---
OA_place: publisher
_id: '19271'
abstract:
- lang: eng
text: "The medial habenula (MHb) is implicated in regulating emotional responses\r\nto
aversive events. Studies in zebrafish have identified a remarkable morphological\r\nleft-right
asymmetry in the dorsal habenula (zebrafish equivalent of mammalian\r\nMHb)-to-interpeduncular
nucleus (IPN) pathway and its left-side specific role in\r\nmodulating fear responses.
However, there is little evidence for structural or\r\nfunctional lateralization
in the mammalian MHb-IPN pathway.\r\nHere, I investigated the synaptic properties
of the left and right MHb\r\nafferents to the IPN in mice and addressed whether
these synaptic connections\r\nselectively influence the expression of conditioned
fear in mice. My findings reveal\r\nthat each individual IPN neuron receives inputs
from both left and right MHb.\r\nElectrophysiological recordings from the same
postsynaptic IPN neurons\r\ndemonstrate that the left MHb-originating synapses
exhibit lower release\r\nprobability and higher \U0001D6FE-aminobutyric acid type
B receptor (GABABR)-mediated\r\npotentiation compared to the right MHb-originating
synapses. Interestingly,\r\nchemogenetic inhibition of cholinergic neurons in
the left but not the right MHb\r\nsignificantly attenuated cue-dependent fear
recall. Furthermore, conditional\r\ndeletion of GABABR in the left MHb interfered
with the recall of cued fear memory,\r\nwhereas that in the right MHb neurons
spared fear memory expression.\r\nCollectively, I demonstrate a functional asymmetry
of the MHb in mice,\r\nrevealing a predominant role for GABABR-mediated signaling
in the left MHb-IPN\r\npathway in the modulation of fear memories. These findings
suggest that\r\nlateralized pathways could represent a fundamental principle in
the neural\r\nregulation of emotion across species."
acknowledged_ssus:
- _id: PreCl
- _id: M-Shop
acknowledgement: "I would like to thank the European Research Council and European
Commission, under the European Union’s Horizon 2020 research and innovation program
(ERC grant agreement no. 694539 to Ryuichi Shigemoto and the Marie Skłodowska-Curie
grant agreement no. 665385 to Cihan Önal), and the Austrian Neuroscience Association
for providing financial support and opportunities, which were important in allowing
me to present my work. I also wish to thank the\r\nPreclinical Facility, especially
Michael Schunn, for always welcoming me from my earliest days as an intern. My gratitude
goes as well to the Miba Machine Shop, in particular Todor Asenov, Astrit Arslani,
and Thomas Menner, whose technical expertise often saved the day."
alternative_title:
- ISTA Thesis
article_processing_charge: No
author:
- first_name: Hüseyin C
full_name: Önal, Hüseyin C
id: 4659D740-F248-11E8-B48F-1D18A9856A87
last_name: Önal
orcid: 0000-0002-2771-2011
citation:
ama: Önal C. Asymmetrical modulation of fear expression via GABAB receptors in the
mouse medial habenula. 2025. doi:10.15479/AT-ISTA-19271
apa: Önal, C. (2025). Asymmetrical modulation of fear expression via GABAB receptors
in the mouse medial habenula. Institute of Science and Technology Austria.
https://doi.org/10.15479/AT-ISTA-19271
chicago: Önal, Cihan. “Asymmetrical Modulation of Fear Expression via GABAB Receptors
in the Mouse Medial Habenula.” Institute of Science and Technology Austria, 2025.
https://doi.org/10.15479/AT-ISTA-19271.
ieee: C. Önal, “Asymmetrical modulation of fear expression via GABAB receptors in
the mouse medial habenula,” Institute of Science and Technology Austria, 2025.
ista: Önal C. 2025. Asymmetrical modulation of fear expression via GABAB receptors
in the mouse medial habenula. Institute of Science and Technology Austria.
mla: Önal, Cihan. Asymmetrical Modulation of Fear Expression via GABAB Receptors
in the Mouse Medial Habenula. Institute of Science and Technology Austria,
2025, doi:10.15479/AT-ISTA-19271.
short: C. Önal, Asymmetrical Modulation of Fear Expression via GABAB Receptors in
the Mouse Medial Habenula, Institute of Science and Technology Austria, 2025.
corr_author: '1'
date_created: 2025-02-28T14:15:53Z
date_published: 2025-03-04T00:00:00Z
date_updated: 2026-04-07T12:40:42Z
day: '04'
ddc:
- '570'
- '571'
- '573'
- '599'
degree_awarded: PhD
department:
- _id: GradSch
- _id: RySh
doi: 10.15479/AT-ISTA-19271
ec_funded: 1
file:
- access_level: closed
checksum: c1a4d75a7471de9f954697b06cd18d28
content_type: application/vnd.openxmlformats-officedocument.wordprocessingml.document
creator: hoenal
date_created: 2025-02-28T13:57:01Z
date_updated: 2026-02-01T23:30:02Z
embargo_to: open_access
file_id: '19272'
file_name: Cihan_Onal_Thesis_Final.docx
file_size: 25869143
relation: source_file
- access_level: open_access
checksum: de4e62147ab9f04098dc8cd898c630da
content_type: application/pdf
creator: hoenal
date_created: 2025-02-28T13:57:04Z
date_updated: 2026-02-01T23:30:02Z
embargo: 2026-02-01
file_id: '19273'
file_name: Cihan_Onal_Thesis_Final_pdfa.pdf
file_size: 12077596
relation: main_file
file_date_updated: 2026-02-01T23:30:02Z
has_accepted_license: '1'
language:
- iso: eng
month: '03'
oa: 1
oa_version: Published Version
project:
- _id: 25CA28EA-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '694539'
name: 'In situ analysis of single channel subunit composition in neurons: physiological
implication in synaptic plasticity and behaviour'
- _id: 2564DBCA-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '665385'
name: International IST Doctoral Program
publication_identifier:
eissn:
- 2663-337X
publication_status: published
publisher: Institute of Science and Technology Austria
related_material:
record:
- id: '9437'
relation: part_of_dissertation
status: public
- id: '15084'
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: Asymmetrical modulation of fear expression via GABAB receptors in the mouse
medial habenula
tmp:
image: /images/cc_by_nc.png
legal_code_url: https://creativecommons.org/licenses/by-nc/4.0/legalcode
name: Creative Commons Attribution-NonCommercial 4.0 International (CC BY-NC 4.0)
short: CC BY-NC (4.0)
type: dissertation
user_id: ba8df636-2132-11f1-aed0-ed93e2281fdd
year: '2025'
...
---
OA_type: closed access
_id: '19302'
abstract:
- lang: eng
text: "Social interaction networks of insect colonies facilitate efficient information
exchange and\r\ndemonstrate adaptive changes to mitigate disease transmission.
While circadian rhythms\r\ninfluence individual behaviour, their role in shaping
colony-level defences against pathogens\r\nremains unexplored. Here, we investigate
whether social networks of the black garden ant,\r\nLasius niger, exhibit circadian
rhythms and how these rhythms influence disease vulnerability\r\nwhen colonies
are exposed to a pathogen during the day or the night.\r\nWe first establish baseline
daily variations in activity and network dynamics in pathogen-free\r\ncolonies,
revealing constitutive daily fluctuations in disease susceptibility. Subsequently,
we\r\nexamine pathogen-induced changes in sanitary care and network dynamics by
exposing\r\nforagers to a natural pathogen (Metarhizium brunneum) during either
the day or the night.\r\nIndividual pathogen loads were measured after a nine-hour
post-exposure period to evaluate\r\ntransmission outcomes.\r\nOur results demonstrate
that diurnal ant colonies maintain robust circadian patterns in network\r\nproperties
while flexibly adapting to pathogen exposure. Ants upregulate sanitary care\r\nirrespective
of exposure timing, prioritising the protection of the valuable colony centre\r\nconsisting
of nurses and the queen. These findings underscore the robustness and adaptability\r\nof
ant colonies in balancing circadian rhythms with effective social immune responses."
acknowledged_ssus:
- _id: LifeSc
acknowledgement: Thank you to the Lab Support Facility at ISTA. Thank you to the European
Research Council (ERC) for their funding under the European Union’s Horizon 2020
research and innovation program (ERC Consolidator Grant EPIDEMICSonCHIP, No. 771402,
to Sylvia Cremer, and ERC Starting Grant DISEASE, No. 802628, to Nathalie Stroeymeyt).
alternative_title:
- ISTA Thesis
article_processing_charge: No
author:
- first_name: Linda
full_name: Sartoris, Linda
id: 2B9284CA-F248-11E8-B48F-1D18A9856A87
last_name: Sartoris
citation:
ama: Sartoris L. The effect of circadian rhythm on organisational immunity of ant
colonies. 2025. doi:10.15479/AT-ISTA-19302
apa: Sartoris, L. (2025). The effect of circadian rhythm on organisational immunity
of ant colonies. Institute of Science and Technology Austria. https://doi.org/10.15479/AT-ISTA-19302
chicago: Sartoris, Linda. “The Effect of Circadian Rhythm on Organisational Immunity
of Ant Colonies.” Institute of Science and Technology Austria, 2025. https://doi.org/10.15479/AT-ISTA-19302.
ieee: L. Sartoris, “The effect of circadian rhythm on organisational immunity of
ant colonies,” Institute of Science and Technology Austria, 2025.
ista: Sartoris L. 2025. The effect of circadian rhythm on organisational immunity
of ant colonies. Institute of Science and Technology Austria.
mla: Sartoris, Linda. The Effect of Circadian Rhythm on Organisational Immunity
of Ant Colonies. Institute of Science and Technology Austria, 2025, doi:10.15479/AT-ISTA-19302.
short: L. Sartoris, The Effect of Circadian Rhythm on Organisational Immunity of
Ant Colonies, Institute of Science and Technology Austria, 2025.
corr_author: '1'
date_created: 2025-03-06T12:16:54Z
date_published: 2025-02-24T00:00:00Z
date_updated: 2026-03-02T23:31:14Z
day: '24'
ddc:
- '577'
degree_awarded: PhD
department:
- _id: GradSch
- _id: SyCr
doi: 10.15479/AT-ISTA-19302
ec_funded: 1
file:
- access_level: closed
checksum: 7e9466dcf3681454211b74b5107e9f7b
content_type: application/vnd.openxmlformats-officedocument.wordprocessingml.document
creator: lsartori
date_created: 2025-03-07T10:16:11Z
date_updated: 2026-02-23T23:30:03Z
embargo_to: open_access
file_id: '19310'
file_name: Thesis_Linda_Sartoris.docx
file_size: 7129583
relation: source_file
- access_level: closed
checksum: 2ccfcf32f0590bb0ec1a488e606a73f5
content_type: application/pdf
creator: lsartori
date_created: 2025-03-11T10:42:20Z
date_updated: 2026-03-02T23:31:13Z
description: for printing purposes only
embargo_to: open_access
file_id: '19384'
file_name: thesis_Sartoris_for_print.pdf
file_size: 3199703
relation: other
- access_level: open_access
checksum: 1d1f3c1279065b1a7f407ff6d1ee1503
content_type: application/pdf
creator: lsartori
date_created: 2025-03-11T10:52:00Z
date_updated: 2026-02-23T23:30:03Z
embargo: 2026-02-23
file_id: '19385'
file_name: Thesis_Linda_Sartoris.pdf
file_size: 3183186
relation: main_file
file_date_updated: 2026-03-02T23:31:13Z
has_accepted_license: '1'
language:
- iso: eng
month: '02'
oa: 1
oa_version: Published Version
page: '85'
project:
- _id: 2649B4DE-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '771402'
name: Epidemics in ant societies on a chip
publication_identifier:
eissn:
- 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: The effect of circadian rhythm on organisational immunity of ant colonies
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: '2025'
...
---
OA_embargo: '12'
OA_place: publisher
_id: '19386'
abstract:
- lang: eng
text: "Crustaceans are a large group of arthropods with a great diversity of species
and\r\ndifferent types of sex determination systems and reproductive modes (Subramoniam,
2017).\r\nThis makes them a great model for exploring the evolution of sex chromosomes
and sexual\r\ndimorphism and investigating the evolutionary mechanisms driving
and maintaining the\r\ndiversity of reproductive systems. Within this taxon, Brine
shrimp of the genus Artemia, a\r\nbranchiopod crustacean, are well suited for
such explorations, as they have both highly\r\ndimorphic traits and closely related
sexual and asexual species. Although brine shrimp are\r\nknown to have ZW sex
chromosomes (Bowen, 1963; Parraguez et al., 2009), the sex\r\nchromosomes are
still not well characterized at the genomic level, the sex-determination gene\r\nis
unknown, and it is still unclear whether the same sex chromosomes as shared by
the\r\ndifferent species.\r\nThe first part of this thesis was to characterize
the Z and W chromosomes in Artemia\r\nusing an array of methods, from generating
multiple chromosome and contig level genome\r\nassemblies to identifying W-linked
scaffolds and transcripts in multiple species using k-mer\r\nbased approaches.\r\nThe
second part tackles the conservation of the cell type specific regulatory pathways\r\nin
the female reproductive system between Artemia and Drosophila, and the expression
of the\r\nZ-specific region throughout meiosis using single-nucleus RNA-seq data.
Our results show\r\nthat germline cells lack dosage compensation, with a subset
of cells showing evidence of\r\nextreme repression of the Z chromosome.\r\nWith
multiple sexual species and several asexual lineages of parthenogenetic females\r\nthat
produce rare males at low frequencies, Brine shrimp present the perfect opportunity
to\r\nexplore the transition to asexuality and shed light on the prerequisites
and repercussions of\r\nthe form of modified meiosis maintaining the asexual lineages.
The last chapter is an\r\ninvestigation of the molecular pathways involved in
asexual reproduction in Artemia using\r\nnewly generated single nucleus RNAseq
and WGS data and previously published data. "
acknowledged_ssus:
- _id: ScienComp
acknowledgement: My PhD work was funded by the Austrian science fund (FWF), as part
of the SFB Meiosis consortium (https://sfbmeiosis.org/, grant ID FWF SFB F88-10).
alternative_title:
- ISTA Thesis
article_processing_charge: No
author:
- first_name: Marwan N
full_name: Elkrewi, Marwan N
id: 0B46FACA-A8E1-11E9-9BD3-79D1E5697425
last_name: Elkrewi
orcid: 0000-0002-5328-7231
citation:
ama: Elkrewi MN. Evolution of sex chromosomes, sex determination and asexuality
in Artemia brine shrimp. 2025. doi:10.15479/AT-ISTA-19386
apa: Elkrewi, M. N. (2025). Evolution of sex chromosomes, sex determination and
asexuality in Artemia brine shrimp. Institute of Science and Technology Austria.
https://doi.org/10.15479/AT-ISTA-19386
chicago: Elkrewi, Marwan N. “Evolution of Sex Chromosomes, Sex Determination and
Asexuality in Artemia Brine Shrimp.” Institute of Science and Technology Austria,
2025. https://doi.org/10.15479/AT-ISTA-19386.
ieee: M. N. Elkrewi, “Evolution of sex chromosomes, sex determination and asexuality
in Artemia brine shrimp,” Institute of Science and Technology Austria, 2025.
ista: Elkrewi MN. 2025. Evolution of sex chromosomes, sex determination and asexuality
in Artemia brine shrimp. Institute of Science and Technology Austria.
mla: Elkrewi, Marwan N. Evolution of Sex Chromosomes, Sex Determination and Asexuality
in Artemia Brine Shrimp. Institute of Science and Technology Austria, 2025,
doi:10.15479/AT-ISTA-19386.
short: M.N. Elkrewi, Evolution of Sex Chromosomes, Sex Determination and Asexuality
in Artemia Brine Shrimp, Institute of Science and Technology Austria, 2025.
corr_author: '1'
date_created: 2025-03-11T12:54:31Z
date_published: 2025-03-14T00:00:00Z
date_updated: 2026-04-16T12:20:41Z
day: '14'
ddc:
- '570'
- '576'
degree_awarded: PhD
department:
- _id: GradSch
- _id: BeVi
doi: 10.15479/AT-ISTA-19386
file:
- access_level: closed
checksum: 5549a8216c07e4c39281648912d72246
content_type: application/vnd.openxmlformats-officedocument.wordprocessingml.document
creator: melkrewi
date_created: 2025-03-26T07:06:56Z
date_updated: 2026-03-26T23:30:03Z
embargo_to: open_access
file_id: '19462'
file_name: Thesis_Marwan_Elkrewi.docx
file_size: 25019680
relation: source_file
- access_level: open_access
checksum: aed2ba9965aa89b3414deae1ae9f4321
content_type: application/pdf
creator: melkrewi
date_created: 2025-03-26T07:06:22Z
date_updated: 2026-03-26T23:30:03Z
embargo: 2026-03-26
file_id: '19463'
file_name: Thesis_Marwan_Elkrewi.pdf
file_size: 17294844
relation: main_file
file_date_updated: 2026-03-26T23:30:03Z
has_accepted_license: '1'
language:
- iso: eng
month: '03'
oa: 1
oa_version: Published Version
page: '170'
project:
- _id: 34ae1506-11ca-11ed-8bc3-c14f4c474396
grant_number: F8810
name: The highjacking of meiosis for asexual reproduction
publication_identifier:
eissn:
- 2663-337X
isbn:
- '9783990780534'
publication_status: published
publisher: Institute of Science and Technology Austria
related_material:
record:
- id: '12248'
relation: part_of_dissertation
status: public
- id: '10167'
relation: part_of_dissertation
status: public
- id: '10767'
relation: part_of_dissertation
status: public
- id: '15009'
relation: part_of_dissertation
status: public
- id: '14613'
relation: part_of_dissertation
status: public
- id: '17890'
relation: part_of_dissertation
status: public
status: public
supervisor:
- first_name: Beatriz
full_name: Vicoso, Beatriz
id: 49E1C5C6-F248-11E8-B48F-1D18A9856A87
last_name: Vicoso
orcid: 0000-0002-4579-8306
title: Evolution of sex chromosomes, sex determination and asexuality in Artemia brine
shrimp
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: '2025'
...
---
OA_place: publisher
_id: '19431'
abstract:
- lang: eng
text: "Gene expression is crucial for cell differentiation, development and survival
of\r\norganisms. It consists of several steps, starting with transcription that
is mediated by\r\nRNA polymerases. These are protein machineries transcribing
and producing different\r\ntypes of RNAs. Although, the individual steps of transcription
by RNA polymerase II\r\n(Pol II) as well as the structure of Pol II has been extensively
studied, surprisingly,\r\nthere is still little known about its regulation and
assembly in cytoplasm. Among the\r\nproteins that are important in biogenesis
of Pol II are RNA polymerase II associating\r\nproteins (RPAP) and small GPN-loop
GTPases (GPN). Both of these protein groups\r\nwere shown to take essential part
in assembly of Pol II.\r\nThe aim of this project was to deepen our knowledge
in regulation of Pol II in\r\nthe cytoplasm as well as the proteins involved in
this process. Techniques of structural\r\nbiology, biochemistry and cell biology
were employed to study and characterize cytoplasmic Pol II and its interacting
partners.\r\nThis study shows for the first time the structure of cytoplasmic
Pol II at high\r\nresolution. The structure also reveals proteins interacting
with Pol II in cytoplasm,\r\nnamely GDOWN1, RPAP2. Comparing the structure of
cytoplasmic Pol II with transcribing Pol II revealed striking difference in clamp
region that is not in closed state.\r\nFurthermore, GDOWN1 and RPAP2 make steric
clashes with various transcription\r\nfactors bound to Pol II during different
stages of transcription. Even though GPN1 and\r\nGPN3 proteins were not resolved
in the cytoplasmic Pol II structure, they are part of\r\nthe complex and their
interaction with Pol II was confirmed in vitro. RPAP2 stabilizes\r\nthese proteins
on Pol II and several experiments suggest that they interact with the\r\nclamp
region. In addition, GDOWN1, RPAP2 and GPNs might keep clamp in open or\r\npartially
open state. Based on these results I propose a novel model of regulation of\r\nPol
II in cytoplasm. GDOWN1, RPAP2, GPN1 and GPN3 bind to Pol II in cytoplasm\r\nand
doing so they can prevent pre-mature binding of DNA or RNA and different transcription
factors to Pol II in cytoplasm or before engaging in transcription nucleus.\r\nThis
research contributes to the current knowledge of molecular mechanisms\r\nof Pol
II regulation in cytoplasm."
acknowledged_ssus:
- _id: LifeSc
- _id: EM-Fac
- _id: ScienComp
acknowledgement: 'I would also like to acknowledge the ISTA Facilities: Lab Support
Facility, Protein Services and Electron Microscopy Facility (EMF) and Scientific
Computing. EMF for their support during data collections and troubleshooting, especially
Valentin. Scientific Computing for solving quickly any issues related with cluster.'
alternative_title:
- ISTA Thesis
article_processing_charge: No
author:
- first_name: Annamaria
full_name: Hlavata, Annamaria
id: 36062FEC-F248-11E8-B48F-1D18A9856A87
last_name: Hlavata
citation:
ama: Hlavata A. Regulation of Cytoplasmic RNA Polymerase II. 2025. doi:10.15479/10.15479/AT-ISTA-19431
apa: Hlavata, A. (2025). Regulation of Cytoplasmic RNA Polymerase II. Institute
of Science and Technology Austria. https://doi.org/10.15479/10.15479/AT-ISTA-19431
chicago: Hlavata, Annamaria. “Regulation of Cytoplasmic RNA Polymerase II.” Institute
of Science and Technology Austria, 2025. https://doi.org/10.15479/10.15479/AT-ISTA-19431.
ieee: A. Hlavata, “Regulation of Cytoplasmic RNA Polymerase II,” Institute of Science
and Technology Austria, 2025.
ista: Hlavata A. 2025. Regulation of Cytoplasmic RNA Polymerase II. Institute of
Science and Technology Austria.
mla: Hlavata, Annamaria. Regulation of Cytoplasmic RNA Polymerase II. Institute
of Science and Technology Austria, 2025, doi:10.15479/10.15479/AT-ISTA-19431.
short: A. Hlavata, Regulation of Cytoplasmic RNA Polymerase II, Institute of Science
and Technology Austria, 2025.
corr_author: '1'
date_created: 2025-03-20T12:52:47Z
date_published: 2025-03-20T00:00:00Z
date_updated: 2026-04-07T11:46:32Z
day: '20'
ddc:
- '572'
degree_awarded: PhD
department:
- _id: GradSch
- _id: CaBe
doi: 10.15479/10.15479/AT-ISTA-19431
file:
- access_level: closed
checksum: b7ddf424ffe95f8c767c53c8bb62d4f3
content_type: application/vnd.openxmlformats-officedocument.wordprocessingml.document
creator: ahlavata
date_created: 2025-03-24T12:48:36Z
date_updated: 2026-03-20T23:30:04Z
embargo_to: open_access
file_id: '19448'
file_name: PhD_Thesis_Hlavata_final_submission.docx
file_size: 23506747
relation: source_file
- access_level: open_access
checksum: 6c5a59c9bac467c3d0b3ffb8ea6d9fd4
content_type: application/pdf
creator: ahlavata
date_created: 2025-03-24T12:51:10Z
date_updated: 2026-03-20T23:30:04Z
embargo: 2026-03-20
file_id: '19449'
file_name: PhD_Thesis_Hlavata_final_submission_update.pdf
file_size: 9478591
relation: main_file
file_date_updated: 2026-03-20T23:30:04Z
has_accepted_license: '1'
language:
- iso: eng
month: '03'
oa: 1
oa_version: Published Version
page: '83'
publication_identifier:
eissn:
- 2663-337X
isbn:
- 978-3-99078-055-8
publication_status: published
publisher: Institute of Science and Technology Austria
status: public
supervisor:
- first_name: Carrie A
full_name: Bernecky, Carrie A
id: 2CB9DFE2-F248-11E8-B48F-1D18A9856A87
last_name: Bernecky
orcid: 0000-0003-0893-7036
title: Regulation of Cytoplasmic RNA Polymerase II
type: dissertation
user_id: ba8df636-2132-11f1-aed0-ed93e2281fdd
year: '2025'
...
---
OA_embargo: 6 months
OA_place: publisher
_id: '19456'
abstract:
- lang: eng
text: "Making decisions requires flexibly adapting to changing environments, a process
that\r\ndepends on accurately interpreting current contingencies and integrating
them with\r\npast experience. Two brain regions are particularly critical for
this process, the medial\r\nprefrontal cortex (mPFC) and the hippocampus. Using
contextual information from the\r\nhippocampus, the mPFC selects relevant cognitive
frameworks and suppresses\r\nirrelevant ones to guide appropriate actions. Several
studies have shown that some\r\nmPFC pyramidal neurons become spatially tuned
when spatial information is required\r\nto guide goal-directed behavior. However,
the role of prefrontal spatial representations\r\nin learning and decision making
is not well understood. This work aims to characterize\r\nthe role of mPFC spatial
tuning in supporting a contextual association task. Rats were\r\ntrained to learn
two cue–location associations on a radial arm maze over multiple days,\r\nwhile
we simultaneously recorded from dorsal CA1 of the hippocampus and the\r\nprelimbic
area of the mPFC. We describe a subset of spatially tuned hippocampal and\r\nprefrontal
pyramidal neurons that “flicker” between multiple spatial representations on\r\ndifferent
trials, suggesting dynamic, context-dependent coding. This flickering may\r\nprovide
a substrate for how the network reorganizes in response to task demands,\r\nlikely
by enabling the flexible evaluation of competing representations. "
acknowledged_ssus:
- _id: PreCl
- _id: Bio
- _id: LifeSc
- _id: M-Shop
alternative_title:
- ISTA Thesis
article_processing_charge: No
author:
- first_name: Andrea D
full_name: Cumpelik, Andrea D
id: 3F158B32-F248-11E8-B48F-1D18A9856A87
last_name: Cumpelik
orcid: 0000-0003-1727-6612
citation:
ama: Cumpelik AD. The role of prefrontal spatial coding in supporting a contextual
association task. 2025. doi:10.15479/AT-ISTA-19456
apa: Cumpelik, A. D. (2025). The role of prefrontal spatial coding in supporting
a contextual association task. Institute of Science and Technology Austria.
https://doi.org/10.15479/AT-ISTA-19456
chicago: Cumpelik, Andrea D. “The Role of Prefrontal Spatial Coding in Supporting
a Contextual Association Task.” Institute of Science and Technology Austria, 2025.
https://doi.org/10.15479/AT-ISTA-19456.
ieee: A. D. Cumpelik, “The role of prefrontal spatial coding in supporting a contextual
association task,” Institute of Science and Technology Austria, 2025.
ista: Cumpelik AD. 2025. The role of prefrontal spatial coding in supporting a contextual
association task. Institute of Science and Technology Austria.
mla: Cumpelik, Andrea D. The Role of Prefrontal Spatial Coding in Supporting
a Contextual Association Task. Institute of Science and Technology Austria,
2025, doi:10.15479/AT-ISTA-19456.
short: A.D. Cumpelik, The Role of Prefrontal Spatial Coding in Supporting a Contextual
Association Task, Institute of Science and Technology Austria, 2025.
corr_author: '1'
date_created: 2025-03-25T11:22:38Z
date_published: 2025-02-18T00:00:00Z
date_updated: 2026-04-07T12:37:58Z
day: '18'
ddc:
- '612'
degree_awarded: PhD
department:
- _id: GradSch
- _id: JoCs
doi: 10.15479/AT-ISTA-19456
file:
- access_level: open_access
checksum: 1c7573303d8e5f6da3eb03d59055390f
content_type: application/pdf
creator: acumpeli
date_created: 2025-03-25T11:07:55Z
date_updated: 2025-09-30T22:30:02Z
embargo: 2025-09-30
file_id: '19457'
file_name: 2025_Thesis_Cumpelik_corrections_PDFA.pdf
file_size: 11869040
relation: main_file
- access_level: closed
checksum: b93265ebd9a53f7a14100d0d48b4ff5b
content_type: application/vnd.openxmlformats-officedocument.wordprocessingml.document
creator: acumpeli
date_created: 2025-03-25T11:08:05Z
date_updated: 2025-09-30T22:30:02Z
embargo_to: open_access
file_id: '19458'
file_name: 2025_Thesis_Cumpelik_corrections.docx
file_size: 20436467
relation: source_file
file_date_updated: 2025-09-30T22:30:02Z
has_accepted_license: '1'
keyword:
- neuroscience
- decision making
- learning
- cognitive flexibility
- medial prefrontal cortex
- hippocampus
- electrophysiology
language:
- iso: eng
month: '02'
oa: 1
oa_version: Published Version
page: '96'
publication_identifier:
isbn:
- 978-3-99078-056-5
issn:
- 2663-337X
publication_status: published
publisher: Institute of Science and Technology Austria
status: public
supervisor:
- first_name: Jozsef L
full_name: Csicsvari, Jozsef L
id: 3FA14672-F248-11E8-B48F-1D18A9856A87
last_name: Csicsvari
orcid: 0000-0002-5193-4036
title: The role of prefrontal spatial coding in supporting a contextual association
task
type: dissertation
user_id: ba8df636-2132-11f1-aed0-ed93e2281fdd
year: '2025'
...
---
OA_embargo: '6'
OA_place: publisher
_id: '19745'
abstract:
- lang: eng
text: "Cell migration is a crucial process in animal development and maintenance.
It is incredibly\r\nheterogeneous, with different cell types utilizing fundamentally
distinct migration strategies.\r\nThe strategies also depend on the cellular microenvironment,
where cells can switch between\r\nmigration modes as they encounter new environmental
cues. In this thesis, we investigated\r\nhow dendritic cells adapt their migration
strategy when encountering geometrically,\r\nmechanically and chemically distinct
environments.\r\nWhen dendritic cells are embedded in a homogeneous fibrous network,
they migrate in a fast\r\nand directional amoeboid manner. In this migration strategy,
extracellular proteolysis and\r\nintegrin-mediated adhesions are dispensable.
Instead, the cells use topography of the\r\nenvironment to propel their cell body
forward. To migrate efficiently in the maze of different\r\npore sizes, they position
the nucleus ahead of the microtubule organizing center (MTOC) and\r\nuse it to
gauge the pores to identify the path of least resistance. Our aim was to identify\r\nwhether
dendritic cells adapt their migration strategy when encountering asymmetrical\r\ntransitions
into much denser environments with limited choice of large pores. In such invasive\r\ntransitions
it is unclear if the cells can cross tight pores without the use of adhesions
and\r\nextracellular proteolysis and whether they maintain the nucleus in the
cell front.\r\nUsing various cell migration assays such as fibrous 3D collagen
gels, geometrically defined\r\nmicrochannels with constrictions and simplistic
under agarose migration assay, we provide\r\na comprehensive characterization
of invasive migration of dendritic cells. We show that\r\nduring invasion the
cells stall and stretch, reflecting the difficulty to translocate the bulky cell\r\nbody
into the dense environment. In collagen gels, we show that dendritic cells can
invade\r\nwithout proteolysis and adhesions. Instead, they utilize contractility,
which can lead to largescale collagen compressions. During invasion, the nucleus
stalls at tight constrictions, leading\r\nto a transient organelle reorientation.
To resolve the stalling, upregulated rear contractility is\r\nrequired. This contractile
force is simultaneously necessary for reverting the nucleus back to\r\nthe cell
front after invasion and maintaining this positioning during permissive migration.\r\nA
functional role of the reorientation was uncovered in the first collaboration
project.\r\nA prominent central actin pool was identified around the MTOC, especially
pronounced in\r\ndense and compressive environments. The actin pool was shown
to generate pushing forces\r\nto dilate the space for cell translocation. These
forces are only necessary in non-permissive\r\nenvironments, where the nucleus
reorients to the cell rear, allowing the actin pool to\r\ngenerate space. In permissive
environments where space generation is dispensable, the\r\nMTOC is located behind
the nucleus and the actin cloud has reduced intensity, allowing more\r\nactin
to be incorporated into the lamellipodium, speeding up migration.\r\nIn the second
collaboration project, we investigated the effects of distinct chemical\r\nenvironments
on dendritic cell migration. The strikingly persistent migration of these cells\r\nwas
explained by their ability to modulate and even self-generate chemokine gradients.
This\r\nallows the cells to migrate faster and more persistent in uniform chemokine
fields compared\r\nto imposed chemokine gradients. The chemokine receptor CCR7
was identified as a crucial\r\nplayer in this process, both sensing the signal
and internalizing the chemokine to create a sink."
acknowledgement: "This project has received funding from the Austrian Science Fund
(FWF) via the doctorate\r\ncollege DK NanoCell and from the European Union’s Horizon
2020 research and innovation\r\nprogramme under the Marie Skłodowska-Curie Grant
Agreement No. 665385.\r\n"
alternative_title:
- ISTA Thesis
article_processing_charge: No
author:
- first_name: Nikola
full_name: Canigova, Nikola
id: 3795523E-F248-11E8-B48F-1D18A9856A87
last_name: Canigova
orcid: 0000-0002-8518-5926
citation:
ama: Canigova N. Adaptive strategies of dendritic cell migration in response to
environmental cues. 2025. doi:10.15479/AT-ISTA-19745
apa: Canigova, N. (2025). Adaptive strategies of dendritic cell migration in
response to environmental cues. Institute of Science and Technology Austria.
https://doi.org/10.15479/AT-ISTA-19745
chicago: Canigova, Nikola. “Adaptive Strategies of Dendritic Cell Migration in Response
to Environmental Cues.” Institute of Science and Technology Austria, 2025. https://doi.org/10.15479/AT-ISTA-19745.
ieee: N. Canigova, “Adaptive strategies of dendritic cell migration in response
to environmental cues,” Institute of Science and Technology Austria, 2025.
ista: Canigova N. 2025. Adaptive strategies of dendritic cell migration in response
to environmental cues. Institute of Science and Technology Austria.
mla: Canigova, Nikola. Adaptive Strategies of Dendritic Cell Migration in Response
to Environmental Cues. Institute of Science and Technology Austria, 2025,
doi:10.15479/AT-ISTA-19745.
short: N. Canigova, Adaptive Strategies of Dendritic Cell Migration in Response
to Environmental Cues, Institute of Science and Technology Austria, 2025.
corr_author: '1'
date_created: 2025-05-26T08:49:00Z
date_published: 2025-05-27T00:00:00Z
date_updated: 2026-06-18T17:34:48Z
day: '27'
ddc:
- '570'
degree_awarded: PhD
department:
- _id: MiSi
- _id: GradSch
doi: 10.15479/AT-ISTA-19745
ec_funded: 1
file:
- access_level: closed
checksum: 1a2d1525d19347fbb879ef57c02951bf
content_type: application/vnd.openxmlformats-officedocument.wordprocessingml.document
creator: cchlebak
date_created: 2025-05-28T07:38:17Z
date_updated: 2025-11-27T23:30:02Z
embargo_to: open_access
file_id: '19748'
file_name: NikolaCanigova_Thesis_final.docx
file_size: 103879193
relation: source_file
- access_level: open_access
checksum: c1d8f9a40a8e19fcf895373f4b773a46
content_type: application/pdf
creator: cchlebak
date_created: 2025-05-28T07:39:53Z
date_updated: 2025-11-27T23:30:02Z
embargo: 2025-11-27
file_id: '19749'
file_name: NikolaCanigova_Thesis_final_PDFA2a_fixed.pdf
file_size: 194530600
relation: main_file
file_date_updated: 2025-11-27T23:30:02Z
has_accepted_license: '1'
language:
- iso: eng
month: '05'
oa: 1
oa_version: Published Version
page: '133'
project:
- _id: 2564DBCA-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '665385'
name: International IST Doctoral Program
- _id: 265E2996-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: W01250-B20
name: Nano-Analytics of Cellular Systems
publication_identifier:
isbn:
- 978-3-99078-058-9
issn:
- 2663-337X
publication_status: published
publisher: Institute of Science and Technology Austria
related_material:
record:
- id: '14274'
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: Adaptive strategies of dendritic cell migration in response to environmental
cues
type: dissertation
user_id: ba8df636-2132-11f1-aed0-ed93e2281fdd
year: '2025'
...
---
OA_place: publisher
_id: '19533'
abstract:
- lang: eng
text: "This thesis explores advancements in quantum remote sensing and non-equilibrium
phase\r\ntransitions in the microwave regime, with a focus on dissipative phase
transitions and quantumenhanced sensing.\r\nIn the first project, I experimentally
studied photon blockade breakdown as a dissipative phase\r\ntransition in a zero-dimensional
cavity-qubit system. By defining an appropriate thermodynamic\r\nlimit, we demonstrated
that the observed bistability is a genuine signature of a first-order\r\nphase
transition in this system. This work provides insight into non-equilibrium quantum\r\ndynamics
and phase transitions in driven-dissipative open quantum systems.\r\nThe second
project focuses on the experimental realization of a phase-conjugate receiver
for\r\nquantum illumination (QI), a quantum sensing protocol that enhances target
detection in noisy\r\nenvironments using entangled light. While an ideal spontaneous
parametric down-conversion\r\n(SPDC) source and receiver could, in theory, provide
up to a 6 dB advantage over classical\r\nillumination, no such ideal receiver
exists. Instead, we explore an experimental realization of a\r\nphase-conjugate
receiver for QI in the microwave regime at millikelvin temperatures using a\r\nJosephson
parametric converter (JPC) as a source of continuous-variable Gaussian entangled\r\nsignal-idler
pairs, where a maximum 3 dB advantage is theoretically achievable. We investigate\r\nkey
experimental limitations that constrain practical QI performance, contributing
to the\r\ndevelopment of quantum-enhanced sensing.\r\nAdditionally, this thesis
presents efficient digital signal processing (DSP) techniques implemented in C++
and Python in collaboration with Przemysław Zieliński and Luka Drmić. These\r\nmethods,
optimized using the Intel Integrated Performance Primitives (IPP) library, have
been\r\nessential in data acquisition, noise filtering, and correlation analysis
across multiple research\r\nprojects. Although not real-time, these DSP techniques
significantly enhance the accuracy of\r\nquantum measurements.\r\nOverall, this
thesis advances quantum-enhanced sensing by establishing the thermodynamic\r\nlimit
in a single transmon-cavity system and experimentally exploring a phase-conjugate
receiver\r\nfor QI. These findings contribute to quantum metrology, particularly
for weak signal detection\r\nand remote sensing in noisy environments.\r\n"
acknowledged_ssus:
- _id: ScienComp
- _id: M-Shop
- _id: NanoFab
- _id: LifeSc
- _id: SSU
acknowledgement: "I acknowledge the generous financial support of the Austrian Science
Fund (FWF) via BeyondC\r\n(F7105) and the European Union’s Horizon 2020 research
and innovation program (FETopen\r\nQUARTET, Grant Agreement No. 862644), which made
this research possible. I also extend\r\nmy sincere appreciation to the MIBA workshop
and the Institute of Science and Technology\r\nAustria nanofabrication facility
for their technical assistance, which was instrumental in realizing\r\nthis work."
alternative_title:
- ISTA Thesis
article_processing_charge: No
author:
- first_name: Riya
full_name: Sett, Riya
id: 2E6D040E-F248-11E8-B48F-1D18A9856A87
last_name: Sett
orcid: 0000-0001-7641-8348
citation:
ama: Sett R. Quantum remote sensing and non-equilibrium phase transitions in the
microwave regime. 2025. doi:10.15479/AT-ISTA-19533
apa: Sett, R. (2025). Quantum remote sensing and non-equilibrium phase transitions
in the microwave regime. Institute of Science and Technology Austria. https://doi.org/10.15479/AT-ISTA-19533
chicago: Sett, Riya. “ Quantum Remote Sensing and Non-Equilibrium Phase Transitions
in the Microwave Regime.” Institute of Science and Technology Austria, 2025. https://doi.org/10.15479/AT-ISTA-19533.
ieee: R. Sett, “ Quantum remote sensing and non-equilibrium phase transitions in
the microwave regime,” Institute of Science and Technology Austria, 2025.
ista: Sett R. 2025. Quantum remote sensing and non-equilibrium phase transitions
in the microwave regime. Institute of Science and Technology Austria.
mla: Sett, Riya. Quantum Remote Sensing and Non-Equilibrium Phase Transitions
in the Microwave Regime. Institute of Science and Technology Austria, 2025,
doi:10.15479/AT-ISTA-19533.
short: R. Sett, Quantum Remote Sensing and Non-Equilibrium Phase Transitions in
the Microwave Regime, Institute of Science and Technology Austria, 2025.
corr_author: '1'
date_created: 2025-04-09T16:44:26Z
date_published: 2025-04-01T00:00:00Z
date_updated: 2026-06-03T07:16:05Z
day: '1'
ddc:
- '530'
degree_awarded: PhD
department:
- _id: GradSch
- _id: JoFi
doi: 10.15479/AT-ISTA-19533
ec_funded: 1
file:
- access_level: open_access
checksum: ba6cd2289d0141a160a14fc97df1632f
content_type: application/pdf
creator: rsett
date_created: 2025-04-10T11:33:22Z
date_updated: 2025-10-11T22:30:02Z
embargo: 2025-10-11
file_id: '19538'
file_name: PhD_Thesis_Riya_Sett_pdfa.pdf
file_size: 4129208
relation: main_file
- access_level: closed
checksum: ee63a94cb8f7adf5e766903028b81ed6
content_type: application/x-zip-compressed
creator: rsett
date_created: 2025-04-10T11:34:08Z
date_updated: 2025-10-11T22:30:02Z
embargo_to: open_access
file_id: '19539'
file_name: PhD Thesis Riya Sett.zip
file_size: 6646110
relation: source_file
file_date_updated: 2025-10-11T22:30:02Z
has_accepted_license: '1'
keyword:
- phase transition
- open quantum system
- phase diagram
- cavity quantum electrodynamics
- superconducting qubits
- semiclassical physics
- quantum optics
- josephson junction
- parametric converter
- phase conjugation
- quantum radar
- quantum entanglement
- correlation
- quantum sensing
language:
- iso: eng
month: '04'
oa: 1
oa_version: Published Version
page: '109'
project:
- _id: 237CBA6C-32DE-11EA-91FC-C7463DDC885E
call_identifier: H2020
grant_number: '862644'
name: Quantum readout techniques and technologies
- _id: bdb108fd-d553-11ed-ba76-83dc74a9864f
grant_number: F07105
name: QUANTUM INFORMATION SYSTEMS BEYOND CLASSICAL CAPABILITIES / P5- Integration
of Superconducting Quantum Circuits
publication_identifier:
issn:
- 2663-337X
publication_status: published
publisher: Institute of Science and Technology Austria
related_material:
record:
- id: '18978'
relation: research_data
status: public
- id: '19280'
relation: part_of_dissertation
status: public
- id: '17183'
relation: part_of_dissertation
status: public
- id: '13117'
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: ' Quantum remote sensing and non-equilibrium phase transitions in the microwave
regime'
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: '2025'
...
---
OA_embargo: '12'
OA_place: publisher
_id: '19722'
abstract:
- lang: eng
text: "As root epidermal cells progress from a phase of elongation to differentiation,
their\r\ncortical microtubule (MT) arrays exhibit a transversal-to-longitudinal
reorientation. The\r\nhormone cytokinin, a key regulator of root development,
facilitates these cytoskeletal\r\nchanges. However, the molecular mechanisms underlying
hormone-mediated MT\r\nreorientation during root development are still unknown.
Here, we find that MT reorientation\r\nin root cells differs from the existing
model in hypocotyl cells, as it does not rely on MT plusend rescue. We show that
cytokinin facilitates MT array reorganization during cell\r\ndifferentiation by
promoting katanin’s (KTN1) severing activity, and by modulating KTN1’s\r\nassociation
with microtubules. Cytokinin regulates SPIRAL2 (SPR2) in a phosphorylationdependent
manner, directing its localization to, and stabilization of, the new MT minus-end\r\ncreated
by katanin-mediated severing at crossovers. Notably, our findings suggest that\r\ndynamic
and reversible phosphorylation at S579 of SPR2 is crucial for the proper functioning\r\nof
the MT severing machinery. Finally, we identify MAP65-1 and CLASP as additional
targets\r\nof cytokinin-dependent phosphoregulation. Cytokinin treatment decreases
MT-MAP65-1\r\nassociation in elongating cells, likely to expose MTs to KTN1-mediated
severing, whereas it\r\nincreases MT-CLASP association to stabilize the growing
plus-end. In this way, cytokinin drives\r\nMT reorganization during cell development
by simultaneously modulating several\r\nmicrotubule-associated proteins. These
results reveal key molecular players in hormonemediated cytoskeletal regulation,
and highlight protein phosphorylation as a powerful tool\r\nduring this process."
acknowledged_ssus:
- _id: Bio
- _id: LifeSc
acknowledgement: Special thanks to the Plant Facility.
alternative_title:
- ISTA Thesis
article_processing_charge: No
author:
- first_name: Syamala
full_name: Inumella, Syamala
id: F8660870-D756-11E9-98C5-34DFE5697425
last_name: Inumella
orcid: 0009-0002-5890-120X
citation:
ama: Inumella S. Molecular mechanisms of microtubule reorganization in elongating
root epidermal cells. 2025. doi:10.15479/AT-ISTA-19722
apa: Inumella, S. (2025). Molecular mechanisms of microtubule reorganization
in elongating root epidermal cells. Institute of Science and Technology Austria.
https://doi.org/10.15479/AT-ISTA-19722
chicago: Inumella, Syamala. “Molecular Mechanisms of Microtubule Reorganization
in Elongating Root Epidermal Cells.” Institute of Science and Technology Austria,
2025. https://doi.org/10.15479/AT-ISTA-19722.
ieee: S. Inumella, “Molecular mechanisms of microtubule reorganization in elongating
root epidermal cells,” Institute of Science and Technology Austria, 2025.
ista: Inumella S. 2025. Molecular mechanisms of microtubule reorganization in elongating
root epidermal cells. Institute of Science and Technology Austria.
mla: Inumella, Syamala. Molecular Mechanisms of Microtubule Reorganization in
Elongating Root Epidermal Cells. Institute of Science and Technology Austria,
2025, doi:10.15479/AT-ISTA-19722.
short: S. Inumella, Molecular Mechanisms of Microtubule Reorganization in Elongating
Root Epidermal Cells, Institute of Science and Technology Austria, 2025.
corr_author: '1'
date_created: 2025-05-23T15:21:29Z
date_published: 2025-05-23T00:00:00Z
date_updated: 2026-06-12T08:34:29Z
day: '23'
ddc:
- '580'
degree_awarded: PhD
department:
- _id: GradSch
- _id: EvBe
doi: 10.15479/AT-ISTA-19722
file:
- access_level: open_access
checksum: 847ec70b2e40f50e0ddc7b8da201d52c
content_type: application/pdf
creator: sinumell
date_created: 2025-05-28T11:59:11Z
date_updated: 2026-05-23T22:30:02Z
embargo: 2026-05-23
file_id: '19757'
file_name: Final Thesis_Syamala Inumella.pdf
file_size: 8292363
relation: main_file
- access_level: closed
checksum: 17cdffdae13a5f65bdad9c84e9e0e3bd
content_type: application/vnd.openxmlformats-officedocument.wordprocessingml.document
creator: sinumell
date_created: 2025-05-28T11:59:11Z
date_updated: 2026-05-23T22:30:02Z
embargo_to: open_access
file_id: '19758'
file_name: Final Thesis_Syamala Inumella.docx
file_size: 7145703
relation: source_file
file_date_updated: 2026-05-23T22:30:02Z
has_accepted_license: '1'
language:
- iso: eng
month: '05'
oa: 1
oa_version: Published Version
page: '113'
publication_identifier:
isbn:
- 978-3-99078-059-6
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: Molecular mechanisms of microtubule reorganization in elongating root epidermal
cells
type: dissertation
user_id: 8b945eb4-e2f2-11eb-945a-df72226e66a9
year: '2025'
...
---
OA_place: publisher
_id: '19763'
abstract:
- lang: eng
text: "Pattern formation in developing organs is controlled by morphogens. These
signalling\r\nmolecules form concentration gradients across tissues, thereby providing
positional\r\ninformation that instructs the pattern of cell differentiation.
Morphogen gradients are highly\r\ndynamic in space and time. Many factors such
as morphogen production, spreading,\r\ndegradation, cellular rearrangements and
others could contribute to changes in the gradient\r\nshape, yet how the spatiotemporal
signalling dynamics arise in many systems is still unclear.\r\nWe studied the
dynamics of morphogen signalling and tissue patterning in the developing\r\nvertebrate
neural tube. In this system, neural crest, roof plate and distinct dorsal progenitor\r\nsubtypes
are specified in a spatially and temporally ordered manner in response to dorsal-toventral
gradients of BMP and WNT signalling activity. How the BMP and WNT gradients are\r\nestablished
and interpreted to ensure ordered cell specification is poorly understood.\r\nTo
address this question, we developed a 2D embryonic stem cell differentiation system
that\r\ncaptures key features of dorsal neural tube development. In this system,
differentiated\r\ncolonies display remarkable self-organised pattern formation
in response to uniformly\r\napplied BMP ligand. We established a method of differentiating
the colonies using\r\nmicrofabricated stencils, which allowed us to control the
initial size and shape of colonies\r\nwithout confining cell migration and colony
growth. This led to highly reproducible pattern\r\nformation that facilitates
quantification.\r\nUsing this approach, we observed striking two-phase temporal
dynamics of BMP signalling in\r\nour colonies: a BMP gradient rapidly forms from
the periphery to the centre of colonies,\r\nsubsequently disappears and is re-established
again in the second phase. By combining our\r\nquantitative data with a data-driven
theoretical model, we uncovered a temporal relay\r\nmechanism that underlies this
biphasic BMP signalling dynamics. The first signalling phase is\r\ncontrolled
by fast tissue-autonomous negative feedback that restricts the duration of the\r\ninitial
response to BMP. The early BMP activity gradient moreover controls the spatial\r\norganisation
of the cell type pattern: the absence of a first phase results in disordered cell\r\ntype
pattern. The second phase is controlled by slow positive regulation of BMP signalling
by\r\nthe transcription factor LMX1A, a key regulator of roof plate identity.
WNT promotes the\r\nsecond phase of BMP signalling via positive feedback on LMX1A.\r\nAltogether,
the mechanism that we uncovered ensures the coupling of sequential\r\ndevelopmental
events, making pattern formation spatially and temporally organised.\r\nFurthermore,
this mechanism allows the BMP signalling pathway to be reused in different\r\ncontexts
– first for the establishment of the neural plate border, and subsequently for
dorsal\r\nneural progenitor patterning. Our study supports a general developmental
principle in which\r\nmultiple morphogens interact with transcriptional networks
resulting in complex\r\nspatiotemporal signalling dynamics that ultimately drive
organised pattern formation."
acknowledged_ssus:
- _id: Bio
- _id: PreCl
- _id: LifeSc
acknowledgement: "My work would also not have been possible without the Imaging and
Optics, the Life Science\r\nand the Preclinical Facility of ISTA. Your support has
facilitated my research substantially. I\r\nalso want to thank the Graduate School
Office for their never-ending support and their sincere\r\neffort to improve the
PhD programme of the ISTA even further.\r\nThis work was supported by the Gesellschaft
für Forschungsförderung Niederösterreich\r\nm.b.H. fellowship (SC19-011). Thank
you for recognizing the importance of this project."
alternative_title:
- ISTA Thesis
article_processing_charge: No
author:
- first_name: Stefanie
full_name: Rus, Stefanie
id: 4D9EC9B6-F248-11E8-B48F-1D18A9856A87
last_name: Rus
orcid: 0000-0001-8703-1093
citation:
ama: Rus S. Dynamics of morphogen signalling and cell fate decisions in the dorsal
neural tube. 2025. doi:10.15479/AT-ISTA-19763
apa: Rus, S. (2025). Dynamics of morphogen signalling and cell fate decisions
in the dorsal neural tube. Institute of Science and Technology Austria. https://doi.org/10.15479/AT-ISTA-19763
chicago: Rus, Stefanie. “Dynamics of Morphogen Signalling and Cell Fate Decisions
in the Dorsal Neural Tube.” Institute of Science and Technology Austria, 2025.
https://doi.org/10.15479/AT-ISTA-19763.
ieee: S. Rus, “Dynamics of morphogen signalling and cell fate decisions in the dorsal
neural tube,” Institute of Science and Technology Austria, 2025.
ista: Rus S. 2025. Dynamics of morphogen signalling and cell fate decisions in the
dorsal neural tube. Institute of Science and Technology Austria.
mla: Rus, Stefanie. Dynamics of Morphogen Signalling and Cell Fate Decisions
in the Dorsal Neural Tube. Institute of Science and Technology Austria, 2025,
doi:10.15479/AT-ISTA-19763.
short: S. Rus, Dynamics of Morphogen Signalling and Cell Fate Decisions in the Dorsal
Neural Tube, Institute of Science and Technology Austria, 2025.
corr_author: '1'
date_created: 2025-05-30T09:14:58Z
date_published: 2025-05-29T00:00:00Z
date_updated: 2026-04-14T09:50:53Z
day: '29'
ddc:
- '570'
degree_awarded: PhD
department:
- _id: AnKi
- _id: GradSch
doi: 10.15479/AT-ISTA-19763
file:
- access_level: open_access
checksum: 8cd7fe3ca990adbcafdece119aa0973d
content_type: application/pdf
creator: cchlebak
date_created: 2025-05-30T09:10:22Z
date_updated: 2025-11-30T23:30:02Z
embargo: 2025-11-30
file_id: '19764'
file_name: Thesis_Lehr_PDFA.pdf
file_size: 42879974
relation: main_file
- access_level: closed
checksum: 0c87dd5fc803450a47b20736b5f86a2f
content_type: application/vnd.openxmlformats-officedocument.wordprocessingml.document
creator: cchlebak
date_created: 2025-05-30T09:31:15Z
date_updated: 2025-11-30T23:30:02Z
embargo_to: open_access
file_id: '19765'
file_name: Thesis_Lehr_emptyPages.docx
file_size: 18731094
relation: source_file
file_date_updated: 2025-11-30T23:30:02Z
has_accepted_license: '1'
language:
- iso: eng
month: '05'
oa: 1
oa_version: Published Version
page: '129'
project:
- _id: 9B9B39FA-BA93-11EA-9121-9846C619BF3A
grant_number: SC19-011
name: The regulatory logic of pattern formation in the vertebrate dorsal neural
tube
publication_identifier:
issn:
- 2663-337X
publication_status: published
publisher: Institute of Science and Technology Austria
related_material:
record:
- id: '18601'
relation: part_of_dissertation
status: public
- id: '17148'
relation: part_of_dissertation
status: public
- id: '18807'
relation: part_of_dissertation
status: public
- id: '13136'
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: Dynamics of morphogen signalling and cell fate decisions in the dorsal neural
tube
tmp:
image: /images/cc_by_nc_nd.png
legal_code_url: https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode
name: Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International
(CC BY-NC-ND 4.0)
short: CC BY-NC-ND (4.0)
type: dissertation
user_id: ba8df636-2132-11f1-aed0-ed93e2281fdd
year: '2025'
...
---
OA_place: publisher
_id: '19836'
abstract:
- lang: eng
text: "Over the past century, researchers have been fascinated by the quantum nature
of the\r\nphysical world, initially striving to understand its fundamental principles
and consequences, and\r\neventually progressing toward engineering systems that
can control and manipulate quantum\r\nproperties. Today, we stand at the dawn
of the quantum technology era. While some quantum\r\ntechnologies follow well-defined
roadmaps, others are still in the exciting and uncertain early\r\nstages of development.
In the fields of quantum computing and quantum simulation, research\r\nis being
conducted across a wide variety of platforms. Each of these demonstrates control
over\r\nquantum properties but also faces challenges in scaling up to the level
of a mature technology.\r\nThis thesis explores some of the fundamental properties
of hole spin qubits in planar germanium.\r\nSemiconductor spin qubits are considered
strong candidates for the realization of quantum\r\nprocessors, owing to their
long relaxation and coherence times, as well as their compatibility\r\nwith existing
semiconductor industry infrastructure. Among these, hole spin qubits in planar\r\ngermanium
are particularly promising. Their advantages include a large effective mass, which\r\neases
fabrication constraints; inherent protection from hyperfine noise; and strong
spin-orbit\r\ninteraction, which enables fast and purely electrical control. However,
spin-orbit coupling also\r\nintroduces site-dependent variability across qubits,
particularly in the g-tensors and spin-flip\r\ntunneling, which might cause that
the quantization axes are not aligned. In this thesis, we\r\ninvestigate the tilt
between the quantization axes of two hole spins hosted in a double quantum\r\ndot
as a function of both the magnetic field direction and various electrostatic configurations,\r\ndemonstrating
that both parameters influence this tilt. We conclude by introducing a machine-learning-assisted
routine to automatically tune baseband spin qubits. This approach may prove\r\nto
be a powerful tool for characterizing spin-orbit effects and gaining deeper insight
into the\r\nphysics governing spin qubit behavior.\r\n"
acknowledged_ssus:
- _id: NanoFab
- _id: M-Shop
acknowledgement: "This research was supported by the Scientific Service Units of ISTA
through resources provided\r\nby the MIBA Machine Shop and the Nanofabrication facility.
We acknowledge the support from\r\nthe European Commission with the project Integrated
Germanium Quantum Technology (with\r\nDOI:10.3030/101069515), the NOMIS Foundation,
the HORIZON-RIA 101069515 project and\r\nthe FWF Projects Center for Correlated
Quantum Materials and Solid State Quantum Systems:\r\nConventional and unconventional
topological superconductors (with DOI:10.55776/F86) and\r\nHigh impedance circuit
quantum electrodynamics with hole spins (with DOI:10.55776/I5060).\r\n"
alternative_title:
- ISTA Thesis
article_processing_charge: No
author:
- first_name: Jaime
full_name: Saez Mollejo, Jaime
id: e0390f72-f6e0-11ea-865d-862393336714
last_name: Saez Mollejo
citation:
ama: 'Saez Mollejo J. Singlet-triplet qubits in planar Germanium : From exchange
anisotropies to autonomous tuning . 2025. doi:10.15479/AT-ISTA-19836'
apa: 'Saez Mollejo, J. (2025). Singlet-triplet qubits in planar Germanium : From
exchange anisotropies to autonomous tuning . Institute of Science and Technology
Austria. https://doi.org/10.15479/AT-ISTA-19836'
chicago: 'Saez Mollejo, Jaime. “Singlet-Triplet Qubits in Planar Germanium : From
Exchange Anisotropies to Autonomous Tuning .” Institute of Science and Technology
Austria, 2025. https://doi.org/10.15479/AT-ISTA-19836.'
ieee: 'J. Saez Mollejo, “Singlet-triplet qubits in planar Germanium : From exchange
anisotropies to autonomous tuning ,” Institute of Science and Technology Austria,
2025.'
ista: 'Saez Mollejo J. 2025. Singlet-triplet qubits in planar Germanium : From exchange
anisotropies to autonomous tuning . Institute of Science and Technology Austria.'
mla: 'Saez Mollejo, Jaime. Singlet-Triplet Qubits in Planar Germanium : From
Exchange Anisotropies to Autonomous Tuning . Institute of Science and Technology
Austria, 2025, doi:10.15479/AT-ISTA-19836.'
short: 'J. Saez Mollejo, Singlet-Triplet Qubits in Planar Germanium : From Exchange
Anisotropies to Autonomous Tuning , Institute of Science and Technology Austria,
2025.'
corr_author: '1'
date_created: 2025-06-13T09:01:50Z
date_published: 2025-06-13T00:00:00Z
date_updated: 2026-05-20T06:42:16Z
day: '13'
ddc:
- '530'
- '539'
degree_awarded: PhD
department:
- _id: GradSch
- _id: GeKa
doi: 10.15479/AT-ISTA-19836
file:
- access_level: closed
checksum: 643bfddead59857536cce4d57c775b32
content_type: application/x-zip-compressed
creator: jsaezmol
date_created: 2025-06-16T09:38:49Z
date_updated: 2026-04-01T22:30:07Z
embargo_to: open_access
file_id: '19849'
file_name: istaustriathesis-master - Copy.zip
file_size: 59892829
relation: source_file
- access_level: open_access
checksum: e3dcb767fcc2b1787a455fdda991cefb
content_type: application/pdf
creator: jsaezmol
date_created: 2025-06-18T08:50:16Z
date_updated: 2026-04-01T22:30:07Z
embargo: 2026-04-01
file_id: '19851'
file_name: SaezMollejo_PhDFinal_pdfa-1b.pdf
file_size: 22382376
relation: main_file
file_date_updated: 2026-04-01T22:30:07Z
has_accepted_license: '1'
language:
- iso: eng
month: '06'
oa: 1
oa_version: Published Version
page: '175'
project:
- _id: 34c0acea-11ca-11ed-8bc3-8775e10fd452
grant_number: '101069515'
name: Integrated Germanium Quantum Technology
- _id: 34a66131-11ca-11ed-8bc3-a31681c6b03e
grant_number: F8606
name: 'Center for Correlated Quantum Materials and Solid State Quantum Systems:
Conventional and unconventional topological superconductors'
- _id: c0977eea-5a5b-11eb-8a69-a862db0cf4d1
grant_number: I05060
name: High impedance circuit quantum electrodynamics with hole spins
publication_identifier:
issn:
- 2663-337X
publication_status: published
publisher: Institute of Science and Technology Austria
related_material:
record:
- id: '19424'
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 in planar Germanium : From exchange anisotropies to
autonomous tuning '
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: '2025'
...
---
OA_place: publisher
_id: '20449'
abstract:
- lang: eng
text: "Males and females of many species differ in morphology, physiology, and
behavior. In taxa\r\nwith genetic sex determination, sexual differentiation arises
largely from sex-biased gene\r\nexpression, which varies across tissues, developmental
stages, and lineages. Increasing\r\nevidence highlights chromatin configuration,
which can exist in open or closed states, and can\r\nbe shaped by sex-determination
path ways, as a key regulatory layer of this dimorphism.\r\nDegeneration of the
Y or W chromosome further contributes to sex -specific differences by\r\naltering
gene copy numbers relative to autosomes in heterogametic sex. To mitigate these\r\nimbalances,
many eukaryotes have independently evolved dosage compensation mechanisms,\r\noften
mediated through chromatin -level regulation. In this thesis, we investigate the\r\nevolutionary
dynamics of sex chromosome differentiation in two species, Artemia franciscana\r\nand
Cameraria ohridella , with a particular focus on the extent of dosage compensation\r\nfollowing
gene loss in the heterogametic sex and the potential chromatin-based mechanisms\r\nunderlying
this process. We further characterize sex -biased gene expression and its regulation\r\nthrough
histone modifications. Our analyses also reveal that the A. franciscana genome
is\r\nhighly repetitive, with many genes containing intronic transposable elements.
We find that\r\nenrichment of histonemo difications associated with constitutive
heterochromatin, positively\r\ncorrelates with variation in gene expression levels.
Collectively, these findings underscore role\r\nof chromatin regulation in shaping
the evolution of sex chromosomes and sexual\r\ndifferentiation. "
acknowledged_ssus:
- _id: ScienComp
acknowledgement: "This work was supported by the Austrian Science Fund (FWF) through
grants PAT8748323\r\nand SFB F88-10 awarded to Professor Beatriz Vicoso."
alternative_title:
- ISTA Thesis
article_processing_charge: No
author:
- first_name: Vincent K
full_name: Bett, Vincent K
id: 57854184-AAE0-11E9-8D04-98D6E5697425
last_name: Bett
citation:
ama: Bett VK. Evolution and regulation of the Z chromosome. 2025. doi:10.15479/AT-ISTA-20449
apa: Bett, V. K. (2025). Evolution and regulation of the Z chromosome. Institute
of Science and Technology Austria. https://doi.org/10.15479/AT-ISTA-20449
chicago: Bett, Vincent K. “Evolution and Regulation of the Z Chromosome.” Institute
of Science and Technology Austria, 2025. https://doi.org/10.15479/AT-ISTA-20449.
ieee: V. K. Bett, “Evolution and regulation of the Z chromosome,” Institute of Science
and Technology Austria, 2025.
ista: Bett VK. 2025. Evolution and regulation of the Z chromosome. Institute of
Science and Technology Austria.
mla: Bett, Vincent K. Evolution and Regulation of the Z Chromosome. Institute
of Science and Technology Austria, 2025, doi:10.15479/AT-ISTA-20449.
short: V.K. Bett, Evolution and Regulation of the Z Chromosome, Institute of Science
and Technology Austria, 2025.
corr_author: '1'
date_created: 2025-10-11T08:18:51Z
date_published: 2025-10-10T00:00:00Z
date_updated: 2026-06-12T08:32:16Z
day: '10'
ddc:
- '576'
degree_awarded: PhD
department:
- _id: GradSch
- _id: BeVi
doi: 10.15479/AT-ISTA-20449
file:
- access_level: open_access
checksum: 26905c22bca417198a733d792d8ce422
content_type: application/pdf
creator: vbett
date_created: 2025-10-20T13:32:29Z
date_updated: 2026-06-01T22:30:04Z
embargo: 2026-06-01
file_id: '20507'
file_name: 2025_Bett_Vincent_Thesis.pdf
file_size: 18507283
relation: main_file
- access_level: closed
checksum: 6a09a8d126d3628bfd8a35202735f267
content_type: application/vnd.openxmlformats-officedocument.wordprocessingml.document
creator: vbett
date_created: 2025-10-20T13:35:34Z
date_updated: 2026-06-01T22:30:04Z
embargo_to: open_access
file_id: '20508'
file_name: 2025_Bett_Vincent_Thesis.docx
file_size: 17163921
relation: source_file
file_date_updated: 2026-06-01T22:30:04Z
has_accepted_license: '1'
language:
- iso: eng
month: '10'
oa: 1
oa_version: Published Version
page: '114'
project:
- _id: 8ed82125-16d5-11f0-9cad-fbcae312235b
grant_number: PAT 8748323
name: Sex chromosomes in evolution and development
- _id: 34ae1506-11ca-11ed-8bc3-c14f4c474396
grant_number: F8810
name: The highjacking of meiosis for asexual reproduction
publication_identifier:
issn:
- 2663-337X
publication_status: published
publisher: Institute of Science and Technology Austria
related_material:
record:
- id: '19735'
relation: part_of_dissertation
status: public
- id: '15009'
relation: part_of_dissertation
status: public
status: public
supervisor:
- first_name: Beatriz
full_name: Vicoso, Beatriz
id: 49E1C5C6-F248-11E8-B48F-1D18A9856A87
last_name: Vicoso
orcid: 0000-0002-4579-8306
title: Evolution and regulation of the Z chromosome
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: dissertation
user_id: 8b945eb4-e2f2-11eb-945a-df72226e66a9
year: '2025'
...
---
OA_place: publisher
_id: '19993'
abstract:
- lang: eng
text: "Ants are frequently challenged by different pathogens, which they counter
with\r\nindividual and collective responses. Usually, the pathogens like fungi
or viruses are\r\nsolitary and passive pathogens transmitted from host to host.
Here, we use a nematobacterial pathogen complex to study worm-borne disease in
black garden ants. These\r\nentomopathogenic nematodes are active parasites with
an own behavior and chasing\r\npray.\r\nIn the first chapter, we investigated
the basic biology of the host-pathogen relationship.\r\nWe tested different ant
life stages and found that adult ants display defense behaviors\r\nand are generally
resistant to nematode infection, whereas brood is highly susceptible.\r\nIn the
case of worker pupae, we found a slight protective effect of the cocoon. When\r\nlarvae
are accompanied by adults, meaning a queen or a group of workers, survival is\r\nsignificantly
enhanced. Moreover, we found that nematodes can transmit from infected\r\ncadavers
to healthy worker larvae, confirming a transmissible disease in ants. Again,\r\nworker
presence significantly reduces transmission risk. In the end, we were also able\r\nto
disentangle the pathogen system and investigate the pathogenic effect of the\r\nbacterial
and nematode components.\r\nIn the second chapter, we studied the effect of multiple
infections in adult queens and\r\nqueen larvae. By multiple exposures in the mode
of coinfection and superinfections,\r\nwe wanted to assess the detrimental effect
of combined fungal and nematode\r\nexposure to better understand how the pathogens
interact with each other in an ant\r\nhost. We found instances where combined
exposure lead to higher mortality in a given\r\ntime frame in both, adult queens
and queen larvae.\r\nOverall entomopathogenic nematodes are a promising model
to study worm infections\r\nin ants which extend our knowledge on collective disease
defense."
acknowledged_ssus:
- _id: LifeSc
alternative_title:
- ISTA Thesis
article_processing_charge: No
author:
- first_name: Florian
full_name: Strahodinsky, Florian
id: 979E35EE-C996-11E9-8C7C-CF13E6697425
last_name: Strahodinsky
citation:
ama: Strahodinsky F. Social immunity in a tri-partite host-pathogen relationship.
2025. doi:10.15479/AT-ISTA-19993
apa: Strahodinsky, F. (2025). Social immunity in a tri-partite host-pathogen
relationship. Institute of Science and Technology Austria. https://doi.org/10.15479/AT-ISTA-19993
chicago: Strahodinsky, Florian. “Social Immunity in a Tri-Partite Host-Pathogen
Relationship.” Institute of Science and Technology Austria, 2025. https://doi.org/10.15479/AT-ISTA-19993.
ieee: F. Strahodinsky, “Social immunity in a tri-partite host-pathogen relationship,”
Institute of Science and Technology Austria, 2025.
ista: Strahodinsky F. 2025. Social immunity in a tri-partite host-pathogen relationship.
Institute of Science and Technology Austria.
mla: Strahodinsky, Florian. Social Immunity in a Tri-Partite Host-Pathogen Relationship.
Institute of Science and Technology Austria, 2025, doi:10.15479/AT-ISTA-19993.
short: F. Strahodinsky, Social Immunity in a Tri-Partite Host-Pathogen Relationship,
Institute of Science and Technology Austria, 2025.
corr_author: '1'
date_created: 2025-07-10T14:12:20Z
date_published: 2025-07-11T00:00:00Z
date_updated: 2026-04-07T12:39:58Z
day: '11'
ddc:
- '570'
degree_awarded: PhD
department:
- _id: GradSch
- _id: SyCr
doi: 10.15479/AT-ISTA-19993
file:
- access_level: closed
checksum: df3a02f0d937ea9a3d79d5fb94fff097
content_type: application/vnd.openxmlformats-officedocument.wordprocessingml.document
creator: fstrahod
date_created: 2025-07-14T13:18:37Z
date_updated: 2026-01-15T23:30:03Z
embargo_to: open_access
file_id: '20021'
file_name: Thesis_Florian_Strahodinsky_DOCX.docx
file_size: 9857392
relation: source_file
- access_level: open_access
checksum: 7164c21fe1946e839f7b8acd255ce803
content_type: application/pdf
creator: fstrahod
date_created: 2025-07-14T13:18:38Z
date_updated: 2026-01-15T23:30:03Z
embargo: 2026-01-15
file_id: '20022'
file_name: Thesis_Florian_Strahodinsky_PDF.pdf
file_size: 6439602
relation: main_file
file_date_updated: 2026-01-15T23:30:03Z
has_accepted_license: '1'
language:
- iso: eng
month: '07'
oa: 1
oa_version: Published Version
page: '138'
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: Social immunity in a tri-partite host-pathogen relationship
tmp:
image: /images/cc_by_nc_nd.png
legal_code_url: https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode
name: Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International
(CC BY-NC-ND 4.0)
short: CC BY-NC-ND (4.0)
type: dissertation
user_id: ba8df636-2132-11f1-aed0-ed93e2281fdd
year: '2025'
...
---
OA_place: publisher
_id: '19906'
abstract:
- lang: eng
text: "Flows of ordinary fluids such as water or air transition from laminar to
turbulent\r\nmotion as the velocity increases. This simple dependence of the flow
state\r\nsolely on inertia, does not apply to more complex substances such as
polymericand biofluids which commonly have elastic as well as viscous properties.
Here\r\nvarious different instabilities and turbulent states can arise at low
and even\r\nvanishing inertia, while high inertia turbulence counterintuitively
is suppressed\r\nand its drag strongly reduced. We here show in experiments of
a viscoelastic\r\nmodel fluid that the phenomena observed at low and high inertia
have a\r\ncommon origin and that the same dynamical state, elasto-inertial turbulence,\r\npersists
across four orders of magnitude in Reynolds number, ranging from\r\nvery low inertia,
all the way to high inertia Maximum drag reduction (MDR)\r\nasymptote. We also
explore the transitions from Newtonian turbulence to\r\nMDR, and specific cases
of flow at high polymer concentrations, exploring the\r\nrelationship between
flow at these wide range of control parameters.\r\n"
acknowledged_ssus:
- _id: M-Shop
acknowledgement: "This work was partially funded by the European Union’s Horizon 2020
research\r\nand innovation programme under the Marie Skłodowska-Curie grant agreement\r\nNo.
665385."
alternative_title:
- ISTA Thesis
article_processing_charge: No
author:
- first_name: Sarath S
full_name: Suresh, Sarath S
id: 3D126CC4-F248-11E8-B48F-1D18A9856A87
last_name: Suresh
citation:
ama: 'Suresh SS. Turbulence in polymeric flows : A characterisation of elasto-inertial
turbulence and the maximum drag reduction asymptote. 2025. doi:10.15479/AT-ISTA-19906'
apa: 'Suresh, S. S. (2025). Turbulence in polymeric flows : A characterisation
of elasto-inertial turbulence and the maximum drag reduction asymptote. Institute
of Science and Technology Austria. https://doi.org/10.15479/AT-ISTA-19906'
chicago: 'Suresh, Sarath S. “Turbulence in Polymeric Flows : A Characterisation
of Elasto-Inertial Turbulence and the Maximum Drag Reduction Asymptote.” Institute
of Science and Technology Austria, 2025. https://doi.org/10.15479/AT-ISTA-19906.'
ieee: 'S. S. Suresh, “Turbulence in polymeric flows : A characterisation of elasto-inertial
turbulence and the maximum drag reduction asymptote,” Institute of Science and
Technology Austria, 2025.'
ista: 'Suresh SS. 2025. Turbulence in polymeric flows : A characterisation of elasto-inertial
turbulence and the maximum drag reduction asymptote. Institute of Science and
Technology Austria.'
mla: 'Suresh, Sarath S. Turbulence in Polymeric Flows : A Characterisation of
Elasto-Inertial Turbulence and the Maximum Drag Reduction Asymptote. Institute
of Science and Technology Austria, 2025, doi:10.15479/AT-ISTA-19906.'
short: 'S.S. Suresh, Turbulence in Polymeric Flows : A Characterisation of Elasto-Inertial
Turbulence and the Maximum Drag Reduction Asymptote, Institute of Science and
Technology Austria, 2025.'
corr_author: '1'
date_created: 2025-06-26T08:39:08Z
date_published: 2025-06-26T00:00:00Z
date_updated: 2026-04-07T12:39:19Z
day: '26'
ddc:
- '530'
degree_awarded: PhD
department:
- _id: GradSch
- _id: BjHo
doi: 10.15479/AT-ISTA-19906
ec_funded: 1
file:
- access_level: open_access
checksum: 302a07605a9e64ac247c2036d5f5b1cd
content_type: application/pdf
creator: cchlebak
date_created: 2025-06-26T08:40:53Z
date_updated: 2025-12-27T23:30:02Z
embargo: 2025-12-27
file_id: '19907'
file_name: Thesis_v9_PDFA2b.pdf
file_size: 6504571
relation: main_file
- access_level: closed
checksum: 5d69d10bdacc24c27f02924379405bd9
content_type: application/x-zip-compressed
creator: cchlebak
date_created: 2025-06-26T08:41:24Z
date_updated: 2025-12-27T23:30:02Z
embargo_to: open_access
file_id: '19908'
file_name: Thesis Template - ISTA [istaustriathesis].zip
file_size: 59092991
relation: source_file
file_date_updated: 2025-12-27T23:30:02Z
has_accepted_license: '1'
language:
- iso: eng
license: https://creativecommons.org/licenses/by-nc-sa/4.0/
month: '06'
oa: 1
oa_version: Published Version
page: '82'
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: '10299'
relation: part_of_dissertation
status: public
status: public
supervisor:
- first_name: Björn
full_name: Hof, Björn
id: 3A374330-F248-11E8-B48F-1D18A9856A87
last_name: Hof
orcid: 0000-0003-2057-2754
title: 'Turbulence in polymeric flows : A characterisation of elasto-inertial turbulence
and the maximum drag reduction asymptote'
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: '2025'
...
---
OA_place: publisher
_id: '20470'
abstract:
- lang: eng
text: "Systems design has classically relied on composable systems, in which individual
subsystems\r\nhave defined inputs, outputs, and interactions with each other;
however, attempts at\r\ndesigning complex systems in synthetic biology has often
run in to issues of crosstalk and\r\ninterference, given that these systems must
function within the context of the host. In nature,\r\nmobile genetic elements
are systems that have evolved to travel between hosts, and thus\r\nappear to be
a good candidate with which to evaluate composability. Selecting temperate\r\nphages
as a model system, I used mathematical modelling to identify sources of information\r\nthat
temperate phages should respond to. I found that essential proteins of temperate
phages\r\ncan interfere with potential hosts, indicating limitations to composability.
I also designed a\r\nlysogeny reporter construct and characterize its behavior
across various laboratory and\r\nenvironmental strains, finding differences in
phage lambda lysogens, and potential\r\ninterference from prophages that already
exist within the environmental strains. Although\r\nthe information gathered is
not conclusive, it suggests that composability is not a key property\r\nof temperate
phages, implying that biological systems may not be composable, and that other\r\nsystem
design principles should be considered when designing synthetic systems."
alternative_title:
- ISTA Thesis
article_processing_charge: No
author:
- first_name: Bryan
full_name: Wu, Bryan
id: 3C521EBA-F248-11E8-B48F-1D18A9856A87
last_name: Wu
citation:
ama: Wu B. An examination on phages as a naturally composable system. 2025. doi:10.15479/AT-ISTA-20470
apa: Wu, B. (2025). An examination on phages as a naturally composable system.
Institute of Science and Technology Austria. https://doi.org/10.15479/AT-ISTA-20470
chicago: Wu, Bryan. “An Examination on Phages as a Naturally Composable System.”
Institute of Science and Technology Austria, 2025. https://doi.org/10.15479/AT-ISTA-20470.
ieee: B. Wu, “An examination on phages as a naturally composable system,” Institute
of Science and Technology Austria, 2025.
ista: Wu B. 2025. An examination on phages as a naturally composable system. Institute
of Science and Technology Austria.
mla: Wu, Bryan. An Examination on Phages as a Naturally Composable System.
Institute of Science and Technology Austria, 2025, doi:10.15479/AT-ISTA-20470.
short: B. Wu, An Examination on Phages as a Naturally Composable System, Institute
of Science and Technology Austria, 2025.
corr_author: '1'
date_created: 2025-10-15T13:30:21Z
date_published: 2025-10-30T00:00:00Z
date_updated: 2026-05-06T08:01:28Z
day: '30'
ddc:
- '579'
degree_awarded: PhD
department:
- _id: GradSch
- _id: CaGu
doi: 10.15479/AT-ISTA-20470
file:
- access_level: closed
checksum: d32ea83f259f6b0506325cd57b1d44c3
content_type: application/vnd.openxmlformats-officedocument.wordprocessingml.document
creator: brwu
date_created: 2025-10-21T17:33:27Z
date_updated: 2026-04-30T22:30:02Z
embargo_to: open_access
file_id: '20516'
file_name: 2025_Wu_Bryan_Thesis.docx
file_size: 10603235
relation: source_file
- access_level: open_access
checksum: 53590046fd3244c5550b4022282449d2
content_type: application/pdf
creator: brwu
date_created: 2025-10-21T17:33:26Z
date_updated: 2026-04-30T22:30:02Z
embargo: 2026-04-30
file_id: '20517'
file_name: 2025_Wu_Bryan_Thesis.pdf
file_size: 6251936
relation: main_file
file_date_updated: 2026-04-30T22:30:02Z
has_accepted_license: '1'
language:
- iso: eng
month: '10'
oa: 1
oa_version: Published Version
page: '102'
publication_identifier:
issn:
- 2663-337X
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
title: An examination on phages as a naturally composable system
type: dissertation
user_id: 8b945eb4-e2f2-11eb-945a-df72226e66a9
year: '2025'
...
---
OA_place: publisher
_id: '20694'
abstract:
- lang: eng
text: "Understanding the mechanisms underlying speciation is a central aim of evolutionary
biology.\r\nA persistent challenge in the field is to identify loci that contribute
to reproductive isolation,\r\nwhile disentangling signals of selection from demography,
linkage and intrinsic genomic\r\nfeatures. Traditional population genomic approaches
that rely on site-based statistics in\r\narbitrary fixed windows face inherent
limitations, as they conflate historical and\r\ncontemporary processes of divergence
and overlook haplotype structure. Recent advances in\r\nwhole-genome sequencing
and methods to infer ancestral recombination graphs (ARGs) now\r\noffer the opportunity
to study genealogical relationships explicitly, revealing how lineages\r\ncoalesce
and recombine through time. By directly analysing haplotype clustering by species\r\nor
phenotype and their patterns of coalescence, ARG-based methods show promise for\r\ndiagnosing
sweeps, identifying barrier loci maintained under divergent selection amid gene\r\nflow,
and tracing their evolutionary history.\r\nIn this thesis, I explore the utility
of genealogical approaches for studying species\r\ndivergence. In chapter 2, I
propose a conceptual framework for defining haplotype blocks\r\nthrough the structure
of the ARG, using simulations and empirical data to highlight how\r\ngenealogical
processes generate rich and often overlooked haplotypic patterns.\r\nIn chapter
3, I examine the genomic basis of a key evolutionary innovation in marine\r\nsnails
Littorina. These snails offer a unique opportunity to study an innovation because
they\r\ninclude a very recent transition from egg-laying to live bearing, yet
snails with the different\r\nreproductive modes are not reciprocally monophyletic.
I exploited this by using topology\r\nclustering in ARG-derived local genealogical
trees to pinpoint narrow genomic regions or\r\nhaplotype blocks that carry swept
alleles, thus revealing that the transition from egg-laying\r\nto live-bearing
involves multiple, live-bearer-specific sweeps.\r\nChapter 4 establishes a population-scale,
phased genomic resource for Antirrhinum\r\nmajus, using cost-effective haplotagging,
then optimizes imputation from low-coverage data\r\nagainst high-accuracy KASP
sequencing to maximize sequence completeness with modest\r\naccuracy trade-offs
against a traditional short-read sequence pipeline. A hybrid phasing\r\nstrategy
combines molecular phasing with statistical phasing to generate phased whole\r\ngenome
sequences of 1084 Antirrhinum individuals at a fraction of long-read sequencing\r\ncosts.\r\nIn
chapter 5, I analyse hybridising populations from two replicate hybrid zones to
find\r\na parallel genetic basis of flower colour, amidst the noise in genomic
differentiation landscape\r\ndriven by variation in demographic history. While
outlier genome scans of FST failed to dissect\r\nthe causes of differentiation,
ARG-based topology clustering revealed a reuse of colour\r\nassociated haplotypes
across hybrid zones. In addition to the biological insight, this chapter\r\nalso
presents a comparison of the latest ARG inference tools, showing that signals
of\r\nAbstract\r\nviii\r\ntopological clustering qualitatively agree between methods,
despite differences in the tree\r\nsequences.\r\nNext, in chapter 6, by leveraging
~1000 individuals in one of the hybrid zones, I\r\nintegrated genome-wide association
studies of floral pigmentation with genealogical\r\ninference, to test for additional
colour loci, and confirm the effect of previously described loci.\r\nThis work
demonstrates that flower colour variation is driven by a small number of large
effect\r\nloci, while also hinting at the presence of a new candidate regulatory
factor.\r\nFinally in chapter 7, in a preliminary analysis, I begin to dissect
the genomic island of\r\nspeciation around Rosea/Eluta to understand its evolutionary
origins. My results show that it\r\nconsists of 5 highly divergent loci, each
of which is associated with flower colour. Using\r\npatterns of coalescence in
genealogical trees, I find evidence of staggered selective sweeps\r\nand a persistent
localized barrier to gene flow within an otherwise permeable genome.\r\nTogether,
these chapters add to the increasing pool of studies using genealogical\r\napproaches
to complement and extend site-based statistics to use haplotype structures in\r\nspeciation
research. By tracking haplotypes directly and connecting genealogical clustering
to\r\npopulation processes, ARG-based inference promises to provide new insights
into how local\r\nselective pressures, demographic history, and long-term barriers
interact to shape the\r\ngenomic architecture of divergence. By underscoring the
value of ARGs in revealing the finescale origins and maintenance of biodiversity,
this thesis presents cautious optimism about\r\nthe benefits of using genealogical
inference to learn more than what site-based statistics\r\ncould tell us."
acknowledged_ssus:
- _id: ScienComp
alternative_title:
- ISTA Thesis
article_processing_charge: No
author:
- first_name: Arka
full_name: Pal, Arka
id: 6AAB2240-CA9A-11E9-9C1A-D9D1E5697425
last_name: Pal
orcid: 0000-0002-4530-8469
citation:
ama: Pal A. Using genealogies to study the genomic basis of species divergence.
2025. doi:10.15479/AT-ISTA-20694
apa: Pal, A. (2025). Using genealogies to study the genomic basis of species
divergence. Institute of Science and Technology Austria. https://doi.org/10.15479/AT-ISTA-20694
chicago: Pal, Arka. “Using Genealogies to Study the Genomic Basis of Species Divergence.”
Institute of Science and Technology Austria, 2025. https://doi.org/10.15479/AT-ISTA-20694.
ieee: A. Pal, “Using genealogies to study the genomic basis of species divergence,”
Institute of Science and Technology Austria, 2025.
ista: Pal A. 2025. Using genealogies to study the genomic basis of species divergence.
Institute of Science and Technology Austria.
mla: Pal, Arka. Using Genealogies to Study the Genomic Basis of Species Divergence.
Institute of Science and Technology Austria, 2025, doi:10.15479/AT-ISTA-20694.
short: A. Pal, Using Genealogies to Study the Genomic Basis of Species Divergence,
Institute of Science and Technology Austria, 2025.
corr_author: '1'
date_created: 2025-11-25T13:19:11Z
date_published: 2025-11-25T00:00:00Z
date_updated: 2026-04-28T13:20:36Z
day: '25'
ddc:
- '576'
- '578'
degree_awarded: PhD
department:
- _id: GradSch
- _id: NiBa
doi: 10.15479/AT-ISTA-20694
file:
- access_level: open_access
checksum: 7a10a738d58524aebb5dcbd9b34c21c5
content_type: application/pdf
creator: apal
date_created: 2025-12-01T13:53:36Z
date_updated: 2026-03-01T23:30:03Z
embargo: 2026-03-01
file_id: '20721'
file_name: 2025_Pal_Arka_Thesis.pdf
file_size: 42723135
relation: main_file
- access_level: closed
checksum: 166d832b08d0434ce407f8f3cb930fe5
content_type: application/vnd.openxmlformats-officedocument.wordprocessingml.document
creator: apal
date_created: 2025-12-01T13:53:39Z
date_updated: 2026-03-01T23:30:03Z
embargo_to: open_access
file_id: '20722'
file_name: 2025_Pal_Arka_Thesis.docx
file_size: 60632116
relation: source_file
file_date_updated: 2026-03-01T23:30:03Z
has_accepted_license: '1'
language:
- iso: eng
month: '11'
oa: 1
oa_version: Published Version
page: '268'
project:
- _id: bd6958e0-d553-11ed-ba76-86eba6a76c00
grant_number: '101055327'
name: Understanding the evolution of continuous genomes
- _id: 05959E1C-7A3F-11EA-A408-12923DDC885E
grant_number: P32166
name: Snapdragon Speciation
publication_identifier:
issn:
- 2663-337X
publication_status: published
publisher: Institute of Science and Technology Austria
related_material:
record:
- id: '12159'
relation: part_of_dissertation
status: public
- id: '14796'
relation: part_of_dissertation
status: public
- id: '20190'
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: Using genealogies to study the genomic basis of species divergence
tmp:
image: /images/cc_by_nc_nd.png
legal_code_url: https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode
name: Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International
(CC BY-NC-ND 4.0)
short: CC BY-NC-ND (4.0)
type: dissertation
user_id: ba8df636-2132-11f1-aed0-ed93e2281fdd
year: '2025'
...
---
OA_place: publisher
_id: '20563'
abstract:
- lang: eng
text: "The theory of optimal transport provides an elegant and powerful description
of many evolution\r\nequations as gradient flows. The primary objective of this
thesis is to adapt and extend the\r\ntheory to deal with important equations that
are not covered by the classical framework,\r\nspecifically boundary value problems
and kinetic equations. Additionally, we establish new\r\nresults in periodic homogenization
for discrete dynamical optimal transport and in quantization\r\nof measures.\r\nSection
1.1 serves as an invitation to the classical theory of optimal transport, including
the\r\nmain definitions and a selection of well-established theorems. Sections
1.2-1.5 introduce the\r\nmain results of this thesis, outline the motivations,
and review the current state of the art.\r\nIn Chapter 2, we consider the Fokker–Planck
equation on a bounded set with positive Dirichlet\r\nboundary conditions. We construct
a time-discrete scheme involving a modification of the\r\nWasserstein distance
and, under weak assumptions, prove its convergence to a solution of this\r\nboundary
value problem. In dimension 1, we show that this solution is a gradient flow in
a\r\nsuitable space of measures.\r\nChapter 3 presents joint work with Giovanni
Brigati and Jan Maas. We introduce a new theory\r\nof optimal transport to describe
and study particle systems at the mesoscopic scale. We prove\r\nadapted versions
of some fundamental theorems, including the Benamou–Brenier formula and\r\nthe
identification of absolutely continuous curves of measures.\r\nChapter 4 presents
joint work with Lorenzo Portinale. We prove convergence of dynamical\r\ntransportation
functionals on periodic graphs in the large-scale limit when the cost functional\r\nis
asymptotically linear. Additionally, we show that discrete 1-Wasserstein distances
converge\r\nto 1-Wasserstein distances constructed from crystalline norms on R\r\nd\r\n.\r\nChapter
5 concerns optimal empirical quantization: the problem of approximating a measure\r\nby
the sum of n equally weighted Dirac deltas, so as to minimize the error in the
p-Wasserstein\r\ndistance. Our main result is an analog of Zador’s theorem, providing
asymptotic bounds for\r\nthe minimal error as n tends to infinity.\r\n"
acknowledgement: "The research contained in this thesis has received funding from
the Austrian Science\r\nFund (FWF) project 10.55776/F65."
alternative_title:
- ISTA Thesis
article_processing_charge: No
author:
- first_name: Filippo
full_name: Quattrocchi, Filippo
id: 3ebd6ba8-edfb-11eb-afb5-91a9745ba308
last_name: Quattrocchi
orcid: 0009-0000-9773-1931
citation:
ama: Quattrocchi F. Optimal transport methods for kinetic equations, boundary value
problems, and discretization of measures. 2025. doi:10.15479/AT-ISTA-20563
apa: Quattrocchi, F. (2025). Optimal transport methods for kinetic equations,
boundary value problems, and discretization of measures. Institute of Science
and Technology Austria. https://doi.org/10.15479/AT-ISTA-20563
chicago: Quattrocchi, Filippo. “Optimal Transport Methods for Kinetic Equations,
Boundary Value Problems, and Discretization of Measures.” Institute of Science
and Technology Austria, 2025. https://doi.org/10.15479/AT-ISTA-20563.
ieee: F. Quattrocchi, “Optimal transport methods for kinetic equations, boundary
value problems, and discretization of measures,” Institute of Science and Technology
Austria, 2025.
ista: Quattrocchi F. 2025. Optimal transport methods for kinetic equations, boundary
value problems, and discretization of measures. Institute of Science and Technology
Austria.
mla: Quattrocchi, Filippo. Optimal Transport Methods for Kinetic Equations, Boundary
Value Problems, and Discretization of Measures. Institute of Science and Technology
Austria, 2025, doi:10.15479/AT-ISTA-20563.
short: F. Quattrocchi, Optimal Transport Methods for Kinetic Equations, Boundary
Value Problems, and Discretization of Measures, Institute of Science and Technology
Austria, 2025.
corr_author: '1'
date_created: 2025-10-28T13:10:49Z
date_published: 2025-11-03T00:00:00Z
date_updated: 2026-06-18T18:02:13Z
day: '03'
ddc:
- '515'
- '519'
degree_awarded: PhD
department:
- _id: GradSch
- _id: JaMa
doi: 10.15479/AT-ISTA-20563
file:
- access_level: open_access
checksum: 6f55275bdf99992be3a6457d949dd664
content_type: application/pdf
creator: fquattro
date_created: 2025-11-17T21:04:15Z
date_updated: 2026-01-01T23:30:03Z
embargo: 2026-01-01
file_id: '20653'
file_name: 2025_quattrocchi_filippo_thesis.pdf
file_size: 4326411
relation: main_file
- access_level: closed
checksum: 707e580f5d993a214c0dba456b75837b
content_type: application/zip
creator: fquattro
date_created: 2025-11-17T21:05:43Z
date_updated: 2026-01-01T23:30:03Z
embargo_to: open_access
file_id: '20654'
file_name: 2025_quattrocchi_thesis.zip
file_size: 11726509
relation: source_file
file_date_updated: 2026-01-01T23:30:03Z
has_accepted_license: '1'
keyword:
- optimal transport
- kinetic equations
- boundary value problems
- quantization
- gradient flows
- homogenization
language:
- iso: eng
month: '11'
oa: 1
oa_version: Published Version
page: '240'
project:
- _id: 260482E2-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: F06504
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: '20569'
relation: part_of_dissertation
status: public
- id: '20571'
relation: part_of_dissertation
status: public
- id: '20570'
relation: part_of_dissertation
status: public
- id: '18706'
relation: part_of_dissertation
status: public
status: public
supervisor:
- first_name: Jan
full_name: Maas, Jan
id: 4C5696CE-F248-11E8-B48F-1D18A9856A87
last_name: Maas
orcid: 0000-0002-0845-1338
title: Optimal transport methods for kinetic equations, boundary value problems, and
discretization 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: ba8df636-2132-11f1-aed0-ed93e2281fdd
year: '2025'
...
---
OA_place: repository
OA_type: green
_id: '20569'
abstract:
- lang: eng
text: 'This is the first part of a general description in terms of mass transport
for time-evolving interacting particles systems, at a mesoscopic level. Beyond
kinetic theory, our framework naturally applies in biology, computer vision, and
engineering. The central object of our study is a new discrepancy d between two
probability distributions in position and velocity states, which is reminiscent
of the 2-Wasserstein distance, but of second-order nature. We construct d in two
steps. First, we optimise over transport plans. The cost function is given by
the minimal acceleration between two coupled states on a fixed time horizon T.
Second, we further optimise over the time horizon T > 0. We prove the existence
of optimal transport plans and maps, and study two time-continuous characterisations
of d. One is given in terms of dynamical transport plans. The other one -- in
the spirit of the Benamou--Brenier formula -- is formulated as the minimisation
of an action of the acceleration field, constrained by Vlasov''s equations. Equivalence
of static and dynamical formulations of d holds true. While part of this result
can be derived from recent, parallel developments in optimal control between measures,
we give an original proof relying on two new ingredients: Galilean regularisation
of Vlasov''s equations and a kinetic Monge--Mather shortening principle. Finally,
we establish a first-order differential calculus in the geometry induced by d,
and identify solutions to Vlasov''s equations with curves of measures satisfying
a certain d-absolute continuity condition. One consequence is an explicit formula
for the d-derivative of such curves.'
acknowledgement: "This work was partially inspired by an unpublished note from 2014
by Guillaume Carlier,\r\nJean Dolbeault, and Bruno Nazaret. GB deeply thanks Jean
Dolbeault for proposing\r\nthis problem to him, guiding him into the subject, and
sharing the aforementioned note.\r\nWe are grateful to Karthik Elamvazhuthi for
making us aware of the work [20].\r\nThe work of GB has received funding from the
European Union’s Horizon 2020 research and innovation programme under the Marie
Sklodowska-Curie grant agreement\r\nNo 101034413.\r\nJM and FQ gratefully acknowledge
support from the Austrian Science Fund (FWF)\r\nproject 10.55776/F65."
article_number: '2502.15665'
article_processing_charge: No
arxiv: 1
author:
- first_name: Giovanni
full_name: Brigati, Giovanni
id: 63ff57e8-1fbb-11ee-88f2-f558ffc59cf1
last_name: Brigati
- first_name: Jan
full_name: Maas, Jan
id: 4C5696CE-F248-11E8-B48F-1D18A9856A87
last_name: Maas
orcid: 0000-0002-0845-1338
- first_name: Filippo
full_name: Quattrocchi, Filippo
id: 3ebd6ba8-edfb-11eb-afb5-91a9745ba308
last_name: Quattrocchi
orcid: 0009-0000-9773-1931
citation:
ama: 'Brigati G, Maas J, Quattrocchi F. Kinetic Optimal Transport (OTIKIN) -- Part
1: Second-order discrepancies between probability measures. arXiv. doi:10.48550/arXiv.2502.15665'
apa: 'Brigati, G., Maas, J., & Quattrocchi, F. (n.d.). Kinetic Optimal Transport
(OTIKIN) -- Part 1: Second-order discrepancies between probability measures. arXiv.
https://doi.org/10.48550/arXiv.2502.15665'
chicago: 'Brigati, Giovanni, Jan Maas, and Filippo Quattrocchi. “Kinetic Optimal
Transport (OTIKIN) -- Part 1: Second-Order Discrepancies between Probability Measures.”
ArXiv, n.d. https://doi.org/10.48550/arXiv.2502.15665.'
ieee: 'G. Brigati, J. Maas, and F. Quattrocchi, “Kinetic Optimal Transport (OTIKIN)
-- Part 1: Second-order discrepancies between probability measures,” arXiv.
.'
ista: 'Brigati G, Maas J, Quattrocchi F. Kinetic Optimal Transport (OTIKIN) -- Part
1: Second-order discrepancies between probability measures. arXiv, 2502.15665.'
mla: 'Brigati, Giovanni, et al. “Kinetic Optimal Transport (OTIKIN) -- Part 1: Second-Order
Discrepancies between Probability Measures.” ArXiv, 2502.15665, doi:10.48550/arXiv.2502.15665.'
short: G. Brigati, J. Maas, F. Quattrocchi, ArXiv (n.d.).
corr_author: '1'
date_created: 2025-10-28T13:12:08Z
date_published: 2025-08-10T00:00:00Z
date_updated: 2026-06-29T22:30:42Z
day: '10'
department:
- _id: GradSch
- _id: JaMa
doi: 10.48550/arXiv.2502.15665
ec_funded: 1
external_id:
arxiv:
- '2502.15665'
keyword:
- optimal transport
- kinetic theory
- second-order discrepancy
- Vlasov equation
- Wasserstein splines.
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.48550/arXiv.2502.15665
month: '08'
oa: 1
oa_version: Preprint
project:
- _id: fc31cba2-9c52-11eb-aca3-ff467d239cd2
grant_number: F6504
name: Taming Complexity in Partial Differential Systems
- _id: fc2ed2f7-9c52-11eb-aca3-c01059dda49c
call_identifier: H2020
grant_number: '101034413'
name: 'IST-BRIDGE: International postdoctoral program'
publication: arXiv
publication_status: draft
related_material:
record:
- id: '20563'
relation: dissertation_contains
status: public
status: public
title: 'Kinetic Optimal Transport (OTIKIN) -- Part 1: Second-order discrepancies between
probability measures'
type: preprint
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
year: '2025'
...
---
OA_embargo: '6'
OA_place: publisher
_id: '20798'
alternative_title:
- ISTA Thesis
article_processing_charge: No
author:
- first_name: Sebastian
full_name: Wald, Sebastian
id: 133F200A-B015-11E9-AD41-0EDAE5697425
last_name: Wald
orcid: 0000-0002-5869-1604
citation:
ama: Wald S. Atoms in a propagating-wave cavity for squeezed Mach-Zehnder atom interferometry.
2025. doi:10.15479/AT-ISTA-20798
apa: Wald, S. (2025). Atoms in a propagating-wave cavity for squeezed Mach-Zehnder
atom interferometry. Institute of Science and Technology Austria. https://doi.org/10.15479/AT-ISTA-20798
chicago: Wald, Sebastian. “Atoms in a Propagating-Wave Cavity for Squeezed Mach-Zehnder
Atom Interferometry.” Institute of Science and Technology Austria, 2025. https://doi.org/10.15479/AT-ISTA-20798.
ieee: S. Wald, “Atoms in a propagating-wave cavity for squeezed Mach-Zehnder atom
interferometry,” Institute of Science and Technology Austria, 2025.
ista: Wald S. 2025. Atoms in a propagating-wave cavity for squeezed Mach-Zehnder
atom interferometry. Institute of Science and Technology Austria.
mla: Wald, Sebastian. Atoms in a Propagating-Wave Cavity for Squeezed Mach-Zehnder
Atom Interferometry. Institute of Science and Technology Austria, 2025, doi:10.15479/AT-ISTA-20798.
short: S. Wald, Atoms in a Propagating-Wave Cavity for Squeezed Mach-Zehnder Atom
Interferometry, Institute of Science and Technology Austria, 2025.
corr_author: '1'
date_created: 2025-12-11T11:48:11Z
date_published: 2025-12-11T00:00:00Z
date_updated: 2026-06-15T22:30:04Z
day: '11'
ddc:
- '530'
degree_awarded: PhD
department:
- _id: GradSch
- _id: OnHo
doi: 10.15479/AT-ISTA-20798
file:
- access_level: open_access
checksum: 1be72faf529a5e8a2d03cb3d5f808b77
content_type: application/pdf
creator: swald
date_created: 2025-12-12T11:53:42Z
date_updated: 2026-06-15T22:30:03Z
embargo: 2026-06-15
file_id: '20809'
file_name: 2025_Wald_Sebastian_Thesis.pdf
file_size: 47536855
relation: main_file
- access_level: closed
checksum: 8c3a1904dceb4bcd04bc9f14b2594bab
content_type: application/x-zip-compressed
creator: swald
date_created: 2025-12-12T11:54:55Z
date_updated: 2026-06-15T22:30:03Z
embargo_to: open_access
file_id: '20810'
file_name: 2025_Wald_Sebastian_Thesis.zip
file_size: 40127601
relation: source_file
file_date_updated: 2026-06-15T22:30:03Z
has_accepted_license: '1'
keyword:
- entanglement-enhanced atom interferometry
- cavity QED
- spin-squeezing
- dipole trap
- quantum optics
language:
- iso: eng
month: '12'
oa: 1
oa_version: Published Version
page: '152'
publication_identifier:
isbn:
- 978-3-99078-075-6
issn:
- 2663-337X
publication_status: published
publisher: Institute of Science and Technology Austria
related_material:
record:
- id: '14759'
relation: part_of_dissertation
status: public
status: public
supervisor:
- first_name: Onur
full_name: Hosten, Onur
id: 4C02D85E-F248-11E8-B48F-1D18A9856A87
last_name: Hosten
orcid: 0000-0002-2031-204X
title: Atoms in a propagating-wave cavity for squeezed Mach-Zehnder atom interferometry
tmp:
image: /images/cc_by_nc.png
legal_code_url: https://creativecommons.org/licenses/by-nc/4.0/legalcode
name: Creative Commons Attribution-NonCommercial 4.0 International (CC BY-NC 4.0)
short: CC BY-NC (4.0)
type: dissertation
user_id: ba8df636-2132-11f1-aed0-ed93e2281fdd
year: '2025'
...
---
OA_place: publisher
_id: '20777'
acknowledgement: "My work has been funded through the project \"Functional Advantages
of Critical Brain\r\nDynamics\" of the ISTA interdisciplinary fund and through the
FWF.\r\n"
alternative_title:
- ISTA Thesis
article_processing_charge: No
author:
- first_name: Predrag
full_name: Zivadinovic, Predrag
id: 68AA0E5A-AFDA-11E9-9994-141DE6697425
last_name: Zivadinovic
citation:
ama: Zivadinovic P. Scale-free activity as a basis for spatial learning and memory
in the brain. 2025. doi:10.15479/AT-ISTA-20777
apa: Zivadinovic, P. (2025). Scale-free activity as a basis for spatial learning
and memory in the brain. Institute of Science and Technology Austria. https://doi.org/10.15479/AT-ISTA-20777
chicago: Zivadinovic, Predrag. “Scale-Free Activity as a Basis for Spatial Learning
and Memory in the Brain.” Institute of Science and Technology Austria, 2025. https://doi.org/10.15479/AT-ISTA-20777.
ieee: P. Zivadinovic, “Scale-free activity as a basis for spatial learning and memory
in the brain,” Institute of Science and Technology Austria, 2025.
ista: Zivadinovic P. 2025. Scale-free activity as a basis for spatial learning and
memory in the brain. Institute of Science and Technology Austria.
mla: Zivadinovic, Predrag. Scale-Free Activity as a Basis for Spatial Learning
and Memory in the Brain. Institute of Science and Technology Austria, 2025,
doi:10.15479/AT-ISTA-20777.
short: P. Zivadinovic, Scale-Free Activity as a Basis for Spatial Learning and Memory
in the Brain, Institute of Science and Technology Austria, 2025.
corr_author: '1'
date_created: 2025-12-10T19:37:41Z
date_published: 2025-12-11T00:00:00Z
date_updated: 2026-06-11T22:30:03Z
day: '11'
ddc:
- '570'
- '539'
- '571'
degree_awarded: PhD
department:
- _id: GradSch
- _id: JoCs
doi: 10.15479/AT-ISTA-20777
file:
- access_level: open_access
checksum: aae9d1ed53f7b67f75e289c26a02b72f
content_type: application/pdf
creator: pzivadin
date_created: 2025-12-10T19:28:20Z
date_updated: 2026-06-11T22:30:02Z
embargo: 2026-06-11
file_id: '20778'
file_name: 2025_Zivadinovic_Predrag_PhD_thesis.pdf
file_size: 8105379
relation: main_file
- access_level: closed
checksum: 8a08a3804ce7d9d625fdf1631113da8c
content_type: application/zip
creator: pzivadin
date_created: 2025-12-10T19:28:10Z
date_updated: 2026-06-11T22:30:02Z
embargo_to: open_access
file_id: '20779'
file_name: 2025_Zivadinovic_Predrag_PhD_thesis_source.zip
file_size: 8512240
relation: source_file
file_date_updated: 2026-06-11T22:30:02Z
has_accepted_license: '1'
language:
- iso: eng
month: '12'
oa: 1
oa_version: Published Version
page: '104'
project:
- _id: eb943429-77a9-11ec-83b8-9f471cdf5c67
grant_number: M03318
name: Functional Advantages of Critical Brain Dynamics
publication_identifier:
issn:
- 2663-337X
publication_status: published
publisher: Institute of Science and Technology Austria
status: public
supervisor:
- first_name: Jozsef L
full_name: Csicsvari, Jozsef L
id: 3FA14672-F248-11E8-B48F-1D18A9856A87
last_name: Csicsvari
orcid: 0000-0002-5193-4036
title: Scale-free activity as a basis for spatial learning and memory in the brain
type: dissertation
user_id: ba8df636-2132-11f1-aed0-ed93e2281fdd
year: '2025'
...
---
OA_place: repository
OA_type: green
_id: '12846'
abstract:
- lang: eng
text: We present a formula for the signed area of a spherical polygon via prequantization.
In contrast to the traditional formula based on the Gauss-Bonnet theorem that
requires measuring angles, the new formula mimics Green's theorem and is applicable
to a wider range of degenerate spherical curves and polygons.
acknowledgement: This work was funded by European Research Council Consolidator grant
101045083 CoDiNA and National Science Foundation CAREER award 2239062. Some figures
in the article were generated by the software Houdini and its education license
was provided by SideFX. The authors acknowledge anonymous referees for their reviews
and insightful suggestions, and Chris Wojtan for his continuous support through
discussions. The second author thanks Anna Sisak for a fruitful discussion on prequantum
bundles.
article_processing_charge: No
article_type: original
arxiv: 1
author:
- first_name: Albert
full_name: Chern, Albert
last_name: Chern
- first_name: Sadashige
full_name: Ishida, Sadashige
id: 6F7C4B96-A8E9-11E9-A7CA-09ECE5697425
last_name: Ishida
orcid: 0000-0002-3121-3100
citation:
ama: Chern A, Ishida S. Area formula for spherical polygons via prequantization.
SIAM Journal on Applied Algebra and Geometry. 2024;8(3):782-796. doi:10.1137/23M1565255
apa: Chern, A., & Ishida, S. (2024). Area formula for spherical polygons via
prequantization. SIAM Journal on Applied Algebra and Geometry. Society
for Industrial and Applied Mathematics. https://doi.org/10.1137/23M1565255
chicago: Chern, Albert, and Sadashige Ishida. “Area Formula for Spherical Polygons
via Prequantization.” SIAM Journal on Applied Algebra and Geometry. Society
for Industrial and Applied Mathematics, 2024. https://doi.org/10.1137/23M1565255.
ieee: A. Chern and S. Ishida, “Area formula for spherical polygons via prequantization,”
SIAM Journal on Applied Algebra and Geometry, vol. 8, no. 3. Society for
Industrial and Applied Mathematics, pp. 782–796, 2024.
ista: Chern A, Ishida S. 2024. Area formula for spherical polygons via prequantization.
SIAM Journal on Applied Algebra and Geometry. 8(3), 782–796.
mla: Chern, Albert, and Sadashige Ishida. “Area Formula for Spherical Polygons via
Prequantization.” SIAM Journal on Applied Algebra and Geometry, vol. 8,
no. 3, Society for Industrial and Applied Mathematics, 2024, pp. 782–96, doi:10.1137/23M1565255.
short: A. Chern, S. Ishida, SIAM Journal on Applied Algebra and Geometry 8 (2024)
782–796.
corr_author: '1'
date_created: 2023-04-18T19:16:06Z
date_published: 2024-09-23T00:00:00Z
date_updated: 2026-04-07T12:02:22Z
day: '23'
ddc:
- '516'
department:
- _id: GradSch
- _id: ChWo
doi: 10.1137/23M1565255
external_id:
arxiv:
- '2303.14555'
isi:
- '001342265800009'
has_accepted_license: '1'
intvolume: ' 8'
isi: 1
issue: '3'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.48550/arXiv.2303.14555
month: '09'
oa: 1
oa_version: Preprint
page: 782-796
project:
- _id: 34bc2376-11ca-11ed-8bc3-9a3b3961a088
grant_number: '101045083'
name: Computational Discovery of Numerical Algorithms for Animation and Simulation
of Natural Phenomena
publication: SIAM Journal on Applied Algebra and Geometry
publication_identifier:
eissn:
- 2470-6566
publication_status: published
publisher: Society for Industrial and Applied Mathematics
quality_controlled: '1'
related_material:
record:
- id: '20551'
relation: dissertation_contains
status: public
scopus_import: '1'
status: public
title: Area formula for spherical polygons via prequantization
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 8
year: '2024'
...