---
OA_place: publisher
_id: '17156'
abstract:
- lang: eng
text: "This dissertation is the summary of the author’s work, concerning the relations
between\r\ncohomology rings of algebraic varieties and rings of functions on zero
schemes and fixed\r\npoint schemes. For most of the thesis, the focus is on smooth
complex varieties with\r\nan action of a principally paired group, e.g. a parabolic
subgroup of a reductive group.\r\nThe fundamental theorem 5.2.11 from co-authored
article [66] says that if the principal\r\nnilpotent has a unique zero, then the
zero scheme over the Kostant section is isomorphic\r\nto the spectrum of the equivariant
cohomology ring, remembering the grading in terms of\r\na C^* action. A similar
statement is proved also for the G-invariant functions on the total\r\nzero scheme
over the whole Lie algebra. Additionally, we are able to prove an analogous\r\nresult
for the GKM spaces, which poses the question on a joint generalisation.\r\nWe
also tackle the situation of a singular variety. As long as it is embedded in
a smooth\r\nvariety with regular action, we are able to study its cohomology as
well by means of\r\nthe zero scheme. In case of e.g. Schubert varieties this determines
the cohomology ring\r\ncompletely. In largest generality, this allows us to see
a significant part of the cohomology\r\nring.\r\nWe also show (Theorem 6.2.1)
that the cohomology ring of spherical varieties appears as\r\nthe ring of functions
on the zero scheme. The computational aspect is not easy, but one\r\ncan hope
that this can bring some concrete information about such cohomology rings.\r\nLastly,
the K-theory conjecture 6.3.1 is studied, with some results attained for GKM\r\nspaces.\r\nThe
thesis includes also an introduction to group actions on algebraic varieties.
In\r\nparticular, the vector fields associated to the actions are extensively
studied. We also\r\nprovide a version of the Kostant section for arbitrary principally
paired group, which\r\nparametrises the regular orbits in the Lie algebra of an
algebraic group. Before proving\r\nthe main theorem, we also include a historical
overview of the field. In particular we bring\r\ntogether the results of Akyildiz,
Carrell and Lieberman on non-equivariant cohomology\r\nrings."
alternative_title:
- ISTA Thesis
article_processing_charge: No
author:
- first_name: Kamil P
full_name: Rychlewicz, Kamil P
id: 85A07246-A8BF-11E9-B4FA-D9E3E5697425
last_name: Rychlewicz
citation:
ama: Rychlewicz KP. Equivariant cohomology and rings of functions. 2024. doi:10.15479/at:ista:17156
apa: Rychlewicz, K. P. (2024). Equivariant cohomology and rings of functions.
Institute of Science and Technology Austria. https://doi.org/10.15479/at:ista:17156
chicago: Rychlewicz, Kamil P. “Equivariant Cohomology and Rings of Functions.” Institute
of Science and Technology Austria, 2024. https://doi.org/10.15479/at:ista:17156.
ieee: K. P. Rychlewicz, “Equivariant cohomology and rings of functions,” Institute
of Science and Technology Austria, 2024.
ista: Rychlewicz KP. 2024. Equivariant cohomology and rings of functions. Institute
of Science and Technology Austria.
mla: Rychlewicz, Kamil P. Equivariant Cohomology and Rings of Functions.
Institute of Science and Technology Austria, 2024, doi:10.15479/at:ista:17156.
short: K.P. Rychlewicz, Equivariant Cohomology and Rings of Functions, Institute
of Science and Technology Austria, 2024.
corr_author: '1'
date_created: 2024-06-23T15:07:06Z
date_published: 2024-06-25T00:00:00Z
date_updated: 2026-04-07T12:55:46Z
day: '25'
ddc:
- '516'
degree_awarded: PhD
department:
- _id: TaHa
- _id: GradSch
doi: 10.15479/at:ista:17156
file:
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checksum: 1610063569f5452f8a5acef728c2fc26
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date_updated: 2024-06-26T21:00:14Z
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creator: krychlew
date_created: 2024-06-26T20:58:24Z
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file_size: 3695952
relation: main_file
file_date_updated: 2024-06-26T21:00:14Z
has_accepted_license: '1'
keyword:
- equivariant cohomology
- zero schemes
- algebraic groups
- Lie algebras
language:
- iso: eng
license: https://creativecommons.org/licenses/by-nc-sa/4.0/
month: '06'
oa: 1
oa_version: Published Version
page: '117'
project:
- _id: 34cd0f74-11ca-11ed-8bc3-bf0492a14a24
grant_number: '26525'
name: Topology of open smooth varieties with a torus action
publication_identifier:
issn:
- 2663-337X
publication_status: published
publisher: Institute of Science and Technology Austria
related_material:
record:
- id: '17157'
relation: part_of_dissertation
status: public
status: public
supervisor:
- first_name: Tamás
full_name: Hausel, Tamás
id: 4A0666D8-F248-11E8-B48F-1D18A9856A87
last_name: Hausel
orcid: 0000-0002-9582-2634
title: Equivariant cohomology and rings of functions
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
OA_type: gold
_id: '18515'
abstract:
- lang: eng
text: "Understanding the role of evolutionary processes in shaping genetic variation
has been a\r\nprimary goal in evolutionary genetics. In this regard, a key question
is how genetically\r\ndistinct populations evolve in the face of gene flow, thereby
generating genetic and\r\nphenotypic divergence and reproductive isolation (RI).
This requires quantifying the role\r\nand relative contributions of prezygotic
and postzygotic isolating mechanisms on the\r\nreduction of gene exchange between
populations, and identifying regions in the genome\r\nthat mediate RI, which is
often polygenic. Further, this needs distinguishing neutral and\r\nselected regions
in the genome, and discerning how selection influences patterns of neutral\r\ndivergence.\r\nPopulation
structure, defined as any deviation from panmixia, such as geographic distribution,
movement and mating patterns of individuals, influences how genetic variation
is\r\nstructured in space and shapes the neutral null model. Availability of large
scale spatial\r\ngenomic datasets now enables us to detect signatures of population
structure in genetic\r\ndata and infer population genetic parameters. Such inferences
are crucial and have wide\r\napplications in biodiversity, conservation genetics,
population management and medical\r\ngenetics. However, inferences are based on
assumptions that do not always match the\r\ncomplex reality, thus leading to erroneous
conclusions. Moreover, the role and interaction\r\nof heterogeneous population
density and dispersal, which are ubiquitous in nature, has\r\nbeen challenging
to study owing to their mathematical complexity. In such scenarios,\r\nfeedback
between theory, data and simulations can prove to be useful.\r\nIn this thesis,
I examine the effect of population structure on neutral genetic variation\r\nand
barriers to gene exchange in hybridising populations, thereby bridging together
the\r\nfields of spatial population genetics and speciation.\r\nDespite being
a key concept in speciation, reproductive isolation (RI) lacks a quantitative\r\ndefinition
and has been used and measured differently across different fields. Chapter 2\r\ngives
a quantitative definition of RI, in terms of the effect of genetic differences
on gene\r\nflow. We give analytical predictions for RI in a range of scenarios,
in terms of effective migration rates for discrete populations and barrier strength
for continuous populations.\r\nIn addition to this, we discuss current measures
of RI and their limitations, and propose\r\nthe need for new measures that combine
organismal and genetic perspectives of RI.\r\nIn chapter 3, I examine the combined
effect of assortative mating, sexual selection\r\nand viability selection on RI.
For this, we consider a polygenic ‘magic’ trait under a\r\nmainland-island model.
We obtain novel theoretical predictions for molecular divergence\r\nin terms of
effective migration rates, which bears a simple relationship to measurable\r\nfitness
components of migrants and various early generation hybrids. We explore the\r\nconditions
under which local adaptation can be maintained despite maladaptive gene flow\r\nand
quantify the relative contributions of viability and sexual selection to genome-wide\r\nbarriers
to gene flow.\r\nThe next two chapters of the thesis focus on a hybrid zone of
Antirrhinum majus that\r\nconsist of two subspecies- the magenta flowered A. m.
pseudomajus and the yellow\r\nflowered A.m. striatum. Previous studies have suggested
that flower colour is target of\r\npollinator mediated selection and is influenced
only by few genes. While these regions\r\nshow high genetic differentiation between
the subspecies, the rest of the genome is seen\r\nto be well mixed. Chapter 4
examines the effects of heterogeneous population density\r\nand leptokurtic dispersal
on isolation by distance and the distribution of heterozygosity\r\nby focusing
on non-flower colour markers.\r\nChapter 5 analyses cline shapes and associations
among 6 focal flower colour markers to\r\nunderstand how selection and dispersal
maintain this hybrid zone. We see sharp coincident\r\nstepped clines at all loci
and positive associations throughout the hybrid zone, contrary to\r\nthe expected
patterns from diffusive gene flow. With a novel scheme of inferring dispersal\r\ncombined
with multilocus simulations, we show that stepped clines do not reflect genetic\r\nbarriers
to gene flow, but are rather a result of long-distance migration. This framework\r\nallows
us to get realistic estimates gene flow and selection and shows how traditional
cline\r\nanalysis may lead to inaccurate conclusions when assumptions of the theory
are not met.\r\nOverall, this thesis investigates how different features of population
structure leave\r\ndetectable signatures in genetic variation, namely in patterns
of isolation by distance,\r\nlinkage disequilibrium and genetic divergence. It
also highlights how effective migration\r\nrates provide useful way of analysing
polygenic architectures and shed new light into\r\nhybrid zones. In doing so,
I identify scenarios when simple models become insufficient\r\nand suggest possibe
directions by combining genetic data with simulations."
acknowledged_ssus:
- _id: ScienComp
acknowledgement: "I also acknowledge the funding agencies Marie Curie COFUND Doctoral
Fellowship,\r\nAustrian Science Fund FWF (grant P32166) and ERC (grant PR1000ERC02)
for financially\r\nsupporting my research over the years."
alternative_title:
- ISTA Thesis
article_processing_charge: No
author:
- first_name: Parvathy
full_name: Surendranadh, Parvathy
id: 455235B8-F248-11E8-B48F-1D18A9856A87
last_name: Surendranadh
orcid: 0000-0001-6395-386X
citation:
ama: Surendranadh P. Effect of population structure on neutral genetic variation
and barriers to gene exchange. 2024. doi:10.15479/at:ista:18515
apa: Surendranadh, P. (2024). Effect of population structure on neutral genetic
variation and barriers to gene exchange. Institute of Science and Technology
Austria. https://doi.org/10.15479/at:ista:18515
chicago: Surendranadh, Parvathy. “Effect of Population Structure on Neutral Genetic
Variation and Barriers to Gene Exchange.” Institute of Science and Technology
Austria, 2024. https://doi.org/10.15479/at:ista:18515.
ieee: P. Surendranadh, “Effect of population structure on neutral genetic variation
and barriers to gene exchange,” Institute of Science and Technology Austria, 2024.
ista: Surendranadh P. 2024. Effect of population structure on neutral genetic variation
and barriers to gene exchange. Institute of Science and Technology Austria.
mla: Surendranadh, Parvathy. Effect of Population Structure on Neutral Genetic
Variation and Barriers to Gene Exchange. Institute of Science and Technology
Austria, 2024, doi:10.15479/at:ista:18515.
short: P. Surendranadh, Effect of Population Structure on Neutral Genetic Variation
and Barriers to Gene Exchange, Institute of Science and Technology Austria, 2024.
corr_author: '1'
date_created: 2024-11-06T21:25:37Z
date_published: 2024-11-07T00:00:00Z
date_updated: 2026-04-07T12:56:52Z
day: '07'
ddc:
- '576'
degree_awarded: PhD
department:
- _id: GradSch
- _id: NiBa
doi: 10.15479/at:ista:18515
file:
- access_level: open_access
checksum: c32cf7bc75748d9c551d8eb70178bbec
content_type: application/pdf
creator: psurendr
date_created: 2024-11-07T10:59:29Z
date_updated: 2024-11-07T10:59:29Z
file_id: '18519'
file_name: PhD_Thesis__Parvathy_071124_PDFA.pdf
file_size: 37019760
relation: main_file
success: 1
- access_level: closed
checksum: 4417e02d54084d89e75734e18caaa96d
content_type: application/zip
creator: psurendr
date_created: 2024-11-07T10:59:42Z
date_updated: 2024-11-07T10:59:42Z
file_id: '18520'
file_name: PhD Thesis- Parvathy_071124.zip
file_size: 41198857
relation: source_file
file_date_updated: 2024-11-07T10:59:42Z
has_accepted_license: '1'
language:
- iso: eng
month: '11'
oa: 1
oa_version: Published Version
page: '219'
project:
- _id: 05959E1C-7A3F-11EA-A408-12923DDC885E
grant_number: P32166
name: Snapdragon Speciation
- _id: bd6958e0-d553-11ed-ba76-86eba6a76c00
grant_number: '101055327'
name: Understanding the evolution of continuous genomes
publication_identifier:
issn:
- 2663-337X
publication_status: published
publisher: Institute of Science and Technology Austria
status: public
supervisor:
- first_name: Nicholas H
full_name: Barton, Nicholas H
id: 4880FE40-F248-11E8-B48F-1D18A9856A87
last_name: Barton
orcid: 0000-0002-8548-5240
title: Effect of population structure on neutral genetic variation and barriers to
gene exchange
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: repository
_id: '18689'
abstract:
- lang: eng
text: Multiplexed fluorescence microscopy imaging is widely used in biomedical applications.
However, simultaneous imaging of multiple fluorophores can result in spectral
leaks and overlapping, which greatly degrades image quality and subsequent analysis.
Existing popular spectral unmixing methods are mainly based on computational intensive
linear models and the performance is heavily dependent on the reference spectra,
which may greatly preclude its further applications. In this paper, we propose
a deep learning-based blindly spectral unmixing method, termed AutoUnmix, to imitate
the physical spectral mixing process. A tranfer learning framework is further
devised to allow our AutoUnmix adapting to a variety of imaging systems without
retraining the network. Our proposed method has demonstrated real-time unmixing
capabilities, surpassing existing methods by up to 100-fold in terms of unmixing
speed. We further validate the reconstruction performance on both synthetic datasets
and biological samples. The unmixing results of AutoUnmix achieve a highest SSIM
of 0.99 in both three- and four-color imaging, with nearly up to 20% higher than
other popular unmixing methods. Due to the desirable property of data independency
and superior blind unmixing performance, we believe AutoUnmix is a powerful tool
to study the interaction process of different organelles labeled by multiple fluorophores.
acknowledged_ssus:
- _id: Bio
- _id: LifeSc
- _id: M-Shop
- _id: E-Lib
acknowledgement: "We gratefully acknowledge support by the Scientific Service Units
at ISTA, including the Imaging and Optics and Lab Support facilities and the mechanical
workshop and Library. We thank Philipp Velicky for STED microscope alignment.\r\n\r\nThis
project has received funding from the Austrian Science Fund (FWF): I 3630-B25 (J.G.D)
and the European Research Council (ERC) under the European Union’s Horizon 2020
research and innovation programme (grant agreement No 742985, J.F.). It has also
received funding from the European Union’s Horizon 2020 research and innovation
programme under the Marie Skłodowska-Curie Grant Agreement No. 665385. S.T. has
received funding as an ISTplus Fellow from the European Union’s Horizon 2020 Research
and Innovation Programme under Marie Skłodowska-Curie grant agreement no. 754411
and from an EMBO Long-Term Fellowship (grant number ALTF 679-2018). It has further
received funding from the Austrian Science Fund (FWF) grant DK W1232 (M.T, N.A-D.,
J.G.D). W.J. received funding via a Human Frontier Science Program postdoctoral
fellowship LT000557/2018.\r\n\r\nThe funders had no role in study design, data collection
and analysis, decision to publish or preparation of the manuscript."
article_processing_charge: No
author:
- first_name: Michelle C
full_name: Gallei, Michelle C
id: 35A03822-F248-11E8-B48F-1D18A9856A87
last_name: Gallei
orcid: 0000-0003-1286-7368
- first_name: Sven M
full_name: Truckenbrodt, Sven M
id: 45812BD4-F248-11E8-B48F-1D18A9856A87
last_name: Truckenbrodt
- first_name: Caroline
full_name: Kreuzinger, Caroline
id: 382077BA-F248-11E8-B48F-1D18A9856A87
last_name: Kreuzinger
- first_name: Syamala
full_name: Inumella, Syamala
id: F8660870-D756-11E9-98C5-34DFE5697425
last_name: Inumella
orcid: 0009-0002-5890-120X
- first_name: Vitali
full_name: Vistunou, Vitali
id: 7e146587-8972-11ed-ae7b-d7a32ea86a81
last_name: Vistunou
- first_name: Christoph M
full_name: Sommer, Christoph M
id: 4DF26D8C-F248-11E8-B48F-1D18A9856A87
last_name: Sommer
orcid: 0000-0003-1216-9105
- first_name: Mojtaba
full_name: Tavakoli, Mojtaba
id: 3A0A06F4-F248-11E8-B48F-1D18A9856A87
last_name: Tavakoli
orcid: 0000-0002-7667-6854
- first_name: Nathalie
full_name: Agudelo Duenas, Nathalie
id: 40E7F008-F248-11E8-B48F-1D18A9856A87
last_name: Agudelo Duenas
- first_name: Jakob
full_name: Vorlaufer, Jakob
id: 937696FA-C996-11E9-8C7C-CF13E6697425
last_name: Vorlaufer
orcid: 0009-0000-7590-3501
- first_name: Wiebke
full_name: Jahr, Wiebke
id: 425C1CE8-F248-11E8-B48F-1D18A9856A87
last_name: Jahr
orcid: 0000-0003-0201-2315
- first_name: Marek
full_name: Randuch, Marek
id: 6ac4636d-15b2-11ec-abd3-fb8df79972ae
last_name: Randuch
- first_name: Alexander J
full_name: Johnson, Alexander J
id: 46A62C3A-F248-11E8-B48F-1D18A9856A87
last_name: Johnson
orcid: 0000-0002-2739-8843
- first_name: Eva
full_name: Benková, Eva
id: 38F4F166-F248-11E8-B48F-1D18A9856A87
last_name: Benková
orcid: 0000-0002-8510-9739
- first_name: Jiří
full_name: Friml, Jiří
id: 4159519E-F248-11E8-B48F-1D18A9856A87
last_name: Friml
orcid: 0000-0002-8302-7596
- first_name: Johann G
full_name: Danzl, Johann G
id: 42EFD3B6-F248-11E8-B48F-1D18A9856A87
last_name: Danzl
orcid: 0000-0001-8559-3973
citation:
ama: Gallei MC, Truckenbrodt SM, Kreuzinger C, et al. Super-resolution expansion
microscopy in plant roots. bioRxiv. doi:10.1101/2024.02.21.581330
apa: Gallei, M. C., Truckenbrodt, S. M., Kreuzinger, C., Inumella, S., Vistunou,
V., Sommer, C. M., … Danzl, J. G. (n.d.). Super-resolution expansion microscopy
in plant roots. bioRxiv. https://doi.org/10.1101/2024.02.21.581330
chicago: Gallei, Michelle C, Sven M Truckenbrodt, Caroline Kreuzinger, Syamala Inumella,
Vitali Vistunou, Christoph M Sommer, Mojtaba Tavakoli, et al. “Super-Resolution
Expansion Microscopy in Plant Roots.” BioRxiv, n.d. https://doi.org/10.1101/2024.02.21.581330.
ieee: M. C. Gallei et al., “Super-resolution expansion microscopy in plant
roots,” bioRxiv. .
ista: Gallei MC, Truckenbrodt SM, Kreuzinger C, Inumella S, Vistunou V, Sommer CM,
Tavakoli M, Agudelo Duenas N, Vorlaufer J, Jahr W, Randuch M, Johnson AJ, Benková
E, Friml J, Danzl JG. Super-resolution expansion microscopy in plant roots. bioRxiv,
10.1101/2024.02.21.581330.
mla: Gallei, Michelle C., et al. “Super-Resolution Expansion Microscopy in Plant
Roots.” BioRxiv, doi:10.1101/2024.02.21.581330.
short: M.C. Gallei, S.M. Truckenbrodt, C. Kreuzinger, S. Inumella, V. Vistunou,
C.M. Sommer, M. Tavakoli, N. Agudelo Duenas, J. Vorlaufer, W. Jahr, M. Randuch,
A.J. Johnson, E. Benková, J. Friml, J.G. Danzl, BioRxiv (n.d.).
corr_author: '1'
date_created: 2024-12-19T12:28:00Z
date_published: 2024-02-21T00:00:00Z
date_updated: 2026-04-07T12:56:36Z
day: '21'
department:
- _id: EvBe
- _id: JoDa
- _id: JiFr
doi: 10.1101/2024.02.21.581330
ec_funded: 1
language:
- iso: eng
license: https://creativecommons.org/licenses/by-nc/4.0/
main_file_link:
- open_access: '1'
url: https://doi.org/10.1101/2024.02.21.581330
month: '02'
oa: 1
oa_version: Preprint
project:
- _id: 261099A6-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '742985'
name: Tracing Evolution of Auxin Transport and Polarity in Plants
- _id: 2564DBCA-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '665385'
name: International IST Doctoral Program
- _id: 260C2330-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '754411'
name: ISTplus - Postdoctoral Fellowships
- _id: 26AA4EF2-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: W1232-B24
name: Molecular Drug Targets
- _id: 269B5B22-B435-11E9-9278-68D0E5697425
grant_number: ALTF 679-2018
name: UltraX - achieving sub-nanometer resolution in light microscopy using iterative
X10 microscopy in combination with nanobodies and STED
publication: bioRxiv
publication_status: draft
related_material:
record:
- id: '19003'
relation: later_version
status: public
- id: '18681'
relation: dissertation_contains
status: public
status: public
title: Super-resolution expansion microscopy in plant roots
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: preprint
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
year: '2024'
...
---
OA_embargo: '20'
OA_place: publisher
_id: '18681'
acknowledged_ssus:
- _id: Bio
- _id: PreCl
- _id: LifeSc
alternative_title:
- ISTA Thesis
article_processing_charge: No
author:
- first_name: Mojtaba
full_name: Tavakoli, Mojtaba
id: 3A0A06F4-F248-11E8-B48F-1D18A9856A87
last_name: Tavakoli
orcid: 0000-0002-7667-6854
citation:
ama: 'Tavakoli M. Developing molecular and structural tools for studying brain architecture
with super resolution expansion microscopy. LICONN: Molecularly-informed connectomics
reconstruction with light microscopy. 2024. doi:10.15479/at:ista:18681'
apa: 'Tavakoli, M. (2024). Developing molecular and structural tools for studying
brain architecture with super resolution expansion microscopy. LICONN: Molecularly-informed
connectomics reconstruction with light microscopy. Institute of Science and
Technology Austria. https://doi.org/10.15479/at:ista:18681'
chicago: 'Tavakoli, Mojtaba. “Developing Molecular and Structural Tools for Studying
Brain Architecture with Super Resolution Expansion Microscopy. LICONN: Molecularly-Informed
Connectomics Reconstruction with Light Microscopy.” Institute of Science and Technology
Austria, 2024. https://doi.org/10.15479/at:ista:18681.'
ieee: 'M. Tavakoli, “Developing molecular and structural tools for studying brain
architecture with super resolution expansion microscopy. LICONN: Molecularly-informed
connectomics reconstruction with light microscopy,” Institute of Science and Technology
Austria, 2024.'
ista: 'Tavakoli M. 2024. Developing molecular and structural tools for studying
brain architecture with super resolution expansion microscopy. LICONN: Molecularly-informed
connectomics reconstruction with light microscopy. Institute of Science and Technology
Austria.'
mla: 'Tavakoli, Mojtaba. Developing Molecular and Structural Tools for Studying
Brain Architecture with Super Resolution Expansion Microscopy. LICONN: Molecularly-Informed
Connectomics Reconstruction with Light Microscopy. Institute of Science and
Technology Austria, 2024, doi:10.15479/at:ista:18681.'
short: 'M. Tavakoli, Developing Molecular and Structural Tools for Studying Brain
Architecture with Super Resolution Expansion Microscopy. LICONN: Molecularly-Informed
Connectomics Reconstruction with Light Microscopy, Institute of Science and Technology
Austria, 2024.'
corr_author: '1'
date_created: 2024-12-19T02:30:39Z
date_published: 2024-12-20T00:00:00Z
date_updated: 2026-04-07T12:56:37Z
day: '20'
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oa_version: Published Version
page: '230'
project:
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grant_number: '26137'
name: Studying Organelle Structure and Function at Nanoscale Resolution with Expansion
Microscopy
- _id: 26AA4EF2-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: W1232-B24
name: Molecular Drug Targets
publication_identifier:
isbn:
- 978-3-99078-048-0
issn:
- 2663-337X
publication_status: published
publisher: Institute of Science and Technology Austria
related_material:
record:
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relation: part_of_dissertation
status: public
- id: '18689'
relation: part_of_dissertation
status: public
status: public
supervisor:
- first_name: Johann G
full_name: Danzl, Johann G
id: 42EFD3B6-F248-11E8-B48F-1D18A9856A87
last_name: Danzl
orcid: 0000-0001-8559-3973
title: 'Developing molecular and structural tools for studying brain architecture
with super resolution expansion microscopy. LICONN: Molecularly-informed connectomics
reconstruction with light microscopy'
tmp:
image: /images/cc_by_nc_nd.png
legal_code_url: https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode
name: Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International
(CC BY-NC-ND 4.0)
short: CC BY-NC-ND (4.0)
type: dissertation
user_id: ba8df636-2132-11f1-aed0-ed93e2281fdd
year: '2024'
...
---
OA_place: repository
_id: '18677'
abstract:
- lang: eng
text: The information-processing capability of the brain’s cellular network depends
on the physical wiring pattern between neurons and their molecular and functional
characteristics. Mapping neurons and resolving their individual synaptic connections
can be achieved by volumetric imaging at nanoscale resolution with dense cellular
labeling. Light microscopy is uniquely positioned to visualize specific molecules
but dense, synapse-level circuit reconstruction by light microscopy has been out
of reach due to limitations in resolution, contrast, and volumetric imaging capability.
Here we developed light-microscopy based connectomics (LICONN). We integrated
specifically engineered hydrogel embedding and expansion with comprehensive deep-learning
based segmentation and analysis of connectivity, thus directly incorporating molecular
information in synapse-level brain tissue reconstructions. LICONN will allow synapse-level
brain tissue phenotyping in biological experiments in a readily adoptable manner.
acknowledged_ssus:
- _id: E-Lib
- _id: M-Shop
- _id: LifeSc
- _id: Bio
- _id: ScienComp
acknowledgement: "We thank Sven Dorkenwald and Peter Li for critical reading of the\r\nmanuscript.
We acknowledge expert support by ISTA’s scientific service units: Imaging and\r\nOptics,
Lab Support, Scientific Computing, Preclinical Facility, Miba Machine Shop, and
Library.\r\nWe gratefully acknowledge funding by the following sources:\r\nAustrian
Science Fund (FWF) grant DK W1232 (JGD, MRT)\r\nAustrian Academy of Sciences DOC
fellowship 26137 (MRT)\r\nEU Horizon 2020 program, Marie Skłodowska-Curie Actions
Fellowship 665385 (JL)\r\nGesellschaft für Forschungsförderung NÖ (NFB) grant LSC18-022
(JGD)\r\nEuropean Union’s Horizon 2020 research and innovation programme, European
Research\r\nCouncil (ERC) grant 101044865 “SecretAutism.”\r\n"
article_processing_charge: No
author:
- first_name: Mojtaba
full_name: Tavakoli, Mojtaba
id: 3A0A06F4-F248-11E8-B48F-1D18A9856A87
last_name: Tavakoli
orcid: 0000-0002-7667-6854
- first_name: Julia
full_name: Lyudchik, Julia
id: 46E28B80-F248-11E8-B48F-1D18A9856A87
last_name: Lyudchik
- first_name: Michał
full_name: Januszewski, Michał
last_name: Januszewski
- first_name: Vitali
full_name: Vistunou, Vitali
id: 7e146587-8972-11ed-ae7b-d7a32ea86a81
last_name: Vistunou
- first_name: Nathalie
full_name: Agudelo Duenas, Nathalie
id: 40E7F008-F248-11E8-B48F-1D18A9856A87
last_name: Agudelo Duenas
- first_name: Jakob
full_name: Vorlaufer, Jakob
id: 937696FA-C996-11E9-8C7C-CF13E6697425
last_name: Vorlaufer
orcid: 0009-0000-7590-3501
- first_name: Christoph M
full_name: Sommer, Christoph M
id: 4DF26D8C-F248-11E8-B48F-1D18A9856A87
last_name: Sommer
orcid: 0000-0003-1216-9105
- first_name: Caroline
full_name: Kreuzinger, Caroline
id: 382077BA-F248-11E8-B48F-1D18A9856A87
last_name: Kreuzinger
- first_name: Bárbara
full_name: Oliveira, Bárbara
id: 3B03AA1A-F248-11E8-B48F-1D18A9856A87
last_name: Oliveira
- first_name: Alban
full_name: Cenameri, Alban
id: 9ac8f577-2357-11eb-997a-e566c5550886
last_name: Cenameri
- first_name: Gaia
full_name: Novarino, Gaia
id: 3E57A680-F248-11E8-B48F-1D18A9856A87
last_name: Novarino
orcid: 0000-0002-7673-7178
- first_name: Viren
full_name: Jain, Viren
last_name: Jain
- first_name: Johann G
full_name: Danzl, Johann G
id: 42EFD3B6-F248-11E8-B48F-1D18A9856A87
last_name: Danzl
orcid: 0000-0001-8559-3973
citation:
ama: Tavakoli M, Lyudchik J, Januszewski M, et al. Light-microscopy based dense
connectomic reconstruction of mammalian brain tissue. bioRxiv. doi:10.1101/2024.03.01.582884
apa: Tavakoli, M., Lyudchik, J., Januszewski, M., Vistunou, V., Agudelo Duenas,
N., Vorlaufer, J., … Danzl, J. G. (n.d.). Light-microscopy based dense connectomic
reconstruction of mammalian brain tissue. bioRxiv. https://doi.org/10.1101/2024.03.01.582884
chicago: Tavakoli, Mojtaba, Julia Lyudchik, Michał Januszewski, Vitali Vistunou,
Nathalie Agudelo Duenas, Jakob Vorlaufer, Christoph M Sommer, et al. “Light-Microscopy
Based Dense Connectomic Reconstruction of Mammalian Brain Tissue.” BioRxiv,
n.d. https://doi.org/10.1101/2024.03.01.582884.
ieee: M. Tavakoli et al., “Light-microscopy based dense connectomic reconstruction
of mammalian brain tissue,” bioRxiv. .
ista: Tavakoli M, Lyudchik J, Januszewski M, Vistunou V, Agudelo Duenas N, Vorlaufer
J, Sommer CM, Kreuzinger C, Oliveira B, Cenameri A, Novarino G, Jain V, Danzl
JG. Light-microscopy based dense connectomic reconstruction of mammalian brain
tissue. bioRxiv, 10.1101/2024.03.01.582884.
mla: Tavakoli, Mojtaba, et al. “Light-Microscopy Based Dense Connectomic Reconstruction
of Mammalian Brain Tissue.” BioRxiv, doi:10.1101/2024.03.01.582884.
short: M. Tavakoli, J. Lyudchik, M. Januszewski, V. Vistunou, N. Agudelo Duenas,
J. Vorlaufer, C.M. Sommer, C. Kreuzinger, B. Oliveira, A. Cenameri, G. Novarino,
V. Jain, J.G. Danzl, BioRxiv (n.d.).
corr_author: '1'
date_created: 2024-12-18T14:48:24Z
date_published: 2024-07-08T00:00:00Z
date_updated: 2026-04-07T12:58:30Z
day: '08'
department:
- _id: GaNo
- _id: JoDa
doi: 10.1101/2024.03.01.582884
ec_funded: 1
language:
- iso: eng
main_file_link:
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month: '07'
oa: 1
oa_version: Preprint
project:
- _id: 6285a163-2b32-11ec-9570-8e204ca2dba5
grant_number: '26137'
name: Studying Organelle Structure and Function at Nanoscale Resolution with Expansion
Microscopy
- _id: 2564DBCA-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '665385'
name: International IST Doctoral Program
- _id: 34ba8964-11ca-11ed-8bc3-e15864e7e9a6
grant_number: '101044865'
name: Toward an understanding of the brain interstitial system and the extracellular
proteome in health and autism spectrum disorders
- _id: 26AA4EF2-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: W1232-B24
name: Molecular Drug Targets
publication: bioRxiv
publication_status: draft
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status: public
title: Light-microscopy based dense connectomic reconstruction of mammalian brain
tissue
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short: CC BY-NC-ND (4.0)
type: preprint
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
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: 2026-04-07T12:58:48Z
day: '08'
ddc:
- '514'
- '500'
- '516'
degree_awarded: PhD
department:
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- _id: HeEd
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ec_funded: 1
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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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relation: part_of_dissertation
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- id: '15090'
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- id: '15093'
relation: part_of_dissertation
status: public
- id: '13182'
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status: public
- id: '11658'
relation: part_of_dissertation
status: public
status: public
supervisor:
- first_name: Herbert
full_name: Edelsbrunner, Herbert
id: 3FB178DA-F248-11E8-B48F-1D18A9856A87
last_name: Edelsbrunner
orcid: 0000-0002-9823-6833
title: Persistence and Morse theory for discrete geometric structures
tmp:
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legal_code_url: https://creativecommons.org/licenses/by-nc-sa/4.0/legalcode
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short: CC BY-NC-SA (4.0)
type: dissertation
user_id: ba8df636-2132-11f1-aed0-ed93e2281fdd
year: '2024'
...
---
OA_place: publisher
OA_type: hybrid
_id: '13182'
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: 2026-04-07T12:58:47Z
day: '01'
ddc:
- '000'
department:
- _id: HeEd
doi: 10.1007/s41468-023-00126-9
ec_funded: 1
external_id:
pmid:
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month: '10'
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
- _id: 268116B8-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: Z00342
name: Mathematics, Computer Science
publication: Journal of Applied and Computational Topology
publication_identifier:
eissn:
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issn:
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publisher: Springer Nature
quality_controlled: '1'
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status: public
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: '15093'
abstract:
- lang: eng
text: We present a dynamic data structure for maintaining the persistent homology
of a time series of real numbers. The data structure supports local operations,
including the insertion and deletion of an item and the cutting and concatenating
of lists, each in time O(log n + k), in which n counts the critical items and
k the changes in the augmented persistence diagram. To achieve this, we design
a tailor-made tree structure with an unconventional representation, referred to
as banana tree, which may be useful in its own right.
acknowledgement: The first and second authors are funded by the European Research Council under the
European Union’s Horizon 2020 research and innovation programme, ERC grant no. 788183,“Alpha
Shape Theory Extended (Alpha)”, by the Wittgenstein Prize, FWF grant no. Z 342-N31,
and by the DFG Collaborative Research Center TRR 109, FWF grant no. I 02979-N35.The
third author received funding by the European Research Council under the European
Union’s Horizon 2020research and innovation programme, ERC grant no. 101019564, “The Design of Modern Fully Dynamic DataStructures
(MoDynStruct)”, and by the Austrian Science Fund through the Wittgenstein Prize
with FWF grant no. Z 422-N, and also by FWF grant no. I 5982-N, and by FWF grant
no. P 33775-N, with additional funding from the netidee SCIENCE Stiftung, 2020–2024. The
fourth author is funded by the Vienna Graduate School on Computational Optimization,
FWF project no. W1260-N35.
article_processing_charge: No
arxiv: 1
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
- first_name: Herbert
full_name: Edelsbrunner, Herbert
id: 3FB178DA-F248-11E8-B48F-1D18A9856A87
last_name: Edelsbrunner
orcid: 0000-0002-9823-6833
- first_name: Monika H
full_name: Henzinger, Monika H
id: 540c9bbd-f2de-11ec-812d-d04a5be85630
last_name: Henzinger
orcid: 0000-0002-5008-6530
- first_name: Lara
full_name: Ost, Lara
last_name: Ost
citation:
ama: 'Cultrera di Montesano S, Edelsbrunner H, Henzinger M, Ost L. Dynamically maintaining
the persistent homology of time series. In: Woodruff DP, ed. Proceedings of
the 2024 Annual ACM-SIAM Symposium on Discrete Algorithms (SODA). Society
for Industrial and Applied Mathematics; 2024:243-295. doi:10.1137/1.9781611977912.11'
apa: 'Cultrera di Montesano, S., Edelsbrunner, H., Henzinger, M., & Ost, L.
(2024). Dynamically maintaining the persistent homology of time series. In D.
P. Woodruff (Ed.), Proceedings of the 2024 Annual ACM-SIAM Symposium on Discrete
Algorithms (SODA) (pp. 243–295). Alexandria, VA, USA: Society for Industrial
and Applied Mathematics. https://doi.org/10.1137/1.9781611977912.11'
chicago: Cultrera di Montesano, Sebastiano, Herbert Edelsbrunner, Monika Henzinger,
and Lara Ost. “Dynamically Maintaining the Persistent Homology of Time Series.”
In Proceedings of the 2024 Annual ACM-SIAM Symposium on Discrete Algorithms
(SODA), edited by David P. Woodruff, 243–95. Society for Industrial and Applied
Mathematics, 2024. https://doi.org/10.1137/1.9781611977912.11.
ieee: S. Cultrera di Montesano, H. Edelsbrunner, M. Henzinger, and L. Ost, “Dynamically
maintaining the persistent homology of time series,” in Proceedings of the
2024 Annual ACM-SIAM Symposium on Discrete Algorithms (SODA), Alexandria,
VA, USA, 2024, pp. 243–295.
ista: 'Cultrera di Montesano S, Edelsbrunner H, Henzinger M, Ost L. 2024. Dynamically
maintaining the persistent homology of time series. Proceedings of the 2024 Annual
ACM-SIAM Symposium on Discrete Algorithms (SODA). SODA: Symposium on Discrete
Algorithms, 243–295.'
mla: Cultrera di Montesano, Sebastiano, et al. “Dynamically Maintaining the Persistent
Homology of Time Series.” Proceedings of the 2024 Annual ACM-SIAM Symposium
on Discrete Algorithms (SODA), edited by David P. Woodruff, Society for Industrial
and Applied Mathematics, 2024, pp. 243–95, doi:10.1137/1.9781611977912.11.
short: S. Cultrera di Montesano, H. Edelsbrunner, M. Henzinger, L. Ost, in:, D.P.
Woodruff (Ed.), Proceedings of the 2024 Annual ACM-SIAM Symposium on Discrete
Algorithms (SODA), Society for Industrial and Applied Mathematics, 2024, pp. 243–295.
conference:
end_date: 2024-01-10
location: Alexandria, VA, USA
name: 'SODA: Symposium on Discrete Algorithms'
start_date: 2024-01-07
corr_author: '1'
date_created: 2024-03-08T10:27:39Z
date_published: 2024-01-04T00:00:00Z
date_updated: 2026-04-07T12:58:47Z
day: '04'
department:
- _id: HeEd
- _id: MoHe
doi: 10.1137/1.9781611977912.11
ec_funded: 1
editor:
- first_name: David P.
full_name: Woodruff, David P.
last_name: Woodruff
external_id:
arxiv:
- '2311.01115'
language:
- iso: eng
main_file_link:
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url: https://arxiv.org/abs/2311.01115
month: '01'
oa: 1
oa_version: Preprint
page: 243 - 295
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: bd9ca328-d553-11ed-ba76-dc4f890cfe62
call_identifier: H2020
grant_number: '101019564'
name: The design and evaluation of modern fully dynamic data structures
- _id: 34def286-11ca-11ed-8bc3-da5948e1613c
grant_number: Z00422
name: Efficient algorithms
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grant_number: P33775
name: Fast Algorithms for a Reactive Network Layer
publication: Proceedings of the 2024 Annual ACM-SIAM Symposium on Discrete Algorithms
(SODA)
publication_identifier:
eisbn:
- '9781611977912'
publication_status: published
publisher: Society for Industrial and Applied Mathematics
quality_controlled: '1'
related_material:
record:
- id: '15094'
relation: dissertation_contains
status: public
scopus_import: '1'
status: public
title: Dynamically maintaining the persistent homology of time series
type: conference
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
year: '2024'
...
---
OA_place: repository
_id: '15091'
abstract:
- lang: eng
text: "Motivated by applications in the medical sciences, we study finite chromatic\r\nsets
in Euclidean space from a topological perspective. Based on the persistent\r\nhomology
for images, kernels and cokernels, we design provably stable\r\nhomological quantifiers
that describe the geometric micro- and macro-structure\r\nof how the color classes
mingle. These can be efficiently computed using\r\nchromatic variants of Delaunay
and alpha complexes, and code that does these\r\ncomputations is provided."
article_number: '2212.03128'
article_processing_charge: No
arxiv: 1
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
- first_name: Ondrej
full_name: Draganov, Ondrej
id: 2B23F01E-F248-11E8-B48F-1D18A9856A87
last_name: Draganov
orcid: 0000-0003-0464-3823
- 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: Cultrera di Montesano S, Draganov O, Edelsbrunner H, Saghafian M. Chromatic
alpha complexes. arXiv. doi:10.48550/arXiv.2212.03128
apa: Cultrera di Montesano, S., Draganov, O., Edelsbrunner, H., & Saghafian,
M. (n.d.). Chromatic alpha complexes. arXiv. https://doi.org/10.48550/arXiv.2212.03128
chicago: Cultrera di Montesano, Sebastiano, Ondrej Draganov, Herbert Edelsbrunner,
and Morteza Saghafian. “Chromatic Alpha Complexes.” ArXiv, n.d. https://doi.org/10.48550/arXiv.2212.03128.
ieee: S. Cultrera di Montesano, O. Draganov, H. Edelsbrunner, and M. Saghafian,
“Chromatic alpha complexes,” arXiv. .
ista: Cultrera di Montesano S, Draganov O, Edelsbrunner H, Saghafian M. Chromatic
alpha complexes. arXiv, 2212.03128.
mla: Cultrera di Montesano, Sebastiano, et al. “Chromatic Alpha Complexes.” ArXiv,
2212.03128, doi:10.48550/arXiv.2212.03128.
short: S. Cultrera di Montesano, O. Draganov, H. Edelsbrunner, M. Saghafian, ArXiv
(n.d.).
corr_author: '1'
date_created: 2024-03-08T10:13:59Z
date_published: 2024-02-07T00:00:00Z
date_updated: 2026-04-07T12:58:47Z
day: '07'
department:
- _id: HeEd
doi: 10.48550/arXiv.2212.03128
external_id:
arxiv:
- '2212.03128'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/2212.03128
month: '02'
oa: 1
oa_version: Preprint
publication: arXiv
publication_status: draft
related_material:
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- id: '15094'
relation: dissertation_contains
status: public
status: public
title: Chromatic alpha complexes
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: 8b945eb4-e2f2-11eb-945a-df72226e66a9
year: '2024'
...
---
OA_place: publisher
_id: '18766'
abstract:
- lang: eng
text: Poxviruses are large pleomorphic double-stranded DNA viruses that include
well known members such as variola virus, the causative agent of smallpox, Mpox
virus, as well as Vaccinia virus (VACV), which serves as a vaccination strain
for formerly mentioned viruses. VACV is a valuable model for studying large pleomorphic
DNA viruses in general and poxviruses specifically, as many features, such as
core morphology and structural proteins, are well conserved within this family.
Despite decades of research, our understanding of the structural components and
proteins that comprise the poxvirus core in mature virions remains limited. Although
major core proteins were identified via indirect experimental evidence, the core's
complexity, with its large size, structure and number of involved proteins, has
hindered efforts to achieve high-resolution insights and to define the roles of
the individual proteins. The specific protein composition of the core's individual
layers, including the palisade layer and the inner core wall, has remained unclear.
In this study, we have merged multiple approaches, including single particle cryo
electron microscopy of purified virus cores, cryo-electron tomography and subtomogram
averaging of mature virions and molecular modeling to elucidate the structural
determinants of the VACV core. Due to the lack of experimentally derived structures,
either in situ or reconstituted in vitro, we used Alphafold to predict models
of the putative major core protein candidates, A10, 23k, A3, A4, and L4. Our results
show that the VACV core is composed of several layers with varying local symmetries,
forming more intricate interactions than observed previously. This allowed us
to identify several molecular building blocks forming the viral core lattice.
In particular, we identified trimers of protein A10 as a major core structure
that forms the palisade layer of the viral core. Additionally, we revealed that
six petals of a flower shaped core pore within the core wall are composed of A10
trimers. Furthermore, we obtained a cryo-EM density for the inner core wall that
could potentially accommodate an A3 dimer. Integrating descriptions of protein
interactions from previous studies enabled us to provide a detailed structural
model of the poxvirus core wall, and our findings indicate that the interactions
within A10 trimers are likely consistent across orthopox- and parapoxviruses.
This combined application of cryo-SPA and cryo-ET can help overcome obstacles
in studying complex virus structures in the future, including their key assembly
proteins, interactions, and the formation into a core lattice. Our work provides
important fundamental new insights into poxvirus core architecture, also considering
the recent re-emergence of poxviruses.
acknowledged_ssus:
- _id: EM-Fac
- _id: LifeSc
- _id: ScienComp
acknowledgement: "This work was funded by the Austrian Science Fund (FWF) grant P31445
and ISTA. I\r\nwould like to express my gratitude to the Scientific Service Units,
particularly the Lab\r\nSupport Facility, the Scientific Computing Facility and
the Electron Microscopy Facility\r\nfor their tremendous support. I want to especially
thank Alois for assisting me with the\r\ninstallation of countless new software
and for troubleshooting cluster issues. A special\r\nthanks goes to Valentin for
his outstanding support in cryo-EM data acquisition and\r\nhis ongoing help in improving
the process to ensure that I obtained the best possible\r\ndata from my sample."
alternative_title:
- ISTA thesis
article_processing_charge: No
author:
- first_name: Julia
full_name: Datler, Julia
id: 3B12E2E6-F248-11E8-B48F-1D18A9856A87
last_name: Datler
orcid: 0000-0002-3616-8580
citation:
ama: Datler J. Elucidating the structural determinants of the poxvirus core using
multi-modal cryo-EM. 2024. doi:10.15479/at:ista:18766
apa: Datler, J. (2024). Elucidating the structural determinants of the poxvirus
core using multi-modal cryo-EM. Institute of Science and Technology Austria.
https://doi.org/10.15479/at:ista:18766
chicago: Datler, Julia. “Elucidating the Structural Determinants of the Poxvirus
Core Using Multi-Modal Cryo-EM.” Institute of Science and Technology Austria,
2024. https://doi.org/10.15479/at:ista:18766.
ieee: J. Datler, “Elucidating the structural determinants of the poxvirus core using
multi-modal cryo-EM,” Institute of Science and Technology Austria, 2024.
ista: Datler J. 2024. Elucidating the structural determinants of the poxvirus core
using multi-modal cryo-EM. Institute of Science and Technology Austria.
mla: Datler, Julia. Elucidating the Structural Determinants of the Poxvirus Core
Using Multi-Modal Cryo-EM. Institute of Science and Technology Austria, 2024,
doi:10.15479/at:ista:18766.
short: J. Datler, Elucidating the Structural Determinants of the Poxvirus Core Using
Multi-Modal Cryo-EM, Institute of Science and Technology Austria, 2024.
corr_author: '1'
date_created: 2025-01-07T10:23:12Z
date_published: 2024-12-30T00:00:00Z
date_updated: 2026-04-07T12:59:44Z
day: '30'
ddc:
- '570'
degree_awarded: PhD
department:
- _id: GradSch
- _id: FlSc
doi: 10.15479/at:ista:18766
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file_size: 38814932
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file_date_updated: 2025-01-07T12:15:14Z
has_accepted_license: '1'
keyword:
- cryo-EM
- cryo-ET
- cryo-SPA
- Structural Virology
- Poxvirus
- Vaccinia Virus
- Structural Biology
language:
- iso: eng
month: '12'
oa: 1
oa_version: Published Version
page: '106'
project:
- _id: 26736D6A-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: P31445
name: Structural conservation and diversity in retroviral capsid
publication_identifier:
isbn:
- 978-3-99078-049-7
issn:
- 2663-337X
publication_status: published
publisher: Institute of Science and Technology Austria
related_material:
record:
- id: '12334'
relation: part_of_dissertation
status: public
- id: '14979'
relation: part_of_dissertation
status: public
status: public
supervisor:
- first_name: Florian KM
full_name: Schur, Florian KM
id: 48AD8942-F248-11E8-B48F-1D18A9856A87
last_name: Schur
orcid: 0000-0003-4790-8078
title: Elucidating the structural determinants of the poxvirus core using multi-modal
cryo-EM
tmp:
image: /images/cc_by_nc_nd.png
legal_code_url: https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode
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short: CC BY-NC-ND (4.0)
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year: '2024'
...
---
APC_amount: 11700 EUR
OA_place: publisher
OA_type: hybrid
_id: '14979'
abstract:
- lang: eng
text: Poxviruses are among the largest double-stranded DNA viruses, with members
such as variola virus, monkeypox virus and the vaccination strain vaccinia virus
(VACV). Knowledge about the structural proteins that form the viral core has remained
sparse. While major core proteins have been annotated via indirect experimental
evidence, their structures have remained elusive and they could not be assigned
to individual core features. Hence, which proteins constitute which layers of
the core, such as the palisade layer and the inner core wall, has remained enigmatic.
Here we show, using a multi-modal cryo-electron microscopy (cryo-EM) approach
in combination with AlphaFold molecular modeling, that trimers formed by the cleavage
product of VACV protein A10 are the key component of the palisade layer. This
allows us to place previously obtained descriptions of protein interactions within
the core wall into perspective and to provide a detailed model of poxvirus core
architecture. Importantly, we show that interactions within A10 trimers are likely
generalizable over members of orthopox- and parapoxviruses.
acknowledged_ssus:
- _id: ScienComp
- _id: LifeSc
- _id: EM-Fac
acknowledgement: "We thank A. Bergthaler (Research Center for Molecular Medicine of
the Austrian Academy of Sciences) for providing VACV WR. We thank A. Nicholas and
his team at the ISTA proteomics facility, and S. Elefante at the ISTA Scientific
Computing facility for their support. We also thank F. Fäßler, D. Porley, T. Muthspiel
and other members of the Schur group for support and helpful discussions. We also
thank D. Castaño-Díez for support with Dynamo. We thank D. Farrell for his help
optimizing the Rosetta protocol to refine the atomic model into the cryo-EM map
with symmetry.\r\n\r\nF.K.M.S. acknowledges support from ISTA and EMBO. F.K.M.S.
also received support from the Austrian Science Fund (FWF) grant P31445. This publication
has been made possible in part by CZI grant DAF2021-234754 and grant https://doi.org/10.37921/812628ebpcwg
from the Chan Zuckerberg Initiative DAF, an advised fund of Silicon Valley Community
Foundation (funder https://doi.org/10.13039/100014989) awarded to F.K.M.S.\r\n\r\nThis
research was also supported by the Scientific Service Units (SSUs) of ISTA through
resources provided by Scientific Computing (SciComp), the Life Science Facility
(LSF), and the Electron Microscopy Facility (EMF). We also acknowledge the use of
COSMIC45 and Colabfold46."
article_processing_charge: Yes (in subscription journal)
article_type: original
author:
- first_name: Julia
full_name: Datler, Julia
id: 3B12E2E6-F248-11E8-B48F-1D18A9856A87
last_name: Datler
orcid: 0000-0002-3616-8580
- first_name: Jesse
full_name: Hansen, Jesse
id: 1063c618-6f9b-11ec-9123-f912fccded63
last_name: Hansen
orcid: 0000-0001-7967-2085
- first_name: Andreas
full_name: Thader, Andreas
id: 3A18A7B8-F248-11E8-B48F-1D18A9856A87
last_name: Thader
- first_name: Alois
full_name: Schlögl, Alois
id: 45BF87EE-F248-11E8-B48F-1D18A9856A87
last_name: Schlögl
orcid: 0000-0002-5621-8100
- first_name: Lukas W
full_name: Bauer, Lukas W
id: 0c894dcf-897b-11ed-a09c-8186353224b0
last_name: Bauer
- first_name: Victor-Valentin
full_name: Hodirnau, Victor-Valentin
id: 3661B498-F248-11E8-B48F-1D18A9856A87
last_name: Hodirnau
orcid: 0000-0003-3904-947X
- first_name: Florian KM
full_name: Schur, Florian KM
id: 48AD8942-F248-11E8-B48F-1D18A9856A87
last_name: Schur
orcid: 0000-0003-4790-8078
citation:
ama: Datler J, Hansen J, Thader A, et al. Multi-modal cryo-EM reveals trimers of
protein A10 to form the palisade layer in poxvirus cores. Nature Structural
& Molecular Biology. 2024;31:1114-1123. doi:10.1038/s41594-023-01201-6
apa: Datler, J., Hansen, J., Thader, A., Schlögl, A., Bauer, L. W., Hodirnau, V.-V.,
& Schur, F. K. (2024). Multi-modal cryo-EM reveals trimers of protein A10
to form the palisade layer in poxvirus cores. Nature Structural & Molecular
Biology. Springer Nature. https://doi.org/10.1038/s41594-023-01201-6
chicago: Datler, Julia, Jesse Hansen, Andreas Thader, Alois Schlögl, Lukas W Bauer,
Victor-Valentin Hodirnau, and Florian KM Schur. “Multi-Modal Cryo-EM Reveals Trimers
of Protein A10 to Form the Palisade Layer in Poxvirus Cores.” Nature Structural
& Molecular Biology. Springer Nature, 2024. https://doi.org/10.1038/s41594-023-01201-6.
ieee: J. Datler et al., “Multi-modal cryo-EM reveals trimers of protein A10
to form the palisade layer in poxvirus cores,” Nature Structural & Molecular
Biology, vol. 31. Springer Nature, pp. 1114–1123, 2024.
ista: Datler J, Hansen J, Thader A, Schlögl A, Bauer LW, Hodirnau V-V, Schur FK.
2024. Multi-modal cryo-EM reveals trimers of protein A10 to form the palisade
layer in poxvirus cores. Nature Structural & Molecular Biology. 31, 1114–1123.
mla: Datler, Julia, et al. “Multi-Modal Cryo-EM Reveals Trimers of Protein A10 to
Form the Palisade Layer in Poxvirus Cores.” Nature Structural & Molecular
Biology, vol. 31, Springer Nature, 2024, pp. 1114–23, doi:10.1038/s41594-023-01201-6.
short: J. Datler, J. Hansen, A. Thader, A. Schlögl, L.W. Bauer, V.-V. Hodirnau,
F.K. Schur, Nature Structural & Molecular Biology 31 (2024) 1114–1123.
corr_author: '1'
date_created: 2024-02-12T09:59:45Z
date_published: 2024-07-01T00:00:00Z
date_updated: 2026-04-07T12:59:44Z
day: '01'
ddc:
- '570'
department:
- _id: FlSc
- _id: ScienComp
- _id: EM-Fac
doi: 10.1038/s41594-023-01201-6
external_id:
isi:
- '001158144600002'
pmid:
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creator: dernst
date_created: 2024-07-22T11:27:22Z
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file_name: 2024_NatureStrucBio_Datler.pdf
file_size: 17485494
relation: main_file
success: 1
file_date_updated: 2024-07-22T11:27:22Z
has_accepted_license: '1'
intvolume: ' 31'
isi: 1
keyword:
- Molecular Biology
- Structural Biology
language:
- iso: eng
month: '07'
oa: 1
oa_version: Published Version
page: 1114-1123
pmid: 1
project:
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call_identifier: FWF
grant_number: P31445
name: Structural conservation and diversity in retroviral capsid
publication: Nature Structural & Molecular Biology
publication_identifier:
eissn:
- 1545-9985
issn:
- 1545-9993
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
related_material:
link:
- description: News on ISTA Website
relation: press_release
url: https://ista.ac.at/en/news/down-to-the-core-of-poxviruses/
record:
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scopus_import: '1'
status: public
title: Multi-modal cryo-EM reveals trimers of protein A10 to form the palisade layer
in poxvirus cores
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: journal_article
user_id: 317138e5-6ab7-11ef-aa6d-ffef3953e345
volume: 31
year: '2024'
...
---
OA_place: publisher
_id: '15020'
abstract:
- lang: eng
text: "This thesis consists of four distinct pieces of work within theoretical biology,
with two themes in common: the concept of optimization in biological systems,
and the use of information-theoretic tools to quantify biological stochasticity
and statistical uncertainty.\r\nChapter 2 develops a statistical framework for
studying biological systems which we believe to be optimized for a particular
utility function, such as retinal neurons conveying information about visual stimuli.
We formalize such beliefs as maximum-entropy Bayesian priors, constrained by the
expected utility. We explore how such priors aid inference of system parameters
with limited data and enable optimality hypothesis testing: is the utility higher
than by chance?\r\nChapter 3 examines the ultimate biological optimization process:
evolution by natural selection. As some individuals survive and reproduce more
successfully than others, populations evolve towards fitter genotypes and phenotypes.
We formalize this as accumulation of genetic information, and use population genetics
theory to study how much such information can be accumulated per generation and
maintained in the face of random mutation and genetic drift. We identify the population
size and fitness variance as the key quantities that control information accumulation
and maintenance.\r\nChapter 4 reuses the concept of genetic information from Chapter
3, but from a different perspective: we ask how much genetic information organisms
actually need, in particular in the context of gene regulation. For example, how
much information is needed to bind transcription factors at correct locations
within the genome? Population genetics provides us with a refined answer: with
an increasing population size, populations achieve higher fitness by maintaining
more genetic information. Moreover, regulatory parameters experience selection
pressure to optimize the fitness-information trade-off, i.e. minimize the information
needed for a given fitness. This provides an evolutionary derivation of the optimization
priors introduced in Chapter 2.\r\nChapter 5 proves an upper bound on mutual information
between a signal and a communication channel output (such as neural activity).
Mutual information is an important utility measure for biological systems, but
its practical use can be difficult due to the large dimensionality of many biological
channels. Sometimes, a lower bound on mutual information is computed by replacing
the high-dimensional channel outputs with decodes (signal estimates). Our result
provides a corresponding upper bound, provided that the decodes are the maximum
posterior estimates of the signal."
acknowledged_ssus:
- _id: ScienComp
alternative_title:
- ISTA Thesis
article_processing_charge: No
author:
- first_name: Michal
full_name: Hledik, Michal
id: 4171253A-F248-11E8-B48F-1D18A9856A87
last_name: Hledik
citation:
ama: Hledik M. Genetic information and biological optimization. 2024. doi:10.15479/at:ista:15020
apa: Hledik, M. (2024). Genetic information and biological optimization.
Institute of Science and Technology Austria. https://doi.org/10.15479/at:ista:15020
chicago: Hledik, Michal. “Genetic Information and Biological Optimization.” Institute
of Science and Technology Austria, 2024. https://doi.org/10.15479/at:ista:15020.
ieee: M. Hledik, “Genetic information and biological optimization,” Institute of
Science and Technology Austria, 2024.
ista: Hledik M. 2024. Genetic information and biological optimization. Institute
of Science and Technology Austria.
mla: Hledik, Michal. Genetic Information and Biological Optimization. Institute
of Science and Technology Austria, 2024, doi:10.15479/at:ista:15020.
short: M. Hledik, Genetic Information and Biological Optimization, Institute of
Science and Technology Austria, 2024.
corr_author: '1'
date_created: 2024-02-23T14:02:04Z
date_published: 2024-02-23T00:00:00Z
date_updated: 2026-04-07T12:59:25Z
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keyword:
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- Optimality
- Evolution
- Information
language:
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oa: 1
oa_version: Published Version
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name: International IST Doctoral Program
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grant_number: RGP0034/2018
name: Can evolution minimize spurious signaling crosstalk to reach optimal performance?
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supervisor:
- first_name: Nicholas H
full_name: Barton, Nicholas H
id: 4880FE40-F248-11E8-B48F-1D18A9856A87
last_name: Barton
orcid: 0000-0002-8548-5240
- first_name: Gašper
full_name: Tkačik, Gašper
id: 3D494DCA-F248-11E8-B48F-1D18A9856A87
last_name: Tkačik
orcid: 0000-0002-6699-1455
title: Genetic information and biological optimization
type: dissertation
user_id: ba8df636-2132-11f1-aed0-ed93e2281fdd
year: '2024'
...
---
OA_place: publisher
_id: '18568'
abstract:
- lang: eng
text: "Locomotion is ubiquitous in the animal kingdom because an animal's survival
depends on its ability to navigate its environment to find food, avoid predators
and locate potential mates. These behaviours require control mechanisms that can
extract information from the environment, particularly visual cues. Selective
evolutionary pressures have thus refined such visuomotor transformations in a
species-specific manner to meet the specific ecological and ethological challenges
of each organism. However, a common challenge across organisms as visual information
processing\r\nbecomes increasingly detailed is the mechanisms required to synthesise
disparate pieces of information into a coherent percept or unified picture of
the world. In this thesis, I investigate how disparate visual information is combined
in the brain of Drosophila melanogaster to effectively guide locomotion.\r\nFor
this, I first designed and built a behavioural setup to record locomotion and
present visual stimuli to freely-walking fruit flies in a closed-loop manner.
This setup allowed the investigation of innate visually-guided behaviours, including
the optomotor reflex and courtship.\r\nSecond, taking advantage of my system I
investigated the optomotor response, a reflexive visual stabilisation behaviour
in which flies turn in the direction of global motion to minimise retinal slip.
This behaviour is thought to be mediated by Lobula plate tangential cells (LPTCs);
a complex network of optic-flow-sensitive neurons essential for self-motion estimation.
Using a novel genetic mutant, I demonstrate that electrical coupling between two
LPTC subtypes, contralateral HS and H2 neurons, regulates the balance between
smooth optomotor turning and saccadic anti-optomotor responses. These findings
underscore the critical role of binocular motion cue integration in guiding course
control. Finally, I developed a novel behavioural paradigm in which a sexually
aroused male fruit fly is presented with an optomotor distractor. This setup creates
competition between two visual behaviours, courtship tracking and the optomotor
response, enabling me to explore how the visual system resolves this conflict.
In this setting, males\r\nengaged in courtship selectively suppress their optomotor
response based on the female's location. Furthermore, when this experiment is
replicated with an “artificial female”, optogenetically aroused males alternate
between tracking and optomotor responses. The probability and dynamics of this
switching are determined by the relative strengths of the two competing stimuli.
In summary, the results presented in this thesis explore two mechanisms – integration
and competition - through which visual information is combined in the brain of
the fruit fly to drive locomotion."
acknowledged_ssus:
- _id: M-Shop
acknowledgement: I am incredibly thankful for the outstanding support provided by
ISTA, especially the Machine Shop team, who made conducting research much easier
and more efficient. I am also grateful for the funding provided by European Union’s
Horizon 2020 research and innovation program under the Marie Skłodowska-Curie programme
(665385) and The German Research Foundation grant DFG (SPP2205) “Evolutionary optimization
of neuronal processing”.
alternative_title:
- ISTA Thesis
article_processing_charge: No
author:
- first_name: Roshan K
full_name: Satapathy, Roshan K
id: 46046B7A-F248-11E8-B48F-1D18A9856A87
last_name: Satapathy
orcid: 0009-0006-2974-5075
citation:
ama: Satapathy RK. Mechanisms of visual integration and competition in innate behaviours
in Drosophila melanogaster. 2024. doi:10.15479/at:ista:18568
apa: Satapathy, R. K. (2024). Mechanisms of visual integration and competition
in innate behaviours in Drosophila melanogaster. Institute of Science and
Technology Austria. https://doi.org/10.15479/at:ista:18568
chicago: Satapathy, Roshan K. “Mechanisms of Visual Integration and Competition
in Innate Behaviours in Drosophila Melanogaster.” Institute of Science and Technology
Austria, 2024. https://doi.org/10.15479/at:ista:18568.
ieee: R. K. Satapathy, “Mechanisms of visual integration and competition in innate
behaviours in Drosophila melanogaster,” Institute of Science and Technology Austria,
2024.
ista: Satapathy RK. 2024. Mechanisms of visual integration and competition in innate
behaviours in Drosophila melanogaster. Institute of Science and Technology Austria.
mla: Satapathy, Roshan K. Mechanisms of Visual Integration and Competition in
Innate Behaviours in Drosophila Melanogaster. Institute of Science and Technology
Austria, 2024, doi:10.15479/at:ista:18568.
short: R.K. Satapathy, Mechanisms of Visual Integration and Competition in Innate
Behaviours in Drosophila Melanogaster, Institute of Science and Technology Austria,
2024.
corr_author: '1'
date_created: 2024-11-19T12:34:30Z
date_published: 2024-11-20T00:00:00Z
date_updated: 2026-04-07T13:00:36Z
day: '20'
ddc:
- '573'
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department:
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- _id: MaJö
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supervisor:
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full_name: Jösch, Maximilian A
id: 2BD278E6-F248-11E8-B48F-1D18A9856A87
last_name: Jösch
orcid: 0000-0002-3937-1330
title: Mechanisms of visual integration and competition in innate behaviours in Drosophila
melanogaster
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abstract:
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text: Animals rely on compensatory actions to maintain stability and navigate their
environment efficiently. These actions depend on global visual motion cues known
as optic-flow. While the optomotor response has been the traditional focus for
studying optic-flow compensation in insects, its simplicity has been insufficient
to determine the role of the intricate optic-flow processing network involved
in visual course control. Here, we reveal a series of course control behaviours
in Drosophila and link them to specific neural circuits. We show that bilateral
electrical coupling of optic-flow-sensitive neurons in the fly’s lobula plate
are required for a proper course control. This electrical interaction works alongside
chemical synapses within the HS-H2 network to control the dynamics and direction
of turning behaviours. Our findings reveal how insects use bilateral motion cues
for navigation, assigning a new functional significance to the HS-H2 network and
suggesting a previously unknown role for gap junctions in non-linear operations.
acknowledged_ssus:
- _id: Bio
- _id: M-Shop
- _id: LifeSc
acknowledgement: We thank Georg Ammer and Alexander Borst for sharing anti-ShakB serum
antibodies. We thank Nélia Varela and Eugenia Chiappe for the w1118;+;10XUAS-IVS-eGFPKir2.1/TM6B
fly line, Augustin Hrvoje for the shakB[2] line, as well as Jesse Isaacman-Beck
and Thomas R Clandinin for the gift of y1,w*;20XUAS-IVS-PhiC31;+ fly line. We also
thank Armel Nicolas and Tomas Masson for the proteomic analysis, Ece Sönmez for
help with fly crosses and dissections for protein analysis, and Lisa Hofer for assistance
with the reconstruction experiments. We would also like to thank Laura Burnett for
drawing scientific illustrations used in the figures. We are particularly grateful
to members of the Siekhaus, the Kondrashov, and the Chiappe group for providing
material support and technical advice. We are grateful to Daria Siekhaus, Eugenia
Chiappe, Alexander Borst, Ben deBivort, and all the members of the Joesch laboratory
for valuable discussions and comments on the manuscript. Stocks from the Bloomington
Drosophila Stock Center (NIH P40OD018537) and the Vienna Drosophila Resource Center
were used in this study. The Scientific Service Units of ISTA supported the project
through resources provided by the Imaging and Optics Facility, MIBA Machine Shop,
and the Lab Support Facility, as well as Vienna Drosophila Research Centre. This
work was funded by the Deutsche Forschungsgemeinschaft (DFG, German Research Foundation)
as part of the SPP 2205 – 429960716 (M.J.).
article_number: '8830'
article_processing_charge: Yes
article_type: original
author:
- first_name: Victoria
full_name: Pokusaeva, Victoria
id: 3184041C-F248-11E8-B48F-1D18A9856A87
last_name: Pokusaeva
orcid: 0000-0001-7660-444X
- first_name: Roshan K
full_name: Satapathy, Roshan K
id: 46046B7A-F248-11E8-B48F-1D18A9856A87
last_name: Satapathy
orcid: 0009-0006-2974-5075
- first_name: Olga
full_name: Symonova, Olga
id: 3C0C7BC6-F248-11E8-B48F-1D18A9856A87
last_name: Symonova
orcid: 0000-0003-2012-9947
- first_name: Maximilian A
full_name: Jösch, Maximilian A
id: 2BD278E6-F248-11E8-B48F-1D18A9856A87
last_name: Jösch
orcid: 0000-0002-3937-1330
citation:
ama: Pokusaeva V, Satapathy RK, Symonova O, Jösch MA. Bilateral interactions of
optic-flow sensitive neurons coordinate course control in flies. Nature Communications.
2024;15. doi:10.1038/s41467-024-53173-w
apa: Pokusaeva, V., Satapathy, R. K., Symonova, O., & Jösch, M. A. (2024). Bilateral
interactions of optic-flow sensitive neurons coordinate course control in flies.
Nature Communications. Springer Nature. https://doi.org/10.1038/s41467-024-53173-w
chicago: Pokusaeva, Victoria, Roshan K Satapathy, Olga Symonova, and Maximilian
A Jösch. “Bilateral Interactions of Optic-Flow Sensitive Neurons Coordinate Course
Control in Flies.” Nature Communications. Springer Nature, 2024. https://doi.org/10.1038/s41467-024-53173-w.
ieee: V. Pokusaeva, R. K. Satapathy, O. Symonova, and M. A. Jösch, “Bilateral interactions
of optic-flow sensitive neurons coordinate course control in flies,” Nature
Communications, vol. 15. Springer Nature, 2024.
ista: Pokusaeva V, Satapathy RK, Symonova O, Jösch MA. 2024. Bilateral interactions
of optic-flow sensitive neurons coordinate course control in flies. Nature Communications.
15, 8830.
mla: Pokusaeva, Victoria, et al. “Bilateral Interactions of Optic-Flow Sensitive
Neurons Coordinate Course Control in Flies.” Nature Communications, vol.
15, 8830, Springer Nature, 2024, doi:10.1038/s41467-024-53173-w.
short: V. Pokusaeva, R.K. Satapathy, O. Symonova, M.A. Jösch, Nature Communications
15 (2024).
corr_author: '1'
date_created: 2024-10-20T22:02:05Z
date_published: 2024-10-12T00:00:00Z
date_updated: 2026-04-07T13:00:35Z
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department:
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doi: 10.1038/s41467-024-53173-w
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title: Bilateral interactions of optic-flow sensitive neurons coordinate course control
in flies
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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)
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---
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_id: '17336'
abstract:
- lang: eng
text: "This thesis deals with the study of stochastic processes and their ergodicity
properties. The\r\nvariety of problems encountered calls for a set of different
approaches, ranging from classical to\r\nmodern ones: a special place is held
by probabilistic methods based on couplings, by functional\r\ninequalities, and
by the theory of gradient flows in the space of measures.\r\n\r\nThe material
is organized as follows. Chapter 1 contains the introduction to this thesis, starting\r\nwith
a general presentation of some of the relevant topics. Section 1.1 is dedicated
to the\r\ntheory of gradient flows in metric spaces, and introduces the first
contribution of this thesis\r\n[DSMP24], which is presented in detail in Chapter
2. Section 1.2 moves to the topic of\r\ncurvature of Markov chains, concluding
with a brief description of our second contribution\r\n[Ped23], which is included
in Chapter 3. Section 1.3 discusses applications of stochastic\r\nprocesses to
the theory of sampling, in particular the recent framework of score-based diffusion\r\nmodels,
and our contribution [PMM24], which is contained in Chapter 4. Section 1.4 discusses\r\nsome
related problems, concerning the regularization properties of the heat flow. It
serves\r\nas a motivation for the work [BP24], which we report in Chapter 5. Finally,
Section 1.5\r\ndiscusses the last contribution of this thesis, which can be found
in Chapter 6. It deals with\r\nthe convergence to equilibrium of a particular
stochastic model from quantitative genetics:\r\nthis is established via some functional
inequalities, which we prove with probabilistic arguments\r\nbased on couplings.\r\n"
alternative_title:
- ISTA Thesis
article_processing_charge: No
author:
- first_name: Francesco
full_name: Pedrotti, Francesco
id: d3ac8ac6-dc8d-11ea-abe3-e2a9628c4c3c
last_name: Pedrotti
citation:
ama: Pedrotti F. Functional inequalities and convergence of stochastic processes.
2024. doi:10.15479/at:ista:17336
apa: Pedrotti, F. (2024). Functional inequalities and convergence of stochastic
processes. Institute of Science and Technology Austria. https://doi.org/10.15479/at:ista:17336
chicago: Pedrotti, Francesco. “Functional Inequalities and Convergence of Stochastic
Processes.” Institute of Science and Technology Austria, 2024. https://doi.org/10.15479/at:ista:17336.
ieee: F. Pedrotti, “Functional inequalities and convergence of stochastic processes,”
Institute of Science and Technology Austria, 2024.
ista: Pedrotti F. 2024. Functional inequalities and convergence of stochastic processes.
Institute of Science and Technology Austria.
mla: Pedrotti, Francesco. Functional Inequalities and Convergence of Stochastic
Processes. Institute of Science and Technology Austria, 2024, doi:10.15479/at:ista:17336.
short: F. Pedrotti, Functional Inequalities and Convergence of Stochastic Processes,
Institute of Science and Technology Austria, 2024.
corr_author: '1'
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date_published: 2024-07-31T00:00:00Z
date_updated: 2026-04-07T13:00:03Z
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ddc:
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- '510'
- '515'
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supervisor:
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full_name: Maas, Jan
id: 4C5696CE-F248-11E8-B48F-1D18A9856A87
last_name: Maas
orcid: 0000-0002-0845-1338
title: Functional inequalities and convergence of stochastic processes
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abstract:
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text: "This paper deals with local criteria for the convergence to a global minimiser
for gradient flow trajectories and their discretisations. To obtain quantitative
estimates on the speed of convergence, we consider variations on the classical
Kurdyka–Łojasiewicz inequality for a large class of parameter functions. Our assumptions
are given in terms of the initial data, without any reference to an equilibrium
point. The main results are convergence statements for gradient flow curves and
proximal point sequences to a global minimiser, together with sharp quantitative
estimates on the speed of convergence. These convergence results apply in the
general setting of lower semicontinuous functionals on complete metric spaces,
generalising recent results for smooth functionals on Rn. While the non-smooth
setting covers very general spaces, it is also useful for (non)-smooth functionals
on Rn.\r\n."
acknowledgement: The authors gratefully acknowledges support by the European Research
Council (ERC) under the European Union’s Horizon 2020 research and innovation programme
(grant agreement No. 716117). This research was funded in part by the Austrian Science
Fund (FWF) project 10.55776/ESP208. This research was funded in part by the Austrian
Science Fund (FWF) project 10.55776/F65
article_processing_charge: No
article_type: original
arxiv: 1
author:
- first_name: Lorenzo
full_name: Dello Schiavo, Lorenzo
id: ECEBF480-9E4F-11EA-B557-B0823DDC885E
last_name: Dello Schiavo
orcid: 0000-0002-9881-6870
- first_name: Jan
full_name: Maas, Jan
id: 4C5696CE-F248-11E8-B48F-1D18A9856A87
last_name: Maas
orcid: 0000-0002-0845-1338
- first_name: Francesco
full_name: Pedrotti, Francesco
id: d3ac8ac6-dc8d-11ea-abe3-e2a9628c4c3c
last_name: Pedrotti
citation:
ama: Dello Schiavo L, Maas J, Pedrotti F. Local conditions for global convergence
of gradient flows and proximal point sequences in metric spaces. Transactions
of the American Mathematical Society. 2024;377(6):3779-3804. doi:10.1090/tran/9156
apa: Dello Schiavo, L., Maas, J., & Pedrotti, F. (2024). Local conditions for
global convergence of gradient flows and proximal point sequences in metric spaces.
Transactions of the American Mathematical Society. American Mathematical
Society. https://doi.org/10.1090/tran/9156
chicago: Dello Schiavo, Lorenzo, Jan Maas, and Francesco Pedrotti. “Local Conditions
for Global Convergence of Gradient Flows and Proximal Point Sequences in Metric
Spaces.” Transactions of the American Mathematical Society. American Mathematical
Society, 2024. https://doi.org/10.1090/tran/9156.
ieee: L. Dello Schiavo, J. Maas, and F. Pedrotti, “Local conditions for global convergence
of gradient flows and proximal point sequences in metric spaces,” Transactions
of the American Mathematical Society, vol. 377, no. 6. American Mathematical
Society, pp. 3779–3804, 2024.
ista: Dello Schiavo L, Maas J, Pedrotti F. 2024. Local conditions for global convergence
of gradient flows and proximal point sequences in metric spaces. Transactions
of the American Mathematical Society. 377(6), 3779–3804.
mla: Dello Schiavo, Lorenzo, et al. “Local Conditions for Global Convergence of
Gradient Flows and Proximal Point Sequences in Metric Spaces.” Transactions
of the American Mathematical Society, vol. 377, no. 6, American Mathematical
Society, 2024, pp. 3779–804, doi:10.1090/tran/9156.
short: L. Dello Schiavo, J. Maas, F. Pedrotti, Transactions of the American Mathematical
Society 377 (2024) 3779–3804.
date_created: 2024-06-16T22:01:06Z
date_published: 2024-06-01T00:00:00Z
date_updated: 2026-04-07T13:00:02Z
day: '01'
department:
- _id: JaMa
doi: 10.1090/tran/9156
ec_funded: 1
external_id:
arxiv:
- '2304.05239'
isi:
- '001203273300001'
intvolume: ' 377'
isi: 1
issue: '6'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.48550/arXiv.2304.05239
month: '06'
oa: 1
oa_version: Preprint
page: 3779-3804
project:
- _id: 256E75B8-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '716117'
name: Optimal Transport and Stochastic Dynamics
- _id: fc31cba2-9c52-11eb-aca3-ff467d239cd2
grant_number: F6504
name: Taming Complexity in Partial Differential Systems
- _id: 34dbf174-11ca-11ed-8bc3-afe9d43d4b9c
grant_number: E208
name: Configuration Spaces over Non-Smooth Spaces
publication: Transactions of the American Mathematical Society
publication_identifier:
eissn:
- 1088-6850
issn:
- 0002-9947
publication_status: published
publisher: American Mathematical Society
quality_controlled: '1'
related_material:
record:
- id: '17336'
relation: dissertation_contains
status: public
scopus_import: '1'
status: public
title: Local conditions for global convergence of gradient flows and proximal point
sequences in metric spaces
type: journal_article
user_id: 317138e5-6ab7-11ef-aa6d-ffef3953e345
volume: 377
year: '2024'
...
---
OA_place: repository
_id: '17350'
abstract:
- lang: eng
text: "Score-based generative models (SGMs) are powerful tools to sample from\r\ncomplex
data distributions. Their underlying idea is to (i) run a forward\r\nprocess for
time $T_1$ by adding noise to the data, (ii) estimate its score\r\nfunction, and
(iii) use such estimate to run a reverse process. As the reverse\r\nprocess is
initialized with the stationary distribution of the forward one, the\r\nexisting
analysis paradigm requires $T_1\\to\\infty$. This is however\r\nproblematic: from
a theoretical viewpoint, for a given precision of the score\r\napproximation,
the convergence guarantee fails as $T_1$ diverges; from a\r\npractical viewpoint,
a large $T_1$ increases computational costs and leads to\r\nerror propagation.
This paper addresses the issue by considering a version of\r\nthe popular predictor-corrector
scheme: after running the forward process, we\r\nfirst estimate the final distribution
via an inexact Langevin dynamics and then\r\nrevert the process. Our key technical
contribution is to provide convergence\r\nguarantees which require to run the
forward process only for a fixed finite\r\ntime $T_1$. Our bounds exhibit a mild
logarithmic dependence on the input\r\ndimension and the subgaussian norm of the
target distribution, have minimal\r\nassumptions on the data, and require only
to control the $L^2$ loss on the\r\nscore approximation, which is the quantity
minimized in practice."
article_processing_charge: No
arxiv: 1
author:
- first_name: Francesco
full_name: Pedrotti, Francesco
id: d3ac8ac6-dc8d-11ea-abe3-e2a9628c4c3c
last_name: Pedrotti
- first_name: Jan
full_name: Maas, Jan
id: 4C5696CE-F248-11E8-B48F-1D18A9856A87
last_name: Maas
orcid: 0000-0002-0845-1338
- first_name: Marco
full_name: Mondelli, Marco
id: 27EB676C-8706-11E9-9510-7717E6697425
last_name: Mondelli
orcid: 0000-0002-3242-7020
citation:
ama: Pedrotti F, Maas J, Mondelli M. Improved convergence of score-based diffusion
models via prediction-correction. arXiv. doi:10.48550/arXiv.2305.14164
apa: Pedrotti, F., Maas, J., & Mondelli, M. (n.d.). Improved convergence of
score-based diffusion models via prediction-correction. arXiv. https://doi.org/10.48550/arXiv.2305.14164
chicago: Pedrotti, Francesco, Jan Maas, and Marco Mondelli. “Improved Convergence
of Score-Based Diffusion Models via Prediction-Correction.” ArXiv, n.d.
https://doi.org/10.48550/arXiv.2305.14164.
ieee: F. Pedrotti, J. Maas, and M. Mondelli, “Improved convergence of score-based
diffusion models via prediction-correction,” arXiv. .
ista: Pedrotti F, Maas J, Mondelli M. Improved convergence of score-based diffusion
models via prediction-correction. arXiv, 10.48550/arXiv.2305.14164.
mla: Pedrotti, Francesco, et al. “Improved Convergence of Score-Based Diffusion
Models via Prediction-Correction.” ArXiv, doi:10.48550/arXiv.2305.14164.
short: F. Pedrotti, J. Maas, M. Mondelli, ArXiv (n.d.).
corr_author: '1'
date_created: 2024-07-31T07:56:40Z
date_published: 2024-06-06T00:00:00Z
date_updated: 2026-04-07T13:00:02Z
day: '06'
department:
- _id: JaMa
- _id: MaMo
doi: 10.48550/arXiv.2305.14164
external_id:
arxiv:
- '2305.14164'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.48550/arXiv.2305.14164
month: '06'
oa: 1
oa_version: Preprint
project:
- _id: fc31cba2-9c52-11eb-aca3-ff467d239cd2
grant_number: F6504
name: Taming Complexity in Partial Differential Systems
- _id: 059876FA-7A3F-11EA-A408-12923DDC885E
name: Prix Lopez-Loretta 2019 - Marco Mondelli
publication: arXiv
publication_status: draft
related_material:
record:
- id: '18897'
relation: later_version
status: public
- id: '17336'
relation: dissertation_contains
status: public
status: public
title: Improved convergence of score-based diffusion models via prediction-correction
type: preprint
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
year: '2024'
...
---
OA_place: repository
_id: '17352'
abstract:
- lang: eng
text: "We prove upper bounds on the $L^\\infty$-Wasserstein distance from optimal\r\ntransport
between strongly log-concave probability densities and log-Lipschitz\r\nperturbations.
In the simplest setting, such a bound amounts to a\r\ntransport-information inequality
involving the $L^\\infty$-Wasserstein metric\r\nand the relative $L^\\infty$-Fisher
information. We show that this inequality\r\ncan be sharpened significantly in
situations where the involved densities are\r\nanisotropic. Our proof is based
on probabilistic techniques using Langevin\r\ndynamics. As an application of these
results, we obtain sharp exponential rates\r\nof convergence in Fisher's infinitesimal
model from quantitative genetics,\r\ngeneralising recent results by Calvez, Poyato,
and Santambrogio in dimension 1\r\nto arbitrary dimensions."
article_number: '2402.04151'
article_processing_charge: No
arxiv: 1
author:
- first_name: Kseniia
full_name: Khudiakova, Kseniia
id: 4E6DC800-AE37-11E9-AC72-31CAE5697425
last_name: Khudiakova
orcid: 0000-0002-6246-1465
- first_name: Jan
full_name: Maas, Jan
id: 4C5696CE-F248-11E8-B48F-1D18A9856A87
last_name: Maas
orcid: 0000-0002-0845-1338
- first_name: Francesco
full_name: Pedrotti, Francesco
id: d3ac8ac6-dc8d-11ea-abe3-e2a9628c4c3c
last_name: Pedrotti
citation:
ama: Khudiakova K, Maas J, Pedrotti F. L∞-optimal transport of anisotropic log-concave
measures and exponential convergence in Fisher’s infinitesimal model. arXiv.
doi:10.48550/arXiv.2402.04151
apa: Khudiakova, K., Maas, J., & Pedrotti, F. (n.d.). L∞-optimal transport of
anisotropic log-concave measures and exponential convergence in Fisher’s infinitesimal
model. arXiv. https://doi.org/10.48550/arXiv.2402.04151
chicago: Khudiakova, Kseniia, Jan Maas, and Francesco Pedrotti. “L∞-Optimal Transport
of Anisotropic Log-Concave Measures and Exponential Convergence in Fisher’s Infinitesimal
Model.” ArXiv, n.d. https://doi.org/10.48550/arXiv.2402.04151.
ieee: K. Khudiakova, J. Maas, and F. Pedrotti, “L∞-optimal transport of anisotropic
log-concave measures and exponential convergence in Fisher’s infinitesimal model,”
arXiv. .
ista: Khudiakova K, Maas J, Pedrotti F. L∞-optimal transport of anisotropic log-concave
measures and exponential convergence in Fisher’s infinitesimal model. arXiv, 2402.04151.
mla: Khudiakova, Kseniia, et al. “L∞-Optimal Transport of Anisotropic Log-Concave
Measures and Exponential Convergence in Fisher’s Infinitesimal Model.” ArXiv,
2402.04151, doi:10.48550/arXiv.2402.04151.
short: K. Khudiakova, J. Maas, F. Pedrotti, ArXiv (n.d.).
corr_author: '1'
date_created: 2024-07-31T08:07:40Z
date_published: 2024-02-07T00:00:00Z
date_updated: 2026-04-07T13:00:02Z
day: '07'
department:
- _id: JaMa
doi: 10.48550/arXiv.2402.04151
external_id:
arxiv:
- '2402.04151'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.48550/arXiv.2402.04151
month: '02'
oa: 1
oa_version: Preprint
project:
- _id: fc31cba2-9c52-11eb-aca3-ff467d239cd2
grant_number: F6504
name: Taming Complexity in Partial Differential Systems
- _id: 34d33d68-11ca-11ed-8bc3-ec13763c0ca8
grant_number: '26293'
name: The impact of deleterious mutations on small populations
publication: arXiv
publication_status: draft
related_material:
record:
- id: '20050'
relation: later_version
status: public
- id: '17336'
relation: dissertation_contains
status: public
status: public
title: L∞-optimal transport of anisotropic log-concave measures and exponential convergence
in Fisher's infinitesimal model
type: preprint
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
year: '2024'
...
---
OA_place: repository
_id: '17353'
abstract:
- lang: eng
text: "In this paper we derive estimates for the Hessian of the logarithm\r\n(log-Hessian)
for solutions to the heat equation. For initial data in the form\r\nof log-Lipschitz
perturbation of strongly log-concave measures, the log-Hessian\r\nadmits an explicit,
uniform (in space) lower bound. This yields a new estimate\r\nfor the Lipschitz
constant of a transport map pushing forward the standard\r\nGaussian to a measure
in this class. Further connections are discussed with\r\nscore-based diffusion
models and improved Gaussian logarithmic Sobolev\r\ninequalities. Finally, we
show that assuming only fast decay of the tails of\r\nthe initial datum does not
suffice to guarantee uniform log-Hessian upper\r\nbounds."
article_number: '2404.15205'
article_processing_charge: No
arxiv: 1
author:
- first_name: Giovanni
full_name: Brigati, Giovanni
id: 63ff57e8-1fbb-11ee-88f2-f558ffc59cf1
last_name: Brigati
- first_name: Francesco
full_name: Pedrotti, Francesco
id: d3ac8ac6-dc8d-11ea-abe3-e2a9628c4c3c
last_name: Pedrotti
citation:
ama: Brigati G, Pedrotti F. Heat flow, log-concavity, and Lipschitz transport maps.
arXiv. doi:10.48550/arXiv.2404.15205
apa: Brigati, G., & Pedrotti, F. (n.d.). Heat flow, log-concavity, and Lipschitz
transport maps. arXiv. https://doi.org/10.48550/arXiv.2404.15205
chicago: Brigati, Giovanni, and Francesco Pedrotti. “Heat Flow, Log-Concavity, and
Lipschitz Transport Maps.” ArXiv, n.d. https://doi.org/10.48550/arXiv.2404.15205.
ieee: G. Brigati and F. Pedrotti, “Heat flow, log-concavity, and Lipschitz transport
maps,” arXiv. .
ista: Brigati G, Pedrotti F. Heat flow, log-concavity, and Lipschitz transport maps.
arXiv, 2404.15205.
mla: Brigati, Giovanni, and Francesco Pedrotti. “Heat Flow, Log-Concavity, and Lipschitz
Transport Maps.” ArXiv, 2404.15205, doi:10.48550/arXiv.2404.15205.
short: G. Brigati, F. Pedrotti, ArXiv (n.d.).
corr_author: '1'
date_created: 2024-07-31T08:17:14Z
date_published: 2024-05-08T00:00:00Z
date_updated: 2026-04-07T13:00:02Z
day: '08'
department:
- _id: JaMa
doi: 10.48550/arXiv.2404.15205
external_id:
arxiv:
- '2404.15205'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.48550/arXiv.2404.15205
month: '05'
oa: 1
oa_version: Preprint
publication: arXiv
publication_status: draft
related_material:
record:
- id: '20591'
relation: later_version
status: public
- id: '17336'
relation: dissertation_contains
status: public
status: public
title: Heat flow, log-concavity, and Lipschitz transport maps
type: preprint
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
year: '2024'
...
---
OA_place: publisher
_id: '18088'
abstract:
- lang: eng
text: "Instant messaging applications like Whatsapp, Signal or Telegram have become
ubiquitous in today's society.\r\nMany of them provide not only end-to-end encryption,
but also security guarantees even when the key material gets compromised.\r\nThese
are achieved through frequent key update performed by users.\r\nIn particular,
the compromise of a group key should preserve confidentiality of previously exchanged
messages (forward secrecy), and a subsequent key update will ensure security for
future ones (post-compromise security).\r\nThough great protocols for one-on-one
communication have been known for some time, the design of ones that scale efficiently
for larger groups while achieving akin security guarantees is a hard problem.\r\nA
great deal of research has been aimed at this topic, much of it under the umbrella
of the Messaging Layer Security (MLS) working group at the IETF. \r\nStarted in
2018, this joint effort by academics and industry culminated in 2023 with the
publication of the first standard for secure group messaging [IETF, RFC9420].\r\n\r\nAt
the core of secure group messaging is a cryptographic primitive termed Continuous
Group Key Agreement, or CGKA [Alwen et al. 2021], that essentially allows a changing
group of users to agree on a common key with the added functionality security
against compromises is achieved by users asynchronously issuing a key update.
In this thesis we contribute to the understanding of CGKA across different angles.\r\nFirst,
we present a new technique to effect dynamic operations in groups, i.e., add or
remove members, that can be more efficient that the one employed by MLS in certain
settings.\r\nConsidering the setting of users belonging to multiple overlapping
groups, we then show lowerbounds on the communication cost of constructions that
leverage said overlap, at the same time showing protocols that are asymptotically
optimal and efficient for practical settings, respectively. Along the way, we
show that the communication cost of key updates in MLS is average-cost optimal.\r\nAn
important feature in CGKA protocols, particularly for big groups, is the possibility
of executing several group operations concurrently. While later versions of MLS
support this, they do at the cost of worsening the communication efficiency of
future group operations.\r\nIn this thesis we introduce two new protocols that
permit concurrency without any negative effect on efficiency. Our protocols circumvent
previously existing lower bounds by satisfying a new notion of post-compromise
security that only asks for security to be re-established after a certain number
of key updates have taken place. While this can be slower than MLS in terms of
rounds of communication, we show that it leads to more efficient overall communication.
\r\nAdditionally, we introduce a new technique that allows group members to decrease
the information they need to store and download, which makes one of our protocols
enjoy much lower download cost than any other existing CGKA constructions. "
alternative_title:
- ISTA Thesis
article_processing_charge: No
author:
- first_name: Guillermo
full_name: Pascual Perez, Guillermo
id: 2D7ABD02-F248-11E8-B48F-1D18A9856A87
last_name: Pascual Perez
orcid: 0000-0001-8630-415X
citation:
ama: Pascual Perez G. On the efficiency and security of secure group messaging.
2024. doi:10.15479/at:ista:18088
apa: Pascual Perez, G. (2024). On the efficiency and security of secure group
messaging. Institute of Science and Technology Austria. https://doi.org/10.15479/at:ista:18088
chicago: Pascual Perez, Guillermo. “On the Efficiency and Security of Secure Group
Messaging.” Institute of Science and Technology Austria, 2024. https://doi.org/10.15479/at:ista:18088.
ieee: G. Pascual Perez, “On the efficiency and security of secure group messaging,”
Institute of Science and Technology Austria, 2024.
ista: Pascual Perez G. 2024. On the efficiency and security of secure group messaging.
Institute of Science and Technology Austria.
mla: Pascual Perez, Guillermo. On the Efficiency and Security of Secure Group
Messaging. Institute of Science and Technology Austria, 2024, doi:10.15479/at:ista:18088.
short: G. Pascual Perez, On the Efficiency and Security of Secure Group Messaging,
Institute of Science and Technology Austria, 2024.
corr_author: '1'
date_created: 2024-09-18T12:59:49Z
date_published: 2024-09-18T00:00:00Z
date_updated: 2026-04-07T13:01:26Z
day: '18'
ddc:
- '000'
degree_awarded: PhD
department:
- _id: KrPi
- _id: GradSch
doi: 10.15479/at:ista:18088
ec_funded: 1
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project:
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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
related_material:
record:
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- id: '11476'
relation: part_of_dissertation
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- id: '18086'
relation: part_of_dissertation
status: public
- id: '10049'
relation: part_of_dissertation
status: public
status: public
supervisor:
- first_name: Krzysztof Z
full_name: Pietrzak, Krzysztof Z
id: 3E04A7AA-F248-11E8-B48F-1D18A9856A87
last_name: Pietrzak
orcid: 0000-0002-9139-1654
title: On the efficiency and security of secure group messaging
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'
...