---
_id: '14979'
abstract:
- lang: eng
text: Poxviruses are among the largest double-stranded DNA viruses, with members
such as variola virus, monkeypox virus and the vaccination strain vaccinia virus
(VACV). Knowledge about the structural proteins that form the viral core has remained
sparse. While major core proteins have been annotated via indirect experimental
evidence, their structures have remained elusive and they could not be assigned
to individual core features. Hence, which proteins constitute which layers of
the core, such as the palisade layer and the inner core wall, has remained enigmatic.
Here we show, using a multi-modal cryo-electron microscopy (cryo-EM) approach
in combination with AlphaFold molecular modeling, that trimers formed by the cleavage
product of VACV protein A10 are the key component of the palisade layer. This
allows us to place previously obtained descriptions of protein interactions within
the core wall into perspective and to provide a detailed model of poxvirus core
architecture. Importantly, we show that interactions within A10 trimers are likely
generalizable over members of orthopox- and parapoxviruses.
acknowledged_ssus:
- _id: ScienComp
- _id: LifeSc
- _id: EM-Fac
acknowledgement: "We thank A. Bergthaler (Research Center for Molecular Medicine of
the Austrian Academy of Sciences) for providing VACV WR. We thank A. Nicholas and
his team at the ISTA proteomics facility, and S. Elefante at the ISTA Scientific
Computing facility for their support. We also thank F. Fäßler, D. Porley, T. Muthspiel
and other members of the Schur group for support and helpful discussions. We also
thank D. Castaño-Díez for support with Dynamo. We thank D. Farrell for his help
optimizing the Rosetta protocol to refine the atomic model into the cryo-EM map
with symmetry.\r\n\r\nF.K.M.S. acknowledges support from ISTA and EMBO. F.K.M.S.
also received support from the Austrian Science Fund (FWF) grant P31445. This publication
has been made possible in part by CZI grant DAF2021-234754 and grant https://doi.org/10.37921/812628ebpcwg
from the Chan Zuckerberg Initiative DAF, an advised fund of Silicon Valley Community
Foundation (funder https://doi.org/10.13039/100014989) awarded to F.K.M.S.\r\n\r\nThis
research was also supported by the Scientific Service Units (SSUs) of ISTA through
resources provided by Scientific Computing (SciComp), the Life Science Facility
(LSF), and the Electron Microscopy Facility (EMF). We also acknowledge the use of
COSMIC45 and Colabfold46."
article_processing_charge: Yes (in subscription journal)
article_type: original
author:
- first_name: Julia
full_name: Datler, Julia
id: 3B12E2E6-F248-11E8-B48F-1D18A9856A87
last_name: Datler
orcid: 0000-0002-3616-8580
- first_name: Jesse
full_name: Hansen, Jesse
id: 1063c618-6f9b-11ec-9123-f912fccded63
last_name: Hansen
- first_name: Andreas
full_name: Thader, Andreas
id: 3A18A7B8-F248-11E8-B48F-1D18A9856A87
last_name: Thader
- first_name: Alois
full_name: Schlögl, Alois
id: 45BF87EE-F248-11E8-B48F-1D18A9856A87
last_name: Schlögl
orcid: 0000-0002-5621-8100
- first_name: Lukas W
full_name: Bauer, Lukas W
id: 0c894dcf-897b-11ed-a09c-8186353224b0
last_name: Bauer
- first_name: Victor-Valentin
full_name: Hodirnau, Victor-Valentin
id: 3661B498-F248-11E8-B48F-1D18A9856A87
last_name: Hodirnau
- first_name: Florian KM
full_name: Schur, Florian KM
id: 48AD8942-F248-11E8-B48F-1D18A9856A87
last_name: Schur
orcid: 0000-0003-4790-8078
citation:
ama: Datler J, Hansen J, Thader A, et al. Multi-modal cryo-EM reveals trimers of
protein A10 to form the palisade layer in poxvirus cores. Nature Structural
& Molecular Biology. 2024. doi:10.1038/s41594-023-01201-6
apa: Datler, J., Hansen, J., Thader, A., Schlögl, A., Bauer, L. W., Hodirnau, V.-V.,
& Schur, F. K. (2024). Multi-modal cryo-EM reveals trimers of protein A10
to form the palisade layer in poxvirus cores. Nature Structural & Molecular
Biology. Springer Nature. https://doi.org/10.1038/s41594-023-01201-6
chicago: Datler, Julia, Jesse Hansen, Andreas Thader, Alois Schlögl, Lukas W Bauer,
Victor-Valentin Hodirnau, and Florian KM Schur. “Multi-Modal Cryo-EM Reveals Trimers
of Protein A10 to Form the Palisade Layer in Poxvirus Cores.” Nature Structural
& Molecular Biology. Springer Nature, 2024. https://doi.org/10.1038/s41594-023-01201-6.
ieee: J. Datler et al., “Multi-modal cryo-EM reveals trimers of protein A10
to form the palisade layer in poxvirus cores,” Nature Structural & Molecular
Biology. Springer Nature, 2024.
ista: Datler J, Hansen J, Thader A, Schlögl A, Bauer LW, Hodirnau V-V, Schur FK.
2024. Multi-modal cryo-EM reveals trimers of protein A10 to form the palisade
layer in poxvirus cores. Nature Structural & Molecular Biology.
mla: Datler, Julia, et al. “Multi-Modal Cryo-EM Reveals Trimers of Protein A10 to
Form the Palisade Layer in Poxvirus Cores.” Nature Structural & Molecular
Biology, Springer Nature, 2024, doi:10.1038/s41594-023-01201-6.
short: J. Datler, J. Hansen, A. Thader, A. Schlögl, L.W. Bauer, V.-V. Hodirnau,
F.K. Schur, Nature Structural & Molecular Biology (2024).
date_created: 2024-02-12T09:59:45Z
date_published: 2024-02-05T00:00:00Z
date_updated: 2024-03-05T09:27:47Z
day: '05'
ddc:
- '570'
department:
- _id: FlSc
- _id: ScienComp
- _id: EM-Fac
doi: 10.1038/s41594-023-01201-6
external_id:
pmid:
- '38316877'
has_accepted_license: '1'
keyword:
- Molecular Biology
- Structural Biology
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.1038/s41594-023-01201-6
month: '02'
oa: 1
oa_version: Published Version
pmid: 1
project:
- _id: 26736D6A-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: P31445
name: Structural conservation and diversity in retroviral capsid
publication: Nature Structural & Molecular Biology
publication_identifier:
eissn:
- 1545-9985
issn:
- 1545-9993
publication_status: epub_ahead
publisher: Springer Nature
quality_controlled: '1'
related_material:
link:
- description: News on ISTA Website
relation: press_release
url: https://ista.ac.at/en/news/down-to-the-core-of-poxviruses/
status: public
title: Multi-modal cryo-EM reveals trimers of protein A10 to form the palisade layer
in poxvirus cores
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: '2024'
...
---
_id: '15020'
abstract:
- lang: eng
text: "This thesis consists of four distinct pieces of work within theoretical biology,
with two themes in common: the concept of optimization in biological systems,
and the use of information-theoretic tools to quantify biological stochasticity
and statistical uncertainty.\r\nChapter 2 develops a statistical framework for
studying biological systems which we believe to be optimized for a particular
utility function, such as retinal neurons conveying information about visual stimuli.
We formalize such beliefs as maximum-entropy Bayesian priors, constrained by the
expected utility. We explore how such priors aid inference of system parameters
with limited data and enable optimality hypothesis testing: is the utility higher
than by chance?\r\nChapter 3 examines the ultimate biological optimization process:
evolution by natural selection. As some individuals survive and reproduce more
successfully than others, populations evolve towards fitter genotypes and phenotypes.
We formalize this as accumulation of genetic information, and use population genetics
theory to study how much such information can be accumulated per generation and
maintained in the face of random mutation and genetic drift. We identify the population
size and fitness variance as the key quantities that control information accumulation
and maintenance.\r\nChapter 4 reuses the concept of genetic information from Chapter
3, but from a different perspective: we ask how much genetic information organisms
actually need, in particular in the context of gene regulation. For example, how
much information is needed to bind transcription factors at correct locations
within the genome? Population genetics provides us with a refined answer: with
an increasing population size, populations achieve higher fitness by maintaining
more genetic information. Moreover, regulatory parameters experience selection
pressure to optimize the fitness-information trade-off, i.e. minimize the information
needed for a given fitness. This provides an evolutionary derivation of the optimization
priors introduced in Chapter 2.\r\nChapter 5 proves an upper bound on mutual information
between a signal and a communication channel output (such as neural activity).
Mutual information is an important utility measure for biological systems, but
its practical use can be difficult due to the large dimensionality of many biological
channels. Sometimes, a lower bound on mutual information is computed by replacing
the high-dimensional channel outputs with decodes (signal estimates). Our result
provides a corresponding upper bound, provided that the decodes are the maximum
posterior estimates of the signal."
acknowledged_ssus:
- _id: ScienComp
alternative_title:
- ISTA Thesis
article_processing_charge: No
author:
- first_name: Michal
full_name: Hledik, Michal
id: 4171253A-F248-11E8-B48F-1D18A9856A87
last_name: Hledik
citation:
ama: Hledik M. Genetic information and biological optimization. 2024. doi:10.15479/at:ista:15020
apa: Hledik, M. (2024). Genetic information and biological optimization.
Institute of Science and Technology Austria. https://doi.org/10.15479/at:ista:15020
chicago: Hledik, Michal. “Genetic Information and Biological Optimization.” Institute
of Science and Technology Austria, 2024. https://doi.org/10.15479/at:ista:15020.
ieee: M. Hledik, “Genetic information and biological optimization,” Institute of
Science and Technology Austria, 2024.
ista: Hledik M. 2024. Genetic information and biological optimization. Institute
of Science and Technology Austria.
mla: Hledik, Michal. Genetic Information and Biological Optimization. Institute
of Science and Technology Austria, 2024, doi:10.15479/at:ista:15020.
short: M. Hledik, Genetic Information and Biological Optimization, Institute of
Science and Technology Austria, 2024.
date_created: 2024-02-23T14:02:04Z
date_published: 2024-02-23T00:00:00Z
date_updated: 2025-06-30T13:21:09Z
day: '23'
ddc:
- '576'
- '519'
department:
- _id: GradSch
- _id: NiBa
- _id: GaTk
doi: 10.15479/at:ista:15020
ec_funded: 1
file:
- access_level: open_access
checksum: b2d3da47c98d481577a4baf68944fe41
content_type: application/pdf
creator: mhledik
date_created: 2024-02-23T13:50:53Z
date_updated: 2024-02-23T13:50:53Z
file_id: '15021'
file_name: hledik thesis pdfa 2b.pdf
file_size: 7102089
relation: main_file
success: 1
- access_level: closed
checksum: eda9b9430da2610fee7ce1c1419a479a
content_type: application/zip
creator: mhledik
date_created: 2024-02-23T13:50:54Z
date_updated: 2024-02-23T14:20:16Z
file_id: '15022'
file_name: hledik thesis source.zip
file_size: 14014790
relation: source_file
file_date_updated: 2024-02-23T14:20:16Z
has_accepted_license: '1'
keyword:
- Theoretical biology
- Optimality
- Evolution
- Information
language:
- iso: eng
month: '02'
oa: 1
oa_version: Published Version
page: '158'
project:
- _id: 2564DBCA-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '665385'
name: International IST Doctoral Program
- _id: 2665AAFE-B435-11E9-9278-68D0E5697425
grant_number: RGP0034/2018
name: Can evolution minimize spurious signaling crosstalk to reach optimal performance?
- _id: bd6958e0-d553-11ed-ba76-86eba6a76c00
grant_number: '101055327'
name: Understanding the evolution of continuous genomes
publication_identifier:
issn:
- 2663 - 337X
publication_status: published
publisher: Institute of Science and Technology Austria
related_material:
record:
- id: '7553'
relation: part_of_dissertation
status: public
- id: '7606'
relation: part_of_dissertation
status: public
- id: '12081'
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: Gašper
full_name: Tkačik, Gašper
id: 3D494DCA-F248-11E8-B48F-1D18A9856A87
last_name: Tkačik
orcid: 0000-0002-6699-1455
title: Genetic information and biological optimization
type: dissertation
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
year: '2024'
...
---
_id: '14341'
abstract:
- lang: eng
text: Flows through pipes and channels are, in practice, almost always turbulent,
and the multiscale eddying motion is responsible for a major part of the encountered
friction losses and pumping costs1. Conversely, for pulsatile flows, in particular
for aortic blood flow, turbulence levels remain low despite relatively large peak
velocities. For aortic blood flow, high turbulence levels are intolerable as they
would damage the shear-sensitive endothelial cell layer2,3,4,5. Here we show that
turbulence in ordinary pipe flow is diminished if the flow is driven in a pulsatile
mode that incorporates all the key features of the cardiac waveform. At Reynolds
numbers comparable to those of aortic blood flow, turbulence is largely inhibited,
whereas at much higher speeds, the turbulent drag is reduced by more than 25%.
This specific operation mode is more efficient when compared with steady driving,
which is the present situation for virtually all fluid transport processes ranging
from heating circuits to water, gas and oil pipelines.
acknowledged_ssus:
- _id: M-Shop
- _id: ScienComp
acknowledgement: We acknowledge the assistance of the Miba machine shop and the team
of the ISTA-HPC cluster. We thank M. Quadrio for the discussions. The work was supported
by the Simons Foundation (grant no. 662960) and by the Austrian Science Fund (grant
no. I4188-N30), within Deutsche Forschungsgemeinschaft research unit FOR 2688.
article_processing_charge: No
article_type: original
author:
- first_name: Davide
full_name: Scarselli, Davide
id: 40315C30-F248-11E8-B48F-1D18A9856A87
last_name: Scarselli
orcid: 0000-0001-5227-4271
- first_name: Jose M
full_name: Lopez Alonso, Jose M
id: 40770848-F248-11E8-B48F-1D18A9856A87
last_name: Lopez Alonso
orcid: 0000-0002-0384-2022
- first_name: Atul
full_name: Varshney, Atul
id: 2A2006B2-F248-11E8-B48F-1D18A9856A87
last_name: Varshney
orcid: 0000-0002-3072-5999
- first_name: Björn
full_name: Hof, Björn
id: 3A374330-F248-11E8-B48F-1D18A9856A87
last_name: Hof
orcid: 0000-0003-2057-2754
citation:
ama: Scarselli D, Lopez Alonso JM, Varshney A, Hof B. Turbulence suppression by
cardiac-cycle-inspired driving of pipe flow. Nature. 2023;621(7977):71-74.
doi:10.1038/s41586-023-06399-5
apa: Scarselli, D., Lopez Alonso, J. M., Varshney, A., & Hof, B. (2023). Turbulence
suppression by cardiac-cycle-inspired driving of pipe flow. Nature. Springer
Nature. https://doi.org/10.1038/s41586-023-06399-5
chicago: Scarselli, Davide, Jose M Lopez Alonso, Atul Varshney, and Björn Hof. “Turbulence
Suppression by Cardiac-Cycle-Inspired Driving of Pipe Flow.” Nature. Springer
Nature, 2023. https://doi.org/10.1038/s41586-023-06399-5.
ieee: D. Scarselli, J. M. Lopez Alonso, A. Varshney, and B. Hof, “Turbulence suppression
by cardiac-cycle-inspired driving of pipe flow,” Nature, vol. 621, no.
7977. Springer Nature, pp. 71–74, 2023.
ista: Scarselli D, Lopez Alonso JM, Varshney A, Hof B. 2023. Turbulence suppression
by cardiac-cycle-inspired driving of pipe flow. Nature. 621(7977), 71–74.
mla: Scarselli, Davide, et al. “Turbulence Suppression by Cardiac-Cycle-Inspired
Driving of Pipe Flow.” Nature, vol. 621, no. 7977, Springer Nature, 2023,
pp. 71–74, doi:10.1038/s41586-023-06399-5.
short: D. Scarselli, J.M. Lopez Alonso, A. Varshney, B. Hof, Nature 621 (2023) 71–74.
date_created: 2023-09-17T22:01:09Z
date_published: 2023-09-07T00:00:00Z
date_updated: 2023-09-20T12:10:22Z
day: '07'
department:
- _id: BjHo
doi: 10.1038/s41586-023-06399-5
external_id:
pmid:
- '37673988'
intvolume: ' 621'
issue: '7977'
language:
- iso: eng
month: '09'
oa_version: None
page: 71-74
pmid: 1
project:
- _id: 238598C6-32DE-11EA-91FC-C7463DDC885E
grant_number: '662960'
name: 'Revisiting the Turbulence Problem Using Statistical Mechanics: Experimental
Studies on Transitional and Turbulent Flows'
- _id: 238B8092-32DE-11EA-91FC-C7463DDC885E
call_identifier: FWF
grant_number: I04188
name: Instabilities in pulsating pipe flow of Newtonian and complex fluids
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://www.ista.ac.at/en/news/pumping-like-the-heart/
scopus_import: '1'
status: public
title: Turbulence suppression by cardiac-cycle-inspired driving of pipe flow
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 621
year: '2023'
...
---
_id: '14458'
abstract:
- lang: eng
text: 'We show for the first time that large-scale generative pretrained transformer
(GPT) family models can be pruned to at least 50% sparsity in one-shot, without
any retraining, at minimal loss of accuracy. This is achieved via a new pruning
method called SparseGPT, specifically designed to work efficiently and accurately
on massive GPT-family models. We can execute SparseGPT on the largest available
open-source models, OPT-175B and BLOOM-176B, in under 4.5 hours, and can reach
60% unstructured sparsity with negligible increase in perplexity: remarkably,
more than 100 billion weights from these models can be ignored at inference time.
SparseGPT generalizes to semi-structured (2:4 and 4:8) patterns, and is compatible
with weight quantization approaches. The code is available at: https://github.com/IST-DASLab/sparsegpt.'
acknowledged_ssus:
- _id: ScienComp
acknowledgement: The authors gratefully acknowledge funding from the European Research
Council (ERC) under the European Union’s Horizon 2020 programme (grant agreement
No. 805223 ScaleML), as well as experimental support from Eldar Kurtic, and from
the IST Austria IT department, in particular Stefano Elefante, Andrei Hornoiu, and
Alois Schloegl.
alternative_title:
- PMLR
article_processing_charge: No
arxiv: 1
author:
- first_name: Elias
full_name: Frantar, Elias
id: 09a8f98d-ec99-11ea-ae11-c063a7b7fe5f
last_name: Frantar
- 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: 'Frantar E, Alistarh D-A. SparseGPT: Massive language models can be accurately
pruned in one-shot. In: Proceedings of the 40th International Conference on
Machine Learning. Vol 202. ML Research Press; 2023:10323-10337.'
apa: 'Frantar, E., & Alistarh, D.-A. (2023). SparseGPT: Massive language models
can be accurately pruned in one-shot. In Proceedings of the 40th International
Conference on Machine Learning (Vol. 202, pp. 10323–10337). Honolulu, Hawaii,
HI, United States: ML Research Press.'
chicago: 'Frantar, Elias, and Dan-Adrian Alistarh. “SparseGPT: Massive Language
Models Can Be Accurately Pruned in One-Shot.” In Proceedings of the 40th International
Conference on Machine Learning, 202:10323–37. ML Research Press, 2023.'
ieee: 'E. Frantar and D.-A. Alistarh, “SparseGPT: Massive language models can be
accurately pruned in one-shot,” in Proceedings of the 40th International Conference
on Machine Learning, Honolulu, Hawaii, HI, United States, 2023, vol. 202,
pp. 10323–10337.'
ista: 'Frantar E, Alistarh D-A. 2023. SparseGPT: Massive language models can be
accurately pruned in one-shot. Proceedings of the 40th International Conference
on Machine Learning. ICML: International Conference on Machine Learning, PMLR,
vol. 202, 10323–10337.'
mla: 'Frantar, Elias, and Dan-Adrian Alistarh. “SparseGPT: Massive Language Models
Can Be Accurately Pruned in One-Shot.” Proceedings of the 40th International
Conference on Machine Learning, vol. 202, ML Research Press, 2023, pp. 10323–37.'
short: E. Frantar, D.-A. Alistarh, in:, Proceedings of the 40th International Conference
on Machine Learning, ML Research Press, 2023, pp. 10323–10337.
conference:
end_date: 2023-07-29
location: Honolulu, Hawaii, HI, United States
name: 'ICML: International Conference on Machine Learning'
start_date: 2023-07-23
date_created: 2023-10-29T23:01:16Z
date_published: 2023-07-30T00:00:00Z
date_updated: 2023-10-31T09:59:42Z
day: '30'
department:
- _id: DaAl
ec_funded: 1
external_id:
arxiv:
- '2301.00774'
intvolume: ' 202'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.48550/arXiv.2301.00774
month: '07'
oa: 1
oa_version: Preprint
page: 10323-10337
project:
- _id: 268A44D6-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '805223'
name: Elastic Coordination for Scalable Machine Learning
publication: Proceedings of the 40th International Conference on Machine Learning
publication_identifier:
eissn:
- 2640-3498
publication_status: published
publisher: ML Research Press
quality_controlled: '1'
scopus_import: '1'
status: public
title: 'SparseGPT: Massive language models can be accurately pruned in one-shot'
type: conference
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 202
year: '2023'
...
---
_id: '14461'
abstract:
- lang: eng
text: 'Communication-reduction techniques are a popular way to improve scalability
in data-parallel training of deep neural networks (DNNs). The recent emergence
of large language models such as GPT has created the need for new approaches to
exploit data-parallelism. Among these, fully-sharded data parallel (FSDP) training
is highly popular, yet it still encounters scalability bottlenecks. One reason
is that applying compression techniques to FSDP is challenging: as the vast majority
of the communication involves the model’s weights, direct compression alters convergence
and leads to accuracy loss. We present QSDP, a variant of FSDP which supports
both gradient and weight quantization with theoretical guarantees, is simple to
implement and has essentially no overheads. To derive QSDP we prove that a natural
modification of SGD achieves convergence even when we only maintain quantized
weights, and thus the domain over which we train consists of quantized points
and is, therefore, highly non-convex. We validate this approach by training GPT-family
models with up to 1.3 billion parameters on a multi-node cluster. Experiments
show that QSDP preserves model accuracy, while completely removing the communication
bottlenecks of FSDP, providing end-to-end speedups of up to 2.2x.'
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 programme
(grant agreement No 805223 ScaleML), as well as experimental support from the IST
Austria IT department, in particular Stefano Elefante, Andrei Hornoiu, and Alois
Schloegl. AV acknowledges the support of the French Agence Nationale de la Recherche
(ANR), under grant ANR-21-CE48-0016 (project COMCOPT), the support of Fondation
Hadamard with a PRMO grant, and the support of CNRS with a CoopIntEER IEA grant
(project ALFRED).
alternative_title:
- PMLR
article_processing_charge: No
arxiv: 1
author:
- first_name: Ilia
full_name: Markov, Ilia
id: D0CF4148-C985-11E9-8066-0BDEE5697425
last_name: Markov
- first_name: Adrian
full_name: Vladu, Adrian
last_name: Vladu
- first_name: Qi
full_name: Guo, Qi
last_name: Guo
- 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: 'Markov I, Vladu A, Guo Q, Alistarh D-A. Quantized distributed training of
large models with convergence guarantees. In: Proceedings of the 40th International
Conference on Machine Learning. Vol 202. ML Research Press; 2023:24020-24044.'
apa: 'Markov, I., Vladu, A., Guo, Q., & Alistarh, D.-A. (2023). Quantized distributed
training of large models with convergence guarantees. In Proceedings of the
40th International Conference on Machine Learning (Vol. 202, pp. 24020–24044).
Honolulu, Hawaii, HI, United States: ML Research Press.'
chicago: Markov, Ilia, Adrian Vladu, Qi Guo, and Dan-Adrian Alistarh. “Quantized
Distributed Training of Large Models with Convergence Guarantees.” In Proceedings
of the 40th International Conference on Machine Learning, 202:24020–44. ML
Research Press, 2023.
ieee: I. Markov, A. Vladu, Q. Guo, and D.-A. Alistarh, “Quantized distributed training
of large models with convergence guarantees,” in Proceedings of the 40th International
Conference on Machine Learning, Honolulu, Hawaii, HI, United States, 2023,
vol. 202, pp. 24020–24044.
ista: 'Markov I, Vladu A, Guo Q, Alistarh D-A. 2023. Quantized distributed training
of large models with convergence guarantees. Proceedings of the 40th International
Conference on Machine Learning. ICML: International Conference on Machine Learning,
PMLR, vol. 202, 24020–24044.'
mla: Markov, Ilia, et al. “Quantized Distributed Training of Large Models with Convergence
Guarantees.” Proceedings of the 40th International Conference on Machine Learning,
vol. 202, ML Research Press, 2023, pp. 24020–44.
short: I. Markov, A. Vladu, Q. Guo, D.-A. Alistarh, in:, Proceedings of the 40th
International Conference on Machine Learning, ML Research Press, 2023, pp. 24020–24044.
conference:
end_date: 2023-07-29
location: Honolulu, Hawaii, HI, United States
name: 'ICML: International Conference on Machine Learning'
start_date: 2023-07-23
date_created: 2023-10-29T23:01:17Z
date_published: 2023-07-30T00:00:00Z
date_updated: 2023-10-31T09:40:45Z
day: '30'
department:
- _id: DaAl
ec_funded: 1
external_id:
arxiv:
- '2302.02390'
intvolume: ' 202'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.48550/arXiv.2302.02390
month: '07'
oa: 1
oa_version: Preprint
page: 24020-24044
project:
- _id: 268A44D6-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '805223'
name: Elastic Coordination for Scalable Machine Learning
publication: Proceedings of the 40th International Conference on Machine Learning
publication_identifier:
eissn:
- 2640-3498
publication_status: published
publisher: ML Research Press
quality_controlled: '1'
scopus_import: '1'
status: public
title: Quantized distributed training of large models with convergence guarantees
type: conference
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 202
year: '2023'
...
---
_id: '14562'
abstract:
- lang: eng
text: "Regulation of the Arp2/3 complex is required for productive nucleation of
branched actin networks. An emerging aspect of regulation is the incorporation
of subunit isoforms into the Arp2/3 complex. Specifically, both ArpC5 subunit
isoforms, ArpC5 and ArpC5L, have been reported to fine-tune nucleation activity
and branch junction stability. We have combined reverse genetics and cellular
structural biology to describe how ArpC5 and ArpC5L differentially affect cell
migration. Both define the structural stability of ArpC1 in branch junctions and,
in turn, by determining protrusion characteristics, affect protein dynamics and
actin network ultrastructure. ArpC5 isoforms also affect the positioning of members
of the Ena/Vasodilator-stimulated phosphoprotein (VASP) family of actin filament
elongators, which mediate ArpC5 isoform–specific effects on the actin assembly
level. Our results suggest that ArpC5 and Ena/VASP proteins are part of a signaling
pathway enhancing cell migration.\r\n"
acknowledged_ssus:
- _id: LifeSc
- _id: Bio
- _id: ScienComp
- _id: EM-Fac
acknowledgement: "We would like to thank K. von Peinen and B. Denker (Helmholtz Centre
for Infection Research, Braunschweig, Germany) for experimental and technical assistance,
respectively.\r\nFunding: This research was supported by the Scientific Service
Units (SSUs) of ISTA through resources provided by Scientific Computing (SciComp),
the Life Science Facility (LSF), the Imaging and Optics facility (IOF), and the
Electron Microscopy Facility (EMF). We acknowledge support from ISTA and from the
Austrian Science Fund (FWF) (P33367) to F.K.M.S., from the Research Training Group
GRK2223 and the Helmholtz Society to K.R,. and from the Deutsche Forschungsgemeinschaft
(DFG) to J.F. and K.R."
article_processing_charge: No
author:
- first_name: Florian KM
full_name: Schur, Florian KM
id: 48AD8942-F248-11E8-B48F-1D18A9856A87
last_name: Schur
orcid: 0000-0003-4790-8078
citation:
ama: Schur FK. Research data of the publication “ArpC5 isoforms regulate Arp2/3
complex-dependent protrusion through differential Ena/VASP positioning.” 2023.
doi:10.15479/AT:ISTA:14562
apa: Schur, F. K. (2023). Research data of the publication “ArpC5 isoforms regulate
Arp2/3 complex-dependent protrusion through differential Ena/VASP positioning.”
Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:14562
chicago: Schur, Florian KM. “Research Data of the Publication ‘ArpC5 Isoforms Regulate
Arp2/3 Complex-Dependent Protrusion through Differential Ena/VASP Positioning.’”
Institute of Science and Technology Austria, 2023. https://doi.org/10.15479/AT:ISTA:14562.
ieee: F. K. Schur, “Research data of the publication ‘ArpC5 isoforms regulate Arp2/3
complex-dependent protrusion through differential Ena/VASP positioning.’” Institute
of Science and Technology Austria, 2023.
ista: Schur FK. 2023. Research data of the publication ‘ArpC5 isoforms regulate
Arp2/3 complex-dependent protrusion through differential Ena/VASP positioning’,
Institute of Science and Technology Austria, 10.15479/AT:ISTA:14562.
mla: Schur, Florian KM. Research Data of the Publication “ArpC5 Isoforms Regulate
Arp2/3 Complex-Dependent Protrusion through Differential Ena/VASP Positioning.”
Institute of Science and Technology Austria, 2023, doi:10.15479/AT:ISTA:14562.
short: F.K. Schur, (2023).
contributor:
- contributor_type: researcher
first_name: Florian
id: 404F5528-F248-11E8-B48F-1D18A9856A87
last_name: Fäßler
orcid: 0000-0001-7149-769X
- contributor_type: researcher
first_name: Manjunath
id: 305ab18b-dc7d-11ea-9b2f-b58195228ea2
last_name: Javoor
- contributor_type: researcher
first_name: Julia
id: 3B12E2E6-F248-11E8-B48F-1D18A9856A87
last_name: Datler
orcid: 0000-0002-3616-8580
- contributor_type: researcher
first_name: Hermann
last_name: Döring
- contributor_type: researcher
first_name: Florian
id: b9d234ba-9e33-11ed-95b6-cd561df280e6
last_name: Hofer
- contributor_type: researcher
first_name: Georgi A
id: 38C393BE-F248-11E8-B48F-1D18A9856A87
last_name: Dimchev
orcid: 0000-0001-8370-6161
- contributor_type: researcher
first_name: Victor-Valentin
id: 3661B498-F248-11E8-B48F-1D18A9856A87
last_name: Hodirnau
- contributor_type: researcher
first_name: Jan
last_name: Faix
- contributor_type: researcher
first_name: Klemens
last_name: Rottner
- contributor_type: researcher
first_name: Florian KM
id: 48AD8942-F248-11E8-B48F-1D18A9856A87
last_name: Schur
orcid: 0000-0003-4790-8078
date_created: 2023-11-20T09:22:33Z
date_published: 2023-11-21T00:00:00Z
date_updated: 2023-11-21T08:05:34Z
day: '21'
ddc:
- '570'
department:
- _id: FlSc
doi: 10.15479/AT:ISTA:14562
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has_accepted_license: '1'
license: https://creativecommons.org/licenses/by-sa/4.0/
month: '11'
oa: 1
oa_version: Published Version
project:
- _id: 9B954C5C-BA93-11EA-9121-9846C619BF3A
grant_number: P33367
name: Structure and isoform diversity of the Arp2/3 complex
publisher: Institute of Science and Technology Austria
related_material:
record:
- id: '12334'
relation: used_in_publication
status: public
status: public
title: Research data of the publication "ArpC5 isoforms regulate Arp2/3 complex-dependent
protrusion through differential Ena/VASP positioning"
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: 2DF688A6-F248-11E8-B48F-1D18A9856A87
year: '2023'
...
---
_id: '14613'
abstract:
- lang: eng
text: 'Many insects carry an ancient X chromosome - the Drosophila Muller element
F - that likely predates their origin. Interestingly, the X has undergone turnover
in multiple fly species (Diptera) after being conserved for more than 450 MY.
The long evolutionary distance between Diptera and other sequenced insect clades
makes it difficult to infer what could have contributed to this sudden increase
in rate of turnover. Here, we produce the first genome and transcriptome of a
long overlooked sister-order to Diptera: Mecoptera. We compare the scorpionfly
Panorpa cognata X-chromosome gene content, expression, and structure, to that
of several dipteran species as well as more distantly-related insect orders (Orthoptera
and Blattodea). We find high conservation of gene content between the mecopteran
X and the dipteran Muller F element, as well as several shared biological features,
such as the presence of dosage compensation and a low amount of genetic diversity,
consistent with a low recombination rate. However, the two homologous X chromosomes
differ strikingly in their size and number of genes they carry. Our results therefore
support a common ancestry of the mecopteran and ancestral dipteran X chromosomes,
and suggest that Muller element F shrank in size and gene content after the split
of Diptera and Mecoptera, which may have contributed to its turnover in dipteran
insects.'
acknowledged_ssus:
- _id: ScienComp
acknowledgement: "We thank the Vicoso lab for their assistance with specimen collection,
and Tim Connallon for valuable comments and suggestions on earlier versions of the
manuscript. Computational resources and support were provided by the Scientific
Computing unit at the ISTA. This research was supported by grants from the Austrian
Science Foundation to C.L.\r\n(FWF ESP 39), and to B.V. (FWF SFB F88-10)."
article_number: msad245
article_processing_charge: Yes (via OA deal)
article_type: original
author:
- first_name: Clementine
full_name: Lasne, Clementine
id: 02225f57-50d2-11eb-9ed8-8c92b9a34237
last_name: Lasne
orcid: 0000-0002-1197-8616
- first_name: Marwan N
full_name: Elkrewi, Marwan N
id: 0B46FACA-A8E1-11E9-9BD3-79D1E5697425
last_name: Elkrewi
orcid: 0000-0002-5328-7231
- first_name: Melissa A
full_name: Toups, Melissa A
id: 4E099E4E-F248-11E8-B48F-1D18A9856A87
last_name: Toups
orcid: 0000-0002-9752-7380
- first_name: Lorena Alexandra
full_name: Layana Franco, Lorena Alexandra
id: 02814589-eb8f-11eb-b029-a70074f3f18f
last_name: Layana Franco
orcid: 0000-0002-1253-6297
- first_name: Ariana
full_name: Macon, Ariana
id: 2A0848E2-F248-11E8-B48F-1D18A9856A87
last_name: Macon
- first_name: Beatriz
full_name: Vicoso, Beatriz
id: 49E1C5C6-F248-11E8-B48F-1D18A9856A87
last_name: Vicoso
orcid: 0000-0002-4579-8306
citation:
ama: Lasne C, Elkrewi MN, Toups MA, Layana Franco LA, Macon A, Vicoso B. The scorpionfly
(Panorpa cognata) genome highlights conserved and derived features of the peculiar
dipteran X chromosome. Molecular Biology and Evolution. 2023;40(12). doi:10.1093/molbev/msad245
apa: Lasne, C., Elkrewi, M. N., Toups, M. A., Layana Franco, L. A., Macon, A., &
Vicoso, B. (2023). The scorpionfly (Panorpa cognata) genome highlights conserved
and derived features of the peculiar dipteran X chromosome. Molecular Biology
and Evolution. Oxford University Press. https://doi.org/10.1093/molbev/msad245
chicago: Lasne, Clementine, Marwan N Elkrewi, Melissa A Toups, Lorena Alexandra
Layana Franco, Ariana Macon, and Beatriz Vicoso. “The Scorpionfly (Panorpa Cognata)
Genome Highlights Conserved and Derived Features of the Peculiar Dipteran X Chromosome.”
Molecular Biology and Evolution. Oxford University Press, 2023. https://doi.org/10.1093/molbev/msad245.
ieee: C. Lasne, M. N. Elkrewi, M. A. Toups, L. A. Layana Franco, A. Macon, and B.
Vicoso, “The scorpionfly (Panorpa cognata) genome highlights conserved and derived
features of the peculiar dipteran X chromosome,” Molecular Biology and Evolution,
vol. 40, no. 12. Oxford University Press, 2023.
ista: Lasne C, Elkrewi MN, Toups MA, Layana Franco LA, Macon A, Vicoso B. 2023.
The scorpionfly (Panorpa cognata) genome highlights conserved and derived features
of the peculiar dipteran X chromosome. Molecular Biology and Evolution. 40(12),
msad245.
mla: Lasne, Clementine, et al. “The Scorpionfly (Panorpa Cognata) Genome Highlights
Conserved and Derived Features of the Peculiar Dipteran X Chromosome.” Molecular
Biology and Evolution, vol. 40, no. 12, msad245, Oxford University Press,
2023, doi:10.1093/molbev/msad245.
short: C. Lasne, M.N. Elkrewi, M.A. Toups, L.A. Layana Franco, A. Macon, B. Vicoso,
Molecular Biology and Evolution 40 (2023).
date_created: 2023-11-27T16:14:37Z
date_published: 2023-12-01T00:00:00Z
date_updated: 2024-02-21T12:18:35Z
day: '01'
ddc:
- '570'
department:
- _id: BeVi
doi: 10.1093/molbev/msad245
external_id:
pmid:
- '37988296'
file:
- access_level: open_access
checksum: 47c1c72fb499f26ea52d216b242208c8
content_type: application/pdf
creator: dernst
date_created: 2024-01-02T11:39:38Z
date_updated: 2024-01-02T11:39:38Z
file_id: '14727'
file_name: 2023_MolecularBioEvo_Lasne.pdf
file_size: 8623505
relation: main_file
success: 1
file_date_updated: 2024-01-02T11:39:38Z
has_accepted_license: '1'
intvolume: ' 40'
issue: '12'
keyword:
- Genetics
- Molecular Biology
- Ecology
- Evolution
- Behavior and Systematics
language:
- iso: eng
month: '12'
oa: 1
oa_version: Published Version
pmid: 1
project:
- _id: 34ae1506-11ca-11ed-8bc3-c14f4c474396
grant_number: F8810
name: The highjacking of meiosis for asexual reproduction
- _id: ebb230e0-77a9-11ec-83b8-87a37e0241d3
grant_number: ESP39 49461
name: Mechanisms and Evolution of Reproductive Plasticity
publication: Molecular Biology and Evolution
publication_identifier:
eissn:
- 1537-1719
issn:
- 0737-4038
publication_status: published
publisher: Oxford University Press
quality_controlled: '1'
related_material:
link:
- description: News on ISTA webpage
relation: press_release
url: https://ista.ac.at/en/news/on-the-hunt/
record:
- id: '14614'
relation: research_data
status: public
scopus_import: '1'
status: public
title: The scorpionfly (Panorpa cognata) genome highlights conserved and derived features
of the peculiar dipteran X chromosome
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: 40
year: '2023'
...
---
_id: '14651'
abstract:
- lang: eng
text: 'For self-incompatibility (SI) to be stable in a population, theory predicts
that sufficient inbreeding depression (ID) is required: the fitness of offspring
from self-mated individuals must be low enough to prevent the spread of self-compatibility
(SC). Reviews of natural plant populations have supported this theory, with SI
species generally showing high levels of ID. However, there is thought to be an
under-sampling of self-incompatible taxa in the current literature. In this thesis,
I study inbreeding depression in the SI plant species Antirrhinum majus using
both greenhouse crosses and a large collected field dataset. Additionally, the
gametophytic S-locus of A. majus is highly heterozygous and polymorphic, thus
making assembly and discovery of S-alleles very difficult. Here, 206 new alleles
of the male component SLFs are presented, along with a phylogeny showing the high
conservation with alleles from another Antirrhinum species. Lastly, selected sites
within the protein structure of SLFs are investigated, with one site in particular
highlighted as potentially being involved in the SI recognition mechanism.'
acknowledged_ssus:
- _id: ScienComp
alternative_title:
- ISTA Thesis
article_processing_charge: No
author:
- first_name: Louise S
full_name: Arathoon, Louise S
id: 2CFCFF98-F248-11E8-B48F-1D18A9856A87
last_name: Arathoon
orcid: 0000-0003-1771-714X
citation:
ama: Arathoon LS. Investigating inbreeding depression and the self-incompatibility
locus of Antirrhinum majus. 2023. doi:10.15479/at:ista:14651
apa: Arathoon, L. S. (2023). Investigating inbreeding depression and the self-incompatibility
locus of Antirrhinum majus. Institute of Science and Technology Austria. https://doi.org/10.15479/at:ista:14651
chicago: Arathoon, Louise S. “Investigating Inbreeding Depression and the Self-Incompatibility
Locus of Antirrhinum Majus.” Institute of Science and Technology Austria, 2023.
https://doi.org/10.15479/at:ista:14651.
ieee: L. S. Arathoon, “Investigating inbreeding depression and the self-incompatibility
locus of Antirrhinum majus,” Institute of Science and Technology Austria, 2023.
ista: Arathoon LS. 2023. Investigating inbreeding depression and the self-incompatibility
locus of Antirrhinum majus. Institute of Science and Technology Austria.
mla: Arathoon, Louise S. Investigating Inbreeding Depression and the Self-Incompatibility
Locus of Antirrhinum Majus. Institute of Science and Technology Austria, 2023,
doi:10.15479/at:ista:14651.
short: L.S. Arathoon, Investigating Inbreeding Depression and the Self-Incompatibility
Locus of Antirrhinum Majus, Institute of Science and Technology Austria, 2023.
date_created: 2023-12-11T19:30:37Z
date_published: 2023-12-12T00:00:00Z
date_updated: 2023-12-22T11:04:45Z
day: '12'
ddc:
- '570'
degree_awarded: PhD
department:
- _id: GradSch
- _id: NiBa
doi: 10.15479/at:ista:14651
ec_funded: 1
file:
- access_level: open_access
checksum: 520bdb61e95e66070e02824947d2c5fa
content_type: application/pdf
creator: larathoo
date_created: 2023-12-13T15:37:55Z
date_updated: 2023-12-13T15:37:55Z
file_id: '14684'
file_name: Phd_Thesis_LA.pdf
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language:
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month: '12'
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oa_version: Published Version
page: '96'
project:
- _id: 2564DBCA-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '665385'
name: International IST Doctoral Program
publication_identifier:
issn:
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publication_status: published
publisher: Institute of Science and Technology Austria
related_material:
record:
- id: '11411'
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
title: Investigating inbreeding depression and the self-incompatibility locus of Antirrhinum
majus
type: dissertation
user_id: 8b945eb4-e2f2-11eb-945a-df72226e66a9
year: '2023'
...
---
_id: '14748'
acknowledged_ssus:
- _id: ScienComp
acknowledgement: We thank the anonymous reviewers and the members of the Visual Computing
Group at ISTA for their helpful comments. 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: '5'
article_processing_charge: No
author:
- first_name: Yi-Lu
full_name: Chen, Yi-Lu
id: 0b467602-dbcd-11ea-9d1d-ed480aa46b70
last_name: Chen
- first_name: Mickaël
full_name: Ly, Mickaël
id: 6340d7f0-b48d-11eb-b10d-b7487e71d9f1
last_name: Ly
- first_name: Christopher J
full_name: Wojtan, Christopher J
id: 3C61F1D2-F248-11E8-B48F-1D18A9856A87
last_name: Wojtan
orcid: 0000-0001-6646-5546
citation:
ama: 'Chen Y-L, Ly M, Wojtan C. Unified treatment of contact, friction and shock-propagation
in rigid body animation. In: Proceedings of the ACM SIGGRAPH/Eurographics Symposium
on Computer Animation. Association for Computing Machinery; 2023. doi:10.1145/3606037.3606836'
apa: 'Chen, Y.-L., Ly, M., & Wojtan, C. (2023). Unified treatment of contact,
friction and shock-propagation in rigid body animation. In Proceedings of the
ACM SIGGRAPH/Eurographics Symposium on Computer Animation. Los Angeles, CA,
United States: Association for Computing Machinery. https://doi.org/10.1145/3606037.3606836'
chicago: Chen, Yi-Lu, Mickaël Ly, and Chris Wojtan. “Unified Treatment of Contact,
Friction and Shock-Propagation in Rigid Body Animation.” In Proceedings of
the ACM SIGGRAPH/Eurographics Symposium on Computer Animation. Association
for Computing Machinery, 2023. https://doi.org/10.1145/3606037.3606836.
ieee: Y.-L. Chen, M. Ly, and C. Wojtan, “Unified treatment of contact, friction
and shock-propagation in rigid body animation,” in Proceedings of the ACM SIGGRAPH/Eurographics
Symposium on Computer Animation, Los Angeles, CA, United States, 2023.
ista: 'Chen Y-L, Ly M, Wojtan C. 2023. Unified treatment of contact, friction and
shock-propagation in rigid body animation. Proceedings of the ACM SIGGRAPH/Eurographics
Symposium on Computer Animation. SCA: Symposium on Computer Animation, 5.'
mla: Chen, Yi-Lu, et al. “Unified Treatment of Contact, Friction and Shock-Propagation
in Rigid Body Animation.” Proceedings of the ACM SIGGRAPH/Eurographics Symposium
on Computer Animation, 5, Association for Computing Machinery, 2023, doi:10.1145/3606037.3606836.
short: Y.-L. Chen, M. Ly, C. Wojtan, in:, Proceedings of the ACM SIGGRAPH/Eurographics
Symposium on Computer Animation, Association for Computing Machinery, 2023.
conference:
end_date: 2023-08-06
location: Los Angeles, CA, United States
name: 'SCA: Symposium on Computer Animation'
start_date: 2023-08-04
date_created: 2024-01-08T13:00:24Z
date_published: 2023-08-01T00:00:00Z
date_updated: 2024-02-28T12:51:40Z
day: '01'
department:
- _id: ChWo
doi: 10.1145/3606037.3606836
language:
- iso: eng
month: '08'
oa_version: None
project:
- _id: 34bc2376-11ca-11ed-8bc3-9a3b3961a088
grant_number: '101045083'
name: Computational Discovery of Numerical Algorithms for Animation and Simulation
of Natural Phenomena
publication: Proceedings of the ACM SIGGRAPH/Eurographics Symposium on Computer Animation
publication_identifier:
isbn:
- '9798400702686'
publication_status: published
publisher: Association for Computing Machinery
quality_controlled: '1'
status: public
title: Unified treatment of contact, friction and shock-propagation in rigid body
animation
type: conference_abstract
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
year: '2023'
...
---
_id: '13053'
abstract:
- lang: eng
text: 'Deep neural networks (DNNs) often have to be compressed, via pruning and/or
quantization, before they can be deployed in practical settings. In this work
we propose a new compression-aware minimizer dubbed CrAM that modifies the optimization
step in a principled way, in order to produce models whose local loss behavior
is stable under compression operations such as pruning. Thus, dense models trained
via CrAM should be compressible post-training, in a single step, without significant
accuracy loss. Experimental results on standard benchmarks, such as residual networks
for ImageNet classification and BERT models for language modelling, show that
CrAM produces dense models that can be more accurate than the standard SGD/Adam-based
baselines, but which are stable under weight pruning: specifically, we can prune
models in one-shot to 70-80% sparsity with almost no accuracy loss, and to 90%
with reasonable (∼1%) accuracy loss, which is competitive with gradual compression
methods. Additionally, CrAM can produce sparse models which perform well for transfer
learning, and it also works for semi-structured 2:4 pruning patterns supported
by GPU hardware. The code for reproducing the results is available at this https
URL .'
acknowledged_ssus:
- _id: ScienComp
acknowledgement: "AP, EK, DA received funding from the European Research Council (ERC)
under the European\r\nUnion’s Horizon 2020 research and innovation programme (grant
agreement No 805223 ScaleML). AV acknowledges the support of the French Agence Nationale
de la Recherche (ANR), under grant ANR-21-CE48-0016 (project COMCOPT). We further
acknowledge the support from the Scientific Service Units (SSU) of ISTA through
resources provided by Scientific Computing (SciComp)-"
article_processing_charge: No
arxiv: 1
author:
- first_name: Elena-Alexandra
full_name: Peste, Elena-Alexandra
id: 32D78294-F248-11E8-B48F-1D18A9856A87
last_name: Peste
- first_name: Adrian
full_name: Vladu, Adrian
last_name: Vladu
- first_name: Eldar
full_name: Kurtic, Eldar
id: 47beb3a5-07b5-11eb-9b87-b108ec578218
last_name: Kurtic
- first_name: Christoph
full_name: Lampert, Christoph
id: 40C20FD2-F248-11E8-B48F-1D18A9856A87
last_name: Lampert
orcid: 0000-0001-8622-7887
- 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: 'Peste E-A, Vladu A, Kurtic E, Lampert C, Alistarh D-A. CrAM: A Compression-Aware
Minimizer. In: 11th International Conference on Learning Representations .'
apa: 'Peste, E.-A., Vladu, A., Kurtic, E., Lampert, C., & Alistarh, D.-A. (n.d.).
CrAM: A Compression-Aware Minimizer. In 11th International Conference on Learning
Representations . Kigali, Rwanda .'
chicago: 'Peste, Elena-Alexandra, Adrian Vladu, Eldar Kurtic, Christoph Lampert,
and Dan-Adrian Alistarh. “CrAM: A Compression-Aware Minimizer.” In 11th International
Conference on Learning Representations , n.d.'
ieee: 'E.-A. Peste, A. Vladu, E. Kurtic, C. Lampert, and D.-A. Alistarh, “CrAM:
A Compression-Aware Minimizer,” in 11th International Conference on Learning
Representations , Kigali, Rwanda .'
ista: 'Peste E-A, Vladu A, Kurtic E, Lampert C, Alistarh D-A. CrAM: A Compression-Aware
Minimizer. 11th International Conference on Learning Representations . ICLR: International
Conference on Learning Representations.'
mla: 'Peste, Elena-Alexandra, et al. “CrAM: A Compression-Aware Minimizer.” 11th
International Conference on Learning Representations .'
short: E.-A. Peste, A. Vladu, E. Kurtic, C. Lampert, D.-A. Alistarh, in:, 11th International
Conference on Learning Representations , n.d.
conference:
end_date: 2023-05-05
location: 'Kigali, Rwanda '
name: 'ICLR: International Conference on Learning Representations'
start_date: 2023-05-01
date_created: 2023-05-23T11:36:18Z
date_published: 2023-05-01T00:00:00Z
date_updated: 2023-06-01T12:54:45Z
department:
- _id: GradSch
- _id: DaAl
- _id: ChLa
ec_funded: 1
external_id:
arxiv:
- '2207.14200'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://openreview.net/pdf?id=_eTZBs-yedr
month: '05'
oa: 1
oa_version: Preprint
project:
- _id: 268A44D6-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '805223'
name: Elastic Coordination for Scalable Machine Learning
publication: '11th International Conference on Learning Representations '
publication_status: accepted
quality_controlled: '1'
related_material:
record:
- id: '13074'
relation: dissertation_contains
status: public
status: public
title: 'CrAM: A Compression-Aware Minimizer'
type: conference
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
year: '2023'
...
---
_id: '13074'
abstract:
- lang: eng
text: "Deep learning has become an integral part of a large number of important
applications, and many of the recent breakthroughs have been enabled by the ability
to train very large models, capable to capture complex patterns and relationships
from the data. At the same time, the massive sizes of modern deep learning models
have made their deployment to smaller devices more challenging; this is particularly
important, as in many applications the users rely on accurate deep learning predictions,
but they only have access to devices with limited memory and compute power. One
solution to this problem is to prune neural networks, by setting as many of their
parameters as possible to zero, to obtain accurate sparse models with lower memory
footprint. Despite the great research progress in obtaining sparse models that
preserve accuracy, while satisfying memory and computational constraints, there
are still many challenges associated with efficiently training sparse models,
as well as understanding their generalization properties.\r\n\r\nThe focus of
this thesis is to investigate how the training process of sparse models can be
made more efficient, and to understand the differences between sparse and dense
models in terms of how well they can generalize to changes in the data distribution.
We first study a method for co-training sparse and dense models, at a lower cost
compared to regular training. With our method we can obtain very accurate sparse
networks, and dense models that can recover the baseline accuracy. Furthermore,
we are able to more easily analyze the differences, at prediction level, between
the sparse-dense model pairs. Next, we investigate the generalization properties
of sparse neural networks in more detail, by studying how well different sparse
models trained on a larger task can adapt to smaller, more specialized tasks,
in a transfer learning scenario. Our analysis across multiple pruning methods
and sparsity levels reveals that sparse models provide features that can transfer
similarly to or better than the dense baseline. However, the choice of the pruning
method plays an important role, and can influence the results when the features
are fixed (linear finetuning), or when they are allowed to adapt to the new task
(full finetuning). Using sparse models with fixed masks for finetuning on new
tasks has an important practical advantage, as it enables training neural networks
on smaller devices. However, one drawback of current pruning methods is that the
entire training cycle has to be repeated to obtain the initial sparse model, for
every sparsity target; in consequence, the entire training process is costly and
also multiple models need to be stored. In the last part of the thesis we propose
a method that can train accurate dense models that are compressible in a single
step, to multiple sparsity levels, without additional finetuning. Our method results
in sparse models that can be competitive with existing pruning methods, and which
can also successfully generalize to new tasks."
acknowledged_ssus:
- _id: ScienComp
alternative_title:
- ISTA Thesis
article_processing_charge: No
author:
- first_name: Elena-Alexandra
full_name: Peste, Elena-Alexandra
id: 32D78294-F248-11E8-B48F-1D18A9856A87
last_name: Peste
citation:
ama: Peste E-A. Efficiency and generalization of sparse neural networks. 2023. doi:10.15479/at:ista:13074
apa: Peste, E.-A. (2023). Efficiency and generalization of sparse neural networks.
Institute of Science and Technology Austria. https://doi.org/10.15479/at:ista:13074
chicago: Peste, Elena-Alexandra. “Efficiency and Generalization of Sparse Neural
Networks.” Institute of Science and Technology Austria, 2023. https://doi.org/10.15479/at:ista:13074.
ieee: E.-A. Peste, “Efficiency and generalization of sparse neural networks,” Institute
of Science and Technology Austria, 2023.
ista: Peste E-A. 2023. Efficiency and generalization of sparse neural networks.
Institute of Science and Technology Austria.
mla: Peste, Elena-Alexandra. Efficiency and Generalization of Sparse Neural Networks.
Institute of Science and Technology Austria, 2023, doi:10.15479/at:ista:13074.
short: E.-A. Peste, Efficiency and Generalization of Sparse Neural Networks, Institute
of Science and Technology Austria, 2023.
date_created: 2023-05-23T17:07:53Z
date_published: 2023-05-23T00:00:00Z
date_updated: 2023-08-04T10:33:27Z
day: '23'
ddc:
- '000'
degree_awarded: PhD
department:
- _id: GradSch
- _id: DaAl
- _id: ChLa
doi: 10.15479/at:ista:13074
ec_funded: 1
file:
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file_id: '13088'
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language:
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month: '05'
oa: 1
oa_version: Published Version
page: '147'
project:
- _id: 2564DBCA-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '665385'
name: International IST Doctoral Program
- _id: 268A44D6-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '805223'
name: Elastic Coordination for Scalable Machine Learning
publication_identifier:
issn:
- 2663-337X
publication_status: published
publisher: Institute of Science and Technology Austria
related_material:
record:
- id: '11458'
relation: part_of_dissertation
status: public
- id: '13053'
relation: part_of_dissertation
status: public
- id: '12299'
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
- first_name: Dan-Adrian
full_name: Alistarh, Dan-Adrian
id: 4A899BFC-F248-11E8-B48F-1D18A9856A87
last_name: Alistarh
orcid: 0000-0003-3650-940X
title: Efficiency and generalization of sparse neural networks
type: dissertation
user_id: 8b945eb4-e2f2-11eb-945a-df72226e66a9
year: '2023'
...
---
_id: '13126'
abstract:
- lang: eng
text: Mapping the complex and dense arrangement of cells and their connectivity
in brain tissue demands nanoscale spatial resolution imaging. Super-resolution
optical microscopy excels at visualizing specific molecules and individual cells
but fails to provide tissue context. Here, we developed Comprehensive Analysis
of Tissues across Scales (CATS), a technology to densely map brain tissue architecture
from millimeter regional to nanometer synaptic scales in diverse chemically fixed
brain preparations, including rodent and human. CATS uses fixation-compatible
extracellular labeling and optical imaging, including stimulated emission depletion
or expansion microscopy, to comprehensively delineate cellular structures. It
enables three-dimensional reconstruction of single synapses and mapping of synaptic
connectivity by identification and analysis of putative synaptic cleft regions.
Applying CATS to the mouse hippocampal mossy fiber circuitry, we reconstructed
and quantified the synaptic input and output structure of identified neurons.
We furthermore demonstrate applicability to clinically derived human tissue samples,
including formalin-fixed paraffin-embedded routine diagnostic specimens, for visualizing
the cellular architecture of brain tissue in health and disease.
acknowledged_ssus:
- _id: ScienComp
- _id: Bio
- _id: PreCl
- _id: LifeSc
- _id: M-Shop
- _id: E-Lib
acknowledgement: "We thank Jakob Vorlaufer, Nathalie Agudelo-Dueñas, Wiebke Jahr,
Andreas Wartak for microscope maintenance and troubleshooting, Caroline Kreuzinger,
Anna Freeman, and Irene Erber for technical assistance and Matthias Tomschik for
support with obtaining human samples. We gratefully acknowledge Eder Miguel for
setting up webKnossos and Marek Šuplata for computational support and hardware control.
We are grateful to Ryuichi Shigemoto and Bernd Bickel for generous support, and
Michael Sixt and Scott Boyd (Stanford University) for discussions and critical reading
of the manuscript. PSD95-HaloTag mice were kindly provided by Seth Grant (University
of Edinburgh). We acknowledge expert support by IST Austria’s scientific computing,
imaging and optics, preclinical, and lab support facilities, and by the Library
and Miba machine shop.\r\nWe gratefully acknowledge funding by the following sources:
\r\nAustrian Science Fund (FWF) grant I3600-B27 (JGD)\r\nAustrian Science Fund (FWF)
grant DK W1232 (JGD, JMM)\r\nAustrian Science Fund (FWF) grant Z 312-B27, Wittgenstein
award (PJ)\r\nAustrian Science Funds (FWF) projects I4685-B, I6565-B (SYNABS) and
DOC 33-B27 (RH)\r\nGesellschaft für Forschungsförderung NÖ (NFB) grant LSC18-022
(JGD)\r\nEuropean Union’s Horizon 2020 research and innovation programme, European
Research Council (ERC) grant 715508 – REVERSEAUTISM (GN)\r\nEuropean Union’s Horizon
2020 research and innovation programme, European Research Council (ERC) grant 692692
– GIANTSYN (PJ)\r\nMarie Skłodowska-Curie Actions Fellowship GA no. 665385 under
the EU Horizon 2020 program (JMM, JL)\r\nMarie Skłodowska-Curie Actions Individual
Fellowship 101026635 under the EU Horizon 2020 program (JFW)"
article_processing_charge: No
author:
- first_name: Johann G
full_name: Danzl, Johann G
id: 42EFD3B6-F248-11E8-B48F-1D18A9856A87
last_name: Danzl
orcid: 0000-0001-8559-3973
citation:
ama: Danzl JG. Research data for the publication “Imaging brain tissue architecture
across millimeter to nanometer scales.” 2023. doi:10.15479/AT:ISTA:13126
apa: Danzl, J. G. (2023). Research data for the publication “Imaging brain tissue
architecture across millimeter to nanometer scales.” Institute of Science and
Technology Austria. https://doi.org/10.15479/AT:ISTA:13126
chicago: Danzl, Johann G. “Research Data for the Publication ‘Imaging Brain Tissue
Architecture across Millimeter to Nanometer Scales.’” Institute of Science and
Technology Austria, 2023. https://doi.org/10.15479/AT:ISTA:13126.
ieee: J. G. Danzl, “Research data for the publication ‘Imaging brain tissue architecture
across millimeter to nanometer scales.’” Institute of Science and Technology Austria,
2023.
ista: Danzl JG. 2023. Research data for the publication ‘Imaging brain tissue architecture
across millimeter to nanometer scales’, Institute of Science and Technology Austria,
10.15479/AT:ISTA:13126.
mla: Danzl, Johann G. Research Data for the Publication “Imaging Brain Tissue
Architecture across Millimeter to Nanometer Scales.” Institute of Science
and Technology Austria, 2023, doi:10.15479/AT:ISTA:13126.
short: J.G. Danzl, (2023).
contributor:
- first_name: Julia M
id: 443DB6DE-F248-11E8-B48F-1D18A9856A87
last_name: Michalska
- first_name: Julia
id: 46E28B80-F248-11E8-B48F-1D18A9856A87
last_name: Lyudchik
- first_name: Philipp
id: 39BDC62C-F248-11E8-B48F-1D18A9856A87
last_name: Velicky
orcid: 0000-0002-2340-7431
- first_name: Hana
id: ee3cb6ca-ec98-11ea-ae11-ff703e2254ed
last_name: Stefanickova
- first_name: Jake
id: 63836096-4690-11EA-BD4E-32803DDC885E
last_name: Watson
orcid: 0000-0002-8698-3823
- first_name: Alban
id: 9ac8f577-2357-11eb-997a-e566c5550886
last_name: Cenameri
- first_name: Christoph M
id: 4DF26D8C-F248-11E8-B48F-1D18A9856A87
last_name: Sommer
orcid: 0000-0003-1216-9105
- first_name: Nicole
id: 4CD6AAC6-F248-11E8-B48F-1D18A9856A87
last_name: Amberg
orcid: 0000-0002-3183-8207
- first_name: Alessandro
id: 41CB84B2-F248-11E8-B48F-1D18A9856A87
last_name: Venturino
orcid: 0000-0003-2356-9403
- first_name: Karl
last_name: Roessler
- first_name: Thomas
last_name: Czech
- first_name: Romana
last_name: Höftberger
- first_name: Sandra
id: 36ACD32E-F248-11E8-B48F-1D18A9856A87
last_name: Siegert
orcid: 0000-0001-8635-0877
- first_name: Gaia
id: 3E57A680-F248-11E8-B48F-1D18A9856A87
last_name: Novarino
orcid: 0000-0002-7673-7178
- first_name: Peter M
id: 353C1B58-F248-11E8-B48F-1D18A9856A87
last_name: Jonas
orcid: 0000-0001-5001-4804
date_created: 2023-06-07T07:15:12Z
date_published: 2023-08-04T00:00:00Z
date_updated: 2024-02-21T12:18:19Z
day: '04'
ddc:
- '610'
department:
- _id: JoDa
- _id: SaSi
- _id: GaNo
- _id: PeJo
- _id: Bio
- _id: RySh
doi: 10.15479/AT:ISTA:13126
ec_funded: 1
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and in vitro Models
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name: Synaptic computations of the hippocampal CA3 circuitry
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related_material:
link:
- description: 'Original data for Fig. 5d, Fig. 5d (N2V) and Fig. 5f-i, provided
via an external link due to the large size (>10GB) of the datasets. '
relation: research_data
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status: public
title: Research data for the publication "Imaging brain tissue architecture across
millimeter to nanometer scales"
tmp:
image: /images/cc_by_nc_sa.png
legal_code_url: https://creativecommons.org/licenses/by-nc-sa/4.0/legalcode
name: Creative Commons Attribution-NonCommercial-ShareAlike 4.0 International (CC
BY-NC-SA 4.0)
short: CC BY-NC-SA (4.0)
type: research_data
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
year: '2023'
...
---
_id: '13267'
abstract:
- lang: eng
text: Three-dimensional (3D) reconstruction of living brain tissue down to an individual
synapse level would create opportunities for decoding the dynamics and structure–function
relationships of the brain’s complex and dense information processing network;
however, this has been hindered by insufficient 3D resolution, inadequate signal-to-noise
ratio and prohibitive light burden in optical imaging, whereas electron microscopy
is inherently static. Here we solved these challenges by developing an integrated
optical/machine-learning technology, LIONESS (live information-optimized nanoscopy
enabling saturated segmentation). This leverages optical modifications to stimulated
emission depletion microscopy in comprehensively, extracellularly labeled tissue
and previous information on sample structure via machine learning to simultaneously
achieve isotropic super-resolution, high signal-to-noise ratio and compatibility
with living tissue. This allows dense deep-learning-based instance segmentation
and 3D reconstruction at a synapse level, incorporating molecular, activity and
morphodynamic information. LIONESS opens up avenues for studying the dynamic functional
(nano-)architecture of living brain tissue.
acknowledged_ssus:
- _id: ScienComp
- _id: Bio
- _id: PreCl
- _id: E-Lib
- _id: LifeSc
- _id: M-Shop
acknowledgement: "We thank J. Vorlaufer, N. Agudelo and A. Wartak for microscope maintenance
and troubleshooting, C. Kreuzinger and A. Freeman for technical assistance, M. Šuplata
for hardware control support and M. Cunha dos Santos for initial exploration of
software. We\r\nthank P. Henderson for advice on deep-learning training and M. Sixt,
S. Boyd and T. Weiss for discussions and critical reading of the manuscript. L.
Lavis (Janelia Research Campus) generously provided the JF585-HaloTag ligand. We
acknowledge expert support by IST\r\nAustria’s scientific computing, imaging and
optics, preclinical, library and laboratory support facilities and by the Miba machine
shop. We gratefully acknowledge funding by the following sources: Austrian Science
Fund (F.W.F.) grant no. I3600-B27 (J.G.D.), grant no. DK W1232\r\n(J.G.D. and J.M.M.)
and grant no. Z 312-B27, Wittgenstein award (P.J.); the Gesellschaft für Forschungsförderung
NÖ grant no. LSC18-022 (J.G.D.); an ISTA Interdisciplinary project grant (J.G.D.
and B.B.); the European Union’s Horizon 2020 research and innovation programme,\r\nMarie-Skłodowska
Curie grant 665385 (J.M.M. and J.L.); the European Union’s Horizon 2020 research
and innovation programme, European Research Council grant no. 715767, MATERIALIZABLE
(B.B.); grant no. 715508, REVERSEAUTISM (G.N.); grant no. 695568, SYNNOVATE (S.G.N.G.);
and grant no. 692692, GIANTSYN (P.J.); the Simons\r\nFoundation Autism Research
Initiative grant no. 529085 (S.G.N.G.); the Wellcome Trust Technology Development
grant no. 202932 (S.G.N.G.); the Marie Skłodowska-Curie Actions Individual Fellowship
no. 101026635 under the EU Horizon 2020 program (J.F.W.);\r\nthe Human Frontier
Science Program postdoctoral fellowship LT000557/2018 (W.J.); and the National Science
Foundation grant no. IIS-1835231 (H.P.) and NCS-FO-2124179 (H.P.)."
article_processing_charge: Yes
article_type: original
author:
- first_name: Philipp
full_name: Velicky, Philipp
id: 39BDC62C-F248-11E8-B48F-1D18A9856A87
last_name: Velicky
orcid: 0000-0002-2340-7431
- first_name: Eder
full_name: Miguel Villalba, Eder
id: 3FB91342-F248-11E8-B48F-1D18A9856A87
last_name: Miguel Villalba
orcid: 0000-0001-5665-0430
- first_name: Julia M
full_name: Michalska, Julia M
id: 443DB6DE-F248-11E8-B48F-1D18A9856A87
last_name: Michalska
orcid: 0000-0003-3862-1235
- first_name: Julia
full_name: Lyudchik, Julia
id: 46E28B80-F248-11E8-B48F-1D18A9856A87
last_name: Lyudchik
- first_name: Donglai
full_name: Wei, Donglai
last_name: Wei
- first_name: Zudi
full_name: Lin, Zudi
last_name: Lin
- first_name: Jake
full_name: Watson, Jake
id: 63836096-4690-11EA-BD4E-32803DDC885E
last_name: Watson
orcid: 0000-0002-8698-3823
- first_name: Jakob
full_name: Troidl, Jakob
last_name: Troidl
- first_name: Johanna
full_name: Beyer, Johanna
last_name: Beyer
- first_name: Yoav
full_name: Ben Simon, Yoav
id: 43DF3136-F248-11E8-B48F-1D18A9856A87
last_name: Ben Simon
- first_name: Christoph M
full_name: Sommer, Christoph M
id: 4DF26D8C-F248-11E8-B48F-1D18A9856A87
last_name: Sommer
orcid: 0000-0003-1216-9105
- first_name: Wiebke
full_name: Jahr, Wiebke
id: 425C1CE8-F248-11E8-B48F-1D18A9856A87
last_name: Jahr
- first_name: Alban
full_name: Cenameri, Alban
id: 9ac8f577-2357-11eb-997a-e566c5550886
last_name: Cenameri
- first_name: Johannes
full_name: Broichhagen, Johannes
last_name: Broichhagen
- first_name: Seth G.N.
full_name: Grant, Seth G.N.
last_name: Grant
- first_name: Peter M
full_name: Jonas, Peter M
id: 353C1B58-F248-11E8-B48F-1D18A9856A87
last_name: Jonas
orcid: 0000-0001-5001-4804
- first_name: Gaia
full_name: Novarino, Gaia
id: 3E57A680-F248-11E8-B48F-1D18A9856A87
last_name: Novarino
orcid: 0000-0002-7673-7178
- first_name: Hanspeter
full_name: Pfister, Hanspeter
last_name: Pfister
- first_name: Bernd
full_name: Bickel, Bernd
id: 49876194-F248-11E8-B48F-1D18A9856A87
last_name: Bickel
orcid: 0000-0001-6511-9385
- first_name: Johann G
full_name: Danzl, Johann G
id: 42EFD3B6-F248-11E8-B48F-1D18A9856A87
last_name: Danzl
orcid: 0000-0001-8559-3973
citation:
ama: Velicky P, Miguel Villalba E, Michalska JM, et al. Dense 4D nanoscale reconstruction
of living brain tissue. Nature Methods. 2023;20:1256-1265. doi:10.1038/s41592-023-01936-6
apa: Velicky, P., Miguel Villalba, E., Michalska, J. M., Lyudchik, J., Wei, D.,
Lin, Z., … Danzl, J. G. (2023). Dense 4D nanoscale reconstruction of living brain
tissue. Nature Methods. Springer Nature. https://doi.org/10.1038/s41592-023-01936-6
chicago: Velicky, Philipp, Eder Miguel Villalba, Julia M Michalska, Julia Lyudchik,
Donglai Wei, Zudi Lin, Jake Watson, et al. “Dense 4D Nanoscale Reconstruction
of Living Brain Tissue.” Nature Methods. Springer Nature, 2023. https://doi.org/10.1038/s41592-023-01936-6.
ieee: P. Velicky et al., “Dense 4D nanoscale reconstruction of living brain
tissue,” Nature Methods, vol. 20. Springer Nature, pp. 1256–1265, 2023.
ista: Velicky P, Miguel Villalba E, Michalska JM, Lyudchik J, Wei D, Lin Z, Watson
J, Troidl J, Beyer J, Ben Simon Y, Sommer CM, Jahr W, Cenameri A, Broichhagen
J, Grant SGN, Jonas PM, Novarino G, Pfister H, Bickel B, Danzl JG. 2023. Dense
4D nanoscale reconstruction of living brain tissue. Nature Methods. 20, 1256–1265.
mla: Velicky, Philipp, et al. “Dense 4D Nanoscale Reconstruction of Living Brain
Tissue.” Nature Methods, vol. 20, Springer Nature, 2023, pp. 1256–65, doi:10.1038/s41592-023-01936-6.
short: P. Velicky, E. Miguel Villalba, J.M. Michalska, J. Lyudchik, D. Wei, Z. Lin,
J. Watson, J. Troidl, J. Beyer, Y. Ben Simon, C.M. Sommer, W. Jahr, A. Cenameri,
J. Broichhagen, S.G.N. Grant, P.M. Jonas, G. Novarino, H. Pfister, B. Bickel,
J.G. Danzl, Nature Methods 20 (2023) 1256–1265.
date_created: 2023-07-23T22:01:13Z
date_published: 2023-08-01T00:00:00Z
date_updated: 2024-01-10T08:37:48Z
day: '01'
department:
- _id: PeJo
- _id: GaNo
- _id: BeBi
- _id: JoDa
- _id: Bio
doi: 10.1038/s41592-023-01936-6
ec_funded: 1
external_id:
isi:
- '001025621500001'
pmid:
- '37429995'
intvolume: ' 20'
isi: 1
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.1038/s41592-023-01936-6
month: '08'
oa: 1
oa_version: Published Version
page: 1256-1265
pmid: 1
project:
- _id: 265CB4D0-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: I03600
name: Optical control of synaptic function via adhesion molecules
- _id: 2548AE96-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: W1232-B24
name: Molecular Drug Targets
- _id: 25C5A090-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: Z00312
name: The Wittgenstein Prize
- _id: 23889792-32DE-11EA-91FC-C7463DDC885E
name: High content imaging to decode human immune cell interactions in health and
allergic disease
- _id: 2564DBCA-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '665385'
name: International IST Doctoral Program
- _id: 24F9549A-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '715767'
name: 'MATERIALIZABLE: Intelligent fabrication-oriented Computational Design and
Modeling'
- _id: 25444568-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '715508'
name: Probing the Reversibility of Autism Spectrum Disorders by Employing in vivo
and in vitro Models
- _id: 25B7EB9E-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '692692'
name: Biophysics and circuit function of a giant cortical glumatergic synapse
- _id: fc2be41b-9c52-11eb-aca3-faa90aa144e9
call_identifier: H2020
grant_number: '101026635'
name: Synaptic computations of the hippocampal CA3 circuitry
- _id: 2668BFA0-B435-11E9-9278-68D0E5697425
grant_number: LT00057
name: High-speed 3D-nanoscopy to study the role of adhesion during 3D cell migration
publication: Nature Methods
publication_identifier:
eissn:
- 1548-7105
issn:
- 1548-7091
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
related_material:
link:
- relation: software
url: https://github.com/danzllab/LIONESS
record:
- id: '12817'
relation: research_data
status: public
- id: '14770'
relation: shorter_version
status: public
scopus_import: '1'
status: public
title: Dense 4D nanoscale reconstruction of living brain tissue
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 20
year: '2023'
...
---
_id: '14040'
abstract:
- lang: eng
text: Robust oxygenic photosynthesis requires a suite of accessory factors to ensure
efficient assembly and repair of the oxygen-evolving photosystem two (PSII) complex.
The highly conserved Ycf48 assembly factor binds to the newly synthesized D1 reaction
center polypeptide and promotes the initial steps of PSII assembly, but its binding
site is unclear. Here we use cryo-electron microscopy to determine the structure
of a cyanobacterial PSII D1/D2 reaction center assembly complex with Ycf48 attached.
Ycf48, a 7-bladed beta propeller, binds to the amino-acid residues of D1 that
ultimately ligate the water-oxidising Mn4CaO5 cluster, thereby preventing the
premature binding of Mn2+ and Ca2+ ions and protecting the site from damage. Interactions
with D2 help explain how Ycf48 promotes assembly of the D1/D2 complex. Overall,
our work provides valuable insights into the early stages of PSII assembly and
the structural changes that create the binding site for the Mn4CaO5 cluster.
acknowledged_ssus:
- _id: EM-Fac
- _id: LifeSc
- _id: ScienComp
acknowledgement: P.J.N. and J.W.M. are grateful for the support of the Biotechnology
& Biological Sciences Research Council (awards BB/L003260/1 and BB/P00931X/1). J.
Knoppová, R.S. and J. Komenda were supported by the Czech Science Foundation (project
19-29225X) and by ERC project Photoredesign (no. 854126) and L.A.S. was supported
by the Scientific Service Units (SSU) of IST Austria through resources provided
by the Electron Microscopy Facility (EMF), the Life Science Facility (LSF) and the
IST high-performance computing cluster.
article_number: '4681'
article_processing_charge: Yes
article_type: original
author:
- first_name: Ziyu
full_name: Zhao, Ziyu
last_name: Zhao
- first_name: Irene
full_name: Vercellino, Irene
id: 3ED6AF16-F248-11E8-B48F-1D18A9856A87
last_name: Vercellino
orcid: 0000-0001-5618-3449
- first_name: Jana
full_name: Knoppová, Jana
last_name: Knoppová
- first_name: Roman
full_name: Sobotka, Roman
last_name: Sobotka
- first_name: James W.
full_name: Murray, James W.
last_name: Murray
- first_name: Peter J.
full_name: Nixon, Peter J.
last_name: Nixon
- first_name: Leonid A
full_name: Sazanov, Leonid A
id: 338D39FE-F248-11E8-B48F-1D18A9856A87
last_name: Sazanov
orcid: 0000-0002-0977-7989
- first_name: Josef
full_name: Komenda, Josef
last_name: Komenda
citation:
ama: Zhao Z, Vercellino I, Knoppová J, et al. The Ycf48 accessory factor occupies
the site of the oxygen-evolving manganese cluster during photosystem II biogenesis.
Nature Communications. 2023;14. doi:10.1038/s41467-023-40388-6
apa: Zhao, Z., Vercellino, I., Knoppová, J., Sobotka, R., Murray, J. W., Nixon,
P. J., … Komenda, J. (2023). The Ycf48 accessory factor occupies the site of the
oxygen-evolving manganese cluster during photosystem II biogenesis. Nature
Communications. Springer Nature. https://doi.org/10.1038/s41467-023-40388-6
chicago: Zhao, Ziyu, Irene Vercellino, Jana Knoppová, Roman Sobotka, James W. Murray,
Peter J. Nixon, Leonid A Sazanov, and Josef Komenda. “The Ycf48 Accessory Factor
Occupies the Site of the Oxygen-Evolving Manganese Cluster during Photosystem
II Biogenesis.” Nature Communications. Springer Nature, 2023. https://doi.org/10.1038/s41467-023-40388-6.
ieee: Z. Zhao et al., “The Ycf48 accessory factor occupies the site of the
oxygen-evolving manganese cluster during photosystem II biogenesis,” Nature
Communications, vol. 14. Springer Nature, 2023.
ista: Zhao Z, Vercellino I, Knoppová J, Sobotka R, Murray JW, Nixon PJ, Sazanov
LA, Komenda J. 2023. The Ycf48 accessory factor occupies the site of the oxygen-evolving
manganese cluster during photosystem II biogenesis. Nature Communications. 14,
4681.
mla: Zhao, Ziyu, et al. “The Ycf48 Accessory Factor Occupies the Site of the Oxygen-Evolving
Manganese Cluster during Photosystem II Biogenesis.” Nature Communications,
vol. 14, 4681, Springer Nature, 2023, doi:10.1038/s41467-023-40388-6.
short: Z. Zhao, I. Vercellino, J. Knoppová, R. Sobotka, J.W. Murray, P.J. Nixon,
L.A. Sazanov, J. Komenda, Nature Communications 14 (2023).
date_created: 2023-08-13T22:01:13Z
date_published: 2023-08-04T00:00:00Z
date_updated: 2023-12-13T12:06:56Z
day: '04'
ddc:
- '570'
department:
- _id: LeSa
doi: 10.1038/s41467-023-40388-6
external_id:
isi:
- '001042606700004'
file:
- access_level: open_access
checksum: 3b9043df3d51c300f9be95eac3ff9d0b
content_type: application/pdf
creator: dernst
date_created: 2023-08-14T07:01:12Z
date_updated: 2023-08-14T07:01:12Z
file_id: '14044'
file_name: 2023_NatureComm_Zhao.pdf
file_size: 2315325
relation: main_file
success: 1
file_date_updated: 2023-08-14T07:01:12Z
has_accepted_license: '1'
intvolume: ' 14'
isi: 1
language:
- iso: eng
month: '08'
oa: 1
oa_version: Published Version
publication: Nature Communications
publication_identifier:
eissn:
- 2041-1723
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
scopus_import: '1'
status: public
title: The Ycf48 accessory factor occupies the site of the oxygen-evolving manganese
cluster during photosystem II biogenesis
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: 14
year: '2023'
...
---
_id: '14077'
abstract:
- lang: eng
text: "The regulatory architecture of gene expression is known to differ substantially
between sexes in Drosophila, but most studies performed\r\nso far used whole-body
data and only single crosses, which may have limited their scope to detect patterns
that are robust across tissues\r\nand biological replicates. Here, we use allele-specific
gene expression of parental and reciprocal hybrid crosses between 6 Drosophila\r\nmelanogaster
inbred lines to quantify cis- and trans-regulatory variation in heads and gonads
of both sexes separately across 3 replicate\r\ncrosses. Our results suggest that
female and male heads, as well as ovaries, have a similar regulatory architecture.
On the other hand,\r\ntestes display more and substantially different cis-regulatory
effects, suggesting that sex differences in the regulatory architecture that\r\nhave
been previously observed may largely derive from testis-specific effects. We also
examine the difference in cis-regulatory variation\r\nof genes across different
levels of sex bias in gonads and heads. Consistent with the idea that intersex
correlations constrain expression\r\nand can lead to sexual antagonism, we find
more cis variation in unbiased and moderately biased genes in heads. In ovaries,
reduced cis\r\nvariation is observed for male-biased genes, suggesting that cis
variants acting on these genes in males do not lead to changes in ovary\r\nexpression.
Finally, we examine the dominance patterns of gene expression and find that sex-
and tissue-specific patterns of inheritance\r\nas well as trans-regulatory variation
are highly variable across biological crosses, although these were performed in
highly controlled\r\nexperimental conditions. This highlights the importance of
using various genetic backgrounds to infer generalizable patterns."
acknowledged_ssus:
- _id: ScienComp
acknowledgement: We thank members of the Vicoso Group for comments on the manuscript,
the Scientific Computing Unit at ISTA for technical support, and 2 anonymous reviewers
for useful feedback. GP is the recipient of a DOC Fellowship of the Austrian Academy
of Sciences at the Institute of Science and Technology Austria (DOC 25817) and received
funding from the European Union’s Horizon 2020 research and innovation program under
the Marie Skłodowska-Curie Grant (agreement no. 665385).
article_processing_charge: Yes
article_type: original
author:
- first_name: Gemma
full_name: Puixeu Sala, Gemma
id: 33AB266C-F248-11E8-B48F-1D18A9856A87
last_name: Puixeu Sala
orcid: 0000-0001-8330-1754
- first_name: Ariana
full_name: Macon, Ariana
id: 2A0848E2-F248-11E8-B48F-1D18A9856A87
last_name: Macon
- first_name: Beatriz
full_name: Vicoso, Beatriz
id: 49E1C5C6-F248-11E8-B48F-1D18A9856A87
last_name: Vicoso
orcid: 0000-0002-4579-8306
citation:
ama: 'Puixeu Sala G, Macon A, Vicoso B. Sex-specific estimation of cis and trans
regulation of gene expression in heads and gonads of Drosophila melanogaster.
G3: Genes, Genomes, Genetics. 2023;13(8). doi:10.1093/g3journal/jkad121'
apa: 'Puixeu Sala, G., Macon, A., & Vicoso, B. (2023). Sex-specific estimation
of cis and trans regulation of gene expression in heads and gonads of Drosophila
melanogaster. G3: Genes, Genomes, Genetics. Oxford University Press. https://doi.org/10.1093/g3journal/jkad121'
chicago: 'Puixeu Sala, Gemma, Ariana Macon, and Beatriz Vicoso. “Sex-Specific Estimation
of Cis and Trans Regulation of Gene Expression in Heads and Gonads of Drosophila
Melanogaster.” G3: Genes, Genomes, Genetics. Oxford University Press, 2023.
https://doi.org/10.1093/g3journal/jkad121.'
ieee: 'G. Puixeu Sala, A. Macon, and B. Vicoso, “Sex-specific estimation of cis
and trans regulation of gene expression in heads and gonads of Drosophila melanogaster,”
G3: Genes, Genomes, Genetics, vol. 13, no. 8. Oxford University Press,
2023.'
ista: 'Puixeu Sala G, Macon A, Vicoso B. 2023. Sex-specific estimation of cis and
trans regulation of gene expression in heads and gonads of Drosophila melanogaster.
G3: Genes, Genomes, Genetics. 13(8).'
mla: 'Puixeu Sala, Gemma, et al. “Sex-Specific Estimation of Cis and Trans Regulation
of Gene Expression in Heads and Gonads of Drosophila Melanogaster.” G3: Genes,
Genomes, Genetics, vol. 13, no. 8, Oxford University Press, 2023, doi:10.1093/g3journal/jkad121.'
short: 'G. Puixeu Sala, A. Macon, B. Vicoso, G3: Genes, Genomes, Genetics 13 (2023).'
date_created: 2023-08-18T06:52:14Z
date_published: 2023-08-01T00:00:00Z
date_updated: 2023-12-13T12:15:37Z
day: '01'
ddc:
- '570'
department:
- _id: BeVi
- _id: NiBa
- _id: GradSch
doi: 10.1093/g3journal/jkad121
ec_funded: 1
external_id:
isi:
- '001002997200001'
file:
- access_level: open_access
checksum: c62e29fc7c5efbf8356f4c60cab4a2d1
content_type: application/pdf
creator: dernst
date_created: 2023-11-07T09:00:19Z
date_updated: 2023-11-07T09:00:19Z
file_id: '14498'
file_name: 2023_G3_Puixeu.pdf
file_size: 845642
relation: main_file
success: 1
file_date_updated: 2023-11-07T09:00:19Z
has_accepted_license: '1'
intvolume: ' 13'
isi: 1
issue: '8'
keyword:
- Genetics (clinical)
- Genetics
- Molecular Biology
language:
- iso: eng
month: '08'
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: 9B9DFC9E-BA93-11EA-9121-9846C619BF3A
grant_number: '25817'
name: 'Sexual conflict: resolution, constraints and biomedical implications'
publication: 'G3: Genes, Genomes, Genetics'
publication_identifier:
issn:
- 2160-1836
publication_status: published
publisher: Oxford University Press
quality_controlled: '1'
related_material:
record:
- id: '12933'
relation: research_data
status: public
- id: '14058'
relation: dissertation_contains
status: public
scopus_import: '1'
status: public
title: Sex-specific estimation of cis and trans regulation of gene expression in heads
and gonads of 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: 13
year: '2023'
...
---
_id: '14240'
abstract:
- lang: eng
text: This paper introduces a novel method for simulating large bodies of water
as a height field. At the start of each time step, we partition the waves into
a bulk flow (which approximately satisfies the assumptions of the shallow water
equations) and surface waves (which approximately satisfy the assumptions of Airy
wave theory). We then solve the two wave regimes separately using appropriate
state-of-the-art techniques, and re-combine the resulting wave velocities at the
end of each step. This strategy leads to the first heightfield wave model capable
of simulating complex interactions between both deep and shallow water effects,
like the waves from a boat wake sloshing up onto a beach, or a dam break producing
wave interference patterns and eddies. We also analyze the numerical dispersion
created by our method and derive an exact correction factor for waves at a constant
water depth, giving us a numerically perfect re-creation of theoretical water
wave dispersion patterns.
acknowledged_ssus:
- _id: ScienComp
acknowledgement: "We thank Georg Sperl for helping with early research for this paper,
Mickael Ly and Yi-Lu Chen for proofreading, and members of the ISTA Visual Computing
Group for general feedback. This project was funded in part by the European Research
Council (ERC Consolidator Grant 101045083 CoDiNA).\r\nThe motorboat and sailboat
were modeled by Sergei and the palmtrees by YadroGames. The environment map was
created by Emil Persson."
article_number: '83'
article_processing_charge: Yes (in subscription journal)
article_type: original
author:
- first_name: Stefan
full_name: Jeschke, Stefan
id: 44D6411A-F248-11E8-B48F-1D18A9856A87
last_name: Jeschke
- first_name: Christopher J
full_name: Wojtan, Christopher J
id: 3C61F1D2-F248-11E8-B48F-1D18A9856A87
last_name: Wojtan
orcid: 0000-0001-6646-5546
citation:
ama: Jeschke S, Wojtan C. Generalizing shallow water simulations with dispersive
surface waves. ACM Transactions on Graphics. 2023;42(4). doi:10.1145/3592098
apa: Jeschke, S., & Wojtan, C. (2023). Generalizing shallow water simulations
with dispersive surface waves. ACM Transactions on Graphics. Association
for Computing Machinery. https://doi.org/10.1145/3592098
chicago: Jeschke, Stefan, and Chris Wojtan. “Generalizing Shallow Water Simulations
with Dispersive Surface Waves.” ACM Transactions on Graphics. Association
for Computing Machinery, 2023. https://doi.org/10.1145/3592098.
ieee: S. Jeschke and C. Wojtan, “Generalizing shallow water simulations with dispersive
surface waves,” ACM Transactions on Graphics, vol. 42, no. 4. Association
for Computing Machinery, 2023.
ista: Jeschke S, Wojtan C. 2023. Generalizing shallow water simulations with dispersive
surface waves. ACM Transactions on Graphics. 42(4), 83.
mla: Jeschke, Stefan, and Chris Wojtan. “Generalizing Shallow Water Simulations
with Dispersive Surface Waves.” ACM Transactions on Graphics, vol. 42,
no. 4, 83, Association for Computing Machinery, 2023, doi:10.1145/3592098.
short: S. Jeschke, C. Wojtan, ACM Transactions on Graphics 42 (2023).
date_created: 2023-08-27T22:01:17Z
date_published: 2023-08-01T00:00:00Z
date_updated: 2024-01-02T09:35:55Z
day: '01'
ddc:
- '000'
department:
- _id: ChWo
doi: 10.1145/3592098
external_id:
isi:
- '001044671300049'
file:
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checksum: 1d178bb2f8011d9f5aedda6427e18c7a
content_type: video/mp4
creator: sjeschke
date_created: 2023-12-21T12:26:40Z
date_updated: 2023-12-21T12:26:40Z
file_id: '14704'
file_name: PaperVideo_final.mp4
file_size: 511572575
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checksum: a49b2e744d5cd1276bb8b2e0ce6dc638
content_type: application/pdf
creator: dernst
date_created: 2024-01-02T09:34:27Z
date_updated: 2024-01-02T09:34:27Z
file_id: '14725'
file_name: 2023_ACMToG_Jeschke.pdf
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has_accepted_license: '1'
intvolume: ' 42'
isi: 1
issue: '4'
language:
- iso: eng
month: '08'
oa: 1
oa_version: Published Version
project:
- _id: 34bc2376-11ca-11ed-8bc3-9a3b3961a088
grant_number: '101045083'
name: Computational Discovery of Numerical Algorithms for Animation and Simulation
of Natural Phenomena
publication: ACM Transactions on Graphics
publication_identifier:
eissn:
- 1557-7368
issn:
- 0730-0301
publication_status: published
publisher: Association for Computing Machinery
quality_controlled: '1'
scopus_import: '1'
status: public
title: Generalizing shallow water simulations with dispersive surface waves
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: 42
year: '2023'
...
---
_id: '14257'
abstract:
- lang: eng
text: Mapping the complex and dense arrangement of cells and their connectivity
in brain tissue demands nanoscale spatial resolution imaging. Super-resolution
optical microscopy excels at visualizing specific molecules and individual cells
but fails to provide tissue context. Here we developed Comprehensive Analysis
of Tissues across Scales (CATS), a technology to densely map brain tissue architecture
from millimeter regional to nanometer synaptic scales in diverse chemically fixed
brain preparations, including rodent and human. CATS uses fixation-compatible
extracellular labeling and optical imaging, including stimulated emission depletion
or expansion microscopy, to comprehensively delineate cellular structures. It
enables three-dimensional reconstruction of single synapses and mapping of synaptic
connectivity by identification and analysis of putative synaptic cleft regions.
Applying CATS to the mouse hippocampal mossy fiber circuitry, we reconstructed
and quantified the synaptic input and output structure of identified neurons.
We furthermore demonstrate applicability to clinically derived human tissue samples,
including formalin-fixed paraffin-embedded routine diagnostic specimens, for visualizing
the cellular architecture of brain tissue in health and disease.
acknowledged_ssus:
- _id: ScienComp
- _id: Bio
- _id: PreCl
- _id: LifeSc
- _id: M-Shop
- _id: E-Lib
acknowledgement: 'We thank J. Vorlaufer, N. Agudelo-Dueñas, W. Jahr and A. Wartak
for microscope maintenance and troubleshooting; C. Kreuzinger, A. Freeman and I.
Erber for technical assistance; and M. Tomschik for support with obtaining human
samples. We gratefully acknowledge E. Miguel for setting up webKnossos and M. Šuplata
for computational support and hardware control. We are grateful to R. Shigemoto
and B. Bickel for generous support and M. Sixt and S. Boyd (Stanford University)
for discussions and critical reading of the paper. PSD95-HaloTag mice were kindly
provided by S. Grant (University of Edinburgh). We acknowledge expert support by
Institute of Science and Technology Austria’s scientific computing, imaging and
optics, preclinical and lab support facilities and by the Miba machine shop and
library. We gratefully acknowledge funding by the following sources: Austrian Science
Fund (FWF) grant I3600-B27 (J.G.D.); Austrian Science Fund (FWF) grant DK W1232
(J.G.D. and J.M.M.); Austrian Science Fund (FWF) grant Z 312-B27, Wittgenstein award
(P.J.); Austrian Science Fund (FWF) projects I4685-B, I6565-B (SYNABS) and DOC 33-B27
(R.H.); Gesellschaft für Forschungsförderung NÖ (NFB) grant LSC18-022 (J.G.D.);
European Union’s Horizon 2020 research and innovation programme, European Research
Council (ERC) grant 715508 – REVERSEAUTISM (G.N.); European Union’s Horizon 2020
research and innovation programme, European Research Council (ERC) grant 692692
– GIANTSYN (P.J.); Marie Skłodowska-Curie Actions Fellowship GA no. 665385 under
the EU Horizon 2020 program (J.M.M. and J.L.); and Marie Skłodowska-Curie Actions
Individual Fellowship no. 101026635 under the EU Horizon 2020 program (J.F.W.).'
article_processing_charge: Yes (in subscription journal)
article_type: original
author:
- first_name: Julia M
full_name: Michalska, Julia M
id: 443DB6DE-F248-11E8-B48F-1D18A9856A87
last_name: Michalska
orcid: 0000-0003-3862-1235
- first_name: Julia
full_name: Lyudchik, Julia
id: 46E28B80-F248-11E8-B48F-1D18A9856A87
last_name: Lyudchik
- first_name: Philipp
full_name: Velicky, Philipp
id: 39BDC62C-F248-11E8-B48F-1D18A9856A87
last_name: Velicky
orcid: 0000-0002-2340-7431
- first_name: Hana
full_name: Korinkova, Hana
id: ee3cb6ca-ec98-11ea-ae11-ff703e2254ed
last_name: Korinkova
- first_name: Jake
full_name: Watson, Jake
id: 63836096-4690-11EA-BD4E-32803DDC885E
last_name: Watson
orcid: 0000-0002-8698-3823
- first_name: Alban
full_name: Cenameri, Alban
id: 9ac8f577-2357-11eb-997a-e566c5550886
last_name: Cenameri
- first_name: Christoph M
full_name: Sommer, Christoph M
id: 4DF26D8C-F248-11E8-B48F-1D18A9856A87
last_name: Sommer
orcid: 0000-0003-1216-9105
- first_name: Nicole
full_name: Amberg, Nicole
id: 4CD6AAC6-F248-11E8-B48F-1D18A9856A87
last_name: Amberg
orcid: 0000-0002-3183-8207
- first_name: Alessandro
full_name: Venturino, Alessandro
id: 41CB84B2-F248-11E8-B48F-1D18A9856A87
last_name: Venturino
orcid: 0000-0003-2356-9403
- first_name: Karl
full_name: Roessler, Karl
last_name: Roessler
- first_name: Thomas
full_name: Czech, Thomas
last_name: Czech
- first_name: Romana
full_name: Höftberger, Romana
last_name: Höftberger
- first_name: Sandra
full_name: Siegert, Sandra
id: 36ACD32E-F248-11E8-B48F-1D18A9856A87
last_name: Siegert
orcid: 0000-0001-8635-0877
- first_name: Gaia
full_name: Novarino, Gaia
id: 3E57A680-F248-11E8-B48F-1D18A9856A87
last_name: Novarino
orcid: 0000-0002-7673-7178
- first_name: Peter M
full_name: Jonas, Peter M
id: 353C1B58-F248-11E8-B48F-1D18A9856A87
last_name: Jonas
orcid: 0000-0001-5001-4804
- first_name: Johann G
full_name: Danzl, Johann G
id: 42EFD3B6-F248-11E8-B48F-1D18A9856A87
last_name: Danzl
orcid: 0000-0001-8559-3973
citation:
ama: Michalska JM, Lyudchik J, Velicky P, et al. Imaging brain tissue architecture
across millimeter to nanometer scales. Nature Biotechnology. 2023. doi:10.1038/s41587-023-01911-8
apa: Michalska, J. M., Lyudchik, J., Velicky, P., Korinkova, H., Watson, J., Cenameri,
A., … Danzl, J. G. (2023). Imaging brain tissue architecture across millimeter
to nanometer scales. Nature Biotechnology. Springer Nature. https://doi.org/10.1038/s41587-023-01911-8
chicago: Michalska, Julia M, Julia Lyudchik, Philipp Velicky, Hana Korinkova, Jake
Watson, Alban Cenameri, Christoph M Sommer, et al. “Imaging Brain Tissue Architecture
across Millimeter to Nanometer Scales.” Nature Biotechnology. Springer
Nature, 2023. https://doi.org/10.1038/s41587-023-01911-8.
ieee: J. M. Michalska et al., “Imaging brain tissue architecture across millimeter
to nanometer scales,” Nature Biotechnology. Springer Nature, 2023.
ista: Michalska JM, Lyudchik J, Velicky P, Korinkova H, Watson J, Cenameri A, Sommer
CM, Amberg N, Venturino A, Roessler K, Czech T, Höftberger R, Siegert S, Novarino
G, Jonas PM, Danzl JG. 2023. Imaging brain tissue architecture across millimeter
to nanometer scales. Nature Biotechnology.
mla: Michalska, Julia M., et al. “Imaging Brain Tissue Architecture across Millimeter
to Nanometer Scales.” Nature Biotechnology, Springer Nature, 2023, doi:10.1038/s41587-023-01911-8.
short: J.M. Michalska, J. Lyudchik, P. Velicky, H. Korinkova, J. Watson, A. Cenameri,
C.M. Sommer, N. Amberg, A. Venturino, K. Roessler, T. Czech, R. Höftberger, S.
Siegert, G. Novarino, P.M. Jonas, J.G. Danzl, Nature Biotechnology (2023).
date_created: 2023-09-03T22:01:15Z
date_published: 2023-08-31T00:00:00Z
date_updated: 2024-02-21T12:18:18Z
day: '31'
department:
- _id: SaSi
- _id: GaNo
- _id: PeJo
- _id: JoDa
- _id: Bio
- _id: RySh
doi: 10.1038/s41587-023-01911-8
ec_funded: 1
external_id:
isi:
- '001065254200001'
isi: 1
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.1038/s41587-023-01911-8
month: '08'
oa: 1
oa_version: Published Version
project:
- _id: 265CB4D0-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: I03600
name: Optical control of synaptic function via adhesion molecules
- _id: 2548AE96-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: W1232-B24
name: Molecular Drug Targets
- _id: 25C5A090-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: Z00312
name: The Wittgenstein Prize
- _id: 23889792-32DE-11EA-91FC-C7463DDC885E
name: High content imaging to decode human immune cell interactions in health and
allergic disease
- _id: 25444568-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '715508'
name: Probing the Reversibility of Autism Spectrum Disorders by Employing in vivo
and in vitro Models
- _id: 25B7EB9E-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '692692'
name: Biophysics and circuit function of a giant cortical glumatergic synapse
- _id: 2564DBCA-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '665385'
name: International IST Doctoral Program
- _id: fc2be41b-9c52-11eb-aca3-faa90aa144e9
call_identifier: H2020
grant_number: '101026635'
name: Synaptic computations of the hippocampal CA3 circuitry
publication: Nature Biotechnology
publication_identifier:
eissn:
- 1546-1696
issn:
- 1087-0156
publication_status: epub_ahead
publisher: Springer Nature
quality_controlled: '1'
related_material:
link:
- relation: software
url: https://github.com/danzllab/CATS
record:
- id: '13126'
relation: research_data
status: public
scopus_import: '1'
status: public
title: Imaging brain tissue architecture across millimeter to nanometer scales
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
year: '2023'
...
---
_id: '12334'
abstract:
- lang: eng
text: Regulation of the Arp2/3 complex is required for productive nucleation of
branched actin networks. An emerging aspect of regulation is the incorporation
of subunit isoforms into the Arp2/3 complex. Specifically, both ArpC5 subunit
isoforms, ArpC5 and ArpC5L, have been reported to fine-tune nucleation activity
and branch junction stability. We have combined reverse genetics and cellular
structural biology to describe how ArpC5 and ArpC5L differentially affect cell
migration. Both define the structural stability of ArpC1 in branch junctions and,
in turn, by determining protrusion characteristics, affect protein dynamics and
actin network ultrastructure. ArpC5 isoforms also affect the positioning of members
of the Ena/Vasodilator-stimulated phosphoprotein (VASP) family of actin filament
elongators, which mediate ArpC5 isoform–specific effects on the actin assembly
level. Our results suggest that ArpC5 and Ena/VASP proteins are part of a signaling
pathway enhancing cell migration.
acknowledged_ssus:
- _id: ScienComp
- _id: LifeSc
- _id: Bio
- _id: EM-Fac
acknowledgement: "We would like to thank K. von Peinen and B. Denker (Helmholtz Centre
for Infection Research, Braunschweig, Germany) for experimental and technical assistance,
respectively.\r\nThis research was supported by the Scientific Service Units (SSUs)
of ISTA through resources provided by Scientific Computing (SciComp), the Life Science
Facility (LSF), the Imaging and Optics facility (IOF), and the Electron Microscopy
Facility (EMF). We acknowledge support from ISTA and from the Austrian Science Fund
(FWF) (P33367) to F.K.M.S., from the Research Training Group GRK2223 and the Helmholtz
Society to K.R,. and from the Deutsche Forschungsgemeinschaft (DFG) to J.F. and
K.R."
article_number: add6495
article_processing_charge: No
article_type: original
author:
- first_name: Florian
full_name: Fäßler, Florian
id: 404F5528-F248-11E8-B48F-1D18A9856A87
last_name: Fäßler
orcid: 0000-0001-7149-769X
- first_name: Manjunath
full_name: Javoor, Manjunath
id: 305ab18b-dc7d-11ea-9b2f-b58195228ea2
last_name: Javoor
- first_name: Julia
full_name: Datler, Julia
id: 3B12E2E6-F248-11E8-B48F-1D18A9856A87
last_name: Datler
orcid: 0000-0002-3616-8580
- first_name: Hermann
full_name: Döring, Hermann
last_name: Döring
- first_name: Florian
full_name: Hofer, Florian
id: b9d234ba-9e33-11ed-95b6-cd561df280e6
last_name: Hofer
- first_name: Georgi A
full_name: Dimchev, Georgi A
id: 38C393BE-F248-11E8-B48F-1D18A9856A87
last_name: Dimchev
orcid: 0000-0001-8370-6161
- first_name: Victor-Valentin
full_name: Hodirnau, Victor-Valentin
id: 3661B498-F248-11E8-B48F-1D18A9856A87
last_name: Hodirnau
- first_name: Jan
full_name: Faix, Jan
last_name: Faix
- first_name: Klemens
full_name: Rottner, Klemens
last_name: Rottner
- first_name: Florian KM
full_name: Schur, Florian KM
id: 48AD8942-F248-11E8-B48F-1D18A9856A87
last_name: Schur
orcid: 0000-0003-4790-8078
citation:
ama: Fäßler F, Javoor M, Datler J, et al. ArpC5 isoforms regulate Arp2/3 complex–dependent
protrusion through differential Ena/VASP positioning. Science Advances.
2023;9(3). doi:10.1126/sciadv.add6495
apa: Fäßler, F., Javoor, M., Datler, J., Döring, H., Hofer, F., Dimchev, G. A.,
… Schur, F. K. (2023). ArpC5 isoforms regulate Arp2/3 complex–dependent protrusion
through differential Ena/VASP positioning. Science Advances. American Association
for the Advancement of Science. https://doi.org/10.1126/sciadv.add6495
chicago: Fäßler, Florian, Manjunath Javoor, Julia Datler, Hermann Döring, Florian
Hofer, Georgi A Dimchev, Victor-Valentin Hodirnau, Jan Faix, Klemens Rottner,
and Florian KM Schur. “ArpC5 Isoforms Regulate Arp2/3 Complex–Dependent Protrusion
through Differential Ena/VASP Positioning.” Science Advances. American
Association for the Advancement of Science, 2023. https://doi.org/10.1126/sciadv.add6495.
ieee: F. Fäßler et al., “ArpC5 isoforms regulate Arp2/3 complex–dependent
protrusion through differential Ena/VASP positioning,” Science Advances,
vol. 9, no. 3. American Association for the Advancement of Science, 2023.
ista: Fäßler F, Javoor M, Datler J, Döring H, Hofer F, Dimchev GA, Hodirnau V-V,
Faix J, Rottner K, Schur FK. 2023. ArpC5 isoforms regulate Arp2/3 complex–dependent
protrusion through differential Ena/VASP positioning. Science Advances. 9(3),
add6495.
mla: Fäßler, Florian, et al. “ArpC5 Isoforms Regulate Arp2/3 Complex–Dependent Protrusion
through Differential Ena/VASP Positioning.” Science Advances, vol. 9, no.
3, add6495, American Association for the Advancement of Science, 2023, doi:10.1126/sciadv.add6495.
short: F. Fäßler, M. Javoor, J. Datler, H. Döring, F. Hofer, G.A. Dimchev, V.-V.
Hodirnau, J. Faix, K. Rottner, F.K. Schur, Science Advances 9 (2023).
date_created: 2023-01-23T07:26:42Z
date_published: 2023-01-20T00:00:00Z
date_updated: 2023-11-21T08:05:35Z
day: '20'
ddc:
- '570'
department:
- _id: FlSc
- _id: EM-Fac
doi: 10.1126/sciadv.add6495
external_id:
isi:
- '000964550100015'
file:
- access_level: open_access
checksum: ce81a6d0b84170e5e8c62f6acfa15d9e
content_type: application/pdf
creator: dernst
date_created: 2023-01-23T07:45:54Z
date_updated: 2023-01-23T07:45:54Z
file_id: '12335'
file_name: 2023_ScienceAdvances_Faessler.pdf
file_size: 1756234
relation: main_file
success: 1
file_date_updated: 2023-01-23T07:45:54Z
has_accepted_license: '1'
intvolume: ' 9'
isi: 1
issue: '3'
keyword:
- Multidisciplinary
language:
- iso: eng
month: '01'
oa: 1
oa_version: Published Version
project:
- _id: 9B954C5C-BA93-11EA-9121-9846C619BF3A
grant_number: P33367
name: Structure and isoform diversity of the Arp2/3 complex
publication: Science Advances
publication_identifier:
issn:
- 2375-2548
publication_status: published
publisher: American Association for the Advancement of Science
quality_controlled: '1'
related_material:
record:
- id: '14562'
relation: research_data
status: public
scopus_import: '1'
status: public
title: ArpC5 isoforms regulate Arp2/3 complex–dependent protrusion through differential
Ena/VASP positioning
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: 9
year: '2023'
...
---
_id: '12349'
abstract:
- lang: eng
text: Statistics of natural scenes are not uniform - their structure varies dramatically
from ground to sky. It remains unknown whether these non-uniformities are reflected
in the large-scale organization of the early visual system and what benefits such
adaptations would confer. Here, by relying on the efficient coding hypothesis,
we predict that changes in the structure of receptive fields across visual space
increase the efficiency of sensory coding. We show experimentally that, in agreement
with our predictions, receptive fields of retinal ganglion cells change their
shape along the dorsoventral retinal axis, with a marked surround asymmetry at
the visual horizon. Our work demonstrates that, according to principles of efficient
coding, the panoramic structure of natural scenes is exploited by the retina across
space and cell-types.
acknowledged_ssus:
- _id: ScienComp
- _id: PreCl
- _id: LifeSc
- _id: Bio
acknowledgement: We thank Hiroki Asari for sharing the dataset of naturalistic images,
Anton Sumser for sharing visual stimulus code, Yoav Ben Simon for initial explorative
work with the generation of AAVs, and Tomas Vega-Zuñiga for help with immunostainings.
We also thank Gasper Tkacik and members of the Neuroethology group for their comments
on the manuscript. This research was supported by the Scientific Service Units of
IST Austria through resources provided by Scientific Computing, the Preclinical
Facility, the Lab Support Facility, and the Imaging and Optics Facility. This work
was supported by European Union Horizon 2020 Marie Skłodowska-Curie grant 665385
(DG), Austrian Science Fund (FWF) stand-alone grant P 34015 (WM), Human Frontiers
Science Program LT000256/2018-L (AS), EMBO ALTF 1098-2017 (AS) and the European
Research Council Starting Grant 756502 (MJ).
article_processing_charge: Yes (in subscription journal)
article_type: original
author:
- first_name: Divyansh
full_name: Gupta, Divyansh
id: 2A485EBE-F248-11E8-B48F-1D18A9856A87
last_name: Gupta
orcid: 0000-0001-7400-6665
- first_name: Wiktor F
full_name: Mlynarski, Wiktor F
id: 358A453A-F248-11E8-B48F-1D18A9856A87
last_name: Mlynarski
- first_name: Anton L
full_name: Sumser, Anton L
id: 3320A096-F248-11E8-B48F-1D18A9856A87
last_name: Sumser
orcid: 0000-0002-4792-1881
- first_name: Olga
full_name: Symonova, Olga
id: 3C0C7BC6-F248-11E8-B48F-1D18A9856A87
last_name: Symonova
orcid: 0000-0003-2012-9947
- first_name: Jan
full_name: Svaton, Jan
id: f7f724c3-9d6f-11ed-9f44-e5c5f3a5bee2
last_name: Svaton
orcid: 0000-0002-6198-2939
- first_name: Maximilian A
full_name: Jösch, Maximilian A
id: 2BD278E6-F248-11E8-B48F-1D18A9856A87
last_name: Jösch
orcid: 0000-0002-3937-1330
citation:
ama: Gupta D, Mlynarski WF, Sumser AL, Symonova O, Svaton J, Jösch MA. Panoramic
visual statistics shape retina-wide organization of receptive fields. Nature
Neuroscience. 2023;26:606-614. doi:10.1038/s41593-023-01280-0
apa: Gupta, D., Mlynarski, W. F., Sumser, A. L., Symonova, O., Svaton, J., &
Jösch, M. A. (2023). Panoramic visual statistics shape retina-wide organization
of receptive fields. Nature Neuroscience. Springer Nature. https://doi.org/10.1038/s41593-023-01280-0
chicago: Gupta, Divyansh, Wiktor F Mlynarski, Anton L Sumser, Olga Symonova, Jan
Svaton, and Maximilian A Jösch. “Panoramic Visual Statistics Shape Retina-Wide
Organization of Receptive Fields.” Nature Neuroscience. Springer Nature,
2023. https://doi.org/10.1038/s41593-023-01280-0.
ieee: D. Gupta, W. F. Mlynarski, A. L. Sumser, O. Symonova, J. Svaton, and M. A.
Jösch, “Panoramic visual statistics shape retina-wide organization of receptive
fields,” Nature Neuroscience, vol. 26. Springer Nature, pp. 606–614, 2023.
ista: Gupta D, Mlynarski WF, Sumser AL, Symonova O, Svaton J, Jösch MA. 2023. Panoramic
visual statistics shape retina-wide organization of receptive fields. Nature Neuroscience.
26, 606–614.
mla: Gupta, Divyansh, et al. “Panoramic Visual Statistics Shape Retina-Wide Organization
of Receptive Fields.” Nature Neuroscience, vol. 26, Springer Nature, 2023,
pp. 606–14, doi:10.1038/s41593-023-01280-0.
short: D. Gupta, W.F. Mlynarski, A.L. Sumser, O. Symonova, J. Svaton, M.A. Jösch,
Nature Neuroscience 26 (2023) 606–614.
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title: Panoramic visual statistics shape retina-wide organization of receptive fields
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abstract:
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text: 'Statistics of natural scenes are not uniform - their structure varies dramatically
from ground to sky. It remains unknown whether these non-uniformities are reflected
in the large-scale organization of the early visual system and what benefits such
adaptations would confer. Here, by relying on the efficient coding hypothesis,
we predict that changes in the structure of receptive fields across visual space
increase the efficiency of sensory coding. We show experimentally that, in agreement
with our predictions, receptive fields of retinal ganglion cells change their
shape along the dorsoventral retinal axis, with a marked surround asymmetry at
the visual horizon. Our work demonstrates that, according to principles of efficient
coding, the panoramic structure of natural scenes is exploited by the retina across
space and cell-types. '
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shape retina-wide organization of receptive fields. 2023. doi:10.15479/AT:ISTA:12370'
apa: 'Gupta, D., Sumser, A. L., & Jösch, M. A. (2023). Research Data for: Panoramic
visual statistics shape retina-wide organization of receptive fields. Institute
of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:12370'
chicago: 'Gupta, Divyansh, Anton L Sumser, and Maximilian A Jösch. “Research Data
for: Panoramic Visual Statistics Shape Retina-Wide Organization of Receptive Fields.”
Institute of Science and Technology Austria, 2023. https://doi.org/10.15479/AT:ISTA:12370.'
ieee: 'D. Gupta, A. L. Sumser, and M. A. Jösch, “Research Data for: Panoramic visual
statistics shape retina-wide organization of receptive fields.” Institute of Science
and Technology Austria, 2023.'
ista: 'Gupta D, Sumser AL, Jösch MA. 2023. Research Data for: Panoramic visual statistics
shape retina-wide organization of receptive fields, Institute of Science and Technology
Austria, 10.15479/AT:ISTA:12370.'
mla: 'Gupta, Divyansh, et al. Research Data for: Panoramic Visual Statistics
Shape Retina-Wide Organization of Receptive Fields. Institute of Science and
Technology Austria, 2023, doi:10.15479/AT:ISTA:12370.'
short: D. Gupta, A.L. Sumser, M.A. Jösch, (2023).
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