---
DOAJ_listed: '1'
OA_place: publisher
OA_type: gold
PlanS_conform: '1'
_id: '21013'
abstract:
- lang: eng
text: We have addressed convective self‐aggregation (CSA) in steady and oscillating
sea surface temperature (SST) and solar radiation (SOLIN) cloud‐resolving model
simulations in a non‐rotating radiative‐convective equilibrium (RCE) framework.
Our experiment designs are motivated by land‐ocean heterogeneity of atmospheric
convection. The steady and oscillating forcings are idealizations of ocean and
land conditions, respectively, based on their differences in heat capacities.
In both kinds of simulations, the diurnal mean SST and SOLIN are the same, and
both SST and SOLIN are only varied in time (i.e., they are spatially homogeneous
at any given time). We find that diurnally oscillating forcing accelerates CSA.
Stronger long‐wave cooling in dry regions at night and during the warm SST phase
(late afternoon) both allow the long‐wave feedback, known to favor aggregation,
to intensify compared to steady forcing simulations. In addition to the long‐wave,
reduced short‐wave warming in dry regions (during the day) further enhances radiative
cooling there compared to moist regions. Overall, the radiative cooling is enhanced
in dry regions compared to neighboring moist convective regions. A dry subsidence
is driven by this net radiative (short‐wave plus long‐wave) cooling, consistent
with earlier work on CSA. Stronger radiative cooling allows stronger subsidence
which allows low‐level circulation to more efficiently transport moisture and
energy up‐gradient, driving convection to aggregate faster. We also note a sensitivity
of our experimental setup to initial conditions, more so at warmer SST. This stochastic
behavior might be critical in reconciling the differences of opinion regarding
the response of convection aggregation to oscillating SST forcing.
acknowledged_ssus:
- _id: ScienComp
acknowledgement: The authors gratefully acknowledge funding from the European Research
Council (ERC) under the European Union's Horizon 2020 research and innovation program
(Project CLUSTER, Grant Agreement No. 805041). This research was supported by the
Scientific Service Units (SSU) of ISTA through resources provided by Scientific
Computing (SciComp). We are grateful to three anonymous reviewer(s) for their insightful
suggestions that have improved the quality of our manuscript. Open Access funding
provided by Institute of Science and Technology Austria/KEMÖ.
article_number: e2024MS004576
article_processing_charge: Yes
article_type: original
author:
- first_name: BIDYUT B
full_name: GOSWAMI, BIDYUT B
id: 3a4ac09c-6d61-11ec-bf66-884cde66b64b
last_name: GOSWAMI
orcid: 0000-0001-8602-3083
- first_name: Ziyin
full_name: Lu, Ziyin
id: a6e549c6-8972-11ed-ae7b-a336d97ac043
last_name: Lu
orcid: 0009-0008-5320-7730
- first_name: Caroline J
full_name: Muller, Caroline J
id: f978ccb0-3f7f-11eb-b193-b0e2bd13182b
last_name: Muller
orcid: 0000-0001-5836-5350
citation:
ama: GOSWAMI BB, Lu Z, Muller CJ. Convective self‐aggregation in diurnally oscillating
sea surface temperature and solar forcing experiments. Journal of Advances
in Modeling Earth Systems. 2026;18(1). doi:10.1029/2024ms004576
apa: GOSWAMI, B. B., Lu, Z., & Muller, C. J. (2026). Convective self‐aggregation
in diurnally oscillating sea surface temperature and solar forcing experiments.
Journal of Advances in Modeling Earth Systems. Wiley. https://doi.org/10.1029/2024ms004576
chicago: GOSWAMI, BIDYUT B, Ziyin Lu, and Caroline J Muller. “Convective Self‐aggregation
in Diurnally Oscillating Sea Surface Temperature and Solar Forcing Experiments.”
Journal of Advances in Modeling Earth Systems. Wiley, 2026. https://doi.org/10.1029/2024ms004576.
ieee: B. B. GOSWAMI, Z. Lu, and C. J. Muller, “Convective self‐aggregation in diurnally
oscillating sea surface temperature and solar forcing experiments,” Journal
of Advances in Modeling Earth Systems, vol. 18, no. 1. Wiley, 2026.
ista: GOSWAMI BB, Lu Z, Muller CJ. 2026. Convective self‐aggregation in diurnally
oscillating sea surface temperature and solar forcing experiments. Journal of
Advances in Modeling Earth Systems. 18(1), e2024MS004576.
mla: GOSWAMI, BIDYUT B., et al. “Convective Self‐aggregation in Diurnally Oscillating
Sea Surface Temperature and Solar Forcing Experiments.” Journal of Advances
in Modeling Earth Systems, vol. 18, no. 1, e2024MS004576, Wiley, 2026, doi:10.1029/2024ms004576.
short: B.B. GOSWAMI, Z. Lu, C.J. Muller, Journal of Advances in Modeling Earth Systems
18 (2026).
corr_author: '1'
date_created: 2026-01-20T10:08:54Z
date_published: 2026-01-12T00:00:00Z
date_updated: 2026-01-21T08:41:19Z
day: '12'
ddc:
- '550'
department:
- _id: CaMu
- _id: BjHo
- _id: GradSch
doi: 10.1029/2024ms004576
ec_funded: 1
file:
- access_level: open_access
checksum: 6ea369e3b46bea58efab4f38b6c671a7
content_type: application/pdf
creator: dernst
date_created: 2026-01-21T08:39:01Z
date_updated: 2026-01-21T08:39:01Z
file_id: '21027'
file_name: 2026_JAMES_Goswami.pdf
file_size: 19509786
relation: main_file
success: 1
file_date_updated: 2026-01-21T08:39:01Z
fulldoi: https://doi.org/10.1029/2024ms004576
has_accepted_license: '1'
intvolume: ' 18'
issue: '1'
language:
- iso: eng
license: https://creativecommons.org/licenses/by-nc-nd/4.0/
month: '01'
oa: 1
oa_version: Published Version
project:
- _id: 629205d8-2b32-11ec-9570-e1356ff73576
call_identifier: H2020
grant_number: '805041'
name: Organization of CLoUdS, and implications of Tropical cyclones and for the
Energetics of the tropics, in current and waRming climate
publication: Journal of Advances in Modeling Earth Systems
publication_identifier:
eissn:
- 1942-2466
publication_status: published
publisher: Wiley
quality_controlled: '1'
scopus_import: '1'
status: public
title: Convective self‐aggregation in diurnally oscillating sea surface temperature
and solar forcing experiments
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: 18
year: '2026'
...
---
OA_place: publisher
OA_type: hybrid
PlanS_conform: '1'
_id: '21015'
abstract:
- lang: eng
text: Early embryo geometry is one of the most invariant species-specific traits,
yet its role in ensuring developmental reproducibility and robustness remains
underexplored. Here we show that in zebrafish, the geometry of the fertilized
egg—specifically its curvature and volume—serves as a critical initial condition
triggering a cascade of events that influence development. The embryo geometry
guides patterned asymmetric cell divisions in the blastoderm, generating radial
gradients of cell volume and nucleocytoplasmic ratio. These gradients generate
mitotic phase waves, with the nucleocytoplasmic ratio determining individual cell
cycle periods independently of other cells. We demonstrate that reducing cell
autonomy reshapes these waves, emphasizing the instructive role of geometry-derived
volume patterns in setting the intrinsic period of the cell cycle oscillator.
In addition to organizing cell cycles, early embryo geometry spatially patterns
zygotic genome activation at the midblastula transition, a key step in establishing
embryonic autonomy. Disrupting the embryo shape alters the zygotic genome activation
pattern and causes ectopic germ layer specification, underscoring the developmental
significance of geometry. Together, our findings reveal a symmetry-breaking function
of early embryo geometry in coordinating cell cycle and transcriptional patterning.
acknowledged_ssus:
- _id: PreCl
- _id: Bio
- _id: ScienComp
- _id: LifeSc
acknowledgement: We thank N. Petridou (EMBL) for sharing results before publication.
N.M. was supported by funding from the European Union’s Horizon 2020 programme under
the Marie Skłodowska-Curie COFUND Actions ISTplus grant agreement number 754411.
Y.I.L. acknowledges funding from the European Union’s Horizon 2020 research and
innovation programme under the Marie Skłodowska-Curie grant agreement number 101034413.
The research was supported by funding to C.-P.H. from the NOMIS Foundation, Project
ID 1.844. We would like to thank past and present members of the Heisenberg and
Hannezo groups for discussions, particularly S. Shamipour, V. Doddihal, M. Jovic,
N. Hino, F. N. Arslan, R. Kobylinska and C. Camelo for feedback on the draft manuscript.
This research was supported by the Scientific Service Units (SSU) of Institute of
Science and Technology Austria through resources provided by the Aquatics Facility,
Imaging & Optics Facility (IOF), Scientific Computing (SciComp) facility and Lab
Support Facility (LSF). Open access funding provided by Institute of Science and
Technology (IST Austria).
article_processing_charge: Yes (via OA deal)
article_type: original
author:
- first_name: Nikhil
full_name: Mishra, Nikhil
id: C4D70E82-1081-11EA-B3ED-9A4C3DDC885E
last_name: Mishra
orcid: 0000-0002-6425-5788
- first_name: Yuting I
full_name: Li, Yuting I
id: ee7a5ca8-8b71-11ed-b662-b3341c05b7eb
last_name: Li
- first_name: Edouard B
full_name: Hannezo, Edouard B
id: 3A9DB764-F248-11E8-B48F-1D18A9856A87
last_name: Hannezo
orcid: 0000-0001-6005-1561
- first_name: Carl-Philipp J
full_name: Heisenberg, Carl-Philipp J
id: 39427864-F248-11E8-B48F-1D18A9856A87
last_name: Heisenberg
orcid: 0000-0002-0912-4566
citation:
ama: Mishra N, Li YI, Hannezo EB, Heisenberg C-PJ. Geometry-driven asymmetric cell
divisions pattern cell cycles and zygotic genome activation in the zebrafish embryo.
Nature Physics. 2026;22:139-150. doi:10.1038/s41567-025-03122-1
apa: Mishra, N., Li, Y. I., Hannezo, E. B., & Heisenberg, C.-P. J. (2026). Geometry-driven
asymmetric cell divisions pattern cell cycles and zygotic genome activation in
the zebrafish embryo. Nature Physics. Springer Nature. https://doi.org/10.1038/s41567-025-03122-1
chicago: Mishra, Nikhil, Yuting I Li, Edouard B Hannezo, and Carl-Philipp J Heisenberg.
“Geometry-Driven Asymmetric Cell Divisions Pattern Cell Cycles and Zygotic Genome
Activation in the Zebrafish Embryo.” Nature Physics. Springer Nature, 2026.
https://doi.org/10.1038/s41567-025-03122-1.
ieee: N. Mishra, Y. I. Li, E. B. Hannezo, and C.-P. J. Heisenberg, “Geometry-driven
asymmetric cell divisions pattern cell cycles and zygotic genome activation in
the zebrafish embryo,” Nature Physics, vol. 22. Springer Nature, pp. 139–150,
2026.
ista: Mishra N, Li YI, Hannezo EB, Heisenberg C-PJ. 2026. Geometry-driven asymmetric
cell divisions pattern cell cycles and zygotic genome activation in the zebrafish
embryo. Nature Physics. 22, 139–150.
mla: Mishra, Nikhil, et al. “Geometry-Driven Asymmetric Cell Divisions Pattern Cell
Cycles and Zygotic Genome Activation in the Zebrafish Embryo.” Nature Physics,
vol. 22, Springer Nature, 2026, pp. 139–50, doi:10.1038/s41567-025-03122-1.
short: N. Mishra, Y.I. Li, E.B. Hannezo, C.-P.J. Heisenberg, Nature Physics 22 (2026)
139–150.
corr_author: '1'
date_created: 2026-01-20T10:12:19Z
date_published: 2026-01-05T00:00:00Z
date_updated: 2026-04-28T12:55:30Z
day: '05'
ddc:
- '570'
department:
- _id: EdHa
- _id: CaHe
doi: 10.1038/s41567-025-03122-1
ec_funded: 1
external_id:
oaworkid:
- W7118187193
file:
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creator: dernst
date_created: 2026-01-21T08:21:11Z
date_updated: 2026-01-21T08:21:11Z
file_id: '21026'
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file_size: 7335694
relation: main_file
success: 1
file_date_updated: 2026-01-21T08:21:11Z
fulldoi: https://doi.org/10.1038/s41567-025-03122-1
has_accepted_license: '1'
intvolume: ' 22'
language:
- iso: eng
month: '01'
oa: 1
oa_version: Published Version
oaworkid: 1
page: 139-150
project:
- _id: 260C2330-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '754411'
name: ISTplus - Postdoctoral Fellowships
- _id: fc2ed2f7-9c52-11eb-aca3-c01059dda49c
call_identifier: H2020
grant_number: '101034413'
name: 'IST-BRIDGE: International postdoctoral program'
- _id: 917c023a-16d5-11f0-9cad-eb5cafc52090
name: Cytoplasmic self-organization into cell-like compartments as a common guiding
principle in early animal development
publication: Nature Physics
publication_identifier:
eissn:
- 1745-2481
issn:
- 1745-2473
issnl:
- ' 1745-2473'
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
related_material:
link:
- description: News on ISTA website
relation: research_data
url: https://ista.ac.at/en/news/geometry-shapes-life/
scopus_import: '1'
status: public
title: Geometry-driven asymmetric cell divisions pattern cell cycles and zygotic genome
activation in the zebrafish embryo
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: ba8df636-2132-11f1-aed0-ed93e2281fdd
volume: 22
year: '2026'
...
---
OA_place: repository
_id: '21137'
acknowledged_ssus:
- _id: Bio
- _id: EM-Fac
- _id: ScienComp
- _id: LifeSc
acknowledgement: We thank all members of the Heisenberg, Henkes, and Hannezo groups
for their support. We are also grateful to the Imaging and Optics, Scientific Computing,
Life Science Support, and Cryo-Electron Microscopy facilities at ISTA for their
technical assistance and support. Numerical simulations were performed using the
computational resources from Lorentz Institute and the Academic Leiden Interdisciplinary
Cluster Environment (ALICE) provided by Leiden University, and from PMMH provided
by Sorbonne Université. S.N has received funding from European Union’s Horizon 2020
research and innovation programme (grant agreement No. 665385). This work was supported
by the Austrian Science Fund (FWF) under projects PAT5044023 and W1250 awarded to
C.-P.H.
article_processing_charge: No
author:
- first_name: Suyash
full_name: Naik, Suyash
id: 2C0B105C-F248-11E8-B48F-1D18A9856A87
last_name: Naik
orcid: 0000-0001-8421-5508
citation:
ama: Naik S. Data associated with Keratins coordinate tissue spreading . 2026. doi:10.15479/AT-ISTA-21137
apa: Naik, S. (2026). Data associated with Keratins coordinate tissue spreading
. Institute of Science and Technology Austria. https://doi.org/10.15479/AT-ISTA-21137
chicago: Naik, Suyash. “Data Associated with Keratins Coordinate Tissue Spreading
.” Institute of Science and Technology Austria, 2026. https://doi.org/10.15479/AT-ISTA-21137.
ieee: S. Naik, “Data associated with Keratins coordinate tissue spreading .” Institute
of Science and Technology Austria, 2026.
ista: Naik S. 2026. Data associated with Keratins coordinate tissue spreading ,
Institute of Science and Technology Austria, 10.15479/AT-ISTA-21137.
mla: Naik, Suyash. Data Associated with Keratins Coordinate Tissue Spreading
. Institute of Science and Technology Austria, 2026, doi:10.15479/AT-ISTA-21137.
short: S. Naik, (2026).
contributor:
- contributor_type: researcher
first_name: Yann-Edwin
last_name: Keta
- contributor_type: supervisor
first_name: 'Silke '
last_name: Henkes
- contributor_type: supervisor
first_name: Carl-Philipp J
id: 39427864-F248-11E8-B48F-1D18A9856A87
last_name: Heisenberg
orcid: 0000-0002-0912-4566
- contributor_type: supervisor
first_name: Edouard B
id: 3A9DB764-F248-11E8-B48F-1D18A9856A87
last_name: Hannezo
orcid: 0000-0001-6005-1561
corr_author: '1'
date_created: 2026-02-04T16:38:02Z
date_published: 2026-03-24T00:00:00Z
date_updated: 2026-06-10T09:44:10Z
day: '24'
department:
- _id: GradSch
- _id: CaHe
- _id: EdHa
doi: 10.15479/AT-ISTA-21137
ec_funded: 1
file:
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checksum: 5d1fda7e410f24c311fcf6bcf725698f
content_type: application/zip
creator: snaik
date_created: 2026-03-16T11:51:10Z
date_updated: 2026-03-16T11:51:10Z
description: 'Python3 library written in C++20 to integrate vertex models. Please
read the readme at https://github.com/yketa/cells/blob/main/README.md for detailed
instructions for installation and usage of the code in this repository. '
file_id: '21461'
file_name: cells-main.zip
file_size: 725916
relation: main_file
title: Cell git repository
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checksum: ee350c8eaed99f3ca348c47c8b190d3c
content_type: application/x-zip-compressed
creator: snaik
date_created: 2026-03-18T14:52:02Z
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creator: snaik
date_created: 2026-03-18T15:01:32Z
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file_name: ReadMe.md
file_size: 2231
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creator: snaik
date_created: 2026-03-18T15:12:57Z
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date_created: 2026-03-21T03:37:43Z
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creator: snaik
date_created: 2026-03-24T07:21:43Z
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file_id: '21495'
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file_date_updated: 2026-03-24T07:21:43Z
fulldoi: https://doi.org/10.15479/AT-ISTA-21137
has_accepted_license: '1'
license: https://creativecommons.org/licenses/by-sa/4.0/
month: '3'
oa: 1
oa_version: Published Version
project:
- _id: 2564DBCA-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '665385'
name: International IST Doctoral Program
- _id: 8f060199-16d5-11f0-9cad-f3253b266c46
grant_number: PAT 5044023
name: Keratins in epithelial tissue spreading
- _id: 252C3B08-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: W1250-B20
name: Nano-Analytics of Cellular Systems
publisher: Institute of Science and Technology Austria
status: public
title: 'Data associated with Keratins coordinate tissue spreading '
tmp:
image: /images/cc_by_sa.png
legal_code_url: https://creativecommons.org/licenses/by-sa/4.0/legalcode
name: Creative Commons Attribution-ShareAlike 4.0 International Public License (CC
BY-SA 4.0)
short: CC BY-SA (4.0)
type: research_data
user_id: 68b8ca59-c5b3-11ee-8790-cd641c68093d
year: '2026'
...
---
OA_place: publisher
OA_type: hybrid
PlanS_conform: '1'
_id: '21485'
abstract:
- lang: eng
text: Insulating oxides are among the most abundant solid materials in the universe1,2,3.
Of the many ways in which they influence natural phenomena, perhaps the most consequential
is their capacity to transfer electrical charge during contact4,5,6,7,8,9,10—which
occurs even between samples of the same oxide—yet the symmetry-breaking parameter
that causes this remains unidentified11,12. Here we show that adventitious carbonaceous
molecules adsorbed from the environment are the symmetry-breaking factor in same-material
oxide contact electrification (CE). We use acoustic levitation to measure charge
exchange between a sphere and a plate composed of identical amorphous silicon
dioxide (SiO2). Although charging polarity is random for co-prepared samples,
we control it with baking or plasma treatment. Observing the charge-exchange relaxation
afterwards, we see dynamics over a timescale of hours and connect this directly
to the presence of adventitious carbon with time-of-flight mass spectrometry,
low-energy ion scattering and infrared spectroscopy. Going further, we confirm
that adventitious carbon can even determine charge exchange among different oxides.
Our results identify the symmetry-breaking parameter that causes insulating oxides
to exchange charge in settings ranging from desert sands4 to volcanic plumes5,6,
while simultaneously highlighting an overlooked factor in CE more broadly.
acknowledged_ssus:
- _id: M-Shop
- _id: NanoFab
- _id: ScienComp
- _id: LifeSc
acknowledgement: This project has received support from the European Research Council
(ERC) under the European Union’s Horizon 2020 research and innovation programme
(grant agreement no. 949120) and from the Marie Skłodowska-Curie programme (grant
agreement no. 754411). We acknowledge the state of Lower Austria and the European
Regional Development Fund under grant no. WST3-F-542638/004-2021. N.M. acknowledges
support from grant Fondecyt 1221597. G.G. is a Serra Húnter fellow. This research
was supported by the Scientific Service Units of the Institute of Science and Technology
Austria through resources provided by the Miba Machine Shop, Nanofabrication Facility,
Scientific Computing facility and Lab Support Facility. We thank the Modic group
for the use of the Laue camera, T. Zauner for the photography of the experimental
set-up and R. Möller for insightful discussions. Open access funding provided by
Institute of Science and Technology (IST Austria).
article_processing_charge: Yes (via OA deal)
article_type: original
author:
- first_name: Galien M
full_name: Grosjean, Galien M
id: 0C5FDA4A-9CF6-11E9-8939-FF05E6697425
last_name: Grosjean
orcid: 0000-0001-5154-417X
- first_name: Markus
full_name: Ostermann, Markus
last_name: Ostermann
- first_name: Markus
full_name: Sauer, Markus
last_name: Sauer
- first_name: Michael
full_name: Hahn, Michael
last_name: Hahn
- first_name: Christian M.
full_name: Pichler, Christian M.
last_name: Pichler
- first_name: Florian
full_name: Fahrnberger, Florian
last_name: Fahrnberger
- first_name: Felix
full_name: Pertl, Felix
id: 6313aec0-15b2-11ec-abd3-ed67d16139af
last_name: Pertl
orcid: 0000-0003-0463-5794
- first_name: Daniel
full_name: Balazs, Daniel
id: 302BADF6-85FC-11EA-9E3B-B9493DDC885E
last_name: Balazs
orcid: 0000-0001-7597-043X
- first_name: Mason M.
full_name: Link, Mason M.
last_name: Link
- first_name: Seong H.
full_name: Kim, Seong H.
last_name: Kim
- first_name: Devin L.
full_name: Schrader, Devin L.
last_name: Schrader
- first_name: Adriana
full_name: Blanco, Adriana
last_name: Blanco
- first_name: Francisco
full_name: Gracia, Francisco
last_name: Gracia
- first_name: Nicolás
full_name: Mujica, Nicolás
last_name: Mujica
- first_name: Scott R
full_name: Waitukaitis, Scott R
id: 3A1FFC16-F248-11E8-B48F-1D18A9856A87
last_name: Waitukaitis
orcid: 0000-0002-2299-3176
citation:
ama: Grosjean GM, Ostermann M, Sauer M, et al. Adventitious carbon breaks symmetry
in oxide contact electrification. Nature. 2026;651(8106):626-631. doi:10.1038/s41586-025-10088-w
apa: Grosjean, G. M., Ostermann, M., Sauer, M., Hahn, M., Pichler, C. M., Fahrnberger,
F., … Waitukaitis, S. R. (2026). Adventitious carbon breaks symmetry in oxide
contact electrification. Nature. Springer Nature. https://doi.org/10.1038/s41586-025-10088-w
chicago: Grosjean, Galien M, Markus Ostermann, Markus Sauer, Michael Hahn, Christian
M. Pichler, Florian Fahrnberger, Felix Pertl, et al. “Adventitious Carbon Breaks
Symmetry in Oxide Contact Electrification.” Nature. Springer Nature, 2026.
https://doi.org/10.1038/s41586-025-10088-w.
ieee: G. M. Grosjean et al., “Adventitious carbon breaks symmetry in oxide
contact electrification,” Nature, vol. 651, no. 8106. Springer Nature,
pp. 626–631, 2026.
ista: Grosjean GM, Ostermann M, Sauer M, Hahn M, Pichler CM, Fahrnberger F, Pertl
F, Balazs D, Link MM, Kim SH, Schrader DL, Blanco A, Gracia F, Mujica N, Waitukaitis
SR. 2026. Adventitious carbon breaks symmetry in oxide contact electrification.
Nature. 651(8106), 626–631.
mla: Grosjean, Galien M., et al. “Adventitious Carbon Breaks Symmetry in Oxide Contact
Electrification.” Nature, vol. 651, no. 8106, Springer Nature, 2026, pp.
626–31, doi:10.1038/s41586-025-10088-w.
short: G.M. Grosjean, M. Ostermann, M. Sauer, M. Hahn, C.M. Pichler, F. Fahrnberger,
F. Pertl, D. Balazs, M.M. Link, S.H. Kim, D.L. Schrader, A. Blanco, F. Gracia,
N. Mujica, S.R. Waitukaitis, Nature 651 (2026) 626–631.
corr_author: '1'
date_created: 2026-03-23T15:04:00Z
date_published: 2026-03-18T00:00:00Z
date_updated: 2026-04-28T12:06:01Z
day: '18'
ddc:
- '540'
department:
- _id: ScWa
- _id: GradSch
- _id: LifeSc
doi: 10.1038/s41586-025-10088-w
ec_funded: 1
external_id:
pmid:
- '41851325'
file:
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issue: '8106'
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oa_version: Published Version
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call_identifier: H2020
grant_number: '754411'
name: ISTplus - Postdoctoral Fellowships
publication: Nature
publication_identifier:
eissn:
- 1476-4687
issn:
- 0028-0836
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
related_material:
link:
- description: News on ISTA website
relation: press_release
url: https://ista.ac.at/en/news/colliding-dust-and-the-sparks-of-creation/
status: public
title: Adventitious carbon breaks symmetry in oxide contact electrification
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: ba8df636-2132-11f1-aed0-ed93e2281fdd
volume: 651
year: '2026'
...
---
OA_place: publisher
_id: '21918'
acknowledged_ssus:
- _id: ScienComp
acknowledgement: "At different stages of my PhD, my work was supported by several
grants: the\r\nDOC fellowship of the Austrian Academy of Sciences (26293, awarded
to me),\r\nthe FWF-SFB grant (PT1032F06504 n. F65, awarded to Jan Maas), and the
ERC\r\ngrant (PR1032ERC01 n. 716117, awarded to Jan Maas). I also appreciate the
help\r\nfrom the Scientific Computing unit for their advice on the cluster usage."
alternative_title:
- ISTA Thesis
article_processing_charge: No
author:
- first_name: Kseniia
full_name: Khudiakova, Kseniia
id: 4E6DC800-AE37-11E9-AC72-31CAE5697425
last_name: Khudiakova
orcid: 0000-0002-6246-1465
citation:
ama: Khudiakova K. How epistasis and purifying selection shape genetic diversity.
2026. doi:10.15479/AT-ISTA-21918
apa: Khudiakova, K. (2026). How epistasis and purifying selection shape genetic
diversity. Institute of Science and Technology Austria. https://doi.org/10.15479/AT-ISTA-21918
chicago: Khudiakova, Kseniia. “How Epistasis and Purifying Selection Shape Genetic
Diversity.” Institute of Science and Technology Austria, 2026. https://doi.org/10.15479/AT-ISTA-21918.
ieee: K. Khudiakova, “How epistasis and purifying selection shape genetic diversity,”
Institute of Science and Technology Austria, 2026.
ista: Khudiakova K. 2026. How epistasis and purifying selection shape genetic diversity.
Institute of Science and Technology Austria.
mla: Khudiakova, Kseniia. How Epistasis and Purifying Selection Shape Genetic
Diversity. Institute of Science and Technology Austria, 2026, doi:10.15479/AT-ISTA-21918.
short: K. Khudiakova, How Epistasis and Purifying Selection Shape Genetic Diversity,
Institute of Science and Technology Austria, 2026.
corr_author: '1'
date_created: 2026-05-27T06:26:08Z
date_published: 2026-06-07T00:00:00Z
date_updated: 2026-06-12T12:43:35Z
day: '07'
ddc:
- '576'
degree_awarded: PhD
department:
- _id: GradSch
- _id: NiBa
- _id: JaMa
doi: 10.15479/AT-ISTA-21918
ec_funded: 1
file:
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creator: kkhudiak
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file_size: 20549813
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date_created: 2026-06-09T12:28:51Z
date_updated: 2026-06-11T12:14:53Z
embargo: 2027-06-10
embargo_to: open_access
file_id: '21969'
file_name: 2026_Khudiakova_Ksenia_Thesis.pdf
file_size: 9387029
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file_date_updated: 2026-06-11T12:14:53Z
fulldoi: https://doi.org/10.15479/AT-ISTA-21918
has_accepted_license: '1'
language:
- iso: eng
month: '06'
oa_version: Published Version
page: '89'
project:
- _id: 256E75B8-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '716117'
name: Optimal Transport and Stochastic Dynamics
- _id: 34d33d68-11ca-11ed-8bc3-ec13763c0ca8
grant_number: '26293'
name: The impact of deleterious mutations on small populations
- _id: fc31cba2-9c52-11eb-aca3-ff467d239cd2
grant_number: F6504
name: Taming Complexity in Partial Differential Systems
publication_identifier:
issn:
- 2663-337X
publication_status: published
publisher: Institute of Science and Technology Austria
related_material:
record:
- id: '11447'
relation: part_of_dissertation
status: public
- id: '12513'
relation: part_of_dissertation
status: deleted
- id: '21967'
relation: part_of_dissertation
status: public
- id: '21968'
relation: part_of_dissertation
status: public
status: public
supervisor:
- first_name: Nicholas H
full_name: Barton, Nicholas H
id: 4880FE40-F248-11E8-B48F-1D18A9856A87
last_name: Barton
orcid: 0000-0002-8548-5240
- first_name: Jan
full_name: Maas, Jan
id: 4C5696CE-F248-11E8-B48F-1D18A9856A87
last_name: Maas
orcid: 0000-0002-0845-1338
title: How epistasis and purifying selection shape genetic diversity
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: dissertation
user_id: 8b945eb4-e2f2-11eb-945a-df72226e66a9
year: '2026'
...
---
DOAJ_listed: '1'
OA_place: publisher
OA_type: gold
PlanS_conform: '1'
_id: '22229'
abstract:
- lang: eng
text: Hippocampal CA3 pyramidal neurons (PNs) form the largest autoassociative network
in the mammalian brain. Whether CA3–CA3 recurrent connectivity is genetically
preconfigured or environmentally shaped during ongoing memory storage is currently
unknown. To address this question, we performed multicellular patch-clamp-based
circuit mapping of up to eight CA3 PNs in the mouse hippocampus at multiple postnatal
time points (P7–8, P18–25, and P45–50). Here, we show that the hippocampal CA3
network undergoes a developmental transformation from local, dense, and random
connectivity to a distributed, sparse, and structured configuration. Thus, sparse
and structured connectivity may emerge via experience-dependent mechanisms. In
parallel, the strength of single synapses is downregulated; single synaptic events
are sufficient to trigger postsynaptic spiking early in development, whereas spatial
summation of several inputs is required at later time points. Biologically inspired
models of memory storage by Hebbian synaptic plasticity and retrieval via pattern
completion suggest that developmental changes improve specific aspects of memory
storage and retrieval. Our results imply a developmental transformation of the
neuronal code and the memory functions in the hippocampal CA3 network.
acknowledged_ssus:
- _id: PreCl
- _id: Bio
- _id: M-Shop
- _id: ScienComp
acknowledgement: 'We thank Jose Guzman, Simon Hippenmeyer, and Tim Vogels for critically
reading the manuscript, Jozsef Csicsvari for useful discussions, Florian Marr for
technical assistance, and Eleftheria Kralli-Beller for manuscript editing. This
research was supported by the Scientific Services Units (SSUs) of ISTA: the preclinical
facility (PCF) provided housing and breeding of the animals, the imaging and optics
facility (IOF) offered technical training and state of the art equipment, the Miba
machine shop contributed to the construction and maintenance of multicellular recording
setups, and the scientific computing unit helped with the large-scale simulations.
The project received funding from the European Union’s Horizon 2020 research and
innovation programme (ERC Advanced Grants No 692692 GIANTSYN and 101199096 CA3-SYNGRAM
to P.J.; Marie Skłodowska-Curie Grant 754411 to V.V.B.; Marie Skłodowska-Curie Grant
101026635 to J.F.W.), the Fond zur Förderung der Wissenschaftlichen Forschung (P
36232-B, PAT4178023, and 10.55776/CoE16 to P.J.), and the Nomis Foundation (fellowship
to A.N.-O.). V.V.B. received funding from a CONACyT fellowship (289638).'
article_number: '5540'
article_processing_charge: Yes
article_type: original
author:
- first_name: Victor M
full_name: Vargas Barroso, Victor M
id: 2F55A9DE-F248-11E8-B48F-1D18A9856A87
last_name: Vargas Barroso
- first_name: Jake
full_name: Watson, Jake
id: 63836096-4690-11EA-BD4E-32803DDC885E
last_name: Watson
orcid: 0000-0002-8698-3823
- first_name: Andrea C
full_name: Navas Olivé, Andrea C
id: 739d26c9-52e8-11ee-8d72-f14d3893b4ce
last_name: Navas Olivé
orcid: 0000-0002-9280-8597
- first_name: Alois
full_name: Schlögl, Alois
id: 45BF87EE-F248-11E8-B48F-1D18A9856A87
last_name: Schlögl
orcid: 0000-0002-5621-8100
- first_name: Peter M
full_name: Jonas, Peter M
id: 353C1B58-F248-11E8-B48F-1D18A9856A87
last_name: Jonas
orcid: 0000-0001-5001-4804
citation:
ama: Vargas Barroso VM, Watson J, Navas Olivé AC, Schlögl A, Jonas PM. Developmental
emergence of sparse and structured synaptic connectivity in the hippocampal CA3
memory circuit. Nature Communications. 2026;17. doi:10.1038/s41467-026-71914-x
apa: Vargas Barroso, V. M., Watson, J., Navas Olivé, A. C., Schlögl, A., & Jonas,
P. M. (2026). Developmental emergence of sparse and structured synaptic connectivity
in the hippocampal CA3 memory circuit. Nature Communications. Springer
Nature. https://doi.org/10.1038/s41467-026-71914-x
chicago: Vargas Barroso, Victor M, Jake Watson, Andrea C Navas Olivé, Alois Schlögl,
and Peter M Jonas. “Developmental Emergence of Sparse and Structured Synaptic
Connectivity in the Hippocampal CA3 Memory Circuit.” Nature Communications.
Springer Nature, 2026. https://doi.org/10.1038/s41467-026-71914-x.
ieee: V. M. Vargas Barroso, J. Watson, A. C. Navas Olivé, A. Schlögl, and P. M.
Jonas, “Developmental emergence of sparse and structured synaptic connectivity
in the hippocampal CA3 memory circuit,” Nature Communications, vol. 17.
Springer Nature, 2026.
ista: Vargas Barroso VM, Watson J, Navas Olivé AC, Schlögl A, Jonas PM. 2026. Developmental
emergence of sparse and structured synaptic connectivity in the hippocampal CA3
memory circuit. Nature Communications. 17, 5540.
mla: Vargas Barroso, Victor M., et al. “Developmental Emergence of Sparse and Structured
Synaptic Connectivity in the Hippocampal CA3 Memory Circuit.” Nature Communications,
vol. 17, 5540, Springer Nature, 2026, doi:10.1038/s41467-026-71914-x.
short: V.M. Vargas Barroso, J. Watson, A.C. Navas Olivé, A. Schlögl, P.M. Jonas,
Nature Communications 17 (2026).
corr_author: '1'
das_tickbox: '1'
dataavailabilitystatement: Source data are provided with this paper. Additional original
data are available from the corresponding author upon request. Code is available
from https://doi.org/10.15479/AT-ISTA-21442 under the link https://research-explorer.ista.ac.at/download/21442/21443/ca3simu-vargas2026v1.tar.gz
date_created: 2026-06-30T13:05:52Z
date_published: 2026-06-23T00:00:00Z
date_updated: 2026-07-01T06:47:49Z
day: '23'
ddc:
- '570'
department:
- _id: PeJo
- _id: ScienComp
doi: 10.1038/s41467-026-71914-x
ec_funded: 1
external_id:
pmid:
- '42014695'
file:
- access_level: open_access
checksum: d0b0093493926985b4c268662ff4d556
content_type: application/pdf
creator: dernst
date_created: 2026-07-01T06:46:06Z
date_updated: 2026-07-01T06:46:06Z
file_id: '22231'
file_name: 2026_NatureComm_VargasBarroso.pdf
file_size: 18304997
relation: main_file
success: 1
file_date_updated: 2026-07-01T06:46:06Z
fulldoi: https://doi.org/10.1038/s41467-026-71914-x
has_accepted_license: '1'
intvolume: ' 17'
language:
- iso: eng
month: '06'
oa: 1
oa_version: Published Version
pmid: 1
project:
- _id: 25B7EB9E-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '692692'
name: Biophysics and circuit function of a giant cortical glutamatergic synapse
- _id: e62b56fe-ab3c-11f0-94c7-d181dd352b3b
grant_number: '101199096'
name: Synaptic mechanisms of engram storage and retrieval in CA3 hippocampal microcircuits
- _id: 260C2330-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '754411'
name: ISTplus - Postdoctoral Fellowships
- _id: fc2be41b-9c52-11eb-aca3-faa90aa144e9
call_identifier: H2020
grant_number: '101026635'
name: Synaptic computations of the hippocampal CA3 circuitry
- _id: bd88be38-d553-11ed-ba76-81d5a70a6ef5
grant_number: P36232
name: Mechanisms of GABA release in hippocampal circuits
- _id: 8d9195e9-16d5-11f0-9cad-d075be887a1e
grant_number: PAT 4178023
name: Synaptic networks of human brain
- _id: 26366136-B435-11E9-9278-68D0E5697425
name: Reglas de Conectividad funcional en el hipocampo
publication: Nature Communications
publication_identifier:
eissn:
- 2041-1723
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
related_material:
record:
- id: '21442'
relation: research_data
status: public
researchdata_availability: yes
scopus_import: '1'
status: public
supplementarymaterial: yes
title: Developmental emergence of sparse and structured synaptic connectivity in the
hippocampal CA3 memory circuit
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: 17
year: '2026'
...
---
OA_place: publisher
OA_type: hybrid
PlanS_conform: '1'
_id: '21161'
abstract:
- lang: eng
text: In many species, sex-biased expression is widespread and thought to contribute
to sexual dimorphism. While bulk RNA-sequencing has been instrumental in identifying
strongly sex-biased genes, it lacks resolution to assess variation across cell-types
and tissue compartments. Using single-nucleus expression data from the Fly Cell
Atlas, we investigate sex differences in adult Drosophila melanogaster. We find
that differences in cell-type composition between the sexes are not a major source
of sex-bias, as for the vast majority of genes, the degree of sex-bias is similar
regardless of whether sex differences in cell-type composition are controlled
for or not. Our analysis confirms a deficit of X-linked male-biased genes in the
body’s somatic tissues that is widespread across cell-types. We also find the
excess of X-linked female-biased genes to be associated with nervous system cells
in the head but with epithelial cells in the body’s somatic tissues, showing that
single-nucleus data crucially resolves sex-bias at the cell-type level. We investigate
dosage compensation (DC) across 15 tissues and 17 cell-types. We observe that
it varies throughout the body. Surprisingly, we observe a lack of DC in a cluster
of main cells within the male accessory glands. This result highlights the importance
of understanding context-dependent DC.
acknowledged_ssus:
- _id: ScienComp
- _id: Bio
acknowledgement: This work was partly funded by an Austrian Science Foundation FWF
ESPRIT fellowship (10.55776/ESP6331524) to C.B. We would like to thank the Vicoso
group for their invaluable input and discussions throughout this work. We thank
Filip Ruzicka for his insightful comments on the manuscript. All computational resources
were provided by the Scientific Computing Unit at ISTA. This research was also supported
through resources provided by the Imaging & Optics Facility (IOF) at ISTA.
article_number: '20252471'
article_processing_charge: Yes (via OA deal)
article_type: original
author:
- first_name: Carolina
full_name: De Castro Barbosa Rodrigues Barata, Carolina
id: 20565186-803f-11ed-ab7e-96a4ff7694ef
last_name: De Castro Barbosa Rodrigues Barata
orcid: 0000-0003-1945-2245
- first_name: Beatriz
full_name: Vicoso, Beatriz
id: 49E1C5C6-F248-11E8-B48F-1D18A9856A87
last_name: Vicoso
orcid: 0000-0002-4579-8306
citation:
ama: de Castro Barbosa Rodrigues Barata C, Vicoso B. Single-nucleus resolution of
sex-biased expression and dosage compensation in Drosophila melanogaster. Proceedings
of the Royal Society B Biological Sciences. 2026;293(2063). doi:10.1098/rspb.2025.2471
apa: de Castro Barbosa Rodrigues Barata, C., & Vicoso, B. (2026). Single-nucleus
resolution of sex-biased expression and dosage compensation in Drosophila melanogaster.
Proceedings of the Royal Society B Biological Sciences. Royal Society of
London. https://doi.org/10.1098/rspb.2025.2471
chicago: Castro Barbosa Rodrigues Barata, Carolina de, and Beatriz Vicoso. “Single-Nucleus
Resolution of Sex-Biased Expression and Dosage Compensation in Drosophila Melanogaster.”
Proceedings of the Royal Society B Biological Sciences. Royal Society of
London, 2026. https://doi.org/10.1098/rspb.2025.2471.
ieee: C. de Castro Barbosa Rodrigues Barata and B. Vicoso, “Single-nucleus resolution
of sex-biased expression and dosage compensation in Drosophila melanogaster,”
Proceedings of the Royal Society B Biological Sciences, vol. 293, no. 2063.
Royal Society of London, 2026.
ista: de Castro Barbosa Rodrigues Barata C, Vicoso B. 2026. Single-nucleus resolution
of sex-biased expression and dosage compensation in Drosophila melanogaster. Proceedings
of the Royal Society B Biological Sciences. 293(2063), 20252471.
mla: de Castro Barbosa Rodrigues Barata, Carolina, and Beatriz Vicoso. “Single-Nucleus
Resolution of Sex-Biased Expression and Dosage Compensation in Drosophila Melanogaster.”
Proceedings of the Royal Society B Biological Sciences, vol. 293, no. 2063,
20252471, Royal Society of London, 2026, doi:10.1098/rspb.2025.2471.
short: C. de Castro Barbosa Rodrigues Barata, B. Vicoso, Proceedings of the Royal
Society B Biological Sciences 293 (2026).
corr_author: '1'
das_tickbox: '1'
date_created: 2026-02-08T23:02:49Z
date_published: 2026-01-28T00:00:00Z
date_updated: 2026-07-08T09:17:41Z
day: '28'
ddc:
- '570'
department:
- _id: BeVi
doi: 10.1098/rspb.2025.2471
external_id:
pmid:
- '41592777'
file:
- access_level: open_access
checksum: d76afebca0a6f112df0146ae2d929f36
content_type: application/pdf
creator: dernst
date_created: 2026-02-16T09:26:02Z
date_updated: 2026-02-16T09:26:02Z
file_id: '21226'
file_name: 2026_RoyalSocPubProceedingsB_Barata.pdf
file_size: 2230841
relation: main_file
success: 1
file_date_updated: 2026-02-16T09:26:02Z
fulldoi: https://doi.org/10.1098/rspb.2025.2471
has_accepted_license: '1'
intvolume: ' 293'
issue: '2063'
language:
- iso: eng
month: '01'
oa: 1
oa_version: Published Version
pmid: 1
project:
- _id: 90ef7108-16d5-11f0-9cad-e6e116913473
grant_number: ESP 6331524
name: Does genetic drift set a limit on the adaptive evolution of sex-biased expression?
publication: Proceedings of the Royal Society B Biological Sciences
publication_identifier:
eissn:
- 1471-2954
publication_status: published
publisher: Royal Society of London
quality_controlled: '1'
scopus_import: '1'
status: public
title: Single-nucleus resolution of sex-biased expression and dosage compensation
in Drosophila melanogaster
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: 293
year: '2026'
...
---
DOAJ_listed: '1'
OA_place: publisher
OA_type: gold
PlanS_conform: '1'
_id: '22333'
abstract:
- lang: eng
text: RNA polymerase II (Pol II) must be assembled in the cytoplasm before it enters
the nucleus, where it transcribes protein-coding genes. Although transcription
by Pol II is intensively studied, how this central multi-subunit enzyme is made
and the role of dedicated assembly factors remains unclear. Here, we report the
integrative structural analysis of a native human Pol II from the cytoplasm captured
near the end of biogenesis. The complex contains Gdown1 and three biogenesis factors
– RPAP2 and the critical small GTPases GPN1 and GPN3. Cryo-EM analysis of the
complex reveals how Gdown1 and RPAP2 associate with Pol II and prevent the premature
association of transcription factors. Further biochemical and cryo-EM analysis
reveals how RPAP2 tethers GPN1–GPN3 to the complex and how the assembly of the
RPAP2–GPN1–GPN3 complex is controlled by GTP hydrolysis. The combined results
uncover a network of interactions that chaperone cytoplasmic Pol II to prevent
aberrant interactions, reveal a molecular switch regulating biogenesis factor
association, and suggest a general mechanism for the action of GPN-loop GTPase
family of enzymes.
acknowledged_ssus:
- _id: LifeSc
- _id: EM-Fac
- _id: ScienComp
- _id: PreCl
acknowledgement: We thank A. Salmazo for assistance with Pol II purification. We thank
staff at the Vienna BioCenter Core Facilities (VBCF) Proteomics facility for immunoprecipitation-mass
spectrometry analysis, and J.A. Stopp for assistance with IP-MS data visualization.
This research was further supported by the Scientific Service Units (SSUs) of ISTA
through resources provided by the Lab Support Facility (LSF), Electron Microscopy
Facility (EMF), Scientific Computing (SciComp), and the Preclinical Facility (PCF).
F.H. was funded by the Endowed Professorship of the Lower Austria Research Funding
Agency (GFF NÖ) and by the Austrian Research Promotion Agency (FFG) through the
COIN Establishment Grant n.o. 45624401.
article_processing_charge: Yes
article_type: original
author:
- first_name: Annamaria
full_name: Hlavata, Annamaria
id: 36062FEC-F248-11E8-B48F-1D18A9856A87
last_name: Hlavata
- first_name: Benjamin
full_name: Neuditschko, Benjamin
last_name: Neuditschko
- first_name: Ulla
full_name: Schellhaas, Ulla
last_name: Schellhaas
- first_name: Clemens
full_name: Plaschka, Clemens
last_name: Plaschka
- first_name: Franz
full_name: Herzog, Franz
last_name: Herzog
- first_name: Carrie A
full_name: Bernecky, Carrie A
id: 2CB9DFE2-F248-11E8-B48F-1D18A9856A87
last_name: Bernecky
orcid: 0000-0003-0893-7036
biorxivid: 1
citation:
ama: Hlavata A, Neuditschko B, Schellhaas U, Plaschka C, Herzog F, Bernecky C. Structure
of cytoplasmic RNA polymerase II. Nature Communications. 2026. doi:10.1038/s41467-026-75416-8
apa: Hlavata, A., Neuditschko, B., Schellhaas, U., Plaschka, C., Herzog, F., &
Bernecky, C. (2026). Structure of cytoplasmic RNA polymerase II. Nature Communications.
Springer Nature. https://doi.org/10.1038/s41467-026-75416-8
chicago: Hlavata, Annamaria, Benjamin Neuditschko, Ulla Schellhaas, Clemens Plaschka,
Franz Herzog, and Carrie Bernecky. “Structure of Cytoplasmic RNA Polymerase II.”
Nature Communications. Springer Nature, 2026. https://doi.org/10.1038/s41467-026-75416-8.
ieee: A. Hlavata, B. Neuditschko, U. Schellhaas, C. Plaschka, F. Herzog, and C.
Bernecky, “Structure of cytoplasmic RNA polymerase II,” Nature Communications.
Springer Nature, 2026.
ista: Hlavata A, Neuditschko B, Schellhaas U, Plaschka C, Herzog F, Bernecky C.
2026. Structure of cytoplasmic RNA polymerase II. Nature Communications.
mla: Hlavata, Annamaria, et al. “Structure of Cytoplasmic RNA Polymerase II.” Nature
Communications, Springer Nature, 2026, doi:10.1038/s41467-026-75416-8.
short: A. Hlavata, B. Neuditschko, U. Schellhaas, C. Plaschka, F. Herzog, C. Bernecky,
Nature Communications (2026).
corr_author: '1'
das_tickbox: '1'
dataavailabilitystatement: "The\r\nc ryo EM maps generated in this study were deposited
to the EM Data Bank under the\r\naccession codes: EMD 55583 [https://www.ebi.ac.uk/pdbe/entry/emdb/EMD
55583\r\n(Pol II Gdown1 RPAP2 composite map), EMD 55578\r\n[https://www.ebi.ac.uk/pdbe/entry/emdb/EMD
55578 Pol II Gdown1 RPAP2 Pol II core\r\nmap EMD 55579 [https://www.ebi.ac.uk/pdbe/entry/emdb/EMD
55579 Pol II\r\nGdown1 RPAP2 Pol II stalk map EMD 55580\r\n[https://www.ebi.ac.uk/pdbe/entry/emdb/EMD
55580 Pol II Gdown1 RPAP2 RPAP2\r\nmap EMD 55581 [https://www.ebi.ac.uk/pdbe/entry/emdb/EMD
55 581 Pol II\r\nGdown1 RPAP2 Gdown1 N terminus map EMD 55582\r\n[https://www.ebi.ac.uk/pdbe/entry/emdb/EMD
55582 Pol II Gdown1 RPAP2 Gdown1\r\nC terminus map and EMD 55585 [https://www.ebi.ac.uk/pdbe/entry/emdb/EMD\r\n55585
RPAP2 GPN1 GPN3 map Model coordi nates were deposited to the PDBe under\r\nthe accession
codes: 9T5H [http://doi.org/10.2210/pdb 9T5H / (Pol II Gdown1\r\nRPAP2 complex structure)
and 9T5J [http://doi.org/10.2210/pdb 9T5H / (GPN1\r\nGPN3 RPAP2 structure). Immunoprecipitation
mass spectrometry and crosslinking mass\r\nspectrometry proteomics data have been
deposited to the ProteomeXchange Consortium\r\nvia the PRIDE partner repository
with the dataset identifiers PXD071638\r\n[http://proteomecentral.proteomexchange.org/cgi/GetDataset?ID=PXD
071638 and\r\nP XD070852\r\n[http://proteomecentral.proteomexchange.org/cgi/GetDataset?ID=PXD
070852\r\nAlphaFold3 structure predictions have been deposited to the Zenodo repository\r\nhttps://doi.org/10.5281/zenodo.20687910
P reviously published model coordinates\r\nwere utilized and are available at the
PDB under the accession codes 8QEP\r\n[http://doi.org/10.2210/pdb 8QEP / 9BZ 0 [http://doi.org/10.2210/pdb
9BZ 0 /\r\nand 7B7U [http://doi.org/10.2210/pdb 7B7U / Source Data are provided
with this\r\npaper."
date_created: 2026-07-14T07:27:59Z
date_published: 2026-07-13T00:00:00Z
date_updated: 2026-07-16T11:29:31Z
day: '13'
ddc:
- '570'
department:
- _id: CaBe
doi: 10.1038/s41467-026-75416-8
external_id:
biorxivid:
- 10.64898/2025.12.10.692585
fulldoi: https://doi.org/10.1038/s41467-026-75416-8
has_accepted_license: '1'
language:
- iso: eng
main_file_link:
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url: https://doi.org/10.1038/s41467-026-75416-8
month: '07'
oa: 1
oa_version: Published Version
publication: Nature Communications
publication_identifier:
eissn:
- 2041-1723
publication_status: epub_ahead
publisher: Springer Nature
quality_controlled: '1'
researchdata_availability: yes
scopus_import: '1'
status: public
supplementarymaterial: yes
title: Structure of cytoplasmic RNA polymerase II
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: publisher
_id: '21021'
abstract:
- lang: eng
text: This thesis examines how geometry and topology intersect in the representation,
transformation, and analysis of complex shapes. It considers how continuous manifolds
relate to their discrete analogues, how topological structures evolve in persistence
vineyards, and how tools from topological data analysis can illuminate problems
in mathematical physics. Central to this exploration is the question of how structure,
both geometric and topological, persists or changes under approximation, sampling,
or deformation. The work develops new approaches to skeletal and grid-based representations
of surfaces, reveals the full expressive capacity of persistence vineyards, and
applies topological methods to the longstanding problem of equilibria in electrostatic
fields. These threads braid together into a broader understanding of how topology
and geometry inform one another across theory, computation, and application.
acknowledged_ssus:
- _id: M-Shop
- _id: ScienComp
acknowledgement: "The research presented in this thesis was funded by the DFG Collaborative
Research\r\nCenter TRR 109, ‘Discretization in Geometry and Dynamics’.\r\n"
alternative_title:
- ISTA Thesis
article_processing_charge: No
author:
- first_name: Christopher D
full_name: Fillmore, Christopher D
id: 35638A5C-AAC7-11E9-B0BF-5503E6697425
last_name: Fillmore
citation:
ama: Fillmore CD. Braiding geometry and topology to study shapes and data. 2026.
doi:10.15479/AT-ISTA-21021
apa: Fillmore, C. D. (2026). Braiding geometry and topology to study shapes and
data. Institute of Science and Technology Austria. https://doi.org/10.15479/AT-ISTA-21021
chicago: Fillmore, Christopher D. “Braiding Geometry and Topology to Study Shapes
and Data.” Institute of Science and Technology Austria, 2026. https://doi.org/10.15479/AT-ISTA-21021.
ieee: C. D. Fillmore, “Braiding geometry and topology to study shapes and data,”
Institute of Science and Technology Austria, 2026.
ista: Fillmore CD. 2026. Braiding geometry and topology to study shapes and data.
Institute of Science and Technology Austria.
mla: Fillmore, Christopher D. Braiding Geometry and Topology to Study Shapes
and Data. Institute of Science and Technology Austria, 2026, doi:10.15479/AT-ISTA-21021.
short: C.D. Fillmore, Braiding Geometry and Topology to Study Shapes and Data, Institute
of Science and Technology Austria, 2026.
corr_author: '1'
date_created: 2026-01-20T21:38:40Z
date_published: 2026-01-21T00:00:00Z
date_updated: 2026-07-22T06:33:54Z
day: '21'
ddc:
- '514'
- '516'
degree_awarded: PhD
department:
- _id: GradSch
- _id: HeEd
- _id: UlWa
doi: 10.15479/AT-ISTA-21021
file:
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date_created: 2026-01-26T19:46:20Z
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file_name: Thesis.zip
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language:
- iso: eng
month: '01'
oa: 1
oa_version: Published Version
page: '122'
publication_identifier:
issn:
- 2663-337X
publication_status: published
publisher: Institute of Science and Technology Austria
related_material:
record:
- id: '20260'
relation: part_of_dissertation
status: public
- id: '21051'
relation: part_of_dissertation
status: public
- id: '21050'
relation: part_of_dissertation
status: public
status: public
supervisor:
- first_name: Herbert
full_name: Edelsbrunner, Herbert
id: 3FB178DA-F248-11E8-B48F-1D18A9856A87
last_name: Edelsbrunner
orcid: 0000-0002-9823-6833
- first_name: Uli
full_name: Wagner, Uli
id: 36690CA2-F248-11E8-B48F-1D18A9856A87
last_name: Wagner
orcid: 0000-0002-1494-0568
title: Braiding geometry and topology to study shapes and data
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: dissertation
user_id: ba8df636-2132-11f1-aed0-ed93e2281fdd
year: '2026'
...
---
OA_place: publisher
OA_type: hybrid
PlanS_conform: '1'
_id: '20590'
abstract:
- lang: eng
text: 'Moist convection is a fundamental process occurring in the Earth''s atmosphere.
It plays a central role in the weather and climate of the Tropics, where, to first
order, the heating of the atmosphere by convection is in balance with the cooling
of the atmosphere by the emission of radiation to outer space. In this study,
we use a cloud-resolving model in radiative–convective equilibrium with an imposed
constant rate of radiative cooling and study the response of moist convection
to varying this rate of radiative cooling. In particular, we study two types of
simulation: varying air temperature (VAT) simulations, where the air temperature
is allowed to adjust to the imposed radiative cooling, and constant air temperature
(CAT) simulations, where the surface temperature is tuned to ensure that the atmospheric
temperature profile in the domain is constant. We recover the previously known
result that, in response to increasing radiative cooling, the area of convection
expands rapidly, while the intensity of convection does not change. We find that
this response is explained by the increased boundary-layer variability in simulations
with greater radiative cooling, which compensates for the decreasing temperature
by adding a larger initial velocity close to the cloud base. We also propose a
fundamental scaling of the non-dimensional cumulus mass flux in moist convection,
which is robust across models of different complexity. We aim to bridge the gap
between highly idealised prototypes of moist convection, such as the “Rainy–Bénard
convection” introduced by Vallis et al., and comprehensive cloud-resolving models.'
acknowledged_ssus:
- _id: ScienComp
acknowledgement: "The authors gratefully acknowledge discussions with Professor Robert
Plant (University of Reading, UK), Professor Steve Sherwood (University of New South
Wales, Australia), Professor Steve Tobias, Professor Douglas Parker, and Gregory
Dritschel (University of Leeds, UK). Discussions with colleagues at the Institute
of Science and Technology Austria played a large role in shaping this study. The
authors are particularly grateful for inputs and discussions from Dr. Jiawei Bao,
Dr. Alejandro Casallas, and Alzbeta Pechacova.\r\nThis project has received funding
from the European Union's Horizon 2020 research and innovation programme under the
Marie Sklodowska–Curie grant agreement No. 101034413. C. Muller gratefully acknowledges
funding from the European Research Council (ERC) under the European Union's Horizon
2020 research and innovation program (Project CLUSTER, Grant Agreement No. 805041).
This research was supported by the Scientific Service Units (SSU) of IST Austria
through resources provided by Scientific Computing (SciComp). Open Access funding
provided by Institute of Science and Technology Austria/KEMÖ."
article_number: e70044
article_processing_charge: Yes (via OA deal)
article_type: original
author:
- first_name: Lokahith N
full_name: Agasthya, Lokahith N
id: cd100965-0804-11ed-9c55-f4878ff4e877
last_name: Agasthya
- first_name: Caroline J
full_name: Muller, Caroline J
id: f978ccb0-3f7f-11eb-b193-b0e2bd13182b
last_name: Muller
orcid: 0000-0001-5836-5350
citation:
ama: 'Agasthya LN, Muller CJ. Moist convection and radiative cooling: Dynamical
response and scaling. Quarterly Journal of the Royal Meteorological Society.
2026;152(775). doi:10.1002/qj.70044'
apa: 'Agasthya, L. N., & Muller, C. J. (2026). Moist convection and radiative
cooling: Dynamical response and scaling. Quarterly Journal of the Royal Meteorological
Society. Wiley. https://doi.org/10.1002/qj.70044'
chicago: 'Agasthya, Lokahith N, and Caroline J Muller. “Moist Convection and Radiative
Cooling: Dynamical Response and Scaling.” Quarterly Journal of the Royal Meteorological
Society. Wiley, 2026. https://doi.org/10.1002/qj.70044.'
ieee: 'L. N. Agasthya and C. J. Muller, “Moist convection and radiative cooling:
Dynamical response and scaling,” Quarterly Journal of the Royal Meteorological
Society, vol. 152, no. 775. Wiley, 2026.'
ista: 'Agasthya LN, Muller CJ. 2026. Moist convection and radiative cooling: Dynamical
response and scaling. Quarterly Journal of the Royal Meteorological Society. 152(775),
e70044.'
mla: 'Agasthya, Lokahith N., and Caroline J. Muller. “Moist Convection and Radiative
Cooling: Dynamical Response and Scaling.” Quarterly Journal of the Royal Meteorological
Society, vol. 152, no. 775, e70044, Wiley, 2026, doi:10.1002/qj.70044.'
short: L.N. Agasthya, C.J. Muller, Quarterly Journal of the Royal Meteorological
Society 152 (2026).
corr_author: '1'
das_tickbox: '1'
dataavailabilitystatement: The data that support the findings of this study are available
from the corresponding author, L. Agasthya, upon reasonable request.
date_created: 2025-11-02T23:01:34Z
date_published: 2026-01-01T00:00:00Z
date_updated: 2026-07-23T12:11:25Z
day: '01'
ddc:
- '550'
department:
- _id: CaMu
doi: 10.1002/qj.70044
ec_funded: 1
external_id:
isi:
- '001595821400001'
file:
- access_level: open_access
checksum: 8dd4d4d3ad027a4d26cbe5b1d66371e9
content_type: application/pdf
creator: dernst
date_created: 2026-07-23T12:10:28Z
date_updated: 2026-07-23T12:10:28Z
file_id: '22398'
file_name: 2026_QuartJourRoyalMeteorobiolSoc_Agasthya.pdf
file_size: 2665988
relation: main_file
success: 1
file_date_updated: 2026-07-23T12:10:28Z
fulldoi: https://doi.org/10.1002/qj.70044
has_accepted_license: '1'
intvolume: ' 152'
isi: 1
issue: '775'
language:
- iso: eng
month: '01'
oa: 1
oa_version: Published Version
project:
- _id: fc2ed2f7-9c52-11eb-aca3-c01059dda49c
call_identifier: H2020
grant_number: '101034413'
name: 'IST-BRIDGE: International postdoctoral program'
- _id: 629205d8-2b32-11ec-9570-e1356ff73576
call_identifier: H2020
grant_number: '805041'
name: Organization of CLoUdS, and implications of Tropical cyclones and for the
Energetics of the tropics, in current and waRming climate
publication: Quarterly Journal of the Royal Meteorological Society
publication_identifier:
eissn:
- 1477-870X
issn:
- 0035-9009
publication_status: published
publisher: Wiley
quality_controlled: '1'
researchdata_availability: no
scopus_import: '1'
status: public
supplementarymaterial: yes
title: 'Moist convection and radiative cooling: Dynamical response and scaling'
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: 152
year: '2026'
...
---
DOAJ_listed: '1'
OA_place: publisher
OA_type: gold
_id: '21486'
abstract:
- lang: eng
text: Sex-chromosome systems are highly variable across animals, but how they transition
from one to another is not well understood. Diptera have undergone multiple sex-chromosome
turnovers and expansions while maintaining their general chromosomal content,
which makes them an ideal clade to study such transitions. We analyzed more than
100 dipteran whole-genome assemblies and identified 4 new lineages that underwent
sex-chromosome turnover (in addition to the 5 previously reported). We find that
the majority of turnovers happened in the group Schizophora, which tend to have
fewer genes on Muller element F (the chromosome homologous to the ancestral insect
X chromosome) than lower dipterans, a factor previously hypothesized to facilitate
turnover. Most derived X chromosomes have higher GC content than autosomes, consistent
with a high prevalence of male achiasmy in Diptera. In addition, an excess of
gene movement out of the X is detected for most of these new X chromosomes, and
many of these moved genes have high testis expression in Drosophila, suggesting
that out-of-X gene movement contributes to the long-term demasculinization of
X chromosomes.
acknowledged_ssus:
- _id: ScienComp
acknowledgement: This work was supported by a grant from the Austrian Science Fund
(FWF, grant number PAT 8748323) to B.V. We thank the Vicoso group for their feedback
on an early version of the manuscript. We are grateful to Kamil Jaron and Julia
Gries for helpful discussions and for sharing their unpublished work. Computational
resources and support were provided by the Scientific Computing Unit at ISTA.
article_number: qrag003
article_processing_charge: Yes
article_type: original
author:
- first_name: Lorena Alexandra
full_name: Layana Franco, Lorena Alexandra
id: 02814589-eb8f-11eb-b029-a70074f3f18f
last_name: Layana Franco
orcid: 0000-0002-1253-6297
- first_name: Melissa A
full_name: Toups, Melissa A
id: 4E099E4E-F248-11E8-B48F-1D18A9856A87
last_name: Toups
orcid: 0000-0002-9752-7380
- first_name: Beatriz
full_name: Vicoso, Beatriz
id: 49E1C5C6-F248-11E8-B48F-1D18A9856A87
last_name: Vicoso
orcid: 0000-0002-4579-8306
citation:
ama: Layana Franco LA, Toups MA, Vicoso B. Causes and consequences of sex-chromosome
turnovers in Diptera. Evolution Letters. 2026;10(3). doi:10.1093/evlett/qrag003
apa: Layana Franco, L. A., Toups, M. A., & Vicoso, B. (2026). Causes and consequences
of sex-chromosome turnovers in Diptera. Evolution Letters. Oxford University
Press. https://doi.org/10.1093/evlett/qrag003
chicago: Layana Franco, Lorena Alexandra, Melissa A Toups, and Beatriz Vicoso. “Causes
and Consequences of Sex-Chromosome Turnovers in Diptera.” Evolution Letters.
Oxford University Press, 2026. https://doi.org/10.1093/evlett/qrag003.
ieee: L. A. Layana Franco, M. A. Toups, and B. Vicoso, “Causes and consequences
of sex-chromosome turnovers in Diptera,” Evolution Letters, vol. 10, no.
3. Oxford University Press, 2026.
ista: Layana Franco LA, Toups MA, Vicoso B. 2026. Causes and consequences of sex-chromosome
turnovers in Diptera. Evolution Letters. 10(3), qrag003.
mla: Layana Franco, Lorena Alexandra, et al. “Causes and Consequences of Sex-Chromosome
Turnovers in Diptera.” Evolution Letters, vol. 10, no. 3, qrag003, Oxford
University Press, 2026, doi:10.1093/evlett/qrag003.
short: L.A. Layana Franco, M.A. Toups, B. Vicoso, Evolution Letters 10 (2026).
corr_author: '1'
dataavailabilitystatement: Scripts, Supplementary Datasets 1–7, and Tables S1, S2,
S5 and S6 are also available at https://doi.org/10.15479/AT-ISTA-21116. Pipelines
are available at https://git.ista.ac.at/llayanaf/transitions_diptera.
date_created: 2026-03-23T15:05:42Z
date_published: 2026-06-01T00:00:00Z
date_updated: 2026-07-27T12:00:11Z
day: '01'
ddc:
- '570'
department:
- _id: BeVi
- _id: GradSch
doi: 10.1093/evlett/qrag003
file:
- access_level: open_access
checksum: 7c929e78c369a5e6e064bcf263e955ad
content_type: application/pdf
creator: dernst
date_created: 2026-07-27T11:59:40Z
date_updated: 2026-07-27T11:59:40Z
file_id: '22426'
file_name: 2026_EvolutionLetters_Layana.pdf
file_size: 1895786
relation: main_file
success: 1
file_date_updated: 2026-07-27T11:59:40Z
fulldoi: https://doi.org/10.1093/evlett/qrag003
has_accepted_license: '1'
intvolume: ' 10'
issue: '3'
language:
- iso: eng
month: '06'
oa: 1
oa_version: Published Version
project:
- _id: 8ed82125-16d5-11f0-9cad-fbcae312235b
grant_number: PAT 8748323
name: Sex chromosomes in evolution and development
publication: Evolution Letters
publication_identifier:
eissn:
- 2056-3744
publication_status: published
publisher: Oxford University Press
quality_controlled: '1'
researchdata_availability: yes
status: public
supplementarymaterial: yes
title: Causes and consequences of sex-chromosome turnovers in Diptera
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: 10
year: '2026'
...
---
OA_place: repository
OA_type: green
_id: '21859'
abstract:
- lang: eng
text: As artificial neural networks, and specifically large language models, have
improved rapidly in capabilities and quality, they have increasingly been deployed
in real-world applications, from customer service to Google search, despite the
fact that they frequently make factually incorrect or undesirable statements.
This trend has inspired practical and academic interest in model editing, that
is, in adjusting the weights of the model to modify its likely outputs for queries
relating to a specific fact or set of facts. This may be done either to amend
a fact or set of facts, for instance, to fix a frequent error in the training
data, or to suppress a fact or set of facts entirely, for instance, in case of
dangerous knowledge. Multiple methods have been proposed to do such edits. However,
at the same time, it has been shown that such model editing can be brittle and
incomplete. Moreover the effectiveness of any model editing method necessarily
depends on the data on which the model is trained, and, therefore, a good understanding
of the interaction of the training data distribution and the way it is stored
in the network is necessary and helpful to reliably perform model editing. However,
working with large language models trained on real-world data does not allow us
to understand this relationship or fully measure the effects of model editing.
We therefore propose Behemoth, a fully synthetic data generation framework. To
demonstrate the practical insights from the framework, we explore model editing
in the context of simple tabular data, demonstrating surprising findings that,
in some cases, echo real-world results, for instance, that in some cases restricting
the update rank results in a more effective update.
acknowledged_ssus:
- _id: ScienComp
acknowledgement: "EI thanks Weiwei Yang, Janardhan Kulkani, and Kate Lytvynets for
their advice and support in\r\ndeveloping an earlier version of the Behemoth library.
This research was supported by the Scientific\r\nService Units (SSU) of IST Austria
through resources provided by Scientific Computing (SciComp).\r\nEI was supported
in part by the FWF DK VGSCO, grant agreement number W1260-N35.\r\n"
article_processing_charge: No
arxiv: 1
author:
- first_name: Eugenia B
full_name: Iofinova, Eugenia B
id: f9a17499-f6e0-11ea-865d-fdf9a3f77117
last_name: Iofinova
orcid: 0000-0002-7778-3221
- first_name: Dan-Adrian
full_name: Alistarh, Dan-Adrian
id: 4A899BFC-F248-11E8-B48F-1D18A9856A87
last_name: Alistarh
orcid: 0000-0003-3650-940X
citation:
ama: 'Iofinova EB, Alistarh D-A. Behemoth: Benchmarking unlearning in LLMs using
fully synthetic data. arXiv. doi:10.48550/arXiv.2601.23153'
apa: 'Iofinova, E. B., & Alistarh, D.-A. (n.d.). Behemoth: Benchmarking unlearning
in LLMs using fully synthetic data. arXiv. https://doi.org/10.48550/arXiv.2601.23153'
chicago: 'Iofinova, Eugenia B, and Dan-Adrian Alistarh. “Behemoth: Benchmarking
Unlearning in LLMs Using Fully Synthetic Data.” ArXiv, n.d. https://doi.org/10.48550/arXiv.2601.23153.'
ieee: 'E. B. Iofinova and D.-A. Alistarh, “Behemoth: Benchmarking unlearning in
LLMs using fully synthetic data,” arXiv. .'
ista: 'Iofinova EB, Alistarh D-A. Behemoth: Benchmarking unlearning in LLMs using
fully synthetic data. arXiv, 10.48550/arXiv.2601.23153.'
mla: 'Iofinova, Eugenia B., and Dan-Adrian Alistarh. “Behemoth: Benchmarking Unlearning
in LLMs Using Fully Synthetic Data.” ArXiv, doi:10.48550/arXiv.2601.23153.'
short: E.B. Iofinova, D.-A. Alistarh, ArXiv (n.d.).
corr_author: '1'
date_created: 2026-05-11T08:58:07Z
date_published: 2026-01-30T00:00:00Z
date_updated: 2026-07-27T12:50:03Z
day: '30'
department:
- _id: GradSch
- _id: DaAl
doi: 10.48550/arXiv.2601.23153
external_id:
arxiv:
- '2601.23153'
fulldoi: https://doi.org/10.48550/arXiv.2601.23153
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.48550/arXiv.2601.23153
month: '01'
oa: 1
oa_version: Preprint
project:
- _id: 9B9290DE-BA93-11EA-9121-9846C619BF3A
grant_number: W1260-N35
name: Vienna Graduate School on Computational Optimization
publication: arXiv
publication_status: draft
related_material:
record:
- id: '21854'
relation: dissertation_contains
status: public
status: public
title: 'Behemoth: Benchmarking unlearning in LLMs using fully synthetic data'
type: preprint
user_id: 8b945eb4-e2f2-11eb-945a-df72226e66a9
year: '2026'
...
---
OA_place: publisher
_id: '22258'
abstract:
- lang: eng
text: "Uncovering the genetic architecture of complex traits and pinpointing causal
molecular drivers require the ability to distinguish true signals from noise within
massive, high-dimensional omics datasets. To extract meaningful biological insights
from these datasets, such as identifying causal genetic variants and proteins,
scalable and accurate inference methods are essential. To this end, this thesis
develops novel Bayesian inference frameworks based on Vector Approximate Message
Passing and demonstrates their effectiveness in the modeling of disease onset
times and quantitative physical and clinical measures.\r\n\r\nFirst, we introduce
gVAMP, a Bayesian framework tailored for Genome-Wide Association Studies that
enables the joint modeling of quantitative complex traits across millions of genetic
variants. gVAMP demonstrates superior accuracy in variable selection and out-of-sample
polygenic risk prediction compared to state-of-the-art approaches. We model human
height using 17 million whole-genome sequence variants from the UK Biobank, incorporating
a vast number of rare variants and revealing novel associations. gVAMP achieves
a prediction accuracy of approximately 46% for human height, representing the
highest reported performance for this trait to date. \r\n\r\nSecond, we present
vampW, a Bayesian framework for survival analysis applied to proteomic data. By
effectively handling right-censoring and complex protein dependencies within the
UK Biobank Pharma Proteomics Project dataset, vampW identifies 219 protein associations
across 24 disease outcomes, the majority of which are not among the top marginal
discoveries. We further adjust protein levels for exponential age effects, yielding
1,308 associations and highlighting the sensitivity of the analysis to the chosen
age-correction methodology. Finally, vampW improves upon the variable selection
capabilities of the commonly used (penalized) variants of the Cox proportional
hazards model and delivers state-of-the-art out-of-sample prediction of disease
onset times.\r\n\r\nCollectively, these methods provide powerful tools for dissecting
the genetic architecture of complex traits and the proteomic drivers of disease
onset. Furthermore, by delivering accurate polygenic risk scores and precise predictions
of onset times, this work advances the capabilities of personalized medicine and
clinical risk stratification."
acknowledged_ssus:
- _id: ScienComp
acknowledgement: "This work was supported in part by the Swiss National Science Foundation
through the\r\nEccellenza Grant \"Improving estimation and prediction of common
complex disease risk\"\r\n(grant number PCEGP3_181181); the European Research Council
through the grant\r\n\"Inference in High Dimensions: Light-speed Algorithms and
Information Limits\" (grant\r\nnumber 101161364); and the Fondation Jean-Jacques
et Felicia Lopez-Loreta through the\r\nPrix Lopez-Loretta 2019.\r\n"
alternative_title:
- ISTA Thesis
article_processing_charge: No
author:
- first_name: Al
full_name: Depope, Al
id: 0b77531d-dbcd-11ea-9d1d-a8eee0bf3830
last_name: Depope
citation:
ama: 'Depope A. From sparse selection to risk prediction: Approximate message passing
for proteomic survival models and large-scale genomics. 2026. doi:10.15479/AT-ISTA-22258'
apa: 'Depope, A. (2026). From sparse selection to risk prediction: Approximate
message passing for proteomic survival models and large-scale genomics. Institute
of Science and Technology Austria. https://doi.org/10.15479/AT-ISTA-22258'
chicago: 'Depope, Al. “From Sparse Selection to Risk Prediction: Approximate Message
Passing for Proteomic Survival Models and Large-Scale Genomics.” Institute of
Science and Technology Austria, 2026. https://doi.org/10.15479/AT-ISTA-22258.'
ieee: 'A. Depope, “From sparse selection to risk prediction: Approximate message
passing for proteomic survival models and large-scale genomics,” Institute of
Science and Technology Austria, 2026.'
ista: 'Depope A. 2026. From sparse selection to risk prediction: Approximate message
passing for proteomic survival models and large-scale genomics. Institute of Science
and Technology Austria.'
mla: 'Depope, Al. From Sparse Selection to Risk Prediction: Approximate Message
Passing for Proteomic Survival Models and Large-Scale Genomics. Institute
of Science and Technology Austria, 2026, doi:10.15479/AT-ISTA-22258.'
short: 'A. Depope, From Sparse Selection to Risk Prediction: Approximate Message
Passing for Proteomic Survival Models and Large-Scale Genomics, Institute of Science
and Technology Austria, 2026.'
corr_author: '1'
das_tickbox: '1'
date_created: 2026-07-10T13:27:20Z
date_published: 2026-07-11T00:00:00Z
date_updated: 2026-07-28T07:08:15Z
day: '11'
ddc:
- '576'
- '610'
- '006'
degree_awarded: PhD
department:
- _id: GradSch
- _id: MaRo
- _id: MaMo
doi: 10.15479/AT-ISTA-22258
doi_confirm: '1'
file:
- access_level: open_access
checksum: 9ab386790515628d957a194f30a7ccb4
content_type: application/pdf
creator: adepope
date_created: 2026-07-13T14:52:19Z
date_updated: 2026-07-13T14:52:19Z
file_id: '22316'
file_name: 2026_Depope_Al_Thesis.pdf
file_size: 25109878
relation: main_file
- access_level: closed
checksum: 8ed8fb63f76a695d5b6fec35343f4b90
content_type: application/zip
creator: adepope
date_created: 2026-07-13T14:56:41Z
date_updated: 2026-07-13T14:56:41Z
file_id: '22317'
file_name: 2026_Depope_Al_Thesis.zip
file_size: 1203199939
relation: source_file
file_date_updated: 2026-07-13T14:56:41Z
fulldoi: https://doi.org/10.15479/AT-ISTA-22258
has_accepted_license: '1'
keyword:
- Approximate Message Passing
- GWAS
- Genomics
- Proteomics
- Survival modeling
language:
- iso: eng
month: '07'
oa: 1
oa_version: Published Version
page: '169'
project:
- _id: 059876FA-7A3F-11EA-A408-12923DDC885E
name: Prix Lopez-Loretta 2019 - Marco Mondelli
- _id: 911e6d1f-16d5-11f0-9cad-c5c68c6a1cdf
grant_number: '101161364'
name: 'Inference in High Dimensions: Light-speed Algorithms and Information Limits'
- _id: 9B8D11D6-BA93-11EA-9121-9846C619BF3A
grant_number: PCEGP3_181181
name: Improving estimation and prediction of common complex disease risk
publication_identifier:
issn:
- 2663-337X
publication_status: published
publisher: Institute of Science and Technology Austria
related_material:
record:
- id: '21488'
relation: part_of_dissertation
status: public
status: public
supervisor:
- first_name: Matthew Richard
full_name: Robinson, Matthew Richard
id: E5D42276-F5DA-11E9-8E24-6303E6697425
last_name: Robinson
orcid: 0000-0001-8982-8813
- first_name: Marco
full_name: Mondelli, Marco
id: 27EB676C-8706-11E9-9510-7717E6697425
last_name: Mondelli
orcid: 0000-0002-3242-7020
title: 'From sparse selection to risk prediction: Approximate message passing for
proteomic survival models and large-scale genomics'
type: dissertation
user_id: 8b945eb4-e2f2-11eb-945a-df72226e66a9
year: '2026'
...
---
OA_place: publisher
OA_type: gold
PlanS_conform: '1'
_id: '22608'
abstract:
- lang: eng
text: For tissues to spread, they must deform while staying intact. How spreading
tissues balance flexibility with integrity is not yet well understood. Here, we
show that keratin intermediate filaments adapt tissue mechanical resilience to
the stresses arising in epithelial tissues during spreading. By analyzing the
expansion of the enveloping cell layer (EVL) over the yolk cell in zebrafish embryos
in vivo, we find that keratin network maturation in EVL cells is promoted by stresses
building up within the spreading tissue. Through genetic interference and tissue
rheology experiments, complemented by a vertex model with mechanochemical feedback,
we demonstrate that stress-induced keratin network maturation in the EVL increases
tissue viscosity, to prevent tissue rupture. Further, keratins are required in
the yolk cell for mechanosensitive actomyosin network contraction and flow, the
forces pulling the EVL. These dual mechanosensitive functions of keratins enable
a balance between pulling force production and EVL mechanical resilience, ensuring
uniform and robust tissue spreading.
acknowledged_ssus:
- _id: Bio
- _id: ScienComp
- _id: LifeSc
- _id: EM-Fac
acknowledgement: We thank all members of the Heisenberg, Henkes, and Hannezo groups
for their support. We are also grateful to the Imaging and Optics, Scientific Computing,
Life Science Support, and Cryo-Electron Microscopy facilities at ISTA for their
technical assistance and support. Numerical simulations were performed using the
computational resources from Lorentz Institute and the Academic Leiden Interdisciplinary
Cluster Environment (ALICE) provided by Leiden University, and from PMMH provided
by Sorbonne Université. S.N has received funding from European Union’s Horizon 2020
research and innovation programme (grant agreement No. 665385). This work was supported
by the Austrian Science Fund (FWF) under projects PAT5044023 and W1250 awarded to
C.-P.H.
article_number: '6499'
article_processing_charge: Yes
article_type: original
author:
- first_name: Suyash
full_name: Naik, Suyash
id: 2C0B105C-F248-11E8-B48F-1D18A9856A87
last_name: Naik
orcid: 0000-0001-8421-5508
- first_name: Yann-Edwin
full_name: Keta, Yann-Edwin
last_name: Keta
- first_name: Kornelija
full_name: Pranjic-Ferscha, Kornelija
id: 4362B3C2-F248-11E8-B48F-1D18A9856A87
last_name: Pranjic-Ferscha
- first_name: Edouard B
full_name: Hannezo, Edouard B
id: 3A9DB764-F248-11E8-B48F-1D18A9856A87
last_name: Hannezo
orcid: 0000-0001-6005-1561
- first_name: Silke
full_name: Henkes, Silke
last_name: Henkes
- first_name: Carl-Philipp J
full_name: Heisenberg, Carl-Philipp J
id: 39427864-F248-11E8-B48F-1D18A9856A87
last_name: Heisenberg
orcid: 0000-0002-0912-4566
citation:
ama: Naik S, Keta Y-E, Pranjic-Ferscha K, Hannezo EB, Henkes S, Heisenberg C-PJ.
Keratins coordinate tissue spreading by balancing spreading forces with tissue
material properties. Nature Communications. 2026;17. doi:10.1038/s41467-026-72366-z
apa: Naik, S., Keta, Y.-E., Pranjic-Ferscha, K., Hannezo, E. B., Henkes, S., &
Heisenberg, C.-P. J. (2026). Keratins coordinate tissue spreading by balancing
spreading forces with tissue material properties. Nature Communications.
Springer Nature. https://doi.org/10.1038/s41467-026-72366-z
chicago: Naik, Suyash, Yann-Edwin Keta, Kornelija Pranjic-Ferscha, Edouard B Hannezo,
Silke Henkes, and Carl-Philipp J Heisenberg. “Keratins Coordinate Tissue Spreading
by Balancing Spreading Forces with Tissue Material Properties.” Nature Communications.
Springer Nature, 2026. https://doi.org/10.1038/s41467-026-72366-z.
ieee: S. Naik, Y.-E. Keta, K. Pranjic-Ferscha, E. B. Hannezo, S. Henkes, and C.-P.
J. Heisenberg, “Keratins coordinate tissue spreading by balancing spreading forces
with tissue material properties,” Nature Communications, vol. 17. Springer
Nature, 2026.
ista: Naik S, Keta Y-E, Pranjic-Ferscha K, Hannezo EB, Henkes S, Heisenberg C-PJ.
2026. Keratins coordinate tissue spreading by balancing spreading forces with
tissue material properties. Nature Communications. 17, 6499.
mla: Naik, Suyash, et al. “Keratins Coordinate Tissue Spreading by Balancing Spreading
Forces with Tissue Material Properties.” Nature Communications, vol. 17,
6499, Springer Nature, 2026, doi:10.1038/s41467-026-72366-z.
short: S. Naik, Y.-E. Keta, K. Pranjic-Ferscha, E.B. Hannezo, S. Henkes, C.-P.J.
Heisenberg, Nature Communications 17 (2026).
corr_author: '1'
das_tickbox: '1'
dataavailabilitystatement: "The authors declare that the minimum dataset that is necessary
to\r\ninterpret, verify, and extend the research in this article is included in\r\nthe
supplementary information, the source data, and the archived data\r\nrepository
(https://doi.org/10.15479/AT-ISTA-21137). This is also available\r\non GitHub at
https://github.com/Suyash-Naik/2026-\r\nKeratinepithlialspreadingcoordinate-Data.
Source data are provided\r\nwith this paper. The framework to develop the vertex
models used in this paper are\r\navailable online on GitHub and archived in the
source data provided.\r\nCustom scripts used for analysis of imaging and simulation
data are\r\nprovided along with data files for all panels in the source data for
this\r\nmanuscript on GitHub and in data repo (https://doi.org/10.15479/ATISTA-\r\n21137).
Framework for the vertex model is available at https://\r\ngithub.com/yketta/cells.
Code for analysis is available on GitHub\r\nhttps://github.com/Suyash-Naik/2026-\r\nKeratinepithlialspreadingcoordinate-Data."
date_created: 2026-07-29T09:10:35Z
date_published: 2026-07-17T00:00:00Z
date_updated: 2026-07-29T10:33:31Z
day: '17'
ddc:
- '570'
department:
- _id: Bio
- _id: CaHe
- _id: EdHa
doi: 10.1038/s41467-026-72366-z
external_id:
pmid:
- '42143048'
file:
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content_type: application/pdf
creator: dernst
date_created: 2026-07-29T10:27:25Z
date_updated: 2026-07-29T10:27:25Z
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file_size: 15363936
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success: 1
file_date_updated: 2026-07-29T10:27:25Z
fulldoi: https://doi.org/10.1038/s41467-026-72366-z
has_accepted_license: '1'
intvolume: ' 17'
language:
- iso: eng
month: '07'
oa: 1
oa_version: Published Version
pmid: 1
project:
- _id: 8f060199-16d5-11f0-9cad-f3253b266c46
grant_number: PAT 5044023
name: Keratins in epithelial tissue spreading
- _id: 252C3B08-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: W1250-B20
name: Nano-Analytics of Cellular Systems
publication: Nature Communications
publication_identifier:
eissn:
- 2041-1723
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
related_material:
record:
- id: '20465'
relation: earlier_version
status: public
researchdata_availability: yes
scopus_import: '1'
status: public
supplementarymaterial: yes
title: Keratins coordinate tissue spreading by balancing spreading forces with tissue
material properties
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: 17
year: '2026'
...
---
OA_place: publisher
OA_type: gold
_id: '21923'
abstract:
- lang: eng
text: "The appearance of simulated natural phenomena heavily depends on the way
surfaces are textured. However, applying texture maps to dynamic deformable surfaces
presents a significant challenge, due to ever-shifting differences in length scales
involved. When these surfaces move and advect the texture along with them, their
final appearance degrades as deformed regions dramatically distort their texture
map. Modifications to the texture directly at the pixel level in response to the
deformation may introduce ghosting artifacts and look unnatural. In the real world,
the appearance of surface details on a deforming material changes through the
interplay of physical processes such as rupturing, exposure of internal structure,
or wrinkling. Motivated by these behaviors, in this work we explore how physical
principles can guide the texturing methods based on the measure of surface deformation.\r\nWe
present two novel wave-based procedural texturing algorithms which reproduce common
physical properties like advection and self-similarity, enabling the plausible
animation of deforming objects with extreme texture map distortions. Our algorithms
are fully procedural, require no actual physics simulation, and store no state
or history of deformation besides the input UV map, making them highly parallelizable
on the GPU and efficient enough for real-time applications. We show the versatility
of the method by animating physical phenomena with extreme deformations such as
flowing lava, stretching putty and outpouring sludge."
acknowledged_ssus:
- _id: ScienComp
acknowledgement: "We thank the anonymous reviewers for their helpful comments, the
members of the Visual Computing Group at ISTA for their feedback. We also thank
Jonathan Gagnon for their help with running the Lapped Textures codes and SideFX
for the Houdini Education software licenses.\r\nImages in Fig. 2 by Kisoulou and
Vultured on Unsplash, Michal Jarmoluk and Public Domain Pictures from Pixabay and
Hawai‘i Volcanoes NPS on flickr. This research was supported by the Scientific Service
Units (SSU) of ISTA through resources provided by Scientific Computing and was funded
in part by the European Union (ERC-2021-COG 101045083 CoDiNA)."
article_number: '154'
article_processing_charge: Yes
article_type: original
author:
- first_name: Aleksei
full_name: Kalinov, Aleksei
id: 44b7120e-eb97-11eb-a6c2-e1557aa81d02
last_name: Kalinov
orcid: 0000-0003-2189-3904
- first_name: Mickaël
full_name: Ly, Mickaël
id: 6340d7f0-b48d-11eb-b10d-b7487e71d9f1
last_name: Ly
- first_name: Christian
full_name: Hafner, Christian
id: 400429CC-F248-11E8-B48F-1D18A9856A87
last_name: Hafner
- first_name: Christopher J
full_name: Wojtan, Christopher J
id: 3C61F1D2-F248-11E8-B48F-1D18A9856A87
last_name: Wojtan
orcid: 0000-0001-6646-5546
citation:
ama: Kalinov A, Ly M, Hafner C, Wojtan C. Physics-inspired procedural texturing
of extremely deformable surfaces. ACM Transactions on Graphics. 2026;45(4).
doi:10.1145/3811353
apa: 'Kalinov, A., Ly, M., Hafner, C., & Wojtan, C. (2026). Physics-inspired
procedural texturing of extremely deformable surfaces. ACM Transactions on
Graphics. Los Angeles, CA, United States: Association for Computing Machinery.
https://doi.org/10.1145/3811353'
chicago: Kalinov, Aleksei, Mickaël Ly, Christian Hafner, and Chris Wojtan. “Physics-Inspired
Procedural Texturing of Extremely Deformable Surfaces.” ACM Transactions on
Graphics. Association for Computing Machinery, 2026. https://doi.org/10.1145/3811353.
ieee: A. Kalinov, M. Ly, C. Hafner, and C. Wojtan, “Physics-inspired procedural
texturing of extremely deformable surfaces,” ACM Transactions on Graphics,
vol. 45, no. 4. Association for Computing Machinery, 2026.
ista: Kalinov A, Ly M, Hafner C, Wojtan C. 2026. Physics-inspired procedural texturing
of extremely deformable surfaces. ACM Transactions on Graphics. 45(4), 154.
mla: Kalinov, Aleksei, et al. “Physics-Inspired Procedural Texturing of Extremely
Deformable Surfaces.” ACM Transactions on Graphics, vol. 45, no. 4, 154,
Association for Computing Machinery, 2026, doi:10.1145/3811353.
short: A. Kalinov, M. Ly, C. Hafner, C. Wojtan, ACM Transactions on Graphics 45
(2026).
conference:
end_date: 2026-07-23
location: Los Angeles, CA, United States
name: 'SIGGRAPH: International Conference and Exhibition on Computer Graphics and
Interactive Techniques'
start_date: 2026-07-19
corr_author: '1'
das_tickbox: '0'
date_created: 2026-05-29T13:25:16Z
date_published: 2026-07-01T00:00:00Z
date_updated: 2026-08-04T09:07:44Z
day: '01'
ddc:
- '006'
department:
- _id: GradSch
- _id: ChWo
doi: 10.1145/3811353
file:
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checksum: ea165bf731ddd3045f83878dcb833672
content_type: video/mp4
creator: akalinov
date_created: 2026-05-29T13:19:33Z
date_updated: 2026-05-29T13:19:33Z
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file_size: 77337231
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success: 1
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content_type: video/mp4
creator: akalinov
date_created: 2026-05-29T13:19:37Z
date_updated: 2026-05-29T13:19:37Z
file_id: '21925'
file_name: tog454-article154-video.mp4
file_size: 226633977
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success: 1
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creator: akalinov
date_created: 2026-05-29T13:19:33Z
date_updated: 2026-05-29T13:19:33Z
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fulldoi: https://doi.org/10.1145/3811353
has_accepted_license: '1'
intvolume: ' 45'
issue: '4'
keyword:
- Procedural animation
language:
- iso: eng
month: '07'
oa: 1
oa_version: Published Version
project:
- _id: 34bc2376-11ca-11ed-8bc3-9a3b3961a088
grant_number: '101045083'
name: Computational Discovery of Numerical Algorithms for Animation and Simulation
of Natural Phenomena
publication: ACM Transactions on Graphics
publication_identifier:
issn:
- 0730-0301
publication_status: published
publisher: Association for Computing Machinery
quality_controlled: '1'
related_material:
link:
- description: News on ISTA website
relation: press_release
url: https://ista.ac.at/en/news/infinite-deformation-and-shape-computation/
researchdata_availability: no
scopus_import: '1'
status: public
supplementarymaterial: yes
title: Physics-inspired procedural texturing of extremely deformable surfaces
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: ba8df636-2132-11f1-aed0-ed93e2281fdd
volume: 45
year: '2026'
...
---
DOAJ_listed: '1'
OA_place: publisher
OA_type: gold
_id: '21987'
abstract:
- lang: eng
text: 'We introduce JODIE, a genetic joint modeling approach that estimates how
DNA loci influence human traits by partitioning genetic effects into four components:
direct effects (from a child’s alleles), indirect maternal and paternal effects
(from parents’ alleles), and parent-of-origin (PofO) effects (dependent on parental
transmission of alleles), while uniquely accounting for assortative mating. We
analyze 30,000 child-mother-father trios from the Estonian Biobank and the Norwegian
Mother, Father, and Child Cohort, focusing on height, body mass index, and childhood
educational test scores. We find direct effects to be the largest contributor
to trait variation, but combined, indirect parental and PofO effects are similarly
substantial. We support our results by within-family genome-wide association testing
and identify 276 independently associated DNA regions with a complex interplay
between direct, indirect, and PofO effects. By joint modeling, we show that direct,
indirect, and PofO effects collectively shape human phenotypic variation across
loci genome-wide.'
acknowledged_ssus:
- _id: ScienComp
acknowledgement: "We thank Zoltan Kutalik, Peter Visscher, and members of the Robinson
group at ISTA for their comments, which improved this manuscript. This work was
funded by an SNSF Eccellenza Grant to M.R.R. (PCEGP3-181181) and by core funding
from the Institute of Science and Technology Austria.\r\nThe Norwegian Mother, Father,
and Child Cohort Study is supported by the Norwegian Ministry of Health and Care
Services and the Ministry of Education and Research. We are grateful to all the
participating families in Norway who take part in this on-going cohort study. We
thank the Norwegian Institute of Public Health (NIPH) for generating high-quality
genomic data. The research is part of the HARVEST collaboration, supported by the
Research Council of Norway (#229624). We also thank the NORMENT Center for providing
genotype data, funded by the Research Council of Norway (#223273), South East Norway
Health Authorities, and Stiftelsen Kristian Gerhard Jebsen, and in collaboration
with deCODE Genetics. We further thank the Center for Diabetes Research, the University
of Bergen for providing genotype data funded by the ERC AdG project SELECTionPREDISPOSED,
Stiftelsen Kristian Gerhard Jebsen, Trond Mohn Foundation, the Research Council
of Norway, the Novo Nordisk Foundation, the University of Bergen, and the Western
Norway Health Authorities. The MoBa work was performed on the TSD (Tjeneste for
Sensitive Data) facilities, owned by the University of Oslo, operated and developed
by the TSD service group at the University of Oslo, IT Department (USIT, tsd-drift@usit.uio.no).
E.Y. is supported by the European Union (grant numbers 101045526 and 101073237)
and the Research Council of Norway (grant numbers 336078, 288083, and 331640).\r\nWe
would like to acknowledge the participants and investigators of the Generation Scotland
Cohort study. Generation Scotland received core support from the Chief Scientist
Office of the Scottish Government Health Directorates (CZD/16/6) and the Scottish
Funding Council (HR03006). Genotyping and methylation typing of the GS:SFHS samples
was carried out by the Genetics Core Laboratory at the Wellcome Trust Clinical Research
Facility, Edinburgh, Scotland and was funded by the Medical Research Council UK
and the Wellcome Trust (Wellcome Trust Strategic Award “STratifying Resilience and
Depression Longitudinally” [STRADL] ref. 104036/Z/14/Z).\r\nWe would like to thank
and acknowledge the participants and investigators of the Estonian Biobank (EstBB)
study. The research was conducted using the Estonian Center of Genomics/Roadmap
II funded by the Estonian Research Council (project number TT17).\r\nNorwegian analyses
were performed on resources provided by Sigma2 - the National Infrastructure for
High-Performance Computing and Data Storage in Norway. Estonian Data analysis was
carried out in the High-Performance Computing Center cloud provided by University
of Tartu. Analysis of the Generation Scotland data and the summary statistics obtained
from the other analyses was conducted at IST Austria and is supported by the Scientific
Service Units (SSU) of IST Austria through resources provided by Scientific Computing
(SciComp)."
article_number: '101277'
article_processing_charge: Yes
article_type: original
author:
- first_name: Ilse
full_name: Krätschmer, Ilse
id: 30d4014e-7753-11eb-b44b-db6d61112e73
last_name: Krätschmer
orcid: 0000-0002-5636-9259
- first_name: Laura
full_name: Hegemann, Laura
last_name: Hegemann
- first_name: Robin J.
full_name: Hofmeister, Robin J.
last_name: Hofmeister
- first_name: Elizabeth C.
full_name: Corfield, Elizabeth C.
last_name: Corfield
- first_name: Mahdi
full_name: Mahmoudi, Mahdi
last_name: Mahmoudi
- first_name: Olivier
full_name: Delaneau, Olivier
last_name: Delaneau
- first_name: Ole A.
full_name: Andreassen, Ole A.
last_name: Andreassen
- first_name: Archie
full_name: Campbell, Archie
last_name: Campbell
- first_name: Caroline
full_name: Hayward, Caroline
last_name: Hayward
- first_name: Riccardo E.
full_name: Marioni, Riccardo E.
last_name: Marioni
- first_name: Eivind
full_name: Ystrom, Eivind
last_name: Ystrom
- first_name: Alexandra
full_name: Havdahl, Alexandra
last_name: Havdahl
- first_name: Matthew Richard
full_name: Robinson, Matthew Richard
id: E5D42276-F5DA-11E9-8E24-6303E6697425
last_name: Robinson
orcid: 0000-0001-8982-8813
citation:
ama: Krätschmer I, Hegemann L, Hofmeister RJ, et al. Separating direct, indirect,
and parent-of-origin genetic effects in the human population. Cell Genomics.
2026;6(7). doi:10.1016/j.xgen.2026.101277
apa: Krätschmer, I., Hegemann, L., Hofmeister, R. J., Corfield, E. C., Mahmoudi,
M., Delaneau, O., … Robinson, M. R. (2026). Separating direct, indirect, and parent-of-origin
genetic effects in the human population. Cell Genomics. Elsevier. https://doi.org/10.1016/j.xgen.2026.101277
chicago: Krätschmer, Ilse, Laura Hegemann, Robin J. Hofmeister, Elizabeth C. Corfield,
Mahdi Mahmoudi, Olivier Delaneau, Ole A. Andreassen, et al. “Separating Direct,
Indirect, and Parent-of-Origin Genetic Effects in the Human Population.” Cell
Genomics. Elsevier, 2026. https://doi.org/10.1016/j.xgen.2026.101277.
ieee: I. Krätschmer et al., “Separating direct, indirect, and parent-of-origin
genetic effects in the human population,” Cell Genomics, vol. 6, no. 7.
Elsevier, 2026.
ista: Krätschmer I, Hegemann L, Hofmeister RJ, Corfield EC, Mahmoudi M, Delaneau
O, Andreassen OA, Campbell A, Hayward C, Marioni RE, Ystrom E, Havdahl A, Robinson
MR. 2026. Separating direct, indirect, and parent-of-origin genetic effects in
the human population. Cell Genomics. 6(7), 101277.
mla: Krätschmer, Ilse, et al. “Separating Direct, Indirect, and Parent-of-Origin
Genetic Effects in the Human Population.” Cell Genomics, vol. 6, no. 7,
101277, Elsevier, 2026, doi:10.1016/j.xgen.2026.101277.
short: I. Krätschmer, L. Hegemann, R.J. Hofmeister, E.C. Corfield, M. Mahmoudi,
O. Delaneau, O.A. Andreassen, A. Campbell, C. Hayward, R.E. Marioni, E. Ystrom,
A. Havdahl, M.R. Robinson, Cell Genomics 6 (2026).
corr_author: '1'
das_tickbox: '1'
dataavailabilitystatement: "Information on how to access the MoBaPsychGen post-imputation
QC data are available here: https://www.fhi.no/en/me/the-psychgen-centre-for-genetic-epidemiology-and-mental-health/access-to-genetic-data-after-quality-control-by-the-mobapsychgen-pipeline-v/.\r\nEstonian
Biobank data (https://genomics.ut.ee/en/content/estonian-biobank) were used in this
project. For access to be granted to the Estonian Biobank genotypic and corresponding
phenotypic data, a preliminary application must be presented to the oversight committee,
who must first approve the project. Ethics permission must then be obtained from
the Estonian Committee on Bioethics and Human Research. Finally, a full project
must be submitted and approved by the Estonian Biobank.\r\nAccess to the Generation
Scotland data is available with appropriate permission from the Generation Scotland
Access Committee. Applications should be made to access@generationscotland.org (https://genscot.ed.ac.uk/).\r\nThe
code for JODIE developed in this work is open source and is publicly available on
zenodo (https://doi.org/10.5281/zenodo.19593928) and GitHub (https://github.com/medical-genomics-group/JODIE).\r\nHaplotype
Reference Consortium Release 1.1 data (https://ega-archive.org/datasets/EGAD00001002729)
are available by application to a Data Access Committee (DAC) of the Wellcome Trust
Sanger Institute.\r\nThe Common Metabolic Diseases Atlas can be accessed here: https://cmdga.org."
date_created: 2026-06-10T07:39:08Z
date_published: 2026-07-08T00:00:00Z
date_updated: 2026-08-04T09:34:08Z
day: '08'
ddc:
- '570'
department:
- _id: MaRo
doi: 10.1016/j.xgen.2026.101277
external_id:
pmid:
- '40909755'
file:
- access_level: open_access
checksum: f896b510480d2d4e4a7fd46c2e2761f4
content_type: application/pdf
creator: dernst
date_created: 2026-07-28T07:24:50Z
date_updated: 2026-07-28T07:24:50Z
file_id: '22597'
file_name: 2026_CellGenomics_Kraetschmer.pdf
file_size: 3679297
relation: main_file
success: 1
file_date_updated: 2026-07-28T07:24:50Z
fulldoi: https://doi.org/10.1016/j.xgen.2026.101277
has_accepted_license: '1'
intvolume: ' 6'
issue: '7'
keyword:
- direct genetic effects
- DGE
- indirect genetic effects
- IGE
- parent-of-origin effects
- phenotypic variation
- assortative mating
- within-family GWAS
- MoBa
- EstBB
language:
- iso: eng
month: '07'
oa: 1
oa_version: Published Version
pmid: 1
project:
- _id: 9B8D11D6-BA93-11EA-9121-9846C619BF3A
grant_number: PCEGP3_181181
name: Improving estimation and prediction of common complex disease risk
publication: Cell Genomics
publication_identifier:
eissn:
- 2666-979X
publication_status: published
publisher: Elsevier
quality_controlled: '1'
related_material:
link:
- description: News on ISTA website
relation: press_release
url: https://ista.ac.at/en/news/human-traits-beyond-inherited-genes/
researchdata_availability: yes
scopus_import: '1'
status: public
supplementarymaterial: yes
title: Separating direct, indirect, and parent-of-origin genetic effects in the human
population
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: ba8df636-2132-11f1-aed0-ed93e2281fdd
volume: 6
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
fulldoi: https://doi.org/10.1016/j.molcel.2026.05.026
has_accepted_license: '1'
language:
- iso: eng
license: https://creativecommons.org/licenses/by-nc/4.0/
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: '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
_id: '22684'
abstract:
- lang: eng
text: "Contact electrification (CE) is a simple yet elusive phenomenon that occurs
when two materials come into contact and separate, leaving behind net electrical
charge. Despite its ubiquity, the microscopic origin of CE remains unclear. In
this thesis, we investigate CE from three complementary perspectives: developing
a quantitative method to measure charge at the nanoscale, exploring the dynamic
behavior of charge on insulating surfaces, and uncovering the role of mechanical
history in forming a triboelectric series.\r\n\r\nIn the first part, we establish
a rigorous framework for converting qualitative Kelvin probe force microscopy
(KPFM) voltage maps into quantitative charge density distributions. Using finite
element method (FEM) simulations, we determine the point-spread function of the
KPFM tip–sample geometry and demonstrate that the true surface charge can be reconstructed
by numerical deconvolution. This procedure enables the recovery of both the magnitude
and sign of charge density with high fidelity, resolving nanoscale features that
are otherwise obscured. Applying the method to contact-charged SiO$_2$ surfaces,
we show that existing analytical approximations, such as parallel plate or spherical
models, can miscalculate charge magnitude by orders of magnitude. Our hybrid FEM/KPFM
approach therefore provides a fast and general method to convert qualitative KPFM
signals into quantitative charge data, enabling nanoscale charge mapping under
realistic experimental conditions.\r\n\r\nIn the second part, we study the temporal
stability of CE-induced charges and identify the key material factors that determine
whether KPFM can capture meaningful charge patterns. Through time-resolved experiments
combining a custom-built transfer system with both microscopic and macroscopic
measurements, we demonstrate that only the best insulators, such as SiO$_2$, preserve
CE charge long enough for stationary imaging. For less conductive polymers, such
as PDMS, charge decays within the duration of a single KPFM scan due to bulk conduction.
Using a simple capacitor-based model, we reproduce the observed decay dynamics
and confirm that the transferred charge decays characteristic to the sample's
bulk conductivity. Further, we always observe homogeneous charge transfer.\r\n\r\nIn
the third part, we address the question: can we form a triboelectric series with
identical materials? Using controlled repetitive contact experiments, we show
that nominally identical materials can progressively order themselves into a triboelectric
series, where surfaces with more contact history charge negatively relative to
fresher ones. By constructing a minimal model based on this ``contact bias'',
we replicate the evolution from random to ordered charging observed in experiments.
Supporting surface analyses, including atomic force microscopy, reveal that repeated
contact induces nanoscale morphological changes, suggesting a mechanism tightly
coupled to mechanical strain. These results highlight the crucial role of surface
history and nanoscale mechanics in dictating charge transfer, motivating further
exploration of mechanisms such as mechanochemical bond cleavage and flexoelectric
polarization."
acknowledged_ssus:
- _id: NanoFab
- _id: ScienComp
- _id: LifeSc
- _id: M-Shop
- _id: EM-Fac
acknowledgement: "This project has received financing from the European Research Council
grant agreement\r\nno. 949120 under the European Union’s Horizon 2020 research and
innovation programme.\r\nThis research was supported by the Scientific Service Units
of The Institute of Science\r\nand Technology Austria (ISTA) through resources provided
by the Miba Machine Shop, the\r\nNanofabrication Facility, the Lab Support Facility,
the Scientific Computing Facility and the\r\nElectron Microscopy Facility. We thank
Florian Stumpf from Park Systems for useful discussions\r\nand support with scanning
probe microscopy. We thank Joaquin Garcia-Suarez and Guillaume\r\nAnciaux for the
suggestion to look into the roughness power spectral density. We thank\r\nIrina-Malina
Strugaru for help with testing the device for Young’s modulus measurements.\r\n"
alternative_title:
- ISTA Thesis
article_processing_charge: No
author:
- first_name: Felix
full_name: Pertl, Felix
id: 6313aec0-15b2-11ec-abd3-ed67d16139af
last_name: Pertl
orcid: 0000-0003-0463-5794
citation:
ama: Pertl F. Experimental probing of nanoscale charge features and surface morphology
changes during tribocharging. 2026. doi:10.15479/AT-ISTA-22684
apa: Pertl, F. (2026). Experimental probing of nanoscale charge features and
surface morphology changes during tribocharging. Institute of Science and
Technology Austria. https://doi.org/10.15479/AT-ISTA-22684
chicago: Pertl, Felix. “Experimental Probing of Nanoscale Charge Features and Surface
Morphology Changes during Tribocharging.” Institute of Science and Technology
Austria, 2026. https://doi.org/10.15479/AT-ISTA-22684.
ieee: F. Pertl, “Experimental probing of nanoscale charge features and surface morphology
changes during tribocharging,” Institute of Science and Technology Austria, 2026.
ista: Pertl F. 2026. Experimental probing of nanoscale charge features and surface
morphology changes during tribocharging. Institute of Science and Technology Austria.
mla: Pertl, Felix. Experimental Probing of Nanoscale Charge Features and Surface
Morphology Changes during Tribocharging. Institute of Science and Technology
Austria, 2026, doi:10.15479/AT-ISTA-22684.
short: F. Pertl, Experimental Probing of Nanoscale Charge Features and Surface Morphology
Changes during Tribocharging, Institute of Science and Technology Austria, 2026.
corr_author: '1'
date_created: 2026-08-12T09:44:40Z
date_published: 2026-08-12T00:00:00Z
date_updated: 2026-08-27T11:42:44Z
day: '12'
ddc:
- '530'
degree_awarded: PhD
department:
- _id: GradSch
- _id: ScWa
doi: 10.15479/AT-ISTA-22684
doi_confirm: '1'
ec_funded: 1
file:
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checksum: 0a4f5a941c40b921447e72291d72bc6f
content_type: application/x-zip-compressed
creator: fpertl
date_created: 2026-08-12T13:04:21Z
date_updated: 2026-08-12T13:04:21Z
file_id: '22690'
file_name: 2026_Pertl_Felix_Thesis.zip
file_size: 31192621
relation: source_file
- access_level: open_access
checksum: ae60dcdb363222138886b2857643d4e3
content_type: application/pdf
creator: fpertl
date_created: 2026-08-12T13:04:21Z
date_updated: 2026-08-12T13:04:21Z
file_id: '22691'
file_name: 2026_Pertl_Felix_Thesis.pdf
file_size: 27882509
relation: main_file
file_date_updated: 2026-08-12T13:04:21Z
fulldoi: https://doi.org/10.15479/AT-ISTA-22684
has_accepted_license: '1'
language:
- iso: eng
month: '08'
oa: 1
oa_version: Published Version
page: '107'
project:
- _id: 0aa60e99-070f-11eb-9043-a6de6bdc3afa
call_identifier: H2020
grant_number: '949120'
name: 'Tribocharge: a multi-scale approach to an enduring problem in physics'
publication_identifier:
isbn:
- 978-3-99078-083-1
issn:
- 2663-337X
publication_status: published
publisher: Institute of Science and Technology Austria
related_material:
record:
- id: '20481'
relation: part_of_dissertation
status: public
- id: '12109'
relation: part_of_dissertation
status: public
- id: '19278'
relation: part_of_dissertation
status: public
- id: '17373'
relation: part_of_dissertation
status: public
status: public
supervisor:
- first_name: Scott R
full_name: Waitukaitis, Scott R
id: 3A1FFC16-F248-11E8-B48F-1D18A9856A87
last_name: Waitukaitis
orcid: 0000-0002-2299-3176
title: Experimental probing of nanoscale charge features and surface morphology changes
during tribocharging
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: dissertation
user_id: 8b945eb4-e2f2-11eb-945a-df72226e66a9
year: '2026'
...
---
OA_type: closed access
_id: '21762'
abstract:
- lang: eng
text: Bacteria, like eukaryotes, use conserved cytoskeletal systems for intracellular
organization. The plasmid-encoded ParMRC system forms actin-like filaments that
segregate low–copy number plasmids. In multicellular cyanobacteria such as Anabaena
sp., we found that a chromosomally encoded ParMR system has evolved into a cytoskeletal
system named CorMR with a function in cell shape control rather than DNA segregation.
Live-cell imaging, in vitro reconstitution, and cryo–electron microscopy revealed
that CorM formed dynamically unstable, antiparallel double-stranded filaments
that were recruited to the membrane by CorR through an amphipathic helix conserved
in multicellular cyanobacteria. CorMR filaments were regulated by MinC, which
excluded them from the poles and division plane. Comparative genomics indicated
that the repurposing of ParMR and Min systems coevolved with cyanobacterial multicellularity,
highlighting the evolutionary plasticity of cytoskeletal systems in bacteria.
acknowledged_ssus:
- _id: Bio
- _id: ScienComp
- _id: EM-Fac
- _id: LifeSc
acknowledgement: "We thank all members of the Loose lab at ISTA for helpful discussions;
M. Kojic for critical reading of the manuscript; A. Herrero (Sevilla University)
for sharing her extensive BACTH plasmid library and other plasmids, as well as cyanobacterial
strains; T. Dagan and F. Nies (both Kiel University) for sharing cyanobacterial
strains and plasmids and for valuable discussions; N. Sapay and A. Michon for providing
the Amphipaseek code, which enabled us to perform our large-scale amphipathic helix
screen of cyanobacterial CorR proteins; V.-V. Hodirnau for support in cryo-ET data
collection; and J. Hansen for advice about cryo-EM data processing.\r\nThis work
was supported by the Scientific Service Units (SSU) of ISTA through resources provided
by the Imaging & Optics Facility (IOF), the Scientific Computing (SciComp), the
Electron Microscopy Facility (EMF), and the Lab Support Facility (LSF). This work
was funded by the European Union’s Horizon 2020 research and innovation program
(Marie Skłodowska-Curie grant 101034413 to B.L.S.); the European Research Council
(ERC) of the European Union (grant ActinID 101076260 to F.K.M.S.); the Swiss National
Science Foundation (starting grant TMSGI3_226208 to G.L.W.); and the Jean-Jacques
et Letitia Lopez-Loreta Foundation (G.L.W.)."
article_number: eaea6343
article_processing_charge: No
article_type: original
author:
- first_name: Benjamin L
full_name: Springstein, Benjamin L
id: b4eb62ef-ac72-11ed-9503-ed3b4d66c083
last_name: Springstein
orcid: 0000-0002-3461-5391
- first_name: Manjunath
full_name: Javoor, Manjunath
id: 305ab18b-dc7d-11ea-9b2f-b58195228ea2
last_name: Javoor
orcid: 0000-0003-2311-2112
- first_name: Daniela
full_name: Megrian, Daniela
last_name: Megrian
- first_name: Roman
full_name: Hajdu, Roman
id: ffab949d-133f-11ed-8f02-94de21ace503
last_name: Hajdu
- first_name: Dustin M.
full_name: Hanke, Dustin M.
last_name: Hanke
- first_name: Bettina
full_name: Zens, Bettina
id: 45FD126C-F248-11E8-B48F-1D18A9856A87
last_name: Zens
orcid: 0000-0002-9561-1239
- first_name: Gregor L.
full_name: Weiss, Gregor L.
last_name: Weiss
- first_name: Florian Km
full_name: Schur, Florian Km
id: 48AD8942-F248-11E8-B48F-1D18A9856A87
last_name: Schur
orcid: 0000-0003-4790-8078
- first_name: Martin
full_name: Loose, Martin
id: 462D4284-F248-11E8-B48F-1D18A9856A87
last_name: Loose
orcid: 0000-0001-7309-9724
citation:
ama: Springstein BL, Javoor M, Megrian D, et al. Repurposing of a DNA segregation
machinery into a cytoskeletal system controlling cell shape. Science. 2026;392(6795).
doi:10.1126/science.aea6343
apa: Springstein, B. L., Javoor, M., Megrian, D., Hajdu, R., Hanke, D. M., Zens,
B., … Loose, M. (2026). Repurposing of a DNA segregation machinery into a cytoskeletal
system controlling cell shape. Science. AAAS. https://doi.org/10.1126/science.aea6343
chicago: Springstein, Benjamin L, Manjunath Javoor, Daniela Megrian, Roman Hajdu,
Dustin M. Hanke, Bettina Zens, Gregor L. Weiss, Florian KM Schur, and Martin Loose.
“Repurposing of a DNA Segregation Machinery into a Cytoskeletal System Controlling
Cell Shape.” Science. AAAS, 2026. https://doi.org/10.1126/science.aea6343.
ieee: B. L. Springstein et al., “Repurposing of a DNA segregation machinery
into a cytoskeletal system controlling cell shape,” Science, vol. 392,
no. 6795. AAAS, 2026.
ista: Springstein BL, Javoor M, Megrian D, Hajdu R, Hanke DM, Zens B, Weiss GL,
Schur FK, Loose M. 2026. Repurposing of a DNA segregation machinery into a cytoskeletal
system controlling cell shape. Science. 392(6795), eaea6343.
mla: Springstein, Benjamin L., et al. “Repurposing of a DNA Segregation Machinery
into a Cytoskeletal System Controlling Cell Shape.” Science, vol. 392,
no. 6795, eaea6343, AAAS, 2026, doi:10.1126/science.aea6343.
short: B.L. Springstein, M. Javoor, D. Megrian, R. Hajdu, D.M. Hanke, B. Zens, G.L.
Weiss, F.K. Schur, M. Loose, Science 392 (2026).
corr_author: '1'
date_created: 2026-04-26T22:01:46Z
date_published: 2026-04-16T00:00:00Z
date_updated: 2026-09-03T09:36:24Z
day: '16'
department:
- _id: MaLo
- _id: FlSc
- _id: GradSch
- _id: EM-Fac
doi: 10.1126/science.aea6343
ec_funded: 1
external_id:
pmid:
- '41990175'
fulldoi: https://doi.org/10.1126/science.aea6343
intvolume: ' 392'
issue: '6795'
language:
- iso: eng
month: '04'
oa_version: None
pmid: 1
project:
- _id: fc2ed2f7-9c52-11eb-aca3-c01059dda49c
call_identifier: H2020
grant_number: '101034413'
name: 'IST-BRIDGE: International postdoctoral program'
- _id: bd980d18-d553-11ed-ba76-ceaa645c97eb
grant_number: '101076260'
name: A molecular atlas of Actin filament IDentities in the cell motility machinery
publication: Science
publication_identifier:
eissn:
- 1095-9203
issn:
- 0036-8075
publication_status: published
publisher: AAAS
quality_controlled: '1'
related_material:
record:
- id: '22744'
relation: dissertation_contains
status: public
scopus_import: '1'
status: public
title: Repurposing of a DNA segregation machinery into a cytoskeletal system controlling
cell shape
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 392
year: '2026'
...