---
OA_place: publisher
_id: '20964'
acknowledged_ssus:
- _id: LifeSc
- _id: Bio
alternative_title:
- ISTA Master’s Thesis
article_processing_charge: No
author:
- first_name: Dmitrii
full_name: Vladimirtsev, Dmitrii
id: 60466724-5355-11ee-ae5a-fa55e8f99c3d
last_name: Vladimirtsev
citation:
ama: Vladimirtsev D. Armadillo repeat only proteins are master regulators of plant
cyclic-nucleotide gated channels. 2026. doi:10.15479/AT-ISTA-20964
apa: Vladimirtsev, D. (2026). Armadillo repeat only proteins are master regulators
of plant cyclic-nucleotide gated channels. Institute of Science and Technology
Austria. https://doi.org/10.15479/AT-ISTA-20964
chicago: Vladimirtsev, Dmitrii. “Armadillo Repeat Only Proteins Are Master Regulators
of Plant Cyclic-Nucleotide Gated Channels.” Institute of Science and Technology
Austria, 2026. https://doi.org/10.15479/AT-ISTA-20964.
ieee: D. Vladimirtsev, “Armadillo repeat only proteins are master regulators of
plant cyclic-nucleotide gated channels,” Institute of Science and Technology Austria,
2026.
ista: Vladimirtsev D. 2026. Armadillo repeat only proteins are master regulators
of plant cyclic-nucleotide gated channels. Institute of Science and Technology
Austria.
mla: Vladimirtsev, Dmitrii. Armadillo Repeat Only Proteins Are Master Regulators
of Plant Cyclic-Nucleotide Gated Channels. Institute of Science and Technology
Austria, 2026, doi:10.15479/AT-ISTA-20964.
short: D. Vladimirtsev, Armadillo Repeat Only Proteins Are Master Regulators of
Plant Cyclic-Nucleotide Gated Channels, Institute of Science and Technology Austria,
2026.
corr_author: '1'
date_created: 2026-01-09T09:22:48Z
date_published: 2026-01-14T00:00:00Z
date_updated: 2026-04-07T11:41:44Z
day: '14'
ddc:
- '570'
degree_awarded: MS
department:
- _id: GradSch
- _id: JiFr
doi: 10.15479/AT-ISTA-20964
file:
- access_level: closed
checksum: 812857b2fbe3f6113bef22fd04bccd3e
content_type: application/pdf
creator: dvladimi
date_created: 2026-01-21T14:12:13Z
date_updated: 2026-01-21T14:12:13Z
embargo: 2027-01-01
embargo_to: open_access
file_id: '21033'
file_name: 2026_Vladimirtsev_Dmitrii_Thesis.pdf
file_size: 2867531
relation: main_file
- access_level: closed
checksum: 2b969f97f8d7461bea3d255f48c2219c
content_type: application/x-zip-compressed
creator: dvladimi
date_created: 2026-01-21T14:41:58Z
date_updated: 2026-01-28T12:38:19Z
file_id: '21034'
file_name: Source Files.zip
file_size: 25023066
relation: source_file
file_date_updated: 2026-01-28T12:38:19Z
has_accepted_license: '1'
language:
- iso: eng
month: '01'
oa_version: Published Version
page: '22'
project:
- _id: 8f347782-16d5-11f0-9cad-8c19706ee739
grant_number: '101142681'
name: Cyclic nucleotides as second messengers in plants
publication_identifier:
issn:
- 2791-4585
publication_status: published
publisher: Institute of Science and Technology Austria
related_material:
record:
- id: '20982'
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: Armadillo repeat only proteins are master regulators of plant cyclic-nucleotide
gated channels
type: dissertation
user_id: ba8df636-2132-11f1-aed0-ed93e2281fdd
year: '2026'
...
---
OA_place: repository
_id: '21401'
abstract:
- lang: eng
text: "Runtime verification offers scalable solutions to improve the safety and
reliability of systems. However, systems that require verification or monitoring
by a third party to ensure compliance with a specification might contain sensitive
information, causing privacy concerns when usual runtime verification approaches
are used. Privacy is compromised if protected information about the system, or
sensitive data that is processed by the system, is revealed. In addition, revealing
the specification being monitored may undermine the essence of third-party verification.\r\n\r\nIn
this thesis, we propose a protocol for privacy-preserving runtime verification
of systems against formal sequential specifications. We develop the protocol in
two steps. In the first step, the monitor verifies whether the system satisfies
the specification without learning anything else, though both parties are aware
of the specification. In the second step, we extend the protocol to ensure that
the system remains oblivious to the monitored specification, while the monitor
learns only whether the system satisfies the specification and nothing more. Our
protocol adapts and improves existing techniques used in cryptography, and more
specifically, multi-party computation.\r\n\r\nThe sequential specification defines
the observation step of the monitor, whose granularity depends on the situation
(e.g., banks may be monitored on a daily basis). Our protocol exchanges a single
message per observation step, after an initialization phase. This design minimizes
communication overhead, enabling relatively lightweight privacy-preserving monitoring.
We implement our approach for monitoring specifications described by register
automata and evaluate it experimentally.\r\n"
acknowledgement: "This work is part of the project VAMOS, which has received funding
from the European\r\nResearch Council (ERC) under grant agreement No. 101020093,
and the Austrian Science\r\nFund (FWF) SFB project SpyCoDe F8502.\r\n"
alternative_title:
- ISTA Master’s Thesis
article_processing_charge: No
author:
- first_name: Mahyar
full_name: Karimi, Mahyar
id: 6e5417ba-5355-11ee-ae5a-94c2e510b26b
last_name: Karimi
orcid: 0009-0005-0820-1696
citation:
ama: Karimi M. Privacy-preserving runtime verification. 2026. doi:10.15479/AT-ISTA-21401
apa: Karimi, M. (2026). Privacy-preserving runtime verification. Institute
of Science and Technology Austria. https://doi.org/10.15479/AT-ISTA-21401
chicago: Karimi, Mahyar. “Privacy-Preserving Runtime Verification.” Institute of
Science and Technology Austria, 2026. https://doi.org/10.15479/AT-ISTA-21401.
ieee: M. Karimi, “Privacy-preserving runtime verification,” Institute of Science
and Technology Austria, 2026.
ista: Karimi M. 2026. Privacy-preserving runtime verification. Institute of Science
and Technology Austria.
mla: Karimi, Mahyar. Privacy-Preserving Runtime Verification. Institute of
Science and Technology Austria, 2026, doi:10.15479/AT-ISTA-21401.
short: M. Karimi, Privacy-Preserving Runtime Verification, Institute of Science
and Technology Austria, 2026.
corr_author: '1'
date_created: 2026-03-05T15:20:47Z
date_published: 2026-03-05T00:00:00Z
date_updated: 2026-03-13T13:37:20Z
day: '05'
ddc:
- '000'
degree_awarded: MS
department:
- _id: GradSch
- _id: ToHe
doi: 10.15479/AT-ISTA-21401
ec_funded: 1
file:
- access_level: open_access
checksum: 3f49f05c9d123e14d7adb73d3bc50fe2
content_type: application/pdf
creator: mkarimi
date_created: 2026-03-06T14:06:25Z
date_updated: 2026-03-10T15:20:09Z
file_id: '21404'
file_name: 2026_Karimi_Mahyar_Thesis.pdf
file_size: 766048
relation: main_file
- access_level: closed
checksum: 8fb9db4b4187e26443369a993427a5ff
content_type: application/zip
creator: mkarimi
date_created: 2026-03-06T14:06:25Z
date_updated: 2026-03-06T14:06:25Z
file_id: '21405'
file_name: 2026_Karimi_Mahyar_Thesis_src.zip
file_size: 1243394
relation: source_file
file_date_updated: 2026-03-10T15:20:09Z
has_accepted_license: '1'
keyword:
- Privacy-preserving verification
- Runtime verification
- Monitoring
- Reactive functionalities
- Cryptographic protocols
language:
- iso: eng
month: '03'
oa: 1
oa_version: Published Version
page: '60'
project:
- _id: 62781420-2b32-11ec-9570-8d9b63373d4d
call_identifier: H2020
grant_number: '101020093'
name: Vigilant Algorithmic Monitoring of Software
- _id: 34a4ce89-11ca-11ed-8bc3-8cc37fb6e11f
grant_number: F8512
name: Security and Privacy by Design for Complex Systems
publication_identifier:
issn:
- 2791-4585
publication_status: published
publisher: Institute of Science and Technology Austria
related_material:
record:
- id: '21020'
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: Privacy-preserving runtime verification
type: dissertation
user_id: 8b945eb4-e2f2-11eb-945a-df72226e66a9
year: '2026'
...
---
OA_place: publisher
_id: '22399'
abstract:
- lang: eng
text: "Gaining an understanding of how biological regulation evolves is a fundamental
research \r\nquestion in both evolutionary biology and molecular genetics. In
order to gain more insight \r\ninto this topic, we focus on studying the simple
gene regulatory system of the lac operon in \r\nE. coli. We show that simple population
genetic models can shed light on evolution \r\nexperiments and that this combined
approach of modelling the experimental system gives \r\ninsight to better understand
the causes of evolutionary change in the experiment. We also \r\nstudy the natural
diversity in the lac operon from 308 publicly available E. coli genomes that \r\ncome
from various host species and different regions of the world. Evidence that selection
is \r\ngenerally maintaining the function of the lac operon across the sample
regardless of host \r\nspecies is provided and we show that different protein
coding genes in the operon are under \r\ndifferent selective constraints on protein
sequence preservation. A similar frameshift \r\nmutation found in experimental
evolution studies is shown to be present in the sample we \r\nanalyzed, indicating
that selectively relevant variants in evolution experiments are also \r\npresent
in natural populations. We show that there is no simple phylogenetic relationship
\r\nbetween host species, geographical location and the lac operon sequence. Finally,
we argue \r\nthat a combined approach of comparative genomics, experimental evolution
and theoretical \r\nmodelling contributes to a more complete understanding of
molecular evolution. "
alternative_title:
- ISTA Master’s Thesis
article_processing_charge: No
author:
- first_name: Aleksa
full_name: Spasić, Aleksa
id: ecee9d38-4040-11ef-8843-b941efb445d6
last_name: Spasić
citation:
ama: Spasić A. Studying the evolutionary systems biology of the lac operon. 2026.
doi:10.15479/AT-ISTA-22399
apa: Spasić, A. (2026). Studying the evolutionary systems biology of the lac
operon. Institute of Science and Technology Austria. https://doi.org/10.15479/AT-ISTA-22399
chicago: Spasić, Aleksa. “Studying the Evolutionary Systems Biology of the Lac Operon.”
Institute of Science and Technology Austria, 2026. https://doi.org/10.15479/AT-ISTA-22399.
ieee: A. Spasić, “Studying the evolutionary systems biology of the lac operon,”
Institute of Science and Technology Austria, 2026.
ista: Spasić A. 2026. Studying the evolutionary systems biology of the lac operon.
Institute of Science and Technology Austria.
mla: Spasić, Aleksa. Studying the Evolutionary Systems Biology of the Lac Operon.
Institute of Science and Technology Austria, 2026, doi:10.15479/AT-ISTA-22399.
short: A. Spasić, Studying the Evolutionary Systems Biology of the Lac Operon, Institute
of Science and Technology Austria, 2026.
corr_author: '1'
das_tickbox: '0'
date_created: 2026-07-25T13:08:32Z
date_published: 2026-07-27T00:00:00Z
date_updated: 2026-07-31T10:52:08Z
day: '27'
ddc:
- '576'
degree_awarded: MS
department:
- _id: GradSch
- _id: GaTk
- _id: CaGu
doi: 10.15479/AT-ISTA-22399
doi_confirm: '1'
file:
- access_level: open_access
checksum: c29880dd71fcc37f23ac6e2843066ede
content_type: application/pdf
creator: aspasic
date_created: 2026-07-27T13:00:07Z
date_updated: 2026-07-27T13:00:07Z
file_id: '22588'
file_name: Aleksa_Spasic_Thesis_final.pdf
file_size: 1986078
relation: main_file
success: 1
- access_level: closed
checksum: 4ebe3bd2d833d913c0756343cca5e5f0
content_type: application/vnd.openxmlformats-officedocument.wordprocessingml.document
creator: aspasic
date_created: 2026-07-27T13:00:22Z
date_updated: 2026-07-27T13:07:23Z
file_id: '22589'
file_name: Thesis_final.docx
file_size: 1868853
relation: source_file
file_date_updated: 2026-07-27T13:07:23Z
has_accepted_license: '1'
language:
- iso: eng
month: '07'
oa: 1
oa_version: Published Version
page: '32'
publication_identifier:
issn:
- 2791-4585
publication_status: published
publisher: Institute of Science and Technology Austria
status: public
supervisor:
- first_name: Calin C
full_name: Guet, Calin C
id: 47F8433E-F248-11E8-B48F-1D18A9856A87
last_name: Guet
orcid: 0000-0001-6220-2052
- first_name: Gašper
full_name: Tkačik, Gašper
id: 3D494DCA-F248-11E8-B48F-1D18A9856A87
last_name: Tkačik
orcid: 0000-0002-6699-1455
title: Studying the evolutionary systems biology of the lac operon
type: dissertation
user_id: 8b945eb4-e2f2-11eb-945a-df72226e66a9
year: '2026'
...
---
OA_place: publisher
_id: '19853'
abstract:
- lang: eng
text: "The internal dynamical properties of red giant stars have been explored extensively
in recent\r\nyears as a result of the increase in high precision data availability
from the space missions\r\nKepler and TESS (Transiting Exoplanet Survey Satellite),
and in this exploration, it has been\r\ndiscovered that some of these stars are
not behaving as expected. Red giants are stars that have\r\nevolved off of the
main sequence after having completed fusing hydrogen into helium in their\r\ncore.
Observational data shows that the cores are rotating significantly slower than
models can\r\nrecreate consistently across evolutionary stages. This discrepancy
has prompted investigation\r\ninto the efficiency of angular momentum transport
mechanisms and mixing processes including\r\nmeridional circulation, shear instability,
internal gravity waves, Tayler-Spruit dynamo, fossil\r\nmagnetic fields etc.,
to explain this behavior.\r\nAnalyzing seismic oscillations in stars, via asteroseismology,
is a powerful tool as it is the only\r\nway in which the deep stellar interior
can be probed and subsequently characterized; this is\r\npossible as global oscillations
modulating the stellar surface are effected by internal processes.\r\nFor red
giants, p-modes (pressure modes; resonating through the entire star) and g-modes\r\n(gravity-modes;
resonating in the radiative interior) couple to create mixed modes. These\r\nmixed
modes give access to the otherwise hidden stellar interior as g-modes couple to
p-modes,\r\ndelivering information from the interior to the surface.\r\nInternal
magnetic signatures have been observationally confirmed in red giant stars via\r\nasteroseismology
and characterized in two ways. One being that dipole mixed modes with\r\nℓ = 1
will display a global asymmetric frequency shift of its azimuthal components;
where\r\nthe m = 0 and m = ±1 components of the ℓ = 1 dipole mode will be shifted
by two\r\ndifferent power laws, respectively. And the other being a reduced visibility
of dipole mixed\r\nmode amplitudes in the power spectra, where stars presenting
with this feature are denoted as\r\nsuppressed.\r\nSeveral studies of the suppressed
dipole mixed mode amplitudes have been carried out, but thus\r\nfar, no dedicated
studies of the asymmetric frequency shifts of suppressed red giants have been\r\nconducted;
one reason being that the asymmetric frequency shifts cannot be characterized\r\nwhen
the dipole mixed mode amplitudes are severely reduced in many of the suppressed
stars.\r\nSincefullysuppressedstarsdonothavedetectablemixed-modestoevaluate, partiallysuppressed\r\nstars,
that is, red giant stars presenting with suppressed dipole mixed modes in select
parts of\r\ntheir power spectra rather than across the entire spectra, will be
the subject of this study as\r\nthe respective mode amplitudes are still visible
at high frequencies.\r\nAs such, this study will search for asymmetric frequency
shifts on the dipole mixed\r\nmodes of partially suppressed red giant stars; the
aim here is to investigate if both\r\nmode suppression and magnetic shifting of
dipole mixed modes occur simultaneously.\r\nThisstudywillbeconductedbycreatingapipelinetoestimatepriorsofasteroseismicparameters,\r\nuse
the priors to model the power spectra with the stellar modeling code sloscillations_ISTA,\r\nand
perform a Bayesian fit of the parameters with the simulated data on the star KIC
6975038,\r\na target with partially suppressed dipolar mode amplitudes identified
in the literature, to fit its\r\nmagnetic parameters. I present a novel method
to model the stellar power spectra of\r\npartially suppressed red giants by application
of a sigmoid profile to the ℓ= 1 dipolar\r\nmode component of the spectra. With
the results of this study I aim at constraining\r\nthe cause of this partial dipole
mode amplitude suppression, allowing for more detailed\r\nstudies regarding their
astrophysical nature. Furthermore, the long term hope for the method\r\nused in
this study will be to expand the sample of partially suppressed red giants and
fit their\r\nasteroseismic parameters accordingly."
acknowledgement: "I would like to give thanks to myself for my hard work on this document.
This paper includes data collected by the Kepler mission and obtained from the MAST
data\r\narchive at the Space Telescope Science Institute (STScI). Funding for the
Kepler mission is\r\nprovided by the NASA Science Mission Directorate. STScI is
operated by the Association of\r\nUniversities for Research in Astronomy, Inc.,
under NASA contract NAS 5–26555.\r\n"
alternative_title:
- ISTA Master's Thesis
article_processing_charge: No
author:
- first_name: Kanah
full_name: Smith, Kanah
id: 7703505d-3211-11ee-a6a9-a2ab9d936c15
last_name: Smith
citation:
ama: Smith K. Exploring internal magnetism in partially suppressed red giant stars.
2025. doi:10.15479/AT-ISTA-19853
apa: Smith, K. (2025). Exploring internal magnetism in partially suppressed red
giant stars. Institute of Science and Technology Austria. https://doi.org/10.15479/AT-ISTA-19853
chicago: Smith, Kanah. “Exploring Internal Magnetism in Partially Suppressed Red
Giant Stars.” Institute of Science and Technology Austria, 2025. https://doi.org/10.15479/AT-ISTA-19853.
ieee: K. Smith, “Exploring internal magnetism in partially suppressed red giant
stars,” Institute of Science and Technology Austria, 2025.
ista: Smith K. 2025. Exploring internal magnetism in partially suppressed red giant
stars. Institute of Science and Technology Austria.
mla: Smith, Kanah. Exploring Internal Magnetism in Partially Suppressed Red Giant
Stars. Institute of Science and Technology Austria, 2025, doi:10.15479/AT-ISTA-19853.
short: K. Smith, Exploring Internal Magnetism in Partially Suppressed Red Giant
Stars, Institute of Science and Technology Austria, 2025.
corr_author: '1'
date_created: 2025-06-20T13:27:08Z
date_published: 2025-10-08T00:00:00Z
date_updated: 2026-04-07T12:01:37Z
day: '08'
ddc:
- '520'
degree_awarded: MS
department:
- _id: GradSch
- _id: LiBu
doi: 10.15479/AT-ISTA-19853
file:
- access_level: closed
checksum: 80d241d11b69af771c1fab0998be4f19
content_type: application/zip
creator: ksmith
date_created: 2025-10-08T08:01:42Z
date_updated: 2025-10-08T09:45:33Z
file_id: '20434'
file_name: 2025_Smith_Kanah_Thesis.zip
file_size: 8263624
relation: source_file
- access_level: open_access
checksum: 13cb48cc98e00fdfe32f3ff66f17aa26
content_type: application/pdf
creator: ksmith
date_created: 2025-10-09T14:38:57Z
date_updated: 2025-10-09T14:38:57Z
file_id: '20439'
file_name: 2025_Smith_Kanah_Thesis.pdf
file_size: 9748339
relation: main_file
success: 1
file_date_updated: 2025-10-09T14:38:57Z
has_accepted_license: '1'
keyword:
- asteroseismology
- stellar physics
- red giant
- magnetism
- suppressed
language:
- iso: eng
month: '10'
oa: 1
oa_version: Published Version
page: '38'
publication_identifier:
issn:
- 2791-4585
publication_status: published
publisher: Institute of Science and Technology Austria
status: public
supervisor:
- first_name: Lisa Annabelle
full_name: Bugnet, Lisa Annabelle
id: d9edb345-f866-11ec-9b37-d119b5234501
last_name: Bugnet
orcid: 0000-0003-0142-4000
title: Exploring internal magnetism in partially suppressed red giant stars
type: dissertation
user_id: ba8df636-2132-11f1-aed0-ed93e2281fdd
year: '2025'
...
---
OA_place: publisher
_id: '20735'
abstract:
- lang: eng
text: "Left–right alternation is a defining feature of spinal locomotor circuits,
yet the level of neuronal\r\ndetail required to generate and maintain this pattern
remains unclear. This thesis investigates how\r\nmodels spanning multiple levels
of abstraction—from biophysically detailed Hodgkin–Huxley (HH)\r\nneurons to adaptive
integrate–and–fire (I&F) formulations and synfire-chain modules—can account\r\nfor
the generation of fictive swimming in the spinal cord of the Xenopus laevis tadpole.
The guiding\r\nhypothesis is that a small set of neuronal mechanisms is sufficient
to reproduce the essential features\r\nof rhythmic alternation, and that moving
between modeling scales helps distinguish core principles\r\nfrom biological detail.\r\nA
minimal bilateral HH network comprising only four canonical neuron classes—excitatory\r\ndescending
interneurons (dINs), inhibitory commissural interneurons (cINs), ipsilateral inhibitory\r\ninterneurons
(aINs) and motoneurons—served as a biophysical proof of concept. Tuned to reproduce\r\nexperimentally
observed firing modes, the model demonstrated that rebound-prone dIN excitability,\r\ncontralateral
inhibition and modest electrical coupling are sufficient to generate stable alternating\r\nactivity,
even in very small networks. These results motivated the transition to simpler
models\r\ncapable of efficient analysis and scaling.\r\nAdaptive exponential I&F
(AdEx) neurons were calibrated to physiological recordings using\r\nsimulation-based
inference, yielding tonic and phasic/rebound templates that preserved the key\r\ndynamical
signatures of the HH model. Phase-plane analysis clarified the mechanisms underlying\r\nsingle-spike
responses and rebound firing in dINs. At network level, the I&F models robustly\r\nreproduced
left–right alternation, while highlighting constraints on synaptic kinetics and
adaptation\r\nneeded to avoid multi-spike responses.\r\nFinally, a synfire-chain
framework provided a complementary, timing-centric perspective, demonstrating
how precise spike synchrony, synaptic delays and minimal inhibitory coupling can
generate\r\nalternating left–right sequences in a feedforward setting. Together,
these approaches converge on a\r\ncommon conclusion: rebound-prone ipsilateral
excitation combined with precisely timed contralateral inhibition constitutes
a sufficient substrate for alternating spinal rhythms.\r\nBy integrating bottom-up
and top-down modeling strategies, this thesis provides a unified, extensible framework
for studying spinal pattern generation. The results show that essential locomotor\r\ndynamics
can be captured across multiple abstraction levels, offering both mechanistic
insight and\r\npractical tools for future data-driven investigations of spinal
circuit development, robustness and\r\nmodulation."
alternative_title:
- ISTA Master's Thesis
article_processing_charge: No
author:
- first_name: Alexia C
full_name: Wilson, Alexia C
id: 5230e794-15b2-11ec-abd3-e2d5335ebd1d
last_name: Wilson
orcid: 0000-0001-6191-1367
citation:
ama: 'Wilson AC. Modelling the spinal cord of a tadpole: Exploring different ways
to model the spinal cord in the Xenopus frog. 2025. doi:10.15479/AT-ISTA-20735'
apa: 'Wilson, A. C. (2025). Modelling the spinal cord of a tadpole: Exploring
different ways to model the spinal cord in the Xenopus frog. Institute of
Science and Technology Austria. https://doi.org/10.15479/AT-ISTA-20735'
chicago: 'Wilson, Alexia C. “Modelling the Spinal Cord of a Tadpole: Exploring Different
Ways to Model the Spinal Cord in the Xenopus Frog.” Institute of Science and Technology
Austria, 2025. https://doi.org/10.15479/AT-ISTA-20735.'
ieee: 'A. C. Wilson, “Modelling the spinal cord of a tadpole: Exploring different
ways to model the spinal cord in the Xenopus frog,” Institute of Science and Technology
Austria, 2025.'
ista: 'Wilson AC. 2025. Modelling the spinal cord of a tadpole: Exploring different
ways to model the spinal cord in the Xenopus frog. Institute of Science and Technology
Austria.'
mla: 'Wilson, Alexia C. Modelling the Spinal Cord of a Tadpole: Exploring Different
Ways to Model the Spinal Cord in the Xenopus Frog. Institute of Science and
Technology Austria, 2025, doi:10.15479/AT-ISTA-20735.'
short: 'A.C. Wilson, Modelling the Spinal Cord of a Tadpole: Exploring Different
Ways to Model the Spinal Cord in the Xenopus Frog, Institute of Science and Technology
Austria, 2025.'
corr_author: '1'
date_created: 2025-12-08T09:49:41Z
date_published: 2025-12-09T00:00:00Z
date_updated: 2026-07-29T12:55:12Z
day: '09'
ddc:
- '570'
- '596'
- '005'
degree_awarded: MS
department:
- _id: GradSch
- _id: TiVo
- _id: LoSw
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language:
- iso: eng
month: '12'
oa: 1
oa_version: Published Version
page: '110'
publication_identifier:
issn:
- 2791-4585
publication_status: published
publisher: Institute of Science and Technology Austria
related_material:
record:
- id: '13097'
relation: part_of_dissertation
status: public
status: public
supervisor:
- first_name: Tim P
full_name: Vogels, Tim P
id: CB6FF8D2-008F-11EA-8E08-2637E6697425
last_name: Vogels
orcid: 0000-0003-3295-6181
- first_name: Lora Beatrice Jaeger
full_name: Sweeney, Lora Beatrice Jaeger
id: 56BE8254-C4F0-11E9-8E45-0B23E6697425
last_name: Sweeney
orcid: 0000-0001-9242-5601
title: 'Modelling the spinal cord of a tadpole: Exploring different ways to model
the spinal cord in the Xenopus frog'
type: dissertation
user_id: 8b945eb4-e2f2-11eb-945a-df72226e66a9
year: '2025'
...
---
OA_place: publisher
_id: '18588'
abstract:
- lang: eng
text: "This thesis is an experimental work about two distinct research projects
that evolved from a single project: non-equilibrium dynamics of an acoustically
vibrated particle and microfabrication of particles with nano-scale 3D printing.
The first project explores non equilibrium dynamics of a particle driven by ultrasonic
vibrations. We design an experimental system consisting of an electromechanical
vibration scheme to drive the particle’s vibrations and an imaging scheme to track
its trajectories. We study the trajectories to determine how the particle’s dynamics
evolve under the driven conditions, considering out of equilibrium systems in
the context of equilibrium statistical mechanics. Using a Langevin framework and
the Boltzmann factor, we characterize the particle’s dynamics as complex; the
particle motion\r\nis not purely diffusive. We extract physical parameters like
spring constant, effective temperature, damping coefficient and resonance frequency.\r\n\r\nIn
the second project, we explore and develop techniques in the design and microfabrication
of particles across scales. Microfabrication involves building structures at the
micron or submicron scale. These designed miniaturized patterns, objects, or devices
are useful in biophysics, pharmacology, medical biology, and nanotechnology. We
specifically apply two-photon polymerization, a form of 3D nano printing. We print
millimetric particles, characterizing different designs to evaluate and showcase
the resolution, aspect ratio integrity and print quality of the printing process.
We also design and fabricate a microsensor to deflect under applicable force of
order 0.1 pN. We present fundamental concepts needed to design the microsensor,
showcasing 3D printing at considerably smaller scales down to the µm or below."
acknowledged_ssus:
- _id: NanoFab
- _id: M-Shop
acknowledgement: "I would like to acknowledge Scott Waitukaitis and Jérémie Palacci,
for their supervision, and their extensive support of my learning. \r\n\r\nFor the
beautiful characterization images used in this work, I would like to thank Dr. Daniel
Grober, Samuel Hajek and Felix Pertl.\r\n\r\nThe Palacci group, particularly Malina
Strugaru and Dan Grober, for their continuous guidance in decoding and following
my streams of thought.\r\n\r\nTo the Waitukaitis group, for helping me find my footing
in science, and making me feel at\r\nhome.\r\n\r\nTo the Nanofabrication Facility
(NFF) at ISTA, for training me in significant aspects of my research. The MIBA Facility,
and particularly Todor Asenov for consistently picking up the phone for my machining
and designing needs.\r\n\r\nTo my friends, Mariana, Lenka, Aaron, Rebecca, Eavan
who provided an ear, wine, and a lot more when I needed to vent, talk through my
crises as well as experiment. For the walks, for the coffees, for reading through
my work and providing edits, for dinners to take me out of blocks and binds and
for cheering me on when it felt insurmountable. \r\n\r\nFinally, I am grateful to
Griff and Fletcher, whose music helped me through several blocks, especially with
my writing.\r\n\r\nMy science would not have been possible without the guidance,
support and contributions of\r\nall these people, and more."
alternative_title:
- ISTA Master's Thesis
article_processing_charge: No
author:
- first_name: Cecelia N
full_name: Mweka, Cecelia N
id: 2a69ab4b-896a-11ed-bdf8-cb8641cf2b21
last_name: Mweka
citation:
ama: Mweka CN. Non equilibrium dynamics of driven individual particles and 3D printing
across scales. 2024. doi:10.15479/at:ista:18588
apa: Mweka, C. N. (2024). Non equilibrium dynamics of driven individual particles
and 3D printing across scales. Institute of Science and Technology Austria.
https://doi.org/10.15479/at:ista:18588
chicago: Mweka, Cecelia N. “Non Equilibrium Dynamics of Driven Individual Particles
and 3D Printing across Scales.” Institute of Science and Technology Austria, 2024.
https://doi.org/10.15479/at:ista:18588.
ieee: C. N. Mweka, “Non equilibrium dynamics of driven individual particles and
3D printing across scales,” Institute of Science and Technology Austria, 2024.
ista: Mweka CN. 2024. Non equilibrium dynamics of driven individual particles and
3D printing across scales. Institute of Science and Technology Austria.
mla: Mweka, Cecelia N. Non Equilibrium Dynamics of Driven Individual Particles
and 3D Printing across Scales. Institute of Science and Technology Austria,
2024, doi:10.15479/at:ista:18588.
short: C.N. Mweka, Non Equilibrium Dynamics of Driven Individual Particles and 3D
Printing across Scales, Institute of Science and Technology Austria, 2024.
corr_author: '1'
date_created: 2024-11-27T09:12:02Z
date_published: 2024-11-29T00:00:00Z
date_updated: 2026-04-07T12:42:13Z
day: '29'
ddc:
- '530'
degree_awarded: MS
department:
- _id: GradSch
doi: 10.15479/at:ista:18588
file:
- access_level: open_access
checksum: 054ed7a5e5ae6e7220e6bb37ea57a3c3
content_type: application/pdf
creator: cmweka
date_created: 2024-11-28T12:50:32Z
date_updated: 2024-11-28T12:50:32Z
file_id: '18597'
file_name: Cecelia Mweka Master Thesis.pdf
file_size: 3836671
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success: 1
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creator: cmweka
date_created: 2024-11-28T12:51:43Z
date_updated: 2024-12-13T11:30:53Z
file_id: '18598'
file_name: Cecelia Mweka Master Thesis.docx
file_size: 7068210
relation: source_file
file_date_updated: 2024-12-13T11:30:53Z
has_accepted_license: '1'
language:
- iso: eng
month: '11'
oa: 1
oa_version: Published Version
page: '61'
publication_identifier:
issn:
- 2791-4585
publication_status: published
publisher: Institute of Science and Technology Austria
status: public
supervisor:
- first_name: Scott R
full_name: Waitukaitis, Scott R
id: 3A1FFC16-F248-11E8-B48F-1D18A9856A87
last_name: Waitukaitis
orcid: 0000-0002-2299-3176
- first_name: Jérémie A
full_name: Palacci, Jérémie A
id: 8fb92548-2b22-11eb-b7c1-a3f0d08d7c7d
last_name: Palacci
orcid: 0000-0002-7253-9465
title: Non equilibrium dynamics of driven individual particles and 3D printing across
scales
type: dissertation
user_id: ba8df636-2132-11f1-aed0-ed93e2281fdd
year: '2024'
...
---
OA_place: publisher
_id: '18301'
abstract:
- lang: eng
text: Physics simulation in computer graphics can bring triangle meshes into topologically
invalid states. The method in this thesis contributed to Heiss-Synak* and Kalinov*
et al. [2024] who devised a non-manifold hybrid surface tracker—a surface tracker
that repairs explicit non-manifold triangle meshes with the help of the implicit
domain. Specifically, this thesis provides an algorithm for filling the holes
that are left after removing problematic parts of the mesh.
alternative_title:
- ISTA Master's Thesis
article_processing_charge: No
author:
- first_name: Arian
full_name: Etemadihaghighi, Arian
id: 36cea3aa-f38e-11ec-8ae0-c65ae6f6098f
last_name: Etemadihaghighi
citation:
ama: Etemadi A. Filling the holes of non-manifold self-intersecting meshes for implicit
topology changes in surface tracking. 2024. doi:10.15479/at:ista:18301
apa: Etemadi, A. (2024). Filling the holes of non-manifold self-intersecting
meshes for implicit topology changes in surface tracking. Institute of Science
and Technology Austria. https://doi.org/10.15479/at:ista:18301
chicago: Etemadi, Arian. “Filling the Holes of Non-Manifold Self-Intersecting Meshes
for Implicit Topology Changes in Surface Tracking.” Institute of Science and Technology
Austria, 2024. https://doi.org/10.15479/at:ista:18301.
ieee: A. Etemadi, “Filling the holes of non-manifold self-intersecting meshes for
implicit topology changes in surface tracking,” Institute of Science and Technology
Austria, 2024.
ista: Etemadi A. 2024. Filling the holes of non-manifold self-intersecting meshes
for implicit topology changes in surface tracking. Institute of Science and Technology
Austria.
mla: Etemadi, Arian. Filling the Holes of Non-Manifold Self-Intersecting Meshes
for Implicit Topology Changes in Surface Tracking. Institute of Science and
Technology Austria, 2024, doi:10.15479/at:ista:18301.
short: A. Etemadi, Filling the Holes of Non-Manifold Self-Intersecting Meshes for
Implicit Topology Changes in Surface Tracking, Institute of Science and Technology
Austria, 2024.
corr_author: '1'
date_created: 2024-10-11T19:52:20Z
date_published: 2024-10-15T00:00:00Z
date_updated: 2026-04-07T13:02:36Z
day: '15'
ddc:
- '000'
degree_awarded: MS
department:
- _id: GradSch
- _id: ChWo
doi: 10.15479/at:ista:18301
file:
- access_level: open_access
checksum: 80fb7923e229ad9d39253d7c8a8083d0
content_type: application/pdf
creator: aetemadi
date_created: 2024-10-24T14:34:42Z
date_updated: 2024-10-24T14:34:42Z
file_id: '18469'
file_name: thesis-arian-etemadi.pdf
file_size: 8914218
relation: main_file
success: 1
- access_level: closed
checksum: 1c02586ed7d441d5ec441867650568d1
content_type: application/x-zip-compressed
creator: aetemadi
date_created: 2024-10-24T14:34:54Z
date_updated: 2024-10-24T14:34:54Z
file_id: '18470'
file_name: thesis-arian-etemadi-latex-source.zip
file_size: 9802650
relation: source_file
file_date_updated: 2024-10-24T14:34:54Z
has_accepted_license: '1'
keyword:
- surface tracking
- non-manifold
- hole-filling
- topology change
- multi-material
- solid-modeling
language:
- iso: eng
license: https://creativecommons.org/licenses/by-sa/4.0/
month: '10'
oa: 1
oa_version: Published Version
page: '39'
publication_identifier:
issn:
- 2791-4585
publication_status: published
publisher: Institute of Science and Technology Austria
related_material:
record:
- id: '17219'
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: Filling the holes of non-manifold self-intersecting meshes for implicit topology
changes in surface tracking
tmp:
image: /images/cc_by_sa.png
legal_code_url: https://creativecommons.org/licenses/by-sa/4.0/legalcode
name: Creative Commons Attribution-ShareAlike 4.0 International Public License (CC
BY-SA 4.0)
short: CC BY-SA (4.0)
type: dissertation
user_id: ba8df636-2132-11f1-aed0-ed93e2281fdd
year: '2024'
...
---
OA_place: publisher
_id: '15352'
abstract:
- lang: eng
text: "Epilepsy affects about 50 to 65 million people globally. It summarizes a
spectrum of neurological\r\ndisorders that have in common a hyperactivity of the
neuronal network resulting in seizures. A common\r\nassumption is that an imbalance
between neuronal excitation and inhibition is a key mechanism in\r\nseizure generation
and epileptogeneisis. In at least one-third of the patients, current therapies
have\r\nproven unsuccessful in treating seizure progression. One potential reason
could be that the therapies\r\nonly focus on neurons. Recent studies suggest that
neuronal hyperactivity causes a microglial\r\nresponse, which reinstates brain
homeostasis. Additionally, interactions between microglia and neurons\r\nhave
been shown to inhibit neuronal firing and dampen seizure activity. However, the
exact relationship\r\nbetween microglia and seizure progression in epilepsy is
yet to be elucidated. A main bottleneck is that\r\nseveral studies investigate
microglia dynamics in ex vivo slice models, which can severely affect the\r\nmicroglia
dynamics due to their rapid response to environmental changes. On the other hand,
in vivo\r\nstudies focus mostly on behavior characterization of the epileptic
seizure phenotype and their long-term\r\nconsequences on microglia activity leaving
out the direct consequences of acute seizure activity on\r\nmicroglia dynamics.\r\nHere,
we perform a pilot study to combine electroencephalography (EEG) and in vivo live
imaging to\r\ndirectly monitor and correlate the onset of seizure activity with
microglia response. To induce seizures,\r\nwe take advantage of the kainic acid
(KA) model, which represents similar neuropathological and\r\nelectroencephalographic
features seen in human patients with temporal lobe epilepsy (TLE). After\r\nconfirmation
of induction of the seizure and microglia activity in the hippocampus as a focal
point, we\r\ninvestigated whether these changes also reached the primary visual
cortex (V1) as a secondary\r\ngeneralized seizure activity. Indeed, we found that
microglia changed their morphology at high doses\r\nof KA in the V1. Next, we
optimized each of the two methodological components: for the EEG recording,\r\nour
initial attempts under the microscope suffered from extensive electrical noise,
which overlaid the\r\nactual signal. Thus, we built a customized Faraday-cage
and confirmed that the signal-to-noise ratio\r\nwas sufficiently reduced to be
able to record brain oscillatory activity. For the in vivo live imaging of\r\nmicroglia,
we had to optimize the imaging parameters, so that we would be able to detect
microglial\r\nprocesses in a sufficient resolution to track their process changes.
Finally, we combined both\r\nmethodologies with the KA model. We confirmed that
KA induced seizure activity and found first\r\nindication that those correlate
with microglia volume changes.\r\nOverall, we have developed a first methodological
approach, which allows the analysis of the acute\r\neffects of seizure onset on
microglia. Future studies will have to continue to optimize the drift during\r\nimaging
recording and the post-image analysis. "
acknowledged_ssus:
- _id: Bio
- _id: LifeSc
- _id: PreCl
alternative_title:
- ISTA Master's Thesis
article_processing_charge: No
author:
- first_name: Julie Stefanie
full_name: Murmann, Julie Stefanie
id: 1d390868-f128-11eb-9611-a0ca5f7833b5
last_name: Murmann
citation:
ama: 'Murmann JS. Investigating acute microglia response to seizure activity in
vivo: Combining 2-Photon imaging and EEG recording. 2024. doi:10.15479/at:ista:15352'
apa: 'Murmann, J. S. (2024). Investigating acute microglia response to seizure
activity in vivo: Combining 2-Photon imaging and EEG recording. Institute
of Science and Technology Austria. https://doi.org/10.15479/at:ista:15352'
chicago: 'Murmann, Julie Stefanie. “Investigating Acute Microglia Response to Seizure
Activity in Vivo: Combining 2-Photon Imaging and EEG Recording.” Institute of
Science and Technology Austria, 2024. https://doi.org/10.15479/at:ista:15352.'
ieee: 'J. S. Murmann, “Investigating acute microglia response to seizure activity
in vivo: Combining 2-Photon imaging and EEG recording,” Institute of Science and
Technology Austria, 2024.'
ista: 'Murmann JS. 2024. Investigating acute microglia response to seizure activity
in vivo: Combining 2-Photon imaging and EEG recording. Institute of Science and
Technology Austria.'
mla: 'Murmann, Julie Stefanie. Investigating Acute Microglia Response to Seizure
Activity in Vivo: Combining 2-Photon Imaging and EEG Recording. Institute
of Science and Technology Austria, 2024, doi:10.15479/at:ista:15352.'
short: 'J.S. Murmann, Investigating Acute Microglia Response to Seizure Activity
in Vivo: Combining 2-Photon Imaging and EEG Recording, Institute of Science and
Technology Austria, 2024.'
corr_author: '1'
date_created: 2024-05-02T08:31:38Z
date_published: 2024-05-02T00:00:00Z
date_updated: 2026-04-07T13:05:00Z
day: '02'
ddc:
- '570'
degree_awarded: MS
department:
- _id: SaSi
- _id: GradSch
doi: 10.15479/at:ista:15352
file:
- access_level: open_access
checksum: 095817a6c944954ac3f277e547031a33
content_type: application/pdf
creator: cchlebak
date_created: 2024-05-02T12:26:13Z
date_updated: 2025-05-02T22:30:04Z
embargo: 2025-05-02
file_id: '15354'
file_name: Murmann_Thesis_final_2024_2.pdf
file_size: 5936142
relation: main_file
- access_level: closed
checksum: 43b632255372973a437ac87739cfd4db
content_type: application/x-zip-compressed
creator: cchlebak
date_created: 2024-05-02T12:37:56Z
date_updated: 2025-05-02T22:30:04Z
embargo_to: open_access
file_id: '15355'
file_name: Murmann_Thesis_final_2024.zip
file_size: 20645510
relation: source_file
file_date_updated: 2025-05-02T22:30:04Z
has_accepted_license: '1'
language:
- iso: eng
license: https://creativecommons.org/licenses/by/4.0/
month: '05'
oa: 1
oa_version: Published Version
page: '54'
publication_identifier:
issn:
- 2791-4585
publication_status: published
publisher: Institute of Science and Technology Austria
status: public
supervisor:
- first_name: Sandra
full_name: Siegert, Sandra
id: 36ACD32E-F248-11E8-B48F-1D18A9856A87
last_name: Siegert
orcid: 0000-0001-8635-0877
title: 'Investigating acute microglia response to seizure activity in vivo: Combining
2-Photon imaging and EEG recording'
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: dissertation
user_id: ba8df636-2132-11f1-aed0-ed93e2281fdd
year: '2024'
...
---
OA_place: publisher
_id: '17368'
abstract:
- lang: eng
text: "Recent advancements in molecular diagnostic techniques have enabled the collection
of\r\nmultiple types of omics data from patients, including genomics, epigenomics,
proteomics,\r\nand transcriptomics. However, we lack effective methods for integrating
all these different\r\ndata types and combining them with clinical outcomes to
study the molecular mechanisms\r\nthat govern pathological phenotypes. We present
multi-omics BayesW, a penalized Bayesian\r\nregression method that can handle
general omics data for survival analysis of time-to-event\r\nphenotypes. Our method
can: (1) accommodate incomplete data by allowing censored\r\nindividuals, (2)
use continuous time-to-event data to test associations of markers with a\r\nphenotype
and (3) estimate effects jointly while allowing for independent groups of biological\r\nmarkers.
Extensive simulations using planted signals on real data demonstrate that our
model\r\naccurately retrieves the true parameters of the model while controlling
for false discoveries\r\nand maintaining the expected prediction accuracy. We
address data correlations by estimating\r\nthe effects jointly, even between omic
groups, while also estimating the individual variance\r\nexplained by each group.
We apply our model to two datasets. Using 18,000 individuals from\r\nthe Generation
Scotland study we model the association of time at onset of Type 2 Diabetes,\r\nStroke,
Ischemic Disease, and Osteoarthritis from baseline study entry, with 831,724 CpG\r\nmethylation
probes. We find that large proportions of variation in disease onset times can\r\nbe
attributed to methylation as measured in whole blood at baseline in individuals
without\r\ndisease symptoms. We then apply our model to The Cancer Genome Atlas
(TCGA) pan-cancer\r\ndataset, in which we use 5 types of omics: copy number variation,
epigenetics, somatic\r\nmutations, miRNA, and gene expression. For cancer survival
age-at-onset we find that, when\r\nfitting the 5 groups together, almost all variation
attributable to \"omics\" data is explained by\r\nDNA methylation. When considering
progression times, both methylation and gene expression\r\nexplain a large part
of the variance. We found 2 genes that are significantly associated (95%\r\nposterior
inclusion probability) with cancer survival time, conditional on all other genome-wide\r\nomics
data variation. Owing to the vast variability of mechanisms characterizing different\r\ncancers,
there are likely few specific genes with a strong signal in a pan-cancer setting.
Taken\r\ntogether, we showed the applicability of our multi-omics BayesW model
to a wide-range of\r\nbiological questions in multi-omics data.\r\n"
alternative_title:
- ISTA Master's Thesis
article_processing_charge: No
author:
- first_name: Ariadna
full_name: Villanueva Marijuan, Ariadna
id: e0ae4864-133f-11ed-8f02-adaa8dd27540
last_name: Villanueva Marijuan
citation:
ama: Villanueva Marijuan A. Bayesian linear regression for analyzing general omics
data with time-to-event phenotypes. 2024. doi:10.15479/at:ista:17368
apa: Villanueva Marijuan, A. (2024). Bayesian linear regression for analyzing
general omics data with time-to-event phenotypes. Institute of Science and
Technology Austria. https://doi.org/10.15479/at:ista:17368
chicago: Villanueva Marijuan, Ariadna. “Bayesian Linear Regression for Analyzing
General Omics Data with Time-to-Event Phenotypes.” Institute of Science and Technology
Austria, 2024. https://doi.org/10.15479/at:ista:17368.
ieee: A. Villanueva Marijuan, “Bayesian linear regression for analyzing general
omics data with time-to-event phenotypes,” Institute of Science and Technology
Austria, 2024.
ista: Villanueva Marijuan A. 2024. Bayesian linear regression for analyzing general
omics data with time-to-event phenotypes. Institute of Science and Technology
Austria.
mla: Villanueva Marijuan, Ariadna. Bayesian Linear Regression for Analyzing General
Omics Data with Time-to-Event Phenotypes. Institute of Science and Technology
Austria, 2024, doi:10.15479/at:ista:17368.
short: A. Villanueva Marijuan, Bayesian Linear Regression for Analyzing General
Omics Data with Time-to-Event Phenotypes, Institute of Science and Technology
Austria, 2024.
corr_author: '1'
date_created: 2024-08-02T10:52:40Z
date_published: 2024-08-13T00:00:00Z
date_updated: 2026-04-07T13:03:41Z
day: '13'
ddc:
- '610'
degree_awarded: MS
department:
- _id: GradSch
- _id: MaRo
doi: 10.15479/at:ista:17368
file:
- access_level: open_access
checksum: 0c2daa174609f0c00919dccc5701d375
content_type: application/pdf
creator: avillanu
date_created: 2024-08-14T11:51:24Z
date_updated: 2025-02-14T23:30:03Z
embargo: 2025-02-14
file_id: '17433'
file_name: Masters_thesis_AriadnaVillanueva.pdf
file_size: 13052436
relation: main_file
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checksum: e9ed4465dfa539ac4c3a8d4d0b6271a1
content_type: application/zip
creator: avillanu
date_created: 2024-08-14T11:51:57Z
date_updated: 2025-02-14T23:30:03Z
embargo_to: open_access
file_id: '17434'
file_name: Masters thesis-AriadnaVillanueva.zip
file_size: 45642547
relation: source_file
file_date_updated: 2025-02-14T23:30:03Z
has_accepted_license: '1'
keyword:
- Epigenetics
- Multi-omics
- Bayesian regression
language:
- iso: eng
license: https://creativecommons.org/licenses/by-nc-sa/4.0/
month: '08'
oa: 1
oa_version: Published Version
page: '60'
publication_identifier:
issn:
- 2791-4585
publication_status: published
publisher: Institute of Science and Technology Austria
status: public
supervisor:
- first_name: Matthew Richard
full_name: Robinson, Matthew Richard
id: E5D42276-F5DA-11E9-8E24-6303E6697425
last_name: Robinson
orcid: 0000-0001-8982-8813
title: Bayesian linear regression for analyzing general omics data with time-to-event
phenotypes
tmp:
image: /images/cc_by_nc_sa.png
legal_code_url: https://creativecommons.org/licenses/by-nc-sa/4.0/legalcode
name: Creative Commons Attribution-NonCommercial-ShareAlike 4.0 International (CC
BY-NC-SA 4.0)
short: CC BY-NC-SA (4.0)
type: dissertation
user_id: ba8df636-2132-11f1-aed0-ed93e2281fdd
year: '2024'
...
---
OA_place: publisher
_id: '13331'
abstract:
- lang: eng
text: "The extension of extremal combinatorics to the setting of exterior algebra
is a work\r\nin progress that gained attention recently. In this thesis, we study
the combinatorial structure of exterior algebra by introducing a dictionary that
translates the notions from the set systems into the framework of exterior algebra.
We show both generalizations of celebrated Erdös--Ko--Rado theorem and Hilton--Milner
theorem to the setting of exterior algebra in the simplest non-trivial case of
two-forms.\r\n"
alternative_title:
- ISTA Master's Thesis
article_processing_charge: No
author:
- first_name: Seyda
full_name: Köse, Seyda
id: 8ba3170d-dc85-11ea-9058-c4251c96a6eb
last_name: Köse
orcid: 0009-0008-0457-9730
citation:
ama: Köse S. Exterior algebra and combinatorics. 2023. doi:10.15479/at:ista:13331
apa: Köse, S. (2023). Exterior algebra and combinatorics. Institute of Science
and Technology Austria. https://doi.org/10.15479/at:ista:13331
chicago: Köse, Seyda. “Exterior Algebra and Combinatorics.” Institute of Science
and Technology Austria, 2023. https://doi.org/10.15479/at:ista:13331.
ieee: S. Köse, “Exterior algebra and combinatorics,” Institute of Science and Technology
Austria, 2023.
ista: Köse S. 2023. Exterior algebra and combinatorics. Institute of Science and
Technology Austria.
mla: Köse, Seyda. Exterior Algebra and Combinatorics. Institute of Science
and Technology Austria, 2023, doi:10.15479/at:ista:13331.
short: S. Köse, Exterior Algebra and Combinatorics, Institute of Science and Technology
Austria, 2023.
corr_author: '1'
date_created: 2023-07-31T10:20:55Z
date_published: 2023-07-31T00:00:00Z
date_updated: 2026-04-07T13:29:29Z
day: '31'
ddc:
- '510'
- '516'
degree_awarded: MS
department:
- _id: GradSch
- _id: UlWa
doi: 10.15479/at:ista:13331
file:
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checksum: 96ee518d796d02af71395622c45de03c
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date_created: 2023-07-31T10:16:32Z
date_updated: 2023-07-31T10:16:32Z
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creator: skoese
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date_updated: 2023-08-03T15:28:55Z
file_id: '13480'
file_name: thesis-pdfa.pdf
file_size: 4953418
relation: main_file
success: 1
file_date_updated: 2023-08-03T15:28:55Z
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language:
- iso: eng
month: '07'
oa: 1
oa_version: Published Version
page: '26'
publication_identifier:
issn:
- 2791-4585
publication_status: published
publisher: Institute of Science and Technology Austria
related_material:
record:
- id: '12680'
relation: part_of_dissertation
status: public
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: Exterior algebra and combinatorics
type: dissertation
user_id: ba8df636-2132-11f1-aed0-ed93e2281fdd
year: '2023'
...
---
OA_place: publisher
_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.
corr_author: '1'
date_created: 2023-02-09T07:45:05Z
date_published: 2023-02-08T00:00:00Z
date_updated: 2026-04-07T14:06:26Z
day: '08'
ddc:
- '570'
degree_awarded: MS
department:
- _id: GradSch
- _id: MaJö
doi: 10.15479/at:ista:12531
file:
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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
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date_updated: 2024-02-09T23:30:03Z
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file_size: 11204408
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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: ba8df636-2132-11f1-aed0-ed93e2281fdd
year: '2023'
...
---
OA_place: publisher
_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.
corr_author: '1'
date_created: 2023-04-04T18:57:11Z
date_published: 2023-04-05T00:00:00Z
date_updated: 2026-04-07T14:01:51Z
day: '05'
ddc:
- '576'
degree_awarded: MS
department:
- _id: GradSch
- _id: NiBa
doi: 10.15479/at:ista:12800
file:
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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
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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
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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
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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: ba8df636-2132-11f1-aed0-ed93e2281fdd
year: '2023'
...
---
OA_place: publisher
_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.
corr_author: '1'
date_created: 2023-08-24T13:01:18Z
date_published: 2023-08-24T00:00:00Z
date_updated: 2026-04-07T14:02:30Z
day: '24'
ddc:
- '500'
degree_awarded: MS
department:
- _id: GradSch
- _id: HeEd
doi: 10.15479/at:ista:14226
file:
- access_level: closed
checksum: 453caf851d75c3478c10ed09bd242a91
content_type: application/x-zip-compressed
creator: cchlebak
date_created: 2023-08-24T13:02:49Z
date_updated: 2024-02-26T23:30:03Z
embargo_to: open_access
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file_size: 15501411
relation: source_file
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checksum: 7349d29963d6695e555e171748648d9a
content_type: application/pdf
creator: cchlebak
date_created: 2023-08-24T13:03:42Z
date_updated: 2024-02-26T23:30:03Z
embargo: 2024-02-25
file_id: '14228'
file_name: thesis_pdf_a.pdf
file_size: 6854783
relation: main_file
file_date_updated: 2024-02-26T23:30:03Z
has_accepted_license: '1'
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: ba8df636-2132-11f1-aed0-ed93e2281fdd
year: '2023'
...
---
OA_place: publisher
_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.
corr_author: '1'
date_created: 2021-12-07T10:48:06Z
date_published: 2021-12-07T00:00:00Z
date_updated: 2026-04-08T06:58:55Z
day: '07'
ddc:
- '530'
degree_awarded: MS
department:
- _id: GradSch
- _id: CaGo
doi: 10.15479/at:ista:10422
file:
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date_created: 2021-12-07T11:14:01Z
date_updated: 2022-03-10T12:10:25Z
file_id: '10425'
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file_size: 47638
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content_type: application/pdf
creator: cchlebak
date_created: 2021-12-07T11:20:35Z
date_updated: 2021-12-07T11:20:35Z
file_id: '10426'
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: ba8df636-2132-11f1-aed0-ed93e2281fdd
year: '2021'
...