---
_id: '14280'
abstract:
- lang: eng
text: "Cell division in Escherichia coli is performed by the divisome, a multi-protein
complex composed of more than 30 proteins. The divisome spans from the cytoplasm
through the inner membrane to the cell wall and the outer membrane. Divisome assembly
is initiated by a cytoskeletal structure, the so-called Z-ring, which localizes
at the center of the E. coli cell and determines the position of the future cell
septum. The Z-ring is composed of the highly conserved bacterial tubulin homologue
FtsZ, which forms treadmilling filaments. These filaments are recruited to the
inner membrane by FtsA, a highly conserved bacterial actin homologue. FtsA interacts
with other proteins in the periplasm and thus connects the cytoplasmic and periplasmic
components of the divisome. \r\nA previous model postulated that FtsA regulates
maturation of the divisome by switching from an oligomeric, inactive state to
a monomeric and active state. This model was based mostly on in vivo studies,
as a biochemical characterization of FtsA has been hampered by difficulties in
purifying the protein. Here, we studied FtsA using an in vitro reconstitution
approach and aimed to answer two questions: (i) How are dynamics from cytoplasmic,
treadmilling FtsZ filaments coupled to proteins acting in the periplasmic space
and (ii) How does FtsA regulate the maturation of the divisome?\r\nWe found that
the cytoplasmic peptides of the transmembrane proteins FtsN and FtsQ interact
directly with FtsA and can follow the spatiotemporal signal of FtsA/Z filaments.
When we investigated the underlying mechanism by imaging single molecules of FtsNcyto,
we found the peptide to interact transiently with FtsA. An in depth analysis of
the single molecule trajectories helped to postulate a model where PG synthases
follow the dynamics of FtsZ by a diffusion and capture mechanism. \r\nFollowing
up on these findings we were interested in how the self-interaction of FtsA changes
when it encounters FtsNcyto and if we can confirm the proposed oligomer-monomer
switch. For this, we compared the behavior of the previously identified, hyperactive
mutant FtsA R286W with wildtype FtsA. The mutant outperforms WT in mirroring and
transmitting the spatiotemporal signal of treadmilling FtsZ filaments. Surprisingly
however, we found that this was not due to a difference in the self-interaction
strength of the two variants, but a difference in their membrane residence time.
Furthermore, in contrast to our expectations, upon binding of FtsNcyto the measured
self-interaction of FtsA actually increased. \r\nWe propose that FtsNcyto induces
a rearrangement of the oligomeric architecture of FtsA. In further consequence
this change leads to more persistent FtsZ filaments which results in a defined
signalling zone, allowing formation of the mature divisome. The observed difference
between FtsA WT and R286W is due to the vastly different membrane turnover of
the proteins. R286W cycles 5-10x faster compared to WT which allows to sample
FtsZ filaments at faster frequencies. These findings can explain the observed
differences in toxicity for overexpression of FtsA WT and R286W and help to understand
how FtsA regulates divisome maturation."
acknowledged_ssus:
- _id: Bio
- _id: LifeSc
alternative_title:
- ISTA Thesis
article_processing_charge: No
author:
- first_name: Philipp
full_name: Radler, Philipp
id: 40136C2A-F248-11E8-B48F-1D18A9856A87
last_name: Radler
orcid: '0000-0001-9198-2182 '
citation:
ama: Radler P. Spatiotemporal signaling during assembly of the bacterial divisome.
2023. doi:10.15479/at:ista:14280
apa: Radler, P. (2023). Spatiotemporal signaling during assembly of the bacterial
divisome. Institute of Science and Technology Austria. https://doi.org/10.15479/at:ista:14280
chicago: Radler, Philipp. “Spatiotemporal Signaling during Assembly of the Bacterial
Divisome.” Institute of Science and Technology Austria, 2023. https://doi.org/10.15479/at:ista:14280.
ieee: P. Radler, “Spatiotemporal signaling during assembly of the bacterial divisome,”
Institute of Science and Technology Austria, 2023.
ista: Radler P. 2023. Spatiotemporal signaling during assembly of the bacterial
divisome. Institute of Science and Technology Austria.
mla: Radler, Philipp. Spatiotemporal Signaling during Assembly of the Bacterial
Divisome. Institute of Science and Technology Austria, 2023, doi:10.15479/at:ista:14280.
short: P. Radler, Spatiotemporal Signaling during Assembly of the Bacterial Divisome,
Institute of Science and Technology Austria, 2023.
date_created: 2023-09-06T10:58:25Z
date_published: 2023-09-25T00:00:00Z
date_updated: 2024-02-21T12:35:18Z
day: '25'
ddc:
- '572'
degree_awarded: PhD
department:
- _id: GradSch
- _id: MaLo
doi: 10.15479/at:ista:14280
ec_funded: 1
file:
- access_level: closed
checksum: 87eef11fbc5c7df0826f12a3a629b444
content_type: application/vnd.openxmlformats-officedocument.wordprocessingml.document
creator: pradler
date_created: 2023-10-04T10:11:53Z
date_updated: 2023-10-04T10:28:35Z
file_id: '14390'
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file_size: 114932847
relation: source_file
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checksum: 3253e099b7126469d941fd9419d68b4f
content_type: application/pdf
creator: pradler
date_created: 2023-10-04T10:11:21Z
date_updated: 2023-10-04T10:28:35Z
embargo: 2024-10-04
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file_id: '14391'
file_name: PhD Thesis_Philipp Radler_20231004.pdf
file_size: 37838778
relation: main_file
file_date_updated: 2023-10-04T10:28:35Z
has_accepted_license: '1'
keyword:
- Cell Division
- Reconstitution
- FtsZ
- FtsA
- Divisome
- E.coli
language:
- iso: eng
license: https://creativecommons.org/licenses/by/4.0/
month: '09'
oa_version: Published Version
page: '156'
project:
- _id: 2595697A-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '679239'
name: Self-Organization of the Bacterial Cell
- _id: fc38323b-9c52-11eb-aca3-ff8afb4a011d
grant_number: P34607
name: "Understanding bacterial cell division by in vitro\r\nreconstitution"
- _id: 2596EAB6-B435-11E9-9278-68D0E5697425
grant_number: ALTF 2015-1163
name: Synthesis of bacterial cell wall
- _id: 259B655A-B435-11E9-9278-68D0E5697425
grant_number: LT000824/2016
name: Reconstitution of bacterial cell wall sythesis
publication_identifier:
isbn:
- 978-3-99078-033-6
issn:
- 2663-337X
publication_status: published
publisher: Institute of Science and Technology Austria
related_material:
record:
- id: '11373'
relation: part_of_dissertation
status: public
- id: '7387'
relation: part_of_dissertation
status: public
- id: '10934'
relation: research_data
status: public
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: Spatiotemporal signaling during assembly of the bacterial divisome
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: '2023'
...
---
_id: '13286'
abstract:
- lang: eng
text: Semiconductor-superconductor hybrid systems are the harbour of many intriguing
mesoscopic phenomena. This material combination leads to spatial variations of
the superconducting properties, which gives rise to Andreev bound states (ABSs).
Some of these states might exhibit remarkable properties that render them highly
desirable for topological quantum computing. The most prominent and hunted of
such states are Majorana zero modes (MZMs), quasiparticles equals to their own
quasiparticles that they follow non-abelian statistics. In this thesis, we first
introduce the general framework of such hybrid systems and, then, we unveil a
series of mesoscopic phenomena that we discovered. Firstly, we show tunneling
spectroscopy experiments on full-shell nanowires (NWs) showing that unwanted quantum-dot
states coupled to superconductors (Yu-Shiba-Rusinov states) can mimic MZMs signatures.
Then, we introduce a novel protocol which allowed the integration of tunneling
spectroscopy with Coulomb spectroscopy within the same device. Employing this
approach on both full-shell NWs and partial-shell NWs, we demonstrated that longitudinally
confined states reveal charge transport phenomenology similar to the one expected
for MZMs. These findings shed light on the intricate interplay between superconductivity
and quantum confinement, which brought us to explore another material platform,
i.e. a two-dimensional Germanium hole gas. After developing a robust way to induce
superconductivity in such system, we showed how to engineer the proximity effect
and we revealed a superconducting hard gap. Finally, we created a superconducting
radio frequency driven ideal diode and a generator of non-sinusoidal current-phase
relations. Our results open the path for the exploration of protected superconducting
qubits and more complex hybrid devices in planar Germanium, like Kitaev chains
and hybrid qubit devices.
acknowledged_ssus:
- _id: NanoFab
- _id: M-Shop
alternative_title:
- ISTA Thesis
article_processing_charge: No
author:
- first_name: Marco
full_name: Valentini, Marco
id: C0BB2FAC-D767-11E9-B658-BC13E6697425
last_name: Valentini
citation:
ama: 'Valentini M. Mesoscopic phenomena in hybrid semiconductor-superconductor nanodevices :
From full-shell nanowires to two-dimensional hole gas in germanium. 2023. doi:10.15479/at:ista:13286'
apa: 'Valentini, M. (2023). Mesoscopic phenomena in hybrid semiconductor-superconductor
nanodevices : From full-shell nanowires to two-dimensional hole gas in germanium.
Institute of Science and Technology Austria. https://doi.org/10.15479/at:ista:13286'
chicago: 'Valentini, Marco. “Mesoscopic Phenomena in Hybrid Semiconductor-Superconductor
Nanodevices : From Full-Shell Nanowires to Two-Dimensional Hole Gas in Germanium.”
Institute of Science and Technology Austria, 2023. https://doi.org/10.15479/at:ista:13286.'
ieee: 'M. Valentini, “Mesoscopic phenomena in hybrid semiconductor-superconductor
nanodevices : From full-shell nanowires to two-dimensional hole gas in germanium,”
Institute of Science and Technology Austria, 2023.'
ista: 'Valentini M. 2023. Mesoscopic phenomena in hybrid semiconductor-superconductor
nanodevices : From full-shell nanowires to two-dimensional hole gas in germanium.
Institute of Science and Technology Austria.'
mla: 'Valentini, Marco. Mesoscopic Phenomena in Hybrid Semiconductor-Superconductor
Nanodevices : From Full-Shell Nanowires to Two-Dimensional Hole Gas in Germanium.
Institute of Science and Technology Austria, 2023, doi:10.15479/at:ista:13286.'
short: 'M. Valentini, Mesoscopic Phenomena in Hybrid Semiconductor-Superconductor
Nanodevices : From Full-Shell Nanowires to Two-Dimensional Hole Gas in Germanium,
Institute of Science and Technology Austria, 2023.'
date_created: 2023-07-24T14:10:45Z
date_published: 2023-07-21T00:00:00Z
date_updated: 2024-02-21T12:35:34Z
day: '21'
ddc:
- '530'
degree_awarded: PhD
department:
- _id: GradSch
- _id: GeKa
doi: 10.15479/at:ista:13286
ec_funded: 1
file:
- access_level: closed
checksum: 666ee31c7eade89679806287c062fa14
content_type: application/x-zip-compressed
creator: mvalenti
date_created: 2023-08-11T09:27:39Z
date_updated: 2023-08-11T10:01:34Z
file_id: '14033'
file_name: PhD_thesis_Valentini_final.zip
file_size: 56121429
relation: source_file
- access_level: open_access
checksum: 0992f2ebef152dee8e70055350ebbb55
content_type: application/pdf
creator: mvalenti
date_created: 2023-08-11T14:39:17Z
date_updated: 2023-08-11T14:39:17Z
file_id: '14035'
file_name: PhD_thesis_Valentini_final_validated.pdf
file_size: 38199711
relation: main_file
file_date_updated: 2023-08-11T14:39:17Z
has_accepted_license: '1'
language:
- iso: eng
license: https://creativecommons.org/licenses/by-nc-sa/4.0/
month: '07'
oa: 1
oa_version: Published Version
page: '184'
project:
- _id: 262116AA-B435-11E9-9278-68D0E5697425
name: Hybrid Semiconductor - Superconductor Quantum Devices
- _id: 237E5020-32DE-11EA-91FC-C7463DDC885E
call_identifier: H2020
grant_number: '862046'
name: TOPOLOGICALLY PROTECTED AND SCALABLE QUANTUM BITS
- _id: 34a66131-11ca-11ed-8bc3-a31681c6b03e
grant_number: F8606
name: Conventional and unconventional topological superconductors
publication_identifier:
issn:
- 2663 - 337X
publication_status: published
publisher: Institute of Science and Technology Austria
related_material:
record:
- id: '13312'
relation: part_of_dissertation
status: public
- id: '12118'
relation: part_of_dissertation
status: public
- id: '8910'
relation: part_of_dissertation
status: public
- id: '12522'
relation: research_data
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: 'Mesoscopic phenomena in hybrid semiconductor-superconductor nanodevices :
From full-shell nanowires to two-dimensional hole gas in germanium'
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: 8b945eb4-e2f2-11eb-945a-df72226e66a9
year: '2023'
...
---
_id: '13984'
abstract:
- lang: eng
text: "Social insects fight disease using their individual immune systems and the
cooperative\r\nsanitary behaviors of colony members. These social defenses are
well explored against\r\nexternally-infecting pathogens, but little is known about
defense strategies against\r\ninternally-infecting pathogens, such as viruses.
Viruses are ubiquitous and in the last decades\r\nit has become evident that also
many ant species harbor viruses. We present one of the first\r\nstudies addressing
transmission dynamics and collective disease defenses against viruses in\r\nants
on a mechanistic level. I successfully established an experimental ant host –
viral\r\npathogen system as a model for the defense strategies used by social
insects against internal\r\npathogen infections, as outlined in the third chapter.
In particular, we studied how garden ants\r\n(Lasius neglectus) defend themselves
and their colonies against the generalist insect virus\r\nCrPV (cricket paralysis
virus). We chose microinjections of virus directly into the ants’\r\nhemolymph
because it allowed us to use a defined exposure dose. Here we show that this is
a\r\ngood model system, as the virus is replicating and thus infecting the host.
The ants mount a\r\nclear individual immune response against the viral infection,
which is characterized by a\r\nspecific siRNA pattern, namely siRNAs mapping against
the viral genome with a peak of 21\r\nand 22 bp long fragments. The onset of this
immune response is consistent with the timeline\r\nof viral replication that starts
already within two days post injection. The disease manifests in\r\ndecreased
survival over a course of two to three weeks.\r\nRegarding group living, we find
that infected ants show a strong individual immune response,\r\nbut that their
course of disease is little affected by nestmate presence, as described in chapter\r\nfour.
Hence, we do not find social immunity in the context of viral infections in ants.\r\nNestmates,
however, can contract the virus. Using Drosophila S2R+ cells in culture, we\r\nshowed
that 94 % of the nestmates contract active virus within four days of social contact
to\r\nan infected individual. Virus is transmitted in low doses, thus not causing
disease\r\ntransmission within the colony. While virus can be transmitted during
short direct contacts,\r\nwe also assume transmission from deceased ants and show
that the nestmates’ immune\r\nsystem gets activated after contracting a low viral
dose. We find considerable potential for\r\nindirect transmission via the nest
space. Virus is shed to the nest, where it stays viable for one\r\nweek and is
also picked up by other ants. Apart from that, we want to underline the potential\r\nof
ant poison as antiviral agent. We determined that ant poison successfully inactivates
CrPV\r\nin vitro. However, we found no evidence for effective poison use to sanitize
the nest space.\r\nOn the other hand, local application of ant poison by oral
poison uptake, which is part of the\r\nants prophylactic behavioral repertoire,
probably contributes to keeping the gut of each\r\nindividual sanitized. We hypothesize
that oral poison uptake might be the reason why we did\r\nnot find viable virus
in the trophallactic fluid.\r\nThe fifth chapter encompasses preliminary data
on potential social immunization. However,\r\nour experiments do not confirm an
actual survival benefit for the nestmates upon pathogen\r\nchallenge under the
given experimental settings. Nevertheless, we do not want to rule out the\r\npossibility
for nestmate immunization, but rather emphasize that considering different\r\nexperimental
timelines and viral doses would provide a multitude of options for follow-up\r\nexperiments.\r\nIn
conclusion, we find that prophylactic individual behaviors, such as oral poison
uptake,\r\nmight play a role in preventing viral disease transmission. Compared
to colony defense\r\nagainst external pathogens, internal pathogen infections
require a stronger component of\r\nindividual physiological immunity than behavioral
social immunity, yet could still lead to\r\ncollective protection."
acknowledged_ssus:
- _id: LifeSc
alternative_title:
- ISTA Thesis
article_processing_charge: No
author:
- first_name: Anna
full_name: Franschitz, Anna
id: 480826C8-F248-11E8-B48F-1D18A9856A87
last_name: Franschitz
citation:
ama: Franschitz A. Individual and social immunity against viral infections in ants.
2023. doi:10.15479/at:ista:13984
apa: Franschitz, A. (2023). Individual and social immunity against viral infections
in ants. Institute of Science and Technology Austria. https://doi.org/10.15479/at:ista:13984
chicago: Franschitz, Anna. “Individual and Social Immunity against Viral Infections
in Ants.” Institute of Science and Technology Austria, 2023. https://doi.org/10.15479/at:ista:13984.
ieee: A. Franschitz, “Individual and social immunity against viral infections in
ants,” Institute of Science and Technology Austria, 2023.
ista: Franschitz A. 2023. Individual and social immunity against viral infections
in ants. Institute of Science and Technology Austria.
mla: Franschitz, Anna. Individual and Social Immunity against Viral Infections
in Ants. Institute of Science and Technology Austria, 2023, doi:10.15479/at:ista:13984.
short: A. Franschitz, Individual and Social Immunity against Viral Infections in
Ants, Institute of Science and Technology Austria, 2023.
date_created: 2023-08-08T15:33:29Z
date_published: 2023-08-08T00:00:00Z
date_updated: 2024-03-01T15:25:17Z
day: '08'
ddc:
- '570'
- '577'
degree_awarded: PhD
department:
- _id: GradSch
- _id: SyCr
doi: 10.15479/at:ista:13984
file:
- access_level: closed
checksum: 27220243d5d51c3b0d7d61c0879d7a0c
content_type: application/pdf
creator: afransch
date_created: 2023-08-08T18:01:28Z
date_updated: 2024-03-01T08:51:42Z
embargo: 2024-08-08
embargo_to: open_access
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file_name: Thesis_AnnaFranschitz_202308.pdf
file_size: 10797612
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content_type: application/vnd.openxmlformats-officedocument.wordprocessingml.document
creator: afransch
date_created: 2023-08-08T18:02:25Z
date_updated: 2023-08-09T07:25:27Z
file_id: '13987'
file_name: Thesis_AnnaFranschitz_202308.docx
file_size: 2619085
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content_type: application/pdf
creator: cchlebak
date_created: 2024-03-01T08:37:15Z
date_updated: 2024-03-01T12:13:29Z
description: Minor modifications and clarifications - Feb 2024
embargo: 2024-08-08
embargo_to: open_access
file_id: '15042'
file_name: Addendum_AnnaFranschitz202402.pdf
file_size: 85956
relation: erratum
title: Addendum
- access_level: closed
checksum: 66745aa01f960f17472c024875c049ed
content_type: application/vnd.openxmlformats-officedocument.wordprocessingml.document
creator: cchlebak
date_created: 2024-03-01T08:39:20Z
date_updated: 2024-03-01T08:51:42Z
file_id: '15043'
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file_size: 11818
relation: source_file
title: Addendum - source file
- access_level: closed
checksum: 55c876b73d49db15228a7f571592ec77
content_type: application/pdf
creator: cchlebak
date_created: 2024-03-01T08:56:06Z
date_updated: 2024-03-01T12:58:14Z
description: For printing purposes
file_id: '15044'
file_name: Print_Version_Franschitz_Anna_Thesis.pdf
file_size: 10416761
relation: other
title: Print Version
file_date_updated: 2024-03-01T12:58:14Z
has_accepted_license: '1'
language:
- iso: eng
month: '08'
oa_version: Published Version
page: '89'
publication_identifier:
isbn:
- 978-3-99078-034-3
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: Individual and social immunity against viral infections in ants
type: dissertation
user_id: 8b945eb4-e2f2-11eb-945a-df72226e66a9
year: '2023'
...
---
_id: '14323'
abstract:
- lang: eng
text: Morphogens are signaling molecules that are known for their prominent role
in pattern formation within developing tissues. In addition to patterning, morphogens
also control tissue growth. However, the underlying mechanisms are poorly understood.
We studied the role of morphogens in regulating tissue growth in the developing
vertebrate neural tube. In this system, opposing morphogen gradients of Shh and
BMP establish the dorsoventral pattern of neural progenitor domains. Perturbations
in these morphogen pathways result in alterations in tissue growth and cell cycle
progression, however, it has been unclear what cellular process is affected. To
address this, we analysed the rates of cell proliferation and cell death in mouse
mutants in which signaling is perturbed, as well as in chick neural plate explants
exposed to defined concentrations of signaling activators or inhibitors. Our results
indicated that the rate of cell proliferation was not altered in these assays.
By contrast, both the Shh and BMP signaling pathways had profound effects on neural
progenitor survival. Our results indicate that these pathways synergise to promote
cell survival within neural progenitors. Consistent with this, we found that progenitors
within the intermediate region of the neural tube, where the combined levels of
Shh and BMP are the lowest, are most prone to cell death when signaling activity
is inhibited. In addition, we found that downregulation of Shh results in increased
apoptosis within the roof plate, which is the dorsal source of BMP ligand production.
This revealed a cross-interaction between the Shh and BMP morphogen signaling
pathways that may be relevant for understanding how gradients scale in neural
tubes with different overall sizes. We further studied the mechanism acting downstream
of Shh in cell survival regulation using genetic and genomic approaches. We propose
that Shh transcriptionally regulates a non-canonical apoptotic pathway. Altogether,
our study points to a novel role of opposing morphogen gradients in tissue size
regulation and provides new insights into complex interactions between Shh and
BMP signaling gradients in the neural tube.
acknowledged_ssus:
- _id: Bio
- _id: PreCl
alternative_title:
- ISTA Thesis
article_processing_charge: No
author:
- first_name: Katarzyna
full_name: Kuzmicz-Kowalska, Katarzyna
id: 4CED352A-F248-11E8-B48F-1D18A9856A87
last_name: Kuzmicz-Kowalska
citation:
ama: Kuzmicz-Kowalska K. Regulation of neural progenitor survival by Shh and BMP
in the developing spinal cord. 2023. doi:10.15479/at:ista:14323
apa: Kuzmicz-Kowalska, K. (2023). Regulation of neural progenitor survival by
Shh and BMP in the developing spinal cord. Institute of Science and Technology
Austria. https://doi.org/10.15479/at:ista:14323
chicago: Kuzmicz-Kowalska, Katarzyna. “Regulation of Neural Progenitor Survival
by Shh and BMP in the Developing Spinal Cord.” Institute of Science and Technology
Austria, 2023. https://doi.org/10.15479/at:ista:14323.
ieee: K. Kuzmicz-Kowalska, “Regulation of neural progenitor survival by Shh and
BMP in the developing spinal cord,” Institute of Science and Technology Austria,
2023.
ista: Kuzmicz-Kowalska K. 2023. Regulation of neural progenitor survival by Shh
and BMP in the developing spinal cord. Institute of Science and Technology Austria.
mla: Kuzmicz-Kowalska, Katarzyna. Regulation of Neural Progenitor Survival by
Shh and BMP in the Developing Spinal Cord. Institute of Science and Technology
Austria, 2023, doi:10.15479/at:ista:14323.
short: K. Kuzmicz-Kowalska, Regulation of Neural Progenitor Survival by Shh and
BMP in the Developing Spinal Cord, Institute of Science and Technology Austria,
2023.
date_created: 2023-09-13T10:07:18Z
date_published: 2023-09-13T00:00:00Z
date_updated: 2024-03-07T15:02:59Z
day: '13'
ddc:
- '570'
degree_awarded: PhD
department:
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name: The role of morphogens in the regulation of neural tube growth
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
status: public
supervisor:
- first_name: Anna
full_name: Kicheva, Anna
id: 3959A2A0-F248-11E8-B48F-1D18A9856A87
last_name: Kicheva
orcid: 0000-0003-4509-4998
title: Regulation of neural progenitor survival by Shh and BMP in the developing spinal
cord
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short: CC BY-NC-ND (4.0)
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year: '2023'
...
---
_id: '14641'
acknowledged_ssus:
- _id: LifeSc
- _id: Bio
- _id: CampIT
alternative_title:
- ISTA Thesis
article_processing_charge: No
author:
- first_name: Mike
full_name: Hennessey-Wesen, Mike
id: 3F338C72-F248-11E8-B48F-1D18A9856A87
last_name: Hennessey-Wesen
citation:
ama: Hennessey-Wesen M. Adaptive mutation in E. coli modulated by luxS. 2023. doi:10.15479/at:ista:14641
apa: Hennessey-Wesen, M. (2023). Adaptive mutation in E. coli modulated by luxS.
Institute of Science and Technology Austria. https://doi.org/10.15479/at:ista:14641
chicago: Hennessey-Wesen, Mike. “Adaptive Mutation in E. Coli Modulated by LuxS.”
Institute of Science and Technology Austria, 2023. https://doi.org/10.15479/at:ista:14641.
ieee: M. Hennessey-Wesen, “Adaptive mutation in E. coli modulated by luxS,” Institute
of Science and Technology Austria, 2023.
ista: Hennessey-Wesen M. 2023. Adaptive mutation in E. coli modulated by luxS. Institute
of Science and Technology Austria.
mla: Hennessey-Wesen, Mike. Adaptive Mutation in E. Coli Modulated by LuxS.
Institute of Science and Technology Austria, 2023, doi:10.15479/at:ista:14641.
short: M. Hennessey-Wesen, Adaptive Mutation in E. Coli Modulated by LuxS, Institute
of Science and Technology Austria, 2023.
date_created: 2023-12-04T13:17:37Z
date_published: 2023-11-30T00:00:00Z
date_updated: 2024-03-22T13:21:17Z
day: '30'
ddc:
- '570'
degree_awarded: PhD
department:
- _id: GradSch
- _id: BjHo
doi: 10.15479/at:ista:14641
ec_funded: 1
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file_size: 2930287
relation: other
file_date_updated: 2024-03-20T13:19:36Z
has_accepted_license: '1'
keyword:
- microfluidics
- miceobiology
- mutations
- quorum sensing
language:
- iso: eng
month: '11'
oa_version: Published Version
page: '104'
project:
- _id: 2564DBCA-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '665385'
name: International IST Doctoral Program
publication_identifier:
issn:
- 2663 - 337X
publication_status: published
publisher: Institute of Science and Technology Austria
status: public
supervisor:
- first_name: Björn
full_name: Hof, Björn
id: 3A374330-F248-11E8-B48F-1D18A9856A87
last_name: Hof
orcid: 0000-0003-2057-2754
title: Adaptive mutation in E. coli modulated by luxS
type: dissertation
user_id: 8b945eb4-e2f2-11eb-945a-df72226e66a9
year: '2023'
...
---
_id: '14587'
abstract:
- lang: eng
text: "This thesis concerns the application of variational methods to the study
of evolution problems arising in fluid mechanics and in material sciences. The
main focus is on weak-strong stability properties of some curvature driven interface
evolution problems, such as the two-phase Navier–Stokes flow with surface tension
and multiphase mean curvature flow, and on the phase-field approximation of the
latter. Furthermore, we discuss a variational approach to the study of a class
of doubly nonlinear wave equations.\r\nFirst, we consider the two-phase Navier–Stokes
flow with surface tension within a bounded domain. The two fluids are immiscible
and separated by a sharp interface, which intersects the boundary of the domain
at a constant contact angle of ninety degree. We devise a suitable concept of
varifolds solutions for the associated interface evolution problem and we establish
a weak-strong uniqueness principle in case of a two dimensional ambient space.
In order to focus on the boundary effects and on the singular geometry of the
evolving domains, we work for simplicity in the regime of same viscosities for
the two fluids.\r\nThe core of the thesis consists in the rigorous proof of the
convergence of the vectorial Allen-Cahn equation towards multiphase mean curvature
flow for a suitable class of multi- well potentials and for well-prepared initial
data. We even establish a rate of convergence. Our relative energy approach relies
on the concept of gradient-flow calibration for branching singularities in multiphase
mean curvature flow and thus enables us to overcome the limitations of other approaches.
To the best of the author’s knowledge, our result is the first quantitative and
unconditional one available in the literature for the vectorial/multiphase setting.\r\nThis
thesis also contains a first study of weak-strong stability for planar multiphase
mean curvature flow beyond the singularity resulting from a topology change. Previous
weak-strong results are indeed limited to time horizons before the first topology
change of the strong solution. We consider circular topology changes and we prove
weak-strong stability for BV solutions to planar multiphase mean curvature flow
beyond the associated singular times by dynamically adapting the strong solutions
to the weak one by means of a space-time shift.\r\nIn the context of interface
evolution problems, our proofs for the main results of this thesis are based on
the relative energy technique, relying on novel suitable notions of relative energy
functionals, which in particular measure the interface error. Our statements follow
from the resulting stability estimates for the relative energy associated to the
problem.\r\nAt last, we introduce a variational approach to the study of nonlinear
evolution problems. This approach hinges on the minimization of a parameter dependent
family of convex functionals over entire trajectories, known as Weighted Inertia-Dissipation-Energy
(WIDE) functionals. We consider a class of doubly nonlinear wave equations and
establish the convergence, up to subsequences, of the associated WIDE minimizers
to a solution of the target problem as the parameter goes to zero."
acknowledgement: The research projects contained in this thesis have received funding
from the European Research Council (ERC) under the European Union’s Horizon 2020
research and innovation programme (grant agreement No 948819).
alternative_title:
- ISTA Thesis
article_processing_charge: No
author:
- first_name: Alice
full_name: Marveggio, Alice
id: 25647992-AA84-11E9-9D75-8427E6697425
last_name: Marveggio
citation:
ama: Marveggio A. Weak-strong stability and phase-field approximation of interface
evolution problems in fluid mechanics and in material sciences. 2023. doi:10.15479/at:ista:14587
apa: Marveggio, A. (2023). Weak-strong stability and phase-field approximation
of interface evolution problems in fluid mechanics and in material sciences.
Institute of Science and Technology Austria. https://doi.org/10.15479/at:ista:14587
chicago: Marveggio, Alice. “Weak-Strong Stability and Phase-Field Approximation
of Interface Evolution Problems in Fluid Mechanics and in Material Sciences.”
Institute of Science and Technology Austria, 2023. https://doi.org/10.15479/at:ista:14587.
ieee: A. Marveggio, “Weak-strong stability and phase-field approximation of interface
evolution problems in fluid mechanics and in material sciences,” Institute of
Science and Technology Austria, 2023.
ista: Marveggio A. 2023. Weak-strong stability and phase-field approximation of
interface evolution problems in fluid mechanics and in material sciences. Institute
of Science and Technology Austria.
mla: Marveggio, Alice. Weak-Strong Stability and Phase-Field Approximation of
Interface Evolution Problems in Fluid Mechanics and in Material Sciences.
Institute of Science and Technology Austria, 2023, doi:10.15479/at:ista:14587.
short: A. Marveggio, Weak-Strong Stability and Phase-Field Approximation of Interface
Evolution Problems in Fluid Mechanics and in Material Sciences, Institute of Science
and Technology Austria, 2023.
date_created: 2023-11-21T11:41:05Z
date_published: 2023-11-21T00:00:00Z
date_updated: 2024-03-22T13:21:28Z
day: '21'
ddc:
- '515'
degree_awarded: PhD
department:
- _id: GradSch
- _id: JuFi
doi: 10.15479/at:ista:14587
ec_funded: 1
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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:
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status: public
- id: '14597'
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: Weak-strong stability and phase-field approximation of interface evolution
problems in fluid mechanics and in material sciences
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short: CC BY-NC-SA (4.0)
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...
---
_id: '12491'
abstract:
- lang: eng
text: "The extracellular matrix (ECM) is a hydrated and complex three-dimensional
network consisting of proteins, polysaccharides, and water. It provides structural
scaffolding for the cells embedded within it and is essential in regulating numerous
physiological processes, including cell migration and proliferation, wound healing,
and stem cell fate. \r\nDespite extensive study, detailed structural knowledge
of ECM components in physiologically relevant conditions is still rudimentary.
This is due to methodological limitations in specimen preparation protocols which
are incompatible with keeping large samples, such as the ECM, in their native
state for subsequent imaging. Conventional electron microscopy (EM) techniques
rely on fixation, dehydration, contrasting, and sectioning. This results in the
alteration of a highly hydrated environment and the potential introduction of
artifacts. Other structural biology techniques, such as nuclear magnetic resonance
(NMR) spectroscopy and X-ray crystallography, allow high-resolution analysis of
protein structures but only work on homogenous and purified samples, hence lacking
contextual information. Currently, no approach exists for the ultrastructural
and structural study of extracellular components under native conditions in a
physiological, 3D environment. \r\nIn this thesis, I have developed a workflow
that allows for the ultrastructural analysis of the ECM in near-native conditions
at molecular resolution. The developments I introduced include implementing a
novel specimen preparation workflow for cell-derived matrices (CDMs) to render
them compatible with ion-beam milling and subsequent high-resolution cryo-electron
tomography (ET). \r\nTo this end, I have established protocols to generate CDMs
grown over several weeks on EM grids that are compatible with downstream cryo-EM
sample preparation and imaging techniques. Characterization of these ECMs confirmed
that they contain essential ECM components such as collagen I, collagen VI, and
fibronectin I in high abundance and hence represent a bona fide biologically-relevant
sample. I successfully optimized vitrification of these specimens by testing various
vitrification techniques and cryoprotectants. \r\nIn order to obtain high-resolution
molecular insights into the ultrastructure and organization of CDMs, I established
cryo-focused ion beam scanning electron microscopy (FIBSEM) on these challenging
and complex specimens. I explored different approaches for the creation of thin
cryo-lamellae by FIB milling and succeeded in optimizing the cryo-lift-out technique,
resulting in high-quality lamellae of approximately 200 nm thickness. \r\nHigh-resolution
Cryo-ET of these lamellae revealed for the first time the architecture of native
CDM in the context of matrix-secreting cells. This allowed for the in situ visualization
of fibrillar matrix proteins such as collagen, laying the foundation for future
structural and ultrastructural characterization of these proteins in their near-native
environment. \r\nIn summary, in this thesis, I present a novel workflow that combines
state-of-the-art cryo-EM specimen preparation and imaging technologies to permit
characterization of the ECM, an important tissue component in higher organisms.
This innovative and highly versatile workflow will enable addressing far-reaching
questions on ECM architecture, composition, and reciprocal ECM-cell interactions."
acknowledged_ssus:
- _id: EM-Fac
- _id: LifeSc
- _id: Bio
alternative_title:
- ISTA Thesis
article_processing_charge: No
author:
- first_name: Bettina
full_name: Zens, Bettina
id: 45FD126C-F248-11E8-B48F-1D18A9856A87
last_name: Zens
orcid: 0000-0002-9561-1239
citation:
ama: Zens B. Ultrastructural characterization of natively preserved extracellular
matrix by cryo-electron tomography. 2023. doi:10.15479/at:ista:12491
apa: Zens, B. (2023). Ultrastructural characterization of natively preserved
extracellular matrix by cryo-electron tomography. Institute of Science and
Technology Austria. https://doi.org/10.15479/at:ista:12491
chicago: Zens, Bettina. “Ultrastructural Characterization of Natively Preserved
Extracellular Matrix by Cryo-Electron Tomography.” Institute of Science and Technology
Austria, 2023. https://doi.org/10.15479/at:ista:12491.
ieee: B. Zens, “Ultrastructural characterization of natively preserved extracellular
matrix by cryo-electron tomography,” Institute of Science and Technology Austria,
2023.
ista: Zens B. 2023. Ultrastructural characterization of natively preserved extracellular
matrix by cryo-electron tomography. Institute of Science and Technology Austria.
mla: Zens, Bettina. Ultrastructural Characterization of Natively Preserved Extracellular
Matrix by Cryo-Electron Tomography. Institute of Science and Technology Austria,
2023, doi:10.15479/at:ista:12491.
short: B. Zens, Ultrastructural Characterization of Natively Preserved Extracellular
Matrix by Cryo-Electron Tomography, Institute of Science and Technology Austria,
2023.
date_created: 2023-02-02T14:50:20Z
date_published: 2023-02-02T00:00:00Z
date_updated: 2024-03-25T23:30:05Z
day: '02'
ddc:
- '570'
degree_awarded: PhD
department:
- _id: GradSch
- _id: FlSc
doi: 10.15479/at:ista:12491
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keyword:
- cryo-EM
- cryo-ET
- FIB milling
- method development
- FIBSEM
- extracellular matrix
- ECM
- cell-derived matrices
- CDMs
- cell culture
- high pressure freezing
- HPF
- structural biology
- tomography
- collagen
language:
- iso: eng
month: '02'
oa: 1
oa_version: Published Version
page: '187'
project:
- _id: eba3b5f6-77a9-11ec-83b8-cf0905748aa3
name: Integrated visual proteomics of reciprocal cell-extracellular matrix interactions
- _id: 059B463C-7A3F-11EA-A408-12923DDC885E
name: NÖ-Fonds Preis für die Jungforscherin des Jahres am IST Austria
publication_identifier:
isbn:
- 978-3-99078-027-5
issn:
- 2663-337X
publication_status: published
publisher: Institute of Science and Technology Austria
related_material:
record:
- id: '8586'
relation: part_of_dissertation
status: public
status: public
supervisor:
- first_name: Florian KM
full_name: Schur, Florian KM
id: 48AD8942-F248-11E8-B48F-1D18A9856A87
last_name: Schur
orcid: 0000-0003-4790-8078
title: Ultrastructural characterization of natively preserved extracellular matrix
by cryo-electron tomography
type: dissertation
user_id: 8b945eb4-e2f2-11eb-945a-df72226e66a9
year: '2023'
...
---
_id: '14226'
abstract:
- lang: eng
text: "We introduce the notion of a Faustian interchange in a 1-parameter family
of smooth\r\nfunctions to generalize the medial axis to critical points of index
larger than 0.\r\nWe construct and implement a general purpose algorithm for approximating
such\r\ngeneralized medial axes."
alternative_title:
- ISTA Master's Thesis
article_processing_charge: No
author:
- first_name: Elizabeth R
full_name: Stephenson, Elizabeth R
id: 2D04F932-F248-11E8-B48F-1D18A9856A87
last_name: Stephenson
orcid: 0000-0002-6862-208X
citation:
ama: Stephenson ER. Generalizing medial axes with homology switches. 2023. doi:10.15479/at:ista:14226
apa: Stephenson, E. R. (2023). Generalizing medial axes with homology switches.
Institute of Science and Technology Austria. https://doi.org/10.15479/at:ista:14226
chicago: Stephenson, Elizabeth R. “Generalizing Medial Axes with Homology Switches.”
Institute of Science and Technology Austria, 2023. https://doi.org/10.15479/at:ista:14226.
ieee: E. R. Stephenson, “Generalizing medial axes with homology switches,” Institute
of Science and Technology Austria, 2023.
ista: Stephenson ER. 2023. Generalizing medial axes with homology switches. Institute
of Science and Technology Austria.
mla: Stephenson, Elizabeth R. Generalizing Medial Axes with Homology Switches.
Institute of Science and Technology Austria, 2023, doi:10.15479/at:ista:14226.
short: E.R. Stephenson, Generalizing Medial Axes with Homology Switches, Institute
of Science and Technology Austria, 2023.
date_created: 2023-08-24T13:01:18Z
date_published: 2023-08-24T00:00:00Z
date_updated: 2024-02-26T23:30:04Z
day: '24'
ddc:
- '500'
degree_awarded: MS
department:
- _id: GradSch
- _id: HeEd
doi: 10.15479/at:ista:14226
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date_created: 2023-08-24T13:02:49Z
date_updated: 2024-02-26T23:30:03Z
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date_updated: 2024-02-26T23:30:03Z
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language:
- iso: eng
month: '08'
oa: 1
oa_version: Published Version
page: '43'
publication_identifier:
issn:
- 2791-4585
publication_status: published
publisher: Institute of Science and Technology Austria
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: Generalizing medial axes with homology switches
type: dissertation
user_id: 8b945eb4-e2f2-11eb-945a-df72226e66a9
year: '2023'
...
---
_id: '12470'
abstract:
- lang: eng
text: "The brain is an exceptionally sophisticated organ consisting of billions
of cells and trillions of \r\nconnections that orchestrate our cognition and behavior.
To decode its complex connectivity, it is \r\npivotal to disentangle its intricate
architecture spanning from cm-sized circuits down to tens of \r\nnm-small synapses.\r\nTo
achieve this goal, I developed CATS – Comprehensive Analysis of nervous Tissue
across \r\nScales, a versatile toolbox for obtaining a holistic view of nervous
tissue context with (super\x02resolution) fluorescence microscopy. CATS combines
comprehensive labeling of the extracellular\r\nspace, that is compatible with
chemical fixation, with information on molecular markers, super\x02resolved data
acquisition and machine-learning based data analysis for segmentation and synapse
\r\nidentification.\r\nI used CATS to analyze key features of nervous tissue connectivity,
ranging from whole tissue \r\narchitecture, neuronal in- and output-fields, down
to synapse morphology.\r\nFocusing on the hippocampal circuitry, I quantified
synaptic transmission properties of mossy \r\nfiber boutons and analyzed the connectivity
pattern of dentate gyrus granule cells with CA3 \r\npyramidal neurons. This shows
that CATS is a viable tool to study hallmarks of neuronal \r\nconnectivity with
light microscopy."
acknowledged_ssus:
- _id: Bio
- _id: LifeSc
- _id: PreCl
- _id: EM-Fac
- _id: M-Shop
- _id: ScienComp
alternative_title:
- ISTA Thesis
article_processing_charge: No
author:
- first_name: Julia M
full_name: Michalska, Julia M
id: 443DB6DE-F248-11E8-B48F-1D18A9856A87
last_name: Michalska
orcid: 0000-0003-3862-1235
citation:
ama: Michalska JM. A versatile toolbox for the comprehensive analysis of nervous
tissue organization with light microscopy. 2023. doi:10.15479/at:ista:12470
apa: Michalska, J. M. (2023). A versatile toolbox for the comprehensive analysis
of nervous tissue organization with light microscopy. Institute of Science
and Technology Austria. https://doi.org/10.15479/at:ista:12470
chicago: Michalska, Julia M. “A Versatile Toolbox for the Comprehensive Analysis
of Nervous Tissue Organization with Light Microscopy.” Institute of Science and
Technology Austria, 2023. https://doi.org/10.15479/at:ista:12470.
ieee: J. M. Michalska, “A versatile toolbox for the comprehensive analysis of nervous
tissue organization with light microscopy,” Institute of Science and Technology
Austria, 2023.
ista: Michalska JM. 2023. A versatile toolbox for the comprehensive analysis of
nervous tissue organization with light microscopy. Institute of Science and Technology
Austria.
mla: Michalska, Julia M. A Versatile Toolbox for the Comprehensive Analysis of
Nervous Tissue Organization with Light Microscopy. Institute of Science and
Technology Austria, 2023, doi:10.15479/at:ista:12470.
short: J.M. Michalska, A Versatile Toolbox for the Comprehensive Analysis of Nervous
Tissue Organization with Light Microscopy, Institute of Science and Technology
Austria, 2023.
date_created: 2023-01-31T15:10:53Z
date_published: 2023-01-09T00:00:00Z
date_updated: 2023-08-31T12:26:58Z
day: '09'
ddc:
- '610'
degree_awarded: PhD
department:
- _id: GradSch
- _id: JoDa
doi: 10.15479/at:ista:12470
ec_funded: 1
file:
- access_level: open_access
checksum: 1a2306e5f59f52df598e7ecfadf921ac
content_type: application/pdf
creator: cchlebak
date_created: 2023-01-31T15:11:42Z
date_updated: 2023-07-27T22:30:54Z
embargo: 2023-07-09
file_id: '12471'
file_name: 20230109_PhD_thesis_JM_final.pdf
file_size: 41771714
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creator: cchlebak
date_created: 2023-01-31T15:11:51Z
date_updated: 2023-07-10T22:30:04Z
embargo_to: open_access
file_id: '12472'
file_name: 20230109_PhD_thesis_JM_final.docx
file_size: 66983464
relation: source_file
file_date_updated: 2023-07-27T22:30:54Z
has_accepted_license: '1'
language:
- iso: eng
month: '01'
oa: 1
oa_version: Published Version
page: '201'
project:
- _id: 2564DBCA-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '665385'
name: International IST Doctoral Program
- _id: 26AA4EF2-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: W1232-B24
name: Molecular Drug Targets
publication_identifier:
isbn:
- ' 978-3-99078-026-8'
issn:
- 2663-337X
publication_status: published
publisher: Institute of Science and Technology Austria
related_material:
record:
- id: '11943'
relation: part_of_dissertation
status: public
- id: '11950'
relation: part_of_dissertation
status: public
status: public
supervisor:
- first_name: Johann G
full_name: Danzl, Johann G
id: 42EFD3B6-F248-11E8-B48F-1D18A9856A87
last_name: Danzl
orcid: 0000-0001-8559-3973
title: A versatile toolbox for the comprehensive analysis of nervous tissue organization
with light microscopy
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: '2023'
...
---
_id: '12531'
abstract:
- lang: eng
text: "All visual experiences of the vertebrates begin with light being converted
into electrical signals\r\nby the eye retina. Retinal ganglion cells (RGCs) are
the neurons of the innermost layer of the\r\nmammal retina, and they transmit
visual information to the rest of the brain.\r\nIt has been shown that RGCs vary
in their morphology and genetic profiles, moreover they can\r\nbe unambiguously
grouped into subtypes that share the same morphological and/or molecular\r\nproperties.
However, in terms of RGCs function, it remains unclear how many distinct types\r\nthere
are and what response properties their typology relies on. Even given the recent
studies\r\nthat successfully classified RGCs in a patch of the retina [1] and
in scotopic conditions [2], the\r\nquestion remains whether the found subtypes
persist across the entire retina.\r\nIn this work, using a novel imaging method,
we show that, when sampled from a large portion\r\nof the retina, RGCs can not
be clearly divided into functional subtypes. We found that in\r\nphotopic conditions,
which implies more prominent natural scene statistic differences across\r\nthe
visual field, response properties can be exhibited by cells differently depending
on their\r\nlocation in the retina, which leads to formation of a gradient of
features rather than distinct\r\nclasses.\r\nThis finding suggests that RGCs follow
a global organization across the visual field of the\r\nanimal, adapting each
RGC subtype to the requirements imposed by the natural scene statistics."
alternative_title:
- ISTA Master's Thesis
article_processing_charge: No
author:
- first_name: Kseniia
full_name: Kirillova, Kseniia
id: 8e3f931e-dc85-11ea-9058-e7b957bf23f0
last_name: Kirillova
citation:
ama: Kirillova K. Panoramic functional gradients across the mouse retina. 2023.
doi:10.15479/at:ista:12531
apa: Kirillova, K. (2023). Panoramic functional gradients across the mouse retina.
Institute of Science and Technology Austria. https://doi.org/10.15479/at:ista:12531
chicago: Kirillova, Kseniia. “Panoramic Functional Gradients across the Mouse Retina.”
Institute of Science and Technology Austria, 2023. https://doi.org/10.15479/at:ista:12531.
ieee: K. Kirillova, “Panoramic functional gradients across the mouse retina,” Institute
of Science and Technology Austria, 2023.
ista: Kirillova K. 2023. Panoramic functional gradients across the mouse retina.
Institute of Science and Technology Austria.
mla: Kirillova, Kseniia. Panoramic Functional Gradients across the Mouse Retina.
Institute of Science and Technology Austria, 2023, doi:10.15479/at:ista:12531.
short: K. Kirillova, Panoramic Functional Gradients across the Mouse Retina, Institute
of Science and Technology Austria, 2023.
date_created: 2023-02-09T07:45:05Z
date_published: 2023-02-08T00:00:00Z
date_updated: 2024-02-09T23:30:04Z
day: '08'
ddc:
- '570'
degree_awarded: MS
department:
- _id: GradSch
- _id: MaJö
doi: 10.15479/at:ista:12531
file:
- access_level: open_access
checksum: 57d8da3a6c749eb1556b7435fe266a5f
content_type: application/pdf
creator: cchlebak
date_created: 2023-02-09T08:03:32Z
date_updated: 2024-02-09T23:30:03Z
embargo: 2024-02-08
file_id: '12532'
file_name: Thesis_Kseniia___ISTA__istaustriathesis_PDF-A.pdf
file_size: 8369317
relation: main_file
- access_level: closed
checksum: 87fb44318e4f9eb9da2ad9ad6ca8e76f
content_type: application/x-zip-compressed
creator: cchlebak
date_created: 2023-02-10T09:32:06Z
date_updated: 2024-02-09T23:30:03Z
embargo_to: open_access
file_id: '12535'
file_name: Thesis Kseniia - ISTA [istaustriathesis]-FINAL.zip
file_size: 11204408
relation: source_file
file_date_updated: 2024-02-09T23:30:03Z
has_accepted_license: '1'
language:
- iso: eng
month: '02'
oa: 1
oa_version: Published Version
page: '46'
publication_identifier:
issn:
- 2791-4585
publication_status: published
publisher: Institute of Science and Technology Austria
status: public
supervisor:
- first_name: Maximilian A
full_name: Jösch, Maximilian A
id: 2BD278E6-F248-11E8-B48F-1D18A9856A87
last_name: Jösch
orcid: 0000-0002-3937-1330
title: Panoramic functional gradients across the mouse retina
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: '2023'
...
---
_id: '12800'
abstract:
- lang: eng
text: 'The evolutionary processes that brought about today’s plethora of living
species and the many billions more ancient ones all underlie biology. Evolutionary
pathways are neither directed nor deterministic, but rather an interplay between
selection, migration, mutation, genetic drift and other environmental factors.
Hybrid zones, as natural crossing experiments, offer a great opportunity to use
cline analysis to deduce different evolutionary processes - for example, selection
strength. Theoretical cline models, largely assuming uniform distribution of individuals,
often lack the capability of incorporating population structure. Since in reality
organisms mostly live in patchy distributions and their dispersal is hardly ever
Gaussian, it is necessary to unravel the effect of these different elements of
population structure on cline parameters and shape. In this thesis, I develop
a simulation inspired by the A. majus hybrid zone of a single selected locus under
frequency dependent selection. This simulation enables us to untangle the effects
of different elements of population structure as for example a low-density center
and long-range dispersal. This thesis is therefore a first step towards theoretically
untangling the effects of different elements of population structure on cline
parameters and shape. '
alternative_title:
- ISTA Master's Thesis
article_processing_charge: No
author:
- first_name: Mara
full_name: Julseth, Mara
id: 1cf464b2-dc7d-11ea-9b2f-f9b1aa9417d1
last_name: Julseth
citation:
ama: Julseth M. The effect of local population structure on genetic variation at
selected loci in the A. majus hybrid zone. 2023. doi:10.15479/at:ista:12800
apa: Julseth, M. (2023). The effect of local population structure on genetic
variation at selected loci in the A. majus hybrid zone. Institute of Science
and Technology Austria. https://doi.org/10.15479/at:ista:12800
chicago: Julseth, Mara. “The Effect of Local Population Structure on Genetic Variation
at Selected Loci in the A. Majus Hybrid Zone.” Institute of Science and Technology
Austria, 2023. https://doi.org/10.15479/at:ista:12800.
ieee: M. Julseth, “The effect of local population structure on genetic variation
at selected loci in the A. majus hybrid zone,” Institute of Science and Technology
Austria, 2023.
ista: Julseth M. 2023. The effect of local population structure on genetic variation
at selected loci in the A. majus hybrid zone. Institute of Science and Technology
Austria.
mla: Julseth, Mara. The Effect of Local Population Structure on Genetic Variation
at Selected Loci in the A. Majus Hybrid Zone. Institute of Science and Technology
Austria, 2023, doi:10.15479/at:ista:12800.
short: M. Julseth, The Effect of Local Population Structure on Genetic Variation
at Selected Loci in the A. Majus Hybrid Zone, Institute of Science and Technology
Austria, 2023.
date_created: 2023-04-04T18:57:11Z
date_published: 2023-04-05T00:00:00Z
date_updated: 2023-06-02T22:30:05Z
day: '05'
ddc:
- '576'
degree_awarded: MS
department:
- _id: GradSch
- _id: NiBa
doi: 10.15479/at:ista:12800
file:
- access_level: closed
checksum: b76cf6d69f2093d8248f6a3f9d4654a4
content_type: application/vnd.openxmlformats-officedocument.spreadsheetml.sheet
creator: mjulseth
date_created: 2023-04-06T06:09:40Z
date_updated: 2023-06-02T22:30:04Z
embargo_to: open_access
file_id: '12805'
file_name: Dispersaldata.xlsx
file_size: 52795
relation: supplementary_material
- access_level: open_access
checksum: 5a13b6d204371572e249f03795bc0d04
content_type: application/vnd.wolfram.nb
creator: mjulseth
date_created: 2023-04-06T06:11:27Z
date_updated: 2023-06-02T22:30:04Z
embargo: 2023-06-01
file_id: '12806'
file_name: 2023_MSc_ThesisMaraJulseth_Notebook.nb
file_size: 787239
relation: supplementary_material
- access_level: closed
checksum: c3ec842839ed1e66bf2618ae33047df8
content_type: application/vnd.openxmlformats-officedocument.wordprocessingml.document
creator: mjulseth
date_created: 2023-04-06T08:26:12Z
date_updated: 2023-06-02T22:30:04Z
embargo_to: open_access
file_id: '12812'
file_name: ThesisMaraJulseth_04_23.docx
file_size: 1061763
relation: source_file
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checksum: 3132cc998fbe3ae2a3a83c2a69367f37
content_type: application/pdf
creator: mjulseth
date_created: 2023-04-06T08:26:37Z
date_updated: 2023-06-02T22:30:04Z
embargo: 2023-06-01
file_id: '12813'
file_name: ThesisMaraJulseth_04_23.pdf
file_size: 1741364
relation: main_file
file_date_updated: 2023-06-02T22:30:04Z
has_accepted_license: '1'
language:
- iso: eng
month: '04'
oa: 1
oa_version: Published Version
page: '21'
publication_identifier:
issn:
- 2791-4585
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: The effect of local population structure on genetic variation at selected loci
in the A. majus hybrid zone
type: dissertation
user_id: 8b945eb4-e2f2-11eb-945a-df72226e66a9
year: '2023'
...
---
_id: '14510'
acknowledged_ssus:
- _id: EM-Fac
- _id: Bio
- _id: LifeSc
alternative_title:
- ISTA Thesis
article_processing_charge: No
author:
- first_name: Nataliia
full_name: Gnyliukh, Nataliia
id: 390C1120-F248-11E8-B48F-1D18A9856A87
last_name: Gnyliukh
orcid: 0000-0002-2198-0509
citation:
ama: Gnyliukh N. Mechanism of clathrin-coated vesicle formation during endocytosis
in plants. 2023. doi:10.15479/at:ista:14510
apa: Gnyliukh, N. (2023). Mechanism of clathrin-coated vesicle formation during
endocytosis in plants. Institute of Science and Technology Austria. https://doi.org/10.15479/at:ista:14510
chicago: Gnyliukh, Nataliia. “Mechanism of Clathrin-Coated Vesicle Formation during
Endocytosis in Plants.” Institute of Science and Technology Austria, 2023. https://doi.org/10.15479/at:ista:14510.
ieee: N. Gnyliukh, “Mechanism of clathrin-coated vesicle formation during endocytosis
in plants,” Institute of Science and Technology Austria, 2023.
ista: Gnyliukh N. 2023. Mechanism of clathrin-coated vesicle formation during endocytosis
in plants. Institute of Science and Technology Austria.
mla: Gnyliukh, Nataliia. Mechanism of Clathrin-Coated Vesicle Formation during
Endocytosis in Plants. Institute of Science and Technology Austria, 2023,
doi:10.15479/at:ista:14510.
short: N. Gnyliukh, Mechanism of Clathrin-Coated Vesicle Formation during Endocytosis
in Plants, Institute of Science and Technology Austria, 2023.
date_created: 2023-11-10T09:10:06Z
date_published: 2023-11-10T00:00:00Z
date_updated: 2024-03-27T23:30:45Z
day: '10'
ddc:
- '570'
degree_awarded: PhD
department:
- _id: GradSch
- _id: JiFr
- _id: MaLo
doi: 10.15479/at:ista:14510
ec_funded: 1
file:
- access_level: closed
checksum: 3d5e680bfc61f98e308c434f45cc9bd6
content_type: application/vnd.openxmlformats-officedocument.wordprocessingml.document
creator: ngnyliuk
date_created: 2023-11-20T09:18:51Z
date_updated: 2023-11-20T09:18:51Z
file_id: '14567'
file_name: Thesis_Gnyliukh_final_08_11_23.docx
file_size: 20824903
relation: source_file
- access_level: closed
checksum: bfc96d47fc4e7e857dd71656097214a4
content_type: application/pdf
creator: ngnyliuk
date_created: 2023-11-20T09:23:11Z
date_updated: 2023-11-23T13:10:55Z
embargo: 2024-11-23
embargo_to: open_access
file_id: '14568'
file_name: Thesis_Gnyliukh_final_20_11_23.pdf
file_size: 24871844
relation: main_file
file_date_updated: 2023-11-23T13:10:55Z
has_accepted_license: '1'
keyword:
- Clathrin-Mediated Endocytosis
- vesicle scission
- Dynamin-Related Protein 2
- SH3P2
- TPLATE complex
- Total internal reflection fluorescence microscopy
- Arabidopsis thaliana
language:
- iso: eng
month: '11'
oa_version: Published Version
page: '180'
project:
- _id: 2564DBCA-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '665385'
name: International IST Doctoral Program
publication_identifier:
isbn:
- 978-3-99078-037-4
issn:
- 2663-337X
publication_status: published
publisher: Institute of Science and Technology Austria
related_material:
record:
- id: '14591'
relation: part_of_dissertation
status: public
- id: '9887'
relation: part_of_dissertation
status: public
- id: '8139'
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: Martin
full_name: Loose, Martin
id: 462D4284-F248-11E8-B48F-1D18A9856A87
last_name: Loose
orcid: 0000-0001-7309-9724
title: Mechanism of clathrin-coated vesicle formation during endocytosis in plants
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: '2023'
...
---
_id: '12897'
abstract:
- lang: eng
text: "Inverse design problems in fabrication-aware shape optimization are typically
solved on discrete representations such as polygonal meshes. This thesis argues
that there are benefits to treating these problems in the same domain as human
designers, namely, the parametric one. One reason is that discretizing a parametric
model usually removes the capability of making further manual changes to the design,
because the human intent is captured by the shape parameters. Beyond this, knowledge
about a design problem can sometimes reveal a structure that is present in a smooth
representation, but is fundamentally altered by discretizing. In this case, working
in the parametric domain may even simplify the optimization task. We present two
lines of research that explore both of these aspects of fabrication-aware shape
optimization on parametric representations.\r\n\r\nThe first project studies the
design of plane elastic curves and Kirchhoff rods, which are common mathematical
models for describing the deformation of thin elastic rods such as beams, ribbons,
cables, and hair. Our main contribution is a characterization of all curved shapes
that can be attained by bending and twisting elastic rods having a stiffness that
is allowed to vary across the length. Elements like these can be manufactured
using digital fabrication devices such as 3d printers and digital cutters, and
have applications in free-form architecture and soft robotics.\r\n\r\nWe show
that the family of curved shapes that can be produced this way admits geometric
description that is concise and computationally convenient. In the case of plane
curves, the geometric description is intuitive enough to allow a designer to determine
whether a curved shape is physically achievable by visual inspection alone. We
also present shape optimization algorithms that convert a user-defined curve in
the plane or in three dimensions into the geometry of an elastic rod that will
naturally deform to follow this curve when its endpoints are attached to a support
structure. Implemented in an interactive software design tool, the rod geometry
is generated in real time as the user edits a curve and enables fast prototyping.
\r\n\r\nThe second project tackles the problem of general-purpose shape optimization
on CAD models using a novel variant of the extended finite element method (XFEM).
Our goal is the decoupling between the simulation mesh and the CAD model, so no
geometry-dependent meshing or remeshing needs to be performed when the CAD parameters
change during optimization. This is achieved by discretizing the embedding space
of the CAD model, and using a new high-accuracy numerical integration method to
enable XFEM on free-form elements bounded by the parametric surface patches of
the model. Our simulation is differentiable from the CAD parameters to the simulation
output, which enables us to use off-the-shelf gradient-based optimization procedures.
The result is a method that fits seamlessly into the CAD workflow because it works
on the same representation as the designer, enabling the alternation of manual
editing and fabrication-aware optimization at will."
acknowledged_ssus:
- _id: M-Shop
alternative_title:
- ISTA Thesis
article_processing_charge: No
author:
- first_name: Christian
full_name: Hafner, Christian
id: 400429CC-F248-11E8-B48F-1D18A9856A87
last_name: Hafner
citation:
ama: 'Hafner C. Inverse shape design with parametric representations: Kirchhoff
Rods and parametric surface models. 2023. doi:10.15479/at:ista:12897'
apa: 'Hafner, C. (2023). Inverse shape design with parametric representations:
Kirchhoff Rods and parametric surface models. Institute of Science and Technology
Austria. https://doi.org/10.15479/at:ista:12897'
chicago: 'Hafner, Christian. “Inverse Shape Design with Parametric Representations:
Kirchhoff Rods and Parametric Surface Models.” Institute of Science and Technology
Austria, 2023. https://doi.org/10.15479/at:ista:12897.'
ieee: 'C. Hafner, “Inverse shape design with parametric representations: Kirchhoff
Rods and parametric surface models,” Institute of Science and Technology Austria,
2023.'
ista: 'Hafner C. 2023. Inverse shape design with parametric representations: Kirchhoff
Rods and parametric surface models. Institute of Science and Technology Austria.'
mla: 'Hafner, Christian. Inverse Shape Design with Parametric Representations:
Kirchhoff Rods and Parametric Surface Models. Institute of Science and Technology
Austria, 2023, doi:10.15479/at:ista:12897.'
short: 'C. Hafner, Inverse Shape Design with Parametric Representations: Kirchhoff
Rods and Parametric Surface Models, Institute of Science and Technology Austria,
2023.'
date_created: 2023-05-05T10:40:14Z
date_published: 2023-05-05T00:00:00Z
date_updated: 2024-01-29T10:47:51Z
day: '05'
ddc:
- '516'
- '004'
- '518'
- '531'
degree_awarded: PhD
department:
- _id: GradSch
- _id: BeBi
doi: 10.15479/at:ista:12897
ec_funded: 1
file:
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checksum: cc2094e92fa27000b70eb4bfb76d6b5a
content_type: application/pdf
creator: chafner
date_created: 2023-05-11T10:43:20Z
date_updated: 2023-12-08T23:30:04Z
embargo: 2023-12-07
file_id: '12942'
file_name: thesis-hafner-2023may11-a2b.pdf
file_size: 50714445
relation: main_file
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checksum: a6b51334be2b81672357b1549afab40c
content_type: application/pdf
creator: chafner
date_created: 2023-05-11T10:43:44Z
date_updated: 2023-12-08T23:30:04Z
embargo_to: open_access
file_id: '12943'
file_name: thesis-release-form.pdf
file_size: 265319
relation: source_file
file_date_updated: 2023-12-08T23:30:04Z
has_accepted_license: '1'
language:
- iso: eng
month: '05'
oa: 1
oa_version: Published Version
page: '180'
project:
- _id: 24F9549A-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '715767'
name: 'MATERIALIZABLE: Intelligent fabrication-oriented Computational Design and
Modeling'
publication_identifier:
isbn:
- 978-3-99078-031-2
issn:
- 2663-337X
publication_status: published
publisher: Institute of Science and Technology Austria
related_material:
record:
- id: '9817'
relation: part_of_dissertation
status: public
- id: '7117'
relation: part_of_dissertation
status: public
- id: '13188'
relation: dissertation_contains
status: public
status: public
supervisor:
- first_name: Bernd
full_name: Bickel, Bernd
id: 49876194-F248-11E8-B48F-1D18A9856A87
last_name: Bickel
orcid: 0000-0001-6511-9385
title: 'Inverse shape design with parametric representations: Kirchhoff Rods and parametric
surface models'
type: dissertation
user_id: 400429CC-F248-11E8-B48F-1D18A9856A87
year: '2023'
...
---
_id: '12072'
abstract:
- lang: eng
text: "In this thesis, we study two of the most important questions in Arithmetic
geometry: that of the existence and density of solutions to Diophantine equations.
In order for a Diophantine equation to have any solutions over the rational numbers,
it must have solutions everywhere locally, i.e., over R and over Qp for every
prime p. The converse, called the Hasse principle, is known to fail in general.
However, it is still a central question in Arithmetic geometry to determine for
which varieties the Hasse principle does hold. In this work, we establish the
Hasse principle for a wide new family of varieties of the form f(t) = NK/Q(x)
̸= 0, where f is a polynomial with integer coefficients and NK/Q denotes the norm\r\nform
associated to a number field K. Our results cover products of arbitrarily many
linear, quadratic or cubic factors, and generalise an argument of Irving [69],
which makes use of the beta sieve of Rosser and Iwaniec. We also demonstrate how
our main sieve results can be applied to treat new cases of a conjecture of Harpaz
and Wittenberg on locally split values of polynomials over number fields, and
discuss consequences for rational points in fibrations.\r\nIn the second question,
about the density of solutions, one defines a height function and seeks to estimate
asymptotically the number of points of height bounded by B as B → ∞. Traditionally,
one either counts rational points, or\r\nintegral points with respect to a suitable
model. However, in this thesis, we study an emerging area of interest in Arithmetic
geometry known as Campana points, which in some sense interpolate between rational
and integral points.\r\nMore precisely, we count the number of nonzero integers
z1, z2, z3 such that gcd(z1, z2, z3) = 1, and z1, z2, z3, z1 + z2 + z3 are all
squareful and bounded by B. Using the circle method, we obtain an asymptotic formula
which agrees in\r\nthe power of B and log B with a bold new generalisation of
Manin’s conjecture to the setting of Campana points, recently formulated by Pieropan,
Smeets, Tanimoto and Várilly-Alvarado [96]. However, in this thesis we also provide
the first known counterexamples to leading constant predicted by their conjecture. "
acknowledgement: I acknowledge the received funding from the European Union’s Horizon
2020 research and innovation programme under the Marie Sklodowska Curie Grant Agreement
No. 665385.
alternative_title:
- ISTA Thesis
article_processing_charge: No
author:
- first_name: Alec L
full_name: Shute, Alec L
id: 440EB050-F248-11E8-B48F-1D18A9856A87
last_name: Shute
orcid: 0000-0002-1812-2810
citation:
ama: 'Shute AL. Existence and density problems in Diophantine geometry: From norm
forms to Campana points. 2022. doi:10.15479/at:ista:12072'
apa: 'Shute, A. L. (2022). Existence and density problems in Diophantine geometry:
From norm forms to Campana points. Institute of Science and Technology Austria.
https://doi.org/10.15479/at:ista:12072'
chicago: 'Shute, Alec L. “Existence and Density Problems in Diophantine Geometry:
From Norm Forms to Campana Points.” Institute of Science and Technology Austria,
2022. https://doi.org/10.15479/at:ista:12072.'
ieee: 'A. L. Shute, “Existence and density problems in Diophantine geometry: From
norm forms to Campana points,” Institute of Science and Technology Austria, 2022.'
ista: 'Shute AL. 2022. Existence and density problems in Diophantine geometry: From
norm forms to Campana points. Institute of Science and Technology Austria.'
mla: 'Shute, Alec L. Existence and Density Problems in Diophantine Geometry:
From Norm Forms to Campana Points. Institute of Science and Technology Austria,
2022, doi:10.15479/at:ista:12072.'
short: 'A.L. Shute, Existence and Density Problems in Diophantine Geometry: From
Norm Forms to Campana Points, Institute of Science and Technology Austria, 2022.'
date_created: 2022-09-08T21:53:03Z
date_published: 2022-09-08T00:00:00Z
date_updated: 2023-02-21T16:37:35Z
day: '08'
ddc:
- '512'
degree_awarded: PhD
department:
- _id: GradSch
- _id: TiBr
doi: 10.15479/at:ista:12072
ec_funded: 1
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language:
- iso: eng
month: '09'
oa: 1
oa_version: Published Version
page: '208'
project:
- _id: 2564DBCA-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '665385'
name: International IST Doctoral Program
publication_identifier:
isbn:
- 978-3-99078-023-7
issn:
- 2663-337X
publication_status: published
publisher: Institute of Science and Technology Austria
related_material:
record:
- id: '12076'
relation: part_of_dissertation
status: public
- id: '12077'
relation: part_of_dissertation
status: public
status: public
supervisor:
- first_name: Timothy D
full_name: Browning, Timothy D
id: 35827D50-F248-11E8-B48F-1D18A9856A87
last_name: Browning
orcid: 0000-0002-8314-0177
title: 'Existence and density problems in Diophantine geometry: From norm forms to
Campana points'
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: 2DF688A6-F248-11E8-B48F-1D18A9856A87
year: '2022'
...
---
_id: '11777'
abstract:
- lang: eng
text: "In this dissertation we study coboundary expansion of simplicial complex
with a view of giving geometric applications.\r\nOur main novel tool is an equivariant
version of Gromov's celebrated Topological Overlap Theorem. The equivariant topological
overlap theorem leads to various geometric applications including a quantitative
non-embeddability result for sufficiently thick buildings (which partially resolves
a conjecture of Tancer and Vorwerk) and an improved lower bound on the pair-crossing
number of (bounded degree) expander graphs. Additionally, we will give new proofs
for several known lower bounds for geometric problems such as the number of Tverberg
partitions or the crossing number of complete bipartite graphs.\r\nFor the aforementioned
applications one is naturally lead to study expansion properties of joins of simplicial
complexes. In the presence of a special certificate for expansion (as it is the
case, e.g., for spherical buildings), the join of two expanders is an expander.
On the flip-side, we report quite some evidence that coboundary expansion exhibits
very non-product-like behaviour under taking joins. For instance, we exhibit infinite
families of graphs $(G_n)_{n\\in \\mathbb{N}}$ and $(H_n)_{n\\in\\mathbb{N}}$
whose join $G_n*H_n$ has expansion of lower order than the product of the expansion
constant of the graphs. Moreover, we show an upper bound of $(d+1)/2^d$ on the
normalized coboundary expansion constants for the complete multipartite complex
$[n]^{*(d+1)}$ (under a mild divisibility condition on $n$).\r\nVia the probabilistic
method the latter result extends to an upper bound of $(d+1)/2^d+\\varepsilon$
on the coboundary expansion constant of the spherical building associated with
$\\mathrm{PGL}_{d+2}(\\mathbb{F}_q)$ for any $\\varepsilon>0$ and sufficiently
large $q=q(\\varepsilon)$. This disproves a conjecture of Lubotzky, Meshulam and
Mozes -- in a rather strong sense.\r\nBy improving on existing lower bounds we
make further progress towards closing the gap between the known lower and upper
bounds on the coboundary expansion constants of $[n]^{*(d+1)}$. The best improvements
we achieve using computer-aided proofs and flag algebras. The exact value even
for the complete $3$-partite $2$-dimensional complex $[n]^{*3}$ remains unknown
but we are happy to conjecture a precise value for every $n$. %Moreover, we show
that a previously shown lower bound on the expansion constant of the spherical
building associated with $\\mathrm{PGL}_{2}(\\mathbb{F}_q)$ is not tight.\r\nIn
a loosely structured, last chapter of this thesis we collect further smaller observations
related to expansion. We point out a link between discrete Morse theory and a
technique for showing coboundary expansion, elaborate a bit on the hardness of
computing coboundary expansion constants, propose a new criterion for coboundary
expansion (in a very dense setting) and give one way of making the folklore result
that expansion of links is a necessary condition for a simplicial complex to be
an expander precise."
alternative_title:
- ISTA Thesis
article_processing_charge: No
author:
- first_name: Pascal
full_name: Wild, Pascal
id: 4C20D868-F248-11E8-B48F-1D18A9856A87
last_name: Wild
citation:
ama: Wild P. High-dimensional expansion and crossing numbers of simplicial complexes.
2022. doi:10.15479/at:ista:11777
apa: Wild, P. (2022). High-dimensional expansion and crossing numbers of simplicial
complexes. Institute of Science and Technology. https://doi.org/10.15479/at:ista:11777
chicago: Wild, Pascal. “High-Dimensional Expansion and Crossing Numbers of Simplicial
Complexes.” Institute of Science and Technology, 2022. https://doi.org/10.15479/at:ista:11777.
ieee: P. Wild, “High-dimensional expansion and crossing numbers of simplicial complexes,”
Institute of Science and Technology, 2022.
ista: Wild P. 2022. High-dimensional expansion and crossing numbers of simplicial
complexes. Institute of Science and Technology.
mla: Wild, Pascal. High-Dimensional Expansion and Crossing Numbers of Simplicial
Complexes. Institute of Science and Technology, 2022, doi:10.15479/at:ista:11777.
short: P. Wild, High-Dimensional Expansion and Crossing Numbers of Simplicial Complexes,
Institute of Science and Technology, 2022.
date_created: 2022-08-10T15:51:19Z
date_published: 2022-08-11T00:00:00Z
date_updated: 2023-06-22T09:56:36Z
day: '11'
ddc:
- '500'
- '516'
- '514'
degree_awarded: PhD
department:
- _id: GradSch
- _id: UlWa
doi: 10.15479/at:ista:11777
ec_funded: 1
file:
- access_level: open_access
checksum: f5f3af1fb7c8a24b71ddc88ad7f7c5b4
content_type: text/x-python
creator: pwild
date_created: 2022-08-10T15:34:04Z
date_updated: 2022-08-10T15:34:04Z
description: Code for computer-assisted proofs in Section 8.4.7 in Thesis
file_id: '11780'
file_name: flags.py
file_size: 16828
relation: supplementary_material
- access_level: open_access
checksum: 1f7c12dfe3bdaa9b147e4fbc3d34e3d5
content_type: text/x-c++src
creator: pwild
date_created: 2022-08-10T15:34:10Z
date_updated: 2022-08-10T15:34:10Z
description: Code for proof of Lemma 8.20 in Thesis
file_id: '11781'
file_name: lowerbound.cpp
file_size: 12226
relation: supplementary_material
- access_level: open_access
checksum: 4cf81455c49e5dec3b9b2e3980137eeb
content_type: text/x-python
creator: pwild
date_created: 2022-08-10T15:34:17Z
date_updated: 2022-08-10T15:34:17Z
description: Code for proof of Proposition 7.9 in Thesis
file_id: '11782'
file_name: upperbound.py
file_size: 3240
relation: supplementary_material
- access_level: open_access
checksum: 4e96575b10cbe4e0d0db2045b2847774
content_type: application/pdf
creator: pwild
date_created: 2022-08-11T16:08:33Z
date_updated: 2022-08-11T16:08:33Z
file_id: '11809'
file_name: finalthesisPascalWildPDFA.pdf
file_size: 5086282
relation: main_file
title: High-Dimensional Expansion and Crossing Numbers of Simplicial Complexes
- access_level: closed
checksum: 92d94842a1fb6dca5808448137573b2e
content_type: application/zip
creator: pwild
date_created: 2022-08-11T16:09:19Z
date_updated: 2022-08-11T16:09:19Z
file_id: '11810'
file_name: ThesisSubmission.zip
file_size: 18150068
relation: source_file
file_date_updated: 2022-08-11T16:09:19Z
has_accepted_license: '1'
language:
- iso: eng
month: '08'
oa: 1
oa_version: Published Version
page: '170'
project:
- _id: 2564DBCA-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '665385'
name: International IST Doctoral Program
publication_identifier:
isbn:
- 978-3-99078-021-3
issn:
- 2663-337X
publication_status: published
publisher: Institute of Science and Technology
status: public
supervisor:
- first_name: Uli
full_name: Wagner, Uli
id: 36690CA2-F248-11E8-B48F-1D18A9856A87
last_name: Wagner
orcid: 0000-0002-1494-0568
title: High-dimensional expansion and crossing numbers of simplicial complexes
type: dissertation
user_id: 8b945eb4-e2f2-11eb-945a-df72226e66a9
year: '2022'
...
---
_id: '11128'
abstract:
- lang: eng
text: "Although we often see studies focusing on simple or even discrete traits
in studies of colouration,\r\nthe variation of “appearance” phenotypes found in
nature is often more complex, continuous\r\nand high-dimensional. Therefore, we
developed automated methods suitable for large datasets\r\nof genomes and images,
striving to account for their complex nature, while minimising human\r\nbias.
We used these methods on a dataset of more than 20, 000 plant SNP genomes and\r\ncorresponding
fower images from a hybrid zone of two subspecies of Antirrhinum majus with\r\ndistinctly
coloured fowers to improve our understanding of the genetic nature of the fower\r\ncolour
in our study system.\r\nFirstly, we use the advantage of large numbers of genotyped
plants to estimate the haplotypes in\r\nthe main fower colour regulating region.
We study colour- and geography-related characteristics\r\nof the estimated haplotypes
and how they connect to their relatedness. We show discrepancies\r\nfrom the expected
fower colour distributions given the genotype and identify particular\r\nhaplotypes
leading to unexpected phenotypes. We also confrm a signifcant defcit of the\r\ndouble
recessive recombinant and quite surprisingly, we show that haplotypes of the most\r\nfrequent
parental type are much less variable than others.\r\nSecondly, we introduce our
pipeline capable of processing tens of thousands of full fower\r\nimages without
human interaction and summarising each image into a set of informative scores.\r\nWe
show the compatibility of these machine-measured fower colour scores with the
previously\r\nused manual scores and study impact of external efect on the resulting
scores. Finally, we use\r\nthe machine-measured fower colour scores to ft and
examine a phenotype cline across the\r\nhybrid zone in Planoles using full fower
images as opposed to discrete, manual scores and\r\ncompare it with the genotypic
cline."
acknowledged_ssus:
- _id: ScienComp
- _id: Bio
alternative_title:
- ISTA Thesis
article_processing_charge: No
author:
- first_name: Lenka
full_name: Matejovicova, Lenka
id: 2DFDEC72-F248-11E8-B48F-1D18A9856A87
last_name: Matejovicova
citation:
ama: Matejovicova L. Genetic basis of flower colour as a model for adaptive evolution.
2022. doi:10.15479/at:ista:11128
apa: Matejovicova, L. (2022). Genetic basis of flower colour as a model for adaptive
evolution. Institute of Science and Technology Austria. https://doi.org/10.15479/at:ista:11128
chicago: Matejovicova, Lenka. “Genetic Basis of Flower Colour as a Model for Adaptive
Evolution.” Institute of Science and Technology Austria, 2022. https://doi.org/10.15479/at:ista:11128.
ieee: L. Matejovicova, “Genetic basis of flower colour as a model for adaptive evolution,”
Institute of Science and Technology Austria, 2022.
ista: Matejovicova L. 2022. Genetic basis of flower colour as a model for adaptive
evolution. Institute of Science and Technology Austria.
mla: Matejovicova, Lenka. Genetic Basis of Flower Colour as a Model for Adaptive
Evolution. Institute of Science and Technology Austria, 2022, doi:10.15479/at:ista:11128.
short: L. Matejovicova, Genetic Basis of Flower Colour as a Model for Adaptive Evolution,
Institute of Science and Technology Austria, 2022.
date_created: 2022-04-07T08:19:54Z
date_published: 2022-04-06T00:00:00Z
date_updated: 2023-06-23T06:26:41Z
day: '06'
ddc:
- '576'
- '582'
degree_awarded: PhD
department:
- _id: GradSch
- _id: NiBa
doi: 10.15479/at:ista:11128
file:
- access_level: open_access
checksum: e9609bc4e8f8e20146fc1125fd4f1bf7
content_type: application/pdf
creator: cchlebak
date_created: 2022-04-07T08:11:34Z
date_updated: 2022-04-07T08:11:34Z
file_id: '11129'
file_name: LenkaPhD_Official_PDFA.pdf
file_size: 11906472
relation: main_file
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checksum: 99d67040432fd07a225643a212ee8588
content_type: application/x-zip-compressed
creator: cchlebak
date_created: 2022-04-07T08:11:51Z
date_updated: 2022-04-07T08:11:51Z
file_id: '11130'
file_name: LenkaPhD Official_source.zip
file_size: 23036766
relation: source_file
file_date_updated: 2022-04-07T08:11:51Z
has_accepted_license: '1'
language:
- iso: eng
month: '04'
oa: 1
oa_version: Published Version
page: '112'
publication_identifier:
isbn:
- 978-3-99078-016-9
issn:
- 2663-337X
publication_status: published
publisher: Institute of Science and Technology Austria
status: public
supervisor:
- first_name: Nicholas H
full_name: Barton, Nicholas H
id: 4880FE40-F248-11E8-B48F-1D18A9856A87
last_name: Barton
orcid: 0000-0002-8548-5240
title: Genetic basis of flower colour as a model for adaptive evolution
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: '11945'
abstract:
- lang: eng
text: "G protein-coupled receptors (GPCRs) respond to specific ligands and regulate
multiple processes ranging from cell growth and immune responses to neuronal signal
transmission. However, ligands for many GPCRs remain unknown, suffer from off-target
effects or have poor bioavailability. Additional challenges exist to dissect cell-type
specific responses when the same GPCR is expressed on several cell types within
the body. Here, we overcome these limitations by engineering DREADD-based GPCR
chimeras that selectively bind their agonist clozapine-N-oxide (CNO) and mimic
a GPCR-of-interest in a desired cell type.\r\nWe validated our approach with β2-adrenergic
receptor (β2AR/ADRB2) and show that our chimeric DREADD-β2AR triggers comparable
responses on second messenger and kinase activity, post-translational modifications,
and protein-protein interactions. Since β2AR is also enriched in microglia, which
can drive inflammation in the central nervous system, we expressed chimeric DREADD-β2AR
in primary microglia and successfully recapitulate β2AR-mediated filopodia formation
through CNO stimulation. To dissect the role of selected GPCRs during microglial
inflammation, we additionally generated DREADD-based chimeras for microglia-enriched
GPR65 and GPR109A/HCAR2. In a microglia cell line, DREADD-β2AR and DREADD-GPR65
both modulated the inflammatory response with a similar profile as endogenously
expressed β2AR, while DREADD-GPR109A showed no impact.\r\nOur DREADD-based approach
provides the means to obtain mechanistic and functional insights into GPCR signaling
on a cell-type specific level."
acknowledged_ssus:
- _id: Bio
- _id: PreCl
- _id: LifeSc
alternative_title:
- ISTA Thesis
article_processing_charge: No
author:
- first_name: Rouven
full_name: Schulz, Rouven
id: 4C5E7B96-F248-11E8-B48F-1D18A9856A87
last_name: Schulz
orcid: 0000-0001-5297-733X
citation:
ama: Schulz R. Chimeric G protein-coupled receptors mimic distinct signaling pathways
and modulate microglia function. 2022. doi:10.15479/at:ista:11945
apa: Schulz, R. (2022). Chimeric G protein-coupled receptors mimic distinct signaling
pathways and modulate microglia function. Institute of Science and Technology
Austria. https://doi.org/10.15479/at:ista:11945
chicago: Schulz, Rouven. “Chimeric G Protein-Coupled Receptors Mimic Distinct Signaling
Pathways and Modulate Microglia Function.” Institute of Science and Technology
Austria, 2022. https://doi.org/10.15479/at:ista:11945.
ieee: R. Schulz, “Chimeric G protein-coupled receptors mimic distinct signaling
pathways and modulate microglia function,” Institute of Science and Technology
Austria, 2022.
ista: Schulz R. 2022. Chimeric G protein-coupled receptors mimic distinct signaling
pathways and modulate microglia function. Institute of Science and Technology
Austria.
mla: Schulz, Rouven. Chimeric G Protein-Coupled Receptors Mimic Distinct Signaling
Pathways and Modulate Microglia Function. Institute of Science and Technology
Austria, 2022, doi:10.15479/at:ista:11945.
short: R. Schulz, Chimeric G Protein-Coupled Receptors Mimic Distinct Signaling
Pathways and Modulate Microglia Function, Institute of Science and Technology
Austria, 2022.
date_created: 2022-08-23T11:33:11Z
date_published: 2022-08-23T00:00:00Z
date_updated: 2023-08-03T13:02:26Z
day: '23'
ddc:
- '570'
degree_awarded: PhD
department:
- _id: GradSch
- _id: SaSi
doi: 10.15479/at:ista:11945
file:
- access_level: open_access
checksum: 61b1b666a210ff7cdd0e95ea75207a13
content_type: application/pdf
creator: rschulz
date_created: 2022-08-25T08:59:57Z
date_updated: 2022-08-25T08:59:57Z
file_id: '11970'
file_name: Thesis_Rouven_Schulz_2022_final.pdf
file_size: 28079331
relation: main_file
success: 1
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checksum: 2b8f95ea1c134dbdb927b41b1dbeeeb5
content_type: application/vnd.openxmlformats-officedocument.wordprocessingml.document
creator: rschulz
date_created: 2022-08-25T09:00:11Z
date_updated: 2022-08-25T09:33:31Z
file_id: '11971'
file_name: Thesis_Rouven_Schulz_2022_final.docx
file_size: 27226963
relation: source_file
file_date_updated: 2022-08-25T09:33:31Z
has_accepted_license: '1'
language:
- iso: eng
month: '08'
oa: 1
oa_version: Published Version
page: '133'
project:
- _id: 267F75D8-B435-11E9-9278-68D0E5697425
name: Modulating microglia through G protein-coupled receptor (GPCR) signaling
publication_identifier:
issn:
- 2663-337X
publication_status: published
publisher: Institute of Science and Technology Austria
related_material:
record:
- id: '11995'
relation: dissertation_contains
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: Chimeric G protein-coupled receptors mimic distinct signaling pathways and
modulate microglia function
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: '12390'
abstract:
- lang: eng
text: "The scope of this thesis is to study quantum systems exhibiting a continuous
symmetry that\r\nis broken on the level of the corresponding effective theory.
In particular we are going to\r\ninvestigate translation-invariant Bose gases
in the mean field limit, effectively described by\r\nthe Hartree functional, and
the Fröhlich Polaron in the regime of strong coupling, effectively\r\ndescribed
by the Pekar functional. The latter is a model describing the interaction between
a\r\ncharged particle and the optical modes of a polar crystal. Regarding the
former, we assume in\r\naddition that the particles in the gas are unconfined,
and typically we will consider particles\r\nthat are subject to an attractive
interaction. In both cases the ground state energy of the\r\nHamiltonian is not
a proper eigenvalue due to the underlying translation-invariance, while on\r\nthe
contrary there exists a whole invariant orbit of minimizers for the corresponding
effective\r\nfunctionals. Both, the absence of proper eigenstates and the broken
symmetry of the effective\r\ntheory, make the study significantly more involved
and it is the content of this thesis to\r\ndevelop a frameworks which allows for
a systematic way to circumvent these issues.\r\nIt is a well-established result
that the ground state energy of Bose gases in the mean field limit,\r\nas well
as the ground state energy of the Fröhlich Polaron in the regime of strong coupling,
is\r\nto leading order given by the minimal energy of the corresponding effective
theory. As part\r\nof this thesis we identify the sub-leading term in the expansion
of the ground state energy,\r\nwhich can be interpreted as the quantum correction
to the classical energy, since the effective\r\ntheories under consideration can
be seen as classical counterparts.\r\nWe are further going to establish an asymptotic
expression for the energy-momentum relation\r\nof the Fröhlich Polaron in the
strong coupling limit. In the regime of suitably small momenta,\r\nthis asymptotic
expression agrees with the energy-momentum relation of a free particle having\r\nan
effectively increased mass, and we find that this effectively increased mass agrees
with the\r\nconjectured value in the physics literature.\r\nIn addition we will
discuss two unrelated papers written by the author during his stay at ISTA\r\nin
the appendix. The first one concerns the realization of anyons, which are quasi-particles\r\nacquiring
a non-trivial phase under the exchange of two particles, as molecular impurities.\r\nThe
second one provides a classification of those vector fields defined on a given
manifold\r\nthat can be written as the gradient of a given functional with respect
to a suitable metric,\r\nprovided that some mild smoothness assumptions hold.
This classification is subsequently\r\nused to identify those quantum Markov semigroups
that can be written as a gradient flow of\r\nthe relative entropy.\r\n"
alternative_title:
- ISTA Thesis
article_processing_charge: No
author:
- first_name: Morris
full_name: Brooks, Morris
id: B7ECF9FC-AA38-11E9-AC9A-0930E6697425
last_name: Brooks
orcid: 0000-0002-6249-0928
citation:
ama: Brooks M. Translation-invariant quantum systems with effectively broken symmetry.
2022. doi:10.15479/at:ista:12390
apa: Brooks, M. (2022). Translation-invariant quantum systems with effectively
broken symmetry. Institute of Science and Technology Austria. https://doi.org/10.15479/at:ista:12390
chicago: Brooks, Morris. “Translation-Invariant Quantum Systems with Effectively
Broken Symmetry.” Institute of Science and Technology Austria, 2022. https://doi.org/10.15479/at:ista:12390.
ieee: M. Brooks, “Translation-invariant quantum systems with effectively broken
symmetry,” Institute of Science and Technology Austria, 2022.
ista: Brooks M. 2022. Translation-invariant quantum systems with effectively broken
symmetry. Institute of Science and Technology Austria.
mla: Brooks, Morris. Translation-Invariant Quantum Systems with Effectively Broken
Symmetry. Institute of Science and Technology Austria, 2022, doi:10.15479/at:ista:12390.
short: M. Brooks, Translation-Invariant Quantum Systems with Effectively Broken
Symmetry, Institute of Science and Technology Austria, 2022.
date_created: 2023-01-26T10:00:42Z
date_published: 2022-12-15T00:00:00Z
date_updated: 2023-08-07T13:32:09Z
day: '15'
ddc:
- '500'
degree_awarded: PhD
department:
- _id: GradSch
- _id: RoSe
doi: 10.15479/at:ista:12390
ec_funded: 1
file:
- access_level: open_access
checksum: b31460e937f33b557abb40ebef02b567
content_type: application/pdf
creator: cchlebak
date_created: 2023-01-26T10:02:34Z
date_updated: 2023-01-26T10:02:34Z
file_id: '12391'
file_name: Brooks_Thesis.pdf
file_size: 3095225
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success: 1
- access_level: closed
checksum: 9751869fa5e7981588ad4228f4fd4bd6
content_type: application/octet-stream
creator: cchlebak
date_created: 2023-01-26T10:02:42Z
date_updated: 2023-01-26T10:02:42Z
file_id: '12392'
file_name: Brooks_Thesis.tex
file_size: 809842
relation: source_file
file_date_updated: 2023-01-26T10:02:42Z
has_accepted_license: '1'
language:
- iso: eng
month: '12'
oa: 1
oa_version: Published Version
page: '196'
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: '9005'
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: Translation-invariant quantum systems with effectively broken symmetry
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: 8b945eb4-e2f2-11eb-945a-df72226e66a9
year: '2022'
...
---
_id: '12368'
abstract:
- lang: eng
text: "Metazoan development relies on the formation and remodeling of cell-cell
contacts. The \r\nbinding of adhesion receptors and remodeling of the actomyosin
cell cortex at cell-cell \r\ninteraction sites have been implicated in cell-cell
contact formation. Yet, how these two \r\nprocesses functionally interact to drive
cell-cell contact expansion and strengthening \r\nremains unclear. Here, we study
how primary germ layer progenitor cells from zebrafish \r\nbind to supported lipid
bilayers (SLB) functionalized with E-cadherin ectodomains as an \r\nassay system
for monitoring cell-cell contact formation at high spatiotemporal resolution.
\r\nWe show that cell-cell contact formation represents a two-tiered process:
E-cadherin\x02mediated downregulation of the small GTPase RhoA at the forming
contact leads to both \r\ndepletion of Myosin-2 and decrease of F-actin. This
is followed by centrifugal actin \r\nnetwork flows at the contact triggered by
a sharp gradient of Myosin-2 at the rim of the \r\ncontact zone, with Myosin-2
displaying higher cortical localization outside than inside of \r\nthe contact.
These centrifugal cortical actin flows, in turn, not only further dilute the actin
\r\nnetwork at the contact disc, but also lead to an accumulation of both F-actin
and E\x02cadherin at the contact rim. Eventually, this combination of actomyosin
downregulation \r\nand flows at the contact contribute to the characteristic molecular
organization implicated \r\nin contact formation and maintenance: depletion of
cortical actomyosin at the contact disc, \r\ndriving contact expansion by lowering
interfacial tension at the contact, and accumulation \r\nof both E-cadherin and
F-actin at the contact rim, mechanically linking the contractile \r\ncortices
of the adhering cells. Thus, using a biomimetic assay, we exemplify how \r\nadhesion
signaling and cell mechanics function together to modulate the spatial \r\norganization
of cell-cell contacts."
acknowledged_ssus:
- _id: LifeSc
- _id: Bio
- _id: NanoFab
alternative_title:
- ISTA Thesis
article_processing_charge: No
author:
- first_name: Feyza N
full_name: Arslan, Feyza N
id: 49DA7910-F248-11E8-B48F-1D18A9856A87
last_name: Arslan
orcid: 0000-0001-5809-9566
citation:
ama: Arslan FN. Remodeling of E-cadherin-mediated contacts via cortical flows.
2022. doi:10.15479/at:ista:12153
apa: Arslan, F. N. (2022). Remodeling of E-cadherin-mediated contacts via cortical
flows. Institute of Science and Technology Austria. https://doi.org/10.15479/at:ista:12153
chicago: Arslan, Feyza N. “Remodeling of E-Cadherin-Mediated Contacts via Cortical
Flows.” Institute of Science and Technology Austria, 2022. https://doi.org/10.15479/at:ista:12153.
ieee: F. N. Arslan, “Remodeling of E-cadherin-mediated contacts via cortical flows,”
Institute of Science and Technology Austria, 2022.
ista: Arslan FN. 2022. Remodeling of E-cadherin-mediated contacts via cortical
flows. Institute of Science and Technology Austria.
mla: Arslan, Feyza N. Remodeling of E-Cadherin-Mediated Contacts via Cortical
Flows. Institute of Science and Technology Austria, 2022, doi:10.15479/at:ista:12153.
short: F.N. Arslan, Remodeling of E-Cadherin-Mediated Contacts via Cortical Flows,
Institute of Science and Technology Austria, 2022.
date_created: 2023-01-25T10:43:24Z
date_published: 2022-09-29T00:00:00Z
date_updated: 2023-08-08T13:14:10Z
day: '29'
ddc:
- '570'
degree_awarded: PhD
department:
- _id: GradSch
- _id: CaHe
doi: 10.15479/at:ista:12153
ec_funded: 1
file:
- access_level: open_access
checksum: e54a3e69b83ebf166544164afd25608e
content_type: application/pdf
creator: cchlebak
date_created: 2023-01-25T10:52:46Z
date_updated: 2023-01-25T10:52:46Z
file_id: '12369'
file_name: THESIS_FINAL_FArslan_pdfa.pdf
file_size: 14581024
relation: main_file
success: 1
file_date_updated: 2023-01-25T10:52:46Z
has_accepted_license: '1'
language:
- iso: eng
month: '09'
oa: 1
oa_version: Published Version
page: '113'
project:
- _id: 260F1432-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '742573'
name: Interaction and feedback between cell mechanics and fate specification in
vertebrate gastrulation
publication_identifier:
isbn:
- ' 978-3-99078-025-1 '
issn:
- 2663-337X
publication_status: published
publisher: Institute of Science and Technology Austria
related_material:
record:
- id: '9350'
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: Remodeling of E-cadherin-mediated contacts via cortical 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: 2DF688A6-F248-11E8-B48F-1D18A9856A87
year: '2022'
...
---
_id: '11362'
abstract:
- lang: eng
text: "Deep learning has enabled breakthroughs in challenging computing problems
and has emerged as the standard problem-solving tool for computer vision and natural
language processing tasks.\r\nOne exception to this trend is safety-critical tasks
where robustness and resilience requirements contradict the black-box nature of
neural networks. \r\nTo deploy deep learning methods for these tasks, it is vital
to provide guarantees on neural network agents' safety and robustness criteria.
\r\nThis can be achieved by developing formal verification methods to verify the
safety and robustness properties of neural networks.\r\n\r\nOur goal is to design,
develop and assess safety verification methods for neural networks to improve
their reliability and trustworthiness in real-world applications.\r\nThis thesis
establishes techniques for the verification of compressed and adversarially trained
models as well as the design of novel neural networks for verifiably safe decision-making.\r\n\r\nFirst,
we establish the problem of verifying quantized neural networks. Quantization
is a technique that trades numerical precision for the computational efficiency
of running a neural network and is widely adopted in industry.\r\nWe show that
neglecting the reduced precision when verifying a neural network can lead to wrong
conclusions about the robustness and safety of the network, highlighting that
novel techniques for quantized network verification are necessary. We introduce
several bit-exact verification methods explicitly designed for quantized neural
networks and experimentally confirm on realistic networks that the network's robustness
and other formal properties are affected by the quantization.\r\n\r\nFurthermore,
we perform a case study providing evidence that adversarial training, a standard
technique for making neural networks more robust, has detrimental effects on the
network's performance. This robustness-accuracy tradeoff has been studied before
regarding the accuracy obtained on classification datasets where each data point
is independent of all other data points. On the other hand, we investigate the
tradeoff empirically in robot learning settings where a both, a high accuracy
and a high robustness, are desirable.\r\nOur results suggest that the negative
side-effects of adversarial training outweigh its robustness benefits in practice.\r\n\r\nFinally,
we consider the problem of verifying safety when running a Bayesian neural network
policy in a feedback loop with systems over the infinite time horizon. Bayesian
neural networks are probabilistic models for learning uncertainties in the data
and are therefore often used on robotic and healthcare applications where data
is inherently stochastic.\r\nWe introduce a method for recalibrating Bayesian
neural networks so that they yield probability distributions over safe decisions
only.\r\nOur method learns a safety certificate that guarantees safety over the
infinite time horizon to determine which decisions are safe in every possible
state of the system.\r\nWe demonstrate the effectiveness of our approach on a
series of reinforcement learning benchmarks."
alternative_title:
- ISTA Thesis
article_processing_charge: No
author:
- first_name: Mathias
full_name: Lechner, Mathias
id: 3DC22916-F248-11E8-B48F-1D18A9856A87
last_name: Lechner
citation:
ama: Lechner M. Learning verifiable representations. 2022. doi:10.15479/at:ista:11362
apa: Lechner, M. (2022). Learning verifiable representations. Institute of
Science and Technology Austria. https://doi.org/10.15479/at:ista:11362
chicago: Lechner, Mathias. “Learning Verifiable Representations.” Institute of Science
and Technology Austria, 2022. https://doi.org/10.15479/at:ista:11362.
ieee: M. Lechner, “Learning verifiable representations,” Institute of Science and
Technology Austria, 2022.
ista: Lechner M. 2022. Learning verifiable representations. Institute of Science
and Technology Austria.
mla: Lechner, Mathias. Learning Verifiable Representations. Institute of
Science and Technology Austria, 2022, doi:10.15479/at:ista:11362.
short: M. Lechner, Learning Verifiable Representations, Institute of Science and
Technology Austria, 2022.
date_created: 2022-05-12T07:14:01Z
date_published: 2022-05-12T00:00:00Z
date_updated: 2023-08-17T06:58:38Z
day: '12'
ddc:
- '004'
degree_awarded: PhD
department:
- _id: GradSch
- _id: ToHe
doi: 10.15479/at:ista:11362
ec_funded: 1
file:
- access_level: closed
checksum: 8eefa9c7c10ca7e1a2ccdd731962a645
content_type: application/zip
creator: mlechner
date_created: 2022-05-13T12:33:26Z
date_updated: 2022-05-13T12:49:00Z
file_id: '11378'
file_name: src.zip
file_size: 13210143
relation: source_file
- access_level: open_access
checksum: 1b9e1e5a9a83ed9d89dad2f5133dc026
content_type: application/pdf
creator: mlechner
date_created: 2022-05-16T08:02:28Z
date_updated: 2022-05-17T15:19:39Z
file_id: '11382'
file_name: thesis_main-a2.pdf
file_size: 2732536
relation: main_file
file_date_updated: 2022-05-17T15:19:39Z
has_accepted_license: '1'
keyword:
- neural networks
- verification
- machine learning
language:
- iso: eng
license: https://creativecommons.org/licenses/by-nd/4.0/
month: '05'
oa: 1
oa_version: Published Version
page: '124'
project:
- _id: 25F42A32-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: Z211
name: The Wittgenstein Prize
- _id: 62781420-2b32-11ec-9570-8d9b63373d4d
call_identifier: H2020
grant_number: '101020093'
name: Vigilant Algorithmic Monitoring of Software
publication_identifier:
isbn:
- 978-3-99078-017-6
publication_status: published
publisher: Institute of Science and Technology Austria
related_material:
record:
- id: '10665'
relation: part_of_dissertation
status: public
- id: '10667'
relation: part_of_dissertation
status: public
- id: '11366'
relation: part_of_dissertation
status: public
- id: '7808'
relation: part_of_dissertation
status: public
- id: '10666'
relation: part_of_dissertation
status: public
status: public
supervisor:
- first_name: Thomas A
full_name: Henzinger, Thomas A
id: 40876CD8-F248-11E8-B48F-1D18A9856A87
last_name: Henzinger
orcid: 0000-0002-2985-7724
title: Learning verifiable representations
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: 8b945eb4-e2f2-11eb-945a-df72226e66a9
year: '2022'
...
---
_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
file:
- access_level: open_access
checksum: 7970714a20a6052f75fb27a6c3e9976e
content_type: application/pdf
creator: kmysliwy
date_created: 2022-07-05T08:12:56Z
date_updated: 2022-07-05T08:12:56Z
file_id: '11486'
file_name: thes1_no_isbn_2_1b.pdf
file_size: 1830973
relation: main_file
success: 1
- access_level: closed
checksum: 647a2011fdf56277096c9350fefe1097
content_type: application/zip
creator: kmysliwy
date_created: 2022-07-05T08:15:52Z
date_updated: 2022-07-05T08:17:12Z
file_id: '11487'
file_name: thes_source.zip
file_size: 5831060
relation: source_file
file_date_updated: 2022-07-05T08:17:12Z
has_accepted_license: '1'
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:
record:
- id: '10564'
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
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file_size: 22841103
relation: source_file
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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:
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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:
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date_created: 2022-07-25T09:09:32Z
date_updated: 2022-07-25T09:39:58Z
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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
content_type: application/pdf
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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file_size: 104497530
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creator: cchlebak
date_created: 2023-02-02T09:33:37Z
date_updated: 2023-02-02T09:33:37Z
description: This version of the thesis uses stronger image compression for a smaller
file size of 23MB.
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language:
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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:
record:
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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
file:
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checksum: 0fc54ad1eaede879c665ac9b53c93e22
content_type: application/zip
creator: wrzadkow
date_created: 2022-02-21T13:58:16Z
date_updated: 2022-02-22T07:20:12Z
file_id: '10785'
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file_size: 17668233
relation: source_file
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checksum: 22d2d7af37ca31f6b1730c26cac7bced
content_type: application/pdf
creator: wrzadkow
date_created: 2022-02-21T14:02:54Z
date_updated: 2022-02-21T14:02:54Z
file_id: '10786'
file_name: Rzadkowski_thesis_final.pdf
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relation: main_file
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has_accepted_license: '1'
language:
- iso: eng
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:
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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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date_created: 2022-04-20T14:21:56Z
date_updated: 2023-04-20T22:30:03Z
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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
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call_identifier: FWF
grant_number: W01205
name: Zellkommunikation in Gesundheit und Krankheit
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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
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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:
- access_level: open_access
checksum: a2c2fdc28002538840490bfa6a08b2cb
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date_created: 2022-08-17T12:08:49Z
date_updated: 2023-09-09T22:30:03Z
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date_created: 2022-08-17T12:08:59Z
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file_id: '11908'
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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
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date_created: 2022-05-17T12:09:25Z
date_updated: 2023-05-17T22:30:03Z
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file_size: 4351981
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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:
- access_level: closed
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_id: '11935'
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file_size: 13515457
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creator: mnardin
date_created: 2022-08-22T09:43:50Z
date_updated: 2023-06-20T22:30:04Z
embargo: 2023-06-19
file_id: '11941'
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
- access_level: open_access
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:
- access_level: open_access
checksum: 4d75e6a619df7e8a9d6e840aee182380
content_type: application/pdf
creator: sbelohla
date_created: 2022-05-19T13:03:13Z
date_updated: 2023-05-20T22:30:03Z
embargo: 2023-05-19
file_id: '11398'
file_name: thesis_sb_final_pdfa.pdf
file_size: 8247240
relation: main_file
- access_level: closed
checksum: 7a5d8b6dd0ca00784f860075b0a7d8f0
content_type: application/x-zip-compressed
creator: sbelohla
date_created: 2022-05-19T13:07:47Z
date_updated: 2023-05-20T22:30:03Z
embargo_to: open_access
file_id: '11399'
file_name: thesis_sb_final.zip
file_size: 7094
relation: source_file
file_date_updated: 2023-05-20T22:30:03Z
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
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date_created: 2023-01-26T12:00:10Z
date_updated: 2023-12-21T23:30:03Z
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file_name: Source Files - Saren Tasciyan - PhD Thesis.zip
file_size: 261256696
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has_accepted_license: '1'
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
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date_updated: 2023-04-21T22:30:03Z
embargo: 2023-04-20
file_id: '11195'
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file_size: 8820951
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date_updated: 2023-04-21T22:30:03Z
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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:
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date_created: 2023-01-24T13:15:45Z
date_updated: 2023-09-20T22:30:03Z
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date_created: 2023-02-02T09:15:35Z
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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
day: '01'
ddc:
- '006'
- '514'
- '516'
degree_awarded: PhD
department:
- _id: HeEd
- _id: GradSch
doi: 10.15479/AT:ISTA:9056
file:
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content_type: application/zip
creator: patrickd
date_created: 2021-02-02T14:09:25Z
date_updated: 2021-02-03T10:37:28Z
file_id: '9063'
file_name: thesis_source.zip
file_size: 13446994
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creator: patrickd
date_created: 2021-02-02T14:09:18Z
date_updated: 2021-02-02T14:09:18Z
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file_name: thesis_pdfA2b.pdf
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file_date_updated: 2021-02-03T10:37:28Z
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language:
- iso: eng
month: '02'
oa: 1
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
file:
- access_level: open_access
checksum: 5a93658a5f19478372523ee232887e2b
content_type: application/pdf
creator: gcipollo
date_created: 2021-01-25T14:19:03Z
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language:
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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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- iso: eng
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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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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:
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- id: '9792'
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status: public
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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
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date_updated: 2021-09-06T08:39:47Z
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file_size: 17592425
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has_accepted_license: '1'
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:
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status: public
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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
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date_updated: 2022-03-10T12:10:25Z
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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
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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_name: 2021_Piankov_combined.pdf
file_size: 484965
relation: main_file
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:
- access_level: open_access
checksum: 4f0abe64114cfed264f9d36e8d1197e3
content_type: application/pdf
creator: bphuong
date_created: 2021-05-24T11:22:29Z
date_updated: 2021-05-24T11:22:29Z
file_id: '9419'
file_name: mph-thesis-v519-pdfimages.pdf
file_size: 2673905
relation: main_file
success: 1
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checksum: f5699e876bc770a9b0df8345a77720a2
content_type: application/zip
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:
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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
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date_updated: 2021-11-08T14:12:22Z
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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
day: '09'
ddc:
- '000'
degree_awarded: PhD
department:
- _id: GradSch
- _id: DaAl
doi: 10.15479/at:ista:10429
ec_funded: 1
file:
- access_level: open_access
checksum: 6bf14e9a523387328f016c0689f5e10e
content_type: application/pdf
creator: gnadirad
date_created: 2021-12-09T17:47:49Z
date_updated: 2021-12-09T17:47:49Z
file_id: '10436'
file_name: Thesis_Final_09_12_2021.pdf
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relation: main_file
success: 1
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checksum: 914d6c5ca86bd0add471971a8f4c4341
content_type: application/zip
creator: gnadirad
date_created: 2021-12-09T17:47:49Z
date_updated: 2022-03-28T12:55:12Z
file_id: '10437'
file_name: Thesis_Final_09_12_2021.zip
file_size: 2596924
relation: source_file
file_date_updated: 2022-03-28T12:55:12Z
has_accepted_license: '1'
language:
- iso: eng
month: '12'
oa: 1
oa_version: Published Version
page: '132'
project:
- _id: 268A44D6-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '805223'
name: Elastic Coordination for Scalable Machine Learning
publication_identifier:
issn:
- 2663-337X
publication_status: published
publisher: Institute of Science and Technology Austria
related_material:
record:
- id: '10432'
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
file:
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checksum: e88bb8ca43948abe060eb2d2fa719881
content_type: application/pdf
creator: dfelicia
date_created: 2021-08-19T14:03:48Z
date_updated: 2021-09-06T09:28:56Z
file_id: '9944'
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file_size: 1958710
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checksum: 72810843abee83705853505b3f8348aa
content_type: application/octet-stream
creator: dfelicia
date_created: 2021-08-19T14:06:35Z
date_updated: 2022-03-10T12:13:57Z
file_id: '9945'
file_name: thesis.7z
file_size: 3771669
relation: source_file
file_date_updated: 2022-03-10T12:13:57Z
has_accepted_license: '1'
language:
- iso: eng
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
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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:
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degree_awarded: PhD
department:
- _id: GradSch
- _id: JiFr
doi: 10.15479/at:ista:9992
ec_funded: 1
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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
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short: CC BY-NC-ND (4.0)
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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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has_accepted_license: '1'
language:
- iso: eng
month: '07'
oa: 1
oa_version: Published Version
page: '111'
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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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
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checksum: ad6bcb24083ed7c02baaf1885c9ea3d5
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date_created: 2021-09-30T14:29:14Z
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content_type: application/pdf
creator: djirovec
date_created: 2021-10-05T07:56:49Z
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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- id: '10065'
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
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image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
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type: dissertation
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
year: '2021'
...