---
_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
corr_author: '1'
date_created: 2023-11-22T15:00:57Z
date_published: 2020-12-01T00:00:00Z
date_updated: 2025-06-12T07:35:28Z
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'
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: '14694'
abstract:
- lang: eng
text: We study the unique solution m of the Dyson equation \( -m(z)^{-1} = z\1 -
a + S[m(z)] \) on a von Neumann algebra A with the constraint Imm≥0. Here, z lies
in the complex upper half-plane, a is a self-adjoint element of A and S is a positivity-preserving
linear operator on A. We show that m is the Stieltjes transform of a compactly
supported A-valued measure on R. Under suitable assumptions, we establish that
this measure has a uniformly 1/3-Hölder continuous density with respect to the
Lebesgue measure, which is supported on finitely many intervals, called bands.
In fact, the density is analytic inside the bands with a square-root growth at
the edges and internal cubic root cusps whenever the gap between two bands vanishes.
The shape of these singularities is universal and no other singularity may occur.
We give a precise asymptotic description of m near the singular points. These
asymptotics generalize the analysis at the regular edges given in the companion
paper on the Tracy-Widom universality for the edge eigenvalue statistics for correlated
random matrices [the first author et al., Ann. Probab. 48, No. 2, 963--1001 (2020;
Zbl 1434.60017)] and they play a key role in the proof of the Pearcey universality
at the cusp for Wigner-type matrices [G. Cipolloni et al., Pure Appl. Anal. 1,
No. 4, 615--707 (2019; Zbl 07142203); the second author et al., Commun. Math.
Phys. 378, No. 2, 1203--1278 (2020; Zbl 07236118)]. We also extend the finite
dimensional band mass formula from [the first author et al., loc. cit.] to the
von Neumann algebra setting by showing that the spectral mass of the bands is
topologically rigid under deformations and we conclude that these masses are quantized
in some important cases.
article_processing_charge: Yes
article_type: original
arxiv: 1
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
citation:
ama: 'Alt J, Erdös L, Krüger TH. The Dyson equation with linear self-energy: Spectral
bands, edges and cusps. Documenta Mathematica. 2020;25:1421-1539. doi:10.4171/dm/780'
apa: 'Alt, J., Erdös, L., & Krüger, T. H. (2020). The Dyson equation with linear
self-energy: Spectral bands, edges and cusps. Documenta Mathematica. EMS
Press. https://doi.org/10.4171/dm/780'
chicago: 'Alt, Johannes, László Erdös, and Torben H Krüger. “The Dyson Equation
with Linear Self-Energy: Spectral Bands, Edges and Cusps.” Documenta Mathematica.
EMS Press, 2020. https://doi.org/10.4171/dm/780.'
ieee: 'J. Alt, L. Erdös, and T. H. Krüger, “The Dyson equation with linear self-energy:
Spectral bands, edges and cusps,” Documenta Mathematica, vol. 25. EMS Press,
pp. 1421–1539, 2020.'
ista: 'Alt J, Erdös L, Krüger TH. 2020. The Dyson equation with linear self-energy:
Spectral bands, edges and cusps. Documenta Mathematica. 25, 1421–1539.'
mla: 'Alt, Johannes, et al. “The Dyson Equation with Linear Self-Energy: Spectral
Bands, Edges and Cusps.” Documenta Mathematica, vol. 25, EMS Press, 2020,
pp. 1421–539, doi:10.4171/dm/780.'
short: J. Alt, L. Erdös, T.H. Krüger, Documenta Mathematica 25 (2020) 1421–1539.
corr_author: '1'
date_created: 2023-12-18T10:37:43Z
date_published: 2020-09-01T00:00:00Z
date_updated: 2025-04-15T08:05:00Z
day: '01'
ddc:
- '510'
department:
- _id: LaEr
doi: 10.4171/dm/780
external_id:
arxiv:
- '1804.07752'
file:
- access_level: open_access
checksum: 12aacc1d63b852ff9a51c1f6b218d4a6
content_type: application/pdf
creator: dernst
date_created: 2023-12-18T10:42:32Z
date_updated: 2023-12-18T10:42:32Z
file_id: '14695'
file_name: 2020_DocumentaMathematica_Alt.pdf
file_size: 1374708
relation: main_file
success: 1
file_date_updated: 2023-12-18T10:42:32Z
has_accepted_license: '1'
intvolume: ' 25'
keyword:
- General Mathematics
language:
- iso: eng
license: https://creativecommons.org/licenses/by/4.0/
month: '09'
oa: 1
oa_version: Published Version
page: 1421-1539
publication: Documenta Mathematica
publication_identifier:
eissn:
- 1431-0643
issn:
- 1431-0635
publication_status: published
publisher: EMS Press
quality_controlled: '1'
related_material:
record:
- id: '6183'
relation: earlier_version
status: public
status: public
title: 'The Dyson equation with linear self-energy: Spectral bands, edges and cusps'
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: 25
year: '2020'
...
---
_id: '14891'
abstract:
- lang: eng
text: We give the first mathematically rigorous justification of the local density
approximation in density functional theory. We provide a quantitative estimate
on the difference between the grand-canonical Levy–Lieb energy of a given density
(the lowest possible energy of all quantum states having this density) and the
integral over the uniform electron gas energy of this density. The error involves
gradient terms and justifies the use of the local density approximation in the
situation where the density is very flat on sufficiently large regions in space.
article_processing_charge: No
article_type: original
arxiv: 1
author:
- first_name: Mathieu
full_name: Lewin, Mathieu
last_name: Lewin
- first_name: Elliott H.
full_name: Lieb, Elliott H.
last_name: Lieb
- first_name: Robert
full_name: Seiringer, Robert
id: 4AFD0470-F248-11E8-B48F-1D18A9856A87
last_name: Seiringer
orcid: 0000-0002-6781-0521
citation:
ama: Lewin M, Lieb EH, Seiringer R. The local density approximation in density
functional theory. Pure and Applied Analysis. 2020;2(1):35-73. doi:10.2140/paa.2020.2.35
apa: Lewin, M., Lieb, E. H., & Seiringer, R. (2020). The local density approximation
in density functional theory. Pure and Applied Analysis. Mathematical Sciences
Publishers. https://doi.org/10.2140/paa.2020.2.35
chicago: Lewin, Mathieu, Elliott H. Lieb, and Robert Seiringer. “ The Local Density
Approximation in Density Functional Theory.” Pure and Applied Analysis.
Mathematical Sciences Publishers, 2020. https://doi.org/10.2140/paa.2020.2.35.
ieee: M. Lewin, E. H. Lieb, and R. Seiringer, “ The local density approximation
in density functional theory,” Pure and Applied Analysis, vol. 2, no. 1.
Mathematical Sciences Publishers, pp. 35–73, 2020.
ista: Lewin M, Lieb EH, Seiringer R. 2020. The local density approximation in density
functional theory. Pure and Applied Analysis. 2(1), 35–73.
mla: Lewin, Mathieu, et al. “ The Local Density Approximation in Density Functional
Theory.” Pure and Applied Analysis, vol. 2, no. 1, Mathematical Sciences
Publishers, 2020, pp. 35–73, doi:10.2140/paa.2020.2.35.
short: M. Lewin, E.H. Lieb, R. Seiringer, Pure and Applied Analysis 2 (2020) 35–73.
corr_author: '1'
date_created: 2024-01-28T23:01:44Z
date_published: 2020-01-01T00:00:00Z
date_updated: 2024-10-09T21:08:02Z
day: '01'
department:
- _id: RoSe
doi: 10.2140/paa.2020.2.35
external_id:
arxiv:
- '1903.04046'
intvolume: ' 2'
issue: '1'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.48550/arXiv.1903.04046
month: '01'
oa: 1
oa_version: Preprint
page: 35-73
publication: Pure and Applied Analysis
publication_identifier:
eissn:
- 2578-5885
issn:
- 2578-5893
publication_status: published
publisher: Mathematical Sciences Publishers
quality_controlled: '1'
scopus_import: '1'
status: public
title: ' The local density approximation in density functional theory'
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 2
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: 2026-06-18T17:44:49Z
day: '02'
ddc:
- '570'
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: '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: '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
arxiv: 1
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: 2025-04-15T06:30:08Z
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
license: https://creativecommons.org/licenses/by-nc/4.0/
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: '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: '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 of the United States of America. 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 of the United States of America. 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 of the United States of America.
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 of the United States of America, vol. 117, no. 36. 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 of the United States of America. 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 of the United States of America, vol. 117, no. 36, 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 of the United States of America 117 (2020)
22101–22112.
date_created: 2024-03-04T10:03:52Z
date_published: 2020-09-08T00:00:00Z
date_updated: 2026-06-18T17:45:21Z
day: '08'
ddc:
- '570'
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 of the United States
of America
publication_identifier:
eissn:
- 1091-6490
issn:
- 0027-8424
publication_status: published
publisher: National Academy of Sciences
quality_controlled: '1'
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: '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
arxiv: 1
author:
- first_name: Giorgio
full_name: Cipolloni, Giorgio
id: 42198EFA-F248-11E8-B48F-1D18A9856A87
last_name: Cipolloni
orcid: 0000-0002-4901-7992
- first_name: László
full_name: Erdös, László
id: 4DBD5372-F248-11E8-B48F-1D18A9856A87
last_name: Erdös
orcid: 0000-0001-5366-9603
- first_name: Dominik J
full_name: Schröder, Dominik J
id: 408ED176-F248-11E8-B48F-1D18A9856A87
last_name: Schröder
orcid: 0000-0002-2904-1856
citation:
ama: Cipolloni G, Erdös L, Schröder DJ. 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.
corr_author: '1'
date_created: 2024-03-04T10:27:57Z
date_published: 2020-11-16T00:00:00Z
date_updated: 2025-07-10T11:51:06Z
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:
- 2690-0998
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: '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: '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: '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
arxiv: 1
author:
- first_name: Dan-Adrian
full_name: Alistarh, Dan-Adrian
id: 4A899BFC-F248-11E8-B48F-1D18A9856A87
last_name: Alistarh
orcid: 0000-0003-3650-940X
- first_name: 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: 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: Automata, Languages and Programming'
start_date: 2020-07-08
corr_author: '1'
date_created: 2024-03-05T07:25:37Z
date_published: 2020-06-29T00:00:00Z
date_updated: 2025-07-10T11:55:11Z
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
license: https://creativecommons.org/licenses/by/3.0/
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
corr_author: '1'
date_created: 2024-03-05T08:57:17Z
date_published: 2020-04-01T00:00:00Z
date_updated: 2026-06-18T17:45:52Z
day: '01'
ddc:
- '000'
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: '15086'
abstract:
- lang: eng
text: "Many communication-efficient variants of SGD use gradient quantization schemes.
These schemes are often heuristic and fixed over the course of training. We empirically
observe that the statistics of gradients of deep models change during the training.
Motivated by this observation, we introduce two adaptive quantization schemes,
ALQ and AMQ. In both schemes, processors update their compression schemes in parallel
by efficiently computing sufficient statistics of a parametric distribution. We
improve the validation accuracy by almost 2% on CIFAR-10 and 1% on ImageNet in
challenging low-cost communication setups. Our adaptive methods are also significantly
more robust to the choice of hyperparameters.\r\n\r\n"
acknowledgement: "The authors would like to thank Blair Bilodeau, David Fleet, Mufan
Li, and Jeffrey Negrea for\r\nhelpful discussions. FF was supported by OGS Scholarship.
DA and IM were supported the\r\nEuropean Research Council (ERC) under the European
Union’s Horizon 2020 research and innovation\r\nprogramme (grant agreement No 805223
ScaleML). DMR was supported by an NSERC Discovery\r\nGrant. ARK was supported by
NSERC Postdoctoral Fellowship. Resources used in preparing this research were provided,
in part, by the Province of Ontario, the Government of Canada through CIFAR, and
companies sponsoring the Vector Institute."
alternative_title:
- NeurIPS
article_processing_charge: No
arxiv: 1
author:
- first_name: 'Fartash '
full_name: 'Faghri, Fartash '
last_name: Faghri
- first_name: 'Iman '
full_name: 'Tabrizian, Iman '
last_name: Tabrizian
- first_name: Ilia
full_name: Markov, Ilia
id: D0CF4148-C985-11E9-8066-0BDEE5697425
last_name: Markov
- 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: 'Daniel '
full_name: 'Roy, Daniel '
last_name: Roy
- first_name: 'Ali '
full_name: 'Ramezani-Kebrya, Ali '
last_name: Ramezani-Kebrya
citation:
ama: 'Faghri F, Tabrizian I, Markov I, Alistarh D-A, Roy D, Ramezani-Kebrya A. Adaptive
gradient quantization for data-parallel SGD. In: Advances in Neural Information
Processing Systems. Vol 33. Neural Information Processing Systems Foundation;
2020.'
apa: 'Faghri, F., Tabrizian, I., Markov, I., Alistarh, D.-A., Roy, D., & Ramezani-Kebrya,
A. (2020). Adaptive gradient quantization for data-parallel SGD. In Advances
in Neural Information Processing Systems (Vol. 33). Vancouver, Canada: Neural
Information Processing Systems Foundation.'
chicago: Faghri, Fartash , Iman Tabrizian, Ilia Markov, Dan-Adrian Alistarh, Daniel Roy,
and Ali Ramezani-Kebrya. “Adaptive Gradient Quantization for Data-Parallel SGD.”
In Advances in Neural Information Processing Systems, Vol. 33. Neural Information
Processing Systems Foundation, 2020.
ieee: F. Faghri, I. Tabrizian, I. Markov, D.-A. Alistarh, D. Roy, and A. Ramezani-Kebrya,
“Adaptive gradient quantization for data-parallel SGD,” in Advances in Neural
Information Processing Systems, Vancouver, Canada, 2020, vol. 33.
ista: 'Faghri F, Tabrizian I, Markov I, Alistarh D-A, Roy D, Ramezani-Kebrya A.
2020. Adaptive gradient quantization for data-parallel SGD. Advances in Neural
Information Processing Systems. NeurIPS: Neural Information Processing Systems,
NeurIPS, vol. 33.'
mla: Faghri, Fartash, et al. “Adaptive Gradient Quantization for Data-Parallel SGD.”
Advances in Neural Information Processing Systems, vol. 33, Neural Information
Processing Systems Foundation, 2020.
short: F. Faghri, I. Tabrizian, I. Markov, D.-A. Alistarh, D. Roy, A. Ramezani-Kebrya,
in:, Advances in Neural Information Processing Systems, Neural Information Processing
Systems Foundation, 2020.
conference:
end_date: 2020-12-12
location: Vancouver, Canada
name: 'NeurIPS: Neural Information Processing Systems'
start_date: 2020-12-06
date_created: 2024-03-06T08:35:58Z
date_published: 2020-12-10T00:00:00Z
date_updated: 2025-04-14T07:49:16Z
day: '10'
department:
- _id: DaAl
ec_funded: 1
external_id:
arxiv:
- '2010.12460'
intvolume: ' 33'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.48550/arXiv.2010.12460
month: '12'
oa: 1
oa_version: Preprint
project:
- _id: 268A44D6-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '805223'
name: Elastic Coordination for Scalable Machine Learning
publication: Advances in Neural Information Processing Systems
publication_identifier:
isbn:
- '9781713829546'
publication_status: published
publisher: Neural Information Processing Systems Foundation
quality_controlled: '1'
status: public
title: Adaptive gradient quantization for data-parallel SGD
type: conference
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 33
year: '2020'
...
---
_id: '15142'
abstract:
- lang: eng
text: Bacteria and archaea employ CRISPR (clustered, regularly, interspaced, short
palindromic repeats)-Cas (CRISPR-associated) systems as a type of adaptive immunity
to target and degrade foreign nucleic acids. While a myriad of CRISPR-Cas systems
have been identified to date, type I-C is one of the most commonly found subtypes
in nature. Interestingly, the type I-C system employs a minimal Cascade effector
complex, which encodes only three unique subunits in its operon. Here, we present
a 3.1 Å resolution cryo-EM structure of the Desulfovibrio vulgaris
type I-C Cascade, revealing the molecular mechanisms that underlie RNA-directed
complex assembly. We demonstrate how this minimal Cascade utilizes previously
overlooked, non-canonical small subunits to stabilize R-loop formation. Furthermore,
we describe putative PAM and Cas3 binding sites. These findings provide the structural
basis for harnessing the type I-C Cascade as a genome-engineering tool.
article_number: '5931'
article_processing_charge: Yes
article_type: original
author:
- first_name: Roisin E.
full_name: O’Brien, Roisin E.
last_name: O’Brien
- first_name: Inês C.
full_name: Santos, Inês C.
last_name: Santos
- first_name: Daniel
full_name: Wrapp, Daniel
last_name: Wrapp
- first_name: Jack Peter Kelly
full_name: Bravo, Jack Peter Kelly
id: 96aecfa5-8931-11ee-af30-aa6a5d6eee0e
last_name: Bravo
orcid: 0000-0003-0456-0753
- first_name: Evan A.
full_name: Schwartz, Evan A.
last_name: Schwartz
- first_name: Jennifer S.
full_name: Brodbelt, Jennifer S.
last_name: Brodbelt
- first_name: David W.
full_name: Taylor, David W.
last_name: Taylor
citation:
ama: O’Brien RE, Santos IC, Wrapp D, et al. Structural basis for assembly of non-canonical
small subunits into type I-C Cascade. Nature Communications. 2020;11. doi:10.1038/s41467-020-19785-8
apa: O’Brien, R. E., Santos, I. C., Wrapp, D., Bravo, J. P. K., Schwartz, E. A.,
Brodbelt, J. S., & Taylor, D. W. (2020). Structural basis for assembly of
non-canonical small subunits into type I-C Cascade. Nature Communications.
Springer Nature. https://doi.org/10.1038/s41467-020-19785-8
chicago: O’Brien, Roisin E., Inês C. Santos, Daniel Wrapp, Jack Peter Kelly Bravo,
Evan A. Schwartz, Jennifer S. Brodbelt, and David W. Taylor. “Structural Basis
for Assembly of Non-Canonical Small Subunits into Type I-C Cascade.” Nature
Communications. Springer Nature, 2020. https://doi.org/10.1038/s41467-020-19785-8.
ieee: R. E. O’Brien et al., “Structural basis for assembly of non-canonical
small subunits into type I-C Cascade,” Nature Communications, vol. 11.
Springer Nature, 2020.
ista: O’Brien RE, Santos IC, Wrapp D, Bravo JPK, Schwartz EA, Brodbelt JS, Taylor
DW. 2020. Structural basis for assembly of non-canonical small subunits into type
I-C Cascade. Nature Communications. 11, 5931.
mla: O’Brien, Roisin E., et al. “Structural Basis for Assembly of Non-Canonical
Small Subunits into Type I-C Cascade.” Nature Communications, vol. 11,
5931, Springer Nature, 2020, doi:10.1038/s41467-020-19785-8.
short: R.E. O’Brien, I.C. Santos, D. Wrapp, J.P.K. Bravo, E.A. Schwartz, J.S. Brodbelt,
D.W. Taylor, Nature Communications 11 (2020).
date_created: 2024-03-20T10:43:07Z
date_published: 2020-11-23T00:00:00Z
date_updated: 2024-06-04T05:52:51Z
day: '23'
doi: 10.1038/s41467-020-19785-8
extern: '1'
external_id:
pmid:
- '33230133'
intvolume: ' 11'
keyword:
- General Physics and Astronomy
- General Biochemistry
- Genetics and Molecular Biology
- General Chemistry
- Multidisciplinary
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.1038/s41467-020-19785-8
month: '11'
oa: 1
oa_version: Published Version
pmid: 1
publication: Nature Communications
publication_identifier:
issn:
- 2041-1723
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
scopus_import: '1'
status: public
title: Structural basis for assembly of non-canonical small subunits into type I-C
Cascade
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 11
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: '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: '15220'
abstract:
- lang: eng
text: 'A new window is opening in high-energy astronomy: X-ray polarimetry. With
many missions currently under development and scheduled to launch as early as
2021, observations of the X-ray polarization of accreting X-ray pulsars will soon
be available. As polarization is particularly sensitive to the geometry of the
emission region, the upcoming polarimeters will shed new light on the emission
mechanism of these objects, provided that we have sound theoretical models that
agree with current spectroscopic and timing observation and that can make predictions
of the polarization parameters of the emission. We here present a new model for
the polarized emission of accreting X-ray pulsars in the accretion column scenario
that for the first time takes into account the macroscopic structure and dynamics
of the accretion region and the propagation of the radiation towards the observer,
including relativistic beaming, gravitational lensing, and quantum electrodynamics.
In this paper, we present all the details of the model, while in a companion paper,
we apply our model to predict the polarization parameters of the bright X-ray
pulsar Hercules X-1.'
article_processing_charge: No
article_type: original
arxiv: 1
author:
- first_name: Ilaria
full_name: Caiazzo, Ilaria
id: 8ae5b6e7-2a03-11ee-914d-b58ed7a3b47d
last_name: Caiazzo
orcid: 0000-0002-4770-5388
- first_name: Jeremy
full_name: Heyl, Jeremy
last_name: Heyl
citation:
ama: Caiazzo I, Heyl J. Polarization of accreting X-ray pulsars. I. A new model.
Monthly Notices of the Royal Astronomical Society. 2020;501(1):109-128.
doi:10.1093/mnras/staa3428
apa: Caiazzo, I., & Heyl, J. (2020). Polarization of accreting X-ray pulsars.
I. A new model. Monthly Notices of the Royal Astronomical Society. Oxford
University Press. https://doi.org/10.1093/mnras/staa3428
chicago: Caiazzo, Ilaria, and Jeremy Heyl. “Polarization of Accreting X-Ray Pulsars.
I. A New Model.” Monthly Notices of the Royal Astronomical Society. Oxford
University Press, 2020. https://doi.org/10.1093/mnras/staa3428.
ieee: I. Caiazzo and J. Heyl, “Polarization of accreting X-ray pulsars. I. A new
model,” Monthly Notices of the Royal Astronomical Society, vol. 501, no.
1. Oxford University Press, pp. 109–128, 2020.
ista: Caiazzo I, Heyl J. 2020. Polarization of accreting X-ray pulsars. I. A new
model. Monthly Notices of the Royal Astronomical Society. 501(1), 109–128.
mla: Caiazzo, Ilaria, and Jeremy Heyl. “Polarization of Accreting X-Ray Pulsars.
I. A New Model.” Monthly Notices of the Royal Astronomical Society, vol.
501, no. 1, Oxford University Press, 2020, pp. 109–28, doi:10.1093/mnras/staa3428.
short: I. Caiazzo, J. Heyl, Monthly Notices of the Royal Astronomical Society 501
(2020) 109–128.
date_created: 2024-03-26T10:33:43Z
date_published: 2020-11-05T00:00:00Z
date_updated: 2024-10-14T12:32:49Z
day: '05'
doi: 10.1093/mnras/staa3428
extern: '1'
external_id:
arxiv:
- '2009.00631'
intvolume: ' 501'
issue: '1'
keyword:
- Space and Planetary Science
- Astronomy and Astrophysics
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.48550/arXiv.2009.00631
month: '11'
oa: 1
oa_version: Preprint
page: 109-128
publication: Monthly Notices of the Royal Astronomical Society
publication_identifier:
eissn:
- 1365-2966
issn:
- 0035-8711
publication_status: published
publisher: Oxford University Press
quality_controlled: '1'
scopus_import: '1'
status: public
title: Polarization of accreting X-ray pulsars. I. A new model
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 501
year: '2020'
...
---
_id: '15221'
abstract:
- lang: eng
text: We employ our new model for the polarized emission of accreting X-ray pulsars
to describe the emission from the luminous X-ray pulsar Hercules X-1. In contrast
with previous works, our model predicts the polarization parameters independently
of spectral formation, and considers the structure and dynamics of the accretion
column, as well as the additional effects on propagation due to general relativity
and quantum electrodynamics. We find that our model can describe the observed
pulse fraction and the pulse shape of the main peak, as well as the modulation
of the cyclotron line with phase. We pick two geometries, assuming a single accretion
column or two columns at the magnetic poles, that can describe current observations
of pulse shape and cyclotron modulation with phase. Both models predict a high
polarization fraction, between 60 and 80 per cent in the 1–10 keV range, that
is phase and energy dependent, and that peaks at the same phase as the intensity.
The phase and energy dependence of the polarization fraction and of the polarization
angle can help discern between the different geometries.
article_processing_charge: No
article_type: original
arxiv: 1
author:
- first_name: Ilaria
full_name: Caiazzo, Ilaria
id: 8ae5b6e7-2a03-11ee-914d-b58ed7a3b47d
last_name: Caiazzo
orcid: 0000-0002-4770-5388
- first_name: Jeremy
full_name: Heyl, Jeremy
last_name: Heyl
citation:
ama: Caiazzo I, Heyl J. Polarization of accreting X-ray pulsars – II. Hercules X-1.
Monthly Notices of the Royal Astronomical Society. 2020;501(1):129-136.
doi:10.1093/mnras/staa3429
apa: Caiazzo, I., & Heyl, J. (2020). Polarization of accreting X-ray pulsars
– II. Hercules X-1. Monthly Notices of the Royal Astronomical Society.
Oxford University Press. https://doi.org/10.1093/mnras/staa3429
chicago: Caiazzo, Ilaria, and Jeremy Heyl. “Polarization of Accreting X-Ray Pulsars
– II. Hercules X-1.” Monthly Notices of the Royal Astronomical Society.
Oxford University Press, 2020. https://doi.org/10.1093/mnras/staa3429.
ieee: I. Caiazzo and J. Heyl, “Polarization of accreting X-ray pulsars – II. Hercules
X-1,” Monthly Notices of the Royal Astronomical Society, vol. 501, no.
1. Oxford University Press, pp. 129–136, 2020.
ista: Caiazzo I, Heyl J. 2020. Polarization of accreting X-ray pulsars – II. Hercules
X-1. Monthly Notices of the Royal Astronomical Society. 501(1), 129–136.
mla: Caiazzo, Ilaria, and Jeremy Heyl. “Polarization of Accreting X-Ray Pulsars
– II. Hercules X-1.” Monthly Notices of the Royal Astronomical Society,
vol. 501, no. 1, Oxford University Press, 2020, pp. 129–36, doi:10.1093/mnras/staa3429.
short: I. Caiazzo, J. Heyl, Monthly Notices of the Royal Astronomical Society 501
(2020) 129–136.
date_created: 2024-03-26T10:34:03Z
date_published: 2020-11-05T00:00:00Z
date_updated: 2024-10-14T12:32:58Z
day: '05'
doi: 10.1093/mnras/staa3429
extern: '1'
external_id:
arxiv:
- '2009.00634'
intvolume: ' 501'
issue: '1'
keyword:
- Space and Planetary Science
- Astronomy and Astrophysics
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.48550/arXiv.2009.00634
month: '11'
oa: 1
oa_version: Preprint
page: 129-136
publication: Monthly Notices of the Royal Astronomical Society
publication_identifier:
eissn:
- 1365-2966
issn:
- 0035-8711
publication_status: published
publisher: Oxford University Press
quality_controlled: '1'
scopus_import: '1'
status: public
title: Polarization of accreting X-ray pulsars – II. Hercules X-1
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 501
year: '2020'
...