---
_id: '11473'
abstract:
- lang: eng
text: "The polaron model is a basic model of quantum field theory describing a single
particle\r\ninteracting with a bosonic field. It arises in many physical contexts.
We are mostly concerned\r\nwith models applicable in the context of an impurity
atom in a Bose-Einstein condensate as\r\nwell as the problem of electrons moving
in polar crystals.\r\nThe model has a simple structure in which the interaction
of the particle with the field is given\r\nby a term linear in the field’s creation
and annihilation operators. In this work, we investigate\r\nthe properties of
this model by providing rigorous estimates on various energies relevant to the\r\nproblem.
The estimates are obtained, for the most part, by suitable operator techniques
which\r\nconstitute the principal mathematical substance of the thesis.\r\nThe
first application of these techniques is to derive the polaron model rigorously
from first\r\nprinciples, i.e., from a full microscopic quantum-mechanical many-body
problem involving an\r\nimpurity in an otherwise homogeneous system. We accomplish
this for the N + 1 Bose gas\r\nin the mean-field regime by showing that a suitable
polaron-type Hamiltonian arises at weak\r\ninteractions as a low-energy effective
theory for this problem.\r\nIn the second part, we investigate rigorously the
ground state of the model at fixed momentum\r\nand for large values of the coupling
constant. Qualitatively, the system is expected to display\r\na transition from
the quasi-particle behavior at small momenta, where the dispersion relation\r\nis
parabolic and the particle moves through the medium dragging along a cloud of
phonons, to\r\nthe radiative behavior at larger momenta where the polaron decelerates
and emits free phonons.\r\nAt the same time, in the strong coupling regime, the
bosonic field is expected to behave purely\r\nclassically. Accordingly, the effective
mass of the polaron at strong coupling is conjectured to\r\nbe asymptotically
equal to the one obtained from the semiclassical counterpart of the problem,\r\nfirst
studied by Landau and Pekar in the 1940s. For polaron models with regularized
form\r\nfactors and phonon dispersion relations of superfluid type, i.e., bounded
below by a linear\r\nfunction of the wavenumbers for all phonon momenta as in
the interacting Bose gas, we prove\r\nthat for a large window of momenta below
the radiation threshold, the energy-momentum\r\nrelation at strong coupling is
indeed essentially a parabola with semi-latus rectum equal to the\r\nLandau–Pekar
effective mass, as expected.\r\nFor the Fröhlich polaron describing electrons
in polar crystals where the dispersion relation is\r\nof the optical type and
the form factor is formally UV–singular due to the nature of the point\r\ncharge-dipole
interaction, we are able to give the corresponding upper bound. In contrast to\r\nthe
regular case, this requires the inclusion of the quantum fluctuations of the phonon
field,\r\nwhich makes the problem considerably more difficult.\r\nThe results
are supplemented by studies on the absolute ground-state energy at strong coupling,\r\na
proof of the divergence of the effective mass with the coupling constant for a
wide class of\r\npolaron models, as well as the discussion of the apparent UV
singularity of the Fröhlich model\r\nand the application of the techniques used
for its removal for the energy estimates.\r\n"
acknowledged_ssus:
- _id: SSU
alternative_title:
- ISTA Thesis
article_processing_charge: No
author:
- first_name: Krzysztof
full_name: Mysliwy, Krzysztof
id: 316457FC-F248-11E8-B48F-1D18A9856A87
last_name: Mysliwy
citation:
ama: 'Mysliwy K. Polarons in Bose gases and polar crystals: Some rigorous energy
estimates. 2022. doi:10.15479/at:ista:11473'
apa: 'Mysliwy, K. (2022). Polarons in Bose gases and polar crystals: Some rigorous
energy estimates. Institute of Science and Technology Austria. https://doi.org/10.15479/at:ista:11473'
chicago: 'Mysliwy, Krzysztof. “Polarons in Bose Gases and Polar Crystals: Some Rigorous
Energy Estimates.” Institute of Science and Technology Austria, 2022. https://doi.org/10.15479/at:ista:11473.'
ieee: 'K. Mysliwy, “Polarons in Bose gases and polar crystals: Some rigorous energy
estimates,” Institute of Science and Technology Austria, 2022.'
ista: 'Mysliwy K. 2022. Polarons in Bose gases and polar crystals: Some rigorous
energy estimates. Institute of Science and Technology Austria.'
mla: 'Mysliwy, Krzysztof. Polarons in Bose Gases and Polar Crystals: Some Rigorous
Energy Estimates. Institute of Science and Technology Austria, 2022, doi:10.15479/at:ista:11473.'
short: 'K. Mysliwy, Polarons in Bose Gases and Polar Crystals: Some Rigorous Energy
Estimates, Institute of Science and Technology Austria, 2022.'
date_created: 2022-06-30T12:15:03Z
date_published: 2022-07-01T00:00:00Z
date_updated: 2023-09-07T13:43:52Z
day: '01'
ddc:
- '515'
- '539'
degree_awarded: PhD
department:
- _id: GradSch
- _id: RoSe
doi: 10.15479/at:ista:11473
ec_funded: 1
file:
- access_level: open_access
checksum: 7970714a20a6052f75fb27a6c3e9976e
content_type: application/pdf
creator: kmysliwy
date_created: 2022-07-05T08:12:56Z
date_updated: 2022-07-05T08:12:56Z
file_id: '11486'
file_name: thes1_no_isbn_2_1b.pdf
file_size: 1830973
relation: main_file
success: 1
- access_level: closed
checksum: 647a2011fdf56277096c9350fefe1097
content_type: application/zip
creator: kmysliwy
date_created: 2022-07-05T08:15:52Z
date_updated: 2022-07-05T08:17:12Z
file_id: '11487'
file_name: thes_source.zip
file_size: 5831060
relation: source_file
file_date_updated: 2022-07-05T08:17:12Z
has_accepted_license: '1'
language:
- iso: eng
month: '07'
oa: 1
oa_version: Published Version
page: '138'
project:
- _id: 2564DBCA-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '665385'
name: International IST Doctoral Program
publication_identifier:
issn:
- 2663-337X
publication_status: published
publisher: Institute of Science and Technology Austria
related_material:
record:
- id: '10564'
relation: part_of_dissertation
status: public
- id: '8705'
relation: part_of_dissertation
status: public
status: public
supervisor:
- first_name: Robert
full_name: Seiringer, Robert
id: 4AFD0470-F248-11E8-B48F-1D18A9856A87
last_name: Seiringer
orcid: 0000-0002-6781-0521
title: 'Polarons in Bose gases and polar crystals: Some rigorous energy estimates'
type: dissertation
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
year: '2022'
...
---
_id: '11476'
abstract:
- lang: eng
text: "Messaging platforms like Signal are widely deployed and provide strong security
in an asynchronous setting. It is a challenging problem to construct a protocol
with similar security guarantees that can efficiently scale to large groups. A
major bottleneck are the frequent key rotations users need to perform to achieve
post compromise forward security.\r\n\r\nIn current proposals – most notably in
TreeKEM (which is part of the IETF’s Messaging Layer Security (MLS) protocol draft)
– for users in a group of size n to rotate their keys, they must each craft a
message of size log(n) to be broadcast to the group using an (untrusted) delivery
server.\r\n\r\nIn larger groups, having users sequentially rotate their keys requires
too much bandwidth (or takes too long), so variants allowing any T≤n users to
simultaneously rotate their keys in just 2 communication rounds have been suggested
(e.g. “Propose and Commit” by MLS). Unfortunately, 2-round concurrent updates
are either damaging or expensive (or both); i.e. they either result in future
operations being more costly (e.g. via “blanking” or “tainting”) or are costly
themselves requiring Ω(T) communication for each user [Bienstock et al., TCC’20].\r\n\r\nIn
this paper we propose CoCoA; a new scheme that allows for T concurrent updates
that are neither damaging nor costly. That is, they add no cost to future operations
yet they only require Ω(log2(n)) communication per user. To circumvent the [Bienstock
et al.] lower bound, CoCoA increases the number of rounds needed to complete all
updates from 2 up to (at most) log(n); though typically fewer rounds are needed.\r\n\r\nThe
key insight of our protocol is the following: in the (non-concurrent version of)
TreeKEM, a delivery server which gets T concurrent update requests will approve
one and reject the remaining T−1. In contrast, our server attempts to apply all
of them. If more than one user requests to rotate the same key during a round,
the server arbitrarily picks a winner. Surprisingly, we prove that regardless
of how the server chooses the winners, all previously compromised users will recover
after at most log(n) such update rounds.\r\n\r\nTo keep the communication complexity
low, CoCoA is a server-aided CGKA. That is, the delivery server no longer blindly
forwards packets, but instead actively computes individualized packets tailored
to each user. As the server is untrusted, this change requires us to develop new
mechanisms ensuring robustness of the protocol."
acknowledgement: We thank Marta Mularczyk and Yiannis Tselekounis for their very helpful
feedback on an earlier draft of this paper.
alternative_title:
- LNCS
article_processing_charge: No
author:
- first_name: Joël
full_name: Alwen, Joël
last_name: Alwen
- first_name: Benedikt
full_name: Auerbach, Benedikt
id: D33D2B18-E445-11E9-ABB7-15F4E5697425
last_name: Auerbach
orcid: 0000-0002-7553-6606
- first_name: Miguel
full_name: Cueto Noval, Miguel
id: ffc563a3-f6e0-11ea-865d-e3cce03d17cc
last_name: Cueto Noval
- first_name: Karen
full_name: Klein, Karen
id: 3E83A2F8-F248-11E8-B48F-1D18A9856A87
last_name: Klein
- first_name: Guillermo
full_name: Pascual Perez, Guillermo
id: 2D7ABD02-F248-11E8-B48F-1D18A9856A87
last_name: Pascual Perez
- first_name: Krzysztof Z
full_name: Pietrzak, Krzysztof Z
id: 3E04A7AA-F248-11E8-B48F-1D18A9856A87
last_name: Pietrzak
orcid: 0000-0002-9139-1654
- first_name: Michael
full_name: Walter, Michael
last_name: Walter
citation:
ama: 'Alwen J, Auerbach B, Cueto Noval M, et al. CoCoA: Concurrent continuous group
key agreement. In: Advances in Cryptology – EUROCRYPT 2022. Vol 13276.
Cham: Springer Nature; 2022:815–844. doi:10.1007/978-3-031-07085-3_28'
apa: 'Alwen, J., Auerbach, B., Cueto Noval, M., Klein, K., Pascual Perez, G., Pietrzak,
K. Z., & Walter, M. (2022). CoCoA: Concurrent continuous group key agreement.
In Advances in Cryptology – EUROCRYPT 2022 (Vol. 13276, pp. 815–844). Cham:
Springer Nature. https://doi.org/10.1007/978-3-031-07085-3_28'
chicago: 'Alwen, Joël, Benedikt Auerbach, Miguel Cueto Noval, Karen Klein, Guillermo
Pascual Perez, Krzysztof Z Pietrzak, and Michael Walter. “CoCoA: Concurrent Continuous
Group Key Agreement.” In Advances in Cryptology – EUROCRYPT 2022, 13276:815–844.
Cham: Springer Nature, 2022. https://doi.org/10.1007/978-3-031-07085-3_28.'
ieee: 'J. Alwen et al., “CoCoA: Concurrent continuous group key agreement,”
in Advances in Cryptology – EUROCRYPT 2022, Trondheim, Norway, 2022, vol.
13276, pp. 815–844.'
ista: 'Alwen J, Auerbach B, Cueto Noval M, Klein K, Pascual Perez G, Pietrzak KZ,
Walter M. 2022. CoCoA: Concurrent continuous group key agreement. Advances in
Cryptology – EUROCRYPT 2022. EUROCRYPT: Annual International Conference on the
Theory and Applications of Cryptology and Information Security, LNCS, vol. 13276,
815–844.'
mla: 'Alwen, Joël, et al. “CoCoA: Concurrent Continuous Group Key Agreement.” Advances
in Cryptology – EUROCRYPT 2022, vol. 13276, Springer Nature, 2022, pp. 815–844,
doi:10.1007/978-3-031-07085-3_28.'
short: J. Alwen, B. Auerbach, M. Cueto Noval, K. Klein, G. Pascual Perez, K.Z. Pietrzak,
M. Walter, in:, Advances in Cryptology – EUROCRYPT 2022, Springer Nature, Cham,
2022, pp. 815–844.
conference:
end_date: 2022-06-03
location: Trondheim, Norway
name: 'EUROCRYPT: Annual International Conference on the Theory and Applications
of Cryptology and Information Security'
start_date: 2022-05-30
date_created: 2022-06-30T16:48:00Z
date_published: 2022-05-25T00:00:00Z
date_updated: 2023-08-03T07:25:02Z
day: '25'
department:
- _id: GradSch
- _id: KrPi
doi: 10.1007/978-3-031-07085-3_28
ec_funded: 1
external_id:
isi:
- '000832305300028'
intvolume: ' 13276'
isi: 1
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://eprint.iacr.org/2022/251
month: '05'
oa: 1
oa_version: Preprint
page: 815–844
place: Cham
project:
- _id: 258AA5B2-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '682815'
name: Teaching Old Crypto New Tricks
- _id: 2564DBCA-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '665385'
name: International IST Doctoral Program
publication: Advances in Cryptology – EUROCRYPT 2022
publication_identifier:
eisbn:
- '9783031070853'
eissn:
- 1611-3349
isbn:
- '9783031070846'
issn:
- 0302-9743
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
scopus_import: '1'
status: public
title: 'CoCoA: Concurrent continuous group key agreement'
type: conference
user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
volume: 13276
year: '2022'
...
---
_id: '11478'
abstract:
- lang: eng
text: Cerebral organoids differentiated from human-induced pluripotent stem cells
(hiPSC) provide a unique opportunity to investigate brain development. However,
organoids usually lack microglia, brain-resident immune cells, which are present
in the early embryonic brain and participate in neuronal circuit development.
Here, we find IBA1+ microglia-like cells alongside retinal cups between week 3
and 4 in 2.5D culture with an unguided retinal organoid differentiation protocol.
Microglia do not infiltrate the neuroectoderm and instead enrich within non-pigmented,
3D-cystic compartments that develop in parallel to the 3D-retinal organoids. When
we guide the retinal organoid differentiation with low-dosed BMP4, we prevent
cup development and enhance microglia and 3D-cysts formation. Mass spectrometry
identifies these 3D-cysts to express mesenchymal and epithelial markers. We confirmed
this microglia-preferred environment also within the unguided protocol, providing
insight into microglial behavior and migration and offer a model to study how
they enter and distribute within the human brain.
acknowledged_ssus:
- _id: Bio
- _id: LifeSc
acknowledgement: We thank the scientific service units at ISTA, specifically the lab
support facility and imaging & optics facility for their support; Nicolas Armel
for performing the Mass Spectrometry. We thank Alexandra Lang and Tanja Peilnsteiner
for their help in human brain tissue collection, Rouven Schulz for his insights
into the functional assays We thank all members of the Siegert group for constant
feedback on the project and Margaret Maes, Rouven Schulz, and Marco Benevento for
feedback on the manuscript. This project has received funding from the European
Research Council (ERC) under the European Union’s Horizon 2020 research and innovation
program (grant No. 715571 to S.S.) and from the Gesellschaft für Forschungsförderung
Niederösterreich (grant No. Sc19-017 to V.H.).
article_number: '104580'
article_processing_charge: Yes
article_type: original
author:
- first_name: Katarina
full_name: Bartalska, Katarina
id: 4D883232-F248-11E8-B48F-1D18A9856A87
last_name: Bartalska
- first_name: Verena
full_name: Hübschmann, Verena
id: 32B7C918-F248-11E8-B48F-1D18A9856A87
last_name: Hübschmann
- first_name: Medina
full_name: Korkut, Medina
id: 4B51CE74-F248-11E8-B48F-1D18A9856A87
last_name: Korkut
orcid: 0000-0003-4309-2251
- first_name: Ryan J
full_name: Cubero, Ryan J
id: 850B2E12-9CD4-11E9-837F-E719E6697425
last_name: Cubero
orcid: 0000-0003-0002-1867
- first_name: Alessandro
full_name: Venturino, Alessandro
id: 41CB84B2-F248-11E8-B48F-1D18A9856A87
last_name: Venturino
orcid: 0000-0003-2356-9403
- first_name: Karl
full_name: Rössler, Karl
last_name: Rössler
- first_name: Thomas
full_name: Czech, Thomas
last_name: Czech
- first_name: Sandra
full_name: Siegert, Sandra
id: 36ACD32E-F248-11E8-B48F-1D18A9856A87
last_name: Siegert
orcid: 0000-0001-8635-0877
citation:
ama: Bartalska K, Hübschmann V, Korkut M, et al. A systematic characterization of
microglia-like cell occurrence during retinal organoid differentiation. iScience.
2022;25(7). doi:10.1016/j.isci.2022.104580
apa: Bartalska, K., Hübschmann, V., Korkut, M., Cubero, R. J., Venturino, A., Rössler,
K., … Siegert, S. (2022). A systematic characterization of microglia-like cell
occurrence during retinal organoid differentiation. IScience. Elsevier.
https://doi.org/10.1016/j.isci.2022.104580
chicago: Bartalska, Katarina, Verena Hübschmann, Medina Korkut, Ryan J Cubero, Alessandro
Venturino, Karl Rössler, Thomas Czech, and Sandra Siegert. “A Systematic Characterization
of Microglia-like Cell Occurrence during Retinal Organoid Differentiation.” IScience.
Elsevier, 2022. https://doi.org/10.1016/j.isci.2022.104580.
ieee: K. Bartalska et al., “A systematic characterization of microglia-like
cell occurrence during retinal organoid differentiation,” iScience, vol.
25, no. 7. Elsevier, 2022.
ista: Bartalska K, Hübschmann V, Korkut M, Cubero RJ, Venturino A, Rössler K, Czech
T, Siegert S. 2022. A systematic characterization of microglia-like cell occurrence
during retinal organoid differentiation. iScience. 25(7), 104580.
mla: Bartalska, Katarina, et al. “A Systematic Characterization of Microglia-like
Cell Occurrence during Retinal Organoid Differentiation.” IScience, vol.
25, no. 7, 104580, Elsevier, 2022, doi:10.1016/j.isci.2022.104580.
short: K. Bartalska, V. Hübschmann, M. Korkut, R.J. Cubero, A. Venturino, K. Rössler,
T. Czech, S. Siegert, IScience 25 (2022).
date_created: 2022-07-03T22:01:33Z
date_published: 2022-07-15T00:00:00Z
date_updated: 2023-11-02T12:21:33Z
day: '15'
ddc:
- '610'
department:
- _id: SaSi
doi: 10.1016/j.isci.2022.104580
ec_funded: 1
external_id:
isi:
- '000830428500005'
file:
- access_level: open_access
checksum: a470b74e1b3796c710189c81a4cd4329
content_type: application/pdf
creator: cchlebak
date_created: 2022-07-04T08:19:25Z
date_updated: 2022-07-04T08:19:25Z
file_id: '11480'
file_name: 2022_iScience_Bartalska.pdf
file_size: 19400048
relation: main_file
success: 1
file_date_updated: 2022-07-04T08:19:25Z
has_accepted_license: '1'
intvolume: ' 25'
isi: 1
issue: '7'
language:
- iso: eng
license: https://creativecommons.org/licenses/by/4.0/
month: '07'
oa: 1
oa_version: Published Version
project:
- _id: 25D4A630-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '715571'
name: Microglia action towards neuronal circuit formation and function in health
and disease
- _id: B67AFEDC-15C9-11EA-A837-991A96BB2854
name: IST Austria Open Access Fund
- _id: 9B99D380-BA93-11EA-9121-9846C619BF3A
grant_number: SC19-017
name: How human microglia shape developing neurons during health and inflammation
publication: iScience
publication_identifier:
eissn:
- 2589-0042
publication_status: published
publisher: Elsevier
quality_controlled: '1'
related_material:
record:
- id: '12117'
relation: other
status: public
scopus_import: '1'
status: public
title: A systematic characterization of microglia-like cell occurrence during retinal
organoid differentiation
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: journal_article
user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87
volume: 25
year: '2022'
...
---
_id: '11489'
abstract:
- lang: eng
text: Much of plant development depends on cell-to-cell redistribution of the plant
hormone auxin, which is facilitated by the plasma membrane (PM) localized PIN
FORMED (PIN) proteins. Auxin export activity, developmental roles, subcellular
trafficking, and polarity of PINs have been well studied, but their structure
remains elusive besides a rough outline that they contain two groups of 5 alpha-helices
connected by a large hydrophilic loop (HL). Here, we focus on the PIN1 HL as we
could produce it in sufficient quantities for biochemical investigations to provide
insights into its secondary structure. Circular dichroism (CD) studies revealed
its nature as an intrinsically disordered protein (IDP), manifested by the increase
of structure content upon thermal melting. Consistent with IDPs serving as interaction
platforms, PIN1 loops homodimerize. PIN1 HL cytoplasmic overexpression in Arabidopsis
disrupts early endocytic trafficking of PIN1 and PIN2 and causes defects in the
cotyledon vasculature formation. In summary, we demonstrate that PIN1 HL has an
intrinsically disordered nature, which must be considered to gain further structural
insights. Some secondary structures may form transiently during pairing with known
and yet-to-be-discovered interactors.
acknowledgement: 'We thank Charo del Genio from Coventry University and Richard Napier
from the University of Warwick for helpful discussion concerning protein modeling
and inspiration concerning CD spectroscopy, respectively. We thank Jan Hejatko for
sharing the published AHP2 construct. We also thank Josef Houser from the core facility
BIC CEITEC for valuable assistance, discussions, and ideas relating to CD. We acknowledge
the: Core Facility CELLIM of CEITEC supported by the Czech-BioImaging large RI project
(LM2018129 funded by MEYS CR), part of the Euro-BioImaging (www.eurobioimaging.eu
accessed on 1 January 2016) ALM and medical imaging Node (Brno, CZ), CF Biomolecular
Interactions and Crystallization of CIISB, Instruct-CZ Centre, supported by MEYS
CR (LM2018127) and European Regional Development Fund-Project “UP CIISB“ (No. CZ.02.1.01/0.0/0.0/18_046/0015974)
for their support with obtaining scientific data presented in this paper; Plant
Sciences Core Facility of CEITEC Masaryk University for technical support. Open
Access Funding by the Austrian Science Fund (FWF).'
article_processing_charge: Yes
article_type: original
author:
- first_name: V
full_name: Bilanovičová, V
last_name: Bilanovičová
- first_name: N
full_name: Rýdza, N
last_name: Rýdza
- first_name: L
full_name: Koczka, L
last_name: Koczka
- first_name: M
full_name: Hess, M
last_name: Hess
- first_name: E
full_name: Feraru, E
last_name: Feraru
- first_name: Jiří
full_name: Friml, Jiří
id: 4159519E-F248-11E8-B48F-1D18A9856A87
last_name: Friml
orcid: 0000-0002-8302-7596
- first_name: T
full_name: Nodzyński, T
last_name: Nodzyński
citation:
ama: Bilanovičová V, Rýdza N, Koczka L, et al. The hydrophilic loop of Arabidopsis
PIN1 auxin efflux carrier harbors hallmarks of an intrinsically disordered protein.
International Journal of Molecular Sciences. 2022;23(11):6352. doi:10.3390/ijms23116352
apa: Bilanovičová, V., Rýdza, N., Koczka, L., Hess, M., Feraru, E., Friml, J., &
Nodzyński, T. (2022). The hydrophilic loop of Arabidopsis PIN1 auxin efflux carrier
harbors hallmarks of an intrinsically disordered protein. International Journal
of Molecular Sciences. MDPI. https://doi.org/10.3390/ijms23116352
chicago: Bilanovičová, V, N Rýdza, L Koczka, M Hess, E Feraru, Jiří Friml, and T
Nodzyński. “The Hydrophilic Loop of Arabidopsis PIN1 Auxin Efflux Carrier Harbors
Hallmarks of an Intrinsically Disordered Protein.” International Journal of
Molecular Sciences. MDPI, 2022. https://doi.org/10.3390/ijms23116352.
ieee: V. Bilanovičová et al., “The hydrophilic loop of Arabidopsis PIN1 auxin
efflux carrier harbors hallmarks of an intrinsically disordered protein,” International
Journal of Molecular Sciences, vol. 23, no. 11. MDPI, p. 6352, 2022.
ista: Bilanovičová V, Rýdza N, Koczka L, Hess M, Feraru E, Friml J, Nodzyński T.
2022. The hydrophilic loop of Arabidopsis PIN1 auxin efflux carrier harbors hallmarks
of an intrinsically disordered protein. International Journal of Molecular Sciences.
23(11), 6352.
mla: Bilanovičová, V., et al. “The Hydrophilic Loop of Arabidopsis PIN1 Auxin Efflux
Carrier Harbors Hallmarks of an Intrinsically Disordered Protein.” International
Journal of Molecular Sciences, vol. 23, no. 11, MDPI, 2022, p. 6352, doi:10.3390/ijms23116352.
short: V. Bilanovičová, N. Rýdza, L. Koczka, M. Hess, E. Feraru, J. Friml, T. Nodzyński,
International Journal of Molecular Sciences 23 (2022) 6352.
date_created: 2022-07-05T15:14:34Z
date_published: 2022-06-06T00:00:00Z
date_updated: 2023-08-09T10:13:57Z
day: '06'
ddc:
- '570'
department:
- _id: JiFr
doi: 10.3390/ijms23116352
external_id:
isi:
- '000808733300001'
pmid:
- '35683031'
file:
- access_level: open_access
checksum: e997a57a928ec9d51fad8ce824a05935
content_type: application/pdf
creator: cchlebak
date_created: 2022-07-06T07:36:59Z
date_updated: 2022-07-06T07:36:59Z
file_id: '11492'
file_name: 2022_IntJMolSci_Bilanovicova.pdf
file_size: 2324542
relation: main_file
success: 1
file_date_updated: 2022-07-06T07:36:59Z
has_accepted_license: '1'
intvolume: ' 23'
isi: 1
issue: '11'
language:
- iso: eng
month: '06'
oa: 1
oa_version: Published Version
page: '6352'
pmid: 1
project:
- _id: 262EF96E-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: P29988
name: RNA-directed DNA methylation in plant development
publication: International Journal of Molecular Sciences
publication_identifier:
issn:
- 1422-0067
publication_status: published
publisher: MDPI
quality_controlled: '1'
status: public
title: The hydrophilic loop of Arabidopsis PIN1 auxin efflux carrier harbors hallmarks
of an intrinsically disordered protein
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: journal_article
user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87
volume: 23
year: '2022'
...
---
_id: '11542'
article_processing_charge: No
author:
- first_name: Rouven
full_name: Schulz, Rouven
id: 4C5E7B96-F248-11E8-B48F-1D18A9856A87
last_name: Schulz
orcid: 0000-0001-5297-733X
citation:
ama: Schulz R. Source Data (Chimeric GPCRs mimic distinct signaling pathways and
modulate microglia responses). 2022. doi:10.15479/AT:ISTA:11542
apa: Schulz, R. (2022). Source Data (Chimeric GPCRs mimic distinct signaling pathways
and modulate microglia responses). Institute of Science and Technology Austria.
https://doi.org/10.15479/AT:ISTA:11542
chicago: Schulz, Rouven. “Source Data (Chimeric GPCRs Mimic Distinct Signaling Pathways
and Modulate Microglia Responses).” Institute of Science and Technology Austria,
2022. https://doi.org/10.15479/AT:ISTA:11542.
ieee: R. Schulz, “Source Data (Chimeric GPCRs mimic distinct signaling pathways
and modulate microglia responses).” Institute of Science and Technology Austria,
2022.
ista: Schulz R. 2022. Source Data (Chimeric GPCRs mimic distinct signaling pathways
and modulate microglia responses), Institute of Science and Technology Austria,
10.15479/AT:ISTA:11542.
mla: Schulz, Rouven. Source Data (Chimeric GPCRs Mimic Distinct Signaling Pathways
and Modulate Microglia Responses). Institute of Science and Technology Austria,
2022, doi:10.15479/AT:ISTA:11542.
short: R. Schulz, (2022).
contributor:
- contributor_type: contact_person
first_name: Sandra
id: 36ACD32E-F248-11E8-B48F-1D18A9856A87
last_name: Siegert
orcid: 0000-0001-8635-0877
date_created: 2022-07-08T11:03:02Z
date_published: 2022-01-01T00:00:00Z
date_updated: 2024-02-21T12:34:51Z
department:
- _id: GradSch
- _id: SaSi
doi: 10.15479/AT:ISTA:11542
file:
- access_level: open_access
checksum: 71e8186583f3adbb6c69a88ac9e6e49b
content_type: application/vnd.openxmlformats-officedocument.spreadsheetml.sheet
creator: rschulz
date_created: 2022-07-08T10:56:52Z
date_updated: 2022-07-08T10:56:52Z
file_id: '11543'
file_name: Source Data.xlsx
file_size: 135784571
relation: main_file
success: 1
file_date_updated: 2022-07-08T10:56:52Z
has_accepted_license: '1'
oa: 1
oa_version: None
publisher: Institute of Science and Technology Austria
related_material:
link:
- relation: contains
url: https://www.biorxiv.org/content/10.1101/2021.06.21.449162v1
record:
- id: '11995'
relation: used_in_publication
status: public
status: public
title: Source Data (Chimeric GPCRs mimic distinct signaling pathways and modulate
microglia responses)
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: research_data
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
year: '2022'
...
---
_id: '11545'
abstract:
- lang: eng
text: "We classify contravariant pairings between standard Whittaker modules and
Verma modules over a complex semisimple Lie algebra. These contravariant pairings
are useful in extending several classical techniques for category O to the Miličić–Soergel
category N . We introduce a class of costandard modules which generalize dual
Verma modules, and describe canonical maps from standard to costandard modules
in terms of contravariant pairings.\r\nWe show that costandard modules have unique
irreducible submodules and share the same composition factors as the corresponding
standard Whittaker modules. We show that costandard modules give an algebraic
characterization of the global sections of costandard twisted Harish-Chandra sheaves
on the associated flag variety, which are defined using holonomic duality of D-modules.
We prove that with these costandard modules, blocks of category\r\nN have the
structure of highest weight categories and we establish a BGG reciprocity theorem
for N ."
acknowledgement: We thank Catharina Stroppel and Jens Niklas Eberhardt for interesting
discussions. The first author acknowledges the support of the European Union's Horizon
2020 research and innovation programme under the Marie Skłodowska-Curie Grant Agreement
No. 754411. The second author is supported by the National Science Foundation Award
No. 1803059 and the Australian Research Council grant DP170101579.
article_processing_charge: Yes (via OA deal)
article_type: original
author:
- first_name: Adam
full_name: Brown, Adam
id: 70B7FDF6-608D-11E9-9333-8535E6697425
last_name: Brown
- first_name: Anna
full_name: Romanov, Anna
last_name: Romanov
citation:
ama: Brown A, Romanov A. Contravariant pairings between standard Whittaker modules
and Verma modules. Journal of Algebra. 2022;609(11):145-179. doi:10.1016/j.jalgebra.2022.06.017
apa: Brown, A., & Romanov, A. (2022). Contravariant pairings between standard
Whittaker modules and Verma modules. Journal of Algebra. Elsevier. https://doi.org/10.1016/j.jalgebra.2022.06.017
chicago: Brown, Adam, and Anna Romanov. “Contravariant Pairings between Standard
Whittaker Modules and Verma Modules.” Journal of Algebra. Elsevier, 2022.
https://doi.org/10.1016/j.jalgebra.2022.06.017.
ieee: A. Brown and A. Romanov, “Contravariant pairings between standard Whittaker
modules and Verma modules,” Journal of Algebra, vol. 609, no. 11. Elsevier,
pp. 145–179, 2022.
ista: Brown A, Romanov A. 2022. Contravariant pairings between standard Whittaker
modules and Verma modules. Journal of Algebra. 609(11), 145–179.
mla: Brown, Adam, and Anna Romanov. “Contravariant Pairings between Standard Whittaker
Modules and Verma Modules.” Journal of Algebra, vol. 609, no. 11, Elsevier,
2022, pp. 145–79, doi:10.1016/j.jalgebra.2022.06.017.
short: A. Brown, A. Romanov, Journal of Algebra 609 (2022) 145–179.
date_created: 2022-07-08T11:40:07Z
date_published: 2022-11-01T00:00:00Z
date_updated: 2023-08-03T11:56:30Z
day: '01'
ddc:
- '510'
department:
- _id: HeEd
doi: 10.1016/j.jalgebra.2022.06.017
ec_funded: 1
external_id:
isi:
- '000861841100004'
file:
- access_level: open_access
checksum: 82abaee3d7837f703e499a9ecbb25b7c
content_type: application/pdf
creator: dernst
date_created: 2023-02-02T07:32:48Z
date_updated: 2023-02-02T07:32:48Z
file_id: '12473'
file_name: 2022_JournalAlgebra_Brown.pdf
file_size: 582962
relation: main_file
success: 1
file_date_updated: 2023-02-02T07:32:48Z
has_accepted_license: '1'
intvolume: ' 609'
isi: 1
issue: '11'
keyword:
- Algebra and Number Theory
language:
- iso: eng
month: '11'
oa: 1
oa_version: Published Version
page: 145-179
project:
- _id: 260C2330-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '754411'
name: ISTplus - Postdoctoral Fellowships
publication: Journal of Algebra
publication_identifier:
issn:
- 0021-8693
publication_status: published
publisher: Elsevier
quality_controlled: '1'
scopus_import: '1'
status: public
title: Contravariant pairings between standard Whittaker modules and Verma modules
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: journal_article
user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
volume: 609
year: '2022'
...
---
_id: '11546'
abstract:
- lang: eng
text: Local adaptation leads to differences between populations within a species.
In many systems, similar environmental contrasts occur repeatedly, sometimes driving
parallel phenotypic evolution. Understanding the genomic basis of local adaptation
and parallel evolution is a major goal of evolutionary genomics. It is now known
that by preventing the break-up of favourable combinations of alleles across multiple
loci, genetic architectures that reduce recombination, like chromosomal inversions,
can make an important contribution to local adaptation. However, little is known
about whether inversions also contribute disproportionately to parallel evolution.
Our aim here is to highlight this knowledge gap, to showcase existing studies,
and to illustrate the differences between genomic architectures with and without
inversions using simple models. We predict that by generating stronger effective
selection, inversions can sometimes speed up the parallel adaptive process or
enable parallel adaptation where it would be impossible otherwise, but this is
highly dependent on the spatial setting. We highlight that further empirical work
is needed, in particular to cover a broader taxonomic range and to understand
the relative importance of inversions compared to genomic regions without inversions.
acknowledgement: We thank the editor and two anonymous reviewers for their helpful
and interesting comments on this manuscript.
article_number: '20210203'
article_processing_charge: Yes (via OA deal)
article_type: original
author:
- first_name: Anja M
full_name: Westram, Anja M
id: 3C147470-F248-11E8-B48F-1D18A9856A87
last_name: Westram
orcid: 0000-0003-1050-4969
- first_name: Rui
full_name: Faria, Rui
last_name: Faria
- first_name: Kerstin
full_name: Johannesson, Kerstin
last_name: Johannesson
- first_name: Roger
full_name: Butlin, Roger
last_name: Butlin
- first_name: Nicholas H
full_name: Barton, Nicholas H
id: 4880FE40-F248-11E8-B48F-1D18A9856A87
last_name: Barton
orcid: 0000-0002-8548-5240
citation:
ama: 'Westram AM, Faria R, Johannesson K, Butlin R, Barton NH. Inversions and parallel
evolution. Philosophical Transactions of the Royal Society B: Biological Sciences.
2022;377(1856). doi:10.1098/rstb.2021.0203'
apa: 'Westram, A. M., Faria, R., Johannesson, K., Butlin, R., & Barton, N. H.
(2022). Inversions and parallel evolution. Philosophical Transactions of the
Royal Society B: Biological Sciences. Royal Society of London. https://doi.org/10.1098/rstb.2021.0203'
chicago: 'Westram, Anja M, Rui Faria, Kerstin Johannesson, Roger Butlin, and Nicholas
H Barton. “Inversions and Parallel Evolution.” Philosophical Transactions of
the Royal Society B: Biological Sciences. Royal Society of London, 2022. https://doi.org/10.1098/rstb.2021.0203.'
ieee: 'A. M. Westram, R. Faria, K. Johannesson, R. Butlin, and N. H. Barton, “Inversions
and parallel evolution,” Philosophical Transactions of the Royal Society B:
Biological Sciences, vol. 377, no. 1856. Royal Society of London, 2022.'
ista: 'Westram AM, Faria R, Johannesson K, Butlin R, Barton NH. 2022. Inversions
and parallel evolution. Philosophical Transactions of the Royal Society B: Biological
Sciences. 377(1856), 20210203.'
mla: 'Westram, Anja M., et al. “Inversions and Parallel Evolution.” Philosophical
Transactions of the Royal Society B: Biological Sciences, vol. 377, no. 1856,
20210203, Royal Society of London, 2022, doi:10.1098/rstb.2021.0203.'
short: 'A.M. Westram, R. Faria, K. Johannesson, R. Butlin, N.H. Barton, Philosophical
Transactions of the Royal Society B: Biological Sciences 377 (2022).'
date_created: 2022-07-08T11:41:56Z
date_published: 2022-08-01T00:00:00Z
date_updated: 2023-08-03T11:55:42Z
day: '01'
ddc:
- '570'
department:
- _id: BeVi
- _id: NiBa
doi: 10.1098/rstb.2021.0203
external_id:
isi:
- '000812317300005'
file:
- access_level: open_access
checksum: 49f69428f3dcf5ce3ff281f7d199e9df
content_type: application/pdf
creator: dernst
date_created: 2023-02-02T08:20:29Z
date_updated: 2023-02-02T08:20:29Z
file_id: '12479'
file_name: 2022_PhilosophicalTransactionsB_Westram.pdf
file_size: 920304
relation: main_file
success: 1
file_date_updated: 2023-02-02T08:20:29Z
has_accepted_license: '1'
intvolume: ' 377'
isi: 1
issue: '1856'
keyword:
- General Agricultural and Biological Sciences
- General Biochemistry
- Genetics and Molecular Biology
language:
- iso: eng
month: '08'
oa: 1
oa_version: Published Version
project:
- _id: 05959E1C-7A3F-11EA-A408-12923DDC885E
grant_number: P32166
name: The maintenance of alternative adaptive peaks in snapdragons
publication: 'Philosophical Transactions of the Royal Society B: Biological Sciences'
publication_identifier:
eissn:
- 1471-2970
issn:
- 0962-8436
publication_status: published
publisher: Royal Society of London
quality_controlled: '1'
scopus_import: '1'
status: public
title: Inversions and parallel evolution
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: journal_article
user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
volume: 377
year: '2022'
...
---
_id: '11551'
abstract:
- lang: eng
text: Imbalanced mitochondrial dNTP pools are known players in the pathogenesis
of multiple human diseases. Here we show that, even under physiological conditions,
dGTP is largely overrepresented among other dNTPs in mitochondria of mouse tissues
and human cultured cells. In addition, a vast majority of mitochondrial dGTP is
tightly bound to NDUFA10, an accessory subunit of complex I of the mitochondrial
respiratory chain. NDUFA10 shares a deoxyribonucleoside kinase (dNK) domain with
deoxyribonucleoside kinases in the nucleotide salvage pathway, though no specific
function beyond stabilizing the complex I holoenzyme has been described for this
subunit. We mutated the dNK domain of NDUFA10 in human HEK-293T cells while preserving
complex I assembly and activity. The NDUFA10E160A/R161A shows reduced dGTP binding
capacity in vitro and leads to a 50% reduction in mitochondrial dGTP content,
proving that most dGTP is directly bound to the dNK domain of NDUFA10. This interaction
may represent a hitherto unknown mechanism regulating mitochondrial dNTP availability
and linking oxidative metabolism to DNA maintenance.
acknowledgement: "We thank Dr, Luke Formosa (Department of Biochemistry and Molecular
Biology, Monash Biomedicine Discovery Institute, Monash University, Melbourne, Australia)
for his valuable advice and assistance on NDUFA10 molecular studies and Dr. Francesc
Canals and his team (Proteomics Laboratory, Vall d’Hebron Institute of Oncology
[VHIO], Universitat Autònoma de Barcelona, Barcelona, Spain) for their assistance
with LC-MS/MS analyses. This work was supported by the Spanish Ministry of Industry,
Economy and Competitiveness [grants BFU2014-52618-R, SAF2017-87506, and PID2020-112929RB-I00
to Y.C.], by the Spanish Instituto de Salud Carlos III [grants PI21/00554 and PMP15/00025
to R.M.], co-financed by the European Regional Development Fund (ERDF), and by an
NHMRC Project grant to M.R. (GNT1164459).\r\n"
article_number: '620'
article_processing_charge: No
author:
- first_name: David
full_name: Molina-Granada, David
last_name: Molina-Granada
- first_name: Emiliano
full_name: González-Vioque, Emiliano
last_name: González-Vioque
- first_name: Marris G.
full_name: Dibley, Marris G.
last_name: Dibley
- first_name: Raquel
full_name: Cabrera-Pérez, Raquel
last_name: Cabrera-Pérez
- first_name: Antoni
full_name: Vallbona-Garcia, Antoni
last_name: Vallbona-Garcia
- first_name: Javier
full_name: Torres-Torronteras, Javier
last_name: Torres-Torronteras
- first_name: Leonid A
full_name: Sazanov, Leonid A
id: 338D39FE-F248-11E8-B48F-1D18A9856A87
last_name: Sazanov
orcid: 0000-0002-0977-7989
- first_name: Michael T.
full_name: Ryan, Michael T.
last_name: Ryan
- first_name: Yolanda
full_name: Cámara, Yolanda
last_name: Cámara
- first_name: Ramon
full_name: Martí, Ramon
last_name: Martí
citation:
ama: Molina-Granada D, González-Vioque E, Dibley MG, et al. Most mitochondrial dGTP
is tightly bound to respiratory complex I through the NDUFA10 subunit. Communications
Biology. 2022;5(1). doi:10.1038/s42003-022-03568-6
apa: Molina-Granada, D., González-Vioque, E., Dibley, M. G., Cabrera-Pérez, R.,
Vallbona-Garcia, A., Torres-Torronteras, J., … Martí, R. (2022). Most mitochondrial
dGTP is tightly bound to respiratory complex I through the NDUFA10 subunit. Communications
Biology. Springer Nature. https://doi.org/10.1038/s42003-022-03568-6
chicago: Molina-Granada, David, Emiliano González-Vioque, Marris G. Dibley, Raquel
Cabrera-Pérez, Antoni Vallbona-Garcia, Javier Torres-Torronteras, Leonid A Sazanov,
Michael T. Ryan, Yolanda Cámara, and Ramon Martí. “Most Mitochondrial DGTP Is
Tightly Bound to Respiratory Complex I through the NDUFA10 Subunit.” Communications
Biology. Springer Nature, 2022. https://doi.org/10.1038/s42003-022-03568-6.
ieee: D. Molina-Granada et al., “Most mitochondrial dGTP is tightly bound
to respiratory complex I through the NDUFA10 subunit,” Communications Biology,
vol. 5, no. 1. Springer Nature, 2022.
ista: Molina-Granada D, González-Vioque E, Dibley MG, Cabrera-Pérez R, Vallbona-Garcia
A, Torres-Torronteras J, Sazanov LA, Ryan MT, Cámara Y, Martí R. 2022. Most mitochondrial
dGTP is tightly bound to respiratory complex I through the NDUFA10 subunit. Communications
Biology. 5(1), 620.
mla: Molina-Granada, David, et al. “Most Mitochondrial DGTP Is Tightly Bound to
Respiratory Complex I through the NDUFA10 Subunit.” Communications Biology,
vol. 5, no. 1, 620, Springer Nature, 2022, doi:10.1038/s42003-022-03568-6.
short: D. Molina-Granada, E. González-Vioque, M.G. Dibley, R. Cabrera-Pérez, A.
Vallbona-Garcia, J. Torres-Torronteras, L.A. Sazanov, M.T. Ryan, Y. Cámara, R.
Martí, Communications Biology 5 (2022).
date_created: 2022-07-10T22:01:52Z
date_published: 2022-06-23T00:00:00Z
date_updated: 2023-08-03T11:51:58Z
day: '23'
ddc:
- '570'
department:
- _id: LeSa
doi: 10.1038/s42003-022-03568-6
external_id:
isi:
- '000815098500002'
pmid:
- ' 35739187'
file:
- access_level: open_access
checksum: 965f88bbcef3fd0c3e121340555c4467
content_type: application/pdf
creator: kschuh
date_created: 2022-07-13T07:44:58Z
date_updated: 2022-07-13T07:44:58Z
file_id: '11571'
file_name: 2022_communicationsbiology_Molina-Granada.pdf
file_size: 2335369
relation: main_file
success: 1
file_date_updated: 2022-07-13T07:44:58Z
has_accepted_license: '1'
intvolume: ' 5'
isi: 1
issue: '1'
language:
- iso: eng
month: '06'
oa: 1
oa_version: Published Version
pmid: 1
publication: Communications Biology
publication_identifier:
eissn:
- '23993642'
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
scopus_import: '1'
status: public
title: Most mitochondrial dGTP is tightly bound to respiratory complex I through the
NDUFA10 subunit
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: 5
year: '2022'
...
---
_id: '11552'
abstract:
- lang: eng
text: Rotational dynamics of D2 molecules inside helium nanodroplets is induced
by a moderately intense femtosecond pump pulse and measured as a function of time
by recording the yield of HeD+ ions, created through strong-field dissociative
ionization with a delayed femtosecond probe pulse. The yield oscillates with a
period of 185 fs, reflecting field-free rotational wave packet dynamics, and the
oscillation persists for more than 500 periods. Within the experimental uncertainty,
the rotational constant BHe of the in-droplet D2 molecule, determined by Fourier
analysis, is the same as Bgas for an isolated D2 molecule. Our observations show
that the D2 molecules inside helium nanodroplets essentially rotate as free D2
molecules.
article_number: '243201'
article_processing_charge: No
arxiv: 1
author:
- first_name: Junjie
full_name: Qiang, Junjie
last_name: Qiang
- first_name: Lianrong
full_name: Zhou, Lianrong
last_name: Zhou
- first_name: Peifen
full_name: Lu, Peifen
last_name: Lu
- first_name: Kang
full_name: Lin, Kang
last_name: Lin
- first_name: Yongzhe
full_name: Ma, Yongzhe
last_name: Ma
- first_name: Shengzhe
full_name: Pan, Shengzhe
last_name: Pan
- first_name: Chenxu
full_name: Lu, Chenxu
last_name: Lu
- first_name: Wenyu
full_name: Jiang, Wenyu
last_name: Jiang
- first_name: Fenghao
full_name: Sun, Fenghao
last_name: Sun
- first_name: Wenbin
full_name: Zhang, Wenbin
last_name: Zhang
- first_name: Hui
full_name: Li, Hui
last_name: Li
- first_name: Xiaochun
full_name: Gong, Xiaochun
last_name: Gong
- first_name: Ilya Sh
full_name: Averbukh, Ilya Sh
last_name: Averbukh
- first_name: Yehiam
full_name: Prior, Yehiam
last_name: Prior
- first_name: Constant A.
full_name: Schouder, Constant A.
last_name: Schouder
- first_name: Henrik
full_name: Stapelfeldt, Henrik
last_name: Stapelfeldt
- first_name: Igor
full_name: Cherepanov, Igor
id: 339C7E5A-F248-11E8-B48F-1D18A9856A87
last_name: Cherepanov
- first_name: Mikhail
full_name: Lemeshko, Mikhail
id: 37CB05FA-F248-11E8-B48F-1D18A9856A87
last_name: Lemeshko
orcid: 0000-0002-6990-7802
- first_name: Wolfgang
full_name: Jäger, Wolfgang
last_name: Jäger
- first_name: Jian
full_name: Wu, Jian
last_name: Wu
citation:
ama: Qiang J, Zhou L, Lu P, et al. Femtosecond rotational dynamics of D2 molecules
in superfluid helium nanodroplets. Physical Review Letters. 2022;128(24).
doi:10.1103/PhysRevLett.128.243201
apa: Qiang, J., Zhou, L., Lu, P., Lin, K., Ma, Y., Pan, S., … Wu, J. (2022). Femtosecond
rotational dynamics of D2 molecules in superfluid helium nanodroplets. Physical
Review Letters. American Physical Society. https://doi.org/10.1103/PhysRevLett.128.243201
chicago: Qiang, Junjie, Lianrong Zhou, Peifen Lu, Kang Lin, Yongzhe Ma, Shengzhe
Pan, Chenxu Lu, et al. “Femtosecond Rotational Dynamics of D2 Molecules in Superfluid
Helium Nanodroplets.” Physical Review Letters. American Physical Society,
2022. https://doi.org/10.1103/PhysRevLett.128.243201.
ieee: J. Qiang et al., “Femtosecond rotational dynamics of D2 molecules in
superfluid helium nanodroplets,” Physical Review Letters, vol. 128, no.
24. American Physical Society, 2022.
ista: Qiang J, Zhou L, Lu P, Lin K, Ma Y, Pan S, Lu C, Jiang W, Sun F, Zhang W,
Li H, Gong X, Averbukh IS, Prior Y, Schouder CA, Stapelfeldt H, Cherepanov I,
Lemeshko M, Jäger W, Wu J. 2022. Femtosecond rotational dynamics of D2 molecules
in superfluid helium nanodroplets. Physical Review Letters. 128(24), 243201.
mla: Qiang, Junjie, et al. “Femtosecond Rotational Dynamics of D2 Molecules in Superfluid
Helium Nanodroplets.” Physical Review Letters, vol. 128, no. 24, 243201,
American Physical Society, 2022, doi:10.1103/PhysRevLett.128.243201.
short: J. Qiang, L. Zhou, P. Lu, K. Lin, Y. Ma, S. Pan, C. Lu, W. Jiang, F. Sun,
W. Zhang, H. Li, X. Gong, I.S. Averbukh, Y. Prior, C.A. Schouder, H. Stapelfeldt,
I. Cherepanov, M. Lemeshko, W. Jäger, J. Wu, Physical Review Letters 128 (2022).
date_created: 2022-07-10T22:01:52Z
date_published: 2022-06-16T00:00:00Z
date_updated: 2023-08-03T11:54:14Z
day: '16'
department:
- _id: MiLe
doi: 10.1103/PhysRevLett.128.243201
ec_funded: 1
external_id:
arxiv:
- '2201.09281'
isi:
- '000820659700002'
intvolume: ' 128'
isi: 1
issue: '24'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.48550/arXiv.2201.09281
month: '06'
oa: 1
oa_version: Submitted Version
project:
- _id: 2688CF98-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '801770'
name: 'Angulon: physics and applications of a new quasiparticle'
- _id: 2564DBCA-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '665385'
name: International IST Doctoral Program
publication: Physical Review Letters
publication_identifier:
eissn:
- '10797114'
issn:
- '00319007'
publication_status: published
publisher: American Physical Society
quality_controlled: '1'
scopus_import: '1'
status: public
title: Femtosecond rotational dynamics of D2 molecules in superfluid helium nanodroplets
type: journal_article
user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
volume: 128
year: '2022'
...
---
_id: '11553'
abstract:
- lang: eng
text: "In holomorphic dynamics, complex box mappings arise as first return maps
to wellchosen domains. They are a generalization of polynomial-like mapping, where
the domain of the return map can have infinitely many components. They turned
out to be extremely useful in tackling diverse problems. The purpose of this paper
is:\r\n• To illustrate some pathologies that can occur when a complex box mapping
is not induced by a globally defined map and when its domain has infinitely many
components, and to give conditions to avoid these issues.\r\n• To show that once
one has a box mapping for a rational map, these conditions can be assumed to hold
in a very natural setting. Thus, we call such complex box mappings dynamically
natural. Having such box mappings is the first step in tackling many problems
in one-dimensional dynamics.\r\n• Many results in holomorphic dynamics rely on
an interplay between combinatorial and analytic techniques. In this setting, some
of these tools are:\r\n • the Enhanced Nest (a nest of puzzle pieces around critical
points) from Kozlovski, Shen, van Strien (AnnMath 165:749–841, 2007), referred
to below as KSS;\r\n • the Covering Lemma (which controls the moduli of pullbacks
of annuli) from Kahn and Lyubich (Ann Math 169(2):561–593, 2009);\r\n • the
QC-Criterion and the Spreading Principle from KSS.\r\nThe purpose of this paper
is to make these tools more accessible so that they can be used as a ‘black box’,
so one does not have to redo the proofs in new settings.\r\n• To give an intuitive,
but also rather detailed, outline of the proof from KSS and Kozlovski and van
Strien (Proc Lond Math Soc (3) 99:275–296, 2009) of the following results for
non-renormalizable dynamically natural complex box mappings:\r\n • puzzle pieces
shrink to points,\r\n • (under some assumptions) topologically conjugate non-renormalizable
polynomials and box mappings are quasiconformally conjugate.\r\n• We prove the
fundamental ergodic properties for dynamically natural box mappings. This leads
to some necessary conditions for when such a box mapping supports a measurable
invariant line field on its filled Julia set. These mappings\r\nare the analogues
of Lattès maps in this setting.\r\n• We prove a version of Mañé’s Theorem for
complex box mappings concerning expansion along orbits of points that avoid a
neighborhood of the set of critical points."
acknowledgement: We would also like to thank Dzmitry Dudko and Dierk Schleicher for
many stimulating discussions and encouragement during our work on this project,
and Weixiao Shen, Mikhail Hlushchanka and the referee for helpful comments. We are
grateful to Leon Staresinic who carefully read the revised version of the manuscript
and provided many helpful suggestions.
article_processing_charge: No
article_type: original
author:
- first_name: Trevor
full_name: Clark, Trevor
last_name: Clark
- first_name: Kostiantyn
full_name: Drach, Kostiantyn
id: fe8209e2-906f-11eb-847d-950f8fc09115
last_name: Drach
orcid: 0000-0002-9156-8616
- first_name: Oleg
full_name: Kozlovski, Oleg
last_name: Kozlovski
- first_name: Sebastian Van
full_name: Strien, Sebastian Van
last_name: Strien
citation:
ama: Clark T, Drach K, Kozlovski O, Strien SV. The dynamics of complex box mappings.
Arnold Mathematical Journal. 2022;8(2):319-410. doi:10.1007/s40598-022-00200-7
apa: Clark, T., Drach, K., Kozlovski, O., & Strien, S. V. (2022). The dynamics
of complex box mappings. Arnold Mathematical Journal. Springer Nature.
https://doi.org/10.1007/s40598-022-00200-7
chicago: Clark, Trevor, Kostiantyn Drach, Oleg Kozlovski, and Sebastian Van Strien.
“The Dynamics of Complex Box Mappings.” Arnold Mathematical Journal. Springer
Nature, 2022. https://doi.org/10.1007/s40598-022-00200-7.
ieee: T. Clark, K. Drach, O. Kozlovski, and S. V. Strien, “The dynamics of complex
box mappings,” Arnold Mathematical Journal, vol. 8, no. 2. Springer Nature,
pp. 319–410, 2022.
ista: Clark T, Drach K, Kozlovski O, Strien SV. 2022. The dynamics of complex box
mappings. Arnold Mathematical Journal. 8(2), 319–410.
mla: Clark, Trevor, et al. “The Dynamics of Complex Box Mappings.” Arnold Mathematical
Journal, vol. 8, no. 2, Springer Nature, 2022, pp. 319–410, doi:10.1007/s40598-022-00200-7.
short: T. Clark, K. Drach, O. Kozlovski, S.V. Strien, Arnold Mathematical Journal
8 (2022) 319–410.
date_created: 2022-07-10T22:01:53Z
date_published: 2022-06-01T00:00:00Z
date_updated: 2023-02-16T10:02:12Z
day: '01'
ddc:
- '500'
department:
- _id: VaKa
doi: 10.1007/s40598-022-00200-7
ec_funded: 1
file:
- access_level: open_access
checksum: 16e7c659dee9073c6c8aeb87316ef201
content_type: application/pdf
creator: kschuh
date_created: 2022-07-12T10:04:55Z
date_updated: 2022-07-12T10:04:55Z
file_id: '11559'
file_name: 2022_ArnoldMathematicalJournal_Clark.pdf
file_size: 2509915
relation: main_file
success: 1
file_date_updated: 2022-07-12T10:04:55Z
has_accepted_license: '1'
intvolume: ' 8'
issue: '2'
language:
- iso: eng
month: '06'
oa: 1
oa_version: None
page: 319-410
project:
- _id: 9B8B92DE-BA93-11EA-9121-9846C619BF3A
call_identifier: H2020
grant_number: '885707'
name: Spectral rigidity and integrability for billiards and geodesic flows
publication: Arnold Mathematical Journal
publication_identifier:
eissn:
- 2199-6806
issn:
- 2199-6792
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
related_material:
link:
- relation: erratum
url: https://doi.org/10.1007/s40598-022-00209-y
- relation: erratum
url: https://doi.org/10.1007/s40598-022-00218-x
scopus_import: '1'
status: public
title: The dynamics of complex box mappings
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 8
year: '2022'
...
---
_id: '11556'
abstract:
- lang: eng
text: "We revisit two basic Direct Simulation Monte Carlo Methods to model aggregation
kinetics and extend them for aggregation processes with collisional fragmentation
(shattering). We test the performance and accuracy of the extended methods and
compare their performance with efficient deterministic finite-difference method
applied to the same model. We validate the stochastic methods on the test problems
and apply them to verify the existence of oscillating regimes in the aggregation-fragmentation
kinetics recently detected in deterministic simulations. We confirm the emergence
of steady oscillations of densities in such systems and prove the stability of
the\r\noscillations with respect to fluctuations and noise."
acknowledgement: Zhores supercomputer of Skolkovo Institute of Science and Technology
[68] has been used in the present research. S.A.M. was supported by Moscow Center
for Fundamental and Applied Mathematics (the agreement with the Ministry of Education
and Science of the Russian Federation No. 075-15-2019-1624). A.I.O. acknowledges
RFBR project No. 20-31-90022. N.V.B. acknowledges the support of the Analytical
Center (subsidy agreement 000000D730321P5Q0002, Grant No. 70-2021-00145 02.11.2021).
article_number: '111439'
article_processing_charge: No
article_type: original
arxiv: 1
author:
- first_name: Aleksei
full_name: Kalinov, Aleksei
id: 44b7120e-eb97-11eb-a6c2-e1557aa81d02
last_name: Kalinov
orcid: 0000-0003-2189-3904
- first_name: A.I.
full_name: Osinskiy, A.I.
last_name: Osinskiy
- first_name: S.A.
full_name: Matveev, S.A.
last_name: Matveev
- first_name: W.
full_name: Otieno, W.
last_name: Otieno
- first_name: N.V.
full_name: Brilliantov, N.V.
last_name: Brilliantov
citation:
ama: Kalinov A, Osinskiy AI, Matveev SA, Otieno W, Brilliantov NV. Direct simulation
Monte Carlo for new regimes in aggregation-fragmentation kinetics. Journal
of Computational Physics. 2022;467. doi:10.1016/j.jcp.2022.111439
apa: Kalinov, A., Osinskiy, A. I., Matveev, S. A., Otieno, W., & Brilliantov,
N. V. (2022). Direct simulation Monte Carlo for new regimes in aggregation-fragmentation
kinetics. Journal of Computational Physics. Elsevier. https://doi.org/10.1016/j.jcp.2022.111439
chicago: Kalinov, Aleksei, A.I. Osinskiy, S.A. Matveev, W. Otieno, and N.V. Brilliantov.
“Direct Simulation Monte Carlo for New Regimes in Aggregation-Fragmentation Kinetics.”
Journal of Computational Physics. Elsevier, 2022. https://doi.org/10.1016/j.jcp.2022.111439.
ieee: A. Kalinov, A. I. Osinskiy, S. A. Matveev, W. Otieno, and N. V. Brilliantov,
“Direct simulation Monte Carlo for new regimes in aggregation-fragmentation kinetics,”
Journal of Computational Physics, vol. 467. Elsevier, 2022.
ista: Kalinov A, Osinskiy AI, Matveev SA, Otieno W, Brilliantov NV. 2022. Direct
simulation Monte Carlo for new regimes in aggregation-fragmentation kinetics.
Journal of Computational Physics. 467, 111439.
mla: Kalinov, Aleksei, et al. “Direct Simulation Monte Carlo for New Regimes in
Aggregation-Fragmentation Kinetics.” Journal of Computational Physics,
vol. 467, 111439, Elsevier, 2022, doi:10.1016/j.jcp.2022.111439.
short: A. Kalinov, A.I. Osinskiy, S.A. Matveev, W. Otieno, N.V. Brilliantov, Journal
of Computational Physics 467 (2022).
date_created: 2022-07-11T12:19:59Z
date_published: 2022-10-15T00:00:00Z
date_updated: 2023-08-03T11:55:06Z
day: '15'
ddc:
- '518'
department:
- _id: GradSch
- _id: ChWo
doi: 10.1016/j.jcp.2022.111439
external_id:
arxiv:
- '2103.09481'
isi:
- '000917225500013'
intvolume: ' 467'
isi: 1
keyword:
- Computer Science Applications
- Physics and Astronomy (miscellaneous)
- Applied Mathematics
- Computational Mathematics
- Modeling and Simulation
- Numerical Analysis
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.48550/arXiv.2103.09481
month: '10'
oa: 1
oa_version: Preprint
publication: Journal of Computational Physics
publication_identifier:
issn:
- 0021-9991
publication_status: published
publisher: Elsevier
quality_controlled: '1'
status: public
title: Direct simulation Monte Carlo for new regimes in aggregation-fragmentation
kinetics
type: journal_article
user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
volume: 467
year: '2022'
...
---
_id: '11587'
abstract:
- lang: eng
text: "Background: Accurate and comprehensive annotation of transcript sequences
is essential for transcript quantification and differential gene and transcript
expression analysis. Single-molecule long-read sequencing technologies provide
improved integrity of transcript structures including alternative splicing, and
transcription start and polyadenylation sites. However, accuracy is significantly
affected by sequencing errors, mRNA degradation, or incomplete cDNA synthesis.\r\nResults:
We present a new and comprehensive Arabidopsis thaliana Reference Transcript Dataset
3 (AtRTD3). AtRTD3 contains over 169,000 transcripts—twice that of the best current
Arabidopsis transcriptome and including over 1500 novel genes. Seventy-eight percent
of transcripts are from Iso-seq with accurately defined splice junctions and transcription
start and end sites. We develop novel methods to determine splice junctions and
transcription start and end sites accurately. Mismatch profiles around splice
junctions provide a powerful feature to distinguish correct splice junctions and
remove false splice junctions. Stratified approaches identify high-confidence
transcription start and end sites and remove fragmentary transcripts due to degradation.
AtRTD3 is a major improvement over existing transcriptomes as demonstrated by
analysis of an Arabidopsis cold response RNA-seq time-series. AtRTD3 provides
higher resolution of transcript expression profiling and identifies cold-induced
differential transcription start and polyadenylation site usage.\r\nConclusions:
AtRTD3 is the most comprehensive Arabidopsis transcriptome currently. It improves
the precision of differential gene and transcript expression, differential alternative
splicing, and transcription start/end site usage analysis from RNA-seq data. The
novel methods for identifying accurate splice junctions and transcription start/end
sites are widely applicable and will improve single-molecule sequencing analysis
from any species."
acknowledgement: "This work was jointly supported by funding from the Biotechnology
and Biological Sciences Research Council (BBSRC) BB/P009751/1 to JB; BB/R014582/1
to RW and RZ; BB/S020160/1 to RZ; BB/S004610/1 (16 ERA-CAPS BARN) to RW; the Scottish
Government Rural and Environment Science and Analytical Services division (RESAS)
[to RZ, RW, and JB]; the\r\nNational Science Foundation (MCB-2014408) and the National
Institute of Health (NIH) (GM-114297) to E.H.; S. H. was supported by funding to
K.D. from the University of York; the Austrian Science Fund (FWF) SFB F43 to AB
and MJ and [P26333] to MK; The French Agence Nationale de la Recherche grant ANR-16-CE12-0032
to MC; the Japan Science and\r\nTechnology Agency (JST), the Core Research for Evolutionary
Science and Technology (CREST; Grant Number JPMJCR13B4) to M.S.; the National Science
Foundation (Grant No. DBI1949036 to A.b.H and A.S.N.R, and Grant No. MCB 2014542
to E.H. and A.S.N.R.); and the DOE Office of Science, Office of Biological and Environmental
Research (Grant\r\nNo. DE-SC0010733) to A.S.N.R and A.b.H.; the Deutsche Forschungsgemeinschaft
(DFG) STA653/14-1 and STA653/15-1 to DS; the National Science Foundation grant (IOS-154173)
to Q.Q.L.; the German Research Foundation (DFG) WA2167/8-1 to AW and SFB1101/C03
to AW and TWK; the Research Grants Council (RGC) of Hong Kong (GRF 12103020) to
LX. NSF grant IOS-1849708 and NSF EPSCoR grant 1826836 to RS; the Academia Sinica
to S.-L. T."
article_number: '149'
article_processing_charge: No
article_type: original
author:
- first_name: Runxuan
full_name: Zhang, Runxuan
last_name: Zhang
- first_name: Richard
full_name: Kuo, Richard
last_name: Kuo
- first_name: Max
full_name: Coulter, Max
last_name: Coulter
- first_name: Cristiane P.G.
full_name: Calixto, Cristiane P.G.
last_name: Calixto
- first_name: Juan Carlos
full_name: Entizne, Juan Carlos
last_name: Entizne
- first_name: Wenbin
full_name: Guo, Wenbin
last_name: Guo
- first_name: Yamile
full_name: Marquez, Yamile
last_name: Marquez
- first_name: Linda
full_name: Milne, Linda
last_name: Milne
- first_name: Stefan
full_name: Riegler, Stefan
id: FF6018E0-D806-11E9-8E43-0B14E6697425
last_name: Riegler
orcid: 0000-0003-3413-1343
- first_name: Akihiro
full_name: Matsui, Akihiro
last_name: Matsui
- first_name: Maho
full_name: Tanaka, Maho
last_name: Tanaka
- first_name: Sarah
full_name: Harvey, Sarah
last_name: Harvey
- first_name: Yubang
full_name: Gao, Yubang
last_name: Gao
- first_name: Theresa
full_name: Wießner-Kroh, Theresa
last_name: Wießner-Kroh
- first_name: Alejandro
full_name: Paniagua, Alejandro
last_name: Paniagua
- first_name: Martin
full_name: Crespi, Martin
last_name: Crespi
- first_name: Katherine
full_name: Denby, Katherine
last_name: Denby
- first_name: Asa Ben
full_name: Hur, Asa Ben
last_name: Hur
- first_name: Enamul
full_name: Huq, Enamul
last_name: Huq
- first_name: Michael
full_name: Jantsch, Michael
last_name: Jantsch
- first_name: Artur
full_name: Jarmolowski, Artur
last_name: Jarmolowski
- first_name: Tino
full_name: Koester, Tino
last_name: Koester
- first_name: Sascha
full_name: Laubinger, Sascha
last_name: Laubinger
- first_name: Qingshun Quinn
full_name: Li, Qingshun Quinn
last_name: Li
- first_name: Lianfeng
full_name: Gu, Lianfeng
last_name: Gu
- first_name: Motoaki
full_name: Seki, Motoaki
last_name: Seki
- first_name: Dorothee
full_name: Staiger, Dorothee
last_name: Staiger
- first_name: Ramanjulu
full_name: Sunkar, Ramanjulu
last_name: Sunkar
- first_name: Zofia
full_name: Szweykowska-Kulinska, Zofia
last_name: Szweykowska-Kulinska
- first_name: Shih Long
full_name: Tu, Shih Long
last_name: Tu
- first_name: Andreas
full_name: Wachter, Andreas
last_name: Wachter
- first_name: Robbie
full_name: Waugh, Robbie
last_name: Waugh
- first_name: Liming
full_name: Xiong, Liming
last_name: Xiong
- first_name: Xiao Ning
full_name: Zhang, Xiao Ning
last_name: Zhang
- first_name: Ana
full_name: Conesa, Ana
last_name: Conesa
- first_name: Anireddy S.N.
full_name: Reddy, Anireddy S.N.
last_name: Reddy
- first_name: Andrea
full_name: Barta, Andrea
last_name: Barta
- first_name: Maria
full_name: Kalyna, Maria
last_name: Kalyna
- first_name: John W.S.
full_name: Brown, John W.S.
last_name: Brown
citation:
ama: Zhang R, Kuo R, Coulter M, et al. A high-resolution single-molecule sequencing-based
Arabidopsis transcriptome using novel methods of Iso-seq analysis. Genome Biology.
2022;23. doi:10.1186/s13059-022-02711-0
apa: Zhang, R., Kuo, R., Coulter, M., Calixto, C. P. G., Entizne, J. C., Guo, W.,
… Brown, J. W. S. (2022). A high-resolution single-molecule sequencing-based Arabidopsis
transcriptome using novel methods of Iso-seq analysis. Genome Biology.
BioMed Central. https://doi.org/10.1186/s13059-022-02711-0
chicago: Zhang, Runxuan, Richard Kuo, Max Coulter, Cristiane P.G. Calixto, Juan
Carlos Entizne, Wenbin Guo, Yamile Marquez, et al. “A High-Resolution Single-Molecule
Sequencing-Based Arabidopsis Transcriptome Using Novel Methods of Iso-Seq Analysis.”
Genome Biology. BioMed Central, 2022. https://doi.org/10.1186/s13059-022-02711-0.
ieee: R. Zhang et al., “A high-resolution single-molecule sequencing-based
Arabidopsis transcriptome using novel methods of Iso-seq analysis,” Genome
Biology, vol. 23. BioMed Central, 2022.
ista: Zhang R, Kuo R, Coulter M, Calixto CPG, Entizne JC, Guo W, Marquez Y, Milne
L, Riegler S, Matsui A, Tanaka M, Harvey S, Gao Y, Wießner-Kroh T, Paniagua A,
Crespi M, Denby K, Hur AB, Huq E, Jantsch M, Jarmolowski A, Koester T, Laubinger
S, Li QQ, Gu L, Seki M, Staiger D, Sunkar R, Szweykowska-Kulinska Z, Tu SL, Wachter
A, Waugh R, Xiong L, Zhang XN, Conesa A, Reddy ASN, Barta A, Kalyna M, Brown JWS.
2022. A high-resolution single-molecule sequencing-based Arabidopsis transcriptome
using novel methods of Iso-seq analysis. Genome Biology. 23, 149.
mla: Zhang, Runxuan, et al. “A High-Resolution Single-Molecule Sequencing-Based
Arabidopsis Transcriptome Using Novel Methods of Iso-Seq Analysis.” Genome
Biology, vol. 23, 149, BioMed Central, 2022, doi:10.1186/s13059-022-02711-0.
short: R. Zhang, R. Kuo, M. Coulter, C.P.G. Calixto, J.C. Entizne, W. Guo, Y. Marquez,
L. Milne, S. Riegler, A. Matsui, M. Tanaka, S. Harvey, Y. Gao, T. Wießner-Kroh,
A. Paniagua, M. Crespi, K. Denby, A.B. Hur, E. Huq, M. Jantsch, A. Jarmolowski,
T. Koester, S. Laubinger, Q.Q. Li, L. Gu, M. Seki, D. Staiger, R. Sunkar, Z. Szweykowska-Kulinska,
S.L. Tu, A. Wachter, R. Waugh, L. Xiong, X.N. Zhang, A. Conesa, A.S.N. Reddy,
A. Barta, M. Kalyna, J.W.S. Brown, Genome Biology 23 (2022).
date_created: 2022-07-17T22:01:53Z
date_published: 2022-07-07T00:00:00Z
date_updated: 2023-08-03T12:04:18Z
day: '07'
ddc:
- '570'
department:
- _id: FyKo
doi: 10.1186/s13059-022-02711-0
external_id:
isi:
- '000821915500002'
file:
- access_level: open_access
checksum: 2c30ef84151d257a6b835b4e069b70ac
content_type: application/pdf
creator: dernst
date_created: 2022-07-18T08:15:24Z
date_updated: 2022-07-18T08:15:24Z
file_id: '11597'
file_name: 2022_GenomeBiology_Zhang.pdf
file_size: 3146207
relation: main_file
success: 1
file_date_updated: 2022-07-18T08:15:24Z
has_accepted_license: '1'
intvolume: ' 23'
isi: 1
language:
- iso: eng
month: '07'
oa: 1
oa_version: Published Version
publication: Genome Biology
publication_identifier:
eissn:
- 1474-760X
publication_status: published
publisher: BioMed Central
quality_controlled: '1'
scopus_import: '1'
status: public
title: A high-resolution single-molecule sequencing-based Arabidopsis transcriptome
using novel methods of Iso-seq analysis
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: 23
year: '2022'
...
---
_id: '11588'
abstract:
- lang: eng
text: Visualizing cell behavior and effector function on a single cell level has
been crucial for understanding key aspects of mammalian biology. Due to their
small size, large number and rapid recruitment into thrombi, there is a lack of
data on fate and behavior of individual platelets in thrombosis and hemostasis.
Here we report the use of platelet lineage restricted multi-color reporter mouse
strains to delineate platelet function on a single cell level. We show that genetic
labeling allows for single platelet and megakaryocyte (MK) tracking and morphological
analysis in vivo and in vitro, while not affecting lineage functions. Using Cre-driven
Confetti expression, we provide insights into temporal gene expression patterns
as well as spatial clustering of MK in the bone marrow. In the vasculature, shape
analysis of activated platelets recruited to thrombi identifies ubiquitous filopodia
formation with no evidence of lamellipodia formation. Single cell tracking in
complex thrombi reveals prominent myosin-dependent motility of platelets and highlights
thrombus formation as a highly dynamic process amenable to modification and intervention
of the acto-myosin cytoskeleton. Platelet function assays combining flow cytrometry,
as well as in vivo, ex vivo and in vitro imaging show unaltered platelet functions
of multicolor reporter mice compared to wild-type controls. In conclusion, platelet
lineage multicolor reporter mice prove useful in furthering our understanding
of platelet and MK biology on a single cell level.
acknowledgement: "This study was supported by the Deutsche Forschungsgemeinschaft
(DFG) SFB 914 ( to SM [B02 and Z01]), the DFG SFB 1123 (to SM [B06]), the DFG FOR
2033 (to SM), the German\r\nCenter for Cardiovascular Research (DZHK) (Clinician
Scientist Programme), MHA 1.4VD (to SM), Postdoc Start-up Grant, 81X3600213 (to
FG), 81X3600222 (to LN), the FP7 program\r\n(project 260309, PRESTIGE [to SM]).
This project has received funding from the European Research Council (ERC) under
the European Union’s Horizon 2020 research and innovation programme (grant agreement
No. 83344, ERC-2018-ADG “IMMUNOTHROMBOSIS” [to SM] and the Marie Skłodowska Curie
Individual Fellowship (EU project 747687, LamelliActin [to FG]). "
article_processing_charge: No
article_type: original
author:
- first_name: Leo
full_name: Nicolai, Leo
last_name: Nicolai
- first_name: Rainer
full_name: Kaiser, Rainer
last_name: Kaiser
- first_name: Raphael
full_name: Escaig, Raphael
last_name: Escaig
- first_name: Marie Louise
full_name: Hoffknecht, Marie Louise
last_name: Hoffknecht
- first_name: Afra
full_name: Anjum, Afra
last_name: Anjum
- first_name: Alexander
full_name: Leunig, Alexander
last_name: Leunig
- first_name: Joachim
full_name: Pircher, Joachim
last_name: Pircher
- first_name: Andreas
full_name: Ehrlich, Andreas
last_name: Ehrlich
- first_name: Michael
full_name: Lorenz, Michael
last_name: Lorenz
- first_name: Hellen
full_name: Ishikawa-Ankerhold, Hellen
last_name: Ishikawa-Ankerhold
- first_name: William C.
full_name: Aird, William C.
last_name: Aird
- first_name: Steffen
full_name: Massberg, Steffen
last_name: Massberg
- first_name: Florian R
full_name: Gärtner, Florian R
id: 397A88EE-F248-11E8-B48F-1D18A9856A87
last_name: Gärtner
orcid: 0000-0001-6120-3723
citation:
ama: Nicolai L, Kaiser R, Escaig R, et al. Single platelet and megakaryocyte morpho-dynamics
uncovered by multicolor reporter mouse strains in vitro and in vivo. Haematologica.
2022;107(7):1669-1680. doi:10.3324/haematol.2021.278896
apa: Nicolai, L., Kaiser, R., Escaig, R., Hoffknecht, M. L., Anjum, A., Leunig,
A., … Gärtner, F. R. (2022). Single platelet and megakaryocyte morpho-dynamics
uncovered by multicolor reporter mouse strains in vitro and in vivo. Haematologica.
Ferrata Storti Foundation. https://doi.org/10.3324/haematol.2021.278896
chicago: Nicolai, Leo, Rainer Kaiser, Raphael Escaig, Marie Louise Hoffknecht, Afra
Anjum, Alexander Leunig, Joachim Pircher, et al. “Single Platelet and Megakaryocyte
Morpho-Dynamics Uncovered by Multicolor Reporter Mouse Strains in Vitro and in
Vivo.” Haematologica. Ferrata Storti Foundation, 2022. https://doi.org/10.3324/haematol.2021.278896.
ieee: L. Nicolai et al., “Single platelet and megakaryocyte morpho-dynamics
uncovered by multicolor reporter mouse strains in vitro and in vivo,” Haematologica,
vol. 107, no. 7. Ferrata Storti Foundation, pp. 1669–1680, 2022.
ista: Nicolai L, Kaiser R, Escaig R, Hoffknecht ML, Anjum A, Leunig A, Pircher J,
Ehrlich A, Lorenz M, Ishikawa-Ankerhold H, Aird WC, Massberg S, Gärtner FR. 2022.
Single platelet and megakaryocyte morpho-dynamics uncovered by multicolor reporter
mouse strains in vitro and in vivo. Haematologica. 107(7), 1669–1680.
mla: Nicolai, Leo, et al. “Single Platelet and Megakaryocyte Morpho-Dynamics Uncovered
by Multicolor Reporter Mouse Strains in Vitro and in Vivo.” Haematologica,
vol. 107, no. 7, Ferrata Storti Foundation, 2022, pp. 1669–80, doi:10.3324/haematol.2021.278896.
short: L. Nicolai, R. Kaiser, R. Escaig, M.L. Hoffknecht, A. Anjum, A. Leunig, J.
Pircher, A. Ehrlich, M. Lorenz, H. Ishikawa-Ankerhold, W.C. Aird, S. Massberg,
F.R. Gärtner, Haematologica 107 (2022) 1669–1680.
date_created: 2022-07-17T22:01:54Z
date_published: 2022-07-01T00:00:00Z
date_updated: 2023-08-03T12:01:01Z
day: '01'
ddc:
- '570'
department:
- _id: MiSi
doi: 10.3324/haematol.2021.278896
ec_funded: 1
external_id:
isi:
- '000823746100018'
file:
- access_level: open_access
checksum: 9b47830945f3c30428fe9cfee2dc4a8a
content_type: application/pdf
creator: dernst
date_created: 2022-07-18T07:51:55Z
date_updated: 2022-07-18T07:51:55Z
file_id: '11595'
file_name: 2022_Haematologica_Nicolai.pdf
file_size: 1722094
relation: main_file
success: 1
file_date_updated: 2022-07-18T07:51:55Z
has_accepted_license: '1'
intvolume: ' 107'
isi: 1
issue: '7'
language:
- iso: eng
license: https://creativecommons.org/licenses/by-nc/4.0/
month: '07'
oa: 1
oa_version: Published Version
page: 1669-1680
project:
- _id: 260AA4E2-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '747687'
name: Mechanical Adaptation of Lamellipodial Actin Networks in Migrating Cells
publication: Haematologica
publication_identifier:
eissn:
- 1592-8721
issn:
- 0390-6078
publication_status: published
publisher: Ferrata Storti Foundation
quality_controlled: '1'
scopus_import: '1'
status: public
title: Single platelet and megakaryocyte morpho-dynamics uncovered by multicolor reporter
mouse strains in vitro and in vivo
tmp:
image: /images/cc_by_nc.png
legal_code_url: https://creativecommons.org/licenses/by-nc/4.0/legalcode
name: Creative Commons Attribution-NonCommercial 4.0 International (CC BY-NC 4.0)
short: CC BY-NC (4.0)
type: journal_article
user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
volume: 107
year: '2022'
...
---
_id: '11589'
abstract:
- lang: eng
text: Calcium-dependent protein kinases (CPK) are key components of a wide array
of signaling pathways, translating stress and nutrient signaling into the modulation
of cellular processes such as ion transport and transcription. However, not much
is known about CPKs in endomembrane trafficking. Here, we screened for CPKs that
impact on root growth and gravitropism, by overexpressing constitutively active
forms of CPKs under the control of an inducible promoter in Arabidopsis thaliana.
We found that inducible overexpression of an constitutive active CPK30 (CA-CPK30)
resulted in a loss of root gravitropism and ectopic auxin accumulation in the
root tip. Immunolocalization revealed that CA-CPK30 roots have reduced PIN protein
levels, PIN1 polarity defects and impaired Brefeldin A (BFA)-sensitive trafficking.
Moreover, FM4-64 uptake was reduced, indicative of a defect in endocytosis. The
effects on BFA-sensitive trafficking were not specific to PINs, as BFA could not
induce aggregation of ARF1- and CHC-labeled endosomes in CA-CPK30. Interestingly,
the interference with BFA-body formation, could be reverted by increasing the
extracellular pH, indicating a pH-dependence of this CA-CPK30 effect. Altogether,
our data reveal an important role for CPK30 in root growth regulation and endomembrane
trafficking in Arabidopsis thaliana.
acknowledgement: "RW and JC predoctoral fellows that were supported by the Chinese
Science Counsil. The IPS2 benefits from the support of the LabEx Saclay Plant Sciences-SPS
(ANR-10-LABX-0040-SPS).\r\nWe thank Jen Sheen for establishing and generously sharing
the CKP family clone sets, and for providing useful feedback on the manuscript."
article_number: '862398'
article_processing_charge: No
article_type: original
author:
- first_name: Ren
full_name: Wang, Ren
last_name: Wang
- first_name: Ellie
full_name: Himschoot, Ellie
last_name: Himschoot
- first_name: Jian
full_name: Chen, Jian
last_name: Chen
- first_name: Marie
full_name: Boudsocq, Marie
last_name: Boudsocq
- first_name: Danny
full_name: Geelen, Danny
last_name: Geelen
- first_name: Jiří
full_name: Friml, Jiří
id: 4159519E-F248-11E8-B48F-1D18A9856A87
last_name: Friml
orcid: 0000-0002-8302-7596
- first_name: Tom
full_name: Beeckman, Tom
last_name: Beeckman
- first_name: Steffen
full_name: Vanneste, Steffen
last_name: Vanneste
citation:
ama: Wang R, Himschoot E, Chen J, et al. Constitutive active CPK30 interferes with
root growth and endomembrane trafficking in Arabidopsis thaliana. Frontiers
in Plant Science. 2022;13. doi:10.3389/fpls.2022.862398
apa: Wang, R., Himschoot, E., Chen, J., Boudsocq, M., Geelen, D., Friml, J., … Vanneste,
S. (2022). Constitutive active CPK30 interferes with root growth and endomembrane
trafficking in Arabidopsis thaliana. Frontiers in Plant Science. Frontiers.
https://doi.org/10.3389/fpls.2022.862398
chicago: Wang, Ren, Ellie Himschoot, Jian Chen, Marie Boudsocq, Danny Geelen, Jiří
Friml, Tom Beeckman, and Steffen Vanneste. “Constitutive Active CPK30 Interferes
with Root Growth and Endomembrane Trafficking in Arabidopsis Thaliana.” Frontiers
in Plant Science. Frontiers, 2022. https://doi.org/10.3389/fpls.2022.862398.
ieee: R. Wang et al., “Constitutive active CPK30 interferes with root growth
and endomembrane trafficking in Arabidopsis thaliana,” Frontiers in Plant Science,
vol. 13. Frontiers, 2022.
ista: Wang R, Himschoot E, Chen J, Boudsocq M, Geelen D, Friml J, Beeckman T, Vanneste
S. 2022. Constitutive active CPK30 interferes with root growth and endomembrane
trafficking in Arabidopsis thaliana. Frontiers in Plant Science. 13, 862398.
mla: Wang, Ren, et al. “Constitutive Active CPK30 Interferes with Root Growth and
Endomembrane Trafficking in Arabidopsis Thaliana.” Frontiers in Plant Science,
vol. 13, 862398, Frontiers, 2022, doi:10.3389/fpls.2022.862398.
short: R. Wang, E. Himschoot, J. Chen, M. Boudsocq, D. Geelen, J. Friml, T. Beeckman,
S. Vanneste, Frontiers in Plant Science 13 (2022).
date_created: 2022-07-17T22:01:54Z
date_published: 2022-06-16T00:00:00Z
date_updated: 2023-08-03T12:01:47Z
day: '16'
ddc:
- '580'
department:
- _id: JiFr
doi: 10.3389/fpls.2022.862398
external_id:
isi:
- '000819250500001'
pmid:
- '35783951'
file:
- access_level: open_access
checksum: 95313515637c0f84de591d204375d764
content_type: application/pdf
creator: dernst
date_created: 2022-07-18T08:05:15Z
date_updated: 2022-07-18T08:05:15Z
file_id: '11596'
file_name: 2022_FrontiersPlantScience_Wang.pdf
file_size: 5040638
relation: main_file
success: 1
file_date_updated: 2022-07-18T08:05:15Z
has_accepted_license: '1'
intvolume: ' 13'
isi: 1
language:
- iso: eng
month: '06'
oa: 1
oa_version: Published Version
pmid: 1
publication: Frontiers in Plant Science
publication_identifier:
eissn:
- 1664-462X
publication_status: published
publisher: Frontiers
quality_controlled: '1'
related_material:
link:
- relation: erratum
url: https://doi.org/10.3389/fpls.2022.1100792
scopus_import: '1'
status: public
title: Constitutive active CPK30 interferes with root growth and endomembrane trafficking
in Arabidopsis thaliana
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: '11590'
abstract:
- lang: eng
text: 'We investigate the ground-state properties of weakly repulsive one-dimensional
bosons in the presence of an attractive zero-range impurity potential. First,
we derive mean-field solutions to the problem on a finite ring for the two asymptotic
cases: (i) all bosons are bound to the impurity and (ii) all bosons are in a scattering
state. Moreover, we derive the critical line that separates these regimes in the
parameter space. In the thermodynamic limit, this critical line determines the
maximum number of bosons that can be bound by the impurity potential, forming
an artificial atom. Second, we validate the mean-field results using the flow
equation approach and the multi-layer multi-configuration time-dependent Hartree
method for atomic mixtures. While beyond-mean-field effects destroy long-range
order in the Bose gas, the critical boson number is unaffected. Our findings are
important for understanding such artificial atoms in low-density Bose gases with
static and mobile impurities.'
acknowledgement: This work has received funding from the DFG Project No. 413495248
[VO 2437/1-1] (FB, H-WH, AGV) and European Union's Horizon 2020 research and innovation
programme under the Marie Skĺodowska-Curie Grant Agreement No. 754411 (AGV). ML
acknowledges support by the European Research Council (ERC) Starting Grant No. 801770
(ANGULON). SIM acknowledges support from the NSF through a grant for ITAMP at Harvard
University.
article_number: '063036'
article_processing_charge: No
article_type: original
author:
- first_name: Fabian
full_name: Brauneis, Fabian
last_name: Brauneis
- first_name: Timothy G.
full_name: Backert, Timothy G.
last_name: Backert
- first_name: Simeon I.
full_name: Mistakidis, Simeon I.
last_name: Mistakidis
- first_name: Mikhail
full_name: Lemeshko, Mikhail
id: 37CB05FA-F248-11E8-B48F-1D18A9856A87
last_name: Lemeshko
orcid: 0000-0002-6990-7802
- first_name: Hans Werner
full_name: Hammer, Hans Werner
last_name: Hammer
- first_name: Artem
full_name: Volosniev, Artem
id: 37D278BC-F248-11E8-B48F-1D18A9856A87
last_name: Volosniev
orcid: 0000-0003-0393-5525
citation:
ama: Brauneis F, Backert TG, Mistakidis SI, Lemeshko M, Hammer HW, Volosniev A.
Artificial atoms from cold bosons in one dimension. New Journal of Physics.
2022;24(6). doi:10.1088/1367-2630/ac78d8
apa: Brauneis, F., Backert, T. G., Mistakidis, S. I., Lemeshko, M., Hammer, H. W.,
& Volosniev, A. (2022). Artificial atoms from cold bosons in one dimension.
New Journal of Physics. IOP Publishing. https://doi.org/10.1088/1367-2630/ac78d8
chicago: Brauneis, Fabian, Timothy G. Backert, Simeon I. Mistakidis, Mikhail Lemeshko,
Hans Werner Hammer, and Artem Volosniev. “Artificial Atoms from Cold Bosons in
One Dimension.” New Journal of Physics. IOP Publishing, 2022. https://doi.org/10.1088/1367-2630/ac78d8.
ieee: F. Brauneis, T. G. Backert, S. I. Mistakidis, M. Lemeshko, H. W. Hammer, and
A. Volosniev, “Artificial atoms from cold bosons in one dimension,” New Journal
of Physics, vol. 24, no. 6. IOP Publishing, 2022.
ista: Brauneis F, Backert TG, Mistakidis SI, Lemeshko M, Hammer HW, Volosniev A.
2022. Artificial atoms from cold bosons in one dimension. New Journal of Physics.
24(6), 063036.
mla: Brauneis, Fabian, et al. “Artificial Atoms from Cold Bosons in One Dimension.”
New Journal of Physics, vol. 24, no. 6, 063036, IOP Publishing, 2022, doi:10.1088/1367-2630/ac78d8.
short: F. Brauneis, T.G. Backert, S.I. Mistakidis, M. Lemeshko, H.W. Hammer, A.
Volosniev, New Journal of Physics 24 (2022).
date_created: 2022-07-17T22:01:55Z
date_published: 2022-06-01T00:00:00Z
date_updated: 2023-08-03T11:57:41Z
day: '01'
ddc:
- '530'
department:
- _id: MiLe
doi: 10.1088/1367-2630/ac78d8
ec_funded: 1
external_id:
isi:
- '000818530000001'
file:
- access_level: open_access
checksum: dc67b60f2e50e9ef2bd820ca0d7333d2
content_type: application/pdf
creator: dernst
date_created: 2022-07-18T06:33:13Z
date_updated: 2022-07-18T06:33:13Z
file_id: '11594'
file_name: 2022_NewJournalPhysics_Brauneis.pdf
file_size: 3415721
relation: main_file
success: 1
file_date_updated: 2022-07-18T06:33:13Z
has_accepted_license: '1'
intvolume: ' 24'
isi: 1
issue: '6'
language:
- iso: eng
month: '06'
oa: 1
oa_version: Published Version
project:
- _id: 260C2330-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '754411'
name: ISTplus - Postdoctoral Fellowships
- _id: 2688CF98-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '801770'
name: 'Angulon: physics and applications of a new quasiparticle'
publication: New Journal of Physics
publication_identifier:
issn:
- 1367-2630
publication_status: published
publisher: IOP Publishing
quality_controlled: '1'
scopus_import: '1'
status: public
title: Artificial atoms from cold bosons in one dimension
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: 24
year: '2022'
...
---
_id: '11591'
abstract:
- lang: eng
text: We investigate the deterministic generation and distribution of entanglement
in large quantum networks by driving distant qubits with the output fields of
a nondegenerate parametric amplifier. In this setting, the amplifier produces
a continuous Gaussian two-mode squeezed state, which acts as a quantum-correlated
reservoir for the qubits and relaxes them into a highly entangled steady state.
Here we are interested in the maximal amount of entanglement and the optimal entanglement
generation rates that can be achieved with this scheme under realistic conditions
taking, in particular, the finite amplifier bandwidth, waveguide losses, and propagation
delays into account. By combining exact numerical simulations of the full network
with approximate analytic results, we predict the optimal working point for the
amplifier and the corresponding qubit-qubit entanglement under various conditions.
Our findings show that this passive conversion of Gaussian into discrete-variable
entanglement offers a robust and experimentally very attractive approach for operating
large optical, microwave, or hybrid quantum networks, for which efficient parametric
amplifiers are currently developed.
acknowledgement: We thank T. Mavrogordatos and D. Zhu for initial contribution on
the presented topic and K. Fedorov for stimulating discussions on entangled microwave
beams. This work was supported by the Austrian Science Fund (FWF) through Grant
No. P32299 (PHONED) and the European Union’s Horizon 2020 research and innovation
programme under Grant Agreement No. 899354 (SuperQuLAN). Most of the computational
results presented were obtained using the CLIP cluster [65].
article_number: '062454'
article_processing_charge: No
article_type: original
arxiv: 1
author:
- first_name: J.
full_name: Agustí, J.
last_name: Agustí
- first_name: Y.
full_name: Minoguchi, Y.
last_name: Minoguchi
- 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: P.
full_name: Rabl, P.
last_name: Rabl
citation:
ama: Agustí J, Minoguchi Y, Fink JM, Rabl P. Long-distance distribution of qubit-qubit
entanglement using Gaussian-correlated photonic beams. Physical Review A.
2022;105(6). doi:10.1103/PhysRevA.105.062454
apa: Agustí, J., Minoguchi, Y., Fink, J. M., & Rabl, P. (2022). Long-distance
distribution of qubit-qubit entanglement using Gaussian-correlated photonic beams.
Physical Review A. American Physical Society. https://doi.org/10.1103/PhysRevA.105.062454
chicago: Agustí, J., Y. Minoguchi, Johannes M Fink, and P. Rabl. “Long-Distance
Distribution of Qubit-Qubit Entanglement Using Gaussian-Correlated Photonic Beams.”
Physical Review A. American Physical Society, 2022. https://doi.org/10.1103/PhysRevA.105.062454.
ieee: J. Agustí, Y. Minoguchi, J. M. Fink, and P. Rabl, “Long-distance distribution
of qubit-qubit entanglement using Gaussian-correlated photonic beams,” Physical
Review A, vol. 105, no. 6. American Physical Society, 2022.
ista: Agustí J, Minoguchi Y, Fink JM, Rabl P. 2022. Long-distance distribution of
qubit-qubit entanglement using Gaussian-correlated photonic beams. Physical Review
A. 105(6), 062454.
mla: Agustí, J., et al. “Long-Distance Distribution of Qubit-Qubit Entanglement
Using Gaussian-Correlated Photonic Beams.” Physical Review A, vol. 105,
no. 6, 062454, American Physical Society, 2022, doi:10.1103/PhysRevA.105.062454.
short: J. Agustí, Y. Minoguchi, J.M. Fink, P. Rabl, Physical Review A 105 (2022).
date_created: 2022-07-17T22:01:55Z
date_published: 2022-06-29T00:00:00Z
date_updated: 2023-08-03T11:58:16Z
day: '29'
department:
- _id: JoFi
doi: 10.1103/PhysRevA.105.062454
ec_funded: 1
external_id:
arxiv:
- '2204.02993'
isi:
- '000824330200003'
intvolume: ' 105'
isi: 1
issue: '6'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: ' https://doi.org/10.48550/arXiv.2204.02993'
month: '06'
oa: 1
oa_version: Preprint
project:
- _id: 9B868D20-BA93-11EA-9121-9846C619BF3A
call_identifier: H2020
grant_number: '899354'
name: Quantum Local Area Networks with Superconducting Qubits
publication: Physical Review A
publication_identifier:
eissn:
- 2469-9934
issn:
- 2469-9926
publication_status: published
publisher: American Physical Society
quality_controlled: '1'
scopus_import: '1'
status: public
title: Long-distance distribution of qubit-qubit entanglement using Gaussian-correlated
photonic beams
type: journal_article
user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
volume: 105
year: '2022'
...
---
_id: '11592'
abstract:
- lang: eng
text: 'We compare recent experimental results [Science 375, 528 (2022)] of the superfluid
unitary Fermi gas near the critical temperature with a thermodynamic model based
on the elementary excitations of the system. We find good agreement between experimental
data and our theory for several quantities such as first sound, second sound,
and superfluid fraction. We also show that mode mixing between first and second
sound occurs. Finally, we characterize the response amplitude to a density perturbation:
Close to the critical temperature both first and second sound can be excited through
a density perturbation, whereas at lower temperatures only the first sound mode
exhibits a significant response.'
acknowledgement: The authors gratefully acknowledge stimulating discussions with T.
Enss, and thank an anonymous referee for suggestions and remarks that allowed us
to improve the original manuscript. This work is supported by the Deutsche Forschungsgemeinschaft
(DFG, German Research Foundation) under Germany’s Excellence Strategy EXC2181/1-390900948
(the Heidelberg STRUCTURES Excellence Cluster).
article_number: '063329'
article_processing_charge: No
article_type: original
arxiv: 1
author:
- first_name: Giacomo
full_name: Bighin, Giacomo
id: 4CA96FD4-F248-11E8-B48F-1D18A9856A87
last_name: Bighin
orcid: 0000-0001-8823-9777
- first_name: Alberto
full_name: Cappellaro, Alberto
id: 9d13b3cb-30a2-11eb-80dc-f772505e8660
last_name: Cappellaro
orcid: 0000-0001-6110-2359
- first_name: L.
full_name: Salasnich, L.
last_name: Salasnich
citation:
ama: 'Bighin G, Cappellaro A, Salasnich L. Unitary Fermi superfluid near the critical
temperature: Thermodynamics and sound modes from elementary excitations. Physical
Review A. 2022;105(6). doi:10.1103/PhysRevA.105.063329'
apa: 'Bighin, G., Cappellaro, A., & Salasnich, L. (2022). Unitary Fermi superfluid
near the critical temperature: Thermodynamics and sound modes from elementary
excitations. Physical Review A. American Physical Society. https://doi.org/10.1103/PhysRevA.105.063329'
chicago: 'Bighin, Giacomo, Alberto Cappellaro, and L. Salasnich. “Unitary Fermi
Superfluid near the Critical Temperature: Thermodynamics and Sound Modes from
Elementary Excitations.” Physical Review A. American Physical Society,
2022. https://doi.org/10.1103/PhysRevA.105.063329.'
ieee: 'G. Bighin, A. Cappellaro, and L. Salasnich, “Unitary Fermi superfluid near
the critical temperature: Thermodynamics and sound modes from elementary excitations,”
Physical Review A, vol. 105, no. 6. American Physical Society, 2022.'
ista: 'Bighin G, Cappellaro A, Salasnich L. 2022. Unitary Fermi superfluid near
the critical temperature: Thermodynamics and sound modes from elementary excitations.
Physical Review A. 105(6), 063329.'
mla: 'Bighin, Giacomo, et al. “Unitary Fermi Superfluid near the Critical Temperature:
Thermodynamics and Sound Modes from Elementary Excitations.” Physical Review
A, vol. 105, no. 6, 063329, American Physical Society, 2022, doi:10.1103/PhysRevA.105.063329.'
short: G. Bighin, A. Cappellaro, L. Salasnich, Physical Review A 105 (2022).
date_created: 2022-07-17T22:01:55Z
date_published: 2022-06-30T00:00:00Z
date_updated: 2023-08-03T12:00:11Z
day: '30'
department:
- _id: MiLe
doi: 10.1103/PhysRevA.105.063329
external_id:
arxiv:
- '2206.03924'
isi:
- '000829758500010'
intvolume: ' 105'
isi: 1
issue: '6'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: ' https://doi.org/10.48550/arXiv.2206.03924'
month: '06'
oa: 1
oa_version: Preprint
publication: Physical Review A
publication_identifier:
eissn:
- 2469-9934
issn:
- 2469-9926
publication_status: published
publisher: American Physical Society
quality_controlled: '1'
scopus_import: '1'
status: public
title: 'Unitary Fermi superfluid near the critical temperature: Thermodynamics and
sound modes from elementary excitations'
type: journal_article
user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
volume: 105
year: '2022'
...
---
_id: '11593'
abstract:
- lang: eng
text: 'A drawing of a graph on a surface is independently even if every pair of
nonadjacent edges in the drawing crosses an even number of times. The Z2 -genus
of a graph G is the minimum g such that G has an independently even drawing on
the orientable surface of genus g. An unpublished result by Robertson and Seymour
implies that for every t, every graph of sufficiently large genus contains as
a minor a projective t×t grid or one of the following so-called t -Kuratowski
graphs: K3,t, or t copies of K5 or K3,3 sharing at most two common vertices. We
show that the Z2-genus of graphs in these families is unbounded in t; in fact,
equal to their genus. Together, this implies that the genus of a graph is bounded
from above by a function of its Z2-genus, solving a problem posed by Schaefer
and Štefankovič, and giving an approximate version of the Hanani–Tutte theorem
on orientable surfaces. We also obtain an analogous result for Euler genus and
Euler Z2-genus of graphs.'
acknowledgement: "We thank Zdeněk Dvořák, Xavier Goaoc, and Pavel Paták for helpful
discussions. We also thank Bojan Mohar, Paul Seymour, Gelasio Salazar, Jim Geelen,
and John Maharry for information about their unpublished results related to Conjecture
3.1. Finally we thank the reviewers for corrections and suggestions for improving
the presentation.\r\nSupported by Austrian Science Fund (FWF): M2281-N35. Supported
by project 19-04113Y of the Czech Science Foundation (GAČR), by the Czech-French
collaboration project EMBEDS II (CZ: 7AMB17FR029, FR: 38087RM), and by Charles University
project UNCE/SCI/004."
article_processing_charge: No
article_type: original
arxiv: 1
author:
- first_name: Radoslav
full_name: Fulek, Radoslav
id: 39F3FFE4-F248-11E8-B48F-1D18A9856A87
last_name: Fulek
orcid: 0000-0001-8485-1774
- first_name: Jan
full_name: Kynčl, Jan
last_name: Kynčl
citation:
ama: Fulek R, Kynčl J. The Z2-Genus of Kuratowski minors. Discrete and Computational
Geometry. 2022;68:425-447. doi:10.1007/s00454-022-00412-w
apa: Fulek, R., & Kynčl, J. (2022). The Z2-Genus of Kuratowski minors. Discrete
and Computational Geometry. Springer Nature. https://doi.org/10.1007/s00454-022-00412-w
chicago: Fulek, Radoslav, and Jan Kynčl. “The Z2-Genus of Kuratowski Minors.” Discrete
and Computational Geometry. Springer Nature, 2022. https://doi.org/10.1007/s00454-022-00412-w.
ieee: R. Fulek and J. Kynčl, “The Z2-Genus of Kuratowski minors,” Discrete and
Computational Geometry, vol. 68. Springer Nature, pp. 425–447, 2022.
ista: Fulek R, Kynčl J. 2022. The Z2-Genus of Kuratowski minors. Discrete and Computational
Geometry. 68, 425–447.
mla: Fulek, Radoslav, and Jan Kynčl. “The Z2-Genus of Kuratowski Minors.” Discrete
and Computational Geometry, vol. 68, Springer Nature, 2022, pp. 425–47, doi:10.1007/s00454-022-00412-w.
short: R. Fulek, J. Kynčl, Discrete and Computational Geometry 68 (2022) 425–447.
date_created: 2022-07-17T22:01:56Z
date_published: 2022-09-01T00:00:00Z
date_updated: 2023-08-14T12:43:52Z
day: '01'
department:
- _id: UlWa
doi: 10.1007/s00454-022-00412-w
external_id:
arxiv:
- '1803.05085'
isi:
- '000825014500001'
intvolume: ' 68'
isi: 1
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/1803.05085
month: '09'
oa: 1
oa_version: Preprint
page: 425-447
project:
- _id: 261FA626-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: M02281
name: Eliminating intersections in drawings of graphs
publication: Discrete and Computational Geometry
publication_identifier:
eissn:
- 1432-0444
issn:
- 0179-5376
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
related_material:
record:
- id: '186'
relation: earlier_version
status: public
scopus_import: '1'
status: public
title: The Z2-Genus of Kuratowski minors
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 68
year: '2022'
...
---
_id: '11626'
abstract:
- lang: eng
text: Plant growth and development is well known to be both, flexible and dynamic.
The high capacity for post-embryonic organ formation and tissue regeneration requires
tightly regulated intercellular communication and coordinated tissue polarization.
One of the most important drivers for patterning and polarity in plant development
is the phytohormone auxin. Auxin has the unique characteristic to establish polarized
channels for its own active directional cell to cell transport. This fascinating
phenomenon is called auxin canalization. Those auxin transport channels are characterized
by the expression and polar, subcellular localization of PIN auxin efflux carriers.
PIN proteins have the ability to dynamically change their localization and auxin
itself can affect this by interfering with trafficking. Most of the underlying
molecular mechanisms of canalization still remain enigmatic. What is known so
far is that canonical auxin signaling is indispensable but also other non-canonical
signaling components are thought to play a role. In order to shed light into the
mysteries auf auxin canalization this study revisits the branches of auxin signaling
in detail. Further a new auxin analogue, PISA, is developed which triggers auxin-like
responses but does not directly activate canonical transcriptional auxin signaling.
We revisit the direct auxin effect on PIN trafficking where we found that, contradictory
to previous observations, auxin is very specifically promoting endocytosis of
PIN2 but has no overall effect on endocytosis. Further, we evaluate which cellular
processes related to PIN subcellular dynamics are involved in the establishment
of auxin conducting channels and the formation of vascular tissue. We are re-evaluating
the function of AUXIN BINDING PROTEIN 1 (ABP1) and provide a comprehensive picture
about its developmental phneotypes and involvement in auxin signaling and canalization.
Lastly, we are focusing on the crosstalk between the hormone strigolactone (SL)
and auxin and found that SL is interfering with essentially all processes involved
in auxin canalization in a non-transcriptional manner. Lastly we identify a new
way of SL perception and signaling which is emanating from mitochondria, is independent
of canonical SL signaling and is modulating primary root growth.
alternative_title:
- ISTA Thesis
article_processing_charge: No
author:
- first_name: Michelle C
full_name: Gallei, Michelle C
id: 35A03822-F248-11E8-B48F-1D18A9856A87
last_name: Gallei
orcid: 0000-0003-1286-7368
citation:
ama: Gallei MC. Auxin and strigolactone non-canonical signaling regulating development
in Arabidopsis thaliana. 2022. doi:10.15479/at:ista:11626
apa: Gallei, M. C. (2022). Auxin and strigolactone non-canonical signaling regulating
development in Arabidopsis thaliana. Institute of Science and Technology Austria.
https://doi.org/10.15479/at:ista:11626
chicago: Gallei, Michelle C. “Auxin and Strigolactone Non-Canonical Signaling Regulating
Development in Arabidopsis Thaliana.” Institute of Science and Technology Austria,
2022. https://doi.org/10.15479/at:ista:11626.
ieee: M. C. Gallei, “Auxin and strigolactone non-canonical signaling regulating
development in Arabidopsis thaliana,” Institute of Science and Technology Austria,
2022.
ista: Gallei MC. 2022. Auxin and strigolactone non-canonical signaling regulating
development in Arabidopsis thaliana. Institute of Science and Technology Austria.
mla: Gallei, Michelle C. Auxin and Strigolactone Non-Canonical Signaling Regulating
Development in Arabidopsis Thaliana. Institute of Science and Technology Austria,
2022, doi:10.15479/at:ista:11626.
short: M.C. Gallei, Auxin and Strigolactone Non-Canonical Signaling Regulating Development
in Arabidopsis Thaliana, Institute of Science and Technology Austria, 2022.
date_created: 2022-07-20T11:21:53Z
date_published: 2022-07-20T00:00:00Z
date_updated: 2024-10-29T10:22:45Z
day: '20'
ddc:
- '575'
degree_awarded: PhD
department:
- _id: GradSch
- _id: JiFr
doi: 10.15479/at:ista:11626
ec_funded: 1
file:
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checksum: bd7ac35403cf5b4b2607287d2a104b3a
content_type: application/pdf
creator: mgallei
date_created: 2022-07-25T09:08:47Z
date_updated: 2022-07-25T09:08:47Z
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date_created: 2022-07-25T09:09:09Z
date_updated: 2022-07-25T09:39:58Z
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content_type: application/pdf
creator: mgallei
date_created: 2022-07-25T09:09:32Z
date_updated: 2022-07-25T09:39:58Z
description: This is the print version of the thesis including the full appendix
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creator: mgallei
date_created: 2022-07-25T11:48:45Z
date_updated: 2022-07-25T11:48:45Z
file_id: '11650'
file_name: Thesis_Gallei_Appendix.pdf
file_size: 15435966
relation: main_file
file_date_updated: 2022-07-25T11:48:45Z
has_accepted_license: '1'
language:
- iso: eng
month: '07'
oa: 1
oa_version: Published Version
page: '248'
project:
- _id: 261099A6-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '742985'
name: Tracing Evolution of Auxin Transport and Polarity in Plants
publication_identifier:
isbn:
- 978-3-99078-019-0
issn:
- 2663-337X
publication_status: published
publisher: Institute of Science and Technology Austria
related_material:
record:
- id: '9287'
relation: part_of_dissertation
status: public
- id: '7142'
relation: part_of_dissertation
status: public
- id: '7465'
relation: part_of_dissertation
status: public
- id: '8138'
relation: part_of_dissertation
status: public
- id: '6260'
relation: part_of_dissertation
status: public
- id: '8931'
relation: part_of_dissertation
status: public
- id: '10411'
relation: part_of_dissertation
status: public
status: public
supervisor:
- first_name: Jiří
full_name: Friml, Jiří
id: 4159519E-F248-11E8-B48F-1D18A9856A87
last_name: Friml
orcid: 0000-0002-8302-7596
- first_name: Eva
full_name: Benková, Eva
id: 38F4F166-F248-11E8-B48F-1D18A9856A87
last_name: Benková
orcid: 0000-0002-8510-9739
- first_name: Eilon
full_name: Shani, Eilon
last_name: Shani
title: Auxin and strigolactone non-canonical signaling regulating development in Arabidopsis
thaliana
type: dissertation
user_id: 8b945eb4-e2f2-11eb-945a-df72226e66a9
year: '2022'
...
---
_id: '11636'
abstract:
- lang: eng
text: In [3], Poonen and Slavov recently developed a novel approach to Bertini irreducibility
theorems over an arbitrary field, based on random hyperplane slicing. In this
paper, we extend their work by proving an analogous bound for the dimension of
the exceptional locus in the setting of linear subspaces of higher codimensions.
article_number: '102085'
article_processing_charge: Yes (via OA deal)
article_type: original
arxiv: 1
author:
- first_name: Philip
full_name: Kmentt, Philip
id: c90670c9-0bf0-11ed-86f5-ed522ece2fac
last_name: Kmentt
- first_name: Alec L
full_name: Shute, Alec L
id: 440EB050-F248-11E8-B48F-1D18A9856A87
last_name: Shute
orcid: 0000-0002-1812-2810
citation:
ama: Kmentt P, Shute AL. The Bertini irreducibility theorem for higher codimensional
slices. Finite Fields and their Applications. 2022;83(10). doi:10.1016/j.ffa.2022.102085
apa: Kmentt, P., & Shute, A. L. (2022). The Bertini irreducibility theorem for
higher codimensional slices. Finite Fields and Their Applications. Elsevier.
https://doi.org/10.1016/j.ffa.2022.102085
chicago: Kmentt, Philip, and Alec L Shute. “The Bertini Irreducibility Theorem for
Higher Codimensional Slices.” Finite Fields and Their Applications. Elsevier,
2022. https://doi.org/10.1016/j.ffa.2022.102085.
ieee: P. Kmentt and A. L. Shute, “The Bertini irreducibility theorem for higher
codimensional slices,” Finite Fields and their Applications, vol. 83, no.
10. Elsevier, 2022.
ista: Kmentt P, Shute AL. 2022. The Bertini irreducibility theorem for higher codimensional
slices. Finite Fields and their Applications. 83(10), 102085.
mla: Kmentt, Philip, and Alec L. Shute. “The Bertini Irreducibility Theorem for
Higher Codimensional Slices.” Finite Fields and Their Applications, vol.
83, no. 10, 102085, Elsevier, 2022, doi:10.1016/j.ffa.2022.102085.
short: P. Kmentt, A.L. Shute, Finite Fields and Their Applications 83 (2022).
date_created: 2022-07-24T22:01:41Z
date_published: 2022-10-01T00:00:00Z
date_updated: 2023-08-03T12:12:57Z
day: '01'
ddc:
- '510'
department:
- _id: TiBr
doi: 10.1016/j.ffa.2022.102085
external_id:
arxiv:
- '2111.06697'
isi:
- '000835490600001'
file:
- access_level: open_access
checksum: 3ca88decb1011180dc6de7e0862153e1
content_type: application/pdf
creator: dernst
date_created: 2023-02-02T07:56:34Z
date_updated: 2023-02-02T07:56:34Z
file_id: '12475'
file_name: 2022_FiniteFields_Kmentt.pdf
file_size: 247615
relation: main_file
success: 1
file_date_updated: 2023-02-02T07:56:34Z
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intvolume: ' 83'
isi: 1
issue: '10'
language:
- iso: eng
month: '10'
oa: 1
oa_version: Published Version
publication: Finite Fields and their Applications
publication_identifier:
eissn:
- '10902465'
issn:
- '10715797'
publication_status: published
publisher: Elsevier
quality_controlled: '1'
scopus_import: '1'
status: public
title: The Bertini irreducibility theorem for higher codimensional slices
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: 83
year: '2022'
...