---
_id: '10891'
abstract:
- lang: eng
text: We present a formal framework for the online black-box monitoring of software
using monitors with quantitative verdict functions. Quantitative verdict functions
have several advantages. First, quantitative monitors can be approximate, i.e.,
the value of the verdict function does not need to correspond exactly to the value
of the property under observation. Second, quantitative monitors can be quantified
universally, i.e., for every possible observed behavior, the monitor tries to
make the best effort to estimate the value of the property under observation.
Third, quantitative monitors can watch boolean as well as quantitative properties,
such as average response time. Fourth, quantitative monitors can use non-finite-state
resources, such as counters. As a consequence, quantitative monitors can be compared
according to how many resources they use (e.g., the number of counters) and how
precisely they approximate the property under observation. This allows for a rich
spectrum of cost-precision trade-offs in monitoring software.
acknowledgement: The formal framework for quantitative monitoring which is presented
in this invited talk was defined jointly with N. Ege Saraç at LICS 2021. This work
was supported in part by the Wittgenstein Award Z211-N23 of the Austrian Science
Fund.
article_processing_charge: No
author:
- first_name: Thomas A
full_name: Henzinger, Thomas A
id: 40876CD8-F248-11E8-B48F-1D18A9856A87
last_name: Henzinger
orcid: 0000-0002-2985-7724
citation:
ama: 'Henzinger TA. Quantitative monitoring of software. In: Software Verification.
Vol 13124. LNCS. Springer Nature; 2022:3-6. doi:10.1007/978-3-030-95561-8_1'
apa: 'Henzinger, T. A. (2022). Quantitative monitoring of software. In Software
Verification (Vol. 13124, pp. 3–6). New Haven, CT, United States: Springer
Nature. https://doi.org/10.1007/978-3-030-95561-8_1'
chicago: Henzinger, Thomas A. “Quantitative Monitoring of Software.” In Software
Verification, 13124:3–6. LNCS. Springer Nature, 2022. https://doi.org/10.1007/978-3-030-95561-8_1.
ieee: T. A. Henzinger, “Quantitative monitoring of software,” in Software Verification,
New Haven, CT, United States, 2022, vol. 13124, pp. 3–6.
ista: 'Henzinger TA. 2022. Quantitative monitoring of software. Software Verification.
NSV: Numerical Software VerificationLNCS vol. 13124, 3–6.'
mla: Henzinger, Thomas A. “Quantitative Monitoring of Software.” Software Verification,
vol. 13124, Springer Nature, 2022, pp. 3–6, doi:10.1007/978-3-030-95561-8_1.
short: T.A. Henzinger, in:, Software Verification, Springer Nature, 2022, pp. 3–6.
conference:
end_date: 2021-10-19
location: New Haven, CT, United States
name: 'NSV: Numerical Software Verification'
start_date: 2021-10-18
corr_author: '1'
date_created: 2022-03-20T23:01:40Z
date_published: 2022-02-22T00:00:00Z
date_updated: 2025-04-15T06:25:58Z
day: '22'
department:
- _id: ToHe
doi: 10.1007/978-3-030-95561-8_1
external_id:
isi:
- '000771713200001'
intvolume: ' 13124'
isi: 1
language:
- iso: eng
month: '02'
oa_version: None
page: 3-6
project:
- _id: 25F42A32-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: Z211
name: Formal methods for the design and analysis of complex systems
publication: Software Verification
publication_identifier:
eissn:
- 1611-3349
isbn:
- '9783030955601'
issn:
- 0302-9743
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
scopus_import: '1'
series_title: LNCS
status: public
title: Quantitative monitoring of software
type: conference
user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
volume: 13124
year: '2022'
...
---
_id: '10918'
abstract:
- lang: eng
text: Cellular metabolism must adapt to changing demands to enable homeostasis.
During immune responses or cancer metastasis, cells leading migration into challenging
environments require an energy boost, but what controls this capacity is unclear.
Here, we study a previously uncharacterized nuclear protein, Atossa (encoded by
CG9005), which supports macrophage invasion into the germband of Drosophila by
controlling cellular metabolism. First, nuclear Atossa increases mRNA levels of
Porthos, a DEAD-box protein, and of two metabolic enzymes, lysine-α-ketoglutarate
reductase (LKR/SDH) and NADPH glyoxylate reductase (GR/HPR), thus enhancing mitochondrial
bioenergetics. Then Porthos supports ribosome assembly and thereby raises the
translational efficiency of a subset of mRNAs, including those affecting mitochondrial
functions, the electron transport chain, and metabolism. Mitochondrial respiration
measurements, metabolomics, and live imaging indicate that Atossa and Porthos
power up OxPhos and energy production to promote the forging of a path into tissues
by leading macrophages. Since many crucial physiological responses require increases
in mitochondrial energy output, this previously undescribed genetic program may
modulate a wide range of cellular behaviors.
acknowledged_ssus:
- _id: Bio
acknowledgement: "We thank the DGRC (NIH grant 2P40OD010949-10A1) for plasmids, the
BDSC (NIH grant P40OD018537) and the VDRC for fly stocks, FlyBase for essential
genomic information, the BDGP in situ database for data (Tomancak et al, 2007),
the IST Austria Bioimaging facility for support, the VBC Core Facilities for RNA
sequencing and analysis, and C. Guet, C. Navarro, C. Desplan, T. Lecuit, I. Miguel-Aliaga,
and Siekhaus group members for comments on the manuscript. The VBCF Metabolomics
Facility is funded by the City of Vienna through the Vienna Business Agency. This
work was supported by the Marie Curie CIG 334077/IRTIM (DES), Austrian Science Fund
(FWF) Lise Meitner Fellowship M2379-B28 (MA and DES), Austrian Science Fund (FWF)
grant ASI_FWF01_P29638S (DES), NIH/NIGMS (R01GM111779-06 (PR), RO1GM135628-01 (PR),
European Research Council (ERC) grant no. 677006 “CMIL” (AB), and Natural Sciences
and Engineering Research Council of Canada\r\n(RGPIN-2019-06766) (TRH). "
article_number: e109049
article_processing_charge: Yes (via OA deal)
article_type: original
author:
- first_name: Shamsi
full_name: Emtenani, Shamsi
id: 49D32318-F248-11E8-B48F-1D18A9856A87
last_name: Emtenani
orcid: 0000-0001-6981-6938
- first_name: Elliot T
full_name: Martin, Elliot T
last_name: Martin
- first_name: Attila
full_name: György, Attila
id: 3BCEDBE0-F248-11E8-B48F-1D18A9856A87
last_name: György
orcid: 0000-0002-1819-198X
- first_name: Julia
full_name: Bicher, Julia
id: 3CCBB46E-F248-11E8-B48F-1D18A9856A87
last_name: Bicher
- first_name: Jakob-Wendelin
full_name: Genger, Jakob-Wendelin
last_name: Genger
- first_name: Thomas
full_name: Köcher, Thomas
last_name: Köcher
- first_name: Maria
full_name: Akhmanova, Maria
id: 3425EC26-F248-11E8-B48F-1D18A9856A87
last_name: Akhmanova
orcid: 0000-0003-1522-3162
- first_name: Mariana
full_name: Pereira Guarda, Mariana
id: 6de81d9d-e2f2-11eb-945a-af8bc2a60b26
last_name: Pereira Guarda
orcid: 0000-0001-8238-480X
- first_name: Marko
full_name: Roblek, Marko
id: 3047D808-F248-11E8-B48F-1D18A9856A87
last_name: Roblek
orcid: 0000-0001-9588-1389
- first_name: Andreas
full_name: Bergthaler, Andreas
last_name: Bergthaler
- first_name: Thomas R
full_name: Hurd, Thomas R
last_name: Hurd
- first_name: Prashanth
full_name: Rangan, Prashanth
last_name: Rangan
- first_name: Daria E
full_name: Siekhaus, Daria E
id: 3D224B9E-F248-11E8-B48F-1D18A9856A87
last_name: Siekhaus
orcid: 0000-0001-8323-8353
citation:
ama: Emtenani S, Martin ET, György A, et al. Macrophage mitochondrial bioenergetics
and tissue invasion are boosted by an Atossa-Porthos axis in Drosophila. The
Embo Journal. 2022;41. doi:10.15252/embj.2021109049
apa: Emtenani, S., Martin, E. T., György, A., Bicher, J., Genger, J.-W., Köcher,
T., … Siekhaus, D. E. (2022). Macrophage mitochondrial bioenergetics and tissue
invasion are boosted by an Atossa-Porthos axis in Drosophila. The Embo Journal.
Embo Press. https://doi.org/10.15252/embj.2021109049
chicago: Emtenani, Shamsi, Elliot T Martin, Attila György, Julia Bicher, Jakob-Wendelin
Genger, Thomas Köcher, Maria Akhmanova, et al. “Macrophage Mitochondrial Bioenergetics
and Tissue Invasion Are Boosted by an Atossa-Porthos Axis in Drosophila.” The
Embo Journal. Embo Press, 2022. https://doi.org/10.15252/embj.2021109049.
ieee: S. Emtenani et al., “Macrophage mitochondrial bioenergetics and tissue
invasion are boosted by an Atossa-Porthos axis in Drosophila,” The Embo Journal,
vol. 41. Embo Press, 2022.
ista: Emtenani S, Martin ET, György A, Bicher J, Genger J-W, Köcher T, Akhmanova
M, Pereira Guarda M, Roblek M, Bergthaler A, Hurd TR, Rangan P, Siekhaus DE. 2022.
Macrophage mitochondrial bioenergetics and tissue invasion are boosted by an Atossa-Porthos
axis in Drosophila. The Embo Journal. 41, e109049.
mla: Emtenani, Shamsi, et al. “Macrophage Mitochondrial Bioenergetics and Tissue
Invasion Are Boosted by an Atossa-Porthos Axis in Drosophila.” The Embo Journal,
vol. 41, e109049, Embo Press, 2022, doi:10.15252/embj.2021109049.
short: S. Emtenani, E.T. Martin, A. György, J. Bicher, J.-W. Genger, T. Köcher,
M. Akhmanova, M. Pereira Guarda, M. Roblek, A. Bergthaler, T.R. Hurd, P. Rangan,
D.E. Siekhaus, The Embo Journal 41 (2022).
corr_author: '1'
date_created: 2022-03-24T13:23:09Z
date_published: 2022-03-23T00:00:00Z
date_updated: 2025-06-12T06:20:16Z
day: '23'
ddc:
- '570'
department:
- _id: DaSi
- _id: LoSw
doi: 10.15252/embj.2021109049
ec_funded: 1
external_id:
isi:
- '000771957000001'
pmid:
- '35319107'
file:
- access_level: open_access
checksum: dba48580fe0fefaa4c63078d1d2a35df
content_type: application/pdf
creator: siekhaus
date_created: 2022-03-24T13:22:41Z
date_updated: 2022-03-24T13:22:41Z
file_id: '10919'
file_name: Macrophage mitochondrial bioenergetics and tissue invasion are boosted
by an Atossa-Porthos axis in Drosopila.pdf
file_size: 4344585
relation: main_file
file_date_updated: 2022-03-24T13:22:41Z
has_accepted_license: '1'
intvolume: ' 41'
isi: 1
language:
- iso: eng
license: https://creativecommons.org/licenses/by/4.0/
month: '03'
oa: 1
oa_version: Published Version
pmid: 1
project:
- _id: 2536F660-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '334077'
name: Investigating the role of transporters in invasive migration through junctions
- _id: 264CBBAC-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: M02379
name: Modeling epithelial tissue mechanics during cell invasion
- _id: 253B6E48-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: P29638
name: The role of Drosophila TNF alpha in immune cell invasion
publication: The Embo Journal
publication_identifier:
eissn:
- 1460-2075
publication_status: published
publisher: Embo Press
quality_controlled: '1'
scopus_import: '1'
status: public
title: Macrophage mitochondrial bioenergetics and tissue invasion are boosted by an
Atossa-Porthos axis in Drosophila
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 41
year: '2022'
...
---
_id: '10920'
abstract:
- lang: eng
text: The spin-orbit interaction permits to control the state of a spin qubit via
electric fields. For holes it is particularly strong, allowing for fast all electrical
qubit manipulation, and yet an in-depth understanding of this interaction in hole
systems is missing. Here we investigate, experimentally and theoretically, the
effect of the cubic Rashba spin-orbit interaction on the mixing of the spin states
by studying singlet-triplet oscillations in a planar Ge hole double quantum dot.
Landau-Zener sweeps at different magnetic field directions allow us to disentangle
the effects of the spin-orbit induced spin-flip term from those caused by strongly
site-dependent and anisotropic quantum dot g tensors. Our work, therefore, provides
new insights into the hole spin-orbit interaction, necessary for optimizing future
qubit experiments.
acknowledged_ssus:
- _id: M-Shop
- _id: NanoFab
acknowledgement: "This research was supported by the Scientific Service Units of ISTA
through resources provided by the MIBA Machine Shop and the nanofabrication facility.
This project has received funding from the European Union’s Horizon 2020 research
and innovation program under the Marie\r\nSkłodowska-Curie Grant Agreement No. 844511,
No. 75441, and by the FWF-P 30207, I05060, and M3032-N projects. A. B. acknowledges
support from the EU Horizon-2020 FET project microSPIRE, ID: 766955. P.M. M. and
G. B. acknowledge funding by the Deutsche Forschungsgemeinschaft (DFG—German Research
Foundation) under Project No. 450396347. This work was supported by the Royal Society
(URF\\R1\\191150) and the European Research Council (Grant Agreement No. 948932),
N. A. acknowledges the use of the University of Oxford Advanced Research Computing
(ARC) facility."
article_number: '126803'
article_processing_charge: No
article_type: original
arxiv: 1
author:
- first_name: Daniel
full_name: Jirovec, Daniel
id: 4C473F58-F248-11E8-B48F-1D18A9856A87
last_name: Jirovec
orcid: 0000-0002-7197-4801
- first_name: Philipp M.
full_name: Mutter, Philipp M.
last_name: Mutter
- first_name: Andrea C
full_name: Hofmann, Andrea C
id: 340F461A-F248-11E8-B48F-1D18A9856A87
last_name: Hofmann
- first_name: Alessandro
full_name: Crippa, Alessandro
id: 1F2B21A2-F6E7-11E9-9B82-F7DBE5697425
last_name: Crippa
orcid: 0000-0002-2968-611X
- first_name: Marek
full_name: Rychetsky, Marek
last_name: Rychetsky
- first_name: David L.
full_name: Craig, David L.
last_name: Craig
- first_name: Josip
full_name: Kukucka, Josip
id: 3F5D8856-F248-11E8-B48F-1D18A9856A87
last_name: Kukucka
- first_name: Frederico
full_name: Martins, Frederico
id: 38F80F9A-1CB8-11EA-BC76-B49B3DDC885E
last_name: Martins
orcid: 0000-0003-2668-2401
- first_name: Andrea
full_name: Ballabio, Andrea
last_name: Ballabio
- first_name: Natalia
full_name: Ares, Natalia
last_name: Ares
- first_name: Daniel
full_name: Chrastina, Daniel
last_name: Chrastina
- first_name: Giovanni
full_name: Isella, Giovanni
last_name: Isella
- first_name: 'Guido '
full_name: 'Burkard, Guido '
last_name: Burkard
- first_name: Georgios
full_name: Katsaros, Georgios
id: 38DB5788-F248-11E8-B48F-1D18A9856A87
last_name: Katsaros
orcid: 0000-0001-8342-202X
citation:
ama: Jirovec D, Mutter PM, Hofmann AC, et al. Dynamics of hole singlet-triplet qubits
with large g-factor differences. Physical Review Letters. 2022;128(12).
doi:10.1103/PhysRevLett.128.126803
apa: Jirovec, D., Mutter, P. M., Hofmann, A. C., Crippa, A., Rychetsky, M., Craig,
D. L., … Katsaros, G. (2022). Dynamics of hole singlet-triplet qubits with large
g-factor differences. Physical Review Letters. American Physical Society.
https://doi.org/10.1103/PhysRevLett.128.126803
chicago: Jirovec, Daniel, Philipp M. Mutter, Andrea C Hofmann, Alessandro Crippa,
Marek Rychetsky, David L. Craig, Josip Kukucka, et al. “Dynamics of Hole Singlet-Triplet
Qubits with Large g-Factor Differences.” Physical Review Letters. American
Physical Society, 2022. https://doi.org/10.1103/PhysRevLett.128.126803.
ieee: D. Jirovec et al., “Dynamics of hole singlet-triplet qubits with large
g-factor differences,” Physical Review Letters, vol. 128, no. 12. American
Physical Society, 2022.
ista: Jirovec D, Mutter PM, Hofmann AC, Crippa A, Rychetsky M, Craig DL, Kukucka
J, Martins F, Ballabio A, Ares N, Chrastina D, Isella G, Burkard G, Katsaros G.
2022. Dynamics of hole singlet-triplet qubits with large g-factor differences.
Physical Review Letters. 128(12), 126803.
mla: Jirovec, Daniel, et al. “Dynamics of Hole Singlet-Triplet Qubits with Large
g-Factor Differences.” Physical Review Letters, vol. 128, no. 12, 126803,
American Physical Society, 2022, doi:10.1103/PhysRevLett.128.126803.
short: D. Jirovec, P.M. Mutter, A.C. Hofmann, A. Crippa, M. Rychetsky, D.L. Craig,
J. Kukucka, F. Martins, A. Ballabio, N. Ares, D. Chrastina, G. Isella, G. Burkard,
G. Katsaros, Physical Review Letters 128 (2022).
corr_author: '1'
date_created: 2022-03-24T15:51:11Z
date_published: 2022-03-24T00:00:00Z
date_updated: 2025-04-14T07:44:07Z
day: '24'
ddc:
- '530'
department:
- _id: GradSch
- _id: GeKa
doi: 10.1103/PhysRevLett.128.126803
ec_funded: 1
external_id:
arxiv:
- '2111.05130'
isi:
- '000786542500004'
pmid:
- '35394319'
file:
- access_level: open_access
checksum: 6e66ad548d18db9c131f304acbd5a1f4
content_type: application/pdf
creator: dernst
date_created: 2022-03-28T06:53:39Z
date_updated: 2022-03-28T06:53:39Z
file_id: '10928'
file_name: 2022_PhysRevLetters_Jirovec.pdf
file_size: 1266515
relation: main_file
success: 1
file_date_updated: 2022-03-28T06:53:39Z
has_accepted_license: '1'
intvolume: ' 128'
isi: 1
issue: '12'
language:
- iso: eng
month: '03'
oa: 1
oa_version: Published Version
pmid: 1
project:
- _id: 26A151DA-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '844511'
name: Majorana bound states in Ge/SiGe heterostructures
- _id: 260C2330-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '754411'
name: ISTplus - Postdoctoral Fellowships
- _id: 2641CE5E-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: P30207
name: Hole spin orbit qubits in Ge quantum wells
- _id: c0977eea-5a5b-11eb-8a69-a862db0cf4d1
grant_number: I05060
name: High impedance circuit quantum electrodynamics with hole spins
- _id: c08c05c4-5a5b-11eb-8a69-dc6ce49d7973
grant_number: M03032
name: Long-range spin exchange for 2D qubits architectures
publication: Physical Review Letters
publication_identifier:
eissn:
- 1079-7114
publication_status: published
publisher: American Physical Society
quality_controlled: '1'
related_material:
record:
- id: '18291'
relation: popular_science
status: public
scopus_import: '1'
status: public
title: Dynamics of hole singlet-triplet qubits with large g-factor differences
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 128
year: '2022'
...
---
_id: '10922'
abstract:
- lang: eng
text: We study structural rigidity for assemblies with mechanical joints. Existing
methods identify whether an assembly is structurally rigid by assuming parts are
perfectly rigid. Yet, an assembly identified as rigid may not be that “rigid”
in practice, and existing methods cannot quantify how rigid an assembly is. We
address this limitation by developing a new measure, worst-case rigidity, to quantify
the rigidity of an assembly as the largest possible deformation that the assembly
undergoes for arbitrary external loads of fixed magnitude. Computing worst-case
rigidity is non-trivial due to non-rigid parts and different joint types. We thus
formulate a new computational approach by encoding parts and their connections
into a stiffness matrix, in which parts are modeled as deformable objects and
joints as soft constraints. Based on this, we formulate worst-case rigidity analysis
as an optimization that seeks the worst-case deformation of an assembly for arbitrary
external loads, and solve the optimization problem via an eigenanalysis. Furthermore,
we present methods to optimize the geometry and topology of various assemblies
to enhance their rigidity, as guided by our rigidity measure. In the end, we validate
our method on a variety of assembly structures with physical experiments and demonstrate
its effectiveness by designing and fabricating several structurally rigid assemblies.
acknowledged_ssus:
- _id: M-Shop
acknowledgement: "This work was supported by the Research Grants Council of the Hong
Kong Special Administrative Region, China [Project No.: CUHK 14201921] and the European
Research Council (ERC) under the European Union’s Horizon 2020 research and innovation
programme (grant agreement No 715767 – MATERIALIZABLE). We thank the anonymous reviewers
for their insightful feedback; Christian Hafner for proofreading and discussions;
Ziqi Wang,\r\nHaisen Zhao, and Martin Hafskjold Thoresen for the helpful discussions;
and the Miba Machine Shop at IST Austria for 3D printing the BUNNY and BOOMERANG
models."
article_processing_charge: No
article_type: original
author:
- first_name: Zhenyuan
full_name: Liu, Zhenyuan
id: 70f0d7cf-ae65-11ec-a14f-89dfc5505b19
last_name: Liu
orcid: 0000-0001-9200-5690
- first_name: Jingyu
full_name: Hu, Jingyu
last_name: Hu
- first_name: Hao
full_name: Xu, Hao
last_name: Xu
- first_name: Peng
full_name: Song, Peng
last_name: Song
- first_name: Ran
full_name: Zhang, Ran
last_name: Zhang
- first_name: Bernd
full_name: Bickel, Bernd
id: 49876194-F248-11E8-B48F-1D18A9856A87
last_name: Bickel
orcid: 0000-0001-6511-9385
- first_name: Chi-Wing
full_name: Fu, Chi-Wing
last_name: Fu
citation:
ama: Liu Z, Hu J, Xu H, et al. Worst-case rigidity analysis and optimization for
assemblies with mechanical joints. Computer Graphics Forum. 2022;41(2):507-519.
doi:10.1111/cgf.14490
apa: Liu, Z., Hu, J., Xu, H., Song, P., Zhang, R., Bickel, B., & Fu, C.-W. (2022).
Worst-case rigidity analysis and optimization for assemblies with mechanical joints.
Computer Graphics Forum. Wiley. https://doi.org/10.1111/cgf.14490
chicago: Liu, Zhenyuan, Jingyu Hu, Hao Xu, Peng Song, Ran Zhang, Bernd Bickel, and
Chi-Wing Fu. “Worst-Case Rigidity Analysis and Optimization for Assemblies with
Mechanical Joints.” Computer Graphics Forum. Wiley, 2022. https://doi.org/10.1111/cgf.14490.
ieee: Z. Liu et al., “Worst-case rigidity analysis and optimization for assemblies
with mechanical joints,” Computer Graphics Forum, vol. 41, no. 2. Wiley,
pp. 507–519, 2022.
ista: Liu Z, Hu J, Xu H, Song P, Zhang R, Bickel B, Fu C-W. 2022. Worst-case rigidity
analysis and optimization for assemblies with mechanical joints. Computer Graphics
Forum. 41(2), 507–519.
mla: Liu, Zhenyuan, et al. “Worst-Case Rigidity Analysis and Optimization for Assemblies
with Mechanical Joints.” Computer Graphics Forum, vol. 41, no. 2, Wiley,
2022, pp. 507–19, doi:10.1111/cgf.14490.
short: Z. Liu, J. Hu, H. Xu, P. Song, R. Zhang, B. Bickel, C.-W. Fu, Computer Graphics
Forum 41 (2022) 507–519.
date_created: 2022-03-27T17:34:17Z
date_published: 2022-05-01T00:00:00Z
date_updated: 2025-04-14T07:28:57Z
day: '01'
ddc:
- '000'
department:
- _id: BeBi
doi: 10.1111/cgf.14490
ec_funded: 1
external_id:
isi:
- '000802723900039'
file:
- access_level: open_access
checksum: b62188b07f5c000f1638c782ec92da41
content_type: application/pdf
creator: bbickel
date_created: 2022-03-27T17:34:11Z
date_updated: 2022-03-27T17:34:11Z
file_id: '10923'
file_name: paper.pdf
file_size: 19601689
relation: main_file
file_date_updated: 2022-03-27T17:34:11Z
has_accepted_license: '1'
intvolume: ' 41'
isi: 1
issue: '2'
language:
- iso: eng
month: '05'
oa: 1
oa_version: Submitted Version
page: 507-519
project:
- _id: 24F9549A-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '715767'
name: 'MATERIALIZABLE: Intelligent fabrication-oriented Computational Design and
Modeling'
publication: Computer Graphics Forum
publication_identifier:
eissn:
- 1467-8659
issn:
- 0167-7055
publication_status: published
publisher: Wiley
quality_controlled: '1'
scopus_import: '1'
status: public
title: Worst-case rigidity analysis and optimization for assemblies with mechanical
joints
type: journal_article
user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
volume: 41
year: '2022'
...
---
_id: '10925'
abstract:
- lang: eng
text: Direct numerical simulations (DNS) of turbulent channel flows up to Reτ≈1000 are
conducted to investigate the three-dimensional (consisting of streamwise wavenumber,
spanwise wavenumber and frequency) spectrum of wall pressure fluctuations. To
develop a predictive model of the wavenumber–frequency spectrum from the wavenumber
spectrum, the time decorrelation mechanisms of wall pressure fluctuations are
investigated. It is discovered that the energy-containing part of the wavenumber–frequency
spectrum of wall pressure fluctuations can be well predicted using a similar random
sweeping model for streamwise velocity fluctuations. To refine the investigation,
we further decompose the spectrum of the total wall pressure fluctuations into
the autospectra of rapid and slow pressure fluctuations, and the cross-spectrum
between them. We focus on evaluating the assumption applied in many predictive
models, that is, the magnitude of the cross-spectrum is negligibly small. The
present DNS shows that neglecting the cross-spectrum causes a maximum error up
to 4.7 dB in the subconvective region for all Reynolds numbers under test. Our
analyses indicate that the approximation of neglecting the cross-spectrum needs
to be applied carefully in the investigations of acoustics at low Mach numbers,
in which the subconvective components of wall pressure fluctuations make important
contributions to the radiated acoustic power.
acknowledgement: This research is supported by the NSFC Basic Science Center Program
for ‘Multiscale Problems in Nonlinear Mechanics’ (no. 11988102), National Key Project
(GJXM92579) and the Strategic Priority Research Program (XDB22040104).
article_number: A39
article_processing_charge: No
article_type: original
arxiv: 1
author:
- first_name: Bowen
full_name: Yang, Bowen
id: 71b6ff4b-15b2-11ec-abd3-aef6b028cf7e
last_name: Yang
orcid: 0000-0002-4843-6853
- first_name: Zixuan
full_name: Yang, Zixuan
last_name: Yang
citation:
ama: Yang B, Yang Z. On the wavenumber-frequency spectrum of the wall pressure fluctuations
in turbulent channel flow. Journal of Fluid Mechanics. 2022;937. doi:10.1017/jfm.2022.137
apa: Yang, B., & Yang, Z. (2022). On the wavenumber-frequency spectrum of the
wall pressure fluctuations in turbulent channel flow. Journal of Fluid Mechanics.
Cambridge University Press. https://doi.org/10.1017/jfm.2022.137
chicago: Yang, Bowen, and Zixuan Yang. “On the Wavenumber-Frequency Spectrum of
the Wall Pressure Fluctuations in Turbulent Channel Flow.” Journal of Fluid
Mechanics. Cambridge University Press, 2022. https://doi.org/10.1017/jfm.2022.137.
ieee: B. Yang and Z. Yang, “On the wavenumber-frequency spectrum of the wall pressure
fluctuations in turbulent channel flow,” Journal of Fluid Mechanics, vol.
937. Cambridge University Press, 2022.
ista: Yang B, Yang Z. 2022. On the wavenumber-frequency spectrum of the wall pressure
fluctuations in turbulent channel flow. Journal of Fluid Mechanics. 937, A39.
mla: Yang, Bowen, and Zixuan Yang. “On the Wavenumber-Frequency Spectrum of the
Wall Pressure Fluctuations in Turbulent Channel Flow.” Journal of Fluid Mechanics,
vol. 937, A39, Cambridge University Press, 2022, doi:10.1017/jfm.2022.137.
short: B. Yang, Z. Yang, Journal of Fluid Mechanics 937 (2022).
date_created: 2022-03-27T22:01:45Z
date_published: 2022-04-25T00:00:00Z
date_updated: 2023-08-03T06:20:26Z
day: '25'
department:
- _id: GradSch
doi: 10.1017/jfm.2022.137
external_id:
arxiv:
- '2201.04702'
isi:
- '000763547000001'
intvolume: ' 937'
isi: 1
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.1017/jfm.2022.137
month: '04'
oa: 1
oa_version: Published Version
publication: Journal of Fluid Mechanics
publication_identifier:
eissn:
- 1469-7645
issn:
- 0022-1120
publication_status: published
publisher: Cambridge University Press
quality_controlled: '1'
scopus_import: '1'
status: public
title: On the wavenumber-frequency spectrum of the wall pressure fluctuations in turbulent
channel flow
type: journal_article
user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
volume: 937
year: '2022'
...
---
_id: '10926'
abstract:
- lang: eng
text: Conflict over reproduction between females and males exists because of anisogamy
and promiscuity. Together they generate differences in fitness optima between
the sexes and result in antagonistic coevolution of female and male reproductive
traits. Mounting duration is likely to be a compromise between male and female
interests whose outcome depends on the intensity of sexual selection. The timing
of sperm transfer during mounting is critical. For example, mountings may be interrupted
before sperm is transferred as a consequence of female or male choice, or they
may be prolonged to function as mate guarding. In the highly promiscuous intertidal
snail Littorina saxatilis, mountings vary substantially in duration, from less
than a minute to more than an hour, and it has been assumed that mountings of
a few minutes do not result in any sperm being transferred. Here, we examined
the timing of sperm transfer, a reproductive trait that is likely affected by
sexual conflict. We performed time-controlled mounting trials using L. saxatilis
males and virgin females, aiming to examine indirectly when the transfer of sperm
starts. We observed the relationship between mounting duration and the proportion
of developing embryos out of all eggs and embryos in the brood pouch. Developing
embryos were observed in similar proportions in all treatments (i.e. 1, 5 and
10 or more minutes at which mountings were artificially interrupted), suggesting
that sperm transfer begins rapidly (within 1 min) in L. saxatilis and very short
matings do not result in sperm shortage in the females. We discuss how the observed
pattern can be influenced by predation risk, population density, and female status
and receptivity.
article_number: eyab049
article_processing_charge: No
article_type: original
author:
- first_name: Samuel
full_name: Perini, Samuel
last_name: Perini
- first_name: Rogerk
full_name: Butlin, Rogerk
last_name: Butlin
- 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: Kerstin
full_name: Johannesson, Kerstin
last_name: Johannesson
citation:
ama: Perini S, Butlin R, Westram AM, Johannesson K. Very short mountings are enough
for sperm transfer in Littorina saxatilis. Journal of Molluscan Studies.
2022;88(1). doi:10.1093/mollus/eyab049
apa: Perini, S., Butlin, R., Westram, A. M., & Johannesson, K. (2022). Very
short mountings are enough for sperm transfer in Littorina saxatilis. Journal
of Molluscan Studies. Oxford University Press. https://doi.org/10.1093/mollus/eyab049
chicago: Perini, Samuel, Rogerk Butlin, Anja M Westram, and Kerstin Johannesson.
“Very Short Mountings Are Enough for Sperm Transfer in Littorina Saxatilis.” Journal
of Molluscan Studies. Oxford University Press, 2022. https://doi.org/10.1093/mollus/eyab049.
ieee: S. Perini, R. Butlin, A. M. Westram, and K. Johannesson, “Very short mountings
are enough for sperm transfer in Littorina saxatilis,” Journal of Molluscan
Studies, vol. 88, no. 1. Oxford University Press, 2022.
ista: Perini S, Butlin R, Westram AM, Johannesson K. 2022. Very short mountings
are enough for sperm transfer in Littorina saxatilis. Journal of Molluscan Studies.
88(1), eyab049.
mla: Perini, Samuel, et al. “Very Short Mountings Are Enough for Sperm Transfer
in Littorina Saxatilis.” Journal of Molluscan Studies, vol. 88, no. 1,
eyab049, Oxford University Press, 2022, doi:10.1093/mollus/eyab049.
short: S. Perini, R. Butlin, A.M. Westram, K. Johannesson, Journal of Molluscan
Studies 88 (2022).
date_created: 2022-03-27T22:01:46Z
date_published: 2022-03-01T00:00:00Z
date_updated: 2025-05-14T11:05:28Z
day: '01'
department:
- _id: BeVi
doi: 10.1093/mollus/eyab049
external_id:
isi:
- '000759081600002'
intvolume: ' 88'
isi: 1
issue: '1'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://eprints.whiterose.ac.uk/187332/
month: '03'
oa: 1
oa_version: Submitted Version
publication: Journal of Molluscan Studies
publication_identifier:
eissn:
- 1464-3766
issn:
- 0260-1230
publication_status: published
publisher: Oxford University Press
quality_controlled: '1'
scopus_import: '1'
status: public
title: Very short mountings are enough for sperm transfer in Littorina saxatilis
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 88
year: '2022'
...
---
_id: '10927'
abstract:
- lang: eng
text: "Motivation\r\nHigh plasticity of bacterial genomes is provided by numerous
mechanisms including horizontal gene transfer and recombination via numerous flanking
repeats. Genome rearrangements such as inversions, deletions, insertions and duplications
may independently occur in different strains, providing parallel adaptation or
phenotypic diversity. Specifically, such rearrangements might be responsible for
virulence, antibiotic resistance and antigenic variation. However, identification
of such events requires laborious manual inspection and verification of phyletic
pattern consistency.\r\nResults\r\nHere, we define the term ‘parallel rearrangements’
as events that occur independently in phylogenetically distant bacterial strains
and present a formalization of the problem of parallel rearrangements calling.
We implement an algorithmic solution for the identification of parallel rearrangements
in bacterial populations as a tool PaReBrick. The tool takes a collection of strains
represented as a sequence of oriented synteny blocks and a phylogenetic tree as
input data. It identifies rearrangements, tests them for consistency with a tree,
and sorts the events by their parallelism score. The tool provides diagrams of
the neighbors for each block of interest, allowing the detection of horizontally
transferred blocks or their extra copies and the inversions in which copied blocks
are involved. We demonstrated PaReBrick’s efficiency and accuracy and showed its
potential to detect genome rearrangements responsible for pathogenicity and adaptation
in bacterial genomes."
acknowledgement: "The authors thank the 2020 student class of the Bioinformatics Institute,
who\r\nused the first versions of the tool and provided many valuable suggestions
to\r\nimprove usability. They also thank Louisa Gonzalez Somermeyer for manuscript
proofreading\r\nThis work was supported by the National Center for Cognitive Research
of\r\nITMO University and JetBrains Research [to A.Z and N.A.]; and the European\r\nUnion’s
Horizon 2020 Research and Innovation Programme under the Marie\r\nSkłodowska-Curie
[754411 to O.B.].\r\nPaReBrick is written in Python and is available on GitHub:
https://github.com/ctlab/parallel-rearrangements."
article_processing_charge: No
article_type: original
author:
- first_name: Alexey
full_name: Zabelkin, Alexey
last_name: Zabelkin
- first_name: Yulia
full_name: Yakovleva, Yulia
last_name: Yakovleva
- first_name: Olga
full_name: Bochkareva, Olga
id: C4558D3C-6102-11E9-A62E-F418E6697425
last_name: Bochkareva
orcid: 0000-0003-1006-6639
- first_name: Nikita
full_name: Alexeev, Nikita
last_name: Alexeev
citation:
ama: 'Zabelkin A, Yakovleva Y, Bochkareva O, Alexeev N. PaReBrick: PArallel REarrangements
and BReaks identification toolkit. Bioinformatics. 2022;38(2):357-363.
doi:10.1093/bioinformatics/btab691'
apa: 'Zabelkin, A., Yakovleva, Y., Bochkareva, O., & Alexeev, N. (2022). PaReBrick:
PArallel REarrangements and BReaks identification toolkit. Bioinformatics.
Oxford University Press. https://doi.org/10.1093/bioinformatics/btab691'
chicago: 'Zabelkin, Alexey, Yulia Yakovleva, Olga Bochkareva, and Nikita Alexeev.
“PaReBrick: PArallel REarrangements and BReaks Identification Toolkit.” Bioinformatics.
Oxford University Press, 2022. https://doi.org/10.1093/bioinformatics/btab691.'
ieee: 'A. Zabelkin, Y. Yakovleva, O. Bochkareva, and N. Alexeev, “PaReBrick: PArallel
REarrangements and BReaks identification toolkit,” Bioinformatics, vol.
38, no. 2. Oxford University Press, pp. 357–363, 2022.'
ista: 'Zabelkin A, Yakovleva Y, Bochkareva O, Alexeev N. 2022. PaReBrick: PArallel
REarrangements and BReaks identification toolkit. Bioinformatics. 38(2), 357–363.'
mla: 'Zabelkin, Alexey, et al. “PaReBrick: PArallel REarrangements and BReaks Identification
Toolkit.” Bioinformatics, vol. 38, no. 2, Oxford University Press, 2022,
pp. 357–63, doi:10.1093/bioinformatics/btab691.'
short: A. Zabelkin, Y. Yakovleva, O. Bochkareva, N. Alexeev, Bioinformatics 38 (2022)
357–363.
corr_author: '1'
date_created: 2022-03-27T22:01:46Z
date_published: 2022-01-15T00:00:00Z
date_updated: 2025-05-14T11:05:09Z
day: '15'
ddc:
- '000'
department:
- _id: FyKo
doi: 10.1093/bioinformatics/btab691
ec_funded: 1
external_id:
isi:
- '000743380100008'
file:
- access_level: open_access
checksum: 4b5688ff9ac86180ccdf7f82fa33d926
content_type: application/pdf
creator: dernst
date_created: 2022-03-28T08:07:46Z
date_updated: 2022-03-28T08:07:46Z
file_id: '10930'
file_name: 2022_Bioinformatics_Zabelkin.pdf
file_size: 3425744
relation: main_file
success: 1
file_date_updated: 2022-03-28T08:07:46Z
has_accepted_license: '1'
intvolume: ' 38'
isi: 1
issue: '2'
language:
- iso: eng
month: '01'
oa: 1
oa_version: Published Version
page: 357-363
project:
- _id: 260C2330-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '754411'
name: ISTplus - Postdoctoral Fellowships
publication: Bioinformatics
publication_identifier:
eissn:
- 1460-2059
issn:
- 1367-4803
publication_status: published
publisher: Oxford University Press
quality_controlled: '1'
related_material:
link:
- relation: software
url: https://github.com/ctlab/parallel-rearrangements
scopus_import: '1'
status: public
title: 'PaReBrick: PArallel REarrangements and BReaks identification toolkit'
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 38
year: '2022'
...
---
_id: '10939'
abstract:
- lang: eng
text: Understanding and characterising biochemical processes inside single cells
requires experimental platforms that allow one to perturb and observe the dynamics
of such processes as well as computational methods to build and parameterise models
from the collected data. Recent progress with experimental platforms and optogenetics
has made it possible to expose each cell in an experiment to an individualised
input and automatically record cellular responses over days with fine time resolution.
However, methods to infer parameters of stochastic kinetic models from single-cell
longitudinal data have generally been developed under the assumption that experimental
data is sparse and that responses of cells to at most a few different input perturbations
can be observed. Here, we investigate and compare different approaches for calculating
parameter likelihoods of single-cell longitudinal data based on approximations
of the chemical master equation (CME) with a particular focus on coupling the
linear noise approximation (LNA) or moment closure methods to a Kalman filter.
We show that, as long as cells are measured sufficiently frequently, coupling
the LNA to a Kalman filter allows one to accurately approximate likelihoods and
to infer model parameters from data even in cases where the LNA provides poor
approximations of the CME. Furthermore, the computational cost of filtering-based
iterative likelihood evaluation scales advantageously in the number of measurement
times and different input perturbations and is thus ideally suited for data obtained
from modern experimental platforms. To demonstrate the practical usefulness of
these results, we perform an experiment in which single cells, equipped with an
optogenetic gene expression system, are exposed to various different light-input
sequences and measured at several hundred time points and use parameter inference
based on iterative likelihood evaluation to parameterise a stochastic model of
the system.
acknowledgement: We thank Virgile Andreani for useful discussions about the model
and parameter inference. We thank Johan Paulsson and Jeffrey J Tabor for kind gifts
of plasmids. R was supported by the ANR grant CyberCircuits (ANR-18-CE91-0002).
The funders had no role in study design, data collection and analysis, decision
to publish, or preparation of the manuscript.
article_number: e1009950
article_processing_charge: No
article_type: original
author:
- first_name: Anđela
full_name: Davidović, Anđela
last_name: Davidović
- first_name: Remy P
full_name: Chait, Remy P
id: 3464AE84-F248-11E8-B48F-1D18A9856A87
last_name: Chait
orcid: 0000-0003-0876-3187
- first_name: Gregory
full_name: Batt, Gregory
last_name: Batt
- first_name: Jakob
full_name: Ruess, Jakob
id: 4A245D00-F248-11E8-B48F-1D18A9856A87
last_name: Ruess
orcid: 0000-0003-1615-3282
citation:
ama: Davidović A, Chait RP, Batt G, Ruess J. Parameter inference for stochastic
biochemical models from perturbation experiments parallelised at the single cell
level. PLoS Computational Biology. 2022;18(3). doi:10.1371/journal.pcbi.1009950
apa: Davidović, A., Chait, R. P., Batt, G., & Ruess, J. (2022). Parameter inference
for stochastic biochemical models from perturbation experiments parallelised at
the single cell level. PLoS Computational Biology. Public Library of Science.
https://doi.org/10.1371/journal.pcbi.1009950
chicago: Davidović, Anđela, Remy P Chait, Gregory Batt, and Jakob Ruess. “Parameter
Inference for Stochastic Biochemical Models from Perturbation Experiments Parallelised
at the Single Cell Level.” PLoS Computational Biology. Public Library of
Science, 2022. https://doi.org/10.1371/journal.pcbi.1009950.
ieee: A. Davidović, R. P. Chait, G. Batt, and J. Ruess, “Parameter inference for
stochastic biochemical models from perturbation experiments parallelised at the
single cell level,” PLoS Computational Biology, vol. 18, no. 3. Public
Library of Science, 2022.
ista: Davidović A, Chait RP, Batt G, Ruess J. 2022. Parameter inference for stochastic
biochemical models from perturbation experiments parallelised at the single cell
level. PLoS Computational Biology. 18(3), e1009950.
mla: Davidović, Anđela, et al. “Parameter Inference for Stochastic Biochemical Models
from Perturbation Experiments Parallelised at the Single Cell Level.” PLoS
Computational Biology, vol. 18, no. 3, e1009950, Public Library of Science,
2022, doi:10.1371/journal.pcbi.1009950.
short: A. Davidović, R.P. Chait, G. Batt, J. Ruess, PLoS Computational Biology 18
(2022).
date_created: 2022-04-03T22:01:42Z
date_published: 2022-03-18T00:00:00Z
date_updated: 2025-09-09T14:29:53Z
day: '18'
ddc:
- '570'
- '000'
department:
- _id: CaGu
doi: 10.1371/journal.pcbi.1009950
external_id:
isi:
- '001044208400004'
pmid:
- '35303737'
file:
- access_level: open_access
checksum: 458ef542761fb714ced214f240daf6b2
content_type: application/pdf
creator: dernst
date_created: 2022-04-04T10:14:39Z
date_updated: 2022-04-04T10:14:39Z
file_id: '10947'
file_name: 2022_PLoSCompBio_Davidovic.pdf
file_size: 2958642
relation: main_file
success: 1
file_date_updated: 2022-04-04T10:14:39Z
has_accepted_license: '1'
intvolume: ' 18'
isi: 1
issue: '3'
language:
- iso: eng
month: '03'
oa: 1
oa_version: Published Version
pmid: 1
publication: PLoS Computational Biology
publication_identifier:
eissn:
- 1553-7358
issn:
- 1553-734X
publication_status: published
publisher: Public Library of Science
quality_controlled: '1'
related_material:
link:
- relation: software
url: https://gitlab.pasteur.fr/adavidov/inferencelnakf
scopus_import: '1'
status: public
title: Parameter inference for stochastic biochemical models from perturbation experiments
parallelised at the single cell level
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: journal_article
user_id: 317138e5-6ab7-11ef-aa6d-ffef3953e345
volume: 18
year: '2022'
...
---
_id: '10940'
abstract:
- lang: eng
text: 'Magnetic-field-resilient superconducting circuits enable sensing applications
and hybrid quantum computing architectures involving spin or topological qubits
and electromechanical elements, as well as studying flux noise and quasiparticle
loss. We investigate the effect of in-plane magnetic fields up to 1 T on the spectrum
and coherence times of thin-film three-dimensional aluminum transmons. Using a
copper cavity, unaffected by strong magnetic fields, we can probe solely the effect
of magnetic fields on the transmons. We present data on a single-junction and
a superconducting-quantum-interference-device (SQUID) transmon that are cooled
down in the same cavity. As expected, the transmon frequencies decrease with increasing
field, due to suppression of the superconducting gap and a geometric Fraunhofer-like
contribution. Nevertheless, the thin-film transmons show strong magnetic field
resilience: both transmons display microsecond coherence up to at least 0.65 T,
and T1 remains above 1μs over the entire measurable range. SQUID spectroscopy
is feasible up to 1 T, the limit of our magnet. We conclude that thin-film aluminum
Josephson junctions are suitable hardware for superconducting circuits in the
high-magnetic-field regime.'
acknowledgement: "We would like to thank Ida Milow for her internship in the laboratory
and contributions to our code base. We thank T. Zent and L. Hamdan for technical
assistance, and D. Fan for help with setting up the aluminum evaporator. We thank
A. Salari, M. Rößler, S. Barzanjeh, M. Zemlicka, F. Hassani, and M. Peruzzo for
contributions in the early stages of the experiments. This project has received
funding from the European Research Council (ERC) under the European Union’s Horizon
2020 research and innovation program (Grant Agreement No. 741121) and was also funded
by the Deutsche Forschungsgemeinschaft (DFG, German Research Foundation) under CRC
1238 – 277146847 (Subproject B01), as well as under Germany’s Excellence Strategy
– Cluster of Excellence Matter and Light for Quantum Computing (ML4Q), EXC 2004/1\r\n–
390534769."
article_number: '034032'
article_processing_charge: No
article_type: original
arxiv: 1
author:
- first_name: J.
full_name: Krause, J.
last_name: Krause
- first_name: C.
full_name: Dickel, C.
last_name: Dickel
- first_name: E.
full_name: Vaal, E.
last_name: Vaal
- first_name: M.
full_name: Vielmetter, M.
last_name: Vielmetter
- first_name: J.
full_name: Feng, J.
last_name: Feng
- first_name: R.
full_name: Bounds, R.
last_name: Bounds
- first_name: G.
full_name: Catelani, G.
last_name: Catelani
- first_name: Johannes M
full_name: Fink, Johannes M
id: 4B591CBA-F248-11E8-B48F-1D18A9856A87
last_name: Fink
orcid: 0000-0001-8112-028X
- first_name: Yoichi
full_name: Ando, Yoichi
last_name: Ando
citation:
ama: Krause J, Dickel C, Vaal E, et al. Magnetic field resilience of three-dimensional
transmons with thin-film Al/AlOx/Al Josephson junctions approaching 1 T. Physical
Review Applied. 2022;17(3). doi:10.1103/PhysRevApplied.17.034032
apa: Krause, J., Dickel, C., Vaal, E., Vielmetter, M., Feng, J., Bounds, R., … Ando,
Y. (2022). Magnetic field resilience of three-dimensional transmons with thin-film
Al/AlOx/Al Josephson junctions approaching 1 T. Physical Review Applied.
American Physical Society. https://doi.org/10.1103/PhysRevApplied.17.034032
chicago: Krause, J., C. Dickel, E. Vaal, M. Vielmetter, J. Feng, R. Bounds, G. Catelani,
Johannes M Fink, and Yoichi Ando. “Magnetic Field Resilience of Three-Dimensional
Transmons with Thin-Film Al/AlOx/Al Josephson Junctions Approaching 1 T.” Physical
Review Applied. American Physical Society, 2022. https://doi.org/10.1103/PhysRevApplied.17.034032.
ieee: J. Krause et al., “Magnetic field resilience of three-dimensional transmons
with thin-film Al/AlOx/Al Josephson junctions approaching 1 T,” Physical Review
Applied, vol. 17, no. 3. American Physical Society, 2022.
ista: Krause J, Dickel C, Vaal E, Vielmetter M, Feng J, Bounds R, Catelani G, Fink
JM, Ando Y. 2022. Magnetic field resilience of three-dimensional transmons with
thin-film Al/AlOx/Al Josephson junctions approaching 1 T. Physical Review Applied.
17(3), 034032.
mla: Krause, J., et al. “Magnetic Field Resilience of Three-Dimensional Transmons
with Thin-Film Al/AlOx/Al Josephson Junctions Approaching 1 T.” Physical Review
Applied, vol. 17, no. 3, 034032, American Physical Society, 2022, doi:10.1103/PhysRevApplied.17.034032.
short: J. Krause, C. Dickel, E. Vaal, M. Vielmetter, J. Feng, R. Bounds, G. Catelani,
J.M. Fink, Y. Ando, Physical Review Applied 17 (2022).
date_created: 2022-04-03T22:01:43Z
date_published: 2022-03-11T00:00:00Z
date_updated: 2023-08-03T06:23:58Z
day: '11'
department:
- _id: JoFi
doi: 10.1103/PhysRevApplied.17.034032
external_id:
arxiv:
- '2111.01115'
isi:
- '000770371400003'
intvolume: ' 17'
isi: 1
issue: '3'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.48550/arXiv.2111.01115
month: '03'
oa: 1
oa_version: Preprint
publication: Physical Review Applied
publication_identifier:
eissn:
- 2331-7019
publication_status: published
publisher: American Physical Society
quality_controlled: '1'
scopus_import: '1'
status: public
title: Magnetic field resilience of three-dimensional transmons with thin-film Al/AlOx/Al
Josephson junctions approaching 1 T
type: journal_article
user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
volume: 17
year: '2022'
...
---
DOAJ_listed: '1'
OA_place: publisher
OA_type: gold
_id: '10945'
abstract:
- lang: eng
text: Mica-titania pearlescent pigments (MTs) were previously coated with organic
molecules to obtain combination pigments (CPs) for achieving certain improvements
or functionalities. Anthocyanins (ACNs) are molecules that can be extracted from
natural resources and exhibit color changes via pH modifications of the enclosing
medium. The purpose of the study was to produce a new series of CPs by depositing
ACNs on MTs at different pH values, to observe the changes in color, and to associate
these changes to thermogravimetrically determined deposition efficiencies in light
of spectral differences. The extraction and deposition methods were based on aqueous
chemistry and were straightforward. The ACN deposition generally increased with
increasing pH and correlated with the consistency between the charges of the MT
surfaces and the dominant ACN species at a specific pH value. The fluorescence
of the CPs was inversely correlated with the deposition quantities invoking the
possibility of a quenching effect.
acknowledgement: "This research was partly funded by Hacettepe University (Bilimsel
Ara¸stırma Projeleri\r\nKoordinasyon Birimi), grant number FHD-2015-8094.The authors
are indebted to Ahmet Önal for his supports in acquiring the fluorescence spectra
and the decision of excitation wavelengths. The authors also acknowledge use of
the services and facilities of UNAM-National Nanotechnology Research Center at Bilkent
University and mica donation from Sabuncular Mining Co."
article_processing_charge: Yes
article_type: original
author:
- first_name: Mehmet Orkun
full_name: Çoruh, Mehmet Orkun
id: d25163e5-8d53-11eb-a251-e6dd8ea1b8ef
last_name: Çoruh
orcid: 0000-0002-3219-2022
- first_name: Güngör
full_name: Gündüz, Güngör
last_name: Gündüz
- first_name: Üner
full_name: Çolak, Üner
last_name: Çolak
- first_name: Bora
full_name: Maviş, Bora
last_name: Maviş
citation:
ama: Çoruh MO, Gündüz G, Çolak Ü, Maviş B. pH-dependent coloring of combination
effect pigments with anthocyanins from Brassica oleracea var. capitata F. rubra.
Colorants. 2022;1(2):149-164. doi:10.3390/colorants1020010
apa: Çoruh, M. O., Gündüz, G., Çolak, Ü., & Maviş, B. (2022). pH-dependent coloring
of combination effect pigments with anthocyanins from Brassica oleracea var. capitata
F. rubra. Colorants. MDPI. https://doi.org/10.3390/colorants1020010
chicago: Çoruh, Mehmet Orkun, Güngör Gündüz, Üner Çolak, and Bora Maviş. “PH-Dependent
Coloring of Combination Effect Pigments with Anthocyanins from Brassica Oleracea
Var. Capitata F. Rubra.” Colorants. MDPI, 2022. https://doi.org/10.3390/colorants1020010.
ieee: M. O. Çoruh, G. Gündüz, Ü. Çolak, and B. Maviş, “pH-dependent coloring of
combination effect pigments with anthocyanins from Brassica oleracea var. capitata
F. rubra,” Colorants, vol. 1, no. 2. MDPI, pp. 149–164, 2022.
ista: Çoruh MO, Gündüz G, Çolak Ü, Maviş B. 2022. pH-dependent coloring of combination
effect pigments with anthocyanins from Brassica oleracea var. capitata F. rubra.
Colorants. 1(2), 149–164.
mla: Çoruh, Mehmet Orkun, et al. “PH-Dependent Coloring of Combination Effect Pigments
with Anthocyanins from Brassica Oleracea Var. Capitata F. Rubra.” Colorants,
vol. 1, no. 2, MDPI, 2022, pp. 149–64, doi:10.3390/colorants1020010.
short: M.O. Çoruh, G. Gündüz, Ü. Çolak, B. Maviş, Colorants 1 (2022) 149–164.
date_created: 2022-04-04T09:03:54Z
date_published: 2022-04-01T00:00:00Z
date_updated: 2024-10-14T13:52:09Z
day: '01'
ddc:
- '570'
department:
- _id: LeSa
doi: 10.3390/colorants1020010
file:
- access_level: open_access
checksum: 2c15c8d3041ebc36bc64870247081758
content_type: application/pdf
creator: dernst
date_created: 2022-04-04T10:39:24Z
date_updated: 2022-04-04T10:39:24Z
file_id: '10949'
file_name: 2022_Colorants_Coruh.pdf
file_size: 2437988
relation: main_file
success: 1
file_date_updated: 2022-04-04T10:39:24Z
has_accepted_license: '1'
intvolume: ' 1'
issue: '2'
language:
- iso: eng
month: '04'
oa: 1
oa_version: Published Version
page: 149-164
publication: Colorants
publication_identifier:
issn:
- 2079-6447
publication_status: published
publisher: MDPI
quality_controlled: '1'
status: public
title: pH-dependent coloring of combination effect pigments with anthocyanins from
Brassica oleracea var. capitata F. rubra
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: 0043cee0-e5fc-11ee-9736-f83bc23afbf0
volume: 1
year: '2022'
...
---
_id: '11142'
abstract:
- lang: eng
text: SnTe is a promising Pb-free thermoelectric (TE) material with high electrical
conductivity. We discovered the synergistic effect of Bi2O3 on enhancing the average
power factor (PF) and overall ZT value of the SnTe-based thermoelectric material.
The introduction of Bi2O3 forms plenty of SnO2, Bi2O3, and Bi-rich nanoprecipitates.
These interfaces between the SnTe matrix and the nanoprecipitates can enhance
the average PF through the energy filtering effect. On the other hand, abundant
and diverse nanoprecipitates can significantly diminish the lattice thermal conductivity
(κlat) through enhanced phonon scattering. The synergistic effect of Bi2O3 resulted
in a maximum ZT (ZTmax) value of 0.9 at SnTe-2% Bi2O3 and an average ZT (ZTave)
value of 0.4 for SnTe-4% Bi2O3 from 300 K to 823 K. The work provides an excellent
reference to develop non-toxic high-performance TE materials.
acknowledgement: This work was supported by National Natural Science Foundation of
China (52002042), National Key Research and Development Program of China (2018YFA0702100
and 2018YFB0703600), 111 Project (B17002) and Lise Meitner Project M 2889-N. This
work was also supported by the National Postdoctoral Program for Innovative Talents
(BX20200028). L.D.Z. appreciates the support of the high-performance computing (HPC)
resources at Beihang University, the National Science Fund for Distinguished Young
Scholars (51925101), and center for High Pressure Science and Technology Advanced
Research (HPSTAR) for SEM and TEM measurements.
article_number: '100985'
article_processing_charge: No
article_type: original
author:
- first_name: Tao
full_name: Hong, Tao
last_name: Hong
- first_name: Changrong
full_name: Guo, Changrong
last_name: Guo
- first_name: Dongyang
full_name: Wang, Dongyang
last_name: Wang
- first_name: Bingchao
full_name: Qin, Bingchao
last_name: Qin
- first_name: Cheng
full_name: Chang, Cheng
id: 9E331C2E-9F27-11E9-AE48-5033E6697425
last_name: Chang
orcid: 0000-0002-9515-4277
- first_name: Xiang
full_name: Gao, Xiang
last_name: Gao
- first_name: Li Dong
full_name: Zhao, Li Dong
last_name: Zhao
citation:
ama: Hong T, Guo C, Wang D, et al. Enhanced thermoelectric performance in SnTe due
to the energy filtering effect introduced by Bi2O3. Materials Today Energy.
2022;25. doi:10.1016/j.mtener.2022.100985
apa: Hong, T., Guo, C., Wang, D., Qin, B., Chang, C., Gao, X., & Zhao, L. D.
(2022). Enhanced thermoelectric performance in SnTe due to the energy filtering
effect introduced by Bi2O3. Materials Today Energy. Elsevier. https://doi.org/10.1016/j.mtener.2022.100985
chicago: Hong, Tao, Changrong Guo, Dongyang Wang, Bingchao Qin, Cheng Chang, Xiang
Gao, and Li Dong Zhao. “Enhanced Thermoelectric Performance in SnTe Due to the
Energy Filtering Effect Introduced by Bi2O3.” Materials Today Energy. Elsevier,
2022. https://doi.org/10.1016/j.mtener.2022.100985.
ieee: T. Hong et al., “Enhanced thermoelectric performance in SnTe due to
the energy filtering effect introduced by Bi2O3,” Materials Today Energy,
vol. 25. Elsevier, 2022.
ista: Hong T, Guo C, Wang D, Qin B, Chang C, Gao X, Zhao LD. 2022. Enhanced thermoelectric
performance in SnTe due to the energy filtering effect introduced by Bi2O3. Materials
Today Energy. 25, 100985.
mla: Hong, Tao, et al. “Enhanced Thermoelectric Performance in SnTe Due to the Energy
Filtering Effect Introduced by Bi2O3.” Materials Today Energy, vol. 25,
100985, Elsevier, 2022, doi:10.1016/j.mtener.2022.100985.
short: T. Hong, C. Guo, D. Wang, B. Qin, C. Chang, X. Gao, L.D. Zhao, Materials
Today Energy 25 (2022).
corr_author: '1'
date_created: 2022-04-10T22:01:39Z
date_published: 2022-04-01T00:00:00Z
date_updated: 2025-04-14T09:29:32Z
day: '01'
department:
- _id: MaIb
doi: 10.1016/j.mtener.2022.100985
external_id:
isi:
- '000798679100010'
intvolume: ' 25'
isi: 1
language:
- iso: eng
month: '04'
oa_version: None
project:
- _id: 9B8804FC-BA93-11EA-9121-9846C619BF3A
grant_number: M02889
name: Bottom-up Engineering for Thermoelectric Applications
publication: Materials Today Energy
publication_identifier:
eissn:
- 2468-6069
publication_status: published
publisher: Elsevier
quality_controlled: '1'
scopus_import: '1'
status: public
title: Enhanced thermoelectric performance in SnTe due to the energy filtering effect
introduced by Bi2O3
type: journal_article
user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
volume: 25
year: '2022'
...
---
_id: '11143'
abstract:
- lang: eng
text: 'Dravet syndrome is a neurodevelopmental disorder characterized by epilepsy,
intellectual disability, and sudden death due to pathogenic variants in SCN1A
with loss of function of the sodium channel subunit Nav1.1. Nav1.1-expressing
parvalbumin GABAergic interneurons (PV-INs) from young Scn1a+/− mice show impaired
action potential generation. An approach assessing PV-IN function in the same
mice at two time points shows impaired spike generation in all Scn1a+/− mice at
postnatal days (P) 16–21, whether deceased prior or surviving to P35, with normalization
by P35 in surviving mice. However, PV-IN synaptic transmission is dysfunctional
in young Scn1a+/− mice that did not survive and in Scn1a+/− mice ≥ P35. Modeling
confirms that PV-IN axonal propagation is more sensitive to decreased sodium conductance
than spike generation. These results demonstrate dynamic dysfunction in Dravet
syndrome: combined abnormalities of PV-IN spike generation and propagation drives
early disease severity, while ongoing dysfunction of synaptic transmission contributes
to chronic pathology.'
acknowledgement: We would like to thank Bernardo Rudy, Joanna Mattis, and Laura Mcgarry
for comments on a previous version of the manuscript; Xiaohong Zhang for expert
technical support and mouse colony maintenance; Melody Cheng for assistance with
generation of the graphical abstract; and Jennifer Kearney for the gift of Scn1a+/−
mice. This work was supported by the National Institute of Neurological Disorders
and Stroke of the National Institutes of Health under F31NS111803 (to K.M.G.) and
K08NS097633 and R01NS110869 (to E.M.G.), the Dravet Syndrome Foundation (to A.S.),
an ERC Consolidator Grant (SYNAPSEEK) (to T.P.V.), and the NOMIS Foundation through
the NOMIS Fellowships program at IST Austria (to C.C.). The graphical abstract was
prepared using BioRender software (BioRender.com).
article_number: '110580'
article_processing_charge: No
article_type: original
author:
- first_name: Keisuke
full_name: Kaneko, Keisuke
last_name: Kaneko
- first_name: Christopher
full_name: Currin, Christopher
id: e8321fc5-3091-11eb-8a53-83f309a11ac9
last_name: Currin
orcid: 0000-0002-4809-5059
- first_name: Kevin M.
full_name: Goff, Kevin M.
last_name: Goff
- first_name: Eric R.
full_name: Wengert, Eric R.
last_name: Wengert
- first_name: Ala
full_name: Somarowthu, Ala
last_name: Somarowthu
- first_name: Tim P
full_name: Vogels, Tim P
id: CB6FF8D2-008F-11EA-8E08-2637E6697425
last_name: Vogels
orcid: 0000-0003-3295-6181
- first_name: Ethan M.
full_name: Goldberg, Ethan M.
last_name: Goldberg
citation:
ama: Kaneko K, Currin C, Goff KM, et al. Developmentally regulated impairment of
parvalbumin interneuron synaptic transmission in an experimental model of Dravet
syndrome. Cell Reports. 2022;38(13). doi:10.1016/j.celrep.2022.110580
apa: Kaneko, K., Currin, C., Goff, K. M., Wengert, E. R., Somarowthu, A., Vogels,
T. P., & Goldberg, E. M. (2022). Developmentally regulated impairment of parvalbumin
interneuron synaptic transmission in an experimental model of Dravet syndrome.
Cell Reports. Elsevier. https://doi.org/10.1016/j.celrep.2022.110580
chicago: Kaneko, Keisuke, Christopher Currin, Kevin M. Goff, Eric R. Wengert, Ala
Somarowthu, Tim P Vogels, and Ethan M. Goldberg. “Developmentally Regulated Impairment
of Parvalbumin Interneuron Synaptic Transmission in an Experimental Model of Dravet
Syndrome.” Cell Reports. Elsevier, 2022. https://doi.org/10.1016/j.celrep.2022.110580.
ieee: K. Kaneko et al., “Developmentally regulated impairment of parvalbumin
interneuron synaptic transmission in an experimental model of Dravet syndrome,”
Cell Reports, vol. 38, no. 13. Elsevier, 2022.
ista: Kaneko K, Currin C, Goff KM, Wengert ER, Somarowthu A, Vogels TP, Goldberg
EM. 2022. Developmentally regulated impairment of parvalbumin interneuron synaptic
transmission in an experimental model of Dravet syndrome. Cell Reports. 38(13),
110580.
mla: Kaneko, Keisuke, et al. “Developmentally Regulated Impairment of Parvalbumin
Interneuron Synaptic Transmission in an Experimental Model of Dravet Syndrome.”
Cell Reports, vol. 38, no. 13, 110580, Elsevier, 2022, doi:10.1016/j.celrep.2022.110580.
short: K. Kaneko, C. Currin, K.M. Goff, E.R. Wengert, A. Somarowthu, T.P. Vogels,
E.M. Goldberg, Cell Reports 38 (2022).
date_created: 2022-04-10T22:01:39Z
date_published: 2022-03-29T00:00:00Z
date_updated: 2025-06-11T14:00:11Z
day: '29'
ddc:
- '570'
department:
- _id: TiVo
doi: 10.1016/j.celrep.2022.110580
ec_funded: 1
external_id:
isi:
- '000779794000001'
pmid:
- '35354025'
file:
- access_level: open_access
checksum: 49105c6c27c9af0f37f50a8bbb4d380d
content_type: application/pdf
creator: dernst
date_created: 2022-04-15T11:00:58Z
date_updated: 2022-04-15T11:00:58Z
file_id: '11172'
file_name: 2022_CellReports_Kaneko.pdf
file_size: 4774216
relation: main_file
success: 1
file_date_updated: 2022-04-15T11:00:58Z
has_accepted_license: '1'
intvolume: ' 38'
isi: 1
issue: '13'
language:
- iso: eng
license: https://creativecommons.org/licenses/by-nc-nd/4.0/
month: '03'
oa: 1
oa_version: Published Version
pmid: 1
project:
- _id: 0aacfa84-070f-11eb-9043-d7eb2c709234
call_identifier: H2020
grant_number: '819603'
name: Learning the shape of synaptic plasticity rules for neuronal architectures
and function through machine learning.
- _id: 9B861AAC-BA93-11EA-9121-9846C619BF3A
name: NOMIS Fellowship Program
publication: Cell Reports
publication_identifier:
eissn:
- 2211-1247
publication_status: published
publisher: Elsevier
quality_controlled: '1'
scopus_import: '1'
status: public
title: Developmentally regulated impairment of parvalbumin interneuron synaptic transmission
in an experimental model of Dravet syndrome
tmp:
image: /images/cc_by_nc_nd.png
legal_code_url: https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode
name: Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International
(CC BY-NC-ND 4.0)
short: CC BY-NC-ND (4.0)
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 38
year: '2022'
...
---
_id: '11144'
abstract:
- lang: eng
text: Thermoelectric materials allow for direct conversion between heat and electricity,
offering the potential for power generation. The average dimensionless figure
of merit ZTave determines device efficiency. N-type tin selenide crystals exhibit
outstanding three-dimensional charge and two-dimensional phonon transport along
the out-of-plane direction, contributing to a high maximum figure of merit Zmax
of ~3.6 × 10−3 per kelvin but a moderate ZTave of ~1.1. We found an attractive
high Zmax of ~4.1 × 10−3 per kelvin at 748 kelvin and a ZTave of ~1.7 at 300 to
773 kelvin in chlorine-doped and lead-alloyed tin selenide crystals by phonon-electron
decoupling. The chlorine-induced low deformation potential improved the carrier
mobility. The lead-induced mass and strain fluctuations reduced the lattice thermal
conductivity. Phonon-electron decoupling plays a critical role to achieve high-performance
thermoelectrics.
acknowledgement: This work was supported by the Basic Science Center Project of the
National Natural Science Foundation of China (51788104), the National Key Research
and Development Program of China (2018YFA0702100), the National Science Fund for
Distinguished Young Scholars (51925101), the 111 Project (B17002), the Lise Meitner
Project (M2889-N), and the National Key Research and Development Program of China
(2018YFB0703600). This work is also supported by the National Postdoctoral Program
for Innovative Talents (BX20200028). L.-D.Z. is thankful for the high-performance
computing resources at Beihang University.
article_processing_charge: No
article_type: original
author:
- first_name: Lizhong
full_name: Su, Lizhong
last_name: Su
- first_name: Dongyang
full_name: Wang, Dongyang
last_name: Wang
- first_name: Sining
full_name: Wang, Sining
last_name: Wang
- first_name: Bingchao
full_name: Qin, Bingchao
last_name: Qin
- first_name: Yuping
full_name: Wang, Yuping
last_name: Wang
- first_name: Yongxin
full_name: Qin, Yongxin
last_name: Qin
- first_name: Yang
full_name: Jin, Yang
last_name: Jin
- first_name: Cheng
full_name: Chang, Cheng
id: 9E331C2E-9F27-11E9-AE48-5033E6697425
last_name: Chang
orcid: 0000-0002-9515-4277
- first_name: Li Dong
full_name: Zhao, Li Dong
last_name: Zhao
citation:
ama: Su L, Wang D, Wang S, et al. High thermoelectric performance realized through
manipulating layered phonon-electron decoupling. Science. 2022;375(6587):1385-1389.
doi:10.1126/science.abn8997
apa: Su, L., Wang, D., Wang, S., Qin, B., Wang, Y., Qin, Y., … Zhao, L. D. (2022).
High thermoelectric performance realized through manipulating layered phonon-electron
decoupling. Science. American Association for the Advancement of Science.
https://doi.org/10.1126/science.abn8997
chicago: Su, Lizhong, Dongyang Wang, Sining Wang, Bingchao Qin, Yuping Wang, Yongxin
Qin, Yang Jin, Cheng Chang, and Li Dong Zhao. “High Thermoelectric Performance
Realized through Manipulating Layered Phonon-Electron Decoupling.” Science.
American Association for the Advancement of Science, 2022. https://doi.org/10.1126/science.abn8997.
ieee: L. Su et al., “High thermoelectric performance realized through manipulating
layered phonon-electron decoupling,” Science, vol. 375, no. 6587. American
Association for the Advancement of Science, pp. 1385–1389, 2022.
ista: Su L, Wang D, Wang S, Qin B, Wang Y, Qin Y, Jin Y, Chang C, Zhao LD. 2022.
High thermoelectric performance realized through manipulating layered phonon-electron
decoupling. Science. 375(6587), 1385–1389.
mla: Su, Lizhong, et al. “High Thermoelectric Performance Realized through Manipulating
Layered Phonon-Electron Decoupling.” Science, vol. 375, no. 6587, American
Association for the Advancement of Science, 2022, pp. 1385–89, doi:10.1126/science.abn8997.
short: L. Su, D. Wang, S. Wang, B. Qin, Y. Wang, Y. Qin, Y. Jin, C. Chang, L.D.
Zhao, Science 375 (2022) 1385–1389.
corr_author: '1'
date_created: 2022-04-10T22:01:40Z
date_published: 2022-03-25T00:00:00Z
date_updated: 2025-04-14T09:29:32Z
day: '25'
department:
- _id: MaIb
doi: 10.1126/science.abn8997
external_id:
isi:
- '000778894800038'
pmid:
- '35324303'
intvolume: ' 375'
isi: 1
issue: '6587'
language:
- iso: eng
month: '03'
oa_version: None
page: 1385-1389
pmid: 1
project:
- _id: 9B8804FC-BA93-11EA-9121-9846C619BF3A
grant_number: M02889
name: Bottom-up Engineering for Thermoelectric Applications
publication: Science
publication_identifier:
eissn:
- 1095-9203
publication_status: published
publisher: American Association for the Advancement of Science
quality_controlled: '1'
scopus_import: '1'
status: public
title: High thermoelectric performance realized through manipulating layered phonon-electron
decoupling
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 375
year: '2022'
...
---
_id: '11145'
abstract:
- lang: eng
text: List-decodability of Reed-Solomon codes has re-ceived a lot of attention,
but the best-possible dependence between the parameters is still not well-understood.
In this work, we focus on the case where the list-decoding radius is of the form
r=1−ε for ε tending to zero. Our main result states that there exist Reed-Solomon
codes with rate Ω(ε) which are (1−ε,O(1/ε) -list-decodable, meaning that any Hamming
ball of radius 1−ε contains at most O(1/ε) codewords. This trade-off between rate
and list-decoding radius is best-possible for any code with list size less than
exponential in the block length. By achieving this trade-off between rate and
list-decoding radius we improve a recent result of Guo, Li, Shangguan, Tamo, and
Wootters, and resolve the main motivating question of their work. Moreover, while
their result requires the field to be exponentially large in the block length,
we only need the field size to be polynomially large (and in fact, almost-linear
suffices). We deduce our main result from a more general theorem, in which we
prove good list-decodability properties of random puncturings of any given code
with very large distance.
article_processing_charge: No
arxiv: 1
author:
- first_name: Asaf
full_name: Ferber, Asaf
last_name: Ferber
- first_name: Matthew Alan
full_name: Kwan, Matthew Alan
id: 5fca0887-a1db-11eb-95d1-ca9d5e0453b3
last_name: Kwan
orcid: 0000-0002-4003-7567
- first_name: Lisa
full_name: Sauermann, Lisa
last_name: Sauermann
citation:
ama: 'Ferber A, Kwan MA, Sauermann L. List-decodability with large radius for Reed-Solomon
codes. In: 62nd Annual IEEE Symposium on Foundations of Computer Science.
Vol 2022. IEEE; 2022:720-726. doi:10.1109/FOCS52979.2021.00075'
apa: 'Ferber, A., Kwan, M. A., & Sauermann, L. (2022). List-decodability with
large radius for Reed-Solomon codes. In 62nd Annual IEEE Symposium on Foundations
of Computer Science (Vol. 2022, pp. 720–726). Denver, CO, United States: IEEE.
https://doi.org/10.1109/FOCS52979.2021.00075'
chicago: Ferber, Asaf, Matthew Alan Kwan, and Lisa Sauermann. “List-Decodability
with Large Radius for Reed-Solomon Codes.” In 62nd Annual IEEE Symposium on
Foundations of Computer Science, 2022:720–26. IEEE, 2022. https://doi.org/10.1109/FOCS52979.2021.00075.
ieee: A. Ferber, M. A. Kwan, and L. Sauermann, “List-decodability with large radius
for Reed-Solomon codes,” in 62nd Annual IEEE Symposium on Foundations of Computer
Science, Denver, CO, United States, 2022, vol. 2022, pp. 720–726.
ista: 'Ferber A, Kwan MA, Sauermann L. 2022. List-decodability with large radius
for Reed-Solomon codes. 62nd Annual IEEE Symposium on Foundations of Computer
Science. FOCS: Foundations of Computer Science vol. 2022, 720–726.'
mla: Ferber, Asaf, et al. “List-Decodability with Large Radius for Reed-Solomon
Codes.” 62nd Annual IEEE Symposium on Foundations of Computer Science,
vol. 2022, IEEE, 2022, pp. 720–26, doi:10.1109/FOCS52979.2021.00075.
short: A. Ferber, M.A. Kwan, L. Sauermann, in:, 62nd Annual IEEE Symposium on Foundations
of Computer Science, IEEE, 2022, pp. 720–726.
conference:
end_date: 2022-02-10
location: Denver, CO, United States
name: 'FOCS: Foundations of Computer Science'
start_date: 2022-02-07
date_created: 2022-04-10T22:01:40Z
date_published: 2022-02-01T00:00:00Z
date_updated: 2025-07-10T11:50:08Z
day: '01'
department:
- _id: MaKw
doi: 10.1109/FOCS52979.2021.00075
external_id:
arxiv:
- '2012.10584'
isi:
- '000802209600065'
intvolume: ' 2022'
isi: 1
language:
- iso: eng
main_file_link:
- open_access: '1'
url: ' https://doi.org/10.48550/arXiv.2012.10584'
month: '02'
oa: 1
oa_version: Preprint
page: 720-726
publication: 62nd Annual IEEE Symposium on Foundations of Computer Science
publication_identifier:
isbn:
- '9781665420556'
issn:
- 0272-5428
publication_status: published
publisher: IEEE
quality_controlled: '1'
related_material:
record:
- id: '10775'
relation: later_version
status: public
scopus_import: '1'
status: public
title: List-decodability with large radius for Reed-Solomon codes
type: conference
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 2022
year: '2022'
...
---
_id: '11155'
abstract:
- lang: eng
text: The potential of energy filtering and direct electron detection for cryo-electron
microscopy (cryo-EM) has been well documented. Here, we assess the performance
of recently introduced hardware for cryo-electron tomography (cryo-ET) and subtomogram
averaging (STA), an increasingly popular structural determination method for complex
3D specimens. We acquired cryo-ET datasets of EIAV virus-like particles (VLPs)
on two contemporary cryo-EM systems equipped with different energy filters and
direct electron detectors (DED), specifically a Krios G4, equipped with a cold
field emission gun (CFEG), Thermo Fisher Scientific Selectris X energy filter,
and a Falcon 4 DED; and a Krios G3i, with a Schottky field emission gun (XFEG),
a Gatan Bioquantum energy filter, and a K3 DED. We performed constrained cross-correlation-based
STA on equally sized datasets acquired on the respective systems. The resulting
EIAV CA hexamer reconstructions show that both systems perform comparably in the
4–6 Å resolution range based on Fourier-Shell correlation (FSC). In addition,
by employing a recently introduced multiparticle refinement approach, we obtained
a reconstruction of the EIAV CA hexamer at 2.9 Å. Our results demonstrate the
potential of the new generation of energy filters and DEDs for STA, and the effects
of using different processing pipelines on their STA outcomes.
acknowledged_ssus:
- _id: LifeSc
- _id: ScienComp
- _id: EM-Fac
acknowledgement: This work was funded by the Austrian Science Fund (FWF) grant P31445
to F.K.M.S and the National Institute of Allergy and Infectious Diseases under awards
R01AI147890 to R.A.D. 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). We
thank Dustin Morado for providing the software SubTOM for data processing. We also
thank William Wan for critical reading of the manuscript and valuable feedback.
article_number: '107852'
article_processing_charge: Yes (via OA deal)
article_type: original
author:
- first_name: Martin
full_name: Obr, Martin
id: 4741CA5A-F248-11E8-B48F-1D18A9856A87
last_name: Obr
orcid: 0000-0003-1756-6564
- first_name: Wim J.H.
full_name: Hagen, Wim J.H.
last_name: Hagen
- first_name: Robert A.
full_name: Dick, Robert A.
last_name: Dick
- first_name: Lingbo
full_name: Yu, Lingbo
last_name: Yu
- first_name: Abhay
full_name: Kotecha, Abhay
last_name: Kotecha
- first_name: Florian KM
full_name: Schur, Florian KM
id: 48AD8942-F248-11E8-B48F-1D18A9856A87
last_name: Schur
orcid: 0000-0003-4790-8078
citation:
ama: Obr M, Hagen WJH, Dick RA, Yu L, Kotecha A, Schur FK. Exploring high-resolution
cryo-ET and subtomogram averaging capabilities of contemporary DEDs. Journal
of Structural Biology. 2022;214(2). doi:10.1016/j.jsb.2022.107852
apa: Obr, M., Hagen, W. J. H., Dick, R. A., Yu, L., Kotecha, A., & Schur, F.
K. (2022). Exploring high-resolution cryo-ET and subtomogram averaging capabilities
of contemporary DEDs. Journal of Structural Biology. Elsevier. https://doi.org/10.1016/j.jsb.2022.107852
chicago: Obr, Martin, Wim J.H. Hagen, Robert A. Dick, Lingbo Yu, Abhay Kotecha,
and Florian KM Schur. “Exploring High-Resolution Cryo-ET and Subtomogram Averaging
Capabilities of Contemporary DEDs.” Journal of Structural Biology. Elsevier,
2022. https://doi.org/10.1016/j.jsb.2022.107852.
ieee: M. Obr, W. J. H. Hagen, R. A. Dick, L. Yu, A. Kotecha, and F. K. Schur, “Exploring
high-resolution cryo-ET and subtomogram averaging capabilities of contemporary
DEDs,” Journal of Structural Biology, vol. 214, no. 2. Elsevier, 2022.
ista: Obr M, Hagen WJH, Dick RA, Yu L, Kotecha A, Schur FK. 2022. Exploring high-resolution
cryo-ET and subtomogram averaging capabilities of contemporary DEDs. Journal of
Structural Biology. 214(2), 107852.
mla: Obr, Martin, et al. “Exploring High-Resolution Cryo-ET and Subtomogram Averaging
Capabilities of Contemporary DEDs.” Journal of Structural Biology, vol.
214, no. 2, 107852, Elsevier, 2022, doi:10.1016/j.jsb.2022.107852.
short: M. Obr, W.J.H. Hagen, R.A. Dick, L. Yu, A. Kotecha, F.K. Schur, Journal of
Structural Biology 214 (2022).
corr_author: '1'
date_created: 2022-04-15T07:10:26Z
date_published: 2022-06-01T00:00:00Z
date_updated: 2025-04-15T08:24:50Z
day: '01'
ddc:
- '570'
department:
- _id: FlSc
doi: 10.1016/j.jsb.2022.107852
external_id:
isi:
- '000790733600001'
pmid:
- '35351542'
file:
- access_level: open_access
checksum: 0b1eb53447aae8e95ae4c12d193b0b00
content_type: application/pdf
creator: dernst
date_created: 2022-08-02T11:07:58Z
date_updated: 2022-08-02T11:07:58Z
file_id: '11722'
file_name: 2022_JourStructuralBiology_Obr.pdf
file_size: 7080863
relation: main_file
success: 1
file_date_updated: 2022-08-02T11:07:58Z
has_accepted_license: '1'
intvolume: ' 214'
isi: 1
issue: '2'
keyword:
- Structural Biology
language:
- iso: eng
month: '06'
oa: 1
oa_version: Published Version
pmid: 1
project:
- _id: 26736D6A-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: P31445
name: Structural conservation and diversity in retroviral capsid
publication: Journal of Structural Biology
publication_identifier:
issn:
- 1047-8477
publication_status: published
publisher: Elsevier
quality_controlled: '1'
scopus_import: '1'
status: public
title: Exploring high-resolution cryo-ET and subtomogram averaging capabilities of
contemporary DEDs
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: 214
year: '2022'
...
---
_id: '11167'
abstract:
- lang: eng
text: Complex I is one of the major respiratory complexes, conserved from bacteria
to mammals. It oxidises NADH, reduces quinone and pumps protons across the membrane,
thus playing a central role in the oxidative energy metabolism. In this review
we discuss our current state of understanding the structure of complex I from
various species of mammals, plants, fungi, and bacteria, as well as of several
complex I-related proteins. By comparing the structural evidence from these systems
in different redox states and data from mutagenesis and molecular simulations,
we formulate the mechanisms of electron transfer and proton pumping and explain
how they are conformationally and electrostatically coupled. Finally, we discuss
the structural basis of the deactivation phenomenon in mammalian complex I.
article_number: '102350'
article_processing_charge: Yes (via OA deal)
article_type: original
author:
- first_name: Domen
full_name: Kampjut, Domen
id: 37233050-F248-11E8-B48F-1D18A9856A87
last_name: Kampjut
- first_name: Leonid A
full_name: Sazanov, Leonid A
id: 338D39FE-F248-11E8-B48F-1D18A9856A87
last_name: Sazanov
orcid: 0000-0002-0977-7989
citation:
ama: Kampjut D, Sazanov LA. Structure of respiratory complex I – An emerging blueprint
for the mechanism. Current Opinion in Structural Biology. 2022;74. doi:10.1016/j.sbi.2022.102350
apa: Kampjut, D., & Sazanov, L. A. (2022). Structure of respiratory complex
I – An emerging blueprint for the mechanism. Current Opinion in Structural
Biology. Elsevier. https://doi.org/10.1016/j.sbi.2022.102350
chicago: Kampjut, Domen, and Leonid A Sazanov. “Structure of Respiratory Complex
I – An Emerging Blueprint for the Mechanism.” Current Opinion in Structural
Biology. Elsevier, 2022. https://doi.org/10.1016/j.sbi.2022.102350.
ieee: D. Kampjut and L. A. Sazanov, “Structure of respiratory complex I – An emerging
blueprint for the mechanism,” Current Opinion in Structural Biology, vol.
74. Elsevier, 2022.
ista: Kampjut D, Sazanov LA. 2022. Structure of respiratory complex I – An emerging
blueprint for the mechanism. Current Opinion in Structural Biology. 74, 102350.
mla: Kampjut, Domen, and Leonid A. Sazanov. “Structure of Respiratory Complex I
– An Emerging Blueprint for the Mechanism.” Current Opinion in Structural Biology,
vol. 74, 102350, Elsevier, 2022, doi:10.1016/j.sbi.2022.102350.
short: D. Kampjut, L.A. Sazanov, Current Opinion in Structural Biology 74 (2022).
corr_author: '1'
date_created: 2022-04-15T09:32:35Z
date_published: 2022-06-01T00:00:00Z
date_updated: 2024-10-09T21:02:00Z
day: '01'
ddc:
- '570'
department:
- _id: LeSa
doi: 10.1016/j.sbi.2022.102350
external_id:
isi:
- '000829029500020'
pmid:
- '35316665'
file:
- access_level: open_access
checksum: 72bdde48853643a32d42b75f54965c44
content_type: application/pdf
creator: dernst
date_created: 2022-08-05T05:56:03Z
date_updated: 2022-08-05T05:56:03Z
file_id: '11725'
file_name: 2022_CurrentOpStructBiology_Kampjut.pdf
file_size: 815607
relation: main_file
success: 1
file_date_updated: 2022-08-05T05:56:03Z
has_accepted_license: '1'
intvolume: ' 74'
isi: 1
keyword:
- Molecular Biology
- Structural Biology
language:
- iso: eng
month: '06'
oa: 1
oa_version: Published Version
pmid: 1
publication: Current Opinion in Structural Biology
publication_identifier:
issn:
- 0959-440X
publication_status: published
publisher: Elsevier
quality_controlled: '1'
scopus_import: '1'
status: public
title: Structure of respiratory complex I – An emerging blueprint for the mechanism
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: 74
year: '2022'
...
---
_id: '11179'
abstract:
- lang: eng
text: Large oligomeric enzymes control a myriad of cellular processes, from protein
synthesis and degradation to metabolism. The 0.5 MDa large TET2 aminopeptidase,
a prototypical protease important for cellular homeostasis, degrades peptides
within a ca. 60 Å wide tetrahedral chamber with four lateral openings. The mechanisms
of substrate trafficking and processing remain debated. Here, we integrate magic-angle
spinning (MAS) NMR, mutagenesis, co-evolution analysis and molecular dynamics
simulations and reveal that a loop in the catalytic chamber is a key element for
enzymatic function. The loop is able to stabilize ligands in the active site and
may additionally have a direct role in activating the catalytic water molecule
whereby a conserved histidine plays a key role. Our data provide a strong case
for the functional importance of highly dynamic - and often overlooked - parts
of an enzyme, and the potential of MAS NMR to investigate their dynamics at atomic
resolution.
acknowledgement: "We are grateful to Bernhard Brutscher, Alicia Vallet, and Adrien
Favier for excellent NMR\r\nplatform operation and management. The plasmid coding
for TET2 was kindly provided\r\nby Bruno Franzetti and Jerome Boisbouvier (IBS Grenoble).
We thank Anne-Marie Villard\r\nand the RoBioMol platform for preparing the loop
deletion construct. The RoBioMol\r\nplatform is part of the Grenoble Instruct-ERIC
center (ISBG; UAR 3518 CNRS-CEAUGA-EMBL) within the Grenoble Partnership for Structural
Biology (PSB), supported by FRISBI (ANR-10-INBS-0005-02) and GRAL (ANR-10-LABX-49-01),
financed within the University Grenoble Alpes graduate school (Ecoles Universitaires
de Recherche) CBHEUR-GS (ANR-17-EURE-0003). This work was supported by the European
Research Council (StG-2012-311318-ProtDyn2Function to P. S.) and the French Agence
Nationale de la Recherche (ANR), under grant ANR-14-ACHN-0016 (M.P. and A.B.)."
article_number: '1927'
article_processing_charge: No
article_type: original
author:
- first_name: Diego F.
full_name: Gauto, Diego F.
last_name: Gauto
- first_name: Pavel
full_name: Macek, Pavel
last_name: Macek
- first_name: Duccio
full_name: Malinverni, Duccio
last_name: Malinverni
- first_name: Hugo
full_name: Fraga, Hugo
last_name: Fraga
- first_name: Matteo
full_name: Paloni, Matteo
last_name: Paloni
- first_name: Iva
full_name: Sučec, Iva
last_name: Sučec
- first_name: Audrey
full_name: Hessel, Audrey
last_name: Hessel
- first_name: Juan Pablo
full_name: Bustamante, Juan Pablo
last_name: Bustamante
- first_name: Alessandro
full_name: Barducci, Alessandro
last_name: Barducci
- first_name: Paul
full_name: Schanda, Paul
id: 7B541462-FAF6-11E9-A490-E8DFE5697425
last_name: Schanda
orcid: 0000-0002-9350-7606
citation:
ama: Gauto DF, Macek P, Malinverni D, et al. Functional control of a 0.5 MDa TET
aminopeptidase by a flexible loop revealed by MAS NMR. Nature Communications.
2022;13. doi:10.1038/s41467-022-29423-0
apa: Gauto, D. F., Macek, P., Malinverni, D., Fraga, H., Paloni, M., Sučec, I.,
… Schanda, P. (2022). Functional control of a 0.5 MDa TET aminopeptidase by a
flexible loop revealed by MAS NMR. Nature Communications. Springer Nature.
https://doi.org/10.1038/s41467-022-29423-0
chicago: Gauto, Diego F., Pavel Macek, Duccio Malinverni, Hugo Fraga, Matteo Paloni,
Iva Sučec, Audrey Hessel, Juan Pablo Bustamante, Alessandro Barducci, and Paul
Schanda. “Functional Control of a 0.5 MDa TET Aminopeptidase by a Flexible Loop
Revealed by MAS NMR.” Nature Communications. Springer Nature, 2022. https://doi.org/10.1038/s41467-022-29423-0.
ieee: D. F. Gauto et al., “Functional control of a 0.5 MDa TET aminopeptidase
by a flexible loop revealed by MAS NMR,” Nature Communications, vol. 13.
Springer Nature, 2022.
ista: Gauto DF, Macek P, Malinverni D, Fraga H, Paloni M, Sučec I, Hessel A, Bustamante
JP, Barducci A, Schanda P. 2022. Functional control of a 0.5 MDa TET aminopeptidase
by a flexible loop revealed by MAS NMR. Nature Communications. 13, 1927.
mla: Gauto, Diego F., et al. “Functional Control of a 0.5 MDa TET Aminopeptidase
by a Flexible Loop Revealed by MAS NMR.” Nature Communications, vol. 13,
1927, Springer Nature, 2022, doi:10.1038/s41467-022-29423-0.
short: D.F. Gauto, P. Macek, D. Malinverni, H. Fraga, M. Paloni, I. Sučec, A. Hessel,
J.P. Bustamante, A. Barducci, P. Schanda, Nature Communications 13 (2022).
corr_author: '1'
date_created: 2022-04-17T22:01:45Z
date_published: 2022-04-08T00:00:00Z
date_updated: 2025-06-11T13:31:55Z
day: '08'
ddc:
- '570'
department:
- _id: PaSc
doi: 10.1038/s41467-022-29423-0
external_id:
isi:
- '000781498700009'
pmid:
- '35395851'
file:
- access_level: open_access
checksum: db61d5534e988743d6266d3675d77b08
content_type: application/pdf
creator: dernst
date_created: 2022-05-02T08:48:00Z
date_updated: 2022-05-02T08:48:00Z
file_id: '11348'
file_name: 2022_NatureCommunications_Gauto.pdf
file_size: 2637590
relation: main_file
success: 1
file_date_updated: 2022-05-02T08:48:00Z
has_accepted_license: '1'
intvolume: ' 13'
isi: 1
language:
- iso: eng
month: '04'
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'
related_material:
link:
- relation: erratum
url: https://doi.org/10.1038/s41467-022-31243-1
scopus_import: '1'
status: public
title: Functional control of a 0.5 MDa TET aminopeptidase by a flexible loop revealed
by MAS NMR
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 13
year: '2022'
...
---
_id: '11180'
abstract:
- lang: eng
text: "Designing and implementing efficient parallel priority schedulers is an active
research area. An intriguing proposed design is the Multi-Queue: given n threads
and m ≥ n distinct priority queues, task insertions are performed uniformly at
random, while, to delete, a thread picks two queues uniformly at random, and removes
the observed task of higher priority. This approach scales well, and has probabilistic
rank guarantees: roughly, the rank of each task removed, relative to remaining
tasks in all other queues, is O (m) in expectation. Yet, the performance of this
pattern is below that of well-engineered schedulers, which eschew theoretical
guarantees for practical efficiency.\r\n\r\nWe investigate whether it is possible
to design and implement a Multi-Queue-based task scheduler that is both highly-efficient
and has analytical guarantees. We propose a new variant called the Stealing Multi-Queue
(SMQ), a cache-efficient variant of the Multi-Queue, which leverages both queue
affinity---each thread has a local queue, from which tasks are usually removed;
but, with some probability, threads also attempt to steal higher-priority tasks
from the other queues---and task batching, that is, the processing of several
tasks in a single insert / remove step. These ideas are well-known for task scheduling
without priorities; our theoretical contribution is showing that, despite relaxations,
this design can still provide rank guarantees, which in turn implies bounds on
total work performed. We provide a general SMQ implementation which can surpass
state-of-the-art schedulers such as OBIM and PMOD in terms of performance on popular
graph-processing benchmarks. Notably, the performance improvement comes mainly
from the superior rank guarantees provided by our scheduler, confirming that analytically-reasoned
approaches can still provide performance improvements for priority task scheduling."
acknowledgement: We would like to thank the anonymous reviewers for their useful comments.
This project has received funding from the European Research Council (ERC) under
the European Union’s Horizon 2020 research and innovation programme (grant agreement
No 805223 ScaleML).
article_processing_charge: No
arxiv: 1
author:
- first_name: Anastasiia
full_name: Postnikova, Anastasiia
last_name: Postnikova
- first_name: Nikita
full_name: Koval, Nikita
id: 2F4DB10C-F248-11E8-B48F-1D18A9856A87
last_name: Koval
- first_name: Giorgi
full_name: Nadiradze, Giorgi
id: 3279A00C-F248-11E8-B48F-1D18A9856A87
last_name: Nadiradze
orcid: 0000-0001-5634-0731
- first_name: Dan-Adrian
full_name: Alistarh, Dan-Adrian
id: 4A899BFC-F248-11E8-B48F-1D18A9856A87
last_name: Alistarh
orcid: 0000-0003-3650-940X
citation:
ama: 'Postnikova A, Koval N, Nadiradze G, Alistarh D-A. Multi-queues can be state-of-the-art
priority schedulers. In: Proceedings of the 27th ACM SIGPLAN Symposium on Principles
and Practice of Parallel Programming. Association for Computing Machinery;
2022:353-367. doi:10.1145/3503221.3508432'
apa: 'Postnikova, A., Koval, N., Nadiradze, G., & Alistarh, D.-A. (2022). Multi-queues
can be state-of-the-art priority schedulers. In Proceedings of the 27th ACM
SIGPLAN Symposium on Principles and Practice of Parallel Programming (pp.
353–367). Seoul, Republic of Korea: Association for Computing Machinery. https://doi.org/10.1145/3503221.3508432'
chicago: Postnikova, Anastasiia, Nikita Koval, Giorgi Nadiradze, and Dan-Adrian
Alistarh. “Multi-Queues Can Be State-of-the-Art Priority Schedulers.” In Proceedings
of the 27th ACM SIGPLAN Symposium on Principles and Practice of Parallel Programming,
353–67. Association for Computing Machinery, 2022. https://doi.org/10.1145/3503221.3508432.
ieee: A. Postnikova, N. Koval, G. Nadiradze, and D.-A. Alistarh, “Multi-queues can
be state-of-the-art priority schedulers,” in Proceedings of the 27th ACM SIGPLAN
Symposium on Principles and Practice of Parallel Programming, Seoul, Republic
of Korea, 2022, pp. 353–367.
ista: 'Postnikova A, Koval N, Nadiradze G, Alistarh D-A. 2022. Multi-queues can
be state-of-the-art priority schedulers. Proceedings of the 27th ACM SIGPLAN Symposium
on Principles and Practice of Parallel Programming. PPoPP: Sympopsium on Principles
and Practice of Parallel Programming, 353–367.'
mla: Postnikova, Anastasiia, et al. “Multi-Queues Can Be State-of-the-Art Priority
Schedulers.” Proceedings of the 27th ACM SIGPLAN Symposium on Principles and
Practice of Parallel Programming, Association for Computing Machinery, 2022,
pp. 353–67, doi:10.1145/3503221.3508432.
short: A. Postnikova, N. Koval, G. Nadiradze, D.-A. Alistarh, in:, Proceedings of
the 27th ACM SIGPLAN Symposium on Principles and Practice of Parallel Programming,
Association for Computing Machinery, 2022, pp. 353–367.
conference:
end_date: 2022-04-06
location: Seoul, Republic of Korea
name: 'PPoPP: Sympopsium on Principles and Practice of Parallel Programming'
start_date: 2022-04-02
corr_author: '1'
date_created: 2022-04-17T22:01:46Z
date_published: 2022-04-02T00:00:00Z
date_updated: 2025-04-14T07:49:13Z
day: '02'
department:
- _id: DaAl
doi: 10.1145/3503221.3508432
ec_funded: 1
external_id:
arxiv:
- '2109.00657'
isi:
- '000883318200025'
isi: 1
language:
- iso: eng
main_file_link:
- open_access: '1'
url: ' https://doi.org/10.48550/arXiv.2109.00657'
month: '04'
oa: 1
oa_version: Preprint
page: 353-367
project:
- _id: 268A44D6-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '805223'
name: Elastic Coordination for Scalable Machine Learning
publication: Proceedings of the 27th ACM SIGPLAN Symposium on Principles and Practice
of Parallel Programming
publication_identifier:
isbn:
- '9781450392044'
publication_status: published
publisher: Association for Computing Machinery
quality_controlled: '1'
related_material:
record:
- id: '13076'
relation: research_data
status: public
scopus_import: '1'
status: public
title: Multi-queues can be state-of-the-art priority schedulers
type: conference
user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
year: '2022'
...
---
_id: '11181'
abstract:
- lang: eng
text: 'To maximize the performance of concurrent data structures, researchers have
often turned to highly complex fine-grained techniques, resulting in efficient
and elegant algorithms, which can however be often difficult to understand and
prove correct. While simpler techniques exist, such as transactional memory, they
can have limited performance or portability relative to their fine-grained counterparts.
Approaches at both ends of this complexity-performance spectrum have been extensively
explored, but relatively less is known about the middle ground: approaches that
are willing to sacrifice some performance for simplicity, while remaining competitive
with state-of-the-art handcrafted designs. In this paper, we explore this middle
ground, and present PathCAS, a primitive that combines ideas from multi-word CAS
(KCAS) and transactional memory approaches, while carefully avoiding overhead.
We show how PathCAS can be used to implement efficient search data structures
relatively simply, using an internal binary search tree as an example, then extending
this to an AVL tree. Our best implementations outperform many handcrafted search
trees: in search-heavy workloads, it rivals the BCCO tree [5], the fastest known
concurrent binary tree in terms of search performance [3]. Our results suggest
that PathCAS can yield concurrent data structures that are relatively easy to
build and prove correct, while offering surprisingly high performance.'
acknowledgement: "This work was supported by: the Natural Sciences and Engineering
Research Council of Canada (NSERC) Collaborative Research and Development grant:
CRDPJ 539431-19, the\r\nCanada Foundation for Innovation John R. Evans Leaders Fund
with equal support from the Ontario Research Fund CFI Leaders Opportunity Fund:
38512, Waterloo Huawei Joint Innovation Lab project “Scalable Infrastructure for
Next Generation Data Management Systems”, NSERC Discovery Launch Supplement: DGECR-2019-00048,
NSERC Discovery\r\nProgram under the grants: RGPIN-2019-04227 and RGPIN04512-2018,
and the University of Waterloo. We would also like to thank the reviewers for their
insightful comments."
article_processing_charge: No
author:
- first_name: Trevor A
full_name: Brown, Trevor A
id: 3569F0A0-F248-11E8-B48F-1D18A9856A87
last_name: Brown
- first_name: William
full_name: Sigouin, William
last_name: Sigouin
- first_name: Dan-Adrian
full_name: Alistarh, Dan-Adrian
id: 4A899BFC-F248-11E8-B48F-1D18A9856A87
last_name: Alistarh
orcid: 0000-0003-3650-940X
citation:
ama: 'Brown TA, Sigouin W, Alistarh D-A. PathCAS: An efficient middle ground for
concurrent search data structures. In: Proceedings of the 27th ACM SIGPLAN
Symposium on Principles and Practice of Parallel Programming. Association
for Computing Machinery; 2022:385-399. doi:10.1145/3503221.3508410'
apa: 'Brown, T. A., Sigouin, W., & Alistarh, D.-A. (2022). PathCAS: An efficient
middle ground for concurrent search data structures. In Proceedings of the
27th ACM SIGPLAN Symposium on Principles and Practice of Parallel Programming
(pp. 385–399). Seoul, Republic of Korea: Association for Computing Machinery.
https://doi.org/10.1145/3503221.3508410'
chicago: 'Brown, Trevor A, William Sigouin, and Dan-Adrian Alistarh. “PathCAS: An
Efficient Middle Ground for Concurrent Search Data Structures.” In Proceedings
of the 27th ACM SIGPLAN Symposium on Principles and Practice of Parallel Programming,
385–99. Association for Computing Machinery, 2022. https://doi.org/10.1145/3503221.3508410.'
ieee: 'T. A. Brown, W. Sigouin, and D.-A. Alistarh, “PathCAS: An efficient middle
ground for concurrent search data structures,” in Proceedings of the 27th ACM
SIGPLAN Symposium on Principles and Practice of Parallel Programming, Seoul,
Republic of Korea, 2022, pp. 385–399.'
ista: 'Brown TA, Sigouin W, Alistarh D-A. 2022. PathCAS: An efficient middle ground
for concurrent search data structures. Proceedings of the 27th ACM SIGPLAN Symposium
on Principles and Practice of Parallel Programming. PPoPP: Sympopsium on Principles
and Practice of Parallel Programming, 385–399.'
mla: 'Brown, Trevor A., et al. “PathCAS: An Efficient Middle Ground for Concurrent
Search Data Structures.” Proceedings of the 27th ACM SIGPLAN Symposium on Principles
and Practice of Parallel Programming, Association for Computing Machinery,
2022, pp. 385–99, doi:10.1145/3503221.3508410.'
short: T.A. Brown, W. Sigouin, D.-A. Alistarh, in:, Proceedings of the 27th ACM
SIGPLAN Symposium on Principles and Practice of Parallel Programming, Association
for Computing Machinery, 2022, pp. 385–399.
conference:
end_date: 2022-04-06
location: Seoul, Republic of Korea
name: 'PPoPP: Sympopsium on Principles and Practice of Parallel Programming'
start_date: 2022-04-02
corr_author: '1'
date_created: 2022-04-17T22:01:46Z
date_published: 2022-04-02T00:00:00Z
date_updated: 2024-10-09T21:02:23Z
day: '02'
ddc:
- '000'
department:
- _id: DaAl
doi: 10.1145/3503221.3508410
external_id:
isi:
- '000883318200027'
file:
- access_level: open_access
checksum: 8ceea411fa133795cd4903529498eb6b
content_type: application/pdf
creator: dernst
date_created: 2022-08-05T09:19:29Z
date_updated: 2022-08-05T09:19:29Z
file_id: '11731'
file_name: 2022_PPoPP_Brown.pdf
file_size: 1128343
relation: main_file
success: 1
file_date_updated: 2022-08-05T09:19:29Z
has_accepted_license: '1'
isi: 1
language:
- iso: eng
month: '04'
oa: 1
oa_version: Published Version
page: 385-399
publication: Proceedings of the 27th ACM SIGPLAN Symposium on Principles and Practice
of Parallel Programming
publication_identifier:
isbn:
- '9781450392044'
publication_status: published
publisher: Association for Computing Machinery
quality_controlled: '1'
scopus_import: '1'
status: public
title: 'PathCAS: An efficient middle ground for concurrent search data structures'
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: conference
user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
year: '2022'
...
---
OA_place: publisher
OA_type: hybrid
_id: '11182'
abstract:
- lang: eng
text: Immune cells are constantly on the move through multicellular organisms to
explore and respond to pathogens and other harmful insults. While moving, immune
cells efficiently traverse microenvironments composed of tissue cells and extracellular
fibers, which together form complex environments of various porosity, stiffness,
topography, and chemical composition. In this protocol we describe experimental
procedures to investigate immune cell migration through microenvironments of heterogeneous
porosity. In particular, we describe micro-channels, micro-pillars, and collagen
networks as cell migration paths with alternative pore size choices. Employing
micro-channels or micro-pillars that divide at junctions into alternative paths
with initially differentially sized pores allows us to precisely (1) measure the
cellular translocation time through these porous path junctions, (2) quantify
the cellular preference for individual pore sizes, and (3) image cellular components
like the nucleus and the cytoskeleton. This reductionistic experimental setup
thus can elucidate how immune cells perform decisions in complex microenvironments
of various porosity like the interstitium. The setup further allows investigation
of the underlying forces of cellular squeezing and the consequences of cellular
deformation on the integrity of the cell and its organelles. As a complementary
approach that does not require any micro-engineering expertise, we describe the
usage of three-dimensional collagen networks with different pore sizes. Whereas
we here focus on dendritic cells as a model for motile immune cells, the described
protocols are versatile as they are also applicable for other immune cell types
like neutrophils and non-immune cell types such as mesenchymal and cancer cells.
In summary, we here describe protocols to identify the mechanisms and principles
of cellular probing, decision making, and squeezing during cellular movement through
microenvironments of heterogeneous porosity.
acknowledgement: "We thank Kasia Stefanowski for excellent technical assistance, and
the Core Facility Bioimaging of the Biomedical Center (BMC) of the Ludwig-Maximilian
University for excellent support. We gratefully acknowledge financial support from
the Peter Hans Hofschneider Professorship of the Stiftung Experimentelle Biomedizin
(to J.R), from the DFG (Collaborative Research Center SFB914, project A12; and Priority
Programme SPP2332, project 492014049; both to J.R) and from the LMU Institutional
Strategy LMU-Excellent within the framework of the German Excellence Initiative
(to J.R).\r\nOpen access funding enabled and organized by Projekt DEAL."
article_number: e407
article_processing_charge: No
article_type: original
author:
- first_name: Janina
full_name: Kroll, Janina
last_name: Kroll
- first_name: Mauricio J.A.
full_name: Ruiz-Fernandez, Mauricio J.A.
last_name: Ruiz-Fernandez
- first_name: Malte B.
full_name: Braun, Malte B.
last_name: Braun
- first_name: Jack
full_name: Merrin, Jack
id: 4515C308-F248-11E8-B48F-1D18A9856A87
last_name: Merrin
orcid: 0000-0001-5145-4609
- first_name: Jörg
full_name: Renkawitz, Jörg
id: 3F0587C8-F248-11E8-B48F-1D18A9856A87
last_name: Renkawitz
orcid: 0000-0003-2856-3369
citation:
ama: Kroll J, Ruiz-Fernandez MJA, Braun MB, Merrin J, Renkawitz J. Quantifying the
probing and selection of microenvironmental pores by motile immune cells. Current
Protocols. 2022;2(4). doi:10.1002/cpz1.407
apa: Kroll, J., Ruiz-Fernandez, M. J. A., Braun, M. B., Merrin, J., & Renkawitz,
J. (2022). Quantifying the probing and selection of microenvironmental pores by
motile immune cells. Current Protocols. Wiley. https://doi.org/10.1002/cpz1.407
chicago: Kroll, Janina, Mauricio J.A. Ruiz-Fernandez, Malte B. Braun, Jack Merrin,
and Jörg Renkawitz. “Quantifying the Probing and Selection of Microenvironmental
Pores by Motile Immune Cells.” Current Protocols. Wiley, 2022. https://doi.org/10.1002/cpz1.407.
ieee: J. Kroll, M. J. A. Ruiz-Fernandez, M. B. Braun, J. Merrin, and J. Renkawitz,
“Quantifying the probing and selection of microenvironmental pores by motile immune
cells,” Current Protocols, vol. 2, no. 4. Wiley, 2022.
ista: Kroll J, Ruiz-Fernandez MJA, Braun MB, Merrin J, Renkawitz J. 2022. Quantifying
the probing and selection of microenvironmental pores by motile immune cells.
Current Protocols. 2(4), e407.
mla: Kroll, Janina, et al. “Quantifying the Probing and Selection of Microenvironmental
Pores by Motile Immune Cells.” Current Protocols, vol. 2, no. 4, e407,
Wiley, 2022, doi:10.1002/cpz1.407.
short: J. Kroll, M.J.A. Ruiz-Fernandez, M.B. Braun, J. Merrin, J. Renkawitz, Current
Protocols 2 (2022).
date_created: 2022-04-17T22:01:46Z
date_published: 2022-04-05T00:00:00Z
date_updated: 2024-10-14T13:16:54Z
day: '05'
ddc:
- '570'
department:
- _id: NanoFab
doi: 10.1002/cpz1.407
external_id:
pmid:
- '35384410'
file:
- access_level: open_access
checksum: 72152d005c367777f6cf2f6a477f0d52
content_type: application/pdf
creator: dernst
date_created: 2022-05-02T08:16:10Z
date_updated: 2022-05-02T08:16:10Z
file_id: '11347'
file_name: 2022_CurrentProtocols_Kroll.pdf
file_size: 2142703
relation: main_file
success: 1
file_date_updated: 2022-05-02T08:16:10Z
has_accepted_license: '1'
intvolume: ' 2'
issue: '4'
language:
- iso: eng
month: '04'
oa: 1
oa_version: Published Version
pmid: 1
publication: Current Protocols
publication_identifier:
eissn:
- 2691-1299
publication_status: published
publisher: Wiley
quality_controlled: '1'
scopus_import: '1'
status: public
title: Quantifying the probing and selection of microenvironmental pores by motile
immune cells
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: journal_article
user_id: 0043cee0-e5fc-11ee-9736-f83bc23afbf0
volume: 2
year: '2022'
...