---
OA_place: publisher
OA_type: hybrid
PlanS_conform: '1'
_id: '21948'
abstract:
- lang: eng
text: The cerebral cortex comprises diverse neuron and glial cell types generated
by radial glial progenitors (RGPs) during development. Although RGPs broadly differentiate
according to temporally and spatially regulated molecular logics, the lineage
hierarchies linking individual progenitors to defined cell (sub)types are not
well understood. Clone-resolved transcriptomics, combining molecular barcoding
and single-cell RNA sequencing, allow high-resolution lineage tracing at the single-clone/cell
level across different species and models. In this mini-review, we synthesize
recent advances in this field, uncovering unexpected lineage relationships in
the developing brain, with a particular focus on the cerebral cortex. We further
highlight new insights into species-specific differences in the developmental
programs generating cell-type diversity, linking changes in clonal architecture
to lineage diversification during cortical evolution.
acknowledgement: We wish to thank all members of the Hippenmeyer laboratory at ISTA
for exciting discussions on the subject of this review. We apologize to colleagues
whose work we could not cite and/or discuss in the frame of the available space.
Work in the Hippenmeyer laboratory on the discussed topic is supported by ISTA institutional
funds, an EMBO LTF (ALTF 994–2023) to F.P., FWF SFB F78 (10.55776/F78) to S.H.,
and FWF Cluster of Excellence COE16 (10.55776/COE16) to S.H.
article_number: '102487'
article_processing_charge: Yes (via OA deal)
article_type: original
author:
- first_name: Irene
full_name: Varela Martínez, Irene
id: a69b5985-8829-11f0-8fc2-d0af58f64471
last_name: Varela Martínez
- first_name: Fabrizia
full_name: Pipicelli, Fabrizia
id: 649134fd-d012-11ed-8f82-db1e5050f9ba
last_name: Pipicelli
- first_name: Simon
full_name: Hippenmeyer, Simon
id: 37B36620-F248-11E8-B48F-1D18A9856A87
last_name: Hippenmeyer
orcid: 0000-0003-2279-1061
citation:
ama: 'Varela Martínez I, Pipicelli F, Hippenmeyer S. Tracing cell lineages in the
developing brain: Insights from mosaic analysis and clone-resolved transcriptomics.
Current Opinion in Genetics & Development. 2026;99. doi:10.1016/j.gde.2026.102487'
apa: 'Varela Martínez, I., Pipicelli, F., & Hippenmeyer, S. (2026). Tracing
cell lineages in the developing brain: Insights from mosaic analysis and clone-resolved
transcriptomics. Current Opinion in Genetics & Development. Elsevier.
https://doi.org/10.1016/j.gde.2026.102487'
chicago: 'Varela Martínez, Irene, Fabrizia Pipicelli, and Simon Hippenmeyer. “Tracing
Cell Lineages in the Developing Brain: Insights from Mosaic Analysis and Clone-Resolved
Transcriptomics.” Current Opinion in Genetics & Development. Elsevier,
2026. https://doi.org/10.1016/j.gde.2026.102487.'
ieee: 'I. Varela Martínez, F. Pipicelli, and S. Hippenmeyer, “Tracing cell lineages
in the developing brain: Insights from mosaic analysis and clone-resolved transcriptomics,”
Current Opinion in Genetics & Development, vol. 99. Elsevier, 2026.'
ista: 'Varela Martínez I, Pipicelli F, Hippenmeyer S. 2026. Tracing cell lineages
in the developing brain: Insights from mosaic analysis and clone-resolved transcriptomics.
Current Opinion in Genetics & Development. 99, 102487.'
mla: 'Varela Martínez, Irene, et al. “Tracing Cell Lineages in the Developing Brain:
Insights from Mosaic Analysis and Clone-Resolved Transcriptomics.” Current
Opinion in Genetics & Development, vol. 99, 102487, Elsevier, 2026, doi:10.1016/j.gde.2026.102487.'
short: I. Varela Martínez, F. Pipicelli, S. Hippenmeyer, Current Opinion in Genetics
& Development 99 (2026).
corr_author: '1'
date_created: 2026-06-07T22:01:35Z
date_published: 2026-05-29T00:00:00Z
date_updated: 2026-08-12T09:56:19Z
day: '29'
ddc:
- '570'
department:
- _id: SiHi
doi: 10.1016/j.gde.2026.102487
external_id:
pmid:
- '42214837'
has_accepted_license: '1'
intvolume: ' 99'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.1016/j.gde.2026.102487
month: '05'
oa: 1
oa_version: Published Version
pmid: 1
project:
- _id: 7c084566-9f16-11ee-852c-c88a1dbbf1cf
grant_number: ALTF 994-2023
name: Role of cell lineage in generating cell-type diversity in developing neocortex’
- _id: 059F6AB4-7A3F-11EA-A408-12923DDC885E
grant_number: F7805
name: Stem Cell Modulation in Neural Development and Regeneration/ P05-Molecular
Mechanisms of Neural Stem Cell Lineage Progression
publication: Current Opinion in Genetics & Development
publication_identifier:
eissn:
- 1879-0380
issn:
- 0959-437X
publication_status: epub_ahead
publisher: Elsevier
quality_controlled: '1'
scopus_import: '1'
status: public
title: 'Tracing cell lineages in the developing brain: Insights from mosaic analysis
and clone-resolved transcriptomics'
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: 99
year: '2026'
...
---
OA_place: repository
OA_type: green
_id: '21039'
abstract:
- lang: eng
text: Cellular plasticity, the ability of a differentiated cell to adopt another
phenotypic identity, is restricted under basal conditions, but can be elicited
upon damage. However, the molecular mechanism enabling such plasticity remains
largely unexplored. Here, we report damage-induced cellular plasticity of secretory
enteroendocrine cells (EEs) in the adult Drosophila midgut. Ionizing radiation
induces EE fate conversion and activates stress-responsive programs in EE lineages,
accompanied by the induction of the stress-inducible transcription factor Xrp1
and the cytokine gene upd3. Xrp1 and upd3 are both necessary for radiation-induced
EE plasticity. Under basal conditions, EE-specific Xrp1 overexpression triggers
ectopic expression of progenitor-specific genes, which is necessary for Xrp1 to
drive EE plasticity. Our work identifies Xrp1 as a crucial regulator that coordinates
damage-induced signaling and transcriptional reprogramming, enabling the reactivation
of cellular plasticity in differentiated cells.
acknowledgement: We thank Pierre Léopold, Tatsushi Igaki, Erik Storkebaum, Tobias
Reiff, Masayuki Miura, Xiaohang Yang, Mikio Furuse, Bloomington Drosophila Stock
Center and Developmental Studies Hybridoma Bank for providing us with fly stocks
and reagents. We are also grateful to Hiromi Yanagisawa, Satoru Kobayashi, Md Al
Amin Sheikh and Yaxuan Cui for allowing us to use their equipment, and to Allison
Bardin, Pierre Léopold and Tadashi Uemura for helpful discussions.
article_number: dev205225
article_processing_charge: No
article_type: original
author:
- first_name: Qingyin
full_name: Qian, Qingyin
last_name: Qian
- first_name: Hiroki
full_name: Nagai, Hiroki
id: 608df3e6-e2ab-11ed-8890-c9318cec7da4
last_name: Nagai
orcid: 0000-0003-1671-9434
- first_name: Yuya
full_name: Sanaki, Yuya
last_name: Sanaki
- first_name: Makoto
full_name: Hayashi, Makoto
last_name: Hayashi
- first_name: Kenichi
full_name: Kimura, Kenichi
last_name: Kimura
- first_name: Yu Ichiro
full_name: Nakajima, Yu Ichiro
last_name: Nakajima
- first_name: Ryusuke
full_name: Niwa, Ryusuke
last_name: Niwa
citation:
ama: Qian Q, NAGAI H, Sanaki Y, et al. Xrp1 drives damage-induced cellular plasticity
of enteroendocrine cells in the adult Drosophila midgut. Development. 2026;153(2).
doi:10.1242/dev.205225
apa: Qian, Q., NAGAI, H., Sanaki, Y., Hayashi, M., Kimura, K., Nakajima, Y. I.,
& Niwa, R. (2026). Xrp1 drives damage-induced cellular plasticity of enteroendocrine
cells in the adult Drosophila midgut. Development. Company of Biologists.
https://doi.org/10.1242/dev.205225
chicago: Qian, Qingyin, HIROKI NAGAI, Yuya Sanaki, Makoto Hayashi, Kenichi Kimura,
Yu Ichiro Nakajima, and Ryusuke Niwa. “Xrp1 Drives Damage-Induced Cellular Plasticity
of Enteroendocrine Cells in the Adult Drosophila Midgut.” Development.
Company of Biologists, 2026. https://doi.org/10.1242/dev.205225.
ieee: Q. Qian et al., “Xrp1 drives damage-induced cellular plasticity of
enteroendocrine cells in the adult Drosophila midgut,” Development, vol.
153, no. 2. Company of Biologists, 2026.
ista: Qian Q, NAGAI H, Sanaki Y, Hayashi M, Kimura K, Nakajima YI, Niwa R. 2026.
Xrp1 drives damage-induced cellular plasticity of enteroendocrine cells in the
adult Drosophila midgut. Development. 153(2), dev205225.
mla: Qian, Qingyin, et al. “Xrp1 Drives Damage-Induced Cellular Plasticity of Enteroendocrine
Cells in the Adult Drosophila Midgut.” Development, vol. 153, no. 2, dev205225,
Company of Biologists, 2026, doi:10.1242/dev.205225.
short: Q. Qian, H. NAGAI, Y. Sanaki, M. Hayashi, K. Kimura, Y.I. Nakajima, R. Niwa,
Development 153 (2026).
date_created: 2026-01-25T23:01:39Z
date_published: 2026-01-15T00:00:00Z
date_updated: 2026-08-12T10:01:56Z
day: '15'
department:
- _id: XiFe
doi: 10.1242/dev.205225
external_id:
pmid:
- '41392708'
intvolume: ' 153'
issue: '2'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.1101/2025.07.05.662934
month: '01'
oa: 1
oa_version: Preprint
pmid: 1
publication: Development
publication_identifier:
eissn:
- 1477-9129
issn:
- 0950-1991
publication_status: published
publisher: Company of Biologists
quality_controlled: '1'
scopus_import: '1'
status: public
title: Xrp1 drives damage-induced cellular plasticity of enteroendocrine cells in
the adult Drosophila midgut
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 153
year: '2026'
...
---
OA_place: publisher
OA_type: hybrid
_id: '22148'
abstract:
- lang: eng
text: 'How the twin-arginine translocase (Tat) system transports fully folded substrate
proteins across cellular membranes without disrupting membrane integrity has been
a fundamental question in cell biology for decades. The Tat system, found in prokaryotes
and plant organelles, recognizes a cargo signal peptide via a conserved twin-arginine
motif. The multi-subunit Tat complex facilitates the proton-motive-force-dependent
translocation process, yet its overall architecture has remained unknown. Here,
we present the cryo-electron microscopy (cryo-EM) structure of the Escherichia
coli (E. coli) trimeric TatB₃C₃ complex with bound substrate SufI, assembled in
vivo. The complex adopts an unusual, wide-open, bowl-shaped architecture with
a polar inner cavity. Unexpectedly, the cargo is engaged in a dual-contact mode:
while the signal peptide binds inside one TatBC unit, the folded domain docks
tightly onto an adjacent unit, possibly performing a proofreading function. This
structure provides a mechanistic framework for substrate engagement and suggests
the direct involvement of the entire Tat complex in substrate translocation.'
acknowledged_ssus:
- _id: EM-Fac
- _id: ScienComp
acknowledgement: We thank IST Austria for providing the funding. We thank IST Austria
EM facility for the use of Titan Krios TEM. Data processing was performed using
IST high-performance computer cluster. We thank Dr. R. Roemhild and Professor C.
Guet (ISTA) for help in constructing Tat deletion strains and Dr. A. Charnagalov
(ISTA) for technical help.
article_processing_charge: Yes (via OA deal)
article_type: original
author:
- first_name: Ziyu
full_name: Zhao, Ziyu
id: a63fe682-9f3a-11ee-bf8c-cfdf919b9850
last_name: Zhao
- first_name: Leonid A
full_name: Sazanov, Leonid A
id: 338D39FE-F248-11E8-B48F-1D18A9856A87
last_name: Sazanov
orcid: 0000-0002-0977-7989
biorxivid: 1
citation:
ama: Zhao Z, Sazanov LA. Structure of E. Coli twin-arginine translocase (Tat) complex
with bound cargo. Molecular Cell. doi:10.1016/j.molcel.2026.05.026
apa: Zhao, Z., & Sazanov, L. A. (n.d.). Structure of E. Coli twin-arginine translocase
(Tat) complex with bound cargo. Molecular Cell. Elsevier. https://doi.org/10.1016/j.molcel.2026.05.026
chicago: Zhao, Ziyu, and Leonid A Sazanov. “Structure of E. Coli Twin-Arginine Translocase
(Tat) Complex with Bound Cargo.” Molecular Cell. Elsevier, n.d. https://doi.org/10.1016/j.molcel.2026.05.026.
ieee: Z. Zhao and L. A. Sazanov, “Structure of E. Coli twin-arginine translocase
(Tat) complex with bound cargo,” Molecular Cell. Elsevier.
ista: Zhao Z, Sazanov LA. Structure of E. Coli twin-arginine translocase (Tat) complex
with bound cargo. Molecular Cell.
mla: Zhao, Ziyu, and Leonid A. Sazanov. “Structure of E. Coli Twin-Arginine Translocase
(Tat) Complex with Bound Cargo.” Molecular Cell, Elsevier, doi:10.1016/j.molcel.2026.05.026.
short: Z. Zhao, L.A. Sazanov, Molecular Cell (n.d.).
corr_author: '1'
das_tickbox: '1'
dataavailabilitystatement: "This study did not generate new unique reagents. Strains
and plasmids generated in this study are available from the lead contact without
restrictions.\r\n• Source data are provided within this paper. The cryo-EM map is
deposited in the Electron Microscopy Data Bank under accession number EMD-53848.
The model is deposited in the Protein Data Bank under accession number 9R91. The
structural data are publicly available as of the date of publication. Raw images
of spot assays, SDS-PAGE and BN-PAGE gels with Coomassie staining and immunoblot
images are available at Mendeley Data (https://doi.org/10.17632/v2g3p9n985.1).\r\n•
This paper does not report original code.\r\n• Any additional information required
to reanalyze the data reported in this paper is available from the lead contact
upon request."
date_created: 2026-06-28T22:01:35Z
date_published: 2026-06-22T00:00:00Z
date_updated: 2026-08-12T12:08:44Z
day: '22'
ddc:
- '570'
department:
- _id: LeSa
doi: 10.1016/j.molcel.2026.05.026
external_id:
biorxivid:
- 10.1101/2025.09.16.676506
has_accepted_license: '1'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.1016/j.molcel.2026.05.026
month: '06'
oa: 1
oa_version: Published Version
publication: Molecular Cell
publication_identifier:
eissn:
- 1097-4164
issn:
- 1097-2765
publication_status: inpress
publisher: Elsevier
quality_controlled: '1'
related_material:
link:
- description: News on ISTA website
relation: press_release
url: https://ista.ac.at/en/news/the-gate-for-bulky-cargo/
record:
- id: '22189'
relation: research_data
status: public
researchdata_availability: yes
scopus_import: '1'
status: public
supplementarymaterial: yes
title: Structure of E. Coli twin-arginine translocase (Tat) complex with bound cargo
tmp:
image: /images/cc_by_nc.png
legal_code_url: https://creativecommons.org/licenses/by-nc/4.0/legalcode
name: Creative Commons Attribution-NonCommercial 4.0 International (CC BY-NC 4.0)
short: CC BY-NC (4.0)
type: journal_article
user_id: ba8df636-2132-11f1-aed0-ed93e2281fdd
year: '2026'
...
---
OA_place: publisher
OA_type: gold
_id: '22189'
abstract:
- lang: eng
text: Raw images for SDS and Blue Native gels, western blots and spot growth assays,
related to figures S1 and S2.
article_processing_charge: No
author:
- first_name: Leonid A
full_name: Sazanov, Leonid A
id: 338D39FE-F248-11E8-B48F-1D18A9856A87
last_name: Sazanov
orcid: 0000-0002-0977-7989
citation:
ama: Sazanov LA. Structure of E. coli twin-arginine translocase (Tat) complex with
bound cargo. Zhao et al. 2026. doi:10.17632/V2G3P9N985.1
apa: Sazanov, L. A. (2026). Structure of E. coli twin-arginine translocase (Tat)
complex with bound cargo. Zhao et al. Mendeley Data. https://doi.org/10.17632/V2G3P9N985.1
chicago: Sazanov, Leonid A. “Structure of E. Coli Twin-Arginine Translocase (Tat)
Complex with Bound Cargo. Zhao et Al.” Mendeley Data, 2026. https://doi.org/10.17632/V2G3P9N985.1.
ieee: L. A. Sazanov, “Structure of E. coli twin-arginine translocase (Tat) complex
with bound cargo. Zhao et al.” Mendeley Data, 2026.
ista: Sazanov LA. 2026. Structure of E. coli twin-arginine translocase (Tat) complex
with bound cargo. Zhao et al., Mendeley Data, 10.17632/V2G3P9N985.1.
mla: Sazanov, Leonid A. Structure of E. Coli Twin-Arginine Translocase (Tat)
Complex with Bound Cargo. Zhao et Al. Mendeley Data, 2026, doi:10.17632/V2G3P9N985.1.
short: L.A. Sazanov, (2026).
corr_author: '1'
date_created: 2026-06-29T12:54:45Z
date_published: 2026-05-15T00:00:00Z
date_updated: 2026-08-12T12:08:44Z
day: '15'
ddc:
- '570'
department:
- _id: LeSa
doi: 10.17632/V2G3P9N985.1
has_accepted_license: '1'
keyword:
- Protein Purification
main_file_link:
- open_access: '1'
url: https://doi.org/10.17632/v2g3p9n985.1
month: '05'
oa: 1
oa_version: Published Version
publisher: Mendeley Data
related_material:
record:
- id: '22148'
relation: used_in_publication
status: public
status: public
title: Structure of E. coli twin-arginine translocase (Tat) complex with bound cargo.
Zhao et al.
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_reference
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
year: '2026'
...
---
OA_place: repository
_id: '22704'
abstract:
- lang: eng
text: "The medial habenula (MHb) is implicated in regulating emotional responses
to aversive events. Studies in zebrafish have identified a remarkable morphological
left–right asymmetry in the dorsal habenula (zebrafish equivalent of mammalian
MHb)-interpeduncular nucleus (IPN) pathway and its asymmetrical roles in behavior.
However, there is little evidence for structural or functional lateralization
in the mammalian MHb-IPN pathway. Here, we investigated the synaptic properties
of left- and right-MHb afferents to the IPN and their roles in the expression
of conditioned fear in mice. We found that each IPN neuron receives inputs from
both left and right MHb, but the left MHb-originating synapses exhibit lower release
probability and higher γ-aminobutyric acid type B receptor (GABABR)-mediated potentiation
compared to the right MHb-originating synapses. Interestingly, these asymmetrical
properties persist in the inversus visceral mutant mice with normal internal organ
laterality (situs solitus), but nearly disappear in those with reversed internal
organ laterality (situs inversus). Behaviorally, chemogenetic inhibition of cholinergic
neurons and conditional deletion of GABABR in the left, but not the right, MHb
significantly attenuated cue-dependent fear recall. Our results demonstrate functional
asymmetry of the MHb under partial influence of the nodal flow in mice, revealing
a predominant role of GABABR-mediated signaling in the left MHb-IPN pathway in
modulating fear memories. These findings suggest that lateralized MHb pathways
could represent a fundamental principle in the neural regulation of emotion across
species but that they develop differently in zebrafish and mice.\r\n"
acknowledged_ssus:
- _id: M-Shop
- _id: PreCl
article_processing_charge: No
author:
- first_name: Elodie
full_name: Le Monnier, Elodie
id: 3B59276A-F248-11E8-B48F-1D18A9856A87
last_name: Le Monnier
- first_name: Cihan
full_name: Önal, Cihan
last_name: Önal
citation:
ama: Le Monnier E, Önal C. Asymmetrical modulation of fear expression via GABAB
receptors in the mouse medial habenula. 2026. doi:10.15479/AT-ISTA-22704
apa: Le Monnier, E., & Önal, C. (2026). Asymmetrical modulation of fear expression
via GABAB receptors in the mouse medial habenula. Institute of Science and Technology
Austria. https://doi.org/10.15479/AT-ISTA-22704
chicago: Le Monnier, Elodie, and Cihan Önal. “Asymmetrical Modulation of Fear Expression
via GABAB Receptors in the Mouse Medial Habenula.” Institute of Science and Technology
Austria, 2026. https://doi.org/10.15479/AT-ISTA-22704.
ieee: E. Le Monnier and C. Önal, “Asymmetrical modulation of fear expression via
GABAB receptors in the mouse medial habenula.” Institute of Science and Technology
Austria, 2026.
ista: Le Monnier E, Önal C. 2026. Asymmetrical modulation of fear expression via
GABAB receptors in the mouse medial habenula, Institute of Science and Technology
Austria, 10.15479/AT-ISTA-22704.
mla: Le Monnier, Elodie, and Cihan Önal. Asymmetrical Modulation of Fear Expression
via GABAB Receptors in the Mouse Medial Habenula. Institute of Science and
Technology Austria, 2026, doi:10.15479/AT-ISTA-22704.
short: E. Le Monnier, C. Önal, (2026).
corr_author: '1'
date_created: 2026-08-13T12:20:08Z
date_published: 2026-08-13T00:00:00Z
date_updated: 2026-08-13T13:30:37Z
day: '13'
department:
- _id: RySh
doi: 10.15479/AT-ISTA-22704
doi_confirm: '1'
ec_funded: 1
file:
- access_level: open_access
checksum: 7742bb211a43bb87c2b5ce7bda3068ae
content_type: application/x-zip-compressed
creator: elemonni
date_created: 2026-08-13T12:07:53Z
date_updated: 2026-08-13T12:07:53Z
file_id: '22705'
file_name: Behavior.zip
file_size: 162086
relation: main_file
success: 1
- access_level: open_access
checksum: a162eb6103a770d94536374e02934fcf
content_type: application/x-zip-compressed
creator: elemonni
date_created: 2026-08-13T12:07:57Z
date_updated: 2026-08-13T12:07:57Z
file_id: '22706'
file_name: image_analysis.zip
file_size: 6643
relation: main_file
success: 1
- access_level: open_access
checksum: 608aaf395bba5fd9cf62d8c8940d63aa
content_type: application/x-zip-compressed
creator: elemonni
date_created: 2026-08-13T12:07:59Z
date_updated: 2026-08-13T12:07:59Z
file_id: '22707'
file_name: Recordings.zip
file_size: 1193016
relation: main_file
success: 1
- access_level: open_access
checksum: 2389ebd71238bd7de03d20504a8cf962
content_type: text/plain
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date_created: 2026-08-13T13:06:29Z
date_updated: 2026-08-13T13:06:29Z
file_id: '22708'
file_name: README.txt
file_size: 246
relation: main_file
success: 1
file_date_updated: 2026-08-13T13:06:29Z
has_accepted_license: '1'
month: '08'
oa: 1
oa_version: None
project:
- _id: 2564DBCA-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '665385'
name: International IST Doctoral Program
- _id: 92503f6e-16d5-11f0-9cad-8c571927f3b7
grant_number: PAT 5720324
name: New regime of presynaptic release regulation
publisher: Institute of Science and Technology Austria
status: public
title: Asymmetrical modulation of fear expression via GABAB receptors in the mouse
medial habenula
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: research_data
user_id: 68b8ca59-c5b3-11ee-8790-cd641c68093d
year: '2026'
...
---
OA_place: publisher
OA_type: hybrid
_id: '22717'
abstract:
- lang: eng
text: "We study concurrent graph games where n players cooperate against an opponent
to reach a set of target states. Unlike traditional settings, we study distributed
randomisation: team players do not share a source of randomness, and their private
random sources are hidden from the opponent and from each other.\r\n\r\nWe show
that memoryless strategies are sufficient for the threshold problem (deciding
whether there is a strategy for the team that ensures winning with probability
that exceeds a threshold), a result that not only places the problem in the Existential
Theory of the Reals (ER) but also enables the construction of value iteration
algorithms. We additionally show that the threshold problem is NP-hard. For the
almost-sure reachability problem, we prove NP-completeness.\r\n\r\nWe introduce
Individually Randomised Alternating-time Temporal Logic (IRATL). This logic extends
the standard ATL framework to reason about probability thresholds, with semantics
explicitly designed for coalitions that lack a shared source of randomness. On
the practical side, we implement and evaluate a solver for the threshold and almost-sure
problem based on the algorithms that we develop."
acknowledgement: This work is a part of project VAMOS that has received funding from
the European Research Council (ERC), grant agreement No 101020093. Part of this
work was realised when the first author was an FNRS aspirant at Université libre
de Bruxelles.
article_processing_charge: Yes (in subscription journal)
arxiv: 1
author:
- first_name: Leonard J
full_name: Brice, Leonard J
id: ce3b3409-db6c-11f0-aa64-ad678f7fd937
last_name: Brice
- first_name: Thomas A
full_name: Henzinger, Thomas A
id: 40876CD8-F248-11E8-B48F-1D18A9856A87
last_name: Henzinger
orcid: 0000-0002-2985-7724
- first_name: Alipasha
full_name: Montaseri, Alipasha
id: 709a7f96-8896-11f0-9809-d75612fc0f2e
last_name: Montaseri
- first_name: Ali
full_name: Shafiee, Ali
id: 2783031a-7378-11f0-b2d0-f17f1db2ebad
last_name: Shafiee
- first_name: K. S.
full_name: Thejaswini, K. S.
last_name: Thejaswini
citation:
ama: 'Brice LJ, Henzinger TA, Montaseri A, Shafiee A, Thejaswini KS. Randomise alone,
reach as a team. In: 38th International Conference on Computer Aided Verification.
Vol 16682. Springer Nature; 2026:215-236. doi:10.1007/978-3-032-32519-8_12'
apa: 'Brice, L. J., Henzinger, T. A., Montaseri, A., Shafiee, A., & Thejaswini,
K. S. (2026). Randomise alone, reach as a team. In 38th International Conference
on Computer Aided Verification (Vol. 16682, pp. 215–236). Lisbon, Portugal:
Springer Nature. https://doi.org/10.1007/978-3-032-32519-8_12'
chicago: Brice, Leonard J, Thomas A Henzinger, Alipasha Montaseri, Ali Shafiee,
and K. S. Thejaswini. “Randomise Alone, Reach as a Team.” In 38th International
Conference on Computer Aided Verification, 16682:215–36. Springer Nature,
2026. https://doi.org/10.1007/978-3-032-32519-8_12.
ieee: L. J. Brice, T. A. Henzinger, A. Montaseri, A. Shafiee, and K. S. Thejaswini,
“Randomise alone, reach as a team,” in 38th International Conference on Computer
Aided Verification, Lisbon, Portugal, 2026, vol. 16682, pp. 215–236.
ista: 'Brice LJ, Henzinger TA, Montaseri A, Shafiee A, Thejaswini KS. 2026. Randomise
alone, reach as a team. 38th International Conference on Computer Aided Verification.
CAV: Computer Aided Verification vol. 16682, 215–236.'
mla: Brice, Leonard J., et al. “Randomise Alone, Reach as a Team.” 38th International
Conference on Computer Aided Verification, vol. 16682, Springer Nature, 2026,
pp. 215–36, doi:10.1007/978-3-032-32519-8_12.
short: L.J. Brice, T.A. Henzinger, A. Montaseri, A. Shafiee, K.S. Thejaswini, in:,
38th International Conference on Computer Aided Verification, Springer Nature,
2026, pp. 215–236.
conference:
end_date: 2026-07-29
location: Lisbon, Portugal
name: 'CAV: Computer Aided Verification'
start_date: 2026-07-26
das_tickbox: '1'
dataavailabilitystatement: "The artifact can be accessed at the link: https://doi.
org/10.5281/zenodo.19680359.\r\nThe source code is available at:https://github.com/alipashamontaseri/Team-Concurrent-Game."
date_created: 2026-08-16T22:01:44Z
date_published: 2026-07-24T00:00:00Z
date_updated: 2026-08-18T06:55:38Z
day: '24'
ddc:
- '000'
department:
- _id: ToHe
- _id: GradSch
doi: 10.1007/978-3-032-32519-8_12
ec_funded: 1
external_id:
arxiv:
- '2603.07094'
file:
- access_level: open_access
checksum: 10ded8a3ab9ed34c9e4794c0b277622c
content_type: application/pdf
creator: dernst
date_created: 2026-08-18T06:53:22Z
date_updated: 2026-08-18T06:53:22Z
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file_size: 1902192
relation: main_file
success: 1
file_date_updated: 2026-08-18T06:53:22Z
has_accepted_license: '1'
intvolume: ' 16682'
language:
- iso: eng
month: '07'
oa: 1
oa_version: Published Version
page: 215-236
project:
- _id: 62781420-2b32-11ec-9570-8d9b63373d4d
call_identifier: H2020
grant_number: '101020093'
name: Vigilant Algorithmic Monitoring of Software
publication: 38th International Conference on Computer Aided Verification
publication_identifier:
eissn:
- 1611-3349
isbn:
- '9783032325181'
issn:
- 0302-9743
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
researchdata_availability: yes
scopus_import: '1'
status: public
supplementarymaterial: no
title: Randomise alone, reach as a team
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: conference
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 16682
year: '2026'
...
---
OA_place: publisher
OA_type: gold
_id: '22722'
abstract:
- lang: eng
text: "The local structure of a protein strongly impacts its function and interactions\r\nwith
other molecules. Representing local biomolecular environments remains a\r\nkey
challenge while applying machine learning approaches over protein structures.
The structural and chemical variability of these environments makes them\r\nchallenging
to model, and performing representation learning on these objects\r\nremains largely
under-explored. In this work, we propose representations for\r\nlocal protein
environments that leverage intermediate features from machine learning force fields
(MLFFs). We extensively benchmark state-of-the-art MLFFs,\r\ncomparing their performance
across latent spaces and downstream tasks, and\r\nshow that their embeddings capture
local structural (e.g., secondary motifs) and\r\nchemical features (e.g., amino
acid identity and protonation state), organizing\r\nprotein environments into
a structured manifold. We show that these representations enable zero-shot generalization
and transfer across diverse downstream\r\ntasks. As a case study, we build a physics-informed,
uncertainty-aware chemical shift predictor that achieves state-of-the-art accuracy
in biomolecular NMR\r\nspectroscopy. Our results establish MLFFs as general-purpose,
reusable representation learners for protein modeling, opening new directions
in representation learning for structured physical systems. Code and data are
available at\r\nhttps://github.com/mb012/MLFF_representation.\r\n"
acknowledged_ssus:
- _id: ScienComp
acknowledgement: "This work was supported by the Institute of Science and Technology
Austria (ISTA) through the IPC\r\ngrant “Generative Protein NMR” and by the Israeli
Science Foundation (ISF) under grant number\r\n1834/24. This research used resources
of the Institute of Science and Technology Austria’s scientific\r\ncomputing cluster.
S.V. was supported in part by funding from the Eric and Wendy Schmidt Center at\r\nthe
Broad Institute of MIT and Harvard."
article_processing_charge: No
arxiv: 1
author:
- first_name: Meital I
full_name: Bojan, Meital I
id: 11d88cf5-91ca-11f0-a95f-edf9f08f47b7
last_name: Bojan
- first_name: Sanketh
full_name: Vedula, Sanketh
last_name: Vedula
- first_name: Sai A
full_name: Maddipatla, Sai A
id: e957f5e5-91c9-11f0-a95f-e090f66ecb4d
last_name: Maddipatla
- first_name: Nadav E
full_name: Sellam, Nadav E
id: ef280fe0-91c9-11f0-a95f-8dea3f5bc513
last_name: Sellam
- first_name: Anar
full_name: Rzayev, Anar
id: 2cd60677-9acd-11f1-ae1a-a85ae1c4dd35
last_name: Rzayev
- first_name: Federico
full_name: Napoli, Federico
id: d42e08e7-f4fc-11eb-af0a-d71e26138f1b
last_name: Napoli
orcid: 0000-0002-9043-136X
- first_name: Paul
full_name: Schanda, Paul
id: 7B541462-FAF6-11E9-A490-E8DFE5697425
last_name: Schanda
orcid: 0000-0002-9350-7606
- first_name: Alexander
full_name: Bronstein, Alexander
id: 58f3726e-7cba-11ef-ad8b-e6e8cb3904e6
last_name: Bronstein
orcid: 0000-0001-9699-8730
citation:
ama: 'Bojan MI, Vedula S, Maddipatla SA, et al. Representing local protein environments
with machine learning force fields. In: 14th International Conference on Learning
Representations. Vol 2026. ; 2026:100760-100799.'
apa: Bojan, M. I., Vedula, S., Maddipatla, S. A., Sellam, N. E., Rzayev, A., Napoli,
F., … Bronstein, A. M. (2026). Representing local protein environments with machine
learning force fields. In 14th International Conference on Learning Representations
(Vol. 2026, pp. 100760–100799). Rio de Janeiro, Brazil.
chicago: Bojan, Meital I, Sanketh Vedula, Sai A Maddipatla, Nadav E Sellam, Anar
Rzayev, Federico Napoli, Paul Schanda, and Alex M. Bronstein. “Representing Local
Protein Environments with Machine Learning Force Fields.” In 14th International
Conference on Learning Representations, 2026:100760–99, 2026.
ieee: M. I. Bojan et al., “Representing local protein environments with machine
learning force fields,” in 14th International Conference on Learning Representations,
Rio de Janeiro, Brazil, 2026, vol. 2026, pp. 100760–100799.
ista: 'Bojan MI, Vedula S, Maddipatla SA, Sellam NE, Rzayev A, Napoli F, Schanda
P, Bronstein AM. 2026. Representing local protein environments with machine learning
force fields. 14th International Conference on Learning Representations. ICLR:
International Conference on Learning Representations vol. 2026, 100760–100799.'
mla: Bojan, Meital I., et al. “Representing Local Protein Environments with Machine
Learning Force Fields.” 14th International Conference on Learning Representations,
vol. 2026, 2026, pp. 100760–99.
short: M.I. Bojan, S. Vedula, S.A. Maddipatla, N.E. Sellam, A. Rzayev, F. Napoli,
P. Schanda, A.M. Bronstein, in:, 14th International Conference on Learning Representations,
2026, pp. 100760–100799.
conference:
end_date: 2026-04-27
location: Rio de Janeiro, Brazil
name: 'ICLR: International Conference on Learning Representations'
start_date: 2026-04-23
corr_author: '1'
das_tickbox: '1'
dataavailabilitystatement: "The code, trained models, and data-processing scripts
are publicly available at https://github.\r\ncom/mb012/MLFF_representation. In addition,
complete details of the models and optimization parameters are provided in Appendix
G.3. The hardware resources used to produce the\r\nresults are specified in Appendix
I.4. The loss functions, evaluation metrics, and details regarding\r\nablation studies
are specified in Appendix G. These details ensure that all results reported in the
paper\r\ncan be independently verified."
date_created: 2026-08-17T12:03:24Z
date_published: 2026-05-01T00:00:00Z
date_updated: 2026-08-18T06:36:55Z
day: '01'
ddc:
- '000'
- '570'
department:
- _id: GradSch
- _id: PaSc
- _id: AlBr
external_id:
arxiv:
- '2505.23354'
file:
- access_level: open_access
checksum: 9f43f5469443388ec55388d95c4cf243
content_type: application/pdf
creator: dernst
date_created: 2026-08-18T06:33:14Z
date_updated: 2026-08-18T06:33:14Z
file_id: '22723'
file_name: 2026_ICLR_Bojan.pdf
file_size: 8534339
relation: main_file
success: 1
file_date_updated: 2026-08-18T06:33:14Z
has_accepted_license: '1'
intvolume: ' 2026'
language:
- iso: eng
month: '05'
oa: 1
oa_version: Published Version
page: 100760-100799
publication: 14th International Conference on Learning Representations
publication_status: published
quality_controlled: '1'
related_material:
link:
- relation: software
url: https://github.com/mb012/MLFF_representation
researchdata_availability: yes
status: public
supplementarymaterial: yes
title: Representing local protein environments with machine learning force fields
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: conference
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 2026
year: '2026'
...
---
OA_place: publisher
OA_type: hybrid
_id: '22719'
abstract:
- lang: eng
text: We study the problem of generating paths on a graph that satisfy a collection
of w-regular objectives. We propose a decoupled framework in which each objective
is assigned to an independent agent that selects a local policy, while a scheduler—oblivious
to the graph and objective—dynamically composes these policies into a single path.
We ask when such a composition satisfies all objectives, assuming their conjunction
is realizable. The framework enables modular policy design but raises fundamental
compositional challenges. We show that even extremely fair deterministic schedulers
do not ensure correctness, and that stochastic schedulers, while necessary, are
insufficient without coordination. For safety objectives, we demonstrate that
fully decentralized implementations are impossible, and we introduce a protocol
for synchronizing on maximal safe actions. For non-safety objectives, we introduce
conventions—simple, a priori restrictions agreed upon before the graph or objectives
are revealed—that guarantee satisfaction of all objectives when followed by all
agents. We characterize minimally restrictive conventions for major subclasses
of w-regular objectives. In particular, Büchi objectives admit universal composition
of finite-memory policies without scheduler communication; co-Büchi objectives
require only knowledge of whether the agent was scheduled; and parity objectives
additionally require knowledge of which agent was scheduled.
acknowledgement: 'This work is funded by the following grants: European Research Council
under Grant No.: ERC-2020-AdG 101020093, ISF grant no. 1679/21, grant RYC2024-049116,
MICIU/AEI/10.13039/501100011033, the ESF+, and Volkswagen Foundation within its
Momentum framework under project no. 9C283.'
alternative_title:
- LNCS
article_processing_charge: Yes (in subscription journal)
arxiv: 1
author:
- first_name: Guy
full_name: Avni, Guy
id: 463C8BC2-F248-11E8-B48F-1D18A9856A87
last_name: Avni
orcid: 0000-0001-5588-8287
- first_name: Thomas A
full_name: Henzinger, Thomas A
id: 40876CD8-F248-11E8-B48F-1D18A9856A87
last_name: Henzinger
orcid: 0000-0002-2985-7724
- first_name: Kaushik
full_name: Mallik, Kaushik
id: 0834ff3c-6d72-11ec-94e0-b5b0a4fb8598
last_name: Mallik
orcid: 0000-0001-9864-7475
- first_name: Suman
full_name: Sadhukhan, Suman
last_name: Sadhukhan
- first_name: K. S.
full_name: Thejaswini, K. S.
last_name: Thejaswini
citation:
ama: 'Avni G, Henzinger TA, Mallik K, Sadhukhan S, Thejaswini KS. Decoupled planning
for multiple omega-regular objectives. In: 38th International Conference on
Computer Aided Verification. Vol 16682. Springer Nature; 2026:237-257. doi:10.1007/978-3-032-32519-8_13'
apa: 'Avni, G., Henzinger, T. A., Mallik, K., Sadhukhan, S., & Thejaswini, K.
S. (2026). Decoupled planning for multiple omega-regular objectives. In 38th
International Conference on Computer Aided Verification (Vol. 16682, pp. 237–257).
Lisbon, Portugal: Springer Nature. https://doi.org/10.1007/978-3-032-32519-8_13'
chicago: Avni, Guy, Thomas A Henzinger, Kaushik Mallik, Suman Sadhukhan, and K.
S. Thejaswini. “Decoupled Planning for Multiple Omega-Regular Objectives.” In
38th International Conference on Computer Aided Verification, 16682:237–57.
Springer Nature, 2026. https://doi.org/10.1007/978-3-032-32519-8_13.
ieee: G. Avni, T. A. Henzinger, K. Mallik, S. Sadhukhan, and K. S. Thejaswini, “Decoupled
planning for multiple omega-regular objectives,” in 38th International Conference
on Computer Aided Verification, Lisbon, Portugal, 2026, vol. 16682, pp. 237–257.
ista: 'Avni G, Henzinger TA, Mallik K, Sadhukhan S, Thejaswini KS. 2026. Decoupled
planning for multiple omega-regular objectives. 38th International Conference
on Computer Aided Verification. CAV: Computer Aided Verification, LNCS, vol. 16682,
237–257.'
mla: Avni, Guy, et al. “Decoupled Planning for Multiple Omega-Regular Objectives.”
38th International Conference on Computer Aided Verification, vol. 16682,
Springer Nature, 2026, pp. 237–57, doi:10.1007/978-3-032-32519-8_13.
short: G. Avni, T.A. Henzinger, K. Mallik, S. Sadhukhan, K.S. Thejaswini, in:, 38th
International Conference on Computer Aided Verification, Springer Nature, 2026,
pp. 237–257.
conference:
end_date: 2026-07-29
location: Lisbon, Portugal
name: 'CAV: Computer Aided Verification'
start_date: 2026-07-26
das_tickbox: '0'
date_created: 2026-08-16T22:01:44Z
date_published: 2026-07-24T00:00:00Z
date_updated: 2026-08-18T08:41:44Z
day: '24'
ddc:
- '000'
department:
- _id: ToHe
doi: 10.1007/978-3-032-32519-8_13
ec_funded: 1
external_id:
arxiv:
- '2605.13185'
file:
- access_level: open_access
checksum: f17ba3f82854fdb4eb69fd922965661a
content_type: application/pdf
creator: dernst
date_created: 2026-08-18T08:40:07Z
date_updated: 2026-08-18T08:40:07Z
file_id: '22730'
file_name: 2026_LNCS_Avni.pdf
file_size: 531980
relation: main_file
success: 1
file_date_updated: 2026-08-18T08:40:07Z
has_accepted_license: '1'
intvolume: ' 16682'
language:
- iso: eng
month: '07'
oa: 1
oa_version: Published Version
page: 237-257
project:
- _id: 62781420-2b32-11ec-9570-8d9b63373d4d
call_identifier: H2020
grant_number: '101020093'
name: Vigilant Algorithmic Monitoring of Software
publication: 38th International Conference on Computer Aided Verification
publication_identifier:
eissn:
- 1611-3349
isbn:
- '9783032325181'
issn:
- 0302-9743
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
researchdata_availability: no
scopus_import: '1'
status: public
supplementarymaterial: no
title: Decoupled planning for multiple omega-regular objectives
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: conference
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 16682
year: '2026'
...
---
DOAJ_listed: '1'
OA_place: publisher
OA_type: gold
PlanS_conform: '1'
_id: '22713'
abstract:
- lang: eng
text: Ground-based gravitational-wave (GW) observatories have detected approximately
200 binary black hole (BH) mergers. The astrophysical origin of these events is
debated, with evidence suggesting that at least a subset originated from dynamic
environments characterized by frequent close encounters. Accretion disks in active
galactic nuclei (AGNs) are of particular interest, as certain observed features
could be more readily produced within such environments. In this paper, we investigate
the expected properties of mergers in these environments, and their dependence
on various parameters, using 1D N-body simulations combined with a comprehensive
semianalytical model. In our fiducial model, the distributions of masses (m1 and
m2) and mass ratios (q ≡ m2/m1 ≤ 1) are similar to those observed. However, they
depend strongly on the lifetime and density of the AGN disk and on the number
and accretion efficiency of BHs, with higher masses predicted as these quantities
increase. The most massive mergers, such as GW231123, can be produced either by
efficient gas accretion or by hierarchical mergers among ≥3 generations of BHs.
The observed negative correlation between q and the average effective spin (χeff),
along with the positive correlation between χeff and the chirp mass (Mchirp),
can be explained by a combination of efficient gas accretion, which promotes spin
alignment, and hierarchical mergers, which produce high-∣χeff∣ and low-q binaries.
Hierarchical mergers can also explain the negative correlation between q and the
dispersion of χeff, as well as the positive correlation between ∣χeff∣and Mchirp.
We present a comprehensive study on how the expected distribution of each of these
quantities depends on model parameters and assumptions, which will aid the interpretation
of observed GW population properties.
acknowledgement: H.T. is supported by the National Science and Technology Major Project
of China (No. 2024ZD1100601) and the National Key R&D Program of China (grant No.2024YFC2207700).
Z.H. was supported by NASA grants 80NSSC22K0822 and 80NSSC24K0440. B.K. is supported
by the Science and Technology Facilities Council grant No. ST/W000903/1. Simulations
were carried out on Cray XD2000 at the Center for Computational Astrophysics, National
Astronomical Observatory of Japan.
article_number: '67'
article_processing_charge: Yes
article_type: original
arxiv: 1
author:
- first_name: Hiromichi
full_name: Tagawa, Hiromichi
last_name: Tagawa
- first_name: Zoltán
full_name: Haiman, Zoltán
id: 7c006e8c-cc0d-11ee-8322-cb904ef76f36
last_name: Haiman
orcid: 0000-0003-3633-5403
- first_name: Bence
full_name: Kocsis, Bence
last_name: Kocsis
citation:
ama: Tagawa H, Haiman Z, Kocsis B. Properties of black hole mergers in disks of
active galactic nuclei. The Astrophysical Journal. 2026;1007(1). doi:10.3847/1538-4357/ae8760
apa: Tagawa, H., Haiman, Z., & Kocsis, B. (2026). Properties of black hole mergers
in disks of active galactic nuclei. The Astrophysical Journal. IOP Publishing.
https://doi.org/10.3847/1538-4357/ae8760
chicago: Tagawa, Hiromichi, Zoltán Haiman, and Bence Kocsis. “Properties of Black
Hole Mergers in Disks of Active Galactic Nuclei.” The Astrophysical Journal.
IOP Publishing, 2026. https://doi.org/10.3847/1538-4357/ae8760.
ieee: H. Tagawa, Z. Haiman, and B. Kocsis, “Properties of black hole mergers in
disks of active galactic nuclei,” The Astrophysical Journal, vol. 1007,
no. 1. IOP Publishing, 2026.
ista: Tagawa H, Haiman Z, Kocsis B. 2026. Properties of black hole mergers in disks
of active galactic nuclei. The Astrophysical Journal. 1007(1), 67.
mla: Tagawa, Hiromichi, et al. “Properties of Black Hole Mergers in Disks of Active
Galactic Nuclei.” The Astrophysical Journal, vol. 1007, no. 1, 67, IOP
Publishing, 2026, doi:10.3847/1538-4357/ae8760.
short: H. Tagawa, Z. Haiman, B. Kocsis, The Astrophysical Journal 1007 (2026).
das_tickbox: '0'
date_created: 2026-08-16T22:01:43Z
date_published: 2026-08-10T00:00:00Z
date_updated: 2026-08-18T09:05:25Z
day: '10'
ddc:
- '520'
department:
- _id: ZoHa
doi: 10.3847/1538-4357/ae8760
external_id:
arxiv:
- '2604.25994'
file:
- access_level: open_access
checksum: 1531fd5997b054d26e99d44ccc7f8ff5
content_type: application/pdf
creator: dernst
date_created: 2026-08-18T09:01:50Z
date_updated: 2026-08-18T09:01:50Z
file_id: '22731'
file_name: 2026_AstrophysicalJour_Tagawa.pdf
file_size: 2246236
relation: main_file
success: 1
file_date_updated: 2026-08-18T09:01:50Z
has_accepted_license: '1'
intvolume: ' 1007'
issue: '1'
language:
- iso: eng
month: '08'
oa: 1
oa_version: Published Version
publication: The Astrophysical Journal
publication_identifier:
eissn:
- 1538-4357
issn:
- 000-4637X
publication_status: published
publisher: IOP Publishing
quality_controlled: '1'
researchdata_availability: no
scopus_import: '1'
status: public
supplementarymaterial: no
title: Properties of black hole mergers in disks of active galactic nuclei
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: 1007
year: '2026'
...
---
OA_place: publisher
OA_type: hybrid
PlanS_conform: '1'
_id: '22720'
abstract:
- lang: eng
text: Circadian clocks underlie daily rhythms in physiology by coordinating temporal
patterns of gene expression and protein function throughout the body. At the core
of this system in mammals is CLOCK/BMAL1, a ubiquitously expressed heterodimeric
transcription factor complex that orchestrates tissue-specific circadian gene
expression. The basis for this specificity remains unclear, but tissue-specific
interactions at chromatin could provide one. Here we used chromatin immunoprecipitation
coupled to mass spectrometry to map CLOCK/BMAL1-associated protein complexes on
chromatin in mouse liver, kidney and lung. We detected 1,510 associated proteins,
most of which were tissue-specific and not explained by protein abundance. Among
these, we identified the homeodomain transcription factors PROX1, HNF1B and HOXA5
as tissue-enriched interactors that bind BMAL1, co-occupy most BMAL1 genomic sites
and establish organ-restricted circadian transcription. Our findings demonstrate
that tissue-specific transcription factors confer cellular identity on the core
clock, thereby contributing to organ-specific patterns of rhythmic gene expression.
acknowledgement: We thank all members of the Robles’ group for critical comments on
and edits to this paper. We thank S. Kay for providing dihXY HCC cell lines and
D. Firsov and Y. Bignon for mouse BMAL1-knockout (KO) kidney tissues. This work
was supported by the German Research Foundation (DFG) project no. 213249687—SFB
1064 and RO 5675/1-1 to M.S.R., F.A. and L.A.H. M.S.R was also supported by DFG
INST 86/1800-1 FUGG and LMU Munich’s Institutional Strategy LMU excellent within
the framework of the German Excellence Initiative. J.S.M. was supported by US National
Institutes of Health grant nos. R01GM145737 and R01DK128133. A.K.M. was supported
by an ERC grant ‘ChromaChrono’ 101162145. Open access funding provided by Ludwig-Maximilians-Universität
München.
article_processing_charge: Yes (via OA deal)
article_type: original
author:
- first_name: Fatih
full_name: Aygenli, Fatih
last_name: Aygenli
- first_name: Lukas A.
full_name: Huschet, Lukas A.
last_name: Huschet
- first_name: Tanja
full_name: Popp, Tanja
last_name: Popp
- first_name: Andrea
full_name: Ribeiro, Andrea
last_name: Ribeiro
- first_name: Darina
full_name: Barkhatova, Darina
id: db547c8c-329f-11ee-a353-cde802618f9e
last_name: Barkhatova
orcid: 0000-0002-0062-2817
- first_name: Céline
full_name: Jouffe, Céline
last_name: Jouffe
- first_name: Ricardo
full_name: Trozzo, Ricardo
last_name: Trozzo
- first_name: Jerome S.
full_name: Menet, Jerome S.
last_name: Menet
- first_name: Roland
full_name: Rad, Roland
last_name: Rad
- first_name: Kenneth A.
full_name: Dyar, Kenneth A.
last_name: Dyar
- first_name: Maciej
full_name: Lech, Maciej
last_name: Lech
- first_name: Tobias
full_name: Straub, Tobias
last_name: Straub
- first_name: Alicia
full_name: Michael, Alicia
id: 6437c950-2a03-11ee-914d-d6476dd7b75c
last_name: Michael
orcid: 0000-0002-6080-839X
- first_name: Maria S.
full_name: Robles, Maria S.
last_name: Robles
citation:
ama: Aygenli F, Huschet LA, Popp T, et al. CLOCK/BMAL1 interactome uncovers homeodomain
factors as tissue regulators. Nature Cell Biology. 2026. doi:10.1038/s41556-026-02041-4
apa: Aygenli, F., Huschet, L. A., Popp, T., Ribeiro, A., Barkhatova, D., Jouffe,
C., … Robles, M. S. (2026). CLOCK/BMAL1 interactome uncovers homeodomain factors
as tissue regulators. Nature Cell Biology. Springer Nature. https://doi.org/10.1038/s41556-026-02041-4
chicago: Aygenli, Fatih, Lukas A. Huschet, Tanja Popp, Andrea Ribeiro, Darina Barkhatova,
Céline Jouffe, Ricardo Trozzo, et al. “CLOCK/BMAL1 Interactome Uncovers Homeodomain
Factors as Tissue Regulators.” Nature Cell Biology. Springer Nature, 2026.
https://doi.org/10.1038/s41556-026-02041-4.
ieee: F. Aygenli et al., “CLOCK/BMAL1 interactome uncovers homeodomain factors
as tissue regulators,” Nature Cell Biology. Springer Nature, 2026.
ista: Aygenli F, Huschet LA, Popp T, Ribeiro A, Barkhatova D, Jouffe C, Trozzo R,
Menet JS, Rad R, Dyar KA, Lech M, Straub T, Michael AK, Robles MS. 2026. CLOCK/BMAL1
interactome uncovers homeodomain factors as tissue regulators. Nature Cell Biology.
mla: Aygenli, Fatih, et al. “CLOCK/BMAL1 Interactome Uncovers Homeodomain Factors
as Tissue Regulators.” Nature Cell Biology, Springer Nature, 2026, doi:10.1038/s41556-026-02041-4.
short: F. Aygenli, L.A. Huschet, T. Popp, A. Ribeiro, D. Barkhatova, C. Jouffe,
R. Trozzo, J.S. Menet, R. Rad, K.A. Dyar, M. Lech, T. Straub, A.K. Michael, M.S.
Robles, Nature Cell Biology (2026).
das_tickbox: '1'
dataavailabilitystatement: Proteomics data have been deposited to the ProteomeXchange
Consortium via the PRIDE64 partner repository with the dataset identifiers PXD062751
and PXD077567. RNA-seq data are available in the European Nucleotide Archive (ENA)
under accession no. PRJEB93884, and ChIP–seq data at the Gene Expression Omnibus
(GEO) under accession no. GSE302237. AlphaFold 3 interaction prediction parameters
can be provided during the revision process on editorial and/or review request.
Source data are provided with this paper.
date_created: 2026-08-16T22:01:44Z
date_published: 2026-08-06T00:00:00Z
date_updated: 2026-08-18T08:03:22Z
day: '06'
ddc:
- '570'
department:
- _id: GradSch
- _id: AlMi
doi: 10.1038/s41556-026-02041-4
external_id:
pmid:
- '42562924'
has_accepted_license: '1'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.1038/s41556-026-02041-4
month: '08'
oa: 1
oa_version: Published Version
pmid: 1
project:
- _id: 9136c684-16d5-11f0-9cad-91c0177b365f
grant_number: '101162145'
name: Circadian structural transitions of chromatin
publication: Nature Cell Biology
publication_identifier:
eissn:
- 1476-4679
issn:
- 1465-7392
publication_status: epub_ahead
publisher: Springer Nature
quality_controlled: '1'
researchdata_availability: yes
scopus_import: '1'
status: public
supplementarymaterial: yes
title: CLOCK/BMAL1 interactome uncovers homeodomain factors as tissue regulators
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
year: '2026'
...
---
OA_place: repository
OA_type: green
_id: '22718'
abstract:
- lang: eng
text: Both Newtonian and non-Newtonian fluids may exhibit complex slip behaviour
at the boundary. We examine a broad class of slip boundary conditions that generalises
the commonly used Navier slip, perfect slip, stick-slip and Tresca friction boundary
conditions. In particular, set-valued, nonmonotone, noncoercive and dynamic relations
may occur. For a unifying framework of such relations, we present a fully discrete
numerical scheme for the time-dependent Navier–Stokes equations subject to impermeability
and general slip-type boundary conditions on polyhedral domains. Based on compactness
arguments, we prove convergence of subsequences, finally ensuring the existence
of a weak solution. The numerical scheme uses a general inf-sup stable pair of
finite element spaces for the velocity and pressure, a regularisation approach
for the implicit slip boundary condition and, most importantly, a general Nitsche
method to impose the impermeability and a backward Euler time stepping. One of
the key tools in the convergence proof is an inhomogeneous Korn inequality that
includes a normal trace term.
article_processing_charge: No
article_type: original
arxiv: 1
author:
- first_name: Pablo Alexei
full_name: Gazca-Orozco, Pablo Alexei
last_name: Gazca-Orozco
- first_name: Franz
full_name: Gmeineder, Franz
last_name: Gmeineder
- first_name: Erika
full_name: Maringová, Erika
id: dbabca31-66eb-11eb-963a-fb9c22c880b4
last_name: Maringová
- first_name: Tabea
full_name: Tscherpel, Tabea
last_name: Tscherpel
citation:
ama: Gazca-Orozco PA, Gmeineder F, Maringová E, Tscherpel T. A Nitsche method for
incompressible fluids with general dynamic boundary conditions. Mathematical
Models and Methods in Applied Sciences. 2026. doi:10.1142/S0218202526500508
apa: Gazca-Orozco, P. A., Gmeineder, F., Maringová, E., & Tscherpel, T. (2026).
A Nitsche method for incompressible fluids with general dynamic boundary conditions.
Mathematical Models and Methods in Applied Sciences. World Scientific Publishing.
https://doi.org/10.1142/S0218202526500508
chicago: Gazca-Orozco, Pablo Alexei, Franz Gmeineder, Erika Maringová, and Tabea
Tscherpel. “A Nitsche Method for Incompressible Fluids with General Dynamic Boundary
Conditions.” Mathematical Models and Methods in Applied Sciences. World
Scientific Publishing, 2026. https://doi.org/10.1142/S0218202526500508.
ieee: P. A. Gazca-Orozco, F. Gmeineder, E. Maringová, and T. Tscherpel, “A Nitsche
method for incompressible fluids with general dynamic boundary conditions,” Mathematical
Models and Methods in Applied Sciences. World Scientific Publishing, 2026.
ista: Gazca-Orozco PA, Gmeineder F, Maringová E, Tscherpel T. 2026. A Nitsche method
for incompressible fluids with general dynamic boundary conditions. Mathematical
Models and Methods in Applied Sciences.
mla: Gazca-Orozco, Pablo Alexei, et al. “A Nitsche Method for Incompressible Fluids
with General Dynamic Boundary Conditions.” Mathematical Models and Methods
in Applied Sciences, World Scientific Publishing, 2026, doi:10.1142/S0218202526500508.
short: P.A. Gazca-Orozco, F. Gmeineder, E. Maringová, T. Tscherpel, Mathematical
Models and Methods in Applied Sciences (2026).
date_created: 2026-08-16T22:01:44Z
date_published: 2026-08-04T00:00:00Z
date_updated: 2026-08-18T07:51:59Z
day: '04'
department:
- _id: JuFi
doi: 10.1142/S0218202526500508
external_id:
arxiv:
- '2502.09550'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.48550/arXiv.2502.09550
mathsc:
- 65N30
- 76D07
- 76M10
month: '08'
oa: 1
oa_version: Preprint
publication: Mathematical Models and Methods in Applied Sciences
publication_identifier:
eissn:
- 1793-6314
issn:
- 0218-2025
publication_status: epub_ahead
publisher: World Scientific Publishing
quality_controlled: '1'
scopus_import: '1'
status: public
title: A Nitsche method for incompressible fluids with general dynamic boundary conditions
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
year: '2026'
...
---
OA_place: publisher
OA_type: hybrid
PlanS_conform: '1'
_id: '22734'
abstract:
- lang: eng
text: Silver selenide (Ag2Se) is a promising near-room-temperature thermoelectric
material, but its narrow stoichiometric window and β–α phase transition complicate
reproducible microstructure control. Here, we present a mismatch-assisted microstructure
engineering strategy in which Ag2Se particles are treated with polyanionic ZnSe
complexes and consolidated through the β–α transition to introduce ZnSe nanoprecipitates,
Ag2Se/ZnSe interfaces, and local strain fields. The crystallographic mismatch
between ZnSe and Ag2Se, together with the Zn2+/Ag+ size difference, amplifies
phase-transition-induced deformation and promotes high-density dislocations with
periodic strain modulations. This defect architecture suppresses grain coarsening,
removes excess Ag, limits Ag-interstitial formation, and reduces lattice thermal
conductivity through lattice softening and multiscale phonon scattering. Ag2Se–4%ZnSe
nanocomposites achieve a peak zTmax of 1.13 at 369 K and a zTavg of 1.08 from
300 to 380 K, demonstrating mismatch-driven defect engineering through the β–α
phase transition as a route for optimizing Ag2Se-based thermoelectrics.
acknowledged_ssus:
- _id: EM-Fac
- _id: LifeSc
- _id: NanoFab
- _id: MassSpec
acknowledgement: 'Open access funding provided by Institute of Science and Technology
Austria. M.I. acknowledges financial support from ISTA and the Werner Siemens Foundation.
The Scientific Service Units (SSU) of ISTA supported this work through resources
provided by the Electron Microscopy Facility (EMF), the Lab Support Facility (LSF),
the Nanofabrication Facility (NNF), and the Mass Spectrometry Facility. Y.L. acknowledges
funding from the National Natural Science Foundation of China (NSFC) (grant no.
22209034) and the Fundamental Research Funds for the Central Universities (JZ2024HGTB0239).
M.H. acknowledges funding from Australian Research Council (FT230100316), and the
high-performance computing resources provided by National Computational Infrastructure
(it39) and Pawsey Supercomputing Centre (pawsey1075). ICN2 acknowledges funding
from Generalitat de Catalunya 2021SGR00457. The authors thank support from the project
AMaDE (PID2023-149158OB-C43), funded by MCIN/AEI/10.13039/501100011033/ and by the
“ERDF Away of making Europe”, by the “European Union”. ICN2 is supported by the
Severo Ochoa program from Spanish MCIN/AEI (grant no.: CEX2021-001214-S) and is
funded by the CERCA Programme/Generalitat de Catalunya. Authors acknowledge the
use of instrumentation as well as the technical advice provided by the Joint Electron
Microscopy Center at ALBA (JEMCA). ICN2 acknowledges funding from Grant IU16-014206
(METCAM-FIB) funded by the European Union through the European Regional Development
Fund (ERDF), with the support of the Ministry of Research and Universities, Generalitat
de Catalunya. ICN2 is founding member of e-DREAM. (91)'
article_processing_charge: Yes (via OA deal)
article_type: letter_note
author:
- first_name: Yu
full_name: Liu, Yu
id: 2A70014E-F248-11E8-B48F-1D18A9856A87
last_name: Liu
orcid: 0000-0001-7313-6740
- first_name: Tobias
full_name: Kleinhanns, Tobias
id: 8BD9DE16-AB3C-11E9-9C8C-2A03E6697425
last_name: Kleinhanns
orcid: 0000-0003-1537-7436
- first_name: Maria Chiara
full_name: Spadaro, Maria Chiara
last_name: Spadaro
- first_name: Aziz
full_name: Genç, Aziz
last_name: Genç
- first_name: Sharona
full_name: Horta, Sharona
id: 03a7e858-01b1-11ec-8b71-99ae6c4a05bc
last_name: Horta
- first_name: Navita
full_name: Navita, Navita
id: 6ebe278d-ba0b-11ee-8184-f34cdc671de4
last_name: Navita
orcid: 0000-0001-7408-8197
- first_name: Tommaso
full_name: Costanzo, Tommaso
id: D93824F4-D9BA-11E9-BB12-F207E6697425
last_name: Costanzo
orcid: 0000-0001-9732-3815
- first_name: Ewelina
full_name: Dutkiewicz, Ewelina
id: 0601cc46-c082-11ec-9b07-bb29641d1de9
last_name: Dutkiewicz
- first_name: Jordi
full_name: Arbiol, Jordi
last_name: Arbiol
- first_name: Min
full_name: Hong, Min
last_name: Hong
- first_name: Maria
full_name: Ibáñez, Maria
id: 43C61214-F248-11E8-B48F-1D18A9856A87
last_name: Ibáñez
orcid: 0000-0001-5013-2843
citation:
ama: Liu Y, Kleinhanns T, Spadaro MC, et al. Exploiting mismatch strain and the
β–α phase transition for microstructural engineering in thermoelectric Ag2Se.
ACS Energy Letters. 2026;11(8):5752-5762. doi:10.1021/acsenergylett.6c01499
apa: Liu, Y., Kleinhanns, T., Spadaro, M. C., Genç, A., Horta, S., Jakhar, N., …
Ibáñez, M. (2026). Exploiting mismatch strain and the β–α phase transition for
microstructural engineering in thermoelectric Ag2Se. ACS Energy Letters.
American Chemical Society. https://doi.org/10.1021/acsenergylett.6c01499
chicago: Liu, Yu, Tobias Kleinhanns, Maria Chiara Spadaro, Aziz Genç, Sharona Horta,
Navita Jakhar, Tommaso Costanzo, et al. “Exploiting Mismatch Strain and the β–α
Phase Transition for Microstructural Engineering in Thermoelectric Ag2Se.” ACS
Energy Letters. American Chemical Society, 2026. https://doi.org/10.1021/acsenergylett.6c01499.
ieee: Y. Liu et al., “Exploiting mismatch strain and the β–α phase transition
for microstructural engineering in thermoelectric Ag2Se,” ACS Energy Letters,
vol. 11, no. 8. American Chemical Society, pp. 5752–5762, 2026.
ista: Liu Y, Kleinhanns T, Spadaro MC, Genç A, Horta S, Jakhar N, Costanzo T, Dutkiewicz
E, Arbiol J, Hong M, Ibáñez M. 2026. Exploiting mismatch strain and the β–α phase
transition for microstructural engineering in thermoelectric Ag2Se. ACS Energy
Letters. 11(8), 5752–5762.
mla: Liu, Yu, et al. “Exploiting Mismatch Strain and the β–α Phase Transition for
Microstructural Engineering in Thermoelectric Ag2Se.” ACS Energy Letters,
vol. 11, no. 8, American Chemical Society, 2026, pp. 5752–62, doi:10.1021/acsenergylett.6c01499.
short: Y. Liu, T. Kleinhanns, M.C. Spadaro, A. Genç, S. Horta, N. Jakhar, T. Costanzo,
E. Dutkiewicz, J. Arbiol, M. Hong, M. Ibáñez, ACS Energy Letters 11 (2026) 5752–5762.
corr_author: '1'
das_tickbox: '0'
date_created: 2026-08-18T11:34:03Z
date_published: 2026-08-14T00:00:00Z
date_updated: 2026-08-19T05:53:33Z
day: '14'
ddc:
- '540'
department:
- _id: MassSpec
- _id: MaIb
- _id: GradSch
- _id: EM-Fac
doi: 10.1021/acsenergylett.6c01499
file:
- access_level: open_access
checksum: 4d75c5a79d112c845c9eecba8838db38
content_type: application/pdf
creator: dernst
date_created: 2026-08-19T05:52:41Z
date_updated: 2026-08-19T05:52:41Z
file_id: '22736'
file_name: 2026_ACSEnergyLetters_Liu.pdf
file_size: 6806815
relation: main_file
success: 1
file_date_updated: 2026-08-19T05:52:41Z
has_accepted_license: '1'
intvolume: ' 11'
issue: '8'
language:
- iso: eng
month: '08'
oa: 1
oa_version: Published Version
page: 5752-5762
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: ACS Energy Letters
publication_identifier:
eissn:
- 2380-8195
publication_status: published
publisher: American Chemical Society
quality_controlled: '1'
researchdata_availability: no
scopus_import: '1'
status: public
supplementarymaterial: yes
title: Exploiting mismatch strain and the β–α phase transition for microstructural
engineering in thermoelectric Ag2Se
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 11
year: '2026'
...
---
OA_place: publisher
OA_type: hybrid
PlanS_conform: '1'
_id: '22715'
abstract:
- lang: eng
text: 'Grazing-incidence small-angle scattering (GISAS) is a relatively young technique
with important applications in thin-film technology and untapped potential when
it comes to 2D analysis on an absolute intensity scale. Approaching standardization
and reference methods early is foundational for reproducibility and comparability
across laboratories and reduction of systematic error sources. It underpins trust
in data obtained and accelerates innovation by ensuring that scientists work from
a common methodological baseline. Accordingly, obtaining reproducible results
from different GISAS instruments requires an agreement on how measurements are
performed, instruments calibrated and terms defined. To pave the way for standardization
and reference methods, we surveyed GISAS practitioners on what comes before an
experiment: hardware, software, sample alignment and instrument calibration. Twenty-two
questions were designed to elucidate the state of the art, which can be used for
the development of reference methods. Our data on 27 instruments provide the basis
for standardization. With very few exceptions, we found laboratories prepared
to implement future reference methods, but no consensus emerges naturally for
sample alignment and instrument calibration. We, that is the GISAS community,
are thus in a position to embark on the journey of standardization.'
acknowledgement: "The authors thank all respondents for their participation in the\r\nquestionnaire.
We plan to make further use of the wealth of\r\nthe dataset going forward. We thank
Xenocs for sharing\r\napproximate data on GISAXS equipment sales and Adrian\r\nRennie
for helpful discussions. Open access funding enabled\r\nand organized by Projekt
DEAL."
article_processing_charge: Yes (via OA deal)
article_type: original
author:
- first_name: Anja F.
full_name: Hörmann, Anja F.
last_name: Hörmann
- first_name: Daniel
full_name: Balazs, Daniel
id: 302BADF6-85FC-11EA-9E3B-B9493DDC885E
last_name: Balazs
orcid: 0000-0001-7597-043X
- first_name: Ingo
full_name: Breßler, Ingo
last_name: Breßler
- first_name: Sumea
full_name: Klokic, Sumea
last_name: Klokic
- first_name: Melika
full_name: Moradi, Melika
last_name: Moradi
- first_name: Eduardo
full_name: Solano, Eduardo
last_name: Solano
- first_name: Annika
full_name: Stellhorn, Annika
last_name: Stellhorn
- first_name: Brian R.
full_name: Pauw, Brian R.
last_name: Pauw
citation:
ama: 'Hörmann AF, Balazs D, Breßler I, et al. Grazing-incidence scattering surveyed:
Towards reference methods for alignment and calibration. Journal of Applied
Crystallography. 2026;59(4):1247-1253. doi:10.1107/S1600576726005741'
apa: 'Hörmann, A. F., Balazs, D., Breßler, I., Klokic, S., Moradi, M., Solano, E.,
… Pauw, B. R. (2026). Grazing-incidence scattering surveyed: Towards reference
methods for alignment and calibration. Journal of Applied Crystallography.
International Union of Crystallography. https://doi.org/10.1107/S1600576726005741'
chicago: 'Hörmann, Anja F., Daniel Balazs, Ingo Breßler, Sumea Klokic, Melika Moradi,
Eduardo Solano, Annika Stellhorn, and Brian R. Pauw. “Grazing-Incidence Scattering
Surveyed: Towards Reference Methods for Alignment and Calibration.” Journal
of Applied Crystallography. International Union of Crystallography, 2026.
https://doi.org/10.1107/S1600576726005741.'
ieee: 'A. F. Hörmann et al., “Grazing-incidence scattering surveyed: Towards
reference methods for alignment and calibration,” Journal of Applied Crystallography,
vol. 59, no. 4. International Union of Crystallography, pp. 1247–1253, 2026.'
ista: 'Hörmann AF, Balazs D, Breßler I, Klokic S, Moradi M, Solano E, Stellhorn
A, Pauw BR. 2026. Grazing-incidence scattering surveyed: Towards reference methods
for alignment and calibration. Journal of Applied Crystallography. 59(4), 1247–1253.'
mla: 'Hörmann, Anja F., et al. “Grazing-Incidence Scattering Surveyed: Towards Reference
Methods for Alignment and Calibration.” Journal of Applied Crystallography,
vol. 59, no. 4, International Union of Crystallography, 2026, pp. 1247–53, doi:10.1107/S1600576726005741.'
short: A.F. Hörmann, D. Balazs, I. Breßler, S. Klokic, M. Moradi, E. Solano, A.
Stellhorn, B.R. Pauw, Journal of Applied Crystallography 59 (2026) 1247–1253.
das_tickbox: '1'
dataavailabilitystatement: "The response data are available at https://doi.org/10.5281/\r\nzenodo.18712813.
The literate programming source of this\r\nwork is available at https://doi.org/10.5281/zenodo.18713631."
date_created: 2026-08-16T22:01:43Z
date_published: 2026-08-01T00:00:00Z
date_updated: 2026-08-20T06:14:07Z
day: '01'
ddc:
- '540'
department:
- _id: LifeSc
doi: 10.1107/S1600576726005741
file:
- access_level: open_access
checksum: 8dbad0ab078338021e2cfe722211df7b
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creator: dernst
date_created: 2026-08-20T05:51:36Z
date_updated: 2026-08-20T05:51:36Z
file_id: '22739'
file_name: 2026_JourAppliedCrystallography_Hoermann.pdf
file_size: 6692218
relation: main_file
success: 1
file_date_updated: 2026-08-20T05:51:36Z
has_accepted_license: '1'
intvolume: ' 59'
issue: '4'
keyword:
- grazing incidence
- reference methods
- calibration
- standardization
- community
language:
- iso: eng
month: '08'
oa: 1
oa_version: Published Version
page: 1247-1253
publication: Journal of Applied Crystallography
publication_identifier:
eissn:
- 1600-5767
issn:
- 0021-8898
publication_status: published
publisher: International Union of Crystallography
quality_controlled: '1'
researchdata_availability: yes
scopus_import: '1'
status: public
supplementarymaterial: no
title: 'Grazing-incidence scattering surveyed: Towards reference methods for alignment
and calibration'
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: 59
year: '2026'
...
---
OA_place: publisher
OA_type: gold
PlanS_conform: '1'
_id: '22716'
abstract:
- lang: eng
text: We give an algorithm that, with high probability, maintains a (1-ε)-approximate
s-t maximum flow in undirected, uncapacitated n-vertex graphs undergoing m edge
insertions in Õ(m+ n F^*/ε) total update time, where F^{*} is the maximum flow
on the final graph. This is the first algorithm to achieve polylogarithmic amortized
update time for dense graphs (m = Ω(n²)), and more generally, for graphs where
F^* = Õ(m/n). At the heart of our incremental algorithm is the residual graph
sparsification technique of Karger and Levine [SICOMP '15], originally designed
for computing exact maximum flows in the static setting. Our main contributions
are (i) showing how to maintain such sparsifiers for approximate maximum flows
in the incremental setting and (ii) generalizing the cut sparsification framework
of Fung et al. [SICOMP '19] from undirected graphs to balanced directed graphs.
acknowledgement: "M. Henzinger: This project has received funding from the European
Research Council (ERC) under the European Union’s\r\nHorizon 2020 research and innovation
programme (MoDynStruct, No. 101019564) and the Austrian Science Fund\r\n(FWF)
grant DOI 10.55776/Z422, grant DOI 10.55776/I5982, and grant DOI 10.55776/P33775
with additional funding from the\r\nnetidee SCIENCE Stiftung, 2020–2024. Views and
opinions expressed are those of the author(s) only and do not necessarily\r\nreflect
those of the European Union or the European Research Council Executive Agency. Neither
the European Union nor\r\nthe granting authority can be held responsible for them"
article_number: '31'
article_processing_charge: Yes
article_type: original
arxiv: 1
author:
- first_name: Gramoz
full_name: Goranci, Gramoz
last_name: Goranci
- first_name: Monika H
full_name: Henzinger, Monika H
id: 540c9bbd-f2de-11ec-812d-d04a5be85630
last_name: Henzinger
orcid: 0000-0002-5008-6530
- first_name: Harald
full_name: Räcke, Harald
last_name: Räcke
- first_name: A. R.
full_name: Sricharan, A. R.
last_name: Sricharan
citation:
ama: Goranci G, Henzinger M, Räcke H, Sricharan AR. Incremental approximate maximum
flow via residual graph sparsification. ACM Transactions on Algorithms.
2026;22(3). doi:10.1145/3816252
apa: Goranci, G., Henzinger, M., Räcke, H., & Sricharan, A. R. (2026). Incremental
approximate maximum flow via residual graph sparsification. ACM Transactions
on Algorithms. ACM. https://doi.org/10.1145/3816252
chicago: Goranci, Gramoz, Monika Henzinger, Harald Räcke, and A. R. Sricharan. “Incremental
Approximate Maximum Flow via Residual Graph Sparsification.” ACM Transactions
on Algorithms. ACM, 2026. https://doi.org/10.1145/3816252.
ieee: G. Goranci, M. Henzinger, H. Räcke, and A. R. Sricharan, “Incremental approximate
maximum flow via residual graph sparsification,” ACM Transactions on Algorithms,
vol. 22, no. 3. ACM, 2026.
ista: Goranci G, Henzinger M, Räcke H, Sricharan AR. 2026. Incremental approximate
maximum flow via residual graph sparsification. ACM Transactions on Algorithms.
22(3), 31.
mla: Goranci, Gramoz, et al. “Incremental Approximate Maximum Flow via Residual
Graph Sparsification.” ACM Transactions on Algorithms, vol. 22, no. 3,
31, ACM, 2026, doi:10.1145/3816252.
short: G. Goranci, M. Henzinger, H. Räcke, A.R. Sricharan, ACM Transactions on Algorithms
22 (2026).
corr_author: '1'
das_tickbox: '0'
date_created: 2026-08-16T22:01:43Z
date_published: 2026-07-06T00:00:00Z
date_updated: 2026-08-20T06:28:01Z
day: '06'
ddc:
- '000'
department:
- _id: MoHe
doi: 10.1145/3816252
ec_funded: 1
external_id:
arxiv:
- '2502.09105'
file:
- access_level: open_access
checksum: 97969d26dab25c3a35be3ae4dd0fd9ee
content_type: application/pdf
creator: dernst
date_created: 2026-08-20T06:19:51Z
date_updated: 2026-08-20T06:19:51Z
file_id: '22740'
file_name: 2026_TransactionsAlgorithms_Goranci.pdf
file_size: 2272512
relation: main_file
success: 1
file_date_updated: 2026-08-20T06:19:51Z
has_accepted_license: '1'
intvolume: ' 22'
issue: '3'
language:
- iso: eng
month: '07'
oa: 1
oa_version: Published Version
project:
- _id: bd9ca328-d553-11ed-ba76-dc4f890cfe62
call_identifier: H2020
grant_number: '101019564'
name: The design and evaluation of modern fully dynamic data structures
- _id: 34def286-11ca-11ed-8bc3-da5948e1613c
grant_number: Z00422
name: Efficient algorithms
- _id: bda196b2-d553-11ed-ba76-8e8ee6c21103
grant_number: I05982
name: Static and Dynamic Hierarchical Graph Decompositions
- _id: bd9e3a2e-d553-11ed-ba76-8aa684ce17fe
grant_number: P33775
name: Fast Algorithms for a Reactive Network Layer
publication: ACM Transactions on Algorithms
publication_identifier:
eissn:
- 1549-6333
issn:
- 1549-6325
publication_status: published
publisher: ACM
quality_controlled: '1'
related_material:
record:
- id: '21280'
relation: earlier_version
status: public
researchdata_availability: no
scopus_import: '1'
status: public
supplementarymaterial: yes
title: Incremental approximate maximum flow via residual graph sparsification
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: 22
year: '2026'
...
---
DOAJ_listed: '1'
OA_place: publisher
OA_type: gold
PlanS_conform: '1'
_id: '22714'
abstract:
- lang: eng
text: Radial glial progenitors (RGPs) generate all projection neurons (PNs) in the
cerebral cortex through incompletely understood processes. We combined Mosaic
Analysis with Double Markers at embryonic stages (E)12.5 and E13.5 with early
postnatal callosal tracing to dissect RGP lineage progression. We find that multipotent
RGPs generate all extra-telencephalic (ET) and intra-telencephalic (IT) PNs via
parallel sublineages that emerge simultaneously at neurogenesis onset. ET-PN production
progresses exclusively via small, self-consuming lineages; IT-PN lineages feature
RGPs generating large translaminar outputs. The early emergence of IT-PN–fated
RGPs, coinciding with a switch to direct neurogenesis, contributes to the stereotyped
population-level progression of the multipotent lineage. We also identify POU3F
transcription factors as candidate regulators of IT-PN fate via noncanonical mitotic
chromatin binding. The results support a model whereby IT- and ET-PNs arise from
an early bifurcation and parallel specification within the multipotent RGP lineage.
acknowledgement: 'We thank M. caouyette for the plasmid construction for Pou3f1overexpression;
d. Pinto-Benito for valuable assistance with shRnA validation in n2A cells andqPcR
experiments; c. Varela-Martínez for help with the code for graphical analysis; allmembers
from the nieto’s lab for comment on the manuscript, specially to F. Martín for theinsightful
discussions; J. c. Oliveros and J. A. García from the computational service of the
cnBfor help with the analysis of RnAseq dataset; c. O. Sorzano for help with statistical
analysis; andA. Oña and the service of Advance Optical Microscopy of the cnB for
technical advice.Funding: i.V.-M. holds a fellowship funded by MciciU (PRe-2018-083376)
and 2023 eMBOscientific exchange grant 10214. the work was funded by grants to M.n.
(Pid2020-112831GB- i00 and Pid2023-146322nB- i00 by Mcin/Aei/10.13039/501100011033
and by“eRdF A way of making europe”).'
article_processing_charge: Yes
article_type: original
author:
- first_name: Irene
full_name: Varela Martínez, Irene
id: a69b5985-8829-11f0-8fc2-d0af58f64471
last_name: Varela Martínez
- first_name: Ana
full_name: Villalba Requena, Ana
id: 68cb85a0-39f7-11eb-9559-9aaab4f6a247
last_name: Villalba Requena
orcid: 0000-0002-5615-5277
- first_name: Jorge
full_name: García-Marqués, Jorge
last_name: García-Marqués
- first_name: Alfonso
full_name: Aguilera, Alfonso
last_name: Aguilera
- first_name: Diogo S.
full_name: Castro, Diogo S.
last_name: Castro
- first_name: Simon
full_name: Hippenmeyer, Simon
id: 37B36620-F248-11E8-B48F-1D18A9856A87
last_name: Hippenmeyer
orcid: 0000-0003-2279-1061
- first_name: Marta
full_name: Nieto, Marta
last_name: Nieto
citation:
ama: Varela Martínez I, Villalba Requena A, García-Marqués J, et al. Early fate
diversification of radial glial progenitors during corticogenesis. Science
Advances. 2026;12(32):eadw5487. doi:10.1126/sciadv.adw5487
apa: Varela Martínez, I., Villalba Requena, A., García-Marqués, J., Aguilera, A.,
Castro, D. S., Hippenmeyer, S., & Nieto, M. (2026). Early fate diversification
of radial glial progenitors during corticogenesis. Science Advances. AAAS.
https://doi.org/10.1126/sciadv.adw5487
chicago: Varela Martínez, Irene, Ana Villalba Requena, Jorge García-Marqués, Alfonso
Aguilera, Diogo S. Castro, Simon Hippenmeyer, and Marta Nieto. “Early Fate Diversification
of Radial Glial Progenitors during Corticogenesis.” Science Advances. AAAS,
2026. https://doi.org/10.1126/sciadv.adw5487.
ieee: I. Varela Martínez et al., “Early fate diversification of radial glial
progenitors during corticogenesis,” Science Advances, vol. 12, no. 32.
AAAS, p. eadw5487, 2026.
ista: Varela Martínez I, Villalba Requena A, García-Marqués J, Aguilera A, Castro
DS, Hippenmeyer S, Nieto M. 2026. Early fate diversification of radial glial progenitors
during corticogenesis. Science Advances. 12(32), eadw5487.
mla: Varela Martínez, Irene, et al. “Early Fate Diversification of Radial Glial
Progenitors during Corticogenesis.” Science Advances, vol. 12, no. 32,
AAAS, 2026, p. eadw5487, doi:10.1126/sciadv.adw5487.
short: I. Varela Martínez, A. Villalba Requena, J. García-Marqués, A. Aguilera,
D.S. Castro, S. Hippenmeyer, M. Nieto, Science Advances 12 (2026) eadw5487.
das_tickbox: '1'
dataavailabilitystatement: 'All data and code needed to evaluate and reproduce the
results in the paper are present in the paper and/or the Supplementary Materials.
Source data underlying all figures (including the clonal atlas) are provided in
the Supplementary Materials. RnA-seq analysis code has been deposited in Zenodo
(dOi: 10.5281/zenodo.14609057). this study did not generate new materials.'
date_created: 2026-08-16T22:01:43Z
date_published: 2026-08-07T00:00:00Z
date_updated: 2026-08-20T05:45:28Z
day: '07'
ddc:
- '570'
department:
- _id: SiHi
doi: 10.1126/sciadv.adw5487
external_id:
pmid:
- '42555737'
file:
- access_level: open_access
checksum: 487c3703387080e8f3c4675d67763f0e
content_type: application/pdf
creator: dernst
date_created: 2026-08-20T05:39:32Z
date_updated: 2026-08-20T05:39:32Z
file_id: '22738'
file_name: 2026_ScienceAdv_VarelaMartinez.pdf
file_size: 3056744
relation: main_file
success: 1
file_date_updated: 2026-08-20T05:39:32Z
has_accepted_license: '1'
intvolume: ' 12'
issue: '32'
language:
- iso: eng
month: '08'
oa: 1
oa_version: Published Version
page: eadw5487
pmid: 1
publication: Science Advances
publication_identifier:
eissn:
- 2375-2548
publication_status: published
publisher: AAAS
quality_controlled: '1'
researchdata_availability: yes
scopus_import: '1'
status: public
supplementarymaterial: yes
title: Early fate diversification of radial glial progenitors during corticogenesis
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: 12
year: '2026'
...
---
DOAJ_listed: '1'
OA_place: publisher
OA_type: gold
_id: '22712'
abstract:
- lang: eng
text: Ginseng (Panax ginseng) derives its renowned therapeutic properties from ginsenoside
metabolites. However, the long cultivation cycle and susceptibility to diseases
hinder the advancement of the ginseng industry. Here, we demonstrate that the
embryonic protoderm of ginseng can efficiently produce ginsenosides. Single-cell
transcriptome and mass spectrometry imaging analyses reveal that ginsenosides
accumulate in the protoderm of ginseng embryonic callus (EC) at levels comparable
to those in forest ginseng. Epigenetic analyses indicate that elevated histone
acetylation and enhanced chromatin accessibility at regeneration- and ginsenoside
metabolism-related gene loci are associated with the ginsenoside-producing capacity
of EC. Increasing histone acetylation levels or overexpressing the regeneration-related
WUSCHEL-RELATED HOMEOBOX11 (WOX11) gene further enhances ginsenoside production
in EC. Our findings suggest that the protoderm of EC could serve as an in situ
biological compartment for high-efficiency ginsenoside producion, offering a complementary
approach to traditional ginseng cultivation.
acknowledgement: 'The authors are grateful to Professor Linfeng Li from the School
of Life Science, Fudan University, for his assistance during the ginseng genome
annotation. This work was supported by Key project at central government level:
The ability establishment of sustainable use for valuable Chinese medicine resources
(2060302-2401-08 to L.X. and J.L.), the National Natural Science Foundation of China
(82373987 to J.L., 31701294 to L.X., 32225007 to L.X., and 32300285 to N.Z.), the
Fundamental Research Funds for the Central public welfare research institutes (ZZ13-YQ-093,
ZZXT202508 to J.L.), the CACMS Innovation Fund (CI2025G00-06 to J.L.), the Principle
Investigator Program (HBMUPI202104 to Y.Z.), the Key R&D Program of Shandong Province,
China (2024LZGC025 to L.X.), the National Key R&D Program of China (2024YFF1000700/2023YFE0101100
to L.X.), Strategic Priority Research Program of Chinese Academy of Sciences (XDB0630000
to L.X.), and China Postdoctoral Science Foundation (2023M733490 to N.Z.).'
article_number: '7994'
article_processing_charge: Yes
article_type: original
author:
- first_name: Juan
full_name: Liu, Juan
last_name: Liu
- first_name: Ning
full_name: Zhai, Ning
last_name: Zhai
- first_name: Shiyi
full_name: Zhang, Shiyi
last_name: Zhang
- first_name: Yosuke
full_name: Tamada, Yosuke
last_name: Tamada
- first_name: Tonghui
full_name: Li, Tonghui
last_name: Li
- first_name: Linfan
full_name: Zhang, Linfan
last_name: Zhang
- first_name: Tong
full_name: Chen, Tong
last_name: Chen
- first_name: Chenglin
full_name: Wang, Chenglin
last_name: Wang
- first_name: Jian
full_name: Yang, Jian
last_name: Yang
- first_name: Jiaqi
full_name: Gao, Jiaqi
last_name: Gao
- first_name: Xiang
full_name: Li, Xiang
id: 4B7E523C-F248-11E8-B48F-1D18A9856A87
last_name: Li
- first_name: Junhui
full_name: Zhou, Junhui
last_name: Zhou
- first_name: Yonghong
full_name: Zhang, Yonghong
last_name: Zhang
- first_name: Yu
full_name: Liu, Yu
id: 2A70014E-F248-11E8-B48F-1D18A9856A87
last_name: Liu
orcid: 0000-0001-7313-6740
- first_name: Yuan
full_name: Wang, Yuan
last_name: Wang
- first_name: Jiří
full_name: Friml, Jiří
id: 4159519E-F248-11E8-B48F-1D18A9856A87
last_name: Friml
orcid: 0000-0002-8302-7596
- first_name: Eva
full_name: Benková, Eva
id: 38F4F166-F248-11E8-B48F-1D18A9856A87
last_name: Benková
orcid: 0000-0002-8510-9739
- first_name: Chen
full_name: Li, Chen
last_name: Li
- first_name: Lin
full_name: Xu, Lin
last_name: Xu
- first_name: Luqi
full_name: Huang, Luqi
last_name: Huang
citation:
ama: Liu J, Zhai N, Zhang S, et al. Single-cell analyses identify the ginseng embryonic
protoderm as a native compartment for high-efficiency ginsenoside production.
Nature Communications. 2026;17. doi:10.1038/s41467-026-74881-5
apa: Liu, J., Zhai, N., Zhang, S., Tamada, Y., Li, T., Zhang, L., … Huang, L. (2026).
Single-cell analyses identify the ginseng embryonic protoderm as a native compartment
for high-efficiency ginsenoside production. Nature Communications. Springer
Nature. https://doi.org/10.1038/s41467-026-74881-5
chicago: Liu, Juan, Ning Zhai, Shiyi Zhang, Yosuke Tamada, Tonghui Li, Linfan Zhang,
Tong Chen, et al. “Single-Cell Analyses Identify the Ginseng Embryonic Protoderm
as a Native Compartment for High-Efficiency Ginsenoside Production.” Nature
Communications. Springer Nature, 2026. https://doi.org/10.1038/s41467-026-74881-5.
ieee: J. Liu et al., “Single-cell analyses identify the ginseng embryonic
protoderm as a native compartment for high-efficiency ginsenoside production,”
Nature Communications, vol. 17. Springer Nature, 2026.
ista: Liu J, Zhai N, Zhang S, Tamada Y, Li T, Zhang L, Chen T, Wang C, Yang J, Gao
J, Li X, Zhou J, Zhang Y, Liu Y, Wang Y, Friml J, Benková E, Li C, Xu L, Huang
L. 2026. Single-cell analyses identify the ginseng embryonic protoderm as a native
compartment for high-efficiency ginsenoside production. Nature Communications.
17, 7994.
mla: Liu, Juan, et al. “Single-Cell Analyses Identify the Ginseng Embryonic Protoderm
as a Native Compartment for High-Efficiency Ginsenoside Production.” Nature
Communications, vol. 17, 7994, Springer Nature, 2026, doi:10.1038/s41467-026-74881-5.
short: J. Liu, N. Zhai, S. Zhang, Y. Tamada, T. Li, L. Zhang, T. Chen, C. Wang,
J. Yang, J. Gao, X. Li, J. Zhou, Y. Zhang, Y. Liu, Y. Wang, J. Friml, E. Benková,
C. Li, L. Xu, L. Huang, Nature Communications 17 (2026).
das_tickbox: '1'
dataavailabilitystatement: The RNA-seq data generated in this study have been deposited
in the GSA database under accession code CRA008967. The scRNA-seq data generated
in this study have been deposited in the GSA database under accession code CRA026200.
The ATAC-seq data generated in this study have been deposited in the GSA database
under accession code CRA008969. The ChIP-seq data generated in this study have been
deposited in the GSA database under accession code CRA008968. Single-cell RNA-seq
data and scripts are publicly available on Zenodo (https://zenodo.org/records/20392012).
Primers are in Supplemental Table 5. Source data are provided with this paper.
date_created: 2026-08-16T22:01:42Z
date_published: 2026-08-07T00:00:00Z
date_updated: 2026-08-20T06:45:46Z
day: '07'
ddc:
- '580'
department:
- _id: JiFr
- _id: EvBe
doi: 10.1038/s41467-026-74881-5
external_id:
pmid:
- '42350386'
file:
- access_level: open_access
checksum: 0b4ff29f0d0168b11be32a5f22ded9e4
content_type: application/pdf
creator: dernst
date_created: 2026-08-20T06:44:33Z
date_updated: 2026-08-20T06:44:33Z
file_id: '22742'
file_name: 2026_NatureComm_Liu.pdf
file_size: 2429551
relation: main_file
success: 1
file_date_updated: 2026-08-20T06:44:33Z
has_accepted_license: '1'
intvolume: ' 17'
language:
- iso: eng
month: '08'
oa: 1
oa_version: Published Version
pmid: 1
publication: Nature Communications
publication_identifier:
eissn:
- 2041-1723
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
researchdata_availability: yes
scopus_import: '1'
status: public
supplementarymaterial: yes
title: Single-cell analyses identify the ginseng embryonic protoderm as a native compartment
for high-efficiency ginsenoside production
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: 17
year: '2026'
...
---
DOAJ_listed: '1'
OA_place: publisher
OA_type: gold
_id: '22711'
abstract:
- lang: eng
text: When charge flows through a molecular circuit, it induces a magnetic field
that allows the circuit to behave as a nanoscale electromagnet. However, in single-molecule
circuits this magnetic field is usually weak. Here we show that radially π-conjugated
carbon structures can support amplified circulating currents that generate local
magnetic fields. Within tight-binding and density functional theory (DFT) frameworks,
we first study cycloparaphenylene (CPP) junctions where both electrodes are attached
to the same phenylene unit on the nanohoop. We observe an energy-dependent ring
current component that traverses the whole macrocycle by mapping the local current
density. Importantly, we find that destructive interference near degenerate resonances
can reverse the ring current direction and amplify it strongly relative to the
source–drain current. We show that this interference-driven design principle is
general, and also carries over to C60 junctions. In fullerene, lower-lying degenerate
resonances are more easily accessible through electrostatic gating, reaching a
magnetic field of 14.2 mT under a 100 mV source–drain bias. This work thus provides
new insights into ring currents in radially π-conjugated carbon structures and
highlights their potential as design platforms for single-molecule electromagnets.
acknowledgement: The authors thank Jascha Repp from the University of Regensburg for
helpful discussions. This paper is dedicated to the memory of Prof. Mark Ratner
in appreciation of the encouragement offered many years ago, and whose influence
had endured ever since. This work was supported by the National Science Foundation
under grant NSF-DMR 2241180 and the Institute of Science and Technology Austria.
The collaboration between L.V., R.K., and F.E. was supported by the Humboldt Foundation.
This research was funded in part by the Austrian Science Fund (FWF) [10.55776/COE5]
(Cluster of Excellence MECS).
article_number: '7916'
article_processing_charge: Yes
article_type: original
author:
- first_name: Wanzhuo
full_name: Shi, Wanzhuo
id: a3010425-87c8-11f0-8106-bec32bea74da
last_name: Shi
- first_name: Richard
full_name: Korytár, Richard
last_name: Korytár
- first_name: Ferdinand
full_name: Evers, Ferdinand
last_name: Evers
- first_name: John D.
full_name: Tovar, John D.
last_name: Tovar
- first_name: Latha
full_name: Venkataraman, Latha
id: 9ebb78a5-cc0d-11ee-8322-fae086a32caf
last_name: Venkataraman
orcid: 0000-0002-6957-6089
citation:
ama: Shi W, Korytár R, Evers F, Tovar JD, Venkataraman L. Designing effective single-molecule
electromagnets with radially π-conjugated carbon structures. Nature Communications.
2026;17. doi:10.1038/s41467-026-74365-6
apa: Shi, W., Korytár, R., Evers, F., Tovar, J. D., & Venkataraman, L. (2026).
Designing effective single-molecule electromagnets with radially π-conjugated
carbon structures. Nature Communications. Springer Nature. https://doi.org/10.1038/s41467-026-74365-6
chicago: Shi, Wanzhuo, Richard Korytár, Ferdinand Evers, John D. Tovar, and Latha
Venkataraman. “Designing Effective Single-Molecule Electromagnets with Radially
π-Conjugated Carbon Structures.” Nature Communications. Springer Nature,
2026. https://doi.org/10.1038/s41467-026-74365-6.
ieee: W. Shi, R. Korytár, F. Evers, J. D. Tovar, and L. Venkataraman, “Designing
effective single-molecule electromagnets with radially π-conjugated carbon structures,”
Nature Communications, vol. 17. Springer Nature, 2026.
ista: Shi W, Korytár R, Evers F, Tovar JD, Venkataraman L. 2026. Designing effective
single-molecule electromagnets with radially π-conjugated carbon structures. Nature
Communications. 17, 7916.
mla: Shi, Wanzhuo, et al. “Designing Effective Single-Molecule Electromagnets with
Radially π-Conjugated Carbon Structures.” Nature Communications, vol. 17,
7916, Springer Nature, 2026, doi:10.1038/s41467-026-74365-6.
short: W. Shi, R. Korytár, F. Evers, J.D. Tovar, L. Venkataraman, Nature Communications
17 (2026).
corr_author: '1'
das_tickbox: '1'
dataavailabilitystatement: The data generated in this study have been deposited in
the Code Ocean capsule. The capsule contains the FHI-aims and AITRANSS output matrices
used for post-processing, precomputed cache files, and optimized atomic coordinate
files. These data are sufficient to reproduce the results reported in the paper.
The code used to reproduce the local-current and magnetic-field analyses is available
in the Code Ocean capsule. The capsule includes Python scripts for post-processing
DFT output matrices and Mathematica notebooks for tight-binding calculations and
reproducing visualizations.
date_created: 2026-08-16T22:01:42Z
date_published: 2026-08-06T00:00:00Z
date_updated: 2026-08-20T06:40:49Z
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title: Designing effective single-molecule electromagnets with radially π-conjugated
carbon structures
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abstract:
- lang: eng
text: "Understanding enzyme function requires characterizing not only static structure
but also dynamics and ligand interactions. NMR spectroscopy provides this insight
at atomic resolution, yet for large proteins the difficulty of resonance assignment
has largely confined such studies to systems below ∼50 kDa, or to observing only
methyl groups. Here we present an integrated magic-angle spinning (MAS) and solution
NMR study of the 134 kDa tetrameric malate dehydrogenase from Ignicoccus islandicus
(IiMDH), an enzyme of particular interest as an evolutionary intermediate between
allosteric lactate\r\ndehydrogenases and non-allosteric malate dehydrogenases.
By combining high-dimensional (up to 4D) MAS NMR experiments on sedimented protein
with solution NMR, we achieved 92% backbone heavy- atom assignment and 91% assignment
of all Ile-δ1, Leu-δ1/-δ2, Val-γ1/-γ2, Met-ε and Thr-γ methyl groups. Building
on these assignments, we use various probes of backbone and sidechain dynamics:
elevated MAS NMR 15N rotating-frame relaxation (R1ρ) points to microsecond motions
in functionally critical regions, including the catalytic loop and the mobile
surface loop. Complementary methyl-axis order parameters from solution NMR identified
additional flexible sites in the hydrophobic core. Chemical shift perturbation
experiments upon addition of the substrate analogue oxamate, monitored via backbone
1H-15N TROSY, revealed both active-site contacts and responses in helices α2F
and α3G, regions implicated in allosteric signal transmission. The integrated
approach demonstrated here exploits the distinct strengths of MAS and solution
NMR, and provides a comprehensive view of structure, dynamics, and substrate interactions
in a large oligomeric enzyme that would not be accessible by either technique
alone."
acknowledged_ssus:
- _id: NMR
- _id: LifeSc
acknowledgement: This research was supported by the Scientific Service Units (SSU)
of Institute of Science and Technology Austria (ISTA) through resources provided
by the Nuclear Magnetic Resonance and the Lab Support Facilities. We thank Petra
Rovó, Megha Mohan and Margarita Valhondo Falcón for excellent support of the NMR
facility.
article_processing_charge: No
author:
- first_name: Paul
full_name: Schanda, Paul
id: 7B541462-FAF6-11E9-A490-E8DFE5697425
last_name: Schanda
orcid: 0000-0002-9350-7606
- first_name: Federico
full_name: Napoli, Federico
id: d42e08e7-f4fc-11eb-af0a-d71e26138f1b
last_name: Napoli
orcid: 0000-0002-9043-136X
citation:
ama: 'Schanda P, Napoli F. Data and scripts for: “Integrated solid/solution NMR
assignment allows mapping dynamics and ligand binding in a 134 kDa enzyme.” 2026.
doi:10.15479/AT-ISTA-22687'
apa: 'Schanda, P., & Napoli, F. (2026). Data and scripts for: “Integrated solid/solution
NMR assignment allows mapping dynamics and ligand binding in a 134 kDa enzyme.”
Institute of Science and Technology Austria. https://doi.org/10.15479/AT-ISTA-22687'
chicago: 'Schanda, Paul, and Federico Napoli. “Data and Scripts for: ‘Integrated
Solid/Solution NMR Assignment Allows Mapping Dynamics and Ligand Binding in a
134 KDa Enzyme.’” Institute of Science and Technology Austria, 2026. https://doi.org/10.15479/AT-ISTA-22687.'
ieee: 'P. Schanda and F. Napoli, “Data and scripts for: ‘Integrated solid/solution
NMR assignment allows mapping dynamics and ligand binding in a 134 kDa enzyme.’”
Institute of Science and Technology Austria, 2026.'
ista: 'Schanda P, Napoli F. 2026. Data and scripts for: ‘Integrated solid/solution
NMR assignment allows mapping dynamics and ligand binding in a 134 kDa enzyme’,
Institute of Science and Technology Austria, 10.15479/AT-ISTA-22687.'
mla: 'Schanda, Paul, and Federico Napoli. Data and Scripts for: “Integrated Solid/Solution
NMR Assignment Allows Mapping Dynamics and Ligand Binding in a 134 KDa Enzyme.”
Institute of Science and Technology Austria, 2026, doi:10.15479/AT-ISTA-22687.'
short: P. Schanda, F. Napoli, (2026).
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id: d42e08e7-f4fc-11eb-af0a-d71e26138f1b
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first_name: Paul
id: 7B541462-FAF6-11E9-A490-E8DFE5697425
last_name: Schanda
orcid: 0000-0002-9350-7606
- contributor_type: project_member
first_name: Rajkumar
id: a3089acd-6806-11ee-bacc-f0c7d500ad20
last_name: Singh
- contributor_type: project_member
first_name: Anna
id: 9fb2a840-89e1-11ee-a8b7-cc5c7ba62471
last_name: Kapitonova
- contributor_type: project_member
first_name: Virgil
last_name: Aitenbichler
- contributor_type: project_member
first_name: Giorgia
id: 334a5e40-8747-11f0-b671-ba1f5154b4b4
last_name: Toscano
- contributor_type: data_collector
first_name: Barbara
last_name: Perrone
corr_author: '1'
date_created: 2026-08-12T16:12:19Z
date_published: 2026-08-20T00:00:00Z
date_updated: 2026-08-20T07:40:15Z
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name: AlloSpace. The emergence and mechanisms of allostery
publisher: Institute of Science and Technology Austria
status: public
title: 'Data and scripts for: "Integrated solid/solution NMR assignment allows mapping
dynamics and ligand binding in a 134 kDa enzyme"'
tmp:
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abstract:
- lang: eng
text: As vertebrates transitioned from water to land, locomotion shifted from undulatory
swimming to limb-based movement. How spinal circuits and their cell types evolved
to support this transition remains unclear. We leverage frog metamorphosis, which
recapitulates this transition within a single organism, to define how spinal circuits
generate aquatic versus terrestrial motor patterns. At swim stages, spinal architecture
is uniform, with a transcriptionally and anatomically homogeneous motor and interneurons.
As limbs develop and their movement complexifies, spinal circuits expand in neuron
number and subtype diversity. This expansion is most pronounced for V1 inhibitory
neurons, which increase ∼70-fold and diversify into transcriptionally distinct
subtypes. Disrupting transcription factors defining emerging motor and V1 populations
reveals molecular segregation between swim and limb circuits, highlighting the
role of subtype diversity in motor coordination. A multifold increase in inhibitory
neuron diversity thus underlies the tail-to-limb locomotor transition, providing
a framework for spinal circuit adaptation during vertebrate evolution.
acknowledged_ssus:
- _id: Bio
- _id: LifeSc
acknowledgement: 'We would like to thank the members of the Sweeney Lab, Mario de
Bono, Michael Forsthofer, Katharina Lust, and Meital Oren, for comments on the manuscript.
We are also grateful to Tom Jessell and Chris Kintner for their scientific insight
and mentorship during the conception of this project. It would also have not been
possible without the technical support of the Aquatics and Imaging and Optics Facility
support teams (ISTA). We thank Martin Estermann for preparing the initial draft
of the graphical abstract and Niki Barolini for the final version. In addition,
we thank our funding sources for providing the resources to do these experiments:
GFF NÖ FTI Strategy Lower Austria dissertation grant FT121-D-046 (to D.V.), Horizon
Europe ERC starting grant 101041551 (to Y.I., L.B.S., F.A.T., and D.V.), Special
Research Program (SFB) of the Austrian Science Fund (FWF) project F7814-B (to L.B.S.),
Austrian Science Fund (FWF) 10.55776/COE16 (to Y.I. and L.B.S.), NINDS 5R35NS116858
(to J.S.D.), CZI grant DAF2020-225401 (DOI) 10.37921/120055ratwvi (to R.H.), NIH
grant R01NS123116 (to J.B.B.), American Lebanese Syrian Associated Charities (ALSAC)
(to J.B.B.), German Academic Exchange Service (DAAD) IFI grant 57515251-91853472
(to Z.H.), and Project A.L.S. (to S.B.-M.).'
article_number: '117227'
article_processing_charge: Yes
article_type: original
author:
- first_name: David
full_name: Vijatovic, David
id: cf391e77-ec3c-11ea-a124-d69323410b58
last_name: Vijatovic
orcid: 0000-0002-5494-0941
- first_name: 'Florina Alexandra '
full_name: 'Toma, Florina Alexandra '
id: 2f73f876-f128-11eb-9611-b96b5a30cb0e
last_name: Toma
- first_name: Y
full_name: Ignatyev, Y
last_name: Ignatyev
- first_name: Zoe P
full_name: Harrington, Zoe P
id: a8144562-32c9-11ee-b5ce-d9800628bda2
last_name: Harrington
orcid: 0009-0008-0158-4032
- first_name: Christoph M
full_name: Sommer, Christoph M
id: 4DF26D8C-F248-11E8-B48F-1D18A9856A87
last_name: Sommer
orcid: 0000-0003-1216-9105
- first_name: Robert
full_name: Hauschild, Robert
id: 4E01D6B4-F248-11E8-B48F-1D18A9856A87
last_name: Hauschild
orcid: 0000-0001-9843-3522
- first_name: Matthijs Geert
full_name: Smits, Matthijs Geert
id: 7a231d52-e216-11ee-a0bb-8acd55f8f1f0
last_name: Smits
- first_name: Marco
full_name: Dalla Vecchia, Marco
id: 02a7a869-ff06-11ed-a87f-86649d6077e5
last_name: Dalla Vecchia
- first_name: Alexandra J.
full_name: Trevisan, Alexandra J.
last_name: Trevisan
- first_name: Phillip
full_name: Chapman, Phillip
last_name: Chapman
- first_name: Mara
full_name: Julseth, Mara
id: 1cf464b2-dc7d-11ea-9b2f-f9b1aa9417d1
last_name: Julseth
- first_name: Susan
full_name: Brenner-Morton, Susan
last_name: Brenner-Morton
- first_name: Mariano I.
full_name: Gabitto, Mariano I.
last_name: Gabitto
- first_name: Jeremy S.
full_name: Dasen, Jeremy S.
last_name: Dasen
- first_name: Jay B.
full_name: Bikoff, Jay B.
last_name: Bikoff
- first_name: Lora Beatrice Jaeger
full_name: Sweeney, Lora Beatrice Jaeger
id: 56BE8254-C4F0-11E9-8E45-0B23E6697425
last_name: Sweeney
orcid: 0000-0001-9242-5601
citation:
ama: Vijatovic D, Toma FA, Ignatyev Y, et al. Multifold increase in spinal inhibitory
cell types with emergence of limb movement. Cell Reports. 2026;45(4). doi:10.1016/j.celrep.2026.117227
apa: Vijatovic, D., Toma, F. A., Ignatyev, Y., Harrington, Z. P., Sommer, C. M.,
Hauschild, R., … Sweeney, L. B. (2026). Multifold increase in spinal inhibitory
cell types with emergence of limb movement. Cell Reports. Elsevier. https://doi.org/10.1016/j.celrep.2026.117227
chicago: Vijatovic, David, Florina Alexandra Toma, Y Ignatyev, Zoe P Harrington,
Christoph M Sommer, Robert Hauschild, Matthijs Geert Smits, et al. “Multifold
Increase in Spinal Inhibitory Cell Types with Emergence of Limb Movement.” Cell
Reports. Elsevier, 2026. https://doi.org/10.1016/j.celrep.2026.117227.
ieee: D. Vijatovic et al., “Multifold increase in spinal inhibitory cell
types with emergence of limb movement,” Cell Reports, vol. 45, no. 4. Elsevier,
2026.
ista: Vijatovic D, Toma FA, Ignatyev Y, Harrington ZP, Sommer CM, Hauschild R, Smits
MG, Dalla Vecchia M, Trevisan AJ, Chapman P, Julseth M, Brenner-Morton S, Gabitto
MI, Dasen JS, Bikoff JB, Sweeney LB. 2026. Multifold increase in spinal inhibitory
cell types with emergence of limb movement. Cell Reports. 45(4), 117227.
mla: Vijatovic, David, et al. “Multifold Increase in Spinal Inhibitory Cell Types
with Emergence of Limb Movement.” Cell Reports, vol. 45, no. 4, 117227,
Elsevier, 2026, doi:10.1016/j.celrep.2026.117227.
short: D. Vijatovic, F.A. Toma, Y. Ignatyev, Z.P. Harrington, C.M. Sommer, R. Hauschild,
M.G. Smits, M. Dalla Vecchia, A.J. Trevisan, P. Chapman, M. Julseth, S. Brenner-Morton,
M.I. Gabitto, J.S. Dasen, J.B. Bikoff, L.B. Sweeney, Cell Reports 45 (2026).
corr_author: '1'
date_created: 2026-04-19T22:07:43Z
date_published: 2026-04-28T00:00:00Z
date_updated: 2026-08-20T14:45:18Z
day: '28'
ddc:
- '570'
department:
- _id: LoSw
- _id: GradSch
- _id: TiVo
- _id: Bio
- _id: NiBa
doi: 10.1016/j.celrep.2026.117227
external_id:
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- '41964955 '
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month: '04'
oa: 1
oa_version: Published Version
pmid: 1
project:
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grant_number: '101041551'
name: Development and Evolution of Tetrapod Motor Circuits
- _id: 8da85f50-16d5-11f0-9cad-eab8b0ff6c9e
grant_number: F7814
name: 'Stem Cell Modulation in Neural Development and Regeneration/ P14-Swim-to-limb
transition: cell type to connection diversity'
- _id: c08e9ad1-5a5b-11eb-8a69-9d1cf3b07473
grant_number: CZI01
name: Tools for automation and feedback microscopy
- _id: bd73af52-d553-11ed-ba76-912049f0ac7a
grant_number: FTI21-D-046
name: Development of V1 interneuron diversity during swim-to-walk transition of
Xenopus metamorphosis
publication: Cell Reports
publication_identifier:
eissn:
- 2211-1247
issn:
- 2639-1856
publication_status: published
publisher: Elsevier
quality_controlled: '1'
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title: Multifold increase in spinal inhibitory cell types with emergence of limb movement
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...
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acknowledged_ssus:
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- _id: LifeSc
acknowledgement: "I am also grateful for the financial support that made this work
possible, including the\r\nEuropean Research Council (ERC Starting Grant 101041551),
the Austrian Science\r\nFund (FWF, Cluster of Excellence 10.55776/COE16), the GFF
Lower Austria FTI\r\nStrategy Dissertation Fellowship (FTI21-D-046), and the FENS/IBRO-PERC\r\nExchange
Fellowship. "
alternative_title:
- ISTA Thesis
article_processing_charge: No
author:
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full_name: Vijatovic, David
id: cf391e77-ec3c-11ea-a124-d69323410b58
last_name: Vijatovic
orcid: 0000-0002-5494-0941
citation:
ama: Vijatovic D. Dissecting the molecular and functional basis of motor control
in the frog Xenopus laevis. 2026. doi:10.15479/AT-ISTA-22667
apa: Vijatovic, D. (2026). Dissecting the molecular and functional basis of motor
control in the frog Xenopus laevis. Institute of Science and Technology Austria.
https://doi.org/10.15479/AT-ISTA-22667
chicago: Vijatovic, David. “Dissecting the Molecular and Functional Basis of Motor
Control in the Frog Xenopus Laevis.” Institute of Science and Technology Austria,
2026. https://doi.org/10.15479/AT-ISTA-22667.
ieee: D. Vijatovic, “Dissecting the molecular and functional basis of motor control
in the frog Xenopus laevis,” Institute of Science and Technology Austria, 2026.
ista: Vijatovic D. 2026. Dissecting the molecular and functional basis of motor
control in the frog Xenopus laevis. Institute of Science and Technology Austria.
mla: Vijatovic, David. Dissecting the Molecular and Functional Basis of Motor
Control in the Frog Xenopus Laevis. Institute of Science and Technology Austria,
2026, doi:10.15479/AT-ISTA-22667.
short: D. Vijatovic, Dissecting the Molecular and Functional Basis of Motor Control
in the Frog Xenopus Laevis, Institute of Science and Technology Austria, 2026.
corr_author: '1'
date_created: 2026-08-10T13:44:30Z
date_published: 2026-08-10T00:00:00Z
date_updated: 2026-08-20T14:45:18Z
day: '10'
ddc:
- '573'
degree_awarded: PhD
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- _id: GradSch
- _id: LoSw
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