---
OA_place: repository
OA_type: green
_id: '22234'
abstract:
- lang: eng
text: Lists of nontrivial integral points on some (families of) cubic surfaces.
(2024-07-18)
article_processing_charge: No
author:
- first_name: Timothy D
full_name: Browning, Timothy D
id: 35827D50-F248-11E8-B48F-1D18A9856A87
last_name: Browning
orcid: 0000-0002-8314-0177
- first_name: Andrew
full_name: Sutherland, Andrew
last_name: Sutherland
citation:
ama: 'Browning TD, Sutherland A. Data and code for: Integral points on cubic surfaces:
heuristics and numerics. 2024. doi:10.25625/4FLFH8'
apa: 'Browning, T. D., & Sutherland, A. (2024). Data and code for: Integral
points on cubic surfaces: heuristics and numerics. Göttingen Research Online Data.
https://doi.org/10.25625/4FLFH8'
chicago: 'Browning, Timothy D, and Andrew Sutherland. “Data and Code for: Integral
Points on Cubic Surfaces: Heuristics and Numerics.” Göttingen Research Online
Data, 2024. https://doi.org/10.25625/4FLFH8.'
ieee: 'T. D. Browning and A. Sutherland, “Data and code for: Integral points on
cubic surfaces: heuristics and numerics.” Göttingen Research Online Data, 2024.'
ista: 'Browning TD, Sutherland A. 2024. Data and code for: Integral points on cubic
surfaces: heuristics and numerics, Göttingen Research Online Data, 10.25625/4FLFH8.'
mla: 'Browning, Timothy D., and Andrew Sutherland. Data and Code for: Integral
Points on Cubic Surfaces: Heuristics and Numerics. Göttingen Research Online
Data, 2024, doi:10.25625/4FLFH8.'
short: T.D. Browning, A. Sutherland, (2024).
contributor:
- first_name: Florian Alexander
id: 560601DA-8D36-11E9-A136-7AC1E5697425
last_name: Wilsch
orcid: 0000-0001-7302-8256
corr_author: '1'
date_created: 2026-07-02T10:38:53Z
date_published: 2024-07-22T00:00:00Z
date_updated: 2026-08-12T12:15:33Z
day: '22'
ddc:
- '500'
department:
- _id: TiBr
doi: 10.25625/4FLFH8
has_accepted_license: '1'
license: https://creativecommons.org/licenses/by/4.0/
main_file_link:
- open_access: '1'
url: https://doi.org/10.25625/4FLFH8
month: '07'
oa: 1
oa_version: Published Version
publisher: Göttingen Research Online Data
related_material:
record:
- id: '20249'
relation: used_in_publication
status: public
status: public
title: 'Data and code for: Integral points on cubic surfaces: heuristics and numerics'
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: research_data_reference
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
year: '2024'
...
---
DOAJ_listed: '1'
OA_place: publisher
OA_type: gold
_id: '17457'
abstract:
- lang: eng
text: "Autoantibodies against the protein leucine-rich glioma inactivated 1 (LGI1)
cause the most\r\ncommon subtype of autoimmune encephalitis with predominant involvement
of the limbic\r\nsystem, associated with seizures and memory deficits. LGI1 and
its receptor ADAM22 are part\r\nof a transsynaptic protein complex that includes
several proteins involved in presynaptic\r\nneurotransmitter release and postsynaptic
glutamate sensing. Autoantibodies against LGI1\r\nincrease excitatory synaptic
strength, but studies that genetically disrupt the LGI1-ADAM22\r\ncomplex report
a reduction in postsynaptic glutamate receptor-mediated responses. Thus, the\r\nmechanisms
underlying the increased synaptic strength induced by LGI1 autoantibodies remain
elusive, and the contributions of presynaptic molecules to the LGI1-transsynaptic
complex remain unclear. We therefore investigated the presynaptic mechanisms that
mediate\r\nautoantibody-induced synaptic strengthening."
acknowledged_ssus:
- _id: Bio
- _id: EM-Fac
acknowledgement: 'The authors thank Claudia Sommer for expert technical assistance,
the Electron Microscopy Facility of IST-Austria for resources, and Tereza Belinova
in the Imaging and Optics Facility of IST-Austria for 3D reconstruction. '
article_processing_charge: Yes
article_type: original
author:
- first_name: Andreas
full_name: Ritzau-Jost, Andreas
last_name: Ritzau-Jost
- first_name: Felix
full_name: Gsell, Felix
last_name: Gsell
- first_name: Josefine
full_name: Sell, Josefine
last_name: Sell
- first_name: Stefan
full_name: Sachs, Stefan
last_name: Sachs
- first_name: Jacqueline-Claire
full_name: Montanaro-Punzengruber, Jacqueline-Claire
id: 3786AB44-F248-11E8-B48F-1D18A9856A87
last_name: Montanaro-Punzengruber
- first_name: Toni
full_name: Kirmann, Toni
last_name: Kirmann
- first_name: Sebastian
full_name: Maaß, Sebastian
last_name: Maaß
- first_name: Sarosh R.
full_name: Irani, Sarosh R.
last_name: Irani
- first_name: Christian
full_name: Werner, Christian
last_name: Werner
- first_name: Christian
full_name: Geis, Christian
last_name: Geis
- first_name: Markus
full_name: Sauer, Markus
last_name: Sauer
- first_name: Ryuichi
full_name: Shigemoto, Ryuichi
id: 499F3ABC-F248-11E8-B48F-1D18A9856A87
last_name: Shigemoto
orcid: 0000-0001-8761-9444
- first_name: Stefan
full_name: Hallermann, Stefan
last_name: Hallermann
citation:
ama: Ritzau-Jost A, Gsell F, Sell J, et al. LGI1 autoantibodies enhance synaptic
transmission by presynaptic Kv1 loss and increased action potential broadening.
Neurology, Neuroimmunology & Neuroinflammation. 2024;11(5):e200284.
doi:10.1212/NXI.0000000000200284
apa: Ritzau-Jost, A., Gsell, F., Sell, J., Sachs, S., Montanaro-Punzengruber, J.-C.,
Kirmann, T., … Hallermann, S. (2024). LGI1 autoantibodies enhance synaptic transmission
by presynaptic Kv1 loss and increased action potential broadening. Neurology,
Neuroimmunology & Neuroinflammation. Wolters Kluwer. https://doi.org/10.1212/NXI.0000000000200284
chicago: Ritzau-Jost, Andreas, Felix Gsell, Josefine Sell, Stefan Sachs, Jacqueline-Claire
Montanaro-Punzengruber, Toni Kirmann, Sebastian Maaß, et al. “LGI1 Autoantibodies
Enhance Synaptic Transmission by Presynaptic Kv1 Loss and Increased Action Potential
Broadening.” Neurology, Neuroimmunology & Neuroinflammation. Wolters
Kluwer, 2024. https://doi.org/10.1212/NXI.0000000000200284.
ieee: A. Ritzau-Jost et al., “LGI1 autoantibodies enhance synaptic transmission
by presynaptic Kv1 loss and increased action potential broadening,” Neurology,
Neuroimmunology & Neuroinflammation, vol. 11, no. 5. Wolters Kluwer, p.
e200284, 2024.
ista: Ritzau-Jost A, Gsell F, Sell J, Sachs S, Montanaro-Punzengruber J-C, Kirmann
T, Maaß S, Irani SR, Werner C, Geis C, Sauer M, Shigemoto R, Hallermann S. 2024.
LGI1 autoantibodies enhance synaptic transmission by presynaptic Kv1 loss and
increased action potential broadening. Neurology, Neuroimmunology & Neuroinflammation.
11(5), e200284.
mla: Ritzau-Jost, Andreas, et al. “LGI1 Autoantibodies Enhance Synaptic Transmission
by Presynaptic Kv1 Loss and Increased Action Potential Broadening.” Neurology,
Neuroimmunology & Neuroinflammation, vol. 11, no. 5, Wolters Kluwer, 2024,
p. e200284, doi:10.1212/NXI.0000000000200284.
short: A. Ritzau-Jost, F. Gsell, J. Sell, S. Sachs, J.-C. Montanaro-Punzengruber,
T. Kirmann, S. Maaß, S.R. Irani, C. Werner, C. Geis, M. Sauer, R. Shigemoto, S.
Hallermann, Neurology, Neuroimmunology & Neuroinflammation 11 (2024) e200284.
date_created: 2024-08-25T22:01:07Z
date_published: 2024-09-01T00:00:00Z
date_updated: 2026-08-12T14:17:59Z
day: '01'
ddc:
- '570'
department:
- _id: RySh
doi: 10.1212/NXI.0000000000200284
external_id:
isi:
- '001291908600001'
pmid:
- '39141878'
file:
- access_level: open_access
checksum: 1e6d1230e0387f72752e3268f5330c9e
content_type: application/pdf
creator: dernst
date_created: 2025-01-09T13:42:42Z
date_updated: 2025-01-09T13:42:42Z
file_id: '18815'
file_name: 2024_NeurologyNeuroimmNeuroinflamm_RitzauJost.pdf
file_size: 855818
relation: main_file
success: 1
file_date_updated: 2025-01-09T13:42:42Z
has_accepted_license: '1'
intvolume: ' 11'
isi: 1
issue: '5'
language:
- iso: eng
month: '09'
oa: 1
oa_version: Published Version
page: e200284
pmid: 1
project:
- _id: 05970B30-7A3F-11EA-A408-12923DDC885E
grant_number: I04638
name: LGI1 antibody-induced pathophysiology in synapses
publication: Neurology, Neuroimmunology & Neuroinflammation
publication_identifier:
eissn:
- 2332-7812
publication_status: published
publisher: Wolters Kluwer
quality_controlled: '1'
related_material:
link:
- relation: earlier_version
url: https://doi.org/10.1101/2023.10.04.560631
scopus_import: '1'
status: public
title: LGI1 autoantibodies enhance synaptic transmission by presynaptic Kv1 loss and
increased action potential broadening
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 11
year: '2024'
...
---
OA_place: repository
OA_type: green
_id: '19063'
abstract:
- lang: eng
text: "Instruction-tuned Large Language Models (LLMs) show impressive results in
numerous practical applications, but they lack essential safety features that
are common in other areas of computer science, particularly an explicit separation
of instructions and data. This makes them vulnerable to manipulations such as
indirect prompt injections and generally unsuitable for safety-critical tasks.
Surprisingly, there is currently no established definition or benchmark to quantify
this phenomenon. In this work, we close this gap by introducing a formal measure
for instruction-data separation and an empirical variant that is calculable from
a model's outputs. We also present a new dataset, SEP, that allows estimating
the measure for real-world models. Our results on various LLMs show that the problem
of instruction-data separation is real: all models fail to achieve high separation,
and canonical mitigation techniques, such as prompt engineering and fine-tuning,
either fail to substantially improve separation or reduce model utility. The source
code and SEP dataset are openly accessible at https://github.com/egozverev/Shold-It-Be-Executed-Or-Processed.\r\n"
acknowledged_ssus:
- _id: ScienComp
acknowledgement: The authors would like to sincerely thank Juan Rocamonde for valuable
feedback to our manuscript. We acknowledge the support from the Scientific Service
Units (SSU) of ISTA through resources provided by Scientific Computing (SciComp).
We thank Dan Alistarh for providing us with computational resources. This work was
partially funded by the German Federal Ministry of Education and Research (BMBF)
under the grant AIgenCY (16KIS2012) and ELSA – European Lighthouse on Secure and
Safe AI funded by the European Union under grant agreement No. 101070617. Views
and opinions expressed are however those of the authors only and do not necessarily
reflect those of the European Union or European Commission. Neither the European
Union nor the European Commission can be held responsible for them.
article_number: '2403.06833'
article_processing_charge: No
arxiv: 1
author:
- first_name: Egor
full_name: Zverev, Egor
id: 05162b19-1340-11ed-8f02-fa94e0e8c3bc
last_name: Zverev
- first_name: Sahar
full_name: Abdelnabi, Sahar
last_name: Abdelnabi
- first_name: Soroush
full_name: Tabesh, Soroush
id: 06000900-6068-11ef-8d61-c2472ef2e752
last_name: Tabesh
orcid: 0009-0003-4119-6281
- first_name: Mario
full_name: Fritz, Mario
last_name: Fritz
- first_name: Christoph
full_name: Lampert, Christoph
id: 40C20FD2-F248-11E8-B48F-1D18A9856A87
last_name: Lampert
orcid: 0000-0001-8622-7887
citation:
ama: Zverev E, Abdelnabi S, Tabesh S, Fritz M, Lampert C. Can LLMs separate instructions
from data? And what do we even mean by that? arXiv. doi:10.48550/arXiv.2403.06833
apa: Zverev, E., Abdelnabi, S., Tabesh, S., Fritz, M., & Lampert, C. (n.d.).
Can LLMs separate instructions from data? And what do we even mean by that? arXiv.
https://doi.org/10.48550/arXiv.2403.06833
chicago: Zverev, Egor, Sahar Abdelnabi, Soroush Tabesh, Mario Fritz, and Christoph
Lampert. “Can LLMs Separate Instructions from Data? And What Do We Even Mean by
That?” ArXiv, n.d. https://doi.org/10.48550/arXiv.2403.06833.
ieee: E. Zverev, S. Abdelnabi, S. Tabesh, M. Fritz, and C. Lampert, “Can LLMs separate
instructions from data? And what do we even mean by that?,” arXiv. .
ista: Zverev E, Abdelnabi S, Tabesh S, Fritz M, Lampert C. Can LLMs separate instructions
from data? And what do we even mean by that? arXiv, 2403.06833.
mla: Zverev, Egor, et al. “Can LLMs Separate Instructions from Data? And What Do
We Even Mean by That?” ArXiv, 2403.06833, doi:10.48550/arXiv.2403.06833.
short: E. Zverev, S. Abdelnabi, S. Tabesh, M. Fritz, C. Lampert, ArXiv (n.d.).
corr_author: '1'
date_created: 2025-02-20T10:13:42Z
date_published: 2024-03-01T00:00:00Z
date_updated: 2026-08-13T07:26:54Z
day: '01'
ddc:
- '000'
department:
- _id: GradSch
- _id: ChLa
doi: 10.48550/arXiv.2403.06833
external_id:
arxiv:
- '2403.06833'
file:
- access_level: open_access
checksum: 35eb43968684b87be59144603ef10af0
content_type: application/pdf
creator: ezverev
date_created: 2025-02-20T10:11:45Z
date_updated: 2025-02-20T10:11:45Z
file_id: '19064'
file_name: 2403.06833v3.pdf
file_size: 530972
relation: main_file
success: 1
file_date_updated: 2025-02-20T10:11:45Z
has_accepted_license: '1'
language:
- iso: eng
month: '03'
oa: 1
oa_version: Preprint
publication: arXiv
publication_status: submitted
related_material:
link:
- relation: software
url: ' https://github.com/egozverev/Shold-It-Be-Executed-Or-Processed'
status: public
title: Can LLMs separate instructions from data? And what do we even mean by that?
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: preprint
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
year: '2024'
...
---
APC_amount: 1530 EUR
OA_place: publisher
OA_type: gold
_id: '15401'
abstract:
- lang: eng
text: Amide-proton-detected magic-angle-spinning NMR of deuterated proteins has
become a main technique in NMR-based structural biology. In standard deuteration
protocols that rely on D2O-based culture media, non-exchangeable amide sites remain
deuterated, making these sites unobservable. Here we demonstrate that proteins
produced with a H2O-based culture medium doped with deuterated cell lysate allow
scientists to overcome this “reprotonation bottleneck” while retaining a high
level of deuteration (ca. 80 %) and narrow linewidths. We quantified coherence
lifetimes of several proteins prepared with this labeling pattern over a range
of magic-angle-spinning (MAS) frequencies (40–100 kHz). We demonstrate that under
commonly used conditions (50–60 kHz MAS), the amide 1H linewidths with our labeling
approach are comparable to those of perdeuterated proteins and better than those
of protonated samples at 100 kHz. For three proteins in the 33–50 kDa size range,
many previously unobserved amides become visible. We report how to prepare the
deuterated cell lysate for our approach from fractions of perdeuterated cultures
which are usually discarded, and we show that such media can be used identically
to commercial media. The residual protonation of Hα sites allows for well-resolved
Hα-detected spectra and Hα resonance assignment, exemplified by the de novo assignment
of 168 Hα sites in a 39 kDa protein. The approach based on this H2O/cell-lysate
deuteration and MAS frequencies compatible with 1.3 or 1.9 mm rotors presents
a strong sensitivity benefit over 0.7 mm 100 kHz MAS experiments.
acknowledged_ssus:
- _id: NMR
acknowledgement: "We thank Dominique Madern (IBS Grenoble) for providing the plasmid
for MalDH and feedback on the article, Alicia Vallet for excellent support at the
Grenoble NMR facility, and Petra Rovo and Margarita Valhondo at the IST Austria
NMR Service Unit. We thank Dorothea Anrather in the mass spectrometry facility of
Max Perutz Labs for the mass spectrometry analysis using the instruments of the
Vienna BioCenter Core Facilities (VBCF). We are grateful to Jean-Pierre Andrieu
(Plateforme Seq3A, IBS Grenoble) for the analysis of the amino acid composition
of the in-house-prepared lysates. We are grateful to Rasmus Linser (Technical University
Dortmund) for sharing a paper draft describing a similar study. This work was supported
by the Austrian Science Fund (FWF; project number I5812-B). We thank Tobias Schubeis
(Lyon) and the reviewers for constructive input.\r\nThis research has been supported
by the Austrian Science Fund (grant no. I5812-B). Part of this work used the platforms
of the Grenoble Instruct-ERIC center (ISBG; UAR 3518 CNRS-CEA-UGA-EMBL) within the
Grenoble Partnership for 40 Structural Biology (PSB), supported by FRISBI (ANR-10-INBS-0005-02)
and GRAL, financed within the University Grenoble Alpes graduate school (Ecoles
Universitaires de Recherche) CBH-EUR-GS (ANR-17-EURE-0003). IBS acknowledges integration
into the Interdisciplinary Research Institute of Grenoble (IRIG, 45 CEA). Charles-Adrien
Arnaud was funded by GRAL."
article_processing_charge: Yes
article_type: original
author:
- first_name: Federico
full_name: Napoli, Federico
id: d42e08e7-f4fc-11eb-af0a-d71e26138f1b
last_name: Napoli
orcid: 0000-0002-9043-136X
- first_name: Jia-Ying
full_name: Guan, Jia-Ying
last_name: Guan
- first_name: Charles-Adrien
full_name: Arnaud, Charles-Adrien
last_name: Arnaud
- first_name: Pavel
full_name: Macek, Pavel
last_name: Macek
- first_name: Hugo
full_name: Fraga, Hugo
last_name: Fraga
- first_name: Cécile
full_name: Breyton, Cécile
last_name: Breyton
- first_name: Paul
full_name: Schanda, Paul
id: 7B541462-FAF6-11E9-A490-E8DFE5697425
last_name: Schanda
orcid: 0000-0002-9350-7606
citation:
ama: 'Napoli F, Guan J-Y, Arnaud C-A, et al. Deuteration of proteins boosted by
cell lysates: High-resolution amide and Ha magic-angle-spinning (MAS) NMR without
the reprotonation bottleneck. Magnetic Resonance. 2024;5(1):33-49. doi:10.5194/mr-5-33-2024'
apa: 'Napoli, F., Guan, J.-Y., Arnaud, C.-A., Macek, P., Fraga, H., Breyton, C.,
& Schanda, P. (2024). Deuteration of proteins boosted by cell lysates: High-resolution
amide and Ha magic-angle-spinning (MAS) NMR without the reprotonation bottleneck.
Magnetic Resonance. Copernicus Publications. https://doi.org/10.5194/mr-5-33-2024'
chicago: 'Napoli, Federico, Jia-Ying Guan, Charles-Adrien Arnaud, Pavel Macek, Hugo
Fraga, Cécile Breyton, and Paul Schanda. “Deuteration of Proteins Boosted by Cell
Lysates: High-Resolution Amide and Ha Magic-Angle-Spinning (MAS) NMR without the
Reprotonation Bottleneck.” Magnetic Resonance. Copernicus Publications,
2024. https://doi.org/10.5194/mr-5-33-2024.'
ieee: 'F. Napoli et al., “Deuteration of proteins boosted by cell lysates:
High-resolution amide and Ha magic-angle-spinning (MAS) NMR without the reprotonation
bottleneck,” Magnetic Resonance, vol. 5, no. 1. Copernicus Publications,
pp. 33–49, 2024.'
ista: 'Napoli F, Guan J-Y, Arnaud C-A, Macek P, Fraga H, Breyton C, Schanda P. 2024.
Deuteration of proteins boosted by cell lysates: High-resolution amide and Ha
magic-angle-spinning (MAS) NMR without the reprotonation bottleneck. Magnetic
Resonance. 5(1), 33–49.'
mla: 'Napoli, Federico, et al. “Deuteration of Proteins Boosted by Cell Lysates:
High-Resolution Amide and Ha Magic-Angle-Spinning (MAS) NMR without the Reprotonation
Bottleneck.” Magnetic Resonance, vol. 5, no. 1, Copernicus Publications,
2024, pp. 33–49, doi:10.5194/mr-5-33-2024.'
short: F. Napoli, J.-Y. Guan, C.-A. Arnaud, P. Macek, H. Fraga, C. Breyton, P. Schanda,
Magnetic Resonance 5 (2024) 33–49.
corr_author: '1'
date_created: 2024-05-16T15:02:43Z
date_published: 2024-04-19T00:00:00Z
date_updated: 2025-07-17T08:12:23Z
day: '19'
ddc:
- '530'
department:
- _id: PaSc
doi: 10.5194/mr-5-33-2024
external_id:
pmid:
- '40384771'
file:
- access_level: open_access
checksum: 80ea50114e428461ca9530d3bd5d89e4
content_type: application/pdf
creator: dernst
date_created: 2024-05-22T07:01:15Z
date_updated: 2024-05-22T07:01:15Z
file_id: '15413'
file_name: 2024_MagneticResonance_Napoli.pdf
file_size: 6657865
relation: main_file
success: 1
file_date_updated: 2024-05-22T07:01:15Z
has_accepted_license: '1'
intvolume: ' 5'
issue: '1'
language:
- iso: eng
month: '04'
oa: 1
oa_version: Published Version
page: 33-49
pmid: 1
project:
- _id: eb9c82eb-77a9-11ec-83b8-aadd536561cf
grant_number: I05812
name: AlloSpace. The emergence and mechanisms of allostery
- _id: 3AC91DDA-15DF-11EA-824D-93A3E7B544D1
call_identifier: FWF
name: FWF Open Access Fund
publication: Magnetic Resonance
publication_identifier:
issn:
- 2699-0016
publication_status: published
publisher: Copernicus Publications
quality_controlled: '1'
scopus_import: '1'
status: public
title: 'Deuteration of proteins boosted by cell lysates: High-resolution amide and
Ha magic-angle-spinning (MAS) NMR without the reprotonation bottleneck'
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: 5
year: '2024'
...
---
OA_place: publisher
_id: '15094'
abstract:
- lang: eng
text: "Point sets, geometric networks, and arrangements of hyperplanes are fundamental
objects in\r\ndiscrete geometry that have captivated mathematicians for centuries,
if not millennia. This\r\nthesis seeks to cast new light on these structures by
illustrating specific instances where a\r\ntopological perspective, specifically
through discrete Morse theory and persistent homology,\r\nprovides valuable insights.\r\n\r\nAt
first glance, the topology of these geometric objects might seem uneventful: point
sets\r\nessentially lack of topology, arrangements of hyperplanes are a decomposition
of Rd, which\r\nis a contractible space, and the topology of a network primarily
involves the enumeration\r\nof connected components and cycles within the network.
However, beneath this apparent\r\nsimplicity, there lies an array of intriguing
structures, a small subset of which will be uncovered\r\nin this thesis.\r\n\r\nFocused
on three case studies, each addressing one of the mentioned objects, this work\r\nwill
showcase connections that intertwine topology with diverse fields such as combinatorial\r\ngeometry,
algorithms and data structures, and emerging applications like spatial biology.\r\n\r\n"
alternative_title:
- ISTA Thesis
article_processing_charge: No
author:
- first_name: Sebastiano
full_name: Cultrera di Montesano, Sebastiano
id: 34D2A09C-F248-11E8-B48F-1D18A9856A87
last_name: Cultrera di Montesano
orcid: 0000-0001-6249-0832
citation:
ama: Cultrera di Montesano S. Persistence and Morse theory for discrete geometric
structures. 2024. doi:10.15479/at:ista:15094
apa: Cultrera di Montesano, S. (2024). Persistence and Morse theory for discrete
geometric structures. Institute of Science and Technology Austria. https://doi.org/10.15479/at:ista:15094
chicago: Cultrera di Montesano, Sebastiano. “Persistence and Morse Theory for Discrete
Geometric Structures.” Institute of Science and Technology Austria, 2024. https://doi.org/10.15479/at:ista:15094.
ieee: S. Cultrera di Montesano, “Persistence and Morse theory for discrete geometric
structures,” Institute of Science and Technology Austria, 2024.
ista: Cultrera di Montesano S. 2024. Persistence and Morse theory for discrete geometric
structures. Institute of Science and Technology Austria.
mla: Cultrera di Montesano, Sebastiano. Persistence and Morse Theory for Discrete
Geometric Structures. Institute of Science and Technology Austria, 2024, doi:10.15479/at:ista:15094.
short: S. Cultrera di Montesano, Persistence and Morse Theory for Discrete Geometric
Structures, Institute of Science and Technology Austria, 2024.
corr_author: '1'
date_created: 2024-03-08T15:28:10Z
date_published: 2024-03-08T00:00:00Z
date_updated: 2026-08-13T09:41:57Z
day: '08'
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ec_funded: 1
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language:
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month: '03'
oa: 1
oa_version: Published Version
page: '108'
project:
- _id: 266A2E9E-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '788183'
name: Alpha Shape Theory Extended
- _id: 268116B8-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: Z00342
name: Mathematics, Computer Science
- _id: 0aa4bc98-070f-11eb-9043-e6fff9c6a316
grant_number: I4887
name: Persistent Homology, Algorithms and Stochastic Geometry
- _id: 2561EBF4-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: I02979-N35
name: Persistence and stability of geometric complexes
publication_identifier:
issn:
- 2663-337X
publication_status: published
publisher: Institute of Science and Technology Austria
related_material:
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status: public
status: public
supervisor:
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full_name: Edelsbrunner, Herbert
id: 3FB178DA-F248-11E8-B48F-1D18A9856A87
last_name: Edelsbrunner
orcid: 0000-0002-9823-6833
title: Persistence and Morse theory for discrete geometric structures
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...
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OA_place: publisher
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abstract:
- lang: eng
text: "We characterize critical points of 1-dimensional maps paired in persistent
homology\r\ngeometrically and this way get elementary proofs of theorems about
the symmetry\r\nof persistence diagrams and the variation of such maps. In particular,
we identify\r\nbranching points and endpoints of networks as the sole source of
asymmetry and\r\nrelate the cycle basis in persistent homology with a version
of the stable marriage\r\nproblem. Our analysis provides the foundations of fast
algorithms for maintaining a\r\ncollection of sorted lists together with its persistence
diagram."
acknowledgement: Open access funding provided by Austrian Science Fund (FWF). This
project has received funding from the European Research Council (ERC) under the
European Union’s Horizon 2020 research and innovation programme, grant no. 788183,
from the Wittgenstein Prize, Austrian Science Fund (FWF), Grant No. Z 342-N31, and
from the DFG Collaborative Research Center TRR 109, ‘Discretization in Geometry
and Dynamics’, Austrian Science Fund (FWF), Grant No. I 02979-N35. The authors of
this paper thank anonymous reviewers for their constructive criticism and Monika
Henzinger for detailed comments on an earlier version of this paper.
article_processing_charge: Yes (via OA deal)
article_type: original
author:
- first_name: Ranita
full_name: Biswas, Ranita
id: 3C2B033E-F248-11E8-B48F-1D18A9856A87
last_name: Biswas
orcid: 0000-0002-5372-7890
- first_name: Sebastiano
full_name: Cultrera Di Montesano, Sebastiano
id: 34D2A09C-F248-11E8-B48F-1D18A9856A87
last_name: Cultrera Di Montesano
orcid: 0000-0001-6249-0832
- first_name: Herbert
full_name: Edelsbrunner, Herbert
id: 3FB178DA-F248-11E8-B48F-1D18A9856A87
last_name: Edelsbrunner
orcid: 0000-0002-9823-6833
- first_name: Morteza
full_name: Saghafian, Morteza
id: f86f7148-b140-11ec-9577-95435b8df824
last_name: Saghafian
citation:
ama: Biswas R, Cultrera di Montesano S, Edelsbrunner H, Saghafian M. Geometric characterization
of the persistence of 1D maps. Journal of Applied and Computational Topology.
2024;8:1101-1119. doi:10.1007/s41468-023-00126-9
apa: Biswas, R., Cultrera di Montesano, S., Edelsbrunner, H., & Saghafian, M.
(2024). Geometric characterization of the persistence of 1D maps. Journal of
Applied and Computational Topology. Springer Nature. https://doi.org/10.1007/s41468-023-00126-9
chicago: Biswas, Ranita, Sebastiano Cultrera di Montesano, Herbert Edelsbrunner,
and Morteza Saghafian. “Geometric Characterization of the Persistence of 1D Maps.”
Journal of Applied and Computational Topology. Springer Nature, 2024. https://doi.org/10.1007/s41468-023-00126-9.
ieee: R. Biswas, S. Cultrera di Montesano, H. Edelsbrunner, and M. Saghafian, “Geometric
characterization of the persistence of 1D maps,” Journal of Applied and Computational
Topology, vol. 8. Springer Nature, pp. 1101–1119, 2024.
ista: Biswas R, Cultrera di Montesano S, Edelsbrunner H, Saghafian M. 2024. Geometric
characterization of the persistence of 1D maps. Journal of Applied and Computational
Topology. 8, 1101–1119.
mla: Biswas, Ranita, et al. “Geometric Characterization of the Persistence of 1D
Maps.” Journal of Applied and Computational Topology, vol. 8, Springer
Nature, 2024, pp. 1101–19, doi:10.1007/s41468-023-00126-9.
short: R. Biswas, S. Cultrera di Montesano, H. Edelsbrunner, M. Saghafian, Journal
of Applied and Computational Topology 8 (2024) 1101–1119.
corr_author: '1'
date_created: 2023-07-02T22:00:44Z
date_published: 2024-10-01T00:00:00Z
date_updated: 2026-08-13T09:41:57Z
day: '01'
ddc:
- '000'
department:
- _id: HeEd
doi: 10.1007/s41468-023-00126-9
ec_funded: 1
external_id:
pmid:
- '39678706'
file:
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oa: 1
oa_version: Published Version
page: 1101-1119
pmid: 1
project:
- _id: 266A2E9E-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '788183'
name: Alpha Shape Theory Extended
- _id: 0aa4bc98-070f-11eb-9043-e6fff9c6a316
grant_number: I4887
name: Persistent Homology, Algorithms and Stochastic Geometry
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call_identifier: FWF
grant_number: Z00342
name: Mathematics, Computer Science
publication: Journal of Applied and Computational Topology
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eissn:
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issn:
- 2367-1726
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publisher: Springer Nature
quality_controlled: '1'
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relation: earlier_version
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scopus_import: '1'
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title: Geometric characterization of the persistence of 1D maps
tmp:
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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: 8
year: '2024'
...
---
_id: '14826'
abstract:
- lang: eng
text: The plant-signaling molecule auxin triggers fast and slow cellular responses
across land plants and algae. The nuclear auxin pathway mediates gene expression
and controls growth and development in land plants, but this pathway is absent
from algal sister groups. Several components of rapid responses have been identified
in Arabidopsis, but it is unknown if these are part of a conserved mechanism.
We recently identified a fast, proteome-wide phosphorylation response to auxin.
Here, we show that this response occurs across 5 land plant and algal species
and converges on a core group of shared targets. We found conserved rapid physiological
responses to auxin in the same species and identified rapidly accelerated fibrosarcoma
(RAF)-like protein kinases as central mediators of auxin-triggered phosphorylation
across species. Genetic analysis connects this kinase to both auxin-triggered
protein phosphorylation and rapid cellular response, thus identifying an ancient
mechanism for fast auxin responses in the green lineage.
acknowledgement: 'We are grateful to Asuka Shitaku and Eri Koide for generating and
sharing the Marchantia PRAF-mCitrine line and Peng-Cheng Wang for sharing the Arabidopsis
raf mutant. We are grateful to our team members for discussions and helpful advice.
This work was supported by funding from the Netherlands Organization for Scientific
Research (NWO): VICI grant 865.14.001 and ENW-KLEIN OCENW.KLEIN.027 grants to D.W.;
VENI grant VI.VENI.212.003 to A.K.; the European Research Council AdG DIRNDL (contract
number 833867) to D.W.; CoG CATCH to J.S.; StG CELLONGATE (contract 803048) to M.F.;
and AdG ETAP (contract 742985) to J.F.; MEXT KAKENHI grant number JP19H05675 to
T.K.; JSPS KAKENHI grant number JP20H03275 to R.N.; Takeda Science Foundation to
R.N.; and the Austrian Science Fund (FWF, P29988) to J.F.'
article_processing_charge: Yes (in subscription journal)
article_type: original
author:
- first_name: Andre
full_name: Kuhn, Andre
last_name: Kuhn
- first_name: Mark
full_name: Roosjen, Mark
last_name: Roosjen
- first_name: Sumanth
full_name: Mutte, Sumanth
last_name: Mutte
- first_name: Shiv Mani
full_name: Dubey, Shiv Mani
last_name: Dubey
- first_name: Vanessa Polet
full_name: Carrillo Carrasco, Vanessa Polet
last_name: Carrillo Carrasco
- first_name: Sjef
full_name: Boeren, Sjef
last_name: Boeren
- first_name: Aline
full_name: Monzer, Aline
id: 2DB5D88C-D7B3-11E9-B8FD-7907E6697425
last_name: Monzer
- first_name: Jasper
full_name: Koehorst, Jasper
last_name: Koehorst
- first_name: Takayuki
full_name: Kohchi, Takayuki
last_name: Kohchi
- first_name: Ryuichi
full_name: Nishihama, Ryuichi
last_name: Nishihama
- first_name: Matyas
full_name: Fendrych, Matyas
id: 43905548-F248-11E8-B48F-1D18A9856A87
last_name: Fendrych
orcid: 0000-0002-9767-8699
- first_name: Joris
full_name: Sprakel, Joris
last_name: Sprakel
- first_name: Jiří
full_name: Friml, Jiří
id: 4159519E-F248-11E8-B48F-1D18A9856A87
last_name: Friml
orcid: 0000-0002-8302-7596
- first_name: Dolf
full_name: Weijers, Dolf
last_name: Weijers
citation:
ama: Kuhn A, Roosjen M, Mutte S, et al. RAF-like protein kinases mediate a deeply
conserved, rapid auxin response. Cell. 2024;187(1):130-148.e17. doi:10.1016/j.cell.2023.11.021
apa: Kuhn, A., Roosjen, M., Mutte, S., Dubey, S. M., Carrillo Carrasco, V. P., Boeren,
S., … Weijers, D. (2024). RAF-like protein kinases mediate a deeply conserved,
rapid auxin response. Cell. Elsevier. https://doi.org/10.1016/j.cell.2023.11.021
chicago: Kuhn, Andre, Mark Roosjen, Sumanth Mutte, Shiv Mani Dubey, Vanessa Polet
Carrillo Carrasco, Sjef Boeren, Aline Monzer, et al. “RAF-like Protein Kinases
Mediate a Deeply Conserved, Rapid Auxin Response.” Cell. Elsevier, 2024.
https://doi.org/10.1016/j.cell.2023.11.021.
ieee: A. Kuhn et al., “RAF-like protein kinases mediate a deeply conserved,
rapid auxin response,” Cell, vol. 187, no. 1. Elsevier, p. 130–148.e17,
2024.
ista: Kuhn A, Roosjen M, Mutte S, Dubey SM, Carrillo Carrasco VP, Boeren S, Monzer
A, Koehorst J, Kohchi T, Nishihama R, Fendrych M, Sprakel J, Friml J, Weijers
D. 2024. RAF-like protein kinases mediate a deeply conserved, rapid auxin response.
Cell. 187(1), 130–148.e17.
mla: Kuhn, Andre, et al. “RAF-like Protein Kinases Mediate a Deeply Conserved, Rapid
Auxin Response.” Cell, vol. 187, no. 1, Elsevier, 2024, p. 130–148.e17,
doi:10.1016/j.cell.2023.11.021.
short: A. Kuhn, M. Roosjen, S. Mutte, S.M. Dubey, V.P. Carrillo Carrasco, S. Boeren,
A. Monzer, J. Koehorst, T. Kohchi, R. Nishihama, M. Fendrych, J. Sprakel, J. Friml,
D. Weijers, Cell 187 (2024) 130–148.e17.
date_created: 2024-01-17T12:45:40Z
date_published: 2024-01-04T00:00:00Z
date_updated: 2026-08-14T09:33:45Z
day: '04'
ddc:
- '580'
department:
- _id: JiFr
doi: 10.1016/j.cell.2023.11.021
ec_funded: 1
external_id:
isi:
- '001152705700001'
pmid:
- '38128538'
file:
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checksum: 06fd236a9ee0b46ccb05f44695bfc34b
content_type: application/pdf
creator: dernst
date_created: 2024-01-22T13:41:41Z
date_updated: 2024-01-22T13:41:41Z
file_id: '14874'
file_name: 2024_Cell_Kuhn.pdf
file_size: 13194060
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success: 1
file_date_updated: 2024-01-22T13:41:41Z
has_accepted_license: '1'
intvolume: ' 187'
isi: 1
issue: '1'
keyword:
- General Biochemistry
- Genetics and Molecular Biology
language:
- iso: eng
license: https://creativecommons.org/licenses/by-nc/4.0/
month: '01'
oa: 1
oa_version: Published Version
page: 130-148.e17
pmid: 1
project:
- _id: 261099A6-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '742985'
name: Tracing Evolution of Auxin Transport and Polarity in Plants
- _id: 262EF96E-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: P29988
name: RNA-directed DNA methylation in plant development
publication: Cell
publication_identifier:
eissn:
- 1097-4172
issn:
- 0092-8674
publication_status: published
publisher: Elsevier
quality_controlled: '1'
related_material:
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relation: dissertation_contains
status: public
scopus_import: '1'
status: public
title: RAF-like protein kinases mediate a deeply conserved, rapid auxin response
tmp:
image: /images/cc_by_nc.png
legal_code_url: https://creativecommons.org/licenses/by-nc/4.0/legalcode
name: Creative Commons Attribution-NonCommercial 4.0 International (CC BY-NC 4.0)
short: CC BY-NC (4.0)
type: journal_article
user_id: 317138e5-6ab7-11ef-aa6d-ffef3953e345
volume: 187
year: '2024'
...
---
OA_place: repository
OA_type: green
_id: '18702'
abstract:
- lang: eng
text: 'In this work we prove lower bounds on the (communication) cost of maintaining
a shared key among a dynamic group of users. Being “dynamic” means one can add
and remove users from the group. This captures important protocols like multicast
encryption (ME) and continuous group-key agreement (CGKA), which is the primitive
underlying many group messaging applications. We prove our bounds in a combinatorial
setting where the state of the protocol progresses in rounds. The state of the
protocol in each round is captured by a set system, with each of its elements
specifying a set of users who share a secret key. We show this combinatorial model
implies bounds in symbolic models for ME and CGKA that capture, as building blocks,
PRGs, PRFs, dual PRFs, secret sharing, and symmetric encryption in the setting
of ME, and PRGs, PRFs, dual PRFs, secret sharing, public-key encryption, and key-updatable
public-key encryption in the setting of CGKA. The models are related to the ones
used by Micciancio and Panjwani (Eurocrypt’04) and Bienstock et al. (TCC’20) to
analyze ME and CGKA, respectively. We prove – using the Bollobás’ Set Pairs Inequality
– that the cost (number of uploaded ciphertexts) for replacing a set of d users
in a group of size n is Ω(dln(n/d)). Our lower bound is asymptotically tight and
both improves on a bound of Ω(d) by Bienstock et al. (TCC’20), and generalizes
a result by Micciancio and Panjwani (Eurocrypt’04), who proved a lower bound of
Ω(log(n)) for d=1. '
alternative_title:
- LNCS
article_processing_charge: No
author:
- first_name: Michael
full_name: Anastos, Michael
id: 0b2a4358-bb35-11ec-b7b9-e3279b593dbb
last_name: Anastos
- first_name: Benedikt
full_name: Auerbach, Benedikt
id: D33D2B18-E445-11E9-ABB7-15F4E5697425
last_name: Auerbach
orcid: 0000-0002-7553-6606
- first_name: Mirza Ahad
full_name: Baig, Mirza Ahad
id: 3EDE6DE4-AA5A-11E9-986D-341CE6697425
last_name: Baig
- first_name: Miguel
full_name: Cueto Noval, Miguel
id: ffc563a3-f6e0-11ea-865d-e3cce03d17cc
last_name: Cueto Noval
orcid: 0000-0002-2505-4246
- first_name: Matthew Alan
full_name: Kwan, Matthew Alan
id: 5fca0887-a1db-11eb-95d1-ca9d5e0453b3
last_name: Kwan
orcid: 0000-0002-4003-7567
- first_name: Guillermo
full_name: Pascual Perez, Guillermo
id: 2D7ABD02-F248-11E8-B48F-1D18A9856A87
last_name: Pascual Perez
orcid: 0000-0001-8630-415X
- first_name: Krzysztof Z
full_name: Pietrzak, Krzysztof Z
id: 3E04A7AA-F248-11E8-B48F-1D18A9856A87
last_name: Pietrzak
orcid: 0000-0002-9139-1654
citation:
ama: 'Anastos M, Auerbach B, Baig MA, et al. The cost of maintaining keys in dynamic
groups with applications to multicast encryption and group messaging. In: 22nd
International Conference on Theory of Cryptography. Vol 15364. Springer Nature;
2024:413-443. doi:10.1007/978-3-031-78011-0_14'
apa: 'Anastos, M., Auerbach, B., Baig, M. A., Cueto Noval, M., Kwan, M. A., Pascual
Perez, G., & Pietrzak, K. Z. (2024). The cost of maintaining keys in dynamic
groups with applications to multicast encryption and group messaging. In 22nd
International Conference on Theory of Cryptography (Vol. 15364, pp. 413–443).
Milan, Italy: Springer Nature. https://doi.org/10.1007/978-3-031-78011-0_14'
chicago: Anastos, Michael, Benedikt Auerbach, Mirza Ahad Baig, Miguel Cueto Noval,
Matthew Alan Kwan, Guillermo Pascual Perez, and Krzysztof Z Pietrzak. “The Cost
of Maintaining Keys in Dynamic Groups with Applications to Multicast Encryption
and Group Messaging.” In 22nd International Conference on Theory of Cryptography,
15364:413–43. Springer Nature, 2024. https://doi.org/10.1007/978-3-031-78011-0_14.
ieee: M. Anastos et al., “The cost of maintaining keys in dynamic groups
with applications to multicast encryption and group messaging,” in 22nd International
Conference on Theory of Cryptography, Milan, Italy, 2024, vol. 15364, pp.
413–443.
ista: 'Anastos M, Auerbach B, Baig MA, Cueto Noval M, Kwan MA, Pascual Perez G,
Pietrzak KZ. 2024. The cost of maintaining keys in dynamic groups with applications
to multicast encryption and group messaging. 22nd International Conference on
Theory of Cryptography. TCC: Theory of Cryptography, LNCS, vol. 15364, 413–443.'
mla: Anastos, Michael, et al. “The Cost of Maintaining Keys in Dynamic Groups with Applications
to Multicast Encryption and Group Messaging.” 22nd International Conference
on Theory of Cryptography, vol. 15364, Springer Nature, 2024, pp. 413–43,
doi:10.1007/978-3-031-78011-0_14.
short: M. Anastos, B. Auerbach, M.A. Baig, M. Cueto Noval, M.A. Kwan, G. Pascual
Perez, K.Z. Pietrzak, in:, 22nd International Conference on Theory of Cryptography,
Springer Nature, 2024, pp. 413–443.
conference:
end_date: 2024-12-06
location: Milan, Italy
name: 'TCC: Theory of Cryptography'
start_date: 2024-12-02
corr_author: '1'
date_created: 2024-12-22T23:01:47Z
date_published: 2024-12-02T00:00:00Z
date_updated: 2026-08-21T10:53:16Z
day: '02'
department:
- _id: MaKw
- _id: KrPi
doi: 10.1007/978-3-031-78011-0_14
external_id:
isi:
- '001545628900014'
intvolume: ' 15364'
isi: 1
language:
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main_file_link:
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url: https://eprint.iacr.org/2024/1097
month: '12'
oa: 1
oa_version: Preprint
page: 413-443
publication: 22nd International Conference on Theory of Cryptography
publication_identifier:
eissn:
- 1611-3349
isbn:
- '9783031780103'
issn:
- 0302-9743
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
related_material:
record:
- id: '22664'
relation: dissertation_contains
status: public
scopus_import: '1'
status: public
title: The cost of maintaining keys in dynamic groups with applications to multicast
encryption and group messaging
type: conference
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 15364
year: '2024'
...
---
_id: '17373'
abstract:
- lang: eng
text: Scanning Kelvin probe microscopy (SKPM) is a powerful technique for investigating
the electrostatic properties of material surfaces, enabling the imaging of variations
in work function, topology, surface charge density, or combinations thereof. Regardless
of the underlying signal source, SKPM results in a voltage image, which is spatially
distorted due to the finite size of the probe, long-range electrostatic interactions,
mechanical and electrical noise, and the finite response time of the electronics.
In order to recover the underlying signal, it is necessary to deconvolve the measurement
with an appropriate point spread function (PSF) that accounts the aforementioned
distortions, but determining this PSF is difficult. Here, we describe how such
PSFs can be determined experimentally and show how they can be used to recover
the underlying information of interest. We first consider the physical principles
that enable SKPM and discuss how these affect the system PSF. We then show how
one can experimentally measure PSFs by looking at well-defined features, and that
these compare well to simulated PSFs, provided scans are performed extremely slowly
and carefully. Next, we work at realistic scan speeds and show that the idealized
PSFs fail to capture temporal distortions in the scan direction. While simulating
PSFs for these situations would be quite challenging, we show that measuring PSFs
with similar scan conditions works well. Our approach clarifies the basic principles
and inherent challenges to SKPM measurements and gives practical methods to improve
results.
acknowledged_ssus:
- _id: M-Shop
- _id: NanoFab
- _id: LifeSc
- _id: ScienComp
acknowledgement: This project has received funding from the European Research Council
(ERC) under the European Union’s Horizon 2020 research and innovation program (Grant
Agreement No. 949120). This research was supported by the Scientific Service Units
of the Institute of Science and Technology Austria (ISTA) through resources provided
by the Miba Machine Shop, Nanofabrication Facility, Scientific Computing Facility,
and Lab Support Facility. The authors wish to thank Dmytro Rak and Juan Carlos Sobarzo
for letting us use their equipment. The authors wish to thank the contributions
of the whole Waitukaitis Group for useful discussions and feedback.
article_number: '045305'
article_processing_charge: No
article_type: original
author:
- first_name: Isaac C
full_name: Lenton, Isaac C
id: a550210f-223c-11ec-8182-e2d45e817efb
last_name: Lenton
orcid: 0000-0002-5010-6984
- first_name: Felix
full_name: Pertl, Felix
id: 6313aec0-15b2-11ec-abd3-ed67d16139af
last_name: Pertl
orcid: 0000-0003-0463-5794
- first_name: Lubuna B
full_name: Shafeek, Lubuna B
id: 3CD37A82-F248-11E8-B48F-1D18A9856A87
last_name: Shafeek
orcid: 0000-0001-7180-6050
- first_name: Scott R
full_name: Waitukaitis, Scott R
id: 3A1FFC16-F248-11E8-B48F-1D18A9856A87
last_name: Waitukaitis
orcid: 0000-0002-2299-3176
citation:
ama: 'Lenton IC, Pertl F, Shafeek LB, Waitukaitis SR. Beyond the blur: Using experimentally
determined point spread functions to improve scanning Kelvin probe imaging. Journal
of Applied Physics. 2024;136(4). doi:10.1063/5.0215151'
apa: 'Lenton, I. C., Pertl, F., Shafeek, L. B., & Waitukaitis, S. R. (2024).
Beyond the blur: Using experimentally determined point spread functions to improve
scanning Kelvin probe imaging. Journal of Applied Physics. AIP Publishing.
https://doi.org/10.1063/5.0215151'
chicago: 'Lenton, Isaac C, Felix Pertl, Lubuna B Shafeek, and Scott R Waitukaitis.
“Beyond the Blur: Using Experimentally Determined Point Spread Functions to Improve
Scanning Kelvin Probe Imaging.” Journal of Applied Physics. AIP Publishing,
2024. https://doi.org/10.1063/5.0215151.'
ieee: 'I. C. Lenton, F. Pertl, L. B. Shafeek, and S. R. Waitukaitis, “Beyond the
blur: Using experimentally determined point spread functions to improve scanning
Kelvin probe imaging,” Journal of Applied Physics, vol. 136, no. 4. AIP
Publishing, 2024.'
ista: 'Lenton IC, Pertl F, Shafeek LB, Waitukaitis SR. 2024. Beyond the blur: Using
experimentally determined point spread functions to improve scanning Kelvin probe
imaging. Journal of Applied Physics. 136(4), 045305.'
mla: 'Lenton, Isaac C., et al. “Beyond the Blur: Using Experimentally Determined
Point Spread Functions to Improve Scanning Kelvin Probe Imaging.” Journal of
Applied Physics, vol. 136, no. 4, 045305, AIP Publishing, 2024, doi:10.1063/5.0215151.'
short: I.C. Lenton, F. Pertl, L.B. Shafeek, S.R. Waitukaitis, Journal of Applied
Physics 136 (2024).
corr_author: '1'
date_created: 2024-08-04T22:01:21Z
date_published: 2024-07-28T00:00:00Z
date_updated: 2026-08-27T11:42:44Z
day: '28'
ddc:
- '530'
department:
- _id: ScWa
- _id: NanoFab
doi: 10.1063/5.0215151
ec_funded: 1
external_id:
isi:
- '001281681100003'
file:
- access_level: open_access
checksum: 6141d05cd68d540a7446dce9490975db
content_type: application/pdf
creator: dernst
date_created: 2024-08-05T08:19:58Z
date_updated: 2024-08-05T08:19:58Z
file_id: '17386'
file_name: 2024_JourApplPhysics_Lenton.pdf
file_size: 2537502
relation: main_file
success: 1
file_date_updated: 2024-08-05T08:19:58Z
has_accepted_license: '1'
intvolume: ' 136'
isi: 1
issue: '4'
language:
- iso: eng
license: https://creativecommons.org/licenses/by-nc-nd/4.0/
month: '07'
oa: 1
oa_version: Published Version
project:
- _id: 0aa60e99-070f-11eb-9043-a6de6bdc3afa
call_identifier: H2020
grant_number: '949120'
name: 'Tribocharge: a multi-scale approach to an enduring problem in physics'
publication: Journal of Applied Physics
publication_identifier:
eissn:
- 1089-7550
issn:
- 0021-8979
publication_status: published
publisher: AIP Publishing
quality_controlled: '1'
related_material:
record:
- id: '22684'
relation: dissertation_contains
status: public
scopus_import: '1'
status: public
title: 'Beyond the blur: Using experimentally determined point spread functions to
improve scanning Kelvin probe imaging'
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: 136
year: '2024'
...
---
_id: '17425'
abstract:
- lang: eng
text: Mosaic Analysis with Double Markers (MADM) is a powerful genetic method typically
used for lineage tracing and to disentangle cell autonomous and tissue-wide roles
of candidate genes with single cell resolution. Given the relatively sparse labeling,
depending on which of the 19 MADM chromosomes one chooses, the MADM approach represents
the perfect opportunity for cell morphology analysis. Various MADM studies include
reports of morphological anomalies and phenotypes in the central nervous system
(CNS). MADM for any candidate gene can easily incorporate morphological analysis
within the experimental workflow. Here, we describe the methods of morphological
cell analysis which we developed in the course of diverse recent MADM studies.
This chapter will specifically focus on methods to quantify aspects of the morphology
of neurons and astrocytes within the CNS, but these methods can broadly be applied
to any MADM-labeled cells throughout the entire organism. We will cover two analyses—soma
volume and dendrite characterization—of physical characteristics of pyramidal
neurons in the somatosensory cortex, and two analyses—volume and Sholl analysis—of
astrocyte morphology.
acknowledged_ssus:
- _id: Bio
acknowledgement: We thank all Hippenmeyer lab members for support and discussions.
This work was supported by the Scientific Service Units (SSU) at ISTA through resources
provided by the Imaging & Optics Facility (IOF). O.A.M was a recipient of a DOC
Fellowship (26253) of the Austrian Academy of Sciences. This work was supported
by ISTA institutional funds, and The Austrian Science Fund Special Research Programmes
(FWF SFB F78 Neuro Stem Modulation) to S.H.
alternative_title:
- Methods in Molecular Biology
article_processing_charge: No
author:
- first_name: Osvaldo
full_name: Miranda, Osvaldo
id: 862A3C56-A8BF-11E9-B4FA-D9E3E5697425
last_name: Miranda
orcid: 0000-0001-6618-6889
- first_name: Giselle T
full_name: Cheung, Giselle T
id: 471195F6-F248-11E8-B48F-1D18A9856A87
last_name: Cheung
orcid: 0000-0001-8457-2572
- first_name: Simon
full_name: Hippenmeyer, Simon
id: 37B36620-F248-11E8-B48F-1D18A9856A87
last_name: Hippenmeyer
orcid: 0000-0003-2279-1061
citation:
ama: 'Miranda O, Cheung GT, Hippenmeyer S. Morphological Analysis of Neurons and
Glia Using Mosaic Analysis with Double Markers. In: Toyooka K, ed. Neuronal
Morphogenesis. Vol 2831. 1st ed. MIMB. New York, NY: Springer Nature; 2024:283-299.
doi:10.1007/978-1-0716-3969-6_19'
apa: 'Miranda, O., Cheung, G. T., & Hippenmeyer, S. (2024). Morphological Analysis
of Neurons and Glia Using Mosaic Analysis with Double Markers. In K. Toyooka (Ed.),
Neuronal Morphogenesis (1st ed., Vol. 2831, pp. 283–299). New York, NY:
Springer Nature. https://doi.org/10.1007/978-1-0716-3969-6_19'
chicago: 'Miranda, Osvaldo, Giselle T Cheung, and Simon Hippenmeyer. “Morphological
Analysis of Neurons and Glia Using Mosaic Analysis with Double Markers.” In Neuronal
Morphogenesis, edited by Kazuhito Toyooka, 1st ed., 2831:283–99. MIMB. New
York, NY: Springer Nature, 2024. https://doi.org/10.1007/978-1-0716-3969-6_19.'
ieee: 'O. Miranda, G. T. Cheung, and S. Hippenmeyer, “Morphological Analysis of
Neurons and Glia Using Mosaic Analysis with Double Markers,” in Neuronal Morphogenesis,
1st ed., vol. 2831, K. Toyooka, Ed. New York, NY: Springer Nature, 2024, pp. 283–299.'
ista: 'Miranda O, Cheung GT, Hippenmeyer S. 2024.Morphological Analysis of Neurons
and Glia Using Mosaic Analysis with Double Markers. In: Neuronal Morphogenesis.
Methods in Molecular Biology, vol. 2831, 283–299.'
mla: Miranda, Osvaldo, et al. “Morphological Analysis of Neurons and Glia Using
Mosaic Analysis with Double Markers.” Neuronal Morphogenesis, edited by
Kazuhito Toyooka, 1st ed., vol. 2831, Springer Nature, 2024, pp. 283–99, doi:10.1007/978-1-0716-3969-6_19.
short: O. Miranda, G.T. Cheung, S. Hippenmeyer, in:, K. Toyooka (Ed.), Neuronal
Morphogenesis, 1st ed., Springer Nature, New York, NY, 2024, pp. 283–299.
corr_author: '1'
date_created: 2024-08-13T12:16:41Z
date_published: 2024-08-13T00:00:00Z
date_updated: 2026-08-29T22:30:06Z
day: '13'
department:
- _id: GradSch
- _id: SiHi
doi: 10.1007/978-1-0716-3969-6_19
edition: '1'
editor:
- first_name: Kazuhito
full_name: Toyooka, Kazuhito
last_name: Toyooka
external_id:
pmid:
- '39134857'
intvolume: ' 2831'
language:
- iso: eng
month: '08'
oa_version: None
page: 283-299
place: New York, NY
pmid: 1
project:
- _id: 34c9fbcb-11ca-11ed-8bc3-98fa5658610d
grant_number: '26253'
name: Molecular Mechanisms Regulating Cortical Neural Stem Cell Lineage Progression
and Astrocyte Development
- _id: 059F6AB4-7A3F-11EA-A408-12923DDC885E
grant_number: F7805
name: Stem Cell Modulation in Neural Development and Regeneration/ P05-Molecular
Mechanisms of Neural Stem Cell Lineage Progression
publication: Neuronal Morphogenesis
publication_identifier:
eisbn:
- '9781071639696'
eissn:
- 1940-6029
isbn:
- '9781071639689'
issn:
- 1064-3745
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
related_material:
record:
- id: '20212'
relation: dissertation_contains
status: public
scopus_import: '1'
series_title: MIMB
status: public
title: Morphological Analysis of Neurons and Glia Using Mosaic Analysis with Double
Markers
type: book_chapter
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 2831
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
file_id: '17482'
file_name: thesis_a2b.pdf
file_size: 4468610
relation: main_file
- access_level: closed
checksum: 76a39ef252239560923cdda4ce0a31a4
content_type: application/zip
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'
...
---
_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: 2026-08-29T22:30:17Z
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: 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:
- _id: GradSch
- _id: AnHi
doi: 10.15479/at:ista:17881
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date_updated: 2025-03-13T23:30:04Z
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file_name: PhD_Thesis_Soham_Mukhopadhyay_source.zip
file_size: 29178634
relation: source_file
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has_accepted_license: '1'
language:
- iso: eng
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'
...
---
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: 2026-08-29T22:30:18Z
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:
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relation: dissertation_contains
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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: 2026-08-29T22:30:30Z
day: '30'
ddc:
- '570'
department:
- _id: BeVi
doi: 10.1371/journal.pgen.1011376
external_id:
isi:
- '001304090200001'
pmid:
- '39213449'
file:
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checksum: f5d96b9af57126fc1063e951440477d6
content_type: application/pdf
creator: dernst
date_created: 2024-09-11T07:54:12Z
date_updated: 2024-09-11T07:54:12Z
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file_name: 2024_PloSGenetics_Elkrewi.pdf
file_size: 8962687
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file_date_updated: 2024-09-11T07:54:12Z
has_accepted_license: '1'
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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'
...
---
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
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content_type: application/zip
creator: rkelemen
date_created: 2024-06-07T16:09:17Z
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file_size: 180557931
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date_updated: 2025-01-10T23:30:10Z
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file_id: '17213'
file_name: thesis_to_archive.pdf
file_size: 19405484
relation: main_file
file_date_updated: 2025-01-10T23:30:10Z
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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:
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issn:
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publication_status: published
publisher: Institute of Science and Technology Austria
related_material:
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status: public
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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
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has_accepted_license: '1'
language:
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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
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creator: cchlebak
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date_updated: 2025-05-02T22:30:04Z
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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
_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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date_created: 2024-01-19T11:04:05Z
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date_updated: 2025-01-19T23:30:04Z
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language:
- iso: eng
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
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
date_updated: 2026-08-29T22:30:33Z
day: '06'
ddc:
- '570'
department:
- _id: PeJo
- _id: EM-Fac
- _id: RySh
doi: 10.1016/j.neuron.2023.12.002
ec_funded: 1
external_id:
isi:
- '001202925700001'
pmid:
- '38215739'
file:
- access_level: open_access
checksum: 30098b4f0209556ddfb3540a23d07ca5
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creator: dernst
date_created: 2025-04-23T14:02:08Z
date_updated: 2025-04-23T14:02:08Z
file_id: '19614'
file_name: 2024_Neuron_Chen.pdf
file_size: 8192355
relation: main_file
success: 1
file_date_updated: 2025-04-23T14:02:08Z
has_accepted_license: '1'
intvolume: ' 112'
isi: 1
issue: '5'
language:
- iso: eng
month: '03'
oa: 1
oa_version: Published Version
page: 755-771.e9
pmid: 1
project:
- _id: 25B7EB9E-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '692692'
name: Biophysics and circuit function of a giant cortical glutamatergic synapse
- _id: 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: 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
relation: press_release
url: https://ista.ac.at/en/news/synapses-brought-to-the-point/
record:
- id: '15101'
relation: dissertation_contains
status: public
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'
...