---
_id: '12130'
abstract:
- lang: eng
text: Germline determination is essential for species survival and evolution in
multicellular organisms. In most flowering plants, formation of the female germline
is initiated with specification of one megaspore mother cell (MMC) in each ovule;
however, the molecular mechanism underlying this key event remains unclear. Here
we report that spatially restricted auxin signaling promotes MMC fate in Arabidopsis.
Our results show that the microRNA160 (miR160) targeted gene ARF17 (AUXIN RESPONSE
FACTOR17) is required for promoting MMC specification by genetically interacting
with the SPL/NZZ (SPOROCYTELESS/NOZZLE) gene. Alterations of auxin signaling cause
formation of supernumerary MMCs in an ARF17- and SPL/NZZ-dependent manner. Furthermore,
miR160 and ARF17 are indispensable for attaining a normal auxin maximum at the
ovule apex via modulating the expression domain of PIN1 (PIN-FORMED1) auxin transporter.
Our findings elucidate the mechanism by which auxin signaling promotes the acquisition
of female germline cell fate in plants.
acknowledgement: "We thank A. Cheung,W. Lukowitz, V.Walbot, D.Weijers, and R. Yadegari
for critically reading the manuscript; E. Xiong and G. Zhang for preparing some
experiments, T. Schuck, J. Gonnering, and P. Engevold for plant care, the Arabidopsis
Biological Resource Center (ABRC) for ARF10,ARF16, ARF17, EMS1,MIR160a BAC clones
and cDNAs, the SALK_090804 seed, T. Nakagawa for pGBW vectors, Y. Zhao for the YUC1
cDNA, Q. Chen for the pHEE401E vector, R. Yadegari for pAT5G01860::n1GFP, pAT5G45980:n1GFP,
pAT5G50490::n1GFP, pAT5G56200:n1GFP vectors, and D.Weijers for the pGreenII KAN
SV40-3×GFP and R2D2 vectors, W. Yang for the splmutant, Y. Qin for the pKNU::KNU-VENUS
vector and seed, G. Tang for the STTM160/160-48 vector, and L. Colombo for pPIN1::PIN1-GFP
spl and pin1-5 seeds. This work was supported by the US National Science Foundation
(NSF)-Israel Binational Science Foundation (BSF) research grant to D.Z. (IOS-1322796)
and T.A. (2012756). D.Z. also\r\ngratefully acknowledges supports of the Shaw Scientist
Award from the Greater Milwaukee Foundation, USDA National Institute of Food and
Agriculture (NIFA, 2022-67013-36294), the UWM Discovery and Innovation Grant, the
Bradley Catalyst Award from the UWM Research\r\nFoundation, and WiSys and UW System
Applied Research Funding Programs."
article_number: '6960'
article_processing_charge: No
article_type: original
author:
- first_name: Jian
full_name: Huang, Jian
last_name: Huang
- first_name: Lei
full_name: Zhao, Lei
last_name: Zhao
- first_name: Shikha
full_name: Malik, Shikha
last_name: Malik
- first_name: Benjamin R.
full_name: Gentile, Benjamin R.
last_name: Gentile
- first_name: Va
full_name: Xiong, Va
last_name: Xiong
- first_name: Tzahi
full_name: Arazi, Tzahi
last_name: Arazi
- first_name: Heather A.
full_name: Owen, Heather A.
last_name: Owen
- first_name: Jiří
full_name: Friml, Jiří
id: 4159519E-F248-11E8-B48F-1D18A9856A87
last_name: Friml
orcid: 0000-0002-8302-7596
- first_name: Dazhong
full_name: Zhao, Dazhong
last_name: Zhao
citation:
ama: Huang J, Zhao L, Malik S, et al. Specification of female germline by microRNA
orchestrated auxin signaling in Arabidopsis. Nature Communications. 2022;13.
doi:10.1038/s41467-022-34723-6
apa: Huang, J., Zhao, L., Malik, S., Gentile, B. R., Xiong, V., Arazi, T., … Zhao,
D. (2022). Specification of female germline by microRNA orchestrated auxin signaling
in Arabidopsis. Nature Communications. Springer Nature. https://doi.org/10.1038/s41467-022-34723-6
chicago: Huang, Jian, Lei Zhao, Shikha Malik, Benjamin R. Gentile, Va Xiong, Tzahi
Arazi, Heather A. Owen, Jiří Friml, and Dazhong Zhao. “Specification of Female
Germline by MicroRNA Orchestrated Auxin Signaling in Arabidopsis.” Nature Communications.
Springer Nature, 2022. https://doi.org/10.1038/s41467-022-34723-6.
ieee: J. Huang et al., “Specification of female germline by microRNA orchestrated
auxin signaling in Arabidopsis,” Nature Communications, vol. 13. Springer
Nature, 2022.
ista: Huang J, Zhao L, Malik S, Gentile BR, Xiong V, Arazi T, Owen HA, Friml J,
Zhao D. 2022. Specification of female germline by microRNA orchestrated auxin
signaling in Arabidopsis. Nature Communications. 13, 6960.
mla: Huang, Jian, et al. “Specification of Female Germline by MicroRNA Orchestrated
Auxin Signaling in Arabidopsis.” Nature Communications, vol. 13, 6960,
Springer Nature, 2022, doi:10.1038/s41467-022-34723-6.
short: J. Huang, L. Zhao, S. Malik, B.R. Gentile, V. Xiong, T. Arazi, H.A. Owen,
J. Friml, D. Zhao, Nature Communications 13 (2022).
date_created: 2023-01-12T12:02:41Z
date_published: 2022-11-15T00:00:00Z
date_updated: 2023-08-04T08:52:01Z
day: '15'
ddc:
- '580'
department:
- _id: JiFr
doi: 10.1038/s41467-022-34723-6
external_id:
isi:
- '000884426700001'
pmid:
- '36379956'
file:
- access_level: open_access
checksum: 233922a7b9507d9d48591e6799e4526e
content_type: application/pdf
creator: dernst
date_created: 2023-01-23T11:17:33Z
date_updated: 2023-01-23T11:17:33Z
file_id: '12346'
file_name: 2022_NatureCommunications_Huang.pdf
file_size: 3375249
relation: main_file
success: 1
file_date_updated: 2023-01-23T11:17:33Z
has_accepted_license: '1'
intvolume: ' 13'
isi: 1
keyword:
- General Physics and Astronomy
- General Biochemistry
- Genetics and Molecular Biology
- General Chemistry
- Multidisciplinary
language:
- iso: eng
license: https://creativecommons.org/licenses/by/4.0/
month: '11'
oa: 1
oa_version: Published Version
pmid: 1
publication: Nature Communications
publication_identifier:
issn:
- 2041-1723
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
scopus_import: '1'
status: public
title: Specification of female germline by microRNA orchestrated auxin signaling in
Arabidopsis
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: journal_article
user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
volume: 13
year: '2022'
...
---
_id: '12131'
abstract:
- lang: eng
text: Replication-incompetent adenoviral vectors have been extensively used as a
platform for vaccine design, with at least four anti-COVID-19 vaccines authorized
to date. These vaccines elicit neutralizing antibody responses directed against
SARS-CoV-2 Spike protein and confer significant level of protection against SARS-CoV-2
infection. Immunization with adenovirus-vectored vaccines is known to be accompanied
by the production of anti-vector antibodies, which may translate into reduced
efficacy of booster or repeated rounds of revaccination. Here, we used blood samples
from patients who received an adenovirus-based Gam-COVID-Vac vaccine to address
the question of whether anti-vector antibodies may influence the magnitude of
SARS-CoV-2-specific humoral response after booster vaccination. We observed that
rAd26-based prime vaccination with Gam-COVID-Vac induced the development of Ad26-neutralizing
antibodies, which persisted in circulation for at least 9 months. Our analysis
further indicates that high pre-boost Ad26 neutralizing antibody titers do not
appear to affect the humoral immunogenicity of the Gam-COVID-Vac boost. The titers
of anti-SARS-CoV-2 RBD IgGs and antibodies, which neutralized both the wild type
and the circulating variants of concern of SARS-CoV-2 such as Delta and Omicron,
were independent of the pre-boost levels of Ad26-neutralizing antibodies. Thus,
our results support the development of repeated immunization schedule with adenovirus-based
COVID-19 vaccines.
acknowledgement: We thank Sergey Kulemzin, Grigory Efimov, Yuri Lebedin, Alexander
Taranin and Rudolf Valenta for providing reagents. Figures were created with the
help of BioRender.com. This work was supported by the Russian Science Foundation
(Project 21-15-00286). Byazrova M.G. was supported by the RUDN University Strategic
Academic Leadership Program.
article_number: '145'
article_processing_charge: No
article_type: original
author:
- first_name: Maria G.
full_name: Byazrova, Maria G.
last_name: Byazrova
- first_name: Ekaterina A.
full_name: Astakhova, Ekaterina A.
last_name: Astakhova
- first_name: Aygul
full_name: Minnegalieva, Aygul
id: 87DF77F0-1D9A-11EA-B6AE-CE443DDC885E
last_name: Minnegalieva
- first_name: Maria M.
full_name: Sukhova, Maria M.
last_name: Sukhova
- first_name: Artem A.
full_name: Mikhailov, Artem A.
last_name: Mikhailov
- first_name: Alexey G.
full_name: Prilipov, Alexey G.
last_name: Prilipov
- first_name: Andrey A.
full_name: Gorchakov, Andrey A.
last_name: Gorchakov
- first_name: Alexander V.
full_name: Filatov, Alexander V.
last_name: Filatov
citation:
ama: Byazrova MG, Astakhova EA, Minnegalieva A, et al. Anti-Ad26 humoral immunity
does not compromise SARS-COV-2 neutralizing antibody responses following Gam-COVID-Vac
booster vaccination. npj Vaccines. 2022;7. doi:10.1038/s41541-022-00566-x
apa: Byazrova, M. G., Astakhova, E. A., Minnegalieva, A., Sukhova, M. M., Mikhailov,
A. A., Prilipov, A. G., … Filatov, A. V. (2022). Anti-Ad26 humoral immunity does
not compromise SARS-COV-2 neutralizing antibody responses following Gam-COVID-Vac
booster vaccination. Npj Vaccines. Springer Nature. https://doi.org/10.1038/s41541-022-00566-x
chicago: Byazrova, Maria G., Ekaterina A. Astakhova, Aygul Minnegalieva, Maria M.
Sukhova, Artem A. Mikhailov, Alexey G. Prilipov, Andrey A. Gorchakov, and Alexander
V. Filatov. “Anti-Ad26 Humoral Immunity Does Not Compromise SARS-COV-2 Neutralizing
Antibody Responses Following Gam-COVID-Vac Booster Vaccination.” Npj Vaccines.
Springer Nature, 2022. https://doi.org/10.1038/s41541-022-00566-x.
ieee: M. G. Byazrova et al., “Anti-Ad26 humoral immunity does not compromise
SARS-COV-2 neutralizing antibody responses following Gam-COVID-Vac booster vaccination,”
npj Vaccines, vol. 7. Springer Nature, 2022.
ista: Byazrova MG, Astakhova EA, Minnegalieva A, Sukhova MM, Mikhailov AA, Prilipov
AG, Gorchakov AA, Filatov AV. 2022. Anti-Ad26 humoral immunity does not compromise
SARS-COV-2 neutralizing antibody responses following Gam-COVID-Vac booster vaccination.
npj Vaccines. 7, 145.
mla: Byazrova, Maria G., et al. “Anti-Ad26 Humoral Immunity Does Not Compromise
SARS-COV-2 Neutralizing Antibody Responses Following Gam-COVID-Vac Booster Vaccination.”
Npj Vaccines, vol. 7, 145, Springer Nature, 2022, doi:10.1038/s41541-022-00566-x.
short: M.G. Byazrova, E.A. Astakhova, A. Minnegalieva, M.M. Sukhova, A.A. Mikhailov,
A.G. Prilipov, A.A. Gorchakov, A.V. Filatov, Npj Vaccines 7 (2022).
date_created: 2023-01-12T12:02:54Z
date_published: 2022-11-15T00:00:00Z
date_updated: 2023-08-04T08:52:40Z
day: '15'
ddc:
- '570'
department:
- _id: FyKo
doi: 10.1038/s41541-022-00566-x
external_id:
isi:
- '000884278600004'
pmid:
- '36379998'
file:
- access_level: open_access
checksum: ddaac096381565b2b4b7dcc34cdbc4ee
content_type: application/pdf
creator: dernst
date_created: 2023-01-23T11:22:09Z
date_updated: 2023-01-23T11:22:09Z
file_id: '12347'
file_name: 2022_njpVaccines_Byazrova.pdf
file_size: 1856046
relation: main_file
success: 1
file_date_updated: 2023-01-23T11:22:09Z
has_accepted_license: '1'
intvolume: ' 7'
isi: 1
keyword:
- Pharmacology (medical)
- Infectious Diseases
- Pharmacology
- Immunology
- SARS-COV-2
- COVID
language:
- iso: eng
month: '11'
oa: 1
oa_version: Published Version
pmid: 1
publication: npj Vaccines
publication_identifier:
issn:
- 2059-0105
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
scopus_import: '1'
status: public
title: Anti-Ad26 humoral immunity does not compromise SARS-COV-2 neutralizing antibody
responses following Gam-COVID-Vac booster vaccination
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: journal_article
user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
volume: 7
year: '2022'
...
---
_id: '12133'
abstract:
- lang: eng
text: Social distancing is an effective way to prevent the spread of disease in
societies, whereas infection elimination is a key element of organismal immunity.
Here, we discuss how the study of social insects such as ants — which form a superorganism
of unconditionally cooperative individuals and thus represent a level of organization
that is intermediate between a classical society of individuals and an organism
of cells — can help to determine common principles of disease defence across levels
of organization.
article_processing_charge: No
article_type: letter_note
author:
- first_name: Sylvia
full_name: Cremer, Sylvia
id: 2F64EC8C-F248-11E8-B48F-1D18A9856A87
last_name: Cremer
orcid: 0000-0002-2193-3868
- first_name: Michael K
full_name: Sixt, Michael K
id: 41E9FBEA-F248-11E8-B48F-1D18A9856A87
last_name: Sixt
orcid: 0000-0002-6620-9179
citation:
ama: Cremer S, Sixt MK. Principles of disease defence in organisms, superorganisms
and societies. Nature Reviews Immunology. 2022;22(12):713-714. doi:10.1038/s41577-022-00797-y
apa: Cremer, S., & Sixt, M. K. (2022). Principles of disease defence in organisms,
superorganisms and societies. Nature Reviews Immunology. Springer Nature.
https://doi.org/10.1038/s41577-022-00797-y
chicago: Cremer, Sylvia, and Michael K Sixt. “Principles of Disease Defence in Organisms,
Superorganisms and Societies.” Nature Reviews Immunology. Springer Nature,
2022. https://doi.org/10.1038/s41577-022-00797-y.
ieee: S. Cremer and M. K. Sixt, “Principles of disease defence in organisms, superorganisms
and societies,” Nature Reviews Immunology, vol. 22, no. 12. Springer Nature,
pp. 713–714, 2022.
ista: Cremer S, Sixt MK. 2022. Principles of disease defence in organisms, superorganisms
and societies. Nature Reviews Immunology. 22(12), 713–714.
mla: Cremer, Sylvia, and Michael K. Sixt. “Principles of Disease Defence in Organisms,
Superorganisms and Societies.” Nature Reviews Immunology, vol. 22, no.
12, Springer Nature, 2022, pp. 713–14, doi:10.1038/s41577-022-00797-y.
short: S. Cremer, M.K. Sixt, Nature Reviews Immunology 22 (2022) 713–714.
date_created: 2023-01-12T12:03:14Z
date_published: 2022-12-01T00:00:00Z
date_updated: 2023-08-04T08:53:32Z
day: '01'
department:
- _id: SyCr
- _id: MiSi
doi: 10.1038/s41577-022-00797-y
external_id:
isi:
- '000871836300001'
pmid:
- '36284178'
intvolume: ' 22'
isi: 1
issue: '12'
keyword:
- Energy Engineering and Power Technology
- Fuel Technology
language:
- iso: eng
month: '12'
oa_version: None
page: 713-714
pmid: 1
publication: Nature Reviews Immunology
publication_identifier:
eissn:
- 1474-1741
issn:
- 1474-1733
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
scopus_import: '1'
status: public
title: Principles of disease defence in organisms, superorganisms and societies
type: journal_article
user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
volume: 22
year: '2022'
...
---
_id: '12134'
abstract:
- lang: eng
text: Standard epidemic models exhibit one continuous, second order phase transition
to macroscopic outbreaks. However, interventions to control outbreaks may fundamentally
alter epidemic dynamics. Here we reveal how such interventions modify the type
of phase transition. In particular, we uncover three distinct types of explosive
phase transitions for epidemic dynamics with capacity-limited interventions. Depending
on the capacity limit, interventions may (i) leave the standard second order phase
transition unchanged but exponentially suppress the probability of large outbreaks,
(ii) induce a first-order discontinuous transition to macroscopic outbreaks, or
(iii) cause a secondary explosive yet continuous third-order transition. These
insights highlight inherent limitations in predicting and containing epidemic
outbreaks. More generally our study offers a cornerstone example of a third-order
explosive phase transition in complex systems.
acknowledgement: We acknowledge support from the Volkswagen Foundation under Grant
No. 99720 and the German Federal Ministry for Education and Research (BMBF) under
Grant No. 16ICR01. This research was supported by the Deutsche Forschungsgemeinschaft
(DFG, German Research Foundation) under Germany’s Excellence Strategy—EXC-2068—390729961—Cluster
of Excellence Physics of Life of TU Dresden.
article_number: 04LT02
article_processing_charge: No
article_type: original
author:
- first_name: Georg
full_name: Börner, Georg
last_name: Börner
- first_name: Malte
full_name: Schröder, Malte
last_name: Schröder
- first_name: Davide
full_name: Scarselli, Davide
id: 40315C30-F248-11E8-B48F-1D18A9856A87
last_name: Scarselli
orcid: 0000-0001-5227-4271
- first_name: Nazmi B
full_name: Budanur, Nazmi B
id: 3EA1010E-F248-11E8-B48F-1D18A9856A87
last_name: Budanur
orcid: 0000-0003-0423-5010
- first_name: Björn
full_name: Hof, Björn
id: 3A374330-F248-11E8-B48F-1D18A9856A87
last_name: Hof
orcid: 0000-0003-2057-2754
- first_name: Marc
full_name: Timme, Marc
last_name: Timme
citation:
ama: 'Börner G, Schröder M, Scarselli D, Budanur NB, Hof B, Timme M. Explosive transitions
in epidemic dynamics. Journal of Physics: Complexity. 2022;3(4). doi:10.1088/2632-072x/ac99cd'
apa: 'Börner, G., Schröder, M., Scarselli, D., Budanur, N. B., Hof, B., & Timme,
M. (2022). Explosive transitions in epidemic dynamics. Journal of Physics:
Complexity. IOP Publishing. https://doi.org/10.1088/2632-072x/ac99cd'
chicago: 'Börner, Georg, Malte Schröder, Davide Scarselli, Nazmi B Budanur, Björn
Hof, and Marc Timme. “Explosive Transitions in Epidemic Dynamics.” Journal
of Physics: Complexity. IOP Publishing, 2022. https://doi.org/10.1088/2632-072x/ac99cd.'
ieee: 'G. Börner, M. Schröder, D. Scarselli, N. B. Budanur, B. Hof, and M. Timme,
“Explosive transitions in epidemic dynamics,” Journal of Physics: Complexity,
vol. 3, no. 4. IOP Publishing, 2022.'
ista: 'Börner G, Schröder M, Scarselli D, Budanur NB, Hof B, Timme M. 2022. Explosive
transitions in epidemic dynamics. Journal of Physics: Complexity. 3(4), 04LT02.'
mla: 'Börner, Georg, et al. “Explosive Transitions in Epidemic Dynamics.” Journal
of Physics: Complexity, vol. 3, no. 4, 04LT02, IOP Publishing, 2022, doi:10.1088/2632-072x/ac99cd.'
short: 'G. Börner, M. Schröder, D. Scarselli, N.B. Budanur, B. Hof, M. Timme, Journal
of Physics: Complexity 3 (2022).'
date_created: 2023-01-12T12:03:43Z
date_published: 2022-10-25T00:00:00Z
date_updated: 2023-02-13T09:15:13Z
day: '25'
ddc:
- '530'
department:
- _id: BjHo
doi: 10.1088/2632-072x/ac99cd
file:
- access_level: open_access
checksum: 35c5c5cb0eb17ea1b5184755daab9fc9
content_type: application/pdf
creator: dernst
date_created: 2023-01-24T07:24:37Z
date_updated: 2023-01-24T07:24:37Z
file_id: '12350'
file_name: 2022_JourPhysics_Boerner.pdf
file_size: 1006106
relation: main_file
success: 1
file_date_updated: 2023-01-24T07:24:37Z
has_accepted_license: '1'
intvolume: ' 3'
issue: '4'
keyword:
- Artificial Intelligence
- Computer Networks and Communications
- Computer Science Applications
- Information Systems
language:
- iso: eng
month: '10'
oa: 1
oa_version: Published Version
publication: 'Journal of Physics: Complexity'
publication_identifier:
issn:
- 2632-072X
publication_status: published
publisher: IOP Publishing
quality_controlled: '1'
scopus_import: '1'
status: public
title: Explosive transitions in epidemic dynamics
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: 3
year: '2022'
...
---
_id: '12135'
abstract:
- lang: eng
text: A good match of material appearance between real-world objects and their digital
on-screen representations is critical for many applications such as fabrication,
design, and e-commerce. However, faithful appearance reproduction is challenging,
especially for complex phenomena, such as gloss. In most cases, the view-dependent
nature of gloss and the range of luminance values required for reproducing glossy
materials exceeds the current capabilities of display devices. As a result, appearance
reproduction poses significant problems even with accurately rendered images.
This paper studies the gap between the gloss perceived from real-world objects
and their digital counterparts. Based on our psychophysical experiments on a wide
range of 3D printed samples and their corresponding photographs, we derive insights
on the influence of geometry, illumination, and the display’s brightness and measure
the change in gloss appearance due to the display limitations. Our evaluation
experiments demonstrate that using the prediction to correct material parameters
in a rendering system improves the match of gloss appearance between real objects
and their visualization on a display device.
acknowledgement: This work is supported by FWF Lise Meitner (Grant M 3319), European
Research Council (project CHAMELEON, Grant no. 682080), Swiss National Science Foundation
(Grant no. 200502), and academic gifts from Meta.
article_number: '35'
article_processing_charge: No
author:
- first_name: Bin
full_name: Chen, Bin
last_name: Chen
- first_name: Michael
full_name: Piovarci, Michael
id: 62E473F4-5C99-11EA-A40E-AF823DDC885E
last_name: Piovarci
- first_name: Chao
full_name: Wang, Chao
last_name: Wang
- first_name: Hans-Peter
full_name: Seidel, Hans-Peter
last_name: Seidel
- first_name: Piotr
full_name: Didyk, Piotr
last_name: Didyk
- first_name: Karol
full_name: Myszkowski, Karol
last_name: Myszkowski
- first_name: Ana
full_name: Serrano, Ana
last_name: Serrano
citation:
ama: 'Chen B, Piovarci M, Wang C, et al. Gloss management for consistent reproduction
of real and virtual objects. In: SIGGRAPH Asia 2022 Conference Papers.
Vol 2022. Association for Computing Machinery; 2022. doi:10.1145/3550469.3555406'
apa: 'Chen, B., Piovarci, M., Wang, C., Seidel, H.-P., Didyk, P., Myszkowski, K.,
& Serrano, A. (2022). Gloss management for consistent reproduction of real
and virtual objects. In SIGGRAPH Asia 2022 Conference Papers (Vol. 2022).
Daegu, South Korea: Association for Computing Machinery. https://doi.org/10.1145/3550469.3555406'
chicago: Chen, Bin, Michael Piovarci, Chao Wang, Hans-Peter Seidel, Piotr Didyk,
Karol Myszkowski, and Ana Serrano. “Gloss Management for Consistent Reproduction
of Real and Virtual Objects.” In SIGGRAPH Asia 2022 Conference Papers,
Vol. 2022. Association for Computing Machinery, 2022. https://doi.org/10.1145/3550469.3555406.
ieee: B. Chen et al., “Gloss management for consistent reproduction of real
and virtual objects,” in SIGGRAPH Asia 2022 Conference Papers, Daegu, South
Korea, 2022, vol. 2022.
ista: 'Chen B, Piovarci M, Wang C, Seidel H-P, Didyk P, Myszkowski K, Serrano A.
2022. Gloss management for consistent reproduction of real and virtual objects.
SIGGRAPH Asia 2022 Conference Papers. SIGGRAPH: Computer Graphics and Interactive
Techniques Conference vol. 2022, 35.'
mla: Chen, Bin, et al. “Gloss Management for Consistent Reproduction of Real and
Virtual Objects.” SIGGRAPH Asia 2022 Conference Papers, vol. 2022, 35,
Association for Computing Machinery, 2022, doi:10.1145/3550469.3555406.
short: B. Chen, M. Piovarci, C. Wang, H.-P. Seidel, P. Didyk, K. Myszkowski, A.
Serrano, in:, SIGGRAPH Asia 2022 Conference Papers, Association for Computing
Machinery, 2022.
conference:
end_date: 2022-12-09
location: Daegu, South Korea
name: 'SIGGRAPH: Computer Graphics and Interactive Techniques Conference'
start_date: 2022-12-06
date_created: 2023-01-12T12:03:56Z
date_published: 2022-11-01T00:00:00Z
date_updated: 2023-02-13T09:15:25Z
day: '01'
ddc:
- '000'
department:
- _id: BeBi
doi: 10.1145/3550469.3555406
file:
- access_level: open_access
checksum: f47f3215ab8bb919e3546b3438c34c21
content_type: application/pdf
creator: dernst
date_created: 2023-01-24T07:35:21Z
date_updated: 2023-01-24T07:35:21Z
file_id: '12351'
file_name: 2022_ACM_SIGGRAPH_Chen.pdf
file_size: 28826826
relation: main_file
success: 1
file_date_updated: 2023-01-24T07:35:21Z
has_accepted_license: '1'
intvolume: ' 2022'
language:
- iso: eng
month: '11'
oa: 1
oa_version: Published Version
project:
- _id: eb901961-77a9-11ec-83b8-f5c883a62027
grant_number: M03319
name: Perception-Aware Appearance Fabrication
publication: SIGGRAPH Asia 2022 Conference Papers
publication_identifier:
isbn:
- '9781450394703'
publication_status: published
publisher: Association for Computing Machinery
quality_controlled: '1'
scopus_import: '1'
status: public
title: Gloss management for consistent reproduction of real and virtual objects
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: conference
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 2022
year: '2022'
...
---
_id: '12137'
abstract:
- lang: eng
text: We investigate the local self-sustained process underlying spiral turbulence
in counter-rotating Taylor–Couette flow using a periodic annular domain, shaped
as a parallelogram, two of whose sides are aligned with the cylindrical helix
described by the spiral pattern. The primary focus of the study is placed on the
emergence of drifting–rotating waves (DRW) that capture, in a relatively small
domain, the main features of coherent structures typically observed in developed
turbulence. The transitional dynamics of the subcritical region, far below the
first instability of the laminar circular Couette flow, is determined by the upper
and lower branches of DRW solutions originated at saddle-node bifurcations. The
mechanism whereby these solutions self-sustain, and the chaotic dynamics they
induce, are conspicuously reminiscent of other subcritical shear flows. Remarkably,
the flow properties of DRW persist even as the Reynolds number is increased beyond
the linear stability threshold of the base flow. Simulations in a narrow parallelogram
domain stretched in the azimuthal direction to revolve around the apparatus a
full turn confirm that self-sustained vortices eventually concentrate into a localised
pattern. The resulting statistical steady state satisfactorily reproduces qualitatively,
and to a certain degree also quantitatively, the topology and properties of spiral
turbulence as calculated in a large periodic domain of sufficient aspect ratio
that is representative of the real system.
acknowledgement: "K.D.’s research was supported by an Australian Research Council
Discovery Early Career\r\nResearcher Award (DE170100171). B.W., R.A., F.M. and A.M.
research was supported by the Spanish Ministerio de Economía y Competitivdad (grant
numbers FIS2016-77849-R and FIS2017-85794-P) and Ministerio de Ciencia e Innovación
(grant number PID2020-114043GB-I00) and the Generalitat de Catalunya (grant 2017-SGR-785).
B.W.’s research was also supported by the Chinese Scholarship Council (grant CSC
no. 201806440152)."
article_number: A21
article_processing_charge: No
article_type: original
arxiv: 1
author:
- first_name: B.
full_name: Wang, B.
last_name: Wang
- first_name: Roger
full_name: Ayats López, Roger
id: ab77522d-073b-11ed-8aff-e71b39258362
last_name: Ayats López
orcid: 0000-0001-6572-0621
- first_name: K.
full_name: Deguchi, K.
last_name: Deguchi
- first_name: F.
full_name: Mellibovsky, F.
last_name: Mellibovsky
- first_name: A.
full_name: Meseguer, A.
last_name: Meseguer
citation:
ama: Wang B, Ayats López R, Deguchi K, Mellibovsky F, Meseguer A. Self-sustainment
of coherent structures in counter-rotating Taylor–Couette flow. Journal of
Fluid Mechanics. 2022;951. doi:10.1017/jfm.2022.828
apa: Wang, B., Ayats López, R., Deguchi, K., Mellibovsky, F., & Meseguer, A.
(2022). Self-sustainment of coherent structures in counter-rotating Taylor–Couette
flow. Journal of Fluid Mechanics. Cambridge University Press. https://doi.org/10.1017/jfm.2022.828
chicago: Wang, B., Roger Ayats López, K. Deguchi, F. Mellibovsky, and A. Meseguer.
“Self-Sustainment of Coherent Structures in Counter-Rotating Taylor–Couette Flow.”
Journal of Fluid Mechanics. Cambridge University Press, 2022. https://doi.org/10.1017/jfm.2022.828.
ieee: B. Wang, R. Ayats López, K. Deguchi, F. Mellibovsky, and A. Meseguer, “Self-sustainment
of coherent structures in counter-rotating Taylor–Couette flow,” Journal of
Fluid Mechanics, vol. 951. Cambridge University Press, 2022.
ista: Wang B, Ayats López R, Deguchi K, Mellibovsky F, Meseguer A. 2022. Self-sustainment
of coherent structures in counter-rotating Taylor–Couette flow. Journal of Fluid
Mechanics. 951, A21.
mla: Wang, B., et al. “Self-Sustainment of Coherent Structures in Counter-Rotating
Taylor–Couette Flow.” Journal of Fluid Mechanics, vol. 951, A21, Cambridge
University Press, 2022, doi:10.1017/jfm.2022.828.
short: B. Wang, R. Ayats López, K. Deguchi, F. Mellibovsky, A. Meseguer, Journal
of Fluid Mechanics 951 (2022).
date_created: 2023-01-12T12:04:17Z
date_published: 2022-11-07T00:00:00Z
date_updated: 2023-08-04T08:54:16Z
day: '07'
department:
- _id: BjHo
doi: 10.1017/jfm.2022.828
external_id:
arxiv:
- '2207.12990'
isi:
- '000879446900001'
intvolume: ' 951'
isi: 1
keyword:
- Mechanical Engineering
- Mechanics of Materials
- Condensed Matter Physics
- Applied Mathematics
language:
- iso: eng
main_file_link:
- open_access: '1'
url: ' https://doi.org/10.48550/arXiv.2207.12990'
month: '11'
oa: 1
oa_version: Preprint
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: Self-sustainment of coherent structures in counter-rotating Taylor–Couette
flow
type: journal_article
user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
volume: 951
year: '2022'
...
---
_id: '12138'
abstract:
- lang: eng
text: 'Complex I is the first enzyme in the respiratory chain, which is responsible
for energy production in mitochondria and bacteria1. Complex I couples the transfer
of two electrons from NADH to quinone and the translocation of four protons across
the membrane2, but the coupling mechanism remains contentious. Here we present
cryo-electron microscopy structures of Escherichia coli complex I (EcCI) in different
redox states, including catalytic turnover. EcCI exists mostly in the open state,
in which the quinone cavity is exposed to the cytosol, allowing access for water
molecules, which enable quinone movements. Unlike the mammalian paralogues3, EcCI
can convert to the closed state only during turnover, showing that closed and
open states are genuine turnover intermediates. The open-to-closed transition
results in the tightly engulfed quinone cavity being connected to the central
axis of the membrane arm, a source of substrate protons. Consistently, the proportion
of the closed state increases with increasing pH. We propose a detailed but straightforward
and robust mechanism comprising a ‘domino effect’ series of proton transfers and
electrostatic interactions: the forward wave (‘dominoes stacking’) primes the
pump, and the reverse wave (‘dominoes falling’) results in the ejection of all
pumped protons from the distal subunit NuoL. This mechanism explains why protons
exit exclusively from the NuoL subunit and is supported by our mutagenesis data.
We contend that this is a universal coupling mechanism of complex I and related
enzymes.'
acknowledged_ssus:
- _id: EM-Fac
- _id: LifeSc
- _id: ScienComp
acknowledgement: This research was supported by the Scientific Service Units (SSU)
of IST Austria through resources provided by the Electron Microscopy Facility (EMF),
the Life Science Facility (LSF) and the IST high-performance computing cluster.
We thank V.-V. Hodirnau from IST Austria EMF, M. Babiak from CEITEC for assistance
with collecting cryo-EM data and A. Charnagalov for the assistance with protein
purification. V.K. was a recipient of a DOC Fellowship of the Austrian Academy of
Sciences at the Institute of Science and Technology, Austria. V.K. and O.P. are
funded by the ERC Advanced Grant 101020697 RESPICHAIN to L.S. This work was also
supported by the Medical Research Council (UK).
article_processing_charge: No
article_type: original
author:
- first_name: Vladyslav
full_name: Kravchuk, Vladyslav
id: 4D62F2A6-F248-11E8-B48F-1D18A9856A87
last_name: Kravchuk
- first_name: Olga
full_name: Petrova, Olga
id: 5D8C9660-5D49-11EA-8188-567B3DDC885E
last_name: Petrova
- first_name: Domen
full_name: Kampjut, Domen
id: 37233050-F248-11E8-B48F-1D18A9856A87
last_name: Kampjut
- first_name: Anna
full_name: Wojciechowska-Bason, Anna
last_name: Wojciechowska-Bason
- first_name: Zara
full_name: Breese, Zara
last_name: Breese
- first_name: Leonid A
full_name: Sazanov, Leonid A
id: 338D39FE-F248-11E8-B48F-1D18A9856A87
last_name: Sazanov
orcid: 0000-0002-0977-7989
citation:
ama: Kravchuk V, Petrova O, Kampjut D, Wojciechowska-Bason A, Breese Z, Sazanov
LA. A universal coupling mechanism of respiratory complex I. Nature. 2022;609(7928):808-814.
doi:10.1038/s41586-022-05199-7
apa: Kravchuk, V., Petrova, O., Kampjut, D., Wojciechowska-Bason, A., Breese, Z.,
& Sazanov, L. A. (2022). A universal coupling mechanism of respiratory complex
I. Nature. Springer Nature. https://doi.org/10.1038/s41586-022-05199-7
chicago: Kravchuk, Vladyslav, Olga Petrova, Domen Kampjut, Anna Wojciechowska-Bason,
Zara Breese, and Leonid A Sazanov. “A Universal Coupling Mechanism of Respiratory
Complex I.” Nature. Springer Nature, 2022. https://doi.org/10.1038/s41586-022-05199-7.
ieee: V. Kravchuk, O. Petrova, D. Kampjut, A. Wojciechowska-Bason, Z. Breese, and
L. A. Sazanov, “A universal coupling mechanism of respiratory complex I,” Nature,
vol. 609, no. 7928. Springer Nature, pp. 808–814, 2022.
ista: Kravchuk V, Petrova O, Kampjut D, Wojciechowska-Bason A, Breese Z, Sazanov
LA. 2022. A universal coupling mechanism of respiratory complex I. Nature. 609(7928),
808–814.
mla: Kravchuk, Vladyslav, et al. “A Universal Coupling Mechanism of Respiratory
Complex I.” Nature, vol. 609, no. 7928, Springer Nature, 2022, pp. 808–14,
doi:10.1038/s41586-022-05199-7.
short: V. Kravchuk, O. Petrova, D. Kampjut, A. Wojciechowska-Bason, Z. Breese, L.A.
Sazanov, Nature 609 (2022) 808–814.
date_created: 2023-01-12T12:04:33Z
date_published: 2022-09-22T00:00:00Z
date_updated: 2023-08-04T08:54:52Z
day: '22'
ddc:
- '572'
department:
- _id: LeSa
doi: 10.1038/s41586-022-05199-7
ec_funded: 1
external_id:
isi:
- '000854788200001'
pmid:
- '36104567'
file:
- access_level: open_access
checksum: d42a93e24f59e883ef0b5429832391d0
content_type: application/pdf
creator: lsazanov
date_created: 2023-05-30T17:05:31Z
date_updated: 2023-05-30T17:05:31Z
file_id: '13104'
file_name: EcCxI_manuscript_rev3_noSI_updated_withFigs_opt.pdf
file_size: 1425655
relation: main_file
success: 1
- access_level: open_access
checksum: 5422bc0a73b3daadafa262c7ea6deae3
content_type: application/pdf
creator: lsazanov
date_created: 2023-05-30T17:07:05Z
date_updated: 2023-05-30T17:07:05Z
file_id: '13105'
file_name: EcCxI_manuscript_rev3_SI_All_opt_upd.pdf
file_size: 9842513
relation: main_file
success: 1
file_date_updated: 2023-05-30T17:07:05Z
has_accepted_license: '1'
intvolume: ' 609'
isi: 1
issue: '7928'
keyword:
- Multidisciplinary
language:
- iso: eng
month: '09'
oa: 1
oa_version: Submitted Version
page: 808-814
pmid: 1
project:
- _id: 238A0A5A-32DE-11EA-91FC-C7463DDC885E
grant_number: '25541'
name: 'Structural characterization of E. coli complex I: an important mechanistic
model'
- _id: 627abdeb-2b32-11ec-9570-ec31a97243d3
call_identifier: H2020
grant_number: '101020697'
name: Structure and mechanism of respiratory chain molecular machines
publication: Nature
publication_identifier:
eissn:
- 1476-4687
issn:
- 0028-0836
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
related_material:
link:
- relation: erratum
url: https://doi.org/10.1038/s41586-022-05457-8
- description: News on ISTA website
relation: press_release
url: https://ista.ac.at/en/news/proton-dominos-kick-off-life/
record:
- id: '12781'
relation: dissertation_contains
status: public
scopus_import: '1'
status: public
title: A universal coupling mechanism of respiratory complex I
type: journal_article
user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
volume: 609
year: '2022'
...
---
_id: '12139'
abstract:
- lang: eng
text: We demonstrate the formation of robust zero-energy modes close to magnetic
impurities in the iron-based superconductor FeSe1-z Tez. We find that the Zeeman
field generated by the impurity favors a spin-triplet interorbital pairing as
opposed to the spin-singlet intraorbital pairing prevalent in the bulk. The preferred
spin-triplet pairing preserves time-reversal symmetry and is topological, as robust,
topologically protected zero modes emerge at the boundary between regions with
different pairing states. Moreover, the zero modes form Kramers doublets that
are insensitive to the direction of the spin polarization or to the separation
between impurities. We argue that our theoretical results are consistent with
recent experimental measurements on FeSe1-z Tez.
acknowledgement: "We thank Armin Rahmani, Andrey V. Chubukov, Jay D. Sau and Ruixing
Zhang for fruitful discussions. AK and PG are supported by NSF-DMR2037996. PG also
acknowledges support from NSF-DMR1824265. RMF was supported by the U. S. Department
of Energy, Office\r\nof Science, Basic Energy Sciences, Materials Sciences and Engineering
Division, under Award No. DE-SC0020045. Part of this work was performed at the Aspen
Center for Physics, which is supported by National Science Foundation grant PHY-1607611. "
article_number: L201107
article_processing_charge: No
article_type: original
arxiv: 1
author:
- first_name: Areg
full_name: Ghazaryan, Areg
id: 4AF46FD6-F248-11E8-B48F-1D18A9856A87
last_name: Ghazaryan
orcid: 0000-0001-9666-3543
- first_name: Ammar
full_name: Kirmani, Ammar
last_name: Kirmani
- first_name: Rafael M.
full_name: Fernandes, Rafael M.
last_name: Fernandes
- first_name: Pouyan
full_name: Ghaemi, Pouyan
last_name: Ghaemi
citation:
ama: Ghazaryan A, Kirmani A, Fernandes RM, Ghaemi P. Anomalous Shiba states in topological
iron-based superconductors. Physical Review B. 2022;106(20). doi:10.1103/physrevb.106.l201107
apa: Ghazaryan, A., Kirmani, A., Fernandes, R. M., & Ghaemi, P. (2022). Anomalous
Shiba states in topological iron-based superconductors. Physical Review B.
American Physical Society. https://doi.org/10.1103/physrevb.106.l201107
chicago: Ghazaryan, Areg, Ammar Kirmani, Rafael M. Fernandes, and Pouyan Ghaemi.
“Anomalous Shiba States in Topological Iron-Based Superconductors.” Physical
Review B. American Physical Society, 2022. https://doi.org/10.1103/physrevb.106.l201107.
ieee: A. Ghazaryan, A. Kirmani, R. M. Fernandes, and P. Ghaemi, “Anomalous Shiba
states in topological iron-based superconductors,” Physical Review B, vol.
106, no. 20. American Physical Society, 2022.
ista: Ghazaryan A, Kirmani A, Fernandes RM, Ghaemi P. 2022. Anomalous Shiba states
in topological iron-based superconductors. Physical Review B. 106(20), L201107.
mla: Ghazaryan, Areg, et al. “Anomalous Shiba States in Topological Iron-Based Superconductors.”
Physical Review B, vol. 106, no. 20, L201107, American Physical Society,
2022, doi:10.1103/physrevb.106.l201107.
short: A. Ghazaryan, A. Kirmani, R.M. Fernandes, P. Ghaemi, Physical Review B 106
(2022).
date_created: 2023-01-12T12:04:43Z
date_published: 2022-11-15T00:00:00Z
date_updated: 2023-08-04T08:55:31Z
day: '15'
department:
- _id: MiLe
doi: 10.1103/physrevb.106.l201107
external_id:
arxiv:
- '2207.12425'
isi:
- '000893171800001'
intvolume: ' 106'
isi: 1
issue: '20'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: ' https://doi.org/10.48550/arXiv.2207.12425'
month: '11'
oa: 1
oa_version: Preprint
publication: Physical Review B
publication_identifier:
eissn:
- 2469-9969
issn:
- 2469-9950
publication_status: published
publisher: American Physical Society
quality_controlled: '1'
scopus_import: '1'
status: public
title: Anomalous Shiba states in topological iron-based superconductors
type: journal_article
user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
volume: 106
year: '2022'
...
---
_id: '12140'
abstract:
- lang: eng
text: Microglia are dynamic cells, constantly surveying their surroundings and interacting
with neurons and synapses. Indeed, a wealth of knowledge has revealed a critical
role of microglia in modulating synaptic transmission and plasticity in the developing
brain. In the past decade, novel pharmacological and genetic strategies have allowed
the acute removal of microglia, opening the possibility to explore and understand
the role of microglia also in the adult brain. In this review, we summarized and
discussed the contribution of microglia depletion strategies to the current understanding
of the role of microglia on synaptic function, learning and memory, and behavior
both in physiological and pathological conditions. We first described the available
microglia depletion methods highlighting their main strengths and weaknesses.
We then reviewed the impact of microglia depletion on structural and functional
synaptic plasticity. Next, we focused our analysis on the effects of microglia
depletion on behavior, including general locomotor activity, sensory perception,
motor function, sociability, learning and memory both in healthy animals and animal
models of disease. Finally, we integrated the findings from the reviewed studies
and discussed the emerging roles of microglia on the maintenance of synaptic function,
learning, memory strength and forgetfulness, and the implications of microglia
depletion in models of brain disease.
acknowledgement: "The write-up of the review was supported by Sapienza University
of Rome (Fondi di Ateneo, grant numbers #MA32117A7B698029 and #PH12017270934C3C
to SD), Regione Lazio (POR FSE 2014/20, grant number #19036AP000000019 to SD), Fulbright
2019 (grant number\r\n#FSP-P005556 to SD), Institute Pasteur Italia (Fondi Cenci
Bolognetti #363 to DR), and Network of European Funding for Neuroscience Research
(ERA-NET NEURON Transnational\r\nResearch Projects on Neurodevelopmental Disorders
2021, grant acronym #JTC2021-SHANKAstro to DR)."
article_number: '1022431'
article_processing_charge: No
article_type: original
author:
- first_name: Bernadette
full_name: Basilico, Bernadette
id: 36035796-5ACA-11E9-A75E-7AF2E5697425
last_name: Basilico
orcid: 0000-0003-1843-3173
- first_name: Laura
full_name: Ferrucci, Laura
last_name: Ferrucci
- first_name: Azka
full_name: Khan, Azka
last_name: Khan
- first_name: Silvia
full_name: Di Angelantonio, Silvia
last_name: Di Angelantonio
- first_name: Davide
full_name: Ragozzino, Davide
last_name: Ragozzino
- first_name: Ingrid
full_name: Reverte, Ingrid
last_name: Reverte
citation:
ama: Basilico B, Ferrucci L, Khan A, Di Angelantonio S, Ragozzino D, Reverte I.
What microglia depletion approaches tell us about the role of microglia on synaptic
function and behavior. Frontiers in Cellular Neuroscience. 2022;16. doi:10.3389/fncel.2022.1022431
apa: Basilico, B., Ferrucci, L., Khan, A., Di Angelantonio, S., Ragozzino, D., &
Reverte, I. (2022). What microglia depletion approaches tell us about the role
of microglia on synaptic function and behavior. Frontiers in Cellular Neuroscience.
Frontiers Media. https://doi.org/10.3389/fncel.2022.1022431
chicago: Basilico, Bernadette, Laura Ferrucci, Azka Khan, Silvia Di Angelantonio,
Davide Ragozzino, and Ingrid Reverte. “What Microglia Depletion Approaches Tell
Us about the Role of Microglia on Synaptic Function and Behavior.” Frontiers
in Cellular Neuroscience. Frontiers Media, 2022. https://doi.org/10.3389/fncel.2022.1022431.
ieee: B. Basilico, L. Ferrucci, A. Khan, S. Di Angelantonio, D. Ragozzino, and I.
Reverte, “What microglia depletion approaches tell us about the role of microglia
on synaptic function and behavior,” Frontiers in Cellular Neuroscience,
vol. 16. Frontiers Media, 2022.
ista: Basilico B, Ferrucci L, Khan A, Di Angelantonio S, Ragozzino D, Reverte I.
2022. What microglia depletion approaches tell us about the role of microglia
on synaptic function and behavior. Frontiers in Cellular Neuroscience. 16, 1022431.
mla: Basilico, Bernadette, et al. “What Microglia Depletion Approaches Tell Us about
the Role of Microglia on Synaptic Function and Behavior.” Frontiers in Cellular
Neuroscience, vol. 16, 1022431, Frontiers Media, 2022, doi:10.3389/fncel.2022.1022431.
short: B. Basilico, L. Ferrucci, A. Khan, S. Di Angelantonio, D. Ragozzino, I. Reverte,
Frontiers in Cellular Neuroscience 16 (2022).
date_created: 2023-01-12T12:04:50Z
date_published: 2022-11-04T00:00:00Z
date_updated: 2023-08-04T08:56:10Z
day: '04'
ddc:
- '570'
department:
- _id: GaNo
doi: 10.3389/fncel.2022.1022431
external_id:
isi:
- '000886526600001'
pmid:
- '36406752'
file:
- access_level: open_access
checksum: 84696213ecf99182c58a9f34b9ff2e23
content_type: application/pdf
creator: dernst
date_created: 2023-01-24T09:16:29Z
date_updated: 2023-01-24T09:16:29Z
file_id: '12352'
file_name: 2022_FrontiersNeuroscience_Basilico.pdf
file_size: 6399987
relation: main_file
success: 1
file_date_updated: 2023-01-24T09:16:29Z
has_accepted_license: '1'
intvolume: ' 16'
isi: 1
keyword:
- Cellular and Molecular Neuroscience
language:
- iso: eng
month: '11'
oa: 1
oa_version: Published Version
pmid: 1
publication: Frontiers in Cellular Neuroscience
publication_identifier:
issn:
- 1662-5102
publication_status: published
publisher: Frontiers Media
quality_controlled: '1'
scopus_import: '1'
status: public
title: What microglia depletion approaches tell us about the role of microglia on
synaptic function and behavior
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: journal_article
user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
volume: 16
year: '2022'
...
---
_id: '12142'
abstract:
- lang: eng
text: Theory for liability-scale models of the underlying genetic basis of complex
disease provides an important way to interpret, compare, and understand results
generated from biological studies. In particular, through estimation of the liability-scale
heritability (LSH), liability models facilitate an understanding and comparison
of the relative importance of genetic and environmental risk factors that shape
different clinically important disease outcomes. Increasingly, large-scale biobank
studies that link genetic information to electronic health records, containing
hundreds of disease diagnosis indicators that mostly occur infrequently within
the sample, are becoming available. Here, we propose an extension of the existing
liability-scale model theory suitable for estimating LSH in biobank studies of
low-prevalence disease. In a simulation study, we find that our derived expression
yields lower mean square error (MSE) and is less sensitive to prevalence misspecification
as compared to previous transformations for diseases with =< 2% population prevalence
and LSH of =< 0.45, especially if the biobank sample prevalence is less than that
of the wider population. Applying our expression to 13 diagnostic outcomes of =<
3% prevalence in the UK Biobank study revealed important differences in LSH obtained
from the different theoretical expressions that impact the conclusions made when
comparing LSH across disease outcomes. This demonstrates the importance of careful
consideration for estimation and prediction of low-prevalence disease outcomes
and facilitates improved inference of the underlying genetic basis of =< 2% population
prevalence diseases, especially where biobank sample ascertainment results in
a healthier sample population.
acknowledged_ssus:
- _id: ScienComp
acknowledgement: This project was funded by an SNSF Eccellenza grant to M.R.R. (PCEGP3-181181),
core funding from the Institute of Science and Technology Austria, and core funding
from the Department of Computational Biology of the University of Lausanne. Z.K.
was funded by the Swiss National Science Foundation (310030-189147). This research
was supported by the Scientific Service Units (SSUs) of IST Austria through resources
provided by Scientific Computing (SciComp). We would like to thank the participants
of the UK Biobank.
article_processing_charge: Yes (via OA deal)
article_type: original
author:
- first_name: Sven E.
full_name: Ojavee, Sven E.
last_name: Ojavee
- first_name: Zoltan
full_name: Kutalik, Zoltan
last_name: Kutalik
- first_name: Matthew Richard
full_name: Robinson, Matthew Richard
id: E5D42276-F5DA-11E9-8E24-6303E6697425
last_name: Robinson
orcid: 0000-0001-8982-8813
citation:
ama: Ojavee SE, Kutalik Z, Robinson MR. Liability-scale heritability estimation
for biobank studies of low-prevalence disease. The American Journal of Human
Genetics. 2022;109(11):2009-2017. doi:10.1016/j.ajhg.2022.09.011
apa: Ojavee, S. E., Kutalik, Z., & Robinson, M. R. (2022). Liability-scale heritability
estimation for biobank studies of low-prevalence disease. The American Journal
of Human Genetics. Elsevier. https://doi.org/10.1016/j.ajhg.2022.09.011
chicago: Ojavee, Sven E., Zoltan Kutalik, and Matthew Richard Robinson. “Liability-Scale
Heritability Estimation for Biobank Studies of Low-Prevalence Disease.” The
American Journal of Human Genetics. Elsevier, 2022. https://doi.org/10.1016/j.ajhg.2022.09.011.
ieee: S. E. Ojavee, Z. Kutalik, and M. R. Robinson, “Liability-scale heritability
estimation for biobank studies of low-prevalence disease,” The American Journal
of Human Genetics, vol. 109, no. 11. Elsevier, pp. 2009–2017, 2022.
ista: Ojavee SE, Kutalik Z, Robinson MR. 2022. Liability-scale heritability estimation
for biobank studies of low-prevalence disease. The American Journal of Human Genetics.
109(11), 2009–2017.
mla: Ojavee, Sven E., et al. “Liability-Scale Heritability Estimation for Biobank
Studies of Low-Prevalence Disease.” The American Journal of Human Genetics,
vol. 109, no. 11, Elsevier, 2022, pp. 2009–17, doi:10.1016/j.ajhg.2022.09.011.
short: S.E. Ojavee, Z. Kutalik, M.R. Robinson, The American Journal of Human Genetics
109 (2022) 2009–2017.
date_created: 2023-01-12T12:05:28Z
date_published: 2022-11-03T00:00:00Z
date_updated: 2023-08-04T08:56:46Z
day: '03'
ddc:
- '570'
department:
- _id: MaRo
doi: 10.1016/j.ajhg.2022.09.011
external_id:
isi:
- '000898683500006'
file:
- access_level: open_access
checksum: 4cd7f12bfe21a8237bb095eedfa26361
content_type: application/pdf
creator: dernst
date_created: 2023-01-24T09:23:01Z
date_updated: 2023-01-24T09:23:01Z
file_id: '12353'
file_name: 2022_AJHG_Ojavee.pdf
file_size: 705195
relation: main_file
success: 1
file_date_updated: 2023-01-24T09:23:01Z
has_accepted_license: '1'
intvolume: ' 109'
isi: 1
issue: '11'
keyword:
- Genetics (clinical)
- Genetics
language:
- iso: eng
license: https://creativecommons.org/licenses/by-nc-nd/4.0/
month: '11'
oa: 1
oa_version: Published Version
page: 2009-2017
project:
- _id: 9B8D11D6-BA93-11EA-9121-9846C619BF3A
grant_number: PCEGP3_181181
name: Improving estimation and prediction of common complex disease risk
publication: The American Journal of Human Genetics
publication_identifier:
issn:
- 0002-9297
publication_status: published
publisher: Elsevier
quality_controlled: '1'
scopus_import: '1'
status: public
title: Liability-scale heritability estimation for biobank studies of low-prevalence
disease
tmp:
image: /images/cc_by_nc_nd.png
legal_code_url: https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode
name: Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International
(CC BY-NC-ND 4.0)
short: CC BY-NC-ND (4.0)
type: journal_article
user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
volume: 109
year: '2022'
...
---
_id: '12143'
abstract:
- lang: eng
text: MicroRNA (miRNA) and RNA interference (RNAi) pathways rely on small RNAs produced
by Dicer endonucleases. Mammalian Dicer primarily supports the essential gene-regulating
miRNA pathway, but how it is specifically adapted to miRNA biogenesis is unknown.
We show that the adaptation entails a unique structural role of Dicer’s DExD/H
helicase domain. Although mice tolerate loss of its putative ATPase function,
the complete absence of the domain is lethal because it assures high-fidelity
miRNA biogenesis. Structures of murine Dicer⋅miRNA precursor complexes revealed
that the DExD/H domain has a helicase-unrelated structural function. It locks
Dicer in a closed state, which facilitates miRNA precursor selection. Transition
to a cleavage-competent open state is stimulated by Dicer-binding protein TARBP2.
Absence of the DExD/H domain or its mutations unlocks the closed state, reduces
substrate selectivity, and activates RNAi. Thus, the DExD/H domain structurally
contributes to mammalian miRNA biogenesis and underlies mechanistical partitioning
of miRNA and RNAi pathways.
acknowledged_ssus:
- _id: EM-Fac
acknowledgement: We thank Kristian Vlahovicek (University of Zagreb) for support of
bioinformatics analyses and Vladimir Benes (EMBL Sequencing Facility) and Genomics
and Bioinformatics Core Facility at the Institute of Molecular Genetics for help
with RNA sequencing. The main funding was provided by the Czech Science Foundation
(EXPRO grant 20-03950X to P.S. and 22-19896S to R. Stefl). Early stages of the work
were supported by European Research Council grants under the European Union’s Horizon
2020 Research and Innovation Programme (grants 647403 to P.S. and 649030 to R. Stefl).
V.B., D.F.J., and F.H. were in part supported by PhD student fellowships from the
Charles University; this work will be in part fulfilling requirements for a PhD
degree as “school work.” Funding of D.Z. included the OP RDE project “Internal Grant
Agency of Masaryk University” no. CZ.02.2.69/0.0/0.0/19_073/0016943. The Ministry
of Education, Youth, and Sports of the Czech Republic (MEYS CR) provided institutional
support for CEITEC 2020 project LQ1601. For technical support, we acknowledge EMBL
Monterotondo’s genome engineering and transgenic core facilities, the Czech Centre
for Phenogenomics at the Institute of Molecular Genetics (supported by RVO 68378050
from the Czech Academy of Sciences and LM2018126 and CZ.02.1.01/0.0/0.0/18_046/0015861
CCP Infrastructure Upgrade II from MEYS CR), the Cryo-EM and Proteomics Core Facilities
(CEITEC, Masaryk University) supported by the CIISB research infrastructure (LM2018127
from MEYS CR), and support from the Scientific Service Units of ISTA through resources
from the Electron Microscopy Facility. Computational resources included e-Infrastruktura
CZ (LM2018140) and ELIXIR-CZ (LM2018131) projects by MEYS CR and the Croatian National
Centres of Research Excellence in Personalized Healthcare (#KK.01.1.1.01.0010) and
Data Science and Advanced Cooperative Systems (#KK.01.1.1.01.0009) projects funded
by the European Structural and Investment Funds grants.
article_processing_charge: No
article_type: original
author:
- first_name: David
full_name: Zapletal, David
last_name: Zapletal
- first_name: Eliska
full_name: Taborska, Eliska
last_name: Taborska
- first_name: Josef
full_name: Pasulka, Josef
last_name: Pasulka
- first_name: Radek
full_name: Malik, Radek
last_name: Malik
- first_name: Karel
full_name: Kubicek, Karel
last_name: Kubicek
- first_name: Martina
full_name: Zanova, Martina
last_name: Zanova
- first_name: Christian
full_name: Much, Christian
last_name: Much
- first_name: Marek
full_name: Sebesta, Marek
last_name: Sebesta
- first_name: Valeria
full_name: Buccheri, Valeria
last_name: Buccheri
- first_name: Filip
full_name: Horvat, Filip
last_name: Horvat
- first_name: Irena
full_name: Jenickova, Irena
last_name: Jenickova
- first_name: Michaela
full_name: Prochazkova, Michaela
last_name: Prochazkova
- first_name: Jan
full_name: Prochazka, Jan
last_name: Prochazka
- first_name: Matyas
full_name: Pinkas, Matyas
last_name: Pinkas
- first_name: Jiri
full_name: Novacek, Jiri
last_name: Novacek
- first_name: Diego F.
full_name: Joseph, Diego F.
last_name: Joseph
- first_name: Radislav
full_name: Sedlacek, Radislav
last_name: Sedlacek
- first_name: Carrie A
full_name: Bernecky, Carrie A
id: 2CB9DFE2-F248-11E8-B48F-1D18A9856A87
last_name: Bernecky
orcid: 0000-0003-0893-7036
- first_name: Dónal
full_name: O’Carroll, Dónal
last_name: O’Carroll
- first_name: Richard
full_name: Stefl, Richard
last_name: Stefl
- first_name: Petr
full_name: Svoboda, Petr
last_name: Svoboda
citation:
ama: Zapletal D, Taborska E, Pasulka J, et al. Structural and functional basis of
mammalian microRNA biogenesis by Dicer. Molecular Cell. 2022;82(21):4064-4079.e13.
doi:10.1016/j.molcel.2022.10.010
apa: Zapletal, D., Taborska, E., Pasulka, J., Malik, R., Kubicek, K., Zanova, M.,
… Svoboda, P. (2022). Structural and functional basis of mammalian microRNA biogenesis
by Dicer. Molecular Cell. Elsevier. https://doi.org/10.1016/j.molcel.2022.10.010
chicago: Zapletal, David, Eliska Taborska, Josef Pasulka, Radek Malik, Karel Kubicek,
Martina Zanova, Christian Much, et al. “Structural and Functional Basis of Mammalian
MicroRNA Biogenesis by Dicer.” Molecular Cell. Elsevier, 2022. https://doi.org/10.1016/j.molcel.2022.10.010.
ieee: D. Zapletal et al., “Structural and functional basis of mammalian microRNA
biogenesis by Dicer,” Molecular Cell, vol. 82, no. 21. Elsevier, p. 4064–4079.e13,
2022.
ista: Zapletal D, Taborska E, Pasulka J, Malik R, Kubicek K, Zanova M, Much C, Sebesta
M, Buccheri V, Horvat F, Jenickova I, Prochazkova M, Prochazka J, Pinkas M, Novacek
J, Joseph DF, Sedlacek R, Bernecky C, O’Carroll D, Stefl R, Svoboda P. 2022. Structural
and functional basis of mammalian microRNA biogenesis by Dicer. Molecular Cell.
82(21), 4064–4079.e13.
mla: Zapletal, David, et al. “Structural and Functional Basis of Mammalian MicroRNA
Biogenesis by Dicer.” Molecular Cell, vol. 82, no. 21, Elsevier, 2022,
p. 4064–4079.e13, doi:10.1016/j.molcel.2022.10.010.
short: D. Zapletal, E. Taborska, J. Pasulka, R. Malik, K. Kubicek, M. Zanova, C.
Much, M. Sebesta, V. Buccheri, F. Horvat, I. Jenickova, M. Prochazkova, J. Prochazka,
M. Pinkas, J. Novacek, D.F. Joseph, R. Sedlacek, C. Bernecky, D. O’Carroll, R.
Stefl, P. Svoboda, Molecular Cell 82 (2022) 4064–4079.e13.
date_created: 2023-01-12T12:05:36Z
date_published: 2022-11-03T00:00:00Z
date_updated: 2023-08-04T08:57:17Z
day: '03'
ddc:
- '570'
department:
- _id: CaBe
doi: 10.1016/j.molcel.2022.10.010
external_id:
isi:
- '000898565300011'
pmid:
- '36332606'
file:
- access_level: open_access
checksum: 999e443b54e4fdaa2542ca5a97619731
content_type: application/pdf
creator: dernst
date_created: 2023-01-24T09:29:02Z
date_updated: 2023-01-24T09:29:02Z
file_id: '12354'
file_name: 2022_MolecularCell_Zapletal.pdf
file_size: 7368534
relation: main_file
success: 1
file_date_updated: 2023-01-24T09:29:02Z
has_accepted_license: '1'
intvolume: ' 82'
isi: 1
issue: '21'
keyword:
- Cell Biology
- Molecular Biology
language:
- iso: eng
month: '11'
oa: 1
oa_version: Published Version
page: 4064-4079.e13
pmid: 1
publication: Molecular Cell
publication_identifier:
issn:
- 1097-2765
publication_status: published
publisher: Elsevier
quality_controlled: '1'
scopus_import: '1'
status: public
title: Structural and functional basis of mammalian microRNA biogenesis by Dicer
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: journal_article
user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
volume: 82
year: '2022'
...
---
_id: '12144'
abstract:
- lang: eng
text: The phytohormone auxin is the major coordinative signal in plant development1,
mediating transcriptional reprogramming by a well-established canonical signalling
pathway. TRANSPORT INHIBITOR RESPONSE 1 (TIR1)/AUXIN-SIGNALING F-BOX (AFB) auxin
receptors are F-box subunits of ubiquitin ligase complexes. In response to auxin,
they associate with Aux/IAA transcriptional repressors and target them for degradation
via ubiquitination2,3. Here we identify adenylate cyclase (AC) activity as an
additional function of TIR1/AFB receptors across land plants. Auxin, together
with Aux/IAAs, stimulates cAMP production. Three separate mutations in the AC
motif of the TIR1 C-terminal region, all of which abolish the AC activity, each
render TIR1 ineffective in mediating gravitropism and sustained auxin-induced
root growth inhibition, and also affect auxin-induced transcriptional regulation.
These results highlight the importance of TIR1/AFB AC activity in canonical auxin
signalling. They also identify a unique phytohormone receptor cassette combining
F-box and AC motifs, and the role of cAMP as a second messenger in plants.
acknowledged_ssus:
- _id: LifeSc
- _id: Bio
acknowledgement: This research was supported by the Lab Support Facility (LSF) and
the Imaging and Optics Facility (IOF) of IST Austria. We thank C. Gehring for suggestions
and advice; and K. U. Torii and G. Stacey for seeds and plasmids. This project was
funded by a European Research Council Advanced Grant (ETAP-742985). M.F.K. and R.N.
acknowledge the support of the EU MSCA-IF project CrysPINs (792329). M.K. was supported
by the project POWR.03.05.00-00-Z302/17 Universitas Copernicana Thoruniensis in
Futuro–IDS “Academia Copernicana”. CIDG acknowledges support from UKRI under Future
Leaders Fellowship grant number MR/T020652/1.
article_processing_charge: No
article_type: original
author:
- first_name: Linlin
full_name: Qi, Linlin
id: 44B04502-A9ED-11E9-B6FC-583AE6697425
last_name: Qi
orcid: 0000-0001-5187-8401
- first_name: Mateusz
full_name: Kwiatkowski, Mateusz
last_name: Kwiatkowski
- first_name: Huihuang
full_name: Chen, Huihuang
id: 83c96512-15b2-11ec-abd3-b7eede36184f
last_name: Chen
- first_name: Lukas
full_name: Hörmayer, Lukas
id: 2EEE7A2A-F248-11E8-B48F-1D18A9856A87
last_name: Hörmayer
orcid: 0000-0001-8295-2926
- first_name: Scott A
full_name: Sinclair, Scott A
id: 2D99FE6A-F248-11E8-B48F-1D18A9856A87
last_name: Sinclair
orcid: 0000-0002-4566-0593
- first_name: Minxia
full_name: Zou, Minxia
id: 5c243f41-03f3-11ec-841c-96faf48a7ef9
last_name: Zou
- first_name: Charo I.
full_name: del Genio, Charo I.
last_name: del Genio
- first_name: Martin F.
full_name: Kubeš, Martin F.
last_name: Kubeš
- first_name: Richard
full_name: Napier, Richard
last_name: Napier
- first_name: Krzysztof
full_name: Jaworski, Krzysztof
last_name: Jaworski
- first_name: Jiří
full_name: Friml, Jiří
id: 4159519E-F248-11E8-B48F-1D18A9856A87
last_name: Friml
orcid: 0000-0002-8302-7596
citation:
ama: Qi L, Kwiatkowski M, Chen H, et al. Adenylate cyclase activity of TIR1/AFB
auxin receptors in plants. Nature. 2022;611(7934):133-138. doi:10.1038/s41586-022-05369-7
apa: Qi, L., Kwiatkowski, M., Chen, H., Hörmayer, L., Sinclair, S. A., Zou, M.,
… Friml, J. (2022). Adenylate cyclase activity of TIR1/AFB auxin receptors in
plants. Nature. Springer Nature. https://doi.org/10.1038/s41586-022-05369-7
chicago: Qi, Linlin, Mateusz Kwiatkowski, Huihuang Chen, Lukas Hörmayer, Scott A
Sinclair, Minxia Zou, Charo I. del Genio, et al. “Adenylate Cyclase Activity of
TIR1/AFB Auxin Receptors in Plants.” Nature. Springer Nature, 2022. https://doi.org/10.1038/s41586-022-05369-7.
ieee: L. Qi et al., “Adenylate cyclase activity of TIR1/AFB auxin receptors
in plants,” Nature, vol. 611, no. 7934. Springer Nature, pp. 133–138, 2022.
ista: Qi L, Kwiatkowski M, Chen H, Hörmayer L, Sinclair SA, Zou M, del Genio CI,
Kubeš MF, Napier R, Jaworski K, Friml J. 2022. Adenylate cyclase activity of TIR1/AFB
auxin receptors in plants. Nature. 611(7934), 133–138.
mla: Qi, Linlin, et al. “Adenylate Cyclase Activity of TIR1/AFB Auxin Receptors
in Plants.” Nature, vol. 611, no. 7934, Springer Nature, 2022, pp. 133–38,
doi:10.1038/s41586-022-05369-7.
short: L. Qi, M. Kwiatkowski, H. Chen, L. Hörmayer, S.A. Sinclair, M. Zou, C.I.
del Genio, M.F. Kubeš, R. Napier, K. Jaworski, J. Friml, Nature 611 (2022) 133–138.
date_created: 2023-01-12T12:06:05Z
date_published: 2022-11-03T00:00:00Z
date_updated: 2023-10-03T11:04:53Z
day: '03'
department:
- _id: JiFr
doi: 10.1038/s41586-022-05369-7
ec_funded: 1
external_id:
isi:
- '000875061600013'
pmid:
- '36289340'
intvolume: ' 611'
isi: 1
issue: '7934'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: http://wrap.warwick.ac.uk/168325/1/WRAP-denylate-cyclase-activity-TIR1-AFB-auxin-receptors-root-growth-22.pdf
month: '11'
oa: 1
oa_version: Submitted Version
page: 133-138
pmid: 1
project:
- _id: 261099A6-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '742985'
name: Tracing Evolution of Auxin Transport and Polarity in Plants
publication: Nature
publication_identifier:
eissn:
- 1476-4687
issn:
- 0028-0836
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
scopus_import: '1'
status: public
title: Adenylate cyclase activity of TIR1/AFB auxin receptors in plants
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 611
year: '2022'
...
---
_id: '12145'
abstract:
- lang: eng
text: In the class of strictly convex smooth boundaries each of which has no strip
around its boundary foliated by invariant curves, we prove that the Taylor coefficients
of the “normalized” Mather’s β-function are invariant under C∞-conjugacies. In
contrast, we prove that any two elliptic billiard maps are C0-conjugate near their
respective boundaries, and C∞-conjugate, near the boundary and away from a line
passing through the center of the underlying ellipse. We also prove that, if the
billiard maps corresponding to two ellipses are topologically conjugate, then
the two ellipses are similar.
acknowledgement: "We are grateful to the anonymous referees for their careful reading
and valuable remarks and\r\ncomments which helped to improve the paper significantly.
We gratefully acknowledge support from the European Research Council (ERC) through
the Advanced Grant “SPERIG” (#885707)."
article_processing_charge: No
article_type: original
arxiv: 1
author:
- first_name: Edmond
full_name: Koudjinan, Edmond
id: 52DF3E68-AEFA-11EA-95A4-124A3DDC885E
last_name: Koudjinan
orcid: 0000-0003-2640-4049
- first_name: Vadim
full_name: Kaloshin, Vadim
id: FE553552-CDE8-11E9-B324-C0EBE5697425
last_name: Kaloshin
orcid: 0000-0002-6051-2628
citation:
ama: Koudjinan E, Kaloshin V. On some invariants of Birkhoff billiards under conjugacy.
Regular and Chaotic Dynamics. 2022;27(6):525-537. doi:10.1134/S1560354722050021
apa: Koudjinan, E., & Kaloshin, V. (2022). On some invariants of Birkhoff billiards
under conjugacy. Regular and Chaotic Dynamics. Springer Nature. https://doi.org/10.1134/S1560354722050021
chicago: Koudjinan, Edmond, and Vadim Kaloshin. “On Some Invariants of Birkhoff
Billiards under Conjugacy.” Regular and Chaotic Dynamics. Springer Nature,
2022. https://doi.org/10.1134/S1560354722050021.
ieee: E. Koudjinan and V. Kaloshin, “On some invariants of Birkhoff billiards under
conjugacy,” Regular and Chaotic Dynamics, vol. 27, no. 6. Springer Nature,
pp. 525–537, 2022.
ista: Koudjinan E, Kaloshin V. 2022. On some invariants of Birkhoff billiards under
conjugacy. Regular and Chaotic Dynamics. 27(6), 525–537.
mla: Koudjinan, Edmond, and Vadim Kaloshin. “On Some Invariants of Birkhoff Billiards
under Conjugacy.” Regular and Chaotic Dynamics, vol. 27, no. 6, Springer
Nature, 2022, pp. 525–37, doi:10.1134/S1560354722050021.
short: E. Koudjinan, V. Kaloshin, Regular and Chaotic Dynamics 27 (2022) 525–537.
date_created: 2023-01-12T12:06:49Z
date_published: 2022-10-03T00:00:00Z
date_updated: 2023-08-04T08:59:14Z
day: '03'
department:
- _id: VaKa
doi: 10.1134/S1560354722050021
ec_funded: 1
external_id:
arxiv:
- '2105.14640'
isi:
- '000865267300002'
intvolume: ' 27'
isi: 1
issue: '6'
keyword:
- Mechanical Engineering
- Applied Mathematics
- Mathematical Physics
- Modeling and Simulation
- Statistical and Nonlinear Physics
- Mathematics (miscellaneous)
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.48550/arXiv.2105.14640
month: '10'
oa: 1
oa_version: Preprint
page: 525-537
project:
- _id: 9B8B92DE-BA93-11EA-9121-9846C619BF3A
call_identifier: H2020
grant_number: '885707'
name: Spectral rigidity and integrability for billiards and geodesic flows
publication: Regular and Chaotic Dynamics
publication_identifier:
eissn:
- 1468-4845
issn:
- 1560-3547
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
related_material:
link:
- relation: erratum
url: https://doi.org/10.1134/s1560354722060107
scopus_import: '1'
status: public
title: On some invariants of Birkhoff billiards under conjugacy
type: journal_article
user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
volume: 27
year: '2022'
...
---
_id: '12146'
abstract:
- lang: eng
text: 'In this paper, we explore the stability and dynamical relevance of a wide
variety of steady, time-periodic, quasiperiodic, and chaotic flows arising between
orthogonally stretching parallel plates. We first explore the stability of all
the steady flow solution families formerly identified by Ayats et al. [“Flows
between orthogonally stretching parallel plates,” Phys. Fluids 33, 024103 (2021)],
concluding that only the one that originates from the Stokesian approximation
is actually stable. When both plates are shrinking at identical or nearly the
same deceleration rates, this Stokesian flow exhibits a Hopf bifurcation that
leads to stable time-periodic regimes. The resulting time-periodic orbits or flows
are tracked for different Reynolds numbers and stretching rates while monitoring
their Floquet exponents to identify secondary instabilities. It is found that
these time-periodic flows also exhibit Neimark–Sacker bifurcations, generating
stable quasiperiodic flows (tori) that may sometimes give rise to chaotic dynamics
through a Ruelle–Takens–Newhouse scenario. However, chaotic dynamics is unusually
observed, as the quasiperiodic flows generally become phase-locked through a resonance
mechanism before a strange attractor may arise, thus restoring the time-periodicity
of the flow. In this work, we have identified and tracked four different resonance
regions, also known as Arnold tongues or horns. In particular, the 1 : 4 strong
resonance region is explored in great detail, where the identified scenarios are
in very good agreement with normal form theory. '
acknowledgement: "This work was supported by the Spanish MINECO under Grant Nos. FIS2017-85794-P
and PRX18/00179, the Spanish MICINN through Grant No. PID2020-114043GB-I00, and
the\r\nGeneralitat de Catalunya under Grant No. 2017-SGR-785. B.W.’s research was
also supported by the Chinese Scholarship Council through Grant CSC No. 201806440152."
article_number: '114111'
article_processing_charge: No
article_type: original
author:
- first_name: B.
full_name: Wang, B.
last_name: Wang
- first_name: Roger
full_name: Ayats López, Roger
id: ab77522d-073b-11ed-8aff-e71b39258362
last_name: Ayats López
orcid: 0000-0001-6572-0621
- first_name: A.
full_name: Meseguer, A.
last_name: Meseguer
- first_name: F.
full_name: Marques, F.
last_name: Marques
citation:
ama: Wang B, Ayats López R, Meseguer A, Marques F. Phase-locking flows between orthogonally
stretching parallel plates. Physics of Fluids. 2022;34(11). doi:10.1063/5.0124152
apa: Wang, B., Ayats López, R., Meseguer, A., & Marques, F. (2022). Phase-locking
flows between orthogonally stretching parallel plates. Physics of Fluids.
AIP Publishing. https://doi.org/10.1063/5.0124152
chicago: Wang, B., Roger Ayats López, A. Meseguer, and F. Marques. “Phase-Locking
Flows between Orthogonally Stretching Parallel Plates.” Physics of Fluids.
AIP Publishing, 2022. https://doi.org/10.1063/5.0124152.
ieee: B. Wang, R. Ayats López, A. Meseguer, and F. Marques, “Phase-locking flows
between orthogonally stretching parallel plates,” Physics of Fluids, vol.
34, no. 11. AIP Publishing, 2022.
ista: Wang B, Ayats López R, Meseguer A, Marques F. 2022. Phase-locking flows between
orthogonally stretching parallel plates. Physics of Fluids. 34(11), 114111.
mla: Wang, B., et al. “Phase-Locking Flows between Orthogonally Stretching Parallel
Plates.” Physics of Fluids, vol. 34, no. 11, 114111, AIP Publishing, 2022,
doi:10.1063/5.0124152.
short: B. Wang, R. Ayats López, A. Meseguer, F. Marques, Physics of Fluids 34 (2022).
date_created: 2023-01-12T12:06:58Z
date_published: 2022-11-04T00:00:00Z
date_updated: 2023-10-03T11:07:58Z
day: '04'
department:
- _id: BjHo
doi: 10.1063/5.0124152
external_id:
isi:
- '000880665300024'
intvolume: ' 34'
isi: 1
issue: '11'
keyword:
- Condensed Matter Physics
- Fluid Flow and Transfer Processes
- Mechanics of Materials
- Computational Mechanics
- Mechanical Engineering
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://upcommons.upc.edu/handle/2117/385635
month: '11'
oa: 1
oa_version: Submitted Version
publication: Physics of Fluids
publication_identifier:
eissn:
- 1089-7666
issn:
- 1070-6631
publication_status: published
publisher: AIP Publishing
quality_controlled: '1'
scopus_import: '1'
status: public
title: Phase-locking flows between orthogonally stretching parallel plates
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 34
year: '2022'
...
---
_id: '12147'
abstract:
- lang: eng
text: Continuous-time neural networks are a class of machine learning systems that
can tackle representation learning on spatiotemporal decision-making tasks. These
models are typically represented by continuous differential equations. However,
their expressive power when they are deployed on computers is bottlenecked by
numerical differential equation solvers. This limitation has notably slowed down
the scaling and understanding of numerous natural physical phenomena such as the
dynamics of nervous systems. Ideally, we would circumvent this bottleneck by solving
the given dynamical system in closed form. This is known to be intractable in
general. Here, we show that it is possible to closely approximate the interaction
between neurons and synapses—the building blocks of natural and artificial neural
networks—constructed by liquid time-constant networks efficiently in closed form.
To this end, we compute a tightly bounded approximation of the solution of an
integral appearing in liquid time-constant dynamics that has had no known closed-form
solution so far. This closed-form solution impacts the design of continuous-time
and continuous-depth neural models. For instance, since time appears explicitly
in closed form, the formulation relaxes the need for complex numerical solvers.
Consequently, we obtain models that are between one and five orders of magnitude
faster in training and inference compared with differential equation-based counterparts.
More importantly, in contrast to ordinary differential equation-based continuous
networks, closed-form networks can scale remarkably well compared with other deep
learning instances. Lastly, as these models are derived from liquid networks,
they show good performance in time-series modelling compared with advanced recurrent
neural network models.
acknowledgement: This research was supported in part by the AI2050 program at Schmidt
Futures (grant G-22-63172), the Boeing Company, and the United States Air Force
Research Laboratory and the United States Air Force Artificial Intelligence Accelerator
and was accomplished under cooperative agreement number FA8750-19-2-1000. The views
and conclusions contained in this document are those of the authors and should not
be interpreted as representing the official policies, either expressed or implied,
of the United States Air Force or the U.S. Government. The U.S. Government is authorized
to reproduce and distribute reprints for Government purposes, notwithstanding any
copyright notation herein. This work was further supported by The Boeing Company
and Office of Naval Research grant N00014-18-1-2830. M.T. is supported by the Poul
Due Jensen Foundation, grant 883901. M.L. was supported in part by the Austrian
Science Fund under grant Z211-N23 (Wittgenstein Award). A.A. was supported by the
National Science Foundation Graduate Research Fellowship Program. We thank T.-H.
Wang, P. Kao, M. Chahine, W. Xiao, X. Li, L. Yin and Y. Ben for useful suggestions
and for testing of CfC models to confirm the results across other domains.
article_processing_charge: No
article_type: original
arxiv: 1
author:
- first_name: Ramin
full_name: Hasani, Ramin
last_name: Hasani
- first_name: Mathias
full_name: Lechner, Mathias
id: 3DC22916-F248-11E8-B48F-1D18A9856A87
last_name: Lechner
- first_name: Alexander
full_name: Amini, Alexander
last_name: Amini
- first_name: Lucas
full_name: Liebenwein, Lucas
last_name: Liebenwein
- first_name: Aaron
full_name: Ray, Aaron
last_name: Ray
- first_name: Max
full_name: Tschaikowski, Max
last_name: Tschaikowski
- first_name: Gerald
full_name: Teschl, Gerald
last_name: Teschl
- first_name: Daniela
full_name: Rus, Daniela
last_name: Rus
citation:
ama: Hasani R, Lechner M, Amini A, et al. Closed-form continuous-time neural networks.
Nature Machine Intelligence. 2022;4(11):992-1003. doi:10.1038/s42256-022-00556-7
apa: Hasani, R., Lechner, M., Amini, A., Liebenwein, L., Ray, A., Tschaikowski,
M., … Rus, D. (2022). Closed-form continuous-time neural networks. Nature Machine
Intelligence. Springer Nature. https://doi.org/10.1038/s42256-022-00556-7
chicago: Hasani, Ramin, Mathias Lechner, Alexander Amini, Lucas Liebenwein, Aaron
Ray, Max Tschaikowski, Gerald Teschl, and Daniela Rus. “Closed-Form Continuous-Time
Neural Networks.” Nature Machine Intelligence. Springer Nature, 2022. https://doi.org/10.1038/s42256-022-00556-7.
ieee: R. Hasani et al., “Closed-form continuous-time neural networks,” Nature
Machine Intelligence, vol. 4, no. 11. Springer Nature, pp. 992–1003, 2022.
ista: Hasani R, Lechner M, Amini A, Liebenwein L, Ray A, Tschaikowski M, Teschl
G, Rus D. 2022. Closed-form continuous-time neural networks. Nature Machine Intelligence.
4(11), 992–1003.
mla: Hasani, Ramin, et al. “Closed-Form Continuous-Time Neural Networks.” Nature
Machine Intelligence, vol. 4, no. 11, Springer Nature, 2022, pp. 992–1003,
doi:10.1038/s42256-022-00556-7.
short: R. Hasani, M. Lechner, A. Amini, L. Liebenwein, A. Ray, M. Tschaikowski,
G. Teschl, D. Rus, Nature Machine Intelligence 4 (2022) 992–1003.
date_created: 2023-01-12T12:07:21Z
date_published: 2022-11-15T00:00:00Z
date_updated: 2023-08-04T09:00:10Z
day: '15'
ddc:
- '000'
department:
- _id: ToHe
doi: 10.1038/s42256-022-00556-7
external_id:
arxiv:
- '2106.13898'
isi:
- '000884215600003'
file:
- access_level: open_access
checksum: b4789122ce04bfb4ac042390f59aaa8b
content_type: application/pdf
creator: dernst
date_created: 2023-01-24T09:49:44Z
date_updated: 2023-01-24T09:49:44Z
file_id: '12355'
file_name: 2022_NatureMachineIntelligence_Hasani.pdf
file_size: 3259553
relation: main_file
success: 1
file_date_updated: 2023-01-24T09:49:44Z
has_accepted_license: '1'
intvolume: ' 4'
isi: 1
issue: '11'
keyword:
- Artificial Intelligence
- Computer Networks and Communications
- Computer Vision and Pattern Recognition
- Human-Computer Interaction
- Software
language:
- iso: eng
month: '11'
oa: 1
oa_version: Published Version
page: 992-1003
project:
- _id: 25F42A32-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: Z211
name: The Wittgenstein Prize
publication: Nature Machine Intelligence
publication_identifier:
issn:
- 2522-5839
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
related_material:
link:
- relation: erratum
url: https://doi.org/10.1038/s42256-022-00597-y
scopus_import: '1'
status: public
title: Closed-form continuous-time neural networks
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: journal_article
user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
volume: 4
year: '2022'
...
---
_id: '12148'
abstract:
- lang: eng
text: 'We prove a general local law for Wigner matrices that optimally handles observables
of arbitrary rank and thus unifies the well-known averaged and isotropic local
laws. As an application, we prove a central limit theorem in quantum unique ergodicity
(QUE): that is, we show that the quadratic forms of a general deterministic matrix
A on the bulk eigenvectors of a Wigner matrix have approximately Gaussian fluctuation.
For the bulk spectrum, we thus generalise our previous result [17] as valid for
test matrices A of large rank as well as the result of Benigni and Lopatto [7]
as valid for specific small-rank observables.'
acknowledgement: L.E. acknowledges support by ERC Advanced Grant ‘RMTBeyond’ No. 101020331.
D.S. acknowledges the support of Dr. Max Rössler, the Walter Haefner Foundation
and the ETH Zürich Foundation.
article_number: e96
article_processing_charge: No
article_type: original
author:
- first_name: Giorgio
full_name: Cipolloni, Giorgio
id: 42198EFA-F248-11E8-B48F-1D18A9856A87
last_name: Cipolloni
orcid: 0000-0002-4901-7992
- first_name: László
full_name: Erdös, László
id: 4DBD5372-F248-11E8-B48F-1D18A9856A87
last_name: Erdös
orcid: 0000-0001-5366-9603
- first_name: Dominik J
full_name: Schröder, Dominik J
id: 408ED176-F248-11E8-B48F-1D18A9856A87
last_name: Schröder
orcid: 0000-0002-2904-1856
citation:
ama: Cipolloni G, Erdös L, Schröder DJ. Rank-uniform local law for Wigner matrices.
Forum of Mathematics, Sigma. 2022;10. doi:10.1017/fms.2022.86
apa: Cipolloni, G., Erdös, L., & Schröder, D. J. (2022). Rank-uniform local
law for Wigner matrices. Forum of Mathematics, Sigma. Cambridge University
Press. https://doi.org/10.1017/fms.2022.86
chicago: Cipolloni, Giorgio, László Erdös, and Dominik J Schröder. “Rank-Uniform
Local Law for Wigner Matrices.” Forum of Mathematics, Sigma. Cambridge
University Press, 2022. https://doi.org/10.1017/fms.2022.86.
ieee: G. Cipolloni, L. Erdös, and D. J. Schröder, “Rank-uniform local law for Wigner
matrices,” Forum of Mathematics, Sigma, vol. 10. Cambridge University Press,
2022.
ista: Cipolloni G, Erdös L, Schröder DJ. 2022. Rank-uniform local law for Wigner
matrices. Forum of Mathematics, Sigma. 10, e96.
mla: Cipolloni, Giorgio, et al. “Rank-Uniform Local Law for Wigner Matrices.” Forum
of Mathematics, Sigma, vol. 10, e96, Cambridge University Press, 2022, doi:10.1017/fms.2022.86.
short: G. Cipolloni, L. Erdös, D.J. Schröder, Forum of Mathematics, Sigma 10 (2022).
date_created: 2023-01-12T12:07:30Z
date_published: 2022-10-27T00:00:00Z
date_updated: 2023-08-04T09:00:35Z
day: '27'
ddc:
- '510'
department:
- _id: LaEr
doi: 10.1017/fms.2022.86
ec_funded: 1
external_id:
isi:
- '000873719200001'
file:
- access_level: open_access
checksum: 94a049aeb1eea5497aa097712a73c400
content_type: application/pdf
creator: dernst
date_created: 2023-01-24T10:02:40Z
date_updated: 2023-01-24T10:02:40Z
file_id: '12356'
file_name: 2022_ForumMath_Cipolloni.pdf
file_size: 817089
relation: main_file
success: 1
file_date_updated: 2023-01-24T10:02:40Z
has_accepted_license: '1'
intvolume: ' 10'
isi: 1
keyword:
- Computational Mathematics
- Discrete Mathematics and Combinatorics
- Geometry and Topology
- Mathematical Physics
- Statistics and Probability
- Algebra and Number Theory
- Theoretical Computer Science
- Analysis
language:
- iso: eng
month: '10'
oa: 1
oa_version: Published Version
project:
- _id: 62796744-2b32-11ec-9570-940b20777f1d
call_identifier: H2020
grant_number: '101020331'
name: Random matrices beyond Wigner-Dyson-Mehta
publication: Forum of Mathematics, Sigma
publication_identifier:
issn:
- 2050-5094
publication_status: published
publisher: Cambridge University Press
quality_controlled: '1'
scopus_import: '1'
status: public
title: Rank-uniform local law for Wigner matrices
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: journal_article
user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
volume: 10
year: '2022'
...
---
_id: '12149'
abstract:
- lang: eng
text: Editorial on the Research Topic
acknowledgement: This work was supported by a DFG grant ZA990/1 to DZ. This work was
supported by the MSCA EU proposal 841301 - DREAM, European Commission; Horizon 2020
- Research and Innovation Framework Programme to JFRV.
article_number: '1028154'
article_processing_charge: No
article_type: letter_note
author:
- first_name: Giuditta
full_name: Gambino, Giuditta
last_name: Gambino
- first_name: Rebecca
full_name: Bhik-Ghanie, Rebecca
last_name: Bhik-Ghanie
- first_name: Giuseppe
full_name: Giglia, Giuseppe
last_name: Giglia
- first_name: M. Victoria
full_name: Puig, M. Victoria
last_name: Puig
- first_name: Juan F
full_name: Ramirez Villegas, Juan F
id: 44B06F76-F248-11E8-B48F-1D18A9856A87
last_name: Ramirez Villegas
- first_name: Daniel
full_name: Zaldivar, Daniel
last_name: Zaldivar
citation:
ama: 'Gambino G, Bhik-Ghanie R, Giglia G, Puig MV, Ramirez Villegas JF, Zaldivar
D. Editorial: Neuromodulatory ascending systems: Their influence at the microscopic
and macroscopic levels. Frontiers in Neural Circuits. 2022;16. doi:10.3389/fncir.2022.1028154'
apa: 'Gambino, G., Bhik-Ghanie, R., Giglia, G., Puig, M. V., Ramirez Villegas, J.
F., & Zaldivar, D. (2022). Editorial: Neuromodulatory ascending systems: Their
influence at the microscopic and macroscopic levels. Frontiers in Neural Circuits.
Frontiers Media. https://doi.org/10.3389/fncir.2022.1028154'
chicago: 'Gambino, Giuditta, Rebecca Bhik-Ghanie, Giuseppe Giglia, M. Victoria Puig,
Juan F Ramirez Villegas, and Daniel Zaldivar. “Editorial: Neuromodulatory Ascending
Systems: Their Influence at the Microscopic and Macroscopic Levels.” Frontiers
in Neural Circuits. Frontiers Media, 2022. https://doi.org/10.3389/fncir.2022.1028154.'
ieee: 'G. Gambino, R. Bhik-Ghanie, G. Giglia, M. V. Puig, J. F. Ramirez Villegas,
and D. Zaldivar, “Editorial: Neuromodulatory ascending systems: Their influence
at the microscopic and macroscopic levels,” Frontiers in Neural Circuits,
vol. 16. Frontiers Media, 2022.'
ista: 'Gambino G, Bhik-Ghanie R, Giglia G, Puig MV, Ramirez Villegas JF, Zaldivar
D. 2022. Editorial: Neuromodulatory ascending systems: Their influence at the
microscopic and macroscopic levels. Frontiers in Neural Circuits. 16, 1028154.'
mla: 'Gambino, Giuditta, et al. “Editorial: Neuromodulatory Ascending Systems: Their
Influence at the Microscopic and Macroscopic Levels.” Frontiers in Neural Circuits,
vol. 16, 1028154, Frontiers Media, 2022, doi:10.3389/fncir.2022.1028154.'
short: G. Gambino, R. Bhik-Ghanie, G. Giglia, M.V. Puig, J.F. Ramirez Villegas,
D. Zaldivar, Frontiers in Neural Circuits 16 (2022).
date_created: 2023-01-12T12:07:39Z
date_published: 2022-10-26T00:00:00Z
date_updated: 2023-08-04T09:01:06Z
day: '26'
ddc:
- '570'
department:
- _id: JoCs
doi: 10.3389/fncir.2022.1028154
ec_funded: 1
external_id:
isi:
- '000886671400001'
file:
- access_level: open_access
checksum: 457aa00e1800847abb340853058531de
content_type: application/pdf
creator: dernst
date_created: 2023-01-24T10:10:43Z
date_updated: 2023-01-24T10:10:43Z
file_id: '12357'
file_name: 2022_FrontiersNeuralCircuits_Gambino.pdf
file_size: 110031
relation: main_file
success: 1
file_date_updated: 2023-01-24T10:10:43Z
has_accepted_license: '1'
intvolume: ' 16'
isi: 1
keyword:
- Cellular and Molecular Neuroscience
- Cognitive Neuroscience
- Sensory Systems
- Neuroscience (miscellaneous)
language:
- iso: eng
month: '10'
oa: 1
oa_version: Published Version
project:
- _id: 26BAE2E4-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '841301'
name: 'The Brainstem-Hippocampus Network Uncovered: Dynamics, Reactivation and Memory
Consolidation'
publication: Frontiers in Neural Circuits
publication_identifier:
issn:
- 1662-5110
publication_status: published
publisher: Frontiers Media
quality_controlled: '1'
scopus_import: '1'
status: public
title: 'Editorial: Neuromodulatory ascending systems: Their influence at the microscopic
and macroscopic levels'
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: journal_article
user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
volume: 16
year: '2022'
...
---
_id: '12150'
abstract:
- lang: eng
text: Methods inspired from machine learning have recently attracted great interest
in the computational study of quantum many-particle systems. So far, however,
it has proven challenging to deal with microscopic models in which the total number
of particles is not conserved. To address this issue, we propose a variant of
neural network states, which we term neural coherent states. Taking the Fröhlich
impurity model as a case study, we show that neural coherent states can learn
the ground state of nonadditive systems very well. In particular, we recover exact
diagonalization in all regimes tested and observe substantial improvement over
the standard coherent state estimates in the most challenging intermediate-coupling
regime. Our approach is generic and does not assume specific details of the system,
suggesting wide applications.
acknowledgement: 'We acknowledge fruitful discussions with G. Bighin, G. Fabiani,
A. Ghazaryan, C. Lampert, and A. Volosniev at various stages of this work. W.R.
acknowledges support through a DOC Fellowship of the Austrian Academy of Sciences
and has received funding from the EU Horizon 2020 programme under the Marie Skłodowska-Curie
Grant Agreement No. 665385. M.L. and J.H.M. acknowledge support by the European
Research Council (ERC) Starting Grant No. 801770 (ANGULON) and Synergy Grant No.
856538 (3D-MAGiC), respectively. This work is part of the Shell-NWO/FOMinitiative
“Computational sciences for energy research” of Shell and Chemical Sciences, Earth
and Life Sciences, Physical Sciences, FOM and STW. '
article_number: '155127'
article_processing_charge: No
article_type: original
arxiv: 1
author:
- first_name: Wojciech
full_name: Rzadkowski, Wojciech
id: 48C55298-F248-11E8-B48F-1D18A9856A87
last_name: Rzadkowski
orcid: 0000-0002-1106-4419
- first_name: Mikhail
full_name: Lemeshko, Mikhail
id: 37CB05FA-F248-11E8-B48F-1D18A9856A87
last_name: Lemeshko
orcid: 0000-0002-6990-7802
- first_name: Johan H.
full_name: Mentink, Johan H.
last_name: Mentink
citation:
ama: Rzadkowski W, Lemeshko M, Mentink JH. Artificial neural network states for
nonadditive systems. Physical Review B. 2022;106(15). doi:10.1103/physrevb.106.155127
apa: Rzadkowski, W., Lemeshko, M., & Mentink, J. H. (2022). Artificial neural
network states for nonadditive systems. Physical Review B. American Physical
Society. https://doi.org/10.1103/physrevb.106.155127
chicago: Rzadkowski, Wojciech, Mikhail Lemeshko, and Johan H. Mentink. “Artificial
Neural Network States for Nonadditive Systems.” Physical Review B. American
Physical Society, 2022. https://doi.org/10.1103/physrevb.106.155127.
ieee: W. Rzadkowski, M. Lemeshko, and J. H. Mentink, “Artificial neural network
states for nonadditive systems,” Physical Review B, vol. 106, no. 15. American
Physical Society, 2022.
ista: Rzadkowski W, Lemeshko M, Mentink JH. 2022. Artificial neural network states
for nonadditive systems. Physical Review B. 106(15), 155127.
mla: Rzadkowski, Wojciech, et al. “Artificial Neural Network States for Nonadditive
Systems.” Physical Review B, vol. 106, no. 15, 155127, American Physical
Society, 2022, doi:10.1103/physrevb.106.155127.
short: W. Rzadkowski, M. Lemeshko, J.H. Mentink, Physical Review B 106 (2022).
date_created: 2023-01-12T12:07:49Z
date_published: 2022-10-15T00:00:00Z
date_updated: 2023-08-04T09:01:48Z
day: '15'
department:
- _id: MiLe
doi: 10.1103/physrevb.106.155127
ec_funded: 1
external_id:
arxiv:
- '2105.15193'
isi:
- '000875189100005'
intvolume: ' 106'
isi: 1
issue: '15'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: ' https://doi.org/10.48550/arXiv.2105.15193'
month: '10'
oa: 1
oa_version: Preprint
project:
- _id: 05A235A0-7A3F-11EA-A408-12923DDC885E
grant_number: '25681'
name: Analytic and machine learning approaches to composite quantum impurities
- _id: 2564DBCA-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '665385'
name: International IST Doctoral Program
- _id: 2688CF98-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '801770'
name: 'Angulon: physics and applications of a new quasiparticle'
publication: Physical Review B
publication_identifier:
eissn:
- 2469-9969
issn:
- 2469-9950
publication_status: published
publisher: American Physical Society
quality_controlled: '1'
scopus_import: '1'
status: public
title: Artificial neural network states for nonadditive systems
type: journal_article
user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
volume: 106
year: '2022'
...
---
_id: '12151'
abstract:
- lang: eng
text: The k-sample G(k,W) from a graphon W:[0,1]2→[0,1] is the random graph on {1,…,k},
where we sample x1,…,xk∈[0,1] uniformly at random and make each pair {i,j}⊆{1,…,k}
an edge with probability W(xi,xj), with all these choices being mutually independent.
Let the random variable Xk(W) be the number of edges in G(k,W). Vera T. Sós asked
in 2012 whether two graphons U, W are necessarily weakly isomorphic if the random
variables Xk(U) and Xk(W) have the same distribution for every integer k≥2. This
question when one of the graphons W is a constant function was answered positively
by Endre Csóka and independently by Jacob Fox, Tomasz Łuczak and Vera T. Sós.
Here we investigate the question when W is a 2-step graphon and prove that the
answer is positive for a 3-dimensional family of such graphons. We also present
some related results.
acknowledgement: "Supported by Austrian Science Fund (FWF) Grant I3747. Supported
by ERC Advanced Grant 101020255 and Leverhulme Research Project Grant RPG-2018-424.\r\nAn
extended abstract of this paper appeared in the Proceedings of the European Conference\r\non
Combinatorics, Graph Theory and Applications (EuroComb 2021), CRM Research Perspectives,
Springer."
article_processing_charge: No
article_type: original
arxiv: 1
author:
- first_name: Oliver
full_name: Cooley, Oliver
id: 43f4ddd0-a46b-11ec-8df6-ef3703bd721d
last_name: Cooley
- first_name: M.
full_name: Kang, M.
last_name: Kang
- first_name: O.
full_name: Pikhurko, O.
last_name: Pikhurko
citation:
ama: Cooley O, Kang M, Pikhurko O. On a question of Vera T. Sós about size forcing
of graphons. Acta Mathematica Hungarica. 2022;168:1-26. doi:10.1007/s10474-022-01265-8
apa: Cooley, O., Kang, M., & Pikhurko, O. (2022). On a question of Vera T. Sós
about size forcing of graphons. Acta Mathematica Hungarica. Springer Nature.
https://doi.org/10.1007/s10474-022-01265-8
chicago: Cooley, Oliver, M. Kang, and O. Pikhurko. “On a Question of Vera T. Sós
about Size Forcing of Graphons.” Acta Mathematica Hungarica. Springer Nature,
2022. https://doi.org/10.1007/s10474-022-01265-8.
ieee: O. Cooley, M. Kang, and O. Pikhurko, “On a question of Vera T. Sós about size
forcing of graphons,” Acta Mathematica Hungarica, vol. 168. Springer Nature,
pp. 1–26, 2022.
ista: Cooley O, Kang M, Pikhurko O. 2022. On a question of Vera T. Sós about size
forcing of graphons. Acta Mathematica Hungarica. 168, 1–26.
mla: Cooley, Oliver, et al. “On a Question of Vera T. Sós about Size Forcing of
Graphons.” Acta Mathematica Hungarica, vol. 168, Springer Nature, 2022,
pp. 1–26, doi:10.1007/s10474-022-01265-8.
short: O. Cooley, M. Kang, O. Pikhurko, Acta Mathematica Hungarica 168 (2022) 1–26.
date_created: 2023-01-12T12:07:59Z
date_published: 2022-11-23T00:00:00Z
date_updated: 2023-08-04T09:02:37Z
day: '23'
department:
- _id: MaKw
doi: 10.1007/s10474-022-01265-8
external_id:
arxiv:
- '2103.09114'
isi:
- '000886839900006'
intvolume: ' 168'
isi: 1
keyword:
- graphon
- k-sample
- graphon forcing
- graph container
language:
- iso: eng
main_file_link:
- open_access: '1'
url: ' https://doi.org/10.48550/arXiv.2103.09114'
month: '11'
oa: 1
oa_version: Preprint
page: 1-26
publication: Acta Mathematica Hungarica
publication_identifier:
eissn:
- 1588-2632
issn:
- 0236-5294
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
scopus_import: '1'
status: public
title: On a question of Vera T. Sós about size forcing of graphons
type: journal_article
user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
volume: 168
year: '2022'
...
---
_id: '12152'
abstract:
- lang: eng
text: ESCRT-III filaments are composite cytoskeletal polymers that can constrict
and cut cell membranes from the inside of the membrane neck. Membrane-bound ESCRT-III
filaments undergo a series of dramatic composition and geometry changes in the
presence of an ATP-consuming Vps4 enzyme, which causes stepwise changes in the
membrane morphology. We set out to understand the physical mechanisms involved
in translating the changes in ESCRT-III polymer composition into membrane deformation.
We have built a coarse-grained model in which ESCRT-III polymers of different
geometries and mechanical properties are allowed to copolymerise and bind to a
deformable membrane. By modelling ATP-driven stepwise depolymerisation of specific
polymers, we identify mechanical regimes in which changes in filament composition
trigger the associated membrane transition from a flat to a buckled state, and
then to a tubule state that eventually undergoes scission to release a small cargo-loaded
vesicle. We then characterise how the location and kinetics of polymer loss affects
the extent of membrane deformation and the efficiency of membrane neck scission.
Our results identify the near-minimal mechanical conditions for the operation
of shape-shifting composite polymers that sever membrane necks.
acknowledgement: "A.S . received an award from European Research Council (https://erc.europa.eu,
“NEPA\"\r\n802960), and an award from the Royal Society (https://royalsociety.org,
UF160266). L. H.-K.\r\nreceived an award from the Biotechnology and Biological Sciences
Research Council (https://\r\nwww.ukri.org/councils/bbsrc/). E. L. received an award
from the University College London (https://www.ucl.ac.uk/biophysics/news/2022/feb/applications-biop-brian-duff-and-ipls-summerundergraduate-studentships-now-open,
Brian Duff Undergraduate Summer Research Studentship). B.B. and A.S. received an
award from Volkswagen Foundation https://www.volkswagenstiftung.de/en/foundation,
Az 96727), and an award from Medical Research Council (https://www.ukri.org/councils/mrc,
MC_CF1226). A. R. received an\r\naward from the Swiss National Fund for Research
(https://www.snf.ch/en, 31003A_130520,\r\n31003A_149975, and 31003A_173087) and
an award from the European Research Council\r\nConsolidator (https://erc.europa.eu,
311536). The funders had no role in study design, data collection and analysis,
decision to publish, or preparation of the manuscript."
article_number: e1010586
article_processing_charge: No
article_type: original
author:
- first_name: Xiuyun
full_name: Jiang, Xiuyun
last_name: Jiang
- first_name: Lena
full_name: Harker-Kirschneck, Lena
last_name: Harker-Kirschneck
- first_name: Christian Eduardo
full_name: Vanhille-Campos, Christian Eduardo
id: 3adeca52-9313-11ed-b1ac-c170b2505714
last_name: Vanhille-Campos
- first_name: Anna-Katharina
full_name: Pfitzner, Anna-Katharina
last_name: Pfitzner
- first_name: Elene
full_name: Lominadze, Elene
last_name: Lominadze
- first_name: Aurélien
full_name: Roux, Aurélien
last_name: Roux
- first_name: Buzz
full_name: Baum, Buzz
last_name: Baum
- first_name: Anđela
full_name: Šarić, Anđela
id: bf63d406-f056-11eb-b41d-f263a6566d8b
last_name: Šarić
orcid: 0000-0002-7854-2139
citation:
ama: Jiang X, Harker-Kirschneck L, Vanhille-Campos CE, et al. Modelling membrane
reshaping by staged polymerization of ESCRT-III filaments. PLOS Computational
Biology. 2022;18(10). doi:10.1371/journal.pcbi.1010586
apa: Jiang, X., Harker-Kirschneck, L., Vanhille-Campos, C. E., Pfitzner, A.-K.,
Lominadze, E., Roux, A., … Šarić, A. (2022). Modelling membrane reshaping by staged
polymerization of ESCRT-III filaments. PLOS Computational Biology. Public
Library of Science. https://doi.org/10.1371/journal.pcbi.1010586
chicago: Jiang, Xiuyun, Lena Harker-Kirschneck, Christian Eduardo Vanhille-Campos,
Anna-Katharina Pfitzner, Elene Lominadze, Aurélien Roux, Buzz Baum, and Anđela
Šarić. “Modelling Membrane Reshaping by Staged Polymerization of ESCRT-III Filaments.”
PLOS Computational Biology. Public Library of Science, 2022. https://doi.org/10.1371/journal.pcbi.1010586.
ieee: X. Jiang et al., “Modelling membrane reshaping by staged polymerization
of ESCRT-III filaments,” PLOS Computational Biology, vol. 18, no. 10. Public
Library of Science, 2022.
ista: Jiang X, Harker-Kirschneck L, Vanhille-Campos CE, Pfitzner A-K, Lominadze
E, Roux A, Baum B, Šarić A. 2022. Modelling membrane reshaping by staged polymerization
of ESCRT-III filaments. PLOS Computational Biology. 18(10), e1010586.
mla: Jiang, Xiuyun, et al. “Modelling Membrane Reshaping by Staged Polymerization
of ESCRT-III Filaments.” PLOS Computational Biology, vol. 18, no. 10, e1010586,
Public Library of Science, 2022, doi:10.1371/journal.pcbi.1010586.
short: X. Jiang, L. Harker-Kirschneck, C.E. Vanhille-Campos, A.-K. Pfitzner, E.
Lominadze, A. Roux, B. Baum, A. Šarić, PLOS Computational Biology 18 (2022).
date_created: 2023-01-12T12:08:10Z
date_published: 2022-10-17T00:00:00Z
date_updated: 2023-08-04T09:03:21Z
day: '17'
ddc:
- '570'
department:
- _id: AnSa
doi: 10.1371/journal.pcbi.1010586
ec_funded: 1
external_id:
isi:
- '000924885500005'
file:
- access_level: open_access
checksum: bada6a7865e470cf42bbdfa67dd471d2
content_type: application/pdf
creator: dernst
date_created: 2023-01-24T10:45:01Z
date_updated: 2023-01-24T10:45:01Z
file_id: '12359'
file_name: 2022_PLoSCompBio_Jiang.pdf
file_size: 2641067
relation: main_file
success: 1
file_date_updated: 2023-01-24T10:45:01Z
has_accepted_license: '1'
intvolume: ' 18'
isi: 1
issue: '10'
keyword:
- Computational Theory and Mathematics
- Cellular and Molecular Neuroscience
- Genetics
- Molecular Biology
- Ecology
- Modeling and Simulation
- Ecology
- Evolution
- Behavior and Systematics
language:
- iso: eng
month: '10'
oa: 1
oa_version: Published Version
project:
- _id: eba2549b-77a9-11ec-83b8-a81e493eae4e
call_identifier: H2020
grant_number: '802960'
name: 'Non-Equilibrium Protein Assembly: from Building Blocks to Biological Machines'
- _id: eba0f67c-77a9-11ec-83b8-cc8501b3e222
grant_number: '96752'
name: 'The evolution of trafficking: from archaea to eukaryotes'
publication: PLOS Computational Biology
publication_identifier:
issn:
- 1553-7358
publication_status: published
publisher: Public Library of Science
quality_controlled: '1'
related_material:
link:
- relation: software
url: https://github.com/sharonJXY/3-filament-model
scopus_import: '1'
status: public
title: Modelling membrane reshaping by staged polymerization of ESCRT-III filaments
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: journal_article
user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
volume: 18
year: '2022'
...