---
_id: '14592'
abstract:
- lang: eng
text: Cryo-electron microscopy (cryo-EM) of cellular specimens provides insights
into biological processes and structures within a native context. However, a major
challenge still lies in the efficient and reproducible preparation of adherent
cells for subsequent cryo-EM analysis. This is due to the sensitivity of many
cellular specimens to the varying seeding and culturing conditions required for
EM experiments, the often limited amount of cellular material and also the fragility
of EM grids and their substrate. Here, we present low-cost and reusable 3D printed
grid holders, designed to improve specimen preparation when culturing challenging
cellular samples directly on grids. The described grid holders increase cell culture
reproducibility and throughput, and reduce the resources required for cell culturing.
We show that grid holders can be integrated into various cryo-EM workflows, including
micro-patterning approaches to control cell seeding on grids, and for generating
samples for cryo-focused ion beam milling and cryo-electron tomography experiments.
Their adaptable design allows for the generation of specialized grid holders customized
to a large variety of applications.
article_processing_charge: No
author:
- first_name: Florian KM
full_name: Schur, Florian KM
id: 48AD8942-F248-11E8-B48F-1D18A9856A87
last_name: Schur
orcid: 0000-0003-4790-8078
citation:
ama: Schur FK. STL-files for 3D-printed grid holders described in Fäßler F, Zens
B, et al.; 3D printed cell culture grid holders for improved cellular specimen
preparation in cryo-electron microscopy. 2020. doi:10.15479/AT:ISTA:14592
apa: Schur, F. K. (2020). STL-files for 3D-printed grid holders described in Fäßler
F, Zens B, et al.; 3D printed cell culture grid holders for improved cellular
specimen preparation in cryo-electron microscopy. Institute of Science and Technology
Austria. https://doi.org/10.15479/AT:ISTA:14592
chicago: Schur, Florian KM. “STL-Files for 3D-Printed Grid Holders Described in
Fäßler F, Zens B, et Al.; 3D Printed Cell Culture Grid Holders for Improved Cellular
Specimen Preparation in Cryo-Electron Microscopy.” Institute of Science and Technology
Austria, 2020. https://doi.org/10.15479/AT:ISTA:14592.
ieee: F. K. Schur, “STL-files for 3D-printed grid holders described in Fäßler F,
Zens B, et al.; 3D printed cell culture grid holders for improved cellular specimen
preparation in cryo-electron microscopy.” Institute of Science and Technology
Austria, 2020.
ista: Schur FK. 2020. STL-files for 3D-printed grid holders described in Fäßler
F, Zens B, et al.; 3D printed cell culture grid holders for improved cellular
specimen preparation in cryo-electron microscopy, Institute of Science and Technology
Austria, 10.15479/AT:ISTA:14592.
mla: Schur, Florian KM. STL-Files for 3D-Printed Grid Holders Described in Fäßler
F, Zens B, et Al.; 3D Printed Cell Culture Grid Holders for Improved Cellular
Specimen Preparation in Cryo-Electron Microscopy. Institute of Science and
Technology Austria, 2020, doi:10.15479/AT:ISTA:14592.
short: F.K. Schur, (2020).
contributor:
- contributor_type: researcher
first_name: Florian
id: 404F5528-F248-11E8-B48F-1D18A9856A87
last_name: Fäßler
orcid: 0000-0001-7149-769X
- contributor_type: researcher
first_name: Bettina
id: 45FD126C-F248-11E8-B48F-1D18A9856A87
last_name: Zens
- contributor_type: researcher
first_name: Robert
id: 4E01D6B4-F248-11E8-B48F-1D18A9856A87
last_name: Hauschild
- contributor_type: researcher
first_name: Florian KM
id: 48AD8942-F248-11E8-B48F-1D18A9856A87
last_name: Schur
orcid: 0000-0003-4790-8078
date_created: 2023-11-22T15:00:57Z
date_published: 2020-12-01T00:00:00Z
date_updated: 2024-02-21T12:44:48Z
day: '01'
ddc:
- '570'
department:
- _id: FlSc
doi: 10.15479/AT:ISTA:14592
file:
- access_level: open_access
checksum: 0108616e2a59e51879ea51299a29b091
content_type: application/zip
creator: fschur
date_created: 2023-11-22T14:58:44Z
date_updated: 2023-11-22T14:58:44Z
file_id: '14593'
file_name: 3Dprint-files_download_v2.zip
file_size: 49297
relation: main_file
success: 1
- access_level: open_access
checksum: 4c66ddedee4d01c1c4a7978208350cfc
content_type: text/plain
creator: cchlebak
date_created: 2023-12-01T10:39:59Z
date_updated: 2023-12-01T10:39:59Z
file_id: '14637'
file_name: readme.txt
file_size: 641
relation: main_file
success: 1
file_date_updated: 2023-12-01T10:39:59Z
has_accepted_license: '1'
license: https://creativecommons.org/licenses/by-nc-sa/4.0/
month: '12'
oa: 1
oa_version: Published Version
project:
- _id: 9B954C5C-BA93-11EA-9121-9846C619BF3A
grant_number: P33367
name: Structure and isoform diversity of the Arp2/3 complex
publisher: Institute of Science and Technology Austria
related_material:
record:
- id: '8586'
relation: research_data
status: public
status: public
title: STL-files for 3D-printed grid holders described in Fäßler F, Zens B, et al.;
3D printed cell culture grid holders for improved cellular specimen preparation
in cryo-electron microscopy
tmp:
image: /images/cc_by_nc_sa.png
legal_code_url: https://creativecommons.org/licenses/by-nc-sa/4.0/legalcode
name: Creative Commons Attribution-NonCommercial-ShareAlike 4.0 International (CC
BY-NC-SA 4.0)
short: CC BY-NC-SA (4.0)
type: research_data
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
year: '2020'
...
---
_id: '7213'
abstract:
- lang: eng
text: Persistent homology is a powerful tool in Topological Data Analysis (TDA)
to capture the topological properties of data succinctly at different spatial
resolutions. For graphical data, the shape, and structure of the neighborhood
of individual data items (nodes) are an essential means of characterizing their
properties. We propose the use of persistent homology methods to capture structural
and topological properties of graphs and use it to address the problem of link
prediction. We achieve encouraging results on nine different real-world datasets
that attest to the potential of persistent homology-based methods for network
analysis.
alternative_title:
- SCI
article_processing_charge: No
author:
- first_name: Sumit
full_name: Bhatia, Sumit
last_name: Bhatia
- first_name: Bapi
full_name: Chatterjee, Bapi
id: 3C41A08A-F248-11E8-B48F-1D18A9856A87
last_name: Chatterjee
orcid: 0000-0002-2742-4028
- first_name: Deepak
full_name: Nathani, Deepak
last_name: Nathani
- first_name: Manohar
full_name: Kaul, Manohar
last_name: Kaul
citation:
ama: 'Bhatia S, Chatterjee B, Nathani D, Kaul M. A persistent homology perspective
to the link prediction problem. In: Complex Networks and Their Applications
VIII. Vol 881. Springer Nature; 2020:27-39. doi:10.1007/978-3-030-36687-2_3'
apa: 'Bhatia, S., Chatterjee, B., Nathani, D., & Kaul, M. (2020). A persistent
homology perspective to the link prediction problem. In Complex Networks and
their applications VIII (Vol. 881, pp. 27–39). Lisbon, Portugal: Springer
Nature. https://doi.org/10.1007/978-3-030-36687-2_3'
chicago: Bhatia, Sumit, Bapi Chatterjee, Deepak Nathani, and Manohar Kaul. “A Persistent
Homology Perspective to the Link Prediction Problem.” In Complex Networks and
Their Applications VIII, 881:27–39. Springer Nature, 2020. https://doi.org/10.1007/978-3-030-36687-2_3.
ieee: S. Bhatia, B. Chatterjee, D. Nathani, and M. Kaul, “A persistent homology
perspective to the link prediction problem,” in Complex Networks and their
applications VIII, Lisbon, Portugal, 2020, vol. 881, pp. 27–39.
ista: 'Bhatia S, Chatterjee B, Nathani D, Kaul M. 2020. A persistent homology perspective
to the link prediction problem. Complex Networks and their applications VIII.
COMPLEX: International Conference on Complex Networks and their Applications,
SCI, vol. 881, 27–39.'
mla: Bhatia, Sumit, et al. “A Persistent Homology Perspective to the Link Prediction
Problem.” Complex Networks and Their Applications VIII, vol. 881, Springer
Nature, 2020, pp. 27–39, doi:10.1007/978-3-030-36687-2_3.
short: S. Bhatia, B. Chatterjee, D. Nathani, M. Kaul, in:, Complex Networks and
Their Applications VIII, Springer Nature, 2020, pp. 27–39.
conference:
end_date: 2019-12-12
location: Lisbon, Portugal
name: 'COMPLEX: International Conference on Complex Networks and their Applications'
start_date: 2019-12-10
date_created: 2019-12-29T23:00:45Z
date_published: 2020-01-01T00:00:00Z
date_updated: 2024-02-22T13:16:06Z
day: '01'
ddc:
- '004'
department:
- _id: DaAl
doi: 10.1007/978-3-030-36687-2_3
ec_funded: 1
external_id:
isi:
- '000843927300003'
file:
- access_level: open_access
checksum: 8951f094c8c7dae9ff8db885199bc296
content_type: application/pdf
creator: bchatter
date_created: 2020-10-08T08:16:48Z
date_updated: 2020-10-08T08:16:48Z
file_id: '8625'
file_name: main.pdf
file_size: 310598
relation: main_file
success: 1
file_date_updated: 2020-10-08T08:16:48Z
has_accepted_license: '1'
intvolume: ' 881'
isi: 1
language:
- iso: eng
month: '01'
oa: 1
oa_version: Submitted Version
page: 27-39
project:
- _id: 260C2330-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '754411'
name: ISTplus - Postdoctoral Fellowships
publication: Complex Networks and their applications VIII
publication_identifier:
eissn:
- '18609503'
isbn:
- '9783030366865'
issn:
- 1860949X
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
scopus_import: '1'
status: public
title: A persistent homology perspective to the link prediction problem
type: conference
user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87
volume: 881
year: '2020'
...
---
_id: '10556'
abstract:
- lang: eng
text: In this paper, we present the first Asynchronous Distributed Key Generation
(ADKG) algorithm which is also the first distributed key generation algorithm
that can generate cryptographic keys with a dual (f,2f+1)-threshold (where f is
the number of faulty parties). As a result, using our ADKG we remove the trusted
setup assumption that the most scalable consensus algorithms make. In order to
create a DKG with a dual (f,2f+1)- threshold we first answer in the affirmative
the open question posed by Cachin et al. [7] on how to create an Asynchronous
Verifiable Secret Sharing (AVSS) protocol with a reconstruction threshold of f+1Proceedings of the 2020 ACM SIGSAC Conference on Computer and Communications
Security. Association for Computing Machinery; 2020:1751–1767. doi:10.1145/3372297.3423364'
apa: 'Kokoris Kogias, E., Malkhi, D., & Spiegelman, A. (2020). Asynchronous
distributed key generation for computationally-secure randomness, consensus, and
threshold signatures. In Proceedings of the 2020 ACM SIGSAC Conference on Computer
and Communications Security (pp. 1751–1767). Virtual, United States: Association
for Computing Machinery. https://doi.org/10.1145/3372297.3423364'
chicago: Kokoris Kogias, Eleftherios, Dahlia Malkhi, and Alexander Spiegelman. “Asynchronous
Distributed Key Generation for Computationally-Secure Randomness, Consensus, and
Threshold Signatures.” In Proceedings of the 2020 ACM SIGSAC Conference on
Computer and Communications Security, 1751–1767. Association for Computing
Machinery, 2020. https://doi.org/10.1145/3372297.3423364.
ieee: E. Kokoris Kogias, D. Malkhi, and A. Spiegelman, “Asynchronous distributed
key generation for computationally-secure randomness, consensus, and threshold
signatures,” in Proceedings of the 2020 ACM SIGSAC Conference on Computer and
Communications Security, Virtual, United States, 2020, pp. 1751–1767.
ista: 'Kokoris Kogias E, Malkhi D, Spiegelman A. 2020. Asynchronous distributed
key generation for computationally-secure randomness, consensus, and threshold
signatures. Proceedings of the 2020 ACM SIGSAC Conference on Computer and Communications
Security. CCS: Computer and Communications Security, 1751–1767.'
mla: Kokoris Kogias, Eleftherios, et al. “Asynchronous Distributed Key Generation
for Computationally-Secure Randomness, Consensus, and Threshold Signatures.” Proceedings
of the 2020 ACM SIGSAC Conference on Computer and Communications Security,
Association for Computing Machinery, 2020, pp. 1751–1767, doi:10.1145/3372297.3423364.
short: E. Kokoris Kogias, D. Malkhi, A. Spiegelman, in:, Proceedings of the 2020
ACM SIGSAC Conference on Computer and Communications Security, Association for
Computing Machinery, 2020, pp. 1751–1767.
conference:
end_date: 2020-11-13
location: Virtual, United States
name: 'CCS: Computer and Communications Security'
start_date: 2020-11-09
date_created: 2021-12-16T13:23:27Z
date_published: 2020-10-30T00:00:00Z
date_updated: 2024-02-22T13:10:45Z
day: '30'
department:
- _id: ElKo
doi: 10.1145/3372297.3423364
external_id:
isi:
- '000768470400104'
isi: 1
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://eprint.iacr.org/2019/1015
month: '10'
oa: 1
oa_version: Preprint
page: 1751–1767
publication: Proceedings of the 2020 ACM SIGSAC Conference on Computer and Communications
Security
publication_identifier:
isbn:
- 978-1-4503-7089-9
publication_status: published
publisher: Association for Computing Machinery
quality_controlled: '1'
scopus_import: '1'
status: public
title: Asynchronous distributed key generation for computationally-secure randomness,
consensus, and threshold signatures
type: conference
user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87
year: '2020'
...
---
_id: '9202'
abstract:
- lang: eng
text: We propose a novel hybridization method for stability analysis that over-approximates
nonlinear dynamical systems by switched systems with linear inclusion dynamics.
We observe that existing hybridization techniques for safety analysis that over-approximate
nonlinear dynamical systems by switched affine inclusion dynamics and provide
fixed approximation error, do not suffice for stability analysis. Hence, we propose
a hybridization method that provides a state-dependent error which converges to
zero as the state tends to the equilibrium point. The crux of our hybridization
computation is an elegant recursive algorithm that uses partial derivatives of
a given function to obtain upper and lower bound matrices for the over-approximating
linear inclusion. We illustrate our method on some examples to demonstrate the
application of the theory for stability analysis. In particular, our method is
able to establish stability of a nonlinear system which does not admit a polynomial
Lyapunov function.
acknowledgement: Miriam Garc´ıa Soto was partially supported by the Austrian Science
Fund (FWF) under grant Z211-N23 (Wittgenstein Award). Pavithra Prabhakar was partially
supported by NSF CAREER Award No. 1552668, NSF Award No. 2008957 and ONR YIP Award
No. N000141712577.
article_processing_charge: No
author:
- first_name: Miriam
full_name: Garcia Soto, Miriam
id: 4B3207F6-F248-11E8-B48F-1D18A9856A87
last_name: Garcia Soto
orcid: 0000-0003-2936-5719
- first_name: Pavithra
full_name: Prabhakar, Pavithra
last_name: Prabhakar
citation:
ama: 'Garcia Soto M, Prabhakar P. Hybridization for stability verification of nonlinear
switched systems. In: 2020 IEEE Real-Time Systems Symposium. IEEE; 2020:244-256.
doi:10.1109/RTSS49844.2020.00031'
apa: 'Garcia Soto, M., & Prabhakar, P. (2020). Hybridization for stability verification
of nonlinear switched systems. In 2020 IEEE Real-Time Systems Symposium
(pp. 244–256). Houston, TX, USA : IEEE. https://doi.org/10.1109/RTSS49844.2020.00031'
chicago: Garcia Soto, Miriam, and Pavithra Prabhakar. “Hybridization for Stability
Verification of Nonlinear Switched Systems.” In 2020 IEEE Real-Time Systems
Symposium, 244–56. IEEE, 2020. https://doi.org/10.1109/RTSS49844.2020.00031.
ieee: M. Garcia Soto and P. Prabhakar, “Hybridization for stability verification
of nonlinear switched systems,” in 2020 IEEE Real-Time Systems Symposium,
Houston, TX, USA , 2020, pp. 244–256.
ista: 'Garcia Soto M, Prabhakar P. 2020. Hybridization for stability verification
of nonlinear switched systems. 2020 IEEE Real-Time Systems Symposium. RTTS: Real-Time
Systems Symposium, 244–256.'
mla: Garcia Soto, Miriam, and Pavithra Prabhakar. “Hybridization for Stability Verification
of Nonlinear Switched Systems.” 2020 IEEE Real-Time Systems Symposium,
IEEE, 2020, pp. 244–56, doi:10.1109/RTSS49844.2020.00031.
short: M. Garcia Soto, P. Prabhakar, in:, 2020 IEEE Real-Time Systems Symposium,
IEEE, 2020, pp. 244–256.
conference:
end_date: 2020-12-04
location: 'Houston, TX, USA '
name: 'RTTS: Real-Time Systems Symposium'
start_date: 2020-12-01
date_created: 2021-02-26T16:38:24Z
date_published: 2020-12-01T00:00:00Z
date_updated: 2024-02-22T13:25:19Z
day: '01'
ddc:
- '000'
department:
- _id: ToHe
doi: 10.1109/RTSS49844.2020.00031
external_id:
isi:
- '000680435100021'
file:
- access_level: open_access
checksum: 8f97f229316c3b3a6f0cf99297aa0941
content_type: application/pdf
creator: mgarcias
date_created: 2021-02-26T16:38:14Z
date_updated: 2021-02-26T16:38:14Z
file_id: '9203'
file_name: main.pdf
file_size: 1125794
relation: main_file
file_date_updated: 2021-02-26T16:38:14Z
has_accepted_license: '1'
isi: 1
language:
- iso: eng
month: '12'
oa: 1
oa_version: Submitted Version
page: 244-256
project:
- _id: 25F42A32-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: Z211
name: The Wittgenstein Prize
publication: 2020 IEEE Real-Time Systems Symposium
publication_identifier:
eisbn:
- '9781728183244'
eissn:
- 2576-3172
publication_status: published
publisher: IEEE
quality_controlled: '1'
status: public
title: Hybridization for stability verification of nonlinear switched systems
type: conference
user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87
year: '2020'
...
---
_id: '6906'
abstract:
- lang: eng
text: We consider systems of bosons trapped in a box, in the Gross–Pitaevskii regime.
We show that low-energy states exhibit complete Bose–Einstein condensation with
an optimal bound on the number of orthogonal excitations. This extends recent
results obtained in Boccato et al. (Commun Math Phys 359(3):975–1026, 2018), removing
the assumption of small interaction potential.
acknowledgement: "We would like to thank P. T. Nam and R. Seiringer for several useful
discussions and\r\nfor suggesting us to use the localization techniques from [9].
C. Boccato has received funding from the\r\nEuropean Research Council (ERC) under
the programme Horizon 2020 (Grant Agreement 694227). B. Schlein gratefully acknowledges
support from the NCCR SwissMAP and from the Swiss National Foundation of Science
(Grant No. 200020_1726230) through the SNF Grant “Dynamical and energetic properties
of Bose–Einstein condensates”."
article_processing_charge: No
article_type: original
author:
- first_name: Chiara
full_name: Boccato, Chiara
id: 342E7E22-F248-11E8-B48F-1D18A9856A87
last_name: Boccato
- first_name: Christian
full_name: Brennecke, Christian
last_name: Brennecke
- first_name: Serena
full_name: Cenatiempo, Serena
last_name: Cenatiempo
- first_name: Benjamin
full_name: Schlein, Benjamin
last_name: Schlein
citation:
ama: Boccato C, Brennecke C, Cenatiempo S, Schlein B. Optimal rate for Bose-Einstein
condensation in the Gross-Pitaevskii regime. Communications in Mathematical
Physics. 2020;376:1311-1395. doi:10.1007/s00220-019-03555-9
apa: Boccato, C., Brennecke, C., Cenatiempo, S., & Schlein, B. (2020). Optimal
rate for Bose-Einstein condensation in the Gross-Pitaevskii regime. Communications
in Mathematical Physics. Springer. https://doi.org/10.1007/s00220-019-03555-9
chicago: Boccato, Chiara, Christian Brennecke, Serena Cenatiempo, and Benjamin Schlein.
“Optimal Rate for Bose-Einstein Condensation in the Gross-Pitaevskii Regime.”
Communications in Mathematical Physics. Springer, 2020. https://doi.org/10.1007/s00220-019-03555-9.
ieee: C. Boccato, C. Brennecke, S. Cenatiempo, and B. Schlein, “Optimal rate for
Bose-Einstein condensation in the Gross-Pitaevskii regime,” Communications
in Mathematical Physics, vol. 376. Springer, pp. 1311–1395, 2020.
ista: Boccato C, Brennecke C, Cenatiempo S, Schlein B. 2020. Optimal rate for Bose-Einstein
condensation in the Gross-Pitaevskii regime. Communications in Mathematical Physics.
376, 1311–1395.
mla: Boccato, Chiara, et al. “Optimal Rate for Bose-Einstein Condensation in the
Gross-Pitaevskii Regime.” Communications in Mathematical Physics, vol.
376, Springer, 2020, pp. 1311–95, doi:10.1007/s00220-019-03555-9.
short: C. Boccato, C. Brennecke, S. Cenatiempo, B. Schlein, Communications in Mathematical
Physics 376 (2020) 1311–1395.
date_created: 2019-09-24T17:30:59Z
date_published: 2020-06-01T00:00:00Z
date_updated: 2024-02-22T13:33:02Z
day: '01'
department:
- _id: RoSe
doi: 10.1007/s00220-019-03555-9
ec_funded: 1
external_id:
arxiv:
- '1812.03086'
isi:
- '000536053300012'
intvolume: ' 376'
isi: 1
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/1812.03086
month: '06'
oa: 1
oa_version: Preprint
page: 1311-1395
project:
- _id: 25C6DC12-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '694227'
name: Analysis of quantum many-body systems
publication: Communications in Mathematical Physics
publication_identifier:
eissn:
- 1432-0916
issn:
- 0010-3616
publication_status: published
publisher: Springer
quality_controlled: '1'
scopus_import: '1'
status: public
title: Optimal rate for Bose-Einstein condensation in the Gross-Pitaevskii regime
type: journal_article
user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87
volume: 376
year: '2020'
...
---
_id: '7410'
abstract:
- lang: eng
text: 'Epiboly is a conserved gastrulation movement describing the thinning and
spreading of a sheet or multi-layer of cells. The zebrafish embryo has emerged
as a vital model system to address the cellular and molecular mechanisms that
drive epiboly. In the zebrafish embryo, the blastoderm, consisting of a simple
squamous epithelium (the enveloping layer) and an underlying mass of deep cells,
as well as a yolk nuclear syncytium (the yolk syncytial layer) undergo epiboly
to internalize the yolk cell during gastrulation. The major events during zebrafish
epiboly are: expansion of the enveloping layer and the internal yolk syncytial
layer, reduction and removal of the yolk membrane ahead of the advancing blastoderm
margin and deep cell rearrangements between the enveloping layer and yolk syncytial
layer to thin the blastoderm. Here, work addressing the cellular and molecular
mechanisms as well as the sources of the mechanical forces that underlie these
events is reviewed. The contribution of recent findings to the current model of
epiboly as well as open questions and future prospects are also discussed.'
article_processing_charge: No
author:
- first_name: Ashley E.E.
full_name: Bruce, Ashley E.E.
last_name: Bruce
- first_name: Carl-Philipp J
full_name: Heisenberg, Carl-Philipp J
id: 39427864-F248-11E8-B48F-1D18A9856A87
last_name: Heisenberg
orcid: 0000-0002-0912-4566
citation:
ama: 'Bruce AEE, Heisenberg C-PJ. Mechanisms of zebrafish epiboly: A current view.
In: Solnica-Krezel L, ed. Gastrulation: From Embryonic Pattern to Form.
Vol 136. Current Topics in Developmental Biology. Elsevier; 2020:319-341. doi:10.1016/bs.ctdb.2019.07.001'
apa: 'Bruce, A. E. E., & Heisenberg, C.-P. J. (2020). Mechanisms of zebrafish
epiboly: A current view. In L. Solnica-Krezel (Ed.), Gastrulation: From Embryonic
Pattern to Form (Vol. 136, pp. 319–341). Elsevier. https://doi.org/10.1016/bs.ctdb.2019.07.001'
chicago: 'Bruce, Ashley E.E., and Carl-Philipp J Heisenberg. “Mechanisms of Zebrafish
Epiboly: A Current View.” In Gastrulation: From Embryonic Pattern to Form,
edited by Lilianna Solnica-Krezel, 136:319–41. Current Topics in Developmental
Biology. Elsevier, 2020. https://doi.org/10.1016/bs.ctdb.2019.07.001.'
ieee: 'A. E. E. Bruce and C.-P. J. Heisenberg, “Mechanisms of zebrafish epiboly:
A current view,” in Gastrulation: From Embryonic Pattern to Form, vol.
136, L. Solnica-Krezel, Ed. Elsevier, 2020, pp. 319–341.'
ista: 'Bruce AEE, Heisenberg C-PJ. 2020.Mechanisms of zebrafish epiboly: A current
view. In: Gastrulation: From Embryonic Pattern to Form. vol. 136, 319–341.'
mla: 'Bruce, Ashley E. E., and Carl-Philipp J. Heisenberg. “Mechanisms of Zebrafish
Epiboly: A Current View.” Gastrulation: From Embryonic Pattern to Form,
edited by Lilianna Solnica-Krezel, vol. 136, Elsevier, 2020, pp. 319–41, doi:10.1016/bs.ctdb.2019.07.001.'
short: 'A.E.E. Bruce, C.-P.J. Heisenberg, in:, L. Solnica-Krezel (Ed.), Gastrulation:
From Embryonic Pattern to Form, Elsevier, 2020, pp. 319–341.'
date_created: 2020-01-30T09:24:06Z
date_published: 2020-01-01T00:00:00Z
date_updated: 2024-02-22T13:23:09Z
day: '01'
department:
- _id: CaHe
doi: 10.1016/bs.ctdb.2019.07.001
editor:
- first_name: 'Lilianna '
full_name: 'Solnica-Krezel, Lilianna '
last_name: Solnica-Krezel
external_id:
isi:
- '000611830600012'
intvolume: ' 136'
isi: 1
language:
- iso: eng
month: '01'
oa_version: None
page: 319-341
publication: 'Gastrulation: From Embryonic Pattern to Form'
publication_identifier:
isbn:
- '9780128127988'
issn:
- 0070-2153
publication_status: published
publisher: Elsevier
quality_controlled: '1'
scopus_import: '1'
series_title: Current Topics in Developmental Biology
status: public
title: 'Mechanisms of zebrafish epiboly: A current view'
type: book_chapter
user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87
volume: 136
year: '2020'
...
---
_id: '6944'
abstract:
- lang: eng
text: 'We study the problem of automatically detecting if a given multi-class classifier
operates outside of its specifications (out-of-specs), i.e. on input data from
a different distribution than what it was trained for. This is an important problem
to solve on the road towards creating reliable computer vision systems for real-world
applications, because the quality of a classifier’s predictions cannot be guaranteed
if it operates out-of-specs. Previously proposed methods for out-of-specs detection
make decisions on the level of single inputs. This, however, is insufficient to
achieve low false positive rate and high false negative rates at the same time.
In this work, we describe a new procedure named KS(conf), based on statistical
reasoning. Its main component is a classical Kolmogorov–Smirnov test that is applied
to the set of predicted confidence values for batches of samples. Working with
batches instead of single samples allows increasing the true positive rate without
negatively affecting the false positive rate, thereby overcoming a crucial limitation
of single sample tests. We show by extensive experiments using a variety of convolutional
network architectures and datasets that KS(conf) reliably detects out-of-specs
situations even under conditions where other tests fail. It furthermore has a
number of properties that make it an excellent candidate for practical deployment:
it is easy to implement, adds almost no overhead to the system, works with any
classifier that outputs confidence scores, and requires no a priori knowledge
about how the data distribution could change.'
article_processing_charge: Yes (via OA deal)
article_type: original
author:
- first_name: Rémy
full_name: Sun, Rémy
last_name: Sun
- first_name: Christoph
full_name: Lampert, Christoph
id: 40C20FD2-F248-11E8-B48F-1D18A9856A87
last_name: Lampert
orcid: 0000-0001-8622-7887
citation:
ama: 'Sun R, Lampert C. KS(conf): A light-weight test if a multiclass classifier
operates outside of its specifications. International Journal of Computer Vision.
2020;128(4):970-995. doi:10.1007/s11263-019-01232-x'
apa: 'Sun, R., & Lampert, C. (2020). KS(conf): A light-weight test if a multiclass
classifier operates outside of its specifications. International Journal of
Computer Vision. Springer Nature. https://doi.org/10.1007/s11263-019-01232-x'
chicago: 'Sun, Rémy, and Christoph Lampert. “KS(Conf): A Light-Weight Test If a
Multiclass Classifier Operates Outside of Its Specifications.” International
Journal of Computer Vision. Springer Nature, 2020. https://doi.org/10.1007/s11263-019-01232-x.'
ieee: 'R. Sun and C. Lampert, “KS(conf): A light-weight test if a multiclass classifier
operates outside of its specifications,” International Journal of Computer
Vision, vol. 128, no. 4. Springer Nature, pp. 970–995, 2020.'
ista: 'Sun R, Lampert C. 2020. KS(conf): A light-weight test if a multiclass classifier
operates outside of its specifications. International Journal of Computer Vision.
128(4), 970–995.'
mla: 'Sun, Rémy, and Christoph Lampert. “KS(Conf): A Light-Weight Test If a Multiclass
Classifier Operates Outside of Its Specifications.” International Journal of
Computer Vision, vol. 128, no. 4, Springer Nature, 2020, pp. 970–95, doi:10.1007/s11263-019-01232-x.'
short: R. Sun, C. Lampert, International Journal of Computer Vision 128 (2020) 970–995.
date_created: 2019-10-14T09:14:28Z
date_published: 2020-04-01T00:00:00Z
date_updated: 2024-02-22T14:57:30Z
day: '01'
ddc:
- '004'
department:
- _id: ChLa
doi: 10.1007/s11263-019-01232-x
ec_funded: 1
external_id:
isi:
- '000494406800001'
file:
- access_level: open_access
checksum: 155e63edf664dcacb3bdc1c2223e606f
content_type: application/pdf
creator: dernst
date_created: 2019-11-26T10:30:02Z
date_updated: 2020-07-14T12:47:45Z
file_id: '7110'
file_name: 2019_IJCV_Sun.pdf
file_size: 1715072
relation: main_file
file_date_updated: 2020-07-14T12:47:45Z
has_accepted_license: '1'
intvolume: ' 128'
isi: 1
issue: '4'
language:
- iso: eng
month: '04'
oa: 1
oa_version: Published Version
page: 970-995
project:
- _id: 2532554C-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '308036'
name: Lifelong Learning of Visual Scene Understanding
- _id: B67AFEDC-15C9-11EA-A837-991A96BB2854
name: IST Austria Open Access Fund
publication: International Journal of Computer Vision
publication_identifier:
eissn:
- 1573-1405
issn:
- 0920-5691
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
related_material:
link:
- relation: erratum
url: https://doi.org/10.1007/s11263-019-01262-5
record:
- id: '6482'
relation: earlier_version
status: public
scopus_import: '1'
status: public
title: 'KS(conf): A light-weight test if a multiclass classifier operates outside
of its specifications'
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: journal_article
user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87
volume: 128
year: '2020'
...
---
_id: '8324'
abstract:
- lang: eng
text: The notion of program sensitivity (aka Lipschitz continuity) specifies that
changes in the program input result in proportional changes to the program output.
For probabilistic programs the notion is naturally extended to expected sensitivity.
A previous approach develops a relational program logic framework for proving
expected sensitivity of probabilistic while loops, where the number of iterations
is fixed and bounded. In this work, we consider probabilistic while loops where
the number of iterations is not fixed, but randomized and depends on the initial
input values. We present a sound approach for proving expected sensitivity of
such programs. Our sound approach is martingale-based and can be automated through
existing martingale-synthesis algorithms. Furthermore, our approach is compositional
for sequential composition of while loops under a mild side condition. We demonstrate
the effectiveness of our approach on several classical examples from Gambler's
Ruin, stochastic hybrid systems and stochastic gradient descent. We also present
experimental results showing that our automated approach can handle various probabilistic
programs in the literature.
acknowledgement: We thank anonymous reviewers for helpful comments, especially for
pointing to us a scenario of piecewise-linear approximation (Remark5). The research
was partially supported by the National Natural Science Foundation of China (NSFC)
under Grant No. 61802254, 61672229, 61832015,61772336,11871221 and Austrian Science
Fund (FWF) NFN under Grant No. S11407-N23 (RiSE/SHiNE). We thank Prof. Yuxi Fu,
director of the BASICS Lab at Shanghai Jiao Tong University, for his support.
article_number: '25'
article_processing_charge: No
author:
- first_name: Peixin
full_name: Wang, Peixin
last_name: Wang
- first_name: Hongfei
full_name: Fu, Hongfei
last_name: Fu
- first_name: Krishnendu
full_name: Chatterjee, Krishnendu
id: 2E5DCA20-F248-11E8-B48F-1D18A9856A87
last_name: Chatterjee
orcid: 0000-0002-4561-241X
- first_name: Yuxin
full_name: Deng, Yuxin
last_name: Deng
- first_name: Ming
full_name: Xu, Ming
last_name: Xu
citation:
ama: 'Wang P, Fu H, Chatterjee K, Deng Y, Xu M. Proving expected sensitivity of
probabilistic programs with randomized variable-dependent termination time. In:
Proceedings of the ACM on Programming Languages. Vol 4. ACM; 2020. doi:10.1145/3371093'
apa: Wang, P., Fu, H., Chatterjee, K., Deng, Y., & Xu, M. (2020). Proving expected
sensitivity of probabilistic programs with randomized variable-dependent termination
time. In Proceedings of the ACM on Programming Languages (Vol. 4). ACM.
https://doi.org/10.1145/3371093
chicago: Wang, Peixin, Hongfei Fu, Krishnendu Chatterjee, Yuxin Deng, and Ming Xu.
“Proving Expected Sensitivity of Probabilistic Programs with Randomized Variable-Dependent
Termination Time.” In Proceedings of the ACM on Programming Languages,
Vol. 4. ACM, 2020. https://doi.org/10.1145/3371093.
ieee: P. Wang, H. Fu, K. Chatterjee, Y. Deng, and M. Xu, “Proving expected sensitivity
of probabilistic programs with randomized variable-dependent termination time,”
in Proceedings of the ACM on Programming Languages, 2020, vol. 4, no. POPL.
ista: Wang P, Fu H, Chatterjee K, Deng Y, Xu M. 2020. Proving expected sensitivity
of probabilistic programs with randomized variable-dependent termination time.
Proceedings of the ACM on Programming Languages. vol. 4, 25.
mla: Wang, Peixin, et al. “Proving Expected Sensitivity of Probabilistic Programs
with Randomized Variable-Dependent Termination Time.” Proceedings of the ACM
on Programming Languages, vol. 4, no. POPL, 25, ACM, 2020, doi:10.1145/3371093.
short: P. Wang, H. Fu, K. Chatterjee, Y. Deng, M. Xu, in:, Proceedings of the ACM
on Programming Languages, ACM, 2020.
date_created: 2020-08-30T22:01:12Z
date_published: 2020-01-01T00:00:00Z
date_updated: 2024-02-22T15:16:45Z
day: '01'
ddc:
- '004'
department:
- _id: KrCh
doi: 10.1145/3371093
external_id:
arxiv:
- '1902.04744'
file:
- access_level: open_access
checksum: c6193d109ff4ecb17e7a6513d8eb34c0
content_type: application/pdf
creator: cziletti
date_created: 2020-09-01T11:12:58Z
date_updated: 2020-09-01T11:12:58Z
file_id: '8328'
file_name: 2019_ACM_POPL_Wang.pdf
file_size: 564151
relation: main_file
success: 1
file_date_updated: 2020-09-01T11:12:58Z
has_accepted_license: '1'
intvolume: ' 4'
issue: POPL
language:
- iso: eng
month: '01'
oa: 1
oa_version: Published Version
project:
- _id: 25863FF4-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: S11407
name: Game Theory
publication: Proceedings of the ACM on Programming Languages
publication_identifier:
eissn:
- 2475-1421
publication_status: published
publisher: ACM
quality_controlled: '1'
related_material:
link:
- relation: software
url: https://doi.org/10.5281/zenodo.3533633
scopus_import: '1'
status: public
title: Proving expected sensitivity of probabilistic programs with randomized variable-dependent
termination time
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: conference
user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87
volume: 4
year: '2020'
...
---
_id: '7160'
abstract:
- lang: eng
text: 'Nocturnal animals that rely on their visual system for foraging, mating,
and navigation usually exhibit specific traits associated with living in scotopic
conditions. Most nocturnal birds have several visual specializations, such as
enlarged eyes and an increased orbital convergence. However, the actual role of
binocular vision in nocturnal foraging is still debated. Nightjars (Aves: Caprimulgidae)
are predators that actively pursue and capture flying insects in crepuscular and
nocturnal environments, mainly using a conspicuous “sit-and-wait” tactic on which
pursuit begins with an insect flying over the bird that sits on the ground. In
this study, we describe the visual system of the band-winged nightjar (Systellura
longirostris), with emphasis on anatomical features previously described as relevant
for nocturnal birds. Orbit convergence, determined by 3D scanning of the skull,
was 73.28°. The visual field, determined by ophthalmoscopic reflex, exhibits an
area of maximum binocular overlap of 42°, and it is dorsally oriented. The eyes
showed a nocturnal-like normalized corneal aperture/axial length index. Retinal
ganglion cells (RGCs) were relatively scant, and distributed in an unusual oblique-band
pattern, with higher concentrations in the ventrotemporal quadrant. Together,
these results indicate that the band-winged nightjar exhibits a retinal specialization
associated with the binocular area of their dorsal visual field, a relevant area
for pursuit triggering and prey attacks. The RGC distribution observed is unusual
among birds, but similar to that of some visually dependent insectivorous bats,
suggesting that those features might be convergent in relation to feeding strategies.'
article_processing_charge: No
article_type: original
author:
- first_name: Juan Esteban
full_name: Salazar, Juan Esteban
last_name: Salazar
- first_name: Daniel
full_name: Severin, Daniel
last_name: Severin
- first_name: Tomas A
full_name: Vega Zuniga, Tomas A
id: 2E7C4E78-F248-11E8-B48F-1D18A9856A87
last_name: Vega Zuniga
- first_name: Pedro
full_name: Fernández-Aburto, Pedro
last_name: Fernández-Aburto
- first_name: Alfonso
full_name: Deichler, Alfonso
last_name: Deichler
- first_name: Michel
full_name: Sallaberry A., Michel
last_name: Sallaberry A.
- first_name: Jorge
full_name: Mpodozis, Jorge
last_name: Mpodozis
citation:
ama: 'Salazar JE, Severin D, Vega Zuniga TA, et al. Anatomical specializations related
to foraging in the visual system of a nocturnal insectivorous bird, the band-winged
nightjar (Aves: Caprimulgiformes). Brain, Behavior and Evolution. 2020;94(1-4):27-36.
doi:10.1159/000504162'
apa: 'Salazar, J. E., Severin, D., Vega Zuniga, T. A., Fernández-Aburto, P., Deichler,
A., Sallaberry A., M., & Mpodozis, J. (2020). Anatomical specializations related
to foraging in the visual system of a nocturnal insectivorous bird, the band-winged
nightjar (Aves: Caprimulgiformes). Brain, Behavior and Evolution. Karger
Publishers. https://doi.org/10.1159/000504162'
chicago: 'Salazar, Juan Esteban, Daniel Severin, Tomas A Vega Zuniga, Pedro Fernández-Aburto,
Alfonso Deichler, Michel Sallaberry A., and Jorge Mpodozis. “Anatomical Specializations
Related to Foraging in the Visual System of a Nocturnal Insectivorous Bird, the
Band-Winged Nightjar (Aves: Caprimulgiformes).” Brain, Behavior and Evolution.
Karger Publishers, 2020. https://doi.org/10.1159/000504162.'
ieee: 'J. E. Salazar et al., “Anatomical specializations related to foraging
in the visual system of a nocturnal insectivorous bird, the band-winged nightjar
(Aves: Caprimulgiformes),” Brain, Behavior and Evolution, vol. 94, no.
1–4. Karger Publishers, pp. 27–36, 2020.'
ista: 'Salazar JE, Severin D, Vega Zuniga TA, Fernández-Aburto P, Deichler A, Sallaberry A.
M, Mpodozis J. 2020. Anatomical specializations related to foraging in the visual
system of a nocturnal insectivorous bird, the band-winged nightjar (Aves: Caprimulgiformes).
Brain, Behavior and Evolution. 94(1–4), 27–36.'
mla: 'Salazar, Juan Esteban, et al. “Anatomical Specializations Related to Foraging
in the Visual System of a Nocturnal Insectivorous Bird, the Band-Winged Nightjar
(Aves: Caprimulgiformes).” Brain, Behavior and Evolution, vol. 94, no.
1–4, Karger Publishers, 2020, pp. 27–36, doi:10.1159/000504162.'
short: J.E. Salazar, D. Severin, T.A. Vega Zuniga, P. Fernández-Aburto, A. Deichler,
M. Sallaberry A., J. Mpodozis, Brain, Behavior and Evolution 94 (2020) 27–36.
date_created: 2019-12-09T09:04:13Z
date_published: 2020-01-01T00:00:00Z
date_updated: 2024-02-22T15:18:34Z
day: '01'
department:
- _id: MaJö
doi: 10.1159/000504162
external_id:
isi:
- '000522856600004'
pmid:
- '31751995'
intvolume: ' 94'
isi: 1
issue: 1-4
language:
- iso: eng
month: '01'
oa_version: None
page: 27-36
pmid: 1
publication: Brain, Behavior and Evolution
publication_identifier:
eissn:
- 1421-9743
issn:
- 0006-8977
publication_status: published
publisher: Karger Publishers
quality_controlled: '1'
scopus_import: '1'
status: public
title: 'Anatomical specializations related to foraging in the visual system of a nocturnal
insectivorous bird, the band-winged nightjar (Aves: Caprimulgiformes)'
type: journal_article
user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87
volume: 94
year: '2020'
...
---
_id: '6184'
abstract:
- lang: eng
text: We prove edge universality for a general class of correlated real symmetric
or complex Hermitian Wigner matrices with arbitrary expectation. Our theorem also
applies to internal edges of the self-consistent density of states. In particular,
we establish a strong form of band rigidity which excludes mismatches between
location and label of eigenvalues close to internal edges in these general models.
article_processing_charge: No
article_type: original
author:
- first_name: Johannes
full_name: Alt, Johannes
id: 36D3D8B6-F248-11E8-B48F-1D18A9856A87
last_name: Alt
- first_name: László
full_name: Erdös, László
id: 4DBD5372-F248-11E8-B48F-1D18A9856A87
last_name: Erdös
orcid: 0000-0001-5366-9603
- first_name: Torben H
full_name: Krüger, Torben H
id: 3020C786-F248-11E8-B48F-1D18A9856A87
last_name: Krüger
orcid: 0000-0002-4821-3297
- first_name: Dominik J
full_name: Schröder, Dominik J
id: 408ED176-F248-11E8-B48F-1D18A9856A87
last_name: Schröder
orcid: 0000-0002-2904-1856
citation:
ama: 'Alt J, Erdös L, Krüger TH, Schröder DJ. Correlated random matrices: Band rigidity
and edge universality. Annals of Probability. 2020;48(2):963-1001. doi:10.1214/19-AOP1379'
apa: 'Alt, J., Erdös, L., Krüger, T. H., & Schröder, D. J. (2020). Correlated
random matrices: Band rigidity and edge universality. Annals of Probability.
Institute of Mathematical Statistics. https://doi.org/10.1214/19-AOP1379'
chicago: 'Alt, Johannes, László Erdös, Torben H Krüger, and Dominik J Schröder.
“Correlated Random Matrices: Band Rigidity and Edge Universality.” Annals of
Probability. Institute of Mathematical Statistics, 2020. https://doi.org/10.1214/19-AOP1379.'
ieee: 'J. Alt, L. Erdös, T. H. Krüger, and D. J. Schröder, “Correlated random matrices:
Band rigidity and edge universality,” Annals of Probability, vol. 48, no.
2. Institute of Mathematical Statistics, pp. 963–1001, 2020.'
ista: 'Alt J, Erdös L, Krüger TH, Schröder DJ. 2020. Correlated random matrices:
Band rigidity and edge universality. Annals of Probability. 48(2), 963–1001.'
mla: 'Alt, Johannes, et al. “Correlated Random Matrices: Band Rigidity and Edge
Universality.” Annals of Probability, vol. 48, no. 2, Institute of Mathematical
Statistics, 2020, pp. 963–1001, doi:10.1214/19-AOP1379.'
short: J. Alt, L. Erdös, T.H. Krüger, D.J. Schröder, Annals of Probability 48 (2020)
963–1001.
date_created: 2019-03-28T09:20:08Z
date_published: 2020-03-01T00:00:00Z
date_updated: 2024-02-22T14:34:33Z
day: '01'
department:
- _id: LaEr
doi: 10.1214/19-AOP1379
ec_funded: 1
external_id:
arxiv:
- '1804.07744'
isi:
- '000528269100013'
intvolume: ' 48'
isi: 1
issue: '2'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/1804.07744
month: '03'
oa: 1
oa_version: Preprint
page: 963-1001
project:
- _id: 258DCDE6-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '338804'
name: Random matrices, universality and disordered quantum systems
publication: Annals of Probability
publication_identifier:
issn:
- 0091-1798
publication_status: published
publisher: Institute of Mathematical Statistics
quality_controlled: '1'
related_material:
record:
- id: '149'
relation: dissertation_contains
status: public
- id: '6179'
relation: dissertation_contains
status: public
scopus_import: '1'
status: public
title: 'Correlated random matrices: Band rigidity and edge universality'
type: journal_article
user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87
volume: 48
year: '2020'
...
---
_id: '15037'
abstract:
- lang: eng
text: Protein abundance and localization at the plasma membrane (PM) shapes plant
development and mediates adaptation to changing environmental conditions. It is
regulated by ubiquitination, a post-translational modification crucial for the
proper sorting of endocytosed PM proteins to the vacuole for subsequent degradation.
To understand the significance and the variety of roles played by this reversible
modification, the function of ubiquitin receptors, which translate the ubiquitin
signature into a cellular response, needs to be elucidated. In this study, we
show that TOL (TOM1-like) proteins function in plants as multivalent ubiquitin
receptors, governing ubiquitinated cargo delivery to the vacuole via the conserved
Endosomal Sorting Complex Required for Transport (ESCRT) pathway. TOL2 and TOL6
interact with components of the ESCRT machinery and bind to K63-linked ubiquitin
via two tandemly arranged conserved ubiquitin-binding domains. Mutation of these
domains results not only in a loss of ubiquitin binding but also altered localization,
abolishing TOL6 ubiquitin receptor activity. Function and localization of TOL6
is itself regulated by ubiquitination, whereby TOL6 ubiquitination potentially
modulates degradation of PM-localized cargoes, assisting in the fine-tuning of
the delicate interplay between protein recycling and downregulation. Taken together,
our findings demonstrate the function and regulation of a ubiquitin receptor that
mediates vacuolar degradation of PM proteins in higher plants.
article_processing_charge: No
article_type: original
author:
- first_name: Jeanette
full_name: Moulinier-Anzola, Jeanette
last_name: Moulinier-Anzola
- first_name: Maximilian
full_name: Schwihla, Maximilian
last_name: Schwihla
- first_name: Lucinda
full_name: De-Araújo, Lucinda
last_name: De-Araújo
- first_name: Christina
full_name: Artner, Christina
id: 45DF286A-F248-11E8-B48F-1D18A9856A87
last_name: Artner
- first_name: Lisa
full_name: Jörg, Lisa
last_name: Jörg
- first_name: Nataliia
full_name: Konstantinova, Nataliia
last_name: Konstantinova
- first_name: Christian
full_name: Luschnig, Christian
last_name: Luschnig
- first_name: Barbara
full_name: Korbei, Barbara
last_name: Korbei
citation:
ama: Moulinier-Anzola J, Schwihla M, De-Araújo L, et al. TOLs function as ubiquitin
receptors in the early steps of the ESCRT pathway in higher plants. Molecular
Plant. 2020;13(5):717-731. doi:10.1016/j.molp.2020.02.012
apa: Moulinier-Anzola, J., Schwihla, M., De-Araújo, L., Artner, C., Jörg, L., Konstantinova,
N., … Korbei, B. (2020). TOLs function as ubiquitin receptors in the early steps
of the ESCRT pathway in higher plants. Molecular Plant. Elsevier. https://doi.org/10.1016/j.molp.2020.02.012
chicago: Moulinier-Anzola, Jeanette, Maximilian Schwihla, Lucinda De-Araújo, Christina
Artner, Lisa Jörg, Nataliia Konstantinova, Christian Luschnig, and Barbara Korbei.
“TOLs Function as Ubiquitin Receptors in the Early Steps of the ESCRT Pathway
in Higher Plants.” Molecular Plant. Elsevier, 2020. https://doi.org/10.1016/j.molp.2020.02.012.
ieee: J. Moulinier-Anzola et al., “TOLs function as ubiquitin receptors in
the early steps of the ESCRT pathway in higher plants,” Molecular Plant,
vol. 13, no. 5. Elsevier, pp. 717–731, 2020.
ista: Moulinier-Anzola J, Schwihla M, De-Araújo L, Artner C, Jörg L, Konstantinova
N, Luschnig C, Korbei B. 2020. TOLs function as ubiquitin receptors in the early
steps of the ESCRT pathway in higher plants. Molecular Plant. 13(5), 717–731.
mla: Moulinier-Anzola, Jeanette, et al. “TOLs Function as Ubiquitin Receptors in
the Early Steps of the ESCRT Pathway in Higher Plants.” Molecular Plant,
vol. 13, no. 5, Elsevier, 2020, pp. 717–31, doi:10.1016/j.molp.2020.02.012.
short: J. Moulinier-Anzola, M. Schwihla, L. De-Araújo, C. Artner, L. Jörg, N. Konstantinova,
C. Luschnig, B. Korbei, Molecular Plant 13 (2020) 717–731.
date_created: 2024-02-28T08:55:56Z
date_published: 2020-05-04T00:00:00Z
date_updated: 2024-02-28T12:41:52Z
day: '04'
ddc:
- '580'
department:
- _id: EvBe
doi: 10.1016/j.molp.2020.02.012
external_id:
pmid:
- '32087370'
file:
- access_level: open_access
checksum: c538a5008f7827f62d17d40a3bfabe65
content_type: application/pdf
creator: dernst
date_created: 2024-02-28T12:39:56Z
date_updated: 2024-02-28T12:39:56Z
file_id: '15038'
file_name: 2020_MolecularPlant_MoulinierAnzola.pdf
file_size: 3089212
relation: main_file
success: 1
file_date_updated: 2024-02-28T12:39:56Z
has_accepted_license: '1'
intvolume: ' 13'
issue: '5'
keyword:
- Plant Science
- Molecular Biology
language:
- iso: eng
month: '05'
oa: 1
oa_version: Published Version
page: 717-731
pmid: 1
publication: Molecular Plant
publication_identifier:
issn:
- 1674-2052
publication_status: published
publisher: Elsevier
quality_controlled: '1'
status: public
title: TOLs function as ubiquitin receptors in the early steps of the ESCRT pathway
in higher plants
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: 13
year: '2020'
...
---
_id: '15036'
abstract:
- lang: eng
text: The assembly of a septin filament requires that homologous monomers must distinguish
between one another in establishing appropriate interfaces with their neighbors.
To understand this phenomenon at the molecular level, we present the first four
crystal structures of heterodimeric septin complexes. We describe in detail the
two distinct types of G-interface present within the octameric particles, which
must polymerize to form filaments. These are formed between SEPT2 and SEPT6 and
between SEPT7 and SEPT3, and their description permits an understanding of the
structural basis for the selectivity necessary for correct filament assembly.
By replacing SEPT6 by SEPT8 or SEPT11, it is possible to rationalize Kinoshita's
postulate, which predicts the exchangeability of septins from within a subgroup.
Switches I and II, which in classical small GTPases provide a mechanism for nucleotide-dependent
conformational change, have been repurposed in septins to play a fundamental role
in molecular recognition. Specifically, it is switch I which holds the key to
discriminating between the two different G-interfaces. Moreover, residues which
are characteristic for a given subgroup play subtle, but pivotal, roles in guaranteeing
that the correct interfaces are formed.
article_processing_charge: No
article_type: original
author:
- first_name: Higor Vinícius Dias
full_name: Rosa, Higor Vinícius Dias
last_name: Rosa
- first_name: Diego Antonio
full_name: Leonardo, Diego Antonio
last_name: Leonardo
- first_name: Gabriel
full_name: Brognara, Gabriel
id: D96FFDA0-A884-11E9-9968-DC26E6697425
last_name: Brognara
- first_name: José
full_name: Brandão-Neto, José
last_name: Brandão-Neto
- first_name: Humberto
full_name: D'Muniz Pereira, Humberto
last_name: D'Muniz Pereira
- first_name: Ana Paula Ulian
full_name: Araújo, Ana Paula Ulian
last_name: Araújo
- first_name: Richard Charles
full_name: Garratt, Richard Charles
last_name: Garratt
citation:
ama: 'Rosa HVD, Leonardo DA, Brognara G, et al. Molecular recognition at septin
interfaces: The switches hold the key. Journal of Molecular Biology. 2020;432(21):5784-5801.
doi:10.1016/j.jmb.2020.09.001'
apa: 'Rosa, H. V. D., Leonardo, D. A., Brognara, G., Brandão-Neto, J., D’Muniz Pereira,
H., Araújo, A. P. U., & Garratt, R. C. (2020). Molecular recognition at septin
interfaces: The switches hold the key. Journal of Molecular Biology. Elsevier.
https://doi.org/10.1016/j.jmb.2020.09.001'
chicago: 'Rosa, Higor Vinícius Dias, Diego Antonio Leonardo, Gabriel Brognara, José
Brandão-Neto, Humberto D’Muniz Pereira, Ana Paula Ulian Araújo, and Richard Charles
Garratt. “Molecular Recognition at Septin Interfaces: The Switches Hold the Key.”
Journal of Molecular Biology. Elsevier, 2020. https://doi.org/10.1016/j.jmb.2020.09.001.'
ieee: 'H. V. D. Rosa et al., “Molecular recognition at septin interfaces:
The switches hold the key,” Journal of Molecular Biology, vol. 432, no.
21. Elsevier, pp. 5784–5801, 2020.'
ista: 'Rosa HVD, Leonardo DA, Brognara G, Brandão-Neto J, D’Muniz Pereira H, Araújo
APU, Garratt RC. 2020. Molecular recognition at septin interfaces: The switches
hold the key. Journal of Molecular Biology. 432(21), 5784–5801.'
mla: 'Rosa, Higor Vinícius Dias, et al. “Molecular Recognition at Septin Interfaces:
The Switches Hold the Key.” Journal of Molecular Biology, vol. 432, no.
21, Elsevier, 2020, pp. 5784–801, doi:10.1016/j.jmb.2020.09.001.'
short: H.V.D. Rosa, D.A. Leonardo, G. Brognara, J. Brandão-Neto, H. D’Muniz Pereira,
A.P.U. Araújo, R.C. Garratt, Journal of Molecular Biology 432 (2020) 5784–5801.
date_created: 2024-02-28T08:50:34Z
date_published: 2020-10-02T00:00:00Z
date_updated: 2024-02-28T12:37:54Z
day: '02'
department:
- _id: MaLo
doi: 10.1016/j.jmb.2020.09.001
external_id:
pmid:
- '32910969'
intvolume: ' 432'
issue: '21'
keyword:
- Molecular Biology
- Structural Biology
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.1016/j.jmb.2020.09.001
month: '10'
oa: 1
oa_version: Published Version
page: 5784-5801
pmid: 1
publication: Journal of Molecular Biology
publication_identifier:
issn:
- 0022-2836
publication_status: published
publisher: Elsevier
quality_controlled: '1'
status: public
title: 'Molecular recognition at septin interfaces: The switches hold the key'
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 432
year: '2020'
...
---
_id: '8384'
abstract:
- lang: eng
text: Previous research on animations of soap bubbles, films, and foams largely
focuses on the motion and geometric shape of the bubble surface. These works neglect
the evolution of the bubble’s thickness, which is normally responsible for visual
phenomena like surface vortices, Newton’s interference patterns, capillary waves,
and deformation-dependent rupturing of films in a foam. In this paper, we model
these natural phenomena by introducing the film thickness as a reduced degree
of freedom in the Navier-Stokes equations and deriving their equations of motion.
We discretize the equations on a nonmanifold triangle mesh surface and couple
it to an existing bubble solver. In doing so, we also introduce an incompressible
fluid solver for 2.5D films and a novel advection algorithm for convecting fields
across non-manifold surface junctions. Our simulations enhance state-of-the-art
bubble solvers with additional effects caused by convection, rippling, draining,
and evaporation of the thin film.
acknowledged_ssus:
- _id: ScienComp
acknowledgement: "We wish to thank the anonymous reviewers and the members of the
Visual Computing Group at IST Austria for their valuable feedback, especially Camille
Schreck for her help in rendering. This research was supported by the Scientific
Service Units (SSU) of IST Austria through resources provided by Scientific Computing.
We would like to thank the authors of [Belcour and Barla 2017] for providing their
implementation, the authors of [Atkins and Elliott 2010] and [Seychelles et al.
2008] for allowing us to use their results, and Rok Grah for helpful discussions.
Finally, we thank Ryoichi Ando for many discussions from the beginning of the project
that resulted in important contents of the paper including our formulation, numerical
scheme, and initial implementation. This project has received funding from the\r\nEuropean
Research Council (ERC) under the European Union’s Horizon 2020 research and innovation
programme under grant agreement No. 638176."
article_number: '31'
article_processing_charge: No
article_type: original
author:
- first_name: Sadashige
full_name: Ishida, Sadashige
id: 6F7C4B96-A8E9-11E9-A7CA-09ECE5697425
last_name: Ishida
- first_name: Peter
full_name: Synak, Peter
id: 331776E2-F248-11E8-B48F-1D18A9856A87
last_name: Synak
- first_name: Fumiya
full_name: Narita, Fumiya
last_name: Narita
- first_name: Toshiya
full_name: Hachisuka, Toshiya
last_name: Hachisuka
- first_name: Christopher J
full_name: Wojtan, Christopher J
id: 3C61F1D2-F248-11E8-B48F-1D18A9856A87
last_name: Wojtan
orcid: 0000-0001-6646-5546
citation:
ama: Ishida S, Synak P, Narita F, Hachisuka T, Wojtan C. A model for soap film dynamics
with evolving thickness. ACM Transactions on Graphics. 2020;39(4). doi:10.1145/3386569.3392405
apa: Ishida, S., Synak, P., Narita, F., Hachisuka, T., & Wojtan, C. (2020).
A model for soap film dynamics with evolving thickness. ACM Transactions on
Graphics. Association for Computing Machinery. https://doi.org/10.1145/3386569.3392405
chicago: Ishida, Sadashige, Peter Synak, Fumiya Narita, Toshiya Hachisuka, and Chris
Wojtan. “A Model for Soap Film Dynamics with Evolving Thickness.” ACM Transactions
on Graphics. Association for Computing Machinery, 2020. https://doi.org/10.1145/3386569.3392405.
ieee: S. Ishida, P. Synak, F. Narita, T. Hachisuka, and C. Wojtan, “A model for
soap film dynamics with evolving thickness,” ACM Transactions on Graphics,
vol. 39, no. 4. Association for Computing Machinery, 2020.
ista: Ishida S, Synak P, Narita F, Hachisuka T, Wojtan C. 2020. A model for soap
film dynamics with evolving thickness. ACM Transactions on Graphics. 39(4), 31.
mla: Ishida, Sadashige, et al. “A Model for Soap Film Dynamics with Evolving Thickness.”
ACM Transactions on Graphics, vol. 39, no. 4, 31, Association for Computing
Machinery, 2020, doi:10.1145/3386569.3392405.
short: S. Ishida, P. Synak, F. Narita, T. Hachisuka, C. Wojtan, ACM Transactions
on Graphics 39 (2020).
date_created: 2020-09-13T22:01:18Z
date_published: 2020-07-08T00:00:00Z
date_updated: 2024-02-28T12:57:31Z
day: '08'
ddc:
- '000'
department:
- _id: ChWo
doi: 10.1145/3386569.3392405
ec_funded: 1
external_id:
isi:
- '000583700300004'
file:
- access_level: open_access
checksum: 813831ca91319d794d9748c276b24578
content_type: application/pdf
creator: dernst
date_created: 2020-11-23T09:03:19Z
date_updated: 2020-11-23T09:03:19Z
file_id: '8795'
file_name: 2020_soapfilm_submitted.pdf
file_size: 14935529
relation: main_file
success: 1
file_date_updated: 2020-11-23T09:03:19Z
has_accepted_license: '1'
intvolume: ' 39'
isi: 1
issue: '4'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.1145/3386569.3392405
month: '07'
oa: 1
oa_version: Submitted Version
project:
- _id: 2533E772-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '638176'
name: Efficient Simulation of Natural Phenomena at Extremely Large Scales
publication: ACM Transactions on Graphics
publication_identifier:
eissn:
- '15577368'
issn:
- '07300301'
publication_status: published
publisher: Association for Computing Machinery
quality_controlled: '1'
scopus_import: '1'
status: public
title: A model for soap film dynamics with evolving thickness
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 39
year: '2020'
...
---
_id: '7802'
abstract:
- lang: eng
text: "The Massively Parallel Computation (MPC) model is an emerging model which
distills core aspects of distributed and parallel computation. It has been developed
as a tool to solve (typically graph) problems in systems where the input is distributed
over many machines with limited space.\r\n\t\r\nRecent work has focused on the
regime in which machines have sublinear (in $n$, the number of nodes in the input
graph) space, with randomized algorithms presented for fundamental graph problems
of Maximal Matching and Maximal Independent Set. However, there have been no prior
corresponding deterministic algorithms.\r\n\t\r\n\tA major challenge underlying
the sublinear space setting is that the local space of each machine might be too
small to store all the edges incident to a single node. This poses a considerable
obstacle compared to the classical models in which each node is assumed to know
and have easy access to its incident edges. To overcome this barrier we introduce
a new graph sparsification technique that deterministically computes a low-degree
subgraph with additional desired properties. The degree of the nodes in this subgraph
is small in the sense that the edges of each node can be now stored on a single
machine. This low-degree subgraph also has the property that solving the problem
on this subgraph provides \\emph{significant} global progress, i.e., progress
towards solving the problem for the original input graph.\r\n\t\r\nUsing this
framework to derandomize the well-known randomized algorithm of Luby [SICOMP'86],
we obtain $O(\\log \\Delta+\\log\\log n)$-round deterministic MPC algorithms for
solving the fundamental problems of Maximal Matching and Maximal Independent Set
with $O(n^{\\epsilon})$ space on each machine for any constant $\\epsilon > 0$.
Based on the recent work of Ghaffari et al. [FOCS'18], this additive $O(\\log\\log
n)$ factor is conditionally essential. These algorithms can also be shown to run
in $O(\\log \\Delta)$ rounds in the closely related model of CONGESTED CLIQUE,
improving upon the state-of-the-art bound of $O(\\log^2 \\Delta)$ rounds by Censor-Hillel
et al. [DISC'17]."
article_processing_charge: No
author:
- first_name: Artur
full_name: Czumaj, Artur
last_name: Czumaj
orcid: 0000-0002-5646-9524
- first_name: Peter
full_name: Davies, Peter
id: 11396234-BB50-11E9-B24C-90FCE5697425
last_name: Davies
orcid: 0000-0002-5646-9524
- first_name: Merav
full_name: Parter, Merav
last_name: Parter
citation:
ama: 'Czumaj A, Davies P, Parter M. Graph sparsification for derandomizing massively
parallel computation with low space. In: Proceedings of the 32nd ACM Symposium
on Parallelism in Algorithms and Architectures (SPAA 2020). Association for
Computing Machinery; 2020:175-185. doi:10.1145/3350755.3400282'
apa: 'Czumaj, A., Davies, P., & Parter, M. (2020). Graph sparsification for
derandomizing massively parallel computation with low space. In Proceedings
of the 32nd ACM Symposium on Parallelism in Algorithms and Architectures (SPAA
2020) (pp. 175–185). Virtual Event, United States: Association for Computing
Machinery. https://doi.org/10.1145/3350755.3400282'
chicago: Czumaj, Artur, Peter Davies, and Merav Parter. “Graph Sparsification for
Derandomizing Massively Parallel Computation with Low Space.” In Proceedings
of the 32nd ACM Symposium on Parallelism in Algorithms and Architectures (SPAA
2020), 175–85. Association for Computing Machinery, 2020. https://doi.org/10.1145/3350755.3400282.
ieee: A. Czumaj, P. Davies, and M. Parter, “Graph sparsification for derandomizing
massively parallel computation with low space,” in Proceedings of the 32nd
ACM Symposium on Parallelism in Algorithms and Architectures (SPAA 2020),
Virtual Event, United States, 2020, no. 7, pp. 175–185.
ista: 'Czumaj A, Davies P, Parter M. 2020. Graph sparsification for derandomizing
massively parallel computation with low space. Proceedings of the 32nd ACM Symposium
on Parallelism in Algorithms and Architectures (SPAA 2020). SPAA: Symposium on
Parallelism in Algorithms and Architectures, 175–185.'
mla: Czumaj, Artur, et al. “Graph Sparsification for Derandomizing Massively Parallel
Computation with Low Space.” Proceedings of the 32nd ACM Symposium on Parallelism
in Algorithms and Architectures (SPAA 2020), no. 7, Association for Computing
Machinery, 2020, pp. 175–85, doi:10.1145/3350755.3400282.
short: A. Czumaj, P. Davies, M. Parter, in:, Proceedings of the 32nd ACM Symposium
on Parallelism in Algorithms and Architectures (SPAA 2020), Association for Computing
Machinery, 2020, pp. 175–185.
conference:
end_date: 2020-07-17
location: Virtual Event, United States
name: 'SPAA: Symposium on Parallelism in Algorithms and Architectures'
start_date: 2020-07-15
date_created: 2020-05-06T08:53:34Z
date_published: 2020-07-01T00:00:00Z
date_updated: 2024-02-28T12:53:09Z
day: '01'
department:
- _id: DaAl
doi: 10.1145/3350755.3400282
ec_funded: 1
external_id:
arxiv:
- '1912.05390'
isi:
- '000744436200015'
isi: 1
issue: '7'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/1912.05390
month: '07'
oa: 1
oa_version: Preprint
page: 175-185
project:
- _id: 260C2330-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '754411'
name: ISTplus - Postdoctoral Fellowships
publication: Proceedings of the 32nd ACM Symposium on Parallelism in Algorithms and
Architectures (SPAA 2020)
publication_status: published
publisher: Association for Computing Machinery
quality_controlled: '1'
related_material:
record:
- id: '9541'
relation: later_version
status: public
scopus_import: '1'
status: public
title: Graph sparsification for derandomizing massively parallel computation with
low space
type: conference
user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
year: '2020'
...
---
_id: '7636'
abstract:
- lang: eng
text: "Balanced search trees typically use key comparisons to guide their operations,
and achieve logarithmic running time. By relying on numerical properties of the
keys, interpolation search achieves lower search complexity and better performance.
Although interpolation-based data structures were investigated in the past, their
non-blocking concurrent variants have received very little attention so far.\r\nIn
this paper, we propose the first non-blocking implementation of the classic interpolation
search tree (IST) data structure. For arbitrary key distributions, the data structure
ensures worst-case O(log n + p) amortized time for search, insertion and deletion
traversals. When the input key distributions are smooth, lookups run in expected
O(log log n + p) time, and insertion and deletion run in expected amortized O(log
log n + p) time, where p is a bound on the number of threads. To improve the scalability
of concurrent insertion and deletion, we propose a novel parallel rebuilding technique,
which should be of independent interest.\r\nWe evaluate whether the theoretical
improvements translate to practice by implementing the concurrent interpolation
search tree, and benchmarking it on uniform and nonuniform key distributions,
for dataset sizes in the millions to billions of keys. Relative to the state-of-the-art
concurrent data structures, the concurrent interpolation search tree achieves
performance improvements of up to 15% under high update rates, and of up to 50%
under moderate update rates. Further, ISTs exhibit up to 2X less cache-misses,
and consume 1.2 -- 2.6X less memory compared to the next best alternative on typical
dataset sizes. We find that the results are surprisingly robust to distributional
skew, which suggests that our data structure can be a promising alternative to
classic concurrent search structures."
acknowledgement: "This project has received funding from the European Research Council
(ERC) under the European Union Horizon 2020 research and innovation program, grant
agreement No 805223, ERC Starting Grant ScaleML. We acknowledge the support of the
Natural Sciences and\r\nEngineering Research Council of Canada (NSERC). "
article_processing_charge: No
author:
- first_name: Trevor A
full_name: Brown, Trevor A
id: 3569F0A0-F248-11E8-B48F-1D18A9856A87
last_name: Brown
- first_name: Aleksandar
full_name: Prokopec, Aleksandar
last_name: Prokopec
- first_name: Dan-Adrian
full_name: Alistarh, Dan-Adrian
id: 4A899BFC-F248-11E8-B48F-1D18A9856A87
last_name: Alistarh
orcid: 0000-0003-3650-940X
citation:
ama: 'Brown TA, Prokopec A, Alistarh D-A. Non-blocking interpolation search trees
with doubly-logarithmic running time. In: Proceedings of the ACM SIGPLAN Symposium
on Principles and Practice of Parallel Programming. Association for Computing
Machinery; 2020:276-291. doi:10.1145/3332466.3374542'
apa: 'Brown, T. A., Prokopec, A., & Alistarh, D.-A. (2020). Non-blocking interpolation
search trees with doubly-logarithmic running time. In Proceedings of the ACM
SIGPLAN Symposium on Principles and Practice of Parallel Programming (pp.
276–291). San Diego, CA, United States: Association for Computing Machinery. https://doi.org/10.1145/3332466.3374542'
chicago: Brown, Trevor A, Aleksandar Prokopec, and Dan-Adrian Alistarh. “Non-Blocking
Interpolation Search Trees with Doubly-Logarithmic Running Time.” In Proceedings
of the ACM SIGPLAN Symposium on Principles and Practice of Parallel Programming,
276–91. Association for Computing Machinery, 2020. https://doi.org/10.1145/3332466.3374542.
ieee: T. A. Brown, A. Prokopec, and D.-A. Alistarh, “Non-blocking interpolation
search trees with doubly-logarithmic running time,” in Proceedings of the ACM
SIGPLAN Symposium on Principles and Practice of Parallel Programming, San
Diego, CA, United States, 2020, pp. 276–291.
ista: 'Brown TA, Prokopec A, Alistarh D-A. 2020. Non-blocking interpolation search
trees with doubly-logarithmic running time. Proceedings of the ACM SIGPLAN Symposium
on Principles and Practice of Parallel Programming. PPOPP: Principles and Practice
of Parallel Programming, 276–291.'
mla: Brown, Trevor A., et al. “Non-Blocking Interpolation Search Trees with Doubly-Logarithmic
Running Time.” Proceedings of the ACM SIGPLAN Symposium on Principles and Practice
of Parallel Programming, Association for Computing Machinery, 2020, pp. 276–91,
doi:10.1145/3332466.3374542.
short: T.A. Brown, A. Prokopec, D.-A. Alistarh, in:, Proceedings of the ACM SIGPLAN
Symposium on Principles and Practice of Parallel Programming, Association for
Computing Machinery, 2020, pp. 276–291.
conference:
end_date: 2020-02-26
location: San Diego, CA, United States
name: 'PPOPP: Principles and Practice of Parallel Programming'
start_date: 2020-02-22
date_created: 2020-04-05T22:00:49Z
date_published: 2020-02-19T00:00:00Z
date_updated: 2024-02-28T12:55:14Z
day: '19'
department:
- _id: DaAl
doi: 10.1145/3332466.3374542
ec_funded: 1
external_id:
isi:
- '000564476500020'
isi: 1
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.1145/3332466.3374542
month: '02'
oa: 1
oa_version: Published Version
page: 276-291
project:
- _id: 268A44D6-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '805223'
name: Elastic Coordination for Scalable Machine Learning
publication: Proceedings of the ACM SIGPLAN Symposium on Principles and Practice of
Parallel Programming
publication_identifier:
isbn:
- '9781450368186'
publication_status: published
publisher: Association for Computing Machinery
quality_controlled: '1'
scopus_import: '1'
status: public
title: Non-blocking interpolation search trees with doubly-logarithmic running time
type: conference
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
year: '2020'
...
---
_id: '8191'
abstract:
- lang: eng
text: "There has been a significant amount of research on hardware and software
support for efficient concurrent data structures; yet, the question of how to
build correct, simple, and scalable data structures has not yet been definitively
settled. In this paper, we revisit this question from a minimalist perspective,
and ask: what is the smallest amount of synchronization required for correct and
efficient concurrent search data structures, and how could this minimal synchronization
support be provided in hardware?\r\n\r\nTo address these questions, we introduce
memory tagging, a simple hardware mechanism which enables the programmer to \"tag\"
a dynamic set of memory locations, at cache-line granularity, and later validate
whether the memory has been concurrently modified, with the possibility of updating
one of the underlying locations atomically if validation succeeds. We provide
several examples showing that this mechanism can enable fast and arguably simple
concurrent data structure designs, such as lists, binary search trees, balanced
search trees, range queries, and Software Transactional Memory (STM) implementations.
We provide an implementation of memory tags in the Graphite multi-core simulator,
showing that the mechanism can be implemented entirely at the level of L1 cache,
and that it can enable non-trivial speedups versus existing implementations of
the above data structures."
article_processing_charge: No
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: Trevor A
full_name: Brown, Trevor A
id: 3569F0A0-F248-11E8-B48F-1D18A9856A87
last_name: Brown
- first_name: Nandini
full_name: Singhal, Nandini
last_name: Singhal
citation:
ama: 'Alistarh D-A, Brown TA, Singhal N. Memory tagging: Minimalist synchronization
for scalable concurrent data structures. In: Annual ACM Symposium on Parallelism
in Algorithms and Architectures. Association for Computing Machinery; 2020:37-49.
doi:10.1145/3350755.3400213'
apa: 'Alistarh, D.-A., Brown, T. A., & Singhal, N. (2020). Memory tagging: Minimalist
synchronization for scalable concurrent data structures. In Annual ACM Symposium
on Parallelism in Algorithms and Architectures (pp. 37–49). Virtual Event,
United States: Association for Computing Machinery. https://doi.org/10.1145/3350755.3400213'
chicago: 'Alistarh, Dan-Adrian, Trevor A Brown, and Nandini Singhal. “Memory Tagging:
Minimalist Synchronization for Scalable Concurrent Data Structures.” In Annual
ACM Symposium on Parallelism in Algorithms and Architectures, 37–49. Association
for Computing Machinery, 2020. https://doi.org/10.1145/3350755.3400213.'
ieee: 'D.-A. Alistarh, T. A. Brown, and N. Singhal, “Memory tagging: Minimalist
synchronization for scalable concurrent data structures,” in Annual ACM Symposium
on Parallelism in Algorithms and Architectures, Virtual Event, United States,
2020, no. 7, pp. 37–49.'
ista: 'Alistarh D-A, Brown TA, Singhal N. 2020. Memory tagging: Minimalist synchronization
for scalable concurrent data structures. Annual ACM Symposium on Parallelism in
Algorithms and Architectures. SPAA: Symposium on Parallelism in Algorithms and
Architectures, 37–49.'
mla: 'Alistarh, Dan-Adrian, et al. “Memory Tagging: Minimalist Synchronization for
Scalable Concurrent Data Structures.” Annual ACM Symposium on Parallelism in
Algorithms and Architectures, no. 7, Association for Computing Machinery,
2020, pp. 37–49, doi:10.1145/3350755.3400213.'
short: D.-A. Alistarh, T.A. Brown, N. Singhal, in:, Annual ACM Symposium on Parallelism
in Algorithms and Architectures, Association for Computing Machinery, 2020, pp.
37–49.
conference:
end_date: 2020-07-17
location: Virtual Event, United States
name: 'SPAA: Symposium on Parallelism in Algorithms and Architectures'
start_date: 2020-07-15
date_created: 2020-08-02T22:00:58Z
date_published: 2020-07-06T00:00:00Z
date_updated: 2024-02-28T12:56:32Z
day: '06'
department:
- _id: DaAl
doi: 10.1145/3350755.3400213
external_id:
isi:
- '000744436200004'
isi: 1
issue: '7'
language:
- iso: eng
month: '07'
oa_version: None
page: 37-49
publication: Annual ACM Symposium on Parallelism in Algorithms and Architectures
publication_identifier:
isbn:
- '9781450369350'
publication_status: published
publisher: Association for Computing Machinery
quality_controlled: '1'
scopus_import: '1'
status: public
title: 'Memory tagging: Minimalist synchronization for scalable concurrent data structures'
type: conference
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
year: '2020'
...
---
_id: '7635'
abstract:
- lang: eng
text: Concurrent programming can be notoriously complex and error-prone. Programming
bugs can arise from a variety of sources, such as operation re-reordering, or
incomplete understanding of the memory model. A variety of formal and model checking
methods have been developed to address this fundamental difficulty. While technically
interesting, existing academic methods are still hard to apply to the large codebases
typical of industrial deployments, which limits their practical impact.
article_processing_charge: No
author:
- first_name: Nikita
full_name: Koval, Nikita
id: 2F4DB10C-F248-11E8-B48F-1D18A9856A87
last_name: Koval
- first_name: Mariia
full_name: Sokolova, Mariia
id: 26217AE4-77FF-11EA-8101-AD24D49E41F4
last_name: Sokolova
- first_name: Alexander
full_name: Fedorov, Alexander
last_name: Fedorov
- 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: Dmitry
full_name: Tsitelov, Dmitry
last_name: Tsitelov
citation:
ama: 'Koval N, Sokolova M, Fedorov A, Alistarh D-A, Tsitelov D. Testing concurrency
on the JVM with Lincheck. In: Proceedings of the ACM SIGPLAN Symposium on Principles
and Practice of Parallel Programming, PPOPP. Association for Computing Machinery;
2020:423-424. doi:10.1145/3332466.3374503'
apa: 'Koval, N., Sokolova, M., Fedorov, A., Alistarh, D.-A., & Tsitelov, D.
(2020). Testing concurrency on the JVM with Lincheck. In Proceedings of the
ACM SIGPLAN Symposium on Principles and Practice of Parallel Programming, PPOPP
(pp. 423–424). San Diego, CA, United States: Association for Computing Machinery.
https://doi.org/10.1145/3332466.3374503'
chicago: Koval, Nikita, Mariia Sokolova, Alexander Fedorov, Dan-Adrian Alistarh,
and Dmitry Tsitelov. “Testing Concurrency on the JVM with Lincheck.” In Proceedings
of the ACM SIGPLAN Symposium on Principles and Practice of Parallel Programming,
PPOPP, 423–24. Association for Computing Machinery, 2020. https://doi.org/10.1145/3332466.3374503.
ieee: N. Koval, M. Sokolova, A. Fedorov, D.-A. Alistarh, and D. Tsitelov, “Testing
concurrency on the JVM with Lincheck,” in Proceedings of the ACM SIGPLAN Symposium
on Principles and Practice of Parallel Programming, PPOPP, San Diego, CA,
United States, 2020, pp. 423–424.
ista: 'Koval N, Sokolova M, Fedorov A, Alistarh D-A, Tsitelov D. 2020. Testing concurrency
on the JVM with Lincheck. Proceedings of the ACM SIGPLAN Symposium on Principles
and Practice of Parallel Programming, PPOPP. PPOPP: Principles and Practice of
Parallel Programming, 423–424.'
mla: Koval, Nikita, et al. “Testing Concurrency on the JVM with Lincheck.” Proceedings
of the ACM SIGPLAN Symposium on Principles and Practice of Parallel Programming,
PPOPP, Association for Computing Machinery, 2020, pp. 423–24, doi:10.1145/3332466.3374503.
short: N. Koval, M. Sokolova, A. Fedorov, D.-A. Alistarh, D. Tsitelov, in:, Proceedings
of the ACM SIGPLAN Symposium on Principles and Practice of Parallel Programming,
PPOPP, Association for Computing Machinery, 2020, pp. 423–424.
conference:
end_date: 2020-02-26
location: San Diego, CA, United States
name: 'PPOPP: Principles and Practice of Parallel Programming'
start_date: 2020-02-22
date_created: 2020-04-05T22:00:48Z
date_published: 2020-02-19T00:00:00Z
date_updated: 2024-02-28T12:53:46Z
day: '19'
department:
- _id: DaAl
doi: 10.1145/3332466.3374503
language:
- iso: eng
month: '02'
oa_version: None
page: 423-424
publication: Proceedings of the ACM SIGPLAN Symposium on Principles and Practice of
Parallel Programming, PPOPP
publication_identifier:
isbn:
- '9781450368186'
publication_status: published
publisher: Association for Computing Machinery
quality_controlled: '1'
scopus_import: '1'
status: public
title: Testing concurrency on the JVM with Lincheck
type: conference
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
year: '2020'
...
---
_id: '8383'
abstract:
- lang: eng
text: We introduce extension-based proofs, a class of impossibility proofs that
includes valency arguments. They are modelled as an interaction between a prover
and a protocol. Using proofs based on combinatorial topology, it has been shown
that it is impossible to deterministically solve k-set agreement among n > k ≥
2 processes in a wait-free manner. However, it was unknown whether proofs based
on simpler techniques were possible. We explain why this impossibility result
cannot be obtained by an extension-based proof and, hence, extension-based proofs
are limited in power.
article_processing_charge: No
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: James
full_name: Aspnes, James
last_name: Aspnes
- first_name: Faith
full_name: Ellen, Faith
last_name: Ellen
- first_name: Rati
full_name: Gelashvili, Rati
last_name: Gelashvili
- first_name: Leqi
full_name: Zhu, Leqi
last_name: Zhu
citation:
ama: 'Alistarh D-A, Aspnes J, Ellen F, Gelashvili R, Zhu L. Brief Announcement:
Why Extension-Based Proofs Fail. In: Proceedings of the 39th Symposium on Principles
of Distributed Computing. Association for Computing Machinery; 2020:54-56.
doi:10.1145/3382734.3405743'
apa: 'Alistarh, D.-A., Aspnes, J., Ellen, F., Gelashvili, R., & Zhu, L. (2020).
Brief Announcement: Why Extension-Based Proofs Fail. In Proceedings of the
39th Symposium on Principles of Distributed Computing (pp. 54–56). Virtual,
Italy: Association for Computing Machinery. https://doi.org/10.1145/3382734.3405743'
chicago: 'Alistarh, Dan-Adrian, James Aspnes, Faith Ellen, Rati Gelashvili, and
Leqi Zhu. “Brief Announcement: Why Extension-Based Proofs Fail.” In Proceedings
of the 39th Symposium on Principles of Distributed Computing, 54–56. Association
for Computing Machinery, 2020. https://doi.org/10.1145/3382734.3405743.'
ieee: 'D.-A. Alistarh, J. Aspnes, F. Ellen, R. Gelashvili, and L. Zhu, “Brief Announcement:
Why Extension-Based Proofs Fail,” in Proceedings of the 39th Symposium on Principles
of Distributed Computing, Virtual, Italy, 2020, pp. 54–56.'
ista: 'Alistarh D-A, Aspnes J, Ellen F, Gelashvili R, Zhu L. 2020. Brief Announcement:
Why Extension-Based Proofs Fail. Proceedings of the 39th Symposium on Principles
of Distributed Computing. PODC: Principles of Distributed Computing, 54–56.'
mla: 'Alistarh, Dan-Adrian, et al. “Brief Announcement: Why Extension-Based Proofs
Fail.” Proceedings of the 39th Symposium on Principles of Distributed Computing,
Association for Computing Machinery, 2020, pp. 54–56, doi:10.1145/3382734.3405743.'
short: D.-A. Alistarh, J. Aspnes, F. Ellen, R. Gelashvili, L. Zhu, in:, Proceedings
of the 39th Symposium on Principles of Distributed Computing, Association for
Computing Machinery, 2020, pp. 54–56.
conference:
end_date: 2020-08-07
location: Virtual, Italy
name: 'PODC: Principles of Distributed Computing'
start_date: 2020-08-03
date_created: 2020-09-13T22:01:18Z
date_published: 2020-07-31T00:00:00Z
date_updated: 2024-02-28T12:54:19Z
day: '31'
department:
- _id: DaAl
doi: 10.1145/3382734.3405743
language:
- iso: eng
month: '07'
oa_version: None
page: 54-56
publication: Proceedings of the 39th Symposium on Principles of Distributed Computing
publication_identifier:
isbn:
- '9781450375825'
publication_status: published
publisher: Association for Computing Machinery
quality_controlled: '1'
scopus_import: '1'
status: public
title: 'Brief Announcement: Why Extension-Based Proofs Fail'
type: conference
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
year: '2020'
...
---
_id: '8385'
abstract:
- lang: eng
text: 'We present a method for animating yarn-level cloth effects using a thin-shell
solver. We accomplish this through numerical homogenization: we first use a large
number of yarn-level simulations to build a model of the potential energy density
of the cloth, and then use this energy density function to compute forces in a
thin shell simulator. We model several yarn-based materials, including both woven
and knitted fabrics. Our model faithfully reproduces expected effects like the
stiffness of woven fabrics, and the highly deformable nature and anisotropy of
knitted fabrics. Our approach does not require any real-world experiments nor
measurements; because the method is based entirely on simulations, it can generate
entirely new material models quickly, without the need for testing apparatuses
or human intervention. We provide data-driven models of several woven and knitted
fabrics, which can be used for efficient simulation with an off-the-shelf cloth
solver.'
acknowledged_ssus:
- _id: ScienComp
acknowledgement: "We wish to thank the anonymous reviewers and the members of the
Visual Computing Group at IST Austria for their valuable feedback. We also thank
the creators of the Berkeley Garment Library [de Joya et al. 2012] for providing
garment meshes, [Krishnamurthy and Levoy 1996] and [Turk and Levoy 1994] for the
armadillo and bunny meshes, the creators of libWetCloth [Fei et al. 2018] for their
implementation of discrete elastic rod forces, and Tomáš Skřivan for\r\ninspiring
discussions and help with Mathematica code generation. This research was supported
by the Scientific Service Units (SSU) of IST Austria through resources provided
by Scientific Computing. This project has received funding from the European Research
Council (ERC) under the European Union’s Horizon 2020 research and innovation programme
under grant agreement No. 638176. Rahul Narain is supported by a Pankaj Gupta Young
Faculty Fellowship and a gift from Adobe Inc."
article_number: '48'
article_processing_charge: No
article_type: original
author:
- first_name: Georg
full_name: Sperl, Georg
id: 4DD40360-F248-11E8-B48F-1D18A9856A87
last_name: Sperl
- first_name: Rahul
full_name: Narain, Rahul
last_name: Narain
- first_name: Christopher J
full_name: Wojtan, Christopher J
id: 3C61F1D2-F248-11E8-B48F-1D18A9856A87
last_name: Wojtan
orcid: 0000-0001-6646-5546
citation:
ama: Sperl G, Narain R, Wojtan C. Homogenized yarn-level cloth. ACM Transactions
on Graphics. 2020;39(4). doi:10.1145/3386569.3392412
apa: Sperl, G., Narain, R., & Wojtan, C. (2020). Homogenized yarn-level cloth.
ACM Transactions on Graphics. Association for Computing Machinery. https://doi.org/10.1145/3386569.3392412
chicago: Sperl, Georg, Rahul Narain, and Chris Wojtan. “Homogenized Yarn-Level Cloth.”
ACM Transactions on Graphics. Association for Computing Machinery, 2020.
https://doi.org/10.1145/3386569.3392412.
ieee: G. Sperl, R. Narain, and C. Wojtan, “Homogenized yarn-level cloth,” ACM
Transactions on Graphics, vol. 39, no. 4. Association for Computing Machinery,
2020.
ista: Sperl G, Narain R, Wojtan C. 2020. Homogenized yarn-level cloth. ACM Transactions
on Graphics. 39(4), 48.
mla: Sperl, Georg, et al. “Homogenized Yarn-Level Cloth.” ACM Transactions on
Graphics, vol. 39, no. 4, 48, Association for Computing Machinery, 2020, doi:10.1145/3386569.3392412.
short: G. Sperl, R. Narain, C. Wojtan, ACM Transactions on Graphics 39 (2020).
date_created: 2020-09-13T22:01:18Z
date_published: 2020-07-08T00:00:00Z
date_updated: 2024-02-28T12:57:47Z
day: '08'
ddc:
- '000'
department:
- _id: ChWo
doi: 10.1145/3386569.3392412
ec_funded: 1
external_id:
isi:
- '000583700300021'
file:
- access_level: open_access
checksum: cf4c1d361c3196c4bd424520a5588205
content_type: application/pdf
creator: dernst
date_created: 2020-11-23T09:01:22Z
date_updated: 2020-11-23T09:01:22Z
file_id: '8794'
file_name: 2020_hylc_submitted.pdf
file_size: 38922662
relation: main_file
success: 1
file_date_updated: 2020-11-23T09:01:22Z
has_accepted_license: '1'
intvolume: ' 39'
isi: 1
issue: '4'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.1145/3386569.3392412
month: '07'
oa: 1
oa_version: Submitted Version
project:
- _id: 2533E772-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '638176'
name: Efficient Simulation of Natural Phenomena at Extremely Large Scales
publication: ACM Transactions on Graphics
publication_identifier:
eissn:
- '15577368'
issn:
- '07300301'
publication_status: published
publisher: Association for Computing Machinery
quality_controlled: '1'
related_material:
record:
- id: '12358'
relation: dissertation_contains
status: public
scopus_import: '1'
status: public
title: Homogenized yarn-level cloth
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 39
year: '2020'
...
---
_id: '7956'
abstract:
- lang: eng
text: When short-range attractions are combined with long-range repulsions in colloidal
particle systems, complex microphases can emerge. Here, we study a system of isotropic
particles, which can form lamellar structures or a disordered fluid phase when
temperature is varied. We show that, at equilibrium, the lamellar structure crystallizes,
while out of equilibrium, the system forms a variety of structures at different
shear rates and temperatures above melting. The shear-induced ordering is analyzed
by means of principal component analysis and artificial neural networks, which
are applied to data of reduced dimensionality. Our results reveal the possibility
of inducing ordering by shear, potentially providing a feasible route to the fabrication
of ordered lamellar structures from isotropic particles.
article_number: '204905'
article_processing_charge: No
article_type: original
author:
- first_name: J.
full_name: Pȩkalski, J.
last_name: Pȩkalski
- first_name: Wojciech
full_name: Rzadkowski, Wojciech
id: 48C55298-F248-11E8-B48F-1D18A9856A87
last_name: Rzadkowski
orcid: 0000-0002-1106-4419
- first_name: A. Z.
full_name: Panagiotopoulos, A. Z.
last_name: Panagiotopoulos
citation:
ama: 'Pȩkalski J, Rzadkowski W, Panagiotopoulos AZ. Shear-induced ordering in systems
with competing interactions: A machine learning study. The Journal of chemical
physics. 2020;152(20). doi:10.1063/5.0005194'
apa: 'Pȩkalski, J., Rzadkowski, W., & Panagiotopoulos, A. Z. (2020). Shear-induced
ordering in systems with competing interactions: A machine learning study. The
Journal of Chemical Physics. AIP Publishing. https://doi.org/10.1063/5.0005194'
chicago: 'Pȩkalski, J., Wojciech Rzadkowski, and A. Z. Panagiotopoulos. “Shear-Induced
Ordering in Systems with Competing Interactions: A Machine Learning Study.” The
Journal of Chemical Physics. AIP Publishing, 2020. https://doi.org/10.1063/5.0005194.'
ieee: 'J. Pȩkalski, W. Rzadkowski, and A. Z. Panagiotopoulos, “Shear-induced ordering
in systems with competing interactions: A machine learning study,” The Journal
of chemical physics, vol. 152, no. 20. AIP Publishing, 2020.'
ista: 'Pȩkalski J, Rzadkowski W, Panagiotopoulos AZ. 2020. Shear-induced ordering
in systems with competing interactions: A machine learning study. The Journal
of chemical physics. 152(20), 204905.'
mla: 'Pȩkalski, J., et al. “Shear-Induced Ordering in Systems with Competing Interactions:
A Machine Learning Study.” The Journal of Chemical Physics, vol. 152, no.
20, 204905, AIP Publishing, 2020, doi:10.1063/5.0005194.'
short: J. Pȩkalski, W. Rzadkowski, A.Z. Panagiotopoulos, The Journal of Chemical
Physics 152 (2020).
date_created: 2020-06-14T22:00:49Z
date_published: 2020-05-29T00:00:00Z
date_updated: 2024-02-28T13:00:28Z
day: '29'
department:
- _id: MiLe
doi: 10.1063/5.0005194
ec_funded: 1
external_id:
arxiv:
- '2002.07294'
isi:
- '000537900300001'
intvolume: ' 152'
isi: 1
issue: '20'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.1063/5.0005194
month: '05'
oa: 1
oa_version: Published Version
project:
- _id: 2564DBCA-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '665385'
name: International IST Doctoral Program
publication: The Journal of chemical physics
publication_identifier:
eissn:
- '10897690'
publication_status: published
publisher: AIP Publishing
quality_controlled: '1'
related_material:
record:
- id: '10759'
relation: dissertation_contains
status: public
scopus_import: '1'
status: public
title: 'Shear-induced ordering in systems with competing interactions: A machine learning
study'
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 152
year: '2020'
...
---
_id: '8382'
abstract:
- lang: eng
text: We present the first deterministic wait-free long-lived snapshot algorithm,
using only read and write operations, that guarantees polylogarithmic amortized
step complexity in all executions. This is the first non-blocking snapshot algorithm,
using reads and writes only, that has sub-linear amortized step complexity in
executions of arbitrary length. The key to our construction is a novel implementation
of a 2-component max array object which may be of independent interest.
article_processing_charge: No
author:
- first_name: Mirza Ahad
full_name: Baig, Mirza Ahad
id: 3EDE6DE4-AA5A-11E9-986D-341CE6697425
last_name: Baig
- first_name: Danny
full_name: Hendler, Danny
last_name: Hendler
- first_name: Alessia
full_name: Milani, Alessia
last_name: Milani
- first_name: Corentin
full_name: Travers, Corentin
last_name: Travers
citation:
ama: 'Baig MA, Hendler D, Milani A, Travers C. Long-lived snapshots with polylogarithmic
amortized step complexity. In: Proceedings of the 39th Symposium on Principles
of Distributed Computing. Association for Computing Machinery; 2020:31-40.
doi:10.1145/3382734.3406005'
apa: 'Baig, M. A., Hendler, D., Milani, A., & Travers, C. (2020). Long-lived
snapshots with polylogarithmic amortized step complexity. In Proceedings of
the 39th Symposium on Principles of Distributed Computing (pp. 31–40). Virtual,
Italy: Association for Computing Machinery. https://doi.org/10.1145/3382734.3406005'
chicago: Baig, Mirza Ahad, Danny Hendler, Alessia Milani, and Corentin Travers.
“Long-Lived Snapshots with Polylogarithmic Amortized Step Complexity.” In Proceedings
of the 39th Symposium on Principles of Distributed Computing, 31–40. Association
for Computing Machinery, 2020. https://doi.org/10.1145/3382734.3406005.
ieee: M. A. Baig, D. Hendler, A. Milani, and C. Travers, “Long-lived snapshots with
polylogarithmic amortized step complexity,” in Proceedings of the 39th Symposium
on Principles of Distributed Computing, Virtual, Italy, 2020, pp. 31–40.
ista: 'Baig MA, Hendler D, Milani A, Travers C. 2020. Long-lived snapshots with
polylogarithmic amortized step complexity. Proceedings of the 39th Symposium on
Principles of Distributed Computing. PODC: Principles of Distributed Computing,
31–40.'
mla: Baig, Mirza Ahad, et al. “Long-Lived Snapshots with Polylogarithmic Amortized
Step Complexity.” Proceedings of the 39th Symposium on Principles of Distributed
Computing, Association for Computing Machinery, 2020, pp. 31–40, doi:10.1145/3382734.3406005.
short: M.A. Baig, D. Hendler, A. Milani, C. Travers, in:, Proceedings of the 39th
Symposium on Principles of Distributed Computing, Association for Computing Machinery,
2020, pp. 31–40.
conference:
end_date: 2020-08-07
location: Virtual, Italy
name: 'PODC: Principles of Distributed Computing'
start_date: 2020-08-03
date_created: 2020-09-13T22:01:17Z
date_published: 2020-07-31T00:00:00Z
date_updated: 2024-02-28T12:54:30Z
day: '31'
doi: 10.1145/3382734.3406005
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://hal.archives-ouvertes.fr/hal-02860087/document
month: '07'
oa: 1
oa_version: Preprint
page: 31-40
publication: Proceedings of the 39th Symposium on Principles of Distributed Computing
publication_identifier:
isbn:
- '9781450375825'
publication_status: published
publisher: Association for Computing Machinery
quality_controlled: '1'
scopus_import: '1'
status: public
title: Long-lived snapshots with polylogarithmic amortized step complexity
type: conference
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
year: '2020'
...
---
_id: '7428'
abstract:
- lang: eng
text: In the superconducting regime of FeTe(1−x)Sex, there exist two types of vortices
which are distinguished by the presence or absence of zero-energy states in their
core. To understand their origin, we examine the interplay of Zeeman coupling
and superconducting pairings in three-dimensional metals with band inversion.
Weak Zeeman fields are found to suppress intraorbital spin-singlet pairing, known
to localize the states at the ends of the vortices on the surface. On the other
hand, an orbital-triplet pairing is shown to be stable against Zeeman interactions,
but leads to delocalized zero-energy Majorana modes which extend through the vortex.
In contrast, the finite-energy vortex modes remain localized at the vortex ends
even when the pairing is of orbital-triplet form. Phenomenologically, this manifests
as an observed disappearance of zero-bias peaks within the cores of topological
vortices upon an increase of the applied magnetic field. The presence of magnetic
impurities in FeTe(1−x)Sex, which are attracted to the vortices, would lead to
such Zeeman-induced delocalization of Majorana modes in a fraction of vortices
that capture a large enough number of magnetic impurities. Our results provide
an explanation for the dichotomy between topological and nontopological vortices
recently observed in FeTe(1−x)Sex.
article_number: '020504'
article_processing_charge: No
article_type: original
author:
- first_name: Areg
full_name: Ghazaryan, Areg
id: 4AF46FD6-F248-11E8-B48F-1D18A9856A87
last_name: Ghazaryan
orcid: 0000-0001-9666-3543
- first_name: P. L.S.
full_name: Lopes, P. L.S.
last_name: Lopes
- first_name: Pavan
full_name: Hosur, Pavan
last_name: Hosur
- first_name: Matthew J.
full_name: Gilbert, Matthew J.
last_name: Gilbert
- first_name: Pouyan
full_name: Ghaemi, Pouyan
last_name: Ghaemi
citation:
ama: Ghazaryan A, Lopes PLS, Hosur P, Gilbert MJ, Ghaemi P. Effect of Zeeman coupling
on the Majorana vortex modes in iron-based topological superconductors. Physical
Review B. 2020;101(2). doi:10.1103/PhysRevB.101.020504
apa: Ghazaryan, A., Lopes, P. L. S., Hosur, P., Gilbert, M. J., & Ghaemi, P.
(2020). Effect of Zeeman coupling on the Majorana vortex modes in iron-based topological
superconductors. Physical Review B. American Physical Society. https://doi.org/10.1103/PhysRevB.101.020504
chicago: Ghazaryan, Areg, P. L.S. Lopes, Pavan Hosur, Matthew J. Gilbert, and Pouyan
Ghaemi. “Effect of Zeeman Coupling on the Majorana Vortex Modes in Iron-Based
Topological Superconductors.” Physical Review B. American Physical Society,
2020. https://doi.org/10.1103/PhysRevB.101.020504.
ieee: A. Ghazaryan, P. L. S. Lopes, P. Hosur, M. J. Gilbert, and P. Ghaemi, “Effect
of Zeeman coupling on the Majorana vortex modes in iron-based topological superconductors,”
Physical Review B, vol. 101, no. 2. American Physical Society, 2020.
ista: Ghazaryan A, Lopes PLS, Hosur P, Gilbert MJ, Ghaemi P. 2020. Effect of Zeeman
coupling on the Majorana vortex modes in iron-based topological superconductors.
Physical Review B. 101(2), 020504.
mla: Ghazaryan, Areg, et al. “Effect of Zeeman Coupling on the Majorana Vortex Modes
in Iron-Based Topological Superconductors.” Physical Review B, vol. 101,
no. 2, 020504, American Physical Society, 2020, doi:10.1103/PhysRevB.101.020504.
short: A. Ghazaryan, P.L.S. Lopes, P. Hosur, M.J. Gilbert, P. Ghaemi, Physical Review
B 101 (2020).
date_created: 2020-02-02T23:01:01Z
date_published: 2020-01-13T00:00:00Z
date_updated: 2024-02-28T13:11:13Z
day: '13'
department:
- _id: MiLe
doi: 10.1103/PhysRevB.101.020504
external_id:
arxiv:
- '1907.02077'
isi:
- '000506843500001'
intvolume: ' 101'
isi: 1
issue: '2'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/1907.02077
month: '01'
oa: 1
oa_version: Preprint
publication: Physical Review B
publication_identifier:
eissn:
- '24699969'
issn:
- '24699950'
publication_status: published
publisher: American Physical Society
quality_controlled: '1'
scopus_import: '1'
status: public
title: Effect of Zeeman coupling on the Majorana vortex modes in iron-based topological
superconductors
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 101
year: '2020'
...
---
_id: '8319'
abstract:
- lang: eng
text: We demonstrate that releasing atoms into free space from an optical lattice
does not deteriorate cavity-generated spin squeezing for metrological purposes.
In this work, an ensemble of 500000 spin-squeezed atoms in a high-finesse optical
cavity with near-uniform atom-cavity coupling is prepared, released into free
space, recaptured in the cavity, and probed. Up to ∼10 dB of metrologically relevant
squeezing is retrieved for 700μs free-fall times, and decaying levels of squeezing
are realized for up to 3 ms free-fall times. The degradation of squeezing results
from loss of atom-cavity coupling homogeneity between the initial squeezed state
generation and final collective state readout. A theoretical model is developed
to quantify this degradation and this model is experimentally validated.
acknowledgement: We thank N. Engelsen for comments on the manuscript. This work was
supported by the Office of Naval Research, Vannevar Bush Faculty Fellowship, Department
of Energy, and Defense Threat Reduction Agency. R.K. was partly supported by the
AQT/INQNET program at Caltech.
article_number: '012224'
article_processing_charge: No
article_type: original
author:
- first_name: Yunfan
full_name: Wu, Yunfan
last_name: Wu
- first_name: Rajiv
full_name: Krishnakumar, Rajiv
last_name: Krishnakumar
- first_name: Julián
full_name: Martínez-Rincón, Julián
last_name: Martínez-Rincón
- first_name: Benjamin K.
full_name: Malia, Benjamin K.
last_name: Malia
- first_name: Onur
full_name: Hosten, Onur
id: 4C02D85E-F248-11E8-B48F-1D18A9856A87
last_name: Hosten
orcid: 0000-0002-2031-204X
- first_name: Mark A.
full_name: Kasevich, Mark A.
last_name: Kasevich
citation:
ama: Wu Y, Krishnakumar R, Martínez-Rincón J, Malia BK, Hosten O, Kasevich MA. Retrieval
of cavity-generated atomic spin squeezing after free-space release. Physical
Review A. 2020;102(1). doi:10.1103/PhysRevA.102.012224
apa: Wu, Y., Krishnakumar, R., Martínez-Rincón, J., Malia, B. K., Hosten, O., &
Kasevich, M. A. (2020). Retrieval of cavity-generated atomic spin squeezing after
free-space release. Physical Review A. American Physical Society. https://doi.org/10.1103/PhysRevA.102.012224
chicago: Wu, Yunfan, Rajiv Krishnakumar, Julián Martínez-Rincón, Benjamin K. Malia,
Onur Hosten, and Mark A. Kasevich. “Retrieval of Cavity-Generated Atomic Spin
Squeezing after Free-Space Release.” Physical Review A. American Physical
Society, 2020. https://doi.org/10.1103/PhysRevA.102.012224.
ieee: Y. Wu, R. Krishnakumar, J. Martínez-Rincón, B. K. Malia, O. Hosten, and M.
A. Kasevich, “Retrieval of cavity-generated atomic spin squeezing after free-space
release,” Physical Review A, vol. 102, no. 1. American Physical Society,
2020.
ista: Wu Y, Krishnakumar R, Martínez-Rincón J, Malia BK, Hosten O, Kasevich MA.
2020. Retrieval of cavity-generated atomic spin squeezing after free-space release.
Physical Review A. 102(1), 012224.
mla: Wu, Yunfan, et al. “Retrieval of Cavity-Generated Atomic Spin Squeezing after
Free-Space Release.” Physical Review A, vol. 102, no. 1, 012224, American
Physical Society, 2020, doi:10.1103/PhysRevA.102.012224.
short: Y. Wu, R. Krishnakumar, J. Martínez-Rincón, B.K. Malia, O. Hosten, M.A. Kasevich,
Physical Review A 102 (2020).
date_created: 2020-08-30T22:01:10Z
date_published: 2020-07-30T00:00:00Z
date_updated: 2024-02-28T13:11:28Z
day: '30'
department:
- _id: OnHo
doi: 10.1103/PhysRevA.102.012224
external_id:
arxiv:
- '1912.08334'
isi:
- '000555104200011'
intvolume: ' 102'
isi: 1
issue: '1'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/1912.08334
month: '07'
oa: 1
oa_version: Preprint
publication: Physical Review A
publication_identifier:
eissn:
- '24699934'
issn:
- '24699926'
publication_status: published
publisher: American Physical Society
quality_controlled: '1'
scopus_import: '1'
status: public
title: Retrieval of cavity-generated atomic spin squeezing after free-space release
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 102
year: '2020'
...
---
_id: '8766'
abstract:
- lang: eng
text: "The “procedural” approach to animating ocean waves is the dominant algorithm
for animating larger bodies of water in\r\ninteractive applications as well as
in off-line productions — it provides high visual quality with a low computational
demand. In this paper, we widen the applicability of procedural water wave animation
with an extension that guarantees the satisfaction of boundary conditions imposed
by terrain while still approximating physical wave behavior. In combination with
a particle system that models wave breaking, foam, and spray, this allows us to
naturally model waves interacting with beaches and rocks. Our system is able to
animate waves at large scales at interactive frame rates on a commodity PC."
article_processing_charge: No
article_type: original
author:
- first_name: Stefan
full_name: Jeschke, Stefan
id: 44D6411A-F248-11E8-B48F-1D18A9856A87
last_name: Jeschke
- first_name: Christian
full_name: Hafner, Christian
id: 400429CC-F248-11E8-B48F-1D18A9856A87
last_name: Hafner
- first_name: Nuttapong
full_name: Chentanez, Nuttapong
last_name: Chentanez
- first_name: Miles
full_name: Macklin, Miles
last_name: Macklin
- first_name: Matthias
full_name: Müller-Fischer, Matthias
last_name: Müller-Fischer
- first_name: Christopher J
full_name: Wojtan, Christopher J
id: 3C61F1D2-F248-11E8-B48F-1D18A9856A87
last_name: Wojtan
orcid: 0000-0001-6646-5546
citation:
ama: Jeschke S, Hafner C, Chentanez N, Macklin M, Müller-Fischer M, Wojtan C. Making
procedural water waves boundary-aware. Computer Graphics forum. 2020;39(8):47-54.
doi:10.1111/cgf.14100
apa: 'Jeschke, S., Hafner, C., Chentanez, N., Macklin, M., Müller-Fischer, M., &
Wojtan, C. (2020). Making procedural water waves boundary-aware. Computer Graphics
Forum. Online Symposium: Wiley. https://doi.org/10.1111/cgf.14100'
chicago: Jeschke, Stefan, Christian Hafner, Nuttapong Chentanez, Miles Macklin,
Matthias Müller-Fischer, and Chris Wojtan. “Making Procedural Water Waves Boundary-Aware.”
Computer Graphics Forum. Wiley, 2020. https://doi.org/10.1111/cgf.14100.
ieee: S. Jeschke, C. Hafner, N. Chentanez, M. Macklin, M. Müller-Fischer, and C.
Wojtan, “Making procedural water waves boundary-aware,” Computer Graphics forum,
vol. 39, no. 8. Wiley, pp. 47–54, 2020.
ista: Jeschke S, Hafner C, Chentanez N, Macklin M, Müller-Fischer M, Wojtan C. 2020.
Making procedural water waves boundary-aware. Computer Graphics forum. 39(8),
47–54.
mla: Jeschke, Stefan, et al. “Making Procedural Water Waves Boundary-Aware.” Computer
Graphics Forum, vol. 39, no. 8, Wiley, 2020, pp. 47–54, doi:10.1111/cgf.14100.
short: S. Jeschke, C. Hafner, N. Chentanez, M. Macklin, M. Müller-Fischer, C. Wojtan,
Computer Graphics Forum 39 (2020) 47–54.
conference:
end_date: 2020-10-09
location: Online Symposium
name: 'SCA: Symposium on Computer Animation'
start_date: 2020-10-06
date_created: 2020-11-17T10:47:48Z
date_published: 2020-12-01T00:00:00Z
date_updated: 2024-02-28T13:58:11Z
day: '01'
department:
- _id: ChWo
- _id: BeBi
doi: 10.1111/cgf.14100
ec_funded: 1
external_id:
isi:
- '000591780400005'
intvolume: ' 39'
isi: 1
issue: '8'
language:
- iso: eng
month: '12'
oa_version: None
page: 47-54
project:
- _id: 2533E772-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '638176'
name: Efficient Simulation of Natural Phenomena at Extremely Large Scales
- _id: 24F9549A-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '715767'
name: 'MATERIALIZABLE: Intelligent fabrication-oriented Computational Design and
Modeling'
publication: Computer Graphics forum
publication_status: published
publisher: Wiley
quality_controlled: '1'
scopus_import: '1'
status: public
title: Making procedural water waves boundary-aware
type: journal_article
user_id: 2EBD1598-F248-11E8-B48F-1D18A9856A87
volume: 39
year: '2020'
...
---
_id: '15055'
abstract:
- lang: eng
text: Markov decision processes (MDPs) are the defacto framework for sequential
decision making in the presence of stochastic uncertainty. A classical optimization
criterion for MDPs is to maximize the expected discounted-sum payoff, which ignores
low probability catastrophic events with highly negative impact on the system.
On the other hand, risk-averse policies require the probability of undesirable
events to be below a given threshold, but they do not account for optimization
of the expected payoff. We consider MDPs with discounted-sum payoff with failure
states which represent catastrophic outcomes. The objective of risk-constrained
planning is to maximize the expected discounted-sum payoff among risk-averse policies
that ensure the probability to encounter a failure state is below a desired threshold.
Our main contribution is an efficient risk-constrained planning algorithm that
combines UCT-like search with a predictor learned through interaction with the
MDP (in the style of AlphaZero) and with a risk-constrained action selection via
linear programming. We demonstrate the effectiveness of our approach with experiments
on classical MDPs from the literature, including benchmarks with an order of 106
states.
acknowledgement: Krishnendu Chatterjee is supported by the Austrian Science Fund (FWF)
NFN Grant No. S11407-N23 (RiSE/SHiNE), and COST Action GAMENET. Tomas Brazdil is
supported by the Grant Agency of Masaryk University grant no. MUNI/G/0739/2017 and
by the Czech Science Foundation grant No. 18-11193S. Petr Novotny and Jirı Vahala
are supported by the Czech Science Foundation grant No. GJ19-15134Y.
article_processing_charge: No
article_type: original
author:
- first_name: Tomáš
full_name: Brázdil, Tomáš
last_name: Brázdil
- first_name: Krishnendu
full_name: Chatterjee, Krishnendu
id: 2E5DCA20-F248-11E8-B48F-1D18A9856A87
last_name: Chatterjee
orcid: 0000-0002-4561-241X
- first_name: Petr
full_name: Novotný, Petr
last_name: Novotný
- first_name: Jiří
full_name: Vahala, Jiří
last_name: Vahala
citation:
ama: Brázdil T, Chatterjee K, Novotný P, Vahala J. Reinforcement learning of risk-constrained
policies in Markov decision processes. Proceedings of the 34th AAAI Conference
on Artificial Intelligence. 2020;34(06):9794-9801. doi:10.1609/aaai.v34i06.6531
apa: 'Brázdil, T., Chatterjee, K., Novotný, P., & Vahala, J. (2020). Reinforcement
learning of risk-constrained policies in Markov decision processes. Proceedings
of the 34th AAAI Conference on Artificial Intelligence. New York, NY, United
States: Association for the Advancement of Artificial Intelligence. https://doi.org/10.1609/aaai.v34i06.6531'
chicago: Brázdil, Tomáš, Krishnendu Chatterjee, Petr Novotný, and Jiří Vahala. “Reinforcement
Learning of Risk-Constrained Policies in Markov Decision Processes.” Proceedings
of the 34th AAAI Conference on Artificial Intelligence. Association for the
Advancement of Artificial Intelligence, 2020. https://doi.org/10.1609/aaai.v34i06.6531.
ieee: T. Brázdil, K. Chatterjee, P. Novotný, and J. Vahala, “Reinforcement learning
of risk-constrained policies in Markov decision processes,” Proceedings of
the 34th AAAI Conference on Artificial Intelligence, vol. 34, no. 06. Association
for the Advancement of Artificial Intelligence, pp. 9794–9801, 2020.
ista: Brázdil T, Chatterjee K, Novotný P, Vahala J. 2020. Reinforcement learning
of risk-constrained policies in Markov decision processes. Proceedings of the
34th AAAI Conference on Artificial Intelligence. 34(06), 9794–9801.
mla: Brázdil, Tomáš, et al. “Reinforcement Learning of Risk-Constrained Policies
in Markov Decision Processes.” Proceedings of the 34th AAAI Conference on Artificial
Intelligence, vol. 34, no. 06, Association for the Advancement of Artificial
Intelligence, 2020, pp. 9794–801, doi:10.1609/aaai.v34i06.6531.
short: T. Brázdil, K. Chatterjee, P. Novotný, J. Vahala, Proceedings of the 34th
AAAI Conference on Artificial Intelligence 34 (2020) 9794–9801.
conference:
end_date: 2020-02-12
location: New York, NY, United States
name: 'AAAI: Conference on Artificial Intelligence'
start_date: 2020-02-07
date_created: 2024-03-04T08:07:22Z
date_published: 2020-04-03T00:00:00Z
date_updated: 2024-03-04T08:30:16Z
day: '03'
department:
- _id: KrCh
doi: 10.1609/aaai.v34i06.6531
external_id:
arxiv:
- '2002.12086'
intvolume: ' 34'
issue: '06'
keyword:
- General Medicine
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.48550/arXiv.2002.12086
month: '04'
oa: 1
oa_version: Preprint
page: 9794-9801
project:
- _id: 25863FF4-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: S11407
name: Game Theory
publication: Proceedings of the 34th AAAI Conference on Artificial Intelligence
publication_identifier:
issn:
- 2374-3468
publication_status: published
publisher: Association for the Advancement of Artificial Intelligence
quality_controlled: '1'
status: public
title: Reinforcement learning of risk-constrained policies in Markov decision processes
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 34
year: '2020'
...
---
_id: '15057'
abstract:
- lang: eng
text: Vaccinia virus–related kinase (VRK) is an evolutionarily conserved nuclear
protein kinase. VRK-1, the single Caenorhabditis elegans VRK ortholog, functions
in cell division and germline proliferation. However, the role of VRK-1 in postmitotic
cells and adult life span remains unknown. Here, we show that VRK-1 increases
organismal longevity by activating the cellular energy sensor, AMP-activated protein
kinase (AMPK), via direct phosphorylation. We found that overexpression of vrk-1
in the soma of adult C. elegans increased life span and, conversely, inhibition
of vrk-1 decreased life span. In addition, vrk-1 was required for longevity conferred
by mutations that inhibit C. elegans mitochondrial respiration, which requires
AMPK. VRK-1 directly phosphorylated and up-regulated AMPK in both C. elegans and
cultured human cells. Thus, our data show that the somatic nuclear kinase, VRK-1,
promotes longevity through AMPK activation, and this function appears to be conserved
between C. elegans and humans.
acknowledgement: 'This research was supported by grants NRF-2019R1A3B2067745 and NRF-2017R1A5A1015366
funded by the Korean Government (MSIT) through the National Research Foundation
(NRF) of Korea to S.-J.V.L. and by grant Basic Science Research Program (No. 2019R1A2C2009440)
funded by the Korean Government (MSIT) through the NRF of Korea to K.-T.K. '
article_number: aaw7824
article_processing_charge: No
article_type: original
author:
- first_name: Sangsoon
full_name: Park, Sangsoon
last_name: Park
- first_name: Murat
full_name: Artan, Murat
id: C407B586-6052-11E9-B3AE-7006E6697425
last_name: Artan
orcid: 0000-0001-8945-6992
- first_name: Seung Hyun
full_name: Han, Seung Hyun
last_name: Han
- first_name: Hae-Eun H.
full_name: Park, Hae-Eun H.
last_name: Park
- first_name: Yoonji
full_name: Jung, Yoonji
last_name: Jung
- first_name: Ara B.
full_name: Hwang, Ara B.
last_name: Hwang
- first_name: Won Sik
full_name: Shin, Won Sik
last_name: Shin
- first_name: Kyong-Tai
full_name: Kim, Kyong-Tai
last_name: Kim
- first_name: Seung-Jae V.
full_name: Lee, Seung-Jae V.
last_name: Lee
citation:
ama: Park S, Artan M, Han SH, et al. VRK-1 extends life span by activation of AMPK
via phosphorylation. Science Advances. 2020;6(27). doi:10.1126/sciadv.aaw7824
apa: Park, S., Artan, M., Han, S. H., Park, H.-E. H., Jung, Y., Hwang, A. B., …
Lee, S.-J. V. (2020). VRK-1 extends life span by activation of AMPK via phosphorylation.
Science Advances. American Association for the Advancement of Science.
https://doi.org/10.1126/sciadv.aaw7824
chicago: Park, Sangsoon, Murat Artan, Seung Hyun Han, Hae-Eun H. Park, Yoonji Jung,
Ara B. Hwang, Won Sik Shin, Kyong-Tai Kim, and Seung-Jae V. Lee. “VRK-1 Extends
Life Span by Activation of AMPK via Phosphorylation.” Science Advances.
American Association for the Advancement of Science, 2020. https://doi.org/10.1126/sciadv.aaw7824.
ieee: S. Park et al., “VRK-1 extends life span by activation of AMPK via
phosphorylation,” Science Advances, vol. 6, no. 27. American Association
for the Advancement of Science, 2020.
ista: Park S, Artan M, Han SH, Park H-EH, Jung Y, Hwang AB, Shin WS, Kim K-T, Lee
S-JV. 2020. VRK-1 extends life span by activation of AMPK via phosphorylation.
Science Advances. 6(27), aaw7824.
mla: Park, Sangsoon, et al. “VRK-1 Extends Life Span by Activation of AMPK via Phosphorylation.”
Science Advances, vol. 6, no. 27, aaw7824, American Association for the
Advancement of Science, 2020, doi:10.1126/sciadv.aaw7824.
short: S. Park, M. Artan, S.H. Han, H.-E.H. Park, Y. Jung, A.B. Hwang, W.S. Shin,
K.-T. Kim, S.-J.V. Lee, Science Advances 6 (2020).
date_created: 2024-03-04T09:41:57Z
date_published: 2020-07-01T00:00:00Z
date_updated: 2024-03-04T09:52:09Z
day: '01'
ddc:
- '570'
department:
- _id: MaDe
doi: 10.1126/sciadv.aaw7824
file:
- access_level: open_access
checksum: a37157cd0de709dce5fe03f4a31cd0b6
content_type: application/pdf
creator: dernst
date_created: 2024-03-04T09:46:41Z
date_updated: 2024-03-04T09:46:41Z
file_id: '15058'
file_name: 2020_ScienceAdvances_Park.pdf
file_size: 1864415
relation: main_file
success: 1
file_date_updated: 2024-03-04T09:46:41Z
has_accepted_license: '1'
intvolume: ' 6'
issue: '27'
language:
- iso: eng
month: '07'
oa: 1
oa_version: Published Version
publication: Science Advances
publication_identifier:
eissn:
- 2375-2548
publication_status: published
publisher: American Association for the Advancement of Science
quality_controlled: '1'
status: public
title: VRK-1 extends life span by activation of AMPK via phosphorylation
tmp:
image: /images/cc_by_nc.png
legal_code_url: https://creativecommons.org/licenses/by-nc/4.0/legalcode
name: Creative Commons Attribution-NonCommercial 4.0 International (CC BY-NC 4.0)
short: CC BY-NC (4.0)
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 6
year: '2020'
...
---
_id: '15061'
abstract:
- lang: eng
text: The actin cytoskeleton, a dynamic network of actin filaments and associated
F-actin–binding proteins, is fundamentally important in eukaryotes. α-Actinins
are major F-actin bundlers that are inhibited by Ca2+ in nonmuscle cells. Here
we report the mechanism of Ca2+-mediated regulation of Entamoeba histolytica α-actinin-2
(EhActn2) with features expected for the common ancestor of Entamoeba and higher
eukaryotic α-actinins. Crystal structures of Ca2+-free and Ca2+-bound EhActn2
reveal a calmodulin-like domain (CaMD) uniquely inserted within the rod domain.
Integrative studies reveal an exceptionally high affinity of the EhActn2 CaMD
for Ca2+, binding of which can only be regulated in the presence of physiological
concentrations of Mg2+. Ca2+ binding triggers an increase in protein multidomain
rigidity, reducing conformational flexibility of F-actin–binding domains via interdomain
cross-talk and consequently inhibiting F-actin bundling. In vivo studies uncover
that EhActn2 plays an important role in phagocytic cup formation and might constitute
a new drug target for amoebic dysentery.
acknowledged_ssus:
- _id: LifeSc
acknowledgement: "We thank the staff of the macromolecular crystallography (MX) and
SAXS beamlines at the European Synchrotron Radiation facility, Diamond, and Swiss
Light Source for excellent support, and the Life Sciences Facility of the Institute
of Science and Technology Austria for usage of the rheometer. We thank Life Sciences
editors for editing assistance. EM data were\r\nrecorded at the EM Facility of the
Vienna BioCenter Core Facilities (Austria). Confocal microscopy was carried out
at the Advanced Instrument Research Facility, Jawaharlal Nehru University. K.D.-C.’s
research was supported by the Initial Training Network MUZIC (ITN-MUZIC) (N°238423),
Austrian Science Fund (FWF) Projects I525, I1593, P22276, P19060, and W1221, Laura
Bassi Centre of Optimized Structural Studies (N°253275), a Wellcome Trust Collaborative
Award (201543/Z/16/Z), COST Action BM1405, Vienna Science and Technology Fund (WWTF)
Chemical Biology Project LS17-008, and Christian Doppler Laboratory for High-Content
Structural Biology and Biotechnology. K.Z., J.L.A., C.S., E.A.G., and A.S. were
supported by the University of Vienna, J.K. by a Wellcome Trust Collaborative Award
and by the Centre of Optimized Structural Studies, M.P. by FWF Project I1593, E.d.A.R.
ITN-MUZIC, and FWF Projects I525 and I1593, and T.C.M. and L.C. by FWF Project I
2408-B22. E.A.G. acknowledges the PhD program Structure and Interaction of Biological
Macromolecules. M.B. acknowledges the University Grant Commission, India, for a
senior research fellowship. A.B. acknowledges a JC Bose Fellowship from the Science
Engineering Research Council. "
article_processing_charge: No
article_type: original
author:
- first_name: Nikos
full_name: Pinotsis, Nikos
last_name: Pinotsis
- first_name: Karolina
full_name: Zielinska, Karolina
last_name: Zielinska
- first_name: Mrigya
full_name: Babuta, Mrigya
last_name: Babuta
- first_name: Joan L.
full_name: Arolas, Joan L.
last_name: Arolas
- first_name: Julius
full_name: Kostan, Julius
last_name: Kostan
- first_name: Muhammad Bashir
full_name: Khan, Muhammad Bashir
last_name: Khan
- first_name: Claudia
full_name: Schreiner, Claudia
last_name: Schreiner
- first_name: Anita P
full_name: Testa Salmazo, Anita P
id: 41F1F098-F248-11E8-B48F-1D18A9856A87
last_name: Testa Salmazo
- first_name: Luciano
full_name: Ciccarelli, Luciano
last_name: Ciccarelli
- first_name: Martin
full_name: Puchinger, Martin
last_name: Puchinger
- first_name: Eirini A.
full_name: Gkougkoulia, Eirini A.
last_name: Gkougkoulia
- first_name: Euripedes de Almeida
full_name: Ribeiro, Euripedes de Almeida
last_name: Ribeiro
- first_name: Thomas C.
full_name: Marlovits, Thomas C.
last_name: Marlovits
- first_name: Alok
full_name: Bhattacharya, Alok
last_name: Bhattacharya
- first_name: Kristina
full_name: Djinovic-Carugo, Kristina
last_name: Djinovic-Carugo
citation:
ama: Pinotsis N, Zielinska K, Babuta M, et al. Calcium modulates the domain flexibility
and function of an α-actinin similar to the ancestral α-actinin. Proceedings
of the National Academy of Sciences. 2020;117(36):22101-22112. doi:10.1073/pnas.1917269117
apa: Pinotsis, N., Zielinska, K., Babuta, M., Arolas, J. L., Kostan, J., Khan, M.
B., … Djinovic-Carugo, K. (2020). Calcium modulates the domain flexibility and
function of an α-actinin similar to the ancestral α-actinin. Proceedings of
the National Academy of Sciences. Proceedings of the National Academy of Sciences.
https://doi.org/10.1073/pnas.1917269117
chicago: Pinotsis, Nikos, Karolina Zielinska, Mrigya Babuta, Joan L. Arolas, Julius
Kostan, Muhammad Bashir Khan, Claudia Schreiner, et al. “Calcium Modulates the
Domain Flexibility and Function of an α-Actinin Similar to the Ancestral α-Actinin.”
Proceedings of the National Academy of Sciences. Proceedings of the National
Academy of Sciences, 2020. https://doi.org/10.1073/pnas.1917269117.
ieee: N. Pinotsis et al., “Calcium modulates the domain flexibility and function
of an α-actinin similar to the ancestral α-actinin,” Proceedings of the National
Academy of Sciences, vol. 117, no. 36. Proceedings of the National Academy
of Sciences, pp. 22101–22112, 2020.
ista: Pinotsis N, Zielinska K, Babuta M, Arolas JL, Kostan J, Khan MB, Schreiner
C, Testa Salmazo AP, Ciccarelli L, Puchinger M, Gkougkoulia EA, Ribeiro E de A,
Marlovits TC, Bhattacharya A, Djinovic-Carugo K. 2020. Calcium modulates the domain
flexibility and function of an α-actinin similar to the ancestral α-actinin. Proceedings
of the National Academy of Sciences. 117(36), 22101–22112.
mla: Pinotsis, Nikos, et al. “Calcium Modulates the Domain Flexibility and Function
of an α-Actinin Similar to the Ancestral α-Actinin.” Proceedings of the National
Academy of Sciences, vol. 117, no. 36, Proceedings of the National Academy
of Sciences, 2020, pp. 22101–12, doi:10.1073/pnas.1917269117.
short: N. Pinotsis, K. Zielinska, M. Babuta, J.L. Arolas, J. Kostan, M.B. Khan,
C. Schreiner, A.P. Testa Salmazo, L. Ciccarelli, M. Puchinger, E.A. Gkougkoulia,
E. de A. Ribeiro, T.C. Marlovits, A. Bhattacharya, K. Djinovic-Carugo, Proceedings
of the National Academy of Sciences 117 (2020) 22101–22112.
date_created: 2024-03-04T10:03:52Z
date_published: 2020-09-08T00:00:00Z
date_updated: 2024-03-04T10:14:44Z
day: '08'
department:
- _id: CaBe
doi: 10.1073/pnas.1917269117
external_id:
pmid:
- '32848067'
intvolume: ' 117'
issue: '36'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.1073/pnas.191726911
month: '09'
oa: 1
oa_version: Published Version
page: 22101-22112
pmid: 1
publication: Proceedings of the National Academy of Sciences
publication_identifier:
eissn:
- 1091-6490
issn:
- 0027-8424
publication_status: published
publisher: Proceedings of the National Academy of Sciences
quality_controlled: '1'
status: public
title: Calcium modulates the domain flexibility and function of an α-actinin similar
to the ancestral α-actinin
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 117
year: '2020'
...
---
_id: '15064'
abstract:
- lang: eng
text: We call a continuous self-map that reveals itself through a discrete set of
point-value pairs a sampled dynamical system. Capturing the available information
with chain maps on Delaunay complexes, we use persistent homology to quantify
the evidence of recurrent behavior. We establish a sampling theorem to recover
the eigenspaces of the endomorphism on homology induced by the self-map. Using
a combinatorial gradient flow arising from the discrete Morse theory for Čech
and Delaunay complexes, we construct a chain map to transform the problem from
the natural but expensive Čech complexes to the computationally efficient Delaunay
triangulations. The fast chain map algorithm has applications beyond dynamical
systems.
acknowledgement: This research has been supported by the DFG Collaborative Research
Center SFB/TRR 109 “Discretization in Geometry and Dynamics”, by Polish MNiSzW Grant
No. 2621/7.PR/12/2013/2, by the Polish National Science Center under Maestro Grant
No. 2014/14/A/ST1/00453 and Grant No. DEC-2013/09/N/ST6/02995. Open Access funding
provided by Projekt DEAL.
article_processing_charge: Yes (via OA deal)
article_type: original
author:
- first_name: U.
full_name: Bauer, U.
last_name: Bauer
- first_name: Herbert
full_name: Edelsbrunner, Herbert
id: 3FB178DA-F248-11E8-B48F-1D18A9856A87
last_name: Edelsbrunner
orcid: 0000-0002-9823-6833
- first_name: Grzegorz
full_name: Jablonski, Grzegorz
id: 4483EF78-F248-11E8-B48F-1D18A9856A87
last_name: Jablonski
orcid: 0000-0002-3536-9866
- first_name: M.
full_name: Mrozek, M.
last_name: Mrozek
citation:
ama: Bauer U, Edelsbrunner H, Jablonski G, Mrozek M. Čech-Delaunay gradient flow
and homology inference for self-maps. Journal of Applied and Computational
Topology. 2020;4(4):455-480. doi:10.1007/s41468-020-00058-8
apa: Bauer, U., Edelsbrunner, H., Jablonski, G., & Mrozek, M. (2020). Čech-Delaunay
gradient flow and homology inference for self-maps. Journal of Applied and
Computational Topology. Springer Nature. https://doi.org/10.1007/s41468-020-00058-8
chicago: Bauer, U., Herbert Edelsbrunner, Grzegorz Jablonski, and M. Mrozek. “Čech-Delaunay
Gradient Flow and Homology Inference for Self-Maps.” Journal of Applied and
Computational Topology. Springer Nature, 2020. https://doi.org/10.1007/s41468-020-00058-8.
ieee: U. Bauer, H. Edelsbrunner, G. Jablonski, and M. Mrozek, “Čech-Delaunay gradient
flow and homology inference for self-maps,” Journal of Applied and Computational
Topology, vol. 4, no. 4. Springer Nature, pp. 455–480, 2020.
ista: Bauer U, Edelsbrunner H, Jablonski G, Mrozek M. 2020. Čech-Delaunay gradient
flow and homology inference for self-maps. Journal of Applied and Computational
Topology. 4(4), 455–480.
mla: Bauer, U., et al. “Čech-Delaunay Gradient Flow and Homology Inference for Self-Maps.”
Journal of Applied and Computational Topology, vol. 4, no. 4, Springer
Nature, 2020, pp. 455–80, doi:10.1007/s41468-020-00058-8.
short: U. Bauer, H. Edelsbrunner, G. Jablonski, M. Mrozek, Journal of Applied and
Computational Topology 4 (2020) 455–480.
date_created: 2024-03-04T10:47:49Z
date_published: 2020-12-01T00:00:00Z
date_updated: 2024-03-04T10:54:04Z
day: '01'
ddc:
- '500'
department:
- _id: HeEd
doi: 10.1007/s41468-020-00058-8
file:
- access_level: open_access
checksum: eed1168b6e66cd55272c19bb7fca8a1c
content_type: application/pdf
creator: dernst
date_created: 2024-03-04T10:52:42Z
date_updated: 2024-03-04T10:52:42Z
file_id: '15065'
file_name: 2020_JourApplCompTopology_Bauer.pdf
file_size: 851190
relation: main_file
success: 1
file_date_updated: 2024-03-04T10:52:42Z
has_accepted_license: '1'
intvolume: ' 4'
issue: '4'
language:
- iso: eng
month: '12'
oa: 1
oa_version: Published Version
page: 455-480
publication: Journal of Applied and Computational Topology
publication_identifier:
eissn:
- 2367-1734
issn:
- 2367-1726
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
scopus_import: '1'
status: public
title: Čech-Delaunay gradient flow and homology inference for self-maps
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: 4
year: '2020'
...
---
_id: '15063'
abstract:
- lang: eng
text: We consider the least singular value of a large random matrix with real or
complex i.i.d. Gaussian entries shifted by a constant z∈C. We prove an optimal
lower tail estimate on this singular value in the critical regime where z is around
the spectral edge, thus improving the classical bound of Sankar, Spielman and
Teng (SIAM J. Matrix Anal. Appl. 28:2 (2006), 446–476) for the particular shift-perturbation
in the edge regime. Lacking Brézin–Hikami formulas in the real case, we rely on
the superbosonization formula (Comm. Math. Phys. 283:2 (2008), 343–395).
acknowledgement: Partially supported by ERC Advanced Grant No. 338804. This project
has received funding from the European Union’s Horizon 2020 research and innovation
programme under the Marie Sklodowska-Curie Grant Agreement No. 66538
article_processing_charge: No
article_type: original
author:
- first_name: Giorgio
full_name: Cipolloni, Giorgio
id: 42198EFA-F248-11E8-B48F-1D18A9856A87
last_name: Cipolloni
orcid: 0000-0002-4901-7992
- first_name: László
full_name: Erdös, László
id: 4DBD5372-F248-11E8-B48F-1D18A9856A87
last_name: Erdös
orcid: 0000-0001-5366-9603
- first_name: Dominik J
full_name: Schröder, Dominik J
id: 408ED176-F248-11E8-B48F-1D18A9856A87
last_name: Schröder
orcid: 0000-0002-2904-1856
citation:
ama: Cipolloni G, Erdös L, Schröder DJ. Optimal lower bound on the least singular
value of the shifted Ginibre ensemble. Probability and Mathematical Physics.
2020;1(1):101-146. doi:10.2140/pmp.2020.1.101
apa: Cipolloni, G., Erdös, L., & Schröder, D. J. (2020). Optimal lower bound
on the least singular value of the shifted Ginibre ensemble. Probability and
Mathematical Physics. Mathematical Sciences Publishers. https://doi.org/10.2140/pmp.2020.1.101
chicago: Cipolloni, Giorgio, László Erdös, and Dominik J Schröder. “Optimal Lower
Bound on the Least Singular Value of the Shifted Ginibre Ensemble.” Probability
and Mathematical Physics. Mathematical Sciences Publishers, 2020. https://doi.org/10.2140/pmp.2020.1.101.
ieee: G. Cipolloni, L. Erdös, and D. J. Schröder, “Optimal lower bound on the least
singular value of the shifted Ginibre ensemble,” Probability and Mathematical
Physics, vol. 1, no. 1. Mathematical Sciences Publishers, pp. 101–146, 2020.
ista: Cipolloni G, Erdös L, Schröder DJ. 2020. Optimal lower bound on the least
singular value of the shifted Ginibre ensemble. Probability and Mathematical Physics.
1(1), 101–146.
mla: Cipolloni, Giorgio, et al. “Optimal Lower Bound on the Least Singular Value
of the Shifted Ginibre Ensemble.” Probability and Mathematical Physics,
vol. 1, no. 1, Mathematical Sciences Publishers, 2020, pp. 101–46, doi:10.2140/pmp.2020.1.101.
short: G. Cipolloni, L. Erdös, D.J. Schröder, Probability and Mathematical Physics
1 (2020) 101–146.
date_created: 2024-03-04T10:27:57Z
date_published: 2020-11-16T00:00:00Z
date_updated: 2024-03-04T10:33:15Z
day: '16'
department:
- _id: LaEr
doi: 10.2140/pmp.2020.1.101
ec_funded: 1
external_id:
arxiv:
- '1908.01653'
intvolume: ' 1'
issue: '1'
keyword:
- General Medicine
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.48550/arXiv.1908.01653
month: '11'
oa: 1
oa_version: Preprint
page: 101-146
project:
- _id: 258DCDE6-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '338804'
name: Random matrices, universality and disordered quantum systems
- _id: 2564DBCA-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '665385'
name: International IST Doctoral Program
publication: Probability and Mathematical Physics
publication_identifier:
issn:
- 2690-1005
- 2690-0998
publication_status: published
publisher: Mathematical Sciences Publishers
quality_controlled: '1'
scopus_import: '1'
status: public
title: Optimal lower bound on the least singular value of the shifted Ginibre ensemble
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 1
year: '2020'
...
---
_id: '15059'
abstract:
- lang: eng
text: "In this paper we present a room temperature radiometer that can eliminate
the need of using cryostats in satellite payload reducing its weight and improving
reliability. The proposed radiometer is based on an electro-optic upconverter
that boosts up microwave photons energy by upconverting them into an optical domain
what makes them immune to thermal noise even if operating at room temperature.
The converter uses a high-quality factor whispering gallery\r\nmode (WGM) resonator
providing naturally narrow bandwidth and therefore might be useful for applications
like microwave hyperspectral sensing. The upconversion process is explained by\r\nproviding
essential information about photon conversion efficiency and sensitivity. To prove
the concept, we describe an experiment which shows state-of-the-art photon conversion
efficiency n=10-5 per mW of pump power at the frequency of 80 GHz."
acknowledgement: This work has been financially supported by Comunidad de Madrid S2018/NMT-4333
ARTINLARA-CM projects, and “FUNDACIÓN SENER” REFTA projects.
article_processing_charge: No
author:
- first_name: Michal
full_name: Wasiak, Michal
last_name: Wasiak
- first_name: Gabriel Santamaria
full_name: Botello, Gabriel Santamaria
last_name: Botello
- first_name: Kerlos Atia
full_name: Abdalmalak, Kerlos Atia
last_name: Abdalmalak
- first_name: Florian
full_name: Sedlmeir, Florian
last_name: Sedlmeir
- first_name: Alfredo R
full_name: Rueda Sanchez, Alfredo R
id: 3B82B0F8-F248-11E8-B48F-1D18A9856A87
last_name: Rueda Sanchez
orcid: 0000-0001-6249-5860
- first_name: Daniel
full_name: Segovia-Vargas, Daniel
last_name: Segovia-Vargas
- first_name: Harald G. L.
full_name: Schwefel, Harald G. L.
last_name: Schwefel
- first_name: Luis Enrique Garcia
full_name: Munoz, Luis Enrique Garcia
last_name: Munoz
citation:
ama: 'Wasiak M, Botello GS, Abdalmalak KA, et al. Compact millimeter and submillimeter-wave
photonic radiometer for cubesats. In: 14th European Conference on Antennas
and Propagation. IEEE; 2020. doi:10.23919/eucap48036.2020.9135962'
apa: 'Wasiak, M., Botello, G. S., Abdalmalak, K. A., Sedlmeir, F., Rueda Sanchez,
A. R., Segovia-Vargas, D., … Munoz, L. E. G. (2020). Compact millimeter and submillimeter-wave
photonic radiometer for cubesats. In 14th European Conference on Antennas and
Propagation. Copenhagen, Denmark: IEEE. https://doi.org/10.23919/eucap48036.2020.9135962'
chicago: Wasiak, Michal, Gabriel Santamaria Botello, Kerlos Atia Abdalmalak, Florian
Sedlmeir, Alfredo R Rueda Sanchez, Daniel Segovia-Vargas, Harald G. L. Schwefel,
and Luis Enrique Garcia Munoz. “Compact Millimeter and Submillimeter-Wave Photonic
Radiometer for Cubesats.” In 14th European Conference on Antennas and Propagation.
IEEE, 2020. https://doi.org/10.23919/eucap48036.2020.9135962.
ieee: M. Wasiak et al., “Compact millimeter and submillimeter-wave photonic
radiometer for cubesats,” in 14th European Conference on Antennas and Propagation,
Copenhagen, Denmark, 2020.
ista: 'Wasiak M, Botello GS, Abdalmalak KA, Sedlmeir F, Rueda Sanchez AR, Segovia-Vargas
D, Schwefel HGL, Munoz LEG. 2020. Compact millimeter and submillimeter-wave photonic
radiometer for cubesats. 14th European Conference on Antennas and Propagation.
EuCAP: European Conference on Antennas and Propagation.'
mla: Wasiak, Michal, et al. “Compact Millimeter and Submillimeter-Wave Photonic
Radiometer for Cubesats.” 14th European Conference on Antennas and Propagation,
IEEE, 2020, doi:10.23919/eucap48036.2020.9135962.
short: M. Wasiak, G.S. Botello, K.A. Abdalmalak, F. Sedlmeir, A.R. Rueda Sanchez,
D. Segovia-Vargas, H.G.L. Schwefel, L.E.G. Munoz, in:, 14th European Conference
on Antennas and Propagation, IEEE, 2020.
conference:
end_date: 2020-03-20
location: Copenhagen, Denmark
name: 'EuCAP: European Conference on Antennas and Propagation'
start_date: 2020-03-15
date_created: 2024-03-04T09:57:48Z
date_published: 2020-07-08T00:00:00Z
date_updated: 2024-03-04T10:02:49Z
day: '08'
department:
- _id: JoFi
doi: 10.23919/eucap48036.2020.9135962
language:
- iso: eng
month: '07'
oa_version: None
publication: 14th European Conference on Antennas and Propagation
publication_identifier:
eisbn:
- '9788831299008'
publication_status: published
publisher: IEEE
quality_controlled: '1'
status: public
title: Compact millimeter and submillimeter-wave photonic radiometer for cubesats
type: conference
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
year: '2020'
...
---
_id: '15074'
abstract:
- lang: eng
text: We introduce a new graph problem, the token dropping game, and we show how
to solve it efficiently in a distributed setting. We use the token dropping game
as a tool to design an efficient distributed algorithm for the stable orientation
problem, which is a special case of the more general locally optimal semi-matching
problem. The prior work by Czygrinow et al. (DISC 2012) finds a locally optimal
semi-matching in O(Δ⁵) rounds in graphs of maximum degree Δ, which directly implies
an algorithm with the same runtime for stable orientations. We improve the runtime
to O(Δ⁴) for stable orientations and prove a lower bound of Ω(Δ) rounds.
alternative_title:
- LIPIcs
article_number: '40'
article_processing_charge: No
author:
- first_name: Sebastian
full_name: Brandt, Sebastian
last_name: Brandt
- first_name: Barbara
full_name: Keller, Barbara
last_name: Keller
- first_name: Joel
full_name: Rybicki, Joel
id: 334EFD2E-F248-11E8-B48F-1D18A9856A87
last_name: Rybicki
orcid: 0000-0002-6432-6646
- first_name: Jukka
full_name: Suomela, Jukka
last_name: Suomela
- first_name: Jara
full_name: Uitto, Jara
last_name: Uitto
citation:
ama: 'Brandt S, Keller B, Rybicki J, Suomela J, Uitto J. Brief announcement: Efficient
load-balancing through distributed token dropping. In: 34th International Symposium
on Distributed Computing. Vol 179. Schloss Dagstuhl - Leibniz-Zentrum für
Informatik; 2020. doi:10.4230/LIPIcs.DISC.2020.40'
apa: 'Brandt, S., Keller, B., Rybicki, J., Suomela, J., & Uitto, J. (2020).
Brief announcement: Efficient load-balancing through distributed token dropping.
In 34th International Symposium on Distributed Computing (Vol. 179). Virtual:
Schloss Dagstuhl - Leibniz-Zentrum für Informatik. https://doi.org/10.4230/LIPIcs.DISC.2020.40'
chicago: 'Brandt, Sebastian, Barbara Keller, Joel Rybicki, Jukka Suomela, and Jara
Uitto. “Brief Announcement: Efficient Load-Balancing through Distributed Token
Dropping.” In 34th International Symposium on Distributed Computing, Vol.
179. Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2020. https://doi.org/10.4230/LIPIcs.DISC.2020.40.'
ieee: 'S. Brandt, B. Keller, J. Rybicki, J. Suomela, and J. Uitto, “Brief announcement:
Efficient load-balancing through distributed token dropping,” in 34th International
Symposium on Distributed Computing, Virtual, 2020, vol. 179.'
ista: 'Brandt S, Keller B, Rybicki J, Suomela J, Uitto J. 2020. Brief announcement:
Efficient load-balancing through distributed token dropping. 34th International
Symposium on Distributed Computing. DISC: Symposium on Distributed Computing,
LIPIcs, vol. 179, 40.'
mla: 'Brandt, Sebastian, et al. “Brief Announcement: Efficient Load-Balancing through
Distributed Token Dropping.” 34th International Symposium on Distributed Computing,
vol. 179, 40, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2020, doi:10.4230/LIPIcs.DISC.2020.40.'
short: S. Brandt, B. Keller, J. Rybicki, J. Suomela, J. Uitto, in:, 34th International
Symposium on Distributed Computing, Schloss Dagstuhl - Leibniz-Zentrum für Informatik,
2020.
conference:
end_date: 2020-10-16
location: Virtual
name: 'DISC: Symposium on Distributed Computing'
start_date: 2020-10-12
date_created: 2024-03-05T07:09:12Z
date_published: 2020-10-07T00:00:00Z
date_updated: 2024-03-05T07:13:13Z
day: '07'
ddc:
- '000'
department:
- _id: DaAl
doi: 10.4230/LIPIcs.DISC.2020.40
external_id:
arxiv:
- '2005.07761'
file:
- access_level: open_access
checksum: 23e2d9321aef53092dc1e24a8ab82d72
content_type: application/pdf
creator: dernst
date_created: 2024-03-05T07:08:27Z
date_updated: 2024-03-05T07:08:27Z
file_id: '15075'
file_name: 2020_LIPIcs_Brandt.pdf
file_size: 303529
relation: main_file
success: 1
file_date_updated: 2024-03-05T07:08:27Z
has_accepted_license: '1'
intvolume: ' 179'
language:
- iso: eng
license: https://creativecommons.org/licenses/by/3.0/
month: '10'
oa: 1
oa_version: Published Version
publication: 34th International Symposium on Distributed Computing
publication_status: published
publisher: Schloss Dagstuhl - Leibniz-Zentrum für Informatik
quality_controlled: '1'
related_material:
record:
- id: '9678'
relation: later_version
status: public
scopus_import: '1'
status: public
title: 'Brief announcement: Efficient load-balancing through distributed token dropping'
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/3.0/legalcode
name: Creative Commons Attribution 3.0 Unported (CC BY 3.0)
short: CC BY (3.0)
type: conference
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 179
year: '2020'
...
---
_id: '15077'
abstract:
- lang: eng
text: "We consider the following dynamic load-balancing process: given an underlying
graph G with n nodes, in each step t≥ 0, one unit of load is created, and placed
at a randomly chosen graph node. In the same step, the chosen node picks a random
neighbor, and the two nodes balance their loads by averaging them. We are interested
in the expected gap between the minimum and maximum loads at nodes as the process
progresses, and its dependence on n and on the graph structure. Variants of the
above graphical balanced allocation process have been studied previously by Peres,
Talwar, and Wieder [Peres et al., 2015], and by Sauerwald and Sun [Sauerwald and
Sun, 2015]. These authors left as open the question of characterizing the gap
in the case of cycle graphs in the dynamic case, where weights are created during
the algorithm’s execution. For this case, the only known upper bound is of \U0001D4AA(n
log n), following from a majorization argument due to [Peres et al., 2015], which
analyzes a related graphical allocation process. In this paper, we provide an
upper bound of \U0001D4AA (√n log n) on the expected gap of the above process
for cycles of length n. We introduce a new potential analysis technique, which
enables us to bound the difference in load between k-hop neighbors on the cycle,
for any k ≤ n/2. We complement this with a \"gap covering\" argument, which bounds
the maximum value of the gap by bounding its value across all possible subsets
of a certain structure, and recursively bounding the gaps within each subset.
We provide analytical and experimental evidence that our upper bound on the gap
is tight up to a logarithmic factor."
acknowledgement: "The authors sincerely thank Thomas Sauerwald and George Giakkoupis
for insightful discussions, and Mohsen Ghaffari, Yuval Peres, and Udi Wieder for
feedback on earlier\r\nversions of this draft. We also thank the ICALP anonymous
reviewers for their very useful comments.\r\nFunding: European Research Council
funding award PR1042ERC01"
alternative_title:
- LIPIcs
article_number: '7'
article_processing_charge: No
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: Giorgi
full_name: Nadiradze, Giorgi
id: 3279A00C-F248-11E8-B48F-1D18A9856A87
last_name: Nadiradze
orcid: 0000-0001-5634-0731
- first_name: Amirmojtaba
full_name: Sabour, Amirmojtaba
id: bcc145fd-e77f-11ea-ae8b-80d661dbff67
last_name: Sabour
citation:
ama: 'Alistarh D-A, Nadiradze G, Sabour A. Dynamic averaging load balancing on cycles.
In: 47th International Colloquium on Automata, Languages, and Programming.
Vol 168. Schloss Dagstuhl - Leibniz-Zentrum für Informatik; 2020. doi:10.4230/LIPIcs.ICALP.2020.7'
apa: 'Alistarh, D.-A., Nadiradze, G., & Sabour, A. (2020). Dynamic averaging
load balancing on cycles. In 47th International Colloquium on Automata, Languages,
and Programming (Vol. 168). Saarbrücken, Germany, Virtual: Schloss Dagstuhl
- Leibniz-Zentrum für Informatik. https://doi.org/10.4230/LIPIcs.ICALP.2020.7'
chicago: Alistarh, Dan-Adrian, Giorgi Nadiradze, and Amirmojtaba Sabour. “Dynamic
Averaging Load Balancing on Cycles.” In 47th International Colloquium on Automata,
Languages, and Programming, Vol. 168. Schloss Dagstuhl - Leibniz-Zentrum für
Informatik, 2020. https://doi.org/10.4230/LIPIcs.ICALP.2020.7.
ieee: D.-A. Alistarh, G. Nadiradze, and A. Sabour, “Dynamic averaging load balancing
on cycles,” in 47th International Colloquium on Automata, Languages, and Programming,
Saarbrücken, Germany, Virtual, 2020, vol. 168.
ista: 'Alistarh D-A, Nadiradze G, Sabour A. 2020. Dynamic averaging load balancing
on cycles. 47th International Colloquium on Automata, Languages, and Programming.
ICALP: International Colloquium on Automata, Languages, and Programming, LIPIcs,
vol. 168, 7.'
mla: Alistarh, Dan-Adrian, et al. “Dynamic Averaging Load Balancing on Cycles.”
47th International Colloquium on Automata, Languages, and Programming,
vol. 168, 7, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2020, doi:10.4230/LIPIcs.ICALP.2020.7.
short: D.-A. Alistarh, G. Nadiradze, A. Sabour, in:, 47th International Colloquium
on Automata, Languages, and Programming, Schloss Dagstuhl - Leibniz-Zentrum für
Informatik, 2020.
conference:
end_date: 2020-07-11
location: Saarbrücken, Germany, Virtual
name: 'ICALP: International Colloquium on Automata, Languages, and Programming'
start_date: 2020-07-08
date_created: 2024-03-05T07:25:37Z
date_published: 2020-06-29T00:00:00Z
date_updated: 2024-03-05T07:35:53Z
day: '29'
ddc:
- '000'
department:
- _id: DaAl
doi: 10.4230/LIPIcs.ICALP.2020.7
ec_funded: 1
external_id:
arxiv:
- '2003.09297'
file:
- access_level: open_access
checksum: e5eb16199f4ccfd77a321977eb3f026f
content_type: application/pdf
creator: dernst
date_created: 2024-03-05T07:25:15Z
date_updated: 2024-03-05T07:25:15Z
file_id: '15078'
file_name: 2020_LIPIcs_Alistarh.pdf
file_size: 782987
relation: main_file
success: 1
file_date_updated: 2024-03-05T07:25:15Z
has_accepted_license: '1'
intvolume: ' 168'
language:
- iso: eng
month: '06'
oa: 1
oa_version: Published Version
project:
- _id: 268A44D6-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '805223'
name: Elastic Coordination for Scalable Machine Learning
publication: 47th International Colloquium on Automata, Languages, and Programming
publication_status: published
publisher: Schloss Dagstuhl - Leibniz-Zentrum für Informatik
quality_controlled: '1'
related_material:
record:
- id: '8286'
relation: later_version
status: public
scopus_import: '1'
status: public
title: Dynamic averaging load balancing on cycles
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/3.0/legalcode
name: Creative Commons Attribution 3.0 Unported (CC BY 3.0)
short: CC BY (3.0)
type: conference
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 168
year: '2020'
...
---
_id: '15082'
abstract:
- lang: eng
text: "Two plane drawings of geometric graphs on the same set of points are called
disjoint compatible if their union is plane and they do not have an edge in common.
For a given set S of 2n points two plane drawings of perfect matchings M1 and
M2 (which do not need to be disjoint nor compatible) are disjoint tree-compatible
if there exists a plane drawing of a spanning tree T on S which is disjoint compatible
to both M1 and M2.\r\nWe show that the graph of all disjoint tree-compatible perfect
geometric matchings on 2n points in convex position is connected if and only if
2n ≥ 10. Moreover, in that case the diameter\r\nof this graph is either 4 or 5,
independent of n."
acknowledgement: Research on this work was initiated at the 6th Austrian-Japanese-Mexican-Spanish
Workshop on Discrete Geometry and continued during the 16th European Geometric Graph-Week,
both held near Strobl, Austria. We are grateful to the participants for the inspiring
atmosphere. We especially thank Alexander Pilz for bringing this class of problems
to our attention and Birgit Vogtenhuber for inspiring discussions. D.P. is partially
supported by the FWF grant I 3340-N35 (Collaborative DACH project Arrangements and
Drawings). The research stay of P.P. at IST Austria is funded by the project CZ.02.2.69/0.0/0.0/17_050/0008466
Improvement of internationalization in the field of research and development at
Charles University, through the support of quality projects MSCA-IF. This project
has received funding from the European Union’s Horizon 2020 research and innovation
programme under the Marie Skłodowska-Curie grant agreement No 734922.
article_number: '56'
article_processing_charge: No
author:
- first_name: Oswin
full_name: Aichholzer, Oswin
last_name: Aichholzer
- first_name: Julia
full_name: Obmann, Julia
last_name: Obmann
- first_name: Pavel
full_name: Patak, Pavel
id: B593B804-1035-11EA-B4F1-947645A5BB83
last_name: Patak
- first_name: Daniel
full_name: Perz, Daniel
last_name: Perz
- first_name: Josef
full_name: Tkadlec, Josef
id: 3F24CCC8-F248-11E8-B48F-1D18A9856A87
last_name: Tkadlec
orcid: 0000-0002-1097-9684
citation:
ama: 'Aichholzer O, Obmann J, Patak P, Perz D, Tkadlec J. Disjoint tree-compatible
plane perfect matchings. In: 36th European Workshop on Computational Geometry.
; 2020.'
apa: Aichholzer, O., Obmann, J., Patak, P., Perz, D., & Tkadlec, J. (2020).
Disjoint tree-compatible plane perfect matchings. In 36th European Workshop
on Computational Geometry. Würzburg, Germany, Virtual.
chicago: Aichholzer, Oswin, Julia Obmann, Pavel Patak, Daniel Perz, and Josef Tkadlec.
“Disjoint Tree-Compatible Plane Perfect Matchings.” In 36th European Workshop
on Computational Geometry, 2020.
ieee: O. Aichholzer, J. Obmann, P. Patak, D. Perz, and J. Tkadlec, “Disjoint tree-compatible
plane perfect matchings,” in 36th European Workshop on Computational Geometry,
Würzburg, Germany, Virtual, 2020.
ista: 'Aichholzer O, Obmann J, Patak P, Perz D, Tkadlec J. 2020. Disjoint tree-compatible
plane perfect matchings. 36th European Workshop on Computational Geometry. EuroCG:
European Workshop on Computational Geometry, 56.'
mla: Aichholzer, Oswin, et al. “Disjoint Tree-Compatible Plane Perfect Matchings.”
36th European Workshop on Computational Geometry, 56, 2020.
short: O. Aichholzer, J. Obmann, P. Patak, D. Perz, J. Tkadlec, in:, 36th European
Workshop on Computational Geometry, 2020.
conference:
end_date: 2020-03-18
location: Würzburg, Germany, Virtual
name: 'EuroCG: European Workshop on Computational Geometry'
start_date: 2020-03-16
date_created: 2024-03-05T08:57:17Z
date_published: 2020-04-01T00:00:00Z
date_updated: 2024-03-05T09:00:07Z
day: '01'
department:
- _id: KrCh
- _id: UlWa
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://www1.pub.informatik.uni-wuerzburg.de/eurocg2020/data/uploads/papers/eurocg20_paper_56.pdf
month: '04'
oa: 1
oa_version: Published Version
publication: 36th European Workshop on Computational Geometry
publication_status: published
quality_controlled: '1'
status: public
title: Disjoint tree-compatible plane perfect matchings
type: conference
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
year: '2020'
...
---
_id: '6748'
abstract:
- lang: eng
text: "Fitting a function by using linear combinations of a large number N of `simple'
components is one of the most fruitful ideas in statistical learning. This idea
lies at the core of a variety of methods, from two-layer neural networks to kernel
regression, to boosting. In general, the resulting risk minimization problem is
non-convex and is solved by gradient descent or its variants. Unfortunately, little
is known about global convergence properties of these approaches.\r\nHere we consider
the problem of learning a concave function f on a compact convex domain Ω⊆ℝd,
using linear combinations of `bump-like' components (neurons). The parameters
to be fitted are the centers of N bumps, and the resulting empirical risk minimization
problem is highly non-convex. We prove that, in the limit in which the number
of neurons diverges, the evolution of gradient descent converges to a Wasserstein
gradient flow in the space of probability distributions over Ω. Further, when
the bump width δ tends to 0, this gradient flow has a limit which is a viscous
porous medium equation. Remarkably, the cost function optimized by this gradient
flow exhibits a special property known as displacement convexity, which implies
exponential convergence rates for N→∞, δ→0. Surprisingly, this asymptotic theory
appears to capture well the behavior for moderate values of δ,N. Explaining this
phenomenon, and understanding the dependence on δ,N in a quantitative manner remains
an outstanding challenge."
article_processing_charge: No
article_type: original
author:
- first_name: Adel
full_name: Javanmard, Adel
last_name: Javanmard
- first_name: Marco
full_name: Mondelli, Marco
id: 27EB676C-8706-11E9-9510-7717E6697425
last_name: Mondelli
orcid: 0000-0002-3242-7020
- first_name: Andrea
full_name: Montanari, Andrea
last_name: Montanari
citation:
ama: Javanmard A, Mondelli M, Montanari A. Analysis of a two-layer neural network
via displacement convexity. Annals of Statistics. 2020;48(6):3619-3642.
doi:10.1214/20-AOS1945
apa: Javanmard, A., Mondelli, M., & Montanari, A. (2020). Analysis of a two-layer
neural network via displacement convexity. Annals of Statistics. Institute
of Mathematical Statistics. https://doi.org/10.1214/20-AOS1945
chicago: Javanmard, Adel, Marco Mondelli, and Andrea Montanari. “Analysis of a Two-Layer
Neural Network via Displacement Convexity.” Annals of Statistics. Institute
of Mathematical Statistics, 2020. https://doi.org/10.1214/20-AOS1945.
ieee: A. Javanmard, M. Mondelli, and A. Montanari, “Analysis of a two-layer neural
network via displacement convexity,” Annals of Statistics, vol. 48, no.
6. Institute of Mathematical Statistics, pp. 3619–3642, 2020.
ista: Javanmard A, Mondelli M, Montanari A. 2020. Analysis of a two-layer neural
network via displacement convexity. Annals of Statistics. 48(6), 3619–3642.
mla: Javanmard, Adel, et al. “Analysis of a Two-Layer Neural Network via Displacement
Convexity.” Annals of Statistics, vol. 48, no. 6, Institute of Mathematical
Statistics, 2020, pp. 3619–42, doi:10.1214/20-AOS1945.
short: A. Javanmard, M. Mondelli, A. Montanari, Annals of Statistics 48 (2020) 3619–3642.
date_created: 2019-07-31T09:39:42Z
date_published: 2020-12-11T00:00:00Z
date_updated: 2024-03-06T08:28:50Z
day: '11'
department:
- _id: MaMo
doi: 10.1214/20-AOS1945
external_id:
arxiv:
- '1901.01375'
isi:
- '000598369200021'
intvolume: ' 48'
isi: 1
issue: '6'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/1901.01375
month: '12'
oa: 1
oa_version: Preprint
page: 3619-3642
publication: Annals of Statistics
publication_identifier:
eissn:
- 1941-7330
issn:
- 1932-6157
publication_status: published
publisher: Institute of Mathematical Statistics
quality_controlled: '1'
status: public
title: Analysis of a two-layer neural network via displacement convexity
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 48
year: '2020'
...
---
_id: '15070'
abstract:
- lang: eng
text: This workshop focused on interactions between the various perspectives on
the moduli space of Higgs bundles over a Riemann surface. This subject draws on
algebraic geometry, geometric topology, geometric analysis and mathematical physics,
and the goal was to promote interactions between these various branches of the
subject. The main current directions of research were well represented by the
participants, and the talks included many from both senior and junior participants.
article_processing_charge: No
article_type: original
author:
- first_name: Lara
full_name: Anderson, Lara
last_name: Anderson
- first_name: Tamás
full_name: Hausel, Tamás
id: 4A0666D8-F248-11E8-B48F-1D18A9856A87
last_name: Hausel
- first_name: Rafe
full_name: Mazzeo, Rafe
last_name: Mazzeo
- first_name: Laura
full_name: Schaposnik, Laura
last_name: Schaposnik
citation:
ama: Anderson L, Hausel T, Mazzeo R, Schaposnik L. Geometry and physics of Higgs
bundles. Oberwolfach Reports. 2020;16(2):1357-1417. doi:10.4171/owr/2019/23
apa: Anderson, L., Hausel, T., Mazzeo, R., & Schaposnik, L. (2020). Geometry
and physics of Higgs bundles. Oberwolfach Reports. European Mathematical
Society. https://doi.org/10.4171/owr/2019/23
chicago: Anderson, Lara, Tamás Hausel, Rafe Mazzeo, and Laura Schaposnik. “Geometry
and Physics of Higgs Bundles.” Oberwolfach Reports. European Mathematical
Society, 2020. https://doi.org/10.4171/owr/2019/23.
ieee: L. Anderson, T. Hausel, R. Mazzeo, and L. Schaposnik, “Geometry and physics
of Higgs bundles,” Oberwolfach Reports, vol. 16, no. 2. European Mathematical
Society, pp. 1357–1417, 2020.
ista: Anderson L, Hausel T, Mazzeo R, Schaposnik L. 2020. Geometry and physics of
Higgs bundles. Oberwolfach Reports. 16(2), 1357–1417.
mla: Anderson, Lara, et al. “Geometry and Physics of Higgs Bundles.” Oberwolfach
Reports, vol. 16, no. 2, European Mathematical Society, 2020, pp. 1357–417,
doi:10.4171/owr/2019/23.
short: L. Anderson, T. Hausel, R. Mazzeo, L. Schaposnik, Oberwolfach Reports 16
(2020) 1357–1417.
date_created: 2024-03-04T11:36:31Z
date_published: 2020-06-04T00:00:00Z
date_updated: 2024-03-11T09:20:34Z
day: '04'
department:
- _id: TaHa
doi: 10.4171/owr/2019/23
intvolume: ' 16'
issue: '2'
keyword:
- Organic Chemistry
- Biochemistry
language:
- iso: eng
month: '06'
oa_version: None
page: 1357-1417
publication: Oberwolfach Reports
publication_identifier:
issn:
- 1660-8933
publication_status: published
publisher: European Mathematical Society
quality_controlled: '1'
status: public
title: Geometry and physics of Higgs bundles
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 16
year: '2020'
...
---
_id: '8741'
abstract:
- lang: eng
text: "In ecology, climate and other fields, (sub)systems have been identified that
can transition into a qualitatively different state when a critical threshold
or tipping point in a driving process is crossed. An understanding of those tipping
elements is of great interest given the increasing influence of humans on the
biophysical Earth system. Complex interactions exist between tipping elements,
e.g. physical mechanisms connect subsystems of the climate system. Based on earlier
work on such coupled nonlinear systems, we systematically assessed the qualitative
long-term behaviour of interacting tipping elements. We developed an understanding
of the consequences of interactions\r\non the tipping behaviour allowing for tipping
cascades to emerge under certain conditions. The (narrative) application of\r\nthese
qualitative results to real-world examples of interacting tipping elements indicates
that tipping cascades with profound consequences may occur: the interacting Greenland
ice sheet and thermohaline ocean circulation might tip before the tipping points
of the isolated subsystems are crossed. The eutrophication of the first lake in
a lake chain might propagate through the following lakes without a crossing of
their individual critical nutrient input levels. The possibility of emerging cascading
tipping dynamics calls for the development of a unified theory of interacting
tipping elements and the quantitative analysis of interacting real-world tipping
elements."
acknowledgement: "V.K. thanks the German National Academic Foundation (Studienstiftung
des deutschen Volkes) for financial\r\nsupport. J.F.D. is grateful for financial
support by the Stordalen Foundation via the Planetary Boundary Research\r\nNetwork
(PB.net), the Earth League’s EarthDoc program and the European Research Council
Advanced Grant\r\nproject ERA (Earth Resilience in the Anthropocene). We are thankful
for support by the Leibniz Association\r\n(project DominoES).\r\nAcknowledgements.
This work has been performed in the context of the copan collaboration and the FutureLab
on Earth\r\nResilience in the Anthropocene at the Potsdam Institute for Climate
Impact Research. Furthermore, we acknowledge\r\ndiscussions with and helpful comments
by N. Wunderling, J. Heitzig and M. Wiedermann."
article_number: '200599'
article_processing_charge: No
article_type: original
author:
- first_name: Ann Kristin
full_name: Klose, Ann Kristin
last_name: Klose
- first_name: Volker
full_name: Karle, Volker
id: D7C012AE-D7ED-11E9-95E8-1EC5E5697425
last_name: Karle
orcid: 0000-0002-6963-0129
- first_name: Ricarda
full_name: Winkelmann, Ricarda
last_name: Winkelmann
- first_name: Jonathan F.
full_name: Donges, Jonathan F.
last_name: Donges
citation:
ama: 'Klose AK, Karle V, Winkelmann R, Donges JF. Emergence of cascading dynamics
in interacting tipping elements of ecology and climate: Cascading dynamics in
tipping elements. Royal Society Open Science. 2020;7(6). doi:10.1098/rsos.200599'
apa: 'Klose, A. K., Karle, V., Winkelmann, R., & Donges, J. F. (2020). Emergence
of cascading dynamics in interacting tipping elements of ecology and climate:
Cascading dynamics in tipping elements. Royal Society Open Science. The
Royal Society. https://doi.org/10.1098/rsos.200599'
chicago: 'Klose, Ann Kristin, Volker Karle, Ricarda Winkelmann, and Jonathan F.
Donges. “Emergence of Cascading Dynamics in Interacting Tipping Elements of Ecology
and Climate: Cascading Dynamics in Tipping Elements.” Royal Society Open Science.
The Royal Society, 2020. https://doi.org/10.1098/rsos.200599.'
ieee: 'A. K. Klose, V. Karle, R. Winkelmann, and J. F. Donges, “Emergence of cascading
dynamics in interacting tipping elements of ecology and climate: Cascading dynamics
in tipping elements,” Royal Society Open Science, vol. 7, no. 6. The Royal
Society, 2020.'
ista: 'Klose AK, Karle V, Winkelmann R, Donges JF. 2020. Emergence of cascading
dynamics in interacting tipping elements of ecology and climate: Cascading dynamics
in tipping elements. Royal Society Open Science. 7(6), 200599.'
mla: 'Klose, Ann Kristin, et al. “Emergence of Cascading Dynamics in Interacting
Tipping Elements of Ecology and Climate: Cascading Dynamics in Tipping Elements.”
Royal Society Open Science, vol. 7, no. 6, 200599, The Royal Society, 2020,
doi:10.1098/rsos.200599.'
short: A.K. Klose, V. Karle, R. Winkelmann, J.F. Donges, Royal Society Open Science
7 (2020).
date_created: 2020-11-08T23:01:25Z
date_published: 2020-06-01T00:00:00Z
date_updated: 2024-03-12T12:31:30Z
day: '01'
ddc:
- '530'
- '550'
department:
- _id: MiLe
doi: 10.1098/rsos.200599
external_id:
arxiv:
- '1910.12042'
isi:
- '000545625200001'
file:
- access_level: open_access
checksum: 5505c445de373bfd836eb4d3b48b1f37
content_type: application/pdf
creator: dernst
date_created: 2020-11-09T09:07:11Z
date_updated: 2020-11-09T09:07:11Z
file_id: '8748'
file_name: 2020_RoyalSocOpenScience_Klose.pdf
file_size: 1611485
relation: main_file
success: 1
file_date_updated: 2020-11-09T09:07:11Z
has_accepted_license: '1'
intvolume: ' 7'
isi: 1
issue: '6'
language:
- iso: eng
month: '06'
oa: 1
oa_version: Published Version
publication: Royal Society Open Science
publication_identifier:
eissn:
- '20545703'
publication_status: published
publisher: The Royal Society
quality_controlled: '1'
scopus_import: '1'
status: public
title: 'Emergence of cascading dynamics in interacting tipping elements of ecology
and climate: Cascading dynamics in tipping elements'
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 7
year: '2020'
...
---
_id: '7687'
abstract:
- lang: eng
text: A working group, which was established within the Network of Repository Managers (RepManNet), has dealt with common certifications for repositories. In
addition, current requirements of the research funding agencies FWF and EU were
also taken into account. The Core Trust Seal was examined in more detail. For
this purpose, a questionnaire was sent to those organizations that are already certified
with CTS in Austria. The answers were summarized and evaluated anonymously. It
is recommended to go for a repository certification. Moreover, the development
of a DINI certificate in Austria is strongly suggested.
- lang: ger
text: ' Eine Arbeitsgruppe, die im Rahmen des Netzwerks für RepositorienmanagerInnen
(RepManNet) entstanden ist, hat sich mit gängigen Zertifizierungen für Repositorien
beschäftigt. Weiters wurden aktuelle Vorgaben der Forschungsförderer FWF und EU
herangezogen. Das Core Trust Seal wurde genauer betrachtet. Hierfür wurden jenen Organisationen, die in Österreich bereits mit CTS zertifiziert
sind, ein Fragebogen übermittelt. Die Antworten wurden anonymisiert zusammengefasst
und ausgewertet. Plädiert wird für eine Zertifizierung von Repositorien und die
Entwicklung einer DINI-Zertifizierung in Österreich.'
article_processing_charge: No
article_type: original
author:
- first_name: Doris
full_name: Ernst, Doris
id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
last_name: Ernst
orcid: 0000-0002-2354-0195
- first_name: Gertraud
full_name: Novotny, Gertraud
last_name: Novotny
- first_name: Eva Maria
full_name: Schönher, Eva Maria
last_name: Schönher
citation:
ama: Ernst D, Novotny G, Schönher EM. (Core Trust) Seal your repository! Mitteilungen
der Vereinigung Österreichischer Bibliothekarinnen und Bibliothekare. 2020;73(1):46-59.
doi:10.31263/voebm.v73i1.3491
apa: Ernst, D., Novotny, G., & Schönher, E. M. (2020). (Core Trust) Seal your
repository! Mitteilungen der Vereinigung Österreichischer Bibliothekarinnen
und Bibliothekare. Vereinigung Osterreichischer Bibliothekarinnen und Bibliothekare.
https://doi.org/10.31263/voebm.v73i1.3491
chicago: Ernst, Doris, Gertraud Novotny, and Eva Maria Schönher. “(Core Trust) Seal
your repository!” Mitteilungen der Vereinigung Österreichischer Bibliothekarinnen
und Bibliothekare. Vereinigung Osterreichischer Bibliothekarinnen und Bibliothekare,
2020. https://doi.org/10.31263/voebm.v73i1.3491.
ieee: D. Ernst, G. Novotny, and E. M. Schönher, “(Core Trust) Seal your repository!,”
Mitteilungen der Vereinigung Österreichischer Bibliothekarinnen und Bibliothekare,
vol. 73, no. 1. Vereinigung Osterreichischer Bibliothekarinnen und Bibliothekare,
pp. 46–59, 2020.
ista: Ernst D, Novotny G, Schönher EM. 2020. (Core Trust) Seal your repository!
Mitteilungen der Vereinigung Österreichischer Bibliothekarinnen und Bibliothekare.
73(1), 46–59.
mla: Ernst, Doris, et al. “(Core Trust) Seal your repository!” Mitteilungen der
Vereinigung Österreichischer Bibliothekarinnen und Bibliothekare, vol. 73,
no. 1, Vereinigung Osterreichischer Bibliothekarinnen und Bibliothekare, 2020,
pp. 46–59, doi:10.31263/voebm.v73i1.3491.
short: D. Ernst, G. Novotny, E.M. Schönher, Mitteilungen der Vereinigung Österreichischer
Bibliothekarinnen und Bibliothekare 73 (2020) 46–59.
date_created: 2020-04-28T08:37:38Z
date_published: 2020-04-28T00:00:00Z
date_updated: 2024-03-12T10:12:33Z
day: '28'
ddc:
- '020'
department:
- _id: E-Lib
doi: 10.31263/voebm.v73i1.3491
file:
- access_level: open_access
checksum: fee784f15a489deb7def6ccf8c5bf8c3
content_type: application/pdf
creator: dernst
date_created: 2020-06-17T10:50:13Z
date_updated: 2024-03-12T10:12:33Z
file_id: '7970'
file_name: 2020_VOEB_Ernst.pdf
file_size: 579291
relation: main_file
file_date_updated: 2024-03-12T10:12:33Z
has_accepted_license: '1'
intvolume: ' 73'
issue: '1'
language:
- iso: ger
month: '04'
oa: 1
oa_version: Published Version
page: 46-59
popular_science: '1'
publication: Mitteilungen der Vereinigung Österreichischer Bibliothekarinnen und Bibliothekare
publication_identifier:
issn:
- 1022-2588
publication_status: published
publisher: Vereinigung Osterreichischer Bibliothekarinnen und Bibliothekare
scopus_import: '1'
status: public
title: (Core Trust) Seal your repository!
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: 73
year: '2020'
...
---
_id: '15079'
abstract:
- lang: eng
text: "Large complex systems tend to develop universal patterns that often represent
their essential characteristics. For example, the cumulative effects of independent
or weakly dependent random variables often yield the Gaussian universality class
via the central limit theorem. For non-commutative random variables, e.g. matrices,
the Gaussian behavior is often replaced by another universality class, commonly
called random matrix statistics. Nearby eigenvalues are strongly correlated, and,
remarkably, their correlation structure is universal, depending only on the symmetry
type of the matrix. Even more surprisingly, this feature is not restricted to
matrices; in fact Eugene Wigner, the pioneer of the field, discovered in the 1950s
that distributions of the gaps between energy levels of complicated quantum systems
universally follow the same random matrix statistics. This claim has never been
rigorously proved for any realistic physical system but experimental data and
extensive numerics leave no doubt as to its correctness. Since then random matrices
have proved to be extremely useful phenomenological models in a wide range of
applications beyond quantum physics that include number theory, statistics, neuroscience,
population dynamics, wireless communication and mathematical finance. The ubiquity
of random matrices in natural sciences is still a mystery, but recent years have
witnessed a breakthrough in the mathematical description of the statistical structure
of their spectrum. Random matrices and closely related areas such as log-gases
have become an extremely active research area in probability theory.\r\nThis workshop
brought together outstanding researchers from a variety of mathematical backgrounds
whose areas of research are linked to random matrices. While there are strong
links between their motivations, the techniques used by these researchers span
a large swath of mathematics, ranging from purely algebraic techniques to stochastic
analysis, classical probability theory, operator algebra, supersymmetry, orthogonal
polynomials, etc."
article_processing_charge: No
article_type: original
author:
- first_name: László
full_name: Erdös, László
id: 4DBD5372-F248-11E8-B48F-1D18A9856A87
last_name: Erdös
orcid: 0000-0001-5366-9603
- first_name: Friedrich
full_name: Götze, Friedrich
last_name: Götze
- first_name: Alice
full_name: Guionnet, Alice
last_name: Guionnet
citation:
ama: Erdös L, Götze F, Guionnet A. Random matrices. Oberwolfach Reports.
2020;16(4):3459-3527. doi:10.4171/owr/2019/56
apa: Erdös, L., Götze, F., & Guionnet, A. (2020). Random matrices. Oberwolfach
Reports. European Mathematical Society. https://doi.org/10.4171/owr/2019/56
chicago: Erdös, László, Friedrich Götze, and Alice Guionnet. “Random Matrices.”
Oberwolfach Reports. European Mathematical Society, 2020. https://doi.org/10.4171/owr/2019/56.
ieee: L. Erdös, F. Götze, and A. Guionnet, “Random matrices,” Oberwolfach Reports,
vol. 16, no. 4. European Mathematical Society, pp. 3459–3527, 2020.
ista: Erdös L, Götze F, Guionnet A. 2020. Random matrices. Oberwolfach Reports.
16(4), 3459–3527.
mla: Erdös, László, et al. “Random Matrices.” Oberwolfach Reports, vol. 16,
no. 4, European Mathematical Society, 2020, pp. 3459–527, doi:10.4171/owr/2019/56.
short: L. Erdös, F. Götze, A. Guionnet, Oberwolfach Reports 16 (2020) 3459–3527.
date_created: 2024-03-05T07:54:44Z
date_published: 2020-11-19T00:00:00Z
date_updated: 2024-03-12T12:25:18Z
day: '19'
department:
- _id: LaEr
doi: 10.4171/owr/2019/56
intvolume: ' 16'
issue: '4'
language:
- iso: eng
month: '11'
oa_version: None
page: 3459-3527
publication: Oberwolfach Reports
publication_identifier:
issn:
- 1660-8933
publication_status: published
publisher: European Mathematical Society
quality_controlled: '1'
status: public
title: Random matrices
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 16
year: '2020'
...
---
_id: '15072'
abstract:
- lang: eng
text: The interaction among fundamental particles in nature leads to many interesting
effects in quantum statistical mechanics; examples include superconductivity for
charged systems and superfluidity in cold gases. It is a huge challenge for mathematical
physics to understand the collective behavior of systems containing a large number
of particles, emerging from known microscopic interactions. In this workshop we
brought together researchers working on different aspects of many-body quantum
mechanics to discuss recent developments, exchange ideas and propose new challenges
and research directions.
article_processing_charge: No
article_type: original
author:
- first_name: Christian
full_name: Hainzl, Christian
last_name: Hainzl
- first_name: Benjamin
full_name: Schlein, Benjamin
last_name: Schlein
- first_name: Robert
full_name: Seiringer, Robert
id: 4AFD0470-F248-11E8-B48F-1D18A9856A87
last_name: Seiringer
orcid: 0000-0002-6781-0521
- first_name: Simone
full_name: Warzel, Simone
last_name: Warzel
citation:
ama: Hainzl C, Schlein B, Seiringer R, Warzel S. Many-body quantum systems. Oberwolfach
Reports. 2020;16(3):2541-2603. doi:10.4171/owr/2019/41
apa: Hainzl, C., Schlein, B., Seiringer, R., & Warzel, S. (2020). Many-body
quantum systems. Oberwolfach Reports. European Mathematical Society. https://doi.org/10.4171/owr/2019/41
chicago: Hainzl, Christian, Benjamin Schlein, Robert Seiringer, and Simone Warzel.
“Many-Body Quantum Systems.” Oberwolfach Reports. European Mathematical
Society, 2020. https://doi.org/10.4171/owr/2019/41.
ieee: C. Hainzl, B. Schlein, R. Seiringer, and S. Warzel, “Many-body quantum systems,”
Oberwolfach Reports, vol. 16, no. 3. European Mathematical Society, pp.
2541–2603, 2020.
ista: Hainzl C, Schlein B, Seiringer R, Warzel S. 2020. Many-body quantum systems.
Oberwolfach Reports. 16(3), 2541–2603.
mla: Hainzl, Christian, et al. “Many-Body Quantum Systems.” Oberwolfach Reports,
vol. 16, no. 3, European Mathematical Society, 2020, pp. 2541–603, doi:10.4171/owr/2019/41.
short: C. Hainzl, B. Schlein, R. Seiringer, S. Warzel, Oberwolfach Reports 16 (2020)
2541–2603.
date_created: 2024-03-04T11:46:12Z
date_published: 2020-09-10T00:00:00Z
date_updated: 2024-03-12T12:02:00Z
day: '10'
department:
- _id: RoSe
doi: 10.4171/owr/2019/41
intvolume: ' 16'
issue: '3'
language:
- iso: eng
month: '09'
oa_version: None
page: 2541-2603
publication: Oberwolfach Reports
publication_identifier:
issn:
- 1660-8933
publication_status: published
publisher: European Mathematical Society
quality_controlled: '1'
status: public
title: Many-body quantum systems
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 16
year: '2020'
...
---
_id: '15071'
abstract:
- lang: eng
text: "A mesophilic methanogenic culture, designated JL01, was isolated from Holocene
permafrost in the Russian Arctic [1]. After long-term extensive cultivation at
15°C it turned out to be a tied binary culture of archaeal (JL01) and bacterial
(Sphaerochaeta associata GLS2) strains.\r\nStrain JL01 was a strict anaerobe and
grew on methanol, acetate and methylamines as energy and carbon sources. Cells
were irregular coccoid, non-motile, non-spore-forming, and Gram-stainpositive.
Optimum conditions for growth were 24-28 oC, pH 6.8–7.3 and 0.075-0.1 M NaCl.\r\nPhylogenetic
tree reconstructions based on 16S rRNA and concatenated alignment of broadly\r\nconserved
protein-coding genes revealed its close relation to Methanosarcina mazei S-6\r\nT
(similarity 99.5%). The comparison of whole genomic sequences (ANI) of the isolate
and the type strain of M.mazei was 98.5%, which is higher than the values recommended
for new species. Thus strain JL01 (=VKM B-2370=JCM 31898) represents the first
M. mazei isolated from permanently subzero Arcticsediments. The long-term co-cultivation
of JL01 with S. associata GLS2T showed the methane production without any additional
carbon and energy sources. Genome analysis of S. associata GLS2T revealed putative
genes involved in methanochondroithin catabolism."
acknowledgement: "The work was supported by of Russian Foundation of Basic Research:
grant № 19-04-00831 for Viktoria Shcherbakova and Olga Troshina, grant № 18-34-00334
for Viktoriia Oshurkova and Vladimir Trubitsyn. \r\nWe thank Dr Natalia Suzina (IBPM
RAS, Federal Research Center Pushchino Center for\r\nBiological Research RAS) for
the help with the microscopic studies, respectively; Dr. Margarita Meyer (Division
of Genetics, Department of Medicine, BWH and HMS, USA) and Dr Fedor Kondrashov (IST,
Austria) for their help in obtaining the genomic sequence of strain JL01. "
article_processing_charge: Yes
author:
- first_name: Viktoriia
full_name: Oshurkova, Viktoriia
last_name: Oshurkova
- first_name: Olga
full_name: Troshina, Olga
last_name: Troshina
- first_name: Vladimir
full_name: Trubitsyn, Vladimir
last_name: Trubitsyn
- first_name: Yana
full_name: Ryzhmanova, Yana
last_name: Ryzhmanova
- first_name: Olga
full_name: Bochkareva, Olga
id: C4558D3C-6102-11E9-A62E-F418E6697425
last_name: Bochkareva
orcid: 0000-0003-1006-6639
- first_name: Viktoria
full_name: Shcherbakova, Viktoria
last_name: Shcherbakova
citation:
ama: 'Oshurkova V, Troshina O, Trubitsyn V, Ryzhmanova Y, Bochkareva O, Shcherbakova
V. Characterization of methanosarcina mazei JL01 isolated from holocene arctic
permafrost and study of the archaeon cooperation with bacterium Sphaerochaeta
associata GLS2T. In: Proceedings of 1st International Electronic Conference
on Microbiology. MDPI; 2020. doi:10.3390/ecm2020-07116'
apa: 'Oshurkova, V., Troshina, O., Trubitsyn, V., Ryzhmanova, Y., Bochkareva, O.,
& Shcherbakova, V. (2020). Characterization of methanosarcina mazei JL01 isolated
from holocene arctic permafrost and study of the archaeon cooperation with bacterium
Sphaerochaeta associata GLS2T. In Proceedings of 1st International Electronic
Conference on Microbiology. Virtual: MDPI. https://doi.org/10.3390/ecm2020-07116'
chicago: Oshurkova, Viktoriia, Olga Troshina, Vladimir Trubitsyn, Yana Ryzhmanova,
Olga Bochkareva, and Viktoria Shcherbakova. “Characterization of Methanosarcina
Mazei JL01 Isolated from Holocene Arctic Permafrost and Study of the Archaeon
Cooperation with Bacterium Sphaerochaeta Associata GLS2T.” In Proceedings of
1st International Electronic Conference on Microbiology. MDPI, 2020. https://doi.org/10.3390/ecm2020-07116.
ieee: V. Oshurkova, O. Troshina, V. Trubitsyn, Y. Ryzhmanova, O. Bochkareva, and
V. Shcherbakova, “Characterization of methanosarcina mazei JL01 isolated from
holocene arctic permafrost and study of the archaeon cooperation with bacterium
Sphaerochaeta associata GLS2T,” in Proceedings of 1st International Electronic
Conference on Microbiology, Virtual, 2020.
ista: 'Oshurkova V, Troshina O, Trubitsyn V, Ryzhmanova Y, Bochkareva O, Shcherbakova
V. 2020. Characterization of methanosarcina mazei JL01 isolated from holocene
arctic permafrost and study of the archaeon cooperation with bacterium Sphaerochaeta
associata GLS2T. Proceedings of 1st International Electronic Conference on Microbiology.
ECM: Electronic Conference on Microbiology.'
mla: Oshurkova, Viktoriia, et al. “Characterization of Methanosarcina Mazei JL01
Isolated from Holocene Arctic Permafrost and Study of the Archaeon Cooperation
with Bacterium Sphaerochaeta Associata GLS2T.” Proceedings of 1st International
Electronic Conference on Microbiology, MDPI, 2020, doi:10.3390/ecm2020-07116.
short: V. Oshurkova, O. Troshina, V. Trubitsyn, Y. Ryzhmanova, O. Bochkareva, V.
Shcherbakova, in:, Proceedings of 1st International Electronic Conference on Microbiology,
MDPI, 2020.
conference:
end_date: 2020-11-30
location: Virtual
name: 'ECM: Electronic Conference on Microbiology'
start_date: 2020-11-02
date_created: 2024-03-04T11:41:31Z
date_published: 2020-11-02T00:00:00Z
date_updated: 2024-03-20T08:06:22Z
day: '02'
ddc:
- '570'
department:
- _id: FyKo
doi: 10.3390/ecm2020-07116
file:
- access_level: open_access
checksum: d1914af7811a21a4b2744eb51b5834e3
content_type: application/pdf
creator: dernst
date_created: 2024-03-20T08:05:46Z
date_updated: 2024-03-20T08:05:46Z
file_id: '15127'
file_name: 2020_ECM_Oshurkova.pdf
file_size: 595543
relation: main_file
success: 1
file_date_updated: 2024-03-20T08:05:46Z
has_accepted_license: '1'
language:
- iso: eng
month: '11'
oa: 1
oa_version: Published Version
publication: Proceedings of 1st International Electronic Conference on Microbiology
publication_status: published
publisher: MDPI
quality_controlled: '1'
status: public
title: Characterization of methanosarcina mazei JL01 isolated from holocene arctic
permafrost and study of the archaeon cooperation with bacterium Sphaerochaeta associata
GLS2T
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: conference
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
year: '2020'
...
---
_id: '15153'
abstract:
- lang: eng
text: Mammalian circadian rhythms are generated by a transcription-based feedback
loop in which CLOCK:BMAL1 drives transcription of its repressors (PER1/2, CRY1/2),
which ultimately interact with CLOCK:BMAL1 to close the feedback loop with ~24
hr periodicity. Here we pinpoint a key difference between CRY1 and CRY2 that underlies
their differential strengths as transcriptional repressors. Both cryptochromes
bind the BMAL1 transactivation domain similarly to sequester it from coactivators
and repress CLOCK:BMAL1 activity. However, we find that CRY1 is recruited with
much higher affinity to the PAS domain core of CLOCK:BMAL1, allowing it to serve
as a stronger repressor that lengthens circadian period. We discovered a dynamic
serine-rich loop adjacent to the secondary pocket in the photolyase homology region
(PHR) domain that regulates differential binding of cryptochromes to the PAS domain
core of CLOCK:BMAL1. Notably, binding of the co-repressor PER2 remodels the serine
loop of CRY2, making it more CRY1-like and enhancing its affinity for CLOCK:BMAL1.
article_number: '55275'
article_processing_charge: No
article_type: original
author:
- first_name: Jennifer L
full_name: Fribourgh, Jennifer L
last_name: Fribourgh
- first_name: Ashutosh
full_name: Srivastava, Ashutosh
last_name: Srivastava
- first_name: Colby R
full_name: Sandate, Colby R
last_name: Sandate
- first_name: Alicia Kathleen
full_name: Michael, Alicia Kathleen
id: 6437c950-2a03-11ee-914d-d6476dd7b75c
last_name: Michael
- first_name: Peter L
full_name: Hsu, Peter L
last_name: Hsu
- first_name: Christin
full_name: Rakers, Christin
last_name: Rakers
- first_name: Leslee T
full_name: Nguyen, Leslee T
last_name: Nguyen
- first_name: Megan R
full_name: Torgrimson, Megan R
last_name: Torgrimson
- first_name: Gian Carlo G
full_name: Parico, Gian Carlo G
last_name: Parico
- first_name: Sarvind
full_name: Tripathi, Sarvind
last_name: Tripathi
- first_name: Ning
full_name: Zheng, Ning
last_name: Zheng
- first_name: Gabriel C
full_name: Lander, Gabriel C
last_name: Lander
- first_name: Tsuyoshi
full_name: Hirota, Tsuyoshi
last_name: Hirota
- first_name: Florence
full_name: Tama, Florence
last_name: Tama
- first_name: Carrie L
full_name: Partch, Carrie L
last_name: Partch
citation:
ama: Fribourgh JL, Srivastava A, Sandate CR, et al. Dynamics at the serine loop
underlie differential affinity of cryptochromes for CLOCK:BMAL1 to control circadian
timing. eLife. 2020;9. doi:10.7554/elife.55275
apa: Fribourgh, J. L., Srivastava, A., Sandate, C. R., Michael, A. K., Hsu, P. L.,
Rakers, C., … Partch, C. L. (2020). Dynamics at the serine loop underlie differential
affinity of cryptochromes for CLOCK:BMAL1 to control circadian timing. ELife.
eLife Sciences Publications. https://doi.org/10.7554/elife.55275
chicago: Fribourgh, Jennifer L, Ashutosh Srivastava, Colby R Sandate, Alicia K.
Michael, Peter L Hsu, Christin Rakers, Leslee T Nguyen, et al. “Dynamics at the
Serine Loop Underlie Differential Affinity of Cryptochromes for CLOCK:BMAL1 to
Control Circadian Timing.” ELife. eLife Sciences Publications, 2020. https://doi.org/10.7554/elife.55275.
ieee: J. L. Fribourgh et al., “Dynamics at the serine loop underlie differential
affinity of cryptochromes for CLOCK:BMAL1 to control circadian timing,” eLife,
vol. 9. eLife Sciences Publications, 2020.
ista: Fribourgh JL, Srivastava A, Sandate CR, Michael AK, Hsu PL, Rakers C, Nguyen
LT, Torgrimson MR, Parico GCG, Tripathi S, Zheng N, Lander GC, Hirota T, Tama
F, Partch CL. 2020. Dynamics at the serine loop underlie differential affinity
of cryptochromes for CLOCK:BMAL1 to control circadian timing. eLife. 9, 55275.
mla: Fribourgh, Jennifer L., et al. “Dynamics at the Serine Loop Underlie Differential
Affinity of Cryptochromes for CLOCK:BMAL1 to Control Circadian Timing.” ELife,
vol. 9, 55275, eLife Sciences Publications, 2020, doi:10.7554/elife.55275.
short: J.L. Fribourgh, A. Srivastava, C.R. Sandate, A.K. Michael, P.L. Hsu, C. Rakers,
L.T. Nguyen, M.R. Torgrimson, G.C.G. Parico, S. Tripathi, N. Zheng, G.C. Lander,
T. Hirota, F. Tama, C.L. Partch, ELife 9 (2020).
date_created: 2024-03-21T07:55:12Z
date_published: 2020-02-26T00:00:00Z
date_updated: 2024-03-25T12:25:02Z
day: '26'
doi: 10.7554/elife.55275
extern: '1'
intvolume: ' 9'
keyword:
- General Immunology and Microbiology
- General Biochemistry
- Genetics and Molecular Biology
- General Medicine
- General Neuroscience
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.7554/eLife.55275
month: '02'
oa: 1
oa_version: Published Version
publication: eLife
publication_identifier:
issn:
- 2050-084X
publication_status: published
publisher: eLife Sciences Publications
quality_controlled: '1'
scopus_import: '1'
status: public
title: Dynamics at the serine loop underlie differential affinity of cryptochromes
for CLOCK:BMAL1 to control circadian timing
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 9
year: '2020'
...
---
_id: '15152'
abstract:
- lang: eng
text: Transcription factors (TFs) regulate gene expression through chromatin where
nucleosomes restrict DNA access. To study how TFs bind nucleosome-occupied motifs,
we focused on the reprogramming factors OCT4 and SOX2 in mouse embryonic stem
cells. We determined TF engagement throughout a nucleosome at base-pair resolution
in vitro, enabling structure determination by cryo–electron microscopy at two
preferred positions. Depending on motif location, OCT4 and SOX2 differentially
distort nucleosomal DNA. At one position, OCT4-SOX2 removes DNA from histone H2A
and histone H3; however, at an inverted motif, the TFs only induce local DNA distortions.
OCT4 uses one of its two DNA-binding domains to engage DNA in both structures,
reading out a partial motif. These findings explain site-specific nucleosome engagement
by the pluripotency factors OCT4 and SOX2, and they reveal how TFs distort nucleosomes
to access chromatinized motifs.
article_processing_charge: No
article_type: original
author:
- first_name: Alicia Kathleen
full_name: Michael, Alicia Kathleen
id: 6437c950-2a03-11ee-914d-d6476dd7b75c
last_name: Michael
orcid: 0000-0002-6080-839X
- first_name: Ralph S.
full_name: Grand, Ralph S.
last_name: Grand
- first_name: Luke
full_name: Isbel, Luke
last_name: Isbel
- first_name: Simone
full_name: Cavadini, Simone
last_name: Cavadini
- first_name: Zuzanna
full_name: Kozicka, Zuzanna
last_name: Kozicka
- first_name: Georg
full_name: Kempf, Georg
last_name: Kempf
- first_name: Richard D.
full_name: Bunker, Richard D.
last_name: Bunker
- first_name: Andreas D.
full_name: Schenk, Andreas D.
last_name: Schenk
- first_name: Alexandra
full_name: Graff-Meyer, Alexandra
last_name: Graff-Meyer
- first_name: Ganesh R.
full_name: Pathare, Ganesh R.
last_name: Pathare
- first_name: Joscha
full_name: Weiss, Joscha
last_name: Weiss
- first_name: Syota
full_name: Matsumoto, Syota
last_name: Matsumoto
- first_name: Lukas
full_name: Burger, Lukas
last_name: Burger
- first_name: Dirk
full_name: Schübeler, Dirk
last_name: Schübeler
- first_name: Nicolas H.
full_name: Thomä, Nicolas H.
last_name: Thomä
citation:
ama: Michael AK, Grand RS, Isbel L, et al. Mechanisms of OCT4-SOX2 motif readout
on nucleosomes. Science. 2020;368(6498):1460-1465. doi:10.1126/science.abb0074
apa: Michael, A. K., Grand, R. S., Isbel, L., Cavadini, S., Kozicka, Z., Kempf,
G., … Thomä, N. H. (2020). Mechanisms of OCT4-SOX2 motif readout on nucleosomes.
Science. American Association for the Advancement of Science . https://doi.org/10.1126/science.abb0074
chicago: Michael, Alicia K., Ralph S. Grand, Luke Isbel, Simone Cavadini, Zuzanna
Kozicka, Georg Kempf, Richard D. Bunker, et al. “Mechanisms of OCT4-SOX2 Motif
Readout on Nucleosomes.” Science. American Association for the Advancement
of Science , 2020. https://doi.org/10.1126/science.abb0074.
ieee: A. K. Michael et al., “Mechanisms of OCT4-SOX2 motif readout on nucleosomes,”
Science, vol. 368, no. 6498. American Association for the Advancement of
Science , pp. 1460–1465, 2020.
ista: Michael AK, Grand RS, Isbel L, Cavadini S, Kozicka Z, Kempf G, Bunker RD,
Schenk AD, Graff-Meyer A, Pathare GR, Weiss J, Matsumoto S, Burger L, Schübeler
D, Thomä NH. 2020. Mechanisms of OCT4-SOX2 motif readout on nucleosomes. Science.
368(6498), 1460–1465.
mla: Michael, Alicia K., et al. “Mechanisms of OCT4-SOX2 Motif Readout on Nucleosomes.”
Science, vol. 368, no. 6498, American Association for the Advancement of
Science , 2020, pp. 1460–65, doi:10.1126/science.abb0074.
short: A.K. Michael, R.S. Grand, L. Isbel, S. Cavadini, Z. Kozicka, G. Kempf, R.D.
Bunker, A.D. Schenk, A. Graff-Meyer, G.R. Pathare, J. Weiss, S. Matsumoto, L.
Burger, D. Schübeler, N.H. Thomä, Science 368 (2020) 1460–1465.
date_created: 2024-03-21T07:54:44Z
date_published: 2020-04-23T00:00:00Z
date_updated: 2024-03-25T12:29:34Z
day: '23'
doi: 10.1126/science.abb0074
extern: '1'
intvolume: ' 368'
issue: '6498'
language:
- iso: eng
month: '04'
oa_version: None
page: 1460-1465
publication: Science
publication_identifier:
eissn:
- 1095-9203
issn:
- 0036-8075
publication_status: published
publisher: 'American Association for the Advancement of Science '
quality_controlled: '1'
scopus_import: '1'
status: public
title: Mechanisms of OCT4-SOX2 motif readout on nucleosomes
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 368
year: '2020'
...
---
_id: '7525'
abstract:
- lang: eng
text: "The medial habenula (MHb) is an evolutionary conserved epithalamic structure
important for the modulation of emotional memory. It is involved in regulation
of anxiety, compulsive behavior, addiction (nicotinic and opioid), sexual and
feeding behavior. MHb receives inputs from septal regions and projects exclusively
to the interpeduncular nucleus (IPN). Distinct sub-regions of the septum project
to different subnuclei of MHb: the bed nucleus of anterior commissure projects
to dorsal MHb and the triangular septum projects to ventral MHb. Furthermore,
the dorsal and ventral MHb project to the lateral and rostral/central IPN, respectively.
Importantly, these projections have unique features of prominent co-release of
different neurotransmitters and requirement of a peculiar type of calcium channel
for release. In general, synaptic neurotransmission requires an activity-dependent
influx of Ca2+ into the presynaptic terminal through voltage-gated calcium channels.
The calcium channel family most commonly involved in neurotransmitter release
comprises three members, P/Q-, N- and R-type with Cav2.1, Cav2.2 and Cav2.3 subunits,
respectively. In contrast to most CNS synapses that mainly express Cav2.1 and/or
Cav2.2, MHb terminals in the IPN exclusively express Cav2.3. In other parts of
the brain, such as the hippocampus, Cav2.3 is mostly located to postsynaptic elements.
This unusual presynaptic location of Cav2.3 in the MHb-IPN pathway implies unique
mechanisms of glutamate release in this pathway. One potential example of such
uniqueness is the facilitation of release by GABAB receptor (GBR) activation.
Presynaptic GBRs usually inhibit the release of neurotransmitters by inhibiting
presynaptic calcium channels. MHb shows the highest expression levels of GBR in
the brain. GBRs comprise two subunits, GABAB1 (GB1) and GABAB2 (GB2), and are
associated with auxiliary subunits, called potassium channel tetramerization domain
containing proteins (KCTD) 8, 12, 12b and 16. Among these four subunits, KCTD12b
is exclusively expressed in ventral MHb, and KCTD8 shows the strongest expression
in the whole MHb among other brain regions, indicating that KCTD8 and KCTD12b
may be involved in the unique mechanisms of neurotransmitter release mediated
by Cav2.3 and regulated by GBRs in this pathway. \r\nIn the present study, we
first verified that neurotransmission in both dorsal and ventral MHb-IPN pathways
is mainly mediated by Cav2.3 using a selective blocker of R-type channels, SNX-482.
We next found that baclofen, a GBR agonist, has facilitatory effects on release
from ventral MHb terminal in rostral IPN, whereas it has inhibitory effects on
release from dorsal MHb terminals in lateral IPN, indicating that KCTD12b expressed
exclusively in ventral MHb may have a role in the facilitatory effects of GBR
activation. In a heterologous expression system using HEK cells, we found that
KCTD8 and KCTD12b but not KCTD12 directly bind with Cav2.3. Pre-embedding immunogold
electron microscopy data show that Cav2.3 and KCTD12b are distributed most densely
in presynaptic active zone in IPN with KCTD12b being present only in rostral/central
but not lateral IPN, whereas GABAB, KCTD8 and KCTD12 are distributed most densely
in perisynaptic sites with KCTD12 present more frequently in postsynaptic elements
and only in rostral/central IPN. In freeze-fracture replica labelling, Cav2.3,
KCTD8 and KCTD12b are co-localized with each other in the same active zone indicating
that they may form complexes regulating vesicle release in rostral IPN. \r\nOn
electrophysiological studies of wild type (WT) mice, we found that paired-pulse
ratio in rostral IPN of KCTD12b knock-out (KO) mice is lower than those of WT
and KCTD8 KO mice. Consistent with this finding, in mean variance analysis, release
probability in rostral IPN of KCTD12b KO mice is higher than that of WT and KCTD8
KO mice. Although paired-pulse ratios are not different between WT and KCTD8 KO
mice, the mean variance analysis revealed significantly lower release probability
in rostral IPN of KCTD8 KO than WT mice. These results demonstrate bidirectional
regulation of Cav2.3-mediated release by KCTD8 and KCTD12b without GBR activation
in rostral IPN. Finally, we examined the baclofen effects in rostral IPN of KCTD8
and KCTD12b KO mice, and found the facilitation of release remained in both KO
mice, indicating that the peculiar effects of the GBR activation in this pathway
do not depend on the selective expression of these KCTD subunits in ventral MHb.
However, we found that presynaptic potentiation of evoked EPSC amplitude by baclofen
falls to baseline after washout faster in KCTD12b KO mice than WT, KCTD8 KO and
KCTD8/12b double KO mice. This result indicates that KCTD12b is involved in sustained
potentiation of vesicle release by GBR activation, whereas KCTD8 is involved in
its termination in the absence of KCTD12b. Consistent with these functional findings,
replica labelling revealed an increase in density of KCTD8, but not Cav2.3 or
GBR at active zone in rostral IPN of KCTD12b KO mice compared with that of WT
mice, suggesting that increased association of KCTD8 with Cav2.3 facilitates the
release probability and termination of the GBR effect in the absence of KCTD12b.\r\nIn
summary, our study provided new insights into the physiological roles of presynaptic
Cav2.3, GBRs and their auxiliary subunits KCTDs at an evolutionary conserved neuronal
circuit. Future studies will be required to identify the exact molecular mechanism
underlying the GBR-mediated presynaptic potentiation on ventral MHb terminals.
It remains to be determined whether the prominent presence of presynaptic KCTDs
at active zone could exert similar neuromodulatory functions in different pathways
of the brain.\r\n"
acknowledged_ssus:
- _id: EM-Fac
alternative_title:
- ISTA Thesis
article_processing_charge: No
author:
- first_name: Pradeep
full_name: Bhandari, Pradeep
id: 45EDD1BC-F248-11E8-B48F-1D18A9856A87
last_name: Bhandari
orcid: 0000-0003-0863-4481
citation:
ama: Bhandari P. Localization and functional role of Cav2.3 in the medial habenula
to interpeduncular nucleus pathway. 2020. doi:10.15479/AT:ISTA:7525
apa: Bhandari, P. (2020). Localization and functional role of Cav2.3 in the medial
habenula to interpeduncular nucleus pathway. Institute of Science and Technology
Austria. https://doi.org/10.15479/AT:ISTA:7525
chicago: Bhandari, Pradeep. “Localization and Functional Role of Cav2.3 in the Medial
Habenula to Interpeduncular Nucleus Pathway.” Institute of Science and Technology
Austria, 2020. https://doi.org/10.15479/AT:ISTA:7525.
ieee: P. Bhandari, “Localization and functional role of Cav2.3 in the medial habenula
to interpeduncular nucleus pathway,” Institute of Science and Technology Austria,
2020.
ista: Bhandari P. 2020. Localization and functional role of Cav2.3 in the medial
habenula to interpeduncular nucleus pathway. Institute of Science and Technology
Austria.
mla: Bhandari, Pradeep. Localization and Functional Role of Cav2.3 in the Medial
Habenula to Interpeduncular Nucleus Pathway. Institute of Science and Technology
Austria, 2020, doi:10.15479/AT:ISTA:7525.
short: P. Bhandari, Localization and Functional Role of Cav2.3 in the Medial Habenula
to Interpeduncular Nucleus Pathway, Institute of Science and Technology Austria,
2020.
date_created: 2020-02-26T10:56:37Z
date_published: 2020-02-28T00:00:00Z
date_updated: 2023-09-07T13:20:03Z
day: '28'
ddc:
- '570'
degree_awarded: PhD
department:
- _id: RySh
doi: 10.15479/AT:ISTA:7525
file:
- access_level: open_access
checksum: 4589234fdb12b4ad72273b311723a7b4
content_type: application/pdf
creator: pbhandari
date_created: 2020-02-28T08:37:53Z
date_updated: 2021-03-01T23:30:04Z
embargo: 2021-02-28
file_id: '7538'
file_name: Pradeep Bhandari Thesis.pdf
file_size: 9646346
relation: main_file
title: Localization and functional role of Cav2.3 in the medial habenula to interpeduncular
nucleus pathway
- access_level: closed
checksum: aa79490553ca0a5c9b6fbcd152e93928
content_type: application/vnd.openxmlformats-officedocument.wordprocessingml.document
creator: pbhandari
date_created: 2020-02-28T08:47:14Z
date_updated: 2021-03-01T23:30:04Z
embargo_to: open_access
file_id: '7539'
file_name: Pradeep Bhandari Thesis.docx
file_size: 35252164
relation: source_file
title: Localization and functional role of Cav2.3 in the medial habenula to interpeduncular
nucleus pathway
file_date_updated: 2021-03-01T23:30:04Z
has_accepted_license: '1'
keyword:
- Cav2.3
- medial habenula (MHb)
- interpeduncular nucleus (IPN)
language:
- iso: eng
month: '02'
oa: 1
oa_version: Published Version
page: '79'
publication_identifier:
issn:
- 2663-337X
publication_status: published
publisher: Institute of Science and Technology Austria
status: public
supervisor:
- first_name: Ryuichi
full_name: Shigemoto, Ryuichi
id: 499F3ABC-F248-11E8-B48F-1D18A9856A87
last_name: Shigemoto
orcid: 0000-0001-8761-9444
title: Localization and functional role of Cav2.3 in the medial habenula to interpeduncular
nucleus pathway
type: dissertation
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
year: '2020'
...
---
_id: '8586'
abstract:
- lang: eng
text: Cryo-electron microscopy (cryo-EM) of cellular specimens provides insights
into biological processes and structures within a native context. However, a major
challenge still lies in the efficient and reproducible preparation of adherent
cells for subsequent cryo-EM analysis. This is due to the sensitivity of many
cellular specimens to the varying seeding and culturing conditions required for
EM experiments, the often limited amount of cellular material and also the fragility
of EM grids and their substrate. Here, we present low-cost and reusable 3D printed
grid holders, designed to improve specimen preparation when culturing challenging
cellular samples directly on grids. The described grid holders increase cell culture
reproducibility and throughput, and reduce the resources required for cell culturing.
We show that grid holders can be integrated into various cryo-EM workflows, including
micro-patterning approaches to control cell seeding on grids, and for generating
samples for cryo-focused ion beam milling and cryo-electron tomography experiments.
Their adaptable design allows for the generation of specialized grid holders customized
to a large variety of applications.
acknowledged_ssus:
- _id: ScienComp
- _id: LifeSc
- _id: Bio
- _id: EM-Fac
acknowledgement: This work was supported by the Austrian Science Fund (FWF, P33367)
to FKMS. BZ acknowledges support by the Niederösterreich Fond. This research was
also supported by the Scientific Service Units (SSU) of IST Austria through resources
provided by Scientific Computing (SciComp), the Life Science Facility (LSF), the
BioImaging Facility (BIF) and the Electron Microscopy Facility (EMF). We thank Georgi
Dimchev (IST Austria) and Sonja Jacob (Vienna Biocenter Core Facilities) for testing
our grid holders in different experimental setups and Daniel Gütl and the Kondrashov
group (IST Austria) for granting us repeated access to their 3D printers. We also
thank Jonna Alanko and the Sixt lab (IST Austria) for providing us HeLa cells, primary
BL6 mouse tail fibroblasts, NIH 3T3 fibroblasts and human telomerase immortalised
foreskin fibroblasts for our experiments. We are thankful to Ori Avinoam and William
Wan for helpful comments on the manuscript and also thank Dorotea Fracchiolla (Art&Science)
for illustrating the graphical abstract.
article_number: '107633'
article_processing_charge: Yes (via OA deal)
article_type: original
author:
- first_name: Florian
full_name: Fäßler, Florian
id: 404F5528-F248-11E8-B48F-1D18A9856A87
last_name: Fäßler
orcid: 0000-0001-7149-769X
- first_name: Bettina
full_name: Zens, Bettina
id: 45FD126C-F248-11E8-B48F-1D18A9856A87
last_name: Zens
orcid: 0000-0002-9561-1239
- first_name: Robert
full_name: Hauschild, Robert
id: 4E01D6B4-F248-11E8-B48F-1D18A9856A87
last_name: Hauschild
orcid: 0000-0001-9843-3522
- first_name: Florian KM
full_name: Schur, Florian KM
id: 48AD8942-F248-11E8-B48F-1D18A9856A87
last_name: Schur
orcid: 0000-0003-4790-8078
citation:
ama: Fäßler F, Zens B, Hauschild R, Schur FK. 3D printed cell culture grid holders
for improved cellular specimen preparation in cryo-electron microscopy. Journal
of Structural Biology. 2020;212(3). doi:10.1016/j.jsb.2020.107633
apa: Fäßler, F., Zens, B., Hauschild, R., & Schur, F. K. (2020). 3D printed
cell culture grid holders for improved cellular specimen preparation in cryo-electron
microscopy. Journal of Structural Biology. Elsevier. https://doi.org/10.1016/j.jsb.2020.107633
chicago: Fäßler, Florian, Bettina Zens, Robert Hauschild, and Florian KM Schur.
“3D Printed Cell Culture Grid Holders for Improved Cellular Specimen Preparation
in Cryo-Electron Microscopy.” Journal of Structural Biology. Elsevier,
2020. https://doi.org/10.1016/j.jsb.2020.107633.
ieee: F. Fäßler, B. Zens, R. Hauschild, and F. K. Schur, “3D printed cell culture
grid holders for improved cellular specimen preparation in cryo-electron microscopy,”
Journal of Structural Biology, vol. 212, no. 3. Elsevier, 2020.
ista: Fäßler F, Zens B, Hauschild R, Schur FK. 2020. 3D printed cell culture grid
holders for improved cellular specimen preparation in cryo-electron microscopy.
Journal of Structural Biology. 212(3), 107633.
mla: Fäßler, Florian, et al. “3D Printed Cell Culture Grid Holders for Improved
Cellular Specimen Preparation in Cryo-Electron Microscopy.” Journal of Structural
Biology, vol. 212, no. 3, 107633, Elsevier, 2020, doi:10.1016/j.jsb.2020.107633.
short: F. Fäßler, B. Zens, R. Hauschild, F.K. Schur, Journal of Structural Biology
212 (2020).
date_created: 2020-09-29T13:24:06Z
date_published: 2020-12-01T00:00:00Z
date_updated: 2024-03-27T23:30:05Z
day: '01'
ddc:
- '570'
department:
- _id: FlSc
doi: 10.1016/j.jsb.2020.107633
external_id:
isi:
- '000600997800008'
file:
- access_level: open_access
checksum: c48cbf594e84fc2f91966ffaafc0918c
content_type: application/pdf
creator: dernst
date_created: 2020-12-10T14:01:10Z
date_updated: 2020-12-10T14:01:10Z
file_id: '8937'
file_name: 2020_JourStrucBiology_Faessler.pdf
file_size: 7076870
relation: main_file
success: 1
file_date_updated: 2020-12-10T14:01:10Z
has_accepted_license: '1'
intvolume: ' 212'
isi: 1
issue: '3'
keyword:
- electron microscopy
- cryo-EM
- EM sample preparation
- 3D printing
- cell culture
language:
- iso: eng
month: '12'
oa: 1
oa_version: Published Version
project:
- _id: 9B954C5C-BA93-11EA-9121-9846C619BF3A
grant_number: P33367
name: Structure and isoform diversity of the Arp2/3 complex
- _id: 059B463C-7A3F-11EA-A408-12923DDC885E
name: NÖ-Fonds Preis für die Jungforscherin des Jahres am IST Austria
publication: Journal of Structural Biology
publication_identifier:
issn:
- 1047-8477
publication_status: published
publisher: Elsevier
quality_controlled: '1'
related_material:
record:
- id: '14592'
relation: used_in_publication
status: public
- id: '12491'
relation: dissertation_contains
status: public
scopus_import: '1'
status: public
title: 3D printed cell culture grid holders for improved cellular specimen preparation
in cryo-electron microscopy
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: 212
year: '2020'
...
---
_id: '8657'
abstract:
- lang: eng
text: "Synthesis of proteins – translation – is a fundamental process of life. Quantitative
studies anchor translation into the context of bacterial physiology and reveal
several mathematical relationships, called “growth laws,” which capture physiological
feedbacks between protein synthesis and cell growth. Growth laws describe the
dependency of the ribosome abundance as a function of growth rate, which can change
depending on the growth conditions. Perturbations of translation reveal that bacteria
employ a compensatory strategy in which the reduced translation capability results
in increased expression of the translation machinery.\r\nPerturbations of translation
are achieved in various ways; clinically interesting is the application of translation-targeting
antibiotics – translation inhibitors. The antibiotic effects on bacterial physiology
are often poorly understood. Bacterial responses to two or more simultaneously
applied antibiotics are even more puzzling. The combined antibiotic effect determines
the type of drug interaction, which ranges from synergy (the effect is stronger
than expected) to antagonism (the effect is weaker) and suppression (one of the
drugs loses its potency).\r\nIn the first part of this work, we systematically
measure the pairwise interaction network for translation inhibitors that interfere
with different steps in translation. We find that the interactions are surprisingly
diverse and tend to be more antagonistic. To explore the underlying mechanisms,
we begin with a minimal biophysical model of combined antibiotic action. We base
this model on the kinetics of antibiotic uptake and binding together with the
physiological response described by the growth laws. The biophysical model explains
some drug interactions, but not all; it specifically fails to predict suppression.\r\nIn
the second part of this work, we hypothesize that elusive suppressive drug interactions
result from the interplay between ribosomes halted in different stages of translation.
To elucidate this putative mechanism of drug interactions between translation
inhibitors, we generate translation bottlenecks genetically using in- ducible
control of translation factors that regulate well-defined translation cycle steps.
These perturbations accurately mimic antibiotic action and drug interactions,
supporting that the interplay of different translation bottlenecks partially causes
these interactions.\r\nWe extend this approach by varying two translation bottlenecks
simultaneously. This approach reveals the suppression of translocation inhibition
by inhibited translation. We rationalize this effect by modeling dense traffic
of ribosomes that move on transcripts in a translation factor-mediated manner.
This model predicts a dissolution of traffic jams caused by inhibited translocation
when the density of ribosome traffic is reduced by lowered initiation. We base
this model on the growth laws and quantitative relationships between different
translation and growth parameters.\r\nIn the final part of this work, we describe
a set of tools aimed at quantification of physiological and translation parameters.
We further develop a simple model that directly connects the abundance of a translation
factor with the growth rate, which allows us to extract physiological parameters
describing initiation. We demonstrate the development of tools for measuring translation
rate.\r\nThis thesis showcases how a combination of high-throughput growth rate
mea- surements, genetics, and modeling can reveal mechanisms of drug interactions.
Furthermore, by a gradual transition from combinations of antibiotics to precise
genetic interventions, we demonstrated the equivalency between genetic and chemi-
cal perturbations of translation. These findings tile the path for quantitative
studies of antibiotic combinations and illustrate future approaches towards the
quantitative description of translation."
acknowledged_ssus:
- _id: LifeSc
- _id: M-Shop
acknowledgement: I thank Life Science Facilities for their continuous support with
providing top-notch laboratory materials, keeping the devices humming, and coordinating
the repairs and building of custom-designed laboratory equipment with the MIBA Machine
shop.
alternative_title:
- ISTA Thesis
article_processing_charge: No
author:
- first_name: Bor
full_name: Kavcic, Bor
id: 350F91D2-F248-11E8-B48F-1D18A9856A87
last_name: Kavcic
orcid: 0000-0001-6041-254X
citation:
ama: 'Kavcic B. Perturbations of protein synthesis: from antibiotics to genetics
and physiology. 2020. doi:10.15479/AT:ISTA:8657'
apa: 'Kavcic, B. (2020). Perturbations of protein synthesis: from antibiotics
to genetics and physiology. Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:8657'
chicago: 'Kavcic, Bor. “Perturbations of Protein Synthesis: From Antibiotics to
Genetics and Physiology.” Institute of Science and Technology Austria, 2020. https://doi.org/10.15479/AT:ISTA:8657.'
ieee: 'B. Kavcic, “Perturbations of protein synthesis: from antibiotics to genetics
and physiology,” Institute of Science and Technology Austria, 2020.'
ista: 'Kavcic B. 2020. Perturbations of protein synthesis: from antibiotics to genetics
and physiology. Institute of Science and Technology Austria.'
mla: 'Kavcic, Bor. Perturbations of Protein Synthesis: From Antibiotics to Genetics
and Physiology. Institute of Science and Technology Austria, 2020, doi:10.15479/AT:ISTA:8657.'
short: 'B. Kavcic, Perturbations of Protein Synthesis: From Antibiotics to Genetics
and Physiology, Institute of Science and Technology Austria, 2020.'
date_created: 2020-10-13T16:46:14Z
date_published: 2020-10-14T00:00:00Z
date_updated: 2023-09-07T13:20:48Z
day: '14'
ddc:
- '571'
- '530'
- '570'
degree_awarded: PhD
department:
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doi: 10.15479/AT:ISTA:8657
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date_updated: 2021-10-07T22:30:03Z
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file_date_updated: 2021-10-07T22:30:03Z
has_accepted_license: '1'
language:
- iso: eng
month: '10'
oa: 1
oa_version: Published Version
page: '271'
publication_identifier:
isbn:
- 978-3-99078-011-4
issn:
- 2663-337X
publication_status: published
publisher: Institute of Science and Technology Austria
related_material:
record:
- id: '7673'
relation: part_of_dissertation
status: public
- id: '8250'
relation: part_of_dissertation
status: public
status: public
supervisor:
- first_name: Gašper
full_name: Tkačik, Gašper
id: 3D494DCA-F248-11E8-B48F-1D18A9856A87
last_name: Tkačik
orcid: 0000-0002-6699-1455
- first_name: Mark Tobias
full_name: Bollenbach, Mark Tobias
id: 3E6DB97A-F248-11E8-B48F-1D18A9856A87
last_name: Bollenbach
orcid: 0000-0003-4398-476X
title: 'Perturbations of protein synthesis: from antibiotics to genetics and physiology'
type: dissertation
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
year: '2020'
...
---
_id: '7473'
abstract:
- lang: eng
text: How structural and functional properties of synapses relate to each other
is a fundamental question in neuroscience. Electrophysiology has elucidated mechanisms
of synaptic transmission, and electron microscopy (EM) has provided insight into
morphological properties of synapses. Here we describe an enhanced method for
functional EM (“flash and freeze”), combining optogenetic stimulation with high-pressure
freezing. We demonstrate that the improved method can be applied to intact networks
in acute brain slices and organotypic slice cultures from mice. As a proof of
concept, we probed vesicle pool changes during synaptic transmission at the hippocampal
mossy fiber-CA3 pyramidal neuron synapse. Our findings show overlap of the docked
vesicle pool and the functionally defined readily releasable pool and provide
evidence of fast endocytosis at this synapse. Functional EM with acute slices
and slice cultures has the potential to reveal the structural and functional mechanisms
of transmission in intact, genetically perturbed, and disease-affected synapses.
acknowledgement: This project has received funding from the European Research Council
(ERC) and European Commission (EC), under the European Union’s Horizon 2020 research
and innovation programme (ERC grant agreement No. 692692 and Marie Sklodowska-Curie
708497) and from Fonds zur Förderung der Wissenschaftlichen Forschung (Z 312-B27
Wittgenstein award and DK W1205-B09). We thank Johann Danzl and Ryuichi Shigemoto
for critically reading the manuscript; Walter Kaufmann, Daniel Gutl, and Vanessa
Zheden for extensive EM training, advice, and experimental assistance; Benjamin
Suter for substantial help with light stimulation, ImageJ plugins for analysis,
and manuscript editing; Florian Marr and Christina Altmutter for technical support;
Eleftheria Kralli-Beller for manuscript editing; Julia König and Paul Wurzinger
(Leica Microsystems) for helpful technical discussions; and Taija Makinen for providing
the Prox1-CreERT2 mouse line.
article_processing_charge: No
article_type: original
author:
- first_name: Carolina
full_name: Borges Merjane, Carolina
id: 4305C450-F248-11E8-B48F-1D18A9856A87
last_name: Borges Merjane
orcid: 0000-0003-0005-401X
- first_name: Olena
full_name: Kim, Olena
id: 3F8ABDDA-F248-11E8-B48F-1D18A9856A87
last_name: Kim
- first_name: Peter M
full_name: Jonas, Peter M
id: 353C1B58-F248-11E8-B48F-1D18A9856A87
last_name: Jonas
orcid: 0000-0001-5001-4804
citation:
ama: Borges Merjane C, Kim O, Jonas PM. Functional electron microscopy (“Flash and
Freeze”) of identified cortical synapses in acute brain slices. Neuron.
2020;105:992-1006. doi:10.1016/j.neuron.2019.12.022
apa: Borges Merjane, C., Kim, O., & Jonas, P. M. (2020). Functional electron
microscopy (“Flash and Freeze”) of identified cortical synapses in acute brain
slices. Neuron. Elsevier. https://doi.org/10.1016/j.neuron.2019.12.022
chicago: Borges Merjane, Carolina, Olena Kim, and Peter M Jonas. “Functional Electron
Microscopy (‘Flash and Freeze’) of Identified Cortical Synapses in Acute Brain
Slices.” Neuron. Elsevier, 2020. https://doi.org/10.1016/j.neuron.2019.12.022.
ieee: C. Borges Merjane, O. Kim, and P. M. Jonas, “Functional electron microscopy
(‘Flash and Freeze’) of identified cortical synapses in acute brain slices,” Neuron,
vol. 105. Elsevier, pp. 992–1006, 2020.
ista: Borges Merjane C, Kim O, Jonas PM. 2020. Functional electron microscopy (“Flash
and Freeze”) of identified cortical synapses in acute brain slices. Neuron. 105,
992–1006.
mla: Borges Merjane, Carolina, et al. “Functional Electron Microscopy (‘Flash and
Freeze’) of Identified Cortical Synapses in Acute Brain Slices.” Neuron,
vol. 105, Elsevier, 2020, pp. 992–1006, doi:10.1016/j.neuron.2019.12.022.
short: C. Borges Merjane, O. Kim, P.M. Jonas, Neuron 105 (2020) 992–1006.
date_created: 2020-02-10T15:59:45Z
date_published: 2020-03-18T00:00:00Z
date_updated: 2024-03-27T23:30:07Z
day: '18'
ddc:
- '570'
department:
- _id: PeJo
doi: 10.1016/j.neuron.2019.12.022
ec_funded: 1
external_id:
isi:
- '000520854700008'
pmid:
- '31928842'
file:
- access_level: open_access
checksum: 3582664addf26859e86ac5bec3e01416
content_type: application/pdf
creator: dernst
date_created: 2020-11-20T08:58:53Z
date_updated: 2020-11-20T08:58:53Z
file_id: '8778'
file_name: 2020_Neuron_BorgesMerjane.pdf
file_size: 9712957
relation: main_file
success: 1
file_date_updated: 2020-11-20T08:58:53Z
has_accepted_license: '1'
intvolume: ' 105'
isi: 1
language:
- iso: eng
month: '03'
oa: 1
oa_version: Published Version
page: 992-1006
pmid: 1
project:
- _id: 25B7EB9E-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '692692'
name: Biophysics and circuit function of a giant cortical glumatergic synapse
- _id: 25BAF7B2-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '708497'
name: Presynaptic calcium channels distribution and impact on coupling at the hippocampal
mossy fiber synapse
- _id: 25C5A090-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: Z00312
name: The Wittgenstein Prize
- _id: 25C3DBB6-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: W01205
name: Zellkommunikation in Gesundheit und Krankheit
publication: Neuron
publication_identifier:
issn:
- 0896-6273
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/flash-and-freeze-reveals-dynamics-of-nerve-connections/
record:
- id: '11196'
relation: dissertation_contains
status: public
scopus_import: '1'
status: public
title: Functional electron microscopy (“Flash and Freeze”) of identified cortical
synapses in acute brain slices
tmp:
image: /images/cc_by_nc_nd.png
legal_code_url: https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode
name: Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International
(CC BY-NC-ND 4.0)
short: CC BY-NC-ND (4.0)
type: journal_article
user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
volume: 105
year: '2020'
...
---
_id: '8250'
abstract:
- lang: eng
text: 'Antibiotics that interfere with translation, when combined, interact in diverse
and difficult-to-predict ways. Here, we explain these interactions by “translation
bottlenecks”: points in the translation cycle where antibiotics block ribosomal
progression. To elucidate the underlying mechanisms of drug interactions between
translation inhibitors, we generate translation bottlenecks genetically using
inducible control of translation factors that regulate well-defined translation
cycle steps. These perturbations accurately mimic antibiotic action and drug interactions,
supporting that the interplay of different translation bottlenecks causes these
interactions. We further show that growth laws, combined with drug uptake and
binding kinetics, enable the direct prediction of a large fraction of observed
interactions, yet fail to predict suppression. However, varying two translation
bottlenecks simultaneously supports that dense traffic of ribosomes and competition
for translation factors account for the previously unexplained suppression. These
results highlight the importance of “continuous epistasis” in bacterial physiology.'
acknowledgement: "We thank M. Hennessey-Wesen, I. Tomanek, K. Jain, A. Staron, K.
Tomasek, M. Scott,\r\nK.C. Huang, and Z. Gitai for reading the manuscript and constructive
comments. B.K. is\r\nindebted to C. Guet for additional guidance and generous support,
which rendered this\r\nwork possible. B.K. thanks all members of Guet group for
many helpful discussions and\r\nsharing of resources. B.K. additionally acknowledges
the tremendous support from A.\r\nAngermayr and K. Mitosch with experimental work.
We further thank E. Brown for\r\nhelpful comments regarding lamotrigine, and A.
Buskirk for valuable suggestions\r\nregarding the ribosome footprint size. This
work was supported in part by Austrian\r\nScience Fund (FWF) standalone grants P
27201-B22 (to T.B.) and P 28844 (to G.T.),\r\nHFSP program Grant RGP0042/2013 (to
T.B.), German Research Foundation (DFG)\r\nstandalone grant BO 3502/2-1 (to T.B.),
and German Research Foundation (DFG)\r\nCollaborative Research Centre (SFB) 1310
(to T.B.). Open access funding provided by\r\nProjekt DEAL."
article_number: '4013'
article_processing_charge: No
article_type: original
author:
- first_name: Bor
full_name: Kavcic, Bor
id: 350F91D2-F248-11E8-B48F-1D18A9856A87
last_name: Kavcic
orcid: 0000-0001-6041-254X
- first_name: Gašper
full_name: Tkačik, Gašper
id: 3D494DCA-F248-11E8-B48F-1D18A9856A87
last_name: Tkačik
orcid: 0000-0002-6699-1455
- first_name: Tobias
full_name: Bollenbach, Tobias
id: 3E6DB97A-F248-11E8-B48F-1D18A9856A87
last_name: Bollenbach
orcid: 0000-0003-4398-476X
citation:
ama: Kavcic B, Tkačik G, Bollenbach MT. Mechanisms of drug interactions between
translation-inhibiting antibiotics. Nature Communications. 2020;11. doi:10.1038/s41467-020-17734-z
apa: Kavcic, B., Tkačik, G., & Bollenbach, M. T. (2020). Mechanisms of drug
interactions between translation-inhibiting antibiotics. Nature Communications.
Springer Nature. https://doi.org/10.1038/s41467-020-17734-z
chicago: Kavcic, Bor, Gašper Tkačik, and Mark Tobias Bollenbach. “Mechanisms of
Drug Interactions between Translation-Inhibiting Antibiotics.” Nature Communications.
Springer Nature, 2020. https://doi.org/10.1038/s41467-020-17734-z.
ieee: B. Kavcic, G. Tkačik, and M. T. Bollenbach, “Mechanisms of drug interactions
between translation-inhibiting antibiotics,” Nature Communications, vol.
11. Springer Nature, 2020.
ista: Kavcic B, Tkačik G, Bollenbach MT. 2020. Mechanisms of drug interactions between
translation-inhibiting antibiotics. Nature Communications. 11, 4013.
mla: Kavcic, Bor, et al. “Mechanisms of Drug Interactions between Translation-Inhibiting
Antibiotics.” Nature Communications, vol. 11, 4013, Springer Nature, 2020,
doi:10.1038/s41467-020-17734-z.
short: B. Kavcic, G. Tkačik, M.T. Bollenbach, Nature Communications 11 (2020).
date_created: 2020-08-12T09:13:50Z
date_published: 2020-08-11T00:00:00Z
date_updated: 2024-03-27T23:30:08Z
day: '11'
ddc:
- '570'
department:
- _id: GaTk
doi: 10.1038/s41467-020-17734-z
external_id:
isi:
- '000562769300008'
file:
- access_level: open_access
checksum: 986bebb308850a55850028d3d2b5b664
content_type: application/pdf
creator: dernst
date_created: 2020-08-17T07:36:57Z
date_updated: 2020-08-17T07:36:57Z
file_id: '8275'
file_name: 2020_NatureComm_Kavcic.pdf
file_size: 1965672
relation: main_file
success: 1
file_date_updated: 2020-08-17T07:36:57Z
has_accepted_license: '1'
intvolume: ' 11'
isi: 1
language:
- iso: eng
month: '08'
oa: 1
oa_version: Published Version
project:
- _id: 25E9AF9E-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: P27201-B22
name: Revealing the mechanisms underlying drug interactions
- _id: 254E9036-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: P28844-B27
name: Biophysics of information processing in gene regulation
publication: Nature Communications
publication_identifier:
issn:
- 2041-1723
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
related_material:
record:
- id: '8657'
relation: dissertation_contains
status: public
status: public
title: Mechanisms of drug interactions between translation-inhibiting antibiotics
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: journal_article
user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
volume: 11
year: '2020'
...
---
_id: '7673'
abstract:
- lang: eng
text: Combining drugs can improve the efficacy of treatments. However, predicting
the effect of drug combinations is still challenging. The combined potency of
drugs determines the drug interaction, which is classified as synergistic, additive,
antagonistic, or suppressive. While probabilistic, non-mechanistic models exist,
there is currently no biophysical model that can predict antibiotic interactions.
Here, we present a physiologically relevant model of the combined action of antibiotics
that inhibit protein synthesis by targeting the ribosome. This model captures
the kinetics of antibiotic binding and transport, and uses bacterial growth laws
to predict growth in the presence of antibiotic combinations. We find that this
biophysical model can produce all drug interaction types except suppression. We
show analytically that antibiotics which cannot bind to the ribosome simultaneously
generally act as substitutes for one another, leading to additive drug interactions.
Previously proposed null expectations for higher-order drug interactions follow
as a limiting case of our model. We further extend the model to include the effects
of direct physical or allosteric interactions between individual drugs on the
ribosome. Notably, such direct interactions profoundly change the combined drug
effect, depending on the kinetic parameters of the drugs used. The model makes
additional predictions for the effects of resistance genes on drug interactions
and for interactions between ribosome-targeting antibiotics and antibiotics with
other targets. These findings enhance our understanding of the interplay between
drug action and cell physiology and are a key step toward a general framework
for predicting drug interactions.
article_processing_charge: No
author:
- first_name: Bor
full_name: Kavcic, Bor
id: 350F91D2-F248-11E8-B48F-1D18A9856A87
last_name: Kavcic
orcid: 0000-0001-6041-254X
- first_name: Gašper
full_name: Tkačik, Gašper
id: 3D494DCA-F248-11E8-B48F-1D18A9856A87
last_name: Tkačik
orcid: 0000-0002-6699-1455
- first_name: Tobias
full_name: Bollenbach, Tobias
id: 3E6DB97A-F248-11E8-B48F-1D18A9856A87
last_name: Bollenbach
orcid: 0000-0003-4398-476X
citation:
ama: Kavcic B, Tkačik G, Bollenbach MT. A minimal biophysical model of combined
antibiotic action. bioRxiv. 2020. doi:10.1101/2020.04.18.047886
apa: Kavcic, B., Tkačik, G., & Bollenbach, M. T. (2020). A minimal biophysical
model of combined antibiotic action. bioRxiv. Cold Spring Harbor Laboratory.
https://doi.org/10.1101/2020.04.18.047886
chicago: Kavcic, Bor, Gašper Tkačik, and Mark Tobias Bollenbach. “A Minimal Biophysical
Model of Combined Antibiotic Action.” BioRxiv. Cold Spring Harbor Laboratory,
2020. https://doi.org/10.1101/2020.04.18.047886.
ieee: B. Kavcic, G. Tkačik, and M. T. Bollenbach, “A minimal biophysical model of
combined antibiotic action,” bioRxiv. Cold Spring Harbor Laboratory, 2020.
ista: Kavcic B, Tkačik G, Bollenbach MT. 2020. A minimal biophysical model of combined
antibiotic action. bioRxiv, 10.1101/2020.04.18.047886.
mla: Kavcic, Bor, et al. “A Minimal Biophysical Model of Combined Antibiotic Action.”
BioRxiv, Cold Spring Harbor Laboratory, 2020, doi:10.1101/2020.04.18.047886.
short: B. Kavcic, G. Tkačik, M.T. Bollenbach, BioRxiv (2020).
date_created: 2020-04-22T08:27:56Z
date_published: 2020-04-18T00:00:00Z
date_updated: 2024-03-27T23:30:08Z
day: '18'
department:
- _id: GaTk
doi: 10.1101/2020.04.18.047886
language:
- iso: eng
main_file_link:
- open_access: '1'
url: 'https://doi.org/10.1101/2020.04.18.047886 '
month: '04'
oa: 1
oa_version: Preprint
project:
- _id: 25E9AF9E-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: P27201-B22
name: Revealing the mechanisms underlying drug interactions
- _id: 254E9036-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: P28844-B27
name: Biophysics of information processing in gene regulation
publication: bioRxiv
publication_status: published
publisher: Cold Spring Harbor Laboratory
related_material:
record:
- id: '8997'
relation: later_version
status: public
- id: '8657'
relation: dissertation_contains
status: public
status: public
title: A minimal biophysical model of combined antibiotic action
type: preprint
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
year: '2020'
...
---
_id: '8002'
abstract:
- lang: eng
text: Wound healing in plant tissues, consisting of rigid cell wall-encapsulated
cells, represents a considerable challenge and occurs through largely unknown
mechanisms distinct from those in animals. Owing to their inability to migrate,
plant cells rely on targeted cell division and expansion to regenerate wounds.
Strict coordination of these wound-induced responses is essential to ensure efficient,
spatially restricted wound healing. Single-cell tracking by live imaging allowed
us to gain mechanistic insight into the wound perception and coordination of wound
responses after laser-based wounding in Arabidopsis root. We revealed a crucial
contribution of the collapse of damaged cells in wound perception and detected
an auxin increase specific to cells immediately adjacent to the wound. This localized
auxin increase balances wound-induced cell expansion and restorative division
rates in a dose-dependent manner, leading to tumorous overproliferation when the
canonical TIR1 auxin signaling is disrupted. Auxin and wound-induced turgor pressure
changes together also spatially define the activation of key components of regeneration,
such as the transcription regulator ERF115. Our observations suggest that the
wound signaling involves the sensing of collapse of damaged cells and a local
auxin signaling activation to coordinate the downstream transcriptional responses
in the immediate wound vicinity.
acknowledged_ssus:
- _id: Bio
- _id: LifeSc
article_number: '202003346'
article_processing_charge: No
article_type: original
author:
- first_name: Lukas
full_name: Hörmayer, Lukas
id: 2EEE7A2A-F248-11E8-B48F-1D18A9856A87
last_name: Hörmayer
orcid: 0000-0001-8295-2926
- first_name: Juan C
full_name: Montesinos López, Juan C
id: 310A8E3E-F248-11E8-B48F-1D18A9856A87
last_name: Montesinos López
orcid: 0000-0001-9179-6099
- first_name: Petra
full_name: Marhavá, Petra
id: 44E59624-F248-11E8-B48F-1D18A9856A87
last_name: Marhavá
- first_name: Eva
full_name: Benková, Eva
id: 38F4F166-F248-11E8-B48F-1D18A9856A87
last_name: Benková
orcid: 0000-0002-8510-9739
- first_name: Saiko
full_name: Yoshida, Saiko
id: 2E46069C-F248-11E8-B48F-1D18A9856A87
last_name: Yoshida
- first_name: Jiří
full_name: Friml, Jiří
id: 4159519E-F248-11E8-B48F-1D18A9856A87
last_name: Friml
orcid: 0000-0002-8302-7596
citation:
ama: Hörmayer L, Montesinos López JC, Marhavá P, Benková E, Yoshida S, Friml J.
Wounding-induced changes in cellular pressure and localized auxin signalling spatially
coordinate restorative divisions in roots. Proceedings of the National Academy
of Sciences. 2020;117(26). doi:10.1073/pnas.2003346117
apa: Hörmayer, L., Montesinos López, J. C., Marhavá, P., Benková, E., Yoshida, S.,
& Friml, J. (2020). Wounding-induced changes in cellular pressure and localized
auxin signalling spatially coordinate restorative divisions in roots. Proceedings
of the National Academy of Sciences. Proceedings of the National Academy of
Sciences. https://doi.org/10.1073/pnas.2003346117
chicago: Hörmayer, Lukas, Juan C Montesinos López, Petra Marhavá, Eva Benková, Saiko
Yoshida, and Jiří Friml. “Wounding-Induced Changes in Cellular Pressure and Localized
Auxin Signalling Spatially Coordinate Restorative Divisions in Roots.” Proceedings
of the National Academy of Sciences. Proceedings of the National Academy of
Sciences, 2020. https://doi.org/10.1073/pnas.2003346117.
ieee: L. Hörmayer, J. C. Montesinos López, P. Marhavá, E. Benková, S. Yoshida, and
J. Friml, “Wounding-induced changes in cellular pressure and localized auxin signalling
spatially coordinate restorative divisions in roots,” Proceedings of the National
Academy of Sciences, vol. 117, no. 26. Proceedings of the National Academy
of Sciences, 2020.
ista: Hörmayer L, Montesinos López JC, Marhavá P, Benková E, Yoshida S, Friml J.
2020. Wounding-induced changes in cellular pressure and localized auxin signalling
spatially coordinate restorative divisions in roots. Proceedings of the National
Academy of Sciences. 117(26), 202003346.
mla: Hörmayer, Lukas, et al. “Wounding-Induced Changes in Cellular Pressure and
Localized Auxin Signalling Spatially Coordinate Restorative Divisions in Roots.”
Proceedings of the National Academy of Sciences, vol. 117, no. 26, 202003346,
Proceedings of the National Academy of Sciences, 2020, doi:10.1073/pnas.2003346117.
short: L. Hörmayer, J.C. Montesinos López, P. Marhavá, E. Benková, S. Yoshida, J.
Friml, Proceedings of the National Academy of Sciences 117 (2020).
date_created: 2020-06-22T13:33:52Z
date_published: 2020-06-30T00:00:00Z
date_updated: 2024-03-27T23:30:11Z
day: '30'
ddc:
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department:
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- _id: EvBe
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issue: '26'
language:
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month: '06'
oa: 1
oa_version: None
pmid: 1
project:
- _id: 261099A6-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '742985'
name: Tracing Evolution of Auxin Transport and Polarity in Plants
- _id: 262EF96E-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: P29988
name: RNA-directed DNA methylation in plant development
publication: Proceedings of the National Academy of Sciences
publication_identifier:
eissn:
- 1091-6490
issn:
- 0027-8424
publication_status: published
publisher: Proceedings of the National Academy of Sciences
quality_controlled: '1'
related_material:
link:
- description: News on IST Homepage
relation: press_release
url: https://ist.ac.at/en/news/how-wounded-plants-coordinate-their-healing/
record:
- id: '9992'
relation: dissertation_contains
status: public
scopus_import: '1'
status: public
title: Wounding-induced changes in cellular pressure and localized auxin signalling
spatially coordinate restorative divisions in roots
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: c635000d-4b10-11ee-a964-aac5a93f6ac1
volume: 117
year: '2020'
...
---
_id: '7680'
abstract:
- lang: eng
text: "Proteins and their complex dynamic interactions regulate cellular mechanisms
from sensing and transducing extracellular signals, to mediating genetic responses,
and sustaining or changing cell morphology. To manipulate these protein-protein
interactions (PPIs) that govern the behavior and fate of cells, synthetically
constructed, genetically encoded tools provide the means to precisely target proteins
of interest (POIs), and control their subcellular localization and activity in
vitro and in vivo. Ideal synthetic tools react to an orthogonal cue, i.e. a trigger
that does not activate any other endogenous process, thereby allowing manipulation
of the POI alone.\r\nIn optogenetics, naturally occurring photosensory domain
from plants, algae and bacteria are re-purposed and genetically fused to POIs.
Illumination with light of a specific wavelength triggers a conformational change
that can mediate PPIs, such as dimerization or oligomerization. By using light
as a trigger, these tools can be activated with high spatial and temporal precision,
on subcellular and millisecond scales. Chemogenetic tools consist of protein domains
that recognize and bind small molecules. By genetic fusion to POIs, these domains
can mediate PPIs upon addition of their specific ligands, which are often synthetically
designed to provide highly specific interactions and exhibit good bioavailability.\r\nMost
optogenetic tools to mediate PPIs are based on well-studied photoreceptors responding
to red, blue or near-UV light, leaving a striking gap in the green band of the
visible light spectrum. Among both optogenetic and chemogenetic tools, there is
an abundance of methods to induce PPIs, but tools to disrupt them require UV illumination,
rely on covalent linkage and subsequent enzymatic cleavage or initially result
in protein clustering of unknown stoichiometry.\r\nThis work describes how the
recently structurally and photochemically characterized green-light responsive
cobalamin-binding domains (CBDs) from bacterial transcription factors were re-purposed
to function as a green-light responsive optogenetic tool. In contrast to previously
engineered optogenetic tools, CBDs do not induce PPI, but rather confer a PPI
already upon expression, which can be rapidly disrupted by illumination. This
was employed to mimic inhibition of constitutive activity of a growth factor receptor,
and successfully implement for cell signalling in mammalian cells and in vivo
to rescue development in zebrafish. This work further describes the development
and application of a chemically induced de-dimerizer (CDD) based on a recently
identified and structurally described bacterial oxyreductase. CDD forms a dimer
upon expression in absence of its cofactor, the flavin derivative F420. Safety
and of domain expression and ligand exposure are demonstrated in vitro and in
vivo in zebrafish. The system is further applied to inhibit cell signalling output
from a chimeric receptor upon F420 treatment.\r\nCBDs and CDD expand the repertoire
of synthetic tools by providing novel mechanisms of mediating PPIs, and by recognizing
previously not utilized cues. In the future, they can readily be combined with
existing synthetic tools to functionally manipulate PPIs in vitro and in vivo."
alternative_title:
- ISTA Thesis
article_processing_charge: No
author:
- first_name: Stephanie
full_name: Kainrath, Stephanie
id: 32CFBA64-F248-11E8-B48F-1D18A9856A87
last_name: Kainrath
citation:
ama: Kainrath S. Synthetic tools for optogenetic and chemogenetic inhibition of
cellular signals. 2020. doi:10.15479/AT:ISTA:7680
apa: Kainrath, S. (2020). Synthetic tools for optogenetic and chemogenetic inhibition
of cellular signals. Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:7680
chicago: Kainrath, Stephanie. “Synthetic Tools for Optogenetic and Chemogenetic
Inhibition of Cellular Signals.” Institute of Science and Technology Austria,
2020. https://doi.org/10.15479/AT:ISTA:7680.
ieee: S. Kainrath, “Synthetic tools for optogenetic and chemogenetic inhibition
of cellular signals,” Institute of Science and Technology Austria, 2020.
ista: Kainrath S. 2020. Synthetic tools for optogenetic and chemogenetic inhibition
of cellular signals. Institute of Science and Technology Austria.
mla: Kainrath, Stephanie. Synthetic Tools for Optogenetic and Chemogenetic Inhibition
of Cellular Signals. Institute of Science and Technology Austria, 2020, doi:10.15479/AT:ISTA:7680.
short: S. Kainrath, Synthetic Tools for Optogenetic and Chemogenetic Inhibition
of Cellular Signals, Institute of Science and Technology Austria, 2020.
date_created: 2020-04-24T16:00:51Z
date_published: 2020-04-24T00:00:00Z
date_updated: 2023-09-22T09:20:10Z
day: '24'
ddc:
- '570'
degree_awarded: PhD
department:
- _id: CaGu
doi: 10.15479/AT:ISTA:7680
file:
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checksum: fb9a4468eb27be92690728e35c823796
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date_updated: 2021-10-31T23:30:05Z
embargo: 2021-10-30
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date_updated: 2021-10-31T23:30:05Z
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file_size: 5167703
relation: source_file
file_date_updated: 2021-10-31T23:30:05Z
has_accepted_license: '1'
language:
- iso: eng
month: '04'
oa: 1
oa_version: None
page: '98'
publication_identifier:
eissn:
- 2663-337X
publication_status: published
publisher: Institute of Science and Technology Austria
related_material:
record:
- id: '1028'
relation: dissertation_contains
status: public
status: public
supervisor:
- first_name: Harald L
full_name: Janovjak, Harald L
id: 33BA6C30-F248-11E8-B48F-1D18A9856A87
last_name: Janovjak
orcid: 0000-0002-8023-9315
title: Synthetic tools for optogenetic and chemogenetic inhibition of cellular signals
type: dissertation
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
year: '2020'
...