---
OA_place: repository
_id: '18874'
abstract:
- lang: eng
text: "Despite extensive research since the community learned about adversarial\r\nexamples
10 years ago, we still do not know how to train high-accuracy\r\nclassifiers that
are guaranteed to be robust to small perturbations of their\r\ninputs. Previous
works often argued that this might be because no classifier\r\nexists that is
robust and accurate at the same time. However, in computer\r\nvision this assumption
does not match reality where humans are usually accurate\r\nand robust on most
tasks of interest. We offer an alternative explanation and\r\nshow that in certain
settings robust generalization is only possible with\r\nunrealistically large
amounts of data. More precisely we find a setting where a\r\nrobust classifier
exists, it is easy to learn an accurate classifier, yet it\r\nrequires an exponential
amount of data to learn a robust classifier. Based on\r\nthis theoretical result,
we explore how well robust classifiers generalize on\r\ndatasets such as CIFAR-10.
We come to the conclusion that on this datasets, the\r\nlimitation of current
robust models also lies in the generalization, and that\r\nthey require a lot
of data to do well on the test set. We also show that the\r\nproblem is not in
the expressiveness or generalization capabilities of current\r\narchitectures,
and that there are low magnitude features in the data which are\r\nuseful for
non-robust generalization but are not available for robust\r\nclassifiers."
article_number: '2412.04245'
article_processing_charge: No
arxiv: 1
author:
- first_name: Bernd
full_name: Prach, Bernd
id: 2D561D42-C427-11E9-89B4-9C1AE6697425
last_name: Prach
- first_name: Christoph
full_name: Lampert, Christoph
id: 40C20FD2-F248-11E8-B48F-1D18A9856A87
last_name: Lampert
orcid: 0000-0001-8622-7887
citation:
ama: Prach B, Lampert C. Intriguing properties of robust classification. arXiv.
doi:10.48550/arXiv.2412.04245
apa: Prach, B., & Lampert, C. (n.d.). Intriguing properties of robust classification.
arXiv. https://doi.org/10.48550/arXiv.2412.04245
chicago: Prach, Bernd, and Christoph Lampert. “Intriguing Properties of Robust Classification.”
ArXiv, n.d. https://doi.org/10.48550/arXiv.2412.04245.
ieee: B. Prach and C. Lampert, “Intriguing properties of robust classification,”
arXiv. .
ista: Prach B, Lampert C. Intriguing properties of robust classification. arXiv,
2412.04245.
mla: Prach, Bernd, and Christoph Lampert. “Intriguing Properties of Robust Classification.”
ArXiv, 2412.04245, doi:10.48550/arXiv.2412.04245.
short: B. Prach, C. Lampert, ArXiv (n.d.).
corr_author: '1'
date_created: 2025-01-24T16:57:29Z
date_published: 2024-12-05T00:00:00Z
date_updated: 2026-07-27T12:47:43Z
day: '05'
department:
- _id: GradSch
- _id: ChLa
doi: 10.48550/arXiv.2412.04245
external_id:
arxiv:
- '2412.04245'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.48550/arXiv.2412.04245
month: '12'
oa: 1
oa_version: Preprint
publication: arXiv
publication_status: draft
related_material:
record:
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relation: later_version
status: public
- id: '19759'
relation: dissertation_contains
status: public
status: public
title: Intriguing properties of robust classification
type: preprint
user_id: 8b945eb4-e2f2-11eb-945a-df72226e66a9
year: '2024'
...
---
APC_amount: 2748 EUR
OA_place: publisher
OA_type: hybrid
_id: '17634'
abstract:
- lang: eng
text: System behaviors are traditionally evaluated through binary classifications
of correctness, which do not suffice for properties involving quantitative aspects
of systems and executions. Quantitative automata offer a more nuanced approach,
mapping each execution to a real number by incorporating weighted transitions
and value functions generalizing acceptance conditions. In this paper, we introduce
QuAK, the first tool designed to automate the analysis of quantitative automata.
QuAK currently supports a variety of quantitative automaton types, including Inf,
Sup, LimInf, LimSup, LimInfAvg, and LimSupAvg automata, and implements decision
procedures for problems such as emptiness, universality, inclusion, equivalence,
as well as for checking whether an automaton is safe, live, or constant. Additionally,
QuAK is able to compute extremal values when possible, construct safety-liveness
decompositions, and monitor system behaviors. We demonstrate the effectiveness
of QuAK through experiments focusing on the inclusion, constant-function check,
and monitoring problems.
acknowledgement: This work was supported in part by the ERC-2020-AdG 101020093. N.
Mazzocchi was affiliated with ISTA when his collaboration started.
alternative_title:
- LNCS
article_processing_charge: Yes (in subscription journal)
arxiv: 1
author:
- first_name: Marek
full_name: Chalupa, Marek
id: 87e34708-d6c6-11ec-9f5b-9391e7be2463
last_name: Chalupa
- first_name: Thomas A
full_name: Henzinger, Thomas A
id: 40876CD8-F248-11E8-B48F-1D18A9856A87
last_name: Henzinger
orcid: 0000-0002-2985-7724
- first_name: Nicolas Adrien
full_name: Mazzocchi, Nicolas Adrien
id: b26baa86-3308-11ec-87b0-8990f34baa85
last_name: Mazzocchi
- first_name: Naci E
full_name: Sarac, Naci E
id: 8C6B42F8-C8E6-11E9-A03A-F2DCE5697425
last_name: Sarac
citation:
ama: 'Chalupa M, Henzinger TA, Mazzocchi NA, Sarac NE. QuAK: Quantitative Automata
Kit. In: 12th International Symposium on Leveraging Applications of Formal
Methods, Verification and Validation. Vol 15222. Springer Nature; 2024:3-20.
doi:10.1007/978-3-031-75387-9_1'
apa: 'Chalupa, M., Henzinger, T. A., Mazzocchi, N. A., & Sarac, N. E. (2024).
QuAK: Quantitative Automata Kit. In 12th International Symposium on Leveraging
Applications of Formal Methods, Verification and Validation (Vol. 15222, pp.
3–20). Crete, Greece: Springer Nature. https://doi.org/10.1007/978-3-031-75387-9_1'
chicago: 'Chalupa, Marek, Thomas A Henzinger, Nicolas Adrien Mazzocchi, and Naci
E Sarac. “QuAK: Quantitative Automata Kit.” In 12th International Symposium
on Leveraging Applications of Formal Methods, Verification and Validation,
15222:3–20. Springer Nature, 2024. https://doi.org/10.1007/978-3-031-75387-9_1.'
ieee: 'M. Chalupa, T. A. Henzinger, N. A. Mazzocchi, and N. E. Sarac, “QuAK: Quantitative
Automata Kit,” in 12th International Symposium on Leveraging Applications of
Formal Methods, Verification and Validation, Crete, Greece, 2024, vol. 15222,
pp. 3–20.'
ista: 'Chalupa M, Henzinger TA, Mazzocchi NA, Sarac NE. 2024. QuAK: Quantitative
Automata Kit. 12th International Symposium on Leveraging Applications of Formal
Methods, Verification and Validation. ISoLA: International Symposium on Leveraging
Applications, LNCS, vol. 15222, 3–20.'
mla: 'Chalupa, Marek, et al. “QuAK: Quantitative Automata Kit.” 12th International
Symposium on Leveraging Applications of Formal Methods, Verification and Validation,
vol. 15222, Springer Nature, 2024, pp. 3–20, doi:10.1007/978-3-031-75387-9_1.'
short: M. Chalupa, T.A. Henzinger, N.A. Mazzocchi, N.E. Sarac, in:, 12th International
Symposium on Leveraging Applications of Formal Methods, Verification and Validation,
Springer Nature, 2024, pp. 3–20.
conference:
end_date: 2024-10-31
location: Crete, Greece
name: 'ISoLA: International Symposium on Leveraging Applications'
start_date: 2024-10-27
corr_author: '1'
date_created: 2024-09-05T14:27:08Z
date_published: 2024-10-26T00:00:00Z
date_updated: 2026-07-27T12:48:18Z
day: '26'
ddc:
- '000'
department:
- _id: GradSch
- _id: ToHe
doi: 10.1007/978-3-031-75387-9_1
ec_funded: 1
external_id:
arxiv:
- '2409.03569'
isi:
- '001419008700001'
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file_date_updated: 2025-01-21T14:39:49Z
has_accepted_license: '1'
intvolume: ' 15222'
isi: 1
language:
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month: '10'
oa: 1
oa_version: Published Version
page: 3-20
project:
- _id: 62781420-2b32-11ec-9570-8d9b63373d4d
call_identifier: H2020
grant_number: '101020093'
name: Vigilant Algorithmic Monitoring of Software
publication: 12th International Symposium on Leveraging Applications of Formal Methods,
Verification and Validation
publication_identifier:
eissn:
- 1611-3349
isbn:
- '9783031753862'
issn:
- 0302-9743
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
related_material:
record:
- id: '20147'
relation: dissertation_contains
status: public
scopus_import: '1'
status: public
title: 'QuAK: Quantitative Automata Kit'
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: conference
user_id: 317138e5-6ab7-11ef-aa6d-ffef3953e345
volume: 15222
year: '2024'
...
---
_id: '18121'
abstract:
- lang: eng
text: It is known that sparsity can improve interpretability for deep neural networks.
However, existing methods in the area either require networks that are pre-trained
with sparsity constraints, or impose sparsity after the fact, altering the network’s
general behavior. In this paper, we demonstrate, for the first time, that sparsity
can instead be incorporated into the interpretation process itself, as a sample-specific
preprocessing step. Unlike previous work, this approach, which we call SPADE,
does not place constraints on the trained model and does not affect its behavior
during inference on the sample. Given a trained model and a target sample, SPADE
uses sample-targeted pruning to provide a "trace" of the network’s execution on
the sample, reducing the network to the most important connections prior to computing
an interpretation. We demonstrate that preprocessing with SPADE significantly
increases the accuracy of image saliency maps across several interpretability
methods. Additionally, SPADE improves the usefulness of neuron visualizations,
aiding humans in reasoning about network behavior. Our code is available at https://github.com/IST-DASLab/SPADE.
acknowledged_ssus:
- _id: ScienComp
acknowledgement: The authors would like to thank Stephen Casper and Tony Wang for
their feedback on this work, and Eldar Kurtic for his advice on aspects of the project.
This research was supported by the Scientific Service Units (SSU) of IST Austria
through resources provided by Scientific Computing (SciComp). EI was supported in
part by the FWF DK VGSCO, grant agreement number W1260-N35.
alternative_title:
- PMLR
article_processing_charge: No
arxiv: 1
author:
- first_name: Arshia Soltani
full_name: Moakhar, Arshia Soltani
last_name: Moakhar
- first_name: Eugenia B
full_name: Iofinova, Eugenia B
id: f9a17499-f6e0-11ea-865d-fdf9a3f77117
last_name: Iofinova
orcid: 0000-0002-7778-3221
- first_name: 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: 'Moakhar AS, Iofinova EB, Frantar E, Alistarh D-A. SPADE: Sparsity-guided debugging
for deep neural networks. In: Proceedings of the 41st International Conference
on Machine Learning. Vol 235. ML Research Press; 2024:45955-45987.'
apa: 'Moakhar, A. S., Iofinova, E. B., Frantar, E., & Alistarh, D.-A. (2024).
SPADE: Sparsity-guided debugging for deep neural networks. In Proceedings of
the 41st International Conference on Machine Learning (Vol. 235, pp. 45955–45987).
Vienna, Austria: ML Research Press.'
chicago: 'Moakhar, Arshia Soltani, Eugenia B Iofinova, Elias Frantar, and Dan-Adrian
Alistarh. “SPADE: Sparsity-Guided Debugging for Deep Neural Networks.” In Proceedings
of the 41st International Conference on Machine Learning, 235:45955–87. ML
Research Press, 2024.'
ieee: 'A. S. Moakhar, E. B. Iofinova, E. Frantar, and D.-A. Alistarh, “SPADE: Sparsity-guided
debugging for deep neural networks,” in Proceedings of the 41st International
Conference on Machine Learning, Vienna, Austria, 2024, vol. 235, pp. 45955–45987.'
ista: 'Moakhar AS, Iofinova EB, Frantar E, Alistarh D-A. 2024. SPADE: Sparsity-guided
debugging for deep neural networks. Proceedings of the 41st International Conference
on Machine Learning. ICML: International Conference on Machine Learning, PMLR,
vol. 235, 45955–45987.'
mla: 'Moakhar, Arshia Soltani, et al. “SPADE: Sparsity-Guided Debugging for Deep
Neural Networks.” Proceedings of the 41st International Conference on Machine
Learning, vol. 235, ML Research Press, 2024, pp. 45955–87.'
short: A.S. Moakhar, E.B. Iofinova, E. Frantar, D.-A. Alistarh, in:, Proceedings
of the 41st International Conference on Machine Learning, ML Research Press, 2024,
pp. 45955–45987.
conference:
end_date: 2024-07-27
location: Vienna, Austria
name: 'ICML: International Conference on Machine Learning'
start_date: 2024-07-21
corr_author: '1'
date_created: 2024-09-22T22:01:46Z
date_published: 2024-09-01T00:00:00Z
date_updated: 2026-07-27T12:50:03Z
day: '01'
department:
- _id: DaAl
external_id:
arxiv:
- '2310.04519'
intvolume: ' 235'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.48550/arXiv.2310.04519
month: '09'
oa: 1
oa_version: Preprint
page: 45955-45987
project:
- _id: 9B9290DE-BA93-11EA-9121-9846C619BF3A
grant_number: W1260-N35
name: Vienna Graduate School on Computational Optimization
publication: Proceedings of the 41st International Conference on Machine Learning
publication_identifier:
eissn:
- 2640-3498
publication_status: published
publisher: ML Research Press
quality_controlled: '1'
related_material:
link:
- relation: software
url: https://github.com/IST-DASLab/SPADE
record:
- id: '21854'
relation: dissertation_contains
status: public
scopus_import: '1'
status: public
title: 'SPADE: Sparsity-guided debugging for deep neural networks'
type: conference
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 235
year: '2024'
...
---
APC_amount: 3149,96 EUR
DOAJ_listed: '1'
OA_place: publisher
OA_type: gold
_id: '15297'
abstract:
- lang: eng
text: Populations evolve by accumulating advantageous mutations. Every population
has some spatial structure that can be modeled by an underlying network. The network
then influences the probability that new advantageous mutations fixate. Amplifiers
of selection are networks that increase the fixation probability of advantageous
mutants, as compared to the unstructured fully-connected network. Whether or not
a network is an amplifier depends on the choice of the random process that governs
the evolutionary dynamics. Two popular choices are Moran process with Birth-death
updating and Moran process with death-Birth updating. Interestingly, while some
networks are amplifiers under Birth-death updating and other networks are amplifiers
under death-Birth updating, so far no spatial structures have been found that
function as an amplifier under both types of updating simultaneously. In this
work, we identify networks that act as amplifiers of selection under both versions
of the Moran process. The amplifiers are robust, modular, and increase fixation
probability for any mutant fitness advantage in a range r ∈ (1, 1.2). To complement
this positive result, we also prove that for certain quantities closely related
to fixation probability, it is impossible to improve them simultaneously for both
versions of the Moran process. Together, our results highlight how the two versions
of the Moran process differ and what they have in common.
acknowledgement: "We thank Gavin Rees for helpful discussions. J.S., S.J., and K.C
were supported by\r\nEuropean Research Council (ERC) CoG 863818 (ForM-SMArt). J.T
was supported by Center for Foundations of Modern Computer Science (Charles University
project UNCE/SCI/004) and by the project PRIMUS/24/SCI/012 from Charles University. "
article_number: e1012008
article_processing_charge: Yes
article_type: original
arxiv: 1
author:
- first_name: Jakub
full_name: Svoboda, Jakub
id: 130759D2-D7DD-11E9-87D2-DE0DE6697425
last_name: Svoboda
orcid: 0000-0002-1419-3267
- first_name: Soham Shrikant
full_name: Joshi, Soham Shrikant
id: f97aac0e-f57c-11ee-93d0-a5a82d8df168
last_name: Joshi
- first_name: Josef
full_name: Tkadlec, Josef
id: 3F24CCC8-F248-11E8-B48F-1D18A9856A87
last_name: Tkadlec
orcid: 0000-0002-1097-9684
- first_name: Krishnendu
full_name: Chatterjee, Krishnendu
id: 2E5DCA20-F248-11E8-B48F-1D18A9856A87
last_name: Chatterjee
orcid: 0000-0002-4561-241X
citation:
ama: Svoboda J, Joshi SS, Tkadlec J, Chatterjee K. Amplifiers of selection for the
Moran process with both Birth-death and death-Birth updating. PLoS Computational
Biology. 2024;20(3). doi:10.1371/journal.pcbi.1012008
apa: Svoboda, J., Joshi, S. S., Tkadlec, J., & Chatterjee, K. (2024). Amplifiers
of selection for the Moran process with both Birth-death and death-Birth updating.
PLoS Computational Biology. Public Library of Science. https://doi.org/10.1371/journal.pcbi.1012008
chicago: Svoboda, Jakub, Soham Shrikant Joshi, Josef Tkadlec, and Krishnendu Chatterjee.
“Amplifiers of Selection for the Moran Process with Both Birth-Death and Death-Birth
Updating.” PLoS Computational Biology. Public Library of Science, 2024.
https://doi.org/10.1371/journal.pcbi.1012008.
ieee: J. Svoboda, S. S. Joshi, J. Tkadlec, and K. Chatterjee, “Amplifiers of selection
for the Moran process with both Birth-death and death-Birth updating,” PLoS
Computational Biology, vol. 20, no. 3. Public Library of Science, 2024.
ista: Svoboda J, Joshi SS, Tkadlec J, Chatterjee K. 2024. Amplifiers of selection
for the Moran process with both Birth-death and death-Birth updating. PLoS Computational
Biology. 20(3), e1012008.
mla: Svoboda, Jakub, et al. “Amplifiers of Selection for the Moran Process with
Both Birth-Death and Death-Birth Updating.” PLoS Computational Biology,
vol. 20, no. 3, e1012008, Public Library of Science, 2024, doi:10.1371/journal.pcbi.1012008.
short: J. Svoboda, S.S. Joshi, J. Tkadlec, K. Chatterjee, PLoS Computational Biology
20 (2024).
corr_author: '1'
date_created: 2024-04-07T22:00:55Z
date_published: 2024-03-29T00:00:00Z
date_updated: 2026-07-27T12:52:03Z
day: '29'
ddc:
- '000'
department:
- _id: KrCh
doi: 10.1371/journal.pcbi.1012008
ec_funded: 1
external_id:
arxiv:
- '2401.14914'
isi:
- '001194482400002'
file:
- access_level: open_access
checksum: a511cf369d9172beb123fe73f291b5cc
content_type: application/pdf
creator: dernst
date_created: 2024-08-20T10:52:28Z
date_updated: 2024-08-20T10:52:28Z
file_id: '17450'
file_name: 2024_PloSComBio_Svoboda.pdf
file_size: 1425292
relation: main_file
success: 1
file_date_updated: 2024-08-20T10:52:28Z
has_accepted_license: '1'
intvolume: ' 20'
isi: 1
issue: '3'
language:
- iso: eng
month: '03'
oa: 1
oa_version: Published Version
project:
- _id: 0599E47C-7A3F-11EA-A408-12923DDC885E
call_identifier: H2020
grant_number: '863818'
name: 'Formal Methods for Stochastic Models: Algorithms and Applications'
publication: PLoS Computational Biology
publication_identifier:
eissn:
- 1553-7358
issn:
- 1553-734X
publication_status: published
publisher: Public Library of Science
quality_controlled: '1'
related_material:
record:
- id: '20138'
relation: dissertation_contains
status: public
scopus_import: '1'
status: public
title: Amplifiers of selection for the Moran process with both Birth-death and death-Birth
updating
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: 317138e5-6ab7-11ef-aa6d-ffef3953e345
volume: 20
year: '2024'
...
---
APC_amount: 3143,76 EUR
OA_place: publisher
OA_type: hybrid
_id: '18703'
abstract:
- lang: eng
text: 'Spatial games provide a simple and elegant mathematical model to study the
evolution of cooperation in networks. In spatial games, individuals reside in
vertices, adopt simple strategies, and interact with neighbors to receive a payoff.
Depending on their own and neighbors’ payoffs, individuals can change their strategy.
The payoff is determined by the Prisoners’ Dilemma, a classical matrix game, where
players cooperate or defect. While cooperation is the desired behavior, defection
provides a higher payoff for a selfish individual. There are many theoretical
and empirical studies related to the role of the network in the evolution of cooperation.
However, the fundamental question of whether there exist networks that for low
initial cooperation rate ensure a high chance of fixation, i.e., cooperation spreads
across the whole population, has remained elusive for spatial games with strong
selection. In this work, we answer this fundamental question in the affirmative
by presenting network structures that ensure high fixation probability for cooperators
in the strong selection regime. Besides, our structures have many desirable properties:
(a) they ensure the spread of cooperation even for a low initial density of cooperation
and high temptation of defection, (b) they have constant degrees, and (c) the
number of steps, until cooperation spreads, is at most quadratic in the size of
the network.'
acknowledgement: J.S. and K.C. were supported by the European Research Council CoG
863818 (ForM-SMArt) and Austrian Science Fund 10.55776/COE12.
article_number: e2405605121
article_processing_charge: Yes
article_type: original
author:
- first_name: Jakub
full_name: Svoboda, Jakub
id: 130759D2-D7DD-11E9-87D2-DE0DE6697425
last_name: Svoboda
orcid: 0000-0002-1419-3267
- first_name: Krishnendu
full_name: Chatterjee, Krishnendu
id: 2E5DCA20-F248-11E8-B48F-1D18A9856A87
last_name: Chatterjee
orcid: 0000-0002-4561-241X
citation:
ama: Svoboda J, Chatterjee K. Density amplifiers of cooperation for spatial games.
Proceedings of the National Academy of Sciences of the United States of America.
2024;121(50). doi:10.1073/pnas.2405605121
apa: Svoboda, J., & Chatterjee, K. (2024). Density amplifiers of cooperation
for spatial games. Proceedings of the National Academy of Sciences of the United
States of America. National Academy of Sciences. https://doi.org/10.1073/pnas.2405605121
chicago: Svoboda, Jakub, and Krishnendu Chatterjee. “Density Amplifiers of Cooperation
for Spatial Games.” Proceedings of the National Academy of Sciences of the
United States of America. National Academy of Sciences, 2024. https://doi.org/10.1073/pnas.2405605121.
ieee: J. Svoboda and K. Chatterjee, “Density amplifiers of cooperation for spatial
games,” Proceedings of the National Academy of Sciences of the United States
of America, vol. 121, no. 50. National Academy of Sciences, 2024.
ista: Svoboda J, Chatterjee K. 2024. Density amplifiers of cooperation for spatial
games. Proceedings of the National Academy of Sciences of the United States of
America. 121(50), e2405605121.
mla: Svoboda, Jakub, and Krishnendu Chatterjee. “Density Amplifiers of Cooperation
for Spatial Games.” Proceedings of the National Academy of Sciences of the
United States of America, vol. 121, no. 50, e2405605121, National Academy
of Sciences, 2024, doi:10.1073/pnas.2405605121.
short: J. Svoboda, K. Chatterjee, Proceedings of the National Academy of Sciences
of the United States of America 121 (2024).
corr_author: '1'
date_created: 2024-12-22T23:01:47Z
date_published: 2024-12-10T00:00:00Z
date_updated: 2026-07-27T12:52:03Z
day: '10'
ddc:
- '000'
department:
- _id: KrCh
doi: 10.1073/pnas.2405605121
ec_funded: 1
external_id:
isi:
- '001379596100014'
pmid:
- '39642209'
file:
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checksum: 0115e9090b478e0644308c6dab58605b
content_type: application/pdf
creator: dernst
date_created: 2025-01-02T12:14:15Z
date_updated: 2025-01-02T12:14:15Z
file_id: '18721'
file_name: 2024_PNAS_Svoboda.pdf
file_size: 2491151
relation: main_file
success: 1
file_date_updated: 2025-01-02T12:14:15Z
has_accepted_license: '1'
intvolume: ' 121'
isi: 1
issue: '50'
language:
- iso: eng
month: '12'
oa: 1
oa_version: Published Version
pmid: 1
project:
- _id: 0599E47C-7A3F-11EA-A408-12923DDC885E
call_identifier: H2020
grant_number: '863818'
name: 'Formal Methods for Stochastic Models: Algorithms and Applications'
publication: Proceedings of the National Academy of Sciences of the United States
of America
publication_identifier:
eissn:
- 1091-6490
issn:
- 0027-8424
publication_status: published
publisher: National Academy of Sciences
quality_controlled: '1'
related_material:
record:
- id: '20138'
relation: dissertation_contains
status: public
scopus_import: '1'
status: public
title: Density amplifiers of cooperation for spatial games
tmp:
image: /images/cc_by_nc_nd.png
legal_code_url: https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode
name: Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International
(CC BY-NC-ND 4.0)
short: CC BY-NC-ND (4.0)
type: journal_article
user_id: 317138e5-6ab7-11ef-aa6d-ffef3953e345
volume: 121
year: '2024'
...
---
_id: '14687'
abstract:
- lang: eng
text: The short history of research on Li-O2 batteries has seen a remarkable number
of mechanistic U-turns over the years. From the initial use of carbonate electrolytes,
that were then found to be entirely unsuitable, to the belief that (su)peroxide
was solely responsible for degradation, before the more reactive singlet oxygen
was found to form, to the hypothesis that capacity depends on a competing surface/solution
mechanism before a practically exclusive solution mechanism was identified. Herein,
we argue for an ever-fresh look at the reported data without bias towards supposedly
established explanations. We explain how the latest findings on rate and capacity
limits, as well as the origin of side reactions, are connected via the disproportionation
(DISP) step in the (dis)charge mechanism. Therefrom, directions emerge for the
design of electrolytes and mediators on how to suppress side reactions and to
enable high rate and high reversible capacity.
acknowledgement: S.A.F. is indebted to ISTA for support. R.B.J. thanks the European
Union's Horizon 2020 research and innovation programme under the Marie Skłodowska-Curie
grant agreement No 101034413 for funding. B.P. thanks Alistore ERI for providing
a PhD scholarship.
article_number: e202316476
article_processing_charge: Yes (via OA deal)
article_type: review
author:
- first_name: Rajesh B
full_name: Jethwa, Rajesh B
id: 4cc538d5-803f-11ed-ab7e-8139573aad8f
last_name: Jethwa
orcid: 0000-0002-0404-4356
- first_name: Soumyadip
full_name: Mondal, Soumyadip
id: d25d21ef-dc8d-11ea-abe3-ec4576307f48
last_name: Mondal
- first_name: Bhargavi
full_name: Pant, Bhargavi
id: 50c64d4d-eb97-11eb-a6c2-d33e5e14f112
last_name: Pant
- first_name: Stefan Alexander
full_name: Freunberger, Stefan Alexander
id: A8CA28E6-CE23-11E9-AD2D-EC27E6697425
last_name: Freunberger
orcid: 0000-0003-2902-5319
citation:
ama: Jethwa RB, Mondal S, Pant B, Freunberger SA. To DISP or not? The far‐reaching
reaction mechanisms underpinning Lithium‐air batteries. Angewandte Chemie International
Edition. 2024;63(28). doi:10.1002/anie.202316476
apa: Jethwa, R. B., Mondal, S., Pant, B., & Freunberger, S. A. (2024). To DISP
or not? The far‐reaching reaction mechanisms underpinning Lithium‐air batteries.
Angewandte Chemie International Edition. Wiley. https://doi.org/10.1002/anie.202316476
chicago: Jethwa, Rajesh B, Soumyadip Mondal, Bhargavi Pant, and Stefan Alexander
Freunberger. “To DISP or Not? The Far‐reaching Reaction Mechanisms Underpinning
Lithium‐air Batteries.” Angewandte Chemie International Edition. Wiley,
2024. https://doi.org/10.1002/anie.202316476.
ieee: R. B. Jethwa, S. Mondal, B. Pant, and S. A. Freunberger, “To DISP or not?
The far‐reaching reaction mechanisms underpinning Lithium‐air batteries,” Angewandte
Chemie International Edition, vol. 63, no. 28. Wiley, 2024.
ista: Jethwa RB, Mondal S, Pant B, Freunberger SA. 2024. To DISP or not? The far‐reaching
reaction mechanisms underpinning Lithium‐air batteries. Angewandte Chemie International
Edition. 63(28), e202316476.
mla: Jethwa, Rajesh B., et al. “To DISP or Not? The Far‐reaching Reaction Mechanisms
Underpinning Lithium‐air Batteries.” Angewandte Chemie International Edition,
vol. 63, no. 28, e202316476, Wiley, 2024, doi:10.1002/anie.202316476.
short: R.B. Jethwa, S. Mondal, B. Pant, S.A. Freunberger, Angewandte Chemie International
Edition 63 (2024).
corr_author: '1'
date_created: 2023-12-15T16:10:13Z
date_published: 2024-07-08T00:00:00Z
date_updated: 2026-07-27T14:29:01Z
day: '08'
ddc:
- '540'
department:
- _id: StFr
- _id: GradSch
doi: 10.1002/anie.202316476
ec_funded: 1
external_id:
isi:
- '001241932700001'
pmid:
- '38095355'
file:
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checksum: fe2c23454279eb9d76ed6ca9970c21c7
content_type: application/pdf
creator: dernst
date_created: 2024-07-16T11:54:46Z
date_updated: 2024-07-16T11:54:46Z
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file_name: 2024_AngChemieInt_Jethwa.pdf
file_size: 4766445
relation: main_file
success: 1
file_date_updated: 2024-07-16T11:54:46Z
has_accepted_license: '1'
intvolume: ' 63'
isi: 1
issue: '28'
keyword:
- General Chemistry
- Catalysis
language:
- iso: eng
month: '07'
oa: 1
oa_version: Published Version
pmid: 1
project:
- _id: fc2ed2f7-9c52-11eb-aca3-c01059dda49c
call_identifier: H2020
grant_number: '101034413'
name: 'IST-BRIDGE: International postdoctoral program'
publication: Angewandte Chemie International Edition
publication_identifier:
eissn:
- 1521-3773
issn:
- 1433-7851
publication_status: published
publisher: Wiley
quality_controlled: '1'
related_material:
record:
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relation: dissertation_contains
status: public
scopus_import: '1'
status: public
title: To DISP or not? The far‐reaching reaction mechanisms underpinning Lithium‐air
batteries
tmp:
image: /images/cc_by_nc_nd.png
legal_code_url: https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode
name: Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International
(CC BY-NC-ND 4.0)
short: CC BY-NC-ND (4.0)
type: journal_article
user_id: 317138e5-6ab7-11ef-aa6d-ffef3953e345
volume: 63
year: '2024'
...
---
_id: '13044'
abstract:
- lang: eng
text: Singlet oxygen (1O2) formation is now recognised as a key aspect of non-aqueous
oxygen redox chemistry. For identifying 1O2, chemical trapping via 9,10-dimethylanthracene
(DMA) to form the endoperoxide (DMA-O2) has become the mainstay method due to
its sensitivity, selectivity, and ease of use. While DMA has been shown to be
selective for 1O2, rather than forming DMA-O2 with a wide variety of potentially
reactive O-containing species, false positives might hypothetically be obtained
in the presence of previously overlooked species. Here, we first give unequivocal
direct spectroscopic proof by the 1O2-specific near infrared (NIR) emission at
1270 nm for the previously proposed 1O2 formation pathways, which centre around
superoxide disproportionation. We then show that peroxocarbonates, common intermediates
in metal-O2 and metal carbonate electrochemistry, do not produce false-positive
DMA-O2. Moreover, we identify a previously unreported 1O2-forming pathway through
the reaction of CO2 with superoxide. Overall, we give unequivocal proof for 1O2
formation in non-aqueous oxygen redox and show that chemical trapping with DMA
is a reliable method to assess 1O2 formation.
article_processing_charge: Yes (via OA deal)
article_type: original
author:
- first_name: Soumyadip
full_name: Mondal, Soumyadip
id: d25d21ef-dc8d-11ea-abe3-ec4576307f48
last_name: Mondal
- first_name: Rajesh B
full_name: Jethwa, Rajesh B
id: 4cc538d5-803f-11ed-ab7e-8139573aad8f
last_name: Jethwa
orcid: 0000-0002-0404-4356
- first_name: Bhargavi
full_name: Pant, Bhargavi
id: 50c64d4d-eb97-11eb-a6c2-d33e5e14f112
last_name: Pant
- first_name: Robert
full_name: Hauschild, Robert
id: 4E01D6B4-F248-11E8-B48F-1D18A9856A87
last_name: Hauschild
orcid: 0000-0001-9843-3522
- first_name: Stefan Alexander
full_name: Freunberger, Stefan Alexander
id: A8CA28E6-CE23-11E9-AD2D-EC27E6697425
last_name: Freunberger
orcid: 0000-0003-2902-5319
citation:
ama: 'Mondal S, Jethwa RB, Pant B, Hauschild R, Freunberger SA. Singlet oxygen in
non-aqueous oxygen redox: Direct spectroscopic evidence for formation pathways
and reliability of chemical probes. Faraday Discussions. 2024;248:175-189.
doi:10.1039/d3fd00088e'
apa: 'Mondal, S., Jethwa, R. B., Pant, B., Hauschild, R., & Freunberger, S.
A. (2024). Singlet oxygen in non-aqueous oxygen redox: Direct spectroscopic evidence
for formation pathways and reliability of chemical probes. Faraday Discussions.
Royal Society of Chemistry. https://doi.org/10.1039/d3fd00088e'
chicago: 'Mondal, Soumyadip, Rajesh B Jethwa, Bhargavi Pant, Robert Hauschild, and
Stefan Alexander Freunberger. “Singlet Oxygen in Non-Aqueous Oxygen Redox: Direct
Spectroscopic Evidence for Formation Pathways and Reliability of Chemical Probes.”
Faraday Discussions. Royal Society of Chemistry, 2024. https://doi.org/10.1039/d3fd00088e.'
ieee: 'S. Mondal, R. B. Jethwa, B. Pant, R. Hauschild, and S. A. Freunberger, “Singlet
oxygen in non-aqueous oxygen redox: Direct spectroscopic evidence for formation
pathways and reliability of chemical probes,” Faraday Discussions, vol.
248. Royal Society of Chemistry, pp. 175–189, 2024.'
ista: 'Mondal S, Jethwa RB, Pant B, Hauschild R, Freunberger SA. 2024. Singlet oxygen
in non-aqueous oxygen redox: Direct spectroscopic evidence for formation pathways
and reliability of chemical probes. Faraday Discussions. 248, 175–189.'
mla: 'Mondal, Soumyadip, et al. “Singlet Oxygen in Non-Aqueous Oxygen Redox: Direct
Spectroscopic Evidence for Formation Pathways and Reliability of Chemical Probes.”
Faraday Discussions, vol. 248, Royal Society of Chemistry, 2024, pp. 175–89,
doi:10.1039/d3fd00088e.'
short: S. Mondal, R.B. Jethwa, B. Pant, R. Hauschild, S.A. Freunberger, Faraday
Discussions 248 (2024) 175–189.
corr_author: '1'
date_created: 2023-05-22T06:53:34Z
date_published: 2024-01-01T00:00:00Z
date_updated: 2026-07-27T14:29:01Z
day: '01'
ddc:
- '540'
department:
- _id: StFr
- _id: Bio
doi: 10.1039/d3fd00088e
external_id:
isi:
- '001070423500001'
pmid:
- '37750344'
file:
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checksum: 6515a227ed3e8942496fe6a1feeffd18
content_type: application/pdf
creator: dernst
date_created: 2024-07-16T07:46:39Z
date_updated: 2024-07-16T07:46:39Z
file_id: '17249'
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file_size: 1303733
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file_date_updated: 2024-07-16T07:46:39Z
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intvolume: ' 248'
isi: 1
keyword:
- Physical and Theoretical Chemistry
language:
- iso: eng
month: '01'
oa: 1
oa_version: Published Version
page: 175-189
pmid: 1
publication: Faraday Discussions
publication_identifier:
eissn:
- 1364-5498
issn:
- 1359-6640
publication_status: published
publisher: Royal Society of Chemistry
quality_controlled: '1'
related_material:
record:
- id: '20607'
relation: dissertation_contains
status: public
scopus_import: '1'
status: public
title: 'Singlet oxygen in non-aqueous oxygen redox: Direct spectroscopic evidence
for formation pathways and reliability of chemical probes'
tmp:
image: /images/cc_by_nc.png
legal_code_url: https://creativecommons.org/licenses/by-nc/3.0/legalcode
name: Creative Commons Attribution-NonCommercial 3.0 Unported (CC BY-NC 3.0)
short: CC BY-NC (3.0)
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 248
year: '2024'
...
---
OA_place: repository
_id: '17465'
abstract:
- lang: eng
text: "In the modern age of machine learning, artificial neural networks have become
an integral part\r\nof many practical systems. One of the key ingredients of the
success of the deep learning\r\napproach is recent computational advances which
allowed the training of models with billions\r\nof parameters on large-scale data.
Such over-parameterized and data-hungry regimes pose a\r\nchallenge for the theoretical
analysis of modern models since “classical” statistical wisdom\r\nis no longer
applicable. In this view, it is paramount to extend or develop new machinery\r\nthat
will allow tackling the neural network analysis under new challenging asymptotic
regimes,\r\nwhich is the focus of this thesis.\r\nLarge neural network systems
are usually optimized via “local” search algorithms, such\r\nas stochastic gradient
descent (SGD). However, given the high-dimensional nature of the\r\nparameter
space, it is a priori not clear why such a crude “local” approach works so remarkably\r\nwell
in practice. We take a step towards demystifying this phenomenon by showing that\r\nthe
landscape of the SGD training dynamics exhibits a few beneficial properties for
the\r\noptimization. First, we show that along the SGD trajectory an over-parameterized
network\r\nis dropout stable. The emergence of dropout stability allows to conclude
that the minima\r\nfound by SGD are connected via a continuous path of small loss.
This in turn means that\r\nthe high-dimensional landscape of the neural network
optimization problem is provably not so\r\nunfavourable to gradient-based training,
due to mode connectivity. Next, we show that SGD\r\nfor an over-parameterized
network tends to find solutions that are functionally more “simple”.\r\nThis in
turn means that the SGD minima are more robust, since a less complicated solution\r\nwill
less likely overfit the data. More formally, for a prototypical example of a wide
two-layer\r\nReLU network on a 1d regression task we show that the SGD algorithm
is implicitly selective in\r\nits choice of an interpolating solution. Namely,
at convergence the neural network implements\r\na piece-wise linear function with
the number of linear regions depending only on the amount\r\nof training data.
This is in contrast to a “smooth”-like behaviour which one would expect\r\ngiven
such a severe over-parameterization of the model.\r\nDiverging from the generic
supervised setting of classification and regression problems, we\r\nanalyze an
auto-encoder model that is commonly used for representation learning and data\r\ncompression.
Despite the wide applicability of the auto-encoding paradigm, the theoretical\r\nunderstanding
of their behaviour is limited even in the simplistic shallow case. The related\r\nwork
is restricted to extreme asymptotic regimes in which the auto-encoder is either
severely\r\nover-parameterized or under-parameterized. In contrast, we provide
a tight characterization\r\nfor the 1-bit compression of Gaussian signals in the
challenging proportional regime, i.e., the\r\ninput dimension and the size of
the compressed representation obey the same asymptotics.\r\nWe also show that
gradient-based methods are able to find a globally optimal solution and\r\nthat
the predictions made for Gaussian data extrapolate beyond - to the case of compression\r\nof
natural images. Next, we relax the Gaussian assumption and study more structured
input\r\nsources. We show that the shallow model is sometimes agnostic to the
structure of the data\r\nvii\r\nwhich results in a Gaussian-like behaviour. We
prove that making the decoding component\r\nslightly less shallow is already enough
to escape the “curse” of Gaussian performance.\r\n"
acknowledged_ssus:
- _id: ScienComp
alternative_title:
- ISTA Thesis
article_processing_charge: No
author:
- first_name: Aleksandr
full_name: Shevchenko, Aleksandr
id: F2B06EC2-C99E-11E9-89F0-752EE6697425
last_name: Shevchenko
citation:
ama: Shevchenko A. High-dimensional limits in artificial neural networks. 2024.
doi:10.15479/at:ista:17465
apa: Shevchenko, A. (2024). High-dimensional limits in artificial neural networks.
Institute of Science and Technology Austria. https://doi.org/10.15479/at:ista:17465
chicago: Shevchenko, Alexander. “High-Dimensional Limits in Artificial Neural Networks.”
Institute of Science and Technology Austria, 2024. https://doi.org/10.15479/at:ista:17465.
ieee: A. Shevchenko, “High-dimensional limits in artificial neural networks,” Institute
of Science and Technology Austria, 2024.
ista: Shevchenko A. 2024. High-dimensional limits in artificial neural networks.
Institute of Science and Technology Austria.
mla: Shevchenko, Alexander. High-Dimensional Limits in Artificial Neural Networks.
Institute of Science and Technology Austria, 2024, doi:10.15479/at:ista:17465.
short: A. Shevchenko, High-Dimensional Limits in Artificial Neural Networks, Institute
of Science and Technology Austria, 2024.
corr_author: '1'
date_created: 2024-08-28T15:14:25Z
date_published: 2024-08-29T00:00:00Z
date_updated: 2026-06-18T17:55:53Z
day: '29'
ddc:
- '519'
degree_awarded: PhD
department:
- _id: GradSch
- _id: DaAl
- _id: MaMo
doi: 10.15479/at:ista:17465
file:
- access_level: open_access
checksum: da6dd3166078934577f6af93d27000e2
content_type: application/pdf
creator: ashevche
date_created: 2024-09-02T09:23:32Z
date_updated: 2024-10-05T22:30:05Z
embargo: 2024-10-04
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file_size: 4468610
relation: main_file
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checksum: 76a39ef252239560923cdda4ce0a31a4
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creator: ashevche
date_created: 2024-09-02T09:23:46Z
date_updated: 2024-10-05T22:30:05Z
embargo_to: open_access
file_id: '17483'
file_name: Thesis Alex - ISTA.zip
file_size: 15930999
relation: source_file
file_date_updated: 2024-10-05T22:30:05Z
has_accepted_license: '1'
language:
- iso: eng
month: '08'
oa: 1
oa_version: Published Version
page: '232'
project:
- _id: 059876FA-7A3F-11EA-A408-12923DDC885E
name: Prix Lopez-Loretta 2019 - Marco Mondelli
- _id: 9B9290DE-BA93-11EA-9121-9846C619BF3A
grant_number: W1260-N35
name: Vienna Graduate School on Computational Optimization
publication_identifier:
issn:
- 2663-337X
publication_status: published
publisher: Institute of Science and Technology Austria
related_material:
record:
- id: '11420'
relation: part_of_dissertation
status: public
- id: '14459'
relation: part_of_dissertation
status: public
- id: '9198'
relation: part_of_dissertation
status: public
- id: '17469'
relation: part_of_dissertation
status: public
status: public
supervisor:
- first_name: Marco
full_name: Mondelli, Marco
id: 27EB676C-8706-11E9-9510-7717E6697425
last_name: Mondelli
orcid: 0000-0002-3242-7020
- first_name: Dan-Adrian
full_name: Alistarh, Dan-Adrian
id: 4A899BFC-F248-11E8-B48F-1D18A9856A87
last_name: Alistarh
orcid: 0000-0003-3650-940X
title: High-dimensional limits in artificial neural networks
type: dissertation
user_id: 8b945eb4-e2f2-11eb-945a-df72226e66a9
year: '2024'
...
---
OA_place: publisher
_id: '17881'
abstract:
- lang: eng
text: "This work can be broadly classified into the study of critical phenomena
in a one dimensional\r\narray of Josephson junctions. While we study quantum criticality
when the array is in thermal\r\nequilibrium at zero bias, the non-equilibrium
study involves understanding the bistability of the\r\narray at a critical non-zero
bias. This work furthers our knowledge in understanding quantum\r\ncritical behaviour
at finite temperatures in a one dimensional Josephson array, while also\r\nestablishing
relaxation behaviour dual to that observed in a single Josephson junction.\r\nChapter
1 briefly introduces the model to understand superconductor-insulator phase transition\r\nin
a one dimensional Josephson array and points out the state of the field from where
we\r\nstarted our zero-bias experiments. In this context it discusses the phase-charge
duality observed\r\nin a Josephson array and its dual hysteretic behaviour to
that of a single junction, setting the\r\nground for our non-equilibrium study
of the array.\r\nChapter 2 shows the experimental setup and the chip layout of
the device we measured.\r\nIn chapter 3 we show that, unlike the typical quantum-critical
broadening scenario, in one dimensional Josephson arrays temperature dramatically
shifts the critical region. This shift leads\r\nto a regime of superconductivity
at high temperature, arising from the melted zero-temperature\r\ninsulator. Our
results quantitatively explain the low-temperature onset of superconductivity
in\r\nnominally insulating regimes, and the transition to the strongly insulating
phase. We further\r\npresent, to our knowledge, the first understanding of the
onset of anomalous-metallic resistance\r\nsaturation [30]. This work demonstrates
a non-trivial interplay between thermal effects and\r\nquantum criticality. A
practical consequence is that, counterintuitively, the coherence of\r\nhigh-impedance
quantum circuits is expected to be stabilized by thermal fluctuations.\r\nIn chapter
4, we show relaxation oscillations in a current-biased one dimensional array of\r\nJosephson
junctions. These oscillations are well described by a circuit model, dual to the\r\nordinary
Josephson relaxation oscillations [72]. Injection locking these oscillations results
in\r\ncurrent plateaux. The relaxation step is found to obey a characteristic
self-consistent relation,\r\nsuggesting that it is governed by overheating effects.\r\nChapter
5 describes the various checks and analysis we performed to support our conclusions\r\nmade
in chapters 3 and 4.\r\nFinally, chapter 6 describes the nanofabrication steps
and the finite element electromagnetic\r\nsimulations we performed to fabricate
our devices."
acknowledged_ssus:
- _id: NanoFab
- _id: M-Shop
alternative_title:
- ISTA Thesis
article_processing_charge: No
author:
- first_name: Soham
full_name: Mukhopadhyay, Soham
id: FDE60288-A89D-11E9-947F-1AF6E5697425
last_name: Mukhopadhyay
orcid: 0000-0001-5263-5559
citation:
ama: Mukhopadhyay S. Thermal effects in one dimensional Josephson chains. 2024.
doi:10.15479/at:ista:17881
apa: Mukhopadhyay, S. (2024). Thermal effects in one dimensional Josephson chains.
Institute of Science and Technology Austria. https://doi.org/10.15479/at:ista:17881
chicago: Mukhopadhyay, Soham. “Thermal Effects in One Dimensional Josephson Chains.”
Institute of Science and Technology Austria, 2024. https://doi.org/10.15479/at:ista:17881.
ieee: S. Mukhopadhyay, “Thermal effects in one dimensional Josephson chains,” Institute
of Science and Technology Austria, 2024.
ista: Mukhopadhyay S. 2024. Thermal effects in one dimensional Josephson chains.
Institute of Science and Technology Austria.
mla: Mukhopadhyay, Soham. Thermal Effects in One Dimensional Josephson Chains.
Institute of Science and Technology Austria, 2024, doi:10.15479/at:ista:17881.
short: S. Mukhopadhyay, Thermal Effects in One Dimensional Josephson Chains, Institute
of Science and Technology Austria, 2024.
corr_author: '1'
date_created: 2024-09-08T10:23:25Z
date_published: 2024-09-10T00:00:00Z
date_updated: 2026-06-03T07:16:04Z
day: '10'
ddc:
- '539'
degree_awarded: PhD
department:
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- _id: AnHi
doi: 10.15479/at:ista:17881
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language:
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month: '09'
oa: 1
oa_version: Published Version
page: '82'
project:
- _id: 0aa3608a-070f-11eb-9043-e9cd8a2bd931
grant_number: P33692
name: Cavity electromechanics across a quantum phase transition
publication_identifier:
isbn:
- 978-3-99078-043-5
issn:
- 2663-337X
publication_status: published
publisher: Institute of Science and Technology Austria
related_material:
record:
- id: '14032'
relation: part_of_dissertation
status: public
- id: '18057'
relation: part_of_dissertation
status: public
status: public
supervisor:
- first_name: Andrew P
full_name: Higginbotham, Andrew P
id: 4AD6785A-F248-11E8-B48F-1D18A9856A87
last_name: Higginbotham
orcid: 0000-0003-2607-2363
title: Thermal effects in one dimensional Josephson chains
type: dissertation
user_id: ba8df636-2132-11f1-aed0-ed93e2281fdd
year: '2024'
...
---
_id: '17469'
abstract:
- lang: eng
text: 'Autoencoders are a prominent model in many empirical branches of machine
learning and lossy data compression. However, basic theoretical questions remain
unanswered even in a shallow two-layer setting. In particular, to what degree
does a shallow autoencoder capture the structure of the underlying data distribution?
For the prototypical case of the 1-bit compression of sparse Gaussian data, we
prove that gradient descent converges to a solution that completely disregards
the sparse structure of the input. Namely, the performance of the algorithm is
the same as if it was compressing a Gaussian source - with no sparsity. For general
data distributions, we give evidence of a phase transition phenomenon in the shape
of the gradient descent minimizer, as a function of the data sparsity: below the
critical sparsity level, the minimizer is a rotation taken uniformly at random
(just like in the compression of non-sparse data); above the critical sparsity,
the minimizer is the identity (up to a permutation). Finally, by exploiting a
connection with approximate message passing algorithms, we show how to improve
upon Gaussian performance for the compression of sparse data: adding a denoising
function to a shallow architecture already reduces the loss provably, and a suitable
multi-layer decoder leads to a further improvement. We validate our findings on
image datasets, such as CIFAR-10 and MNIST.'
acknowledgement: "Kevin Kogler, Alexander Shevchenko and Marco Mondelli are supported
by the 2019 Lopez-Loreta Prize. Hamed\r\nHassani acknowledges the support by the
NSF CIF award (1910056) and the NSF Institute for CORE Emerging Methods in Data
Science (EnCORE)."
alternative_title:
- PMLR
article_processing_charge: No
arxiv: 1
author:
- first_name: Kevin
full_name: Kögler, Kevin
id: 94ec913c-dc85-11ea-9058-e5051ab2428b
last_name: Kögler
- first_name: Aleksandr
full_name: Shevchenko, Aleksandr
id: F2B06EC2-C99E-11E9-89F0-752EE6697425
last_name: Shevchenko
- first_name: Hamed
full_name: Hassani, Hamed
last_name: Hassani
- first_name: Marco
full_name: Mondelli, Marco
id: 27EB676C-8706-11E9-9510-7717E6697425
last_name: Mondelli
orcid: 0000-0002-3242-7020
citation:
ama: 'Kögler K, Shevchenko A, Hassani H, Mondelli M. Compression of structured data
with autoencoders: Provable benefit of nonlinearities and depth. In: Proceedings
of the 41st International Conference on Machine Learning. Vol 235. ML Research
Press; 2024:24964-25015.'
apa: 'Kögler, K., Shevchenko, A., Hassani, H., & Mondelli, M. (2024). Compression
of structured data with autoencoders: Provable benefit of nonlinearities and depth.
In Proceedings of the 41st International Conference on Machine Learning
(Vol. 235, pp. 24964–25015). Vienna, Austria: ML Research Press.'
chicago: 'Kögler, Kevin, Alexander Shevchenko, Hamed Hassani, and Marco Mondelli.
“Compression of Structured Data with Autoencoders: Provable Benefit of Nonlinearities
and Depth.” In Proceedings of the 41st International Conference on Machine
Learning, 235:24964–15. ML Research Press, 2024.'
ieee: 'K. Kögler, A. Shevchenko, H. Hassani, and M. Mondelli, “Compression of structured
data with autoencoders: Provable benefit of nonlinearities and depth,” in Proceedings
of the 41st International Conference on Machine Learning, Vienna, Austria,
2024, vol. 235, pp. 24964–25015.'
ista: 'Kögler K, Shevchenko A, Hassani H, Mondelli M. 2024. Compression of structured
data with autoencoders: Provable benefit of nonlinearities and depth. Proceedings
of the 41st International Conference on Machine Learning. ICML: International
Conference on Machine Learning, PMLR, vol. 235, 24964–25015.'
mla: 'Kögler, Kevin, et al. “Compression of Structured Data with Autoencoders: Provable
Benefit of Nonlinearities and Depth.” Proceedings of the 41st International
Conference on Machine Learning, vol. 235, ML Research Press, 2024, pp. 24964–5015.'
short: K. Kögler, A. Shevchenko, H. Hassani, M. Mondelli, in:, Proceedings of the
41st International Conference on Machine Learning, ML Research Press, 2024, pp.
24964–25015.
conference:
end_date: 2024-07-27
location: Vienna, Austria
name: 'ICML: International Conference on Machine Learning'
start_date: 2024-07-21
corr_author: '1'
date_created: 2024-08-29T11:47:57Z
date_published: 2024-07-01T00:00:00Z
date_updated: 2026-07-27T22:30:47Z
day: '01'
ddc:
- '000'
department:
- _id: DaAl
- _id: MaMo
external_id:
arxiv:
- '2402.05013'
intvolume: ' 235'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://proceedings.mlr.press/v235/kogler24a.html
month: '07'
oa: 1
oa_version: Published Version
page: 24964-25015
project:
- _id: 059876FA-7A3F-11EA-A408-12923DDC885E
name: Prix Lopez-Loretta 2019 - Marco Mondelli
publication: Proceedings of the 41st International Conference on Machine Learning
publication_status: published
publisher: ML Research Press
quality_controlled: '1'
related_material:
record:
- id: '17465'
relation: dissertation_contains
status: public
scopus_import: '1'
status: public
title: 'Compression of structured data with autoencoders: Provable benefit of nonlinearities
and depth'
type: conference
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 235
year: '2024'
...
---
OA_place: repository
_id: '18057'
abstract:
- lang: eng
text: "We report relaxation oscillations in a one-dimensional array of Josephson\r\njunctions.
The oscillations are circuit-dual to those ordinarily observed in\r\nsingle junctions.
The dual circuit quantitatively accounts for temporal\r\ndynamics of the array,
including the dependence on biasing conditions.\r\nInjection locking the oscillations
results in well-developed current plateaux.\r\nA thermal model explains the relaxation
step of the oscillations."
acknowledged_ssus:
- _id: NanoFab
- _id: M-Shop
acknowledgement: "We gratefully acknowledge support from the MIBA machine shop and
Nanofabrication Facility at IST Austria. Work was supported by Austrian FWF grant
P33692-N (S.M., J.S. and A.P.H.), the European Union’s Horizon 2020 Research and
Innovation program under the Marie Sk lodowska-Curie Grant Agreement No. 754411
(J.S.), and a NOMIS foundation research grant (A.P.H.).\r\n"
article_number: '2408.07829'
article_processing_charge: No
arxiv: 1
author:
- first_name: Soham
full_name: Mukhopadhyay, Soham
id: FDE60288-A89D-11E9-947F-1AF6E5697425
last_name: Mukhopadhyay
orcid: 0000-0001-5263-5559
- first_name: Diego A
full_name: Lancheros Naranjo, Diego A
id: 6c55e976-15b2-11ec-abd3-d790e8937fde
last_name: Lancheros Naranjo
- first_name: Jorden L
full_name: Senior, Jorden L
id: 5479D234-2D30-11EA-89CC-40953DDC885E
last_name: Senior
orcid: 0000-0002-0672-9295
- first_name: Andrew P
full_name: Higginbotham, Andrew P
id: 4AD6785A-F248-11E8-B48F-1D18A9856A87
last_name: Higginbotham
orcid: 0000-0003-2607-2363
citation:
ama: Mukhopadhyay S, Lancheros Naranjo DA, Senior JL, Higginbotham AP. Dual relaxation
oscillations in a Josephson junction array. arXiv. doi:10.48550/arXiv.2408.07829
apa: Mukhopadhyay, S., Lancheros Naranjo, D. A., Senior, J. L., & Higginbotham,
A. P. (n.d.). Dual relaxation oscillations in a Josephson junction array. arXiv.
https://doi.org/10.48550/arXiv.2408.07829
chicago: Mukhopadhyay, Soham, Diego A Lancheros Naranjo, Jorden L Senior, and Andrew
P Higginbotham. “Dual Relaxation Oscillations in a Josephson Junction Array.”
ArXiv, n.d. https://doi.org/10.48550/arXiv.2408.07829.
ieee: S. Mukhopadhyay, D. A. Lancheros Naranjo, J. L. Senior, and A. P. Higginbotham,
“Dual relaxation oscillations in a Josephson junction array,” arXiv. .
ista: Mukhopadhyay S, Lancheros Naranjo DA, Senior JL, Higginbotham AP. Dual relaxation
oscillations in a Josephson junction array. arXiv, 2408.07829.
mla: Mukhopadhyay, Soham, et al. “Dual Relaxation Oscillations in a Josephson Junction
Array.” ArXiv, 2408.07829, doi:10.48550/arXiv.2408.07829.
short: S. Mukhopadhyay, D.A. Lancheros Naranjo, J.L. Senior, A.P. Higginbotham,
ArXiv (n.d.).
corr_author: '1'
date_created: 2024-09-11T09:25:22Z
date_published: 2024-08-14T00:00:00Z
date_updated: 2026-07-27T22:30:47Z
day: '14'
department:
- _id: AnHi
- _id: GradSch
doi: 10.48550/arXiv.2408.07829
ec_funded: 1
external_id:
arxiv:
- '2408.07829'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.48550/arXiv.2408.07829
month: '08'
oa: 1
oa_version: Preprint
project:
- _id: 260C2330-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '754411'
name: ISTplus - Postdoctoral Fellowships
- _id: 0aa3608a-070f-11eb-9043-e9cd8a2bd931
grant_number: P33692
name: Cavity electromechanics across a quantum phase transition
- _id: eb9b30ac-77a9-11ec-83b8-871f581d53d2
name: Protected states of quantum matter
publication: arXiv
publication_status: draft
related_material:
record:
- id: '20324'
relation: later_version
status: public
- id: '17881'
relation: dissertation_contains
status: public
status: public
title: Dual relaxation oscillations in a Josephson junction array
type: preprint
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
year: '2024'
...
---
APC_amount: 3145,39 EUR
DOAJ_listed: '1'
OA_place: publisher
OA_type: gold
_id: '17890'
abstract:
- lang: eng
text: Our understanding of the molecular pathways that regulate oogenesis and define
cellular identity in the Arthropod female reproductive system and the extent of
their conservation is currently very limited. This is due to the focus on model
systems, including Drosophila and Daphnia, which do not reflect the observed diversity
of morphologies, reproductive modes, and sex chromosome systems. We use single-nucleus
RNA and ATAC sequencing to produce a comprehensive single nucleus atlas of the
adult Artemia franciscana female reproductive system. We map our data to the Fly
Cell Atlas single-nucleus dataset of the Drosophila melanogaster ovary, shedding
light on the conserved regulatory programs between the two distantly related Arthropod
species. We identify the major cell types known to be present in the Artemia ovary,
including germ cells, follicle cells, and ovarian muscle cells. Additionally,
we use the germ cells to explore gene regulation and expression of the Z chromosome
during meiosis, highlighting its unique regulatory dynamics and allowing us to
explore the presence of meiotic sex chromosome silencing in this group.
acknowledged_ssus:
- _id: ScienComp
acknowledgement: "We thank the Vicoso group for their valuable comments on the earlier
draft of the manuscript. We would also like to thank the Vienna BioCenter Next Generation
Sequencing (NGS) facility staff, and in particular, Thomas Grentzinger for his support
with the handling and sequencing of the samples, the scientific computing unit at
ISTA for the computational resources, Brittney Wick for the help with hosting our
data on the UCSC Cell Browser, and Lora B. Sweeney for her valuable input at the
different stages of the project.\r\nThis research was funded by the Austrian science
fund (FWF), as part of the SFB Meiosis consortium https://sfbmeiosis.org/, grant
ID FWF SFB F88-10) to BV. "
article_number: e1011376
article_processing_charge: Yes
article_type: original
author:
- 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: Beatriz
full_name: Vicoso, Beatriz
id: 49E1C5C6-F248-11E8-B48F-1D18A9856A87
last_name: Vicoso
orcid: 0000-0002-4579-8306
citation:
ama: Elkrewi MN, Vicoso B. Single-nucleus atlas of the Artemia female reproductive
system suggests germline repression of the Z chromosome. PLoS Genetics.
2024;20(8). doi:10.1371/journal.pgen.1011376
apa: Elkrewi, M. N., & Vicoso, B. (2024). Single-nucleus atlas of the Artemia
female reproductive system suggests germline repression of the Z chromosome. PLoS
Genetics. Public Library of Science. https://doi.org/10.1371/journal.pgen.1011376
chicago: Elkrewi, Marwan N, and Beatriz Vicoso. “Single-Nucleus Atlas of the Artemia
Female Reproductive System Suggests Germline Repression of the Z Chromosome.”
PLoS Genetics. Public Library of Science, 2024. https://doi.org/10.1371/journal.pgen.1011376.
ieee: M. N. Elkrewi and B. Vicoso, “Single-nucleus atlas of the Artemia female reproductive
system suggests germline repression of the Z chromosome,” PLoS Genetics,
vol. 20, no. 8. Public Library of Science, 2024.
ista: Elkrewi MN, Vicoso B. 2024. Single-nucleus atlas of the Artemia female reproductive
system suggests germline repression of the Z chromosome. PLoS Genetics. 20(8),
e1011376.
mla: Elkrewi, Marwan N., and Beatriz Vicoso. “Single-Nucleus Atlas of the Artemia
Female Reproductive System Suggests Germline Repression of the Z Chromosome.”
PLoS Genetics, vol. 20, no. 8, e1011376, Public Library of Science, 2024,
doi:10.1371/journal.pgen.1011376.
short: M.N. Elkrewi, B. Vicoso, PLoS Genetics 20 (2024).
corr_author: '1'
date_created: 2024-09-08T22:01:11Z
date_published: 2024-08-30T00:00:00Z
date_updated: 2026-07-27T22:31:13Z
day: '30'
ddc:
- '570'
department:
- _id: BeVi
doi: 10.1371/journal.pgen.1011376
external_id:
isi:
- '001304090200001'
pmid:
- '39213449'
file:
- access_level: open_access
checksum: f5d96b9af57126fc1063e951440477d6
content_type: application/pdf
creator: dernst
date_created: 2024-09-11T07:54:12Z
date_updated: 2024-09-11T07:54:12Z
file_id: '18056'
file_name: 2024_PloSGenetics_Elkrewi.pdf
file_size: 8962687
relation: main_file
success: 1
file_date_updated: 2024-09-11T07:54:12Z
has_accepted_license: '1'
intvolume: ' 20'
isi: 1
issue: '8'
language:
- iso: eng
month: '08'
oa: 1
oa_version: Published Version
pmid: 1
project:
- _id: 3AC91DDA-15DF-11EA-824D-93A3E7B544D1
call_identifier: FWF
name: FWF Open Access Fund
- _id: 34ae1506-11ca-11ed-8bc3-c14f4c474396
grant_number: F8810
name: The highjacking of meiosis for asexual reproduction
publication: PLoS Genetics
publication_identifier:
eissn:
- 1553-7404
issn:
- 1553-7390
publication_status: published
publisher: Public Library of Science
quality_controlled: '1'
related_material:
link:
- relation: software
url: https://github.com/Melkrewi/Artemia-snRNAseq-Project
record:
- id: '17362'
relation: research_data
status: public
- id: '19386'
relation: dissertation_contains
status: public
scopus_import: '1'
status: public
title: Single-nucleus atlas of the Artemia female reproductive system suggests germline
repression of the Z 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: 317138e5-6ab7-11ef-aa6d-ffef3953e345
volume: 20
year: '2024'
...
---
DOAJ_listed: '1'
OA_place: publisher
OA_type: gold
_id: '15009'
abstract:
- lang: eng
text: Since the commercialization of brine shrimp (genus Artemia) in the 1950s,
this lineage, and in particular the model species Artemia franciscana, has been
the subject of extensive research. However, our understanding of the genetic mechanisms
underlying various aspects of their reproductive biology, including sex determination,
is still lacking. This is partly due to the scarcity of genomic resources for
Artemia species and crustaceans in general. Here, we present a chromosome-level
genome assembly of A. franciscana (Kellogg 1906), from the Great Salt Lake, United
States. The genome is 1 GB, and the majority of the genome (81%) is scaffolded
into 21 linkage groups using a previously published high-density linkage map.
We performed coverage and FST analyses using male and female genomic and transcriptomic
reads to quantify the extent of differentiation between the Z and W chromosomes.
Additionally, we quantified the expression levels in male and female heads and
gonads and found further evidence for dosage compensation in this species.
article_number: evae006
article_processing_charge: Yes
article_type: original
author:
- first_name: Vincent K
full_name: Bett, Vincent K
id: 57854184-AAE0-11E9-8D04-98D6E5697425
last_name: Bett
- 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
- first_name: Marwan N
full_name: Elkrewi, Marwan N
id: 0B46FACA-A8E1-11E9-9BD3-79D1E5697425
last_name: Elkrewi
orcid: 0000-0002-5328-7231
citation:
ama: Bett VK, Macon A, Vicoso B, Elkrewi MN. Chromosome-level assembly of Artemia
franciscana sheds light on sex chromosome differentiation. Genome Biology and
Evolution. 2024;16(1). doi:10.1093/gbe/evae006
apa: Bett, V. K., Macon, A., Vicoso, B., & Elkrewi, M. N. (2024). Chromosome-level
assembly of Artemia franciscana sheds light on sex chromosome differentiation.
Genome Biology and Evolution. Oxford University Press. https://doi.org/10.1093/gbe/evae006
chicago: Bett, Vincent K, Ariana Macon, Beatriz Vicoso, and Marwan N Elkrewi. “Chromosome-Level
Assembly of Artemia Franciscana Sheds Light on Sex Chromosome Differentiation.”
Genome Biology and Evolution. Oxford University Press, 2024. https://doi.org/10.1093/gbe/evae006.
ieee: V. K. Bett, A. Macon, B. Vicoso, and M. N. Elkrewi, “Chromosome-level assembly
of Artemia franciscana sheds light on sex chromosome differentiation,” Genome
Biology and Evolution, vol. 16, no. 1. Oxford University Press, 2024.
ista: Bett VK, Macon A, Vicoso B, Elkrewi MN. 2024. Chromosome-level assembly of
Artemia franciscana sheds light on sex chromosome differentiation. Genome Biology
and Evolution. 16(1), evae006.
mla: Bett, Vincent K., et al. “Chromosome-Level Assembly of Artemia Franciscana
Sheds Light on Sex Chromosome Differentiation.” Genome Biology and Evolution,
vol. 16, no. 1, evae006, Oxford University Press, 2024, doi:10.1093/gbe/evae006.
short: V.K. Bett, A. Macon, B. Vicoso, M.N. Elkrewi, Genome Biology and Evolution
16 (2024).
corr_author: '1'
date_created: 2024-02-18T23:01:02Z
date_published: 2024-01-20T00:00:00Z
date_updated: 2026-07-27T22:31:13Z
day: '20'
ddc:
- '570'
department:
- _id: BeVi
doi: 10.1093/gbe/evae006
external_id:
isi:
- '001153952800001'
pmid:
- '38245839'
file:
- access_level: open_access
checksum: 106a40f10443b2e7ba66749844ebbdf1
content_type: application/pdf
creator: dernst
date_created: 2024-02-26T09:54:59Z
date_updated: 2024-02-26T09:54:59Z
file_id: '15029'
file_name: 2024_GBE_Bett.pdf
file_size: 5213306
relation: main_file
success: 1
file_date_updated: 2024-02-26T09:54:59Z
has_accepted_license: '1'
intvolume: ' 16'
isi: 1
issue: '1'
language:
- iso: eng
month: '01'
oa: 1
oa_version: Published Version
pmid: 1
publication: Genome Biology and Evolution
publication_identifier:
eissn:
- 1759-6653
publication_status: published
publisher: Oxford University Press
quality_controlled: '1'
related_material:
record:
- id: '14705'
relation: research_data
status: public
- id: '20449'
relation: dissertation_contains
status: public
- id: '20444'
relation: dissertation_contains
status: deleted
- id: '19386'
relation: dissertation_contains
status: public
scopus_import: '1'
status: public
title: Chromosome-level assembly of Artemia franciscana sheds light on sex chromosome
differentiation
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: 317138e5-6ab7-11ef-aa6d-ffef3953e345
volume: 16
year: '2024'
...
---
OA_place: publisher
_id: '17119'
abstract:
- lang: eng
text: "Genomes are shaped by natural selection at the level of the organism, as
genomic variants that\r\nhave a beneficial effect on the viability or fecundity
of their carriers are on average expected\r\nto be passed on to more offspring
than less beneficial alleles. However, selection also favors\r\ngenomic variants
that drive their own transmission to the next generation above the mendelian\r\nexpectation
of 50 percent in heterozygotes, even if these self-promoting variants are less\r\nbeneficial
to the organism than other variants at the same locus. Such variants, called meiotic\r\ndrivers,
are found in diverse taxa, and often impose fitness costs on their host organisms.
As\r\nmeiotic drivers often require multiple genes and sequences for transmission
ratio distortion,\r\nthey are often found in regions of low recombination, such
as inversions, which prevent their\r\nrecombination with the non-driving homologous
regions. Reduced recombination rates are\r\nexpected to lead to the accumulation
of deleterious mutations, which may affect hundreds\r\nof genes trapped in the
inversions of meiotic drivers. Although the observed fitness costs of\r\nself-promoting
haplotypes are thought to possibly reflect sequence degeneration, no study has\r\nsystematically
investigated the level of degeneration on a meiotic driver. Further, the low\r\nrates
of recombination between driving and non-driving haplotypes have limited the power
of\r\ntraditional genetic studies in uncovering the gene content of meiotic drivers,
and made the\r\nthe identification of the genes causing transmission ratio distortion
difficult.\r\nAfter an introduction to meiotic drivers in Chapter 1, this thesis
presents three studies that\r\nmake use of next generation sequencing data to
characterize the sequence and expression\r\nevolution of genes on the t-haplotype,
a large and ancient meiotic driver in house mice that is\r\ntransmitted to up
to 100% of the offspring in males heterozygous for it. Chapter 2 presents\r\na
comprehensive assessment of the t-haplotype’s sequence evolution, which shows
signs of\r\nsequence degeneration counteracted by occasional recombination with
the non-driving homolog\r\nover large parts of the meiotic driver, proposing an
explanation for its long-term survival.\r\nChapter 3 investigates the sequence
and expression evolution of genes on the t-haplotype,\r\nand finds widespread
expression and copy number changes and signs of less efficient purifying\r\nselection
compared to the genes on the non-driving homolog. Further, this chapter finds\r\ncandidates
for involvment in drive: two positively selected genes on the t-haplotype, and\r\nthe
discovery of a t-specific gene duplicate, which was gained from another chromosome,\r\nand
which acquired novel sequence and testis-specific expression on the t-haplotype.
Finally,\r\nChapter 4 provides unprecedented insights into the gene expression
landscape in testes of\r\nt-carrier mice, using single nucleus sequencing. Cell-resolved
RNA-sequencing allows the\r\ncomparison of expression in spermatids carrying or
not carrying the t-haplotype as well as the\r\ntiming of t-haplotype-induced expression
changes along spermatogenesis. This study shows\r\nthe timing of previously found
drive-associated genes, and uncovers novel candidate genes and\r\nbiological processes
that may underlie the complex biology of transmission ratio distortion of\r\nthe
t-haplotype. Chapter 5 synthesizes the findings of the three studies, and discusses
them in\r\nthe context of the current state of meiotic drive research."
alternative_title:
- ISTA Thesis
article_processing_charge: No
author:
- first_name: Réka K
full_name: Kelemen, Réka K
id: 48D3F8DE-F248-11E8-B48F-1D18A9856A87
last_name: Kelemen
orcid: 0000-0002-8489-9281
citation:
ama: Kelemen RK. Characterizing the sequence and expression evolution of the t-haplotype,
a model meiotic driver. 2024. doi:10.15479/at:ista:17119
apa: Kelemen, R. K. (2024). Characterizing the sequence and expression evolution
of the t-haplotype, a model meiotic driver. Institute of Science and Technology
Austria. https://doi.org/10.15479/at:ista:17119
chicago: Kelemen, Réka K. “Characterizing the Sequence and Expression Evolution
of the T-Haplotype, a Model Meiotic Driver.” Institute of Science and Technology
Austria, 2024. https://doi.org/10.15479/at:ista:17119.
ieee: R. K. Kelemen, “Characterizing the sequence and expression evolution of the
t-haplotype, a model meiotic driver,” Institute of Science and Technology Austria,
2024.
ista: Kelemen RK. 2024. Characterizing the sequence and expression evolution of
the t-haplotype, a model meiotic driver. Institute of Science and Technology Austria.
mla: Kelemen, Réka K. Characterizing the Sequence and Expression Evolution of
the T-Haplotype, a Model Meiotic Driver. Institute of Science and Technology
Austria, 2024, doi:10.15479/at:ista:17119.
short: R.K. Kelemen, Characterizing the Sequence and Expression Evolution of the
T-Haplotype, a Model Meiotic Driver, Institute of Science and Technology Austria,
2024.
corr_author: '1'
date_created: 2024-06-07T16:14:13Z
date_published: 2024-06-20T00:00:00Z
date_updated: 2026-04-07T13:21:37Z
day: '20'
ddc:
- '576'
degree_awarded: PhD
department:
- _id: GradSch
- _id: BeVi
doi: 10.15479/at:ista:17119
ec_funded: 1
file:
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checksum: fab59146e3b3dc2e5d214576984a2a63
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date_created: 2024-06-07T16:09:17Z
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date_updated: 2025-01-10T23:30:10Z
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file_size: 19405484
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file_date_updated: 2025-01-10T23:30:10Z
has_accepted_license: '1'
keyword:
- meiotic driver
- neofunctionalization
- single nucleus sequencing
language:
- iso: eng
month: '06'
oa: 1
oa_version: Published Version
page: '105'
project:
- _id: 250BDE62-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '715257'
name: Prevalence and Influence of Sexual Antagonism on Genome Evolution
- _id: 34ae1506-11ca-11ed-8bc3-c14f4c474396
grant_number: F8810
name: The highjacking of meiosis for asexual reproduction
publication_identifier:
isbn:
- 978-3-99078-039-8
issn:
- 2663-337X
publication_status: published
publisher: Institute of Science and Technology Austria
related_material:
record:
- id: '542'
relation: part_of_dissertation
status: public
- id: '10767'
relation: part_of_dissertation
status: public
status: public
supervisor:
- first_name: Beatriz
full_name: Vicoso, Beatriz
id: 49E1C5C6-F248-11E8-B48F-1D18A9856A87
last_name: Vicoso
orcid: 0000-0002-4579-8306
title: Characterizing the sequence and expression evolution of the t-haplotype, a
model meiotic driver
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: dissertation
user_id: ba8df636-2132-11f1-aed0-ed93e2281fdd
year: '2024'
...
---
OA_place: publisher
_id: '18477'
abstract:
- lang: eng
text: "ADAR1 is broadly expressed across various tissues and is vital in regulating
pathways\r\nassociated with innate immune responses. ADAR1 marks double-stranded
RNA as \"self\"\r\nthrough its A-to-I editing activity, effectively repressing
autoimmunity and maintaining\r\nimmune tolerance. This editing process has been
detected at millions of sites across the\r\nhuman genome. However, the mechanism
underlying ADAR1's substrate selectivity\r\nproperties remains largely unclear,
with much of the current knowledge derived from\r\ncomparisons to its more extensively
studied homolog, ADAR2. By studying ADAR1 in complex\r\nwith its RNA substrates
and applying a combination of biochemical techniques and structural\r\nstudies
using CryoEM, we aim to gain a more comprehensive understanding of the substrate\r\nselectivity
characteristics of ADAR1.\r\nIn this thesis, the purification protocol for ADAR1
was successfully optimized, resulting in the\r\nfirst report in the literature
to achieve high protein purity and activity. This advancement\r\nenabled the investigation
of complex formation between ADAR1 and various RNA substrates,\r\nleading to the
identification of optimal conditions for preparing the cryoEM sample. However,\r\ndespite
comprehensive optimization of the cryo-EM conditions, the resulting data lacked
the\r\ndesired quality, highlighting the need for similar rigorous optimization
of the RNA substrates\r\nto facilitate structural studies of the ADAR1-RNA complex.
The study was complemented by\r\nAlphaFold predictions, which provided some insights
into this mechanism.\r\nMoreover, during this project I established a collaboration
with a research group focused on\r\nstudying ADAR homologs. Notably ADAR homologs
were identified in bivalve species, and it\r\nwas further demonstrated that ADAR
and its A-to-I editing activity are upregulated in Pacific\r\noysters during infections
with Ostreid herpesvirus-1—a highly infectious virus that leads to\r\nsignificant
losses in oyster populations globally. I successfully purified oyster ADAR and\r\nprepared
in vitro edited RNA for nanopore sequencing—a direct sequencing technology\r\ncapable
of detecting modified nucleotides without the need for reverse transcription.
The\r\ncollaborators initiated optimization of this nanopore-based approach. However,
current\r\ntechnological limitations still constrain the reliable detection of
modified nucleotides.\r\nThe project also examined the impact of RNA editing on
RNA binding and filament formation\r\nby MDA5, a key cytosolic dsRNA sensor that
triggers an interferon response. A primary target\r\nof ADAR1's editing activity
is RNA derived from repetitive elements present in the genome,\r\nparticularly
Alu elements forming double-stranded RNA. When unedited, these RNA\r\nsequences
are recognized by MDA5. However, the mechanisms by which MDA5 interacts with\r\nAlu
RNAs, as well as the role of A-to-I editing in influencing this binding, are still
not well\r\nunderstood.\r\nThe interaction between MDA5 and Alu elements, was
successfully established. This was\r\nachieved through the testing of different
RNA variants and the evaluation of filament\r\nformation using binding techniques
and electron microscopy imaging. This groundwork has\r\nset the conditions for
further evaluation using CryoEM. Furthermore, the effects of A-to-I\r\nediting
on the binding properties of MDA5 with Alu RNA were investigated. Given the recent\r\nresearch
that has provided new insights into MDA5's interaction with dsRNA, it is essential
to\r\nrevise the experimental setup to integrate these findings before moving
forward with the\r\nCryoEM sample analysis."
acknowledged_ssus:
- _id: EM-Fac
- _id: LifeSc
alternative_title:
- ISTA Thesis
article_processing_charge: No
author:
- first_name: Beata M
full_name: Kaczmarek, Beata M
id: 36FA4AFA-F248-11E8-B48F-1D18A9856A87
last_name: Kaczmarek
citation:
ama: Kaczmarek BM. Biochemical and structural insights into ADAR1 RNA editing. 2024.
doi:10.15479/at:ista:18477
apa: Kaczmarek, B. M. (2024). Biochemical and structural insights into ADAR1
RNA editing. Institute of Science and Technology Austria. https://doi.org/10.15479/at:ista:18477
chicago: Kaczmarek, Beata M. “Biochemical and Structural Insights into ADAR1 RNA
Editing.” Institute of Science and Technology Austria, 2024. https://doi.org/10.15479/at:ista:18477.
ieee: B. M. Kaczmarek, “Biochemical and structural insights into ADAR1 RNA editing,”
Institute of Science and Technology Austria, 2024.
ista: Kaczmarek BM. 2024. Biochemical and structural insights into ADAR1 RNA editing.
Institute of Science and Technology Austria.
mla: Kaczmarek, Beata M. Biochemical and Structural Insights into ADAR1 RNA Editing.
Institute of Science and Technology Austria, 2024, doi:10.15479/at:ista:18477.
short: B.M. Kaczmarek, Biochemical and Structural Insights into ADAR1 RNA Editing,
Institute of Science and Technology Austria, 2024.
corr_author: '1'
date_created: 2024-10-27T07:35:13Z
date_published: 2024-10-29T00:00:00Z
date_updated: 2026-04-07T13:23:59Z
day: '29'
ddc:
- '572'
degree_awarded: PhD
department:
- _id: GradSch
- _id: CaBe
doi: 10.15479/at:ista:18477
file:
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checksum: 2053294ea4d770c495e4cc501e2a218b
content_type: application/vnd.openxmlformats-officedocument.wordprocessingml.document
creator: bkaczmar
date_created: 2024-10-29T11:56:36Z
date_updated: 2025-10-29T23:30:02Z
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date_created: 2024-10-29T11:56:44Z
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file_date_updated: 2025-10-29T23:30:02Z
has_accepted_license: '1'
language:
- iso: eng
month: '10'
oa: 1
oa_version: Published Version
page: '124'
publication_identifier:
isbn:
- 978-3-99078-045-9
issn:
- 2663-337X
publication_status: published
publisher: Institute of Science and Technology Austria
status: public
supervisor:
- first_name: Carrie A
full_name: Bernecky, Carrie A
id: 2CB9DFE2-F248-11E8-B48F-1D18A9856A87
last_name: Bernecky
orcid: 0000-0003-0893-7036
title: Biochemical and structural insights into ADAR1 RNA editing
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: dissertation
user_id: ba8df636-2132-11f1-aed0-ed93e2281fdd
year: '2024'
...
---
OA_place: publisher
_id: '15352'
abstract:
- lang: eng
text: "Epilepsy affects about 50 to 65 million people globally. It summarizes a
spectrum of neurological\r\ndisorders that have in common a hyperactivity of the
neuronal network resulting in seizures. A common\r\nassumption is that an imbalance
between neuronal excitation and inhibition is a key mechanism in\r\nseizure generation
and epileptogeneisis. In at least one-third of the patients, current therapies
have\r\nproven unsuccessful in treating seizure progression. One potential reason
could be that the therapies\r\nonly focus on neurons. Recent studies suggest that
neuronal hyperactivity causes a microglial\r\nresponse, which reinstates brain
homeostasis. Additionally, interactions between microglia and neurons\r\nhave
been shown to inhibit neuronal firing and dampen seizure activity. However, the
exact relationship\r\nbetween microglia and seizure progression in epilepsy is
yet to be elucidated. A main bottleneck is that\r\nseveral studies investigate
microglia dynamics in ex vivo slice models, which can severely affect the\r\nmicroglia
dynamics due to their rapid response to environmental changes. On the other hand,
in vivo\r\nstudies focus mostly on behavior characterization of the epileptic
seizure phenotype and their long-term\r\nconsequences on microglia activity leaving
out the direct consequences of acute seizure activity on\r\nmicroglia dynamics.\r\nHere,
we perform a pilot study to combine electroencephalography (EEG) and in vivo live
imaging to\r\ndirectly monitor and correlate the onset of seizure activity with
microglia response. To induce seizures,\r\nwe take advantage of the kainic acid
(KA) model, which represents similar neuropathological and\r\nelectroencephalographic
features seen in human patients with temporal lobe epilepsy (TLE). After\r\nconfirmation
of induction of the seizure and microglia activity in the hippocampus as a focal
point, we\r\ninvestigated whether these changes also reached the primary visual
cortex (V1) as a secondary\r\ngeneralized seizure activity. Indeed, we found that
microglia changed their morphology at high doses\r\nof KA in the V1. Next, we
optimized each of the two methodological components: for the EEG recording,\r\nour
initial attempts under the microscope suffered from extensive electrical noise,
which overlaid the\r\nactual signal. Thus, we built a customized Faraday-cage
and confirmed that the signal-to-noise ratio\r\nwas sufficiently reduced to be
able to record brain oscillatory activity. For the in vivo live imaging of\r\nmicroglia,
we had to optimize the imaging parameters, so that we would be able to detect
microglial\r\nprocesses in a sufficient resolution to track their process changes.
Finally, we combined both\r\nmethodologies with the KA model. We confirmed that
KA induced seizure activity and found first\r\nindication that those correlate
with microglia volume changes.\r\nOverall, we have developed a first methodological
approach, which allows the analysis of the acute\r\neffects of seizure onset on
microglia. Future studies will have to continue to optimize the drift during\r\nimaging
recording and the post-image analysis. "
acknowledged_ssus:
- _id: Bio
- _id: LifeSc
- _id: PreCl
alternative_title:
- ISTA Master's Thesis
article_processing_charge: No
author:
- first_name: Julie Stefanie
full_name: Murmann, Julie Stefanie
id: 1d390868-f128-11eb-9611-a0ca5f7833b5
last_name: Murmann
citation:
ama: 'Murmann JS. Investigating acute microglia response to seizure activity in
vivo: Combining 2-Photon imaging and EEG recording. 2024. doi:10.15479/at:ista:15352'
apa: 'Murmann, J. S. (2024). Investigating acute microglia response to seizure
activity in vivo: Combining 2-Photon imaging and EEG recording. Institute
of Science and Technology Austria. https://doi.org/10.15479/at:ista:15352'
chicago: 'Murmann, Julie Stefanie. “Investigating Acute Microglia Response to Seizure
Activity in Vivo: Combining 2-Photon Imaging and EEG Recording.” Institute of
Science and Technology Austria, 2024. https://doi.org/10.15479/at:ista:15352.'
ieee: 'J. S. Murmann, “Investigating acute microglia response to seizure activity
in vivo: Combining 2-Photon imaging and EEG recording,” Institute of Science and
Technology Austria, 2024.'
ista: 'Murmann JS. 2024. Investigating acute microglia response to seizure activity
in vivo: Combining 2-Photon imaging and EEG recording. Institute of Science and
Technology Austria.'
mla: 'Murmann, Julie Stefanie. Investigating Acute Microglia Response to Seizure
Activity in Vivo: Combining 2-Photon Imaging and EEG Recording. Institute
of Science and Technology Austria, 2024, doi:10.15479/at:ista:15352.'
short: 'J.S. Murmann, Investigating Acute Microglia Response to Seizure Activity
in Vivo: Combining 2-Photon Imaging and EEG Recording, Institute of Science and
Technology Austria, 2024.'
corr_author: '1'
date_created: 2024-05-02T08:31:38Z
date_published: 2024-05-02T00:00:00Z
date_updated: 2026-04-07T13:05:00Z
day: '02'
ddc:
- '570'
degree_awarded: MS
department:
- _id: SaSi
- _id: GradSch
doi: 10.15479/at:ista:15352
file:
- access_level: open_access
checksum: 095817a6c944954ac3f277e547031a33
content_type: application/pdf
creator: cchlebak
date_created: 2024-05-02T12:26:13Z
date_updated: 2025-05-02T22:30:04Z
embargo: 2025-05-02
file_id: '15354'
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file_size: 5936142
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checksum: 43b632255372973a437ac87739cfd4db
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creator: cchlebak
date_created: 2024-05-02T12:37:56Z
date_updated: 2025-05-02T22:30:04Z
embargo_to: open_access
file_id: '15355'
file_name: Murmann_Thesis_final_2024.zip
file_size: 20645510
relation: source_file
file_date_updated: 2025-05-02T22:30:04Z
has_accepted_license: '1'
language:
- iso: eng
month: '05'
oa: 1
oa_version: Published Version
page: '54'
publication_identifier:
issn:
- 2791-4585
publication_status: published
publisher: Institute of Science and Technology Austria
status: public
supervisor:
- first_name: Sandra
full_name: Siegert, Sandra
id: 36ACD32E-F248-11E8-B48F-1D18A9856A87
last_name: Siegert
orcid: 0000-0001-8635-0877
title: 'Investigating acute microglia response to seizure activity in vivo: Combining
2-Photon imaging and EEG recording'
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: dissertation
user_id: ba8df636-2132-11f1-aed0-ed93e2281fdd
year: '2024'
...
---
OA_place: publisher
OA_type: hybrid
PlanS_conform: '1'
_id: '14843'
abstract:
- lang: eng
text: The coupling between Ca2+ channels and release sensors is a key factor defining
the signaling properties of a synapse. However, the coupling nanotopography at
many synapses remains unknown, and it is unclear how it changes during development.
To address these questions, we examined coupling at the cerebellar inhibitory
basket cell (BC)-Purkinje cell (PC) synapse. Biophysical analysis of transmission
by paired recording and intracellular pipette perfusion revealed that the effects
of exogenous Ca2+ chelators decreased during development, despite constant reliance
of release on P/Q-type Ca2+ channels. Structural analysis by freeze-fracture replica
labeling (FRL) and transmission electron microscopy (EM) indicated that presynaptic
P/Q-type Ca2+ channels formed nanoclusters throughout development, whereas docked
vesicles were only clustered at later developmental stages. Modeling suggested
a developmental transformation from a more random to a more clustered coupling
nanotopography. Thus, presynaptic signaling developmentally approaches a point-to-point
configuration, optimizing speed, reliability, and energy efficiency of synaptic
transmission.
acknowledged_ssus:
- _id: EM-Fac
- _id: PreCl
- _id: M-Shop
acknowledgement: We thank Drs. David DiGregorio and Erwin Neher for critically reading
an earlier version of the manuscript, Ralf Schneggenburger for helpful discussions,
Benjamin Suter and Katharina Lichter for support with image analysis, Chris Wojtan
for advice on numerical solution of partial differential equations, Maria Reva for
help with Ripley analysis, Alois Schlögl for programming, and Akari Hagiwara and
Toshihisa Ohtsuka for anti-ELKS antibody. We are grateful to Florian Marr, Christina
Altmutter, and Vanessa Zheden for excellent technical assistance and to Eleftheria
Kralli-Beller for manuscript editing. This research was supported by the Scientific
Services Units (SSUs) of ISTA (Electron Microscopy Facility, Preclinical Facility,
and Machine Shop). The project received funding from the European Research Council
(ERC) under the European Union’s Horizon 2020 research and innovation program (grant
agreement no. 692692), the Fonds zur Förderung der Wissenschaftlichen Forschung
(Z 312-B27, Wittgenstein award; P 36232-B), all to P.J., and a DOC fellowship of
the Austrian Academy of Sciences to J.-J.C.
article_processing_charge: Yes (via OA deal)
article_type: original
author:
- first_name: JingJing
full_name: Chen, JingJing
id: 2C4E65C8-F248-11E8-B48F-1D18A9856A87
last_name: Chen
- first_name: Walter
full_name: Kaufmann, Walter
id: 3F99E422-F248-11E8-B48F-1D18A9856A87
last_name: Kaufmann
orcid: 0000-0001-9735-5315
- first_name: Chong
full_name: Chen, Chong
id: 3DFD581A-F248-11E8-B48F-1D18A9856A87
last_name: Chen
- first_name: Itaru
full_name: Arai, Itaru
id: 32A73F6C-F248-11E8-B48F-1D18A9856A87
last_name: Arai
- first_name: Olena
full_name: Kim, Olena
id: 3F8ABDDA-F248-11E8-B48F-1D18A9856A87
last_name: Kim
orcid: 0000-0003-2344-1039
- first_name: Ryuichi
full_name: Shigemoto, Ryuichi
id: 499F3ABC-F248-11E8-B48F-1D18A9856A87
last_name: Shigemoto
orcid: 0000-0001-8761-9444
- first_name: Peter M
full_name: Jonas, Peter M
id: 353C1B58-F248-11E8-B48F-1D18A9856A87
last_name: Jonas
orcid: 0000-0001-5001-4804
citation:
ama: Chen J, Kaufmann W, Chen C, et al. Developmental transformation of Ca2+ channel-vesicle
nanotopography at a central GABAergic synapse. Neuron. 2024;112(5):755-771.e9.
doi:10.1016/j.neuron.2023.12.002
apa: Chen, J., Kaufmann, W., Chen, C., Arai, itaru, Kim, O., Shigemoto, R., &
Jonas, P. M. (2024). Developmental transformation of Ca2+ channel-vesicle nanotopography
at a central GABAergic synapse. Neuron. Elsevier. https://doi.org/10.1016/j.neuron.2023.12.002
chicago: Chen, JingJing, Walter Kaufmann, Chong Chen, itaru Arai, Olena Kim, Ryuichi
Shigemoto, and Peter M Jonas. “Developmental Transformation of Ca2+ Channel-Vesicle
Nanotopography at a Central GABAergic Synapse.” Neuron. Elsevier, 2024.
https://doi.org/10.1016/j.neuron.2023.12.002.
ieee: J. Chen et al., “Developmental transformation of Ca2+ channel-vesicle
nanotopography at a central GABAergic synapse,” Neuron, vol. 112, no. 5.
Elsevier, p. 755–771.e9, 2024.
ista: Chen J, Kaufmann W, Chen C, Arai itaru, Kim O, Shigemoto R, Jonas PM. 2024.
Developmental transformation of Ca2+ channel-vesicle nanotopography at a central
GABAergic synapse. Neuron. 112(5), 755–771.e9.
mla: Chen, JingJing, et al. “Developmental Transformation of Ca2+ Channel-Vesicle
Nanotopography at a Central GABAergic Synapse.” Neuron, vol. 112, no. 5,
Elsevier, 2024, p. 755–771.e9, doi:10.1016/j.neuron.2023.12.002.
short: J. Chen, W. Kaufmann, C. Chen, itaru Arai, O. Kim, R. Shigemoto, P.M. Jonas,
Neuron 112 (2024) 755–771.e9.
corr_author: '1'
date_created: 2024-01-21T23:00:56Z
date_published: 2024-03-06T00:00:00Z
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call_identifier: H2020
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name: Biophysics and circuit function of a giant cortical glutamatergic synapse
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call_identifier: FWF
grant_number: Z00312
name: Synaptic communication in neuronal microcircuits
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grant_number: P36232
name: Mechanisms of GABA release in hippocampal circuits
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grant_number: '25383'
name: Development of nanodomain coupling between Ca2+ channels and release sensors
at a central inhibitory synapse
publication: Neuron
publication_identifier:
eissn:
- 1097-4199
issn:
- 0896-6273
publication_status: published
publisher: Elsevier
quality_controlled: '1'
related_material:
link:
- description: News on ISTA Website
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url: https://ista.ac.at/en/news/synapses-brought-to-the-point/
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scopus_import: '1'
status: public
title: Developmental transformation of Ca2+ channel-vesicle nanotopography at a central
GABAergic synapse
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 112
year: '2024'
...
---
OA_place: publisher
_id: '14821'
abstract:
- lang: eng
text: "The hippocampus is central to memory formation, storage and retrieval over
many\r\ntimescales. Neurons in this brain area are highly selective to spatial
position as well as to many\r\nother variables of the environment. It is believed
that the selectivity patterns of hippocampal\r\nneurons reflect the structure
of tasks an animal performs. However, especially at timescales\r\nlonger than
a few minutes or hours it is not fully known how these representations evolve,
nor\r\nhow they map to behaviour in the process. In this thesis, I monitored the
evolution of\r\nhippocampal representations in a novel spatial-associative memory
task for rats. Reward\r\nlocations were associated with global sensory cues (i.e.
context); animals had to remember the\r\nassociations and dig for food in those
locations only. I used in vivo electrophysiology to record\r\nthe activity of
the hippocampus dorsal CA1 neurons during the learning period of a few days.\r\nI
report here a novel and simple method to classify behaviour performance to account\r\nfor
individual variability in learning speed and spurious performance unrelated to
true task rule\r\nlearning. Using this classification I was then able to investigate
neural responses on different\r\nstages of learning matched across animals. On
the first day of learning, I observed a fast\r\nformation of single-cell selectivity
to task variables which remained stable over days. I also\r\nobserved that reward
tuning was not a single process but dependent on task-related cognitive\r\nload.
At the population level, a linear decoding approach revealed a hierarchy in the\r\nrepresentation
of task variables that changed with learning. In the high-dimensional space of\r\npopulation
activity, the representation of contexts was specific to each position in the
maze, and\r\ncould thus be better decoded if the position was known. The decoding
of position did not improve\r\nwith knowledge of other variables. As learning
progressed, the hippocampal code underwent a\r\nreorganisation of high-variance
directions in population activity, identified by principal\r\ncomponent analysis.
I found that dominant dimensions started carrying increasing amounts of\r\ninformation
about task context specifically at those positions where it mattered for task\r\nperformance.
When I contrasted this with variables less relevant to task performance (e.g.\r\nmovement
direction), I did not observe differences in decoding quality over positions nor
a\r\nreduction of dimensionality with learning.\r\nOverall, the largest changes
in CA1 neural response with task learning happened in a\r\nmatter of a few trials;
over days, changes undetectable in single-cell statistics were responsible\r\nfor
re-structuring the hierarchy of neural representations at the population level;
these changes\r\nwere task-specific and reflected different stages of learning.
This indicates that complex task\r\nlearning may involve different magnitudes
of response modulation in CA1, which happen at\r\nspecific time scales linked
to behaviour."
alternative_title:
- ISTA Thesis
article_processing_charge: No
author:
- first_name: Heloisa
full_name: Chiossi, Heloisa
id: 2BBA502C-F248-11E8-B48F-1D18A9856A87
last_name: Chiossi
orcid: 0009-0004-2973-278X
citation:
ama: Chiossi HSC. Adaptive hierarchical representations in the hippocampus. 2024.
doi:10.15479/at:ista:14821
apa: Chiossi, H. S. C. (2024). Adaptive hierarchical representations in the hippocampus.
Institute of Science and Technology Austria. https://doi.org/10.15479/at:ista:14821
chicago: Chiossi, Heloisa S. C. “Adaptive Hierarchical Representations in the Hippocampus.”
Institute of Science and Technology Austria, 2024. https://doi.org/10.15479/at:ista:14821.
ieee: H. S. C. Chiossi, “Adaptive hierarchical representations in the hippocampus,”
Institute of Science and Technology Austria, 2024.
ista: Chiossi HSC. 2024. Adaptive hierarchical representations in the hippocampus.
Institute of Science and Technology Austria.
mla: Chiossi, Heloisa S. C. Adaptive Hierarchical Representations in the Hippocampus.
Institute of Science and Technology Austria, 2024, doi:10.15479/at:ista:14821.
short: H.S.C. Chiossi, Adaptive Hierarchical Representations in the Hippocampus,
Institute of Science and Technology Austria, 2024.
corr_author: '1'
date_created: 2024-01-16T14:25:21Z
date_published: 2024-01-19T00:00:00Z
date_updated: 2026-04-07T13:21:56Z
day: '19'
ddc:
- '570'
degree_awarded: PhD
department:
- _id: GradSch
- _id: JoCs
doi: 10.15479/at:ista:14821
ec_funded: 1
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file_date_updated: 2025-01-19T23:30:04Z
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language:
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month: '01'
oa: 1
oa_version: Published Version
page: '89'
project:
- _id: 2564DBCA-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '665385'
name: International IST Doctoral Program
publication_identifier:
issn:
- 2663-337X
publication_status: published
publisher: Institute of Science and Technology Austria
status: public
supervisor:
- first_name: Jozsef L
full_name: Csicsvari, Jozsef L
id: 3FA14672-F248-11E8-B48F-1D18A9856A87
last_name: Csicsvari
orcid: 0000-0002-5193-4036
title: Adaptive hierarchical representations in the hippocampus
type: dissertation
user_id: ba8df636-2132-11f1-aed0-ed93e2281fdd
year: '2024'
...
---
OA_place: publisher
_id: '15101'
abstract:
- lang: eng
text: "The coupling between presynaptic Ca2+ channels and release sensors is a key
factor that\r\ndetermines speed and efficacy of synapse transmission. At some
excitatory synapses,\r\nchannel–sensor coupling becomes tighter during development,
and tightening is often\r\nassociated with a switch in the reliance on different
Ca2+ channel subtypes. However, the\r\ncoupling topography at many synapses remains
unknown, and it is unclear how it changes\r\nduring development. To address this
question, we analyzed the coupling configuration at the\r\ncerebellar basket cell
(BC) to Purkinje cell (PC) synapse at different developmental stages,\r\ncombining
biophysical analysis, structural analysis, and modeling.\r\nQuantal analysis of
BC–PC indicated that release probability decreased, while the\r\nnumber of functional
sites increased during development. Although transmitter release\r\npersistently
relied on P/Q-type Ca2+ channels in the time period postnatal day 7–23, effects\r\nof
the Ca2+ chelator EGTA and BAPTA applied by intracellular pipette perfusion decreased\r\nduring
development, indicative of tightening of source-sensor coupling. Furthermore,\r\npresynaptic
action potentials became shorter during development, suggesting reduced\r\nefficacy
of Ca2+ channel activation.\r\nStructural analysis by freeze-fracture replica
labeling (FRL) and transmission electron\r\nmicroscopy (EM) indicated that presynaptic
P/Q-type Ca2+ channels formed nanoclusters\r\nthroughout development, whereas
docked vesicles were only clustered at later\r\ndevelopmental stages. The number
of functional release sites correlated better with the AZ\r\nnumber early in development,
but match better with the Ca2+ channel cluster number at later\r\nstages.\r\nModeling
suggested a developmental transformation from a more random to a more\r\nclustered
coupling nanotopography. Thus, presynaptic signaling developmentally approaches\r\na
point-to-point configuration, optimizing speed, reliability, and energy efficiency
of synaptic\r\ntransmission."
acknowledged_ssus:
- _id: EM-Fac
alternative_title:
- ISTA Thesis
article_processing_charge: No
author:
- first_name: JingJing
full_name: Chen, JingJing
id: 2C4E65C8-F248-11E8-B48F-1D18A9856A87
last_name: Chen
citation:
ama: Chen J. Developmental transformation of nanodomain coupling between Ca2+ channels
and release sensors at a central GABAergic synapse. 2024. doi:10.15479/at:ista:15101
apa: Chen, J. (2024). Developmental transformation of nanodomain coupling between
Ca2+ channels and release sensors at a central GABAergic synapse. Institute
of Science and Technology Austria. https://doi.org/10.15479/at:ista:15101
chicago: Chen, JingJing. “Developmental Transformation of Nanodomain Coupling between
Ca2+ Channels and Release Sensors at a Central GABAergic Synapse.” Institute of
Science and Technology Austria, 2024. https://doi.org/10.15479/at:ista:15101.
ieee: J. Chen, “Developmental transformation of nanodomain coupling between Ca2+
channels and release sensors at a central GABAergic synapse,” Institute of Science
and Technology Austria, 2024.
ista: Chen J. 2024. Developmental transformation of nanodomain coupling between
Ca2+ channels and release sensors at a central GABAergic synapse. Institute of
Science and Technology Austria.
mla: Chen, JingJing. Developmental Transformation of Nanodomain Coupling between
Ca2+ Channels and Release Sensors at a Central GABAergic Synapse. Institute
of Science and Technology Austria, 2024, doi:10.15479/at:ista:15101.
short: J. Chen, Developmental Transformation of Nanodomain Coupling between Ca2+
Channels and Release Sensors at a Central GABAergic Synapse, Institute of Science
and Technology Austria, 2024.
corr_author: '1'
date_created: 2024-03-11T10:09:54Z
date_published: 2024-03-11T00:00:00Z
date_updated: 2026-04-07T13:24:22Z
day: '11'
ddc:
- '570'
degree_awarded: PhD
department:
- _id: GradSch
- _id: PeJo
doi: 10.15479/at:ista:15101
ec_funded: 1
file:
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date_updated: 2024-04-02T22:30:03Z
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file_date_updated: 2024-04-02T22:30:03Z
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language:
- iso: eng
month: '03'
oa: 1
oa_version: Published Version
page: '84'
project:
- _id: 25B7EB9E-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '692692'
name: Biophysics and circuit function of a giant cortical glutamatergic synapse
- _id: 25C5A090-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: Z00312
name: Synaptic communication in neuronal microcircuits
- _id: bd88be38-d553-11ed-ba76-81d5a70a6ef5
grant_number: P36232
name: Mechanisms of GABA release in hippocampal circuits
- _id: 26B66A3E-B435-11E9-9278-68D0E5697425
grant_number: '25383'
name: Development of nanodomain coupling between Ca2+ channels and release sensors
at a central inhibitory synapse
publication_identifier:
issn:
- 2663-337X
publication_status: published
publisher: Institute of Science and Technology Austria
related_material:
record:
- id: '14843'
relation: part_of_dissertation
status: public
status: public
supervisor:
- first_name: Peter M
full_name: Jonas, Peter M
id: 353C1B58-F248-11E8-B48F-1D18A9856A87
last_name: Jonas
orcid: 0000-0001-5001-4804
title: Developmental transformation of nanodomain coupling between Ca2+ channels and
release sensors at a central GABAergic synapse
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: dissertation
user_id: ba8df636-2132-11f1-aed0-ed93e2281fdd
year: '2024'
...
---
OA_place: publisher
_id: '18471'
abstract:
- lang: eng
text: "Spatial omics technologies are enriching our understanding of complex biological
samples, by\r\nallowing us to study their molecular composition while preserving
the spatial relationships\r\nbetween molecules in their native context. As the
field continues to advance, there are\r\ntechnical challenges that need to be
addressed in order to take full advantage of the spatial\r\ncapabilities of these
methods. In this work, I present two technical developments that I\r\nestablished
for multiplexed error robust FISH (MERFISH) throughout my PhD: (1) pushing the\r\nspatial
resolution limits to the nanoscale, and (2) adding rich tissue context to the
mouse brain\r\ntranscriptome. To achieve nanoscale resolution with MERFISH in
cultured cells, I combined it\r\nwith stimulated emission depletion (STED) and
expansion microscopy (ExM) to achieve a\r\nspatial resolution as low as ~20 nm,
and explored the compatibility of MERFISH with singlemolecule localization microscopy
(SMLM) techniques. To visualize targeted mRNAs in mouse\r\nbrain tissue, I applied
the comprehensive analysis of tissues across scales (CATS) toolbox, which\r\nprovides
an unbiased morphological readout by labeling the extracellular domain. I\r\nsuccessfully
established this method, which we call CATS-MERFISH-ExM, to work with thick\r\nmouse
brain slices, being able to extract transcriptomics information with 3D tissue
context.\r\nCATS-MERFISH-ExM enabled us to identify cell types and further visualize
the subcellular\r\ndistribution of transcripts in mouse brain tissue, shedding
light on the neuropil-specific\r\ntranscriptome. This method provides integrated
information on cellular structure and\r\ntranscriptomes in situ, and could potentially
be applied with other modalities, opening new\r\navenues for scientific discovery. "
acknowledged_ssus:
- _id: Bio
- _id: LifeSc
- _id: PreCl
- _id: M-Shop
- _id: ScienComp
alternative_title:
- ISTA Thesis
article_processing_charge: No
author:
- first_name: Nathalie
full_name: Agudelo Duenas, Nathalie
id: 40E7F008-F248-11E8-B48F-1D18A9856A87
last_name: Agudelo Duenas
citation:
ama: Agudelo Duenas N. Visualizing the neuronal transcriptional landscape with tissue
context. 2024. doi:10.15479/at:ista:18471
apa: Agudelo Duenas, N. (2024). Visualizing the neuronal transcriptional landscape
with tissue context. Institute of Science and Technology Austria. https://doi.org/10.15479/at:ista:18471
chicago: Agudelo Duenas, Nathalie. “Visualizing the Neuronal Transcriptional Landscape
with Tissue Context.” Institute of Science and Technology Austria, 2024. https://doi.org/10.15479/at:ista:18471.
ieee: N. Agudelo Duenas, “Visualizing the neuronal transcriptional landscape with
tissue context,” Institute of Science and Technology Austria, 2024.
ista: Agudelo Duenas N. 2024. Visualizing the neuronal transcriptional landscape
with tissue context. Institute of Science and Technology Austria.
mla: Agudelo Duenas, Nathalie. Visualizing the Neuronal Transcriptional Landscape
with Tissue Context. Institute of Science and Technology Austria, 2024, doi:10.15479/at:ista:18471.
short: N. Agudelo Duenas, Visualizing the Neuronal Transcriptional Landscape with
Tissue Context, Institute of Science and Technology Austria, 2024.
corr_author: '1'
date_created: 2024-10-26T20:02:42Z
date_published: 2024-10-28T00:00:00Z
date_updated: 2026-04-14T08:34:37Z
day: '28'
ddc:
- '570'
degree_awarded: PhD
department:
- _id: GradSch
- _id: JoDa
doi: 10.15479/at:ista:18471
ec_funded: 1
file:
- access_level: closed
checksum: 6d7c7725d040d8debc070dcb35ac965d
content_type: application/vnd.openxmlformats-officedocument.wordprocessingml.document
creator: nagudelo
date_created: 2024-10-26T22:29:06Z
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file_date_updated: 2025-05-05T22:30:04Z
has_accepted_license: '1'
language:
- iso: eng
month: '10'
oa: 1
oa_version: Published Version
page: '97'
project:
- _id: 2564DBCA-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '665385'
name: International IST Doctoral Program
- _id: 2548AE96-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: W1232
name: Molecular Drug Targets
publication_identifier:
isbn:
- 978-3-99078-044-2
issn:
- 2663-337X
publication_status: published
publisher: Institute of Science and Technology Austria
status: public
supervisor:
- first_name: Johann G
full_name: Danzl, Johann G
id: 42EFD3B6-F248-11E8-B48F-1D18A9856A87
last_name: Danzl
orcid: 0000-0001-8559-3973
title: Visualizing the neuronal transcriptional landscape with tissue context
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: dissertation
user_id: ba8df636-2132-11f1-aed0-ed93e2281fdd
year: '2024'
...