published
publisher: Elsevier
quality_controlled: '1'
scopus_import: '1'
status: public
title: Simultaneous brain cell type and lineage determined by scRNA-seq reveals stereotyped
cortical development
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 13
year: '2022'
...
---
_id: '11417'
abstract:
- lang: eng
text: "Over the past few years, the field of quantum information science has seen
tremendous progress toward realizing large-scale quantum computers. With demonstrations
of quantum computers outperforming classical computers for a select range of problems,1–3
we have finally entered the noisy, intermediate-scale quantum (NISQ) computing
era. While the quantum computers of today are technological marvels, they are
not yet error corrected, and it is unclear whether any system will scale beyond
a few hundred logical qubits without significant changes to architecture and control
schemes. Today's quantum systems are analogous to the ENIAC (Electronic Numerical
Integrator And Computer) and EDVAC (Electronic Discrete Variable Automatic Computer)
systems of the 1940s, which ran on vacuum tubes. These machines were built on
a solid, nominally scalable architecture and when they were developed, nobody
could have predicted the development of the transistor and the impact of the resulting
semiconductor industry. Simply put, the computers of today are nothing like the
early computers of the 1940s. We believe that the qubits of future fault-tolerant
quantum systems will look quite different from the qubits of the NISQ machines
in operation today. This Special Topic issue is devoted to new and emerging quantum
systems with a focus on enabling technologies that can eventually lead to the
quantum analog to the transistor. We have solicited both research4–18 and perspective
articles19–21 to discuss new and emerging qubit systems with a focus on novel
materials, encodings, and architectures. We are proud to present a collection
that touches on a wide range of technologies including superconductors,7–13,21
semiconductors,15–17,19 and individual atomic qubits.18\r\n"
acknowledgement: "We would like to thank all of the authors who contributed to\r\nthis
Special Topic. We would also like to thank the editorial team at\r\nAPL including
Jessica Trudeau, Emma Van Burns, Martin Weides,\r\nand Lesley Cohen."
article_number: '190401'
article_processing_charge: No
article_type: letter_note
author:
- first_name: Anthony J.
full_name: Sigillito, Anthony J.
last_name: Sigillito
- first_name: Jacob P.
full_name: Covey, Jacob P.
last_name: Covey
- first_name: Johannes M
full_name: Fink, Johannes M
id: 4B591CBA-F248-11E8-B48F-1D18A9856A87
last_name: Fink
orcid: 0000-0001-8112-028X
- first_name: Karl
full_name: Petersson, Karl
last_name: Petersson
- first_name: Stefan
full_name: Preble, Stefan
last_name: Preble
citation:
ama: 'Sigillito AJ, Covey JP, Fink JM, Petersson K, Preble S. Emerging qubit systems:
Guest editorial. Applied Physics Letters. 2022;120(19). doi:10.1063/5.0097339'
apa: 'Sigillito, A. J., Covey, J. P., Fink, J. M., Petersson, K., & Preble,
S. (2022). Emerging qubit systems: Guest editorial. Applied Physics Letters.
American Institute of Physics. https://doi.org/10.1063/5.0097339'
chicago: 'Sigillito, Anthony J., Jacob P. Covey, Johannes M Fink, Karl Petersson,
and Stefan Preble. “Emerging Qubit Systems: Guest Editorial.” Applied Physics
Letters. American Institute of Physics, 2022. https://doi.org/10.1063/5.0097339.'
ieee: 'A. J. Sigillito, J. P. Covey, J. M. Fink, K. Petersson, and S. Preble, “Emerging
qubit systems: Guest editorial,” Applied Physics Letters, vol. 120, no.
19. American Institute of Physics, 2022.'
ista: 'Sigillito AJ, Covey JP, Fink JM, Petersson K, Preble S. 2022. Emerging qubit
systems: Guest editorial. Applied Physics Letters. 120(19), 190401.'
mla: 'Sigillito, Anthony J., et al. “Emerging Qubit Systems: Guest Editorial.” Applied
Physics Letters, vol. 120, no. 19, 190401, American Institute of Physics,
2022, doi:10.1063/5.0097339.'
short: A.J. Sigillito, J.P. Covey, J.M. Fink, K. Petersson, S. Preble, Applied Physics
Letters 120 (2022).
date_created: 2022-05-29T22:01:53Z
date_published: 2022-05-12T00:00:00Z
date_updated: 2026-06-18T17:14:33Z
day: '12'
ddc:
- '530'
department:
- _id: JoFi
doi: 10.1063/5.0097339
external_id:
isi:
- '000796002100002'
intvolume: ' 120'
isi: 1
issue: '19'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.1063/5.0097339
month: '05'
oa: 1
oa_version: Published Version
publication: Applied Physics Letters
publication_identifier:
issn:
- 0003-6951
publication_status: published
publisher: American Institute of Physics
quality_controlled: '1'
scopus_import: '1'
status: public
title: 'Emerging qubit systems: Guest editorial'
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 120
year: '2022'
...
---
_id: '11356'
acknowledgement: This work was supported by the National Science Fund for Distinguished
Young Scholars (51925101), National Key Research and Development Program of China
(2018YFA0702100), 111 Project (B17002), and Lise Meitner Project (M2889-N).
article_processing_charge: No
article_type: letter_note
author:
- first_name: Cheng
full_name: Chang, Cheng
id: 9E331C2E-9F27-11E9-AE48-5033E6697425
last_name: Chang
orcid: 0000-0002-9515-4277
- first_name: Bingchao
full_name: Qin, Bingchao
last_name: Qin
- first_name: Lizhong
full_name: Su, Lizhong
last_name: Su
- first_name: Li Dong
full_name: Zhao, Li Dong
last_name: Zhao
citation:
ama: Chang C, Qin B, Su L, Zhao LD. Distinct electron and hole transports in SnSe
crystals. Science Bulletin. 2022;67(11):1105-1107. doi:10.1016/j.scib.2022.04.007
apa: Chang, C., Qin, B., Su, L., & Zhao, L. D. (2022). Distinct electron and
hole transports in SnSe crystals. Science Bulletin. Elsevier. https://doi.org/10.1016/j.scib.2022.04.007
chicago: Chang, Cheng, Bingchao Qin, Lizhong Su, and Li Dong Zhao. “Distinct Electron
and Hole Transports in SnSe Crystals.” Science Bulletin. Elsevier, 2022.
https://doi.org/10.1016/j.scib.2022.04.007.
ieee: C. Chang, B. Qin, L. Su, and L. D. Zhao, “Distinct electron and hole transports
in SnSe crystals,” Science Bulletin, vol. 67, no. 11. Elsevier, pp. 1105–1107,
2022.
ista: Chang C, Qin B, Su L, Zhao LD. 2022. Distinct electron and hole transports
in SnSe crystals. Science Bulletin. 67(11), 1105–1107.
mla: Chang, Cheng, et al. “Distinct Electron and Hole Transports in SnSe Crystals.”
Science Bulletin, vol. 67, no. 11, Elsevier, 2022, pp. 1105–07, doi:10.1016/j.scib.2022.04.007.
short: C. Chang, B. Qin, L. Su, L.D. Zhao, Science Bulletin 67 (2022) 1105–1107.
date_created: 2022-05-08T22:01:44Z
date_published: 2022-06-15T00:00:00Z
date_updated: 2026-06-18T10:50:26Z
day: '15'
ddc:
- '530'
department:
- _id: MaIb
doi: 10.1016/j.scib.2022.04.007
external_id:
isi:
- '000835291100006'
pmid:
- '36545972'
intvolume: ' 67'
isi: 1
issue: '11'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.1016/j.scib.2022.04.007
month: '06'
oa: 1
oa_version: Published Version
page: 1105-1107
pmid: 1
project:
- _id: 9B8804FC-BA93-11EA-9121-9846C619BF3A
grant_number: M02889
name: Bottom-up Engineering for Thermoelectric Applications
publication: Science Bulletin
publication_identifier:
eissn:
- 2095-9281
issn:
- 2095-9273
publication_status: published
publisher: Elsevier
quality_controlled: '1'
scopus_import: '1'
status: public
title: Distinct electron and hole transports in SnSe crystals
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 67
year: '2022'
...
---
_id: '11736'
abstract:
- lang: eng
text: "This paper introduces a methodology for inverse-modeling of yarn-level mechanics
of cloth, based on the mechanical response of fabrics in the real world. We compiled
a database from physical tests of several different knitted fabrics used in the
textile industry. These data span different types of complex knit patterns, yarn
compositions, and fabric finishes, and the results demonstrate diverse physical
properties like stiffness, nonlinearity, and anisotropy.\r\n\r\nWe then develop
a system for approximating these mechanical responses with yarn-level cloth simulation.
To do so, we introduce an efficient pipeline for converting between fabric-level
data and yarn-level simulation, including a novel swatch-level approximation for
speeding up computation, and some small-but-necessary extensions to yarn-level
models used in computer graphics. The dataset used for this paper can be found
at http://mslab.es/projects/YarnLevelFabrics."
acknowledged_ssus:
- _id: ScienComp
acknowledgement: We wish to thank the anonymous reviewers for their helpful comments.
To develop this project, we were helped by many people both at Under Armour (Clay
Dean, Randall Harward, Kyle Blakely, Craig Simile, Michael Seiz, Brooke Malone,
Brittainy McFarland, Emilie Phan, Lindsey Kern, Courtney Oswald, Haley Barkley,
Bob Chin, Adam Bayer, Connie Kwok, Marielle Newman, Nick Pence, Allison Hicks, Allison
White, Candace Rubenstein, Jeremy Stangland, Fred Fagergren, Michael Mazzoleni,
Nathaniel Berry, Manuel Frank) and SEDDI (Gabriel Cirio, Alejandro Rodríguez, Sofía
Dominguez, Alicia Nicas, Elena Garcés, Daniel Rodríguez, David Pascual, Manuel Godoy,
Sergio Suja, Sergio Ruiz, Roberto Condori, Alberto Martín, Graham Sullivan). We
also thank the members of the Visual Computing Group at IST Austria and the Multimodal
Simulation Lab at URJC for their feedback. This research was supported by the Scientific
Service Units (SSU) of IST Austria through resources provided by Scientific Computing,
and it was funded in part by the European Research Council (ERC Consolidator Grant
772738 TouchDesign).
article_number: '65'
article_processing_charge: No
article_type: original
author:
- first_name: Georg
full_name: Sperl, Georg
id: 4DD40360-F248-11E8-B48F-1D18A9856A87
last_name: Sperl
- first_name: Rosa M.
full_name: Sánchez-Banderas, Rosa M.
last_name: Sánchez-Banderas
- first_name: Manwen
full_name: Li, Manwen
last_name: Li
- first_name: Christopher J
full_name: Wojtan, Christopher J
id: 3C61F1D2-F248-11E8-B48F-1D18A9856A87
last_name: Wojtan
orcid: 0000-0001-6646-5546
- first_name: Miguel A.
full_name: Otaduy, Miguel A.
last_name: Otaduy
citation:
ama: Sperl G, Sánchez-Banderas RM, Li M, Wojtan C, Otaduy MA. Estimation of yarn-level
simulation models for production fabrics. ACM Transactions on Graphics.
2022;41(4). doi:10.1145/3528223.3530167
apa: Sperl, G., Sánchez-Banderas, R. M., Li, M., Wojtan, C., & Otaduy, M. A.
(2022). Estimation of yarn-level simulation models for production fabrics. ACM
Transactions on Graphics. Association for Computing Machinery. https://doi.org/10.1145/3528223.3530167
chicago: Sperl, Georg, Rosa M. Sánchez-Banderas, Manwen Li, Chris Wojtan, and Miguel
A. Otaduy. “Estimation of Yarn-Level Simulation Models for Production Fabrics.”
ACM Transactions on Graphics. Association for Computing Machinery, 2022.
https://doi.org/10.1145/3528223.3530167.
ieee: G. Sperl, R. M. Sánchez-Banderas, M. Li, C. Wojtan, and M. A. Otaduy, “Estimation
of yarn-level simulation models for production fabrics,” ACM Transactions on
Graphics, vol. 41, no. 4. Association for Computing Machinery, 2022.
ista: Sperl G, Sánchez-Banderas RM, Li M, Wojtan C, Otaduy MA. 2022. Estimation
of yarn-level simulation models for production fabrics. ACM Transactions on Graphics.
41(4), 65.
mla: Sperl, Georg, et al. “Estimation of Yarn-Level Simulation Models for Production
Fabrics.” ACM Transactions on Graphics, vol. 41, no. 4, 65, Association
for Computing Machinery, 2022, doi:10.1145/3528223.3530167.
short: G. Sperl, R.M. Sánchez-Banderas, M. Li, C. Wojtan, M.A. Otaduy, ACM Transactions
on Graphics 41 (2022).
date_created: 2022-08-07T22:01:58Z
date_published: 2022-07-22T00:00:00Z
date_updated: 2026-06-18T17:20:41Z
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title: Estimation of yarn-level simulation models for production fabrics
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