---
OA_place: repository
OA_type: gold
_id: '18697'
abstract:
- lang: eng
text: The information-processing capability of the brain’s cellular network depends
on the physical wiring pattern between neurons and their molecular and functional
characteristics. Mapping neurons and resolving their individual synaptic connections
can be achieved by volumetric imaging at nanoscale resolution with dense cellular
labelling. Light microscopy is uniquely positioned to visualize specific molecules
but dense, synapse-level circuit reconstruction by light microscopy has been out
of reach due to limitations in resolution, contrast, and volumetric imaging capability.
Here we developed light-microscopy based connectomics (LICONN). We integrated
specifically engineered hydrogel embedding and expansion with comprehensive deep-learning
based segmentation and analysis of connectivity, thus directly incorporating molecular
information in synapse-level brain tissue reconstructions. LICONN will allow synapse-level
brain tissue phenotyping in biological experiments in a readily adoptable manner.
acknowledged_ssus:
- _id: Bio
- _id: LifeSc
- _id: ScienComp
- _id: PreCl
- _id: M-Shop
- _id: E-Lib
article_processing_charge: No
author:
- first_name: Johann G
full_name: Danzl, Johann G
id: 42EFD3B6-F248-11E8-B48F-1D18A9856A87
last_name: Danzl
orcid: 0000-0001-8559-3973
- first_name: Julia
full_name: Lyudchik, Julia
id: 46E28B80-F248-11E8-B48F-1D18A9856A87
last_name: Lyudchik
- first_name: Caroline
full_name: Kreuzinger, Caroline
id: 382077BA-F248-11E8-B48F-1D18A9856A87
last_name: Kreuzinger
citation:
ama: Danzl JG, Lyudchik J, Kreuzinger C. Light-microscopy based connectomic reconstruction
of mammalian brain tissue. 2025. doi:10.15479/AT:ISTA:18697
apa: Danzl, J. G., Lyudchik, J., & Kreuzinger, C. (2025). Light-microscopy based
connectomic reconstruction of mammalian brain tissue. Institute of Science and
Technology Austria. https://doi.org/10.15479/AT:ISTA:18697
chicago: Danzl, Johann G, Julia Lyudchik, and Caroline Kreuzinger. “Light-Microscopy
Based Connectomic Reconstruction of Mammalian Brain Tissue.” Institute of Science
and Technology Austria, 2025. https://doi.org/10.15479/AT:ISTA:18697.
ieee: J. G. Danzl, J. Lyudchik, and C. Kreuzinger, “Light-microscopy based connectomic
reconstruction of mammalian brain tissue.” Institute of Science and Technology
Austria, 2025.
ista: Danzl JG, Lyudchik J, Kreuzinger C. 2025. Light-microscopy based connectomic
reconstruction of mammalian brain tissue, Institute of Science and Technology
Austria, 10.15479/AT:ISTA:18697.
mla: Danzl, Johann G., et al. Light-Microscopy Based Connectomic Reconstruction
of Mammalian Brain Tissue. Institute of Science and Technology Austria, 2025,
doi:10.15479/AT:ISTA:18697.
short: J.G. Danzl, J. Lyudchik, C. Kreuzinger, (2025).
contributor:
- contributor_type: researcher
first_name: Mojtaba
id: 3A0A06F4-F248-11E8-B48F-1D18A9856A87
last_name: Tavakoli
orcid: 0000-0002-7667-6854
- contributor_type: researcher
first_name: Julia
id: 46E28B80-F248-11E8-B48F-1D18A9856A87
last_name: Lyudchik
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first_name: Michal
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first_name: Vitali
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last_name: Vistunou
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first_name: Nathalie
id: 40E7F008-F248-11E8-B48F-1D18A9856A87
last_name: Agudelo Duenas
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first_name: Jakob
id: 937696FA-C996-11E9-8C7C-CF13E6697425
last_name: Vorlaufer
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first_name: Christoph M
id: 4DF26D8C-F248-11E8-B48F-1D18A9856A87
last_name: Sommer
orcid: 0000-0003-1216-9105
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first_name: Caroline
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last_name: Kreuzinger
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id: 42EFD3B6-F248-11E8-B48F-1D18A9856A87
last_name: Danzl
orcid: 0000-0001-8559-3973
corr_author: '1'
date_created: 2024-12-20T09:22:20Z
date_published: 2025-03-03T00:00:00Z
date_updated: 2026-04-28T13:33:34Z
day: '03'
ddc:
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department:
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doi: 10.15479/AT:ISTA:18697
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fulldoi: https://doi.org/10.15479/AT:ISTA:18697
has_accepted_license: '1'
month: '03'
oa: 1
oa_version: Published Version
publisher: Institute of Science and Technology Austria
related_material:
link:
- description: Original datasets of large size (>10GB) and datasets in zarr/n5/ims/npz
format are provided via this external link.
relation: research_data
url: https://pub.ista.ac.at/group_danzl/data/LICONN/
record:
- id: '19704'
relation: used_in_publication
status: public
status: public
title: Light-microscopy based connectomic reconstruction of mammalian brain tissue
tmp:
image: /images/cc_by_nc_sa.png
legal_code_url: https://creativecommons.org/licenses/by-nc-sa/4.0/legalcode
name: Creative Commons Attribution-NonCommercial-ShareAlike 4.0 International (CC
BY-NC-SA 4.0)
short: CC BY-NC-SA (4.0)
type: research_data
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
year: '2025'
...
---
OA_type: closed access
_id: '18701'
abstract:
- lang: eng
text: We developed in-situ engineered polycrystalline polythiophene (PTh) and its
composite with reduced graphene oxide (PTh-rGO) via a simple chemical synthesis.
The PTh-rGO-based electrodes in a symmetrical device with xanthan gum in 1 M aq.
Na2SO4 as an electrolyte, delivers a specific capacitance (Csp) of 114.7 F g–1
(electrode) and 28.7 F g–1 (cell) at an applied current density of 0.2 A g−1.
The maximum energy and power densities recorded from the device were 588.0 mWh
kg−1 and 1.1 kW kg−1 at 1.5 A g−1. The device exhibited a remarkable retention
of Csp of 98.9 % over 10,000 continuous galvanostatic charge–discharge cycles
highlighting an excellent performance. Electrochemical impedance spectroscopy
analysis emphasizes material’s excellent structural integrity. This is attributed
to the crystalline phases present in the matrix.
acknowledgement: This work was partly supported by the Institute of Information &
Communications Technology Planning & Evaluation (IITP) grant funded by the Korea
government (MSIT) (No.RS-2021-II210077) and Korea Institute of Energy Technology
Evaluation and Planning (KETEP) grant funded by the Korea government (MOTIE)(RS-2024-00398346,
ESS BigData-Based O&M and Asset Management Technical Manpower Training).
article_number: '137869'
article_processing_charge: No
article_type: original
author:
- first_name: Neelima
full_name: Mahato, Neelima
last_name: Mahato
- first_name: Saurabh
full_name: Singh, Saurabh
id: 12d625da-9cb3-11ed-9667-af09d37d3f0a
last_name: Singh
orcid: 0000-0003-2209-5269
- first_name: T. V.M.
full_name: Sreekanth, T. V.M.
last_name: Sreekanth
- first_name: Kisoo
full_name: Yoo, Kisoo
last_name: Yoo
- first_name: Jonghoon
full_name: Kim, Jonghoon
last_name: Kim
citation:
ama: 'Mahato N, Singh S, Sreekanth TVM, Yoo K, Kim J. In-situ engineered highly-crystalline
Polythiophene empowered electrochemical capacitor-II: Anomalous electrochemical
charge storage behavior of Polythiophene-rGO composite. Materials Letters.
2025;382. doi:10.1016/j.matlet.2024.137869'
apa: 'Mahato, N., Singh, S., Sreekanth, T. V. M., Yoo, K., & Kim, J. (2025).
In-situ engineered highly-crystalline Polythiophene empowered electrochemical
capacitor-II: Anomalous electrochemical charge storage behavior of Polythiophene-rGO
composite. Materials Letters. Elsevier. https://doi.org/10.1016/j.matlet.2024.137869'
chicago: 'Mahato, Neelima, Saurabh Singh, T. V.M. Sreekanth, Kisoo Yoo, and Jonghoon
Kim. “In-Situ Engineered Highly-Crystalline Polythiophene Empowered Electrochemical
Capacitor-II: Anomalous Electrochemical Charge Storage Behavior of Polythiophene-RGO
Composite.” Materials Letters. Elsevier, 2025. https://doi.org/10.1016/j.matlet.2024.137869.'
ieee: 'N. Mahato, S. Singh, T. V. M. Sreekanth, K. Yoo, and J. Kim, “In-situ engineered
highly-crystalline Polythiophene empowered electrochemical capacitor-II: Anomalous
electrochemical charge storage behavior of Polythiophene-rGO composite,” Materials
Letters, vol. 382. Elsevier, 2025.'
ista: 'Mahato N, Singh S, Sreekanth TVM, Yoo K, Kim J. 2025. In-situ engineered
highly-crystalline Polythiophene empowered electrochemical capacitor-II: Anomalous
electrochemical charge storage behavior of Polythiophene-rGO composite. Materials
Letters. 382, 137869.'
mla: 'Mahato, Neelima, et al. “In-Situ Engineered Highly-Crystalline Polythiophene
Empowered Electrochemical Capacitor-II: Anomalous Electrochemical Charge Storage
Behavior of Polythiophene-RGO Composite.” Materials Letters, vol. 382,
137869, Elsevier, 2025, doi:10.1016/j.matlet.2024.137869.'
short: N. Mahato, S. Singh, T.V.M. Sreekanth, K. Yoo, J. Kim, Materials Letters
382 (2025).
date_created: 2024-12-22T23:01:47Z
date_published: 2025-03-01T00:00:00Z
date_updated: 2025-05-19T14:05:22Z
day: '01'
department:
- _id: MaIb
doi: 10.1016/j.matlet.2024.137869
external_id:
isi:
- '001433664000001'
fulldoi: https://doi.org/10.1016/j.matlet.2024.137869
intvolume: ' 382'
isi: 1
language:
- iso: eng
month: '03'
oa_version: None
publication: Materials Letters
publication_identifier:
eissn:
- 1873-4979
issn:
- 0167-577X
publication_status: published
publisher: Elsevier
quality_controlled: '1'
scopus_import: '1'
status: public
title: 'In-situ engineered highly-crystalline Polythiophene empowered electrochemical
capacitor-II: Anomalous electrochemical charge storage behavior of Polythiophene-rGO
composite'
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 382
year: '2025'
...
---
OA_type: closed access
_id: '18707'
abstract:
- lang: eng
text: Lead Sulfide (PbS) has garnered attention as a promising thermoelectric (TE)
material due to its natural abundance and cost-effectiveness. However, its practical
application is hindered by inherently high lattice thermal conductivity and low
electrical conductivity. In this study, we address these challenges by surface
functionalization of PbS nanocrystals using Cu2S molecular complexes-based ligand
displacement. The molecular complexes facilitate the incorporation of Cu into
the PbS matrix and leads to the formation of nanoscale defects, dislocations,
and strain fields while optimizing the charge carrier transport. The structural
modulations enhance the phonon scattering and lead to a significant reduction
in lattice thermal conductivity of 0.60 W m−1K−1 at 867 K in the PbS-Cu2S system.
Simultaneously, the Cu incorporation improves electrical conductivity by increasing
both carrier concentration and mobility with carefully optimized the content of
Cu2S molecular complexes. These synergistic modifications yield a peak figure-of-merit
(zT) of 1.05 at 867 K for the PbS-1.0 %Cu2S sample, representing an almost twofold
enhancement in TE performance compared to pristine PbS. This work highlights the
effectiveness of surface treatment in overcoming the intrinsic limitations of
PbS-based materials and presents a promising strategy for the development of high-efficiency
TE systems.
acknowledgement: Y.L. acknowledges funding from the National Natural Science Foundation
of China (NSFC) (Grants No. 22209034), the Innovation and Entrepreneurship Project
of Overseas Returnees in Anhui Province (Grant No. 2022LCX002) and the Fundamental
Research Funds for the Central Universities (JZ2024HGTB0239). M.I. acknowledges
financial support from ISTA and the Werner Siemens Foundation. K.H.L. acknowledges
financial support from the National Natural Science Foundation of China (NSFC) (Grant
No. 22208293). M.H acknowledges funding from Australian Research Council (FT230100316
and IH200100035) and iLAuNCH, Trailblazer Universities Program. L. H. and S. W.
acknowledge the Fundamental Research Funds for the Central Universities (JZ2023HGTA0179,
JZ2024HGTA0170).
article_processing_charge: No
article_type: original
author:
- first_name: Haibo
full_name: Shu, Haibo
last_name: Shu
- first_name: Mingjun
full_name: Zhao, Mingjun
last_name: Zhao
- first_name: Shaoqing
full_name: Lu, Shaoqing
last_name: Lu
- first_name: Shanhong
full_name: Wan, Shanhong
last_name: Wan
- first_name: Aziz
full_name: Genç, Aziz
last_name: Genç
- first_name: Lulu
full_name: Huang, Lulu
last_name: Huang
- first_name: Maria
full_name: Ibáñez, Maria
id: 43C61214-F248-11E8-B48F-1D18A9856A87
last_name: Ibáñez
orcid: 0000-0001-5013-2843
- first_name: Khak Ho
full_name: Lim, Khak Ho
last_name: Lim
- first_name: Min
full_name: Hong, Min
last_name: Hong
- first_name: Yu
full_name: Liu, Yu
id: 2A70014E-F248-11E8-B48F-1D18A9856A87
last_name: Liu
orcid: 0000-0001-7313-6740
citation:
ama: Shu H, Zhao M, Lu S, et al. Influence of surface engineering on the transport
properties of lead sulfide nanomaterials. Journal of Colloid and Interface
Science. 2025;683:703-712. doi:10.1016/j.jcis.2024.12.067
apa: Shu, H., Zhao, M., Lu, S., Wan, S., Genç, A., Huang, L., … Liu, Y. (2025).
Influence of surface engineering on the transport properties of lead sulfide nanomaterials.
Journal of Colloid and Interface Science. Elsevier. https://doi.org/10.1016/j.jcis.2024.12.067
chicago: Shu, Haibo, Mingjun Zhao, Shaoqing Lu, Shanhong Wan, Aziz Genç, Lulu Huang,
Maria Ibáñez, Khak Ho Lim, Min Hong, and Yu Liu. “Influence of Surface Engineering
on the Transport Properties of Lead Sulfide Nanomaterials.” Journal of Colloid
and Interface Science. Elsevier, 2025. https://doi.org/10.1016/j.jcis.2024.12.067.
ieee: H. Shu et al., “Influence of surface engineering on the transport properties
of lead sulfide nanomaterials,” Journal of Colloid and Interface Science,
vol. 683. Elsevier, pp. 703–712, 2025.
ista: Shu H, Zhao M, Lu S, Wan S, Genç A, Huang L, Ibáñez M, Lim KH, Hong M, Liu
Y. 2025. Influence of surface engineering on the transport properties of lead
sulfide nanomaterials. Journal of Colloid and Interface Science. 683, 703–712.
mla: Shu, Haibo, et al. “Influence of Surface Engineering on the Transport Properties
of Lead Sulfide Nanomaterials.” Journal of Colloid and Interface Science,
vol. 683, Elsevier, 2025, pp. 703–12, doi:10.1016/j.jcis.2024.12.067.
short: H. Shu, M. Zhao, S. Lu, S. Wan, A. Genç, L. Huang, M. Ibáñez, K.H. Lim, M.
Hong, Y. Liu, Journal of Colloid and Interface Science 683 (2025) 703–712.
date_created: 2024-12-29T23:01:56Z
date_published: 2025-04-01T00:00:00Z
date_updated: 2025-05-19T14:03:54Z
day: '01'
department:
- _id: MaIb
doi: 10.1016/j.jcis.2024.12.067
external_id:
isi:
- '001393340800001'
pmid:
- '39706089'
fulldoi: https://doi.org/10.1016/j.jcis.2024.12.067
intvolume: ' 683'
isi: 1
language:
- iso: eng
month: '04'
oa_version: None
page: 703-712
pmid: 1
project:
- _id: 9B8F7476-BA93-11EA-9121-9846C619BF3A
name: 'HighTE: The Werner Siemens Laboratory for the High Throughput Discovery of
Semiconductors for Waste Heat Recovery'
publication: Journal of Colloid and Interface Science
publication_identifier:
eissn:
- 1095-7103
issn:
- 0021-9797
publication_status: published
publisher: Elsevier
quality_controlled: '1'
scopus_import: '1'
status: public
title: Influence of surface engineering on the transport properties of lead sulfide
nanomaterials
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 683
year: '2025'
...
---
_id: '18712'
abstract:
- lang: eng
text: 'This file contains the code associated with the manuscript ''Effect of assortative
mating and sexual selection on polygenic barriers to gene flow''. '
acknowledged_ssus:
- _id: ScienComp
article_processing_charge: No
author:
- first_name: Parvathy
full_name: Surendranadh, Parvathy
id: 455235B8-F248-11E8-B48F-1D18A9856A87
last_name: Surendranadh
orcid: 0000-0001-6395-386X
- first_name: Himani
full_name: Sachdeva, Himani
last_name: Sachdeva
citation:
ama: Surendranadh P, Sachdeva H. Mathematica notebook and Fortran code for “Effect
of assortative mating and sexual selection on polygenic barriers to gene flow.”
2025. doi:10.15479/AT:ISTA:17344
apa: Surendranadh, P., & Sachdeva, H. (2025). Mathematica notebook and Fortran
code for “Effect of assortative mating and sexual selection on polygenic barriers
to gene flow.” Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:17344
chicago: Surendranadh, Parvathy, and Himani Sachdeva. “Mathematica Notebook and
Fortran Code for ‘Effect of Assortative Mating and Sexual Selection on Polygenic
Barriers to Gene Flow.’” Institute of Science and Technology Austria, 2025. https://doi.org/10.15479/AT:ISTA:17344.
ieee: P. Surendranadh and H. Sachdeva, “Mathematica notebook and Fortran code for
‘Effect of assortative mating and sexual selection on polygenic barriers to gene
flow.’” Institute of Science and Technology Austria, 2025.
ista: Surendranadh P, Sachdeva H. 2025. Mathematica notebook and Fortran code for
‘Effect of assortative mating and sexual selection on polygenic barriers to gene
flow’, Institute of Science and Technology Austria, 10.15479/AT:ISTA:17344.
mla: Surendranadh, Parvathy, and Himani Sachdeva. Mathematica Notebook and Fortran
Code for “Effect of Assortative Mating and Sexual Selection on Polygenic Barriers
to Gene Flow.” Institute of Science and Technology Austria, 2025, doi:10.15479/AT:ISTA:17344.
short: P. Surendranadh, H. Sachdeva, (2025).
corr_author: '1'
date_created: 2025-01-01T15:28:27Z
date_published: 2025-01-07T00:00:00Z
date_updated: 2025-12-30T08:44:12Z
day: '07'
ddc:
- '576'
department:
- _id: GradSch
- _id: NiBa
doi: 10.15479/AT:ISTA:17344
file:
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checksum: 9c5f91876014706990a0728c3675cd2a
content_type: application/zip
creator: psurendr
date_created: 2025-01-02T12:30:27Z
date_updated: 2025-01-02T12:30:27Z
file_id: '18722'
file_name: Codes.zip
file_size: 326835
relation: main_file
success: 1
- access_level: open_access
checksum: 47fe98b7cc526e634e42de58f5eae288
content_type: text/plain
creator: psurendr
date_created: 2025-01-02T12:30:39Z
date_updated: 2025-01-02T12:30:39Z
file_id: '18723'
file_name: ReadMe.txt
file_size: 620
relation: main_file
success: 1
file_date_updated: 2025-01-02T12:30:39Z
fulldoi: https://doi.org/10.15479/AT:ISTA:17344
has_accepted_license: '1'
month: '01'
oa: 1
oa_version: Published Version
publisher: Institute of Science and Technology Austria
related_material:
record:
- id: '19876'
relation: used_in_publication
status: public
status: public
title: Mathematica notebook and Fortran code for 'Effect of assortative mating and
sexual selection on polygenic barriers to gene flow'
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: research_data
user_id: 9947682f-b9fa-11ee-9c4a-b3ffaafe6614
year: '2025'
...
---
OA_place: publisher
OA_type: hybrid
_id: '18753'
abstract:
- lang: eng
text: "We continue a line of research which studies which hereditary families of
digraphs have bounded dichromatic number. For a class of digraphs C, a hero in
\ C is any digraph H\r\n such that H -free digraphs in C have bounded dichromatic
number. We show that if F\r\n is an oriented star of degree at least five, the
only heroes for the class of F -free digraphs are transitive tournaments. For
oriented stars F of degree exactly four, we show the only heroes in F -free
digraphs are transitive tournaments, or possibly special joins of transitive tournaments.
Aboulker et al. characterized the set of heroes of {H,K1+P2→} -free digraphs
almost completely, and we show the same characterization for the class of {H,rK1+P3→}
-free digraphs. Lastly, we show that if we forbid two \"valid\" orientations of
brooms, then every transitive tournament is a hero for this class of digraphs."
acknowledgement: "We thank the anonymous referees for their careful proofreading which
helped improve the presentation of this paper. We also thank one of the anonymous
referees for pointing out our construction implies Theorem 1.7!\r\nBenjamin Moore
finished this project while a postdoctoral researcher at Charles University, and
was supported by project 22-17398S (Flows and cycles in graphs on surfaces) of the
Czech Science Foundation. Benjamin Moore is currently funded by RANDSTRUCT No. 101076777,
and appreciates the gracious support. We acknowledge the support of the Natural
Sciences and Engineering Research Council of Canada (NSERC), [funding reference
number RGPIN-2020-03912]. Cette recherche a été financée par le Conseil de recherches
en sciences naturelles et en génie du Canada (CRSNG), [numéro de référence RGPIN-2020-03912].
This project was funded in part by the Government of Ontario ."
article_number: '104104'
article_processing_charge: Yes (in subscription journal)
article_type: original
arxiv: 1
author:
- first_name: Alvaro
full_name: Carbonero, Alvaro
last_name: Carbonero
- first_name: Hidde
full_name: Koerts, Hidde
last_name: Koerts
- first_name: Benjamin
full_name: Moore, Benjamin
id: 6dc1a1be-bf1c-11ed-8d2b-d044840f49d6
last_name: Moore
- first_name: Sophie
full_name: Spirkl, Sophie
last_name: Spirkl
citation:
ama: Carbonero A, Koerts H, Moore B, Spirkl S. On heroes in digraphs with forbidden
induced forests. European Journal of Combinatorics. 2025;125. doi:10.1016/j.ejc.2024.104104
apa: Carbonero, A., Koerts, H., Moore, B., & Spirkl, S. (2025). On heroes in
digraphs with forbidden induced forests. European Journal of Combinatorics.
Elsevier. https://doi.org/10.1016/j.ejc.2024.104104
chicago: Carbonero, Alvaro, Hidde Koerts, Benjamin Moore, and Sophie Spirkl. “On
Heroes in Digraphs with Forbidden Induced Forests.” European Journal of Combinatorics.
Elsevier, 2025. https://doi.org/10.1016/j.ejc.2024.104104.
ieee: A. Carbonero, H. Koerts, B. Moore, and S. Spirkl, “On heroes in digraphs with
forbidden induced forests,” European Journal of Combinatorics, vol. 125.
Elsevier, 2025.
ista: Carbonero A, Koerts H, Moore B, Spirkl S. 2025. On heroes in digraphs with
forbidden induced forests. European Journal of Combinatorics. 125, 104104.
mla: Carbonero, Alvaro, et al. “On Heroes in Digraphs with Forbidden Induced Forests.”
European Journal of Combinatorics, vol. 125, 104104, Elsevier, 2025, doi:10.1016/j.ejc.2024.104104.
short: A. Carbonero, H. Koerts, B. Moore, S. Spirkl, European Journal of Combinatorics
125 (2025).
corr_author: '1'
date_created: 2025-01-05T23:01:55Z
date_published: 2025-03-01T00:00:00Z
date_updated: 2025-05-19T14:06:00Z
day: '01'
ddc:
- '510'
department:
- _id: MaKw
doi: 10.1016/j.ejc.2024.104104
external_id:
arxiv:
- '2306.04710'
isi:
- '001400113700001'
file:
- access_level: open_access
checksum: 2c75f78f40ebb93d16fe3765bda2905a
content_type: application/pdf
creator: dernst
date_created: 2025-04-16T09:16:25Z
date_updated: 2025-04-16T09:16:25Z
file_id: '19577'
file_name: 2025_EuropJournCombinatorics_Carbonero.pdf
file_size: 1110657
relation: main_file
success: 1
file_date_updated: 2025-04-16T09:16:25Z
fulldoi: https://doi.org/10.1016/j.ejc.2024.104104
has_accepted_license: '1'
intvolume: ' 125'
isi: 1
language:
- iso: eng
month: '03'
oa: 1
oa_version: Published Version
project:
- _id: bd95085b-d553-11ed-ba76-e55d3349be45
grant_number: '101076777'
name: Randomness and structure in combinatorics
publication: European Journal of Combinatorics
publication_identifier:
issn:
- 0195-6698
publication_status: published
publisher: Elsevier
quality_controlled: '1'
scopus_import: '1'
status: public
title: On heroes in digraphs with forbidden induced forests
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: 125
year: '2025'
...
---
OA_place: publisher
OA_type: hybrid
_id: '18754'
abstract:
- lang: eng
text: 'Exploring the molecular correlates of metabolic health measures may identify
their shared and unique biological processes and pathways. Molecular proxies of
these traits may also provide a more objective approach to their measurement.
Here, DNA methylation (DNAm) data were used in epigenome-wide association studies
(EWASs) and for training epigenetic scores (EpiScores) of six metabolic traits:
body mass index (BMI), body fat percentage, waist-hip ratio, and blood-based measures
of glucose, high-density lipoprotein cholesterol, and total cholesterol in >17,000
volunteers from the Generation Scotland (GS) cohort. We observed a maximum of
12,033 significant findings (p < 3.6 × 10−8) for BMI in a marginal linear regression
EWAS. By contrast, a joint and conditional Bayesian penalized regression approach
yielded 27 high-confidence associations with BMI. EpiScores trained in GS performed
well in both Scottish and Singaporean test cohorts (Lothian Birth Cohort 1936
[LBC1936] and Health for Life in Singapore [HELIOS]). The EpiScores for BMI and
total cholesterol performed best in HELIOS, explaining 20.8% and 7.1% of the variance
in the measured traits, respectively. The corresponding results in LBC1936 were
14.4% and 3.2%, respectively. Differences were observed in HELIOS for body fat,
where the EpiScore explained ∼9% of the variance in Chinese and Malay -subgroups
but ∼3% in the Indian subgroup. The EpiScores also correlated with cognitive function
in LBC1936 (standardized βrange: 0.08–0.12, false discovery rate p [pFDR] < 0.05).
Accounting for the correlation structure across the methylome can vastly affect
the number of lead findings in EWASs. The EpiScores of metabolic traits are broadly
applicable across populations and can reflect differences in cognition.'
article_processing_charge: No
article_type: original
author:
- first_name: Hannah M.
full_name: Smith, Hannah M.
last_name: Smith
- first_name: Hong Kiat
full_name: Ng, Hong Kiat
last_name: Ng
- first_name: Joanna E.
full_name: Moodie, Joanna E.
last_name: Moodie
- first_name: Danni A.
full_name: Gadd, Danni A.
last_name: Gadd
- first_name: Daniel L.
full_name: Mccartney, Daniel L.
last_name: Mccartney
- first_name: Elena
full_name: Bernabeu, Elena
last_name: Bernabeu
- first_name: Archie
full_name: Campbell, Archie
last_name: Campbell
- first_name: Paul
full_name: Redmond, Paul
last_name: Redmond
- first_name: Adele
full_name: Taylor, Adele
last_name: Taylor
- first_name: Danielle
full_name: Page, Danielle
last_name: Page
- first_name: Janie
full_name: Corley, Janie
last_name: Corley
- first_name: Sarah E.
full_name: Harris, Sarah E.
last_name: Harris
- first_name: Darwin
full_name: Tay, Darwin
last_name: Tay
- first_name: Ian J.
full_name: Deary, Ian J.
last_name: Deary
- first_name: Kathryn L.
full_name: Evans, Kathryn L.
last_name: Evans
- first_name: Matthew Richard
full_name: Robinson, Matthew Richard
id: E5D42276-F5DA-11E9-8E24-6303E6697425
last_name: Robinson
orcid: 0000-0001-8982-8813
- first_name: John C.
full_name: Chambers, John C.
last_name: Chambers
- first_name: Marie
full_name: Loh, Marie
last_name: Loh
- first_name: Simon R.
full_name: Cox, Simon R.
last_name: Cox
- first_name: Riccardo E.
full_name: Marioni, Riccardo E.
last_name: Marioni
- first_name: Robert F.
full_name: Hillary, Robert F.
last_name: Hillary
citation:
ama: Smith HM, Ng HK, Moodie JE, et al. DNA methylation-based predictors of metabolic
traits in Scottish and Singaporean cohorts. American Journal of Human Genetics.
2025;112(1):106-115. doi:10.1016/j.ajhg.2024.11.012
apa: Smith, H. M., Ng, H. K., Moodie, J. E., Gadd, D. A., Mccartney, D. L., Bernabeu,
E., … Hillary, R. F. (2025). DNA methylation-based predictors of metabolic traits
in Scottish and Singaporean cohorts. American Journal of Human Genetics.
Elsevier. https://doi.org/10.1016/j.ajhg.2024.11.012
chicago: Smith, Hannah M., Hong Kiat Ng, Joanna E. Moodie, Danni A. Gadd, Daniel
L. Mccartney, Elena Bernabeu, Archie Campbell, et al. “DNA Methylation-Based Predictors
of Metabolic Traits in Scottish and Singaporean Cohorts.” American Journal
of Human Genetics. Elsevier, 2025. https://doi.org/10.1016/j.ajhg.2024.11.012.
ieee: H. M. Smith et al., “DNA methylation-based predictors of metabolic
traits in Scottish and Singaporean cohorts,” American Journal of Human Genetics,
vol. 112, no. 1. Elsevier, pp. 106–115, 2025.
ista: Smith HM, Ng HK, Moodie JE, Gadd DA, Mccartney DL, Bernabeu E, Campbell A,
Redmond P, Taylor A, Page D, Corley J, Harris SE, Tay D, Deary IJ, Evans KL, Robinson
MR, Chambers JC, Loh M, Cox SR, Marioni RE, Hillary RF. 2025. DNA methylation-based
predictors of metabolic traits in Scottish and Singaporean cohorts. American Journal
of Human Genetics. 112(1), 106–115.
mla: Smith, Hannah M., et al. “DNA Methylation-Based Predictors of Metabolic Traits
in Scottish and Singaporean Cohorts.” American Journal of Human Genetics,
vol. 112, no. 1, Elsevier, 2025, pp. 106–15, doi:10.1016/j.ajhg.2024.11.012.
short: H.M. Smith, H.K. Ng, J.E. Moodie, D.A. Gadd, D.L. Mccartney, E. Bernabeu,
A. Campbell, P. Redmond, A. Taylor, D. Page, J. Corley, S.E. Harris, D. Tay, I.J.
Deary, K.L. Evans, M.R. Robinson, J.C. Chambers, M. Loh, S.R. Cox, R.E. Marioni,
R.F. Hillary, American Journal of Human Genetics 112 (2025) 106–115.
date_created: 2025-01-05T23:01:56Z
date_published: 2025-01-02T00:00:00Z
date_updated: 2025-02-27T12:38:23Z
day: '02'
ddc:
- '570'
department:
- _id: MaRo
doi: 10.1016/j.ajhg.2024.11.012
external_id:
isi:
- '001412498600001'
pmid:
- '39706196'
file:
- access_level: open_access
checksum: 891d120554f07da2c35d38388c29a690
content_type: application/pdf
creator: dernst
date_created: 2025-01-08T09:26:42Z
date_updated: 2025-01-08T09:26:42Z
file_id: '18776'
file_name: 2025_AJHG_Smith.pdf
file_size: 2266488
relation: main_file
success: 1
file_date_updated: 2025-01-08T09:26:42Z
fulldoi: https://doi.org/10.1016/j.ajhg.2024.11.012
has_accepted_license: '1'
intvolume: ' 112'
isi: 1
issue: '1'
language:
- iso: eng
month: '01'
oa: 1
oa_version: Published Version
page: 106-115
pmid: 1
publication: American Journal of Human Genetics
publication_identifier:
eissn:
- 1537-6605
issn:
- 0002-9297
publication_status: published
publisher: Elsevier
quality_controlled: '1'
related_material:
link:
- relation: software
url: https://github.com/marioni-group/Metabolic_trait
scopus_import: '1'
status: public
title: DNA methylation-based predictors of metabolic traits in Scottish and Singaporean
cohorts
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: 112
year: '2025'
...
---
OA_type: closed access
_id: '18765'
abstract:
- lang: eng
text: Mosaic Analysis with Double Markers (MADM) represents a mouse genetic approach
coupling differential fluorescent labeling to genetic manipulations in dividing
cells and their lineages. MADM uniquely enables the generation and visualization
of individual control or homozygous mutant cells in a heterozygous genetic environment.
Among its diverse applications, MADM has been used to dissect cell-autonomous
gene functions important for cortical development and neural development in general.
The high cellular resolution offered by MADM also permits the analysis of transcriptomic
changes of individual cells upon genetic manipulations. In this chapter, we describe
an experimental protocol combining the generation and isolation of MADM-labeled
cells with downstream single-cell RNA-sequencing technologies to probe cell-type
specific phenotypes due to genetic mutations at single-cell resolution.
acknowledged_ssus:
- _id: Bio
acknowledgement: 'We thank all Hippenmeyer lab members for support and discussions.
Experimental steps described were optimized with support provided by the Imaging
& Optics Facility (IOF) and Preclinical Facility (PCF) at ISTA, Vienna BioCenter
Core Facilities (VBCF), and Christoph Bock lab at Center for Molecular Medicine
(CeMM). G.C. received funding from European Commission (IST plus postdoctoral fellowship).
This work was supported by ISTA institutional funds: The Austrian Science Fund Special
Research Programmes (FWF SFB F78 Neuro Stem Modulation) to S.H.'
alternative_title:
- Methods in Molecular Biology
article_processing_charge: No
author:
- first_name: Giselle T
full_name: Cheung, Giselle T
id: 471195F6-F248-11E8-B48F-1D18A9856A87
last_name: Cheung
orcid: 0000-0001-8457-2572
- first_name: Florian
full_name: Pauler, Florian
id: 48EA0138-F248-11E8-B48F-1D18A9856A87
last_name: Pauler
orcid: 0000-0002-7462-0048
- first_name: Simon
full_name: Hippenmeyer, Simon
id: 37B36620-F248-11E8-B48F-1D18A9856A87
last_name: Hippenmeyer
orcid: 0000-0003-2279-1061
citation:
ama: 'Cheung GT, Pauler F, Hippenmeyer S. Probing Cell-Type Specificity of Mutant
Phenotype at Transcriptomic Level Using Mosaic Analysis with Double Markers (MADM).
In: Garcia-Marques J, Lee T, eds. Lineage Tracing. Vol 2886. MIMB. New
York, NY: Springer Nature; 2025:139-151. doi:10.1007/978-1-0716-4310-5_7'
apa: 'Cheung, G. T., Pauler, F., & Hippenmeyer, S. (2025). Probing Cell-Type
Specificity of Mutant Phenotype at Transcriptomic Level Using Mosaic Analysis
with Double Markers (MADM). In J. Garcia-Marques & T. Lee (Eds.), Lineage
Tracing (Vol. 2886, pp. 139–151). New York, NY: Springer Nature. https://doi.org/10.1007/978-1-0716-4310-5_7'
chicago: 'Cheung, Giselle T, Florian Pauler, and Simon Hippenmeyer. “Probing Cell-Type
Specificity of Mutant Phenotype at Transcriptomic Level Using Mosaic Analysis
with Double Markers (MADM).” In Lineage Tracing, edited by Jorge Garcia-Marques
and Tzumin Lee, 2886:139–51. MIMB. New York, NY: Springer Nature, 2025. https://doi.org/10.1007/978-1-0716-4310-5_7.'
ieee: 'G. T. Cheung, F. Pauler, and S. Hippenmeyer, “Probing Cell-Type Specificity
of Mutant Phenotype at Transcriptomic Level Using Mosaic Analysis with Double
Markers (MADM),” in Lineage Tracing, vol. 2886, J. Garcia-Marques and T.
Lee, Eds. New York, NY: Springer Nature, 2025, pp. 139–151.'
ista: 'Cheung GT, Pauler F, Hippenmeyer S. 2025.Probing Cell-Type Specificity of
Mutant Phenotype at Transcriptomic Level Using Mosaic Analysis with Double Markers
(MADM). In: Lineage Tracing. Methods in Molecular Biology, vol. 2886, 139–151.'
mla: Cheung, Giselle T., et al. “Probing Cell-Type Specificity of Mutant Phenotype
at Transcriptomic Level Using Mosaic Analysis with Double Markers (MADM).” Lineage
Tracing, edited by Jorge Garcia-Marques and Tzumin Lee, vol. 2886, Springer
Nature, 2025, pp. 139–51, doi:10.1007/978-1-0716-4310-5_7.
short: G.T. Cheung, F. Pauler, S. Hippenmeyer, in:, J. Garcia-Marques, T. Lee (Eds.),
Lineage Tracing, Springer Nature, New York, NY, 2025, pp. 139–151.
corr_author: '1'
date_created: 2025-01-07T08:36:47Z
date_published: 2025-01-03T00:00:00Z
date_updated: 2025-04-14T07:43:46Z
day: '03'
department:
- _id: SiHi
doi: 10.1007/978-1-0716-4310-5_7
ec_funded: 1
editor:
- first_name: Jorge
full_name: Garcia-Marques, Jorge
last_name: Garcia-Marques
- first_name: Tzumin
full_name: Lee, Tzumin
last_name: Lee
external_id:
pmid:
- '39745639'
fulldoi: https://doi.org/10.1007/978-1-0716-4310-5_7
intvolume: ' 2886'
language:
- iso: eng
month: '01'
oa_version: None
page: 139-151
place: New York, NY
pmid: 1
project:
- _id: 260C2330-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '754411'
name: ISTplus - Postdoctoral Fellowships
publication: Lineage Tracing
publication_identifier:
eisbn:
- '9781071643105'
eissn:
- 1940-6029
isbn:
- '9781071643099'
issn:
- 1064-3745
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
scopus_import: '1'
series_title: MIMB
status: public
title: Probing Cell-Type Specificity of Mutant Phenotype at Transcriptomic Level Using
Mosaic Analysis with Double Markers (MADM)
type: book_chapter
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 2886
year: '2025'
...
---
APC_amount: 12348 EUR
OA_place: publisher
OA_type: hybrid
_id: '18778'
abstract:
- lang: eng
text: Transcription by RNA polymerase II (Pol II) can be repressed by noncoding
RNA, including the human RNA Alu. However, the mechanism by which endogenous RNAs
repress transcription remains unclear. Here we present cryogenic-electron microscopy
structures of Pol II bound to Alu RNA, which reveal that Alu RNA mimics how DNA
and RNA bind to Pol II during transcription elongation. Further, we show how distinct
domains of the general transcription factor TFIIF control repressive activity.
Together, we reveal how a noncoding RNA can regulate mammalian gene expression.
acknowledged_ssus:
- _id: LifeSc
- _id: EM-Fac
- _id: ScienComp
- _id: PreCl
acknowledgement: We thank the members of the Bernecky laboratory for helpful discussions
and A. Hlavata for providing Pol II for use in the fluorescence anisotropy binding
assay. We thank V.-V. Hodirnau for SerialEM data collection and support with EPU
data collection. We thank D. Slade (Max Perutz Laboratories and Medical University
of Vienna, Vienna, Austria) for the wild-type TFIIF expression plasmid. We thank
N. Thompson and R. Burgess (McArdle Laboratory for Cancer Research, University of
Wisconsin-Madison, Madison, WI, USA) for the 8WG16 hybridoma cell line. We thank
C. Plaschka and M. Loose for critical reading of the manuscript. This work was supported
by Austrian Science Fund (FWF) grant no. P34185 (DOI 10.55776/P34185) (C.B.). The
funders had no role in study design, data collection and analysis, decision to publish
or preparation of the manuscript. This research was further supported by the Scientific
Service Units of ISTA through resources provided by the Laboratory Support Facility,
Electron Microscopy Facility, Scientific Computing and the Preclinical Facility.
article_processing_charge: Yes (in subscription journal)
article_type: original
author:
- first_name: Katarina
full_name: Tluckova, Katarina
id: 4AC7D980-F248-11E8-B48F-1D18A9856A87
last_name: Tluckova
- first_name: Beata M
full_name: Kaczmarek, Beata M
id: 36FA4AFA-F248-11E8-B48F-1D18A9856A87
last_name: Kaczmarek
- first_name: Anita P
full_name: Testa Salmazo, Anita P
id: 41F1F098-F248-11E8-B48F-1D18A9856A87
last_name: Testa Salmazo
- first_name: Carrie A
full_name: Bernecky, Carrie A
id: 2CB9DFE2-F248-11E8-B48F-1D18A9856A87
last_name: Bernecky
orcid: 0000-0003-0893-7036
citation:
ama: Tluckova K, Kaczmarek BM, Testa Salmazo AP, Bernecky C. Mechanism of mammalian
transcriptional repression by noncoding RNA. Nature Structural & Molecular
Biology. 2025;32:607-612. doi:10.1038/s41594-024-01448-7
apa: Tluckova, K., Kaczmarek, B. M., Testa Salmazo, A. P., & Bernecky, C. (2025).
Mechanism of mammalian transcriptional repression by noncoding RNA. Nature
Structural & Molecular Biology. Springer Nature. https://doi.org/10.1038/s41594-024-01448-7
chicago: Tluckova, Katarina, Beata M Kaczmarek, Anita P Testa Salmazo, and Carrie
Bernecky. “Mechanism of Mammalian Transcriptional Repression by Noncoding RNA.”
Nature Structural & Molecular Biology. Springer Nature, 2025. https://doi.org/10.1038/s41594-024-01448-7.
ieee: K. Tluckova, B. M. Kaczmarek, A. P. Testa Salmazo, and C. Bernecky, “Mechanism
of mammalian transcriptional repression by noncoding RNA,” Nature Structural
& Molecular Biology, vol. 32. Springer Nature, pp. 607–612, 2025.
ista: Tluckova K, Kaczmarek BM, Testa Salmazo AP, Bernecky C. 2025. Mechanism of
mammalian transcriptional repression by noncoding RNA. Nature Structural &
Molecular Biology. 32, 607–612.
mla: Tluckova, Katarina, et al. “Mechanism of Mammalian Transcriptional Repression
by Noncoding RNA.” Nature Structural & Molecular Biology, vol. 32,
Springer Nature, 2025, pp. 607–12, doi:10.1038/s41594-024-01448-7.
short: K. Tluckova, B.M. Kaczmarek, A.P. Testa Salmazo, C. Bernecky, Nature Structural
& Molecular Biology 32 (2025) 607–612.
corr_author: '1'
date_created: 2025-01-08T11:20:20Z
date_published: 2025-04-01T00:00:00Z
date_updated: 2025-11-20T10:28:36Z
day: '01'
ddc:
- '570'
department:
- _id: CaBe
doi: 10.1038/s41594-024-01448-7
external_id:
isi:
- '001390268000001'
pmid:
- '39762629'
file:
- access_level: open_access
checksum: 2919b30b271f395888e880076a680d73
content_type: application/pdf
creator: dernst
date_created: 2025-04-16T08:17:27Z
date_updated: 2025-04-16T08:17:27Z
file_id: '19573'
file_name: 2025_NatureStrucMolBiol_Tluckova.pdf
file_size: 9306639
relation: main_file
success: 1
file_date_updated: 2025-04-16T08:17:27Z
fulldoi: https://doi.org/10.1038/s41594-024-01448-7
has_accepted_license: '1'
intvolume: ' 32'
isi: 1
language:
- iso: eng
month: '04'
oa: 1
oa_version: Published Version
page: 607-612
pmid: 1
project:
- _id: c08a6700-5a5b-11eb-8a69-82a722b2bc30
grant_number: P34185
name: Regulation of mammalian transcription by noncoding RNA
publication: Nature Structural & Molecular Biology
publication_identifier:
eissn:
- 1545-9985
issn:
- 1545-9993
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
related_material:
record:
- id: '14644'
relation: earlier_version
status: public
scopus_import: '1'
status: public
title: Mechanism of mammalian transcriptional repression by noncoding RNA
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: '2025'
...
---
OA_place: repository
OA_type: green
_id: '18821'
abstract:
- lang: eng
text: 'Even though the one-dimensional contact interaction requires no regularization,
renormalization methods have been shown to improve the convergence of numerical
calculations considerably. In this work, we compare and contrast these methods:
“the running coupling constant” where the two-body ground-state energy is used
as a renormalization condition, and two effective interaction approaches that
include information about the ground as well as excited states. In particular,
we calculate the energies and densities of few-fermion systems in a harmonic oscillator
with the configuration-interaction method and compare the results based upon renormalized
and bare interactions. We find that the use of the running coupling constant instead
of the bare interaction improves convergence significantly. A comparison with
an effective interaction, which is designed to reproduce the relative part of
the energy spectrum of two particles, showed a similar improvement. The effective
interaction provides an additional improvement if the center-of-mass excitations
are included in the construction. Finally, we discuss the transformation of observables
alongside the renormalization of the potential, and demonstrate that this might
be an essential ingredient for accurate numerical calculations.'
acknowledgement: We thank J. Cremon and J. Bjerlin for earlier contributions to the
configuration-interaction calculations used in this work (see Refs. [49,50]). F.B.
and S.M.R. acknowledge helpful discussions with Carl Heintze, Sandra Brandstetter,
and Lila Chergui. We further want to thank Lila Chergui for helpful comments on
the paper. This research was financially supported by the Knut and Alice Wallenberg
Foundation (Grant No. KAW 2018.0217) and the Swedish Research Council (Grant No.
2022-03654 VR).
article_number: '013303'
article_processing_charge: No
article_type: original
arxiv: 1
author:
- first_name: Fabian
full_name: Brauneis, Fabian
last_name: Brauneis
- first_name: Hans Werner
full_name: Hammer, Hans Werner
last_name: Hammer
- first_name: Stephanie M.
full_name: Reimann, Stephanie M.
last_name: Reimann
- first_name: Artem
full_name: Volosniev, Artem
id: 37D278BC-F248-11E8-B48F-1D18A9856A87
last_name: Volosniev
orcid: 0000-0003-0393-5525
citation:
ama: Brauneis F, Hammer HW, Reimann SM, Volosniev A. Comparison of renormalized
interactions using one-dimensional few-body systems as a testbed. Physical
Review A. 2025;111(1). doi:10.1103/PhysRevA.111.013303
apa: Brauneis, F., Hammer, H. W., Reimann, S. M., & Volosniev, A. (2025). Comparison
of renormalized interactions using one-dimensional few-body systems as a testbed.
Physical Review A. American Physical Society. https://doi.org/10.1103/PhysRevA.111.013303
chicago: Brauneis, Fabian, Hans Werner Hammer, Stephanie M. Reimann, and Artem Volosniev.
“Comparison of Renormalized Interactions Using One-Dimensional Few-Body Systems
as a Testbed.” Physical Review A. American Physical Society, 2025. https://doi.org/10.1103/PhysRevA.111.013303.
ieee: F. Brauneis, H. W. Hammer, S. M. Reimann, and A. Volosniev, “Comparison of
renormalized interactions using one-dimensional few-body systems as a testbed,”
Physical Review A, vol. 111, no. 1. American Physical Society, 2025.
ista: Brauneis F, Hammer HW, Reimann SM, Volosniev A. 2025. Comparison of renormalized
interactions using one-dimensional few-body systems as a testbed. Physical Review
A. 111(1), 013303.
mla: Brauneis, Fabian, et al. “Comparison of Renormalized Interactions Using One-Dimensional
Few-Body Systems as a Testbed.” Physical Review A, vol. 111, no. 1, 013303,
American Physical Society, 2025, doi:10.1103/PhysRevA.111.013303.
short: F. Brauneis, H.W. Hammer, S.M. Reimann, A. Volosniev, Physical Review A 111
(2025).
date_created: 2025-01-12T23:04:00Z
date_published: 2025-01-03T00:00:00Z
date_updated: 2025-02-27T12:41:58Z
day: '03'
department:
- _id: MiLe
doi: 10.1103/PhysRevA.111.013303
external_id:
arxiv:
- '2408.10052'
isi:
- '001398791400004'
fulldoi: https://doi.org/10.1103/PhysRevA.111.013303
intvolume: ' 111'
isi: 1
issue: '1'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: ' https://doi.org/10.48550/arXiv.2408.10052'
month: '01'
oa: 1
oa_version: Preprint
publication: Physical Review A
publication_identifier:
eissn:
- 2469-9934
issn:
- 2469-9926
publication_status: published
publisher: American Physical Society
quality_controlled: '1'
scopus_import: '1'
status: public
title: Comparison of renormalized interactions using one-dimensional few-body systems
as a testbed
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 111
year: '2025'
...
---
OA_place: publisher
OA_type: hybrid
_id: '18823'
article_number: kiae651
article_processing_charge: Yes (in subscription journal)
article_type: original
author:
- first_name: Dechang
full_name: Cao, Dechang
last_name: Cao
- first_name: Joke G
full_name: De Jaeger-Braet, Joke G
id: 26bd38d3-c59a-11ee-a1af-d7a988cafcc5
last_name: De Jaeger-Braet
citation:
ama: 'Cao D, De Jaeger-Braet JG. Memory of maternal temperatures: DNA methylation
alterations across generations. Plant Physiology. 2025;197(1). doi:10.1093/plphys/kiae651'
apa: 'Cao, D., & De Jaeger-Braet, J. G. (2025). Memory of maternal temperatures:
DNA methylation alterations across generations. Plant Physiology. Oxford
University Press. https://doi.org/10.1093/plphys/kiae651'
chicago: 'Cao, Dechang, and Joke G De Jaeger-Braet. “Memory of Maternal Temperatures:
DNA Methylation Alterations across Generations.” Plant Physiology. Oxford
University Press, 2025. https://doi.org/10.1093/plphys/kiae651.'
ieee: 'D. Cao and J. G. De Jaeger-Braet, “Memory of maternal temperatures: DNA methylation
alterations across generations,” Plant Physiology, vol. 197, no. 1. Oxford
University Press, 2025.'
ista: 'Cao D, De Jaeger-Braet JG. 2025. Memory of maternal temperatures: DNA methylation
alterations across generations. Plant Physiology. 197(1), kiae651.'
mla: 'Cao, Dechang, and Joke G. De Jaeger-Braet. “Memory of Maternal Temperatures:
DNA Methylation Alterations across Generations.” Plant Physiology, vol.
197, no. 1, kiae651, Oxford University Press, 2025, doi:10.1093/plphys/kiae651.'
short: D. Cao, J.G. De Jaeger-Braet, Plant Physiology 197 (2025).
corr_author: '1'
date_created: 2025-01-12T23:04:02Z
date_published: 2025-01-01T00:00:00Z
date_updated: 2025-07-15T08:18:19Z
day: '01'
ddc:
- '580'
department:
- _id: XiFe
doi: 10.1093/plphys/kiae651
external_id:
isi:
- '001382979900001'
pmid:
- '39691053'
file:
- access_level: open_access
checksum: a9b2a12d7bc6174f27e28413e9c77a9c
content_type: application/pdf
creator: dernst
date_created: 2025-07-15T08:17:25Z
date_updated: 2025-07-15T08:17:25Z
file_id: '20023'
file_name: 2025_PlantPhysiology_Cao.pdf
file_size: 1214018
relation: main_file
success: 1
file_date_updated: 2025-07-15T08:17:25Z
fulldoi: https://doi.org/10.1093/plphys/kiae651
has_accepted_license: '1'
intvolume: ' 197'
isi: 1
issue: '1'
language:
- iso: eng
month: '01'
oa: 1
oa_version: Published Version
pmid: 1
publication: Plant Physiology
publication_identifier:
eissn:
- 1532-2548
publication_status: published
publisher: Oxford University Press
quality_controlled: '1'
scopus_import: '1'
status: public
title: 'Memory of maternal temperatures: DNA methylation alterations across generations'
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: 197
year: '2025'
...
---
_id: '18837'
abstract:
- lang: eng
text: Super-resolution methods provide far better spatial resolution than the optical
diffraction limit of about half the wavelength of light (∼200-300 nm). Nevertheless,
they have yet to attain widespread use in plants, largely due to plants’ challenging
optical properties. Expansion microscopy improves effective resolution by isotropically
increasing the physical distances between sample structures while preserving relative
spatial arrangements and clearing the sample. However, its application to plants
has been hindered by the rigid, mechanically cohesive structure of plant tissues.
Here, we report on whole-mount expansion microscopy of thale cress (Arabidopsis
thaliana) root tissues (PlantEx), achieving a four-fold resolution increase over
conventional microscopy. Our results highlight the microtubule cytoskeleton organization
and interaction between molecularly defined cellular constituents. Combining PlantEx
with stimulated emission depletion (STED) microscopy, we increase nanoscale resolution
and visualize the complex organization of subcellular organelles from intact tissues
by example of the densely packed COPI-coated vesicles associated with the Golgi
apparatus and put these into a cellular structural context. Our results show that
expansion microscopy can be applied to increase effective imaging resolution in
Arabidopsis root specimens.
article_processing_charge: No
author:
- first_name: Johann G
full_name: Danzl, Johann G
id: 42EFD3B6-F248-11E8-B48F-1D18A9856A87
last_name: Danzl
orcid: 0000-0001-8559-3973
- first_name: Caroline
full_name: Kreuzinger, Caroline
id: 382077BA-F248-11E8-B48F-1D18A9856A87
last_name: Kreuzinger
citation:
ama: Danzl JG, Kreuzinger C. Research Data for the publication “Super-resolution
expansion microscopy in plant roots.” 2025. doi:10.15479/AT:ISTA:18837
apa: Danzl, J. G., & Kreuzinger, C. (2025). Research Data for the publication
“Super-resolution expansion microscopy in plant roots.” Institute of Science and
Technology Austria. https://doi.org/10.15479/AT:ISTA:18837
chicago: Danzl, Johann G, and Caroline Kreuzinger. “Research Data for the Publication
‘Super-Resolution Expansion Microscopy in Plant Roots.’” Institute of Science
and Technology Austria, 2025. https://doi.org/10.15479/AT:ISTA:18837.
ieee: J. G. Danzl and C. Kreuzinger, “Research Data for the publication ‘Super-resolution
expansion microscopy in plant roots.’” Institute of Science and Technology Austria,
2025.
ista: Danzl JG, Kreuzinger C. 2025. Research Data for the publication ‘Super-resolution
expansion microscopy in plant roots’, Institute of Science and Technology Austria,
10.15479/AT:ISTA:18837.
mla: Danzl, Johann G., and Caroline Kreuzinger. Research Data for the Publication
“Super-Resolution Expansion Microscopy in Plant Roots.” Institute of Science
and Technology Austria, 2025, doi:10.15479/AT:ISTA:18837.
short: J.G. Danzl, C. Kreuzinger, (2025).
contributor:
- contributor_type: researcher
first_name: Michelle C
id: 35A03822-F248-11E8-B48F-1D18A9856A87
last_name: Gallei
orcid: 0000-0003-1286-7368
- contributor_type: researcher
first_name: Sven M
id: 45812BD4-F248-11E8-B48F-1D18A9856A87
last_name: Truckenbrodt
- contributor_type: researcher
first_name: Caroline
id: 382077BA-F248-11E8-B48F-1D18A9856A87
last_name: Kreuzinger
- contributor_type: researcher
first_name: Syamala
id: F8660870-D756-11E9-98C5-34DFE5697425
last_name: Inumella
- contributor_type: researcher
first_name: Vitali
id: 7e146587-8972-11ed-ae7b-d7a32ea86a81
last_name: Vistunou
- contributor_type: researcher
first_name: Christoph M
id: 4DF26D8C-F248-11E8-B48F-1D18A9856A87
last_name: Sommer
orcid: 0000-0003-1216-9105
- contributor_type: researcher
first_name: Mojtaba
id: 3A0A06F4-F248-11E8-B48F-1D18A9856A87
last_name: Tavakoli
orcid: 0000-0002-7667-6854
- contributor_type: researcher
first_name: Nathalie
id: 40E7F008-F248-11E8-B48F-1D18A9856A87
last_name: Agudelo Duenas
- contributor_type: researcher
first_name: Jakob
id: 937696FA-C996-11E9-8C7C-CF13E6697425
last_name: Vorlaufer
- contributor_type: researcher
first_name: Wiebke
id: 425C1CE8-F248-11E8-B48F-1D18A9856A87
last_name: Jahr
- contributor_type: researcher
first_name: Marek
id: 6ac4636d-15b2-11ec-abd3-fb8df79972ae
last_name: Randuch
- contributor_type: researcher
first_name: Alexander J
id: 46A62C3A-F248-11E8-B48F-1D18A9856A87
last_name: Johnson
orcid: 0000-0002-2739-8843
- contributor_type: researcher
first_name: Eva
id: 38F4F166-F248-11E8-B48F-1D18A9856A87
last_name: Benková
orcid: 0000-0002-8510-9739
- contributor_type: researcher
first_name: Jiří
id: 4159519E-F248-11E8-B48F-1D18A9856A87
last_name: Friml
orcid: 0000-0002-8302-7596
- contributor_type: researcher
first_name: Johann G
id: 42EFD3B6-F248-11E8-B48F-1D18A9856A87
last_name: Danzl
orcid: 0000-0001-8559-3973
corr_author: '1'
date_created: 2025-01-13T09:51:29Z
date_published: 2025-04-01T00:00:00Z
date_updated: 2026-06-10T08:30:20Z
department:
- _id: JoDa
doi: 10.15479/AT:ISTA:18837
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title: Research Data for the publication "Super-resolution expansion microscopy in
plant roots"
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_id: '18848'
abstract:
- lang: eng
text: Type II CRISPR endonucleases are widely used programmable genome editing tools.
Recently, CRISPR-Cas systems with highly compact nucleases have been discovered,
including Cas9d (a type II-D nuclease). Here, we report the cryo-EM structures
of a Cas9d nuclease (747 amino acids in length) in multiple functional states,
revealing a stepwise process of DNA targeting involving a conformational switch
in a REC2 domain insertion. Our structures provide insights into the intricately
folded guide RNA which acts as a structural scaffold to anchor small, flexible
protein domains for DNA recognition. The sgRNA can be truncated by up to ~25%
yet still retain activity in vivo. Using ancestral sequence reconstruction, we
generated compact nucleases capable of efficient genome editing in mammalian cells.
Collectively, our results provide mechanistic insights into the evolution and
DNA targeting of diverse type II CRISPR-Cas systems, providing a blueprint for
future re-engineering of minimal RNA-guided DNA endonucleases.
acknowledgement: We would like to thank M. Ocampo Camacho and M.F. Canedo Ocampo for
assistance with the figures. We thank M. Hooper for assistance developing the GFP
assay and operating the CE machine for in vitro cleavage analysis. We thank E. Schwartz
and A. Brilot for expert cryo-EM support in the Sauer Structural Biology Laboratory
at UT Austin. This work was funded, in part, by a sponsored research agreement with
Metagenomi, Inc. (to D.W.T), a Welch Foundation Research Grant F-1938 (to D.W.T),
and the Robert J. Kleberg, Jr. and Helen C. Kleberg Foundation Medical Research
Grant (to D.W.T), and a grant from the National Institute of Allergy and Infectious
Diseases (NIAID 1R01AI110577 to K.A.J.).
article_number: '457'
article_processing_charge: Yes
article_type: original
author:
- first_name: Rodrigo Fregoso
full_name: Ocampo, Rodrigo Fregoso
last_name: Ocampo
- 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: Tyler L.
full_name: Dangerfield, Tyler L.
last_name: Dangerfield
- first_name: Isabel
full_name: Nocedal, Isabel
last_name: Nocedal
- first_name: Samatar A.
full_name: Jirde, Samatar A.
last_name: Jirde
- first_name: Lisa M.
full_name: Alexander, Lisa M.
last_name: Alexander
- first_name: Nicole C.
full_name: Thomas, Nicole C.
last_name: Thomas
- first_name: Anjali
full_name: Das, Anjali
last_name: Das
- first_name: Sarah
full_name: Nielson, Sarah
last_name: Nielson
- first_name: Kenneth A.
full_name: Johnson, Kenneth A.
last_name: Johnson
- first_name: Christopher T.
full_name: Brown, Christopher T.
last_name: Brown
- first_name: Cristina N.
full_name: Butterfield, Cristina N.
last_name: Butterfield
- first_name: Daniela S.A.
full_name: Goltsman, Daniela S.A.
last_name: Goltsman
- first_name: David W.
full_name: Taylor, David W.
last_name: Taylor
citation:
ama: Ocampo RF, Bravo JPK, Dangerfield TL, et al. DNA targeting by compact Cas9d
and its resurrected ancestor. Nature Communications. 2025;16. doi:10.1038/s41467-024-55573-4
apa: Ocampo, R. F., Bravo, J. P. K., Dangerfield, T. L., Nocedal, I., Jirde, S.
A., Alexander, L. M., … Taylor, D. W. (2025). DNA targeting by compact Cas9d and
its resurrected ancestor. Nature Communications. Springer Nature. https://doi.org/10.1038/s41467-024-55573-4
chicago: Ocampo, Rodrigo Fregoso, Jack Peter Kelly Bravo, Tyler L. Dangerfield,
Isabel Nocedal, Samatar A. Jirde, Lisa M. Alexander, Nicole C. Thomas, et al.
“DNA Targeting by Compact Cas9d and Its Resurrected Ancestor.” Nature Communications.
Springer Nature, 2025. https://doi.org/10.1038/s41467-024-55573-4.
ieee: R. F. Ocampo et al., “DNA targeting by compact Cas9d and its resurrected
ancestor,” Nature Communications, vol. 16. Springer Nature, 2025.
ista: Ocampo RF, Bravo JPK, Dangerfield TL, Nocedal I, Jirde SA, Alexander LM, Thomas
NC, Das A, Nielson S, Johnson KA, Brown CT, Butterfield CN, Goltsman DSA, Taylor
DW. 2025. DNA targeting by compact Cas9d and its resurrected ancestor. Nature
Communications. 16, 457.
mla: Ocampo, Rodrigo Fregoso, et al. “DNA Targeting by Compact Cas9d and Its Resurrected
Ancestor.” Nature Communications, vol. 16, 457, Springer Nature, 2025,
doi:10.1038/s41467-024-55573-4.
short: R.F. Ocampo, J.P.K. Bravo, T.L. Dangerfield, I. Nocedal, S.A. Jirde, L.M.
Alexander, N.C. Thomas, A. Das, S. Nielson, K.A. Johnson, C.T. Brown, C.N. Butterfield,
D.S.A. Goltsman, D.W. Taylor, Nature Communications 16 (2025).
date_created: 2025-01-19T23:01:50Z
date_published: 2025-01-07T00:00:00Z
date_updated: 2025-07-03T11:58:22Z
day: '07'
ddc:
- '570'
department:
- _id: JaBr
doi: 10.1038/s41467-024-55573-4
external_id:
pmid:
- '39774105'
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creator: dernst
date_created: 2025-01-22T14:35:22Z
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language:
- iso: eng
month: '01'
oa: 1
oa_version: Published Version
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publication: Nature Communications
publication_identifier:
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quality_controlled: '1'
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title: DNA targeting by compact Cas9d and its resurrected ancestor
tmp:
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legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
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type: journal_article
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year: '2025'
...
---
OA_place: publisher
OA_type: hybrid
_id: '18849'
abstract:
- lang: eng
text: Many biological systems operate near the physical limits to their performance,
suggesting that aspects of their behavior and underlying mechanisms could be derived
from optimization principles. However, such principles have often been applied
only in simplified models. Here, we explore a detailed mechanistic model of the
gap gene network in the Drosophila embryo, optimizing its 50+ parameters to maximize
the information that gene expression levels provide about nuclear positions. This
optimization is conducted under realistic constraints, such as limits on the number
of available molecules. Remarkably, the optimal networks we derive closely match
the architecture and spatial gene expression profiles observed in the real organism.
Our framework quantifies the tradeoffs involved in maximizing functional performance
and allows for the exploration of alternative network configurations, addressing
the question of which features are necessary and which are contingent. Our results
suggest that multiple solutions to the optimization problem might exist across
closely related organisms, offering insights into the evolution of gene regulatory
networks.
acknowledgement: We thank Nicholas H. Barton for his comments on the manuscript, Benjamin
Zoller for helpful discussions, and Aleksandra Walczak and Curtis Callan for early
collaborations that shaped this work. Special thanks to Eric F. Wieschaus for many
persistently inspiring conversations. This work was supported in part by the Human
Frontiers Science Program; the Austrian Science Fund (FWF P28844); by the European
Research Council grant DynaTrans (101118866); by U.S. NSF, through the Center for
the Physics of Biological Function (PHY–1734030); by NIH Grants R01GM097275, U01DA047730,
and U01DK127429; by the John Simon Guggenheim Memorial Foundation; and by the LOEWE
priority program “Center for Multiscale Modeling in Life Sciences” (CMMS), sponsored
by the Hessian Ministry for Science and Research, Arts and Culture (HMWK).
article_number: e2402925121
article_processing_charge: Yes (in subscription journal)
article_type: original
author:
- first_name: Thomas R
full_name: Sokolowski, Thomas R
id: 3E999752-F248-11E8-B48F-1D18A9856A87
last_name: Sokolowski
orcid: 0000-0002-1287-3779
- first_name: Thomas
full_name: Gregor, Thomas
last_name: Gregor
- first_name: William
full_name: Bialek, William
last_name: Bialek
- first_name: Gašper
full_name: Tkačik, Gašper
id: 3D494DCA-F248-11E8-B48F-1D18A9856A87
last_name: Tkačik
orcid: 0000-0002-6699-1455
citation:
ama: Sokolowski TR, Gregor T, Bialek W, Tkačik G. Deriving a genetic regulatory
network from an optimization principle. Proceedings of the National Academy
of Sciences. 2025;122(1). doi:10.1073/pnas.2402925121
apa: Sokolowski, T. R., Gregor, T., Bialek, W., & Tkačik, G. (2025). Deriving
a genetic regulatory network from an optimization principle. Proceedings of
the National Academy of Sciences. National Academy of Sciences. https://doi.org/10.1073/pnas.2402925121
chicago: Sokolowski, Thomas R, Thomas Gregor, William Bialek, and Gašper Tkačik.
“Deriving a Genetic Regulatory Network from an Optimization Principle.” Proceedings
of the National Academy of Sciences. National Academy of Sciences, 2025. https://doi.org/10.1073/pnas.2402925121.
ieee: T. R. Sokolowski, T. Gregor, W. Bialek, and G. Tkačik, “Deriving a genetic
regulatory network from an optimization principle,” Proceedings of the National
Academy of Sciences, vol. 122, no. 1. National Academy of Sciences, 2025.
ista: Sokolowski TR, Gregor T, Bialek W, Tkačik G. 2025. Deriving a genetic regulatory
network from an optimization principle. Proceedings of the National Academy of
Sciences. 122(1), e2402925121.
mla: Sokolowski, Thomas R., et al. “Deriving a Genetic Regulatory Network from an
Optimization Principle.” Proceedings of the National Academy of Sciences,
vol. 122, no. 1, e2402925121, National Academy of Sciences, 2025, doi:10.1073/pnas.2402925121.
short: T.R. Sokolowski, T. Gregor, W. Bialek, G. Tkačik, Proceedings of the National
Academy of Sciences 122 (2025).
corr_author: '1'
date_created: 2025-01-19T23:01:50Z
date_published: 2025-01-07T00:00:00Z
date_updated: 2026-02-16T12:26:51Z
day: '07'
ddc:
- '570'
department:
- _id: GaTk
doi: 10.1073/pnas.2402925121
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pmid:
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creator: dernst
date_created: 2025-01-20T10:10:04Z
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file_date_updated: 2025-01-20T10:10:04Z
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intvolume: ' 122'
isi: 1
issue: '1'
language:
- iso: eng
month: '01'
oa: 1
oa_version: Published Version
pmid: 1
project:
- _id: 254E9036-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: P28844-B27
name: Biophysics of information processing in gene regulation
- _id: 7bfe6a29-9f16-11ee-852c-c0da5e2045d9
grant_number: '101118866'
name: 'Transcription in 4D: the dynamic interplay between chromatin architecture
and gene expression in developing pseudo-embryos'
- _id: 2665AAFE-B435-11E9-9278-68D0E5697425
grant_number: RGP0034/2018
name: Can evolution minimize spurious signaling crosstalk to reach optimal performance?
publication: Proceedings of the National Academy of Sciences
publication_identifier:
eissn:
- 1091-6490
issn:
- 0027-8424
publication_status: published
publisher: National Academy of Sciences
quality_controlled: '1'
scopus_import: '1'
status: public
title: Deriving a genetic regulatory network from an optimization principle
tmp:
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(CC BY-NC-ND 4.0)
short: CC BY-NC-ND (4.0)
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volume: 122
year: '2025'
...
---
APC_amount: 3261,23 EUR
OA_place: publisher
OA_type: hybrid
_id: '18850'
abstract:
- lang: eng
text: 'Biophysical constraints limit the specificity with which transcription factors
(TFs) can target regulatory DNA. While individual nontarget binding events may
be low affinity, the sheer number of such interactions could present a challenge
for gene regulation by degrading its precision or possibly leading to an erroneous
induction state. Chromatin can prevent nontarget binding by rendering DNA physically
inaccessible to TFs, at the cost of energy-consuming remodeling orchestrated by
pioneer factors (PFs). Under what conditions and by how much can chromatin reduce
regulatory errors on a global scale? We use a theoretical approach to compare
two scenarios for gene regulation: one that relies on TF binding to free DNA alone
and one that uses a combination of TFs and chromatin-regulating PFs to achieve
desired gene expression patterns. We find, first, that chromatin effectively silences
groups of genes that should be simultaneously OFF, thereby allowing more accurate
graded control of expression for the remaining ON genes. Second, chromatin buffers
the deleterious consequences of nontarget binding as the number of OFF genes grows,
permitting a substantial expansion in regulatory complexity. Third, chromatin-based
regulation productively co-opts nontarget TF binding for ON genes in order to
establish a “leaky” baseline expression level, which targeted activator or repressor
binding subsequently up- or down-modulates. Thus, on a global scale, using chromatin
simultaneously alleviates pressure for high specificity of regulatory interactions
and enables an increase in genome size with minimal impact on global expression
error.'
acknowledgement: M.L.P. was supported by the European Molecular Biology Laboratory
(EMBL) Interdisciplinary Postdoc Programme (EIPOD4 fellowships), cofunded by Marie
Skłodowska-Curie Actions (Grant Agreement No. 847543). J.C. and M.L.P. were supported
by EMBL Core Funding and Theory@EMBL. This work is supported by European Research
Council Grant DynaTrans (101118866) to G.T. We would like to thank the members of
the J.C. and G.T. groups, especially Natalia Misunou, Michal Hledík, and Réka Borbély,
for helpful feedback and discussion. We also thank EMBL IT Services for the use
of high performance computing resources.
article_number: e2411887121
article_processing_charge: No
article_type: original
author:
- first_name: Mindy Liu
full_name: Perkins, Mindy Liu
last_name: Perkins
- first_name: Justin
full_name: Crocker, Justin
last_name: Crocker
- first_name: Gašper
full_name: Tkačik, Gašper
id: 3D494DCA-F248-11E8-B48F-1D18A9856A87
last_name: Tkačik
orcid: 0000-0002-6699-1455
citation:
ama: Perkins ML, Crocker J, Tkačik G. Chromatin enables precise and scalable gene
regulation with factors of limited specificity. Proceedings of the National
Academy of Sciences. 2025;122(1). doi:10.1073/pnas.2411887121
apa: Perkins, M. L., Crocker, J., & Tkačik, G. (2025). Chromatin enables precise
and scalable gene regulation with factors of limited specificity. Proceedings
of the National Academy of Sciences. National Academy of Sciences. https://doi.org/10.1073/pnas.2411887121
chicago: Perkins, Mindy Liu, Justin Crocker, and Gašper Tkačik. “Chromatin Enables
Precise and Scalable Gene Regulation with Factors of Limited Specificity.” Proceedings
of the National Academy of Sciences. National Academy of Sciences, 2025. https://doi.org/10.1073/pnas.2411887121.
ieee: M. L. Perkins, J. Crocker, and G. Tkačik, “Chromatin enables precise and scalable
gene regulation with factors of limited specificity,” Proceedings of the National
Academy of Sciences, vol. 122, no. 1. National Academy of Sciences, 2025.
ista: Perkins ML, Crocker J, Tkačik G. 2025. Chromatin enables precise and scalable
gene regulation with factors of limited specificity. Proceedings of the National
Academy of Sciences. 122(1), e2411887121.
mla: Perkins, Mindy Liu, et al. “Chromatin Enables Precise and Scalable Gene Regulation
with Factors of Limited Specificity.” Proceedings of the National Academy of
Sciences, vol. 122, no. 1, e2411887121, National Academy of Sciences, 2025,
doi:10.1073/pnas.2411887121.
short: M.L. Perkins, J. Crocker, G. Tkačik, Proceedings of the National Academy
of Sciences 122 (2025).
corr_author: '1'
date_created: 2025-01-19T23:01:51Z
date_published: 2025-01-07T00:00:00Z
date_updated: 2026-05-06T12:43:59Z
day: '07'
ddc:
- '570'
department:
- _id: GaTk
doi: 10.1073/pnas.2411887121
external_id:
isi:
- '001392765300001'
pmid:
- '39793086'
file:
- access_level: open_access
checksum: 86a8d25a6e282aeb4128f1d0b86ff911
content_type: application/pdf
creator: dernst
date_created: 2025-01-20T09:38:32Z
date_updated: 2025-01-20T09:38:32Z
file_id: '18859'
file_name: 2025_PNAS_Perkins.pdf
file_size: 30943709
relation: main_file
success: 1
file_date_updated: 2025-01-20T09:38:32Z
fulldoi: https://doi.org/10.1073/pnas.2411887121
has_accepted_license: '1'
intvolume: ' 122'
isi: 1
issue: '1'
language:
- iso: eng
month: '01'
oa: 1
oa_version: Published Version
pmid: 1
project:
- _id: 7bfe6a29-9f16-11ee-852c-c0da5e2045d9
grant_number: '101118866'
name: 'Transcription in 4D: the dynamic interplay between chromatin architecture
and gene expression in developing pseudo-embryos'
publication: Proceedings of the National Academy of Sciences
publication_identifier:
eissn:
- 1091-6490
issn:
- 0027-8424
publication_status: published
publisher: National Academy of Sciences
quality_controlled: '1'
related_material:
link:
- relation: software
url: https://github.com/officerredshirt/network_crosstalk
scopus_import: '1'
status: public
title: Chromatin enables precise and scalable gene regulation with factors of limited
specificity
tmp:
image: /images/cc_by_nc_nd.png
legal_code_url: https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode
name: Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International
(CC BY-NC-ND 4.0)
short: CC BY-NC-ND (4.0)
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 122
year: '2025'
...
---
OA_place: publisher
OA_type: hybrid
_id: '18851'
abstract:
- lang: eng
text: 'We present volume-limited samples of cataclysmic variables (CVs) and AM CVn
binaries jointly selected from SRG/eROSITA eRASS1 and Gaia DR3 using an X-ray
+ optical color–color diagram (the "X-ray Main Sequence"). This tool identifies
all CV subtypes, including magnetic and low-accretion rate systems, in contrast
to most previous surveys. We find 23 CVs, 3 of which are AM CVns, out to 150 pc
in the Western Galactic Hemisphere. Our 150 pc sample is spectroscopically verified
and complete down to LX = 1.3 × 1029 erg s−1 in the 0.2–2.3 keV band, and we also
present CV candidates out to 300 pc and 1000 pc. We discovered two previously
unknown systems in our 150 pc sample: the third nearest AM CVn and a magnetic
period bouncer. We find the mean LX of CVs to be 〈LX〉 ≈ 4.6 × 1030 erg s−1, in
contrast to previous surveys which yielded 〈LX〉 ∼ 1031−1032 erg s−1. We construct
X-ray luminosity functions that, for the first time, flatten out at LX ∼ 1030
erg s−1. We infer average number, mass, and luminosity densities of ρN,CV = (3.7
± 0.7) × 10−6pc−3, (math formular), and (math formular), respectively, in the
solar neighborhood. Our uniform selection method also allows us to place meaningful
estimates on the space density of AM CVns, ρN,AM CVn = (5.5 ± 3.7) × 10−7 pc−3.
Magnetic CVs and period bouncers make up 35% and 25% of our sample, respectively.
This work, through a novel discovery technique, shows that the observed number
densities of CVs and AM CVns, as well as the fraction of period bouncers, are
still in tension with population synthesis estimates.'
acknowledgement: "We thank Roman Krivonos for insightful feedback, Kevin Burdge, Dovi
Poznanski, and Jim Fuller for useful discussions, and Sunny Wong for providing AM
CVn evolutionary models. A.C.R. acknowledges support from an NSF Graduate Fellowship.\r\n\r\nA.C.R.
thanks the LSST-DA Data Science Fellowship Program, which is funded by LSST-DA,
the Brinson Foundation, and the Moore Foundation; his participation in the program
has benefited this work. RLO is a Research Fellow of the Brazilian institution CNPq
(PQ-315632/2023-2).\r\n\r\nThis work is based on data from eROSITA, the soft X-ray
instrument aboard SRG, a joint Russian-German science mission supported by the Russian
Space Agency (Roskosmos), in the interests of the Russian Academy of Sciences represented
by its Space Research Institute (IKI), and the Deutsches Zentrum für Luft- und Raumfahrt
(DLR). The SRG spacecraft was built by Lavochkin Association (NPOL) and its subcontractors,
and is operated by NPOL with support from the Max Planck Institute for Extraterrestrial
Physics (MPE). The development and construction of the eROSITA X-ray instrument
was led by MPE, with contributions from the Dr. Karl Remeis Observatory Bamberg
& ECAP (FAU Erlangen-Nuernberg), the University of Hamburg Observatory, the Leibniz
Institute for Astrophysics Potsdam (AIP), and the Institute for Astronomy and Astrophysics
of the University of Tübingen, with the support of DLR and the Max Planck Society.
The Argelander Institute for Astronomy of the University of Bonn and the Ludwig
Maximilians Universität Munich also participated in the science preparation for
eROSITA.\r\n\r\nThis work presents results from the European Space Agency (ESA)
space mission Gaia. Gaia data are being processed by the Gaia Data Processing and
Analysis Consortium (DPAC). Funding for the DPAC is provided by national institutions,
in particular the institutions participating in the Gaia MultiLateral Agreement
(MLA). The Gaia mission website is https://www.cosmos.esa.int/gaia. The Gaia archive
website is https://archives.esac.esa.int/gaia.\r\n\r\nSome of the data presented
herein were obtained at Keck Observatory, which is a private 501(c)3 non-profit
organization operated as a scientific partnership among the California Institute
of Technology, the University of California, and the National Aeronautics and Space
Administration. The Observatory was made possible by the generous financial support
of the W. M. Keck Foundation. The authors wish to recognize and acknowledge the
very significant cultural role and reverence that the summit of Maunakea has always
had within the Native Hawaiian community. We are most fortunate to have the opportunity
to conduct observations from this mountain. We are also grateful to the staff of
Palomar Observatory and that of Lick Observatory for their assistance in carrying
out observations used in this work.\r\n\r\nBased on observations obtained with the
Samuel Oschin Telescope 48 inch and the 60 inch Telescope at the Palomar Observatory
as part of the Zwicky Transient Facility project. ZTF is supported by the National
Science Foundation under grants No. AST-1440341 and AST-2034437 and a collaboration
including current partners Caltech, IPAC, the Weizmann Institute of Science, the
Oskar Klein Center at Stockholm University, the University of Maryland, Deutsches
Elektronen-Synchrotron and Humboldt University, the TANGO Consortium of Taiwan,
the University of Wisconsin at Milwaukee, Trinity College Dublin, Lawrence Livermore
National Laboratories, IN2P3, University of Warwick, Ruhr University Bochum, Northwestern
University and former partners the University of Washington, Los Alamos National
Laboratories, and Lawrence Berkeley National Laboratories. Operations are conducted
by COO, IPAC, and UW.\r\n\r\nSoftware: used: Python and the following libraries:
matplotlib (Hunter 2007), scipy (Virtanen et al. 2020), astropy (Astropy Collaboration
et al. 2013), numpy (van der Walt et al. 2011). PypeIt (Prochaska et al. 2020),
lpipe (Perley 2019), and Tool for OPerations on Catalogues And Tables (TOPCAT) (Taylor
2005)."
article_number: '014201'
article_processing_charge: No
article_type: original
arxiv: 1
author:
- first_name: Antonio C.
full_name: Rodriguez, Antonio C.
last_name: Rodriguez
- first_name: Kareem
full_name: El-Badry, Kareem
last_name: El-Badry
- first_name: Valery
full_name: Suleimanov, Valery
last_name: Suleimanov
- first_name: Anna F.
full_name: Pala, Anna F.
last_name: Pala
- first_name: Shrinivas R.
full_name: Kulkarni, Shrinivas R.
last_name: Kulkarni
- first_name: Boris
full_name: Gaensicke, Boris
last_name: Gaensicke
- first_name: Kaya
full_name: Mori, Kaya
last_name: Mori
- first_name: R. Michael
full_name: Rich, R. Michael
last_name: Rich
- first_name: Arnab
full_name: Sarkar, Arnab
last_name: Sarkar
- first_name: Tong
full_name: Bao, Tong
last_name: Bao
- first_name: Raimundo Lopes
full_name: De Oliveira, Raimundo Lopes
last_name: De Oliveira
- first_name: Gavin
full_name: Ramsay, Gavin
last_name: Ramsay
- first_name: Paula
full_name: Szkody, Paula
last_name: Szkody
- first_name: Matthew
full_name: Graham, Matthew
last_name: Graham
- first_name: Thomas A.
full_name: Prince, Thomas A.
last_name: Prince
- first_name: Ilaria
full_name: Caiazzo, Ilaria
id: 8ae5b6e7-2a03-11ee-914d-b58ed7a3b47d
last_name: Caiazzo
orcid: 0000-0002-4770-5388
- first_name: Zachary P.
full_name: Vanderbosch, Zachary P.
last_name: Vanderbosch
- first_name: Jan Van
full_name: Roestel, Jan Van
last_name: Roestel
- first_name: Kaustav K.
full_name: Das, Kaustav K.
last_name: Das
- first_name: Yu Jing
full_name: Qin, Yu Jing
last_name: Qin
- first_name: Mansi M.
full_name: Kasliwal, Mansi M.
last_name: Kasliwal
- first_name: Avery
full_name: Wold, Avery
last_name: Wold
- first_name: Steven L.
full_name: Groom, Steven L.
last_name: Groom
- first_name: Daniel
full_name: Reiley, Daniel
last_name: Reiley
- first_name: Reed
full_name: Riddle, Reed
last_name: Riddle
citation:
ama: 'Rodriguez AC, El-Badry K, Suleimanov V, et al. Cataclysmic variables and AM
CVn binaries in SRG/eROSITA + Gaia: Volume limited samples, X-ray luminosity functions,
and space densities. Publications of the Astronomical Society of the Pacific.
2025;137(1). doi:10.1088/1538-3873/ada185'
apa: 'Rodriguez, A. C., El-Badry, K., Suleimanov, V., Pala, A. F., Kulkarni, S.
R., Gaensicke, B., … Riddle, R. (2025). Cataclysmic variables and AM CVn binaries
in SRG/eROSITA + Gaia: Volume limited samples, X-ray luminosity functions, and
space densities. Publications of the Astronomical Society of the Pacific.
IOP Publishing. https://doi.org/10.1088/1538-3873/ada185'
chicago: 'Rodriguez, Antonio C., Kareem El-Badry, Valery Suleimanov, Anna F. Pala,
Shrinivas R. Kulkarni, Boris Gaensicke, Kaya Mori, et al. “Cataclysmic Variables
and AM CVn Binaries in SRG/EROSITA + Gaia: Volume Limited Samples, X-Ray Luminosity
Functions, and Space Densities.” Publications of the Astronomical Society of
the Pacific. IOP Publishing, 2025. https://doi.org/10.1088/1538-3873/ada185.'
ieee: 'A. C. Rodriguez et al., “Cataclysmic variables and AM CVn binaries
in SRG/eROSITA + Gaia: Volume limited samples, X-ray luminosity functions, and
space densities,” Publications of the Astronomical Society of the Pacific,
vol. 137, no. 1. IOP Publishing, 2025.'
ista: 'Rodriguez AC, El-Badry K, Suleimanov V, Pala AF, Kulkarni SR, Gaensicke B,
Mori K, Rich RM, Sarkar A, Bao T, De Oliveira RL, Ramsay G, Szkody P, Graham M,
Prince TA, Caiazzo I, Vanderbosch ZP, Roestel JV, Das KK, Qin YJ, Kasliwal MM,
Wold A, Groom SL, Reiley D, Riddle R. 2025. Cataclysmic variables and AM CVn binaries
in SRG/eROSITA + Gaia: Volume limited samples, X-ray luminosity functions, and
space densities. Publications of the Astronomical Society of the Pacific. 137(1),
014201.'
mla: 'Rodriguez, Antonio C., et al. “Cataclysmic Variables and AM CVn Binaries in
SRG/EROSITA + Gaia: Volume Limited Samples, X-Ray Luminosity Functions, and Space
Densities.” Publications of the Astronomical Society of the Pacific, vol.
137, no. 1, 014201, IOP Publishing, 2025, doi:10.1088/1538-3873/ada185.'
short: A.C. Rodriguez, K. El-Badry, V. Suleimanov, A.F. Pala, S.R. Kulkarni, B.
Gaensicke, K. Mori, R.M. Rich, A. Sarkar, T. Bao, R.L. De Oliveira, G. Ramsay,
P. Szkody, M. Graham, T.A. Prince, I. Caiazzo, Z.P. Vanderbosch, J.V. Roestel,
K.K. Das, Y.J. Qin, M.M. Kasliwal, A. Wold, S.L. Groom, D. Reiley, R. Riddle,
Publications of the Astronomical Society of the Pacific 137 (2025).
date_created: 2025-01-19T23:01:51Z
date_published: 2025-01-01T00:00:00Z
date_updated: 2025-02-27T12:46:32Z
day: '01'
ddc:
- '520'
department:
- _id: IlCa
doi: 10.1088/1538-3873/ada185
external_id:
arxiv:
- '2408.16053'
isi:
- '001393204700001'
file:
- access_level: open_access
checksum: 02a9be04a6704fc272ed5a976e5fa8c5
content_type: application/pdf
creator: dernst
date_created: 2025-01-20T09:52:34Z
date_updated: 2025-01-20T09:52:34Z
file_id: '18860'
file_name: 2025_PASP_Rodriguez.pdf
file_size: 5155631
relation: main_file
success: 1
file_date_updated: 2025-01-20T09:52:34Z
fulldoi: https://doi.org/10.1088/1538-3873/ada185
has_accepted_license: '1'
intvolume: ' 137'
isi: 1
issue: '1'
language:
- iso: eng
month: '01'
oa: 1
oa_version: Published Version
publication: Publications of the Astronomical Society of the Pacific
publication_identifier:
issn:
- 0004-6280
publication_status: published
publisher: IOP Publishing
quality_controlled: '1'
scopus_import: '1'
status: public
title: 'Cataclysmic variables and AM CVn binaries in SRG/eROSITA + Gaia: Volume limited
samples, X-ray luminosity functions, and space densities'
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/3.0/legalcode
name: Creative Commons Attribution 3.0 Unported (CC BY 3.0)
short: CC BY (3.0)
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 137
year: '2025'
...
---
OA_place: publisher
OA_type: diamond
_id: '18852'
abstract:
- lang: eng
text: 'Recent observations have found a growing number of hypervelocity stars with
speeds of ≈1500 − 2500 km s−1 that could have only been produced through thermonuclear
supernovae in white dwarf binaries. Most of the observed hypervelocity runaways
in this class display a surprising inflated structure: their current radii are
roughly an order of magnitude greater than they would have been as white dwarfs
filling their Roche lobe. While many simulations exist studying the dynamical
phase leading to supernova detonation in these systems, no detailed calculations
of the long-term structure of the runaways have yet been performed. We used an
existing AREPO hydrodynamical simulation of a supernova in a white dwarf binary
as a starting point for the evolution of these stars with the one-dimensional
stellar evolution code MESA. We show that the supernova shock is not energetic
enough to inflate the white dwarf over timescales longer than a few thousand years,
significantly shorter than the 105 − 6 year lifetimes inferred for observed hypervelocity
runaways. Although they experience a shock from a supernova less than ≈0.02 R⊙
away, our models do not experience significant interior heating, and all contract
back to radii of around 0.01 R⊙ within about 104 years. Explaining the observed
inflated states requires either an additional source of significant heating or
some other physics that is not yet accounted for in the subsequent evolution.'
acknowledgement: 'This project was originally started as part of the Kavli Summer
Program which took place in the Max Planck Institute for Astrophysics in Garching
in July 2023, supported by the Kavli Foundation. We are grateful to Stephen Justham,
Selma de Mink, and Jim Fuller for enriching discussions. We would like to thank
the anonymous referee for their helpful report. A.B. was supported by the Deutsche
Forschungsgemeinschaft (DFG) through grant GE2506/18-1. K.J.S. was supported by
NASA through the Astrophysics Theory Program (80NSSC20K0544) and by NASA/ESA Hubble
Space Telescope programs #15871 and #15918. W.E.K. was supported by NSF Grants OAC-2311323,
AST-2206523, and NASA/ESA HST-AR-Theory HSTAR-16613.002-A. K.E. was supported in
part by HST-GO-17441.001-A. AB and ASR would like to thank Rob Farmer for his support
with PyMESA.'
article_number: A114
article_processing_charge: No
article_type: original
arxiv: 1
author:
- first_name: Aakash
full_name: Bhat, Aakash
last_name: Bhat
- first_name: Evan B.
full_name: Bauer, Evan B.
last_name: Bauer
- first_name: Rüdiger
full_name: Pakmor, Rüdiger
last_name: Pakmor
- first_name: Ken J.
full_name: Shen, Ken J.
last_name: Shen
- first_name: Ilaria
full_name: Caiazzo, Ilaria
id: 8ae5b6e7-2a03-11ee-914d-b58ed7a3b47d
last_name: Caiazzo
orcid: 0000-0002-4770-5388
- first_name: Abinaya Swaruba
full_name: Rajamuthukumar, Abinaya Swaruba
last_name: Rajamuthukumar
- first_name: Kareem
full_name: El-Badry, Kareem
last_name: El-Badry
- first_name: Wolfgang E.
full_name: Kerzendorf, Wolfgang E.
last_name: Kerzendorf
citation:
ama: Bhat A, Bauer EB, Pakmor R, et al. Supernova shocks cannot explain the inflated
state of hypervelocity runaways from white dwarf binaries. Astronomy &
Astrophysics. 2025;693(1). doi:10.1051/0004-6361/202451371
apa: Bhat, A., Bauer, E. B., Pakmor, R., Shen, K. J., Caiazzo, I., Rajamuthukumar,
A. S., … Kerzendorf, W. E. (2025). Supernova shocks cannot explain the inflated
state of hypervelocity runaways from white dwarf binaries. Astronomy &
Astrophysics. EDP Sciences. https://doi.org/10.1051/0004-6361/202451371
chicago: Bhat, Aakash, Evan B. Bauer, Rüdiger Pakmor, Ken J. Shen, Ilaria Caiazzo,
Abinaya Swaruba Rajamuthukumar, Kareem El-Badry, and Wolfgang E. Kerzendorf. “Supernova
Shocks Cannot Explain the Inflated State of Hypervelocity Runaways from White
Dwarf Binaries.” Astronomy & Astrophysics. EDP Sciences, 2025. https://doi.org/10.1051/0004-6361/202451371.
ieee: A. Bhat et al., “Supernova shocks cannot explain the inflated state
of hypervelocity runaways from white dwarf binaries,” Astronomy & Astrophysics,
vol. 693, no. 1. EDP Sciences, 2025.
ista: Bhat A, Bauer EB, Pakmor R, Shen KJ, Caiazzo I, Rajamuthukumar AS, El-Badry
K, Kerzendorf WE. 2025. Supernova shocks cannot explain the inflated state of
hypervelocity runaways from white dwarf binaries. Astronomy & Astrophysics.
693(1), A114.
mla: Bhat, Aakash, et al. “Supernova Shocks Cannot Explain the Inflated State of
Hypervelocity Runaways from White Dwarf Binaries.” Astronomy & Astrophysics,
vol. 693, no. 1, A114, EDP Sciences, 2025, doi:10.1051/0004-6361/202451371.
short: A. Bhat, E.B. Bauer, R. Pakmor, K.J. Shen, I. Caiazzo, A.S. Rajamuthukumar,
K. El-Badry, W.E. Kerzendorf, Astronomy & Astrophysics 693 (2025).
date_created: 2025-01-19T23:01:51Z
date_published: 2025-01-07T00:00:00Z
date_updated: 2026-02-16T12:08:05Z
day: '07'
ddc:
- '520'
department:
- _id: IlCa
doi: 10.1051/0004-6361/202451371
external_id:
arxiv:
- '2407.03424'
isi:
- '001406577300001'
file:
- access_level: open_access
checksum: e532b9c8123c29cfb0ee758e6d00453c
content_type: application/pdf
creator: dernst
date_created: 2025-01-20T09:57:00Z
date_updated: 2025-01-20T09:57:00Z
file_id: '18861'
file_name: 2025_AstronomyAstrophysics_Bhat.pdf
file_size: 1692527
relation: main_file
success: 1
file_date_updated: 2025-01-20T09:57:00Z
fulldoi: https://doi.org/10.1051/0004-6361/202451371
has_accepted_license: '1'
intvolume: ' 693'
isi: 1
issue: '1'
language:
- iso: eng
month: '01'
oa: 1
oa_version: Published Version
publication: Astronomy & Astrophysics
publication_identifier:
eissn:
- 1432-0746
issn:
- 0004-6361
publication_status: published
publisher: EDP Sciences
quality_controlled: '1'
scopus_import: '1'
status: public
title: Supernova shocks cannot explain the inflated state of hypervelocity runaways
from white dwarf binaries
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: 693
year: '2025'
...
---
OA_type: closed access
_id: '18853'
abstract:
- lang: eng
text: Electrolyte additives are extensively validated effective in mitigating dendrite
growth and parasitic reactions in aqueous zinc-ion batteries (AZIBs). Nonetheless,
the mechanisms by which additives influence the formation and characteristics
of the inorganic solid–electrolyte interphase (SEI) are not yet fully elucidated.
Herein, we investigate how Zn(CF3COO)2 additives influence solvation structure
and elucidate the mechanism by which these additives promote the dual reduction
of anions. Through cryo-transmission electron microscopy analysis, we identified
the SEI as a highly amorphous ZnS/ZnF2 phase. This amorphous hybrid SEI demonstrates
exceptional stability, mechanical robustness, and high Zn2+ conductivity, effectively
mitigating parasitic reactions and enhancing Zn plating/stripping reversibility.
Even under elevated current densities, the Zn anode exhibits ultra-stable longevity
and ultra-high reversibility. This study provides a comprehensive understanding
of the intrinsic mechanisms governing solvation structure modulation that lead
to the formation of amorphous hybrid SEI, underscoring their efficacy in enhancing
the performance and durability of AZIBs.
acknowledged_ssus:
- _id: EM-Fac
- _id: NanoFab
acknowledgement: The authors acknowledge financial support from the Joint Fund of
Henan Province Science and Technology R&D Program (235200810097) and the Generalitat
de Catalunya (2021SGR01581). This research was supported by the Scientific Service
Units (SSU) of ISTA Austria through resources provided by the Electron Microscopy
Facility (EMF) and the Nanofabrication Facility (NFF). G. Z. and J. L. thank the
China Scholarship Council (CSC) for the scholarship support.
article_processing_charge: No
article_type: original
author:
- first_name: Guifang
full_name: Zeng, Guifang
last_name: Zeng
- first_name: Qing
full_name: Sun, Qing
last_name: Sun
- first_name: Sharona
full_name: Horta, Sharona
id: 03a7e858-01b1-11ec-8b71-99ae6c4a05bc
last_name: Horta
- first_name: Paulina R.
full_name: Martínez-Alanis, Paulina R.
last_name: Martínez-Alanis
- first_name: Peng
full_name: Wu, Peng
last_name: Wu
- first_name: Jing
full_name: Li, Jing
last_name: Li
- first_name: Shang
full_name: Wang, Shang
last_name: Wang
- first_name: Maria
full_name: Ibáñez, Maria
id: 43C61214-F248-11E8-B48F-1D18A9856A87
last_name: Ibáñez
orcid: 0000-0001-5013-2843
- first_name: Yanhong
full_name: Tian, Yanhong
last_name: Tian
- first_name: Lijie
full_name: Ci, Lijie
last_name: Ci
- first_name: Andreu
full_name: Cabot, Andreu
last_name: Cabot
citation:
ama: Zeng G, Sun Q, Horta S, et al. Modulating the solvation structure to enhance
amorphous solid electrolyte interface formation for ultra-stable aqueous zinc
anode. Energy and Environmental Science. 2025;18(4):1683-1695. doi:10.1039/d4ee03750b
apa: Zeng, G., Sun, Q., Horta, S., Martínez-Alanis, P. R., Wu, P., Li, J., … Cabot,
A. (2025). Modulating the solvation structure to enhance amorphous solid electrolyte
interface formation for ultra-stable aqueous zinc anode. Energy and Environmental
Science. Royal Society of Chemistry. https://doi.org/10.1039/d4ee03750b
chicago: Zeng, Guifang, Qing Sun, Sharona Horta, Paulina R. Martínez-Alanis, Peng
Wu, Jing Li, Shang Wang, et al. “Modulating the Solvation Structure to Enhance
Amorphous Solid Electrolyte Interface Formation for Ultra-Stable Aqueous Zinc
Anode.” Energy and Environmental Science. Royal Society of Chemistry, 2025.
https://doi.org/10.1039/d4ee03750b.
ieee: G. Zeng et al., “Modulating the solvation structure to enhance amorphous
solid electrolyte interface formation for ultra-stable aqueous zinc anode,” Energy
and Environmental Science, vol. 18, no. 4. Royal Society of Chemistry, pp.
1683–1695, 2025.
ista: Zeng G, Sun Q, Horta S, Martínez-Alanis PR, Wu P, Li J, Wang S, Ibáñez M,
Tian Y, Ci L, Cabot A. 2025. Modulating the solvation structure to enhance amorphous
solid electrolyte interface formation for ultra-stable aqueous zinc anode. Energy
and Environmental Science. 18(4), 1683–1695.
mla: Zeng, Guifang, et al. “Modulating the Solvation Structure to Enhance Amorphous
Solid Electrolyte Interface Formation for Ultra-Stable Aqueous Zinc Anode.” Energy
and Environmental Science, vol. 18, no. 4, Royal Society of Chemistry, 2025,
pp. 1683–95, doi:10.1039/d4ee03750b.
short: G. Zeng, Q. Sun, S. Horta, P.R. Martínez-Alanis, P. Wu, J. Li, S. Wang, M.
Ibáñez, Y. Tian, L. Ci, A. Cabot, Energy and Environmental Science 18 (2025) 1683–1695.
date_created: 2025-01-19T23:01:52Z
date_published: 2025-02-21T00:00:00Z
date_updated: 2025-07-10T11:51:27Z
day: '21'
department:
- _id: MaIb
doi: 10.1039/d4ee03750b
external_id:
isi:
- '001389898000001'
fulldoi: https://doi.org/10.1039/d4ee03750b
intvolume: ' 18'
isi: 1
issue: '4'
language:
- iso: eng
month: '02'
oa_version: None
page: 1683-1695
publication: Energy and Environmental Science
publication_identifier:
eissn:
- 1754-5706
issn:
- 1754-5692
publication_status: published
publisher: Royal Society of Chemistry
quality_controlled: '1'
scopus_import: '1'
status: public
title: Modulating the solvation structure to enhance amorphous solid electrolyte interface
formation for ultra-stable aqueous zinc anode
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 18
year: '2025'
...
---
OA_place: publisher
OA_type: diamond
_id: '18854'
abstract:
- lang: eng
text: "Context. One of the surprising early findings with JWST has been the discovery
of a strong “roll-over” or a softening of the absorption edge of Lyα in a large
number of galaxies at z ≳ 6, in addition to systematic offsets from photometric
redshift estimates and fundamental galaxy scaling relations. This has been interpreted
as strong cumulative damped Lyα absorption (DLA) wings from high column densities
of neutral atomic hydrogen (H I), signifying major gas accretion events in the
formation of these galaxies.\r\nAims. To explore this new phenomenon systematically,
we assembled the JWST/NIRSpec PRImordial gas Mass AssembLy (PRIMAL) legacy survey
of 584 galaxies at z = 5.0 − 13.4, designed to study the physical properties and
gas in and around galaxies during the reionization epoch.\r\nMethods. We characterized
this benchmark sample in full and spectroscopically derived the galaxy redshifts,
metallicities, star formation rates, and ultraviolet (UV) slopes. We defined a
new diagnostic, the Lyα damping parameter DLyα, to measure and quantify the net
effect of Lyα emission strength, the H I fraction in the intergalactic medium,
or the local H I column density for each source. The JWST-PRIMAL survey is based
on the spectroscopic DAWN JWST Archive (DJA-Spec). We describe DJA-Spec in this
paper, detailing the reduction methods, the post-processing steps, and basic analysis
tools. All the software, reduced spectra, and spectroscopically derived quantities
and catalogs are made publicly available in dedicated repositories.\r\nResults.
We find that the fraction of galaxies showing strong integrated DLAs with NHI > 1021 cm−2
only increases slightly from ≈60% at z ≈ 6 up to ≈65 − 90% at z > 8. Similarly,
the prevalence and prominence of Lyα emission is found to increase with decreasing
redshift, in qualitative agreement with previous observational results. Strong
Lyα emitters (LAEs) are predominantly found to be associated with low-metallicity
and UV faint galaxies. By contrast, strong DLAs are observed in galaxies with
a variety of intrinsic physical properties, but predominantly at high redshifts
and low metallicities.\r\nConclusions. Our results indicate that strong DLAs likely
reflect a particular early assembly phase of reionization-era galaxies, at which
point they are largely dominated by pristine H I gas accretion. At z = 8 − 10,
this gas gradually cools and forms into stars that ionize their local surroundings,
forming large ionized bubbles and producing strong observed Lyα emission at z < 8."
acknowledgement: 'We would like to thank the referee for a detailed and constructive
report, greatly improving the presentation of the results in this work. We would
like to thank Peter Jakobsen for his vision and heroic endeavor in optimally designing
the JWST/NIRSpec instrument and some of its first on-sky observations and for enlightening
discussions about the intricacies of the NIRSpec data. Further, we would like to
thank John Chisholm for helpful clarifications and discussions related to the escape
fraction of ionizing photons and Aayush Saxena for enlightening conversations on
the escape and absorption of Lyman-α photons. This work has received funding from
the Swiss State Secretariat for Education, Research and Innovation (SERI) under
contract number MB22.00072. The Cosmic Dawn Center (DAWN) is funded by the Danish
National Research Foundation under grant DNRF140. The data products presented herein
were retrieved from the DAWN JWST Archive (DJA). DJA is an initiative of the Cosmic
Dawn Center, which is funded by the Danish National Research Foundation under grant
DNRF140. P.D. acknowledge support from the NWO grant 016.VIDI.189.162 (“ODIN") and
warmly thanks the European Commission’s and University of Groningen’s CO-FUND Rosalind
Franklin program. Support from the ERC Advanced Grant INTERSTELLAR H2020/740120
is kindly acknowledged (A.F.). S.G. acknowledges financial support from the Villum
Young Investigator grants 37440 and 13160 and the Cosmic Dawn Center. M.K. was supported
by the ANID BASAL project FB210003. G.E.M. acknowledges financial support from the
Villum Young Investigator grants 37440 and 13160 and the Cosmic Dawn Center. J.W.
acknowledges support from the Science and Technology Facilities Council (STFC),
by the ERC through Advanced Grant 695671 “QUENCH”, by the UKRI Frontier Research
grant RISEandFALL. Support for this work was provided by NASA through the NASA Hubble
Fellowship grant HST-HF2-51515.001-A awarded by the Space Telescope Science Institute,
which is operated by the Association of Universities for Research in Astronomy,
Incorporated, under NASA contract NAS5-26555. F.C. acknowledges support from a UKRI
Frontier Research Guarantee Grant (PI Cullen; grant reference EP/X021025/1). J.H.W.
acknowledges support by NSF grant AST-2108020 and NASA grants 80NSSC20K0520 and
80NSSC21K1053. NRT acknowledges support through STFC consolidated grant ST/W000857/1.
M.J.H. is supported by the Swedish Research Council, VetenskapsrÅdet, and is fellow
of the Knut & Alice Wallenberg foundation. This work is based in part on observations
made with the NASA/ESA/CSA James Webb Space Telescope. The data were obtained from
the Mikulski Archive for Space Telescopes (MAST) at the Space Telescope Science
Institute, which is operated by the Association of Universities for Research in
Astronomy, Inc., under NASA contract NAS 5-03127 for JWST. Software: This work made
use of and acknowledge the following software: NumPy (Harris et al. 2020), Matplotlib
(Hunter 2007), LMfit (Newville et al. 2014), SciPy (Virtanen et al. 2020), grizli
(Brammer 2023a), Astrodrizzle (Gonzaga et al. 2012), and MsaExp (v0.3; Brammer 2023b).'
article_number: A60
article_processing_charge: No
article_type: original
author:
- first_name: K. E.
full_name: Heintz, K. E.
last_name: Heintz
- first_name: G. B.
full_name: Brammer, G. B.
last_name: Brammer
- first_name: D.
full_name: Watson, D.
last_name: Watson
- first_name: P. A.
full_name: Oesch, P. A.
last_name: Oesch
- first_name: L. C.
full_name: Keating, L. C.
last_name: Keating
- first_name: M. J.
full_name: Hayes, M. J.
last_name: Hayes
- first_name: Unknown
full_name: Abdurro'Uf, Unknown
last_name: Abdurro'Uf
- first_name: K. Z.
full_name: Arellano-Córdova, K. Z.
last_name: Arellano-Córdova
- first_name: A. C.
full_name: Carnall, A. C.
last_name: Carnall
- first_name: C. R.
full_name: Christiansen, C. R.
last_name: Christiansen
- first_name: F.
full_name: Cullen, F.
last_name: Cullen
- first_name: R.
full_name: Davé, R.
last_name: Davé
- first_name: P.
full_name: Dayal, P.
last_name: Dayal
- first_name: A.
full_name: Ferrara, A.
last_name: Ferrara
- first_name: K.
full_name: Finlator, K.
last_name: Finlator
- first_name: J. P.U.
full_name: Fynbo, J. P.U.
last_name: Fynbo
- first_name: S. R.
full_name: Flury, S. R.
last_name: Flury
- first_name: V.
full_name: Gelli, V.
last_name: Gelli
- first_name: S.
full_name: Gillman, S.
last_name: Gillman
- first_name: R.
full_name: Gottumukkala, R.
last_name: Gottumukkala
- first_name: K.
full_name: Gould, K.
last_name: Gould
- first_name: T. R.
full_name: Greve, T. R.
last_name: Greve
- first_name: S. E.
full_name: Hardin, S. E.
last_name: Hardin
- first_name: T. Y.Y.
full_name: Hsiao, T. Y.Y.
last_name: Hsiao
- first_name: A.
full_name: Hutter, A.
last_name: Hutter
- first_name: P.
full_name: Jakobsson, P.
last_name: Jakobsson
- first_name: M.
full_name: Killi, M.
last_name: Killi
- first_name: N.
full_name: Khosravaninezhad, N.
last_name: Khosravaninezhad
- first_name: P.
full_name: Laursen, P.
last_name: Laursen
- first_name: M. M.
full_name: Lee, M. M.
last_name: Lee
- first_name: G. E.
full_name: Magdis, G. E.
last_name: Magdis
- 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: R. P.
full_name: Naidu, R. P.
last_name: Naidu
- first_name: D.
full_name: Narayanan, D.
last_name: Narayanan
- first_name: C.
full_name: Pollock, C.
last_name: Pollock
- first_name: M. K.M.
full_name: Prescott, M. K.M.
last_name: Prescott
- first_name: V.
full_name: Rusakov, V.
last_name: Rusakov
- first_name: M.
full_name: Shuntov, M.
last_name: Shuntov
- first_name: A.
full_name: Sneppen, A.
last_name: Sneppen
- first_name: R.
full_name: Smit, R.
last_name: Smit
- first_name: N. R.
full_name: Tanvir, N. R.
last_name: Tanvir
- first_name: C.
full_name: Terp, C.
last_name: Terp
- first_name: S.
full_name: Toft, S.
last_name: Toft
- first_name: F.
full_name: Valentino, F.
last_name: Valentino
- first_name: A. P.
full_name: Vijayan, A. P.
last_name: Vijayan
- first_name: J. R.
full_name: Weaver, J. R.
last_name: Weaver
- first_name: J. H.
full_name: Wise, J. H.
last_name: Wise
- first_name: J.
full_name: Witstok, J.
last_name: Witstok
citation:
ama: 'Heintz KE, Brammer GB, Watson D, et al. The JWST-PRIMAL archival survey: A
JWST/NIRSpec reference sample for the physical properties and Lyman-α absorption
and emission of ∼600 galaxies at z = 5.0-13.4. Astronomy & Astrophysics.
2025;693. doi:10.1051/0004-6361/202450243'
apa: 'Heintz, K. E., Brammer, G. B., Watson, D., Oesch, P. A., Keating, L. C., Hayes,
M. J., … Witstok, J. (2025). The JWST-PRIMAL archival survey: A JWST/NIRSpec reference
sample for the physical properties and Lyman-α absorption and emission of ∼600
galaxies at z = 5.0-13.4. Astronomy & Astrophysics. EDP Sciences. https://doi.org/10.1051/0004-6361/202450243'
chicago: 'Heintz, K. E., G. B. Brammer, D. Watson, P. A. Oesch, L. C. Keating, M.
J. Hayes, Unknown Abdurro’Uf, et al. “The JWST-PRIMAL Archival Survey: A JWST/NIRSpec
Reference Sample for the Physical Properties and Lyman-α Absorption and Emission
of ∼600 Galaxies at z = 5.0-13.4.” Astronomy & Astrophysics. EDP Sciences,
2025. https://doi.org/10.1051/0004-6361/202450243.'
ieee: 'K. E. Heintz et al., “The JWST-PRIMAL archival survey: A JWST/NIRSpec
reference sample for the physical properties and Lyman-α absorption and emission
of ∼600 galaxies at z = 5.0-13.4,” Astronomy & Astrophysics, vol. 693.
EDP Sciences, 2025.'
ista: 'Heintz KE, Brammer GB, Watson D, Oesch PA, Keating LC, Hayes MJ, Abdurro’Uf
U, Arellano-Córdova KZ, Carnall AC, Christiansen CR, Cullen F, Davé R, Dayal P,
Ferrara A, Finlator K, Fynbo JPU, Flury SR, Gelli V, Gillman S, Gottumukkala R,
Gould K, Greve TR, Hardin SE, Hsiao TYY, Hutter A, Jakobsson P, Killi M, Khosravaninezhad
N, Laursen P, Lee MM, Magdis GE, Matthee JJ, Naidu RP, Narayanan D, Pollock C,
Prescott MKM, Rusakov V, Shuntov M, Sneppen A, Smit R, Tanvir NR, Terp C, Toft
S, Valentino F, Vijayan AP, Weaver JR, Wise JH, Witstok J. 2025. The JWST-PRIMAL
archival survey: A JWST/NIRSpec reference sample for the physical properties and
Lyman-α absorption and emission of ∼600 galaxies at z = 5.0-13.4. Astronomy &
Astrophysics. 693, A60.'
mla: 'Heintz, K. E., et al. “The JWST-PRIMAL Archival Survey: A JWST/NIRSpec Reference
Sample for the Physical Properties and Lyman-α Absorption and Emission of ∼600
Galaxies at z = 5.0-13.4.” Astronomy & Astrophysics, vol. 693, A60,
EDP Sciences, 2025, doi:10.1051/0004-6361/202450243.'
short: K.E. Heintz, G.B. Brammer, D. Watson, P.A. Oesch, L.C. Keating, M.J. Hayes,
U. Abdurro’Uf, K.Z. Arellano-Córdova, A.C. Carnall, C.R. Christiansen, F. Cullen,
R. Davé, P. Dayal, A. Ferrara, K. Finlator, J.P.U. Fynbo, S.R. Flury, V. Gelli,
S. Gillman, R. Gottumukkala, K. Gould, T.R. Greve, S.E. Hardin, T.Y.Y. Hsiao,
A. Hutter, P. Jakobsson, M. Killi, N. Khosravaninezhad, P. Laursen, M.M. Lee,
G.E. Magdis, J.J. Matthee, R.P. Naidu, D. Narayanan, C. Pollock, M.K.M. Prescott,
V. Rusakov, M. Shuntov, A. Sneppen, R. Smit, N.R. Tanvir, C. Terp, S. Toft, F.
Valentino, A.P. Vijayan, J.R. Weaver, J.H. Wise, J. Witstok, Astronomy & Astrophysics
693 (2025).
date_created: 2025-01-19T23:01:52Z
date_published: 2025-01-06T00:00:00Z
date_updated: 2026-02-16T12:07:37Z
day: '06'
ddc:
- '520'
department:
- _id: JoMa
doi: 10.1051/0004-6361/202450243
external_id:
isi:
- '001390856800001'
file:
- access_level: open_access
checksum: 67a791080ade9bfb449d249de2af7456
content_type: application/pdf
creator: dernst
date_created: 2025-01-20T09:17:33Z
date_updated: 2025-01-20T09:17:33Z
file_id: '18858'
file_name: 2025_AstronomyAstrophysics_Heintz.pdf
file_size: 4513466
relation: main_file
success: 1
file_date_updated: 2025-01-20T09:17:33Z
fulldoi: https://doi.org/10.1051/0004-6361/202450243
has_accepted_license: '1'
intvolume: ' 693'
isi: 1
language:
- iso: eng
month: '01'
oa: 1
oa_version: Published Version
publication: Astronomy & Astrophysics
publication_identifier:
eissn:
- 1432-0746
issn:
- 0004-6361
publication_status: published
publisher: EDP Sciences
quality_controlled: '1'
scopus_import: '1'
status: public
title: 'The JWST-PRIMAL archival survey: A JWST/NIRSpec reference sample for the physical
properties and Lyman-α absorption and emission of ∼600 galaxies at z = 5.0-13.4'
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: 693
year: '2025'
...
---
OA_place: repository
OA_type: green
_id: '18855'
abstract:
- lang: eng
text: "A central problem in computational statistics is to convert a procedure for
sampling combinatorial objects into a procedure for counting those objects, and
vice versa. We consider sampling problems which come from Gibbs distributions,
which are families of probability distributions over a discrete space Ω with probability
mass function of the form μ^Ω_β(ω) ∝ e^{β H(ω)} for β in an interval [β_min, β_max]
and H(ω) ∈ {0} ∪ [1, n]. Two important parameters are the partition function,
which is the normalization factor Z(β) = ∑_{ω ∈ Ω} e^{β H(ω)}, and the vector
of pre-image counts c_x=|H^-1(x)|.\r\nWe develop black-box sampling algorithms
to estimate the counts roughly Õ(n²/ε²) samples for integer-valued distributions
and Õ(q/ε²) samples for general distributions, where q = (log Z(β_max))/Z(β_min)
\ (ignoring some second-order terms and parameters). We show this is optimal up
to logarithmic factors. We illustrate with improved algorithms for counting connected
subgraphs, independent sets, and perfect matchings. As a key subroutine, we estimate
all values of the partition function using Õ(n²/ε²) samples for integer-valued
distributions and Õ(q/ε²) samples for general distributions. This improves over
a prior algorithm of Huber (2015) which computes a single point estimate Z(β_max)
and which uses a slightly larger amount of samples. We show matching lower bounds,
demonstrating this complexity is optimal as a function of n and q up to logarithmic
terms."
acknowledgement: "We thank Heng Guo for helpful explanations of algorithms for sampling
connected subgraphs and matchings, and Maksym Serbyn for bringing to our attention
the WL algorithm and its use in physics.\r\nThis is an extended version, which includes
work under the same name from ICALP 2023, as well as the earlier work [22] appearing
in COLT 2018.\r\nV. Kolmogorov was supported by the European Research Council under
the European Unions Seventh Framework Programme (FP7/2007-2013)/ERC grant agreement
no 616160"
article_number: '3'
article_processing_charge: No
article_type: original
arxiv: 1
author:
- first_name: David G.
full_name: Harris, David G.
last_name: Harris
- first_name: Vladimir
full_name: Kolmogorov, Vladimir
id: 3D50B0BA-F248-11E8-B48F-1D18A9856A87
last_name: Kolmogorov
citation:
ama: Harris DG, Kolmogorov V. Parameter estimation for Gibbs distributions. ACM
Transactions on Algorithms. 2025;21(1). doi:10.1145/3685676
apa: Harris, D. G., & Kolmogorov, V. (2025). Parameter estimation for Gibbs
distributions. ACM Transactions on Algorithms. Association for Computing
Machinery. https://doi.org/10.1145/3685676
chicago: Harris, David G., and Vladimir Kolmogorov. “Parameter Estimation for Gibbs
Distributions.” ACM Transactions on Algorithms. Association for Computing
Machinery, 2025. https://doi.org/10.1145/3685676.
ieee: D. G. Harris and V. Kolmogorov, “Parameter estimation for Gibbs distributions,”
ACM Transactions on Algorithms, vol. 21, no. 1. Association for Computing
Machinery, 2025.
ista: Harris DG, Kolmogorov V. 2025. Parameter estimation for Gibbs distributions.
ACM Transactions on Algorithms. 21(1), 3.
mla: Harris, David G., and Vladimir Kolmogorov. “Parameter Estimation for Gibbs
Distributions.” ACM Transactions on Algorithms, vol. 21, no. 1, 3, Association
for Computing Machinery, 2025, doi:10.1145/3685676.
short: D.G. Harris, V. Kolmogorov, ACM Transactions on Algorithms 21 (2025).
corr_author: '1'
date_created: 2025-01-19T23:01:52Z
date_published: 2025-01-01T00:00:00Z
date_updated: 2025-07-10T11:50:44Z
day: '01'
department:
- _id: VlKo
doi: 10.1145/3685676
ec_funded: 1
external_id:
arxiv:
- '2007.10824'
isi:
- '001399998600008'
fulldoi: https://doi.org/10.1145/3685676
intvolume: ' 21'
isi: 1
issue: '1'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.48550/arXiv.2007.10824
month: '01'
oa: 1
oa_version: Preprint
project:
- _id: 25FBA906-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '616160'
name: 'Discrete Optimization in Computer Vision: Theory and Practice'
publication: ACM Transactions on Algorithms
publication_identifier:
eissn:
- 1549-6333
issn:
- 1549-6325
publication_status: published
publisher: Association for Computing Machinery
quality_controlled: '1'
related_material:
record:
- id: '14084'
relation: earlier_version
status: public
scopus_import: '1'
status: public
title: Parameter estimation for Gibbs distributions
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 21
year: '2025'
...
---
OA_type: closed access
_id: '18878'
abstract:
- lang: eng
text: Thermoelectric (TE) materials, with the ability to convert heat into electrical
energy, can generate micro-electrical fields at electronic interfaces with biological
systems, making them applicable in electric-catalyzing as nanozymes, and modulate
the infected microenvironment of skin wounds. Thereby, by harnessing temperature
differences in vitro or in vivo, TE nanomaterials can provide antimicrobial reactive
oxygen species (ROS) by catalyzing redox reactions, thereby accelerating wound
healing by suppressing infection. However, despite their promising potential,
there is still a lack of comprehensive understanding of the antimicrobial mechanisms,
biocompatibility, and practical applications of TE nanomaterials in wound healing,
as this is a newly-emerged sub-area of energy-related biomedical applications.
This review aims to address this gap by highlighting the emerging progress of
TE materials in wound healing, clarifying their mechanism and advances, emphasizing
their potential challenges for commercialization and clinical use, and proposing
novel design strategies of TE nanomaterials for effective antibacterial performance.
acknowledgement: This work was financially supported by the Sichuan Science and Technology
Program (Nos. 2023ZYD0064 and 2023YFG0220), the Fundamental Research Funds for the
Central Universities (No. YJ202242), and the Research Funding from West China School/Hospital
of Stomatology, Sichuan University (No. QDJF2022–2).
article_processing_charge: No
article_type: review
author:
- first_name: Shiyu
full_name: Jia, Shiyu
last_name: Jia
- first_name: Cai
full_name: Qi, Cai
last_name: Qi
- first_name: Shengduo
full_name: Xu, Shengduo
id: 12ab8624-4c8a-11ec-9e11-e1ac2438f22f
last_name: Xu
- first_name: Lei
full_name: Yang, Lei
last_name: Yang
- first_name: Qiang
full_name: Sun, Qiang
last_name: Sun
citation:
ama: Jia S, Qi C, Xu S, Yang L, Sun Q. Advancements of thermoelectric nanomaterials
in ROS-mediated broad-spectrum antibacterial therapies for wound healing. Journal
of Materials Science and Technology. 2025;225(08):212-226. doi:10.1016/j.jmst.2024.11.039
apa: Jia, S., Qi, C., Xu, S., Yang, L., & Sun, Q. (2025). Advancements of thermoelectric
nanomaterials in ROS-mediated broad-spectrum antibacterial therapies for wound
healing. Journal of Materials Science and Technology. Elsevier. https://doi.org/10.1016/j.jmst.2024.11.039
chicago: Jia, Shiyu, Cai Qi, Shengduo Xu, Lei Yang, and Qiang Sun. “Advancements
of Thermoelectric Nanomaterials in ROS-Mediated Broad-Spectrum Antibacterial Therapies
for Wound Healing.” Journal of Materials Science and Technology. Elsevier,
2025. https://doi.org/10.1016/j.jmst.2024.11.039.
ieee: S. Jia, C. Qi, S. Xu, L. Yang, and Q. Sun, “Advancements of thermoelectric
nanomaterials in ROS-mediated broad-spectrum antibacterial therapies for wound
healing,” Journal of Materials Science and Technology, vol. 225, no. 08.
Elsevier, pp. 212–226, 2025.
ista: Jia S, Qi C, Xu S, Yang L, Sun Q. 2025. Advancements of thermoelectric nanomaterials
in ROS-mediated broad-spectrum antibacterial therapies for wound healing. Journal
of Materials Science and Technology. 225(08), 212–226.
mla: Jia, Shiyu, et al. “Advancements of Thermoelectric Nanomaterials in ROS-Mediated
Broad-Spectrum Antibacterial Therapies for Wound Healing.” Journal of Materials
Science and Technology, vol. 225, no. 08, Elsevier, 2025, pp. 212–26, doi:10.1016/j.jmst.2024.11.039.
short: S. Jia, C. Qi, S. Xu, L. Yang, Q. Sun, Journal of Materials Science and Technology
225 (2025) 212–226.
date_created: 2025-01-26T23:01:49Z
date_published: 2025-08-01T00:00:00Z
date_updated: 2025-12-30T07:19:04Z
day: '01'
department:
- _id: MaIb
doi: 10.1016/j.jmst.2024.11.039
external_id:
isi:
- '001407204300001'
fulldoi: https://doi.org/10.1016/j.jmst.2024.11.039
intvolume: ' 225'
isi: 1
issue: '08'
language:
- iso: eng
month: '08'
oa_version: None
page: 212-226
publication: Journal of Materials Science and Technology
publication_identifier:
issn:
- 1005-0302
publication_status: published
publisher: Elsevier
quality_controlled: '1'
scopus_import: '1'
status: public
title: Advancements of thermoelectric nanomaterials in ROS-mediated broad-spectrum
antibacterial therapies for wound healing
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 225
year: '2025'
...