---
_id: '11473'
abstract:
- lang: eng
text: "The polaron model is a basic model of quantum field theory describing a single
particle\r\ninteracting with a bosonic field. It arises in many physical contexts.
We are mostly concerned\r\nwith models applicable in the context of an impurity
atom in a Bose-Einstein condensate as\r\nwell as the problem of electrons moving
in polar crystals.\r\nThe model has a simple structure in which the interaction
of the particle with the field is given\r\nby a term linear in the field’s creation
and annihilation operators. In this work, we investigate\r\nthe properties of
this model by providing rigorous estimates on various energies relevant to the\r\nproblem.
The estimates are obtained, for the most part, by suitable operator techniques
which\r\nconstitute the principal mathematical substance of the thesis.\r\nThe
first application of these techniques is to derive the polaron model rigorously
from first\r\nprinciples, i.e., from a full microscopic quantum-mechanical many-body
problem involving an\r\nimpurity in an otherwise homogeneous system. We accomplish
this for the N + 1 Bose gas\r\nin the mean-field regime by showing that a suitable
polaron-type Hamiltonian arises at weak\r\ninteractions as a low-energy effective
theory for this problem.\r\nIn the second part, we investigate rigorously the
ground state of the model at fixed momentum\r\nand for large values of the coupling
constant. Qualitatively, the system is expected to display\r\na transition from
the quasi-particle behavior at small momenta, where the dispersion relation\r\nis
parabolic and the particle moves through the medium dragging along a cloud of
phonons, to\r\nthe radiative behavior at larger momenta where the polaron decelerates
and emits free phonons.\r\nAt the same time, in the strong coupling regime, the
bosonic field is expected to behave purely\r\nclassically. Accordingly, the effective
mass of the polaron at strong coupling is conjectured to\r\nbe asymptotically
equal to the one obtained from the semiclassical counterpart of the problem,\r\nfirst
studied by Landau and Pekar in the 1940s. For polaron models with regularized
form\r\nfactors and phonon dispersion relations of superfluid type, i.e., bounded
below by a linear\r\nfunction of the wavenumbers for all phonon momenta as in
the interacting Bose gas, we prove\r\nthat for a large window of momenta below
the radiation threshold, the energy-momentum\r\nrelation at strong coupling is
indeed essentially a parabola with semi-latus rectum equal to the\r\nLandau–Pekar
effective mass, as expected.\r\nFor the Fröhlich polaron describing electrons
in polar crystals where the dispersion relation is\r\nof the optical type and
the form factor is formally UV–singular due to the nature of the point\r\ncharge-dipole
interaction, we are able to give the corresponding upper bound. In contrast to\r\nthe
regular case, this requires the inclusion of the quantum fluctuations of the phonon
field,\r\nwhich makes the problem considerably more difficult.\r\nThe results
are supplemented by studies on the absolute ground-state energy at strong coupling,\r\na
proof of the divergence of the effective mass with the coupling constant for a
wide class of\r\npolaron models, as well as the discussion of the apparent UV
singularity of the Fröhlich model\r\nand the application of the techniques used
for its removal for the energy estimates.\r\n"
acknowledged_ssus:
- _id: SSU
alternative_title:
- ISTA Thesis
article_processing_charge: No
author:
- first_name: Krzysztof
full_name: Mysliwy, Krzysztof
id: 316457FC-F248-11E8-B48F-1D18A9856A87
last_name: Mysliwy
citation:
ama: 'Mysliwy K. Polarons in Bose gases and polar crystals: Some rigorous energy
estimates. 2022. doi:10.15479/at:ista:11473'
apa: 'Mysliwy, K. (2022). Polarons in Bose gases and polar crystals: Some rigorous
energy estimates. Institute of Science and Technology Austria. https://doi.org/10.15479/at:ista:11473'
chicago: 'Mysliwy, Krzysztof. “Polarons in Bose Gases and Polar Crystals: Some Rigorous
Energy Estimates.” Institute of Science and Technology Austria, 2022. https://doi.org/10.15479/at:ista:11473.'
ieee: 'K. Mysliwy, “Polarons in Bose gases and polar crystals: Some rigorous energy
estimates,” Institute of Science and Technology Austria, 2022.'
ista: 'Mysliwy K. 2022. Polarons in Bose gases and polar crystals: Some rigorous
energy estimates. Institute of Science and Technology Austria.'
mla: 'Mysliwy, Krzysztof. Polarons in Bose Gases and Polar Crystals: Some Rigorous
Energy Estimates. Institute of Science and Technology Austria, 2022, doi:10.15479/at:ista:11473.'
short: 'K. Mysliwy, Polarons in Bose Gases and Polar Crystals: Some Rigorous Energy
Estimates, Institute of Science and Technology Austria, 2022.'
date_created: 2022-06-30T12:15:03Z
date_published: 2022-07-01T00:00:00Z
date_updated: 2023-09-07T13:43:52Z
day: '01'
ddc:
- '515'
- '539'
degree_awarded: PhD
department:
- _id: GradSch
- _id: RoSe
doi: 10.15479/at:ista:11473
ec_funded: 1
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creator: kmysliwy
date_created: 2022-07-05T08:15:52Z
date_updated: 2022-07-05T08:17:12Z
file_id: '11487'
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language:
- iso: eng
month: '07'
oa: 1
oa_version: Published Version
page: '138'
project:
- _id: 2564DBCA-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '665385'
name: International IST Doctoral Program
publication_identifier:
issn:
- 2663-337X
publication_status: published
publisher: Institute of Science and Technology Austria
related_material:
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relation: part_of_dissertation
status: public
- id: '8705'
relation: part_of_dissertation
status: public
status: public
supervisor:
- first_name: Robert
full_name: Seiringer, Robert
id: 4AFD0470-F248-11E8-B48F-1D18A9856A87
last_name: Seiringer
orcid: 0000-0002-6781-0521
title: 'Polarons in Bose gases and polar crystals: Some rigorous energy estimates'
type: dissertation
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
year: '2022'
...
---
_id: '10799'
abstract:
- lang: eng
text: "Because of the increasing popularity of machine learning methods, it is becoming
important to understand the impact of learned components on automated decision-making
systems and to guarantee that their consequences are beneficial to society. In
other words, it is necessary to ensure that machine learning is sufficiently trustworthy
to be used in real-world applications. This thesis studies two properties of machine
learning models that are highly desirable for the\r\nsake of reliability: robustness
and fairness. In the first part of the thesis we study the robustness of learning
algorithms to training data corruption. Previous work has shown that machine learning
models are vulnerable to a range\r\nof training set issues, varying from label
noise through systematic biases to worst-case data manipulations. This is an especially
relevant problem from a present perspective, since modern machine learning methods
are particularly data hungry and therefore practitioners often have to rely on
data collected from various external sources, e.g. from the Internet, from app
users or via crowdsourcing. Naturally, such sources vary greatly in the quality
and reliability of the\r\ndata they provide. With these considerations in mind,
we study the problem of designing machine learning algorithms that are robust
to corruptions in data coming from multiple sources. We show that, in contrast
to the case of a single dataset with outliers, successful learning within this
model is possible both theoretically and practically, even under worst-case data
corruptions. The second part of this thesis deals with fairness-aware machine
learning. There are multiple areas where machine learning models have shown promising
results, but where careful considerations are required, in order to avoid discrimanative
decisions taken by such learned components. Ensuring fairness can be particularly
challenging, because real-world training datasets are expected to contain various
forms of historical bias that may affect the learning process. In this thesis
we show that data corruption can indeed render the problem of achieving fairness
impossible, by tightly characterizing the theoretical limits of fair learning
under worst-case data manipulations. However, assuming access to clean data, we
also show how fairness-aware learning can be made practical in contexts beyond
binary classification, in particular in the challenging learning to rank setting."
alternative_title:
- ISTA Thesis
article_processing_charge: No
author:
- first_name: Nikola H
full_name: Konstantinov, Nikola H
id: 4B9D76E4-F248-11E8-B48F-1D18A9856A87
last_name: Konstantinov
citation:
ama: Konstantinov NH. Robustness and fairness in machine learning. 2022. doi:10.15479/at:ista:10799
apa: Konstantinov, N. H. (2022). Robustness and fairness in machine learning.
Institute of Science and Technology Austria. https://doi.org/10.15479/at:ista:10799
chicago: Konstantinov, Nikola H. “Robustness and Fairness in Machine Learning.”
Institute of Science and Technology Austria, 2022. https://doi.org/10.15479/at:ista:10799.
ieee: N. H. Konstantinov, “Robustness and fairness in machine learning,” Institute
of Science and Technology Austria, 2022.
ista: Konstantinov NH. 2022. Robustness and fairness in machine learning. Institute
of Science and Technology Austria.
mla: Konstantinov, Nikola H. Robustness and Fairness in Machine Learning.
Institute of Science and Technology Austria, 2022, doi:10.15479/at:ista:10799.
short: N.H. Konstantinov, Robustness and Fairness in Machine Learning, Institute
of Science and Technology Austria, 2022.
date_created: 2022-02-28T13:03:49Z
date_published: 2022-03-08T00:00:00Z
date_updated: 2023-10-17T12:31:54Z
day: '08'
ddc:
- '000'
degree_awarded: PhD
department:
- _id: GradSch
- _id: ChLa
doi: 10.15479/at:ista:10799
ec_funded: 1
file:
- access_level: open_access
checksum: 626bc523ae8822d20e635d0e2d95182e
content_type: application/pdf
creator: nkonstan
date_created: 2022-03-06T11:42:54Z
date_updated: 2022-03-06T11:42:54Z
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date_created: 2022-03-06T11:42:57Z
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file_size: 22841103
relation: source_file
file_date_updated: 2022-03-10T12:11:48Z
has_accepted_license: '1'
keyword:
- robustness
- fairness
- machine learning
- PAC learning
- adversarial learning
language:
- iso: eng
month: '03'
oa: 1
oa_version: Published Version
page: '176'
project:
- _id: 2564DBCA-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '665385'
name: International IST Doctoral Program
publication_identifier:
isbn:
- 978-3-99078-015-2
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: '10803'
relation: part_of_dissertation
status: public
- id: '10802'
relation: part_of_dissertation
status: public
- id: '6590'
relation: part_of_dissertation
status: public
status: public
supervisor:
- first_name: Christoph
full_name: Lampert, Christoph
id: 40C20FD2-F248-11E8-B48F-1D18A9856A87
last_name: Lampert
orcid: 0000-0001-8622-7887
title: Robustness and fairness in machine learning
type: dissertation
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
year: '2022'
...
---
_id: '11626'
abstract:
- lang: eng
text: Plant growth and development is well known to be both, flexible and dynamic.
The high capacity for post-embryonic organ formation and tissue regeneration requires
tightly regulated intercellular communication and coordinated tissue polarization.
One of the most important drivers for patterning and polarity in plant development
is the phytohormone auxin. Auxin has the unique characteristic to establish polarized
channels for its own active directional cell to cell transport. This fascinating
phenomenon is called auxin canalization. Those auxin transport channels are characterized
by the expression and polar, subcellular localization of PIN auxin efflux carriers.
PIN proteins have the ability to dynamically change their localization and auxin
itself can affect this by interfering with trafficking. Most of the underlying
molecular mechanisms of canalization still remain enigmatic. What is known so
far is that canonical auxin signaling is indispensable but also other non-canonical
signaling components are thought to play a role. In order to shed light into the
mysteries auf auxin canalization this study revisits the branches of auxin signaling
in detail. Further a new auxin analogue, PISA, is developed which triggers auxin-like
responses but does not directly activate canonical transcriptional auxin signaling.
We revisit the direct auxin effect on PIN trafficking where we found that, contradictory
to previous observations, auxin is very specifically promoting endocytosis of
PIN2 but has no overall effect on endocytosis. Further, we evaluate which cellular
processes related to PIN subcellular dynamics are involved in the establishment
of auxin conducting channels and the formation of vascular tissue. We are re-evaluating
the function of AUXIN BINDING PROTEIN 1 (ABP1) and provide a comprehensive picture
about its developmental phneotypes and involvement in auxin signaling and canalization.
Lastly, we are focusing on the crosstalk between the hormone strigolactone (SL)
and auxin and found that SL is interfering with essentially all processes involved
in auxin canalization in a non-transcriptional manner. Lastly we identify a new
way of SL perception and signaling which is emanating from mitochondria, is independent
of canonical SL signaling and is modulating primary root growth.
alternative_title:
- ISTA Thesis
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
citation:
ama: Gallei MC. Auxin and strigolactone non-canonical signaling regulating development
in Arabidopsis thaliana. 2022. doi:10.15479/at:ista:11626
apa: Gallei, M. C. (2022). Auxin and strigolactone non-canonical signaling regulating
development in Arabidopsis thaliana. Institute of Science and Technology Austria.
https://doi.org/10.15479/at:ista:11626
chicago: Gallei, Michelle C. “Auxin and Strigolactone Non-Canonical Signaling Regulating
Development in Arabidopsis Thaliana.” Institute of Science and Technology Austria,
2022. https://doi.org/10.15479/at:ista:11626.
ieee: M. C. Gallei, “Auxin and strigolactone non-canonical signaling regulating
development in Arabidopsis thaliana,” Institute of Science and Technology Austria,
2022.
ista: Gallei MC. 2022. Auxin and strigolactone non-canonical signaling regulating
development in Arabidopsis thaliana. Institute of Science and Technology Austria.
mla: Gallei, Michelle C. Auxin and Strigolactone Non-Canonical Signaling Regulating
Development in Arabidopsis Thaliana. Institute of Science and Technology Austria,
2022, doi:10.15479/at:ista:11626.
short: M.C. Gallei, Auxin and Strigolactone Non-Canonical Signaling Regulating Development
in Arabidopsis Thaliana, Institute of Science and Technology Austria, 2022.
date_created: 2022-07-20T11:21:53Z
date_published: 2022-07-20T00:00:00Z
date_updated: 2023-11-07T08:20:13Z
day: '20'
ddc:
- '575'
degree_awarded: PhD
department:
- _id: GradSch
- _id: JiFr
doi: 10.15479/at:ista:11626
ec_funded: 1
file:
- access_level: open_access
checksum: bd7ac35403cf5b4b2607287d2a104b3a
content_type: application/pdf
creator: mgallei
date_created: 2022-07-25T09:08:47Z
date_updated: 2022-07-25T09:08:47Z
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date_updated: 2022-07-25T09:39:58Z
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date_created: 2022-07-25T09:09:32Z
date_updated: 2022-07-25T09:39:58Z
description: This is the print version of the thesis including the full appendix
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content_type: application/pdf
creator: mgallei
date_created: 2022-07-25T11:48:45Z
date_updated: 2022-07-25T11:48:45Z
file_id: '11650'
file_name: Thesis_Gallei_Appendix.pdf
file_size: 15435966
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file_date_updated: 2022-07-25T11:48:45Z
has_accepted_license: '1'
language:
- iso: eng
month: '07'
oa: 1
oa_version: Published Version
page: '248'
project:
- _id: 261099A6-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '742985'
name: Tracing Evolution of Auxin Transport and Polarity in Plants
publication_identifier:
isbn:
- 978-3-99078-019-0
issn:
- 2663-337X
publication_status: published
publisher: Institute of Science and Technology Austria
related_material:
record:
- id: '8931'
relation: part_of_dissertation
status: public
- id: '9287'
relation: part_of_dissertation
status: public
- id: '7142'
relation: part_of_dissertation
status: public
- id: '7465'
relation: part_of_dissertation
status: public
- id: '8138'
relation: part_of_dissertation
status: public
- id: '6260'
relation: part_of_dissertation
status: public
- id: '10411'
relation: part_of_dissertation
status: public
status: public
supervisor:
- first_name: Jiří
full_name: Friml, Jiří
id: 4159519E-F248-11E8-B48F-1D18A9856A87
last_name: Friml
orcid: 0000-0002-8302-7596
- first_name: Eva
full_name: Benková, Eva
id: 38F4F166-F248-11E8-B48F-1D18A9856A87
last_name: Benková
orcid: 0000-0002-8510-9739
- first_name: Eilon
full_name: Shani, Eilon
last_name: Shani
title: Auxin and strigolactone non-canonical signaling regulating development in Arabidopsis
thaliana
type: dissertation
user_id: 8b945eb4-e2f2-11eb-945a-df72226e66a9
year: '2022'
...
---
_id: '12358'
abstract:
- lang: eng
text: "The complex yarn structure of knitted and woven fabrics gives rise to both
a mechanical and\r\nvisual complexity. The small-scale interactions of yarns colliding
with and pulling on each\r\nother result in drastically different large-scale
stretching and bending behavior, introducing\r\nanisotropy, curling, and more.
While simulating cloth as individual yarns can reproduce this\r\ncomplexity and
match the quality of real fabric, it may be too computationally expensive for\r\nlarge
fabrics. On the other hand, continuum-based approaches do not need to discretize
the\r\ncloth at a stitch-level, but it is non-trivial to find a material model
that would replicate the\r\nlarge-scale behavior of yarn fabrics, and they discard
the intricate visual detail. In this thesis,\r\nwe discuss three methods to try
and bridge the gap between small-scale and large-scale yarn\r\nmechanics using
numerical homogenization: fitting a continuum model to periodic yarn simulations,
adding mechanics-aware yarn detail onto thin-shell simulations, and quantitatively\r\nfitting
yarn parameters to physical measurements of real fabric.\r\nTo start, we present
a method for animating yarn-level cloth effects using a thin-shell solver.\r\nWe
first use a large number of periodic yarn-level simulations to build a model of
the potential\r\nenergy density of the cloth, and then use it to compute forces
in a thin-shell simulator. The\r\nresulting simulations faithfully reproduce expected
effects like the stiffening of woven fabrics\r\nand the highly deformable nature
and anisotropy of knitted fabrics at a fraction of the cost of\r\nfull yarn-level
simulation.\r\nWhile our thin-shell simulations are able to capture large-scale
yarn mechanics, they lack\r\nthe rich visual detail of yarn-level simulations.
Therefore, we propose a method to animate\r\nyarn-level cloth geometry on top
of an underlying deforming mesh in a mechanics-aware\r\nfashion in real time.
Using triangle strains to interpolate precomputed yarn geometry, we are\r\nable
to reproduce effects such as knit loops tightening under stretching at negligible
cost.\r\nFinally, we introduce a methodology for inverse-modeling of yarn-level
mechanics of cloth,\r\nbased on the mechanical response of fabrics in the real
world. We compile a database from\r\nphysical tests of several knitted fabrics
used in the textile industry spanning diverse physical\r\nproperties like stiffness,
nonlinearity, and anisotropy. We then develop a system for approximating these
mechanical responses with yarn-level cloth simulation, using homogenized\r\nshell
models to speed up computation and adding some small-but-necessary extensions
to\r\nyarn-level models used in computer graphics.\r\n"
acknowledged_ssus:
- _id: SSU
alternative_title:
- ISTA Thesis
article_processing_charge: No
author:
- first_name: Georg
full_name: Sperl, Georg
id: 4DD40360-F248-11E8-B48F-1D18A9856A87
last_name: Sperl
citation:
ama: 'Sperl G. Homogenizing yarn simulations: Large-scale mechanics, small-scale
detail, and quantitative fitting. 2022. doi:10.15479/at:ista:12103'
apa: 'Sperl, G. (2022). Homogenizing yarn simulations: Large-scale mechanics,
small-scale detail, and quantitative fitting. Institute of Science and Technology
Austria. https://doi.org/10.15479/at:ista:12103'
chicago: 'Sperl, Georg. “Homogenizing Yarn Simulations: Large-Scale Mechanics, Small-Scale
Detail, and Quantitative Fitting.” Institute of Science and Technology Austria,
2022. https://doi.org/10.15479/at:ista:12103.'
ieee: 'G. Sperl, “Homogenizing yarn simulations: Large-scale mechanics, small-scale
detail, and quantitative fitting,” Institute of Science and Technology Austria,
2022.'
ista: 'Sperl G. 2022. Homogenizing yarn simulations: Large-scale mechanics, small-scale
detail, and quantitative fitting. Institute of Science and Technology Austria.'
mla: 'Sperl, Georg. Homogenizing Yarn Simulations: Large-Scale Mechanics, Small-Scale
Detail, and Quantitative Fitting. Institute of Science and Technology Austria,
2022, doi:10.15479/at:ista:12103.'
short: 'G. Sperl, Homogenizing Yarn Simulations: Large-Scale Mechanics, Small-Scale
Detail, and Quantitative Fitting, Institute of Science and Technology Austria,
2022.'
date_created: 2023-01-24T10:49:46Z
date_published: 2022-09-22T00:00:00Z
date_updated: 2024-02-28T12:57:46Z
day: '22'
ddc:
- '000'
- '620'
degree_awarded: PhD
department:
- _id: GradSch
- _id: ChWo
doi: 10.15479/at:ista:12103
ec_funded: 1
file:
- access_level: open_access
checksum: 083722acbb8115e52e3b0fdec6226769
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creator: cchlebak
date_created: 2023-01-25T12:04:41Z
date_updated: 2023-02-02T09:29:57Z
description: 'This is the main PDF file of the thesis. File size: 105 MB'
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date_created: 2023-02-02T09:33:37Z
date_updated: 2023-02-02T09:33:37Z
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has_accepted_license: '1'
language:
- iso: eng
month: '09'
oa: 1
oa_version: Published Version
page: '138'
project:
- _id: 2533E772-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '638176'
name: Efficient Simulation of Natural Phenomena at Extremely Large Scales
publication_identifier:
isbn:
- 978-3-99078-020-6
issn:
- 2663-337X
publication_status: published
publisher: Institute of Science and Technology Austria
related_material:
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relation: part_of_dissertation
status: public
- id: '9818'
relation: part_of_dissertation
status: public
- id: '8385'
relation: part_of_dissertation
status: public
status: public
supervisor:
- first_name: Christopher J
full_name: Wojtan, Christopher J
id: 3C61F1D2-F248-11E8-B48F-1D18A9856A87
last_name: Wojtan
orcid: 0000-0001-6646-5546
title: 'Homogenizing yarn simulations: Large-scale mechanics, small-scale detail,
and quantitative fitting'
type: dissertation
user_id: 8b945eb4-e2f2-11eb-945a-df72226e66a9
year: '2022'
...
---
_id: '10759'
abstract:
- lang: eng
text: In this Thesis, I study composite quantum impurities with variational techniques,
both inspired by machine learning as well as fully analytic. I supplement this
with exploration of other applications of machine learning, in particular artificial
neural networks, in many-body physics. In Chapters 3 and 4, I study quasiparticle
systems with variational approach. I derive a Hamiltonian describing the angulon
quasiparticle in the presence of a magnetic field. I apply analytic variational
treatment to this Hamiltonian. Then, I introduce a variational approach for non-additive
systems, based on artificial neural networks. I exemplify this approach on the
example of the polaron quasiparticle (Fröhlich Hamiltonian). In Chapter 5, I continue
using artificial neural networks, albeit in a different setting. I apply artificial
neural networks to detect phases from snapshots of two types physical systems.
Namely, I study Monte Carlo snapshots of multilayer classical spin models as well
as molecular dynamics maps of colloidal systems. The main type of networks that
I use here are convolutional neural networks, known for their applicability to
image data.
alternative_title:
- ISTA Thesis
article_processing_charge: No
author:
- first_name: Wojciech
full_name: Rzadkowski, Wojciech
id: 48C55298-F248-11E8-B48F-1D18A9856A87
last_name: Rzadkowski
orcid: 0000-0002-1106-4419
citation:
ama: Rzadkowski W. Analytic and machine learning approaches to composite quantum
impurities. 2022. doi:10.15479/at:ista:10759
apa: Rzadkowski, W. (2022). Analytic and machine learning approaches to composite
quantum impurities. Institute of Science and Technology Austria. https://doi.org/10.15479/at:ista:10759
chicago: Rzadkowski, Wojciech. “Analytic and Machine Learning Approaches to Composite
Quantum Impurities.” Institute of Science and Technology Austria, 2022. https://doi.org/10.15479/at:ista:10759.
ieee: W. Rzadkowski, “Analytic and machine learning approaches to composite quantum
impurities,” Institute of Science and Technology Austria, 2022.
ista: Rzadkowski W. 2022. Analytic and machine learning approaches to composite
quantum impurities. Institute of Science and Technology Austria.
mla: Rzadkowski, Wojciech. Analytic and Machine Learning Approaches to Composite
Quantum Impurities. Institute of Science and Technology Austria, 2022, doi:10.15479/at:ista:10759.
short: W. Rzadkowski, Analytic and Machine Learning Approaches to Composite Quantum
Impurities, Institute of Science and Technology Austria, 2022.
date_created: 2022-02-16T13:27:37Z
date_published: 2022-02-21T00:00:00Z
date_updated: 2024-02-28T13:01:59Z
day: '21'
ddc:
- '530'
degree_awarded: PhD
department:
- _id: GradSch
- _id: MiLe
doi: 10.15479/at:ista:10759
ec_funded: 1
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month: '02'
oa: 1
oa_version: Published Version
page: '120'
project:
- _id: 2564DBCA-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '665385'
name: International IST Doctoral Program
publication_identifier:
issn:
- 2663-337X
publication_status: published
publisher: Institute of Science and Technology Austria
related_material:
record:
- id: '10762'
relation: part_of_dissertation
status: public
- id: '8644'
relation: part_of_dissertation
status: public
- id: '7956'
relation: part_of_dissertation
status: public
- id: '415'
relation: part_of_dissertation
status: public
status: public
supervisor:
- first_name: Mikhail
full_name: Lemeshko, Mikhail
id: 37CB05FA-F248-11E8-B48F-1D18A9856A87
last_name: Lemeshko
orcid: 0000-0002-6990-7802
title: Analytic and machine learning approaches to composite quantum impurities
type: dissertation
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
year: '2022'
...
---
_id: '11196'
abstract:
- lang: eng
text: "One of the fundamental questions in Neuroscience is how the structure of
synapses and their physiological properties are related. While synaptic transmission
remains a dynamic process, electron microscopy provides images with comparably
low temporal resolution (Studer et al., 2014). The current work overcomes this
challenge and describes an improved “Flash and Freeze” technique (Watanabe et
al., 2013a; Watanabe et al., 2013b) to study synaptic transmission at the hippocampal
mossy fiber-CA3 pyramidal neuron synapses, using mouse acute brain slices and
organotypic slices culture. The improved method allowed for selective stimulation
of presynaptic mossy fiber boutons and the observation of synaptic vesicle pool
dynamics at the active zones. Our results uncovered several intriguing morphological
features of mossy fiber boutons. First, the docked vesicle pool was largely depleted
(more than 70%) after stimulation, implying that the docked synaptic vesicles
pool and readily releasable pool are vastly overlapping in mossy fiber boutons.
Second, the synaptic vesicles are skewed towards larger diameters, displaying
a wide range of sizes. An increase in the mean diameter of synaptic vesicles,
after single and repetitive stimulation, suggests that smaller vesicles have a
higher release probability. Third, we observed putative endocytotic structures
after moderate light stimulation, matching the timing of previously described
ultrafast endocytosis (Watanabe et al., 2013a; Delvendahl et al., 2016). \r\n\tIn
addition, synaptic transmission depends on a sophisticated system of protein machinery
and calcium channels (Südhof, 2013b), which amplifies the challenge in studying
synaptic communication as these interactions can be potentially modified during
synaptic plasticity. And although recent study elucidated the potential correlation
between physiological and morphological properties of synapses during synaptic
plasticity (Vandael et al., 2020), the molecular underpinning of it remains unknown.
Thus, the presented work tries to overcome this challenge and aims to pinpoint
changes in the molecular architecture at hippocampal mossy fiber bouton synapses
during short- and long-term potentiation (STP and LTP), we combined chemical potentiation,
with the application of a cyclic adenosine monophosphate agonist (i.e. forskolin)
and freeze-fracture replica immunolabelling. This method allowed the localization
of membrane-bound proteins with nanometer precision within the active zone, in
particular, P/Q-type calcium channels and synaptic vesicle priming proteins Munc13-1/2.
First, we found that the number of clusters of Munc13-1 in the mossy fiber bouton
active zone increased significantly during STP, but decreased to lower than the
control value during LTP. Secondly, although the distance between the calcium
channels and Munc13-1s did not change after induction of STP, it shortened during
the LTP phase. Additionally, forskolin did not affect Munc13-2 distribution during
STP and LTP. These results indicate the existence of two distinct mechanisms that
govern STP and LTP at mossy fiber bouton synapses: an increase in the readily
realizable pool in the case of STP and a potential increase in release probability
during LTP. “Flash and freeze” and functional electron microscopy, are versatile
methods that can be successfully applied to intact brain circuits to study synaptic
transmission even at the molecular level.\r\n"
acknowledged_ssus:
- _id: EM-Fac
- _id: PreCl
alternative_title:
- ISTA Thesis
article_processing_charge: No
author:
- first_name: Olena
full_name: Kim, Olena
id: 3F8ABDDA-F248-11E8-B48F-1D18A9856A87
last_name: Kim
citation:
ama: Kim O. Nanoarchitecture of hippocampal mossy fiber-CA3 pyramidal neuron synapses.
2022. doi:10.15479/at:ista:11196
apa: Kim, O. (2022). Nanoarchitecture of hippocampal mossy fiber-CA3 pyramidal
neuron synapses. Institute of Science and Technology Austria. https://doi.org/10.15479/at:ista:11196
chicago: Kim, Olena. “Nanoarchitecture of Hippocampal Mossy Fiber-CA3 Pyramidal
Neuron Synapses.” Institute of Science and Technology Austria, 2022. https://doi.org/10.15479/at:ista:11196.
ieee: O. Kim, “Nanoarchitecture of hippocampal mossy fiber-CA3 pyramidal neuron
synapses,” Institute of Science and Technology Austria, 2022.
ista: Kim O. 2022. Nanoarchitecture of hippocampal mossy fiber-CA3 pyramidal neuron
synapses. Institute of Science and Technology Austria.
mla: Kim, Olena. Nanoarchitecture of Hippocampal Mossy Fiber-CA3 Pyramidal Neuron
Synapses. Institute of Science and Technology Austria, 2022, doi:10.15479/at:ista:11196.
short: O. Kim, Nanoarchitecture of Hippocampal Mossy Fiber-CA3 Pyramidal Neuron
Synapses, Institute of Science and Technology Austria, 2022.
date_created: 2022-04-20T09:47:12Z
date_published: 2022-04-20T00:00:00Z
date_updated: 2023-08-18T06:31:52Z
day: '20'
ddc:
- '570'
degree_awarded: PhD
department:
- _id: PeJo
- _id: GradSch
doi: 10.15479/at:ista:11196
ec_funded: 1
file:
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content_type: application/pdf
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date_created: 2022-04-20T14:21:56Z
date_updated: 2023-04-20T22:30:03Z
embargo: 2023-04-19
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language:
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month: '04'
oa: 1
oa_version: Published Version
page: '132'
project:
- _id: 25BAF7B2-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '708497'
name: Presynaptic calcium channels distribution and impact on coupling at the hippocampal
mossy fiber synapse
- _id: 25B7EB9E-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '692692'
name: Biophysics and circuit function of a giant cortical glumatergic synapse
- _id: 25C3DBB6-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: W01205
name: Zellkommunikation in Gesundheit und Krankheit
- _id: 25C5A090-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: Z00312
name: The Wittgenstein Prize
publication_identifier:
issn:
- 2663-337X
publication_status: published
publisher: Institute of Science and Technology Austria
related_material:
record:
- id: '11222'
relation: part_of_dissertation
status: public
- id: '7473'
relation: part_of_dissertation
status: public
status: public
supervisor:
- first_name: Peter M
full_name: Jonas, Peter M
id: 353C1B58-F248-11E8-B48F-1D18A9856A87
last_name: Jonas
orcid: 0000-0001-5001-4804
title: Nanoarchitecture of hippocampal mossy fiber-CA3 pyramidal neuron synapses
tmp:
image: /images/cc_by_nc_nd.png
legal_code_url: https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode
name: Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International
(CC BY-NC-ND 4.0)
short: CC BY-NC-ND (4.0)
type: dissertation
user_id: 8b945eb4-e2f2-11eb-945a-df72226e66a9
year: '2022'
...
---
_id: '10727'
abstract:
- lang: eng
text: "Social insects are a common model to study disease dynamics in social animals.
Even though pathogens should thrive in social insect colonies as the hosts engage
in frequent social interactions, are closely related and live in a pathogen-rich
environment, disease outbreaks are rare. This is because social insects have evolved
mechanisms to keep pathogens at bay – and fight disease as a collective. Social
insect colonies are often viewed as “superorganisms” with division of labor between
reproductive “germ-like” queens and males and “somatic” workers, which together
form an interdependent reproductive unit that parallels a multicellular body.
Superorganisms possess a “social immune system” that comprises of collective disease
defenses performed by the workers - summarized as “social immunity”. In social
groups immunization (reduced susceptibility to a parasite upon secondary exposure
to the same parasite) can e.g. be triggered by social interactions (“social immunization”).
Social immunization can be caused by (i) asymptomatic low-level infections that
are acquired during caregiving to a contagious individual that can give an immune
boost, which can induce protection upon later encounter with the same pathogen
(active immunization) or (ii) by transfer of immune effectors between individuals
(passive immunization).\r\nIn the second chapter, I built up on a study that I
co-authored that found that low-level infections can not only be protective, but
also be costly and make the host more susceptible to detrimental superinfections
after contact to a very dissimilar pathogen. I here now tested different degrees
of phylogenetically-distant fungal strains of M. brunneum and M. robertsii in
L. neglectus and can describe the occurrence of cross-protection of social immunization
if the first and second pathogen are from the same level. Interestingly, low-level
infections only provided protection when the first strain was less virulent than
the second strain and elicited higher immune gene expression.\r\nIn the third
and fourth chapters, I expanded on the role of social immunity in sexual selection,
a so far unstudied field. I used the fungus Metarhizium robertsii and the ant
Cardiocondyla obscurior as a model, as in this species mating occurs in the presence
of workers and can be studied under laboratory conditions. Before males mate with
virgin queens in the nest they engage in fierce combat over the access to their
mating partners.\r\nFirst, I focused on male-male competition in the third chapter
and found that fighting with a contagious male is costly as it can lead to contamination
of the rival, but that workers can decrease the risk of disease contraction by
performing sanitary care.\r\nIn the fourth chapter, I studied the effect of fungal
infection on survival and mating success of sexuals (freshly emerged queens and
males) and found that worker-performed sanitary care can buffer the negative effect
that a pathogenic contagion would have on sexuals by spore removal from the exposed
individuals. When social immunity was prevented and queens could contract spores
from their mating partner, very low dosages led to negative consequences: their
lifespan was reduced and they produced fewer offspring with poor immunocompetence
compared to healthy queens. Interestingly, cohabitation with a late-stage infected
male where no spore transfer was possible had a positive effect on offspring immunity
– male offspring of mothers that apparently perceived an infected partner in their
vicinity reacted more sensitively to fungal challenge than male offspring without
paternal pathogen history."
acknowledged_ssus:
- _id: LifeSc
alternative_title:
- ISTA Thesis
article_processing_charge: No
author:
- first_name: Sina
full_name: Metzler, Sina
id: 48204546-F248-11E8-B48F-1D18A9856A87
last_name: Metzler
orcid: 0000-0002-9547-2494
citation:
ama: Metzler S. Pathogen-mediated sexual selection and immunization in ant colonies.
2022. doi:10.15479/AT:ISTA:10727
apa: Metzler, S. (2022). Pathogen-mediated sexual selection and immunization
in ant colonies. Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:10727
chicago: Metzler, Sina. “Pathogen-Mediated Sexual Selection and Immunization in
Ant Colonies.” Institute of Science and Technology Austria, 2022. https://doi.org/10.15479/AT:ISTA:10727.
ieee: S. Metzler, “Pathogen-mediated sexual selection and immunization in ant colonies,”
Institute of Science and Technology Austria, 2022.
ista: Metzler S. 2022. Pathogen-mediated sexual selection and immunization in ant
colonies. Institute of Science and Technology Austria.
mla: Metzler, Sina. Pathogen-Mediated Sexual Selection and Immunization in Ant
Colonies. Institute of Science and Technology Austria, 2022, doi:10.15479/AT:ISTA:10727.
short: S. Metzler, Pathogen-Mediated Sexual Selection and Immunization in Ant Colonies,
Institute of Science and Technology Austria, 2022.
date_created: 2022-02-04T15:45:12Z
date_published: 2022-02-07T00:00:00Z
date_updated: 2023-09-07T13:43:23Z
day: '07'
ddc:
- '570'
degree_awarded: PhD
department:
- _id: GradSch
- _id: SyCr
doi: 10.15479/AT:ISTA:10727
ec_funded: 1
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date_created: 2022-02-04T15:36:12Z
date_updated: 2023-02-03T23:30:03Z
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creator: smetzler
date_created: 2022-02-04T15:36:43Z
date_updated: 2023-02-03T23:30:03Z
embargo: 2023-02-02
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creator: smetzler
date_created: 2022-02-07T10:35:02Z
date_updated: 2023-02-04T23:30:03Z
embargo: 2023-02-02
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file_date_updated: 2023-02-04T23:30:03Z
has_accepted_license: '1'
language:
- iso: eng
month: '02'
oa: 1
oa_version: Published Version
project:
- _id: 2649B4DE-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '771402'
name: Epidemics in ant societies on a chip
publication_identifier:
issn:
- 2663-337X
publication_status: published
publisher: Institute of Science and Technology Austria
status: public
supervisor:
- first_name: Sylvia
full_name: Cremer, Sylvia
id: 2F64EC8C-F248-11E8-B48F-1D18A9856A87
last_name: Cremer
orcid: 0000-0002-2193-3868
title: Pathogen-mediated sexual selection and immunization in ant colonies
type: dissertation
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
year: '2022'
...
---
_id: '11879'
abstract:
- lang: eng
text: "As the overall global mean surface temperature is increasing due to climate
change, plant\r\nadaptation to those stressful conditions is of utmost importance
for their survival. Plants are\r\nsessile organisms, thus to compensate for their
lack of mobility, they evolved a variety of\r\nmechanisms enabling them to flexibly
adjust their physiological, growth and developmental\r\nprocesses to fluctuating
temperatures and to survive in harsh environments. While these unique\r\nadaptation
abilities provide an important evolutionary advantage, overall modulation of plant\r\ngrowth
and developmental program due to non-optimal temperature negatively affects biomass\r\nproduction,
crop productivity or sensitivity to pathogens. Thus, understanding molecular\r\nprocesses
underlying plant adaptation to increased temperature can provide important\r\nresources
for breeding strategies to ensure sufficient agricultural food production.\r\nAn
increase in ambient temperature by a few degrees leads to profound changes in
organ growth\r\nincluding enhanced hypocotyl elongation, expansion of petioles,
hyponastic growth of leaves and\r\ncotyledons, collectively named thermomorphogenesis
(Casal & Balasubramanian, 2019). Auxin,\r\none of the best-studied growth hormones,
plays an essential role in this process by direct\r\nactivation of transcriptional
and non-transcriptional processes resulting in elongation growth\r\n(Majda & Robert,
2018).To modulate hypocotyl growth in response to high ambient temperature\r\n(hAT),
auxin needs to be redistributed accordingly. PINs, auxin efflux transporters,
are key\r\ncomponents of the polar auxin transport (PAT) machinery, which controls
the amount and\r\ndirection of auxin translocated in the plant tissues and organs(Adamowski
& Friml, 2015). Hence,\r\nPIN-mediated transport is tightly linked with thermo-morphogenesis,
and interference with PAT\r\nthrough either chemical or genetic means dramatically
affecting the adaptive responses to hAT.\r\nIntriguingly, despite the key role
of PIN mediated transport in growth response to hAT, whether\r\nand how PINs at
the level of expression adapt to fluctuation in temperature is scarcely\r\nunderstood.\r\nWith
genetic, molecular and advanced bio-imaging approaches, we demonstrate the role
of PIN\r\nauxin transporters in the regulation of hypocotyl growth in response
to hAT. We show that via\r\nadjustment of PIN3, PIN4 and PIN7 expression in cotyledons
and hypocotyls, auxin distribution is modulated thereby determining elongation
pattern of epidermal cells at hAT. Furthermore, we\r\nidentified three Zinc-Finger
(ZF) transcription factors as novel molecular components of the\r\nthermo-regulatory
network, which through negative regulation of PIN transcription adjust the\r\ntransport
of auxin at hAT. Our results suggest that the ZF-PIN module might be a part of
the\r\nnegative feedback loop attenuating the activity of the thermo-sensing pathway
to restrain\r\nexaggerated growth and developmental responses to hAT."
acknowledged_ssus:
- _id: Bio
- _id: LifeSc
- _id: SSU
acknowledgement: I would like to acknowledge ISTA and all the people from the Scientific
Service Units and at ISTA, in particular Dorota Jaworska for excellent technical
and scientific support as well as ÖAW for funding my research for over 3 years (DOC
ÖAW Fellowship PR1022OEAW02).
alternative_title:
- ISTA Thesis
article_processing_charge: No
author:
- first_name: Christina
full_name: Artner, Christina
id: 45DF286A-F248-11E8-B48F-1D18A9856A87
last_name: Artner
citation:
ama: Artner C. Modulation of auxin transport via ZF proteins adjust plant response
to high ambient temperature. 2022. doi:10.15479/at:ista:11879
apa: Artner, C. (2022). Modulation of auxin transport via ZF proteins adjust
plant response to high ambient temperature. Institute of Science and Technology
Austria. https://doi.org/10.15479/at:ista:11879
chicago: Artner, Christina. “Modulation of Auxin Transport via ZF Proteins Adjust
Plant Response to High Ambient Temperature.” Institute of Science and Technology
Austria, 2022. https://doi.org/10.15479/at:ista:11879.
ieee: C. Artner, “Modulation of auxin transport via ZF proteins adjust plant response
to high ambient temperature,” Institute of Science and Technology Austria, 2022.
ista: Artner C. 2022. Modulation of auxin transport via ZF proteins adjust plant
response to high ambient temperature. Institute of Science and Technology Austria.
mla: Artner, Christina. Modulation of Auxin Transport via ZF Proteins Adjust
Plant Response to High Ambient Temperature. Institute of Science and Technology
Austria, 2022, doi:10.15479/at:ista:11879.
short: C. Artner, Modulation of Auxin Transport via ZF Proteins Adjust Plant Response
to High Ambient Temperature, Institute of Science and Technology Austria, 2022.
date_created: 2022-08-17T07:58:53Z
date_published: 2022-08-17T00:00:00Z
date_updated: 2023-09-09T22:30:04Z
day: '17'
ddc:
- '580'
degree_awarded: PhD
department:
- _id: GradSch
- _id: EvBe
doi: 10.15479/at:ista:11879
file:
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date_created: 2022-08-17T12:08:59Z
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file_size: 19097730
relation: source_file
file_date_updated: 2023-09-09T22:30:03Z
has_accepted_license: '1'
keyword:
- high ambient temperature
- auxin
- PINs
- Zinc-Finger proteins
- thermomorphogenesis
- stress
language:
- iso: eng
month: '08'
oa: 1
oa_version: Published Version
page: '128'
project:
- _id: 2685A872-B435-11E9-9278-68D0E5697425
name: Hormonal regulation of plant adaptive responses to environmental signals
publication_identifier:
isbn:
- 978-3-99078-022-0
issn:
- 2663-337X
publication_status: published
publisher: Institute of Science and Technology Austria
status: public
supervisor:
- first_name: Eva
full_name: Benková, Eva
id: 38F4F166-F248-11E8-B48F-1D18A9856A87
last_name: Benková
orcid: 0000-0002-8510-9739
title: Modulation of auxin transport via ZF proteins adjust plant response to high
ambient temperature
type: dissertation
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
year: '2022'
...
---
_id: '11393'
abstract:
- lang: eng
text: "AMPA receptors (AMPARs) mediate fast excitatory neurotransmission and their
role is\r\nimplicated in complex processes such as learning and memory and various
neurological\r\ndiseases. These receptors are composed of different subunits and
the subunit composition can\r\naffect channel properties, receptor trafficking
and interaction with other associated proteins.\r\nUsing the high sensitivity
SDS-digested freeze-fracture replica labeling (SDS-FRL) for\r\nelectron microscopy
I investigated the number, density, and localization of AMPAR subunits,\r\nGluA1,
GluA2, GluA3, and GluA1-3 (panAMPA) in pyramidal cells in the CA1 area of mouse\r\nhippocampus.
I have found that the immunogold labeling for all of these subunits in the\r\npostsynaptic
sites was highest in stratum radiatum and lowest in stratum lacunosummoleculare.
The labeling density for the all subunits in the extrasynaptic sites showed a
gradual\r\nincrease from the pyramidal cell soma towards the distal part of stratum
radiatum. The densities\r\nof extrasynaptic GluA1, GluA2 and panAMPA labeling
reached 10-15% of synaptic densities,\r\nwhile the ratio of extrasynaptic labeling
for GluA3 was significantly lower compared than those\r\nfor other subunits. The
labeling patterns for GluA1, GluA2 and GluA1-3 are similar and their\r\ndensities
were higher in the periphery than center of synapses. In contrast, the GluA3-\r\ncontaining
receptors were more centrally localized compared to the GluA1- and GluA2-\r\ncontaining
receptors.\r\nThe hippocampus plays a central role in learning and memory. Contextual
learning has been\r\nshown to require the delivery of AMPA receptors to CA1 synapses
in the dorsal hippocampus.\r\nHowever, proximodistal heterogeneity of this plasticity
and particular contribution of different\r\nAMPA receptor subunits are not fully
understood. By combining inhibitory avoidance task, a\r\nhippocampus-dependent
contextual fear-learning paradigm, with SDS-FRL, I have revealed an\r\nincrease
in synaptic density specific to GluA1-containing AMPA receptors in the CA1 area.\r\nThe
intrasynaptic distribution of GluA1 also changed from the periphery to center-preferred\r\npattern.
Furthermore, this synaptic plasticity was evident selectively in stratum radiatum
but\r\nnot stratum oriens, and in the CA1 subregion proximal but not distal to
CA2. These findings\r\nfurther contribute to our understanding of how specific
hippocampal subregions and AMPA\r\nreceptor subunits are involved in physiological
learning.\r\nAlthough the immunolabeling results above shed light on subunit-specific
plasticity in\r\nAMPAR distribution, no tools to visualize and study the subunit
composition at the single\r\nchannel level in situ have been available. Electron
microscopy with conventional immunogold\r\nlabeling approaches has limitations
in the single channel analysis because of the large size of\r\nantibodies and
steric hindrance hampering multiple subunit labeling of single channels. I\r\nmanaged
to develop a new chemical labeling system using a short peptide tag and small\r\nsynthetic
probes, which form specific covalent bond with a cysteine residue in the tag fused
to\r\nproteins of interest (reactive tag system). I additionally made substantial
progress into adapting\r\nthis system for AMPA receptor subunits."
acknowledged_ssus:
- _id: EM-Fac
alternative_title:
- ISTA Thesis
article_processing_charge: No
author:
- first_name: Marijo
full_name: Jevtic, Marijo
id: 4BE3BC94-F248-11E8-B48F-1D18A9856A87
last_name: Jevtic
citation:
ama: Jevtic M. Contextual fear learning induced changes in AMPA receptor subtypes
along the proximodistal axis in dorsal hippocampus. 2022. doi:10.15479/at:ista:11393
apa: Jevtic, M. (2022). Contextual fear learning induced changes in AMPA receptor
subtypes along the proximodistal axis in dorsal hippocampus. Institute of
Science and Technology Austria. https://doi.org/10.15479/at:ista:11393
chicago: Jevtic, Marijo. “Contextual Fear Learning Induced Changes in AMPA Receptor
Subtypes along the Proximodistal Axis in Dorsal Hippocampus.” Institute of Science
and Technology Austria, 2022. https://doi.org/10.15479/at:ista:11393.
ieee: M. Jevtic, “Contextual fear learning induced changes in AMPA receptor subtypes
along the proximodistal axis in dorsal hippocampus,” Institute of Science and
Technology Austria, 2022.
ista: Jevtic M. 2022. Contextual fear learning induced changes in AMPA receptor
subtypes along the proximodistal axis in dorsal hippocampus. Institute of Science
and Technology Austria.
mla: Jevtic, Marijo. Contextual Fear Learning Induced Changes in AMPA Receptor
Subtypes along the Proximodistal Axis in Dorsal Hippocampus. Institute of
Science and Technology Austria, 2022, doi:10.15479/at:ista:11393.
short: M. Jevtic, Contextual Fear Learning Induced Changes in AMPA Receptor Subtypes
along the Proximodistal Axis in Dorsal Hippocampus, Institute of Science and Technology
Austria, 2022.
date_created: 2022-05-17T08:57:41Z
date_published: 2022-05-16T00:00:00Z
date_updated: 2023-09-07T14:53:44Z
day: '16'
ddc:
- '570'
degree_awarded: PhD
department:
- _id: GradSch
- _id: RySh
doi: 10.15479/at:ista:11393
file:
- access_level: closed
checksum: 8fc695d88020d70d231dad0e9f10b138
content_type: application/vnd.openxmlformats-officedocument.wordprocessingml.document
creator: cchlebak
date_created: 2022-05-17T09:08:06Z
date_updated: 2023-05-17T22:30:03Z
embargo_to: open_access
file_id: '11395'
file_name: MJ thesis.docx
file_size: 56427603
relation: source_file
- access_level: open_access
checksum: c1dd20a1aece521b3500607b00e463d6
content_type: application/pdf
creator: cchlebak
date_created: 2022-05-17T12:09:25Z
date_updated: 2023-05-17T22:30:03Z
embargo: 2023-05-16
file_id: '11397'
file_name: MJ_thesis_PDFA.pdf
file_size: 4351981
relation: main_file
file_date_updated: 2023-05-17T22:30:03Z
has_accepted_license: '1'
language:
- iso: eng
month: '05'
oa: 1
oa_version: Published Version
page: '108'
publication_identifier:
issn:
- 2663-337X
publication_status: published
publisher: Institute of Science and Technology Austria
related_material:
record:
- id: '7391'
relation: part_of_dissertation
status: public
status: public
supervisor:
- first_name: Ryuichi
full_name: Shigemoto, Ryuichi
id: 499F3ABC-F248-11E8-B48F-1D18A9856A87
last_name: Shigemoto
orcid: 0000-0001-8761-9444
title: Contextual fear learning induced changes in AMPA receptor subtypes along the
proximodistal axis in dorsal hippocampus
type: dissertation
user_id: 8b945eb4-e2f2-11eb-945a-df72226e66a9
year: '2022'
...
---
_id: '12366'
abstract:
- lang: eng
text: "Recent substantial advances in the feld of superconducting circuits have
shown its\r\npotential as a leading platform for future quantum computing. In
contrast to classical\r\ncomputers based on bits that are represented by a single
binary value, 0 or 1, quantum\r\nbits (or qubits) can be in a superposition of
both. Thus, quantum computers can store\r\nand handle more information at the
same time and a quantum advantage has already\r\nbeen demonstrated for two types
of computational tasks. Rapid progress in academic\r\nand industry labs accelerates
the development of superconducting processors which may\r\nsoon fnd applications
in complex computations, chemical simulations, cryptography, and\r\noptimization.
Now that these machines are scaled up to tackle such problems the questions\r\nof
qubit interconnects and networks becomes very relevant. How to route signals on-chip\r\nbetween
diferent processor components? What is the most efcient way to entangle\r\nqubits?
And how to then send and process entangled signals between distant cryostats\r\nhosting
superconducting processors?\r\nIn this thesis, we are looking for solutions to
these problems by studying the collective\r\nbehavior of superconducting qubit
ensembles. We frst demonstrate on-demand tunable\r\ndirectional scattering of
microwave photons from a pair of qubits in a waveguide. Such a\r\ndevice can route
microwave photons on-chip with a high diode efciency. Then we focus\r\non studying
ultra-strong coupling regimes between light (microwave photons) and matter\r\n(superconducting
qubits), a regime that could be promising for extremely fast multi-qubit\r\nentanglement
generation. Finally, we show coherent pulse storage and periodic revivals\r\nin
a fve qubit ensemble strongly coupled to a resonator. Such a reconfgurable storage\r\ndevice
could be used as part of a quantum repeater that is needed for longer-distance\r\nquantum
communication.\r\nThe achieved high degree of control over multi-qubit ensembles
highlights not only the\r\nbeautiful physics of circuit quantum electrodynamics,
it also represents the frst step\r\ntoward new quantum simulation and communication
methods, and certain techniques\r\nmay also fnd applications in future superconducting
quantum computing hardware.\r\n"
acknowledged_ssus:
- _id: NanoFab
- _id: M-Shop
- _id: EM-Fac
alternative_title:
- ISTA Thesis
article_processing_charge: No
author:
- first_name: Elena
full_name: Redchenko, Elena
id: 2C21D6E8-F248-11E8-B48F-1D18A9856A87
last_name: Redchenko
citation:
ama: Redchenko E. Controllable states of superconducting Qubit ensembles. 2022.
doi:10.15479/at:ista:12132
apa: Redchenko, E. (2022). Controllable states of superconducting Qubit ensembles.
Institute of Science and Technology Austria. https://doi.org/10.15479/at:ista:12132
chicago: Redchenko, Elena. “Controllable States of Superconducting Qubit Ensembles.”
Institute of Science and Technology Austria, 2022. https://doi.org/10.15479/at:ista:12132.
ieee: E. Redchenko, “Controllable states of superconducting Qubit ensembles,” Institute
of Science and Technology Austria, 2022.
ista: Redchenko E. 2022. Controllable states of superconducting Qubit ensembles.
Institute of Science and Technology Austria.
mla: Redchenko, Elena. Controllable States of Superconducting Qubit Ensembles.
Institute of Science and Technology Austria, 2022, doi:10.15479/at:ista:12132.
short: E. Redchenko, Controllable States of Superconducting Qubit Ensembles, Institute
of Science and Technology Austria, 2022.
date_created: 2023-01-25T09:17:02Z
date_published: 2022-09-26T00:00:00Z
date_updated: 2023-05-26T09:29:07Z
day: '26'
ddc:
- '530'
degree_awarded: PhD
department:
- _id: GradSch
- _id: JoFi
doi: 10.15479/at:ista:12132
ec_funded: 1
file:
- access_level: open_access
checksum: 39eabb1e006b41335f17f3b29af09648
content_type: application/pdf
creator: cchlebak
date_created: 2023-01-25T09:41:49Z
date_updated: 2023-01-26T23:30:44Z
embargo: 2022-12-28
file_id: '12367'
file_name: Final_Thesis_ES_Redchenko.pdf
file_size: 56076868
relation: main_file
file_date_updated: 2023-01-26T23:30:44Z
has_accepted_license: '1'
language:
- iso: eng
month: '09'
oa: 1
oa_version: Published Version
page: '168'
project:
- _id: 2564DBCA-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '665385'
name: International IST Doctoral Program
- _id: 26336814-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '758053'
name: A Fiber Optic Transceiver for Superconducting Qubits
- _id: 237CBA6C-32DE-11EA-91FC-C7463DDC885E
call_identifier: H2020
grant_number: '862644'
name: Quantum readout techniques and technologies
publication_identifier:
isbn:
- 978-3-99078-024-4
issn:
- 2663-337X
publication_status: published
publisher: Institute of Science and Technology Austria
status: public
supervisor:
- first_name: Johannes M
full_name: Fink, Johannes M
id: 4B591CBA-F248-11E8-B48F-1D18A9856A87
last_name: Fink
orcid: 0000-0001-8112-028X
title: Controllable states of superconducting Qubit ensembles
type: dissertation
user_id: 8b945eb4-e2f2-11eb-945a-df72226e66a9
year: '2022'
...
---
_id: '11932'
abstract:
- lang: eng
text: "The ability to form and retrieve memories is central to survival. In mammals,
the hippocampus\r\nis a brain region essential to the acquisition and consolidation
of new memories. It is also\r\ninvolved in keeping track of one’s position in
space and aids navigation. Although this\r\nspace-memory has been a source of
contradiction, evidence supports the view that the role of\r\nthe hippocampus
in navigation is memory, thanks to the formation of cognitive maps. First\r\nintroduced
by Tolman in 1948, cognitive maps are generally used to organize experiences in\r\nmemory;
however, the detailed mechanisms by which these maps are formed and stored are
not\r\nyet agreed upon. Some influential theories describe this process as involving
three fundamental\r\nsteps: initial encoding by the hippocampus, interactions
between the hippocampus and other\r\ncortical areas, and long-term extra-hippocampal
consolidation. In this thesis, I will show how\r\nthe investigation of cognitive
maps of space helped to shed light on each of these three memory\r\nprocesses.\r\nThe
first study included in this thesis deals with the initial encoding of spatial
memories in\r\nthe hippocampus. Much is known about encoding at the level of single
cells, but less about\r\ntheir co-activity or joint contribution to the encoding
of novel spatial information. I will\r\ndescribe the structure of an interaction
network that allows for efficient encoding of noisy\r\nspatial information during
the first exploration of a novel environment.\r\nThe second study describes the
interactions between the hippocampus and the prefrontal\r\ncortex (PFC), two areas
directly and indirectly connected. It is known that the PFC, in concert\r\nwith
the hippocampus, is involved in various processes, including memory storage and
spatial\r\nnavigation. Nonetheless, the detailed mechanisms by which PFC receives
information from the\r\nhippocampus are not clear. I will show how a transient
improvement in theta phase locking of\r\nPFC cells enables interactions of cell
pairs across the two regions.\r\nThe third study describes the learning of behaviorally-relevant
spatial locations in the hippocampus and the medial entorhinal cortex. I will
show how the accumulation of firing around\r\ngoal locations, a correlate of learning,
can shed light on the transition from short- to long-term\r\nspatial memories
and the speed of consolidation in different brain areas.\r\nThe studies included
in this thesis represent the main scientific contributions of my Ph.D. They\r\ninvolve
statistical analyses and models of neural responses of cells in different brain
areas of\r\nrats executing spatial tasks. I will conclude the thesis by discussing
the impact of the findings\r\non principles of memory formation and retention,
including the mechanisms, the speed, and\r\nthe duration of these processes."
acknowledgement: I acknowledge the support from the European Union’s Horizon 2020
research and innovation program under the Marie Skłodowska-Curie Grant Agreement
No. 665385.
alternative_title:
- ISTA Thesis
article_processing_charge: No
author:
- first_name: Michele
full_name: Nardin, Michele
id: 30BD0376-F248-11E8-B48F-1D18A9856A87
last_name: Nardin
orcid: 0000-0001-8849-6570
citation:
ama: Nardin M. On the encoding, transfer, and consolidation of spatial memories.
2022. doi:10.15479/at:ista:11932
apa: Nardin, M. (2022). On the encoding, transfer, and consolidation of spatial
memories. Institute of Science and Technology Austria. https://doi.org/10.15479/at:ista:11932
chicago: Nardin, Michele. “On the Encoding, Transfer, and Consolidation of Spatial
Memories.” Institute of Science and Technology Austria, 2022. https://doi.org/10.15479/at:ista:11932.
ieee: M. Nardin, “On the encoding, transfer, and consolidation of spatial memories,”
Institute of Science and Technology Austria, 2022.
ista: Nardin M. 2022. On the encoding, transfer, and consolidation of spatial memories.
Institute of Science and Technology Austria.
mla: Nardin, Michele. On the Encoding, Transfer, and Consolidation of Spatial
Memories. Institute of Science and Technology Austria, 2022, doi:10.15479/at:ista:11932.
short: M. Nardin, On the Encoding, Transfer, and Consolidation of Spatial Memories,
Institute of Science and Technology Austria, 2022.
date_created: 2022-08-19T08:52:30Z
date_published: 2022-08-19T00:00:00Z
date_updated: 2023-09-05T12:02:14Z
day: '19'
ddc:
- '573'
degree_awarded: PhD
department:
- _id: GradSch
- _id: JoCs
doi: 10.15479/at:ista:11932
ec_funded: 1
file:
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checksum: 2dbb70c74aaa3b64c1f463e943baf09c
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creator: mnardin
date_created: 2022-08-19T16:31:34Z
date_updated: 2023-06-20T22:30:04Z
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file_size: 13515457
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date_created: 2022-08-22T09:43:50Z
date_updated: 2023-06-20T22:30:04Z
embargo: 2023-06-19
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file_name: Michele_Nardin_Phd_Thesis_PDFA.pdf
file_size: 9906458
relation: main_file
file_date_updated: 2023-06-20T22:30:04Z
has_accepted_license: '1'
language:
- iso: eng
month: '08'
oa: 1
oa_version: Published Version
page: '136'
project:
- _id: 2564DBCA-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '665385'
name: International IST Doctoral Program
publication_identifier:
issn:
- 2663-337X
publication_status: published
publisher: Institute of Science and Technology Austria
related_material:
record:
- id: '10077'
relation: part_of_dissertation
status: public
- id: '6194'
relation: part_of_dissertation
status: public
status: public
supervisor:
- first_name: Jozsef L
full_name: Csicsvari, Jozsef L
id: 3FA14672-F248-11E8-B48F-1D18A9856A87
last_name: Csicsvari
orcid: 0000-0002-5193-4036
title: On the encoding, transfer, and consolidation of spatial memories
type: dissertation
user_id: 8b945eb4-e2f2-11eb-945a-df72226e66a9
year: '2022'
...
---
_id: '12378'
abstract:
- lang: eng
text: "Environmental cues influence the highly dynamic morphology of microglia.
Strategies to \r\ncharacterize these changes usually involve user-selected morphometric
features, which \r\npreclude the identification of a spectrum of context-dependent
morphological phenotypes. \r\nHere, we develop MorphOMICs, a topological data
analysis approach, which enables semi\x02automatic mapping of microglial morphology
into an atlas of cue-dependent phenotypes,\r\novercomes feature-selection bias
and minimizes biological variability. \r\nFirst, with MorphOMICs we derive the
morphological spectrum of microglia across seven \r\nbrain regions during postnatal
development and in two distinct Alzheimer’s disease \r\ndegeneration mouse models.
We uncover region-specific and sexually dimorphic\r\nmorphological trajectories,
with females showing an earlier morphological shift than males in \r\nthe degenerating
brain. Overall, we demonstrate that both long primary- and short terminal \r\nprocesses
provide distinct insights to morphological phenotypes. Moreover, using machine
\r\nlearning to map novel condition on the spectrum, we observe that microglia
morphologies \r\nreflect a dose-dependent adaptation upon ketamine anesthesia
and do not recover to control \r\nmorphologies.\r\nNext, we took advantage of
MorphOMICs to build a high-resolution and layer-specific map of \r\nmicroglial
morphological spectrum in the retina, covering postnatal development and rd10
\r\ndegeneration. Here, following photoreceptor death, microglia assume an early
development\x02like morphology. Finally, we map microglial morphology following
optic nerve crush on the \r\nretinal spectrum and observe a layer- and sex-dependent
response. \r\nOverall, MorphOMICs opens a new perspective to analyze microglial
morphology across \r\nmultiple conditions, and provides a novel tool to characterize
microglial morphology beyond \r\nthe traditionally dichotomized view of microglia."
acknowledged_ssus:
- _id: PreCl
- _id: Bio
- _id: ScienComp
alternative_title:
- ISTA Thesis
article_processing_charge: No
author:
- first_name: Gloria
full_name: Colombo, Gloria
id: 3483CF6C-F248-11E8-B48F-1D18A9856A87
last_name: Colombo
orcid: 0000-0001-9434-8902
citation:
ama: Colombo G. MorphOMICs, a tool for mapping microglial morphology, reveals brain
region- and sex-dependent phenotypes. 2022. doi:10.15479/at:ista:12378
apa: Colombo, G. (2022). MorphOMICs, a tool for mapping microglial morphology,
reveals brain region- and sex-dependent phenotypes. Institute of Science and
Technology Austria. https://doi.org/10.15479/at:ista:12378
chicago: Colombo, Gloria. “MorphOMICs, a Tool for Mapping Microglial Morphology,
Reveals Brain Region- and Sex-Dependent Phenotypes.” Institute of Science and
Technology Austria, 2022. https://doi.org/10.15479/at:ista:12378.
ieee: G. Colombo, “MorphOMICs, a tool for mapping microglial morphology, reveals
brain region- and sex-dependent phenotypes,” Institute of Science and Technology
Austria, 2022.
ista: Colombo G. 2022. MorphOMICs, a tool for mapping microglial morphology, reveals
brain region- and sex-dependent phenotypes. Institute of Science and Technology
Austria.
mla: Colombo, Gloria. MorphOMICs, a Tool for Mapping Microglial Morphology, Reveals
Brain Region- and Sex-Dependent Phenotypes. Institute of Science and Technology
Austria, 2022, doi:10.15479/at:ista:12378.
short: G. Colombo, MorphOMICs, a Tool for Mapping Microglial Morphology, Reveals
Brain Region- and Sex-Dependent Phenotypes, Institute of Science and Technology
Austria, 2022.
date_created: 2023-01-25T14:27:43Z
date_published: 2022-11-11T00:00:00Z
date_updated: 2023-08-04T09:40:37Z
day: '11'
ddc:
- '570'
degree_awarded: PhD
department:
- _id: GradSch
- _id: SaSi
doi: 10.15479/at:ista:12378
ec_funded: 1
file:
- access_level: closed
checksum: 8cd3ddfe9b53381dcf086023d8d8893a
content_type: application/vnd.openxmlformats-officedocument.wordprocessingml.document
creator: cchlebak
date_created: 2023-01-25T14:31:32Z
date_updated: 2023-04-12T22:30:03Z
embargo_to: open_access
file_id: '12379'
file_name: Gloria_Colombo_Thesis.docx
file_size: 23890382
relation: source_file
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checksum: 8af4319c18b516e8758e9a6cb02b103b
content_type: application/pdf
creator: cchlebak
date_created: 2023-01-25T14:31:36Z
date_updated: 2023-04-12T22:30:03Z
embargo: 2023-04-11
file_id: '12380'
file_name: Gloria_Colombo_Thesis.pdf
file_size: 13802421
relation: main_file
file_date_updated: 2023-04-12T22:30:03Z
has_accepted_license: '1'
language:
- iso: eng
month: '11'
oa: 1
oa_version: Published Version
page: '142'
project:
- _id: 2564DBCA-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '665385'
name: International IST Doctoral Program
publication_identifier:
issn:
- 2663-337X
publication_status: published
publisher: Institute of Science and Technology Austria
related_material:
record:
- id: '12244'
relation: part_of_dissertation
status: public
status: public
supervisor:
- first_name: Sandra
full_name: Siegert, Sandra
id: 36ACD32E-F248-11E8-B48F-1D18A9856A87
last_name: Siegert
orcid: 0000-0001-8635-0877
title: MorphOMICs, a tool for mapping microglial morphology, reveals brain region-
and sex-dependent phenotypes
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: dissertation
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
year: '2022'
...
---
_id: '11388'
abstract:
- lang: eng
text: "In evolve and resequence experiments, a population is sequenced, subjected
to selection and\r\nthen sequenced again, so that genetic changes before and after
selection can be observed at\r\nthe genetic level. Here, I use these studies to
better understand the genetic basis of complex\r\ntraits - traits which depend
on more than a few genes.\r\nIn the first chapter, I discuss the first evolve
and resequence experiment, in which a population\r\nof mice, the so-called \"Longshanks\"
mice, were selected for tibia length while their body mass\r\nwas kept constant.
The full pedigree is known. We observed a selection response on all\r\nchromosomes
and used the infinitesimal model with linkage, a model which assumes an infinite\r\nnumber
of genes with infinitesimally small effect sizes, as a null model. Results implied
a very\r\npolygenic basis with a few loci of major effect standing out and changing
in parallel. There\r\nwas large variability between the different chromosomes
in this study, probably due to LD.\r\nIn chapter two, I go on to discuss the impact
of LD, on the variability in an allele-frequency\r\nbased summary statistic, giving
an equation based on the initial allele frequencies, average\r\npairwise LD, and
the first four moments of the haplotype block copy number distribution. I\r\ndescribe
this distribution by referring back to the founder generation. I then demonstrate\r\nhow
to infer selection via a maximum likelihood scheme on the example of a single
locus and\r\ndiscuss how to extend this to more realistic scenarios.\r\nIn chapter
three, I discuss the second evolve and resequence experiment, in which a small\r\npopulation
of Drosophila melanogaster was selected for increased pupal case size over 6\r\ngenerations.
The experiment was highly replicated with 27 lines selected within family and
a\r\nknown pedigree. We observed a phenotypic selection response of over one standard
deviation.\r\nI describe the patterns in allele frequency data, including allele
frequency changes and patterns\r\nof heterozygosity, and give ideas for future
work."
alternative_title:
- ISTA Thesis
article_processing_charge: No
author:
- first_name: Stefanie
full_name: Belohlavy, Stefanie
id: 43FE426A-F248-11E8-B48F-1D18A9856A87
last_name: Belohlavy
orcid: 0000-0002-9849-498X
citation:
ama: Belohlavy S. The genetic basis of complex traits studied via analysis of evolve
and resequence experiments. 2022. doi:10.15479/at:ista:11388
apa: Belohlavy, S. (2022). The genetic basis of complex traits studied via analysis
of evolve and resequence experiments. Institute of Science and Technology
Austria. https://doi.org/10.15479/at:ista:11388
chicago: Belohlavy, Stefanie. “The Genetic Basis of Complex Traits Studied via Analysis
of Evolve and Resequence Experiments.” Institute of Science and Technology Austria,
2022. https://doi.org/10.15479/at:ista:11388.
ieee: S. Belohlavy, “The genetic basis of complex traits studied via analysis of
evolve and resequence experiments,” Institute of Science and Technology Austria,
2022.
ista: Belohlavy S. 2022. The genetic basis of complex traits studied via analysis
of evolve and resequence experiments. Institute of Science and Technology Austria.
mla: Belohlavy, Stefanie. The Genetic Basis of Complex Traits Studied via Analysis
of Evolve and Resequence Experiments. Institute of Science and Technology
Austria, 2022, doi:10.15479/at:ista:11388.
short: S. Belohlavy, The Genetic Basis of Complex Traits Studied via Analysis of
Evolve and Resequence Experiments, Institute of Science and Technology Austria,
2022.
date_created: 2022-05-16T16:49:18Z
date_published: 2022-05-18T00:00:00Z
date_updated: 2023-08-29T06:41:51Z
day: '18'
ddc:
- '576'
degree_awarded: PhD
department:
- _id: GradSch
- _id: NiBa
doi: 10.15479/at:ista:11388
file:
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date_updated: 2023-05-20T22:30:03Z
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date_updated: 2023-05-20T22:30:03Z
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has_accepted_license: '1'
language:
- iso: eng
month: '05'
oa: 1
oa_version: Published Version
page: '98'
publication_identifier:
isbn:
- 978-3-99078-018-3
publication_status: published
publisher: Institute of Science and Technology Austria
related_material:
record:
- id: '6713'
relation: part_of_dissertation
status: public
status: public
supervisor:
- first_name: Nicholas H
full_name: Barton, Nicholas H
id: 4880FE40-F248-11E8-B48F-1D18A9856A87
last_name: Barton
orcid: 0000-0002-8548-5240
title: The genetic basis of complex traits studied via analysis of evolve and resequence
experiments
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: dissertation
user_id: 8b945eb4-e2f2-11eb-945a-df72226e66a9
year: '2022'
...
---
_id: '12401'
abstract:
- lang: eng
text: "Detachment of the cancer cells from the bulk of the tumor is the first step
of metastasis, which\r\nis the primary cause of cancer related deaths. It is unclear,
which factors contribute to this step.\r\nRecent studies indicate a crucial role
of the tumor microenvironment in malignant\r\ntransformation and metastasis. Studying
cancer cell invasion and detachments quantitatively in\r\nthe context of its physiological
microenvironment is technically challenging. Especially, precise\r\ncontrol of
microenvironmental properties in vivo is currently not possible. Here, I studied
the\r\nrole of microenvironment geometry in the invasion and detachment of cancer
cells from the\r\nbulk with a simplistic and reductionist approach. In this approach,
I engineered microfluidic\r\ndevices to mimic a pseudo 3D extracellular matrix
environment, where I was able to\r\nquantitatively tune the geometrical configuration
of the microenvironment and follow tumor\r\ncells with fluorescence live imaging.
To aid quantitative analysis I developed a widely applicable\r\nsoftware application
to automatically analyze and visualize particle tracking data.\r\nQuantitative
analysis of tumor cell invasion in isotropic and anisotropic microenvironments\r\nshowed
that heterogeneity in the microenvironment promotes faster invasion and more\r\nfrequent
detachment of cells. These observations correlated with overall higher speed of
cells at\r\nthe edge of the bulk of the cells. In heterogeneous microenvironments
cells preferentially\r\npassed through larger pores, thus invading areas of least
resistance and generating finger-like\r\ninvasive structures. The detachments
occurred mostly at the tips of these structures.\r\nTo investigate the potential
mechanism, we established a two dimensional model to simulate\r\nactive Brownian
particles representing the cell nuclei dynamics. These simulations backed our
in\r\nvitro observations without the need of precise fitting the simulation parameters.
Our model\r\nsuggests the importance of the pore heterogeneity in the direction
perpendicular to the\r\norientation of bias field (lateral heterogeneity), which
causes the interface roughening."
alternative_title:
- ISTA Thesis
article_processing_charge: No
author:
- first_name: Saren
full_name: Tasciyan, Saren
id: 4323B49C-F248-11E8-B48F-1D18A9856A87
last_name: Tasciyan
orcid: 0000-0003-1671-393X
citation:
ama: Tasciyan S. Role of microenvironment heterogeneity in cancer cell invasion.
2022. doi:10.15479/at:ista:12401
apa: Tasciyan, S. (2022). Role of microenvironment heterogeneity in cancer cell
invasion. Institute of Science and Technology Austria. https://doi.org/10.15479/at:ista:12401
chicago: Tasciyan, Saren. “Role of Microenvironment Heterogeneity in Cancer Cell
Invasion.” Institute of Science and Technology Austria, 2022. https://doi.org/10.15479/at:ista:12401.
ieee: S. Tasciyan, “Role of microenvironment heterogeneity in cancer cell invasion,”
Institute of Science and Technology Austria, 2022.
ista: Tasciyan S. 2022. Role of microenvironment heterogeneity in cancer cell invasion.
Institute of Science and Technology Austria.
mla: Tasciyan, Saren. Role of Microenvironment Heterogeneity in Cancer Cell Invasion.
Institute of Science and Technology Austria, 2022, doi:10.15479/at:ista:12401.
short: S. Tasciyan, Role of Microenvironment Heterogeneity in Cancer Cell Invasion,
Institute of Science and Technology Austria, 2022.
date_created: 2023-01-26T11:55:16Z
date_published: 2022-12-22T00:00:00Z
date_updated: 2023-12-21T23:30:04Z
day: '22'
ddc:
- '610'
degree_awarded: PhD
department:
- _id: GradSch
- _id: MiSi
doi: 10.15479/at:ista:12401
file:
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date_updated: 2023-12-21T23:30:03Z
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date_created: 2023-01-26T12:00:10Z
date_updated: 2023-12-21T23:30:03Z
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language:
- iso: eng
month: '12'
oa: 1
oa_version: Published Version
page: '105'
publication_identifier:
issn:
- 2663-337X
publication_status: published
publisher: Institute of Science and Technology Austria
related_material:
record:
- id: '679'
relation: part_of_dissertation
status: public
- id: '10703'
relation: part_of_dissertation
status: public
- id: '9429'
relation: part_of_dissertation
status: public
- id: '7885'
relation: part_of_dissertation
status: public
status: public
supervisor:
- first_name: Michael K
full_name: Sixt, Michael K
id: 41E9FBEA-F248-11E8-B48F-1D18A9856A87
last_name: Sixt
orcid: 0000-0002-6620-9179
title: Role of microenvironment heterogeneity in cancer cell invasion
type: dissertation
user_id: 8b945eb4-e2f2-11eb-945a-df72226e66a9
year: '2022'
...
---
_id: '11193'
abstract:
- lang: eng
text: "The infiltration of immune cells into tissues underlies the establishment
of tissue-resident\r\nmacrophages and responses to infections and tumors. However,
the mechanisms immune\r\ncells utilize to collectively migrate through tissue
barriers in vivo are not yet well understood.\r\nIn this thesis, I describe two
mechanisms that Drosophila immune cells (hemocytes) use to\r\novercome the tissue
barrier of the germband in the embryo. One strategy is the strengthening\r\nof
the actin cortex through developmentally controlled transcriptional regulation
induced by\r\nthe Drosophila proto-oncogene family member Dfos, which I show in
Chapter 2. Dfos induces\r\nexpression of the tetraspanin TM4SF and the filamin
Cher leading to higher levels of the\r\nactivated formin Dia at the cortex and
increased cortical F-actin. This enhanced cortical\r\nstrength allows hemocytes
to overcome the physical resistance of the surrounding tissue and\r\ntranslocate
their nucleus to move forward. This mechanism affects the speed of migration\r\nwhen
hemocytes face a confined environment in vivo.\r\nAnother aspect of the invasion
process is the initial step of the leading hemocytes entering\r\nthe tissue, which
potentially guides the follower cells. In Chapter 3, I describe a novel\r\nsubpopulation
of hemocytes activated by BMP signaling prior to tissue invasion that leads\r\npenetration
into the germband. Hemocytes that are deficient in BMP signaling activation\r\nshow
impaired persistence at the tissue entry, while their migration speed remains\r\nunaffected.\r\nThis
suggests that there might be different mechanisms controlling immune cell migration\r\nwithin
the confined environment in vivo, one of these being the general ability to overcome\r\nthe
resistance of the surrounding tissue and another affecting the order of hemocytes
that\r\ncollectively invade the tissue in a stream of individual cells.\r\nTogether,
my findings provide deeper insights into transcriptional changes in immune\r\ncells
that enable efficient tissue invasion and pave the way for future studies investigating
the\r\nearly colonization of tissues by macrophages in higher organisms. Moreover,
they extend the\r\ncurrent view of Drosophila immune cell heterogeneity and point
toward a potentially\r\nconserved role for canonical BMP signaling in specifying
immune cells that lead the migration\r\nof tissue resident macrophages during
embryogenesis."
acknowledged_ssus:
- _id: LifeSc
alternative_title:
- ISTA Thesis
article_processing_charge: No
author:
- first_name: Stephanie
full_name: Wachner, Stephanie
id: 2A95E7B0-F248-11E8-B48F-1D18A9856A87
last_name: Wachner
citation:
ama: Wachner S. Transcriptional regulation by Dfos and BMP-signaling support tissue
invasion of Drosophila immune cells. 2022. doi:10.15479/at:ista:11193
apa: Wachner, S. (2022). Transcriptional regulation by Dfos and BMP-signaling
support tissue invasion of Drosophila immune cells. Institute of Science and
Technology Austria. https://doi.org/10.15479/at:ista:11193
chicago: Wachner, Stephanie. “Transcriptional Regulation by Dfos and BMP-Signaling
Support Tissue Invasion of Drosophila Immune Cells.” Institute of Science and
Technology Austria, 2022. https://doi.org/10.15479/at:ista:11193.
ieee: S. Wachner, “Transcriptional regulation by Dfos and BMP-signaling support
tissue invasion of Drosophila immune cells,” Institute of Science and Technology
Austria, 2022.
ista: Wachner S. 2022. Transcriptional regulation by Dfos and BMP-signaling support
tissue invasion of Drosophila immune cells. Institute of Science and Technology
Austria.
mla: Wachner, Stephanie. Transcriptional Regulation by Dfos and BMP-Signaling
Support Tissue Invasion of Drosophila Immune Cells. Institute of Science and
Technology Austria, 2022, doi:10.15479/at:ista:11193.
short: S. Wachner, Transcriptional Regulation by Dfos and BMP-Signaling Support
Tissue Invasion of Drosophila Immune Cells, Institute of Science and Technology
Austria, 2022.
date_created: 2022-04-20T08:59:07Z
date_published: 2022-04-20T00:00:00Z
date_updated: 2023-09-19T10:15:54Z
day: '20'
ddc:
- '570'
degree_awarded: PhD
department:
- _id: GradSch
- _id: DaSi
doi: 10.15479/at:ista:11193
file:
- access_level: open_access
checksum: 999ab16884c4522486136ebc5ae8dbff
content_type: application/pdf
creator: cchlebak
date_created: 2022-04-20T09:03:57Z
date_updated: 2023-04-21T22:30:03Z
embargo: 2023-04-20
file_id: '11195'
file_name: Thesis_Stephanie_Wachner_20200414_formatted.pdf
file_size: 8820951
relation: main_file
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date_created: 2022-04-22T12:41:00Z
date_updated: 2023-04-21T22:30:03Z
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file_id: '11329'
file_name: Thesis_Stephanie_Wachner_20200414.zip
file_size: 65864612
relation: source_file
file_date_updated: 2023-04-21T22:30:03Z
has_accepted_license: '1'
language:
- iso: eng
month: '04'
oa: 1
oa_version: Published Version
page: '170'
project:
- _id: 26199CA4-B435-11E9-9278-68D0E5697425
grant_number: '24800'
name: Tissue barrier penetration is crucial for immunity and metastasis
publication_identifier:
issn:
- 2663-337X
publication_status: published
publisher: Institute of Science and Technology Austria
related_material:
record:
- id: '10614'
relation: part_of_dissertation
status: public
- id: '544'
relation: part_of_dissertation
status: public
status: public
supervisor:
- first_name: Daria E
full_name: Siekhaus, Daria E
id: 3D224B9E-F248-11E8-B48F-1D18A9856A87
last_name: Siekhaus
orcid: 0000-0001-8323-8353
title: Transcriptional regulation by Dfos and BMP-signaling support tissue invasion
of Drosophila immune cells
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: dissertation
user_id: 8b945eb4-e2f2-11eb-945a-df72226e66a9
year: '2022'
...
---
_id: '12364'
abstract:
- lang: eng
text: "Autism spectrum disorders (ASDs) are a group of neurodevelopmental disorders
character\x02ized by behavioral symptoms such as problems in social communication
and interaction, as\r\nwell as repetitive, restricted behaviors and interests.
These disorders show a high degree\r\nof heritability and hundreds of risk genes
have been identifed using high throughput\r\nsequencing technologies. This genetic
heterogeneity has hampered eforts in understanding\r\nthe pathogenesis of ASD
but at the same time given rise to the concept of convergent\r\nmechanisms. Previous
studies have identifed that risk genes for ASD broadly converge\r\nonto specifc
functional categories with transcriptional regulation being one of the biggest\r\ngroups.
In this thesis, I focus on this subgroup of genes and investigate the gene regulatory\r\nconsequences
of some of them in the context of neurodevelopment.\r\nFirst, we showed that mutations
in the ASD and intellectual disability risk gene Setd5 lead\r\nto perturbations
of gene regulatory programs in early cell fate specifcation. In addition,\r\nadult
animals display abnormal learning behavior which is mirrored at the transcriptional\r\nlevel
by altered activity dependent regulation of postsynaptic gene expression. Lastly,\r\nwe
link the regulatory function of Setd5 to its interaction with the Paf1 and the
NCoR\r\ncomplex.\r\nSecond, by modeling the heterozygous loss of the top ASD gene
CHD8 in human cerebral\r\norganoids we demonstrate profound changes in the developmental
trajectories of both\r\ninhibitory and excitatory neurons using single cell RNA-sequencing.
While the former\r\nwere generated earlier in CHD8+/- organoids, the generation
of the latter was shifted to\r\nlater times in favor of a prolonged progenitor
expansion phase and ultimately increased\r\norganoid size.\r\nFinally, by modeling
heterozygous mutations for four ASD associated chromatin modifers,\r\nASH1L, KDM6B,
KMT5B, and SETD5 in human cortical spheroids we show evidence of\r\nregulatory
convergence across three of those genes. We observe a shift from dorsal cortical\r\nexcitatory
neuron fates towards partially ventralized cell types resembling cells from the\r\nlateral
ganglionic eminence. As this project is still ongoing at the time of writing,
future\r\nexperiments will aim at elucidating the regulatory mechanisms underlying
this shift with\r\nthe aim of linking these three ASD risk genes through biological
convergence."
alternative_title:
- ISTA Thesis
article_processing_charge: No
author:
- first_name: Christoph
full_name: Dotter, Christoph
id: 4C66542E-F248-11E8-B48F-1D18A9856A87
last_name: Dotter
orcid: 0000-0002-9033-9096
citation:
ama: Dotter C. Transcriptional consequences of mutations in genes associated with
Autism Spectrum Disorder. 2022. doi:10.15479/at:ista:12094
apa: Dotter, C. (2022). Transcriptional consequences of mutations in genes associated
with Autism Spectrum Disorder. Institute of Science and Technology Austria.
https://doi.org/10.15479/at:ista:12094
chicago: Dotter, Christoph. “Transcriptional Consequences of Mutations in Genes
Associated with Autism Spectrum Disorder.” Institute of Science and Technology
Austria, 2022. https://doi.org/10.15479/at:ista:12094.
ieee: C. Dotter, “Transcriptional consequences of mutations in genes associated
with Autism Spectrum Disorder,” Institute of Science and Technology Austria, 2022.
ista: Dotter C. 2022. Transcriptional consequences of mutations in genes associated
with Autism Spectrum Disorder. Institute of Science and Technology Austria.
mla: Dotter, Christoph. Transcriptional Consequences of Mutations in Genes Associated
with Autism Spectrum Disorder. Institute of Science and Technology Austria,
2022, doi:10.15479/at:ista:12094.
short: C. Dotter, Transcriptional Consequences of Mutations in Genes Associated
with Autism Spectrum Disorder, Institute of Science and Technology Austria, 2022.
date_created: 2023-01-24T13:09:57Z
date_published: 2022-09-19T00:00:00Z
date_updated: 2023-11-16T13:10:22Z
day: '19'
ddc:
- '570'
degree_awarded: PhD
department:
- _id: GradSch
- _id: GaNo
doi: 10.15479/at:ista:12094
ec_funded: 1
file:
- access_level: open_access
checksum: 896f4cac9adb6d3f26a6605772f4e1a3
content_type: application/pdf
creator: cchlebak
date_created: 2023-01-24T13:15:45Z
date_updated: 2023-09-20T22:30:03Z
embargo: 2023-09-19
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file_name: 220923_Thesis_CDotter_Final.pdf
file_size: 20457465
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creator: cchlebak
date_created: 2023-02-02T09:15:35Z
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has_accepted_license: '1'
language:
- iso: eng
month: '09'
oa: 1
oa_version: Published Version
page: '152'
project:
- _id: 254BA948-B435-11E9-9278-68D0E5697425
grant_number: '401299'
name: Probing development and reversibility of autism spectrum disorders
- _id: 9B91375C-BA93-11EA-9121-9846C619BF3A
grant_number: '707964'
name: Critical windows and reversibility of ASD associated with mutations in chromatin
remodelers
- _id: 25444568-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '715508'
name: Probing the Reversibility of Autism Spectrum Disorders by Employing in vivo
and in vitro Models
- _id: 2690FEAC-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: I04205
name: Identification of converging Molecular Pathways Across Chromatinopathies as
Targets for Therapy
publication_identifier:
issn:
- 2663-337X
publication_status: published
publisher: Institute of Science and Technology Austria
related_material:
record:
- id: '3'
relation: part_of_dissertation
status: public
- id: '11160'
relation: part_of_dissertation
status: public
status: public
supervisor:
- first_name: Gaia
full_name: Novarino, Gaia
id: 3E57A680-F248-11E8-B48F-1D18A9856A87
last_name: Novarino
orcid: 0000-0002-7673-7178
title: Transcriptional consequences of mutations in genes associated with Autism Spectrum
Disorder
type: dissertation
user_id: 8b945eb4-e2f2-11eb-945a-df72226e66a9
year: '2022'
...
---
_id: '9056'
abstract:
- lang: eng
text: "In this thesis we study persistence of multi-covers of Euclidean balls and
the geometric structures underlying their computation, in particular Delaunay
mosaics and Voronoi tessellations. The k-fold cover for some discrete input point
set consists of the space where at least k balls of radius r around the input
points overlap. Persistence is a notion that captures, in some sense, the topology
of the shape underlying the input. While persistence is usually computed for the
union of balls, the k-fold cover is of interest as it captures local density,\r\nand
thus might approximate the shape of the input better if the input data is noisy.
To compute persistence of these k-fold covers, we need a discretization that is
provided by higher-order Delaunay mosaics. We present and implement a simple and
efficient algorithm for the computation of higher-order Delaunay mosaics, and
use it to give experimental results for their combinatorial properties. The algorithm
makes use of a new geometric structure, the rhomboid tiling. It contains the higher-order
Delaunay mosaics as slices, and by introducing a filtration\r\nfunction on the
tiling, we also obtain higher-order α-shapes as slices. These allow us to compute
persistence of the multi-covers for varying radius r; the computation for varying
k is less straight-foward and involves the rhomboid tiling directly. We apply
our algorithms to experimental sphere packings to shed light on their structural
properties. Finally, inspired by periodic structures in packings and materials,
we propose and implement an algorithm for periodic Delaunay triangulations to
be integrated into the Computational Geometry Algorithms Library (CGAL), and discuss
the implications on persistence for periodic data sets."
alternative_title:
- ISTA Thesis
article_processing_charge: No
author:
- first_name: Georg F
full_name: Osang, Georg F
id: 464B40D6-F248-11E8-B48F-1D18A9856A87
last_name: Osang
orcid: 0000-0002-8882-5116
citation:
ama: Osang GF. Multi-cover persistence and Delaunay mosaics. 2021. doi:10.15479/AT:ISTA:9056
apa: Osang, G. F. (2021). Multi-cover persistence and Delaunay mosaics. Institute
of Science and Technology Austria, Klosterneuburg. https://doi.org/10.15479/AT:ISTA:9056
chicago: Osang, Georg F. “Multi-Cover Persistence and Delaunay Mosaics.” Institute
of Science and Technology Austria, 2021. https://doi.org/10.15479/AT:ISTA:9056.
ieee: G. F. Osang, “Multi-cover persistence and Delaunay mosaics,” Institute of
Science and Technology Austria, Klosterneuburg, 2021.
ista: 'Osang GF. 2021. Multi-cover persistence and Delaunay mosaics. Klosterneuburg:
Institute of Science and Technology Austria.'
mla: Osang, Georg F. Multi-Cover Persistence and Delaunay Mosaics. Institute
of Science and Technology Austria, 2021, doi:10.15479/AT:ISTA:9056.
short: G.F. Osang, Multi-Cover Persistence and Delaunay Mosaics, Institute of Science
and Technology Austria, 2021.
date_created: 2021-02-02T14:11:06Z
date_published: 2021-02-01T00:00:00Z
date_updated: 2023-09-07T13:29:01Z
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oa_version: Published Version
page: '134'
place: Klosterneuburg
publication_identifier:
issn:
- 2663-337X
publication_status: published
publisher: Institute of Science and Technology Austria
related_material:
record:
- id: '187'
relation: part_of_dissertation
status: public
- id: '8703'
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: Multi-cover persistence and Delaunay mosaics
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: dissertation
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
year: '2021'
...
---
_id: '9022'
abstract:
- lang: eng
text: "In the first part of the thesis we consider Hermitian random matrices. Firstly,
we consider sample covariance matrices XX∗ with X having independent identically
distributed (i.i.d.) centred entries. We prove a Central Limit Theorem for differences
of linear statistics of XX∗ and its minor after removing the first column of X.
Secondly, we consider Wigner-type matrices and prove that the eigenvalue statistics
near cusp singularities of the limiting density of states are universal and that
they form a Pearcey process. Since the limiting eigenvalue distribution admits
only square root (edge) and cubic root (cusp) singularities, this concludes the
third and last remaining case of the Wigner-Dyson-Mehta universality conjecture.
The main technical ingredients are an optimal local law at the cusp, and the proof
of the fast relaxation to equilibrium of the Dyson Brownian motion in the cusp
regime.\r\nIn the second part we consider non-Hermitian matrices X with centred
i.i.d. entries. We normalise the entries of X to have variance N −1. It is well
known that the empirical eigenvalue density converges to the uniform distribution
on the unit disk (circular law). In the first project, we prove universality of
the local eigenvalue statistics close to the edge of the spectrum. This is the
non-Hermitian analogue of the TracyWidom universality at the Hermitian edge. Technically
we analyse the evolution of the spectral distribution of X along the Ornstein-Uhlenbeck
flow for very long time\r\n(up to t = +∞). In the second project, we consider
linear statistics of eigenvalues for macroscopic test functions f in the Sobolev
space H2+ϵ and prove their convergence to the projection of the Gaussian Free
Field on the unit disk. We prove this result for non-Hermitian matrices with real
or complex entries. The main technical ingredients are: (i) local law for products
of two resolvents at different spectral parameters, (ii) analysis of correlated
Dyson Brownian motions.\r\nIn the third and final part we discuss the mathematically
rigorous application of supersymmetric techniques (SUSY ) to give a lower tail
estimate of the lowest singular value of X − z, with z ∈ C. More precisely, we
use superbosonisation formula to give an integral representation of the resolvent
of (X − z)(X − z)∗ which reduces to two and three contour integrals in the complex
and real case, respectively. The rigorous analysis of these integrals is quite
challenging since simple saddle point analysis cannot be applied (the main contribution
comes from a non-trivial manifold). Our result\r\nimproves classical smoothing
inequalities in the regime |z| ≈ 1; this result is essential to prove edge universality
for i.i.d. non-Hermitian matrices."
acknowledgement: I gratefully acknowledge the financial support from the European
Union’s Horizon 2020 research and innovation programme under the Marie Skłodowska-Curie
Grant Agreement No. 665385 and my advisor’s ERC Advanced Grant No. 338804.
alternative_title:
- ISTA Thesis
article_processing_charge: No
author:
- first_name: Giorgio
full_name: Cipolloni, Giorgio
id: 42198EFA-F248-11E8-B48F-1D18A9856A87
last_name: Cipolloni
orcid: 0000-0002-4901-7992
citation:
ama: Cipolloni G. Fluctuations in the spectrum of random matrices. 2021. doi:10.15479/AT:ISTA:9022
apa: Cipolloni, G. (2021). Fluctuations in the spectrum of random matrices.
Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:9022
chicago: Cipolloni, Giorgio. “Fluctuations in the Spectrum of Random Matrices.”
Institute of Science and Technology Austria, 2021. https://doi.org/10.15479/AT:ISTA:9022.
ieee: G. Cipolloni, “Fluctuations in the spectrum of random matrices,” Institute
of Science and Technology Austria, 2021.
ista: Cipolloni G. 2021. Fluctuations in the spectrum of random matrices. Institute
of Science and Technology Austria.
mla: Cipolloni, Giorgio. Fluctuations in the Spectrum of Random Matrices.
Institute of Science and Technology Austria, 2021, doi:10.15479/AT:ISTA:9022.
short: G. Cipolloni, Fluctuations in the Spectrum of Random Matrices, Institute
of Science and Technology Austria, 2021.
date_created: 2021-01-21T18:16:54Z
date_published: 2021-01-25T00:00:00Z
date_updated: 2023-09-07T13:29:32Z
day: '25'
ddc:
- '510'
degree_awarded: PhD
department:
- _id: GradSch
- _id: LaEr
doi: 10.15479/AT:ISTA:9022
ec_funded: 1
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date_updated: 2021-01-25T14:19:10Z
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month: '01'
oa: 1
oa_version: Published Version
page: '380'
project:
- _id: 2564DBCA-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '665385'
name: International IST Doctoral Program
- _id: 258DCDE6-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '338804'
name: Random matrices, universality and disordered quantum systems
publication_identifier:
issn:
- 2663-337X
publication_status: published
publisher: Institute of Science and Technology Austria
status: public
supervisor:
- first_name: László
full_name: Erdös, László
id: 4DBD5372-F248-11E8-B48F-1D18A9856A87
last_name: Erdös
orcid: 0000-0001-5366-9603
title: Fluctuations in the spectrum of random matrices
type: dissertation
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
year: '2021'
...
---
_id: '10007'
abstract:
- lang: eng
text: The present thesis is concerned with the derivation of weak-strong uniqueness
principles for curvature driven interface evolution problems not satisfying a
comparison principle. The specific examples being treated are two-phase Navier-Stokes
flow with surface tension, modeling the evolution of two incompressible, viscous
and immiscible fluids separated by a sharp interface, and multiphase mean curvature
flow, which serves as an idealized model for the motion of grain boundaries in
an annealing polycrystalline material. Our main results - obtained in joint works
with Julian Fischer, Tim Laux and Theresa M. Simon - state that prior to the formation
of geometric singularities due to topology changes, the weak solution concept
of Abels (Interfaces Free Bound. 9, 2007) to two-phase Navier-Stokes flow with
surface tension and the weak solution concept of Laux and Otto (Calc. Var. Partial
Differential Equations 55, 2016) to multiphase mean curvature flow (for networks
in R^2 or double bubbles in R^3) represents the unique solution to these interface
evolution problems within the class of classical solutions, respectively. To the
best of the author's knowledge, for interface evolution problems not admitting
a geometric comparison principle the derivation of a weak-strong uniqueness principle
represented an open problem, so that the works contained in the present thesis
constitute the first positive results in this direction. The key ingredient of
our approach consists of the introduction of a novel concept of relative entropies
for a class of curvature driven interface evolution problems, for which the associated
energy contains an interfacial contribution being proportional to the surface
area of the evolving (network of) interface(s). The interfacial part of the relative
entropy gives sufficient control on the interface error between a weak and a classical
solution, and its time evolution can be computed, at least in principle, for any
energy dissipating weak solution concept. A resulting stability estimate for the
relative entropy essentially entails the above mentioned weak-strong uniqueness
principles. The present thesis contains a detailed introduction to our relative
entropy approach, which in particular highlights potential applications to other
problems in curvature driven interface evolution not treated in this thesis.
alternative_title:
- ISTA Thesis
article_processing_charge: No
author:
- first_name: Sebastian
full_name: Hensel, Sebastian
id: 4D23B7DA-F248-11E8-B48F-1D18A9856A87
last_name: Hensel
orcid: 0000-0001-7252-8072
citation:
ama: 'Hensel S. Curvature driven interface evolution: Uniqueness properties of weak
solution concepts. 2021. doi:10.15479/at:ista:10007'
apa: 'Hensel, S. (2021). Curvature driven interface evolution: Uniqueness properties
of weak solution concepts. Institute of Science and Technology Austria. https://doi.org/10.15479/at:ista:10007'
chicago: 'Hensel, Sebastian. “Curvature Driven Interface Evolution: Uniqueness Properties
of Weak Solution Concepts.” Institute of Science and Technology Austria, 2021.
https://doi.org/10.15479/at:ista:10007.'
ieee: 'S. Hensel, “Curvature driven interface evolution: Uniqueness properties of
weak solution concepts,” Institute of Science and Technology Austria, 2021.'
ista: 'Hensel S. 2021. Curvature driven interface evolution: Uniqueness properties
of weak solution concepts. Institute of Science and Technology Austria.'
mla: 'Hensel, Sebastian. Curvature Driven Interface Evolution: Uniqueness Properties
of Weak Solution Concepts. Institute of Science and Technology Austria, 2021,
doi:10.15479/at:ista:10007.'
short: 'S. Hensel, Curvature Driven Interface Evolution: Uniqueness Properties of
Weak Solution Concepts, Institute of Science and Technology Austria, 2021.'
date_created: 2021-09-13T11:12:34Z
date_published: 2021-09-14T00:00:00Z
date_updated: 2023-09-07T13:30:45Z
day: '14'
ddc:
- '515'
degree_awarded: PhD
department:
- _id: GradSch
- _id: JuFi
doi: 10.15479/at:ista:10007
ec_funded: 1
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oa: 1
oa_version: Published Version
page: '300'
project:
- _id: 2564DBCA-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '665385'
name: International IST Doctoral Program
- _id: 0aa76401-070f-11eb-9043-b5bb049fa26d
call_identifier: H2020
grant_number: '948819'
name: Bridging Scales in Random Materials
publication_identifier:
issn:
- 2663-337X
publication_status: published
publisher: Institute of Science and Technology Austria
related_material:
record:
- id: '10012'
relation: part_of_dissertation
status: public
- id: '10013'
relation: part_of_dissertation
status: public
- id: '7489'
relation: part_of_dissertation
status: public
status: public
supervisor:
- first_name: Julian L
full_name: Fischer, Julian L
id: 2C12A0B0-F248-11E8-B48F-1D18A9856A87
last_name: Fischer
orcid: 0000-0002-0479-558X
title: 'Curvature driven interface evolution: Uniqueness properties of weak solution
concepts'
type: dissertation
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
year: '2021'
...
---
_id: '10030'
abstract:
- lang: eng
text: "This PhD thesis is primarily focused on the study of discrete transport problems,
introduced for the first time in the seminal works of Maas [Maa11] and Mielke
[Mie11] on finite state Markov chains and reaction-diffusion equations, respectively.
More in detail, my research focuses on the study of transport costs on graphs,
in particular the convergence and the stability of such problems in the discrete-to-continuum
limit. This thesis also includes some results concerning\r\nnon-commutative optimal
transport. The first chapter of this thesis consists of a general introduction
to the optimal transport problems, both in the discrete, the continuous, and the
non-commutative setting. Chapters 2 and 3 present the content of two works, obtained
in collaboration with Peter Gladbach, Eva Kopfer, and Jan Maas, where we have
been able to show the convergence of discrete transport costs on periodic graphs
to suitable continuous ones, which can be described by means of a homogenisation
result. We first focus on the particular case of quadratic costs on the real line
and then extending the result to more general costs in arbitrary dimension. Our
results are the first complete characterisation of limits of transport costs on
periodic graphs in arbitrary dimension which do not rely on any additional symmetry.
In Chapter 4 we turn our attention to one of the intriguing connection between
evolution equations and optimal transport, represented by the theory of gradient
flows. We show that discrete gradient flow structures associated to a finite volume
approximation of a certain class of diffusive equations (Fokker–Planck) is stable
in the limit of vanishing meshes, reproving the convergence of the scheme via
the method of evolutionary Γ-convergence and exploiting a more variational point
of view on the problem. This is based on a collaboration with Dominik Forkert
and Jan Maas. Chapter 5 represents a change of perspective, moving away from the
discrete world and reaching the non-commutative one. As in the discrete case,
we discuss how classical tools coming from the commutative optimal transport can
be translated into the setting of density matrices. In particular, in this final
chapter we present a non-commutative version of the Schrödinger problem (or entropic
regularised optimal transport problem) and discuss existence and characterisation
of minimisers, a duality result, and present a non-commutative version of the
well-known Sinkhorn algorithm to compute the above mentioned optimisers. This
is based on a joint work with Dario Feliciangeli and Augusto Gerolin. Finally,
Appendix A and B contain some additional material and discussions, with particular
attention to Harnack inequalities and the regularity of flows on discrete spaces."
acknowledged_ssus:
- _id: M-Shop
- _id: NanoFab
acknowledgement: The author gratefully acknowledges support by the Austrian Science
Fund (FWF), grants No W1245.
alternative_title:
- ISTA Thesis
article_processing_charge: No
author:
- first_name: Lorenzo
full_name: Portinale, Lorenzo
id: 30AD2CBC-F248-11E8-B48F-1D18A9856A87
last_name: Portinale
citation:
ama: Portinale L. Discrete-to-continuum limits of transport problems and gradient
flows in the space of measures. 2021. doi:10.15479/at:ista:10030
apa: Portinale, L. (2021). Discrete-to-continuum limits of transport problems
and gradient flows in the space of measures. Institute of Science and Technology
Austria. https://doi.org/10.15479/at:ista:10030
chicago: Portinale, Lorenzo. “Discrete-to-Continuum Limits of Transport Problems
and Gradient Flows in the Space of Measures.” Institute of Science and Technology
Austria, 2021. https://doi.org/10.15479/at:ista:10030.
ieee: L. Portinale, “Discrete-to-continuum limits of transport problems and gradient
flows in the space of measures,” Institute of Science and Technology Austria,
2021.
ista: Portinale L. 2021. Discrete-to-continuum limits of transport problems and
gradient flows in the space of measures. Institute of Science and Technology Austria.
mla: Portinale, Lorenzo. Discrete-to-Continuum Limits of Transport Problems and
Gradient Flows in the Space of Measures. Institute of Science and Technology
Austria, 2021, doi:10.15479/at:ista:10030.
short: L. Portinale, Discrete-to-Continuum Limits of Transport Problems and Gradient
Flows in the Space of Measures, Institute of Science and Technology Austria, 2021.
date_created: 2021-09-21T09:14:15Z
date_published: 2021-09-22T00:00:00Z
date_updated: 2023-09-07T13:31:06Z
day: '22'
ddc:
- '515'
degree_awarded: PhD
department:
- _id: GradSch
- _id: JaMa
doi: 10.15479/at:ista:10030
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creator: cchlebak
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date_updated: 2021-09-27T11:14:31Z
file_id: '10047'
file_name: thesis_portinale_Final (1).pdf
file_size: 2532673
relation: main_file
file_date_updated: 2022-03-10T12:14:42Z
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language:
- iso: eng
month: '09'
oa: 1
oa_version: Published Version
project:
- _id: 260788DE-B435-11E9-9278-68D0E5697425
call_identifier: FWF
name: Dissipation and Dispersion in Nonlinear Partial Differential Equations
- _id: fc31cba2-9c52-11eb-aca3-ff467d239cd2
grant_number: F6504
name: Taming Complexity in Partial Differential Systems
publication_identifier:
issn:
- 2663-337X
publication_status: published
publisher: Institute of Science and Technology Austria
related_material:
record:
- id: '10022'
relation: part_of_dissertation
status: public
- id: '9792'
relation: part_of_dissertation
status: public
- id: '7573'
relation: part_of_dissertation
status: public
status: public
supervisor:
- first_name: Jan
full_name: Maas, Jan
id: 4C5696CE-F248-11E8-B48F-1D18A9856A87
last_name: Maas
orcid: 0000-0002-0845-1338
title: Discrete-to-continuum limits of transport problems and gradient flows in the
space of measures
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: dissertation
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
year: '2021'
...
---
_id: '9920'
abstract:
- lang: eng
text: 'This work is concerned with two fascinating circuit quantum electrodynamics
components, the Josephson junction and the geometric superinductor, and the interesting
experiments that can be done by combining the two. The Josephson junction has
revolutionized the field of superconducting circuits as a non-linear dissipation-less
circuit element and is used in almost all superconducting qubit implementations
since the 90s. On the other hand, the superinductor is a relatively new circuit
element introduced as a key component of the fluxonium qubit in 2009. This is
an inductor with characteristic impedance larger than the resistance quantum and
self-resonance frequency in the GHz regime. The combination of these two elements
can occur in two fundamental ways: in parallel and in series. When connected in
parallel the two create the fluxonium qubit, a loop with large inductance and
a rich energy spectrum reliant on quantum tunneling. On the other hand placing
the two elements in series aids with the measurement of the IV curve of a single
Josephson junction in a high impedance environment. In this limit theory predicts
that the junction will behave as its dual element: the phase-slip junction. While
the Josephson junction acts as a non-linear inductor the phase-slip junction has
the behavior of a non-linear capacitance and can be used to measure new Josephson
junction phenomena, namely Coulomb blockade of Cooper pairs and phase-locked Bloch
oscillations. The latter experiment allows for a direct link between frequency
and current which is an elusive connection in quantum metrology. This work introduces
the geometric superinductor, a superconducting circuit element where the high
inductance is due to the geometry rather than the material properties of the superconductor,
realized from a highly miniaturized superconducting planar coil. These structures
will be described and characterized as resonators and qubit inductors and progress
towards the measurement of phase-locked Bloch oscillations will be presented.'
acknowledged_ssus:
- _id: NanoFab
- _id: M-Shop
alternative_title:
- ISTA Thesis
article_processing_charge: No
author:
- first_name: Matilda
full_name: Peruzzo, Matilda
id: 3F920B30-F248-11E8-B48F-1D18A9856A87
last_name: Peruzzo
orcid: 0000-0002-3415-4628
citation:
ama: Peruzzo M. Geometric superinductors and their applications in circuit quantum
electrodynamics. 2021. doi:10.15479/at:ista:9920
apa: Peruzzo, M. (2021). Geometric superinductors and their applications in circuit
quantum electrodynamics. Institute of Science and Technology Austria. https://doi.org/10.15479/at:ista:9920
chicago: Peruzzo, Matilda. “Geometric Superinductors and Their Applications in Circuit
Quantum Electrodynamics.” Institute of Science and Technology Austria, 2021. https://doi.org/10.15479/at:ista:9920.
ieee: M. Peruzzo, “Geometric superinductors and their applications in circuit quantum
electrodynamics,” Institute of Science and Technology Austria, 2021.
ista: Peruzzo M. 2021. Geometric superinductors and their applications in circuit
quantum electrodynamics. Institute of Science and Technology Austria.
mla: Peruzzo, Matilda. Geometric Superinductors and Their Applications in Circuit
Quantum Electrodynamics. Institute of Science and Technology Austria, 2021,
doi:10.15479/at:ista:9920.
short: M. Peruzzo, Geometric Superinductors and Their Applications in Circuit Quantum
Electrodynamics, Institute of Science and Technology Austria, 2021.
date_created: 2021-08-16T09:44:09Z
date_published: 2021-08-19T00:00:00Z
date_updated: 2023-09-07T13:31:22Z
day: '19'
ddc:
- '539'
degree_awarded: PhD
department:
- _id: GradSch
- _id: JoFi
doi: 10.15479/at:ista:9920
file:
- access_level: closed
checksum: 3cd1986efde5121d7581f6fcf9090da8
content_type: application/x-zip-compressed
creator: mperuzzo
date_created: 2021-08-16T09:33:21Z
date_updated: 2021-09-06T08:39:47Z
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file_size: 151387283
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content_type: application/pdf
creator: mperuzzo
date_created: 2021-08-18T14:20:06Z
date_updated: 2021-09-06T08:39:47Z
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date_created: 2021-08-18T14:20:09Z
date_updated: 2021-09-06T08:39:47Z
description: Extra copy of the thesis as PDF/A-2b
file_id: '9940'
file_name: GeometricSuperinductorsAndTheirApplicationsIncQED-2b.pdf
file_size: 17592425
relation: other
file_date_updated: 2021-09-06T08:39:47Z
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keyword:
- quantum computing
- superinductor
- quantum metrology
language:
- iso: eng
month: '08'
oa: 1
oa_version: Published Version
page: '149'
publication_identifier:
isbn:
- 978-3-99078-013-8
issn:
- 2663-337X
publication_status: published
publisher: Institute of Science and Technology Austria
related_material:
record:
- id: '9928'
relation: part_of_dissertation
status: public
- id: '8755'
relation: part_of_dissertation
status: public
status: public
supervisor:
- first_name: Johannes M
full_name: Fink, Johannes M
id: 4B591CBA-F248-11E8-B48F-1D18A9856A87
last_name: Fink
orcid: 0000-0001-8112-028X
title: Geometric superinductors and their applications in circuit quantum electrodynamics
type: dissertation
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
year: '2021'
...
---
_id: '10422'
abstract:
- lang: eng
text: Those who aim to devise new materials with desirable properties usually examine
present methods first. However, they will find out that some approaches can exist
only conceptually without high chances to become practically useful. It seems
that a numerical technique called automatic differentiation together with increasing
supply of computational accelerators will soon shift many methods of the material
design from the category ”unimaginable” to the category ”expensive but possible”.
Approach we suggest is not an exception. Our overall goal is to have an efficient
and generalizable approach allowing to solve inverse design problems. In this
thesis we scratch its surface. We consider jammed systems of identical particles.
And ask ourselves how the shape of those particles (or the parameters codifying
it) may affect mechanical properties of the system. An indispensable part of reaching
the answer is an appropriate particle parametrization. We come up with a simple,
yet generalizable and purposeful scheme for it. Using our generalizable shape
parameterization, we simulate the formation of a solid composed of pentagonal-like
particles and measure anisotropy in the resulting elastic response. Through automatic
differentiation techniques, we directly connect the shape parameters with the
elastic response. Interestingly, for our system we find that less isotropic particles
lead to a more isotropic elastic response. Together with other results known about
our method it seems that it can be successfully generalized for different inverse
design problems.
alternative_title:
- ISTA Master's Thesis
article_processing_charge: No
author:
- first_name: Anton
full_name: Piankov, Anton
id: 865E3C26-AA8C-11E9-A409-C4C4E5697425
last_name: Piankov
citation:
ama: Piankov A. Towards designer materials using customizable particle shape. 2021.
doi:10.15479/at:ista:10422
apa: Piankov, A. (2021). Towards designer materials using customizable particle
shape. Institute of Science and Technology Austria. https://doi.org/10.15479/at:ista:10422
chicago: Piankov, Anton. “Towards Designer Materials Using Customizable Particle
Shape.” Institute of Science and Technology Austria, 2021. https://doi.org/10.15479/at:ista:10422.
ieee: A. Piankov, “Towards designer materials using customizable particle shape,”
Institute of Science and Technology Austria, 2021.
ista: Piankov A. 2021. Towards designer materials using customizable particle shape.
Institute of Science and Technology Austria.
mla: Piankov, Anton. Towards Designer Materials Using Customizable Particle Shape.
Institute of Science and Technology Austria, 2021, doi:10.15479/at:ista:10422.
short: A. Piankov, Towards Designer Materials Using Customizable Particle Shape,
Institute of Science and Technology Austria, 2021.
date_created: 2021-12-07T10:48:06Z
date_published: 2021-12-07T00:00:00Z
date_updated: 2023-09-07T13:34:12Z
day: '07'
ddc:
- '530'
degree_awarded: MS
department:
- _id: GradSch
- _id: CaGo
doi: 10.15479/at:ista:10422
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creator: cchlebak
date_created: 2021-12-07T11:13:52Z
date_updated: 2022-03-10T12:10:25Z
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file_name: Thesis.zip
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creator: cchlebak
date_created: 2021-12-07T11:14:01Z
date_updated: 2022-03-10T12:10:25Z
file_id: '10425'
file_name: Preliminary_pages_Piankov.docx
file_size: 47638
relation: source_file
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content_type: application/pdf
creator: cchlebak
date_created: 2021-12-07T11:20:35Z
date_updated: 2021-12-07T11:20:35Z
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file_size: 484965
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success: 1
file_date_updated: 2022-03-10T12:10:25Z
has_accepted_license: '1'
language:
- iso: eng
month: '12'
oa: 1
oa_version: Published Version
publication_identifier:
issn:
- 2791-4585
publication_status: published
publisher: Institute of Science and Technology Austria
status: public
supervisor:
- first_name: Carl Peter
full_name: Goodrich, Carl Peter
id: EB352CD2-F68A-11E9-89C5-A432E6697425
last_name: Goodrich
orcid: 0000-0002-1307-5074
title: Towards designer materials using customizable particle shape
type: dissertation
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
year: '2021'
...
---
_id: '9418'
abstract:
- lang: eng
text: "Deep learning is best known for its empirical success across a wide range
of applications\r\nspanning computer vision, natural language processing and speech.
Of equal significance,\r\nthough perhaps less known, are its ramifications for
learning theory: deep networks have\r\nbeen observed to perform surprisingly well
in the high-capacity regime, aka the overfitting\r\nor underspecified regime.
Classically, this regime on the far right of the bias-variance curve\r\nis associated
with poor generalisation; however, recent experiments with deep networks\r\nchallenge
this view.\r\n\r\nThis thesis is devoted to investigating various aspects of underspecification
in deep learning.\r\nFirst, we argue that deep learning models are underspecified
on two levels: a) any given\r\ntraining dataset can be fit by many different functions,
and b) any given function can be\r\nexpressed by many different parameter configurations.
We refer to the second kind of\r\nunderspecification as parameterisation redundancy
and we precisely characterise its extent.\r\nSecond, we characterise the implicit
criteria (the inductive bias) that guide learning in the\r\nunderspecified regime.
Specifically, we consider a nonlinear but tractable classification\r\nsetting,
and show that given the choice, neural networks learn classifiers with a large
margin.\r\nThird, we consider learning scenarios where the inductive bias is not
by itself sufficient to\r\ndeal with underspecification. We then study different
ways of ‘tightening the specification’: i)\r\nIn the setting of representation
learning with variational autoencoders, we propose a hand-\r\ncrafted regulariser
based on mutual information. ii) In the setting of binary classification, we\r\nconsider
soft-label (real-valued) supervision. We derive a generalisation bound for linear\r\nnetworks
supervised in this way and verify that soft labels facilitate fast learning. Finally,
we\r\nexplore an application of soft-label supervision to the training of multi-exit
models."
acknowledged_ssus:
- _id: ScienComp
- _id: CampIT
- _id: E-Lib
alternative_title:
- ISTA Thesis
article_processing_charge: No
author:
- first_name: Phuong
full_name: Bui Thi Mai, Phuong
id: 3EC6EE64-F248-11E8-B48F-1D18A9856A87
last_name: Bui Thi Mai
citation:
ama: Phuong M. Underspecification in deep learning. 2021. doi:10.15479/AT:ISTA:9418
apa: Phuong, M. (2021). Underspecification in deep learning. Institute of
Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:9418
chicago: Phuong, Mary. “Underspecification in Deep Learning.” Institute of Science
and Technology Austria, 2021. https://doi.org/10.15479/AT:ISTA:9418.
ieee: M. Phuong, “Underspecification in deep learning,” Institute of Science and
Technology Austria, 2021.
ista: Phuong M. 2021. Underspecification in deep learning. Institute of Science
and Technology Austria.
mla: Phuong, Mary. Underspecification in Deep Learning. Institute of Science
and Technology Austria, 2021, doi:10.15479/AT:ISTA:9418.
short: M. Phuong, Underspecification in Deep Learning, Institute of Science and
Technology Austria, 2021.
date_created: 2021-05-24T13:06:23Z
date_published: 2021-05-30T00:00:00Z
date_updated: 2023-09-08T11:11:12Z
day: '30'
ddc:
- '000'
degree_awarded: PhD
department:
- _id: GradSch
- _id: ChLa
doi: 10.15479/AT:ISTA:9418
file:
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checksum: 4f0abe64114cfed264f9d36e8d1197e3
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creator: bphuong
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date_updated: 2021-05-24T11:22:29Z
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file_size: 2673905
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creator: bphuong
date_created: 2021-05-24T11:56:02Z
date_updated: 2021-05-24T11:56:02Z
file_id: '9420'
file_name: thesis.zip
file_size: 92995100
relation: source_file
file_date_updated: 2021-05-24T11:56:02Z
has_accepted_license: '1'
language:
- iso: eng
month: '05'
oa: 1
oa_version: Published Version
page: '125'
publication_identifier:
issn:
- 2663-337X
publication_status: published
publisher: Institute of Science and Technology Austria
related_material:
record:
- id: '7435'
relation: part_of_dissertation
status: deleted
- id: '7481'
relation: part_of_dissertation
status: public
- id: '9416'
relation: part_of_dissertation
status: public
- id: '7479'
relation: part_of_dissertation
status: public
status: public
supervisor:
- first_name: Christoph
full_name: Lampert, Christoph
id: 40C20FD2-F248-11E8-B48F-1D18A9856A87
last_name: Lampert
orcid: 0000-0001-8622-7887
title: Underspecification in deep learning
type: dissertation
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
year: '2021'
...
---
_id: '10199'
abstract:
- lang: eng
text: The design and verification of concurrent systems remains an open challenge
due to the non-determinism that arises from the inter-process communication. In
particular, concurrent programs are notoriously difficult both to be written correctly
and to be analyzed formally, as complex thread interaction has to be accounted
for. The difficulties are further exacerbated when concurrent programs get executed
on modern-day hardware, which contains various buffering and caching mechanisms
for efficiency reasons. This causes further subtle non-determinism, which can
often produce very unintuitive behavior of the concurrent programs. Model checking
is at the forefront of tackling the verification problem, where the task is to
decide, given as input a concurrent system and a desired property, whether the
system satisfies the property. The inherent state-space explosion problem in model
checking of concurrent systems causes naïve explicit methods not to scale, thus
more inventive methods are required. One such method is stateless model checking
(SMC), which explores in memory-efficient manner the program executions rather
than the states of the program. State-of-the-art SMC is typically coupled with
partial order reduction (POR) techniques, which argue that certain executions
provably produce identical system behavior, thus limiting the amount of executions
one needs to explore in order to cover all possible behaviors. Another method
to tackle the state-space explosion is symbolic model checking, where the considered
techniques operate on a succinct implicit representation of the input system rather
than explicitly accessing the system. In this thesis we present new techniques
for verification of concurrent systems. We present several novel POR methods for
SMC of concurrent programs under various models of semantics, some of which account
for write-buffering mechanisms. Additionally, we present novel algorithms for
symbolic model checking of finite-state concurrent systems, where the desired
property of the systems is to ensure a formally defined notion of fairness.
acknowledged_ssus:
- _id: SSU
alternative_title:
- ISTA Thesis
article_processing_charge: No
author:
- first_name: Viktor
full_name: Toman, Viktor
id: 3AF3DA7C-F248-11E8-B48F-1D18A9856A87
last_name: Toman
orcid: 0000-0001-9036-063X
citation:
ama: Toman V. Improved verification techniques for concurrent systems. 2021. doi:10.15479/at:ista:10199
apa: Toman, V. (2021). Improved verification techniques for concurrent systems.
Institute of Science and Technology Austria. https://doi.org/10.15479/at:ista:10199
chicago: Toman, Viktor. “Improved Verification Techniques for Concurrent Systems.”
Institute of Science and Technology Austria, 2021. https://doi.org/10.15479/at:ista:10199.
ieee: V. Toman, “Improved verification techniques for concurrent systems,” Institute
of Science and Technology Austria, 2021.
ista: Toman V. 2021. Improved verification techniques for concurrent systems. Institute
of Science and Technology Austria.
mla: Toman, Viktor. Improved Verification Techniques for Concurrent Systems.
Institute of Science and Technology Austria, 2021, doi:10.15479/at:ista:10199.
short: V. Toman, Improved Verification Techniques for Concurrent Systems, Institute
of Science and Technology Austria, 2021.
date_created: 2021-10-29T20:09:01Z
date_published: 2021-10-31T00:00:00Z
date_updated: 2023-09-19T09:59:54Z
day: '31'
ddc:
- '000'
degree_awarded: PhD
department:
- _id: GradSch
- _id: KrCh
doi: 10.15479/at:ista:10199
ec_funded: 1
file:
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checksum: 4f412a1ee60952221b499a4b1268df35
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creator: vtoman
date_created: 2021-11-08T14:12:22Z
date_updated: 2021-11-08T14:12:22Z
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file_size: 2915234
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checksum: 9584943f99127be2dd2963f6784c37d4
content_type: application/zip
creator: vtoman
date_created: 2021-11-08T14:12:46Z
date_updated: 2021-11-09T09:00:50Z
file_id: '10226'
file_name: toman_thesis.zip
file_size: 8616056
relation: source_file
file_date_updated: 2021-11-09T09:00:50Z
has_accepted_license: '1'
keyword:
- concurrency
- verification
- model checking
language:
- iso: eng
month: '10'
oa: 1
oa_version: Published Version
page: '166'
project:
- _id: 2564DBCA-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '665385'
name: International IST Doctoral Program
- _id: 25F2ACDE-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: S11402-N23
name: Rigorous Systems Engineering
- _id: 25892FC0-B435-11E9-9278-68D0E5697425
grant_number: ICT15-003
name: Efficient Algorithms for Computer Aided Verification
- _id: 0599E47C-7A3F-11EA-A408-12923DDC885E
call_identifier: H2020
grant_number: '863818'
name: 'Formal Methods for Stochastic Models: Algorithms and Applications'
publication_identifier:
issn:
- 2663-337X
publication_status: published
publisher: Institute of Science and Technology Austria
related_material:
record:
- id: '10190'
relation: part_of_dissertation
status: public
- id: '10191'
relation: part_of_dissertation
status: public
- id: '9987'
relation: part_of_dissertation
status: public
- id: '141'
relation: part_of_dissertation
status: public
status: public
supervisor:
- first_name: Krishnendu
full_name: Chatterjee, Krishnendu
id: 2E5DCA20-F248-11E8-B48F-1D18A9856A87
last_name: Chatterjee
orcid: 0000-0002-4561-241X
title: Improved verification techniques for concurrent systems
type: dissertation
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
year: '2021'
...
---
_id: '10035'
abstract:
- lang: eng
text: 'Many security definitions come in two flavors: a stronger “adaptive” flavor,
where the adversary can arbitrarily make various choices during the course of
the attack, and a weaker “selective” flavor where the adversary must commit to
some or all of their choices a-priori. For example, in the context of identity-based
encryption, selective security requires the adversary to decide on the identity
of the attacked party at the very beginning of the game whereas adaptive security
allows the attacker to first see the master public key and some secret keys before
making this choice. Often, it appears to be much easier to achieve selective security
than it is to achieve adaptive security. A series of several recent works shows
how to cleverly achieve adaptive security in several such scenarios including
generalized selective decryption [Pan07][FJP15], constrained PRFs [FKPR14], and
Yao’s garbled circuits [JW16]. Although the above works expressed vague intuition
that they share a common technique, the connection was never made precise. In
this work we present a new framework (published at Crypto ’17 [JKK+17a]) that
connects all of these works and allows us to present them in a unified and simplified
fashion. Having the framework in place, we show how to achieve adaptive security
for proxy re-encryption schemes (published at PKC ’19 [FKKP19]) and provide the
first adaptive security proofs for continuous group key agreement protocols (published
at S&P ’21 [KPW+21]). Questioning optimality of our framework, we then show that
currently used proof techniques cannot lead to significantly better security guarantees
for "graph-building" games (published at TCC ’21 [KKPW21a]). These games cover
generalized selective decryption, as well as the security of prominent constructions
for constrained PRFs, continuous group key agreement, and proxy re-encryption.
Finally, we revisit the adaptive security of Yao’s garbled circuits and extend
the analysis of Jafargholi and Wichs in two directions: While they prove adaptive
security only for a modified construction with increased online complexity, we
provide the first positive results for the original construction by Yao (published
at TCC ’21 [KKP21a]). On the negative side, we prove that the results of Jafargholi
and Wichs are essentially optimal by showing that no black-box reduction can provide
a significantly better security bound (published at Crypto ’21 [KKPW21c]).'
acknowledgement: "I want to acknowledge the funding by the European Research Council
(ERC) under the European Union’s Horizon 2020 research and innovation programme
(682815 - TOCNeT).\r\n"
alternative_title:
- ISTA Thesis
article_processing_charge: No
author:
- first_name: Karen
full_name: Klein, Karen
id: 3E83A2F8-F248-11E8-B48F-1D18A9856A87
last_name: Klein
citation:
ama: Klein K. On the adaptive security of graph-based games. 2021. doi:10.15479/at:ista:10035
apa: Klein, K. (2021). On the adaptive security of graph-based games. Institute
of Science and Technology Austria. https://doi.org/10.15479/at:ista:10035
chicago: Klein, Karen. “On the Adaptive Security of Graph-Based Games.” Institute
of Science and Technology Austria, 2021. https://doi.org/10.15479/at:ista:10035.
ieee: K. Klein, “On the adaptive security of graph-based games,” Institute of Science
and Technology Austria, 2021.
ista: Klein K. 2021. On the adaptive security of graph-based games. Institute of
Science and Technology Austria.
mla: Klein, Karen. On the Adaptive Security of Graph-Based Games. Institute
of Science and Technology Austria, 2021, doi:10.15479/at:ista:10035.
short: K. Klein, On the Adaptive Security of Graph-Based Games, Institute of Science
and Technology Austria, 2021.
date_created: 2021-09-23T07:31:44Z
date_published: 2021-09-23T00:00:00Z
date_updated: 2023-10-17T09:24:07Z
day: '23'
ddc:
- '519'
degree_awarded: PhD
department:
- _id: GradSch
- _id: KrPi
doi: 10.15479/at:ista:10035
ec_funded: 1
file:
- access_level: open_access
checksum: 73a44345c683e81f3e765efbf86fdcc5
content_type: application/pdf
creator: cchlebak
date_created: 2021-10-04T12:22:33Z
date_updated: 2021-10-04T12:22:33Z
file_id: '10082'
file_name: thesis_pdfa.pdf
file_size: 2104726
relation: main_file
success: 1
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checksum: 7b80df30a0e686c3ef6a56d4e1c59e29
content_type: application/x-zip-compressed
creator: cchlebak
date_created: 2021-10-05T07:04:37Z
date_updated: 2022-03-10T12:15:18Z
file_id: '10085'
file_name: thesis_final (1).zip
file_size: 9538359
relation: source_file
file_date_updated: 2022-03-10T12:15:18Z
has_accepted_license: '1'
language:
- iso: eng
month: '09'
oa: 1
oa_version: Published Version
page: '276'
project:
- _id: 258AA5B2-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '682815'
name: Teaching Old Crypto New Tricks
publication_identifier:
issn:
- 2663-337X
publication_status: published
publisher: Institute of Science and Technology Austria
related_material:
record:
- id: '10044'
relation: part_of_dissertation
status: public
- id: '10049'
relation: part_of_dissertation
status: public
- id: '637'
relation: part_of_dissertation
status: public
- id: '10041'
relation: part_of_dissertation
status: public
- id: '6430'
relation: part_of_dissertation
status: public
- id: '10048'
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 adaptive security of graph-based games
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: dissertation
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
year: '2021'
...
---
_id: '10429'
abstract:
- lang: eng
text: "The scalability of concurrent data structures and distributed algorithms
strongly depends on\r\nreducing the contention for shared resources and the costs
of synchronization and communication. We show how such cost reductions can be
attained by relaxing the strict consistency conditions required by sequential
implementations. In the first part of the thesis, we consider relaxation in the
context of concurrent data structures. Specifically, in data structures \r\nsuch
as priority queues, imposing strong semantics renders scalability impossible,
since a correct implementation of the remove operation should return only the
element with highest priority. Intuitively, attempting to invoke remove operations
concurrently creates a race condition. This bottleneck can be circumvented by
relaxing semantics of the affected data structure, thus allowing removal of the
elements which are no longer required to have the highest priority. We prove that
the randomized implementations of relaxed data structures provide provable guarantees
on the priority of the removed elements even under concurrency. Additionally,
we show that in some cases the relaxed data structures can be used to scale the
classical algorithms which are usually implemented with the exact ones. In the
second part, we study parallel variants of the stochastic gradient descent (SGD)
algorithm, which distribute computation among the multiple processors, thus reducing
the running time. Unfortunately, in order for standard parallel SGD to succeed,
each processor has to maintain a local copy of the necessary model parameter,
which is identical to the local copies of other processors; the overheads from
this perfect consistency in terms of communication and synchronization can negate
the speedup gained by distributing the computation. We show that the consistency
conditions required by SGD can be relaxed, allowing the algorithm to be more
flexible in terms of tolerating quantized communication, asynchrony, or even crash
faults, while its convergence remains asymptotically the same."
alternative_title:
- ISTA Thesis
article_processing_charge: No
author:
- first_name: Giorgi
full_name: Nadiradze, Giorgi
id: 3279A00C-F248-11E8-B48F-1D18A9856A87
last_name: Nadiradze
orcid: 0000-0001-5634-0731
citation:
ama: Nadiradze G. On achieving scalability through relaxation. 2021. doi:10.15479/at:ista:10429
apa: Nadiradze, G. (2021). On achieving scalability through relaxation. Institute
of Science and Technology Austria. https://doi.org/10.15479/at:ista:10429
chicago: Nadiradze, Giorgi. “On Achieving Scalability through Relaxation.” Institute
of Science and Technology Austria, 2021. https://doi.org/10.15479/at:ista:10429.
ieee: G. Nadiradze, “On achieving scalability through relaxation,” Institute of
Science and Technology Austria, 2021.
ista: Nadiradze G. 2021. On achieving scalability through relaxation. Institute
of Science and Technology Austria.
mla: Nadiradze, Giorgi. On Achieving Scalability through Relaxation. Institute
of Science and Technology Austria, 2021, doi:10.15479/at:ista:10429.
short: G. Nadiradze, On Achieving Scalability through Relaxation, Institute of Science
and Technology Austria, 2021.
date_created: 2021-12-08T21:52:28Z
date_published: 2021-12-09T00:00:00Z
date_updated: 2023-10-17T11:48:55Z
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oa_version: Published Version
page: '132'
project:
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call_identifier: H2020
grant_number: '805223'
name: Elastic Coordination for Scalable Machine Learning
publication_identifier:
issn:
- 2663-337X
publication_status: published
publisher: Institute of Science and Technology Austria
related_material:
record:
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relation: part_of_dissertation
status: public
- id: '6673'
relation: part_of_dissertation
status: public
- id: '5965'
relation: part_of_dissertation
status: public
- id: '10435'
relation: part_of_dissertation
status: public
status: public
supervisor:
- first_name: Dan-Adrian
full_name: Alistarh, Dan-Adrian
id: 4A899BFC-F248-11E8-B48F-1D18A9856A87
last_name: Alistarh
orcid: 0000-0003-3650-940X
title: On achieving scalability through relaxation
type: dissertation
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
year: '2021'
...
---
_id: '9733'
abstract:
- lang: eng
text: This thesis is the result of the research carried out by the author during
his PhD at IST Austria between 2017 and 2021. It mainly focuses on the Fröhlich
polaron model, specifically to its regime of strong coupling. This model, which
is rigorously introduced and discussed in the introduction, has been of great
interest in condensed matter physics and field theory for more than eighty years.
It is used to describe an electron interacting with the atoms of a solid material
(the strength of this interaction is modeled by the presence of a coupling constant
α in the Hamiltonian of the system). The particular regime examined here, which
is mathematically described by considering the limit α →∞, displays many interesting
features related to the emergence of classical behavior, which allows for a simplified
effective description of the system under analysis. The properties, the range
of validity and a quantitative analysis of the precision of such classical approximations
are the main object of the present work. We specify our investigation to the study
of the ground state energy of the system, its dynamics and its effective mass.
For each of these problems, we provide in the introduction an overview of the
previously known results and a detailed account of the original contributions
by the author.
alternative_title:
- ISTA Thesis
article_processing_charge: No
author:
- first_name: Dario
full_name: Feliciangeli, Dario
id: 41A639AA-F248-11E8-B48F-1D18A9856A87
last_name: Feliciangeli
orcid: 0000-0003-0754-8530
citation:
ama: Feliciangeli D. The polaron at strong coupling. 2021. doi:10.15479/at:ista:9733
apa: Feliciangeli, D. (2021). The polaron at strong coupling. Institute of
Science and Technology Austria. https://doi.org/10.15479/at:ista:9733
chicago: Feliciangeli, Dario. “The Polaron at Strong Coupling.” Institute of Science
and Technology Austria, 2021. https://doi.org/10.15479/at:ista:9733.
ieee: D. Feliciangeli, “The polaron at strong coupling,” Institute of Science and
Technology Austria, 2021.
ista: Feliciangeli D. 2021. The polaron at strong coupling. Institute of Science
and Technology Austria.
mla: Feliciangeli, Dario. The Polaron at Strong Coupling. Institute of Science
and Technology Austria, 2021, doi:10.15479/at:ista:9733.
short: D. Feliciangeli, The Polaron at Strong Coupling, Institute of Science and
Technology Austria, 2021.
date_created: 2021-07-27T15:48:30Z
date_published: 2021-08-20T00:00:00Z
date_updated: 2024-03-06T12:30:44Z
day: '20'
ddc:
- '515'
- '519'
- '539'
degree_awarded: PhD
department:
- _id: GradSch
- _id: RoSe
- _id: JaMa
doi: 10.15479/at:ista:9733
ec_funded: 1
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language:
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month: '08'
oa: 1
oa_version: Published Version
page: '180'
project:
- _id: 256E75B8-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '716117'
name: Optimal Transport and Stochastic Dynamics
- _id: 25C6DC12-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '694227'
name: Analysis of quantum many-body systems
- _id: fc31cba2-9c52-11eb-aca3-ff467d239cd2
grant_number: F6504
name: Taming Complexity in Partial Differential Systems
publication_identifier:
issn:
- 2663-337X
publication_status: published
publisher: Institute of Science and Technology Austria
related_material:
record:
- id: '9787'
relation: part_of_dissertation
status: public
- id: '9792'
relation: part_of_dissertation
status: public
- id: '9225'
relation: part_of_dissertation
status: public
- id: '9781'
relation: part_of_dissertation
status: public
- id: '9791'
relation: part_of_dissertation
status: public
status: public
supervisor:
- first_name: Robert
full_name: Seiringer, Robert
id: 4AFD0470-F248-11E8-B48F-1D18A9856A87
last_name: Seiringer
orcid: 0000-0002-6781-0521
- first_name: Jan
full_name: Maas, Jan
id: 4C5696CE-F248-11E8-B48F-1D18A9856A87
last_name: Maas
orcid: 0000-0002-0845-1338
title: The polaron at strong coupling
tmp:
image: /image/cc_by_nd.png
legal_code_url: https://creativecommons.org/licenses/by-nd/4.0/legalcode
name: Creative Commons Attribution-NoDerivatives 4.0 International (CC BY-ND 4.0)
short: CC BY-ND (4.0)
type: dissertation
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
year: '2021'
...
---
_id: '9992'
abstract:
- lang: eng
text: "Blood – this is what animals use to heal wounds fast and efficient. Plants
do not have blood circulation and their cells cannot move. However, plants have
evolved remarkable capacities to regenerate tissues and organs preventing further
damage. In my PhD research, I studied the wound healing in the Arabidopsis root.
I used a UV laser to ablate single cells in the root tip and observed the consequent
wound healing. Interestingly, the inner adjacent cells induced a\r\ndivision plane
switch and subsequently adopted the cell type of the killed cell to replace it.
We termed this form of wound healing “restorative divisions”. This initial observation
triggered the questions of my PhD studies: How and why do cells orient their division
planes, how do they feel the wound and why does this happen only in inner adjacent
cells.\r\nFor answering these questions, I used a quite simple experimental setup:
5 day - old seedlings were stained with propidium iodide to visualize cell walls
and dead cells; ablation was carried out using a special laser cutter and a confocal
microscope. Adaptation of the novel vertical microscope system made it possible
to observe wounds in real time. This revealed that restorative divisions occur
at increased frequency compared to normal divisions. Additionally,\r\nthe major
plant hormone auxin accumulates in wound adjacent cells and drives the expression
of the wound-stress responsive transcription factor ERF115. Using this as a marker
gene for wound responses, we found that an important part of wound signalling
is the sensing of the collapse of the ablated cell. The collapse causes a radical
pressure drop, which results in strong tissue deformations. These deformations
manifest in an invasion of the now free spot specifically by the inner adjacent
cells within seconds, probably because of higher pressure of the inner tissues.
Long-term imaging revealed that those deformed cells continuously expand towards
the wound hole and that this is crucial for the restorative division. These wound-expanding
cells exhibit an abnormal, biphasic polarity of microtubule arrays\r\nbefore the
division. Experiments inhibiting cell expansion suggest that it is the biphasic
stretching that induces those MT arrays. Adapting the micromanipulator aspiration
system from animal scientists at our institute confirmed the hypothesis that stretching
influences microtubule stability. In conclusion, this shows that microtubules
react to tissue deformation\r\nand this facilitates the observed division plane
switch. This puts mechanical cues and tensions at the most prominent position
for explaining the growth and wound healing properties of plants. Hence, it shines
light onto the importance of understanding mechanical signal transduction. "
acknowledged_ssus:
- _id: Bio
- _id: LifeSc
alternative_title:
- ISTA Thesis
article_processing_charge: No
author:
- first_name: Lukas
full_name: Hörmayer, Lukas
id: 2EEE7A2A-F248-11E8-B48F-1D18A9856A87
last_name: Hörmayer
orcid: 0000-0001-8295-2926
citation:
ama: Hörmayer L. Wound healing in the Arabidopsis root meristem. 2021. doi:10.15479/at:ista:9992
apa: Hörmayer, L. (2021). Wound healing in the Arabidopsis root meristem.
Institute of Science and Technology Austria. https://doi.org/10.15479/at:ista:9992
chicago: Hörmayer, Lukas. “Wound Healing in the Arabidopsis Root Meristem.” Institute
of Science and Technology Austria, 2021. https://doi.org/10.15479/at:ista:9992.
ieee: L. Hörmayer, “Wound healing in the Arabidopsis root meristem,” Institute of
Science and Technology Austria, 2021.
ista: Hörmayer L. 2021. Wound healing in the Arabidopsis root meristem. Institute
of Science and Technology Austria.
mla: Hörmayer, Lukas. Wound Healing in the Arabidopsis Root Meristem. Institute
of Science and Technology Austria, 2021, doi:10.15479/at:ista:9992.
short: L. Hörmayer, Wound Healing in the Arabidopsis Root Meristem, Institute of
Science and Technology Austria, 2021.
date_created: 2021-09-09T07:37:20Z
date_published: 2021-09-13T00:00:00Z
date_updated: 2023-09-07T13:38:33Z
day: '13'
ddc:
- '575'
degree_awarded: PhD
department:
- _id: GradSch
- _id: JiFr
doi: 10.15479/at:ista:9992
ec_funded: 1
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file_size: 25179004
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creator: lhoermaye
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date_updated: 2021-09-15T22:30:26Z
embargo: 2021-09-09
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file_date_updated: 2021-09-15T22:30:26Z
has_accepted_license: '1'
language:
- iso: eng
month: '09'
oa: 1
oa_version: Published Version
page: '168'
project:
- _id: 262EF96E-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: P29988
name: RNA-directed DNA methylation in plant development
- _id: 261099A6-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '742985'
name: Tracing Evolution of Auxin Transport and Polarity in Plants
publication_identifier:
issn:
- 2663-337X
publication_status: published
publisher: Institute of Science and Technology Austria
related_material:
record:
- id: '6351'
relation: part_of_dissertation
status: public
- id: '6943'
relation: part_of_dissertation
status: public
- id: '8002'
relation: part_of_dissertation
status: public
status: public
supervisor:
- first_name: Jiří
full_name: Friml, Jiří
id: 4159519E-F248-11E8-B48F-1D18A9856A87
last_name: Friml
orcid: 0000-0002-8302-7596
title: Wound healing in the Arabidopsis root meristem
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: c635000d-4b10-11ee-a964-aac5a93f6ac1
year: '2021'
...
---
_id: '9623'
abstract:
- lang: eng
text: "Cytoplasmic reorganizations are essential for morphogenesis. In large cells
like oocytes, these reorganizations become crucial in patterning the oocyte for
later stages of embryonic development. Ascidians oocytes reorganize their cytoplasm
(ooplasm) in a spectacular manner. Ooplasmic reorganization is initiated at fertilization
with the contraction of the actomyosin cortex along the animal-vegetal axis of
the oocyte, driving the accumulation of cortical endoplasmic reticulum (cER),
maternal mRNAs associated to it and a mitochondria-rich subcortical layer – the
myoplasm – in a region of the vegetal pole termed contraction pole (CP). Here
we have used the species Phallusia mammillata to investigate the changes in cell
shape that accompany these reorganizations and the mechanochemical mechanisms
underlining CP formation.\r\nWe report that the length of the animal-vegetal (AV)
axis oscillates upon fertilization: it first undergoes a cycle of fast elongation-lengthening
followed by a slow expansion of mainly the vegetal pole (VP) of the cell. We show
that the fast oscillation corresponds to a dynamic polarization of the actin cortex
as a result of a fertilization-induced increase in cortical tension in the oocyte
that triggers a rupture of the cortex at the animal pole and the establishment
of vegetal-directed cortical flows. These flows are responsible for the vegetal
accumulation of actin causing the VP to flatten. \r\nWe find that the slow expansion
of the VP, leading to CP formation, correlates with a relaxation of the vegetal
cortex and that the myoplasm plays a role in the expansion. We show that the myoplasm
is a solid-like layer that buckles under compression forces arising from the contracting
actin cortex at the VP. Straightening of the myoplasm when actin flows stops,
facilitates the expansion of the VP and the CP. Altogether, our results present
a previously unrecognized role for the myoplasm in ascidian ooplasmic segregation.
\r\n"
acknowledged_ssus:
- _id: Bio
- _id: EM-Fac
- _id: NanoFab
- _id: M-Shop
alternative_title:
- ISTA Thesis
article_processing_charge: No
author:
- first_name: Silvia
full_name: Caballero Mancebo, Silvia
id: 2F1E1758-F248-11E8-B48F-1D18A9856A87
last_name: Caballero Mancebo
orcid: 0000-0002-5223-3346
citation:
ama: Caballero Mancebo S. Fertilization-induced deformations are controlled by the
actin cortex and a mitochondria-rich subcortical layer in ascidian oocytes. 2021.
doi:10.15479/at:ista:9623
apa: Caballero Mancebo, S. (2021). Fertilization-induced deformations are controlled
by the actin cortex and a mitochondria-rich subcortical layer in ascidian oocytes.
Institute of Science and Technology Austria. https://doi.org/10.15479/at:ista:9623
chicago: Caballero Mancebo, Silvia. “Fertilization-Induced Deformations Are Controlled
by the Actin Cortex and a Mitochondria-Rich Subcortical Layer in Ascidian Oocytes.”
Institute of Science and Technology Austria, 2021. https://doi.org/10.15479/at:ista:9623.
ieee: S. Caballero Mancebo, “Fertilization-induced deformations are controlled by
the actin cortex and a mitochondria-rich subcortical layer in ascidian oocytes,”
Institute of Science and Technology Austria, 2021.
ista: Caballero Mancebo S. 2021. Fertilization-induced deformations are controlled
by the actin cortex and a mitochondria-rich subcortical layer in ascidian oocytes.
Institute of Science and Technology Austria.
mla: Caballero Mancebo, Silvia. Fertilization-Induced Deformations Are Controlled
by the Actin Cortex and a Mitochondria-Rich Subcortical Layer in Ascidian Oocytes.
Institute of Science and Technology Austria, 2021, doi:10.15479/at:ista:9623.
short: S. Caballero Mancebo, Fertilization-Induced Deformations Are Controlled by
the Actin Cortex and a Mitochondria-Rich Subcortical Layer in Ascidian Oocytes,
Institute of Science and Technology Austria, 2021.
date_created: 2021-07-01T14:50:17Z
date_published: 2021-07-01T00:00:00Z
date_updated: 2023-09-07T13:33:27Z
ddc:
- '570'
degree_awarded: PhD
department:
- _id: GradSch
- _id: CaHe
doi: 10.15479/at:ista:9623
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oa: 1
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publication_identifier:
isbn:
- 978-3-99078-012-1
issn:
- 2663-337X
publication_status: published
publisher: Institute of Science and Technology Austria
related_material:
record:
- id: '9750'
relation: part_of_dissertation
status: public
- id: '9006'
relation: part_of_dissertation
status: public
status: public
supervisor:
- first_name: Carl-Philipp J
full_name: Heisenberg, Carl-Philipp J
id: 39427864-F248-11E8-B48F-1D18A9856A87
last_name: Heisenberg
orcid: 0000-0002-0912-4566
title: Fertilization-induced deformations are controlled by the actin cortex and a
mitochondria-rich subcortical layer in ascidian oocytes
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image: /images/cc_by_nc_nd.png
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short: CC BY-NC-ND (4.0)
type: dissertation
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
year: '2021'
...
---
_id: '10058'
abstract:
- lang: eng
text: 'Quantum information and computation has become a vast field paved with opportunities
for researchers and investors. As large multinational companies and international
funds are heavily investing in quantum technologies it is still a question which
platform is best suited for the task of realizing a scalable quantum processor.
In this work we investigate hole spins in Ge quantum wells. These hold great promise
as they possess several favorable properties: a small effective mass, a strong
spin-orbit coupling, long relaxation time and an inherent immunity to hyperfine
noise. All these characteristics helped Ge hole spin qubits to evolve from a single
qubit to a fully entangled four qubit processor in only 3 years. Here, we investigated
a qubit approach leveraging the large out-of-plane g-factors of heavy hole states
in Ge quantum dots. We found this qubit to be reproducibly operable at extremely
low magnetic field and at large speeds while maintaining coherence. This was possible
because large differences of g-factors in adjacent dots can be achieved in the
out-of-plane direction. In the in-plane direction the small g-factors, on the
other hand, can be altered very effectively by the confinement potentials. Here,
we found that this can even lead to a sign change of the g-factors. The resulting
g-factor difference alters the dynamics of the system drastically and produces
effects typically attributed to a spin-orbit induced spin-flip term. The investigations
carried out in this thesis give further insights into the possibilities of holes
in Ge and reveal new physical properties that need to be considered when designing
future spin qubit experiments.'
acknowledged_ssus:
- _id: M-Shop
- _id: NanoFab
acknowledgement: The author gratefully acknowledges support by the Austrian Science
Fund (FWF), grants No P30207, and the Nomis foundation.
alternative_title:
- ISTA Thesis
article_processing_charge: No
author:
- first_name: Daniel
full_name: Jirovec, Daniel
id: 4C473F58-F248-11E8-B48F-1D18A9856A87
last_name: Jirovec
orcid: 0000-0002-7197-4801
citation:
ama: Jirovec D. Singlet-Triplet qubits and spin-orbit interaction in 2-dimensional
Ge hole gases. 2021. doi:10.15479/at:ista:10058
apa: Jirovec, D. (2021). Singlet-Triplet qubits and spin-orbit interaction in
2-dimensional Ge hole gases. Institute of Science and Technology Austria.
https://doi.org/10.15479/at:ista:10058
chicago: Jirovec, Daniel. “Singlet-Triplet Qubits and Spin-Orbit Interaction in
2-Dimensional Ge Hole Gases.” Institute of Science and Technology Austria, 2021.
https://doi.org/10.15479/at:ista:10058.
ieee: D. Jirovec, “Singlet-Triplet qubits and spin-orbit interaction in 2-dimensional
Ge hole gases,” Institute of Science and Technology Austria, 2021.
ista: Jirovec D. 2021. Singlet-Triplet qubits and spin-orbit interaction in 2-dimensional
Ge hole gases. Institute of Science and Technology Austria.
mla: Jirovec, Daniel. Singlet-Triplet Qubits and Spin-Orbit Interaction in 2-Dimensional
Ge Hole Gases. Institute of Science and Technology Austria, 2021, doi:10.15479/at:ista:10058.
short: D. Jirovec, Singlet-Triplet Qubits and Spin-Orbit Interaction in 2-Dimensional
Ge Hole Gases, Institute of Science and Technology Austria, 2021.
date_created: 2021-09-30T07:53:49Z
date_published: 2021-10-05T00:00:00Z
date_updated: 2023-09-08T11:41:08Z
day: '05'
ddc:
- '621'
- '539'
degree_awarded: PhD
department:
- _id: GradSch
- _id: GeKa
doi: 10.15479/at:ista:10058
file:
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date_created: 2021-09-30T14:29:14Z
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relation: source_file
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content_type: application/pdf
creator: djirovec
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date_updated: 2022-12-20T23:30:07Z
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file_date_updated: 2022-12-20T23:30:07Z
has_accepted_license: '1'
keyword:
- qubits
- quantum computing
- holes
language:
- iso: eng
month: '10'
oa: 1
oa_version: Published Version
page: '151'
project:
- _id: 2641CE5E-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: P30207
name: Hole spin orbit qubits in Ge quantum wells
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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relation: part_of_dissertation
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- id: '10066'
relation: part_of_dissertation
status: public
- id: '8909'
relation: part_of_dissertation
status: public
- id: '5816'
relation: part_of_dissertation
status: public
status: public
supervisor:
- first_name: Georgios
full_name: Katsaros, Georgios
id: 38DB5788-F248-11E8-B48F-1D18A9856A87
last_name: Katsaros
orcid: 0000-0001-8342-202X
title: Singlet-Triplet qubits and spin-orbit interaction in 2-dimensional Ge hole
gases
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: dissertation
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
year: '2021'
...
---
_id: '9397'
abstract:
- lang: eng
text: Accumulation of interstitial fluid (IF) between embryonic cells is a common
phenomenon in vertebrate embryogenesis. Unlike other model systems, where these
accumulations coalesce into a large central cavity – the blastocoel, in zebrafish,
IF is more uniformly distributed between the deep cells (DC) before the onset
of gastrulation. This is likely due to the presence of a large extraembryonic
structure – the yolk cell (YC) at the position where the blastocoel typically
forms in other model organisms. IF has long been speculated to play a role in
tissue morphogenesis during embryogenesis, but direct evidence supporting such
function is still sparse. Here we show that the relocalization of IF to the interface
between the YC and DC/epiblast is critical for axial mesendoderm (ME) cell protrusion
formation and migration along this interface, a key process in embryonic axis
formation. We further demonstrate that axial ME cell migration and IF relocalization
engage in a positive feedback loop, where axial ME migration triggers IF accumulation
ahead of the advancing axial ME tissue by mechanically compressing the overlying
epiblast cell layer. Upon compression, locally induced flow relocalizes the IF
through the porous epiblast tissue resulting in an IF accumulation ahead of the
leading axial ME. This IF accumulation, in turn, promotes cell protrusion formation
and migration of the leading axial ME cells, thereby facilitating axial ME extension.
Our findings reveal a central role of dynamic IF relocalization in orchestrating
germ layer morphogenesis during gastrulation.
alternative_title:
- ISTA Thesis
article_processing_charge: No
author:
- first_name: Karla
full_name: Huljev, Karla
id: 44C6F6A6-F248-11E8-B48F-1D18A9856A87
last_name: Huljev
citation:
ama: Huljev K. Coordinated spatiotemporal reorganization of interstitial fluid is
required for axial mesendoderm migration in zebrafish gastrulation. 2021. doi:10.15479/at:ista:9397
apa: Huljev, K. (2021). Coordinated spatiotemporal reorganization of interstitial
fluid is required for axial mesendoderm migration in zebrafish gastrulation.
Institute of Science and Technology Austria. https://doi.org/10.15479/at:ista:9397
chicago: Huljev, Karla. “Coordinated Spatiotemporal Reorganization of Interstitial
Fluid Is Required for Axial Mesendoderm Migration in Zebrafish Gastrulation.”
Institute of Science and Technology Austria, 2021. https://doi.org/10.15479/at:ista:9397.
ieee: K. Huljev, “Coordinated spatiotemporal reorganization of interstitial fluid
is required for axial mesendoderm migration in zebrafish gastrulation,” Institute
of Science and Technology Austria, 2021.
ista: Huljev K. 2021. Coordinated spatiotemporal reorganization of interstitial
fluid is required for axial mesendoderm migration in zebrafish gastrulation. Institute
of Science and Technology Austria.
mla: Huljev, Karla. Coordinated Spatiotemporal Reorganization of Interstitial
Fluid Is Required for Axial Mesendoderm Migration in Zebrafish Gastrulation.
Institute of Science and Technology Austria, 2021, doi:10.15479/at:ista:9397.
short: K. Huljev, Coordinated Spatiotemporal Reorganization of Interstitial Fluid
Is Required for Axial Mesendoderm Migration in Zebrafish Gastrulation, Institute
of Science and Technology Austria, 2021.
date_created: 2021-05-17T12:31:30Z
date_published: 2021-05-18T00:00:00Z
date_updated: 2023-09-07T13:32:32Z
day: '18'
ddc:
- '571'
degree_awarded: PhD
department:
- _id: CaHe
- _id: GradSch
doi: 10.15479/at:ista:9397
file:
- access_level: closed
checksum: 7f98532f5324a0b2f3fa8de2967baa19
content_type: application/vnd.openxmlformats-officedocument.wordprocessingml.document
creator: khuljev
date_created: 2021-05-17T12:29:12Z
date_updated: 2022-05-21T22:30:04Z
embargo_to: open_access
file_id: '9398'
file_name: KHuljev_Thesis_corrections.docx
file_size: 47799741
relation: source_file
- access_level: open_access
checksum: bf512f8a1e572a543778fc4b227c01ba
content_type: application/pdf
creator: khuljev
date_created: 2021-05-18T14:50:28Z
date_updated: 2022-05-21T22:30:04Z
embargo: 2022-05-20
file_id: '9401'
file_name: new_KHuljev_Thesis_corrections.pdf
file_size: 16542131
relation: main_file
file_date_updated: 2022-05-21T22:30:04Z
has_accepted_license: '1'
language:
- iso: eng
month: '05'
oa: 1
oa_version: Published Version
page: '101'
publication_identifier:
issn:
- 2663-337X
publication_status: published
publisher: Institute of Science and Technology Austria
status: public
supervisor:
- first_name: Carl-Philipp J
full_name: Heisenberg, Carl-Philipp J
id: 39427864-F248-11E8-B48F-1D18A9856A87
last_name: Heisenberg
orcid: 0000-0002-0912-4566
title: Coordinated spatiotemporal reorganization of interstitial fluid is required
for axial mesendoderm migration in zebrafish gastrulation
type: dissertation
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
year: '2021'
...
---
_id: '9562'
abstract:
- lang: eng
text: Left-right asymmetries can be considered a fundamental organizational principle
of the vertebrate central nervous system. The hippocampal CA3-CA1 pyramidal cell
synaptic connection shows an input-side dependent asymmetry where the hemispheric
location of the presynaptic CA3 neuron determines the synaptic properties. Left-input
synapses terminating on apical dendrites in stratum radiatum have a higher density
of NMDA receptor subunit GluN2B, a lower density of AMPA receptor subunit GluA1
and smaller areas with less often perforated PSDs. On the other hand, left-input
synapses terminating on basal dendrites in stratum oriens have lower GluN2B densities
than right-input ones. Apical and basal synapses further employ different signaling
pathways involved in LTP. SDS-digested freeze-fracture replica labeling can visualize
synaptic membrane proteins with high sensitivity and resolution, and has been
used to reveal the asymmetry at the electron microscopic level. However, it requires
time-consuming manual demarcation of the synaptic surface for quantitative measurements.
To facilitate the analysis of replica labeling, I first developed a software named
Darea, which utilizes deep-learning to automatize this demarcation. With Darea
I characterized the synaptic distribution of NMDA and AMPA receptors as well as
the voltage-gated Ca2+ channels in CA1 stratum radiatum and oriens. Second, I
explored the role of GluN2B and its carboxy-terminus in the establishment of input-side
dependent hippocampal asymmetry. In conditional knock-out mice lacking GluN2B
expression in CA1 and GluN2B-2A swap mice, where GluN2B carboxy-terminus was exchanged
to that of GluN2A, no significant asymmetries of GluN2B, GluA1 and PSD area were
detected. We further discovered a previously unknown functional asymmetry of GluN2A,
which was also lost in the swap mouse. These results demonstrate that GluN2B carboxy-terminus
plays a critical role in normal formation of input-side dependent asymmetry.
acknowledged_ssus:
- _id: EM-Fac
alternative_title:
- ISTA Thesis
article_processing_charge: No
author:
- first_name: David
full_name: Kleindienst, David
id: 42E121A4-F248-11E8-B48F-1D18A9856A87
last_name: Kleindienst
citation:
ama: 'Kleindienst D. 2B or not 2B: Hippocampal asymmetries mediated by NMDA receptor
subunit GluN2B C-terminus and high-throughput image analysis by Deep-Learning.
2021. doi:10.15479/at:ista:9562'
apa: 'Kleindienst, D. (2021). 2B or not 2B: Hippocampal asymmetries mediated
by NMDA receptor subunit GluN2B C-terminus and high-throughput image analysis
by Deep-Learning. Institute of Science and Technology Austria. https://doi.org/10.15479/at:ista:9562'
chicago: 'Kleindienst, David. “2B or Not 2B: Hippocampal Asymmetries Mediated by
NMDA Receptor Subunit GluN2B C-Terminus and High-Throughput Image Analysis by
Deep-Learning.” Institute of Science and Technology Austria, 2021. https://doi.org/10.15479/at:ista:9562.'
ieee: 'D. Kleindienst, “2B or not 2B: Hippocampal asymmetries mediated by NMDA receptor
subunit GluN2B C-terminus and high-throughput image analysis by Deep-Learning,”
Institute of Science and Technology Austria, 2021.'
ista: 'Kleindienst D. 2021. 2B or not 2B: Hippocampal asymmetries mediated by NMDA
receptor subunit GluN2B C-terminus and high-throughput image analysis by Deep-Learning.
Institute of Science and Technology Austria.'
mla: 'Kleindienst, David. 2B or Not 2B: Hippocampal Asymmetries Mediated by NMDA
Receptor Subunit GluN2B C-Terminus and High-Throughput Image Analysis by Deep-Learning.
Institute of Science and Technology Austria, 2021, doi:10.15479/at:ista:9562.'
short: 'D. Kleindienst, 2B or Not 2B: Hippocampal Asymmetries Mediated by NMDA Receptor
Subunit GluN2B C-Terminus and High-Throughput Image Analysis by Deep-Learning,
Institute of Science and Technology Austria, 2021.'
date_created: 2021-06-17T14:10:47Z
date_published: 2021-06-01T00:00:00Z
date_updated: 2023-09-11T12:55:53Z
day: '01'
ddc:
- '570'
degree_awarded: PhD
department:
- _id: GradSch
- _id: RySh
doi: 10.15479/at:ista:9562
file:
- access_level: open_access
checksum: 659df5518db495f679cb1df9e9bd1d94
content_type: application/pdf
creator: dkleindienst
date_created: 2021-06-17T14:03:14Z
date_updated: 2022-07-02T22:30:04Z
embargo: 2022-07-01
file_id: '9563'
file_name: Thesis.pdf
file_size: 77299142
relation: main_file
- access_level: closed
checksum: 3bcf63a2b19e5b6663be051bea332748
content_type: application/zip
creator: dkleindienst
date_created: 2021-06-17T14:04:30Z
date_updated: 2022-07-02T22:30:04Z
embargo_to: open_access
file_id: '9564'
file_name: Thesis_source.zip
file_size: 369804895
relation: source_file
file_date_updated: 2022-07-02T22:30:04Z
has_accepted_license: '1'
language:
- iso: eng
month: '06'
oa: 1
oa_version: Published Version
page: '124'
publication_identifier:
issn:
- 2663-337X
publication_status: published
publisher: Institute of Science and Technology Austria
related_material:
record:
- id: '9756'
relation: part_of_dissertation
status: public
- id: '9437'
relation: part_of_dissertation
status: public
- id: '8532'
relation: part_of_dissertation
status: public
- id: '612'
relation: part_of_dissertation
status: public
status: public
supervisor:
- first_name: Ryuichi
full_name: Shigemoto, Ryuichi
id: 499F3ABC-F248-11E8-B48F-1D18A9856A87
last_name: Shigemoto
orcid: 0000-0001-8761-9444
title: '2B or not 2B: Hippocampal asymmetries mediated by NMDA receptor subunit GluN2B
C-terminus and high-throughput image analysis by Deep-Learning'
type: dissertation
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
year: '2021'
...
---
_id: '8934'
abstract:
- lang: eng
text: "In this thesis, we consider several of the most classical and fundamental
problems in static analysis and formal verification, including invariant generation,
reachability analysis, termination analysis of probabilistic programs, data-flow
analysis, quantitative analysis of Markov chains and Markov decision processes,
and the problem of data packing in cache management.\r\nWe use techniques from
parameterized complexity theory, polyhedral geometry, and real algebraic geometry
to significantly improve the state-of-the-art, in terms of both scalability and
completeness guarantees, for the mentioned problems. In some cases, our results
are the first theoretical improvements for the respective problems in two or three
decades."
acknowledgement: 'The research was partially supported by an IBM PhD fellowship, a
Facebook PhD fellowship, and DOC fellowship #24956 of the Austrian Academy of Sciences
(OeAW).'
alternative_title:
- ISTA Thesis
article_processing_charge: No
author:
- first_name: Amir Kafshdar
full_name: Goharshady, Amir Kafshdar
id: 391365CE-F248-11E8-B48F-1D18A9856A87
last_name: Goharshady
orcid: 0000-0003-1702-6584
citation:
ama: Goharshady AK. Parameterized and algebro-geometric advances in static program
analysis. 2021. doi:10.15479/AT:ISTA:8934
apa: Goharshady, A. K. (2021). Parameterized and algebro-geometric advances in
static program analysis. Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:8934
chicago: Goharshady, Amir Kafshdar. “Parameterized and Algebro-Geometric Advances
in Static Program Analysis.” Institute of Science and Technology Austria, 2021.
https://doi.org/10.15479/AT:ISTA:8934.
ieee: A. K. Goharshady, “Parameterized and algebro-geometric advances in static
program analysis,” Institute of Science and Technology Austria, 2021.
ista: Goharshady AK. 2021. Parameterized and algebro-geometric advances in static
program analysis. Institute of Science and Technology Austria.
mla: Goharshady, Amir Kafshdar. Parameterized and Algebro-Geometric Advances
in Static Program Analysis. Institute of Science and Technology Austria, 2021,
doi:10.15479/AT:ISTA:8934.
short: A.K. Goharshady, Parameterized and Algebro-Geometric Advances in Static Program
Analysis, Institute of Science and Technology Austria, 2021.
date_created: 2020-12-10T12:17:07Z
date_published: 2021-01-01T00:00:00Z
date_updated: 2023-09-22T10:03:21Z
day: '01'
ddc:
- '005'
degree_awarded: PhD
department:
- _id: KrCh
- _id: GradSch
doi: 10.15479/AT:ISTA:8934
file:
- access_level: open_access
checksum: d1b9db3725aed34dadd81274aeb9426c
content_type: application/pdf
creator: akafshda
date_created: 2020-12-22T20:08:44Z
date_updated: 2021-12-23T23:30:04Z
embargo: 2021-12-22
file_id: '8969'
file_name: Thesis-pdfa.pdf
file_size: 5251507
relation: main_file
- access_level: closed
checksum: 1661df7b393e6866d2460eba3c905130
content_type: application/zip
creator: akafshda
date_created: 2020-12-22T20:08:50Z
date_updated: 2021-03-04T23:30:04Z
embargo_to: open_access
file_id: '8970'
file_name: source.zip
file_size: 10636756
relation: source_file
file_date_updated: 2021-12-23T23:30:04Z
has_accepted_license: '1'
language:
- iso: eng
license: https://creativecommons.org/publicdomain/zero/1.0/
month: '01'
oa: 1
oa_version: Published Version
page: '278'
project:
- _id: 267066CE-B435-11E9-9278-68D0E5697425
name: Quantitative Analysis of Probablistic Systems with a focus on Crypto-currencies
- _id: 266EEEC0-B435-11E9-9278-68D0E5697425
name: Quantitative Game-theoretic Analysis of Blockchain Applications and Smart
Contracts
publication_identifier:
issn:
- 2663-337X
publication_status: published
publisher: Institute of Science and Technology Austria
related_material:
record:
- id: '1386'
relation: part_of_dissertation
status: public
- id: '1437'
relation: part_of_dissertation
status: public
- id: '311'
relation: part_of_dissertation
status: public
- id: '6056'
relation: part_of_dissertation
status: public
- id: '6380'
relation: part_of_dissertation
status: public
- id: '639'
relation: part_of_dissertation
status: public
- id: '66'
relation: part_of_dissertation
status: public
- id: '6780'
relation: part_of_dissertation
status: public
- id: '6918'
relation: part_of_dissertation
status: public
- id: '7810'
relation: part_of_dissertation
status: public
- id: '6175'
relation: part_of_dissertation
status: public
- id: '6378'
relation: part_of_dissertation
status: public
- id: '6490'
relation: part_of_dissertation
status: public
- id: '7014'
relation: part_of_dissertation
status: public
- id: '8089'
relation: part_of_dissertation
status: public
- id: '8728'
relation: part_of_dissertation
status: public
- id: '7158'
relation: part_of_dissertation
status: public
- id: '5977'
relation: part_of_dissertation
status: public
- id: '6009'
relation: part_of_dissertation
status: public
- id: '6340'
relation: part_of_dissertation
status: public
- id: '949'
relation: part_of_dissertation
status: public
status: public
supervisor:
- first_name: Krishnendu
full_name: Chatterjee, Krishnendu
id: 2E5DCA20-F248-11E8-B48F-1D18A9856A87
last_name: Chatterjee
orcid: 0000-0002-4561-241X
title: Parameterized and algebro-geometric advances in static program analysis
tmp:
image: /images/cc_0.png
legal_code_url: https://creativecommons.org/publicdomain/zero/1.0/legalcode
name: Creative Commons Public Domain Dedication (CC0 1.0)
short: CC0 (1.0)
type: dissertation
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
year: '2021'
...
---
_id: '10307'
abstract:
- lang: eng
text: Bacteria-host interactions represent a continuous trade-off between benefit
and risk. Thus, the host immune response is faced with a non-trivial problem –
accommodate beneficial commensals and remove harmful pathogens. This is especially
difficult as molecular patterns, such as lipopolysaccharide or specific surface
organelles such as pili, are conserved in both, commensal and pathogenic bacteria.
Type 1 pili, tightly regulated by phase variation, are considered an important
virulence factor of pathogenic bacteria as they facilitate invasion into host
cells. While invasion represents a de facto passive mechanism for pathogens to
escape the host immune response, we demonstrate a fundamental role of type 1 pili
as active modulators of the innate and adaptive immune response.
acknowledged_ssus:
- _id: LifeSc
- _id: Bio
- _id: PreCl
- _id: EM-Fac
alternative_title:
- ISTA Thesis
article_processing_charge: No
author:
- first_name: Kathrin
full_name: Tomasek, Kathrin
id: 3AEC8556-F248-11E8-B48F-1D18A9856A87
last_name: Tomasek
orcid: 0000-0003-3768-877X
citation:
ama: Tomasek K. Pathogenic Escherichia coli hijack the host immune response. 2021.
doi:10.15479/at:ista:10307
apa: Tomasek, K. (2021). Pathogenic Escherichia coli hijack the host immune response.
Institute of Science and Technology Austria. https://doi.org/10.15479/at:ista:10307
chicago: Tomasek, Kathrin. “Pathogenic Escherichia Coli Hijack the Host Immune Response.”
Institute of Science and Technology Austria, 2021. https://doi.org/10.15479/at:ista:10307.
ieee: K. Tomasek, “Pathogenic Escherichia coli hijack the host immune response,”
Institute of Science and Technology Austria, 2021.
ista: Tomasek K. 2021. Pathogenic Escherichia coli hijack the host immune response.
Institute of Science and Technology Austria.
mla: Tomasek, Kathrin. Pathogenic Escherichia Coli Hijack the Host Immune Response.
Institute of Science and Technology Austria, 2021, doi:10.15479/at:ista:10307.
short: K. Tomasek, Pathogenic Escherichia Coli Hijack the Host Immune Response,
Institute of Science and Technology Austria, 2021.
date_created: 2021-11-18T15:05:06Z
date_published: 2021-11-18T00:00:00Z
date_updated: 2023-09-07T13:34:38Z
day: '18'
ddc:
- '570'
degree_awarded: PhD
department:
- _id: MiSi
- _id: CaGu
- _id: GradSch
doi: 10.15479/at:ista:10307
file:
- access_level: open_access
checksum: b39c9e0ef18d0484d537a67551effd02
content_type: application/pdf
creator: ktomasek
date_created: 2021-11-18T15:07:31Z
date_updated: 2022-12-20T23:30:05Z
embargo: 2022-11-18
file_id: '10308'
file_name: ThesisTomasekKathrin.pdf
file_size: 13266088
relation: main_file
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checksum: c0c440ee9e5ef1102a518a4f9f023e7c
content_type: application/vnd.openxmlformats-officedocument.wordprocessingml.document
creator: ktomasek
date_created: 2021-11-18T15:07:46Z
date_updated: 2022-12-20T23:30:05Z
embargo_to: open_access
file_id: '10309'
file_name: ThesisTomasekKathrin.docx
file_size: 7539509
relation: source_file
file_date_updated: 2022-12-20T23:30:05Z
has_accepted_license: '1'
language:
- iso: eng
month: '11'
oa: 1
oa_version: Published Version
page: '73'
publication_identifier:
issn:
- 2663-337X
publication_status: published
publisher: Institute of Science and Technology Austria
related_material:
record:
- id: '10316'
relation: part_of_dissertation
status: public
status: public
supervisor:
- first_name: Michael K
full_name: Sixt, Michael K
id: 41E9FBEA-F248-11E8-B48F-1D18A9856A87
last_name: Sixt
orcid: 0000-0002-4561-241X
- first_name: Calin C
full_name: Guet, Calin C
id: 47F8433E-F248-11E8-B48F-1D18A9856A87
last_name: Guet
orcid: 0000-0001-6220-2052
title: Pathogenic Escherichia coli hijack the host immune response
type: dissertation
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
year: '2021'
...
---
_id: '10303'
abstract:
- lang: eng
text: 'Nitrogen is an essential macronutrient determining plant growth, development
and affecting agricultural productivity. Root, as a hub that perceives and integrates
local and systemic signals on the plant’s external and endogenous nitrogen resources,
communicates with other plant organs to consolidate their physiology and development
in accordance with actual nitrogen balance. Over the last years, numerous studies
demonstrated that these comprehensive developmental adaptations rely on the interaction
between pathways controlling nitrogen homeostasis and hormonal networks acting
globally in the plant body. However, molecular insights into how the information
about the nitrogen status is translated through hormonal pathways into specific
developmental output are lacking. In my work, I addressed so far poorly understood
mechanisms underlying root-to-shoot communication that lead to a rapid re-adjustment
of shoot growth and development after nitrate provision. Applying a combination
of molecular, cell, and developmental biology approaches, genetics and grafting
experiments as well as hormonal analytics, I identified and characterized an unknown
molecular framework orchestrating shoot development with a root nitrate sensory
system. '
acknowledged_ssus:
- _id: LifeSc
- _id: Bio
alternative_title:
- ISTA Thesis
article_processing_charge: No
author:
- first_name: Rashed
full_name: Abualia, Rashed
id: 4827E134-F248-11E8-B48F-1D18A9856A87
last_name: Abualia
orcid: 0000-0002-9357-9415
citation:
ama: Abualia R. Role of hormones in nitrate regulated growth. 2021. doi:10.15479/at:ista:10303
apa: Abualia, R. (2021). Role of hormones in nitrate regulated growth. Institute
of Science and Technology Austria. https://doi.org/10.15479/at:ista:10303
chicago: Abualia, Rashed. “Role of Hormones in Nitrate Regulated Growth.” Institute
of Science and Technology Austria, 2021. https://doi.org/10.15479/at:ista:10303.
ieee: R. Abualia, “Role of hormones in nitrate regulated growth,” Institute of Science
and Technology Austria, 2021.
ista: Abualia R. 2021. Role of hormones in nitrate regulated growth. Institute of
Science and Technology Austria.
mla: Abualia, Rashed. Role of Hormones in Nitrate Regulated Growth. Institute
of Science and Technology Austria, 2021, doi:10.15479/at:ista:10303.
short: R. Abualia, Role of Hormones in Nitrate Regulated Growth, Institute of Science
and Technology Austria, 2021.
date_created: 2021-11-18T11:20:59Z
date_published: 2021-11-22T00:00:00Z
date_updated: 2023-09-19T14:42:45Z
day: '22'
ddc:
- '580'
- '581'
degree_awarded: PhD
department:
- _id: GradSch
- _id: EvBe
doi: 10.15479/at:ista:10303
file:
- access_level: open_access
checksum: dea38b98aa4da1cea03dcd0f10862818
content_type: application/pdf
creator: rabualia
date_created: 2021-11-22T14:48:21Z
date_updated: 2022-12-20T23:30:06Z
embargo: 2022-11-23
file_id: '10331'
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status: public
supervisor:
- first_name: Eva
full_name: Benková, Eva
id: 38F4F166-F248-11E8-B48F-1D18A9856A87
last_name: Benková
orcid: 0000-0002-8510-9739
title: Role of hormones in nitrate regulated growth
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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: dissertation
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
year: '2021'
...
---
_id: '9962'
abstract:
- lang: eng
text: The brain is one of the largest and most complex organs and it is composed
of billions of neurons that communicate together enabling e.g. consciousness.
The cerebral cortex is the largest site of neural integration in the central nervous
system. Concerted radial migration of newly born cortical projection neurons,
from their birthplace to their final position, is a key step in the assembly of
the cerebral cortex. The cellular and molecular mechanisms regulating radial neuronal
migration in vivo are however still unclear. Recent evidence suggests that distinct
signaling cues act cell-autonomously but differentially at certain steps during
the overall migration process. Moreover, functional analysis of genetic mosaics
(mutant neurons present in wild-type/heterozygote environment) using the MADM
(Mosaic Analysis with Double Markers) analyses in comparison to global knockout
also indicate a significant degree of non-cell-autonomous and/or community effects
in the control of cortical neuron migration. The interactions of cell-intrinsic
(cell-autonomous) and cell-extrinsic (non-cell-autonomous) components are largely
unknown. In part of this thesis work we established a MADM-based experimental
strategy for the quantitative analysis of cell-autonomous gene function versus
non-cell-autonomous and/or community effects. The direct comparison of mutant
neurons from the genetic mosaic (cell-autonomous) to mutant neurons in the conditional
and/or global knockout (cell-autonomous + non-cell-autonomous) allows to quantitatively
analyze non-cell-autonomous effects. Such analysis enable the high-resolution
analysis of projection neuron migration dynamics in distinct environments with
concomitant isolation of genomic and proteomic profiles. Using these experimental
paradigms and in combination with computational modeling we show and characterize
the nature of non-cell-autonomous effects to coordinate radial neuron migration.
Furthermore, this thesis discusses recent developments in neurodevelopment with
focus on neuronal polarization and non-cell-autonomous mechanisms in neuronal
migration.
alternative_title:
- ISTA Thesis
article_processing_charge: No
author:
- first_name: Andi H
full_name: Hansen, Andi H
id: 38853E16-F248-11E8-B48F-1D18A9856A87
last_name: Hansen
citation:
ama: Hansen AH. Cell-autonomous gene function and non-cell-autonomous effects in
radial projection neuron migration. 2021. doi:10.15479/at:ista:9962
apa: Hansen, A. H. (2021). Cell-autonomous gene function and non-cell-autonomous
effects in radial projection neuron migration. Institute of Science and Technology
Austria. https://doi.org/10.15479/at:ista:9962
chicago: Hansen, Andi H. “Cell-Autonomous Gene Function and Non-Cell-Autonomous
Effects in Radial Projection Neuron Migration.” Institute of Science and Technology
Austria, 2021. https://doi.org/10.15479/at:ista:9962.
ieee: A. H. Hansen, “Cell-autonomous gene function and non-cell-autonomous effects
in radial projection neuron migration,” Institute of Science and Technology Austria,
2021.
ista: Hansen AH. 2021. Cell-autonomous gene function and non-cell-autonomous effects
in radial projection neuron migration. Institute of Science and Technology Austria.
mla: Hansen, Andi H. Cell-Autonomous Gene Function and Non-Cell-Autonomous Effects
in Radial Projection Neuron Migration. Institute of Science and Technology
Austria, 2021, doi:10.15479/at:ista:9962.
short: A.H. Hansen, Cell-Autonomous Gene Function and Non-Cell-Autonomous Effects
in Radial Projection Neuron Migration, Institute of Science and Technology Austria,
2021.
date_created: 2021-08-29T12:36:50Z
date_published: 2021-09-02T00:00:00Z
date_updated: 2023-09-22T09:58:30Z
day: '02'
ddc:
- '570'
degree_awarded: PhD
department:
- _id: GradSch
- _id: SiHi
doi: 10.15479/at:ista:9962
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keyword:
- Neuronal migration
- Non-cell-autonomous
- Cell-autonomous
- Neurodevelopmental disease
language:
- iso: eng
month: '09'
oa: 1
oa_version: Published Version
page: '182'
project:
- _id: 2625A13E-B435-11E9-9278-68D0E5697425
grant_number: '24812'
name: Molecular Mechanisms of Radial Neuronal Migration
publication_identifier:
issn:
- 2663-337X
publication_status: published
publisher: Institute of Science and Technology Austria
related_material:
record:
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status: public
- id: '960'
relation: part_of_dissertation
status: public
status: public
supervisor:
- first_name: Simon
full_name: Hippenmeyer, Simon
id: 37B36620-F248-11E8-B48F-1D18A9856A87
last_name: Hippenmeyer
orcid: 0000-0003-2279-1061
title: Cell-autonomous gene function and non-cell-autonomous effects in radial projection
neuron migration
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: dissertation
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
year: '2021'
...
---
_id: '10083'
abstract:
- lang: eng
text: "Plant motions occur across a wide spectrum of timescales, ranging from seed
dispersal through bursting (milliseconds) and stomatal opening (minutes) to long-term
adaptation of gross architecture. Relatively fast motions include water-driven
growth as exemplified by root cell expansion under abiotic/biotic stresses or
during gravitropism. A showcase is a root growth inhibition in 30 seconds triggered
by the phytohormone auxin. However, the cellular and molecular mechanisms are
still largely unknown. This thesis covers the studies about this topic as follows.
By taking advantage of microfluidics combined with live imaging, pharmaceutical
tools, and transgenic lines, we examined the kinetics of and causal relationship
among various auxininduced rapid cellular changes in root growth, apoplastic pH,
cytosolic Ca2+, cortical microtubule (CMT) orientation, and vacuolar morphology.
We revealed that CMT reorientation and vacuolar constriction are the consequence
of growth itself instead of responding directly to auxin. In contrast, auxin induces
apoplast alkalinization to rapidly inhibit root growth in 30 seconds. This auxin-triggered
apoplast alkalinization results from rapid H+- influx that is contributed by Ca2+
inward channel CYCLIC NUCLEOTIDE-GATED CHANNEL 14 (CNGC14)-dependent Ca2+ signaling.
To dissect which auxin signaling mediates the rapid apoplast alkalinization, we\r\ncombined
microfluidics and genetic engineering to verify that TIR1/AFB receptors conduct
a non-transcriptional regulation on Ca2+ and H+ -influx. This non-canonical pathway
is mostly mediated by the cytosolic portion of TIR1/AFB. On the other hand, we
uncovered, using biochemical and phospho-proteomic analysis, that auxin cell surface
signaling component TRANSMEMBRANE KINASE 1 (TMK1) plays a negative role during
auxin-trigger apoplast\r\nalkalinization and root growth inhibition through directly
activating PM H+ -ATPases. Therefore, we discovered that PM H+ -ATPases counteract
instead of mediate the auxintriggered rapid H+ -influx, and that TIR1/AFB and
TMK1 regulate root growth antagonistically. This opposite effect of TIR1/AFB and
TMK1 is consistent during auxin-induced hypocotyl elongation, leading us to explore
the relation of two signaling pathways. Assisted with biochemistry and fluorescent
imaging, we verified for the first time that TIR1/AFB and TMK1 can interact with
each other. The ability of TIR1/AFB binding to membrane lipid provides a basis
for the interaction of plasma membrane- and cytosol-localized proteins.\r\nBesides,
transgenic analysis combined with genetic engineering and biochemistry showed
that vi\r\nthey do function in the same pathway. Particularly, auxin-induced
TMK1 increase is TIR1/AFB dependent, suggesting TIR1/AFB regulation on TMK1. Conversely,
TMK1 also regulates TIR1/AFB protein levels and thus auxin canonical signaling.
To follow the study of rapid growth regulation, we analyzed another rapid growth
regulator, signaling peptide RALF1. We showed that RALF1 also triggers a rapid
and reversible growth inhibition caused by H + influx, highly resembling but not
dependent on auxin. Besides, RALF1 promotes auxin biosynthesis by increasing expression
of auxin biosynthesis enzyme YUCCAs and thus induces auxin signaling in ca. 1
hour, contributing to the sustained RALF1-triggered growth inhibition. These studies
collectively contribute to understanding rapid regulation on plant cell\r\ngrowth,
novel auxin signaling pathway as well as auxin-peptide crosstalk. "
alternative_title:
- ISTA Thesis
article_processing_charge: No
author:
- first_name: Lanxin
full_name: Li, Lanxin
last_name: Li
citation:
ama: Li L. Rapid cell growth regulation in Arabidopsis. 2021. doi:10.15479/at:ista:10083
apa: Li, L. (2021). Rapid cell growth regulation in Arabidopsis. Institute
of Science and Technology Austria. https://doi.org/10.15479/at:ista:10083
chicago: Li, Lanxin. “Rapid Cell Growth Regulation in Arabidopsis.” Institute of
Science and Technology Austria, 2021. https://doi.org/10.15479/at:ista:10083.
ieee: L. Li, “Rapid cell growth regulation in Arabidopsis,” Institute of Science
and Technology Austria, 2021.
ista: Li L. 2021. Rapid cell growth regulation in Arabidopsis. Institute of Science
and Technology Austria.
mla: Li, Lanxin. Rapid Cell Growth Regulation in Arabidopsis. Institute of
Science and Technology Austria, 2021, doi:10.15479/at:ista:10083.
short: L. Li, Rapid Cell Growth Regulation in Arabidopsis, Institute of Science
and Technology Austria, 2021.
date_created: 2021-10-04T13:33:10Z
date_published: 2021-10-06T00:00:00Z
date_updated: 2023-10-31T19:30:02Z
day: '06'
ddc:
- '575'
degree_awarded: PhD
department:
- _id: GradSch
- _id: JiFr
doi: 10.15479/at:ista:10083
ec_funded: 1
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language:
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month: '10'
oa: 1
oa_version: Published Version
project:
- _id: 2564DBCA-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '665385'
name: International IST Doctoral Program
- _id: 26B4D67E-B435-11E9-9278-68D0E5697425
grant_number: '25351'
name: 'A Case Study of Plant Growth Regulation: Molecular Mechanism of Auxin-mediated
Rapid Growth Inhibition in Arabidopsis Root'
publication_identifier:
issn:
- 2663-337X
publication_status: published
publisher: Institute of Science and Technology Austria
related_material:
record:
- id: '442'
relation: part_of_dissertation
status: public
- id: '8931'
relation: part_of_dissertation
status: public
- id: '9287'
relation: part_of_dissertation
status: public
- id: '8283'
relation: part_of_dissertation
status: public
- id: '8986'
relation: part_of_dissertation
status: public
- id: '6627'
relation: part_of_dissertation
status: public
- id: '10095'
relation: part_of_dissertation
status: public
- id: '10015'
relation: part_of_dissertation
status: public
status: public
supervisor:
- first_name: Jiří
full_name: Friml, Jiří
id: 4159519E-F248-11E8-B48F-1D18A9856A87
last_name: Friml
orcid: 0000-0002-8302-7596
title: Rapid cell growth regulation in Arabidopsis
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: c635000d-4b10-11ee-a964-aac5a93f6ac1
year: '2021'
...
---
_id: '10293'
abstract:
- lang: eng
text: "Indirect reciprocity in evolutionary game theory is a prominent mechanism
for explaining the evolution of cooperation among unrelated individuals. In contrast
to direct reciprocity, which is based on individuals meeting repeatedly, and conditionally
cooperating by using their own experiences, indirect reciprocity is based on individuals’
reputations. If a player helps another, this increases the helper’s public standing,
benefitting them in the future. This lets cooperation in the population emerge
without individuals having to meet more than once. While the two modes of reciprocity
are intertwined, they are difficult to compare. Thus, they are usually studied
in isolation. Direct reciprocity can maintain cooperation with simple strategies,
and is robust against noise even when players do not remember more\r\nthan their
partner’s last action. Meanwhile, indirect reciprocity requires its successful
strategies, or social norms, to be more complex. Exhaustive search previously
identified eight such norms, called the “leading eight”, which excel at maintaining
cooperation. However, as the first result of this thesis, we show that the leading
eight break down once we remove the fundamental assumption that information is
synchronized and public, such that everyone agrees on reputations. Once we consider
a more realistic scenario of imperfect information, where reputations are private,
and individuals occasionally misinterpret or miss observations, the leading eight
do not promote cooperation anymore. Instead, minor initial disagreements can proliferate,
fragmenting populations into subgroups. In a next step, we consider ways to mitigate
this issue. We first explore whether introducing “generosity” can stabilize cooperation
when players use the leading eight strategies in noisy environments. This approach
of modifying strategies to include probabilistic elements for coping with errors
is known to work well in direct reciprocity. However, as we show here, it fails
for the more complex norms of indirect reciprocity. Imperfect information still
prevents cooperation from evolving. On the other hand, we succeeded to show in
this thesis that modifying the leading eight to use “quantitative assessment”,
i.e. tracking reputation scores on a scale beyond good and bad, and making overall
judgments of others based on a threshold, is highly successful, even when noise
increases in the environment. Cooperation can flourish when reputations\r\nare
more nuanced, and players have a broader understanding what it means to be “good.”
Finally, we present a single theoretical framework that unites the two modes of
reciprocity despite their differences. Within this framework, we identify a novel
simple and successful strategy for indirect reciprocity, which can cope with noisy
environments and has an analogue in direct reciprocity. We can also analyze decision
making when different sources of information are available. Our results help highlight
that for sustaining cooperation, already the most simple rules of reciprocity
can be sufficient."
alternative_title:
- ISTA Thesis
article_processing_charge: No
author:
- first_name: Laura
full_name: Schmid, Laura
id: 38B437DE-F248-11E8-B48F-1D18A9856A87
last_name: Schmid
orcid: 0000-0002-6978-7329
citation:
ama: Schmid L. Evolution of cooperation via (in)direct reciprocity under imperfect
information. 2021. doi:10.15479/at:ista:10293
apa: Schmid, L. (2021). Evolution of cooperation via (in)direct reciprocity under
imperfect information. Institute of Science and Technology Austria. https://doi.org/10.15479/at:ista:10293
chicago: Schmid, Laura. “Evolution of Cooperation via (in)Direct Reciprocity under
Imperfect Information.” Institute of Science and Technology Austria, 2021. https://doi.org/10.15479/at:ista:10293.
ieee: L. Schmid, “Evolution of cooperation via (in)direct reciprocity under imperfect
information,” Institute of Science and Technology Austria, 2021.
ista: Schmid L. 2021. Evolution of cooperation via (in)direct reciprocity under
imperfect information. Institute of Science and Technology Austria.
mla: Schmid, Laura. Evolution of Cooperation via (in)Direct Reciprocity under
Imperfect Information. Institute of Science and Technology Austria, 2021,
doi:10.15479/at:ista:10293.
short: L. Schmid, Evolution of Cooperation via (in)Direct Reciprocity under Imperfect
Information, Institute of Science and Technology Austria, 2021.
date_created: 2021-11-15T17:12:57Z
date_published: 2021-11-17T00:00:00Z
date_updated: 2023-11-07T08:28:29Z
day: '17'
ddc:
- '519'
- '576'
degree_awarded: PhD
department:
- _id: GradSch
- _id: KrCh
doi: 10.15479/at:ista:10293
ec_funded: 1
file:
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language:
- iso: eng
month: '11'
oa: 1
oa_version: Published Version
page: '171'
project:
- _id: 2581B60A-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '279307'
name: 'Quantitative Graph Games: Theory and Applications'
- _id: 0599E47C-7A3F-11EA-A408-12923DDC885E
call_identifier: H2020
grant_number: '863818'
name: 'Formal Methods for Stochastic Models: Algorithms and Applications'
- _id: 25F42A32-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: Z211
name: The Wittgenstein Prize
- _id: 2584A770-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: P 23499-N23
name: Modern Graph Algorithmic Techniques in Formal Verification
- _id: 25832EC2-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: S 11407_N23
name: Rigorous Systems Engineering
publication_identifier:
issn:
- 2663-337X
publication_status: published
publisher: Institute of Science and Technology Austria
related_material:
record:
- id: '9997'
relation: part_of_dissertation
status: public
- id: '2'
relation: part_of_dissertation
status: public
- id: '9402'
relation: part_of_dissertation
status: public
status: public
supervisor:
- first_name: Krishnendu
full_name: Chatterjee, Krishnendu
id: 2E5DCA20-F248-11E8-B48F-1D18A9856A87
last_name: Chatterjee
orcid: 0000-0002-4561-241X
title: Evolution of cooperation via (in)direct reciprocity under imperfect information
type: dissertation
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
year: '2021'
...
---
_id: '10135'
abstract:
- lang: eng
text: "Plants maintain the capacity to develop new organs e.g. lateral roots post-embryonically
throughout their whole life and thereby flexibly adapt to ever-changing environmental
conditions. Plant hormones auxin and cytokinin are the main regulators of the
lateral root organogenesis. Additionally to their solo activities, the interaction
between auxin and\r\ncytokinin plays crucial role in fine-tuning of lateral root
development and growth. In particular, cytokinin modulates auxin distribution
within the developing lateral root by affecting the endomembrane trafficking of
auxin transporter PIN1 and promoting its vacuolar degradation (Marhavý et al.,
2011, 2014). This effect is independent of transcription and\r\ntranslation. Therefore,
it suggests novel, non-canonical cytokinin activity occuring possibly on the posttranslational
level. Impact of cytokinin and other plant hormones on auxin transporters (including
PIN1) on the posttranslational level is described in detail in the introduction
part of this thesis in a form of a review (Semeradova et al., 2020). To gain insights
into the molecular machinery underlying cytokinin effect on the endomembrane trafficking
in the plant cell, in particular on the PIN1 degradation, we conducted two large
proteomic screens: 1) Identification of cytokinin binding proteins using\r\nchemical
proteomics. 2) Monitoring of proteomic and phosphoproteomic changes upon cytokinin
treatment. In the first screen, we identified DYNAMIN RELATED PROTEIN 2A (DRP2A).
We found that DRP2A plays a role in cytokinin regulated processes during the plant
growth and that cytokinin treatment promotes destabilization of DRP2A protein.
However, the role of DRP2A in the PIN1 degradation remains to be elucidated. In
the second screen, we found VACUOLAR PROTEIN SORTING 9A (VPS9A). VPS9a plays crucial
role in plant’s response to cytokin and in cytokinin mediated PIN1 degradation.
Altogether, we identified proteins, which bind to cytokinin and proteins that
in response to\r\ncytokinin exhibit significantly changed abundance or phosphorylation
pattern. By combining information from these two screens, we can pave our way
towards understanding of noncanonical cytokinin effects."
alternative_title:
- ISTA Thesis
article_processing_charge: No
author:
- first_name: Hana
full_name: Semerádová, Hana
id: 42FE702E-F248-11E8-B48F-1D18A9856A87
last_name: Semerádová
citation:
ama: Semerádová H. Molecular mechanisms of the cytokinin-regulated endomembrane
trafficking to coordinate plant organogenesis. 2021. doi:10.15479/at:ista:10135
apa: Semerádová, H. (2021). Molecular mechanisms of the cytokinin-regulated endomembrane
trafficking to coordinate plant organogenesis. Institute of Science and Technology
Austria. https://doi.org/10.15479/at:ista:10135
chicago: Semerádová, Hana. “Molecular Mechanisms of the Cytokinin-Regulated Endomembrane
Trafficking to Coordinate Plant Organogenesis.” Institute of Science and Technology
Austria, 2021. https://doi.org/10.15479/at:ista:10135.
ieee: H. Semerádová, “Molecular mechanisms of the cytokinin-regulated endomembrane
trafficking to coordinate plant organogenesis,” Institute of Science and Technology
Austria, 2021.
ista: Semerádová H. 2021. Molecular mechanisms of the cytokinin-regulated endomembrane
trafficking to coordinate plant organogenesis. Institute of Science and Technology
Austria.
mla: Semerádová, Hana. Molecular Mechanisms of the Cytokinin-Regulated Endomembrane
Trafficking to Coordinate Plant Organogenesis. Institute of Science and Technology
Austria, 2021, doi:10.15479/at:ista:10135.
short: H. Semerádová, Molecular Mechanisms of the Cytokinin-Regulated Endomembrane
Trafficking to Coordinate Plant Organogenesis, Institute of Science and Technology
Austria, 2021.
date_created: 2021-10-13T13:42:48Z
date_published: 2021-10-13T00:00:00Z
date_updated: 2024-01-25T10:53:29Z
day: '13'
ddc:
- '570'
degree_awarded: PhD
department:
- _id: GradSch
- _id: EvBe
doi: 10.15479/at:ista:10135
file:
- access_level: closed
checksum: ce7108853e6cec6224f17cd6429b51fe
content_type: application/vnd.openxmlformats-officedocument.wordprocessingml.document
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date_created: 2021-10-27T07:45:37Z
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language:
- iso: eng
month: '10'
oa: 1
oa_version: Published Version
project:
- _id: 261821BC-B435-11E9-9278-68D0E5697425
grant_number: '24746'
name: Molecular mechanisms of the cytokinin regulated endomembrane trafficking to
coordinate plant organogenesis.
publication_identifier:
isbn:
- 978-3-99078-014-5
issn:
- 2663-337X
publication_status: published
publisher: Institute of Science and Technology Austria
related_material:
record:
- id: '9160'
relation: part_of_dissertation
status: public
status: public
supervisor:
- first_name: Eva
full_name: Benková, Eva
id: 38F4F166-F248-11E8-B48F-1D18A9856A87
last_name: Benková
orcid: 0000-0002-8510-9739
title: Molecular mechanisms of the cytokinin-regulated endomembrane trafficking to
coordinate plant organogenesis
type: dissertation
user_id: 8b945eb4-e2f2-11eb-945a-df72226e66a9
year: '2021'
...
---
_id: '9728'
abstract:
- lang: eng
text: "Most real-world flows are multiphase, yet we know little about them compared
to their single-phase counterparts. Multiphase flows are more difficult to investigate
as their dynamics occur in large parameter space and involve complex phenomena
such as preferential concentration, turbulence modulation, non-Newtonian rheology,
etc. Over the last few decades, experiments in particle-laden flows have taken
a back seat in favour of ever-improving computational resources. However, computers
are still not powerful enough to simulate a real-world fluid with millions of
finite-size particles. Experiments are essential not only because they offer a
reliable way to investigate real-world multiphase flows but also because they
serve to validate numerical studies and steer the research in a relevant direction.
In this work, we have experimentally investigated particle-laden flows in pipes,
and in particular, examined the effect of particles on the laminar-turbulent transition
and the drag scaling in turbulent flows.\r\n\r\nFor particle-laden pipe flows,
an earlier study [Matas et al., 2003] reported how the sub-critical (i.e., hysteretic)
transition that occurs via localised turbulent structures called puffs is affected
by the addition of particles. In this study, in addition to this known transition,
we found a super-critical transition to a globally fluctuating state with increasing
particle concentration. At the same time, the Newtonian-type transition via puffs
is delayed to larger Reynolds numbers. At an even higher concentration, only the
globally fluctuating state is found. The dynamics of particle-laden flows are
hence determined by two competing instabilities that give rise to three flow regimes:
Newtonian-type turbulence at low, a particle-induced globally fluctuating state
at high, and a coexistence state at intermediate concentrations.\r\n\r\nThe effect
of particles on turbulent drag is ambiguous, with studies reporting drag reduction,
no net change, and even drag increase. The ambiguity arises because, in addition
to particle concentration, particle shape, size, and density also affect the net
drag. Even similar particles might affect the flow dissimilarly in different Reynolds
number and concentration ranges. In the present study, we explored a wide range
of both Reynolds number and concentration, using spherical as well as cylindrical
particles. We found that the spherical particles do not reduce drag while the
cylindrical particles are drag-reducing within a specific Reynolds number interval.
The interval strongly depends on the particle concentration and the relative size
of the pipe and particles. Within this interval, the magnitude of drag reduction
reaches a maximum. These drag reduction maxima appear to fall onto a distinct
power-law curve irrespective of the pipe diameter and particle concentration,
and this curve can be considered as the maximum drag reduction asymptote for a
given fibre shape. Such an asymptote is well known for polymeric flows but had
not been identified for particle-laden flows prior to this work."
acknowledged_ssus:
- _id: M-Shop
alternative_title:
- ISTA Thesis
article_processing_charge: No
author:
- first_name: Nishchal
full_name: Agrawal, Nishchal
id: 469E6004-F248-11E8-B48F-1D18A9856A87
last_name: Agrawal
citation:
ama: Agrawal N. Transition to turbulence and drag reduction in particle-laden pipe
flows. 2021. doi:10.15479/at:ista:9728
apa: Agrawal, N. (2021). Transition to turbulence and drag reduction in particle-laden
pipe flows. Institute of Science and Technology Austria. https://doi.org/10.15479/at:ista:9728
chicago: Agrawal, Nishchal. “Transition to Turbulence and Drag Reduction in Particle-Laden
Pipe Flows.” Institute of Science and Technology Austria, 2021. https://doi.org/10.15479/at:ista:9728.
ieee: N. Agrawal, “Transition to turbulence and drag reduction in particle-laden
pipe flows,” Institute of Science and Technology Austria, 2021.
ista: Agrawal N. 2021. Transition to turbulence and drag reduction in particle-laden
pipe flows. Institute of Science and Technology Austria.
mla: Agrawal, Nishchal. Transition to Turbulence and Drag Reduction in Particle-Laden
Pipe Flows. Institute of Science and Technology Austria, 2021, doi:10.15479/at:ista:9728.
short: N. Agrawal, Transition to Turbulence and Drag Reduction in Particle-Laden
Pipe Flows, Institute of Science and Technology Austria, 2021.
date_created: 2021-07-27T13:40:30Z
date_published: 2021-07-29T00:00:00Z
date_updated: 2024-02-28T13:14:39Z
day: '29'
ddc:
- '532'
degree_awarded: PhD
department:
- _id: GradSch
- _id: BjHo
doi: 10.15479/at:ista:9728
file:
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date_updated: 2022-07-29T22:30:05Z
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date_created: 2021-07-28T13:32:05Z
date_updated: 2022-07-29T22:30:05Z
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file_size: 18658048
relation: main_file
file_date_updated: 2022-07-29T22:30:05Z
has_accepted_license: '1'
keyword:
- Drag Reduction
- Transition to Turbulence
- Multiphase Flows
- particle Laden Flows
- Complex Flows
- Experiments
- Fluid Dynamics
language:
- iso: eng
month: '07'
oa: 1
oa_version: Published Version
page: '118'
publication_identifier:
issn:
- 2663-337X
publication_status: published
publisher: Institute of Science and Technology Austria
related_material:
record:
- id: '6189'
relation: part_of_dissertation
status: public
status: public
supervisor:
- first_name: Björn
full_name: Hof, Björn
id: 3A374330-F248-11E8-B48F-1D18A9856A87
last_name: Hof
orcid: 0000-0003-2057-2754
title: Transition to turbulence and drag reduction in particle-laden pipe flows
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: dissertation
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
year: '2021'
...
---
_id: '7629'
abstract:
- lang: eng
text: "This thesis is based on three main topics: In the first part, we study convergence
of discrete gradient flow structures associated with regular finite-volume discretisations
of Fokker-Planck equations. We show evolutionary I convergence of the discrete
gradient flows to the L2-Wasserstein gradient flow corresponding to the solution
of a Fokker-Planck\r\nequation in arbitrary dimension d >= 1. Along the argument,
we prove Mosco- and I-convergence results for discrete energy functionals, which
are of independent interest for convergence of equivalent gradient flow structures
in Hilbert spaces.\r\nThe second part investigates L2-Wasserstein flows on metric
graph. The starting point is a Benamou-Brenier formula for the L2-Wasserstein
distance, which is proved via a regularisation scheme for solutions of the continuity
equation, adapted to the peculiar geometric structure of metric graphs. Based
on those results, we show that the L2-Wasserstein space over a metric graph admits
a gradient flow which may be identified as a solution of a Fokker-Planck equation.\r\nIn
the third part, we focus again on the discrete gradient flows, already encountered
in the first part. We propose a variational structure which extends the gradient
flow structure to Markov chains violating the detailed-balance conditions. Using
this structure, we characterise contraction estimates for the discrete heat flow
in terms of convexity of\r\ncorresponding path-dependent energy functionals. In
addition, we use this approach to derive several functional inequalities for said
functionals."
alternative_title:
- ISTA Thesis
article_processing_charge: No
author:
- first_name: Dominik L
full_name: Forkert, Dominik L
id: 35C79D68-F248-11E8-B48F-1D18A9856A87
last_name: Forkert
citation:
ama: Forkert DL. Gradient flows in spaces of probability measures for finite-volume
schemes, metric graphs and non-reversible Markov chains. 2020. doi:10.15479/AT:ISTA:7629
apa: Forkert, D. L. (2020). Gradient flows in spaces of probability measures
for finite-volume schemes, metric graphs and non-reversible Markov chains.
Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:7629
chicago: Forkert, Dominik L. “Gradient Flows in Spaces of Probability Measures for
Finite-Volume Schemes, Metric Graphs and Non-Reversible Markov Chains.” Institute
of Science and Technology Austria, 2020. https://doi.org/10.15479/AT:ISTA:7629.
ieee: D. L. Forkert, “Gradient flows in spaces of probability measures for finite-volume
schemes, metric graphs and non-reversible Markov chains,” Institute of Science
and Technology Austria, 2020.
ista: Forkert DL. 2020. Gradient flows in spaces of probability measures for finite-volume
schemes, metric graphs and non-reversible Markov chains. Institute of Science
and Technology Austria.
mla: Forkert, Dominik L. Gradient Flows in Spaces of Probability Measures for
Finite-Volume Schemes, Metric Graphs and Non-Reversible Markov Chains. Institute
of Science and Technology Austria, 2020, doi:10.15479/AT:ISTA:7629.
short: D.L. Forkert, Gradient Flows in Spaces of Probability Measures for Finite-Volume
Schemes, Metric Graphs and Non-Reversible Markov Chains, Institute of Science
and Technology Austria, 2020.
date_created: 2020-04-02T06:40:23Z
date_published: 2020-03-31T00:00:00Z
date_updated: 2023-09-07T13:03:12Z
day: '31'
ddc:
- '510'
degree_awarded: PhD
department:
- _id: JaMa
doi: 10.15479/AT:ISTA:7629
ec_funded: 1
file:
- access_level: open_access
checksum: c814a1a6195269ca6fe48b0dca45ae8a
content_type: application/pdf
creator: dernst
date_created: 2020-04-14T10:47:59Z
date_updated: 2020-07-14T12:48:01Z
file_id: '7657'
file_name: Thesis_Forkert_PDFA.pdf
file_size: 3297129
relation: main_file
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checksum: ceafb53f923d1b5bdf14b2b0f22e4a81
content_type: application/x-zip-compressed
creator: dernst
date_created: 2020-04-14T10:47:59Z
date_updated: 2020-07-14T12:48:01Z
file_id: '7658'
file_name: Thesis_Forkert_source.zip
file_size: 1063908
relation: source_file
file_date_updated: 2020-07-14T12:48:01Z
has_accepted_license: '1'
language:
- iso: eng
month: '03'
oa: 1
oa_version: Published Version
page: '154'
project:
- _id: 256E75B8-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '716117'
name: Optimal Transport and Stochastic Dynamics
publication_identifier:
issn:
- 2663-337X
publication_status: published
publisher: Institute of Science and Technology Austria
status: public
supervisor:
- first_name: Jan
full_name: Maas, Jan
id: 4C5696CE-F248-11E8-B48F-1D18A9856A87
last_name: Maas
orcid: 0000-0002-0845-1338
title: Gradient flows in spaces of probability measures for finite-volume schemes,
metric graphs and non-reversible Markov chains
type: dissertation
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
year: '2020'
...
---
_id: '8574'
abstract:
- lang: eng
text: "This thesis concerns itself with the interactions of evolutionary and ecological
forces and the consequences on genetic diversity and the ultimate survival of
populations. It is important to understand what signals processes \r\nleave on
the genome and what we can infer from such data, which is usually abundant but
noisy. Furthermore, understanding how and when populations adapt or go extinct
is important for practical purposes, such as the genetic management of populations,
as well as for theoretical questions, since local adaptation can be the first
step toward speciation. \r\nIn Chapter 2, we introduce the method of maximum entropy
to approximate the demographic changes of a population in a simple setting, namely
the logistic growth model with immigration. We show that this method is not only
a powerful \r\ntool in physics but can be gainfully applied in an ecological framework.
We investigate how well it approximates the real \r\nbehavior of the system, and
find that is does so, even in unexpected situations. Finally, we illustrate how
it can model changing environments.\r\nIn Chapter 3, we analyze the co-evolution
of allele frequencies and population sizes in an infinite island model.\r\nWe
give conditions under which polygenic adaptation to a rare habitat is possible.
The model we use is based on the diffusion approximation, considers eco-evolutionary
feedback mechanisms (hard selection), and treats both \r\ndrift and environmental
fluctuations explicitly. We also look at limiting scenarios, for which we derive
analytical expressions. \r\nIn Chapter 4, we present a coalescent based simulation
tool to obtain patterns of diversity in a spatially explicit subdivided population,
in which the demographic history of each subpopulation can be specified. We compare
\r\nthe results to existing predictions, and explore the relative importance of
time and space under a variety of spatial arrangements and demographic histories,
such as expansion and extinction. \r\nIn the last chapter, we give a brief outlook
to further research. "
alternative_title:
- ISTA Thesis
article_processing_charge: No
author:
- first_name: Eniko
full_name: Szep, Eniko
id: 485BB5A4-F248-11E8-B48F-1D18A9856A87
last_name: Szep
citation:
ama: Szep E. Local adaptation in metapopulations. 2020. doi:10.15479/AT:ISTA:8574
apa: Szep, E. (2020). Local adaptation in metapopulations. Institute of Science
and Technology Austria. https://doi.org/10.15479/AT:ISTA:8574
chicago: Szep, Eniko. “Local Adaptation in Metapopulations.” Institute of Science
and Technology Austria, 2020. https://doi.org/10.15479/AT:ISTA:8574.
ieee: E. Szep, “Local adaptation in metapopulations,” Institute of Science and Technology
Austria, 2020.
ista: Szep E. 2020. Local adaptation in metapopulations. Institute of Science and
Technology Austria.
mla: Szep, Eniko. Local Adaptation in Metapopulations. Institute of Science
and Technology Austria, 2020, doi:10.15479/AT:ISTA:8574.
short: E. Szep, Local Adaptation in Metapopulations, Institute of Science and Technology
Austria, 2020.
date_created: 2020-09-28T07:33:38Z
date_published: 2020-09-20T00:00:00Z
date_updated: 2023-09-07T13:11:39Z
day: '20'
ddc:
- '570'
degree_awarded: PhD
department:
- _id: NiBa
doi: 10.15479/AT:ISTA:8574
file:
- access_level: open_access
checksum: 20e71f015fbbd78fea708893ad634ed0
content_type: application/pdf
creator: dernst
date_created: 2020-09-28T07:25:35Z
date_updated: 2020-09-28T07:25:35Z
file_id: '8575'
file_name: thesis_EnikoSzep_final.pdf
file_size: 6354833
relation: main_file
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creator: dernst
date_created: 2020-09-28T07:25:37Z
date_updated: 2020-09-28T07:25:37Z
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language:
- iso: eng
month: '09'
oa: 1
oa_version: Published Version
page: '158'
publication_identifier:
eissn:
- 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: Local adaptation in metapopulations
type: dissertation
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
year: '2020'
...
---
_id: '7514'
abstract:
- lang: eng
text: "We study the interacting homogeneous Bose gas in two spatial dimensions in
the thermodynamic limit at fixed density. We shall be concerned with some mathematical
aspects of this complicated problem in many-body quantum mechanics. More specifically,
we consider the dilute limit where the scattering length of the interaction potential,
which is a measure for the effective range of the potential, is small compared
to the average distance between the particles. We are interested in a setting
with positive (i.e., non-zero) temperature. After giving a survey of the relevant
literature in the field, we provide some facts and examples to set expectations
for the two-dimensional system. The crucial difference to the three-dimensional
system is that there is no Bose–Einstein condensate at positive temperature due
to the Hohenberg–Mermin–Wagner theorem. However, it turns out that an asymptotic
formula for the free energy holds similarly to the three-dimensional case.\r\nWe
motivate this formula by considering a toy model with δ interaction potential.
By restricting this model Hamiltonian to certain trial states with a quasi-condensate
we obtain an upper bound for the free energy that still has the quasi-condensate
fraction as a free parameter. When minimizing over the quasi-condensate fraction,
we obtain the Berezinskii–Kosterlitz–Thouless critical temperature for superfluidity,
which plays an important role in our rigorous contribution. The mathematically
rigorous result that we prove concerns the specific free energy in the dilute
limit. We give upper and lower bounds on the free energy in terms of the free
energy of the non-interacting system and a correction term coming from the interaction.
Both bounds match and thus we obtain the leading term of an asymptotic approximation
in the dilute limit, provided the thermal wavelength of the particles is of the
same order (or larger) than the average distance between the particles. The remarkable
feature of this result is its generality: the correction term depends on the interaction
potential only through its scattering length and it holds for all nonnegative
interaction potentials with finite scattering length that are measurable. In particular,
this allows to model an interaction of hard disks."
alternative_title:
- ISTA Thesis
article_processing_charge: No
author:
- first_name: Simon
full_name: Mayer, Simon
id: 30C4630A-F248-11E8-B48F-1D18A9856A87
last_name: Mayer
citation:
ama: Mayer S. The free energy of a dilute two-dimensional Bose gas. 2020. doi:10.15479/AT:ISTA:7514
apa: Mayer, S. (2020). The free energy of a dilute two-dimensional Bose gas.
Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:7514
chicago: Mayer, Simon. “The Free Energy of a Dilute Two-Dimensional Bose Gas.” Institute
of Science and Technology Austria, 2020. https://doi.org/10.15479/AT:ISTA:7514.
ieee: S. Mayer, “The free energy of a dilute two-dimensional Bose gas,” Institute
of Science and Technology Austria, 2020.
ista: Mayer S. 2020. The free energy of a dilute two-dimensional Bose gas. Institute
of Science and Technology Austria.
mla: Mayer, Simon. The Free Energy of a Dilute Two-Dimensional Bose Gas.
Institute of Science and Technology Austria, 2020, doi:10.15479/AT:ISTA:7514.
short: S. Mayer, The Free Energy of a Dilute Two-Dimensional Bose Gas, Institute
of Science and Technology Austria, 2020.
date_created: 2020-02-24T09:17:27Z
date_published: 2020-02-24T00:00:00Z
date_updated: 2023-09-07T13:12:42Z
day: '24'
ddc:
- '510'
degree_awarded: PhD
department:
- _id: RoSe
- _id: GradSch
doi: 10.15479/AT:ISTA:7514
ec_funded: 1
file:
- access_level: open_access
checksum: b4de7579ddc1dbdd44ff3f17c48395f6
content_type: application/pdf
creator: dernst
date_created: 2020-02-24T09:15:06Z
date_updated: 2020-07-14T12:47:59Z
file_id: '7515'
file_name: thesis.pdf
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checksum: ad7425867b52d7d9e72296e87bc9cb67
content_type: application/x-zip-compressed
creator: dernst
date_created: 2020-02-24T09:15:16Z
date_updated: 2020-07-14T12:47:59Z
file_id: '7516'
file_name: thesis_source.zip
file_size: 2028038
relation: source_file
file_date_updated: 2020-07-14T12:47:59Z
has_accepted_license: '1'
language:
- iso: eng
month: '02'
oa: 1
oa_version: Published Version
page: '148'
project:
- _id: 25C6DC12-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '694227'
name: Analysis of quantum many-body systems
publication_identifier:
issn:
- 2663-337X
publication_status: published
publisher: Institute of Science and Technology Austria
related_material:
record:
- id: '7524'
relation: part_of_dissertation
status: public
status: public
supervisor:
- first_name: Robert
full_name: Seiringer, Robert
id: 4AFD0470-F248-11E8-B48F-1D18A9856A87
last_name: Seiringer
orcid: 0000-0002-6781-0521
title: The free energy of a dilute two-dimensional Bose gas
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: dissertation
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
year: '2020'
...
---
_id: '8353'
abstract:
- lang: eng
text: "Mrp (Multi resistance and pH adaptation) are broadly distributed secondary
active antiporters that catalyze the transport of monovalent ions such as sodium
and potassium outside of the cell coupled to the inward translocation of protons.
Mrp antiporters are unique in a way that they are composed of seven subunits (MrpABCDEFG)
encoded in a single operon, whereas other antiporters catalyzing the same reaction
are mostly encoded by a single gene. Mrp exchangers are crucial for intracellular
pH homeostasis and Na+ efflux, essential mechanisms for H+ uptake under alkaline
environments and for reduction of the intracellular concentration of toxic cations.
Mrp displays no homology to any other monovalent Na+(K+)/H+ antiporters but Mrp
subunits have primary sequence similarity to essential redox-driven proton pumps,
such as respiratory complex I and membrane-bound hydrogenases. This similarity
reinforces the hypothesis that these present day redox-driven proton pumps are
descended from the Mrp antiporter. The Mrp structure serves as a model to understand
the yet obscure coupling mechanism between ion or electron transfer and proton
translocation in this large group of proteins. In the thesis, I am presenting
the purification, biochemical analysis, cryo-EM analysis and molecular structure
of the Mrp complex from Anoxybacillus flavithermus solved by cryo-EM at 3.0 Å
resolution. Numerous conditions were screened to purify Mrp to high homogeneity
and to obtain an appropriate distribution of single particles on cryo-EM grids
covered with a continuous layer of ultrathin carbon. A preferred particle orientation
problem was solved by performing a tilted data collection. The activity assays
showed the specific pH-dependent\r\nprofile of secondary active antiporters. The
molecular structure shows that Mrp is a dimer of seven-subunit protomers with
50 trans-membrane helices each. The dimer interface is built by many short and
tilted transmembrane helices, probably causing a thinning of the bacterial membrane.
The surface charge distribution shows an extraordinary asymmetry within each monomer,
revealing presumable proton and sodium translocation pathways. The two largest\r\nand
homologous Mrp subunits MrpA and MrpD probably translocate one proton each into
the cell. The sodium ion is likely being translocated in the opposite direction
within the small subunits along a ladder of charged and conserved residues. Based
on the structure, we propose a mechanism were the antiport activity is accomplished
via electrostatic interactions between the charged cations and key charged residues.
The flexible key TM helices coordinate these\r\nelectrostatic interactions, while
the membrane thinning between the monomers enables the translocation of sodium
across the charged membrane. The entire family of redox-driven proton pumps is
likely to perform their mechanism in a likewise manner."
acknowledged_ssus:
- _id: LifeSc
- _id: EM-Fac
- _id: ScienComp
acknowledgement: "I acknowledge the scientific service units of the IST Austria for
providing resources by the Life Science Facility, the Electron Microscopy Facility
and the high-performance computer cluster. Special thanks to the cryo-EM specialists
Valentin Hodirnau and Daniel Johann Gütl for spending many hours with me in front
of the microscope and for supporting me to collect the data presented here. I also
want to thank Professor Masahiro Ito for providing plasmid DNA\r\nencoding Mrp from
Anoxybacillus flavithermus WK1. I am a recipient of a DOC Fellowship of the Austrian
Academy of Sciences."
alternative_title:
- ISTA Thesis
article_processing_charge: No
author:
- first_name: Julia
full_name: Steiner, Julia
id: 3BB67EB0-F248-11E8-B48F-1D18A9856A87
last_name: Steiner
orcid: 0000-0003-0493-3775
citation:
ama: Steiner J. Biochemical and structural investigation of the Mrp antiporter,
an ancestor of complex I. 2020. doi:10.15479/AT:ISTA:8353
apa: Steiner, J. (2020). Biochemical and structural investigation of the Mrp
antiporter, an ancestor of complex I. Institute of Science and Technology
Austria. https://doi.org/10.15479/AT:ISTA:8353
chicago: Steiner, Julia. “Biochemical and Structural Investigation of the Mrp Antiporter,
an Ancestor of Complex I.” Institute of Science and Technology Austria, 2020.
https://doi.org/10.15479/AT:ISTA:8353.
ieee: J. Steiner, “Biochemical and structural investigation of the Mrp antiporter,
an ancestor of complex I,” Institute of Science and Technology Austria, 2020.
ista: Steiner J. 2020. Biochemical and structural investigation of the Mrp antiporter,
an ancestor of complex I. Institute of Science and Technology Austria.
mla: Steiner, Julia. Biochemical and Structural Investigation of the Mrp Antiporter,
an Ancestor of Complex I. Institute of Science and Technology Austria, 2020,
doi:10.15479/AT:ISTA:8353.
short: J. Steiner, Biochemical and Structural Investigation of the Mrp Antiporter,
an Ancestor of Complex I, Institute of Science and Technology Austria, 2020.
date_created: 2020-09-09T14:27:01Z
date_published: 2020-09-09T00:00:00Z
date_updated: 2023-09-07T13:14:09Z
day: '09'
ddc:
- '572'
degree_awarded: PhD
department:
- _id: LeSa
doi: 10.15479/AT:ISTA:8353
file:
- access_level: open_access
checksum: 2388d7e6e7a4d364c096fa89f305c3de
content_type: application/pdf
creator: jsteiner
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date_updated: 2021-09-16T12:40:56Z
file_id: '8354'
file_name: Thesis_Julia_Steiner_pdfA.pdf
file_size: 117547589
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checksum: ba112f957b7145462d0ab79044873ee9
content_type: application/vnd.openxmlformats-officedocument.wordprocessingml.document
creator: jsteiner
date_created: 2020-09-09T14:23:25Z
date_updated: 2020-09-15T08:48:37Z
file_id: '8355'
file_name: Thesis_Julia_Steiner.docx
file_size: 223328668
relation: source_file
file_date_updated: 2021-09-16T12:40:56Z
has_accepted_license: '1'
language:
- iso: eng
month: '09'
oa: 1
oa_version: None
page: '191'
project:
- _id: 26169496-B435-11E9-9278-68D0E5697425
grant_number: '24741'
name: Revealing the functional mechanism of Mrp antiporter, an ancestor of complex
I
publication_identifier:
issn:
- 2663-337X
publication_status: published
publisher: Institute of Science and Technology Austria
related_material:
record:
- id: '8284'
relation: part_of_dissertation
status: public
status: public
supervisor:
- first_name: Leonid A
full_name: Sazanov, Leonid A
id: 338D39FE-F248-11E8-B48F-1D18A9856A87
last_name: Sazanov
orcid: 0000-0002-0977-7989
title: Biochemical and structural investigation of the Mrp antiporter, an ancestor
of complex I
type: dissertation
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
year: '2020'
...
---
_id: '8589'
abstract:
- lang: eng
text: The plant hormone auxin plays indispensable roles in plant growth and development.
An essential level of regulation in auxin action is the directional auxin transport
within cells. The establishment of auxin gradient in plant tissue has been attributed
to local auxin biosynthesis and directional intercellular auxin transport, which
both are controlled by various environmental and developmental signals. It is
well established that asymmetric auxin distribution in cells is achieved by polarly
localized PIN-FORMED (PIN) auxin efflux transporters. Despite the initial insights
into cellular mechanisms of PIN polarization obtained from the last decades, the
molecular mechanism and specific regulators mediating PIN polarization remains
elusive. In this thesis, we aim to find novel players in PIN subcellular polarity
regulation during Arabidopsis development. We first characterize the physiological
effect of piperonylic acid (PA) on Arabidopsis hypocotyl gravitropic bending and
PIN polarization. Secondly, we reveal the importance of SCFTIR1/AFB auxin signaling
pathway in shoot gravitropism bending termination. In addition, we also explore
the role of myosin XI complex, and actin cytoskeleton in auxin feedback regulation
on PIN polarity. In Chapter 1, we give an overview of the current knowledge about
PIN-mediated auxin fluxes in various plant tropic responses. In Chapter 2, we
study the physiological effect of PA on shoot gravitropic bending. Our results
show that PA treatment inhibits auxin-mediated PIN3 repolarization by interfering
with PINOID and PIN3 phosphorylation status, ultimately leading to hyperbending
hypocotyls. In Chapter 3, we provide evidence to show that the SCFTIR1/AFB nuclear
auxin signaling pathway is crucial and required for auxin-mediated PIN3 repolarization
and shoot gravitropic bending termination. In Chapter 4, we perform a phosphoproteomics
approach and identify the motor protein Myosin XI and its binding protein, the
MadB2 family, as an essential regulator of PIN polarity for auxin-canalization
related developmental processes. In Chapter 5, we demonstrate the vital role of
actin cytoskeleton in auxin feedback on PIN polarity by regulating PIN subcellular
trafficking. Overall, the data presented in this PhD thesis brings novel insights
into the PIN polar localization regulation that resulted in the (re)establishment
of the polar auxin flow and gradient in response to environmental stimuli during
plant development.
acknowledged_ssus:
- _id: Bio
- _id: LifeSc
acknowledgement: I also want to thank the China Scholarship Council for supporting
my study during the year from 2015 to 2019. I also want to thank IST facilities
– the Bioimaging facility, the media kitchen, the plant facility and all of the
campus services, for their support.
alternative_title:
- ISTA Thesis
article_processing_charge: No
author:
- first_name: Huibin
full_name: Han, Huibin
id: 31435098-F248-11E8-B48F-1D18A9856A87
last_name: Han
citation:
ama: Han H. Novel insights into PIN polarity regulation during Arabidopsis development.
2020. doi:10.15479/AT:ISTA:8589
apa: Han, H. (2020). Novel insights into PIN polarity regulation during Arabidopsis
development. Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:8589
chicago: Han, Huibin. “Novel Insights into PIN Polarity Regulation during Arabidopsis
Development.” Institute of Science and Technology Austria, 2020. https://doi.org/10.15479/AT:ISTA:8589.
ieee: H. Han, “Novel insights into PIN polarity regulation during Arabidopsis development,”
Institute of Science and Technology Austria, 2020.
ista: Han H. 2020. Novel insights into PIN polarity regulation during Arabidopsis
development. Institute of Science and Technology Austria.
mla: Han, Huibin. Novel Insights into PIN Polarity Regulation during Arabidopsis
Development. Institute of Science and Technology Austria, 2020, doi:10.15479/AT:ISTA:8589.
short: H. Han, Novel Insights into PIN Polarity Regulation during Arabidopsis Development,
Institute of Science and Technology Austria, 2020.
date_created: 2020-09-30T14:50:51Z
date_published: 2020-09-30T00:00:00Z
date_updated: 2023-09-07T13:13:05Z
day: '30'
ddc:
- '580'
degree_awarded: PhD
department:
- _id: JiFr
doi: 10.15479/AT:ISTA:8589
file:
- access_level: closed
checksum: c4bda1947d4c09c428ac9ce667b02327
content_type: application/vnd.openxmlformats-officedocument.wordprocessingml.document
creator: dernst
date_created: 2020-09-30T14:50:20Z
date_updated: 2020-09-30T14:50:20Z
file_id: '8590'
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content_type: application/pdf
creator: dernst
date_created: 2020-09-30T14:49:59Z
date_updated: 2021-10-01T13:33:02Z
file_id: '8591'
file_name: 2020_Han_Thesis.pdf
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file_date_updated: 2021-10-01T13:33:02Z
has_accepted_license: '1'
language:
- iso: eng
month: '09'
oa: 1
oa_version: Published Version
page: '164'
publication_identifier:
issn:
- 2663-337X
publication_status: published
publisher: Institute of Science and Technology Austria
related_material:
record:
- id: '7643'
relation: part_of_dissertation
status: public
status: public
supervisor:
- first_name: Jiří
full_name: Friml, Jiří
id: 4159519E-F248-11E8-B48F-1D18A9856A87
last_name: Friml
orcid: 0000-0002-8302-7596
title: Novel insights into PIN polarity regulation during Arabidopsis development
type: dissertation
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
year: '2020'
...
---
_id: '8155'
abstract:
- lang: eng
text: "In the thesis we focus on the interplay of the biophysics and evolution of
gene regulation. We start by addressing how the type of prokaryotic gene regulation
– activation and repression – affects spurious binding to DNA, also known as\r\ntranscriptional
crosstalk. We propose that regulatory interference caused by excess regulatory
proteins in the dense cellular medium – global crosstalk – could be a factor in
determining which type of gene regulatory network is evolutionarily preferred.
Next,we use a normative approach in eukaryotic gene regulation to describe minimal\r\nnon-equilibrium
enhancer models that optimize so-called regulatory phenotypes. We find a class
of models that differ from standard thermodynamic equilibrium models by a single
parameter that notably increases the regulatory performance. Next chapter addresses
the question of genotype-phenotype-fitness maps of higher dimensional phenotypes.
We show that our biophysically realistic approach allows us to understand how
the mechanisms of promoter function constrain genotypephenotype maps, and how
they affect the evolutionary trajectories of promoters.\r\nIn the last chapter
we ask whether the intrinsic instability of gene duplication and amplification
provides a generic alternative to canonical gene regulation. Using mathematical
modeling, we show that amplifications can tune gene expression in many environments,
including those where transcription factor-based schemes are\r\nhard to evolve
or maintain. "
acknowledgement: For the duration of his PhD, Rok was a recipient of a DOC fellowship
of the Austrian Academy of Sciences.
alternative_title:
- ISTA Thesis
article_processing_charge: No
author:
- first_name: Rok
full_name: Grah, Rok
id: 483E70DE-F248-11E8-B48F-1D18A9856A87
last_name: Grah
orcid: 0000-0003-2539-3560
citation:
ama: Grah R. Gene regulation across scales – how biophysical constraints shape evolution.
2020. doi:10.15479/AT:ISTA:8155
apa: Grah, R. (2020). Gene regulation across scales – how biophysical constraints
shape evolution. Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:8155
chicago: Grah, Rok. “Gene Regulation across Scales – How Biophysical Constraints
Shape Evolution.” Institute of Science and Technology Austria, 2020. https://doi.org/10.15479/AT:ISTA:8155.
ieee: R. Grah, “Gene regulation across scales – how biophysical constraints shape
evolution,” Institute of Science and Technology Austria, 2020.
ista: Grah R. 2020. Gene regulation across scales – how biophysical constraints
shape evolution. Institute of Science and Technology Austria.
mla: Grah, Rok. Gene Regulation across Scales – How Biophysical Constraints Shape
Evolution. Institute of Science and Technology Austria, 2020, doi:10.15479/AT:ISTA:8155.
short: R. Grah, Gene Regulation across Scales – How Biophysical Constraints Shape
Evolution, Institute of Science and Technology Austria, 2020.
date_created: 2020-07-23T09:51:28Z
date_published: 2020-07-24T00:00:00Z
date_updated: 2023-09-07T13:13:27Z
day: '24'
ddc:
- '530'
- '570'
degree_awarded: PhD
department:
- _id: CaGu
- _id: GaTk
doi: 10.15479/AT:ISTA:8155
file:
- access_level: open_access
content_type: application/pdf
creator: rgrah
date_created: 2020-07-27T12:00:07Z
date_updated: 2020-07-27T12:00:07Z
file_id: '8176'
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file_size: 16638998
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content_type: application/zip
creator: rgrah
date_created: 2020-07-27T12:02:23Z
date_updated: 2020-07-30T13:04:55Z
file_id: '8177'
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file_size: 347459978
relation: main_file
file_date_updated: 2020-07-30T13:04:55Z
has_accepted_license: '1'
language:
- iso: eng
month: '07'
oa: 1
oa_version: Published Version
page: '310'
project:
- _id: 267C84F4-B435-11E9-9278-68D0E5697425
name: Biophysically realistic genotype-phenotype maps for regulatory networks
publication_identifier:
issn:
- 2663-337X
publication_status: published
publisher: Institute of Science and Technology Austria
related_material:
record:
- id: '7675'
relation: part_of_dissertation
status: public
- id: '7569'
relation: part_of_dissertation
status: public
- id: '7652'
relation: part_of_dissertation
status: public
status: public
supervisor:
- first_name: Calin C
full_name: Guet, Calin C
id: 47F8433E-F248-11E8-B48F-1D18A9856A87
last_name: Guet
orcid: 0000-0001-6220-2052
- first_name: Gašper
full_name: Tkačik, Gašper
id: 3D494DCA-F248-11E8-B48F-1D18A9856A87
last_name: Tkačik
orcid: 0000-0002-6699-1455
title: Gene regulation across scales – how biophysical constraints shape evolution
type: dissertation
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
year: '2020'
...
---
_id: '7460'
abstract:
- lang: eng
text: "Many methods for the reconstruction of shapes from sets of points produce
ordered simplicial complexes, which are collections of vertices, edges, triangles,
and their higher-dimensional analogues, called simplices, in which every simplex
gets assigned a real value measuring its size. This thesis studies ordered simplicial
complexes, with a focus on their topology, which reflects the connectedness of
the represented shapes and the presence of holes. We are interested both in understanding
better the structure of these complexes, as well as in developing algorithms for
applications.\r\n\r\nFor the Delaunay triangulation, the most popular measure
for a simplex is the radius of the smallest empty circumsphere. Based on it, we
revisit Alpha and Wrap complexes and experimentally determine their probabilistic
properties for random data. Also, we prove the existence of tri-partitions, propose
algorithms to open and close holes, and extend the concepts from Euclidean to
Bregman geometries."
alternative_title:
- ISTA Thesis
article_processing_charge: No
author:
- first_name: Katharina
full_name: Ölsböck, Katharina
id: 4D4AA390-F248-11E8-B48F-1D18A9856A87
last_name: Ölsböck
orcid: 0000-0002-4672-8297
citation:
ama: Ölsböck K. The hole system of triangulated shapes. 2020. doi:10.15479/AT:ISTA:7460
apa: Ölsböck, K. (2020). The hole system of triangulated shapes. Institute
of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:7460
chicago: Ölsböck, Katharina. “The Hole System of Triangulated Shapes.” Institute
of Science and Technology Austria, 2020. https://doi.org/10.15479/AT:ISTA:7460.
ieee: K. Ölsböck, “The hole system of triangulated shapes,” Institute of Science
and Technology Austria, 2020.
ista: Ölsböck K. 2020. The hole system of triangulated shapes. Institute of Science
and Technology Austria.
mla: Ölsböck, Katharina. The Hole System of Triangulated Shapes. Institute
of Science and Technology Austria, 2020, doi:10.15479/AT:ISTA:7460.
short: K. Ölsböck, The Hole System of Triangulated Shapes, Institute of Science
and Technology Austria, 2020.
date_created: 2020-02-06T14:56:53Z
date_published: 2020-02-10T00:00:00Z
date_updated: 2023-09-07T13:15:30Z
day: '10'
ddc:
- '514'
degree_awarded: PhD
department:
- _id: HeEd
- _id: GradSch
doi: 10.15479/AT:ISTA:7460
file:
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checksum: 1df9f8c530b443c0e63a3f2e4fde412e
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creator: koelsboe
date_created: 2020-02-06T14:43:54Z
date_updated: 2020-07-14T12:47:58Z
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content_type: application/x-zip-compressed
creator: koelsboe
date_created: 2020-02-06T14:52:45Z
date_updated: 2020-07-14T12:47:58Z
description: latex source files, figures
file_id: '7462'
file_name: latex-files.zip
file_size: 122103715
relation: source_file
file_date_updated: 2020-07-14T12:47:58Z
has_accepted_license: '1'
keyword:
- shape reconstruction
- hole manipulation
- ordered complexes
- Alpha complex
- Wrap complex
- computational topology
- Bregman geometry
language:
- iso: eng
license: https://creativecommons.org/licenses/by-nc-sa/4.0/
month: '02'
oa: 1
oa_version: Published Version
page: '155'
publication_identifier:
issn:
- 2663-337X
publication_status: published
publisher: Institute of Science and Technology Austria
related_material:
record:
- id: '6608'
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: The hole system of triangulated shapes
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: c635000d-4b10-11ee-a964-aac5a93f6ac1
year: '2020'
...
---
_id: '7896'
abstract:
- lang: eng
text: "A search problem lies in the complexity class FNP if a solution to the given
instance of the problem can be verified efficiently. The complexity class TFNP
consists of all search problems in FNP that are total in the sense that a solution
is guaranteed to exist. TFNP contains a host of interesting problems from fields
such as algorithmic game theory, computational topology, number theory and combinatorics.
Since TFNP is a semantic class, it is unlikely to have a complete problem. Instead,
one studies its syntactic subclasses which are defined based on the combinatorial
principle used to argue totality. Of particular interest is the subclass PPAD,
which contains important problems\r\nlike computing Nash equilibrium for bimatrix
games and computational counterparts of several fixed-point theorems as complete.
In the thesis, we undertake the study of averagecase hardness of TFNP, and in
particular its subclass PPAD.\r\nAlmost nothing was known about average-case hardness
of PPAD before a series of recent results showed how to achieve it using a cryptographic
primitive called program obfuscation.\r\nHowever, it is currently not known how
to construct program obfuscation from standard cryptographic assumptions. Therefore,
it is desirable to relax the assumption under which average-case hardness of PPAD
can be shown. In the thesis we take a step in this direction. First, we show that
assuming the (average-case) hardness of a numbertheoretic\r\nproblem related to
factoring of integers, which we call Iterated-Squaring, PPAD is hard-on-average
in the random-oracle model. Then we strengthen this result to show that the average-case
hardness of PPAD reduces to the (adaptive) soundness of the Fiat-Shamir Transform,
a well-known technique used to compile a public-coin interactive protocol into
a non-interactive one. As a corollary, we obtain average-case hardness for PPAD
in the random-oracle model assuming the worst-case hardness of #SAT. Moreover,
the above results can all be strengthened to obtain average-case hardness for
the class CLS ⊆ PPAD.\r\nOur main technical contribution is constructing incrementally-verifiable
procedures for computing Iterated-Squaring and #SAT. By incrementally-verifiable,
we mean that every intermediate state of the computation includes a proof of its
correctness, and the proof can be updated and verified in polynomial time. Previous
constructions of such procedures relied on strong, non-standard assumptions. Instead,
we introduce a technique called recursive proof-merging to obtain the same from
weaker assumptions. "
alternative_title:
- ISTA Thesis
article_processing_charge: No
author:
- first_name: Chethan
full_name: Kamath Hosdurg, Chethan
id: 4BD3F30E-F248-11E8-B48F-1D18A9856A87
last_name: Kamath Hosdurg
citation:
ama: Kamath Hosdurg C. On the average-case hardness of total search problems. 2020.
doi:10.15479/AT:ISTA:7896
apa: Kamath Hosdurg, C. (2020). On the average-case hardness of total search
problems. Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:7896
chicago: Kamath Hosdurg, Chethan. “On the Average-Case Hardness of Total Search
Problems.” Institute of Science and Technology Austria, 2020. https://doi.org/10.15479/AT:ISTA:7896.
ieee: C. Kamath Hosdurg, “On the average-case hardness of total search problems,”
Institute of Science and Technology Austria, 2020.
ista: Kamath Hosdurg C. 2020. On the average-case hardness of total search problems.
Institute of Science and Technology Austria.
mla: Kamath Hosdurg, Chethan. On the Average-Case Hardness of Total Search Problems.
Institute of Science and Technology Austria, 2020, doi:10.15479/AT:ISTA:7896.
short: C. Kamath Hosdurg, On the Average-Case Hardness of Total Search Problems,
Institute of Science and Technology Austria, 2020.
date_created: 2020-05-26T14:08:55Z
date_published: 2020-05-25T00:00:00Z
date_updated: 2023-09-07T13:15:55Z
day: '25'
ddc:
- '000'
degree_awarded: PhD
department:
- _id: KrPi
doi: 10.15479/AT:ISTA:7896
ec_funded: 1
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has_accepted_license: '1'
language:
- iso: eng
month: '05'
oa: 1
oa_version: Published Version
page: '126'
project:
- _id: 258C570E-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '259668'
name: Provable Security for Physical Cryptography
- _id: 258AA5B2-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '682815'
name: Teaching Old Crypto New Tricks
publication_identifier:
issn:
- 2663-337X
publication_status: published
publisher: Institute of Science and Technology Austria
related_material:
record:
- id: '6677'
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 average-case hardness of total search problems
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: dissertation
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
year: '2020'
...
---
_id: '7944'
abstract:
- lang: eng
text: "This thesis considers two examples of reconfiguration problems: flipping
edges in edge-labelled triangulations of planar point sets and swapping labelled
tokens placed on vertices of a graph. In both cases the studied structures – all
the triangulations of a given point set or all token placements on a given graph
– can be thought of as vertices of the so-called reconfiguration graph, in which
two vertices are adjacent if the corresponding structures differ by a single elementary
operation – by a flip of a diagonal in a triangulation or by a swap of tokens
on adjacent vertices, respectively. We study the reconfiguration of one instance
of a structure into another via (shortest) paths in the reconfiguration graph.\r\n\r\nFor
triangulations of point sets in which each edge has a unique label and a flip
transfers the label from the removed edge to the new edge, we prove a polynomial-time
testable condition, called the Orbit Theorem, that characterizes when two triangulations
of the same point set lie in the same connected component of the reconfiguration
graph. The condition was first conjectured by Bose, Lubiw, Pathak and Verdonschot.
We additionally provide a polynomial time algorithm that computes a reconfiguring
flip sequence, if it exists. Our proof of the Orbit Theorem uses topological properties
of a certain high-dimensional cell complex that has the usual reconfiguration
graph as its 1-skeleton.\r\n\r\nIn the context of token swapping on a tree graph,
we make partial progress on the problem of finding shortest reconfiguration sequences.
We disprove the so-called Happy Leaf Conjecture and demonstrate the importance
of swapping tokens that are already placed at the correct vertices. We also prove
that a generalization of the problem to weighted coloured token swapping is NP-hard
on trees but solvable in polynomial time on paths and stars."
alternative_title:
- ISTA Thesis
article_processing_charge: No
author:
- first_name: Zuzana
full_name: Masárová, Zuzana
id: 45CFE238-F248-11E8-B48F-1D18A9856A87
last_name: Masárová
orcid: 0000-0002-6660-1322
citation:
ama: Masárová Z. Reconfiguration problems. 2020. doi:10.15479/AT:ISTA:7944
apa: Masárová, Z. (2020). Reconfiguration problems. Institute of Science
and Technology Austria. https://doi.org/10.15479/AT:ISTA:7944
chicago: Masárová, Zuzana. “Reconfiguration Problems.” Institute of Science and
Technology Austria, 2020. https://doi.org/10.15479/AT:ISTA:7944.
ieee: Z. Masárová, “Reconfiguration problems,” Institute of Science and Technology
Austria, 2020.
ista: Masárová Z. 2020. Reconfiguration problems. Institute of Science and Technology
Austria.
mla: Masárová, Zuzana. Reconfiguration Problems. Institute of Science and
Technology Austria, 2020, doi:10.15479/AT:ISTA:7944.
short: Z. Masárová, Reconfiguration Problems, Institute of Science and Technology
Austria, 2020.
date_created: 2020-06-08T00:49:46Z
date_published: 2020-06-09T00:00:00Z
date_updated: 2023-09-07T13:17:37Z
day: '09'
ddc:
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- '514'
degree_awarded: PhD
department:
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- _id: UlWa
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has_accepted_license: '1'
keyword:
- reconfiguration
- reconfiguration graph
- triangulations
- flip
- constrained triangulations
- shellability
- piecewise-linear balls
- token swapping
- trees
- coloured weighted token swapping
language:
- iso: eng
license: https://creativecommons.org/licenses/by-sa/4.0/
month: '06'
oa: 1
oa_version: Published Version
page: '160'
publication_identifier:
isbn:
- 978-3-99078-005-3
issn:
- 2663-337X
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supervisor:
- first_name: Uli
full_name: Wagner, Uli
id: 36690CA2-F248-11E8-B48F-1D18A9856A87
last_name: Wagner
orcid: 0000-0002-1494-0568
- first_name: Herbert
full_name: Edelsbrunner, Herbert
id: 3FB178DA-F248-11E8-B48F-1D18A9856A87
last_name: Edelsbrunner
orcid: 0000-0002-9823-6833
title: Reconfiguration problems
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...
---
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abstract:
- lang: eng
text: "One of the most striking hallmarks of the eukaryotic cell is the presence
of intracellular vesicles and organelles. Each of these membrane-enclosed compartments
has a distinct composition of lipids and proteins, which is essential for accurate
membrane traffic and homeostasis. Interestingly, their biochemical identities
are achieved with the help\r\nof small GTPases of the Rab family, which cycle
between GDP- and GTP-bound forms on the selected membrane surface. While this
activity switch is well understood for an individual protein, how Rab GTPases
collectively transition between states to generate decisive signal propagation
in space and time is unclear. In my PhD thesis, I present\r\nin vitro reconstitution
experiments with theoretical modeling to systematically study a minimal Rab5 activation
network from bottom-up. We find that positive feedback based on known molecular
interactions gives rise to bistable GTPase activity switching on system’s scale.
Furthermore, we determine that collective transition near the critical\r\npoint
is intrinsically stochastic and provide evidence that the inactive Rab5 abundance
on the membrane can shape the network response. Finally, we demonstrate that collective
switching can spread on the lipid bilayer as a traveling activation wave, representing
a possible emergent activity pattern in endosomal maturation. Together, our\r\nfindings
reveal new insights into the self-organization properties of signaling networks
away from chemical equilibrium. Our work highlights the importance of systematic
characterization of biochemical systems in well-defined physiological conditions.
This way, we were able to answer long-standing open questions in the field and
close the gap between regulatory processes on a molecular scale and emergent responses
on system’s level."
acknowledged_ssus:
- _id: Bio
- _id: LifeSc
- _id: NanoFab
acknowledgement: My thanks goes to the Loose lab members, BioImaging, Life Science
and Nanofabrication Facilities and the wonderful international community at IST
for sharing this experience with me.
alternative_title:
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article_processing_charge: No
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full_name: Bezeljak, Urban
id: 2A58201A-F248-11E8-B48F-1D18A9856A87
last_name: Bezeljak
orcid: 0000-0003-1365-5631
citation:
ama: Bezeljak U. In vitro reconstitution of a Rab activation switch. 2020. doi:10.15479/AT:ISTA:8341
apa: Bezeljak, U. (2020). In vitro reconstitution of a Rab activation switch.
Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:8341
chicago: Bezeljak, Urban. “In Vitro Reconstitution of a Rab Activation Switch.”
Institute of Science and Technology Austria, 2020. https://doi.org/10.15479/AT:ISTA:8341.
ieee: U. Bezeljak, “In vitro reconstitution of a Rab activation switch,” Institute
of Science and Technology Austria, 2020.
ista: Bezeljak U. 2020. In vitro reconstitution of a Rab activation switch. Institute
of Science and Technology Austria.
mla: Bezeljak, Urban. In Vitro Reconstitution of a Rab Activation Switch.
Institute of Science and Technology Austria, 2020, doi:10.15479/AT:ISTA:8341.
short: U. Bezeljak, In Vitro Reconstitution of a Rab Activation Switch, Institute
of Science and Technology Austria, 2020.
date_created: 2020-09-08T08:53:53Z
date_published: 2020-09-08T00:00:00Z
date_updated: 2023-09-07T13:17:06Z
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publication_identifier:
issn:
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publisher: Institute of Science and Technology Austria
related_material:
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relation: part_of_dissertation
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status: public
supervisor:
- first_name: Martin
full_name: Loose, Martin
id: 462D4284-F248-11E8-B48F-1D18A9856A87
last_name: Loose
orcid: 0000-0001-7309-9724
title: In vitro reconstitution of a Rab activation switch
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name: Creative Commons Attribution-NonCommercial-ShareAlike 4.0 International (CC
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short: CC BY-NC-SA (4.0)
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...