---
_id: '9822'
abstract:
- lang: eng
text: Attachment of adhesive molecules on cell culture surfaces to restrict cell
adhesion to defined areas and shapes has been vital for the progress of in vitro
research. In currently existing patterning methods, a combination of pattern properties
such as stability, precision, specificity, high-throughput outcome, and spatiotemporal
control is highly desirable but challenging to achieve. Here, we introduce a versatile
and high-throughput covalent photoimmobilization technique, comprising a light-dose-dependent
patterning step and a subsequent functionalization of the pattern via click chemistry.
This two-step process is feasible on arbitrary surfaces and allows for generation
of sustainable patterns and gradients. The method is validated in different biological
systems by patterning adhesive ligands on cell-repellent surfaces, thereby constraining
the growth and migration of cells to the designated areas. We then implement a
sequential photopatterning approach by adding a second switchable patterning step,
allowing for spatiotemporal control over two distinct surface patterns. As a proof
of concept, we reconstruct the dynamics of the tip/stalk cell switch during angiogenesis.
Our results show that the spatiotemporal control provided by our “sequential photopatterning”
system is essential for mimicking dynamic biological processes and that our innovative
approach has great potential for further applications in cell science.
acknowledgement: We would like to thank Charlott Leu for the production of our chromium
wafers, Louise Ritter for her contribution of the IF stainings in Figure 4, Shokoufeh
Teymouri for her help with the Bioinert coated slides, and finally Prof. Dr. Joachim
Rädler for his valuable scientific guidance.
article_processing_charge: Yes (in subscription journal)
article_type: original
author:
- first_name: Themistoklis
full_name: Zisis, Themistoklis
last_name: Zisis
- first_name: Jan
full_name: Schwarz, Jan
id: 346C1EC6-F248-11E8-B48F-1D18A9856A87
last_name: Schwarz
- first_name: Miriam
full_name: Balles, Miriam
last_name: Balles
- first_name: Maibritt
full_name: Kretschmer, Maibritt
last_name: Kretschmer
- first_name: Maria
full_name: Nemethova, Maria
id: 34E27F1C-F248-11E8-B48F-1D18A9856A87
last_name: Nemethova
- first_name: Remy P
full_name: Chait, Remy P
id: 3464AE84-F248-11E8-B48F-1D18A9856A87
last_name: Chait
orcid: 0000-0003-0876-3187
- first_name: Robert
full_name: Hauschild, Robert
id: 4E01D6B4-F248-11E8-B48F-1D18A9856A87
last_name: Hauschild
orcid: 0000-0001-9843-3522
- first_name: Janina
full_name: Lange, Janina
last_name: Lange
- first_name: Calin C
full_name: Guet, Calin C
id: 47F8433E-F248-11E8-B48F-1D18A9856A87
last_name: Guet
orcid: 0000-0001-6220-2052
- first_name: Michael K
full_name: Sixt, Michael K
id: 41E9FBEA-F248-11E8-B48F-1D18A9856A87
last_name: Sixt
orcid: 0000-0002-4561-241X
- first_name: Stefan
full_name: Zahler, Stefan
last_name: Zahler
citation:
ama: Zisis T, Schwarz J, Balles M, et al. Sequential and switchable patterning for
studying cellular processes under spatiotemporal control. ACS Applied Materials
and Interfaces. 2021;13(30):35545–35560. doi:10.1021/acsami.1c09850
apa: Zisis, T., Schwarz, J., Balles, M., Kretschmer, M., Nemethova, M., Chait, R.
P., … Zahler, S. (2021). Sequential and switchable patterning for studying cellular
processes under spatiotemporal control. ACS Applied Materials and Interfaces.
American Chemical Society. https://doi.org/10.1021/acsami.1c09850
chicago: Zisis, Themistoklis, Jan Schwarz, Miriam Balles, Maibritt Kretschmer, Maria
Nemethova, Remy P Chait, Robert Hauschild, et al. “Sequential and Switchable Patterning
for Studying Cellular Processes under Spatiotemporal Control.” ACS Applied
Materials and Interfaces. American Chemical Society, 2021. https://doi.org/10.1021/acsami.1c09850.
ieee: T. Zisis et al., “Sequential and switchable patterning for studying
cellular processes under spatiotemporal control,” ACS Applied Materials and
Interfaces, vol. 13, no. 30. American Chemical Society, pp. 35545–35560, 2021.
ista: Zisis T, Schwarz J, Balles M, Kretschmer M, Nemethova M, Chait RP, Hauschild
R, Lange J, Guet CC, Sixt MK, Zahler S. 2021. Sequential and switchable patterning
for studying cellular processes under spatiotemporal control. ACS Applied Materials
and Interfaces. 13(30), 35545–35560.
mla: Zisis, Themistoklis, et al. “Sequential and Switchable Patterning for Studying
Cellular Processes under Spatiotemporal Control.” ACS Applied Materials and
Interfaces, vol. 13, no. 30, American Chemical Society, 2021, pp. 35545–35560,
doi:10.1021/acsami.1c09850.
short: T. Zisis, J. Schwarz, M. Balles, M. Kretschmer, M. Nemethova, R.P. Chait,
R. Hauschild, J. Lange, C.C. Guet, M.K. Sixt, S. Zahler, ACS Applied Materials
and Interfaces 13 (2021) 35545–35560.
corr_author: '1'
date_created: 2021-08-08T22:01:28Z
date_published: 2021-08-04T00:00:00Z
date_updated: 2025-07-10T12:02:02Z
day: '04'
ddc:
- '620'
- '570'
department:
- _id: MiSi
- _id: GaTk
- _id: Bio
- _id: CaGu
doi: 10.1021/acsami.1c09850
ec_funded: 1
external_id:
isi:
- '000683741400026'
pmid:
- '34283577'
file:
- access_level: open_access
checksum: b043a91d9f9200e467b970b692687ed3
content_type: application/pdf
creator: asandaue
date_created: 2021-08-09T09:44:03Z
date_updated: 2021-08-09T09:44:03Z
file_id: '9833'
file_name: 2021_ACSAppliedMaterialsAndInterfaces_Zisis.pdf
file_size: 7123293
relation: main_file
success: 1
file_date_updated: 2021-08-09T09:44:03Z
has_accepted_license: '1'
intvolume: ' 13'
isi: 1
issue: '30'
language:
- iso: eng
month: '08'
oa: 1
oa_version: Published Version
page: 35545–35560
pmid: 1
project:
- _id: 25FE9508-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '724373'
name: Cellular Navigation Along Spatial Gradients
publication: ACS Applied Materials and Interfaces
publication_identifier:
eissn:
- 1944-8252
issn:
- 1944-8244
publication_status: published
publisher: American Chemical Society
quality_controlled: '1'
scopus_import: '1'
status: public
title: Sequential and switchable patterning for studying cellular processes under
spatiotemporal control
tmp:
image: /images/cc_by_nc_nd.png
legal_code_url: https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode
name: Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International
(CC BY-NC-ND 4.0)
short: CC BY-NC-ND (4.0)
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 13
year: '2021'
...
---
_id: '9823'
abstract:
- lang: eng
text: "Approximate agreement is one of the few variants of consensus that can be
solved in a wait-free manner in asynchronous systems where processes communicate
by reading and writing to shared memory. In this work, we consider a natural generalisation
of approximate agreement on arbitrary undirected connected graphs. Each process
is given a vertex of the graph as input and, if non-faulty, must output a vertex
such that\r\nall the outputs are within distance 1 of one another, and\r\n\r\neach
output value lies on a shortest path between two input values.\r\n\r\nFrom prior
work, it is known that there is no wait-free algorithm among \U0001D45B≥3 processes
for this problem on any cycle of length \U0001D450≥4 , by reduction from 2-set
agreement (Castañeda et al. 2018).\r\n\r\nIn this work, we investigate the solvability
and complexity of this task on general graphs. We give a new, direct proof of
the impossibility of approximate agreement on cycles of length \U0001D450≥4
, via a generalisation of Sperner’s Lemma to convex polygons. We also extend the
reduction from 2-set agreement to a larger class of graphs, showing that approximate
agreement on these graphs is unsolvable. On the positive side, we present a wait-free
algorithm for a class of graphs that properly contains the class of chordal graphs."
alternative_title:
- LNCS
article_processing_charge: No
arxiv: 1
author:
- first_name: Dan-Adrian
full_name: Alistarh, Dan-Adrian
id: 4A899BFC-F248-11E8-B48F-1D18A9856A87
last_name: Alistarh
orcid: 0000-0003-3650-940X
- first_name: Faith
full_name: Ellen, Faith
last_name: Ellen
- first_name: Joel
full_name: Rybicki, Joel
id: 334EFD2E-F248-11E8-B48F-1D18A9856A87
last_name: Rybicki
orcid: 0000-0002-6432-6646
citation:
ama: 'Alistarh D-A, Ellen F, Rybicki J. Wait-free approximate agreement on graphs.
In: Structural Information and Communication Complexity. Vol 12810. Springer
Nature; 2021:87-105. doi:10.1007/978-3-030-79527-6_6'
apa: 'Alistarh, D.-A., Ellen, F., & Rybicki, J. (2021). Wait-free approximate
agreement on graphs. In Structural Information and Communication Complexity
(Vol. 12810, pp. 87–105). Wrocław, Poland: Springer Nature. https://doi.org/10.1007/978-3-030-79527-6_6'
chicago: Alistarh, Dan-Adrian, Faith Ellen, and Joel Rybicki. “Wait-Free Approximate
Agreement on Graphs.” In Structural Information and Communication Complexity,
12810:87–105. Springer Nature, 2021. https://doi.org/10.1007/978-3-030-79527-6_6.
ieee: D.-A. Alistarh, F. Ellen, and J. Rybicki, “Wait-free approximate agreement
on graphs,” in Structural Information and Communication Complexity, Wrocław,
Poland, 2021, vol. 12810, pp. 87–105.
ista: 'Alistarh D-A, Ellen F, Rybicki J. 2021. Wait-free approximate agreement on graphs.
Structural Information and Communication Complexity. SIROCCO: Structural Information
and Communication Complexity, LNCS, vol. 12810, 87–105.'
mla: Alistarh, Dan-Adrian, et al. “Wait-Free Approximate Agreement on Graphs.” Structural
Information and Communication Complexity, vol. 12810, Springer Nature, 2021,
pp. 87–105, doi:10.1007/978-3-030-79527-6_6.
short: D.-A. Alistarh, F. Ellen, J. Rybicki, in:, Structural Information and Communication
Complexity, Springer Nature, 2021, pp. 87–105.
conference:
end_date: 2021-07-01
location: Wrocław, Poland
name: 'SIROCCO: Structural Information and Communication Complexity'
start_date: 2021-06-28
date_created: 2021-08-08T22:01:29Z
date_published: 2021-06-20T00:00:00Z
date_updated: 2026-04-16T09:26:11Z
day: '20'
department:
- _id: DaAl
doi: 10.1007/978-3-030-79527-6_6
external_id:
arxiv:
- '2103.08949'
isi:
- '001292788400006'
intvolume: ' 12810'
isi: 1
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/2103.08949
month: '06'
oa: 1
oa_version: Preprint
page: 87-105
publication: Structural Information and Communication Complexity
publication_identifier:
eissn:
- 1611-3349
isbn:
- '9783030795269'
issn:
- 0302-9743
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
scopus_import: '1'
status: public
title: Wait-free approximate agreement on graphs
type: conference
user_id: ba8df636-2132-11f1-aed0-ed93e2281fdd
volume: 12810
year: '2021'
...
---
_id: '9824'
abstract:
- lang: eng
text: We define a new compact coordinate system in which each integer triplet addresses
a voxel in the BCC grid, and we investigate some of its properties. We propose
a characterization of 3D discrete analytical planes with their topological features
(in the Cartesian and in the new coordinate system) such as the interrelation
between the thickness of the plane and the separability constraint we aim to obtain.
acknowledgement: 'This work has been partially supported by the Ministry of Education,
Science and Technological Development of the Republic of Serbia through the project
no. 451-03-68/2020-14/200156: “Innovative scientific and artistic research from
the FTS (activity) domain” (LČ), the European Research Council (ERC) under the European
Union’s Horizon 2020 research and innovation programme, grant no. 788183 (RB), and
the DFG Collaborative Research Center TRR 109, ‘Discretization in Geometry and Dynamics’,
Austrian Science Fund (FWF), grant no. I 02979-N35 (RB).'
alternative_title:
- LNCS
article_processing_charge: No
author:
- first_name: Lidija
full_name: Čomić, Lidija
last_name: Čomić
- first_name: Rita
full_name: Zrour, Rita
last_name: Zrour
- first_name: Gaëlle
full_name: Largeteau-Skapin, Gaëlle
last_name: Largeteau-Skapin
- first_name: Ranita
full_name: Biswas, Ranita
id: 3C2B033E-F248-11E8-B48F-1D18A9856A87
last_name: Biswas
orcid: 0000-0002-5372-7890
- first_name: Eric
full_name: Andres, Eric
last_name: Andres
citation:
ama: 'Čomić L, Zrour R, Largeteau-Skapin G, Biswas R, Andres E. Body centered cubic
grid - coordinate system and discrete analytical plane definition. In: Discrete
Geometry and Mathematical Morphology. Vol 12708. Springer Nature; 2021:152-163.
doi:10.1007/978-3-030-76657-3_10'
apa: 'Čomić, L., Zrour, R., Largeteau-Skapin, G., Biswas, R., & Andres, E. (2021).
Body centered cubic grid - coordinate system and discrete analytical plane definition.
In Discrete Geometry and Mathematical Morphology (Vol. 12708, pp. 152–163).
Uppsala, Sweden: Springer Nature. https://doi.org/10.1007/978-3-030-76657-3_10'
chicago: Čomić, Lidija, Rita Zrour, Gaëlle Largeteau-Skapin, Ranita Biswas, and
Eric Andres. “Body Centered Cubic Grid - Coordinate System and Discrete Analytical
Plane Definition.” In Discrete Geometry and Mathematical Morphology, 12708:152–63.
Springer Nature, 2021. https://doi.org/10.1007/978-3-030-76657-3_10.
ieee: L. Čomić, R. Zrour, G. Largeteau-Skapin, R. Biswas, and E. Andres, “Body centered
cubic grid - coordinate system and discrete analytical plane definition,” in Discrete
Geometry and Mathematical Morphology, Uppsala, Sweden, 2021, vol. 12708, pp.
152–163.
ista: 'Čomić L, Zrour R, Largeteau-Skapin G, Biswas R, Andres E. 2021. Body centered
cubic grid - coordinate system and discrete analytical plane definition. Discrete
Geometry and Mathematical Morphology. DGMM: International Conference on Discrete
Geometry and Mathematical Morphology, LNCS, vol. 12708, 152–163.'
mla: Čomić, Lidija, et al. “Body Centered Cubic Grid - Coordinate System and Discrete
Analytical Plane Definition.” Discrete Geometry and Mathematical Morphology,
vol. 12708, Springer Nature, 2021, pp. 152–63, doi:10.1007/978-3-030-76657-3_10.
short: L. Čomić, R. Zrour, G. Largeteau-Skapin, R. Biswas, E. Andres, in:, Discrete
Geometry and Mathematical Morphology, Springer Nature, 2021, pp. 152–163.
conference:
end_date: 2021-05-27
location: Uppsala, Sweden
name: 'DGMM: International Conference on Discrete Geometry and Mathematical Morphology'
start_date: 2021-05-24
date_created: 2021-08-08T22:01:29Z
date_published: 2021-05-16T00:00:00Z
date_updated: 2026-04-16T09:26:30Z
day: '16'
department:
- _id: HeEd
doi: 10.1007/978-3-030-76657-3_10
ec_funded: 1
external_id:
isi:
- '001286400400010'
intvolume: ' 12708'
isi: 1
language:
- iso: eng
month: '05'
oa_version: None
page: 152-163
project:
- _id: 266A2E9E-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '788183'
name: Alpha Shape Theory Extended
- _id: 2561EBF4-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: I02979-N35
name: Persistence and stability of geometric complexes
publication: Discrete Geometry and Mathematical Morphology
publication_identifier:
eissn:
- 1611-3349
isbn:
- '9783030766566'
issn:
- 0302-9743
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
scopus_import: '1'
status: public
title: Body centered cubic grid - coordinate system and discrete analytical plane
definition
type: conference
user_id: ba8df636-2132-11f1-aed0-ed93e2281fdd
volume: 12708
year: '2021'
...
---
_id: '9825'
abstract:
- lang: eng
text: "The dual attack has long been considered a relevant attack on lattice-based
cryptographic schemes relying on the hardness of learning with errors (LWE) and
its structured variants. As solving LWE corresponds to finding a nearest point
on a lattice, one may naturally wonder how efficient this dual approach is for
solving more general closest vector problems, such as the classical closest vector
problem (CVP), the variants bounded distance decoding (BDD) and approximate CVP,
and preprocessing versions of these problems. While primal, sieving-based solutions
to these problems (with preprocessing) were recently studied in a series of works
on approximate Voronoi cells [Laa16b, DLdW19, Laa20, DLvW20], for the dual attack
no such overview exists, especially for problems with preprocessing. With one
of the take-away messages of the approximate Voronoi cell line of work being that
primal attacks work well for approximate CVP(P) but scale poorly for BDD(P), one
may further wonder if the dual attack suffers the same drawbacks, or if it is
perhaps a better solution when trying to solve BDD(P).\r\n\r\nIn this work we
provide an overview of cost estimates for dual algorithms for solving these “classical”
closest lattice vector problems. Heuristically we expect to solve the search version
of average-case CVPP in time and space 20.293\U0001D451+\U0001D45C(\U0001D451)
\ in the single-target model. The distinguishing version of average-case CVPP,
where we wish to distinguish between random targets and targets planted at distance
(say) 0.99⋅\U0001D454\U0001D451 from the lattice, has the same complexity in
the single-target model, but can be solved in time and space 20.195\U0001D451+\U0001D45C(\U0001D451)
\ in the multi-target setting, when given a large number of targets from either
target distribution. This suggests an inequivalence between distinguishing and
searching, as we do not expect a similar improvement in the multi-target setting
to hold for search-CVPP. We analyze three slightly different decoders, both for
distinguishing and searching, and experimentally obtain concrete cost estimates
for the dual attack in dimensions 50 to 80, which confirm our heuristic assumptions,
and show that the hidden order terms in the asymptotic estimates are quite small.\r\n\r\nOur
main take-away message is that the dual attack appears to mirror the approximate
Voronoi cell line of work – whereas using approximate Voronoi cells works well
for approximate CVP(P) but scales poorly for BDD(P), the dual approach scales
well for BDD(P) instances but performs poorly on approximate CVP(P)."
acknowledgement: The authors thank Sauvik Bhattacharya, L´eo Ducas, Rachel Player,
and Christine van Vredendaal for early discussions on this topic and on preliminary
results. The authors further thank the reviewers of CT-RSA 2021 for their valuable
feedback.
alternative_title:
- LNCS
article_processing_charge: No
author:
- first_name: Thijs
full_name: Laarhoven, Thijs
last_name: Laarhoven
- first_name: Michael
full_name: Walter, Michael
id: 488F98B0-F248-11E8-B48F-1D18A9856A87
last_name: Walter
orcid: 0000-0003-3186-2482
citation:
ama: 'Laarhoven T, Walter M. Dual lattice attacks for closest vector problems (with
preprocessing). In: Topics in Cryptology – CT-RSA 2021. Vol 12704. Springer
Nature; 2021:478-502. doi:10.1007/978-3-030-75539-3_20'
apa: 'Laarhoven, T., & Walter, M. (2021). Dual lattice attacks for closest vector
problems (with preprocessing). In Topics in Cryptology – CT-RSA 2021 (Vol.
12704, pp. 478–502). Virtual Event: Springer Nature. https://doi.org/10.1007/978-3-030-75539-3_20'
chicago: Laarhoven, Thijs, and Michael Walter. “Dual Lattice Attacks for Closest
Vector Problems (with Preprocessing).” In Topics in Cryptology – CT-RSA 2021,
12704:478–502. Springer Nature, 2021. https://doi.org/10.1007/978-3-030-75539-3_20.
ieee: T. Laarhoven and M. Walter, “Dual lattice attacks for closest vector problems
(with preprocessing),” in Topics in Cryptology – CT-RSA 2021, Virtual Event,
2021, vol. 12704, pp. 478–502.
ista: 'Laarhoven T, Walter M. 2021. Dual lattice attacks for closest vector problems
(with preprocessing). Topics in Cryptology – CT-RSA 2021. CT-RSA: Cryptographers’
Track at the RSA Conference, LNCS, vol. 12704, 478–502.'
mla: Laarhoven, Thijs, and Michael Walter. “Dual Lattice Attacks for Closest Vector
Problems (with Preprocessing).” Topics in Cryptology – CT-RSA 2021, vol.
12704, Springer Nature, 2021, pp. 478–502, doi:10.1007/978-3-030-75539-3_20.
short: T. Laarhoven, M. Walter, in:, Topics in Cryptology – CT-RSA 2021, Springer
Nature, 2021, pp. 478–502.
conference:
end_date: 2021-05-20
location: Virtual Event
name: 'CT-RSA: Cryptographers’ Track at the RSA Conference'
start_date: 2021-05-17
date_created: 2021-08-08T22:01:30Z
date_published: 2021-05-11T00:00:00Z
date_updated: 2026-04-16T09:28:30Z
day: '11'
department:
- _id: KrPi
doi: 10.1007/978-3-030-75539-3_20
intvolume: ' 12704'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://eprint.iacr.org/2021/557
month: '05'
oa: 1
oa_version: Preprint
page: 478-502
publication: Topics in Cryptology – CT-RSA 2021
publication_identifier:
eissn:
- 1611-3349
isbn:
- '9783030755386'
issn:
- 0302-9743
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
scopus_import: '1'
status: public
title: Dual lattice attacks for closest vector problems (with preprocessing)
type: conference
user_id: ba8df636-2132-11f1-aed0-ed93e2281fdd
volume: 12704
year: '2021'
...
---
_id: '9826'
abstract:
- lang: eng
text: "Automated contract tracing aims at supporting manual contact tracing during
pandemics by alerting users of encounters with infected people. There are currently
many proposals for protocols (like the “decentralized” DP-3T and PACT or the “centralized”
ROBERT and DESIRE) to be run on mobile phones, where the basic idea is to regularly
broadcast (using low energy Bluetooth) some values, and at the same time store
(a function of) incoming messages broadcasted by users in their proximity. In
the existing proposals one can trigger false positives on a massive scale by an
“inverse-Sybil” attack, where a large number of devices (malicious users or hacked
phones) pretend to be the same user, such that later, just a single person needs
to be diagnosed (and allowed to upload) to trigger an alert for all users who
were in proximity to any of this large group of devices.\r\n\r\nWe propose the
first protocols that do not succumb to such attacks assuming the devices involved
in the attack do not constantly communicate, which we observe is a necessary assumption.
The high level idea of the protocols is to derive the values to be broadcasted
by a hash chain, so that two (or more) devices who want to launch an inverse-Sybil
attack will not be able to connect their respective chains and thus only one of
them will be able to upload. Our protocols also achieve security against replay,
belated replay, and one of them even against relay attacks."
acknowledgement: Guillermo Pascual-Perez and Michelle Yeo were funded by the European
Union’s Horizon 2020 research and innovation programme under the Marie Skłodowska–Curie
Grant Agreement No. 665385; the remaining contributors to this project have received
funding from the European Research Council (ERC) under the European Union’s Horizon
2020 research and innovation programme (682815 - TOCNeT).
alternative_title:
- LNCS
article_processing_charge: No
author:
- first_name: Benedikt
full_name: Auerbach, Benedikt
id: D33D2B18-E445-11E9-ABB7-15F4E5697425
last_name: Auerbach
orcid: 0000-0002-7553-6606
- first_name: Suvradip
full_name: Chakraborty, Suvradip
id: B9CD0494-D033-11E9-B219-A439E6697425
last_name: Chakraborty
- first_name: Karen
full_name: Klein, Karen
id: 3E83A2F8-F248-11E8-B48F-1D18A9856A87
last_name: Klein
- first_name: Guillermo
full_name: Pascual Perez, Guillermo
id: 2D7ABD02-F248-11E8-B48F-1D18A9856A87
last_name: Pascual Perez
orcid: 0000-0001-8630-415X
- first_name: Krzysztof Z
full_name: Pietrzak, Krzysztof Z
id: 3E04A7AA-F248-11E8-B48F-1D18A9856A87
last_name: Pietrzak
orcid: 0000-0002-9139-1654
- first_name: Michael
full_name: Walter, Michael
id: 488F98B0-F248-11E8-B48F-1D18A9856A87
last_name: Walter
orcid: 0000-0003-3186-2482
- first_name: Michelle X
full_name: Yeo, Michelle X
id: 2D82B818-F248-11E8-B48F-1D18A9856A87
last_name: Yeo
orcid: 0009-0001-3676-4809
citation:
ama: 'Auerbach B, Chakraborty S, Klein K, et al. Inverse-Sybil attacks in automated
contact tracing. In: Topics in Cryptology – CT-RSA 2021. Vol 12704. Springer
Nature; 2021:399-421. doi:10.1007/978-3-030-75539-3_17'
apa: 'Auerbach, B., Chakraborty, S., Klein, K., Pascual Perez, G., Pietrzak, K.
Z., Walter, M., & Yeo, M. X. (2021). Inverse-Sybil attacks in automated contact
tracing. In Topics in Cryptology – CT-RSA 2021 (Vol. 12704, pp. 399–421).
Virtual Event: Springer Nature. https://doi.org/10.1007/978-3-030-75539-3_17'
chicago: Auerbach, Benedikt, Suvradip Chakraborty, Karen Klein, Guillermo Pascual
Perez, Krzysztof Z Pietrzak, Michael Walter, and Michelle X Yeo. “Inverse-Sybil
Attacks in Automated Contact Tracing.” In Topics in Cryptology – CT-RSA 2021,
12704:399–421. Springer Nature, 2021. https://doi.org/10.1007/978-3-030-75539-3_17.
ieee: B. Auerbach et al., “Inverse-Sybil attacks in automated contact tracing,”
in Topics in Cryptology – CT-RSA 2021, Virtual Event, 2021, vol. 12704,
pp. 399–421.
ista: 'Auerbach B, Chakraborty S, Klein K, Pascual Perez G, Pietrzak KZ, Walter
M, Yeo MX. 2021. Inverse-Sybil attacks in automated contact tracing. Topics in
Cryptology – CT-RSA 2021. CT-RSA: Cryptographers’ Track at the RSA Conference,
LNCS, vol. 12704, 399–421.'
mla: Auerbach, Benedikt, et al. “Inverse-Sybil Attacks in Automated Contact Tracing.”
Topics in Cryptology – CT-RSA 2021, vol. 12704, Springer Nature, 2021,
pp. 399–421, doi:10.1007/978-3-030-75539-3_17.
short: B. Auerbach, S. Chakraborty, K. Klein, G. Pascual Perez, K.Z. Pietrzak, M.
Walter, M.X. Yeo, in:, Topics in Cryptology – CT-RSA 2021, Springer Nature, 2021,
pp. 399–421.
conference:
end_date: 2021-05-20
location: Virtual Event
name: 'CT-RSA: Cryptographers’ Track at the RSA Conference'
start_date: 2021-05-17
corr_author: '1'
date_created: 2021-08-08T22:01:30Z
date_published: 2021-05-11T00:00:00Z
date_updated: 2026-04-16T09:28:46Z
day: '11'
department:
- _id: KrPi
- _id: GradSch
doi: 10.1007/978-3-030-75539-3_17
ec_funded: 1
intvolume: ' 12704'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://eprint.iacr.org/2020/670
month: '05'
oa: 1
oa_version: Submitted Version
page: 399-421
project:
- _id: 2564DBCA-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '665385'
name: International IST Doctoral Program
- _id: 258AA5B2-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '682815'
name: Teaching Old Crypto New Tricks
publication: Topics in Cryptology – CT-RSA 2021
publication_identifier:
eissn:
- 1611-3349
isbn:
- '9783030755386'
issn:
- 0302-9743
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
scopus_import: '1'
status: public
title: Inverse-Sybil attacks in automated contact tracing
type: conference
user_id: ba8df636-2132-11f1-aed0-ed93e2281fdd
volume: 12704
year: '2021'
...
---
_id: '9827'
abstract:
- lang: eng
text: 'The Nearest neighbour search (NNS) is a fundamental problem in many application
domains dealing with multidimensional data. In a concurrent setting, where dynamic
modifications are allowed, a linearizable implementation of the NNS is highly
desirable.This paper introduces the LockFree-kD-tree (LFkD-tree ): a lock-free
concurrent kD-tree, which implements an abstract data type (ADT) that provides
the operations Add, Remove, Contains, and NNS. Our implementation is linearizable.
The operations in the LFkD-tree use single-word read and compare-and-swap (Image
1 ) atomic primitives, which are readily supported on available multi-core processors.
We experimentally evaluate the LFkD-tree using several benchmarks comprising real-world
and synthetic datasets. The experiments show that the presented design is scalable
and achieves significant speed-up compared to the implementations of an existing
sequential kD-tree and a recently proposed multidimensional indexing structure,
PH-tree.'
article_processing_charge: No
article_type: original
author:
- first_name: Bapi
full_name: Chatterjee, Bapi
id: 3C41A08A-F248-11E8-B48F-1D18A9856A87
last_name: Chatterjee
orcid: 0000-0002-2742-4028
- first_name: Ivan
full_name: Walulya, Ivan
last_name: Walulya
- first_name: Philippas
full_name: Tsigas, Philippas
last_name: Tsigas
citation:
ama: Chatterjee B, Walulya I, Tsigas P. Concurrent linearizable nearest neighbour
search in LockFree-kD-tree. Theoretical Computer Science. 2021;886:27-48.
doi:10.1016/j.tcs.2021.06.041
apa: Chatterjee, B., Walulya, I., & Tsigas, P. (2021). Concurrent linearizable
nearest neighbour search in LockFree-kD-tree. Theoretical Computer Science.
Elsevier. https://doi.org/10.1016/j.tcs.2021.06.041
chicago: Chatterjee, Bapi, Ivan Walulya, and Philippas Tsigas. “Concurrent Linearizable
Nearest Neighbour Search in LockFree-KD-Tree.” Theoretical Computer Science.
Elsevier, 2021. https://doi.org/10.1016/j.tcs.2021.06.041.
ieee: B. Chatterjee, I. Walulya, and P. Tsigas, “Concurrent linearizable nearest
neighbour search in LockFree-kD-tree,” Theoretical Computer Science, vol.
886. Elsevier, pp. 27–48, 2021.
ista: Chatterjee B, Walulya I, Tsigas P. 2021. Concurrent linearizable nearest neighbour
search in LockFree-kD-tree. Theoretical Computer Science. 886, 27–48.
mla: Chatterjee, Bapi, et al. “Concurrent Linearizable Nearest Neighbour Search
in LockFree-KD-Tree.” Theoretical Computer Science, vol. 886, Elsevier,
2021, pp. 27–48, doi:10.1016/j.tcs.2021.06.041.
short: B. Chatterjee, I. Walulya, P. Tsigas, Theoretical Computer Science 886 (2021)
27–48.
corr_author: '1'
date_created: 2021-08-08T22:01:31Z
date_published: 2021-09-13T00:00:00Z
date_updated: 2024-10-09T21:00:45Z
day: '13'
department:
- _id: DaAl
doi: 10.1016/j.tcs.2021.06.041
external_id:
isi:
- '000694718900004'
intvolume: ' 886'
isi: 1
keyword:
- Concurrent data structure
- kD-tree
- Nearest neighbor search
- Similarity search
- Lock-free
- Linearizability
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://publications.lib.chalmers.se/records/fulltext/232185/232185.pdf
month: '09'
oa: 1
oa_version: Submitted Version
page: 27-48
publication: Theoretical Computer Science
publication_identifier:
issn:
- 0304-3975
publication_status: published
publisher: Elsevier
quality_controlled: '1'
scopus_import: '1'
status: public
title: Concurrent linearizable nearest neighbour search in LockFree-kD-tree
type: journal_article
user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
volume: 886
year: '2021'
...
---
_id: '9829'
abstract:
- lang: eng
text: In 2020, many in-person scientific events were canceled due to the COVID-19
pandemic, creating a vacuum in networking and knowledge exchange between scientists.
To fill this void in scientific communication, a group of early career nanocrystal
enthusiasts launched the virtual seminar series, News in Nanocrystals, in the
summer of 2020. By the end of the year, the series had attracted over 850 participants
from 46 countries. In this Nano Focus, we describe the process of organizing the
News in Nanocrystals seminar series; discuss its growth, emphasizing what the
organizers have learned in terms of diversity and accessibility; and provide an
outlook for the next steps and future opportunities. This summary and analysis
of experiences and learned lessons are intended to inform the broader scientific
community, especially those who are looking for avenues to continue fostering
discussion and scientific engagement virtually, both during the pandemic and after.
acknowledgement: K. E. Shulenberger, M. D. Klein, T. Šverko, and H. R. Keller would
like to thank Professors Moungi Bawendi (MIT) and Gordana Dukovic (CU Boulder) for
their feedback and support of the News in Nanocrystals initiative. The authors thank
Madison Jilek (CU Boulder) and Dhananjeya Kumaar (ETH Zurich) for their help in
the organization of the seminar, and Professors Brandi Cossairt (University of Washington)
and Gordana Dukovic for their feedback on an earlier version of this manuscript.
The authors thank all the seminar speakers and attendees for their interest and
continuing participation in the seminar series.
article_processing_charge: No
article_type: original
author:
- first_name: Dmitry
full_name: Baranov, Dmitry
last_name: Baranov
- first_name: Tara
full_name: Šverko, Tara
last_name: Šverko
- first_name: Taylor
full_name: Moot, Taylor
last_name: Moot
- first_name: Helena R.
full_name: Keller, Helena R.
last_name: Keller
- first_name: Megan D.
full_name: Klein, Megan D.
last_name: Klein
- first_name: E. K.
full_name: Vishnu, E. K.
last_name: Vishnu
- first_name: Daniel
full_name: Balazs, Daniel
id: 302BADF6-85FC-11EA-9E3B-B9493DDC885E
last_name: Balazs
orcid: 0000-0001-7597-043X
- first_name: Katherine E.
full_name: Shulenberger, Katherine E.
last_name: Shulenberger
citation:
ama: 'Baranov D, Šverko T, Moot T, et al. News in Nanocrystals seminar: Self-assembly
of early career researchers toward globally accessible nanoscience. ACS Nano.
2021;15(7):10743–10747. doi:10.1021/acsnano.1c03276'
apa: 'Baranov, D., Šverko, T., Moot, T., Keller, H. R., Klein, M. D., Vishnu, E.
K., … Shulenberger, K. E. (2021). News in Nanocrystals seminar: Self-assembly
of early career researchers toward globally accessible nanoscience. ACS Nano.
American Chemical Society. https://doi.org/10.1021/acsnano.1c03276'
chicago: 'Baranov, Dmitry, Tara Šverko, Taylor Moot, Helena R. Keller, Megan D.
Klein, E. K. Vishnu, Daniel Balazs, and Katherine E. Shulenberger. “News in Nanocrystals
Seminar: Self-Assembly of Early Career Researchers toward Globally Accessible
Nanoscience.” ACS Nano. American Chemical Society, 2021. https://doi.org/10.1021/acsnano.1c03276.'
ieee: 'D. Baranov et al., “News in Nanocrystals seminar: Self-assembly of
early career researchers toward globally accessible nanoscience,” ACS Nano,
vol. 15, no. 7. American Chemical Society, pp. 10743–10747, 2021.'
ista: 'Baranov D, Šverko T, Moot T, Keller HR, Klein MD, Vishnu EK, Balazs D, Shulenberger
KE. 2021. News in Nanocrystals seminar: Self-assembly of early career researchers
toward globally accessible nanoscience. ACS Nano. 15(7), 10743–10747.'
mla: 'Baranov, Dmitry, et al. “News in Nanocrystals Seminar: Self-Assembly of Early
Career Researchers toward Globally Accessible Nanoscience.” ACS Nano, vol.
15, no. 7, American Chemical Society, 2021, pp. 10743–10747, doi:10.1021/acsnano.1c03276.'
short: D. Baranov, T. Šverko, T. Moot, H.R. Keller, M.D. Klein, E.K. Vishnu, D.
Balazs, K.E. Shulenberger, ACS Nano 15 (2021) 10743–10747.
date_created: 2021-08-08T22:01:31Z
date_published: 2021-07-06T00:00:00Z
date_updated: 2026-06-18T19:58:29Z
day: '06'
ddc:
- '540'
department:
- _id: MaIb
doi: 10.1021/acsnano.1c03276
external_id:
isi:
- '000679406500002'
pmid:
- '34228432'
intvolume: ' 15'
isi: 1
issue: '7'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.1021/acsnano.1c03276
month: '07'
oa: 1
oa_version: Published Version
page: 10743–10747
pmid: 1
publication: ACS Nano
publication_identifier:
eissn:
- 1936-086X
issn:
- 1936-0851
publication_status: published
publisher: American Chemical Society
quality_controlled: '1'
scopus_import: '1'
status: public
title: 'News in Nanocrystals seminar: Self-assembly of early career researchers toward
globally accessible nanoscience'
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 15
year: '2021'
...
---
_id: '6965'
abstract:
- lang: eng
text: The central object of investigation of this paper is the Hirzebruch class,
a deformation of the Todd class, given by Hirzebruch (for smooth varieties). The
generalization for singular varieties is due to Brasselet–Schürmann–Yokura. Following
the work of Weber, we investigate its equivariant version for (possibly singular)
toric varieties. The local decomposition of the Hirzebruch class to the fixed
points of the torus action and a formula for the local class in terms of the defining
fan are recalled. After this review part, we prove the positivity of local Hirzebruch
classes for all toric varieties, thus proving false the alleged counterexample
given by Weber.
article_processing_charge: No
article_type: original
arxiv: 1
author:
- first_name: Kamil P
full_name: Rychlewicz, Kamil P
id: 85A07246-A8BF-11E9-B4FA-D9E3E5697425
last_name: Rychlewicz
citation:
ama: Rychlewicz KP. The positivity of local equivariant Hirzebruch class for toric
varieties. Bulletin of the London Mathematical Society. 2021;53(2):560-574.
doi:10.1112/blms.12442
apa: Rychlewicz, K. P. (2021). The positivity of local equivariant Hirzebruch class
for toric varieties. Bulletin of the London Mathematical Society. Wiley.
https://doi.org/10.1112/blms.12442
chicago: Rychlewicz, Kamil P. “The Positivity of Local Equivariant Hirzebruch Class
for Toric Varieties.” Bulletin of the London Mathematical Society. Wiley,
2021. https://doi.org/10.1112/blms.12442.
ieee: K. P. Rychlewicz, “The positivity of local equivariant Hirzebruch class for
toric varieties,” Bulletin of the London Mathematical Society, vol. 53,
no. 2. Wiley, pp. 560–574, 2021.
ista: Rychlewicz KP. 2021. The positivity of local equivariant Hirzebruch class
for toric varieties. Bulletin of the London Mathematical Society. 53(2), 560–574.
mla: Rychlewicz, Kamil P. “The Positivity of Local Equivariant Hirzebruch Class
for Toric Varieties.” Bulletin of the London Mathematical Society, vol.
53, no. 2, Wiley, 2021, pp. 560–74, doi:10.1112/blms.12442.
short: K.P. Rychlewicz, Bulletin of the London Mathematical Society 53 (2021) 560–574.
corr_author: '1'
date_created: 2019-10-24T08:04:09Z
date_published: 2021-04-01T00:00:00Z
date_updated: 2024-10-09T20:59:03Z
day: '01'
department:
- _id: TaHa
doi: 10.1112/blms.12442
external_id:
arxiv:
- '1910.10435'
isi:
- '000594805800001'
intvolume: ' 53'
isi: 1
issue: '2'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/1910.10435
month: '04'
oa: 1
oa_version: Preprint
page: 560-574
publication: Bulletin of the London Mathematical Society
publication_identifier:
eissn:
- 1469-2120
issn:
- 0024-6093
publication_status: published
publisher: Wiley
quality_controlled: '1'
scopus_import: '1'
status: public
title: The positivity of local equivariant Hirzebruch class for toric varieties
type: journal_article
user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
volume: 53
year: '2021'
...
---
OA_place: publisher
OA_type: green
_id: '6995'
abstract:
- lang: eng
text: Human brain organoids represent a powerful tool for the study of human neurological
diseases particularly those that impact brain growth and structure. However, many
neurological diseases lack obvious anatomical abnormalities, yet significantly
impact neural network functions, raising the question of whether organoids possess
sufficient neural network architecture and complexity to model these conditions.
Here, we explore the network level functions of brain organoids using calcium
sensor imaging and extracellular recording approaches that together reveal the
existence of complex oscillatory network behaviors reminiscent of intact brain
preparations. We further demonstrate strikingly abnormal epileptiform network
activity in organoids derived from a Rett Syndrome patient despite only modest
anatomical differences from isogenically matched controls, and rescue with an
unconventional neuromodulatory drug Pifithrin-α. Together, these findings provide
an essential foundation for the utilization of human brain organoids to study
intact and disordered human brain network formation and illustrate their utility
in therapeutic discovery.
acknowledgement: We thank S. Butler, T. Carmichael and members of the laboratory of
B.G.N. for helpful discussions and comments on the manuscript; N. Vishlaghi and
F. Turcios-Hernandez for technical assistance, and J. Lee, S.-K. Lee, H. Shinagawa
and K. Yoshikawa for valuable reagents. We also thank the UCLA Eli and Edythe Broad
Stem Cell Research Center (BSCRC) and Intellectual and Developmental Disabilities
Research Center microscopy cores for access to imaging facilities. This work was
supported by grants from the California Institute for Regenerative Medicine (CIRM)
(DISC1-08819 to B.G.N.), the National Institute of Health (R01NS089817, R01DA051897
and P50HD103557 to B.G.N.; K08NS119747 to R.A.S.; K99HD096105 to M.W.; R01MH123922,
R01MH121521 and P50HD103557 to M.J.G.; R01GM099134 to K.P.; R01NS103788 to W.E.L.;
R01NS088571 to J.M.P.; R01NS030549 and R01AG050474 to I.M.), and research awards
from the UCLA Jonsson Comprehensive Cancer Center and BSCRC Ablon Scholars Program
(to B.G.N.), the BSCRC Innovation Program (to B.G.N., K.P. and W.E.L.), the UCLA
BSCRC Steffy Brain Aging Research Fund (to B.G.N. and W.E.L.) and the UCLA Clinical
and Translational Science Institute (to B.G.N.), Paul Allen Family Foundation Frontiers
Group (to K.P. and W.E.L.), the March of Dimes Foundation (to W.E.L.) and the Simons
Foundation Autism Research Initiative Bridge to Independence Program (to R.A.S.
and M.J.G.). R.A.S. was also supported by the UCLA/NINDS Translational Neuroscience
Training Grant (R25NS065723), a Research and Training Fellowship from the American
Epilepsy Society, a Taking Flight Award from CURE Epilepsy and a Clinician Scientist
training award from the UCLA BSCRC. J.E.B. was supported by the UCLA BSCRC Rose
Hills Foundation Graduate Scholarship Training Program. M.W. was supported by postdoctoral
training awards provided by the UCLA BSCRC and the Uehara Memorial Foundation. O.A.M.
and A.K. were supported in part by the UCLA-California State University Northridge
CIRM-Bridges training program (EDUC2-08411). We also acknowledge the support of
the IDDRC Cells, Circuits and Systems Analysis, Microscopy and Genetics and Genomics
Cores of the Semel Institute of Neuroscience at UCLA, which are supported by the
NICHD (U54HD087101 and P50HD10355701). We lastly acknowledge support from a Quantitative
and Computational Biosciences Collaboratory Postdoctoral Fellowship to S.M. and
the Quantitative and Computational Biosciences Collaboratory community, directed
by M. Pellegrini.
article_processing_charge: No
article_type: review
author:
- first_name: Ranmal A.
full_name: Samarasinghe, Ranmal A.
last_name: Samarasinghe
- first_name: Osvaldo
full_name: Miranda, Osvaldo
id: 862A3C56-A8BF-11E9-B4FA-D9E3E5697425
last_name: Miranda
orcid: 0000-0001-6618-6889
- first_name: Jessie E.
full_name: Buth, Jessie E.
last_name: Buth
- first_name: Simon
full_name: Mitchell, Simon
last_name: Mitchell
- first_name: Isabella
full_name: Ferando, Isabella
last_name: Ferando
- first_name: Momoko
full_name: Watanabe, Momoko
last_name: Watanabe
- first_name: Arinnae
full_name: Kurdian, Arinnae
last_name: Kurdian
- first_name: Peyman
full_name: Golshani, Peyman
last_name: Golshani
- first_name: Kathrin
full_name: Plath, Kathrin
last_name: Plath
- first_name: William E.
full_name: Lowry, William E.
last_name: Lowry
- first_name: Jack M.
full_name: Parent, Jack M.
last_name: Parent
- first_name: Istvan
full_name: Mody, Istvan
last_name: Mody
- first_name: Bennett G.
full_name: Novitch, Bennett G.
last_name: Novitch
citation:
ama: Samarasinghe RA, Miranda O, Buth JE, et al. Identification of neural oscillations
and epileptiform changes in human brain organoids. Nature Neuroscience.
2021;24:32. doi:10.1038/s41593-021-00906-5
apa: Samarasinghe, R. A., Miranda, O., Buth, J. E., Mitchell, S., Ferando, I., Watanabe,
M., … Novitch, B. G. (2021). Identification of neural oscillations and epileptiform
changes in human brain organoids. Nature Neuroscience. Springer Nature.
https://doi.org/10.1038/s41593-021-00906-5
chicago: Samarasinghe, Ranmal A., Osvaldo Miranda, Jessie E. Buth, Simon Mitchell,
Isabella Ferando, Momoko Watanabe, Arinnae Kurdian, et al. “Identification of
Neural Oscillations and Epileptiform Changes in Human Brain Organoids.” Nature
Neuroscience. Springer Nature, 2021. https://doi.org/10.1038/s41593-021-00906-5.
ieee: R. A. Samarasinghe et al., “Identification of neural oscillations and
epileptiform changes in human brain organoids,” Nature Neuroscience, vol.
24. Springer Nature, p. 32, 2021.
ista: Samarasinghe RA, Miranda O, Buth JE, Mitchell S, Ferando I, Watanabe M, Kurdian
A, Golshani P, Plath K, Lowry WE, Parent JM, Mody I, Novitch BG. 2021. Identification
of neural oscillations and epileptiform changes in human brain organoids. Nature
Neuroscience. 24, 32.
mla: Samarasinghe, Ranmal A., et al. “Identification of Neural Oscillations and
Epileptiform Changes in Human Brain Organoids.” Nature Neuroscience, vol.
24, Springer Nature, 2021, p. 32, doi:10.1038/s41593-021-00906-5.
short: R.A. Samarasinghe, O. Miranda, J.E. Buth, S. Mitchell, I. Ferando, M. Watanabe,
A. Kurdian, P. Golshani, K. Plath, W.E. Lowry, J.M. Parent, I. Mody, B.G. Novitch,
Nature Neuroscience 24 (2021) 32.
date_created: 2019-11-10T11:23:58Z
date_published: 2021-08-23T00:00:00Z
date_updated: 2025-07-09T09:00:12Z
day: '23'
department:
- _id: GradSch
- _id: SiHi
doi: 10.1038/s41593-021-00906-5
external_id:
isi:
- '000687516300001'
pmid:
- '34426698 '
intvolume: ' 24'
isi: 1
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.1101/820183
month: '08'
oa: 1
oa_version: Preprint
page: '32'
pmid: 1
publication: Nature Neuroscience
publication_identifier:
eissn:
- 1546-1726
issn:
- 1097-6256
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
scopus_import: '1'
status: public
title: Identification of neural oscillations and epileptiform changes in human brain
organoids
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 24
year: '2021'
...
---
_id: '7463'
abstract:
- lang: eng
text: Resting-state brain activity is characterized by the presence of neuronal
avalanches showing absence of characteristic size. Such evidence has been interpreted
in the context of criticality and associated with the normal functioning of the
brain. A distinctive attribute of systems at criticality is the presence of long-range
correlations. Thus, to verify the hypothesis that the brain operates close to
a critical point and consequently assess deviations from criticality for diagnostic
purposes, it is of primary importance to robustly and reliably characterize correlations
in resting-state brain activity. Recent works focused on the analysis of narrow-band
electroencephalography (EEG) and magnetoencephalography (MEG) signal amplitude
envelope, showing evidence of long-range temporal correlations (LRTC) in neural
oscillations. However, brain activity is a broadband phenomenon, and a significant
piece of information useful to precisely discriminate between normal (critical)
and pathological behavior (non-critical), may be encoded in the broadband spatio-temporal
cortical dynamics. Here we propose to characterize the temporal correlations in
the broadband brain activity through the lens of neuronal avalanches. To this
end, we consider resting-state EEG and long-term MEG recordings, extract the corresponding
neuronal avalanche sequences, and study their temporal correlations. We demonstrate
that the broadband resting-state brain activity consistently exhibits long-range
power-law correlations in both EEG and MEG recordings, with similar values of
the scaling exponents. Importantly, although we observe that the avalanche size
distribution depends on scale parameters, scaling exponents characterizing long-range
correlations are quite robust. In particular, they are independent of the temporal
binning (scale of analysis), indicating that our analysis captures intrinsic characteristics
of the underlying dynamics. Because neuronal avalanches constitute a fundamental
feature of neural systems with universal characteristics, the proposed approach
may serve as a general, systems- and experiment-independent procedure to infer
the existence of underlying long-range correlations in extended neural systems,
and identify pathological behaviors in the complex spatio-temporal interplay of
cortical rhythms.
acknowledgement: LdA would like to acknowledge the financial support from MIUR-PRIN2017
WZFTZP and VALERE:VAnviteLli pEr la RicErca 2019. FL acknowledges support from the
European Union’s Horizon 2020 research and innovation programme under the Marie
Sklodowska-Curie Grant Agreement No. 754411. HJH would like to thank the Agencies
CAPES and FUNCAP for financial support.
article_processing_charge: No
article_type: original
author:
- first_name: Fabrizio
full_name: Lombardi, Fabrizio
id: A057D288-3E88-11E9-986D-0CF4E5697425
last_name: Lombardi
orcid: 0000-0003-2623-5249
- first_name: Oren
full_name: Shriki, Oren
last_name: Shriki
- first_name: Hans J
full_name: Herrmann, Hans J
last_name: Herrmann
- first_name: Lucilla
full_name: de Arcangelis, Lucilla
last_name: de Arcangelis
citation:
ama: Lombardi F, Shriki O, Herrmann HJ, de Arcangelis L. Long-range temporal correlations
in the broadband resting state activity of the human brain revealed by neuronal
avalanches. Neurocomputing. 2021;461:657-666. doi:10.1016/j.neucom.2020.05.126
apa: Lombardi, F., Shriki, O., Herrmann, H. J., & de Arcangelis, L. (2021).
Long-range temporal correlations in the broadband resting state activity of the
human brain revealed by neuronal avalanches. Neurocomputing. Elsevier.
https://doi.org/10.1016/j.neucom.2020.05.126
chicago: Lombardi, Fabrizio, Oren Shriki, Hans J Herrmann, and Lucilla de Arcangelis.
“Long-Range Temporal Correlations in the Broadband Resting State Activity of the
Human Brain Revealed by Neuronal Avalanches.” Neurocomputing. Elsevier,
2021. https://doi.org/10.1016/j.neucom.2020.05.126.
ieee: F. Lombardi, O. Shriki, H. J. Herrmann, and L. de Arcangelis, “Long-range
temporal correlations in the broadband resting state activity of the human brain
revealed by neuronal avalanches,” Neurocomputing, vol. 461. Elsevier, pp.
657–666, 2021.
ista: Lombardi F, Shriki O, Herrmann HJ, de Arcangelis L. 2021. Long-range temporal
correlations in the broadband resting state activity of the human brain revealed
by neuronal avalanches. Neurocomputing. 461, 657–666.
mla: Lombardi, Fabrizio, et al. “Long-Range Temporal Correlations in the Broadband
Resting State Activity of the Human Brain Revealed by Neuronal Avalanches.” Neurocomputing,
vol. 461, Elsevier, 2021, pp. 657–66, doi:10.1016/j.neucom.2020.05.126.
short: F. Lombardi, O. Shriki, H.J. Herrmann, L. de Arcangelis, Neurocomputing 461
(2021) 657–666.
date_created: 2020-02-06T16:09:14Z
date_published: 2021-05-13T00:00:00Z
date_updated: 2025-04-14T07:44:02Z
day: '13'
department:
- _id: GaTk
doi: 10.1016/j.neucom.2020.05.126
ec_funded: 1
external_id:
isi:
- '000704086300015'
intvolume: ' 461'
isi: 1
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.1101/2020.02.03.930966
month: '05'
oa: 1
oa_version: Preprint
page: 657-666
project:
- _id: 260C2330-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '754411'
name: ISTplus - Postdoctoral Fellowships
publication: Neurocomputing
publication_identifier:
eissn:
- 1872-8286
issn:
- 0925-2312
publication_status: published
publisher: Elsevier
quality_controlled: '1'
scopus_import: '1'
status: public
title: Long-range temporal correlations in the broadband resting state activity of
the human brain revealed by neuronal avalanches
type: journal_article
user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
volume: 461
year: '2021'
...
---
_id: '7551'
abstract:
- lang: eng
text: Novelty facilitates formation of memories. The detection of novelty and storage
of contextual memories are both mediated by the hippocampus, yet the mechanisms
that link these two functions remain to be defined. Dentate granule cells (GCs)
of the dorsal hippocampus fire upon novelty exposure forming engrams of contextual
memory. However, their key excitatory inputs from the entorhinal cortex are not
responsive to novelty and are insufficient to make dorsal GCs fire reliably. Here
we uncover a powerful glutamatergic pathway to dorsal GCs from ventral hippocampal
mossy cells (MCs) that relays novelty, and is necessary and sufficient for driving
dorsal GCs activation. Furthermore, manipulation of ventral MCs activity bidirectionally
regulates novelty-induced contextual memory acquisition. Our results show that
ventral MCs activity controls memory formation through an intra-hippocampal interaction
mechanism gated by novelty.
acknowledgement: We thank Peter Jonas and Peter Somogyi for critically reading the
manuscript, Satoshi Kida for helpful discussion, Taijia Makinen for providing the
Prox1-creERT2 mouse line, and Hiromu Yawo for the VAMP2-Venus construct. We also
thank Vivek Jayaraman, Ph.D.; Rex A. Kerr, Ph.D.; Douglas S. Kim, Ph.D.; Loren L.
Looger, Ph.D.; and Karel Svoboda, Ph.D. from the GENIE Project, Janelia Farm Research
Campus, Howard Hughes Medical Institute for the viral constructs used for GCaMP6s
expression. We also thank Jacqueline Montanaro, Vanessa Zheden, David Kleindienst,
and Laura Burnett for technical assistance, as well as Robert Beattie for imaging
assistance. This work was supported by a European Research Council Advanced Grant
694539 to R.S.
article_processing_charge: No
article_type: original
author:
- first_name: Felipe A
full_name: Fredes Tolorza, Felipe A
id: 384825DA-F248-11E8-B48F-1D18A9856A87
last_name: Fredes Tolorza
- first_name: Maria A
full_name: Silva Sifuentes, Maria A
id: 371B3D6E-F248-11E8-B48F-1D18A9856A87
last_name: Silva Sifuentes
- first_name: Peter
full_name: Koppensteiner, Peter
id: 3B8B25A8-F248-11E8-B48F-1D18A9856A87
last_name: Koppensteiner
orcid: 0000-0002-3509-1948
- first_name: Kenta
full_name: Kobayashi, Kenta
last_name: Kobayashi
- first_name: Maximilian A
full_name: Jösch, Maximilian A
id: 2BD278E6-F248-11E8-B48F-1D18A9856A87
last_name: Jösch
orcid: 0000-0002-3937-1330
- first_name: Ryuichi
full_name: Shigemoto, Ryuichi
id: 499F3ABC-F248-11E8-B48F-1D18A9856A87
last_name: Shigemoto
orcid: 0000-0001-8761-9444
citation:
ama: Fredes Tolorza FA, Silva Sifuentes MA, Koppensteiner P, Kobayashi K, Jösch
MA, Shigemoto R. Ventro-dorsal hippocampal pathway gates novelty-induced contextual
memory formation. Current Biology. 2021;31(1):P25-38.E5. doi:10.1016/j.cub.2020.09.074
apa: Fredes Tolorza, F. A., Silva Sifuentes, M. A., Koppensteiner, P., Kobayashi,
K., Jösch, M. A., & Shigemoto, R. (2021). Ventro-dorsal hippocampal pathway
gates novelty-induced contextual memory formation. Current Biology. Elsevier.
https://doi.org/10.1016/j.cub.2020.09.074
chicago: Fredes Tolorza, Felipe A, Maria A Silva Sifuentes, Peter Koppensteiner,
Kenta Kobayashi, Maximilian A Jösch, and Ryuichi Shigemoto. “Ventro-Dorsal Hippocampal
Pathway Gates Novelty-Induced Contextual Memory Formation.” Current Biology.
Elsevier, 2021. https://doi.org/10.1016/j.cub.2020.09.074.
ieee: F. A. Fredes Tolorza, M. A. Silva Sifuentes, P. Koppensteiner, K. Kobayashi,
M. A. Jösch, and R. Shigemoto, “Ventro-dorsal hippocampal pathway gates novelty-induced
contextual memory formation,” Current Biology, vol. 31, no. 1. Elsevier,
p. P25–38.E5, 2021.
ista: Fredes Tolorza FA, Silva Sifuentes MA, Koppensteiner P, Kobayashi K, Jösch
MA, Shigemoto R. 2021. Ventro-dorsal hippocampal pathway gates novelty-induced
contextual memory formation. Current Biology. 31(1), P25–38.E5.
mla: Fredes Tolorza, Felipe A., et al. “Ventro-Dorsal Hippocampal Pathway Gates
Novelty-Induced Contextual Memory Formation.” Current Biology, vol. 31,
no. 1, Elsevier, 2021, p. P25–38.E5, doi:10.1016/j.cub.2020.09.074.
short: F.A. Fredes Tolorza, M.A. Silva Sifuentes, P. Koppensteiner, K. Kobayashi,
M.A. Jösch, R. Shigemoto, Current Biology 31 (2021) P25–38.E5.
date_created: 2020-02-28T10:56:18Z
date_published: 2021-01-11T00:00:00Z
date_updated: 2025-06-12T06:54:22Z
day: '11'
ddc:
- '570'
department:
- _id: MaJö
- _id: RySh
doi: 10.1016/j.cub.2020.09.074
ec_funded: 1
external_id:
isi:
- '000614361000020'
pmid:
- '33065009'
file:
- access_level: open_access
checksum: b7b9c8bc84a08befce365c675229a7d1
content_type: application/pdf
creator: dernst
date_created: 2020-10-19T13:31:28Z
date_updated: 2020-10-19T13:31:28Z
file_id: '8678'
file_name: 2021_CurrentBiology_Fredes.pdf
file_size: 4915964
relation: main_file
success: 1
file_date_updated: 2020-10-19T13:31:28Z
has_accepted_license: '1'
intvolume: ' 31'
isi: 1
issue: '1'
language:
- iso: eng
month: '01'
oa: 1
oa_version: Published Version
page: P25-38.E5
pmid: 1
project:
- _id: 25CA28EA-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '694539'
name: 'In situ analysis of single channel subunit composition in neurons: physiological
implication in synaptic plasticity and behaviour'
publication: Current Biology
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/remembering-novelty/
scopus_import: '1'
status: public
title: Ventro-dorsal hippocampal pathway gates novelty-induced contextual memory formation
tmp:
image: /images/cc_by_nc_nd.png
legal_code_url: https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode
name: Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International
(CC BY-NC-ND 4.0)
short: CC BY-NC-ND (4.0)
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 31
year: '2021'
...
---
_id: '7553'
abstract:
- lang: eng
text: Normative theories and statistical inference provide complementary approaches
for the study of biological systems. A normative theory postulates that organisms
have adapted to efficiently solve essential tasks, and proceeds to mathematically
work out testable consequences of such optimality; parameters that maximize the
hypothesized organismal function can be derived ab initio, without reference to
experimental data. In contrast, statistical inference focuses on efficient utilization
of data to learn model parameters, without reference to any a priori notion of
biological function, utility, or fitness. Traditionally, these two approaches
were developed independently and applied separately. Here we unify them in a coherent
Bayesian framework that embeds a normative theory into a family of maximum-entropy
“optimization priors.” This family defines a smooth interpolation between a data-rich
inference regime (characteristic of “bottom-up” statistical models), and a data-limited
ab inito prediction regime (characteristic of “top-down” normative theory). We
demonstrate the applicability of our framework using data from the visual cortex,
and argue that the flexibility it affords is essential to address a number of
fundamental challenges relating to inference and prediction in complex, high-dimensional
biological problems.
acknowledgement: The authors thank Dario Ringach for providing the V1 receptive fields
and Olivier Marre for providing the retinal receptive fields. W.M. was funded by
the European Union’s Horizon 2020 research and innovation programme under the Marie
Skłodowska-Curie grant agreement no. 754411. M.H. was funded in part by Human Frontiers
Science grant no. HFSP RGP0032/2018.
article_processing_charge: No
author:
- first_name: Wiktor F
full_name: Mlynarski, Wiktor F
id: 358A453A-F248-11E8-B48F-1D18A9856A87
last_name: Mlynarski
- first_name: Michal
full_name: Hledik, Michal
id: 4171253A-F248-11E8-B48F-1D18A9856A87
last_name: Hledik
- first_name: Thomas R
full_name: Sokolowski, Thomas R
id: 3E999752-F248-11E8-B48F-1D18A9856A87
last_name: Sokolowski
orcid: 0000-0002-1287-3779
- first_name: Gašper
full_name: Tkačik, Gašper
id: 3D494DCA-F248-11E8-B48F-1D18A9856A87
last_name: Tkačik
orcid: 0000-0002-6699-1455
citation:
ama: Mlynarski WF, Hledik M, Sokolowski TR, Tkačik G. Statistical analysis and optimality
of neural systems. Neuron. 2021;109(7):1227-1241.e5. doi:10.1016/j.neuron.2021.01.020
apa: Mlynarski, W. F., Hledik, M., Sokolowski, T. R., & Tkačik, G. (2021). Statistical
analysis and optimality of neural systems. Neuron. Cell Press. https://doi.org/10.1016/j.neuron.2021.01.020
chicago: Mlynarski, Wiktor F, Michal Hledik, Thomas R Sokolowski, and Gašper Tkačik.
“Statistical Analysis and Optimality of Neural Systems.” Neuron. Cell Press,
2021. https://doi.org/10.1016/j.neuron.2021.01.020.
ieee: W. F. Mlynarski, M. Hledik, T. R. Sokolowski, and G. Tkačik, “Statistical
analysis and optimality of neural systems,” Neuron, vol. 109, no. 7. Cell
Press, p. 1227–1241.e5, 2021.
ista: Mlynarski WF, Hledik M, Sokolowski TR, Tkačik G. 2021. Statistical analysis
and optimality of neural systems. Neuron. 109(7), 1227–1241.e5.
mla: Mlynarski, Wiktor F., et al. “Statistical Analysis and Optimality of Neural
Systems.” Neuron, vol. 109, no. 7, Cell Press, 2021, p. 1227–1241.e5, doi:10.1016/j.neuron.2021.01.020.
short: W.F. Mlynarski, M. Hledik, T.R. Sokolowski, G. Tkačik, Neuron 109 (2021)
1227–1241.e5.
corr_author: '1'
date_created: 2020-02-28T11:00:12Z
date_published: 2021-04-07T00:00:00Z
date_updated: 2026-04-07T12:59:24Z
day: '07'
department:
- _id: GaTk
doi: 10.1016/j.neuron.2021.01.020
ec_funded: 1
external_id:
isi:
- '000637809600006'
pmid:
- '33592180'
intvolume: ' 109'
isi: 1
issue: '7'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.1101/848374
month: '04'
oa: 1
oa_version: Preprint
page: 1227-1241.e5
pmid: 1
project:
- _id: 260C2330-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '754411'
name: ISTplus - Postdoctoral Fellowships
publication: Neuron
publication_status: published
publisher: Cell Press
quality_controlled: '1'
related_material:
link:
- description: News on IST Homepage
relation: press_release
url: https://ist.ac.at/en/news/can-evolution-be-predicted/
record:
- id: '15020'
relation: dissertation_contains
status: public
scopus_import: '1'
status: public
title: Statistical analysis and optimality of neural systems
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 109
year: '2021'
...
---
_id: '9874'
abstract:
- lang: eng
text: Myocardial regeneration is restricted to early postnatal life, when mammalian
cardiomyocytes still retain the ability to proliferate. The molecular cues that
induce cell cycle arrest of neonatal cardiomyocytes towards terminally differentiated
adult heart muscle cells remain obscure. Here we report that the miR-106b~25 cluster
is higher expressed in the early postnatal myocardium and decreases in expression
towards adulthood, especially under conditions of overload, and orchestrates the
transition of cardiomyocyte hyperplasia towards cell cycle arrest and hypertrophy
by virtue of its targetome. In line, gene delivery of miR-106b~25 to the mouse
heart provokes cardiomyocyte proliferation by targeting a network of negative
cell cycle regulators including E2f5, Cdkn1c, Ccne1 and Wee1. Conversely, gene-targeted
miR-106b~25 null mice display spontaneous hypertrophic remodeling and exaggerated
remodeling to overload by derepression of the prohypertrophic transcription factors
Hand2 and Mef2d. Taking advantage of the regulatory function of miR-106b~25 on
cardiomyocyte hyperplasia and hypertrophy, viral gene delivery of miR-106b~25
provokes nearly complete regeneration of the adult myocardium after ischemic injury.
Our data demonstrate that exploitation of conserved molecular programs can enhance
the regenerative capacity of the injured heart.
acknowledgement: E.D. is supported by a VENI award 916-150-16 from the Netherlands
Organization for Health Research and Development (ZonMW), an EMBO Long-term Fellowship
(EMBO ALTF 848-2013) and a FP7 Marie Curie Intra-European Fellowship (Project number
627539). V.S.P. was funded by a fellowship from the FCT/ Ministério da Ciência,
Tecnologia e Inovação SFRH/BD/111799/2015. P.D.C.M. is an Established Investigator
of the Dutch Heart Foundation. L.D.W. acknowledges support from the Dutch CardioVascular
Alliance (ARENA-PRIME). L.D.W. was further supported by grant 311549 from the European
Research Council (ERC), a VICI award 918-156-47 from the Dutch Research Council
and Marie Sklodowska-Curie grant agreement no. 813716 (TRAIN-HEART).
article_number: '4808'
article_processing_charge: Yes
article_type: original
author:
- first_name: Andrea
full_name: Raso, Andrea
last_name: Raso
- first_name: Ellen
full_name: Dirkx, Ellen
last_name: Dirkx
- first_name: Vasco
full_name: Sampaio-Pinto, Vasco
last_name: Sampaio-Pinto
- first_name: Hamid
full_name: el Azzouzi, Hamid
last_name: el Azzouzi
- first_name: Ryan J
full_name: Cubero, Ryan J
id: 850B2E12-9CD4-11E9-837F-E719E6697425
last_name: Cubero
orcid: 0000-0003-0002-1867
- first_name: Daniel W.
full_name: Sorensen, Daniel W.
last_name: Sorensen
- first_name: Lara
full_name: Ottaviani, Lara
last_name: Ottaviani
- first_name: Servé
full_name: Olieslagers, Servé
last_name: Olieslagers
- first_name: Manon M.
full_name: Huibers, Manon M.
last_name: Huibers
- first_name: Roel
full_name: de Weger, Roel
last_name: de Weger
- first_name: Sailay
full_name: Siddiqi, Sailay
last_name: Siddiqi
- first_name: Silvia
full_name: Moimas, Silvia
last_name: Moimas
- first_name: Consuelo
full_name: Torrini, Consuelo
last_name: Torrini
- first_name: Lorena
full_name: Zentillin, Lorena
last_name: Zentillin
- first_name: Luca
full_name: Braga, Luca
last_name: Braga
- first_name: Diana S.
full_name: Nascimento, Diana S.
last_name: Nascimento
- first_name: Paula A.
full_name: da Costa Martins, Paula A.
last_name: da Costa Martins
- first_name: Jop H.
full_name: van Berlo, Jop H.
last_name: van Berlo
- first_name: Serena
full_name: Zacchigna, Serena
last_name: Zacchigna
- first_name: Mauro
full_name: Giacca, Mauro
last_name: Giacca
- first_name: Leon J.
full_name: De Windt, Leon J.
last_name: De Windt
citation:
ama: Raso A, Dirkx E, Sampaio-Pinto V, et al. A microRNA program regulates the balance
between cardiomyocyte hyperplasia and hypertrophy and stimulates cardiac regeneration.
Nature Communications. 2021;12. doi:10.1038/s41467-021-25211-4
apa: Raso, A., Dirkx, E., Sampaio-Pinto, V., el Azzouzi, H., Cubero, R. J., Sorensen,
D. W., … De Windt, L. J. (2021). A microRNA program regulates the balance between
cardiomyocyte hyperplasia and hypertrophy and stimulates cardiac regeneration.
Nature Communications. Springer Nature. https://doi.org/10.1038/s41467-021-25211-4
chicago: Raso, Andrea, Ellen Dirkx, Vasco Sampaio-Pinto, Hamid el Azzouzi, Ryan
J Cubero, Daniel W. Sorensen, Lara Ottaviani, et al. “A MicroRNA Program Regulates
the Balance between Cardiomyocyte Hyperplasia and Hypertrophy and Stimulates Cardiac
Regeneration.” Nature Communications. Springer Nature, 2021. https://doi.org/10.1038/s41467-021-25211-4.
ieee: A. Raso et al., “A microRNA program regulates the balance between cardiomyocyte
hyperplasia and hypertrophy and stimulates cardiac regeneration,” Nature Communications,
vol. 12. Springer Nature, 2021.
ista: Raso A, Dirkx E, Sampaio-Pinto V, el Azzouzi H, Cubero RJ, Sorensen DW, Ottaviani
L, Olieslagers S, Huibers MM, de Weger R, Siddiqi S, Moimas S, Torrini C, Zentillin
L, Braga L, Nascimento DS, da Costa Martins PA, van Berlo JH, Zacchigna S, Giacca
M, De Windt LJ. 2021. A microRNA program regulates the balance between cardiomyocyte
hyperplasia and hypertrophy and stimulates cardiac regeneration. Nature Communications.
12, 4808.
mla: Raso, Andrea, et al. “A MicroRNA Program Regulates the Balance between Cardiomyocyte
Hyperplasia and Hypertrophy and Stimulates Cardiac Regeneration.” Nature Communications,
vol. 12, 4808, Springer Nature, 2021, doi:10.1038/s41467-021-25211-4.
short: A. Raso, E. Dirkx, V. Sampaio-Pinto, H. el Azzouzi, R.J. Cubero, D.W. Sorensen,
L. Ottaviani, S. Olieslagers, M.M. Huibers, R. de Weger, S. Siddiqi, S. Moimas,
C. Torrini, L. Zentillin, L. Braga, D.S. Nascimento, P.A. da Costa Martins, J.H.
van Berlo, S. Zacchigna, M. Giacca, L.J. De Windt, Nature Communications 12 (2021).
date_created: 2021-08-10T11:49:20Z
date_published: 2021-08-10T00:00:00Z
date_updated: 2023-08-11T10:27:03Z
day: '10'
ddc:
- '610'
- '570'
department:
- _id: SaSi
doi: 10.1038/s41467-021-25211-4
external_id:
isi:
- '000683910200042'
pmid:
- '34376683'
file:
- access_level: open_access
checksum: 48d8562e8229e4282f3f354b329722c5
content_type: application/pdf
creator: asandaue
date_created: 2021-08-10T12:29:59Z
date_updated: 2021-08-10T12:29:59Z
file_id: '9876'
file_name: 2021_NatureCommunications_Raso.pdf
file_size: 4364333
relation: main_file
success: 1
file_date_updated: 2021-08-10T12:29:59Z
genbank:
- GSE178867
has_accepted_license: '1'
intvolume: ' 12'
isi: 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:
- relation: erratum
url: https://doi.org/10.1038/s41467-022-32785-0
scopus_import: '1'
status: public
title: A microRNA program regulates the balance between cardiomyocyte hyperplasia
and hypertrophy and stimulates cardiac regeneration
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: journal_article
user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
volume: 12
year: '2021'
...
---
_id: '9877'
abstract:
- lang: eng
text: 'Parent-of-origin–dependent gene expression in mammals and flowering plants
results from differing chromatin imprints (genomic imprinting) between maternally
and paternally inherited alleles. Imprinted gene expression in the endosperm of
seeds is associated with localized hypomethylation of maternally but not paternally
inherited DNA, with certain small RNAs also displaying parent-of-origin–specific
expression. To understand the evolution of imprinting mechanisms in Oryza sativa
(rice), we analyzed imprinting divergence among four cultivars that span both
japonica and indica subspecies: Nipponbare, Kitaake, 93-11, and IR64. Most imprinted
genes are imprinted across cultivars and enriched for functions in chromatin and
transcriptional regulation, development, and signaling. However, 4 to 11% of imprinted
genes display divergent imprinting. Analyses of DNA methylation and small RNAs
revealed that endosperm-specific 24-nt small RNA–producing loci show weak RNA-directed
DNA methylation, frequently overlap genes, and are imprinted four times more often
than genes. However, imprinting divergence most often correlated with local DNA
methylation epimutations (9 of 17 assessable loci), which were largely stable
within subspecies. Small insertion/deletion events and transposable element insertions
accompanied 4 of the 9 locally epimutated loci and associated with imprinting
divergence at another 4 of the remaining 8 loci. Correlating epigenetic and genetic
variation occurred at key regulatory regions—the promoter and transcription start
site of maternally biased genes, and the promoter and gene body of paternally
biased genes. Our results reinforce models for the role of maternal-specific DNA
hypomethylation in imprinting of both maternally and paternally biased genes,
and highlight the role of transposition and epimutation in rice imprinting evolution.'
acknowledgement: We thank W. Schackwitz, M. Joel, and the Joint Genome Institute sequencing
team for generating the IR64 genome sequence and initial analysis; L. Bartley and
E. Marvinney for genomic DNA preparation for IR64 resequencing; and the University
of California (UC), Berkeley Sanger sequencing team for technical advice and service.
This work was partially funded by NSF Grant IOS-1025890 (to R.L.F. and D.Z.), NIH
Grant GM69415 (to R.L.F. and D.Z.), NIH Grant GM122968 (to P.C.R.), a Young Investigator
Grant from the Arnold and Mabel Beckman Foundation (to D.Z.), an International Fulbright
Science and Technology Award (to J.A.R.), and a Taiwan Ministry of Education Studying
Abroad Scholarship (to P.-H.H.). This work used the Vincent J. Coates Genomics Sequencing
Laboratory at UC Berkeley, supported by NIH Instrumentation Grant S10 OD018174.
article_number: e2104445118
article_processing_charge: Yes (in subscription journal)
article_type: original
author:
- first_name: Jessica A.
full_name: Rodrigues, Jessica A.
last_name: Rodrigues
- first_name: Ping-Hung
full_name: Hsieh, Ping-Hung
last_name: Hsieh
- first_name: Deling
full_name: Ruan, Deling
last_name: Ruan
- first_name: Toshiro
full_name: Nishimura, Toshiro
last_name: Nishimura
- first_name: Manoj K.
full_name: Sharma, Manoj K.
last_name: Sharma
- first_name: Rita
full_name: Sharma, Rita
last_name: Sharma
- first_name: XinYi
full_name: Ye, XinYi
last_name: Ye
- first_name: Nicholas D.
full_name: Nguyen, Nicholas D.
last_name: Nguyen
- first_name: Sukhranjan
full_name: Nijjar, Sukhranjan
last_name: Nijjar
- first_name: Pamela C.
full_name: Ronald, Pamela C.
last_name: Ronald
- first_name: Robert L.
full_name: Fischer, Robert L.
last_name: Fischer
- first_name: Daniel
full_name: Zilberman, Daniel
id: 6973db13-dd5f-11ea-814e-b3e5455e9ed1
last_name: Zilberman
orcid: 0000-0002-0123-8649
citation:
ama: Rodrigues JA, Hsieh P-H, Ruan D, et al. Divergence among rice cultivars reveals
roles for transposition and epimutation in ongoing evolution of genomic imprinting.
Proceedings of the National Academy of Sciences of the United States of America.
2021;118(29). doi:10.1073/pnas.2104445118
apa: Rodrigues, J. A., Hsieh, P.-H., Ruan, D., Nishimura, T., Sharma, M. K., Sharma,
R., … Zilberman, D. (2021). Divergence among rice cultivars reveals roles for
transposition and epimutation in ongoing evolution of genomic imprinting. Proceedings
of the National Academy of Sciences of the United States of America. National
Academy of Sciences. https://doi.org/10.1073/pnas.2104445118
chicago: Rodrigues, Jessica A., Ping-Hung Hsieh, Deling Ruan, Toshiro Nishimura,
Manoj K. Sharma, Rita Sharma, XinYi Ye, et al. “Divergence among Rice Cultivars
Reveals Roles for Transposition and Epimutation in Ongoing Evolution of Genomic
Imprinting.” Proceedings of the National Academy of Sciences of the United
States of America. National Academy of Sciences, 2021. https://doi.org/10.1073/pnas.2104445118.
ieee: J. A. Rodrigues et al., “Divergence among rice cultivars reveals roles
for transposition and epimutation in ongoing evolution of genomic imprinting,”
Proceedings of the National Academy of Sciences of the United States of America,
vol. 118, no. 29. National Academy of Sciences, 2021.
ista: Rodrigues JA, Hsieh P-H, Ruan D, Nishimura T, Sharma MK, Sharma R, Ye X, Nguyen
ND, Nijjar S, Ronald PC, Fischer RL, Zilberman D. 2021. Divergence among rice
cultivars reveals roles for transposition and epimutation in ongoing evolution
of genomic imprinting. Proceedings of the National Academy of Sciences of the
United States of America. 118(29), e2104445118.
mla: Rodrigues, Jessica A., et al. “Divergence among Rice Cultivars Reveals Roles
for Transposition and Epimutation in Ongoing Evolution of Genomic Imprinting.”
Proceedings of the National Academy of Sciences of the United States of America,
vol. 118, no. 29, e2104445118, National Academy of Sciences, 2021, doi:10.1073/pnas.2104445118.
short: J.A. Rodrigues, P.-H. Hsieh, D. Ruan, T. Nishimura, M.K. Sharma, R. Sharma,
X. Ye, N.D. Nguyen, S. Nijjar, P.C. Ronald, R.L. Fischer, D. Zilberman, Proceedings
of the National Academy of Sciences of the United States of America 118 (2021).
date_created: 2021-08-10T19:30:41Z
date_published: 2021-07-16T00:00:00Z
date_updated: 2025-05-14T10:59:43Z
day: '16'
ddc:
- '580'
- '570'
department:
- _id: DaZi
doi: 10.1073/pnas.2104445118
external_id:
isi:
- '000685037700012'
pmid:
- '34272287'
file:
- access_level: open_access
checksum: 19e84ad8c03c60222744ee8e16cd6998
content_type: application/pdf
creator: asandaue
date_created: 2021-08-11T09:31:41Z
date_updated: 2021-08-11T09:31:41Z
file_id: '9879'
file_name: 2021_ProceedingsOfTheNationalAcademyOfSciences_Rodrigues.pdf
file_size: 1898360
relation: main_file
success: 1
file_date_updated: 2021-08-11T09:31:41Z
has_accepted_license: '1'
intvolume: ' 118'
isi: 1
issue: '29'
language:
- iso: eng
month: '07'
oa: 1
oa_version: Published Version
pmid: 1
publication: Proceedings of the National Academy of Sciences of the United States
of America
publication_identifier:
eissn:
- 1091-6490
issn:
- 0027-8424
publication_status: published
publisher: National Academy of Sciences
quality_controlled: '1'
scopus_import: '1'
status: public
title: Divergence among rice cultivars reveals roles for transposition and epimutation
in ongoing evolution of genomic imprinting
tmp:
image: /images/cc_by_nc_nd.png
legal_code_url: https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode
name: Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International
(CC BY-NC-ND 4.0)
short: CC BY-NC-ND (4.0)
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 118
year: '2021'
...
---
_id: '9891'
abstract:
- lang: eng
text: 'Extending on ideas of Lewin, Lieb, and Seiringer [Phys. Rev. B 100, 035127
(2019)], we present a modified “floating crystal” trial state for jellium (also
known as the classical homogeneous electron gas) with density equal to a characteristic
function. This allows us to show that three definitions of the jellium energy
coincide in dimensions d ≥ 2, thus extending the result of Cotar and Petrache
[“Equality of the Jellium and uniform electron gas next-order asymptotic terms
for Coulomb and Riesz potentials,” arXiv: 1707.07664 (2019)] and Lewin, Lieb,
and Seiringer [Phys. Rev. B 100, 035127 (2019)] that the three definitions coincide
in dimension d ≥ 3. We show that the jellium energy is also equivalent to a “renormalized
energy” studied in a series of papers by Serfaty and others, and thus, by the
work of Bétermin and Sandier [Constr. Approximation 47, 39–74 (2018)], we relate
the jellium energy to the order n term in the logarithmic energy of n points on
the unit 2-sphere. We improve upon known lower bounds for this renormalized energy.
Additionally, we derive formulas for the jellium energy of periodic configurations.'
acknowledgement: The author would like to thank Robert Seiringer for guidance and
many helpful comments on this project. The author would also like to thank Mathieu
Lewin for his comments on the manuscript and Lorenzo Portinale for providing his
lecture notes for the course “Mathematics of quantum many-body systems” in spring
2020, taught by Robert Seiringer. The Proof of Theorem III.1 is inspired by these
lecture notes.
article_number: '083305'
article_processing_charge: No
article_type: original
arxiv: 1
author:
- first_name: Asbjørn Bækgaard
full_name: Lauritsen, Asbjørn Bækgaard
id: e1a2682f-dc8d-11ea-abe3-81da9ac728f1
last_name: Lauritsen
orcid: 0000-0003-4476-2288
citation:
ama: Lauritsen AB. Floating Wigner crystal and periodic jellium configurations.
Journal of Mathematical Physics. 2021;62(8). doi:10.1063/5.0053494
apa: Lauritsen, A. B. (2021). Floating Wigner crystal and periodic jellium configurations.
Journal of Mathematical Physics. AIP Publishing. https://doi.org/10.1063/5.0053494
chicago: Lauritsen, Asbjørn Bækgaard. “Floating Wigner Crystal and Periodic Jellium
Configurations.” Journal of Mathematical Physics. AIP Publishing, 2021.
https://doi.org/10.1063/5.0053494.
ieee: A. B. Lauritsen, “Floating Wigner crystal and periodic jellium configurations,”
Journal of Mathematical Physics, vol. 62, no. 8. AIP Publishing, 2021.
ista: Lauritsen AB. 2021. Floating Wigner crystal and periodic jellium configurations.
Journal of Mathematical Physics. 62(8), 083305.
mla: Lauritsen, Asbjørn Bækgaard. “Floating Wigner Crystal and Periodic Jellium
Configurations.” Journal of Mathematical Physics, vol. 62, no. 8, 083305,
AIP Publishing, 2021, doi:10.1063/5.0053494.
short: A.B. Lauritsen, Journal of Mathematical Physics 62 (2021).
corr_author: '1'
date_created: 2021-08-12T07:08:36Z
date_published: 2021-08-01T00:00:00Z
date_updated: 2024-10-09T21:00:48Z
day: '01'
ddc:
- '530'
department:
- _id: GradSch
- _id: RoSe
doi: 10.1063/5.0053494
external_id:
arxiv:
- '2103.07975'
isi:
- '000683960800003'
file:
- access_level: open_access
checksum: d035be2b894c4d50d90ac5ce252e27cd
content_type: application/pdf
creator: cziletti
date_created: 2021-10-27T12:57:06Z
date_updated: 2021-10-27T12:57:06Z
file_id: '10188'
file_name: 2021_JMathPhy_Lauritsen.pdf
file_size: 4352640
relation: main_file
success: 1
file_date_updated: 2021-10-27T12:57:06Z
has_accepted_license: '1'
intvolume: ' 62'
isi: 1
issue: '8'
keyword:
- Mathematical Physics
- Statistical and Nonlinear Physics
language:
- iso: eng
month: '08'
oa: 1
oa_version: Published Version
publication: Journal of Mathematical Physics
publication_identifier:
eissn:
- 1089-7658
issn:
- 0022-2488
publication_status: published
publisher: AIP Publishing
quality_controlled: '1'
scopus_import: '1'
status: public
title: Floating Wigner crystal and periodic jellium configurations
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: journal_article
user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
volume: 62
year: '2021'
...
---
_id: '9903'
abstract:
- lang: eng
text: Eigenstate thermalization in quantum many-body systems implies that eigenstates
at high energy are similar to random vectors. Identifying systems where at least
some eigenstates are nonthermal is an outstanding question. In this Letter we
show that interacting quantum models that have a nullspace—a degenerate subspace
of eigenstates at zero energy (zero modes), which corresponds to infinite temperature,
provide a route to nonthermal eigenstates. We analytically show the existence
of a zero mode which can be represented as a matrix product state for a certain
class of local Hamiltonians. In the more general case we use a subspace disentangling
algorithm to generate an orthogonal basis of zero modes characterized by increasing
entanglement entropy. We show evidence for an area-law entanglement scaling of
the least-entangled zero mode in the broad parameter regime, leading to a conjecture
that all local Hamiltonians with the nullspace feature zero modes with area-law
entanglement scaling and, as such, break the strong thermalization hypothesis.
Finally, we find zero modes in constrained models and propose a setup for observing
their experimental signatures.
acknowledgement: "We acknowledge useful discussions with V. Gritsev and A. Garkun
and suggestions on implementation of the\r\nPPXPP model by D. Bluvstein. A. M. and
M. S. were supported by the European Research Council (ERC) under\r\nthe European
Union’s Horizon 2020 research and innovation program (Grant Agreement No. 850899)"
article_number: '060602'
article_processing_charge: Yes (in subscription journal)
article_type: letter_note
arxiv: 1
author:
- first_name: Volker
full_name: Karle, Volker
id: D7C012AE-D7ED-11E9-95E8-1EC5E5697425
last_name: Karle
orcid: 0000-0002-6963-0129
- first_name: Maksym
full_name: Serbyn, Maksym
id: 47809E7E-F248-11E8-B48F-1D18A9856A87
last_name: Serbyn
orcid: 0000-0002-2399-5827
- first_name: Alexios
full_name: Michailidis, Alexios
id: 36EBAD38-F248-11E8-B48F-1D18A9856A87
last_name: Michailidis
orcid: 0000-0002-8443-1064
citation:
ama: Karle V, Serbyn M, Michailidis A. Area-law entangled eigenstates from nullspaces
of local Hamiltonians. Physical Review Letters. 2021;127(6). doi:10.1103/physrevlett.127.060602
apa: Karle, V., Serbyn, M., & Michailidis, A. (2021). Area-law entangled eigenstates
from nullspaces of local Hamiltonians. Physical Review Letters. American
Physical Society. https://doi.org/10.1103/physrevlett.127.060602
chicago: Karle, Volker, Maksym Serbyn, and Alexios Michailidis. “Area-Law Entangled
Eigenstates from Nullspaces of Local Hamiltonians.” Physical Review Letters.
American Physical Society, 2021. https://doi.org/10.1103/physrevlett.127.060602.
ieee: V. Karle, M. Serbyn, and A. Michailidis, “Area-law entangled eigenstates from
nullspaces of local Hamiltonians,” Physical Review Letters, vol. 127, no.
6. American Physical Society, 2021.
ista: Karle V, Serbyn M, Michailidis A. 2021. Area-law entangled eigenstates from
nullspaces of local Hamiltonians. Physical Review Letters. 127(6), 060602.
mla: Karle, Volker, et al. “Area-Law Entangled Eigenstates from Nullspaces of Local
Hamiltonians.” Physical Review Letters, vol. 127, no. 6, 060602, American
Physical Society, 2021, doi:10.1103/physrevlett.127.060602.
short: V. Karle, M. Serbyn, A. Michailidis, Physical Review Letters 127 (2021).
date_created: 2021-08-13T09:27:39Z
date_published: 2021-08-06T00:00:00Z
date_updated: 2026-04-07T11:48:53Z
day: '06'
ddc:
- '539'
department:
- _id: MaSe
- _id: GradSch
- _id: MiLe
doi: 10.1103/physrevlett.127.060602
ec_funded: 1
external_id:
arxiv:
- '2102.13633'
isi:
- '000684276000002'
file:
- access_level: open_access
checksum: 51218f302dcef99d90d1209809fcc874
content_type: application/pdf
creator: mserbyn
date_created: 2021-08-13T09:28:08Z
date_updated: 2021-08-13T09:28:08Z
file_id: '9904'
file_name: PhysRevLett.127.060602_SOM.pdf
file_size: 5064231
relation: main_file
success: 1
file_date_updated: 2021-08-13T09:28:08Z
has_accepted_license: '1'
intvolume: ' 127'
isi: 1
issue: '6'
language:
- iso: eng
month: '08'
oa: 1
oa_version: Published Version
project:
- _id: 23841C26-32DE-11EA-91FC-C7463DDC885E
call_identifier: H2020
grant_number: '850899'
name: 'Non-Ergodic Quantum Matter: Universality, Dynamics and Control'
publication: Physical Review Letters
publication_identifier:
eissn:
- 1079-7114
issn:
- 0031-9007
publication_status: published
publisher: American Physical Society
quality_controlled: '1'
related_material:
record:
- id: '19393'
relation: dissertation_contains
status: public
scopus_import: '1'
status: public
title: Area-law entangled eigenstates from nullspaces of local Hamiltonians
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: journal_article
user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
volume: 127
year: '2021'
...
---
_id: '9906'
abstract:
- lang: eng
text: Endometriosis is a common gynecological disorder characterized by ectopic
growth of endometrium outside the uterus and is associated with chronic pain and
infertility. We investigated the role of the long intergenic noncoding RNA 01133
(LINC01133) in endometriosis, an lncRNA that has been implicated in several types
of cancer. We found that LINC01133 is upregulated in ectopic endometriotic lesions.
As expression appeared higher in the epithelial endometrial layer, we performed
a siRNA knockdown of LINC01133 in an endometriosis epithelial cell line. Phenotypic
assays indicated that LINC01133 may promote proliferation and suppress cellular
migration, and affect the cytoskeleton and morphology of the cells. Gene ontology
analysis of differentially expressed genes indicated that cell proliferation and
migration pathways were affected in line with the observed phenotype. We validated
upregulation of p21 and downregulation of Cyclin A at the protein level, which
together with the quantification of the DNA content using fluorescence-activated
cell sorting (FACS) analysis indicated that the observed effects on cellular proliferation
may be due to changes in cell cycle. Further, we found testis-specific protein
kinase 1 (TESK1) kinase upregulation corresponding with phosphorylation and inactivation
of actin severing protein Cofilin, which could explain changes in the cytoskeleton
and cellular migration. These results indicate that endometriosis is associated
with LINC01133 upregulation, which may affect pathogenesis via the cellular proliferation
and migration pathways.
acknowledgement: "Open access funding provided by Medical University of Vienna. The
authors would like to thank all the participants and health professionals involved
in the present study. We want to thank our technical assistants Barbara Widmar and
Matthias Witzmann-Stern for their diligent work and constant assistance. We would
like to thank Simon Hippenmeyer for access to\r\nbioinformatic infrastructure and
resources."
article_number: '8385'
article_processing_charge: Yes
article_type: original
author:
- first_name: Iveta
full_name: Yotova, Iveta
last_name: Yotova
- first_name: Quanah J.
full_name: Hudson, Quanah J.
last_name: Hudson
- first_name: Florian
full_name: Pauler, Florian
id: 48EA0138-F248-11E8-B48F-1D18A9856A87
last_name: Pauler
orcid: 0000-0002-7462-0048
- first_name: Katharina
full_name: Proestling, Katharina
last_name: Proestling
- first_name: Isabella
full_name: Haslinger, Isabella
last_name: Haslinger
- first_name: Lorenz
full_name: Kuessel, Lorenz
last_name: Kuessel
- first_name: Alexandra
full_name: Perricos, Alexandra
last_name: Perricos
- first_name: Heinrich
full_name: Husslein, Heinrich
last_name: Husslein
- first_name: René
full_name: Wenzl, René
last_name: Wenzl
citation:
ama: Yotova I, Hudson QJ, Pauler F, et al. LINC01133 inhibits invasion and promotes
proliferation in an endometriosis epithelial cell line. International Journal
of Molecular Sciences. 2021;22(16). doi:10.3390/ijms22168385
apa: Yotova, I., Hudson, Q. J., Pauler, F., Proestling, K., Haslinger, I., Kuessel,
L., … Wenzl, R. (2021). LINC01133 inhibits invasion and promotes proliferation
in an endometriosis epithelial cell line. International Journal of Molecular
Sciences. MDPI. https://doi.org/10.3390/ijms22168385
chicago: Yotova, Iveta, Quanah J. Hudson, Florian Pauler, Katharina Proestling,
Isabella Haslinger, Lorenz Kuessel, Alexandra Perricos, Heinrich Husslein, and
René Wenzl. “LINC01133 Inhibits Invasion and Promotes Proliferation in an Endometriosis
Epithelial Cell Line.” International Journal of Molecular Sciences. MDPI,
2021. https://doi.org/10.3390/ijms22168385.
ieee: I. Yotova et al., “LINC01133 inhibits invasion and promotes proliferation
in an endometriosis epithelial cell line,” International Journal of Molecular
Sciences, vol. 22, no. 16. MDPI, 2021.
ista: Yotova I, Hudson QJ, Pauler F, Proestling K, Haslinger I, Kuessel L, Perricos
A, Husslein H, Wenzl R. 2021. LINC01133 inhibits invasion and promotes proliferation
in an endometriosis epithelial cell line. International Journal of Molecular Sciences.
22(16), 8385.
mla: Yotova, Iveta, et al. “LINC01133 Inhibits Invasion and Promotes Proliferation
in an Endometriosis Epithelial Cell Line.” International Journal of Molecular
Sciences, vol. 22, no. 16, 8385, MDPI, 2021, doi:10.3390/ijms22168385.
short: I. Yotova, Q.J. Hudson, F. Pauler, K. Proestling, I. Haslinger, L. Kuessel,
A. Perricos, H. Husslein, R. Wenzl, International Journal of Molecular Sciences
22 (2021).
date_created: 2021-08-15T22:01:27Z
date_published: 2021-08-04T00:00:00Z
date_updated: 2025-06-12T06:29:07Z
day: '04'
ddc:
- '570'
department:
- _id: SiHi
doi: 10.3390/ijms22168385
external_id:
isi:
- '000689147400001'
pmid:
- '34445100'
file:
- access_level: open_access
checksum: be7f0042607ca60549cb27513c19c6af
content_type: application/pdf
creator: asandaue
date_created: 2021-08-16T09:29:17Z
date_updated: 2021-08-16T09:29:17Z
file_id: '9922'
file_name: 2021_InternationalJournalOfMolecularSciences_Yotova.pdf
file_size: 2646018
relation: main_file
success: 1
file_date_updated: 2021-08-16T09:29:17Z
has_accepted_license: '1'
intvolume: ' 22'
isi: 1
issue: '16'
language:
- iso: eng
month: '08'
oa: 1
oa_version: Published Version
pmid: 1
publication: International Journal of Molecular Sciences
publication_identifier:
eissn:
- 1422-0067
issn:
- 1661-6596
publication_status: published
publisher: MDPI
quality_controlled: '1'
scopus_import: '1'
status: public
title: LINC01133 inhibits invasion and promotes proliferation in an endometriosis
epithelial cell line
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 22
year: '2021'
...
---
_id: '9907'
abstract:
- lang: eng
text: 'DivIVA is a protein initially identified as a spatial regulator of cell division
in the model organism Bacillus subtilis, but its homologues are present in many
other Gram-positive bacteria, including Clostridia species. Besides its role as
topological regulator of the Min system during bacterial cell division, DivIVA
is involved in chromosome segregation during sporulation, genetic competence,
and cell wall synthesis. DivIVA localizes to regions of high membrane curvature,
such as the cell poles and cell division site, where it recruits distinct binding
partners. Previously, it was suggested that negative curvature sensing is the
main mechanism by which DivIVA binds to these specific regions. Here, we show
that Clostridioides difficile DivIVA binds preferably to membranes containing
negatively charged phospholipids, especially cardiolipin. Strikingly, we observed
that upon binding, DivIVA modifies the lipid distribution and induces changes
to lipid bilayers containing cardiolipin. Our observations indicate that DivIVA
might play a more complex and so far unknown active role during the formation
of the cell division septal membrane. '
acknowledged_ssus:
- _id: Bio
- _id: LifeSc
acknowledgement: "We thank Daniela Krajˇcíkova, Katarína Muchová, Zuzana Chromíkova
and other members of Barák’s laboratory for useful discussions, suggestions and
help. Special thanks also to Emília Chovancová for technical support. We are grateful
to Juraj Labaj for drawing the model and for help with graphics. Many thanks to
all members of Loose’s laboratory: Maria del Mar\r\nLópez, Paulo Caldas, Philipp
Radler, and other members of the Loose’s laboratory for sharing their knowledge
of SLB preparation and TIRF experiment chambers, for sharing coverslips and for
help with the TIRF microscope and data analysis. We also thank the members of the
Dept. of Biochemistry of Biomembranes at the Institute of Animal Biochemistry and
Genetics, CBs SAS for their help with preparing the lipid mixtures. We thank J.
Bauer for critically reading the manuscript."
article_number: '8350'
article_processing_charge: Yes
article_type: original
author:
- first_name: Naďa
full_name: Labajová, Naďa
last_name: Labajová
- first_name: Natalia S.
full_name: Baranova, Natalia S.
id: 38661662-F248-11E8-B48F-1D18A9856A87
last_name: Baranova
orcid: 0000-0002-3086-9124
- first_name: Miroslav
full_name: Jurásek, Miroslav
last_name: Jurásek
- first_name: Robert
full_name: Vácha, Robert
last_name: Vácha
- first_name: Martin
full_name: Loose, Martin
id: 462D4284-F248-11E8-B48F-1D18A9856A87
last_name: Loose
orcid: 0000-0001-7309-9724
- first_name: Imrich
full_name: Barák, Imrich
last_name: Barák
citation:
ama: Labajová N, Baranova NS, Jurásek M, Vácha R, Loose M, Barák I. Cardiolipin-containing
lipid membranes attract the bacterial cell division protein diviva. International
Journal of Molecular Sciences. 2021;22(15). doi:10.3390/ijms22158350
apa: Labajová, N., Baranova, N. S., Jurásek, M., Vácha, R., Loose, M., & Barák,
I. (2021). Cardiolipin-containing lipid membranes attract the bacterial cell division
protein diviva. International Journal of Molecular Sciences. MDPI. https://doi.org/10.3390/ijms22158350
chicago: Labajová, Naďa, Natalia S. Baranova, Miroslav Jurásek, Robert Vácha, Martin
Loose, and Imrich Barák. “Cardiolipin-Containing Lipid Membranes Attract the Bacterial
Cell Division Protein Diviva.” International Journal of Molecular Sciences.
MDPI, 2021. https://doi.org/10.3390/ijms22158350.
ieee: N. Labajová, N. S. Baranova, M. Jurásek, R. Vácha, M. Loose, and I. Barák,
“Cardiolipin-containing lipid membranes attract the bacterial cell division protein
diviva,” International Journal of Molecular Sciences, vol. 22, no. 15.
MDPI, 2021.
ista: Labajová N, Baranova NS, Jurásek M, Vácha R, Loose M, Barák I. 2021. Cardiolipin-containing
lipid membranes attract the bacterial cell division protein diviva. International
Journal of Molecular Sciences. 22(15), 8350.
mla: Labajová, Naďa, et al. “Cardiolipin-Containing Lipid Membranes Attract the
Bacterial Cell Division Protein Diviva.” International Journal of Molecular
Sciences, vol. 22, no. 15, 8350, MDPI, 2021, doi:10.3390/ijms22158350.
short: N. Labajová, N.S. Baranova, M. Jurásek, R. Vácha, M. Loose, I. Barák, International
Journal of Molecular Sciences 22 (2021).
date_created: 2021-08-15T22:01:27Z
date_published: 2021-08-01T00:00:00Z
date_updated: 2025-07-10T12:02:05Z
day: '01'
ddc:
- '570'
department:
- _id: MaLo
doi: 10.3390/ijms22158350
ec_funded: 1
external_id:
isi:
- '000681815400001'
pmid:
- '34361115'
file:
- access_level: open_access
checksum: a4bc06e9a2c803ceff5a91f10b174054
content_type: application/pdf
creator: asandaue
date_created: 2021-08-16T09:35:56Z
date_updated: 2021-08-16T09:35:56Z
file_id: '9923'
file_name: 2021_InternationalJournalOfMolecularSciences_Labajová .pdf
file_size: 6132410
relation: main_file
success: 1
file_date_updated: 2021-08-16T09:35:56Z
has_accepted_license: '1'
intvolume: ' 22'
isi: 1
issue: '15'
language:
- iso: eng
month: '08'
oa: 1
oa_version: Published Version
pmid: 1
project:
- _id: 2595697A-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '679239'
name: Self-Organization of the Bacterial Cell
publication: International Journal of Molecular Sciences
publication_identifier:
eissn:
- 1422-0067
issn:
- 1661-6596
publication_status: published
publisher: MDPI
quality_controlled: '1'
scopus_import: '1'
status: public
title: Cardiolipin-containing lipid membranes attract the bacterial cell division
protein diviva
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 22
year: '2021'
...
---
_id: '9908'
abstract:
- lang: eng
text: About eight million animal species are estimated to live on Earth, and all
except those belonging to one subphylum are invertebrates. Invertebrates are incredibly
diverse in their morphologies, life histories, and in the range of the ecological
niches that they occupy. A great variety of modes of reproduction and sex determination
systems is also observed among them, and their mosaic-distribution across the
phylogeny shows that transitions between them occur frequently and rapidly. Genetic
conflict in its various forms is a long-standing theory to explain what drives
those evolutionary transitions. Here, we review (1) the different modes of reproduction
among invertebrate species, highlighting sexual reproduction as the probable ancestral
state; (2) the paradoxical diversity of sex determination systems; (3) the different
types of genetic conflicts that could drive the evolution of such different systems.
article_number: '1136'
article_processing_charge: Yes
article_type: review
author:
- first_name: Marion A L
full_name: Picard, Marion A L
id: 2C921A7A-F248-11E8-B48F-1D18A9856A87
last_name: Picard
orcid: 0000-0002-8101-2518
- first_name: Beatriz
full_name: Vicoso, Beatriz
id: 49E1C5C6-F248-11E8-B48F-1D18A9856A87
last_name: Vicoso
orcid: 0000-0002-4579-8306
- first_name: Stéphanie
full_name: Bertrand, Stéphanie
last_name: Bertrand
- first_name: Hector
full_name: Escriva, Hector
last_name: Escriva
citation:
ama: Picard MAL, Vicoso B, Bertrand S, Escriva H. Diversity of modes of reproduction
and sex determination systems in invertebrates, and the putative contribution
of genetic conflict. Genes. 2021;12(8). doi:10.3390/genes12081136
apa: Picard, M. A. L., Vicoso, B., Bertrand, S., & Escriva, H. (2021). Diversity
of modes of reproduction and sex determination systems in invertebrates, and the
putative contribution of genetic conflict. Genes. MDPI. https://doi.org/10.3390/genes12081136
chicago: Picard, Marion A L, Beatriz Vicoso, Stéphanie Bertrand, and Hector Escriva.
“Diversity of Modes of Reproduction and Sex Determination Systems in Invertebrates,
and the Putative Contribution of Genetic Conflict.” Genes. MDPI, 2021.
https://doi.org/10.3390/genes12081136.
ieee: M. A. L. Picard, B. Vicoso, S. Bertrand, and H. Escriva, “Diversity of modes
of reproduction and sex determination systems in invertebrates, and the putative
contribution of genetic conflict,” Genes, vol. 12, no. 8. MDPI, 2021.
ista: Picard MAL, Vicoso B, Bertrand S, Escriva H. 2021. Diversity of modes of reproduction
and sex determination systems in invertebrates, and the putative contribution
of genetic conflict. Genes. 12(8), 1136.
mla: Picard, Marion A. L., et al. “Diversity of Modes of Reproduction and Sex Determination
Systems in Invertebrates, and the Putative Contribution of Genetic Conflict.”
Genes, vol. 12, no. 8, 1136, MDPI, 2021, doi:10.3390/genes12081136.
short: M.A.L. Picard, B. Vicoso, S. Bertrand, H. Escriva, Genes 12 (2021).
date_created: 2021-08-15T22:01:27Z
date_published: 2021-08-01T00:00:00Z
date_updated: 2026-04-02T14:05:14Z
day: '01'
ddc:
- '570'
department:
- _id: BeVi
doi: 10.3390/genes12081136
ec_funded: 1
external_id:
isi:
- '000690475900001'
pmid:
- '34440310'
file:
- access_level: open_access
checksum: 744e60e56d290a96da3c91a9779f886f
content_type: application/pdf
creator: asandaue
date_created: 2021-08-16T09:49:35Z
date_updated: 2021-08-16T09:49:35Z
file_id: '9926'
file_name: 2021_Genes_Picard.pdf
file_size: 2297655
relation: main_file
success: 1
file_date_updated: 2021-08-16T09:49:35Z
has_accepted_license: '1'
intvolume: ' 12'
isi: 1
issue: '8'
language:
- iso: eng
month: '08'
oa: 1
oa_version: Published Version
pmid: 1
project:
- _id: 250BDE62-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '715257'
name: Prevalence and Influence of Sexual Antagonism on Genome Evolution
publication: Genes
publication_identifier:
eissn:
- 2073-4425
publication_status: published
publisher: MDPI
quality_controlled: '1'
scopus_import: '1'
status: public
title: Diversity of modes of reproduction and sex determination systems in invertebrates,
and the putative contribution of genetic conflict
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: 12
year: '2021'
...
---
_id: '9909'
abstract:
- lang: eng
text: Roots are composed of different root types and, in the dicotyledonous Arabidopsis,
typically consist of a primary root that branches into lateral roots. Adventitious
roots emerge from non-root tissue and are formed upon wounding or other types
of abiotic stress. Here, we investigated adventitious root (AR) formation in Arabidopsis
hypocotyls under conditions of altered abscisic acid (ABA) signaling. Exogenously
applied ABA suppressed AR formation at 0.25 µM or higher doses. AR formation was
less sensitive to the synthetic ABA analog pyrabactin (PB). However, PB was a
more potent inhibitor at concentrations above 1 µM, suggesting that it was more
selective in triggering a root inhibition response. Analysis of a series of phosphonamide
and phosphonate pyrabactin analogs suggested that adventitious root formation
and lateral root branching are differentially regulated by ABA signaling. ABA
biosynthesis and signaling mutants affirmed a general inhibitory role of ABA and
point to PYL1 and PYL2 as candidate ABA receptors that regulate AR inhibition.
acknowledgement: We thank S. Cutler (Riverside, USA) for providing the ABA biosynthesis
mutants and ABA signaling mutants.
article_number: '1141'
article_processing_charge: Yes
article_type: original
author:
- first_name: Yinwei
full_name: Zeng, Yinwei
last_name: Zeng
- first_name: Inge
full_name: Verstraeten, Inge
id: 362BF7FE-F248-11E8-B48F-1D18A9856A87
last_name: Verstraeten
orcid: 0000-0001-7241-2328
- first_name: Hoang Khai
full_name: Trinh, Hoang Khai
last_name: Trinh
- first_name: Thomas
full_name: Heugebaert, Thomas
last_name: Heugebaert
- first_name: Christian V.
full_name: Stevens, Christian V.
last_name: Stevens
- first_name: Irene
full_name: Garcia-Maquilon, Irene
last_name: Garcia-Maquilon
- first_name: Pedro L.
full_name: Rodriguez, Pedro L.
last_name: Rodriguez
- first_name: Steffen
full_name: Vanneste, Steffen
last_name: Vanneste
- first_name: Danny
full_name: Geelen, Danny
last_name: Geelen
citation:
ama: Zeng Y, Verstraeten I, Trinh HK, et al. Arabidopsis hypocotyl adventitious
root formation is suppressed by ABA signaling. Genes. 2021;12(8). doi:10.3390/genes12081141
apa: Zeng, Y., Verstraeten, I., Trinh, H. K., Heugebaert, T., Stevens, C. V., Garcia-Maquilon,
I., … Geelen, D. (2021). Arabidopsis hypocotyl adventitious root formation is
suppressed by ABA signaling. Genes. MDPI. https://doi.org/10.3390/genes12081141
chicago: Zeng, Yinwei, Inge Verstraeten, Hoang Khai Trinh, Thomas Heugebaert, Christian
V. Stevens, Irene Garcia-Maquilon, Pedro L. Rodriguez, Steffen Vanneste, and Danny
Geelen. “Arabidopsis Hypocotyl Adventitious Root Formation Is Suppressed by ABA
Signaling.” Genes. MDPI, 2021. https://doi.org/10.3390/genes12081141.
ieee: Y. Zeng et al., “Arabidopsis hypocotyl adventitious root formation
is suppressed by ABA signaling,” Genes, vol. 12, no. 8. MDPI, 2021.
ista: Zeng Y, Verstraeten I, Trinh HK, Heugebaert T, Stevens CV, Garcia-Maquilon
I, Rodriguez PL, Vanneste S, Geelen D. 2021. Arabidopsis hypocotyl adventitious
root formation is suppressed by ABA signaling. Genes. 12(8), 1141.
mla: Zeng, Yinwei, et al. “Arabidopsis Hypocotyl Adventitious Root Formation Is
Suppressed by ABA Signaling.” Genes, vol. 12, no. 8, 1141, MDPI, 2021,
doi:10.3390/genes12081141.
short: Y. Zeng, I. Verstraeten, H.K. Trinh, T. Heugebaert, C.V. Stevens, I. Garcia-Maquilon,
P.L. Rodriguez, S. Vanneste, D. Geelen, Genes 12 (2021).
date_created: 2021-08-15T22:01:28Z
date_published: 2021-07-27T00:00:00Z
date_updated: 2026-04-02T13:57:06Z
day: '27'
ddc:
- '580'
- '570'
department:
- _id: JiFr
doi: 10.3390/genes12081141
external_id:
isi:
- '000690558000001'
file:
- access_level: open_access
checksum: 3d99535618cf9a5b14d264408fa52e97
content_type: application/pdf
creator: asandaue
date_created: 2021-08-16T09:02:40Z
date_updated: 2021-08-16T09:02:40Z
file_id: '9919'
file_name: 2021_Genes_Zeng.pdf
file_size: 1340305
relation: main_file
success: 1
file_date_updated: 2021-08-16T09:02:40Z
has_accepted_license: '1'
intvolume: ' 12'
isi: 1
issue: '8'
language:
- iso: eng
month: '07'
oa: 1
oa_version: Published Version
publication: Genes
publication_identifier:
eissn:
- 2073-4425
publication_status: published
publisher: MDPI
quality_controlled: '1'
scopus_import: '1'
status: public
title: Arabidopsis hypocotyl adventitious root formation is suppressed by ABA signaling
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: 12
year: '2021'
...