---
_id: '13136'
abstract:
- lang: eng
text: Despite its fundamental importance for development, the question of how organs
achieve their correct size and shape is poorly understood. This complex process
requires coordination between the generation of cell mass and the morphogenetic
mechanisms that sculpt tissues. These processes are regulated by morphogen signalling
pathways and mechanical forces. Yet, in many systems, it is unclear how biochemical
and mechanical signalling are quantitatively interpreted to determine the behaviours
of individual cells and how they contribute to growth and morphogenesis at the
tissue scale. In this review, we discuss the development of the vertebrate neural
tube and somites as an example of the state of knowledge, as well as the challenges
in understanding the mechanisms of tissue size control in vertebrate organogenesis.
We highlight how the recent advances in stem cell differentiation and organoid
approaches can be harnessed to provide new insights into this question.
acknowledgement: 'We thank J. Briscoe for comments on the manuscript. Work in the
AK lab is supported by ISTA, the European Research Council under Horizon Europe:
grant 101044579, and Austrian Science Fund (FWF): F78 (Stem Cell Modulation). SR
is supported by Gesellschaft für Forschungsförderung Niederösterreich m.b.H. fellowship
SC19-011.'
article_number: '100459'
article_processing_charge: Yes (via OA deal)
article_type: original
author:
- first_name: Thomas
full_name: Minchington, Thomas
id: 7d1648cb-19e9-11eb-8e7a-f8c037fb3e3f
last_name: Minchington
- first_name: Stefanie
full_name: Rus, Stefanie
id: 4D9EC9B6-F248-11E8-B48F-1D18A9856A87
last_name: Rus
orcid: 0000-0001-8703-1093
- first_name: Anna
full_name: Kicheva, Anna
id: 3959A2A0-F248-11E8-B48F-1D18A9856A87
last_name: Kicheva
orcid: 0000-0003-4509-4998
citation:
ama: Minchington T, Rus S, Kicheva A. Control of tissue dimensions in the developing
neural tube and somites. Current Opinion in Systems Biology. 2023;35. doi:10.1016/j.coisb.2023.100459
apa: Minchington, T., Rus, S., & Kicheva, A. (2023). Control of tissue dimensions
in the developing neural tube and somites. Current Opinion in Systems Biology.
Elsevier. https://doi.org/10.1016/j.coisb.2023.100459
chicago: Minchington, Thomas, Stefanie Rus, and Anna Kicheva. “Control of Tissue
Dimensions in the Developing Neural Tube and Somites.” Current Opinion in Systems
Biology. Elsevier, 2023. https://doi.org/10.1016/j.coisb.2023.100459.
ieee: T. Minchington, S. Rus, and A. Kicheva, “Control of tissue dimensions in the
developing neural tube and somites,” Current Opinion in Systems Biology,
vol. 35. Elsevier, 2023.
ista: Minchington T, Rus S, Kicheva A. 2023. Control of tissue dimensions in the
developing neural tube and somites. Current Opinion in Systems Biology. 35, 100459.
mla: Minchington, Thomas, et al. “Control of Tissue Dimensions in the Developing
Neural Tube and Somites.” Current Opinion in Systems Biology, vol. 35,
100459, Elsevier, 2023, doi:10.1016/j.coisb.2023.100459.
short: T. Minchington, S. Rus, A. Kicheva, Current Opinion in Systems Biology 35
(2023).
corr_author: '1'
date_created: 2023-06-18T22:00:46Z
date_published: 2023-09-01T00:00:00Z
date_updated: 2026-04-23T22:30:52Z
day: '01'
ddc:
- '570'
department:
- _id: AnKi
doi: 10.1016/j.coisb.2023.100459
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month: '09'
oa: 1
oa_version: Published Version
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grant_number: '101044579'
name: Mechanisms of tissue size regulation in spinal cord development
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grant_number: F7802
name: Stem Cell Modulation in Neural Development and Regeneration/ P02-Morphogen
control of growth and pattern in the spinal cord
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grant_number: SC19-011
name: The regulatory logic of pattern formation in the vertebrate dorsal neural
tube
publication: Current Opinion in Systems Biology
publication_identifier:
eissn:
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publication_status: published
publisher: Elsevier
quality_controlled: '1'
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title: Control of tissue dimensions in the developing neural tube and somites
tmp:
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short: CC BY-NC-ND (4.0)
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 35
year: '2023'
...
---
_id: '12837'
abstract:
- lang: eng
text: As developing tissues grow in size and undergo morphogenetic changes, their
material properties may be altered. Such changes result from tension dynamics
at cell contacts or cellular jamming. Yet, in many cases, the cellular mechanisms
controlling the physical state of growing tissues are unclear. We found that at
early developmental stages, the epithelium in the developing mouse spinal cord
maintains both high junctional tension and high fluidity. This is achieved via
a mechanism in which interkinetic nuclear movements generate cell area dynamics
that drive extensive cell rearrangements. Over time, the cell proliferation rate
declines, effectively solidifying the tissue. Thus, unlike well-studied jamming
transitions, the solidification uncovered here resembles a glass transition that
depends on the dynamical stresses generated by proliferation and differentiation.
Our finding that the fluidity of developing epithelia is linked to interkinetic
nuclear movements and the dynamics of growth is likely to be relevant to multiple
developing tissues.
acknowledgement: 'We thank S. Hippenmeyer for the reagents and C. P. Heisenberg, J.
Briscoe and K. Page for comments on the manuscript. This work was supported by IST
Austria; the European Research Council under Horizon 2020 research and innovation
programme grant no. 680037 and Horizon Europe grant 101044579 (A.K.); Austrian Science
Fund (FWF): F78 (Stem Cell Modulation) (A.K.); ISTFELLOW postdoctoral program (A.S.);
Narodowe Centrum Nauki, Poland SONATA, 2017/26/D/NZ2/00454 (M.Z.); and the Polish
National Agency for Academic Exchange (M.Z.).'
article_processing_charge: No
article_type: original
author:
- first_name: Laura
full_name: Bocanegra, Laura
id: 4896F754-F248-11E8-B48F-1D18A9856A87
last_name: Bocanegra
- first_name: Amrita
full_name: Singh, Amrita
id: 76250f9f-3a21-11eb-9a80-a6180a0d7958
last_name: Singh
- first_name: Edouard B
full_name: Hannezo, Edouard B
id: 3A9DB764-F248-11E8-B48F-1D18A9856A87
last_name: Hannezo
orcid: 0000-0001-6005-1561
- first_name: Marcin P
full_name: Zagórski, Marcin P
id: 343DA0DC-F248-11E8-B48F-1D18A9856A87
last_name: Zagórski
orcid: 0000-0001-7896-7762
- first_name: Anna
full_name: Kicheva, Anna
id: 3959A2A0-F248-11E8-B48F-1D18A9856A87
last_name: Kicheva
orcid: 0000-0003-4509-4998
citation:
ama: Bocanegra L, Singh A, Hannezo EB, Zagórski MP, Kicheva A. Cell cycle dynamics
control fluidity of the developing mouse neuroepithelium. Nature Physics.
2023;19:1050-1058. doi:10.1038/s41567-023-01977-w
apa: Bocanegra, L., Singh, A., Hannezo, E. B., Zagórski, M. P., & Kicheva, A.
(2023). Cell cycle dynamics control fluidity of the developing mouse neuroepithelium.
Nature Physics. Springer Nature. https://doi.org/10.1038/s41567-023-01977-w
chicago: Bocanegra, Laura, Amrita Singh, Edouard B Hannezo, Marcin P Zagórski, and
Anna Kicheva. “Cell Cycle Dynamics Control Fluidity of the Developing Mouse Neuroepithelium.”
Nature Physics. Springer Nature, 2023. https://doi.org/10.1038/s41567-023-01977-w.
ieee: L. Bocanegra, A. Singh, E. B. Hannezo, M. P. Zagórski, and A. Kicheva, “Cell
cycle dynamics control fluidity of the developing mouse neuroepithelium,” Nature
Physics, vol. 19. Springer Nature, pp. 1050–1058, 2023.
ista: Bocanegra L, Singh A, Hannezo EB, Zagórski MP, Kicheva A. 2023. Cell cycle
dynamics control fluidity of the developing mouse neuroepithelium. Nature Physics.
19, 1050–1058.
mla: Bocanegra, Laura, et al. “Cell Cycle Dynamics Control Fluidity of the Developing
Mouse Neuroepithelium.” Nature Physics, vol. 19, Springer Nature, 2023,
pp. 1050–58, doi:10.1038/s41567-023-01977-w.
short: L. Bocanegra, A. Singh, E.B. Hannezo, M.P. Zagórski, A. Kicheva, Nature Physics
19 (2023) 1050–1058.
corr_author: '1'
date_created: 2023-04-16T22:01:09Z
date_published: 2023-07-01T00:00:00Z
date_updated: 2026-04-23T22:30:54Z
day: '01'
ddc:
- '570'
department:
- _id: EdHa
- _id: AnKi
doi: 10.1038/s41567-023-01977-w
ec_funded: 1
external_id:
isi:
- '000964029300003'
pmid:
- '37456593'
file:
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creator: dernst
date_created: 2023-10-04T11:13:28Z
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file_id: '14392'
file_name: 2023_NaturePhysics_Boncanegra.pdf
file_size: 5532285
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isi: 1
language:
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month: '07'
oa: 1
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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
- _id: 25681D80-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '291734'
name: International IST Postdoc Fellowship Programme
publication: Nature Physics
publication_identifier:
eissn:
- 1745-2481
issn:
- 1745-2473
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
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title: Cell cycle dynamics control fluidity of the developing mouse neuroepithelium
tmp:
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legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 19
year: '2023'
...
---
OA_place: publisher
_id: '13081'
abstract:
- lang: eng
text: During development, tissues undergo changes in size and shape to form functional
organs. Distinct cellular processes such as cell division and cell rearrangements
underlie tissue morphogenesis. Yet how the distinct processes are controlled and
coordinated, and how they contribute to morphogenesis is poorly understood. In
our study, we addressed these questions using the developing mouse neural tube.
This epithelial organ transforms from a flat epithelial sheet to an epithelial
tube while increasing in size and undergoing morpho-gen-mediated patterning. The
extent and mechanism of neural progenitor rearrangement within the developing
mouse neuroepithelium is unknown. To investigate this, we per-formed high resolution
lineage tracing analysis to quantify the extent of epithelial rear-rangement at
different stages of neural tube development. We quantitatively described the relationship
between apical cell size with cell cycle dependent interkinetic nuclear migra-tions
(IKNM) and performed high cellular resolution live imaging of the neuroepithelium
to study the dynamics of junctional remodeling. Furthermore, developed a vertex
model of the neuroepithelium to investigate the quantitative contribution of cell
proliferation, cell differentiation and mechanical properties to the epithelial
rearrangement dynamics and validated the model predictions through functional
experiments. Our analysis revealed that at early developmental stages, the apical
cell area kinetics driven by IKNM induce high lev-els of cell rearrangements in
a regime of high junctional tension and contractility. After E9.5, there is a
sharp decline in the extent of cell rearrangements, suggesting that the epi-thelium
transitions from a fluid-like to a solid-like state. We found that this transition
is regulated by the growth rate of the tissue, rather than by changes in cell-cell
adhesion and contractile forces. Overall, our study provides a quantitative description
of the relationship between tissue growth, cell cycle dynamics, epithelia rearrangements
and the emergent tissue material properties, and novel insights on how epithelial
cell dynamics influences tissue morphogenesis.
acknowledged_ssus:
- _id: Bio
- _id: LifeSc
alternative_title:
- ISTA Thesis
article_processing_charge: No
author:
- first_name: Laura
full_name: Bocanegra, Laura
id: 4896F754-F248-11E8-B48F-1D18A9856A87
last_name: Bocanegra
citation:
ama: Bocanegra L. Epithelial dynamics during mouse neural tube development. 2023.
doi:10.15479/at:ista:13081
apa: Bocanegra, L. (2023). Epithelial dynamics during mouse neural tube development.
Institute of Science and Technology Austria. https://doi.org/10.15479/at:ista:13081
chicago: Bocanegra, Laura. “Epithelial Dynamics during Mouse Neural Tube Development.”
Institute of Science and Technology Austria, 2023. https://doi.org/10.15479/at:ista:13081.
ieee: L. Bocanegra, “Epithelial dynamics during mouse neural tube development,”
Institute of Science and Technology Austria, 2023.
ista: Bocanegra L. 2023. Epithelial dynamics during mouse neural tube development.
Institute of Science and Technology Austria.
mla: Bocanegra, Laura. Epithelial Dynamics during Mouse Neural Tube Development.
Institute of Science and Technology Austria, 2023, doi:10.15479/at:ista:13081.
short: L. Bocanegra, Epithelial Dynamics during Mouse Neural Tube Development, Institute
of Science and Technology Austria, 2023.
corr_author: '1'
date_created: 2023-05-23T19:10:42Z
date_published: 2023-05-23T00:00:00Z
date_updated: 2026-04-14T09:50:54Z
day: '23'
ddc:
- '570'
degree_awarded: PhD
department:
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- _id: AnKi
doi: 10.15479/at:ista:13081
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relation: part_of_dissertation
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status: public
supervisor:
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full_name: Kicheva, Anna
id: 3959A2A0-F248-11E8-B48F-1D18A9856A87
last_name: Kicheva
orcid: 0000-0003-4509-4998
title: Epithelial dynamics during mouse neural tube development
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...
---
_id: '14613'
abstract:
- lang: eng
text: 'Many insects carry an ancient X chromosome - the Drosophila Muller element
F - that likely predates their origin. Interestingly, the X has undergone turnover
in multiple fly species (Diptera) after being conserved for more than 450 MY.
The long evolutionary distance between Diptera and other sequenced insect clades
makes it difficult to infer what could have contributed to this sudden increase
in rate of turnover. Here, we produce the first genome and transcriptome of a
long overlooked sister-order to Diptera: Mecoptera. We compare the scorpionfly
Panorpa cognata X-chromosome gene content, expression, and structure, to that
of several dipteran species as well as more distantly-related insect orders (Orthoptera
and Blattodea). We find high conservation of gene content between the mecopteran
X and the dipteran Muller F element, as well as several shared biological features,
such as the presence of dosage compensation and a low amount of genetic diversity,
consistent with a low recombination rate. However, the two homologous X chromosomes
differ strikingly in their size and number of genes they carry. Our results therefore
support a common ancestry of the mecopteran and ancestral dipteran X chromosomes,
and suggest that Muller element F shrank in size and gene content after the split
of Diptera and Mecoptera, which may have contributed to its turnover in dipteran
insects.'
acknowledged_ssus:
- _id: ScienComp
acknowledgement: "We thank the Vicoso lab for their assistance with specimen collection,
and Tim Connallon for valuable comments and suggestions on earlier versions of the
manuscript. Computational resources and support were provided by the Scientific
Computing unit at the ISTA. This research was supported by grants from the Austrian
Science Foundation to C.L.\r\n(FWF ESP 39), and to B.V. (FWF SFB F88-10)."
article_number: msad245
article_processing_charge: Yes
article_type: original
author:
- first_name: Clementine
full_name: Lasne, Clementine
id: 02225f57-50d2-11eb-9ed8-8c92b9a34237
last_name: Lasne
orcid: 0000-0002-1197-8616
- first_name: Marwan N
full_name: Elkrewi, Marwan N
id: 0B46FACA-A8E1-11E9-9BD3-79D1E5697425
last_name: Elkrewi
orcid: 0000-0002-5328-7231
- first_name: Melissa A
full_name: Toups, Melissa A
id: 4E099E4E-F248-11E8-B48F-1D18A9856A87
last_name: Toups
orcid: 0000-0002-9752-7380
- first_name: Lorena Alexandra
full_name: Layana Franco, Lorena Alexandra
id: 02814589-eb8f-11eb-b029-a70074f3f18f
last_name: Layana Franco
orcid: 0000-0002-1253-6297
- first_name: Ariana
full_name: Macon, Ariana
id: 2A0848E2-F248-11E8-B48F-1D18A9856A87
last_name: Macon
- first_name: Beatriz
full_name: Vicoso, Beatriz
id: 49E1C5C6-F248-11E8-B48F-1D18A9856A87
last_name: Vicoso
orcid: 0000-0002-4579-8306
citation:
ama: Lasne C, Elkrewi MN, Toups MA, Layana Franco LA, Macon A, Vicoso B. The scorpionfly
(Panorpa cognata) genome highlights conserved and derived features of the peculiar
dipteran X chromosome. Molecular Biology and Evolution. 2023;40(12). doi:10.1093/molbev/msad245
apa: Lasne, C., Elkrewi, M. N., Toups, M. A., Layana Franco, L. A., Macon, A., &
Vicoso, B. (2023). The scorpionfly (Panorpa cognata) genome highlights conserved
and derived features of the peculiar dipteran X chromosome. Molecular Biology
and Evolution. Oxford University Press. https://doi.org/10.1093/molbev/msad245
chicago: Lasne, Clementine, Marwan N Elkrewi, Melissa A Toups, Lorena Alexandra
Layana Franco, Ariana Macon, and Beatriz Vicoso. “The Scorpionfly (Panorpa Cognata)
Genome Highlights Conserved and Derived Features of the Peculiar Dipteran X Chromosome.”
Molecular Biology and Evolution. Oxford University Press, 2023. https://doi.org/10.1093/molbev/msad245.
ieee: C. Lasne, M. N. Elkrewi, M. A. Toups, L. A. Layana Franco, A. Macon, and B.
Vicoso, “The scorpionfly (Panorpa cognata) genome highlights conserved and derived
features of the peculiar dipteran X chromosome,” Molecular Biology and Evolution,
vol. 40, no. 12. Oxford University Press, 2023.
ista: Lasne C, Elkrewi MN, Toups MA, Layana Franco LA, Macon A, Vicoso B. 2023.
The scorpionfly (Panorpa cognata) genome highlights conserved and derived features
of the peculiar dipteran X chromosome. Molecular Biology and Evolution. 40(12),
msad245.
mla: Lasne, Clementine, et al. “The Scorpionfly (Panorpa Cognata) Genome Highlights
Conserved and Derived Features of the Peculiar Dipteran X Chromosome.” Molecular
Biology and Evolution, vol. 40, no. 12, msad245, Oxford University Press,
2023, doi:10.1093/molbev/msad245.
short: C. Lasne, M.N. Elkrewi, M.A. Toups, L.A. Layana Franco, A. Macon, B. Vicoso,
Molecular Biology and Evolution 40 (2023).
corr_author: '1'
date_created: 2023-11-27T16:14:37Z
date_published: 2023-12-01T00:00:00Z
date_updated: 2026-04-23T22:31:00Z
day: '01'
ddc:
- '570'
department:
- _id: BeVi
doi: 10.1093/molbev/msad245
external_id:
isi:
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pmid:
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checksum: 47c1c72fb499f26ea52d216b242208c8
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intvolume: ' 40'
isi: 1
issue: '12'
keyword:
- Genetics
- Molecular Biology
- Ecology
- Evolution
- Behavior and Systematics
language:
- iso: eng
month: '12'
oa: 1
oa_version: Published Version
pmid: 1
project:
- _id: 34ae1506-11ca-11ed-8bc3-c14f4c474396
grant_number: F8810
name: The highjacking of meiosis for asexual reproduction
- _id: ebb230e0-77a9-11ec-83b8-87a37e0241d3
grant_number: ESP39 49461
name: Mechanisms and Evolution of Reproductive Plasticity
publication: Molecular Biology and Evolution
publication_identifier:
eissn:
- 1537-1719
issn:
- 0737-4038
publication_status: published
publisher: Oxford University Press
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short: CC BY (4.0)
type: journal_article
user_id: 317138e5-6ab7-11ef-aa6d-ffef3953e345
volume: 40
year: '2023'
...
---
APC_amount: 6228 EUR
DOAJ_listed: '1'
OA_place: publisher
OA_type: gold
_id: '13200'
abstract:
- lang: eng
text: Recent quantum technologies have established precise quantum control of various
microscopic systems using electromagnetic waves. Interfaces based on cryogenic
cavity electro-optic systems are particularly promising, due to the direct interaction
between microwave and optical fields in the quantum regime. Quantum optical control
of superconducting microwave circuits has been precluded so far due to the weak
electro-optical coupling as well as quasi-particles induced by the pump laser.
Here we report the coherent control of a superconducting microwave cavity using
laser pulses in a multimode electro-optical device at millikelvin temperature
with near-unity cooperativity. Both the stationary and instantaneous responses
of the microwave and optical modes comply with the coherent electro-optical interaction,
and reveal only minuscule amount of excess back-action with an unanticipated time
delay. Our demonstration enables wide ranges of applications beyond quantum transductions,
from squeezing and quantum non-demolition measurements of microwave fields, to
entanglement generation and hybrid quantum networks.
acknowledgement: This work was supported by the European Research Council under grant
agreement no. 758053 (ERC StG QUNNECT), the European Union’s Horizon 2020 research
and innovation program under grant agreement no. 899354 (FETopen SuperQuLAN), and
the Austrian Science Fund (FWF) through BeyondC (F7105). L.Q. acknowledges generous
support from the ISTFELLOW programme. W.H. is the recipient of an ISTplus postdoctoral
fellowship with funding from the European Union’s Horizon 2020 research and innovation
program under the Marie Skłodowska-Curie grant agreement no. 754411. G.A. is the
recipient of a DOC fellowship of the Austrian Academy of Sciences at IST Austria.
article_number: '3784'
article_processing_charge: Yes
article_type: original
arxiv: 1
author:
- first_name: Liu
full_name: Qiu, Liu
id: 45e99c0d-1eb1-11eb-9b96-ed8ab2983cac
last_name: Qiu
orcid: 0000-0003-4345-4267
- first_name: Rishabh
full_name: Sahu, Rishabh
id: 47D26E34-F248-11E8-B48F-1D18A9856A87
last_name: Sahu
orcid: 0000-0001-6264-2162
- 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: Johannes M
full_name: Fink, Johannes M
id: 4B591CBA-F248-11E8-B48F-1D18A9856A87
last_name: Fink
orcid: 0000-0001-8112-028X
citation:
ama: Qiu L, Sahu R, Hease WJ, Arnold GM, Fink JM. Coherent optical control of a
superconducting microwave cavity via electro-optical dynamical back-action. Nature
Communications. 2023;14. doi:10.1038/s41467-023-39493-3
apa: Qiu, L., Sahu, R., Hease, W. J., Arnold, G. M., & Fink, J. M. (2023). Coherent
optical control of a superconducting microwave cavity via electro-optical dynamical
back-action. Nature Communications. Nature Research. https://doi.org/10.1038/s41467-023-39493-3
chicago: Qiu, Liu, Rishabh Sahu, William J Hease, Georg M Arnold, and Johannes M
Fink. “Coherent Optical Control of a Superconducting Microwave Cavity via Electro-Optical
Dynamical Back-Action.” Nature Communications. Nature Research, 2023. https://doi.org/10.1038/s41467-023-39493-3.
ieee: L. Qiu, R. Sahu, W. J. Hease, G. M. Arnold, and J. M. Fink, “Coherent optical
control of a superconducting microwave cavity via electro-optical dynamical back-action,”
Nature Communications, vol. 14. Nature Research, 2023.
ista: Qiu L, Sahu R, Hease WJ, Arnold GM, Fink JM. 2023. Coherent optical control
of a superconducting microwave cavity via electro-optical dynamical back-action.
Nature Communications. 14, 3784.
mla: Qiu, Liu, et al. “Coherent Optical Control of a Superconducting Microwave Cavity
via Electro-Optical Dynamical Back-Action.” Nature Communications, vol.
14, 3784, Nature Research, 2023, doi:10.1038/s41467-023-39493-3.
short: L. Qiu, R. Sahu, W.J. Hease, G.M. Arnold, J.M. Fink, Nature Communications
14 (2023).
corr_author: '1'
date_created: 2023-07-09T22:01:11Z
date_published: 2023-06-24T00:00:00Z
date_updated: 2026-04-23T22:31:01Z
day: '24'
ddc:
- '000'
department:
- _id: JoFi
doi: 10.1038/s41467-023-39493-3
ec_funded: 1
external_id:
arxiv:
- '2210.12443'
isi:
- '001018100800002'
pmid:
- '37355691'
file:
- access_level: open_access
checksum: ec7ccd2c08f90d59cab302fd0d7776a4
content_type: application/pdf
creator: alisjak
date_created: 2023-07-10T10:10:54Z
date_updated: 2023-07-10T10:10:54Z
file_id: '13206'
file_name: 2023_NatureComms_Qiu.pdf
file_size: 1349134
relation: main_file
success: 1
file_date_updated: 2023-07-10T10:10:54Z
has_accepted_license: '1'
intvolume: ' 14'
isi: 1
language:
- iso: eng
month: '06'
oa: 1
oa_version: Published Version
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: bdb108fd-d553-11ed-ba76-83dc74a9864f
grant_number: F07105
name: QUANTUM INFORMATION SYSTEMS BEYOND CLASSICAL CAPABILITIES / P5- Integration
of Superconducting Quantum Circuits
- _id: 260C2330-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '754411'
name: ISTplus - Postdoctoral Fellowships
- _id: 25681D80-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '291734'
name: International IST Postdoc Fellowship Programme
- _id: 2671EB66-B435-11E9-9278-68D0E5697425
name: Coherent on-chip conversion of superconducting qubit signals from microwaves
to optical frequencies
- _id: 3AC91DDA-15DF-11EA-824D-93A3E7B544D1
call_identifier: FWF
name: FWF Open Access Fund
publication: Nature Communications
publication_identifier:
eissn:
- 2041-1723
publication_status: published
publisher: Nature Research
quality_controlled: '1'
related_material:
record:
- id: '18871'
relation: dissertation_contains
status: public
scopus_import: '1'
status: public
title: Coherent optical control of a superconducting microwave cavity via electro-optical
dynamical back-action
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
year: '2023'
...
---
OA_place: repository
_id: '18953'
abstract:
- lang: eng
text: The rapid development of superconducting quantum hardware is expected to run
into significant I/O restrictions due to the need for large-scale error correction
in a cryogenic environment. Classical data centers rely on fiber-optic interconnects
to remove similar networking bottlenecks and to allow for reconfigurable, software-defined
infrastructures. In the same spirit, ultra-cold electro-optic links have been
proposed and used to generate qubit control signals, or to replace cryogenic readout
electronics. So far, the latter suffered from either low efficiency, low bandwidth
and the need for additional microwave drives, or breaking of Cooper pairs and
qubit states. In this work we realize electro-optic microwave photonics at millikelvin
temperatures to implement a radio-over-fiber qubit readout that does not require
any active or passive cryogenic microwave equipment. We demonstrate all-optical
single-shot-readout by means of the Jaynes-Cummings nonlinearity in a circulator-free
readout scheme. Importantly, we do not observe any direct radiation impact on
the qubit state as verified with high-fidelity quantum-non-demolition measurements
despite the absence of shielding elements. This compatibility between superconducting
circuits and telecom wavelength light is not only a prerequisite to establish
modular quantum networks, it is also relevant for multiplexed readout of superconducting
photon detectors and classical superconducting logic. Moreover, this experiment
showcases the potential of electro-optic radiometry in harsh environments - an
electronics-free sensing principle that extends into the THz regime with applications
in radio astronomy, planetary missions and earth observation.
acknowledgement: "We thank F. Hassani and M. Zemlicka for assistance\r\nwith qubit
design and high power readout respectively,\r\nand P. Winkel and I. Pop at KIT for
providing the JPA.\r\nThis work was supported by the European Research\r\nCouncil
under grant agreement no. 758053 (ERC StG\r\nQUNNECT) and no. 101089099 (ERC CoG
cQEO), the\r\nEuropean Union’s Horizon 2020 research and innovation\r\nprogram under
grant agreement no. 899354 (FETopen\r\nSuperQuLAN) and the Austrian Science Fund
(FWF)\r\nthrough BeyondC (grant no. F7105). L.Q. acknowledges\r\ngenerous support
from the ISTFELLOW programme\r\nand G.A. is the recipient of a DOC fellowship of
the\r\nAustrian Academy of Sciences at IST Austria."
article_processing_charge: No
arxiv: 1
author:
- 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: Thomas
full_name: Werner, Thomas
id: 1fcd8497-dba3-11ea-a45e-c6fbd715f7c7
last_name: Werner
orcid: 0009-0001-2346-5236
- first_name: Rishabh
full_name: Sahu, Rishabh
id: 47D26E34-F248-11E8-B48F-1D18A9856A87
last_name: Sahu
orcid: 0000-0001-6264-2162
- first_name: Lucky
full_name: Kapoor, Lucky
id: 84b9700b-15b2-11ec-abd3-831089e67615
last_name: Kapoor
orcid: 0000-0001-8319-2148
- first_name: Liu
full_name: Qiu, Liu
id: 45e99c0d-1eb1-11eb-9b96-ed8ab2983cac
last_name: Qiu
orcid: 0000-0003-4345-4267
- 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: Arnold GM, Werner T, Sahu R, Kapoor L, Qiu L, Fink JM. All-optical single-shot
readout of a superconducting qubit. arXiv. doi:10.48550/ARXIV.2310.16817
apa: Arnold, G. M., Werner, T., Sahu, R., Kapoor, L., Qiu, L., & Fink, J. M.
(n.d.). All-optical single-shot readout of a superconducting qubit. arXiv.
https://doi.org/10.48550/ARXIV.2310.16817
chicago: Arnold, Georg M, Thomas Werner, Rishabh Sahu, Lucky Kapoor, Liu Qiu, and
Johannes M Fink. “All-Optical Single-Shot Readout of a Superconducting Qubit.”
ArXiv, n.d. https://doi.org/10.48550/ARXIV.2310.16817.
ieee: G. M. Arnold, T. Werner, R. Sahu, L. Kapoor, L. Qiu, and J. M. Fink, “All-optical
single-shot readout of a superconducting qubit,” arXiv. .
ista: Arnold GM, Werner T, Sahu R, Kapoor L, Qiu L, Fink JM. All-optical single-shot
readout of a superconducting qubit. arXiv, 10.48550/ARXIV.2310.16817.
mla: Arnold, Georg M., et al. “All-Optical Single-Shot Readout of a Superconducting
Qubit.” ArXiv, doi:10.48550/ARXIV.2310.16817.
short: G.M. Arnold, T. Werner, R. Sahu, L. Kapoor, L. Qiu, J.M. Fink, ArXiv (n.d.).
corr_author: '1'
date_created: 2025-01-29T11:11:34Z
date_published: 2023-10-25T00:00:00Z
date_updated: 2026-04-23T22:31:01Z
day: '25'
department:
- _id: JoFi
doi: 10.48550/ARXIV.2310.16817
ec_funded: 1
external_id:
arxiv:
- '2310.16817'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.48550/arXiv.2310.16817
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: bdadfa0d-d553-11ed-ba76-fb85edbd456a
grant_number: '101089099'
name: 'Cavity Quantum Electro Optics: Microwave photonics with nonclassical states'
- _id: 9B868D20-BA93-11EA-9121-9846C619BF3A
call_identifier: H2020
grant_number: '899354'
name: Quantum Local Area Networks with Superconducting Qubits
- _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: arXiv
publication_status: draft
related_material:
record:
- id: '19073'
relation: later_version
status: public
- id: '18871'
relation: dissertation_contains
status: public
status: public
title: All-optical single-shot readout of a superconducting qubit
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: preprint
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
year: '2023'
...
---
_id: '13117'
abstract:
- lang: eng
text: The ability to control the direction of scattered light is crucial to provide
flexibility and scalability for a wide range of on-chip applications, such as
integrated photonics, quantum information processing, and nonlinear optics. Tunable
directionality can be achieved by applying external magnetic fields that modify
optical selection rules, by using nonlinear effects, or interactions with vibrations.
However, these approaches are less suitable to control microwave photon propagation
inside integrated superconducting quantum devices. Here, we demonstrate on-demand
tunable directional scattering based on two periodically modulated transmon qubits
coupled to a transmission line at a fixed distance. By changing the relative phase
between the modulation tones, we realize unidirectional forward or backward photon
scattering. Such an in-situ switchable mirror represents a versatile tool for
intra- and inter-chip microwave photonic processors. In the future, a lattice
of qubits can be used to realize topological circuits that exhibit strong nonreciprocity
or chirality.
acknowledged_ssus:
- _id: M-Shop
- _id: NanoFab
acknowledgement: The authors thank W.D. Oliver for discussions, L. Drmic and P. Zielinski
for software development, and the MIBA workshop and the IST nanofabrication facility
for technical support. This work was supported by the Austrian Science Fund (FWF)
through BeyondC (F7105) and IST Austria. E.R. is the recipient of a DOC fellowship
of the Austrian Academy of Sciences at IST Austria. J.M.F. and M.Z. acknowledge
support from the European Research Council under grant agreement No 758053 (ERC
StG QUNNECT) and a NOMIS foundation research grant. The work of A.N.P. and A.V.P.
has been supported by the Russian Science Foundation under the grant No 20-12-00194.
article_number: '2998'
article_processing_charge: No
article_type: original
arxiv: 1
author:
- first_name: Elena
full_name: Redchenko, Elena
id: 2C21D6E8-F248-11E8-B48F-1D18A9856A87
last_name: Redchenko
- first_name: Alexander V.
full_name: Poshakinskiy, Alexander V.
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 N.
full_name: Poddubny, Alexander N.
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 AV, Sett R, Zemlicka M, Poddubny AN, Fink JM. Tunable
directional photon scattering from a pair of superconducting qubits. Nature
Communications. 2023;14. doi:10.1038/s41467-023-38761-6
apa: Redchenko, E., Poshakinskiy, A. V., Sett, R., Zemlicka, M., Poddubny, A. N.,
& Fink, J. M. (2023). Tunable directional photon scattering from a pair of
superconducting qubits. Nature Communications. Springer Nature. https://doi.org/10.1038/s41467-023-38761-6
chicago: Redchenko, Elena, Alexander V. Poshakinskiy, Riya Sett, Martin Zemlicka,
Alexander N. Poddubny, and Johannes M Fink. “Tunable Directional Photon Scattering
from a Pair of Superconducting Qubits.” Nature Communications. Springer
Nature, 2023. https://doi.org/10.1038/s41467-023-38761-6.
ieee: E. Redchenko, A. V. Poshakinskiy, R. Sett, M. Zemlicka, A. N. Poddubny, and
J. M. Fink, “Tunable directional photon scattering from a pair of superconducting
qubits,” Nature Communications, vol. 14. Springer Nature, 2023.
ista: Redchenko E, Poshakinskiy AV, Sett R, Zemlicka M, Poddubny AN, Fink JM. 2023.
Tunable directional photon scattering from a pair of superconducting qubits. Nature
Communications. 14, 2998.
mla: Redchenko, Elena, et al. “Tunable Directional Photon Scattering from a Pair
of Superconducting Qubits.” Nature Communications, vol. 14, 2998, Springer
Nature, 2023, doi:10.1038/s41467-023-38761-6.
short: E. Redchenko, A.V. Poshakinskiy, R. Sett, M. Zemlicka, A.N. Poddubny, J.M.
Fink, Nature Communications 14 (2023).
corr_author: '1'
date_created: 2023-06-04T22:01:02Z
date_published: 2023-05-24T00:00:00Z
date_updated: 2026-04-23T22:31:02Z
day: '24'
ddc:
- '530'
department:
- _id: JoFi
doi: 10.1038/s41467-023-38761-6
ec_funded: 1
external_id:
arxiv:
- '2205.03293'
isi:
- '001001099700002'
pmid:
- '37225689'
file:
- access_level: open_access
checksum: a857df40f0882859c48a1ff1e2001ec2
content_type: application/pdf
creator: dernst
date_created: 2023-06-06T07:31:20Z
date_updated: 2023-06-06T07:31:20Z
file_id: '13123'
file_name: 2023_NaturePhysics_Redchenko.pdf
file_size: 1654389
relation: main_file
success: 1
file_date_updated: 2023-06-06T07:31:20Z
has_accepted_license: '1'
intvolume: ' 14'
isi: 1
language:
- iso: eng
month: '05'
oa: 1
oa_version: Published Version
pmid: 1
project:
- _id: 26336814-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '758053'
name: A Fiber Optic Transceiver for Superconducting Qubits
- _id: 26B354CA-B435-11E9-9278-68D0E5697425
name: Controllable Collective States of Superconducting Qubit Ensembles
- _id: eb9b30ac-77a9-11ec-83b8-871f581d53d2
name: Protected states of quantum matter
- _id: bdb108fd-d553-11ed-ba76-83dc74a9864f
grant_number: F07105
name: QUANTUM INFORMATION SYSTEMS BEYOND CLASSICAL CAPABILITIES / P5- Integration
of Superconducting Quantum Circuits
publication: Nature Communications
publication_identifier:
eissn:
- 2041-1723
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
related_material:
record:
- id: '13124'
relation: research_data
status: public
- id: '19533'
relation: dissertation_contains
status: public
scopus_import: '1'
status: public
title: Tunable directional photon scattering from a pair of superconducting qubits
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
year: '2023'
...
---
OA_place: publisher
OA_type: hybrid
PlanS_conform: '1'
_id: '11442'
abstract:
- lang: eng
text: "Enabling additive manufacturing to employ a wide range of novel, functional
materials can be a major boost to this technology. However, making such materials
printable requires painstaking trial-and-error by an expert operator,\r\nas they
typically tend to exhibit peculiar rheological or hysteresis properties. Even
in the case of successfully finding the process parameters, there is no guarantee
of print-to-print consistency due to material differences between batches. These
challenges make closed-loop feedback an attractive option where the process parameters
are adjusted on-the-fly. There are several challenges for designing an efficient
controller: the deposition parameters are complex and highly coupled, artifacts
occur after long time horizons, simulating the deposition is computationally costly,
and learning on hardware is intractable. In this work, we demonstrate the feasibility
of learning a closed-loop control policy for additive manufacturing using reinforcement
learning. We show that approximate, but efficient, numerical simulation is\r\nsufficient
as long as it allows learning the behavioral patterns of deposition that translate
to real-world experiences. In combination with reinforcement learning, our model
can be used to discover control policies that outperform\r\nbaseline controllers.
Furthermore, the recovered policies have a minimal sim-to-real gap. We showcase
this by applying our control policy in-vivo on a single-layer, direct ink writing
printer. "
acknowledgement: "This work is graciously supported by the following grant agencies:
FWF Lise Meitner (Grant M 3319), SNSF (Grant 200502), ERC Starting Grant (MATERIALIZABLE-715767),
NSF (Grant IIS-181507).\r\n"
article_number: '112'
article_processing_charge: No
article_type: original
arxiv: 1
author:
- first_name: Michael
full_name: Piovarci, Michael
id: 62E473F4-5C99-11EA-A40E-AF823DDC885E
last_name: Piovarci
orcid: 0000-0002-5062-4474
- first_name: Michael
full_name: Foshey, Michael
last_name: Foshey
- first_name: Jie
full_name: Xu, Jie
last_name: Xu
- first_name: Timothy
full_name: Erps, Timothy
last_name: Erps
- first_name: Vahid
full_name: Babaei, Vahid
last_name: Babaei
- first_name: Piotr
full_name: Didyk, Piotr
last_name: Didyk
- first_name: Szymon
full_name: Rusinkiewicz, Szymon
last_name: Rusinkiewicz
- first_name: Wojciech
full_name: Matusik, Wojciech
last_name: Matusik
- first_name: Bernd
full_name: Bickel, Bernd
id: 49876194-F248-11E8-B48F-1D18A9856A87
last_name: Bickel
orcid: 0000-0001-6511-9385
citation:
ama: Piovarci M, Foshey M, Xu J, et al. Closed-loop control of direct ink writing
via reinforcement learning. ACM Transactions on Graphics. 2022;41(4). doi:10.1145/3528223.3530144
apa: Piovarci, M., Foshey, M., Xu, J., Erps, T., Babaei, V., Didyk, P., … Bickel,
B. (2022). Closed-loop control of direct ink writing via reinforcement learning.
ACM Transactions on Graphics. Association for Computing Machinery. https://doi.org/10.1145/3528223.3530144
chicago: Piovarci, Michael, Michael Foshey, Jie Xu, Timothy Erps, Vahid Babaei,
Piotr Didyk, Szymon Rusinkiewicz, Wojciech Matusik, and Bernd Bickel. “Closed-Loop
Control of Direct Ink Writing via Reinforcement Learning.” ACM Transactions
on Graphics. Association for Computing Machinery, 2022. https://doi.org/10.1145/3528223.3530144.
ieee: M. Piovarci et al., “Closed-loop control of direct ink writing via
reinforcement learning,” ACM Transactions on Graphics, vol. 41, no. 4.
Association for Computing Machinery, 2022.
ista: Piovarci M, Foshey M, Xu J, Erps T, Babaei V, Didyk P, Rusinkiewicz S, Matusik
W, Bickel B. 2022. Closed-loop control of direct ink writing via reinforcement
learning. ACM Transactions on Graphics. 41(4), 112.
mla: Piovarci, Michael, et al. “Closed-Loop Control of Direct Ink Writing via Reinforcement
Learning.” ACM Transactions on Graphics, vol. 41, no. 4, 112, Association
for Computing Machinery, 2022, doi:10.1145/3528223.3530144.
short: M. Piovarci, M. Foshey, J. Xu, T. Erps, V. Babaei, P. Didyk, S. Rusinkiewicz,
W. Matusik, B. Bickel, ACM Transactions on Graphics 41 (2022).
corr_author: '1'
date_created: 2022-06-10T06:41:47Z
date_published: 2022-06-01T00:00:00Z
date_updated: 2025-09-10T09:36:45Z
day: '01'
ddc:
- '000'
department:
- _id: BeBi
doi: 10.1145/3528223.3530144
ec_funded: 1
external_id:
arxiv:
- '2201.11819'
isi:
- '000830989200091'
file:
- access_level: open_access
checksum: 27f6fe41c6ff84d50445cc9b0176d45b
content_type: application/pdf
creator: dernst
date_created: 2022-06-28T08:32:58Z
date_updated: 2022-06-28T08:32:58Z
file_id: '11467'
file_name: 2022_ACM_acceptedversion_Piovarci.pdf
file_size: 33994829
relation: main_file
success: 1
file_date_updated: 2022-06-28T08:32:58Z
has_accepted_license: '1'
intvolume: ' 41'
isi: 1
issue: '4'
language:
- iso: eng
month: '06'
oa: 1
oa_version: Submitted Version
project:
- _id: eb901961-77a9-11ec-83b8-f5c883a62027
grant_number: M03319
name: Perception-Aware Appearance Fabrication
- _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:
link:
- description: News on ISTA website
relation: press_release
url: https://ista.ac.at/en/news/machine-learning-3d-printing-fluids/
scopus_import: '1'
status: public
title: Closed-loop control of direct ink writing via reinforcement learning
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: 41
year: '2022'
...
---
_id: '11443'
abstract:
- lang: eng
text: Sometimes, it is possible to represent a complicated polytope as a projection
of a much simpler polytope. To quantify this phenomenon, the extension complexity
of a polytope P is defined to be the minimum number of facets of a (possibly higher-dimensional)
polytope from which P can be obtained as a (linear) projection. This notion is
motivated by its relevance to combinatorial optimisation, and has been studied
intensively for various specific polytopes associated with important optimisation
problems. In this paper we study extension complexity as a parameter of general
polytopes, more specifically considering various families of low-dimensional polytopes.
First, we prove that for a fixed dimension d, the extension complexity of a random
d-dimensional polytope (obtained as the convex hull of random points in a ball
or on a sphere) is typically on the order of the square root of its number of
vertices. Second, we prove that any cyclic n-vertex polygon (whose vertices lie
on a circle) has extension complexity at most 24√n. This bound is tight up to
the constant factor 24. Finally, we show that there exists an no(1)-dimensional
polytope with at most n vertices and extension complexity n1−o(1). Our theorems
are proved with a range of different techniques, which we hope will be of further
interest.
acknowledgement: "The research of the first author was supported by SNSF Project 178493
and NSF Award DMS-1953990. The research of the second author supported by NSF Award
DMS-1953772.\r\nThe research of the third author was supported by NSF Award DMS-1764176,
NSF CAREER Award DMS-2044606, a Sloan Research Fellowship, and the MIT Solomon Buchsbaum
Fund. "
article_processing_charge: No
article_type: original
arxiv: 1
author:
- first_name: Matthew Alan
full_name: Kwan, Matthew Alan
id: 5fca0887-a1db-11eb-95d1-ca9d5e0453b3
last_name: Kwan
orcid: 0000-0002-4003-7567
- first_name: Lisa
full_name: Sauermann, Lisa
last_name: Sauermann
- first_name: Yufei
full_name: Zhao, Yufei
last_name: Zhao
citation:
ama: Kwan MA, Sauermann L, Zhao Y. Extension complexity of low-dimensional polytopes.
Transactions of the American Mathematical Society. 2022;375(6):4209-4250.
doi:10.1090/tran/8614
apa: Kwan, M. A., Sauermann, L., & Zhao, Y. (2022). Extension complexity of
low-dimensional polytopes. Transactions of the American Mathematical Society.
American Mathematical Society. https://doi.org/10.1090/tran/8614
chicago: Kwan, Matthew Alan, Lisa Sauermann, and Yufei Zhao. “Extension Complexity
of Low-Dimensional Polytopes.” Transactions of the American Mathematical Society.
American Mathematical Society, 2022. https://doi.org/10.1090/tran/8614.
ieee: M. A. Kwan, L. Sauermann, and Y. Zhao, “Extension complexity of low-dimensional
polytopes,” Transactions of the American Mathematical Society, vol. 375,
no. 6. American Mathematical Society, pp. 4209–4250, 2022.
ista: Kwan MA, Sauermann L, Zhao Y. 2022. Extension complexity of low-dimensional
polytopes. Transactions of the American Mathematical Society. 375(6), 4209–4250.
mla: Kwan, Matthew Alan, et al. “Extension Complexity of Low-Dimensional Polytopes.”
Transactions of the American Mathematical Society, vol. 375, no. 6, American
Mathematical Society, 2022, pp. 4209–50, doi:10.1090/tran/8614.
short: M.A. Kwan, L. Sauermann, Y. Zhao, Transactions of the American Mathematical
Society 375 (2022) 4209–4250.
corr_author: '1'
date_created: 2022-06-12T22:01:45Z
date_published: 2022-06-01T00:00:00Z
date_updated: 2024-10-09T21:02:31Z
day: '01'
department:
- _id: MaKw
doi: 10.1090/tran/8614
external_id:
arxiv:
- '2006.08836'
isi:
- '000798461500001'
intvolume: ' 375'
isi: 1
issue: '6'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: ' https://doi.org/10.48550/arXiv.2006.08836'
month: '06'
oa: 1
oa_version: Preprint
page: 4209-4250
publication: Transactions of the American Mathematical Society
publication_identifier:
eissn:
- 1088-6850
issn:
- 0002-9947
publication_status: published
publisher: American Mathematical Society
quality_controlled: '1'
scopus_import: '1'
status: public
title: Extension complexity of low-dimensional polytopes
type: journal_article
user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
volume: 375
year: '2022'
...
---
_id: '11449'
abstract:
- lang: eng
text: Mutations are acquired frequently, such that each cell's genome inscribes
its history of cell divisions. Common genomic alterations involve loss of heterozygosity
(LOH). LOH accumulates throughout the genome, offering large encoding capacity
for inferring cell lineage. Using only single-cell RNA sequencing (scRNA-seq)
of mouse brain cells, we found that LOH events spanning multiple genes are revealed
as tracts of monoallelically expressed, constitutionally heterozygous single-nucleotide
variants (SNVs). We simultaneously inferred cell lineage and marked developmental
time points based on X chromosome inactivation and the total number of LOH events
while identifying cell types from gene expression patterns. Our results are consistent
with progenitor cells giving rise to multiple cortical cell types through stereotyped
expansion and distinct waves of neurogenesis. This type of retrospective analysis
could be incorporated into scRNA-seq pipelines and, compared with experimental
approaches for determining lineage in model organisms, is applicable where genetic
engineering is prohibited, such as humans.
acknowledgement: D.J.A. thanks Wayne K. Potts, Alan R. Rogers, Kristen Hawkes, Ryk
Ward, and Jon Seger for inspiring a young undergraduate to apply evolutionary theory
to intraorganism development. Supported by the Paul G. Allen Frontiers Group (University
of Washington); NIH R00HG010152 (Dartmouth); and NÖ Forschung und Bildung n[f+b]
life science call grant (C13-002) and the European Research Council (ERC) under
the European Union’s Horizon 2020 research and innovation program 725780 LinPro
to S.H.
article_processing_charge: No
article_type: original
author:
- first_name: Donovan J.
full_name: Anderson, Donovan J.
last_name: Anderson
- first_name: Florian
full_name: Pauler, Florian
id: 48EA0138-F248-11E8-B48F-1D18A9856A87
last_name: Pauler
orcid: 0000-0002-7462-0048
- first_name: Aaron
full_name: Mckenna, Aaron
last_name: Mckenna
- first_name: Jay
full_name: Shendure, Jay
last_name: Shendure
- first_name: Simon
full_name: Hippenmeyer, Simon
id: 37B36620-F248-11E8-B48F-1D18A9856A87
last_name: Hippenmeyer
orcid: 0000-0003-2279-1061
- first_name: Marshall S.
full_name: Horwitz, Marshall S.
last_name: Horwitz
citation:
ama: Anderson DJ, Pauler F, Mckenna A, Shendure J, Hippenmeyer S, Horwitz MS. Simultaneous
brain cell type and lineage determined by scRNA-seq reveals stereotyped cortical
development. Cell Systems. 2022;13(6):438-453.e5. doi:10.1016/j.cels.2022.03.006
apa: Anderson, D. J., Pauler, F., Mckenna, A., Shendure, J., Hippenmeyer, S., &
Horwitz, M. S. (2022). Simultaneous brain cell type and lineage determined by
scRNA-seq reveals stereotyped cortical development. Cell Systems. Elsevier.
https://doi.org/10.1016/j.cels.2022.03.006
chicago: Anderson, Donovan J., Florian Pauler, Aaron Mckenna, Jay Shendure, Simon
Hippenmeyer, and Marshall S. Horwitz. “Simultaneous Brain Cell Type and Lineage
Determined by ScRNA-Seq Reveals Stereotyped Cortical Development.” Cell Systems.
Elsevier, 2022. https://doi.org/10.1016/j.cels.2022.03.006.
ieee: D. J. Anderson, F. Pauler, A. Mckenna, J. Shendure, S. Hippenmeyer, and M.
S. Horwitz, “Simultaneous brain cell type and lineage determined by scRNA-seq
reveals stereotyped cortical development,” Cell Systems, vol. 13, no. 6.
Elsevier, p. 438–453.e5, 2022.
ista: Anderson DJ, Pauler F, Mckenna A, Shendure J, Hippenmeyer S, Horwitz MS. 2022.
Simultaneous brain cell type and lineage determined by scRNA-seq reveals stereotyped
cortical development. Cell Systems. 13(6), 438–453.e5.
mla: Anderson, Donovan J., et al. “Simultaneous Brain Cell Type and Lineage Determined
by ScRNA-Seq Reveals Stereotyped Cortical Development.” Cell Systems, vol.
13, no. 6, Elsevier, 2022, p. 438–453.e5, doi:10.1016/j.cels.2022.03.006.
short: D.J. Anderson, F. Pauler, A. Mckenna, J. Shendure, S. Hippenmeyer, M.S. Horwitz,
Cell Systems 13 (2022) 438–453.e5.
date_created: 2022-06-19T22:01:57Z
date_published: 2022-06-15T00:00:00Z
date_updated: 2025-04-14T07:43:05Z
day: '15'
department:
- _id: SiHi
doi: 10.1016/j.cels.2022.03.006
ec_funded: 1
external_id:
isi:
- '000814124400002'
pmid:
- '35452605'
intvolume: ' 13'
isi: 1
issue: '6'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.1016/j.cels.2022.03.006
month: '06'
oa: 1
oa_version: Published Version
page: 438-453.e5
pmid: 1
project:
- _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: 25D92700-B435-11E9-9278-68D0E5697425
grant_number: LS13-002
name: Mapping Cell-Type Specificity of the Genomic Imprintome in the Brain
publication: Cell Systems
publication_identifier:
eissn:
- 2405-4720
issn:
- 2405-4712
publication_status: published
publisher: Elsevier
quality_controlled: '1'
scopus_import: '1'
status: public
title: Simultaneous brain cell type and lineage determined by scRNA-seq reveals stereotyped
cortical development
type: journal_article
user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
volume: 13
year: '2022'
...
---
_id: '11451'
abstract:
- lang: eng
text: The precursor conversion chemistry and surface chemistry of Cu3N and Cu3PdN
nanocrystals are unknown or contested. Here, we first obtain phase-pure, colloidally
stable nanocubes. Second, we elucidate the pathway by which copper(II) nitrate
and oleylamine form Cu3N. We find that oleylamine is both a reductant and a nitrogen
source. Oleylamine is oxidized by nitrate to a primary aldimine, which reacts
further with excess oleylamine to a secondary aldimine, eliminating ammonia. Ammonia
reacts with CuI to form Cu3N. Third, we investigated the surface chemistry and
find a mixed ligand shell of aliphatic amines and carboxylates (formed in situ).
While the carboxylates appear tightly bound, the amines are easily desorbed from
the surface. Finally, we show that doping with palladium decreases the band gap
and the material becomes semi-metallic. These results bring insight into the chemistry
of metal nitrides and might help the development of other metal nitride nanocrystals.
acknowledgement: 'J.D.R. and M.P. acknowledge the SNF Eccellenza funding scheme (project
number: 194172). We acknowledge DESY (Hamburg, Germany), a member of the Helmholtz
Association HGF, for the provision of experimental facilities. Parts of this research
were carried out at beamline P21.1, PETRA III. We thank Dr. Soham Banerjee for acquiring
the PDF data and helpful advice. A.R. acknowledges the support from the Analytical
Chemistry Trust Fund for her CAMS-UK Fellowship. C.K. acknowledges the support from
the Department of Chemistry, UCL. The authors acknowledge Dr Stephan Lany from NREL
for providing the Cu3N DFT calculations. The authors thank Prof. Raymond Schaak
and Dr. Robert William Lord for helpful advice and suggestions regarding the purification
procedure. Open access funding provided by Universitat Basel.'
article_number: e202207013
article_processing_charge: No
article_type: original
author:
- first_name: Mahsa
full_name: Parvizian, Mahsa
last_name: Parvizian
- first_name: Alejandra
full_name: Duràn Balsa, Alejandra
last_name: Duràn Balsa
- first_name: Rohan
full_name: Pokratath, Rohan
last_name: Pokratath
- first_name: Curran
full_name: Kalha, Curran
last_name: Kalha
- first_name: Seungho
full_name: Lee, Seungho
id: BB243B88-D767-11E9-B658-BC13E6697425
last_name: Lee
orcid: 0000-0002-6962-8598
- first_name: Dietger
full_name: Van Den Eynden, Dietger
last_name: Van Den Eynden
- first_name: Maria
full_name: Ibáñez, Maria
id: 43C61214-F248-11E8-B48F-1D18A9856A87
last_name: Ibáñez
orcid: 0000-0001-5013-2843
- first_name: Anna
full_name: Regoutz, Anna
last_name: Regoutz
- first_name: Jonathan
full_name: De Roo, Jonathan
last_name: De Roo
citation:
ama: Parvizian M, Duràn Balsa A, Pokratath R, et al. The chemistry of Cu₃N and Cu₃PdN
nanocrystals. Angewandte Chemie - International Edition. 2022;61(31). doi:10.1002/anie.202207013
apa: Parvizian, M., Duràn Balsa, A., Pokratath, R., Kalha, C., Lee, S., Van Den
Eynden, D., … De Roo, J. (2022). The chemistry of Cu₃N and Cu₃PdN nanocrystals.
Angewandte Chemie - International Edition. Wiley. https://doi.org/10.1002/anie.202207013
chicago: Parvizian, Mahsa, Alejandra Duràn Balsa, Rohan Pokratath, Curran Kalha,
Seungho Lee, Dietger Van Den Eynden, Maria Ibáñez, Anna Regoutz, and Jonathan
De Roo. “The Chemistry of Cu₃N and Cu₃PdN Nanocrystals.” Angewandte Chemie
- International Edition. Wiley, 2022. https://doi.org/10.1002/anie.202207013.
ieee: M. Parvizian et al., “The chemistry of Cu₃N and Cu₃PdN nanocrystals,”
Angewandte Chemie - International Edition, vol. 61, no. 31. Wiley, 2022.
ista: Parvizian M, Duràn Balsa A, Pokratath R, Kalha C, Lee S, Van Den Eynden D,
Ibáñez M, Regoutz A, De Roo J. 2022. The chemistry of Cu₃N and Cu₃PdN nanocrystals.
Angewandte Chemie - International Edition. 61(31), e202207013.
mla: Parvizian, Mahsa, et al. “The Chemistry of Cu₃N and Cu₃PdN Nanocrystals.” Angewandte
Chemie - International Edition, vol. 61, no. 31, e202207013, Wiley, 2022,
doi:10.1002/anie.202207013.
short: M. Parvizian, A. Duràn Balsa, R. Pokratath, C. Kalha, S. Lee, D. Van Den
Eynden, M. Ibáñez, A. Regoutz, J. De Roo, Angewandte Chemie - International Edition
61 (2022).
date_created: 2022-06-19T22:01:58Z
date_published: 2022-08-01T00:00:00Z
date_updated: 2023-08-03T07:19:12Z
day: '01'
ddc:
- '540'
department:
- _id: MaIb
doi: 10.1002/anie.202207013
external_id:
isi:
- '000811084000001'
pmid:
- '35612297'
file:
- access_level: open_access
checksum: 2a3ee0bb59e044b808ebe85cd94ac899
content_type: application/pdf
creator: dernst
date_created: 2022-07-29T09:29:20Z
date_updated: 2022-07-29T09:29:20Z
file_id: '11696'
file_name: 2022_AngewandteChemieInternat_Parvizian.pdf
file_size: 1303202
relation: main_file
success: 1
file_date_updated: 2022-07-29T09:29:20Z
has_accepted_license: '1'
intvolume: ' 61'
isi: 1
issue: '31'
language:
- iso: eng
month: '08'
oa: 1
oa_version: Published Version
pmid: 1
publication: Angewandte Chemie - International Edition
publication_identifier:
eissn:
- 1521-3773
issn:
- 1433-7851
publication_status: published
publisher: Wiley
quality_controlled: '1'
related_material:
record:
- id: '11695'
relation: research_data
status: public
scopus_import: '1'
status: public
title: The chemistry of Cu₃N and Cu₃PdN nanocrystals
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: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
volume: 61
year: '2022'
...
---
_id: '11456'
abstract:
- lang: eng
text: The proteomes of specialized structures, and the interactomes of proteins
of interest, provide entry points to elucidate the functions of molecular machines.
Here, we review a proximity-labeling strategy that uses the improved E. coli biotin
ligase TurboID to characterize C. elegans protein complexes. Although the focus
is on C. elegans neurons, the method is applicable regardless of cell type. We
describe detailed extraction procedures that solubilize the bulk of C. elegans
proteins and highlight the importance of tagging endogenous genes, to ensure physiological
expression levels. We review issues associated with non-specific background noise
and the importance of appropriate controls. As proof of principle, we review our
analysis of the interactome of a presynaptic active zone protein, ELKS-1. Our
aim is to provide a detailed protocol for TurboID-based proximity labeling in
C. elegans and to highlight its potential and its limitations to characterize
protein complexes and subcellular compartments in this animal.
acknowledgement: We thank de Bono lab members for the helpful comments on the manuscript.
The biotin-auxotrophic E. coli strain MG1655bioB:kan was a generous gift from J.
Cronan (University of Illinois) and was kindly sent to us by Jessica Feldman and
Ariana Sanchez (Stanford University). dg398 pEntryslot2_mNeongreen::3XFLAG::stop
and dg397 pEntryslot3_mNeongreen::3XFLAG::stop::unc-54 3’UTR entry vector were kindly
sent by Dr. Dominique Glauser (University of Fribourg). This work was supported
by an Advanced ERC Grant (269058 ACMO) and a Wellcome Investigator Award (209504/Z/17/Z)
to MdB and an ISTplus Fellowship to MA (Marie Sklodowska-Curie agreement No 754411).
alternative_title:
- Neuromethods
article_processing_charge: No
author:
- first_name: Murat
full_name: Artan, Murat
id: C407B586-6052-11E9-B3AE-7006E6697425
last_name: Artan
orcid: 0000-0001-8945-6992
- first_name: Mario
full_name: de Bono, Mario
id: 4E3FF80E-F248-11E8-B48F-1D18A9856A87
last_name: de Bono
orcid: 0000-0001-8347-0443
citation:
ama: 'Artan M, de Bono M. Proteomic Analysis of C. Elegans Neurons Using TurboID-Based
Proximity Labeling. In: Yamamoto D, ed. Behavioral Neurogenetics. Vol 181.
NM. New York: Springer Nature; 2022:277-294. doi:10.1007/978-1-0716-2321-3_15'
apa: 'Artan, M., & de Bono, M. (2022). Proteomic Analysis of C. Elegans Neurons
Using TurboID-Based Proximity Labeling. In D. Yamamoto (Ed.), Behavioral Neurogenetics
(Vol. 181, pp. 277–294). New York: Springer Nature. https://doi.org/10.1007/978-1-0716-2321-3_15'
chicago: 'Artan, Murat, and Mario de Bono. “Proteomic Analysis of C. Elegans Neurons
Using TurboID-Based Proximity Labeling.” In Behavioral Neurogenetics, edited
by Daisuke Yamamoto, 181:277–94. NM. New York: Springer Nature, 2022. https://doi.org/10.1007/978-1-0716-2321-3_15.'
ieee: 'M. Artan and M. de Bono, “Proteomic Analysis of C. Elegans Neurons Using
TurboID-Based Proximity Labeling,” in Behavioral Neurogenetics, vol. 181,
D. Yamamoto, Ed. New York: Springer Nature, 2022, pp. 277–294.'
ista: 'Artan M, de Bono M. 2022.Proteomic Analysis of C. Elegans Neurons Using TurboID-Based
Proximity Labeling. In: Behavioral Neurogenetics. Neuromethods, vol. 181, 277–294.'
mla: Artan, Murat, and Mario de Bono. “Proteomic Analysis of C. Elegans Neurons
Using TurboID-Based Proximity Labeling.” Behavioral Neurogenetics, edited
by Daisuke Yamamoto, vol. 181, Springer Nature, 2022, pp. 277–94, doi:10.1007/978-1-0716-2321-3_15.
short: M. Artan, M. de Bono, in:, D. Yamamoto (Ed.), Behavioral Neurogenetics, Springer
Nature, New York, 2022, pp. 277–294.
corr_author: '1'
date_created: 2022-06-20T08:10:34Z
date_published: 2022-06-04T00:00:00Z
date_updated: 2025-04-14T07:43:58Z
day: '04'
department:
- _id: MaDe
doi: 10.1007/978-1-0716-2321-3_15
ec_funded: 1
editor:
- first_name: Daisuke
full_name: Yamamoto, Daisuke
last_name: Yamamoto
intvolume: ' 181'
language:
- iso: eng
month: '06'
oa_version: None
page: 277-294
place: New York
project:
- _id: 23870BE8-32DE-11EA-91FC-C7463DDC885E
grant_number: 209504/A/17/Z
name: Molecular mechanisms of neural circuit function
- _id: 260C2330-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '754411'
name: ISTplus - Postdoctoral Fellowships
publication: Behavioral Neurogenetics
publication_identifier:
eisbn:
- '9781071623213'
eissn:
- 1940-6045
isbn:
- '9781071623206'
issn:
- 0893-2336
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
scopus_import: '1'
series_title: NM
status: public
title: Proteomic Analysis of C. Elegans Neurons Using TurboID-Based Proximity Labeling
type: book_chapter
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 181
year: '2022'
...
---
_id: '11459'
abstract:
- lang: eng
text: 'We present a novel approach to differential cost analysis that, given a program
revision, attempts to statically bound the difference in resource usage, or cost,
between the two program versions. Differential cost analysis is particularly interesting
because of the many compelling applications for it, such as detecting resource-use
regressions at code-review time or proving the absence of certain side-channel
vulnerabilities. One prior approach to differential cost analysis is to apply
relational reasoning that conceptually constructs a product program on which one
can over-approximate the difference in costs between the two program versions.
However, a significant challenge in any relational approach is effectively aligning
the program versions to get precise results. In this paper, our key insight is
that we can avoid the need for and the limitations of program alignment if, instead,
we bound the difference of two cost-bound summaries rather than directly bounding
the concrete cost difference. In particular, our method computes a threshold value
for the maximal difference in cost between two program versions simultaneously
using two kinds of cost-bound summaries---a potential function that evaluates
to an upper bound for the cost incurred in the first program and an anti-potential
function that evaluates to a lower bound for the cost incurred in the second.
Our method has a number of desirable properties: it can be fully automated, it
allows optimizing the threshold value on relative cost, it is suitable for programs
that are not syntactically similar, and it supports non-determinism. We have evaluated
an implementation of our approach on a number of program pairs collected from
the literature, and we find that our method computes tight threshold values on
relative cost in most examples.'
acknowledgement: "We thank Shaun Willows, Thomas Lugnet, and the Living Room Application
Vending team for suggesting threshold\r\nbounds as a developer-friendly way to interact
with a differential cost analyzer, and we thank Jim Christy, Daniel\r\nSchoepe,
and the Prime Video Automated Reasoning team for their support and helpful suggestions
throughout the\r\nproject. We also thank Michael Emmi for feedback on an earlier
version of this paper. And finally, we thank the anonymous reviewers for their useful
feedback and Aws Albarghouthi for shepherding the final version of the paper. Ðorđe
Žikelić was also partially supported by ERC CoG 863818 (FoRM-SMArt)."
article_processing_charge: No
arxiv: 1
author:
- first_name: Dorde
full_name: Zikelic, Dorde
id: 294AA7A6-F248-11E8-B48F-1D18A9856A87
last_name: Zikelic
orcid: 0000-0002-4681-1699
- first_name: Bor-Yuh Evan
full_name: Chang, Bor-Yuh Evan
last_name: Chang
- first_name: Pauline
full_name: Bolignano, Pauline
last_name: Bolignano
- first_name: Franco
full_name: Raimondi, Franco
last_name: Raimondi
citation:
ama: 'Zikelic D, Chang B-YE, Bolignano P, Raimondi F. Differential cost analysis
with simultaneous potentials and anti-potentials. In: Proceedings of the 43rd
ACM SIGPLAN International Conference on Programming Language Design and Implementation.
Association for Computing Machinery; 2022:442-457. doi:10.1145/3519939.3523435'
apa: 'Zikelic, D., Chang, B.-Y. E., Bolignano, P., & Raimondi, F. (2022). Differential
cost analysis with simultaneous potentials and anti-potentials. In Proceedings
of the 43rd ACM SIGPLAN International Conference on Programming Language Design
and Implementation (pp. 442–457). San Diego, CA, United States: Association
for Computing Machinery. https://doi.org/10.1145/3519939.3523435'
chicago: Zikelic, Dorde, Bor-Yuh Evan Chang, Pauline Bolignano, and Franco Raimondi.
“Differential Cost Analysis with Simultaneous Potentials and Anti-Potentials.”
In Proceedings of the 43rd ACM SIGPLAN International Conference on Programming
Language Design and Implementation, 442–57. Association for Computing Machinery,
2022. https://doi.org/10.1145/3519939.3523435.
ieee: D. Zikelic, B.-Y. E. Chang, P. Bolignano, and F. Raimondi, “Differential cost
analysis with simultaneous potentials and anti-potentials,” in Proceedings
of the 43rd ACM SIGPLAN International Conference on Programming Language Design
and Implementation, San Diego, CA, United States, 2022, pp. 442–457.
ista: 'Zikelic D, Chang B-YE, Bolignano P, Raimondi F. 2022. Differential cost analysis
with simultaneous potentials and anti-potentials. Proceedings of the 43rd ACM
SIGPLAN International Conference on Programming Language Design and Implementation.
PLDI: Programming Language Design and Implementation, 442–457.'
mla: Zikelic, Dorde, et al. “Differential Cost Analysis with Simultaneous Potentials
and Anti-Potentials.” Proceedings of the 43rd ACM SIGPLAN International Conference
on Programming Language Design and Implementation, Association for Computing
Machinery, 2022, pp. 442–57, doi:10.1145/3519939.3523435.
short: D. Zikelic, B.-Y.E. Chang, P. Bolignano, F. Raimondi, in:, Proceedings of
the 43rd ACM SIGPLAN International Conference on Programming Language Design and
Implementation, Association for Computing Machinery, 2022, pp. 442–457.
conference:
end_date: 2022-06-17
location: San Diego, CA, United States
name: 'PLDI: Programming Language Design and Implementation'
start_date: 2022-06-13
corr_author: '1'
date_created: 2022-06-21T09:26:15Z
date_published: 2022-06-09T00:00:00Z
date_updated: 2025-04-14T07:52:47Z
day: '09'
ddc:
- '000'
department:
- _id: GradSch
- _id: KrCh
doi: 10.1145/3519939.3523435
ec_funded: 1
external_id:
arxiv:
- '2204.00870'
isi:
- '000850435600030'
file:
- access_level: open_access
checksum: 7eb915a2ca5b5ce4729321f33b2e16e1
content_type: application/pdf
creator: dernst
date_created: 2022-06-27T07:38:21Z
date_updated: 2022-06-27T07:38:21Z
file_id: '11466'
file_name: 2022_PLDI_Zikelic.pdf
file_size: 318697
relation: main_file
success: 1
file_date_updated: 2022-06-27T07:38:21Z
has_accepted_license: '1'
isi: 1
language:
- iso: eng
month: '06'
oa: 1
oa_version: Published Version
page: 442-457
project:
- _id: 0599E47C-7A3F-11EA-A408-12923DDC885E
call_identifier: H2020
grant_number: '863818'
name: 'Formal Methods for Stochastic Models: Algorithms and Applications'
publication: Proceedings of the 43rd ACM SIGPLAN International Conference on Programming
Language Design and Implementation
publication_identifier:
isbn:
- '9781450392655'
publication_status: published
publisher: Association for Computing Machinery
quality_controlled: '1'
scopus_import: '1'
status: public
title: Differential cost analysis with simultaneous potentials and anti-potentials
tmp:
image: /images/cc_by_nc_nd.png
legal_code_url: https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode
name: Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International
(CC BY-NC-ND 4.0)
short: CC BY-NC-ND (4.0)
type: conference
user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
year: '2022'
...
---
_id: '11460'
abstract:
- lang: eng
text: "Background: Proper cerebral cortical development depends on the tightly orchestrated
migration of newly born neurons from the inner ventricular and subventricular
zones to the outer cortical plate. Any disturbance in this process during prenatal
stages may lead to neuronal migration disorders (NMDs), which can vary in extent
from focal to global. Furthermore, NMDs show a substantial comorbidity with other
neurodevelopmental disorders, notably autism spectrum disorders (ASDs). Our previous
work demonstrated focal neuronal migration defects in mice carrying loss-of-function
alleles of the recognized autism risk gene WDFY3. However, the cellular origins
of these defects in Wdfy3 mutant mice remain elusive and uncovering it will provide
critical insight into WDFY3-dependent disease pathology.\r\nMethods: Here, in
an effort to untangle the origins of NMDs in Wdfy3lacZ mice, we employed mosaic
analysis with double markers (MADM). MADM technology enabled us to genetically
distinctly track and phenotypically analyze mutant and wild-type cells concomitantly
in vivo using immunofluorescent techniques.\r\nResults: We revealed a cell autonomous
requirement of WDFY3 for accurate laminar positioning of cortical projection neurons
and elimination of mispositioned cells during early postnatal life. In addition,
we identified significant deviations in dendritic arborization, as well as synaptic
density and morphology between wild type, heterozygous, and homozygous Wdfy3 mutant
neurons in Wdfy3-MADM reporter mice at postnatal stages.\r\nLimitations: While
Wdfy3 mutant mice have provided valuable insight into prenatal aspects of ASD
pathology that remain inaccessible to investigation in humans, like most animal
models, they do not a perfectly replicate all aspects of human ASD biology. The
lack of human data makes it indeterminate whether morphological deviations described
here apply to ASD patients or some of the other neurodevelopmental conditions
associated with WDFY3 mutation.\r\nConclusions: Our genetic approach revealed
several cell autonomous requirements of WDFY3 in neuronal development that could
underlie the pathogenic mechanisms of WDFY3-related neurodevelopmental conditions.
The results are also consistent with findings in other ASD animal models and patients
and suggest an important role for WDFY3 in regulating neuronal function and interconnectivity
in postnatal life."
acknowledgement: "This study was funded by NIMH R21MH115347 to KSZ. KSZ is further
supported by Shriners Hospitals for Children.\r\nWe would like to thank Angelo Harlan
de Crescenzo for early contributions to this project."
article_number: '27'
article_processing_charge: No
article_type: original
author:
- first_name: Zachary A.
full_name: Schaaf, Zachary A.
last_name: Schaaf
- first_name: Lyvin
full_name: Tat, Lyvin
last_name: Tat
- first_name: Noemi
full_name: Cannizzaro, Noemi
last_name: Cannizzaro
- first_name: Ralph
full_name: Green, Ralph
last_name: Green
- first_name: Thomas
full_name: Rülicke, Thomas
last_name: Rülicke
- first_name: Simon
full_name: Hippenmeyer, Simon
id: 37B36620-F248-11E8-B48F-1D18A9856A87
last_name: Hippenmeyer
orcid: 0000-0003-2279-1061
- first_name: Konstantinos S.
full_name: Zarbalis, Konstantinos S.
last_name: Zarbalis
citation:
ama: Schaaf ZA, Tat L, Cannizzaro N, et al. WDFY3 mutation alters laminar position
and morphology of cortical neurons. Molecular Autism. 2022;13. doi:10.1186/s13229-022-00508-3
apa: Schaaf, Z. A., Tat, L., Cannizzaro, N., Green, R., Rülicke, T., Hippenmeyer,
S., & Zarbalis, K. S. (2022). WDFY3 mutation alters laminar position and morphology
of cortical neurons. Molecular Autism. Springer Nature. https://doi.org/10.1186/s13229-022-00508-3
chicago: Schaaf, Zachary A., Lyvin Tat, Noemi Cannizzaro, Ralph Green, Thomas Rülicke,
Simon Hippenmeyer, and Konstantinos S. Zarbalis. “WDFY3 Mutation Alters Laminar
Position and Morphology of Cortical Neurons.” Molecular Autism. Springer
Nature, 2022. https://doi.org/10.1186/s13229-022-00508-3.
ieee: Z. A. Schaaf et al., “WDFY3 mutation alters laminar position and morphology
of cortical neurons,” Molecular Autism, vol. 13. Springer Nature, 2022.
ista: Schaaf ZA, Tat L, Cannizzaro N, Green R, Rülicke T, Hippenmeyer S, Zarbalis
KS. 2022. WDFY3 mutation alters laminar position and morphology of cortical neurons.
Molecular Autism. 13, 27.
mla: Schaaf, Zachary A., et al. “WDFY3 Mutation Alters Laminar Position and Morphology
of Cortical Neurons.” Molecular Autism, vol. 13, 27, Springer Nature, 2022,
doi:10.1186/s13229-022-00508-3.
short: Z.A. Schaaf, L. Tat, N. Cannizzaro, R. Green, T. Rülicke, S. Hippenmeyer,
K.S. Zarbalis, Molecular Autism 13 (2022).
date_created: 2022-06-23T14:28:55Z
date_published: 2022-06-22T00:00:00Z
date_updated: 2025-06-11T13:34:57Z
day: '22'
ddc:
- '570'
department:
- _id: SiHi
doi: 10.1186/s13229-022-00508-3
external_id:
isi:
- '000814641400001'
pmid:
- '35733184'
file:
- access_level: open_access
checksum: 525d2618e855139089bbfc3e3d49d1b2
content_type: application/pdf
creator: dernst
date_created: 2022-06-24T08:22:59Z
date_updated: 2022-06-24T08:22:59Z
file_id: '11461'
file_name: 2022_MolecularAutism_Schaaf.pdf
file_size: 7552298
relation: main_file
success: 1
file_date_updated: 2022-06-24T08:22:59Z
has_accepted_license: '1'
intvolume: ' 13'
isi: 1
keyword:
- Psychiatry and Mental health
- Developmental Biology
- Developmental Neuroscience
- Molecular Biology
language:
- iso: eng
month: '06'
oa: 1
oa_version: Published Version
pmid: 1
publication: Molecular Autism
publication_identifier:
issn:
- 2040-2392
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
related_material:
link:
- relation: erratum
url: https://doi.org/10.1186/s13229-023-00539-4
scopus_import: '1'
status: public
title: WDFY3 mutation alters laminar position and morphology of cortical neurons
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: 13
year: '2022'
...
---
_id: '11462'
abstract:
- lang: eng
text: Nanobodies (VHH) from camelid antibody libraries hold great promise as therapeutic
agents and components of immunoassay systems. Synthetic antibody libraries that
could be designed and generated once and for various applications could yield
binders to virtually any targets, even for non-immunogenic or toxic ones, in a
short term. One of the most difficult tasks is to obtain antibodies with a high
affinity and specificity to polyglycosylated proteins. It requires antibody libraries
with extremely high functional diversity and the use of sophisticated selection
techniques. Here we report a development of a novel sandwich immunoassay involving
a combination of the synthetic library-derived VHH-Fc fusion protein as a capture
antibody and the immune single-chain fragment variable (scFv) as a tracer for
the detection of pregnancy-associated glycoprotein (PAG) of cattle (Bos taurus).
We succeeded in the generation of a number of specific scFv antibodies against
PAG from the mouse immune library. Subsequent selection using the immobilized
scFv-Fc capture antibody allowed to isolate 1.9 nM VHH binder from the diverse
synthetic library without any overlapping with the capture antibody binding site.
The prototype sandwich ELISA based on the synthetic VHH and the immune scFv was
established. This is the first successful example of the combination of synthetic
and immune antibody libraries in a single sandwich immunoassay. Thus, our approach
could be used for the express isolation of antibody pairs and the development
of sandwich immunoassays for challenging antigens.
acknowledgement: This study was financially supported by the State Committee on Science
and Technology. We would like to thank Elena Tumar and Elena Kisileva at the Institute
of Bioorganic Chemistry of NASB for their kind assistance with mouse immunizations.
article_processing_charge: No
article_type: original
author:
- first_name: Dmitri
full_name: Dormeshkin, Dmitri
last_name: Dormeshkin
- first_name: Michail
full_name: Shapira, Michail
last_name: Shapira
- first_name: Alena
full_name: Karputs, Alena
last_name: Karputs
- first_name: Anton
full_name: Kavaleuski, Anton
id: 62304f89-eb97-11eb-a6c2-8903dd183976
last_name: Kavaleuski
orcid: 0000-0003-2091-526X
- first_name: Ivan
full_name: Kuzminski, Ivan
last_name: Kuzminski
- first_name: Elena
full_name: Stepanova, Elena
last_name: Stepanova
- first_name: Andrei
full_name: Gilep, Andrei
last_name: Gilep
citation:
ama: Dormeshkin D, Shapira M, Karputs A, et al. Combining of synthetic VHH and immune
scFv libraries for pregnancy-associated glycoproteins ELISA development. Applied
Microbiology and Biotechnology. 2022;106:5093-5103. doi:10.1007/s00253-022-12022-w
apa: Dormeshkin, D., Shapira, M., Karputs, A., Kavaleuski, A., Kuzminski, I., Stepanova,
E., & Gilep, A. (2022). Combining of synthetic VHH and immune scFv libraries
for pregnancy-associated glycoproteins ELISA development. Applied Microbiology
and Biotechnology. Springer Nature. https://doi.org/10.1007/s00253-022-12022-w
chicago: Dormeshkin, Dmitri, Michail Shapira, Alena Karputs, Anton Kavaleuski, Ivan
Kuzminski, Elena Stepanova, and Andrei Gilep. “Combining of Synthetic VHH and
Immune ScFv Libraries for Pregnancy-Associated Glycoproteins ELISA Development.”
Applied Microbiology and Biotechnology. Springer Nature, 2022. https://doi.org/10.1007/s00253-022-12022-w.
ieee: D. Dormeshkin et al., “Combining of synthetic VHH and immune scFv libraries
for pregnancy-associated glycoproteins ELISA development,” Applied Microbiology
and Biotechnology, vol. 106. Springer Nature, pp. 5093–5103, 2022.
ista: Dormeshkin D, Shapira M, Karputs A, Kavaleuski A, Kuzminski I, Stepanova E,
Gilep A. 2022. Combining of synthetic VHH and immune scFv libraries for pregnancy-associated
glycoproteins ELISA development. Applied Microbiology and Biotechnology. 106,
5093–5103.
mla: Dormeshkin, Dmitri, et al. “Combining of Synthetic VHH and Immune ScFv Libraries
for Pregnancy-Associated Glycoproteins ELISA Development.” Applied Microbiology
and Biotechnology, vol. 106, Springer Nature, 2022, pp. 5093–103, doi:10.1007/s00253-022-12022-w.
short: D. Dormeshkin, M. Shapira, A. Karputs, A. Kavaleuski, I. Kuzminski, E. Stepanova,
A. Gilep, Applied Microbiology and Biotechnology 106 (2022) 5093–5103.
date_created: 2022-06-26T22:01:34Z
date_published: 2022-08-01T00:00:00Z
date_updated: 2023-10-10T07:15:02Z
day: '01'
department:
- _id: GradSch
- _id: LeSa
doi: 10.1007/s00253-022-12022-w
external_id:
isi:
- '000813677500001'
pmid:
- '35723693'
intvolume: ' 106'
isi: 1
language:
- iso: eng
month: '08'
oa_version: None
page: 5093-5103
pmid: 1
publication: Applied Microbiology and Biotechnology
publication_identifier:
eissn:
- 1432-0614
issn:
- 0175-7598
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
scopus_import: '1'
status: public
title: Combining of synthetic VHH and immune scFv libraries for pregnancy-associated
glycoproteins ELISA development
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 106
year: '2022'
...
---
_id: '11489'
abstract:
- lang: eng
text: Much of plant development depends on cell-to-cell redistribution of the plant
hormone auxin, which is facilitated by the plasma membrane (PM) localized PIN
FORMED (PIN) proteins. Auxin export activity, developmental roles, subcellular
trafficking, and polarity of PINs have been well studied, but their structure
remains elusive besides a rough outline that they contain two groups of 5 alpha-helices
connected by a large hydrophilic loop (HL). Here, we focus on the PIN1 HL as we
could produce it in sufficient quantities for biochemical investigations to provide
insights into its secondary structure. Circular dichroism (CD) studies revealed
its nature as an intrinsically disordered protein (IDP), manifested by the increase
of structure content upon thermal melting. Consistent with IDPs serving as interaction
platforms, PIN1 loops homodimerize. PIN1 HL cytoplasmic overexpression in Arabidopsis
disrupts early endocytic trafficking of PIN1 and PIN2 and causes defects in the
cotyledon vasculature formation. In summary, we demonstrate that PIN1 HL has an
intrinsically disordered nature, which must be considered to gain further structural
insights. Some secondary structures may form transiently during pairing with known
and yet-to-be-discovered interactors.
acknowledgement: 'We thank Charo del Genio from Coventry University and Richard Napier
from the University of Warwick for helpful discussion concerning protein modeling
and inspiration concerning CD spectroscopy, respectively. We thank Jan Hejatko for
sharing the published AHP2 construct. We also thank Josef Houser from the core facility
BIC CEITEC for valuable assistance, discussions, and ideas relating to CD. We acknowledge
the: Core Facility CELLIM of CEITEC supported by the Czech-BioImaging large RI project
(LM2018129 funded by MEYS CR), part of the Euro-BioImaging (www.eurobioimaging.eu
accessed on 1 January 2016) ALM and medical imaging Node (Brno, CZ), CF Biomolecular
Interactions and Crystallization of CIISB, Instruct-CZ Centre, supported by MEYS
CR (LM2018127) and European Regional Development Fund-Project “UP CIISB“ (No. CZ.02.1.01/0.0/0.0/18_046/0015974)
for their support with obtaining scientific data presented in this paper; Plant
Sciences Core Facility of CEITEC Masaryk University for technical support. Open
Access Funding by the Austrian Science Fund (FWF).'
article_processing_charge: Yes
article_type: original
author:
- first_name: V
full_name: Bilanovičová, V
last_name: Bilanovičová
- first_name: N
full_name: Rýdza, N
last_name: Rýdza
- first_name: L
full_name: Koczka, L
last_name: Koczka
- first_name: M
full_name: Hess, M
last_name: Hess
- first_name: E
full_name: Feraru, E
last_name: Feraru
- first_name: Jiří
full_name: Friml, Jiří
id: 4159519E-F248-11E8-B48F-1D18A9856A87
last_name: Friml
orcid: 0000-0002-8302-7596
- first_name: T
full_name: Nodzyński, T
last_name: Nodzyński
citation:
ama: Bilanovičová V, Rýdza N, Koczka L, et al. The hydrophilic loop of Arabidopsis
PIN1 auxin efflux carrier harbors hallmarks of an intrinsically disordered protein.
International Journal of Molecular Sciences. 2022;23(11):6352. doi:10.3390/ijms23116352
apa: Bilanovičová, V., Rýdza, N., Koczka, L., Hess, M., Feraru, E., Friml, J., &
Nodzyński, T. (2022). The hydrophilic loop of Arabidopsis PIN1 auxin efflux carrier
harbors hallmarks of an intrinsically disordered protein. International Journal
of Molecular Sciences. MDPI. https://doi.org/10.3390/ijms23116352
chicago: Bilanovičová, V, N Rýdza, L Koczka, M Hess, E Feraru, Jiří Friml, and T
Nodzyński. “The Hydrophilic Loop of Arabidopsis PIN1 Auxin Efflux Carrier Harbors
Hallmarks of an Intrinsically Disordered Protein.” International Journal of
Molecular Sciences. MDPI, 2022. https://doi.org/10.3390/ijms23116352.
ieee: V. Bilanovičová et al., “The hydrophilic loop of Arabidopsis PIN1 auxin
efflux carrier harbors hallmarks of an intrinsically disordered protein,” International
Journal of Molecular Sciences, vol. 23, no. 11. MDPI, p. 6352, 2022.
ista: Bilanovičová V, Rýdza N, Koczka L, Hess M, Feraru E, Friml J, Nodzyński T.
2022. The hydrophilic loop of Arabidopsis PIN1 auxin efflux carrier harbors hallmarks
of an intrinsically disordered protein. International Journal of Molecular Sciences.
23(11), 6352.
mla: Bilanovičová, V., et al. “The Hydrophilic Loop of Arabidopsis PIN1 Auxin Efflux
Carrier Harbors Hallmarks of an Intrinsically Disordered Protein.” International
Journal of Molecular Sciences, vol. 23, no. 11, MDPI, 2022, p. 6352, doi:10.3390/ijms23116352.
short: V. Bilanovičová, N. Rýdza, L. Koczka, M. Hess, E. Feraru, J. Friml, T. Nodzyński,
International Journal of Molecular Sciences 23 (2022) 6352.
corr_author: '1'
date_created: 2022-07-05T15:14:34Z
date_published: 2022-06-06T00:00:00Z
date_updated: 2025-04-15T08:12:07Z
day: '06'
ddc:
- '570'
department:
- _id: JiFr
doi: 10.3390/ijms23116352
external_id:
isi:
- '000808733300001'
pmid:
- '35683031'
file:
- access_level: open_access
checksum: e997a57a928ec9d51fad8ce824a05935
content_type: application/pdf
creator: cchlebak
date_created: 2022-07-06T07:36:59Z
date_updated: 2022-07-06T07:36:59Z
file_id: '11492'
file_name: 2022_IntJMolSci_Bilanovicova.pdf
file_size: 2324542
relation: main_file
success: 1
file_date_updated: 2022-07-06T07:36:59Z
has_accepted_license: '1'
intvolume: ' 23'
isi: 1
issue: '11'
language:
- iso: eng
month: '06'
oa: 1
oa_version: Published Version
page: '6352'
pmid: 1
project:
- _id: 262EF96E-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: P29988
name: RNA-directed DNA methylation in plant development
publication: International Journal of Molecular Sciences
publication_identifier:
issn:
- 1422-0067
publication_status: published
publisher: MDPI
quality_controlled: '1'
scopus_import: '1'
status: public
title: The hydrophilic loop of Arabidopsis PIN1 auxin efflux carrier harbors hallmarks
of an intrinsically disordered protein
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: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87
volume: 23
year: '2022'
...
---
_id: '11542'
article_processing_charge: No
author:
- first_name: Rouven
full_name: Schulz, Rouven
id: 4C5E7B96-F248-11E8-B48F-1D18A9856A87
last_name: Schulz
orcid: 0000-0001-5297-733X
citation:
ama: Schulz R. Source Data (Chimeric GPCRs mimic distinct signaling pathways and
modulate microglia responses). 2022. doi:10.15479/AT:ISTA:11542
apa: Schulz, R. (2022). Source Data (Chimeric GPCRs mimic distinct signaling pathways
and modulate microglia responses). Institute of Science and Technology Austria.
https://doi.org/10.15479/AT:ISTA:11542
chicago: Schulz, Rouven. “Source Data (Chimeric GPCRs Mimic Distinct Signaling Pathways
and Modulate Microglia Responses).” Institute of Science and Technology Austria,
2022. https://doi.org/10.15479/AT:ISTA:11542.
ieee: R. Schulz, “Source Data (Chimeric GPCRs mimic distinct signaling pathways
and modulate microglia responses).” Institute of Science and Technology Austria,
2022.
ista: Schulz R. 2022. Source Data (Chimeric GPCRs mimic distinct signaling pathways
and modulate microglia responses), Institute of Science and Technology Austria,
10.15479/AT:ISTA:11542.
mla: Schulz, Rouven. Source Data (Chimeric GPCRs Mimic Distinct Signaling Pathways
and Modulate Microglia Responses). Institute of Science and Technology Austria,
2022, doi:10.15479/AT:ISTA:11542.
short: R. Schulz, (2022).
contributor:
- contributor_type: contact_person
first_name: Sandra
id: 36ACD32E-F248-11E8-B48F-1D18A9856A87
last_name: Siegert
orcid: 0000-0001-8635-0877
corr_author: '1'
date_created: 2022-07-08T11:03:02Z
date_published: 2022-01-01T00:00:00Z
date_updated: 2025-04-15T07:27:21Z
department:
- _id: GradSch
- _id: SaSi
doi: 10.15479/AT:ISTA:11542
file:
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date_created: 2022-07-08T10:56:52Z
date_updated: 2022-07-08T10:56:52Z
file_id: '11543'
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file_date_updated: 2022-07-08T10:56:52Z
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oa: 1
oa_version: None
publisher: Institute of Science and Technology Austria
related_material:
link:
- relation: contains
url: https://www.biorxiv.org/content/10.1101/2021.06.21.449162v1
record:
- id: '11995'
relation: used_in_publication
status: public
status: public
title: Source Data (Chimeric GPCRs mimic distinct signaling pathways and modulate
microglia responses)
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: research_data
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
year: '2022'
...
---
_id: '11545'
abstract:
- lang: eng
text: "We classify contravariant pairings between standard Whittaker modules and
Verma modules over a complex semisimple Lie algebra. These contravariant pairings
are useful in extending several classical techniques for category O to the Miličić–Soergel
category N . We introduce a class of costandard modules which generalize dual
Verma modules, and describe canonical maps from standard to costandard modules
in terms of contravariant pairings.\r\nWe show that costandard modules have unique
irreducible submodules and share the same composition factors as the corresponding
standard Whittaker modules. We show that costandard modules give an algebraic
characterization of the global sections of costandard twisted Harish-Chandra sheaves
on the associated flag variety, which are defined using holonomic duality of D-modules.
We prove that with these costandard modules, blocks of category\r\nN have the
structure of highest weight categories and we establish a BGG reciprocity theorem
for N ."
acknowledgement: We thank Catharina Stroppel and Jens Niklas Eberhardt for interesting
discussions. The first author acknowledges the support of the European Union's Horizon
2020 research and innovation programme under the Marie Skłodowska-Curie Grant Agreement
No. 754411. The second author is supported by the National Science Foundation Award
No. 1803059 and the Australian Research Council grant DP170101579.
article_processing_charge: Yes (via OA deal)
article_type: original
author:
- first_name: Adam
full_name: Brown, Adam
id: 70B7FDF6-608D-11E9-9333-8535E6697425
last_name: Brown
- first_name: Anna
full_name: Romanov, Anna
last_name: Romanov
citation:
ama: Brown A, Romanov A. Contravariant pairings between standard Whittaker modules
and Verma modules. Journal of Algebra. 2022;609(11):145-179. doi:10.1016/j.jalgebra.2022.06.017
apa: Brown, A., & Romanov, A. (2022). Contravariant pairings between standard
Whittaker modules and Verma modules. Journal of Algebra. Elsevier. https://doi.org/10.1016/j.jalgebra.2022.06.017
chicago: Brown, Adam, and Anna Romanov. “Contravariant Pairings between Standard
Whittaker Modules and Verma Modules.” Journal of Algebra. Elsevier, 2022.
https://doi.org/10.1016/j.jalgebra.2022.06.017.
ieee: A. Brown and A. Romanov, “Contravariant pairings between standard Whittaker
modules and Verma modules,” Journal of Algebra, vol. 609, no. 11. Elsevier,
pp. 145–179, 2022.
ista: Brown A, Romanov A. 2022. Contravariant pairings between standard Whittaker
modules and Verma modules. Journal of Algebra. 609(11), 145–179.
mla: Brown, Adam, and Anna Romanov. “Contravariant Pairings between Standard Whittaker
Modules and Verma Modules.” Journal of Algebra, vol. 609, no. 11, Elsevier,
2022, pp. 145–79, doi:10.1016/j.jalgebra.2022.06.017.
short: A. Brown, A. Romanov, Journal of Algebra 609 (2022) 145–179.
corr_author: '1'
date_created: 2022-07-08T11:40:07Z
date_published: 2022-11-01T00:00:00Z
date_updated: 2025-04-14T07:43:58Z
day: '01'
ddc:
- '510'
department:
- _id: HeEd
doi: 10.1016/j.jalgebra.2022.06.017
ec_funded: 1
external_id:
isi:
- '000861841100004'
file:
- access_level: open_access
checksum: 82abaee3d7837f703e499a9ecbb25b7c
content_type: application/pdf
creator: dernst
date_created: 2023-02-02T07:32:48Z
date_updated: 2023-02-02T07:32:48Z
file_id: '12473'
file_name: 2022_JournalAlgebra_Brown.pdf
file_size: 582962
relation: main_file
success: 1
file_date_updated: 2023-02-02T07:32:48Z
has_accepted_license: '1'
intvolume: ' 609'
isi: 1
issue: '11'
keyword:
- Algebra and Number Theory
language:
- iso: eng
month: '11'
oa: 1
oa_version: Published Version
page: 145-179
project:
- _id: 260C2330-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '754411'
name: ISTplus - Postdoctoral Fellowships
publication: Journal of Algebra
publication_identifier:
issn:
- 0021-8693
publication_status: published
publisher: Elsevier
quality_controlled: '1'
scopus_import: '1'
status: public
title: Contravariant pairings between standard Whittaker modules and Verma modules
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: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
volume: 609
year: '2022'
...
---
_id: '11546'
abstract:
- lang: eng
text: Local adaptation leads to differences between populations within a species.
In many systems, similar environmental contrasts occur repeatedly, sometimes driving
parallel phenotypic evolution. Understanding the genomic basis of local adaptation
and parallel evolution is a major goal of evolutionary genomics. It is now known
that by preventing the break-up of favourable combinations of alleles across multiple
loci, genetic architectures that reduce recombination, like chromosomal inversions,
can make an important contribution to local adaptation. However, little is known
about whether inversions also contribute disproportionately to parallel evolution.
Our aim here is to highlight this knowledge gap, to showcase existing studies,
and to illustrate the differences between genomic architectures with and without
inversions using simple models. We predict that by generating stronger effective
selection, inversions can sometimes speed up the parallel adaptive process or
enable parallel adaptation where it would be impossible otherwise, but this is
highly dependent on the spatial setting. We highlight that further empirical work
is needed, in particular to cover a broader taxonomic range and to understand
the relative importance of inversions compared to genomic regions without inversions.
acknowledgement: We thank the editor and two anonymous reviewers for their helpful
and interesting comments on this manuscript.
article_number: '20210203'
article_processing_charge: Yes (via OA deal)
article_type: original
author:
- first_name: Anja M
full_name: Westram, Anja M
id: 3C147470-F248-11E8-B48F-1D18A9856A87
last_name: Westram
orcid: 0000-0003-1050-4969
- first_name: Rui
full_name: Faria, Rui
last_name: Faria
- first_name: Kerstin
full_name: Johannesson, Kerstin
last_name: Johannesson
- first_name: Roger
full_name: Butlin, Roger
last_name: Butlin
- 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: 'Westram AM, Faria R, Johannesson K, Butlin R, Barton NH. Inversions and parallel
evolution. Philosophical Transactions of the Royal Society B: Biological Sciences.
2022;377(1856). doi:10.1098/rstb.2021.0203'
apa: 'Westram, A. M., Faria, R., Johannesson, K., Butlin, R., & Barton, N. H.
(2022). Inversions and parallel evolution. Philosophical Transactions of the
Royal Society B: Biological Sciences. Royal Society of London. https://doi.org/10.1098/rstb.2021.0203'
chicago: 'Westram, Anja M, Rui Faria, Kerstin Johannesson, Roger Butlin, and Nicholas
H Barton. “Inversions and Parallel Evolution.” Philosophical Transactions of
the Royal Society B: Biological Sciences. Royal Society of London, 2022. https://doi.org/10.1098/rstb.2021.0203.'
ieee: 'A. M. Westram, R. Faria, K. Johannesson, R. Butlin, and N. H. Barton, “Inversions
and parallel evolution,” Philosophical Transactions of the Royal Society B:
Biological Sciences, vol. 377, no. 1856. Royal Society of London, 2022.'
ista: 'Westram AM, Faria R, Johannesson K, Butlin R, Barton NH. 2022. Inversions
and parallel evolution. Philosophical Transactions of the Royal Society B: Biological
Sciences. 377(1856), 20210203.'
mla: 'Westram, Anja M., et al. “Inversions and Parallel Evolution.” Philosophical
Transactions of the Royal Society B: Biological Sciences, vol. 377, no. 1856,
20210203, Royal Society of London, 2022, doi:10.1098/rstb.2021.0203.'
short: 'A.M. Westram, R. Faria, K. Johannesson, R. Butlin, N.H. Barton, Philosophical
Transactions of the Royal Society B: Biological Sciences 377 (2022).'
corr_author: '1'
date_created: 2022-07-08T11:41:56Z
date_published: 2022-08-01T00:00:00Z
date_updated: 2025-06-12T06:10:18Z
day: '01'
ddc:
- '570'
department:
- _id: BeVi
- _id: NiBa
doi: 10.1098/rstb.2021.0203
external_id:
isi:
- '000812317300005'
pmid:
- '35694747'
file:
- access_level: open_access
checksum: 49f69428f3dcf5ce3ff281f7d199e9df
content_type: application/pdf
creator: dernst
date_created: 2023-02-02T08:20:29Z
date_updated: 2023-02-02T08:20:29Z
file_id: '12479'
file_name: 2022_PhilosophicalTransactionsB_Westram.pdf
file_size: 920304
relation: main_file
success: 1
file_date_updated: 2023-02-02T08:20:29Z
has_accepted_license: '1'
intvolume: ' 377'
isi: 1
issue: '1856'
keyword:
- General Agricultural and Biological Sciences
- General Biochemistry
- Genetics and Molecular Biology
language:
- iso: eng
month: '08'
oa: 1
oa_version: Published Version
pmid: 1
project:
- _id: 05959E1C-7A3F-11EA-A408-12923DDC885E
grant_number: P32166
name: Snapdragon Speciation
publication: 'Philosophical Transactions of the Royal Society B: Biological Sciences'
publication_identifier:
eissn:
- 1471-2970
issn:
- 0962-8436
publication_status: published
publisher: Royal Society of London
quality_controlled: '1'
scopus_import: '1'
status: public
title: Inversions and parallel evolution
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 377
year: '2022'
...
---
OA_place: publisher
OA_type: hybrid
_id: '11553'
abstract:
- lang: eng
text: "In holomorphic dynamics, complex box mappings arise as first return maps
to wellchosen domains. They are a generalization of polynomial-like mapping, where
the domain of the return map can have infinitely many components. They turned
out to be extremely useful in tackling diverse problems. The purpose of this paper
is:\r\n• To illustrate some pathologies that can occur when a complex box mapping
is not induced by a globally defined map and when its domain has infinitely many
components, and to give conditions to avoid these issues.\r\n• To show that once
one has a box mapping for a rational map, these conditions can be assumed to hold
in a very natural setting. Thus, we call such complex box mappings dynamically
natural. Having such box mappings is the first step in tackling many problems
in one-dimensional dynamics.\r\n• Many results in holomorphic dynamics rely on
an interplay between combinatorial and analytic techniques. In this setting, some
of these tools are:\r\n • the Enhanced Nest (a nest of puzzle pieces around critical
points) from Kozlovski, Shen, van Strien (AnnMath 165:749–841, 2007), referred
to below as KSS;\r\n • the Covering Lemma (which controls the moduli of pullbacks
of annuli) from Kahn and Lyubich (Ann Math 169(2):561–593, 2009);\r\n • the
QC-Criterion and the Spreading Principle from KSS.\r\nThe purpose of this paper
is to make these tools more accessible so that they can be used as a ‘black box’,
so one does not have to redo the proofs in new settings.\r\n• To give an intuitive,
but also rather detailed, outline of the proof from KSS and Kozlovski and van
Strien (Proc Lond Math Soc (3) 99:275–296, 2009) of the following results for
non-renormalizable dynamically natural complex box mappings:\r\n • puzzle pieces
shrink to points,\r\n • (under some assumptions) topologically conjugate non-renormalizable
polynomials and box mappings are quasiconformally conjugate.\r\n• We prove the
fundamental ergodic properties for dynamically natural box mappings. This leads
to some necessary conditions for when such a box mapping supports a measurable
invariant line field on its filled Julia set. These mappings\r\nare the analogues
of Lattès maps in this setting.\r\n• We prove a version of Mañé’s Theorem for
complex box mappings concerning expansion along orbits of points that avoid a
neighborhood of the set of critical points."
acknowledgement: We would also like to thank Dzmitry Dudko and Dierk Schleicher for
many stimulating discussions and encouragement during our work on this project,
and Weixiao Shen, Mikhail Hlushchanka and the referee for helpful comments. We are
grateful to Leon Staresinic who carefully read the revised version of the manuscript
and provided many helpful suggestions.
article_processing_charge: No
article_type: original
author:
- first_name: Trevor
full_name: Clark, Trevor
last_name: Clark
- first_name: Kostiantyn
full_name: Drach, Kostiantyn
id: fe8209e2-906f-11eb-847d-950f8fc09115
last_name: Drach
orcid: 0000-0002-9156-8616
- first_name: Oleg
full_name: Kozlovski, Oleg
last_name: Kozlovski
- first_name: Sebastian Van
full_name: Strien, Sebastian Van
last_name: Strien
citation:
ama: Clark T, Drach K, Kozlovski O, Strien SV. The dynamics of complex box mappings.
Arnold Mathematical Journal. 2022;8(2):319-410. doi:10.1007/s40598-022-00200-7
apa: Clark, T., Drach, K., Kozlovski, O., & Strien, S. V. (2022). The dynamics
of complex box mappings. Arnold Mathematical Journal. Springer Nature.
https://doi.org/10.1007/s40598-022-00200-7
chicago: Clark, Trevor, Kostiantyn Drach, Oleg Kozlovski, and Sebastian Van Strien.
“The Dynamics of Complex Box Mappings.” Arnold Mathematical Journal. Springer
Nature, 2022. https://doi.org/10.1007/s40598-022-00200-7.
ieee: T. Clark, K. Drach, O. Kozlovski, and S. V. Strien, “The dynamics of complex
box mappings,” Arnold Mathematical Journal, vol. 8, no. 2. Springer Nature,
pp. 319–410, 2022.
ista: Clark T, Drach K, Kozlovski O, Strien SV. 2022. The dynamics of complex box
mappings. Arnold Mathematical Journal. 8(2), 319–410.
mla: Clark, Trevor, et al. “The Dynamics of Complex Box Mappings.” Arnold Mathematical
Journal, vol. 8, no. 2, Springer Nature, 2022, pp. 319–410, doi:10.1007/s40598-022-00200-7.
short: T. Clark, K. Drach, O. Kozlovski, S.V. Strien, Arnold Mathematical Journal
8 (2022) 319–410.
date_created: 2022-07-10T22:01:53Z
date_published: 2022-06-01T00:00:00Z
date_updated: 2025-07-10T11:50:12Z
day: '01'
ddc:
- '500'
department:
- _id: VaKa
doi: 10.1007/s40598-022-00200-7
ec_funded: 1
file:
- access_level: open_access
checksum: 16e7c659dee9073c6c8aeb87316ef201
content_type: application/pdf
creator: kschuh
date_created: 2022-07-12T10:04:55Z
date_updated: 2022-07-12T10:04:55Z
file_id: '11559'
file_name: 2022_ArnoldMathematicalJournal_Clark.pdf
file_size: 2509915
relation: main_file
success: 1
file_date_updated: 2022-07-12T10:04:55Z
has_accepted_license: '1'
intvolume: ' 8'
issue: '2'
language:
- iso: eng
month: '06'
oa: 1
oa_version: Published Version
page: 319-410
project:
- _id: 9B8B92DE-BA93-11EA-9121-9846C619BF3A
call_identifier: H2020
grant_number: '885707'
name: Spectral rigidity and integrability for billiards and geodesic flows
publication: Arnold Mathematical Journal
publication_identifier:
eissn:
- 2199-6806
issn:
- 2199-6792
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
related_material:
link:
- relation: erratum
url: https://doi.org/10.1007/s40598-022-00209-y
- relation: erratum
url: https://doi.org/10.1007/s40598-022-00218-x
scopus_import: '1'
status: public
title: The dynamics of complex box mappings
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 8
year: '2022'
...