---
_id: '11184'
abstract:
- lang: eng
text: "Let G be a graph on n nodes. In the stochastic population protocol model,
a collection of n indistinguishable, resource-limited nodes collectively solve
tasks via pairwise interactions. In each interaction, two randomly chosen neighbors
first read each other’s states, and then update their local states. A rich line
of research has established tight upper and lower bounds on the complexity of
fundamental tasks, such as majority and leader election, in this model, when G
is a clique. Specifically, in the clique, these tasks can be solved fast, i.e.,
in n polylog n pairwise interactions, with high probability, using at most polylog
n states per node.\r\nIn this work, we consider the more general setting where
G is an arbitrary regular graph, and present a technique for simulating protocols
designed for fully-connected networks in any connected regular graph. Our main
result is a simulation that is efficient on many interesting graph families: roughly,
the simulation overhead is polylogarithmic in the number of nodes, and quadratic
in the conductance of the graph. As a sample application, we show that, in any
regular graph with conductance φ, both leader election and exact majority can
be solved in φ^{-2} ⋅ n polylog n pairwise interactions, with high probability,
using at most φ^{-2} ⋅ polylog n states per node. This shows that there are fast
and space-efficient population protocols for leader election and exact majority
on graphs with good expansion properties. We believe our results will prove generally
useful, as they allow efficient technology transfer between the well-mixed (clique)
case, and the under-explored spatial setting."
acknowledgement: "Dan Alistarh: This project has received funding from the European
Research Council (ERC)\r\nunder the European Union’s Horizon 2020 research and innovation
programme (grant agreement No.805223 ScaleML).\r\nJoel Rybicki: This project has
received from the European Union’s Horizon 2020 research and\r\ninnovation programme
under the Marie Skłodowska-Curie grant agreement No. 840605.\r\nAcknowledgements
We grateful to Giorgi Nadiradze for pointing out a generalisation of the phase clock
construction to non-regular graphs. We also thank anonymous reviewers for their
useful comments on earlier versions of this manuscript."
alternative_title:
- LIPIcs
article_number: '14'
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: Rati
full_name: Gelashvili, Rati
last_name: Gelashvili
- first_name: Joel
full_name: Rybicki, Joel
id: 334EFD2E-F248-11E8-B48F-1D18A9856A87
last_name: Rybicki
orcid: 0000-0002-6432-6646
citation:
ama: 'Alistarh D-A, Gelashvili R, Rybicki J. Fast graphical population protocols.
In: Bramas Q, Gramoli V, Milani A, eds. 25th International Conference on Principles
of Distributed Systems. Vol 217. Schloss Dagstuhl - Leibniz-Zentrum für Informatik;
2022. doi:10.4230/LIPIcs.OPODIS.2021.14'
apa: 'Alistarh, D.-A., Gelashvili, R., & Rybicki, J. (2022). Fast graphical
population protocols. In Q. Bramas, V. Gramoli, & A. Milani (Eds.), 25th
International Conference on Principles of Distributed Systems (Vol. 217).
Strasbourg, France: Schloss Dagstuhl - Leibniz-Zentrum für Informatik. https://doi.org/10.4230/LIPIcs.OPODIS.2021.14'
chicago: Alistarh, Dan-Adrian, Rati Gelashvili, and Joel Rybicki. “Fast Graphical
Population Protocols.” In 25th International Conference on Principles of Distributed
Systems, edited by Quentin Bramas, Vincent Gramoli, and Alessia Milani, Vol.
217. Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2022. https://doi.org/10.4230/LIPIcs.OPODIS.2021.14.
ieee: D.-A. Alistarh, R. Gelashvili, and J. Rybicki, “Fast graphical population
protocols,” in 25th International Conference on Principles of Distributed Systems,
Strasbourg, France, 2022, vol. 217.
ista: Alistarh D-A, Gelashvili R, Rybicki J. 2022. Fast graphical population protocols.
25th International Conference on Principles of Distributed Systems. OPODIS, LIPIcs,
vol. 217, 14.
mla: Alistarh, Dan-Adrian, et al. “Fast Graphical Population Protocols.” 25th
International Conference on Principles of Distributed Systems, edited by Quentin
Bramas et al., vol. 217, 14, Schloss Dagstuhl - Leibniz-Zentrum für Informatik,
2022, doi:10.4230/LIPIcs.OPODIS.2021.14.
short: D.-A. Alistarh, R. Gelashvili, J. Rybicki, in:, Q. Bramas, V. Gramoli, A.
Milani (Eds.), 25th International Conference on Principles of Distributed Systems,
Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2022.
conference:
end_date: 2021-12-15
location: Strasbourg, France
name: OPODIS
start_date: 2021-12-13
date_created: 2022-04-17T22:01:47Z
date_published: 2022-02-01T00:00:00Z
date_updated: 2022-05-02T08:09:39Z
day: '01'
ddc:
- '510'
department:
- _id: DaAl
doi: 10.4230/LIPIcs.OPODIS.2021.14
ec_funded: 1
editor:
- first_name: Quentin
full_name: Bramas, Quentin
last_name: Bramas
- first_name: Vincent
full_name: Gramoli, Vincent
last_name: Gramoli
- first_name: Alessia
full_name: Milani, Alessia
last_name: Milani
external_id:
arxiv:
- '2102.08808'
file:
- access_level: open_access
checksum: 2c7c982174c6f98c4ca6e92539d15086
content_type: application/pdf
creator: dernst
date_created: 2022-05-02T08:06:33Z
date_updated: 2022-05-02T08:06:33Z
file_id: '11346'
file_name: 2022_LIPICs_Alistarh.pdf
file_size: 959406
relation: main_file
success: 1
file_date_updated: 2022-05-02T08:06:33Z
has_accepted_license: '1'
intvolume: ' 217'
language:
- iso: eng
license: https://creativecommons.org/licenses/by/4.0/
month: '02'
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
- _id: 26A5D39A-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '840605'
name: Coordination in constrained and natural distributed systems
publication: 25th International Conference on Principles of Distributed Systems
publication_identifier:
isbn:
- '9783959772198'
issn:
- 1868-8969
publication_status: published
publisher: Schloss Dagstuhl - Leibniz-Zentrum für Informatik
quality_controlled: '1'
scopus_import: '1'
status: public
title: Fast graphical population protocols
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
volume: 217
year: '2022'
...
---
_id: '11185'
abstract:
- lang: eng
text: Bundling crossings is a strategy which can enhance the readability of graph
drawings. In this paper we consider bundlings for families of pseudosegments,
i.e., simple curves such that any two have share at most one point at which they
cross. Our main result is that there is a polynomial-time algorithm to compute
an 8-approximation of the bundled crossing number of such instances (up to adding
a term depending on the facial structure). This 8-approximation also holds for
bundlings of good drawings of graphs. In the special case of circular drawings
the approximation factor is 8 (no extra term), this improves upon the 10-approximation
of Fink et al. [6]. We also show how to compute a 92-approximation when the intersection
graph of the pseudosegments is bipartite.
acknowledgement: This work was initiated during the Workshop on Geometric Graphs in
November 2019 in Strobl, Austria. We would like to thank Oswin Aichholzer, Fabian
Klute, Man-Kwun Chiu, Martin Balko, Pavel Valtr for their avid discussions during
the workshop. The first author has received funding from the European Union’s Horizon
2020 research and innovation programme under the Marie Sklodowska Curie grant agreement
No 754411. The second author has been supported by the German Research Foundation
DFG Project FE 340/12-1.
article_processing_charge: No
arxiv: 1
author:
- first_name: Alan M
full_name: Arroyo Guevara, Alan M
id: 3207FDC6-F248-11E8-B48F-1D18A9856A87
last_name: Arroyo Guevara
orcid: 0000-0003-2401-8670
- first_name: Stefan
full_name: Felsner, Stefan
last_name: Felsner
citation:
ama: 'Arroyo Guevara AM, Felsner S. Approximating the bundled crossing number. In:
WALCOM 2022: Algorithms and Computation. Vol 13174. LNCS. Springer Nature;
2022:383-395. doi:10.1007/978-3-030-96731-4_31'
apa: 'Arroyo Guevara, A. M., & Felsner, S. (2022). Approximating the bundled
crossing number. In WALCOM 2022: Algorithms and Computation (Vol. 13174,
pp. 383–395). Jember, Indonesia: Springer Nature. https://doi.org/10.1007/978-3-030-96731-4_31'
chicago: 'Arroyo Guevara, Alan M, and Stefan Felsner. “Approximating the Bundled
Crossing Number.” In WALCOM 2022: Algorithms and Computation, 13174:383–95.
LNCS. Springer Nature, 2022. https://doi.org/10.1007/978-3-030-96731-4_31.'
ieee: 'A. M. Arroyo Guevara and S. Felsner, “Approximating the bundled crossing
number,” in WALCOM 2022: Algorithms and Computation, Jember, Indonesia,
2022, vol. 13174, pp. 383–395.'
ista: 'Arroyo Guevara AM, Felsner S. 2022. Approximating the bundled crossing number.
WALCOM 2022: Algorithms and Computation. WALCOM: Algorithms and ComputationLNCS
vol. 13174, 383–395.'
mla: 'Arroyo Guevara, Alan M., and Stefan Felsner. “Approximating the Bundled Crossing
Number.” WALCOM 2022: Algorithms and Computation, vol. 13174, Springer
Nature, 2022, pp. 383–95, doi:10.1007/978-3-030-96731-4_31.'
short: 'A.M. Arroyo Guevara, S. Felsner, in:, WALCOM 2022: Algorithms and Computation,
Springer Nature, 2022, pp. 383–395.'
conference:
end_date: 2022-03-26
location: Jember, Indonesia
name: 'WALCOM: Algorithms and Computation'
start_date: 2022-03-24
date_created: 2022-04-17T22:01:47Z
date_published: 2022-03-16T00:00:00Z
date_updated: 2023-09-25T10:56:10Z
day: '16'
department:
- _id: UlWa
doi: 10.1007/978-3-030-96731-4_31
ec_funded: 1
external_id:
arxiv:
- '2109.14892'
intvolume: ' 13174'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: ' https://doi.org/10.48550/arXiv.2109.14892'
month: '03'
oa: 1
oa_version: Preprint
page: 383-395
project:
- _id: 260C2330-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '754411'
name: ISTplus - Postdoctoral Fellowships
publication: 'WALCOM 2022: Algorithms and Computation'
publication_identifier:
eissn:
- 1611-3349
isbn:
- '9783030967307'
issn:
- 0302-9743
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
related_material:
record:
- id: '13969'
relation: later_version
status: public
scopus_import: '1'
series_title: LNCS
status: public
title: Approximating the bundled crossing number
type: conference
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 13174
year: '2022'
...
---
_id: '11186'
abstract:
- lang: eng
text: "In this note, we study large deviations of the number \U0001D40D of intercalates
( 2×2 combinatorial subsquares which are themselves Latin squares) in a random
\ \U0001D45B×\U0001D45B Latin square. In particular, for constant \U0001D6FF>0
\ we prove that exp(−\U0001D442(\U0001D45B2log\U0001D45B))⩽Pr(\U0001D40D⩽(1−\U0001D6FF)\U0001D45B2/4)⩽exp(−Ω(\U0001D45B2))
\ and exp(−\U0001D442(\U0001D45B4/3(log\U0001D45B)))⩽Pr(\U0001D40D⩾(1+\U0001D6FF)\U0001D45B2/4)⩽exp(−Ω(\U0001D45B4/3(log\U0001D45B)2/3))
. As a consequence, we deduce that a typical order- \U0001D45B Latin square has
\ (1+\U0001D45C(1))\U0001D45B2/4 intercalates, matching a lower bound due to
Kwan and Sudakov and resolving an old conjecture of McKay and Wanless."
acknowledgement: "We thank Zach Hunter for pointing out some important typographical
errors. We also thank the referee for several remarks which helped improve the paper
substantially.\r\nKwan was supported by NSF grant DMS-1953990. Sah and Sawhney were
supported by NSF Graduate Research Fellowship Program DGE-1745302."
article_processing_charge: No
article_type: original
arxiv: 1
author:
- first_name: Matthew Alan
full_name: Kwan, Matthew Alan
id: 5fca0887-a1db-11eb-95d1-ca9d5e0453b3
last_name: Kwan
orcid: 0000-0002-4003-7567
- first_name: Ashwin
full_name: Sah, Ashwin
last_name: Sah
- first_name: Mehtaab
full_name: Sawhney, Mehtaab
last_name: Sawhney
citation:
ama: Kwan MA, Sah A, Sawhney M. Large deviations in random latin squares. Bulletin
of the London Mathematical Society. 2022;54(4):1420-1438. doi:10.1112/blms.12638
apa: Kwan, M. A., Sah, A., & Sawhney, M. (2022). Large deviations in random
latin squares. Bulletin of the London Mathematical Society. Wiley. https://doi.org/10.1112/blms.12638
chicago: Kwan, Matthew Alan, Ashwin Sah, and Mehtaab Sawhney. “Large Deviations
in Random Latin Squares.” Bulletin of the London Mathematical Society.
Wiley, 2022. https://doi.org/10.1112/blms.12638.
ieee: M. A. Kwan, A. Sah, and M. Sawhney, “Large deviations in random latin squares,”
Bulletin of the London Mathematical Society, vol. 54, no. 4. Wiley, pp.
1420–1438, 2022.
ista: Kwan MA, Sah A, Sawhney M. 2022. Large deviations in random latin squares.
Bulletin of the London Mathematical Society. 54(4), 1420–1438.
mla: Kwan, Matthew Alan, et al. “Large Deviations in Random Latin Squares.” Bulletin
of the London Mathematical Society, vol. 54, no. 4, Wiley, 2022, pp. 1420–38,
doi:10.1112/blms.12638.
short: M.A. Kwan, A. Sah, M. Sawhney, Bulletin of the London Mathematical Society
54 (2022) 1420–1438.
date_created: 2022-04-17T22:01:48Z
date_published: 2022-08-01T00:00:00Z
date_updated: 2023-08-03T06:47:29Z
day: '01'
ddc:
- '510'
department:
- _id: MaKw
doi: 10.1112/blms.12638
external_id:
arxiv:
- '2106.11932'
isi:
- '000779920900001'
file:
- access_level: open_access
checksum: 02d74e7ae955ba3c808e2a8aebe6ef98
content_type: application/pdf
creator: dernst
date_created: 2023-02-03T09:43:38Z
date_updated: 2023-02-03T09:43:38Z
file_id: '12499'
file_name: 2022_BulletinMathSociety_Kwan.pdf
file_size: 233758
relation: main_file
success: 1
file_date_updated: 2023-02-03T09:43:38Z
has_accepted_license: '1'
intvolume: ' 54'
isi: 1
issue: '4'
language:
- iso: eng
license: https://creativecommons.org/licenses/by-nc/4.0/
month: '08'
oa: 1
oa_version: Published Version
page: 1420-1438
publication: Bulletin of the London Mathematical Society
publication_identifier:
eissn:
- 1469-2120
issn:
- 0024-6093
publication_status: published
publisher: Wiley
quality_controlled: '1'
scopus_import: '1'
status: public
title: Large deviations in random latin squares
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: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
volume: 54
year: '2022'
...
---
_id: '11187'
abstract:
- lang: eng
text: During the COVID-19 pandemic, genomics and bioinformatics have emerged as
essential public health tools. The genomic data acquired using these methods have
supported the global health response, facilitated the development of testing methods
and allowed the timely tracking of novel SARS-CoV-2 variants. Yet the virtually
unlimited potential for rapid generation and analysis of genomic data is also
coupled with unique technical, scientific and organizational challenges. Here,
we discuss the application of genomic and computational methods for efficient
data-driven COVID-19 response, the advantages of the democratization of viral
sequencing around the world and the challenges associated with viral genome data
collection and processing.
acknowledgement: 'Our paper is dedicated to all freedom-loving people around the world,
and to the people of Ukraine who fight for our freedom. We thank William M. Switzer
and Ellsworth M. Campbell from the Division of HIV/AIDS Prevention, Centers for
Disease Control and Prevention (CDC), Atlanta, GA, USA, for discussions and suggestions.
We thank Jason Ladner from the Pathogen and Microbiome Institute, Northern Arizona
University, Flagstaff, AZ, for providing suggestions and feedback. S.M. was partially
supported by National Science Foundation grants 2041984. T.L. is supported by the
NSFC Excellent Young Scientists Fund (Hong Kong and Macau; 31922087), Research Grants
Council (RGC) Collaborative Research Fund (C7144-20GF), RGC Research Impact Fund
(R7021-20), Innovation and Technology Commission’s InnoHK funding (D24H) and Health
and Medical Research Fund (COVID190223). P.S. was supported by US National Institutes
of Health (NIH) grant 1R01EB025022 and National Science Foundation (NSF) grant 2047828.
M.A. acknowledges King Abdulaziz City for Science and Technology and the Saudi Human
Genome Project for technical and financial support (https://shgp.kacst.edu.sa) N.W.
was supported by US NIH grants R00 AI139445, DP2 AT011966 and R01 AI167910. A.S.
acknowledge funding from NSF grant no. 2029025. A.Z. has been partially supported
by NIH grants 1R01EB025022-01 and 1R21CA241044-01A1. S. Knyazev has been partly
supported by Molecular Basis of Disease at Georgia State University and NIH awards
R01 HG009120, R01 MH115676, R01 AI153827 and U01 HG011715. A.W. has been supported
by the CAMS Innovation Fund for Medical Sciences (2021-I2M-1-061). R.K. was supported
by NSF project 2038509, RAPID: Improving QIIME 2 and UniFrac for Viruses to Respond
to COVID-19, CDC project 30055281 with Scripps led by Kristian Andersen, Genomic
sequencing of SARS-CoV-2 to investigate local and cross-border emergence and spread.
J.O.W. was supported by NIH–National Institute of Allergy and Infectious Diseases
(NIAID) R01 AI135992 and receives funding from the CDC unrelated to this work. T.I.V.
is supported by the Branco Weiss Fellowship. Y.P. was supported by the Ministry
of Science and Higher Education of the Russian Federation within the framework of
state support for the creation and development of World-Class Research Centers “Digital
biodesign and personalized healthcare” N◦075-15-2020-926. E.B. was supported by
a US National Institute of General Medical Sciences IDeA Alaska INBRE (P20GM103395)
and NIAID CEIRR (75N93019R00028). C.E.M. thanks Testing for America (501c3), OpenCovidScreen
Foundation, Igor Tulchinsky and the WorldQuant Foundation, Bill Ackman and Olivia
Flatto and the Pershing Square Foundation, Ken Griffin and Citadel, the US National
Institutes of Health (R01AI125416, R01AI151059, R21AI129851, U01DA053941), and the
Alfred P. Sloan Foundation (G-2015-13964). C.Y.C. is supported by US CDC Epidemiology
and Laboratory Capacity (ELC) for Infectious Diseases grant 6NU50CK000539 to the
California Department of Public Health, the Innovative Genomics Institute (IGI)
at the University of California, Berkeley, and University of California, San Francisco,
NIH grant R33AI12945 and US CDC contract 75D30121C10991. A.K. was partly supported
by RFBR grant 20-515-80017. P.L. acknowledges support from the European Research
Council (ERC) under the European Union’s Horizon 2020 research and innovation program
(grant agreement no. ~725422 - ReservoirDOCS), the Wellcome Trust through project
206298/Z/17/Z (Artic Network) and NIH grants R01 AI153044 and U19 AI135995. K.C.
acknowledges support from the US NSF award EEID-IOS-2109688. F.K.’s work was supported
by an ERC Consolidator grant to F.K. (771209–CharFL).'
article_processing_charge: No
article_type: letter_note
author:
- first_name: Sergey
full_name: Knyazev, Sergey
last_name: Knyazev
- first_name: Karishma
full_name: Chhugani, Karishma
last_name: Chhugani
- first_name: Varuni
full_name: Sarwal, Varuni
last_name: Sarwal
- first_name: Ram
full_name: Ayyala, Ram
last_name: Ayyala
- first_name: Harman
full_name: Singh, Harman
last_name: Singh
- first_name: Smruthi
full_name: Karthikeyan, Smruthi
last_name: Karthikeyan
- first_name: Dhrithi
full_name: Deshpande, Dhrithi
last_name: Deshpande
- first_name: Pelin Icer
full_name: Baykal, Pelin Icer
last_name: Baykal
- first_name: Zoia
full_name: Comarova, Zoia
last_name: Comarova
- first_name: Angela
full_name: Lu, Angela
last_name: Lu
- first_name: Yuri
full_name: Porozov, Yuri
last_name: Porozov
- first_name: Tetyana I.
full_name: Vasylyeva, Tetyana I.
last_name: Vasylyeva
- first_name: Joel O.
full_name: Wertheim, Joel O.
last_name: Wertheim
- first_name: Braden T.
full_name: Tierney, Braden T.
last_name: Tierney
- first_name: Charles Y.
full_name: Chiu, Charles Y.
last_name: Chiu
- first_name: Ren
full_name: Sun, Ren
last_name: Sun
- first_name: Aiping
full_name: Wu, Aiping
last_name: Wu
- first_name: Malak S.
full_name: Abedalthagafi, Malak S.
last_name: Abedalthagafi
- first_name: Victoria M.
full_name: Pak, Victoria M.
last_name: Pak
- first_name: Shivashankar H.
full_name: Nagaraj, Shivashankar H.
last_name: Nagaraj
- first_name: Adam L.
full_name: Smith, Adam L.
last_name: Smith
- first_name: Pavel
full_name: Skums, Pavel
last_name: Skums
- first_name: Bogdan
full_name: Pasaniuc, Bogdan
last_name: Pasaniuc
- first_name: Andrey
full_name: Komissarov, Andrey
last_name: Komissarov
- first_name: Christopher E.
full_name: Mason, Christopher E.
last_name: Mason
- first_name: Eric
full_name: Bortz, Eric
last_name: Bortz
- first_name: Philippe
full_name: Lemey, Philippe
last_name: Lemey
- first_name: Fyodor
full_name: Kondrashov, Fyodor
id: 44FDEF62-F248-11E8-B48F-1D18A9856A87
last_name: Kondrashov
orcid: 0000-0001-8243-4694
- first_name: Niko
full_name: Beerenwinkel, Niko
last_name: Beerenwinkel
- first_name: Tommy Tsan Yuk
full_name: Lam, Tommy Tsan Yuk
last_name: Lam
- first_name: Nicholas C.
full_name: Wu, Nicholas C.
last_name: Wu
- first_name: Alex
full_name: Zelikovsky, Alex
last_name: Zelikovsky
- first_name: Rob
full_name: Knight, Rob
last_name: Knight
- first_name: Keith A.
full_name: Crandall, Keith A.
last_name: Crandall
- first_name: Serghei
full_name: Mangul, Serghei
last_name: Mangul
citation:
ama: Knyazev S, Chhugani K, Sarwal V, et al. Unlocking capacities of genomics for
the COVID-19 response and future pandemics. Nature Methods. 2022;19(4):374-380.
doi:10.1038/s41592-022-01444-z
apa: Knyazev, S., Chhugani, K., Sarwal, V., Ayyala, R., Singh, H., Karthikeyan,
S., … Mangul, S. (2022). Unlocking capacities of genomics for the COVID-19 response
and future pandemics. Nature Methods. Springer Nature. https://doi.org/10.1038/s41592-022-01444-z
chicago: Knyazev, Sergey, Karishma Chhugani, Varuni Sarwal, Ram Ayyala, Harman Singh,
Smruthi Karthikeyan, Dhrithi Deshpande, et al. “Unlocking Capacities of Genomics
for the COVID-19 Response and Future Pandemics.” Nature Methods. Springer
Nature, 2022. https://doi.org/10.1038/s41592-022-01444-z.
ieee: S. Knyazev et al., “Unlocking capacities of genomics for the COVID-19
response and future pandemics,” Nature Methods, vol. 19, no. 4. Springer
Nature, pp. 374–380, 2022.
ista: Knyazev S, Chhugani K, Sarwal V, Ayyala R, Singh H, Karthikeyan S, Deshpande
D, Baykal PI, Comarova Z, Lu A, Porozov Y, Vasylyeva TI, Wertheim JO, Tierney
BT, Chiu CY, Sun R, Wu A, Abedalthagafi MS, Pak VM, Nagaraj SH, Smith AL, Skums
P, Pasaniuc B, Komissarov A, Mason CE, Bortz E, Lemey P, Kondrashov F, Beerenwinkel
N, Lam TTY, Wu NC, Zelikovsky A, Knight R, Crandall KA, Mangul S. 2022. Unlocking
capacities of genomics for the COVID-19 response and future pandemics. Nature
Methods. 19(4), 374–380.
mla: Knyazev, Sergey, et al. “Unlocking Capacities of Genomics for the COVID-19
Response and Future Pandemics.” Nature Methods, vol. 19, no. 4, Springer
Nature, 2022, pp. 374–80, doi:10.1038/s41592-022-01444-z.
short: S. Knyazev, K. Chhugani, V. Sarwal, R. Ayyala, H. Singh, S. Karthikeyan,
D. Deshpande, P.I. Baykal, Z. Comarova, A. Lu, Y. Porozov, T.I. Vasylyeva, J.O.
Wertheim, B.T. Tierney, C.Y. Chiu, R. Sun, A. Wu, M.S. Abedalthagafi, V.M. Pak,
S.H. Nagaraj, A.L. Smith, P. Skums, B. Pasaniuc, A. Komissarov, C.E. Mason, E.
Bortz, P. Lemey, F. Kondrashov, N. Beerenwinkel, T.T.Y. Lam, N.C. Wu, A. Zelikovsky,
R. Knight, K.A. Crandall, S. Mangul, Nature Methods 19 (2022) 374–380.
date_created: 2022-04-17T22:01:48Z
date_published: 2022-04-08T00:00:00Z
date_updated: 2023-08-03T06:46:09Z
day: '08'
department:
- _id: FyKo
doi: 10.1038/s41592-022-01444-z
ec_funded: 1
external_id:
isi:
- '000781199600011'
pmid:
- '35396471'
intvolume: ' 19'
isi: 1
issue: '4'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.1038/s41592-022-01444-z
month: '04'
oa: 1
oa_version: Published Version
page: 374-380
pmid: 1
project:
- _id: 26580278-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '771209'
name: Characterizing the fitness landscape on population and global scales
publication: Nature Methods
publication_identifier:
eissn:
- 1548-7105
issn:
- 1548-7091
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
scopus_import: '1'
status: public
title: Unlocking capacities of genomics for the COVID-19 response and future pandemics
type: journal_article
user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
volume: 19
year: '2022'
...
---
_id: '11193'
abstract:
- lang: eng
text: "The infiltration of immune cells into tissues underlies the establishment
of tissue-resident\r\nmacrophages and responses to infections and tumors. However,
the mechanisms immune\r\ncells utilize to collectively migrate through tissue
barriers in vivo are not yet well understood.\r\nIn this thesis, I describe two
mechanisms that Drosophila immune cells (hemocytes) use to\r\novercome the tissue
barrier of the germband in the embryo. One strategy is the strengthening\r\nof
the actin cortex through developmentally controlled transcriptional regulation
induced by\r\nthe Drosophila proto-oncogene family member Dfos, which I show in
Chapter 2. Dfos induces\r\nexpression of the tetraspanin TM4SF and the filamin
Cher leading to higher levels of the\r\nactivated formin Dia at the cortex and
increased cortical F-actin. This enhanced cortical\r\nstrength allows hemocytes
to overcome the physical resistance of the surrounding tissue and\r\ntranslocate
their nucleus to move forward. This mechanism affects the speed of migration\r\nwhen
hemocytes face a confined environment in vivo.\r\nAnother aspect of the invasion
process is the initial step of the leading hemocytes entering\r\nthe tissue, which
potentially guides the follower cells. In Chapter 3, I describe a novel\r\nsubpopulation
of hemocytes activated by BMP signaling prior to tissue invasion that leads\r\npenetration
into the germband. Hemocytes that are deficient in BMP signaling activation\r\nshow
impaired persistence at the tissue entry, while their migration speed remains\r\nunaffected.\r\nThis
suggests that there might be different mechanisms controlling immune cell migration\r\nwithin
the confined environment in vivo, one of these being the general ability to overcome\r\nthe
resistance of the surrounding tissue and another affecting the order of hemocytes
that\r\ncollectively invade the tissue in a stream of individual cells.\r\nTogether,
my findings provide deeper insights into transcriptional changes in immune\r\ncells
that enable efficient tissue invasion and pave the way for future studies investigating
the\r\nearly colonization of tissues by macrophages in higher organisms. Moreover,
they extend the\r\ncurrent view of Drosophila immune cell heterogeneity and point
toward a potentially\r\nconserved role for canonical BMP signaling in specifying
immune cells that lead the migration\r\nof tissue resident macrophages during
embryogenesis."
acknowledged_ssus:
- _id: LifeSc
alternative_title:
- ISTA Thesis
article_processing_charge: No
author:
- first_name: Stephanie
full_name: Wachner, Stephanie
id: 2A95E7B0-F248-11E8-B48F-1D18A9856A87
last_name: Wachner
citation:
ama: Wachner S. Transcriptional regulation by Dfos and BMP-signaling support tissue
invasion of Drosophila immune cells. 2022. doi:10.15479/at:ista:11193
apa: Wachner, S. (2022). Transcriptional regulation by Dfos and BMP-signaling
support tissue invasion of Drosophila immune cells. Institute of Science and
Technology Austria. https://doi.org/10.15479/at:ista:11193
chicago: Wachner, Stephanie. “Transcriptional Regulation by Dfos and BMP-Signaling
Support Tissue Invasion of Drosophila Immune Cells.” Institute of Science and
Technology Austria, 2022. https://doi.org/10.15479/at:ista:11193.
ieee: S. Wachner, “Transcriptional regulation by Dfos and BMP-signaling support
tissue invasion of Drosophila immune cells,” Institute of Science and Technology
Austria, 2022.
ista: Wachner S. 2022. Transcriptional regulation by Dfos and BMP-signaling support
tissue invasion of Drosophila immune cells. Institute of Science and Technology
Austria.
mla: Wachner, Stephanie. Transcriptional Regulation by Dfos and BMP-Signaling
Support Tissue Invasion of Drosophila Immune Cells. Institute of Science and
Technology Austria, 2022, doi:10.15479/at:ista:11193.
short: S. Wachner, Transcriptional Regulation by Dfos and BMP-Signaling Support
Tissue Invasion of Drosophila Immune Cells, Institute of Science and Technology
Austria, 2022.
date_created: 2022-04-20T08:59:07Z
date_published: 2022-04-20T00:00:00Z
date_updated: 2023-09-19T10:15:54Z
day: '20'
ddc:
- '570'
degree_awarded: PhD
department:
- _id: GradSch
- _id: DaSi
doi: 10.15479/at:ista:11193
file:
- access_level: open_access
checksum: 999ab16884c4522486136ebc5ae8dbff
content_type: application/pdf
creator: cchlebak
date_created: 2022-04-20T09:03:57Z
date_updated: 2023-04-21T22:30:03Z
embargo: 2023-04-20
file_id: '11195'
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file_size: 8820951
relation: main_file
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checksum: fd92b1e38d53bdf8b458213882d41383
content_type: application/x-zip-compressed
creator: cchlebak
date_created: 2022-04-22T12:41:00Z
date_updated: 2023-04-21T22:30:03Z
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file_name: Thesis_Stephanie_Wachner_20200414.zip
file_size: 65864612
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file_date_updated: 2023-04-21T22:30:03Z
has_accepted_license: '1'
language:
- iso: eng
month: '04'
oa: 1
oa_version: Published Version
page: '170'
project:
- _id: 26199CA4-B435-11E9-9278-68D0E5697425
grant_number: '24800'
name: Tissue barrier penetration is crucial for immunity and metastasis
publication_identifier:
issn:
- 2663-337X
publication_status: published
publisher: Institute of Science and Technology Austria
related_material:
record:
- id: '10614'
relation: part_of_dissertation
status: public
- id: '544'
relation: part_of_dissertation
status: public
status: public
supervisor:
- first_name: Daria E
full_name: Siekhaus, Daria E
id: 3D224B9E-F248-11E8-B48F-1D18A9856A87
last_name: Siekhaus
orcid: 0000-0001-8323-8353
title: Transcriptional regulation by Dfos and BMP-signaling support tissue invasion
of Drosophila immune cells
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: dissertation
user_id: 8b945eb4-e2f2-11eb-945a-df72226e66a9
year: '2022'
...
---
_id: '11196'
abstract:
- lang: eng
text: "One of the fundamental questions in Neuroscience is how the structure of
synapses and their physiological properties are related. While synaptic transmission
remains a dynamic process, electron microscopy provides images with comparably
low temporal resolution (Studer et al., 2014). The current work overcomes this
challenge and describes an improved “Flash and Freeze” technique (Watanabe et
al., 2013a; Watanabe et al., 2013b) to study synaptic transmission at the hippocampal
mossy fiber-CA3 pyramidal neuron synapses, using mouse acute brain slices and
organotypic slices culture. The improved method allowed for selective stimulation
of presynaptic mossy fiber boutons and the observation of synaptic vesicle pool
dynamics at the active zones. Our results uncovered several intriguing morphological
features of mossy fiber boutons. First, the docked vesicle pool was largely depleted
(more than 70%) after stimulation, implying that the docked synaptic vesicles
pool and readily releasable pool are vastly overlapping in mossy fiber boutons.
Second, the synaptic vesicles are skewed towards larger diameters, displaying
a wide range of sizes. An increase in the mean diameter of synaptic vesicles,
after single and repetitive stimulation, suggests that smaller vesicles have a
higher release probability. Third, we observed putative endocytotic structures
after moderate light stimulation, matching the timing of previously described
ultrafast endocytosis (Watanabe et al., 2013a; Delvendahl et al., 2016). \r\n\tIn
addition, synaptic transmission depends on a sophisticated system of protein machinery
and calcium channels (Südhof, 2013b), which amplifies the challenge in studying
synaptic communication as these interactions can be potentially modified during
synaptic plasticity. And although recent study elucidated the potential correlation
between physiological and morphological properties of synapses during synaptic
plasticity (Vandael et al., 2020), the molecular underpinning of it remains unknown.
Thus, the presented work tries to overcome this challenge and aims to pinpoint
changes in the molecular architecture at hippocampal mossy fiber bouton synapses
during short- and long-term potentiation (STP and LTP), we combined chemical potentiation,
with the application of a cyclic adenosine monophosphate agonist (i.e. forskolin)
and freeze-fracture replica immunolabelling. This method allowed the localization
of membrane-bound proteins with nanometer precision within the active zone, in
particular, P/Q-type calcium channels and synaptic vesicle priming proteins Munc13-1/2.
First, we found that the number of clusters of Munc13-1 in the mossy fiber bouton
active zone increased significantly during STP, but decreased to lower than the
control value during LTP. Secondly, although the distance between the calcium
channels and Munc13-1s did not change after induction of STP, it shortened during
the LTP phase. Additionally, forskolin did not affect Munc13-2 distribution during
STP and LTP. These results indicate the existence of two distinct mechanisms that
govern STP and LTP at mossy fiber bouton synapses: an increase in the readily
realizable pool in the case of STP and a potential increase in release probability
during LTP. “Flash and freeze” and functional electron microscopy, are versatile
methods that can be successfully applied to intact brain circuits to study synaptic
transmission even at the molecular level.\r\n"
acknowledged_ssus:
- _id: EM-Fac
- _id: PreCl
alternative_title:
- ISTA Thesis
article_processing_charge: No
author:
- first_name: Olena
full_name: Kim, Olena
id: 3F8ABDDA-F248-11E8-B48F-1D18A9856A87
last_name: Kim
citation:
ama: Kim O. Nanoarchitecture of hippocampal mossy fiber-CA3 pyramidal neuron synapses.
2022. doi:10.15479/at:ista:11196
apa: Kim, O. (2022). Nanoarchitecture of hippocampal mossy fiber-CA3 pyramidal
neuron synapses. Institute of Science and Technology Austria. https://doi.org/10.15479/at:ista:11196
chicago: Kim, Olena. “Nanoarchitecture of Hippocampal Mossy Fiber-CA3 Pyramidal
Neuron Synapses.” Institute of Science and Technology Austria, 2022. https://doi.org/10.15479/at:ista:11196.
ieee: O. Kim, “Nanoarchitecture of hippocampal mossy fiber-CA3 pyramidal neuron
synapses,” Institute of Science and Technology Austria, 2022.
ista: Kim O. 2022. Nanoarchitecture of hippocampal mossy fiber-CA3 pyramidal neuron
synapses. Institute of Science and Technology Austria.
mla: Kim, Olena. Nanoarchitecture of Hippocampal Mossy Fiber-CA3 Pyramidal Neuron
Synapses. Institute of Science and Technology Austria, 2022, doi:10.15479/at:ista:11196.
short: O. Kim, Nanoarchitecture of Hippocampal Mossy Fiber-CA3 Pyramidal Neuron
Synapses, Institute of Science and Technology Austria, 2022.
date_created: 2022-04-20T09:47:12Z
date_published: 2022-04-20T00:00:00Z
date_updated: 2023-08-18T06:31:52Z
day: '20'
ddc:
- '570'
degree_awarded: PhD
department:
- _id: PeJo
- _id: GradSch
doi: 10.15479/at:ista:11196
ec_funded: 1
file:
- access_level: open_access
checksum: 1616a8bf6f13a57c892dac873dcd0936
content_type: application/pdf
creator: okim
date_created: 2022-04-20T14:21:56Z
date_updated: 2023-04-20T22:30:03Z
embargo: 2023-04-19
file_id: '11220'
file_name: Olena_KIM_thesis_final.pdf
file_size: 21273537
relation: main_file
- access_level: closed
checksum: 1acb433f98dc42abb0b4b0cbb0c4b918
content_type: application/x-zip-compressed
creator: okim
date_created: 2022-04-20T14:22:56Z
date_updated: 2023-04-20T22:30:03Z
embargo_to: open_access
file_id: '11221'
file_name: KIM_thesis_final.zip
file_size: 59248569
relation: source_file
file_date_updated: 2023-04-20T22:30:03Z
has_accepted_license: '1'
language:
- iso: eng
license: https://creativecommons.org/licenses/by-nc-nd/4.0/
month: '04'
oa: 1
oa_version: Published Version
page: '132'
project:
- _id: 25BAF7B2-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '708497'
name: Presynaptic calcium channels distribution and impact on coupling at the hippocampal
mossy fiber synapse
- _id: 25B7EB9E-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '692692'
name: Biophysics and circuit function of a giant cortical glumatergic synapse
- _id: 25C3DBB6-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: W01205
name: Zellkommunikation in Gesundheit und Krankheit
- _id: 25C5A090-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: Z00312
name: The Wittgenstein Prize
publication_identifier:
issn:
- 2663-337X
publication_status: published
publisher: Institute of Science and Technology Austria
related_material:
record:
- id: '11222'
relation: part_of_dissertation
status: public
- id: '7473'
relation: part_of_dissertation
status: public
status: public
supervisor:
- first_name: Peter M
full_name: Jonas, Peter M
id: 353C1B58-F248-11E8-B48F-1D18A9856A87
last_name: Jonas
orcid: 0000-0001-5001-4804
title: Nanoarchitecture of hippocampal mossy fiber-CA3 pyramidal neuron synapses
tmp:
image: /images/cc_by_nc_nd.png
legal_code_url: https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode
name: Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International
(CC BY-NC-ND 4.0)
short: CC BY-NC-ND (4.0)
type: dissertation
user_id: 8b945eb4-e2f2-11eb-945a-df72226e66a9
year: '2022'
...
---
_id: '11321'
abstract:
- lang: eng
text: 'Here are the research data underlying the publication "Effects of fine-scale
population structure on the distribution of heterozygosity in a long-term study
of Antirrhinum majus" Further information are summed up in the README document. '
article_processing_charge: No
author:
- first_name: Parvathy
full_name: Surendranadh, Parvathy
id: 455235B8-F248-11E8-B48F-1D18A9856A87
last_name: Surendranadh
- first_name: Louise S
full_name: Arathoon, Louise S
id: 2CFCFF98-F248-11E8-B48F-1D18A9856A87
last_name: Arathoon
orcid: 0000-0003-1771-714X
- first_name: Carina
full_name: Baskett, Carina
id: 3B4A7CE2-F248-11E8-B48F-1D18A9856A87
last_name: Baskett
orcid: 0000-0002-7354-8574
- first_name: David
full_name: Field, David
id: 419049E2-F248-11E8-B48F-1D18A9856A87
last_name: Field
orcid: 0000-0002-4014-8478
- first_name: Melinda
full_name: Pickup, Melinda
id: 2C78037E-F248-11E8-B48F-1D18A9856A87
last_name: Pickup
orcid: 0000-0001-6118-0541
- first_name: Nicholas H
full_name: Barton, Nicholas H
id: 4880FE40-F248-11E8-B48F-1D18A9856A87
last_name: Barton
orcid: 0000-0002-8548-5240
citation:
ama: Surendranadh P, Arathoon LS, Baskett C, Field D, Pickup M, Barton NH. Effects
of fine-scale population structure on the distribution of heterozygosity in a
long-term study of Antirrhinum majus. 2022. doi:10.15479/at:ista:11321
apa: Surendranadh, P., Arathoon, L. S., Baskett, C., Field, D., Pickup, M., &
Barton, N. H. (2022). Effects of fine-scale population structure on the distribution
of heterozygosity in a long-term study of Antirrhinum majus. Institute of Science
and Technology Austria. https://doi.org/10.15479/at:ista:11321
chicago: Surendranadh, Parvathy, Louise S Arathoon, Carina Baskett, David Field,
Melinda Pickup, and Nicholas H Barton. “Effects of Fine-Scale Population Structure
on the Distribution of Heterozygosity in a Long-Term Study of Antirrhinum Majus.”
Institute of Science and Technology Austria, 2022. https://doi.org/10.15479/at:ista:11321.
ieee: P. Surendranadh, L. S. Arathoon, C. Baskett, D. Field, M. Pickup, and N. H.
Barton, “Effects of fine-scale population structure on the distribution of heterozygosity
in a long-term study of Antirrhinum majus.” Institute of Science and Technology
Austria, 2022.
ista: Surendranadh P, Arathoon LS, Baskett C, Field D, Pickup M, Barton NH. 2022.
Effects of fine-scale population structure on the distribution of heterozygosity
in a long-term study of Antirrhinum majus, Institute of Science and Technology
Austria, 10.15479/at:ista:11321.
mla: Surendranadh, Parvathy, et al. Effects of Fine-Scale Population Structure
on the Distribution of Heterozygosity in a Long-Term Study of Antirrhinum Majus.
Institute of Science and Technology Austria, 2022, doi:10.15479/at:ista:11321.
short: P. Surendranadh, L.S. Arathoon, C. Baskett, D. Field, M. Pickup, N.H. Barton,
(2022).
contributor:
- contributor_type: project_member
first_name: Louise S
id: 2CFCFF98-F248-11E8-B48F-1D18A9856A87
last_name: Arathoon
- contributor_type: project_member
first_name: Carina
id: 3B4A7CE2-F248-11E8-B48F-1D18A9856A87
last_name: Baskett
orcid: 0000-0002-7354-8574
- contributor_type: project_member
first_name: David
id: 419049E2-F248-11E8-B48F-1D18A9856A87
last_name: Field
orcid: 0000-0002-4014-8478
- contributor_type: project_member
first_name: Melinda
id: 2C78037E-F248-11E8-B48F-1D18A9856A87
last_name: Pickup
orcid: 0000-0001-6118-0541
- contributor_type: project_member
first_name: Nicholas H
id: 4880FE40-F248-11E8-B48F-1D18A9856A87
last_name: Barton
orcid: 0000-0002-8548-5240
date_created: 2022-04-22T09:42:24Z
date_published: 2022-04-28T00:00:00Z
date_updated: 2024-02-21T12:41:09Z
day: '28'
ddc:
- '570'
department:
- _id: GradSch
- _id: NiBa
doi: 10.15479/at:ista:11321
file:
- access_level: open_access
checksum: 96c1b86cdf25481f2a52972fcc45ca7f
content_type: application/x-zip-compressed
creator: larathoo
date_created: 2022-04-22T09:39:03Z
date_updated: 2022-04-22T09:39:03Z
file_id: '11326'
file_name: Data_Code.zip
file_size: 13260571
relation: main_file
success: 1
file_date_updated: 2022-04-22T09:39:03Z
has_accepted_license: '1'
month: '04'
oa: 1
oa_version: Published Version
publisher: Institute of Science and Technology Austria
related_material:
record:
- id: '11411'
relation: used_in_publication
status: public
- id: '9192'
relation: earlier_version
status: public
- id: '8254'
relation: earlier_version
status: public
status: public
title: Effects of fine-scale population structure on the distribution of heterozygosity
in a long-term study of Antirrhinum majus
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: research_data
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
year: '2022'
...
---
_id: '11330'
abstract:
- lang: eng
text: In this article we study the noncommutative transport distance introduced
by Carlen and Maas and its entropic regularization defined by Becker and Li. We
prove a duality formula that can be understood as a quantum version of the dual
Benamou–Brenier formulation of the Wasserstein distance in terms of subsolutions
of a Hamilton–Jacobi–Bellmann equation.
acknowledgement: "The author wants to thank Jan Maas for helpful comments. He also
acknowledges financial support from the Austrian Science Fund (FWF) through Grant
Number F65 and from the European Research Council (ERC) under the European Union’s
Horizon 2020 Research and Innovation Programme (Grant Agreement No. 716117).\r\nOpen
access funding provided by Institute of Science and Technology (IST Austria)."
article_number: '19'
article_processing_charge: Yes (via OA deal)
article_type: original
author:
- first_name: Melchior
full_name: Wirth, Melchior
id: 88644358-0A0E-11EA-8FA5-49A33DDC885E
last_name: Wirth
orcid: 0000-0002-0519-4241
citation:
ama: Wirth M. A dual formula for the noncommutative transport distance. Journal
of Statistical Physics. 2022;187(2). doi:10.1007/s10955-022-02911-9
apa: Wirth, M. (2022). A dual formula for the noncommutative transport distance.
Journal of Statistical Physics. Springer Nature. https://doi.org/10.1007/s10955-022-02911-9
chicago: Wirth, Melchior. “A Dual Formula for the Noncommutative Transport Distance.”
Journal of Statistical Physics. Springer Nature, 2022. https://doi.org/10.1007/s10955-022-02911-9.
ieee: M. Wirth, “A dual formula for the noncommutative transport distance,” Journal
of Statistical Physics, vol. 187, no. 2. Springer Nature, 2022.
ista: Wirth M. 2022. A dual formula for the noncommutative transport distance. Journal
of Statistical Physics. 187(2), 19.
mla: Wirth, Melchior. “A Dual Formula for the Noncommutative Transport Distance.”
Journal of Statistical Physics, vol. 187, no. 2, 19, Springer Nature, 2022,
doi:10.1007/s10955-022-02911-9.
short: M. Wirth, Journal of Statistical Physics 187 (2022).
date_created: 2022-04-24T22:01:43Z
date_published: 2022-04-08T00:00:00Z
date_updated: 2023-08-03T06:37:49Z
day: '08'
ddc:
- '510'
- '530'
department:
- _id: JaMa
doi: 10.1007/s10955-022-02911-9
ec_funded: 1
external_id:
isi:
- '000780305000001'
file:
- access_level: open_access
checksum: f3e0b00884b7dde31347a3756788b473
content_type: application/pdf
creator: dernst
date_created: 2022-04-29T11:24:23Z
date_updated: 2022-04-29T11:24:23Z
file_id: '11338'
file_name: 2022_JourStatisticalPhysics_Wirth.pdf
file_size: 362119
relation: main_file
success: 1
file_date_updated: 2022-04-29T11:24:23Z
has_accepted_license: '1'
intvolume: ' 187'
isi: 1
issue: '2'
language:
- iso: eng
month: '04'
oa: 1
oa_version: Published Version
project:
- _id: fc31cba2-9c52-11eb-aca3-ff467d239cd2
grant_number: F6504
name: Taming Complexity in Partial Differential Systems
- _id: 256E75B8-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '716117'
name: Optimal Transport and Stochastic Dynamics
publication: Journal of Statistical Physics
publication_identifier:
eissn:
- '15729613'
issn:
- '00224715'
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
scopus_import: '1'
status: public
title: A dual formula for the noncommutative transport distance
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: journal_article
user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
volume: 187
year: '2022'
...
---
_id: '11331'
abstract:
- lang: eng
text: "We propose separating the task of reliable transaction dissemination from
transaction ordering, to enable high-performance Byzantine fault-tolerant quorum-based
consensus. We design and evaluate a mempool protocol, Narwhal, specializing in
high-throughput reliable dissemination and storage of causal histories of transactions.
Narwhal tolerates an asynchronous network and maintains high performance despite
failures. Narwhal is designed to easily scale-out using multiple workers at each
validator, and we demonstrate that there is no foreseeable limit to the throughput
we can achieve.\r\nComposing Narwhal with a partially synchronous consensus protocol
(Narwhal-HotStuff) yields significantly better throughput even in the presence
of faults or intermittent loss of liveness due to asynchrony. However, loss of
liveness can result in higher latency. To achieve overall good performance when
faults occur we design Tusk, a zero-message overhead asynchronous consensus protocol,
to work with Narwhal. We demonstrate its high performance under a variety of configurations
and faults.\r\nAs a summary of results, on a WAN, Narwhal-Hotstuff achieves over
130,000 tx/sec at less than 2-sec latency compared with 1,800 tx/sec at 1-sec
latency for Hotstuff. Additional workers increase throughput linearly to 600,000
tx/sec without any latency increase. Tusk achieves 160,000 tx/sec with about 3
seconds latency. Under faults, both protocols maintain high throughput, but Narwhal-HotStuff
suffers from increased latency."
article_processing_charge: No
arxiv: 1
author:
- first_name: George
full_name: Danezis, George
last_name: Danezis
- first_name: Eleftherios
full_name: Kokoris Kogias, Eleftherios
id: f5983044-d7ef-11ea-ac6d-fd1430a26d30
last_name: Kokoris Kogias
- first_name: Alberto
full_name: Sonnino, Alberto
last_name: Sonnino
- first_name: Alexander
full_name: Spiegelman, Alexander
last_name: Spiegelman
citation:
ama: 'Danezis G, Kokoris Kogias E, Sonnino A, Spiegelman A. Narwhal and Tusk: A
DAG-based mempool and efficient BFT consensus. In: Proceedings of the 17th
European Conference on Computer Systems. Association for Computing Machinery;
2022:34-50. doi:10.1145/3492321.3519594'
apa: 'Danezis, G., Kokoris Kogias, E., Sonnino, A., & Spiegelman, A. (2022).
Narwhal and Tusk: A DAG-based mempool and efficient BFT consensus. In Proceedings
of the 17th European Conference on Computer Systems (pp. 34–50). Rennes, France:
Association for Computing Machinery. https://doi.org/10.1145/3492321.3519594'
chicago: 'Danezis, George, Eleftherios Kokoris Kogias, Alberto Sonnino, and Alexander
Spiegelman. “Narwhal and Tusk: A DAG-Based Mempool and Efficient BFT Consensus.”
In Proceedings of the 17th European Conference on Computer Systems, 34–50.
Association for Computing Machinery, 2022. https://doi.org/10.1145/3492321.3519594.'
ieee: 'G. Danezis, E. Kokoris Kogias, A. Sonnino, and A. Spiegelman, “Narwhal and
Tusk: A DAG-based mempool and efficient BFT consensus,” in Proceedings of the
17th European Conference on Computer Systems, Rennes, France, 2022, pp. 34–50.'
ista: 'Danezis G, Kokoris Kogias E, Sonnino A, Spiegelman A. 2022. Narwhal and Tusk:
A DAG-based mempool and efficient BFT consensus. Proceedings of the 17th European
Conference on Computer Systems. EuroSys: European Conference on Computer Systems,
34–50.'
mla: 'Danezis, George, et al. “Narwhal and Tusk: A DAG-Based Mempool and Efficient
BFT Consensus.” Proceedings of the 17th European Conference on Computer Systems,
Association for Computing Machinery, 2022, pp. 34–50, doi:10.1145/3492321.3519594.'
short: G. Danezis, E. Kokoris Kogias, A. Sonnino, A. Spiegelman, in:, Proceedings
of the 17th European Conference on Computer Systems, Association for Computing
Machinery, 2022, pp. 34–50.
conference:
end_date: 2022-04-08
location: Rennes, France
name: 'EuroSys: European Conference on Computer Systems'
start_date: 2022-04-05
date_created: 2022-04-24T22:01:43Z
date_published: 2022-03-28T00:00:00Z
date_updated: 2023-08-03T06:38:40Z
day: '28'
department:
- _id: ElKo
doi: 10.1145/3492321.3519594
external_id:
arxiv:
- '2105.11827'
isi:
- '000926506800003'
isi: 1
language:
- iso: eng
main_file_link:
- open_access: '1'
url: ' https://doi.org/10.48550/arXiv.2105.11827'
month: '03'
oa: 1
oa_version: Preprint
page: 34-50
publication: Proceedings of the 17th European Conference on Computer Systems
publication_identifier:
isbn:
- '9781450391627'
publication_status: published
publisher: Association for Computing Machinery
quality_controlled: '1'
scopus_import: '1'
status: public
title: 'Narwhal and Tusk: A DAG-based mempool and efficient BFT consensus'
type: conference
user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
year: '2022'
...
---
_id: '11332'
abstract:
- lang: eng
text: We show that the fluctuations of the largest eigenvalue of a real symmetric
or complex Hermitian Wigner matrix of size N converge to the Tracy–Widom laws
at a rate O(N^{-1/3+\omega }), as N tends to infinity. For Wigner matrices this
improves the previous rate O(N^{-2/9+\omega }) obtained by Bourgade (J Eur Math
Soc, 2021) for generalized Wigner matrices. Our result follows from a Green function
comparison theorem, originally introduced by Erdős et al. (Adv Math 229(3):1435–1515,
2012) to prove edge universality, on a finer spectral parameter scale with improved
error estimates. The proof relies on the continuous Green function flow induced
by a matrix-valued Ornstein–Uhlenbeck process. Precise estimates on leading contributions
from the third and fourth order moments of the matrix entries are obtained using
iterative cumulant expansions and recursive comparisons for correlation functions,
along with uniform convergence estimates for correlation kernels of the Gaussian
invariant ensembles.
acknowledgement: Kevin Schnelli is supported in parts by the Swedish Research Council
Grant VR-2017-05195, and the Knut and Alice Wallenberg Foundation. Yuanyuan Xu is
supported by the Swedish Research Council Grant VR-2017-05195 and the ERC Advanced
Grant “RMTBeyond” No. 101020331.
article_processing_charge: No
article_type: original
arxiv: 1
author:
- first_name: Kevin
full_name: Schnelli, Kevin
id: 434AD0AE-F248-11E8-B48F-1D18A9856A87
last_name: Schnelli
orcid: 0000-0003-0954-3231
- first_name: Yuanyuan
full_name: Xu, Yuanyuan
id: 7902bdb1-a2a4-11eb-a164-c9216f71aea3
last_name: Xu
citation:
ama: Schnelli K, Xu Y. Convergence rate to the Tracy–Widom laws for the largest
Eigenvalue of Wigner matrices. Communications in Mathematical Physics.
2022;393:839-907. doi:10.1007/s00220-022-04377-y
apa: Schnelli, K., & Xu, Y. (2022). Convergence rate to the Tracy–Widom laws
for the largest Eigenvalue of Wigner matrices. Communications in Mathematical
Physics. Springer Nature. https://doi.org/10.1007/s00220-022-04377-y
chicago: Schnelli, Kevin, and Yuanyuan Xu. “Convergence Rate to the Tracy–Widom
Laws for the Largest Eigenvalue of Wigner Matrices.” Communications in Mathematical
Physics. Springer Nature, 2022. https://doi.org/10.1007/s00220-022-04377-y.
ieee: K. Schnelli and Y. Xu, “Convergence rate to the Tracy–Widom laws for the largest
Eigenvalue of Wigner matrices,” Communications in Mathematical Physics,
vol. 393. Springer Nature, pp. 839–907, 2022.
ista: Schnelli K, Xu Y. 2022. Convergence rate to the Tracy–Widom laws for the largest
Eigenvalue of Wigner matrices. Communications in Mathematical Physics. 393, 839–907.
mla: Schnelli, Kevin, and Yuanyuan Xu. “Convergence Rate to the Tracy–Widom Laws
for the Largest Eigenvalue of Wigner Matrices.” Communications in Mathematical
Physics, vol. 393, Springer Nature, 2022, pp. 839–907, doi:10.1007/s00220-022-04377-y.
short: K. Schnelli, Y. Xu, Communications in Mathematical Physics 393 (2022) 839–907.
date_created: 2022-04-24T22:01:44Z
date_published: 2022-07-01T00:00:00Z
date_updated: 2023-08-03T06:34:24Z
day: '01'
ddc:
- '510'
department:
- _id: LaEr
doi: 10.1007/s00220-022-04377-y
ec_funded: 1
external_id:
arxiv:
- '2102.04330'
isi:
- '000782737200001'
file:
- access_level: open_access
checksum: bee0278c5efa9a33d9a2dc8d354a6c51
content_type: application/pdf
creator: dernst
date_created: 2022-08-05T06:01:13Z
date_updated: 2022-08-05T06:01:13Z
file_id: '11726'
file_name: 2022_CommunMathPhys_Schnelli.pdf
file_size: 1141462
relation: main_file
success: 1
file_date_updated: 2022-08-05T06:01:13Z
has_accepted_license: '1'
intvolume: ' 393'
isi: 1
language:
- iso: eng
month: '07'
oa: 1
oa_version: Published Version
page: 839-907
project:
- _id: 62796744-2b32-11ec-9570-940b20777f1d
call_identifier: H2020
grant_number: '101020331'
name: Random matrices beyond Wigner-Dyson-Mehta
publication: Communications in Mathematical Physics
publication_identifier:
eissn:
- 1432-0916
issn:
- 0010-3616
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
scopus_import: '1'
status: public
title: Convergence rate to the Tracy–Widom laws for the largest Eigenvalue of Wigner
matrices
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: journal_article
user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
volume: 393
year: '2022'
...
---
_id: '11333'
abstract:
- lang: eng
text: Adenosine triphosphate (ATP) is the energy source for various biochemical
processes and biomolecular motors in living things. Development of ATP antagonists
and their stimuli-controlled actions offer a novel approach to regulate biological
processes. Herein, we developed azobenzene-based photoswitchable ATP antagonists
for controlling the activity of motor proteins; cytoplasmic and axonemal dyneins.
The new ATP antagonists showed reversible photoswitching of cytoplasmic dynein
activity in an in vitro dynein-microtubule system due to the trans and cis photoisomerization
of their azobenzene segment. Importantly, our ATP antagonists reversibly regulated
the axonemal dynein motor activity for the force generation in a demembranated
model of Chlamydomonas reinhardtii. We found that the trans and cis isomers of
ATP antagonists significantly differ in their affinity to the ATP binding site.
article_number: e202200807
article_processing_charge: No
article_type: original
author:
- first_name: Sampreeth
full_name: Thayyil, Sampreeth
last_name: Thayyil
- first_name: Yukinori
full_name: Nishigami, Yukinori
last_name: Nishigami
- first_name: Muhammad J
full_name: Islam, Muhammad J
id: C94881D2-008F-11EA-8E08-2637E6697425
last_name: Islam
- first_name: P. K.
full_name: Hashim, P. K.
last_name: Hashim
- first_name: Ken'Ya
full_name: Furuta, Ken'Ya
last_name: Furuta
- first_name: Kazuhiro
full_name: Oiwa, Kazuhiro
last_name: Oiwa
- first_name: Jian
full_name: Yu, Jian
last_name: Yu
- first_name: Min
full_name: Yao, Min
last_name: Yao
- first_name: Toshiyuki
full_name: Nakagaki, Toshiyuki
last_name: Nakagaki
- first_name: Nobuyuki
full_name: Tamaoki, Nobuyuki
last_name: Tamaoki
citation:
ama: Thayyil S, Nishigami Y, Islam MJ, et al. Dynamic control of microbial movement
by photoswitchable ATP antagonists. Chemistry - A European Journal. 2022;28(30).
doi:10.1002/chem.202200807
apa: Thayyil, S., Nishigami, Y., Islam, M. J., Hashim, P. K., Furuta, K., Oiwa,
K., … Tamaoki, N. (2022). Dynamic control of microbial movement by photoswitchable
ATP antagonists. Chemistry - A European Journal. Wiley. https://doi.org/10.1002/chem.202200807
chicago: Thayyil, Sampreeth, Yukinori Nishigami, Muhammad J Islam, P. K. Hashim,
Ken’Ya Furuta, Kazuhiro Oiwa, Jian Yu, Min Yao, Toshiyuki Nakagaki, and Nobuyuki
Tamaoki. “Dynamic Control of Microbial Movement by Photoswitchable ATP Antagonists.”
Chemistry - A European Journal. Wiley, 2022. https://doi.org/10.1002/chem.202200807.
ieee: S. Thayyil et al., “Dynamic control of microbial movement by photoswitchable
ATP antagonists,” Chemistry - A European Journal, vol. 28, no. 30. Wiley,
2022.
ista: Thayyil S, Nishigami Y, Islam MJ, Hashim PK, Furuta K, Oiwa K, Yu J, Yao M,
Nakagaki T, Tamaoki N. 2022. Dynamic control of microbial movement by photoswitchable
ATP antagonists. Chemistry - A European Journal. 28(30), e202200807.
mla: Thayyil, Sampreeth, et al. “Dynamic Control of Microbial Movement by Photoswitchable
ATP Antagonists.” Chemistry - A European Journal, vol. 28, no. 30, e202200807,
Wiley, 2022, doi:10.1002/chem.202200807.
short: S. Thayyil, Y. Nishigami, M.J. Islam, P.K. Hashim, K. Furuta, K. Oiwa, J.
Yu, M. Yao, T. Nakagaki, N. Tamaoki, Chemistry - A European Journal 28 (2022).
date_created: 2022-04-24T22:01:44Z
date_published: 2022-05-25T00:00:00Z
date_updated: 2023-10-03T10:58:31Z
day: '25'
department:
- _id: RySh
doi: 10.1002/chem.202200807
external_id:
isi:
- '000781658800001'
pmid:
- '35332959'
intvolume: ' 28'
isi: 1
issue: '30'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.1002/chem.202200807
month: '05'
oa: 1
oa_version: Published Version
pmid: 1
publication: Chemistry - A European Journal
publication_identifier:
eissn:
- '15213765'
issn:
- '09476539'
publication_status: published
publisher: Wiley
quality_controlled: '1'
scopus_import: '1'
status: public
title: Dynamic control of microbial movement by photoswitchable ATP antagonists
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 28
year: '2022'
...
---
_id: '11334'
abstract:
- lang: eng
text: Hybridization is a common evolutionary process with multiple possible outcomes.
In vertebrates, interspecific hybridization has repeatedly generated parthenogenetic
hybrid species. However, it is unknown whether the generation of parthenogenetic
hybrids is a rare outcome of frequent hybridization between sexual species within
a genus or the typical outcome of rare hybridization events. Darevskia is a genus
of rock lizards with both hybrid parthenogenetic and sexual species. Using capture
sequencing, we estimate phylogenetic relationships and gene flow among the sexual
species, to determine how introgressive hybridization relates to the origins of
parthenogenetic hybrids. We find evidence for widespread hybridization with gene
flow, both between recently diverged species and deep branches. Surprisingly,
we find no signal of gene flow between parental species of the parthenogenetic
hybrids, suggesting that the parental pairs were either reproductively or geographically
isolated early in their divergence. The generation of parthenogenetic hybrids
in Darevskia is, then, a rare outcome of the total occurrence of hybridization
within the genus, but the typical outcome when specific species pairs hybridize.
Our results question the conventional view that parthenogenetic lineages are generated
by hybridization in a window of divergence. Instead, they suggest that some lineages
possess specific properties that underpin successful parthenogenetic reproduction.
acknowledgement: "The authors thank A. van der Meijden and F. Ahmadzadeh for providing
specimens and tissue samples, and A. Vardanyan, C. Corti, F. Jorge, and S. Drovetski
for support during field work. The authors also thank S. Qiu for assistance with
python scripting, S. Rocha for her support in BEAST analysis, and B. Wielstra for
his comments on\r\na previous version of the manuscript. SF was funded by FCT grant
SFRH/BD/81483/2011 (a PhD individual grant). AMW was funded by the European Union’s
Horizon 2020 research and innovation programme under Marie Skłodowska-Curie grant
agreement no. 797747. TS acknowledges funding from the Swiss National Science Foundation
(grants\r\nPP00P3_170627 and 31003A_182495). The work was carried out under financial
support of the projects “Preserving Armenian biodiversity: Joint Portuguese – Armenian
program for training in modern conservation biology” of Gulbenkian Foundation (Portugal)
and PTDC/BIABEC/101256/2008 of Fundação para a Ciência e a Tecnologia (FCT, Portugal)."
article_processing_charge: No
article_type: original
author:
- first_name: Susana
full_name: Freitas, Susana
last_name: Freitas
- first_name: Anja M
full_name: Westram, Anja M
id: 3C147470-F248-11E8-B48F-1D18A9856A87
last_name: Westram
orcid: 0000-0003-1050-4969
- first_name: Tanja
full_name: Schwander, Tanja
last_name: Schwander
- first_name: Marine
full_name: Arakelyan, Marine
last_name: Arakelyan
- first_name: Çetin
full_name: Ilgaz, Çetin
last_name: Ilgaz
- first_name: Yusuf
full_name: Kumlutas, Yusuf
last_name: Kumlutas
- first_name: David James
full_name: Harris, David James
last_name: Harris
- first_name: Miguel A.
full_name: Carretero, Miguel A.
last_name: Carretero
- first_name: Roger K.
full_name: Butlin, Roger K.
last_name: Butlin
citation:
ama: 'Freitas S, Westram AM, Schwander T, et al. Parthenogenesis in Darevskia lizards:
A rare outcome of common hybridization, not a common outcome of rare hybridization.
Evolution. 2022;76(5):899-914. doi:10.1111/evo.14462'
apa: 'Freitas, S., Westram, A. M., Schwander, T., Arakelyan, M., Ilgaz, Ç., Kumlutas,
Y., … Butlin, R. K. (2022). Parthenogenesis in Darevskia lizards: A rare outcome
of common hybridization, not a common outcome of rare hybridization. Evolution.
Wiley. https://doi.org/10.1111/evo.14462'
chicago: 'Freitas, Susana, Anja M Westram, Tanja Schwander, Marine Arakelyan, Çetin
Ilgaz, Yusuf Kumlutas, David James Harris, Miguel A. Carretero, and Roger K. Butlin.
“Parthenogenesis in Darevskia Lizards: A Rare Outcome of Common Hybridization,
Not a Common Outcome of Rare Hybridization.” Evolution. Wiley, 2022. https://doi.org/10.1111/evo.14462.'
ieee: 'S. Freitas et al., “Parthenogenesis in Darevskia lizards: A rare outcome
of common hybridization, not a common outcome of rare hybridization,” Evolution,
vol. 76, no. 5. Wiley, pp. 899–914, 2022.'
ista: 'Freitas S, Westram AM, Schwander T, Arakelyan M, Ilgaz Ç, Kumlutas Y, Harris
DJ, Carretero MA, Butlin RK. 2022. Parthenogenesis in Darevskia lizards: A rare
outcome of common hybridization, not a common outcome of rare hybridization. Evolution.
76(5), 899–914.'
mla: 'Freitas, Susana, et al. “Parthenogenesis in Darevskia Lizards: A Rare Outcome
of Common Hybridization, Not a Common Outcome of Rare Hybridization.” Evolution,
vol. 76, no. 5, Wiley, 2022, pp. 899–914, doi:10.1111/evo.14462.'
short: S. Freitas, A.M. Westram, T. Schwander, M. Arakelyan, Ç. Ilgaz, Y. Kumlutas,
D.J. Harris, M.A. Carretero, R.K. Butlin, Evolution 76 (2022) 899–914.
date_created: 2022-04-24T22:01:44Z
date_published: 2022-05-01T00:00:00Z
date_updated: 2023-08-03T07:00:28Z
day: '01'
ddc:
- '570'
department:
- _id: NiBa
- _id: BeVi
doi: 10.1111/evo.14462
ec_funded: 1
external_id:
isi:
- '000781632500001'
pmid:
- '35323995'
file:
- access_level: open_access
checksum: c27c025ae9afcf6c804d46a909775ee5
content_type: application/pdf
creator: dernst
date_created: 2022-08-05T06:19:28Z
date_updated: 2022-08-05T06:19:28Z
file_id: '11729'
file_name: 2022_Evolution_Freitas.pdf
file_size: 2855214
relation: main_file
success: 1
file_date_updated: 2022-08-05T06:19:28Z
has_accepted_license: '1'
intvolume: ' 76'
isi: 1
issue: '5'
language:
- iso: eng
month: '05'
oa: 1
oa_version: Published Version
page: 899-914
pmid: 1
project:
- _id: 265B41B8-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '797747'
name: Theoretical and empirical approaches to understanding Parallel Adaptation
publication: Evolution
publication_identifier:
eissn:
- 1558-5646
issn:
- 0014-3820
publication_status: published
publisher: Wiley
quality_controlled: '1'
scopus_import: '1'
status: public
title: 'Parthenogenesis in Darevskia lizards: A rare outcome of common hybridization,
not a common outcome of rare hybridization'
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: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
volume: 76
year: '2022'
...
---
_id: '11336'
abstract:
- lang: eng
text: The generation of a correctly-sized cerebral cortex with all-embracing neuronal
and glial cell-type diversity critically depends on faithful radial glial progenitor
(RGP) cell proliferation/differentiation programs. Temporal RGP lineage progression
is regulated by Polycomb Repressive Complex 2 (PRC2) and loss of PRC2 activity
results in severe neurogenesis defects and microcephaly. How PRC2-dependent gene
expression instructs RGP lineage progression is unknown. Here we utilize Mosaic
Analysis with Double Markers (MADM)-based single cell technology and demonstrate
that PRC2 is not cell-autonomously required in neurogenic RGPs but rather acts
at the global tissue-wide level. Conversely, cortical astrocyte production and
maturation is cell-autonomously controlled by PRC2-dependent transcriptional regulation.
We thus reveal highly distinct and sequential PRC2 functions in RGP lineage progression
that are dependent on complex interplays between intrinsic and tissue-wide properties.
In a broader context our results imply a critical role for the genetic and cellular
niche environment in neural stem cell behavior.
acknowledged_ssus:
- _id: PreCl
- _id: Bio
- _id: LifeSc
acknowledgement: We thank A. Heger (IST Austria Preclinical Facility), A. Sommer and
C. Czepe (VBCF GmbH, NGS Unit) and S. Gharagozlou for technical support. This research was supported by the Scientific Service Units (SSU) of IST Austria through resources provided by the Imaging & Optics
Facility (IOF), Lab Support Facility (LSF), and Preclinical Facility (PCF). N.A.
received funding from the FWF Firnberg-Programm (T 1031). The work was supported by IST institutional funds and by the European Research Council (ERC) under the European Union’s Horizon
2020 research and innovation program (grant agreement 725780 LinPro) to S.H.
article_number: abq1263
article_processing_charge: No
article_type: original
author:
- first_name: Nicole
full_name: Amberg, Nicole
id: 4CD6AAC6-F248-11E8-B48F-1D18A9856A87
last_name: Amberg
orcid: 0000-0002-3183-8207
- first_name: Florian
full_name: Pauler, Florian
id: 48EA0138-F248-11E8-B48F-1D18A9856A87
last_name: Pauler
- first_name: Carmen
full_name: Streicher, Carmen
id: 36BCB99C-F248-11E8-B48F-1D18A9856A87
last_name: Streicher
- first_name: Simon
full_name: Hippenmeyer, Simon
id: 37B36620-F248-11E8-B48F-1D18A9856A87
last_name: Hippenmeyer
orcid: 0000-0003-2279-1061
citation:
ama: Amberg N, Pauler F, Streicher C, Hippenmeyer S. Tissue-wide genetic and cellular
landscape shapes the execution of sequential PRC2 functions in neural stem cell
lineage progression. Science Advances. 2022;8(44). doi:10.1126/sciadv.abq1263
apa: Amberg, N., Pauler, F., Streicher, C., & Hippenmeyer, S. (2022). Tissue-wide
genetic and cellular landscape shapes the execution of sequential PRC2 functions
in neural stem cell lineage progression. Science Advances. American Association
for the Advancement of Science. https://doi.org/10.1126/sciadv.abq1263
chicago: Amberg, Nicole, Florian Pauler, Carmen Streicher, and Simon Hippenmeyer.
“Tissue-Wide Genetic and Cellular Landscape Shapes the Execution of Sequential
PRC2 Functions in Neural Stem Cell Lineage Progression.” Science Advances.
American Association for the Advancement of Science, 2022. https://doi.org/10.1126/sciadv.abq1263.
ieee: N. Amberg, F. Pauler, C. Streicher, and S. Hippenmeyer, “Tissue-wide genetic
and cellular landscape shapes the execution of sequential PRC2 functions in neural
stem cell lineage progression,” Science Advances, vol. 8, no. 44. American
Association for the Advancement of Science, 2022.
ista: Amberg N, Pauler F, Streicher C, Hippenmeyer S. 2022. Tissue-wide genetic
and cellular landscape shapes the execution of sequential PRC2 functions in neural
stem cell lineage progression. Science Advances. 8(44), abq1263.
mla: Amberg, Nicole, et al. “Tissue-Wide Genetic and Cellular Landscape Shapes the
Execution of Sequential PRC2 Functions in Neural Stem Cell Lineage Progression.”
Science Advances, vol. 8, no. 44, abq1263, American Association for the
Advancement of Science, 2022, doi:10.1126/sciadv.abq1263.
short: N. Amberg, F. Pauler, C. Streicher, S. Hippenmeyer, Science Advances 8 (2022).
date_created: 2022-04-26T15:04:50Z
date_published: 2022-11-01T00:00:00Z
date_updated: 2023-05-31T12:24:10Z
day: '01'
ddc:
- '570'
department:
- _id: SiHi
doi: 10.1126/sciadv.abq1263
ec_funded: 1
file:
- access_level: open_access
checksum: 0117023e188542082ca6693cf39e7f03
content_type: application/pdf
creator: patrickd
date_created: 2023-03-21T14:18:10Z
date_updated: 2023-03-21T14:18:10Z
file_id: '12742'
file_name: sciadv.abq1263.pdf
file_size: 2973998
relation: main_file
success: 1
file_date_updated: 2023-03-21T14:18:10Z
has_accepted_license: '1'
intvolume: ' 8'
issue: '44'
language:
- iso: eng
month: '11'
oa: 1
oa_version: Published Version
project:
- _id: 260018B0-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '725780'
name: Principles of Neural Stem Cell Lineage Progression in Cerebral Cortex Development
- _id: 268F8446-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: T0101031
name: Role of Eed in neural stem cell lineage progression
publication: Science Advances
publication_identifier:
issn:
- 2375-2548
publication_status: published
publisher: American Association for the Advancement of Science
quality_controlled: '1'
related_material:
link:
- description: News on ISTA website
relation: press_release
url: https://ista.ac.at/en/news/whole-tissue-shapes-brain-development/
scopus_import: '1'
status: public
title: Tissue-wide genetic and cellular landscape shapes the execution of sequential
PRC2 functions in neural stem cell lineage progression
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: 8
year: '2022'
...
---
_id: '11337'
abstract:
- lang: eng
text: 'Nonanalytic points in the return probability of a quantum state as a function
of time, known as dynamical quantum phase transitions (DQPTs), have received great
attention in recent years, but the understanding of their mechanism is still incomplete.
In our recent work [Phys. Rev. Lett. 126, 040602 (2021)], we demonstrated that
one-dimensional DQPTs can be produced by two distinct mechanisms, namely semiclassical
precession and entanglement generation, leading to the definition of precession
(pDQPTs) and entanglement (eDQPTs) dynamical quantum phase transitions. In this
manuscript, we extend and investigate the notion of p- and eDQPTs in two-dimensional
systems by considering semi-infinite ladders of varying width. For square lattices,
we find that pDQPTs and eDQPTs persist and are characterized by similar phenomenology
as in 1D: pDQPTs are associated with a magnetization sign change and a wide entanglement
gap, while eDQPTs correspond to suppressed local observables and avoided crossings
in the entanglement spectrum. However, DQPTs show higher sensitivity to the ladder
width and other details, challenging the extrapolation to the thermodynamic limit
especially for eDQPTs. Moving to honeycomb lattices, we also demonstrate that
lattices with an odd number of nearest neighbors give rise to phenomenologies
beyond the one-dimensional classification.'
acknowledgement: "We acknowledge support by the European Research Council (ERC) under
the European Union’s Horizon 2020 research and innovation programme (Grant Agreement
No. 850899).\r\nS.D.N. also acknowledges funding from the Institute of Science and
Technology (IST) Austria, and from the European Union’s Horizon 2020 Research and
Innovation Programme under the Marie Skłodowska-Curie Grant Agreement No. 754411."
article_number: '165149'
article_processing_charge: No
article_type: original
arxiv: 1
author:
- first_name: Stefano
full_name: De Nicola, Stefano
id: 42832B76-F248-11E8-B48F-1D18A9856A87
last_name: De Nicola
orcid: 0000-0002-4842-6671
- first_name: Alexios
full_name: Michailidis, Alexios
id: 36EBAD38-F248-11E8-B48F-1D18A9856A87
last_name: Michailidis
- first_name: Maksym
full_name: Serbyn, Maksym
id: 47809E7E-F248-11E8-B48F-1D18A9856A87
last_name: Serbyn
orcid: 0000-0002-2399-5827
citation:
ama: De Nicola S, Michailidis A, Serbyn M. Entanglement and precession in two-dimensional
dynamical quantum phase transitions. Physical Review B. 2022;105. doi:10.1103/PhysRevB.105.165149
apa: De Nicola, S., Michailidis, A., & Serbyn, M. (2022). Entanglement and precession
in two-dimensional dynamical quantum phase transitions. Physical Review B.
American Physical Society. https://doi.org/10.1103/PhysRevB.105.165149
chicago: De Nicola, Stefano, Alexios Michailidis, and Maksym Serbyn. “Entanglement
and Precession in Two-Dimensional Dynamical Quantum Phase Transitions.” Physical
Review B. American Physical Society, 2022. https://doi.org/10.1103/PhysRevB.105.165149.
ieee: S. De Nicola, A. Michailidis, and M. Serbyn, “Entanglement and precession
in two-dimensional dynamical quantum phase transitions,” Physical Review B,
vol. 105. American Physical Society, 2022.
ista: De Nicola S, Michailidis A, Serbyn M. 2022. Entanglement and precession in
two-dimensional dynamical quantum phase transitions. Physical Review B. 105, 165149.
mla: De Nicola, Stefano, et al. “Entanglement and Precession in Two-Dimensional
Dynamical Quantum Phase Transitions.” Physical Review B, vol. 105, 165149,
American Physical Society, 2022, doi:10.1103/PhysRevB.105.165149.
short: S. De Nicola, A. Michailidis, M. Serbyn, Physical Review B 105 (2022).
date_created: 2022-04-28T08:06:10Z
date_published: 2022-04-15T00:00:00Z
date_updated: 2023-08-03T06:33:33Z
day: '15'
department:
- _id: MaSe
doi: 10.1103/PhysRevB.105.165149
ec_funded: 1
external_id:
arxiv:
- '2112.11273'
isi:
- '000806812400004'
intvolume: ' 105'
isi: 1
language:
- iso: eng
main_file_link:
- open_access: '1'
url: ' https://doi.org/10.48550/arXiv.2112.11273'
month: '04'
oa: 1
oa_version: Preprint
project:
- _id: 23841C26-32DE-11EA-91FC-C7463DDC885E
call_identifier: H2020
grant_number: '850899'
name: 'Non-Ergodic Quantum Matter: Universality, Dynamics and Control'
- _id: 260C2330-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '754411'
name: ISTplus - Postdoctoral Fellowships
publication: Physical Review B
publication_identifier:
eisbn:
- 2469-9969
issn:
- 2469-9950
publication_status: published
publisher: American Physical Society
quality_controlled: '1'
status: public
title: Entanglement and precession in two-dimensional dynamical quantum phase transitions
type: journal_article
user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
volume: 105
year: '2022'
...
---
_id: '11339'
abstract:
- lang: eng
text: The interaction between a cell and its environment shapes fundamental intracellular
processes such as cellular metabolism. In most cases growth rate is treated as
a proximal metric for understanding the cellular metabolic status. However, changes
in growth rate might not reflect metabolic variations in individuals responding
to environmental fluctuations. Here we use single-cell microfluidics-microscopy
combined with transcriptomics, proteomics and mathematical modelling to quantify
the accumulation of glucose within Escherichia coli cells. In contrast to the
current consensus, we reveal that environmental conditions which are comparatively
unfavourable for growth, where both nutrients and salinity are depleted, increase
glucose accumulation rates in individual bacteria and population subsets. We find
that these changes in metabolic function are underpinned by variations at the
translational and posttranslational level but not at the transcriptional level
and are not dictated by changes in cell size. The metabolic response-characteristics
identified greatly advance our fundamental understanding of the interactions between
bacteria and their environment and have important ramifications when investigating
cellular processes where salinity plays an important role.
acknowledgement: G.G. was supported by an EPSRC DTP PhD studentship (EP/M506527/1).
M.V. and K.T.A. gratefully acknowledge financial support from the EPSRC (EP/N014391/1).
U.L. was supported through a BBSRC grant (BB/V008021/1) and an MRC Proximity to
Discovery EXCITEME2 grant (MCPC17189). This work was further supported by a Royal
Society Research Grant (RG180007) awarded to S.P. and a QUEX Initiator grant awarded
to S.P. and K.T.A.. D.S.M., T.A.R. and S.P.’s work in this area is also supported
by a Marie Skłodowska-Curie project SINGEK (H2020-MSCA-ITN-2015-675752) and the
Gordon and Betty Moore Foundation Marine Microbiology Initiative (GBMF5514). B.M.I.
acknowledges support from a Wellcome Trust Institutional Strategic Support Award
to the University of Exeter (204909/Z/16/Z). This project utilised equipment funded
by the Wellcome Trust Institutional Strategic Support Fund (WT097835MF), Wellcome
Trust Multi User Equipment Award (WT101650MA) and BBSRC LOLA award (BB/K003240/1).
article_number: '385'
article_processing_charge: No
article_type: original
author:
- first_name: Georgina
full_name: Glover, Georgina
last_name: Glover
- first_name: Margaritis
full_name: Voliotis, Margaritis
last_name: Voliotis
- first_name: Urszula
full_name: Łapińska, Urszula
last_name: Łapińska
- first_name: Brandon M.
full_name: Invergo, Brandon M.
last_name: Invergo
- first_name: Darren
full_name: Soanes, Darren
last_name: Soanes
- first_name: Paul
full_name: O’Neill, Paul
last_name: O’Neill
- first_name: Karen
full_name: Moore, Karen
last_name: Moore
- first_name: Nela
full_name: Nikolic, Nela
id: 42D9CABC-F248-11E8-B48F-1D18A9856A87
last_name: Nikolic
orcid: 0000-0001-9068-6090
- first_name: Peter
full_name: Petrov, Peter
last_name: Petrov
- first_name: David S.
full_name: Milner, David S.
last_name: Milner
- first_name: Sumita
full_name: Roy, Sumita
last_name: Roy
- first_name: Kate
full_name: Heesom, Kate
last_name: Heesom
- first_name: Thomas A.
full_name: Richards, Thomas A.
last_name: Richards
- first_name: Krasimira
full_name: Tsaneva-Atanasova, Krasimira
last_name: Tsaneva-Atanasova
- first_name: Stefano
full_name: Pagliara, Stefano
last_name: Pagliara
citation:
ama: Glover G, Voliotis M, Łapińska U, et al. Nutrient and salt depletion synergistically
boosts glucose metabolism in individual Escherichia coli cells. Communications
Biology. 2022;5. doi:10.1038/s42003-022-03336-6
apa: Glover, G., Voliotis, M., Łapińska, U., Invergo, B. M., Soanes, D., O’Neill,
P., … Pagliara, S. (2022). Nutrient and salt depletion synergistically boosts
glucose metabolism in individual Escherichia coli cells. Communications Biology.
Springer Nature. https://doi.org/10.1038/s42003-022-03336-6
chicago: Glover, Georgina, Margaritis Voliotis, Urszula Łapińska, Brandon M. Invergo,
Darren Soanes, Paul O’Neill, Karen Moore, et al. “Nutrient and Salt Depletion
Synergistically Boosts Glucose Metabolism in Individual Escherichia Coli Cells.”
Communications Biology. Springer Nature, 2022. https://doi.org/10.1038/s42003-022-03336-6.
ieee: G. Glover et al., “Nutrient and salt depletion synergistically boosts
glucose metabolism in individual Escherichia coli cells,” Communications Biology,
vol. 5. Springer Nature, 2022.
ista: Glover G, Voliotis M, Łapińska U, Invergo BM, Soanes D, O’Neill P, Moore K,
Nikolic N, Petrov P, Milner DS, Roy S, Heesom K, Richards TA, Tsaneva-Atanasova
K, Pagliara S. 2022. Nutrient and salt depletion synergistically boosts glucose
metabolism in individual Escherichia coli cells. Communications Biology. 5, 385.
mla: Glover, Georgina, et al. “Nutrient and Salt Depletion Synergistically Boosts
Glucose Metabolism in Individual Escherichia Coli Cells.” Communications Biology,
vol. 5, 385, Springer Nature, 2022, doi:10.1038/s42003-022-03336-6.
short: G. Glover, M. Voliotis, U. Łapińska, B.M. Invergo, D. Soanes, P. O’Neill,
K. Moore, N. Nikolic, P. Petrov, D.S. Milner, S. Roy, K. Heesom, T.A. Richards,
K. Tsaneva-Atanasova, S. Pagliara, Communications Biology 5 (2022).
date_created: 2022-05-01T22:01:41Z
date_published: 2022-04-20T00:00:00Z
date_updated: 2023-08-03T06:45:26Z
day: '20'
ddc:
- '570'
department:
- _id: CaGu
doi: 10.1038/s42003-022-03336-6
external_id:
isi:
- '000784143400001'
pmid:
- '35444215'
file:
- access_level: open_access
checksum: 7c6f76ab17393d650825cc240edc84b3
content_type: application/pdf
creator: dernst
date_created: 2022-05-02T06:26:26Z
date_updated: 2022-05-02T06:26:26Z
file_id: '11342'
file_name: 2022_CommBiology_Glover.pdf
file_size: 2827723
relation: main_file
success: 1
file_date_updated: 2022-05-02T06:26:26Z
has_accepted_license: '1'
intvolume: ' 5'
isi: 1
language:
- iso: eng
month: '04'
oa: 1
oa_version: Published Version
pmid: 1
publication: Communications Biology
publication_identifier:
eissn:
- 2399-3642
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
scopus_import: '1'
status: public
title: Nutrient and salt depletion synergistically boosts glucose metabolism in individual
Escherichia coli cells
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: journal_article
user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
volume: 5
year: '2022'
...
---
_id: '11340'
abstract:
- lang: eng
text: Like-charge attraction, driven by ionic correlations, challenges our understanding
of electrostatics both in soft and hard matter. For two charged planar surfaces
confining counterions and water, we prove that, even at relatively low correlation
strength, the relevant physics is the ground-state one, oblivious of fluctuations.
Based on this, we derive a simple and accurate interaction pressure that fulfills
known exact requirements and can be used as an effective potential. We test this
equation against implicit-solvent Monte Carlo simulations and against explicit-solvent
simulations of cement and several types of clays. We argue that water destructuring
under nanometric confinement drastically reduces dielectric screening, enhancing
ionic correlations. Our equation of state at reduced permittivity therefore explains
the exotic attractive regime reported for these materials, even in the absence
of multivalent counterions.
acknowledgement: We thank Martin Trulsson for useful discussions and for providing
us with simulation data. This work has received funding from the European Union’s
Horizon 2020 research and innovation programme under the Marie Sklodowska-Curie
grant agreement 674979-NANOTRANS. The support received from VEGA Grant No. 2/0092/21
is acknowledged.
article_processing_charge: No
article_type: original
arxiv: 1
author:
- first_name: Ivan
full_name: Palaia, Ivan
id: 9c805cd2-4b75-11ec-a374-db6dd0ed57fa
last_name: Palaia
orcid: ' 0000-0002-8843-9485 '
- first_name: Abhay
full_name: Goyal, Abhay
last_name: Goyal
- first_name: Emanuela
full_name: Del Gado, Emanuela
last_name: Del Gado
- first_name: Ladislav
full_name: Šamaj, Ladislav
last_name: Šamaj
- first_name: Emmanuel
full_name: Trizac, Emmanuel
last_name: Trizac
citation:
ama: 'Palaia I, Goyal A, Del Gado E, Šamaj L, Trizac E. Like-charge attraction at
the nanoscale: Ground-state correlations and water destructuring. Journal of
Physical Chemistry B. 2022;126(16):3143-3149. doi:10.1021/acs.jpcb.2c00028'
apa: 'Palaia, I., Goyal, A., Del Gado, E., Šamaj, L., & Trizac, E. (2022). Like-charge
attraction at the nanoscale: Ground-state correlations and water destructuring.
Journal of Physical Chemistry B. American Chemical Society. https://doi.org/10.1021/acs.jpcb.2c00028'
chicago: 'Palaia, Ivan, Abhay Goyal, Emanuela Del Gado, Ladislav Šamaj, and Emmanuel
Trizac. “Like-Charge Attraction at the Nanoscale: Ground-State Correlations and
Water Destructuring.” Journal of Physical Chemistry B. American Chemical
Society, 2022. https://doi.org/10.1021/acs.jpcb.2c00028.'
ieee: 'I. Palaia, A. Goyal, E. Del Gado, L. Šamaj, and E. Trizac, “Like-charge attraction
at the nanoscale: Ground-state correlations and water destructuring,” Journal
of Physical Chemistry B, vol. 126, no. 16. American Chemical Society, pp.
3143–3149, 2022.'
ista: 'Palaia I, Goyal A, Del Gado E, Šamaj L, Trizac E. 2022. Like-charge attraction
at the nanoscale: Ground-state correlations and water destructuring. Journal of
Physical Chemistry B. 126(16), 3143–3149.'
mla: 'Palaia, Ivan, et al. “Like-Charge Attraction at the Nanoscale: Ground-State
Correlations and Water Destructuring.” Journal of Physical Chemistry B,
vol. 126, no. 16, American Chemical Society, 2022, pp. 3143–49, doi:10.1021/acs.jpcb.2c00028.'
short: I. Palaia, A. Goyal, E. Del Gado, L. Šamaj, E. Trizac, Journal of Physical
Chemistry B 126 (2022) 3143–3149.
date_created: 2022-05-01T22:01:42Z
date_published: 2022-04-14T00:00:00Z
date_updated: 2023-08-03T06:42:50Z
day: '14'
department:
- _id: AnSa
doi: 10.1021/acs.jpcb.2c00028
external_id:
arxiv:
- '2203.10524'
isi:
- '000796953700022'
intvolume: ' 126'
isi: 1
issue: '16'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: ' https://doi.org/10.48550/arXiv.2203.10524'
month: '04'
oa: 1
oa_version: Preprint
page: 3143-3149
publication: Journal of Physical Chemistry B
publication_identifier:
eissn:
- 1520-5207
issn:
- 1520-6106
publication_status: published
publisher: American Chemical Society
quality_controlled: '1'
scopus_import: '1'
status: public
title: 'Like-charge attraction at the nanoscale: Ground-state correlations and water
destructuring'
type: journal_article
user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
volume: 126
year: '2022'
...
---
_id: '11343'
abstract:
- lang: eng
text: Multistable systems are characterized by exhibiting domain coexistence, where
each domain accounts for the different equilibrium states. In case these systems
are described by vectorial fields, domains can be connected through topological
defects. Vortices are one of the most frequent and studied topological defect
points. Optical vortices are equally relevant for their fundamental features as
beams with topological features and their applications in image processing, telecommunications,
optical tweezers, and quantum information. A natural source of optical vortices
is the interaction of light beams with matter vortices in liquid crystal cells.
The rhythms that govern the emergence of matter vortices due to fluctuations are
not established. Here, we investigate the nucleation mechanisms of the matter
vortices in liquid crystal cells and establish statistical laws that govern them.
Based on a stochastic amplitude equation, the law for the number of nucleated
vortices as a function of anisotropy, voltage, and noise level intensity is set.
Experimental observations in a nematic liquid crystal cell with homeotropic anchoring
and a negative anisotropic dielectric constant under the influence of a transversal
electric field show a qualitative agreement with the theoretical findings.
acknowledgement: "The authors thank Enrique Calisto,Michal Kowalczyk, and Michel Ferre
for fructified discussions. This work was funded by ANID—Millennium Science Initiative
Program—ICN17_012. MGC is thankful for financial support from the Fondecyt 1210353
project.\r\nOpen access funding provided by Institute of Science and Technology
(IST Austria)."
article_processing_charge: Yes (via OA deal)
article_type: original
author:
- first_name: Esteban
full_name: Aguilera, Esteban
last_name: Aguilera
- first_name: Marcel G.
full_name: Clerc, Marcel G.
last_name: Clerc
- first_name: Valeska
full_name: Zambra, Valeska
id: 467ed36b-dc96-11ea-b7c8-b043a380b282
last_name: Zambra
citation:
ama: Aguilera E, Clerc MG, Zambra V. Vortices nucleation by inherent fluctuations
in nematic liquid crystal cells. Nonlinear Dynamics. 2022;108:3209-3218.
doi:10.1007/s11071-022-07396-5
apa: Aguilera, E., Clerc, M. G., & Zambra, V. (2022). Vortices nucleation by
inherent fluctuations in nematic liquid crystal cells. Nonlinear Dynamics.
Springer Nature. https://doi.org/10.1007/s11071-022-07396-5
chicago: Aguilera, Esteban, Marcel G. Clerc, and Valeska Zambra. “Vortices Nucleation
by Inherent Fluctuations in Nematic Liquid Crystal Cells.” Nonlinear Dynamics.
Springer Nature, 2022. https://doi.org/10.1007/s11071-022-07396-5.
ieee: E. Aguilera, M. G. Clerc, and V. Zambra, “Vortices nucleation by inherent
fluctuations in nematic liquid crystal cells,” Nonlinear Dynamics, vol.
108. Springer Nature, pp. 3209–3218, 2022.
ista: Aguilera E, Clerc MG, Zambra V. 2022. Vortices nucleation by inherent fluctuations
in nematic liquid crystal cells. Nonlinear Dynamics. 108, 3209–3218.
mla: Aguilera, Esteban, et al. “Vortices Nucleation by Inherent Fluctuations in
Nematic Liquid Crystal Cells.” Nonlinear Dynamics, vol. 108, Springer Nature,
2022, pp. 3209–18, doi:10.1007/s11071-022-07396-5.
short: E. Aguilera, M.G. Clerc, V. Zambra, Nonlinear Dynamics 108 (2022) 3209–3218.
date_created: 2022-05-02T07:01:59Z
date_published: 2022-06-01T00:00:00Z
date_updated: 2023-08-03T06:46:54Z
day: '01'
ddc:
- '530'
department:
- _id: KiMo
doi: 10.1007/s11071-022-07396-5
external_id:
isi:
- '000784871800001'
file:
- access_level: open_access
checksum: 7d80cdece4e1b1c2106e6772a9622f60
content_type: application/pdf
creator: dernst
date_created: 2022-08-05T06:13:19Z
date_updated: 2022-08-05T06:13:19Z
file_id: '11728'
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file_size: 1416049
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file_date_updated: 2022-08-05T06:13:19Z
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intvolume: ' 108'
isi: 1
keyword:
- Electrical and Electronic Engineering
- Applied Mathematics
- Mechanical Engineering
- Ocean Engineering
- Aerospace Engineering
- Control and Systems Engineering
language:
- iso: eng
month: '06'
oa: 1
oa_version: Published Version
page: 3209-3218
publication: Nonlinear Dynamics
publication_identifier:
eissn:
- 1573-269X
issn:
- 0924-090X
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
scopus_import: '1'
status: public
title: Vortices nucleation by inherent fluctuations in nematic liquid crystal cells
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: journal_article
user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
volume: 108
year: '2022'
...
---
_id: '11344'
abstract:
- lang: eng
text: Until recently, Shigella and enteroinvasive Escherichia coli were thought
to be primate-restricted pathogens. The base of their pathogenicity is the type
3 secretion system (T3SS) encoded by the pINV virulence plasmid, which facilitates
host cell invasion and subsequent proliferation. A large family of T3SS effectors,
E3 ubiquitin-ligases encoded by the ipaH genes, have a key role in the Shigella
pathogenicity through the modulation of cellular ubiquitination that degrades
host proteins. However, recent genomic studies identified ipaH genes in the genomes
of Escherichia marmotae, a potential marmot pathogen, and an E. coli extracted
from fecal samples of bovine calves, suggesting that non-human hosts may also
be infected by these strains, potentially pathogenic to humans. We performed a
comparative genomic study of the functional repertoires in the ipaH gene family
in Shigella and enteroinvasive Escherichia from human and predicted non-human
hosts. We found that fewer than half of Shigella genomes had a complete set of
ipaH genes, with frequent gene losses and duplications that were not consistent
with the species tree and nomenclature. Non-human host IpaH proteins had a diverse
set of substrate-binding domains and, in contrast to the Shigella proteins, two
variants of the NEL C-terminal domain. Inconsistencies between strains phylogeny
and composition of effectors indicate horizontal gene transfer between E. coli
adapted to different hosts. These results provide a framework for understanding
of ipaH-mediated host-pathogens interactions and suggest a need for a genomic
study of fecal samples from diseased animals.
acknowledgement: 'The project was initiated with Aygul Minnegalieva and Yulia Yakovleva
at the Summer School of Molecular and Theoretical Biology (SMTB-2020), supported
by the Zimin Foundation. We thank Inna Shapovalenko, Daria Abuzova, Elizaveta Kaminskaya,
and Dmitriy Zvezdin for their contribution to the project during SMTB-2020. We also
thank Peter Vlasov for fruitful discussions.This study was supported by the Russian
Foundation for Basic Research (RFBR), Grant # 20-54-14005 and Fonds zur Förderung
der wissenschaftlichen Forschung (FWF), Grant # I5127-B. The work of OB is supported
by the European Union’s Horizon 2020 Research and Innovation Programme under the
Marie Skłodowska-Curie Grant Agreement No. 754411. '
article_number: '6868'
article_processing_charge: No
article_type: original
author:
- first_name: NO
full_name: Dranenko, NO
last_name: Dranenko
- first_name: MN
full_name: Tutukina, MN
last_name: Tutukina
- first_name: MS
full_name: Gelfand, MS
last_name: Gelfand
- first_name: Fyodor
full_name: Kondrashov, Fyodor
id: 44FDEF62-F248-11E8-B48F-1D18A9856A87
last_name: Kondrashov
orcid: 0000-0001-8243-4694
- first_name: Olga
full_name: Bochkareva, Olga
id: C4558D3C-6102-11E9-A62E-F418E6697425
last_name: Bochkareva
orcid: 0000-0003-1006-6639
citation:
ama: Dranenko N, Tutukina M, Gelfand M, Kondrashov F, Bochkareva O. Chromosome-encoded
IpaH ubiquitin ligases indicate non-human enteroinvasive Escherichia. Scientific
Reports. 2022;12. doi:10.1038/s41598-022-10827-3
apa: Dranenko, N., Tutukina, M., Gelfand, M., Kondrashov, F., & Bochkareva,
O. (2022). Chromosome-encoded IpaH ubiquitin ligases indicate non-human enteroinvasive
Escherichia. Scientific Reports. Springer Nature. https://doi.org/10.1038/s41598-022-10827-3
chicago: Dranenko, NO, MN Tutukina, MS Gelfand, Fyodor Kondrashov, and Olga Bochkareva.
“Chromosome-Encoded IpaH Ubiquitin Ligases Indicate Non-Human Enteroinvasive Escherichia.”
Scientific Reports. Springer Nature, 2022. https://doi.org/10.1038/s41598-022-10827-3.
ieee: N. Dranenko, M. Tutukina, M. Gelfand, F. Kondrashov, and O. Bochkareva, “Chromosome-encoded
IpaH ubiquitin ligases indicate non-human enteroinvasive Escherichia,” Scientific
Reports, vol. 12. Springer Nature, 2022.
ista: Dranenko N, Tutukina M, Gelfand M, Kondrashov F, Bochkareva O. 2022. Chromosome-encoded
IpaH ubiquitin ligases indicate non-human enteroinvasive Escherichia. Scientific
Reports. 12, 6868.
mla: Dranenko, NO, et al. “Chromosome-Encoded IpaH Ubiquitin Ligases Indicate Non-Human
Enteroinvasive Escherichia.” Scientific Reports, vol. 12, 6868, Springer
Nature, 2022, doi:10.1038/s41598-022-10827-3.
short: N. Dranenko, M. Tutukina, M. Gelfand, F. Kondrashov, O. Bochkareva, Scientific
Reports 12 (2022).
date_created: 2022-05-02T07:08:42Z
date_published: 2022-04-27T00:00:00Z
date_updated: 2023-08-03T06:59:49Z
day: '27'
ddc:
- '570'
department:
- _id: FyKo
doi: 10.1038/s41598-022-10827-3
ec_funded: 1
external_id:
isi:
- '000788639400032'
pmid:
- '35477739'
file:
- access_level: open_access
checksum: 12601b8a5c6b83bb618f92bcb963ecc9
content_type: application/pdf
creator: dernst
date_created: 2022-05-02T09:05:20Z
date_updated: 2022-05-02T09:05:20Z
file_id: '11349'
file_name: 2022_ScientificReports_Dranenko.pdf
file_size: 3564155
relation: main_file
success: 1
file_date_updated: 2022-05-02T09:05:20Z
has_accepted_license: '1'
intvolume: ' 12'
isi: 1
language:
- iso: eng
month: '04'
oa: 1
oa_version: Published Version
pmid: 1
project:
- _id: c098eddd-5a5b-11eb-8a69-abe27170a68f
grant_number: I05127
name: Evolutionary analysis of gene regulation
- _id: 260C2330-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '754411'
name: ISTplus - Postdoctoral Fellowships
publication: Scientific Reports
publication_identifier:
issn:
- 2045-2322
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
scopus_import: '1'
status: public
title: Chromosome-encoded IpaH ubiquitin ligases indicate non-human enteroinvasive
Escherichia
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: journal_article
user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
volume: 12
year: '2022'
...
---
_id: '11351'
abstract:
- lang: eng
text: 'One hallmark of plant cells is their cell wall. They protect cells against
the environment and high turgor and mediate morphogenesis through the dynamics
of their mechanical and chemical properties. The walls are a complex polysaccharidic
structure. Although their biochemical composition is well known, how the different
components organize in the volume of the cell wall and interact with each other
is not well understood and yet is key to the wall’s mechanical properties. To
investigate the ultrastructure of the plant cell wall, we imaged the walls of
onion (Allium cepa) bulbs in a near-native state via cryo-focused ion beam milling
(cryo-FIB milling) and cryo-electron tomography (cryo-ET). This allowed the high-resolution
visualization of cellulose fibers in situ. We reveal the coexistence of dense
fiber fields bathed in a reticulated matrix we termed “meshing,” which is more
abundant at the inner surface of the cell wall. The fibers adopted a regular bimodal
angular distribution at all depths in the cell wall and bundled according to their
orientation, creating layers within the cell wall. Concomitantly, employing homogalacturonan
(HG)-specific enzymatic digestion, we observed changes in the meshing, suggesting
that it is—at least in part—composed of HG pectins. We propose the following model
for the construction of the abaxial epidermal primary cell wall: the cell deposits
successive layers of cellulose fibers at −45° and +45° relative to the cell’s
long axis and secretes the surrounding HG-rich meshing proximal to the plasma
membrane, which then migrates to more distal regions of the cell wall.'
acknowledgement: This work was supported by the Howard Hughes Medical Institute (HHMI)
and grant R35 GM122588 to G.J. and the Austrian Science Fund (FWF) P33367 to F.K.M.S.
We thank Noé Cochetel for his guidance and great help in data analysis, discovery,
and representation with the R software. We thank Hans-Ulrich Endress for graciously
providing us with the purified citrus pectin and Jozef Mravec for generating and
providing the COS488 probe. Cryo-EM work was done in the Beckman Institute Resource
Center for Transmission Electron Microscopy at Caltech. This article is subject
to HHMI’s Open Access to Publications policy. HHMI lab heads have previously granted
a nonexclusive CC BY 4.0 license to the public and a sublicensable license to HHMI
in their research articles. Pursuant to those licenses, the author accepted manuscript
of this article can be made freely available under a CC BY 4.0 license immediately
upon publication.
article_processing_charge: No
article_type: original
author:
- first_name: William J.
full_name: Nicolas, William J.
last_name: Nicolas
- first_name: Florian
full_name: Fäßler, Florian
id: 404F5528-F248-11E8-B48F-1D18A9856A87
last_name: Fäßler
orcid: 0000-0001-7149-769X
- first_name: Przemysław
full_name: Dutka, Przemysław
last_name: Dutka
- first_name: Florian KM
full_name: Schur, Florian KM
id: 48AD8942-F248-11E8-B48F-1D18A9856A87
last_name: Schur
orcid: 0000-0003-4790-8078
- first_name: Grant
full_name: Jensen, Grant
last_name: Jensen
- first_name: Elliot
full_name: Meyerowitz, Elliot
last_name: Meyerowitz
citation:
ama: Nicolas WJ, Fäßler F, Dutka P, Schur FK, Jensen G, Meyerowitz E. Cryo-electron
tomography of the onion cell wall shows bimodally oriented cellulose fibers and
reticulated homogalacturonan networks. Current Biology. 2022;32(11):P2375-2389.
doi:10.1016/j.cub.2022.04.024
apa: Nicolas, W. J., Fäßler, F., Dutka, P., Schur, F. K., Jensen, G., & Meyerowitz,
E. (2022). Cryo-electron tomography of the onion cell wall shows bimodally oriented
cellulose fibers and reticulated homogalacturonan networks. Current Biology.
Elsevier. https://doi.org/10.1016/j.cub.2022.04.024
chicago: Nicolas, William J., Florian Fäßler, Przemysław Dutka, Florian KM Schur,
Grant Jensen, and Elliot Meyerowitz. “Cryo-Electron Tomography of the Onion Cell
Wall Shows Bimodally Oriented Cellulose Fibers and Reticulated Homogalacturonan
Networks.” Current Biology. Elsevier, 2022. https://doi.org/10.1016/j.cub.2022.04.024.
ieee: W. J. Nicolas, F. Fäßler, P. Dutka, F. K. Schur, G. Jensen, and E. Meyerowitz,
“Cryo-electron tomography of the onion cell wall shows bimodally oriented cellulose
fibers and reticulated homogalacturonan networks,” Current Biology, vol.
32, no. 11. Elsevier, pp. P2375-2389, 2022.
ista: Nicolas WJ, Fäßler F, Dutka P, Schur FK, Jensen G, Meyerowitz E. 2022. Cryo-electron
tomography of the onion cell wall shows bimodally oriented cellulose fibers and
reticulated homogalacturonan networks. Current Biology. 32(11), P2375-2389.
mla: Nicolas, William J., et al. “Cryo-Electron Tomography of the Onion Cell Wall
Shows Bimodally Oriented Cellulose Fibers and Reticulated Homogalacturonan Networks.”
Current Biology, vol. 32, no. 11, Elsevier, 2022, pp. P2375-2389, doi:10.1016/j.cub.2022.04.024.
short: W.J. Nicolas, F. Fäßler, P. Dutka, F.K. Schur, G. Jensen, E. Meyerowitz,
Current Biology 32 (2022) P2375-2389.
date_created: 2022-05-04T06:22:06Z
date_published: 2022-06-06T00:00:00Z
date_updated: 2023-08-03T07:05:36Z
day: '06'
ddc:
- '570'
department:
- _id: FlSc
doi: 10.1016/j.cub.2022.04.024
external_id:
isi:
- '000822399200019'
pmid:
- '35508170'
file:
- access_level: open_access
checksum: af3f24d97c016d844df237abef987639
content_type: application/pdf
creator: dernst
date_created: 2022-08-05T06:29:18Z
date_updated: 2022-08-05T06:29:18Z
file_id: '11730'
file_name: 2022_CurrentBiology_Nicolas.pdf
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relation: main_file
success: 1
file_date_updated: 2022-08-05T06:29:18Z
has_accepted_license: '1'
intvolume: ' 32'
isi: 1
issue: '11'
keyword:
- General Agricultural and Biological Sciences
- General Biochemistry
- Genetics and Molecular Biology
language:
- iso: eng
month: '06'
oa: 1
oa_version: Published Version
page: P2375-2389
pmid: 1
project:
- _id: 9B954C5C-BA93-11EA-9121-9846C619BF3A
grant_number: P33367
name: Structure and isoform diversity of the Arp2/3 complex
publication: Current Biology
publication_identifier:
issn:
- 0960-9822
publication_status: published
publisher: Elsevier
quality_controlled: '1'
scopus_import: '1'
status: public
title: Cryo-electron tomography of the onion cell wall shows bimodally oriented cellulose
fibers and reticulated homogalacturonan networks
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: journal_article
user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
volume: 32
year: '2022'
...
---
_id: '11353'
abstract:
- lang: eng
text: Micro- and nanoscale optical or microwave cavities are used in a wide range
of classical applications and quantum science experiments, ranging from precision
measurements, laser technologies to quantum control of mechanical motion. The
dissipative photon loss via absorption, present to some extent in any optical
cavity, is known to introduce thermo-optical effects and thereby impose fundamental
limits on precision measurements. Here, we theoretically and experimentally reveal
that such dissipative photon absorption can result in quantum feedback via in-loop
field detection of the absorbed optical field, leading to the intracavity field
fluctuations to be squashed or antisquashed. A closed-loop dissipative quantum
feedback to the cavity field arises. Strikingly, this modifies the optical cavity
susceptibility in coherent response measurements (capable of both increasing or
decreasing the bare cavity linewidth) and causes excess noise and correlations
in incoherent interferometric optomechanical measurements using a cavity, that
is parametrically coupled to a mechanical oscillator. We experimentally observe
such unanticipated dissipative dynamics in optomechanical spectroscopy of sideband-cooled
optomechanical crystal cavitiess at both cryogenic temperature (approximately
8 K) and ambient conditions. The dissipative feedback introduces effective modifications
to the optical cavity linewidth and the optomechanical scattering rate and gives
rise to excess imprecision noise in the interferometric quantum measurement of
mechanical motion. Such dissipative feedback differs fundamentally from a quantum
nondemolition feedback, e.g., optical Kerr squeezing. The dissipative feedback
itself always results in an antisqueezed out-of-loop optical field, while it can
enhance the coexisting Kerr squeezing under certain conditions. Our result applies
to cavity spectroscopy in both optical and superconducting microwave cavities,
and equally applies to any dissipative feedback mechanism of different bandwidth
inside the cavity. It has wide-ranging implications for future dissipation engineering,
such as dissipation enhanced sideband cooling and Kerr squeezing, quantum frequency
conversion, and nonreciprocity in photonic systems.
acknowledgement: "L.Q. acknowledges fruitful discussions with D. Vitali, R. Schnabel,
P.K. Lam, A. Nunnenkamp, and D. Malz. This work is supported by the EUH2020 research
and innovation programme under Grant No. 732894 (FET Proactive HOT), and the European
Research Council through \r\nGrant No. 835329 (ExCOM-cCEO). This work was further
supported by Swiss National Science Foundation under Grant Agreements No. 185870
(Ambizione) and No. 204927. Samples were fabricated at the Center of MicroNanoTechnology
(CMi) at EPFL and the Binnig and Rohrer Nanotechnology Center at IBM Research-Zurich."
article_number: '020309'
article_processing_charge: No
article_type: original
author:
- first_name: Liu
full_name: Qiu, Liu
id: 45e99c0d-1eb1-11eb-9b96-ed8ab2983cac
last_name: Qiu
orcid: 0000-0003-4345-4267
- first_name: Guanhao
full_name: Huang, Guanhao
last_name: Huang
- first_name: Itay
full_name: Shomroni, Itay
last_name: Shomroni
- first_name: Jiahe
full_name: Pan, Jiahe
last_name: Pan
- first_name: Paul
full_name: Seidler, Paul
last_name: Seidler
- first_name: Tobias J.
full_name: Kippenberg, Tobias J.
last_name: Kippenberg
citation:
ama: Qiu L, Huang G, Shomroni I, Pan J, Seidler P, Kippenberg TJ. Dissipative quantum
feedback in measurements using a parametrically coupled microcavity. PRX Quantum.
2022;3(2). doi:10.1103/PRXQuantum.3.020309
apa: Qiu, L., Huang, G., Shomroni, I., Pan, J., Seidler, P., & Kippenberg, T.
J. (2022). Dissipative quantum feedback in measurements using a parametrically
coupled microcavity. PRX Quantum. American Physical Society. https://doi.org/10.1103/PRXQuantum.3.020309
chicago: Qiu, Liu, Guanhao Huang, Itay Shomroni, Jiahe Pan, Paul Seidler, and Tobias
J. Kippenberg. “Dissipative Quantum Feedback in Measurements Using a Parametrically
Coupled Microcavity.” PRX Quantum. American Physical Society, 2022. https://doi.org/10.1103/PRXQuantum.3.020309.
ieee: L. Qiu, G. Huang, I. Shomroni, J. Pan, P. Seidler, and T. J. Kippenberg, “Dissipative
quantum feedback in measurements using a parametrically coupled microcavity,”
PRX Quantum, vol. 3, no. 2. American Physical Society, 2022.
ista: Qiu L, Huang G, Shomroni I, Pan J, Seidler P, Kippenberg TJ. 2022. Dissipative
quantum feedback in measurements using a parametrically coupled microcavity. PRX
Quantum. 3(2), 020309.
mla: Qiu, Liu, et al. “Dissipative Quantum Feedback in Measurements Using a Parametrically
Coupled Microcavity.” PRX Quantum, vol. 3, no. 2, 020309, American Physical
Society, 2022, doi:10.1103/PRXQuantum.3.020309.
short: L. Qiu, G. Huang, I. Shomroni, J. Pan, P. Seidler, T.J. Kippenberg, PRX Quantum
3 (2022).
date_created: 2022-05-08T22:01:43Z
date_published: 2022-04-13T00:00:00Z
date_updated: 2023-08-03T07:05:00Z
day: '13'
ddc:
- '530'
department:
- _id: JoFi
doi: 10.1103/PRXQuantum.3.020309
ec_funded: 1
external_id:
isi:
- '000789316700001'
file:
- access_level: open_access
checksum: 35ff9ddf1d54f64432e435b660edaeb6
content_type: application/pdf
creator: dernst
date_created: 2022-05-09T07:10:51Z
date_updated: 2022-05-09T07:10:51Z
file_id: '11358'
file_name: 2022_PRXQuantum_Qiu.pdf
file_size: 1657177
relation: main_file
success: 1
file_date_updated: 2022-05-09T07:10:51Z
has_accepted_license: '1'
intvolume: ' 3'
isi: 1
issue: '2'
language:
- iso: eng
month: '04'
oa: 1
oa_version: Published Version
project:
- _id: 257EB838-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '732894'
name: Hybrid Optomechanical Technologies
publication: PRX Quantum
publication_identifier:
eissn:
- '26913399'
publication_status: published
publisher: American Physical Society
quality_controlled: '1'
scopus_import: '1'
status: public
title: Dissipative quantum feedback in measurements using a parametrically coupled
microcavity
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: journal_article
user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
volume: 3
year: '2022'
...