---
_id: '8669'
abstract:
- lang: eng
text: Pancreatic islets play an essential role in regulating blood glucose level.
Although the molecular pathways underlying islet cell differentiation are beginning
to be resolved, the cellular basis of islet morphogenesis and fate allocation
remain unclear. By combining unbiased and targeted lineage tracing, we address
the events leading to islet formation in the mouse. From the statistical analysis
of clones induced at multiple embryonic timepoints, here we show that, during
the secondary transition, islet formation involves the aggregation of multiple
equipotent endocrine progenitors that transition from a phase of stochastic amplification
by cell division into a phase of sublineage restriction and limited islet fission.
Together, these results explain quantitatively the heterogeneous size distribution
and degree of polyclonality of maturing islets, as well as dispersion of progenitors
within and between islets. Further, our results show that, during the secondary
transition, α- and β-cells are generated in a contemporary manner. Together, these
findings provide insight into the cellular basis of islet development.
article_number: '5037'
article_processing_charge: No
article_type: original
author:
- first_name: Magdalena K.
full_name: Sznurkowska, Magdalena K.
last_name: Sznurkowska
- 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: Roberta
full_name: Azzarelli, Roberta
last_name: Azzarelli
- first_name: Lemonia
full_name: Chatzeli, Lemonia
last_name: Chatzeli
- first_name: Tatsuro
full_name: Ikeda, Tatsuro
last_name: Ikeda
- first_name: Shosei
full_name: Yoshida, Shosei
last_name: Yoshida
- first_name: Anna
full_name: Philpott, Anna
last_name: Philpott
- first_name: Benjamin D
full_name: Simons, Benjamin D
last_name: Simons
citation:
ama: Sznurkowska MK, Hannezo EB, Azzarelli R, et al. Tracing the cellular basis
of islet specification in mouse pancreas. Nature Communications. 2020;11.
doi:10.1038/s41467-020-18837-3
apa: Sznurkowska, M. K., Hannezo, E. B., Azzarelli, R., Chatzeli, L., Ikeda, T.,
Yoshida, S., … Simons, B. D. (2020). Tracing the cellular basis of islet specification
in mouse pancreas. Nature Communications. Springer Nature. https://doi.org/10.1038/s41467-020-18837-3
chicago: Sznurkowska, Magdalena K., Edouard B Hannezo, Roberta Azzarelli, Lemonia
Chatzeli, Tatsuro Ikeda, Shosei Yoshida, Anna Philpott, and Benjamin D Simons.
“Tracing the Cellular Basis of Islet Specification in Mouse Pancreas.” Nature
Communications. Springer Nature, 2020. https://doi.org/10.1038/s41467-020-18837-3.
ieee: M. K. Sznurkowska et al., “Tracing the cellular basis of islet specification
in mouse pancreas,” Nature Communications, vol. 11. Springer Nature, 2020.
ista: Sznurkowska MK, Hannezo EB, Azzarelli R, Chatzeli L, Ikeda T, Yoshida S, Philpott
A, Simons BD. 2020. Tracing the cellular basis of islet specification in mouse
pancreas. Nature Communications. 11, 5037.
mla: Sznurkowska, Magdalena K., et al. “Tracing the Cellular Basis of Islet Specification
in Mouse Pancreas.” Nature Communications, vol. 11, 5037, Springer Nature,
2020, doi:10.1038/s41467-020-18837-3.
short: M.K. Sznurkowska, E.B. Hannezo, R. Azzarelli, L. Chatzeli, T. Ikeda, S. Yoshida,
A. Philpott, B.D. Simons, Nature Communications 11 (2020).
date_created: 2020-10-18T22:01:35Z
date_published: 2020-10-07T00:00:00Z
date_updated: 2026-04-02T14:29:58Z
day: '07'
ddc:
- '570'
department:
- _id: EdHa
doi: 10.1038/s41467-020-18837-3
external_id:
isi:
- '000577244600003'
pmid:
- '33028844'
file:
- access_level: open_access
checksum: 0ecc0eab72d2d50694852579611a6624
content_type: application/pdf
creator: dernst
date_created: 2020-10-19T11:27:46Z
date_updated: 2020-10-19T11:27:46Z
file_id: '8677'
file_name: 2020_NatureComm_Sznurkowska.pdf
file_size: 5540540
relation: main_file
success: 1
file_date_updated: 2020-10-19T11:27:46Z
has_accepted_license: '1'
intvolume: ' 11'
isi: 1
language:
- iso: eng
month: '10'
oa: 1
oa_version: Published Version
pmid: 1
publication: Nature Communications
publication_identifier:
eissn:
- 2041-1723
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
scopus_import: '1'
status: public
title: Tracing the cellular basis of islet specification in mouse pancreas
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: ba8df636-2132-11f1-aed0-ed93e2281fdd
volume: 11
year: '2020'
...
---
_id: '8697'
abstract:
- lang: eng
text: In the computation of the material properties of random alloys, the method
of 'special quasirandom structures' attempts to approximate the properties of
the alloy on a finite volume with higher accuracy by replicating certain statistics
of the random atomic lattice in the finite volume as accurately as possible. In
the present work, we provide a rigorous justification for a variant of this method
in the framework of the Thomas–Fermi–von Weizsäcker (TFW) model. Our approach
is based on a recent analysis of a related variance reduction method in stochastic
homogenization of linear elliptic PDEs and the locality properties of the TFW
model. Concerning the latter, we extend an exponential locality result by Nazar
and Ortner to include point charges, a result that may be of independent interest.
article_processing_charge: Yes (via OA deal)
article_type: original
arxiv: 1
author:
- first_name: Julian L
full_name: Fischer, Julian L
id: 2C12A0B0-F248-11E8-B48F-1D18A9856A87
last_name: Fischer
orcid: 0000-0002-0479-558X
- first_name: Michael
full_name: Kniely, Michael
id: 2CA2C08C-F248-11E8-B48F-1D18A9856A87
last_name: Kniely
orcid: 0000-0001-5645-4333
citation:
ama: Fischer JL, Kniely M. Variance reduction for effective energies of random lattices
in the Thomas-Fermi-von Weizsäcker model. Nonlinearity. 2020;33(11):5733-5772.
doi:10.1088/1361-6544/ab9728
apa: Fischer, J. L., & Kniely, M. (2020). Variance reduction for effective energies
of random lattices in the Thomas-Fermi-von Weizsäcker model. Nonlinearity.
IOP Publishing. https://doi.org/10.1088/1361-6544/ab9728
chicago: Fischer, Julian L, and Michael Kniely. “Variance Reduction for Effective
Energies of Random Lattices in the Thomas-Fermi-von Weizsäcker Model.” Nonlinearity.
IOP Publishing, 2020. https://doi.org/10.1088/1361-6544/ab9728.
ieee: J. L. Fischer and M. Kniely, “Variance reduction for effective energies of
random lattices in the Thomas-Fermi-von Weizsäcker model,” Nonlinearity,
vol. 33, no. 11. IOP Publishing, pp. 5733–5772, 2020.
ista: Fischer JL, Kniely M. 2020. Variance reduction for effective energies of random
lattices in the Thomas-Fermi-von Weizsäcker model. Nonlinearity. 33(11), 5733–5772.
mla: Fischer, Julian L., and Michael Kniely. “Variance Reduction for Effective Energies
of Random Lattices in the Thomas-Fermi-von Weizsäcker Model.” Nonlinearity,
vol. 33, no. 11, IOP Publishing, 2020, pp. 5733–72, doi:10.1088/1361-6544/ab9728.
short: J.L. Fischer, M. Kniely, Nonlinearity 33 (2020) 5733–5772.
corr_author: '1'
date_created: 2020-10-25T23:01:16Z
date_published: 2020-11-01T00:00:00Z
date_updated: 2026-04-02T14:31:34Z
day: '01'
ddc:
- '510'
department:
- _id: JuFi
doi: 10.1088/1361-6544/ab9728
external_id:
arxiv:
- '1906.12245'
isi:
- '000576492700001'
file:
- access_level: open_access
checksum: ed90bc6eb5f32ee6157fef7f3aabc057
content_type: application/pdf
creator: cziletti
date_created: 2020-10-27T12:09:57Z
date_updated: 2020-10-27T12:09:57Z
file_id: '8710'
file_name: 2020_Nonlinearity_Fischer.pdf
file_size: 1223899
relation: main_file
success: 1
file_date_updated: 2020-10-27T12:09:57Z
has_accepted_license: '1'
intvolume: ' 33'
isi: 1
issue: '11'
language:
- iso: eng
license: https://creativecommons.org/licenses/by/3.0/
month: '11'
oa: 1
oa_version: Published Version
page: 5733-5772
publication: Nonlinearity
publication_identifier:
eissn:
- 1361-6544
issn:
- 0951-7715
publication_status: published
publisher: IOP Publishing
quality_controlled: '1'
scopus_import: '1'
status: public
title: Variance reduction for effective energies of random lattices in the Thomas-Fermi-von
Weizsäcker model
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/3.0/legalcode
name: Creative Commons Attribution 3.0 Unported (CC BY 3.0)
short: CC BY (3.0)
type: journal_article
user_id: ba8df636-2132-11f1-aed0-ed93e2281fdd
volume: 33
year: '2020'
...
---
_id: '9208'
abstract:
- lang: eng
text: 'Bending-active structures are able to efficiently produce complex curved
shapes from flat panels. The desired deformation of the panels derives from the
proper selection of their elastic properties. Optimized panels, called FlexMaps,
are designed such that, once they are bent and assembled, the resulting static
equilibrium configuration matches a desired input 3D shape. The FlexMaps elastic
properties are controlled by locally varying spiraling geometric mesostructures,
which are optimized in size and shape to match specific bending requests, namely
the global curvature of the target shape. The design pipeline starts from a quad
mesh representing the input 3D shape, which defines the edge size and the total
amount of spirals: every quad will embed one spiral. Then, an optimization algorithm
tunes the geometry of the spirals by using a simplified pre-computed rod model.
This rod model is derived from a non-linear regression algorithm which approximates
the non-linear behavior of solid FEM spiral models subject to hundreds of load
combinations. This innovative pipeline has been applied to the project of a lightweight
plywood pavilion named FlexMaps Pavilion, which is a single-layer piecewise twisted
arch that fits a bounding box of 3.90x3.96x3.25 meters. This case study serves
to test the applicability of this methodology at the architectural scale. The
structure is validated via FE analyses and the fabrication of the full scale prototype.'
acknowledgement: 'The FlexMaps Pavilion has been awarded First Prize at the “Competition
and Exhibition of innovative lightweight structures” organized by the IASS Working
Group 21 within the FORM and FORCE, joint international conference of IASS Symposium
2019 and Structural Membranes 2019 (Barcelona, 7-11 October 2019) with the following
motivation: “for its structural innovation of bending-twisting system, connection
constructability and exquisite craftmanship”[20]. The authors would like to acknowledge
the Visual Computing Lab Staff of ISTI - CNR, in particular Thomas Alderighi, Marco
Callieri, Paolo Pingi; Antonio Rizzo of IPCF - CNR; and the Administrative Staff
of ISTI - CNR. This research was partially funded by the EU H2020 Programme EVOCATION:
Advanced Visual and Geometric Computing for 3D Capture, Display, and Fabrication
(grant no. 813170).'
article_number: '1505'
article_processing_charge: No
article_type: original
author:
- first_name: Francesco
full_name: Laccone, Francesco
last_name: Laccone
- first_name: Luigi
full_name: Malomo, Luigi
last_name: Malomo
- first_name: Jesus
full_name: Perez Rodriguez, Jesus
id: 2DC83906-F248-11E8-B48F-1D18A9856A87
last_name: Perez Rodriguez
- first_name: Nico
full_name: Pietroni, Nico
last_name: Pietroni
- first_name: Federico
full_name: Ponchio, Federico
last_name: Ponchio
- first_name: Bernd
full_name: Bickel, Bernd
id: 49876194-F248-11E8-B48F-1D18A9856A87
last_name: Bickel
orcid: 0000-0001-6511-9385
- first_name: Paolo
full_name: Cignoni, Paolo
last_name: Cignoni
citation:
ama: 'Laccone F, Malomo L, Perez Rodriguez J, et al. A bending-active twisted-arch
plywood structure: Computational design and fabrication of the FlexMaps Pavilion.
SN Applied Sciences. 2020;2(9). doi:10.1007/s42452-020-03305-w'
apa: 'Laccone, F., Malomo, L., Perez Rodriguez, J., Pietroni, N., Ponchio, F., Bickel,
B., & Cignoni, P. (2020). A bending-active twisted-arch plywood structure:
Computational design and fabrication of the FlexMaps Pavilion. SN Applied Sciences.
Springer Nature. https://doi.org/10.1007/s42452-020-03305-w'
chicago: 'Laccone, Francesco, Luigi Malomo, Jesus Perez Rodriguez, Nico Pietroni,
Federico Ponchio, Bernd Bickel, and Paolo Cignoni. “A Bending-Active Twisted-Arch
Plywood Structure: Computational Design and Fabrication of the FlexMaps Pavilion.”
SN Applied Sciences. Springer Nature, 2020. https://doi.org/10.1007/s42452-020-03305-w.'
ieee: 'F. Laccone et al., “A bending-active twisted-arch plywood structure:
Computational design and fabrication of the FlexMaps Pavilion,” SN Applied
Sciences, vol. 2, no. 9. Springer Nature, 2020.'
ista: 'Laccone F, Malomo L, Perez Rodriguez J, Pietroni N, Ponchio F, Bickel B,
Cignoni P. 2020. A bending-active twisted-arch plywood structure: Computational
design and fabrication of the FlexMaps Pavilion. SN Applied Sciences. 2(9), 1505.'
mla: 'Laccone, Francesco, et al. “A Bending-Active Twisted-Arch Plywood Structure:
Computational Design and Fabrication of the FlexMaps Pavilion.” SN Applied
Sciences, vol. 2, no. 9, 1505, Springer Nature, 2020, doi:10.1007/s42452-020-03305-w.'
short: F. Laccone, L. Malomo, J. Perez Rodriguez, N. Pietroni, F. Ponchio, B. Bickel,
P. Cignoni, SN Applied Sciences 2 (2020).
date_created: 2021-02-28T23:01:25Z
date_published: 2020-09-01T00:00:00Z
date_updated: 2026-04-02T14:31:49Z
day: '01'
department:
- _id: BeBi
doi: 10.1007/s42452-020-03305-w
intvolume: ' 2'
issue: '9'
language:
- iso: eng
month: '09'
oa_version: None
publication: SN Applied Sciences
publication_identifier:
eissn:
- 2523-3971
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
scopus_import: '1'
status: public
title: 'A bending-active twisted-arch plywood structure: Computational design and
fabrication of the FlexMaps Pavilion'
type: journal_article
user_id: ba8df636-2132-11f1-aed0-ed93e2281fdd
volume: 2
year: '2020'
...
---
_id: '8336'
abstract:
- lang: eng
text: Plant hormone cytokinins are perceived by a subfamily of sensor histidine
kinases (HKs), which via a two-component phosphorelay cascade activate transcriptional
responses in the nucleus. Subcellular localization of the receptors proposed the
endoplasmic reticulum (ER) membrane as a principal cytokinin perception site,
while study of cytokinin transport pointed to the plasma membrane (PM)-mediated
cytokinin signalling. Here, by detailed monitoring of subcellular localizations
of the fluorescently labelled natural cytokinin probe and the receptor ARABIDOPSIS
HISTIDINE KINASE 4 (CRE1/AHK4) fused to GFP reporter, we show that pools of the
ER-located cytokinin receptors can enter the secretory pathway and reach the PM
in cells of the root apical meristem, and the cell plate of dividing meristematic
cells. Brefeldin A (BFA) experiments revealed vesicular recycling of the receptor
and its accumulation in BFA compartments. We provide a revised view on cytokinin
signalling and the possibility of multiple sites of perception at PM and ER.
acknowledged_ssus:
- _id: Bio
- _id: LifeSc
acknowledgement: This paper is dedicated to deceased P. Galuszka for his support and
contribution to the project. This research was supported by the Scientific Service
Units (SSU) of IST-Austria through resources provided by the Bioimaging Facility
(BIF), the Life Science Facility (LSF) and by Centre of the Region Haná (CRH), Palacký
University. We thank Lucia Hlusková, Zuzana Pěkná and Martin Hönig for technical
assistance, and Fernando Aniento, Rashed Abualia and Andrej Hurný for sharing material.
The work was supported from ERDF project “Plants as a tool for sustainable global
development” (No. CZ.02.1.01/0.0/0.0/16_019/0000827), from Czech Science Foundation
via projects 16-04184S (O.P., K.K. and K.D.), 18-23972Y (D.Z., K.K.), 17-21122S
(K.B.), Erasmus+ (K.K.), Endowment Fund of Palacký University (K.K.) and EMBO Long-Term
Fellowship, ALTF number 710-2016 (J.C.M.); People Programme (Marie Curie Actions)
of the European Union’s Seventh Framework Programme (FP7/2007-2013) under REA grant
agreement no. [291734] (N.C.); DOC Fellowship of the Austrian Academy of Sciences
at the Institute of Science and Technology, Austria (H.S.).
article_number: '4285'
article_processing_charge: No
article_type: original
author:
- first_name: Karolina
full_name: Kubiasova, Karolina
id: 946011F4-3E71-11EA-860B-C7A73DDC885E
last_name: Kubiasova
orcid: 0000-0001-5630-9419
- first_name: Juan C
full_name: Montesinos López, Juan C
id: 310A8E3E-F248-11E8-B48F-1D18A9856A87
last_name: Montesinos López
orcid: 0000-0001-9179-6099
- first_name: Olga
full_name: Šamajová, Olga
last_name: Šamajová
- first_name: Jaroslav
full_name: Nisler, Jaroslav
last_name: Nisler
- first_name: Václav
full_name: Mik, Václav
last_name: Mik
- first_name: Hana
full_name: Semeradova, Hana
id: 42FE702E-F248-11E8-B48F-1D18A9856A87
last_name: Semeradova
- first_name: Lucie
full_name: Plíhalová, Lucie
last_name: Plíhalová
- first_name: Ondřej
full_name: Novák, Ondřej
last_name: Novák
- first_name: Peter
full_name: Marhavý, Peter
id: 3F45B078-F248-11E8-B48F-1D18A9856A87
last_name: Marhavý
orcid: 0000-0001-5227-5741
- first_name: Nicola
full_name: Cavallari, Nicola
id: 457160E6-F248-11E8-B48F-1D18A9856A87
last_name: Cavallari
- first_name: David
full_name: Zalabák, David
last_name: Zalabák
- first_name: Karel
full_name: Berka, Karel
last_name: Berka
- first_name: Karel
full_name: Doležal, Karel
last_name: Doležal
- first_name: Petr
full_name: Galuszka, Petr
last_name: Galuszka
- first_name: Jozef
full_name: Šamaj, Jozef
last_name: Šamaj
- first_name: Miroslav
full_name: Strnad, Miroslav
last_name: Strnad
- first_name: Eva
full_name: Benková, Eva
id: 38F4F166-F248-11E8-B48F-1D18A9856A87
last_name: Benková
orcid: 0000-0002-8510-9739
- first_name: Ondřej
full_name: Plíhal, Ondřej
last_name: Plíhal
- first_name: Lukáš
full_name: Spíchal, Lukáš
last_name: Spíchal
citation:
ama: Kubiasova K, Montesinos López JC, Šamajová O, et al. Cytokinin fluoroprobe
reveals multiple sites of cytokinin perception at plasma membrane and endoplasmic
reticulum. Nature Communications. 2020;11. doi:10.1038/s41467-020-17949-0
apa: Kubiasova, K., Montesinos López, J. C., Šamajová, O., Nisler, J., Mik, V.,
Semerádová, H., … Spíchal, L. (2020). Cytokinin fluoroprobe reveals multiple sites
of cytokinin perception at plasma membrane and endoplasmic reticulum. Nature
Communications. Springer Nature. https://doi.org/10.1038/s41467-020-17949-0
chicago: Kubiasova, Karolina, Juan C Montesinos López, Olga Šamajová, Jaroslav Nisler,
Václav Mik, Hana Semerádová, Lucie Plíhalová, et al. “Cytokinin Fluoroprobe Reveals
Multiple Sites of Cytokinin Perception at Plasma Membrane and Endoplasmic Reticulum.”
Nature Communications. Springer Nature, 2020. https://doi.org/10.1038/s41467-020-17949-0.
ieee: K. Kubiasova et al., “Cytokinin fluoroprobe reveals multiple sites
of cytokinin perception at plasma membrane and endoplasmic reticulum,” Nature
Communications, vol. 11. Springer Nature, 2020.
ista: Kubiasova K, Montesinos López JC, Šamajová O, Nisler J, Mik V, Semerádová
H, Plíhalová L, Novák O, Marhavý P, Cavallari N, Zalabák D, Berka K, Doležal K,
Galuszka P, Šamaj J, Strnad M, Benková E, Plíhal O, Spíchal L. 2020. Cytokinin
fluoroprobe reveals multiple sites of cytokinin perception at plasma membrane
and endoplasmic reticulum. Nature Communications. 11, 4285.
mla: Kubiasova, Karolina, et al. “Cytokinin Fluoroprobe Reveals Multiple Sites of
Cytokinin Perception at Plasma Membrane and Endoplasmic Reticulum.” Nature
Communications, vol. 11, 4285, Springer Nature, 2020, doi:10.1038/s41467-020-17949-0.
short: K. Kubiasova, J.C. Montesinos López, O. Šamajová, J. Nisler, V. Mik, H. Semerádová,
L. Plíhalová, O. Novák, P. Marhavý, N. Cavallari, D. Zalabák, K. Berka, K. Doležal,
P. Galuszka, J. Šamaj, M. Strnad, E. Benková, O. Plíhal, L. Spíchal, Nature Communications
11 (2020).
corr_author: '1'
date_created: 2020-09-06T22:01:12Z
date_published: 2020-08-27T00:00:00Z
date_updated: 2026-04-02T14:35:13Z
day: '27'
ddc:
- '580'
department:
- _id: EvBe
doi: 10.1038/s41467-020-17949-0
ec_funded: 1
external_id:
isi:
- '000567931000002'
pmid:
- '32855390'
file:
- access_level: open_access
checksum: 7494b7665b3d2bf2d8edb13e4f12b92d
content_type: application/pdf
creator: dernst
date_created: 2020-09-10T08:05:19Z
date_updated: 2020-09-10T08:05:19Z
file_id: '8357'
file_name: 2020_NatureComm_Kubiasova.pdf
file_size: 3455704
relation: main_file
success: 1
file_date_updated: 2020-09-10T08:05:19Z
has_accepted_license: '1'
intvolume: ' 11'
isi: 1
language:
- iso: eng
month: '08'
oa: 1
oa_version: Published Version
pmid: 1
project:
- _id: 25681D80-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '291734'
name: International IST Postdoc Fellowship Programme
- _id: 261821BC-B435-11E9-9278-68D0E5697425
grant_number: '24746'
name: Molecular mechanisms of the cytokinin regulated endomembrane trafficking to
coordinate plant organogenesis
- _id: 253E54C8-B435-11E9-9278-68D0E5697425
grant_number: ALTF710-2016
name: Molecular mechanism of auxindriven formative divisions delineating lateral
root organogenesis in plants
publication: Nature Communications
publication_identifier:
eissn:
- 2041-1723
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
scopus_import: '1'
status: public
title: Cytokinin fluoroprobe reveals multiple sites of cytokinin perception at plasma
membrane and endoplasmic reticulum
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: ba8df636-2132-11f1-aed0-ed93e2281fdd
volume: 11
year: '2020'
...
---
_id: '7582'
abstract:
- lang: eng
text: Small RNAs (smRNA, 19–25 nucleotides long), which are transcribed by RNA polymerase
II, regulate the expression of genes involved in a multitude of processes in eukaryotes.
miRNA biogenesis and the proteins involved in the biogenesis pathway differ across
plant and animal lineages. The major proteins constituting the biogenesis pathway,
namely, the Dicers (DCL/DCR) and Argonautes (AGOs), have been extensively studied.
However, the accessory proteins (DAWDLE (DDL), SERRATE (SE), and TOUGH (TGH))
of the pathway that differs across the two lineages remain largely uncharacterized.
We present the first detailed report on the molecular evolution and divergence
of these proteins across eukaryotes. Although DDL is present in eukaryotes and
prokaryotes, SE and TGH appear to be specific to eukaryotes. The addition/deletion
of specific domains and/or domain-specific sequence divergence in the three proteins
points to the observed functional divergence of these proteins across the two
lineages, which correlates with the differences in miRNA length across the two
lineages. Our data enhance the current understanding of the structure–function
relationship of these proteins and reveals previous unexplored crucial residues
in the three proteins that can be used as a basis for further functional characterization.
The data presented here on the number of miRNAs in crown eukaryotic lineages are
consistent with the notion of the expansion of the number of miRNA-coding genes
in animal and plant lineages correlating with organismal complexity. Whether this
difference in functionally correlates with the diversification (or presence/absence)
of the three proteins studied here or the miRNA signaling in the plant and animal
lineages is unclear. Based on our results of the three proteins studied here and
previously available data concerning the evolution of miRNA genes in the plant
and animal lineages, we believe that miRNAs probably evolved once in the ancestor
to crown eukaryotes and have diversified independently in the eukaryotes.
article_number: '299'
article_processing_charge: No
article_type: original
author:
- first_name: Taraka Ramji
full_name: Moturu, Taraka Ramji
last_name: Moturu
- first_name: Sansrity
full_name: Sinha, Sansrity
last_name: Sinha
- first_name: Hymavathi
full_name: Salava, Hymavathi
last_name: Salava
- first_name: Sravankumar
full_name: Thula, Sravankumar
last_name: Thula
- first_name: Tomasz
full_name: Nodzyński, Tomasz
last_name: Nodzyński
- first_name: Radka Svobodová
full_name: Vařeková, Radka Svobodová
last_name: Vařeková
- first_name: Jiří
full_name: Friml, Jiří
id: 4159519E-F248-11E8-B48F-1D18A9856A87
last_name: Friml
orcid: 0000-0002-8302-7596
- first_name: Sibu
full_name: Simon, Sibu
id: 4542EF9A-F248-11E8-B48F-1D18A9856A87
last_name: Simon
orcid: 0000-0002-1998-6741
citation:
ama: Moturu TR, Sinha S, Salava H, et al. Molecular evolution and diversification
of proteins involved in miRNA maturation pathway. Plants. 2020;9(3). doi:10.3390/plants9030299
apa: Moturu, T. R., Sinha, S., Salava, H., Thula, S., Nodzyński, T., Vařeková, R.
S., … Simon, S. (2020). Molecular evolution and diversification of proteins involved
in miRNA maturation pathway. Plants. MDPI. https://doi.org/10.3390/plants9030299
chicago: Moturu, Taraka Ramji, Sansrity Sinha, Hymavathi Salava, Sravankumar Thula,
Tomasz Nodzyński, Radka Svobodová Vařeková, Jiří Friml, and Sibu Simon. “Molecular
Evolution and Diversification of Proteins Involved in MiRNA Maturation Pathway.”
Plants. MDPI, 2020. https://doi.org/10.3390/plants9030299.
ieee: T. R. Moturu et al., “Molecular evolution and diversification of proteins
involved in miRNA maturation pathway,” Plants, vol. 9, no. 3. MDPI, 2020.
ista: Moturu TR, Sinha S, Salava H, Thula S, Nodzyński T, Vařeková RS, Friml J,
Simon S. 2020. Molecular evolution and diversification of proteins involved in
miRNA maturation pathway. Plants. 9(3), 299.
mla: Moturu, Taraka Ramji, et al. “Molecular Evolution and Diversification of Proteins
Involved in MiRNA Maturation Pathway.” Plants, vol. 9, no. 3, 299, MDPI,
2020, doi:10.3390/plants9030299.
short: T.R. Moturu, S. Sinha, H. Salava, S. Thula, T. Nodzyński, R.S. Vařeková,
J. Friml, S. Simon, Plants 9 (2020).
corr_author: '1'
date_created: 2020-03-15T23:00:52Z
date_published: 2020-03-01T00:00:00Z
date_updated: 2026-04-02T14:35:47Z
day: '01'
ddc:
- '580'
department:
- _id: JiFr
doi: 10.3390/plants9030299
ec_funded: 1
external_id:
isi:
- '000525315000035'
pmid:
- '32121542'
file:
- access_level: open_access
checksum: 6d5af3e17266a48996b4af4e67e88a85
content_type: application/pdf
creator: dernst
date_created: 2020-03-23T13:37:00Z
date_updated: 2020-07-14T12:48:00Z
file_id: '7614'
file_name: 2020_Plants_Moturu.pdf
file_size: 2373484
relation: main_file
file_date_updated: 2020-07-14T12:48:00Z
has_accepted_license: '1'
intvolume: ' 9'
isi: 1
issue: '3'
language:
- iso: eng
month: '03'
oa: 1
oa_version: Published Version
pmid: 1
project:
- _id: 25716A02-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '282300'
name: Polarity and subcellular dynamics in plants
publication: Plants
publication_identifier:
eissn:
- 2223-7747
publication_status: published
publisher: MDPI
quality_controlled: '1'
scopus_import: '1'
status: public
title: Molecular evolution and diversification of proteins involved in miRNA maturation
pathway
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: ba8df636-2132-11f1-aed0-ed93e2281fdd
volume: 9
year: '2020'
...
---
_id: '7957'
abstract:
- lang: eng
text: "Neurodevelopmental disorders (NDDs) are a class of disorders affecting brain
development and function and are characterized by wide genetic and clinical variability.
In this review, we discuss the multiple factors that influence the clinical presentation
of NDDs, with particular attention to gene vulnerability, mutational load, and
the two-hit model. Despite the complex architecture of\r\nmutational events associated
with NDDs, the various proteins involved appear to converge on common pathways,
such as synaptic plasticity/function, chromatin remodelers and the mammalian target
of rapamycin (mTOR) pathway. A thorough understanding of the mechanisms behind
these pathways will hopefully lead to the identification of candidates that could
be targeted for treatment approaches."
acknowledgement: We wish to thank Jasmin Morandell for generously sharing Figure 2.
This work was supported by the European Research Council Starting Grant (grant 715508
) to G.N.
article_processing_charge: No
article_type: original
author:
- first_name: Ilaria
full_name: Parenti, Ilaria
id: D93538B0-5B71-11E9-AC62-02EBE5697425
last_name: Parenti
- first_name: Luis E
full_name: Garcia Rabaneda, Luis E
id: 33D1B084-F248-11E8-B48F-1D18A9856A87
last_name: Garcia Rabaneda
- first_name: Hanna
full_name: Schön, Hanna
id: C8E17EDC-D7AA-11E9-B7B7-45ECE5697425
last_name: Schön
- first_name: Gaia
full_name: Novarino, Gaia
id: 3E57A680-F248-11E8-B48F-1D18A9856A87
last_name: Novarino
orcid: 0000-0002-7673-7178
citation:
ama: 'Parenti I, Garcia Rabaneda LE, Schön H, Novarino G. Neurodevelopmental disorders:
From genetics to functional pathways. Trends in Neurosciences. 2020;43(8):608-621.
doi:10.1016/j.tins.2020.05.004'
apa: 'Parenti, I., Garcia Rabaneda, L. E., Schön, H., & Novarino, G. (2020).
Neurodevelopmental disorders: From genetics to functional pathways. Trends
in Neurosciences. Elsevier. https://doi.org/10.1016/j.tins.2020.05.004'
chicago: 'Parenti, Ilaria, Luis E Garcia Rabaneda, Hanna Schön, and Gaia Novarino.
“Neurodevelopmental Disorders: From Genetics to Functional Pathways.” Trends
in Neurosciences. Elsevier, 2020. https://doi.org/10.1016/j.tins.2020.05.004.'
ieee: 'I. Parenti, L. E. Garcia Rabaneda, H. Schön, and G. Novarino, “Neurodevelopmental
disorders: From genetics to functional pathways,” Trends in Neurosciences,
vol. 43, no. 8. Elsevier, pp. 608–621, 2020.'
ista: 'Parenti I, Garcia Rabaneda LE, Schön H, Novarino G. 2020. Neurodevelopmental
disorders: From genetics to functional pathways. Trends in Neurosciences. 43(8),
608–621.'
mla: 'Parenti, Ilaria, et al. “Neurodevelopmental Disorders: From Genetics to Functional
Pathways.” Trends in Neurosciences, vol. 43, no. 8, Elsevier, 2020, pp.
608–21, doi:10.1016/j.tins.2020.05.004.'
short: I. Parenti, L.E. Garcia Rabaneda, H. Schön, G. Novarino, Trends in Neurosciences
43 (2020) 608–621.
corr_author: '1'
date_created: 2020-06-14T22:00:49Z
date_published: 2020-08-01T00:00:00Z
date_updated: 2026-04-02T14:36:06Z
day: '01'
ddc:
- '570'
department:
- _id: GaNo
doi: 10.1016/j.tins.2020.05.004
ec_funded: 1
external_id:
isi:
- '000553090600008'
pmid:
- '32507511'
file:
- access_level: open_access
checksum: 67db0251b1d415ae59005f876fcf9e34
content_type: application/pdf
creator: dernst
date_created: 2020-11-25T09:43:40Z
date_updated: 2020-11-25T09:43:40Z
file_id: '8805'
file_name: 2020_TrendsNeuroscience_Parenti.pdf
file_size: 1439550
relation: main_file
success: 1
file_date_updated: 2020-11-25T09:43:40Z
has_accepted_license: '1'
intvolume: ' 43'
isi: 1
issue: '8'
language:
- iso: eng
month: '08'
oa: 1
oa_version: Published Version
page: 608-621
pmid: 1
project:
- _id: 25444568-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '715508'
name: Probing the Reversibility of Autism Spectrum Disorders by Employing in vivo
and in vitro Models
publication: Trends in Neurosciences
publication_identifier:
eissn:
- 1878-108X
issn:
- 0166-2236
publication_status: published
publisher: Elsevier
quality_controlled: '1'
scopus_import: '1'
status: public
title: 'Neurodevelopmental disorders: From genetics to functional pathways'
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: ba8df636-2132-11f1-aed0-ed93e2281fdd
volume: 43
year: '2020'
...
---
_id: '8318'
abstract:
- lang: eng
text: Complex I is the first and the largest enzyme of respiratory chains in bacteria
and mitochondria. The mechanism which couples spatially separated transfer of
electrons to proton translocation in complex I is not known. Here we report five
crystal structures of T. thermophilus enzyme in complex with NADH or quinone-like
compounds. We also determined cryo-EM structures of major and minor native states
of the complex, differing in the position of the peripheral arm. Crystal structures
show that binding of quinone-like compounds (but not of NADH) leads to a related
global conformational change, accompanied by local re-arrangements propagating
from the quinone site to the nearest proton channel. Normal mode and molecular
dynamics analyses indicate that these are likely to represent the first steps
in the proton translocation mechanism. Our results suggest that quinone binding
and chemistry play a key role in the coupling mechanism of complex I.
acknowledgement: This work was funded by the Medical Research Council, UK and IST
Austria. We thank the European Synchrotron Radiation Facility and the Diamond Light
Source for provision of synchrotron radiation facilities. We are grateful to the
staff of beamlines ID29, ID23-2 (ESRF, Grenoble, France) and I03 (Diamond Light
Source, Didcot, UK) for assistance. Data processing was performed at the IST high-performance
computing cluster.
article_number: '4135'
article_processing_charge: No
article_type: original
author:
- first_name: Javier
full_name: Gutierrez-Fernandez, Javier
id: 3D9511BA-F248-11E8-B48F-1D18A9856A87
last_name: Gutierrez-Fernandez
- first_name: Karol
full_name: Kaszuba, Karol
id: 3FDF9472-F248-11E8-B48F-1D18A9856A87
last_name: Kaszuba
- first_name: Gurdeep S.
full_name: Minhas, Gurdeep S.
last_name: Minhas
- first_name: Rozbeh
full_name: Baradaran, Rozbeh
last_name: Baradaran
- first_name: Margherita
full_name: Tambalo, Margherita
id: 4187dfe4-ec23-11ea-ae46-f08ab378313a
last_name: Tambalo
- first_name: David T.
full_name: Gallagher, David T.
last_name: Gallagher
- first_name: Leonid A
full_name: Sazanov, Leonid A
id: 338D39FE-F248-11E8-B48F-1D18A9856A87
last_name: Sazanov
orcid: 0000-0002-0977-7989
citation:
ama: Gutierrez-Fernandez J, Kaszuba K, Minhas GS, et al. Key role of quinone in
the mechanism of respiratory complex I. Nature Communications. 2020;11(1).
doi:10.1038/s41467-020-17957-0
apa: Gutierrez-Fernandez, J., Kaszuba, K., Minhas, G. S., Baradaran, R., Tambalo,
M., Gallagher, D. T., & Sazanov, L. A. (2020). Key role of quinone in the
mechanism of respiratory complex I. Nature Communications. Springer Nature.
https://doi.org/10.1038/s41467-020-17957-0
chicago: Gutierrez-Fernandez, Javier, Karol Kaszuba, Gurdeep S. Minhas, Rozbeh Baradaran,
Margherita Tambalo, David T. Gallagher, and Leonid A Sazanov. “Key Role of Quinone
in the Mechanism of Respiratory Complex I.” Nature Communications. Springer
Nature, 2020. https://doi.org/10.1038/s41467-020-17957-0.
ieee: J. Gutierrez-Fernandez et al., “Key role of quinone in the mechanism
of respiratory complex I,” Nature Communications, vol. 11, no. 1. Springer
Nature, 2020.
ista: Gutierrez-Fernandez J, Kaszuba K, Minhas GS, Baradaran R, Tambalo M, Gallagher
DT, Sazanov LA. 2020. Key role of quinone in the mechanism of respiratory complex
I. Nature Communications. 11(1), 4135.
mla: Gutierrez-Fernandez, Javier, et al. “Key Role of Quinone in the Mechanism of
Respiratory Complex I.” Nature Communications, vol. 11, no. 1, 4135, Springer
Nature, 2020, doi:10.1038/s41467-020-17957-0.
short: J. Gutierrez-Fernandez, K. Kaszuba, G.S. Minhas, R. Baradaran, M. Tambalo,
D.T. Gallagher, L.A. Sazanov, Nature Communications 11 (2020).
date_created: 2020-08-30T22:01:10Z
date_published: 2020-08-18T00:00:00Z
date_updated: 2026-04-02T14:36:31Z
day: '18'
ddc:
- '570'
department:
- _id: LeSa
doi: 10.1038/s41467-020-17957-0
external_id:
isi:
- '000607072900001'
pmid:
- '32811817'
file:
- access_level: open_access
checksum: 52b96f41d7d0db9728064c08da00d030
content_type: application/pdf
creator: cziletti
date_created: 2020-08-31T13:40:00Z
date_updated: 2020-08-31T13:40:00Z
file_id: '8326'
file_name: 2020_NatComm_Gutierrez-Fernandez.pdf
file_size: 7527373
relation: main_file
success: 1
file_date_updated: 2020-08-31T13:40:00Z
has_accepted_license: '1'
intvolume: ' 11'
isi: 1
issue: '1'
language:
- iso: eng
month: '08'
oa: 1
oa_version: Published Version
pmid: 1
publication: Nature Communications
publication_identifier:
eissn:
- 2041-1723
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
related_material:
link:
- description: News on IST Homepage
relation: press_release
url: https://ist.ac.at/en/news/mystery-of-giant-proton-pump-solved/
scopus_import: '1'
status: public
title: Key role of quinone in the mechanism of respiratory complex I
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: ba8df636-2132-11f1-aed0-ed93e2281fdd
volume: 11
year: '2020'
...
---
_id: '7882'
abstract:
- lang: eng
text: A few-body cluster is a building block of a many-body system in a gas phase
provided the temperature at most is of the order of the binding energy of this
cluster. Here we illustrate this statement by considering a system of tubes filled
with dipolar distinguishable particles. We calculate the partition function, which
determines the probability to find a few-body cluster at a given temperature.
The input for our calculations—the energies of few-body clusters—is estimated
using the harmonic approximation. We first describe and demonstrate the validity
of our numerical procedure. Then we discuss the results featuring melting of the
zero-temperature many-body state into a gas of free particles and few-body clusters.
For temperature higher than its binding energy threshold, the dimers overwhelmingly
dominate the ensemble, where the remaining probability is in free particles. At
very high temperatures free (harmonic oscillator trap-bound) particle dominance
is eventually reached. This structure evolution appears both for one and two particles
in each layer providing crucial information about the behavior of ultracold dipolar
gases. The investigation addresses the transition region between few- and many-body
physics as a function of temperature using a system of ten dipoles in five tubes.
article_number: '484'
article_processing_charge: No
article_type: original
author:
- first_name: Jeremy R.
full_name: Armstrong, Jeremy R.
last_name: Armstrong
- first_name: Aksel S.
full_name: Jensen, Aksel S.
last_name: Jensen
- first_name: Artem
full_name: Volosniev, Artem
id: 37D278BC-F248-11E8-B48F-1D18A9856A87
last_name: Volosniev
orcid: 0000-0003-0393-5525
- first_name: Nikolaj T.
full_name: Zinner, Nikolaj T.
last_name: Zinner
citation:
ama: Armstrong JR, Jensen AS, Volosniev A, Zinner NT. Clusters in separated tubes
of tilted dipoles. Mathematics. 2020;8(4). doi:10.3390/math8040484
apa: Armstrong, J. R., Jensen, A. S., Volosniev, A., & Zinner, N. T. (2020).
Clusters in separated tubes of tilted dipoles. Mathematics. MDPI. https://doi.org/10.3390/math8040484
chicago: Armstrong, Jeremy R., Aksel S. Jensen, Artem Volosniev, and Nikolaj T.
Zinner. “Clusters in Separated Tubes of Tilted Dipoles.” Mathematics. MDPI,
2020. https://doi.org/10.3390/math8040484.
ieee: J. R. Armstrong, A. S. Jensen, A. Volosniev, and N. T. Zinner, “Clusters in
separated tubes of tilted dipoles,” Mathematics, vol. 8, no. 4. MDPI, 2020.
ista: Armstrong JR, Jensen AS, Volosniev A, Zinner NT. 2020. Clusters in separated
tubes of tilted dipoles. Mathematics. 8(4), 484.
mla: Armstrong, Jeremy R., et al. “Clusters in Separated Tubes of Tilted Dipoles.”
Mathematics, vol. 8, no. 4, 484, MDPI, 2020, doi:10.3390/math8040484.
short: J.R. Armstrong, A.S. Jensen, A. Volosniev, N.T. Zinner, Mathematics 8 (2020).
date_created: 2020-05-24T22:01:00Z
date_published: 2020-04-01T00:00:00Z
date_updated: 2026-04-02T14:33:47Z
day: '01'
ddc:
- '510'
department:
- _id: MiLe
doi: 10.3390/math8040484
ec_funded: 1
external_id:
isi:
- '000531824100024'
file:
- access_level: open_access
checksum: a05a7df724522203d079673a0d4de4bc
content_type: application/pdf
creator: dernst
date_created: 2020-05-25T14:42:22Z
date_updated: 2020-07-14T12:48:04Z
file_id: '7887'
file_name: 2020_Mathematics_Armstrong.pdf
file_size: 990540
relation: main_file
file_date_updated: 2020-07-14T12:48:04Z
has_accepted_license: '1'
intvolume: ' 8'
isi: 1
issue: '4'
language:
- iso: eng
month: '04'
oa: 1
oa_version: Published Version
project:
- _id: 260C2330-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '754411'
name: ISTplus - Postdoctoral Fellowships
publication: Mathematics
publication_identifier:
eissn:
- 2227-7390
publication_status: published
publisher: MDPI
quality_controlled: '1'
scopus_import: '1'
status: public
title: Clusters in separated tubes of tilted dipoles
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: ba8df636-2132-11f1-aed0-ed93e2281fdd
volume: 8
year: '2020'
...
---
_id: '8036'
abstract:
- lang: eng
text: When tiny soft ferromagnetic particles are placed along a liquid interface
and exposed to a vertical magnetic field, the balance between capillary attraction
and magnetic repulsion leads to self-organization into well-defined patterns.
Here, we demonstrate experimentally that precessing magnetic fields induce metachronal
waves on the periphery of these assemblies, similar to the ones observed in ciliates
and some arthropods. The outermost layer of particles behaves like an array of
cilia or legs whose sequential movement causes a net and controllable locomotion.
This bioinspired many-particle swimming strategy is effective even at low Reynolds
number, using only spatially uniform fields to generate the waves.
article_number: '112'
article_processing_charge: No
article_type: original
author:
- first_name: Ylona
full_name: Collard, Ylona
last_name: Collard
- first_name: Galien M
full_name: Grosjean, Galien M
id: 0C5FDA4A-9CF6-11E9-8939-FF05E6697425
last_name: Grosjean
orcid: 0000-0001-5154-417X
- first_name: Nicolas
full_name: Vandewalle, Nicolas
last_name: Vandewalle
citation:
ama: Collard Y, Grosjean GM, Vandewalle N. Magnetically powered metachronal waves
induce locomotion in self-assemblies. Communications Physics. 2020;3. doi:10.1038/s42005-020-0380-9
apa: Collard, Y., Grosjean, G. M., & Vandewalle, N. (2020). Magnetically powered
metachronal waves induce locomotion in self-assemblies. Communications Physics.
Springer Nature. https://doi.org/10.1038/s42005-020-0380-9
chicago: Collard, Ylona, Galien M Grosjean, and Nicolas Vandewalle. “Magnetically
Powered Metachronal Waves Induce Locomotion in Self-Assemblies.” Communications
Physics. Springer Nature, 2020. https://doi.org/10.1038/s42005-020-0380-9.
ieee: Y. Collard, G. M. Grosjean, and N. Vandewalle, “Magnetically powered metachronal
waves induce locomotion in self-assemblies,” Communications Physics, vol.
3. Springer Nature, 2020.
ista: Collard Y, Grosjean GM, Vandewalle N. 2020. Magnetically powered metachronal
waves induce locomotion in self-assemblies. Communications Physics. 3, 112.
mla: Collard, Ylona, et al. “Magnetically Powered Metachronal Waves Induce Locomotion
in Self-Assemblies.” Communications Physics, vol. 3, 112, Springer Nature,
2020, doi:10.1038/s42005-020-0380-9.
short: Y. Collard, G.M. Grosjean, N. Vandewalle, Communications Physics 3 (2020).
date_created: 2020-06-29T07:59:35Z
date_published: 2020-06-19T00:00:00Z
date_updated: 2026-04-02T14:34:21Z
day: '19'
ddc:
- '530'
department:
- _id: ScWa
doi: 10.1038/s42005-020-0380-9
ec_funded: 1
external_id:
isi:
- '000543328000002'
file:
- access_level: open_access
checksum: ed984f7a393f19140b5279a54a3336ad
content_type: application/pdf
creator: cziletti
date_created: 2020-06-29T13:21:24Z
date_updated: 2020-07-14T12:48:08Z
file_id: '8045'
file_name: 2020_CommunicationsPhysics_Collard.pdf
file_size: 1907821
relation: main_file
file_date_updated: 2020-07-14T12:48:08Z
has_accepted_license: '1'
intvolume: ' 3'
isi: 1
language:
- iso: eng
month: '06'
oa: 1
oa_version: Published Version
project:
- _id: 260C2330-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '754411'
name: ISTplus - Postdoctoral Fellowships
publication: Communications Physics
publication_identifier:
eissn:
- 2399-3650
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
scopus_import: '1'
status: public
title: Magnetically powered metachronal waves induce locomotion in self-assemblies
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: ba8df636-2132-11f1-aed0-ed93e2281fdd
volume: 3
year: '2020'
...
---
_id: '9630'
abstract:
- lang: eng
text: Various kinds of data are routinely represented as discrete probability distributions.
Examples include text documents summarized by histograms of word occurrences and
images represented as histograms of oriented gradients. Viewing a discrete probability
distribution as a point in the standard simplex of the appropriate dimension,
we can understand collections of such objects in geometric and topological terms. Importantly,
instead of using the standard Euclidean distance, we look into dissimilarity measures
with information-theoretic justification, and we develop the theory needed for
applying topological data analysis in this setting. In doing so, we emphasize
constructions that enable the usage of existing computational topology software
in this context.
acknowledgement: This research is partially supported by the Office of Naval Research,
through grant no. N62909-18-1-2038, and the DFG Collaborative Research Center TRR
109, ‘Discretization in Geometry and Dynamics’, through grant no. I02979-N35 of
the Austrian Science Fund (FWF).
article_processing_charge: Yes
article_type: original
author:
- first_name: Herbert
full_name: Edelsbrunner, Herbert
id: 3FB178DA-F248-11E8-B48F-1D18A9856A87
last_name: Edelsbrunner
orcid: 0000-0002-9823-6833
- first_name: Ziga
full_name: Virk, Ziga
id: 2E36B656-F248-11E8-B48F-1D18A9856A87
last_name: Virk
- first_name: Hubert
full_name: Wagner, Hubert
id: 379CA8B8-F248-11E8-B48F-1D18A9856A87
last_name: Wagner
orcid: 0009-0009-9111-8429
citation:
ama: Edelsbrunner H, Virk Z, Wagner H. Topological data analysis in information
space. Journal of Computational Geometry. 2020;11(2):162-182. doi:10.20382/jocg.v11i2a7
apa: Edelsbrunner, H., Virk, Z., & Wagner, H. (2020). Topological data analysis
in information space. Journal of Computational Geometry. Carleton University.
https://doi.org/10.20382/jocg.v11i2a7
chicago: Edelsbrunner, Herbert, Ziga Virk, and Hubert Wagner. “Topological Data
Analysis in Information Space.” Journal of Computational Geometry. Carleton
University, 2020. https://doi.org/10.20382/jocg.v11i2a7.
ieee: H. Edelsbrunner, Z. Virk, and H. Wagner, “Topological data analysis in information
space,” Journal of Computational Geometry, vol. 11, no. 2. Carleton University,
pp. 162–182, 2020.
ista: Edelsbrunner H, Virk Z, Wagner H. 2020. Topological data analysis in information
space. Journal of Computational Geometry. 11(2), 162–182.
mla: Edelsbrunner, Herbert, et al. “Topological Data Analysis in Information Space.”
Journal of Computational Geometry, vol. 11, no. 2, Carleton University,
2020, pp. 162–82, doi:10.20382/jocg.v11i2a7.
short: H. Edelsbrunner, Z. Virk, H. Wagner, Journal of Computational Geometry 11
(2020) 162–182.
corr_author: '1'
date_created: 2021-07-04T22:01:26Z
date_published: 2020-12-14T00:00:00Z
date_updated: 2026-04-02T14:35:31Z
day: '14'
ddc:
- '510'
- '000'
department:
- _id: HeEd
doi: 10.20382/jocg.v11i2a7
file:
- access_level: open_access
checksum: f02d0b2b3838e7891a6c417fc34ffdcd
content_type: application/pdf
creator: asandaue
date_created: 2021-08-11T11:55:11Z
date_updated: 2021-08-11T11:55:11Z
file_id: '9882'
file_name: 2020_JournalOfComputationalGeometry_Edelsbrunner.pdf
file_size: 1449234
relation: main_file
success: 1
file_date_updated: 2021-08-11T11:55:11Z
has_accepted_license: '1'
intvolume: ' 11'
issue: '2'
language:
- iso: eng
month: '12'
oa: 1
oa_version: Published Version
page: 162-182
project:
- _id: 0aa4bc98-070f-11eb-9043-e6fff9c6a316
grant_number: I4887
name: Persistent Homology, Algorithms and Stochastic Geometry
publication: Journal of Computational Geometry
publication_identifier:
eissn:
- 1920-180X
publication_status: published
publisher: Carleton University
quality_controlled: '1'
scopus_import: '1'
status: public
title: Topological data analysis in information space
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/3.0/legalcode
name: Creative Commons Attribution 3.0 Unported (CC BY 3.0)
short: CC BY (3.0)
type: journal_article
user_id: ba8df636-2132-11f1-aed0-ed93e2281fdd
volume: 11
year: '2020'
...
---
_id: '8788'
abstract:
- lang: eng
text: 'We consider a real-time setting where an environment releases sequences of
firm-deadline tasks, and an online scheduler chooses on-the-fly the ones to execute
on a single processor so as to maximize cumulated utility. The competitive ratio
is a well-known performance measure for the scheduler: it gives the worst-case
ratio, among all possible choices for the environment, of the cumulated utility
of the online scheduler versus an offline scheduler that knows these choices in
advance. Traditionally, competitive analysis is performed by hand, while automated
techniques are rare and only handle static environments with independent tasks.
We present a quantitative-verification framework for precedence-aware competitive
analysis, where task releases may depend on preceding scheduling choices, i.e.,
the environment can respond to scheduling decisions dynamically . We consider
two general classes of precedences: 1) follower precedences force the release
of a dependent task upon the completion of a set of precursor tasks, while and
2) pairing precedences modify the characteristics of a dependent task provided
the completion of a set of precursor tasks. Precedences make competitive analysis
challenging, as the online and offline schedulers operate on diverging sequences.
We make a formal presentation of our framework, and use a GPU-based implementation
to analyze ten well-known schedulers on precedence-based application examples
taken from the existing literature: 1) a handshake protocol (HP); 2) network packet-switching;
3) query scheduling (QS); and 4) a sporadic-interrupt setting. Our experimental
results show that precedences and task parameters can vary drastically the best
scheduler. Our framework thus supports application designers in choosing the best
scheduler among a given set automatically.'
acknowledgement: 'This work was supported by the Austrian Science Foundation (FWF)
under the NFN RiSE/SHiNE under Grant S11405 and Grant S11407. This article was presented
in the International Conference on Embedded Software 2020 and appears as part of
the ESWEEK-TCAD special issue. '
article_processing_charge: No
article_type: original
author:
- first_name: Andreas
full_name: Pavlogiannis, Andreas
id: 49704004-F248-11E8-B48F-1D18A9856A87
last_name: Pavlogiannis
orcid: 0000-0002-8943-0722
- first_name: Nico
full_name: Schaumberger, Nico
last_name: Schaumberger
- first_name: Ulrich
full_name: Schmid, Ulrich
last_name: Schmid
- first_name: Krishnendu
full_name: Chatterjee, Krishnendu
id: 2E5DCA20-F248-11E8-B48F-1D18A9856A87
last_name: Chatterjee
orcid: 0000-0002-4561-241X
citation:
ama: Pavlogiannis A, Schaumberger N, Schmid U, Chatterjee K. Precedence-aware automated
competitive analysis of real-time scheduling. IEEE Transactions on Computer-Aided
Design of Integrated Circuits and Systems. 2020;39(11):3981-3992. doi:10.1109/TCAD.2020.3012803
apa: Pavlogiannis, A., Schaumberger, N., Schmid, U., & Chatterjee, K. (2020).
Precedence-aware automated competitive analysis of real-time scheduling. IEEE
Transactions on Computer-Aided Design of Integrated Circuits and Systems.
IEEE. https://doi.org/10.1109/TCAD.2020.3012803
chicago: Pavlogiannis, Andreas, Nico Schaumberger, Ulrich Schmid, and Krishnendu
Chatterjee. “Precedence-Aware Automated Competitive Analysis of Real-Time Scheduling.”
IEEE Transactions on Computer-Aided Design of Integrated Circuits and Systems.
IEEE, 2020. https://doi.org/10.1109/TCAD.2020.3012803.
ieee: A. Pavlogiannis, N. Schaumberger, U. Schmid, and K. Chatterjee, “Precedence-aware
automated competitive analysis of real-time scheduling,” IEEE Transactions
on Computer-Aided Design of Integrated Circuits and Systems, vol. 39, no.
11. IEEE, pp. 3981–3992, 2020.
ista: Pavlogiannis A, Schaumberger N, Schmid U, Chatterjee K. 2020. Precedence-aware
automated competitive analysis of real-time scheduling. IEEE Transactions on Computer-Aided
Design of Integrated Circuits and Systems. 39(11), 3981–3992.
mla: Pavlogiannis, Andreas, et al. “Precedence-Aware Automated Competitive Analysis
of Real-Time Scheduling.” IEEE Transactions on Computer-Aided Design of Integrated
Circuits and Systems, vol. 39, no. 11, IEEE, 2020, pp. 3981–92, doi:10.1109/TCAD.2020.3012803.
short: A. Pavlogiannis, N. Schaumberger, U. Schmid, K. Chatterjee, IEEE Transactions
on Computer-Aided Design of Integrated Circuits and Systems 39 (2020) 3981–3992.
date_created: 2020-11-22T23:01:24Z
date_published: 2020-11-01T00:00:00Z
date_updated: 2026-04-02T14:37:50Z
day: '01'
department:
- _id: KrCh
doi: 10.1109/TCAD.2020.3012803
external_id:
isi:
- '000587712700069'
intvolume: ' 39'
isi: 1
issue: '11'
language:
- iso: eng
month: '11'
oa_version: None
page: 3981-3992
project:
- _id: 25832EC2-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: S 11407_N23
name: Rigorous Systems Engineering
- _id: 25863FF4-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: S11407
name: Game Theory
publication: IEEE Transactions on Computer-Aided Design of Integrated Circuits and
Systems
publication_identifier:
eissn:
- 1937-4151
issn:
- 0278-0070
publication_status: published
publisher: IEEE
quality_controlled: '1'
scopus_import: '1'
status: public
title: Precedence-aware automated competitive analysis of real-time scheduling
type: journal_article
user_id: ba8df636-2132-11f1-aed0-ed93e2281fdd
volume: 39
year: '2020'
...
---
_id: '8337'
abstract:
- lang: eng
text: Cytokinins are mobile multifunctional plant hormones with roles in development
and stress resilience. Although their Histidine Kinase receptors are substantially
localised to the endoplasmic reticulum, cellular sites of cytokinin perception
and importance of spatially heterogeneous cytokinin distribution continue to be
debated. Here we show that cytokinin perception by plasma membrane receptors is
an effective additional path for cytokinin response. Readout from a Two Component
Signalling cytokinin-specific reporter (TCSn::GFP) closely matches intracellular
cytokinin content in roots, yet we also find cytokinins in extracellular fluid,
potentially enabling action at the cell surface. Cytokinins covalently linked
to beads that could not pass the plasma membrane increased expression of both
TCSn::GFP and Cytokinin Response Factors. Super-resolution microscopy of GFP-labelled
receptors and diminished TCSn::GFP response to immobilised cytokinins in cytokinin
receptor mutants, further indicate that receptors can function at the cell surface.
We argue that dual intracellular and surface locations may augment flexibility
of cytokinin responses.
acknowledged_ssus:
- _id: Bio
acknowledgement: 'We thank Bruno Müller and Aaron Rashotte for critical discussions
and provision of plant lines used in this work, Roger Granbom and Tamara Hernández
Verdeja (UPSC, Umeå, Sweden) for technical assistance and providing materials, Zuzana
Pěkná and Karolina Wojewodová (CRH, Palacký University, Olomouc, Czech Republic)
for help with cytokinin receptor binding assays, and David Zalabák (CRH, Palacký
University, Olomouc, Czech Republic) for provision of vector pINIIIΔEH expressing
CRE1/AHK4. The bioimaging facility of IST Austria, the Swedish Metabolomics Centre
and the IST Austria Bio-Imaging facility are acknowledged for support. The work
was funded by the European Molecular Biology Organization (EMBO ASTF 297-2013) (I.A.),
Development—The Company of Biologists (DEVTF2012) (I.A.; C.T.), Plant Fellows (the
International Post doc Fellowship Programme in Plant Sciences, 267423) (I.A.; K.L.),
the Swedish Research Council (621-2014-4514) (K.L.), UPSC Berzelii Center for Forest
Biotechnology (Vinnova 2012-01560), Kempestiftelserna (JCK-2711) (K.L.) and (JCK-1811)
(E.-M.B., K.L.). The Ministry of Education, Youth and Sports of the Czech Republic
via the European Regional Development Fund-Project “Plants as a tool for sustainable
global development” (CZ.02.1.01/0.0/0.0/16_019/0000827) (O.N., O.P., R.S., V.M.,
L.P., K.D.) and project CEITEC 2020 (LQ1601) (M.P., J.H.) provided support, as did
the Czech Science Foundation via projects GP14-30004P (M.P.) and 16-04184S (O.P.,
K.D., O.N.), Vetenskapsrådet and Vinnova (Verket för Innovationssystem) (T.V., S.R.),
Knut och Alice Wallenbergs Stiftelse via “Shapesystem” grant number 2012.0050. A.J.
was supported by the Austria Science Fund (FWF): I03630 to J.F. The research leading
to these results received funding from European Union’s Horizon 2020 programme (ERC
grant no. 742985) and FWO-FWF joint project G0E5718N to J.F.'
article_number: '4284'
article_processing_charge: No
article_type: original
author:
- first_name: Ioanna
full_name: Antoniadi, Ioanna
last_name: Antoniadi
- first_name: Ondřej
full_name: Novák, Ondřej
last_name: Novák
- first_name: Zuzana
full_name: Gelová, Zuzana
id: 0AE74790-0E0B-11E9-ABC7-1ACFE5697425
last_name: Gelová
orcid: 0000-0003-4783-1752
- first_name: Alexander J
full_name: Johnson, Alexander J
id: 46A62C3A-F248-11E8-B48F-1D18A9856A87
last_name: Johnson
orcid: 0000-0002-2739-8843
- first_name: Ondřej
full_name: Plíhal, Ondřej
last_name: Plíhal
- first_name: Radim
full_name: Simerský, Radim
last_name: Simerský
- first_name: Václav
full_name: Mik, Václav
last_name: Mik
- first_name: Thomas
full_name: Vain, Thomas
last_name: Vain
- first_name: Eduardo
full_name: Mateo-Bonmatí, Eduardo
last_name: Mateo-Bonmatí
- first_name: Michal
full_name: Karady, Michal
last_name: Karady
- first_name: Markéta
full_name: Pernisová, Markéta
last_name: Pernisová
- first_name: Lenka
full_name: Plačková, Lenka
last_name: Plačková
- first_name: Korawit
full_name: Opassathian, Korawit
last_name: Opassathian
- first_name: Jan
full_name: Hejátko, Jan
last_name: Hejátko
- first_name: Stéphanie
full_name: Robert, Stéphanie
last_name: Robert
- first_name: Jiří
full_name: Friml, Jiří
id: 4159519E-F248-11E8-B48F-1D18A9856A87
last_name: Friml
orcid: 0000-0002-8302-7596
- first_name: Karel
full_name: Doležal, Karel
last_name: Doležal
- first_name: Karin
full_name: Ljung, Karin
last_name: Ljung
- first_name: Colin
full_name: Turnbull, Colin
last_name: Turnbull
citation:
ama: Antoniadi I, Novák O, Gelová Z, et al. Cell-surface receptors enable perception
of extracellular cytokinins. Nature Communications. 2020;11. doi:10.1038/s41467-020-17700-9
apa: Antoniadi, I., Novák, O., Gelová, Z., Johnson, A. J., Plíhal, O., Simerský,
R., … Turnbull, C. (2020). Cell-surface receptors enable perception of extracellular
cytokinins. Nature Communications. Springer Nature. https://doi.org/10.1038/s41467-020-17700-9
chicago: Antoniadi, Ioanna, Ondřej Novák, Zuzana Gelová, Alexander J Johnson, Ondřej
Plíhal, Radim Simerský, Václav Mik, et al. “Cell-Surface Receptors Enable Perception
of Extracellular Cytokinins.” Nature Communications. Springer Nature, 2020.
https://doi.org/10.1038/s41467-020-17700-9.
ieee: I. Antoniadi et al., “Cell-surface receptors enable perception of extracellular
cytokinins,” Nature Communications, vol. 11. Springer Nature, 2020.
ista: Antoniadi I, Novák O, Gelová Z, Johnson AJ, Plíhal O, Simerský R, Mik V, Vain
T, Mateo-Bonmatí E, Karady M, Pernisová M, Plačková L, Opassathian K, Hejátko
J, Robert S, Friml J, Doležal K, Ljung K, Turnbull C. 2020. Cell-surface receptors
enable perception of extracellular cytokinins. Nature Communications. 11, 4284.
mla: Antoniadi, Ioanna, et al. “Cell-Surface Receptors Enable Perception of Extracellular
Cytokinins.” Nature Communications, vol. 11, 4284, Springer Nature, 2020,
doi:10.1038/s41467-020-17700-9.
short: I. Antoniadi, O. Novák, Z. Gelová, A.J. Johnson, O. Plíhal, R. Simerský,
V. Mik, T. Vain, E. Mateo-Bonmatí, M. Karady, M. Pernisová, L. Plačková, K. Opassathian,
J. Hejátko, S. Robert, J. Friml, K. Doležal, K. Ljung, C. Turnbull, Nature Communications
11 (2020).
date_created: 2020-09-06T22:01:13Z
date_published: 2020-08-27T00:00:00Z
date_updated: 2026-04-03T09:25:48Z
day: '27'
ddc:
- '580'
department:
- _id: JiFr
doi: 10.1038/s41467-020-17700-9
ec_funded: 1
external_id:
isi:
- '000567931000001'
pmid:
- '32855409'
file:
- access_level: open_access
checksum: 5b96f39b598de7510cfefefb819b9a6d
content_type: application/pdf
creator: dernst
date_created: 2020-12-10T12:23:56Z
date_updated: 2020-12-10T12:23:56Z
file_id: '8936'
file_name: 2020_NatureComm_Antoniadi.pdf
file_size: 3526415
relation: main_file
success: 1
file_date_updated: 2020-12-10T12:23:56Z
has_accepted_license: '1'
intvolume: ' 11'
isi: 1
language:
- iso: eng
month: '08'
oa: 1
oa_version: Published Version
pmid: 1
project:
- _id: 26538374-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: I03630
name: Molecular mechanisms of endocytic cargo recognition in plants
- _id: 261099A6-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '742985'
name: Tracing Evolution of Auxin Transport and Polarity in Plants
publication: Nature Communications
publication_identifier:
eissn:
- 2041-1723
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
scopus_import: '1'
status: public
title: Cell-surface receptors enable perception of extracellular cytokinins
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: ba8df636-2132-11f1-aed0-ed93e2281fdd
volume: 11
year: '2020'
...
---
_id: '8643'
abstract:
- lang: eng
text: The parabigeminal nucleus (PBG) is the mammalian homologue to the isthmic
complex of other vertebrates. Optogenetic stimulation of the PBG induces freezing
and escape in mice, a result thought to be caused by a PBG projection to the central
nucleus of the amygdala. However, the isthmic complex, including the PBG, has
been classically considered satellite nuclei of the Superior Colliculus (SC),
which upon stimulation of its medial part also triggers fear and avoidance reactions.
As the PBG-SC connectivity is not well characterized, we investigated whether
the topology of the PBG projection to the SC could be related to the behavioral
consequences of PBG stimulation. To that end, we performed immunohistochemistry,
in situ hybridization and neural tracer injections in the SC and PBG in a diurnal
rodent, the Octodon degus. We found that all PBG neurons expressed both glutamatergic
and cholinergic markers and were distributed in clearly defined anterior (aPBG)
and posterior (pPBG) subdivisions. The pPBG is connected reciprocally and topographically
to the ipsilateral SC, whereas the aPBG receives afferent axons from the ipsilateral
SC and projected exclusively to the contralateral SC. This contralateral projection
forms a dense field of terminals that is restricted to the medial SC, in correspondence
with the SC representation of the aerial binocular field which, we also found,
in O. degus prompted escape reactions upon looming stimulation. Therefore, this
specialized topography allows binocular interactions in the SC region controlling
responses to aerial predators, suggesting a link between the mechanisms by which
the SC and PBG produce defensive behaviors.
acknowledgement: 'We thank Elisa Sentis and Solano Henriquez for their expert technical
assistance. Dr. David Sterratt for his helpful advice in using the Retistruct package.
Dr. Joao Botelho for his valuable assistance in scanning the retinas. To Mrs. Diane
Greenstein for kindly reading and correcting our manuscript. Macarena Ruiz for her
helpful comments during figures elaboration. Dr. Alexia Nunez-Parra for kindly providing
us with the transgenic mouse line. Dr. Harald Luksch for granting us access to the
confocal microscope at his lab. This study was supported by: FONDECYT 1151432 (to
G.M.), FONDECYT 1170027 (to J.M.) and Doctoral fellowship CONICYT 21161599 (to A.D.).'
article_number: '16220'
article_processing_charge: No
article_type: original
author:
- first_name: Alfonso
full_name: Deichler, Alfonso
last_name: Deichler
- first_name: Denisse
full_name: Carrasco, Denisse
last_name: Carrasco
- first_name: Luciana
full_name: Lopez-Jury, Luciana
last_name: Lopez-Jury
- first_name: Tomas A
full_name: Vega Zuniga, Tomas A
id: 2E7C4E78-F248-11E8-B48F-1D18A9856A87
last_name: Vega Zuniga
- first_name: Natalia
full_name: Marquez, Natalia
last_name: Marquez
- first_name: Jorge
full_name: Mpodozis, Jorge
last_name: Mpodozis
- first_name: Gonzalo
full_name: Marin, Gonzalo
last_name: Marin
citation:
ama: Deichler A, Carrasco D, Lopez-Jury L, et al. A specialized reciprocal connectivity
suggests a link between the mechanisms by which the superior colliculus and parabigeminal
nucleus produce defensive behaviors in rodents. Scientific Reports. 2020;10.
doi:10.1038/s41598-020-72848-0
apa: Deichler, A., Carrasco, D., Lopez-Jury, L., Vega Zuniga, T. A., Marquez, N.,
Mpodozis, J., & Marin, G. (2020). A specialized reciprocal connectivity suggests
a link between the mechanisms by which the superior colliculus and parabigeminal
nucleus produce defensive behaviors in rodents. Scientific Reports. Springer
Nature. https://doi.org/10.1038/s41598-020-72848-0
chicago: Deichler, Alfonso, Denisse Carrasco, Luciana Lopez-Jury, Tomas A Vega Zuniga,
Natalia Marquez, Jorge Mpodozis, and Gonzalo Marin. “A Specialized Reciprocal
Connectivity Suggests a Link between the Mechanisms by Which the Superior Colliculus
and Parabigeminal Nucleus Produce Defensive Behaviors in Rodents.” Scientific
Reports. Springer Nature, 2020. https://doi.org/10.1038/s41598-020-72848-0.
ieee: A. Deichler et al., “A specialized reciprocal connectivity suggests
a link between the mechanisms by which the superior colliculus and parabigeminal
nucleus produce defensive behaviors in rodents,” Scientific Reports, vol.
10. Springer Nature, 2020.
ista: Deichler A, Carrasco D, Lopez-Jury L, Vega Zuniga TA, Marquez N, Mpodozis
J, Marin G. 2020. A specialized reciprocal connectivity suggests a link between
the mechanisms by which the superior colliculus and parabigeminal nucleus produce
defensive behaviors in rodents. Scientific Reports. 10, 16220.
mla: Deichler, Alfonso, et al. “A Specialized Reciprocal Connectivity Suggests a
Link between the Mechanisms by Which the Superior Colliculus and Parabigeminal
Nucleus Produce Defensive Behaviors in Rodents.” Scientific Reports, vol.
10, 16220, Springer Nature, 2020, doi:10.1038/s41598-020-72848-0.
short: A. Deichler, D. Carrasco, L. Lopez-Jury, T.A. Vega Zuniga, N. Marquez, J.
Mpodozis, G. Marin, Scientific Reports 10 (2020).
date_created: 2020-10-11T22:01:14Z
date_published: 2020-10-01T00:00:00Z
date_updated: 2026-04-03T09:26:41Z
day: '01'
ddc:
- '570'
department:
- _id: MaJö
doi: 10.1038/s41598-020-72848-0
external_id:
isi:
- '000577142600032'
pmid:
- '33004866'
file:
- access_level: open_access
checksum: f6dd99954f1c0ffb4da5a1d2d739bf31
content_type: application/pdf
creator: dernst
date_created: 2020-10-12T12:39:10Z
date_updated: 2020-10-12T12:39:10Z
file_id: '8651'
file_name: 2020_ScientificReport_Deichler.pdf
file_size: 3906744
relation: main_file
success: 1
file_date_updated: 2020-10-12T12:39:10Z
has_accepted_license: '1'
intvolume: ' 10'
isi: 1
language:
- iso: eng
month: '10'
oa: 1
oa_version: Published Version
pmid: 1
publication: Scientific Reports
publication_identifier:
eissn:
- 2045-2322
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
scopus_import: '1'
status: public
title: A specialized reciprocal connectivity suggests a link between the mechanisms
by which the superior colliculus and parabigeminal nucleus produce defensive behaviors
in rodents
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: ba8df636-2132-11f1-aed0-ed93e2281fdd
volume: 10
year: '2020'
...
---
_id: '8741'
abstract:
- lang: eng
text: "In ecology, climate and other fields, (sub)systems have been identified that
can transition into a qualitatively different state when a critical threshold
or tipping point in a driving process is crossed. An understanding of those tipping
elements is of great interest given the increasing influence of humans on the
biophysical Earth system. Complex interactions exist between tipping elements,
e.g. physical mechanisms connect subsystems of the climate system. Based on earlier
work on such coupled nonlinear systems, we systematically assessed the qualitative
long-term behaviour of interacting tipping elements. We developed an understanding
of the consequences of interactions\r\non the tipping behaviour allowing for tipping
cascades to emerge under certain conditions. The (narrative) application of\r\nthese
qualitative results to real-world examples of interacting tipping elements indicates
that tipping cascades with profound consequences may occur: the interacting Greenland
ice sheet and thermohaline ocean circulation might tip before the tipping points
of the isolated subsystems are crossed. The eutrophication of the first lake in
a lake chain might propagate through the following lakes without a crossing of
their individual critical nutrient input levels. The possibility of emerging cascading
tipping dynamics calls for the development of a unified theory of interacting
tipping elements and the quantitative analysis of interacting real-world tipping
elements."
acknowledgement: "V.K. thanks the German National Academic Foundation (Studienstiftung
des deutschen Volkes) for financial\r\nsupport. J.F.D. is grateful for financial
support by the Stordalen Foundation via the Planetary Boundary Research\r\nNetwork
(PB.net), the Earth League’s EarthDoc program and the European Research Council
Advanced Grant\r\nproject ERA (Earth Resilience in the Anthropocene). We are thankful
for support by the Leibniz Association\r\n(project DominoES).\r\nAcknowledgements.
This work has been performed in the context of the copan collaboration and the FutureLab
on Earth\r\nResilience in the Anthropocene at the Potsdam Institute for Climate
Impact Research. Furthermore, we acknowledge\r\ndiscussions with and helpful comments
by N. Wunderling, J. Heitzig and M. Wiedermann."
article_number: '200599'
article_processing_charge: No
article_type: original
arxiv: 1
author:
- first_name: Ann Kristin
full_name: Klose, Ann Kristin
last_name: Klose
- first_name: Volker
full_name: Karle, Volker
id: D7C012AE-D7ED-11E9-95E8-1EC5E5697425
last_name: Karle
orcid: 0000-0002-6963-0129
- first_name: Ricarda
full_name: Winkelmann, Ricarda
last_name: Winkelmann
- first_name: Jonathan F.
full_name: Donges, Jonathan F.
last_name: Donges
citation:
ama: 'Klose AK, Karle V, Winkelmann R, Donges JF. Emergence of cascading dynamics
in interacting tipping elements of ecology and climate: Cascading dynamics in
tipping elements. Royal Society Open Science. 2020;7(6). doi:10.1098/rsos.200599'
apa: 'Klose, A. K., Karle, V., Winkelmann, R., & Donges, J. F. (2020). Emergence
of cascading dynamics in interacting tipping elements of ecology and climate:
Cascading dynamics in tipping elements. Royal Society Open Science. The
Royal Society. https://doi.org/10.1098/rsos.200599'
chicago: 'Klose, Ann Kristin, Volker Karle, Ricarda Winkelmann, and Jonathan F.
Donges. “Emergence of Cascading Dynamics in Interacting Tipping Elements of Ecology
and Climate: Cascading Dynamics in Tipping Elements.” Royal Society Open Science.
The Royal Society, 2020. https://doi.org/10.1098/rsos.200599.'
ieee: 'A. K. Klose, V. Karle, R. Winkelmann, and J. F. Donges, “Emergence of cascading
dynamics in interacting tipping elements of ecology and climate: Cascading dynamics
in tipping elements,” Royal Society Open Science, vol. 7, no. 6. The Royal
Society, 2020.'
ista: 'Klose AK, Karle V, Winkelmann R, Donges JF. 2020. Emergence of cascading
dynamics in interacting tipping elements of ecology and climate: Cascading dynamics
in tipping elements. Royal Society Open Science. 7(6), 200599.'
mla: 'Klose, Ann Kristin, et al. “Emergence of Cascading Dynamics in Interacting
Tipping Elements of Ecology and Climate: Cascading Dynamics in Tipping Elements.”
Royal Society Open Science, vol. 7, no. 6, 200599, The Royal Society, 2020,
doi:10.1098/rsos.200599.'
short: A.K. Klose, V. Karle, R. Winkelmann, J.F. Donges, Royal Society Open Science
7 (2020).
date_created: 2020-11-08T23:01:25Z
date_published: 2020-06-01T00:00:00Z
date_updated: 2026-04-03T09:26:55Z
day: '01'
ddc:
- '530'
- '550'
department:
- _id: MiLe
doi: 10.1098/rsos.200599
external_id:
arxiv:
- '1910.12042'
isi:
- '000545625200001'
pmid:
- '32742700'
file:
- access_level: open_access
checksum: 5505c445de373bfd836eb4d3b48b1f37
content_type: application/pdf
creator: dernst
date_created: 2020-11-09T09:07:11Z
date_updated: 2020-11-09T09:07:11Z
file_id: '8748'
file_name: 2020_RoyalSocOpenScience_Klose.pdf
file_size: 1611485
relation: main_file
success: 1
file_date_updated: 2020-11-09T09:07:11Z
has_accepted_license: '1'
intvolume: ' 7'
isi: 1
issue: '6'
language:
- iso: eng
month: '06'
oa: 1
oa_version: Published Version
pmid: 1
publication: Royal Society Open Science
publication_identifier:
eissn:
- 2054-5703
publication_status: published
publisher: The Royal Society
quality_controlled: '1'
scopus_import: '1'
status: public
title: 'Emergence of cascading dynamics in interacting tipping elements of ecology
and climate: Cascading dynamics in tipping elements'
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: ba8df636-2132-11f1-aed0-ed93e2281fdd
volume: 7
year: '2020'
...
---
_id: '7466'
abstract:
- lang: eng
text: Unpaired ligands are secreted signals that act via a GP130-like receptor,
domeless, to activate JAK/STAT signalling in Drosophila. Like many mammalian cytokines,
unpaireds can be activated by infection and other stresses and can promote insulin
resistance in target tissues. However, the importance of this effect in non-inflammatory
physiology is unknown. Here, we identify a requirement for unpaired-JAK signalling
as a metabolic regulator in healthy adult Drosophila muscle. Adult muscles show
basal JAK-STAT signalling activity in the absence of any immune challenge. Plasmatocytes
(Drosophila macrophages) are an important source of this tonic signal. Loss of
the dome receptor on adult muscles significantly reduces lifespan and causes local
and systemic metabolic pathology. These pathologies result from hyperactivation
of AKT and consequent deregulation of metabolism. Thus, we identify a cytokine
signal that must be received in muscle to control AKT activity and metabolic homeostasis.
article_number: e51595
article_processing_charge: No
article_type: original
author:
- first_name: Katrin
full_name: Kierdorf, Katrin
last_name: Kierdorf
- first_name: Fabian
full_name: Hersperger, Fabian
last_name: Hersperger
- first_name: Jessica
full_name: Sharrock, Jessica
last_name: Sharrock
- first_name: Crystal M.
full_name: Vincent, Crystal M.
last_name: Vincent
- first_name: Pinar
full_name: Ustaoglu, Pinar
last_name: Ustaoglu
- first_name: Jiawen
full_name: Dou, Jiawen
last_name: Dou
- first_name: Attila
full_name: György, Attila
id: 3BCEDBE0-F248-11E8-B48F-1D18A9856A87
last_name: György
orcid: 0000-0002-1819-198X
- first_name: Olaf
full_name: Groß, Olaf
last_name: Groß
- 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: Marc S.
full_name: Dionne, Marc S.
last_name: Dionne
citation:
ama: Kierdorf K, Hersperger F, Sharrock J, et al. Muscle function and homeostasis
require cytokine inhibition of AKT activity in Drosophila. eLife. 2020;9.
doi:10.7554/eLife.51595
apa: Kierdorf, K., Hersperger, F., Sharrock, J., Vincent, C. M., Ustaoglu, P., Dou,
J., … Dionne, M. S. (2020). Muscle function and homeostasis require cytokine inhibition
of AKT activity in Drosophila. ELife. eLife Sciences Publications. https://doi.org/10.7554/eLife.51595
chicago: Kierdorf, Katrin, Fabian Hersperger, Jessica Sharrock, Crystal M. Vincent,
Pinar Ustaoglu, Jiawen Dou, Attila György, Olaf Groß, Daria E Siekhaus, and Marc
S. Dionne. “Muscle Function and Homeostasis Require Cytokine Inhibition of AKT
Activity in Drosophila.” ELife. eLife Sciences Publications, 2020. https://doi.org/10.7554/eLife.51595.
ieee: K. Kierdorf et al., “Muscle function and homeostasis require cytokine
inhibition of AKT activity in Drosophila,” eLife, vol. 9. eLife Sciences
Publications, 2020.
ista: Kierdorf K, Hersperger F, Sharrock J, Vincent CM, Ustaoglu P, Dou J, György
A, Groß O, Siekhaus DE, Dionne MS. 2020. Muscle function and homeostasis require
cytokine inhibition of AKT activity in Drosophila. eLife. 9, e51595.
mla: Kierdorf, Katrin, et al. “Muscle Function and Homeostasis Require Cytokine
Inhibition of AKT Activity in Drosophila.” ELife, vol. 9, e51595, eLife
Sciences Publications, 2020, doi:10.7554/eLife.51595.
short: K. Kierdorf, F. Hersperger, J. Sharrock, C.M. Vincent, P. Ustaoglu, J. Dou,
A. György, O. Groß, D.E. Siekhaus, M.S. Dionne, ELife 9 (2020).
date_created: 2020-02-09T23:00:51Z
date_published: 2020-01-20T00:00:00Z
date_updated: 2026-04-03T09:24:34Z
day: '20'
ddc:
- '570'
department:
- _id: DaSi
doi: 10.7554/eLife.51595
external_id:
isi:
- '000512304800001'
file:
- access_level: open_access
checksum: 3a072be843f416c7a7d532a51dc0addb
content_type: application/pdf
creator: dernst
date_created: 2020-02-10T08:53:16Z
date_updated: 2020-07-14T12:47:59Z
file_id: '7470'
file_name: 2020_eLife_Kierdorf.pdf
file_size: 4959933
relation: main_file
file_date_updated: 2020-07-14T12:47:59Z
has_accepted_license: '1'
intvolume: ' 9'
isi: 1
language:
- iso: eng
month: '01'
oa: 1
oa_version: Published Version
project:
- _id: 253B6E48-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: P29638
name: The role of Drosophila TNF alpha in immune cell invasion
publication: eLife
publication_identifier:
eissn:
- 2050-084X
publication_status: published
publisher: eLife Sciences Publications
quality_controlled: '1'
scopus_import: '1'
status: public
title: Muscle function and homeostasis require cytokine inhibition of AKT activity
in Drosophila
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: ba8df636-2132-11f1-aed0-ed93e2281fdd
volume: 9
year: '2020'
...
---
_id: '7931'
abstract:
- lang: eng
text: In the course of sample preparation for Next Generation Sequencing (NGS),
DNA is fragmented by various methods. Fragmentation shows a persistent bias with
regard to the cleavage rates of various dinucleotides. With the exception of CpG
dinucleotides the previously described biases were consistent with results of
the DNA cleavage in solution. Here we computed cleavage rates of all dinucleotides
including the methylated CpG and unmethylated CpG dinucleotides using data of
the Whole Genome Sequencing datasets of the 1000 Genomes project. We found that
the cleavage rate of CpG is significantly higher for the methylated CpG dinucleotides.
Using this information, we developed a classifier for distinguishing cancer and
healthy tissues based on their CpG islands statuses of the fragmentation. A simple
Support Vector Machine classifier based on this algorithm shows an accuracy of
84%. The proposed method allows the detection of epigenetic markers purely based
on mechanochemical DNA fragmentation, which can be detected by a simple analysis
of the NGS sequencing data.
article_number: '8635'
article_processing_charge: No
article_type: original
author:
- first_name: Leonid A.
full_name: Uroshlev, Leonid A.
last_name: Uroshlev
- first_name: Eldar T.
full_name: Abdullaev, Eldar T.
last_name: Abdullaev
- first_name: Iren R.
full_name: Umarova, Iren R.
last_name: Umarova
- first_name: Irina A.
full_name: Il’Icheva, Irina A.
last_name: Il’Icheva
- first_name: Larisa A.
full_name: Panchenko, Larisa A.
last_name: Panchenko
- first_name: Robert V.
full_name: Polozov, Robert V.
last_name: Polozov
- first_name: Fyodor
full_name: Kondrashov, Fyodor
id: 44FDEF62-F248-11E8-B48F-1D18A9856A87
last_name: Kondrashov
orcid: 0000-0001-8243-4694
- first_name: Yury D.
full_name: Nechipurenko, Yury D.
last_name: Nechipurenko
- first_name: Sergei L.
full_name: Grokhovsky, Sergei L.
last_name: Grokhovsky
citation:
ama: Uroshlev LA, Abdullaev ET, Umarova IR, et al. A method for identification of
the methylation level of CpG islands from NGS data. Scientific Reports.
2020;10. doi:10.1038/s41598-020-65406-1
apa: Uroshlev, L. A., Abdullaev, E. T., Umarova, I. R., Il’Icheva, I. A., Panchenko,
L. A., Polozov, R. V., … Grokhovsky, S. L. (2020). A method for identification
of the methylation level of CpG islands from NGS data. Scientific Reports.
Springer Nature. https://doi.org/10.1038/s41598-020-65406-1
chicago: Uroshlev, Leonid A., Eldar T. Abdullaev, Iren R. Umarova, Irina A. Il’Icheva,
Larisa A. Panchenko, Robert V. Polozov, Fyodor Kondrashov, Yury D. Nechipurenko,
and Sergei L. Grokhovsky. “A Method for Identification of the Methylation Level
of CpG Islands from NGS Data.” Scientific Reports. Springer Nature, 2020.
https://doi.org/10.1038/s41598-020-65406-1.
ieee: L. A. Uroshlev et al., “A method for identification of the methylation
level of CpG islands from NGS data,” Scientific Reports, vol. 10. Springer
Nature, 2020.
ista: Uroshlev LA, Abdullaev ET, Umarova IR, Il’Icheva IA, Panchenko LA, Polozov
RV, Kondrashov F, Nechipurenko YD, Grokhovsky SL. 2020. A method for identification
of the methylation level of CpG islands from NGS data. Scientific Reports. 10,
8635.
mla: Uroshlev, Leonid A., et al. “A Method for Identification of the Methylation
Level of CpG Islands from NGS Data.” Scientific Reports, vol. 10, 8635,
Springer Nature, 2020, doi:10.1038/s41598-020-65406-1.
short: L.A. Uroshlev, E.T. Abdullaev, I.R. Umarova, I.A. Il’Icheva, L.A. Panchenko,
R.V. Polozov, F. Kondrashov, Y.D. Nechipurenko, S.L. Grokhovsky, Scientific Reports
10 (2020).
date_created: 2020-06-07T22:00:51Z
date_published: 2020-05-25T00:00:00Z
date_updated: 2026-04-03T09:26:06Z
day: '25'
ddc:
- '570'
department:
- _id: FyKo
doi: 10.1038/s41598-020-65406-1
external_id:
isi:
- '000560774200007'
pmid:
- '32451390'
file:
- access_level: open_access
checksum: 099e51611a5b7ca04244d03b2faddf33
content_type: application/pdf
creator: dernst
date_created: 2020-06-08T06:27:32Z
date_updated: 2020-07-14T12:48:05Z
file_id: '7947'
file_name: 2020_ScientificReports_Uroshlev.pdf
file_size: 1001724
relation: main_file
file_date_updated: 2020-07-14T12:48:05Z
has_accepted_license: '1'
intvolume: ' 10'
isi: 1
language:
- iso: eng
month: '05'
oa: 1
oa_version: Published Version
pmid: 1
publication: Scientific Reports
publication_identifier:
eissn:
- 2045-2322
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
scopus_import: '1'
status: public
title: A method for identification of the methylation level of CpG islands from NGS
data
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: ba8df636-2132-11f1-aed0-ed93e2281fdd
volume: 10
year: '2020'
...
---
_id: '8706'
abstract:
- lang: eng
text: As part of the Austrian Transition to Open Access (AT2OA) project, subproject
TP1-B is working on designing a monitoring solution for the output of Open Access
publications in Austria. This report on a potential Open Access monitoring approach
in Austria is one of the results of these efforts and can serve as a basis for
discussion on an international level.
- lang: ger
text: Als Teil des Hochschulraumstrukturmittel-Projekts Austrian Transition to Open
Access (AT2OA) befasst sich das Teilprojekt TP1-B mit der Konzeption einer Monitoring-Lösung
für den Open Access-Publikationsoutput in Österreich. Der nun vorliegende Bericht
zu einem potentiellen Open Access-Monitoring in Österreich ist eines der Ergebnisse
dieser Bemühungen und kann als Grundlage einer Diskussion auf internationaler
Ebene dienen.
article_processing_charge: No
article_type: original
author:
- first_name: Patrick
full_name: Danowski, Patrick
id: 2EBD1598-F248-11E8-B48F-1D18A9856A87
last_name: Danowski
orcid: 0000-0002-6026-4409
- first_name: Andreas
full_name: Ferus, Andreas
last_name: Ferus
- first_name: Anna-Laetitia
full_name: Hikl, Anna-Laetitia
last_name: Hikl
- first_name: Gerda
full_name: McNeill, Gerda
last_name: McNeill
- first_name: Clemens
full_name: Miniberger, Clemens
last_name: Miniberger
- first_name: Steve
full_name: Reding, Steve
last_name: Reding
- first_name: Tobias
full_name: Zarka, Tobias
last_name: Zarka
- first_name: Michael
full_name: Zojer, Michael
last_name: Zojer
citation:
ama: Danowski P, Ferus A, Hikl A-L, et al. „Recommendation“ for the further procedure
for open access monitoring. Deliverable of the AT2OA subproject TP1-B. Mitteilungen
der Vereinigung Österreichischer Bibliothekarinnen und Bibliothekare. 2020;73(2):278-284.
doi:10.31263/voebm.v73i2.3941
apa: Danowski, P., Ferus, A., Hikl, A.-L., McNeill, G., Miniberger, C., Reding,
S., … Zojer, M. (2020). „Recommendation“ for the further procedure for open access
monitoring. Deliverable of the AT2OA subproject TP1-B. Mitteilungen der Vereinigung
Österreichischer Bibliothekarinnen und Bibliothekare. Vereinigung Österreichischer
Bibliothekarinnen und Bibliothekare. https://doi.org/10.31263/voebm.v73i2.3941
chicago: Danowski, Patrick, Andreas Ferus, Anna-Laetitia Hikl, Gerda McNeill, Clemens
Miniberger, Steve Reding, Tobias Zarka, and Michael Zojer. “„Recommendation“ for
the further procedure for open access monitoring. Deliverable of the AT2OA subproject
TP1-B.” Mitteilungen der Vereinigung Österreichischer Bibliothekarinnen und
Bibliothekare. Vereinigung Österreichischer Bibliothekarinnen und Bibliothekare,
2020. https://doi.org/10.31263/voebm.v73i2.3941.
ieee: P. Danowski et al., “„Recommendation“ for the further procedure for
open access monitoring. Deliverable of the AT2OA subproject TP1-B,” Mitteilungen
der Vereinigung Österreichischer Bibliothekarinnen und Bibliothekare, vol.
73, no. 2. Vereinigung Österreichischer Bibliothekarinnen und Bibliothekare, pp.
278–284, 2020.
ista: Danowski P, Ferus A, Hikl A-L, McNeill G, Miniberger C, Reding S, Zarka T,
Zojer M. 2020. „Recommendation“ for the further procedure for open access monitoring.
Deliverable of the AT2OA subproject TP1-B. Mitteilungen der Vereinigung Österreichischer
Bibliothekarinnen und Bibliothekare. 73(2), 278–284.
mla: Danowski, Patrick, et al. “„Recommendation“ for the further procedure for open
access monitoring. Deliverable of the AT2OA subproject TP1-B.” Mitteilungen
der Vereinigung Österreichischer Bibliothekarinnen und Bibliothekare, vol.
73, no. 2, Vereinigung Österreichischer Bibliothekarinnen und Bibliothekare, 2020,
pp. 278–84, doi:10.31263/voebm.v73i2.3941.
short: P. Danowski, A. Ferus, A.-L. Hikl, G. McNeill, C. Miniberger, S. Reding,
T. Zarka, M. Zojer, Mitteilungen der Vereinigung Österreichischer Bibliothekarinnen
und Bibliothekare 73 (2020) 278–284.
corr_author: '1'
date_created: 2020-10-25T23:01:19Z
date_published: 2020-07-14T00:00:00Z
date_updated: 2026-04-03T09:25:27Z
day: '14'
ddc:
- '020'
department:
- _id: E-Lib
doi: 10.31263/voebm.v73i2.3941
file:
- access_level: open_access
checksum: 37443c34d91d5bdbeb38c78b14792537
content_type: application/pdf
creator: kschuh
date_created: 2020-10-27T16:27:25Z
date_updated: 2020-10-27T16:27:25Z
file_id: '8714'
file_name: 2020_VOEB_Danowski.pdf
file_size: 960317
relation: main_file
success: 1
file_date_updated: 2020-10-27T16:27:25Z
has_accepted_license: '1'
intvolume: ' 73'
issue: '2'
language:
- iso: ger
month: '07'
oa: 1
oa_version: Published Version
page: 278-284
publication: Mitteilungen der Vereinigung Österreichischer Bibliothekarinnen und Bibliothekare
publication_identifier:
eissn:
- 1022-2588
publication_status: published
publisher: Vereinigung Österreichischer Bibliothekarinnen und Bibliothekare
quality_controlled: '1'
scopus_import: '1'
status: public
title: „Recommendation“ for the further procedure for open access monitoring. Deliverable
of the AT2OA subproject TP1-B
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: ba8df636-2132-11f1-aed0-ed93e2281fdd
volume: 73
year: '2020'
...
---
OA_place: repository
OA_type: green
_id: '8132'
abstract:
- lang: eng
text: The WAVE regulatory complex (WRC) is crucial for assembly of the peripheral
branched actin network constituting one of the main drivers of eukaryotic cell
migration. Here, we uncover an essential role of the hematopoietic-specific WRC
component HEM1 for immune cell development. Germline-encoded HEM1 deficiency underlies
an inborn error of immunity with systemic autoimmunity, at cellular level marked
by WRC destabilization, reduced filamentous actin, and failure to assemble lamellipodia.
Hem1−/− mice display systemic autoimmunity, phenocopying the human disease. In
the absence of Hem1, B cells become deprived of extracellular stimuli necessary
to maintain the strength of B cell receptor signaling at a level permissive for
survival of non-autoreactive B cells. This shifts the balance of B cell fate choices
toward autoreactive B cells and thus autoimmunity.
article_number: eabc3979
article_processing_charge: No
article_type: original
author:
- first_name: Elisabeth
full_name: Salzer, Elisabeth
last_name: Salzer
- first_name: Samaneh
full_name: Zoghi, Samaneh
last_name: Zoghi
- first_name: Máté G.
full_name: Kiss, Máté G.
last_name: Kiss
- first_name: Frieda
full_name: Kage, Frieda
last_name: Kage
- first_name: Christina
full_name: Rashkova, Christina
last_name: Rashkova
- first_name: Stephanie
full_name: Stahnke, Stephanie
last_name: Stahnke
- first_name: Matthias
full_name: Haimel, Matthias
last_name: Haimel
- first_name: René
full_name: Platzer, René
last_name: Platzer
- first_name: Michael
full_name: Caldera, Michael
last_name: Caldera
- first_name: Rico Chandra
full_name: Ardy, Rico Chandra
last_name: Ardy
- first_name: Birgit
full_name: Hoeger, Birgit
last_name: Hoeger
- first_name: Jana
full_name: Block, Jana
last_name: Block
- first_name: David
full_name: Medgyesi, David
last_name: Medgyesi
- first_name: Celine
full_name: Sin, Celine
last_name: Sin
- first_name: Sepideh
full_name: Shahkarami, Sepideh
last_name: Shahkarami
- first_name: Renate
full_name: Kain, Renate
last_name: Kain
- first_name: Vahid
full_name: Ziaee, Vahid
last_name: Ziaee
- first_name: Peter
full_name: Hammerl, Peter
last_name: Hammerl
- first_name: Christoph
full_name: Bock, Christoph
last_name: Bock
- first_name: Jörg
full_name: Menche, Jörg
last_name: Menche
- first_name: Loïc
full_name: Dupré, Loïc
last_name: Dupré
- first_name: Johannes B.
full_name: Huppa, Johannes B.
last_name: Huppa
- first_name: Michael K
full_name: Sixt, Michael K
id: 41E9FBEA-F248-11E8-B48F-1D18A9856A87
last_name: Sixt
orcid: 0000-0002-6620-9179
- first_name: Alexis
full_name: Lomakin, Alexis
last_name: Lomakin
- first_name: Klemens
full_name: Rottner, Klemens
last_name: Rottner
- first_name: Christoph J.
full_name: Binder, Christoph J.
last_name: Binder
- first_name: Theresia E.B.
full_name: Stradal, Theresia E.B.
last_name: Stradal
- first_name: Nima
full_name: Rezaei, Nima
last_name: Rezaei
- first_name: Kaan
full_name: Boztug, Kaan
last_name: Boztug
citation:
ama: Salzer E, Zoghi S, Kiss MG, et al. The cytoskeletal regulator HEM1 governs
B cell development and prevents autoimmunity. Science Immunology. 2020;5(49).
doi:10.1126/sciimmunol.abc3979
apa: Salzer, E., Zoghi, S., Kiss, M. G., Kage, F., Rashkova, C., Stahnke, S., …
Boztug, K. (2020). The cytoskeletal regulator HEM1 governs B cell development
and prevents autoimmunity. Science Immunology. AAAS. https://doi.org/10.1126/sciimmunol.abc3979
chicago: Salzer, Elisabeth, Samaneh Zoghi, Máté G. Kiss, Frieda Kage, Christina
Rashkova, Stephanie Stahnke, Matthias Haimel, et al. “The Cytoskeletal Regulator
HEM1 Governs B Cell Development and Prevents Autoimmunity.” Science Immunology.
AAAS, 2020. https://doi.org/10.1126/sciimmunol.abc3979.
ieee: E. Salzer et al., “The cytoskeletal regulator HEM1 governs B cell development
and prevents autoimmunity,” Science Immunology, vol. 5, no. 49. AAAS, 2020.
ista: Salzer E, Zoghi S, Kiss MG, Kage F, Rashkova C, Stahnke S, Haimel M, Platzer
R, Caldera M, Ardy RC, Hoeger B, Block J, Medgyesi D, Sin C, Shahkarami S, Kain
R, Ziaee V, Hammerl P, Bock C, Menche J, Dupré L, Huppa JB, Sixt MK, Lomakin A,
Rottner K, Binder CJ, Stradal TEB, Rezaei N, Boztug K. 2020. The cytoskeletal
regulator HEM1 governs B cell development and prevents autoimmunity. Science Immunology.
5(49), eabc3979.
mla: Salzer, Elisabeth, et al. “The Cytoskeletal Regulator HEM1 Governs B Cell Development
and Prevents Autoimmunity.” Science Immunology, vol. 5, no. 49, eabc3979,
AAAS, 2020, doi:10.1126/sciimmunol.abc3979.
short: E. Salzer, S. Zoghi, M.G. Kiss, F. Kage, C. Rashkova, S. Stahnke, M. Haimel,
R. Platzer, M. Caldera, R.C. Ardy, B. Hoeger, J. Block, D. Medgyesi, C. Sin, S.
Shahkarami, R. Kain, V. Ziaee, P. Hammerl, C. Bock, J. Menche, L. Dupré, J.B.
Huppa, M.K. Sixt, A. Lomakin, K. Rottner, C.J. Binder, T.E.B. Stradal, N. Rezaei,
K. Boztug, Science Immunology 5 (2020).
date_created: 2020-07-19T22:00:58Z
date_published: 2020-07-10T00:00:00Z
date_updated: 2026-04-03T09:25:04Z
day: '10'
department:
- _id: MiSi
doi: 10.1126/sciimmunol.abc3979
external_id:
isi:
- '000546994600004'
pmid:
- '32646852'
intvolume: ' 5'
isi: 1
issue: '49'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7116756
month: '07'
oa: 1
oa_version: Submitted Version
pmid: 1
publication: Science Immunology
publication_identifier:
eissn:
- 2470-9468
publication_status: published
publisher: AAAS
quality_controlled: '1'
scopus_import: '1'
status: public
title: The cytoskeletal regulator HEM1 governs B cell development and prevents autoimmunity
type: journal_article
user_id: ba8df636-2132-11f1-aed0-ed93e2281fdd
volume: 5
year: '2020'
...
---
_id: '8943'
abstract:
- lang: eng
text: The widely used non-steroidal anti-inflammatory drugs (NSAIDs) are derivatives
of the phytohormone salicylic acid (SA). SA is well known to regulate plant immunity
and development, whereas there have been few reports focusing on the effects of
NSAIDs in plants. Our studies here reveal that NSAIDs exhibit largely overlapping
physiological activities to SA in the model plant Arabidopsis. NSAID treatments
lead to shorter and agravitropic primary roots and inhibited lateral root organogenesis.
Notably, in addition to the SA-like action, which in roots involves binding to
the protein phosphatase 2A (PP2A), NSAIDs also exhibit PP2A-independent effects.
Cell biological and biochemical analyses reveal that many NSAIDs bind directly
to and inhibit the chaperone activity of TWISTED DWARF1, thereby regulating actin
cytoskeleton dynamics and subsequent endosomal trafficking. Our findings uncover
an unexpected bioactivity of human pharmaceuticals in plants and provide insights
into the molecular mechanism underlying the cellular action of this class of anti-inflammatory
compounds.
acknowledged_ssus:
- _id: LifeSc
- _id: Bio
acknowledgement: "We thank Drs. Sebastian Bednarek (University of Wisconsin-Madison),
Niko Geldner (University of Lausanne), and Karin Schumacher (Heidelberg University)
for kindly sharing published Arabidopsis lines; Dr. Satoshi Naramoto for the pPIN2::PIN2-GFP;
pVHA-a1::VHA-a1-mRFP reporter; the staff at the Life Science Facility and Bioimaging
Facility, Monika Hrtyan, and Dorota Jaworska at IST Austria for technical support;
and Drs. Su Tang (Texas A&M University),\r\nMelinda Abas (BOKU), Eva Benkova´ (IST
Austria), Christian Luschnig (BOKU), Bartel Vanholme (Gent University), and the
Friml group for valuable discussions. The research leading to these findings was
funded by the European Union’s Horizon 2020 program (ERC grant agreement no. 742985,
to J.F.), the People Programme (Marie Curie Actions) of the European Union’s Seventh
Framework Programme (FP7/2007-2013) under REA grant agreement no.\r\n291734, the
Swiss National Funds (31003A_165877, to M.G.), the Ministry of Education, Youth,
and Sports of the Czech Republic (project no. CZ.02.1.01/0.0/0.0/16_019/0000738,
EU Operational Programme ‘‘Research, development and education and Centre for Plant
Experimental Biology’’), and the EU Operational Programme Prague - Competitiveness
(project no. CZ.2.16/3.1.00/21519). S.T. was funded by a European Molecular Biology
Organization (EMBO) long-term postdoctoral fellowship (ALTF 723-2015). X.Z. was
partly supported by a PhD scholarship from the China Scholarship Council."
article_number: '108463'
article_processing_charge: Yes
article_type: original
author:
- first_name: Shutang
full_name: Tan, Shutang
id: 2DE75584-F248-11E8-B48F-1D18A9856A87
last_name: Tan
orcid: 0000-0002-0471-8285
- first_name: Martin
full_name: Di Donato, Martin
last_name: Di Donato
- first_name: Matous
full_name: Glanc, Matous
id: 1AE1EA24-02D0-11E9-9BAA-DAF4881429F2
last_name: Glanc
orcid: 0000-0003-0619-7783
- first_name: Xixi
full_name: Zhang, Xixi
id: 61A66458-47E9-11EA-85BA-8AEAAF14E49A
last_name: Zhang
orcid: 0000-0001-7048-4627
- first_name: Petr
full_name: Klíma, Petr
last_name: Klíma
- first_name: Jie
full_name: Liu, Jie
last_name: Liu
- first_name: Aurélien
full_name: Bailly, Aurélien
last_name: Bailly
- first_name: Noel
full_name: Ferro, Noel
last_name: Ferro
- first_name: Jan
full_name: Petrášek, Jan
last_name: Petrášek
- first_name: Markus
full_name: Geisler, Markus
last_name: Geisler
- first_name: Jiří
full_name: Friml, Jiří
id: 4159519E-F248-11E8-B48F-1D18A9856A87
last_name: Friml
orcid: 0000-0002-8302-7596
citation:
ama: Tan S, Di Donato M, Glanc M, et al. Non-steroidal anti-inflammatory drugs target
TWISTED DWARF1-regulated actin dynamics and auxin transport-mediated plant development.
Cell Reports. 2020;33(9). doi:10.1016/j.celrep.2020.108463
apa: Tan, S., Di Donato, M., Glanc, M., Zhang, X., Klíma, P., Liu, J., … Friml,
J. (2020). Non-steroidal anti-inflammatory drugs target TWISTED DWARF1-regulated
actin dynamics and auxin transport-mediated plant development. Cell Reports.
Elsevier. https://doi.org/10.1016/j.celrep.2020.108463
chicago: Tan, Shutang, Martin Di Donato, Matous Glanc, Xixi Zhang, Petr Klíma, Jie
Liu, Aurélien Bailly, et al. “Non-Steroidal Anti-Inflammatory Drugs Target TWISTED
DWARF1-Regulated Actin Dynamics and Auxin Transport-Mediated Plant Development.”
Cell Reports. Elsevier, 2020. https://doi.org/10.1016/j.celrep.2020.108463.
ieee: S. Tan et al., “Non-steroidal anti-inflammatory drugs target TWISTED
DWARF1-regulated actin dynamics and auxin transport-mediated plant development,”
Cell Reports, vol. 33, no. 9. Elsevier, 2020.
ista: Tan S, Di Donato M, Glanc M, Zhang X, Klíma P, Liu J, Bailly A, Ferro N, Petrášek
J, Geisler M, Friml J. 2020. Non-steroidal anti-inflammatory drugs target TWISTED
DWARF1-regulated actin dynamics and auxin transport-mediated plant development.
Cell Reports. 33(9), 108463.
mla: Tan, Shutang, et al. “Non-Steroidal Anti-Inflammatory Drugs Target TWISTED
DWARF1-Regulated Actin Dynamics and Auxin Transport-Mediated Plant Development.”
Cell Reports, vol. 33, no. 9, 108463, Elsevier, 2020, doi:10.1016/j.celrep.2020.108463.
short: S. Tan, M. Di Donato, M. Glanc, X. Zhang, P. Klíma, J. Liu, A. Bailly, N.
Ferro, J. Petrášek, M. Geisler, J. Friml, Cell Reports 33 (2020).
corr_author: '1'
date_created: 2020-12-13T23:01:21Z
date_published: 2020-12-01T00:00:00Z
date_updated: 2026-04-03T09:30:47Z
day: '01'
ddc:
- '580'
department:
- _id: JiFr
doi: 10.1016/j.celrep.2020.108463
ec_funded: 1
external_id:
isi:
- '000595658100018'
pmid:
- '33264621'
file:
- access_level: open_access
checksum: ed18cba0fb48ed2e789381a54cc21904
content_type: application/pdf
creator: dernst
date_created: 2020-12-14T07:33:39Z
date_updated: 2020-12-14T07:33:39Z
file_id: '8948'
file_name: 2020_CellReports_Tan.pdf
file_size: 8056434
relation: main_file
success: 1
file_date_updated: 2020-12-14T07:33:39Z
has_accepted_license: '1'
intvolume: ' 33'
isi: 1
issue: '9'
language:
- iso: eng
month: '12'
oa: 1
oa_version: Published 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
- _id: 25681D80-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '291734'
name: International IST Postdoc Fellowship Programme
- _id: 256FEF10-B435-11E9-9278-68D0E5697425
grant_number: 723-2015
name: Molecular Mechanism underlying Salicylic Acid Regulation of Endocytic Trafficking
in Arabidopsis
publication: Cell Reports
publication_identifier:
eissn:
- 2211-1247
publication_status: published
publisher: Elsevier
quality_controlled: '1'
related_material:
link:
- description: News on IST Homepage
relation: press_release
url: https://ist.ac.at/en/news/plants-on-aspirin/
scopus_import: '1'
status: public
title: Non-steroidal anti-inflammatory drugs target TWISTED DWARF1-regulated actin
dynamics and auxin transport-mediated plant development
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: ba8df636-2132-11f1-aed0-ed93e2281fdd
volume: 33
year: '2020'
...
---
_id: '8220'
abstract:
- lang: eng
text: Understanding to what extent stem cell potential is a cell-intrinsic property
or an emergent behavior coming from global tissue dynamics and geometry is a key
outstanding question of systems and stem cell biology. Here, we propose a theory
of stem cell dynamics as a stochastic competition for access to a spatially localized
niche, giving rise to a stochastic conveyor-belt model. Cell divisions produce
a steady cellular stream which advects cells away from the niche, while random
rearrangements enable cells away from the niche to be favorably repositioned.
Importantly, even when assuming that all cells in a tissue are molecularly equivalent,
we predict a common (“universal”) functional dependence of the long-term clonal
survival probability on distance from the niche, as well as the emergence of a
well-defined number of functional stem cells, dependent only on the rate of random
movements vs. mitosis-driven advection. We test the predictions of this theory
on datasets of pubertal mammary gland tips and embryonic kidney tips, as well
as homeostatic intestinal crypts. Importantly, we find good agreement for the
predicted functional dependency of the competition as a function of position,
and thus functional stem cell number in each organ. This argues for a key role
of positional fluctuations in dictating stem cell number and dynamics, and we
discuss the applicability of this theory to other settings.
acknowledgement: "We thank all members of the E.H., B.D.S., and J.v.R. groups for
stimulating discussions. This project was supported by\r\nthe European Research
Council (648804 to J.v.R. and 851288 to E.H.). It has also received support from
the CancerGenomics.nl (Netherlands Organization for Scientific Research) program
(J.v.R.) and the Doctor Josef Steiner Foundation (J.v.R). B.D.S. was supported by
Royal Society E. P. Abraham Research Professorship RP/R1/180165 and Wellcome Trust
Grant 098357/Z/12/Z."
article_processing_charge: No
article_type: original
author:
- first_name: Bernat
full_name: Corominas-Murtra, Bernat
id: 43BE2298-F248-11E8-B48F-1D18A9856A87
last_name: Corominas-Murtra
orcid: 0000-0001-9806-5643
- first_name: Colinda L.G.J.
full_name: Scheele, Colinda L.G.J.
last_name: Scheele
- first_name: Kasumi
full_name: Kishi, Kasumi
id: 3065DFC4-F248-11E8-B48F-1D18A9856A87
last_name: Kishi
orcid: 0000-0001-6060-4795
- first_name: Saskia I.J.
full_name: Ellenbroek, Saskia I.J.
last_name: Ellenbroek
- first_name: Benjamin D.
full_name: Simons, Benjamin D.
last_name: Simons
- first_name: Jacco
full_name: Van Rheenen, Jacco
last_name: Van Rheenen
- first_name: Edouard B
full_name: Hannezo, Edouard B
id: 3A9DB764-F248-11E8-B48F-1D18A9856A87
last_name: Hannezo
orcid: 0000-0001-6005-1561
citation:
ama: Corominas-Murtra B, Scheele CLGJ, Kishi K, et al. Stem cell lineage survival
as a noisy competition for niche access. Proceedings of the National Academy
of Sciences of the United States of America. 2020;117(29):16969-16975. doi:10.1073/pnas.1921205117
apa: Corominas-Murtra, B., Scheele, C. L. G. J., Kishi, K., Ellenbroek, S. I. J.,
Simons, B. D., Van Rheenen, J., & Hannezo, E. B. (2020). Stem cell lineage
survival as a noisy competition for niche access. Proceedings of the National
Academy of Sciences of the United States of America. National Academy of Sciences.
https://doi.org/10.1073/pnas.1921205117
chicago: Corominas-Murtra, Bernat, Colinda L.G.J. Scheele, Kasumi Kishi, Saskia
I.J. Ellenbroek, Benjamin D. Simons, Jacco Van Rheenen, and Edouard B Hannezo.
“Stem Cell Lineage Survival as a Noisy Competition for Niche Access.” Proceedings
of the National Academy of Sciences of the United States of America. National
Academy of Sciences, 2020. https://doi.org/10.1073/pnas.1921205117.
ieee: B. Corominas-Murtra et al., “Stem cell lineage survival as a noisy
competition for niche access,” Proceedings of the National Academy of Sciences
of the United States of America, vol. 117, no. 29. National Academy of Sciences,
pp. 16969–16975, 2020.
ista: Corominas-Murtra B, Scheele CLGJ, Kishi K, Ellenbroek SIJ, Simons BD, Van
Rheenen J, Hannezo EB. 2020. Stem cell lineage survival as a noisy competition
for niche access. Proceedings of the National Academy of Sciences of the United
States of America. 117(29), 16969–16975.
mla: Corominas-Murtra, Bernat, et al. “Stem Cell Lineage Survival as a Noisy Competition
for Niche Access.” Proceedings of the National Academy of Sciences of the United
States of America, vol. 117, no. 29, National Academy of Sciences, 2020, pp.
16969–75, doi:10.1073/pnas.1921205117.
short: B. Corominas-Murtra, C.L.G.J. Scheele, K. Kishi, S.I.J. Ellenbroek, B.D.
Simons, J. Van Rheenen, E.B. Hannezo, Proceedings of the National Academy of Sciences
of the United States of America 117 (2020) 16969–16975.
corr_author: '1'
date_created: 2020-08-09T22:00:52Z
date_published: 2020-07-21T00:00:00Z
date_updated: 2026-04-03T09:29:04Z
day: '21'
ddc:
- '570'
department:
- _id: EdHa
doi: 10.1073/pnas.1921205117
ec_funded: 1
external_id:
isi:
- '000553292900014'
pmid:
- '32611816'
file:
- access_level: open_access
content_type: application/pdf
creator: dernst
date_created: 2020-08-10T06:50:28Z
date_updated: 2020-08-10T06:50:28Z
file_id: '8223'
file_name: 2020_PNAS_Corominas.pdf
file_size: 1111604
relation: main_file
success: 1
file_date_updated: 2020-08-10T06:50:28Z
has_accepted_license: '1'
intvolume: ' 117'
isi: 1
issue: '29'
language:
- iso: eng
month: '07'
oa: 1
oa_version: Published Version
page: 16969-16975
pmid: 1
project:
- _id: 05943252-7A3F-11EA-A408-12923DDC885E
call_identifier: H2020
grant_number: '851288'
name: Design Principles of Branching Morphogenesis
publication: Proceedings of the National Academy of Sciences of the United States
of America
publication_identifier:
eissn:
- 1091-6490
publication_status: published
publisher: National Academy of Sciences
quality_controlled: '1'
related_material:
link:
- relation: press_release
url: https://ist.ac.at/en/news/order-from-noise/
scopus_import: '1'
status: public
title: Stem cell lineage survival as a noisy competition for niche access
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: ba8df636-2132-11f1-aed0-ed93e2281fdd
volume: 117
year: '2020'
...