---
_id: '13230'
abstract:
- lang: eng
text: 'To interpret the sensory environment, the brain combines ambiguous sensory
measurements with knowledge that reflects context-specific prior experience. But
environmental contexts can change abruptly and unpredictably, resulting in uncertainty
about the current context. Here we address two questions: how should context-specific
prior knowledge optimally guide the interpretation of sensory stimuli in changing
environments, and do human decision-making strategies resemble this optimum? We
probe these questions with a task in which subjects report the orientation of
ambiguous visual stimuli that were drawn from three dynamically switching distributions,
representing different environmental contexts. We derive predictions for an ideal
Bayesian observer that leverages knowledge about the statistical structure of
the task to maximize decision accuracy, including knowledge about the dynamics
of the environment. We show that its decisions are biased by the dynamically changing
task context. The magnitude of this decision bias depends on the observer’s continually
evolving belief about the current context. The model therefore not only predicts
that decision bias will grow as the context is indicated more reliably, but also
as the stability of the environment increases, and as the number of trials since
the last context switch grows. Analysis of human choice data validates all three
predictions, suggesting that the brain leverages knowledge of the statistical
structure of environmental change when interpreting ambiguous sensory signals.'
acknowledgement: The authors thank Corey Ziemba and Zoe Boundy-Singer for valuable
discussion and feedback.
article_number: e1011104
article_processing_charge: No
article_type: original
author:
- first_name: Julie A.
full_name: Charlton, Julie A.
last_name: Charlton
- first_name: Wiktor F
full_name: Mlynarski, Wiktor F
id: 358A453A-F248-11E8-B48F-1D18A9856A87
last_name: Mlynarski
- first_name: Yoon H.
full_name: Bai, Yoon H.
last_name: Bai
- first_name: Ann M.
full_name: Hermundstad, Ann M.
last_name: Hermundstad
- first_name: Robbe L.T.
full_name: Goris, Robbe L.T.
last_name: Goris
citation:
ama: Charlton JA, Mlynarski WF, Bai YH, Hermundstad AM, Goris RLT. Environmental
dynamics shape perceptual decision bias. PLoS Computational Biology. 2023;19(6).
doi:10.1371/journal.pcbi.1011104
apa: Charlton, J. A., Mlynarski, W. F., Bai, Y. H., Hermundstad, A. M., & Goris,
R. L. T. (2023). Environmental dynamics shape perceptual decision bias. PLoS
Computational Biology. Public Library of Science. https://doi.org/10.1371/journal.pcbi.1011104
chicago: Charlton, Julie A., Wiktor F Mlynarski, Yoon H. Bai, Ann M. Hermundstad,
and Robbe L.T. Goris. “Environmental Dynamics Shape Perceptual Decision Bias.”
PLoS Computational Biology. Public Library of Science, 2023. https://doi.org/10.1371/journal.pcbi.1011104.
ieee: J. A. Charlton, W. F. Mlynarski, Y. H. Bai, A. M. Hermundstad, and R. L. T.
Goris, “Environmental dynamics shape perceptual decision bias,” PLoS Computational
Biology, vol. 19, no. 6. Public Library of Science, 2023.
ista: Charlton JA, Mlynarski WF, Bai YH, Hermundstad AM, Goris RLT. 2023. Environmental
dynamics shape perceptual decision bias. PLoS Computational Biology. 19(6), e1011104.
mla: Charlton, Julie A., et al. “Environmental Dynamics Shape Perceptual Decision
Bias.” PLoS Computational Biology, vol. 19, no. 6, e1011104, Public Library
of Science, 2023, doi:10.1371/journal.pcbi.1011104.
short: J.A. Charlton, W.F. Mlynarski, Y.H. Bai, A.M. Hermundstad, R.L.T. Goris,
PLoS Computational Biology 19 (2023).
date_created: 2023-07-16T22:01:09Z
date_published: 2023-06-08T00:00:00Z
date_updated: 2023-08-02T06:33:50Z
day: '08'
ddc:
- '570'
department:
- _id: MaJö
doi: 10.1371/journal.pcbi.1011104
external_id:
isi:
- '001003410200003'
pmid:
- '37289753'
file:
- access_level: open_access
checksum: 800761fa2c647fabd6ad034589bc526e
content_type: application/pdf
creator: dernst
date_created: 2023-07-18T08:07:59Z
date_updated: 2023-07-18T08:07:59Z
file_id: '13247'
file_name: 2023_PloSCompBio_Charlton.pdf
file_size: 2281868
relation: main_file
success: 1
file_date_updated: 2023-07-18T08:07:59Z
has_accepted_license: '1'
intvolume: ' 19'
isi: 1
issue: '6'
language:
- iso: eng
month: '06'
oa: 1
oa_version: Published Version
pmid: 1
publication: PLoS Computational Biology
publication_identifier:
eissn:
- 1553-7358
publication_status: published
publisher: Public Library of Science
quality_controlled: '1'
scopus_import: '1'
status: public
title: Environmental dynamics shape perceptual decision bias
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: 19
year: '2023'
...
---
_id: '13231'
abstract:
- lang: eng
text: We study ab initio approaches for calculating x-ray Thomson scattering spectra
from density functional theory molecular dynamics simulations based on a modified
Chihara formula that expresses the inelastic contribution in terms of the dielectric
function. We study the electronic dynamic structure factor computed from the Mermin
dielectric function using an ab initio electron-ion collision frequency in comparison
to computations using a linear-response time-dependent density functional theory
(LR-TDDFT) framework for hydrogen and beryllium and investigate the dispersion
of free-free and bound-free contributions to the scattering signal. A separate
treatment of these contributions, where only the free-free part follows the Mermin
dispersion, shows good agreement with LR-TDDFT results for ambient-density beryllium,
but breaks down for highly compressed matter where the bound states become pressure
ionized. LR-TDDFT is used to reanalyze x-ray Thomson scattering experiments on
beryllium demonstrating strong deviations from the plasma conditions inferred
with traditional analytic models at small scattering angles.
acknowledgement: "We want to thank P. Sperling, B. Witte, M. French, G. Röpke, H.
J. Lee and A. Cangi for many helpful discussions. M. S. and R. R. acknowledge support
by the Deutsche Forschungsgemeinschaft (DFG) within the Research Unit FOR 2440.
All simulations and analyses were performed at the North-German Supercomputing Alliance
(HLRN) and the ITMZ of the University of Rostock. M. B. gratefully acknowledges
support by the European Horizon 2020 programme within the Marie Sklodowska-Curie
actions (xICE grant 894725) and the\r\nNOMIS foundation. The work of T. D. was performed
under the auspices of the U.S. Department of Energy by Lawrence Livermore National
Laboratory under Contract No. DE-AC52-07NA27344."
article_number: '065207'
article_processing_charge: No
article_type: original
arxiv: 1
author:
- first_name: Maximilian
full_name: Schörner, Maximilian
last_name: Schörner
- first_name: Mandy
full_name: Bethkenhagen, Mandy
id: 201939f4-803f-11ed-ab7e-d8da4bd1517f
last_name: Bethkenhagen
orcid: 0000-0002-1838-2129
- first_name: Tilo
full_name: Döppner, Tilo
last_name: Döppner
- first_name: Dominik
full_name: Kraus, Dominik
last_name: Kraus
- first_name: Luke B.
full_name: Fletcher, Luke B.
last_name: Fletcher
- first_name: Siegfried H.
full_name: Glenzer, Siegfried H.
last_name: Glenzer
- first_name: Ronald
full_name: Redmer, Ronald
last_name: Redmer
citation:
ama: Schörner M, Bethkenhagen M, Döppner T, et al. X-ray Thomson scattering spectra
from density functional theory molecular dynamics simulations based on a modified
Chihara formula. Physical Review E. 2023;107(6). doi:10.1103/PhysRevE.107.065207
apa: Schörner, M., Bethkenhagen, M., Döppner, T., Kraus, D., Fletcher, L. B., Glenzer,
S. H., & Redmer, R. (2023). X-ray Thomson scattering spectra from density
functional theory molecular dynamics simulations based on a modified Chihara formula.
Physical Review E. American Physical Society. https://doi.org/10.1103/PhysRevE.107.065207
chicago: Schörner, Maximilian, Mandy Bethkenhagen, Tilo Döppner, Dominik Kraus,
Luke B. Fletcher, Siegfried H. Glenzer, and Ronald Redmer. “X-Ray Thomson Scattering
Spectra from Density Functional Theory Molecular Dynamics Simulations Based on
a Modified Chihara Formula.” Physical Review E. American Physical Society,
2023. https://doi.org/10.1103/PhysRevE.107.065207.
ieee: M. Schörner et al., “X-ray Thomson scattering spectra from density
functional theory molecular dynamics simulations based on a modified Chihara formula,”
Physical Review E, vol. 107, no. 6. American Physical Society, 2023.
ista: Schörner M, Bethkenhagen M, Döppner T, Kraus D, Fletcher LB, Glenzer SH, Redmer
R. 2023. X-ray Thomson scattering spectra from density functional theory molecular
dynamics simulations based on a modified Chihara formula. Physical Review E. 107(6),
065207.
mla: Schörner, Maximilian, et al. “X-Ray Thomson Scattering Spectra from Density
Functional Theory Molecular Dynamics Simulations Based on a Modified Chihara Formula.”
Physical Review E, vol. 107, no. 6, 065207, American Physical Society,
2023, doi:10.1103/PhysRevE.107.065207.
short: M. Schörner, M. Bethkenhagen, T. Döppner, D. Kraus, L.B. Fletcher, S.H. Glenzer,
R. Redmer, Physical Review E 107 (2023).
date_created: 2023-07-16T22:01:10Z
date_published: 2023-06-14T00:00:00Z
date_updated: 2023-08-02T06:30:46Z
day: '14'
department:
- _id: BiCh
doi: 10.1103/PhysRevE.107.065207
external_id:
arxiv:
- '2301.01545'
isi:
- '001020265000002'
intvolume: ' 107'
isi: 1
issue: '6'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.48550/arXiv.2301.01545
month: '06'
oa: 1
oa_version: Preprint
publication: Physical Review E
publication_identifier:
eissn:
- 2470-0053
issn:
- 2470-0045
publication_status: published
publisher: American Physical Society
quality_controlled: '1'
scopus_import: '1'
status: public
title: X-ray Thomson scattering spectra from density functional theory molecular dynamics
simulations based on a modified Chihara formula
type: journal_article
user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
volume: 107
year: '2023'
...
---
_id: '13232'
abstract:
- lang: eng
text: The potential of immune-evasive mutation accumulation in the SARS-CoV-2 virus
has led to its rapid spread, causing over 600 million confirmed cases and more
than 6.5 million confirmed deaths. The huge demand for the rapid development and
deployment of low-cost and effective vaccines against emerging variants has renewed
interest in DNA vaccine technology. Here, we report the rapid generation and immunological
evaluation of novel DNA vaccine candidates against the Wuhan-Hu-1 and Omicron
variants based on the RBD protein fused with the Potato virus X coat protein (PVXCP).
The delivery of DNA vaccines using electroporation in a two-dose regimen induced
high-antibody titers and profound cellular responses in mice. The antibody titers
induced against the Omicron variant of the vaccine were sufficient for effective
protection against both Omicron and Wuhan-Hu-1 virus infections. The PVXCP protein
in the vaccine construct shifted the immune response to the favorable Th1-like
type and provided the oligomerization of RBD-PVXCP protein. Naked DNA delivery
by needle-free injection allowed us to achieve antibody titers comparable with
mRNA-LNP delivery in rabbits. These data identify the RBD-PVXCP DNA vaccine platform
as a promising solution for robust and effective SARS-CoV-2 protection, supporting
further translational study.
acknowledgement: The authors declare that this study received funding from Immunofusion.
The funder was not involved in the study design, collection, analysis, interpretation
of data, the writing of this article, or the decision to submit it for publication.
The authors express their gratitude to the Institute of Physiology of the National
Academy of Sciences of Belarus for providing assistance in keeping laboratory animals.
article_number: '1014'
article_processing_charge: No
article_type: original
author:
- first_name: Dmitri
full_name: Dormeshkin, Dmitri
last_name: Dormeshkin
- first_name: Mikalai
full_name: Katsin, Mikalai
last_name: Katsin
- first_name: Maria
full_name: Stegantseva, Maria
last_name: Stegantseva
- first_name: Sergey
full_name: Golenchenko, Sergey
last_name: Golenchenko
- first_name: Michail
full_name: Shapira, Michail
last_name: Shapira
- first_name: Simon
full_name: Dubovik, Simon
last_name: Dubovik
- first_name: Dzmitry
full_name: Lutskovich, Dzmitry
last_name: Lutskovich
- first_name: Anton
full_name: Kavaleuski, Anton
id: 62304f89-eb97-11eb-a6c2-8903dd183976
last_name: Kavaleuski
orcid: 0000-0003-2091-526X
- first_name: Alexander
full_name: Meleshko, Alexander
last_name: Meleshko
citation:
ama: Dormeshkin D, Katsin M, Stegantseva M, et al. Design and immunogenicity of
SARS-CoV-2 DNA vaccine encoding RBD-PVXCP fusion protein. Vaccines. 2023;11(6).
doi:10.3390/vaccines11061014
apa: Dormeshkin, D., Katsin, M., Stegantseva, M., Golenchenko, S., Shapira, M.,
Dubovik, S., … Meleshko, A. (2023). Design and immunogenicity of SARS-CoV-2 DNA
vaccine encoding RBD-PVXCP fusion protein. Vaccines. MDPI. https://doi.org/10.3390/vaccines11061014
chicago: Dormeshkin, Dmitri, Mikalai Katsin, Maria Stegantseva, Sergey Golenchenko,
Michail Shapira, Simon Dubovik, Dzmitry Lutskovich, Anton Kavaleuski, and Alexander
Meleshko. “Design and Immunogenicity of SARS-CoV-2 DNA Vaccine Encoding RBD-PVXCP
Fusion Protein.” Vaccines. MDPI, 2023. https://doi.org/10.3390/vaccines11061014.
ieee: D. Dormeshkin et al., “Design and immunogenicity of SARS-CoV-2 DNA
vaccine encoding RBD-PVXCP fusion protein,” Vaccines, vol. 11, no. 6. MDPI,
2023.
ista: Dormeshkin D, Katsin M, Stegantseva M, Golenchenko S, Shapira M, Dubovik S,
Lutskovich D, Kavaleuski A, Meleshko A. 2023. Design and immunogenicity of SARS-CoV-2
DNA vaccine encoding RBD-PVXCP fusion protein. Vaccines. 11(6), 1014.
mla: Dormeshkin, Dmitri, et al. “Design and Immunogenicity of SARS-CoV-2 DNA Vaccine
Encoding RBD-PVXCP Fusion Protein.” Vaccines, vol. 11, no. 6, 1014, MDPI,
2023, doi:10.3390/vaccines11061014.
short: D. Dormeshkin, M. Katsin, M. Stegantseva, S. Golenchenko, M. Shapira, S.
Dubovik, D. Lutskovich, A. Kavaleuski, A. Meleshko, Vaccines 11 (2023).
date_created: 2023-07-16T22:01:10Z
date_published: 2023-06-01T00:00:00Z
date_updated: 2023-08-02T06:31:19Z
day: '01'
ddc:
- '570'
department:
- _id: LeSa
doi: 10.3390/vaccines11061014
external_id:
isi:
- '001017740000001'
file:
- access_level: open_access
checksum: 8f484c0f30f8699c589b1c29a0fd7d7f
content_type: application/pdf
creator: dernst
date_created: 2023-07-18T07:25:43Z
date_updated: 2023-07-18T07:25:43Z
file_id: '13244'
file_name: 2023_Vaccines_Dormeshkin.pdf
file_size: 2339746
relation: main_file
success: 1
file_date_updated: 2023-07-18T07:25:43Z
has_accepted_license: '1'
intvolume: ' 11'
isi: 1
issue: '6'
language:
- iso: eng
month: '06'
oa: 1
oa_version: Published Version
publication: Vaccines
publication_identifier:
eissn:
- 2076-393X
publication_status: published
publisher: MDPI
quality_controlled: '1'
scopus_import: '1'
status: public
title: Design and immunogenicity of SARS-CoV-2 DNA vaccine encoding RBD-PVXCP fusion
protein
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: journal_article
user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
volume: 11
year: '2023'
...
---
_id: '13233'
abstract:
- lang: eng
text: We study the impact of finite-range physics on the zero-range-model analysis
of three-body recombination in ultracold atoms. We find that temperature dependence
of the zero-range parameters can vary from one set of measurements to another
as it may be driven by the distribution of error bars in the experiment, and not
by the underlying three-body physics. To study finite-temperature effects in three-body
recombination beyond the zero-range physics, we introduce and examine a finite-range
model based upon a hyperspherical formalism. The systematic error discussed in
this Letter may provide a significant contribution to the error bars of measured
three-body parameters.
acknowledgement: We thank Jan Arlt, Hans-Werner Hammer, and Karsten Riisager for useful
discussions. M.L. acknowledges support by the European Research Council (ERC) Starting
Grant No. 801770 (ANGULON).
article_number: L061304
article_processing_charge: No
article_type: letter_note
arxiv: 1
author:
- first_name: Sofya
full_name: Agafonova, Sofya
id: 09501ff6-dca7-11ea-a8ae-b3e0b9166e80
last_name: Agafonova
- first_name: Mikhail
full_name: Lemeshko, Mikhail
id: 37CB05FA-F248-11E8-B48F-1D18A9856A87
last_name: Lemeshko
orcid: 0000-0002-6990-7802
- first_name: Artem
full_name: Volosniev, Artem
id: 37D278BC-F248-11E8-B48F-1D18A9856A87
last_name: Volosniev
orcid: 0000-0003-0393-5525
citation:
ama: Agafonova S, Lemeshko M, Volosniev A. Finite-range bias in fitting three-body
loss to the zero-range model. Physical Review A. 2023;107(6). doi:10.1103/PhysRevA.107.L061304
apa: Agafonova, S., Lemeshko, M., & Volosniev, A. (2023). Finite-range bias
in fitting three-body loss to the zero-range model. Physical Review A.
American Physical Society. https://doi.org/10.1103/PhysRevA.107.L061304
chicago: Agafonova, Sofya, Mikhail Lemeshko, and Artem Volosniev. “Finite-Range
Bias in Fitting Three-Body Loss to the Zero-Range Model.” Physical Review A.
American Physical Society, 2023. https://doi.org/10.1103/PhysRevA.107.L061304.
ieee: S. Agafonova, M. Lemeshko, and A. Volosniev, “Finite-range bias in fitting
three-body loss to the zero-range model,” Physical Review A, vol. 107,
no. 6. American Physical Society, 2023.
ista: Agafonova S, Lemeshko M, Volosniev A. 2023. Finite-range bias in fitting three-body
loss to the zero-range model. Physical Review A. 107(6), L061304.
mla: Agafonova, Sofya, et al. “Finite-Range Bias in Fitting Three-Body Loss to the
Zero-Range Model.” Physical Review A, vol. 107, no. 6, L061304, American
Physical Society, 2023, doi:10.1103/PhysRevA.107.L061304.
short: S. Agafonova, M. Lemeshko, A. Volosniev, Physical Review A 107 (2023).
date_created: 2023-07-16T22:01:10Z
date_published: 2023-06-20T00:00:00Z
date_updated: 2023-08-02T06:31:52Z
day: '20'
department:
- _id: MiLe
- _id: OnHo
doi: 10.1103/PhysRevA.107.L061304
ec_funded: 1
external_id:
arxiv:
- '2302.01022'
isi:
- '001019748000005'
intvolume: ' 107'
isi: 1
issue: '6'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.48550/arXiv.2302.01022
month: '06'
oa: 1
oa_version: Preprint
project:
- _id: 2688CF98-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '801770'
name: 'Angulon: physics and applications of a new quasiparticle'
publication: Physical Review A
publication_identifier:
eissn:
- 2469-9934
issn:
- 2469-9926
publication_status: published
publisher: American Physical Society
quality_controlled: '1'
scopus_import: '1'
status: public
title: Finite-range bias in fitting three-body loss to the zero-range model
type: journal_article
user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
volume: 107
year: '2023'
...
---
_id: '13234'
abstract:
- lang: eng
text: Neural-network classifiers achieve high accuracy when predicting the class
of an input that they were trained to identify. Maintaining this accuracy in dynamic
environments, where inputs frequently fall outside the fixed set of initially
known classes, remains a challenge. We consider the problem of monitoring the
classification decisions of neural networks in the presence of novel classes.
For this purpose, we generalize our recently proposed abstraction-based monitor
from binary output to real-valued quantitative output. This quantitative output
enables new applications, two of which we investigate in the paper. As our first
application, we introduce an algorithmic framework for active monitoring of a
neural network, which allows us to learn new classes dynamically and yet maintain
high monitoring performance. As our second application, we present an offline
procedure to retrain the neural network to improve the monitor’s detection performance
without deteriorating the network’s classification accuracy. Our experimental
evaluation demonstrates both the benefits of our active monitoring framework in
dynamic scenarios and the effectiveness of the retraining procedure.
acknowledgement: This work was supported in part by the ERC-2020-AdG 101020093, by
DIREC - Digital Research Centre Denmark, and by the Villum Investigator Grant S4OS.
article_processing_charge: Yes (in subscription journal)
article_type: original
arxiv: 1
author:
- first_name: Konstantin
full_name: Kueffner, Konstantin
id: 8121a2d0-dc85-11ea-9058-af578f3b4515
last_name: Kueffner
orcid: 0000-0001-8974-2542
- first_name: Anna
full_name: Lukina, Anna
id: CBA4D1A8-0FE8-11E9-BDE6-07BFE5697425
last_name: Lukina
- first_name: Christian
full_name: Schilling, Christian
id: 3A2F4DCE-F248-11E8-B48F-1D18A9856A87
last_name: Schilling
orcid: 0000-0003-3658-1065
- 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: 'Kueffner K, Lukina A, Schilling C, Henzinger TA. Into the unknown: Active
monitoring of neural networks (extended version). International Journal on
Software Tools for Technology Transfer. 2023;25:575-592. doi:10.1007/s10009-023-00711-4'
apa: 'Kueffner, K., Lukina, A., Schilling, C., & Henzinger, T. A. (2023). Into
the unknown: Active monitoring of neural networks (extended version). International
Journal on Software Tools for Technology Transfer. Springer Nature. https://doi.org/10.1007/s10009-023-00711-4'
chicago: 'Kueffner, Konstantin, Anna Lukina, Christian Schilling, and Thomas A Henzinger.
“Into the Unknown: Active Monitoring of Neural Networks (Extended Version).” International
Journal on Software Tools for Technology Transfer. Springer Nature, 2023.
https://doi.org/10.1007/s10009-023-00711-4.'
ieee: 'K. Kueffner, A. Lukina, C. Schilling, and T. A. Henzinger, “Into the unknown:
Active monitoring of neural networks (extended version),” International Journal
on Software Tools for Technology Transfer, vol. 25. Springer Nature, pp. 575–592,
2023.'
ista: 'Kueffner K, Lukina A, Schilling C, Henzinger TA. 2023. Into the unknown:
Active monitoring of neural networks (extended version). International Journal
on Software Tools for Technology Transfer. 25, 575–592.'
mla: 'Kueffner, Konstantin, et al. “Into the Unknown: Active Monitoring of Neural
Networks (Extended Version).” International Journal on Software Tools for Technology
Transfer, vol. 25, Springer Nature, 2023, pp. 575–92, doi:10.1007/s10009-023-00711-4.'
short: K. Kueffner, A. Lukina, C. Schilling, T.A. Henzinger, International Journal
on Software Tools for Technology Transfer 25 (2023) 575–592.
date_created: 2023-07-16T22:01:11Z
date_published: 2023-08-01T00:00:00Z
date_updated: 2024-01-30T12:06:57Z
day: '01'
ddc:
- '000'
department:
- _id: ToHe
doi: 10.1007/s10009-023-00711-4
ec_funded: 1
external_id:
arxiv:
- '2009.06429'
isi:
- '001020160000001'
file:
- access_level: open_access
checksum: 3c4b347f39412a76872f9a6f30101f94
content_type: application/pdf
creator: dernst
date_created: 2024-01-30T12:06:07Z
date_updated: 2024-01-30T12:06:07Z
file_id: '14903'
file_name: 2023_JourSoftwareTools_Kueffner.pdf
file_size: 13387667
relation: main_file
success: 1
file_date_updated: 2024-01-30T12:06:07Z
has_accepted_license: '1'
intvolume: ' 25'
isi: 1
language:
- iso: eng
month: '08'
oa: 1
oa_version: Published Version
page: 575-592
project:
- _id: 62781420-2b32-11ec-9570-8d9b63373d4d
call_identifier: H2020
grant_number: '101020093'
name: Vigilant Algorithmic Monitoring of Software
publication: International Journal on Software Tools for Technology Transfer
publication_identifier:
eissn:
- 1433-2787
issn:
- 1433-2779
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
related_material:
record:
- id: '10206'
relation: shorter_version
status: public
scopus_import: '1'
status: public
title: 'Into the unknown: Active monitoring of neural networks (extended version)'
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: 25
year: '2023'
...
---
_id: '13235'
abstract:
- lang: eng
text: AgSbSe2 is a promising thermoelectric (TE) p-type material for applications
in the middle-temperature range. AgSbSe2 is characterized by relatively low thermal
conductivities and high Seebeck coefficients, but its main limitation is moderate
electrical conductivity. Herein, we detail an efficient and scalable hot-injection
synthesis route to produce AgSbSe2 nanocrystals (NCs). To increase the carrier
concentration and improve the electrical conductivity, these NCs are doped with
Sn2+ on Sb3+ sites. Upon processing, the Sn2+ chemical state is conserved using
a reducing NaBH4 solution to displace the organic ligand and anneal the material
under a forming gas flow. The TE properties of the dense materials obtained from
the consolidation of the NCs using a hot pressing are then characterized. The
presence of Sn2+ ions replacing Sb3+ significantly increases the charge carrier
concentration and, consequently, the electrical conductivity. Opportunely, the
measured Seebeck coefficient varied within a small range upon Sn doping. The excellent
performance obtained when Sn2+ ions are prevented from oxidation is rationalized
by modeling the system. Calculated band structures disclosed that Sn doping induces
convergence of the AgSbSe2 valence bands, accounting for an enhanced electronic
effective mass. The dramatically enhanced carrier transport leads to a maximized
power factor for AgSb0.98Sn0.02Se2 of 0.63 mW m–1 K–2 at 640 K. Thermally, phonon
scattering is significantly enhanced in the NC-based materials, yielding an ultralow
thermal conductivity of 0.3 W mK–1 at 666 K. Overall, a record-high figure of
merit (zT) is obtained at 666 K for AgSb0.98Sn0.02Se2 at zT = 1.37, well above
the values obtained for undoped AgSbSe2, at zT = 0.58 and state-of-art Pb- and
Te-free materials, which makes AgSb0.98Sn0.02Se2 an excellent p-type candidate
for medium-temperature TE applications.
acknowledgement: Y.L. acknowledges funding from the National Natural Science Foundation
of China (NSFC) (Grants No. 22209034), the Innovation and Entrepreneurship Project
of Overseas Returnees in Anhui Province (Grant No. 2022LCX002). K.H.L. acknowledges
financial support from the National Natural Science Foundation of China (Grant No.
22208293). Y.Z. acknowledges support from the SBIR program NanoOhmics. J.L. is grateful
for the project supported by the Natural Science Foundation of Sichuan (2022NSFSC1229).
M.I. acknowledges financial support from ISTA and the Werner Siemens Foundation.
article_processing_charge: No
article_type: original
author:
- first_name: Yu
full_name: Liu, Yu
id: 2A70014E-F248-11E8-B48F-1D18A9856A87
last_name: Liu
orcid: 0000-0001-7313-6740
- first_name: Mingquan
full_name: Li, Mingquan
last_name: Li
- first_name: Shanhong
full_name: Wan, Shanhong
last_name: Wan
- first_name: Khak Ho
full_name: Lim, Khak Ho
last_name: Lim
- first_name: Yu
full_name: Zhang, Yu
last_name: Zhang
- first_name: Mengyao
full_name: Li, Mengyao
last_name: Li
- first_name: Junshan
full_name: Li, Junshan
last_name: Li
- first_name: Maria
full_name: Ibáñez, Maria
id: 43C61214-F248-11E8-B48F-1D18A9856A87
last_name: Ibáñez
orcid: 0000-0001-5013-2843
- first_name: Min
full_name: Hong, Min
last_name: Hong
- first_name: Andreu
full_name: Cabot, Andreu
last_name: Cabot
citation:
ama: 'Liu Y, Li M, Wan S, et al. Surface chemistry and band engineering in AgSbSe₂:
Toward high thermoelectric performance. ACS Nano. 2023;17(12):11923–11934.
doi:10.1021/acsnano.3c03541'
apa: 'Liu, Y., Li, M., Wan, S., Lim, K. H., Zhang, Y., Li, M., … Cabot, A. (2023).
Surface chemistry and band engineering in AgSbSe₂: Toward high thermoelectric
performance. ACS Nano. American Chemical Society. https://doi.org/10.1021/acsnano.3c03541'
chicago: 'Liu, Yu, Mingquan Li, Shanhong Wan, Khak Ho Lim, Yu Zhang, Mengyao Li,
Junshan Li, Maria Ibáñez, Min Hong, and Andreu Cabot. “Surface Chemistry and Band
Engineering in AgSbSe₂: Toward High Thermoelectric Performance.” ACS Nano.
American Chemical Society, 2023. https://doi.org/10.1021/acsnano.3c03541.'
ieee: 'Y. Liu et al., “Surface chemistry and band engineering in AgSbSe₂:
Toward high thermoelectric performance,” ACS Nano, vol. 17, no. 12. American
Chemical Society, pp. 11923–11934, 2023.'
ista: 'Liu Y, Li M, Wan S, Lim KH, Zhang Y, Li M, Li J, Ibáñez M, Hong M, Cabot
A. 2023. Surface chemistry and band engineering in AgSbSe₂: Toward high thermoelectric
performance. ACS Nano. 17(12), 11923–11934.'
mla: 'Liu, Yu, et al. “Surface Chemistry and Band Engineering in AgSbSe₂: Toward
High Thermoelectric Performance.” ACS Nano, vol. 17, no. 12, American Chemical
Society, 2023, pp. 11923–11934, doi:10.1021/acsnano.3c03541.'
short: Y. Liu, M. Li, S. Wan, K.H. Lim, Y. Zhang, M. Li, J. Li, M. Ibáñez, M. Hong,
A. Cabot, ACS Nano 17 (2023) 11923–11934.
date_created: 2023-07-16T22:01:11Z
date_published: 2023-06-13T00:00:00Z
date_updated: 2023-08-02T06:29:55Z
day: '13'
department:
- _id: MaIb
doi: 10.1021/acsnano.3c03541
external_id:
isi:
- '001008564800001'
pmid:
- '37310395'
intvolume: ' 17'
isi: 1
issue: '12'
language:
- iso: eng
month: '06'
oa_version: None
page: 11923–11934
pmid: 1
project:
- _id: 9B8F7476-BA93-11EA-9121-9846C619BF3A
name: 'HighTE: The Werner Siemens Laboratory for the High Throughput Discovery of
Semiconductors for Waste Heat Recovery'
publication: ACS Nano
publication_identifier:
eissn:
- 1936-086X
issn:
- 1936-0851
publication_status: published
publisher: American Chemical Society
quality_controlled: '1'
scopus_import: '1'
status: public
title: 'Surface chemistry and band engineering in AgSbSe₂: Toward high thermoelectric
performance'
type: journal_article
user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
volume: 17
year: '2023'
...
---
_id: '13236'
abstract:
- lang: eng
text: We present an auction algorithm using multiplicative instead of constant weight
updates to compute a (1−ε)-approximate maximum weight matching (MWM) in a bipartite
graph with n vertices and m edges in time O(mε−1log(ε−1)), matching the running
time of the linear-time approximation algorithm of Duan and Pettie [JACM ’14].
Our algorithm is very simple and it can be extended to give a dynamic data structure
that maintains a (1−ε)-approximate maximum weight matching under (1) one-sided
vertex deletions (with incident edges) and (2) one-sided vertex insertions (with
incident edges sorted by weight) to the other side. The total time time used is
O(mε−1log(ε−1)), where m is the sum of the number of initially existing and inserted
edges.
acknowledgement: The first author thanks to Chandra Chekuri for useful discussions
about this paper. 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. 101019564 “The Design of Modern Fully Dynamic Data Structures
(MoDynStruct)” and from the Austrian Science Fund (FWF) project “Fast Algorithms
for a Reactive Network Layer (ReactNet)”, P 33775-N, with additional funding from
the netidee SCIENCE Stiftung, 2020–2024.
alternative_title:
- LNCS
article_processing_charge: No
arxiv: 1
author:
- first_name: Da Wei
full_name: Zheng, Da Wei
last_name: Zheng
- first_name: Monika H
full_name: Henzinger, Monika H
id: 540c9bbd-f2de-11ec-812d-d04a5be85630
last_name: Henzinger
orcid: 0000-0002-5008-6530
citation:
ama: 'Zheng DW, Henzinger MH. Multiplicative auction algorithm for approximate maximum
weight bipartite matching. In: International Conference on Integer Programming
and Combinatorial Optimization. Vol 13904. Springer Nature; 2023:453-465.
doi:10.1007/978-3-031-32726-1_32'
apa: 'Zheng, D. W., & Henzinger, M. H. (2023). Multiplicative auction algorithm
for approximate maximum weight bipartite matching. In International Conference
on Integer Programming and Combinatorial Optimization (Vol. 13904, pp. 453–465).
Madison, WI, United States: Springer Nature. https://doi.org/10.1007/978-3-031-32726-1_32'
chicago: Zheng, Da Wei, and Monika H Henzinger. “Multiplicative Auction Algorithm
for Approximate Maximum Weight Bipartite Matching.” In International Conference
on Integer Programming and Combinatorial Optimization, 13904:453–65. Springer
Nature, 2023. https://doi.org/10.1007/978-3-031-32726-1_32.
ieee: D. W. Zheng and M. H. Henzinger, “Multiplicative auction algorithm for approximate
maximum weight bipartite matching,” in International Conference on Integer
Programming and Combinatorial Optimization, Madison, WI, United States, 2023,
vol. 13904, pp. 453–465.
ista: 'Zheng DW, Henzinger MH. 2023. Multiplicative auction algorithm for approximate
maximum weight bipartite matching. International Conference on Integer Programming
and Combinatorial Optimization. IPCO: Integer Programming and Combinatorial Optimization,
LNCS, vol. 13904, 453–465.'
mla: Zheng, Da Wei, and Monika H. Henzinger. “Multiplicative Auction Algorithm for Approximate
Maximum Weight Bipartite Matching.” International Conference on Integer Programming
and Combinatorial Optimization, vol. 13904, Springer Nature, 2023, pp. 453–65,
doi:10.1007/978-3-031-32726-1_32.
short: D.W. Zheng, M.H. Henzinger, in:, International Conference on Integer Programming
and Combinatorial Optimization, Springer Nature, 2023, pp. 453–465.
conference:
end_date: 2023-06-23
location: Madison, WI, United States
name: 'IPCO: Integer Programming and Combinatorial Optimization'
start_date: 2023-06-21
date_created: 2023-07-16T22:01:11Z
date_published: 2023-05-22T00:00:00Z
date_updated: 2023-07-18T07:08:51Z
day: '22'
department:
- _id: MoHe
doi: 10.1007/978-3-031-32726-1_32
ec_funded: 1
external_id:
arxiv:
- '2301.09217'
intvolume: ' 13904'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.48550/arXiv.2301.09217
month: '05'
oa: 1
oa_version: Preprint
page: 453-465
project:
- _id: bd9ca328-d553-11ed-ba76-dc4f890cfe62
call_identifier: H2020
grant_number: '101019564'
name: The design and evaluation of modern fully dynamic data structures
- _id: bd9e3a2e-d553-11ed-ba76-8aa684ce17fe
grant_number: 'P33775 '
name: Fast Algorithms for a Reactive Network Layer
publication: International Conference on Integer Programming and Combinatorial Optimization
publication_identifier:
eissn:
- 1611-3349
isbn:
- '9783031327254'
issn:
- 0302-9743
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
scopus_import: '1'
status: public
title: Multiplicative auction algorithm for approximate maximum weight bipartite matching
type: conference
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 13904
year: '2023'
...
---
_id: '13237'
abstract:
- lang: eng
text: The formation of amyloid fibrils is a general class of protein self-assembly
behaviour, which is associated with both functional biology and the development
of a number of disorders, such as Alzheimer and Parkinson diseases. In this Review,
we discuss how general physical concepts from the study of phase transitions can
be used to illuminate the fundamental mechanisms of amyloid self-assembly. We
summarize progress in the efforts to describe the essential biophysical features
of amyloid self-assembly as a nucleation-and-growth process and discuss how master
equation approaches can reveal the key molecular pathways underlying this process,
including the role of secondary nucleation. Additionally, we outline how non-classical
aspects of aggregate formation involving oligomers or biomolecular condensates
have emerged, inspiring developments in understanding, modelling and modulating
complex protein assembly pathways. Finally, we consider how these concepts can
be applied to kinetics-based drug discovery and therapeutic design to develop
treatments for protein aggregation diseases.
acknowledgement: The authors acknowledge support from the Institute for the Physics
of Living Systems, University College London (T.C.T.M.), the Swedish Research Council
(2015-00143) (S.L.), the European Research Council under the European Union’s Seventh
Framework Programme (FP7/2007-2013) through the ERC grant PhysProt (agreement no.
337969) (T.P.J.K.), the BBSRC (T.P.J.K.), the Newman Foundation (T.P.J.K.) and the
Wellcome Trust Collaborative Award 203249/Z/16/Z (T.P.J.K.). The authors thank C.
Flandoli for help with illustrations.
article_processing_charge: No
article_type: original
author:
- first_name: Thomas C.T.
full_name: Michaels, Thomas C.T.
last_name: Michaels
- first_name: Daoyuan
full_name: Qian, Daoyuan
last_name: Qian
- first_name: Anđela
full_name: Šarić, Anđela
id: bf63d406-f056-11eb-b41d-f263a6566d8b
last_name: Šarić
orcid: 0000-0002-7854-2139
- first_name: Michele
full_name: Vendruscolo, Michele
last_name: Vendruscolo
- first_name: Sara
full_name: Linse, Sara
last_name: Linse
- first_name: Tuomas P.J.
full_name: Knowles, Tuomas P.J.
last_name: Knowles
citation:
ama: Michaels TCT, Qian D, Šarić A, Vendruscolo M, Linse S, Knowles TPJ. Amyloid
formation as a protein phase transition. Nature Reviews Physics. 2023;5:379–397.
doi:10.1038/s42254-023-00598-9
apa: Michaels, T. C. T., Qian, D., Šarić, A., Vendruscolo, M., Linse, S., &
Knowles, T. P. J. (2023). Amyloid formation as a protein phase transition. Nature
Reviews Physics. Springer Nature. https://doi.org/10.1038/s42254-023-00598-9
chicago: Michaels, Thomas C.T., Daoyuan Qian, Anđela Šarić, Michele Vendruscolo,
Sara Linse, and Tuomas P.J. Knowles. “Amyloid Formation as a Protein Phase Transition.”
Nature Reviews Physics. Springer Nature, 2023. https://doi.org/10.1038/s42254-023-00598-9.
ieee: T. C. T. Michaels, D. Qian, A. Šarić, M. Vendruscolo, S. Linse, and T. P.
J. Knowles, “Amyloid formation as a protein phase transition,” Nature Reviews
Physics, vol. 5. Springer Nature, pp. 379–397, 2023.
ista: Michaels TCT, Qian D, Šarić A, Vendruscolo M, Linse S, Knowles TPJ. 2023.
Amyloid formation as a protein phase transition. Nature Reviews Physics. 5, 379–397.
mla: Michaels, Thomas C. T., et al. “Amyloid Formation as a Protein Phase Transition.”
Nature Reviews Physics, vol. 5, Springer Nature, 2023, pp. 379–397, doi:10.1038/s42254-023-00598-9.
short: T.C.T. Michaels, D. Qian, A. Šarić, M. Vendruscolo, S. Linse, T.P.J. Knowles,
Nature Reviews Physics 5 (2023) 379–397.
date_created: 2023-07-16T22:01:12Z
date_published: 2023-07-01T00:00:00Z
date_updated: 2023-08-02T06:28:38Z
day: '01'
department:
- _id: AnSa
doi: 10.1038/s42254-023-00598-9
external_id:
isi:
- '001017539800001'
intvolume: ' 5'
isi: 1
language:
- iso: eng
month: '07'
oa_version: None
page: 379–397
publication: Nature Reviews Physics
publication_identifier:
eissn:
- 2522-5820
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
scopus_import: '1'
status: public
title: Amyloid formation as a protein phase transition
type: journal_article
user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
volume: 5
year: '2023'
...
---
_id: '13238'
abstract:
- lang: eng
text: "We consider a natural problem dealing with weighted packet selection across
a rechargeable link, which e.g., finds applications in cryptocurrency networks.
The capacity of a link (u, v) is determined by how much nodes u and v allocate
for this link. Specifically, the input is a finite ordered sequence of packets
that arrive in both directions along a link. Given (u, v) and a packet of weight
x going from u to v, node u can either accept or reject the packet. If u accepts
the packet, the capacity on link (u, v) decreases by x. Correspondingly, v’s capacity
on (u, v) increases by x. If a node rejects the packet, this will entail a cost
affinely linear in the weight of the packet. A link is “rechargeable” in the sense
that the total capacity of the link has to remain constant, but the allocation
of capacity at the ends of the link can depend arbitrarily on the nodes’ decisions.
The goal is to minimise the sum of the capacity injected into the link and the
cost of rejecting packets. We show that the problem is NP-hard, but can be approximated
efficiently with a ratio of (1+ε)⋅(1+3–√) for some arbitrary ε>0.\r\n."
acknowledgement: We thank Mahsa Bastankhah and Mohammad Ali Maddah-Ali for fruitful
discussions about different variants of the problem. This work is supported by the
European Research Council (ERC) Consolidator Project 864228 (AdjustNet), 2020-2025,
the ERC CoG 863818 (ForM-SMArt), and the German Research Foundation (DFG) grant
470029389 (FlexNets), 2021–2024.
alternative_title:
- LNCS
article_processing_charge: No
arxiv: 1
author:
- first_name: Stefan
full_name: Schmid, Stefan
last_name: Schmid
- first_name: Jakub
full_name: Svoboda, Jakub
id: 130759D2-D7DD-11E9-87D2-DE0DE6697425
last_name: Svoboda
orcid: 0000-0002-1419-3267
- first_name: Michelle X
full_name: Yeo, Michelle X
id: 2D82B818-F248-11E8-B48F-1D18A9856A87
last_name: Yeo
orcid: 0009-0001-3676-4809
citation:
ama: 'Schmid S, Svoboda J, Yeo MX. Weighted packet selection for rechargeable links
in cryptocurrency networks: Complexity and approximation. In: SIROCCO 2023:
Structural Information and Communication Complexity . Vol 13892. Springer
Nature; 2023:576-594. doi:10.1007/978-3-031-32733-9_26'
apa: 'Schmid, S., Svoboda, J., & Yeo, M. X. (2023). Weighted packet selection
for rechargeable links in cryptocurrency networks: Complexity and approximation.
In SIROCCO 2023: Structural Information and Communication Complexity (Vol.
13892, pp. 576–594). Alcala de Henares, Spain: Springer Nature. https://doi.org/10.1007/978-3-031-32733-9_26'
chicago: 'Schmid, Stefan, Jakub Svoboda, and Michelle X Yeo. “Weighted Packet Selection
for Rechargeable Links in Cryptocurrency Networks: Complexity and Approximation.”
In SIROCCO 2023: Structural Information and Communication Complexity ,
13892:576–94. Springer Nature, 2023. https://doi.org/10.1007/978-3-031-32733-9_26.'
ieee: 'S. Schmid, J. Svoboda, and M. X. Yeo, “Weighted packet selection for rechargeable
links in cryptocurrency networks: Complexity and approximation,” in SIROCCO
2023: Structural Information and Communication Complexity , Alcala de Henares,
Spain, 2023, vol. 13892, pp. 576–594.'
ista: 'Schmid S, Svoboda J, Yeo MX. 2023. Weighted packet selection for rechargeable
links in cryptocurrency networks: Complexity and approximation. SIROCCO 2023:
Structural Information and Communication Complexity . SIROCCO: Structural Information
and Communication Complexity, LNCS, vol. 13892, 576–594.'
mla: 'Schmid, Stefan, et al. “Weighted Packet Selection for Rechargeable Links in Cryptocurrency
Networks: Complexity and Approximation.” SIROCCO 2023: Structural Information
and Communication Complexity , vol. 13892, Springer Nature, 2023, pp. 576–94,
doi:10.1007/978-3-031-32733-9_26.'
short: 'S. Schmid, J. Svoboda, M.X. Yeo, in:, SIROCCO 2023: Structural Information
and Communication Complexity , Springer Nature, 2023, pp. 576–594.'
conference:
end_date: 2023-06-09
location: Alcala de Henares, Spain
name: 'SIROCCO: Structural Information and Communication Complexity'
start_date: 2023-06-06
date_created: 2023-07-16T22:01:12Z
date_published: 2023-05-25T00:00:00Z
date_updated: 2025-07-14T09:09:53Z
day: '25'
department:
- _id: KrPi
- _id: KrCh
doi: 10.1007/978-3-031-32733-9_26
ec_funded: 1
external_id:
arxiv:
- '2204.13459'
intvolume: ' 13892'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.48550/arXiv.2204.13459
month: '05'
oa: 1
oa_version: Preprint
page: 576-594
project:
- _id: 0599E47C-7A3F-11EA-A408-12923DDC885E
call_identifier: H2020
grant_number: '863818'
name: 'Formal Methods for Stochastic Models: Algorithms and Applications'
publication: 'SIROCCO 2023: Structural Information and Communication Complexity '
publication_identifier:
eissn:
- 1611-3349
isbn:
- '9783031327322'
issn:
- 0302-9743
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
related_material:
record:
- id: '14506'
relation: dissertation_contains
status: public
scopus_import: '1'
status: public
title: 'Weighted packet selection for rechargeable links in cryptocurrency networks:
Complexity and approximation'
type: conference
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 13892
year: '2023'
...
---
_id: '13251'
abstract:
- lang: eng
text: A rotating organic cation and a dynamically disordered soft inorganic cage
are the hallmark features of organic-inorganic lead-halide perovskites. Understanding
the interplay between these two subsystems is a challenging problem, but it is
this coupling that is widely conjectured to be responsible for the unique behavior
of photocarriers in these materials. In this work, we use the fact that the polarizability
of the organic cation strongly depends on the ambient electrostatic environment
to put the molecule forward as a sensitive probe of the local crystal fields inside
the lattice cell. We measure the average polarizability of the C/N–H bond stretching
mode by means of infrared spectroscopy, which allows us to deduce the character
of the motion of the cation molecule, find the magnitude of the local crystal
field, and place an estimate on the strength of the hydrogen bond between the
hydrogen and halide atoms. Our results pave the way for understanding electric
fields in lead-halide perovskites using infrared bond spectroscopy.
acknowledgement: "We thank Bingqing Cheng and Hong-Zhou Ye for valuable discussions;
Y.W.’s work at IST Austria was supported through ISTernship summer internship program
funded by OeADGmbH; D.L. and Z.A. acknowledge support by IST Austria (ISTA); M.L.
acknowledges support by the European Research Council (ERC) Starting Grant No. 801770
(ANGULON).\r\nA.A.Z. and O.M.B. acknowledge support by KAUST."
article_processing_charge: Yes (via OA deal)
article_type: original
arxiv: 1
author:
- first_name: Yujing
full_name: Wei, Yujing
id: 0c5ff007-2600-11ee-b896-98bd8d663294
last_name: Wei
orcid: 0000-0001-8913-9719
- first_name: Artem
full_name: Volosniev, Artem
id: 37D278BC-F248-11E8-B48F-1D18A9856A87
last_name: Volosniev
orcid: 0000-0003-0393-5525
- first_name: Dusan
full_name: Lorenc, Dusan
id: 40D8A3E6-F248-11E8-B48F-1D18A9856A87
last_name: Lorenc
- first_name: Ayan A.
full_name: Zhumekenov, Ayan A.
last_name: Zhumekenov
- first_name: Osman M.
full_name: Bakr, Osman M.
last_name: Bakr
- first_name: Mikhail
full_name: Lemeshko, Mikhail
id: 37CB05FA-F248-11E8-B48F-1D18A9856A87
last_name: Lemeshko
orcid: 0000-0002-6990-7802
- first_name: Zhanybek
full_name: Alpichshev, Zhanybek
id: 45E67A2A-F248-11E8-B48F-1D18A9856A87
last_name: Alpichshev
orcid: 0000-0002-7183-5203
citation:
ama: Wei Y, Volosniev A, Lorenc D, et al. Bond polarizability as a probe of local
crystal fields in hybrid lead-halide perovskites. The Journal of Physical Chemistry
Letters. 2023;14(27):6309-6314. doi:10.1021/acs.jpclett.3c01158
apa: Wei, Y., Volosniev, A., Lorenc, D., Zhumekenov, A. A., Bakr, O. M., Lemeshko,
M., & Alpichshev, Z. (2023). Bond polarizability as a probe of local crystal
fields in hybrid lead-halide perovskites. The Journal of Physical Chemistry
Letters. American Chemical Society. https://doi.org/10.1021/acs.jpclett.3c01158
chicago: Wei, Yujing, Artem Volosniev, Dusan Lorenc, Ayan A. Zhumekenov, Osman M.
Bakr, Mikhail Lemeshko, and Zhanybek Alpichshev. “Bond Polarizability as a Probe
of Local Crystal Fields in Hybrid Lead-Halide Perovskites.” The Journal of
Physical Chemistry Letters. American Chemical Society, 2023. https://doi.org/10.1021/acs.jpclett.3c01158.
ieee: Y. Wei et al., “Bond polarizability as a probe of local crystal fields
in hybrid lead-halide perovskites,” The Journal of Physical Chemistry Letters,
vol. 14, no. 27. American Chemical Society, pp. 6309–6314, 2023.
ista: Wei Y, Volosniev A, Lorenc D, Zhumekenov AA, Bakr OM, Lemeshko M, Alpichshev
Z. 2023. Bond polarizability as a probe of local crystal fields in hybrid lead-halide
perovskites. The Journal of Physical Chemistry Letters. 14(27), 6309–6314.
mla: Wei, Yujing, et al. “Bond Polarizability as a Probe of Local Crystal Fields
in Hybrid Lead-Halide Perovskites.” The Journal of Physical Chemistry Letters,
vol. 14, no. 27, American Chemical Society, 2023, pp. 6309–14, doi:10.1021/acs.jpclett.3c01158.
short: Y. Wei, A. Volosniev, D. Lorenc, A.A. Zhumekenov, O.M. Bakr, M. Lemeshko,
Z. Alpichshev, The Journal of Physical Chemistry Letters 14 (2023) 6309–6314.
date_created: 2023-07-18T11:13:17Z
date_published: 2023-07-05T00:00:00Z
date_updated: 2023-07-19T06:59:19Z
day: '05'
ddc:
- '530'
department:
- _id: MiLe
- _id: ZhAl
doi: 10.1021/acs.jpclett.3c01158
ec_funded: 1
external_id:
arxiv:
- '2304.14198'
isi:
- '001022811500001'
file:
- access_level: open_access
checksum: c0c040063f06a51b9c463adc504f1a23
content_type: application/pdf
creator: dernst
date_created: 2023-07-19T06:55:39Z
date_updated: 2023-07-19T06:55:39Z
file_id: '13253'
file_name: 2023_JourPhysChemistry_Wei.pdf
file_size: 2121252
relation: main_file
success: 1
file_date_updated: 2023-07-19T06:55:39Z
has_accepted_license: '1'
intvolume: ' 14'
isi: 1
issue: '27'
keyword:
- General Materials Science
- Physical and Theoretical Chemistry
language:
- iso: eng
month: '07'
oa: 1
oa_version: Published Version
page: 6309-6314
project:
- _id: 2688CF98-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '801770'
name: 'Angulon: physics and applications of a new quasiparticle'
publication: The Journal of Physical Chemistry Letters
publication_identifier:
eissn:
- 1948-7185
publication_status: published
publisher: American Chemical Society
quality_controlled: '1'
status: public
title: Bond polarizability as a probe of local crystal fields in hybrid lead-halide
perovskites
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 14
year: '2023'
...
---
_id: '13256'
abstract:
- lang: eng
text: The El Niño-Southern Oscillation (ENSO) and the Indian summer monsoon (ISM,
or monsoon) are two giants of tropical climate. Here we assess the future evolution
of the ENSO-monsoon teleconnection in climate simulations with idealized forcing
of CO2 increment at a rate of 1% year-1 starting from a present-day condition
(367 p.p.m.) until quadrupling. We find a monotonous weakening of the ENSO-monsoon
teleconnection with the increase in CO2. Increased co-occurrences of El Niño and
positive Indian Ocean Dipoles (pIODs) in a warmer climate weaken the teleconnection.
Co-occurrences of El Niño and pIOD are attributable to mean sea surface temperature
(SST) warming that resembles a pIOD-type warming pattern in the Indian Ocean and
an El Niño-type warming in the Pacific. Since ENSO is a critical precursor of
the strength of the Indian monsoon, a weakening of this relation may mean a less
predictable Indian monsoon in a warmer climate.
acknowledgement: This work was supported by National Research Foundation of Korea
(NRF) grants funded by the Korean government (MSIT) (NRF-2018R1A5A1024958, RS-2023-00208000).
Model simulation and data transfer were supported by the National Supercomputing
Center with supercomputing resources including technical support (KSC-2019-CHA-0005),
the National Center for Meteorological Supercomputer of the Korea Meteorological
Administration (KMA), and by the Korea Research Environment Open NETwork (KREONET),
respectively. We sincerely thank Dr. Jongsoo Shin of Pohang University of Science
and Technology, Pohang, South Korea for the model simulations.
article_number: '82'
article_processing_charge: Yes
article_type: original
author:
- first_name: Bidyut B
full_name: Goswami, Bidyut B
id: 3a4ac09c-6d61-11ec-bf66-884cde66b64b
last_name: Goswami
- first_name: Soon Il
full_name: An, Soon Il
last_name: An
citation:
ama: GOSWAMI BB, An SI. An assessment of the ENSO-monsoon teleconnection in a warming
climate. npj Climate and Atmospheric Science. 2023;6. doi:10.1038/s41612-023-00411-5
apa: GOSWAMI, B. B., & An, S. I. (2023). An assessment of the ENSO-monsoon teleconnection
in a warming climate. Npj Climate and Atmospheric Science. Springer Nature.
https://doi.org/10.1038/s41612-023-00411-5
chicago: GOSWAMI, BIDYUT B, and Soon Il An. “An Assessment of the ENSO-Monsoon Teleconnection
in a Warming Climate.” Npj Climate and Atmospheric Science. Springer Nature,
2023. https://doi.org/10.1038/s41612-023-00411-5.
ieee: B. B. GOSWAMI and S. I. An, “An assessment of the ENSO-monsoon teleconnection
in a warming climate,” npj Climate and Atmospheric Science, vol. 6. Springer
Nature, 2023.
ista: GOSWAMI BB, An SI. 2023. An assessment of the ENSO-monsoon teleconnection
in a warming climate. npj Climate and Atmospheric Science. 6, 82.
mla: GOSWAMI, BIDYUT B., and Soon Il An. “An Assessment of the ENSO-Monsoon Teleconnection
in a Warming Climate.” Npj Climate and Atmospheric Science, vol. 6, 82,
Springer Nature, 2023, doi:10.1038/s41612-023-00411-5.
short: B.B. GOSWAMI, S.I. An, Npj Climate and Atmospheric Science 6 (2023).
date_created: 2023-07-23T22:01:10Z
date_published: 2023-07-08T00:00:00Z
date_updated: 2023-08-02T06:38:07Z
day: '08'
ddc:
- '550'
department:
- _id: CaMu
doi: 10.1038/s41612-023-00411-5
external_id:
isi:
- '001024920300002'
file:
- access_level: open_access
checksum: e9967d436a83b8ffcc6f58782e1f7500
content_type: application/pdf
creator: dernst
date_created: 2023-07-31T08:00:01Z
date_updated: 2023-07-31T08:00:01Z
file_id: '13326'
file_name: 2023_npjclimate_Goswami.pdf
file_size: 1750712
relation: main_file
success: 1
file_date_updated: 2023-07-31T08:00:01Z
has_accepted_license: '1'
intvolume: ' 6'
isi: 1
language:
- iso: eng
month: '07'
oa: 1
oa_version: Published Version
publication: npj Climate and Atmospheric Science
publication_identifier:
eissn:
- 2397-3722
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
scopus_import: '1'
status: public
title: An assessment of the ENSO-monsoon teleconnection in a warming climate
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: 6
year: '2023'
...
---
_id: '13257'
abstract:
- lang: eng
text: The magnetotropic susceptibility is the thermodynamic coefficient associated
with the rotational anisotropy of the free energy in an external magnetic field
and is closely related to the magnetic susceptibility. It emerges naturally in
frequency-shift measurements of oscillating mechanical cantilevers, which are
becoming an increasingly important tool in the quantitative study of the thermodynamics
of modern condensed-matter systems. Here we discuss the basic properties of the
magnetotropic susceptibility as they relate to the experimental aspects of frequency-shift
measurements, as well as to the interpretation of those experiments in terms of
the intrinsic properties of the system under study.
acknowledgement: "We thank Aharon Kapitulnik, Philip Moll, and Andreas Rydh for illuminating
discussions. The work at the Los Alamos National Laboratory is supported by National
Science Foundation Cooperative Agreements No. DMR-1157490 and No. DMR-1644779, the
state of Florida, and the U.S. Department of Energy. A.S. acknowledges support from
the DOE/BES Science of 100T grant. B.J.R. acknowledges funding from the National
Science Foundation under Grant No.\r\nDMR-1752784."
article_number: '035111'
article_processing_charge: No
article_type: original
arxiv: 1
author:
- first_name: A.
full_name: Shekhter, A.
last_name: Shekhter
- first_name: R. D.
full_name: Mcdonald, R. D.
last_name: Mcdonald
- first_name: B. J.
full_name: Ramshaw, B. J.
last_name: Ramshaw
- first_name: Kimberly A
full_name: Modic, Kimberly A
id: 13C26AC0-EB69-11E9-87C6-5F3BE6697425
last_name: Modic
orcid: 0000-0001-9760-3147
citation:
ama: Shekhter A, Mcdonald RD, Ramshaw BJ, Modic KA. Magnetotropic susceptibility.
Physical Review B. 2023;108(3). doi:10.1103/PhysRevB.108.035111
apa: Shekhter, A., Mcdonald, R. D., Ramshaw, B. J., & Modic, K. A. (2023). Magnetotropic
susceptibility. Physical Review B. American Physical Society. https://doi.org/10.1103/PhysRevB.108.035111
chicago: Shekhter, A., R. D. Mcdonald, B. J. Ramshaw, and Kimberly A Modic. “Magnetotropic
Susceptibility.” Physical Review B. American Physical Society, 2023. https://doi.org/10.1103/PhysRevB.108.035111.
ieee: A. Shekhter, R. D. Mcdonald, B. J. Ramshaw, and K. A. Modic, “Magnetotropic
susceptibility,” Physical Review B, vol. 108, no. 3. American Physical
Society, 2023.
ista: Shekhter A, Mcdonald RD, Ramshaw BJ, Modic KA. 2023. Magnetotropic susceptibility.
Physical Review B. 108(3), 035111.
mla: Shekhter, A., et al. “Magnetotropic Susceptibility.” Physical Review B,
vol. 108, no. 3, 035111, American Physical Society, 2023, doi:10.1103/PhysRevB.108.035111.
short: A. Shekhter, R.D. Mcdonald, B.J. Ramshaw, K.A. Modic, Physical Review B 108
(2023).
date_created: 2023-07-23T22:01:10Z
date_published: 2023-07-15T00:00:00Z
date_updated: 2023-12-13T11:58:57Z
day: '15'
department:
- _id: KiMo
doi: 10.1103/PhysRevB.108.035111
external_id:
arxiv:
- '2208.10038'
isi:
- '001062708600002'
intvolume: ' 108'
isi: 1
issue: '3'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.48550/arXiv.2208.10038
month: '07'
oa: 1
oa_version: Preprint
publication: Physical Review B
publication_identifier:
eissn:
- 2469-9969
issn:
- 2469-9950
publication_status: published
publisher: American Physical Society
quality_controlled: '1'
scopus_import: '1'
status: public
title: Magnetotropic susceptibility
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 108
year: '2023'
...
---
_id: '13258'
abstract:
- lang: eng
text: Many human interactions feature the characteristics of social dilemmas where
individual actions have consequences for the group and the environment. The feedback
between behavior and environment can be studied with the framework of stochastic
games. In stochastic games, the state of the environment can change, depending
on the choices made by group members. Past work suggests that such feedback can
reinforce cooperative behaviors. In particular, cooperation can evolve in stochastic
games even if it is infeasible in each separate repeated game. In stochastic games,
participants have an interest in conditioning their strategies on the state of
the environment. Yet in many applications, precise information about the state
could be scarce. Here, we study how the availability of information (or lack thereof)
shapes evolution of cooperation. Already for simple examples of two state games
we find surprising effects. In some cases, cooperation is only possible if there
is precise information about the state of the environment. In other cases, cooperation
is most abundant when there is no information about the state of the environment.
We systematically analyze all stochastic games of a given complexity class, to
determine when receiving information about the environment is better, neutral,
or worse for evolution of cooperation.
acknowledgement: 'This work was supported by the European Research Council CoG 863818
(ForM-SMArt) (to K.C.), the European Research Council Starting Grant 850529: E-DIRECT
(to C.H.), the European Union’s Horizon 2020 research and innovation program under
the Marie Sklodowska-Curie Grant Agreement #754411 and the French Agence Nationale
de la Recherche (under the Investissement d’Avenir programme, ANR-17-EURE-0010)
(to M.K.).'
article_number: '4153'
article_processing_charge: Yes
article_type: original
author:
- first_name: Maria
full_name: Kleshnina, Maria
id: 4E21749C-F248-11E8-B48F-1D18A9856A87
last_name: Kleshnina
- first_name: Christian
full_name: Hilbe, Christian
id: 2FDF8F3C-F248-11E8-B48F-1D18A9856A87
last_name: Hilbe
orcid: 0000-0001-5116-955X
- first_name: Stepan
full_name: Simsa, Stepan
id: 409d615c-2f95-11ee-b934-90a352102c1e
last_name: Simsa
orcid: 0000-0001-6687-1210
- first_name: Krishnendu
full_name: Chatterjee, Krishnendu
id: 2E5DCA20-F248-11E8-B48F-1D18A9856A87
last_name: Chatterjee
orcid: 0000-0002-4561-241X
- first_name: Martin A.
full_name: Nowak, Martin A.
last_name: Nowak
citation:
ama: Kleshnina M, Hilbe C, Simsa S, Chatterjee K, Nowak MA. The effect of environmental
information on evolution of cooperation in stochastic games. Nature Communications.
2023;14. doi:10.1038/s41467-023-39625-9
apa: Kleshnina, M., Hilbe, C., Simsa, S., Chatterjee, K., & Nowak, M. A. (2023).
The effect of environmental information on evolution of cooperation in stochastic
games. Nature Communications. Springer Nature. https://doi.org/10.1038/s41467-023-39625-9
chicago: Kleshnina, Maria, Christian Hilbe, Stepan Simsa, Krishnendu Chatterjee,
and Martin A. Nowak. “The Effect of Environmental Information on Evolution of
Cooperation in Stochastic Games.” Nature Communications. Springer Nature,
2023. https://doi.org/10.1038/s41467-023-39625-9.
ieee: M. Kleshnina, C. Hilbe, S. Simsa, K. Chatterjee, and M. A. Nowak, “The effect
of environmental information on evolution of cooperation in stochastic games,”
Nature Communications, vol. 14. Springer Nature, 2023.
ista: Kleshnina M, Hilbe C, Simsa S, Chatterjee K, Nowak MA. 2023. The effect of
environmental information on evolution of cooperation in stochastic games. Nature
Communications. 14, 4153.
mla: Kleshnina, Maria, et al. “The Effect of Environmental Information on Evolution
of Cooperation in Stochastic Games.” Nature Communications, vol. 14, 4153,
Springer Nature, 2023, doi:10.1038/s41467-023-39625-9.
short: M. Kleshnina, C. Hilbe, S. Simsa, K. Chatterjee, M.A. Nowak, Nature Communications
14 (2023).
date_created: 2023-07-23T22:01:11Z
date_published: 2023-07-12T00:00:00Z
date_updated: 2025-07-14T09:09:53Z
day: '12'
ddc:
- '000'
department:
- _id: KrCh
doi: 10.1038/s41467-023-39625-9
ec_funded: 1
external_id:
isi:
- '001029450400031'
pmid:
- '37438341'
file:
- access_level: open_access
checksum: 5aceefdfe76686267b93ae4fe81899f1
content_type: application/pdf
creator: dernst
date_created: 2023-07-31T11:32:36Z
date_updated: 2023-07-31T11:32:36Z
file_id: '13337'
file_name: 2023_NatureComm_Kleshnina.pdf
file_size: 1601682
relation: main_file
success: 1
file_date_updated: 2023-07-31T11:32:36Z
has_accepted_license: '1'
intvolume: ' 14'
isi: 1
language:
- iso: eng
month: '07'
oa: 1
oa_version: Published Version
pmid: 1
project:
- _id: 0599E47C-7A3F-11EA-A408-12923DDC885E
call_identifier: H2020
grant_number: '863818'
name: 'Formal Methods for Stochastic Models: Algorithms and Applications'
- _id: 260C2330-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '754411'
name: ISTplus - Postdoctoral Fellowships
publication: Nature Communications
publication_identifier:
eissn:
- 2041-1723
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
related_material:
record:
- id: '13336'
relation: research_data
status: public
scopus_import: '1'
status: public
title: The effect of environmental information on evolution of cooperation in stochastic
games
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 14
year: '2023'
...
---
_id: '13259'
abstract:
- lang: eng
text: Plants can regenerate their bodies via de novo establishment of shoot apical
meristems (SAMs) from pluripotent callus. Only a small fraction of callus cells
is eventually specified into SAMs but the molecular mechanisms underlying fate
specification remain obscure. The expression of WUSCHEL (WUS) is an early hallmark
of SAM fate acquisition. Here, we show that a WUS paralog, WUSCHEL-RELATED HOMEOBOX
13 (WOX13), negatively regulates SAM formation from callus in Arabidopsis thaliana.
WOX13 promotes non-meristematic cell fate via transcriptional repression of WUS
and other SAM regulators and activation of cell wall modifiers. Our Quartz-Seq2–based
single cell transcriptome revealed that WOX13 plays key roles in determining cellular
identity of callus cell population. We propose that reciprocal inhibition between
WUS and WOX13 mediates critical cell fate determination in pluripotent cell population,
which has a major impact on regeneration efficiency.
acknowledgement: Wethank Y.Iwayama, K.Ohtawa, K.Fukumoto,andN. Mataga (RIKENRRD) for
technical assistance in Quartz-Seq2analyses; M. Mouri(RIKENCSRS)for technical support
with plasmid construction and transactivation assay; Y. Ikeda (NAIST) for technical
support with tissue culture; and A. Furuta for technical support in bulk RNA-seq
analysis. We also thank the Single-cell Omics Laboratory for technical consultation
in scRNA-seq analyses, the members of the Laboratory for Bioinformatics Research
at the RIKEN Center for Biosystems Dynamics Research, and A. Matsushima and T. Ichikawa
for IT infrastructure management. This work was supported by JSPS KAKENHI(17K15146,19H05670,20K06712,20H04894,20H05431,and
22H04713 to M.I. and 20H03284 and 20H05911 to K.S.), by the JST FOREST Program (JPMJFR214H
to M.I.), by The Naito Foundation to M.I.; by Takeda Science Foundation to M.I,and
by the Shiseido Female Researcher Science Grant to M.I. This work was partially
supported by RIKENE pigenome Control Program, Medical Research Center Initiative
for High Depth Omics, and JST CREST(JPMJCR16G3and JPMJCR1926)to I.N.
article_processing_charge: Yes
article_type: original
author:
- first_name: Nao
full_name: Ogura, Nao
last_name: Ogura
- first_name: Yohei
full_name: Sasagawa, Yohei
last_name: Sasagawa
- first_name: Tasuku
full_name: Ito, Tasuku
id: d5a17a4a-e534-11eb-93ec-91fa2aa9bd57
last_name: Ito
orcid: 0000-0002-2482-9089
- first_name: Toshiaki
full_name: Tameshige, Toshiaki
last_name: Tameshige
- first_name: Satomi
full_name: Kawai, Satomi
last_name: Kawai
- first_name: Masaki
full_name: Sano, Masaki
last_name: Sano
- first_name: Yuki
full_name: Doll, Yuki
last_name: Doll
- first_name: Akira
full_name: Iwase, Akira
last_name: Iwase
- first_name: Ayako
full_name: Kawamura, Ayako
last_name: Kawamura
- first_name: Takamasa
full_name: Suzuki, Takamasa
last_name: Suzuki
- first_name: Itoshi
full_name: Nikaido, Itoshi
last_name: Nikaido
- first_name: Keiko
full_name: Sugimoto, Keiko
last_name: Sugimoto
- first_name: Momoko
full_name: Ikeuchi, Momoko
last_name: Ikeuchi
citation:
ama: Ogura N, Sasagawa Y, Ito T, et al. WUSCHEL-RELATED HOMEOBOX 13 suppresses de
novo shoot regeneration via cell fate control of pluripotent callus. Science
Advances. 2023;9(27):eadg6983. doi:10.1126/sciadv.adg6983
apa: Ogura, N., Sasagawa, Y., Ito, T., Tameshige, T., Kawai, S., Sano, M., … Ikeuchi,
M. (2023). WUSCHEL-RELATED HOMEOBOX 13 suppresses de novo shoot regeneration via
cell fate control of pluripotent callus. Science Advances. American Association
for the Advancement of Science. https://doi.org/10.1126/sciadv.adg6983
chicago: Ogura, Nao, Yohei Sasagawa, Tasuku Ito, Toshiaki Tameshige, Satomi Kawai,
Masaki Sano, Yuki Doll, et al. “WUSCHEL-RELATED HOMEOBOX 13 Suppresses de Novo
Shoot Regeneration via Cell Fate Control of Pluripotent Callus.” Science Advances.
American Association for the Advancement of Science, 2023. https://doi.org/10.1126/sciadv.adg6983.
ieee: N. Ogura et al., “WUSCHEL-RELATED HOMEOBOX 13 suppresses de novo shoot
regeneration via cell fate control of pluripotent callus,” Science Advances,
vol. 9, no. 27. American Association for the Advancement of Science, p. eadg6983,
2023.
ista: Ogura N, Sasagawa Y, Ito T, Tameshige T, Kawai S, Sano M, Doll Y, Iwase A,
Kawamura A, Suzuki T, Nikaido I, Sugimoto K, Ikeuchi M. 2023. WUSCHEL-RELATED
HOMEOBOX 13 suppresses de novo shoot regeneration via cell fate control of pluripotent
callus. Science Advances. 9(27), eadg6983.
mla: Ogura, Nao, et al. “WUSCHEL-RELATED HOMEOBOX 13 Suppresses de Novo Shoot Regeneration
via Cell Fate Control of Pluripotent Callus.” Science Advances, vol. 9,
no. 27, American Association for the Advancement of Science, 2023, p. eadg6983,
doi:10.1126/sciadv.adg6983.
short: N. Ogura, Y. Sasagawa, T. Ito, T. Tameshige, S. Kawai, M. Sano, Y. Doll,
A. Iwase, A. Kawamura, T. Suzuki, I. Nikaido, K. Sugimoto, M. Ikeuchi, Science
Advances 9 (2023) eadg6983.
date_created: 2023-07-23T22:01:11Z
date_published: 2023-07-07T00:00:00Z
date_updated: 2023-12-13T11:59:29Z
day: '07'
ddc:
- '580'
doi: 10.1126/sciadv.adg6983
external_id:
isi:
- '001030983100012'
pmid:
- '37418524'
file:
- access_level: open_access
checksum: f59217e1083767777318b5d0cc5e141d
content_type: application/pdf
creator: dernst
date_created: 2023-08-01T06:40:35Z
date_updated: 2023-08-01T06:40:35Z
file_id: '13338'
file_name: 2023_ScienceAdvance_Ogura.pdf
file_size: 1759993
relation: main_file
success: 1
file_date_updated: 2023-08-01T06:40:35Z
has_accepted_license: '1'
intvolume: ' 9'
isi: 1
issue: '27'
language:
- iso: eng
month: '07'
oa: 1
oa_version: Published Version
page: eadg6983
pmid: 1
publication: Science Advances
publication_identifier:
eissn:
- 2375-2548
publication_status: published
publisher: American Association for the Advancement of Science
quality_controlled: '1'
scopus_import: '1'
status: public
title: WUSCHEL-RELATED HOMEOBOX 13 suppresses de novo shoot regeneration via cell
fate control of pluripotent callus
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: 9
year: '2023'
...
---
_id: '13260'
abstract:
- lang: eng
text: Experimental evolution studies are powerful approaches to examine the evolutionary
history of lab populations. Such studies have shed light on how selection changes
phenotypes and genotypes. Most of these studies have not examined the time course
of adaptation under sexual selection manipulation, by resequencing the populations’
genomes at multiple time points. Here, we analyze allele frequency trajectories
in Drosophila pseudoobscura where we altered their sexual selection regime for
200 generations and sequenced pooled populations at 5 time points. The intensity
of sexual selection was either relaxed in monogamous populations (M) or elevated
in polyandrous lines (E). We present a comprehensive study of how selection alters
population genetics parameters at the chromosome and gene level. We investigate
differences in the effective population size—Ne—between the treatments, and perform
a genome-wide scan to identify signatures of selection from the time-series data.
We found genomic signatures of adaptation to both regimes in D. pseudoobscura.
There are more significant variants in E lines as expected from stronger sexual
selection. However, we found that the response on the X chromosome was substantial
in both treatments, more pronounced in E and restricted to the more recently sex-linked
chromosome arm XR in M. In the first generations of experimental evolution, we
estimate Ne to be lower on the X in E lines, which might indicate a swift adaptive
response at the onset of selection. Additionally, the third chromosome was affected
by elevated polyandry whereby its distal end harbors a region showing a strong
signal of adaptive evolution especially in E lines.
acknowledgement: This work was supported by the Vienna Science and Technology Fund
(WWTF)(10.47379/MA16061). C.K. received funding from the Royal Society (RG170315)
and the Carnegie Trust (RIG007474). M.G.R. and R.R.S. have been supported by NERC
(UK) grants NE/I014632/1 and NE/V001566/1. Bioinformatics analyses were performed
on the computer cluster at the University of St Andrews Bioinformatics Unit, which
is funded by Wellcome Trust ISSF awards 105621/Z/14/Z. Complementary data parsing
was carried out with the computational resources provided by the Research/Scientific
Computing teams at The James Hutton Institute and the National Institute of Agricultural
Botany (NIAB)—UK’s Crop Diversity Bioinformatics HPC, BBSRC grant BB/S019669/1.
We are thankful to Paris Veltsos and R. Axel W. Wiberg for useful discussions about
the project as well as providing us with the resequencing data they had produced
as a result of previous work on this experiment. We are especially grateful to Tanya
Sneddon for her help with the DNA extraction process and shipping.
article_number: evad113
article_processing_charge: Yes
article_type: original
author:
- first_name: Carolina
full_name: De Castro Barbosa Rodrigues Barata, Carolina
id: 20565186-803f-11ed-ab7e-96a4ff7694ef
last_name: De Castro Barbosa Rodrigues Barata
- first_name: Rhonda R.
full_name: Snook, Rhonda R.
last_name: Snook
- first_name: Michael G.
full_name: Ritchie, Michael G.
last_name: Ritchie
- first_name: Carolin
full_name: Kosiol, Carolin
last_name: Kosiol
citation:
ama: 'de Castro Barbosa Rodrigues Barata C, Snook RR, Ritchie MG, Kosiol C. Selection
on the fly: Short-term adaptation to an altered sexual selection regime in Drosophila
pseudoobscura. Genome biology and evolution. 2023;15(7). doi:10.1093/gbe/evad113'
apa: 'de Castro Barbosa Rodrigues Barata, C., Snook, R. R., Ritchie, M. G., &
Kosiol, C. (2023). Selection on the fly: Short-term adaptation to an altered sexual
selection regime in Drosophila pseudoobscura. Genome Biology and Evolution.
Oxford Academic. https://doi.org/10.1093/gbe/evad113'
chicago: 'Castro Barbosa Rodrigues Barata, Carolina de, Rhonda R. Snook, Michael
G. Ritchie, and Carolin Kosiol. “Selection on the Fly: Short-Term Adaptation to
an Altered Sexual Selection Regime in Drosophila Pseudoobscura.” Genome Biology
and Evolution. Oxford Academic, 2023. https://doi.org/10.1093/gbe/evad113.'
ieee: 'C. de Castro Barbosa Rodrigues Barata, R. R. Snook, M. G. Ritchie, and C.
Kosiol, “Selection on the fly: Short-term adaptation to an altered sexual selection
regime in Drosophila pseudoobscura,” Genome biology and evolution, vol.
15, no. 7. Oxford Academic, 2023.'
ista: 'de Castro Barbosa Rodrigues Barata C, Snook RR, Ritchie MG, Kosiol C. 2023.
Selection on the fly: Short-term adaptation to an altered sexual selection regime
in Drosophila pseudoobscura. Genome biology and evolution. 15(7), evad113.'
mla: 'de Castro Barbosa Rodrigues Barata, Carolina, et al. “Selection on the Fly:
Short-Term Adaptation to an Altered Sexual Selection Regime in Drosophila Pseudoobscura.”
Genome Biology and Evolution, vol. 15, no. 7, evad113, Oxford Academic,
2023, doi:10.1093/gbe/evad113.'
short: C. de Castro Barbosa Rodrigues Barata, R.R. Snook, M.G. Ritchie, C. Kosiol,
Genome Biology and Evolution 15 (2023).
date_created: 2023-07-23T22:01:11Z
date_published: 2023-07-01T00:00:00Z
date_updated: 2023-08-02T06:42:35Z
day: '01'
ddc:
- '570'
department:
- _id: BeVi
doi: 10.1093/gbe/evad113
external_id:
isi:
- '001023444700003'
pmid:
- '37341535'
file:
- access_level: open_access
checksum: 70de3c4878de6efe00dc56de2df8812f
content_type: application/pdf
creator: dernst
date_created: 2023-08-01T06:58:34Z
date_updated: 2023-08-01T06:58:34Z
file_id: '13339'
file_name: 2023_GBE_Barata.pdf
file_size: 2382587
relation: main_file
success: 1
file_date_updated: 2023-08-01T06:58:34Z
has_accepted_license: '1'
intvolume: ' 15'
isi: 1
issue: '7'
language:
- iso: eng
month: '07'
oa: 1
oa_version: Published Version
pmid: 1
publication: Genome biology and evolution
publication_identifier:
eissn:
- 1759-6653
publication_status: published
publisher: Oxford Academic
quality_controlled: '1'
related_material:
link:
- relation: software
url: https://github.com/carolbarata/dpseudo-n-beyond
scopus_import: '1'
status: public
title: 'Selection on the fly: Short-term adaptation to an altered sexual selection
regime in Drosophila pseudoobscura'
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: 15
year: '2023'
...
---
_id: '13261'
abstract:
- lang: eng
text: Chromosomes in the eukaryotic nucleus are highly compacted. However, for many
functional processes, including transcription initiation, the pairwise motion
of distal chromosomal elements such as enhancers and promoters is essential and
necessitates dynamic fluidity. Here, we used a live-imaging assay to simultaneously
measure the positions of pairs of enhancers and promoters and their transcriptional
output while systematically varying the genomic separation between these two DNA
loci. Our analysis reveals the coexistence of a compact globular organization
and fast subdiffusive dynamics. These combined features cause an anomalous scaling
of polymer relaxation times with genomic separation leading to long-ranged correlations.
Thus, encounter times of DNA loci are much less dependent on genomic distance
than predicted by existing polymer models, with potential consequences for eukaryotic
gene expression.
acknowledgement: This work was supported in part by the U.S. National Science Foundation,
the Center for the Physics of Biological Function (grant PHY-1734030), and the National
Institutes of Health (grants R01GM097275, U01DA047730, and U01DK127429). D.B.B.
was supported by the NOMIS Foundation as a fellow and by an EMBO postdoctoral fellowship
(ALTF 343-2022). H.C. was supported by a Charles H. Revson Biomedical Science Fellowship.
article_processing_charge: No
article_type: original
author:
- first_name: David
full_name: Brückner, David
id: e1e86031-6537-11eb-953a-f7ab92be508d
last_name: Brückner
orcid: 0000-0001-7205-2975
- first_name: Hongtao
full_name: Chen, Hongtao
last_name: Chen
- first_name: Lev
full_name: Barinov, Lev
last_name: Barinov
- first_name: Benjamin
full_name: Zoller, Benjamin
last_name: Zoller
- first_name: Thomas
full_name: Gregor, Thomas
last_name: Gregor
citation:
ama: Brückner D, Chen H, Barinov L, Zoller B, Gregor T. Stochastic motion and transcriptional
dynamics of pairs of distal DNA loci on a compacted chromosome. Science.
2023;380(6652):1357-1362. doi:10.1126/science.adf5568
apa: Brückner, D., Chen, H., Barinov, L., Zoller, B., & Gregor, T. (2023). Stochastic
motion and transcriptional dynamics of pairs of distal DNA loci on a compacted
chromosome. Science. American Association for the Advancement of Science.
https://doi.org/10.1126/science.adf5568
chicago: Brückner, David, Hongtao Chen, Lev Barinov, Benjamin Zoller, and Thomas
Gregor. “Stochastic Motion and Transcriptional Dynamics of Pairs of Distal DNA
Loci on a Compacted Chromosome.” Science. American Association for the
Advancement of Science, 2023. https://doi.org/10.1126/science.adf5568.
ieee: D. Brückner, H. Chen, L. Barinov, B. Zoller, and T. Gregor, “Stochastic motion
and transcriptional dynamics of pairs of distal DNA loci on a compacted chromosome,”
Science, vol. 380, no. 6652. American Association for the Advancement of
Science, pp. 1357–1362, 2023.
ista: Brückner D, Chen H, Barinov L, Zoller B, Gregor T. 2023. Stochastic motion
and transcriptional dynamics of pairs of distal DNA loci on a compacted chromosome.
Science. 380(6652), 1357–1362.
mla: Brückner, David, et al. “Stochastic Motion and Transcriptional Dynamics of
Pairs of Distal DNA Loci on a Compacted Chromosome.” Science, vol. 380,
no. 6652, American Association for the Advancement of Science, 2023, pp. 1357–62,
doi:10.1126/science.adf5568.
short: D. Brückner, H. Chen, L. Barinov, B. Zoller, T. Gregor, Science 380 (2023)
1357–1362.
date_created: 2023-07-23T22:01:12Z
date_published: 2023-06-29T00:00:00Z
date_updated: 2023-12-13T11:41:07Z
day: '29'
department:
- _id: EdHa
doi: 10.1126/science.adf5568
external_id:
isi:
- '001106405600028'
intvolume: ' 380'
isi: 1
issue: '6652'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.1126/science.adf5568
month: '06'
oa: 1
oa_version: Preprint
page: 1357-1362
project:
- _id: 34e2a5b5-11ca-11ed-8bc3-b2265616ef0b
grant_number: 343-2022
name: A mechano-chemical theory for stem cell fate decisions in organoid development
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: Stochastic motion and transcriptional dynamics of pairs of distal DNA loci
on a compacted chromosome
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 380
year: '2023'
...
---
_id: '13262'
abstract:
- lang: eng
text: 'Determining the degree of inherent parallelism in classical sequential algorithms
and leveraging it for fast parallel execution is a key topic in parallel computing,
and detailed analyses are known for a wide range of classical algorithms. In this
paper, we perform the first such analysis for the fundamental Union-Find problem,
in which we are given a graph as a sequence of edges, and must maintain its connectivity
structure under edge additions. We prove that classic sequential algorithms for
this problem are well-parallelizable under reasonable assumptions, addressing
a conjecture by [Blelloch, 2017]. More precisely, we show via a new potential
argument that, under uniform random edge ordering, parallel union-find operations
are unlikely to interfere: T concurrent threads processing the graph in parallel
will encounter memory contention O(T2 · log |V| · log |E|) times in expectation,
where |E| and |V| are the number of edges and nodes in the graph, respectively.
We leverage this result to design a new parallel Union-Find algorithm that is
both internally deterministic, i.e., its results are guaranteed to match those
of a sequential execution, but also work-efficient and scalable, as long as the
number of threads T is O(|E|1 over 3 - ε), for an arbitrarily small constant ε
> 0, which holds for most large real-world graphs. We present lower bounds which
show that our analysis is close to optimal, and experimental results suggesting
that the performance cost of internal determinism is limited.'
article_processing_charge: Yes (in subscription journal)
arxiv: 1
author:
- first_name: Alexander
full_name: Fedorov, Alexander
id: 2e711909-896a-11ed-bdf8-eb0f5a2984c6
last_name: Fedorov
- first_name: Diba
full_name: Hashemi, Diba
id: ed9595ea-2f8f-11ee-ba95-d2b546540783
last_name: Hashemi
- first_name: Giorgi
full_name: Nadiradze, Giorgi
id: 3279A00C-F248-11E8-B48F-1D18A9856A87
last_name: Nadiradze
- 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: 'Fedorov A, Hashemi D, Nadiradze G, Alistarh D-A. Provably-efficient and internally-deterministic
parallel Union-Find. In: Proceedings of the 35th ACM Symposium on Parallelism
in Algorithms and Architectures. Association for Computing Machinery; 2023:261-271.
doi:10.1145/3558481.3591082'
apa: 'Fedorov, A., Hashemi, D., Nadiradze, G., & Alistarh, D.-A. (2023). Provably-efficient
and internally-deterministic parallel Union-Find. In Proceedings of the 35th
ACM Symposium on Parallelism in Algorithms and Architectures (pp. 261–271).
Orlando, FL, United States: Association for Computing Machinery. https://doi.org/10.1145/3558481.3591082'
chicago: Fedorov, Alexander, Diba Hashemi, Giorgi Nadiradze, and Dan-Adrian Alistarh.
“Provably-Efficient and Internally-Deterministic Parallel Union-Find.” In Proceedings
of the 35th ACM Symposium on Parallelism in Algorithms and Architectures,
261–71. Association for Computing Machinery, 2023. https://doi.org/10.1145/3558481.3591082.
ieee: A. Fedorov, D. Hashemi, G. Nadiradze, and D.-A. Alistarh, “Provably-efficient
and internally-deterministic parallel Union-Find,” in Proceedings of the 35th
ACM Symposium on Parallelism in Algorithms and Architectures, Orlando, FL,
United States, 2023, pp. 261–271.
ista: 'Fedorov A, Hashemi D, Nadiradze G, Alistarh D-A. 2023. Provably-efficient
and internally-deterministic parallel Union-Find. Proceedings of the 35th ACM
Symposium on Parallelism in Algorithms and Architectures. SPAA: Symposium on Parallelism
in Algorithms and Architectures, 261–271.'
mla: Fedorov, Alexander, et al. “Provably-Efficient and Internally-Deterministic
Parallel Union-Find.” Proceedings of the 35th ACM Symposium on Parallelism
in Algorithms and Architectures, Association for Computing Machinery, 2023,
pp. 261–71, doi:10.1145/3558481.3591082.
short: A. Fedorov, D. Hashemi, G. Nadiradze, D.-A. Alistarh, in:, Proceedings of
the 35th ACM Symposium on Parallelism in Algorithms and Architectures, Association
for Computing Machinery, 2023, pp. 261–271.
conference:
end_date: 2023-06-19
location: Orlando, FL, United States
name: 'SPAA: Symposium on Parallelism in Algorithms and Architectures'
start_date: 2023-06-17
date_created: 2023-07-23T22:01:12Z
date_published: 2023-06-17T00:00:00Z
date_updated: 2023-07-31T10:54:32Z
day: '17'
ddc:
- '000'
department:
- _id: DaAl
- _id: GradSch
doi: 10.1145/3558481.3591082
external_id:
arxiv:
- '2304.09331'
file:
- access_level: open_access
checksum: 72e312aabf0c5248c99b5cd3a88e4c88
content_type: application/pdf
creator: dernst
date_created: 2023-07-31T10:53:08Z
date_updated: 2023-07-31T10:53:08Z
file_id: '13334'
file_name: 2023_SPAA_Fedorov.pdf
file_size: 2087937
relation: main_file
success: 1
file_date_updated: 2023-07-31T10:53:08Z
has_accepted_license: '1'
language:
- iso: eng
month: '06'
oa: 1
oa_version: Published Version
page: 261-271
publication: Proceedings of the 35th ACM Symposium on Parallelism in Algorithms and
Architectures
publication_identifier:
isbn:
- '9781450395458'
publication_status: published
publisher: Association for Computing Machinery
quality_controlled: '1'
scopus_import: '1'
status: public
title: Provably-efficient and internally-deterministic parallel Union-Find
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: 2DF688A6-F248-11E8-B48F-1D18A9856A87
year: '2023'
...
---
_id: '13263'
abstract:
- lang: eng
text: "Motivation: Boolean networks are simple but efficient mathematical formalism
for modelling complex biological systems. However, having only two levels of activation
is sometimes not enough to fully capture the dynamics of real-world biological
systems. Hence, the need for multi-valued networks (MVNs), a generalization of
Boolean networks. Despite the importance of MVNs for modelling biological systems,
only limited progress has been made on developing theories, analysis methods,
and tools that can support them. In particular, the recent use of trap spaces
in Boolean networks made a great impact on the field of systems biology, but there
has been no similar concept defined and studied for MVNs to date.\r\n\r\nResults:
In this work, we generalize the concept of trap spaces in Boolean networks to
that in MVNs. We then develop the theory and the analysis methods for trap spaces
in MVNs. In particular, we implement all proposed methods in a Python package
called trapmvn. Not only showing the applicability of our approach via a realistic
case study, we also evaluate the time efficiency of the method on a large collection
of real-world models. The experimental results confirm the time efficiency, which
we believe enables more accurate analysis on larger and more complex multi-valued
models."
acknowledgement: This work was supported by L’Institut Carnot STAR, Marseille, France,
and by the European Union’s Horizon 2020 research and innovation programme under
the Marie Skłodowska-Curie Grant Agreement No. [101034413].
article_processing_charge: Yes
article_type: original
author:
- first_name: Van Giang
full_name: Trinh, Van Giang
last_name: Trinh
- first_name: Belaid
full_name: Benhamou, Belaid
last_name: Benhamou
- first_name: Thomas A
full_name: Henzinger, Thomas A
id: 40876CD8-F248-11E8-B48F-1D18A9856A87
last_name: Henzinger
orcid: 0000-0002-2985-7724
- first_name: Samuel
full_name: Pastva, Samuel
id: 07c5ea74-f61c-11ec-a664-aa7c5d957b2b
last_name: Pastva
orcid: 0000-0003-1993-0331
citation:
ama: 'Trinh VG, Benhamou B, Henzinger TA, Pastva S. Trap spaces of multi-valued
networks: Definition, computation, and applications. Bioinformatics. 2023;39(Supplement_1):i513-i522.
doi:10.1093/bioinformatics/btad262'
apa: 'Trinh, V. G., Benhamou, B., Henzinger, T. A., & Pastva, S. (2023). Trap
spaces of multi-valued networks: Definition, computation, and applications. Bioinformatics.
Oxford Academic. https://doi.org/10.1093/bioinformatics/btad262'
chicago: 'Trinh, Van Giang, Belaid Benhamou, Thomas A Henzinger, and Samuel Pastva.
“Trap Spaces of Multi-Valued Networks: Definition, Computation, and Applications.”
Bioinformatics. Oxford Academic, 2023. https://doi.org/10.1093/bioinformatics/btad262.'
ieee: 'V. G. Trinh, B. Benhamou, T. A. Henzinger, and S. Pastva, “Trap spaces of
multi-valued networks: Definition, computation, and applications,” Bioinformatics,
vol. 39, no. Supplement_1. Oxford Academic, pp. i513–i522, 2023.'
ista: 'Trinh VG, Benhamou B, Henzinger TA, Pastva S. 2023. Trap spaces of multi-valued
networks: Definition, computation, and applications. Bioinformatics. 39(Supplement_1),
i513–i522.'
mla: 'Trinh, Van Giang, et al. “Trap Spaces of Multi-Valued Networks: Definition,
Computation, and Applications.” Bioinformatics, vol. 39, no. Supplement_1,
Oxford Academic, 2023, pp. i513–22, doi:10.1093/bioinformatics/btad262.'
short: V.G. Trinh, B. Benhamou, T.A. Henzinger, S. Pastva, Bioinformatics 39 (2023)
i513–i522.
date_created: 2023-07-23T22:01:12Z
date_published: 2023-06-30T00:00:00Z
date_updated: 2023-12-13T11:41:52Z
day: '30'
ddc:
- '000'
department:
- _id: ToHe
doi: 10.1093/bioinformatics/btad262
ec_funded: 1
external_id:
isi:
- '001027457000060'
pmid:
- '37387165'
file:
- access_level: open_access
checksum: ba3abe1171df1958413b7c7f957f5486
content_type: application/pdf
creator: dernst
date_created: 2023-07-31T11:09:05Z
date_updated: 2023-07-31T11:09:05Z
file_id: '13335'
file_name: 2023_Bioinformatics_Trinh.pdf
file_size: 641736
relation: main_file
success: 1
file_date_updated: 2023-07-31T11:09:05Z
has_accepted_license: '1'
intvolume: ' 39'
isi: 1
issue: Supplement_1
language:
- iso: eng
month: '06'
oa: 1
oa_version: Published Version
page: i513-i522
pmid: 1
project:
- _id: fc2ed2f7-9c52-11eb-aca3-c01059dda49c
call_identifier: H2020
grant_number: '101034413'
name: 'IST-BRIDGE: International postdoctoral program'
publication: Bioinformatics
publication_identifier:
eissn:
- 1367-4811
issn:
- 1367-4803
publication_status: published
publisher: Oxford Academic
quality_controlled: '1'
related_material:
link:
- relation: software
url: https://github.com/giang-trinh/trap-mvn
scopus_import: '1'
status: public
title: 'Trap spaces of multi-valued networks: Definition, computation, and applications'
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: 39
year: '2023'
...
---
_id: '13264'
abstract:
- lang: eng
text: "We build a parametric amplifier with a Josephson field-effect transistor
(JoFET) as the active element. The resonant frequency of the device is field-effect
tunable over a range of 2 GHz. The JoFET amplifier has 20 dB of gain, 4 MHz of
instantaneous bandwidth, and a 1-dB compression point of -125.5 dBm when operated
at a fixed resonance frequency.\r\n\r\n"
acknowledged_ssus:
- _id: NanoFab
- _id: M-Shop
acknowledgement: We thank Shyam Shankar for helpful feedback on the manuscript. We
gratefully acknowledge the support of the ISTA nanofabrication facility, the Miba
Machine Shop, and the eMachine Shop. The NYU team acknowledges support from Army
Research Office Grant No. W911NF2110303.
article_number: '064032'
article_processing_charge: No
article_type: original
arxiv: 1
author:
- first_name: Duc T
full_name: Phan, Duc T
id: 29C8C0B4-F248-11E8-B48F-1D18A9856A87
last_name: Phan
- first_name: Paul
full_name: Falthansl-Scheinecker, Paul
id: 85b43b21-15b2-11ec-abd3-e2c252cc2285
last_name: Falthansl-Scheinecker
- first_name: Umang
full_name: Mishra, Umang
id: 4328fa4c-f128-11eb-9611-c107b0fe4d51
last_name: Mishra
- first_name: W. M.
full_name: Strickland, W. M.
last_name: Strickland
- first_name: D.
full_name: Langone, D.
last_name: Langone
- first_name: J.
full_name: Shabani, J.
last_name: Shabani
- first_name: Andrew P
full_name: Higginbotham, Andrew P
id: 4AD6785A-F248-11E8-B48F-1D18A9856A87
last_name: Higginbotham
orcid: 0000-0003-2607-2363
citation:
ama: Phan DT, Falthansl-Scheinecker P, Mishra U, et al. Gate-tunable superconductor-semiconductor
parametric amplifier. Physical Review Applied. 2023;19(6). doi:10.1103/PhysRevApplied.19.064032
apa: Phan, D. T., Falthansl-Scheinecker, P., Mishra, U., Strickland, W. M., Langone,
D., Shabani, J., & Higginbotham, A. P. (2023). Gate-tunable superconductor-semiconductor
parametric amplifier. Physical Review Applied. American Physical Society.
https://doi.org/10.1103/PhysRevApplied.19.064032
chicago: Phan, Duc T, Paul Falthansl-Scheinecker, Umang Mishra, W. M. Strickland,
D. Langone, J. Shabani, and Andrew P Higginbotham. “Gate-Tunable Superconductor-Semiconductor
Parametric Amplifier.” Physical Review Applied. American Physical Society,
2023. https://doi.org/10.1103/PhysRevApplied.19.064032.
ieee: D. T. Phan et al., “Gate-tunable superconductor-semiconductor parametric
amplifier,” Physical Review Applied, vol. 19, no. 6. American Physical
Society, 2023.
ista: Phan DT, Falthansl-Scheinecker P, Mishra U, Strickland WM, Langone D, Shabani
J, Higginbotham AP. 2023. Gate-tunable superconductor-semiconductor parametric
amplifier. Physical Review Applied. 19(6), 064032.
mla: Phan, Duc T., et al. “Gate-Tunable Superconductor-Semiconductor Parametric
Amplifier.” Physical Review Applied, vol. 19, no. 6, 064032, American Physical
Society, 2023, doi:10.1103/PhysRevApplied.19.064032.
short: D.T. Phan, P. Falthansl-Scheinecker, U. Mishra, W.M. Strickland, D. Langone,
J. Shabani, A.P. Higginbotham, Physical Review Applied 19 (2023).
date_created: 2023-07-23T22:01:12Z
date_published: 2023-06-09T00:00:00Z
date_updated: 2023-11-30T10:56:03Z
day: '09'
department:
- _id: AnHi
- _id: OnHo
doi: 10.1103/PhysRevApplied.19.064032
external_id:
arxiv:
- '2206.05746'
isi:
- '001012022600004'
intvolume: ' 19'
isi: 1
issue: '6'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/2206.05746
month: '06'
oa: 1
oa_version: Preprint
publication: Physical Review Applied
publication_identifier:
eissn:
- 2331-7019
publication_status: published
publisher: American Physical Society
quality_controlled: '1'
related_material:
record:
- id: '14547'
relation: dissertation_contains
status: public
scopus_import: '1'
status: public
title: Gate-tunable superconductor-semiconductor parametric amplifier
type: journal_article
user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
volume: 19
year: '2023'
...
---
_id: '13265'
abstract:
- lang: eng
text: In this study, we propose a computational framework for optimizing the continuity
of the toolpath in fabricating surface models on an extrusion-based 3D printer.
Toolpath continuity is a critical issue that influences both the quality and the
efficiency of extrusion-based fabrication. Transfer moves lead to rough and bumpy
surfaces, where this phenomenon worsens for materials with large viscosity, like
clay. The effects of continuity on the surface models are even more severe in
terms of the quality of the surface and the stability of the model. We introduce
a criterion called the one–path patch (OPP) to represent a patch on the surface
of the shell that can be traversed along one path by considering the constraints
on fabrication. We study the properties of the OPPs and their merging operations
to propose a bottom-up OPP merging procedure to decompose the given shell surface
into a minimal number of OPPs, and to generate the “as-continuous-as-possible”
(ACAP) toolpath. Furthermore, we augment the path planning algorithm with a curved-layer
printing scheme that reduces staircase defects and improves the continuity of
the toolpath by connecting multiple segments. We evaluated the ACAP algorithm
on ceramic and thermoplastic materials, and the results showed that it improves
the fabrication of surface models in terms of both efficiency and surface quality.
acknowledgement: 'This work was supported in part by grants from the NSFC (61972232),
Science and Technology Program of Shenzhen, China (CJGJZD20200617102202007). '
article_number: '26'
article_processing_charge: No
article_type: original
arxiv: 1
author:
- first_name: Fanchao
full_name: Zhong, Fanchao
last_name: Zhong
- first_name: Yonglai
full_name: Xu, Yonglai
last_name: Xu
- first_name: Haisen
full_name: Zhao, Haisen
id: fb7f793a-80d1-11eb-8869-d56e5b2a8ff4
last_name: Zhao
orcid: 0000-0002-6389-1045
- first_name: Lin
full_name: Lu, Lin
last_name: Lu
citation:
ama: Zhong F, Xu Y, Zhao H, Lu L. As-Continuous-As-Possible extrusion-based fabrication
of surface models. ACM Transactions on Graphics. 2023;42(3). doi:10.1145/3575859
apa: Zhong, F., Xu, Y., Zhao, H., & Lu, L. (2023). As-Continuous-As-Possible
extrusion-based fabrication of surface models. ACM Transactions on Graphics.
Association for Computing Machinery. https://doi.org/10.1145/3575859
chicago: Zhong, Fanchao, Yonglai Xu, Haisen Zhao, and Lin Lu. “As-Continuous-As-Possible
Extrusion-Based Fabrication of Surface Models.” ACM Transactions on Graphics.
Association for Computing Machinery, 2023. https://doi.org/10.1145/3575859.
ieee: F. Zhong, Y. Xu, H. Zhao, and L. Lu, “As-Continuous-As-Possible extrusion-based
fabrication of surface models,” ACM Transactions on Graphics, vol. 42,
no. 3. Association for Computing Machinery, 2023.
ista: Zhong F, Xu Y, Zhao H, Lu L. 2023. As-Continuous-As-Possible extrusion-based
fabrication of surface models. ACM Transactions on Graphics. 42(3), 26.
mla: Zhong, Fanchao, et al. “As-Continuous-As-Possible Extrusion-Based Fabrication
of Surface Models.” ACM Transactions on Graphics, vol. 42, no. 3, 26, Association
for Computing Machinery, 2023, doi:10.1145/3575859.
short: F. Zhong, Y. Xu, H. Zhao, L. Lu, ACM Transactions on Graphics 42 (2023).
date_created: 2023-07-23T22:01:13Z
date_published: 2023-03-17T00:00:00Z
date_updated: 2023-12-13T11:34:59Z
day: '17'
department:
- _id: BeBi
doi: 10.1145/3575859
external_id:
arxiv:
- '2201.02374'
isi:
- '001018739600002'
intvolume: ' 42'
isi: 1
issue: '3'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.48550/arXiv.2201.02374
month: '03'
oa: 1
oa_version: Preprint
publication: ACM Transactions on Graphics
publication_identifier:
eissn:
- 1557-7368
issn:
- 0730-0301
publication_status: published
publisher: Association for Computing Machinery
quality_controlled: '1'
scopus_import: '1'
status: public
title: As-Continuous-As-Possible extrusion-based fabrication of surface models
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 42
year: '2023'
...