---
_id: '11343'
abstract:
- lang: eng
text: Multistable systems are characterized by exhibiting domain coexistence, where
each domain accounts for the different equilibrium states. In case these systems
are described by vectorial fields, domains can be connected through topological
defects. Vortices are one of the most frequent and studied topological defect
points. Optical vortices are equally relevant for their fundamental features as
beams with topological features and their applications in image processing, telecommunications,
optical tweezers, and quantum information. A natural source of optical vortices
is the interaction of light beams with matter vortices in liquid crystal cells.
The rhythms that govern the emergence of matter vortices due to fluctuations are
not established. Here, we investigate the nucleation mechanisms of the matter
vortices in liquid crystal cells and establish statistical laws that govern them.
Based on a stochastic amplitude equation, the law for the number of nucleated
vortices as a function of anisotropy, voltage, and noise level intensity is set.
Experimental observations in a nematic liquid crystal cell with homeotropic anchoring
and a negative anisotropic dielectric constant under the influence of a transversal
electric field show a qualitative agreement with the theoretical findings.
acknowledgement: "The authors thank Enrique Calisto,Michal Kowalczyk, and Michel Ferre
for fructified discussions. This work was funded by ANID—Millennium Science Initiative
Program—ICN17_012. MGC is thankful for financial support from the Fondecyt 1210353
project.\r\nOpen access funding provided by Institute of Science and Technology
(IST Austria)."
article_processing_charge: Yes (via OA deal)
article_type: original
author:
- first_name: Esteban
full_name: Aguilera, Esteban
last_name: Aguilera
- first_name: Marcel G.
full_name: Clerc, Marcel G.
last_name: Clerc
- first_name: Valeska
full_name: Zambra, Valeska
id: 467ed36b-dc96-11ea-b7c8-b043a380b282
last_name: Zambra
citation:
ama: Aguilera E, Clerc MG, Zambra V. Vortices nucleation by inherent fluctuations
in nematic liquid crystal cells. Nonlinear Dynamics. 2022;108:3209-3218.
doi:10.1007/s11071-022-07396-5
apa: Aguilera, E., Clerc, M. G., & Zambra, V. (2022). Vortices nucleation by
inherent fluctuations in nematic liquid crystal cells. Nonlinear Dynamics.
Springer Nature. https://doi.org/10.1007/s11071-022-07396-5
chicago: Aguilera, Esteban, Marcel G. Clerc, and Valeska Zambra. “Vortices Nucleation
by Inherent Fluctuations in Nematic Liquid Crystal Cells.” Nonlinear Dynamics.
Springer Nature, 2022. https://doi.org/10.1007/s11071-022-07396-5.
ieee: E. Aguilera, M. G. Clerc, and V. Zambra, “Vortices nucleation by inherent
fluctuations in nematic liquid crystal cells,” Nonlinear Dynamics, vol.
108. Springer Nature, pp. 3209–3218, 2022.
ista: Aguilera E, Clerc MG, Zambra V. 2022. Vortices nucleation by inherent fluctuations
in nematic liquid crystal cells. Nonlinear Dynamics. 108, 3209–3218.
mla: Aguilera, Esteban, et al. “Vortices Nucleation by Inherent Fluctuations in
Nematic Liquid Crystal Cells.” Nonlinear Dynamics, vol. 108, Springer Nature,
2022, pp. 3209–18, doi:10.1007/s11071-022-07396-5.
short: E. Aguilera, M.G. Clerc, V. Zambra, Nonlinear Dynamics 108 (2022) 3209–3218.
date_created: 2022-05-02T07:01:59Z
date_published: 2022-06-01T00:00:00Z
date_updated: 2023-08-03T06:46:54Z
day: '01'
ddc:
- '530'
department:
- _id: KiMo
doi: 10.1007/s11071-022-07396-5
external_id:
isi:
- '000784871800001'
file:
- access_level: open_access
checksum: 7d80cdece4e1b1c2106e6772a9622f60
content_type: application/pdf
creator: dernst
date_created: 2022-08-05T06:13:19Z
date_updated: 2022-08-05T06:13:19Z
file_id: '11728'
file_name: 2022_NonlinearDyn_Aguilera.pdf
file_size: 1416049
relation: main_file
success: 1
file_date_updated: 2022-08-05T06:13:19Z
has_accepted_license: '1'
intvolume: ' 108'
isi: 1
keyword:
- Electrical and Electronic Engineering
- Applied Mathematics
- Mechanical Engineering
- Ocean Engineering
- Aerospace Engineering
- Control and Systems Engineering
language:
- iso: eng
month: '06'
oa: 1
oa_version: Published Version
page: 3209-3218
publication: Nonlinear Dynamics
publication_identifier:
eissn:
- 1573-269X
issn:
- 0924-090X
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
scopus_import: '1'
status: public
title: Vortices nucleation by inherent fluctuations in nematic liquid crystal cells
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: 108
year: '2022'
...
---
_id: '11344'
abstract:
- lang: eng
text: Until recently, Shigella and enteroinvasive Escherichia coli were thought
to be primate-restricted pathogens. The base of their pathogenicity is the type
3 secretion system (T3SS) encoded by the pINV virulence plasmid, which facilitates
host cell invasion and subsequent proliferation. A large family of T3SS effectors,
E3 ubiquitin-ligases encoded by the ipaH genes, have a key role in the Shigella
pathogenicity through the modulation of cellular ubiquitination that degrades
host proteins. However, recent genomic studies identified ipaH genes in the genomes
of Escherichia marmotae, a potential marmot pathogen, and an E. coli extracted
from fecal samples of bovine calves, suggesting that non-human hosts may also
be infected by these strains, potentially pathogenic to humans. We performed a
comparative genomic study of the functional repertoires in the ipaH gene family
in Shigella and enteroinvasive Escherichia from human and predicted non-human
hosts. We found that fewer than half of Shigella genomes had a complete set of
ipaH genes, with frequent gene losses and duplications that were not consistent
with the species tree and nomenclature. Non-human host IpaH proteins had a diverse
set of substrate-binding domains and, in contrast to the Shigella proteins, two
variants of the NEL C-terminal domain. Inconsistencies between strains phylogeny
and composition of effectors indicate horizontal gene transfer between E. coli
adapted to different hosts. These results provide a framework for understanding
of ipaH-mediated host-pathogens interactions and suggest a need for a genomic
study of fecal samples from diseased animals.
acknowledgement: 'The project was initiated with Aygul Minnegalieva and Yulia Yakovleva
at the Summer School of Molecular and Theoretical Biology (SMTB-2020), supported
by the Zimin Foundation. We thank Inna Shapovalenko, Daria Abuzova, Elizaveta Kaminskaya,
and Dmitriy Zvezdin for their contribution to the project during SMTB-2020. We also
thank Peter Vlasov for fruitful discussions.This study was supported by the Russian
Foundation for Basic Research (RFBR), Grant # 20-54-14005 and Fonds zur Förderung
der wissenschaftlichen Forschung (FWF), Grant # I5127-B. The work of OB is supported
by the European Union’s Horizon 2020 Research and Innovation Programme under the
Marie Skłodowska-Curie Grant Agreement No. 754411. '
article_number: '6868'
article_processing_charge: No
article_type: original
author:
- first_name: NO
full_name: Dranenko, NO
last_name: Dranenko
- first_name: MN
full_name: Tutukina, MN
last_name: Tutukina
- first_name: MS
full_name: Gelfand, MS
last_name: Gelfand
- first_name: Fyodor
full_name: Kondrashov, Fyodor
id: 44FDEF62-F248-11E8-B48F-1D18A9856A87
last_name: Kondrashov
orcid: 0000-0001-8243-4694
- first_name: Olga
full_name: Bochkareva, Olga
id: C4558D3C-6102-11E9-A62E-F418E6697425
last_name: Bochkareva
orcid: 0000-0003-1006-6639
citation:
ama: Dranenko N, Tutukina M, Gelfand M, Kondrashov F, Bochkareva O. Chromosome-encoded
IpaH ubiquitin ligases indicate non-human enteroinvasive Escherichia. Scientific
Reports. 2022;12. doi:10.1038/s41598-022-10827-3
apa: Dranenko, N., Tutukina, M., Gelfand, M., Kondrashov, F., & Bochkareva,
O. (2022). Chromosome-encoded IpaH ubiquitin ligases indicate non-human enteroinvasive
Escherichia. Scientific Reports. Springer Nature. https://doi.org/10.1038/s41598-022-10827-3
chicago: Dranenko, NO, MN Tutukina, MS Gelfand, Fyodor Kondrashov, and Olga Bochkareva.
“Chromosome-Encoded IpaH Ubiquitin Ligases Indicate Non-Human Enteroinvasive Escherichia.”
Scientific Reports. Springer Nature, 2022. https://doi.org/10.1038/s41598-022-10827-3.
ieee: N. Dranenko, M. Tutukina, M. Gelfand, F. Kondrashov, and O. Bochkareva, “Chromosome-encoded
IpaH ubiquitin ligases indicate non-human enteroinvasive Escherichia,” Scientific
Reports, vol. 12. Springer Nature, 2022.
ista: Dranenko N, Tutukina M, Gelfand M, Kondrashov F, Bochkareva O. 2022. Chromosome-encoded
IpaH ubiquitin ligases indicate non-human enteroinvasive Escherichia. Scientific
Reports. 12, 6868.
mla: Dranenko, NO, et al. “Chromosome-Encoded IpaH Ubiquitin Ligases Indicate Non-Human
Enteroinvasive Escherichia.” Scientific Reports, vol. 12, 6868, Springer
Nature, 2022, doi:10.1038/s41598-022-10827-3.
short: N. Dranenko, M. Tutukina, M. Gelfand, F. Kondrashov, O. Bochkareva, Scientific
Reports 12 (2022).
date_created: 2022-05-02T07:08:42Z
date_published: 2022-04-27T00:00:00Z
date_updated: 2023-08-03T06:59:49Z
day: '27'
ddc:
- '570'
department:
- _id: FyKo
doi: 10.1038/s41598-022-10827-3
ec_funded: 1
external_id:
isi:
- '000788639400032'
pmid:
- '35477739'
file:
- access_level: open_access
checksum: 12601b8a5c6b83bb618f92bcb963ecc9
content_type: application/pdf
creator: dernst
date_created: 2022-05-02T09:05:20Z
date_updated: 2022-05-02T09:05:20Z
file_id: '11349'
file_name: 2022_ScientificReports_Dranenko.pdf
file_size: 3564155
relation: main_file
success: 1
file_date_updated: 2022-05-02T09:05:20Z
has_accepted_license: '1'
intvolume: ' 12'
isi: 1
language:
- iso: eng
month: '04'
oa: 1
oa_version: Published Version
pmid: 1
project:
- _id: c098eddd-5a5b-11eb-8a69-abe27170a68f
grant_number: I05127
name: Evolutionary analysis of gene regulation
- _id: 260C2330-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '754411'
name: ISTplus - Postdoctoral Fellowships
publication: Scientific Reports
publication_identifier:
issn:
- 2045-2322
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
scopus_import: '1'
status: public
title: Chromosome-encoded IpaH ubiquitin ligases indicate non-human enteroinvasive
Escherichia
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: 12
year: '2022'
...
---
_id: '11351'
abstract:
- lang: eng
text: 'One hallmark of plant cells is their cell wall. They protect cells against
the environment and high turgor and mediate morphogenesis through the dynamics
of their mechanical and chemical properties. The walls are a complex polysaccharidic
structure. Although their biochemical composition is well known, how the different
components organize in the volume of the cell wall and interact with each other
is not well understood and yet is key to the wall’s mechanical properties. To
investigate the ultrastructure of the plant cell wall, we imaged the walls of
onion (Allium cepa) bulbs in a near-native state via cryo-focused ion beam milling
(cryo-FIB milling) and cryo-electron tomography (cryo-ET). This allowed the high-resolution
visualization of cellulose fibers in situ. We reveal the coexistence of dense
fiber fields bathed in a reticulated matrix we termed “meshing,” which is more
abundant at the inner surface of the cell wall. The fibers adopted a regular bimodal
angular distribution at all depths in the cell wall and bundled according to their
orientation, creating layers within the cell wall. Concomitantly, employing homogalacturonan
(HG)-specific enzymatic digestion, we observed changes in the meshing, suggesting
that it is—at least in part—composed of HG pectins. We propose the following model
for the construction of the abaxial epidermal primary cell wall: the cell deposits
successive layers of cellulose fibers at −45° and +45° relative to the cell’s
long axis and secretes the surrounding HG-rich meshing proximal to the plasma
membrane, which then migrates to more distal regions of the cell wall.'
acknowledgement: This work was supported by the Howard Hughes Medical Institute (HHMI)
and grant R35 GM122588 to G.J. and the Austrian Science Fund (FWF) P33367 to F.K.M.S.
We thank Noé Cochetel for his guidance and great help in data analysis, discovery,
and representation with the R software. We thank Hans-Ulrich Endress for graciously
providing us with the purified citrus pectin and Jozef Mravec for generating and
providing the COS488 probe. Cryo-EM work was done in the Beckman Institute Resource
Center for Transmission Electron Microscopy at Caltech. This article is subject
to HHMI’s Open Access to Publications policy. HHMI lab heads have previously granted
a nonexclusive CC BY 4.0 license to the public and a sublicensable license to HHMI
in their research articles. Pursuant to those licenses, the author accepted manuscript
of this article can be made freely available under a CC BY 4.0 license immediately
upon publication.
article_processing_charge: No
article_type: original
author:
- first_name: William J.
full_name: Nicolas, William J.
last_name: Nicolas
- first_name: Florian
full_name: Fäßler, Florian
id: 404F5528-F248-11E8-B48F-1D18A9856A87
last_name: Fäßler
orcid: 0000-0001-7149-769X
- first_name: Przemysław
full_name: Dutka, Przemysław
last_name: Dutka
- first_name: Florian KM
full_name: Schur, Florian KM
id: 48AD8942-F248-11E8-B48F-1D18A9856A87
last_name: Schur
orcid: 0000-0003-4790-8078
- first_name: Grant
full_name: Jensen, Grant
last_name: Jensen
- first_name: Elliot
full_name: Meyerowitz, Elliot
last_name: Meyerowitz
citation:
ama: Nicolas WJ, Fäßler F, Dutka P, Schur FK, Jensen G, Meyerowitz E. Cryo-electron
tomography of the onion cell wall shows bimodally oriented cellulose fibers and
reticulated homogalacturonan networks. Current Biology. 2022;32(11):P2375-2389.
doi:10.1016/j.cub.2022.04.024
apa: Nicolas, W. J., Fäßler, F., Dutka, P., Schur, F. K., Jensen, G., & Meyerowitz,
E. (2022). Cryo-electron tomography of the onion cell wall shows bimodally oriented
cellulose fibers and reticulated homogalacturonan networks. Current Biology.
Elsevier. https://doi.org/10.1016/j.cub.2022.04.024
chicago: Nicolas, William J., Florian Fäßler, Przemysław Dutka, Florian KM Schur,
Grant Jensen, and Elliot Meyerowitz. “Cryo-Electron Tomography of the Onion Cell
Wall Shows Bimodally Oriented Cellulose Fibers and Reticulated Homogalacturonan
Networks.” Current Biology. Elsevier, 2022. https://doi.org/10.1016/j.cub.2022.04.024.
ieee: W. J. Nicolas, F. Fäßler, P. Dutka, F. K. Schur, G. Jensen, and E. Meyerowitz,
“Cryo-electron tomography of the onion cell wall shows bimodally oriented cellulose
fibers and reticulated homogalacturonan networks,” Current Biology, vol.
32, no. 11. Elsevier, pp. P2375-2389, 2022.
ista: Nicolas WJ, Fäßler F, Dutka P, Schur FK, Jensen G, Meyerowitz E. 2022. Cryo-electron
tomography of the onion cell wall shows bimodally oriented cellulose fibers and
reticulated homogalacturonan networks. Current Biology. 32(11), P2375-2389.
mla: Nicolas, William J., et al. “Cryo-Electron Tomography of the Onion Cell Wall
Shows Bimodally Oriented Cellulose Fibers and Reticulated Homogalacturonan Networks.”
Current Biology, vol. 32, no. 11, Elsevier, 2022, pp. P2375-2389, doi:10.1016/j.cub.2022.04.024.
short: W.J. Nicolas, F. Fäßler, P. Dutka, F.K. Schur, G. Jensen, E. Meyerowitz,
Current Biology 32 (2022) P2375-2389.
date_created: 2022-05-04T06:22:06Z
date_published: 2022-06-06T00:00:00Z
date_updated: 2023-08-03T07:05:36Z
day: '06'
ddc:
- '570'
department:
- _id: FlSc
doi: 10.1016/j.cub.2022.04.024
external_id:
isi:
- '000822399200019'
pmid:
- '35508170'
file:
- access_level: open_access
checksum: af3f24d97c016d844df237abef987639
content_type: application/pdf
creator: dernst
date_created: 2022-08-05T06:29:18Z
date_updated: 2022-08-05T06:29:18Z
file_id: '11730'
file_name: 2022_CurrentBiology_Nicolas.pdf
file_size: 12827717
relation: main_file
success: 1
file_date_updated: 2022-08-05T06:29:18Z
has_accepted_license: '1'
intvolume: ' 32'
isi: 1
issue: '11'
keyword:
- General Agricultural and Biological Sciences
- General Biochemistry
- Genetics and Molecular Biology
language:
- iso: eng
month: '06'
oa: 1
oa_version: Published Version
page: P2375-2389
pmid: 1
project:
- _id: 9B954C5C-BA93-11EA-9121-9846C619BF3A
grant_number: P33367
name: Structure and isoform diversity of the Arp2/3 complex
publication: Current Biology
publication_identifier:
issn:
- 0960-9822
publication_status: published
publisher: Elsevier
quality_controlled: '1'
scopus_import: '1'
status: public
title: Cryo-electron tomography of the onion cell wall shows bimodally oriented cellulose
fibers and reticulated homogalacturonan networks
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: 32
year: '2022'
...
---
_id: '11353'
abstract:
- lang: eng
text: Micro- and nanoscale optical or microwave cavities are used in a wide range
of classical applications and quantum science experiments, ranging from precision
measurements, laser technologies to quantum control of mechanical motion. The
dissipative photon loss via absorption, present to some extent in any optical
cavity, is known to introduce thermo-optical effects and thereby impose fundamental
limits on precision measurements. Here, we theoretically and experimentally reveal
that such dissipative photon absorption can result in quantum feedback via in-loop
field detection of the absorbed optical field, leading to the intracavity field
fluctuations to be squashed or antisquashed. A closed-loop dissipative quantum
feedback to the cavity field arises. Strikingly, this modifies the optical cavity
susceptibility in coherent response measurements (capable of both increasing or
decreasing the bare cavity linewidth) and causes excess noise and correlations
in incoherent interferometric optomechanical measurements using a cavity, that
is parametrically coupled to a mechanical oscillator. We experimentally observe
such unanticipated dissipative dynamics in optomechanical spectroscopy of sideband-cooled
optomechanical crystal cavitiess at both cryogenic temperature (approximately
8 K) and ambient conditions. The dissipative feedback introduces effective modifications
to the optical cavity linewidth and the optomechanical scattering rate and gives
rise to excess imprecision noise in the interferometric quantum measurement of
mechanical motion. Such dissipative feedback differs fundamentally from a quantum
nondemolition feedback, e.g., optical Kerr squeezing. The dissipative feedback
itself always results in an antisqueezed out-of-loop optical field, while it can
enhance the coexisting Kerr squeezing under certain conditions. Our result applies
to cavity spectroscopy in both optical and superconducting microwave cavities,
and equally applies to any dissipative feedback mechanism of different bandwidth
inside the cavity. It has wide-ranging implications for future dissipation engineering,
such as dissipation enhanced sideband cooling and Kerr squeezing, quantum frequency
conversion, and nonreciprocity in photonic systems.
acknowledgement: "L.Q. acknowledges fruitful discussions with D. Vitali, R. Schnabel,
P.K. Lam, A. Nunnenkamp, and D. Malz. This work is supported by the EUH2020 research
and innovation programme under Grant No. 732894 (FET Proactive HOT), and the European
Research Council through \r\nGrant No. 835329 (ExCOM-cCEO). This work was further
supported by Swiss National Science Foundation under Grant Agreements No. 185870
(Ambizione) and No. 204927. Samples were fabricated at the Center of MicroNanoTechnology
(CMi) at EPFL and the Binnig and Rohrer Nanotechnology Center at IBM Research-Zurich."
article_number: '020309'
article_processing_charge: No
article_type: original
author:
- first_name: Liu
full_name: Qiu, Liu
id: 45e99c0d-1eb1-11eb-9b96-ed8ab2983cac
last_name: Qiu
orcid: 0000-0003-4345-4267
- first_name: Guanhao
full_name: Huang, Guanhao
last_name: Huang
- first_name: Itay
full_name: Shomroni, Itay
last_name: Shomroni
- first_name: Jiahe
full_name: Pan, Jiahe
last_name: Pan
- first_name: Paul
full_name: Seidler, Paul
last_name: Seidler
- first_name: Tobias J.
full_name: Kippenberg, Tobias J.
last_name: Kippenberg
citation:
ama: Qiu L, Huang G, Shomroni I, Pan J, Seidler P, Kippenberg TJ. Dissipative quantum
feedback in measurements using a parametrically coupled microcavity. PRX Quantum.
2022;3(2). doi:10.1103/PRXQuantum.3.020309
apa: Qiu, L., Huang, G., Shomroni, I., Pan, J., Seidler, P., & Kippenberg, T.
J. (2022). Dissipative quantum feedback in measurements using a parametrically
coupled microcavity. PRX Quantum. American Physical Society. https://doi.org/10.1103/PRXQuantum.3.020309
chicago: Qiu, Liu, Guanhao Huang, Itay Shomroni, Jiahe Pan, Paul Seidler, and Tobias
J. Kippenberg. “Dissipative Quantum Feedback in Measurements Using a Parametrically
Coupled Microcavity.” PRX Quantum. American Physical Society, 2022. https://doi.org/10.1103/PRXQuantum.3.020309.
ieee: L. Qiu, G. Huang, I. Shomroni, J. Pan, P. Seidler, and T. J. Kippenberg, “Dissipative
quantum feedback in measurements using a parametrically coupled microcavity,”
PRX Quantum, vol. 3, no. 2. American Physical Society, 2022.
ista: Qiu L, Huang G, Shomroni I, Pan J, Seidler P, Kippenberg TJ. 2022. Dissipative
quantum feedback in measurements using a parametrically coupled microcavity. PRX
Quantum. 3(2), 020309.
mla: Qiu, Liu, et al. “Dissipative Quantum Feedback in Measurements Using a Parametrically
Coupled Microcavity.” PRX Quantum, vol. 3, no. 2, 020309, American Physical
Society, 2022, doi:10.1103/PRXQuantum.3.020309.
short: L. Qiu, G. Huang, I. Shomroni, J. Pan, P. Seidler, T.J. Kippenberg, PRX Quantum
3 (2022).
date_created: 2022-05-08T22:01:43Z
date_published: 2022-04-13T00:00:00Z
date_updated: 2023-08-03T07:05:00Z
day: '13'
ddc:
- '530'
department:
- _id: JoFi
doi: 10.1103/PRXQuantum.3.020309
ec_funded: 1
external_id:
isi:
- '000789316700001'
file:
- access_level: open_access
checksum: 35ff9ddf1d54f64432e435b660edaeb6
content_type: application/pdf
creator: dernst
date_created: 2022-05-09T07:10:51Z
date_updated: 2022-05-09T07:10:51Z
file_id: '11358'
file_name: 2022_PRXQuantum_Qiu.pdf
file_size: 1657177
relation: main_file
success: 1
file_date_updated: 2022-05-09T07:10:51Z
has_accepted_license: '1'
intvolume: ' 3'
isi: 1
issue: '2'
language:
- iso: eng
month: '04'
oa: 1
oa_version: Published Version
project:
- _id: 257EB838-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '732894'
name: Hybrid Optomechanical Technologies
publication: PRX Quantum
publication_identifier:
eissn:
- '26913399'
publication_status: published
publisher: American Physical Society
quality_controlled: '1'
scopus_import: '1'
status: public
title: Dissipative quantum feedback in measurements using a parametrically coupled
microcavity
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: 3
year: '2022'
...
---
_id: '11354'
abstract:
- lang: eng
text: We construct a recurrent diffusion process with values in the space of probability
measures over an arbitrary closed Riemannian manifold of dimension d≥2. The process
is associated with the Dirichlet form defined by integration of the Wasserstein
gradient w.r.t. the Dirichlet–Ferguson measure, and is the counterpart on multidimensional
base spaces to the modified massive Arratia flow over the unit interval described
in V. Konarovskyi and M.-K. von Renesse (Comm. Pure Appl. Math. 72 (2019) 764–800).
Together with two different constructions of the process, we discuss its ergodicity,
invariant sets, finite-dimensional approximations, and Varadhan short-time asymptotics.
acknowledgement: Research supported by the Sonderforschungsbereich 1060 and the Hausdorff
Center for Mathematics. The author gratefully acknowledges funding of his current
position at IST Austria by the Austrian Science Fund (FWF) grant F65 and by the
European Research Council (ERC, Grant agreement No. 716117, awarded to Prof. Dr.
Jan Maas).
article_processing_charge: No
article_type: original
arxiv: 1
author:
- first_name: Lorenzo
full_name: Dello Schiavo, Lorenzo
id: ECEBF480-9E4F-11EA-B557-B0823DDC885E
last_name: Dello Schiavo
orcid: 0000-0002-9881-6870
citation:
ama: Dello Schiavo L. The Dirichlet–Ferguson diffusion on the space of probability
measures over a closed Riemannian manifold. Annals of Probability. 2022;50(2):591-648.
doi:10.1214/21-AOP1541
apa: Dello Schiavo, L. (2022). The Dirichlet–Ferguson diffusion on the space of
probability measures over a closed Riemannian manifold. Annals of Probability.
Institute of Mathematical Statistics. https://doi.org/10.1214/21-AOP1541
chicago: Dello Schiavo, Lorenzo. “The Dirichlet–Ferguson Diffusion on the Space
of Probability Measures over a Closed Riemannian Manifold.” Annals of Probability.
Institute of Mathematical Statistics, 2022. https://doi.org/10.1214/21-AOP1541.
ieee: L. Dello Schiavo, “The Dirichlet–Ferguson diffusion on the space of probability
measures over a closed Riemannian manifold,” Annals of Probability, vol.
50, no. 2. Institute of Mathematical Statistics, pp. 591–648, 2022.
ista: Dello Schiavo L. 2022. The Dirichlet–Ferguson diffusion on the space of probability
measures over a closed Riemannian manifold. Annals of Probability. 50(2), 591–648.
mla: Dello Schiavo, Lorenzo. “The Dirichlet–Ferguson Diffusion on the Space of Probability
Measures over a Closed Riemannian Manifold.” Annals of Probability, vol.
50, no. 2, Institute of Mathematical Statistics, 2022, pp. 591–648, doi:10.1214/21-AOP1541.
short: L. Dello Schiavo, Annals of Probability 50 (2022) 591–648.
date_created: 2022-05-08T22:01:44Z
date_published: 2022-03-01T00:00:00Z
date_updated: 2023-10-17T12:50:24Z
day: '01'
department:
- _id: JaMa
doi: 10.1214/21-AOP1541
ec_funded: 1
external_id:
arxiv:
- '1811.11598'
isi:
- '000773518500005'
intvolume: ' 50'
isi: 1
issue: '2'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: ' https://doi.org/10.48550/arXiv.1811.11598'
month: '03'
oa: 1
oa_version: Preprint
page: 591-648
project:
- _id: 256E75B8-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '716117'
name: Optimal Transport and Stochastic Dynamics
- _id: fc31cba2-9c52-11eb-aca3-ff467d239cd2
grant_number: F6504
name: Taming Complexity in Partial Differential Systems
publication: Annals of Probability
publication_identifier:
eissn:
- 2168-894X
issn:
- 0091-1798
publication_status: published
publisher: Institute of Mathematical Statistics
quality_controlled: '1'
scopus_import: '1'
status: public
title: The Dirichlet–Ferguson diffusion on the space of probability measures over
a closed Riemannian manifold
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 50
year: '2022'
...
---
_id: '11355'
abstract:
- lang: eng
text: "Contract-based design is a promising methodology for taming the complexity
of developing sophisticated systems. A formal contract distinguishes between assumptions,
which are constraints that the designer of a component puts on the environments
in which the component can be used safely, and guarantees, which are promises
that the designer asks from the team that implements the component. A theory of
formal contracts can be formalized as an interface theory, which supports the
composition and refinement of both assumptions and guarantees.\r\nAlthough there
is a rich landscape of contract-based design methods that address functional and
extra-functional properties, we present the first interface theory that is designed
for ensuring system-wide security properties. Our framework provides a refinement
relation and a composition operation that support both incremental design and
independent implementability. We develop our theory for both stateless and stateful
interfaces. We illustrate the applicability of our framework with an example inspired
from the automotive domain."
acknowledgement: This project has received funding from the European Union’s Horizon
2020 research and innovation programme under grant agreement No 956123 and was funded
in part by the FWF project W1255-N23 and by the ERC-2020-AdG 101020093.
alternative_title:
- LNCS
article_processing_charge: No
author:
- first_name: Ezio
full_name: Bartocci, Ezio
last_name: Bartocci
- first_name: Thomas
full_name: Ferrere, Thomas
id: 40960E6E-F248-11E8-B48F-1D18A9856A87
last_name: Ferrere
orcid: 0000-0001-5199-3143
- first_name: Thomas A
full_name: Henzinger, Thomas A
id: 40876CD8-F248-11E8-B48F-1D18A9856A87
last_name: Henzinger
orcid: 0000-0002-2985-7724
- first_name: Dejan
full_name: Nickovic, Dejan
id: 41BCEE5C-F248-11E8-B48F-1D18A9856A87
last_name: Nickovic
- first_name: Ana Oliveira
full_name: Da Costa, Ana Oliveira
last_name: Da Costa
citation:
ama: 'Bartocci E, Ferrere T, Henzinger TA, Nickovic D, Da Costa AO. Information-flow
interfaces. In: Fundamental Approaches to Software Engineering. Vol 13241.
Springer Nature; 2022:3-22. doi:10.1007/978-3-030-99429-7_1'
apa: 'Bartocci, E., Ferrere, T., Henzinger, T. A., Nickovic, D., & Da Costa,
A. O. (2022). Information-flow interfaces. In Fundamental Approaches to Software
Engineering (Vol. 13241, pp. 3–22). Munich, Germany: Springer Nature. https://doi.org/10.1007/978-3-030-99429-7_1'
chicago: Bartocci, Ezio, Thomas Ferrere, Thomas A Henzinger, Dejan Nickovic, and
Ana Oliveira Da Costa. “Information-Flow Interfaces.” In Fundamental Approaches
to Software Engineering, 13241:3–22. Springer Nature, 2022. https://doi.org/10.1007/978-3-030-99429-7_1.
ieee: E. Bartocci, T. Ferrere, T. A. Henzinger, D. Nickovic, and A. O. Da Costa,
“Information-flow interfaces,” in Fundamental Approaches to Software Engineering,
Munich, Germany, 2022, vol. 13241, pp. 3–22.
ista: 'Bartocci E, Ferrere T, Henzinger TA, Nickovic D, Da Costa AO. 2022. Information-flow
interfaces. Fundamental Approaches to Software Engineering. FASE: Fundamental
Approaches to Software Engineering, LNCS, vol. 13241, 3–22.'
mla: Bartocci, Ezio, et al. “Information-Flow Interfaces.” Fundamental Approaches
to Software Engineering, vol. 13241, Springer Nature, 2022, pp. 3–22, doi:10.1007/978-3-030-99429-7_1.
short: E. Bartocci, T. Ferrere, T.A. Henzinger, D. Nickovic, A.O. Da Costa, in:,
Fundamental Approaches to Software Engineering, Springer Nature, 2022, pp. 3–22.
conference:
end_date: 2022-04-07
location: Munich, Germany
name: 'FASE: Fundamental Approaches to Software Engineering'
start_date: 2022-04-02
date_created: 2022-05-08T22:01:44Z
date_published: 2022-03-29T00:00:00Z
date_updated: 2023-08-03T07:03:40Z
day: '29'
ddc:
- '000'
department:
- _id: ToHe
doi: 10.1007/978-3-030-99429-7_1
ec_funded: 1
external_id:
isi:
- '000782393600001'
file:
- access_level: open_access
checksum: 7f6f860b20b8de2a249e9c1b4eee15cf
content_type: application/pdf
creator: dernst
date_created: 2022-05-09T06:52:44Z
date_updated: 2022-05-09T06:52:44Z
file_id: '11357'
file_name: 2022_LNCS_Bartocci.pdf
file_size: 479146
relation: main_file
success: 1
file_date_updated: 2022-05-09T06:52:44Z
has_accepted_license: '1'
intvolume: ' 13241'
isi: 1
language:
- iso: eng
month: '03'
oa: 1
oa_version: Published Version
page: 3-22
project:
- _id: 62781420-2b32-11ec-9570-8d9b63373d4d
call_identifier: H2020
grant_number: '101020093'
name: Vigilant Algorithmic Monitoring of Software
publication: Fundamental Approaches to Software Engineering
publication_identifier:
eissn:
- 1611-3349
isbn:
- '9783030994280'
issn:
- 0302-9743
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
scopus_import: '1'
status: public
title: Information-flow interfaces
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: conference
user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
volume: 13241
year: '2022'
...
---
_id: '11356'
acknowledgement: This work was supported by the National Science Fund for Distinguished
Young Scholars (51925101), National Key Research and Development Program of China
(2018YFA0702100), 111 Project (B17002), and Lise Meitner Project (M2889-N).
article_processing_charge: No
article_type: letter_note
author:
- first_name: Cheng
full_name: Chang, Cheng
id: 9E331C2E-9F27-11E9-AE48-5033E6697425
last_name: Chang
orcid: 0000-0002-9515-4277
- first_name: Bingchao
full_name: Qin, Bingchao
last_name: Qin
- first_name: Lizhong
full_name: Su, Lizhong
last_name: Su
- first_name: Li Dong
full_name: Zhao, Li Dong
last_name: Zhao
citation:
ama: Chang C, Qin B, Su L, Zhao LD. Distinct electron and hole transports in SnSe
crystals. Science Bulletin. 2022;67(11):1105-1107. doi:10.1016/j.scib.2022.04.007
apa: Chang, C., Qin, B., Su, L., & Zhao, L. D. (2022). Distinct electron and
hole transports in SnSe crystals. Science Bulletin. Elsevier. https://doi.org/10.1016/j.scib.2022.04.007
chicago: Chang, Cheng, Bingchao Qin, Lizhong Su, and Li Dong Zhao. “Distinct Electron
and Hole Transports in SnSe Crystals.” Science Bulletin. Elsevier, 2022.
https://doi.org/10.1016/j.scib.2022.04.007.
ieee: C. Chang, B. Qin, L. Su, and L. D. Zhao, “Distinct electron and hole transports
in SnSe crystals,” Science Bulletin, vol. 67, no. 11. Elsevier, pp. 1105–1107,
2022.
ista: Chang C, Qin B, Su L, Zhao LD. 2022. Distinct electron and hole transports
in SnSe crystals. Science Bulletin. 67(11), 1105–1107.
mla: Chang, Cheng, et al. “Distinct Electron and Hole Transports in SnSe Crystals.”
Science Bulletin, vol. 67, no. 11, Elsevier, 2022, pp. 1105–07, doi:10.1016/j.scib.2022.04.007.
short: C. Chang, B. Qin, L. Su, L.D. Zhao, Science Bulletin 67 (2022) 1105–1107.
date_created: 2022-05-08T22:01:44Z
date_published: 2022-06-15T00:00:00Z
date_updated: 2023-08-03T07:04:10Z
day: '15'
department:
- _id: MaIb
doi: 10.1016/j.scib.2022.04.007
external_id:
isi:
- '000835291100006'
intvolume: ' 67'
isi: 1
issue: '11'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.1016/j.scib.2022.04.007
month: '06'
oa: 1
oa_version: Published Version
page: 1105-1107
project:
- _id: 9B8804FC-BA93-11EA-9121-9846C619BF3A
grant_number: M02889
name: Bottom-up Engineering for Thermoelectric Applications
publication: Science Bulletin
publication_identifier:
eissn:
- 2095-9281
issn:
- 2095-9273
publication_status: published
publisher: Elsevier
quality_controlled: '1'
scopus_import: '1'
status: public
title: Distinct electron and hole transports in SnSe crystals
type: journal_article
user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
volume: 67
year: '2022'
...
---
_id: '11362'
abstract:
- lang: eng
text: "Deep learning has enabled breakthroughs in challenging computing problems
and has emerged as the standard problem-solving tool for computer vision and natural
language processing tasks.\r\nOne exception to this trend is safety-critical tasks
where robustness and resilience requirements contradict the black-box nature of
neural networks. \r\nTo deploy deep learning methods for these tasks, it is vital
to provide guarantees on neural network agents' safety and robustness criteria.
\r\nThis can be achieved by developing formal verification methods to verify the
safety and robustness properties of neural networks.\r\n\r\nOur goal is to design,
develop and assess safety verification methods for neural networks to improve
their reliability and trustworthiness in real-world applications.\r\nThis thesis
establishes techniques for the verification of compressed and adversarially trained
models as well as the design of novel neural networks for verifiably safe decision-making.\r\n\r\nFirst,
we establish the problem of verifying quantized neural networks. Quantization
is a technique that trades numerical precision for the computational efficiency
of running a neural network and is widely adopted in industry.\r\nWe show that
neglecting the reduced precision when verifying a neural network can lead to wrong
conclusions about the robustness and safety of the network, highlighting that
novel techniques for quantized network verification are necessary. We introduce
several bit-exact verification methods explicitly designed for quantized neural
networks and experimentally confirm on realistic networks that the network's robustness
and other formal properties are affected by the quantization.\r\n\r\nFurthermore,
we perform a case study providing evidence that adversarial training, a standard
technique for making neural networks more robust, has detrimental effects on the
network's performance. This robustness-accuracy tradeoff has been studied before
regarding the accuracy obtained on classification datasets where each data point
is independent of all other data points. On the other hand, we investigate the
tradeoff empirically in robot learning settings where a both, a high accuracy
and a high robustness, are desirable.\r\nOur results suggest that the negative
side-effects of adversarial training outweigh its robustness benefits in practice.\r\n\r\nFinally,
we consider the problem of verifying safety when running a Bayesian neural network
policy in a feedback loop with systems over the infinite time horizon. Bayesian
neural networks are probabilistic models for learning uncertainties in the data
and are therefore often used on robotic and healthcare applications where data
is inherently stochastic.\r\nWe introduce a method for recalibrating Bayesian
neural networks so that they yield probability distributions over safe decisions
only.\r\nOur method learns a safety certificate that guarantees safety over the
infinite time horizon to determine which decisions are safe in every possible
state of the system.\r\nWe demonstrate the effectiveness of our approach on a
series of reinforcement learning benchmarks."
alternative_title:
- ISTA Thesis
article_processing_charge: No
author:
- first_name: Mathias
full_name: Lechner, Mathias
id: 3DC22916-F248-11E8-B48F-1D18A9856A87
last_name: Lechner
citation:
ama: Lechner M. Learning verifiable representations. 2022. doi:10.15479/at:ista:11362
apa: Lechner, M. (2022). Learning verifiable representations. Institute of
Science and Technology Austria. https://doi.org/10.15479/at:ista:11362
chicago: Lechner, Mathias. “Learning Verifiable Representations.” Institute of Science
and Technology Austria, 2022. https://doi.org/10.15479/at:ista:11362.
ieee: M. Lechner, “Learning verifiable representations,” Institute of Science and
Technology Austria, 2022.
ista: Lechner M. 2022. Learning verifiable representations. Institute of Science
and Technology Austria.
mla: Lechner, Mathias. Learning Verifiable Representations. Institute of
Science and Technology Austria, 2022, doi:10.15479/at:ista:11362.
short: M. Lechner, Learning Verifiable Representations, Institute of Science and
Technology Austria, 2022.
date_created: 2022-05-12T07:14:01Z
date_published: 2022-05-12T00:00:00Z
date_updated: 2025-07-14T09:10:11Z
day: '12'
ddc:
- '004'
degree_awarded: PhD
department:
- _id: GradSch
- _id: ToHe
doi: 10.15479/at:ista:11362
ec_funded: 1
file:
- access_level: closed
checksum: 8eefa9c7c10ca7e1a2ccdd731962a645
content_type: application/zip
creator: mlechner
date_created: 2022-05-13T12:33:26Z
date_updated: 2022-05-13T12:49:00Z
file_id: '11378'
file_name: src.zip
file_size: 13210143
relation: source_file
- access_level: open_access
checksum: 1b9e1e5a9a83ed9d89dad2f5133dc026
content_type: application/pdf
creator: mlechner
date_created: 2022-05-16T08:02:28Z
date_updated: 2022-05-17T15:19:39Z
file_id: '11382'
file_name: thesis_main-a2.pdf
file_size: 2732536
relation: main_file
file_date_updated: 2022-05-17T15:19:39Z
has_accepted_license: '1'
keyword:
- neural networks
- verification
- machine learning
language:
- iso: eng
license: https://creativecommons.org/licenses/by-nd/4.0/
month: '05'
oa: 1
oa_version: Published Version
page: '124'
project:
- _id: 25F42A32-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: Z211
name: The Wittgenstein Prize
- _id: 62781420-2b32-11ec-9570-8d9b63373d4d
call_identifier: H2020
grant_number: '101020093'
name: Vigilant Algorithmic Monitoring of Software
publication_identifier:
isbn:
- 978-3-99078-017-6
publication_status: published
publisher: Institute of Science and Technology Austria
related_material:
record:
- id: '11366'
relation: part_of_dissertation
status: public
- id: '7808'
relation: part_of_dissertation
status: public
- id: '10666'
relation: part_of_dissertation
status: public
- id: '10665'
relation: part_of_dissertation
status: public
- id: '10667'
relation: part_of_dissertation
status: public
status: public
supervisor:
- first_name: Thomas A
full_name: Henzinger, Thomas A
id: 40876CD8-F248-11E8-B48F-1D18A9856A87
last_name: Henzinger
orcid: 0000-0002-2985-7724
title: Learning verifiable representations
tmp:
image: /image/cc_by_nd.png
legal_code_url: https://creativecommons.org/licenses/by-nd/4.0/legalcode
name: Creative Commons Attribution-NoDerivatives 4.0 International (CC BY-ND 4.0)
short: CC BY-ND (4.0)
type: dissertation
user_id: 8b945eb4-e2f2-11eb-945a-df72226e66a9
year: '2022'
...
---
_id: '11366'
abstract:
- lang: eng
text: "Adversarial training (i.e., training on adversarially perturbed input data)
is a well-studied method for making neural networks robust to potential adversarial
attacks during inference. However, the improved robustness does not\r\ncome for
free but rather is accompanied by a decrease in overall model accuracy and performance.
Recent work has shown that, in practical robot learning applications, the effects
of adversarial training do not pose a fair trade-off\r\nbut inflict a net loss
when measured in holistic robot performance. This work revisits the robustness-accuracy
trade-off in robot learning by systematically analyzing if recent advances in
robust training methods and theory in\r\nconjunction with adversarial robot learning
can make adversarial training suitable for real-world robot applications. We evaluate
a wide variety of robot learning tasks ranging from autonomous driving in a high-fidelity
environment\r\namenable to sim-to-real deployment, to mobile robot gesture recognition.
Our results demonstrate that, while these techniques make incremental improvements
on the trade-off on a relative scale, the negative side-effects caused by\r\nadversarial
training still outweigh the improvements by an order of magnitude. We conclude
that more substantial advances in robust learning methods are necessary before
they can benefit robot learning tasks in practice."
acknowledgement: "This work was supported in parts by the ERC-2020-AdG 101020093,
National Science Foundation (NSF), and JP\r\nMorgan Graduate Fellowships. We thank
Christoph Lampert for inspiring this work.\r\n"
article_number: '2204.07373'
article_processing_charge: No
arxiv: 1
author:
- first_name: Mathias
full_name: Lechner, Mathias
id: 3DC22916-F248-11E8-B48F-1D18A9856A87
last_name: Lechner
- first_name: Alexander
full_name: Amini, Alexander
last_name: Amini
- first_name: Daniela
full_name: Rus, Daniela
last_name: Rus
- first_name: Thomas A
full_name: Henzinger, Thomas A
id: 40876CD8-F248-11E8-B48F-1D18A9856A87
last_name: Henzinger
orcid: 0000-0002-2985-7724
citation:
ama: Lechner M, Amini A, Rus D, Henzinger TA. Revisiting the adversarial robustness-accuracy
tradeoff in robot learning. arXiv. doi:10.48550/arXiv.2204.07373
apa: Lechner, M., Amini, A., Rus, D., & Henzinger, T. A. (n.d.). Revisiting
the adversarial robustness-accuracy tradeoff in robot learning. arXiv.
https://doi.org/10.48550/arXiv.2204.07373
chicago: Lechner, Mathias, Alexander Amini, Daniela Rus, and Thomas A Henzinger.
“Revisiting the Adversarial Robustness-Accuracy Tradeoff in Robot Learning.” ArXiv,
n.d. https://doi.org/10.48550/arXiv.2204.07373.
ieee: M. Lechner, A. Amini, D. Rus, and T. A. Henzinger, “Revisiting the adversarial
robustness-accuracy tradeoff in robot learning,” arXiv. .
ista: Lechner M, Amini A, Rus D, Henzinger TA. Revisiting the adversarial robustness-accuracy
tradeoff in robot learning. arXiv, 2204.07373.
mla: Lechner, Mathias, et al. “Revisiting the Adversarial Robustness-Accuracy Tradeoff
in Robot Learning.” ArXiv, 2204.07373, doi:10.48550/arXiv.2204.07373.
short: M. Lechner, A. Amini, D. Rus, T.A. Henzinger, ArXiv (n.d.).
date_created: 2022-05-12T13:20:17Z
date_published: 2022-04-15T00:00:00Z
date_updated: 2023-08-01T13:36:50Z
day: '15'
department:
- _id: ToHe
doi: 10.48550/arXiv.2204.07373
ec_funded: 1
external_id:
arxiv:
- '2204.07373'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.48550/arXiv.2204.07373
month: '04'
oa: 1
oa_version: Preprint
project:
- _id: 62781420-2b32-11ec-9570-8d9b63373d4d
call_identifier: H2020
grant_number: '101020093'
name: Vigilant Algorithmic Monitoring of Software
publication: arXiv
publication_status: submitted
related_material:
record:
- id: '11362'
relation: dissertation_contains
status: public
- id: '12704'
relation: later_version
status: public
status: public
title: Revisiting the adversarial robustness-accuracy tradeoff in robot learning
type: preprint
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
year: '2022'
...
---
_id: '11373'
abstract:
- lang: eng
text: The actin-homologue FtsA is essential for E. coli cell division, as it links
FtsZ filaments in the Z-ring to transmembrane proteins. FtsA is thought to initiate
cell constriction by switching from an inactive polymeric to an active monomeric
conformation, which recruits downstream proteins and stabilizes the Z-ring. However,
direct biochemical evidence for this mechanism is missing. Here, we use reconstitution
experiments and quantitative fluorescence microscopy to study divisome activation
in vitro. By comparing wild-type FtsA with FtsA R286W, we find that this hyperactive
mutant outperforms FtsA WT in replicating FtsZ treadmilling dynamics, FtsZ filament
stabilization and recruitment of FtsN. We could attribute these differences to
a faster exchange and denser packing of FtsA R286W below FtsZ filaments. Using
FRET microscopy, we also find that FtsN binding promotes FtsA self-interaction.
We propose that in the active divisome FtsA and FtsN exist as a dynamic copolymer
that follows treadmilling filaments of FtsZ.
acknowledged_ssus:
- _id: Bio
- _id: LifeSc
acknowledgement: We acknowledge members of the Loose laboratory at IST Austria for
helpful discussions—in particular L. Lindorfer for his assistance with cloning and
purifications. We thank J. Löwe and T. Nierhaus (MRC-LMB Cambridge, UK) for sharing
unpublished work and helpful discussions, as well as D. Vavylonis and D. Rutkowski
(Lehigh University, Bethlehem, PA, USA) and S. Martin (University of Lausanne, Switzerland)
for sharing their code for FRAP analysis. We are also thankful for the support by
the Scientific Service Units (SSU) of IST Austria through resources provided by
the Imaging and Optics Facility (IOF) and the Lab Support Facility (LSF). This work
was supported by the European Research Council through grant ERC 2015-StG-679239
and by the Austrian Science Fund (FWF) StandAlone P34607 to M.L. and HFSP LT 000824/2016-L4
to N.B. For the purpose of open access, we have applied a CC BY public copyright
licence to any Author Accepted Manuscript version arising from this submission.
article_number: '2635'
article_processing_charge: No
article_type: original
author:
- first_name: Philipp
full_name: Radler, Philipp
id: 40136C2A-F248-11E8-B48F-1D18A9856A87
last_name: Radler
orcid: '0000-0001-9198-2182 '
- first_name: Natalia S.
full_name: Baranova, Natalia S.
id: 38661662-F248-11E8-B48F-1D18A9856A87
last_name: Baranova
orcid: 0000-0002-3086-9124
- first_name: Paulo R
full_name: Dos Santos Caldas, Paulo R
id: 38FCDB4C-F248-11E8-B48F-1D18A9856A87
last_name: Dos Santos Caldas
orcid: 0000-0001-6730-4461
- first_name: Christoph M
full_name: Sommer, Christoph M
id: 4DF26D8C-F248-11E8-B48F-1D18A9856A87
last_name: Sommer
orcid: 0000-0003-1216-9105
- first_name: Maria D
full_name: Lopez Pelegrin, Maria D
id: 319AA9CE-F248-11E8-B48F-1D18A9856A87
last_name: Lopez Pelegrin
- first_name: David
full_name: Michalik, David
id: B9577E20-AA38-11E9-AC9A-0930E6697425
last_name: Michalik
- first_name: Martin
full_name: Loose, Martin
id: 462D4284-F248-11E8-B48F-1D18A9856A87
last_name: Loose
orcid: 0000-0001-7309-9724
citation:
ama: Radler P, Baranova NS, Dos Santos Caldas PR, et al. In vitro reconstitution
of Escherichia coli divisome activation. Nature Communications. 2022;13.
doi:10.1038/s41467-022-30301-y
apa: Radler, P., Baranova, N. S., Dos Santos Caldas, P. R., Sommer, C. M., Lopez
Pelegrin, M. D., Michalik, D., & Loose, M. (2022). In vitro reconstitution
of Escherichia coli divisome activation. Nature Communications. Springer
Nature. https://doi.org/10.1038/s41467-022-30301-y
chicago: Radler, Philipp, Natalia S. Baranova, Paulo R Dos Santos Caldas, Christoph
M Sommer, Maria D Lopez Pelegrin, David Michalik, and Martin Loose. “In Vitro
Reconstitution of Escherichia Coli Divisome Activation.” Nature Communications.
Springer Nature, 2022. https://doi.org/10.1038/s41467-022-30301-y.
ieee: P. Radler et al., “In vitro reconstitution of Escherichia coli divisome
activation,” Nature Communications, vol. 13. Springer Nature, 2022.
ista: Radler P, Baranova NS, Dos Santos Caldas PR, Sommer CM, Lopez Pelegrin MD,
Michalik D, Loose M. 2022. In vitro reconstitution of Escherichia coli divisome
activation. Nature Communications. 13, 2635.
mla: Radler, Philipp, et al. “In Vitro Reconstitution of Escherichia Coli Divisome
Activation.” Nature Communications, vol. 13, 2635, Springer Nature, 2022,
doi:10.1038/s41467-022-30301-y.
short: P. Radler, N.S. Baranova, P.R. Dos Santos Caldas, C.M. Sommer, M.D. Lopez
Pelegrin, D. Michalik, M. Loose, Nature Communications 13 (2022).
date_created: 2022-05-13T09:06:28Z
date_published: 2022-05-12T00:00:00Z
date_updated: 2024-02-21T12:35:18Z
day: '12'
ddc:
- '570'
department:
- _id: MaLo
doi: 10.1038/s41467-022-30301-y
ec_funded: 1
external_id:
isi:
- '000795171100037'
file:
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checksum: 5af863ee1b95a0710f6ee864d68dc7a6
content_type: application/pdf
creator: dernst
date_created: 2022-05-13T09:10:51Z
date_updated: 2022-05-13T09:10:51Z
file_id: '11374'
file_name: 2022_NatureCommunications_Radler.pdf
file_size: 6945191
relation: main_file
success: 1
file_date_updated: 2022-05-13T09:10:51Z
has_accepted_license: '1'
intvolume: ' 13'
isi: 1
keyword:
- General Physics and Astronomy
- General Biochemistry
- Genetics and Molecular Biology
- General Chemistry
language:
- iso: eng
month: '05'
oa: 1
oa_version: Published Version
project:
- _id: 2595697A-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '679239'
name: Self-Organization of the Bacterial Cell
- _id: fc38323b-9c52-11eb-aca3-ff8afb4a011d
grant_number: P34607
name: "Understanding bacterial cell division by in vitro\r\nreconstitution"
publication: Nature Communications
publication_identifier:
issn:
- 2041-1723
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
related_material:
link:
- relation: erratum
url: https://doi.org/10.1038/s41467-022-34485-1
record:
- id: '14280'
relation: dissertation_contains
status: public
- id: '10934'
relation: research_data
status: public
scopus_import: '1'
status: public
title: In vitro reconstitution of Escherichia coli divisome activation
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: 13
year: '2022'
...
---
_id: '11379'
abstract:
- lang: eng
text: Bernal-stacked multilayer graphene is a versatile platform to explore quantum
transport phenomena and interaction physics due to its exceptional tunability
via electrostatic gating. For instance, upon applying a perpendicular electric
field, its band structure exhibits several off-center Dirac points (so-called
Dirac gullies) in each valley. Here, the formation of Dirac gullies and the interaction-induced
breakdown of gully coherence is explored via magnetotransport measurements in
high-quality Bernal-stacked (ABA) trilayer graphene. At zero magnetic field, multiple
Lifshitz transitions indicating the formation of Dirac gullies are identified.
In the quantum Hall regime, the emergence of Dirac gullies is evident as an increase
in Landau level degeneracy. When tuning both electric and magnetic fields, electron–electron
interactions can be controllably enhanced until, beyond critical electric and
magnetic fields, the gully degeneracy is eventually lifted. The arising correlated
ground state is consistent with a previously predicted nematic phase that spontaneously
breaks the rotational gully symmetry.
acknowledgement: "We acknowledge funding from the Center for Nanoscience (CeNS) and
by the Deutsche\r\nForschungsgemeinschaft (DFG, German Research Foundation) under
Germany’s Excellence Strategy-EXC-2111-390814868 (MCQST). K.W. and T.T. acknowledge
support from the Elemental Strategy Initiative conducted by the MEXT, Japan (Grant
Number PMXP0112101001) and JSPS KAKENHI (Grant Numbers 19H05790 and JP20H00354)."
article_processing_charge: No
article_type: original
arxiv: 1
author:
- first_name: Felix
full_name: Winterer, Felix
last_name: Winterer
- first_name: Anna M.
full_name: Seiler, Anna M.
last_name: Seiler
- first_name: Areg
full_name: Ghazaryan, Areg
id: 4AF46FD6-F248-11E8-B48F-1D18A9856A87
last_name: Ghazaryan
orcid: 0000-0001-9666-3543
- first_name: Fabian R.
full_name: Geisenhof, Fabian R.
last_name: Geisenhof
- first_name: Kenji
full_name: Watanabe, Kenji
last_name: Watanabe
- first_name: Takashi
full_name: Taniguchi, Takashi
last_name: Taniguchi
- first_name: Maksym
full_name: Serbyn, Maksym
id: 47809E7E-F248-11E8-B48F-1D18A9856A87
last_name: Serbyn
orcid: 0000-0002-2399-5827
- first_name: R. Thomas
full_name: Weitz, R. Thomas
last_name: Weitz
citation:
ama: Winterer F, Seiler AM, Ghazaryan A, et al. Spontaneous gully-polarized quantum
hall states in ABA trilayer graphene. Nano Letters. 2022;22(8):3317-3322.
doi:10.1021/acs.nanolett.2c00435
apa: Winterer, F., Seiler, A. M., Ghazaryan, A., Geisenhof, F. R., Watanabe, K.,
Taniguchi, T., … Weitz, R. T. (2022). Spontaneous gully-polarized quantum hall
states in ABA trilayer graphene. Nano Letters. American Chemical Society.
https://doi.org/10.1021/acs.nanolett.2c00435
chicago: Winterer, Felix, Anna M. Seiler, Areg Ghazaryan, Fabian R. Geisenhof, Kenji
Watanabe, Takashi Taniguchi, Maksym Serbyn, and R. Thomas Weitz. “Spontaneous
Gully-Polarized Quantum Hall States in ABA Trilayer Graphene.” Nano Letters.
American Chemical Society, 2022. https://doi.org/10.1021/acs.nanolett.2c00435.
ieee: F. Winterer et al., “Spontaneous gully-polarized quantum hall states
in ABA trilayer graphene,” Nano Letters, vol. 22, no. 8. American Chemical
Society, pp. 3317–3322, 2022.
ista: Winterer F, Seiler AM, Ghazaryan A, Geisenhof FR, Watanabe K, Taniguchi T,
Serbyn M, Weitz RT. 2022. Spontaneous gully-polarized quantum hall states in ABA
trilayer graphene. Nano Letters. 22(8), 3317–3322.
mla: Winterer, Felix, et al. “Spontaneous Gully-Polarized Quantum Hall States in
ABA Trilayer Graphene.” Nano Letters, vol. 22, no. 8, American Chemical
Society, 2022, pp. 3317–22, doi:10.1021/acs.nanolett.2c00435.
short: F. Winterer, A.M. Seiler, A. Ghazaryan, F.R. Geisenhof, K. Watanabe, T. Taniguchi,
M. Serbyn, R.T. Weitz, Nano Letters 22 (2022) 3317–3322.
date_created: 2022-05-15T22:01:41Z
date_published: 2022-04-27T00:00:00Z
date_updated: 2023-08-03T07:12:45Z
day: '27'
department:
- _id: MaSe
doi: 10.1021/acs.nanolett.2c00435
external_id:
arxiv:
- '2109.00556'
isi:
- '000809056900019'
intvolume: ' 22'
isi: 1
issue: '8'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: ' https://doi.org/10.48550/arXiv.2109.00556'
month: '04'
oa: 1
oa_version: Preprint
page: 3317-3322
publication: Nano Letters
publication_identifier:
eissn:
- '15306992'
issn:
- '15306984'
publication_status: published
publisher: American Chemical Society
quality_controlled: '1'
scopus_import: '1'
status: public
title: Spontaneous gully-polarized quantum hall states in ABA trilayer graphene
type: journal_article
user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
volume: 22
year: '2022'
...
---
_id: '11388'
abstract:
- lang: eng
text: "In evolve and resequence experiments, a population is sequenced, subjected
to selection and\r\nthen sequenced again, so that genetic changes before and after
selection can be observed at\r\nthe genetic level. Here, I use these studies to
better understand the genetic basis of complex\r\ntraits - traits which depend
on more than a few genes.\r\nIn the first chapter, I discuss the first evolve
and resequence experiment, in which a population\r\nof mice, the so-called \"Longshanks\"
mice, were selected for tibia length while their body mass\r\nwas kept constant.
The full pedigree is known. We observed a selection response on all\r\nchromosomes
and used the infinitesimal model with linkage, a model which assumes an infinite\r\nnumber
of genes with infinitesimally small effect sizes, as a null model. Results implied
a very\r\npolygenic basis with a few loci of major effect standing out and changing
in parallel. There\r\nwas large variability between the different chromosomes
in this study, probably due to LD.\r\nIn chapter two, I go on to discuss the impact
of LD, on the variability in an allele-frequency\r\nbased summary statistic, giving
an equation based on the initial allele frequencies, average\r\npairwise LD, and
the first four moments of the haplotype block copy number distribution. I\r\ndescribe
this distribution by referring back to the founder generation. I then demonstrate\r\nhow
to infer selection via a maximum likelihood scheme on the example of a single
locus and\r\ndiscuss how to extend this to more realistic scenarios.\r\nIn chapter
three, I discuss the second evolve and resequence experiment, in which a small\r\npopulation
of Drosophila melanogaster was selected for increased pupal case size over 6\r\ngenerations.
The experiment was highly replicated with 27 lines selected within family and
a\r\nknown pedigree. We observed a phenotypic selection response of over one standard
deviation.\r\nI describe the patterns in allele frequency data, including allele
frequency changes and patterns\r\nof heterozygosity, and give ideas for future
work."
alternative_title:
- ISTA Thesis
article_processing_charge: No
author:
- first_name: Stefanie
full_name: Belohlavy, Stefanie
id: 43FE426A-F248-11E8-B48F-1D18A9856A87
last_name: Belohlavy
orcid: 0000-0002-9849-498X
citation:
ama: Belohlavy S. The genetic basis of complex traits studied via analysis of evolve
and resequence experiments. 2022. doi:10.15479/at:ista:11388
apa: Belohlavy, S. (2022). The genetic basis of complex traits studied via analysis
of evolve and resequence experiments. Institute of Science and Technology
Austria. https://doi.org/10.15479/at:ista:11388
chicago: Belohlavy, Stefanie. “The Genetic Basis of Complex Traits Studied via Analysis
of Evolve and Resequence Experiments.” Institute of Science and Technology Austria,
2022. https://doi.org/10.15479/at:ista:11388.
ieee: S. Belohlavy, “The genetic basis of complex traits studied via analysis of
evolve and resequence experiments,” Institute of Science and Technology Austria,
2022.
ista: Belohlavy S. 2022. The genetic basis of complex traits studied via analysis
of evolve and resequence experiments. Institute of Science and Technology Austria.
mla: Belohlavy, Stefanie. The Genetic Basis of Complex Traits Studied via Analysis
of Evolve and Resequence Experiments. Institute of Science and Technology
Austria, 2022, doi:10.15479/at:ista:11388.
short: S. Belohlavy, The Genetic Basis of Complex Traits Studied via Analysis of
Evolve and Resequence Experiments, Institute of Science and Technology Austria,
2022.
date_created: 2022-05-16T16:49:18Z
date_published: 2022-05-18T00:00:00Z
date_updated: 2023-08-29T06:41:51Z
day: '18'
ddc:
- '576'
degree_awarded: PhD
department:
- _id: GradSch
- _id: NiBa
doi: 10.15479/at:ista:11388
file:
- access_level: open_access
checksum: 4d75e6a619df7e8a9d6e840aee182380
content_type: application/pdf
creator: sbelohla
date_created: 2022-05-19T13:03:13Z
date_updated: 2023-05-20T22:30:03Z
embargo: 2023-05-19
file_id: '11398'
file_name: thesis_sb_final_pdfa.pdf
file_size: 8247240
relation: main_file
- access_level: closed
checksum: 7a5d8b6dd0ca00784f860075b0a7d8f0
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date_updated: 2023-05-20T22:30:03Z
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file_id: '11399'
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file_size: 7094
relation: source_file
file_date_updated: 2023-05-20T22:30:03Z
has_accepted_license: '1'
language:
- iso: eng
month: '05'
oa: 1
oa_version: Published Version
page: '98'
publication_identifier:
isbn:
- 978-3-99078-018-3
publication_status: published
publisher: Institute of Science and Technology Austria
related_material:
record:
- id: '6713'
relation: part_of_dissertation
status: public
status: public
supervisor:
- first_name: Nicholas H
full_name: Barton, Nicholas H
id: 4880FE40-F248-11E8-B48F-1D18A9856A87
last_name: Barton
orcid: 0000-0002-8548-5240
title: The genetic basis of complex traits studied via analysis of evolve and resequence
experiments
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: dissertation
user_id: 8b945eb4-e2f2-11eb-945a-df72226e66a9
year: '2022'
...
---
_id: '11393'
abstract:
- lang: eng
text: "AMPA receptors (AMPARs) mediate fast excitatory neurotransmission and their
role is\r\nimplicated in complex processes such as learning and memory and various
neurological\r\ndiseases. These receptors are composed of different subunits and
the subunit composition can\r\naffect channel properties, receptor trafficking
and interaction with other associated proteins.\r\nUsing the high sensitivity
SDS-digested freeze-fracture replica labeling (SDS-FRL) for\r\nelectron microscopy
I investigated the number, density, and localization of AMPAR subunits,\r\nGluA1,
GluA2, GluA3, and GluA1-3 (panAMPA) in pyramidal cells in the CA1 area of mouse\r\nhippocampus.
I have found that the immunogold labeling for all of these subunits in the\r\npostsynaptic
sites was highest in stratum radiatum and lowest in stratum lacunosummoleculare.
The labeling density for the all subunits in the extrasynaptic sites showed a
gradual\r\nincrease from the pyramidal cell soma towards the distal part of stratum
radiatum. The densities\r\nof extrasynaptic GluA1, GluA2 and panAMPA labeling
reached 10-15% of synaptic densities,\r\nwhile the ratio of extrasynaptic labeling
for GluA3 was significantly lower compared than those\r\nfor other subunits. The
labeling patterns for GluA1, GluA2 and GluA1-3 are similar and their\r\ndensities
were higher in the periphery than center of synapses. In contrast, the GluA3-\r\ncontaining
receptors were more centrally localized compared to the GluA1- and GluA2-\r\ncontaining
receptors.\r\nThe hippocampus plays a central role in learning and memory. Contextual
learning has been\r\nshown to require the delivery of AMPA receptors to CA1 synapses
in the dorsal hippocampus.\r\nHowever, proximodistal heterogeneity of this plasticity
and particular contribution of different\r\nAMPA receptor subunits are not fully
understood. By combining inhibitory avoidance task, a\r\nhippocampus-dependent
contextual fear-learning paradigm, with SDS-FRL, I have revealed an\r\nincrease
in synaptic density specific to GluA1-containing AMPA receptors in the CA1 area.\r\nThe
intrasynaptic distribution of GluA1 also changed from the periphery to center-preferred\r\npattern.
Furthermore, this synaptic plasticity was evident selectively in stratum radiatum
but\r\nnot stratum oriens, and in the CA1 subregion proximal but not distal to
CA2. These findings\r\nfurther contribute to our understanding of how specific
hippocampal subregions and AMPA\r\nreceptor subunits are involved in physiological
learning.\r\nAlthough the immunolabeling results above shed light on subunit-specific
plasticity in\r\nAMPAR distribution, no tools to visualize and study the subunit
composition at the single\r\nchannel level in situ have been available. Electron
microscopy with conventional immunogold\r\nlabeling approaches has limitations
in the single channel analysis because of the large size of\r\nantibodies and
steric hindrance hampering multiple subunit labeling of single channels. I\r\nmanaged
to develop a new chemical labeling system using a short peptide tag and small\r\nsynthetic
probes, which form specific covalent bond with a cysteine residue in the tag fused
to\r\nproteins of interest (reactive tag system). I additionally made substantial
progress into adapting\r\nthis system for AMPA receptor subunits."
acknowledged_ssus:
- _id: EM-Fac
alternative_title:
- ISTA Thesis
article_processing_charge: No
author:
- first_name: Marijo
full_name: Jevtic, Marijo
id: 4BE3BC94-F248-11E8-B48F-1D18A9856A87
last_name: Jevtic
citation:
ama: Jevtic M. Contextual fear learning induced changes in AMPA receptor subtypes
along the proximodistal axis in dorsal hippocampus. 2022. doi:10.15479/at:ista:11393
apa: Jevtic, M. (2022). Contextual fear learning induced changes in AMPA receptor
subtypes along the proximodistal axis in dorsal hippocampus. Institute of
Science and Technology Austria. https://doi.org/10.15479/at:ista:11393
chicago: Jevtic, Marijo. “Contextual Fear Learning Induced Changes in AMPA Receptor
Subtypes along the Proximodistal Axis in Dorsal Hippocampus.” Institute of Science
and Technology Austria, 2022. https://doi.org/10.15479/at:ista:11393.
ieee: M. Jevtic, “Contextual fear learning induced changes in AMPA receptor subtypes
along the proximodistal axis in dorsal hippocampus,” Institute of Science and
Technology Austria, 2022.
ista: Jevtic M. 2022. Contextual fear learning induced changes in AMPA receptor
subtypes along the proximodistal axis in dorsal hippocampus. Institute of Science
and Technology Austria.
mla: Jevtic, Marijo. Contextual Fear Learning Induced Changes in AMPA Receptor
Subtypes along the Proximodistal Axis in Dorsal Hippocampus. Institute of
Science and Technology Austria, 2022, doi:10.15479/at:ista:11393.
short: M. Jevtic, Contextual Fear Learning Induced Changes in AMPA Receptor Subtypes
along the Proximodistal Axis in Dorsal Hippocampus, Institute of Science and Technology
Austria, 2022.
date_created: 2022-05-17T08:57:41Z
date_published: 2022-05-16T00:00:00Z
date_updated: 2023-09-07T14:53:44Z
day: '16'
ddc:
- '570'
degree_awarded: PhD
department:
- _id: GradSch
- _id: RySh
doi: 10.15479/at:ista:11393
file:
- access_level: closed
checksum: 8fc695d88020d70d231dad0e9f10b138
content_type: application/vnd.openxmlformats-officedocument.wordprocessingml.document
creator: cchlebak
date_created: 2022-05-17T09:08:06Z
date_updated: 2023-05-17T22:30:03Z
embargo_to: open_access
file_id: '11395'
file_name: MJ thesis.docx
file_size: 56427603
relation: source_file
- access_level: open_access
checksum: c1dd20a1aece521b3500607b00e463d6
content_type: application/pdf
creator: cchlebak
date_created: 2022-05-17T12:09:25Z
date_updated: 2023-05-17T22:30:03Z
embargo: 2023-05-16
file_id: '11397'
file_name: MJ_thesis_PDFA.pdf
file_size: 4351981
relation: main_file
file_date_updated: 2023-05-17T22:30:03Z
has_accepted_license: '1'
language:
- iso: eng
month: '05'
oa: 1
oa_version: Published Version
page: '108'
publication_identifier:
issn:
- 2663-337X
publication_status: published
publisher: Institute of Science and Technology Austria
related_material:
record:
- id: '7391'
relation: part_of_dissertation
status: public
status: public
supervisor:
- first_name: Ryuichi
full_name: Shigemoto, Ryuichi
id: 499F3ABC-F248-11E8-B48F-1D18A9856A87
last_name: Shigemoto
orcid: 0000-0001-8761-9444
title: Contextual fear learning induced changes in AMPA receptor subtypes along the
proximodistal axis in dorsal hippocampus
type: dissertation
user_id: 8b945eb4-e2f2-11eb-945a-df72226e66a9
year: '2022'
...
---
_id: '11400'
abstract:
- lang: eng
text: By varying the concentration of molecules in the cytoplasm or on the membrane,
cells can induce the formation of condensates and liquid droplets, similar to
phase separation. Their thermodynamics, much studied, depends on the mutual interactions
between microscopic constituents. Here, we focus on the kinetics and size control
of 2D clusters, forming on membranes. Using molecular dynamics of patchy colloids,
we model a system of two species of proteins, giving origin to specific heterotypic
bonds. We find that concentrations, together with valence and bond strength, control
both the size and the growth time rate of the clusters. In particular, if one
species is in large excess, it gradually saturates the binding sites of the other
species; the system then becomes kinetically arrested and cluster coarsening slows
down or stops, thus yielding effective size selection. This phenomenology is observed
both in solid and fluid clusters, which feature additional generic homotypic interactions
and are reminiscent of the ones observed on biological membranes.
acknowledgement: "The authors thank Longhui Zeng and Xiaolei Su (Yale University)
for bringing the topic to their attention and for useful comments. This work has
received funding from the European Research Council under the European Union’s Horizon\r\n2020
research and innovation program (ERC Grant No. 802960 and Marie Skłodowska-Curie
Grant No. 101034413). The authors are grateful to the UK Materials and Molecular
Modeling Hub for computational resources, which is partially funded by EPSRC (Grant
Nos. EP/P020194/1 and EP/T022213/1). The authors acknowledge support from ISTA and
from the Royal Society (Grant No. UF160266)."
article_number: '194902'
article_processing_charge: No
article_type: original
author:
- first_name: Ivan
full_name: Palaia, Ivan
id: 9c805cd2-4b75-11ec-a374-db6dd0ed57fa
last_name: Palaia
orcid: ' 0000-0002-8843-9485 '
- first_name: Anđela
full_name: Šarić, Anđela
id: bf63d406-f056-11eb-b41d-f263a6566d8b
last_name: Šarić
orcid: 0000-0002-7854-2139
citation:
ama: Palaia I, Šarić A. Controlling cluster size in 2D phase-separating binary mixtures
with specific interactions. The Journal of Chemical Physics. 2022;156(19).
doi:10.1063/5.0087769
apa: Palaia, I., & Šarić, A. (2022). Controlling cluster size in 2D phase-separating
binary mixtures with specific interactions. The Journal of Chemical Physics.
AIP Publishing. https://doi.org/10.1063/5.0087769
chicago: Palaia, Ivan, and Anđela Šarić. “Controlling Cluster Size in 2D Phase-Separating
Binary Mixtures with Specific Interactions.” The Journal of Chemical Physics.
AIP Publishing, 2022. https://doi.org/10.1063/5.0087769.
ieee: I. Palaia and A. Šarić, “Controlling cluster size in 2D phase-separating binary
mixtures with specific interactions,” The Journal of Chemical Physics,
vol. 156, no. 19. AIP Publishing, 2022.
ista: Palaia I, Šarić A. 2022. Controlling cluster size in 2D phase-separating binary
mixtures with specific interactions. The Journal of Chemical Physics. 156(19),
194902.
mla: Palaia, Ivan, and Anđela Šarić. “Controlling Cluster Size in 2D Phase-Separating
Binary Mixtures with Specific Interactions.” The Journal of Chemical Physics,
vol. 156, no. 19, 194902, AIP Publishing, 2022, doi:10.1063/5.0087769.
short: I. Palaia, A. Šarić, The Journal of Chemical Physics 156 (2022).
date_created: 2022-05-22T17:04:48Z
date_published: 2022-05-16T00:00:00Z
date_updated: 2023-09-05T11:59:00Z
day: '16'
ddc:
- '540'
department:
- _id: AnSa
doi: 10.1063/5.0087769
ec_funded: 1
external_id:
isi:
- '000797236000004'
file:
- access_level: open_access
checksum: 7fada58059676a4bb0944b82247af740
content_type: application/pdf
creator: dernst
date_created: 2022-05-23T07:45:33Z
date_updated: 2022-05-23T07:45:33Z
file_id: '11405'
file_name: 2022_JourChemPhysics_Palaia.pdf
file_size: 6387208
relation: main_file
success: 1
file_date_updated: 2022-05-23T07:45:33Z
has_accepted_license: '1'
intvolume: ' 156'
isi: 1
issue: '19'
keyword:
- Physical and Theoretical Chemistry
- General Physics and Astronomy
language:
- iso: eng
month: '05'
oa: 1
oa_version: Published Version
project:
- _id: eba2549b-77a9-11ec-83b8-a81e493eae4e
call_identifier: H2020
grant_number: '802960'
name: 'Non-Equilibrium Protein Assembly: from Building Blocks to Biological Machines'
- _id: fc2ed2f7-9c52-11eb-aca3-c01059dda49c
call_identifier: H2020
grant_number: '101034413'
name: 'IST-BRIDGE: International postdoctoral program'
publication: The Journal of Chemical Physics
publication_identifier:
eissn:
- 1089-7690
issn:
- 0021-9606
publication_status: published
publisher: AIP Publishing
quality_controlled: '1'
status: public
title: Controlling cluster size in 2D phase-separating binary mixtures with specific
interactions
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: c635000d-4b10-11ee-a964-aac5a93f6ac1
volume: 156
year: '2022'
...
---
_id: '11401'
abstract:
- lang: eng
text: Tin selenide (SnSe) is considered a robust candidate for thermoelectric applications
due to its very high thermoelectric figure of merit, ZT, with values of 2.6 in
p-type and 2.8 in n-type single crystals. Sn has been replaced with various lower
group dopants to achieve successful p-type doping in SnSe with high ZT values.
A known, facile, and powerful alternative way to introduce a hole carrier is to
use a natural single Sn vacancy, VSn. Through transport and scanning tunneling
microscopy studies, we discovered that VSn are dominant in high-quality (slow
cooling rate) SnSe single crystals, while multiple vacancies, Vmulti, are dominant
in low-quality (high cooling rate) single crystals. Surprisingly, both VSn and
Vmulti help to increase the power factors of SnSe, whereas samples with dominant
VSn have superior thermoelectric properties in SnSe single crystals. Additionally,
the observation that Vmulti are good p-type sources observed in relatively low-quality
single crystals is useful in thermoelectric applications because polycrystalline
SnSe can be used due to its mechanical strength; this substance is usually fabricated
at very high cooling speeds.
acknowledgement: This work was supported by the National Research Foundation of Korea
[NRF-2019R1F1A1058473, NRF-2019R1A6A1A11053838, and NRF-2020K1A4A7A02095438].
article_number: '42'
article_processing_charge: No
article_type: original
author:
- first_name: Van Quang
full_name: Nguyen, Van Quang
last_name: Nguyen
- first_name: Thi Ly
full_name: Trinh, Thi Ly
last_name: Trinh
- first_name: Cheng
full_name: Chang, Cheng
id: 9E331C2E-9F27-11E9-AE48-5033E6697425
last_name: Chang
orcid: 0000-0002-9515-4277
- first_name: Li Dong
full_name: Zhao, Li Dong
last_name: Zhao
- first_name: Thi Huong
full_name: Nguyen, Thi Huong
last_name: Nguyen
- first_name: Van Thiet
full_name: Duong, Van Thiet
last_name: Duong
- first_name: Anh Tuan
full_name: Duong, Anh Tuan
last_name: Duong
- first_name: Jong Ho
full_name: Park, Jong Ho
last_name: Park
- first_name: Sudong
full_name: Park, Sudong
last_name: Park
- first_name: Jungdae
full_name: Kim, Jungdae
last_name: Kim
- first_name: Sunglae
full_name: Cho, Sunglae
last_name: Cho
citation:
ama: 'Nguyen VQ, Trinh TL, Chang C, et al. Unidentified major p-type source in SnSe:
Multivacancies. NPG Asia Materials. 2022;14. doi:10.1038/s41427-022-00393-5'
apa: 'Nguyen, V. Q., Trinh, T. L., Chang, C., Zhao, L. D., Nguyen, T. H., Duong,
V. T., … Cho, S. (2022). Unidentified major p-type source in SnSe: Multivacancies.
NPG Asia Materials. Springer Nature. https://doi.org/10.1038/s41427-022-00393-5'
chicago: 'Nguyen, Van Quang, Thi Ly Trinh, Cheng Chang, Li Dong Zhao, Thi Huong
Nguyen, Van Thiet Duong, Anh Tuan Duong, et al. “Unidentified Major P-Type Source
in SnSe: Multivacancies.” NPG Asia Materials. Springer Nature, 2022. https://doi.org/10.1038/s41427-022-00393-5.'
ieee: 'V. Q. Nguyen et al., “Unidentified major p-type source in SnSe: Multivacancies,”
NPG Asia Materials, vol. 14. Springer Nature, 2022.'
ista: 'Nguyen VQ, Trinh TL, Chang C, Zhao LD, Nguyen TH, Duong VT, Duong AT, Park
JH, Park S, Kim J, Cho S. 2022. Unidentified major p-type source in SnSe: Multivacancies.
NPG Asia Materials. 14, 42.'
mla: 'Nguyen, Van Quang, et al. “Unidentified Major P-Type Source in SnSe: Multivacancies.”
NPG Asia Materials, vol. 14, 42, Springer Nature, 2022, doi:10.1038/s41427-022-00393-5.'
short: V.Q. Nguyen, T.L. Trinh, C. Chang, L.D. Zhao, T.H. Nguyen, V.T. Duong, A.T.
Duong, J.H. Park, S. Park, J. Kim, S. Cho, NPG Asia Materials 14 (2022).
date_created: 2022-05-22T22:01:40Z
date_published: 2022-05-13T00:00:00Z
date_updated: 2023-08-03T07:13:58Z
day: '13'
ddc:
- '540'
department:
- _id: MaIb
doi: 10.1038/s41427-022-00393-5
external_id:
isi:
- '000794880200001'
file:
- access_level: open_access
checksum: 0579997cc1d28bf66e29357e08e3e39d
content_type: application/pdf
creator: dernst
date_created: 2022-05-23T06:47:57Z
date_updated: 2022-05-23T06:47:57Z
file_id: '11404'
file_name: 2022_NPGAsiaMaterials_Nguyen.pdf
file_size: 6202545
relation: main_file
success: 1
file_date_updated: 2022-05-23T06:47:57Z
has_accepted_license: '1'
intvolume: ' 14'
isi: 1
language:
- iso: eng
month: '05'
oa: 1
oa_version: Published Version
publication: NPG Asia Materials
publication_identifier:
eissn:
- 1884-4057
issn:
- 1884-4049
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
scopus_import: '1'
status: public
title: 'Unidentified major p-type source in SnSe: Multivacancies'
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: 14
year: '2022'
...
---
_id: '11402'
abstract:
- lang: eng
text: Fixed-horizon planning considers a weighted graph and asks to construct a
path that maximizes the sum of weights for a given time horizon T. However, in
many scenarios, the time horizon is not fixed, but the stopping time is chosen
according to some distribution such that the expected stopping time is T. If the
stopping-time distribution is not known, then to ensure robustness, the distribution
is chosen by an adversary as the worst-case scenario. A stationary plan for every
vertex always chooses the same outgoing edge. For fixed horizon or fixed stopping-time
distribution, stationary plans are not sufficient for optimality. Quite surprisingly
we show that when an adversary chooses the stopping-time distribution with expected
stopping-time T, then stationary plans are sufficient. While computing optimal
stationary plans for fixed horizon is NP-complete, we show that computing optimal
stationary plans under adversarial stopping-time distribution can be achieved
in polynomial time.
acknowledgement: This work was partially supported by Austrian Science Fund (FWF)
NFN Grant No RiSE/SHiNE S11407 and by the grant ERC CoG 863818 (ForM-SMArt).
article_processing_charge: No
article_type: original
arxiv: 1
author:
- first_name: Krishnendu
full_name: Chatterjee, Krishnendu
id: 2E5DCA20-F248-11E8-B48F-1D18A9856A87
last_name: Chatterjee
orcid: 0000-0002-4561-241X
- first_name: Laurent
full_name: Doyen, Laurent
last_name: Doyen
citation:
ama: Chatterjee K, Doyen L. Graph planning with expected finite horizon. Journal
of Computer and System Sciences. 2022;129:1-21. doi:10.1016/j.jcss.2022.04.003
apa: Chatterjee, K., & Doyen, L. (2022). Graph planning with expected finite
horizon. Journal of Computer and System Sciences. Elsevier. https://doi.org/10.1016/j.jcss.2022.04.003
chicago: Chatterjee, Krishnendu, and Laurent Doyen. “Graph Planning with Expected
Finite Horizon.” Journal of Computer and System Sciences. Elsevier, 2022.
https://doi.org/10.1016/j.jcss.2022.04.003.
ieee: K. Chatterjee and L. Doyen, “Graph planning with expected finite horizon,”
Journal of Computer and System Sciences, vol. 129. Elsevier, pp. 1–21,
2022.
ista: Chatterjee K, Doyen L. 2022. Graph planning with expected finite horizon.
Journal of Computer and System Sciences. 129, 1–21.
mla: Chatterjee, Krishnendu, and Laurent Doyen. “Graph Planning with Expected Finite
Horizon.” Journal of Computer and System Sciences, vol. 129, Elsevier,
2022, pp. 1–21, doi:10.1016/j.jcss.2022.04.003.
short: K. Chatterjee, L. Doyen, Journal of Computer and System Sciences 129 (2022)
1–21.
date_created: 2022-05-22T22:01:40Z
date_published: 2022-11-01T00:00:00Z
date_updated: 2025-07-14T09:09:54Z
day: '01'
department:
- _id: KrCh
doi: 10.1016/j.jcss.2022.04.003
ec_funded: 1
external_id:
arxiv:
- '1802.03642'
isi:
- '000805002800001'
intvolume: ' 129'
isi: 1
language:
- iso: eng
main_file_link:
- open_access: '1'
url: ' https://doi.org/10.48550/arXiv.1802.03642'
month: '11'
oa: 1
oa_version: Preprint
page: 1-21
project:
- _id: 25863FF4-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: S11407
name: Game Theory
- _id: 0599E47C-7A3F-11EA-A408-12923DDC885E
call_identifier: H2020
grant_number: '863818'
name: 'Formal Methods for Stochastic Models: Algorithms and Applications'
publication: Journal of Computer and System Sciences
publication_identifier:
eissn:
- 1090-2724
issn:
- 0022-0000
publication_status: published
publisher: Elsevier
quality_controlled: '1'
related_material:
record:
- id: '7402'
relation: earlier_version
status: public
scopus_import: '1'
status: public
title: Graph planning with expected finite horizon
type: journal_article
user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
volume: 129
year: '2022'
...
---
_id: '11411'
abstract:
- lang: eng
text: Many studies have quantified the distribution of heterozygosity and relatedness
in natural populations, but few have examined the demographic processes driving
these patterns. In this study, we take a novel approach by studying how population
structure affects both pairwise identity and the distribution of heterozygosity
in a natural population of the self-incompatible plant Antirrhinum majus. Excess
variance in heterozygosity between individuals is due to identity disequilibrium,
which reflects the variance in inbreeding between individuals; it is measured
by the statistic g2. We calculated g2 together with FST and pairwise relatedness
(Fij) using 91 SNPs in 22,353 individuals collected over 11 years. We find that
pairwise Fij declines rapidly over short spatial scales, and the excess variance
in heterozygosity between individuals reflects significant variation in inbreeding.
Additionally, we detect an excess of individuals with around half the average
heterozygosity, indicating either selfing or matings between close relatives.
We use 2 types of simulation to ask whether variation in heterozygosity is consistent
with fine-scale spatial population structure. First, by simulating offspring using
parents drawn from a range of spatial scales, we show that the known pollen dispersal
kernel explains g2. Second, we simulate a 1,000-generation pedigree using the
known dispersal and spatial distribution and find that the resulting g2 is consistent
with that observed from the field data. In contrast, a simulated population with
uniform density underestimates g2, indicating that heterogeneous density promotes
identity disequilibrium. Our study shows that heterogeneous density and leptokurtic
dispersal can together explain the distribution of heterozygosity.
acknowledged_ssus:
- _id: ScienComp
acknowledgement: "Part of this work was funded by Marie Curie COFUND Doctoral Fellowship
and Austrian Science Fund FWF (grant P32166).\r\nWe thank the many volunteers and
friends who have contributed to data collection in the field site over the years,
in particular those who have managed field seasons: Barbora Trubenova, Maria Clara
Melo, Tom Ellis, Eva Cereghetti, Lenka Matejovicova, Beatriz Pablo Carmona. Frederic
Ferrer and Eva Salmerón Mateu have been immensely helpful with logistics at our
informal field station, El Serrat de Planoles. We thank Sean Stankowski for technical
help in\r\nproducing figure 1. This research was also supported by the Scientific
Service Units (SSU) of IST Austria through resources provided by Scientific Computing
(SciComp)."
article_number: iyac083
article_processing_charge: No
article_type: original
author:
- first_name: Parvathy
full_name: Surendranadh, Parvathy
id: 455235B8-F248-11E8-B48F-1D18A9856A87
last_name: Surendranadh
- first_name: Louise S
full_name: Arathoon, Louise S
id: 2CFCFF98-F248-11E8-B48F-1D18A9856A87
last_name: Arathoon
orcid: 0000-0003-1771-714X
- first_name: Carina
full_name: Baskett, Carina
id: 3B4A7CE2-F248-11E8-B48F-1D18A9856A87
last_name: Baskett
orcid: 0000-0002-7354-8574
- first_name: David
full_name: Field, David
id: 419049E2-F248-11E8-B48F-1D18A9856A87
last_name: Field
orcid: 0000-0002-4014-8478
- first_name: Melinda
full_name: Pickup, Melinda
id: 2C78037E-F248-11E8-B48F-1D18A9856A87
last_name: Pickup
orcid: 0000-0001-6118-0541
- 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: Surendranadh P, Arathoon LS, Baskett C, Field D, Pickup M, Barton NH. Effects
of fine-scale population structure on the distribution of heterozygosity in a
long-term study of Antirrhinum majus. Genetics. 2022;221(3). doi:10.1093/genetics/iyac083
apa: Surendranadh, P., Arathoon, L. S., Baskett, C., Field, D., Pickup, M., &
Barton, N. H. (2022). Effects of fine-scale population structure on the distribution
of heterozygosity in a long-term study of Antirrhinum majus. Genetics.
Oxford University Press. https://doi.org/10.1093/genetics/iyac083
chicago: Surendranadh, Parvathy, Louise S Arathoon, Carina Baskett, David Field,
Melinda Pickup, and Nicholas H Barton. “Effects of Fine-Scale Population Structure
on the Distribution of Heterozygosity in a Long-Term Study of Antirrhinum Majus.”
Genetics. Oxford University Press, 2022. https://doi.org/10.1093/genetics/iyac083.
ieee: P. Surendranadh, L. S. Arathoon, C. Baskett, D. Field, M. Pickup, and N. H.
Barton, “Effects of fine-scale population structure on the distribution of heterozygosity
in a long-term study of Antirrhinum majus,” Genetics, vol. 221, no. 3.
Oxford University Press, 2022.
ista: Surendranadh P, Arathoon LS, Baskett C, Field D, Pickup M, Barton NH. 2022.
Effects of fine-scale population structure on the distribution of heterozygosity
in a long-term study of Antirrhinum majus. Genetics. 221(3), iyac083.
mla: Surendranadh, Parvathy, et al. “Effects of Fine-Scale Population Structure
on the Distribution of Heterozygosity in a Long-Term Study of Antirrhinum Majus.”
Genetics, vol. 221, no. 3, iyac083, Oxford University Press, 2022, doi:10.1093/genetics/iyac083.
short: P. Surendranadh, L.S. Arathoon, C. Baskett, D. Field, M. Pickup, N.H. Barton,
Genetics 221 (2022).
date_created: 2022-05-26T13:44:50Z
date_published: 2022-07-01T00:00:00Z
date_updated: 2024-02-21T12:38:33Z
day: '01'
ddc:
- '576'
department:
- _id: GradSch
- _id: NiBa
doi: 10.1093/genetics/iyac083
external_id:
isi:
- '000803735800001'
pmid:
- '35639938'
file:
- access_level: open_access
checksum: cc2d56deb608bd53c5cc02f03a875107
content_type: application/pdf
creator: larathoo
date_created: 2022-05-26T12:48:15Z
date_updated: 2022-05-26T12:48:15Z
file_id: '11412'
file_name: Manuscript.pdf
file_size: 885374
relation: main_file
success: 1
- access_level: open_access
checksum: 693742595b6c7ed809423be01460d083
content_type: application/pdf
creator: larathoo
date_created: 2022-05-26T12:48:21Z
date_updated: 2022-05-26T12:48:21Z
file_id: '11413'
file_name: SupplementalMaterial.pdf
file_size: 1401704
relation: main_file
success: 1
file_date_updated: 2022-05-26T12:48:21Z
has_accepted_license: '1'
intvolume: ' 221'
isi: 1
issue: '3'
language:
- iso: eng
month: '07'
oa: 1
oa_version: Submitted Version
pmid: 1
project:
- _id: 05959E1C-7A3F-11EA-A408-12923DDC885E
grant_number: P32166
name: The maintenance of alternative adaptive peaks in snapdragons
publication: Genetics
publication_identifier:
eissn:
- 1943-2631
publication_status: published
publisher: Oxford University Press
quality_controlled: '1'
related_material:
record:
- id: '14651'
relation: dissertation_contains
status: public
- id: '11321'
relation: research_data
status: public
- id: '9192'
relation: research_data
status: public
scopus_import: '1'
status: public
title: Effects of fine-scale population structure on the distribution of heterozygosity
in a long-term study of Antirrhinum majus
type: journal_article
user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
volume: 221
year: '2022'
...
---
_id: '11417'
abstract:
- lang: eng
text: "Over the past few years, the field of quantum information science has seen
tremendous progress toward realizing large-scale quantum computers. With demonstrations
of quantum computers outperforming classical computers for a select range of problems,1–3
we have finally entered the noisy, intermediate-scale quantum (NISQ) computing
era. While the quantum computers of today are technological marvels, they are
not yet error corrected, and it is unclear whether any system will scale beyond
a few hundred logical qubits without significant changes to architecture and control
schemes. Today's quantum systems are analogous to the ENIAC (Electronic Numerical
Integrator And Computer) and EDVAC (Electronic Discrete Variable Automatic Computer)
systems of the 1940s, which ran on vacuum tubes. These machines were built on
a solid, nominally scalable architecture and when they were developed, nobody
could have predicted the development of the transistor and the impact of the resulting
semiconductor industry. Simply put, the computers of today are nothing like the
early computers of the 1940s. We believe that the qubits of future fault-tolerant
quantum systems will look quite different from the qubits of the NISQ machines
in operation today. This Special Topic issue is devoted to new and emerging quantum
systems with a focus on enabling technologies that can eventually lead to the
quantum analog to the transistor. We have solicited both research4–18 and perspective
articles19–21 to discuss new and emerging qubit systems with a focus on novel
materials, encodings, and architectures. We are proud to present a collection
that touches on a wide range of technologies including superconductors,7–13,21
semiconductors,15–17,19 and individual atomic qubits.18\r\n"
acknowledgement: "We would like to thank all of the authors who contributed to\r\nthis
Special Topic. We would also like to thank the editorial team at\r\nAPL including
Jessica Trudeau, Emma Van Burns, Martin Weides,\r\nand Lesley Cohen."
article_number: '190401'
article_processing_charge: No
article_type: letter_note
author:
- first_name: Anthony J.
full_name: Sigillito, Anthony J.
last_name: Sigillito
- first_name: Jacob P.
full_name: Covey, Jacob P.
last_name: Covey
- first_name: Johannes M
full_name: Fink, Johannes M
id: 4B591CBA-F248-11E8-B48F-1D18A9856A87
last_name: Fink
orcid: 0000-0001-8112-028X
- first_name: Karl
full_name: Petersson, Karl
last_name: Petersson
- first_name: Stefan
full_name: Preble, Stefan
last_name: Preble
citation:
ama: 'Sigillito AJ, Covey JP, Fink JM, Petersson K, Preble S. Emerging qubit systems:
Guest editorial. Applied Physics Letters. 2022;120(19). doi:10.1063/5.0097339'
apa: 'Sigillito, A. J., Covey, J. P., Fink, J. M., Petersson, K., & Preble,
S. (2022). Emerging qubit systems: Guest editorial. Applied Physics Letters.
American Institute of Physics. https://doi.org/10.1063/5.0097339'
chicago: 'Sigillito, Anthony J., Jacob P. Covey, Johannes M Fink, Karl Petersson,
and Stefan Preble. “Emerging Qubit Systems: Guest Editorial.” Applied Physics
Letters. American Institute of Physics, 2022. https://doi.org/10.1063/5.0097339.'
ieee: 'A. J. Sigillito, J. P. Covey, J. M. Fink, K. Petersson, and S. Preble, “Emerging
qubit systems: Guest editorial,” Applied Physics Letters, vol. 120, no.
19. American Institute of Physics, 2022.'
ista: 'Sigillito AJ, Covey JP, Fink JM, Petersson K, Preble S. 2022. Emerging qubit
systems: Guest editorial. Applied Physics Letters. 120(19), 190401.'
mla: 'Sigillito, Anthony J., et al. “Emerging Qubit Systems: Guest Editorial.” Applied
Physics Letters, vol. 120, no. 19, 190401, American Institute of Physics,
2022, doi:10.1063/5.0097339.'
short: A.J. Sigillito, J.P. Covey, J.M. Fink, K. Petersson, S. Preble, Applied Physics
Letters 120 (2022).
date_created: 2022-05-29T22:01:53Z
date_published: 2022-05-12T00:00:00Z
date_updated: 2023-08-03T07:16:20Z
day: '12'
department:
- _id: JoFi
doi: 10.1063/5.0097339
external_id:
isi:
- '000796002100002'
intvolume: ' 120'
isi: 1
issue: '19'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.1063/5.0097339
month: '05'
oa: 1
oa_version: Published Version
publication: Applied Physics Letters
publication_identifier:
issn:
- 0003-6951
publication_status: published
publisher: American Institute of Physics
quality_controlled: '1'
scopus_import: '1'
status: public
title: 'Emerging qubit systems: Guest editorial'
type: journal_article
user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
volume: 120
year: '2022'
...
---
_id: '11418'
abstract:
- lang: eng
text: "We consider the quadratic form of a general high-rank deterministic matrix
on the eigenvectors of an N×N\r\nWigner matrix and prove that it has Gaussian
fluctuation for each bulk eigenvector in the large N limit. The proof is a combination
of the energy method for the Dyson Brownian motion inspired by Marcinek and Yau
(2021) and our recent multiresolvent local laws (Comm. Math. Phys. 388 (2021)
1005–1048)."
acknowledgement: L.E. would like to thank Zhigang Bao for many illuminating discussions
in an early stage of this research. The authors are also grateful to Paul Bourgade
for his comments on the manuscript and the anonymous referee for several useful
suggestions.
article_processing_charge: No
article_type: original
arxiv: 1
author:
- first_name: Giorgio
full_name: Cipolloni, Giorgio
id: 42198EFA-F248-11E8-B48F-1D18A9856A87
last_name: Cipolloni
orcid: 0000-0002-4901-7992
- first_name: László
full_name: Erdös, László
id: 4DBD5372-F248-11E8-B48F-1D18A9856A87
last_name: Erdös
orcid: 0000-0001-5366-9603
- first_name: Dominik J
full_name: Schröder, Dominik J
id: 408ED176-F248-11E8-B48F-1D18A9856A87
last_name: Schröder
orcid: 0000-0002-2904-1856
citation:
ama: Cipolloni G, Erdös L, Schröder DJ. Normal fluctuation in quantum ergodicity
for Wigner matrices. Annals of Probability. 2022;50(3):984-1012. doi:10.1214/21-AOP1552
apa: Cipolloni, G., Erdös, L., & Schröder, D. J. (2022). Normal fluctuation
in quantum ergodicity for Wigner matrices. Annals of Probability. Institute
of Mathematical Statistics. https://doi.org/10.1214/21-AOP1552
chicago: Cipolloni, Giorgio, László Erdös, and Dominik J Schröder. “Normal Fluctuation
in Quantum Ergodicity for Wigner Matrices.” Annals of Probability. Institute
of Mathematical Statistics, 2022. https://doi.org/10.1214/21-AOP1552.
ieee: G. Cipolloni, L. Erdös, and D. J. Schröder, “Normal fluctuation in quantum
ergodicity for Wigner matrices,” Annals of Probability, vol. 50, no. 3.
Institute of Mathematical Statistics, pp. 984–1012, 2022.
ista: Cipolloni G, Erdös L, Schröder DJ. 2022. Normal fluctuation in quantum ergodicity
for Wigner matrices. Annals of Probability. 50(3), 984–1012.
mla: Cipolloni, Giorgio, et al. “Normal Fluctuation in Quantum Ergodicity for Wigner
Matrices.” Annals of Probability, vol. 50, no. 3, Institute of Mathematical
Statistics, 2022, pp. 984–1012, doi:10.1214/21-AOP1552.
short: G. Cipolloni, L. Erdös, D.J. Schröder, Annals of Probability 50 (2022) 984–1012.
date_created: 2022-05-29T22:01:53Z
date_published: 2022-05-01T00:00:00Z
date_updated: 2023-08-03T07:16:53Z
day: '01'
department:
- _id: LaEr
doi: 10.1214/21-AOP1552
external_id:
arxiv:
- '2103.06730'
isi:
- '000793963400005'
intvolume: ' 50'
isi: 1
issue: '3'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/2103.06730
month: '05'
oa: 1
oa_version: Preprint
page: 984-1012
publication: Annals of Probability
publication_identifier:
eissn:
- 2168-894X
issn:
- 0091-1798
publication_status: published
publisher: Institute of Mathematical Statistics
quality_controlled: '1'
scopus_import: '1'
status: public
title: Normal fluctuation in quantum ergodicity for Wigner matrices
type: journal_article
user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
volume: 50
year: '2022'
...
---
_id: '11419'
abstract:
- lang: eng
text: Elevation of soluble wild-type (WT) tau occurs in synaptic compartments in
Alzheimer’s disease. We addressed whether tau elevation affects synaptic transmission
at the calyx of Held in slices from mice brainstem. Whole-cell loading of WT human
tau (h-tau) in presynaptic terminals at 10–20 µM caused microtubule (MT) assembly
and activity-dependent rundown of excitatory neurotransmission. Capacitance measurements
revealed that the primary target of WT h-tau is vesicle endocytosis. Blocking
MT assembly using nocodazole prevented tau-induced impairments of endocytosis
and neurotransmission. Immunofluorescence imaging analyses revealed that MT assembly
by WT h-tau loading was associated with an increased MT-bound fraction of the
endocytic protein dynamin. A synthetic dodecapeptide corresponding to dynamin
1-pleckstrin-homology domain inhibited MT-dynamin interaction and rescued tau-induced
impairments of endocytosis and neurotransmission. We conclude that elevation of
presynaptic WT tau induces de novo assembly of MTs, thereby sequestering free
dynamins. As a result, endocytosis and subsequent vesicle replenishment are impaired,
causing activity-dependent rundown of neurotransmission.
acknowledgement: We thank Yasuo Ihara, Nobuyuki Nukina, and Takeshi Sakaba for comments
and Patrick Stoney for editing this paper. We also thank Shota Okuda and Mikako
Matsubara for their contributions in the early stage of this study, and Satoko Wada-Kakuda
for technical assistant with in vitro analysis of tau. This research was supported
by funding from Okinawa Institute of Science and Technology and from Technology
(OIST) and Core Research for the Evolutional Science and Technology of Japan Science
and Technology Agency (CREST) to TT, and by Scientific Research on Innovative Areas
to TM (Brain Protein Aging and Dementia Control 26117004).
article_number: e73542
article_processing_charge: No
article_type: original
author:
- first_name: Tetsuya
full_name: Hori, Tetsuya
last_name: Hori
- first_name: Kohgaku
full_name: Eguchi, Kohgaku
id: 2B7846DC-F248-11E8-B48F-1D18A9856A87
last_name: Eguchi
orcid: 0000-0002-6170-2546
- first_name: Han Ying
full_name: Wang, Han Ying
last_name: Wang
- first_name: Tomohiro
full_name: Miyasaka, Tomohiro
last_name: Miyasaka
- first_name: Laurent
full_name: Guillaud, Laurent
last_name: Guillaud
- first_name: Zacharie
full_name: Taoufiq, Zacharie
last_name: Taoufiq
- first_name: Satyajit
full_name: Mahapatra, Satyajit
last_name: Mahapatra
- first_name: Hiroshi
full_name: Yamada, Hiroshi
last_name: Yamada
- first_name: Kohji
full_name: Takei, Kohji
last_name: Takei
- first_name: Tomoyuki
full_name: Takahashi, Tomoyuki
last_name: Takahashi
citation:
ama: Hori T, Eguchi K, Wang HY, et al. Microtubule assembly by tau impairs endocytosis
and neurotransmission via dynamin sequestration in Alzheimer’s disease synapse
model. eLife. 2022;11. doi:10.7554/eLife.73542
apa: Hori, T., Eguchi, K., Wang, H. Y., Miyasaka, T., Guillaud, L., Taoufiq, Z.,
… Takahashi, T. (2022). Microtubule assembly by tau impairs endocytosis and neurotransmission
via dynamin sequestration in Alzheimer’s disease synapse model. ELife.
eLife Sciences Publications. https://doi.org/10.7554/eLife.73542
chicago: Hori, Tetsuya, Kohgaku Eguchi, Han Ying Wang, Tomohiro Miyasaka, Laurent
Guillaud, Zacharie Taoufiq, Satyajit Mahapatra, Hiroshi Yamada, Kohji Takei, and
Tomoyuki Takahashi. “Microtubule Assembly by Tau Impairs Endocytosis and Neurotransmission
via Dynamin Sequestration in Alzheimer’s Disease Synapse Model.” ELife.
eLife Sciences Publications, 2022. https://doi.org/10.7554/eLife.73542.
ieee: T. Hori et al., “Microtubule assembly by tau impairs endocytosis and
neurotransmission via dynamin sequestration in Alzheimer’s disease synapse model,”
eLife, vol. 11. eLife Sciences Publications, 2022.
ista: Hori T, Eguchi K, Wang HY, Miyasaka T, Guillaud L, Taoufiq Z, Mahapatra S,
Yamada H, Takei K, Takahashi T. 2022. Microtubule assembly by tau impairs endocytosis
and neurotransmission via dynamin sequestration in Alzheimer’s disease synapse
model. eLife. 11, e73542.
mla: Hori, Tetsuya, et al. “Microtubule Assembly by Tau Impairs Endocytosis and
Neurotransmission via Dynamin Sequestration in Alzheimer’s Disease Synapse Model.”
ELife, vol. 11, e73542, eLife Sciences Publications, 2022, doi:10.7554/eLife.73542.
short: T. Hori, K. Eguchi, H.Y. Wang, T. Miyasaka, L. Guillaud, Z. Taoufiq, S. Mahapatra,
H. Yamada, K. Takei, T. Takahashi, ELife 11 (2022).
date_created: 2022-05-29T22:01:54Z
date_published: 2022-05-05T00:00:00Z
date_updated: 2023-08-03T07:15:49Z
day: '05'
ddc:
- '616'
department:
- _id: RySh
doi: 10.7554/eLife.73542
external_id:
isi:
- '000876231600001'
pmid:
- '35471147 '
file:
- access_level: open_access
checksum: ccddbd167e00ff8375f12998af497152
content_type: application/pdf
creator: cchlebak
date_created: 2022-05-30T08:09:16Z
date_updated: 2022-05-30T08:09:16Z
file_id: '11421'
file_name: elife-73542-v2.pdf
file_size: 2466296
relation: main_file
success: 1
file_date_updated: 2022-05-30T08:09:16Z
has_accepted_license: '1'
intvolume: ' 11'
isi: 1
language:
- iso: eng
month: '05'
oa: 1
oa_version: Published Version
pmid: 1
publication: eLife
publication_identifier:
eissn:
- 2050-084X
publication_status: published
publisher: eLife Sciences Publications
quality_controlled: '1'
scopus_import: '1'
status: public
title: Microtubule assembly by tau impairs endocytosis and neurotransmission via dynamin
sequestration in Alzheimer's disease synapse model
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: 11
year: '2022'
...