---
OA_place: publisher
OA_type: hybrid
_id: '17886'
abstract:
- lang: eng
text: 'Thin pancake-like neuronal networks cultured on top of a planar microelectrode
array have been extensively tried out in neuroengineering, as a substrate for
the mobile robot’s control unit, i.e., as a cyborg’s brain. Most of these attempts
failed due to intricate self-organizing dynamics in the neuronal systems. In particular,
the networks may exhibit an emergent spatial map of steady nucleation sites (“n-sites”)
of spontaneous population spikes. Being unpredictable and independent of the surface
electrode locations, the n-sites drastically change local ability of the network
to generate spikes. Here, using a spiking neuronal network model with generative
spatially-embedded connectome, we systematically show in simulations that the
number, location, and relative activity of spontaneously formed n-sites (“the
vitals”) crucially depend on the samplings of three distributions: (1) the network
distribution of neuronal excitability, (2) the distribution of connections between
neurons of the network, and (3) the distribution of maximal amplitudes of a single
synaptic current pulse. Moreover, blocking the dynamics of a small fraction (about
4%) of non-pacemaker neurons having the highest excitability was enough to completely
suppress the occurrence of population spikes and their n-sites. This key result
is explained theoretically. Remarkably, the n-sites occur taking into account
only short-term synaptic plasticity, i.e., without a Hebbian-type plasticity.
As the spiking network model used in this study is strictly deterministic, all
simulation results can be accurately reproduced. The model, which has already
demonstrated a very high richness-to-complexity ratio, can also be directly extended
into the three-dimensional case, e.g., for targeting peculiarities of spiking
dynamics in cerebral (or brain) organoids. We recommend the model as an excellent
illustrative tool for teaching network-level computational neuroscience, complementing
a few benchmark models.'
acknowledgement: A.P. is grateful to Chaitanya Chintaluri, Douglas Feitosa Tomé, and
Tim P. Vogels for useful discussions. This work was supported by a European Research
Council Consolidator Grant (SYNAPSEEK, 819603, to Tim P. Vogels).
article_number: '106589'
article_processing_charge: Yes (via OA deal)
article_type: original
author:
- first_name: Dmitrii
full_name: Zendrikov, Dmitrii
last_name: Zendrikov
- first_name: Alexander
full_name: Paraskevov, Alexander
id: d05e3c56-9262-11ed-9231-be692464e5ac
last_name: Paraskevov
citation:
ama: Zendrikov D, Paraskevov A. The vitals for steady nucleation maps of spontaneous
spiking coherence in autonomous two-dimensional neuronal networks. Neural Networks.
2024;180. doi:10.1016/j.neunet.2024.106589
apa: Zendrikov, D., & Paraskevov, A. (2024). The vitals for steady nucleation
maps of spontaneous spiking coherence in autonomous two-dimensional neuronal networks.
Neural Networks. Elsevier. https://doi.org/10.1016/j.neunet.2024.106589
chicago: Zendrikov, Dmitrii, and Alexander Paraskevov. “The Vitals for Steady Nucleation
Maps of Spontaneous Spiking Coherence in Autonomous Two-Dimensional Neuronal Networks.”
Neural Networks. Elsevier, 2024. https://doi.org/10.1016/j.neunet.2024.106589.
ieee: D. Zendrikov and A. Paraskevov, “The vitals for steady nucleation maps of
spontaneous spiking coherence in autonomous two-dimensional neuronal networks,”
Neural Networks, vol. 180. Elsevier, 2024.
ista: Zendrikov D, Paraskevov A. 2024. The vitals for steady nucleation maps of
spontaneous spiking coherence in autonomous two-dimensional neuronal networks.
Neural Networks. 180, 106589.
mla: Zendrikov, Dmitrii, and Alexander Paraskevov. “The Vitals for Steady Nucleation
Maps of Spontaneous Spiking Coherence in Autonomous Two-Dimensional Neuronal Networks.”
Neural Networks, vol. 180, 106589, Elsevier, 2024, doi:10.1016/j.neunet.2024.106589.
short: D. Zendrikov, A. Paraskevov, Neural Networks 180 (2024).
corr_author: '1'
date_created: 2024-09-08T22:01:10Z
date_published: 2024-12-01T00:00:00Z
date_updated: 2025-09-08T09:12:20Z
day: '01'
ddc:
- '570'
department:
- _id: TiVo
doi: 10.1016/j.neunet.2024.106589
ec_funded: 1
external_id:
isi:
- '001316474600001'
pmid:
- '39217864'
file:
- access_level: open_access
checksum: 6a194323234e01d4ae725f674529cdb1
content_type: application/pdf
creator: dernst
date_created: 2025-01-13T08:26:08Z
date_updated: 2025-01-13T08:26:08Z
file_id: '18825'
file_name: 2024_NeuralNetworks_Zendrikov.pdf
file_size: 6162281
relation: main_file
success: 1
file_date_updated: 2025-01-13T08:26:08Z
has_accepted_license: '1'
intvolume: ' 180'
isi: 1
language:
- iso: eng
license: https://creativecommons.org/licenses/by/4.0/
month: '12'
oa: 1
oa_version: Published Version
pmid: 1
project:
- _id: 0aacfa84-070f-11eb-9043-d7eb2c709234
call_identifier: H2020
grant_number: '819603'
name: Learning the shape of synaptic plasticity rules for neuronal architectures
and function through machine learning.
publication: Neural Networks
publication_identifier:
eissn:
- 1879-2782
issn:
- 0893-6080
publication_status: published
publisher: Elsevier
quality_controlled: '1'
scopus_import: '1'
status: public
title: The vitals for steady nucleation maps of spontaneous spiking coherence in autonomous
two-dimensional neuronal networks
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: journal_article
user_id: 317138e5-6ab7-11ef-aa6d-ffef3953e345
volume: 180
year: '2024'
...
---
_id: '17887'
abstract:
- lang: eng
text: We show convergence of the Navier-Stokes/Allen-Cahn system to a classical
sharp interface model for the two-phase flow of two viscous incompressible fluids
with same viscosities in a smooth bounded domain in two and three space dimensions
as long as a smooth solution of the limit system exists. Moreover, we obtain error
estimates with the aid of a relative entropy method. Our results hold provided
that the mobility mε>0 in the Allen-Cahn equation tends to zero in a subcritical
way, i.e., mε=m0εβ for some β∈(0,2) and m0>0 . The proof proceeds by showing
via a relative entropy argument that the solution to the Navier-Stokes/Allen-Cahn
system remains close to the solution of a perturbed version of the two-phase flow
problem, augmented by an extra mean curvature flow term mεHΓt in the interface
motion. In a second step, it is easy to see that the solution to the perturbed
problem is close to the original two-phase flow.
acknowledgement: "J. Fischer and M. Moser have received funding from the European
Research Council (ERC) under the European Union’s Horizon 2020 research and innovation
programme (grant agreement No 948819).\r\nOpen Access funding enabled and organized
by Projekt DEAL."
article_number: '77'
article_processing_charge: Yes (via OA deal)
article_type: original
arxiv: 1
author:
- first_name: Helmut
full_name: Abels, Helmut
last_name: Abels
- first_name: Julian L
full_name: Fischer, Julian L
id: 2C12A0B0-F248-11E8-B48F-1D18A9856A87
last_name: Fischer
orcid: 0000-0002-0479-558X
- first_name: Maximilian
full_name: Moser, Maximilian
id: a60047a9-da77-11eb-85b4-c4dc385ebb8c
last_name: Moser
citation:
ama: Abels H, Fischer JL, Moser M. Approximation of classical two-phase flows of
viscous incompressible fluids by a Navier–Stokes/Allen–Cahn system. Archive
for Rational Mechanics and Analysis. 2024;248(5). doi:10.1007/s00205-024-02020-9
apa: Abels, H., Fischer, J. L., & Moser, M. (2024). Approximation of classical
two-phase flows of viscous incompressible fluids by a Navier–Stokes/Allen–Cahn
system. Archive for Rational Mechanics and Analysis. Springer Nature. https://doi.org/10.1007/s00205-024-02020-9
chicago: Abels, Helmut, Julian L Fischer, and Maximilian Moser. “Approximation of
Classical Two-Phase Flows of Viscous Incompressible Fluids by a Navier–Stokes/Allen–Cahn
System.” Archive for Rational Mechanics and Analysis. Springer Nature,
2024. https://doi.org/10.1007/s00205-024-02020-9.
ieee: H. Abels, J. L. Fischer, and M. Moser, “Approximation of classical two-phase
flows of viscous incompressible fluids by a Navier–Stokes/Allen–Cahn system,”
Archive for Rational Mechanics and Analysis, vol. 248, no. 5. Springer
Nature, 2024.
ista: Abels H, Fischer JL, Moser M. 2024. Approximation of classical two-phase flows
of viscous incompressible fluids by a Navier–Stokes/Allen–Cahn system. Archive
for Rational Mechanics and Analysis. 248(5), 77.
mla: Abels, Helmut, et al. “Approximation of Classical Two-Phase Flows of Viscous
Incompressible Fluids by a Navier–Stokes/Allen–Cahn System.” Archive for Rational
Mechanics and Analysis, vol. 248, no. 5, 77, Springer Nature, 2024, doi:10.1007/s00205-024-02020-9.
short: H. Abels, J.L. Fischer, M. Moser, Archive for Rational Mechanics and Analysis
248 (2024).
date_created: 2024-09-08T22:01:10Z
date_published: 2024-09-03T00:00:00Z
date_updated: 2025-09-08T09:11:41Z
day: '03'
ddc:
- '510'
department:
- _id: JuFi
doi: 10.1007/s00205-024-02020-9
ec_funded: 1
external_id:
arxiv:
- '2311.02997'
isi:
- '001305530600001'
pmid:
- '39239088'
file:
- access_level: open_access
checksum: 98493a05b84e4513b6394dfad4851ddf
content_type: application/pdf
creator: dernst
date_created: 2024-09-09T08:43:32Z
date_updated: 2024-09-09T08:43:32Z
file_id: '17938'
file_name: 2024_ArchiveRatAnalysis_Abels.pdf
file_size: 811131
relation: main_file
success: 1
file_date_updated: 2024-09-09T08:43:32Z
has_accepted_license: '1'
intvolume: ' 248'
isi: 1
issue: '5'
language:
- iso: eng
month: '09'
oa: 1
oa_version: Published Version
pmid: 1
project:
- _id: 0aa76401-070f-11eb-9043-b5bb049fa26d
call_identifier: H2020
grant_number: '948819'
name: Bridging Scales in Random Materials
publication: Archive for Rational Mechanics and Analysis
publication_identifier:
eissn:
- 1432-0673
issn:
- 0003-9527
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
scopus_import: '1'
status: public
title: Approximation of classical two-phase flows of viscous incompressible fluids
by a Navier–Stokes/Allen–Cahn system
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: 317138e5-6ab7-11ef-aa6d-ffef3953e345
volume: 248
year: '2024'
...
---
_id: '17888'
abstract:
- lang: eng
text: "Context: Biotic resource exploitation is a critical determinant of species’
distributions. However, quantifying resource exploitation patterns through space
and time can be difficult, complicating their incorporation in spatial ecology
studies. Therefore, understanding the local drivers of spatial patterns of resource
exploitation may contribute to better large-scale species distribution models.\r\nObjectives:
We investigated (1) how the resource exploitation patterns of two trophic interactions
(plant–insect) are explained by insect behaviour, resource aggregation, and potential
insect-insect interactions. We also analyzed how (2) resource patch size and (3)
resource accessibility in a heterogeneous landscape affected host exploitation
patterns.\r\nMethods: We quantified nectar robbing by insects in the genus Bombus
(bumblebees) and seed predation by Brachypterolus vestitus larvae (Antirrhinum
beetle) on Antirrhinum majus L. (wild snapdragons) in the Pyrenees Mountains,
Catalonia, Spain. We tested hypotheses about resource exploitation by integrating
spatial analyses at multiple scales.\r\nResults: Both trophic interactions were
aggregated, explained by the aggregation of their resource. At some scales, nectar
robbing is more aggregated than the resource. Trophic interaction abundance is
proportional to resource patch size, following the ideal free distribution model.
Landscape features do not explain the locations exploited. Nectar robbing and
seed predation occur together more often than expected.\r\nConclusions: Our findings
suggest that multiple biotic and ecological spatial factors may simultaneously
affect resource exploitation at a local scale. These findings should be considered
when developing agricultural projects, management plans and conservation policies."
acknowledgement: "For the beetle barcoding, we are very thankful to Brent Emerson’s
laboratory at the Consejo Superior de Investigaciones Científicas (CSIC) at the
Instituto de Productos Naturales y Agrobiología (IPNA) in La Laguna, Tenerife. Many
thanks to numerous field assistants, especially Sandra Cuevas Gallego, Beatriz Pablo
Carmona, Luís Santos Cid and Alex Fuster, for their assistance in data collection.
Finally, we thank Jesús Muñoz, Virgilio Gómez-Rubio, and two anonymous reviewers
for comments that greatly improved the quality of the manuscript.\r\nOpen access
funding provided by Institute of Science and Technology (IST Austria). CB received
funding from the European Union’s Horizon 2020 research and innovation programme
under the Marie Skłodowska-Curie Grant Agreement No. 754411. NB was funded by the
FWF grant “Löwenmaul speciation” P 32166-B32."
article_number: '172'
article_processing_charge: Yes (via OA deal)
article_type: original
author:
- first_name: Guillem
full_name: Pocull Belles, Guillem
id: 54359172-700c-11ef-a103-c1d91ceac6d6
last_name: Pocull Belles
- first_name: Carina
full_name: Baskett, Carina
id: 3B4A7CE2-F248-11E8-B48F-1D18A9856A87
last_name: Baskett
orcid: 0000-0002-7354-8574
- first_name: Nicholas H
full_name: Barton, Nicholas H
id: 4880FE40-F248-11E8-B48F-1D18A9856A87
last_name: Barton
orcid: 0000-0002-8548-5240
citation:
ama: 'Pocull Belles G, Baskett C, Barton NH. Multiscale spatial analysis of two
plant–insect interactions: Effects of landscape, resource distribution, and other
insects. Landscape Ecology. 2024;39(9). doi:10.1007/s10980-024-01899-9'
apa: 'Pocull Belles, G., Baskett, C., & Barton, N. H. (2024). Multiscale spatial
analysis of two plant–insect interactions: Effects of landscape, resource distribution,
and other insects. Landscape Ecology. Springer Nature. https://doi.org/10.1007/s10980-024-01899-9'
chicago: 'Pocull Belles, Guillem, Carina Baskett, and Nicholas H Barton. “Multiscale
Spatial Analysis of Two Plant–Insect Interactions: Effects of Landscape, Resource
Distribution, and Other Insects.” Landscape Ecology. Springer Nature, 2024.
https://doi.org/10.1007/s10980-024-01899-9.'
ieee: 'G. Pocull Belles, C. Baskett, and N. H. Barton, “Multiscale spatial analysis
of two plant–insect interactions: Effects of landscape, resource distribution,
and other insects,” Landscape Ecology, vol. 39, no. 9. Springer Nature,
2024.'
ista: 'Pocull Belles G, Baskett C, Barton NH. 2024. Multiscale spatial analysis
of two plant–insect interactions: Effects of landscape, resource distribution,
and other insects. Landscape Ecology. 39(9), 172.'
mla: 'Pocull Belles, Guillem, et al. “Multiscale Spatial Analysis of Two Plant–Insect
Interactions: Effects of Landscape, Resource Distribution, and Other Insects.”
Landscape Ecology, vol. 39, no. 9, 172, Springer Nature, 2024, doi:10.1007/s10980-024-01899-9.'
short: G. Pocull Belles, C. Baskett, N.H. Barton, Landscape Ecology 39 (2024).
corr_author: '1'
date_created: 2024-09-08T22:01:11Z
date_published: 2024-09-01T00:00:00Z
date_updated: 2025-09-08T09:20:11Z
day: '01'
ddc:
- '570'
department:
- _id: NiBa
doi: 10.1007/s10980-024-01899-9
ec_funded: 1
external_id:
isi:
- '001304011900001'
file:
- access_level: open_access
checksum: 2e1cbc320ec1b4447a5a8562a90bcbc3
content_type: application/pdf
creator: dernst
date_created: 2024-09-11T07:14:03Z
date_updated: 2024-09-11T07:14:03Z
file_id: '18054'
file_name: 2024_LandscapeEcology_Pocull.pdf
file_size: 1494987
relation: main_file
success: 1
file_date_updated: 2024-09-11T07:14:03Z
has_accepted_license: '1'
intvolume: ' 39'
isi: 1
issue: '9'
language:
- iso: eng
month: '09'
oa: 1
oa_version: Published Version
project:
- _id: 260C2330-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '754411'
name: ISTplus - Postdoctoral Fellowships
- _id: 05959E1C-7A3F-11EA-A408-12923DDC885E
grant_number: P32166
name: Snapdragon Speciation
publication: Landscape Ecology
publication_identifier:
eissn:
- 1572-9761
issn:
- 0921-2973
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
scopus_import: '1'
status: public
title: 'Multiscale spatial analysis of two plant–insect interactions: Effects of landscape,
resource distribution, and other insects'
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: 317138e5-6ab7-11ef-aa6d-ffef3953e345
volume: 39
year: '2024'
...
---
_id: '17891'
abstract:
- lang: eng
text: "Abstract\r\nMethods used in topological data analysis naturally capture higher-order
interactions in point cloud data embedded in a metric space. This methodology
was recently extended to data living in an information space, by which we mean
a space measured with an information theoretical distance. One such setting is
a finite collection of discrete probability distributions embedded in the probability
simplex measured with the relative entropy (Kullback–Leibler divergence). More
generally, one can work with a Bregman divergence parameterized by a different
notion of entropy. While theoretical algorithms exist for this setup, there is
a paucity of implementations for exploring and comparing geometric-topological
properties of various information spaces. The interest of this work is therefore
twofold. First, we propose the first robust algorithms and software for geometric
and topological data analysis in information space. Perhaps surprisingly, despite
working with Bregman divergences, our design reuses robust libraries for the Euclidean
case. Second, using the new software, we take the first steps towards understanding
the geometric-topological structure of these spaces. In particular, we compare
them with the more familiar spaces equipped with the Euclidean and Fisher metrics."
acknowledgement: We thank Anton Nikitenko for first observing that the Wrap complex
can be characterized as stated in Claim (ii) of the Wrap Complex Lemma, and Ondrej
Draganov for correcting a critical mistake in one of our formulas in Section 2.
article_number: '637'
article_processing_charge: Yes
article_type: original
author:
- first_name: Herbert
full_name: Edelsbrunner, Herbert
id: 3FB178DA-F248-11E8-B48F-1D18A9856A87
last_name: Edelsbrunner
orcid: 0000-0002-9823-6833
- first_name: Katharina
full_name: Ölsböck, Katharina
id: 4D4AA390-F248-11E8-B48F-1D18A9856A87
last_name: Ölsböck
orcid: 0000-0002-4672-8297
- first_name: Hubert
full_name: Wagner, Hubert
id: 379CA8B8-F248-11E8-B48F-1D18A9856A87
last_name: Wagner
citation:
ama: Edelsbrunner H, Ölsböck K, Wagner H. Understanding higher-order interactions
in information space. Entropy. 2024;26(8). doi:10.3390/e26080637
apa: Edelsbrunner, H., Ölsböck, K., & Wagner, H. (2024). Understanding higher-order
interactions in information space. Entropy. MDPI. https://doi.org/10.3390/e26080637
chicago: Edelsbrunner, Herbert, Katharina Ölsböck, and Hubert Wagner. “Understanding
Higher-Order Interactions in Information Space.” Entropy. MDPI, 2024. https://doi.org/10.3390/e26080637.
ieee: H. Edelsbrunner, K. Ölsböck, and H. Wagner, “Understanding higher-order interactions
in information space,” Entropy, vol. 26, no. 8. MDPI, 2024.
ista: Edelsbrunner H, Ölsböck K, Wagner H. 2024. Understanding higher-order interactions
in information space. Entropy. 26(8), 637.
mla: Edelsbrunner, Herbert, et al. “Understanding Higher-Order Interactions in Information
Space.” Entropy, vol. 26, no. 8, 637, MDPI, 2024, doi:10.3390/e26080637.
short: H. Edelsbrunner, K. Ölsböck, H. Wagner, Entropy 26 (2024).
date_created: 2024-09-08T22:01:11Z
date_published: 2024-08-01T00:00:00Z
date_updated: 2025-09-08T09:13:44Z
day: '01'
ddc:
- '510'
department:
- _id: HeEd
doi: 10.3390/e26080637
external_id:
isi:
- '001305543500001'
pmid:
- '39202107'
file:
- access_level: open_access
checksum: 624a9e2c5b49d6c38b88b0f675467ba3
content_type: application/pdf
creator: dernst
date_created: 2024-09-09T09:01:12Z
date_updated: 2024-09-09T09:01:12Z
file_id: '17948'
file_name: 2024_Entropy_Edelsbrunner.pdf
file_size: 8025139
relation: main_file
success: 1
file_date_updated: 2024-09-09T09:01:12Z
has_accepted_license: '1'
intvolume: ' 26'
isi: 1
issue: '8'
language:
- iso: eng
month: '08'
oa: 1
oa_version: Published Version
pmid: 1
publication: Entropy
publication_identifier:
eissn:
- 1099-4300
publication_status: published
publisher: MDPI
quality_controlled: '1'
related_material:
link:
- relation: software
url: https://git.ista.ac.at/katharina.oelsboeck/wrap_2_3-public/
scopus_import: '1'
status: public
title: Understanding higher-order interactions in information space
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: 317138e5-6ab7-11ef-aa6d-ffef3953e345
volume: 26
year: '2024'
...
---
_id: '17892'
abstract:
- lang: eng
text: "Enzyme-substrate kinetics form the basis of many biomolecular processes.
The interplay between substrate binding and substrate geometry can give rise to
long-range interactions between enzyme binding events. Here we study a general
model of enzyme-substrate kinetics with restricted long-range interactions described
by an exponent −\U0001D6FE. We employ a coherent-state path integral and renormalization
group approach to calculate the first moment and two-point correlation function
of the enzyme-binding profile. We show that starting from an empty substrate the
average occupancy follows a power law with an exponent 1/(1−\U0001D6FE) over time.
The correlation function decays algebraically with two distinct spatial regimes
characterized by exponents −\U0001D6FE on short distances and −(2/3)(2−\U0001D6FE)
on long distances. The crossover between both regimes scales inversely with the
average substrate occupancy. Our work allows associating experimental measurements
of bound enzyme locations with their binding kinetics and the spatial conformation
of the substrate."
acknowledgement: We thank F. Piazza, M. Henkel, and F. Jülicher for helpful feedback
and the entire Rulands group for fruitful discussions. We thank W. Reik, S. Clark,
T. Lohoff, and I. Kafetzopoulos for fruitful discussions about the biological aspects
of this work. This project has received funding from the European Research Council
(ERC) under the European Union's Horizon 2020 research and innovation program (Grant
No. 950349). This project has received funding from the European Union's Horizon
2020 research and innovation programme under the Marie Skłodowska-Curie Grant No.
101034413.
article_number: '024404'
article_processing_charge: Yes (in subscription journal)
article_type: original
author:
- first_name: Fabrizio
full_name: Olmeda, Fabrizio
id: 69dbf5fb-8a76-11ed-866b-fb486d8b5689
last_name: Olmeda
- first_name: Steffen
full_name: Rulands, Steffen
last_name: Rulands
citation:
ama: Olmeda F, Rulands S. Field theory of enzyme-substrate systems with restricted
long-range interactions. Physical Review E. 2024;110(2). doi:10.1103/PhysRevE.110.024404
apa: Olmeda, F., & Rulands, S. (2024). Field theory of enzyme-substrate systems
with restricted long-range interactions. Physical Review E. American Physical
Society. https://doi.org/10.1103/PhysRevE.110.024404
chicago: Olmeda, Fabrizio, and Steffen Rulands. “Field Theory of Enzyme-Substrate
Systems with Restricted Long-Range Interactions.” Physical Review E. American
Physical Society, 2024. https://doi.org/10.1103/PhysRevE.110.024404.
ieee: F. Olmeda and S. Rulands, “Field theory of enzyme-substrate systems with restricted
long-range interactions,” Physical Review E, vol. 110, no. 2. American
Physical Society, 2024.
ista: Olmeda F, Rulands S. 2024. Field theory of enzyme-substrate systems with restricted
long-range interactions. Physical Review E. 110(2), 024404.
mla: Olmeda, Fabrizio, and Steffen Rulands. “Field Theory of Enzyme-Substrate Systems
with Restricted Long-Range Interactions.” Physical Review E, vol. 110,
no. 2, 024404, American Physical Society, 2024, doi:10.1103/PhysRevE.110.024404.
short: F. Olmeda, S. Rulands, Physical Review E 110 (2024).
corr_author: '1'
date_created: 2024-09-08T22:01:12Z
date_published: 2024-08-01T00:00:00Z
date_updated: 2025-09-08T09:17:18Z
day: '01'
ddc:
- '530'
department:
- _id: EdHa
doi: 10.1103/PhysRevE.110.024404
ec_funded: 1
external_id:
isi:
- '001299670100004'
pmid:
- '39294986'
file:
- access_level: open_access
checksum: 67fc2cc8eee3155e5c3b7380307d8284
content_type: application/pdf
creator: dernst
date_created: 2024-09-11T05:59:36Z
date_updated: 2024-09-11T05:59:36Z
file_id: '18053'
file_name: 2024_PhysReviewE_Olmeda.pdf
file_size: 445696
relation: main_file
success: 1
file_date_updated: 2024-09-11T05:59:36Z
has_accepted_license: '1'
intvolume: ' 110'
isi: 1
issue: '2'
language:
- iso: eng
month: '08'
oa: 1
oa_version: Published Version
pmid: 1
project:
- _id: fc2ed2f7-9c52-11eb-aca3-c01059dda49c
call_identifier: H2020
grant_number: '101034413'
name: 'IST-BRIDGE: International postdoctoral program'
publication: Physical Review E
publication_identifier:
eissn:
- 2470-0053
issn:
- 2470-0045
publication_status: published
publisher: American Physical Society
quality_controlled: '1'
scopus_import: '1'
status: public
title: Field theory of enzyme-substrate systems with restricted long-range interactions
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: 317138e5-6ab7-11ef-aa6d-ffef3953e345
volume: 110
year: '2024'
...
---
OA_type: closed access
_id: '17896'
abstract:
- lang: eng
text: Broadband photodetectors that can decipher the wavelength (λ) and intensity
(I) of an unknown incident light are urgently demanded. Photothermoelectric (PTE)
detectors can achieve ultrabroadband photodetection surpassing the bandgap limitation;
however, their practical application is severely hampered by the lack of deciphering
strategy. In this work, we report a variable elimination method to decipher λ
and I of the incident lights based on an integrated Ag2Se film-based PTE detector.
Nanostructured Ag2Se films with controlled thickness are synthesized using an
ion sputtering of Ag and a room-temperature selenization method and then assembled
into a detector. Under identical illumination, Ag2Se films of different thicknesses
produce varying output photothermal voltages, influenced by factors including
λ. By establishing a direct relationship between the photothermal voltage and
the absorption of Ag2Se films of varied thickness, we successfully eliminate variables
independent of λ, thus determining λ. Subsequently, I is determined by the calibrated
responsivity relationship using obtained λ. Our PTE detector achieves a broadband
spectrum from 400 to 950 nm and high accuracy, with deviations as low as ∼2.63
and ∼0.53% for deciphered λ and I, respectively. This method allows for self-powered
broadband decipherable photodetection without a complex device architecture or
computational assistance, which could boost the research enthusiasm and promote
the commercialization of PTE broadband detectors.
acknowledgement: The authors appreciate the Analytical & Testing Center of Sichuan
University and Ceshigo Research Service for their supports on material characterization.
This study is financial supported by the fund of the State Key Laboratory of Solidification
Processing in Northwestern Polytechnical University (NWPU, Grant SKLSP202315), the
State Key Laboratory for Mechanical Behavior of Materials (Grant 20232509), and
the International Scientific and Technological Innovation Cooperation of Sichuan
Province (2024YFHZ0309).
article_processing_charge: No
article_type: original
author:
- first_name: Jiamin
full_name: Zhou, Jiamin
last_name: Zhou
- first_name: Shengduo
full_name: Xu, Shengduo
id: 12ab8624-4c8a-11ec-9e11-e1ac2438f22f
last_name: Xu
- first_name: Yi
full_name: Shuai, Yi
last_name: Shuai
- first_name: Qiang
full_name: Sun, Qiang
last_name: Sun
- first_name: Huangshui
full_name: Ma, Huangshui
last_name: Ma
- first_name: Chao
full_name: Wang, Chao
last_name: Wang
- first_name: Haijuan
full_name: Wu, Haijuan
last_name: Wu
- first_name: Shanshan
full_name: Tan, Shanshan
last_name: Tan
- first_name: Zegao
full_name: Wang, Zegao
last_name: Wang
- first_name: Lei
full_name: Yang, Lei
last_name: Yang
citation:
ama: Zhou J, Xu S, Shuai Y, et al. Decipher the wavelength and intensity using photothermoelectric
detectors. ACS Applied Materials and Interfaces. 2024;16(36):47923-47930.
doi:10.1021/acsami.4c10489
apa: Zhou, J., Xu, S., Shuai, Y., Sun, Q., Ma, H., Wang, C., … Yang, L. (2024).
Decipher the wavelength and intensity using photothermoelectric detectors. ACS
Applied Materials and Interfaces. American Chemical Society. https://doi.org/10.1021/acsami.4c10489
chicago: Zhou, Jiamin, Shengduo Xu, Yi Shuai, Qiang Sun, Huangshui Ma, Chao Wang,
Haijuan Wu, Shanshan Tan, Zegao Wang, and Lei Yang. “Decipher the Wavelength and
Intensity Using Photothermoelectric Detectors.” ACS Applied Materials and Interfaces.
American Chemical Society, 2024. https://doi.org/10.1021/acsami.4c10489.
ieee: J. Zhou et al., “Decipher the wavelength and intensity using photothermoelectric
detectors,” ACS Applied Materials and Interfaces, vol. 16, no. 36. American
Chemical Society, pp. 47923–47930, 2024.
ista: Zhou J, Xu S, Shuai Y, Sun Q, Ma H, Wang C, Wu H, Tan S, Wang Z, Yang L. 2024.
Decipher the wavelength and intensity using photothermoelectric detectors. ACS
Applied Materials and Interfaces. 16(36), 47923–47930.
mla: Zhou, Jiamin, et al. “Decipher the Wavelength and Intensity Using Photothermoelectric
Detectors.” ACS Applied Materials and Interfaces, vol. 16, no. 36, American
Chemical Society, 2024, pp. 47923–30, doi:10.1021/acsami.4c10489.
short: J. Zhou, S. Xu, Y. Shuai, Q. Sun, H. Ma, C. Wang, H. Wu, S. Tan, Z. Wang,
L. Yang, ACS Applied Materials and Interfaces 16 (2024) 47923–47930.
date_created: 2024-09-08T22:01:13Z
date_published: 2024-09-11T00:00:00Z
date_updated: 2025-09-08T09:15:07Z
day: '11'
department:
- _id: MaIb
doi: 10.1021/acsami.4c10489
external_id:
isi:
- '001300770000001'
pmid:
- '39194354'
intvolume: ' 16'
isi: 1
issue: '36'
language:
- iso: eng
month: '09'
oa_version: None
page: 47923-47930
pmid: 1
publication: ACS Applied Materials and Interfaces
publication_identifier:
eissn:
- 1944-8252
issn:
- 1944-8244
publication_status: published
publisher: American Chemical Society
quality_controlled: '1'
scopus_import: '1'
status: public
title: Decipher the wavelength and intensity using photothermoelectric detectors
type: journal_article
user_id: 317138e5-6ab7-11ef-aa6d-ffef3953e345
volume: 16
year: '2024'
...
---
OA_type: closed access
_id: '17897'
abstract:
- lang: eng
text: High-entropy materials (HEMs) offer a quasi-continuous spectrum of active
sites and have generated great expectations in fields such as electrocatalysis
and energy storage. Despite their potential, the complex composition and associated
surface phenomena of HEMs pose challenges to their rational design and development.
In this context, we have synthesized FeCoNiPdWP high entropy phosphide (HEP) nanoparticles
using a low-temperature colloidal method, and explored their application as bifunctional
electrocatalysts for the oxygen evolution and reduction reactions (OER/ORR). Our
analysis provides a detailed understanding of the individual roles and transformations
of each element during OER/ORR operation. Notably, the HEPs exhibit an exceptionally
low OER overpotential of 227 mV at 10 mA cm−2, attributed to the reconstructed
HEP surface into a FeCoNiPdW high entropy oxyhydroxide with high oxidation states
of Fe, Co, and Ni serving as the active sites. Additionally, Pd and W play crucial
roles in modulating the electronic structure to optimize the adsorption energy
of oxygen intermediates. For the ORR, Pd emerges as the most active component.
In the reconstructed catalyst, the strong d–d orbital coupling of especially Pd,
Co, and W fine-tunes ORR electron transfer pathways, delivering an ORR half-wave
potential of 0.81 V with a pure four-electron reduction mechanism. The practicality
of these HEPs catalysts is showcased through the assembly of aqueous zinc–air
batteries. These batteries demonstrate a superior specific capacity of 886 mA
h gZn−1 and maintain excellent stability over more than 700 hours of continuous
operation. Overall, this study not only elucidates the role of each element in
HEMs but also establishes a foundational framework for the design and development
of next-generation bifunctional oxygen catalysts, broadening the potential applications
of these complex materials in advanced energy systems.
acknowledgement: This work was financially supported by the SyDEC at project from
the Spanish MCIN/AEI/FEDER (PID2022-136883OB-C22) and Generalitat de Catalunya 2021SGR01581.
J. N. H. and P. W. M. acknowledge support from the German Federal Ministry of Education
and Research in the framework of the project “Catlab” (03EW0015A/B). L. Yang thanks
the China Scholarship Council (CSC) for the scholarship support (202008130132).
This work was supported by the European Union Horizon 2020 research and innovation
program (No. 857470) and the European Regional Development Fund via the Foundation
for Polish Science International Research Agenda PLUS program (No. MAB PLUS/2018/8).
The publication was created within the framework of the project of the Minister
of Science and Higher Education, Poland “Support for the activities of Centres of
Excellence established in Poland under Horizon 2020” under contract no. MEiN/2023/DIR/3795.
H. D. and S. M. thank the German Federal Ministry of Education and Research (BMBF)
for supporting the Live-XAS project (05K22KE1) and the Deutsche Forschungsgemeinschaft
(DFG, German Research Foundation) for support under Germany's Excellence Strategy
– EXC 2008/1 – 390540038 – UniSysCat. The authors thank the Helmholtz-Zentrum Berlin
(HZB) for beamtime allocation at the KMC-3 synchrotron beamline of the BESSY synchrotron
in Berlin-Adlershof and Dr Ivo Zizak as well as Dr Michael Haumann for technical
support.
article_processing_charge: No
article_type: original
author:
- first_name: Ren
full_name: He, Ren
last_name: He
- first_name: Shiqi
full_name: Wang, Shiqi
last_name: Wang
- first_name: Linlin
full_name: Yang, Linlin
last_name: Yang
- first_name: Sharona
full_name: Horta, Sharona
id: 03a7e858-01b1-11ec-8b71-99ae6c4a05bc
last_name: Horta
- first_name: Yang
full_name: Ding, Yang
last_name: Ding
- first_name: Chong
full_name: Di, Chong
last_name: Di
- first_name: Xuesong
full_name: Zhang, Xuesong
last_name: Zhang
- first_name: Ying
full_name: Xu, Ying
last_name: Xu
- first_name: Maria
full_name: Ibáñez, Maria
id: 43C61214-F248-11E8-B48F-1D18A9856A87
last_name: Ibáñez
orcid: 0000-0001-5013-2843
- first_name: Yingtang
full_name: Zhou, Yingtang
last_name: Zhou
- first_name: Stefan
full_name: Mebs, Stefan
last_name: Mebs
- first_name: Holger
full_name: Dau, Holger
last_name: Dau
- first_name: Jan Niklas
full_name: Hausmann, Jan Niklas
last_name: Hausmann
- first_name: Wenyi
full_name: Huo, Wenyi
last_name: Huo
- first_name: Prashanth W.
full_name: Menezes, Prashanth W.
last_name: Menezes
- first_name: Andreu
full_name: Cabot, Andreu
last_name: Cabot
citation:
ama: He R, Wang S, Yang L, et al. Active site switching on high entropy phosphides
as bifunctional oxygen electrocatalysts for rechargeable/robust Zn-air battery.
Energy and Environmental Science. 2024;17(19):7193-7208. doi:10.1039/d4ee01912a
apa: He, R., Wang, S., Yang, L., Horta, S., Ding, Y., Di, C., … Cabot, A. (2024).
Active site switching on high entropy phosphides as bifunctional oxygen electrocatalysts
for rechargeable/robust Zn-air battery. Energy and Environmental Science.
Royal Society of Chemistry. https://doi.org/10.1039/d4ee01912a
chicago: He, Ren, Shiqi Wang, Linlin Yang, Sharona Horta, Yang Ding, Chong Di, Xuesong
Zhang, et al. “Active Site Switching on High Entropy Phosphides as Bifunctional
Oxygen Electrocatalysts for Rechargeable/Robust Zn-Air Battery.” Energy and
Environmental Science. Royal Society of Chemistry, 2024. https://doi.org/10.1039/d4ee01912a.
ieee: R. He et al., “Active site switching on high entropy phosphides as
bifunctional oxygen electrocatalysts for rechargeable/robust Zn-air battery,”
Energy and Environmental Science, vol. 17, no. 19. Royal Society of Chemistry,
pp. 7193–7208, 2024.
ista: He R, Wang S, Yang L, Horta S, Ding Y, Di C, Zhang X, Xu Y, Ibáñez M, Zhou
Y, Mebs S, Dau H, Hausmann JN, Huo W, Menezes PW, Cabot A. 2024. Active site switching
on high entropy phosphides as bifunctional oxygen electrocatalysts for rechargeable/robust
Zn-air battery. Energy and Environmental Science. 17(19), 7193–7208.
mla: He, Ren, et al. “Active Site Switching on High Entropy Phosphides as Bifunctional
Oxygen Electrocatalysts for Rechargeable/Robust Zn-Air Battery.” Energy and
Environmental Science, vol. 17, no. 19, Royal Society of Chemistry, 2024,
pp. 7193–208, doi:10.1039/d4ee01912a.
short: R. He, S. Wang, L. Yang, S. Horta, Y. Ding, C. Di, X. Zhang, Y. Xu, M. Ibáñez,
Y. Zhou, S. Mebs, H. Dau, J.N. Hausmann, W. Huo, P.W. Menezes, A. Cabot, Energy
and Environmental Science 17 (2024) 7193–7208.
date_created: 2024-09-08T22:01:13Z
date_published: 2024-08-22T00:00:00Z
date_updated: 2025-09-08T09:15:49Z
day: '22'
department:
- _id: MaIb
doi: 10.1039/d4ee01912a
external_id:
isi:
- '001298924700001'
intvolume: ' 17'
isi: 1
issue: '19'
language:
- iso: eng
month: '08'
oa_version: None
page: 7193-7208
publication: Energy and Environmental Science
publication_identifier:
eissn:
- 1754-5706
issn:
- 1754-5692
publication_status: published
publisher: Royal Society of Chemistry
quality_controlled: '1'
scopus_import: '1'
status: public
title: Active site switching on high entropy phosphides as bifunctional oxygen electrocatalysts
for rechargeable/robust Zn-air battery
type: journal_article
user_id: 317138e5-6ab7-11ef-aa6d-ffef3953e345
volume: 17
year: '2024'
...
---
_id: '18052'
abstract:
- lang: eng
text: Sodium dodecyl sulfate-digested freeze-fracture replica labeling (SDS-FRL)
is an electron microscope (EM) sample preparation technique which allows for high-resolution
visualization of membrane proteins with high sensitivity. However, image acquisition
of specific replica profiles such as synapses in a large field of EM view needs
a valid experience and a long time for manual searching. Here, we describe how
to utilize deep learning for automatizing image acquisition of specific profiles
of interest in replica samples. This protocol facilitates the labor-intensive
collection of EM images, in particular for rare profiles. We provide instructions
for using SerialEM image acquisition software in conjunction with object detection
by our newly developed deep learning software DarEM, to automatically acquire
tilt series of all synapses in a selected region. We then show how to perform
a mostly automated analysis of gold particle labeling in the acquired images by
utilizing Darea software.
acknowledged_ssus:
- _id: EM-Fac
acknowledgement: This research was supported by the European Research Council Advanced
Grant 694539 to RS and by the Scientific Service Units of IST Austria through resources
provided by the Electron Microscopy Facility.
alternative_title:
- Neuromethods
article_processing_charge: No
author:
- first_name: David
full_name: Kleindienst, David
id: 42E121A4-F248-11E8-B48F-1D18A9856A87
last_name: Kleindienst
- first_name: Tommaso
full_name: Costanzo, Tommaso
id: D93824F4-D9BA-11E9-BB12-F207E6697425
last_name: Costanzo
orcid: 0000-0001-9732-3815
- first_name: Ryuichi
full_name: Shigemoto, Ryuichi
id: 499F3ABC-F248-11E8-B48F-1D18A9856A87
last_name: Shigemoto
orcid: 0000-0001-8761-9444
citation:
ama: 'Kleindienst D, Costanzo T, Shigemoto R. Automated Imaging and Analysis of
Synapses in Freeze-Fracture Replica Samples with Deep Learning. In: Lübke JHR,
Rollenhagen A, eds. New Aspects in Analyzing the Synaptic Organization of the
Brain. 1st ed. New York: Springer Nature; 2024:123-137. doi:10.1007/978-1-0716-4019-7_8'
apa: 'Kleindienst, D., Costanzo, T., & Shigemoto, R. (2024). Automated Imaging
and Analysis of Synapses in Freeze-Fracture Replica Samples with Deep Learning.
In J. H. R. Lübke & A. Rollenhagen (Eds.), New Aspects in Analyzing the
Synaptic Organization of the Brain (1st ed., pp. 123–137). New York: Springer
Nature. https://doi.org/10.1007/978-1-0716-4019-7_8'
chicago: 'Kleindienst, David, Tommaso Costanzo, and Ryuichi Shigemoto. “Automated
Imaging and Analysis of Synapses in Freeze-Fracture Replica Samples with Deep
Learning.” In New Aspects in Analyzing the Synaptic Organization of the Brain,
edited by Joachim H.R. Lübke and Astrid Rollenhagen, 1st ed., 123–37. New York:
Springer Nature, 2024. https://doi.org/10.1007/978-1-0716-4019-7_8.'
ieee: 'D. Kleindienst, T. Costanzo, and R. Shigemoto, “Automated Imaging and Analysis
of Synapses in Freeze-Fracture Replica Samples with Deep Learning,” in New
Aspects in Analyzing the Synaptic Organization of the Brain, 1st ed., J. H.
R. Lübke and A. Rollenhagen, Eds. New York: Springer Nature, 2024, pp. 123–137.'
ista: 'Kleindienst D, Costanzo T, Shigemoto R. 2024.Automated Imaging and Analysis
of Synapses in Freeze-Fracture Replica Samples with Deep Learning. In: New Aspects
in Analyzing the Synaptic Organization of the Brain. Neuromethods, , 123–137.'
mla: Kleindienst, David, et al. “Automated Imaging and Analysis of Synapses in Freeze-Fracture
Replica Samples with Deep Learning.” New Aspects in Analyzing the Synaptic
Organization of the Brain, edited by Joachim H.R. Lübke and Astrid Rollenhagen,
1st ed., Springer Nature, 2024, pp. 123–37, doi:10.1007/978-1-0716-4019-7_8.
short: D. Kleindienst, T. Costanzo, R. Shigemoto, in:, J.H.R. Lübke, A. Rollenhagen
(Eds.), New Aspects in Analyzing the Synaptic Organization of the Brain, 1st ed.,
Springer Nature, New York, 2024, pp. 123–137.
corr_author: '1'
date_created: 2024-09-10T12:32:38Z
date_published: 2024-08-27T00:00:00Z
date_updated: 2025-04-14T07:27:15Z
day: '27'
department:
- _id: EM-Fac
- _id: RySh
doi: 10.1007/978-1-0716-4019-7_8
ec_funded: 1
edition: '1'
editor:
- first_name: 'Joachim H.R. '
full_name: 'Lübke, Joachim H.R. '
last_name: Lübke
- first_name: Astrid
full_name: Rollenhagen, Astrid
last_name: Rollenhagen
language:
- iso: eng
month: '08'
oa_version: None
page: 123-137
place: New York
project:
- _id: 25CA28EA-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '694539'
name: 'In situ analysis of single channel subunit composition in neurons: physiological
implication in synaptic plasticity and behaviour'
publication: New Aspects in Analyzing the Synaptic Organization of the Brain
publication_identifier:
eisbn:
- '9781071640197'
eissn:
- 1940-6045
isbn:
- '9781071640180'
issn:
- 0893-2336
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
scopus_import: '1'
status: public
title: Automated Imaging and Analysis of Synapses in Freeze-Fracture Replica Samples
with Deep Learning
type: book_chapter
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
year: '2024'
...
---
_id: '18058'
abstract:
- lang: eng
text: DNA cloning is a core technique in biomedical and biotechnological research
and is used to assemble and modify DNA fragments at will. While DNA cloning has
traditionally relied on restriction enzymes, recent homology-based methods offer
improved protocols together with seamless and directional assembly of desired
products, overcoming the main disadvantages of restriction enzyme DNA cloning.
This chapter provides a historical perspective on DNA cloning, presents a detailed
discussion on state-of-the-art in vitro and in vivo homology-based methodologies,
covering the basics of how to perform all major plasmid modifications (sub-cloning,
site-directed mutagenesis, insertions, and deletions), and gives examples of how
to apply these techniques for complex DNA cloning projects.
article_processing_charge: No
author:
- first_name: Jake
full_name: Watson, Jake
id: 63836096-4690-11EA-BD4E-32803DDC885E
last_name: Watson
orcid: 0000-0002-8698-3823
- first_name: Sandra
full_name: Arroyo-Urea, Sandra
last_name: Arroyo-Urea
- first_name: Javier
full_name: García-Nafría, Javier
last_name: García-Nafría
citation:
ama: 'Watson J, Arroyo-Urea S, García-Nafría J. DNA Cloning. In: Liu D, ed. Handbook
of Molecular Biotechnology. 1st ed. Boca Raton: CRC Press; 2024:66-72. doi:10.1201/9781003055211-8'
apa: 'Watson, J., Arroyo-Urea, S., & García-Nafría, J. (2024). DNA Cloning.
In D. Liu (Ed.), Handbook of Molecular Biotechnology (1st ed., pp. 66–72).
Boca Raton: CRC Press. https://doi.org/10.1201/9781003055211-8'
chicago: 'Watson, Jake, Sandra Arroyo-Urea, and Javier García-Nafría. “DNA Cloning.”
In Handbook of Molecular Biotechnology, edited by Dongyou Liu, 1st ed.,
66–72. Boca Raton: CRC Press, 2024. https://doi.org/10.1201/9781003055211-8.'
ieee: 'J. Watson, S. Arroyo-Urea, and J. García-Nafría, “DNA Cloning,” in Handbook
of Molecular Biotechnology, 1st ed., D. Liu, Ed. Boca Raton: CRC Press, 2024,
pp. 66–72.'
ista: 'Watson J, Arroyo-Urea S, García-Nafría J. 2024.DNA Cloning. In: Handbook
of Molecular Biotechnology. , 66–72.'
mla: Watson, Jake, et al. “DNA Cloning.” Handbook of Molecular Biotechnology,
edited by Dongyou Liu, 1st ed., CRC Press, 2024, pp. 66–72, doi:10.1201/9781003055211-8.
short: J. Watson, S. Arroyo-Urea, J. García-Nafría, in:, D. Liu (Ed.), Handbook
of Molecular Biotechnology, 1st ed., CRC Press, Boca Raton, 2024, pp. 66–72.
date_created: 2024-09-11T10:40:36Z
date_published: 2024-09-05T00:00:00Z
date_updated: 2024-09-11T11:16:58Z
day: '05'
department:
- _id: PeJo
doi: 10.1201/9781003055211-8
edition: '1'
editor:
- first_name: Dongyou
full_name: Liu, Dongyou
last_name: Liu
language:
- iso: eng
month: '09'
oa_version: None
page: 66-72
place: Boca Raton
publication: Handbook of Molecular Biotechnology
publication_identifier:
eisbn:
- '9781003055211'
publication_status: published
publisher: CRC Press
quality_controlled: '1'
scopus_import: '1'
status: public
title: DNA Cloning
type: book_chapter
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
year: '2024'
...
---
_id: '18063'
abstract:
- lang: eng
text: The developmental plasticity of the root system plays an essential role in
the adaptation of plants to the environment. Among many other signals, auxin and
its directional, intercellular transport are critical in regulating root growth
and development. In particular, the PIN-FORMED2 (PIN2) auxin exporter acts as
a key regulator of root gravitropic growth. Multiple regulators have been reported
to be involved in PIN2-mediated root growth; however, our information remains
incomplete. Here, we identified ROWY Bro1-domain proteins as important regulators
of PIN2 sorting control. Genetic analysis revealed that Arabidopsis rowy1 single
mutants and higher-order rowy1 rowy2 rowy3 triple mutants presented a wavy root
growth phenotype. Cell biological experiments revealed that ROWY1 and PIN2 colocalized
to the apical side of the plasma membrane in the root epidermis and that ROWYs
are required for correct PM targeting of PIN2. In addition, ROWYs also affected
PIN3 protein abundance in the stele, suggesting the potential involvement of additional
PIN transporters as well as other proteins. A global transcriptome analysis revealed
that ROWY genes are involved in the Fe2+ availability perception pathway. This
work establishes ROWYs as important novel regulators of root gravitropic growth
by connecting micronutrient availability to the proper subcellular targeting of
PIN auxin transporters.
acknowledgement: We thank Drs. Erika Isono (University of Constance), Grégory Vert
(University of Toulouse), and Liwen Jiang (The Chinese University of Hong Kong)
for kindly sharing published Arabidopsis lines; Dr. Yuzhou Zhang (ISTA) for help
with molecular cloning, and Drs. Melinda Abas (BOKU), Eugenia Russinova (Ghent University),
and Zhaojun Ding (Shandong University) for valuable discussions. This work was supported
by grants to S.T. from the National Natural Science Foundation of China (32321001),
the USTC Research Funds of the Double First-Class Initiative (YD9100002016), the
Research Funds from the Center for Advanced Interdisciplinary Science and Biomedicine
of IHM, the Division of Life Sciences and Medicine, the University of Science and
Technology of China (QYPY20220012), the Fundamental Research Funds for the Central
Universities (WK9100000021), and start-up funding from the University of Science
and Technology of China and the Chinese Academy of Sciences (GG9100007007, KY9100000026,
KY9100000051, and KJ2070000079). J.S. was supported by the National Natural Science
Foundation of China (31970181 and 32170342). J.F. was supported by Austrian Science
Fund (FWF; projects I6123 and P37051-B).
article_number: '1085'
article_processing_charge: Yes
article_type: original
author:
- first_name: Yakun
full_name: Peng, Yakun
last_name: Peng
- first_name: Kangkang
full_name: Ji, Kangkang
last_name: Ji
- first_name: Yanbo
full_name: Mao, Yanbo
last_name: Mao
- first_name: Yiqun
full_name: Wang, Yiqun
id: 82F537F2-B517-11E9-84D7-6433E6697425
last_name: Wang
- first_name: Barbara
full_name: Korbei, Barbara
last_name: Korbei
- first_name: Christian
full_name: Luschnig, Christian
last_name: Luschnig
- first_name: Jinbo
full_name: Shen, Jinbo
last_name: Shen
- first_name: Eva
full_name: Benková, Eva
id: 38F4F166-F248-11E8-B48F-1D18A9856A87
last_name: Benková
orcid: 0000-0002-8510-9739
- first_name: Jiří
full_name: Friml, Jiří
id: 4159519E-F248-11E8-B48F-1D18A9856A87
last_name: Friml
orcid: 0000-0002-8302-7596
- first_name: Shutang
full_name: Tan, Shutang
id: 2DE75584-F248-11E8-B48F-1D18A9856A87
last_name: Tan
orcid: 0000-0002-0471-8285
citation:
ama: Peng Y, Ji K, Mao Y, et al. Polarly localized Bro1 domain proteins regulate
PIN-FORMED abundance and root gravitropic growth in Arabidopsis. Communications
Biology. 2024;7. doi:10.1038/s42003-024-06747-9
apa: Peng, Y., Ji, K., Mao, Y., Wang, Y., Korbei, B., Luschnig, C., … Tan, S. (2024).
Polarly localized Bro1 domain proteins regulate PIN-FORMED abundance and root
gravitropic growth in Arabidopsis. Communications Biology. Springer Nature.
https://doi.org/10.1038/s42003-024-06747-9
chicago: Peng, Yakun, Kangkang Ji, Yanbo Mao, Yiqun Wang, Barbara Korbei, Christian
Luschnig, Jinbo Shen, Eva Benková, Jiří Friml, and Shutang Tan. “Polarly Localized
Bro1 Domain Proteins Regulate PIN-FORMED Abundance and Root Gravitropic Growth
in Arabidopsis.” Communications Biology. Springer Nature, 2024. https://doi.org/10.1038/s42003-024-06747-9.
ieee: Y. Peng et al., “Polarly localized Bro1 domain proteins regulate PIN-FORMED
abundance and root gravitropic growth in Arabidopsis,” Communications Biology,
vol. 7. Springer Nature, 2024.
ista: Peng Y, Ji K, Mao Y, Wang Y, Korbei B, Luschnig C, Shen J, Benková E, Friml
J, Tan S. 2024. Polarly localized Bro1 domain proteins regulate PIN-FORMED abundance
and root gravitropic growth in Arabidopsis. Communications Biology. 7, 1085.
mla: Peng, Yakun, et al. “Polarly Localized Bro1 Domain Proteins Regulate PIN-FORMED
Abundance and Root Gravitropic Growth in Arabidopsis.” Communications Biology,
vol. 7, 1085, Springer Nature, 2024, doi:10.1038/s42003-024-06747-9.
short: Y. Peng, K. Ji, Y. Mao, Y. Wang, B. Korbei, C. Luschnig, J. Shen, E. Benková,
J. Friml, S. Tan, Communications Biology 7 (2024).
date_created: 2024-09-15T22:01:38Z
date_published: 2024-09-04T00:00:00Z
date_updated: 2026-04-07T11:49:33Z
day: '04'
ddc:
- '570'
department:
- _id: EvBe
- _id: JiFr
doi: 10.1038/s42003-024-06747-9
external_id:
isi:
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pmid:
- '39232040'
file:
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checksum: 7d66af41c90e73d1b8a375eb652a9561
content_type: application/pdf
creator: dernst
date_created: 2024-09-17T09:44:29Z
date_updated: 2024-09-17T09:44:29Z
file_id: '18084'
file_name: 2024_CommBiology_Peng.pdf
file_size: 7718758
relation: main_file
success: 1
file_date_updated: 2024-09-17T09:44:29Z
has_accepted_license: '1'
intvolume: ' 7'
isi: 1
language:
- iso: eng
month: '09'
oa: 1
oa_version: Published Version
pmid: 1
project:
- _id: bd76d395-d553-11ed-ba76-f678c14f9033
grant_number: I06123
name: Peptide receptors for auxin canalization in Arabidopsis
- _id: 7bcece63-9f16-11ee-852c-ae94e099eeb6
grant_number: P37051
name: Guanylate cyclase activity of TIR1/AFBs auxin receptors
publication: Communications Biology
publication_identifier:
eissn:
- 2399-3642
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
related_material:
record:
- id: '20117'
relation: dissertation_contains
status: public
scopus_import: '1'
status: public
title: Polarly localized Bro1 domain proteins regulate PIN-FORMED abundance and root
gravitropic growth in Arabidopsis
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: 317138e5-6ab7-11ef-aa6d-ffef3953e345
volume: 7
year: '2024'
...
---
OA_place: publisher
OA_type: hybrid
_id: '18065'
abstract:
- lang: eng
text: We establish a close connection between acceleration and dynamical degree
for one-frequency quasi-periodic compact cocycles, by showing that two vectors
derived separately from each coincide. Based on this, we provide a dynamical classification
of one-frequency quasi-periodic SO(3, R)-cocycles.
acknowledgement: "X. Hou is partially supported by National Natural Science Foundation
of China (Grant \r\n12071083) and Funds for Distinguished Youths of Hubei Province
of China (\r\n2019CFA680). Y. Pan is supported by ERC Advanced Grant (#885707).
Q. Zhou is partially supported by National Key R&D Program of China (2020YFA0713300),
NSFC grant (\r\n12071232) and Nankai Zhide Foundation."
article_number: '109943'
article_processing_charge: Yes (via OA deal)
article_type: original
arxiv: 1
author:
- first_name: Xuanji
full_name: Hou, Xuanji
last_name: Hou
- first_name: Yi
full_name: Pan, Yi
id: 1e21c7f7-9070-11eb-847d-8b04c7169523
last_name: Pan
- first_name: Qi
full_name: Zhou, Qi
last_name: Zhou
citation:
ama: Hou X, Pan Y, Zhou Q. Dynamical classification of analytic one-frequency quasi-periodic
SO(3,R)-cocycles. Advances in Mathematics. 2024;457. doi:10.1016/j.aim.2024.109943
apa: Hou, X., Pan, Y., & Zhou, Q. (2024). Dynamical classification of analytic
one-frequency quasi-periodic SO(3,R)-cocycles. Advances in Mathematics.
Elsevier. https://doi.org/10.1016/j.aim.2024.109943
chicago: Hou, Xuanji, Yi Pan, and Qi Zhou. “Dynamical Classification of Analytic
One-Frequency Quasi-Periodic SO(3,R)-Cocycles.” Advances in Mathematics.
Elsevier, 2024. https://doi.org/10.1016/j.aim.2024.109943.
ieee: X. Hou, Y. Pan, and Q. Zhou, “Dynamical classification of analytic one-frequency
quasi-periodic SO(3,R)-cocycles,” Advances in Mathematics, vol. 457. Elsevier,
2024.
ista: Hou X, Pan Y, Zhou Q. 2024. Dynamical classification of analytic one-frequency
quasi-periodic SO(3,R)-cocycles. Advances in Mathematics. 457, 109943.
mla: Hou, Xuanji, et al. “Dynamical Classification of Analytic One-Frequency Quasi-Periodic
SO(3,R)-Cocycles.” Advances in Mathematics, vol. 457, 109943, Elsevier,
2024, doi:10.1016/j.aim.2024.109943.
short: X. Hou, Y. Pan, Q. Zhou, Advances in Mathematics 457 (2024).
corr_author: '1'
date_created: 2024-09-15T22:01:39Z
date_published: 2024-11-01T00:00:00Z
date_updated: 2025-09-08T09:44:19Z
day: '01'
ddc:
- '510'
department:
- _id: VaKa
doi: 10.1016/j.aim.2024.109943
ec_funded: 1
external_id:
arxiv:
- '2311.17537'
isi:
- '001315306500001'
file:
- access_level: open_access
checksum: 1c80b844a91d93cf4799f4a65873b18d
content_type: application/pdf
creator: dernst
date_created: 2025-01-13T08:29:27Z
date_updated: 2025-01-13T08:29:27Z
file_id: '18826'
file_name: 2024_AdvancesMath_Hou.pdf
file_size: 713659
relation: main_file
success: 1
file_date_updated: 2025-01-13T08:29:27Z
has_accepted_license: '1'
intvolume: ' 457'
isi: 1
language:
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month: '11'
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:
eissn:
- 1090-2082
issn:
- 0001-8708
publication_status: published
publisher: Elsevier
quality_controlled: '1'
scopus_import: '1'
status: public
title: Dynamical classification of analytic one-frequency quasi-periodic SO(3,R)-cocycles
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: 317138e5-6ab7-11ef-aa6d-ffef3953e345
volume: 457
year: '2024'
...
---
_id: '18066'
abstract:
- lang: eng
text: 'Graph games lie at the algorithmic core of many automated design problems
in computer science. These are games usually played between two players on a given
graph, where the players keep moving a token along the edges according to pre-determined
rules (turn-based, concurrent, etc.), and the winner is decided based on the infinite
path (aka play) traversed by the token from a given initial position. In bidding
games, the players initially get some monetary budgets which they need to use
to bid for the privilege of moving the token at each step. Each round of bidding
affects the players'' available budgets, which is the only form of update that
the budgets experience. We introduce bidding games with charging where the players
can additionally improve their budgets during the game by collecting vertex-dependent
monetary rewards, aka the "charges." Unlike traditional bidding games (where all
charges are zero), bidding games with charging allow non-trivial recurrent behaviors.
For example, a reachability objective may require multiple detours to vertices
with high charges to earn additional budget. We show that, nonetheless, the central
property of traditional bidding games generalizes to bidding games with charging:
For each vertex there exists a threshold ratio, which is the necessary and sufficient
fraction of the total budget for winning the game from that vertex. While the
thresholds of traditional bidding games correspond to unique fixed points of linear
systems of equations, in games with charging, these fixed points are no longer
unique. This significantly complicates the proof of existence and the algorithmic
computation of thresholds for infinite-duration objectives. We also provide the
lower complexity bounds for computing thresholds for Rabin and Streett objectives,
which are the first known lower bounds in any form of bidding games (with or without
charging), and we solve the following repair problem for safety and reachability
games that have unsatisfiable objectives: Can we distribute a given amount of
charge to the players in a way such that the objective can be satisfied?'
acknowledgement: This work was supported in part by the ERC projects ERC-2020-AdG
101020093 and CoG 863818 (ForM-SMArt) and by ISF grant no. 1679/21.
alternative_title:
- LIPIcs
article_number: '8'
article_processing_charge: Yes
arxiv: 1
author:
- first_name: Guy
full_name: Avni, Guy
id: 463C8BC2-F248-11E8-B48F-1D18A9856A87
last_name: Avni
orcid: 0000-0001-5588-8287
- first_name: Ehsan Kafshdar
full_name: Goharshady, Ehsan Kafshdar
last_name: Goharshady
- first_name: Thomas A
full_name: Henzinger, Thomas A
id: 40876CD8-F248-11E8-B48F-1D18A9856A87
last_name: Henzinger
orcid: 0000-0002-2985-7724
- first_name: Kaushik
full_name: Mallik, Kaushik
id: 0834ff3c-6d72-11ec-94e0-b5b0a4fb8598
last_name: Mallik
orcid: 0000-0001-9864-7475
citation:
ama: 'Avni G, Goharshady EK, Henzinger TA, Mallik K. Bidding games with charging.
In: 35th International Conference on Concurrency Theory. Vol 311. Schloss
Dagstuhl - Leibniz-Zentrum für Informatik; 2024. doi:10.4230/LIPIcs.CONCUR.2024.8'
apa: 'Avni, G., Goharshady, E. K., Henzinger, T. A., & Mallik, K. (2024). Bidding
games with charging. In 35th International Conference on Concurrency Theory
(Vol. 311). Calgary, Canada: Schloss Dagstuhl - Leibniz-Zentrum für Informatik.
https://doi.org/10.4230/LIPIcs.CONCUR.2024.8'
chicago: Avni, Guy, Ehsan Kafshdar Goharshady, Thomas A Henzinger, and Kaushik Mallik.
“Bidding Games with Charging.” In 35th International Conference on Concurrency
Theory, Vol. 311. Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2024.
https://doi.org/10.4230/LIPIcs.CONCUR.2024.8.
ieee: G. Avni, E. K. Goharshady, T. A. Henzinger, and K. Mallik, “Bidding games
with charging,” in 35th International Conference on Concurrency Theory,
Calgary, Canada, 2024, vol. 311.
ista: 'Avni G, Goharshady EK, Henzinger TA, Mallik K. 2024. Bidding games with charging.
35th International Conference on Concurrency Theory. CONCUR: Conference on Concurrency
Theory, LIPIcs, vol. 311, 8.'
mla: Avni, Guy, et al. “Bidding Games with Charging.” 35th International Conference
on Concurrency Theory, vol. 311, 8, Schloss Dagstuhl - Leibniz-Zentrum für
Informatik, 2024, doi:10.4230/LIPIcs.CONCUR.2024.8.
short: G. Avni, E.K. Goharshady, T.A. Henzinger, K. Mallik, in:, 35th International
Conference on Concurrency Theory, Schloss Dagstuhl - Leibniz-Zentrum für Informatik,
2024.
conference:
end_date: 2024-09-13
location: Calgary, Canada
name: 'CONCUR: Conference on Concurrency Theory'
start_date: 2024-09-09
corr_author: '1'
date_created: 2024-09-15T22:01:39Z
date_published: 2024-09-01T00:00:00Z
date_updated: 2025-12-02T13:46:11Z
day: '01'
ddc:
- '000'
department:
- _id: ToHe
doi: 10.4230/LIPIcs.CONCUR.2024.8
ec_funded: 1
external_id:
arxiv:
- '2407.06288'
isi:
- '001556847400008'
file:
- access_level: open_access
checksum: cb6f2254b84922cd7bf224f550b73f4a
content_type: application/pdf
creator: dernst
date_created: 2024-09-17T09:35:03Z
date_updated: 2024-09-17T09:35:03Z
file_id: '18083'
file_name: 2024_LIPICS_Avni.pdf
file_size: 854430
relation: main_file
success: 1
file_date_updated: 2024-09-17T09:35:03Z
has_accepted_license: '1'
intvolume: ' 311'
isi: 1
language:
- iso: eng
month: '09'
oa: 1
oa_version: Published Version
project:
- _id: 62781420-2b32-11ec-9570-8d9b63373d4d
call_identifier: H2020
grant_number: '101020093'
name: Vigilant Algorithmic Monitoring of Software
- _id: 0599E47C-7A3F-11EA-A408-12923DDC885E
call_identifier: H2020
grant_number: '863818'
name: 'Formal Methods for Stochastic Models: Algorithms and Applications'
publication: 35th International Conference on Concurrency Theory
publication_identifier:
isbn:
- '9783959773393'
issn:
- 1868-8969
publication_status: published
publisher: Schloss Dagstuhl - Leibniz-Zentrum für Informatik
quality_controlled: '1'
scopus_import: '1'
status: public
title: Bidding games with charging
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: conference
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 311
year: '2024'
...
---
_id: '18067'
abstract:
- lang: eng
text: "An automaton \U0001D49C is history-deterministic if its nondeterminism can
be resolved on the fly, only using the prefix of the word read so far. This mild
form of nondeterminism has attracted particular attention for its applications
in synthesis problems. An automaton \U0001D49C is guidable with respect to a class
C of automata if it can fairly simulate every automaton in C, whose language is
contained in that of \U0001D49C. In other words, guidable automata are those for
which inclusion and simulation coincide, making them particularly interesting
for model-checking. We study the connection between these two notions, and specifically
the question of when they coincide. For classes of automata on which they do,
deciding guidability, an otherwise challenging decision problem, reduces to deciding
history-determinism, a problem that is starting to be well-understood for many
classes. We provide a selection of sufficient criteria for a class of automata
to guarantee the coincidence of the notions, and use them to show that the notions
coincide for the most common automata classes, among which are ω-regular automata
and many infinite-state automata with safety and reachability acceptance conditions,
including vector addition systems with states, one-counter nets, pushdown-, Parikh-,
and timed-automata. We also demonstrate that history-determinism and guidability
do not always coincide, for example, for the classes of timed automata with a
fixed number of clocks."
acknowledgement: "Udi Boker: Israel Science Foundation grant 2410/22\r\nThomas A.
Henzinger: ERC-2020-AdG 101020093 (VAMOS)\r\nKaroliina Lehtinen: ANR QUASY 23-CE48-0008-01\r\nAditya
Prakash: Chancellors’ International Scholarship from the University of Warwick and
Centre for Discrete Mathematics and Its Applications (DIMAP)"
alternative_title:
- LIPIcs
article_number: '12'
article_processing_charge: No
arxiv: 1
author:
- first_name: Udi
full_name: Boker, Udi
id: 31E297B6-F248-11E8-B48F-1D18A9856A87
last_name: Boker
- first_name: Thomas A
full_name: Henzinger, Thomas A
id: 40876CD8-F248-11E8-B48F-1D18A9856A87
last_name: Henzinger
orcid: 0000-0002-2985-7724
- first_name: Karoliina
full_name: Lehtinen, Karoliina
last_name: Lehtinen
- first_name: Aditya
full_name: Prakash, Aditya
last_name: Prakash
citation:
ama: 'Boker U, Henzinger TA, Lehtinen K, Prakash A. History-determinism vs fair
simulation. In: 35th International Conference on Concurrency Theory. Vol
311. Schloss Dagstuhl - Leibniz-Zentrum für Informatik; 2024. doi:10.4230/LIPIcs.CONCUR.2024.12'
apa: 'Boker, U., Henzinger, T. A., Lehtinen, K., & Prakash, A. (2024). History-determinism
vs fair simulation. In 35th International Conference on Concurrency Theory
(Vol. 311). Calgary, Canada: Schloss Dagstuhl - Leibniz-Zentrum für Informatik.
https://doi.org/10.4230/LIPIcs.CONCUR.2024.12'
chicago: Boker, Udi, Thomas A Henzinger, Karoliina Lehtinen, and Aditya Prakash.
“History-Determinism vs Fair Simulation.” In 35th International Conference
on Concurrency Theory, Vol. 311. Schloss Dagstuhl - Leibniz-Zentrum für Informatik,
2024. https://doi.org/10.4230/LIPIcs.CONCUR.2024.12.
ieee: U. Boker, T. A. Henzinger, K. Lehtinen, and A. Prakash, “History-determinism
vs fair simulation,” in 35th International Conference on Concurrency Theory,
Calgary, Canada, 2024, vol. 311.
ista: 'Boker U, Henzinger TA, Lehtinen K, Prakash A. 2024. History-determinism vs
fair simulation. 35th International Conference on Concurrency Theory. CONCUR:
Conference on Concurrency Theory, LIPIcs, vol. 311, 12.'
mla: Boker, Udi, et al. “History-Determinism vs Fair Simulation.” 35th International
Conference on Concurrency Theory, vol. 311, 12, Schloss Dagstuhl - Leibniz-Zentrum
für Informatik, 2024, doi:10.4230/LIPIcs.CONCUR.2024.12.
short: U. Boker, T.A. Henzinger, K. Lehtinen, A. Prakash, in:, 35th International
Conference on Concurrency Theory, Schloss Dagstuhl - Leibniz-Zentrum für Informatik,
2024.
conference:
end_date: 2024-09-13
location: Calgary, Canada
name: 'CONCUR: Conference on Concurrency Theory'
start_date: 2024-09-09
corr_author: '1'
date_created: 2024-09-15T22:01:40Z
date_published: 2024-09-01T00:00:00Z
date_updated: 2025-12-02T13:44:54Z
day: '01'
ddc:
- '000'
department:
- _id: ToHe
doi: 10.4230/LIPIcs.CONCUR.2024.12
ec_funded: 1
external_id:
arxiv:
- '2407.08620'
isi:
- '001556847400012'
file:
- access_level: open_access
checksum: 66db11ef8e600a434079c278050c3f09
content_type: application/pdf
creator: dernst
date_created: 2024-09-17T07:31:18Z
date_updated: 2024-09-17T07:31:18Z
file_id: '18080'
file_name: 2024_LIPICS_Boker.pdf
file_size: 766902
relation: main_file
success: 1
file_date_updated: 2024-09-17T07:31:18Z
has_accepted_license: '1'
intvolume: ' 311'
isi: 1
language:
- iso: eng
month: '09'
oa: 1
oa_version: Published Version
project:
- _id: 62781420-2b32-11ec-9570-8d9b63373d4d
call_identifier: H2020
grant_number: '101020093'
name: Vigilant Algorithmic Monitoring of Software
publication: 35th International Conference on Concurrency Theory
publication_identifier:
isbn:
- '9783959773393'
issn:
- 1868-8969
publication_status: published
publisher: Schloss Dagstuhl - Leibniz-Zentrum für Informatik
quality_controlled: '1'
scopus_import: '1'
status: public
title: History-determinism vs fair simulation
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: conference
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 311
year: '2024'
...
---
OA_place: publisher
OA_type: gold
_id: '18068'
abstract:
- lang: eng
text: "We study the following refinement relation between nondeterministic state-transition
models: model ℬ strategically dominates model \U0001D49C iff every deterministic
refinement of \U0001D49C is language contained in some deterministic refinement
of ℬ. While language containment is trace inclusion, and the (fair) simulation
preorder coincides with tree inclusion, strategic dominance falls strictly between
the two and can be characterized as \"strategy inclusion\" between \U0001D49C
and ℬ: every strategy that resolves the nondeterminism of \U0001D49C is dominated
by a strategy that resolves the nondeterminism of ℬ. Strategic dominance can be
checked in 2-ExpTime by a decidable first-order Presburger logic with quantification
over words and strategies, called resolver logic. We give several other applications
of resolver logic, including checking the co-safety, co-liveness, and history-determinism
of boolean and quantitative automata, and checking the inclusion between hyperproperties
that are specified by nondeterministic boolean and quantitative automata."
acknowledgement: This work was supported in part by the ERC-2020-AdG 101020093. N.
Mazzocchi was affiliated with ISTA when this work was submitted for publication.
alternative_title:
- LIPIcs
article_number: '29'
article_processing_charge: Yes
arxiv: 1
author:
- first_name: Thomas A
full_name: Henzinger, Thomas A
id: 40876CD8-F248-11E8-B48F-1D18A9856A87
last_name: Henzinger
orcid: 0000-0002-2985-7724
- first_name: Nicolas Adrien
full_name: Mazzocchi, Nicolas Adrien
id: b26baa86-3308-11ec-87b0-8990f34baa85
last_name: Mazzocchi
- first_name: Naci E
full_name: Sarac, Naci E
id: 8C6B42F8-C8E6-11E9-A03A-F2DCE5697425
last_name: Sarac
citation:
ama: 'Henzinger TA, Mazzocchi NA, Sarac NE. Strategic dominance: A new preorder
for nondeterministic processes. In: 35th International Conference on Concurrency
Theory. Vol 311. Schloss Dagstuhl - Leibniz-Zentrum für Informatik; 2024.
doi:10.4230/LIPIcs.CONCUR.2024.29'
apa: 'Henzinger, T. A., Mazzocchi, N. A., & Sarac, N. E. (2024). Strategic dominance:
A new preorder for nondeterministic processes. In 35th International Conference
on Concurrency Theory (Vol. 311). Calgary, Canada: Schloss Dagstuhl - Leibniz-Zentrum
für Informatik. https://doi.org/10.4230/LIPIcs.CONCUR.2024.29'
chicago: 'Henzinger, Thomas A, Nicolas Adrien Mazzocchi, and Naci E Sarac. “Strategic
Dominance: A New Preorder for Nondeterministic Processes.” In 35th International
Conference on Concurrency Theory, Vol. 311. Schloss Dagstuhl - Leibniz-Zentrum
für Informatik, 2024. https://doi.org/10.4230/LIPIcs.CONCUR.2024.29.'
ieee: 'T. A. Henzinger, N. A. Mazzocchi, and N. E. Sarac, “Strategic dominance:
A new preorder for nondeterministic processes,” in 35th International Conference
on Concurrency Theory, Calgary, Canada, 2024, vol. 311.'
ista: 'Henzinger TA, Mazzocchi NA, Sarac NE. 2024. Strategic dominance: A new preorder
for nondeterministic processes. 35th International Conference on Concurrency Theory.
CONCUR: Conference on Concurrency Theory, LIPIcs, vol. 311, 29.'
mla: 'Henzinger, Thomas A., et al. “Strategic Dominance: A New Preorder for Nondeterministic
Processes.” 35th International Conference on Concurrency Theory, vol. 311,
29, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2024, doi:10.4230/LIPIcs.CONCUR.2024.29.'
short: T.A. Henzinger, N.A. Mazzocchi, N.E. Sarac, in:, 35th International Conference
on Concurrency Theory, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2024.
conference:
end_date: 2024-09-13
location: Calgary, Canada
name: 'CONCUR: Conference on Concurrency Theory'
start_date: 2024-09-09
corr_author: '1'
date_created: 2024-09-15T22:01:40Z
date_published: 2024-09-01T00:00:00Z
date_updated: 2025-12-02T13:45:38Z
day: '01'
ddc:
- '000'
department:
- _id: ToHe
- _id: GradSch
doi: 10.4230/LIPIcs.CONCUR.2024.29
ec_funded: 1
external_id:
arxiv:
- '2407.10473'
isi:
- '001556847400029'
file:
- access_level: open_access
checksum: 555bd343e1fb38adeab8fc465ff4fad8
content_type: application/pdf
creator: dernst
date_created: 2024-09-17T07:48:56Z
date_updated: 2024-09-17T07:48:56Z
file_id: '18081'
file_name: 2024_LIPICS_Henzinger.pdf
file_size: 964124
relation: main_file
success: 1
file_date_updated: 2024-09-17T07:48:56Z
has_accepted_license: '1'
intvolume: ' 311'
isi: 1
language:
- iso: eng
month: '09'
oa: 1
oa_version: Published Version
project:
- _id: 62781420-2b32-11ec-9570-8d9b63373d4d
call_identifier: H2020
grant_number: '101020093'
name: Vigilant Algorithmic Monitoring of Software
publication: 35th International Conference on Concurrency Theory
publication_identifier:
isbn:
- '9783959773393'
issn:
- 1868-8969
publication_status: published
publisher: Schloss Dagstuhl - Leibniz-Zentrum für Informatik
quality_controlled: '1'
scopus_import: '1'
status: public
title: 'Strategic dominance: A new preorder for nondeterministic processes'
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: conference
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 311
year: '2024'
...
---
DOAJ_listed: '1'
_id: '18069'
abstract:
- lang: eng
text: We present results from the JWST First Reionization Epoch Spectroscopically
Complete Observations survey on the star-forming sequence (SFS) of galaxies at
1.0 < z < 1.7, around the peak of the cosmic star formation history. Star formation
rates (SFRs) are measured from the redshifted, relatively dust-insensitive Paschen-α
emission line, and stellar mass measurements include the F444W (4.4 μm; rest-frame
H) band. We find SFRs of galaxies with log(M*/M⊙) > 9.5 that are lower than found
in many earlier studies by up to 0.6 dex, but in good agreement with recent results
obtained with the Prospector fitting framework. The difference (log(SFR(Paα)-SFR(Prospector))
is −0.09 ± 0.04 dex at 1010−11M⊙. We also measure the empirical relation between
Paschen-α luminosity and rest-frame H-band magnitude and find that the scatter
is only 0.04 dex lower than that of the SFR–M* relation and is much lower than
the systematic differences among relations in the literature due to various methods
of converting observed measurements to physical properties. We additionally identify
examples of sources—that, with standard cutoffs via the UVJ diagram, would be
deemed quiescent—with significant (log(sSFR)> −11 yr−1), typically extended, Paschen-α
emission. Our results may be indicative of the potential unification of methods
used to derive the SFS with careful selection of star-forming galaxies and independent
SFR and stellar mass indicators.
acknowledgement: "The authors thank the anonymous referee whose comments and suggestions
improved the quality of this work.\r\nThis work is based on observations made with
the NASA/ESA/CSA James Webb Space Telescope. The data were obtained from the Mikulski
Archive for Space Telescopes at the Space Telescope Science Institute, which is
operated by the Association of Universities for Research in Astronomy, Inc., under
NASA contract NAS 5-03127 for JWST. These observations are associated with program
No. 1895.\r\nSupport for this work was provided by NASA through grant JWST-GO-01895
awarded by the Space Telescope Science Institute, which is operated by the Association
of Universities for Research in Astronomy, Inc., under NASA contract NAS 5-26555.\r\nThis
work has received funding from the Swiss State Secretariat for Education, Research,
and Innovation (SERI) under contract No. MB22.00072, as well as from the Swiss National
Science Foundation (SNSF) through project grant 200020_207349. The Cosmic Dawn Center
(DAWN) is funded by the Danish National Research Foundation under grant No. 140.\r\nR.P.N.
acknowledges funding from JWST programs GO-1933 and GO-2279. Support for this work
was provided by NASA through the NASA Hubble Fellowship grant HST-HF2-51515.001-A
awarded by the Space Telescope Science Institute, which is operated by the Association
of Universities for Research in Astronomy, Inc., under NASA contract NAS 5-26555\r\nCloud-based
data processing and file storage for this work is provided by the AWS Cloud Credits
for Research program.\r\nThis paper made use of several publicly available software
packages. We thank the respective authors for sharing their work: IPython (Pérez
& Granger 2007), matplotlib (Hunter 2007), seaborn (Waskom et al. 2018), NumPy (Harris
et al. 2020), SciPy (Virtanen et al. 2020), jupyter (Kluyver et al. 2016), Astropy
(Astropy Collaboration et al. 2013, 2018, 2022), grizli (Brammer 2018; Brammer et
al. 2022), Prospector (Leja et al. 2019, 2017; Johnson et al. 2021), FSPS (Conroy
et al. 2009a, 2010; Conroy & Gunn 2010a, 2010b; Foreman-Mackey et al. 2014), dynesty
(Speagle 2020), EAZY (Brammer et al. 2008), Bagpipes (Carnall et al. 2018), and
SExtractor (Bertin & Arnouts 1996)."
article_number: '156'
article_processing_charge: Yes
article_type: original
author:
- first_name: Chloe
full_name: Neufeld, Chloe
last_name: Neufeld
- first_name: Pieter
full_name: Van Dokkum, Pieter
last_name: Van Dokkum
- first_name: Yasmeen
full_name: Asali, Yasmeen
last_name: Asali
- first_name: Alba
full_name: Covelo-Paz, Alba
last_name: Covelo-Paz
- first_name: Joel
full_name: Leja, Joel
last_name: Leja
- first_name: Jamie
full_name: Lin, Jamie
last_name: Lin
- first_name: Jorryt J
full_name: Matthee, Jorryt J
id: 7439a258-f3c0-11ec-9501-9df22fe06720
last_name: Matthee
orcid: 0000-0003-2871-127X
- first_name: Pascal A.
full_name: Oesch, Pascal A.
last_name: Oesch
- first_name: Naveen A.
full_name: Reddy, Naveen A.
last_name: Reddy
- first_name: Irene
full_name: Shivaei, Irene
last_name: Shivaei
- first_name: Katherine E.
full_name: Whitaker, Katherine E.
last_name: Whitaker
- first_name: Stijn
full_name: Wuyts, Stijn
last_name: Wuyts
- first_name: Gabriel
full_name: Brammer, Gabriel
last_name: Brammer
- first_name: Danilo
full_name: Marchesini, Danilo
last_name: Marchesini
- first_name: Michael V.
full_name: Maseda, Michael V.
last_name: Maseda
- first_name: Rohan P.
full_name: Naidu, Rohan P.
last_name: Naidu
- first_name: Erica J.
full_name: Nelson, Erica J.
last_name: Nelson
- first_name: Anna
full_name: Velichko, Anna
last_name: Velichko
- first_name: Andrea
full_name: Weibel, Andrea
last_name: Weibel
- first_name: Mengyuan
full_name: Xiao, Mengyuan
last_name: Xiao
citation:
ama: 'Neufeld C, Van Dokkum P, Asali Y, et al. FRESCO: The Paschen-α star-forming
sequence at cosmic noon. Astrophysical Journal. 2024;972(2). doi:10.3847/1538-4357/ad6158'
apa: 'Neufeld, C., Van Dokkum, P., Asali, Y., Covelo-Paz, A., Leja, J., Lin, J.,
… Xiao, M. (2024). FRESCO: The Paschen-α star-forming sequence at cosmic noon.
Astrophysical Journal. IOP Publishing. https://doi.org/10.3847/1538-4357/ad6158'
chicago: 'Neufeld, Chloe, Pieter Van Dokkum, Yasmeen Asali, Alba Covelo-Paz, Joel
Leja, Jamie Lin, Jorryt J Matthee, et al. “FRESCO: The Paschen-α Star-Forming
Sequence at Cosmic Noon.” Astrophysical Journal. IOP Publishing, 2024.
https://doi.org/10.3847/1538-4357/ad6158.'
ieee: 'C. Neufeld et al., “FRESCO: The Paschen-α star-forming sequence at
cosmic noon,” Astrophysical Journal, vol. 972, no. 2. IOP Publishing, 2024.'
ista: 'Neufeld C, Van Dokkum P, Asali Y, Covelo-Paz A, Leja J, Lin J, Matthee JJ,
Oesch PA, Reddy NA, Shivaei I, Whitaker KE, Wuyts S, Brammer G, Marchesini D,
Maseda MV, Naidu RP, Nelson EJ, Velichko A, Weibel A, Xiao M. 2024. FRESCO: The
Paschen-α star-forming sequence at cosmic noon. Astrophysical Journal. 972(2),
156.'
mla: 'Neufeld, Chloe, et al. “FRESCO: The Paschen-α Star-Forming Sequence at Cosmic
Noon.” Astrophysical Journal, vol. 972, no. 2, 156, IOP Publishing, 2024,
doi:10.3847/1538-4357/ad6158.'
short: C. Neufeld, P. Van Dokkum, Y. Asali, A. Covelo-Paz, J. Leja, J. Lin, J.J.
Matthee, P.A. Oesch, N.A. Reddy, I. Shivaei, K.E. Whitaker, S. Wuyts, G. Brammer,
D. Marchesini, M.V. Maseda, R.P. Naidu, E.J. Nelson, A. Velichko, A. Weibel, M.
Xiao, Astrophysical Journal 972 (2024).
date_created: 2024-09-15T22:01:40Z
date_published: 2024-09-01T00:00:00Z
date_updated: 2025-09-08T09:43:41Z
day: '01'
ddc:
- '520'
department:
- _id: JoMa
doi: 10.3847/1538-4357/ad6158
external_id:
isi:
- '001305987600001'
file:
- access_level: open_access
checksum: 754b58c1d79adb9670ca76fa8c20ab16
content_type: application/pdf
creator: dernst
date_created: 2024-09-17T08:23:59Z
date_updated: 2024-09-17T08:23:59Z
file_id: '18082'
file_name: 2024_AstrophysicalJourn_Neufeld.pdf
file_size: 9960685
relation: main_file
success: 1
file_date_updated: 2024-09-17T08:23:59Z
has_accepted_license: '1'
intvolume: ' 972'
isi: 1
issue: '2'
language:
- iso: eng
month: '09'
oa: 1
oa_version: Published Version
publication: Astrophysical Journal
publication_identifier:
eissn:
- 1538-4357
issn:
- 0004-637X
publication_status: published
publisher: IOP Publishing
quality_controlled: '1'
scopus_import: '1'
status: public
title: 'FRESCO: The Paschen-α star-forming sequence at cosmic noon'
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: 317138e5-6ab7-11ef-aa6d-ffef3953e345
volume: 972
year: '2024'
...
---
_id: '18070'
abstract:
- lang: eng
text: Parallel SGD in a shared-memory setting is oft-represented by the popular
Hogwild! algorithm, in which lock-free updates are asynchronously performed by
multiple computing processes. Unfortunately, scaling Hogwild! to distributed workers
is largely unexplored. Specifically, it is unknown if any adaptation of Hogwild!
to the popular decentralized multi-GPU setting offers any competitive speedup,
either empirically or theoretically. In this work, we investigate the potential
of decentralizing Hogwild! by incorporating simultaneously (a) asynchronous local
gradient updates on the shared memory of GPUs, and (b) non-blocking asynchronous
decentralized federated averaging. A naive direct implementation shows degradation
in performance, arising from scheduling overheads and concurrent write conflicts
on GPUs. To mitigate these drawbacks, we investigate and propose a new method,
based on careful block selection rules, which update only portions of the parameter
vectors. Our experiments show that the resulting decentralized training method
exhibits improved throughput and competitive accuracy for standard image classification
benchmarks on the CIFAR-10, CIFAR-100, and Imagenet datasets. On the theoretical
side, we prove that our method guarantees sublinear ergodic convergence rates
for non-convex objectives.
article_processing_charge: No
author:
- first_name: Bapi
full_name: Chatterjee, Bapi
id: 3C41A08A-F248-11E8-B48F-1D18A9856A87
last_name: Chatterjee
orcid: 0000-0002-2742-4028
- first_name: Vyacheslav
full_name: Kungurtsev, Vyacheslav
last_name: Kungurtsev
- first_name: Dan-Adrian
full_name: Alistarh, Dan-Adrian
id: 4A899BFC-F248-11E8-B48F-1D18A9856A87
last_name: Alistarh
orcid: 0000-0003-3650-940X
citation:
ama: 'Chatterjee B, Kungurtsev V, Alistarh D-A. Federated SGD with local asynchrony.
In: Proceedings of the 44th International Conference on Distributed Computing
Systems. IEEE; 2024:857-868. doi:10.1109/ICDCS60910.2024.00084'
apa: 'Chatterjee, B., Kungurtsev, V., & Alistarh, D.-A. (2024). Federated SGD
with local asynchrony. In Proceedings of the 44th International Conference
on Distributed Computing Systems (pp. 857–868). Jersey City, NJ, United States:
IEEE. https://doi.org/10.1109/ICDCS60910.2024.00084'
chicago: Chatterjee, Bapi, Vyacheslav Kungurtsev, and Dan-Adrian Alistarh. “Federated
SGD with Local Asynchrony.” In Proceedings of the 44th International Conference
on Distributed Computing Systems, 857–68. IEEE, 2024. https://doi.org/10.1109/ICDCS60910.2024.00084.
ieee: B. Chatterjee, V. Kungurtsev, and D.-A. Alistarh, “Federated SGD with local
asynchrony,” in Proceedings of the 44th International Conference on Distributed
Computing Systems, Jersey City, NJ, United States, 2024, pp. 857–868.
ista: 'Chatterjee B, Kungurtsev V, Alistarh D-A. 2024. Federated SGD with local
asynchrony. Proceedings of the 44th International Conference on Distributed Computing
Systems. ICDCS: International Conference on Distributed Computing Systems, 857–868.'
mla: Chatterjee, Bapi, et al. “Federated SGD with Local Asynchrony.” Proceedings
of the 44th International Conference on Distributed Computing Systems, IEEE,
2024, pp. 857–68, doi:10.1109/ICDCS60910.2024.00084.
short: B. Chatterjee, V. Kungurtsev, D.-A. Alistarh, in:, Proceedings of the 44th
International Conference on Distributed Computing Systems, IEEE, 2024, pp. 857–868.
conference:
end_date: 2024-07-26
location: Jersey City, NJ, United States
name: 'ICDCS: International Conference on Distributed Computing Systems'
start_date: 2024-07-23
corr_author: '1'
date_created: 2024-09-15T22:01:41Z
date_published: 2024-07-26T00:00:00Z
date_updated: 2025-09-08T09:23:48Z
day: '26'
department:
- _id: DaAl
doi: 10.1109/ICDCS60910.2024.00084
external_id:
isi:
- '001304430200075'
isi: 1
language:
- iso: eng
month: '07'
oa_version: None
page: 857-868
publication: Proceedings of the 44th International Conference on Distributed Computing
Systems
publication_identifier:
eissn:
- 2575-8411
isbn:
- '9798350386059'
issn:
- 1063-6927
publication_status: published
publisher: IEEE
quality_controlled: '1'
scopus_import: '1'
status: public
title: Federated SGD with local asynchrony
type: conference
user_id: 317138e5-6ab7-11ef-aa6d-ffef3953e345
year: '2024'
...
---
_id: '18071'
abstract:
- lang: eng
text: Recent advancements on DAG-based consensus protocols allow for blockchains
with improved metrics and properties, such as throughput and censorship-resistance.
Variants of the Bullshark [18] consensus protocol are adopted for practical use
by the Sui blockchain, for improved latency. However, the protocol is leader-based,
and is strongly affected by crashed leaders that can lead to various performance
issues, for example, decreased transaction throughput. In this paper, we propose
HammerHead, a DAG-based consensus protocol, that is inspired by Carousel [8] and
provides Leader-Utilization. Our proposal differs from Carousel, which is built
for a chained consensus protocol; in HammerHead chain quality is inherited by
the DAG. HammerHead needs to preserve safety and liveness, despite validators
committing leader vertices asynchronously. The key idea is to update leader schedules
dynamically, based on the validators' scores during the previous schedule. We
implement HammerHead and show a minor improvement in performance for cases without
faults. The major improvements in comparison to Bullshark appear in faulty settings.
Specifically, we show a drastic, 2x-latency improvement and up to 40% increased
throughput when crash faults occur (100 validators, 33 faults).
acknowledgement: This work is supported by Mysten Labs. We thank the Mysten Labs Engineering
teams for valuable feedback broadly, and specifically to Laura Makdah for helping
implementing the early reputation score system for validators and Dmitry Perelman
for managing the overall implementation effort.
article_processing_charge: No
arxiv: 1
author:
- first_name: Giorgos
full_name: Tsimos, Giorgos
last_name: Tsimos
- first_name: Anastasios
full_name: Kichidis, Anastasios
last_name: Kichidis
- first_name: Alberto
full_name: Sonnino, Alberto
last_name: Sonnino
- first_name: Eleftherios
full_name: Kokoris Kogias, Eleftherios
id: f5983044-d7ef-11ea-ac6d-fd1430a26d30
last_name: Kokoris Kogias
citation:
ama: 'Tsimos G, Kichidis A, Sonnino A, Kokoris Kogias E. HammerHead: Leader reputation
for dynamic scheduling. In: Proceedings - International Conference on Distributed
Computing Systems. IEEE; 2024:1377-1387. doi:10.1109/ICDCS60910.2024.00129'
apa: 'Tsimos, G., Kichidis, A., Sonnino, A., & Kokoris Kogias, E. (2024). HammerHead:
Leader reputation for dynamic scheduling. In Proceedings - International Conference
on Distributed Computing Systems (pp. 1377–1387). Jersey City, NJ, United
States: IEEE. https://doi.org/10.1109/ICDCS60910.2024.00129'
chicago: 'Tsimos, Giorgos, Anastasios Kichidis, Alberto Sonnino, and Eleftherios
Kokoris Kogias. “HammerHead: Leader Reputation for Dynamic Scheduling.” In Proceedings
- International Conference on Distributed Computing Systems, 1377–87. IEEE,
2024. https://doi.org/10.1109/ICDCS60910.2024.00129.'
ieee: 'G. Tsimos, A. Kichidis, A. Sonnino, and E. Kokoris Kogias, “HammerHead: Leader
reputation for dynamic scheduling,” in Proceedings - International Conference
on Distributed Computing Systems, Jersey City, NJ, United States, 2024, pp.
1377–1387.'
ista: 'Tsimos G, Kichidis A, Sonnino A, Kokoris Kogias E. 2024. HammerHead: Leader
reputation for dynamic scheduling. Proceedings - International Conference on Distributed
Computing Systems. ICDCS: International Conference on Distributed Computing Systems,
1377–1387.'
mla: 'Tsimos, Giorgos, et al. “HammerHead: Leader Reputation for Dynamic Scheduling.”
Proceedings - International Conference on Distributed Computing Systems,
IEEE, 2024, pp. 1377–87, doi:10.1109/ICDCS60910.2024.00129.'
short: G. Tsimos, A. Kichidis, A. Sonnino, E. Kokoris Kogias, in:, Proceedings -
International Conference on Distributed Computing Systems, IEEE, 2024, pp. 1377–1387.
conference:
end_date: 2024-07-26
location: Jersey City, NJ, United States
name: 'ICDCS: International Conference on Distributed Computing Systems'
start_date: 2024-07-23
date_created: 2024-09-15T22:01:41Z
date_published: 2024-07-26T00:00:00Z
date_updated: 2025-09-08T09:42:36Z
day: '26'
department:
- _id: ElKo
doi: 10.1109/ICDCS60910.2024.00129
external_id:
arxiv:
- '2309.12713'
isi:
- '001304430200120'
isi: 1
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/2309.12713
month: '07'
oa: 1
oa_version: Preprint
page: 1377-1387
publication: Proceedings - International Conference on Distributed Computing Systems
publication_identifier:
eissn:
- 2575-8411
isbn:
- '9798350386059'
issn:
- 1063-6927
publication_status: published
publisher: IEEE
quality_controlled: '1'
scopus_import: '1'
status: public
title: 'HammerHead: Leader reputation for dynamic scheduling'
type: conference
user_id: 317138e5-6ab7-11ef-aa6d-ffef3953e345
year: '2024'
...
---
_id: '18072'
abstract:
- lang: eng
text: The individualization of chromosomes during early mitosis and their clustering
upon exit from cell division are two key transitions that ensure efficient segregation
of eukaryotic chromosomes. Both processes are regulated by the surfactant-like
protein Ki-67, but how Ki-67 achieves these diametric functions has remained unknown.
Here, we report that Ki-67 radically switches from a chromosome repellent to a
chromosome attractant during anaphase in human cells. We show that Ki-67 dephosphorylation
during mitotic exit and the simultaneous exposure of a conserved basic patch induce
the RNA-dependent formation of a liquid-like condensed phase on the chromosome
surface. Experiments and coarse-grained simulations support a model in which the
coalescence of chromosome surfaces, driven by co-condensation of Ki-67 and RNA,
promotes clustering of chromosomes. Our study reveals how the switch of Ki-67
from a surfactant to a liquid-like condensed phase can generate mechanical forces
during genome segregation that are required for re-establishing nuclear-cytoplasmic
compartmentalization after mitosis.
acknowledgement: We thank Daniel W. Gerlich for providing cell lines, the EMBL Advanced
Light Microscopy Facility (ALMF) for support, Christian H. Haering and Thomas Quail
for input on the manuscript, and Martina Dees for cloning several Ki-67 constructs.
This work was supported by the German Research Foundation (DFG project number 402723784)
and the Human Frontier Science Program (CDA00045/2019). A.H.-A. and A.B. have received
PhD fellowships from the Boehringer Ingelheim Fonds, V.S. and A.Š. were supported
by the European Research Council (ERC) under the European Union’s Horizon 2020 research
and innovation programme (grant no. 802960), and Y.H. was supported by a fellowship
from the EMBL interdisciplinary Postdoc (EIPOD) program (Marie Sklodowska-Curie
Actions, COFUND grant agreement 664726).
article_processing_charge: Yes (in subscription journal)
article_type: original
author:
- first_name: Alberto
full_name: Hernandez-Armendariz, Alberto
last_name: Hernandez-Armendariz
- first_name: Valerio
full_name: Sorichetti, Valerio
id: ef8a92cb-c7b6-11ec-8bea-e1fd5847bc5b
last_name: Sorichetti
orcid: 0000-0002-9645-6576
- first_name: Yuki
full_name: Hayashi, Yuki
last_name: Hayashi
- first_name: Zuzana
full_name: Koskova, Zuzana
last_name: Koskova
- first_name: Andreas
full_name: Brunner, Andreas
last_name: Brunner
- first_name: Jan
full_name: Ellenberg, Jan
last_name: Ellenberg
- first_name: Anđela
full_name: Šarić, Anđela
id: bf63d406-f056-11eb-b41d-f263a6566d8b
last_name: Šarić
orcid: 0000-0002-7854-2139
- first_name: Sara
full_name: Cuylen-Haering, Sara
last_name: Cuylen-Haering
citation:
ama: Hernandez-Armendariz A, Sorichetti V, Hayashi Y, et al. A liquid-like coat
mediates chromosome clustering during mitotic exit. Molecular Cell. 2024;84(17):P3254-3270.E9.
doi:10.1016/j.molcel.2024.07.022
apa: Hernandez-Armendariz, A., Sorichetti, V., Hayashi, Y., Koskova, Z., Brunner,
A., Ellenberg, J., … Cuylen-Haering, S. (2024). A liquid-like coat mediates chromosome
clustering during mitotic exit. Molecular Cell. Cell Press. https://doi.org/10.1016/j.molcel.2024.07.022
chicago: Hernandez-Armendariz, Alberto, Valerio Sorichetti, Yuki Hayashi, Zuzana
Koskova, Andreas Brunner, Jan Ellenberg, Anđela Šarić, and Sara Cuylen-Haering.
“A Liquid-like Coat Mediates Chromosome Clustering during Mitotic Exit.” Molecular
Cell. Cell Press, 2024. https://doi.org/10.1016/j.molcel.2024.07.022.
ieee: A. Hernandez-Armendariz et al., “A liquid-like coat mediates chromosome
clustering during mitotic exit,” Molecular Cell, vol. 84, no. 17. Cell
Press, p. P3254–3270.E9, 2024.
ista: Hernandez-Armendariz A, Sorichetti V, Hayashi Y, Koskova Z, Brunner A, Ellenberg
J, Šarić A, Cuylen-Haering S. 2024. A liquid-like coat mediates chromosome clustering
during mitotic exit. Molecular Cell. 84(17), P3254–3270.E9.
mla: Hernandez-Armendariz, Alberto, et al. “A Liquid-like Coat Mediates Chromosome
Clustering during Mitotic Exit.” Molecular Cell, vol. 84, no. 17, Cell
Press, 2024, p. P3254–3270.E9, doi:10.1016/j.molcel.2024.07.022.
short: A. Hernandez-Armendariz, V. Sorichetti, Y. Hayashi, Z. Koskova, A. Brunner,
J. Ellenberg, A. Šarić, S. Cuylen-Haering, Molecular Cell 84 (2024) P3254–3270.E9.
date_created: 2024-09-15T22:01:41Z
date_published: 2024-09-05T00:00:00Z
date_updated: 2025-09-08T09:23:02Z
day: '05'
ddc:
- '570'
department:
- _id: AnSa
doi: 10.1016/j.molcel.2024.07.022
ec_funded: 1
external_id:
isi:
- '001309051100001'
pmid:
- '39153474'
file:
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checksum: 3f360e0287b8ec79fb2b8b02b5070360
content_type: application/pdf
creator: dernst
date_created: 2024-09-16T07:38:38Z
date_updated: 2024-09-16T07:38:38Z
file_id: '18075'
file_name: 2024_MolecularCell_HernandezArmendariz.pdf
file_size: 11654644
relation: main_file
success: 1
file_date_updated: 2024-09-16T07:38:38Z
has_accepted_license: '1'
intvolume: ' 84'
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issue: '17'
language:
- iso: eng
month: '09'
oa: 1
oa_version: Published Version
page: P3254-3270.E9
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: Molecular Cell
publication_identifier:
eissn:
- 1097-4164
issn:
- 1097-2765
publication_status: published
publisher: Cell Press
quality_controlled: '1'
scopus_import: '1'
status: public
title: A liquid-like coat mediates chromosome clustering during mitotic exit
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: 317138e5-6ab7-11ef-aa6d-ffef3953e345
volume: 84
year: '2024'
...
---
OA_place: publisher
OA_type: gold
_id: '18073'
abstract:
- lang: eng
text: Conserved signaling cascades monitor protein-folding homeostasis to ensure
proper cellular function. One of the evolutionary conserved key players is IRE1,
which maintains endoplasmic reticulum (ER) homeostasis through the unfolded protein
response (UPR). Upon accumulation of misfolded proteins in the ER, IRE1 forms
clusters on the ER membrane to initiate UPR signaling. What regulates IRE1 cluster
formation is not fully understood. Here, we show that the ER lumenal domain (LD)
of human IRE1α forms biomolecular condensates in vitro. IRE1α LD condensates were
stabilized both by binding to unfolded polypeptides as well as by tethering to
model membranes, suggesting their role in assembling IRE1α into signaling-competent
stable clusters. Molecular dynamics simulations indicated that weak multivalent
interactions drive IRE1α LD clustering. Mutagenesis experiments identified disordered
regions in IRE1α LD to control its clustering in vitro and in cells. Importantly,
dysregulated clustering of IRE1α mutants led to defects in IRE1α signaling. Our
results revealed that disordered regions in IRE1α LD control its clustering and
suggest their role as a common strategy in regulating protein assembly on membranes.
acknowledgement: We thank late Thomas Peterbauer at the Max Perutz Labs Biooptics
Light Microscopy Facility for his help and support. We are grateful to Kitti Csalyi
and Thomas Sauer at Max Perutz Labs Biooptics FACS facility for their help. We thank
Grzegorz Scibisz and Sertan Atilla for their support with the expression and purification
of mCherry-IRE1α LD-10His. We are grateful to Aleksandra S Anisimova with her help
in the generation of stable cell lines and the statistical analyses of the data.
We thank Venja Vieweger for her help with the characterization of the WLLI and D123P
IRE1 mutants in cells. We are thankful to Monika Kubickova for the help with the
AUC experiments. We acknowledge CF BIC of CIISB, Instruct-CZ Centre, supported by
MEYS CR (LM2023042)) and European Regional Development Fund-Project, UP CIISB“ (No.
CZ.02.1.01/0.0/0.0/18_046/0015974). We thank the members of the Karagöz lab for
the critical reading and editing of the manuscript. We are thankful to our colleagues
Diego Acosta-Alvear, Vladislav Belyy, Jirka Peschek, Yasin Dagdas, Javier Martinez,
Sascha Martens and Alwin Köhler for their invaluable input on the manuscript. We
are grateful to Life Science Editors, especially Katrina Woolcock for her useful
edits and comments on the manuscript. We acknowledge funding from Austrian Science
Fund (FWF-SFB F79 and FWF-W 1261) to GEK. PK acknowledges the support of the Max
Perutz PhD fellowship. GAV is funded by Stand-Alone grants (P30231-B, P30415-B,
P36572), Special Research Grant (SFB grant F79), and Doctoral School grant (DK grant
W1261) from the Austrian Science Fund (FWF). ES and RC acknowledge support and funding
by the Frankfurt Institute of Advanced Studies, the LOEWE Center for Multiscale
Modelling in Life Sciences of the state of Hesse, the Collaborative Research Center
1507 “Membrane-associated Protein Assemblies, Machineries, and Supercomplexes” (Project
ID 450648163), and the International Max Planck Research School on Cellular Biophysics
(to RC), the Center for Scientific Computing of the Goethe University and the Jülich
Supercomputing Centre for computational resources and support.
article_processing_charge: Yes
article_type: original
author:
- first_name: Paulina
full_name: Kettel, Paulina
last_name: Kettel
- first_name: Laura
full_name: Marosits, Laura
last_name: Marosits
- first_name: Elena
full_name: Spinetti, Elena
last_name: Spinetti
- first_name: Michael
full_name: Rechberger, Michael
last_name: Rechberger
- first_name: Caterina
full_name: Giannini, Caterina
id: e3fdddd5-f6e0-11ea-865d-ca99ee6367f4
last_name: Giannini
- first_name: Philipp
full_name: Radler, Philipp
id: 40136C2A-F248-11E8-B48F-1D18A9856A87
last_name: Radler
orcid: '0000-0001-9198-2182 '
- first_name: Isabell
full_name: Niedermoser, Isabell
last_name: Niedermoser
- first_name: Irmgard
full_name: Fischer, Irmgard
last_name: Fischer
- first_name: Gijs A.
full_name: Versteeg, Gijs A.
last_name: Versteeg
- first_name: Martin
full_name: Loose, Martin
id: 462D4284-F248-11E8-B48F-1D18A9856A87
last_name: Loose
orcid: 0000-0001-7309-9724
- first_name: Roberto
full_name: Covino, Roberto
last_name: Covino
- first_name: G. Elif
full_name: Karagöz, G. Elif
last_name: Karagöz
citation:
ama: Kettel P, Marosits L, Spinetti E, et al. Disordered regions in the IRE1α ER
lumenal domain mediate its stress-induced clustering. EMBO Journal. 2024;43(20):4668-4698.
doi:10.1038/s44318-024-00207-0
apa: Kettel, P., Marosits, L., Spinetti, E., Rechberger, M., Giannini, C., Radler,
P., … Karagöz, G. E. (2024). Disordered regions in the IRE1α ER lumenal domain
mediate its stress-induced clustering. EMBO Journal. Embo Press. https://doi.org/10.1038/s44318-024-00207-0
chicago: Kettel, Paulina, Laura Marosits, Elena Spinetti, Michael Rechberger, Caterina
Giannini, Philipp Radler, Isabell Niedermoser, et al. “Disordered Regions in the
IRE1α ER Lumenal Domain Mediate Its Stress-Induced Clustering.” EMBO Journal.
Embo Press, 2024. https://doi.org/10.1038/s44318-024-00207-0.
ieee: P. Kettel et al., “Disordered regions in the IRE1α ER lumenal domain
mediate its stress-induced clustering,” EMBO Journal, vol. 43, no. 20.
Embo Press, pp. 4668–4698, 2024.
ista: Kettel P, Marosits L, Spinetti E, Rechberger M, Giannini C, Radler P, Niedermoser
I, Fischer I, Versteeg GA, Loose M, Covino R, Karagöz GE. 2024. Disordered regions
in the IRE1α ER lumenal domain mediate its stress-induced clustering. EMBO Journal.
43(20), 4668–4698.
mla: Kettel, Paulina, et al. “Disordered Regions in the IRE1α ER Lumenal Domain
Mediate Its Stress-Induced Clustering.” EMBO Journal, vol. 43, no. 20,
Embo Press, 2024, pp. 4668–98, doi:10.1038/s44318-024-00207-0.
short: P. Kettel, L. Marosits, E. Spinetti, M. Rechberger, C. Giannini, P. Radler,
I. Niedermoser, I. Fischer, G.A. Versteeg, M. Loose, R. Covino, G.E. Karagöz,
EMBO Journal 43 (2024) 4668–4698.
date_created: 2024-09-15T22:01:42Z
date_published: 2024-10-15T00:00:00Z
date_updated: 2025-09-08T09:22:11Z
day: '15'
ddc:
- '570'
department:
- _id: MaLo
- _id: JiFr
doi: 10.1038/s44318-024-00207-0
external_id:
isi:
- '001306286100002'
pmid:
- '39232130'
file:
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checksum: 04f4df1a561083f2846676442fc4eb3c
content_type: application/pdf
creator: dernst
date_created: 2025-01-13T08:43:20Z
date_updated: 2025-01-13T08:43:20Z
file_id: '18827'
file_name: 2024_Embo_Kettel.pdf
file_size: 10080854
relation: main_file
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file_date_updated: 2025-01-13T08:43:20Z
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month: '10'
oa: 1
oa_version: Published Version
page: 4668-4698
pmid: 1
publication: EMBO Journal
publication_identifier:
eissn:
- 1460-2075
issn:
- 0261-4189
publication_status: published
publisher: Embo Press
quality_controlled: '1'
scopus_import: '1'
status: public
title: Disordered regions in the IRE1α ER lumenal domain mediate its stress-induced
clustering
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: 317138e5-6ab7-11ef-aa6d-ffef3953e345
volume: 43
year: '2024'
...
---
OA_place: publisher
_id: '18076'
abstract:
- lang: eng
text: "The new era of Ge has opened up new possibilities in quantum computing. The
maturity of Ge\r\nspin qubits is unquestioned, while hybrid semiconductor-superconductor
Ge circuits are on track\r\nto enter the game. Gate-tunable transmons (gatemons)
employing semiconductor Josephson\r\njunctions have recently emerged as building
blocks for such hybrid quantum circuits. In this\r\nthesis, we present a gatemon
fabricated in planar Germanium. We induce superconductivity\r\nin a two-dimensional
hole gas by evaporating aluminum atop a thin spacer, which separates\r\nthe superconductor
from the Ge quantum well. The Josephson junction is then integrated\r\ninto an
Xmon circuit and capacitively coupled to a transmission line resonator. We showcase\r\nthe
qubit tunability in a broad frequency range with resonator and two-tone spectroscopy.\r\nTime-domain
characterizations reveal energy relaxation and coherence times up to 75 ns. Our\r\nresults,
combined with the recent advances in the spin qubit field, pave the way towards
novel\r\nhybrid and protected qubits in a group IV, CMOS-compatible material."
acknowledged_ssus:
- _id: NanoFab
- _id: M-Shop
alternative_title:
- ISTA Thesis
article_processing_charge: No
author:
- first_name: Oliver
full_name: Sagi, Oliver
id: 71616374-A8E9-11E9-A7CA-09ECE5697425
last_name: Sagi
citation:
ama: Sagi O. Hybrid circuits on planar Germanium. 2024. doi:10.15479/at:ista:18076
apa: Sagi, O. (2024). Hybrid circuits on planar Germanium. Institute of Science
and Technology Austria. https://doi.org/10.15479/at:ista:18076
chicago: Sagi, Oliver. “Hybrid Circuits on Planar Germanium.” Institute of Science
and Technology Austria, 2024. https://doi.org/10.15479/at:ista:18076.
ieee: O. Sagi, “Hybrid circuits on planar Germanium,” Institute of Science and Technology
Austria, 2024.
ista: Sagi O. 2024. Hybrid circuits on planar Germanium. Institute of Science and
Technology Austria.
mla: Sagi, Oliver. Hybrid Circuits on Planar Germanium. Institute of Science
and Technology Austria, 2024, doi:10.15479/at:ista:18076.
short: O. Sagi, Hybrid Circuits on Planar Germanium, Institute of Science and Technology
Austria, 2024.
corr_author: '1'
date_created: 2024-09-16T12:58:36Z
date_published: 2024-09-18T00:00:00Z
date_updated: 2026-04-16T12:20:39Z
day: '18'
ddc:
- '539'
degree_awarded: PhD
department:
- _id: GradSch
- _id: GeKa
doi: 10.15479/at:ista:18076
ec_funded: 1
file:
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checksum: d01d0e2846c2f3ac5bb14d321554a4cd
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creator: osagi
date_created: 2024-09-18T14:14:02Z
date_updated: 2024-09-19T09:20:33Z
file_id: '18094'
file_name: Thesis_OliverSagi.zip
file_size: 172098524
relation: source_file
file_date_updated: 2024-09-19T09:20:33Z
has_accepted_license: '1'
language:
- iso: eng
license: https://creativecommons.org/licenses/by-nc-sa/4.0/
month: '09'
oa: 1
oa_version: Published Version
page: '111'
project:
- _id: bd8bd29e-d553-11ed-ba76-f0070d4b237a
grant_number: P36507
name: Merging spin and superconducting qubits in planar Ge
- _id: c0977eea-5a5b-11eb-8a69-a862db0cf4d1
grant_number: I05060
name: High impedance circuit quantum electrodynamics with hole spins
- _id: 262116AA-B435-11E9-9278-68D0E5697425
name: Hybrid Semiconductor - Superconductor Quantum Devices
- _id: 237E5020-32DE-11EA-91FC-C7463DDC885E
call_identifier: H2020
grant_number: '862046'
name: TOPOLOGICALLY PROTECTED AND SCALABLE QUANTUM BITS
publication_identifier:
issn:
- 2663-337X
publication_status: published
publisher: Institute of Science and Technology Austria
related_material:
record:
- id: '17202'
relation: part_of_dissertation
status: public
status: public
supervisor:
- first_name: Georgios
full_name: Katsaros, Georgios
id: 38DB5788-F248-11E8-B48F-1D18A9856A87
last_name: Katsaros
orcid: 0000-0001-8342-202X
title: Hybrid circuits on planar Germanium
tmp:
image: /images/cc_by_nc_sa.png
legal_code_url: https://creativecommons.org/licenses/by-nc-sa/4.0/legalcode
name: Creative Commons Attribution-NonCommercial-ShareAlike 4.0 International (CC
BY-NC-SA 4.0)
short: CC BY-NC-SA (4.0)
type: dissertation
user_id: ba8df636-2132-11f1-aed0-ed93e2281fdd
year: '2024'
...