---
_id: '11704'
abstract:
- lang: eng
text: In Fall 2020, several European countries reported rapid increases in COVID-19
cases along with growing estimates of the effective reproduction rates. Such an
acceleration in epidemic spread is usually attributed to time-dependent effects,
e.g. human travel, seasonal behavioral changes, mutations of the pathogen etc.
In this case however the acceleration occurred when counter measures such as testing
and contact tracing exceeded their capacity limit. Considering Austria as an example,
here we show that this dynamics can be captured by a time-independent, i.e. autonomous,
compartmental model that incorporates these capacity limits. In this model, the
epidemic acceleration coincides with the exhaustion of mitigation efforts, resulting
in an increasing fraction of undetected cases that drive the effective reproduction
rate progressively higher. We demonstrate that standard models which does not
include this effect necessarily result in a systematic underestimation of the
effective reproduction rate.
article_number: e0269975
article_processing_charge: No
article_type: original
author:
- first_name: Nazmi B
full_name: Budanur, Nazmi B
id: 3EA1010E-F248-11E8-B48F-1D18A9856A87
last_name: Budanur
orcid: 0000-0003-0423-5010
- first_name: Björn
full_name: Hof, Björn
id: 3A374330-F248-11E8-B48F-1D18A9856A87
last_name: Hof
orcid: 0000-0003-2057-2754
citation:
ama: Budanur NB, Hof B. An autonomous compartmental model for accelerating epidemics.
PLoS ONE. 2022;17(7). doi:10.1371/journal.pone.0269975
apa: Budanur, N. B., & Hof, B. (2022). An autonomous compartmental model for
accelerating epidemics. PLoS ONE. Public Library of Science. https://doi.org/10.1371/journal.pone.0269975
chicago: Budanur, Nazmi B, and Björn Hof. “An Autonomous Compartmental Model for
Accelerating Epidemics.” PLoS ONE. Public Library of Science, 2022. https://doi.org/10.1371/journal.pone.0269975.
ieee: N. B. Budanur and B. Hof, “An autonomous compartmental model for accelerating
epidemics,” PLoS ONE, vol. 17, no. 7. Public Library of Science, 2022.
ista: Budanur NB, Hof B. 2022. An autonomous compartmental model for accelerating
epidemics. PLoS ONE. 17(7), e0269975.
mla: Budanur, Nazmi B., and Björn Hof. “An Autonomous Compartmental Model for Accelerating
Epidemics.” PLoS ONE, vol. 17, no. 7, e0269975, Public Library of Science,
2022, doi:10.1371/journal.pone.0269975.
short: N.B. Budanur, B. Hof, PLoS ONE 17 (2022).
corr_author: '1'
date_created: 2022-07-31T22:01:48Z
date_published: 2022-07-18T00:00:00Z
date_updated: 2025-06-11T13:37:36Z
day: '18'
ddc:
- '510'
department:
- _id: BjHo
doi: 10.1371/journal.pone.0269975
external_id:
isi:
- '000911392100055'
pmid:
- '35849565'
file:
- access_level: open_access
checksum: 1ddd9b91e6dec31ab0e7a8433ca2d452
content_type: application/pdf
creator: dernst
date_created: 2022-08-01T08:02:38Z
date_updated: 2022-08-01T08:02:38Z
file_id: '11712'
file_name: 2022_PLoSONE_Budanur.pdf
file_size: 1421256
relation: main_file
success: 1
file_date_updated: 2022-08-01T08:02:38Z
has_accepted_license: '1'
intvolume: ' 17'
isi: 1
issue: '7'
language:
- iso: eng
month: '07'
oa: 1
oa_version: Published Version
pmid: 1
publication: PLoS ONE
publication_identifier:
eissn:
- 1932-6203
publication_status: published
publisher: Public Library of Science
quality_controlled: '1'
related_material:
record:
- id: '11711'
relation: research_data
status: public
scopus_import: '1'
status: public
title: An autonomous compartmental model for accelerating epidemics
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: 17
year: '2022'
...
---
_id: '11705'
abstract:
- lang: eng
text: 'The broad implementation of thermoelectricity requires high-performance and
low-cost materials. One possibility is employing surfactant-free solution synthesis
to produce nanopowders. We propose the strategy of functionalizing “naked” particles’
surface by inorganic molecules to control the nanostructure and, consequently,
thermoelectric performance. In particular, we use bismuth thiolates to functionalize
surfactant-free SnTe particles’ surfaces. Upon thermal processing, bismuth thiolates
decomposition renders SnTe-Bi2S3 nanocomposites with synergistic functions: 1)
carrier concentration optimization by Bi doping; 2) Seebeck coefficient enhancement
and bipolar effect suppression by energy filtering; and 3) lattice thermal conductivity
reduction by small grain domains, grain boundaries and nanostructuration. Overall,
the SnTe-Bi2S3 nanocomposites exhibit peak z T up to 1.3 at 873 K and an average
z T of ≈0.6 at 300–873 K, which is among the highest reported for solution-processed
SnTe.'
acknowledged_ssus:
- _id: EM-Fac
- _id: NanoFab
acknowledgement: This research was supported by the Scientific Service Units (SSU)
of IST Austria through resources provided by Electron Microscopy Facility (EMF)
and the Nanofabrication Facility (NNF). This work was financially supported by IST
Austria and the Werner Siemens Foundation. C.C. acknowledges funding from the FWF
“Lise Meitner Fellowship” grant agreement M 2889-N. Lise Meitner Project (M2889-N).
Y.L. acknowledges funding from the European Union's Horizon 2020 research and innovation
program under the Marie Sklodowska-Curie grant agreement No. 754411. R.L.B. thanks
the National Science Foundation for support under DMR-1904719. MCS acknowledge MINECO
Juan de la Cierva Incorporation fellowship (JdlCI 2019) and Severo Ochoa. M.C.S.
and J.A. acknowledge funding from Generalitat de Catalunya 2017 SGR 327. ICN2 is
supported by the Severo Ochoa program from Spanish MINECO (Grant no. SEV-2017-0706)
and is funded by the CERCA Programme/Generalitat de Catalunya. This study was supported
by MCIN with funding from European Union NextGenerationEU (PRTR-C17.I1) and Generalitat
de Catalunya.
article_number: e202207002
article_processing_charge: Yes (via OA deal)
article_type: original
author:
- first_name: Cheng
full_name: Chang, Cheng
id: 9E331C2E-9F27-11E9-AE48-5033E6697425
last_name: Chang
orcid: 0000-0002-9515-4277
- first_name: Yu
full_name: Liu, Yu
id: 2A70014E-F248-11E8-B48F-1D18A9856A87
last_name: Liu
orcid: 0000-0001-7313-6740
- first_name: Seungho
full_name: Lee, Seungho
id: BB243B88-D767-11E9-B658-BC13E6697425
last_name: Lee
orcid: 0000-0002-6962-8598
- first_name: Maria
full_name: Spadaro, Maria
last_name: Spadaro
- first_name: Kristopher M.
full_name: Koskela, Kristopher M.
last_name: Koskela
- first_name: Tobias
full_name: Kleinhanns, Tobias
id: 8BD9DE16-AB3C-11E9-9C8C-2A03E6697425
last_name: Kleinhanns
- first_name: Tommaso
full_name: Costanzo, Tommaso
id: D93824F4-D9BA-11E9-BB12-F207E6697425
last_name: Costanzo
orcid: 0000-0001-9732-3815
- first_name: Jordi
full_name: Arbiol, Jordi
last_name: Arbiol
- first_name: Richard L.
full_name: Brutchey, Richard L.
last_name: Brutchey
- first_name: Maria
full_name: Ibáñez, Maria
id: 43C61214-F248-11E8-B48F-1D18A9856A87
last_name: Ibáñez
orcid: 0000-0001-5013-2843
citation:
ama: 'Chang C, Liu Y, Lee S, et al. Surface functionalization of surfactant-free
particles: A strategy to tailor the properties of nanocomposites for enhanced
thermoelectric performance. Angewandte Chemie - International Edition.
2022;61(35). doi:10.1002/anie.202207002'
apa: 'Chang, C., Liu, Y., Lee, S., Spadaro, M., Koskela, K. M., Kleinhanns, T.,
… Ibáñez, M. (2022). Surface functionalization of surfactant-free particles: A
strategy to tailor the properties of nanocomposites for enhanced thermoelectric
performance. Angewandte Chemie - International Edition. Wiley. https://doi.org/10.1002/anie.202207002'
chicago: 'Chang, Cheng, Yu Liu, Seungho Lee, Maria Spadaro, Kristopher M. Koskela,
Tobias Kleinhanns, Tommaso Costanzo, Jordi Arbiol, Richard L. Brutchey, and Maria
Ibáñez. “Surface Functionalization of Surfactant-Free Particles: A Strategy to
Tailor the Properties of Nanocomposites for Enhanced Thermoelectric Performance.”
Angewandte Chemie - International Edition. Wiley, 2022. https://doi.org/10.1002/anie.202207002.'
ieee: 'C. Chang et al., “Surface functionalization of surfactant-free particles:
A strategy to tailor the properties of nanocomposites for enhanced thermoelectric
performance,” Angewandte Chemie - International Edition, vol. 61, no. 35.
Wiley, 2022.'
ista: 'Chang C, Liu Y, Lee S, Spadaro M, Koskela KM, Kleinhanns T, Costanzo T, Arbiol
J, Brutchey RL, Ibáñez M. 2022. Surface functionalization of surfactant-free particles:
A strategy to tailor the properties of nanocomposites for enhanced thermoelectric
performance. Angewandte Chemie - International Edition. 61(35), e202207002.'
mla: 'Chang, Cheng, et al. “Surface Functionalization of Surfactant-Free Particles:
A Strategy to Tailor the Properties of Nanocomposites for Enhanced Thermoelectric
Performance.” Angewandte Chemie - International Edition, vol. 61, no. 35,
e202207002, Wiley, 2022, doi:10.1002/anie.202207002.'
short: C. Chang, Y. Liu, S. Lee, M. Spadaro, K.M. Koskela, T. Kleinhanns, T. Costanzo,
J. Arbiol, R.L. Brutchey, M. Ibáñez, Angewandte Chemie - International Edition
61 (2022).
corr_author: '1'
date_created: 2022-07-31T22:01:48Z
date_published: 2022-08-26T00:00:00Z
date_updated: 2025-04-14T07:44:07Z
day: '26'
ddc:
- '540'
department:
- _id: MaIb
- _id: EM-Fac
doi: 10.1002/anie.202207002
ec_funded: 1
external_id:
isi:
- '000828274200001'
pmid:
- '38505739'
file:
- access_level: open_access
checksum: ad601f2b9e26e46ab4785162be58b5ed
content_type: application/pdf
creator: dernst
date_created: 2023-02-02T08:01:00Z
date_updated: 2023-02-02T08:01:00Z
file_id: '12476'
file_name: 2022_AngewandteChemieInternat_Chang.pdf
file_size: 4072650
relation: main_file
success: 1
file_date_updated: 2023-02-02T08:01:00Z
has_accepted_license: '1'
intvolume: ' 61'
isi: 1
issue: '35'
language:
- iso: eng
month: '08'
oa: 1
oa_version: Published Version
pmid: 1
project:
- _id: 9B8804FC-BA93-11EA-9121-9846C619BF3A
grant_number: M02889
name: Bottom-up Engineering for Thermoelectric Applications
- _id: 260C2330-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '754411'
name: ISTplus - Postdoctoral Fellowships
publication: Angewandte Chemie - International Edition
publication_identifier:
eissn:
- 1521-3773
issn:
- 1433-7851
publication_status: published
publisher: Wiley
quality_controlled: '1'
scopus_import: '1'
status: public
title: 'Surface functionalization of surfactant-free particles: A strategy to tailor
the properties of nanocomposites for enhanced thermoelectric performance'
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: 61
year: '2022'
...
---
_id: '11707'
abstract:
- lang: eng
text: 'In this work we introduce the graph-theoretic notion of mendability: for
each locally checkable graph problem we can define its mending radius, which captures
the idea of how far one needs to modify a partial solution in order to “patch
a hole.” We explore how mendability is connected to the existence of efficient
algorithms, especially in distributed, parallel, and fault-tolerant settings.
It is easy to see that O(1)-mendable problems are also solvable in O(log∗n) rounds
in the LOCAL model of distributed computing. One of the surprises is that in paths
and cycles, a converse also holds in the following sense: if a problem Π can be
solved in O(log∗n), there is always a restriction Π′⊆Π that is still efficiently
solvable but that is also O(1)-mendable. We also explore the structure of the
landscape of mendability. For example, we show that in trees, the mending radius
of any locally checkable problem is O(1), Θ(logn), or Θ(n), while in general graphs
the structure is much more diverse.'
acknowledgement: This project has received funding from the European Union’s Horizon
2020 research and innovation programme under the Marie Skłodowska-Curie grant agreement
No 840605. This work was supported in part by the Academy of Finland, Grants 314888
and 333837. The authors would also like to thank David Harris, Neven Villani, and
the anonymous reviewers for their very helpful comments and feedback on previous
versions of this work.
article_processing_charge: No
arxiv: 1
author:
- first_name: Alkida
full_name: Balliu, Alkida
last_name: Balliu
- first_name: Juho
full_name: Hirvonen, Juho
last_name: Hirvonen
- first_name: Darya
full_name: Melnyk, Darya
last_name: Melnyk
- first_name: Dennis
full_name: Olivetti, Dennis
last_name: Olivetti
- first_name: Joel
full_name: Rybicki, Joel
id: 334EFD2E-F248-11E8-B48F-1D18A9856A87
last_name: Rybicki
orcid: 0000-0002-6432-6646
- first_name: Jukka
full_name: Suomela, Jukka
last_name: Suomela
citation:
ama: 'Balliu A, Hirvonen J, Melnyk D, Olivetti D, Rybicki J, Suomela J. Local mending.
In: Parter M, ed. International Colloquium on Structural Information and Communication
Complexity. Vol 13298. LNCS. Springer Nature; 2022:1-20. doi:10.1007/978-3-031-09993-9_1'
apa: 'Balliu, A., Hirvonen, J., Melnyk, D., Olivetti, D., Rybicki, J., & Suomela,
J. (2022). Local mending. In M. Parter (Ed.), International Colloquium on Structural
Information and Communication Complexity (Vol. 13298, pp. 1–20). Paderborn,
Germany: Springer Nature. https://doi.org/10.1007/978-3-031-09993-9_1'
chicago: Balliu, Alkida, Juho Hirvonen, Darya Melnyk, Dennis Olivetti, Joel Rybicki,
and Jukka Suomela. “Local Mending.” In International Colloquium on Structural
Information and Communication Complexity, edited by Merav Parter, 13298:1–20.
LNCS. Springer Nature, 2022. https://doi.org/10.1007/978-3-031-09993-9_1.
ieee: A. Balliu, J. Hirvonen, D. Melnyk, D. Olivetti, J. Rybicki, and J. Suomela,
“Local mending,” in International Colloquium on Structural Information and
Communication Complexity, Paderborn, Germany, 2022, vol. 13298, pp. 1–20.
ista: 'Balliu A, Hirvonen J, Melnyk D, Olivetti D, Rybicki J, Suomela J. 2022. Local
mending. International Colloquium on Structural Information and Communication
Complexity. SIROCCO: Structural Information and Communication ComplexityLNCS vol.
13298, 1–20.'
mla: Balliu, Alkida, et al. “Local Mending.” International Colloquium on Structural
Information and Communication Complexity, edited by Merav Parter, vol. 13298,
Springer Nature, 2022, pp. 1–20, doi:10.1007/978-3-031-09993-9_1.
short: A. Balliu, J. Hirvonen, D. Melnyk, D. Olivetti, J. Rybicki, J. Suomela, in:,
M. Parter (Ed.), International Colloquium on Structural Information and Communication
Complexity, Springer Nature, 2022, pp. 1–20.
conference:
end_date: 2022-06-29
location: Paderborn, Germany
name: 'SIROCCO: Structural Information and Communication Complexity'
start_date: 2022-06-27
date_created: 2022-07-31T22:01:49Z
date_published: 2022-06-25T00:00:00Z
date_updated: 2025-04-14T07:50:55Z
day: '25'
department:
- _id: DaAl
doi: 10.1007/978-3-031-09993-9_1
ec_funded: 1
editor:
- first_name: Merav
full_name: Parter, Merav
last_name: Parter
external_id:
arxiv:
- '2102.08703'
isi:
- '000876977400001'
intvolume: ' 13298'
isi: 1
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/2102.08703
month: '06'
oa: 1
oa_version: Preprint
page: 1-20
project:
- _id: 26A5D39A-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '840605'
name: Coordination in constrained and natural distributed systems
publication: International Colloquium on Structural Information and Communication
Complexity
publication_identifier:
eissn:
- 1611-3349
isbn:
- '9783031099922'
issn:
- 0302-9743
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
scopus_import: '1'
series_title: LNCS
status: public
title: Local mending
type: conference
user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
volume: 13298
year: '2022'
...
---
_id: '11711'
abstract:
- lang: eng
text: Codes and data for reproducing the results of N. B. Budanur and B. Hof "An
autonomous compartmental model for accelerating epidemics"
article_processing_charge: No
author:
- first_name: Nazmi B
full_name: Budanur, Nazmi B
id: 3EA1010E-F248-11E8-B48F-1D18A9856A87
last_name: Budanur
orcid: 0000-0003-0423-5010
citation:
ama: Budanur NB. burakbudanur/autoacc-public. 2022. doi:10.5281/ZENODO.6802720
apa: Budanur, N. B. (2022). burakbudanur/autoacc-public. Zenodo. https://doi.org/10.5281/ZENODO.6802720
chicago: Budanur, Nazmi B. “Burakbudanur/Autoacc-Public.” Zenodo, 2022. https://doi.org/10.5281/ZENODO.6802720.
ieee: N. B. Budanur, “burakbudanur/autoacc-public.” Zenodo, 2022.
ista: Budanur NB. 2022. burakbudanur/autoacc-public, Zenodo, 10.5281/ZENODO.6802720.
mla: Budanur, Nazmi B. Burakbudanur/Autoacc-Public. Zenodo, 2022, doi:10.5281/ZENODO.6802720.
short: N.B. Budanur, (2022).
corr_author: '1'
date_created: 2022-08-01T08:06:33Z
date_published: 2022-07-06T00:00:00Z
date_updated: 2025-06-11T13:37:36Z
day: '06'
ddc:
- '000'
department:
- _id: BjHo
doi: 10.5281/ZENODO.6802720
has_accepted_license: '1'
license: https://creativecommons.org/publicdomain/zero/1.0/
main_file_link:
- open_access: '1'
url: https://doi.org/10.5281/ZENODO.6802720
month: '07'
oa: 1
oa_version: Published Version
publisher: Zenodo
related_material:
record:
- id: '11704'
relation: used_in_publication
status: public
status: public
title: burakbudanur/autoacc-public
tmp:
image: /images/cc_0.png
legal_code_url: https://creativecommons.org/publicdomain/zero/1.0/legalcode
name: Creative Commons Public Domain Dedication (CC0 1.0)
short: CC0 (1.0)
type: research_data_reference
user_id: 6785fbc1-c503-11eb-8a32-93094b40e1cf
year: '2022'
...
---
_id: '11713'
abstract:
- lang: eng
text: "Objective: MazF is a sequence-specific endoribonuclease-toxin of the MazEF
toxin–antitoxin system. MazF cleaves single-stranded ribonucleic acid (RNA) regions
at adenine–cytosine–adenine (ACA) sequences in the bacterium Escherichia coli.
The MazEF system has been used in various biotechnology and synthetic biology
applications. In this study, we infer how ectopic mazF overexpression affects
production of heterologous proteins. To this end, we quantified the levels of
fluorescent proteins expressed in E. coli from reporters translated from the ACA-containing
or ACA-less messenger RNAs (mRNAs). Additionally, we addressed the impact of the
5′-untranslated region of these reporter mRNAs under the same conditions by comparing
expression from mRNAs that comprise (canonical mRNA) or lack this region (leaderless
mRNA).\r\nResults: Flow cytometry analysis indicates that during mazF overexpression,
fluorescent proteins are translated from the canonical as well as leaderless mRNAs.
Our analysis further indicates that longer mazF overexpression generally increases
the concentration of fluorescent proteins translated from ACA-less mRNAs, however
it also substantially increases bacterial population heterogeneity. Finally, our
results suggest that the strength and duration of mazF overexpression should be
optimized for each experimental setup, to maximize the heterologous protein production
and minimize the amount of phenotypic heterogeneity in bacterial populations,
which is unfavorable in biotechnological processes."
acknowledgement: "We acknowledge the Max Perutz Labs FACS Facility together with Thomas
Sauer. NN is grateful to Călin C. Guet for his support.\r\nThis work was funded
by the Elise Richter grant V738 of the Austrian Science Fund (FWF), and the FWF
Lise Meitner grant M1697, to NN; and by the FWF grant P22249, FWF Special Research
Program RNA-REG F43 (subproject F4316), and FWF doctoral program RNA Biology (W1207),
to IM. Open access funding provided by the Austrian Science Fund."
article_number: '173'
article_processing_charge: No
article_type: letter_note
author:
- first_name: Nela
full_name: Nikolic, Nela
id: 42D9CABC-F248-11E8-B48F-1D18A9856A87
last_name: Nikolic
orcid: 0000-0001-9068-6090
- first_name: Martina
full_name: Sauert, Martina
last_name: Sauert
- first_name: Tanino G.
full_name: Albanese, Tanino G.
last_name: Albanese
- first_name: Isabella
full_name: Moll, Isabella
last_name: Moll
citation:
ama: Nikolic N, Sauert M, Albanese TG, Moll I. Quantifying heterologous gene expression
during ectopic MazF production in Escherichia coli. BMC Research Notes.
2022;15. doi:10.1186/s13104-022-06061-9
apa: Nikolic, N., Sauert, M., Albanese, T. G., & Moll, I. (2022). Quantifying
heterologous gene expression during ectopic MazF production in Escherichia coli.
BMC Research Notes. Springer Nature. https://doi.org/10.1186/s13104-022-06061-9
chicago: Nikolic, Nela, Martina Sauert, Tanino G. Albanese, and Isabella Moll. “Quantifying
Heterologous Gene Expression during Ectopic MazF Production in Escherichia Coli.”
BMC Research Notes. Springer Nature, 2022. https://doi.org/10.1186/s13104-022-06061-9.
ieee: N. Nikolic, M. Sauert, T. G. Albanese, and I. Moll, “Quantifying heterologous
gene expression during ectopic MazF production in Escherichia coli,” BMC Research
Notes, vol. 15. Springer Nature, 2022.
ista: Nikolic N, Sauert M, Albanese TG, Moll I. 2022. Quantifying heterologous gene
expression during ectopic MazF production in Escherichia coli. BMC Research Notes.
15, 173.
mla: Nikolic, Nela, et al. “Quantifying Heterologous Gene Expression during Ectopic
MazF Production in Escherichia Coli.” BMC Research Notes, vol. 15, 173,
Springer Nature, 2022, doi:10.1186/s13104-022-06061-9.
short: N. Nikolic, M. Sauert, T.G. Albanese, I. Moll, BMC Research Notes 15 (2022).
corr_author: '1'
date_created: 2022-08-01T09:04:27Z
date_published: 2022-05-13T00:00:00Z
date_updated: 2025-04-14T09:24:53Z
day: '13'
ddc:
- '570'
department:
- _id: CaGu
doi: 10.1186/s13104-022-06061-9
external_id:
pmid:
- '35562780'
file:
- access_level: open_access
checksum: 008156e5340e9789f0f6d82bde4d347a
content_type: application/pdf
creator: dernst
date_created: 2022-08-01T09:24:42Z
date_updated: 2022-08-01T09:24:42Z
file_id: '11714'
file_name: 2022_BMCResearchNotes_Nikolic.pdf
file_size: 1545310
relation: main_file
success: 1
file_date_updated: 2022-08-01T09:24:42Z
has_accepted_license: '1'
intvolume: ' 15'
keyword:
- General Biochemistry
- Genetics and Molecular Biology
- General Medicine
language:
- iso: eng
month: '05'
oa: 1
oa_version: Published Version
pmid: 1
project:
- _id: 26956E74-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: V00738
name: Bacterial toxin-antitoxin systems as antiphage defense mechanisms
publication: BMC Research Notes
publication_identifier:
issn:
- 1756-0500
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
related_material:
link:
- relation: erratum
url: https://doi.org/10.1186/s13104-022-06152-7
scopus_import: '1'
status: public
title: Quantifying heterologous gene expression during ectopic MazF production in
Escherichia coli
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: 15
year: '2022'
...
---
_id: '11717'
abstract:
- lang: eng
text: "We study rigidity of rational maps that come from Newton's root finding method
for polynomials of arbitrary degrees. We establish dynamical rigidity of these
maps: each point in the Julia set of a Newton map is either rigid (i.e. its orbit
can be distinguished in combinatorial terms from all other orbits), or the orbit
of this point eventually lands in the filled-in Julia set of a polynomial-like
restriction of the original map. As a corollary, we show that the Julia sets of
Newton maps in many non-trivial cases are locally connected; in particular, every
cubic Newton map without Siegel points has locally connected Julia set.\r\nIn
the parameter space of Newton maps of arbitrary degree we obtain the following
rigidity result: any two combinatorially equivalent Newton maps are quasiconformally
conjugate in a neighborhood of their Julia sets provided that they either non-renormalizable,
or they are both renormalizable “in the same way”.\r\nOur main tool is a generalized
renormalization concept called “complex box mappings” for which we extend a dynamical
rigidity result by Kozlovski and van Strien so as to include irrationally indifferent
and renormalizable situations."
acknowledgement: 'We are grateful to a number of colleagues for helpful and inspiring
discussions during the time when we worked on this project, in particular Dima Dudko,
Misha Hlushchanka, John Hubbard, Misha Lyubich, Oleg Kozlovski, and Sebastian van
Strien. Finally, we would like to thank our dynamics research group for numerous
helpful and enjoyable discussions: Konstantin Bogdanov, Roman Chernov, Russell Lodge,
Steffen Maaß, David Pfrang, Bernhard Reinke, Sergey Shemyakov, and Maik Sowinski.
We gratefully acknowledge support by the Advanced Grant “HOLOGRAM” (#695 621) of
the European Research Council (ERC), as well as hospitality of Cornell University
in the spring of 2018 while much of this work was prepared. The first-named author
also acknowledges the support of the ERC Advanced Grant “SPERIG” (#885 707).'
article_number: '108591'
article_processing_charge: Yes (via OA deal)
article_type: original
author:
- first_name: Kostiantyn
full_name: Drach, Kostiantyn
id: fe8209e2-906f-11eb-847d-950f8fc09115
last_name: Drach
orcid: 0000-0002-9156-8616
- first_name: Dierk
full_name: Schleicher, Dierk
last_name: Schleicher
citation:
ama: Drach K, Schleicher D. Rigidity of Newton dynamics. Advances in Mathematics.
2022;408(Part A). doi:10.1016/j.aim.2022.108591
apa: Drach, K., & Schleicher, D. (2022). Rigidity of Newton dynamics. Advances
in Mathematics. Elsevier. https://doi.org/10.1016/j.aim.2022.108591
chicago: Drach, Kostiantyn, and Dierk Schleicher. “Rigidity of Newton Dynamics.”
Advances in Mathematics. Elsevier, 2022. https://doi.org/10.1016/j.aim.2022.108591.
ieee: K. Drach and D. Schleicher, “Rigidity of Newton dynamics,” Advances in
Mathematics, vol. 408, no. Part A. Elsevier, 2022.
ista: Drach K, Schleicher D. 2022. Rigidity of Newton dynamics. Advances in Mathematics.
408(Part A), 108591.
mla: Drach, Kostiantyn, and Dierk Schleicher. “Rigidity of Newton Dynamics.” Advances
in Mathematics, vol. 408, no. Part A, 108591, Elsevier, 2022, doi:10.1016/j.aim.2022.108591.
short: K. Drach, D. Schleicher, Advances in Mathematics 408 (2022).
corr_author: '1'
date_created: 2022-08-01T17:08:16Z
date_published: 2022-10-29T00:00:00Z
date_updated: 2025-04-14T07:53:45Z
day: '29'
ddc:
- '510'
department:
- _id: VaKa
doi: 10.1016/j.aim.2022.108591
ec_funded: 1
external_id:
isi:
- '000860924200005'
file:
- access_level: open_access
checksum: 2710e6f5820f8c20a676ddcbb30f0e8d
content_type: application/pdf
creator: dernst
date_created: 2023-02-02T07:39:09Z
date_updated: 2023-02-02T07:39:09Z
file_id: '12474'
file_name: 2022_AdvancesMathematics_Drach.pdf
file_size: 2164036
relation: main_file
success: 1
file_date_updated: 2023-02-02T07:39:09Z
has_accepted_license: '1'
intvolume: ' 408'
isi: 1
issue: Part A
keyword:
- General Mathematics
language:
- iso: eng
month: '10'
oa: 1
oa_version: Published Version
project:
- _id: 9B8B92DE-BA93-11EA-9121-9846C619BF3A
call_identifier: H2020
grant_number: '885707'
name: Spectral rigidity and integrability for billiards and geodesic flows
publication: Advances in Mathematics
publication_identifier:
issn:
- 0001-8708
publication_status: published
publisher: Elsevier
quality_controlled: '1'
scopus_import: '1'
status: public
title: Rigidity of Newton dynamics
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: 408
year: '2022'
...
---
_id: '11723'
abstract:
- lang: eng
text: Plant cell growth responds rapidly to various stimuli, adapting architecture
to environmental changes. Two major endogenous signals regulating growth are the
phytohormone auxin and the secreted peptides rapid alkalinization factors (RALFs).
Both trigger very rapid cellular responses and also exert long-term effects [Du
et al., Annu. Rev. Plant Biol. 71, 379–402 (2020); Blackburn et al., Plant Physiol.
182, 1657–1666 (2020)]. However, the way, in which these distinct signaling pathways
converge to regulate growth, remains unknown. Here, using vertical confocal microscopy
combined with a microfluidic chip, we addressed the mechanism of RALF action on
growth. We observed correlation between RALF1-induced rapid Arabidopsis thaliana
root growth inhibition and apoplast alkalinization during the initial phase of
the response, and revealed that RALF1 reversibly inhibits primary root growth
through apoplast alkalinization faster than within 1 min. This rapid apoplast
alkalinization was the result of RALF1-induced net H+ influx and was mediated
by the receptor FERONIA (FER). Furthermore, we investigated the cross-talk between
RALF1 and the auxin signaling pathways during root growth regulation. The results
showed that RALF-FER signaling triggered auxin signaling with a delay of approximately
1 h by up-regulating auxin biosynthesis, thus contributing to sustained RALF1-induced
growth inhibition. This biphasic RALF1 action on growth allows plants to respond
rapidly to environmental stimuli and also reprogram growth and development in
the long term.
acknowledgement: We thank Sarah M. Assmann, Kris Vissenberg, and Nadine Paris for
kindly sharing seeds; Matyáš Fendrych for initiating this project and providing
constant support; Lukas Fiedler for revising the manuscript; and Huibin Han and
Arseny Savin for contributing to genotyping. This work was supported by the Austrian
Science Fund (FWF) I 3630-B25 (to J.F.) and the Doctoral Fellowship Progrmme of
the Austrian Academy of Sciences (to L.L.) We also acknowledge Taif University Researchers
Supporting Project TURSP-HC2021/02 and funding “Plants as a tool for sustainable
global development (no. CZ.02.1.01/0.0/0.0/16_019/0000827).”
article_number: e2121058119
article_processing_charge: No
article_type: original
author:
- first_name: Lanxin
full_name: Li, Lanxin
id: 367EF8FA-F248-11E8-B48F-1D18A9856A87
last_name: Li
orcid: 0000-0002-5607-272X
- first_name: Huihuang
full_name: Chen, Huihuang
id: 83c96512-15b2-11ec-abd3-b7eede36184f
last_name: Chen
- first_name: Saqer S.
full_name: Alotaibi, Saqer S.
last_name: Alotaibi
- first_name: Aleš
full_name: Pěnčík, Aleš
last_name: Pěnčík
- first_name: Maciek
full_name: Adamowski, Maciek
id: 45F536D2-F248-11E8-B48F-1D18A9856A87
last_name: Adamowski
orcid: 0000-0001-6463-5257
- first_name: Ondřej
full_name: Novák, Ondřej
last_name: Novák
- first_name: Jiří
full_name: Friml, Jiří
id: 4159519E-F248-11E8-B48F-1D18A9856A87
last_name: Friml
orcid: 0000-0002-8302-7596
citation:
ama: Li L, Chen H, Alotaibi SS, et al. RALF1 peptide triggers biphasic root growth
inhibition upstream of auxin biosynthesis. Proceedings of the National Academy
of Sciences of the United States of America. 2022;119(31). doi:10.1073/pnas.2121058119
apa: Li, L., Chen, H., Alotaibi, S. S., Pěnčík, A., Adamowski, M., Novák, O., &
Friml, J. (2022). RALF1 peptide triggers biphasic root growth inhibition upstream
of auxin biosynthesis. Proceedings of the National Academy of Sciences of the
United States of America. National Academy of Sciences. https://doi.org/10.1073/pnas.2121058119
chicago: Li, Lanxin, Huihuang Chen, Saqer S. Alotaibi, Aleš Pěnčík, Maciek Adamowski,
Ondřej Novák, and Jiří Friml. “RALF1 Peptide Triggers Biphasic Root Growth Inhibition
Upstream of Auxin Biosynthesis.” Proceedings of the National Academy of Sciences
of the United States of America. National Academy of Sciences, 2022. https://doi.org/10.1073/pnas.2121058119.
ieee: L. Li et al., “RALF1 peptide triggers biphasic root growth inhibition
upstream of auxin biosynthesis,” Proceedings of the National Academy of Sciences
of the United States of America, vol. 119, no. 31. National Academy of Sciences,
2022.
ista: Li L, Chen H, Alotaibi SS, Pěnčík A, Adamowski M, Novák O, Friml J. 2022.
RALF1 peptide triggers biphasic root growth inhibition upstream of auxin biosynthesis.
Proceedings of the National Academy of Sciences of the United States of America.
119(31), e2121058119.
mla: Li, Lanxin, et al. “RALF1 Peptide Triggers Biphasic Root Growth Inhibition
Upstream of Auxin Biosynthesis.” Proceedings of the National Academy of Sciences
of the United States of America, vol. 119, no. 31, e2121058119, National Academy
of Sciences, 2022, doi:10.1073/pnas.2121058119.
short: L. Li, H. Chen, S.S. Alotaibi, A. Pěnčík, M. Adamowski, O. Novák, J. Friml,
Proceedings of the National Academy of Sciences of the United States of America
119 (2022).
corr_author: '1'
date_created: 2022-08-04T20:06:49Z
date_published: 2022-07-25T00:00:00Z
date_updated: 2025-05-14T11:01:00Z
day: '25'
ddc:
- '580'
department:
- _id: GradSch
- _id: JiFr
doi: 10.1073/pnas.2121058119
external_id:
isi:
- '000881496900002'
pmid:
- '35878023'
file:
- access_level: open_access
checksum: ae6f19b0d9efba6687f9e4dc1bab1d6e
content_type: application/pdf
creator: dernst
date_created: 2022-08-08T07:42:09Z
date_updated: 2022-08-08T07:42:09Z
file_id: '11747'
file_name: 2022_PNAS_Li.pdf
file_size: 2506262
relation: main_file
success: 1
file_date_updated: 2022-08-08T07:42:09Z
has_accepted_license: '1'
intvolume: ' 119'
isi: 1
issue: '31'
keyword:
- Multidisciplinary
language:
- iso: eng
month: '07'
oa: 1
oa_version: Published Version
pmid: 1
project:
- _id: 26538374-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: I03630
name: Molecular mechanisms of endocytic cargo recognition in plants
- _id: 26B4D67E-B435-11E9-9278-68D0E5697425
grant_number: '25351'
name: 'A Case Study of Plant Growth Regulation: Molecular Mechanism of Auxin-mediated
Rapid Growth Inhibition in Arabidopsis Root'
publication: Proceedings of the National Academy of Sciences of the United States
of America
publication_identifier:
eissn:
- 1091-6490
issn:
- 0027-8424
publication_status: published
publisher: National Academy of Sciences
quality_controlled: '1'
scopus_import: '1'
status: public
title: RALF1 peptide triggers biphasic root growth inhibition upstream of auxin biosynthesis
tmp:
image: /images/cc_by_nc_nd.png
legal_code_url: https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode
name: Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International
(CC BY-NC-ND 4.0)
short: CC BY-NC-ND (4.0)
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 119
year: '2022'
...
---
_id: '11733'
abstract:
- lang: eng
text: Genetically informed, deep-phenotyped biobanks are an important research resource
and it is imperative that the most powerful, versatile, and efficient analysis
approaches are used. Here, we apply our recently developed Bayesian grouped mixture
of regressions model (GMRM) in the UK and Estonian Biobanks and obtain the highest
genomic prediction accuracy reported to date across 21 heritable traits. When
compared to other approaches, GMRM accuracy was greater than annotation prediction
models run in the LDAK or LDPred-funct software by 15% (SE 7%) and 14% (SE 2%),
respectively, and was 18% (SE 3%) greater than a baseline BayesR model without
single-nucleotide polymorphism (SNP) markers grouped into minor allele frequency–linkage
disequilibrium (MAF-LD) annotation categories. For height, the prediction accuracy
R2 was 47% in a UK Biobank holdout sample, which was 76% of the estimated h2SNP.
We then extend our GMRM prediction model to provide mixed-linear model association
(MLMA) SNP marker estimates for genome-wide association (GWAS) discovery, which
increased the independent loci detected to 16,162 in unrelated UK Biobank individuals,
compared to 10,550 from BoltLMM and 10,095 from Regenie, a 62 and 65% increase,
respectively. The average χ2 value of the leading markers increased by 15.24 (SE
0.41) for every 1% increase in prediction accuracy gained over a baseline BayesR
model across the traits. Thus, we show that modeling genetic associations accounting
for MAF and LD differences among SNP markers, and incorporating prior knowledge
of genomic function, is important for both genomic prediction and discovery in
large-scale individual-level studies.
acknowledgement: This project was funded by Swiss National Science Foundation Eccellenza
Grant PCEGP3-181181(toM.R.R.) and by core funding from the Institute of Science
and Technology Austria. P.M.V. acknowledges funding from the Australian National
Health and Medical Research Council (1113400) and the Australian Research Council
(FL180100072). K.L. and R.M. were supported by the Estonian Research Council Grant
PRG687. Estonian Biobank computations were performed in the High-Performance Computing
Centre, University of Tartu.
article_number: e2121279119
article_processing_charge: No
article_type: original
author:
- first_name: Etienne J.
full_name: Orliac, Etienne J.
last_name: Orliac
- first_name: Daniel
full_name: Trejo Banos, Daniel
last_name: Trejo Banos
- first_name: Sven E.
full_name: Ojavee, Sven E.
last_name: Ojavee
- first_name: Kristi
full_name: Läll, Kristi
last_name: Läll
- first_name: Reedik
full_name: Mägi, Reedik
last_name: Mägi
- first_name: Peter M.
full_name: Visscher, Peter M.
last_name: Visscher
- first_name: Matthew Richard
full_name: Robinson, Matthew Richard
id: E5D42276-F5DA-11E9-8E24-6303E6697425
last_name: Robinson
orcid: 0000-0001-8982-8813
citation:
ama: Orliac EJ, Trejo Banos D, Ojavee SE, et al. Improving GWAS discovery and genomic
prediction accuracy in biobank data. Proceedings of the National Academy of
Sciences of the United States of America. 2022;119(31). doi:10.1073/pnas.2121279119
apa: Orliac, E. J., Trejo Banos, D., Ojavee, S. E., Läll, K., Mägi, R., Visscher,
P. M., & Robinson, M. R. (2022). Improving GWAS discovery and genomic prediction
accuracy in biobank data. Proceedings of the National Academy of Sciences of
the United States of America. National Academy of Sciences. https://doi.org/10.1073/pnas.2121279119
chicago: Orliac, Etienne J., Daniel Trejo Banos, Sven E. Ojavee, Kristi Läll, Reedik
Mägi, Peter M. Visscher, and Matthew Richard Robinson. “Improving GWAS Discovery
and Genomic Prediction Accuracy in Biobank Data.” Proceedings of the National
Academy of Sciences of the United States of America. National Academy of Sciences,
2022. https://doi.org/10.1073/pnas.2121279119.
ieee: E. J. Orliac et al., “Improving GWAS discovery and genomic prediction
accuracy in biobank data,” Proceedings of the National Academy of Sciences
of the United States of America, vol. 119, no. 31. National Academy of Sciences,
2022.
ista: Orliac EJ, Trejo Banos D, Ojavee SE, Läll K, Mägi R, Visscher PM, Robinson
MR. 2022. Improving GWAS discovery and genomic prediction accuracy in biobank
data. Proceedings of the National Academy of Sciences of the United States of
America. 119(31), e2121279119.
mla: Orliac, Etienne J., et al. “Improving GWAS Discovery and Genomic Prediction
Accuracy in Biobank Data.” Proceedings of the National Academy of Sciences
of the United States of America, vol. 119, no. 31, e2121279119, National Academy
of Sciences, 2022, doi:10.1073/pnas.2121279119.
short: E.J. Orliac, D. Trejo Banos, S.E. Ojavee, K. Läll, R. Mägi, P.M. Visscher,
M.R. Robinson, Proceedings of the National Academy of Sciences of the United States
of America 119 (2022).
corr_author: '1'
date_created: 2022-08-07T22:01:56Z
date_published: 2022-07-29T00:00:00Z
date_updated: 2025-06-12T06:22:37Z
day: '29'
ddc:
- '570'
department:
- _id: MaRo
doi: 10.1073/pnas.2121279119
external_id:
isi:
- '000881496900003'
pmid:
- '35905320'
file:
- access_level: open_access
checksum: b5d2024e19fbad6f85a5e384e44d0f3b
content_type: application/pdf
creator: dernst
date_created: 2022-08-08T07:31:19Z
date_updated: 2022-08-08T07:31:19Z
file_id: '11745'
file_name: 2022_PNAS_Orliac.pdf
file_size: 1001164
relation: main_file
success: 1
file_date_updated: 2022-08-08T07:31:19Z
has_accepted_license: '1'
intvolume: ' 119'
isi: 1
issue: '31'
language:
- iso: eng
month: '07'
oa: 1
oa_version: Published Version
pmid: 1
publication: Proceedings of the National Academy of Sciences of the United States
of America
publication_identifier:
eissn:
- 1091-6490
publication_status: published
publisher: National Academy of Sciences
quality_controlled: '1'
related_material:
record:
- id: '13064'
relation: research_data
status: public
scopus_import: '1'
status: public
title: Improving GWAS discovery and genomic prediction accuracy in biobank data
tmp:
image: /images/cc_by_nc_nd.png
legal_code_url: https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode
name: Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International
(CC BY-NC-ND 4.0)
short: CC BY-NC-ND (4.0)
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 119
year: '2022'
...
---
_id: '11734'
abstract:
- lang: eng
text: Mineral nutrition is one of the key environmental factors determining plant
development and growth. Nitrate is the major form of macronutrient nitrogen that
plants take up from the soil. Fluctuating availability or deficiency of this element
severely limits plant growth and negatively affects crop production in the agricultural
system. To cope with the heterogeneity of nitrate distribution in soil, plants
evolved a complex regulatory mechanism that allows rapid adjustment of physiological
and developmental processes to the status of this nutrient. The root, as a major
exploitation organ that controls the uptake of nitrate to the plant body, acts
as a regulatory hub that, according to nitrate availability, coordinates the growth
and development of other plant organs. Here, we identified a regulatory framework,
where cytokinin response factors (CRFs) play a central role as a molecular readout
of the nitrate status in roots to guide shoot adaptive developmental response.
We show that nitrate-driven activation of NLP7, a master regulator of nitrate
response in plants, fine tunes biosynthesis of cytokinin in roots and its translocation
to shoots where it enhances expression of CRFs. CRFs, through direct transcriptional
regulation of PIN auxin transporters, promote the flow of auxin and thereby stimulate
the development of shoot organs.
acknowledged_ssus:
- _id: Bio
- _id: LifeSc
acknowledgement: "We acknowledge Hana Semeradova, Juan Carlos Montesinos, Nicola Cavallari,
Marc¸al Gallem\x03ı, Kaori Tabata, Andrej Hurn\x03y, and Sascha Waidmann for sharing
materials; and Marina Borges Osorio for critical reading of the manuscript. Work
in the E. Benkova laboratory was supported by the Austrian Science Fund (FWF01_I1774S)
to K.O., R.A., and E. Benkova. We acknowledge the Bioimaging Facility and Life Science
Facilities of the Institute of Science\r\nand Technology Austria. We give sincere
thanks to Hana Martınkova and Petra Amakorova for their help with cytokinin analyses.
This work was funded by the Czech Science Foundation (Project No. 19-00973S)."
article_number: e2122460119
article_processing_charge: No
article_type: original
author:
- first_name: Rashed
full_name: Abualia, Rashed
id: 4827E134-F248-11E8-B48F-1D18A9856A87
last_name: Abualia
orcid: 0000-0002-9357-9415
- first_name: Krisztina
full_name: Ötvös, Krisztina
id: 29B901B0-F248-11E8-B48F-1D18A9856A87
last_name: Ötvös
orcid: 0000-0002-5503-4983
- first_name: Ondřej
full_name: Novák, Ondřej
last_name: Novák
- first_name: Eleonore
full_name: Bouguyon, Eleonore
last_name: Bouguyon
- first_name: Kevin
full_name: Domanegg, Kevin
id: a24c7829-16e8-11ed-8527-c4d36ffb7539
last_name: Domanegg
orcid: 0000-0002-1215-4264
- first_name: Anne
full_name: Krapp, Anne
last_name: Krapp
- first_name: Philip
full_name: Nacry, Philip
last_name: Nacry
- first_name: Alain
full_name: Gojon, Alain
last_name: Gojon
- first_name: Benoit
full_name: Lacombe, Benoit
last_name: Lacombe
- first_name: Eva
full_name: Benková, Eva
id: 38F4F166-F248-11E8-B48F-1D18A9856A87
last_name: Benková
orcid: 0000-0002-8510-9739
citation:
ama: Abualia R, Ötvös K, Novák O, et al. Molecular framework integrating nitrate
sensing in root and auxin-guided shoot adaptive responses. Proceedings of the
National Academy of Sciences of the United States of America. 2022;119(31).
doi:10.1073/pnas.2122460119
apa: Abualia, R., Ötvös, K., Novák, O., Bouguyon, E., Domanegg, K., Krapp, A., …
Benková, E. (2022). Molecular framework integrating nitrate sensing in root and
auxin-guided shoot adaptive responses. Proceedings of the National Academy
of Sciences of the United States of America. National Academy of Sciences.
https://doi.org/10.1073/pnas.2122460119
chicago: Abualia, Rashed, Krisztina Ötvös, Ondřej Novák, Eleonore Bouguyon, Kevin
Domanegg, Anne Krapp, Philip Nacry, Alain Gojon, Benoit Lacombe, and Eva Benková.
“Molecular Framework Integrating Nitrate Sensing in Root and Auxin-Guided Shoot
Adaptive Responses.” Proceedings of the National Academy of Sciences of the
United States of America. National Academy of Sciences, 2022. https://doi.org/10.1073/pnas.2122460119.
ieee: R. Abualia et al., “Molecular framework integrating nitrate sensing
in root and auxin-guided shoot adaptive responses,” Proceedings of the National
Academy of Sciences of the United States of America, vol. 119, no. 31. National
Academy of Sciences, 2022.
ista: Abualia R, Ötvös K, Novák O, Bouguyon E, Domanegg K, Krapp A, Nacry P, Gojon
A, Lacombe B, Benková E. 2022. Molecular framework integrating nitrate sensing
in root and auxin-guided shoot adaptive responses. Proceedings of the National
Academy of Sciences of the United States of America. 119(31), e2122460119.
mla: Abualia, Rashed, et al. “Molecular Framework Integrating Nitrate Sensing in
Root and Auxin-Guided Shoot Adaptive Responses.” Proceedings of the National
Academy of Sciences of the United States of America, vol. 119, no. 31, e2122460119,
National Academy of Sciences, 2022, doi:10.1073/pnas.2122460119.
short: R. Abualia, K. Ötvös, O. Novák, E. Bouguyon, K. Domanegg, A. Krapp, P. Nacry,
A. Gojon, B. Lacombe, E. Benková, Proceedings of the National Academy of Sciences
of the United States of America 119 (2022).
corr_author: '1'
date_created: 2022-08-07T22:01:57Z
date_published: 2022-07-25T00:00:00Z
date_updated: 2025-05-14T11:00:29Z
day: '25'
ddc:
- '570'
department:
- _id: EvBe
doi: 10.1073/pnas.2122460119
external_id:
isi:
- '000881496900007'
pmid:
- '35878040'
file:
- access_level: open_access
checksum: 6e97dedc281247fc3fe238a209f14af0
content_type: application/pdf
creator: dernst
date_created: 2022-08-08T07:09:58Z
date_updated: 2022-08-08T07:09:58Z
file_id: '11744'
file_name: 2022_PNAS_Abualia.pdf
file_size: 3092330
relation: main_file
success: 1
file_date_updated: 2022-08-08T07:09:58Z
has_accepted_license: '1'
intvolume: ' 119'
isi: 1
issue: '31'
language:
- iso: eng
month: '07'
oa: 1
oa_version: Published Version
pmid: 1
project:
- _id: 2542D156-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: I 1774-B16
name: Hormone cross-talk drives nutrient dependent plant development
publication: Proceedings of the National Academy of Sciences of the United States
of America
publication_identifier:
eissn:
- 1091-6490
publication_status: published
publisher: National Academy of Sciences
quality_controlled: '1'
scopus_import: '1'
status: public
title: Molecular framework integrating nitrate sensing in root and auxin-guided shoot
adaptive responses
tmp:
image: /images/cc_by_nc_nd.png
legal_code_url: https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode
name: Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International
(CC BY-NC-ND 4.0)
short: CC BY-NC-ND (4.0)
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 119
year: '2022'
...
---
_id: '11735'
abstract:
- lang: eng
text: "Interlocking puzzles are intriguing geometric games where the puzzle pieces
are held together based on their geometric arrangement, preventing the puzzle
from falling apart. High-level-of-difficulty, or simply high-level, interlocking
puzzles are a subclass of interlocking puzzles that require multiple moves to
take out the first subassembly from the puzzle. Solving a high-level interlocking
puzzle is a challenging task since one has to explore many different configurations
of the puzzle pieces until reaching a configuration where the first subassembly
can be taken out. Designing a high-level interlocking puzzle with a user-specified
level of difficulty is even harder since the puzzle pieces have to be interlocking
in all the configurations before the first subassembly is taken out.\r\n\r\nIn
this paper, we present a computational approach to design high-level interlocking
puzzles. The core idea is to represent all possible configurations of an interlocking
puzzle as well as transitions among these configurations using a rooted, undirected
graph called a disassembly graph and leverage this graph to find a disassembly
plan that requires a minimal number of moves to take out the first subassembly
from the puzzle. At the design stage, our algorithm iteratively constructs the
geometry of each puzzle piece to expand the disassembly graph incrementally, aiming
to achieve a user-specified level of difficulty. We show that our approach allows
efficient generation of high-level interlocking puzzles of various shape complexities,
including new solutions not attainable by state-of-the-art approaches."
acknowledgement: "We thank the reviewers for the valuable comments, David Gontier
for sharing the source code of the baseline design approach, Christian Hafner for
proofreading the paper, Keenan Crane for the 3D model of Cow, and Thingiverse for
the 3D models of Moai and Owl. This work was supported by the SUTD Start-up Research
Grant (Number: SRG ISTD 2019 148), the Swiss National Science Foundation (NCCR Digital
Fabrication Agreement #51NF40-141853), and\r\nthe European Research Council (ERC)
under the European Union’s Horizon 2020 research and innovation programme (Grant
Agreement No 715767 – MATERIALIZABLE)."
article_number: '150'
article_processing_charge: No
article_type: original
author:
- first_name: Rulin
full_name: Chen, Rulin
last_name: Chen
- first_name: Ziqi
full_name: Wang, Ziqi
last_name: Wang
- first_name: Peng
full_name: Song, Peng
last_name: Song
- first_name: Bernd
full_name: Bickel, Bernd
id: 49876194-F248-11E8-B48F-1D18A9856A87
last_name: Bickel
orcid: 0000-0001-6511-9385
citation:
ama: Chen R, Wang Z, Song P, Bickel B. Computational design of high-level interlocking
puzzles. ACM Transactions on Graphics. 2022;41(4). doi:10.1145/3528223.3530071
apa: Chen, R., Wang, Z., Song, P., & Bickel, B. (2022). Computational design
of high-level interlocking puzzles. ACM Transactions on Graphics. Association
for Computing Machinery. https://doi.org/10.1145/3528223.3530071
chicago: Chen, Rulin, Ziqi Wang, Peng Song, and Bernd Bickel. “Computational Design
of High-Level Interlocking Puzzles.” ACM Transactions on Graphics. Association
for Computing Machinery, 2022. https://doi.org/10.1145/3528223.3530071.
ieee: R. Chen, Z. Wang, P. Song, and B. Bickel, “Computational design of high-level
interlocking puzzles,” ACM Transactions on Graphics, vol. 41, no. 4. Association
for Computing Machinery, 2022.
ista: Chen R, Wang Z, Song P, Bickel B. 2022. Computational design of high-level
interlocking puzzles. ACM Transactions on Graphics. 41(4), 150.
mla: Chen, Rulin, et al. “Computational Design of High-Level Interlocking Puzzles.”
ACM Transactions on Graphics, vol. 41, no. 4, 150, Association for Computing
Machinery, 2022, doi:10.1145/3528223.3530071.
short: R. Chen, Z. Wang, P. Song, B. Bickel, ACM Transactions on Graphics 41 (2022).
date_created: 2022-08-07T22:01:57Z
date_published: 2022-07-22T00:00:00Z
date_updated: 2025-04-14T07:28:57Z
day: '22'
ddc:
- '000'
department:
- _id: BeBi
doi: 10.1145/3528223.3530071
ec_funded: 1
external_id:
isi:
- '000830989200018'
file:
- access_level: open_access
checksum: 0b51651be45b1b33f2072bd5d2686c69
content_type: application/pdf
creator: bbickel
date_created: 2022-08-28T07:56:19Z
date_updated: 2022-08-28T07:56:19Z
file_id: '11992'
file_name: Chen-2022-High-LevelPuzzle_authorVersion.pdf
file_size: 16896871
relation: main_file
success: 1
file_date_updated: 2022-08-28T07:56:19Z
has_accepted_license: '1'
intvolume: ' 41'
isi: 1
issue: '4'
language:
- iso: eng
month: '07'
oa: 1
oa_version: Submitted Version
project:
- _id: 24F9549A-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '715767'
name: 'MATERIALIZABLE: Intelligent fabrication-oriented Computational Design and
Modeling'
publication: ACM Transactions on Graphics
publication_identifier:
eissn:
- 1557-7368
issn:
- 0730-0301
publication_status: published
publisher: Association for Computing Machinery
quality_controlled: '1'
related_material:
link:
- description: News on ISTA website
relation: press_release
url: https://ista.ac.at/en/news/unlocking-interlocking-riddles/
scopus_import: '1'
status: public
title: Computational design of high-level interlocking puzzles
type: journal_article
user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
volume: 41
year: '2022'
...
---
_id: '11737'
abstract:
- lang: eng
text: Spin-orbit coupling in thin HgTe quantum wells results in a relativistic-like
electron band structure, making it a versatile solid state platform to observe
and control nontrivial electrodynamic phenomena. Here we report an observation
of universal terahertz (THz) transparency determined by fine-structure constant
α≈1/137 in 6.5-nm-thick HgTe layer, close to the critical thickness separating
phases with topologically different electronic band structure. Using THz spectroscopy
in a magnetic field we obtain direct evidence of asymmetric spin splitting of
the Dirac cone. This particle-hole asymmetry facilitates optical control of edge
spin currents in the quantum wells.
acknowledgement: This work was supported by the Austrian Science Funds (W 1243, I
3456-N27, I 5539-N).
article_number: '045302'
article_processing_charge: No
article_type: original
author:
- first_name: Uladzislau
full_name: Dziom, Uladzislau
id: 6A9A37C2-8C5C-11E9-AE53-F2FDE5697425
last_name: Dziom
orcid: 0000-0002-1648-0999
- first_name: A.
full_name: Shuvaev, A.
last_name: Shuvaev
- first_name: J.
full_name: Gospodarič, J.
last_name: Gospodarič
- first_name: E. G.
full_name: Novik, E. G.
last_name: Novik
- first_name: A. A.
full_name: Dobretsova, A. A.
last_name: Dobretsova
- first_name: N. N.
full_name: Mikhailov, N. N.
last_name: Mikhailov
- first_name: Z. D.
full_name: Kvon, Z. D.
last_name: Kvon
- first_name: Zhanybek
full_name: Alpichshev, Zhanybek
id: 45E67A2A-F248-11E8-B48F-1D18A9856A87
last_name: Alpichshev
orcid: 0000-0002-7183-5203
- first_name: A.
full_name: Pimenov, A.
last_name: Pimenov
citation:
ama: Dziom U, Shuvaev A, Gospodarič J, et al. Universal transparency and asymmetric
spin splitting near the Dirac point in HgTe quantum wells. Physical Review
B. 2022;106(4). doi:10.1103/PhysRevB.106.045302
apa: Dziom, U., Shuvaev, A., Gospodarič, J., Novik, E. G., Dobretsova, A. A., Mikhailov,
N. N., … Pimenov, A. (2022). Universal transparency and asymmetric spin splitting
near the Dirac point in HgTe quantum wells. Physical Review B. American
Physical Society. https://doi.org/10.1103/PhysRevB.106.045302
chicago: Dziom, Uladzislau, A. Shuvaev, J. Gospodarič, E. G. Novik, A. A. Dobretsova,
N. N. Mikhailov, Z. D. Kvon, Zhanybek Alpichshev, and A. Pimenov. “Universal Transparency
and Asymmetric Spin Splitting near the Dirac Point in HgTe Quantum Wells.” Physical
Review B. American Physical Society, 2022. https://doi.org/10.1103/PhysRevB.106.045302.
ieee: U. Dziom et al., “Universal transparency and asymmetric spin splitting
near the Dirac point in HgTe quantum wells,” Physical Review B, vol. 106,
no. 4. American Physical Society, 2022.
ista: Dziom U, Shuvaev A, Gospodarič J, Novik EG, Dobretsova AA, Mikhailov NN, Kvon
ZD, Alpichshev Z, Pimenov A. 2022. Universal transparency and asymmetric spin
splitting near the Dirac point in HgTe quantum wells. Physical Review B. 106(4),
045302.
mla: Dziom, Uladzislau, et al. “Universal Transparency and Asymmetric Spin Splitting
near the Dirac Point in HgTe Quantum Wells.” Physical Review B, vol. 106,
no. 4, 045302, American Physical Society, 2022, doi:10.1103/PhysRevB.106.045302.
short: U. Dziom, A. Shuvaev, J. Gospodarič, E.G. Novik, A.A. Dobretsova, N.N. Mikhailov,
Z.D. Kvon, Z. Alpichshev, A. Pimenov, Physical Review B 106 (2022).
date_created: 2022-08-07T22:01:58Z
date_published: 2022-07-15T00:00:00Z
date_updated: 2023-08-03T12:38:57Z
day: '15'
ddc:
- '530'
department:
- _id: ZhAl
doi: 10.1103/PhysRevB.106.045302
external_id:
isi:
- '000834349200010'
file:
- access_level: open_access
checksum: 115aff9e0cde2f806cb26953d7262791
content_type: application/pdf
creator: dernst
date_created: 2022-08-08T06:58:22Z
date_updated: 2022-08-08T06:58:22Z
file_id: '11743'
file_name: 2022_PhysRevB_Dziom.pdf
file_size: 774455
relation: main_file
success: 1
file_date_updated: 2022-08-08T06:58:22Z
has_accepted_license: '1'
intvolume: ' 106'
isi: 1
issue: '4'
language:
- iso: eng
month: '07'
oa: 1
oa_version: Published Version
publication: Physical Review B
publication_identifier:
eissn:
- 2469-9969
issn:
- 2469-9950
publication_status: published
publisher: American Physical Society
quality_controlled: '1'
scopus_import: '1'
status: public
title: Universal transparency and asymmetric spin splitting near the Dirac point in
HgTe quantum wells
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: 106
year: '2022'
...
---
_id: '11739'
abstract:
- lang: eng
text: We consider finite-volume approximations of Fokker--Planck equations on bounded
convex domains in $\mathbb{R}^d$ and study the corresponding gradient flow structures.
We reprove the convergence of the discrete to continuous Fokker--Planck equation
via the method of evolutionary $\Gamma$-convergence, i.e., we pass to the limit
at the level of the gradient flow structures, generalizing the one-dimensional
result obtained by Disser and Liero. The proof is of variational nature and relies
on a Mosco convergence result for functionals in the discrete-to-continuum limit
that is of independent interest. Our results apply to arbitrary regular meshes,
even though the associated discrete transport distances may fail to converge to
the Wasserstein distance in this generality.
acknowledgement: This work was supported by the European Research Council (ERC) under
the European Union's Horizon 2020 Research and Innovation Programme grant 716117
and by the AustrianScience Fund (FWF) through grants F65 and W1245.
article_processing_charge: No
article_type: original
arxiv: 1
author:
- first_name: Dominik L
full_name: Forkert, Dominik L
id: 35C79D68-F248-11E8-B48F-1D18A9856A87
last_name: Forkert
- first_name: Jan
full_name: Maas, Jan
id: 4C5696CE-F248-11E8-B48F-1D18A9856A87
last_name: Maas
orcid: 0000-0002-0845-1338
- first_name: Lorenzo
full_name: Portinale, Lorenzo
id: 30AD2CBC-F248-11E8-B48F-1D18A9856A87
last_name: Portinale
citation:
ama: Forkert DL, Maas J, Portinale L. Evolutionary $\Gamma$-convergence of entropic
gradient flow structures for Fokker-Planck equations in multiple dimensions. SIAM
Journal on Mathematical Analysis. 2022;54(4):4297-4333. doi:10.1137/21M1410968
apa: Forkert, D. L., Maas, J., & Portinale, L. (2022). Evolutionary $\Gamma$-convergence
of entropic gradient flow structures for Fokker-Planck equations in multiple dimensions.
SIAM Journal on Mathematical Analysis. Society for Industrial and Applied
Mathematics. https://doi.org/10.1137/21M1410968
chicago: Forkert, Dominik L, Jan Maas, and Lorenzo Portinale. “Evolutionary $\Gamma$-Convergence
of Entropic Gradient Flow Structures for Fokker-Planck Equations in Multiple Dimensions.”
SIAM Journal on Mathematical Analysis. Society for Industrial and Applied
Mathematics, 2022. https://doi.org/10.1137/21M1410968.
ieee: D. L. Forkert, J. Maas, and L. Portinale, “Evolutionary $\Gamma$-convergence
of entropic gradient flow structures for Fokker-Planck equations in multiple dimensions,”
SIAM Journal on Mathematical Analysis, vol. 54, no. 4. Society for Industrial
and Applied Mathematics, pp. 4297–4333, 2022.
ista: Forkert DL, Maas J, Portinale L. 2022. Evolutionary $\Gamma$-convergence of
entropic gradient flow structures for Fokker-Planck equations in multiple dimensions.
SIAM Journal on Mathematical Analysis. 54(4), 4297–4333.
mla: Forkert, Dominik L., et al. “Evolutionary $\Gamma$-Convergence of Entropic
Gradient Flow Structures for Fokker-Planck Equations in Multiple Dimensions.”
SIAM Journal on Mathematical Analysis, vol. 54, no. 4, Society for Industrial
and Applied Mathematics, 2022, pp. 4297–333, doi:10.1137/21M1410968.
short: D.L. Forkert, J. Maas, L. Portinale, SIAM Journal on Mathematical Analysis
54 (2022) 4297–4333.
corr_author: '1'
date_created: 2022-08-07T22:01:59Z
date_published: 2022-07-18T00:00:00Z
date_updated: 2025-04-15T08:31:31Z
day: '18'
department:
- _id: JaMa
doi: 10.1137/21M1410968
ec_funded: 1
external_id:
arxiv:
- '2008.10962'
isi:
- '000889274600001'
intvolume: ' 54'
isi: 1
issue: '4'
keyword:
- Fokker--Planck equation
- gradient flow
- evolutionary $\Gamma$-convergence
language:
- iso: eng
main_file_link:
- open_access: '1'
url: ' https://doi.org/10.48550/arXiv.2008.10962'
month: '07'
oa: 1
oa_version: Preprint
page: 4297-4333
project:
- _id: 256E75B8-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '716117'
name: Optimal Transport and Stochastic Dynamics
- _id: fc31cba2-9c52-11eb-aca3-ff467d239cd2
grant_number: F6504
name: Taming Complexity in Partial Differential Systems
- _id: 260788DE-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: W1245
name: Dissipation and dispersion in nonlinear partial differential equations
publication: SIAM Journal on Mathematical Analysis
publication_identifier:
eissn:
- 1095-7154
issn:
- 0036-1410
publication_status: published
publisher: Society for Industrial and Applied Mathematics
quality_controlled: '1'
related_material:
record:
- id: '10022'
relation: earlier_version
status: public
scopus_import: '1'
status: public
title: Evolutionary $\Gamma$-convergence of entropic gradient flow structures for
Fokker-Planck equations in multiple dimensions
type: journal_article
user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
volume: 54
year: '2022'
...
---
_id: '11740'
abstract:
- lang: eng
text: "We consider a generalised model of a random simplicial complex, which arises
from a random hypergraph. Our model is generated by taking the downward-closure
of a non-uniform binomial random hypergraph, in which for each k, each set of
k+1 vertices forms an edge with some probability pk independently. As a special
case, this contains an extensively studied model of a (uniform) random simplicial
complex, introduced by Meshulam and Wallach [Random Structures & Algorithms 34
(2009), no. 3, pp. 408–417].\r\nWe consider a higher-dimensional notion of connectedness
on this new model according to the vanishing of cohomology groups over an arbitrary
abelian group R. We prove that this notion of connectedness displays a phase transition
and determine the threshold. We also prove a hitting time result for a natural
process interpretation, in which simplices and their downward-closure are added
one by one. In addition, we determine the asymptotic behaviour of cohomology groups
inside the critical window around the time of the phase transition."
acknowledgement: 'Supported by Austrian Science Fund (FWF): I3747, W1230.'
article_number: P3.27
article_processing_charge: No
article_type: original
arxiv: 1
author:
- first_name: Oliver
full_name: Cooley, Oliver
id: 43f4ddd0-a46b-11ec-8df6-ef3703bd721d
last_name: Cooley
- first_name: Nicola
full_name: Del Giudice, Nicola
last_name: Del Giudice
- first_name: Mihyun
full_name: Kang, Mihyun
last_name: Kang
- first_name: Philipp
full_name: Sprüssel, Philipp
last_name: Sprüssel
citation:
ama: Cooley O, Del Giudice N, Kang M, Sprüssel P. Phase transition in cohomology
groups of non-uniform random simplicial complexes. Electronic Journal of Combinatorics.
2022;29(3). doi:10.37236/10607
apa: Cooley, O., Del Giudice, N., Kang, M., & Sprüssel, P. (2022). Phase transition
in cohomology groups of non-uniform random simplicial complexes. Electronic
Journal of Combinatorics. Electronic Journal of Combinatorics. https://doi.org/10.37236/10607
chicago: Cooley, Oliver, Nicola Del Giudice, Mihyun Kang, and Philipp Sprüssel.
“Phase Transition in Cohomology Groups of Non-Uniform Random Simplicial Complexes.”
Electronic Journal of Combinatorics. Electronic Journal of Combinatorics,
2022. https://doi.org/10.37236/10607.
ieee: O. Cooley, N. Del Giudice, M. Kang, and P. Sprüssel, “Phase transition in
cohomology groups of non-uniform random simplicial complexes,” Electronic Journal
of Combinatorics, vol. 29, no. 3. Electronic Journal of Combinatorics, 2022.
ista: Cooley O, Del Giudice N, Kang M, Sprüssel P. 2022. Phase transition in cohomology
groups of non-uniform random simplicial complexes. Electronic Journal of Combinatorics.
29(3), P3.27.
mla: Cooley, Oliver, et al. “Phase Transition in Cohomology Groups of Non-Uniform
Random Simplicial Complexes.” Electronic Journal of Combinatorics, vol.
29, no. 3, P3.27, Electronic Journal of Combinatorics, 2022, doi:10.37236/10607.
short: O. Cooley, N. Del Giudice, M. Kang, P. Sprüssel, Electronic Journal of Combinatorics
29 (2022).
corr_author: '1'
date_created: 2022-08-07T22:01:59Z
date_published: 2022-07-29T00:00:00Z
date_updated: 2024-10-09T21:03:03Z
day: '29'
ddc:
- '510'
department:
- _id: MaKw
doi: 10.37236/10607
external_id:
arxiv:
- '2005.07103'
isi:
- '000836200300001'
file:
- access_level: open_access
checksum: 057c676dcee70236aa234d4ce6138c69
content_type: application/pdf
creator: dernst
date_created: 2022-08-08T06:28:52Z
date_updated: 2022-08-08T06:28:52Z
file_id: '11742'
file_name: 2022_ElecJournCombinatorics_Cooley.pdf
file_size: 1768663
relation: main_file
success: 1
file_date_updated: 2022-08-08T06:28:52Z
has_accepted_license: '1'
intvolume: ' 29'
isi: 1
issue: '3'
language:
- iso: eng
month: '07'
oa: 1
oa_version: Published Version
publication: Electronic Journal of Combinatorics
publication_identifier:
eissn:
- 1077-8926
publication_status: published
publisher: Electronic Journal of Combinatorics
quality_controlled: '1'
scopus_import: '1'
status: public
title: Phase transition in cohomology groups of non-uniform random simplicial complexes
tmp:
image: /image/cc_by_nd.png
legal_code_url: https://creativecommons.org/licenses/by-nd/4.0/legalcode
name: Creative Commons Attribution-NoDerivatives 4.0 International (CC BY-ND 4.0)
short: CC BY-ND (4.0)
type: journal_article
user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
volume: 29
year: '2022'
...
---
_id: '11783'
abstract:
- lang: eng
text: We consider a gas of N bosons with interactions in the mean-field scaling
regime. We review the proof of an asymptotic expansion of its low-energy spectrum,
eigenstates, and dynamics, which provides corrections to Bogoliubov theory to
all orders in 1/ N. This is based on joint works with Petrat, Pickl, Seiringer,
and Soffer. In addition, we derive a full asymptotic expansion of the ground state
one-body reduced density matrix.
acknowledgement: "The author thanks Nataˇsa Pavlovic, Sören Petrat, Peter Pickl, Robert
Seiringer, and Avy Soffer for the collaboration on Refs. 1, 2 and 21. Funding from
the European Union’s Horizon 2020 Research and Innovation Programme under Marie
Skℓodowska-Curie Grant Agreement\r\nNo. 754411 is gratefully acknowledged."
article_number: '061102'
article_processing_charge: Yes (via OA deal)
article_type: original
arxiv: 1
author:
- first_name: Lea
full_name: Bossmann, Lea
id: A2E3BCBE-5FCC-11E9-AA4B-76F3E5697425
last_name: Bossmann
orcid: 0000-0002-6854-1343
citation:
ama: Bossmann L. Low-energy spectrum and dynamics of the weakly interacting Bose
gas. Journal of Mathematical Physics. 2022;63(6). doi:10.1063/5.0089983
apa: Bossmann, L. (2022). Low-energy spectrum and dynamics of the weakly interacting
Bose gas. Journal of Mathematical Physics. AIP Publishing. https://doi.org/10.1063/5.0089983
chicago: Bossmann, Lea. “Low-Energy Spectrum and Dynamics of the Weakly Interacting
Bose Gas.” Journal of Mathematical Physics. AIP Publishing, 2022. https://doi.org/10.1063/5.0089983.
ieee: L. Bossmann, “Low-energy spectrum and dynamics of the weakly interacting Bose
gas,” Journal of Mathematical Physics, vol. 63, no. 6. AIP Publishing,
2022.
ista: Bossmann L. 2022. Low-energy spectrum and dynamics of the weakly interacting
Bose gas. Journal of Mathematical Physics. 63(6), 061102.
mla: Bossmann, Lea. “Low-Energy Spectrum and Dynamics of the Weakly Interacting
Bose Gas.” Journal of Mathematical Physics, vol. 63, no. 6, 061102, AIP
Publishing, 2022, doi:10.1063/5.0089983.
short: L. Bossmann, Journal of Mathematical Physics 63 (2022).
corr_author: '1'
date_created: 2022-08-11T06:37:52Z
date_published: 2022-06-10T00:00:00Z
date_updated: 2025-04-14T07:43:58Z
day: '10'
ddc:
- '530'
department:
- _id: RoSe
doi: 10.1063/5.0089983
ec_funded: 1
external_id:
arxiv:
- '2203.00730'
isi:
- '000809648100002'
file:
- access_level: open_access
checksum: d0d32c338c1896680174be88c70968fa
content_type: application/pdf
creator: dernst
date_created: 2022-08-11T07:03:02Z
date_updated: 2022-08-11T07:03:02Z
file_id: '11784'
file_name: 2022_JourMathPhysics_Bossmann.pdf
file_size: 5957888
relation: main_file
success: 1
file_date_updated: 2022-08-11T07:03:02Z
has_accepted_license: '1'
intvolume: ' 63'
isi: 1
issue: '6'
keyword:
- Mathematical Physics
- Statistical and Nonlinear Physics
language:
- iso: eng
month: '06'
oa: 1
oa_version: Published Version
project:
- _id: 260C2330-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '754411'
name: ISTplus - Postdoctoral Fellowships
publication: Journal of Mathematical Physics
publication_identifier:
eissn:
- 1089-7658
issn:
- 0022-2488
publication_status: published
publisher: AIP Publishing
quality_controlled: '1'
scopus_import: '1'
status: public
title: Low-energy spectrum and dynamics of the weakly interacting Bose gas
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: 63
year: '2022'
...
---
_id: '11808'
abstract:
- lang: eng
text: In recent years, significant advances have been made in the design and analysis
of fully dynamic algorithms. However, these theoretical results have received
very little attention from the practical perspective. Few of the algorithms are
implemented and tested on real datasets, and their practical potential is far
from understood. Here, we present a quick reference guide to recent engineering
and theory results in the area of fully dynamic graph algorithms.
alternative_title:
- LIPIcs
article_number: '1'
article_processing_charge: No
arxiv: 1
author:
- first_name: Kathrin
full_name: Hanauer, Kathrin
last_name: Hanauer
- first_name: Monika H
full_name: Henzinger, Monika H
id: 540c9bbd-f2de-11ec-812d-d04a5be85630
last_name: Henzinger
orcid: 0000-0002-5008-6530
- first_name: Christian
full_name: Schulz, Christian
last_name: Schulz
citation:
ama: 'Hanauer K, Henzinger M, Schulz C. Recent advances in fully dynamic graph algorithms.
In: 1st Symposium on Algorithmic Foundations of Dynamic Networks. Vol 221.
Schloss Dagstuhl - Leibniz-Zentrum für Informatik; 2022. doi:10.4230/LIPIcs.SAND.2022.1'
apa: 'Hanauer, K., Henzinger, M., & Schulz, C. (2022). Recent advances in fully
dynamic graph algorithms. In 1st Symposium on Algorithmic Foundations of Dynamic
Networks (Vol. 221). Virtual: Schloss Dagstuhl - Leibniz-Zentrum für Informatik.
https://doi.org/10.4230/LIPIcs.SAND.2022.1'
chicago: Hanauer, Kathrin, Monika Henzinger, and Christian Schulz. “Recent Advances
in Fully Dynamic Graph Algorithms.” In 1st Symposium on Algorithmic Foundations
of Dynamic Networks, Vol. 221. Schloss Dagstuhl - Leibniz-Zentrum für Informatik,
2022. https://doi.org/10.4230/LIPIcs.SAND.2022.1.
ieee: K. Hanauer, M. Henzinger, and C. Schulz, “Recent advances in fully dynamic
graph algorithms,” in 1st Symposium on Algorithmic Foundations of Dynamic Networks,
Virtual, 2022, vol. 221.
ista: 'Hanauer K, Henzinger M, Schulz C. 2022. Recent advances in fully dynamic
graph algorithms. 1st Symposium on Algorithmic Foundations of Dynamic Networks.
SAND: Symposium on Algorithmic Foundations of Dynamic Networks, LIPIcs, vol. 221,
1.'
mla: Hanauer, Kathrin, et al. “Recent Advances in Fully Dynamic Graph Algorithms.”
1st Symposium on Algorithmic Foundations of Dynamic Networks, vol. 221,
1, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2022, doi:10.4230/LIPIcs.SAND.2022.1.
short: K. Hanauer, M. Henzinger, C. Schulz, in:, 1st Symposium on Algorithmic Foundations
of Dynamic Networks, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2022.
conference:
end_date: 2022-03-30
location: Virtual
name: 'SAND: Symposium on Algorithmic Foundations of Dynamic Networks'
start_date: 2022-03-28
date_created: 2022-08-11T14:35:52Z
date_published: 2022-04-29T00:00:00Z
date_updated: 2024-11-06T08:23:49Z
day: '29'
doi: 10.4230/LIPIcs.SAND.2022.1
extern: '1'
external_id:
arxiv:
- '2102.11169'
intvolume: ' 221'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.4230/LIPIcs.SAND.2022.1
month: '04'
oa: 1
oa_version: Published Version
publication: 1st Symposium on Algorithmic Foundations of Dynamic Networks
publication_identifier:
eissn:
- 1868-8969
isbn:
- '9783959772242'
publication_status: published
publisher: Schloss Dagstuhl - Leibniz-Zentrum für Informatik
quality_controlled: '1'
scopus_import: '1'
status: public
title: Recent advances in fully dynamic graph algorithms
type: conference
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 221
year: '2022'
...
---
_id: '11812'
abstract:
- lang: eng
text: "This paper presents a comprehensive study of algorithms for maintaining the
number of all connected four-vertex subgraphs in a dynamic graph. Specifically,
our algorithms maintain the number of paths of length three in deterministic amortized
O(m^{1/2}) update time, and any other connected four-vertex subgraph which is
not a clique in deterministic amortized update time O(m^{2/3}). Queries can be
answered in constant time. We also study the query times for subgraphs containing
an arbitrary edge that is supplied only with the query as well as the case where
only subgraphs containing a vertex s that is fixed beforehand are considered.
For length-3 paths, paws, 4-cycles, and diamonds our bounds match or are not far
from (conditional) lower bounds: Based on the OMv conjecture we show that any
dynamic algorithm that detects the existence of paws, diamonds, or 4-cycles or
that counts length-3 paths takes update time Ω(m^{1/2-δ}).\r\nAdditionally, for
4-cliques and all connected induced subgraphs, we show a lower bound of Ω(m^{1-δ})
for any small constant δ > 0 for the amortized update time, assuming the static
combinatorial 4-clique conjecture holds. This shows that the O(m) algorithm by
Eppstein et al. [David Eppstein et al., 2012] for these subgraphs cannot be improved
by a polynomial factor."
alternative_title:
- LIPIcs
article_number: '18'
article_processing_charge: No
arxiv: 1
author:
- first_name: Kathrin
full_name: Hanauer, Kathrin
last_name: Hanauer
- first_name: Monika H
full_name: Henzinger, Monika H
id: 540c9bbd-f2de-11ec-812d-d04a5be85630
last_name: Henzinger
orcid: 0000-0002-5008-6530
- first_name: Qi Cheng
full_name: Hua, Qi Cheng
last_name: Hua
citation:
ama: 'Hanauer K, Henzinger M, Hua QC. Fully dynamic four-vertex subgraph counting.
In: 1st Symposium on Algorithmic Foundations of Dynamic Networks. Vol 221.
Schloss Dagstuhl - Leibniz-Zentrum für Informatik; 2022. doi:10.4230/LIPIcs.SAND.2022.18'
apa: 'Hanauer, K., Henzinger, M., & Hua, Q. C. (2022). Fully dynamic four-vertex
subgraph counting. In 1st Symposium on Algorithmic Foundations of Dynamic Networks
(Vol. 221). Virtual: Schloss Dagstuhl - Leibniz-Zentrum für Informatik. https://doi.org/10.4230/LIPIcs.SAND.2022.18'
chicago: Hanauer, Kathrin, Monika Henzinger, and Qi Cheng Hua. “Fully Dynamic Four-Vertex
Subgraph Counting.” In 1st Symposium on Algorithmic Foundations of Dynamic
Networks, Vol. 221. Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2022.
https://doi.org/10.4230/LIPIcs.SAND.2022.18.
ieee: K. Hanauer, M. Henzinger, and Q. C. Hua, “Fully dynamic four-vertex subgraph
counting,” in 1st Symposium on Algorithmic Foundations of Dynamic Networks,
Virtual, 2022, vol. 221.
ista: 'Hanauer K, Henzinger M, Hua QC. 2022. Fully dynamic four-vertex subgraph
counting. 1st Symposium on Algorithmic Foundations of Dynamic Networks. SAND:
Symposium on Algorithmic Foundations of Dynamic Networks, LIPIcs, vol. 221, 18.'
mla: Hanauer, Kathrin, et al. “Fully Dynamic Four-Vertex Subgraph Counting.” 1st
Symposium on Algorithmic Foundations of Dynamic Networks, vol. 221, 18, Schloss
Dagstuhl - Leibniz-Zentrum für Informatik, 2022, doi:10.4230/LIPIcs.SAND.2022.18.
short: K. Hanauer, M. Henzinger, Q.C. Hua, in:, 1st Symposium on Algorithmic Foundations
of Dynamic Networks, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2022.
conference:
end_date: 2022-04-30
location: Virtual
name: 'SAND: Symposium on Algorithmic Foundations of Dynamic Networks'
start_date: 2022-04-28
date_created: 2022-08-12T06:57:55Z
date_published: 2022-04-29T00:00:00Z
date_updated: 2024-11-06T08:22:47Z
day: '29'
doi: 10.4230/LIPIcs.SAND.2022.18
extern: '1'
external_id:
arxiv:
- '2106.15524'
intvolume: ' 221'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.4230/LIPIcs.SAND.2022.18
month: '04'
oa: 1
oa_version: Published Version
publication: 1st Symposium on Algorithmic Foundations of Dynamic Networks
publication_identifier:
isbn:
- '9783959772242'
issn:
- 1868-8969
publication_status: published
publisher: Schloss Dagstuhl - Leibniz-Zentrum für Informatik
quality_controlled: '1'
scopus_import: '1'
status: public
title: Fully dynamic four-vertex subgraph counting
type: conference
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 221
year: '2022'
...
---
_id: '11841'
abstract:
- lang: eng
text: Primary nucleation is the fundamental event that initiates the conversion
of proteins from their normal physiological forms into pathological amyloid aggregates
associated with the onset and development of disorders including systemic amyloidosis,
as well as the neurodegenerative conditions Alzheimer’s and Parkinson’s diseases.
It has become apparent that the presence of surfaces can dramatically modulate
nucleation. However, the underlying physicochemical parameters governing this
process have been challenging to elucidate, with interfaces in some cases having
been found to accelerate aggregation, while in others they can inhibit the kinetics
of this process. Here we show through kinetic analysis that for three different
fibril-forming proteins, interfaces affect the aggregation reaction mainly through
modulating the primary nucleation step. Moreover, we show through direct measurements
of the Gibbs free energy of adsorption, combined with theory and coarse-grained
computer simulations, that overall nucleation rates are suppressed at high and
at low surface interaction strengths but significantly enhanced at intermediate
strengths, and we verify these regimes experimentally. Taken together, these results
provide a quantitative description of the fundamental process which triggers amyloid
formation and shed light on the key factors that control this process.
acknowledgement: "The research leading to these results has received funding from
the European Research Council (ERC) under the European Union’s Seventh Framework
Programme (FP7/2007-2013) through the ERC grant PhysProt\r\n(agreement 337969).
We are grateful for financial support from the Biotechnology and Biological Sciences
Research Council (BBSRC) (T.P.J.K.), the Newman\r\nFoundation (T.P.J.K.), the Wellcome
Trust (T.P.J.K. and M.V.), Peterhouse College\r\nCambridge (T.C.T.M.), the ERC Starting
Grant (StG) Non-Equilibrium Protein Assembly (NEPA) (A.S.), the Royal Society (A.S.),
the Academy of Medical Sciences\r\n(A.S. and J.K.), and the Cambridge Centre for
Misfolding Diseases (CMD)."
article_number: e2109718119
article_processing_charge: No
article_type: original
author:
- first_name: Zenon
full_name: Toprakcioglu, Zenon
last_name: Toprakcioglu
- first_name: Ayaka
full_name: Kamada, Ayaka
last_name: Kamada
- first_name: Thomas C.T.
full_name: Michaels, Thomas C.T.
last_name: Michaels
- first_name: Mengqi
full_name: Xie, Mengqi
last_name: Xie
- first_name: Johannes
full_name: Krausser, Johannes
last_name: Krausser
- first_name: Jiapeng
full_name: Wei, Jiapeng
last_name: Wei
- first_name: Anđela
full_name: Šarić, Anđela
id: bf63d406-f056-11eb-b41d-f263a6566d8b
last_name: Šarić
orcid: 0000-0002-7854-2139
- first_name: Michele
full_name: Vendruscolo, Michele
last_name: Vendruscolo
- first_name: Tuomas P.J.
full_name: Knowles, Tuomas P.J.
last_name: Knowles
citation:
ama: Toprakcioglu Z, Kamada A, Michaels TCT, et al. Adsorption free energy predicts
amyloid protein nucleation rates. Proceedings of the National Academy of Sciences
of the United States of America. 2022;119(31). doi:10.1073/pnas.2109718119
apa: Toprakcioglu, Z., Kamada, A., Michaels, T. C. T., Xie, M., Krausser, J., Wei,
J., … Knowles, T. P. J. (2022). Adsorption free energy predicts amyloid protein
nucleation rates. Proceedings of the National Academy of Sciences of the United
States of America. National Academy of Sciences. https://doi.org/10.1073/pnas.2109718119
chicago: Toprakcioglu, Zenon, Ayaka Kamada, Thomas C.T. Michaels, Mengqi Xie, Johannes
Krausser, Jiapeng Wei, Anđela Šarić, Michele Vendruscolo, and Tuomas P.J. Knowles.
“Adsorption Free Energy Predicts Amyloid Protein Nucleation Rates.” Proceedings
of the National Academy of Sciences of the United States of America. National
Academy of Sciences, 2022. https://doi.org/10.1073/pnas.2109718119.
ieee: Z. Toprakcioglu et al., “Adsorption free energy predicts amyloid protein
nucleation rates,” Proceedings of the National Academy of Sciences of the United
States of America, vol. 119, no. 31. National Academy of Sciences, 2022.
ista: Toprakcioglu Z, Kamada A, Michaels TCT, Xie M, Krausser J, Wei J, Šarić A,
Vendruscolo M, Knowles TPJ. 2022. Adsorption free energy predicts amyloid protein
nucleation rates. Proceedings of the National Academy of Sciences of the United
States of America. 119(31), e2109718119.
mla: Toprakcioglu, Zenon, et al. “Adsorption Free Energy Predicts Amyloid Protein
Nucleation Rates.” Proceedings of the National Academy of Sciences of the United
States of America, vol. 119, no. 31, e2109718119, National Academy of Sciences,
2022, doi:10.1073/pnas.2109718119.
short: Z. Toprakcioglu, A. Kamada, T.C.T. Michaels, M. Xie, J. Krausser, J. Wei,
A. Šarić, M. Vendruscolo, T.P.J. Knowles, Proceedings of the National Academy
of Sciences of the United States of America 119 (2022).
date_created: 2022-08-14T22:01:45Z
date_published: 2022-07-28T00:00:00Z
date_updated: 2025-06-12T06:21:34Z
day: '28'
ddc:
- '570'
department:
- _id: AnSa
doi: 10.1073/pnas.2109718119
ec_funded: 1
external_id:
isi:
- '000903753500002'
pmid:
- '35901206'
file:
- access_level: open_access
checksum: 0fe3878896cbeb6c44e29222ec2f336a
content_type: application/pdf
creator: dernst
date_created: 2023-10-04T09:05:44Z
date_updated: 2023-10-04T09:05:44Z
file_id: '14386'
file_name: 2022_PNAS_Toprakcioglu.pdf
file_size: 2476021
relation: main_file
success: 1
file_date_updated: 2023-10-04T09:05:44Z
has_accepted_license: '1'
intvolume: ' 119'
isi: 1
issue: '31'
language:
- iso: eng
month: '07'
oa: 1
oa_version: Published Version
pmid: 1
project:
- _id: eba2549b-77a9-11ec-83b8-a81e493eae4e
call_identifier: H2020
grant_number: '802960'
name: 'Non-Equilibrium Protein Assembly: from Building Blocks to Biological Machines'
publication: Proceedings of the National Academy of Sciences of the United States
of America
publication_identifier:
eissn:
- 1091-6490
issn:
- 0027-8424
publication_status: published
publisher: National Academy of Sciences
quality_controlled: '1'
scopus_import: '1'
status: public
title: Adsorption free energy predicts amyloid protein nucleation rates
tmp:
image: /images/cc_by_nc_nd.png
legal_code_url: https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode
name: Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International
(CC BY-NC-ND 4.0)
short: CC BY-NC-ND (4.0)
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 119
year: '2022'
...
---
_id: '11843'
abstract:
- lang: eng
text: A key attribute of persistent or recurring bacterial infections is the ability
of the pathogen to evade the host’s immune response. Many Enterobacteriaceae express
type 1 pili, a pre-adapted virulence trait, to invade host epithelial cells and
establish persistent infections. However, the molecular mechanisms and strategies
by which bacteria actively circumvent the immune response of the host remain poorly
understood. Here, we identified CD14, the major co-receptor for lipopolysaccharide
detection, on mouse dendritic cells (DCs) as a binding partner of FimH, the protein
located at the tip of the type 1 pilus of Escherichia coli. The FimH amino acids
involved in CD14 binding are highly conserved across pathogenic and non-pathogenic
strains. Binding of the pathogenic strain CFT073 to CD14 reduced DC migration
by overactivation of integrins and blunted expression of co-stimulatory molecules
by overactivating the NFAT (nuclear factor of activated T-cells) pathway, both
rate-limiting factors of T cell activation. This response was binary at the single-cell
level, but averaged in larger populations exposed to both piliated and non-piliated
pathogens, presumably via the exchange of immunomodulatory cytokines. While defining
an active molecular mechanism of immune evasion by pathogens, the interaction
between FimH and CD14 represents a potential target to interfere with persistent
and recurrent infections, such as urinary tract infections or Crohn’s disease.
acknowledged_ssus:
- _id: Bio
- _id: PreCl
- _id: EM-Fac
acknowledgement: We thank Ulrich Dobrindt for providing UPEC strains CFT073, UTI89,
and 536, Frank Assen, Vlad Gavra, Maximilian Götz, Bor Kavčič, Jonna Alanko, and
Eva Kiermaier for help with experiments and Robert Hauschild, Julian Stopp, and
Saren Tasciyan for help with data analysis. We thank the IST Austria Scientific
Service Units, especially the Bioimaging facility, the Preclinical facility and
the Electron microscopy facility for technical support, Jakob Wallner and all members
of the Guet and Sixt lab for fruitful discussions and Daria Siekhaus for critically
reading the manuscript. This work was supported by grants from the Austrian Research
Promotion Agency (FEMtech 868984) to IG, the European Research Council (CoG 724373),
and the Austrian Science Fund (FWF P29911) to MS.
article_number: e78995
article_processing_charge: Yes
article_type: original
author:
- first_name: Kathrin
full_name: Tomasek, Kathrin
id: 3AEC8556-F248-11E8-B48F-1D18A9856A87
last_name: Tomasek
orcid: 0000-0003-3768-877X
- first_name: Alexander F
full_name: Leithner, Alexander F
id: 3B1B77E4-F248-11E8-B48F-1D18A9856A87
last_name: Leithner
orcid: 0000-0002-1073-744X
- first_name: Ivana
full_name: Glatzová, Ivana
id: 727b3c7d-4939-11ec-89b3-b9b0750ab74d
last_name: Glatzová
- first_name: Michael S.
full_name: Lukesch, Michael S.
last_name: Lukesch
- first_name: Calin C
full_name: Guet, Calin C
id: 47F8433E-F248-11E8-B48F-1D18A9856A87
last_name: Guet
orcid: 0000-0001-6220-2052
- first_name: Michael K
full_name: Sixt, Michael K
id: 41E9FBEA-F248-11E8-B48F-1D18A9856A87
last_name: Sixt
orcid: 0000-0002-6620-9179
citation:
ama: Tomasek K, Leithner AF, Glatzová I, Lukesch MS, Guet CC, Sixt MK. Type 1 piliated
uropathogenic Escherichia coli hijack the host immune response by binding to CD14.
eLife. 2022;11. doi:10.7554/eLife.78995
apa: Tomasek, K., Leithner, A. F., Glatzová, I., Lukesch, M. S., Guet, C. C., &
Sixt, M. K. (2022). Type 1 piliated uropathogenic Escherichia coli hijack the
host immune response by binding to CD14. ELife. eLife Sciences Publications.
https://doi.org/10.7554/eLife.78995
chicago: Tomasek, Kathrin, Alexander F Leithner, Ivana Glatzová, Michael S. Lukesch,
Calin C Guet, and Michael K Sixt. “Type 1 Piliated Uropathogenic Escherichia Coli
Hijack the Host Immune Response by Binding to CD14.” ELife. eLife Sciences
Publications, 2022. https://doi.org/10.7554/eLife.78995.
ieee: K. Tomasek, A. F. Leithner, I. Glatzová, M. S. Lukesch, C. C. Guet, and M.
K. Sixt, “Type 1 piliated uropathogenic Escherichia coli hijack the host immune
response by binding to CD14,” eLife, vol. 11. eLife Sciences Publications,
2022.
ista: Tomasek K, Leithner AF, Glatzová I, Lukesch MS, Guet CC, Sixt MK. 2022. Type
1 piliated uropathogenic Escherichia coli hijack the host immune response by binding
to CD14. eLife. 11, e78995.
mla: Tomasek, Kathrin, et al. “Type 1 Piliated Uropathogenic Escherichia Coli Hijack
the Host Immune Response by Binding to CD14.” ELife, vol. 11, e78995, eLife
Sciences Publications, 2022, doi:10.7554/eLife.78995.
short: K. Tomasek, A.F. Leithner, I. Glatzová, M.S. Lukesch, C.C. Guet, M.K. Sixt,
ELife 11 (2022).
corr_author: '1'
date_created: 2022-08-14T22:01:46Z
date_published: 2022-07-26T00:00:00Z
date_updated: 2025-04-15T07:17:32Z
day: '26'
ddc:
- '570'
department:
- _id: MiSi
- _id: CaGu
doi: 10.7554/eLife.78995
ec_funded: 1
external_id:
isi:
- '000838410200001'
pmid:
- '35881547'
file:
- access_level: open_access
checksum: 002a3c7c7ea5caa9af9cfbea308f6ea4
content_type: application/pdf
creator: cchlebak
date_created: 2022-08-16T08:57:37Z
date_updated: 2022-08-16T08:57:37Z
file_id: '11861'
file_name: 2022_eLife_Tomasek.pdf
file_size: 2057577
relation: main_file
success: 1
file_date_updated: 2022-08-16T08:57:37Z
has_accepted_license: '1'
intvolume: ' 11'
isi: 1
language:
- iso: eng
month: '07'
oa: 1
oa_version: Published Version
pmid: 1
project:
- _id: 25FE9508-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '724373'
name: Cellular Navigation Along Spatial Gradients
- _id: 26018E70-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: P29911
name: Mechanical adaptation of lamellipodial actin
publication: eLife
publication_identifier:
eissn:
- 2050-084X
publication_status: published
publisher: eLife Sciences Publications
quality_controlled: '1'
related_material:
record:
- id: '10316'
relation: earlier_version
status: public
scopus_import: '1'
status: public
title: Type 1 piliated uropathogenic Escherichia coli hijack the host immune response
by binding to CD14
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: 11
year: '2022'
...
---
_id: '11844'
abstract:
- lang: eng
text: "In the stochastic population protocol model, we are given a connected graph
with n nodes, and in every time step, a scheduler samples an edge of the graph
uniformly at random and the nodes connected by this edge interact. A fundamental
task in this model is stable leader election, in which all nodes start in an identical
state and the aim is to reach a configuration in which (1) exactly one node is
elected as leader and (2) this node remains as the unique leader no matter what
sequence of interactions follows. On cliques, the complexity of this problem has
recently been settled: time-optimal protocols stabilize in Θ(n log n) expected
steps using Θ(log log n) states, whereas protocols that use O(1) states require
Θ(n2) expected steps.\r\n\r\nIn this work, we investigate the complexity of stable
leader election on general graphs. We provide the first non-trivial time lower
bounds for leader election on general graphs, showing that, when moving beyond
cliques, the complexity landscape of leader election becomes very diverse: the
time required to elect a leader can range from O(1) to Θ(n3) expected steps. On
the upper bound side, we first observe that there exists a protocol that is time-optimal
on many graph families, but uses polynomially-many states. In contrast, we give
a near-time-optimal protocol that uses only O(log2n) states that is at most a
factor log n slower. Finally, we show that the constant-state protocol of Beauquier
et al. [OPODIS 2013] is at most a factor n log n slower than the fast polynomial-state
protocol. Moreover, among constant-state protocols, this protocol has near-optimal
average case complexity on dense random graphs."
acknowledgement: We thank the anonymous reviewers for their helpful comments. We gratefully
acknowledge funding from the European Research Council (ERC) under the European
Union’s Horizon 2020 research and innovation programme (grant agreement No 805223
ScaleML).
article_processing_charge: Yes (via OA deal)
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: Joel
full_name: Rybicki, Joel
id: 334EFD2E-F248-11E8-B48F-1D18A9856A87
last_name: Rybicki
orcid: 0000-0002-6432-6646
- first_name: Sasha
full_name: Voitovych, Sasha
last_name: Voitovych
citation:
ama: 'Alistarh D-A, Rybicki J, Voitovych S. Near-optimal leader election in population
protocols on graphs. In: Proceedings of the Annual ACM Symposium on Principles
of Distributed Computing. Association for Computing Machinery; 2022:246-256.
doi:10.1145/3519270.3538435'
apa: 'Alistarh, D.-A., Rybicki, J., & Voitovych, S. (2022). Near-optimal leader
election in population protocols on graphs. In Proceedings of the Annual ACM
Symposium on Principles of Distributed Computing (pp. 246–256). Salerno, Italy:
Association for Computing Machinery. https://doi.org/10.1145/3519270.3538435'
chicago: Alistarh, Dan-Adrian, Joel Rybicki, and Sasha Voitovych. “Near-Optimal
Leader Election in Population Protocols on Graphs.” In Proceedings of the Annual
ACM Symposium on Principles of Distributed Computing, 246–56. Association
for Computing Machinery, 2022. https://doi.org/10.1145/3519270.3538435.
ieee: D.-A. Alistarh, J. Rybicki, and S. Voitovych, “Near-optimal leader election
in population protocols on graphs,” in Proceedings of the Annual ACM Symposium
on Principles of Distributed Computing, Salerno, Italy, 2022, pp. 246–256.
ista: 'Alistarh D-A, Rybicki J, Voitovych S. 2022. Near-optimal leader election
in population protocols on graphs. Proceedings of the Annual ACM Symposium on
Principles of Distributed Computing. PODC: Symposium on Principles of Distributed
Computing, 246–256.'
mla: Alistarh, Dan-Adrian, et al. “Near-Optimal Leader Election in Population Protocols
on Graphs.” Proceedings of the Annual ACM Symposium on Principles of Distributed
Computing, Association for Computing Machinery, 2022, pp. 246–56, doi:10.1145/3519270.3538435.
short: D.-A. Alistarh, J. Rybicki, S. Voitovych, in:, Proceedings of the Annual
ACM Symposium on Principles of Distributed Computing, Association for Computing
Machinery, 2022, pp. 246–256.
conference:
end_date: 2022-07-29
location: Salerno, Italy
name: 'PODC: Symposium on Principles of Distributed Computing'
start_date: 2022-07-25
corr_author: '1'
date_created: 2022-08-14T22:01:46Z
date_published: 2022-07-21T00:00:00Z
date_updated: 2025-12-30T09:04:17Z
day: '21'
ddc:
- '000'
department:
- _id: DaAl
doi: 10.1145/3519270.3538435
ec_funded: 1
external_id:
arxiv:
- '2205.12597'
isi:
- '001031439100030'
file:
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language:
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month: '07'
oa: 1
oa_version: Published Version
page: 246-256
project:
- _id: 268A44D6-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '805223'
name: Elastic Coordination for Scalable Machine Learning
publication: Proceedings of the Annual ACM Symposium on Principles of Distributed
Computing
publication_identifier:
isbn:
- '9781450392624'
publication_status: published
publisher: Association for Computing Machinery
quality_controlled: '1'
related_material:
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relation: later_version
status: public
scopus_import: '1'
status: public
title: Near-optimal leader election in population protocols on graphs
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: 317138e5-6ab7-11ef-aa6d-ffef3953e345
year: '2022'
...
---
_id: '11858'
abstract:
- lang: eng
text: "This paper is a continuation of Part I of this project, where we developed
a new local well-posedness theory for nonlinear stochastic PDEs with Gaussian
noise. In the current Part II we consider blow-up criteria and regularization
phenomena. As in Part I we can allow nonlinearities with polynomial growth and
rough initial values from critical spaces. In the first main result we obtain
several new blow-up criteria for quasi- and semilinear stochastic evolution equations.
In particular, for semilinear equations we obtain a Serrin type blow-up criterium,
which extends a recent result of Prüss–Simonett–Wilke (J Differ Equ 264(3):2028–2074,
2018) to the stochastic setting. Blow-up criteria can be used to prove global
well-posedness for SPDEs. As in Part I, maximal regularity techniques and weights
in time play a central role in the proofs. Our second contribution is a new method
to bootstrap Sobolev and Hölder regularity in time and space, which does not require
smoothness of the initial data. The blow-up criteria are at the basis of these
new methods. Moreover, in applications the bootstrap results can be combined with
our blow-up criteria, to obtain efficient ways to prove global existence. This
gives new results even in classical \U0001D43F2-settings, which we illustrate
for a concrete SPDE. In future works in preparation we apply the results of the
current paper to obtain global well-posedness results and regularity for several
concrete SPDEs. These include stochastic Navier–Stokes equations, reaction– diffusion
equations and the Allen–Cahn equation. Our setting allows to put these SPDEs into
a more flexible framework, where less restrictions on the nonlinearities are needed,
and we are able to treat rough initial values from critical spaces. Moreover,
we will obtain higher-order regularity results."
acknowledgement: "The authors thank Emiel Lorist for helpful comments. The authors
thank the anonymous referees for their helpful remarks to improve the presentation.\r\nOpen
access funding provided by Institute of Science and Technology (IST Austria)."
article_number: '56'
article_processing_charge: Yes (via OA deal)
article_type: original
author:
- first_name: Antonio
full_name: Agresti, Antonio
id: 673cd0cc-9b9a-11eb-b144-88f30e1fbb72
last_name: Agresti
orcid: 0000-0002-9573-2962
- first_name: Mark
full_name: Veraar, Mark
last_name: Veraar
citation:
ama: Agresti A, Veraar M. Nonlinear parabolic stochastic evolution equations in
critical spaces part II. Journal of Evolution Equations. 2022;22(2). doi:10.1007/s00028-022-00786-7
apa: Agresti, A., & Veraar, M. (2022). Nonlinear parabolic stochastic evolution
equations in critical spaces part II. Journal of Evolution Equations. Springer
Nature. https://doi.org/10.1007/s00028-022-00786-7
chicago: Agresti, Antonio, and Mark Veraar. “Nonlinear Parabolic Stochastic Evolution
Equations in Critical Spaces Part II.” Journal of Evolution Equations.
Springer Nature, 2022. https://doi.org/10.1007/s00028-022-00786-7.
ieee: A. Agresti and M. Veraar, “Nonlinear parabolic stochastic evolution equations
in critical spaces part II,” Journal of Evolution Equations, vol. 22, no.
2. Springer Nature, 2022.
ista: Agresti A, Veraar M. 2022. Nonlinear parabolic stochastic evolution equations
in critical spaces part II. Journal of Evolution Equations. 22(2), 56.
mla: Agresti, Antonio, and Mark Veraar. “Nonlinear Parabolic Stochastic Evolution
Equations in Critical Spaces Part II.” Journal of Evolution Equations,
vol. 22, no. 2, 56, Springer Nature, 2022, doi:10.1007/s00028-022-00786-7.
short: A. Agresti, M. Veraar, Journal of Evolution Equations 22 (2022).
corr_author: '1'
date_created: 2022-08-16T08:39:43Z
date_published: 2022-06-01T00:00:00Z
date_updated: 2024-10-09T21:03:06Z
day: '01'
ddc:
- '510'
department:
- _id: JuFi
doi: 10.1007/s00028-022-00786-7
external_id:
isi:
- '000809108500001'
file:
- access_level: open_access
checksum: 59b99d1b48b6bd40983e7ce298524a21
content_type: application/pdf
creator: kschuh
date_created: 2022-08-16T08:52:46Z
date_updated: 2022-08-16T08:52:46Z
file_id: '11862'
file_name: 2022_Journal of Evolution Equations_Agresti.pdf
file_size: 1758371
relation: main_file
success: 1
file_date_updated: 2022-08-16T08:52:46Z
has_accepted_license: '1'
intvolume: ' 22'
isi: 1
issue: '2'
keyword:
- Mathematics (miscellaneous)
language:
- iso: eng
month: '06'
oa: 1
oa_version: Published Version
publication: Journal of Evolution Equations
publication_identifier:
eissn:
- 1424-3202
issn:
- 1424-3199
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
scopus_import: '1'
status: public
title: Nonlinear parabolic stochastic evolution equations in critical spaces part
II
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: 22
year: '2022'
...