---
_id: '10705'
abstract:
- lang: eng
text: Although rigidity and jamming transitions have been widely studied in physics
and material science, their importance in a number of biological processes, including
embryo development, tissue homeostasis, wound healing, and disease progression,
has only begun to be recognized in the past few years. The hypothesis that biological
systems can undergo rigidity/jamming transitions is attractive, as it would allow
these systems to change their material properties rapidly and strongly. However,
whether such transitions indeed occur in biological systems, how they are being
regulated, and what their physiological relevance might be, is still being debated.
Here, we review theoretical and experimental advances from the past few years,
focusing on the regulation and role of potential tissue rigidity transitions in
different biological processes.
acknowledgement: We thank present and former members of the Heisenberg and Hannezo
groups, in particular Bernat Corominas-Murtra and Nicoletta Petridou, for helpful
discussions, and Claudia Flandoli for the artwork. We apologize for not being able
to cite a number of highly relevant studies, to stay within the maximum allowed
number of citations.
article_processing_charge: No
article_type: original
author:
- first_name: Edouard B
full_name: Hannezo, Edouard B
id: 3A9DB764-F248-11E8-B48F-1D18A9856A87
last_name: Hannezo
orcid: 0000-0001-6005-1561
- first_name: Carl-Philipp J
full_name: Heisenberg, Carl-Philipp J
id: 39427864-F248-11E8-B48F-1D18A9856A87
last_name: Heisenberg
orcid: 0000-0002-0912-4566
citation:
ama: Hannezo EB, Heisenberg C-PJ. Rigidity transitions in development and disease.
Trends in Cell Biology. 2022;32(5):P433-444. doi:10.1016/j.tcb.2021.12.006
apa: Hannezo, E. B., & Heisenberg, C.-P. J. (2022). Rigidity transitions in
development and disease. Trends in Cell Biology. Cell Press. https://doi.org/10.1016/j.tcb.2021.12.006
chicago: Hannezo, Edouard B, and Carl-Philipp J Heisenberg. “Rigidity Transitions
in Development and Disease.” Trends in Cell Biology. Cell Press, 2022.
https://doi.org/10.1016/j.tcb.2021.12.006.
ieee: E. B. Hannezo and C.-P. J. Heisenberg, “Rigidity transitions in development
and disease,” Trends in Cell Biology, vol. 32, no. 5. Cell Press, pp. P433-444,
2022.
ista: Hannezo EB, Heisenberg C-PJ. 2022. Rigidity transitions in development and
disease. Trends in Cell Biology. 32(5), P433-444.
mla: Hannezo, Edouard B., and Carl-Philipp J. Heisenberg. “Rigidity Transitions
in Development and Disease.” Trends in Cell Biology, vol. 32, no. 5, Cell
Press, 2022, pp. P433-444, doi:10.1016/j.tcb.2021.12.006.
short: E.B. Hannezo, C.-P.J. Heisenberg, Trends in Cell Biology 32 (2022) P433-444.
date_created: 2022-01-30T23:01:34Z
date_published: 2022-05-01T00:00:00Z
date_updated: 2023-08-02T14:03:53Z
day: '01'
department:
- _id: EdHa
- _id: CaHe
doi: 10.1016/j.tcb.2021.12.006
external_id:
isi:
- '000795773900009'
pmid:
- '35058104'
intvolume: ' 32'
isi: 1
issue: '5'
language:
- iso: eng
month: '05'
oa_version: None
page: P433-444
pmid: 1
publication: Trends in Cell Biology
publication_identifier:
eissn:
- 1879-3088
issn:
- 0962-8924
publication_status: published
publisher: Cell Press
quality_controlled: '1'
scopus_import: '1'
status: public
title: Rigidity transitions in development and disease
type: journal_article
user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
volume: 32
year: '2022'
...
---
_id: '10706'
abstract:
- lang: eng
text: This is a collection of problems composed by some participants of the workshop
“Differential Geometry, Billiards, and Geometric Optics” that took place at CIRM
on October 4–8, 2021.
article_processing_charge: No
article_type: original
arxiv: 1
author:
- first_name: Misha
full_name: Bialy, Misha
last_name: Bialy
- first_name: Corentin
full_name: Fiorebe, Corentin
id: 06619f18-9070-11eb-847d-d1ee780bd88b
last_name: Fiorebe
- first_name: Alexey
full_name: Glutsyuk, Alexey
last_name: Glutsyuk
- first_name: Mark
full_name: Levi, Mark
last_name: Levi
- first_name: Alexander
full_name: Plakhov, Alexander
last_name: Plakhov
- first_name: Serge
full_name: Tabachnikov, Serge
last_name: Tabachnikov
citation:
ama: Bialy M, Fiorebe C, Glutsyuk A, Levi M, Plakhov A, Tabachnikov S. Open problems
on billiards and geometric optics. Arnold Mathematical Journal. 2022;8:411-422.
doi:10.1007/s40598-022-00198-y
apa: 'Bialy, M., Fiorebe, C., Glutsyuk, A., Levi, M., Plakhov, A., & Tabachnikov,
S. (2022). Open problems on billiards and geometric optics. Arnold Mathematical
Journal. Hybrid: Springer Nature. https://doi.org/10.1007/s40598-022-00198-y'
chicago: Bialy, Misha, Corentin Fiorebe, Alexey Glutsyuk, Mark Levi, Alexander Plakhov,
and Serge Tabachnikov. “Open Problems on Billiards and Geometric Optics.” Arnold
Mathematical Journal. Springer Nature, 2022. https://doi.org/10.1007/s40598-022-00198-y.
ieee: M. Bialy, C. Fiorebe, A. Glutsyuk, M. Levi, A. Plakhov, and S. Tabachnikov,
“Open problems on billiards and geometric optics,” Arnold Mathematical Journal,
vol. 8. Springer Nature, pp. 411–422, 2022.
ista: Bialy M, Fiorebe C, Glutsyuk A, Levi M, Plakhov A, Tabachnikov S. 2022. Open
problems on billiards and geometric optics. Arnold Mathematical Journal. 8, 411–422.
mla: Bialy, Misha, et al. “Open Problems on Billiards and Geometric Optics.” Arnold
Mathematical Journal, vol. 8, Springer Nature, 2022, pp. 411–22, doi:10.1007/s40598-022-00198-y.
short: M. Bialy, C. Fiorebe, A. Glutsyuk, M. Levi, A. Plakhov, S. Tabachnikov, Arnold
Mathematical Journal 8 (2022) 411–422.
conference:
end_date: 2021-10-08
location: Hybrid
name: 'CIRM: Centre International de Rencontres Mathématiques'
start_date: 2021-10-04
date_created: 2022-01-30T23:01:34Z
date_published: 2022-10-01T00:00:00Z
date_updated: 2023-02-27T07:34:08Z
day: '01'
department:
- _id: VaKa
doi: 10.1007/s40598-022-00198-y
external_id:
arxiv:
- '2110.10750'
intvolume: ' 8'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/2110.10750
month: '10'
oa: 1
oa_version: Preprint
page: 411-422
publication: Arnold Mathematical Journal
publication_identifier:
eissn:
- 2199-6806
issn:
- 2199-6792
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
related_material:
link:
- relation: earlier_version
url: https://conferences.cirm-math.fr/2383.html
scopus_import: '1'
status: public
title: Open problems on billiards and geometric optics
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 8
year: '2022'
...
---
_id: '10712'
abstract:
- lang: eng
text: Solute carriers are increasingly recognized as participating in a plethora
of pathologies, including cancer. We describe here the involvement of the orphan
solute carrier MFSD1 in the regulation of tumor cell migration. Loss of MFSD1
enabled higher levels of metastasis in a mouse model. We identified an increased
migratory potential in MFSD1-/- tumor cells which was mediated by increased focal
adhesion turn-over, reduced stability of mature inactive β1 integrin, and the
resulting increased integrin activation index. We show that MFSD1 promoted recycling
to the cell surface of endocytosed inactive β1 integrin and thereby protected
β1 integrin from proteolytic degradation; this led to dampening of the integrin
activation index. Furthermore, down-regulation of MFSD1 expression was observed
during early steps of tumorigenesis and higher MFSD1 expression levels correlate
with a better cancer patient prognosis. In sum, we describe a requirement for
endolysosomal MFSD1 in efficient β1 integrin recycling to suppress tumor spread.
acknowledged_ssus:
- _id: Bio
acknowledgement: We thank M. Sixt, A. Leithner, and J. Alanko for helpful advice and
the BioImaging Facility at IST Austria for technical support and assistance. We
thank the Siekhaus Lab for the careful review of the manuscript and their input.
MR and DS were funded by the NO Forschungs- und Bildungsges.m.b.H. (LS16-021) and
IST core funding. MD was funded by Deutsche Forschungsgemeinschaft (DA 1785-1).
article_number: '777634'
article_processing_charge: Yes (via OA deal)
article_type: original
author:
- first_name: Marko
full_name: Roblek, Marko
id: 3047D808-F248-11E8-B48F-1D18A9856A87
last_name: Roblek
orcid: 0000-0001-9588-1389
- first_name: Julia
full_name: Bicher, Julia
id: 3CCBB46E-F248-11E8-B48F-1D18A9856A87
last_name: Bicher
- first_name: Merel
full_name: van Gogh, Merel
last_name: van Gogh
- first_name: Attila
full_name: György, Attila
id: 3BCEDBE0-F248-11E8-B48F-1D18A9856A87
last_name: György
orcid: 0000-0002-1819-198X
- first_name: Rita
full_name: Seeböck, Rita
last_name: Seeböck
- first_name: Bozena
full_name: Szulc, Bozena
last_name: Szulc
- first_name: Markus
full_name: Damme, Markus
last_name: Damme
- first_name: Mariusz
full_name: Olczak, Mariusz
last_name: Olczak
- first_name: Lubor
full_name: Borsig, Lubor
last_name: Borsig
- first_name: Daria E
full_name: Siekhaus, Daria E
id: 3D224B9E-F248-11E8-B48F-1D18A9856A87
last_name: Siekhaus
orcid: 0000-0001-8323-8353
citation:
ama: Roblek M, Bicher J, van Gogh M, et al. The solute carrier MFSD1 decreases β1
integrin’s activation status and thus tumor metastasis. Frontiers in Oncology.
2022;12. doi:10.3389/fonc.2022.777634
apa: Roblek, M., Bicher, J., van Gogh, M., György, A., Seeböck, R., Szulc, B., …
Siekhaus, D. E. (2022). The solute carrier MFSD1 decreases β1 integrin’s activation
status and thus tumor metastasis. Frontiers in Oncology. Frontiers. https://doi.org/10.3389/fonc.2022.777634
chicago: Roblek, Marko, Julia Bicher, Merel van Gogh, Attila György, Rita Seeböck,
Bozena Szulc, Markus Damme, Mariusz Olczak, Lubor Borsig, and Daria E Siekhaus.
“The Solute Carrier MFSD1 Decreases Β1 Integrin’s Activation Status and Thus Tumor
Metastasis.” Frontiers in Oncology. Frontiers, 2022. https://doi.org/10.3389/fonc.2022.777634.
ieee: M. Roblek et al., “The solute carrier MFSD1 decreases β1 integrin’s
activation status and thus tumor metastasis,” Frontiers in Oncology, vol.
12. Frontiers, 2022.
ista: Roblek M, Bicher J, van Gogh M, György A, Seeböck R, Szulc B, Damme M, Olczak
M, Borsig L, Siekhaus DE. 2022. The solute carrier MFSD1 decreases β1 integrin’s
activation status and thus tumor metastasis. Frontiers in Oncology. 12, 777634.
mla: Roblek, Marko, et al. “The Solute Carrier MFSD1 Decreases Β1 Integrin’s Activation
Status and Thus Tumor Metastasis.” Frontiers in Oncology, vol. 12, 777634,
Frontiers, 2022, doi:10.3389/fonc.2022.777634.
short: M. Roblek, J. Bicher, M. van Gogh, A. György, R. Seeböck, B. Szulc, M. Damme,
M. Olczak, L. Borsig, D.E. Siekhaus, Frontiers in Oncology 12 (2022).
date_created: 2022-02-01T10:33:50Z
date_published: 2022-02-08T00:00:00Z
date_updated: 2023-08-02T14:05:44Z
day: '08'
ddc:
- '570'
department:
- _id: DaSi
doi: 10.3389/fonc.2022.777634
external_id:
isi:
- '000760618800001'
file:
- access_level: open_access
checksum: 63dfecf30c5bbf9408b3512bd603f78c
content_type: application/pdf
creator: cchlebak
date_created: 2022-02-08T13:26:40Z
date_updated: 2022-02-08T13:26:40Z
file_id: '10751'
file_name: 2022_FrontiersOncol_Roblek.pdf
file_size: 6303227
relation: main_file
success: 1
file_date_updated: 2022-02-08T13:26:40Z
has_accepted_license: '1'
intvolume: ' 12'
isi: 1
language:
- iso: eng
month: '02'
oa: 1
oa_version: Published Version
project:
- _id: 2637E9C0-B435-11E9-9278-68D0E5697425
grant_number: 'LSC16-021 '
name: Investigating the role of the novel major superfamily facilitator transporter
family member MFSD1 in metastasis
publication: Frontiers in Oncology
publication_identifier:
issn:
- 2234-943X
publication_status: published
publisher: Frontiers
quality_controlled: '1'
related_material:
link:
- description: News on IST Homepage
relation: confirmation
url: https://ist.ac.at/en/news/suppressing-the-spread-of-tumors/
scopus_import: '1'
status: public
title: The solute carrier MFSD1 decreases β1 integrin’s activation status and thus
tumor metastasis
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: 12
year: '2022'
...
---
_id: '10713'
abstract:
- lang: eng
text: Cells migrate through crowded microenvironments within tissues during normal
development, immune response, and cancer metastasis. Although migration through
pores and tracks in the extracellular matrix (ECM) has been well studied, little
is known about cellular traversal into confining cell-dense tissues. We find that
embryonic tissue invasion by Drosophila macrophages requires division of an epithelial
ectodermal cell at the site of entry. Dividing ectodermal cells disassemble ECM
attachment formed by integrin-mediated focal adhesions next to mesodermal cells,
allowing macrophages to move their nuclei ahead and invade between two immediately
adjacent tissues. Invasion efficiency depends on division frequency, but reduction
of adhesion strength allows macrophage entry independently of division. This work
demonstrates that tissue dynamics can regulate cellular infiltration.
acknowledged_ssus:
- _id: Bio
acknowledgement: 'We thank J. Friml, C. Guet, T. Hurd, M. Fendrych and members of
the laboratory for comments on the manuscript; the Bioimaging Facility of IST Austria
for excellent support and T. Lecuit, E. Hafen, R. Levayer and A. Martin for fly
strains. This work was supported by a grant from the Austrian Science Fund FWF:
Lise Meitner Fellowship M2379-B28 to M.A and D.S., and internal funding from IST
Austria to D.S. and EMBL to S.D.R.'
article_processing_charge: No
article_type: original
author:
- first_name: Maria
full_name: Akhmanova, Maria
id: 3425EC26-F248-11E8-B48F-1D18A9856A87
last_name: Akhmanova
orcid: 0000-0003-1522-3162
- first_name: Shamsi
full_name: Emtenani, Shamsi
id: 49D32318-F248-11E8-B48F-1D18A9856A87
last_name: Emtenani
orcid: 0000-0001-6981-6938
- first_name: Daniel
full_name: Krueger, Daniel
last_name: Krueger
- first_name: Attila
full_name: György, Attila
id: 3BCEDBE0-F248-11E8-B48F-1D18A9856A87
last_name: György
orcid: 0000-0002-1819-198X
- first_name: Mariana
full_name: Pereira Guarda, Mariana
id: 6de81d9d-e2f2-11eb-945a-af8bc2a60b26
last_name: Pereira Guarda
- first_name: Mikhail
full_name: Vlasov, Mikhail
last_name: Vlasov
- first_name: Fedor
full_name: Vlasov, Fedor
last_name: Vlasov
- first_name: Andrei
full_name: Akopian, Andrei
last_name: Akopian
- first_name: Aparna
full_name: Ratheesh, Aparna
id: 2F064CFE-F248-11E8-B48F-1D18A9856A87
last_name: Ratheesh
- first_name: Stefano
full_name: De Renzis, Stefano
last_name: De Renzis
- first_name: Daria E
full_name: Siekhaus, Daria E
id: 3D224B9E-F248-11E8-B48F-1D18A9856A87
last_name: Siekhaus
orcid: 0000-0001-8323-8353
citation:
ama: Akhmanova M, Emtenani S, Krueger D, et al. Cell division in tissues enables
macrophage infiltration. Science. 2022;376(6591):394-396. doi:10.1126/science.abj0425
apa: Akhmanova, M., Emtenani, S., Krueger, D., György, A., Pereira Guarda, M., Vlasov,
M., … Siekhaus, D. E. (2022). Cell division in tissues enables macrophage infiltration.
Science. American Association for the Advancement of Science. https://doi.org/10.1126/science.abj0425
chicago: Akhmanova, Maria, Shamsi Emtenani, Daniel Krueger, Attila György, Mariana
Pereira Guarda, Mikhail Vlasov, Fedor Vlasov, et al. “Cell Division in Tissues
Enables Macrophage Infiltration.” Science. American Association for the
Advancement of Science, 2022. https://doi.org/10.1126/science.abj0425.
ieee: M. Akhmanova et al., “Cell division in tissues enables macrophage infiltration,”
Science, vol. 376, no. 6591. American Association for the Advancement of
Science, pp. 394–396, 2022.
ista: Akhmanova M, Emtenani S, Krueger D, György A, Pereira Guarda M, Vlasov M,
Vlasov F, Akopian A, Ratheesh A, De Renzis S, Siekhaus DE. 2022. Cell division
in tissues enables macrophage infiltration. Science. 376(6591), 394–396.
mla: Akhmanova, Maria, et al. “Cell Division in Tissues Enables Macrophage Infiltration.”
Science, vol. 376, no. 6591, American Association for the Advancement of
Science, 2022, pp. 394–96, doi:10.1126/science.abj0425.
short: M. Akhmanova, S. Emtenani, D. Krueger, A. György, M. Pereira Guarda, M. Vlasov,
F. Vlasov, A. Akopian, A. Ratheesh, S. De Renzis, D.E. Siekhaus, Science 376 (2022)
394–396.
date_created: 2022-02-01T11:23:18Z
date_published: 2022-04-22T00:00:00Z
date_updated: 2023-08-02T14:06:15Z
day: '22'
department:
- _id: DaSi
doi: 10.1126/science.abj0425
external_id:
isi:
- '000788553700039'
pmid:
- '35446632'
intvolume: ' 376'
isi: 1
issue: '6591'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.1101/2021.04.19.438995
month: '04'
oa: 1
oa_version: Preprint
page: 394-396
pmid: 1
project:
- _id: 264CBBAC-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: M02379
name: Modeling epithelial tissue mechanics during cell invasion
publication: Science
publication_identifier:
issn:
- 0036-8075
publication_status: published
publisher: American Association for the Advancement of Science
quality_controlled: '1'
status: public
title: Cell division in tissues enables macrophage infiltration
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: 376
year: '2022'
...
---
_id: '10714'
abstract:
- lang: eng
text: Ribosomal defects perturb stem cell differentiation, causing diseases called
ribosomopathies. How ribosome levels control stem cell differentiation is not
fully known. Here, we discovered three RNA helicases are required for ribosome
biogenesis and for Drosophila oogenesis. Loss of these helicases, which we named
Aramis, Athos and Porthos, lead to aberrant stabilization of p53, cell cycle arrest
and stalled GSC differentiation. Unexpectedly, Aramis is required for efficient
translation of a cohort of mRNAs containing a 5’-Terminal-Oligo-Pyrimidine (TOP)-motif,
including mRNAs that encode ribosomal proteins and a conserved p53 inhibitor,
Novel Nucleolar protein 1 (Non1). The TOP-motif co-regulates the translation of
growth-related mRNAs in mammals. As in mammals, the La-related protein co-regulates
the translation of TOP-motif containing RNAs during Drosophila oogenesis. Thus,
a previously unappreciated TOP-motif in Drosophila responds to reduced ribosome
biogenesis to co-regulate the translation of ribosomal proteins and a p53 repressor,
thus coupling ribosome biogenesis to GSC differentiation.
acknowledgement: We are grateful to all members of the Rangan and Fuchs labs for their
discussion and comments on the manuscript. We also thanks Dr. Sammons, Dr. Marlow,
Life Science Editors, for their thoughts and comments the manuscript Additionally,
we thank the Bloomington Stock Center, the Vienna Drosophila Resource Center, the
BDGP Gene Disruption Project, and Flybase for fly stocks, reagents, and other resources.
P.R. is funded by the NIH/NIGMS (R01GM111779-06 and RO1GM135628-01), G.F. is funded
by NSF MCB-2047629 and NIH RO3 AI144839, D.E.S. was funded by Marie Curie CIG 334077/IRTIM
and the Austrian Science Fund (FWF) grant ASI_FWF01_P29638S, and A.B is funded by
NIH R01GM116889 and American Cancer Society RSG-17-197-01-RMC.
article_processing_charge: No
article_type: original
author:
- first_name: Elliot T.
full_name: Martin, Elliot T.
last_name: Martin
- first_name: Patrick
full_name: Blatt, Patrick
last_name: Blatt
- first_name: Elaine
full_name: Ngyuen, Elaine
last_name: Ngyuen
- first_name: Roni
full_name: Lahr, Roni
last_name: Lahr
- first_name: Sangeetha
full_name: Selvam, Sangeetha
last_name: Selvam
- first_name: Hyun Ah M.
full_name: Yoon, Hyun Ah M.
last_name: Yoon
- first_name: Tyler
full_name: Pocchiari, Tyler
last_name: Pocchiari
- first_name: Shamsi
full_name: Emtenani, Shamsi
id: 49D32318-F248-11E8-B48F-1D18A9856A87
last_name: Emtenani
orcid: 0000-0001-6981-6938
- first_name: Daria E
full_name: Siekhaus, Daria E
id: 3D224B9E-F248-11E8-B48F-1D18A9856A87
last_name: Siekhaus
orcid: 0000-0001-8323-8353
- first_name: Andrea
full_name: Berman, Andrea
last_name: Berman
- first_name: Gabriele
full_name: Fuchs, Gabriele
last_name: Fuchs
- first_name: Prashanth
full_name: Rangan, Prashanth
last_name: Rangan
citation:
ama: Martin ET, Blatt P, Ngyuen E, et al. A translation control module coordinates
germline stem cell differentiation with ribosome biogenesis during Drosophila
oogenesis. Developmental Cell. 2022;57(7):883-900.e10. doi:10.1016/j.devcel.2022.03.005
apa: Martin, E. T., Blatt, P., Ngyuen, E., Lahr, R., Selvam, S., Yoon, H. A. M.,
… Rangan, P. (2022). A translation control module coordinates germline stem cell
differentiation with ribosome biogenesis during Drosophila oogenesis. Developmental
Cell. Elsevier. https://doi.org/10.1016/j.devcel.2022.03.005
chicago: Martin, Elliot T., Patrick Blatt, Elaine Ngyuen, Roni Lahr, Sangeetha Selvam,
Hyun Ah M. Yoon, Tyler Pocchiari, et al. “A Translation Control Module Coordinates
Germline Stem Cell Differentiation with Ribosome Biogenesis during Drosophila
Oogenesis.” Developmental Cell. Elsevier, 2022. https://doi.org/10.1016/j.devcel.2022.03.005.
ieee: E. T. Martin et al., “A translation control module coordinates germline
stem cell differentiation with ribosome biogenesis during Drosophila oogenesis,”
Developmental Cell, vol. 57, no. 7. Elsevier, p. 883–900.e10, 2022.
ista: Martin ET, Blatt P, Ngyuen E, Lahr R, Selvam S, Yoon HAM, Pocchiari T, Emtenani
S, Siekhaus DE, Berman A, Fuchs G, Rangan P. 2022. A translation control module
coordinates germline stem cell differentiation with ribosome biogenesis during
Drosophila oogenesis. Developmental Cell. 57(7), 883–900.e10.
mla: Martin, Elliot T., et al. “A Translation Control Module Coordinates Germline
Stem Cell Differentiation with Ribosome Biogenesis during Drosophila Oogenesis.”
Developmental Cell, vol. 57, no. 7, Elsevier, 2022, p. 883–900.e10, doi:10.1016/j.devcel.2022.03.005.
short: E.T. Martin, P. Blatt, E. Ngyuen, R. Lahr, S. Selvam, H.A.M. Yoon, T. Pocchiari,
S. Emtenani, D.E. Siekhaus, A. Berman, G. Fuchs, P. Rangan, Developmental Cell
57 (2022) 883–900.e10.
date_created: 2022-02-01T13:15:05Z
date_published: 2022-04-11T00:00:00Z
date_updated: 2023-08-02T14:07:13Z
day: '11'
department:
- _id: DaSi
doi: 10.1016/j.devcel.2022.03.005
ec_funded: 1
external_id:
isi:
- '000789021800005'
intvolume: ' 57'
isi: 1
issue: '7'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.1101/2021.04.04.438367
month: '04'
oa: 1
oa_version: Preprint
page: 883-900.e10
project:
- _id: 2536F660-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '334077'
name: Investigating the role of transporters in invasive migration through junctions
- _id: 253B6E48-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: P29638
name: Drosophila TNFa´s Funktion in Immunzellen
publication: Developmental Cell
publication_identifier:
eissn:
- 1878-1551
issn:
- 1534-5807
publication_status: published
publisher: Elsevier
quality_controlled: '1'
scopus_import: '1'
status: public
title: A translation control module coordinates germline stem cell differentiation
with ribosome biogenesis during Drosophila oogenesis
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: 57
year: '2022'
...
---
_id: '10717'
abstract:
- lang: eng
text: Much of what we know about the role of auxin in plant development derives
from exogenous manipulations of auxin distribution and signaling, using inhibitors,
auxins and auxin analogs. In this context, synthetic auxin analogs, such as 1-Naphtalene
Acetic Acid (1-NAA), are often favored over the endogenous auxin indole-3-acetic
acid (IAA), in part due to their higher stability. While such auxin analogs have
proven to be instrumental to reveal the various faces of auxin, they display in
some cases distinct bioactivities compared to IAA. Here, we focused on the effect
of auxin analogs on the accumulation of PIN proteins in Brefeldin A-sensitive
endosomal aggregations (BFA bodies), and the correlation with the ability to elicit
Ca 2+ responses. For a set of commonly used auxin analogs, we evaluated if auxin-analog
induced Ca 2+ signaling inhibits PIN accumulation. Not all auxin analogs elicited
a Ca 2+ response, and their differential ability to elicit Ca 2+ responses correlated
partially with their ability to inhibit BFA-body formation. However, in tir1/afb
and cngc14, 1-NAA-induced Ca 2+ signaling was strongly impaired, yet 1-NAA still
could inhibit PIN accumulation in BFA bodies. This demonstrates that TIR1/AFB-CNGC14-dependent
Ca 2+ signaling does not inhibit BFA body formation in Arabidopsis roots.
acknowledgement: "We thank Joerg Kudla (WWU Munster, Germany), Petra Dietrich (F.A.
University of Erlangen-Nurnberg, Germany) for sharing published materials, and NASC
for providing seeds. We thank Veronique Storme for help with the statistical analyses.
Part of the imaging analysis was carried out at NOLIMITS, an advanced imaging facility
established by the University of Milan.\r\nThis work was supported by grants of
the China Scholarship Council (CSC) to RW and JC; Fonds Wetenschappelijk Onderzoek
(FWO) to TB and (G002220N) SV; the special research fund of Ghent University to
EH; the Deutsche Forschungsgemeinschaft (DFG) through Grants within FOR964 (MK and
KS); Piano di Sviluppo di Ateneo 2019 (University of Milan) to AC; the European
Research Council (ERC) T-Rex project 682436 to DVD; the ERC ETAP project 742985
to JF, and by a PhD fellowship from the University of Milan to MG."
article_number: erac019
article_processing_charge: No
article_type: original
author:
- first_name: R
full_name: Wang, R
last_name: Wang
- first_name: E
full_name: Himschoot, E
last_name: Himschoot
- first_name: M
full_name: Grenzi, M
last_name: Grenzi
- first_name: J
full_name: Chen, J
last_name: Chen
- first_name: A
full_name: Safi, A
last_name: Safi
- first_name: M
full_name: Krebs, M
last_name: Krebs
- first_name: K
full_name: Schumacher, K
last_name: Schumacher
- first_name: MK
full_name: Nowack, MK
last_name: Nowack
- first_name: W
full_name: Moeder, W
last_name: Moeder
- first_name: K
full_name: Yoshioka, K
last_name: Yoshioka
- first_name: D
full_name: Van Damme, D
last_name: Van Damme
- first_name: I
full_name: De Smet, I
last_name: De Smet
- first_name: D
full_name: Geelen, D
last_name: Geelen
- first_name: T
full_name: Beeckman, T
last_name: Beeckman
- first_name: Jiří
full_name: Friml, Jiří
id: 4159519E-F248-11E8-B48F-1D18A9856A87
last_name: Friml
orcid: 0000-0002-8302-7596
- first_name: A
full_name: Costa, A
last_name: Costa
- first_name: S
full_name: Vanneste, S
last_name: Vanneste
citation:
ama: Wang R, Himschoot E, Grenzi M, et al. Auxin analog-induced Ca2+ signaling is
independent of inhibition of endosomal aggregation in Arabidopsis roots. Journal
of Experimental Botany. 2022;73(8). doi:10.1093/jxb/erac019
apa: Wang, R., Himschoot, E., Grenzi, M., Chen, J., Safi, A., Krebs, M., … Vanneste,
S. (2022). Auxin analog-induced Ca2+ signaling is independent of inhibition of
endosomal aggregation in Arabidopsis roots. Journal of Experimental Botany.
Oxford Academic. https://doi.org/10.1093/jxb/erac019
chicago: Wang, R, E Himschoot, M Grenzi, J Chen, A Safi, M Krebs, K Schumacher,
et al. “Auxin Analog-Induced Ca2+ Signaling Is Independent of Inhibition of Endosomal
Aggregation in Arabidopsis Roots.” Journal of Experimental Botany. Oxford
Academic, 2022. https://doi.org/10.1093/jxb/erac019.
ieee: R. Wang et al., “Auxin analog-induced Ca2+ signaling is independent
of inhibition of endosomal aggregation in Arabidopsis roots,” Journal of Experimental
Botany, vol. 73, no. 8. Oxford Academic, 2022.
ista: Wang R, Himschoot E, Grenzi M, Chen J, Safi A, Krebs M, Schumacher K, Nowack
M, Moeder W, Yoshioka K, Van Damme D, De Smet I, Geelen D, Beeckman T, Friml J,
Costa A, Vanneste S. 2022. Auxin analog-induced Ca2+ signaling is independent
of inhibition of endosomal aggregation in Arabidopsis roots. Journal of Experimental
Botany. 73(8), erac019.
mla: Wang, R., et al. “Auxin Analog-Induced Ca2+ Signaling Is Independent of Inhibition
of Endosomal Aggregation in Arabidopsis Roots.” Journal of Experimental Botany,
vol. 73, no. 8, erac019, Oxford Academic, 2022, doi:10.1093/jxb/erac019.
short: R. Wang, E. Himschoot, M. Grenzi, J. Chen, A. Safi, M. Krebs, K. Schumacher,
M. Nowack, W. Moeder, K. Yoshioka, D. Van Damme, I. De Smet, D. Geelen, T. Beeckman,
J. Friml, A. Costa, S. Vanneste, Journal of Experimental Botany 73 (2022).
date_created: 2022-02-03T09:19:01Z
date_published: 2022-04-18T00:00:00Z
date_updated: 2023-08-02T14:07:58Z
day: '18'
department:
- _id: JiFr
doi: 10.1093/jxb/erac019
ec_funded: 1
external_id:
isi:
- '000764220900001'
pmid:
- '35085386'
intvolume: ' 73'
isi: 1
issue: '8'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://biblio.ugent.be/publication/8738721
month: '04'
oa: 1
oa_version: Submitted Version
pmid: 1
project:
- _id: 261099A6-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '742985'
name: Tracing Evolution of Auxin Transport and Polarity in Plants
publication: Journal of Experimental Botany
publication_identifier:
eissn:
- 1460-2431
issn:
- 0022-0957
publication_status: published
publisher: Oxford Academic
quality_controlled: '1'
scopus_import: '1'
status: public
title: Auxin analog-induced Ca2+ signaling is independent of inhibition of endosomal
aggregation in Arabidopsis roots
type: journal_article
user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
volume: 73
year: '2022'
...
---
_id: '10719'
abstract:
- lang: eng
text: Auxin, one of the first identified and most widely studied phytohormones,
has been and will remain a hot topic in plant biology. After more than a century
of passionate exploration, the mysteries of its synthesis, transport, signaling,
and metabolism have largely been unlocked. Due to the rapid development of new
technologies, new methods, and new genetic materials, the study of auxin has entered
the fast lane over the past 30 years. Here, we highlight advances in understanding
auxin signaling, including auxin perception, rapid auxin responses, TRANSPORT
INHIBITOR RESPONSE 1 and AUXIN SIGNALING F-boxes (TIR1/AFBs)-mediated transcriptional
and non-transcriptional branches, and the epigenetic regulation of auxin signaling.
We also focus on feedback inhibition mechanisms that prevent the over-amplification
of auxin signals. In addition, we cover the TRANSMEMBRANE KINASEs (TMKs)-mediated
non-canonical signaling, which converges with TIR1/AFBs-mediated transcriptional
regulation to coordinate plant growth and development. The identification of additional
auxin signaling components and their regulation will continue to open new avenues
of research in this field, leading to an increasingly deeper, more comprehensive
understanding of how auxin signals are interpreted at the cellular level to regulate
plant growth and development.
acknowledgement: "This research was financially supported by the National Natural
Science Foundation of China and the Israel Science Foundation (NSFC-ISF; 32061143005),
National Natural Science Foundation of China (32000225), Natural Science Foundation
of Shandong Province (ZR2020QC036), and China Postdoctoral Science Foundation (2020M682165).\r\n"
article_processing_charge: No
article_type: review
author:
- first_name: Z
full_name: Yu, Z
last_name: Yu
- first_name: F
full_name: Zhang, F
last_name: Zhang
- first_name: Jiří
full_name: Friml, Jiří
id: 4159519E-F248-11E8-B48F-1D18A9856A87
last_name: Friml
orcid: 0000-0002-8302-7596
- first_name: Z
full_name: Ding, Z
last_name: Ding
citation:
ama: 'Yu Z, Zhang F, Friml J, Ding Z. Auxin signaling: Research advances over the
past 30 years. Journal of Integrative Plant Biology. 2022;64(2):371-392.
doi:10.1111/jipb.13225'
apa: 'Yu, Z., Zhang, F., Friml, J., & Ding, Z. (2022). Auxin signaling: Research
advances over the past 30 years. Journal of Integrative Plant Biology.
Wiley. https://doi.org/10.1111/jipb.13225'
chicago: 'Yu, Z, F Zhang, Jiří Friml, and Z Ding. “Auxin Signaling: Research Advances
over the Past 30 Years.” Journal of Integrative Plant Biology. Wiley, 2022.
https://doi.org/10.1111/jipb.13225.'
ieee: 'Z. Yu, F. Zhang, J. Friml, and Z. Ding, “Auxin signaling: Research advances
over the past 30 years,” Journal of Integrative Plant Biology, vol. 64,
no. 2. Wiley, pp. 371–392, 2022.'
ista: 'Yu Z, Zhang F, Friml J, Ding Z. 2022. Auxin signaling: Research advances
over the past 30 years. Journal of Integrative Plant Biology. 64(2), 371–392.'
mla: 'Yu, Z., et al. “Auxin Signaling: Research Advances over the Past 30 Years.”
Journal of Integrative Plant Biology, vol. 64, no. 2, Wiley, 2022, pp.
371–92, doi:10.1111/jipb.13225.'
short: Z. Yu, F. Zhang, J. Friml, Z. Ding, Journal of Integrative Plant Biology
64 (2022) 371–392.
date_created: 2022-02-03T09:52:59Z
date_published: 2022-02-01T00:00:00Z
date_updated: 2023-08-02T14:08:30Z
day: '01'
department:
- _id: JiFr
doi: 10.1111/jipb.13225
external_id:
isi:
- '000761281200011'
pmid:
- '35018726'
intvolume: ' 64'
isi: 1
issue: '2'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.1111/jipb.13225
month: '02'
oa: 1
oa_version: Published Version
page: 371-392
pmid: 1
publication: Journal of Integrative Plant Biology
publication_identifier:
eissn:
- 1744-7909
issn:
- 1672-9072
publication_status: published
publisher: Wiley
quality_controlled: '1'
scopus_import: '1'
status: public
title: 'Auxin signaling: Research advances over the past 30 years'
type: journal_article
user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
volume: 64
year: '2022'
...
---
_id: '10727'
abstract:
- lang: eng
text: "Social insects are a common model to study disease dynamics in social animals.
Even though pathogens should thrive in social insect colonies as the hosts engage
in frequent social interactions, are closely related and live in a pathogen-rich
environment, disease outbreaks are rare. This is because social insects have evolved
mechanisms to keep pathogens at bay – and fight disease as a collective. Social
insect colonies are often viewed as “superorganisms” with division of labor between
reproductive “germ-like” queens and males and “somatic” workers, which together
form an interdependent reproductive unit that parallels a multicellular body.
Superorganisms possess a “social immune system” that comprises of collective disease
defenses performed by the workers - summarized as “social immunity”. In social
groups immunization (reduced susceptibility to a parasite upon secondary exposure
to the same parasite) can e.g. be triggered by social interactions (“social immunization”).
Social immunization can be caused by (i) asymptomatic low-level infections that
are acquired during caregiving to a contagious individual that can give an immune
boost, which can induce protection upon later encounter with the same pathogen
(active immunization) or (ii) by transfer of immune effectors between individuals
(passive immunization).\r\nIn the second chapter, I built up on a study that I
co-authored that found that low-level infections can not only be protective, but
also be costly and make the host more susceptible to detrimental superinfections
after contact to a very dissimilar pathogen. I here now tested different degrees
of phylogenetically-distant fungal strains of M. brunneum and M. robertsii in
L. neglectus and can describe the occurrence of cross-protection of social immunization
if the first and second pathogen are from the same level. Interestingly, low-level
infections only provided protection when the first strain was less virulent than
the second strain and elicited higher immune gene expression.\r\nIn the third
and fourth chapters, I expanded on the role of social immunity in sexual selection,
a so far unstudied field. I used the fungus Metarhizium robertsii and the ant
Cardiocondyla obscurior as a model, as in this species mating occurs in the presence
of workers and can be studied under laboratory conditions. Before males mate with
virgin queens in the nest they engage in fierce combat over the access to their
mating partners.\r\nFirst, I focused on male-male competition in the third chapter
and found that fighting with a contagious male is costly as it can lead to contamination
of the rival, but that workers can decrease the risk of disease contraction by
performing sanitary care.\r\nIn the fourth chapter, I studied the effect of fungal
infection on survival and mating success of sexuals (freshly emerged queens and
males) and found that worker-performed sanitary care can buffer the negative effect
that a pathogenic contagion would have on sexuals by spore removal from the exposed
individuals. When social immunity was prevented and queens could contract spores
from their mating partner, very low dosages led to negative consequences: their
lifespan was reduced and they produced fewer offspring with poor immunocompetence
compared to healthy queens. Interestingly, cohabitation with a late-stage infected
male where no spore transfer was possible had a positive effect on offspring immunity
– male offspring of mothers that apparently perceived an infected partner in their
vicinity reacted more sensitively to fungal challenge than male offspring without
paternal pathogen history."
acknowledged_ssus:
- _id: LifeSc
alternative_title:
- ISTA Thesis
article_processing_charge: No
author:
- first_name: Sina
full_name: Metzler, Sina
id: 48204546-F248-11E8-B48F-1D18A9856A87
last_name: Metzler
orcid: 0000-0002-9547-2494
citation:
ama: Metzler S. Pathogen-mediated sexual selection and immunization in ant colonies.
2022. doi:10.15479/AT:ISTA:10727
apa: Metzler, S. (2022). Pathogen-mediated sexual selection and immunization
in ant colonies. Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:10727
chicago: Metzler, Sina. “Pathogen-Mediated Sexual Selection and Immunization in
Ant Colonies.” Institute of Science and Technology Austria, 2022. https://doi.org/10.15479/AT:ISTA:10727.
ieee: S. Metzler, “Pathogen-mediated sexual selection and immunization in ant colonies,”
Institute of Science and Technology Austria, 2022.
ista: Metzler S. 2022. Pathogen-mediated sexual selection and immunization in ant
colonies. Institute of Science and Technology Austria.
mla: Metzler, Sina. Pathogen-Mediated Sexual Selection and Immunization in Ant
Colonies. Institute of Science and Technology Austria, 2022, doi:10.15479/AT:ISTA:10727.
short: S. Metzler, Pathogen-Mediated Sexual Selection and Immunization in Ant Colonies,
Institute of Science and Technology Austria, 2022.
date_created: 2022-02-04T15:45:12Z
date_published: 2022-02-07T00:00:00Z
date_updated: 2023-09-07T13:43:23Z
day: '07'
ddc:
- '570'
degree_awarded: PhD
department:
- _id: GradSch
- _id: SyCr
doi: 10.15479/AT:ISTA:10727
ec_funded: 1
file:
- access_level: closed
checksum: 47ba18bb270dd6cc266e0a3f7c69d0e4
content_type: application/vnd.openxmlformats-officedocument.wordprocessingml.document
creator: smetzler
date_created: 2022-02-04T15:36:12Z
date_updated: 2023-02-03T23:30:03Z
embargo_to: open_access
file_id: '10728'
file_name: Thesis_Sina_Metzler.docx
file_size: 6757886
relation: source_file
- access_level: open_access
checksum: f3ec07d5d6b20ae6e46bfeedebce9027
content_type: application/pdf
creator: smetzler
date_created: 2022-02-04T15:36:43Z
date_updated: 2023-02-03T23:30:03Z
embargo: 2023-02-02
file_id: '10730'
file_name: Thesis_Sina_Metzler_A2.pdf
file_size: 6314921
relation: main_file
- access_level: open_access
checksum: dedd14b7be7a75d63018dbfc68dd8113
content_type: application/pdf
creator: smetzler
date_created: 2022-02-07T10:35:02Z
date_updated: 2023-02-04T23:30:03Z
embargo: 2023-02-02
file_id: '10742'
file_name: Thesis_Sina_Metzler_print.pdf
file_size: 6882557
relation: main_file
file_date_updated: 2023-02-04T23:30:03Z
has_accepted_license: '1'
language:
- iso: eng
month: '02'
oa: 1
oa_version: Published Version
project:
- _id: 2649B4DE-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '771402'
name: Epidemics in ant societies on a chip
publication_identifier:
issn:
- 2663-337X
publication_status: published
publisher: Institute of Science and Technology Austria
status: public
supervisor:
- first_name: Sylvia
full_name: Cremer, Sylvia
id: 2F64EC8C-F248-11E8-B48F-1D18A9856A87
last_name: Cremer
orcid: 0000-0002-2193-3868
title: Pathogen-mediated sexual selection and immunization in ant colonies
type: dissertation
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
year: '2022'
...
---
_id: '10731'
abstract:
- lang: eng
text: Motivated by COVID-19, we develop and analyze a simple stochastic model for
the spread of disease in human population. We track how the number of infected
and critically ill people develops over time in order to estimate the demand that
is imposed on the hospital system. To keep this demand under control, we consider
a class of simple policies for slowing down and reopening society and we compare
their efficiency in mitigating the spread of the virus from several different
points of view. We find that in order to avoid overwhelming of the hospital system,
a policy must impose a harsh lockdown or it must react swiftly (or both). While
reacting swiftly is universally beneficial, being harsh pays off only when the
country is patient about reopening and when the neighboring countries coordinate
their mitigation efforts. Our work highlights the importance of acting decisively
when closing down and the importance of patience and coordination between neighboring
countries when reopening.
acknowledgement: 'K.C. acknowledges support from ERC Consolidator Grant No. (863818:
ForM-SMart). A.P. acknowledges support from FWF Grant No. J-4220. M.A.N. acknowledges
support from Office of Naval Research grant N00014-16-1-2914 and from the John Templeton
Foundation.'
article_number: '1526'
article_processing_charge: No
article_type: original
arxiv: 1
author:
- first_name: Jakub
full_name: Svoboda, Jakub
id: 130759D2-D7DD-11E9-87D2-DE0DE6697425
last_name: Svoboda
orcid: 0000-0002-1419-3267
- first_name: Josef
full_name: Tkadlec, Josef
last_name: Tkadlec
- first_name: Andreas
full_name: Pavlogiannis, Andreas
id: 49704004-F248-11E8-B48F-1D18A9856A87
last_name: Pavlogiannis
orcid: 0000-0002-8943-0722
- first_name: Krishnendu
full_name: Chatterjee, Krishnendu
id: 2E5DCA20-F248-11E8-B48F-1D18A9856A87
last_name: Chatterjee
orcid: 0000-0002-4561-241X
- first_name: Martin A.
full_name: Nowak, Martin A.
last_name: Nowak
citation:
ama: Svoboda J, Tkadlec J, Pavlogiannis A, Chatterjee K, Nowak MA. Infection dynamics
of COVID-19 virus under lockdown and reopening. Scientific Reports. 2022;12(1).
doi:10.1038/s41598-022-05333-5
apa: Svoboda, J., Tkadlec, J., Pavlogiannis, A., Chatterjee, K., & Nowak, M.
A. (2022). Infection dynamics of COVID-19 virus under lockdown and reopening.
Scientific Reports. Springer Nature. https://doi.org/10.1038/s41598-022-05333-5
chicago: Svoboda, Jakub, Josef Tkadlec, Andreas Pavlogiannis, Krishnendu Chatterjee,
and Martin A. Nowak. “Infection Dynamics of COVID-19 Virus under Lockdown and
Reopening.” Scientific Reports. Springer Nature, 2022. https://doi.org/10.1038/s41598-022-05333-5.
ieee: J. Svoboda, J. Tkadlec, A. Pavlogiannis, K. Chatterjee, and M. A. Nowak, “Infection
dynamics of COVID-19 virus under lockdown and reopening,” Scientific Reports,
vol. 12, no. 1. Springer Nature, 2022.
ista: Svoboda J, Tkadlec J, Pavlogiannis A, Chatterjee K, Nowak MA. 2022. Infection
dynamics of COVID-19 virus under lockdown and reopening. Scientific Reports. 12(1),
1526.
mla: Svoboda, Jakub, et al. “Infection Dynamics of COVID-19 Virus under Lockdown
and Reopening.” Scientific Reports, vol. 12, no. 1, 1526, Springer Nature,
2022, doi:10.1038/s41598-022-05333-5.
short: J. Svoboda, J. Tkadlec, A. Pavlogiannis, K. Chatterjee, M.A. Nowak, Scientific
Reports 12 (2022).
date_created: 2022-02-06T23:01:30Z
date_published: 2022-01-27T00:00:00Z
date_updated: 2025-07-14T09:10:12Z
day: '27'
ddc:
- '570'
department:
- _id: KrCh
doi: 10.1038/s41598-022-05333-5
ec_funded: 1
external_id:
arxiv:
- '2012.15155'
isi:
- '000749198000039'
file:
- access_level: open_access
checksum: 247afd30c173390940f099ead35a28ed
content_type: application/pdf
creator: alisjak
date_created: 2022-02-07T14:57:59Z
date_updated: 2022-02-07T14:57:59Z
file_id: '10744'
file_name: 2022_ScientificReports_Svoboda.pdf
file_size: 2971922
relation: main_file
success: 1
file_date_updated: 2022-02-07T14:57:59Z
has_accepted_license: '1'
intvolume: ' 12'
isi: 1
issue: '1'
language:
- iso: eng
month: '01'
oa: 1
oa_version: Published Version
project:
- _id: 0599E47C-7A3F-11EA-A408-12923DDC885E
call_identifier: H2020
grant_number: '863818'
name: 'Formal Methods for Stochastic Models: Algorithms and Applications'
publication: Scientific Reports
publication_identifier:
eissn:
- 2045-2322
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
scopus_import: '1'
status: public
title: Infection dynamics of COVID-19 virus under lockdown and reopening
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: 12
year: '2022'
...
---
_id: '10732'
abstract:
- lang: eng
text: We compute the deterministic approximation of products of Sobolev functions
of large Wigner matrices W and provide an optimal error bound on their fluctuation
with very high probability. This generalizes Voiculescu's seminal theorem from
polynomials to general Sobolev functions, as well as from tracial quantities to
individual matrix elements. Applying the result to eitW for large t, we obtain
a precise decay rate for the overlaps of several deterministic matrices with temporally
well separated Heisenberg time evolutions; thus we demonstrate the thermalisation
effect of the unitary group generated by Wigner matrices.
acknowledgement: We compute the deterministic approximation of products of Sobolev
functions of large Wigner matrices W and provide an optimal error bound on their
fluctuation with very high probability. This generalizes Voiculescu's seminal theorem
from polynomials to general Sobolev functions, as well as from tracial quantities
to individual matrix elements. Applying the result to for large t, we obtain a
precise decay rate for the overlaps of several deterministic matrices with temporally
well separated Heisenberg time evolutions; thus we demonstrate the thermalisation
effect of the unitary group generated by Wigner matrices.
article_number: '109394'
article_processing_charge: Yes (via OA deal)
article_type: original
arxiv: 1
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. Thermalisation for Wigner matrices. Journal
of Functional Analysis. 2022;282(8). doi:10.1016/j.jfa.2022.109394
apa: Cipolloni, G., Erdös, L., & Schröder, D. J. (2022). Thermalisation for
Wigner matrices. Journal of Functional Analysis. Elsevier. https://doi.org/10.1016/j.jfa.2022.109394
chicago: Cipolloni, Giorgio, László Erdös, and Dominik J Schröder. “Thermalisation
for Wigner Matrices.” Journal of Functional Analysis. Elsevier, 2022. https://doi.org/10.1016/j.jfa.2022.109394.
ieee: G. Cipolloni, L. Erdös, and D. J. Schröder, “Thermalisation for Wigner matrices,”
Journal of Functional Analysis, vol. 282, no. 8. Elsevier, 2022.
ista: Cipolloni G, Erdös L, Schröder DJ. 2022. Thermalisation for Wigner matrices.
Journal of Functional Analysis. 282(8), 109394.
mla: Cipolloni, Giorgio, et al. “Thermalisation for Wigner Matrices.” Journal
of Functional Analysis, vol. 282, no. 8, 109394, Elsevier, 2022, doi:10.1016/j.jfa.2022.109394.
short: G. Cipolloni, L. Erdös, D.J. Schröder, Journal of Functional Analysis 282
(2022).
date_created: 2022-02-06T23:01:30Z
date_published: 2022-04-15T00:00:00Z
date_updated: 2023-08-02T14:12:35Z
day: '15'
ddc:
- '500'
department:
- _id: LaEr
doi: 10.1016/j.jfa.2022.109394
external_id:
arxiv:
- '2102.09975'
isi:
- '000781239100004'
file:
- access_level: open_access
checksum: b75fdad606ab507dc61109e0907d86c0
content_type: application/pdf
creator: dernst
date_created: 2022-07-29T07:22:08Z
date_updated: 2022-07-29T07:22:08Z
file_id: '11690'
file_name: 2022_JourFunctionalAnalysis_Cipolloni.pdf
file_size: 652573
relation: main_file
success: 1
file_date_updated: 2022-07-29T07:22:08Z
has_accepted_license: '1'
intvolume: ' 282'
isi: 1
issue: '8'
language:
- iso: eng
month: '04'
oa: 1
oa_version: Published Version
publication: Journal of Functional Analysis
publication_identifier:
eissn:
- 1096-0783
issn:
- 0022-1236
publication_status: published
publisher: Elsevier
quality_controlled: '1'
scopus_import: '1'
status: public
title: Thermalisation 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: 282
year: '2022'
...
---
_id: '10733'
abstract:
- lang: eng
text: 'When a cylindrical object penetrates granular matter near a vertical boundary,
it experiences two effects: its center of mass moves horizontally away from the
wall, and it rotates around its symmetry axis. Here we show experimentally that,
if two identical intruders instead of one are released side-by-side near the wall,
both effects are also detected. However, unexpected phenomena appear due to a
cooperative dynamics between the intruders. The net horizontal distance traveled
by the common center of mass of the twin intruders is much larger than that traveled
by one intruder released at the same initial distance from the wall, and the rotation
is also larger. The experimental results are well described by the Discrete Element
Method (DEM), which reveals that, as the number of intruders horizontally released
side-by-side increases, the total energy dissipation per intruder decreases. Finally,
DEM simulations demonstrate that the horizontal repulsion is substantially enhanced
if groups of intruders are released forming a column near the wall.'
acknowledgement: 'We acknowledge the University of Havana’s institutional project
“Granular media: creating tools for the prevention of catastrophes”. The Institute
“Pedro Kourí” is thanked for allowing us using their computing cluster. E. Altshuler
found inspiration in the late M. Álvarez-Ponte.'
article_number: '39'
article_processing_charge: No
article_type: original
arxiv: 1
author:
- first_name: M.
full_name: Espinosa, M.
last_name: Espinosa
- first_name: Vicente L
full_name: Diaz Melian, Vicente L
id: b6798902-eea0-11ea-9cbc-a8e14286c631
last_name: Diaz Melian
- first_name: A.
full_name: Serrano-Muñoz, A.
last_name: Serrano-Muñoz
- first_name: E.
full_name: Altshuler, E.
last_name: Altshuler
citation:
ama: Espinosa M, Diaz Melian VL, Serrano-Muñoz A, Altshuler E. Intruders cooperatively
interact with a wall into granular matter. Granular Matter. 2022;24(1).
doi:10.1007/s10035-021-01200-8
apa: Espinosa, M., Diaz Melian, V. L., Serrano-Muñoz, A., & Altshuler, E. (2022).
Intruders cooperatively interact with a wall into granular matter. Granular
Matter. Springer Nature. https://doi.org/10.1007/s10035-021-01200-8
chicago: Espinosa, M., Vicente L Diaz Melian, A. Serrano-Muñoz, and E. Altshuler.
“Intruders Cooperatively Interact with a Wall into Granular Matter.” Granular
Matter. Springer Nature, 2022. https://doi.org/10.1007/s10035-021-01200-8.
ieee: M. Espinosa, V. L. Diaz Melian, A. Serrano-Muñoz, and E. Altshuler, “Intruders
cooperatively interact with a wall into granular matter,” Granular Matter,
vol. 24, no. 1. Springer Nature, 2022.
ista: Espinosa M, Diaz Melian VL, Serrano-Muñoz A, Altshuler E. 2022. Intruders
cooperatively interact with a wall into granular matter. Granular Matter. 24(1),
39.
mla: Espinosa, M., et al. “Intruders Cooperatively Interact with a Wall into Granular
Matter.” Granular Matter, vol. 24, no. 1, 39, Springer Nature, 2022, doi:10.1007/s10035-021-01200-8.
short: M. Espinosa, V.L. Diaz Melian, A. Serrano-Muñoz, E. Altshuler, Granular Matter
24 (2022).
date_created: 2022-02-06T23:01:30Z
date_published: 2022-01-24T00:00:00Z
date_updated: 2023-08-02T14:10:13Z
day: '24'
department:
- _id: ScWa
doi: 10.1007/s10035-021-01200-8
external_id:
arxiv:
- '2110.15311'
isi:
- '000746623000001'
intvolume: ' 24'
isi: 1
issue: '1'
keyword:
- granular matter
- boundary effects
- intruder penetration
- sedimentation
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/2110.15311
month: '01'
oa: 1
oa_version: Preprint
publication: Granular Matter
publication_identifier:
eissn:
- 1434-7636
issn:
- 1434-5021
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
scopus_import: '1'
status: public
title: Intruders cooperatively interact with a wall into granular matter
type: journal_article
user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
volume: 24
year: '2022'
...
---
_id: '10735'
abstract:
- lang: eng
text: Magnetic anisotropy in strontium iridate (Sr2IrO4) is essential because of
its strong spin–orbit coupling and crystal field effect. In this paper, we present
a detailed mapping of the out-of-plane (OOP) magnetic anisotropy in Sr2IrO4 for
different sample orientations using torque magnetometry measurements in the low-magnetic-field
region before the isospins are completely ordered. Dominant in-plane anisotropy
was identified at low fields, confirming the b axis as an easy magnetization axis.
Based on the fitting analysis of the strong uniaxial magnetic anisotropy, we observed
that the main anisotropic effect arises from a spin–orbit-coupled magnetic exchange
interaction affecting the OOP interaction. The effect of interlayer exchange interaction
results in additional anisotropic terms owing to the tilting of the isospins.
The results are relevant for understanding OOP magnetic anisotropy and provide
a new way to analyze the effects of spin–orbit-coupling and interlayer magnetic
exchange interactions. This study provides insight into the understanding of bulk
magnetic, magnetotransport, and spintronic behavior on Sr2IrO4 for future studies.
acknowledgement: 'YJ was supported by the National Research Foundation of Korea (NRF)
(Grant Nos. NRF-2018K2A9A1A06069211 and NRF-2019R1A2C1089017). The work at Yonsei
was supported by the NRF (Grant Nos. NRF-2017R1A5A-1014862 (SRC program: vdWMRC
center), NRF-2019R1A2C2002601, and NRF-2021R1A2C1006375). WK acknowledges the support
by the NRF (Grant Nos. 2018R1D1A1B07050087, 2018R1A6A1A03025340).'
article_number: '135802'
article_processing_charge: No
article_type: original
author:
- first_name: Muhammad
full_name: Nauman, Muhammad
id: 32c21954-2022-11eb-9d5f-af9f93c24e71
last_name: Nauman
orcid: 0000-0002-2111-4846
- first_name: Tayyaba
full_name: Hussain, Tayyaba
last_name: Hussain
- first_name: Joonyoung
full_name: Choi, Joonyoung
last_name: Choi
- first_name: Nara
full_name: Lee, Nara
last_name: Lee
- first_name: Young Jai
full_name: Choi, Young Jai
last_name: Choi
- first_name: Woun
full_name: Kang, Woun
last_name: Kang
- first_name: Younjung
full_name: Jo, Younjung
last_name: Jo
citation:
ama: 'Nauman M, Hussain T, Choi J, et al. Low-field magnetic anisotropy of Sr2IrO4.
Journal of physics: Condensed matter. 2022;34(13). doi:10.1088/1361-648X/ac484d'
apa: 'Nauman, M., Hussain, T., Choi, J., Lee, N., Choi, Y. J., Kang, W., & Jo,
Y. (2022). Low-field magnetic anisotropy of Sr2IrO4. Journal of Physics: Condensed
Matter. IOP Publishing. https://doi.org/10.1088/1361-648X/ac484d'
chicago: 'Nauman, Muhammad, Tayyaba Hussain, Joonyoung Choi, Nara Lee, Young Jai
Choi, Woun Kang, and Younjung Jo. “Low-Field Magnetic Anisotropy of Sr2IrO4.”
Journal of Physics: Condensed Matter. IOP Publishing, 2022. https://doi.org/10.1088/1361-648X/ac484d.'
ieee: 'M. Nauman et al., “Low-field magnetic anisotropy of Sr2IrO4,” Journal
of physics: Condensed matter, vol. 34, no. 13. IOP Publishing, 2022.'
ista: 'Nauman M, Hussain T, Choi J, Lee N, Choi YJ, Kang W, Jo Y. 2022. Low-field
magnetic anisotropy of Sr2IrO4. Journal of physics: Condensed matter. 34(13),
135802.'
mla: 'Nauman, Muhammad, et al. “Low-Field Magnetic Anisotropy of Sr2IrO4.” Journal
of Physics: Condensed Matter, vol. 34, no. 13, 135802, IOP Publishing, 2022,
doi:10.1088/1361-648X/ac484d.'
short: 'M. Nauman, T. Hussain, J. Choi, N. Lee, Y.J. Choi, W. Kang, Y. Jo, Journal
of Physics: Condensed Matter 34 (2022).'
date_created: 2022-02-06T23:01:31Z
date_published: 2022-01-20T00:00:00Z
date_updated: 2023-08-02T14:12:01Z
day: '20'
ddc:
- '530'
department:
- _id: KiMo
doi: 10.1088/1361-648X/ac484d
external_id:
isi:
- '000775191800001'
pmid:
- '34986467'
file:
- access_level: open_access
checksum: b6c705c7f03dcb1dbcb06b1b4d4938d6
content_type: application/pdf
creator: cchlebak
date_created: 2022-02-07T10:35:28Z
date_updated: 2022-02-07T10:35:28Z
file_id: '10741'
file_name: 2022_JPhysCondensMatter_Nauman.pdf
file_size: 1742414
relation: main_file
success: 1
file_date_updated: 2022-02-07T10:35:28Z
has_accepted_license: '1'
intvolume: ' 34'
isi: 1
issue: '13'
language:
- iso: eng
month: '01'
oa: 1
oa_version: Published Version
pmid: 1
publication: 'Journal of physics: Condensed matter'
publication_identifier:
eissn:
- 1361-648X
publication_status: published
publisher: IOP Publishing
quality_controlled: '1'
scopus_import: '1'
status: public
title: Low-field magnetic anisotropy of Sr2IrO4
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: 34
year: '2022'
...
---
_id: '10736'
abstract:
- lang: eng
text: Predicting function from sequence is a central problem of biology. Currently,
this is possible only locally in a narrow mutational neighborhood around a wildtype
sequence rather than globally from any sequence. Using random mutant libraries,
we developed a biophysical model that accounts for multiple features of σ70 binding
bacterial promoters to predict constitutive gene expression levels from any sequence.
We experimentally and theoretically estimated that 10–20% of random sequences
lead to expression and ~80% of non-expressing sequences are one mutation away
from a functional promoter. The potential for generating expression from random
sequences is so pervasive that selection acts against σ70-RNA polymerase binding
sites even within inter-genic, promoter-containing regions. This pervasiveness
of σ70-binding sites implies that emergence of promoters is not the limiting step
in gene regulatory evolution. Ultimately, the inclusion of novel features of promoter
function into a mechanistic model enabled not only more accurate predictions of
gene expression levels, but also identified that promoters evolve more rapidly
than previously thought.
acknowledgement: 'We thank Hande Acar, Nicholas H Barton, Rok Grah, Tiago Paixao,
Maros Pleska, Anna Staron, and Murat Tugrul for insightful comments and input on
the manuscript. This work was supported by: Sir Henry Dale Fellowship jointly funded
by the Wellcome Trust and the Royal Society (grant number 216779/Z/19/Z) to ML;
IPC Grant from IST Austria to ML and SS; European Research Council Funding Programme
7 (2007–2013, grant agreement number 648440) to JPB.'
article_number: e64543
article_processing_charge: No
article_type: original
author:
- first_name: Mato
full_name: Lagator, Mato
id: 345D25EC-F248-11E8-B48F-1D18A9856A87
last_name: Lagator
- first_name: Srdjan
full_name: Sarikas, Srdjan
id: 35F0286E-F248-11E8-B48F-1D18A9856A87
last_name: Sarikas
- first_name: Magdalena
full_name: Steinrueck, Magdalena
last_name: Steinrueck
- first_name: David
full_name: Toledo-Aparicio, David
last_name: Toledo-Aparicio
- first_name: Jonathan P
full_name: Bollback, Jonathan P
id: 2C6FA9CC-F248-11E8-B48F-1D18A9856A87
last_name: Bollback
orcid: 0000-0002-4624-4612
- first_name: Calin C
full_name: Guet, Calin C
id: 47F8433E-F248-11E8-B48F-1D18A9856A87
last_name: Guet
orcid: 0000-0001-6220-2052
- first_name: Gašper
full_name: Tkačik, Gašper
id: 3D494DCA-F248-11E8-B48F-1D18A9856A87
last_name: Tkačik
orcid: 0000-0002-6699-1455
citation:
ama: Lagator M, Sarikas S, Steinrueck M, et al. Predicting bacterial promoter function
and evolution from random sequences. eLife. 2022;11. doi:10.7554/eLife.64543
apa: Lagator, M., Sarikas, S., Steinrueck, M., Toledo-Aparicio, D., Bollback, J.
P., Guet, C. C., & Tkačik, G. (2022). Predicting bacterial promoter function
and evolution from random sequences. ELife. eLife Sciences Publications.
https://doi.org/10.7554/eLife.64543
chicago: Lagator, Mato, Srdjan Sarikas, Magdalena Steinrueck, David Toledo-Aparicio,
Jonathan P Bollback, Calin C Guet, and Gašper Tkačik. “Predicting Bacterial Promoter
Function and Evolution from Random Sequences.” ELife. eLife Sciences Publications,
2022. https://doi.org/10.7554/eLife.64543.
ieee: M. Lagator et al., “Predicting bacterial promoter function and evolution
from random sequences,” eLife, vol. 11. eLife Sciences Publications, 2022.
ista: Lagator M, Sarikas S, Steinrueck M, Toledo-Aparicio D, Bollback JP, Guet CC,
Tkačik G. 2022. Predicting bacterial promoter function and evolution from random
sequences. eLife. 11, e64543.
mla: Lagator, Mato, et al. “Predicting Bacterial Promoter Function and Evolution
from Random Sequences.” ELife, vol. 11, e64543, eLife Sciences Publications,
2022, doi:10.7554/eLife.64543.
short: M. Lagator, S. Sarikas, M. Steinrueck, D. Toledo-Aparicio, J.P. Bollback,
C.C. Guet, G. Tkačik, ELife 11 (2022).
date_created: 2022-02-06T23:01:32Z
date_published: 2022-01-26T00:00:00Z
date_updated: 2023-08-02T14:09:02Z
day: '26'
ddc:
- '576'
department:
- _id: CaGu
- _id: GaTk
- _id: NiBa
doi: 10.7554/eLife.64543
ec_funded: 1
external_id:
isi:
- '000751104400001'
pmid:
- '35080492'
file:
- access_level: open_access
checksum: decdcdf600ff51e9a9703b49ca114170
content_type: application/pdf
creator: cchlebak
date_created: 2022-02-07T07:14:09Z
date_updated: 2022-02-07T07:14:09Z
file_id: '10739'
file_name: 2022_ELife_Lagator.pdf
file_size: 5604343
relation: main_file
success: 1
file_date_updated: 2022-02-07T07:14:09Z
has_accepted_license: '1'
intvolume: ' 11'
isi: 1
language:
- iso: eng
month: '01'
oa: 1
oa_version: Published Version
pmid: 1
project:
- _id: 2578D616-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '648440'
name: Selective Barriers to Horizontal Gene Transfer
publication: eLife
publication_identifier:
eissn:
- 2050-084X
publication_status: published
publisher: eLife Sciences Publications
quality_controlled: '1'
scopus_import: '1'
status: public
title: Predicting bacterial promoter function and evolution from random sequences
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: 11
year: '2022'
...
---
_id: '10737'
abstract:
- lang: eng
text: We consider two models for the sequence labeling (tagging) problem. The first
one is a Pattern-Based Conditional Random Field (PB), in which the energy of a
string (chain labeling) x=x1…xn∈Dn is a sum of terms over intervals [i,j] where
each term is non-zero only if the substring xi…xj equals a prespecified word
w∈Λ. The second model is a Weighted Context-Free Grammar (WCFG) frequently used
for natural language processing. PB and WCFG encode local and non-local interactions
respectively, and thus can be viewed as complementary. We propose a Grammatical
Pattern-Based CRF model (GPB) that combines the two in a natural way. We argue
that it has certain advantages over existing approaches such as the Hybrid model
of Benedí and Sanchez that combines N-grams and WCFGs. The focus of this paper
is to analyze the complexity of inference tasks in a GPB such as computing MAP.
We present a polynomial-time algorithm for general GPBs and a faster version for
a special case that we call Interaction Grammars.
article_processing_charge: No
article_type: original
arxiv: 1
author:
- first_name: Rustem
full_name: Takhanov, Rustem
id: 2CCAC26C-F248-11E8-B48F-1D18A9856A87
last_name: Takhanov
- first_name: Vladimir
full_name: Kolmogorov, Vladimir
id: 3D50B0BA-F248-11E8-B48F-1D18A9856A87
last_name: Kolmogorov
citation:
ama: Takhanov R, Kolmogorov V. Combining pattern-based CRFs and weighted context-free
grammars. Intelligent Data Analysis. 2022;26(1):257-272. doi:10.3233/IDA-205623
apa: Takhanov, R., & Kolmogorov, V. (2022). Combining pattern-based CRFs and
weighted context-free grammars. Intelligent Data Analysis. IOS Press. https://doi.org/10.3233/IDA-205623
chicago: Takhanov, Rustem, and Vladimir Kolmogorov. “Combining Pattern-Based CRFs
and Weighted Context-Free Grammars.” Intelligent Data Analysis. IOS Press,
2022. https://doi.org/10.3233/IDA-205623.
ieee: R. Takhanov and V. Kolmogorov, “Combining pattern-based CRFs and weighted
context-free grammars,” Intelligent Data Analysis, vol. 26, no. 1. IOS
Press, pp. 257–272, 2022.
ista: Takhanov R, Kolmogorov V. 2022. Combining pattern-based CRFs and weighted
context-free grammars. Intelligent Data Analysis. 26(1), 257–272.
mla: Takhanov, Rustem, and Vladimir Kolmogorov. “Combining Pattern-Based CRFs and
Weighted Context-Free Grammars.” Intelligent Data Analysis, vol. 26, no.
1, IOS Press, 2022, pp. 257–72, doi:10.3233/IDA-205623.
short: R. Takhanov, V. Kolmogorov, Intelligent Data Analysis 26 (2022) 257–272.
date_created: 2022-02-06T23:01:32Z
date_published: 2022-01-14T00:00:00Z
date_updated: 2023-08-02T14:09:41Z
day: '14'
department:
- _id: VlKo
doi: 10.3233/IDA-205623
external_id:
arxiv:
- '1404.5475'
isi:
- '000749997700015'
intvolume: ' 26'
isi: 1
issue: '1'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/1404.5475
month: '01'
oa: 1
oa_version: Preprint
page: 257-272
publication: Intelligent Data Analysis
publication_identifier:
eissn:
- 1571-4128
issn:
- 1088-467X
publication_status: published
publisher: IOS Press
quality_controlled: '1'
scopus_import: '1'
status: public
title: Combining pattern-based CRFs and weighted context-free grammars
type: journal_article
user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
volume: 26
year: '2022'
...
---
_id: '10752'
abstract:
- lang: eng
text: 'The digitalization of almost all aspects of our everyday lives has led to
unprecedented amounts of data being freely available on the Internet. In particular
social media platforms provide rich sources of user-generated data, though typically
in unstructured form, and with high diversity, such as written in many different
languages. Automatically identifying meaningful information in such big data resources
and extracting it efficiently is one of the ongoing challenges of our time. A
common step for this is sentiment analysis, which forms the foundation for tasks
such as opinion mining or trend prediction. Unfortunately, publicly available
tools for this task are almost exclusively available for English-language texts.
Consequently, a large fraction of the Internet users, who do not communicate in
English, are ignored in automatized studies, a phenomenon called rare-language
discrimination.In this work we propose a technique to overcome this problem by
a truly multi-lingual model, which can be trained automatically without linguistic
knowledge or even the ability to read the many target languages. The main step
is to combine self-annotation, specifically the use of emoticons as a proxy for
labels, with multi-lingual sentence representations.To evaluate our method we
curated several large datasets from data obtained via the free Twitter streaming
API. The results show that our proposed multi-lingual training is able to achieve
sentiment predictions at the same quality level for rare languages as for frequent
ones, and in particular clearly better than what mono-lingual training achieves
on the same data. '
article_processing_charge: No
author:
- first_name: Jasmin
full_name: Lampert, Jasmin
last_name: Lampert
- first_name: Christoph
full_name: Lampert, Christoph
id: 40C20FD2-F248-11E8-B48F-1D18A9856A87
last_name: Lampert
orcid: 0000-0002-4561-241X
citation:
ama: 'Lampert J, Lampert C. Overcoming rare-language discrimination in multi-lingual
sentiment analysis. In: 2021 IEEE International Conference on Big Data.
IEEE; 2022:5185-5192. doi:10.1109/bigdata52589.2021.9672003'
apa: 'Lampert, J., & Lampert, C. (2022). Overcoming rare-language discrimination
in multi-lingual sentiment analysis. In 2021 IEEE International Conference
on Big Data (pp. 5185–5192). Orlando, FL, United States: IEEE. https://doi.org/10.1109/bigdata52589.2021.9672003'
chicago: Lampert, Jasmin, and Christoph Lampert. “Overcoming Rare-Language Discrimination
in Multi-Lingual Sentiment Analysis.” In 2021 IEEE International Conference
on Big Data, 5185–92. IEEE, 2022. https://doi.org/10.1109/bigdata52589.2021.9672003.
ieee: J. Lampert and C. Lampert, “Overcoming rare-language discrimination in multi-lingual
sentiment analysis,” in 2021 IEEE International Conference on Big Data,
Orlando, FL, United States, 2022, pp. 5185–5192.
ista: 'Lampert J, Lampert C. 2022. Overcoming rare-language discrimination in multi-lingual
sentiment analysis. 2021 IEEE International Conference on Big Data. Big Data:
International Conference on Big Data, 5185–5192.'
mla: Lampert, Jasmin, and Christoph Lampert. “Overcoming Rare-Language Discrimination
in Multi-Lingual Sentiment Analysis.” 2021 IEEE International Conference on
Big Data, IEEE, 2022, pp. 5185–92, doi:10.1109/bigdata52589.2021.9672003.
short: J. Lampert, C. Lampert, in:, 2021 IEEE International Conference on Big Data,
IEEE, 2022, pp. 5185–5192.
conference:
end_date: 2021-12-18
location: Orlando, FL, United States
name: 'Big Data: International Conference on Big Data'
start_date: 2021-12-15
date_created: 2022-02-10T14:08:23Z
date_published: 2022-01-13T00:00:00Z
date_updated: 2023-08-02T14:27:50Z
day: '13'
department:
- _id: ChLa
doi: 10.1109/bigdata52589.2021.9672003
external_id:
isi:
- '000800559505036'
isi: 1
language:
- iso: eng
month: '01'
oa_version: None
page: 5185-5192
publication: 2021 IEEE International Conference on Big Data
publication_identifier:
isbn:
- '9781665439022'
publication_status: published
publisher: IEEE
quality_controlled: '1'
status: public
title: Overcoming rare-language discrimination in multi-lingual sentiment analysis
type: conference
user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
year: '2022'
...
---
_id: '10753'
abstract:
- lang: eng
text: This is a comment on "Meta-learning synaptic plasticity and memory addressing
for continual familiarity detection." Neuron. 2022 Feb 2;110(3):544-557.e8.
article_processing_charge: No
article_type: letter_note
author:
- first_name: Basile J
full_name: Confavreux, Basile J
id: C7610134-B532-11EA-BD9F-F5753DDC885E
last_name: Confavreux
- first_name: Tim P
full_name: Vogels, Tim P
id: CB6FF8D2-008F-11EA-8E08-2637E6697425
last_name: Vogels
orcid: 0000-0003-3295-6181
citation:
ama: 'Confavreux BJ, Vogels TP. A familiar thought: Machines that replace us? Neuron.
2022;110(3):361-362. doi:10.1016/j.neuron.2022.01.014'
apa: 'Confavreux, B. J., & Vogels, T. P. (2022). A familiar thought: Machines
that replace us? Neuron. Elsevier. https://doi.org/10.1016/j.neuron.2022.01.014'
chicago: 'Confavreux, Basile J, and Tim P Vogels. “A Familiar Thought: Machines
That Replace Us?” Neuron. Elsevier, 2022. https://doi.org/10.1016/j.neuron.2022.01.014.'
ieee: 'B. J. Confavreux and T. P. Vogels, “A familiar thought: Machines that replace
us?,” Neuron, vol. 110, no. 3. Elsevier, pp. 361–362, 2022.'
ista: 'Confavreux BJ, Vogels TP. 2022. A familiar thought: Machines that replace
us? Neuron. 110(3), 361–362.'
mla: 'Confavreux, Basile J., and Tim P. Vogels. “A Familiar Thought: Machines That
Replace Us?” Neuron, vol. 110, no. 3, Elsevier, 2022, pp. 361–62, doi:10.1016/j.neuron.2022.01.014.'
short: B.J. Confavreux, T.P. Vogels, Neuron 110 (2022) 361–362.
date_created: 2022-02-13T23:01:34Z
date_published: 2022-02-02T00:00:00Z
date_updated: 2023-10-03T10:53:17Z
day: '02'
department:
- _id: TiVo
doi: 10.1016/j.neuron.2022.01.014
external_id:
isi:
- '000751819100005'
pmid:
- '35114107'
intvolume: ' 110'
isi: 1
issue: '3'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.1016/j.neuron.2022.01.014
month: '02'
oa: 1
oa_version: Published Version
page: 361-362
pmid: 1
publication: Neuron
publication_identifier:
eissn:
- 1097-4199
publication_status: published
publisher: Elsevier
quality_controlled: '1'
scopus_import: '1'
status: public
title: 'A familiar thought: Machines that replace us?'
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 110
year: '2022'
...
---
_id: '10754'
abstract:
- lang: eng
text: Targeting dysregulated Ca2+ signaling in cancer cells is an emerging chemotherapy
approach. We previously reported that store-operated Ca2+ entry (SOCE) blockers,
such as RP4010, are promising antitumor drugs for esophageal cancer. As a tyrosine
kinase inhibitor (TKI), afatinib received FDA approval to be used in targeted
therapy for patients with EGFR mutation-positive cancers. While preclinical studies
and clinical trials have shown that afatinib has benefits for esophageal cancer
patients, it is not known whether a combination of afatinib and RP4010 could achieve
better anticancer effects. Since TKI can alter intracellular Ca2+ dynamics through
EGFR/phospholipase C-γ pathway, in this study, we evaluated the inhibitory effect
of afatinib and RP4010 on intracellular Ca2+ oscillations in KYSE-150, a human
esophageal squamous cell carcinoma cell line, using both experimental and mathematical
simulations. Our mathematical simulation of Ca2+ oscillations could fit well with
experimental data responding to afatinib or RP4010, both separately or in combination.
Guided by simulation, we were able to identify a proper ratio of afatinib and
RP4010 for combined treatment, and such a combination presented synergistic anticancer-effect
evidence by experimental measurement of intracellular Ca2+ and cell proliferation.
This intracellular Ca2+ dynamic-based mathematical simulation approach could be
useful for a rapid and cost-effective evaluation of combined targeting therapy
drugs.
acknowledgement: "This work was partially supported by grants from National Institutes
of Health (NIH) (R01 CA185055, S10OD0252300) and The University of Texas System
STARs Award (to Z.P.),\r\nThe University of Texas at Arlington Interdisciplinary
Research Program (to B.C., H.V.K. and Z.P.). "
article_number: '1763'
article_processing_charge: Yes
article_type: original
author:
- first_name: Yan
full_name: Chang, Yan
last_name: Chang
- first_name: Marah
full_name: Funk, Marah
last_name: Funk
- first_name: Souvik
full_name: Roy, Souvik
last_name: Roy
- first_name: Elizabeth R
full_name: Stephenson, Elizabeth R
id: 2D04F932-F248-11E8-B48F-1D18A9856A87
last_name: Stephenson
orcid: 0000-0002-6862-208X
- first_name: Sangyong
full_name: Choi, Sangyong
last_name: Choi
- first_name: Hristo V.
full_name: Kojouharov, Hristo V.
last_name: Kojouharov
- first_name: Benito
full_name: Chen, Benito
last_name: Chen
- first_name: Zui
full_name: Pan, Zui
last_name: Pan
citation:
ama: Chang Y, Funk M, Roy S, et al. Developing a mathematical model of intracellular
Calcium dynamics for evaluating combined anticancer effects of afatinib and RP4010
in esophageal cancer. International Journal of Molecular Sciences. 2022;23(3).
doi:10.3390/ijms23031763
apa: Chang, Y., Funk, M., Roy, S., Stephenson, E. R., Choi, S., Kojouharov, H. V.,
… Pan, Z. (2022). Developing a mathematical model of intracellular Calcium dynamics
for evaluating combined anticancer effects of afatinib and RP4010 in esophageal
cancer. International Journal of Molecular Sciences. MDPI. https://doi.org/10.3390/ijms23031763
chicago: Chang, Yan, Marah Funk, Souvik Roy, Elizabeth R Stephenson, Sangyong Choi,
Hristo V. Kojouharov, Benito Chen, and Zui Pan. “Developing a Mathematical Model
of Intracellular Calcium Dynamics for Evaluating Combined Anticancer Effects of
Afatinib and RP4010 in Esophageal Cancer.” International Journal of Molecular
Sciences. MDPI, 2022. https://doi.org/10.3390/ijms23031763.
ieee: Y. Chang et al., “Developing a mathematical model of intracellular
Calcium dynamics for evaluating combined anticancer effects of afatinib and RP4010
in esophageal cancer,” International Journal of Molecular Sciences, vol.
23, no. 3. MDPI, 2022.
ista: Chang Y, Funk M, Roy S, Stephenson ER, Choi S, Kojouharov HV, Chen B, Pan
Z. 2022. Developing a mathematical model of intracellular Calcium dynamics for
evaluating combined anticancer effects of afatinib and RP4010 in esophageal cancer.
International Journal of Molecular Sciences. 23(3), 1763.
mla: Chang, Yan, et al. “Developing a Mathematical Model of Intracellular Calcium
Dynamics for Evaluating Combined Anticancer Effects of Afatinib and RP4010 in
Esophageal Cancer.” International Journal of Molecular Sciences, vol. 23,
no. 3, 1763, MDPI, 2022, doi:10.3390/ijms23031763.
short: Y. Chang, M. Funk, S. Roy, E.R. Stephenson, S. Choi, H.V. Kojouharov, B.
Chen, Z. Pan, International Journal of Molecular Sciences 23 (2022).
date_created: 2022-02-13T23:01:35Z
date_published: 2022-02-01T00:00:00Z
date_updated: 2023-08-09T10:17:07Z
day: '01'
ddc:
- '510'
- '576'
department:
- _id: HeEd
doi: 10.3390/ijms23031763
external_id:
isi:
- '000754773500001'
file:
- access_level: open_access
checksum: 8890ad20c54e90dc58ad5ea97c902998
content_type: application/pdf
creator: dernst
date_created: 2022-02-14T07:46:30Z
date_updated: 2022-02-14T07:46:30Z
file_id: '10756'
file_name: 2022_IJMS_Chang.pdf
file_size: 24416183
relation: main_file
success: 1
file_date_updated: 2022-02-14T07:46:30Z
has_accepted_license: '1'
intvolume: ' 23'
isi: 1
issue: '3'
language:
- iso: eng
month: '02'
oa: 1
oa_version: Published Version
publication: International Journal of Molecular Sciences
publication_identifier:
eissn:
- '14220067'
issn:
- '16616596'
publication_status: published
publisher: MDPI
quality_controlled: '1'
scopus_import: '1'
status: public
title: Developing a mathematical model of intracellular Calcium dynamics for evaluating
combined anticancer effects of afatinib and RP4010 in esophageal cancer
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: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87
volume: 23
year: '2022'
...
---
_id: '10755'
abstract:
- lang: eng
text: We provide a definition of the effective mass for the classical polaron described
by the Landau–Pekar (LP) equations. It is based on a novel variational principle,
minimizing the energy functional over states with given (initial) velocity. The
resulting formula for the polaron's effective mass agrees with the prediction
by LP (1948 J. Exp. Theor. Phys. 18 419–423).
acknowledgement: "We thank Herbert Spohn for helpful comments. Funding from the European
Union’s Horizon\r\n2020 research and innovation programme under the ERC Grant Agreement
No. 694227\r\n(DF and RS) and under the Marie Skłodowska-Curie Grant Agreement No.
754411 (SR) is\r\ngratefully acknowledged."
article_number: '015201'
article_processing_charge: Yes (via OA deal)
article_type: original
arxiv: 1
author:
- first_name: Dario
full_name: Feliciangeli, Dario
id: 41A639AA-F248-11E8-B48F-1D18A9856A87
last_name: Feliciangeli
orcid: 0000-0003-0754-8530
- first_name: Simone Anna Elvira
full_name: Rademacher, Simone Anna Elvira
id: 856966FE-A408-11E9-977E-802DE6697425
last_name: Rademacher
orcid: 0000-0001-5059-4466
- first_name: Robert
full_name: Seiringer, Robert
id: 4AFD0470-F248-11E8-B48F-1D18A9856A87
last_name: Seiringer
orcid: 0000-0002-6781-0521
citation:
ama: 'Feliciangeli D, Rademacher SAE, Seiringer R. The effective mass problem for
the Landau-Pekar equations. Journal of Physics A: Mathematical and Theoretical.
2022;55(1). doi:10.1088/1751-8121/ac3947'
apa: 'Feliciangeli, D., Rademacher, S. A. E., & Seiringer, R. (2022). The effective
mass problem for the Landau-Pekar equations. Journal of Physics A: Mathematical
and Theoretical. IOP Publishing. https://doi.org/10.1088/1751-8121/ac3947'
chicago: 'Feliciangeli, Dario, Simone Anna Elvira Rademacher, and Robert Seiringer.
“The Effective Mass Problem for the Landau-Pekar Equations.” Journal of Physics
A: Mathematical and Theoretical. IOP Publishing, 2022. https://doi.org/10.1088/1751-8121/ac3947.'
ieee: 'D. Feliciangeli, S. A. E. Rademacher, and R. Seiringer, “The effective mass
problem for the Landau-Pekar equations,” Journal of Physics A: Mathematical
and Theoretical, vol. 55, no. 1. IOP Publishing, 2022.'
ista: 'Feliciangeli D, Rademacher SAE, Seiringer R. 2022. The effective mass problem
for the Landau-Pekar equations. Journal of Physics A: Mathematical and Theoretical.
55(1), 015201.'
mla: 'Feliciangeli, Dario, et al. “The Effective Mass Problem for the Landau-Pekar
Equations.” Journal of Physics A: Mathematical and Theoretical, vol. 55,
no. 1, 015201, IOP Publishing, 2022, doi:10.1088/1751-8121/ac3947.'
short: 'D. Feliciangeli, S.A.E. Rademacher, R. Seiringer, Journal of Physics A:
Mathematical and Theoretical 55 (2022).'
date_created: 2022-02-13T23:01:35Z
date_published: 2022-01-19T00:00:00Z
date_updated: 2024-03-06T12:30:44Z
day: '19'
ddc:
- '510'
department:
- _id: RoSe
doi: 10.1088/1751-8121/ac3947
ec_funded: 1
external_id:
arxiv:
- '2107.03720'
file:
- access_level: open_access
checksum: 0875e562705563053d6dd98fba4d8578
content_type: application/pdf
creator: dernst
date_created: 2022-02-14T08:20:19Z
date_updated: 2022-02-14T08:20:19Z
file_id: '10757'
file_name: 2022_JournalPhysicsA_Feliciangeli.pdf
file_size: 1132380
relation: main_file
success: 1
file_date_updated: 2022-02-14T08:20:19Z
has_accepted_license: '1'
intvolume: ' 55'
issue: '1'
language:
- iso: eng
month: '01'
oa: 1
oa_version: Published Version
project:
- _id: 25C6DC12-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '694227'
name: Analysis of quantum many-body systems
- _id: 260C2330-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '754411'
name: ISTplus - Postdoctoral Fellowships
publication: 'Journal of Physics A: Mathematical and Theoretical'
publication_identifier:
eissn:
- 1751-8121
issn:
- 1751-8113
publication_status: published
publisher: IOP Publishing
quality_controlled: '1'
related_material:
record:
- id: '9791'
relation: earlier_version
status: public
scopus_import: '1'
status: public
title: The effective mass problem for the Landau-Pekar equations
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: 55
year: '2022'
...
---
_id: '10759'
abstract:
- lang: eng
text: In this Thesis, I study composite quantum impurities with variational techniques,
both inspired by machine learning as well as fully analytic. I supplement this
with exploration of other applications of machine learning, in particular artificial
neural networks, in many-body physics. In Chapters 3 and 4, I study quasiparticle
systems with variational approach. I derive a Hamiltonian describing the angulon
quasiparticle in the presence of a magnetic field. I apply analytic variational
treatment to this Hamiltonian. Then, I introduce a variational approach for non-additive
systems, based on artificial neural networks. I exemplify this approach on the
example of the polaron quasiparticle (Fröhlich Hamiltonian). In Chapter 5, I continue
using artificial neural networks, albeit in a different setting. I apply artificial
neural networks to detect phases from snapshots of two types physical systems.
Namely, I study Monte Carlo snapshots of multilayer classical spin models as well
as molecular dynamics maps of colloidal systems. The main type of networks that
I use here are convolutional neural networks, known for their applicability to
image data.
alternative_title:
- ISTA Thesis
article_processing_charge: No
author:
- first_name: Wojciech
full_name: Rzadkowski, Wojciech
id: 48C55298-F248-11E8-B48F-1D18A9856A87
last_name: Rzadkowski
orcid: 0000-0002-1106-4419
citation:
ama: Rzadkowski W. Analytic and machine learning approaches to composite quantum
impurities. 2022. doi:10.15479/at:ista:10759
apa: Rzadkowski, W. (2022). Analytic and machine learning approaches to composite
quantum impurities. Institute of Science and Technology Austria. https://doi.org/10.15479/at:ista:10759
chicago: Rzadkowski, Wojciech. “Analytic and Machine Learning Approaches to Composite
Quantum Impurities.” Institute of Science and Technology Austria, 2022. https://doi.org/10.15479/at:ista:10759.
ieee: W. Rzadkowski, “Analytic and machine learning approaches to composite quantum
impurities,” Institute of Science and Technology Austria, 2022.
ista: Rzadkowski W. 2022. Analytic and machine learning approaches to composite
quantum impurities. Institute of Science and Technology Austria.
mla: Rzadkowski, Wojciech. Analytic and Machine Learning Approaches to Composite
Quantum Impurities. Institute of Science and Technology Austria, 2022, doi:10.15479/at:ista:10759.
short: W. Rzadkowski, Analytic and Machine Learning Approaches to Composite Quantum
Impurities, Institute of Science and Technology Austria, 2022.
date_created: 2022-02-16T13:27:37Z
date_published: 2022-02-21T00:00:00Z
date_updated: 2024-08-07T07:16:53Z
day: '21'
ddc:
- '530'
degree_awarded: PhD
department:
- _id: GradSch
- _id: MiLe
doi: 10.15479/at:ista:10759
ec_funded: 1
file:
- access_level: closed
checksum: 0fc54ad1eaede879c665ac9b53c93e22
content_type: application/zip
creator: wrzadkow
date_created: 2022-02-21T13:58:16Z
date_updated: 2022-02-22T07:20:12Z
file_id: '10785'
file_name: Rzadkowski_thesis_final_source.zip
file_size: 17668233
relation: source_file
- access_level: open_access
checksum: 22d2d7af37ca31f6b1730c26cac7bced
content_type: application/pdf
creator: wrzadkow
date_created: 2022-02-21T14:02:54Z
date_updated: 2022-02-21T14:02:54Z
file_id: '10786'
file_name: Rzadkowski_thesis_final.pdf
file_size: 13307331
relation: main_file
success: 1
file_date_updated: 2022-02-22T07:20:12Z
has_accepted_license: '1'
language:
- iso: eng
month: '02'
oa: 1
oa_version: Published Version
page: '120'
project:
- _id: 2564DBCA-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '665385'
name: International IST Doctoral Program
publication_identifier:
issn:
- 2663-337X
publication_status: published
publisher: Institute of Science and Technology Austria
related_material:
record:
- id: '10762'
relation: part_of_dissertation
status: public
- id: '7956'
relation: part_of_dissertation
status: public
- id: '415'
relation: part_of_dissertation
status: public
- id: '8644'
relation: part_of_dissertation
status: public
status: public
supervisor:
- first_name: Mikhail
full_name: Lemeshko, Mikhail
id: 37CB05FA-F248-11E8-B48F-1D18A9856A87
last_name: Lemeshko
orcid: 0000-0002-6990-7802
title: Analytic and machine learning approaches to composite quantum impurities
type: dissertation
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
year: '2022'
...
---
_id: '10763'
abstract:
- lang: eng
text: "AMPA-type glutamate receptors (AMPARs) mediate rapid signal transmission
at excitatory\r\nsynapses in the brain. Glutamate binding to the receptor’s ligand-binding
domains (LBDs)\r\nleads to ion channel activation and desensitization. Gating
kinetics shape synaptic transmission\r\nand are strongly modulated by transmembrane
AMPAR regulatory proteins (TARPs)\r\nthrough currently incompletely resolved mechanisms.
Here, electron cryo-microscopy\r\nstructures of the GluA1/2 TARP-γ8 complex, in
both open and desensitized states\r\n(at 3.5 Å), reveal state-selective engagement
of the LBDs by the large TARP-γ8 loop (‘β1’),\r\nelucidating how this TARP stabilizes
specific gating states. We further show how TARPs alter\r\nchannel rectification,
by interacting with the pore helix of the selectivity filter. Lastly, we\r\nreveal
that the Q/R-editing site couples the channel constriction at the filter entrance
to the\r\ngate, and forms the major cation binding site in the conduction path.
Our results provide a\r\nmechanistic framework of how TARPs modulate AMPAR gating
and conductance."
acknowledgement: "We thank Ondrej Cais for critical reading of the manuscript. We
are grateful to LMB\r\nscientific computing and the EM facility for support, Paul
Emsley for help with model\r\nbuilding and Takanori Nakane for helpful comments
with Relion 3.1. This work was\r\nsupported by grants from the Medical Research
Council (MC_U105174197) and BBSRC\r\n(BB/N002113/1) to I.H.G, and grants from the
MCIN/AEI/ 10.13039/501100011033 and\r\n“ESF Investing in your future” to B.H (PID2019-106284GA-I00
and RYC2018-025720-I)."
article_number: '734'
article_processing_charge: No
article_type: original
author:
- first_name: Beatriz
full_name: Herguedas, Beatriz
last_name: Herguedas
- first_name: Bianka K.
full_name: Kohegyi, Bianka K.
last_name: Kohegyi
- first_name: Jan Niklas
full_name: Dohrke, Jan Niklas
last_name: Dohrke
- first_name: Jake
full_name: Watson, Jake
id: 63836096-4690-11EA-BD4E-32803DDC885E
last_name: Watson
orcid: 0000-0002-8698-3823
- first_name: Danyang
full_name: Zhang, Danyang
last_name: Zhang
- first_name: Hinze
full_name: Ho, Hinze
last_name: Ho
- first_name: Saher A.
full_name: Shaikh, Saher A.
last_name: Shaikh
- first_name: Remigijus
full_name: Lape, Remigijus
last_name: Lape
- first_name: James M.
full_name: Krieger, James M.
last_name: Krieger
- first_name: Ingo H.
full_name: Greger, Ingo H.
last_name: Greger
citation:
ama: Herguedas B, Kohegyi BK, Dohrke JN, et al. Mechanisms underlying TARP modulation
of the GluA1/2-γ8 AMPA receptor. Nature Communications. 2022;13. doi:10.1038/s41467-022-28404-7
apa: Herguedas, B., Kohegyi, B. K., Dohrke, J. N., Watson, J., Zhang, D., Ho, H.,
… Greger, I. H. (2022). Mechanisms underlying TARP modulation of the GluA1/2-γ8
AMPA receptor. Nature Communications. Springer Nature. https://doi.org/10.1038/s41467-022-28404-7
chicago: Herguedas, Beatriz, Bianka K. Kohegyi, Jan Niklas Dohrke, Jake Watson,
Danyang Zhang, Hinze Ho, Saher A. Shaikh, Remigijus Lape, James M. Krieger, and
Ingo H. Greger. “Mechanisms Underlying TARP Modulation of the GluA1/2-Γ8 AMPA
Receptor.” Nature Communications. Springer Nature, 2022. https://doi.org/10.1038/s41467-022-28404-7.
ieee: B. Herguedas et al., “Mechanisms underlying TARP modulation of the
GluA1/2-γ8 AMPA receptor,” Nature Communications, vol. 13. Springer Nature,
2022.
ista: Herguedas B, Kohegyi BK, Dohrke JN, Watson J, Zhang D, Ho H, Shaikh SA, Lape
R, Krieger JM, Greger IH. 2022. Mechanisms underlying TARP modulation of the GluA1/2-γ8
AMPA receptor. Nature Communications. 13, 734.
mla: Herguedas, Beatriz, et al. “Mechanisms Underlying TARP Modulation of the GluA1/2-Γ8
AMPA Receptor.” Nature Communications, vol. 13, 734, Springer Nature, 2022,
doi:10.1038/s41467-022-28404-7.
short: B. Herguedas, B.K. Kohegyi, J.N. Dohrke, J. Watson, D. Zhang, H. Ho, S.A.
Shaikh, R. Lape, J.M. Krieger, I.H. Greger, Nature Communications 13 (2022).
date_created: 2022-02-20T23:01:30Z
date_published: 2022-02-08T00:00:00Z
date_updated: 2023-08-02T14:25:33Z
day: '08'
ddc:
- '570'
department:
- _id: PeJo
doi: 10.1038/s41467-022-28404-7
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title: Mechanisms underlying TARP modulation of the GluA1/2-γ8 AMPA receptor
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legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
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