---
_id: '15358'
abstract:
- lang: eng
text: 'We consider how a population of N haploid individuals responds to directional
selection on standing variation, with no new variation from recombination or mutation.
Individuals have trait values z1,…,zN, which are drawn from a distribution ψ;
the fitness of individual i is proportional to [Formula: see text] . For illustration,
we consider the Laplace and Gaussian distributions, which are parametrised only
by the variance V0, and show that for large N, there is a scaling limit which
depends on a single parameter NV0. When selection is weak relative to drift (NV0≪1),
the variance decreases exponentially at rate 1/N, and the expected ultimate gain
in log fitness (scaled by V0), is just NV0, which is the same as Robertson''s
(1960) prediction for a sexual population. In contrast, when selection is strong
relative to drift (NV0≫1), the ultimate gain can be found by approximating the
establishment of alleles by a branching process in which each allele competes
independently with the population mean and the fittest allele to establish is
certain to fix. Then, if the probability of survival to time t∼1/V0 of an allele
with value z is P(z), with mean P¯, the winning allele is the fittest of NP¯ survivors
drawn from a distribution ψP/P¯. The expected ultimate change is ∼2log(1.15NV0)
for a Gaussian distribution, and ∼-12log0.36NV0-log-log0.36NV0 for a Laplace distribution.
This approach also predicts the variability of the process, and its dynamics;
we show that in the strong selection regime, the expected genetic variance decreases
as ∼t-3 at large times. We discuss how these results may be related to selection
on standing variation that is spread along a linear chromosome.'
acknowledgement: We thank Emmanuel Schertzer and two reviewers for comments on this
manuscript. NB thanks the European Research Council for support via the grant “HaplotypeStructure”
101055327. We would also like to give our sincere thanks to Alison Etheridge for
her insight, inspiration and support over the years.
article_processing_charge: Yes (via OA deal)
article_type: original
author:
- first_name: Nicholas H
full_name: Barton, Nicholas H
id: 4880FE40-F248-11E8-B48F-1D18A9856A87
last_name: Barton
orcid: 0000-0002-8548-5240
- first_name: Himani
full_name: Sachdeva, Himani
id: 42377A0A-F248-11E8-B48F-1D18A9856A87
last_name: Sachdeva
citation:
ama: Barton NH, Sachdeva H. Limits to selection on standing variation in an asexual
population. Theoretical Population Biology. 2024;157:129-137. doi:10.1016/j.tpb.2024.04.001
apa: Barton, N. H., & Sachdeva, H. (2024). Limits to selection on standing variation
in an asexual population. Theoretical Population Biology. Elsevier. https://doi.org/10.1016/j.tpb.2024.04.001
chicago: Barton, Nicholas H, and Himani Sachdeva. “Limits to Selection on Standing
Variation in an Asexual Population.” Theoretical Population Biology. Elsevier,
2024. https://doi.org/10.1016/j.tpb.2024.04.001.
ieee: N. H. Barton and H. Sachdeva, “Limits to selection on standing variation in
an asexual population,” Theoretical Population Biology, vol. 157. Elsevier,
pp. 129–137, 2024.
ista: Barton NH, Sachdeva H. 2024. Limits to selection on standing variation in
an asexual population. Theoretical Population Biology. 157, 129–137.
mla: Barton, Nicholas H., and Himani Sachdeva. “Limits to Selection on Standing
Variation in an Asexual Population.” Theoretical Population Biology, vol.
157, Elsevier, 2024, pp. 129–37, doi:10.1016/j.tpb.2024.04.001.
short: N.H. Barton, H. Sachdeva, Theoretical Population Biology 157 (2024) 129–137.
corr_author: '1'
date_created: 2024-05-05T22:01:03Z
date_published: 2024-06-01T00:00:00Z
date_updated: 2025-09-04T13:56:11Z
day: '01'
ddc:
- '570'
department:
- _id: NiBa
doi: 10.1016/j.tpb.2024.04.001
external_id:
isi:
- '001237016800001'
pmid:
- '38643838'
file:
- access_level: open_access
checksum: 78f36488d24f868d5913624e9c8d88bf
content_type: application/pdf
creator: dernst
date_created: 2024-05-13T08:22:21Z
date_updated: 2024-05-13T08:22:21Z
file_id: '15383'
file_name: 2024_TheorPopulationBiology_Barton.pdf
file_size: 1098292
relation: main_file
success: 1
file_date_updated: 2024-05-13T08:22:21Z
has_accepted_license: '1'
intvolume: ' 157'
isi: 1
language:
- iso: eng
month: '06'
oa: 1
oa_version: Published Version
page: 129-137
pmid: 1
project:
- _id: bd6958e0-d553-11ed-ba76-86eba6a76c00
grant_number: '101055327'
name: Understanding the evolution of continuous genomes
publication: Theoretical Population Biology
publication_identifier:
eissn:
- 1096-0325
issn:
- 0040-5809
publication_status: published
publisher: Elsevier
quality_controlled: '1'
scopus_import: '1'
status: public
title: Limits to selection on standing variation in an asexual population
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: journal_article
user_id: 317138e5-6ab7-11ef-aa6d-ffef3953e345
volume: 157
year: '2024'
...
---
_id: '15360'
abstract:
- lang: eng
text: We investigate superradiant enhancements in the refrigeration performance
of a set of N three-level systems that are collectively coupled to a hot and a
cold thermal reservoir and are additionally subject to collective periodic (circular)
driving. Assuming the system-reservoir coupling to be weak, we explore the regime
of stronger periodic driving strengths by comparing collective weak driving, Floquet-Lindblad,
and Floquet-Redfield master equations. We identify regimes where the power injected
by the periodic driving is used to pump heat from the cold to the hot reservoir
and derive analytic sufficient conditions for them based on a cycle analysis of
the Floquet-Lindblad master equation. In those regimes, we also argue for which
parameters collective enhancements like a quadratic scaling of the cooling current
with N can be expected and support our arguments by numerical simulations.
acknowledgement: "Financial support by the DFG (project ID 278162697 – SFB 1242) is
gratefully acknowledged.\r\n"
article_number: '044050'
article_processing_charge: No
article_type: original
arxiv: 1
author:
- first_name: Dmytro
full_name: Kolisnyk, Dmytro
id: 530a7320-5355-11ee-ae5a-82a46997aaa7
last_name: Kolisnyk
- first_name: Friedemann
full_name: Queißer, Friedemann
last_name: Queißer
- first_name: Gernot
full_name: Schaller, Gernot
last_name: Schaller
- first_name: Ralf
full_name: Schützhold, Ralf
last_name: Schützhold
citation:
ama: Kolisnyk D, Queißer F, Schaller G, Schützhold R. Floquet analysis of a superradiant
many-qutrit refrigerator. Physical Review Applied. 2024;21(4). doi:10.1103/PhysRevApplied.21.044050
apa: Kolisnyk, D., Queißer, F., Schaller, G., & Schützhold, R. (2024). Floquet
analysis of a superradiant many-qutrit refrigerator. Physical Review Applied.
American Physical Society. https://doi.org/10.1103/PhysRevApplied.21.044050
chicago: Kolisnyk, Dmytro, Friedemann Queißer, Gernot Schaller, and Ralf Schützhold.
“Floquet Analysis of a Superradiant Many-Qutrit Refrigerator.” Physical Review
Applied. American Physical Society, 2024. https://doi.org/10.1103/PhysRevApplied.21.044050.
ieee: D. Kolisnyk, F. Queißer, G. Schaller, and R. Schützhold, “Floquet analysis
of a superradiant many-qutrit refrigerator,” Physical Review Applied, vol.
21, no. 4. American Physical Society, 2024.
ista: Kolisnyk D, Queißer F, Schaller G, Schützhold R. 2024. Floquet analysis of
a superradiant many-qutrit refrigerator. Physical Review Applied. 21(4), 044050.
mla: Kolisnyk, Dmytro, et al. “Floquet Analysis of a Superradiant Many-Qutrit Refrigerator.”
Physical Review Applied, vol. 21, no. 4, 044050, American Physical Society,
2024, doi:10.1103/PhysRevApplied.21.044050.
short: D. Kolisnyk, F. Queißer, G. Schaller, R. Schützhold, Physical Review Applied
21 (2024).
date_created: 2024-05-05T22:01:04Z
date_published: 2024-04-26T00:00:00Z
date_updated: 2025-09-04T13:51:06Z
day: '26'
department:
- _id: GradSch
doi: 10.1103/PhysRevApplied.21.044050
external_id:
arxiv:
- '2310.18126'
isi:
- '001226579400001'
intvolume: ' 21'
isi: 1
issue: '4'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.48550/arXiv.2310.18126
month: '04'
oa: 1
oa_version: Preprint
publication: Physical Review Applied
publication_identifier:
eissn:
- 2331-7019
publication_status: published
publisher: American Physical Society
quality_controlled: '1'
scopus_import: '1'
status: public
title: Floquet analysis of a superradiant many-qutrit refrigerator
type: journal_article
user_id: 317138e5-6ab7-11ef-aa6d-ffef3953e345
volume: 21
year: '2024'
...
---
_id: '15361'
abstract:
- lang: eng
text: Bimolecular fluorescence complementation (BiFC) is a powerful tool for studying
protein-protein interactions in living cells. By fusing interacting proteins to
fluorescent protein fragments, BiFC allows visualization of spatial localization
patterns of protein complexes. This method has been adapted to a variety of expression
systems in different organisms and is widely used to study protein interactions
in plant cells. The Agrobacterium-mediated transient expression protocol for BiFC
assays in Nicotiana benthamiana (N. benthamiana) leaf cells is widely used, but
in this chapter, a method for BiFC assay using Arabidopsis thaliana protoplasts
is presented.
acknowledgement: Special thanks to Dr. Marta Zwiewka for the support. Thanks to the
Czech Science Foundation GA 20-20860Y for financial aid and support of A.S.S., respectively.
Thanks go to Core Facility Cellular Imaging (CELLIM), and Plant Sciences Core Facility
of CEITEC Masaryk University is acknowledged for the technical support.
alternative_title:
- Methods in Molecular Biology
article_processing_charge: No
author:
- first_name: Aswathy
full_name: Jayasree, Aswathy
last_name: Jayasree
- first_name: Hymavathi
full_name: Salava, Hymavathi
last_name: Salava
- first_name: Tomasz
full_name: Nodzynski, Tomasz
last_name: Nodzynski
- first_name: Thula
full_name: Sravankumar, Thula
id: 055b7938-0b72-11ef-94eb-d14136011bb5
last_name: Sravankumar
orcid: 0000-0001-6925-6950
citation:
ama: 'Jayasree A, Salava H, Nodzynski T, Sravankumar T. Protein-Protein Interactions
Visualized by Bimolecular Fluorescence Complementation in Arabidopsis thaliana
Protoplasts from Leaf. In: Maghuly F, ed. Plant Functional Genomics. Vol
2787. MIMB. Springer Nature; 2024:305-313. doi:10.1007/978-1-0716-3778-4_21'
apa: Jayasree, A., Salava, H., Nodzynski, T., & Sravankumar, T. (2024). Protein-Protein
Interactions Visualized by Bimolecular Fluorescence Complementation in Arabidopsis
thaliana Protoplasts from Leaf. In F. Maghuly (Ed.), Plant Functional Genomics
(Vol. 2787, pp. 305–313). Springer Nature. https://doi.org/10.1007/978-1-0716-3778-4_21
chicago: Jayasree, Aswathy, Hymavathi Salava, Tomasz Nodzynski, and Thula Sravankumar.
“Protein-Protein Interactions Visualized by Bimolecular Fluorescence Complementation
in Arabidopsis Thaliana Protoplasts from Leaf.” In Plant Functional Genomics,
edited by Fatemeh Maghuly, 2787:305–13. MIMB. Springer Nature, 2024. https://doi.org/10.1007/978-1-0716-3778-4_21.
ieee: A. Jayasree, H. Salava, T. Nodzynski, and T. Sravankumar, “Protein-Protein
Interactions Visualized by Bimolecular Fluorescence Complementation in Arabidopsis
thaliana Protoplasts from Leaf,” in Plant Functional Genomics, vol. 2787,
F. Maghuly, Ed. Springer Nature, 2024, pp. 305–313.
ista: 'Jayasree A, Salava H, Nodzynski T, Sravankumar T. 2024.Protein-Protein Interactions
Visualized by Bimolecular Fluorescence Complementation in Arabidopsis thaliana
Protoplasts from Leaf. In: Plant Functional Genomics. Methods in Molecular Biology,
vol. 2787, 305–313.'
mla: Jayasree, Aswathy, et al. “Protein-Protein Interactions Visualized by Bimolecular
Fluorescence Complementation in Arabidopsis Thaliana Protoplasts from Leaf.” Plant
Functional Genomics, edited by Fatemeh Maghuly, vol. 2787, Springer Nature,
2024, pp. 305–13, doi:10.1007/978-1-0716-3778-4_21.
short: A. Jayasree, H. Salava, T. Nodzynski, T. Sravankumar, in:, F. Maghuly (Ed.),
Plant Functional Genomics, Springer Nature, 2024, pp. 305–313.
date_created: 2024-05-05T22:01:04Z
date_published: 2024-04-25T00:00:00Z
date_updated: 2024-05-06T06:39:10Z
day: '25'
department:
- _id: JiFr
doi: 10.1007/978-1-0716-3778-4_21
editor:
- first_name: Fatemeh
full_name: Maghuly, Fatemeh
last_name: Maghuly
external_id:
pmid:
- '38656499'
intvolume: ' 2787'
language:
- iso: eng
month: '04'
oa_version: None
page: 305-313
pmid: 1
publication: Plant Functional Genomics
publication_identifier:
eissn:
- 1940-6029
isbn:
- '9781071637777'
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
scopus_import: '1'
series_title: MIMB
status: public
title: Protein-Protein Interactions Visualized by Bimolecular Fluorescence Complementation
in Arabidopsis thaliana Protoplasts from Leaf
type: book_chapter
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 2787
year: '2024'
...
---
OA_place: publisher
OA_type: hybrid
_id: '15362'
abstract:
- lang: eng
text: Constitutional heterozygous pathogenic variants in the exonuclease domain
of POLE and POLD1, which affect the proofreading activity of the corresponding
polymerases, cause a cancer predisposition syndrome characterized by increased
risk of gastrointestinal polyposis, colorectal cancer, endometrial cancer and
other tumor types. The generally accepted explanation for the connection between
the disruption of the proofreading activity of polymerases epsilon and delta and
cancer development is through an increase in the somatic mutation rate. Here we
studied an extended family with multiple members heterozygous for the pathogenic
POLD1 variant c.1421T>C p.(Leu474Pro), which segregates with the polyposis and
cancer phenotypes. Through the analysis of mutational patterns of patient-derived
fibroblasts colonies and de novo mutations obtained by parent-offspring comparisons,
we concluded that heterozygous POLD1 L474P just subtly increases the somatic and
germline mutation burden. In contrast, tumors developed in individuals with a
heterozygous mutation in the exonuclease domain of POLD1, including L474P, have
an extremely high mutation rate (>100 mut/Mb) associated with signature SBS10d.
We solved this contradiction through the observation that tumorigenesis involves
somatic inactivation of the wildtype POLD1 allele. These results imply that exonuclease
deficiency of polymerase delta has a recessive effect on mutation rate.
acknowledgement: 'This study was funded by the Spanish Ministry of Science and Innovation
(Agencia Estatal de Investigación), co-funded by FEDER funds a way to build Europe
[PID2020-112595RB-I00 (LV)], Instituto de Salud Carlos III [CIBERONC CB16/12/00234
(LV); ISCIII-AES-2017 PI17/01082 (JLS), PMP22/00064], Government of Catalonia [AGAUR
2021SGR01112, CERCA Program for institutional support (LV)], Scientific Foundation
Asociación Española Contra el Cáncer [AECC Investigador (MT)], Austrian Science
Fund FWF [Grant Agreement # I5127-B (FK)], German Research Foundation DFG [Grant
Agreement # 429960716 (FK)], and ERC Consolidator [Grant Agreement # 771209 ChrFL
(FK)].'
article_processing_charge: No
article_type: original
author:
- first_name: Maria A.
full_name: Andrianova, Maria A.
last_name: Andrianova
- first_name: Vladimir B.
full_name: Seplyarskiy, Vladimir B.
last_name: Seplyarskiy
- first_name: Mariona
full_name: Terradas, Mariona
last_name: Terradas
- first_name: Ana Beatriz
full_name: Sánchez-Heras, Ana Beatriz
last_name: Sánchez-Heras
- first_name: Pilar
full_name: Mur, Pilar
last_name: Mur
- first_name: José Luis
full_name: Soto, José Luis
last_name: Soto
- first_name: Gemma
full_name: Aiza, Gemma
last_name: Aiza
- first_name: Emma
full_name: Borràs, Emma
last_name: Borràs
- first_name: Fyodor
full_name: Kondrashov, Fyodor
id: 44FDEF62-F248-11E8-B48F-1D18A9856A87
last_name: Kondrashov
orcid: 0000-0001-8243-4694
- first_name: Alexey S.
full_name: Kondrashov, Alexey S.
last_name: Kondrashov
- first_name: Georgii A.
full_name: Bazykin, Georgii A.
last_name: Bazykin
- first_name: Laura
full_name: Valle, Laura
last_name: Valle
citation:
ama: Andrianova MA, Seplyarskiy VB, Terradas M, et al. Discovery of recessive effect
of human polymerase δ proofreading deficiency through mutational analysis of POLD1-mutated
normal and cancer cells. European Journal of Human Genetics. 2024;32:837-845.
doi:10.1038/s41431-024-01598-8
apa: Andrianova, M. A., Seplyarskiy, V. B., Terradas, M., Sánchez-Heras, A. B.,
Mur, P., Soto, J. L., … Valle, L. (2024). Discovery of recessive effect of human
polymerase δ proofreading deficiency through mutational analysis of POLD1-mutated
normal and cancer cells. European Journal of Human Genetics. Springer Nature.
https://doi.org/10.1038/s41431-024-01598-8
chicago: Andrianova, Maria A., Vladimir B. Seplyarskiy, Mariona Terradas, Ana Beatriz
Sánchez-Heras, Pilar Mur, José Luis Soto, Gemma Aiza, et al. “Discovery of Recessive
Effect of Human Polymerase δ Proofreading Deficiency through Mutational Analysis
of POLD1-Mutated Normal and Cancer Cells.” European Journal of Human Genetics.
Springer Nature, 2024. https://doi.org/10.1038/s41431-024-01598-8.
ieee: M. A. Andrianova et al., “Discovery of recessive effect of human polymerase
δ proofreading deficiency through mutational analysis of POLD1-mutated normal
and cancer cells,” European Journal of Human Genetics, vol. 32. Springer
Nature, pp. 837–845, 2024.
ista: Andrianova MA, Seplyarskiy VB, Terradas M, Sánchez-Heras AB, Mur P, Soto JL,
Aiza G, Borràs E, Kondrashov F, Kondrashov AS, Bazykin GA, Valle L. 2024. Discovery
of recessive effect of human polymerase δ proofreading deficiency through mutational
analysis of POLD1-mutated normal and cancer cells. European Journal of Human Genetics.
32, 837–845.
mla: Andrianova, Maria A., et al. “Discovery of Recessive Effect of Human Polymerase
δ Proofreading Deficiency through Mutational Analysis of POLD1-Mutated Normal
and Cancer Cells.” European Journal of Human Genetics, vol. 32, Springer
Nature, 2024, pp. 837–45, doi:10.1038/s41431-024-01598-8.
short: M.A. Andrianova, V.B. Seplyarskiy, M. Terradas, A.B. Sánchez-Heras, P. Mur,
J.L. Soto, G. Aiza, E. Borràs, F. Kondrashov, A.S. Kondrashov, G.A. Bazykin, L.
Valle, European Journal of Human Genetics 32 (2024) 837–845.
date_created: 2024-05-05T22:01:04Z
date_published: 2024-07-01T00:00:00Z
date_updated: 2026-04-15T08:51:09Z
day: '01'
ddc:
- '570'
department:
- _id: FyKo
doi: 10.1038/s41431-024-01598-8
ec_funded: 1
external_id:
isi:
- '001207703200001'
pmid:
- '38658779'
file:
- access_level: open_access
checksum: e45fc987f4e9ebafdd0ec4f0e9027de4
content_type: application/pdf
creator: dernst
date_created: 2025-01-09T09:21:25Z
date_updated: 2025-01-09T09:21:25Z
file_id: '18799'
file_name: 2024_EJHG_Andrianova.pdf
file_size: 3060724
relation: main_file
success: 1
file_date_updated: 2025-01-09T09:21:25Z
has_accepted_license: '1'
intvolume: ' 32'
isi: 1
language:
- iso: eng
month: '07'
oa: 1
oa_version: Published Version
page: 837-845
pmid: 1
project:
- _id: 9B767A34-BA93-11EA-9121-9846C619BF3A
grant_number: '429960716'
name: Evolution of Sensorimotor Transformation Across Diptera
- _id: 26580278-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '771209'
name: Characterizing the fitness landscape on population and global scales
- _id: 34e076d6-11ca-11ed-8bc3-aec76c41a181
grant_number: I05127
name: Evolutionary analysis of gene regulation
publication: European Journal of Human Genetics
publication_identifier:
eissn:
- 1476-5438
issn:
- 1018-4813
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
scopus_import: '1'
status: public
title: Discovery of recessive effect of human polymerase δ proofreading deficiency
through mutational analysis of POLD1-mutated normal and cancer cells
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 32
year: '2024'
...
---
_id: '15367'
abstract:
- lang: eng
text: Two-dimensional semiconductor-superconductor heterostructures form the foundation
of numerous nanoscale physical systems. However, measuring the properties of such
heterostructures, and characterizing the semiconductor in-situ is challenging.
A recent experimental study by [Phys. Rev. Lett. 128, 107701 (2022)] was able
to probe the semiconductor within the heterostructure using microwave measurements
of the superfluid density. This work revealed a rapid depletion of superfluid
density in semiconductor, caused by the in-plane magnetic field which in presence
of spin-orbit coupling creates so-called Bogoliubov Fermi surfaces. The experimental
work used a simplified theoretical model that neglected the presence of non-magnetic
disorder in the semiconductor, hence describing the data only qualitatively. Motivated
by experiments, we introduce a theoretical model describing a disordered semiconductor
with strong spin-orbit coupling that is proximitized by a superconductor. Our
model provides specific predictions for the density of states and superfluid density.
Presence of disorder leads to the emergence of a gapless superconducting phase,
that may be viewed as a manifestation of Bogoliubov Fermi surface. When applied
to real experimental data, our model showcases excellent quantitative agreement,
enabling the extraction of material parameters such as mean free path and mobility,
and estimating g-tensor after taking into account the orbital contribution of
magnetic field. Our model can be used to probe in-situ parameters of other superconductor-semiconductor
heterostructures and can be further extended to give access to transport properties.
acknowledgement: "We acknowledge useful discussions with M. Geier, A. Levchenko, B.
Ramshaw, T. Scaffidi, and\r\nJ. Shabani. This research was funded by the Austrian
Science Fund (FWF) F 86.\r\nFor the purpose of open access, authors have applied
a CC BY public copyright licence to any\r\nAuthor Accepted Manuscript version arising
from this submission. MS acknowledges hospitality of KITP supported in part by the
National Science Foundation under Grants No. NSF\r\nPHY-1748958 and PHY-2309135.
APH acknowledges the support of the NOMIS foundation."
article_number: '115'
article_processing_charge: Yes
article_type: original
arxiv: 1
author:
- first_name: Serafim
full_name: Babkin, Serafim
id: 41e64307-6672-11ee-b9ad-cc7a0075a479
last_name: Babkin
orcid: 0009-0003-7382-8036
- first_name: Andrew P
full_name: Higginbotham, Andrew P
id: 4AD6785A-F248-11E8-B48F-1D18A9856A87
last_name: Higginbotham
orcid: 0000-0003-2607-2363
- first_name: Maksym
full_name: Serbyn, Maksym
id: 47809E7E-F248-11E8-B48F-1D18A9856A87
last_name: Serbyn
orcid: 0000-0002-2399-5827
citation:
ama: Babkin S, Higginbotham AP, Serbyn M. Proximity-induced gapless superconductivity
in two-dimensional Rashba semiconductor in magnetic field. SciPost Physics.
2024;16(5). doi:10.21468/scipostphys.16.5.115
apa: Babkin, S., Higginbotham, A. P., & Serbyn, M. (2024). Proximity-induced
gapless superconductivity in two-dimensional Rashba semiconductor in magnetic
field. SciPost Physics. SciPost Foundation. https://doi.org/10.21468/scipostphys.16.5.115
chicago: Babkin, Serafim, Andrew P Higginbotham, and Maksym Serbyn. “Proximity-Induced
Gapless Superconductivity in Two-Dimensional Rashba Semiconductor in Magnetic
Field.” SciPost Physics. SciPost Foundation, 2024. https://doi.org/10.21468/scipostphys.16.5.115.
ieee: S. Babkin, A. P. Higginbotham, and M. Serbyn, “Proximity-induced gapless superconductivity
in two-dimensional Rashba semiconductor in magnetic field,” SciPost Physics,
vol. 16, no. 5. SciPost Foundation, 2024.
ista: Babkin S, Higginbotham AP, Serbyn M. 2024. Proximity-induced gapless superconductivity
in two-dimensional Rashba semiconductor in magnetic field. SciPost Physics. 16(5),
115.
mla: Babkin, Serafim, et al. “Proximity-Induced Gapless Superconductivity in Two-Dimensional
Rashba Semiconductor in Magnetic Field.” SciPost Physics, vol. 16, no.
5, 115, SciPost Foundation, 2024, doi:10.21468/scipostphys.16.5.115.
short: S. Babkin, A.P. Higginbotham, M. Serbyn, SciPost Physics 16 (2024).
corr_author: '1'
date_created: 2024-05-06T09:02:18Z
date_published: 2024-05-01T00:00:00Z
date_updated: 2026-06-03T07:16:00Z
day: '01'
ddc:
- '530'
department:
- _id: MaSe
- _id: AnHi
doi: 10.21468/scipostphys.16.5.115
external_id:
arxiv:
- '2311.09347'
isi:
- '001215855200002'
file:
- access_level: open_access
checksum: f999204856417dcf5a736ac8df432b96
content_type: application/pdf
creator: dernst
date_created: 2024-05-07T12:58:47Z
date_updated: 2024-05-07T12:58:47Z
file_id: '15369'
file_name: 2024_SciPostPhys_Babkin.pdf
file_size: 2733685
relation: main_file
success: 1
file_date_updated: 2024-05-07T12:58:47Z
has_accepted_license: '1'
intvolume: ' 16'
isi: 1
issue: '5'
language:
- iso: eng
month: '05'
oa: 1
oa_version: Published Version
project:
- _id: eb9b30ac-77a9-11ec-83b8-871f581d53d2
name: Protected states of quantum matter
- _id: 34a7f947-11ca-11ed-8bc3-c5dc2bbaae25
grant_number: F8609
name: 'Center for Correlated Quantum Materials and Solid State Quantum Systems: Probing
topology in circuits and quantum materials'
publication: SciPost Physics
publication_identifier:
issn:
- 2542-4653
publication_status: published
publisher: SciPost Foundation
quality_controlled: '1'
scopus_import: '1'
status: public
title: Proximity-induced gapless superconductivity in two-dimensional Rashba semiconductor
in magnetic field
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: journal_article
user_id: 317138e5-6ab7-11ef-aa6d-ffef3953e345
volume: 16
year: '2024'
...
---
DOAJ_listed: '1'
_id: '15372'
abstract:
- lang: eng
text: CRISPR-Cas9 is a powerful tool for genome editing, but the strict requirement
for an NGG protospacer-adjacent motif (PAM) sequence immediately next to the DNA
target limits the number of editable genes. Recently developed Cas9 variants have
been engineered with relaxed PAM requirements, including SpG-Cas9 (SpG) and the
nearly PAM-less SpRY-Cas9 (SpRY). However, the molecular mechanisms of how SpRY
recognizes all potential PAM sequences remains unclear. Here, we combine structural
and biochemical approaches to determine how SpRY interrogates DNA and recognizes
target sites. Divergent PAM sequences can be accommodated through conformational
flexibility within the PAM-interacting region, which facilitates tight binding
to off-target DNA sequences. Nuclease activation occurs ~1000-fold slower than
for Streptococcus pyogenes Cas9, enabling us to directly visualize multiple on-pathway
intermediate states. Experiments with SpG position it as an intermediate enzyme
between Cas9 and SpRY. Our findings shed light on the molecular mechanisms of
PAMless genome editing.
acknowledgement: We thank I. Stohkendl in the Taylor group for insightful discussions.
This work was supported in part by Welch Foundation grants F-1808 (to I.J.F.), and
F-1938 (to D.W.T.), the National Institutes of Health R01GM124141 (to I.J.F.), R01AI110577
(to K.A.J.), and R35GM138348 (to D.W.T.), and a Robert J. Kleberg, Jr. and Helen
C. Kleberg Foundation Medical Research Grant (to D.W.T.). The content is solely
the responsibility of the authors and does not necessarily represent the official
views of the National Institutes of Health.
article_number: '3663'
article_processing_charge: Yes
article_type: original
author:
- first_name: Grace N.
full_name: Hibshman, Grace N.
last_name: Hibshman
- first_name: Jack Peter Kelly
full_name: Bravo, Jack Peter Kelly
id: 96aecfa5-8931-11ee-af30-aa6a5d6eee0e
last_name: Bravo
orcid: 0000-0003-0456-0753
- first_name: Matthew M.
full_name: Hooper, Matthew M.
last_name: Hooper
- first_name: Tyler L.
full_name: Dangerfield, Tyler L.
last_name: Dangerfield
- first_name: Hongshan
full_name: Zhang, Hongshan
last_name: Zhang
- first_name: Ilya J.
full_name: Finkelstein, Ilya J.
last_name: Finkelstein
- first_name: Kenneth A.
full_name: Johnson, Kenneth A.
last_name: Johnson
- first_name: David W.
full_name: Taylor, David W.
last_name: Taylor
citation:
ama: Hibshman GN, Bravo JPK, Hooper MM, et al. Unraveling the mechanisms of PAMless
DNA interrogation by SpRY-Cas9. Nature Communications. 2024;15. doi:10.1038/s41467-024-47830-3
apa: Hibshman, G. N., Bravo, J. P. K., Hooper, M. M., Dangerfield, T. L., Zhang,
H., Finkelstein, I. J., … Taylor, D. W. (2024). Unraveling the mechanisms of PAMless
DNA interrogation by SpRY-Cas9. Nature Communications. Springer Nature.
https://doi.org/10.1038/s41467-024-47830-3
chicago: Hibshman, Grace N., Jack Peter Kelly Bravo, Matthew M. Hooper, Tyler L.
Dangerfield, Hongshan Zhang, Ilya J. Finkelstein, Kenneth A. Johnson, and David
W. Taylor. “Unraveling the Mechanisms of PAMless DNA Interrogation by SpRY-Cas9.”
Nature Communications. Springer Nature, 2024. https://doi.org/10.1038/s41467-024-47830-3.
ieee: G. N. Hibshman et al., “Unraveling the mechanisms of PAMless DNA interrogation
by SpRY-Cas9,” Nature Communications, vol. 15. Springer Nature, 2024.
ista: Hibshman GN, Bravo JPK, Hooper MM, Dangerfield TL, Zhang H, Finkelstein IJ,
Johnson KA, Taylor DW. 2024. Unraveling the mechanisms of PAMless DNA interrogation
by SpRY-Cas9. Nature Communications. 15, 3663.
mla: Hibshman, Grace N., et al. “Unraveling the Mechanisms of PAMless DNA Interrogation
by SpRY-Cas9.” Nature Communications, vol. 15, 3663, Springer Nature, 2024,
doi:10.1038/s41467-024-47830-3.
short: G.N. Hibshman, J.P.K. Bravo, M.M. Hooper, T.L. Dangerfield, H. Zhang, I.J.
Finkelstein, K.A. Johnson, D.W. Taylor, Nature Communications 15 (2024).
corr_author: '1'
date_created: 2024-05-12T22:01:00Z
date_published: 2024-04-30T00:00:00Z
date_updated: 2025-05-14T09:33:21Z
day: '30'
ddc:
- '570'
department:
- _id: JaBr
doi: 10.1038/s41467-024-47830-3
external_id:
pmid:
- '38688943'
file:
- access_level: open_access
checksum: 509c65919067a03ef8ad65c7192cd860
content_type: application/pdf
creator: dernst
date_created: 2024-05-13T11:46:19Z
date_updated: 2024-05-13T11:46:19Z
file_id: '15386'
file_name: 2024_NatureComm_Hibshman.pdf
file_size: 7477013
relation: main_file
success: 1
file_date_updated: 2024-05-13T11:46:19Z
has_accepted_license: '1'
intvolume: ' 15'
language:
- iso: eng
month: '04'
oa: 1
oa_version: Published Version
pmid: 1
publication: Nature Communications
publication_identifier:
eissn:
- 2041-1723
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
scopus_import: '1'
status: public
title: Unraveling the mechanisms of PAMless DNA interrogation by SpRY-Cas9
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 15
year: '2024'
...
---
OA_place: publisher
OA_type: hybrid
_id: '15373'
abstract:
- lang: eng
text: In this article we prove a refined version of the Christensen–Evans theorem
for generators of uniformly continuous GNS-symmetric quantum Markov semigroups.
We use this result to show the existence of GNS-symmetric extensions of GNS-symmetric
quantum Markov semigroups. In particular, this implies that the generators of
GNS-symmetric quantum Markov semigroups on finite-dimensional von Neumann algebra
can be written in the form specified by Alicki's theorem.
article_number: '110475'
article_processing_charge: Yes (via OA deal)
article_type: original
author:
- first_name: Melchior
full_name: Wirth, Melchior
id: 88644358-0A0E-11EA-8FA5-49A33DDC885E
last_name: Wirth
orcid: 0000-0002-0519-4241
citation:
ama: Wirth M. Christensen–Evans theorem and extensions of GNS-symmetric quantum
Markov semigroups. Journal of Functional Analysis. 2024;287(3). doi:10.1016/j.jfa.2024.110475
apa: Wirth, M. (2024). Christensen–Evans theorem and extensions of GNS-symmetric
quantum Markov semigroups. Journal of Functional Analysis. Elsevier. https://doi.org/10.1016/j.jfa.2024.110475
chicago: Wirth, Melchior. “Christensen–Evans Theorem and Extensions of GNS-Symmetric
Quantum Markov Semigroups.” Journal of Functional Analysis. Elsevier, 2024.
https://doi.org/10.1016/j.jfa.2024.110475.
ieee: M. Wirth, “Christensen–Evans theorem and extensions of GNS-symmetric quantum
Markov semigroups,” Journal of Functional Analysis, vol. 287, no. 3. Elsevier,
2024.
ista: Wirth M. 2024. Christensen–Evans theorem and extensions of GNS-symmetric quantum
Markov semigroups. Journal of Functional Analysis. 287(3), 110475.
mla: Wirth, Melchior. “Christensen–Evans Theorem and Extensions of GNS-Symmetric
Quantum Markov Semigroups.” Journal of Functional Analysis, vol. 287, no.
3, 110475, Elsevier, 2024, doi:10.1016/j.jfa.2024.110475.
short: M. Wirth, Journal of Functional Analysis 287 (2024).
corr_author: '1'
date_created: 2024-05-12T22:01:01Z
date_published: 2024-08-01T00:00:00Z
date_updated: 2025-09-08T07:24:07Z
day: '01'
ddc:
- '510'
department:
- _id: JaMa
doi: 10.1016/j.jfa.2024.110475
external_id:
isi:
- '001237916800001'
file:
- access_level: open_access
checksum: 657c9f77dd30bb31ce43a591f58126a2
content_type: application/pdf
creator: dernst
date_created: 2025-01-09T09:33:56Z
date_updated: 2025-01-09T09:33:56Z
file_id: '18802'
file_name: 2024_JourFunctAnalysis_Wirth.pdf
file_size: 503148
relation: main_file
success: 1
file_date_updated: 2025-01-09T09:33:56Z
has_accepted_license: '1'
intvolume: ' 287'
isi: 1
issue: '3'
language:
- iso: eng
month: '08'
oa: 1
oa_version: Published Version
publication: Journal of Functional Analysis
publication_identifier:
eissn:
- 1096-0783
issn:
- 0022-1236
publication_status: published
publisher: Elsevier
quality_controlled: '1'
scopus_import: '1'
status: public
title: Christensen–Evans theorem and extensions of GNS-symmetric quantum Markov semigroups
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: journal_article
user_id: 317138e5-6ab7-11ef-aa6d-ffef3953e345
volume: 287
year: '2024'
...
---
_id: '15374'
abstract:
- lang: eng
text: Clathrin-mediated endocytosis (CME) is an essential process of cargo uptake
operating in all eukaryotes. In animals and yeast, BAR-SH3 domain proteins, endophilins
and amphiphysins, function at the conclusion of CME to recruit factors for vesicle
scission and uncoating. Arabidopsis thaliana contains the BAR-SH3 domain proteins
SH3P1–SH3P3, but their role is poorly understood. Here, we identify SH3Ps as functional
homologs of endophilin/amphiphysin. SH3P1–SH3P3 bind to discrete foci at the plasma
membrane (PM), and SH3P2 recruits late to a subset of clathrin-coated pits. The
SH3P2 PM recruitment pattern is nearly identical to its interactor, a putative
uncoating factor, AUXILIN-LIKE1. Notably, SH3P1–SH3P3 are required for most of
AUXILIN-LIKE1 recruitment to the PM. This indicates a plant-specific modification
of CME, where BAR-SH3 proteins recruit auxilin-like uncoating factors rather than
the uncoating phosphatases, synaptojanins. SH3P1–SH3P3 act redundantly in overall
CME with the plant-specific endocytic adaptor TPLATE complex but not due to an
SH3 domain in its TASH3 subunit.
acknowledgement: 'The authors wish to acknowledge Dr. Daniel van Damme for mRuby3/pDONRP2rP3
and Prof. Qi-Jun Chen for sharing plasmids used for CRISPR-Cas9 mutagenesis. This
work was supported by the Austrian Science Fund (FWF): I 3630-B25.'
article_number: '114195'
article_processing_charge: Yes
article_type: original
author:
- first_name: Maciek
full_name: Adamowski, Maciek
id: 45F536D2-F248-11E8-B48F-1D18A9856A87
last_name: Adamowski
orcid: 0000-0001-6463-5257
- first_name: Marek
full_name: Randuch, Marek
id: 6ac4636d-15b2-11ec-abd3-fb8df79972ae
last_name: Randuch
- first_name: Ivana
full_name: Matijevic, Ivana
id: 83c17ce3-15b2-11ec-abd3-f486545870bd
last_name: Matijevic
- first_name: Madhumitha
full_name: Narasimhan, Madhumitha
id: 44BF24D0-F248-11E8-B48F-1D18A9856A87
last_name: Narasimhan
orcid: 0000-0002-8600-0671
- first_name: Jiří
full_name: Friml, Jiří
id: 4159519E-F248-11E8-B48F-1D18A9856A87
last_name: Friml
orcid: 0000-0002-8302-7596
citation:
ama: Adamowski M, Randuch M, Matijevic I, Narasimhan M, Friml J. SH3Ps recruit auxilin-like
vesicle uncoating factors for clathrin-mediated endocytosis. Cell Reports.
2024;43(5). doi:10.1016/j.celrep.2024.114195
apa: Adamowski, M., Randuch, M., Matijevic, I., Narasimhan, M., & Friml, J.
(2024). SH3Ps recruit auxilin-like vesicle uncoating factors for clathrin-mediated
endocytosis. Cell Reports. Cell Press. https://doi.org/10.1016/j.celrep.2024.114195
chicago: Adamowski, Maciek, Marek Randuch, Ivana Matijevic, Madhumitha Narasimhan,
and Jiří Friml. “SH3Ps Recruit Auxilin-like Vesicle Uncoating Factors for Clathrin-Mediated
Endocytosis.” Cell Reports. Cell Press, 2024. https://doi.org/10.1016/j.celrep.2024.114195.
ieee: M. Adamowski, M. Randuch, I. Matijevic, M. Narasimhan, and J. Friml, “SH3Ps
recruit auxilin-like vesicle uncoating factors for clathrin-mediated endocytosis,”
Cell Reports, vol. 43, no. 5. Cell Press, 2024.
ista: Adamowski M, Randuch M, Matijevic I, Narasimhan M, Friml J. 2024. SH3Ps recruit
auxilin-like vesicle uncoating factors for clathrin-mediated endocytosis. Cell
Reports. 43(5), 114195.
mla: Adamowski, Maciek, et al. “SH3Ps Recruit Auxilin-like Vesicle Uncoating Factors
for Clathrin-Mediated Endocytosis.” Cell Reports, vol. 43, no. 5, 114195,
Cell Press, 2024, doi:10.1016/j.celrep.2024.114195.
short: M. Adamowski, M. Randuch, I. Matijevic, M. Narasimhan, J. Friml, Cell Reports
43 (2024).
corr_author: '1'
date_created: 2024-05-12T22:01:01Z
date_published: 2024-05-28T00:00:00Z
date_updated: 2025-09-08T07:23:07Z
day: '28'
ddc:
- '580'
department:
- _id: JiFr
- _id: MaLo
doi: 10.1016/j.celrep.2024.114195
external_id:
isi:
- '001240362800001'
pmid:
- '38717900'
file:
- access_level: open_access
checksum: a06bb85be4fc765c51554d27ee2da802
content_type: application/pdf
creator: dernst
date_created: 2024-05-13T12:11:22Z
date_updated: 2024-05-13T12:11:22Z
file_id: '15387'
file_name: 2024_CellReports_Adamowski.pdf
file_size: 5698598
relation: main_file
success: 1
file_date_updated: 2024-05-13T12:11:22Z
has_accepted_license: '1'
intvolume: ' 43'
isi: 1
issue: '5'
language:
- iso: eng
month: '05'
oa: 1
oa_version: Published Version
pmid: 1
project:
- _id: 26538374-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: I03630
name: Molecular mechanisms of endocytic cargo recognition in plants
publication: Cell Reports
publication_identifier:
eissn:
- 2211-1247
publication_status: published
publisher: Cell Press
quality_controlled: '1'
scopus_import: '1'
status: public
title: SH3Ps recruit auxilin-like vesicle uncoating factors for clathrin-mediated
endocytosis
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: journal_article
user_id: 317138e5-6ab7-11ef-aa6d-ffef3953e345
volume: 43
year: '2024'
...
---
OA_place: publisher
OA_type: hybrid
_id: '15375'
abstract:
- lang: eng
text: In the eukaryotic nucleus, heterochromatin forms highly condensed, visible
foci known as heterochromatin foci (HF). These HF are enriched with linker histone
H1, a key player in heterochromatin condensation and silencing. However, it is
unknown how H1 aggregates HF and condenses heterochromatin. In this study, we
established that H1 facilitates heterochromatin condensation by enhancing inter-
and intrachromosomal interactions between and within heterochromatic regions of
the Arabidopsis (Arabidopsis thaliana) genome. We demonstrated that H1 drives
HF formation via phase separation, which requires its C-terminal intrinsically
disordered region (C-IDR). A truncated H1 lacking the C-IDR fails to form foci
or recover HF in the h1 mutant background, whereas C-IDR with a short stretch
of the globular domain (18 out of 71 amino acids) is sufficient to rescue both
defects. In addition, C-IDR is essential for H1's roles in regulating nucleosome
repeat length and DNA methylation in Arabidopsis, indicating that phase separation
capability is required for chromatin functions of H1. Our data suggest that bacterial
H1-like proteins, which have been shown to condense DNA, are intrinsically disordered
and capable of mediating phase separation. Therefore, we propose that phase separation
mediated by H1 or H1-like proteins may represent an ancient mechanism for condensing
chromatin and DNA.
acknowledged_ssus:
- _id: Bio
- _id: ScienComp
acknowledgement: "This work was funded by ISTA core support (Y.Y. and X.F.) and grants
from the National Natural Science Foundation of China (31871443 to L.W. and P.L.;
32100417 to L.W.).\r\nWe thank the ISTA Imaging and Optics Facility for assistance
with microscopy and the ISTA Scientific Computing Facility for high-performance
computing resources."
article_processing_charge: Yes (via OA deal)
article_type: original
author:
- first_name: Shengbo
full_name: He, Shengbo
last_name: He
- first_name: Yiming
full_name: Yu, Yiming
id: 318e643b-8b61-11ed-b69e-aafa103ec8dd
last_name: Yu
- first_name: Liang
full_name: Wang, Liang
last_name: Wang
- first_name: Jingyi
full_name: Zhang, Jingyi
last_name: Zhang
- first_name: Zhengyong
full_name: Bai, Zhengyong
last_name: Bai
- first_name: Guohong
full_name: Li, Guohong
last_name: Li
- first_name: Pilong
full_name: Li, Pilong
last_name: Li
- first_name: Xiaoqi
full_name: Feng, Xiaoqi
id: e0164712-22ee-11ed-b12a-d80fcdf35958
last_name: Feng
orcid: 0000-0002-4008-1234
citation:
ama: He S, Yu Y, Wang L, et al. Linker histone H1 drives heterochromatin condensation
via phase separation in Arabidopsis. The Plant Cell. 2024;36(5):1829-1843.
doi:10.1093/plcell/koae034
apa: He, S., Yu, Y., Wang, L., Zhang, J., Bai, Z., Li, G., … Feng, X. (2024). Linker
histone H1 drives heterochromatin condensation via phase separation in Arabidopsis.
The Plant Cell. Oxford University Press. https://doi.org/10.1093/plcell/koae034
chicago: He, Shengbo, Yiming Yu, Liang Wang, Jingyi Zhang, Zhengyong Bai, Guohong
Li, Pilong Li, and Xiaoqi Feng. “Linker Histone H1 Drives Heterochromatin Condensation
via Phase Separation in Arabidopsis.” The Plant Cell. Oxford University
Press, 2024. https://doi.org/10.1093/plcell/koae034.
ieee: S. He et al., “Linker histone H1 drives heterochromatin condensation
via phase separation in Arabidopsis,” The Plant Cell, vol. 36, no. 5. Oxford
University Press, pp. 1829–1843, 2024.
ista: He S, Yu Y, Wang L, Zhang J, Bai Z, Li G, Li P, Feng X. 2024. Linker histone
H1 drives heterochromatin condensation via phase separation in Arabidopsis. The
Plant Cell. 36(5), 1829–1843.
mla: He, Shengbo, et al. “Linker Histone H1 Drives Heterochromatin Condensation
via Phase Separation in Arabidopsis.” The Plant Cell, vol. 36, no. 5, Oxford
University Press, 2024, pp. 1829–43, doi:10.1093/plcell/koae034.
short: S. He, Y. Yu, L. Wang, J. Zhang, Z. Bai, G. Li, P. Li, X. Feng, The Plant
Cell 36 (2024) 1829–1843.
corr_author: '1'
date_created: 2024-05-12T22:01:01Z
date_published: 2024-05-01T00:00:00Z
date_updated: 2025-09-08T07:21:17Z
day: '01'
ddc:
- '580'
department:
- _id: XiFe
doi: 10.1093/plcell/koae034
external_id:
isi:
- '001180817000001'
pmid:
- '38309957'
file:
- access_level: open_access
checksum: eed76c848fe3d8fe9a53943181aaa53c
content_type: application/pdf
creator: dernst
date_created: 2025-04-23T07:43:12Z
date_updated: 2025-04-23T07:43:12Z
file_id: '19611'
file_name: 2024_PlantCell_He.pdf
file_size: 50791962
relation: main_file
success: 1
file_date_updated: 2025-04-23T07:43:12Z
has_accepted_license: '1'
intvolume: ' 36'
isi: 1
issue: '5'
language:
- iso: eng
month: '05'
oa: 1
oa_version: Published Version
page: 1829-1843
pmid: 1
publication: The Plant Cell
publication_identifier:
eissn:
- 1532-298X
publication_status: published
publisher: Oxford University Press
quality_controlled: '1'
scopus_import: '1'
status: public
title: Linker histone H1 drives heterochromatin condensation via phase separation
in Arabidopsis
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: journal_article
user_id: 317138e5-6ab7-11ef-aa6d-ffef3953e345
volume: 36
year: '2024'
...
---
_id: '15376'
abstract:
- lang: eng
text: Sequential decision-making tasks often require satisfaction of multiple, partially-contradictory
objectives. Existing approaches are monolithic, where a single policy fulfills
all objectives. We present auction-based scheduling, a decentralized framework
for multi-objective sequential decision making. Each objective is fulfilled using
a separate and independent policy. Composition of policies is performed at runtime,
where at each step, the policies simultaneously bid from pre-allocated budgets
for the privilege of choosing the next action. The framework allows policies to
be independently created, modified, and replaced. We study path planning problems
on finite graphs with two temporal objectives and present algorithms to synthesize
policies together with bidding policies in a decentralized manner. We consider
three categories of decentralized synthesis problems, parameterized by the assumptions
that the policies make on each other. We identify a class of assumptions called
assume-admissible for which synthesis is always possible for graphs whose every
vertex has at most two outgoing edges.
acknowledgement: This work was supported in part by the ERC project ERC-2020-AdG 101020093
and by ISF grant no. 1679/21.
alternative_title:
- LNCS
article_processing_charge: Yes (in subscription journal)
arxiv: 1
author:
- first_name: Guy
full_name: Avni, Guy
id: 463C8BC2-F248-11E8-B48F-1D18A9856A87
last_name: Avni
orcid: 0000-0001-5588-8287
- first_name: Kaushik
full_name: Mallik, Kaushik
id: 0834ff3c-6d72-11ec-94e0-b5b0a4fb8598
last_name: Mallik
orcid: 0000-0001-9864-7475
- first_name: Suman
full_name: Sadhukhan, Suman
last_name: Sadhukhan
citation:
ama: 'Avni G, Mallik K, Sadhukhan S. Auction-based scheduling. In: 30th International
Conference on Tools and Algorithms for the Construction and Analysis of Systems.
Vol 14572. Springer Nature; 2024:153-172. doi:10.1007/978-3-031-57256-2_8'
apa: 'Avni, G., Mallik, K., & Sadhukhan, S. (2024). Auction-based scheduling.
In 30th International Conference on Tools and Algorithms for the Construction
and Analysis of Systems (Vol. 14572, pp. 153–172). Luxembourg City, Luxembourg:
Springer Nature. https://doi.org/10.1007/978-3-031-57256-2_8'
chicago: Avni, Guy, Kaushik Mallik, and Suman Sadhukhan. “Auction-Based Scheduling.”
In 30th International Conference on Tools and Algorithms for the Construction
and Analysis of Systems, 14572:153–72. Springer Nature, 2024. https://doi.org/10.1007/978-3-031-57256-2_8.
ieee: G. Avni, K. Mallik, and S. Sadhukhan, “Auction-based scheduling,” in 30th
International Conference on Tools and Algorithms for the Construction and Analysis
of Systems, Luxembourg City, Luxembourg, 2024, vol. 14572, pp. 153–172.
ista: 'Avni G, Mallik K, Sadhukhan S. 2024. Auction-based scheduling. 30th International
Conference on Tools and Algorithms for the Construction and Analysis of Systems.
TACAS: Tools and Algorithms for the Construction and Analysis of Systems, LNCS,
vol. 14572, 153–172.'
mla: Avni, Guy, et al. “Auction-Based Scheduling.” 30th International Conference
on Tools and Algorithms for the Construction and Analysis of Systems, vol.
14572, Springer Nature, 2024, pp. 153–72, doi:10.1007/978-3-031-57256-2_8.
short: G. Avni, K. Mallik, S. Sadhukhan, in:, 30th International Conference on Tools
and Algorithms for the Construction and Analysis of Systems, Springer Nature,
2024, pp. 153–172.
conference:
end_date: 2024-04-11
location: Luxembourg City, Luxembourg
name: 'TACAS: Tools and Algorithms for the Construction and Analysis of Systems'
start_date: 2024-04-06
corr_author: '1'
date_created: 2024-05-12T22:01:02Z
date_published: 2024-04-05T00:00:00Z
date_updated: 2025-09-08T07:33:43Z
day: '05'
ddc:
- '000'
department:
- _id: ToHe
doi: 10.1007/978-3-031-57256-2_8
ec_funded: 1
external_id:
arxiv:
- '2310.11798'
isi:
- '001284187100008'
file:
- access_level: open_access
checksum: dbeb123510997886d11925aedbf9c400
content_type: application/pdf
creator: dernst
date_created: 2024-05-22T07:09:24Z
date_updated: 2024-05-22T07:09:24Z
file_id: '15414'
file_name: 2024_LNCS_Avni.pdf
file_size: 508191
relation: main_file
success: 1
file_date_updated: 2024-05-22T07:09:24Z
has_accepted_license: '1'
intvolume: ' 14572'
isi: 1
language:
- iso: eng
month: '04'
oa: 1
oa_version: Published Version
page: 153-172
project:
- _id: 62781420-2b32-11ec-9570-8d9b63373d4d
call_identifier: H2020
grant_number: '101020093'
name: Vigilant Algorithmic Monitoring of Software
publication: 30th International Conference on Tools and Algorithms for the Construction
and Analysis of Systems
publication_identifier:
eissn:
- 1611-3349
isbn:
- '9783031572555'
issn:
- 0302-9743
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
scopus_import: '1'
status: public
title: Auction-based scheduling
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: conference
user_id: 317138e5-6ab7-11ef-aa6d-ffef3953e345
volume: 14572
year: '2024'
...
---
_id: '15377'
abstract:
- lang: eng
text: "We provide an algorithmto solve Rabin and Streett games over graphs\r\nwith
n vertices,m edges, and k colours that runs in ˜O³mn(k!)1+o(1)´time and\r\nO(nk
logk logn) space, where ˜O hides poly-logarithmic factors. Our algorithm\r\nis
an improvement by a super quadratic dependence on k! from the currently\r\nbest
known run time of O³mn2(k!)2+o(1)´, obtained by converting a Rabin\r\ngameinto
a parity game,while simultaneously improving its exponential space\r\nrequirement.\r\nOur
main technical ingredient is a characterisation of progress measures for\r\nRabin
games using colourful trees and a combinatorial construction of succinctlyrepresented,\r\nuniversal
colourful trees. Colourful universal trees are generalisations\r\nof universal
trees used by Jurdzi´nski and Lazi´c (2017) to solve parity\r\ngames, as well
as of Rabin progress measures of Klarlund and Kozen (1991).\r\nOur algorithm for
Rabin games is a progress measure lifting algorithm where\r\nthe lifting is performed
on succinct, colourful, universal trees."
acknowledgement: This work is a part of the project VAMOS that has received funding
from the European Research Council (ERC) under the European Union’s Horizon 2020
research and innovation programme, grant agreements No 101020093. Rupak Majumdar
was partially supported by the DFG project 389792660 TRR 248-CPEC.
alternative_title:
- LNCS
article_processing_charge: Yes (in subscription journal)
arxiv: 1
author:
- first_name: Rupak
full_name: Majumdar, Rupak
last_name: Majumdar
- first_name: Irmak
full_name: Sağlam, Irmak
last_name: Sağlam
- first_name: K. S.
full_name: Thejaswini, K. S.
id: 3807fb92-fdc1-11ee-bb4a-b4d8a431c753
last_name: Thejaswini
citation:
ama: 'Majumdar R, Sağlam I, Thejaswini KS. Rabin games and colourful universal trees.
In: 30th International Conference on Tools and Algorithms for the Construction
and Analysis of Systems. Vol 14572. Springer Nature; 2024:213-231. doi:10.1007/978-3-031-57256-2_11'
apa: Majumdar, R., Sağlam, I., & Thejaswini, K. S. (2024). Rabin games and colourful
universal trees. In 30th International Conference on Tools and Algorithms for
the Construction and Analysis of Systems (Vol. 14572, pp. 213–231). Springer
Nature. https://doi.org/10.1007/978-3-031-57256-2_11
chicago: Majumdar, Rupak, Irmak Sağlam, and K. S. Thejaswini. “Rabin Games and Colourful
Universal Trees.” In 30th International Conference on Tools and Algorithms
for the Construction and Analysis of Systems, 14572:213–31. Springer Nature,
2024. https://doi.org/10.1007/978-3-031-57256-2_11.
ieee: R. Majumdar, I. Sağlam, and K. S. Thejaswini, “Rabin games and colourful universal
trees,” in 30th International Conference on Tools and Algorithms for the Construction
and Analysis of Systems, 2024, vol. 14572, pp. 213–231.
ista: Majumdar R, Sağlam I, Thejaswini KS. 2024. Rabin games and colourful universal
trees. 30th International Conference on Tools and Algorithms for the Construction
and Analysis of Systems. , LNCS, vol. 14572, 213–231.
mla: Majumdar, Rupak, et al. “Rabin Games and Colourful Universal Trees.” 30th
International Conference on Tools and Algorithms for the Construction and Analysis
of Systems, vol. 14572, Springer Nature, 2024, pp. 213–31, doi:10.1007/978-3-031-57256-2_11.
short: R. Majumdar, I. Sağlam, K.S. Thejaswini, in:, 30th International Conference
on Tools and Algorithms for the Construction and Analysis of Systems, Springer
Nature, 2024, pp. 213–231.
corr_author: '1'
date_created: 2024-05-12T22:01:02Z
date_published: 2024-04-06T00:00:00Z
date_updated: 2025-09-08T07:34:49Z
day: '06'
ddc:
- '000'
department:
- _id: ToHe
doi: 10.1007/978-3-031-57256-2_11
ec_funded: 1
external_id:
arxiv:
- '2401.07548'
isi:
- '001284187100011'
file:
- access_level: open_access
checksum: 492be74f69cd6ea42d38681082d0b521
content_type: application/pdf
creator: dernst
date_created: 2024-05-22T07:24:45Z
date_updated: 2024-05-22T07:24:45Z
file_id: '15415'
file_name: 2024_LNCS_Majumdar.pdf
file_size: 462173
relation: main_file
success: 1
file_date_updated: 2024-05-22T07:24:45Z
has_accepted_license: '1'
intvolume: ' 14572'
isi: 1
language:
- iso: eng
month: '04'
oa: 1
oa_version: Published Version
page: 213-231
project:
- _id: 62781420-2b32-11ec-9570-8d9b63373d4d
call_identifier: H2020
grant_number: '101020093'
name: Vigilant Algorithmic Monitoring of Software
publication: 30th International Conference on Tools and Algorithms for the Construction
and Analysis of Systems
publication_identifier:
eissn:
- 1611-3349
isbn:
- '9783031572555'
issn:
- 0302-9743
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
scopus_import: '1'
status: public
title: Rabin games and colourful universal trees
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: conference
user_id: 317138e5-6ab7-11ef-aa6d-ffef3953e345
volume: 14572
year: '2024'
...
---
OA_place: publisher
OA_type: hybrid
_id: '15378'
abstract:
- lang: eng
text: We consider N×N non-Hermitian random matrices of the form X+A, where A is
a general deterministic matrix and N−−√X consists of independent entries with
zero mean, unit variance, and bounded densities. For this ensemble, we prove (i)
a Wegner estimate, i.e. that the local density of eigenvalues is bounded by N1+o(1)
and (ii) that the expected condition number of any bulk eigenvalue is bounded
by N1+o(1); both results are optimal up to the factor No(1). The latter result
complements the very recent matching lower bound obtained in [15] (arXiv:2301.03549)
and improves the N-dependence of the upper bounds in [5,6,32] (arXiv:1906.11819,
arXiv:2005.08930, arXiv:2005.08908). Our main ingredient, a near-optimal lower
tail estimate for the small singular values of X+A−z, is of independent interest.
acknowledgement: László Erdős is partially supported by ERC Advanced Grant “RMTBeyond”
No. 101020331. Hong Chang Ji is supported by ERC Advanced Grant “RMTBeyond” No.
101020331.
article_processing_charge: Yes (via OA deal)
article_type: original
arxiv: 1
author:
- first_name: László
full_name: Erdös, László
id: 4DBD5372-F248-11E8-B48F-1D18A9856A87
last_name: Erdös
orcid: 0000-0001-5366-9603
- first_name: Hong Chang
full_name: Ji, Hong Chang
id: dd216c0a-c1f9-11eb-beaf-e9ea9d2de76d
last_name: Ji
citation:
ama: Erdös L, Ji HC. Wegner estimate and upper bound on the eigenvalue condition
number of non-Hermitian random matrices. Communications on Pure and Applied
Mathematics. 2024;77(9):3785-3840. doi:10.1002/cpa.22201
apa: Erdös, L., & Ji, H. C. (2024). Wegner estimate and upper bound on the eigenvalue
condition number of non-Hermitian random matrices. Communications on Pure and
Applied Mathematics. Wiley. https://doi.org/10.1002/cpa.22201
chicago: Erdös, László, and Hong Chang Ji. “Wegner Estimate and Upper Bound on the
Eigenvalue Condition Number of Non-Hermitian Random Matrices.” Communications
on Pure and Applied Mathematics. Wiley, 2024. https://doi.org/10.1002/cpa.22201.
ieee: L. Erdös and H. C. Ji, “Wegner estimate and upper bound on the eigenvalue
condition number of non-Hermitian random matrices,” Communications on Pure
and Applied Mathematics, vol. 77, no. 9. Wiley, pp. 3785–3840, 2024.
ista: Erdös L, Ji HC. 2024. Wegner estimate and upper bound on the eigenvalue condition
number of non-Hermitian random matrices. Communications on Pure and Applied Mathematics.
77(9), 3785–3840.
mla: Erdös, László, and Hong Chang Ji. “Wegner Estimate and Upper Bound on the Eigenvalue
Condition Number of Non-Hermitian Random Matrices.” Communications on Pure
and Applied Mathematics, vol. 77, no. 9, Wiley, 2024, pp. 3785–840, doi:10.1002/cpa.22201.
short: L. Erdös, H.C. Ji, Communications on Pure and Applied Mathematics 77 (2024)
3785–3840.
corr_author: '1'
date_created: 2024-05-12T22:01:02Z
date_published: 2024-09-01T00:00:00Z
date_updated: 2025-09-08T07:25:47Z
day: '01'
ddc:
- '510'
department:
- _id: LaEr
doi: 10.1002/cpa.22201
ec_funded: 1
external_id:
arxiv:
- '2301.04981'
isi:
- '001217139900001'
file:
- access_level: open_access
checksum: fbcc9cc7bf274f024e4f4afc9c208f96
content_type: application/pdf
creator: dernst
date_created: 2025-01-09T09:36:41Z
date_updated: 2025-01-09T09:36:41Z
file_id: '18803'
file_name: 2024_CommPureApplMath_Erdoes.pdf
file_size: 566963
relation: main_file
success: 1
file_date_updated: 2025-01-09T09:36:41Z
has_accepted_license: '1'
intvolume: ' 77'
isi: 1
issue: '9'
language:
- iso: eng
month: '09'
oa: 1
oa_version: Published Version
page: 3785-3840
project:
- _id: 62796744-2b32-11ec-9570-940b20777f1d
call_identifier: H2020
grant_number: '101020331'
name: Random matrices beyond Wigner-Dyson-Mehta
publication: Communications on Pure and Applied Mathematics
publication_identifier:
eissn:
- 1097-0312
issn:
- 0010-3640
publication_status: published
publisher: Wiley
quality_controlled: '1'
scopus_import: '1'
status: public
title: Wegner estimate and upper bound on the eigenvalue condition number of non-Hermitian
random matrices
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: 317138e5-6ab7-11ef-aa6d-ffef3953e345
volume: 77
year: '2024'
...
---
OA_place: publisher
OA_type: hybrid
_id: '15379'
abstract:
- lang: eng
text: Long-term potentiation (LTP) of excitatory synapses is a leading model to
explain the concept of information storage in the brain. Multiple mechanisms contribute
to LTP, but central amongst them is an increased sensitivity of the postsynaptic
membrane to neurotransmitter release. This sensitivity is predominantly determined
by the abundance and localization of AMPA-type glutamate receptors (AMPARs). A
combination of AMPAR structural data, super-resolution imaging of excitatory synapses,
and an abundance of electrophysiological studies are providing an ever-clearer
picture of how AMPARs are recruited and organized at synaptic junctions. Here,
we review the latest insights into this process, and discuss how both cytoplasmic
and extracellular receptor elements cooperate to tune the AMPAR response at the
hippocampal CA1 synapse.
acknowledgement: The authors thank Alexander Scrutton and James M. Krieger for comments
on the manuscript. The authors also acknowledge Shraddha Nayak for help with Figure
1B design. This work was supported by grants from the Medical Research Council (MC_U105174197),
the BBSRC (BB/N002113/1), and the Wellcome Trust (223194/Z/21/Z) to IHG.
article_number: ' 2400006'
article_processing_charge: Yes (in subscription journal)
article_type: review
author:
- first_name: Imogen
full_name: Stockwell, Imogen
last_name: Stockwell
- first_name: Jake
full_name: Watson, Jake
id: 63836096-4690-11EA-BD4E-32803DDC885E
last_name: Watson
orcid: 0000-0002-8698-3823
- first_name: Ingo H.
full_name: Greger, Ingo H.
last_name: Greger
citation:
ama: Stockwell I, Watson J, Greger IH. Tuning synaptic strength by regulation of
AMPA glutamate receptor localization. BioEssays. 2024;46(7). doi:10.1002/bies.202400006
apa: Stockwell, I., Watson, J., & Greger, I. H. (2024). Tuning synaptic strength
by regulation of AMPA glutamate receptor localization. BioEssays. Wiley.
https://doi.org/10.1002/bies.202400006
chicago: Stockwell, Imogen, Jake Watson, and Ingo H. Greger. “Tuning Synaptic Strength
by Regulation of AMPA Glutamate Receptor Localization.” BioEssays. Wiley,
2024. https://doi.org/10.1002/bies.202400006.
ieee: I. Stockwell, J. Watson, and I. H. Greger, “Tuning synaptic strength by regulation
of AMPA glutamate receptor localization,” BioEssays, vol. 46, no. 7. Wiley,
2024.
ista: Stockwell I, Watson J, Greger IH. 2024. Tuning synaptic strength by regulation
of AMPA glutamate receptor localization. BioEssays. 46(7), 2400006.
mla: Stockwell, Imogen, et al. “Tuning Synaptic Strength by Regulation of AMPA Glutamate
Receptor Localization.” BioEssays, vol. 46, no. 7, 2400006, Wiley, 2024,
doi:10.1002/bies.202400006.
short: I. Stockwell, J. Watson, I.H. Greger, BioEssays 46 (2024).
date_created: 2024-05-12T22:01:02Z
date_published: 2024-07-01T00:00:00Z
date_updated: 2025-09-08T07:25:02Z
day: '01'
ddc:
- '570'
department:
- _id: PeJo
doi: 10.1002/bies.202400006
external_id:
isi:
- '001214545700001'
pmid:
- '38693811'
file:
- access_level: open_access
checksum: dc8be74156657e8aab12a9d613233ee3
content_type: application/pdf
creator: dernst
date_created: 2025-01-09T09:31:05Z
date_updated: 2025-01-09T09:31:05Z
file_id: '18801'
file_name: 2024_BioEssays_Stockwell.pdf
file_size: 775825
relation: main_file
success: 1
file_date_updated: 2025-01-09T09:31:05Z
has_accepted_license: '1'
intvolume: ' 46'
isi: 1
issue: '7'
language:
- iso: eng
month: '07'
oa: 1
oa_version: Published Version
pmid: 1
publication: BioEssays
publication_identifier:
eissn:
- 1521-1878
issn:
- 0265-9247
publication_status: published
publisher: Wiley
quality_controlled: '1'
scopus_import: '1'
status: public
title: Tuning synaptic strength by regulation of AMPA glutamate receptor localization
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: journal_article
user_id: 317138e5-6ab7-11ef-aa6d-ffef3953e345
volume: 46
year: '2024'
...
---
OA_place: publisher
OA_type: hybrid
_id: '15380'
abstract:
- lang: eng
text: The depth of a cell in an arrangement of n (non-vertical) great-spheres in
Sd is the number of great-spheres that pass above the cell. We prove Euler-type
relations, which imply extensions of the classic Dehn–Sommerville relations for
convex polytopes to sublevel sets of the depth function, and we use the relations
to extend the expressions for the number of faces of neighborly polytopes to the
number of cells of levels in neighborly arrangements.
acknowledgement: "The authors thank Uli Wagner and Emo Welzl for comments on an earlier
version of this paper, and for pointing out related work in the prior literature.\r\nOpen
access funding provided by Institute of Science and Technology (IST Austria). This
project has received funding from the European Research Council (ERC) under the
European Union’s Horizon 2020 research and innovation programme, Grant No. 788183,
from the Wittgenstein Prize, Austrian Science Fund (FWF), Grant No. Z 342-N31, and
from the DFG Collaborative Research Center TRR 109, ‘Discretization in Geometry
and Dynamics’, Austrian Science Fund (FWF), Grant No. I 02979-N35."
article_processing_charge: Yes (via OA deal)
article_type: original
author:
- first_name: Ranita
full_name: Biswas, Ranita
id: 3C2B033E-F248-11E8-B48F-1D18A9856A87
last_name: Biswas
orcid: 0000-0002-5372-7890
- 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: Morteza
full_name: Saghafian, Morteza
id: f86f7148-b140-11ec-9577-95435b8df824
last_name: Saghafian
citation:
ama: 'Biswas R, Cultrera di Montesano S, Edelsbrunner H, Saghafian M. Depth in arrangements:
Dehn–Sommerville–Euler relations with applications. Journal of Applied and
Computational Topology. 2024;8:557-578. doi:10.1007/s41468-024-00173-w'
apa: 'Biswas, R., Cultrera di Montesano, S., Edelsbrunner, H., & Saghafian,
M. (2024). Depth in arrangements: Dehn–Sommerville–Euler relations with applications.
Journal of Applied and Computational Topology. Springer Nature. https://doi.org/10.1007/s41468-024-00173-w'
chicago: 'Biswas, Ranita, Sebastiano Cultrera di Montesano, Herbert Edelsbrunner,
and Morteza Saghafian. “Depth in Arrangements: Dehn–Sommerville–Euler Relations
with Applications.” Journal of Applied and Computational Topology. Springer
Nature, 2024. https://doi.org/10.1007/s41468-024-00173-w.'
ieee: 'R. Biswas, S. Cultrera di Montesano, H. Edelsbrunner, and M. Saghafian, “Depth
in arrangements: Dehn–Sommerville–Euler relations with applications,” Journal
of Applied and Computational Topology, vol. 8. Springer Nature, pp. 557–578,
2024.'
ista: 'Biswas R, Cultrera di Montesano S, Edelsbrunner H, Saghafian M. 2024. Depth
in arrangements: Dehn–Sommerville–Euler relations with applications. Journal of
Applied and Computational Topology. 8, 557–578.'
mla: 'Biswas, Ranita, et al. “Depth in Arrangements: Dehn–Sommerville–Euler Relations
with Applications.” Journal of Applied and Computational Topology, vol.
8, Springer Nature, 2024, pp. 557–78, doi:10.1007/s41468-024-00173-w.'
short: R. Biswas, S. Cultrera di Montesano, H. Edelsbrunner, M. Saghafian, Journal
of Applied and Computational Topology 8 (2024) 557–578.
corr_author: '1'
date_created: 2024-05-12T22:01:03Z
date_published: 2024-09-01T00:00:00Z
date_updated: 2025-05-14T09:27:57Z
day: '01'
ddc:
- '510'
department:
- _id: HeEd
doi: 10.1007/s41468-024-00173-w
ec_funded: 1
external_id:
pmid:
- '39308789'
file:
- access_level: open_access
checksum: 0ee15c1493a6413cf356ab2f32c81a9e
content_type: application/pdf
creator: dernst
date_created: 2025-04-23T08:01:36Z
date_updated: 2025-04-23T08:01:36Z
file_id: '19612'
file_name: 2024_JourApplCompTopo_BiswasRa.pdf
file_size: 522831
relation: main_file
success: 1
file_date_updated: 2025-04-23T08:01:36Z
has_accepted_license: '1'
intvolume: ' 8'
language:
- iso: eng
month: '09'
oa: 1
oa_version: Published Version
page: 557-578
pmid: 1
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: Mathematics, Computer Science
- _id: 2561EBF4-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: I02979-N35
name: Persistence and stability of geometric complexes
publication: Journal of Applied and Computational Topology
publication_identifier:
eissn:
- 2367-1734
issn:
- 2367-1726
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
related_material:
record:
- id: '11658'
relation: earlier_version
status: public
scopus_import: '1'
status: public
title: 'Depth in arrangements: Dehn–Sommerville–Euler relations with applications'
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 8
year: '2024'
...
---
OA_place: publisher
OA_type: hybrid
_id: '15381'
abstract:
- lang: eng
text: 'Cholecystokinin-expressing interneurons (CCKIs) are hypothesized to shape
pyramidal cell-firing patterns and regulate network oscillations and related network
state transitions. To directly probe their role in the CA1 region, we silenced
their activity using optogenetic and chemogenetic tools in mice. Opto-tagged CCKIs
revealed a heterogeneous population, and their optogenetic silencing triggered
wide disinhibitory network changes affecting both pyramidal cells and other interneurons.
CCKI silencing enhanced pyramidal cell burst firing and altered the temporal coding
of place cells: theta phase precession was disrupted, whereas sequence reactivation
was enhanced. Chemogenetic CCKI silencing did not alter the acquisition of spatial
reference memories on the Morris water maze but enhanced the recall of contextual
fear memories and enabled selective recall when similar environments were tested.
This work suggests the key involvement of CCKIs in the control of place-cell temporal
coding and the formation of contextual memories.'
acknowledged_ssus:
- _id: M-Shop
- _id: Bio
- _id: LifeSc
- _id: PreCl
acknowledgement: We thank the kind donations from Andrea Varro, Brian Sauer, Edward
Boyden, and Peter Jonas. We thank Jago Wallenschus, Kerstin Kronenbitter, and Didier
Gremelle for outstanding technical support; Laura Bollepalli for initial viral targeting
experiments; Cihan Önal for initial electrophysiology experiments; Yoav Ben-Simon
for histological advice; and Anton Nikitenko for contributing to the analysis. We
acknowledge support from the Miba Machine Shop, Bioimaging-, Life Science- and Pre-Clinical
Facilities at ISTA. This work was supported by the Austrian Science Fund (FWF I3713
to J.C. as part of the FOR 2143 research consortium), the Deutsche Forschungsgemeinschaft
(DFG) (WU 503/2-2 to P.W.), and the Medical Research Council, United Kingdom (grant
G1100546/2 to P.W.).
article_processing_charge: Yes (via OA deal)
article_type: original
author:
- first_name: Dámaris K
full_name: Rangel Guerrero, Dámaris K
id: 4871BCE6-F248-11E8-B48F-1D18A9856A87
last_name: Rangel Guerrero
orcid: 0000-0002-8602-4374
- first_name: Kira
full_name: Balueva, Kira
last_name: Balueva
- first_name: Uladzislau
full_name: Barayeu, Uladzislau
id: b515be12-ec90-11ea-b966-d0b5e15613d2
last_name: Barayeu
- first_name: Peter
full_name: Baracskay, Peter
id: 361CC00E-F248-11E8-B48F-1D18A9856A87
last_name: Baracskay
- first_name: Igor
full_name: Gridchyn, Igor
id: 4B60654C-F248-11E8-B48F-1D18A9856A87
last_name: Gridchyn
orcid: 0000-0002-1807-1929
- first_name: Michele
full_name: Nardin, Michele
id: 30BD0376-F248-11E8-B48F-1D18A9856A87
last_name: Nardin
orcid: 0000-0001-8849-6570
- first_name: Chiara N
full_name: Roth, Chiara N
id: 37BB4FB6-F248-11E8-B48F-1D18A9856A87
last_name: Roth
- first_name: Peer
full_name: Wulff, Peer
last_name: Wulff
- first_name: Jozsef L
full_name: Csicsvari, Jozsef L
id: 3FA14672-F248-11E8-B48F-1D18A9856A87
last_name: Csicsvari
orcid: 0000-0002-5193-4036
citation:
ama: Rangel Guerrero DK, Balueva K, Barayeu U, et al. Hippocampal cholecystokinin-expressing
interneurons regulate temporal coding and contextual learning. Neuron.
2024;112(12):2045-2061.e10. doi:10.1016/j.neuron.2024.03.019
apa: Rangel Guerrero, D. K., Balueva, K., Barayeu, U., Baracskay, P., Gridchyn,
I., Nardin, M., … Csicsvari, J. L. (2024). Hippocampal cholecystokinin-expressing
interneurons regulate temporal coding and contextual learning. Neuron.
Cell Press. https://doi.org/10.1016/j.neuron.2024.03.019
chicago: Rangel Guerrero, Dámaris K, Kira Balueva, Uladzislau Barayeu, Peter Baracskay,
Igor Gridchyn, Michele Nardin, Chiara N Roth, Peer Wulff, and Jozsef L Csicsvari.
“Hippocampal Cholecystokinin-Expressing Interneurons Regulate Temporal Coding
and Contextual Learning.” Neuron. Cell Press, 2024. https://doi.org/10.1016/j.neuron.2024.03.019.
ieee: D. K. Rangel Guerrero et al., “Hippocampal cholecystokinin-expressing
interneurons regulate temporal coding and contextual learning,” Neuron,
vol. 112, no. 12. Cell Press, p. 2045–2061.e10, 2024.
ista: Rangel Guerrero DK, Balueva K, Barayeu U, Baracskay P, Gridchyn I, Nardin
M, Roth CN, Wulff P, Csicsvari JL. 2024. Hippocampal cholecystokinin-expressing
interneurons regulate temporal coding and contextual learning. Neuron. 112(12),
2045–2061.e10.
mla: Rangel Guerrero, Dámaris K., et al. “Hippocampal Cholecystokinin-Expressing
Interneurons Regulate Temporal Coding and Contextual Learning.” Neuron,
vol. 112, no. 12, Cell Press, 2024, p. 2045–2061.e10, doi:10.1016/j.neuron.2024.03.019.
short: D.K. Rangel Guerrero, K. Balueva, U. Barayeu, P. Baracskay, I. Gridchyn,
M. Nardin, C.N. Roth, P. Wulff, J.L. Csicsvari, Neuron 112 (2024) 2045–2061.e10.
corr_author: '1'
date_created: 2024-05-12T22:01:03Z
date_published: 2024-06-19T00:00:00Z
date_updated: 2025-09-08T07:26:42Z
day: '19'
ddc:
- '570'
department:
- _id: JoCs
doi: 10.1016/j.neuron.2024.03.019
external_id:
isi:
- '001300571400001'
pmid:
- '38636524'
file:
- access_level: open_access
checksum: de5b18ff293d42bd90e83a193e889844
content_type: application/pdf
creator: dernst
date_created: 2025-01-09T09:15:31Z
date_updated: 2025-01-09T09:15:31Z
file_id: '18798'
file_name: 2024_Neuron_RangelGuerrero.pdf
file_size: 9149079
relation: main_file
success: 1
file_date_updated: 2025-01-09T09:15:31Z
has_accepted_license: '1'
intvolume: ' 112'
isi: 1
issue: '12'
language:
- iso: eng
month: '06'
oa: 1
oa_version: Published Version
page: 2045-2061.e10
pmid: 1
project:
- _id: 2654F984-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: I 3713-B27
name: Interneuro plasticity during spatial learning
publication: Neuron
publication_identifier:
eissn:
- 1097-4199
issn:
- 0896-6273
publication_status: published
publisher: Cell Press
quality_controlled: '1'
scopus_import: '1'
status: public
title: Hippocampal cholecystokinin-expressing interneurons regulate temporal coding
and contextual learning
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: journal_article
user_id: 317138e5-6ab7-11ef-aa6d-ffef3953e345
volume: 112
year: '2024'
...
---
_id: '15385'
abstract:
- lang: eng
text: "Relevant information about the data can be found in the 'Readme_Data.txt'
file. \r\nA previous version of the publication can be found on BioRxiv: https://www.biorxiv.org/content/10.1101/2022.10.11.511691v4\r\nand
published in Plos Biology (2024)"
acknowledged_ssus:
- _id: PreCl
- _id: M-Shop
- _id: LifeSc
- _id: Bio
acknowledgement: 'We thank Armel Nicolas, Bella Bruszel and Ewelina Dutkiewicz from
the ISTA Mass Spectrometry Service (Lab Services Facilities) for all Proteomics
work, including samples preparation, LC/MS data acquisition, searches and data evaluation.
We thank Prof. Peter Jonas for his suggestion on the involvement of potassium channels
and members of the Neuroethology group for their comments on the manuscript. Katalin
Szigeti and Julie Murmann for experimental help. This research was supported by
the Scientific Service Units of ISTA through resources provided by the Lab Support
Facility, the Imaging and Optics Facility, the Machine Shop Unit and the Preclinical
Facility, especially Freyja Langer and Michael Schunn. '
article_processing_charge: No
author:
- first_name: Laura
full_name: Burnett, Laura
id: 3B717F68-F248-11E8-B48F-1D18A9856A87
last_name: Burnett
orcid: 0000-0002-8937-410X
- first_name: Peter
full_name: Koppensteiner, Peter
id: 3B8B25A8-F248-11E8-B48F-1D18A9856A87
last_name: Koppensteiner
orcid: 0000-0002-3509-1948
- first_name: Olga
full_name: Symonova, Olga
id: 3C0C7BC6-F248-11E8-B48F-1D18A9856A87
last_name: Symonova
orcid: 0000-0003-2012-9947
- first_name: Tomas
full_name: Masson, Tomas
id: 93ac43e8-8599-11eb-9b86-f6efb0a4c207
last_name: Masson
orcid: 0000-0002-2634-6283
- first_name: Tomas A
full_name: Vega Zuniga, Tomas A
id: 2E7C4E78-F248-11E8-B48F-1D18A9856A87
last_name: Vega Zuniga
- first_name: Ximena
full_name: Contreras, Ximena
id: 475990FE-F248-11E8-B48F-1D18A9856A87
last_name: Contreras
- first_name: Thomas
full_name: Rülicke, Thomas
last_name: Rülicke
- first_name: Ryuichi
full_name: Shigemoto, Ryuichi
id: 499F3ABC-F248-11E8-B48F-1D18A9856A87
last_name: Shigemoto
orcid: 0000-0001-8761-9444
- first_name: Gaia
full_name: Novarino, Gaia
id: 3E57A680-F248-11E8-B48F-1D18A9856A87
last_name: Novarino
orcid: 0000-0002-7673-7178
- first_name: Maximilian A
full_name: Jösch, Maximilian A
id: 2BD278E6-F248-11E8-B48F-1D18A9856A87
last_name: Jösch
orcid: 0000-0002-3937-1330
citation:
ama: Burnett L, Koppensteiner P, Symonova O, et al. Shared behavioural impairments
in visual perception and place avoidance across different autism models are driven
by periaqueductal grey hypoexcitability in Setd5 haploinsufficient mice. 2024.
doi:10.15479/AT:ISTA:15385
apa: Burnett, L., Koppensteiner, P., Symonova, O., Masson, T., Vega Zuniga, T. A.,
Contreras, X., … Jösch, M. A. (2024). Shared behavioural impairments in visual
perception and place avoidance across different autism models are driven by periaqueductal
grey hypoexcitability in Setd5 haploinsufficient mice. Institute of Science and
Technology Austria. https://doi.org/10.15479/AT:ISTA:15385
chicago: Burnett, Laura, Peter Koppensteiner, Olga Symonova, Tomas Masson, Tomas
A Vega Zuniga, Ximena Contreras, Thomas Rülicke, Ryuichi Shigemoto, Gaia Novarino,
and Maximilian A Jösch. “Shared Behavioural Impairments in Visual Perception and
Place Avoidance across Different Autism Models Are Driven by Periaqueductal Grey
Hypoexcitability in Setd5 Haploinsufficient Mice.” Institute of Science and Technology
Austria, 2024. https://doi.org/10.15479/AT:ISTA:15385.
ieee: L. Burnett et al., “Shared behavioural impairments in visual perception
and place avoidance across different autism models are driven by periaqueductal
grey hypoexcitability in Setd5 haploinsufficient mice.” Institute of Science and
Technology Austria, 2024.
ista: Burnett L, Koppensteiner P, Symonova O, Masson T, Vega Zuniga TA, Contreras
X, Rülicke T, Shigemoto R, Novarino G, Jösch MA. 2024. Shared behavioural impairments
in visual perception and place avoidance across different autism models are driven
by periaqueductal grey hypoexcitability in Setd5 haploinsufficient mice, Institute
of Science and Technology Austria, 10.15479/AT:ISTA:15385.
mla: Burnett, Laura, et al. Shared Behavioural Impairments in Visual Perception
and Place Avoidance across Different Autism Models Are Driven by Periaqueductal
Grey Hypoexcitability in Setd5 Haploinsufficient Mice. Institute of Science
and Technology Austria, 2024, doi:10.15479/AT:ISTA:15385.
short: L. Burnett, P. Koppensteiner, O. Symonova, T. Masson, T.A. Vega Zuniga, X.
Contreras, T. Rülicke, R. Shigemoto, G. Novarino, M.A. Jösch, (2024).
corr_author: '1'
date_created: 2024-05-13T15:04:04Z
date_published: 2024-05-15T00:00:00Z
date_updated: 2025-09-08T07:57:11Z
day: '15'
ddc:
- '570'
department:
- _id: MaJö
- _id: PreCl
- _id: SiHi
- _id: RySh
- _id: GaNo
doi: 10.15479/AT:ISTA:15385
file:
- access_level: open_access
checksum: 9205eb0876f0f08552dbad80d6884b4b
content_type: application/zip
creator: mjoesch
date_created: 2024-05-15T06:09:17Z
date_updated: 2024-05-15T06:09:17Z
file_id: '15396'
file_name: PatchClamp.zip
file_size: '1149617663'
relation: main_file
success: 1
- access_level: open_access
content_type: application/zip
creator: mjoesch
date_created: 2024-05-15T06:09:12Z
date_updated: 2024-05-15T06:09:12Z
file_id: '15397'
file_name: SiliconProbe.zip
file_size: '564903112'
relation: main_file
success: 1
- access_level: open_access
checksum: 49a807bbab06b5fada38f532e2176e2e
content_type: application/zip
creator: mjoesch
date_created: 2024-05-15T06:09:14Z
date_updated: 2024-05-15T06:09:14Z
file_id: '15398'
file_name: WesternBlot.zip
file_size: '11685703'
relation: main_file
success: 1
- access_level: open_access
checksum: beeeeaa43770090f3b291209ed6b0623
content_type: application/zip
creator: mjoesch
date_created: 2024-05-15T06:09:38Z
date_updated: 2024-05-15T06:09:38Z
file_id: '15399'
file_name: Behaviour.zip
file_size: '1335626779'
relation: main_file
success: 1
- access_level: open_access
checksum: 8862ad7719388304d1d19f8e7db8bb00
content_type: text/plain
creator: mjoesch
date_created: 2024-05-16T09:08:20Z
date_updated: 2024-05-16T09:08:20Z
file_id: '15400'
file_name: Readme_Data.txt
file_size: 18841
relation: main_file
success: 1
file_date_updated: 2024-05-16T09:08:20Z
has_accepted_license: '1'
keyword:
- ASD
- periaqueductal gray
- perception
- behavior
- potassium channels
month: '05'
oa: 1
oa_version: Published Version
publisher: Institute of Science and Technology Austria
related_material:
record:
- id: '17142'
relation: used_in_publication
status: public
status: public
title: Shared behavioural impairments in visual perception and place avoidance across
different autism models are driven by periaqueductal grey hypoexcitability in Setd5
haploinsufficient mice
tmp:
image: /images/cc_by_nc.png
legal_code_url: https://creativecommons.org/licenses/by-nc/4.0/legalcode
name: Creative Commons Attribution-NonCommercial 4.0 International (CC BY-NC 4.0)
short: CC BY-NC (4.0)
type: research_data
user_id: 68b8ca59-c5b3-11ee-8790-cd641c68093d
year: '2024'
...
---
OA_place: repository
OA_type: green
_id: '15404'
abstract:
- lang: eng
text: We used diverse methods to characterize the role of avian lateral spiriform
nucleus (SpL) in basal ganglia motor function. Connectivity analysis showed that
SpL receives input from globus pallidus (GP), and the intrapeduncular nucleus
(INP) located ventromedial to GP, whose neurons express numerous striatal markers.
SpL-projecting GP neurons were large and aspiny, while SpL-projecting INP neurons
were medium sized and spiny. Connectivity analysis further showed that SpL receives
inputs from subthalamic nucleus (STN) and substantia nigra pars reticulata (SNr),
and that the SNr also receives inputs from GP, INP, and STN. Neurochemical analysis
showed that SpL neurons express ENK, GAD, and a variety of pallidal neuron markers,
and receive GABAergic terminals, some of which also contain DARPP32, consistent
with GP pallidal and INP striatal inputs. Connectivity and neurochemical analysis
showed that the SpL input to tectum prominently ends on GABAA receptor-enriched
tectobulbar neurons. Behavioral studies showed that lesions of SpL impair visuomotor
behaviors involving tracking and pecking moving targets. Our results suggest that
SpL modulates brainstem-projecting tectobulbar neurons in a manner comparable
to the demonstrated influence of GP internus on motor thalamus and of SNr on tectobulbar
neurons in mammals. Given published data in amphibians and reptiles, it seems
likely the SpL circuit represents a major direct pathway-type circuit by which
the basal ganglia exerts its motor influence in nonmammalian tetrapods. The present
studies also show that avian striatum is divided into three spatially segregated
territories with differing connectivity, a medial striato-nigral territory, a
dorsolateral striato-GP territory, and the ventrolateral INP motor territory.
acknowledgement: We gratefully thank Marion Joni, Tony Laverghetta, Sherry Cuthbertson,
Gary Henderson, and Patricia Lindaman for technical assistance. The research presented
here has been supported by NIH grants NS-16857, NS-19620, NS-28721, and EY-05298,
and The Methodist Hospitals Endowed Professorship in Neuroscience (A. R.), by grant
number 09/50623-9 from the Fundacao de Amparo a Pesquisa do Estado de Sao Paulo
(C. A. B. T.), by NIH grant EY-00735 (W. H.), and by NIH grants NS-12078 and EY-02145
(H. J. K.).
article_number: e25620
article_processing_charge: No
article_type: original
author:
- first_name: Anton
full_name: Reiner, Anton
last_name: Reiner
- first_name: Loreta
full_name: Medina, Loreta
last_name: Medina
- first_name: Antonio
full_name: Abellan, Antonio
last_name: Abellan
- first_name: Yunping
full_name: Deng, Yunping
last_name: Deng
- first_name: Claudio A.B.
full_name: Toledo, Claudio A.B.
last_name: Toledo
- first_name: Harald
full_name: Luksch, Harald
last_name: Luksch
- first_name: Tomas A
full_name: Vega Zuniga, Tomas A
id: 2E7C4E78-F248-11E8-B48F-1D18A9856A87
last_name: Vega Zuniga
- first_name: Nell B.
full_name: Riley, Nell B.
last_name: Riley
- first_name: William
full_name: Hodos, William
last_name: Hodos
- first_name: Harvey J.
full_name: Karten, Harvey J.
last_name: Karten
citation:
ama: 'Reiner A, Medina L, Abellan A, et al. Neurochemistry and circuit organization
of the lateral spiriform nucleus of birds: A uniquely nonmammalian direct pathway
component of the basal ganglia. Journal of Comparative Neurology. 2024;532(5).
doi:10.1002/cne.25620'
apa: 'Reiner, A., Medina, L., Abellan, A., Deng, Y., Toledo, C. A. B., Luksch, H.,
… Karten, H. J. (2024). Neurochemistry and circuit organization of the lateral
spiriform nucleus of birds: A uniquely nonmammalian direct pathway component of
the basal ganglia. Journal of Comparative Neurology. Wiley. https://doi.org/10.1002/cne.25620'
chicago: 'Reiner, Anton, Loreta Medina, Antonio Abellan, Yunping Deng, Claudio A.B.
Toledo, Harald Luksch, Tomas A Vega Zuniga, Nell B. Riley, William Hodos, and
Harvey J. Karten. “Neurochemistry and Circuit Organization of the Lateral Spiriform
Nucleus of Birds: A Uniquely Nonmammalian Direct Pathway Component of the Basal
Ganglia.” Journal of Comparative Neurology. Wiley, 2024. https://doi.org/10.1002/cne.25620.'
ieee: 'A. Reiner et al., “Neurochemistry and circuit organization of the
lateral spiriform nucleus of birds: A uniquely nonmammalian direct pathway component
of the basal ganglia,” Journal of Comparative Neurology, vol. 532, no.
5. Wiley, 2024.'
ista: 'Reiner A, Medina L, Abellan A, Deng Y, Toledo CAB, Luksch H, Vega Zuniga
TA, Riley NB, Hodos W, Karten HJ. 2024. Neurochemistry and circuit organization
of the lateral spiriform nucleus of birds: A uniquely nonmammalian direct pathway
component of the basal ganglia. Journal of Comparative Neurology. 532(5), e25620.'
mla: 'Reiner, Anton, et al. “Neurochemistry and Circuit Organization of the Lateral
Spiriform Nucleus of Birds: A Uniquely Nonmammalian Direct Pathway Component of
the Basal Ganglia.” Journal of Comparative Neurology, vol. 532, no. 5,
e25620, Wiley, 2024, doi:10.1002/cne.25620.'
short: A. Reiner, L. Medina, A. Abellan, Y. Deng, C.A.B. Toledo, H. Luksch, T.A.
Vega Zuniga, N.B. Riley, W. Hodos, H.J. Karten, Journal of Comparative Neurology
532 (2024).
date_created: 2024-05-19T22:01:12Z
date_published: 2024-05-01T00:00:00Z
date_updated: 2025-09-08T07:29:27Z
day: '01'
department:
- _id: MaJö
doi: 10.1002/cne.25620
external_id:
isi:
- '001217825300001'
pmid:
- '38733146'
intvolume: ' 532'
isi: 1
issue: '5'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://www.ncbi.nlm.nih.gov/pmc/articles/11090467
month: '05'
oa: 1
oa_version: Submitted Version
pmid: 1
publication: Journal of Comparative Neurology
publication_identifier:
eissn:
- 1096-9861
issn:
- 0021-9967
publication_status: published
publisher: Wiley
quality_controlled: '1'
scopus_import: '1'
status: public
title: 'Neurochemistry and circuit organization of the lateral spiriform nucleus of
birds: A uniquely nonmammalian direct pathway component of the basal ganglia'
type: journal_article
user_id: 317138e5-6ab7-11ef-aa6d-ffef3953e345
volume: 532
year: '2024'
...
---
DOAJ_listed: '1'
_id: '15405'
abstract:
- lang: eng
text: We report JWST/NIRCam measurements of quasar host galaxy emissions and supermassive
black hole (SMBH) masses for six quasars at 5.9 < z < 7.1 in the Emission-line
galaxies and Intergalactic Gas in the Epoch of Reionization (EIGER) project. We
obtain deep NIRCam imaging in the F115W, F200W, and F356W bands, as well as F356W
grism spectroscopy of the quasars. We use bright unsaturated stars to construct
models of the point-spread functions (PSFs) and estimate the errors of these PSFs.
We then measure or constrain the fluxes and morphology of the quasar host galaxies
by fitting the quasar images as a point source plus an exponential disk. We successfully
detect the host galaxies of three quasars, which have host-to-quasar-flux ratios
of ∼1%–5%. Spectral energy distribution fitting suggests that these quasar host
galaxies have stellar masses of M* ≳ 1010M⊙. For quasars with host galaxy nondetections,
we estimate the upper limits of their stellar masses. We use the grism spectra
to measure the Hβ line profile and the continuum luminosity, then estimate the
SMBH masses for the quasars. Our results indicate that the positive relation between
SMBH masses and host galaxy stellar masses already exists at redshift z ≳ 6. The
quasars in our sample show a high BH-to-stellar-mass ratio of MBH/M* ∼ 0.15, which
is about ∼2 dex higher than local relations. We find that selection effects only
contribute partially to the high MBH/M* ratios of high-redshift quasars. This
result hints at a possible redshift evolution of the MBH–M* relation.
acknowledgement: "We thank the referee for the valuable comments on this paper. We
thank John Silverman, Madeline Marshall, MingYang Zhuang, Weizhe Liu, and Jinyi
Yang for inspiring discussions and suggestions. D.K. is grateful for the support
from JSPS KAKENHI grant No. JP21K13956. This work is based on observations made
with the NASA/ESA/CSA James Webb Space Telescope. The data were obtained from the
Mikulski Archive for Space Telescopes at the Space Telescope\r\nScience Institute,
which is operated by the Association of Universities for Research in Astronomy,
Inc., under NASA contract NAS 5-03127 for JWST. These observations are\r\nassociated
with program ID #1243. Facility: JWST (NIRCam) Software: astropy (Astropy Collaboration
et al. 2013, 2018), psfMC (Mechtley 2014), webbpsf (Perrin et al. 2014), jwst."
article_number: '176'
article_processing_charge: Yes
article_type: original
author:
- first_name: Minghao
full_name: Yue, Minghao
last_name: Yue
- first_name: Anna Christina
full_name: Eilers, Anna Christina
last_name: Eilers
- first_name: Robert A.
full_name: Simcoe, Robert A.
last_name: Simcoe
- first_name: Ruari
full_name: Mackenzie, Ruari
last_name: Mackenzie
- 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: Daichi
full_name: Kashino, Daichi
last_name: Kashino
- first_name: Rongmon
full_name: Bordoloi, Rongmon
last_name: Bordoloi
- first_name: Simon J.
full_name: Lilly, Simon J.
last_name: Lilly
- first_name: Rohan P.
full_name: Naidu, Rohan P.
last_name: Naidu
citation:
ama: Yue M, Eilers AC, Simcoe RA, et al. EIGER. V. Characterizing the host galaxies
of luminous quasars at z ≳ 6. Astrophysical Journal. 2024;966(2). doi:10.3847/1538-4357/ad3914
apa: Yue, M., Eilers, A. C., Simcoe, R. A., Mackenzie, R., Matthee, J. J., Kashino,
D., … Naidu, R. P. (2024). EIGER. V. Characterizing the host galaxies of luminous
quasars at z ≳ 6. Astrophysical Journal. IOP Publishing. https://doi.org/10.3847/1538-4357/ad3914
chicago: Yue, Minghao, Anna Christina Eilers, Robert A. Simcoe, Ruari Mackenzie,
Jorryt J Matthee, Daichi Kashino, Rongmon Bordoloi, Simon J. Lilly, and Rohan
P. Naidu. “EIGER. V. Characterizing the Host Galaxies of Luminous Quasars at z
≳ 6.” Astrophysical Journal. IOP Publishing, 2024. https://doi.org/10.3847/1538-4357/ad3914.
ieee: M. Yue et al., “EIGER. V. Characterizing the host galaxies of luminous
quasars at z ≳ 6,” Astrophysical Journal, vol. 966, no. 2. IOP Publishing,
2024.
ista: Yue M, Eilers AC, Simcoe RA, Mackenzie R, Matthee JJ, Kashino D, Bordoloi
R, Lilly SJ, Naidu RP. 2024. EIGER. V. Characterizing the host galaxies of luminous
quasars at z ≳ 6. Astrophysical Journal. 966(2), 176.
mla: Yue, Minghao, et al. “EIGER. V. Characterizing the Host Galaxies of Luminous
Quasars at z ≳ 6.” Astrophysical Journal, vol. 966, no. 2, 176, IOP Publishing,
2024, doi:10.3847/1538-4357/ad3914.
short: M. Yue, A.C. Eilers, R.A. Simcoe, R. Mackenzie, J.J. Matthee, D. Kashino,
R. Bordoloi, S.J. Lilly, R.P. Naidu, Astrophysical Journal 966 (2024).
date_created: 2024-05-19T22:01:12Z
date_published: 2024-05-01T00:00:00Z
date_updated: 2025-09-08T07:30:17Z
day: '01'
ddc:
- '520'
department:
- _id: JoMa
doi: 10.3847/1538-4357/ad3914
external_id:
isi:
- '001214916200001'
file:
- access_level: open_access
checksum: 47b428f6209d8a6f9869031d9cb8dae6
content_type: application/pdf
creator: dernst
date_created: 2024-05-21T11:13:25Z
date_updated: 2024-05-21T11:13:25Z
file_id: '15410'
file_name: 2024_AstrophysicalJourn_Yue.pdf
file_size: 4472346
relation: main_file
success: 1
file_date_updated: 2024-05-21T11:13:25Z
has_accepted_license: '1'
intvolume: ' 966'
isi: 1
issue: '2'
language:
- iso: eng
month: '05'
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: EIGER. V. Characterizing the host galaxies of luminous quasars at z ≳ 6
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: journal_article
user_id: 317138e5-6ab7-11ef-aa6d-ffef3953e345
volume: 966
year: '2024'
...
---
DOAJ_listed: '1'
_id: '15406'
abstract:
- lang: eng
text: 'We report on dynamic Shubnikov–de Haas (SdH) oscillations that are measured
in the optical response, subterahertz transmittance of two-dimensional systems,
and reveal two distinct types of oscillation nodes: “universal” nodes at integer
ratios of radiation and cyclotron frequencies and “tunable” nodes at positions
sensitive to all parameters of the structure. The nodes in both real and imaginary
parts of the measured complex transmittance are analyzed using a dynamic version
of the static Lifshitz-Kosevich formula. These results demonstrate that the node
structure of the dynamic SdH oscillations provides an all-optical access to quantization-
and interaction-induced renormalization effects, in addition to parameters one
can obtain from the static SdH oscillations.'
acknowledgement: This research was funded in whole or in part by the Austrian Science
Fund (FWF) [10.55776/I3456,10.55776/I5539]. I.A.D. acknowledges the financial support
of the German Research Foundation (DM 1/6-1). The quantum well growth and transport
measurements were supported by RSF 23-72-30003. For open access purposes, the authors
have applied a CC BY public copyright license to any authoraccepted manuscript version
arising from this submission.
article_number: L022027
article_processing_charge: Yes
article_type: letter_note
arxiv: 1
author:
- first_name: M. L.
full_name: Savchenko, M. L.
last_name: Savchenko
- first_name: J.
full_name: Gospodarič, J.
last_name: Gospodarič
- first_name: A.
full_name: Shuvaev, A.
last_name: Shuvaev
- first_name: I. A.
full_name: Dmitriev, I. A.
last_name: Dmitriev
- first_name: Vlad
full_name: Dziom, Vlad
id: 6A9A37C2-8C5C-11E9-AE53-F2FDE5697425
last_name: Dziom
orcid: 0000-0002-1648-0999
- first_name: A. A.
full_name: Dobretsova, A. A.
last_name: Dobretsova
- first_name: N. N.
full_name: Mikhailov, N. N.
last_name: Mikhailov
- first_name: Z. D.
full_name: Kvon, Z. D.
last_name: Kvon
- first_name: A.
full_name: Pimenov, A.
last_name: Pimenov
citation:
ama: Savchenko ML, Gospodarič J, Shuvaev A, et al. Optical Shubnikov-de Haas oscillations
in two-dimensional electron systems. Physical Review Research. 2024;6(2).
doi:10.1103/PhysRevResearch.6.L022027
apa: Savchenko, M. L., Gospodarič, J., Shuvaev, A., Dmitriev, I. A., Dziom, V.,
Dobretsova, A. A., … Pimenov, A. (2024). Optical Shubnikov-de Haas oscillations
in two-dimensional electron systems. Physical Review Research. American
Physical Society. https://doi.org/10.1103/PhysRevResearch.6.L022027
chicago: Savchenko, M. L., J. Gospodarič, A. Shuvaev, I. A. Dmitriev, Vlad Dziom,
A. A. Dobretsova, N. N. Mikhailov, Z. D. Kvon, and A. Pimenov. “Optical Shubnikov-de
Haas Oscillations in Two-Dimensional Electron Systems.” Physical Review Research.
American Physical Society, 2024. https://doi.org/10.1103/PhysRevResearch.6.L022027.
ieee: M. L. Savchenko et al., “Optical Shubnikov-de Haas oscillations in
two-dimensional electron systems,” Physical Review Research, vol. 6, no.
2. American Physical Society, 2024.
ista: Savchenko ML, Gospodarič J, Shuvaev A, Dmitriev IA, Dziom V, Dobretsova AA,
Mikhailov NN, Kvon ZD, Pimenov A. 2024. Optical Shubnikov-de Haas oscillations
in two-dimensional electron systems. Physical Review Research. 6(2), L022027.
mla: Savchenko, M. L., et al. “Optical Shubnikov-de Haas Oscillations in Two-Dimensional
Electron Systems.” Physical Review Research, vol. 6, no. 2, L022027, American
Physical Society, 2024, doi:10.1103/PhysRevResearch.6.L022027.
short: M.L. Savchenko, J. Gospodarič, A. Shuvaev, I.A. Dmitriev, V. Dziom, A.A.
Dobretsova, N.N. Mikhailov, Z.D. Kvon, A. Pimenov, Physical Review Research 6
(2024).
date_created: 2024-05-19T22:01:12Z
date_published: 2024-04-01T00:00:00Z
date_updated: 2025-05-14T09:31:15Z
day: '01'
ddc:
- '530'
department:
- _id: ZhAl
doi: 10.1103/PhysRevResearch.6.L022027
external_id:
arxiv:
- '2402.05879'
file:
- access_level: open_access
checksum: 78c8c3cf1bda766e3de0db45f143a367
content_type: application/pdf
creator: dernst
date_created: 2024-05-22T06:39:35Z
date_updated: 2024-05-22T06:39:35Z
file_id: '15412'
file_name: 2024_PhysicalReviewResearch_Savchenko.pdf
file_size: 1697856
relation: main_file
success: 1
file_date_updated: 2024-05-22T06:39:35Z
has_accepted_license: '1'
intvolume: ' 6'
issue: '2'
language:
- iso: eng
month: '04'
oa: 1
oa_version: Published Version
publication: Physical Review Research
publication_identifier:
eissn:
- 2643-1564
publication_status: published
publisher: American Physical Society
quality_controlled: '1'
scopus_import: '1'
status: public
title: Optical Shubnikov-de Haas oscillations in two-dimensional electron systems
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'
...
---
DOAJ_listed: '1'
OA_place: publisher
OA_type: gold
_id: '15407'
abstract:
- lang: eng
text: We propose and implement a family of quantum-informed recursive optimization
(QIRO) algorithms for combinatorial optimization problems. Our approach leverages
quantum resources to obtain information that is used in problem-specific classical
reduction steps that recursively simplify the problem. These reduction steps address
the limitations of the quantum component (e.g., locality) and ensure solution
feasibility in constrained optimization problems. Additionally, we use backtracking
techniques to further improve the performance of the algorithm without increasing
the requirements on the quantum hardware. We showcase the capabilities of our
approach by informing QIRO with correlations from classical simulations of shallow
circuits of the quantum approximate optimization algorithm, solving instances
of maximum independent set and maximum satisfiability problems with hundreds of
variables. We also demonstrate how QIRO can be deployed on a neutral atom quantum
processor to find large independent sets of graphs. In summary, our scheme achieves
results comparable to classical heuristics even with relatively weak quantum resources.
Furthermore, enhancing the quality of these quantum resources improves the performance
of the algorithms. Notably, the modular nature of QIRO offers various avenues
for modifications, positioning our work as a template for a broader class of hybrid
quantum-classical algorithms for combinatorial optimization.
acknowledgement: J.R.F. and A.K. thank Libor Caha and Alexander Kliesch for insightful
discussions. The authors thank Lilly Palackal, Maximilian Passek, Carlos Riofrío,
and Gili Rosenberg for thorough reviews of the manuscript, and the Amazon Braket,
BMW, and QuEra teams for their support. C.M. thanks the Munich Quantum Valley initiative,
which is supported by the Bavarian State Government with funds from the Hightech
Agenda Bayern Plus. H.G.K. would like to thank Am Platzl 1A for providing the necessary
environment for creative thinking. An open-source implementation of QIRO is available
online [60].
article_number: '020327'
article_processing_charge: Yes
article_type: original
arxiv: 1
author:
- first_name: Jernej Rudi
full_name: Finžgar, Jernej Rudi
last_name: Finžgar
- first_name: Aron
full_name: Kerschbaumer, Aron
id: ade85a9c-3200-11ee-973b-91c1eb240410
last_name: Kerschbaumer
- first_name: Martin J.A.
full_name: Schuetz, Martin J.A.
last_name: Schuetz
- first_name: Christian B.
full_name: Mendl, Christian B.
last_name: Mendl
- first_name: Helmut G.
full_name: Katzgraber, Helmut G.
last_name: Katzgraber
citation:
ama: Finžgar JR, Kerschbaumer A, Schuetz MJA, Mendl CB, Katzgraber HG. Quantum-informed
recursive optimization algorithms. PRX Quantum. 2024;5(2). doi:10.1103/PRXQuantum.5.020327
apa: Finžgar, J. R., Kerschbaumer, A., Schuetz, M. J. A., Mendl, C. B., & Katzgraber,
H. G. (2024). Quantum-informed recursive optimization algorithms. PRX Quantum.
American Physical Society. https://doi.org/10.1103/PRXQuantum.5.020327
chicago: Finžgar, Jernej Rudi, Aron Kerschbaumer, Martin J.A. Schuetz, Christian
B. Mendl, and Helmut G. Katzgraber. “Quantum-Informed Recursive Optimization Algorithms.”
PRX Quantum. American Physical Society, 2024. https://doi.org/10.1103/PRXQuantum.5.020327.
ieee: J. R. Finžgar, A. Kerschbaumer, M. J. A. Schuetz, C. B. Mendl, and H. G. Katzgraber,
“Quantum-informed recursive optimization algorithms,” PRX Quantum, vol.
5, no. 2. American Physical Society, 2024.
ista: Finžgar JR, Kerschbaumer A, Schuetz MJA, Mendl CB, Katzgraber HG. 2024. Quantum-informed
recursive optimization algorithms. PRX Quantum. 5(2), 020327.
mla: Finžgar, Jernej Rudi, et al. “Quantum-Informed Recursive Optimization Algorithms.”
PRX Quantum, vol. 5, no. 2, 020327, American Physical Society, 2024, doi:10.1103/PRXQuantum.5.020327.
short: J.R. Finžgar, A. Kerschbaumer, M.J.A. Schuetz, C.B. Mendl, H.G. Katzgraber,
PRX Quantum 5 (2024).
corr_author: '1'
date_created: 2024-05-19T22:01:13Z
date_published: 2024-05-01T00:00:00Z
date_updated: 2025-05-14T09:29:40Z
day: '01'
ddc:
- '530'
department:
- _id: GradSch
doi: 10.1103/PRXQuantum.5.020327
external_id:
arxiv:
- '2308.13607'
file:
- access_level: open_access
checksum: 76bdf0b4dc06d59d073a57bd6957a96c
content_type: application/pdf
creator: dernst
date_created: 2024-05-21T09:35:14Z
date_updated: 2024-05-21T09:35:14Z
file_id: '15409'
file_name: 2024_PRXQuantum_Finzgar.pdf
file_size: 2016085
relation: main_file
success: 1
file_date_updated: 2024-05-21T09:35:14Z
has_accepted_license: '1'
intvolume: ' 5'
issue: '2'
language:
- iso: eng
month: '05'
oa: 1
oa_version: Published Version
publication: PRX Quantum
publication_identifier:
eissn:
- 2691-3399
publication_status: published
publisher: American Physical Society
quality_controlled: '1'
scopus_import: '1'
status: public
title: Quantum-informed recursive optimization algorithms
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: 5
year: '2024'
...