---
_id: '21145'
abstract:
- lang: eng
text: 'Protein conformational energy landscapes are shaped not only by intramolecular
interactions but also by their environment. In protein crystals and protein-protein
complexes, intermolecular contacts alter this energy landscape, but the exact
nature of this alteration is difficult to decipher. Understanding how the crystal
lattice affects protein dynamics is crucial for crystallography-based studies
of motion, yet its influence on collective motions remains unclear. Aromatic ring
flips in the hydrophobic core represent sensitive probes of such dynamics. Here,
we compare the kinetics of aromatic ring flips in the protein GB1 in crystals,
in complex with its binding partner IgG, and in solution, combining advanced isotope
labeling with quantitative NMR methods. We show that rings in the core flip nearly
a thousand times less frequently in crystals than in solution. Enhanced-sampling
molecular dynamics simulations, based on a new crystal structure, reproduce these
elevated barriers and reveal how the crystal restrains motions. '
acknowledged_ssus:
- _id: NMR
- _id: LifeSc
acknowledgement: "We thank Nikolai R. Skrynnikov and Olga O. Lebedenko (St. Petersburg)
for insightful discussions and for performing exploratory MD simulations. We are
grateful to Tobias Schubeis (Lyon) for advice with GB1 crystallization, and Rebecca
Schmid for initial crystallization trials.\r\nWe thank Sebastian Falkner for assistance
with constructing the structural model of the IgG:GB1 complex.\r\nThis research
was supported by the Scientific Service Units (SSU) of Institute of Science and
Technology Austria (ISTA) through resources provided by the Nuclear Magnetic Resonance
and the Lab Support Facilities. We thank Petra Rovó and Margarita Valhondo Falcón
for excellent support of the NMR facility.\r\nLea M. Becker is recipient of a DOC
fellowship of the Austrian Academy of Sciences at the Institute of Science and Technology
Austria (grant no. PR10660EAW01). Christophe Chipot acknowledges the European Research
Council (grant project 101097272 ``MilliInMicro'') and the Métropole du Grand Nancy
(grant project ``ARC''). BM07-FIP2 is supported by the French ANR PIA3 (France 2030)
EquipEx+ project MAGNIFIX under grant agreement ANR-21-ESRE-0011."
article_processing_charge: No
author:
- first_name: Lea Marie
full_name: Becker, Lea Marie
id: 36336939-eb97-11eb-a6c2-c83f1214ca79
last_name: Becker
orcid: 0000-0002-6401-5151
- first_name: Paul
full_name: Schanda, Paul
id: 7B541462-FAF6-11E9-A490-E8DFE5697425
last_name: Schanda
orcid: 0000-0002-9350-7606
- first_name: Christophe
full_name: Chipot, Christophe
last_name: Chipot
citation:
ama: Becker LM, Schanda P, Chipot C. Additional Data for “Aromatic Ring Flips Reveal
Reshaping of Protein Dynamics in Crystals and Complexes.” 2026. doi:10.15479/AT-ISTA-21145
apa: Becker, L. M., Schanda, P., & Chipot, C. (2026). Additional Data for “Aromatic
Ring Flips Reveal Reshaping of Protein Dynamics in Crystals and Complexes.” Institute
of Science and Technology Austria. https://doi.org/10.15479/AT-ISTA-21145
chicago: Becker, Lea Marie, Paul Schanda, and Christophe Chipot. “Additional Data
for ‘Aromatic Ring Flips Reveal Reshaping of Protein Dynamics in Crystals and
Complexes.’” Institute of Science and Technology Austria, 2026. https://doi.org/10.15479/AT-ISTA-21145.
ieee: L. M. Becker, P. Schanda, and C. Chipot, “Additional Data for ‘Aromatic Ring
Flips Reveal Reshaping of Protein Dynamics in Crystals and Complexes.’” Institute
of Science and Technology Austria, 2026.
ista: Becker LM, Schanda P, Chipot C. 2026. Additional Data for ‘Aromatic Ring Flips
Reveal Reshaping of Protein Dynamics in Crystals and Complexes’, Institute of
Science and Technology Austria, 10.15479/AT-ISTA-21145.
mla: Becker, Lea Marie, et al. Additional Data for “Aromatic Ring Flips Reveal
Reshaping of Protein Dynamics in Crystals and Complexes.” Institute of Science
and Technology Austria, 2026, doi:10.15479/AT-ISTA-21145.
short: L.M. Becker, P. Schanda, C. Chipot, (2026).
contributor:
- contributor_type: researcher
first_name: Haohao
last_name: Fu
- contributor_type: researcher
first_name: Benjamin
id: 71cda2f3-e604-11ee-a1df-da10587eda3f
last_name: Tatman
- contributor_type: researcher
first_name: Matthias
last_name: Dreydoppel
- contributor_type: researcher
first_name: Anna
id: 9fb2a840-89e1-11ee-a8b7-cc5c7ba62471
last_name: Kapitonova
- contributor_type: researcher
first_name: Daniel
id: 302BADF6-85FC-11EA-9E3B-B9493DDC885E
last_name: Balazs
orcid: 0000-0001-7597-043X
- contributor_type: researcher
first_name: Ulrich
last_name: Weininger
- contributor_type: researcher
first_name: Sylvain
last_name: Engilberge
corr_author: '1'
date_created: 2026-02-05T13:54:39Z
date_published: 2026-02-09T00:00:00Z
date_updated: 2026-06-10T08:25:16Z
day: '09'
ddc:
- '572'
department:
- _id: GradSch
- _id: PaSc
doi: 10.15479/AT-ISTA-21145
file:
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checksum: 02a419cce8cea450bc952f35488d2df5
content_type: text/plain
creator: lbecker
date_created: 2026-02-05T13:52:37Z
date_updated: 2026-02-05T13:52:37Z
file_id: '21146'
file_name: README.txt
file_size: 4263
relation: table_of_contents
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checksum: b0b82b1aa73985b0b308a3fa52d21aea
content_type: application/zip
creator: lbecker
date_created: 2026-02-05T13:52:41Z
date_updated: 2026-02-05T13:52:41Z
file_id: '21147'
file_name: Research_Data.zip
file_size: 50647107
relation: main_file
success: 1
file_date_updated: 2026-02-05T13:52:41Z
has_accepted_license: '1'
license: https://creativecommons.org/licenses/by-nc/4.0/
month: '02'
oa: 1
oa_version: Published Version
project:
- _id: 7be609c4-9f16-11ee-852c-85015ce2b9b0
grant_number: '26777'
name: Exploring protein dynamics by solid-state MAS NMR through specific labeling
approaches
publisher: Institute of Science and Technology Austria
related_material:
record:
- id: '20641'
relation: earlier_version
status: public
status: public
title: Additional Data for "Aromatic Ring Flips Reveal Reshaping of Protein Dynamics
in Crystals and Complexes"
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: research_data
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
year: '2026'
...
---
DOAJ_listed: '1'
OA_place: publisher
OA_type: gold
PlanS_conform: '1'
_id: '20840'
abstract:
- lang: eng
text: Probing the possibility of entanglement generation through gravity offers
a path to tackle the question of whether gravitational fields possess a quantum
mechanical nature. A potential realization necessitates systems with low-frequency
dynamics at an optimal mass scale, for which the microgram-to-milligram range
is a strong contender. Here, after refining a figure-of-merit for the problem,
we present a 1-milligram torsional pendulum operating at 18 Hz. We demonstrate
laser cooling its motion from room temperature to 240 microkelvins, surpassing
by over 20-fold the coldest motions attained for oscillators ranging from micrograms
to kilograms. We quantify and contrast the utility of the current approach with
other platforms. The achieved performance and large improvement potential highlight
milligram-scale torsional pendulums as a powerful platform for precision measurements
relevant to future studies at the quantum-gravity interface.
acknowledgement: We thank Gerard Higgins, Andrei Militaru, Nikolai Kiesel, and Markus
Aspelmeyer for useful discussions on the topic of the figure-of-merit. We thank
Teodor Strömberg for helping with the additional characterizations of the optical
lever noise. We thank Johannes Fink and Scott Waitukaitis for their helpful feedback
on the manuscript. This work was supported by Institute of Science and Technology
Austria and the European Research Council under Grant No. 101087907 (ERC CoG QuHAMP).
article_number: '80'
article_processing_charge: Yes
article_type: original
arxiv: 1
author:
- first_name: Sofya
full_name: Agafonova, Sofya
id: 09501ff6-dca7-11ea-a8ae-b3e0b9166e80
last_name: Agafonova
orcid: 0000-0003-0582-2946
- first_name: Pere
full_name: Rosello, Pere
last_name: Rosello
- first_name: Manuel
full_name: Mekonnen, Manuel
last_name: Mekonnen
- first_name: Onur
full_name: Hosten, Onur
id: 4C02D85E-F248-11E8-B48F-1D18A9856A87
last_name: Hosten
orcid: 0000-0002-2031-204X
citation:
ama: Agafonova S, Rosello P, Mekonnen M, Hosten O. One-milligram torsional pendulum
toward experiments at the quantum-gravity interface. Communications Physics.
2026;9. doi:10.1038/s42005-026-02514-w
apa: Agafonova, S., Rosello, P., Mekonnen, M., & Hosten, O. (2026). One-milligram
torsional pendulum toward experiments at the quantum-gravity interface. Communications
Physics. Springer Nature. https://doi.org/10.1038/s42005-026-02514-w
chicago: Agafonova, Sofia, Pere Rosello, Manuel Mekonnen, and Onur Hosten. “One-Milligram
Torsional Pendulum toward Experiments at the Quantum-Gravity Interface.” Communications
Physics. Springer Nature, 2026. https://doi.org/10.1038/s42005-026-02514-w.
ieee: S. Agafonova, P. Rosello, M. Mekonnen, and O. Hosten, “One-milligram torsional
pendulum toward experiments at the quantum-gravity interface,” Communications
Physics, vol. 9. Springer Nature, 2026.
ista: Agafonova S, Rosello P, Mekonnen M, Hosten O. 2026. One-milligram torsional
pendulum toward experiments at the quantum-gravity interface. Communications Physics.
9, 80.
mla: Agafonova, Sofia, et al. “One-Milligram Torsional Pendulum toward Experiments
at the Quantum-Gravity Interface.” Communications Physics, vol. 9, 80,
Springer Nature, 2026, doi:10.1038/s42005-026-02514-w.
short: S. Agafonova, P. Rosello, M. Mekonnen, O. Hosten, Communications Physics
9 (2026).
corr_author: '1'
date_created: 2025-12-21T11:39:04Z
date_published: 2026-03-04T00:00:00Z
date_updated: 2026-06-10T08:36:06Z
day: '04'
ddc:
- '530'
department:
- _id: GradSch
- _id: OnHo
doi: 10.1038/s42005-026-02514-w
external_id:
arxiv:
- '2408.09445'
file:
- access_level: open_access
checksum: 62e2175e7e3ad49260ae6a7b4e0860a2
content_type: application/pdf
creator: dernst
date_created: 2026-03-16T10:07:46Z
date_updated: 2026-03-16T10:07:46Z
file_id: '21457'
file_name: 2026_CommunicationsPhysics_Agafonova.pdf
file_size: 1901772
relation: main_file
success: 1
file_date_updated: 2026-03-16T10:07:46Z
has_accepted_license: '1'
intvolume: ' 9'
language:
- iso: eng
month: '03'
oa: 1
oa_version: Published Version
project:
- _id: bdb2a702-d553-11ed-ba76-f12e3e5a3bc6
grant_number: '101087907'
name: 'A quantum hybrid of atoms and milligram-scale pendulums: towards gravitational
quantum mechanics'
publication: Communications Physics
publication_identifier:
eissn:
- 2399-3650
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
related_material:
record:
- id: '20842'
relation: research_data
status: public
scopus_import: '1'
status: public
title: One-milligram torsional pendulum toward experiments at the quantum-gravity
interface
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: 9
year: '2026'
...
---
OA_place: repository
OA_type: free access
_id: '21284'
abstract:
- lang: eng
text: The advantageous characteristics attributed to the 19F nucleus have made it
a popular target for NMR once again in recent years. Aside from solution NMR,
an increasing number of studies have been conducted applying solid-state magic-angle-spinning
NMR to fluorine-labeled samples. Here, the high chemical shift anisotropy and
strong dipolar couplings can be utilized to get structural insights into proteins
and measure long distances. Despite increasing popularity and promising benefits,
the sensitivity of biomolecular 19F MAS NMR often suffers from slow longitudinal
T1 relaxation and therefore long recycle delays. In this work, we expand paramagnetic
doping, an approach commonly used to reduce proton T1 relaxation times, to 19F-labeled
biological samples. We study the effect of Gd(DTPA) and Gd(DTPA-BMA) on 19F and
13C T1 and T2 relaxation in a [5-19F13C]-tryptophan-labeled protein via 19F-detected
MAS NMR experiments. The observed paramagnetic relaxation enhancement substantially
reduces measurement times of 19F MAS NMR experiments without compromising resolution.
Additionally, we report the chemical-shift assignments of all four fluorotryptophan
signals in the 12 × 39 kDa large protein using a mutagenesis approach.
acknowledged_ssus:
- _id: NMR
- _id: LifeSc
acknowledgement: We thank Ben P. Tatman for insightful discussions. This research
was supported by the Scientific Service Units (SSU) of Institute of Science and
Technology Austria (ISTA) through resources provided by the Nuclear Magnetic Resonance
Facility and the Lab Support Facility.
article_processing_charge: No
author:
- first_name: Lea Marie
full_name: Becker, Lea Marie
id: 36336939-eb97-11eb-a6c2-c83f1214ca79
last_name: Becker
orcid: 0000-0002-6401-5151
- first_name: Paul
full_name: Schanda, Paul
id: 7B541462-FAF6-11E9-A490-E8DFE5697425
last_name: Schanda
orcid: 0000-0002-9350-7606
citation:
ama: Becker LM, Schanda P. Research data for “Accelerated 19F biomolecular magic-angle
spinning NMR with paramagnetic dopants.” 2026. doi:10.15479/AT-ISTA-21284
apa: Becker, L. M., & Schanda, P. (2026). Research data for “Accelerated 19F
biomolecular magic-angle spinning NMR with paramagnetic dopants.” Institute of
Science and Technology Austria. https://doi.org/10.15479/AT-ISTA-21284
chicago: Becker, Lea Marie, and Paul Schanda. “Research Data for ‘Accelerated 19F
Biomolecular Magic-Angle Spinning NMR with Paramagnetic Dopants.’” Institute of
Science and Technology Austria, 2026. https://doi.org/10.15479/AT-ISTA-21284.
ieee: L. M. Becker and P. Schanda, “Research data for ‘Accelerated 19F biomolecular
magic-angle spinning NMR with paramagnetic dopants.’” Institute of Science and
Technology Austria, 2026.
ista: Becker LM, Schanda P. 2026. Research data for ‘Accelerated 19F biomolecular
magic-angle spinning NMR with paramagnetic dopants’, Institute of Science and
Technology Austria, 10.15479/AT-ISTA-21284.
mla: Becker, Lea Marie, and Paul Schanda. Research Data for “Accelerated 19F
Biomolecular Magic-Angle Spinning NMR with Paramagnetic Dopants.” Institute
of Science and Technology Austria, 2026, doi:10.15479/AT-ISTA-21284.
short: L.M. Becker, P. Schanda, (2026).
contributor:
- contributor_type: researcher
first_name: Giorgia
id: 334a5e40-8747-11f0-b671-ba1f5154b4b4
last_name: Toscano
- contributor_type: researcher
first_name: Anna
id: 9fb2a840-89e1-11ee-a8b7-cc5c7ba62471
last_name: Kapitonova
- contributor_type: researcher
first_name: Rajkumar
id: a3089acd-6806-11ee-bacc-f0c7d500ad20
last_name: Singh
- contributor_type: researcher
first_name: Undina
id: bb74f472-ae54-11eb-9835-bc9c22fb1183
last_name: Guillerm
- contributor_type: researcher
first_name: Roman
last_name: Lichtenecker
corr_author: '1'
date_created: 2026-02-17T10:17:14Z
date_published: 2026-02-18T00:00:00Z
date_updated: 2026-06-10T09:28:41Z
day: '18'
ddc:
- '541'
department:
- _id: GradSch
- _id: PaSc
doi: 10.15479/AT-ISTA-21284
file:
- access_level: open_access
checksum: 2d3105f26be578073b88ee1f2ea0bdb1
content_type: application/zip
creator: lbecker
date_created: 2026-02-17T10:11:14Z
date_updated: 2026-02-17T10:11:14Z
file_id: '21285'
file_name: Research_data.zip
file_size: 36996027
relation: main_file
success: 1
- access_level: open_access
checksum: e24aebcdb8856cb181cbaa02de020ddb
content_type: text/plain
creator: lbecker
date_created: 2026-02-17T10:11:14Z
date_updated: 2026-02-17T10:11:14Z
file_id: '21286'
file_name: README.txt
file_size: 1993
relation: table_of_contents
file_date_updated: 2026-02-17T10:11:14Z
has_accepted_license: '1'
month: '2'
oa: 1
oa_version: Published Version
publisher: Institute of Science and Technology Austria
status: public
title: Research data for "Accelerated 19F biomolecular magic-angle spinning NMR with
paramagnetic dopants"
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: research_data
user_id: 68b8ca59-c5b3-11ee-8790-cd641c68093d
year: '2026'
...
---
OA_place: repository
_id: '21360'
acknowledged_ssus:
- _id: LifeSc
- _id: Bio
acknowledgement: "I would like to acknowledge the Austrian Academy of Sciences (ÖAW)
and European\r\nResearch Executive Agency (REA) for funding my research (DOC ÖAW
Fellowship\r\n26130, Horizon Europe BOLERO Project 101060393). "
alternative_title:
- ISTA Thesis
article_processing_charge: No
author:
- first_name: Stefan
full_name: Riegler, Stefan
id: FF6018E0-D806-11E9-8E43-0B14E6697425
last_name: Riegler
orcid: 0000-0003-3413-1343
citation:
ama: 'Riegler S. Root system plasticity under nutrient limitation : Investigating
hormonal and molecular drivers in Arabidopsis thaliana and Coffea species. 2026.
doi:10.15479/AT-ISTA-21360'
apa: 'Riegler, S. (2026). Root system plasticity under nutrient limitation :
Investigating hormonal and molecular drivers in Arabidopsis thaliana and Coffea
species. Institute of Science and Technology Austria. https://doi.org/10.15479/AT-ISTA-21360'
chicago: 'Riegler, Stefan. “Root System Plasticity under Nutrient Limitation : Investigating
Hormonal and Molecular Drivers in Arabidopsis Thaliana and Coffea Species.” Institute
of Science and Technology Austria, 2026. https://doi.org/10.15479/AT-ISTA-21360.'
ieee: 'S. Riegler, “Root system plasticity under nutrient limitation : Investigating
hormonal and molecular drivers in Arabidopsis thaliana and Coffea species,” Institute
of Science and Technology Austria, 2026.'
ista: 'Riegler S. 2026. Root system plasticity under nutrient limitation : Investigating
hormonal and molecular drivers in Arabidopsis thaliana and Coffea species. Institute
of Science and Technology Austria.'
mla: 'Riegler, Stefan. Root System Plasticity under Nutrient Limitation : Investigating
Hormonal and Molecular Drivers in Arabidopsis Thaliana and Coffea Species.
Institute of Science and Technology Austria, 2026, doi:10.15479/AT-ISTA-21360.'
short: 'S. Riegler, Root System Plasticity under Nutrient Limitation : Investigating
Hormonal and Molecular Drivers in Arabidopsis Thaliana and Coffea Species, Institute
of Science and Technology Austria, 2026.'
corr_author: '1'
date_created: 2026-02-27T09:08:14Z
date_published: 2026-02-26T00:00:00Z
date_updated: 2026-06-10T09:39:12Z
day: '26'
ddc:
- '570'
- '575'
- '583'
degree_awarded: PhD
department:
- _id: GradSch
- _id: EvBe
doi: 10.15479/AT-ISTA-21360
file:
- access_level: closed
checksum: 2f1f44e8536c2538f94a440217452c9f
content_type: application/x-zip-compressed
creator: sriegler
date_created: 2026-03-02T10:59:50Z
date_updated: 2026-03-02T10:59:50Z
file_id: '21386'
file_name: 2026_Riegler_Stefan_Thesis.zip
file_size: 31430022
relation: source_file
- access_level: closed
checksum: 2e8dc39640bc26ae5684c944c619719b
content_type: application/pdf
creator: sriegler
date_created: 2026-03-02T10:59:49Z
date_updated: 2026-03-02T10:59:49Z
embargo: 2027-02-27
embargo_to: open_access
file_id: '21387'
file_name: 2026_Riegler_Stefan_Thesis.pdf
file_size: 11635090
relation: main_file
file_date_updated: 2026-03-02T10:59:50Z
has_accepted_license: '1'
language:
- iso: eng
license: https://creativecommons.org/licenses/by-sa/4.0/
month: '02'
oa_version: Published Version
page: '185'
project:
- _id: 34afa094-11ca-11ed-8bc3-a375845a59fb
grant_number: '101060393'
name: Breeding for coffee and cocoa root resilience in low input farming systems
based on improved rootstocks
publication_identifier:
issn:
- 2663-337X
publication_status: published
publisher: Institute of Science and Technology Austria
related_material:
record:
- id: '21363'
relation: research_data
status: public
status: public
supervisor:
- first_name: Eva
full_name: Benková, Eva
id: 38F4F166-F248-11E8-B48F-1D18A9856A87
last_name: Benková
orcid: 0000-0002-8510-9739
title: 'Root system plasticity under nutrient limitation : Investigating hormonal
and molecular drivers in Arabidopsis thaliana and Coffea species'
tmp:
image: /images/cc_by_sa.png
legal_code_url: https://creativecommons.org/licenses/by-sa/4.0/legalcode
name: Creative Commons Attribution-ShareAlike 4.0 International Public License (CC
BY-SA 4.0)
short: CC BY-SA (4.0)
type: dissertation
user_id: 8b945eb4-e2f2-11eb-945a-df72226e66a9
year: '2026'
...
---
_id: '20833'
abstract:
- lang: eng
text: Sex-chromosome systems are highly variable across animals, but how they transition
from one to another is not well understood. Diptera have undergone multiple sex-chromosome
turnovers and expansions while maintaining their general chromosomal content,
which makes them an ideal clade to study such transitions. We analysed more than
100 dipteran whole-genome assemblies and identified 4 new lineages that underwent
sex-chromosome turnover (in addition to the 5 previously reported). We find the
majority of turnovers happened in the group Schizophora, which tend to have fewer
genes on the F element (the chromosome homologous to the ancestral insect X chromosome)
than lower dipterans, a factor previously hypothesized to facilitate turnover.
Most derived X chromosomes have higher GC content than autosomes, consistent with
a high prevalence of male-achiasmy in Diptera. In addition, an excess of gene
movement out of the X is detected for most of these new X chromosomes, and many
of these moved genes have high testis expression in Drosophila, suggesting that
out-of-X gene movement contributes to the long-term demasculinization of X chromosomes.
article_processing_charge: No
author:
- first_name: Lorena Alexandra
full_name: Layana Franco, Lorena Alexandra
id: 02814589-eb8f-11eb-b029-a70074f3f18f
last_name: Layana Franco
orcid: 0000-0002-1253-6297
- first_name: Melissa A
full_name: Toups, Melissa A
id: 4E099E4E-F248-11E8-B48F-1D18A9856A87
last_name: Toups
orcid: 0000-0002-9752-7380
- first_name: Beatriz
full_name: Vicoso, Beatriz
id: 49E1C5C6-F248-11E8-B48F-1D18A9856A87
last_name: Vicoso
orcid: 0000-0002-4579-8306
citation:
ama: Layana Franco LA, Toups MA, Vicoso B. Research Data for “Causes and consequences
of sex-chromosome turnovers in Diptera.” 2026. doi:10.15479/AT-ISTA-20833
apa: Layana Franco, L. A., Toups, M. A., & Vicoso, B. (2026). Research Data
for “Causes and consequences of sex-chromosome turnovers in Diptera.” Institute
of Science and Technology Austria. https://doi.org/10.15479/AT-ISTA-20833
chicago: Layana Franco, Lorena Alexandra, Melissa A Toups, and Beatriz Vicoso. “Research
Data for ‘Causes and Consequences of Sex-Chromosome Turnovers in Diptera.’” Institute
of Science and Technology Austria, 2026. https://doi.org/10.15479/AT-ISTA-20833.
ieee: L. A. Layana Franco, M. A. Toups, and B. Vicoso, “Research Data for ‘Causes
and consequences of sex-chromosome turnovers in Diptera.’” Institute of Science
and Technology Austria, 2026.
ista: Layana Franco LA, Toups MA, Vicoso B. 2026. Research Data for ‘Causes and
consequences of sex-chromosome turnovers in Diptera’, Institute of Science and
Technology Austria, 10.15479/AT-ISTA-20833.
mla: Layana Franco, Lorena Alexandra, et al. Research Data for “Causes and Consequences
of Sex-Chromosome Turnovers in Diptera.” Institute of Science and Technology
Austria, 2026, doi:10.15479/AT-ISTA-20833.
short: L.A. Layana Franco, M.A. Toups, B. Vicoso, (2026).
corr_author: '1'
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has_accepted_license: '1'
keyword:
- Schizophora
- sex chromosomes
- sex-chromosome turnover
- Diptera
- genomic features
- out-of-X movement.
month: '01'
oa: 1
oa_version: Published Version
publisher: Institute of Science and Technology Austria
status: public
title: Research Data for 'Causes and consequences of sex-chromosome turnovers in Diptera'
tmp:
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legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: research_data
user_id: 68b8ca59-c5b3-11ee-8790-cd641c68093d
year: '2026'
...
---
_id: '21363'
abstract:
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text: The data contains information on coffee differential gene expression as well
as co-expression and trait correlations in two separate experiments. First, contrasting
nitrogen supply, second, intra- and interspecific grafting.
article_processing_charge: No
author:
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orcid: 0000-0003-3413-1343
citation:
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Investigating Hormonal and Molecular Drivers in Arabidopsis thaliana and Coffea
species. 2026. doi:10.15479/AT-ISTA-21363'
apa: 'Riegler, S. (2026). Thesis Data for Root System Plasticity under Nutrient
Limitation: Investigating Hormonal and Molecular Drivers in Arabidopsis thaliana
and Coffea species. Institute of Science and Technology Austria. https://doi.org/10.15479/AT-ISTA-21363'
chicago: 'Riegler, Stefan. “Thesis Data for Root System Plasticity under Nutrient
Limitation: Investigating Hormonal and Molecular Drivers in Arabidopsis Thaliana
and Coffea Species.” Institute of Science and Technology Austria, 2026. https://doi.org/10.15479/AT-ISTA-21363.'
ieee: 'S. Riegler, “Thesis Data for Root System Plasticity under Nutrient Limitation:
Investigating Hormonal and Molecular Drivers in Arabidopsis thaliana and Coffea
species.” Institute of Science and Technology Austria, 2026.'
ista: 'Riegler S. 2026. Thesis Data for Root System Plasticity under Nutrient Limitation:
Investigating Hormonal and Molecular Drivers in Arabidopsis thaliana and Coffea
species, Institute of Science and Technology Austria, 10.15479/AT-ISTA-21363.'
mla: 'Riegler, Stefan. Thesis Data for Root System Plasticity under Nutrient
Limitation: Investigating Hormonal and Molecular Drivers in Arabidopsis Thaliana
and Coffea Species. Institute of Science and Technology Austria, 2026, doi:10.15479/AT-ISTA-21363.'
short: S. Riegler, (2026).
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month: '02'
oa_version: Published Version
publisher: Institute of Science and Technology Austria
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title: 'Thesis Data for Root System Plasticity under Nutrient Limitation: Investigating
Hormonal and Molecular Drivers in Arabidopsis thaliana and Coffea species'
tmp:
image: /images/cc_by_sa.png
legal_code_url: https://creativecommons.org/licenses/by-sa/4.0/legalcode
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BY-SA 4.0)
short: CC BY-SA (4.0)
type: research_data
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...
---
OA_place: repository
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acknowledgement: "Finally, I gratefully acknowledge funding from the DOC Fellowship
of the Austrian Academy\r\nof Sciences (OeAW): grant agreement 26360."
alternative_title:
- ISTA Thesis
article_processing_charge: No
author:
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full_name: Dunajova, Zuzana
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ama: Dunajova Z. Geometry-driven self-organization of migrating cells and chiral
filaments. 2026. doi:10.15479/AT-ISTA-21423
apa: Dunajova, Z. (2026). Geometry-driven self-organization of migrating cells
and chiral filaments. Institute of Science and Technology Austria. https://doi.org/10.15479/AT-ISTA-21423
chicago: Dunajova, Zuzana. “Geometry-Driven Self-Organization of Migrating Cells
and Chiral Filaments.” Institute of Science and Technology Austria, 2026. https://doi.org/10.15479/AT-ISTA-21423.
ieee: Z. Dunajova, “Geometry-driven self-organization of migrating cells and chiral
filaments,” Institute of Science and Technology Austria, 2026.
ista: Dunajova Z. 2026. Geometry-driven self-organization of migrating cells and
chiral filaments. Institute of Science and Technology Austria.
mla: Dunajova, Zuzana. Geometry-Driven Self-Organization of Migrating Cells and
Chiral Filaments. Institute of Science and Technology Austria, 2026, doi:10.15479/AT-ISTA-21423.
short: Z. Dunajova, Geometry-Driven Self-Organization of Migrating Cells and Chiral
Filaments, Institute of Science and Technology Austria, 2026.
corr_author: '1'
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date_published: 2026-03-11T00:00:00Z
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license: https://creativecommons.org/licenses/by-nc-sa/4.0/
month: '03'
oa_version: Published Version
page: '110'
project:
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grant_number: '26360'
name: Motile active matter models of migrating cells and chiral filaments
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isbn:
- 978-3-99078-076-3
issn:
- 2663-337X
publication_status: published
publisher: Institute of Science and Technology Austria
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supervisor:
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full_name: Hannezo, Edouard B
id: 3A9DB764-F248-11E8-B48F-1D18A9856A87
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orcid: 0000-0001-6005-1561
title: Geometry-driven self-organization of migrating cells and chiral filaments
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...
---
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abstract:
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text: Magneto-optic Kerr effect (MOKE) is a powerful probe of broken time-reversal
symmetry (T), typically used to study ferromagnets. While MOKE has been observed
in some antiferromagnets (AFMs) with vanishing magnetization, it is often associated
with structures whose symmetry is lower than basic collinear, bipartite order.
In contrast, theory predicts a mechanism for MOKE intrinsic to all AFMs of A-type,
i.e. layered AFMs in which ferromagnetic layers are antiferromagnetically aligned.
Here we report the experimental confirmation of this mechanism in a bulk AFM.
We achieve this by measuring the imaginary component of MOKE as a function of
photon energy in MnBi2Te4, an A-type AFM where T is preserved in combination with
a translation, and comparing the experimental results with model calculations.
Our model suggests that observable MOKE should be expected in all collinear A-type
AFMs with out-of-plane spin order, thus enabling optical detection of AFM domains
and expanding the scope of MOKE to few-layer AFMs.
acknowledgement: We thank Christine Kuntscher for providing optical conductivity and
reflectance data published in ref. 33, and Nicola Spaldin, Joel Moore and Bevin
Huang for useful discussions. V.S. and J.O. received support from the Gordon and
Betty Moore Foundation’s EPiQS Initiative through Grant GBMF4537 awarded to J.O.
at UC Berkeley. Experimental and theoretical work at LBNL and UC Berkeley was funded
by the Quantum Materials (KC2202) program under the U.S. Department of Energy, Office
of Science, Office of Basic Energy Sciences, Materials Sciences and Engineering
Division under Contract No. DE-AC02-05CH11231. Work at the University of Kansas
was supported by the U.S. Department of Energy, Office of Science, Basic Energy
Sciences, EPSCoR, and Materials Sciences and Engineering Division under Award No.
DE-SC0025319. Parts of device fabrication were performed in the KU Nanofabrication
Facility, which is supported by the National Institutes of Health NIGMS P30GM145499.
Work at ORNL was supported by the U. S. Department of Energy, Office of Science,
Basic Energy Sciences, Materials Sciences and Engineering Division. For the DFT
calculations we used resources provided by the Swedish National Infrastructure for
Computing (SNIC) at C3SE. We acknowledge support from the US National Science Foundation
(NSF) Grant Number 2201516 under the Accelnet program of Office of International
Science and Engineering (OISE). This publication is funded in part by a QuantEmX
grant from ICAM and the Gordon and Betty Moore Foundation through Grant GBMF9616
to S. K.
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author:
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full_name: Sunko, Veronika
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last_name: Sunko
orcid: 0000-0003-2724-3523
- first_name: Salman
full_name: Ahsanullah, Salman
last_name: Ahsanullah
- first_name: Vivek
full_name: Jain, Vivek
last_name: Jain
- first_name: Sophie
full_name: Weber, Sophie
last_name: Weber
- first_name: Sivaloganathan
full_name: Kumaran, Sivaloganathan
last_name: Kumaran
- first_name: Jiaqiang
full_name: Yan, Jiaqiang
last_name: Yan
- first_name: Joseph
full_name: Orenstein, Joseph
last_name: Orenstein
- first_name: Dmitry
full_name: Ovchinnikov, Dmitry
last_name: Ovchinnikov
citation:
ama: Sunko V, Ahsanullah S, Jain V, et al. Magneto-optical Kerr effect in an A-type
antiferromagnet. Nature Communications. 2026. doi:10.1038/s41467-026-72577-4
apa: Sunko, V., Ahsanullah, S., Jain, V., Weber, S., Kumaran, S., Yan, J., … Ovchinnikov,
D. (2026). Magneto-optical Kerr effect in an A-type antiferromagnet. Nature
Communications. Springer Nature. https://doi.org/10.1038/s41467-026-72577-4
chicago: Sunko, Veronika, Salman Ahsanullah, Vivek Jain, Sophie Weber, Sivaloganathan
Kumaran, Jiaqiang Yan, Joseph Orenstein, and Dmitry Ovchinnikov. “Magneto-Optical
Kerr Effect in an A-Type Antiferromagnet.” Nature Communications. Springer
Nature, 2026. https://doi.org/10.1038/s41467-026-72577-4.
ieee: V. Sunko et al., “Magneto-optical Kerr effect in an A-type antiferromagnet,”
Nature Communications. Springer Nature, 2026.
ista: Sunko V, Ahsanullah S, Jain V, Weber S, Kumaran S, Yan J, Orenstein J, Ovchinnikov
D. 2026. Magneto-optical Kerr effect in an A-type antiferromagnet. Nature Communications.
mla: Sunko, Veronika, et al. “Magneto-Optical Kerr Effect in an A-Type Antiferromagnet.”
Nature Communications, Springer Nature, 2026, doi:10.1038/s41467-026-72577-4.
short: V. Sunko, S. Ahsanullah, V. Jain, S. Weber, S. Kumaran, J. Yan, J. Orenstein,
D. Ovchinnikov, Nature Communications (2026).
corr_author: '1'
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date_published: 2026-05-12T00:00:00Z
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eissn:
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publication_status: epub_ahead
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quality_controlled: '1'
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title: Magneto-optical Kerr effect in an A-type antiferromagnet
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type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
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...
---
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acknowledgement: We thank all members of the Heisenberg, Henkes, and Hannezo groups
for their support. We are also grateful to the Imaging and Optics, Scientific Computing,
Life Science Support, and Cryo-Electron Microscopy facilities at ISTA for their
technical assistance and support. Numerical simulations were performed using the
computational resources from Lorentz Institute and the Academic Leiden Interdisciplinary
Cluster Environment (ALICE) provided by Leiden University, and from PMMH provided
by Sorbonne Université. S.N has received funding from European Union’s Horizon 2020
research and innovation programme (grant agreement No. 665385). This work was supported
by the Austrian Science Fund (FWF) under projects PAT5044023 and W1250 awarded to
C.-P.H.
article_processing_charge: No
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citation:
ama: Naik S. Data associated with Keratins coordinate tissue spreading . 2026. doi:10.15479/AT-ISTA-21137
apa: Naik, S. (2026). Data associated with Keratins coordinate tissue spreading
. Institute of Science and Technology Austria. https://doi.org/10.15479/AT-ISTA-21137
chicago: Naik, Suyash. “Data Associated with Keratins Coordinate Tissue Spreading
.” Institute of Science and Technology Austria, 2026. https://doi.org/10.15479/AT-ISTA-21137.
ieee: S. Naik, “Data associated with Keratins coordinate tissue spreading .” Institute
of Science and Technology Austria, 2026.
ista: Naik S. 2026. Data associated with Keratins coordinate tissue spreading ,
Institute of Science and Technology Austria, 10.15479/AT-ISTA-21137.
mla: Naik, Suyash. Data Associated with Keratins Coordinate Tissue Spreading
. Institute of Science and Technology Austria, 2026, doi:10.15479/AT-ISTA-21137.
short: S. Naik, (2026).
contributor:
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first_name: Yann-Edwin
last_name: Keta
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first_name: 'Silke '
last_name: Henkes
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first_name: Carl-Philipp J
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last_name: Heisenberg
orcid: 0000-0002-0912-4566
- contributor_type: supervisor
first_name: Edouard B
id: 3A9DB764-F248-11E8-B48F-1D18A9856A87
last_name: Hannezo
orcid: 0000-0001-6005-1561
corr_author: '1'
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date_updated: 2026-03-16T11:51:10Z
description: 'Python3 library written in C++20 to integrate vertex models. Please
read the readme at https://github.com/yketa/cells/blob/main/README.md for detailed
instructions for installation and usage of the code in this repository. '
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project:
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call_identifier: H2020
grant_number: '665385'
name: International IST Doctoral Program
- _id: 8f060199-16d5-11f0-9cad-f3253b266c46
grant_number: PAT 5044023
name: Keratins in epithelial tissue spreading
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call_identifier: FWF
grant_number: W1250-B20
name: Nano-Analytics of Cellular Systems
publisher: Institute of Science and Technology Austria
status: public
title: 'Data associated with Keratins coordinate tissue spreading '
tmp:
image: /images/cc_by_sa.png
legal_code_url: https://creativecommons.org/licenses/by-sa/4.0/legalcode
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short: CC BY-SA (4.0)
type: research_data
user_id: 68b8ca59-c5b3-11ee-8790-cd641c68093d
year: '2026'
...
---
OA_place: repository
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abstract:
- lang: eng
text: These files contain supplementary movies accompanying the PhD thesis “Geometry-driven
self-organization of migrating cells and chiral filaments” by Zuzana Dunajova
(2026). The videos provide additional visual material supporting the experiments
and results described in the thesis.
acknowledged_ssus:
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- first_name: Zuzana
full_name: Dunajova, Zuzana
id: 4B39F286-F248-11E8-B48F-1D18A9856A87
last_name: Dunajova
citation:
ama: Dunajova Z. Supplementary movies to PhD thesis “Geometry-driven self-organization
of migrating cells and chiral filaments.” 2026. doi:10.15479/AT-ISTA-21439
apa: Dunajova, Z. (2026). Supplementary movies to PhD thesis “Geometry-driven self-organization
of migrating cells and chiral filaments.” Institute of Science and Technology
Austria. https://doi.org/10.15479/AT-ISTA-21439
chicago: Dunajova, Zuzana. “Supplementary Movies to PhD Thesis ‘Geometry-Driven
Self-Organization of Migrating Cells and Chiral Filaments.’” Institute of Science
and Technology Austria, 2026. https://doi.org/10.15479/AT-ISTA-21439.
ieee: Z. Dunajova, “Supplementary movies to PhD thesis ‘Geometry-driven self-organization
of migrating cells and chiral filaments.’” Institute of Science and Technology
Austria, 2026.
ista: Dunajova Z. 2026. Supplementary movies to PhD thesis “Geometry-driven self-organization
of migrating cells and chiral filaments”, Institute of Science and Technology
Austria, 10.15479/AT-ISTA-21439.
mla: Dunajova, Zuzana. Supplementary Movies to PhD Thesis “Geometry-Driven Self-Organization
of Migrating Cells and Chiral Filaments.” Institute of Science and Technology
Austria, 2026, doi:10.15479/AT-ISTA-21439.
short: Z. Dunajova, (2026).
contributor:
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first_name: Saren
id: 4323B49C-F248-11E8-B48F-1D18A9856A87
last_name: Tasciyan
orcid: 0000-0003-1671-393X
- contributor_type: researcher
first_name: Philipp
id: 40136C2A-F248-11E8-B48F-1D18A9856A87
last_name: Radler
orcid: '0000-0001-9198-2182 '
corr_author: '1'
date_created: 2026-03-11T21:05:20Z
date_published: 2026-03-12T00:00:00Z
date_updated: 2026-06-10T09:41:12Z
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grant_number: '26360'
name: Motile active matter models of migrating cells and chiral filaments
publisher: Institute of Science and Technology Austria
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title: Supplementary movies to PhD thesis “Geometry-driven self-organization of migrating
cells and chiral filaments”
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orcid: 0000-0003-2724-3523
citation:
ama: Sunko V. Data underpinning “Magneto-optical Kerr effect in an A-type antiferromagnet.”
2026. doi:10.15479/AT-ISTA-21422
apa: Sunko, V. (2026). Data underpinning “Magneto-optical Kerr effect in an A-type
antiferromagnet.” Institute of Science and Technology Austria. https://doi.org/10.15479/AT-ISTA-21422
chicago: Sunko, Veronika. “Data Underpinning ‘Magneto-Optical Kerr Effect in an
A-Type Antiferromagnet.’” Institute of Science and Technology Austria, 2026. https://doi.org/10.15479/AT-ISTA-21422.
ieee: V. Sunko, “Data underpinning ‘Magneto-optical Kerr effect in an A-type antiferromagnet.’”
Institute of Science and Technology Austria, 2026.
ista: Sunko V. 2026. Data underpinning ‘Magneto-optical Kerr effect in an A-type
antiferromagnet’, Institute of Science and Technology Austria, 10.15479/AT-ISTA-21422.
mla: Sunko, Veronika. Data Underpinning “Magneto-Optical Kerr Effect in an A-Type
Antiferromagnet.” Institute of Science and Technology Austria, 2026, doi:10.15479/AT-ISTA-21422.
short: V. Sunko, (2026).
corr_author: '1'
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date_published: 2026-03-11T00:00:00Z
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title: Data underpinning "Magneto-optical Kerr effect in an A-type antiferromagnet"
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abstract:
- lang: eng
text: Quantifying cell morphology is central to understanding cellular regulation,
fate, and heterogeneity, yet conventional image-based analyses often struggle
with diverse or irregular shapes. We present a computational framework that uses
topological data analysis to characterise and compare single-cell morphologies
from fluorescence microscopy. Each cell is represented by its contour together
with the position of its nucleus, from which we construct a filtration based on
a radial distance function and derive a persistence diagram encoding the shape’s
topological evolution. The similarity between two cells is quantified using the
2-Wasserstein distance between their diagrams, yielding a shape distance we call
the PH distance. We apply this method to two representative experimental systems—primary
human mesenchymal stem cells (hMSCs) and HeLa cells—and show that PH distances
enable the detection of outliers in those systems, the identification of sub-populations,
and the quantification of shape heterogeneity. We benchmark PH against three established
contour-based distances (aspect ratio, Fourier descriptors, and elastic shape
analysis) and show that PH offers better separation between cell types and greater
robustness when clustering heterogeneous populations. Together, these results
demonstrate that persistent-homology-based signatures provide a principled and
sensitive approach for analysing cell morphology in settings where traditional
geometric or image-based descriptors are insufficient.
acknowledgement: We thank Stephan Huckemann, Katharine Turner, Benjamin Eltzner, Stephan
Tillmann, Fariza Rashid, Vanessa Robins, and Lamiae Azizi for many useful discussions
at various stages of this project. FR and PY gratefully acknowledge Matthias Weiss
(Experimental Physics I, University of Bayreuth, Germany) for granting access to
cell culture and laboratories, as well as funding consumables and the fruitful discussion
that contributed to this work. For open access purposes, the author has applied
a CC BY public copyright license to any author-accepted manuscript version arising
from this submission.
article_number: e1013890
article_processing_charge: Yes
article_type: original
author:
- first_name: Yossi
full_name: Bleile, Yossi
id: 920a7385-7995-11ef-9bfd-8c434cd8f3c2
last_name: Bleile
orcid: 0000-0002-4861-9174
- first_name: Pooja
full_name: Yadav, Pooja
last_name: Yadav
- first_name: Patrice
full_name: Koehl, Patrice
last_name: Koehl
- first_name: Florian
full_name: Rehfeldt, Florian
last_name: Rehfeldt
citation:
ama: 'Bokor Bleile Y, Yadav P, Koehl P, Rehfeldt F. Persistence diagrams as morphological
signatures of cells: A method to measure and compare cells within a population.
PLoS Computational Biology. 2026;22. doi:10.1371/journal.pcbi.1013890'
apa: 'Bokor Bleile, Y., Yadav, P., Koehl, P., & Rehfeldt, F. (2026). Persistence
diagrams as morphological signatures of cells: A method to measure and compare
cells within a population. PLoS Computational Biology. Public Library of
Science. https://doi.org/10.1371/journal.pcbi.1013890'
chicago: 'Bokor Bleile, Yossi, Pooja Yadav, Patrice Koehl, and Florian Rehfeldt.
“Persistence Diagrams as Morphological Signatures of Cells: A Method to Measure
and Compare Cells within a Population.” PLoS Computational Biology. Public
Library of Science, 2026. https://doi.org/10.1371/journal.pcbi.1013890.'
ieee: 'Y. Bokor Bleile, P. Yadav, P. Koehl, and F. Rehfeldt, “Persistence diagrams
as morphological signatures of cells: A method to measure and compare cells within
a population,” PLoS Computational Biology, vol. 22. Public Library of Science,
2026.'
ista: 'Bokor Bleile Y, Yadav P, Koehl P, Rehfeldt F. 2026. Persistence diagrams
as morphological signatures of cells: A method to measure and compare cells within
a population. PLoS Computational Biology. 22, e1013890.'
mla: 'Bokor Bleile, Yossi, et al. “Persistence Diagrams as Morphological Signatures
of Cells: A Method to Measure and Compare Cells within a Population.” PLoS
Computational Biology, vol. 22, e1013890, Public Library of Science, 2026,
doi:10.1371/journal.pcbi.1013890.'
short: Y. Bokor Bleile, P. Yadav, P. Koehl, F. Rehfeldt, PLoS Computational Biology
22 (2026).
corr_author: '1'
date_created: 2026-01-30T10:36:32Z
date_published: 2026-01-28T00:00:00Z
date_updated: 2026-06-11T11:51:13Z
day: '28'
ddc:
- '000'
department:
- _id: HeEd
doi: 10.1371/journal.pcbi.1013890
external_id:
pmid:
- '41604421'
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date_updated: 2026-02-10T07:13:06Z
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file_size: 8908746
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month: '01'
oa: 1
oa_version: Published Version
pmid: 1
publication: PLoS Computational Biology
publication_identifier:
issn:
- 1553-7358
publication_status: published
publisher: Public Library of Science
quality_controlled: '1'
related_material:
link:
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url: https://github.com/yossibokorbleile/correa
scopus_import: '1'
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title: 'Persistence diagrams as morphological signatures of cells: A method to measure
and compare cells within a population'
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...
---
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OA_type: hybrid
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abstract:
- lang: eng
text: "Abstract\r\n In this paper,
we consider a simple class of stratified spaces – 2-complexes. We present an algorithm
that learns the abstract structure of an embedded 2-complex from a point cloud
sampled from it. We use tools and inspiration from computational geometry, algebraic
topology, and topological data analysis and prove the correctness of the identified
abstract structure under assumptions on the embedding."
acknowledgement: The author would like to thank Kate Turner, Chris Williams, Jonathan
Spreer, Stephan Tillmann, Vanessa Robins, Vigleik Angeltveit, Martin Helmer, and
James Morgan for very helpful discussions; and thanks Sara Kališnik Hintz and Paul
Bendich for comments on an earlier version. Additonally, the author would like to
thank both reviewers for their very insightful and helpful comments, without which
the paper would be infinitely less coherent than it currently is. Open access funding
provided by Institute of Science and Technology (IST Austria). The work in this
paper was supported by an Australian Federal Government Grant, 2019-2022, Stratified
Space Learning.
article_number: '17'
article_processing_charge: Yes (via OA deal)
article_type: original
arxiv: 1
author:
- first_name: Yossi
full_name: Bleile, Yossi
id: 920a7385-7995-11ef-9bfd-8c434cd8f3c2
last_name: Bleile
orcid: 0000-0002-4861-9174
citation:
ama: 'Bokor Bleile Y. Towards stratified space learning: 2-complexes. La Matematica.
2026;5. doi:10.1007/s44007-025-00183-9'
apa: 'Bokor Bleile, Y. (2026). Towards stratified space learning: 2-complexes. La
Matematica. Springer Nature. https://doi.org/10.1007/s44007-025-00183-9'
chicago: 'Bokor Bleile, Yossi. “Towards Stratified Space Learning: 2-Complexes.”
La Matematica. Springer Nature, 2026. https://doi.org/10.1007/s44007-025-00183-9.'
ieee: 'Y. Bokor Bleile, “Towards stratified space learning: 2-complexes,” La
Matematica, vol. 5. Springer Nature, 2026.'
ista: 'Bokor Bleile Y. 2026. Towards stratified space learning: 2-complexes. La
Matematica. 5, 17.'
mla: 'Bokor Bleile, Yossi. “Towards Stratified Space Learning: 2-Complexes.” La
Matematica, vol. 5, 17, Springer Nature, 2026, doi:10.1007/s44007-025-00183-9.'
short: Y. Bokor Bleile, La Matematica 5 (2026).
corr_author: '1'
date_created: 2026-02-16T10:44:44Z
date_published: 2026-02-08T00:00:00Z
date_updated: 2026-06-11T11:51:14Z
day: '08'
ddc:
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department:
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doi: 10.1007/s44007-025-00183-9
external_id:
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publisher: Springer Nature
quality_controlled: '1'
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title: 'Towards stratified space learning: 2-complexes'
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OA_place: publisher
_id: '21957'
abstract:
- lang: eng
text: "This thesis investigates algorithmic certification and approximation methods
for degenerate semidefinite programs (SDPs) and the singular roots of polynomial
systems. In the first part, we present a hybrid symbolic-numeric algorithm for
certifying the feasibility of weakly feasible, degenerate SDPs. By reformulating
linear matrix inequalities (LMIs) into a structured polynomial system via facial
reduction and incidence varieties, we guarantee the existence of an isolated exact
solution. This algebraic reduction enables the certification of maximum-rank numerical
approximations using methods from algebraic geometry.\r\n\r\nIn the second part,
we address the severe ill-conditioning and loss of quadratic convergence that
plague standard path-tracking methods near isolated singular roots. To overcome
this, we propose tracking algorithms that achieve superlinear convergence without
the computational bloat characteristic of classical deflation techniques. By modeling
the solution path as a generalized fractional Puiseux series, our approach combines
an explicitly derived algebraic predictor with a localized hyperplane desingularization
phase during the corrector step. Furthermore, we introduce a continuous path-limit
method and an extension of the geometric sequence rule to directly extract exact
fractional exponents. This bypasses traditional heuristic trial-and-error methods
and explicitly accommodates sparse series expansions. Numerical experiments confirm
that our method significantly reduces the cumulative number of matrix inversions
while achieving high-accuracy root approximations, even for heavily degenerate
systems exhibiting higher coranks."
acknowledgement: 'Funding: Vienna Graduate School on Computational Optimization (FWF),
grant DOI: 10.55776/W1260.'
alternative_title:
- ISTA Thesis
article_processing_charge: No
author:
- first_name: Jeferson
full_name: Zapata, Jeferson
id: 00223538-AF8F-11E9-A4C7-F729E6697425
last_name: Zapata
citation:
ama: 'Zapata J. Overcoming degeneracy and singularity : Techniques for semidefinite
programs and homotopy continuation endgames. 2026. doi:10.15479/AT-ISTA-21957'
apa: 'Zapata, J. (2026). Overcoming degeneracy and singularity : Techniques for
semidefinite programs and homotopy continuation endgames. Institute of Science
and Technology Austria. https://doi.org/10.15479/AT-ISTA-21957'
chicago: 'Zapata, Jeferson. “Overcoming Degeneracy and Singularity : Techniques
for Semidefinite Programs and Homotopy Continuation Endgames.” Institute of Science
and Technology Austria, 2026. https://doi.org/10.15479/AT-ISTA-21957.'
ieee: 'J. Zapata, “Overcoming degeneracy and singularity : Techniques for semidefinite
programs and homotopy continuation endgames,” Institute of Science and Technology
Austria, 2026.'
ista: 'Zapata J. 2026. Overcoming degeneracy and singularity : Techniques for semidefinite
programs and homotopy continuation endgames. Institute of Science and Technology
Austria.'
mla: 'Zapata, Jeferson. Overcoming Degeneracy and Singularity : Techniques for
Semidefinite Programs and Homotopy Continuation Endgames. Institute of Science
and Technology Austria, 2026, doi:10.15479/AT-ISTA-21957.'
short: 'J. Zapata, Overcoming Degeneracy and Singularity : Techniques for Semidefinite
Programs and Homotopy Continuation Endgames, Institute of Science and Technology
Austria, 2026.'
corr_author: '1'
date_created: 2026-06-08T13:29:52Z
date_published: 2026-06-09T00:00:00Z
date_updated: 2026-06-12T10:37:00Z
day: '09'
ddc:
- '500'
degree_awarded: PhD
department:
- _id: GradSch
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language:
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month: '06'
oa: 1
oa_version: Published Version
page: '89'
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grant_number: W1260-N35
name: Vienna Graduate School on Computational Optimization
publication_identifier:
isbn:
- 978-3-99078-079-4
issn:
- 2663-337X
publication_status: published
publisher: Institute of Science and Technology Austria
related_material:
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relation: part_of_dissertation
status: public
status: public
supervisor:
- first_name: Vladimir
full_name: Kolmogorov, Vladimir
id: 3D50B0BA-F248-11E8-B48F-1D18A9856A87
last_name: Kolmogorov
title: 'Overcoming degeneracy and singularity : Techniques for semidefinite programs
and homotopy continuation endgames'
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legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: dissertation
user_id: 8b945eb4-e2f2-11eb-945a-df72226e66a9
year: '2026'
...
---
OA_place: publisher
_id: '21918'
acknowledged_ssus:
- _id: ScienComp
acknowledgement: "At different stages of my PhD, my work was supported by several
grants: the\r\nDOC fellowship of the Austrian Academy of Sciences (26293, awarded
to me),\r\nthe FWF-SFB grant (PT1032F06504 n. F65, awarded to Jan Maas), and the
ERC\r\ngrant (PR1032ERC01 n. 716117, awarded to Jan Maas). I also appreciate the
help\r\nfrom the Scientific Computing unit for their advice on the cluster usage."
alternative_title:
- ISTA Thesis
article_processing_charge: No
author:
- first_name: Kseniia
full_name: Khudiakova, Kseniia
id: 4E6DC800-AE37-11E9-AC72-31CAE5697425
last_name: Khudiakova
orcid: 0000-0002-6246-1465
citation:
ama: Khudiakova K. How epistasis and purifying selection shape genetic diversity.
2026. doi:10.15479/AT-ISTA-21918
apa: Khudiakova, K. (2026). How epistasis and purifying selection shape genetic
diversity. Institute of Science and Technology Austria. https://doi.org/10.15479/AT-ISTA-21918
chicago: Khudiakova, Kseniia. “How Epistasis and Purifying Selection Shape Genetic
Diversity.” Institute of Science and Technology Austria, 2026. https://doi.org/10.15479/AT-ISTA-21918.
ieee: K. Khudiakova, “How epistasis and purifying selection shape genetic diversity,”
Institute of Science and Technology Austria, 2026.
ista: Khudiakova K. 2026. How epistasis and purifying selection shape genetic diversity.
Institute of Science and Technology Austria.
mla: Khudiakova, Kseniia. How Epistasis and Purifying Selection Shape Genetic
Diversity. Institute of Science and Technology Austria, 2026, doi:10.15479/AT-ISTA-21918.
short: K. Khudiakova, How Epistasis and Purifying Selection Shape Genetic Diversity,
Institute of Science and Technology Austria, 2026.
corr_author: '1'
date_created: 2026-05-27T06:26:08Z
date_published: 2026-06-07T00:00:00Z
date_updated: 2026-06-12T12:43:35Z
day: '07'
ddc:
- '576'
degree_awarded: PhD
department:
- _id: GradSch
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- _id: JaMa
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date_updated: 2026-06-09T08:40:48Z
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file_name: 2026_Khudiakova_Ksenia_Thesis.pdf
file_size: 9387029
relation: main_file
file_date_updated: 2026-06-11T12:14:53Z
has_accepted_license: '1'
language:
- iso: eng
month: '06'
oa_version: Published Version
page: '89'
project:
- _id: 256E75B8-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '716117'
name: Optimal Transport and Stochastic Dynamics
- _id: 34d33d68-11ca-11ed-8bc3-ec13763c0ca8
grant_number: '26293'
name: The impact of deleterious mutations on small populations
- _id: fc31cba2-9c52-11eb-aca3-ff467d239cd2
grant_number: F6504
name: Taming Complexity in Partial Differential Systems
publication_identifier:
issn:
- 2663-337X
publication_status: published
publisher: Institute of Science and Technology Austria
related_material:
record:
- id: '11447'
relation: part_of_dissertation
status: public
- id: '12513'
relation: part_of_dissertation
status: deleted
- id: '21967'
relation: part_of_dissertation
status: public
- id: '21968'
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
- first_name: Jan
full_name: Maas, Jan
id: 4C5696CE-F248-11E8-B48F-1D18A9856A87
last_name: Maas
orcid: 0000-0002-0845-1338
title: How epistasis and purifying selection shape genetic diversity
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: '2026'
...
---
OA_place: repository
OA_type: green
_id: '21968'
abstract:
- lang: eng
text: Balancing selection, a form of selection that maintains genetic diversity,
is difficult to detect, and the importance of balancing selection for the maintenance
of genetic variation may be larger than often assumed. We model the possibility
that the diversity-promoting effects of balancing selection extend to other loci
that show sign epistasis with a locus under balancing selection. Rather than focusing
on overdominance, as was done in previous efforts, we explore the effects of negative
frequency dependence and show that this has important effects on the conditions
under which the diversity-promoting effect of epistasis can occur in diploids.
Our results show that not only recombination rate but also the dominance of sign
epistasis are key parameters that determine the maintenance of polymorphism beyond
the locus under direct balancing selection. We suggest that the effect we explore
may play a significant role, especially when balancing selection acts on major
effect loci.
acknowledgement: This work was funded by grants from the Swedish Research Council
(2023-03730 to G.A.) and the DOC fellowship from the Austrian Academy of Science
(26293 to K.K.).
article_processing_charge: No
author:
- first_name: Kseniia
full_name: Khudiakova, Kseniia
id: 4E6DC800-AE37-11E9-AC72-31CAE5697425
last_name: Khudiakova
orcid: 0000-0002-6246-1465
- first_name: Nicholas H
full_name: Barton, Nicholas H
id: 4880FE40-F248-11E8-B48F-1D18A9856A87
last_name: Barton
orcid: 0000-0002-8548-5240
- first_name: Goran
full_name: Arnqvist, Goran
last_name: Arnqvist
citation:
ama: Khudiakova K, Barton NH, Arnqvist G. Sign epistasis extends the effects of
balancing selection on genetic diversity. bioRxiv. doi:10.1101/2025.04.09.647826
apa: Khudiakova, K., Barton, N. H., & Arnqvist, G. (n.d.). Sign epistasis extends
the effects of balancing selection on genetic diversity. bioRxiv. https://doi.org/10.1101/2025.04.09.647826
chicago: Khudiakova, Kseniia, Nicholas H Barton, and Goran Arnqvist. “Sign Epistasis
Extends the Effects of Balancing Selection on Genetic Diversity.” BioRxiv,
n.d. https://doi.org/10.1101/2025.04.09.647826.
ieee: K. Khudiakova, N. H. Barton, and G. Arnqvist, “Sign epistasis extends the
effects of balancing selection on genetic diversity,” bioRxiv. .
ista: Khudiakova K, Barton NH, Arnqvist G. Sign epistasis extends the effects of
balancing selection on genetic diversity. bioRxiv, 10.1101/2025.04.09.647826.
mla: Khudiakova, Kseniia, et al. “Sign Epistasis Extends the Effects of Balancing
Selection on Genetic Diversity.” BioRxiv, doi:10.1101/2025.04.09.647826.
short: K. Khudiakova, N.H. Barton, G. Arnqvist, BioRxiv (n.d.).
corr_author: '1'
date_created: 2026-06-09T12:26:11Z
date_published: 2026-04-23T00:00:00Z
date_updated: 2026-06-12T12:43:34Z
day: '23'
department:
- _id: NiBa
- _id: JaMa
doi: 10.1101/2025.04.09.647826
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.1101/2025.04.09.647826
month: '04'
oa: 1
oa_version: Preprint
project:
- _id: 34d33d68-11ca-11ed-8bc3-ec13763c0ca8
grant_number: '26293'
name: The impact of deleterious mutations on small populations
publication: bioRxiv
publication_status: draft
related_material:
record:
- id: '21918'
relation: dissertation_contains
status: public
status: public
title: Sign epistasis extends the effects of balancing selection on genetic diversity
tmp:
image: /images/cc_by_nc.png
legal_code_url: https://creativecommons.org/licenses/by-nc/4.0/legalcode
name: Creative Commons Attribution-NonCommercial 4.0 International (CC BY-NC 4.0)
short: CC BY-NC (4.0)
type: preprint
user_id: 8b945eb4-e2f2-11eb-945a-df72226e66a9
year: '2026'
...
---
OA_place: repository
OA_type: green
_id: '21962'
abstract:
- lang: eng
text: The generation of faithful cell-type diversity and correct projection neuron
numbers is essential for cerebral cortex development. Corticogenesis is however
susceptible to genetic interference of critical signaling pathways, including
mutations in Mtor/Rptor that lead to microcephaly. How the loss of Rptor/mTORC1
function affects cortical developmental programs, at single cell level, is still
unknown. Here, we utilized Mosaic Analysis with Double Markers (MADM) technology
to probe Rptor gene function upon sparse single cell- or global tissue-wide ablation.
We found that tissue-wide effects drive the etiology of cortical microcephaly
upon loss of Rptor, rather than deficits in projection neuron genesis. Conversely,
Rptor function is cell-autonomously required for postnatal projection neuron survival
in a highly cell-type-specific manner. Collectively, our results suggest that
the fine balance of precise cell-type-specific cell-autonomous Rptor/mTORC1 function
in concert with non-cell-autonomous tissue-wide effects is essential for the development
of a properly-sized cerebral cortex with accurate projection neuron diversity.
acknowledged_ssus:
- _id: PreCl
- _id: LifeSc
- _id: MassSpec
- _id: Bio
acknowledgement: "We thank A. Heger (IST Austria Preclinical Facility), A. Sommer
(VBCF GmbH, NGS Unit), and A.\r\nNicolas (IST Austria Lab Support Facility / Mass
Spectrometry Facility) for technical support; K. Ferencak,\r\nI. Aykara, P. Hirschfeld,
E. Fisher, S. Laukoter, L. Andersen for initial experiments and/or assistance; and\r\nall
members of the Hippenmeyer lab for discussion. This research was supported by the
Scientific Service\r\nUnits (SSU) of IST Austria through resources provided by the
Imaging and Optics- (IOF), Lab Support-\r\n(LSF) and Preclinical Facilities (PCF).
R.B. received support from FWF Meitner-Programm (M 2416). This\r\nwork was also
supported by IST Austria institutional funds; the People Programme (Marie Curie
Actions)\r\nof the European Union’s Seventh Framework Programme (FP7/2007-2013)
under REA grant agreement\r\nNo 618444 to S.H., and the European Research Council
(ERC) under the European Union’s Horizon 2020\r\nresearch and innovation programme
(grant agreement No 725780 LinPro) to S.H."
article_processing_charge: No
author:
- first_name: Ana
full_name: Villalba Requena, Ana
id: 68cb85a0-39f7-11eb-9559-9aaab4f6a247
last_name: Villalba Requena
orcid: 0000-0002-5615-5277
- first_name: Robert J
full_name: Beattie, Robert J
id: 2E26DF60-F248-11E8-B48F-1D18A9856A87
last_name: Beattie
orcid: 0000-0002-8483-8753
- first_name: Florian
full_name: Pauler, Florian
id: 48EA0138-F248-11E8-B48F-1D18A9856A87
last_name: Pauler
orcid: 0000-0002-7462-0048
- first_name: Carmen
full_name: Streicher, Carmen
id: 36BCB99C-F248-11E8-B48F-1D18A9856A87
last_name: Streicher
- first_name: Osvaldo
full_name: Miranda, Osvaldo
id: 862A3C56-A8BF-11E9-B4FA-D9E3E5697425
last_name: Miranda
orcid: 0000-0001-6618-6889
- first_name: Thomas
full_name: Krausgruber, Thomas
last_name: Krausgruber
- first_name: Martin
full_name: Senekowitsch, Martin
last_name: Senekowitsch
- first_name: Matthias
full_name: Farlik, Matthias
last_name: Farlik
- first_name: Christoph
full_name: Bock, Christoph
last_name: Bock
- first_name: Thomas
full_name: Rülicke, Thomas
last_name: Rülicke
- first_name: Simon
full_name: Hippenmeyer, Simon
id: 37B36620-F248-11E8-B48F-1D18A9856A87
last_name: Hippenmeyer
orcid: 0000-0003-2279-1061
citation:
ama: Villalba Requena A, Beattie RJ, Pauler F, et al. Mtor/Rptor function globally
prevents cortical microcephaly and cell-autonomously promotes postnatal neuron
survival in cell type specific manner. bioRxiv. doi:10.64898/2026.05.01.722172
apa: Villalba Requena, A., Beattie, R. J., Pauler, F., Streicher, C., Miranda, O.,
Krausgruber, T., … Hippenmeyer, S. (n.d.). Mtor/Rptor function globally prevents
cortical microcephaly and cell-autonomously promotes postnatal neuron survival
in cell type specific manner. bioRxiv. https://doi.org/10.64898/2026.05.01.722172
chicago: Villalba Requena, Ana, Robert J Beattie, Florian Pauler, Carmen Streicher,
Osvaldo Miranda, Thomas Krausgruber, Martin Senekowitsch, et al. “Mtor/Rptor Function
Globally Prevents Cortical Microcephaly and Cell-Autonomously Promotes Postnatal
Neuron Survival in Cell Type Specific Manner.” BioRxiv, n.d. https://doi.org/10.64898/2026.05.01.722172.
ieee: A. Villalba Requena et al., “Mtor/Rptor function globally prevents
cortical microcephaly and cell-autonomously promotes postnatal neuron survival
in cell type specific manner,” bioRxiv. .
ista: Villalba Requena A, Beattie RJ, Pauler F, Streicher C, Miranda O, Krausgruber
T, Senekowitsch M, Farlik M, Bock C, Rülicke T, Hippenmeyer S. Mtor/Rptor function
globally prevents cortical microcephaly and cell-autonomously promotes postnatal
neuron survival in cell type specific manner. bioRxiv, 10.64898/2026.05.01.722172.
mla: Villalba Requena, Ana, et al. “Mtor/Rptor Function Globally Prevents Cortical
Microcephaly and Cell-Autonomously Promotes Postnatal Neuron Survival in Cell
Type Specific Manner.” BioRxiv, doi:10.64898/2026.05.01.722172.
short: A. Villalba Requena, R.J. Beattie, F. Pauler, C. Streicher, O. Miranda, T.
Krausgruber, M. Senekowitsch, M. Farlik, C. Bock, T. Rülicke, S. Hippenmeyer,
BioRxiv (n.d.).
date_created: 2026-06-09T08:08:18Z
date_published: 2026-05-05T00:00:00Z
date_updated: 2026-06-16T08:45:25Z
day: '05'
ddc:
- '570'
department:
- _id: SiHi
doi: 10.64898/2026.05.01.722172
ec_funded: 1
has_accepted_license: '1'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.64898/2026.05.01.722172
month: '05'
oa: 1
oa_version: Preprint
project:
- _id: 264E56E2-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: M02416
name: Molecular Mechanisms Regulating Gliogenesis in the Neocortex
- _id: 25D61E48-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '618444'
name: Molecular Mechanisms of Cerebral Cortex Development
- _id: 260018B0-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '725780'
name: Principles of Neural Stem Cell Lineage Progression in Cerebral Cortex Development
publication: bioRxiv
publication_status: submitted
status: public
title: Mtor/Rptor function globally prevents cortical microcephaly and cell-autonomously
promotes postnatal neuron survival in cell type specific manner
tmp:
image: /images/cc_by_nc.png
legal_code_url: https://creativecommons.org/licenses/by-nc/4.0/legalcode
name: Creative Commons Attribution-NonCommercial 4.0 International (CC BY-NC 4.0)
short: CC BY-NC (4.0)
type: preprint
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
year: '2026'
...
---
OA_place: repository
OA_type: green
_id: '21955'
abstract:
- lang: eng
text: 'AgRP neurons cause hunger, the drive to seek and consume food. Their activation
by fasting is key for survival and is thought to be triggered by feedback when
energy stores are low. However, we know that environmental cues can also regulate
AgRP neurons since cues that predict future food intake rapidly inhibit AgRP neurons,
but is the converse true: can the prediction of future fasting rapidly activate
AgRP neurons? Here, we show in mice that such rapid fasting activation of AgRP
neurons does occur. This rapid activation is driven by excitatory input from paraventricular
hypothalamic (PVH) neurons expressing Sim2, which are bidirectionally sensitive
to predictions of future energy state. Thus, cognitively processed contextual
information conveyed by PVHSim2 neurons strongly activates AgRP neurons. Lastly,
chronic silencing of PVHSim2 neurons causes persistent hypophagia. This PVHSim2-to-AgRP-neuron
circuit, by anticipating and preventing negative energy balance, provides an important
new dimension of hunger regulation.'
acknowledgement: "We thank all members of the B.B.L. laboratory for helpful discussions.
We\r\nthank the BADERC and BNORC transgenic cores (NIH P30DK057521 and\r\nP30DK046200)
for performing embryo injections to generate knockin mouse\r\nlines. We also thank
the BIDMC Energy Balance Core (supported by NIH\r\nS10OD028635 and the Boston Area
Diabetes Endocrinology Research Centers, P30DK135043), where Marissa Cortopassi
performed indirect calorimetry experiments and Alexander Banks assisted with data
analysis and interpretation. Confocal imaging was performed at BIDMC’s Confocal
Imaging\r\nCore. We thank Chen Wu for assistance in designing knockin mouse lines.\r\nThis
work was supported by the NIH (R01DK134427, R01DK096010, and\r\nR01DK075632 to B.B.L.).
Authors were supported by an EMBO Long-Term\r\nFellowship (770-2018, S.J.W.), a
T32 Postdoctoral Training Fellowship\r\n(5T32DK007516, E.D.L.), the Charles A. King
Trust Postdoctoral Research\r\nFellowship program (A.M.D.), and a K99 Career Development
Award\r\n(K99HL144923, J.M.R.)."
article_processing_charge: No
article_type: original
author:
- first_name: Samuel J.
full_name: Walker, Samuel J.
last_name: Walker
- first_name: Elijah D.
full_name: Lowenstein, Elijah D.
last_name: Lowenstein
- first_name: Amelia May Barnett
full_name: Douglass, Amelia May Barnett
id: de5f6fda-80fb-11ef-996f-a8c4ecd8e289
last_name: Douglass
orcid: 0000-0001-5398-6473
- first_name: Callum M.P.
full_name: Thomas, Callum M.P.
last_name: Thomas
- first_name: Joseph C.
full_name: Madara, Joseph C.
last_name: Madara
- first_name: Hakan
full_name: Kucukdereli, Hakan
last_name: Kucukdereli
- first_name: Eunice A.
full_name: Barbosa-Meillon, Eunice A.
last_name: Barbosa-Meillon
- first_name: Jenkang
full_name: Tao, Jenkang
last_name: Tao
- first_name: Jon M.
full_name: Resch, Jon M.
last_name: Resch
- first_name: Bradford B.
full_name: Lowell, Bradford B.
last_name: Lowell
citation:
ama: Walker SJ, Lowenstein ED, Douglass AM, et al. A hypothalamic circuit for anticipating
future changes in energy balance. Neuron. doi:10.1016/j.neuron.2026.05.010
apa: Walker, S. J., Lowenstein, E. D., Douglass, A. M., Thomas, C. M. P., Madara,
J. C., Kucukdereli, H., … Lowell, B. B. (n.d.). A hypothalamic circuit for anticipating
future changes in energy balance. Neuron. Elsevier. https://doi.org/10.1016/j.neuron.2026.05.010
chicago: Walker, Samuel J., Elijah D. Lowenstein, Amelia M. Douglass, Callum M.P.
Thomas, Joseph C. Madara, Hakan Kucukdereli, Eunice A. Barbosa-Meillon, Jenkang
Tao, Jon M. Resch, and Bradford B. Lowell. “A Hypothalamic Circuit for Anticipating
Future Changes in Energy Balance.” Neuron. Elsevier, n.d. https://doi.org/10.1016/j.neuron.2026.05.010.
ieee: S. J. Walker et al., “A hypothalamic circuit for anticipating future
changes in energy balance,” Neuron. Elsevier.
ista: Walker SJ, Lowenstein ED, Douglass AM, Thomas CMP, Madara JC, Kucukdereli
H, Barbosa-Meillon EA, Tao J, Resch JM, Lowell BB. A hypothalamic circuit for
anticipating future changes in energy balance. Neuron.
mla: Walker, Samuel J., et al. “A Hypothalamic Circuit for Anticipating Future Changes
in Energy Balance.” Neuron, Elsevier, doi:10.1016/j.neuron.2026.05.010.
short: S.J. Walker, E.D. Lowenstein, A.M. Douglass, C.M.P. Thomas, J.C. Madara,
H. Kucukdereli, E.A. Barbosa-Meillon, J. Tao, J.M. Resch, B.B. Lowell, Neuron
(n.d.).
date_created: 2026-06-08T09:24:25Z
date_published: 2026-06-03T00:00:00Z
date_updated: 2026-06-16T08:35:11Z
day: '03'
department:
- _id: AmDo
doi: 10.1016/j.neuron.2026.05.010
external_id:
pmid:
- '42235510'
keyword:
- hunger
- hypothalamus
- AGRP neurons
- neuroscience
- metabolism
- homeostasis
- feeding
- food intake
- energy balance
- appetite
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.1101/2025.09.27.678865
month: '06'
oa: 1
oa_version: Preprint
pmid: 1
publication: Neuron
publication_identifier:
eissn:
- ' 1097-4199'
issn:
- 0896-6273
publication_status: inpress
publisher: Elsevier
quality_controlled: '1'
scopus_import: '1'
status: public
title: A hypothalamic circuit for anticipating future changes in energy balance
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
year: '2026'
...
---
OA_place: repository
_id: '21960'
abstract:
- lang: eng
text: "Solitons - localized wave packets that travel without spreading - play a
central role in understanding transport and properties of nonlinear systems. In
quantum many-body systems, however, such robust excitations are typically destroyed
by thermalization. Here, we theoretically demonstrate the existence of solitonic
excitations in high-energy states of Rydberg atom chains in the regime of strong
nearest-neighbor Rydberg blockade. \r\nThese localized wave packets propagate
directionally atop a special class of reviving initial states related to quantum
many-body scars and are capable of carrying energy. Exhibiting long coherence
times, these states constitute a form of non-ergodic quantum dynamics and can
be efficiently implemented on Rydberg atom simulators. In this work, in addition
to a phenomenological description of solitons, we identify their counterpart in
a classical nonlinear dynamical system, demonstrate their potential use in quantum
information transfer, and conjecture their relevance for anomalous energy transport
reported in numerical studies of Rydberg atom arrays."
article_processing_charge: No
author:
- first_name: Aron
full_name: Kerschbaumer, Aron
id: ade85a9c-3200-11ee-973b-91c1eb240410
last_name: Kerschbaumer
orcid: 0009-0002-2370-8661
citation:
ama: 'Kerschbaumer A. Research Data: “Quasi-solitons in Rydberg atom chains.” 2026.
doi:10.15479/AT-ISTA-21960'
apa: 'Kerschbaumer, A. (2026). Research Data: “Quasi-solitons in Rydberg atom chains.”
Institute of Science and Technology Austria. https://doi.org/10.15479/AT-ISTA-21960'
chicago: 'Kerschbaumer, Aron. “Research Data: ‘Quasi-Solitons in Rydberg Atom Chains.’”
Institute of Science and Technology Austria, 2026. https://doi.org/10.15479/AT-ISTA-21960.'
ieee: 'A. Kerschbaumer, “Research Data: ‘Quasi-solitons in Rydberg atom chains.’”
Institute of Science and Technology Austria, 2026.'
ista: 'Kerschbaumer A. 2026. Research Data: ‘Quasi-solitons in Rydberg atom chains’,
Institute of Science and Technology Austria, 10.15479/AT-ISTA-21960.'
mla: 'Kerschbaumer, Aron. Research Data: “Quasi-Solitons in Rydberg Atom Chains.”
Institute of Science and Technology Austria, 2026, doi:10.15479/AT-ISTA-21960.'
short: A. Kerschbaumer, (2026).
contributor:
- contributor_type: contact_person
first_name: Aron
id: ade85a9c-3200-11ee-973b-91c1eb240410
last_name: Kerschbaumer
orcid: 0009-0002-2370-8661
- contributor_type: supervisor
first_name: Maksym
id: 47809E7E-F248-11E8-B48F-1D18A9856A87
last_name: Serbyn
orcid: 0000-0002-2399-5827
- contributor_type: researcher
first_name: Jean-Yves Marc
id: 6c292945-a610-11ed-9eec-c3be1ad62a80
last_name: Desaules
orcid: 0000-0002-3749-6375
- contributor_type: researcher
first_name: Marko
last_name: Ljubotina
corr_author: '1'
date_created: 2026-06-09T07:17:50Z
date_published: 2026-06-16T00:00:00Z
date_updated: 2026-06-16T08:00:38Z
day: '16'
department:
- _id: GradSch
- _id: MaSe
doi: 10.15479/AT-ISTA-21960
ec_funded: 1
file:
- access_level: open_access
checksum: 133269a105e996c6c44fdd56128259c7
content_type: text/plain
creator: akerschb
date_created: 2026-06-15T22:01:57Z
date_updated: 2026-06-15T22:01:57Z
file_id: '22010'
file_name: README.txt
file_size: 1940
relation: main_file
success: 1
- access_level: open_access
checksum: 759f9649c3919f4c4ad37a1d104ea32a
content_type: application/zip
creator: akerschb
date_created: 2026-06-15T22:02:07Z
date_updated: 2026-06-15T22:02:07Z
file_id: '22011'
file_name: Soliton_Data.zip
file_size: 13259747
relation: main_file
success: 1
file_date_updated: 2026-06-15T22:02:07Z
has_accepted_license: '1'
month: '06'
oa: 1
oa_version: Published Version
project:
- _id: fc2ed2f7-9c52-11eb-aca3-c01059dda49c
call_identifier: H2020
grant_number: '101034413'
name: 'IST-BRIDGE: International postdoctoral program'
publisher: Institute of Science and Technology Austria
status: public
title: 'Research Data: "Quasi-solitons in Rydberg atom chains"'
tmp:
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year: '2026'
...
---
_id: '21971'
abstract:
- lang: eng
text: "A Rust library for analyzing dendritic structures using quadric matrices.
This project provides efficient tools for representing dendritic trees, computing
quadric error metrics, and visualizing eigenvalue distributions on hexagonal plots.\r\n\r\nThis
library implements quadric-based geometric analysis of dendritic structures, commonly
found in neuroscience applications. Key features include:\r\n\r\nTree data structures:
Hierarchical vertex and edge representations for dendritic trees\r\nQuadric matrices:
Computation of quadric error metrics for edges and vertices\r\nVisualisation:
Hexagonal plot generation using NormPolar transformations\r\nInteractive tools:
Desktop application with plotting capabilities"
author:
- first_name: Yossi
full_name: Bleile, Yossi
id: 920a7385-7995-11ef-9bfd-8c434cd8f3c2
last_name: Bleile
orcid: 0000-0002-4861-9174
- first_name: Emanuele
full_name: Cortinovis, Emanuele
last_name: Cortinovis
citation:
ama: Bokor Bleile Y, Cortinovis E. Quadrix. 2026. doi:10.15479/AT-ISTA-21971
apa: Bokor Bleile, Y., & Cortinovis, E. (2026). Quadrix. Institute of Science
and Technology Austria. https://doi.org/10.15479/AT-ISTA-21971
chicago: Bokor Bleile, Yossi, and Emanuele Cortinovis. “Quadrix.” Institute of Science
and Technology Austria, 2026. https://doi.org/10.15479/AT-ISTA-21971.
ieee: Y. Bokor Bleile and E. Cortinovis, “Quadrix.” Institute of Science and Technology
Austria, 2026.
ista: Bokor Bleile Y, Cortinovis E. 2026. Quadrix, Institute of Science and Technology
Austria, 10.15479/AT-ISTA-21971.
mla: Bokor Bleile, Yossi, and Emanuele Cortinovis. Quadrix. Institute of
Science and Technology Austria, 2026, doi:10.15479/AT-ISTA-21971.
short: Y. Bokor Bleile, E. Cortinovis, (2026).
corr_author: '1'
date_created: 2026-06-09T19:19:13Z
date_published: 2026-06-15T00:00:00Z
date_updated: 2026-06-15T23:00:03Z
day: '15'
department:
- _id: HeEd
doi: 10.15479/AT-ISTA-21971
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has_accepted_license: '1'
keyword:
- quadratics
- mathematics
- dendrites
- geometry
- topology
license: https://opensource.org/licenses/MIT
month: '06'
oa: 1
project:
- _id: 9106a876-16d5-11f0-9cad-bbf11c9952f9
grant_number: ESP 9584724
name: Quantitative Unbiased Shape Analysis with Geometry & Topology
publisher: Institute of Science and Technology Austria
status: public
title: Quadrix
tmp:
legal_code_url: https://opensource.org/licenses/MIT
name: The MIT License
short: MIT
type: software
user_id: 68b8ca59-c5b3-11ee-8790-cd641c68093d
year: '2026'
...