---
_id: '14770'
abstract:
- lang: eng
text: We developed LIONESS, a technology that leverages improvements to optical
super-resolution microscopy and prior information on sample structure via machine
learning to overcome the limitations (in 3D-resolution, signal-to-noise ratio
and light exposure) of optical microscopy of living biological specimens. LIONESS
enables dense reconstruction of living brain tissue and morphodynamics visualization
at the nanoscale.
article_processing_charge: No
article_type: letter_note
author:
- first_name: Johann G
full_name: Danzl, Johann G
id: 42EFD3B6-F248-11E8-B48F-1D18A9856A87
last_name: Danzl
orcid: 0000-0001-8559-3973
- first_name: Philipp
full_name: Velicky, Philipp
id: 39BDC62C-F248-11E8-B48F-1D18A9856A87
last_name: Velicky
orcid: 0000-0002-2340-7431
citation:
ama: Danzl JG, Velicky P. LIONESS enables 4D nanoscale reconstruction of living
brain tissue. Nature Methods. 2023;20(8):1141-1142. doi:10.1038/s41592-023-01937-5
apa: Danzl, J. G., & Velicky, P. (2023). LIONESS enables 4D nanoscale reconstruction
of living brain tissue. Nature Methods. Springer Nature. https://doi.org/10.1038/s41592-023-01937-5
chicago: Danzl, Johann G, and Philipp Velicky. “LIONESS Enables 4D Nanoscale Reconstruction
of Living Brain Tissue.” Nature Methods. Springer Nature, 2023. https://doi.org/10.1038/s41592-023-01937-5.
ieee: J. G. Danzl and P. Velicky, “LIONESS enables 4D nanoscale reconstruction of
living brain tissue,” Nature Methods, vol. 20, no. 8. Springer Nature,
pp. 1141–1142, 2023.
ista: Danzl JG, Velicky P. 2023. LIONESS enables 4D nanoscale reconstruction of
living brain tissue. Nature Methods. 20(8), 1141–1142.
mla: Danzl, Johann G., and Philipp Velicky. “LIONESS Enables 4D Nanoscale Reconstruction
of Living Brain Tissue.” Nature Methods, vol. 20, no. 8, Springer Nature,
2023, pp. 1141–42, doi:10.1038/s41592-023-01937-5.
short: J.G. Danzl, P. Velicky, Nature Methods 20 (2023) 1141–1142.
corr_author: '1'
date_created: 2024-01-10T08:07:15Z
date_published: 2023-08-01T00:00:00Z
date_updated: 2026-04-14T08:34:34Z
day: '01'
department:
- _id: JoDa
doi: 10.1038/s41592-023-01937-5
external_id:
isi:
- '001025621500002'
intvolume: ' 20'
isi: 1
issue: '8'
keyword:
- Cell Biology
- Molecular Biology
- Biochemistry
- Biotechnology
language:
- iso: eng
month: '08'
oa_version: None
page: 1141-1142
publication: Nature Methods
publication_identifier:
eissn:
- 1548-7105
issn:
- 1548-7091
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
related_material:
record:
- id: '13267'
relation: extended_version
status: public
scopus_import: '1'
status: public
title: LIONESS enables 4D nanoscale reconstruction of living brain tissue
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 20
year: '2023'
...
---
OA_place: publisher
_id: '13107'
abstract:
- lang: eng
text: "Within the human body, the brain exhibits the highest rate of energy consumption
amongst all organs, with the majority of generated ATP being utilized to sustain
neuronal activity. Therefore, the metabolism of the mature cerebral cortex is
geared towards preserving metabolic homeostasis whilst generating significant
amounts of energy. This requires a precise interplay between diverse metabolic
pathways, spanning from a tissue-wide scale to the level of individual neurons.
Disturbances to this delicate metabolic equilibrium, such as those resulting from
maternal malnutrition\r\nor mutations affecting metabolic enzymes, often result
in neuropathological variants of neurodevelopment. For instance, mutations in
SLC7A5, a transporter of metabolically essential large neutral amino acids (LNAAs),
have been associated with autism and microcephaly. However, despite recent progress
in the field, the extent of metabolic restructuring that occurs within the developing
brain and the corresponding alterations in nutrient demands during various critical
periods remain largely unknown. To investigate this, we performed metabolomic
profiling of the murine cerebral cortex to characterize the metabolic state of
the forebrain at different developmental stages. We found that the developing
cortex undergoes substantial metabolic reprogramming, with specific sets of metabolites
displaying stage-specific changes. According to our observations, we determined
a distinct temporal period in postnatal development during which the cortex displays
heightened reliance on LNAAs. Hence, using a conditional knock-out mouse model,
we deleted Slc7a5 in neural cells, allowing us to monitor the impact of a perturbed
neuronal metabolic state across multiple developmental stages of corticogenesis.
We found that manipulating the levels of essential LNAAs in cortical neurons in
vivo affects one particular perinatal developmental period critical for cortical
network refinement. Abnormally low intracellular LNAA levels result in cell-autonomous
alterations in neuronal lipid metabolism, excitability, and survival during this
particular time window. Although most of the effects of Slc7a5 deletion on neuronal
physiology are transient, derailment of these processes during this brief but
crucial window leads to long-term circuit dysfunction in mice. In conclusion,
out data indicate that the cerebral cortex undergoes significant metabolic reorganization
during development. This process involves the intricate integration of multiple
metabolic pathways to ensure optimal neuronal function throughout different developmental
stages. Our findings offer a paradigm for understanding how neurons synchronize
the expression of nutrient-related genes with their activity to allow proper brain
maturation. Further, our results demonstrate that disruptions in these precisely
calibrated metabolic processes during critical periods of brain development may
result in neuropathological outcomes in mice and in humans."
acknowledged_ssus:
- _id: PreCl
- _id: Bio
- _id: EM-Fac
alternative_title:
- ISTA Thesis
article_processing_charge: No
author:
- first_name: Lisa
full_name: Knaus, Lisa
id: 3B2ABCF4-F248-11E8-B48F-1D18A9856A87
last_name: Knaus
citation:
ama: 'Knaus L. The metabolism of the developing brain : How large neutral amino
acids modulate perinatal neuronal excitability and survival. 2023. doi:10.15479/at:ista:13107'
apa: 'Knaus, L. (2023). The metabolism of the developing brain : How large neutral
amino acids modulate perinatal neuronal excitability and survival. Institute
of Science and Technology Austria. https://doi.org/10.15479/at:ista:13107'
chicago: 'Knaus, Lisa. “The Metabolism of the Developing Brain : How Large Neutral
Amino Acids Modulate Perinatal Neuronal Excitability and Survival.” Institute
of Science and Technology Austria, 2023. https://doi.org/10.15479/at:ista:13107.'
ieee: 'L. Knaus, “The metabolism of the developing brain : How large neutral amino
acids modulate perinatal neuronal excitability and survival,” Institute of Science
and Technology Austria, 2023.'
ista: 'Knaus L. 2023. The metabolism of the developing brain : How large neutral
amino acids modulate perinatal neuronal excitability and survival. Institute of
Science and Technology Austria.'
mla: 'Knaus, Lisa. The Metabolism of the Developing Brain : How Large Neutral
Amino Acids Modulate Perinatal Neuronal Excitability and Survival. Institute
of Science and Technology Austria, 2023, doi:10.15479/at:ista:13107.'
short: 'L. Knaus, The Metabolism of the Developing Brain : How Large Neutral Amino
Acids Modulate Perinatal Neuronal Excitability and Survival, Institute of Science
and Technology Austria, 2023.'
corr_author: '1'
date_created: 2023-06-01T09:05:24Z
date_published: 2023-05-31T00:00:00Z
date_updated: 2026-04-14T08:34:36Z
day: '31'
ddc:
- '570'
degree_awarded: PhD
department:
- _id: GradSch
- _id: GaNo
doi: 10.15479/at:ista:13107
ec_funded: 1
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language:
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month: '05'
oa: 1
oa_version: Published Version
page: '147'
project:
- _id: 25444568-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '715508'
name: Probing the Reversibility of Autism Spectrum Disorders by Employing in vivo
and in vitro Models
- _id: 2548AE96-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: W1232
name: Molecular Drug Targets
publication_identifier:
issn:
- 2663-337X
publication_status: published
publisher: Institute of Science and Technology Austria
related_material:
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status: public
status: public
supervisor:
- first_name: Gaia
full_name: Novarino, Gaia
id: 3E57A680-F248-11E8-B48F-1D18A9856A87
last_name: Novarino
orcid: 0000-0002-7673-7178
title: 'The metabolism of the developing brain : How large neutral amino acids modulate
perinatal neuronal excitability and survival'
type: dissertation
user_id: ba8df636-2132-11f1-aed0-ed93e2281fdd
year: '2023'
...
---
_id: '12802'
abstract:
- lang: eng
text: Little is known about the critical metabolic changes that neural cells have
to undergo during development and how temporary shifts in this program can influence
brain circuitries and behavior. Inspired by the discovery that mutations in SLC7A5,
a transporter of metabolically essential large neutral amino acids (LNAAs), lead
to autism, we employed metabolomic profiling to study the metabolic states of
the cerebral cortex across different developmental stages. We found that the forebrain
undergoes significant metabolic remodeling throughout development, with certain
groups of metabolites showing stage-specific changes, but what are the consequences
of perturbing this metabolic program? By manipulating Slc7a5 expression in neural
cells, we found that the metabolism of LNAAs and lipids are interconnected in
the cortex. Deletion of Slc7a5 in neurons affects the postnatal metabolic state,
leading to a shift in lipid metabolism. Additionally, it causes stage- and cell-type-specific
alterations in neuronal activity patterns, resulting in a long-term circuit dysfunction.
acknowledged_ssus:
- _id: PreCl
- _id: EM-Fac
- _id: Bio
- _id: LifeSc
acknowledgement: We thank A. Freeman and V. Voronin for technical assistance, S. Deixler,
A. Stichelberger, M. Schunn, and the Preclinical Facility for managing our animal
colony. We thank L. Andersen and J. Sonntag, who were involved in generating the
MADM lines. We thank the ISTA LSF Mass Spectrometry Core Facility for assistance
with the proteomic analysis, as well as the ISTA electron microscopy and Imaging
and Optics facility for technical support. Metabolomics LC-MS/MS analysis was performed
by the Metabolomics Facility at Vienna BioCenter Core Facilities (VBCF). We acknowledge
the support of the EMBL Metabolomics Core Facility (MCF) for lipidomics and intracellular
metabolomics mass spectrometry data acquisition and analysis. RNA sequencing was
performed by the Next Generation Sequencing Facility at VBCF. Schematics were generated
using Biorender.com. This work was supported by the Austrian Science Fund (FWF,
DK W1232-B24) and by the European Union’s Horizon 2020 research and innovation program
(ERC) grant 725780 (LinPro) to S.H. and 715508 (REVERSEAUTISM) to G.N.
article_processing_charge: Yes (via OA deal)
article_type: original
author:
- first_name: Lisa
full_name: Knaus, Lisa
id: 3B2ABCF4-F248-11E8-B48F-1D18A9856A87
last_name: Knaus
- first_name: Bernadette
full_name: Basilico, Bernadette
id: 36035796-5ACA-11E9-A75E-7AF2E5697425
last_name: Basilico
orcid: 0000-0003-1843-3173
- first_name: Daniel
full_name: Malzl, Daniel
last_name: Malzl
- first_name: Maria
full_name: Gerykova Bujalkova, Maria
last_name: Gerykova Bujalkova
- first_name: Mateja
full_name: Smogavec, Mateja
last_name: Smogavec
- first_name: Lena A.
full_name: Schwarz, Lena A.
last_name: Schwarz
- first_name: Sarah
full_name: Gorkiewicz, Sarah
id: f141a35d-15a9-11ec-9fb2-fef6becc7b6f
last_name: Gorkiewicz
- first_name: Nicole
full_name: Amberg, Nicole
id: 4CD6AAC6-F248-11E8-B48F-1D18A9856A87
last_name: Amberg
orcid: 0000-0002-3183-8207
- first_name: Florian
full_name: Pauler, Florian
id: 48EA0138-F248-11E8-B48F-1D18A9856A87
last_name: Pauler
orcid: 0000-0002-7462-0048
- first_name: Christian
full_name: Knittl-Frank, Christian
last_name: Knittl-Frank
- first_name: Marianna
full_name: Tassinari, Marianna
id: 7af593f1-d44a-11ed-bf94-a3646a6bb35e
last_name: Tassinari
- first_name: Nuno
full_name: Maulide, Nuno
last_name: Maulide
- first_name: Thomas
full_name: Rülicke, Thomas
last_name: Rülicke
- first_name: Jörg
full_name: Menche, Jörg
last_name: Menche
- first_name: Simon
full_name: Hippenmeyer, Simon
id: 37B36620-F248-11E8-B48F-1D18A9856A87
last_name: Hippenmeyer
orcid: 0000-0003-2279-1061
- first_name: Gaia
full_name: Novarino, Gaia
id: 3E57A680-F248-11E8-B48F-1D18A9856A87
last_name: Novarino
orcid: 0000-0002-7673-7178
citation:
ama: Knaus L, Basilico B, Malzl D, et al. Large neutral amino acid levels tune perinatal
neuronal excitability and survival. Cell. 2023;186(9):1950-1967.e25. doi:10.1016/j.cell.2023.02.037
apa: Knaus, L., Basilico, B., Malzl, D., Gerykova Bujalkova, M., Smogavec, M., Schwarz,
L. A., … Novarino, G. (2023). Large neutral amino acid levels tune perinatal neuronal
excitability and survival. Cell. Elsevier. https://doi.org/10.1016/j.cell.2023.02.037
chicago: Knaus, Lisa, Bernadette Basilico, Daniel Malzl, Maria Gerykova Bujalkova,
Mateja Smogavec, Lena A. Schwarz, Sarah Gorkiewicz, et al. “Large Neutral Amino
Acid Levels Tune Perinatal Neuronal Excitability and Survival.” Cell. Elsevier,
2023. https://doi.org/10.1016/j.cell.2023.02.037.
ieee: L. Knaus et al., “Large neutral amino acid levels tune perinatal neuronal
excitability and survival,” Cell, vol. 186, no. 9. Elsevier, p. 1950–1967.e25,
2023.
ista: Knaus L, Basilico B, Malzl D, Gerykova Bujalkova M, Smogavec M, Schwarz LA,
Gorkiewicz S, Amberg N, Pauler F, Knittl-Frank C, Tassinari M, Maulide N, Rülicke
T, Menche J, Hippenmeyer S, Novarino G. 2023. Large neutral amino acid levels
tune perinatal neuronal excitability and survival. Cell. 186(9), 1950–1967.e25.
mla: Knaus, Lisa, et al. “Large Neutral Amino Acid Levels Tune Perinatal Neuronal
Excitability and Survival.” Cell, vol. 186, no. 9, Elsevier, 2023, p. 1950–1967.e25,
doi:10.1016/j.cell.2023.02.037.
short: L. Knaus, B. Basilico, D. Malzl, M. Gerykova Bujalkova, M. Smogavec, L.A.
Schwarz, S. Gorkiewicz, N. Amberg, F. Pauler, C. Knittl-Frank, M. Tassinari, N.
Maulide, T. Rülicke, J. Menche, S. Hippenmeyer, G. Novarino, Cell 186 (2023) 1950–1967.e25.
corr_author: '1'
date_created: 2023-04-05T08:15:40Z
date_published: 2023-04-27T00:00:00Z
date_updated: 2026-04-14T08:34:36Z
day: '27'
ddc:
- '570'
department:
- _id: SiHi
- _id: GaNo
doi: 10.1016/j.cell.2023.02.037
ec_funded: 1
external_id:
isi:
- '000991468700001'
pmid:
- '36996814'
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creator: dernst
date_created: 2023-05-02T09:26:21Z
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file_date_updated: 2023-05-02T09:26:21Z
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intvolume: ' 186'
isi: 1
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keyword:
- General Biochemistry
- Genetics and Molecular Biology
language:
- iso: eng
license: https://creativecommons.org/licenses/by/4.0/
month: '04'
oa: 1
oa_version: Published Version
page: 1950-1967.e25
pmid: 1
project:
- _id: 2548AE96-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: W1232
name: Molecular Drug Targets
- _id: 260018B0-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '725780'
name: Principles of Neural Stem Cell Lineage Progression in Cerebral Cortex Development
- _id: 25444568-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '715508'
name: Probing the Reversibility of Autism Spectrum Disorders by Employing in vivo
and in vitro Models
publication: Cell
publication_identifier:
issn:
- 0092-8674
publication_status: published
publisher: Elsevier
quality_controlled: '1'
related_material:
link:
- description: News on ISTA Website
relation: press_release
url: https://ista.ac.at/en/news/feed-them-or-lose-them/
record:
- id: '19557'
relation: dissertation_contains
status: public
- id: '13107'
relation: dissertation_contains
status: public
scopus_import: '1'
status: public
title: Large neutral amino acid levels tune perinatal neuronal excitability and survival
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: 186
year: '2023'
...
---
_id: '14484'
abstract:
- lang: eng
text: Intercellular signaling molecules, known as morphogens, act at a long range
in developing tissues to provide spatial information and control properties such
as cell fate and tissue growth. The production, transport, and removal of morphogens
shape their concentration profiles in time and space. Downstream signaling cascades
and gene regulatory networks within cells then convert the spatiotemporal morphogen
profiles into distinct cellular responses. Current challenges are to understand
the diverse molecular and cellular mechanisms underlying morphogen gradient formation,
as well as the logic of downstream regulatory circuits involved in morphogen interpretation.
This knowledge, combining experimental and theoretical results, is essential to
understand emerging properties of morphogen-controlled systems, such as robustness
and scaling.
acknowledgement: We are grateful to Zena Hadjivasiliou for comments on this article.
A.K. is supported by grants from the European Research Council under the European
Union (EU) Horizon 2020 research and innovation program (680037) and Horizon Europe
(101044579), and the Austrian Science Fund (F78) (Stem Cell Modulation). J.B. is
supported by the Francis Crick Institute, which receives its core funding from Cancer
Research UK (CC001051), the UK Medical Research Council (CC001051), and the Wellcome
Trust (CC001051), and by a grant from the European Research Council under the EU
Horizon 2020 research and innovation program (742138).
article_processing_charge: Yes (in subscription journal)
article_type: review
author:
- first_name: Anna
full_name: Kicheva, Anna
id: 3959A2A0-F248-11E8-B48F-1D18A9856A87
last_name: Kicheva
orcid: 0000-0003-4509-4998
- first_name: James
full_name: Briscoe, James
last_name: Briscoe
citation:
ama: Kicheva A, Briscoe J. Control of tissue development by morphogens. Annual
Review of Cell and Developmental Biology. 2023;39:91-121. doi:10.1146/annurev-cellbio-020823-011522
apa: Kicheva, A., & Briscoe, J. (2023). Control of tissue development by morphogens.
Annual Review of Cell and Developmental Biology. Annual Reviews. https://doi.org/10.1146/annurev-cellbio-020823-011522
chicago: Kicheva, Anna, and James Briscoe. “Control of Tissue Development by Morphogens.”
Annual Review of Cell and Developmental Biology. Annual Reviews, 2023.
https://doi.org/10.1146/annurev-cellbio-020823-011522.
ieee: A. Kicheva and J. Briscoe, “Control of tissue development by morphogens,”
Annual Review of Cell and Developmental Biology, vol. 39. Annual Reviews,
pp. 91–121, 2023.
ista: Kicheva A, Briscoe J. 2023. Control of tissue development by morphogens. Annual
Review of Cell and Developmental Biology. 39, 91–121.
mla: Kicheva, Anna, and James Briscoe. “Control of Tissue Development by Morphogens.”
Annual Review of Cell and Developmental Biology, vol. 39, Annual Reviews,
2023, pp. 91–121, doi:10.1146/annurev-cellbio-020823-011522.
short: A. Kicheva, J. Briscoe, Annual Review of Cell and Developmental Biology 39
(2023) 91–121.
corr_author: '1'
date_created: 2023-11-05T23:00:53Z
date_published: 2023-10-16T00:00:00Z
date_updated: 2025-12-30T10:57:08Z
day: '16'
ddc:
- '570'
department:
- _id: AnKi
doi: 10.1146/annurev-cellbio-020823-011522
ec_funded: 1
external_id:
isi:
- '001082823000006'
pmid:
- '37418774'
file:
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checksum: 461726014cf5907010afbd418d3c13ec
content_type: application/pdf
creator: dernst
date_created: 2023-11-06T09:47:50Z
date_updated: 2023-11-06T09:47:50Z
file_id: '14491'
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language:
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month: '10'
oa: 1
oa_version: Published Version
page: 91-121
pmid: 1
project:
- _id: B6FC0238-B512-11E9-945C-1524E6697425
call_identifier: H2020
grant_number: '680037'
name: Coordination of Patterning And Growth In the Spinal Cord
- _id: bd7e737f-d553-11ed-ba76-d69ffb5ee3aa
grant_number: '101044579'
name: Mechanisms of tissue size regulation in spinal cord development
- _id: 059DF620-7A3F-11EA-A408-12923DDC885E
grant_number: F7802
name: Stem Cell Modulation in Neural Development and Regeneration/ P02-Morphogen
control of growth and pattern in the spinal cord
publication: Annual Review of Cell and Developmental Biology
publication_identifier:
eissn:
- 1530-8995
issn:
- 1081-0706
publication_status: published
publisher: Annual Reviews
quality_controlled: '1'
scopus_import: '1'
status: public
title: Control of tissue development by morphogens
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: 317138e5-6ab7-11ef-aa6d-ffef3953e345
volume: 39
year: '2023'
...
---
_id: '14517'
abstract:
- lang: eng
text: 'State-of-the-art transmon qubits rely on large capacitors, which systematically
improve their coherence due to reduced surface-loss participation. However, this
approach increases both the footprint and the parasitic cross-coupling and is
ultimately limited by radiation losses—a potential roadblock for scaling up quantum
processors to millions of qubits. In this work we present transmon qubits with
sizes as low as 36 × 39 µm2 with 100-nm-wide vacuum-gap capacitors that are micromachined
from commercial silicon-on-insulator wafers and shadow evaporated with aluminum.
We achieve a vacuum participation ratio up to 99.6% in an in-plane design that
is compatible with standard coplanar circuits. Qubit relaxationtime measurements
for small gaps with high zero-point electric field variance of up to 22 V/m reveal
a double exponential decay indicating comparably strong qubit interaction with
long-lived two-level systems. The exceptionally high selectivity of up to 20 dB
to the superconductor-vacuum interface allows us to precisely back out the sub-single-photon
dielectric loss tangent of aluminum oxide previously exposed to ambient conditions.
In terms of future scaling potential, we achieve a ratio of qubit quality factor
to a footprint area equal to 20 µm−2, which is comparable with the highest T1
devices relying on larger geometries, a value that could improve substantially
for lower surface-loss superconductors. '
acknowledged_ssus:
- _id: NanoFab
acknowledgement: "This work was supported by the Austrian Science Fund (FWF) through
BeyondC (F7105), the European Research Council under Grant Agreement No. 758053
(ERC StG QUNNECT) and a NOMIS foundation research grant. M.Z. was the recipient
of a SAIA scholarship, E.R. of\r\na DOC fellowship of the Austrian Academy of Sciences,
and M.P. of a Pöttinger scholarship at IST Austria. S.B. acknowledges support from
Marie Skłodowska Curie Program No. 707438 (MSC-IF SUPEREOM). J.M.F. acknowledges
support from the Horizon Europe Program HORIZON-CL4-2022-QUANTUM-01-SGA via Project
No. 101113946 OpenSuperQPlus100 and the ISTA Nanofabrication Facility."
article_number: '044054'
article_processing_charge: No
article_type: original
arxiv: 1
author:
- first_name: Martin
full_name: Zemlicka, Martin
id: 2DCF8DE6-F248-11E8-B48F-1D18A9856A87
last_name: Zemlicka
orcid: 0009-0005-0878-3032
- first_name: Elena
full_name: Redchenko, Elena
id: 2C21D6E8-F248-11E8-B48F-1D18A9856A87
last_name: Redchenko
- first_name: Matilda
full_name: Peruzzo, Matilda
id: 3F920B30-F248-11E8-B48F-1D18A9856A87
last_name: Peruzzo
orcid: 0000-0002-3415-4628
- first_name: Farid
full_name: Hassani, Farid
id: 2AED110C-F248-11E8-B48F-1D18A9856A87
last_name: Hassani
orcid: 0000-0001-6937-5773
- first_name: Andrea
full_name: Trioni, Andrea
id: 42F71B44-F248-11E8-B48F-1D18A9856A87
last_name: Trioni
- first_name: Shabir
full_name: Barzanjeh, Shabir
id: 2D25E1F6-F248-11E8-B48F-1D18A9856A87
last_name: Barzanjeh
orcid: 0000-0003-0415-1423
- first_name: Johannes M
full_name: Fink, Johannes M
id: 4B591CBA-F248-11E8-B48F-1D18A9856A87
last_name: Fink
orcid: 0000-0001-8112-028X
citation:
ama: 'Zemlicka M, Redchenko E, Peruzzo M, et al. Compact vacuum-gap transmon qubits:
Selective and sensitive probes for superconductor surface losses. Physical
Review Applied. 2023;20(4). doi:10.1103/PhysRevApplied.20.044054'
apa: 'Zemlicka, M., Redchenko, E., Peruzzo, M., Hassani, F., Trioni, A., Barzanjeh,
S., & Fink, J. M. (2023). Compact vacuum-gap transmon qubits: Selective and
sensitive probes for superconductor surface losses. Physical Review Applied.
American Physical Society. https://doi.org/10.1103/PhysRevApplied.20.044054'
chicago: 'Zemlicka, Martin, Elena Redchenko, Matilda Peruzzo, Farid Hassani, Andrea
Trioni, Shabir Barzanjeh, and Johannes M Fink. “Compact Vacuum-Gap Transmon Qubits:
Selective and Sensitive Probes for Superconductor Surface Losses.” Physical
Review Applied. American Physical Society, 2023. https://doi.org/10.1103/PhysRevApplied.20.044054.'
ieee: 'M. Zemlicka et al., “Compact vacuum-gap transmon qubits: Selective
and sensitive probes for superconductor surface losses,” Physical Review Applied,
vol. 20, no. 4. American Physical Society, 2023.'
ista: 'Zemlicka M, Redchenko E, Peruzzo M, Hassani F, Trioni A, Barzanjeh S, Fink
JM. 2023. Compact vacuum-gap transmon qubits: Selective and sensitive probes for
superconductor surface losses. Physical Review Applied. 20(4), 044054.'
mla: 'Zemlicka, Martin, et al. “Compact Vacuum-Gap Transmon Qubits: Selective and
Sensitive Probes for Superconductor Surface Losses.” Physical Review Applied,
vol. 20, no. 4, 044054, American Physical Society, 2023, doi:10.1103/PhysRevApplied.20.044054.'
short: M. Zemlicka, E. Redchenko, M. Peruzzo, F. Hassani, A. Trioni, S. Barzanjeh,
J.M. Fink, Physical Review Applied 20 (2023).
corr_author: '1'
date_created: 2023-11-12T23:00:55Z
date_published: 2023-10-20T00:00:00Z
date_updated: 2026-04-15T06:39:01Z
day: '20'
department:
- _id: JoFi
doi: 10.1103/PhysRevApplied.20.044054
ec_funded: 1
external_id:
arxiv:
- '2206.14104'
isi:
- '001095315600001'
intvolume: ' 20'
isi: 1
issue: '4'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/2206.14104
month: '10'
oa: 1
oa_version: Preprint
project:
- _id: 26336814-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '758053'
name: A Fiber Optic Transceiver for Superconducting Qubits
- _id: eb9b30ac-77a9-11ec-83b8-871f581d53d2
name: Protected states of quantum matter
- _id: 258047B6-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '707438'
name: 'Microwave-to-Optical Quantum Link: Quantum Teleportation and Quantum Illumination
with cavity Optomechanics'
- _id: bdb7cfc1-d553-11ed-ba76-d2eaab167738
grant_number: '101080139'
name: Open Superconducting Quantum Computers (OpenSuperQPlus)
- _id: bdb108fd-d553-11ed-ba76-83dc74a9864f
grant_number: F07105
name: QUANTUM INFORMATION SYSTEMS BEYOND CLASSICAL CAPABILITIES / P5- Integration
of Superconducting Quantum Circuits
publication: Physical Review Applied
publication_identifier:
eissn:
- 2331-7019
publication_status: published
publisher: American Physical Society
quality_controlled: '1'
related_material:
record:
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relation: research_data
status: public
scopus_import: '1'
status: public
title: 'Compact vacuum-gap transmon qubits: Selective and sensitive probes for superconductor
surface losses'
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 20
year: '2023'
...
---
_id: '13106'
abstract:
- lang: eng
text: Quantum entanglement is a key resource in currently developed quantum technologies.
Sharing this fragile property between superconducting microwave circuits and optical
or atomic systems would enable new functionalities, but this has been hindered
by an energy scale mismatch of >104 and the resulting mutually imposed loss and
noise. In this work, we created and verified entanglement between microwave and
optical fields in a millikelvin environment. Using an optically pulsed superconducting
electro-optical device, we show entanglement between propagating microwave and
optical fields in the continuous variable domain. This achievement not only paves
the way for entanglement between superconducting circuits and telecom wavelength
light, but also has wide-ranging implications for hybrid quantum networks in the
context of modularization, scaling, sensing, and cross-platform verification.
acknowledgement: This work was supported by the European Research Council (grant no.
758053, ERC StG QUNNECT) and the European Union’s Horizon 2020 Research and Innovation
Program (grant no. 899354, FETopen SuperQuLAN). L.Q. acknowledges generous support
from the ISTFELLOW program. W.H. is the recipient of an ISTplus postdoctoral fellowship
with funding from the European Union’s Horizon 2020 Research and Innovation Program
(Marie Sklodowska-Curie grant no. 754411). G.A. is the recipient of a DOC fellowship
of the Austrian Academy of Sciences at IST Austria. J.M.F. acknowledges support
from the Austrian Science Fund (FWF) through BeyondC (grant no. F7105) and the European
Union’s Horizon 2020 Research and Innovation Program (grant no. 862644, FETopen
QUARTET).
article_processing_charge: No
article_type: original
arxiv: 1
author:
- first_name: Rishabh
full_name: Sahu, Rishabh
id: 47D26E34-F248-11E8-B48F-1D18A9856A87
last_name: Sahu
orcid: 0000-0001-6264-2162
- first_name: Liu
full_name: Qiu, Liu
id: 45e99c0d-1eb1-11eb-9b96-ed8ab2983cac
last_name: Qiu
orcid: 0000-0003-4345-4267
- first_name: William J
full_name: Hease, William J
id: 29705398-F248-11E8-B48F-1D18A9856A87
last_name: Hease
orcid: 0000-0001-9868-2166
- first_name: Georg M
full_name: Arnold, Georg M
id: 3770C838-F248-11E8-B48F-1D18A9856A87
last_name: Arnold
orcid: 0000-0003-1397-7876
- first_name: Y.
full_name: Minoguchi, Y.
last_name: Minoguchi
- first_name: P.
full_name: Rabl, P.
last_name: Rabl
- first_name: Johannes M
full_name: Fink, Johannes M
id: 4B591CBA-F248-11E8-B48F-1D18A9856A87
last_name: Fink
orcid: 0000-0001-8112-028X
citation:
ama: Sahu R, Qiu L, Hease WJ, et al. Entangling microwaves with light. Science.
2023;380(6646):718-721. doi:10.1126/science.adg3812
apa: Sahu, R., Qiu, L., Hease, W. J., Arnold, G. M., Minoguchi, Y., Rabl, P., &
Fink, J. M. (2023). Entangling microwaves with light. Science. American
Association for the Advancement of Science. https://doi.org/10.1126/science.adg3812
chicago: Sahu, Rishabh, Liu Qiu, William J Hease, Georg M Arnold, Y. Minoguchi,
P. Rabl, and Johannes M Fink. “Entangling Microwaves with Light.” Science.
American Association for the Advancement of Science, 2023. https://doi.org/10.1126/science.adg3812.
ieee: R. Sahu et al., “Entangling microwaves with light,” Science,
vol. 380, no. 6646. American Association for the Advancement of Science, pp. 718–721,
2023.
ista: Sahu R, Qiu L, Hease WJ, Arnold GM, Minoguchi Y, Rabl P, Fink JM. 2023. Entangling
microwaves with light. Science. 380(6646), 718–721.
mla: Sahu, Rishabh, et al. “Entangling Microwaves with Light.” Science, vol.
380, no. 6646, American Association for the Advancement of Science, 2023, pp.
718–21, doi:10.1126/science.adg3812.
short: R. Sahu, L. Qiu, W.J. Hease, G.M. Arnold, Y. Minoguchi, P. Rabl, J.M. Fink,
Science 380 (2023) 718–721.
corr_author: '1'
date_created: 2023-05-31T11:39:24Z
date_published: 2023-05-18T00:00:00Z
date_updated: 2026-04-15T06:39:33Z
day: '18'
department:
- _id: JoFi
doi: 10.1126/science.adg3812
ec_funded: 1
external_id:
arxiv:
- '2301.03315'
isi:
- '000996515200004'
pmid:
- '37200415'
intvolume: ' 380'
isi: 1
issue: '6646'
keyword:
- Multidisciplinary
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.48550/arXiv.2301.03315
month: '05'
oa: 1
oa_version: Preprint
page: 718-721
pmid: 1
project:
- _id: 26336814-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '758053'
name: A Fiber Optic Transceiver for Superconducting Qubits
- _id: 9B868D20-BA93-11EA-9121-9846C619BF3A
call_identifier: H2020
grant_number: '899354'
name: Quantum Local Area Networks with Superconducting Qubits
- _id: 260C2330-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '754411'
name: ISTplus - Postdoctoral Fellowships
- _id: 237CBA6C-32DE-11EA-91FC-C7463DDC885E
call_identifier: H2020
grant_number: '862644'
name: Quantum readout techniques and technologies
- _id: 2671EB66-B435-11E9-9278-68D0E5697425
name: Coherent on-chip conversion of superconducting qubit signals from microwaves
to optical frequencies
- _id: bdb108fd-d553-11ed-ba76-83dc74a9864f
grant_number: F07105
name: QUANTUM INFORMATION SYSTEMS BEYOND CLASSICAL CAPABILITIES / P5- Integration
of Superconducting Quantum Circuits
publication: Science
publication_identifier:
eissn:
- 1095-9203
issn:
- 0036-8075
publication_status: published
publisher: American Association for the Advancement of Science
quality_controlled: '1'
related_material:
link:
- description: News on ISTA Website
relation: press_release
url: https://ista.ac.at/en/news/wiring-up-quantum-circuits-with-light/
record:
- id: '13122'
relation: research_data
status: public
scopus_import: '1'
status: public
title: Entangling microwaves with light
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 380
year: '2023'
...
---
_id: '13122'
abstract:
- lang: eng
text: Data for submitted article "Entangling microwaves with light" at arXiv:2301.03315v1
article_processing_charge: No
author:
- first_name: Rishabh
full_name: Sahu, Rishabh
id: 47D26E34-F248-11E8-B48F-1D18A9856A87
last_name: Sahu
orcid: 0000-0001-6264-2162
citation:
ama: Sahu R. Entangling microwaves with light. 2023. doi:10.5281/ZENODO.7789417
apa: Sahu, R. (2023). Entangling microwaves with light. Zenodo. https://doi.org/10.5281/ZENODO.7789417
chicago: Sahu, Rishabh. “Entangling Microwaves with Light.” Zenodo, 2023. https://doi.org/10.5281/ZENODO.7789417.
ieee: R. Sahu, “Entangling microwaves with light.” Zenodo, 2023.
ista: Sahu R. 2023. Entangling microwaves with light, Zenodo, 10.5281/ZENODO.7789417.
mla: Sahu, Rishabh. Entangling Microwaves with Light. Zenodo, 2023, doi:10.5281/ZENODO.7789417.
short: R. Sahu, (2023).
corr_author: '1'
date_created: 2023-06-06T06:46:16Z
date_published: 2023-03-31T00:00:00Z
date_updated: 2026-04-15T06:39:32Z
day: '31'
department:
- _id: JoFi
doi: 10.5281/ZENODO.7789417
main_file_link:
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month: '03'
oa: 1
oa_version: Published Version
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title: Entangling microwaves with light
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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)
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type: research_data_reference
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
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...
---
_id: '13227'
abstract:
- lang: eng
text: Currently available quantum processors are dominated by noise, which severely
limits their applicability and motivates the search for new physical qubit encodings.
In this work, we introduce the inductively shunted transmon, a weakly flux-tunable
superconducting qubit that offers charge offset protection for all levels and
a 20-fold reduction in flux dispersion compared to the state-of-the-art resulting
in a constant coherence over a full flux quantum. The parabolic confinement provided
by the inductive shunt as well as the linearity of the geometric superinductor
facilitates a high-power readout that resolves quantum jumps with a fidelity and
QND-ness of >90% and without the need for a Josephson parametric amplifier. Moreover,
the device reveals quantum tunneling physics between the two prepared fluxon ground
states with a measured average decay time of up to 3.5 h. In the future, fast
time-domain control of the transition matrix elements could offer a new path forward
to also achieve full qubit control in the decay-protected fluxon basis.
acknowledged_ssus:
- _id: M-Shop
- _id: NanoFab
acknowledgement: The authors thank J. Koch for discussions and support with the scQubits
python package, I. Rozhansky and A. Poddubny for important insights into photon-assisted
tunneling, S. Barzanjeh and G. Arnold for theory, E. Redchenko, S. Pepic, the MIBA
workshop and the IST nanofabrication facility for technical contributions, as well
as L. Drmic, P. Zielinski and R. Sett for software development. We acknowledge the
prompt support of Quantum Machines to implement active state preparation with their
OPX+. This work was supported by a NOMIS foundation research grant (J.F.), the Austrian
Science Fund (FWF) through BeyondC F7105 (J.F.) and IST Austria.
article_number: '3968'
article_processing_charge: No
article_type: original
author:
- first_name: Farid
full_name: Hassani, Farid
id: 2AED110C-F248-11E8-B48F-1D18A9856A87
last_name: Hassani
orcid: 0000-0001-6937-5773
- first_name: Matilda
full_name: Peruzzo, Matilda
id: 3F920B30-F248-11E8-B48F-1D18A9856A87
last_name: Peruzzo
orcid: 0000-0002-3415-4628
- first_name: Lucky
full_name: Kapoor, Lucky
id: 84b9700b-15b2-11ec-abd3-831089e67615
last_name: Kapoor
orcid: 0000-0001-8319-2148
- first_name: Andrea
full_name: Trioni, Andrea
id: 42F71B44-F248-11E8-B48F-1D18A9856A87
last_name: Trioni
- first_name: Martin
full_name: Zemlicka, Martin
id: 2DCF8DE6-F248-11E8-B48F-1D18A9856A87
last_name: Zemlicka
orcid: 0009-0005-0878-3032
- first_name: Johannes M
full_name: Fink, Johannes M
id: 4B591CBA-F248-11E8-B48F-1D18A9856A87
last_name: Fink
orcid: 0000-0001-8112-028X
citation:
ama: Hassani F, Peruzzo M, Kapoor L, Trioni A, Zemlicka M, Fink JM. Inductively
shunted transmons exhibit noise insensitive plasmon states and a fluxon decay
exceeding 3 hours. Nature Communications. 2023;14. doi:10.1038/s41467-023-39656-2
apa: Hassani, F., Peruzzo, M., Kapoor, L., Trioni, A., Zemlicka, M., & Fink,
J. M. (2023). Inductively shunted transmons exhibit noise insensitive plasmon
states and a fluxon decay exceeding 3 hours. Nature Communications. Springer
Nature. https://doi.org/10.1038/s41467-023-39656-2
chicago: Hassani, Farid, Matilda Peruzzo, Lucky Kapoor, Andrea Trioni, Martin Zemlicka,
and Johannes M Fink. “Inductively Shunted Transmons Exhibit Noise Insensitive
Plasmon States and a Fluxon Decay Exceeding 3 Hours.” Nature Communications.
Springer Nature, 2023. https://doi.org/10.1038/s41467-023-39656-2.
ieee: F. Hassani, M. Peruzzo, L. Kapoor, A. Trioni, M. Zemlicka, and J. M. Fink,
“Inductively shunted transmons exhibit noise insensitive plasmon states and a
fluxon decay exceeding 3 hours,” Nature Communications, vol. 14. Springer
Nature, 2023.
ista: Hassani F, Peruzzo M, Kapoor L, Trioni A, Zemlicka M, Fink JM. 2023. Inductively
shunted transmons exhibit noise insensitive plasmon states and a fluxon decay
exceeding 3 hours. Nature Communications. 14, 3968.
mla: Hassani, Farid, et al. “Inductively Shunted Transmons Exhibit Noise Insensitive
Plasmon States and a Fluxon Decay Exceeding 3 Hours.” Nature Communications,
vol. 14, 3968, Springer Nature, 2023, doi:10.1038/s41467-023-39656-2.
short: F. Hassani, M. Peruzzo, L. Kapoor, A. Trioni, M. Zemlicka, J.M. Fink, Nature
Communications 14 (2023).
corr_author: '1'
date_created: 2023-07-16T22:01:08Z
date_published: 2023-07-05T00:00:00Z
date_updated: 2026-04-15T06:39:57Z
day: '05'
ddc:
- '530'
department:
- _id: JoFi
doi: 10.1038/s41467-023-39656-2
external_id:
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pmid:
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creator: dernst
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date_updated: 2023-07-18T08:43:07Z
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file_name: 2023_NatureComm_Hassani.pdf
file_size: 2899592
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has_accepted_license: '1'
intvolume: ' 14'
isi: 1
language:
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oa: 1
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pmid: 1
project:
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name: Hybrid Semiconductor - Superconductor Quantum Devices
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eissn:
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publisher: Springer Nature
quality_controlled: '1'
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status: public
scopus_import: '1'
status: public
title: Inductively shunted transmons exhibit noise insensitive plasmon states and
a fluxon decay exceeding 3 hours
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: 14
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...
---
_id: '13124'
abstract:
- lang: eng
text: This dataset comprises all data shown in the figures of the submitted article
"Tunable directional photon scattering from a pair of superconducting qubits"
at arXiv:2205.03293. Additional raw data are available from the corresponding
author on reasonable request.
article_processing_charge: No
author:
- first_name: Elena
full_name: Redchenko, Elena
id: 2C21D6E8-F248-11E8-B48F-1D18A9856A87
last_name: Redchenko
- first_name: Alexander
full_name: Poshakinskiy, Alexander
last_name: Poshakinskiy
- first_name: Riya
full_name: Sett, Riya
id: 2E6D040E-F248-11E8-B48F-1D18A9856A87
last_name: Sett
orcid: 0000-0001-7641-8348
- first_name: Martin
full_name: Zemlicka, Martin
id: 2DCF8DE6-F248-11E8-B48F-1D18A9856A87
last_name: Zemlicka
orcid: 0009-0005-0878-3032
- first_name: Alexander
full_name: Poddubny, Alexander
last_name: Poddubny
- first_name: Johannes M
full_name: Fink, Johannes M
id: 4B591CBA-F248-11E8-B48F-1D18A9856A87
last_name: Fink
orcid: 0000-0001-8112-028X
citation:
ama: Redchenko E, Poshakinskiy A, Sett R, Zemlicka M, Poddubny A, Fink JM. Tunable
directional photon scattering from a pair of superconducting qubits. 2023. doi:10.5281/ZENODO.7858567
apa: Redchenko, E., Poshakinskiy, A., Sett, R., Zemlicka, M., Poddubny, A., &
Fink, J. M. (2023). Tunable directional photon scattering from a pair of superconducting
qubits. Zenodo. https://doi.org/10.5281/ZENODO.7858567
chicago: Redchenko, Elena, Alexander Poshakinskiy, Riya Sett, Martin Zemlicka, Alexander
Poddubny, and Johannes M Fink. “Tunable Directional Photon Scattering from a Pair
of Superconducting Qubits.” Zenodo, 2023. https://doi.org/10.5281/ZENODO.7858567.
ieee: E. Redchenko, A. Poshakinskiy, R. Sett, M. Zemlicka, A. Poddubny, and J. M.
Fink, “Tunable directional photon scattering from a pair of superconducting qubits.”
Zenodo, 2023.
ista: Redchenko E, Poshakinskiy A, Sett R, Zemlicka M, Poddubny A, Fink JM. 2023.
Tunable directional photon scattering from a pair of superconducting qubits, Zenodo,
10.5281/ZENODO.7858567.
mla: Redchenko, Elena, et al. Tunable Directional Photon Scattering from a Pair
of Superconducting Qubits. Zenodo, 2023, doi:10.5281/ZENODO.7858567.
short: E. Redchenko, A. Poshakinskiy, R. Sett, M. Zemlicka, A. Poddubny, J.M. Fink,
(2023).
corr_author: '1'
date_created: 2023-06-06T07:36:50Z
date_published: 2023-04-28T00:00:00Z
date_updated: 2026-04-15T06:40:27Z
day: '28'
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title: Tunable directional photon scattering from a pair of superconducting qubits
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abstract:
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text: "About a 100 years ago, we discovered that our universe is inherently noisy,
that is, measuring any physical quantity with a precision beyond a certain point
is not possible because of an omnipresent inherent noise. We call this - the quantum
noise. Certain physical processes allow this quantum noise to get correlated in
conjugate physical variables. These quantum correlations can be used to go beyond
the potential of our inherently noisy universe and obtain a quantum advantage
over the classical applications. \r\n\r\nQuantum noise being inherent also means
that, at the fundamental level, the physical quantities are not well defined and
therefore, objects can stay in multiple states at the same time. For example,
the position of a particle not being well defined means that the particle is in
multiple positions at the same time. About 4 decades ago, we started exploring
the possibility of using objects which can be in multiple states at the same time
to increase the dimensionality in computation. Thus, the field of quantum computing
was born. We discovered that using quantum entanglement, a property closely related
to quantum correlations, can be used to speed up computation of certain problems,
such as factorisation of large numbers, faster than any known classical algorithm.
Thus began the pursuit to make quantum computers a reality. \r\n\r\nTill date,
we have explored quantum control over many physical systems including photons,
spins, atoms, ions and even simple circuits made up of superconducting material.
However, there persists one ubiquitous theme. The more readily a system interacts
with an external field or matter, the more easily we can control it. But this
also means that such a system can easily interact with a noisy environment and
quickly lose its coherence. Consequently, such systems like electron spins need
to be protected from the environment to ensure the longevity of their coherence.
Other systems like nuclear spins are naturally protected as they do not interact
easily with the environment. But, due to the same reason, it is harder to interact
with such systems. \r\n\r\nAfter decades of experimentation with various systems,
we are convinced that no one type of quantum system would be the best for all
the quantum applications. We would need hybrid systems which are all interconnected
- much like the current internet where all sorts of devices can all talk to each
other - but now for quantum devices. A quantum internet. \r\n\r\nOptical photons
are the best contenders to carry information for the quantum internet. They can
carry quantum information cheaply and without much loss - the same reasons which
has made them the backbone of our current internet. Following this direction,
many systems, like trapped ions, have already demonstrated successful quantum
links over a large distances using optical photons. However, some of the most
promising contenders for quantum computing which are based on microwave frequencies
have been left behind. This is because high energy optical photons can adversely
affect fragile low-energy microwave systems. \r\n\r\nIn this thesis, we present
substantial progress on this missing quantum link between microwave and optics
using electrooptical nonlinearities in lithium niobate. The nonlinearities are
enhanced by using resonant cavities for all the involved modes leading to observation
of strong direct coupling between optical and microwave frequencies. With this
strong coupling we are not only able to achieve almost 100\\% internal conversion
efficiency with low added noise, thus presenting a quantum-enabled transducer,
but also we are able to observe novel effects such as cooling of a microwave mode
using optics. The strong coupling regime also leads to direct observation of dynamical
backaction effect between microwave and optical frequencies which are studied
in detail here. Finally, we also report first observation of microwave-optics
entanglement in form of two-mode squeezed vacuum squeezed 0.7dB below vacuum level.
\r\nWith this new bridge between microwave and optics, the microwave-based quantum
technologies can finally be a part of a quantum network which is based on optical
photons - putting us one step closer to a future with quantum internet. "
acknowledged_ssus:
- _id: M-Shop
- _id: SSU
- _id: NanoFab
alternative_title:
- ISTA Thesis
article_processing_charge: No
author:
- first_name: Rishabh
full_name: Sahu, Rishabh
id: 47D26E34-F248-11E8-B48F-1D18A9856A87
last_name: Sahu
orcid: 0000-0001-6264-2162
citation:
ama: Sahu R. Cavity quantum electrooptics. 2023. doi:10.15479/at:ista:13175
apa: Sahu, R. (2023). Cavity quantum electrooptics. Institute of Science
and Technology Austria. https://doi.org/10.15479/at:ista:13175
chicago: Sahu, Rishabh. “Cavity Quantum Electrooptics.” Institute of Science and
Technology Austria, 2023. https://doi.org/10.15479/at:ista:13175.
ieee: R. Sahu, “Cavity quantum electrooptics,” Institute of Science and Technology
Austria, 2023.
ista: Sahu R. 2023. Cavity quantum electrooptics. Institute of Science and Technology
Austria.
mla: Sahu, Rishabh. Cavity Quantum Electrooptics. Institute of Science and
Technology Austria, 2023, doi:10.15479/at:ista:13175.
short: R. Sahu, Cavity Quantum Electrooptics, Institute of Science and Technology
Austria, 2023.
corr_author: '1'
date_created: 2023-06-30T08:07:43Z
date_published: 2023-05-05T00:00:00Z
date_updated: 2026-04-15T06:43:26Z
day: '05'
ddc:
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- '535'
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degree_awarded: PhD
department:
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- _id: JoFi
doi: 10.15479/at:ista:13175
ec_funded: 1
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keyword:
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- electrooptics
- quantum networks
- quantum communication
- transduction
language:
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call_identifier: H2020
grant_number: '758053'
name: A Fiber Optic Transceiver for Superconducting Qubits
- _id: 9B868D20-BA93-11EA-9121-9846C619BF3A
call_identifier: H2020
grant_number: '899354'
name: Quantum Local Area Networks with Superconducting Qubits
- _id: bdb108fd-d553-11ed-ba76-83dc74a9864f
grant_number: F07105
name: QUANTUM INFORMATION SYSTEMS BEYOND CLASSICAL CAPABILITIES / P5- Integration
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orcid: 0000-0001-8112-028X
title: Cavity quantum electrooptics
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abstract:
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text: "About a 100 years ago, we discovered that our universe is inherently noisy,
that is, measuring any physical quantity with a precision beyond a certain point
is not possible because of an omnipresent inherent noise. We call this - the quantum
noise. Certain physical processes allow this quantum noise to get correlated in
conjugate physical variables. These quantum correlations can be used to go beyond
the potential of our inherently noisy universe and obtain a quantum advantage
over the classical applications. \r\n\r\nQuantum noise being inherent also means
that, at the fundamental level, the physical quantities are not well defined and
therefore, objects can stay in multiple states at the same time. For example,
the position of a particle not being well defined means that the particle is in
multiple positions at the same time. About 4 decades ago, we started exploring
the possibility of using objects which can be in multiple states at the same time
to increase the dimensionality in computation. Thus, the field of quantum computing
was born. We discovered that using quantum entanglement, a property closely related
to quantum correlations, can be used to speed up computation of certain problems,
such as factorisation of large numbers, faster than any known classical algorithm.
Thus began the pursuit to make quantum computers a reality. \r\n\r\nTill date,
we have explored quantum control over many physical systems including photons,
spins, atoms, ions and even simple circuits made up of superconducting material.
However, there persists one ubiquitous theme. The more readily a system interacts
with an external field or matter, the more easily we can control it. But this
also means that such a system can easily interact with a noisy environment and
quickly lose its coherence. Consequently, such systems like electron spins need
to be protected from the environment to ensure the longevity of their coherence.
Other systems like nuclear spins are naturally protected as they do not interact
easily with the environment. But, due to the same reason, it is harder to interact
with such systems. \r\n\r\nAfter decades of experimentation with various systems,
we are convinced that no one type of quantum system would be the best for all
the quantum applications. We would need hybrid systems which are all interconnected
- much like the current internet where all sorts of devices can all talk to each
other - but now for quantum devices. A quantum internet. \r\n\r\nOptical photons
are the best contenders to carry information for the quantum internet. They can
carry quantum information cheaply and without much loss - the same reasons which
has made them the backbone of our current internet. Following this direction,
many systems, like trapped ions, have already demonstrated successful quantum
links over a large distances using optical photons. However, some of the most
promising contenders for quantum computing which are based on microwave frequencies
have been left behind. This is because high energy optical photons can adversely
affect fragile low-energy microwave systems. \r\n\r\nIn this thesis, we present
substantial progress on this missing quantum link between microwave and optics
using electrooptical nonlinearities in lithium niobate. The nonlinearities are
enhanced by using resonant cavities for all the involved modes leading to observation
of strong direct coupling between optical and microwave frequencies. With this
strong coupling we are not only able to achieve almost 100\\% internal conversion
efficiency with low added noise, thus presenting a quantum-enabled transducer,
but also we are able to observe novel effects such as cooling of a microwave mode
using optics. The strong coupling regime also leads to direct observation of dynamical
backaction effect between microwave and optical frequencies which are studied
in detail here. Finally, we also report first observation of microwave-optics
entanglement in form of two-mode squeezed vacuum squeezed 0.7dB below vacuum level.
\r\nWith this new bridge between microwave and optics, the microwave-based quantum
technologies can finally be a part of a quantum network which is based on optical
photons - putting us one step closer to a future with quantum internet. "
acknowledged_ssus:
- _id: M-Shop
- _id: SSU
- _id: NanoFab
alternative_title:
- ISTA Thesis
article_processing_charge: No
author:
- first_name: Rishabh
full_name: Sahu, Rishabh
id: 47D26E34-F248-11E8-B48F-1D18A9856A87
last_name: Sahu
orcid: 0000-0001-6264-2162
citation:
ama: Sahu R. Cavity quantum electrooptics. 2023. doi:10.15479/at:ista:12900
apa: Sahu, R. (2023). Cavity quantum electrooptics. Institute of Science
and Technology Austria. https://doi.org/10.15479/at:ista:12900
chicago: Sahu, Rishabh. “Cavity Quantum Electrooptics.” Institute of Science and
Technology Austria, 2023. https://doi.org/10.15479/at:ista:12900.
ieee: R. Sahu, “Cavity quantum electrooptics,” Institute of Science and Technology
Austria, 2023.
ista: Sahu R. 2023. Cavity quantum electrooptics. Institute of Science and Technology
Austria.
mla: Sahu, Rishabh. Cavity Quantum Electrooptics. Institute of Science and
Technology Austria, 2023, doi:10.15479/at:ista:12900.
short: R. Sahu, Cavity Quantum Electrooptics, Institute of Science and Technology
Austria, 2023.
corr_author: '1'
date_created: 2023-05-05T11:08:50Z
date_published: 2023-05-05T00:00:00Z
date_updated: 2026-04-15T06:43:26Z
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keyword:
- quantum optics
- electrooptics
- quantum networks
- quantum communication
- transduction
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- iso: eng
month: '05'
oa_version: Published Version
page: '190'
project:
- _id: 26336814-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '758053'
name: A Fiber Optic Transceiver for Superconducting Qubits
- _id: 9B868D20-BA93-11EA-9121-9846C619BF3A
call_identifier: H2020
grant_number: '899354'
name: Quantum Local Area Networks with Superconducting Qubits
- _id: bdb108fd-d553-11ed-ba76-83dc74a9864f
grant_number: F07105
name: QUANTUM INFORMATION SYSTEMS BEYOND CLASSICAL CAPABILITIES / P5- Integration
of Superconducting Quantum Circuits
publication_identifier:
isbn:
- 978-3-99078-030-5
issn:
- 2663-337X
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related_material:
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status: public
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- first_name: Johannes M
full_name: Fink, Johannes M
id: 4B591CBA-F248-11E8-B48F-1D18A9856A87
last_name: Fink
orcid: 0000-0001-8112-028X
title: Cavity quantum electrooptics
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...
---
_id: '12897'
abstract:
- lang: eng
text: "Inverse design problems in fabrication-aware shape optimization are typically
solved on discrete representations such as polygonal meshes. This thesis argues
that there are benefits to treating these problems in the same domain as human
designers, namely, the parametric one. One reason is that discretizing a parametric
model usually removes the capability of making further manual changes to the design,
because the human intent is captured by the shape parameters. Beyond this, knowledge
about a design problem can sometimes reveal a structure that is present in a smooth
representation, but is fundamentally altered by discretizing. In this case, working
in the parametric domain may even simplify the optimization task. We present two
lines of research that explore both of these aspects of fabrication-aware shape
optimization on parametric representations.\r\n\r\nThe first project studies the
design of plane elastic curves and Kirchhoff rods, which are common mathematical
models for describing the deformation of thin elastic rods such as beams, ribbons,
cables, and hair. Our main contribution is a characterization of all curved shapes
that can be attained by bending and twisting elastic rods having a stiffness that
is allowed to vary across the length. Elements like these can be manufactured
using digital fabrication devices such as 3d printers and digital cutters, and
have applications in free-form architecture and soft robotics.\r\n\r\nWe show
that the family of curved shapes that can be produced this way admits geometric
description that is concise and computationally convenient. In the case of plane
curves, the geometric description is intuitive enough to allow a designer to determine
whether a curved shape is physically achievable by visual inspection alone. We
also present shape optimization algorithms that convert a user-defined curve in
the plane or in three dimensions into the geometry of an elastic rod that will
naturally deform to follow this curve when its endpoints are attached to a support
structure. Implemented in an interactive software design tool, the rod geometry
is generated in real time as the user edits a curve and enables fast prototyping.
\r\n\r\nThe second project tackles the problem of general-purpose shape optimization
on CAD models using a novel variant of the extended finite element method (XFEM).
Our goal is the decoupling between the simulation mesh and the CAD model, so no
geometry-dependent meshing or remeshing needs to be performed when the CAD parameters
change during optimization. This is achieved by discretizing the embedding space
of the CAD model, and using a new high-accuracy numerical integration method to
enable XFEM on free-form elements bounded by the parametric surface patches of
the model. Our simulation is differentiable from the CAD parameters to the simulation
output, which enables us to use off-the-shelf gradient-based optimization procedures.
The result is a method that fits seamlessly into the CAD workflow because it works
on the same representation as the designer, enabling the alternation of manual
editing and fabrication-aware optimization at will."
acknowledged_ssus:
- _id: M-Shop
alternative_title:
- ISTA Thesis
article_processing_charge: No
author:
- first_name: Christian
full_name: Hafner, Christian
id: 400429CC-F248-11E8-B48F-1D18A9856A87
last_name: Hafner
citation:
ama: 'Hafner C. Inverse shape design with parametric representations: Kirchhoff
Rods and parametric surface models. 2023. doi:10.15479/at:ista:12897'
apa: 'Hafner, C. (2023). Inverse shape design with parametric representations:
Kirchhoff Rods and parametric surface models. Institute of Science and Technology
Austria. https://doi.org/10.15479/at:ista:12897'
chicago: 'Hafner, Christian. “Inverse Shape Design with Parametric Representations:
Kirchhoff Rods and Parametric Surface Models.” Institute of Science and Technology
Austria, 2023. https://doi.org/10.15479/at:ista:12897.'
ieee: 'C. Hafner, “Inverse shape design with parametric representations: Kirchhoff
Rods and parametric surface models,” Institute of Science and Technology Austria,
2023.'
ista: 'Hafner C. 2023. Inverse shape design with parametric representations: Kirchhoff
Rods and parametric surface models. Institute of Science and Technology Austria.'
mla: 'Hafner, Christian. Inverse Shape Design with Parametric Representations:
Kirchhoff Rods and Parametric Surface Models. Institute of Science and Technology
Austria, 2023, doi:10.15479/at:ista:12897.'
short: 'C. Hafner, Inverse Shape Design with Parametric Representations: Kirchhoff
Rods and Parametric Surface Models, Institute of Science and Technology Austria,
2023.'
corr_author: '1'
date_created: 2023-05-05T10:40:14Z
date_published: 2023-05-05T00:00:00Z
date_updated: 2025-04-15T07:16:15Z
day: '05'
ddc:
- '516'
- '004'
- '518'
- '531'
degree_awarded: PhD
department:
- _id: GradSch
- _id: BeBi
doi: 10.15479/at:ista:12897
ec_funded: 1
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checksum: cc2094e92fa27000b70eb4bfb76d6b5a
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creator: chafner
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month: '05'
oa: 1
oa_version: Published Version
page: '180'
project:
- _id: 24F9549A-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '715767'
name: 'MATERIALIZABLE: Intelligent fabrication-oriented Computational Design and
Modeling'
publication_identifier:
isbn:
- 978-3-99078-031-2
issn:
- 2663-337X
publication_status: published
publisher: Institute of Science and Technology Austria
related_material:
record:
- id: '9817'
relation: part_of_dissertation
status: public
- id: '13188'
relation: dissertation_contains
status: public
- id: '7117'
relation: part_of_dissertation
status: public
status: public
supervisor:
- first_name: Bernd
full_name: Bickel, Bernd
id: 49876194-F248-11E8-B48F-1D18A9856A87
last_name: Bickel
orcid: 0000-0001-6511-9385
title: 'Inverse shape design with parametric representations: Kirchhoff Rods and parametric
surface models'
type: dissertation
user_id: 400429CC-F248-11E8-B48F-1D18A9856A87
year: '2023'
...
---
_id: '13188'
abstract:
- lang: eng
text: "The Kirchhoff rod model describes the bending and twisting of slender elastic
rods in three dimensions, and has been widely studied to enable the prediction
of how a rod will deform, given its geometry and boundary conditions. In this
work, we study a number of inverse problems with the goal of computing the geometry
of a straight rod that will automatically deform to match a curved target shape
after attaching its endpoints to a support structure. Our solution lets us finely
control the static equilibrium state of a rod by varying the cross-sectional profiles
along its length.\r\nWe also show that the set of physically realizable equilibrium
states admits a concise geometric description in terms of linear line complexes,
which leads to very efficient computational design algorithms. Implemented in
an interactive software tool, they allow us to convert three-dimensional hand-drawn
spline curves to elastic rods, and give feedback about the feasibility and practicality
of a design in real time. We demonstrate the efficacy of our method by designing
and manufacturing several physical prototypes with applications to interior design
and soft robotics."
acknowledged_ssus:
- _id: M-Shop
acknowledgement: We thank the anonymous reviewers for their generous feedback, and
Julian Fischer for his help in proving Proposition 1. This project has received
funding from the European Research Council (ERC) under the European Union’s Horizon
2020 research and innovation programme (grant agreement No. 715767).
article_number: '171'
article_processing_charge: No
article_type: original
author:
- first_name: Christian
full_name: Hafner, Christian
id: 400429CC-F248-11E8-B48F-1D18A9856A87
last_name: Hafner
- first_name: Bernd
full_name: Bickel, Bernd
id: 49876194-F248-11E8-B48F-1D18A9856A87
last_name: Bickel
orcid: 0000-0001-6511-9385
citation:
ama: Hafner C, Bickel B. The design space of Kirchhoff rods. ACM Transactions
on Graphics. 2023;42(5). doi:10.1145/3606033
apa: Hafner, C., & Bickel, B. (2023). The design space of Kirchhoff rods. ACM
Transactions on Graphics. Association for Computing Machinery. https://doi.org/10.1145/3606033
chicago: Hafner, Christian, and Bernd Bickel. “The Design Space of Kirchhoff Rods.”
ACM Transactions on Graphics. Association for Computing Machinery, 2023.
https://doi.org/10.1145/3606033.
ieee: C. Hafner and B. Bickel, “The design space of Kirchhoff rods,” ACM Transactions
on Graphics, vol. 42, no. 5. Association for Computing Machinery, 2023.
ista: Hafner C, Bickel B. 2023. The design space of Kirchhoff rods. ACM Transactions
on Graphics. 42(5), 171.
mla: Hafner, Christian, and Bernd Bickel. “The Design Space of Kirchhoff Rods.”
ACM Transactions on Graphics, vol. 42, no. 5, 171, Association for Computing
Machinery, 2023, doi:10.1145/3606033.
short: C. Hafner, B. Bickel, ACM Transactions on Graphics 42 (2023).
corr_author: '1'
date_created: 2023-07-04T07:41:30Z
date_published: 2023-09-20T00:00:00Z
date_updated: 2026-04-25T22:30:04Z
day: '20'
ddc:
- '516'
department:
- _id: BeBi
doi: 10.1145/3606033
ec_funded: 1
external_id:
isi:
- '001086833300010'
file:
- access_level: open_access
checksum: 4954c1cfa487725bc156dcfec872478a
content_type: application/pdf
creator: chafner
date_created: 2023-07-04T08:11:28Z
date_updated: 2023-07-04T08:11:28Z
file_id: '13194'
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file_size: 19635168
relation: main_file
success: 1
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checksum: 79c9975fbc82ff71f1767331d2204cca
content_type: application/pdf
creator: chafner
date_created: 2023-07-04T07:46:28Z
date_updated: 2023-07-04T07:46:28Z
file_id: '13190'
file_name: supp-main.pdf
file_size: 420909
relation: supplementary_material
title: Supplemental Material with Proofs
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checksum: 4ab647e4f03c711e1e6a5fc1eb8684db
content_type: application/pdf
creator: chafner
date_created: 2023-07-04T07:46:30Z
date_updated: 2023-07-04T07:46:30Z
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file_size: 430086
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title: Cheat Sheet for Notation
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checksum: c0fd9a57d012046de90c185ffa904b76
content_type: video/mp4
creator: chafner
date_created: 2023-07-04T07:46:39Z
date_updated: 2023-07-04T07:46:39Z
file_id: '13192'
file_name: kirchhoff-video-final.mp4
file_size: 268088064
relation: supplementary_material
title: Supplemental Video
- access_level: open_access
checksum: 71b00712b489ada2cd9815910ee180a9
content_type: application/x-zip-compressed
creator: chafner
date_created: 2023-07-04T07:47:10Z
date_updated: 2023-07-04T07:47:10Z
file_id: '13193'
file_name: matlab-submission.zip
file_size: 25790
relation: supplementary_material
title: Matlab Source Code with Example
file_date_updated: 2023-07-04T08:11:28Z
has_accepted_license: '1'
intvolume: ' 42'
isi: 1
issue: '5'
keyword:
- Computer Graphics
- Computational Design
- Computational Geometry
- Shape Modeling
language:
- iso: eng
month: '09'
oa: 1
oa_version: Submitted Version
project:
- _id: 24F9549A-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '715767'
name: 'MATERIALIZABLE: Intelligent fabrication-oriented Computational Design and
Modeling'
publication: ACM Transactions on Graphics
publication_identifier:
eissn:
- 1557-7368
issn:
- 0730-0301
publication_status: published
publisher: Association for Computing Machinery
quality_controlled: '1'
related_material:
record:
- id: '12897'
relation: part_of_dissertation
status: public
scopus_import: '1'
status: public
title: The design space of Kirchhoff rods
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 42
year: '2023'
...
---
_id: '12891'
abstract:
- lang: eng
text: "The tight spatiotemporal coordination of signaling activity determining embryo\r\npatterning
and the physical processes driving embryo morphogenesis renders\r\nembryonic development
robust, such that key developmental processes can unfold\r\nrelatively normally
even outside of the full embryonic context. For instance, embryonic\r\nstem cell
cultures can recapitulate the hallmarks of gastrulation, i.e. break symmetry\r\nleading
to germ layer formation and morphogenesis, in a very reduced environment.\r\nThis
leads to questions on specific contributions of embryo-specific features, such
as\r\nthe presence of extraembryonic tissues, which are inherently involved in
gastrulation\r\nin the full embryonic context. To address this, we established
zebrafish embryonic\r\nexplants without the extraembryonic yolk cell, an important
player as a signaling\r\nsource and for morphogenesis during gastrulation, as
a model of ex vivo development.\r\nWe found that dorsal-marginal determinants
are required and sufficient in these\r\nexplants to form and pattern all three
germ layers. However, formation of tissues,\r\nwhich require the highest Nodal-signaling
levels, is variable, demonstrating a\r\ncontribution of extraembryonic tissues
for reaching peak Nodal signaling levels.\r\nBlastoderm explants also undergo
gastrulation-like axis elongation. We found that this\r\nelongation movement shows
hallmarks of oriented mesendoderm cell intercalations\r\ntypically associated
with dorsal tissues in the intact embryo. These are disrupted by\r\nuniform upregulation
of BMP signaling activity and concomitant explant ventralization,\r\nsuggesting
that tight spatial control of BMP signaling is a prerequisite for explant\r\nmorphogenesis.
This control is achieved by Nodal signaling, which is critical for\r\neffectively
downregulating BMP signaling in the mesendoderm, highlighting that Nodal\r\nsignaling
is not only directly required for mesendoderm cell fate specification and\r\nmorphogenesis,
but also by maintaining low levels of BMP signaling at the dorsal side.\r\nCollectively,
we provide insights into the capacity and organization of signaling and\r\nmorphogenetic
domains to recapitulate features of zebrafish gastrulation outside of\r\nthe full
embryonic context."
acknowledged_ssus:
- _id: Bio
- _id: LifeSc
alternative_title:
- ISTA Thesis
article_processing_charge: No
author:
- first_name: Alexandra
full_name: Schauer, Alexandra
id: 30A536BA-F248-11E8-B48F-1D18A9856A87
last_name: Schauer
orcid: 0000-0001-7659-9142
citation:
ama: 'Schauer A. Mesendoderm formation in zebrafish gastrulation: The role of extraembryonic
tissues. 2023. doi:10.15479/at:ista:12891'
apa: 'Schauer, A. (2023). Mesendoderm formation in zebrafish gastrulation: The
role of extraembryonic tissues. Institute of Science and Technology Austria.
https://doi.org/10.15479/at:ista:12891'
chicago: 'Schauer, Alexandra. “Mesendoderm Formation in Zebrafish Gastrulation:
The Role of Extraembryonic Tissues.” Institute of Science and Technology Austria,
2023. https://doi.org/10.15479/at:ista:12891.'
ieee: 'A. Schauer, “Mesendoderm formation in zebrafish gastrulation: The role of
extraembryonic tissues,” Institute of Science and Technology Austria, 2023.'
ista: 'Schauer A. 2023. Mesendoderm formation in zebrafish gastrulation: The role
of extraembryonic tissues. Institute of Science and Technology Austria.'
mla: 'Schauer, Alexandra. Mesendoderm Formation in Zebrafish Gastrulation: The
Role of Extraembryonic Tissues. Institute of Science and Technology Austria,
2023, doi:10.15479/at:ista:12891.'
short: 'A. Schauer, Mesendoderm Formation in Zebrafish Gastrulation: The Role of
Extraembryonic Tissues, Institute of Science and Technology Austria, 2023.'
corr_author: '1'
date_created: 2023-05-05T08:48:20Z
date_published: 2023-05-05T00:00:00Z
date_updated: 2025-06-12T06:56:58Z
day: '05'
ddc:
- '570'
degree_awarded: PhD
department:
- _id: GradSch
- _id: CaHe
doi: 10.15479/at:ista:12891
ec_funded: 1
file:
- access_level: open_access
checksum: 59b0303dc483f40a96a610a90aab7ee9
content_type: application/pdf
creator: aschauer
date_created: 2023-05-05T13:01:14Z
date_updated: 2024-05-06T22:30:03Z
embargo: 2024-05-05
file_id: '12907'
file_name: Thesis_Schauer_final.pdf
file_size: 31434230
relation: main_file
- access_level: closed
checksum: 25f54e12479b6adaabd129a20568e6c1
content_type: application/vnd.openxmlformats-officedocument.wordprocessingml.document
creator: aschauer
date_created: 2023-05-05T13:04:15Z
date_updated: 2024-05-06T22:30:03Z
embargo_to: open_access
file_id: '12908'
file_name: Thesis_Schauer_final.docx
file_size: 43809109
relation: source_file
file_date_updated: 2024-05-06T22:30:03Z
has_accepted_license: '1'
language:
- iso: eng
month: '05'
oa: 1
oa_version: Published Version
page: '190'
project:
- _id: 260F1432-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '742573'
name: Interaction and feedback between cell mechanics and fate specification in
vertebrate gastrulation
- _id: 26B1E39C-B435-11E9-9278-68D0E5697425
grant_number: '25239'
name: 'Mesendoderm specification in zebrafish: The role of extraembryonic tissues'
publication_identifier:
issn:
- 2663-337X
publication_status: published
publisher: Institute of Science and Technology Austria
related_material:
record:
- id: '7888'
relation: part_of_dissertation
status: public
- id: '8966'
relation: part_of_dissertation
status: public
status: public
supervisor:
- first_name: Carl-Philipp J
full_name: Heisenberg, Carl-Philipp J
id: 39427864-F248-11E8-B48F-1D18A9856A87
last_name: Heisenberg
orcid: 0000-0002-0912-4566
title: 'Mesendoderm formation in zebrafish gastrulation: The role of extraembryonic
tissues'
type: dissertation
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
year: '2023'
...
---
_id: '14656'
abstract:
- lang: eng
text: Although much is known about how single neurons in the hippocampus represent
an animal's position, how circuit interactions contribute to spatial coding is
less well understood. Using a novel statistical estimator and theoretical modeling,
both developed in the framework of maximum entropy models, we reveal highly structured
CA1 cell-cell interactions in male rats during open field exploration. The statistics
of these interactions depend on whether the animal is in a familiar or novel environment.
In both conditions the circuit interactions optimize the encoding of spatial information,
but for regimes that differ in the informativeness of their spatial inputs. This
structure facilitates linear decodability, making the information easy to read
out by downstream circuits. Overall, our findings suggest that the efficient coding
hypothesis is not only applicable to individual neuron properties in the sensory
periphery, but also to neural interactions in the central brain.
acknowledgement: M.N. was supported by the European Union Horizon 2020 Grant 665385.
J.C. was supported by the European Research Council Consolidator Grant 281511. G.T.
was supported by the Austrian Science Fund (FWF) Grant P34015. C.S. was supported
by an Institute of Science and Technology fellow award and by the National Science
Foundation (NSF) Award No. 1922658. We thank Peter Baracskay, Karola Kaefer, and
Hugo Malagon-Vina for the acquisition of the data. We also thank Federico Stella,
Wiktor Młynarski, Dori Derdikman, Colin Bredenberg, Roman Huszar, Heloisa Chiossi,
Lorenzo Posani, and Mohamady El-Gaby for comments on an earlier version of the manuscript.
article_processing_charge: Yes (in subscription journal)
article_type: original
author:
- first_name: Michele
full_name: Nardin, Michele
id: 30BD0376-F248-11E8-B48F-1D18A9856A87
last_name: Nardin
orcid: 0000-0001-8849-6570
- first_name: Jozsef L
full_name: Csicsvari, Jozsef L
id: 3FA14672-F248-11E8-B48F-1D18A9856A87
last_name: Csicsvari
orcid: 0000-0002-5193-4036
- first_name: Gašper
full_name: Tkačik, Gašper
id: 3D494DCA-F248-11E8-B48F-1D18A9856A87
last_name: Tkačik
orcid: 0000-0002-6699-1455
- first_name: Cristina
full_name: Savin, Cristina
id: 3933349E-F248-11E8-B48F-1D18A9856A87
last_name: Savin
citation:
ama: Nardin M, Csicsvari JL, Tkačik G, Savin C. The structure of hippocampal CA1
interactions optimizes spatial coding across experience. The Journal of Neuroscience.
2023;43(48):8140-8156. doi:10.1523/JNEUROSCI.0194-23.2023
apa: Nardin, M., Csicsvari, J. L., Tkačik, G., & Savin, C. (2023). The structure
of hippocampal CA1 interactions optimizes spatial coding across experience. The
Journal of Neuroscience. Society for Neuroscience. https://doi.org/10.1523/JNEUROSCI.0194-23.2023
chicago: Nardin, Michele, Jozsef L Csicsvari, Gašper Tkačik, and Cristina Savin.
“The Structure of Hippocampal CA1 Interactions Optimizes Spatial Coding across
Experience.” The Journal of Neuroscience. Society for Neuroscience, 2023.
https://doi.org/10.1523/JNEUROSCI.0194-23.2023.
ieee: M. Nardin, J. L. Csicsvari, G. Tkačik, and C. Savin, “The structure of hippocampal
CA1 interactions optimizes spatial coding across experience,” The Journal of
Neuroscience, vol. 43, no. 48. Society for Neuroscience, pp. 8140–8156, 2023.
ista: Nardin M, Csicsvari JL, Tkačik G, Savin C. 2023. The structure of hippocampal
CA1 interactions optimizes spatial coding across experience. The Journal of Neuroscience.
43(48), 8140–8156.
mla: Nardin, Michele, et al. “The Structure of Hippocampal CA1 Interactions Optimizes
Spatial Coding across Experience.” The Journal of Neuroscience, vol. 43,
no. 48, Society for Neuroscience, 2023, pp. 8140–56, doi:10.1523/JNEUROSCI.0194-23.2023.
short: M. Nardin, J.L. Csicsvari, G. Tkačik, C. Savin, The Journal of Neuroscience
43 (2023) 8140–8156.
date_created: 2023-12-10T23:00:58Z
date_published: 2023-11-29T00:00:00Z
date_updated: 2025-09-09T13:37:51Z
day: '29'
ddc:
- '570'
department:
- _id: JoCs
- _id: GaTk
doi: 10.1523/JNEUROSCI.0194-23.2023
ec_funded: 1
external_id:
isi:
- '001148071000005'
pmid:
- '37758476'
file:
- access_level: open_access
checksum: e2503c8f84be1050e28f64320f1d5bd2
content_type: application/pdf
creator: dernst
date_created: 2023-12-11T11:30:37Z
date_updated: 2024-06-02T22:30:03Z
embargo: 2024-06-01
file_id: '14674'
file_name: 2023_JourNeuroscience_Nardin.pdf
file_size: 2280632
relation: main_file
file_date_updated: 2024-06-02T22:30:03Z
has_accepted_license: '1'
intvolume: ' 43'
isi: 1
issue: '48'
language:
- iso: eng
month: '11'
oa: 1
oa_version: Published Version
page: 8140-8156
pmid: 1
project:
- _id: 257A4776-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '281511'
name: Memory-related information processing in neuronal circuits of the hippocampus
and entorhinal cortex
- _id: 626c45b5-2b32-11ec-9570-e509828c1ba6
grant_number: P34015
name: Efficient coding with biophysical realism
- _id: 2564DBCA-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '665385'
name: International IST Doctoral Program
publication: The Journal of Neuroscience
publication_identifier:
eissn:
- 1529-2401
publication_status: published
publisher: Society for Neuroscience
quality_controlled: '1'
related_material:
record:
- id: '10077'
relation: earlier_version
status: public
scopus_import: '1'
status: public
title: The structure of hippocampal CA1 interactions optimizes spatial coding across
experience
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: 317138e5-6ab7-11ef-aa6d-ffef3953e345
volume: 43
year: '2023'
...
---
_id: '14459'
abstract:
- lang: eng
text: Autoencoders are a popular model in many branches of machine learning and
lossy data compression. However, their fundamental limits, the performance of
gradient methods and the features learnt during optimization remain poorly understood,
even in the two-layer setting. In fact, earlier work has considered either linear
autoencoders or specific training regimes (leading to vanishing or diverging compression
rates). Our paper addresses this gap by focusing on non-linear two-layer autoencoders
trained in the challenging proportional regime in which the input dimension scales
linearly with the size of the representation. Our results characterize the minimizers
of the population risk, and show that such minimizers are achieved by gradient
methods; their structure is also unveiled, thus leading to a concise description
of the features obtained via training. For the special case of a sign activation
function, our analysis establishes the fundamental limits for the lossy compression
of Gaussian sources via (shallow) autoencoders. Finally, while the results are
proved for Gaussian data, numerical simulations on standard datasets display the
universality of the theoretical predictions.
acknowledgement: Aleksandr Shevchenko, Kevin Kogler and Marco Mondelli are supported
by the 2019 Lopez-Loreta Prize. Hamed Hassani acknowledges the support by the NSF
CIF award (1910056) and the NSF Institute for CORE Emerging Methods in Data Science
(EnCORE).
alternative_title:
- PMLR
article_processing_charge: No
arxiv: 1
author:
- first_name: Aleksandr
full_name: Shevchenko, Aleksandr
id: F2B06EC2-C99E-11E9-89F0-752EE6697425
last_name: Shevchenko
- first_name: Kevin
full_name: Kögler, Kevin
id: 94ec913c-dc85-11ea-9058-e5051ab2428b
last_name: Kögler
- first_name: Hamed
full_name: Hassani, Hamed
last_name: Hassani
- first_name: Marco
full_name: Mondelli, Marco
id: 27EB676C-8706-11E9-9510-7717E6697425
last_name: Mondelli
orcid: 0000-0002-3242-7020
citation:
ama: 'Shevchenko A, Kögler K, Hassani H, Mondelli M. Fundamental limits of two-layer
autoencoders, and achieving them with gradient methods. In: Proceedings of
the 40th International Conference on Machine Learning. Vol 202. ML Research
Press; 2023:31151-31209.'
apa: 'Shevchenko, A., Kögler, K., Hassani, H., & Mondelli, M. (2023). Fundamental
limits of two-layer autoencoders, and achieving them with gradient methods. In
Proceedings of the 40th International Conference on Machine Learning (Vol.
202, pp. 31151–31209). Honolulu, Hawaii, HI, United States: ML Research Press.'
chicago: Shevchenko, Alexander, Kevin Kögler, Hamed Hassani, and Marco Mondelli.
“Fundamental Limits of Two-Layer Autoencoders, and Achieving Them with Gradient
Methods.” In Proceedings of the 40th International Conference on Machine Learning,
202:31151–209. ML Research Press, 2023.
ieee: A. Shevchenko, K. Kögler, H. Hassani, and M. Mondelli, “Fundamental limits
of two-layer autoencoders, and achieving them with gradient methods,” in Proceedings
of the 40th International Conference on Machine Learning, Honolulu, Hawaii,
HI, United States, 2023, vol. 202, pp. 31151–31209.
ista: 'Shevchenko A, Kögler K, Hassani H, Mondelli M. 2023. Fundamental limits of
two-layer autoencoders, and achieving them with gradient methods. Proceedings
of the 40th International Conference on Machine Learning. ICML: International
Conference on Machine Learning, PMLR, vol. 202, 31151–31209.'
mla: Shevchenko, Alexander, et al. “Fundamental Limits of Two-Layer Autoencoders,
and Achieving Them with Gradient Methods.” Proceedings of the 40th International
Conference on Machine Learning, vol. 202, ML Research Press, 2023, pp. 31151–209.
short: A. Shevchenko, K. Kögler, H. Hassani, M. Mondelli, in:, Proceedings of the
40th International Conference on Machine Learning, ML Research Press, 2023, pp.
31151–31209.
conference:
end_date: 2023-07-29
location: Honolulu, Hawaii, HI, United States
name: 'ICML: International Conference on Machine Learning'
start_date: 2023-07-23
corr_author: '1'
date_created: 2023-10-29T23:01:17Z
date_published: 2023-07-30T00:00:00Z
date_updated: 2026-04-25T22:30:23Z
day: '30'
department:
- _id: MaMo
- _id: DaAl
external_id:
arxiv:
- '2212.13468'
intvolume: ' 202'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.48550/arXiv.2212.13468
month: '07'
oa: 1
oa_version: Preprint
page: 31151-31209
project:
- _id: 059876FA-7A3F-11EA-A408-12923DDC885E
name: Prix Lopez-Loretta 2019 - Marco Mondelli
publication: Proceedings of the 40th International Conference on Machine Learning
publication_identifier:
eissn:
- 2640-3498
publication_status: published
publisher: ML Research Press
quality_controlled: '1'
related_material:
record:
- id: '17465'
relation: dissertation_contains
status: public
scopus_import: '1'
status: public
title: Fundamental limits of two-layer autoencoders, and achieving them with gradient
methods
type: conference
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 202
year: '2023'
...
---
_id: '13201'
abstract:
- lang: eng
text: As a crucial nitrogen source, nitrate (NO3−) is a key nutrient for plants.
Accordingly, root systems adapt to maximize NO3− availability, a developmental
regulation also involving the phytohormone auxin. Nonetheless, the molecular mechanisms
underlying this regulation remain poorly understood. Here, we identify low-nitrate-resistant
mutant (lonr) in Arabidopsis (Arabidopsis thaliana), whose root growth fails to
adapt to low-NO3− conditions. lonr2 is defective in the high-affinity NO3− transporter
NRT2.1. lonr2 (nrt2.1) mutants exhibit defects in polar auxin transport, and their
low-NO3−-induced root phenotype depends on the PIN7 auxin exporter activity. NRT2.1
directly associates with PIN7 and antagonizes PIN7-mediated auxin efflux depending
on NO3− levels. These results reveal a mechanism by which NRT2.1 in response to
NO3− limitation directly regulates auxin transport activity and, thus, root growth.
This adaptive mechanism contributes to the root developmental plasticity to help
plants cope with changes in NO3− availability.
acknowledgement: We are grateful to Caifu Jiang for providing ethyl metha-nesulfonate-
mutagenized population, Yi Wang for providing Xenopus oocytes, Jun Fan and Zhaosheng
Kong for providing tobacco BY- 2 cells, and Claus Schwechheimer, Alain Gojon, and
Shutang Tan for helpful discussions. This work was supported by the National Key
Research and Development Program of China (2021YFF1000500), the National Natural Science Foundation of China (32170265 and 32022007), Hainan Provincial Natural Science Foundation of China (323CXTD379), Chinese Universities Scientific Fund (2023TC019), Beijing Municipal Natural Science Foundation (5192011), Beijing Outstanding University Discipline Program, and China
Postdoctoral Science Foundation (BH2020259460).
article_number: e2221313120
article_processing_charge: No
article_type: original
author:
- first_name: Yalu
full_name: Wang, Yalu
last_name: Wang
- first_name: Zhi
full_name: Yuan, Zhi
last_name: Yuan
- first_name: Jinyi
full_name: Wang, Jinyi
last_name: Wang
- first_name: Huixin
full_name: Xiao, Huixin
last_name: Xiao
- first_name: Lu
full_name: Wan, Lu
last_name: Wan
- first_name: Lanxin
full_name: Li, Lanxin
id: 367EF8FA-F248-11E8-B48F-1D18A9856A87
last_name: Li
orcid: 0000-0002-5607-272X
- first_name: Yan
full_name: Guo, Yan
last_name: Guo
- first_name: Zhizhong
full_name: Gong, Zhizhong
last_name: Gong
- first_name: Jiří
full_name: Friml, Jiří
id: 4159519E-F248-11E8-B48F-1D18A9856A87
last_name: Friml
orcid: 0000-0002-8302-7596
- first_name: Jing
full_name: Zhang, Jing
last_name: Zhang
citation:
ama: Wang Y, Yuan Z, Wang J, et al. The nitrate transporter NRT2.1 directly antagonizes
PIN7-mediated auxin transport for root growth adaptation. Proceedings of the
National Academy of Sciences of the United States of America. 2023;120(25).
doi:10.1073/pnas.2221313120
apa: Wang, Y., Yuan, Z., Wang, J., Xiao, H., Wan, L., Li, L., … Zhang, J. (2023).
The nitrate transporter NRT2.1 directly antagonizes PIN7-mediated auxin transport
for root growth adaptation. Proceedings of the National Academy of Sciences
of the United States of America. National Academy of Sciences. https://doi.org/10.1073/pnas.2221313120
chicago: Wang, Yalu, Zhi Yuan, Jinyi Wang, Huixin Xiao, Lu Wan, Lanxin Li, Yan Guo,
Zhizhong Gong, Jiří Friml, and Jing Zhang. “The Nitrate Transporter NRT2.1 Directly
Antagonizes PIN7-Mediated Auxin Transport for Root Growth Adaptation.” Proceedings
of the National Academy of Sciences of the United States of America. National
Academy of Sciences, 2023. https://doi.org/10.1073/pnas.2221313120.
ieee: Y. Wang et al., “The nitrate transporter NRT2.1 directly antagonizes
PIN7-mediated auxin transport for root growth adaptation,” Proceedings of the
National Academy of Sciences of the United States of America, vol. 120, no.
25. National Academy of Sciences, 2023.
ista: Wang Y, Yuan Z, Wang J, Xiao H, Wan L, Li L, Guo Y, Gong Z, Friml J, Zhang
J. 2023. The nitrate transporter NRT2.1 directly antagonizes PIN7-mediated auxin
transport for root growth adaptation. Proceedings of the National Academy of Sciences
of the United States of America. 120(25), e2221313120.
mla: Wang, Yalu, et al. “The Nitrate Transporter NRT2.1 Directly Antagonizes PIN7-Mediated
Auxin Transport for Root Growth Adaptation.” Proceedings of the National Academy
of Sciences of the United States of America, vol. 120, no. 25, e2221313120,
National Academy of Sciences, 2023, doi:10.1073/pnas.2221313120.
short: Y. Wang, Z. Yuan, J. Wang, H. Xiao, L. Wan, L. Li, Y. Guo, Z. Gong, J. Friml,
J. Zhang, Proceedings of the National Academy of Sciences of the United States
of America 120 (2023).
date_created: 2023-07-09T22:01:12Z
date_published: 2023-06-12T00:00:00Z
date_updated: 2023-12-13T23:30:04Z
day: '12'
ddc:
- '570'
department:
- _id: JiFr
doi: 10.1073/pnas.2221313120
external_id:
isi:
- '001030689600003'
pmid:
- '37307446'
file:
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checksum: d800e06252eaefba28531fa9440f23f0
content_type: application/pdf
creator: alisjak
date_created: 2023-07-10T08:48:40Z
date_updated: 2023-12-13T23:30:03Z
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file_size: 5244581
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oa_version: Published Version
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of America
publication_identifier:
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issn:
- 0027-8424
publication_status: published
publisher: National Academy of Sciences
quality_controlled: '1'
scopus_import: '1'
status: public
title: The nitrate transporter NRT2.1 directly antagonizes PIN7-mediated auxin transport
for root growth adaptation
tmp:
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(CC BY-NC-ND 4.0)
short: CC BY-NC-ND (4.0)
type: journal_article
user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
volume: 120
year: '2023'
...
---
_id: '12159'
abstract:
- lang: eng
text: The term “haplotype block” is commonly used in the developing field of haplotype-based
inference methods. We argue that the term should be defined based on the structure
of the Ancestral Recombination Graph (ARG), which contains complete information
on the ancestry of a sample. We use simulated examples to demonstrate key features
of the relationship between haplotype blocks and ancestral structure, emphasizing
the stochasticity of the processes that generate them. Even the simplest cases
of neutrality or of a “hard” selective sweep produce a rich structure, often missed
by commonly used statistics. We highlight a number of novel methods for inferring
haplotype structure, based on the full ARG, or on a sequence of trees, and illustrate
how they can be used to define haplotype blocks using an empirical data set. While
the advent of new, computationally efficient methods makes it possible to apply
these concepts broadly, they (and additional new methods) could benefit from adding
features to explore haplotype blocks, as we define them. Understanding and applying
the concept of the haplotype block will be essential to fully exploit long and
linked-read sequencing technologies.
acknowledgement: 'We thank the Barton group for useful discussion and feedback during
the writing of this article. Comments from Roger Butlin, Molly Schumer''s Group,
the tskit development team, editors and three reviewers greatly improved the manuscript.
Funding was provided by SCAS (Natural Sciences Programme, Knut and Alice Wallenberg
Foundation), an FWF Wittgenstein grant (PT1001Z211), an FWF standalone grant (grant
P 32166), and an ERC Advanced Grant. YFC was supported by the Max Planck Society
and an ERC Proof of Concept Grant #101069216 (HAPLOTAGGING).'
article_processing_charge: Yes (via OA deal)
article_type: original
author:
- first_name: Daria
full_name: Shipilina, Daria
id: 428A94B0-F248-11E8-B48F-1D18A9856A87
last_name: Shipilina
orcid: 0000-0002-1145-9226
- first_name: Arka
full_name: Pal, Arka
id: 6AAB2240-CA9A-11E9-9C1A-D9D1E5697425
last_name: Pal
orcid: 0000-0002-4530-8469
- first_name: Sean
full_name: Stankowski, Sean
id: 43161670-5719-11EA-8025-FABC3DDC885E
last_name: Stankowski
- first_name: Yingguang Frank
full_name: Chan, Yingguang Frank
last_name: Chan
- first_name: Nicholas H
full_name: Barton, Nicholas H
id: 4880FE40-F248-11E8-B48F-1D18A9856A87
last_name: Barton
orcid: 0000-0002-8548-5240
citation:
ama: Shipilina D, Pal A, Stankowski S, Chan YF, Barton NH. On the origin and structure
of haplotype blocks. Molecular Ecology. 2023;32(6):1441-1457. doi:10.1111/mec.16793
apa: Shipilina, D., Pal, A., Stankowski, S., Chan, Y. F., & Barton, N. H. (2023).
On the origin and structure of haplotype blocks. Molecular Ecology. Wiley.
https://doi.org/10.1111/mec.16793
chicago: Shipilina, Daria, Arka Pal, Sean Stankowski, Yingguang Frank Chan, and
Nicholas H Barton. “On the Origin and Structure of Haplotype Blocks.” Molecular
Ecology. Wiley, 2023. https://doi.org/10.1111/mec.16793.
ieee: D. Shipilina, A. Pal, S. Stankowski, Y. F. Chan, and N. H. Barton, “On the
origin and structure of haplotype blocks,” Molecular Ecology, vol. 32,
no. 6. Wiley, pp. 1441–1457, 2023.
ista: Shipilina D, Pal A, Stankowski S, Chan YF, Barton NH. 2023. On the origin
and structure of haplotype blocks. Molecular Ecology. 32(6), 1441–1457.
mla: Shipilina, Daria, et al. “On the Origin and Structure of Haplotype Blocks.”
Molecular Ecology, vol. 32, no. 6, Wiley, 2023, pp. 1441–57, doi:10.1111/mec.16793.
short: D. Shipilina, A. Pal, S. Stankowski, Y.F. Chan, N.H. Barton, Molecular Ecology
32 (2023) 1441–1457.
corr_author: '1'
date_created: 2023-01-12T12:09:17Z
date_published: 2023-03-01T00:00:00Z
date_updated: 2026-04-25T22:30:32Z
day: '01'
ddc:
- '570'
department:
- _id: NiBa
doi: 10.1111/mec.16793
external_id:
isi:
- '000900762000001'
pmid:
- '36433653'
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intvolume: ' 32'
isi: 1
issue: '6'
keyword:
- Genetics
- Ecology
- Evolution
- Behavior and Systematics
language:
- iso: eng
month: '03'
oa: 1
oa_version: Published Version
page: 1441-1457
pmid: 1
project:
- _id: 05959E1C-7A3F-11EA-A408-12923DDC885E
grant_number: P32166
name: Snapdragon Speciation
- _id: 25F42A32-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: Z211
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publication: Molecular Ecology
publication_identifier:
eissn:
- 1365-294X
issn:
- 0962-1083
publication_status: published
publisher: Wiley
quality_controlled: '1'
related_material:
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relation: dissertation_contains
status: public
scopus_import: '1'
status: public
title: On the origin and structure of haplotype blocks
tmp:
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type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
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year: '2023'
...
---
OA_place: publisher
_id: '12491'
abstract:
- lang: eng
text: "The extracellular matrix (ECM) is a hydrated and complex three-dimensional
network consisting of proteins, polysaccharides, and water. It provides structural
scaffolding for the cells embedded within it and is essential in regulating numerous
physiological processes, including cell migration and proliferation, wound healing,
and stem cell fate. \r\nDespite extensive study, detailed structural knowledge
of ECM components in physiologically relevant conditions is still rudimentary.
This is due to methodological limitations in specimen preparation protocols which
are incompatible with keeping large samples, such as the ECM, in their native
state for subsequent imaging. Conventional electron microscopy (EM) techniques
rely on fixation, dehydration, contrasting, and sectioning. This results in the
alteration of a highly hydrated environment and the potential introduction of
artifacts. Other structural biology techniques, such as nuclear magnetic resonance
(NMR) spectroscopy and X-ray crystallography, allow high-resolution analysis of
protein structures but only work on homogenous and purified samples, hence lacking
contextual information. Currently, no approach exists for the ultrastructural
and structural study of extracellular components under native conditions in a
physiological, 3D environment. \r\nIn this thesis, I have developed a workflow
that allows for the ultrastructural analysis of the ECM in near-native conditions
at molecular resolution. The developments I introduced include implementing a
novel specimen preparation workflow for cell-derived matrices (CDMs) to render
them compatible with ion-beam milling and subsequent high-resolution cryo-electron
tomography (ET). \r\nTo this end, I have established protocols to generate CDMs
grown over several weeks on EM grids that are compatible with downstream cryo-EM
sample preparation and imaging techniques. Characterization of these ECMs confirmed
that they contain essential ECM components such as collagen I, collagen VI, and
fibronectin I in high abundance and hence represent a bona fide biologically-relevant
sample. I successfully optimized vitrification of these specimens by testing various
vitrification techniques and cryoprotectants. \r\nIn order to obtain high-resolution
molecular insights into the ultrastructure and organization of CDMs, I established
cryo-focused ion beam scanning electron microscopy (FIBSEM) on these challenging
and complex specimens. I explored different approaches for the creation of thin
cryo-lamellae by FIB milling and succeeded in optimizing the cryo-lift-out technique,
resulting in high-quality lamellae of approximately 200 nm thickness. \r\nHigh-resolution
Cryo-ET of these lamellae revealed for the first time the architecture of native
CDM in the context of matrix-secreting cells. This allowed for the in situ visualization
of fibrillar matrix proteins such as collagen, laying the foundation for future
structural and ultrastructural characterization of these proteins in their near-native
environment. \r\nIn summary, in this thesis, I present a novel workflow that combines
state-of-the-art cryo-EM specimen preparation and imaging technologies to permit
characterization of the ECM, an important tissue component in higher organisms.
This innovative and highly versatile workflow will enable addressing far-reaching
questions on ECM architecture, composition, and reciprocal ECM-cell interactions."
acknowledged_ssus:
- _id: EM-Fac
- _id: LifeSc
- _id: Bio
alternative_title:
- ISTA Thesis
article_processing_charge: No
author:
- first_name: Bettina
full_name: Zens, Bettina
id: 45FD126C-F248-11E8-B48F-1D18A9856A87
last_name: Zens
orcid: 0000-0002-9561-1239
citation:
ama: Zens B. Ultrastructural characterization of natively preserved extracellular
matrix by cryo-electron tomography. 2023. doi:10.15479/at:ista:12491
apa: Zens, B. (2023). Ultrastructural characterization of natively preserved
extracellular matrix by cryo-electron tomography. Institute of Science and
Technology Austria. https://doi.org/10.15479/at:ista:12491
chicago: Zens, Bettina. “Ultrastructural Characterization of Natively Preserved
Extracellular Matrix by Cryo-Electron Tomography.” Institute of Science and Technology
Austria, 2023. https://doi.org/10.15479/at:ista:12491.
ieee: B. Zens, “Ultrastructural characterization of natively preserved extracellular
matrix by cryo-electron tomography,” Institute of Science and Technology Austria,
2023.
ista: Zens B. 2023. Ultrastructural characterization of natively preserved extracellular
matrix by cryo-electron tomography. Institute of Science and Technology Austria.
mla: Zens, Bettina. Ultrastructural Characterization of Natively Preserved Extracellular
Matrix by Cryo-Electron Tomography. Institute of Science and Technology Austria,
2023, doi:10.15479/at:ista:12491.
short: B. Zens, Ultrastructural Characterization of Natively Preserved Extracellular
Matrix by Cryo-Electron Tomography, Institute of Science and Technology Austria,
2023.
corr_author: '1'
date_created: 2023-02-02T14:50:20Z
date_published: 2023-02-02T00:00:00Z
date_updated: 2026-04-07T13:49:23Z
day: '02'
ddc:
- '570'
degree_awarded: PhD
department:
- _id: GradSch
- _id: FlSc
doi: 10.15479/at:ista:12491
file:
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keyword:
- cryo-EM
- cryo-ET
- FIB milling
- method development
- FIBSEM
- extracellular matrix
- ECM
- cell-derived matrices
- CDMs
- cell culture
- high pressure freezing
- HPF
- structural biology
- tomography
- collagen
language:
- iso: eng
month: '02'
oa: 1
oa_version: Published Version
page: '187'
project:
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name: Integrated visual proteomics of reciprocal cell-extracellular matrix interactions
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name: "NÃ\x96-Fonds Preis für die Jungforscherin des Jahres am IST Austria"
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- 978-3-99078-027-5
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: Florian KM
full_name: Schur, Florian KM
id: 48AD8942-F248-11E8-B48F-1D18A9856A87
last_name: Schur
orcid: 0000-0003-4790-8078
title: Ultrastructural characterization of natively preserved extracellular matrix
by cryo-electron tomography
type: dissertation
user_id: ba8df636-2132-11f1-aed0-ed93e2281fdd
year: '2023'
...
---
OA_place: publisher
_id: '13984'
abstract:
- lang: eng
text: "Social insects fight disease using their individual immune systems and the
cooperative\r\nsanitary behaviors of colony members. These social defenses are
well explored against\r\nexternally-infecting pathogens, but little is known about
defense strategies against\r\ninternally-infecting pathogens, such as viruses.
Viruses are ubiquitous and in the last decades\r\nit has become evident that also
many ant species harbor viruses. We present one of the first\r\nstudies addressing
transmission dynamics and collective disease defenses against viruses in\r\nants
on a mechanistic level. I successfully established an experimental ant host –
viral\r\npathogen system as a model for the defense strategies used by social
insects against internal\r\npathogen infections, as outlined in the third chapter.
In particular, we studied how garden ants\r\n(Lasius neglectus) defend themselves
and their colonies against the generalist insect virus\r\nCrPV (cricket paralysis
virus). We chose microinjections of virus directly into the ants’\r\nhemolymph
because it allowed us to use a defined exposure dose. Here we show that this is
a\r\ngood model system, as the virus is replicating and thus infecting the host.
The ants mount a\r\nclear individual immune response against the viral infection,
which is characterized by a\r\nspecific siRNA pattern, namely siRNAs mapping against
the viral genome with a peak of 21\r\nand 22 bp long fragments. The onset of this
immune response is consistent with the timeline\r\nof viral replication that starts
already within two days post injection. The disease manifests in\r\ndecreased
survival over a course of two to three weeks.\r\nRegarding group living, we find
that infected ants show a strong individual immune response,\r\nbut that their
course of disease is little affected by nestmate presence, as described in chapter\r\nfour.
Hence, we do not find social immunity in the context of viral infections in ants.\r\nNestmates,
however, can contract the virus. Using Drosophila S2R+ cells in culture, we\r\nshowed
that 94 % of the nestmates contract active virus within four days of social contact
to\r\nan infected individual. Virus is transmitted in low doses, thus not causing
disease\r\ntransmission within the colony. While virus can be transmitted during
short direct contacts,\r\nwe also assume transmission from deceased ants and show
that the nestmates’ immune\r\nsystem gets activated after contracting a low viral
dose. We find considerable potential for\r\nindirect transmission via the nest
space. Virus is shed to the nest, where it stays viable for one\r\nweek and is
also picked up by other ants. Apart from that, we want to underline the potential\r\nof
ant poison as antiviral agent. We determined that ant poison successfully inactivates
CrPV\r\nin vitro. However, we found no evidence for effective poison use to sanitize
the nest space.\r\nOn the other hand, local application of ant poison by oral
poison uptake, which is part of the\r\nants prophylactic behavioral repertoire,
probably contributes to keeping the gut of each\r\nindividual sanitized. We hypothesize
that oral poison uptake might be the reason why we did\r\nnot find viable virus
in the trophallactic fluid.\r\nThe fifth chapter encompasses preliminary data
on potential social immunization. However,\r\nour experiments do not confirm an
actual survival benefit for the nestmates upon pathogen\r\nchallenge under the
given experimental settings. Nevertheless, we do not want to rule out the\r\npossibility
for nestmate immunization, but rather emphasize that considering different\r\nexperimental
timelines and viral doses would provide a multitude of options for follow-up\r\nexperiments.\r\nIn
conclusion, we find that prophylactic individual behaviors, such as oral poison
uptake,\r\nmight play a role in preventing viral disease transmission. Compared
to colony defense\r\nagainst external pathogens, internal pathogen infections
require a stronger component of\r\nindividual physiological immunity than behavioral
social immunity, yet could still lead to\r\ncollective protection."
acknowledged_ssus:
- _id: LifeSc
alternative_title:
- ISTA Thesis
article_processing_charge: No
author:
- first_name: Anna
full_name: Franschitz, Anna
id: 480826C8-F248-11E8-B48F-1D18A9856A87
last_name: Franschitz
citation:
ama: Franschitz A. Individual and social immunity against viral infections in ants.
2023. doi:10.15479/at:ista:13984
apa: Franschitz, A. (2023). Individual and social immunity against viral infections
in ants. Institute of Science and Technology Austria. https://doi.org/10.15479/at:ista:13984
chicago: Franschitz, Anna. “Individual and Social Immunity against Viral Infections
in Ants.” Institute of Science and Technology Austria, 2023. https://doi.org/10.15479/at:ista:13984.
ieee: A. Franschitz, “Individual and social immunity against viral infections in
ants,” Institute of Science and Technology Austria, 2023.
ista: Franschitz A. 2023. Individual and social immunity against viral infections
in ants. Institute of Science and Technology Austria.
mla: Franschitz, Anna. Individual and Social Immunity against Viral Infections
in Ants. Institute of Science and Technology Austria, 2023, doi:10.15479/at:ista:13984.
short: A. Franschitz, Individual and Social Immunity against Viral Infections in
Ants, Institute of Science and Technology Austria, 2023.
corr_author: '1'
date_created: 2023-08-08T15:33:29Z
date_published: 2023-08-08T00:00:00Z
date_updated: 2026-04-07T13:51:29Z
day: '08'
ddc:
- '570'
- '577'
degree_awarded: PhD
department:
- _id: GradSch
- _id: SyCr
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month: '08'
oa: 1
oa_version: Published Version
page: '89'
publication_identifier:
isbn:
- 978-3-99078-034-3
issn:
- 2663-337X
publication_status: published
publisher: Institute of Science and Technology Austria
status: public
supervisor:
- first_name: Sylvia
full_name: Cremer, Sylvia
id: 2F64EC8C-F248-11E8-B48F-1D18A9856A87
last_name: Cremer
orcid: 0000-0002-2193-3868
title: Individual and social immunity against viral infections in ants
type: dissertation
user_id: ba8df636-2132-11f1-aed0-ed93e2281fdd
year: '2023'
...