---
OA_place: publisher
OA_type: hybrid
PlanS_conform: '1'
_id: '21982'
abstract:
- lang: eng
text: A floating Leidenfrost droplet exhibits curvature inversion of its underside,
due to the balance of vapor pressure and surface tension. Using interferometric
imaging, we find different behavior for a levitated hydrogel sphere. Curvature
inversion is observed briefly just after deposition, but quickly gives way to
a steady state with no inversion. We show the essential role of vaporization in
shaping the underbelly of the hydrogel, where changes due to direct mass loss
are more significant than the balance of vapor pressure and elastic forces.
acknowledged_ssus:
- _id: M-Shop
- _id: ScienComp
acknowledgement: This research was supported by the Scientific Service Units of The
Institute of Science and Technology Austria (ISTA) through resources provided by
the Miba Machine Shop and the Scientific Computing Facility. J.B. acknowledges funding
from the European Union's Horizon research and innovation programme under the Marie
Sklodowska-Curie Grant Agreement No. 101106500.
article_number: L053502
article_processing_charge: Yes (via OA deal)
article_type: letter_note
arxiv: 1
author:
- first_name: Vicente L
full_name: Diaz Melian, Vicente L
id: b6798902-eea0-11ea-9cbc-a8e14286c631
last_name: Diaz Melian
- first_name: Isaac C
full_name: Lenton, Isaac C
id: a550210f-223c-11ec-8182-e2d45e817efb
last_name: Lenton
orcid: 0000-0002-5010-6984
- first_name: Jack
full_name: Binysh, Jack
last_name: Binysh
- first_name: Anton
full_name: Souslov, Anton
last_name: Souslov
- 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: Diaz Melian VL, Lenton IC, Binysh J, Souslov A, Waitukaitis SR. Geometry of
the vapor layer under a Leidenfrost hydrogel sphere. Physical Review E.
2026;113(5). doi:10.1103/m7gr-2t6j
apa: Diaz Melian, V. L., Lenton, I. C., Binysh, J., Souslov, A., & Waitukaitis,
S. R. (2026). Geometry of the vapor layer under a Leidenfrost hydrogel sphere.
Physical Review E. American Physical Society. https://doi.org/10.1103/m7gr-2t6j
chicago: Diaz Melian, Vicente L, Isaac C Lenton, Jack Binysh, Anton Souslov, and
Scott R Waitukaitis. “Geometry of the Vapor Layer under a Leidenfrost Hydrogel
Sphere.” Physical Review E. American Physical Society, 2026. https://doi.org/10.1103/m7gr-2t6j.
ieee: V. L. Diaz Melian, I. C. Lenton, J. Binysh, A. Souslov, and S. R. Waitukaitis,
“Geometry of the vapor layer under a Leidenfrost hydrogel sphere,” Physical
Review E, vol. 113, no. 5. American Physical Society, 2026.
ista: Diaz Melian VL, Lenton IC, Binysh J, Souslov A, Waitukaitis SR. 2026. Geometry
of the vapor layer under a Leidenfrost hydrogel sphere. Physical Review E. 113(5),
L053502.
mla: Diaz Melian, Vicente L., et al. “Geometry of the Vapor Layer under a Leidenfrost
Hydrogel Sphere.” Physical Review E, vol. 113, no. 5, L053502, American
Physical Society, 2026, doi:10.1103/m7gr-2t6j.
short: V.L. Diaz Melian, I.C. Lenton, J. Binysh, A. Souslov, S.R. Waitukaitis, Physical
Review E 113 (2026).
corr_author: '1'
date_created: 2026-06-10T07:36:41Z
date_published: 2026-05-14T00:00:00Z
date_updated: 2026-06-16T11:24:18Z
day: '14'
ddc:
- '530'
department:
- _id: ScWa
- _id: GradSch
doi: 10.1103/m7gr-2t6j
external_id:
arxiv:
- '2507.04982'
file:
- access_level: open_access
checksum: 902cc8d177c8d3ae9cfe07c30375c9a9
content_type: application/pdf
creator: dernst
date_created: 2026-06-16T11:21:53Z
date_updated: 2026-06-16T11:21:53Z
file_id: '22014'
file_name: 2026_PhysicalReviewE_DiazMelian.pdf
file_size: 3173197
relation: main_file
success: 1
file_date_updated: 2026-06-16T11:21:53Z
has_accepted_license: '1'
intvolume: ' 113'
issue: '5'
language:
- iso: eng
month: '05'
oa: 1
oa_version: Published Version
publication: Physical Review E
publication_identifier:
eissn:
- 2470-0053
issn:
- 2470-0045
publication_status: published
publisher: American Physical Society
quality_controlled: '1'
scopus_import: '1'
status: public
title: Geometry of the vapor layer under a Leidenfrost hydrogel sphere
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: 113
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.
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. (n.d.). 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, n.d. 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. Elsevier.
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. Separating direct, indirect, and parent-of-origin genetic effects in the human
population. Cell Genomics., 101277.
mla: Krätschmer, Ilse, et al. “Separating Direct, Indirect, and Parent-of-Origin
Genetic Effects in the Human Population.” Cell Genomics, 101277, Elsevier,
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 (n.d.).
corr_author: '1'
date_created: 2026-06-10T07:39:08Z
date_published: 2026-06-09T00:00:00Z
date_updated: 2026-06-19T07:00:47Z
day: '09'
department:
- _id: MaRo
doi: 10.1016/j.xgen.2026.101277
external_id:
pmid:
- '40909755'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.1016/j.xgen.2026.101277
month: '06'
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: inpress
publisher: Elsevier
quality_controlled: '1'
scopus_import: '1'
status: public
title: Separating direct, indirect, and parent-of-origin genetic effects in the human
population
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
year: '2026'
...
---
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
has_accepted_license: '1'
intvolume: ' 18'
issue: '1'
language:
- iso: eng
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:
- access_level: open_access
checksum: 0ab7ac2fbcb61a364dba57152db64ed7
content_type: application/pdf
creator: dernst
date_created: 2026-01-21T08:21:11Z
date_updated: 2026-01-21T08:21:11Z
file_id: '21026'
file_name: 2026_NaturePhysics_Mishra.pdf
file_size: 7335694
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success: 1
file_date_updated: 2026-01-21T08:21:11Z
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:
- access_level: open_access
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
- access_level: open_access
checksum: ee350c8eaed99f3ca348c47c8b190d3c
content_type: application/x-zip-compressed
creator: snaik
date_created: 2026-03-18T14:52:02Z
date_updated: 2026-03-18T14:52:02Z
file_id: '21464'
file_name: DevBranchDataRepo.zip
file_size: 282168895
relation: main_file
success: 1
- access_level: open_access
checksum: 1ecaf2c1a2ce8ff9c75a128cc02d0b8f
content_type: text/markdown
creator: snaik
date_created: 2026-03-18T15:01:32Z
date_updated: 2026-03-18T15:01:32Z
file_id: '21466'
file_name: ReadMe.md
file_size: 2231
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date_created: 2026-03-18T15:12:57Z
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file_name: PaperSchematics.svg
file_size: 1951210
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checksum: 9ac1054b16c212c6f34d402dce2c80e0
content_type: application/octet-stream
creator: snaik
date_created: 2026-03-21T03:37:43Z
date_updated: 2026-03-21T03:37:43Z
file_id: '21468'
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creator: snaik
date_created: 2026-03-24T07:21:43Z
date_updated: 2026-03-24T07:21:43Z
file_id: '21495'
file_name: DataRepo.zip
file_size: 749368723
relation: main_file
success: 1
file_date_updated: 2026-03-24T07:21:43Z
has_accepted_license: '1'
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:
- access_level: open_access
checksum: dafef9ed575b44be4263e948a47ae056
content_type: application/pdf
creator: dernst
date_created: 2026-03-24T06:57:08Z
date_updated: 2026-03-24T06:57:08Z
file_id: '21494'
file_name: 2026_Nature_Grosjean.pdf
file_size: 12245694
relation: main_file
success: 1
file_date_updated: 2026-03-24T06:57:08Z
has_accepted_license: '1'
intvolume: ' 651'
issue: '8106'
language:
- iso: eng
month: '03'
oa: 1
oa_version: Published Version
page: 626-631
pmid: 1
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'
- _id: 260C2330-B435-11E9-9278-68D0E5697425
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_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: 2026-04-28T13:29:05Z
day: '16'
department:
- _id: MaLo
- _id: FlSc
- _id: GradSch
- _id: EM-Fac
doi: 10.1126/science.aea6343
ec_funded: 1
external_id:
pmid:
- '41990175'
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'
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'
...
---
OA_place: publisher
_id: '21854'
abstract:
- lang: eng
text: "As neural-network-based models grow both in size and popularity, interest
has grown in making the models smaller and more efficient to train. To that end,
many methods have been proposed to prune models by reducing their number of nonzero
parameters. Additionally, parameter-efficient fine-tuning, in which a much smaller
number of parameters than the total contained in the model is updated during training,
has become very popular, especially in the space of Large Language Models. At
the same time, the increasingly routine deployment of machine learning in real-world
applications has spurred a drive to make them more trustworthy - in the sense
of, among other things, being unbiased, interpretable, and editable. In this thesis,
we examine the interplay between efficiency and trustworthiness.\r\n\r\nFirst,
we analyze the effects of model pruning on bias in computer vision models, demonstrating
that increased sparsity leads to greater bias, largely as a function of increased
model uncertainty in marginal cases. Based on this observation, we propose several
bias mitigation techniques. Then, we demonstrate that example-specific model pruning
can improve model interpretation methods while improving pruning efficiency to
make example-specific model pruning feasible in real time. Then, we investigate
the effectiveness of parameter-efficient and data-efficient model personalization
via fine-tuning, demonstrating that it is highly feasible with very small computational
and data resources. Finally, we consider efficiency in editing model knowledge
using a custom synthetic data framework, demonstrating that parameter-efficient,
low-rank fine-tuning frequently outperforms full-rank fine-tuning, and, additionally,
that restricting which model blocks are fine-tuned frequently improves results.
Together, the results in this thesis provide new insights and techniques for combining
trustworthiness and efficiency during neural network inference and training.\r\n\r\n-----------------“In
reference to IEEE copyrighted material which is used with permission in this thesis,
the IEEE does not endorse any of [name of university or educational entity]’s
products or services. Internal or personal use of this material is permitted.
If interested in reprinting/republishing IEEE copyrighted material for advertising
or promotional purposes or for creating new collective works for resale or redistribution,
please go to http://www.ieee.org/publications_standards/publications/rights/rights_link.html
to learn how to obtain a License from RightsLink. If applicable, University Microfilms
and/or ProQuest Library, or the Archives of Canada may supply single copies of
the dissertation.”"
acknowledged_ssus:
- _id: ScienComp
acknowledgement: "The research in this Ph.D. was funded in whole\r\nor in part by
the Austrian Science Fund (FWF) W1260-N35 (Vienna Graduate School for\r\nComputational
Optimization). For open access purposes the author has applied a CC BY\r\npublic
copyright license to any author accepted manuscript version arising from this submission\r\nwherever
possible. Additionally, I am grateful to Alois Schlögl, Waleed Khalid, and the rest
of\r\nthe ISTA Scientific Computing team for building and maintaining the infrastructure
I used\r\nto run experiments. I’m also deeply grateful to the Alistarh group’s administrative
assistant,\r\nChristine Francois, who always deals with our nonsense with common
sense and a smile.\r\n"
alternative_title:
- ISTA Thesis
article_processing_charge: No
author:
- first_name: Eugenia B
full_name: Iofinova, Eugenia B
id: f9a17499-f6e0-11ea-865d-fdf9a3f77117
last_name: Iofinova
orcid: 0000-0002-7778-3221
citation:
ama: Iofinova EB. On the utility and effects of efficiency in artificial neural
networks. 2026. doi:10.15479/AT-ISTA-21854
apa: Iofinova, E. B. (2026). On the utility and effects of efficiency in artificial
neural networks. Institute of Science and Technology Austria. https://doi.org/10.15479/AT-ISTA-21854
chicago: Iofinova, Eugenia B. “On the Utility and Effects of Efficiency in Artificial
Neural Networks.” Institute of Science and Technology Austria, 2026. https://doi.org/10.15479/AT-ISTA-21854.
ieee: E. B. Iofinova, “On the utility and effects of efficiency in artificial neural
networks,” Institute of Science and Technology Austria, 2026.
ista: Iofinova EB. 2026. On the utility and effects of efficiency in artificial
neural networks. Institute of Science and Technology Austria.
mla: Iofinova, Eugenia B. On the Utility and Effects of Efficiency in Artificial
Neural Networks. Institute of Science and Technology Austria, 2026, doi:10.15479/AT-ISTA-21854.
short: E.B. Iofinova, On the Utility and Effects of Efficiency in Artificial Neural
Networks, Institute of Science and Technology Austria, 2026.
corr_author: '1'
date_created: 2026-05-11T08:43:22Z
date_published: 2026-05-11T00:00:00Z
date_updated: 2026-05-19T11:20:28Z
day: '11'
ddc:
- '000'
degree_awarded: PhD
department:
- _id: GradSch
- _id: DaAl
doi: 10.15479/AT-ISTA-21854
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date_created: 2026-05-11T08:36:01Z
date_updated: 2026-05-11T08:36:01Z
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file_size: 28479571
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creator: eiofinov
date_created: 2026-05-13T13:10:48Z
date_updated: 2026-05-13T13:10:48Z
file_id: '21877'
file_name: 2026_Iofinova_Eugenia_Thesis.pdf
file_size: 18137757
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language:
- iso: eng
month: '05'
oa: 1
oa_version: Published Version
page: '237'
project:
- _id: 9B9290DE-BA93-11EA-9121-9846C619BF3A
grant_number: W1260-N35
name: Vienna Graduate School on Computational Optimization
publication_identifier:
issn:
- 2663-337X
publication_status: published
publisher: Institute of Science and Technology Austria
related_material:
record:
- id: '14771'
relation: part_of_dissertation
status: public
- id: '18121'
relation: part_of_dissertation
status: public
- id: '21858'
relation: part_of_dissertation
status: public
- id: '21859'
relation: part_of_dissertation
status: public
- id: '21857'
relation: part_of_dissertation
status: public
status: public
supervisor:
- first_name: Dan-Adrian
full_name: Alistarh, Dan-Adrian
id: 4A899BFC-F248-11E8-B48F-1D18A9856A87
last_name: Alistarh
orcid: 0000-0003-3650-940X
title: On the utility and effects of efficiency in artificial neural networks
type: dissertation
user_id: 8b945eb4-e2f2-11eb-945a-df72226e66a9
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: 2026-05-19T11:20:27Z
day: '30'
department:
- _id: GradSch
- _id: DaAl
doi: 10.48550/arXiv.2601.23153
external_id:
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: '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
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date_created: 2026-06-09T08:34:38Z
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date_created: 2026-06-09T12:28:51Z
date_updated: 2026-06-11T12:14:53Z
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relation: main_file
file_date_updated: 2026-06-11T12:14:53Z
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'
...
---
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: 2026-06-29T12:55:19Z
day: '22'
ddc:
- '570'
department:
- _id: LeSa
doi: 10.1016/j.molcel.2026.05.026
external_id:
biorxivid:
- 10.1101/2025.09.16.676506
has_accepted_license: '1'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.1016/j.molcel.2026.05.026
month: '06'
oa: 1
oa_version: Published Version
publication: Molecular Cell
publication_identifier:
eissn:
- 1097-4164
issn:
- 1097-2765
publication_status: inpress
publisher: Elsevier
quality_controlled: '1'
related_material:
record:
- id: '22189'
relation: research_data
status: for_moderation
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: 2DF688A6-F248-11E8-B48F-1D18A9856A87
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'
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title: Developmental emergence of sparse and structured synaptic connectivity in the
hippocampal CA3 memory circuit
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abstract:
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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
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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
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- first_name: Christopher J
full_name: Wojtan, Christopher J
id: 3C61F1D2-F248-11E8-B48F-1D18A9856A87
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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'
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date_published: 2026-07-01T00:00:00Z
date_updated: 2026-07-06T10:30:34Z
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department:
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doi: 10.1145/3811353
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apa: Dunajova, Z. (2026). Geometry-driven self-organization of migrating cells
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and Chiral Filaments.” Institute of Science and Technology Austria, 2026. https://doi.org/10.15479/AT-ISTA-21423.
ieee: Z. Dunajova, “Geometry-driven self-organization of migrating cells and chiral
filaments,” Institute of Science and Technology Austria, 2026.
ista: Dunajova Z. 2026. Geometry-driven self-organization of migrating cells and
chiral filaments. Institute of Science and Technology Austria.
mla: Dunajova, Zuzana. Geometry-Driven Self-Organization of Migrating Cells and
Chiral Filaments. Institute of Science and Technology Austria, 2026, doi:10.15479/AT-ISTA-21423.
short: Z. Dunajova, Geometry-Driven Self-Organization of Migrating Cells and Chiral
Filaments, Institute of Science and Technology Austria, 2026.
corr_author: '1'
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text: These files contain supplementary movies accompanying the PhD thesis “Geometry-driven
self-organization of migrating cells and chiral filaments” by Zuzana Dunajova
(2026). The videos provide additional visual material supporting the experiments
and results described in the thesis.
acknowledged_ssus:
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article_processing_charge: No
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- first_name: Zuzana
full_name: Dunajova, Zuzana
id: 4B39F286-F248-11E8-B48F-1D18A9856A87
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citation:
ama: Dunajova Z. Supplementary movies to PhD thesis “Geometry-driven self-organization
of migrating cells and chiral filaments.” 2026. doi:10.15479/AT-ISTA-21439
apa: Dunajova, Z. (2026). Supplementary movies to PhD thesis “Geometry-driven self-organization
of migrating cells and chiral filaments.” Institute of Science and Technology
Austria. https://doi.org/10.15479/AT-ISTA-21439
chicago: Dunajova, Zuzana. “Supplementary Movies to PhD Thesis ‘Geometry-Driven
Self-Organization of Migrating Cells and Chiral Filaments.’” Institute of Science
and Technology Austria, 2026. https://doi.org/10.15479/AT-ISTA-21439.
ieee: Z. Dunajova, “Supplementary movies to PhD thesis ‘Geometry-driven self-organization
of migrating cells and chiral filaments.’” Institute of Science and Technology
Austria, 2026.
ista: Dunajova Z. 2026. Supplementary movies to PhD thesis “Geometry-driven self-organization
of migrating cells and chiral filaments”, Institute of Science and Technology
Austria, 10.15479/AT-ISTA-21439.
mla: Dunajova, Zuzana. Supplementary Movies to PhD Thesis “Geometry-Driven Self-Organization
of Migrating Cells and Chiral Filaments.” Institute of Science and Technology
Austria, 2026, doi:10.15479/AT-ISTA-21439.
short: Z. Dunajova, (2026).
contributor:
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first_name: Saren
id: 4323B49C-F248-11E8-B48F-1D18A9856A87
last_name: Tasciyan
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first_name: Philipp
id: 40136C2A-F248-11E8-B48F-1D18A9856A87
last_name: Radler
orcid: '0000-0001-9198-2182 '
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date_updated: 2026-07-06T12:38:16Z
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abstract:
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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:
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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
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- _id: BeVi
doi: 10.1098/rspb.2025.2471
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checksum: d76afebca0a6f112df0146ae2d929f36
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creator: dernst
date_created: 2026-02-16T09:26:02Z
date_updated: 2026-02-16T09:26:02Z
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file_size: 2230841
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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
has_accepted_license: '1'
language:
- iso: eng
main_file_link:
- open_access: '1'
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: '21198'
abstract:
- lang: eng
text: "In recent years there has been a massive increase in the amount of data generated
in a\r\ndecentralized manner. Ever more powerful edge devices, such as smartphones,
have become\r\nubiquitous in most societies on earth. Through text typed, photos
taken and apps used,\r\nthese devices, which we refer to as clients, generate
enormous amounts of high quality and\r\ncomplex data. Moreover, the nature of
these devices means the data they generate is often\r\nsensitive and privacy concerns
prevent it being gathered and stored in a central location. This\r\npresents a
challenge to the modern machine learning paradigm that requires central access\r\nto
large amounts of data. Federated learning (FL) has emerged as one of the answers
to\r\nthis problem. Rather than bringing the data to the model, FL sends the model
to the data.\r\nModel training takes place on device, with periodically synchronized
updates, allowing data to\r\nremain locally stored. While this approach offers
significant privacy advantages it comes with\r\nits own set of unique challenges.
These include: data heterogeneity, the notion that different\r\ndevices generate
data in distinct ways which can negatively impact training dynamics; systems\r\nheterogeneity,
meaning that different devices may have differing hardware specifications; high\r\ncommunication
costs, which are induced by the repeated transferring of models over the\r\nnetwork
and low device computational power, which limits the use of larger models on device.\r\nIn
this thesis we present a range of methods for federated learning. We focus primarily
on\r\nthe challenge of data heterogeneity, though the methods presented are designed
to be well\r\nadapted to the other challenges of a federated setting, such as
the constraints of limited\r\ncompute and communication overhead. We first present
a method for explicitly modeling client\r\ndata heterogeneity. The approach formulates
clients as samples from a certain probability\r\ndistribution and infers the parameters
of this distribution from the available training clients.\r\nThis learned distribution
then represents the heterogeneity present among the clients and can\r\nbe sampled
from in order to create new simulated clients that are similar to the real clients
we\r\nhave observed so far. Following this we present two methods for directly
dealing with data\r\nheterogeneity through personalization. Highly heterogeneous
client data distributions can mean\r\nthat learning a single global model becomes
suboptimal, and some form of personalization of\r\nmodels to each individual client
is required. Our approaches are based around hypernetworks,\r\nwhich we use to
generate personalized model parameters without the need for additional\r\ntraining
or finetuning. In the first approach we focus on generating full parameterizations
of\r\nclient models using learned embeddings of client data and labels, with a
hypernetwork located\r\non the central server. In the second approach we address
the more challenging scenario where\r\nwe want to generate a personalized model
for a client without any label information. The\r\nhypernetwork is trained to
generate a low dimensional representation of a client’s personalized\r\nmodel
parameters, allowing it to be transferred to and run on the client devices. In
our final\r\npresented method, we change our focus and rather than aim to directly
address the challenge\r\nof data heterogeneity, we instead ensure we are unaffected
by it. This is done in the context\r\nof k-means clustering and we present a method
for federated clustering with a focus on added\r\nprivacy guarantees."
acknowledged_ssus:
- _id: ScienComp
acknowledgement: "This research was funded in part by the Austrian Science Fund (FWF)\r\n[10.55776/COE12].
Furthermore, the candidate acknowledges the support from the Scientific\r\nService
Units (SSU) of ISTA through resources provided by Scientific Computing (SciComp)."
alternative_title:
- ISTA Thesis
article_processing_charge: No
author:
- first_name: Jonathan A
full_name: Scott, Jonathan A
id: e499926b-f6e0-11ea-865d-9c63db0031e8
last_name: Scott
citation:
ama: Scott JA. Data heterogeneity and personalization in federated learning. 2026.
doi:10.15479/AT-ISTA-21198
apa: Scott, J. A. (2026). Data heterogeneity and personalization in federated
learning. Institute of Science and Technology Austria. https://doi.org/10.15479/AT-ISTA-21198
chicago: Scott, Jonathan A. “Data Heterogeneity and Personalization in Federated
Learning.” Institute of Science and Technology Austria, 2026. https://doi.org/10.15479/AT-ISTA-21198.
ieee: J. A. Scott, “Data heterogeneity and personalization in federated learning,”
Institute of Science and Technology Austria, 2026.
ista: Scott JA. 2026. Data heterogeneity and personalization in federated learning.
Institute of Science and Technology Austria.
mla: Scott, Jonathan A. Data Heterogeneity and Personalization in Federated Learning.
Institute of Science and Technology Austria, 2026, doi:10.15479/AT-ISTA-21198.
short: J.A. Scott, Data Heterogeneity and Personalization in Federated Learning,
Institute of Science and Technology Austria, 2026.
corr_author: '1'
date_created: 2026-02-09T14:59:53Z
date_published: 2026-02-09T00:00:00Z
date_updated: 2026-07-22T06:34:27Z
day: '09'
ddc:
- '005'
degree_awarded: PhD
department:
- _id: GradSch
- _id: ChLa
doi: 10.15479/AT-ISTA-21198
file:
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date_created: 2026-02-17T11:46:22Z
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date_created: 2026-02-27T10:25:41Z
date_updated: 2026-02-27T10:25:41Z
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language:
- iso: eng
month: '02'
oa: 1
oa_version: Published Version
page: '158'
publication_identifier:
issn:
- 2663-337X
publication_status: published
publisher: Institute of Science and Technology Austria
related_material:
record:
- id: '20819'
relation: part_of_dissertation
status: public
- id: '17411'
relation: part_of_dissertation
status: public
- id: '18120'
relation: part_of_dissertation
status: public
- id: '21207'
relation: part_of_dissertation
status: public
status: public
supervisor:
- first_name: Christoph
full_name: Lampert, Christoph
id: 40C20FD2-F248-11E8-B48F-1D18A9856A87
last_name: Lampert
orcid: 0000-0001-8622-7887
title: Data heterogeneity and personalization in federated learning
type: dissertation
user_id: ba8df636-2132-11f1-aed0-ed93e2281fdd
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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checksum: 4c0889130095c31d4e5088c5b8dfd607
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creator: cfillmor
date_created: 2026-01-26T19:44:46Z
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file_size: 55954297
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creator: cfillmor
date_created: 2026-01-26T19:46:20Z
date_updated: 2026-01-26T19:46:20Z
file_id: '21047'
file_name: Thesis.zip
file_size: 166080788
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file_date_updated: 2026-01-30T11:40:09Z
has_accepted_license: '1'
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
_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: 2026-07-23T05:33:50Z
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
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date_created: 2026-07-13T14:56:41Z
date_updated: 2026-07-13T14:56:41Z
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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:
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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'
...