---
_id: '9431'
abstract:
- lang: eng
text: Inositol hexakisphosphate (IP6) is an assembly cofactor for HIV-1. We report
here that IP6 is also used for assembly of Rous sarcoma virus (RSV), a retrovirus
from a different genus. IP6 is ~100-fold more potent at promoting RSV mature capsid
protein (CA) assembly than observed for HIV-1 and removal of IP6 in cells reduces
infectivity by 100-fold. Here, visualized by cryo-electron tomography and subtomogram
averaging, mature capsid-like particles show an IP6-like density in the CA hexamer,
coordinated by rings of six lysines and six arginines. Phosphate and IP6 have
opposing effects on CA in vitro assembly, inducing formation of T = 1 icosahedrons
and tubes, respectively, implying that phosphate promotes pentamer and IP6 hexamer
formation. Subtomogram averaging and classification optimized for analysis of
pleomorphic retrovirus particles reveal that the heterogeneity of mature RSV CA
polyhedrons results from an unexpected, intrinsic CA hexamer flexibility. In contrast,
the CA pentamer forms rigid units organizing the local architecture. These different
features of hexamers and pentamers determine the structural mechanism to form
CA polyhedrons of variable shape in mature RSV particles.
acknowledged_ssus:
- _id: ScienComp
- _id: LifeSc
- _id: EM-Fac
acknowledgement: This work was funded by the National Institute of Allergy and Infectious
Diseases under awards R01AI147890 to R.A.D., R01AI150454 to V.M.V, R35GM136258 in
support of J-P.R.F, and the Austrian Science Fund (FWF) grant P31445 to F.K.M.S.
Access to high-resolution cryo-ET data acquisition at EMBL Heidelberg was supported
by iNEXT (grant no. 653706), funded by the Horizon 2020 program of the European
Union (PID 4246). We thank Wim Hagen and Felix Weis at EMBL Heidelberg for support
in cryo-ET data acquisition. This work made use of the Cornell Center for Materials
Research Shared Facilities, which are supported through the NSF MRSEC program (DMR-179875).
This research was also supported by the Scientific Service Units (SSUs) of IST Austria
through resources provided by Scientific Computing (SciComp), the Life Science Facility
(LSF), and the Electron Microscopy Facility (EMF).
article_number: '3226'
article_processing_charge: No
article_type: original
author:
- first_name: Martin
full_name: Obr, Martin
id: 4741CA5A-F248-11E8-B48F-1D18A9856A87
last_name: Obr
- first_name: Clifton L.
full_name: Ricana, Clifton L.
last_name: Ricana
- first_name: Nadia
full_name: Nikulin, Nadia
last_name: Nikulin
- first_name: Jon-Philip R.
full_name: Feathers, Jon-Philip R.
last_name: Feathers
- first_name: Marco
full_name: Klanschnig, Marco
last_name: Klanschnig
- first_name: Andreas
full_name: Thader, Andreas
id: 3A18A7B8-F248-11E8-B48F-1D18A9856A87
last_name: Thader
- first_name: Marc C.
full_name: Johnson, Marc C.
last_name: Johnson
- first_name: Volker M.
full_name: Vogt, Volker M.
last_name: Vogt
- first_name: Florian KM
full_name: Schur, Florian KM
id: 48AD8942-F248-11E8-B48F-1D18A9856A87
last_name: Schur
orcid: 0000-0003-4790-8078
- first_name: Robert A.
full_name: Dick, Robert A.
last_name: Dick
citation:
ama: Obr M, Ricana CL, Nikulin N, et al. Structure of the mature Rous sarcoma virus
lattice reveals a role for IP6 in the formation of the capsid hexamer. Nature
Communications. 2021;12(1). doi:10.1038/s41467-021-23506-0
apa: Obr, M., Ricana, C. L., Nikulin, N., Feathers, J.-P. R., Klanschnig, M., Thader,
A., … Dick, R. A. (2021). Structure of the mature Rous sarcoma virus lattice reveals
a role for IP6 in the formation of the capsid hexamer. Nature Communications.
Nature Research. https://doi.org/10.1038/s41467-021-23506-0
chicago: Obr, Martin, Clifton L. Ricana, Nadia Nikulin, Jon-Philip R. Feathers,
Marco Klanschnig, Andreas Thader, Marc C. Johnson, Volker M. Vogt, Florian KM
Schur, and Robert A. Dick. “Structure of the Mature Rous Sarcoma Virus Lattice
Reveals a Role for IP6 in the Formation of the Capsid Hexamer.” Nature Communications.
Nature Research, 2021. https://doi.org/10.1038/s41467-021-23506-0.
ieee: M. Obr et al., “Structure of the mature Rous sarcoma virus lattice
reveals a role for IP6 in the formation of the capsid hexamer,” Nature Communications,
vol. 12, no. 1. Nature Research, 2021.
ista: Obr M, Ricana CL, Nikulin N, Feathers J-PR, Klanschnig M, Thader A, Johnson
MC, Vogt VM, Schur FK, Dick RA. 2021. Structure of the mature Rous sarcoma virus
lattice reveals a role for IP6 in the formation of the capsid hexamer. Nature
Communications. 12(1), 3226.
mla: Obr, Martin, et al. “Structure of the Mature Rous Sarcoma Virus Lattice Reveals
a Role for IP6 in the Formation of the Capsid Hexamer.” Nature Communications,
vol. 12, no. 1, 3226, Nature Research, 2021, doi:10.1038/s41467-021-23506-0.
short: M. Obr, C.L. Ricana, N. Nikulin, J.-P.R. Feathers, M. Klanschnig, A. Thader,
M.C. Johnson, V.M. Vogt, F.K. Schur, R.A. Dick, Nature Communications 12 (2021).
date_created: 2021-05-28T14:25:50Z
date_published: 2021-05-28T00:00:00Z
date_updated: 2023-08-08T13:53:53Z
day: '28'
ddc:
- '570'
department:
- _id: FlSc
doi: 10.1038/s41467-021-23506-0
external_id:
isi:
- '000659145000011'
file:
- access_level: open_access
checksum: 53ccc53d09a9111143839dbe7784e663
content_type: application/pdf
creator: kschuh
date_created: 2021-06-09T15:21:14Z
date_updated: 2021-06-09T15:21:14Z
file_id: '9538'
file_name: 2021_NatureCommunications_Obr.pdf
file_size: 6166295
relation: main_file
success: 1
file_date_updated: 2021-06-09T15:21:14Z
has_accepted_license: '1'
intvolume: ' 12'
isi: 1
issue: '1'
keyword:
- General Biochemistry
- Genetics and Molecular Biology
- General Physics and Astronomy
- General Chemistry
language:
- iso: eng
month: '05'
oa: 1
oa_version: Published Version
project:
- _id: 26736D6A-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: P31445
name: Structural conservation and diversity in retroviral capsid
publication: Nature Communications
publication_identifier:
eissn:
- 2041-1723
publication_status: published
publisher: Nature Research
quality_controlled: '1'
related_material:
link:
- description: News on IST Homepage
relation: press_release
url: https://ist.ac.at/en/news/how-retroviruses-become-infectious/
scopus_import: '1'
status: public
title: Structure of the mature Rous sarcoma virus lattice reveals a role for IP6 in
the formation of the capsid hexamer
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: journal_article
user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
volume: 12
year: '2021'
...
---
_id: '9467'
abstract:
- lang: eng
text: "Turbulence in the flow of fluid through a pipe can be suppressed by buoyancy
forces. As the suppression of turbulence leads to severe heat transfer deterioration,
this is an important and undesirable phenomenon in both heating and cooling applications.
Vertical flow is often considered, as the axial buoyancy force can help drive
the flow. With heating measured by the buoyancy parameter \U0001D436, our direct
numerical simulations show that shear-driven turbulence may either be completely
laminarised or it transitions to a relatively quiescent convection-driven state.
Buoyancy forces cause a flattening of the base flow profile, which in isothermal
pipe flow has recently been linked to complete suppression of turbulence (Kühnen
et al., Nat. Phys., vol. 14, 2018, pp. 386–390), and the flattened laminar base
profile has enhanced nonlinear stability (Marensi et al., J. Fluid Mech., vol.
863, 2019, pp. 50–875). In agreement with these findings, the nonlinear lower-branch
travelling-wave solution analysed here, which is believed to mediate transition
to turbulence in isothermal pipe flow, is shown to be suppressed by buoyancy.
A linear instability of the laminar base flow is responsible for the appearance
of the relatively quiescent convection driven state for \U0001D436≳4 across the
range of Reynolds numbers considered. In the suppression of turbulence, however,
i.e. in the transition from turbulence, we find clearer association with the analysis
of He et al. (J. Fluid Mech., vol. 809, 2016, pp. 31–71) than with the above dynamical
systems approach, which describes better the transition to turbulence. The laminarisation
criterion He et al. propose, based on an apparent Reynolds number of the flow
as measured by its driving pressure gradient, is found to capture the critical
\U0001D436=\U0001D436\U0001D450\U0001D45F(\U0001D445\U0001D452) above which the
flow will be laminarised or switch to the convection-driven type. Our analysis
suggests that it is the weakened rolls, rather than the streaks, which appear
to be critical for laminarisation."
acknowledgement: The anonymous referees are kindly acknowledged for their useful suggestions
andcomments.
article_number: A17
article_processing_charge: Yes (via OA deal)
article_type: original
author:
- first_name: Elena
full_name: Marensi, Elena
id: 0BE7553A-1004-11EA-B805-18983DDC885E
last_name: Marensi
- first_name: Shuisheng
full_name: He, Shuisheng
last_name: He
- first_name: Ashley P.
full_name: Willis, Ashley P.
last_name: Willis
citation:
ama: Marensi E, He S, Willis AP. Suppression of turbulence and travelling waves
in a vertical heated pipe. Journal of Fluid Mechanics. 2021;919. doi:10.1017/jfm.2021.371
apa: Marensi, E., He, S., & Willis, A. P. (2021). Suppression of turbulence
and travelling waves in a vertical heated pipe. Journal of Fluid Mechanics.
Cambridge University Press. https://doi.org/10.1017/jfm.2021.371
chicago: Marensi, Elena, Shuisheng He, and Ashley P. Willis. “Suppression of Turbulence
and Travelling Waves in a Vertical Heated Pipe.” Journal of Fluid Mechanics.
Cambridge University Press, 2021. https://doi.org/10.1017/jfm.2021.371.
ieee: E. Marensi, S. He, and A. P. Willis, “Suppression of turbulence and travelling
waves in a vertical heated pipe,” Journal of Fluid Mechanics, vol. 919.
Cambridge University Press, 2021.
ista: Marensi E, He S, Willis AP. 2021. Suppression of turbulence and travelling
waves in a vertical heated pipe. Journal of Fluid Mechanics. 919, A17.
mla: Marensi, Elena, et al. “Suppression of Turbulence and Travelling Waves in a
Vertical Heated Pipe.” Journal of Fluid Mechanics, vol. 919, A17, Cambridge
University Press, 2021, doi:10.1017/jfm.2021.371.
short: E. Marensi, S. He, A.P. Willis, Journal of Fluid Mechanics 919 (2021).
date_created: 2021-06-06T22:01:30Z
date_published: 2021-07-25T00:00:00Z
date_updated: 2023-08-08T13:58:41Z
day: '25'
ddc:
- '530'
department:
- _id: BjHo
doi: 10.1017/jfm.2021.371
external_id:
arxiv:
- '2008.13486'
isi:
- '000653785000001'
file:
- access_level: open_access
checksum: 867ad077e45c181c2c5ec1311ba27c41
content_type: application/pdf
creator: kschuh
date_created: 2021-08-03T09:53:28Z
date_updated: 2021-08-03T09:53:28Z
file_id: '9766'
file_name: 2021_JournalFluidMechanics_Marensi.pdf
file_size: 4087358
relation: main_file
success: 1
file_date_updated: 2021-08-03T09:53:28Z
has_accepted_license: '1'
intvolume: ' 919'
isi: 1
language:
- iso: eng
month: '07'
oa: 1
oa_version: Published Version
publication: Journal of Fluid Mechanics
publication_identifier:
eissn:
- '14697645'
issn:
- '00221120'
publication_status: published
publisher: Cambridge University Press
quality_controlled: '1'
scopus_import: '1'
status: public
title: Suppression of turbulence and travelling waves in a vertical heated pipe
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: 919
year: '2021'
...
---
_id: '9470'
abstract:
- lang: eng
text: A key step in understanding the genetic basis of different evolutionary outcomes
(e.g., adaptation) is to determine the roles played by different mutation types
(e.g., SNPs, translocations and inversions). To do this we must simultaneously
consider different mutation types in an evolutionary framework. Here, we propose
a research framework that directly utilizes the most important characteristics
of mutations, their population genetic effects, to determine their relative evolutionary
significance in a given scenario. We review known population genetic effects of
different mutation types and show how these may be connected to different evolutionary
outcomes. We provide examples of how to implement this framework and pinpoint
areas where more data, theory and synthesis are needed. Linking experimental and
theoretical approaches to examine different mutation types simultaneously is a
critical step towards understanding their evolutionary significance.
acknowledgement: We thank the editor, two helpful reviewers, Roger Butlin, Kerstin
Johannesson, Valentina Peona, Rike Stelkens, Julie Blommaert, Nick Barton, and João
Alpedrinha for helpful comments that improved the manuscript. The authors acknowledge
funding from the Swedish Research Council Formas (2017-01597 to AS), the Swedish
Research Council Vetenskapsrådet (2016-05139 to AS, 2019-04452 to TS) and from the
European Research Council (ERC) under the European Union’s Horizon 2020 research
and innovation programme (grant agreement no. 757451 to TS). ELB was funded by a
Carl Tryggers grant awarded to Tanja Slotte. Anja M. Westram was funded by the European
Union’s Horizon 2020 research and innovation programme under the Marie Sklodowska-Curie
grant agreement No 797747. Inês Fragata was funded by a Junior Researcher contract
from FCT (CEECIND/02616/2018).
article_processing_charge: No
author:
- first_name: Emma L.
full_name: Berdan, Emma L.
last_name: Berdan
- first_name: Alexandre
full_name: Blanckaert, Alexandre
last_name: Blanckaert
- first_name: Tanja
full_name: Slotte, Tanja
last_name: Slotte
- first_name: Alexander
full_name: Suh, Alexander
last_name: Suh
- 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: Inês
full_name: Fragata, Inês
last_name: Fragata
citation:
ama: 'Berdan EL, Blanckaert A, Slotte T, Suh A, Westram AM, Fragata I. Unboxing
mutations: Connecting mutation types with evolutionary consequences. Molecular
Ecology. 2021;30(12):2710-2723. doi:10.1111/mec.15936'
apa: 'Berdan, E. L., Blanckaert, A., Slotte, T., Suh, A., Westram, A. M., &
Fragata, I. (2021). Unboxing mutations: Connecting mutation types with evolutionary
consequences. Molecular Ecology. Wiley. https://doi.org/10.1111/mec.15936'
chicago: 'Berdan, Emma L., Alexandre Blanckaert, Tanja Slotte, Alexander Suh, Anja
M Westram, and Inês Fragata. “Unboxing Mutations: Connecting Mutation Types with
Evolutionary Consequences.” Molecular Ecology. Wiley, 2021. https://doi.org/10.1111/mec.15936.'
ieee: 'E. L. Berdan, A. Blanckaert, T. Slotte, A. Suh, A. M. Westram, and I. Fragata,
“Unboxing mutations: Connecting mutation types with evolutionary consequences,”
Molecular Ecology, vol. 30, no. 12. Wiley, pp. 2710–2723, 2021.'
ista: 'Berdan EL, Blanckaert A, Slotte T, Suh A, Westram AM, Fragata I. 2021. Unboxing
mutations: Connecting mutation types with evolutionary consequences. Molecular
Ecology. 30(12), 2710–2723.'
mla: 'Berdan, Emma L., et al. “Unboxing Mutations: Connecting Mutation Types with
Evolutionary Consequences.” Molecular Ecology, vol. 30, no. 12, Wiley,
2021, pp. 2710–23, doi:10.1111/mec.15936.'
short: E.L. Berdan, A. Blanckaert, T. Slotte, A. Suh, A.M. Westram, I. Fragata,
Molecular Ecology 30 (2021) 2710–2723.
date_created: 2021-06-06T22:01:31Z
date_published: 2021-06-01T00:00:00Z
date_updated: 2023-08-08T13:59:18Z
day: '01'
ddc:
- '570'
department:
- _id: NiBa
doi: 10.1111/mec.15936
ec_funded: 1
external_id:
isi:
- '000652056400001'
file:
- access_level: open_access
checksum: e6f4731365bde2614b333040a08265d8
content_type: application/pdf
creator: kschuh
date_created: 2021-06-11T15:34:53Z
date_updated: 2021-06-11T15:34:53Z
file_id: '9545'
file_name: 2021_MolecularEcology_Berdan.pdf
file_size: 1031978
relation: main_file
success: 1
file_date_updated: 2021-06-11T15:34:53Z
has_accepted_license: '1'
intvolume: ' 30'
isi: 1
issue: '12'
language:
- iso: eng
license: https://creativecommons.org/licenses/by-nc/4.0/
month: '06'
oa: 1
oa_version: Published Version
page: 2710-2723
project:
- _id: 265B41B8-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '797747'
name: Theoretical and empirical approaches to understanding Parallel Adaptation
publication: Molecular Ecology
publication_identifier:
eissn:
- 1365294X
issn:
- '09621083'
publication_status: published
publisher: Wiley
quality_controlled: '1'
scopus_import: '1'
status: public
title: 'Unboxing mutations: Connecting mutation types with evolutionary consequences'
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: 30
year: '2021'
...
---
_id: '9468'
abstract:
- lang: eng
text: "Motivated by the successful application of geometry to proving the Harary--Hill
conjecture for “pseudolinear” drawings of $K_n$, we introduce “pseudospherical”
drawings of graphs. A spherical drawing of a graph $G$ is a drawing in the unit
sphere $\\mathbb{S}^2$ in which the vertices of $G$ are represented as points---no
three on a great circle---and the edges of $G$ are shortest-arcs in $\\mathbb{S}^2$
connecting pairs of vertices. Such a drawing has three properties: (1) every edge
$e$ is contained in a simple closed curve $\\gamma_e$ such that the only vertices
in $\\gamma_e$ are the ends of $e$; (2) if $e\\ne f$, then $\\gamma_e\\cap\\gamma_f$
has precisely two crossings; and (3) if $e\\ne f$, then $e$ intersects $\\gamma_f$
at most once, in either a crossing or an end of $e$. We use properties (1)--(3)
to define a pseudospherical drawing of $G$. Our main result is that for the complete
graph, properties (1)--(3) are equivalent to the same three properties but with
“precisely two crossings” in (2) replaced by “at most two crossings.” The proof
requires a result in the geometric transversal theory of arrangements of pseudocircles.
This is proved using the surprising result that the absence of special arcs (coherent
spirals) in an arrangement of simple closed curves characterizes the fact that
any two curves in the arrangement have at most two crossings. Our studies provide
the necessary ideas for exhibiting a drawing of $K_{10}$ that has no extension
to an arrangement of pseudocircles and a drawing of $K_9$ that does extend to
an arrangement of pseudocircles, but no such extension has all pairs of pseudocircles
crossing twice.\r\n"
article_processing_charge: No
article_type: original
author:
- first_name: Alan M
full_name: Arroyo Guevara, Alan M
id: 3207FDC6-F248-11E8-B48F-1D18A9856A87
last_name: Arroyo Guevara
orcid: 0000-0003-2401-8670
- first_name: R. Bruce
full_name: Richter, R. Bruce
last_name: Richter
- first_name: Matthew
full_name: Sunohara, Matthew
last_name: Sunohara
citation:
ama: Arroyo Guevara AM, Richter RB, Sunohara M. Extending drawings of complete graphs
into arrangements of pseudocircles. SIAM Journal on Discrete Mathematics.
2021;35(2):1050-1076. doi:10.1137/20M1313234
apa: Arroyo Guevara, A. M., Richter, R. B., & Sunohara, M. (2021). Extending
drawings of complete graphs into arrangements of pseudocircles. SIAM Journal
on Discrete Mathematics. Society for Industrial and Applied Mathematics. https://doi.org/10.1137/20M1313234
chicago: Arroyo Guevara, Alan M, R. Bruce Richter, and Matthew Sunohara. “Extending
Drawings of Complete Graphs into Arrangements of Pseudocircles.” SIAM Journal
on Discrete Mathematics. Society for Industrial and Applied Mathematics, 2021.
https://doi.org/10.1137/20M1313234.
ieee: A. M. Arroyo Guevara, R. B. Richter, and M. Sunohara, “Extending drawings
of complete graphs into arrangements of pseudocircles,” SIAM Journal on Discrete
Mathematics, vol. 35, no. 2. Society for Industrial and Applied Mathematics,
pp. 1050–1076, 2021.
ista: Arroyo Guevara AM, Richter RB, Sunohara M. 2021. Extending drawings of complete
graphs into arrangements of pseudocircles. SIAM Journal on Discrete Mathematics.
35(2), 1050–1076.
mla: Arroyo Guevara, Alan M., et al. “Extending Drawings of Complete Graphs into
Arrangements of Pseudocircles.” SIAM Journal on Discrete Mathematics, vol.
35, no. 2, Society for Industrial and Applied Mathematics, 2021, pp. 1050–76,
doi:10.1137/20M1313234.
short: A.M. Arroyo Guevara, R.B. Richter, M. Sunohara, SIAM Journal on Discrete
Mathematics 35 (2021) 1050–1076.
date_created: 2021-06-06T22:01:30Z
date_published: 2021-05-20T00:00:00Z
date_updated: 2023-08-08T13:58:12Z
day: '20'
department:
- _id: UlWa
doi: 10.1137/20M1313234
ec_funded: 1
external_id:
arxiv:
- '2001.06053'
isi:
- '000674142200022'
intvolume: ' 35'
isi: 1
issue: '2'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/2001.06053
month: '05'
oa: 1
oa_version: Preprint
page: 1050-1076
project:
- _id: 260C2330-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '754411'
name: ISTplus - Postdoctoral Fellowships
publication: SIAM Journal on Discrete Mathematics
publication_identifier:
issn:
- '08954801'
publication_status: published
publisher: Society for Industrial and Applied Mathematics
quality_controlled: '1'
scopus_import: '1'
status: public
title: Extending drawings of complete graphs into arrangements of pseudocircles
type: journal_article
user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
volume: 35
year: '2021'
...
---
_id: '9462'
abstract:
- lang: eng
text: We consider a system of N trapped bosons with repulsive interactions in a
combined semiclassical mean-field limit at positive temperature. We show that
the free energy is well approximated by the minimum of the Hartree free energy
functional – a natural extension of the Hartree energy functional to positive
temperatures. The Hartree free energy functional converges in the same limit to
a semiclassical free energy functional, and we show that the system displays Bose–Einstein
condensation if and only if it occurs in the semiclassical free energy functional.
This allows us to show that for weak coupling the critical temperature decreases
due to the repulsive interactions.
acknowledgement: Funding from the European Union's Horizon 2020 research and innovation
programme under the ERC grant agreement No 694227 (R.S.) and under the Marie Sklodowska-Curie
grant agreement No 836146 (A.D.) is gratefully acknowledged. A.D. acknowledges support
of the Swiss National Science Foundation through the Ambizione grant PZ00P2 185851.
article_number: '109096'
article_processing_charge: No
article_type: original
author:
- first_name: Andreas
full_name: Deuchert, Andreas
last_name: Deuchert
- first_name: Robert
full_name: Seiringer, Robert
id: 4AFD0470-F248-11E8-B48F-1D18A9856A87
last_name: Seiringer
orcid: 0000-0002-6781-0521
citation:
ama: Deuchert A, Seiringer R. Semiclassical approximation and critical temperature
shift for weakly interacting trapped bosons. Journal of Functional Analysis.
2021;281(6). doi:10.1016/j.jfa.2021.109096
apa: Deuchert, A., & Seiringer, R. (2021). Semiclassical approximation and critical
temperature shift for weakly interacting trapped bosons. Journal of Functional
Analysis. Elsevier. https://doi.org/10.1016/j.jfa.2021.109096
chicago: Deuchert, Andreas, and Robert Seiringer. “Semiclassical Approximation and
Critical Temperature Shift for Weakly Interacting Trapped Bosons.” Journal
of Functional Analysis. Elsevier, 2021. https://doi.org/10.1016/j.jfa.2021.109096.
ieee: A. Deuchert and R. Seiringer, “Semiclassical approximation and critical temperature
shift for weakly interacting trapped bosons,” Journal of Functional Analysis,
vol. 281, no. 6. Elsevier, 2021.
ista: Deuchert A, Seiringer R. 2021. Semiclassical approximation and critical temperature
shift for weakly interacting trapped bosons. Journal of Functional Analysis. 281(6),
109096.
mla: Deuchert, Andreas, and Robert Seiringer. “Semiclassical Approximation and Critical
Temperature Shift for Weakly Interacting Trapped Bosons.” Journal of Functional
Analysis, vol. 281, no. 6, 109096, Elsevier, 2021, doi:10.1016/j.jfa.2021.109096.
short: A. Deuchert, R. Seiringer, Journal of Functional Analysis 281 (2021).
date_created: 2021-06-06T22:01:28Z
date_published: 2021-09-15T00:00:00Z
date_updated: 2023-08-08T13:56:27Z
day: '15'
department:
- _id: RoSe
doi: 10.1016/j.jfa.2021.109096
ec_funded: 1
external_id:
arxiv:
- '2009.00992'
isi:
- '000656508600008'
intvolume: ' 281'
isi: 1
issue: '6'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/2009.00992
month: '09'
oa: 1
oa_version: Preprint
project:
- _id: 25C6DC12-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '694227'
name: Analysis of quantum many-body systems
publication: Journal of Functional Analysis
publication_identifier:
eissn:
- 1096-0783
issn:
- 0022-1236
publication_status: published
publisher: Elsevier
quality_controlled: '1'
scopus_import: '1'
status: public
title: Semiclassical approximation and critical temperature shift for weakly interacting
trapped bosons
type: journal_article
user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
volume: 281
year: '2021'
...
---
_id: '9469'
abstract:
- lang: eng
text: In this paper, we consider reflected three-operator splitting methods for
monotone inclusion problems in real Hilbert spaces. To do this, we first obtain
weak convergence analysis and nonasymptotic O(1/n) convergence rate of the reflected
Krasnosel'skiĭ-Mann iteration for finding a fixed point of nonexpansive mapping
in real Hilbert spaces under some seemingly easy to implement conditions on the
iterative parameters. We then apply our results to three-operator splitting for
the monotone inclusion problem and consequently obtain the corresponding convergence
analysis. Furthermore, we derive reflected primal-dual algorithms for highly structured
monotone inclusion problems. Some numerical implementations are drawn from splitting
methods to support the theoretical analysis.
acknowledgement: The authors are grateful to the anonymous referees and the handling
Editor for their insightful comments which have improved the earlier version of
the manuscript greatly. The second author is grateful to the University of Hafr
Al Batin. The last author has received funding from the European Research Council
(ERC) under the European Union's Seventh Framework Program (FP7-2007-2013) (Grant
agreement No. 616160).
article_processing_charge: No
article_type: original
author:
- first_name: Olaniyi S.
full_name: Iyiola, Olaniyi S.
last_name: Iyiola
- first_name: Cyril D.
full_name: Enyi, Cyril D.
last_name: Enyi
- first_name: Yekini
full_name: Shehu, Yekini
id: 3FC7CB58-F248-11E8-B48F-1D18A9856A87
last_name: Shehu
orcid: 0000-0001-9224-7139
citation:
ama: Iyiola OS, Enyi CD, Shehu Y. Reflected three-operator splitting method for
monotone inclusion problem. Optimization Methods and Software. 2021. doi:10.1080/10556788.2021.1924715
apa: Iyiola, O. S., Enyi, C. D., & Shehu, Y. (2021). Reflected three-operator
splitting method for monotone inclusion problem. Optimization Methods and Software.
Taylor and Francis. https://doi.org/10.1080/10556788.2021.1924715
chicago: Iyiola, Olaniyi S., Cyril D. Enyi, and Yekini Shehu. “Reflected Three-Operator
Splitting Method for Monotone Inclusion Problem.” Optimization Methods and
Software. Taylor and Francis, 2021. https://doi.org/10.1080/10556788.2021.1924715.
ieee: O. S. Iyiola, C. D. Enyi, and Y. Shehu, “Reflected three-operator splitting
method for monotone inclusion problem,” Optimization Methods and Software.
Taylor and Francis, 2021.
ista: Iyiola OS, Enyi CD, Shehu Y. 2021. Reflected three-operator splitting method
for monotone inclusion problem. Optimization Methods and Software.
mla: Iyiola, Olaniyi S., et al. “Reflected Three-Operator Splitting Method for Monotone
Inclusion Problem.” Optimization Methods and Software, Taylor and Francis,
2021, doi:10.1080/10556788.2021.1924715.
short: O.S. Iyiola, C.D. Enyi, Y. Shehu, Optimization Methods and Software (2021).
date_created: 2021-06-06T22:01:30Z
date_published: 2021-05-12T00:00:00Z
date_updated: 2023-08-08T13:57:43Z
day: '12'
department:
- _id: VlKo
doi: 10.1080/10556788.2021.1924715
ec_funded: 1
external_id:
isi:
- '000650507600001'
isi: 1
language:
- iso: eng
month: '05'
oa_version: None
project:
- _id: 25FBA906-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '616160'
name: 'Discrete Optimization in Computer Vision: Theory and Practice'
publication: Optimization Methods and Software
publication_identifier:
eissn:
- 1029-4937
issn:
- 1055-6788
publication_status: published
publisher: Taylor and Francis
quality_controlled: '1'
scopus_import: '1'
status: public
title: Reflected three-operator splitting method for monotone inclusion problem
type: journal_article
user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
year: '2021'
...
---
_id: '9540'
abstract:
- lang: eng
text: The hexameric AAA-ATPase Drg1 is a key factor in eukaryotic ribosome biogenesis
and initiates cytoplasmic maturation of the large ribosomal subunit by releasing
the shuttling maturation factor Rlp24. Drg1 monomers contain two AAA-domains (D1
and D2) that act in a concerted manner. Rlp24 release is inhibited by the drug
diazaborine which blocks ATP hydrolysis in D2. The mode of inhibition was unknown.
Here we show the first cryo-EM structure of Drg1 revealing the inhibitory mechanism.
Diazaborine forms a covalent bond to the 2′-OH of the nucleotide in D2, explaining
its specificity for this site. As a consequence, the D2 domain is locked in a
rigid, inactive state, stalling the whole Drg1 hexamer. Resistance mechanisms
identified include abolished drug binding and altered positioning of the nucleotide.
Our results suggest nucleotide-modifying compounds as potential novel inhibitors
for AAA-ATPases.
acknowledged_ssus:
- _id: EM-Fac
acknowledgement: We are deeply grateful to the late Gregor Högenauer who built the
foundation for this study with his visionary work on the inhibitor diazaborine and
its bacterial target. We thank Rolf Breinbauer for insightful discussions on boron
chemistry. We thank Anton Meinhart and Tim Clausen for the valuable discussion of
the manuscript. We are indebted to Thomas Köcher for the MS measurement of the diazaborine-ATPγS
adduct. We thank the team of the VBCF for support during early phases of this work
and the IST Austria Electron Microscopy Facility for providing equipment. The lab
of D.H. is supported by Boehringer Ingelheim. The work was funded by FWF projects
P32536 and P32977 (to H.B.).
article_number: '3483'
article_processing_charge: No
article_type: original
author:
- first_name: Michael
full_name: Prattes, Michael
last_name: Prattes
- first_name: Irina
full_name: Grishkovskaya, Irina
last_name: Grishkovskaya
- first_name: Victor-Valentin
full_name: Hodirnau, Victor-Valentin
id: 3661B498-F248-11E8-B48F-1D18A9856A87
last_name: Hodirnau
- first_name: Ingrid
full_name: Rössler, Ingrid
last_name: Rössler
- first_name: Isabella
full_name: Klein, Isabella
last_name: Klein
- first_name: Christina
full_name: Hetzmannseder, Christina
last_name: Hetzmannseder
- first_name: Gertrude
full_name: Zisser, Gertrude
last_name: Zisser
- first_name: Christian C.
full_name: Gruber, Christian C.
last_name: Gruber
- first_name: Karl
full_name: Gruber, Karl
last_name: Gruber
- first_name: David
full_name: Haselbach, David
last_name: Haselbach
- first_name: Helmut
full_name: Bergler, Helmut
last_name: Bergler
citation:
ama: Prattes M, Grishkovskaya I, Hodirnau V-V, et al. Structural basis for inhibition
of the AAA-ATPase Drg1 by diazaborine. Nature Communications. 2021;12(1).
doi:10.1038/s41467-021-23854-x
apa: Prattes, M., Grishkovskaya, I., Hodirnau, V.-V., Rössler, I., Klein, I., Hetzmannseder,
C., … Bergler, H. (2021). Structural basis for inhibition of the AAA-ATPase Drg1
by diazaborine. Nature Communications. Springer Nature. https://doi.org/10.1038/s41467-021-23854-x
chicago: Prattes, Michael, Irina Grishkovskaya, Victor-Valentin Hodirnau, Ingrid
Rössler, Isabella Klein, Christina Hetzmannseder, Gertrude Zisser, et al. “Structural
Basis for Inhibition of the AAA-ATPase Drg1 by Diazaborine.” Nature Communications.
Springer Nature, 2021. https://doi.org/10.1038/s41467-021-23854-x.
ieee: M. Prattes et al., “Structural basis for inhibition of the AAA-ATPase
Drg1 by diazaborine,” Nature Communications, vol. 12, no. 1. Springer Nature,
2021.
ista: Prattes M, Grishkovskaya I, Hodirnau V-V, Rössler I, Klein I, Hetzmannseder
C, Zisser G, Gruber CC, Gruber K, Haselbach D, Bergler H. 2021. Structural basis
for inhibition of the AAA-ATPase Drg1 by diazaborine. Nature Communications. 12(1),
3483.
mla: Prattes, Michael, et al. “Structural Basis for Inhibition of the AAA-ATPase
Drg1 by Diazaborine.” Nature Communications, vol. 12, no. 1, 3483, Springer
Nature, 2021, doi:10.1038/s41467-021-23854-x.
short: M. Prattes, I. Grishkovskaya, V.-V. Hodirnau, I. Rössler, I. Klein, C. Hetzmannseder,
G. Zisser, C.C. Gruber, K. Gruber, D. Haselbach, H. Bergler, Nature Communications
12 (2021).
date_created: 2021-06-10T14:57:45Z
date_published: 2021-06-09T00:00:00Z
date_updated: 2023-08-08T14:05:26Z
day: '09'
ddc:
- '570'
department:
- _id: EM-Fac
doi: 10.1038/s41467-021-23854-x
external_id:
isi:
- '000664874700014'
pmid:
- '34108481'
file:
- access_level: open_access
checksum: 40fc24c1310930990b52a8ad1142ee97
content_type: application/pdf
creator: cziletti
date_created: 2021-06-15T18:55:59Z
date_updated: 2021-06-15T18:55:59Z
file_id: '9556'
file_name: 2021_NatureComm_Prattes.pdf
file_size: 3397292
relation: main_file
success: 1
file_date_updated: 2021-06-15T18:55:59Z
has_accepted_license: '1'
intvolume: ' 12'
isi: 1
issue: '1'
keyword:
- General Biochemistry
- Genetics and Molecular Biology
- General Physics and Astronomy
- General Chemistry
language:
- iso: eng
month: '06'
oa: 1
oa_version: Published Version
pmid: 1
publication: Nature Communications
publication_identifier:
eissn:
- 2041-1723
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
status: public
title: Structural basis for inhibition of the AAA-ATPase Drg1 by diazaborine
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: journal_article
user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
volume: 12
year: '2021'
...
---
_id: '9549'
abstract:
- lang: eng
text: 'AMPA receptors (AMPARs) mediate the majority of excitatory transmission in
the brain and enable the synaptic plasticity that underlies learning1. A diverse
array of AMPAR signalling complexes are established by receptor auxiliary subunits,
which associate with the AMPAR in various combinations to modulate trafficking,
gating and synaptic strength2. However, their mechanisms of action are poorly
understood. Here we determine cryo-electron microscopy structures of the heteromeric
GluA1–GluA2 receptor assembled with both TARP-γ8 and CNIH2, the predominant AMPAR
complex in the forebrain, in both resting and active states. Two TARP-γ8 and two
CNIH2 subunits insert at distinct sites beneath the ligand-binding domains of
the receptor, with site-specific lipids shaping each interaction and affecting
the gating regulation of the AMPARs. Activation of the receptor leads to asymmetry
between GluA1 and GluA2 along the ion conduction path and an outward expansion
of the channel triggers counter-rotations of both auxiliary subunit pairs, promoting
the active-state conformation. In addition, both TARP-γ8 and CNIH2 pivot towards
the pore exit upon activation, extending their reach for cytoplasmic receptor
elements. CNIH2 achieves this through its uniquely extended M2 helix, which has
transformed this endoplasmic reticulum-export factor into a powerful AMPAR modulator
that is capable of providing hippocampal pyramidal neurons with their integrative
synaptic properties. '
acknowledgement: We thank members of the Greger laboratory, B. Herguedas, J. Krieger
and J.-N. Dohrke for comments on the manuscript; J. Krieger and J.-N. Dohrke for
discussion, J. Krieger for help with the normal mode analysis, B. Köhegyi for help
with cryo-EM imaging, V. Chang and K. Suzuki for helping to generate the CNIH2-1D4-HA
stable cell line, M. Carvalho for assistance at early stages of this project, the
LMB scientific computing and the cryo-EM facility for support, P. Emsley for help
with model building, T. Nakane for helpful comments with RELION 3.1 and R. Warshamanage
for helping with EMDA cryo-EM-map processing. We acknowledge the Diamond Light Source
for access and support of the Cryo-EM facilities at the UK national electron bio10
imaging centre (eBIC), proposal EM17434, funded by the Wellcome Trust, MRC and BBSRC.
This work was supported by grants from the Medical Research Council, as part of
United Kingdom Research and Innovation (also known as UK Research and Innovation)
(MC_U105174197) and BBSRC (BB/N002113/1) to I.H.G.
article_processing_charge: No
article_type: original
author:
- first_name: Danyang
full_name: Zhang, Danyang
last_name: Zhang
- first_name: Jake
full_name: Watson, Jake
id: 63836096-4690-11EA-BD4E-32803DDC885E
last_name: Watson
orcid: 0000-0002-8698-3823
- first_name: Peter M.
full_name: Matthews, Peter M.
last_name: Matthews
- first_name: Ondrej
full_name: Cais, Ondrej
last_name: Cais
- first_name: Ingo H.
full_name: Greger, Ingo H.
last_name: Greger
citation:
ama: Zhang D, Watson J, Matthews PM, Cais O, Greger IH. Gating and modulation of
a hetero-octameric AMPA glutamate receptor. Nature. 2021;594:454-458. doi:10.1038/s41586-021-03613-0
apa: Zhang, D., Watson, J., Matthews, P. M., Cais, O., & Greger, I. H. (2021).
Gating and modulation of a hetero-octameric AMPA glutamate receptor. Nature.
Springer Nature. https://doi.org/10.1038/s41586-021-03613-0
chicago: Zhang, Danyang, Jake Watson, Peter M. Matthews, Ondrej Cais, and Ingo H.
Greger. “Gating and Modulation of a Hetero-Octameric AMPA Glutamate Receptor.”
Nature. Springer Nature, 2021. https://doi.org/10.1038/s41586-021-03613-0.
ieee: D. Zhang, J. Watson, P. M. Matthews, O. Cais, and I. H. Greger, “Gating and
modulation of a hetero-octameric AMPA glutamate receptor,” Nature, vol.
594. Springer Nature, pp. 454–458, 2021.
ista: Zhang D, Watson J, Matthews PM, Cais O, Greger IH. 2021. Gating and modulation
of a hetero-octameric AMPA glutamate receptor. Nature. 594, 454–458.
mla: Zhang, Danyang, et al. “Gating and Modulation of a Hetero-Octameric AMPA Glutamate
Receptor.” Nature, vol. 594, Springer Nature, 2021, pp. 454–58, doi:10.1038/s41586-021-03613-0.
short: D. Zhang, J. Watson, P.M. Matthews, O. Cais, I.H. Greger, Nature 594 (2021)
454–458.
date_created: 2021-06-13T22:01:33Z
date_published: 2021-06-02T00:00:00Z
date_updated: 2023-08-08T13:59:51Z
day: '02'
department:
- _id: PeJo
doi: 10.1038/s41586-021-03613-0
external_id:
isi:
- '000657238100003'
pmid:
- '34079129'
intvolume: ' 594'
isi: 1
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.1038/s41586-021-03613-0
month: '06'
oa: 1
oa_version: Published Version
page: 454-458
pmid: 1
publication: Nature
publication_identifier:
eissn:
- 1476-4687
issn:
- 0028-0836
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
scopus_import: '1'
status: public
title: Gating and modulation of a hetero-octameric AMPA glutamate receptor
type: journal_article
user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
volume: 594
year: '2021'
...
---
_id: '9550'
abstract:
- lang: eng
text: 'We prove that the energy of any eigenvector of a sum of several independent
large Wigner matrices is equally distributed among these matrices with very high
precision. This shows a particularly strong microcanonical form of the equipartition
principle for quantum systems whose components are modelled by Wigner matrices. '
acknowledgement: The first author is supported in part by Hong Kong RGC Grant GRF
16301519 and NSFC 11871425. The second author is supported in part by ERC Advanced
Grant RANMAT 338804. The third author is supported in part by Swedish Research Council
Grant VR-2017-05195 and the Knut and Alice Wallenberg Foundation
article_number: e44
article_processing_charge: No
article_type: original
author:
- first_name: Zhigang
full_name: Bao, Zhigang
id: 442E6A6C-F248-11E8-B48F-1D18A9856A87
last_name: Bao
orcid: 0000-0003-3036-1475
- first_name: László
full_name: Erdös, László
id: 4DBD5372-F248-11E8-B48F-1D18A9856A87
last_name: Erdös
orcid: 0000-0001-5366-9603
- first_name: Kevin
full_name: Schnelli, Kevin
id: 434AD0AE-F248-11E8-B48F-1D18A9856A87
last_name: Schnelli
orcid: 0000-0003-0954-3231
citation:
ama: Bao Z, Erdös L, Schnelli K. Equipartition principle for Wigner matrices. Forum
of Mathematics, Sigma. 2021;9. doi:10.1017/fms.2021.38
apa: Bao, Z., Erdös, L., & Schnelli, K. (2021). Equipartition principle for
Wigner matrices. Forum of Mathematics, Sigma. Cambridge University Press.
https://doi.org/10.1017/fms.2021.38
chicago: Bao, Zhigang, László Erdös, and Kevin Schnelli. “Equipartition Principle
for Wigner Matrices.” Forum of Mathematics, Sigma. Cambridge University
Press, 2021. https://doi.org/10.1017/fms.2021.38.
ieee: Z. Bao, L. Erdös, and K. Schnelli, “Equipartition principle for Wigner matrices,”
Forum of Mathematics, Sigma, vol. 9. Cambridge University Press, 2021.
ista: Bao Z, Erdös L, Schnelli K. 2021. Equipartition principle for Wigner matrices.
Forum of Mathematics, Sigma. 9, e44.
mla: Bao, Zhigang, et al. “Equipartition Principle for Wigner Matrices.” Forum
of Mathematics, Sigma, vol. 9, e44, Cambridge University Press, 2021, doi:10.1017/fms.2021.38.
short: Z. Bao, L. Erdös, K. Schnelli, Forum of Mathematics, Sigma 9 (2021).
date_created: 2021-06-13T22:01:33Z
date_published: 2021-05-27T00:00:00Z
date_updated: 2023-08-08T14:03:40Z
day: '27'
ddc:
- '510'
department:
- _id: LaEr
doi: 10.1017/fms.2021.38
ec_funded: 1
external_id:
arxiv:
- '2008.07061'
isi:
- '000654960800001'
file:
- access_level: open_access
checksum: 47c986578de132200d41e6d391905519
content_type: application/pdf
creator: cziletti
date_created: 2021-06-15T14:40:45Z
date_updated: 2021-06-15T14:40:45Z
file_id: '9555'
file_name: 2021_ForumMath_Bao.pdf
file_size: 483458
relation: main_file
success: 1
file_date_updated: 2021-06-15T14:40:45Z
has_accepted_license: '1'
intvolume: ' 9'
isi: 1
language:
- iso: eng
month: '05'
oa: 1
oa_version: Published Version
project:
- _id: 258DCDE6-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '338804'
name: Random matrices, universality and disordered quantum systems
publication: Forum of Mathematics, Sigma
publication_identifier:
eissn:
- '20505094'
publication_status: published
publisher: Cambridge University Press
quality_controlled: '1'
scopus_import: '1'
status: public
title: Equipartition principle for Wigner matrices
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: 9
year: '2021'
...
---
_id: '9570'
abstract:
- lang: eng
text: We present conductance-matrix measurements in long, three-terminal hybrid
superconductor-semiconductor nanowires, and compare with theoretical predictions
of a magnetic-field-driven, topological quantum phase transition. By examining
the nonlocal conductance, we identify the closure of the excitation gap in the
bulk of the semiconductor before the emergence of zero-bias peaks, ruling out
spurious gap-closure signatures from localized states. We observe that after the
gap closes, nonlocal signals and zero-bias peaks fluctuate strongly at both ends,
inconsistent with a simple picture of clean topological superconductivity.
acknowledgement: We acknowledge insightful discussions with K. Flensberg, E. B. Hansen,
T. Karzig, R. Lutchyn, D. Pikulin, E. Prada, and R. Aguado. This work was supported
by Microsoft Project Q and the Danmarks Grundforskningsfond. C.M.M. acknowledges
support from the Villum Fonden. A.P.H. and L.C. contributed equally to this work.
article_number: '235201'
article_processing_charge: No
article_type: original
author:
- first_name: Denise
full_name: Puglia, Denise
id: 4D495994-AE37-11E9-AC72-31CAE5697425
last_name: Puglia
- first_name: E. A.
full_name: Martinez, E. A.
last_name: Martinez
- first_name: G. C.
full_name: Ménard, G. C.
last_name: Ménard
- first_name: A.
full_name: Pöschl, A.
last_name: Pöschl
- first_name: S.
full_name: Gronin, S.
last_name: Gronin
- first_name: G. C.
full_name: Gardner, G. C.
last_name: Gardner
- first_name: R.
full_name: Kallaher, R.
last_name: Kallaher
- first_name: M. J.
full_name: Manfra, M. J.
last_name: Manfra
- first_name: C. M.
full_name: Marcus, C. M.
last_name: Marcus
- first_name: Andrew P
full_name: Higginbotham, Andrew P
id: 4AD6785A-F248-11E8-B48F-1D18A9856A87
last_name: Higginbotham
orcid: 0000-0003-2607-2363
- first_name: L.
full_name: Casparis, L.
last_name: Casparis
citation:
ama: Puglia D, Martinez EA, Ménard GC, et al. Closing of the induced gap in a hybrid
superconductor-semiconductor nanowire. Physical Review B. 2021;103(23).
doi:10.1103/PhysRevB.103.235201
apa: Puglia, D., Martinez, E. A., Ménard, G. C., Pöschl, A., Gronin, S., Gardner,
G. C., … Casparis, L. (2021). Closing of the induced gap in a hybrid superconductor-semiconductor
nanowire. Physical Review B. American Physical Society. https://doi.org/10.1103/PhysRevB.103.235201
chicago: Puglia, Denise, E. A. Martinez, G. C. Ménard, A. Pöschl, S. Gronin, G.
C. Gardner, R. Kallaher, et al. “Closing of the Induced Gap in a Hybrid Superconductor-Semiconductor
Nanowire.” Physical Review B. American Physical Society, 2021. https://doi.org/10.1103/PhysRevB.103.235201.
ieee: D. Puglia et al., “Closing of the induced gap in a hybrid superconductor-semiconductor
nanowire,” Physical Review B, vol. 103, no. 23. American Physical Society,
2021.
ista: Puglia D, Martinez EA, Ménard GC, Pöschl A, Gronin S, Gardner GC, Kallaher
R, Manfra MJ, Marcus CM, Higginbotham AP, Casparis L. 2021. Closing of the induced
gap in a hybrid superconductor-semiconductor nanowire. Physical Review B. 103(23),
235201.
mla: Puglia, Denise, et al. “Closing of the Induced Gap in a Hybrid Superconductor-Semiconductor
Nanowire.” Physical Review B, vol. 103, no. 23, 235201, American Physical
Society, 2021, doi:10.1103/PhysRevB.103.235201.
short: D. Puglia, E.A. Martinez, G.C. Ménard, A. Pöschl, S. Gronin, G.C. Gardner,
R. Kallaher, M.J. Manfra, C.M. Marcus, A.P. Higginbotham, L. Casparis, Physical
Review B 103 (2021).
date_created: 2021-06-20T22:01:33Z
date_published: 2021-06-15T00:00:00Z
date_updated: 2023-08-08T14:08:08Z
day: '15'
department:
- _id: AnHi
doi: 10.1103/PhysRevB.103.235201
external_id:
arxiv:
- '2006.01275'
isi:
- '000661512500002'
intvolume: ' 103'
isi: 1
issue: '23'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/2006.01275
month: '06'
oa: 1
oa_version: Preprint
publication: Physical Review B
publication_identifier:
eissn:
- '24699969'
issn:
- '24699950'
publication_status: published
publisher: American Physical Society
quality_controlled: '1'
related_material:
record:
- id: '13080'
relation: research_data
status: public
scopus_import: '1'
status: public
title: Closing of the induced gap in a hybrid superconductor-semiconductor nanowire
type: journal_article
user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
volume: 103
year: '2021'
...
---
_id: '9548'
abstract:
- lang: eng
text: 'We extend the notion of the minimal volume ellipsoid containing a convex
body in Rd to the setting of logarithmically concave functions. We consider a
vast class of logarithmically concave functions whose superlevel sets are concentric
ellipsoids. For a fixed function from this class, we consider the set of all its
“affine” positions. For any log-concave function f on Rd, we consider functions
belonging to this set of “affine” positions, and find the one with the minimal
integral under the condition that it is pointwise greater than or equal to f.
We study the properties of existence and uniqueness of the solution to this problem.
For any s∈[0,+∞), we consider the construction dual to the recently defined John
s-function (Ivanov and Naszódi in Functional John ellipsoids. arXiv preprint:
arXiv:2006.09934, 2020). We prove that such a construction determines a unique
function and call it the Löwner s-function of f. We study the Löwner s-functions
as s tends to zero and to infinity. Finally, extending the notion of the outer
volume ratio, we define the outer integral ratio of a log-concave function and
give an asymptotically tight bound on it.'
acknowledgement: The authors acknowledge the support of the grant of the Russian Government
N 075-15-2019-1926.
article_processing_charge: No
article_type: original
author:
- first_name: Grigory
full_name: Ivanov, Grigory
id: 87744F66-5C6F-11EA-AFE0-D16B3DDC885E
last_name: Ivanov
- first_name: Igor
full_name: Tsiutsiurupa, Igor
last_name: Tsiutsiurupa
citation:
ama: Ivanov G, Tsiutsiurupa I. Functional Löwner ellipsoids. Journal of Geometric
Analysis. 2021;31:11493-11528. doi:10.1007/s12220-021-00691-4
apa: Ivanov, G., & Tsiutsiurupa, I. (2021). Functional Löwner ellipsoids. Journal
of Geometric Analysis. Springer. https://doi.org/10.1007/s12220-021-00691-4
chicago: Ivanov, Grigory, and Igor Tsiutsiurupa. “Functional Löwner Ellipsoids.”
Journal of Geometric Analysis. Springer, 2021. https://doi.org/10.1007/s12220-021-00691-4.
ieee: G. Ivanov and I. Tsiutsiurupa, “Functional Löwner ellipsoids,” Journal
of Geometric Analysis, vol. 31. Springer, pp. 11493–11528, 2021.
ista: Ivanov G, Tsiutsiurupa I. 2021. Functional Löwner ellipsoids. Journal of Geometric
Analysis. 31, 11493–11528.
mla: Ivanov, Grigory, and Igor Tsiutsiurupa. “Functional Löwner Ellipsoids.” Journal
of Geometric Analysis, vol. 31, Springer, 2021, pp. 11493–528, doi:10.1007/s12220-021-00691-4.
short: G. Ivanov, I. Tsiutsiurupa, Journal of Geometric Analysis 31 (2021) 11493–11528.
date_created: 2021-06-13T22:01:32Z
date_published: 2021-05-31T00:00:00Z
date_updated: 2023-08-08T14:04:49Z
day: '31'
department:
- _id: UlWa
doi: 10.1007/s12220-021-00691-4
external_id:
arxiv:
- '2008.09543'
isi:
- '000656507500001'
intvolume: ' 31'
isi: 1
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/2008.09543
month: '05'
oa: 1
oa_version: Preprint
page: 11493-11528
publication: Journal of Geometric Analysis
publication_identifier:
eissn:
- 1559-002X
issn:
- 1050-6926
publication_status: published
publisher: Springer
quality_controlled: '1'
scopus_import: '1'
status: public
title: Functional Löwner ellipsoids
type: journal_article
user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
volume: 31
year: '2021'
...
---
_id: '13080'
abstract:
- lang: eng
text: "Data for the manuscript 'Closing of the Induced Gap in a Hybrid Superconductor-Semiconductor
Nanowire' ([2006.01275] Closing of the Induced Gap in a Hybrid Superconductor-Semiconductor
Nanowire (arxiv.org))\r\n\r\nWe upload a pdf with extended data sets, and the
raw data for these extended datasets as well."
article_processing_charge: No
author:
- first_name: Denise
full_name: Puglia, Denise
id: 4D495994-AE37-11E9-AC72-31CAE5697425
last_name: Puglia
- first_name: Esteban
full_name: Martinez, Esteban
last_name: Martinez
- first_name: Gerbold
full_name: Menard, Gerbold
last_name: Menard
- first_name: Andreas
full_name: Pöschl, Andreas
last_name: Pöschl
- first_name: Sergei
full_name: Gronin, Sergei
last_name: Gronin
- first_name: Geoffrey
full_name: Gardner, Geoffrey
last_name: Gardner
- first_name: Ray
full_name: Kallaher, Ray
last_name: Kallaher
- first_name: Michael
full_name: Manfra, Michael
last_name: Manfra
- first_name: Charles
full_name: Marcus, Charles
last_name: Marcus
- first_name: Andrew P
full_name: Higginbotham, Andrew P
id: 4AD6785A-F248-11E8-B48F-1D18A9856A87
last_name: Higginbotham
orcid: 0000-0003-2607-2363
- first_name: Lucas
full_name: Casparis, Lucas
last_name: Casparis
citation:
ama: Puglia D, Martinez E, Menard G, et al. Data for ’Closing of the Induced Gap
in a Hybrid Superconductor-Semiconductor Nanowire. 2021. doi:10.5281/ZENODO.4592435
apa: Puglia, D., Martinez, E., Menard, G., Pöschl, A., Gronin, S., Gardner, G.,
… Casparis, L. (2021). Data for ’Closing of the Induced Gap in a Hybrid Superconductor-Semiconductor
Nanowire. Zenodo. https://doi.org/10.5281/ZENODO.4592435
chicago: Puglia, Denise, Esteban Martinez, Gerbold Menard, Andreas Pöschl, Sergei
Gronin, Geoffrey Gardner, Ray Kallaher, et al. “Data for ’Closing of the Induced
Gap in a Hybrid Superconductor-Semiconductor Nanowire.” Zenodo, 2021. https://doi.org/10.5281/ZENODO.4592435.
ieee: D. Puglia et al., “Data for ’Closing of the Induced Gap in a Hybrid
Superconductor-Semiconductor Nanowire.” Zenodo, 2021.
ista: Puglia D, Martinez E, Menard G, Pöschl A, Gronin S, Gardner G, Kallaher R,
Manfra M, Marcus C, Higginbotham AP, Casparis L. 2021. Data for ’Closing of the
Induced Gap in a Hybrid Superconductor-Semiconductor Nanowire, Zenodo, 10.5281/ZENODO.4592435.
mla: Puglia, Denise, et al. Data for ’Closing of the Induced Gap in a Hybrid
Superconductor-Semiconductor Nanowire. Zenodo, 2021, doi:10.5281/ZENODO.4592435.
short: D. Puglia, E. Martinez, G. Menard, A. Pöschl, S. Gronin, G. Gardner, R. Kallaher,
M. Manfra, C. Marcus, A.P. Higginbotham, L. Casparis, (2021).
date_created: 2023-05-23T17:11:28Z
date_published: 2021-03-09T00:00:00Z
date_updated: 2023-08-08T14:08:07Z
day: '09'
ddc:
- '530'
department:
- _id: AnHi
doi: 10.5281/ZENODO.4592435
main_file_link:
- open_access: '1'
url: https://doi.org/10.5281/zenodo.4592460
month: '03'
oa: 1
oa_version: Published Version
publisher: Zenodo
related_material:
link:
- relation: software
url: https://github.com/caslu85/Induced-Gap-Closing-Shared/tree/1.1.3
record:
- id: '9570'
relation: used_in_publication
status: public
status: public
title: Data for 'Closing of the Induced Gap in a Hybrid Superconductor-Semiconductor
Nanowire
type: research_data_reference
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
year: '2021'
...
---
_id: '9569'
abstract:
- lang: eng
text: We report the synthesis and characterization of graphene functionalized with
iron (Fe3+) oxide (G-Fe3O4) nanohybrids for radio-frequency magnetic hyperthermia
application. We adopted the wet chemical procedure, using various contents of
Fe3O4 (magnetite) from 0–100% for making two-dimensional graphene–Fe3O4 nanohybrids.
The homogeneous dispersal of Fe3O4 nanoparticles decorated on the graphene surface
combined with their biocompatibility and high thermal conductivity make them an
excellent material for magnetic hyperthermia. The morphological and magnetic properties
of the nanohybrids were studied using scanning electron microscopy (SEM) and a
vibrating sample magnetometer (VSM), respectively. The smart magnetic platforms
were exposed to an alternating current (AC) magnetic field of 633 kHz and of strength
9.1 mT for studying their hyperthermic performance. The localized antitumor effects
were investigated with artificial neural network modeling. A neural net time-series
model was developed for the assessment of the best nanohybrid composition to serve
the purpose with an accuracy close to 100%. Six Nonlinear Autoregressive with
External Input (NARX) models were obtained, one for each of the components. The
assessment of the accuracy of the predicted results has been done on the basis
of Mean Squared Error (MSE). The highest Mean Squared Error value was obtained
for the nanohybrid containing 45% magnetite and 55% graphene (F45G55) in the training
phase i.e., 0.44703, which is where the model achieved optimal results after 71
epochs. The F45G55 nanohybrid was found to be the best for hyperthermia applications
in low dosage with the highest specific absorption rate (SAR) and mean squared
error values.
acknowledgement: The research is funded by Higher Education Commission (HEC) Pakistan
under start-up research grant program (SRGP) Project no. 2454.
article_processing_charge: No
article_type: original
author:
- first_name: M. S.
full_name: Dar, M. S.
last_name: Dar
- first_name: Khush Bakhat
full_name: Akram, Khush Bakhat
last_name: Akram
- first_name: Ayesha
full_name: Sohail, Ayesha
last_name: Sohail
- first_name: Fatima
full_name: Arif, Fatima
last_name: Arif
- first_name: Fatemeh
full_name: Zabihi, Fatemeh
last_name: Zabihi
- first_name: Shengyuan
full_name: Yang, Shengyuan
last_name: Yang
- first_name: Shamsa
full_name: Munir, Shamsa
last_name: Munir
- first_name: Meifang
full_name: Zhu, Meifang
last_name: Zhu
- first_name: M.
full_name: Abid, M.
last_name: Abid
- first_name: Muhammad
full_name: Nauman, Muhammad
id: 32c21954-2022-11eb-9d5f-af9f93c24e71
last_name: Nauman
orcid: 0000-0002-2111-4846
citation:
ama: Dar MS, Akram KB, Sohail A, et al. Heat induction in two-dimensional graphene–Fe3O4
nanohybrids for magnetic hyperthermia applications with artificial neural network
modeling. RSC Advances. 2021;11(35):21702-21715. doi:10.1039/d1ra03428f
apa: Dar, M. S., Akram, K. B., Sohail, A., Arif, F., Zabihi, F., Yang, S., … Nauman,
M. (2021). Heat induction in two-dimensional graphene–Fe3O4 nanohybrids for magnetic
hyperthermia applications with artificial neural network modeling. RSC Advances.
Royal Society of Chemistry. https://doi.org/10.1039/d1ra03428f
chicago: Dar, M. S., Khush Bakhat Akram, Ayesha Sohail, Fatima Arif, Fatemeh Zabihi,
Shengyuan Yang, Shamsa Munir, Meifang Zhu, M. Abid, and Muhammad Nauman. “Heat
Induction in Two-Dimensional Graphene–Fe3O4 Nanohybrids for Magnetic Hyperthermia
Applications with Artificial Neural Network Modeling.” RSC Advances. Royal
Society of Chemistry, 2021. https://doi.org/10.1039/d1ra03428f.
ieee: M. S. Dar et al., “Heat induction in two-dimensional graphene–Fe3O4
nanohybrids for magnetic hyperthermia applications with artificial neural network
modeling,” RSC Advances, vol. 11, no. 35. Royal Society of Chemistry, pp.
21702–21715, 2021.
ista: Dar MS, Akram KB, Sohail A, Arif F, Zabihi F, Yang S, Munir S, Zhu M, Abid
M, Nauman M. 2021. Heat induction in two-dimensional graphene–Fe3O4 nanohybrids
for magnetic hyperthermia applications with artificial neural network modeling.
RSC Advances. 11(35), 21702–21715.
mla: Dar, M. S., et al. “Heat Induction in Two-Dimensional Graphene–Fe3O4 Nanohybrids
for Magnetic Hyperthermia Applications with Artificial Neural Network Modeling.”
RSC Advances, vol. 11, no. 35, Royal Society of Chemistry, 2021, pp. 21702–15,
doi:10.1039/d1ra03428f.
short: M.S. Dar, K.B. Akram, A. Sohail, F. Arif, F. Zabihi, S. Yang, S. Munir, M.
Zhu, M. Abid, M. Nauman, RSC Advances 11 (2021) 21702–21715.
date_created: 2021-06-19T07:27:45Z
date_published: 2021-06-18T00:00:00Z
date_updated: 2023-08-08T14:23:21Z
day: '18'
ddc:
- '540'
department:
- _id: KiMo
doi: 10.1039/d1ra03428f
external_id:
isi:
- '000665644000048'
file:
- access_level: open_access
checksum: cd582d67ace7151078e46b3a896871a9
content_type: application/pdf
creator: asandaue
date_created: 2021-06-23T13:09:34Z
date_updated: 2021-06-23T13:09:34Z
file_id: '9596'
file_name: 2021_RSCAdvances_Dar.pdf
file_size: 2114557
relation: main_file
success: 1
file_date_updated: 2021-06-23T13:09:34Z
has_accepted_license: '1'
intvolume: ' 11'
isi: 1
issue: '35'
language:
- iso: eng
license: https://creativecommons.org/licenses/by/3.0/
month: '06'
oa: 1
oa_version: Published Version
page: 21702-21715
publication: RSC Advances
publication_identifier:
eissn:
- 2046-2069
publication_status: published
publisher: Royal Society of Chemistry
quality_controlled: '1'
status: public
title: Heat induction in two-dimensional graphene–Fe3O4 nanohybrids for magnetic hyperthermia
applications with artificial neural network modeling
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/3.0/legalcode
name: Creative Commons Attribution 3.0 Unported (CC BY 3.0)
short: CC BY (3.0)
type: journal_article
user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
volume: 11
year: '2021'
...
---
_id: '9558'
abstract:
- lang: eng
text: "We show that turbulent dynamics that arise in simulations of the three-dimensional
Navier--Stokes equations in a triply-periodic domain under sinusoidal forcing
can be described as transient visits to the neighborhoods of unstable time-periodic
solutions. Based on this description, we reduce the original system with more
than 10^5 degrees of freedom to a 17-node Markov chain where each node corresponds
to the neighborhood of a periodic orbit. The model accurately reproduces long-term
averages of the system's observables as weighted sums over the periodic orbits.\r\n"
acknowledged_ssus:
- _id: ScienComp
acknowledgement: "We thank the referees for improving this Letter with their comments.
We acknowledge stimulating discussions with\r\nH. Edelsbrunner. This work was supported
by Grant No. 662960 from the Simons Foundation (B. H.). The numerical calculations
were performed at TUBITAK ULAKBIM High Performance and Grid Computing Center (TRUBA
resources) and IST Austria High Performance Computing cluster."
article_number: '244502'
article_processing_charge: No
article_type: letter_note
author:
- first_name: Gökhan
full_name: Yalniz, Gökhan
id: 66E74FA2-D8BF-11E9-8249-8DE2E5697425
last_name: Yalniz
orcid: 0000-0002-8490-9312
- first_name: Björn
full_name: Hof, Björn
id: 3A374330-F248-11E8-B48F-1D18A9856A87
last_name: Hof
orcid: 0000-0003-2057-2754
- first_name: Nazmi B
full_name: Budanur, Nazmi B
id: 3EA1010E-F248-11E8-B48F-1D18A9856A87
last_name: Budanur
orcid: 0000-0003-0423-5010
citation:
ama: Yalniz G, Hof B, Budanur NB. Coarse graining the state space of a turbulent
flow using periodic orbits. Physical Review Letters. 2021;126(24). doi:10.1103/PhysRevLett.126.244502
apa: Yalniz, G., Hof, B., & Budanur, N. B. (2021). Coarse graining the state
space of a turbulent flow using periodic orbits. Physical Review Letters.
American Physical Society. https://doi.org/10.1103/PhysRevLett.126.244502
chicago: Yalniz, Gökhan, Björn Hof, and Nazmi B Budanur. “Coarse Graining the State
Space of a Turbulent Flow Using Periodic Orbits.” Physical Review Letters.
American Physical Society, 2021. https://doi.org/10.1103/PhysRevLett.126.244502.
ieee: G. Yalniz, B. Hof, and N. B. Budanur, “Coarse graining the state space of
a turbulent flow using periodic orbits,” Physical Review Letters, vol.
126, no. 24. American Physical Society, 2021.
ista: Yalniz G, Hof B, Budanur NB. 2021. Coarse graining the state space of a turbulent
flow using periodic orbits. Physical Review Letters. 126(24), 244502.
mla: Yalniz, Gökhan, et al. “Coarse Graining the State Space of a Turbulent Flow
Using Periodic Orbits.” Physical Review Letters, vol. 126, no. 24, 244502,
American Physical Society, 2021, doi:10.1103/PhysRevLett.126.244502.
short: G. Yalniz, B. Hof, N.B. Budanur, Physical Review Letters 126 (2021).
date_created: 2021-06-16T15:45:36Z
date_published: 2021-06-18T00:00:00Z
date_updated: 2023-08-08T14:08:36Z
day: '18'
department:
- _id: GradSch
- _id: BjHo
doi: 10.1103/PhysRevLett.126.244502
external_id:
arxiv:
- '2007.02584'
isi:
- '000663310100008'
intvolume: ' 126'
isi: 1
issue: '24'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/2007.02584
month: '06'
oa: 1
oa_version: Preprint
project:
- _id: 238598C6-32DE-11EA-91FC-C7463DDC885E
grant_number: '662960'
name: 'Revisiting the Turbulence Problem Using Statistical Mechanics: Experimental
Studies on Transitional and Turbulent Flows'
publication: Physical Review Letters
publication_identifier:
eissn:
- 1079-7114
issn:
- 0031-9007
publication_status: published
publisher: American Physical Society
quality_controlled: '1'
related_material:
link:
- description: News on IST Homepage
relation: press_release
url: https://ist.ac.at/en/news/turbulent-flow-simplified/
status: public
title: Coarse graining the state space of a turbulent flow using periodic orbits
type: journal_article
user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
volume: 126
year: '2021'
...
---
_id: '9607'
abstract:
- lang: eng
text: While high risk of failure is an inherent part of developing innovative therapies,
it can be reduced by adherence to evidence-based rigorous research practices.
Numerous analyses conducted to date have clearly identified measures that need
to be taken to improve research rigor. Supported through the European Union's
Innovative Medicines Initiative, the EQIPD consortium has developed a novel preclinical
research quality system that can be applied in both public and private sectors
and is free for anyone to use. The EQIPD Quality System was designed to be suited
to boost innovation by ensuring the generation of robust and reliable preclinical
data while being lean, effective and not becoming a burden that could negatively
impact the freedom to explore scientific questions. EQIPD defines research quality
as the extent to which research data are fit for their intended use. Fitness,
in this context, is defined by the stakeholders, who are the scientists directly
involved in the research, but also their funders, sponsors, publishers, research
tool manufacturers and collaboration partners such as peers in a multi-site research
project. The essence of the EQIPD Quality System is the set of 18 core requirements
that can be addressed flexibly, according to user-specific needs and following
a user-defined trajectory. The EQIPD Quality System proposes guidance on expectations
for quality-related measures, defines criteria for adequate processes (i.e., performance
standards) and provides examples of how such measures can be developed and implemented.
However, it does not prescribe any pre-determined solutions. EQIPD has also developed
tools (for optional use) to support users in implementing the system and assessment
services for those research units that successfully implement the quality system
and seek formal accreditation. Building upon the feedback from users and continuous
improvement, a sustainable EQIPD Quality System will ultimately serve the entire
community of scientists conducting non-regulated preclinical research, by helping
them generate reliable data that are fit for their intended use.
acknowledgement: This project has received funding from the Innovative Medicines Initiative
2 Joint Undertaking under grant agreement No 777364. This Joint Undertaking receives
support from the European Union’s Horizon 2020 research and innovation programme
and EFPIA. The authors are very grateful to Martin Heinrich (Abbvie, Ludwigshafen,
Germany) for the exceptional IT support and programming the EQIPD Planning Tool
and the Creator Tool and to Dr Shai Silberberg (NINDS, USA), Dr. Renza Roncarati
(PAASP Italy) and Dr Judith Homberg (Radboud University, Nijmegen) for highly stimulating
contributions to the discussions and comments on earlier versions of this manuscript.
We also wish to express our thanks to Dr. Sara Stöber (concentris research management
GmbH, Fürstenfeldbruck, Germany) for excellent and continuous support of this project.
Creation of the EQIPD Stakeholder group was supported by Noldus Information Technology
bv (Wageningen, the Netherlands).
article_processing_charge: No
article_type: original
author:
- first_name: Anton
full_name: Bespalov, Anton
last_name: Bespalov
- first_name: René
full_name: Bernard, René
last_name: Bernard
- first_name: Anja
full_name: Gilis, Anja
last_name: Gilis
- first_name: Björn
full_name: Gerlach, Björn
last_name: Gerlach
- first_name: Javier
full_name: Guillén, Javier
last_name: Guillén
- first_name: Vincent
full_name: Castagné, Vincent
last_name: Castagné
- first_name: Isabel A.
full_name: Lefevre, Isabel A.
last_name: Lefevre
- first_name: Fiona
full_name: Ducrey, Fiona
last_name: Ducrey
- first_name: Lee
full_name: Monk, Lee
last_name: Monk
- first_name: Sandrine
full_name: Bongiovanni, Sandrine
last_name: Bongiovanni
- first_name: Bruce
full_name: Altevogt, Bruce
last_name: Altevogt
- first_name: María
full_name: Arroyo-Araujo, María
last_name: Arroyo-Araujo
- first_name: Lior
full_name: Bikovski, Lior
last_name: Bikovski
- first_name: Natasja
full_name: De Bruin, Natasja
last_name: De Bruin
- first_name: Esmeralda
full_name: Castaños-Vélez, Esmeralda
last_name: Castaños-Vélez
- first_name: Alexander
full_name: Dityatev, Alexander
last_name: Dityatev
- first_name: Christoph H.
full_name: Emmerich, Christoph H.
last_name: Emmerich
- first_name: Raafat
full_name: Fares, Raafat
last_name: Fares
- first_name: Chantelle
full_name: Ferland-Beckham, Chantelle
last_name: Ferland-Beckham
- first_name: Christelle
full_name: Froger-Colléaux, Christelle
last_name: Froger-Colléaux
- first_name: Valerie
full_name: Gailus-Durner, Valerie
last_name: Gailus-Durner
- first_name: Sabine M.
full_name: Hölter, Sabine M.
last_name: Hölter
- first_name: Martine Cj
full_name: Hofmann, Martine Cj
last_name: Hofmann
- first_name: Patricia
full_name: Kabitzke, Patricia
last_name: Kabitzke
- first_name: Martien Jh
full_name: Kas, Martien Jh
last_name: Kas
- first_name: Claudia
full_name: Kurreck, Claudia
last_name: Kurreck
- first_name: Paul
full_name: Moser, Paul
last_name: Moser
- first_name: Malgorzata
full_name: Pietraszek, Malgorzata
last_name: Pietraszek
- first_name: Piotr
full_name: Popik, Piotr
last_name: Popik
- first_name: Heidrun
full_name: Potschka, Heidrun
last_name: Potschka
- first_name: Ernesto
full_name: Prado Montes De Oca, Ernesto
last_name: Prado Montes De Oca
- first_name: Leonardo
full_name: Restivo, Leonardo
last_name: Restivo
- first_name: Gernot
full_name: Riedel, Gernot
last_name: Riedel
- first_name: Merel
full_name: Ritskes-Hoitinga, Merel
last_name: Ritskes-Hoitinga
- first_name: Janko
full_name: Samardzic, Janko
last_name: Samardzic
- first_name: Michael
full_name: Schunn, Michael
id: 4272DB4A-F248-11E8-B48F-1D18A9856A87
last_name: Schunn
orcid: 0000-0003-4326-5300
- first_name: Claudia
full_name: Stöger, Claudia
last_name: Stöger
- first_name: Vootele
full_name: Voikar, Vootele
last_name: Voikar
- first_name: Jan
full_name: Vollert, Jan
last_name: Vollert
- first_name: Kimberley E.
full_name: Wever, Kimberley E.
last_name: Wever
- first_name: Kathleen
full_name: Wuyts, Kathleen
last_name: Wuyts
- first_name: Malcolm R.
full_name: Macleod, Malcolm R.
last_name: Macleod
- first_name: Ulrich
full_name: Dirnagl, Ulrich
last_name: Dirnagl
- first_name: Thomas
full_name: Steckler, Thomas
last_name: Steckler
citation:
ama: Bespalov A, Bernard R, Gilis A, et al. Introduction to the EQIPD quality system.
eLife. 2021;10. doi:10.7554/eLife.63294
apa: Bespalov, A., Bernard, R., Gilis, A., Gerlach, B., Guillén, J., Castagné, V.,
… Steckler, T. (2021). Introduction to the EQIPD quality system. ELife.
eLife Sciences Publications. https://doi.org/10.7554/eLife.63294
chicago: Bespalov, Anton, René Bernard, Anja Gilis, Björn Gerlach, Javier Guillén,
Vincent Castagné, Isabel A. Lefevre, et al. “Introduction to the EQIPD Quality
System.” ELife. eLife Sciences Publications, 2021. https://doi.org/10.7554/eLife.63294.
ieee: A. Bespalov et al., “Introduction to the EQIPD quality system,” eLife,
vol. 10. eLife Sciences Publications, 2021.
ista: Bespalov A, Bernard R, Gilis A, Gerlach B, Guillén J, Castagné V, Lefevre
IA, Ducrey F, Monk L, Bongiovanni S, Altevogt B, Arroyo-Araujo M, Bikovski L,
De Bruin N, Castaños-Vélez E, Dityatev A, Emmerich CH, Fares R, Ferland-Beckham
C, Froger-Colléaux C, Gailus-Durner V, Hölter SM, Hofmann MC, Kabitzke P, Kas
MJ, Kurreck C, Moser P, Pietraszek M, Popik P, Potschka H, Prado Montes De Oca
E, Restivo L, Riedel G, Ritskes-Hoitinga M, Samardzic J, Schunn M, Stöger C, Voikar
V, Vollert J, Wever KE, Wuyts K, Macleod MR, Dirnagl U, Steckler T. 2021. Introduction
to the EQIPD quality system. eLife. 10.
mla: Bespalov, Anton, et al. “Introduction to the EQIPD Quality System.” ELife,
vol. 10, eLife Sciences Publications, 2021, doi:10.7554/eLife.63294.
short: A. Bespalov, R. Bernard, A. Gilis, B. Gerlach, J. Guillén, V. Castagné, I.A.
Lefevre, F. Ducrey, L. Monk, S. Bongiovanni, B. Altevogt, M. Arroyo-Araujo, L.
Bikovski, N. De Bruin, E. Castaños-Vélez, A. Dityatev, C.H. Emmerich, R. Fares,
C. Ferland-Beckham, C. Froger-Colléaux, V. Gailus-Durner, S.M. Hölter, M.C. Hofmann,
P. Kabitzke, M.J. Kas, C. Kurreck, P. Moser, M. Pietraszek, P. Popik, H. Potschka,
E. Prado Montes De Oca, L. Restivo, G. Riedel, M. Ritskes-Hoitinga, J. Samardzic,
M. Schunn, C. Stöger, V. Voikar, J. Vollert, K.E. Wever, K. Wuyts, M.R. Macleod,
U. Dirnagl, T. Steckler, ELife 10 (2021).
date_created: 2021-06-27T22:01:49Z
date_published: 2021-05-24T00:00:00Z
date_updated: 2023-08-10T13:36:50Z
day: '24'
ddc:
- '570'
department:
- _id: PreCl
doi: 10.7554/eLife.63294
external_id:
isi:
- '000661272000001'
pmid:
- '34028353'
file:
- access_level: open_access
checksum: 885b746051a7a6b6e24e3d2781a48fde
content_type: application/pdf
creator: asandaue
date_created: 2021-06-28T11:35:30Z
date_updated: 2021-06-28T11:35:30Z
file_id: '9609'
file_name: 2021_ELife_Bespalov.pdf
file_size: 2500720
relation: main_file
success: 1
file_date_updated: 2021-06-28T11:35:30Z
has_accepted_license: '1'
intvolume: ' 10'
isi: 1
language:
- iso: eng
month: '05'
oa: 1
oa_version: Published Version
pmid: 1
publication: eLife
publication_identifier:
eissn:
- 2050084X
publication_status: published
publisher: eLife Sciences Publications
quality_controlled: '1'
scopus_import: '1'
status: public
title: Introduction to the EQIPD quality system
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: 10
year: '2021'
...
---
_id: '9601'
abstract:
- lang: eng
text: 'In mammalian genomes, differentially methylated regions (DMRs) and histone
marks including trimethylation of histone 3 lysine 27 (H3K27me3) at imprinted
genes are asymmetrically inherited to control parentally-biased gene expression.
However, neither parent-of-origin-specific transcription nor imprints have been
comprehensively mapped at the blastocyst stage of preimplantation development.
Here, we address this by integrating transcriptomic and epigenomic approaches
in mouse preimplantation embryos. We find that seventy-one genes exhibit previously
unreported parent-of-origin-specific expression in blastocysts (nBiX: novel blastocyst-imprinted
expressed). Uniparental expression of nBiX genes disappears soon after implantation.
Micro-whole-genome bisulfite sequencing (µWGBS) of individual uniparental blastocysts
detects 859 DMRs. We further find that 16% of nBiX genes are associated with a
DMR, whereas most are associated with parentally-biased H3K27me3, suggesting a
role for Polycomb-mediated imprinting in blastocysts. nBiX genes are clustered:
five clusters contained at least one published imprinted gene, and five clusters
exclusively contained nBiX genes. These data suggest that early development undergoes
a complex program of stage-specific imprinting involving different tiers of regulation.'
acknowledgement: The authors thank Robert Feil and Anton Wutz for helpful discussions
and comments, Samuel Collombet and Peter Fraser for sharing embryo TAD coordinates,
and Andy Riddel at the Cambridge Stem Cell Institute and Thomas Sauer at the Max
Perutz Laboratories FACS facility for flow-sorting. We thank the team of the Biomedical
Sequencing Facility at the CeMM and the Vienna Biocenter Core Facilities (VBCF)
for support with next-generation sequencing. We are grateful to animal care teams
at the University of Bath and MRC Harwell. A.C.F.P. acknowledges support from the
UK Medical Research Council (MR/N000080/1 and MR/N020294/1) and Biotechnology and
Biological Sciences Research Council (BB/P009506/1). L.S. is part of the FWF doctoral
programme SMICH and supported by an Austrian Academy of Sciences DOC Fellowship.
M.L. is funded by a Vienna Research Group for Young Investigators grant (VRG14-006)
by the Vienna Science and Technology Fund (WWTF) and by the Austrian Science Fund
FWF (I3786 and P31334).
article_number: '3804'
article_processing_charge: No
article_type: original
author:
- first_name: Laura
full_name: Santini, Laura
last_name: Santini
- first_name: Florian
full_name: Halbritter, Florian
last_name: Halbritter
- first_name: Fabian
full_name: Titz-Teixeira, Fabian
last_name: Titz-Teixeira
- first_name: Toru
full_name: Suzuki, Toru
last_name: Suzuki
- first_name: Maki
full_name: Asami, Maki
last_name: Asami
- first_name: Xiaoyan
full_name: Ma, Xiaoyan
last_name: Ma
- first_name: Julia
full_name: Ramesmayer, Julia
last_name: Ramesmayer
- first_name: Andreas
full_name: Lackner, Andreas
last_name: Lackner
- first_name: Nick
full_name: Warr, Nick
last_name: Warr
- first_name: Florian
full_name: Pauler, Florian
id: 48EA0138-F248-11E8-B48F-1D18A9856A87
last_name: Pauler
orcid: 0000-0002-7462-0048
- first_name: Simon
full_name: Hippenmeyer, Simon
id: 37B36620-F248-11E8-B48F-1D18A9856A87
last_name: Hippenmeyer
orcid: 0000-0003-2279-1061
- first_name: Ernest
full_name: Laue, Ernest
last_name: Laue
- first_name: Matthias
full_name: Farlik, Matthias
last_name: Farlik
- first_name: Christoph
full_name: Bock, Christoph
last_name: Bock
- first_name: Andreas
full_name: Beyer, Andreas
last_name: Beyer
- first_name: Anthony C.F.
full_name: Perry, Anthony C.F.
last_name: Perry
- first_name: Martin
full_name: Leeb, Martin
last_name: Leeb
citation:
ama: Santini L, Halbritter F, Titz-Teixeira F, et al. Genomic imprinting in mouse
blastocysts is predominantly associated with H3K27me3. Nature Communications.
2021;12(1). doi:10.1038/s41467-021-23510-4
apa: Santini, L., Halbritter, F., Titz-Teixeira, F., Suzuki, T., Asami, M., Ma,
X., … Leeb, M. (2021). Genomic imprinting in mouse blastocysts is predominantly
associated with H3K27me3. Nature Communications. Springer Nature. https://doi.org/10.1038/s41467-021-23510-4
chicago: Santini, Laura, Florian Halbritter, Fabian Titz-Teixeira, Toru Suzuki,
Maki Asami, Xiaoyan Ma, Julia Ramesmayer, et al. “Genomic Imprinting in Mouse
Blastocysts Is Predominantly Associated with H3K27me3.” Nature Communications.
Springer Nature, 2021. https://doi.org/10.1038/s41467-021-23510-4.
ieee: L. Santini et al., “Genomic imprinting in mouse blastocysts is predominantly
associated with H3K27me3,” Nature Communications, vol. 12, no. 1. Springer
Nature, 2021.
ista: Santini L, Halbritter F, Titz-Teixeira F, Suzuki T, Asami M, Ma X, Ramesmayer
J, Lackner A, Warr N, Pauler F, Hippenmeyer S, Laue E, Farlik M, Bock C, Beyer
A, Perry ACF, Leeb M. 2021. Genomic imprinting in mouse blastocysts is predominantly
associated with H3K27me3. Nature Communications. 12(1), 3804.
mla: Santini, Laura, et al. “Genomic Imprinting in Mouse Blastocysts Is Predominantly
Associated with H3K27me3.” Nature Communications, vol. 12, no. 1, 3804,
Springer Nature, 2021, doi:10.1038/s41467-021-23510-4.
short: L. Santini, F. Halbritter, F. Titz-Teixeira, T. Suzuki, M. Asami, X. Ma,
J. Ramesmayer, A. Lackner, N. Warr, F. Pauler, S. Hippenmeyer, E. Laue, M. Farlik,
C. Bock, A. Beyer, A.C.F. Perry, M. Leeb, Nature Communications 12 (2021).
date_created: 2021-06-27T22:01:46Z
date_published: 2021-07-12T00:00:00Z
date_updated: 2023-08-10T13:53:23Z
day: '12'
ddc:
- '570'
department:
- _id: SiHi
doi: 10.1038/s41467-021-23510-4
external_id:
isi:
- '000667248600005'
file:
- access_level: open_access
checksum: 75dd89d09945185b2d14b2434a0bcb50
content_type: application/pdf
creator: asandaue
date_created: 2021-06-28T08:04:22Z
date_updated: 2021-06-28T08:04:22Z
file_id: '9608'
file_name: 2021_NatureCommunications_Santini.pdf
file_size: 2156554
relation: main_file
success: 1
file_date_updated: 2021-06-28T08:04:22Z
has_accepted_license: '1'
intvolume: ' 12'
isi: 1
issue: '1'
language:
- iso: eng
month: '07'
oa: 1
oa_version: Published Version
publication: Nature Communications
publication_identifier:
eissn:
- '20411723'
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
scopus_import: '1'
status: public
title: Genomic imprinting in mouse blastocysts is predominantly associated with H3K27me3
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: journal_article
user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
volume: 12
year: '2021'
...
---
_id: '9602'
abstract:
- lang: eng
text: "An ordered graph is a graph with a linear ordering on its vertex set. We
prove that for every positive integer k, there exists a constant ck > 0 such that
any ordered graph G on n vertices with the property that neither G nor its complement
contains an induced monotone path of size k, has either a clique or an independent
set of size at least n^ck . This strengthens a result of Bousquet, Lagoutte, and
Thomassé, who proved the analogous result for unordered graphs.\r\nA key idea
of the above paper was to show that any unordered graph on n vertices that does
not contain an induced path of size k, and whose maximum degree is at most c(k)n
for some small c(k) > 0, contains two disjoint linear size subsets with no edge
between them. This approach fails for ordered graphs, because the analogous statement
is false for k ≥ 3, by a construction of Fox. We provide some further examples
showing that this statement also fails for ordered graphs avoiding other ordered
trees."
acknowledgement: We would like to thank the anonymous referees for their useful comments
and suggestions. János Pach is partially supported by Austrian Science Fund (FWF)
grant Z 342-N31 and by ERC Advanced grant “GeoScape.” István Tomon is partially
supported by Swiss National Science Foundation grant no. 200021_196965, and thanks
the support of MIPT Moscow. Both authors are partially supported by The Russian
Government in the framework of MegaGrant no. 075-15-2019-1926.
article_processing_charge: No
article_type: original
author:
- first_name: János
full_name: Pach, János
id: E62E3130-B088-11EA-B919-BF823C25FEA4
last_name: Pach
- first_name: István
full_name: Tomon, István
last_name: Tomon
citation:
ama: Pach J, Tomon I. Erdős-Hajnal-type results for monotone paths. Journal of
Combinatorial Theory Series B. 2021;151:21-37. doi:10.1016/j.jctb.2021.05.004
apa: Pach, J., & Tomon, I. (2021). Erdős-Hajnal-type results for monotone paths.
Journal of Combinatorial Theory. Series B. Elsevier. https://doi.org/10.1016/j.jctb.2021.05.004
chicago: Pach, János, and István Tomon. “Erdős-Hajnal-Type Results for Monotone
Paths.” Journal of Combinatorial Theory. Series B. Elsevier, 2021. https://doi.org/10.1016/j.jctb.2021.05.004.
ieee: J. Pach and I. Tomon, “Erdős-Hajnal-type results for monotone paths,” Journal
of Combinatorial Theory. Series B, vol. 151. Elsevier, pp. 21–37, 2021.
ista: Pach J, Tomon I. 2021. Erdős-Hajnal-type results for monotone paths. Journal
of Combinatorial Theory. Series B. 151, 21–37.
mla: Pach, János, and István Tomon. “Erdős-Hajnal-Type Results for Monotone Paths.”
Journal of Combinatorial Theory. Series B, vol. 151, Elsevier, 2021, pp.
21–37, doi:10.1016/j.jctb.2021.05.004.
short: J. Pach, I. Tomon, Journal of Combinatorial Theory. Series B 151 (2021) 21–37.
date_created: 2021-06-27T22:01:47Z
date_published: 2021-06-09T00:00:00Z
date_updated: 2023-08-10T13:38:00Z
day: '09'
ddc:
- '510'
department:
- _id: HeEd
doi: 10.1016/j.jctb.2021.05.004
external_id:
isi:
- '000702280800002'
file:
- access_level: open_access
checksum: 15fbc9064cd9d1c777ac0043b78c8f12
content_type: application/pdf
creator: asandaue
date_created: 2021-06-28T13:33:23Z
date_updated: 2021-06-28T13:33:23Z
file_id: '9612'
file_name: 2021_JournalOfCombinatorialTheory_Pach.pdf
file_size: 418168
relation: main_file
success: 1
file_date_updated: 2021-06-28T13:33:23Z
has_accepted_license: '1'
intvolume: ' 151'
isi: 1
language:
- iso: eng
month: '06'
oa: 1
oa_version: Published Version
page: 21-37
project:
- _id: 268116B8-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: Z00342
name: The Wittgenstein Prize
publication: Journal of Combinatorial Theory. Series B
publication_identifier:
issn:
- 0095-8956
publication_status: published
publisher: Elsevier
quality_controlled: '1'
scopus_import: '1'
status: public
title: Erdős-Hajnal-type results for monotone paths
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: 151
year: '2021'
...
---
_id: '9606'
abstract:
- lang: eng
text: Sound propagation is a macroscopic manifestation of the interplay between
the equilibrium thermodynamics and the dynamical transport properties of fluids.
Here, for a two-dimensional system of ultracold fermions, we calculate the first
and second sound velocities across the whole BCS-BEC crossover, and we analyze
the system response to an external perturbation. In the low-temperature regime
we reproduce the recent measurements [Phys. Rev. Lett. 124, 240403 (2020)] of
the first sound velocity, which, due to the decoupling of density and entropy
fluctuations, is the sole mode excited by a density probe. Conversely, a heat
perturbation excites only the second sound, which, being sensitive to the superfluid
depletion, vanishes in the deep BCS regime and jumps discontinuously to zero at
the Berezinskii-Kosterlitz-Thouless superfluid transition. A mixing between the
modes occurs only in the finite-temperature BEC regime, where our theory converges
to the purely bosonic results.
acknowledgement: "G.B. acknowledges support from the Austrian Science Fund (FWF),
under Project No. M2641-N27. This work was\r\npartially supported by the University
of Padua, BIRD project “Superfluid properties of Fermi gases in optical potentials.”\r\nThe
authors thank Miki Ota, Tomoki Ozawa, Sandro Stringari, Tilman Enss, Hauke Biss,
Henning Moritz, and Nicolò Defenu for fruitful discussions. The authors thank Henning
Moritz and Markus Bohlen for providing their experimental\r\ndata."
article_number: L061303
article_processing_charge: No
article_type: letter_note
author:
- first_name: A.
full_name: Tononi, A.
last_name: Tononi
- first_name: Alberto
full_name: Cappellaro, Alberto
id: 9d13b3cb-30a2-11eb-80dc-f772505e8660
last_name: Cappellaro
orcid: 0000-0001-6110-2359
- first_name: Giacomo
full_name: Bighin, Giacomo
id: 4CA96FD4-F248-11E8-B48F-1D18A9856A87
last_name: Bighin
orcid: 0000-0001-8823-9777
- first_name: L.
full_name: Salasnich, L.
last_name: Salasnich
citation:
ama: Tononi A, Cappellaro A, Bighin G, Salasnich L. Propagation of first and second
sound in a two-dimensional Fermi superfluid. Physical Review A. 2021;103(6).
doi:10.1103/PhysRevA.103.L061303
apa: Tononi, A., Cappellaro, A., Bighin, G., & Salasnich, L. (2021). Propagation
of first and second sound in a two-dimensional Fermi superfluid. Physical Review
A. American Physical Society. https://doi.org/10.1103/PhysRevA.103.L061303
chicago: Tononi, A., Alberto Cappellaro, Giacomo Bighin, and L. Salasnich. “Propagation
of First and Second Sound in a Two-Dimensional Fermi Superfluid.” Physical
Review A. American Physical Society, 2021. https://doi.org/10.1103/PhysRevA.103.L061303.
ieee: A. Tononi, A. Cappellaro, G. Bighin, and L. Salasnich, “Propagation of first
and second sound in a two-dimensional Fermi superfluid,” Physical Review A,
vol. 103, no. 6. American Physical Society, 2021.
ista: Tononi A, Cappellaro A, Bighin G, Salasnich L. 2021. Propagation of first
and second sound in a two-dimensional Fermi superfluid. Physical Review A. 103(6),
L061303.
mla: Tononi, A., et al. “Propagation of First and Second Sound in a Two-Dimensional
Fermi Superfluid.” Physical Review A, vol. 103, no. 6, L061303, American
Physical Society, 2021, doi:10.1103/PhysRevA.103.L061303.
short: A. Tononi, A. Cappellaro, G. Bighin, L. Salasnich, Physical Review A 103
(2021).
date_created: 2021-06-27T22:01:49Z
date_published: 2021-06-01T00:00:00Z
date_updated: 2023-08-10T13:37:25Z
day: '01'
department:
- _id: MiLe
doi: 10.1103/PhysRevA.103.L061303
external_id:
arxiv:
- '2009.06491'
isi:
- '000662296700014'
intvolume: ' 103'
isi: 1
issue: '6'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/2009.06491
month: '06'
oa: 1
oa_version: Preprint
publication: Physical Review A
publication_identifier:
eissn:
- '24699934'
issn:
- '24699926'
publication_status: published
publisher: American Physical Society
quality_controlled: '1'
scopus_import: '1'
status: public
title: Propagation of first and second sound in a two-dimensional Fermi superfluid
type: journal_article
user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
volume: 103
year: '2021'
...
---
_id: '9642'
abstract:
- lang: eng
text: Perineuronal nets (PNNs), components of the extracellular matrix, preferentially
coat parvalbumin-positive interneurons and constrain critical-period plasticity
in the adult cerebral cortex. Current strategies to remove PNN are long-lasting,
invasive, and trigger neuropsychiatric symptoms. Here, we apply repeated anesthetic
ketamine as a method with minimal behavioral effect. We find that this paradigm
strongly reduces PNN coating in the healthy adult brain and promotes juvenile-like
plasticity. Microglia are critically involved in PNN loss because they engage
with parvalbumin-positive neurons in their defined cortical layer. We identify
external 60-Hz light-flickering entrainment to recapitulate microglia-mediated
PNN removal. Importantly, 40-Hz frequency, which is known to remove amyloid plaques,
does not induce PNN loss, suggesting microglia might functionally tune to distinct
brain frequencies. Thus, our 60-Hz light-entrainment strategy provides an alternative
form of PNN intervention in the healthy adult brain.
acknowledged_ssus:
- _id: Bio
- _id: PreCl
acknowledgement: We thank the scientific service units at IST Austria, especially
the IST bioimaging facility, the preclinical facility, and, specifically, Michael
Schunn and Sonja Haslinger for excellent support; Plexxikon for the PLX food; the
Csicsvari group for advice and equipment for in vivo recording; Jürgen Siegert for
the light-entrainment design; Marco Benevento, Soledad Gonzalo Cogno, Pat King,
and all Siegert group members for constant feedback on the project and manuscript;
Lorena Pantano (PILM Bioinformatics Core) for assisting with sample-size determination
for OD plasticity experiments; and Ana Morello from MIT for technical assistance
with VEPs recordings. This research was supported by a DOC Fellowship from the Austrian
Academy of Sciences at the Institute of Science and Technology Austria to R.S.,
from the European Union Horizon 2020 research and innovation program under the Marie
Skłodowska-Curie Actions program (grants 665385 to G.C.; 754411 to R.J.A.C.), the
European Research Council (grant 715571 to S.S.), and the National Eye Institute
of the National Institutes of Health under award numbers R01EY029245 (to M.F.B.)
and R01EY023037 (diversity supplement to H.D.J-C.).
article_number: '109313'
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author:
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full_name: Venturino, Alessandro
id: 41CB84B2-F248-11E8-B48F-1D18A9856A87
last_name: Venturino
orcid: 0000-0003-2356-9403
- first_name: Rouven
full_name: Schulz, Rouven
id: 4C5E7B96-F248-11E8-B48F-1D18A9856A87
last_name: Schulz
orcid: 0000-0001-5297-733X
- first_name: Héctor
full_name: De Jesús-Cortés, Héctor
last_name: De Jesús-Cortés
- first_name: Margaret E
full_name: Maes, Margaret E
id: 3838F452-F248-11E8-B48F-1D18A9856A87
last_name: Maes
orcid: 0000-0001-9642-1085
- first_name: Balint
full_name: Nagy, Balint
id: 93C65ECC-A6F2-11E9-8DF9-9712E6697425
last_name: Nagy
- first_name: Francis
full_name: Reilly-Andújar, Francis
last_name: Reilly-Andújar
- first_name: Gloria
full_name: Colombo, Gloria
id: 3483CF6C-F248-11E8-B48F-1D18A9856A87
last_name: Colombo
orcid: 0000-0001-9434-8902
- 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: Florianne E
full_name: Schoot Uiterkamp, Florianne E
id: 3526230C-F248-11E8-B48F-1D18A9856A87
last_name: Schoot Uiterkamp
- first_name: Mark F.
full_name: Bear, Mark F.
last_name: Bear
- first_name: Sandra
full_name: Siegert, Sandra
id: 36ACD32E-F248-11E8-B48F-1D18A9856A87
last_name: Siegert
orcid: 0000-0001-8635-0877
citation:
ama: Venturino A, Schulz R, De Jesús-Cortés H, et al. Microglia enable mature perineuronal
nets disassembly upon anesthetic ketamine exposure or 60-Hz light entrainment
in the healthy brain. Cell Reports. 2021;36(1). doi:10.1016/j.celrep.2021.109313
apa: Venturino, A., Schulz, R., De Jesús-Cortés, H., Maes, M. E., Nagy, B., Reilly-Andújar,
F., … Siegert, S. (2021). Microglia enable mature perineuronal nets disassembly
upon anesthetic ketamine exposure or 60-Hz light entrainment in the healthy brain.
Cell Reports. Elsevier. https://doi.org/10.1016/j.celrep.2021.109313
chicago: Venturino, Alessandro, Rouven Schulz, Héctor De Jesús-Cortés, Margaret
E Maes, Balint Nagy, Francis Reilly-Andújar, Gloria Colombo, et al. “Microglia
Enable Mature Perineuronal Nets Disassembly upon Anesthetic Ketamine Exposure
or 60-Hz Light Entrainment in the Healthy Brain.” Cell Reports. Elsevier,
2021. https://doi.org/10.1016/j.celrep.2021.109313.
ieee: A. Venturino et al., “Microglia enable mature perineuronal nets disassembly
upon anesthetic ketamine exposure or 60-Hz light entrainment in the healthy brain,”
Cell Reports, vol. 36, no. 1. Elsevier, 2021.
ista: Venturino A, Schulz R, De Jesús-Cortés H, Maes ME, Nagy B, Reilly-Andújar
F, Colombo G, Cubero RJ, Schoot Uiterkamp FE, Bear MF, Siegert S. 2021. Microglia
enable mature perineuronal nets disassembly upon anesthetic ketamine exposure
or 60-Hz light entrainment in the healthy brain. Cell Reports. 36(1), 109313.
mla: Venturino, Alessandro, et al. “Microglia Enable Mature Perineuronal Nets Disassembly
upon Anesthetic Ketamine Exposure or 60-Hz Light Entrainment in the Healthy Brain.”
Cell Reports, vol. 36, no. 1, 109313, Elsevier, 2021, doi:10.1016/j.celrep.2021.109313.
short: A. Venturino, R. Schulz, H. De Jesús-Cortés, M.E. Maes, B. Nagy, F. Reilly-Andújar,
G. Colombo, R.J. Cubero, F.E. Schoot Uiterkamp, M.F. Bear, S. Siegert, Cell Reports
36 (2021).
date_created: 2021-07-11T22:01:16Z
date_published: 2021-07-06T00:00:00Z
date_updated: 2023-08-10T14:09:39Z
day: '06'
ddc:
- '570'
department:
- _id: SaSi
doi: 10.1016/j.celrep.2021.109313
ec_funded: 1
external_id:
isi:
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pmid:
- '34233180'
file:
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creator: cziletti
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file_id: '9693'
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month: '07'
oa: 1
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pmid: 1
project:
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call_identifier: H2020
grant_number: '665385'
name: International IST Doctoral Program
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call_identifier: H2020
grant_number: '754411'
name: ISTplus - Postdoctoral Fellowships
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call_identifier: H2020
grant_number: '715571'
name: Microglia action towards neuronal circuit formation and function in health
and disease
publication: Cell Reports
publication_identifier:
eissn:
- '22111247'
publication_status: published
publisher: Elsevier
quality_controlled: '1'
related_material:
link:
- description: News on IST Homepage
relation: press_release
url: https://ist.ac.at/en/news/the-twinkle-and-the-brain/
scopus_import: '1'
status: public
title: Microglia enable mature perineuronal nets disassembly upon anesthetic ketamine
exposure or 60-Hz light entrainment in the healthy brain
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)
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type: journal_article
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...
---
_id: '9603'
abstract:
- lang: eng
text: Mosaic analysis with double markers (MADM) offers one approach to visualize
and concomitantly manipulate genetically defined cells in mice with single-cell
resolution. MADM applications include the analysis of lineage, single-cell morphology
and physiology, genomic imprinting phenotypes, and dissection of cell-autonomous
gene functions in vivo in health and disease. Yet, MADM can only be applied to
<25% of all mouse genes on select chromosomes to date. To overcome this limitation,
we generate transgenic mice with knocked-in MADM cassettes near the centromeres
of all 19 autosomes and validate their use across organs. With this resource,
>96% of the entire mouse genome can now be subjected to single-cell genetic mosaic
analysis. Beyond a proof of principle, we apply our MADM library to systematically
trace sister chromatid segregation in distinct mitotic cell lineages. We find
striking chromosome-specific biases in segregation patterns, reflecting a putative
mechanism for the asymmetric segregation of genetic determinants in somatic stem
cell division.
acknowledged_ssus:
- _id: Bio
- _id: LifeSc
- _id: PreCl
acknowledgement: We thank the Bioimaging, Life Science, and Pre-Clinical Facilities
at IST Austria; M.P. Postiglione, C. Simbriger, K. Valoskova, C. Schwayer, T. Hussain,
M. Pieber, and V. Wimmer for initial experiments, technical support, and/or assistance;
R. Shigemoto for sharing iv (Dnah11 mutant) mice; and M. Sixt and all members of
the Hippenmeyer lab for discussion. This work was supported by National Institutes
of Health grants ( R01-NS050580 to L.L. and F32MH096361 to L.A.S.). L.L. is an investigator
of HHMI. N.A. received support from FWF Firnberg-Programm ( T 1031 ). A.H.H. is
a recipient of a DOC Fellowship (24812) of the Austrian Academy of Sciences . This
work also received support from IST Austria institutional funds , FWF SFB F78 to
S.H., the People Programme (Marie Curie Actions) of the European Union’s Seventh
Framework Programme ( FP7/2007-2013 ) under REA grant agreement no 618444 to S.H.,
and the European Research Council (ERC) under the European Union’s Horizon 2020
Research and Innovation Programme (grant agreement no. 725780 LinPro ) to S.H.
article_number: '109274'
article_processing_charge: No
article_type: original
author:
- first_name: Ximena
full_name: Contreras, Ximena
id: 475990FE-F248-11E8-B48F-1D18A9856A87
last_name: Contreras
- first_name: Nicole
full_name: Amberg, Nicole
id: 4CD6AAC6-F248-11E8-B48F-1D18A9856A87
last_name: Amberg
orcid: 0000-0002-3183-8207
- first_name: Amarbayasgalan
full_name: Davaatseren, Amarbayasgalan
id: 70ADC922-B424-11E9-99E3-BA18E6697425
last_name: Davaatseren
- first_name: Andi H
full_name: Hansen, Andi H
id: 38853E16-F248-11E8-B48F-1D18A9856A87
last_name: Hansen
- first_name: Johanna
full_name: Sonntag, Johanna
id: 32FE7D7C-F248-11E8-B48F-1D18A9856A87
last_name: Sonntag
- first_name: Lill
full_name: Andersen, Lill
last_name: Andersen
- first_name: Tina
full_name: Bernthaler, Tina
last_name: Bernthaler
- first_name: Carmen
full_name: Streicher, Carmen
id: 36BCB99C-F248-11E8-B48F-1D18A9856A87
last_name: Streicher
- first_name: Anna-Magdalena
full_name: Heger, Anna-Magdalena
id: 4B76FFD2-F248-11E8-B48F-1D18A9856A87
last_name: Heger
- first_name: Randy L.
full_name: Johnson, Randy L.
last_name: Johnson
- first_name: Lindsay A.
full_name: Schwarz, Lindsay A.
last_name: Schwarz
- first_name: Liqun
full_name: Luo, Liqun
last_name: Luo
- first_name: Thomas
full_name: Rülicke, Thomas
last_name: Rülicke
- first_name: Simon
full_name: Hippenmeyer, Simon
id: 37B36620-F248-11E8-B48F-1D18A9856A87
last_name: Hippenmeyer
orcid: 0000-0003-2279-1061
citation:
ama: Contreras X, Amberg N, Davaatseren A, et al. A genome-wide library of MADM
mice for single-cell genetic mosaic analysis. Cell Reports. 2021;35(12).
doi:10.1016/j.celrep.2021.109274
apa: Contreras, X., Amberg, N., Davaatseren, A., Hansen, A. H., Sonntag, J., Andersen,
L., … Hippenmeyer, S. (2021). A genome-wide library of MADM mice for single-cell
genetic mosaic analysis. Cell Reports. Cell Press. https://doi.org/10.1016/j.celrep.2021.109274
chicago: Contreras, Ximena, Nicole Amberg, Amarbayasgalan Davaatseren, Andi H Hansen,
Johanna Sonntag, Lill Andersen, Tina Bernthaler, et al. “A Genome-Wide Library
of MADM Mice for Single-Cell Genetic Mosaic Analysis.” Cell Reports. Cell
Press, 2021. https://doi.org/10.1016/j.celrep.2021.109274.
ieee: X. Contreras et al., “A genome-wide library of MADM mice for single-cell
genetic mosaic analysis,” Cell Reports, vol. 35, no. 12. Cell Press, 2021.
ista: Contreras X, Amberg N, Davaatseren A, Hansen AH, Sonntag J, Andersen L, Bernthaler
T, Streicher C, Heger A-M, Johnson RL, Schwarz LA, Luo L, Rülicke T, Hippenmeyer
S. 2021. A genome-wide library of MADM mice for single-cell genetic mosaic analysis.
Cell Reports. 35(12), 109274.
mla: Contreras, Ximena, et al. “A Genome-Wide Library of MADM Mice for Single-Cell
Genetic Mosaic Analysis.” Cell Reports, vol. 35, no. 12, 109274, Cell Press,
2021, doi:10.1016/j.celrep.2021.109274.
short: X. Contreras, N. Amberg, A. Davaatseren, A.H. Hansen, J. Sonntag, L. Andersen,
T. Bernthaler, C. Streicher, A.-M. Heger, R.L. Johnson, L.A. Schwarz, L. Luo,
T. Rülicke, S. Hippenmeyer, Cell Reports 35 (2021).
date_created: 2021-06-27T22:01:48Z
date_published: 2021-06-22T00:00:00Z
date_updated: 2023-08-10T13:55:00Z
day: '22'
ddc:
- '570'
department:
- _id: SiHi
- _id: LoSw
- _id: PreCl
doi: 10.1016/j.celrep.2021.109274
ec_funded: 1
external_id:
isi:
- '000664463600016'
file:
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checksum: d49520fdcbbb5c2f883bddb67cee5d77
content_type: application/pdf
creator: asandaue
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date_updated: 2021-06-28T14:06:24Z
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file_name: 2021_CellReports_Contreras.pdf
file_size: 7653149
relation: main_file
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file_date_updated: 2021-06-28T14:06:24Z
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isi: 1
issue: '12'
language:
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license: https://creativecommons.org/licenses/by-nc-nd/4.0/
month: '06'
oa: 1
oa_version: Published Version
project:
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grant_number: '24812'
name: Molecular Mechanisms of Radial Neuronal Migration
- _id: 25D61E48-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '618444'
name: Molecular Mechanisms of Cerebral Cortex Development
- _id: 260018B0-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '725780'
name: Principles of Neural Stem Cell Lineage Progression in Cerebral Cortex Development
publication: Cell Reports
publication_identifier:
eissn:
- '22111247'
publication_status: published
publisher: Cell Press
quality_controlled: '1'
related_material:
link:
- description: News on IST Homepage
relation: press_release
url: https://ist.ac.at/en/news/boost-for-mouse-genetic-analysis/
scopus_import: '1'
status: public
title: A genome-wide library of MADM mice for single-cell genetic mosaic analysis
tmp:
image: /images/cc_by_nc_nd.png
legal_code_url: https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode
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short: CC BY-NC-ND (4.0)
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...