---
_id: '14843'
abstract:
- lang: eng
text: The coupling between Ca2+ channels and release sensors is a key factor defining
the signaling properties of a synapse. However, the coupling nanotopography at
many synapses remains unknown, and it is unclear how it changes during development.
To address these questions, we examined coupling at the cerebellar inhibitory
basket cell (BC)-Purkinje cell (PC) synapse. Biophysical analysis of transmission
by paired recording and intracellular pipette perfusion revealed that the effects
of exogenous Ca2+ chelators decreased during development, despite constant reliance
of release on P/Q-type Ca2+ channels. Structural analysis by freeze-fracture replica
labeling (FRL) and transmission electron microscopy (EM) indicated that presynaptic
P/Q-type Ca2+ channels formed nanoclusters throughout development, whereas docked
vesicles were only clustered at later developmental stages. Modeling suggested
a developmental transformation from a more random to a more clustered coupling
nanotopography. Thus, presynaptic signaling developmentally approaches a point-to-point
configuration, optimizing speed, reliability, and energy efficiency of synaptic
transmission.
acknowledged_ssus:
- _id: EM-Fac
- _id: PreCl
- _id: M-Shop
acknowledgement: We thank Drs. David DiGregorio and Erwin Neher for critically reading
an earlier version of the manuscript, Ralf Schneggenburger for helpful discussions,
Benjamin Suter and Katharina Lichter for support with image analysis, Chris Wojtan
for advice on numerical solution of partial differential equations, Maria Reva for
help with Ripley analysis, Alois Schlögl for programming, and Akari Hagiwara and
Toshihisa Ohtsuka for anti-ELKS antibody. We are grateful to Florian Marr, Christina
Altmutter, and Vanessa Zheden for excellent technical assistance and to Eleftheria
Kralli-Beller for manuscript editing. This research was supported by the Scientific
Services Units (SSUs) of ISTA (Electron Microscopy Facility, Preclinical Facility,
and Machine Shop). The project received funding from the European Research Council
(ERC) under the European Union’s Horizon 2020 research and innovation program (grant
agreement no. 692692), the Fonds zur Förderung der Wissenschaftlichen Forschung
(Z 312-B27, Wittgenstein award; P 36232-B), all to P.J., and a DOC fellowship of
the Austrian Academy of Sciences to J.-J.C.
article_processing_charge: No
article_type: original
author:
- first_name: JingJing
full_name: Chen, JingJing
id: 2C4E65C8-F248-11E8-B48F-1D18A9856A87
last_name: Chen
- first_name: Walter
full_name: Kaufmann, Walter
id: 3F99E422-F248-11E8-B48F-1D18A9856A87
last_name: Kaufmann
orcid: 0000-0001-9735-5315
- first_name: Chong
full_name: Chen, Chong
id: 3DFD581A-F248-11E8-B48F-1D18A9856A87
last_name: Chen
- first_name: Itaru
full_name: Arai, Itaru
id: 32A73F6C-F248-11E8-B48F-1D18A9856A87
last_name: Arai
- first_name: Olena
full_name: Kim, Olena
id: 3F8ABDDA-F248-11E8-B48F-1D18A9856A87
last_name: Kim
- first_name: Ryuichi
full_name: Shigemoto, Ryuichi
id: 499F3ABC-F248-11E8-B48F-1D18A9856A87
last_name: Shigemoto
orcid: 0000-0001-8761-9444
- first_name: Peter M
full_name: Jonas, Peter M
id: 353C1B58-F248-11E8-B48F-1D18A9856A87
last_name: Jonas
orcid: 0000-0001-5001-4804
citation:
ama: Chen J, Kaufmann W, Chen C, et al. Developmental transformation of Ca2+ channel-vesicle
nanotopography at a central GABAergic synapse. Neuron. doi:10.1016/j.neuron.2023.12.002
apa: Chen, J., Kaufmann, W., Chen, C., Arai, itaru, Kim, O., Shigemoto, R., &
Jonas, P. M. (n.d.). Developmental transformation of Ca2+ channel-vesicle nanotopography
at a central GABAergic synapse. Neuron. Elsevier. https://doi.org/10.1016/j.neuron.2023.12.002
chicago: Chen, JingJing, Walter Kaufmann, Chong Chen, itaru Arai, Olena Kim, Ryuichi
Shigemoto, and Peter M Jonas. “Developmental Transformation of Ca2+ Channel-Vesicle
Nanotopography at a Central GABAergic Synapse.” Neuron. Elsevier, n.d.
https://doi.org/10.1016/j.neuron.2023.12.002.
ieee: J. Chen et al., “Developmental transformation of Ca2+ channel-vesicle
nanotopography at a central GABAergic synapse,” Neuron. Elsevier.
ista: Chen J, Kaufmann W, Chen C, Arai itaru, Kim O, Shigemoto R, Jonas PM. Developmental
transformation of Ca2+ channel-vesicle nanotopography at a central GABAergic synapse.
Neuron.
mla: Chen, JingJing, et al. “Developmental Transformation of Ca2+ Channel-Vesicle
Nanotopography at a Central GABAergic Synapse.” Neuron, Elsevier, doi:10.1016/j.neuron.2023.12.002.
short: J. Chen, W. Kaufmann, C. Chen, itaru Arai, O. Kim, R. Shigemoto, P.M. Jonas,
Neuron (n.d.).
date_created: 2024-01-21T23:00:56Z
date_published: 2024-01-11T00:00:00Z
date_updated: 2024-03-14T13:14:18Z
day: '11'
department:
- _id: PeJo
- _id: EM-Fac
- _id: RySh
doi: 10.1016/j.neuron.2023.12.002
ec_funded: 1
external_id:
pmid:
- '38215739'
language:
- iso: eng
month: '01'
oa_version: None
pmid: 1
project:
- _id: 25B7EB9E-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '692692'
name: Biophysics and circuit function of a giant cortical glumatergic synapse
- _id: 25C5A090-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: Z00312
name: The Wittgenstein Prize
- _id: bd88be38-d553-11ed-ba76-81d5a70a6ef5
grant_number: P36232
name: Mechanisms of GABA release in hippocampal circuits
- _id: 26B66A3E-B435-11E9-9278-68D0E5697425
grant_number: '25383'
name: Development of nanodomain coupling between Ca2+ channels and release sensors
at a central inhibitory synapse
publication: Neuron
publication_identifier:
eissn:
- 1097-4199
issn:
- 0896-6273
publication_status: inpress
publisher: Elsevier
quality_controlled: '1'
related_material:
link:
- description: News on ISTA Website
relation: press_release
url: https://ista.ac.at/en/news/synapses-brought-to-the-point/
record:
- id: '15101'
relation: dissertation_contains
status: public
scopus_import: '1'
status: public
title: Developmental transformation of Ca2+ channel-vesicle nanotopography at a central
GABAergic synapse
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
year: '2024'
...
---
_id: '15101'
acknowledged_ssus:
- _id: EM-Fac
alternative_title:
- ISTA Thesis
article_processing_charge: No
author:
- first_name: JingJing
full_name: Chen, JingJing
id: 2C4E65C8-F248-11E8-B48F-1D18A9856A87
last_name: Chen
citation:
ama: Chen J. Developmental transformation of nanodomain coupling between Ca2+ channels
and release sensors at a central GABAergic synapse. 2024. doi:10.15479/at:ista:15101
apa: Chen, J. (2024). Developmental transformation of nanodomain coupling between
Ca2+ channels and release sensors at a central GABAergic synapse. Institute
of Science and Technology Austria. https://doi.org/10.15479/at:ista:15101
chicago: Chen, JingJing. “Developmental Transformation of Nanodomain Coupling between
Ca2+ Channels and Release Sensors at a Central GABAergic Synapse.” Institute of
Science and Technology Austria, 2024. https://doi.org/10.15479/at:ista:15101.
ieee: J. Chen, “Developmental transformation of nanodomain coupling between Ca2+
channels and release sensors at a central GABAergic synapse,” Institute of Science
and Technology Austria, 2024.
ista: Chen J. 2024. Developmental transformation of nanodomain coupling between
Ca2+ channels and release sensors at a central GABAergic synapse. Institute of
Science and Technology Austria.
mla: Chen, JingJing. Developmental Transformation of Nanodomain Coupling between
Ca2+ Channels and Release Sensors at a Central GABAergic Synapse. Institute
of Science and Technology Austria, 2024, doi:10.15479/at:ista:15101.
short: J. Chen, Developmental Transformation of Nanodomain Coupling between Ca2+
Channels and Release Sensors at a Central GABAergic Synapse, Institute of Science
and Technology Austria, 2024.
date_created: 2024-03-11T10:09:54Z
date_published: 2024-03-11T00:00:00Z
date_updated: 2024-03-14T13:14:19Z
day: '11'
ddc:
- '570'
degree_awarded: PhD
department:
- _id: GradSch
- _id: PeJo
doi: 10.15479/at:ista:15101
ec_funded: 1
file:
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checksum: db4947474ffa271e66c254b6fe876a55
content_type: application/vnd.openxmlformats-officedocument.wordprocessingml.document
creator: jchen
date_created: 2024-03-11T14:10:58Z
date_updated: 2024-03-12T07:12:17Z
file_id: '15104'
file_name: Thesis_Jingjing CHEN.docx
file_size: 11271363
relation: source_file
- access_level: closed
checksum: a5eeae8b5702cd540f5d03469bc33dde
content_type: application/pdf
creator: jchen
date_created: 2024-03-11T14:11:06Z
date_updated: 2024-03-11T14:11:06Z
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embargo_to: open_access
file_id: '15105'
file_name: Thesis_Jingjing CHEN_merged.pdf
file_size: 16627311
relation: main_file
file_date_updated: 2024-03-12T07:12:17Z
has_accepted_license: '1'
language:
- iso: eng
month: '03'
oa_version: Published Version
page: '84'
project:
- _id: 25B7EB9E-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '692692'
name: Biophysics and circuit function of a giant cortical glumatergic synapse
- _id: 25C5A090-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: Z00312
name: The Wittgenstein Prize
- _id: bd88be38-d553-11ed-ba76-81d5a70a6ef5
grant_number: P36232
name: Mechanisms of GABA release in hippocampal circuits
- _id: 26B66A3E-B435-11E9-9278-68D0E5697425
grant_number: '25383'
name: Development of nanodomain coupling between Ca2+ channels and release sensors
at a central inhibitory synapse
publication_identifier:
issn:
- 2663 - 337X
publication_status: published
publisher: Institute of Science and Technology Austria
related_material:
record:
- id: '14843'
relation: part_of_dissertation
status: public
status: public
supervisor:
- first_name: Peter M
full_name: Jonas, Peter M
id: 353C1B58-F248-11E8-B48F-1D18A9856A87
last_name: Jonas
orcid: 0000-0001-5001-4804
title: Developmental transformation of nanodomain coupling between Ca2+ channels and
release sensors at a central GABAergic synapse
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: dissertation
user_id: 8b945eb4-e2f2-11eb-945a-df72226e66a9
year: '2024'
...
---
_id: '15122'
abstract:
- lang: eng
text: Quantum computers are increasing in size and quality but are still very noisy.
Error mitigation extends the size of the quantum circuits that noisy devices can
meaningfully execute. However, state-of-the-art error mitigation methods are hard
to implement and the limited qubit connectivity in superconducting qubit devices
restricts most applications to the hardware's native topology. Here we show a
quantum approximate optimization algorithm (QAOA) on nonplanar random regular
graphs with up to 40 nodes enabled by a machine learning-based error mitigation.
We use a swap network with careful decision-variable-to-qubit mapping and a feed-forward
neural network to optimize a depth-two QAOA on up to 40 qubits. We observe a meaningful
parameter optimization for the largest graph which requires running quantum circuits
with 958 two-qubit gates. Our paper emphasizes the need to mitigate samples, and
not only expectation values, in quantum approximate optimization. These results
are a step towards executing quantum approximate optimization at a scale that
is not classically simulable. Reaching such system sizes is key to properly understanding
the true potential of heuristic algorithms like QAOA.
acknowledgement: S.H.S. acknowledges support from the IBM Ph.D. fellowship 2022 in
quantum computing. The authors also thank M. Serbyn, R. Kueng, R. A. Medina, and
S. Woerner for fruitful discussions.
article_number: '013223'
article_processing_charge: Yes
article_type: original
author:
- first_name: Stefan
full_name: Sack, Stefan
id: dd622248-f6e0-11ea-865d-ce382a1c81a5
last_name: Sack
orcid: 0000-0001-5400-8508
- first_name: Daniel J.
full_name: Egger, Daniel J.
last_name: Egger
citation:
ama: Sack S, Egger DJ. Large-scale quantum approximate optimization on nonplanar
graphs with machine learning noise mitigation. Physical Review Research.
2024;6(1). doi:10.1103/PhysRevResearch.6.013223
apa: Sack, S., & Egger, D. J. (2024). Large-scale quantum approximate optimization
on nonplanar graphs with machine learning noise mitigation. Physical Review
Research. American Physical Society. https://doi.org/10.1103/PhysRevResearch.6.013223
chicago: Sack, Stefan, and Daniel J. Egger. “Large-Scale Quantum Approximate Optimization
on Nonplanar Graphs with Machine Learning Noise Mitigation.” Physical Review
Research. American Physical Society, 2024. https://doi.org/10.1103/PhysRevResearch.6.013223.
ieee: S. Sack and D. J. Egger, “Large-scale quantum approximate optimization on
nonplanar graphs with machine learning noise mitigation,” Physical Review Research,
vol. 6, no. 1. American Physical Society, 2024.
ista: Sack S, Egger DJ. 2024. Large-scale quantum approximate optimization on nonplanar
graphs with machine learning noise mitigation. Physical Review Research. 6(1),
013223.
mla: Sack, Stefan, and Daniel J. Egger. “Large-Scale Quantum Approximate Optimization
on Nonplanar Graphs with Machine Learning Noise Mitigation.” Physical Review
Research, vol. 6, no. 1, 013223, American Physical Society, 2024, doi:10.1103/PhysRevResearch.6.013223.
short: S. Sack, D.J. Egger, Physical Review Research 6 (2024).
date_created: 2024-03-17T23:00:59Z
date_published: 2024-03-01T00:00:00Z
date_updated: 2024-03-19T07:24:03Z
day: '01'
ddc:
- '530'
department:
- _id: MaSe
doi: 10.1103/PhysRevResearch.6.013223
external_id:
arxiv:
- '2307.14427'
file:
- access_level: open_access
checksum: 274c9f1b15b3547a10a03f39e4ccc582
content_type: application/pdf
creator: dernst
date_created: 2024-03-19T07:16:38Z
date_updated: 2024-03-19T07:16:38Z
file_id: '15123'
file_name: 2024_PhysicalReviewResearch_Sack.pdf
file_size: 2777593
relation: main_file
success: 1
file_date_updated: 2024-03-19T07:16:38Z
has_accepted_license: '1'
intvolume: ' 6'
issue: '1'
language:
- iso: eng
month: '03'
oa: 1
oa_version: Published Version
project:
- _id: bd660c93-d553-11ed-ba76-fb0fb6f49c0d
name: Quantum_Quantum Circuits and Software_Variational quantum algorithms on NISQ
devices
publication: Physical Review Research
publication_identifier:
issn:
- 2643-1564
publication_status: published
publisher: American Physical Society
quality_controlled: '1'
scopus_import: '1'
status: public
title: Large-scale quantum approximate optimization on nonplanar graphs with machine
learning noise mitigation
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 6
year: '2024'
...
---
_id: '15118'
abstract:
- lang: eng
text: Cell division in all domains of life requires the orchestration of many proteins,
but in Archaea most of the machinery remains poorly characterized. Here we investigate
the FtsZ-based cell division mechanism in Haloferax volcanii and find proteins
containing photosynthetic reaction centre (PRC) barrel domains that play an essential
role in archaeal cell division. We rename these proteins cell division protein
B 1 (CdpB1) and CdpB2. Depletions and deletions in their respective genes cause
severe cell division defects, generating drastically enlarged cells. Fluorescence
microscopy of tagged FtsZ1, FtsZ2 and SepF in CdpB1 and CdpB2 mutant strains revealed
an unusually disordered divisome that is not organized into a distinct ring-like
structure. Biochemical analysis shows that SepF forms a tripartite complex with
CdpB1/2 and crystal structures suggest that these two proteins might form filaments,
possibly aligning SepF and the FtsZ2 ring during cell division. Overall our results
indicate that PRC-domain proteins play essential roles in FtsZ-based cell division
in Archaea.
acknowledged_ssus:
- _id: LifeSc
acknowledgement: We thank X. Ye (ISTA) for providing the His–SUMO expression plasmid
pSVA13429. pCDB302 was a gift from C. Bahl (Addgene plasmid number 113673; http://n2t.net/addgene:113673;
RRID Addgene_113673). We thank B. Ahsan, G. Sharov, G. Cannone and S. Chen from
the Medical Research Council (MRC) LMB Electron Microscopy Facility for help and
support. We thank Scientific Computing at the MRC LMB for their support. We thank
L. Trübestein and N. Krasnici of the protein service unit of the ISTA Lab Support
Facility for help with the SEC coupled with multi-angle light scattering experiments.
We thank D. Grohmann and R. Reichelt from the Archaea Centre at the University of
Regensburg for providing the P. furiosus cell material. P.N. and S.-V.A. were supported
by a Momentum grant from the Volkswagen (VW) Foundation (grant number 94933). D.K.-C.
and D.B. were supported by the VW Stiftung ‘Life?’ programme (to J.L.; grant number
Az 96727) and by the MRC, as part of UK Research and Innovation (UKRI), MRC file
reference number U105184326 (to J.L.). N.T. and S.G. acknowledge support from the
French Government’s Investissement d’Avenir program, Laboratoire d’Excellence ‘Integrative
Biology of Emerging Infectious Diseases’ (grant number ANR-10-LABX-62-IBEID), and
the computational and storage services (Maestro cluster) provided by the IT department
at Institut Pasteur. M.K. and M.L. were supported by the Austrian Science Fund (FWF)
Stand-Alone P34607. For the purpose of open access, the MRC Laboratory of Molecular
Biology has applied a CC BY public copyright licence to any author accepted manuscript
version arising.
article_processing_charge: No
article_type: original
author:
- first_name: Phillip
full_name: Nußbaum, Phillip
last_name: Nußbaum
- first_name: Danguole
full_name: Kureisaite-Ciziene, Danguole
last_name: Kureisaite-Ciziene
- first_name: Dom
full_name: Bellini, Dom
last_name: Bellini
- first_name: Chris
full_name: Van Der Does, Chris
last_name: Van Der Does
- first_name: Marko
full_name: Kojic, Marko
id: 73e7ecd4-dc85-11ea-9058-88a16394b160
last_name: Kojic
- first_name: Najwa
full_name: Taib, Najwa
last_name: Taib
- first_name: Anna
full_name: Yeates, Anna
last_name: Yeates
- first_name: Maxime
full_name: Tourte, Maxime
last_name: Tourte
- first_name: Simonetta
full_name: Gribaldo, Simonetta
last_name: Gribaldo
- first_name: Martin
full_name: Loose, Martin
id: 462D4284-F248-11E8-B48F-1D18A9856A87
last_name: Loose
orcid: 0000-0001-7309-9724
- first_name: Jan
full_name: Löwe, Jan
last_name: Löwe
- first_name: Sonja Verena
full_name: Albers, Sonja Verena
last_name: Albers
citation:
ama: Nußbaum P, Kureisaite-Ciziene D, Bellini D, et al. Proteins containing photosynthetic
reaction centre domains modulate FtsZ-based archaeal cell division. Nature
Microbiology. 2024;9(3):698-711. doi:10.1038/s41564-024-01600-5
apa: Nußbaum, P., Kureisaite-Ciziene, D., Bellini, D., Van Der Does, C., Kojic,
M., Taib, N., … Albers, S. V. (2024). Proteins containing photosynthetic reaction
centre domains modulate FtsZ-based archaeal cell division. Nature Microbiology.
Springer Nature. https://doi.org/10.1038/s41564-024-01600-5
chicago: Nußbaum, Phillip, Danguole Kureisaite-Ciziene, Dom Bellini, Chris Van Der
Does, Marko Kojic, Najwa Taib, Anna Yeates, et al. “Proteins Containing Photosynthetic
Reaction Centre Domains Modulate FtsZ-Based Archaeal Cell Division.” Nature
Microbiology. Springer Nature, 2024. https://doi.org/10.1038/s41564-024-01600-5.
ieee: P. Nußbaum et al., “Proteins containing photosynthetic reaction centre
domains modulate FtsZ-based archaeal cell division,” Nature Microbiology,
vol. 9, no. 3. Springer Nature, pp. 698–711, 2024.
ista: Nußbaum P, Kureisaite-Ciziene D, Bellini D, Van Der Does C, Kojic M, Taib
N, Yeates A, Tourte M, Gribaldo S, Loose M, Löwe J, Albers SV. 2024. Proteins
containing photosynthetic reaction centre domains modulate FtsZ-based archaeal
cell division. Nature Microbiology. 9(3), 698–711.
mla: Nußbaum, Phillip, et al. “Proteins Containing Photosynthetic Reaction Centre
Domains Modulate FtsZ-Based Archaeal Cell Division.” Nature Microbiology,
vol. 9, no. 3, Springer Nature, 2024, pp. 698–711, doi:10.1038/s41564-024-01600-5.
short: P. Nußbaum, D. Kureisaite-Ciziene, D. Bellini, C. Van Der Does, M. Kojic,
N. Taib, A. Yeates, M. Tourte, S. Gribaldo, M. Loose, J. Löwe, S.V. Albers, Nature
Microbiology 9 (2024) 698–711.
date_created: 2024-03-17T23:00:58Z
date_published: 2024-03-04T00:00:00Z
date_updated: 2024-03-19T07:30:53Z
day: '04'
department:
- _id: MaLo
doi: 10.1038/s41564-024-01600-5
external_id:
pmid:
- '38443575'
intvolume: ' 9'
issue: '3'
language:
- iso: eng
month: '03'
oa_version: None
page: 698-711
pmid: 1
project:
- _id: fc38323b-9c52-11eb-aca3-ff8afb4a011d
grant_number: P34607
name: "Understanding bacterial cell division by in vitro\r\nreconstitution"
publication: Nature Microbiology
publication_identifier:
eissn:
- 2058-5276
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
scopus_import: '1'
status: public
title: Proteins containing photosynthetic reaction centre domains modulate FtsZ-based
archaeal cell division
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 9
year: '2024'
...
---
_id: '15119'
abstract:
- lang: eng
text: In this paper we consider an SPDE where the leading term is a second order
operator with periodic boundary conditions, coefficients which are measurable
in (t,ω) , and Hölder continuous in space. Assuming stochastic parabolicity conditions,
we prove Lp((0,T)×Ω,tκdt;Hσ,q(Td)) -estimates. The main novelty is that we do
not require p=q . Moreover, we allow arbitrary σ∈R and weights in time. Such
mixed regularity estimates play a crucial role in applications to nonlinear SPDEs
which is clear from our previous work. To prove our main results we develop a
general perturbation theory for SPDEs. Moreover, we prove a new result on pointwise
multiplication in spaces with fractional smoothness.
acknowledgement: The first author has been partially supported by the Nachwuchsring
– Network for the promotion of young scientists – at TU Kaiserslautern. The second
author is supported by the VIDI subsidy 639.032.427 of the Netherlands Organisation
for Scientific Research (NWO). The authors thank the anonymous referees and Max
Sauerbrey for careful reading and helpful suggestions.
article_processing_charge: No
article_type: original
author:
- first_name: Antonio
full_name: Agresti, Antonio
id: 673cd0cc-9b9a-11eb-b144-88f30e1fbb72
last_name: Agresti
orcid: 0000-0002-9573-2962
- first_name: Mark
full_name: Veraar, Mark
last_name: Veraar
citation:
ama: Agresti A, Veraar M. Stochastic maximal Lp(Lq)-regularity for second order
systems with periodic boundary conditions. Annales de l’institut Henri Poincare
Probability and Statistics. 2024;60(1):413-430. doi:10.1214/22-AIHP1333
apa: Agresti, A., & Veraar, M. (2024). Stochastic maximal Lp(Lq)-regularity
for second order systems with periodic boundary conditions. Annales de l’institut
Henri Poincare Probability and Statistics. Institute of Mathematical Statistics.
https://doi.org/10.1214/22-AIHP1333
chicago: Agresti, Antonio, and Mark Veraar. “Stochastic Maximal Lp(Lq)-Regularity
for Second Order Systems with Periodic Boundary Conditions.” Annales de l’institut
Henri Poincare Probability and Statistics. Institute of Mathematical Statistics,
2024. https://doi.org/10.1214/22-AIHP1333.
ieee: A. Agresti and M. Veraar, “Stochastic maximal Lp(Lq)-regularity for second
order systems with periodic boundary conditions,” Annales de l’institut Henri
Poincare Probability and Statistics, vol. 60, no. 1. Institute of Mathematical
Statistics, pp. 413–430, 2024.
ista: Agresti A, Veraar M. 2024. Stochastic maximal Lp(Lq)-regularity for second
order systems with periodic boundary conditions. Annales de l’institut Henri Poincare
Probability and Statistics. 60(1), 413–430.
mla: Agresti, Antonio, and Mark Veraar. “Stochastic Maximal Lp(Lq)-Regularity for
Second Order Systems with Periodic Boundary Conditions.” Annales de l’institut
Henri Poincare Probability and Statistics, vol. 60, no. 1, Institute of Mathematical
Statistics, 2024, pp. 413–30, doi:10.1214/22-AIHP1333.
short: A. Agresti, M. Veraar, Annales de l’institut Henri Poincare Probability and
Statistics 60 (2024) 413–430.
date_created: 2024-03-17T23:00:58Z
date_published: 2024-02-01T00:00:00Z
date_updated: 2024-03-19T08:14:17Z
day: '01'
department:
- _id: JuFi
doi: 10.1214/22-AIHP1333
external_id:
arxiv:
- '2106.01274'
intvolume: ' 60'
issue: '1'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.48550/arXiv.2106.01274
month: '02'
oa: 1
oa_version: Preprint
page: 413-430
publication: Annales de l'institut Henri Poincare Probability and Statistics
publication_identifier:
issn:
- 0246-0203
publication_status: published
publisher: Institute of Mathematical Statistics
quality_controlled: '1'
scopus_import: '1'
status: public
title: Stochastic maximal Lp(Lq)-regularity for second order systems with periodic
boundary conditions
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 60
year: '2024'
...
---
_id: '14478'
abstract:
- lang: eng
text: Entire chromosomes are typically only transmitted vertically from one generation
to the next. The horizontal transfer of such chromosomes has long been considered
improbable, yet gained recent support in several pathogenic fungi where it may
affect the fitness or host specificity. To date, it is unknown how these transfers
occur, how common they are and whether they can occur between different species.
In this study, we show multiple independent instances of horizontal transfers
of the same accessory chromosome between two distinct strains of the asexual entomopathogenic
fungusMetarhizium robertsiiduring experimental co-infection
of its insect host, the Argentine ant. Notably, only the one chromosome – but
no other – was transferred from the donor to the recipient strain. The recipient
strain, now harboring the accessory chromosome, exhibited a competitive advantage
under certain host conditions. By phylogenetic analysis we further demonstrate
that the same accessory chromosome was horizontally transferred in a natural environment
betweenM. robertsiiand another congeneric insect pathogen,M.
guizhouense. Hence horizontal chromosome transfer is not limited
to the observed frequent events within species during experimental infections
but also occurs naturally across species. The transferred accessory chromosome
contains genes that might be involved in its preferential horizontal transfer,
encoding putative histones and histone-modifying enzymes, but also putative virulence
factors that may support its establishment. Our study reveals that both intra-
and interspecies horizontal transfer of entire chromosomes is more frequent than
previously assumed, likely representing a not uncommon mechanism for gene exchange.Significance
StatementThe enormous success of bacterial pathogens has
been attributed to their ability to exchange genetic material between one another.
Similarly, in eukaryotes, horizontal transfer of genetic material allowed the
spread of virulence factors across species. The horizontal transfer of whole chromosomes
could be an important pathway for such exchange of genetic material, but little
is known about the origin of transferable chromosomes and how frequently they
are exchanged. Here, we show that the transfer of accessory chromosomes - chromosomes
that are non-essential but may provide fitness benefits - is common during fungal
co-infections and is even possible between distant pathogenic species, highlighting
the importance of horizontal gene transfer via chromosome transfer also for the
evolution and function of eukaryotic pathogens.
acknowledgement: We thank Bernhardt Steinwender, Jorgen Eilenberg, and Nicolai V.
Meyling for the fungal strains. We further thank Chengshu Wang for providing the
short sequencing reads for M. guizhouense ARESF977 he used for his published genome
assembly, and Kristian Ullrich for help in the bioinformatics analysis for methylation
pattern in Nanopore reads, and the VBC and the Max Planck Society for the use of
their sequencing centers. We thank Barbara Milutinović and Hinrich Schulenburg for
discussion, and Tal Dagan and Jens Rolff for comments on a previous version of the
manuscript. Fig. 1A was created with BioRender.com. This study received funding
by the European Research Council under the European Union’s Horizon 2020 Research
and Innovation Programme (No. 771402; EPIDEMICSonCHIP) to S.C. and by the German
Research Foundation (DFG grant HA9263/1-1) to M.H.
article_number: e2316284121
article_processing_charge: Yes (in subscription journal)
article_type: original
author:
- first_name: Michael
full_name: Habig, Michael
last_name: Habig
- first_name: Anna V
full_name: Grasse, Anna V
id: 406F989C-F248-11E8-B48F-1D18A9856A87
last_name: Grasse
- first_name: Judith
full_name: Müller, Judith
last_name: Müller
- first_name: Eva H.
full_name: Stukenbrock, Eva H.
last_name: Stukenbrock
- first_name: Hanna
full_name: Leitner, Hanna
id: 8fc5c6f6-5903-11ec-abad-c83f046253e7
last_name: Leitner
- first_name: Sylvia
full_name: Cremer, Sylvia
id: 2F64EC8C-F248-11E8-B48F-1D18A9856A87
last_name: Cremer
orcid: 0000-0002-2193-3868
citation:
ama: Habig M, Grasse AV, Müller J, Stukenbrock EH, Leitner H, Cremer S. Frequent
horizontal chromosome transfer between asexual fungal insect pathogens. Proceedings
of the National Academy of Sciences of the United States of America. 2024;121(11).
doi:10.1073/pnas.2316284121
apa: Habig, M., Grasse, A. V., Müller, J., Stukenbrock, E. H., Leitner, H., &
Cremer, S. (2024). Frequent horizontal chromosome transfer between asexual fungal
insect pathogens. Proceedings of the National Academy of Sciences of the United
States of America. Proceedings of the National Academy of Sciences. https://doi.org/10.1073/pnas.2316284121
chicago: Habig, Michael, Anna V Grasse, Judith Müller, Eva H. Stukenbrock, Hanna
Leitner, and Sylvia Cremer. “Frequent Horizontal Chromosome Transfer between Asexual
Fungal Insect Pathogens.” Proceedings of the National Academy of Sciences of
the United States of America. Proceedings of the National Academy of Sciences,
2024. https://doi.org/10.1073/pnas.2316284121.
ieee: M. Habig, A. V. Grasse, J. Müller, E. H. Stukenbrock, H. Leitner, and S. Cremer,
“Frequent horizontal chromosome transfer between asexual fungal insect pathogens,”
Proceedings of the National Academy of Sciences of the United States of America,
vol. 121, no. 11. Proceedings of the National Academy of Sciences, 2024.
ista: Habig M, Grasse AV, Müller J, Stukenbrock EH, Leitner H, Cremer S. 2024. Frequent
horizontal chromosome transfer between asexual fungal insect pathogens. Proceedings
of the National Academy of Sciences of the United States of America. 121(11),
e2316284121.
mla: Habig, Michael, et al. “Frequent Horizontal Chromosome Transfer between Asexual
Fungal Insect Pathogens.” Proceedings of the National Academy of Sciences of
the United States of America, vol. 121, no. 11, e2316284121, Proceedings of
the National Academy of Sciences, 2024, doi:10.1073/pnas.2316284121.
short: M. Habig, A.V. Grasse, J. Müller, E.H. Stukenbrock, H. Leitner, S. Cremer,
Proceedings of the National Academy of Sciences of the United States of America
121 (2024).
date_created: 2023-10-31T13:30:00Z
date_published: 2024-03-12T00:00:00Z
date_updated: 2024-03-19T09:07:20Z
day: '12'
ddc:
- '570'
department:
- _id: SyCr
doi: 10.1073/pnas.2316284121
ec_funded: 1
external_id:
pmid:
- '38442176'
file:
- access_level: open_access
checksum: f5e871db617b682edc71fcd08670dc81
content_type: application/pdf
creator: dernst
date_created: 2024-03-19T09:02:57Z
date_updated: 2024-03-19T09:02:57Z
file_id: '15124'
file_name: 2024_PNAS_Habig.pdf
file_size: 5750361
relation: main_file
success: 1
file_date_updated: 2024-03-19T09:02:57Z
has_accepted_license: '1'
intvolume: ' 121'
issue: '11'
language:
- iso: eng
month: '03'
oa: 1
oa_version: Published Version
pmid: 1
project:
- _id: 2649B4DE-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '771402'
name: Epidemics in ant societies on a chip
publication: Proceedings of the National Academy of Sciences of the United States
of America
publication_identifier:
eissn:
- 1091-6490
issn:
- 0027-8424
publication_status: published
publisher: Proceedings of the National Academy of Sciences
quality_controlled: '1'
scopus_import: '1'
status: public
title: Frequent horizontal chromosome transfer between asexual fungal insect pathogens
tmp:
image: /images/cc_by_nc_nd.png
legal_code_url: https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode
name: Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International
(CC BY-NC-ND 4.0)
short: CC BY-NC-ND (4.0)
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 121
year: '2024'
...
---
_id: '10045'
abstract:
- lang: eng
text: "Given a fixed finite metric space (V,μ), the {\\em minimum 0-extension problem},
denoted as 0-Ext[μ], is equivalent to the following optimization problem: minimize
function of the form minx∈Vn∑ifi(xi)+∑ijcijμ(xi,xj) where cij,cvi are given nonnegative
costs and fi:V→R are functions given by fi(xi)=∑v∈Vcviμ(xi,v). The computational
complexity of 0-Ext[μ] has been recently established by Karzanov and by Hirai:
if metric μ is {\\em orientable modular} then 0-Ext[μ] can be solved in polynomial
time, otherwise 0-Ext[μ] is NP-hard. To prove the tractability part, Hirai developed
a theory of discrete convex functions on orientable modular graphs generalizing
several known classes of functions in discrete convex analysis, such as L♮-convex
functions. We consider a more general version of the problem in which unary functions
fi(xi) can additionally have terms of the form cuv;iμ(xi,{u,v}) for {u,v}∈F, where
set F⊆(V2) is fixed. We extend the complexity classification above by providing
an explicit condition on (μ,F) for the problem to be tractable. In order to prove
the tractability part, we generalize Hirai's theory and define a larger class
of discrete convex functions. It covers, in particular, another well-known class
of functions, namely submodular functions on an integer lattice. Finally, we improve
the complexity of Hirai's algorithm for solving 0-Ext on orientable modular graphs.\r\n"
acknowledgement: We thank the anonymous reviewers for their careful reading of our
manuscript and their many insightful comments and suggestions. Open access funding
provided by Institute of Science and Technology (IST Austria).
article_number: '2109.10203'
article_processing_charge: Yes (via OA deal)
article_type: original
author:
- first_name: Martin
full_name: Dvorak, Martin
id: 40ED02A8-C8B4-11E9-A9C0-453BE6697425
last_name: Dvorak
orcid: 0000-0001-5293-214X
- first_name: Vladimir
full_name: Kolmogorov, Vladimir
id: 3D50B0BA-F248-11E8-B48F-1D18A9856A87
last_name: Kolmogorov
citation:
ama: Dvorak M, Kolmogorov V. Generalized minimum 0-extension problem and discrete
convexity. Mathematical Programming. 2024. doi:10.1007/s10107-024-02064-5
apa: Dvorak, M., & Kolmogorov, V. (2024). Generalized minimum 0-extension problem
and discrete convexity. Mathematical Programming. Springer Nature. https://doi.org/10.1007/s10107-024-02064-5
chicago: Dvorak, Martin, and Vladimir Kolmogorov. “Generalized Minimum 0-Extension
Problem and Discrete Convexity.” Mathematical Programming. Springer Nature,
2024. https://doi.org/10.1007/s10107-024-02064-5.
ieee: M. Dvorak and V. Kolmogorov, “Generalized minimum 0-extension problem and
discrete convexity,” Mathematical Programming. Springer Nature, 2024.
ista: Dvorak M, Kolmogorov V. 2024. Generalized minimum 0-extension problem and
discrete convexity. Mathematical Programming., 2109.10203.
mla: Dvorak, Martin, and Vladimir Kolmogorov. “Generalized Minimum 0-Extension Problem
and Discrete Convexity.” Mathematical Programming, 2109.10203, Springer
Nature, 2024, doi:10.1007/s10107-024-02064-5.
short: M. Dvorak, V. Kolmogorov, Mathematical Programming (2024).
date_created: 2021-09-27T10:48:23Z
date_published: 2024-03-07T00:00:00Z
date_updated: 2024-03-19T08:20:31Z
day: '07'
ddc:
- '004'
department:
- _id: GradSch
- _id: VlKo
doi: 10.1007/s10107-024-02064-5
external_id:
arxiv:
- '2109.10203'
file:
- access_level: open_access
checksum: e7e83065f7bc18b9c188bf93b5ca5db6
content_type: application/pdf
creator: mdvorak
date_created: 2021-09-27T10:54:51Z
date_updated: 2021-09-27T10:54:51Z
file_id: '10046'
file_name: Generalized-0-Ext.pdf
file_size: 603672
relation: main_file
success: 1
file_date_updated: 2021-09-27T10:54:51Z
has_accepted_license: '1'
keyword:
- minimum 0-extension problem
- metric labeling problem
- discrete metric spaces
- metric extensions
- computational complexity
- valued constraint satisfaction problems
- discrete convex analysis
- L-convex functions
language:
- iso: eng
month: '03'
oa: 1
oa_version: Preprint
publication: Mathematical Programming
publication_identifier:
eissn:
- 1436-4646
issn:
- 0025-5610
publication_status: epub_ahead
publisher: Springer Nature
quality_controlled: '1'
scopus_import: '1'
status: public
title: Generalized minimum 0-extension problem and discrete convexity
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
year: '2024'
...
---
_id: '15121'
abstract:
- lang: eng
text: We present an auction algorithm using multiplicative instead of constant weight
updates to compute a (1-E)-approximate maximum weight matching (MWM) in a bipartite
graph with n vertices and m edges in time 0(mE-1), beating the running time of
the fastest known approximation algorithm of Duan and Pettie [JACM ’14] that runs
in 0(mE-1 log E-1). Our algorithm is very simple and it can be extended to give
a dynamic data structure that maintains a (1-E)-approximate maximum weight matching
under (1) one-sided vertex deletions (with incident edges) and (2) one-sided vertex
insertions (with incident edges sorted by weight) to the other side. The total
time time used is 0(mE-1), where m is the sum of the number of initially existing
and inserted edges.
acknowledgement: The first author thanks Chandra Chekuri for useful discussions about
this paper. This work was done in part at the University of Vienna. This project
has received funding from the European Research Council (ERC) under the European
Union’s Horizon 2020 research and innovation programme (Grant agreement No. 101019564
“The Design of Modern Fully Dynamic Data Structures (MoDynStruct)” and from the
Austrian Science Fund (FWF) project “Fast Algorithms for a Reactive Network Layer
(ReactNet)”, P 33775-N, with additional funding from the netidee SCIENCE Stiftung,
2020–2024.
article_processing_charge: No
article_type: original
author:
- first_name: Da Wei
full_name: Zheng, Da Wei
last_name: Zheng
- first_name: Monika H
full_name: Henzinger, Monika H
id: 540c9bbd-f2de-11ec-812d-d04a5be85630
last_name: Henzinger
orcid: 0000-0002-5008-6530
citation:
ama: Zheng DW, Henzinger MH. Multiplicative auction algorithm for approximate maximum
weight bipartite matching. Mathematical Programming. 2024. doi:10.1007/s10107-024-02066-3
apa: Zheng, D. W., & Henzinger, M. H. (2024). Multiplicative auction algorithm
for approximate maximum weight bipartite matching. Mathematical Programming.
Springer Nature. https://doi.org/10.1007/s10107-024-02066-3
chicago: Zheng, Da Wei, and Monika H Henzinger. “Multiplicative Auction Algorithm
for Approximate Maximum Weight Bipartite Matching.” Mathematical Programming.
Springer Nature, 2024. https://doi.org/10.1007/s10107-024-02066-3.
ieee: D. W. Zheng and M. H. Henzinger, “Multiplicative auction algorithm for approximate
maximum weight bipartite matching,” Mathematical Programming. Springer
Nature, 2024.
ista: Zheng DW, Henzinger MH. 2024. Multiplicative auction algorithm for approximate
maximum weight bipartite matching. Mathematical Programming.
mla: Zheng, Da Wei, and Monika H. Henzinger. “Multiplicative Auction Algorithm for
Approximate Maximum Weight Bipartite Matching.” Mathematical Programming,
Springer Nature, 2024, doi:10.1007/s10107-024-02066-3.
short: D.W. Zheng, M.H. Henzinger, Mathematical Programming (2024).
date_created: 2024-03-17T23:00:58Z
date_published: 2024-03-06T00:00:00Z
date_updated: 2024-03-19T08:32:32Z
day: '06'
department:
- _id: MoHe
doi: 10.1007/s10107-024-02066-3
ec_funded: 1
external_id:
arxiv:
- '2301.09217'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.48550/arXiv.2301.09217
month: '03'
oa: 1
oa_version: Preprint
project:
- _id: bd9ca328-d553-11ed-ba76-dc4f890cfe62
call_identifier: H2020
grant_number: '101019564'
name: The design and evaluation of modern fully dynamic data structures
- _id: bd9e3a2e-d553-11ed-ba76-8aa684ce17fe
grant_number: 'P33775 '
name: Fast Algorithms for a Reactive Network Layer
publication: Mathematical Programming
publication_identifier:
eissn:
- 1436-4646
issn:
- 0025-5610
publication_status: epub_ahead
publisher: Springer Nature
quality_controlled: '1'
related_material:
record:
- id: '13236'
relation: earlier_version
status: public
scopus_import: '1'
status: public
title: Multiplicative auction algorithm for approximate maximum weight bipartite matching
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
year: '2024'
...
---
_id: '15114'
abstract:
- lang: eng
text: As a key liquid organic hydrogen carrier, investigating the decomposition
of formic acid (HCOOH) on the Pd (1 1 1) transition metal surface is imperative
for harnessing hydrogen energy. Despite a multitude of studies, the major mechanisms
and key intermediates involved in the dehydrogenation process of formic acid remain
a great topic of debate due to ambiguous adsorbate interactions. In this research,
we develop an advanced microkinetic model based on first-principles calculations,
accounting for adsorbate–adsorbate interactions. Our study unveils a comprehensive
mechanism for the Pd (1 1 1) surface, highlighting the significance of coverage
effects in formic acid dehydrogenation. Our findings unequivocally demonstrate
that H coverage on the Pd (1 1 1) surface renders formic acid more susceptible
to decompose into H2 and CO2 through COOH intermediates. Consistent with experimental
results, the selectivity of H2 in the decomposition of formic acid on the Pd (1
1 1) surface approaches 100 %. Considering the influence of H coverage, our kinetic
analysis aligns perfectly with experimental values at a temperature of 373 K.
acknowledgement: The authors acknowledge the financial support from the National Key
Research and Development Project of China (2021YFA1500900, 2022YFE0113800), the
National Natural Science Foundation of China (22141001, U21A20298), Zhejiang Innovation
Team (2017R5203).
article_number: '119959'
article_processing_charge: No
article_type: original
author:
- first_name: Zihao
full_name: Yao, Zihao
last_name: Yao
- first_name: Xu
full_name: Liu, Xu
last_name: Liu
- first_name: Rhys
full_name: Bunting, Rhys
id: 91deeae8-1207-11ec-b130-c194ad5b50c6
last_name: Bunting
orcid: 0000-0001-6928-074X
- first_name: Jianguo
full_name: Wang, Jianguo
last_name: Wang
citation:
ama: 'Yao Z, Liu X, Bunting R, Wang J. Unravelling the reaction mechanism for H2
production via formic acid decomposition over Pd: Coverage-dependent microkinetic
modeling. Chemical Engineering Science. 2024;291. doi:10.1016/j.ces.2024.119959'
apa: 'Yao, Z., Liu, X., Bunting, R., & Wang, J. (2024). Unravelling the reaction
mechanism for H2 production via formic acid decomposition over Pd: Coverage-dependent
microkinetic modeling. Chemical Engineering Science. Elsevier. https://doi.org/10.1016/j.ces.2024.119959'
chicago: 'Yao, Zihao, Xu Liu, Rhys Bunting, and Jianguo Wang. “Unravelling the Reaction
Mechanism for H2 Production via Formic Acid Decomposition over Pd: Coverage-Dependent
Microkinetic Modeling.” Chemical Engineering Science. Elsevier, 2024. https://doi.org/10.1016/j.ces.2024.119959.'
ieee: 'Z. Yao, X. Liu, R. Bunting, and J. Wang, “Unravelling the reaction mechanism
for H2 production via formic acid decomposition over Pd: Coverage-dependent microkinetic
modeling,” Chemical Engineering Science, vol. 291. Elsevier, 2024.'
ista: 'Yao Z, Liu X, Bunting R, Wang J. 2024. Unravelling the reaction mechanism
for H2 production via formic acid decomposition over Pd: Coverage-dependent microkinetic
modeling. Chemical Engineering Science. 291, 119959.'
mla: 'Yao, Zihao, et al. “Unravelling the Reaction Mechanism for H2 Production via
Formic Acid Decomposition over Pd: Coverage-Dependent Microkinetic Modeling.”
Chemical Engineering Science, vol. 291, 119959, Elsevier, 2024, doi:10.1016/j.ces.2024.119959.'
short: Z. Yao, X. Liu, R. Bunting, J. Wang, Chemical Engineering Science 291 (2024).
date_created: 2024-03-17T23:00:57Z
date_published: 2024-03-04T00:00:00Z
date_updated: 2024-03-19T08:47:42Z
day: '04'
department:
- _id: MaIb
doi: 10.1016/j.ces.2024.119959
intvolume: ' 291'
language:
- iso: eng
month: '03'
oa_version: None
publication: Chemical Engineering Science
publication_identifier:
issn:
- 0009-2509
publication_status: epub_ahead
publisher: Elsevier
quality_controlled: '1'
scopus_import: '1'
status: public
title: 'Unravelling the reaction mechanism for H2 production via formic acid decomposition
over Pd: Coverage-dependent microkinetic modeling'
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 291
year: '2024'
...
---
_id: '15116'
abstract:
- lang: eng
text: Water is known to play an important role in collagen self-assembly, but it
is still largely unclear how water–collagen interactions influence the assembly
process and determine the fibril network properties. Here, we use the H2O/D2O
isotope effect on the hydrogen-bond strength in water to investigate the role
of hydration in collagen self-assembly. We dissolve collagen in H2O and D2O and
compare the growth kinetics and the structure of the collagen assemblies formed
in these water isotopomers. Surprisingly, collagen assembly occurs ten times faster
in D2O than in H2O, and collagen in D2O self-assembles into much thinner fibrils,
that form a more inhomogeneous and softer network, with a fourfold reduction in
elastic modulus when compared to H2O. Combining spectroscopic measurements with
atomistic simulations, we show that collagen in D2O is less hydrated than in H2O.
This partial dehydration lowers the enthalpic penalty for water removal and reorganization
at the collagen–water interface, increasing the self-assembly rate and the number
of nucleation centers, leading to thinner fibrils and a softer network. Coarse-grained
simulations show that the acceleration in the initial nucleation rate can be reproduced
by the enhancement of electrostatic interactions. These results show that water
acts as a mediator between collagen monomers, by modulating their interactions
so as to optimize the assembly process and, thus, the final network properties.
We believe that isotopically modulating the hydration of proteins can be a valuable
method to investigate the role of water in protein structural dynamics and protein
self-assembly.
acknowledgement: We thank Dr. Steven Roeters (Aarhus University), Dr. Federica Burla,
and Prof. Dr. Mischa Bonn (Institute for Polymer Research, Mainz, Germany) for the
useful discussions. We thank Dr. Wim Roeterdink and Michiel Hilberts for technical
support. G.H.K. acknowledges financial support by the “BaSyC Building a Synthetic
Cell” Gravitation grant (024.003.019) of The Netherlands Ministry of Education,
Culture and Science (OCW) and The Netherlands Organization for Scientific Research
and from NWO grant OCENW.GROOT.2019.022. This work has received support from the
National Research Foundation of Korea (NRF), funded by the Ministry of Science and
ICT, under Grant No. 2022K1A3A1A04062969. This publication is part of the project
(with Project Number VI.Veni.212.240) of the research programme NWO Talent Programme
Veni 2021, which is financed by the Dutch Research Council (NWO). I.M.I. acknowledges
support from the Sectorplan Bèta & Techniek of the Dutch Government and the Dementia
Research - Synapsis Foundation Switzerland. A.Š. and K.K. acknowledge support from
Royal Society and European Research Council Starting Grant. G. Giubertoni kindly
thanks to the Care4Bones community and the Collagen Café community for reminding
that we do not own the knowledge we create, but it is, rather, a collective resource
intended for the advancement of human progress.
article_number: e2313162121
article_processing_charge: Yes (in subscription journal)
article_type: original
author:
- first_name: Giulia
full_name: Giubertoni, Giulia
last_name: Giubertoni
- first_name: Liru
full_name: Feng, Liru
last_name: Feng
- first_name: Kevin
full_name: Klein, Kevin
last_name: Klein
- first_name: Guido
full_name: Giannetti, Guido
last_name: Giannetti
- first_name: Luco
full_name: Rutten, Luco
last_name: Rutten
- first_name: Yeji
full_name: Choi, Yeji
last_name: Choi
- first_name: Anouk
full_name: Van Der Net, Anouk
last_name: Van Der Net
- first_name: Gerard
full_name: Castro-Linares, Gerard
last_name: Castro-Linares
- first_name: Federico
full_name: Caporaletti, Federico
last_name: Caporaletti
- first_name: Dimitra
full_name: Micha, Dimitra
last_name: Micha
- first_name: Johannes
full_name: Hunger, Johannes
last_name: Hunger
- first_name: Antoine
full_name: Deblais, Antoine
last_name: Deblais
- first_name: Daniel
full_name: Bonn, Daniel
last_name: Bonn
- first_name: Nico
full_name: Sommerdijk, Nico
last_name: Sommerdijk
- first_name: Anđela
full_name: Šarić, Anđela
id: bf63d406-f056-11eb-b41d-f263a6566d8b
last_name: Šarić
orcid: 0000-0002-7854-2139
- first_name: Ioana M.
full_name: Ilie, Ioana M.
last_name: Ilie
- first_name: Gijsje H.
full_name: Koenderink, Gijsje H.
last_name: Koenderink
- first_name: Sander
full_name: Woutersen, Sander
last_name: Woutersen
citation:
ama: Giubertoni G, Feng L, Klein K, et al. Elucidating the role of water in collagen
self-assembly by isotopically modulating collagen hydration. Proceedings of
the National Academy of Sciences of the United States of America. 2024;121(11).
doi:10.1073/pnas.2313162121
apa: Giubertoni, G., Feng, L., Klein, K., Giannetti, G., Rutten, L., Choi, Y., …
Woutersen, S. (2024). Elucidating the role of water in collagen self-assembly
by isotopically modulating collagen hydration. Proceedings of the National
Academy of Sciences of the United States of America. Proceedings of the National
Academy of Sciences. https://doi.org/10.1073/pnas.2313162121
chicago: Giubertoni, Giulia, Liru Feng, Kevin Klein, Guido Giannetti, Luco Rutten,
Yeji Choi, Anouk Van Der Net, et al. “Elucidating the Role of Water in Collagen
Self-Assembly by Isotopically Modulating Collagen Hydration.” Proceedings of
the National Academy of Sciences of the United States of America. Proceedings
of the National Academy of Sciences, 2024. https://doi.org/10.1073/pnas.2313162121.
ieee: G. Giubertoni et al., “Elucidating the role of water in collagen self-assembly
by isotopically modulating collagen hydration,” Proceedings of the National
Academy of Sciences of the United States of America, vol. 121, no. 11. Proceedings
of the National Academy of Sciences, 2024.
ista: Giubertoni G, Feng L, Klein K, Giannetti G, Rutten L, Choi Y, Van Der Net
A, Castro-Linares G, Caporaletti F, Micha D, Hunger J, Deblais A, Bonn D, Sommerdijk
N, Šarić A, Ilie IM, Koenderink GH, Woutersen S. 2024. Elucidating the role of
water in collagen self-assembly by isotopically modulating collagen hydration.
Proceedings of the National Academy of Sciences of the United States of America.
121(11), e2313162121.
mla: Giubertoni, Giulia, et al. “Elucidating the Role of Water in Collagen Self-Assembly
by Isotopically Modulating Collagen Hydration.” Proceedings of the National
Academy of Sciences of the United States of America, vol. 121, no. 11, e2313162121,
Proceedings of the National Academy of Sciences, 2024, doi:10.1073/pnas.2313162121.
short: G. Giubertoni, L. Feng, K. Klein, G. Giannetti, L. Rutten, Y. Choi, A. Van
Der Net, G. Castro-Linares, F. Caporaletti, D. Micha, J. Hunger, A. Deblais, D.
Bonn, N. Sommerdijk, A. Šarić, I.M. Ilie, G.H. Koenderink, S. Woutersen, Proceedings
of the National Academy of Sciences of the United States of America 121 (2024).
date_created: 2024-03-17T23:00:57Z
date_published: 2024-03-12T00:00:00Z
date_updated: 2024-03-19T11:41:32Z
day: '12'
ddc:
- '550'
department:
- _id: AnSa
doi: 10.1073/pnas.2313162121
external_id:
pmid:
- '38451946'
file:
- access_level: open_access
checksum: a3f7fdc29dd9f0a38952ab4e322b3a05
content_type: application/pdf
creator: dernst
date_created: 2024-03-19T10:22:42Z
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file_name: 2024_PNAS_Giubertoni.pdf
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pmid: 1
publication: Proceedings of the National Academy of Sciences of the United States
of America
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eissn:
- 1091-6490
issn:
- 0027-8424
publication_status: published
publisher: Proceedings of the National Academy of Sciences
quality_controlled: '1'
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record:
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relation: research_data
status: public
scopus_import: '1'
status: public
title: Elucidating the role of water in collagen self-assembly by isotopically modulating
collagen hydration
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 121
year: '2024'
...
---
_id: '15117'
abstract:
- lang: eng
text: 'The hippocampal mossy fiber synapse, formed between axons of dentate gyrus
granule cells and dendrites of CA3 pyramidal neurons, is a key synapse in the
trisynaptic circuitry of the hippocampus. Because of its comparatively large size,
this synapse is accessible to direct presynaptic recording, allowing a rigorous
investigation of the biophysical mechanisms of synaptic transmission and plasticity.
Furthermore, because of its placement in the very center of the hippocampal memory
circuit, this synapse seems to be critically involved in several higher network
functions, such as learning, memory, pattern separation, and pattern completion.
Recent work based on new technologies in both nanoanatomy and nanophysiology,
including presynaptic patch-clamp recording, paired recording, super-resolution
light microscopy, and freeze-fracture and “flash-and-freeze” electron microscopy,
has provided new insights into the structure, biophysics, and network function
of this intriguing synapse. This brings us one step closer to answering a fundamental
question in neuroscience: how basic synaptic properties shape higher network computations.'
acknowledgement: "We thank previous students, postdocs, and collaborators, particularly
J. Geiger, and (in alphabetical order) H. Alle, J. Bischofberger, C. Borges-Merjane,
D. Engel, M. Frotscher, S. Hallermann, M. Heckmann, S. Jamrichova, O. Kim, L. Li,
K. Lichter, P. Lin, J. Lübke, Y. Okamoto, C. Pawlu, C. Schmidt-Hieber, N. Spruston,
and N. Vyleta for their outstanding experimental contributions. We also thank P.
Castillo, J. Geiger, T. Sakaba, S. Siegert, T. Vogels, and J. Watson for critically
reading the manuscript, E. Kralli-Beller for text editing, and J. Malikovic and
L. Slomianka for useful discussions. We apologize that, due to space constraints,
not all relevant papers could be cited.\r\nThis project was supported by the European
Research Council (ERC) under the European Union’s Horizon 2020 research and innovation
program (grant agreement 692692, AdG “GIANTSYN”) and the Fonds zur Förderung der
Wissenschaftlichen Forschung (Z 312-B27, Wittgenstein Award; P 36232-B, stand-alone
grant), both to P.J."
article_processing_charge: No
article_type: review
author:
- first_name: David H
full_name: Vandael, David H
id: 3AE48E0A-F248-11E8-B48F-1D18A9856A87
last_name: Vandael
orcid: 0000-0001-7577-1676
- first_name: Peter M
full_name: Jonas, Peter M
id: 353C1B58-F248-11E8-B48F-1D18A9856A87
last_name: Jonas
orcid: 0000-0001-5001-4804
citation:
ama: Vandael DH, Jonas PM. Structure, biophysics, and circuit function of a “giant”
cortical presynaptic terminal. Science. 2024;383(6687):eadg6757. doi:10.1126/science.adg6757
apa: Vandael, D. H., & Jonas, P. M. (2024). Structure, biophysics, and circuit
function of a “giant” cortical presynaptic terminal. Science. AAAS. https://doi.org/10.1126/science.adg6757
chicago: Vandael, David H, and Peter M Jonas. “Structure, Biophysics, and Circuit
Function of a ‘Giant’ Cortical Presynaptic Terminal.” Science. AAAS, 2024.
https://doi.org/10.1126/science.adg6757.
ieee: D. H. Vandael and P. M. Jonas, “Structure, biophysics, and circuit function
of a ‘giant’ cortical presynaptic terminal,” Science, vol. 383, no. 6687.
AAAS, p. eadg6757, 2024.
ista: Vandael DH, Jonas PM. 2024. Structure, biophysics, and circuit function of
a ‘giant’ cortical presynaptic terminal. Science. 383(6687), eadg6757.
mla: Vandael, David H., and Peter M. Jonas. “Structure, Biophysics, and Circuit
Function of a ‘Giant’ Cortical Presynaptic Terminal.” Science, vol. 383,
no. 6687, AAAS, 2024, p. eadg6757, doi:10.1126/science.adg6757.
short: D.H. Vandael, P.M. Jonas, Science 383 (2024) eadg6757.
date_created: 2024-03-17T23:00:57Z
date_published: 2024-03-08T00:00:00Z
date_updated: 2024-03-20T07:42:52Z
day: '08'
department:
- _id: PeJo
doi: 10.1126/science.adg6757
ec_funded: 1
external_id:
pmid:
- '38452088'
intvolume: ' 383'
issue: '6687'
language:
- iso: eng
month: '03'
oa_version: None
page: eadg6757
pmid: 1
project:
- _id: 25B7EB9E-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '692692'
name: Biophysics and circuit function of a giant cortical glumatergic synapse
- _id: 25C5A090-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: Z00312
name: The Wittgenstein Prize
- _id: bd88be38-d553-11ed-ba76-81d5a70a6ef5
grant_number: P36232
name: Mechanisms of GABA release in hippocampal circuits
publication: Science
publication_identifier:
eissn:
- 1095-9203
publication_status: published
publisher: AAAS
quality_controlled: '1'
scopus_import: '1'
status: public
title: Structure, biophysics, and circuit function of a "giant" cortical presynaptic
terminal
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 383
year: '2024'
...
---
_id: '15094'
abstract:
- lang: eng
text: "Point sets, geometric networks, and arrangements of hyperplanes are fundamental
objects in\r\ndiscrete geometry that have captivated mathematicians for centuries,
if not millennia. This\r\nthesis seeks to cast new light on these structures by
illustrating specific instances where a\r\ntopological perspective, specifically
through discrete Morse theory and persistent homology,\r\nprovides valuable insights.\r\n\r\nAt
first glance, the topology of these geometric objects might seem uneventful: point
sets\r\nessentially lack of topology, arrangements of hyperplanes are a decomposition
of Rd, which\r\nis a contractible space, and the topology of a network primarily
involves the enumeration\r\nof connected components and cycles within the network.
However, beneath this apparent\r\nsimplicity, there lies an array of intriguing
structures, a small subset of which will be uncovered\r\nin this thesis.\r\n\r\nFocused
on three case studies, each addressing one of the mentioned objects, this work\r\nwill
showcase connections that intertwine topology with diverse fields such as combinatorial\r\ngeometry,
algorithms and data structures, and emerging applications like spatial biology.\r\n\r\n"
alternative_title:
- ISTA Thesis
article_processing_charge: No
author:
- first_name: Sebastiano
full_name: Cultrera di Montesano, Sebastiano
id: 34D2A09C-F248-11E8-B48F-1D18A9856A87
last_name: Cultrera di Montesano
orcid: 0000-0001-6249-0832
citation:
ama: Cultrera di Montesano S. Persistence and Morse theory for discrete geometric
structures. 2024. doi:10.15479/at:ista:15094
apa: Cultrera di Montesano, S. (2024). Persistence and Morse theory for discrete
geometric structures. Institute of Science and Technology Austria. https://doi.org/10.15479/at:ista:15094
chicago: Cultrera di Montesano, Sebastiano. “Persistence and Morse Theory for Discrete
Geometric Structures.” Institute of Science and Technology Austria, 2024. https://doi.org/10.15479/at:ista:15094.
ieee: S. Cultrera di Montesano, “Persistence and Morse theory for discrete geometric
structures,” Institute of Science and Technology Austria, 2024.
ista: Cultrera di Montesano S. 2024. Persistence and Morse theory for discrete geometric
structures. Institute of Science and Technology Austria.
mla: Cultrera di Montesano, Sebastiano. Persistence and Morse Theory for Discrete
Geometric Structures. Institute of Science and Technology Austria, 2024, doi:10.15479/at:ista:15094.
short: S. Cultrera di Montesano, Persistence and Morse Theory for Discrete Geometric
Structures, Institute of Science and Technology Austria, 2024.
date_created: 2024-03-08T15:28:10Z
date_published: 2024-03-08T00:00:00Z
date_updated: 2024-03-20T09:36:57Z
day: '08'
ddc:
- '514'
- '500'
- '516'
degree_awarded: PhD
department:
- _id: GradSch
- _id: HeEd
doi: 10.15479/at:ista:15094
ec_funded: 1
file:
- access_level: open_access
checksum: 1e468bfa42a7dcf04d89f4dadc621c87
content_type: application/pdf
creator: scultrer
date_created: 2024-03-14T08:55:07Z
date_updated: 2024-03-14T08:55:07Z
file_id: '15112'
file_name: Thesis Sebastiano.pdf
file_size: 4106872
relation: main_file
success: 1
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content_type: application/zip
creator: scultrer
date_created: 2024-03-14T08:56:24Z
date_updated: 2024-03-14T14:14:35Z
file_id: '15113'
file_name: Thesis (1).zip
file_size: 4746234
relation: source_file
file_date_updated: 2024-03-14T14:14:35Z
has_accepted_license: '1'
language:
- iso: eng
license: https://creativecommons.org/licenses/by-nc-sa/4.0/
month: '03'
oa: 1
oa_version: Published Version
page: '108'
project:
- _id: 266A2E9E-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '788183'
name: Alpha Shape Theory Extended
- _id: 268116B8-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: Z00342
name: The Wittgenstein Prize
- _id: 0aa4bc98-070f-11eb-9043-e6fff9c6a316
grant_number: I4887
name: Discretization in Geometry and Dynamics
- _id: 2561EBF4-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: I02979-N35
name: Persistence and stability of geometric complexes
publication_identifier:
issn:
- 2663 - 337X
publication_status: published
publisher: Institute of Science and Technology Austria
related_material:
record:
- id: '11660'
relation: part_of_dissertation
status: public
- id: '11658'
relation: part_of_dissertation
status: public
- id: '13182'
relation: part_of_dissertation
status: public
- id: '15090'
relation: part_of_dissertation
status: public
- id: '15091'
relation: part_of_dissertation
status: public
- id: '15093'
relation: part_of_dissertation
status: public
status: public
supervisor:
- first_name: Herbert
full_name: Edelsbrunner, Herbert
id: 3FB178DA-F248-11E8-B48F-1D18A9856A87
last_name: Edelsbrunner
orcid: 0000-0002-9823-6833
title: Persistence and Morse theory for discrete geometric structures
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: 8b945eb4-e2f2-11eb-945a-df72226e66a9
year: '2024'
...
---
_id: '15093'
abstract:
- lang: eng
text: We present a dynamic data structure for maintaining the persistent homology
of a time series of real numbers. The data structure supports local operations,
including the insertion and deletion of an item and the cutting and concatenating
of lists, each in time O(log n + k), in which n counts the critical items and
k the changes in the augmented persistence diagram. To achieve this, we design
a tailor-made tree structure with an unconventional representation, referred to
as banana tree, which may be useful in its own right.
acknowledgement: The first and second authors are funded by the European Research Council under the
European Union’s Horizon 2020 research and innovation programme, ERC grant no. 788183,“Alpha
Shape Theory Extended (Alpha)”, by the Wittgenstein Prize, FWF grant no. Z 342-N31,
and by the DFG Collaborative Research Center TRR 109, FWF grant no. I 02979-N35.The
third author received funding by the European Research Council under the European
Union’s Horizon 2020research and innovation programme, ERC grant no. 101019564, “The Design of Modern Fully Dynamic DataStructures
(MoDynStruct)”, and by the Austrian Science Fund through the Wittgenstein Prize
with FWF grant no. Z 422-N, and also by FWF grant no. I 5982-N, and by FWF grant
no. P 33775-N, with additional funding from the netidee SCIENCE Stiftung, 2020–2024. The
fourth author is funded by the Vienna Graduate School on Computational Optimization,
FWF project no. W1260-N35.
article_processing_charge: No
author:
- first_name: Sebastiano
full_name: Cultrera di Montesano, Sebastiano
id: 34D2A09C-F248-11E8-B48F-1D18A9856A87
last_name: Cultrera di Montesano
orcid: 0000-0001-6249-0832
- first_name: Herbert
full_name: Edelsbrunner, Herbert
id: 3FB178DA-F248-11E8-B48F-1D18A9856A87
last_name: Edelsbrunner
orcid: 0000-0002-9823-6833
- first_name: Monika H
full_name: Henzinger, Monika H
id: 540c9bbd-f2de-11ec-812d-d04a5be85630
last_name: Henzinger
orcid: 0000-0002-5008-6530
- first_name: Lara
full_name: Ost, Lara
last_name: Ost
citation:
ama: 'Cultrera di Montesano S, Edelsbrunner H, Henzinger MH, Ost L. Dynamically
maintaining the persistent homology of time series. In: Woodruff DP, ed. Proceedings
of the 2024 Annual ACM-SIAM Symposium on Discrete Algorithms (SODA). Society
for Industrial and Applied Mathematics; 2024:243-295. doi:10.1137/1.9781611977912.11'
apa: 'Cultrera di Montesano, S., Edelsbrunner, H., Henzinger, M. H., & Ost,
L. (2024). Dynamically maintaining the persistent homology of time series. In
D. P. Woodruff (Ed.), Proceedings of the 2024 Annual ACM-SIAM Symposium on
Discrete Algorithms (SODA) (pp. 243–295). Alexandria, VA, USA: Society for
Industrial and Applied Mathematics. https://doi.org/10.1137/1.9781611977912.11'
chicago: Cultrera di Montesano, Sebastiano, Herbert Edelsbrunner, Monika H Henzinger,
and Lara Ost. “Dynamically Maintaining the Persistent Homology of Time Series.”
In Proceedings of the 2024 Annual ACM-SIAM Symposium on Discrete Algorithms
(SODA), edited by David P. Woodruff, 243–95. Society for Industrial and Applied
Mathematics, 2024. https://doi.org/10.1137/1.9781611977912.11.
ieee: S. Cultrera di Montesano, H. Edelsbrunner, M. H. Henzinger, and L. Ost, “Dynamically
maintaining the persistent homology of time series,” in Proceedings of the
2024 Annual ACM-SIAM Symposium on Discrete Algorithms (SODA), Alexandria,
VA, USA, 2024, pp. 243–295.
ista: 'Cultrera di Montesano S, Edelsbrunner H, Henzinger MH, Ost L. 2024. Dynamically
maintaining the persistent homology of time series. Proceedings of the 2024 Annual
ACM-SIAM Symposium on Discrete Algorithms (SODA). SODA: Symposium on Discrete
Algorigthms, 243–295.'
mla: Cultrera di Montesano, Sebastiano, et al. “Dynamically Maintaining the Persistent
Homology of Time Series.” Proceedings of the 2024 Annual ACM-SIAM Symposium
on Discrete Algorithms (SODA), edited by David P. Woodruff, Society for Industrial
and Applied Mathematics, 2024, pp. 243–95, doi:10.1137/1.9781611977912.11.
short: S. Cultrera di Montesano, H. Edelsbrunner, M.H. Henzinger, L. Ost, in:, D.P.
Woodruff (Ed.), Proceedings of the 2024 Annual ACM-SIAM Symposium on Discrete
Algorithms (SODA), Society for Industrial and Applied Mathematics, 2024, pp. 243–295.
conference:
end_date: 2024-01-10
location: Alexandria, VA, USA
name: 'SODA: Symposium on Discrete Algorigthms'
start_date: 2024-01-07
date_created: 2024-03-08T10:27:39Z
date_published: 2024-01-04T00:00:00Z
date_updated: 2024-03-20T09:36:56Z
day: '04'
department:
- _id: HeEd
- _id: MoHe
doi: 10.1137/1.9781611977912.11
ec_funded: 1
editor:
- first_name: David P.
full_name: Woodruff, David P.
last_name: Woodruff
external_id:
arxiv:
- '2311.01115'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/2311.01115
month: '01'
oa: 1
oa_version: Preprint
page: 243 - 295
project:
- _id: 266A2E9E-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '788183'
name: Alpha Shape Theory Extended
- _id: 268116B8-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: Z00342
name: The Wittgenstein Prize
- _id: bd9ca328-d553-11ed-ba76-dc4f890cfe62
call_identifier: H2020
grant_number: '101019564'
name: The design and evaluation of modern fully dynamic data structures
- _id: 34def286-11ca-11ed-8bc3-da5948e1613c
grant_number: Z00422
name: Wittgenstein Award - Monika Henzinger
- _id: bd9e3a2e-d553-11ed-ba76-8aa684ce17fe
grant_number: 'P33775 '
name: Fast Algorithms for a Reactive Network Layer
publication: Proceedings of the 2024 Annual ACM-SIAM Symposium on Discrete Algorithms
(SODA)
publication_identifier:
eisbn:
- '9781611977912'
publication_status: published
publisher: Society for Industrial and Applied Mathematics
quality_controlled: '1'
related_material:
record:
- id: '15094'
relation: dissertation_contains
status: public
status: public
title: Dynamically maintaining the persistent homology of time series
type: conference
user_id: 8b945eb4-e2f2-11eb-945a-df72226e66a9
year: '2024'
...
---
_id: '15091'
abstract:
- lang: eng
text: "Motivated by applications in the medical sciences, we study finite chromatic\r\nsets
in Euclidean space from a topological perspective. Based on the persistent\r\nhomology
for images, kernels and cokernels, we design provably stable\r\nhomological quantifiers
that describe the geometric micro- and macro-structure\r\nof how the color classes
mingle. These can be efficiently computed using\r\nchromatic variants of Delaunay
and alpha complexes, and code that does these\r\ncomputations is provided."
article_number: '2212.03128'
article_processing_charge: No
author:
- first_name: Sebastiano
full_name: Cultrera di Montesano, Sebastiano
id: 34D2A09C-F248-11E8-B48F-1D18A9856A87
last_name: Cultrera di Montesano
orcid: 0000-0001-6249-0832
- first_name: Ondrej
full_name: Draganov, Ondrej
id: 2B23F01E-F248-11E8-B48F-1D18A9856A87
last_name: Draganov
- first_name: Herbert
full_name: Edelsbrunner, Herbert
id: 3FB178DA-F248-11E8-B48F-1D18A9856A87
last_name: Edelsbrunner
orcid: 0000-0002-9823-6833
- first_name: Morteza
full_name: Saghafian, Morteza
id: f86f7148-b140-11ec-9577-95435b8df824
last_name: Saghafian
citation:
ama: Cultrera di Montesano S, Draganov O, Edelsbrunner H, Saghafian M. Chromatic
alpha complexes. arXiv.
apa: Cultrera di Montesano, S., Draganov, O., Edelsbrunner, H., & Saghafian,
M. (n.d.). Chromatic alpha complexes. arXiv.
chicago: Cultrera di Montesano, Sebastiano, Ondrej Draganov, Herbert Edelsbrunner,
and Morteza Saghafian. “Chromatic Alpha Complexes.” ArXiv, n.d.
ieee: S. Cultrera di Montesano, O. Draganov, H. Edelsbrunner, and M. Saghafian,
“Chromatic alpha complexes,” arXiv. .
ista: Cultrera di Montesano S, Draganov O, Edelsbrunner H, Saghafian M. Chromatic
alpha complexes. arXiv, 2212.03128.
mla: Cultrera di Montesano, Sebastiano, et al. “Chromatic Alpha Complexes.” ArXiv,
2212.03128.
short: S. Cultrera di Montesano, O. Draganov, H. Edelsbrunner, M. Saghafian, ArXiv
(n.d.).
date_created: 2024-03-08T10:13:59Z
date_published: 2024-02-07T00:00:00Z
date_updated: 2024-03-20T09:36:56Z
day: '07'
department:
- _id: HeEd
external_id:
arxiv:
- '2212.03128'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/2212.03128
month: '02'
oa: 1
oa_version: Preprint
publication: arXiv
publication_status: submitted
related_material:
record:
- id: '15094'
relation: dissertation_contains
status: public
status: public
title: Chromatic alpha complexes
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: preprint
user_id: 8b945eb4-e2f2-11eb-945a-df72226e66a9
year: '2024'
...
---
_id: '15171'
abstract:
- lang: eng
text: The brain’s functionality is developed and maintained through synaptic plasticity.
As synapses undergo plasticity, they also affect each other. The nature of such
‘co-dependency’ is difficult to disentangle experimentally, because multiple synapses
must be monitored simultaneously. To help understand the experimentally observed
phenomena, we introduce a framework that formalizes synaptic co-dependency between
different connection types. The resulting model explains how inhibition can gate
excitatory plasticity while neighboring excitatory–excitatory interactions determine
the strength of long-term potentiation. Furthermore, we show how the interplay
between excitatory and inhibitory synapses can account for the quick rise and
long-term stability of a variety of synaptic weight profiles, such as orientation
tuning and dendritic clustering of co-active synapses. In recurrent neuronal networks,
co-dependent plasticity produces rich and stable motor cortex-like dynamics with
high input sensitivity. Our results suggest an essential role for the neighborly
synaptic interaction during learning, connecting micro-level physiology with network-wide
phenomena.
acknowledgement: We thank C. Currin, B. Podlaski and the members of the Vogels group
for fruitful discussions. E.J.A. and T.P.V. were supported by a Research Project
Grant from the Leverhulme Trust (RPG-2016-446; TPV), a Sir Henry Dale Fellowship
from the Wellcome Trust and the Royal Society (WT100000; T.P.V.), a Wellcome Trust
Senior Research Fellowship (214316/Z/18/Z; T.P.V.) and a European Research Council
Consolidator Grant (SYNAPSEEK, 819603; T.P.V.). For the purpose of open access,
the authors have applied a CC BY public copyright license to any author accepted
manuscript version arising from this submission. Open access funding provided by
University of Basel.
article_processing_charge: Yes (via OA deal)
article_type: original
author:
- first_name: Everton J.
full_name: Agnes, Everton J.
last_name: Agnes
- first_name: Tim P
full_name: Vogels, Tim P
id: CB6FF8D2-008F-11EA-8E08-2637E6697425
last_name: Vogels
orcid: 0000-0003-3295-6181
citation:
ama: Agnes EJ, Vogels TP. Co-dependent excitatory and inhibitory plasticity accounts
for quick, stable and long-lasting memories in biological networks. Nature
Neuroscience. 2024. doi:10.1038/s41593-024-01597-4
apa: Agnes, E. J., & Vogels, T. P. (2024). Co-dependent excitatory and inhibitory
plasticity accounts for quick, stable and long-lasting memories in biological
networks. Nature Neuroscience. Springer Nature. https://doi.org/10.1038/s41593-024-01597-4
chicago: Agnes, Everton J., and Tim P Vogels. “Co-Dependent Excitatory and Inhibitory
Plasticity Accounts for Quick, Stable and Long-Lasting Memories in Biological
Networks.” Nature Neuroscience. Springer Nature, 2024. https://doi.org/10.1038/s41593-024-01597-4.
ieee: E. J. Agnes and T. P. Vogels, “Co-dependent excitatory and inhibitory plasticity
accounts for quick, stable and long-lasting memories in biological networks,”
Nature Neuroscience. Springer Nature, 2024.
ista: Agnes EJ, Vogels TP. 2024. Co-dependent excitatory and inhibitory plasticity
accounts for quick, stable and long-lasting memories in biological networks. Nature
Neuroscience.
mla: Agnes, Everton J., and Tim P. Vogels. “Co-Dependent Excitatory and Inhibitory
Plasticity Accounts for Quick, Stable and Long-Lasting Memories in Biological
Networks.” Nature Neuroscience, Springer Nature, 2024, doi:10.1038/s41593-024-01597-4.
short: E.J. Agnes, T.P. Vogels, Nature Neuroscience (2024).
date_created: 2024-03-24T23:01:00Z
date_published: 2024-03-20T00:00:00Z
date_updated: 2024-03-25T07:04:05Z
day: '20'
department:
- _id: TiVo
doi: 10.1038/s41593-024-01597-4
ec_funded: 1
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.1038/s41593-024-01597-4
month: '03'
oa: 1
oa_version: Published Version
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: Nature Neuroscience
publication_identifier:
eissn:
- 1546-1726
issn:
- 1097-6256
publication_status: epub_ahead
publisher: Springer Nature
quality_controlled: '1'
scopus_import: '1'
status: public
title: Co-dependent excitatory and inhibitory plasticity accounts for quick, stable
and long-lasting memories in biological networks
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
year: '2024'
...
---
_id: '15172'
abstract:
- lang: eng
text: 'We propose a novel approach to concentration for non-independent random variables.
The main idea is to “pretend” that the random variables are independent and pay
a multiplicative price measuring how far they are from actually being independent.
This price is encapsulated in the Hellinger integral between the joint and the
product of the marginals, which is then upper bounded leveraging tensorisation
properties. Our bounds represent a natural generalisation of concentration inequalities
in the presence of dependence: we recover exactly the classical bounds (McDiarmid’s
inequality) when the random variables are independent. Furthermore, in a “large
deviations” regime, we obtain the same decay in the probability as for the independent
case, even when the random variables display non-trivial dependencies. To show
this, we consider a number of applications of interest. First, we provide a bound
for Markov chains with finite state space. Then, we consider the Simple Symmetric
Random Walk, which is a non-contracting Markov chain, and a non-Markovian setting
in which the stochastic process depends on its entire past. To conclude, we propose
an application to Markov Chain Monte Carlo methods, where our approach leads to
an improved lower bound on the minimum burn-in period required to reach a certain
accuracy. In all of these settings, we provide a regime of parameters in which
our bound fares better than what the state of the art can provide.'
article_processing_charge: No
article_type: original
author:
- first_name: Amedeo Roberto
full_name: Esposito, Amedeo Roberto
id: 9583e921-e1ad-11ec-9862-cef099626dc9
last_name: Esposito
- first_name: Marco
full_name: Mondelli, Marco
id: 27EB676C-8706-11E9-9510-7717E6697425
last_name: Mondelli
orcid: 0000-0002-3242-7020
citation:
ama: Esposito AR, Mondelli M. Concentration without independence via information
measures. IEEE Transactions on Information Theory. doi:10.1109/TIT.2024.3367767
apa: Esposito, A. R., & Mondelli, M. (n.d.). Concentration without independence
via information measures. IEEE Transactions on Information Theory. IEEE.
https://doi.org/10.1109/TIT.2024.3367767
chicago: Esposito, Amedeo Roberto, and Marco Mondelli. “Concentration without Independence
via Information Measures.” IEEE Transactions on Information Theory. IEEE,
n.d. https://doi.org/10.1109/TIT.2024.3367767.
ieee: A. R. Esposito and M. Mondelli, “Concentration without independence via information
measures,” IEEE Transactions on Information Theory. IEEE.
ista: Esposito AR, Mondelli M. Concentration without independence via information
measures. IEEE Transactions on Information Theory.
mla: Esposito, Amedeo Roberto, and Marco Mondelli. “Concentration without Independence
via Information Measures.” IEEE Transactions on Information Theory, IEEE,
doi:10.1109/TIT.2024.3367767.
short: A.R. Esposito, M. Mondelli, IEEE Transactions on Information Theory (n.d.).
date_created: 2024-03-24T23:01:00Z
date_published: 2024-02-20T00:00:00Z
date_updated: 2024-03-25T07:15:51Z
day: '20'
department:
- _id: MaMo
doi: 10.1109/TIT.2024.3367767
external_id:
arxiv:
- '2303.07245'
language:
- iso: eng
month: '02'
oa_version: None
project:
- _id: 059876FA-7A3F-11EA-A408-12923DDC885E
name: Prix Lopez-Loretta 2019 - Marco Mondelli
publication: IEEE Transactions on Information Theory
publication_identifier:
eissn:
- 1557-9654
issn:
- 0018-9448
publication_status: inpress
publisher: IEEE
quality_controlled: '1'
related_material:
record:
- id: '14922'
relation: earlier_version
status: public
scopus_import: '1'
status: public
title: Concentration without independence via information measures
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
year: '2024'
...
---
_id: '15170'
abstract:
- lang: eng
text: 'The James Webb Space Telescope is revealing a new population of dust-reddened
broad-line active galactic nuclei (AGN) at redshifts z ≳ 5. Here we present deep
NIRSpec/Prism spectroscopy from the Cycle 1 Treasury program Ultradeep NIRSpec
and NIRCam ObserVations before the Epoch of Reionization (UNCOVER) of 15 AGN candidates
selected to be compact, with red continua in the rest-frame optical but with blue
slopes in the UV. From NIRCam photometry alone, they could have been dominated
by dusty star formation or an AGN. Here we show that the majority of the compact
red sources in UNCOVER are dust-reddened AGN: 60% show definitive evidence for
broad-line Hα with a FWHM > 2000 km s −1, 20% of the current data are inconclusive,
and 20% are brown dwarf stars. We propose an updated photometric criterion to
select red z > 5 AGN that excludes brown dwarfs and is expected to yield >80%
AGN. Remarkably, among all zphot > 5 galaxies with F277W – F444W > 1 in UNCOVER
at least 33% are AGN regardless of compactness, climbing to at least 80% AGN for
sources with F277W – F444W > 1.6. The confirmed AGN have black hole masses of
107–109M⊙. While their UV luminosities (−16 > MUV > −20 AB mag) are low compared
to UV-selected AGN at these epochs, consistent with percent-level scattered AGN
light or low levels of unobscured star formation, the inferred bolometric luminosities
are typical of 107–109M⊙ black holes radiating at ∼10%–40% the Eddington limit.
The number densities are surprisingly high at ∼10−5 Mpc−3 mag−1, 100 times more
common than the faintest UV-selected quasars, while accounting for ∼1% of the
UV-selected galaxies. While their UV faintness suggests they may not contribute
strongly to reionization, their ubiquity poses challenges to models of black hole
growth.'
acknowledgement: J.E.G. and A.D.G acknowledge support from NSF/AAG grant No. 1007094,
and J.E.G. also acknowledges support from NSF/AAG grant No. 1007052. A.Z. acknowledges
support by grant No. 2020750 from the United States-Israel Binational Science Foundation
(BSF) and grant No. 2109066 from the United States National Science Foundation (NSF),
and by the Ministry of Science & Technology of Israel. The Cosmic Dawn Center is
funded by the Danish National Research Foundation (DNRF) under grant No. 140. This
work has received funding from the Swiss State Secretariat for Education, Research
and Innovation (SERI) under contract number MB22.00072, as well as from the Swiss
National Science Foundation (SNSF) through project grant 200020_207349. P.D. acknowledges
support from the NWO grant 016.VIDI.189.162 ("ODIN") and from the European Commission's
and University of Groningen's CO-FUND Rosalind Franklin program. K.G. and T.N. acknowledge
support from Australian Research Council Laureate Fellowship FL180100060. H.A. and
I.C. acknowledge support from CNES, focused on the JWST mission, and the Programme
National Cosmology and Galaxies (PNCG) of CNRS/INSU with INP and IN2P3, cofunded
by CEA and CNES. R.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, Incorporated, under
NASA contract NAS5-26555. The research of C.C.W. is supported by NOIRLab, which
is managed by the Association of Universities for Research in Astronomy (AURA) under
a cooperative agreement with the National Science Foundation. B.W. acknowledges
support from JWST-GO-02561.022-A. A.J.B. acknowledges funding support from NASA/ADAP
grant 21-ADAP21-0187. Support for this work was provided by The Brinson Foundation
through a Brinson Prize Fellowship grant. R.P.N. acknowledges support for this work
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, Incorporated, under NASA contract NAS5-26555.
C.P. thanks Marsha and Ralph Schilling for the generous support of this research.
article_number: '39'
article_processing_charge: Yes
article_type: original
author:
- first_name: Jenny E.
full_name: Greene, Jenny E.
last_name: Greene
- first_name: Ivo
full_name: Labbe, Ivo
last_name: Labbe
- first_name: Andy D.
full_name: Goulding, Andy D.
last_name: Goulding
- first_name: Lukas J.
full_name: Furtak, Lukas J.
last_name: Furtak
- first_name: Iryna
full_name: Chemerynska, Iryna
last_name: Chemerynska
- first_name: Vasily
full_name: Kokorev, Vasily
last_name: Kokorev
- first_name: Pratika
full_name: Dayal, Pratika
last_name: Dayal
- first_name: Marta
full_name: Volonteri, Marta
last_name: Volonteri
- first_name: Christina C.
full_name: Williams, Christina C.
last_name: Williams
- first_name: Bingjie
full_name: Wang, Bingjie
last_name: Wang
- first_name: David J.
full_name: Setton, David J.
last_name: Setton
- first_name: Adam J.
full_name: Burgasser, Adam J.
last_name: Burgasser
- first_name: Rachel
full_name: Bezanson, Rachel
last_name: Bezanson
- first_name: Hakim
full_name: Atek, Hakim
last_name: Atek
- first_name: Gabriel
full_name: Brammer, Gabriel
last_name: Brammer
- first_name: Sam E.
full_name: Cutler, Sam E.
last_name: Cutler
- first_name: Robert
full_name: Feldmann, Robert
last_name: Feldmann
- first_name: Seiji
full_name: Fujimoto, Seiji
last_name: Fujimoto
- first_name: Karl
full_name: Glazebrook, Karl
last_name: Glazebrook
- first_name: Anna
full_name: De Graaff, Anna
last_name: De Graaff
- first_name: Gourav
full_name: Khullar, Gourav
last_name: Khullar
- first_name: Joel
full_name: Leja, Joel
last_name: Leja
- first_name: Danilo
full_name: Marchesini, Danilo
last_name: Marchesini
- first_name: Michael V.
full_name: Maseda, Michael V.
last_name: Maseda
- 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: Tim B.
full_name: Miller, Tim B.
last_name: Miller
- first_name: Rohan P.
full_name: Naidu, Rohan P.
last_name: Naidu
- first_name: Themiya
full_name: Nanayakkara, Themiya
last_name: Nanayakkara
- first_name: Pascal A.
full_name: Oesch, Pascal A.
last_name: Oesch
- first_name: Richard
full_name: Pan, Richard
last_name: Pan
- first_name: Casey
full_name: Papovich, Casey
last_name: Papovich
- first_name: Sedona H.
full_name: Price, Sedona H.
last_name: Price
- first_name: Pieter
full_name: Van Dokkum, Pieter
last_name: Van Dokkum
- first_name: John R.
full_name: Weaver, John R.
last_name: Weaver
- first_name: Katherine E.
full_name: Whitaker, Katherine E.
last_name: Whitaker
- first_name: Adi
full_name: Zitrin, Adi
last_name: Zitrin
citation:
ama: Greene JE, Labbe I, Goulding AD, et al. UNCOVER spectroscopy confirms the surprising
ubiquity of active galactic nuclei in red sources at z > 5. Astrophysical
Journal. 2024;964. doi:10.3847/1538-4357/ad1e5f
apa: Greene, J. E., Labbe, I., Goulding, A. D., Furtak, L. J., Chemerynska, I.,
Kokorev, V., … Zitrin, A. (2024). UNCOVER spectroscopy confirms the surprising
ubiquity of active galactic nuclei in red sources at z > 5. Astrophysical
Journal. IOP Publishing. https://doi.org/10.3847/1538-4357/ad1e5f
chicago: Greene, Jenny E., Ivo Labbe, Andy D. Goulding, Lukas J. Furtak, Iryna Chemerynska,
Vasily Kokorev, Pratika Dayal, et al. “UNCOVER Spectroscopy Confirms the Surprising
Ubiquity of Active Galactic Nuclei in Red Sources at z > 5.” Astrophysical
Journal. IOP Publishing, 2024. https://doi.org/10.3847/1538-4357/ad1e5f.
ieee: J. E. Greene et al., “UNCOVER spectroscopy confirms the surprising
ubiquity of active galactic nuclei in red sources at z > 5,” Astrophysical
Journal, vol. 964. IOP Publishing, 2024.
ista: Greene JE, Labbe I, Goulding AD, Furtak LJ, Chemerynska I, Kokorev V, Dayal
P, Volonteri M, Williams CC, Wang B, Setton DJ, Burgasser AJ, Bezanson R, Atek
H, Brammer G, Cutler SE, Feldmann R, Fujimoto S, Glazebrook K, De Graaff A, Khullar
G, Leja J, Marchesini D, Maseda MV, Matthee JJ, Miller TB, Naidu RP, Nanayakkara
T, Oesch PA, Pan R, Papovich C, Price SH, Van Dokkum P, Weaver JR, Whitaker KE,
Zitrin A. 2024. UNCOVER spectroscopy confirms the surprising ubiquity of active
galactic nuclei in red sources at z > 5. Astrophysical Journal. 964, 39.
mla: Greene, Jenny E., et al. “UNCOVER Spectroscopy Confirms the Surprising Ubiquity
of Active Galactic Nuclei in Red Sources at z > 5.” Astrophysical Journal,
vol. 964, 39, IOP Publishing, 2024, doi:10.3847/1538-4357/ad1e5f.
short: J.E. Greene, I. Labbe, A.D. Goulding, L.J. Furtak, I. Chemerynska, V. Kokorev,
P. Dayal, M. Volonteri, C.C. Williams, B. Wang, D.J. Setton, A.J. Burgasser, R.
Bezanson, H. Atek, G. Brammer, S.E. Cutler, R. Feldmann, S. Fujimoto, K. Glazebrook,
A. De Graaff, G. Khullar, J. Leja, D. Marchesini, M.V. Maseda, J.J. Matthee, T.B.
Miller, R.P. Naidu, T. Nanayakkara, P.A. Oesch, R. Pan, C. Papovich, S.H. Price,
P. Van Dokkum, J.R. Weaver, K.E. Whitaker, A. Zitrin, Astrophysical Journal 964
(2024).
date_created: 2024-03-24T23:00:59Z
date_published: 2024-03-01T00:00:00Z
date_updated: 2024-03-25T08:04:13Z
day: '01'
ddc:
- '550'
department:
- _id: JoMa
doi: 10.3847/1538-4357/ad1e5f
external_id:
arxiv:
- '2309.05714'
file:
- access_level: open_access
checksum: 389a880e176799d5c062ea7cb82d08c9
content_type: application/pdf
creator: dernst
date_created: 2024-03-25T08:02:43Z
date_updated: 2024-03-25T08:02:43Z
file_id: '15176'
file_name: 2024_AstrophysicalJourn_Greene.pdf
file_size: 2700137
relation: main_file
success: 1
file_date_updated: 2024-03-25T08:02:43Z
has_accepted_license: '1'
intvolume: ' 964'
language:
- iso: eng
month: '03'
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: UNCOVER spectroscopy confirms the surprising ubiquity of active galactic nuclei
in red sources at z > 5
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 964
year: '2024'
...
---
_id: '15168'
abstract:
- lang: eng
text: 'A linearly ordered (LO) k-colouring of a hypergraph is a colouring of its
vertices with colours 1, … , k such that each edge contains a unique maximal colour.
Deciding whether an input hypergraph admits LO k-colouring with a fixed number
of colours is NP-complete (and in the special case of graphs, LO colouring coincides
with the usual graph colouring). Here, we investigate the complexity of approximating
the "linearly ordered chromatic number" of a hypergraph. We prove that the following
promise problem is NP-complete: Given a 3-uniform hypergraph, distinguish between
the case that it is LO 3-colourable, and the case that it is not even LO 4-colourable.
We prove this result by a combination of algebraic, topological, and combinatorial
methods, building on and extending a topological approach for studying approximate
graph colouring introduced by Krokhin, Opršal, Wrochna, and Živný (2023).'
acknowledgement: "Marek Filakovský: This research was supported by Charles University
(project PRIMUS/\r\n21/SCI/014), the Austrian Science Fund (FWF project P31312-N35),
and MSCAfellow5_MUNI\r\n(CZ.02.01.01/00/22_010/0003229). Tamio-Vesa Nakajima: This
research was funded by UKRI EP/X024431/1 and by a Clarendon Fund Scholarship. All
data is provided in full in the results section of this paper. Jakub Opršal: This
project has received funding from the European Union’s Horizon 2020 research and
innovation programme under the Marie Skłodowska-Curie Grant Agreement No 101034413.
Uli Wagner: This research was supported by the Austrian Science Fund (FWF project
P31312-N35)."
alternative_title:
- LIPIcs
article_number: '34'
article_processing_charge: No
author:
- first_name: Marek
full_name: Filakovský, Marek
id: 3E8AF77E-F248-11E8-B48F-1D18A9856A87
last_name: Filakovský
- first_name: Tamio Vesa
full_name: Nakajima, Tamio Vesa
last_name: Nakajima
- first_name: Jakub
full_name: Opršal, Jakub
id: ec596741-c539-11ec-b829-c79322a91242
last_name: Opršal
orcid: 0000-0003-1245-3456
- first_name: Gianluca
full_name: Tasinato, Gianluca
id: 0433290C-AF8F-11E9-A4C7-F729E6697425
last_name: Tasinato
- first_name: Uli
full_name: Wagner, Uli
id: 36690CA2-F248-11E8-B48F-1D18A9856A87
last_name: Wagner
orcid: 0000-0002-1494-0568
citation:
ama: 'Filakovský M, Nakajima TV, Opršal J, Tasinato G, Wagner U. Hardness of linearly
ordered 4-colouring of 3-colourable 3-uniform hypergraphs. In: 41st International
Symposium on Theoretical Aspects of Computer Science. Vol 289. Schloss Dagstuhl
- Leibniz-Zentrum für Informatik; 2024. doi:10.4230/LIPIcs.STACS.2024.34'
apa: 'Filakovský, M., Nakajima, T. V., Opršal, J., Tasinato, G., & Wagner, U.
(2024). Hardness of linearly ordered 4-colouring of 3-colourable 3-uniform hypergraphs.
In 41st International Symposium on Theoretical Aspects of Computer Science
(Vol. 289). Clermont-Ferrand, France: Schloss Dagstuhl - Leibniz-Zentrum für Informatik.
https://doi.org/10.4230/LIPIcs.STACS.2024.34'
chicago: Filakovský, Marek, Tamio Vesa Nakajima, Jakub Opršal, Gianluca Tasinato,
and Uli Wagner. “Hardness of Linearly Ordered 4-Colouring of 3-Colourable 3-Uniform
Hypergraphs.” In 41st International Symposium on Theoretical Aspects of Computer
Science, Vol. 289. Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2024.
https://doi.org/10.4230/LIPIcs.STACS.2024.34.
ieee: M. Filakovský, T. V. Nakajima, J. Opršal, G. Tasinato, and U. Wagner, “Hardness
of linearly ordered 4-colouring of 3-colourable 3-uniform hypergraphs,” in 41st
International Symposium on Theoretical Aspects of Computer Science, Clermont-Ferrand,
France, 2024, vol. 289.
ista: 'Filakovský M, Nakajima TV, Opršal J, Tasinato G, Wagner U. 2024. Hardness
of linearly ordered 4-colouring of 3-colourable 3-uniform hypergraphs. 41st International
Symposium on Theoretical Aspects of Computer Science. STACS: Symposium on Theoretical
Aspects of Computer Science, LIPIcs, vol. 289, 34.'
mla: Filakovský, Marek, et al. “Hardness of Linearly Ordered 4-Colouring of 3-Colourable
3-Uniform Hypergraphs.” 41st International Symposium on Theoretical Aspects
of Computer Science, vol. 289, 34, Schloss Dagstuhl - Leibniz-Zentrum für
Informatik, 2024, doi:10.4230/LIPIcs.STACS.2024.34.
short: M. Filakovský, T.V. Nakajima, J. Opršal, G. Tasinato, U. Wagner, in:, 41st
International Symposium on Theoretical Aspects of Computer Science, Schloss Dagstuhl
- Leibniz-Zentrum für Informatik, 2024.
conference:
end_date: 2024-03-14
location: Clermont-Ferrand, France
name: 'STACS: Symposium on Theoretical Aspects of Computer Science'
start_date: 2024-03-12
date_created: 2024-03-24T23:00:59Z
date_published: 2024-03-01T00:00:00Z
date_updated: 2024-03-25T07:45:54Z
day: '01'
ddc:
- '510'
department:
- _id: UlWa
doi: 10.4230/LIPIcs.STACS.2024.34
ec_funded: 1
external_id:
arxiv:
- '2312.12981'
file:
- access_level: open_access
checksum: 0524d4189fd1ed08989546511343edf3
content_type: application/pdf
creator: dernst
date_created: 2024-03-25T07:44:30Z
date_updated: 2024-03-25T07:44:30Z
file_id: '15175'
file_name: 2024_LIPICs_Filakovsky.pdf
file_size: 927290
relation: main_file
success: 1
file_date_updated: 2024-03-25T07:44:30Z
has_accepted_license: '1'
intvolume: ' 289'
language:
- iso: eng
month: '03'
oa: 1
oa_version: Published Version
project:
- _id: 26611F5C-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: P31312
name: Algorithms for Embeddings and Homotopy Theory
- _id: fc2ed2f7-9c52-11eb-aca3-c01059dda49c
call_identifier: H2020
grant_number: '101034413'
name: 'IST-BRIDGE: International postdoctoral program'
publication: 41st International Symposium on Theoretical Aspects of Computer Science
publication_identifier:
eissn:
- 1868-8969
isbn:
- '9783959773119'
publication_status: published
publisher: Schloss Dagstuhl - Leibniz-Zentrum für Informatik
quality_controlled: '1'
scopus_import: '1'
status: public
title: Hardness of linearly ordered 4-colouring of 3-colourable 3-uniform hypergraphs
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: 289
year: '2024'
...
---
_id: '15164'
abstract:
- lang: eng
text: Primary implant stability, which refers to the stability of the implant during
the initial healing period is a crucial factor in determining the long-term success
of the implant and lays the foundation for secondary implant stability achieved
through osseointegration. Factors affecting primary stability include implant
design, surgical technique, and patient-specific factors like bone quality and
morphology. In vivo, the cyclic nature of anatomical loading puts osteosynthesis
locking screws under dynamic loads, which can lead to the formation of micro cracks
and defects that slowly degrade the mechanical connection between the bone and
screw, thus compromising the initial stability and secondary stability of the
implant. Monotonic quasi-static loading used for testing the holding capacity
of implanted screws is not well suited to capture this behavior since it cannot
capture the progressive deterioration of peri‑implant bone at small displacements.
In order to address this issue, this study aims to determine a critical point
of loss of primary implant stability in osteosynthesis locking screws under cyclic
overloading by investigating the evolution of damage, dissipated energy, and permanent
deformation. A custom-made test setup was used to test implanted 2.5 mm locking
screws under cyclic overloading test. For each loading cycle, maximum forces and
displacement were recorded as well as initial and final cycle displacements and
used to calculate damage and energy dissipation evolution. The results of this
study demonstrate that for axial, shear, and mixed loading significant damage
and energy dissipation can be observed at approximately 20 % of the failure force.
Additionally, at this load level, permanent deformations on the screw-bone interface
were found to be in the range of 50 to 150 mm which promotes osseointegration
and secondary implant stability. This research can assist surgeons in making informed
preoperative decisions by providing a better understanding of the critical point
of loss of primary implant stability, thus improving the long-term success of
the implant and overall patient satisfaction.
acknowledgement: The authors declare no conflict of interest related to this study.
This project was funded by the Gesellschaft fuer Forschungsfoerderung Niederoesterreich
m.b.H. Life Science Call 2017 Grant No. LS17004 and Science call 2019 Dissertationen
Grant No. SC19014. No ethical approval was required for this study.
article_number: '104143'
article_processing_charge: Yes (in subscription journal)
article_type: original
author:
- first_name: Juan D.
full_name: Silva-Henao, Juan D.
last_name: Silva-Henao
- first_name: Sophie
full_name: Schober, Sophie
id: 80b0a0ef-4b9f-11ec-b119-8d9d94c4a1d8
last_name: Schober
- first_name: Dieter H.
full_name: Pahr, Dieter H.
last_name: Pahr
- first_name: Andreas G.
full_name: Reisinger, Andreas G.
last_name: Reisinger
citation:
ama: Silva-Henao JD, Schober S, Pahr DH, Reisinger AG. Critical loss of primary
implant stability in osteosynthesis locking screws under cyclic overloading. Medical
Engineering and Physics. 2024;126. doi:10.1016/j.medengphy.2024.104143
apa: Silva-Henao, J. D., Schober, S., Pahr, D. H., & Reisinger, A. G. (2024).
Critical loss of primary implant stability in osteosynthesis locking screws under
cyclic overloading. Medical Engineering and Physics. Elsevier. https://doi.org/10.1016/j.medengphy.2024.104143
chicago: Silva-Henao, Juan D., Sophie Schober, Dieter H. Pahr, and Andreas G. Reisinger.
“Critical Loss of Primary Implant Stability in Osteosynthesis Locking Screws under
Cyclic Overloading.” Medical Engineering and Physics. Elsevier, 2024. https://doi.org/10.1016/j.medengphy.2024.104143.
ieee: J. D. Silva-Henao, S. Schober, D. H. Pahr, and A. G. Reisinger, “Critical
loss of primary implant stability in osteosynthesis locking screws under cyclic
overloading,” Medical Engineering and Physics, vol. 126. Elsevier, 2024.
ista: Silva-Henao JD, Schober S, Pahr DH, Reisinger AG. 2024. Critical loss of primary
implant stability in osteosynthesis locking screws under cyclic overloading. Medical
Engineering and Physics. 126, 104143.
mla: Silva-Henao, Juan D., et al. “Critical Loss of Primary Implant Stability in
Osteosynthesis Locking Screws under Cyclic Overloading.” Medical Engineering
and Physics, vol. 126, 104143, Elsevier, 2024, doi:10.1016/j.medengphy.2024.104143.
short: J.D. Silva-Henao, S. Schober, D.H. Pahr, A.G. Reisinger, Medical Engineering
and Physics 126 (2024).
date_created: 2024-03-24T23:00:58Z
date_published: 2024-04-01T00:00:00Z
date_updated: 2024-03-25T08:31:01Z
day: '01'
ddc:
- '610'
department:
- _id: PreCl
doi: 10.1016/j.medengphy.2024.104143
file:
- access_level: open_access
checksum: 974acbf2731e7382dcf5920ac762e551
content_type: application/pdf
creator: dernst
date_created: 2024-03-25T08:29:52Z
date_updated: 2024-03-25T08:29:52Z
file_id: '15177'
file_name: 2024_MedEngineeringPhysics_SilvaHenao.pdf
file_size: 10039402
relation: main_file
success: 1
file_date_updated: 2024-03-25T08:29:52Z
has_accepted_license: '1'
intvolume: ' 126'
language:
- iso: eng
month: '04'
oa: 1
oa_version: Published Version
publication: Medical Engineering and Physics
publication_identifier:
eissn:
- 1873-4030
issn:
- 1350-4533
publication_status: published
publisher: Elsevier
quality_controlled: '1'
scopus_import: '1'
status: public
title: Critical loss of primary implant stability in osteosynthesis locking screws
under cyclic overloading
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 126
year: '2024'
...
---
_id: '15169'
abstract:
- lang: eng
text: Interpretation of extracellular recordings can be challenging due to the long
range of electric field. This challenge can be mitigated by estimating the current
source density (CSD). Here we introduce kCSD-python, an open Python package implementing
Kernel Current Source Density (kCSD) method and related tools to facilitate CSD
analysis of experimental data and the interpretation of results. We show how to
counter the limitations imposed by noise and assumptions in the method itself.
kCSD-python allows CSD estimation for an arbitrary distribution of electrodes
in 1D, 2D, and 3D, assuming distributions of sources in tissue, a slice, or in
a single cell, and includes a range of diagnostic aids. We demonstrate its features
in a Jupyter Notebook tutorial which illustrates a typical analytical workflow
and main functionalities useful in validating analysis results.
acknowledgement: 'The Python implementation of kCSD was started by Grzegorz Parka
during Google Summer of Code project through the International Neuroinformatics
Coordinating Facility. Jan Mąka implemented the first Python version of skCSD class.
This work was supported by the Polish National Science Centre (2013/08/W/NZ4/00691
to DKW; 2015/17/B/ST7/04123 to DKW). '
article_number: e1011941
article_processing_charge: Yes
article_type: original
author:
- first_name: Chaitanya
full_name: Chintaluri, Chaitanya
id: E4EDB536-3485-11EA-98D2-20AF3DDC885E
last_name: Chintaluri
- first_name: Marta
full_name: Bejtka, Marta
last_name: Bejtka
- first_name: Wladyslaw
full_name: Sredniawa, Wladyslaw
last_name: Sredniawa
- first_name: Michal
full_name: Czerwinski, Michal
last_name: Czerwinski
- first_name: Jakub M.
full_name: Dzik, Jakub M.
last_name: Dzik
- first_name: Joanna
full_name: Jedrzejewska-Szmek, Joanna
last_name: Jedrzejewska-Szmek
- first_name: Daniel K.
full_name: Wojciki, Daniel K.
last_name: Wojciki
citation:
ama: Chintaluri C, Bejtka M, Sredniawa W, et al. kCSD-python, reliable current source
density estimation with quality control. PLoS Computational Biology. 2024;20(3).
doi:10.1371/journal.pcbi.1011941
apa: Chintaluri, C., Bejtka, M., Sredniawa, W., Czerwinski, M., Dzik, J. M., Jedrzejewska-Szmek,
J., & Wojciki, D. K. (2024). kCSD-python, reliable current source density
estimation with quality control. PLoS Computational Biology. Public Library
of Science. https://doi.org/10.1371/journal.pcbi.1011941
chicago: Chintaluri, Chaitanya, Marta Bejtka, Wladyslaw Sredniawa, Michal Czerwinski,
Jakub M. Dzik, Joanna Jedrzejewska-Szmek, and Daniel K. Wojciki. “KCSD-Python,
Reliable Current Source Density Estimation with Quality Control.” PLoS Computational
Biology. Public Library of Science, 2024. https://doi.org/10.1371/journal.pcbi.1011941.
ieee: C. Chintaluri et al., “kCSD-python, reliable current source density
estimation with quality control,” PLoS Computational Biology, vol. 20,
no. 3. Public Library of Science, 2024.
ista: Chintaluri C, Bejtka M, Sredniawa W, Czerwinski M, Dzik JM, Jedrzejewska-Szmek
J, Wojciki DK. 2024. kCSD-python, reliable current source density estimation with
quality control. PLoS Computational Biology. 20(3), e1011941.
mla: Chintaluri, Chaitanya, et al. “KCSD-Python, Reliable Current Source Density
Estimation with Quality Control.” PLoS Computational Biology, vol. 20,
no. 3, e1011941, Public Library of Science, 2024, doi:10.1371/journal.pcbi.1011941.
short: C. Chintaluri, M. Bejtka, W. Sredniawa, M. Czerwinski, J.M. Dzik, J. Jedrzejewska-Szmek,
D.K. Wojciki, PLoS Computational Biology 20 (2024).
date_created: 2024-03-24T23:00:59Z
date_published: 2024-03-14T00:00:00Z
date_updated: 2024-03-25T07:54:23Z
day: '14'
department:
- _id: TiVo
doi: 10.1371/journal.pcbi.1011941
intvolume: ' 20'
issue: '3'
language:
- iso: eng
month: '03'
oa_version: Published Version
publication: PLoS Computational Biology
publication_identifier:
eissn:
- 1553-7358
issn:
- 1553-734X
publication_status: published
publisher: Public Library of Science
quality_controlled: '1'
related_material:
link:
- relation: software
url: https://github.com/Neuroinflab/kCSD-python
scopus_import: '1'
status: public
title: kCSD-python, reliable current source density estimation with quality control
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 20
year: '2024'
...