---
_id: '12856'
abstract:
- lang: eng
text: "As the complexity and criticality of software increase every year, so does
the importance of run-time monitoring. Third-party monitoring, with limited knowledge
of the monitored software, and best-effort monitoring, which keeps pace with the
monitored software, are especially valuable, yet underexplored areas of run-time
monitoring. Most existing monitoring frameworks do not support their combination
because they either require access to the monitored code for instrumentation purposes
or the processing of all observed events, or both.\r\n\r\nWe present a middleware
framework, VAMOS, for the run-time monitoring of software which is explicitly
designed to support third-party and best-effort scenarios. The design goals of
VAMOS are (i) efficiency (keeping pace at low overhead), (ii) flexibility (the
ability to monitor black-box code through a variety of different event channels,
and the connectability to monitors written in different specification languages),
and (iii) ease-of-use. To achieve its goals, VAMOS combines aspects of event broker
and event recognition systems with aspects of stream processing systems.\r\nWe
implemented a prototype toolchain for VAMOS and conducted experiments including
a case study of monitoring for data races. The results indicate that VAMOS enables
writing useful yet efficient monitors, is compatible with a variety of event sources
and monitor specifications, and simplifies key aspects of setting up a monitoring
system from scratch."
acknowledgement: This work was supported in part by the ERC-2020-AdG 101020093. The
authors would like to thank the anonymous FASE reviewers for their valuable feedback
and suggestions.
alternative_title:
- LNCS
article_processing_charge: No
author:
- first_name: Marek
full_name: Chalupa, Marek
id: 87e34708-d6c6-11ec-9f5b-9391e7be2463
last_name: Chalupa
- first_name: Fabian
full_name: Mühlböck, Fabian
id: 6395C5F6-89DF-11E9-9C97-6BDFE5697425
last_name: Mühlböck
orcid: 0000-0003-1548-0177
- first_name: Stefanie
full_name: Muroya Lei, Stefanie
id: a376de31-8972-11ed-ae7b-d0251c13c8ff
last_name: Muroya Lei
- 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: 'Chalupa M, Mühlböck F, Muroya Lei S, Henzinger TA. Vamos: Middleware for best-effort
third-party monitoring. In: Fundamental Approaches to Software Engineering.
Vol 13991. Springer Nature; 2023:260-281. doi:10.1007/978-3-031-30826-0_15'
apa: 'Chalupa, M., Mühlböck, F., Muroya Lei, S., & Henzinger, T. A. (2023).
Vamos: Middleware for best-effort third-party monitoring. In Fundamental Approaches
to Software Engineering (Vol. 13991, pp. 260–281). Paris, France: Springer
Nature. https://doi.org/10.1007/978-3-031-30826-0_15'
chicago: 'Chalupa, Marek, Fabian Mühlböck, Stefanie Muroya Lei, and Thomas A Henzinger.
“Vamos: Middleware for Best-Effort Third-Party Monitoring.” In Fundamental
Approaches to Software Engineering, 13991:260–81. Springer Nature, 2023. https://doi.org/10.1007/978-3-031-30826-0_15.'
ieee: 'M. Chalupa, F. Mühlböck, S. Muroya Lei, and T. A. Henzinger, “Vamos: Middleware
for best-effort third-party monitoring,” in Fundamental Approaches to Software
Engineering, Paris, France, 2023, vol. 13991, pp. 260–281.'
ista: 'Chalupa M, Mühlböck F, Muroya Lei S, Henzinger TA. 2023. Vamos: Middleware
for best-effort third-party monitoring. Fundamental Approaches to Software Engineering.
FASE: Fundamental Approaches to Software Engineering, LNCS, vol. 13991, 260–281.'
mla: 'Chalupa, Marek, et al. “Vamos: Middleware for Best-Effort Third-Party Monitoring.”
Fundamental Approaches to Software Engineering, vol. 13991, Springer Nature,
2023, pp. 260–81, doi:10.1007/978-3-031-30826-0_15.'
short: M. Chalupa, F. Mühlböck, S. Muroya Lei, T.A. Henzinger, in:, Fundamental
Approaches to Software Engineering, Springer Nature, 2023, pp. 260–281.
conference:
end_date: 2023-04-27
location: Paris, France
name: 'FASE: Fundamental Approaches to Software Engineering'
start_date: 2023-04-22
corr_author: '1'
date_created: 2023-04-20T08:29:42Z
date_published: 2023-04-20T00:00:00Z
date_updated: 2025-09-09T12:25:29Z
day: '20'
ddc:
- '000'
department:
- _id: ToHe
doi: 10.1007/978-3-031-30826-0_15
ec_funded: 1
external_id:
isi:
- '001284136600015'
file:
- access_level: open_access
checksum: 17a7c8e08be609cf2408d37ea55e322c
content_type: application/pdf
creator: dernst
date_created: 2023-04-25T07:16:36Z
date_updated: 2023-04-25T07:16:36Z
file_id: '12865'
file_name: 2023_LNCS_ChalupaM.pdf
file_size: 580828
relation: main_file
success: 1
file_date_updated: 2023-04-25T07:16:36Z
has_accepted_license: '1'
intvolume: ' 13991'
isi: 1
language:
- iso: eng
license: https://creativecommons.org/licenses/by/4.0/
month: '04'
oa: 1
oa_version: Published Version
page: 260-281
project:
- _id: 62781420-2b32-11ec-9570-8d9b63373d4d
call_identifier: H2020
grant_number: '101020093'
name: Vigilant Algorithmic Monitoring of Software
publication: Fundamental Approaches to Software Engineering
publication_identifier:
eisbn:
- '9783031308260'
eissn:
- 1611-3349
isbn:
- '9783031308253'
issn:
- 0302-9743
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
related_material:
record:
- id: '18169'
relation: later_version
status: public
- id: '12407'
relation: earlier_version
status: public
scopus_import: '1'
status: public
title: 'Vamos: Middleware for best-effort third-party monitoring'
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: 317138e5-6ab7-11ef-aa6d-ffef3953e345
volume: 13991
year: '2023'
...
---
_id: '12859'
abstract:
- lang: eng
text: 'Machine learning models are vulnerable to adversarial perturbations, and
a thought-provoking paper by Bubeck and Sellke has analyzed this phenomenon through
the lens of over-parameterization: interpolating smoothly the data requires significantly
more parameters than simply memorizing it. However, this "universal" law provides
only a necessary condition for robustness, and it is unable to discriminate between
models. In this paper, we address these gaps by focusing on empirical risk minimization
in two prototypical settings, namely, random features and the neural tangent kernel
(NTK). We prove that, for random features, the model is not robust for any degree
of over-parameterization, even when the necessary condition coming from the universal
law of robustness is satisfied. In contrast, for even activations, the NTK model
meets the universal lower bound, and it is robust as soon as the necessary condition
on over-parameterization is fulfilled. This also addresses a conjecture in prior
work by Bubeck, Li and Nagaraj. Our analysis decouples the effect of the kernel
of the model from an "interaction matrix", which describes the interaction with
the test data and captures the effect of the activation. Our theoretical results
are corroborated by numerical evidence on both synthetic and standard datasets
(MNIST, CIFAR-10).'
acknowledgement: "Simone Bombari and Marco Mondelli were partially supported by the
2019 Lopez-Loreta prize, and\r\nthe authors would like to thank Hamed Hassani for
helpful discussions.\r\n"
alternative_title:
- PMLR
article_processing_charge: No
arxiv: 1
author:
- first_name: Simone
full_name: Bombari, Simone
id: ca726dda-de17-11ea-bc14-f9da834f63aa
last_name: Bombari
- first_name: Shayan
full_name: Kiyani, Shayan
id: f5a2b424-e339-11ed-8435-ff3b4fe70cf8
last_name: Kiyani
- first_name: Marco
full_name: Mondelli, Marco
id: 27EB676C-8706-11E9-9510-7717E6697425
last_name: Mondelli
orcid: 0000-0002-3242-7020
citation:
ama: 'Bombari S, Kiyani S, Mondelli M. Beyond the universal law of robustness: Sharper
laws for random features and neural tangent kernels. In: Proceedings of the
40th International Conference on Machine Learning. Vol 202. ML Research Press;
2023:2738-2776.'
apa: 'Bombari, S., Kiyani, S., & Mondelli, M. (2023). Beyond the universal law
of robustness: Sharper laws for random features and neural tangent kernels. In
Proceedings of the 40th International Conference on Machine Learning (Vol.
202, pp. 2738–2776). Honolulu, HI, United States: ML Research Press.'
chicago: 'Bombari, Simone, Shayan Kiyani, and Marco Mondelli. “Beyond the Universal
Law of Robustness: Sharper Laws for Random Features and Neural Tangent Kernels.”
In Proceedings of the 40th International Conference on Machine Learning,
202:2738–76. ML Research Press, 2023.'
ieee: 'S. Bombari, S. Kiyani, and M. Mondelli, “Beyond the universal law of robustness:
Sharper laws for random features and neural tangent kernels,” in Proceedings
of the 40th International Conference on Machine Learning, Honolulu, HI, United
States, 2023, vol. 202, pp. 2738–2776.'
ista: 'Bombari S, Kiyani S, Mondelli M. 2023. Beyond the universal law of robustness:
Sharper laws for random features and neural tangent kernels. Proceedings of the
40th International Conference on Machine Learning. ICML: International Conference
on Machine Learning, PMLR, vol. 202, 2738–2776.'
mla: 'Bombari, Simone, et al. “Beyond the Universal Law of Robustness: Sharper Laws
for Random Features and Neural Tangent Kernels.” Proceedings of the 40th International
Conference on Machine Learning, vol. 202, ML Research Press, 2023, pp. 2738–76.'
short: S. Bombari, S. Kiyani, M. Mondelli, in:, Proceedings of the 40th International
Conference on Machine Learning, ML Research Press, 2023, pp. 2738–2776.
conference:
end_date: 2023-07-29
location: Honolulu, HI, United States
name: 'ICML: International Conference on Machine Learning'
start_date: 2023-07-23
corr_author: '1'
date_created: 2023-04-23T16:11:03Z
date_published: 2023-10-27T00:00:00Z
date_updated: 2025-04-15T07:50:16Z
day: '27'
department:
- _id: GradSch
- _id: MaMo
external_id:
arxiv:
- '2302.01629'
intvolume: ' 202'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/2302.01629
month: '10'
oa: 1
oa_version: Preprint
page: 2738-2776
project:
- _id: 059876FA-7A3F-11EA-A408-12923DDC885E
name: Prix Lopez-Loretta 2019 - Marco Mondelli
publication: Proceedings of the 40th International Conference on Machine Learning
publication_status: published
publisher: ML Research Press
quality_controlled: '1'
related_material:
link:
- relation: software
url: https://github.com/simone-bombari/beyond-universal-robustness
status: public
title: 'Beyond the universal law of robustness: Sharper laws for random features and
neural tangent kernels'
type: conference
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 202
year: '2023'
...
---
_id: '12861'
abstract:
- lang: eng
text: The field of indirect reciprocity investigates how social norms can foster
cooperation when individuals continuously monitor and assess each other’s social
interactions. By adhering to certain social norms, cooperating individuals can
improve their reputation and, in turn, receive benefits from others. Eight social
norms, known as the “leading eight," have been shown to effectively promote the
evolution of cooperation as long as information is public and reliable. These
norms categorize group members as either ’good’ or ’bad’. In this study, we examine
a scenario where individuals instead assign nuanced reputation scores to each
other, and only cooperate with those whose reputation exceeds a certain threshold.
We find both analytically and through simulations that such quantitative assessments
are error-correcting, thus facilitating cooperation in situations where information
is private and unreliable. Moreover, our results identify four specific norms
that are robust to such conditions, and may be relevant for helping to sustain
cooperation in natural populations.
acknowledgement: 'This work was supported by the European Research Council CoG 863818
(ForM-SMArt) (to K.C.) and the European Research Council Starting Grant 850529:
E-DIRECT (to C.H.). L.S. received additional partial support by the Austrian Science
Fund (FWF) under grant Z211-N23 (Wittgenstein Award), and also thanks the support
by the Stochastic Analysis and Application Research Center (SAARC) under National
Research Foundation of Korea grant NRF-2019R1A5A1028324. The authors additionally
thank Stefan Schmid for providing access to his lab infrastructure at the University
of Vienna for the purpose of collecting simulation data.'
article_number: '2086'
article_processing_charge: No
article_type: original
author:
- first_name: Laura
full_name: Schmid, Laura
id: 38B437DE-F248-11E8-B48F-1D18A9856A87
last_name: Schmid
orcid: 0000-0002-6978-7329
- first_name: Farbod
full_name: Ekbatani, Farbod
last_name: Ekbatani
- first_name: Christian
full_name: Hilbe, Christian
id: 2FDF8F3C-F248-11E8-B48F-1D18A9856A87
last_name: Hilbe
orcid: 0000-0001-5116-955X
- first_name: Krishnendu
full_name: Chatterjee, Krishnendu
id: 2E5DCA20-F248-11E8-B48F-1D18A9856A87
last_name: Chatterjee
orcid: 0000-0002-4561-241X
citation:
ama: Schmid L, Ekbatani F, Hilbe C, Chatterjee K. Quantitative assessment can stabilize
indirect reciprocity under imperfect information. Nature Communications.
2023;14. doi:10.1038/s41467-023-37817-x
apa: Schmid, L., Ekbatani, F., Hilbe, C., & Chatterjee, K. (2023). Quantitative
assessment can stabilize indirect reciprocity under imperfect information. Nature
Communications. Springer Nature. https://doi.org/10.1038/s41467-023-37817-x
chicago: Schmid, Laura, Farbod Ekbatani, Christian Hilbe, and Krishnendu Chatterjee.
“Quantitative Assessment Can Stabilize Indirect Reciprocity under Imperfect Information.”
Nature Communications. Springer Nature, 2023. https://doi.org/10.1038/s41467-023-37817-x.
ieee: L. Schmid, F. Ekbatani, C. Hilbe, and K. Chatterjee, “Quantitative assessment
can stabilize indirect reciprocity under imperfect information,” Nature Communications,
vol. 14. Springer Nature, 2023.
ista: Schmid L, Ekbatani F, Hilbe C, Chatterjee K. 2023. Quantitative assessment
can stabilize indirect reciprocity under imperfect information. Nature Communications.
14, 2086.
mla: Schmid, Laura, et al. “Quantitative Assessment Can Stabilize Indirect Reciprocity
under Imperfect Information.” Nature Communications, vol. 14, 2086, Springer
Nature, 2023, doi:10.1038/s41467-023-37817-x.
short: L. Schmid, F. Ekbatani, C. Hilbe, K. Chatterjee, Nature Communications 14
(2023).
date_created: 2023-04-23T22:01:03Z
date_published: 2023-04-12T00:00:00Z
date_updated: 2025-04-15T06:26:15Z
day: '12'
ddc:
- '000'
department:
- _id: KrCh
doi: 10.1038/s41467-023-37817-x
ec_funded: 1
external_id:
isi:
- '001003644100020'
pmid:
- '37045828'
file:
- access_level: open_access
checksum: a4b3b7b36fbef068cabf4fb99501fef6
content_type: application/pdf
creator: dernst
date_created: 2023-04-25T09:13:53Z
date_updated: 2023-04-25T09:13:53Z
file_id: '12868'
file_name: 2023_NatureComm_Schmid.pdf
file_size: 1786475
relation: main_file
success: 1
file_date_updated: 2023-04-25T09:13:53Z
has_accepted_license: '1'
intvolume: ' 14'
isi: 1
language:
- iso: eng
month: '04'
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: 25F42A32-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: Z211
name: Formal methods for the design and analysis of complex systems
publication: Nature Communications
publication_identifier:
eissn:
- 2041-1723
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
scopus_import: '1'
status: public
title: Quantitative assessment can stabilize indirect reciprocity under imperfect
information
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: journal_article
user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
volume: 14
year: '2023'
...
---
_id: '12862'
abstract:
- lang: eng
text: Despite the considerable progress of in vivo neural recording techniques,
inferring the biophysical mechanisms underlying large scale coordination of brain
activity from neural data remains challenging. One obstacle is the difficulty
to link high dimensional functional connectivity measures to mechanistic models
of network activity. We address this issue by investigating spike-field coupling
(SFC) measurements, which quantify the synchronization between, on the one hand,
the action potentials produced by neurons, and on the other hand mesoscopic “field”
signals, reflecting subthreshold activities at possibly multiple recording sites.
As the number of recording sites gets large, the amount of pairwise SFC measurements
becomes overwhelmingly challenging to interpret. We develop Generalized Phase
Locking Analysis (GPLA) as an interpretable dimensionality reduction of this multivariate
SFC. GPLA describes the dominant coupling between field activity and neural ensembles
across space and frequencies. We show that GPLA features are biophysically interpretable
when used in conjunction with appropriate network models, such that we can identify
the influence of underlying circuit properties on these features. We demonstrate
the statistical benefits and interpretability of this approach in various computational
models and Utah array recordings. The results suggest that GPLA, used jointly
with biophysical modeling, can help uncover the contribution of recurrent microcircuits
to the spatio-temporal dynamics observed in multi-channel experimental recordings.
acknowledgement: "We thank Britni Crocker for help with preprocessing of the data
and spike sorting; Joachim Werner and Michael Schnabel for their excellent IT support;
Andreas Tolias for help with the initial implantation’s of the Utah arrays.\r\nAll
authors were supported by the Max Planck Society. M.B. was supported by the German\r\nFederal
Ministry of Education and Research (BMBF) through the funding scheme received by\r\nthe
Tübingen AI Center, FKZ: 01IS18039B. N.K.L. and V.K. acknowledge the support from
the\r\nShanghai Municipal Science and Technology Major Project (Grant No. 2019SHZDZX02).
The funders had no role in study design, data collection and analysis, decision
to publish, or preparation of the manuscript. "
article_number: e1010983
article_processing_charge: No
article_type: original
author:
- first_name: Shervin
full_name: Safavi, Shervin
last_name: Safavi
- first_name: Theofanis I.
full_name: Panagiotaropoulos, Theofanis I.
last_name: Panagiotaropoulos
- first_name: Vishal
full_name: Kapoor, Vishal
last_name: Kapoor
- first_name: Juan F
full_name: Ramirez Villegas, Juan F
id: 44B06F76-F248-11E8-B48F-1D18A9856A87
last_name: Ramirez Villegas
- first_name: Nikos K.
full_name: Logothetis, Nikos K.
last_name: Logothetis
- first_name: Michel
full_name: Besserve, Michel
last_name: Besserve
citation:
ama: Safavi S, Panagiotaropoulos TI, Kapoor V, Ramirez Villegas JF, Logothetis NK,
Besserve M. Uncovering the organization of neural circuits with Generalized Phase
Locking Analysis. PLoS Computational Biology. 2023;19(4). doi:10.1371/journal.pcbi.1010983
apa: Safavi, S., Panagiotaropoulos, T. I., Kapoor, V., Ramirez Villegas, J. F.,
Logothetis, N. K., & Besserve, M. (2023). Uncovering the organization of neural
circuits with Generalized Phase Locking Analysis. PLoS Computational Biology.
Public Library of Science. https://doi.org/10.1371/journal.pcbi.1010983
chicago: Safavi, Shervin, Theofanis I. Panagiotaropoulos, Vishal Kapoor, Juan F
Ramirez Villegas, Nikos K. Logothetis, and Michel Besserve. “Uncovering the Organization
of Neural Circuits with Generalized Phase Locking Analysis.” PLoS Computational
Biology. Public Library of Science, 2023. https://doi.org/10.1371/journal.pcbi.1010983.
ieee: S. Safavi, T. I. Panagiotaropoulos, V. Kapoor, J. F. Ramirez Villegas, N.
K. Logothetis, and M. Besserve, “Uncovering the organization of neural circuits
with Generalized Phase Locking Analysis,” PLoS Computational Biology, vol.
19, no. 4. Public Library of Science, 2023.
ista: Safavi S, Panagiotaropoulos TI, Kapoor V, Ramirez Villegas JF, Logothetis
NK, Besserve M. 2023. Uncovering the organization of neural circuits with Generalized
Phase Locking Analysis. PLoS Computational Biology. 19(4), e1010983.
mla: Safavi, Shervin, et al. “Uncovering the Organization of Neural Circuits with
Generalized Phase Locking Analysis.” PLoS Computational Biology, vol. 19,
no. 4, e1010983, Public Library of Science, 2023, doi:10.1371/journal.pcbi.1010983.
short: S. Safavi, T.I. Panagiotaropoulos, V. Kapoor, J.F. Ramirez Villegas, N.K.
Logothetis, M. Besserve, PLoS Computational Biology 19 (2023).
date_created: 2023-04-23T22:01:03Z
date_published: 2023-04-01T00:00:00Z
date_updated: 2025-04-23T08:54:49Z
day: '01'
ddc:
- '570'
department:
- _id: JoCs
doi: 10.1371/journal.pcbi.1010983
external_id:
isi:
- '000962668700002'
pmid:
- '37011110'
file:
- access_level: open_access
checksum: edeb9d09f3e41ba7c0251308b9e372e7
content_type: application/pdf
creator: dernst
date_created: 2023-04-25T08:59:18Z
date_updated: 2023-04-25T08:59:18Z
file_id: '12867'
file_name: 2023_PLoSCompBio_Safavi.pdf
file_size: 4737671
relation: main_file
success: 1
file_date_updated: 2023-04-25T08:59:18Z
has_accepted_license: '1'
intvolume: ' 19'
isi: 1
issue: '4'
language:
- iso: eng
month: '04'
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'
related_material:
link:
- relation: software
url: https://github.com/shervinsafavi/gpla.git
scopus_import: '1'
status: public
title: Uncovering the organization of neural circuits with Generalized Phase Locking
Analysis
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 19
year: '2023'
...
---
_id: '12863'
abstract:
- lang: eng
text: In the present study, essential and nonessential metal content and biomarker
responses were investigated in the intestine of fish collected from the areas
polluted by mining. Our objective was to determine metal and biomarker levels
in tissue responsible for dietary intake, which is rarely studied in water pollution
research. The study was conducted in the Bregalnica River, reference location,
and in the Zletovska and Kriva Rivers (the Republic of North Macedonia), which
are directly influenced by the active mines Zletovo and Toranica, respectively.
Biological responses were analyzed in Vardar chub (Squalius vardarensis; Karaman,
1928), using for the first time intestinal cytosol as a potentially toxic cell
fraction, since metal sensitivity is mostly associated with cytosol. Cytosolic
metal levels were higher in fish under the influence of mining (Tl, Li, Cs, Mo,
Sr, Cd, Rb, and Cu in the Zletovska River and Cr, Pb, and Se in the Kriva River
compared to the Bregalnica River in both seasons). The same trend was evident
for total proteins, biomarkers of general stress, and metallothioneins, biomarkers
of metal exposure, indicating cellular disturbances in the intestine, the primary
site of dietary metal uptake. The association of cytosolic Cu and Cd at all locations
pointed to similar pathways and homeostasis of these metallothionein-binding metals.
Comparison with other indicator tissues showed that metal concentrations were
higher in the intestine of fish from mining-affected areas than in the liver and
gills. In general, these results indicated the importance of dietary metal pathways,
and cytosolic metal fraction in assessing pollution impacts in freshwater ecosystems.
acknowledgement: 'The authors are grateful to Dr. Nevenka Mikac for the opportunity
to perform metal measurements on HR ICP-MS. This research was funded by the Ministry
of Science, Education and Sport of the Republic of Croatia (projects No. 098–0982934-2721
and 098–1782739-2749). The sampling was carried out as a part of two Croatian-Macedonian
bilateral projects: “The assessment of availability and effects of metals on fish
in the rivers under the impact of mining activities” and “Bacterial and parasitical
communities of chub as indicators of the status of environment exposed to mining
activities.”'
article_processing_charge: No
article_type: original
author:
- first_name: Vlatka
full_name: Filipović Marijić, Vlatka
last_name: Filipović Marijić
- first_name: Nesrete
full_name: Krasnici, Nesrete
id: cb5852d4-287f-11ed-baf0-bc1dd2d5c745
last_name: Krasnici
- first_name: Damir
full_name: Valić, Damir
last_name: Valić
- first_name: Damir
full_name: Kapetanović, Damir
last_name: Kapetanović
- first_name: Irena
full_name: Vardić Smrzlić, Irena
last_name: Vardić Smrzlić
- first_name: Maja
full_name: Jordanova, Maja
last_name: Jordanova
- first_name: Katerina
full_name: Rebok, Katerina
last_name: Rebok
- first_name: Sheriban
full_name: Ramani, Sheriban
last_name: Ramani
- first_name: Vasil
full_name: Kostov, Vasil
last_name: Kostov
- first_name: Rodne
full_name: Nastova, Rodne
last_name: Nastova
- first_name: Zrinka
full_name: Dragun, Zrinka
last_name: Dragun
citation:
ama: Filipović Marijić V, Krasnici N, Valić D, et al. Pollution impact on metal
and biomarker responses in intestinal cytosol of freshwater fish. Environmental
Science and Pollution Research. 2023;30:63510-63521. doi:10.1007/s11356-023-26844-2
apa: Filipović Marijić, V., Krasnici, N., Valić, D., Kapetanović, D., Vardić Smrzlić,
I., Jordanova, M., … Dragun, Z. (2023). Pollution impact on metal and biomarker
responses in intestinal cytosol of freshwater fish. Environmental Science and
Pollution Research. Springer Nature. https://doi.org/10.1007/s11356-023-26844-2
chicago: Filipović Marijić, Vlatka, Nesrete Krasnici, Damir Valić, Damir Kapetanović,
Irena Vardić Smrzlić, Maja Jordanova, Katerina Rebok, et al. “Pollution Impact
on Metal and Biomarker Responses in Intestinal Cytosol of Freshwater Fish.” Environmental
Science and Pollution Research. Springer Nature, 2023. https://doi.org/10.1007/s11356-023-26844-2.
ieee: V. Filipović Marijić et al., “Pollution impact on metal and biomarker
responses in intestinal cytosol of freshwater fish,” Environmental Science
and Pollution Research, vol. 30. Springer Nature, pp. 63510–63521, 2023.
ista: Filipović Marijić V, Krasnici N, Valić D, Kapetanović D, Vardić Smrzlić I,
Jordanova M, Rebok K, Ramani S, Kostov V, Nastova R, Dragun Z. 2023. Pollution
impact on metal and biomarker responses in intestinal cytosol of freshwater fish.
Environmental Science and Pollution Research. 30, 63510–63521.
mla: Filipović Marijić, Vlatka, et al. “Pollution Impact on Metal and Biomarker
Responses in Intestinal Cytosol of Freshwater Fish.” Environmental Science
and Pollution Research, vol. 30, Springer Nature, 2023, pp. 63510–21, doi:10.1007/s11356-023-26844-2.
short: V. Filipović Marijić, N. Krasnici, D. Valić, D. Kapetanović, I. Vardić Smrzlić,
M. Jordanova, K. Rebok, S. Ramani, V. Kostov, R. Nastova, Z. Dragun, Environmental
Science and Pollution Research 30 (2023) 63510–63521.
date_created: 2023-04-23T22:01:03Z
date_published: 2023-05-01T00:00:00Z
date_updated: 2023-10-04T11:23:10Z
day: '01'
department:
- _id: LifeSc
doi: 10.1007/s11356-023-26844-2
external_id:
isi:
- '000970917900012'
pmid:
- '37055686'
intvolume: ' 30'
isi: 1
language:
- iso: eng
month: '05'
oa_version: None
page: 63510-63521
pmid: 1
publication: Environmental Science and Pollution Research
publication_identifier:
eissn:
- 1614-7499
issn:
- 0944-1344
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
scopus_import: '1'
status: public
title: Pollution impact on metal and biomarker responses in intestinal cytosol of
freshwater fish
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 30
year: '2023'
...
---
_id: '12866'
abstract:
- lang: eng
text: "Autism spectrum disorder (ASD) and epilepsy are frequently comorbid neurodevelopmental
disorders. Extensive research has demonstrated shared pathological pathways, etiologies,
and phenotypes. Many risk factors for these disorders, like genetic mutations
and environmental pressures, are linked to changes in childhood brain development,
which is a critical period for their manifestation.\r\nDecades of research have
yielded many signatures for ASD and epilepsy, some shared and others unique or
opposing. The anatomical, physiological, and behavioral correlates of these disorders
are discussed in this chapter in the context of understanding shared pathological
pathways. We end with important takeaways on the presentation, prevention, intervention,
and policy changes for ASD and epilepsy. This chapter aims to explore the complexity
of these disorders, both in etiology and phenotypes, with the further goal of
appreciating the expanse of unknowns still to explore about the brain."
alternative_title:
- 'Vol. 1: Biological Development and Physical Health'
article_processing_charge: No
author:
- first_name: Christopher
full_name: Currin, Christopher
id: e8321fc5-3091-11eb-8a53-83f309a11ac9
last_name: Currin
orcid: 0000-0002-4809-5059
- first_name: Chad
full_name: Beyer, Chad
last_name: Beyer
citation:
ama: 'Currin C, Beyer C. Altered childhood brain development in autism and epilepsy.
In: Halpern-Felsher B, ed. Encyclopedia of Child and Adolescent Health.
1st ed. Elsevier; 2023:86-98. doi:10.1016/b978-0-12-818872-9.00129-1'
apa: Currin, C., & Beyer, C. (2023). Altered childhood brain development in
autism and epilepsy. In B. Halpern-Felsher (Ed.), Encyclopedia of Child and
Adolescent Health (1st ed., pp. 86–98). Elsevier. https://doi.org/10.1016/b978-0-12-818872-9.00129-1
chicago: Currin, Christopher, and Chad Beyer. “Altered Childhood Brain Development
in Autism and Epilepsy.” In Encyclopedia of Child and Adolescent Health,
edited by Bonnie Halpern-Felsher, 1st ed., 86–98. Elsevier, 2023. https://doi.org/10.1016/b978-0-12-818872-9.00129-1.
ieee: C. Currin and C. Beyer, “Altered childhood brain development in autism and
epilepsy,” in Encyclopedia of Child and Adolescent Health, 1st ed., B.
Halpern-Felsher, Ed. Elsevier, 2023, pp. 86–98.
ista: 'Currin C, Beyer C. 2023.Altered childhood brain development in autism and
epilepsy. In: Encyclopedia of Child and Adolescent Health. Vol. 1: Biological
Development and Physical Health, , 86–98.'
mla: Currin, Christopher, and Chad Beyer. “Altered Childhood Brain Development in
Autism and Epilepsy.” Encyclopedia of Child and Adolescent Health, edited
by Bonnie Halpern-Felsher, 1st ed., Elsevier, 2023, pp. 86–98, doi:10.1016/b978-0-12-818872-9.00129-1.
short: C. Currin, C. Beyer, in:, B. Halpern-Felsher (Ed.), Encyclopedia of Child
and Adolescent Health, 1st ed., Elsevier, 2023, pp. 86–98.
corr_author: '1'
date_created: 2023-04-25T07:52:43Z
date_published: 2023-02-01T00:00:00Z
date_updated: 2024-10-21T06:01:23Z
day: '01'
department:
- _id: TiVo
doi: 10.1016/b978-0-12-818872-9.00129-1
edition: '1'
editor:
- first_name: Bonnie
full_name: Halpern-Felsher, Bonnie
last_name: Halpern-Felsher
language:
- iso: eng
month: '02'
oa_version: None
page: 86-98
publication: Encyclopedia of Child and Adolescent Health
publication_identifier:
isbn:
- '9780128188736'
publication_status: published
publisher: Elsevier
quality_controlled: '1'
scopus_import: '1'
status: public
title: Altered childhood brain development in autism and epilepsy
type: book_chapter
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
year: '2023'
...
---
_id: '12869'
abstract:
- lang: eng
text: 'We introduce a stochastic cellular automaton as a model for culture and border
formation. The model can be conceptualized as a game where the expansion rate
of cultures is quantified in terms of their area and perimeter in such a way that
approximately round cultures get a competitive advantage. We first analyse the
model with periodic boundary conditions, where we study how the model can end
up in a fixed state, i.e. freezes. Then we implement the model on the European
geography with mountains and rivers. We see how the model reproduces some qualitative
features of European culture formation, namely that rivers and mountains are more
frequently borders between cultures, mountainous regions tend to have higher cultural
diversity and the central European plain has less clear cultural borders. '
acknowledgement: 'FRK acknowledges support from the Villum Foundation for support
through the QMATH center of Excellence (Grant No. 10059) and the Villum Young Investigator
(Grant No. 25452) programs. '
article_processing_charge: No
author:
- first_name: Frederik Ravn
full_name: Klausen, Frederik Ravn
last_name: Klausen
- first_name: Asbjørn Bækgaard
full_name: Lauritsen, Asbjørn Bækgaard
id: e1a2682f-dc8d-11ea-abe3-81da9ac728f1
last_name: Lauritsen
orcid: 0000-0003-4476-2288
citation:
ama: 'Klausen FR, Lauritsen AB. Research data for: A stochastic cellular automaton
model of culture formation. 2023. doi:10.15479/AT:ISTA:12869'
apa: 'Klausen, F. R., & Lauritsen, A. B. (2023). Research data for: A stochastic
cellular automaton model of culture formation. Institute of Science and Technology
Austria. https://doi.org/10.15479/AT:ISTA:12869'
chicago: 'Klausen, Frederik Ravn, and Asbjørn Bækgaard Lauritsen. “Research Data
for: A Stochastic Cellular Automaton Model of Culture Formation.” Institute of
Science and Technology Austria, 2023. https://doi.org/10.15479/AT:ISTA:12869.'
ieee: 'F. R. Klausen and A. B. Lauritsen, “Research data for: A stochastic cellular
automaton model of culture formation.” Institute of Science and Technology Austria,
2023.'
ista: 'Klausen FR, Lauritsen AB. 2023. Research data for: A stochastic cellular
automaton model of culture formation, Institute of Science and Technology Austria,
10.15479/AT:ISTA:12869.'
mla: 'Klausen, Frederik Ravn, and Asbjørn Bækgaard Lauritsen. Research Data for:
A Stochastic Cellular Automaton Model of Culture Formation. Institute of Science
and Technology Austria, 2023, doi:10.15479/AT:ISTA:12869.'
short: F.R. Klausen, A.B. Lauritsen, (2023).
corr_author: '1'
date_created: 2023-04-26T12:34:49Z
date_published: 2023-04-26T00:00:00Z
date_updated: 2025-09-09T12:26:01Z
day: '26'
ddc:
- '000'
department:
- _id: GradSch
- _id: RoSe
doi: 10.15479/AT:ISTA:12869
file:
- access_level: open_access
checksum: 85ede12d38bb8d944022a8cba4d719f5
content_type: application/octet-stream
creator: alaurits
date_created: 2023-04-26T12:30:06Z
date_updated: 2023-04-26T12:30:06Z
file_id: '12870'
file_name: README.md
file_size: 4567
relation: main_file
success: 1
- access_level: open_access
checksum: 25bf79452ae895f9c8a20571a096b4c3
content_type: application/x-zip-compressed
creator: alaurits
date_created: 2023-04-26T12:27:34Z
date_updated: 2023-04-26T12:27:34Z
file_id: '12871'
file_name: simulations_era=10_flux_varied_europe.zip
file_size: 732586731
relation: main_file
success: 1
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checksum: bca48d80ece73eb169aee7211a4a751a
content_type: application/x-zip-compressed
creator: alaurits
date_created: 2023-04-26T12:29:53Z
date_updated: 2023-04-26T12:29:53Z
file_id: '12872'
file_name: simulations_era=10_flux_varied_torus.zip
file_size: 1743893150
relation: main_file
success: 1
- access_level: open_access
checksum: e77a655db15486a387a36362fbf0b665
content_type: application/x-zip-compressed
creator: alaurits
date_created: 2023-04-26T12:29:19Z
date_updated: 2023-04-26T12:29:19Z
file_id: '12873'
file_name: simulations_era=10_R_varied_torus.zip
file_size: 878391851
relation: main_file
success: 1
- access_level: open_access
checksum: 8556406513adc4aa2e0417f46680f627
content_type: application/x-zip-compressed
creator: alaurits
date_created: 2023-04-26T12:30:05Z
date_updated: 2023-04-26T12:30:05Z
file_id: '12874'
file_name: simulations_era=100.zip
file_size: 201652478
relation: main_file
success: 1
file_date_updated: 2023-04-26T12:30:06Z
has_accepted_license: '1'
license: https://creativecommons.org/publicdomain/zero/1.0/
month: '04'
oa: 1
oa_version: Published Version
publisher: Institute of Science and Technology Austria
related_material:
record:
- id: '14505'
relation: used_in_publication
status: deleted
- id: '12890'
relation: used_in_publication
status: public
status: public
title: 'Research data for: A stochastic cellular automaton model of culture formation'
tmp:
image: /images/cc_0.png
legal_code_url: https://creativecommons.org/publicdomain/zero/1.0/legalcode
name: Creative Commons Public Domain Dedication (CC0 1.0)
short: CC0 (1.0)
type: research_data
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
year: '2023'
...
---
_id: '12876'
abstract:
- lang: eng
text: "Motivation: The problem of model inference is of fundamental importance to
systems biology. Logical models (e.g. Boolean networks; BNs) represent a computationally
attractive approach capable of handling large biological networks. The models
are typically inferred from experimental data. However, even with a substantial
amount of experimental data supported by some prior knowledge, existing inference
methods often focus on a small sample of admissible candidate models only.\r\n\r\nResults:
We propose Boolean network sketches as a new formal instrument for the inference
of Boolean networks. A sketch integrates (typically partial) knowledge about the
network’s topology and the update logic (obtained through, e.g. a biological knowledge
base or a literature search), as well as further assumptions about the properties
of the network’s transitions (e.g. the form of its attractor landscape), and additional
restrictions on the model dynamics given by the measured experimental data. Our
new BNs inference algorithm starts with an ‘initial’ sketch, which is extended
by adding restrictions representing experimental data to a ‘data-informed’ sketch
and subsequently computes all BNs consistent with the data-informed sketch. Our
algorithm is based on a symbolic representation and coloured model-checking. Our
approach is unique in its ability to cover a broad spectrum of knowledge and efficiently
produce a compact representation of all inferred BNs. We evaluate the method on
a non-trivial collection of real-world and simulated data."
acknowledgement: This work was partially supported by GACR [grant No. GA22-10845S];
and Grant Agency of Masaryk University [grant No. MUNI/G/1771/2020]. This work was
partially supported by European Union’s Horizon 2020 research and innovation programme
under the Marie Skłodowska-Curie [Grant Agreement No. 101034413 to S.P.].
article_number: btad158
article_processing_charge: No
article_type: original
author:
- first_name: Nikola
full_name: Beneš, Nikola
last_name: Beneš
- first_name: Luboš
full_name: Brim, Luboš
last_name: Brim
- first_name: Ondřej
full_name: Huvar, Ondřej
last_name: Huvar
- first_name: Samuel
full_name: Pastva, Samuel
id: 07c5ea74-f61c-11ec-a664-aa7c5d957b2b
last_name: Pastva
orcid: 0000-0003-1993-0331
- first_name: David
full_name: Šafránek, David
last_name: Šafránek
citation:
ama: 'Beneš N, Brim L, Huvar O, Pastva S, Šafránek D. Boolean network sketches:
A unifying framework for logical model inference. Bioinformatics. 2023;39(4).
doi:10.1093/bioinformatics/btad158'
apa: 'Beneš, N., Brim, L., Huvar, O., Pastva, S., & Šafránek, D. (2023). Boolean
network sketches: A unifying framework for logical model inference. Bioinformatics.
Oxford University Press. https://doi.org/10.1093/bioinformatics/btad158'
chicago: 'Beneš, Nikola, Luboš Brim, Ondřej Huvar, Samuel Pastva, and David Šafránek.
“Boolean Network Sketches: A Unifying Framework for Logical Model Inference.”
Bioinformatics. Oxford University Press, 2023. https://doi.org/10.1093/bioinformatics/btad158.'
ieee: 'N. Beneš, L. Brim, O. Huvar, S. Pastva, and D. Šafránek, “Boolean network
sketches: A unifying framework for logical model inference,” Bioinformatics,
vol. 39, no. 4. Oxford University Press, 2023.'
ista: 'Beneš N, Brim L, Huvar O, Pastva S, Šafránek D. 2023. Boolean network sketches:
A unifying framework for logical model inference. Bioinformatics. 39(4), btad158.'
mla: 'Beneš, Nikola, et al. “Boolean Network Sketches: A Unifying Framework for
Logical Model Inference.” Bioinformatics, vol. 39, no. 4, btad158, Oxford
University Press, 2023, doi:10.1093/bioinformatics/btad158.'
short: N. Beneš, L. Brim, O. Huvar, S. Pastva, D. Šafránek, Bioinformatics 39 (2023).
date_created: 2023-04-30T22:01:05Z
date_published: 2023-04-03T00:00:00Z
date_updated: 2025-05-14T11:06:50Z
day: '03'
ddc:
- '000'
department:
- _id: ToHe
doi: 10.1093/bioinformatics/btad158
ec_funded: 1
external_id:
isi:
- '000976610800001'
pmid:
- '37004199'
file:
- access_level: open_access
checksum: 2cb90ddf781baefddf47eac4b54e2a03
content_type: application/pdf
creator: dernst
date_created: 2023-05-02T07:39:04Z
date_updated: 2023-05-02T07:39:04Z
file_id: '12886'
file_name: 2023_Bioinformatics_Benes.pdf
file_size: 478740
relation: main_file
success: 1
file_date_updated: 2023-05-02T07:39:04Z
has_accepted_license: '1'
intvolume: ' 39'
isi: 1
issue: '4'
language:
- iso: eng
month: '04'
oa: 1
oa_version: Published Version
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
publication_status: published
publisher: Oxford University Press
quality_controlled: '1'
related_material:
link:
- relation: software
url: https://doi.org/10.5281/zenodo.7688740
scopus_import: '1'
status: public
title: 'Boolean network sketches: A unifying framework for logical model inference'
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: '12877'
abstract:
- lang: eng
text: We consider billiards obtained by removing from the plane finitely many strictly
convex analytic obstacles satisfying the non-eclipse condition. The restriction
of the dynamics to the set of non-escaping orbits is conjugated to a subshift,
which provides a natural labeling of periodic orbits. We show that under suitable
symmetry and genericity assumptions, the Marked Length Spectrum determines the
geometry of the billiard table.
acknowledgement: 'J.D.S. and M.L. have been partially supported by the NSERC Discovery
grant, reference number 502617-2017. M.L. was also supported by the ERC project
692925 NUHGD of Sylvain Crovisier, by the ANR AAPG 2021 PRC CoSyDy: Conformally
symplectic dynamics, beyond symplectic dynamics (ANR-CE40-0014), and by the ANR
JCJC PADAWAN: Parabolic dynamics, bifurcations and wandering domains (ANR-21-CE40-0012).
V.K. acknowledges partial support of the NSF grant DMS-1402164 and ERC Grant # 885707.'
article_processing_charge: No
article_type: original
arxiv: 1
author:
- first_name: Jacopo
full_name: De Simoi, Jacopo
last_name: De Simoi
- first_name: Vadim
full_name: Kaloshin, Vadim
id: FE553552-CDE8-11E9-B324-C0EBE5697425
last_name: Kaloshin
orcid: 0000-0002-6051-2628
- first_name: Martin
full_name: Leguil, Martin
last_name: Leguil
citation:
ama: De Simoi J, Kaloshin V, Leguil M. Marked Length Spectral determination of analytic
chaotic billiards with axial symmetries. Inventiones Mathematicae. 2023;233:829-901.
doi:10.1007/s00222-023-01191-8
apa: De Simoi, J., Kaloshin, V., & Leguil, M. (2023). Marked Length Spectral
determination of analytic chaotic billiards with axial symmetries. Inventiones
Mathematicae. Springer Nature. https://doi.org/10.1007/s00222-023-01191-8
chicago: De Simoi, Jacopo, Vadim Kaloshin, and Martin Leguil. “Marked Length Spectral
Determination of Analytic Chaotic Billiards with Axial Symmetries.” Inventiones
Mathematicae. Springer Nature, 2023. https://doi.org/10.1007/s00222-023-01191-8.
ieee: J. De Simoi, V. Kaloshin, and M. Leguil, “Marked Length Spectral determination
of analytic chaotic billiards with axial symmetries,” Inventiones Mathematicae,
vol. 233. Springer Nature, pp. 829–901, 2023.
ista: De Simoi J, Kaloshin V, Leguil M. 2023. Marked Length Spectral determination
of analytic chaotic billiards with axial symmetries. Inventiones Mathematicae.
233, 829–901.
mla: De Simoi, Jacopo, et al. “Marked Length Spectral Determination of Analytic
Chaotic Billiards with Axial Symmetries.” Inventiones Mathematicae, vol.
233, Springer Nature, 2023, pp. 829–901, doi:10.1007/s00222-023-01191-8.
short: J. De Simoi, V. Kaloshin, M. Leguil, Inventiones Mathematicae 233 (2023)
829–901.
date_created: 2023-04-30T22:01:05Z
date_published: 2023-08-01T00:00:00Z
date_updated: 2025-04-14T07:53:46Z
day: '01'
department:
- _id: VaKa
doi: 10.1007/s00222-023-01191-8
ec_funded: 1
external_id:
arxiv:
- '1905.00890'
isi:
- '000978887600001'
intvolume: ' 233'
isi: 1
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.48550/arXiv.1905.00890
month: '08'
oa: 1
oa_version: Preprint
page: 829-901
project:
- _id: 9B8B92DE-BA93-11EA-9121-9846C619BF3A
call_identifier: H2020
grant_number: '885707'
name: Spectral rigidity and integrability for billiards and geodesic flows
publication: Inventiones Mathematicae
publication_identifier:
eissn:
- 1432-1297
issn:
- 0020-9910
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
scopus_import: '1'
status: public
title: Marked Length Spectral determination of analytic chaotic billiards with axial
symmetries
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 233
year: '2023'
...
---
OA_place: publisher
OA_type: free access
_id: '12878'
abstract:
- lang: eng
text: Salicylic acid (SA) plays important roles in different aspects of plant development,
including root growth, where auxin is also a major player by means of its asymmetric
distribution. However, the mechanism underlying the effect of SA on the development
of rice roots remains poorly understood. Here, we show that SA inhibits rice root
growth by interfering with auxin transport associated with the OsPIN3t- and clathrin-mediated
gene regulatory network (GRN). SA inhibits root growth as well as Brefeldin A-sensitive
trafficking through a non-canonical SA signaling mechanism. Transcriptome analysis
of rice seedlings treated with SA revealed that the OsPIN3t auxin transporter
is at the center of a GRN involving the coat protein clathrin. The root growth
and endocytic trafficking in both the pin3t and clathrin heavy chain mutants were
SA insensitivity. SA inhibitory effect on the endocytosis of OsPIN3t was dependent
on clathrin; however, the root growth and endocytic trafficking mediated by tyrphostin
A23 (TyrA23) were independent of the pin3t mutant under SA treatment. These data
reveal that SA affects rice root growth through the convergence of transcriptional
and non-SA signaling mechanisms involving OsPIN3t-mediated auxin transport and
clathrin-mediated trafficking as key components.
acknowledgement: The authors thank Professor Jianqiang Wu (Kunming Institute of Botany,
Chinese Academy of Sciences) for support with phytohormone measurement. Thanks also
go to Professor Pieter. B. F. Ouwerkerk (Leiden University) and Professor Jean-Benoit
Morel (Plant Health Institute of Montpellier) for provision of the rice lines NB-7B-70
and NB-7B-76 and wild-type NB-61-WT, Professor Zuhua He (Chinese Academy of Sciences)
for provision of the rice OsNPR1-RNAi mutant, and Professor Yinong Yang (The Pennsylvania
State University) for provision of the rice line NahG. This work was supported by
grants from the National Natural Science Foundation of China (Grant Nos. 32260085,
31460453, 31660501, 31860064, 31970609, 31801792 and 31960554), the Key Projects
of the Applied Basic Research Plan of Yunnan Province (202301AS070082), the Major
Special Program for Scientific Research, Education Department of Yunnan Province
(Grant No. ZD2015005), the Start-up fund from Xishuangbanna Tropical Botanical Garden,
and ‘Top Talents Program in Science and Technology’ from Yunnan Province, the SRF
for ROCS, SEM (Grant No. [2013] 1792), and the Major Science and Technology Project
in Yunnan Province (202102AE090042 and 202202AE090036); and the young and middle-aged
academic and technical leaders reserve talent program in Yunnan Province (202205AC160076).
article_processing_charge: No
article_type: original
author:
- first_name: Lihui
full_name: Jiang, Lihui
last_name: Jiang
- first_name: Baolin
full_name: Yao, Baolin
last_name: Yao
- first_name: Xiaoyan
full_name: Zhang, Xiaoyan
last_name: Zhang
- first_name: Lixia
full_name: Wu, Lixia
last_name: Wu
- first_name: Qijing
full_name: Fu, Qijing
last_name: Fu
- first_name: Yiting
full_name: Zhao, Yiting
last_name: Zhao
- first_name: Yuxin
full_name: Cao, Yuxin
last_name: Cao
- first_name: Ruomeng
full_name: Zhu, Ruomeng
last_name: Zhu
- first_name: Xinqi
full_name: Lu, Xinqi
last_name: Lu
- first_name: Wuying
full_name: Huang, Wuying
last_name: Huang
- first_name: Jianping
full_name: Zhao, Jianping
last_name: Zhao
- first_name: Kuixiu
full_name: Li, Kuixiu
last_name: Li
- first_name: Shuanglu
full_name: Zhao, Shuanglu
last_name: Zhao
- first_name: Li
full_name: Han, Li
last_name: Han
- first_name: Xuan
full_name: Zhou, Xuan
last_name: Zhou
- first_name: Chongyu
full_name: Luo, Chongyu
last_name: Luo
- first_name: Haiyan
full_name: Zhu, Haiyan
last_name: Zhu
- first_name: Jing
full_name: Yang, Jing
last_name: Yang
- first_name: Huichuan
full_name: Huang, Huichuan
last_name: Huang
- first_name: Zhengge
full_name: Zhu, Zhengge
last_name: Zhu
- first_name: Xiahong
full_name: He, Xiahong
last_name: He
- first_name: Jiří
full_name: Friml, Jiří
id: 4159519E-F248-11E8-B48F-1D18A9856A87
last_name: Friml
orcid: 0000-0002-8302-7596
- first_name: Zhongkai
full_name: Zhang, Zhongkai
last_name: Zhang
- first_name: Changning
full_name: Liu, Changning
last_name: Liu
- first_name: Yunlong
full_name: Du, Yunlong
last_name: Du
citation:
ama: Jiang L, Yao B, Zhang X, et al. Salicylic acid inhibits rice endocytic protein
trafficking mediated by OsPIN3t and clathrin to affect root growth. Plant Journal.
2023;115(1):155-174. doi:10.1111/tpj.16218
apa: Jiang, L., Yao, B., Zhang, X., Wu, L., Fu, Q., Zhao, Y., … Du, Y. (2023). Salicylic
acid inhibits rice endocytic protein trafficking mediated by OsPIN3t and clathrin
to affect root growth. Plant Journal. Wiley. https://doi.org/10.1111/tpj.16218
chicago: Jiang, Lihui, Baolin Yao, Xiaoyan Zhang, Lixia Wu, Qijing Fu, Yiting Zhao,
Yuxin Cao, et al. “Salicylic Acid Inhibits Rice Endocytic Protein Trafficking
Mediated by OsPIN3t and Clathrin to Affect Root Growth.” Plant Journal.
Wiley, 2023. https://doi.org/10.1111/tpj.16218.
ieee: L. Jiang et al., “Salicylic acid inhibits rice endocytic protein trafficking
mediated by OsPIN3t and clathrin to affect root growth,” Plant Journal,
vol. 115, no. 1. Wiley, pp. 155–174, 2023.
ista: Jiang L, Yao B, Zhang X, Wu L, Fu Q, Zhao Y, Cao Y, Zhu R, Lu X, Huang W,
Zhao J, Li K, Zhao S, Han L, Zhou X, Luo C, Zhu H, Yang J, Huang H, Zhu Z, He
X, Friml J, Zhang Z, Liu C, Du Y. 2023. Salicylic acid inhibits rice endocytic
protein trafficking mediated by OsPIN3t and clathrin to affect root growth. Plant
Journal. 115(1), 155–174.
mla: Jiang, Lihui, et al. “Salicylic Acid Inhibits Rice Endocytic Protein Trafficking
Mediated by OsPIN3t and Clathrin to Affect Root Growth.” Plant Journal,
vol. 115, no. 1, Wiley, 2023, pp. 155–74, doi:10.1111/tpj.16218.
short: L. Jiang, B. Yao, X. Zhang, L. Wu, Q. Fu, Y. Zhao, Y. Cao, R. Zhu, X. Lu,
W. Huang, J. Zhao, K. Li, S. Zhao, L. Han, X. Zhou, C. Luo, H. Zhu, J. Yang, H.
Huang, Z. Zhu, X. He, J. Friml, Z. Zhang, C. Liu, Y. Du, Plant Journal 115 (2023)
155–174.
date_created: 2023-04-30T22:01:06Z
date_published: 2023-07-01T00:00:00Z
date_updated: 2025-06-25T08:50:43Z
day: '01'
department:
- _id: JiFr
doi: 10.1111/tpj.16218
external_id:
isi:
- '000971861400001'
pmid:
- '37025008 '
intvolume: ' 115'
isi: 1
issue: '1'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.1111/tpj.16218
month: '07'
oa: 1
oa_version: Published Version
page: 155-174
pmid: 1
publication: Plant Journal
publication_identifier:
eissn:
- 1365-313X
issn:
- 0960-7412
publication_status: published
publisher: Wiley
quality_controlled: '1'
scopus_import: '1'
status: public
title: Salicylic acid inhibits rice endocytic protein trafficking mediated by OsPIN3t
and clathrin to affect root growth
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 115
year: '2023'
...
---
_id: '12879'
abstract:
- lang: eng
text: Machine learning (ML) has been widely applied to chemical property prediction,
most prominently for the energies and forces in molecules and materials. The strong
interest in predicting energies in particular has led to a ‘local energy’-based
paradigm for modern atomistic ML models, which ensures size-extensivity and a
linear scaling of computational cost with system size. However, many electronic
properties (such as excitation energies or ionization energies) do not necessarily
scale linearly with system size and may even be spatially localized. Using size-extensive
models in these cases can lead to large errors. In this work, we explore different
strategies for learning intensive and localized properties, using HOMO energies
in organic molecules as a representative test case. In particular, we analyze
the pooling functions that atomistic neural networks use to predict molecular
properties, and suggest an orbital weighted average (OWA) approach that enables
the accurate prediction of orbital energies and locations.
acknowledgement: KC acknowledges funding from the China Scholarship Council. KC is
grateful for the TUM graduate school finance support to visit Bingqing Cheng's group
in IST for two months. We also thankfully acknowledge computational resources provided
by the MPCDF Supercomputing Centre.
article_processing_charge: No
article_type: original
author:
- first_name: Ke
full_name: Chen, Ke
id: c636c5ca-e8b8-11ed-b2d4-cc2c37613a8d
last_name: Chen
- first_name: Christian
full_name: Kunkel, Christian
last_name: Kunkel
- first_name: Bingqing
full_name: Cheng, Bingqing
id: cbe3cda4-d82c-11eb-8dc7-8ff94289fcc9
last_name: Cheng
orcid: 0000-0002-3584-9632
- first_name: Karsten
full_name: Reuter, Karsten
last_name: Reuter
- first_name: Johannes T.
full_name: Margraf, Johannes T.
last_name: Margraf
citation:
ama: Chen K, Kunkel C, Cheng B, Reuter K, Margraf JT. Physics-inspired machine learning
of localized intensive properties. Chemical Science. 2023. doi:10.1039/d3sc00841j
apa: Chen, K., Kunkel, C., Cheng, B., Reuter, K., & Margraf, J. T. (2023). Physics-inspired
machine learning of localized intensive properties. Chemical Science. Royal
Society of Chemistry. https://doi.org/10.1039/d3sc00841j
chicago: Chen, Ke, Christian Kunkel, Bingqing Cheng, Karsten Reuter, and Johannes
T. Margraf. “Physics-Inspired Machine Learning of Localized Intensive Properties.”
Chemical Science. Royal Society of Chemistry, 2023. https://doi.org/10.1039/d3sc00841j.
ieee: K. Chen, C. Kunkel, B. Cheng, K. Reuter, and J. T. Margraf, “Physics-inspired
machine learning of localized intensive properties,” Chemical Science.
Royal Society of Chemistry, 2023.
ista: Chen K, Kunkel C, Cheng B, Reuter K, Margraf JT. 2023. Physics-inspired machine
learning of localized intensive properties. Chemical Science.
mla: Chen, Ke, et al. “Physics-Inspired Machine Learning of Localized Intensive
Properties.” Chemical Science, Royal Society of Chemistry, 2023, doi:10.1039/d3sc00841j.
short: K. Chen, C. Kunkel, B. Cheng, K. Reuter, J.T. Margraf, Chemical Science (2023).
date_created: 2023-04-30T22:01:06Z
date_published: 2023-04-10T00:00:00Z
date_updated: 2023-08-01T14:18:10Z
day: '10'
ddc:
- '000'
- '540'
department:
- _id: BiCh
doi: 10.1039/d3sc00841j
external_id:
isi:
- '000971508100001'
file:
- access_level: open_access
checksum: 5eeec69a51e192dcd94b955d84423836
content_type: application/pdf
creator: dernst
date_created: 2023-05-02T07:17:05Z
date_updated: 2023-05-02T07:17:05Z
file_id: '12883'
file_name: 2023_ChemialScience_Chen.pdf
file_size: 1515446
relation: main_file
success: 1
file_date_updated: 2023-05-02T07:17:05Z
has_accepted_license: '1'
isi: 1
language:
- iso: eng
license: https://creativecommons.org/licenses/by/3.0/
month: '04'
oa: 1
oa_version: Published Version
publication: Chemical Science
publication_identifier:
eissn:
- 2041-6539
issn:
- 2041-6520
publication_status: published
publisher: Royal Society of Chemistry
quality_controlled: '1'
scopus_import: '1'
status: public
title: Physics-inspired machine learning of localized intensive properties
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/3.0/legalcode
name: Creative Commons Attribution 3.0 Unported (CC BY 3.0)
short: CC BY (3.0)
type: journal_article
user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
year: '2023'
...
---
_id: '12880'
abstract:
- lang: eng
text: Peripheral heterochromatin positioning depends on nuclear envelope associated
proteins and repressive histone modifications. Here we show that overexpression
(OE) of Lamin B1 (LmnB1) leads to the redistribution of peripheral heterochromatin
into heterochromatic foci within the nucleoplasm. These changes represent a perturbation
of heterochromatin binding at the nuclear periphery (NP) through a mechanism independent
from altering other heterochromatin anchors or histone post-translational modifications.
We further show that LmnB1 OE alters gene expression. These changes do not correlate
with different levels of H3K9me3, but a significant number of the misregulated
genes were likely mislocalized away from the NP upon LmnB1 OE. We also observed
an enrichment of developmental processes amongst the upregulated genes. ~74% of
these genes were normally repressed in our cell type, suggesting that LmnB1 OE
promotes gene de-repression. This demonstrates a broader consequence of LmnB1
OE on cell fate, and highlights the importance of maintaining proper levels of
LmnB1.
acknowledgement: 'We thank members of the Hetzer lab for critical review of the manuscript;
Novogene for mRNA library preparation and sequencing; the Next-Generation Sequencing
Core Facility at the Salk Institute, with funding from NIH-NCI CCSG: P30 014195,
the Chapman Foundation, and the Helmsley Charitable Trust, for sequencing Cut&Run
libraries; and the Waitt Advanced Biophotonics Core Facility at the Salk Institute,
with funding from NIH-NCI CCSG: P30 014195, the Waitt Foundation, and the Chan-Zuckerberg
Initiative Imaging Scientist Award, for electron microscopy sample preparation and
imaging.'
article_number: '2202548'
article_processing_charge: No
article_type: original
author:
- first_name: Jeanae M.
full_name: Kaneshiro, Jeanae M.
last_name: Kaneshiro
- first_name: Juliana S.
full_name: Capitanio, Juliana S.
last_name: Capitanio
- first_name: Martin W
full_name: Hetzer, Martin W
id: 86c0d31b-b4eb-11ec-ac5a-eae7b2e135ed
last_name: Hetzer
orcid: 0000-0002-2111-992X
citation:
ama: Kaneshiro JM, Capitanio JS, Hetzer M. Lamin B1 overexpression alters chromatin
organization and gene expression. Nucleus. 2023;14(1). doi:10.1080/19491034.2023.2202548
apa: Kaneshiro, J. M., Capitanio, J. S., & Hetzer, M. (2023). Lamin B1 overexpression
alters chromatin organization and gene expression. Nucleus. Taylor &
Francis. https://doi.org/10.1080/19491034.2023.2202548
chicago: Kaneshiro, Jeanae M., Juliana S. Capitanio, and Martin Hetzer. “Lamin B1
Overexpression Alters Chromatin Organization and Gene Expression.” Nucleus.
Taylor & Francis, 2023. https://doi.org/10.1080/19491034.2023.2202548.
ieee: J. M. Kaneshiro, J. S. Capitanio, and M. Hetzer, “Lamin B1 overexpression
alters chromatin organization and gene expression,” Nucleus, vol. 14, no.
1. Taylor & Francis, 2023.
ista: Kaneshiro JM, Capitanio JS, Hetzer M. 2023. Lamin B1 overexpression alters
chromatin organization and gene expression. Nucleus. 14(1), 2202548.
mla: Kaneshiro, Jeanae M., et al. “Lamin B1 Overexpression Alters Chromatin Organization
and Gene Expression.” Nucleus, vol. 14, no. 1, 2202548, Taylor & Francis,
2023, doi:10.1080/19491034.2023.2202548.
short: J.M. Kaneshiro, J.S. Capitanio, M. Hetzer, Nucleus 14 (2023).
corr_author: '1'
date_created: 2023-04-30T22:01:06Z
date_published: 2023-04-18T00:00:00Z
date_updated: 2024-10-09T21:05:01Z
day: '18'
ddc:
- '570'
department:
- _id: MaHe
doi: 10.1080/19491034.2023.2202548
external_id:
isi:
- '000971629400001'
pmid:
- '37071033'
file:
- access_level: open_access
checksum: 8e707eda84f64dbad7f03545ae0a83ef
content_type: application/pdf
creator: dernst
date_created: 2023-05-02T07:24:55Z
date_updated: 2023-05-02T07:24:55Z
file_id: '12884'
file_name: 2023_Nucleus_Kaneshiro.pdf
file_size: 3811113
relation: main_file
success: 1
file_date_updated: 2023-05-02T07:24:55Z
has_accepted_license: '1'
intvolume: ' 14'
isi: 1
issue: '1'
language:
- iso: eng
license: https://creativecommons.org/licenses/by-nc/4.0/
month: '04'
oa: 1
oa_version: Published Version
pmid: 1
publication: Nucleus
publication_identifier:
eissn:
- 1949-1042
issn:
- 1949-1034
publication_status: published
publisher: Taylor & Francis
quality_controlled: '1'
scopus_import: '1'
status: public
title: Lamin B1 overexpression alters chromatin organization and gene expression
tmp:
image: /images/cc_by_nc.png
legal_code_url: https://creativecommons.org/licenses/by-nc/4.0/legalcode
name: Creative Commons Attribution-NonCommercial 4.0 International (CC BY-NC 4.0)
short: CC BY-NC (4.0)
type: journal_article
user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
volume: 14
year: '2023'
...
---
_id: '12890'
abstract:
- lang: eng
text: We introduce a stochastic cellular automaton as a model for culture and border
formation. The model can be conceptualized as a game where the expansion rate
of cultures is quantified in terms of their area and perimeter in such a way that
approximately geometrically round cultures get a competitive advantage. We first
analyze the model with periodic boundary conditions, where we study how the model
can end up in a fixed state, i.e., freezes. Then we implement the model on the
European geography with mountains and rivers. We see how the model reproduces
some qualitative features of European culture formation, namely, that rivers and
mountains are more frequently borders between cultures, mountainous regions tend
to have higher cultural diversity, and the central European plain has less clear
cultural borders.
acknowledgement: Thanks to Kim Sneppen, Svend Krøjer, Peter Wildemann, Peter Rasmussen
and Kent Bækgaard Lauritsen for discussions and suggestions. FRK acknowledges support
from the Villum Foundation for support through the QMATH center of Excellence (Grant
No. 10059) and the Villum Young Investigator (Grant No. 25452) programs.
article_number: '054307'
article_processing_charge: No
article_type: original
arxiv: 1
author:
- first_name: Frederik Ravn
full_name: Klausen, Frederik Ravn
last_name: Klausen
- first_name: Asbjørn Bækgaard
full_name: Lauritsen, Asbjørn Bækgaard
id: e1a2682f-dc8d-11ea-abe3-81da9ac728f1
last_name: Lauritsen
orcid: 0000-0003-4476-2288
citation:
ama: Klausen FR, Lauritsen AB. Stochastic cellular automaton model of culture formation.
Physical Review E. 2023;108(5). doi:10.1103/PhysRevE.108.054307
apa: Klausen, F. R., & Lauritsen, A. B. (2023). Stochastic cellular automaton
model of culture formation. Physical Review E. American Physical Society.
https://doi.org/10.1103/PhysRevE.108.054307
chicago: Klausen, Frederik Ravn, and Asbjørn Bækgaard Lauritsen. “Stochastic Cellular
Automaton Model of Culture Formation.” Physical Review E. American Physical
Society, 2023. https://doi.org/10.1103/PhysRevE.108.054307.
ieee: F. R. Klausen and A. B. Lauritsen, “Stochastic cellular automaton model of
culture formation,” Physical Review E, vol. 108, no. 5. American Physical
Society, 2023.
ista: Klausen FR, Lauritsen AB. 2023. Stochastic cellular automaton model of culture
formation. Physical Review E. 108(5), 054307.
mla: Klausen, Frederik Ravn, and Asbjørn Bækgaard Lauritsen. “Stochastic Cellular
Automaton Model of Culture Formation.” Physical Review E, vol. 108, no.
5, 054307, American Physical Society, 2023, doi:10.1103/PhysRevE.108.054307.
short: F.R. Klausen, A.B. Lauritsen, Physical Review E 108 (2023).
corr_author: '1'
date_created: 2023-05-04T08:35:01Z
date_published: 2023-11-08T00:00:00Z
date_updated: 2025-09-09T12:26:01Z
day: '08'
department:
- _id: GradSch
- _id: RoSe
doi: 10.1103/PhysRevE.108.054307
external_id:
arxiv:
- '2305.02153'
isi:
- '001106396300005'
pmid:
- '38115445'
intvolume: ' 108'
isi: 1
issue: '5'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.48550/arXiv.2305.02153
month: '11'
oa: 1
oa_version: Preprint
pmid: 1
publication: Physical Review E
publication_identifier:
eissn:
- 2470-0053
issn:
- 2470-0045
publication_status: published
publisher: American Physical Society
quality_controlled: '1'
related_material:
link:
- relation: software
url: https://github.com/FrederikRavnKlausen/model-for-culture-formation
record:
- id: '12869'
relation: research_data
status: public
scopus_import: '1'
status: public
title: Stochastic cellular automaton model of culture formation
type: journal_article
user_id: 317138e5-6ab7-11ef-aa6d-ffef3953e345
volume: 108
year: '2023'
...
---
_id: '12911'
abstract:
- lang: eng
text: 'This paper establishes new connections between many-body quantum systems,
One-body Reduced Density Matrices Functional Theory (1RDMFT) and Optimal Transport
(OT), by interpreting the problem of computing the ground-state energy of a finite-dimensional
composite quantum system at positive temperature as a non-commutative entropy
regularized Optimal Transport problem. We develop a new approach to fully characterize
the dual-primal solutions in such non-commutative setting. The mathematical formalism
is particularly relevant in quantum chemistry: numerical realizations of the many-electron
ground-state energy can be computed via a non-commutative version of Sinkhorn
algorithm. Our approach allows to prove convergence and robustness of this algorithm,
which, to our best knowledge, were unknown even in the two marginal case. Our
methods are based on a priori estimates in the dual problem, which we believe
to be of independent interest. Finally, the above results are extended in 1RDMFT
setting, where bosonic or fermionic symmetry conditions are enforced on the problem.'
acknowledgement: "This work started when A.G. was visiting the Erwin Schrödinger Institute
and then continued when D.F. and L.P visited the Theoretical Chemistry Department
of the Vrije Universiteit Amsterdam. The authors thank the hospitality of both places
and, especially, P. Gori-Giorgi and K. Giesbertz for fruitful discussions and literature
suggestions in the early state of the project. The authors also thank J. Maas and
R. Seiringer for their feedback and useful comments to a first draft of the article.
Finally, we acknowledge the high quality review done by the anonymous referee of
our paper, who we would like to thank for the excellent work and constructive feedback.\r\nD.F
acknowledges support by the European Research Council (ERC) under the European Union's
Horizon 2020 research and innovation programme (grant agreements No 716117 and No
694227). A.G. acknowledges funding by the HORIZON EUROPE European Research Council
under H2020/MSCA-IF “OTmeetsDFT” [grant ID: 795942] as well as partial support of
his research by the Canada Research Chairs Program (ID 2021-00234) and Natural Sciences
and Engineering Research Council of Canada, RGPIN-2022-05207. L.P. acknowledges
support by the Austrian Science Fund (FWF), grants No W1245 and No F65, and by the
Deutsche Forschungsgemeinschaft (DFG) - Project number 390685813."
article_number: '109963'
article_processing_charge: No
article_type: original
arxiv: 1
author:
- first_name: Dario
full_name: Feliciangeli, Dario
id: 41A639AA-F248-11E8-B48F-1D18A9856A87
last_name: Feliciangeli
orcid: 0000-0003-0754-8530
- first_name: Augusto
full_name: Gerolin, Augusto
last_name: Gerolin
- first_name: Lorenzo
full_name: Portinale, Lorenzo
id: 30AD2CBC-F248-11E8-B48F-1D18A9856A87
last_name: Portinale
citation:
ama: Feliciangeli D, Gerolin A, Portinale L. A non-commutative entropic optimal
transport approach to quantum composite systems at positive temperature. Journal
of Functional Analysis. 2023;285(4). doi:10.1016/j.jfa.2023.109963
apa: Feliciangeli, D., Gerolin, A., & Portinale, L. (2023). A non-commutative
entropic optimal transport approach to quantum composite systems at positive temperature.
Journal of Functional Analysis. Elsevier. https://doi.org/10.1016/j.jfa.2023.109963
chicago: Feliciangeli, Dario, Augusto Gerolin, and Lorenzo Portinale. “A Non-Commutative
Entropic Optimal Transport Approach to Quantum Composite Systems at Positive Temperature.”
Journal of Functional Analysis. Elsevier, 2023. https://doi.org/10.1016/j.jfa.2023.109963.
ieee: D. Feliciangeli, A. Gerolin, and L. Portinale, “A non-commutative entropic
optimal transport approach to quantum composite systems at positive temperature,”
Journal of Functional Analysis, vol. 285, no. 4. Elsevier, 2023.
ista: Feliciangeli D, Gerolin A, Portinale L. 2023. A non-commutative entropic optimal
transport approach to quantum composite systems at positive temperature. Journal
of Functional Analysis. 285(4), 109963.
mla: Feliciangeli, Dario, et al. “A Non-Commutative Entropic Optimal Transport Approach
to Quantum Composite Systems at Positive Temperature.” Journal of Functional
Analysis, vol. 285, no. 4, 109963, Elsevier, 2023, doi:10.1016/j.jfa.2023.109963.
short: D. Feliciangeli, A. Gerolin, L. Portinale, Journal of Functional Analysis
285 (2023).
date_created: 2023-05-07T22:01:02Z
date_published: 2023-08-15T00:00:00Z
date_updated: 2025-04-15T08:31:52Z
day: '15'
department:
- _id: RoSe
- _id: JaMa
doi: 10.1016/j.jfa.2023.109963
ec_funded: 1
external_id:
arxiv:
- '2106.11217'
isi:
- '000990804300001'
intvolume: ' 285'
isi: 1
issue: '4'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.48550/arXiv.2106.11217
month: '08'
oa: 1
oa_version: Preprint
project:
- _id: 256E75B8-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '716117'
name: Optimal Transport and Stochastic Dynamics
- _id: 25C6DC12-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '694227'
name: Analysis of quantum many-body systems
- _id: 260482E2-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: F06504
name: Taming Complexity in Partial Differential Systems
publication: Journal of Functional Analysis
publication_identifier:
eissn:
- 1096-0783
issn:
- 0022-1236
publication_status: published
publisher: Elsevier
quality_controlled: '1'
related_material:
record:
- id: '9792'
relation: earlier_version
status: public
scopus_import: '1'
status: public
title: A non-commutative entropic optimal transport approach to quantum composite
systems at positive temperature
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 285
year: '2023'
...
---
_id: '12912'
abstract:
- lang: eng
text: The chemical potential of adsorbed or confined fluids provides insight into
their unique thermodynamic properties and determines adsorption isotherms. However,
it is often difficult to compute this quantity from atomistic simulations using
existing statistical mechanical methods. We introduce a computational framework
that utilizes static structure factors, thermodynamic integration, and free energy
perturbation for calculating the absolute chemical potential of fluids. For demonstration,
we apply the method to compute the adsorption isotherms of carbon dioxide in a
metal-organic framework and water in carbon nanotubes.
acknowledgement: We thank Aleks Reinhardt and Daan Frenkel for their insightful comments
and suggestions on the article. B.C. acknowledges the resources provided by the
Cambridge Tier-2 system operated by the University of Cambridge Research Computing
Service funded by EPSRC Tier-2 capital Grant No. EP/P020259/1.
article_number: '161101 '
article_processing_charge: No
article_type: original
arxiv: 1
author:
- first_name: Rochus
full_name: Schmid, Rochus
last_name: Schmid
- first_name: Bingqing
full_name: Cheng, Bingqing
id: cbe3cda4-d82c-11eb-8dc7-8ff94289fcc9
last_name: Cheng
orcid: 0000-0002-3584-9632
citation:
ama: Schmid R, Cheng B. Computing chemical potentials of adsorbed or confined fluids.
The Journal of Chemical Physics. 2023;158(16). doi:10.1063/5.0146711
apa: Schmid, R., & Cheng, B. (2023). Computing chemical potentials of adsorbed
or confined fluids. The Journal of Chemical Physics. AIP Publishing. https://doi.org/10.1063/5.0146711
chicago: Schmid, Rochus, and Bingqing Cheng. “Computing Chemical Potentials of Adsorbed
or Confined Fluids.” The Journal of Chemical Physics. AIP Publishing, 2023.
https://doi.org/10.1063/5.0146711.
ieee: R. Schmid and B. Cheng, “Computing chemical potentials of adsorbed or confined
fluids,” The Journal of Chemical Physics, vol. 158, no. 16. AIP Publishing,
2023.
ista: Schmid R, Cheng B. 2023. Computing chemical potentials of adsorbed or confined
fluids. The Journal of Chemical Physics. 158(16), 161101.
mla: Schmid, Rochus, and Bingqing Cheng. “Computing Chemical Potentials of Adsorbed
or Confined Fluids.” The Journal of Chemical Physics, vol. 158, no. 16,
161101, AIP Publishing, 2023, doi:10.1063/5.0146711.
short: R. Schmid, B. Cheng, The Journal of Chemical Physics 158 (2023).
corr_author: '1'
date_created: 2023-05-07T22:01:03Z
date_published: 2023-04-24T00:00:00Z
date_updated: 2024-10-09T21:05:04Z
day: '24'
ddc:
- '540'
department:
- _id: BiCh
doi: 10.1063/5.0146711
external_id:
arxiv:
- '2302.01297'
isi:
- '001010676000010'
pmid:
- '37093149'
file:
- access_level: open_access
checksum: 4ab8c965f2fa4e17920bfa846847f137
content_type: application/pdf
creator: dernst
date_created: 2023-05-08T07:44:49Z
date_updated: 2023-05-08T07:44:49Z
file_id: '12918'
file_name: 2023_JourChemicalPhysics_Schmid.pdf
file_size: 6499468
relation: main_file
success: 1
file_date_updated: 2023-05-08T07:44:49Z
has_accepted_license: '1'
intvolume: ' 158'
isi: 1
issue: '16'
language:
- iso: eng
month: '04'
oa: 1
oa_version: Published Version
pmid: 1
publication: The Journal of Chemical Physics
publication_identifier:
eissn:
- 1089-7690
publication_status: published
publisher: AIP Publishing
quality_controlled: '1'
related_material:
link:
- relation: software
url: https://github.com/BingqingCheng/mu-adsorption
- relation: software
url: https://github.com/BingqingCheng/S0
scopus_import: '1'
status: public
title: Computing chemical potentials of adsorbed or confined fluids
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: 158
year: '2023'
...
---
_id: '12913'
abstract:
- lang: eng
text: The coexistence of gate-tunable superconducting, magnetic and topological
orders in magic-angle twisted bilayer graphene provides opportunities for the
creation of hybrid Josephson junctions. Here we report the fabrication of gate-defined
symmetry-broken Josephson junctions in magic-angle twisted bilayer graphene, where
the weak link is gate-tuned close to the correlated insulator state with a moiré
filling factor of υ = −2. We observe a phase-shifted and asymmetric Fraunhofer
pattern with a pronounced magnetic hysteresis. Our theoretical calculations of
the junction weak link—with valley polarization and orbital magnetization—explain
most of these unconventional features. The effects persist up to the critical
temperature of 3.5 K, with magnetic hysteresis observed below 800 mK. We show
how the combination of magnetization and its current-induced magnetization switching
allows us to realise a programmable zero-field superconducting diode. Our results
represent a major advance towards the creation of future superconducting quantum
electronic devices.
acknowledgement: We are grateful for the fruitful discussions with Allan MacDonald
and Andrei Bernevig. D.K.E. acknowledges support from the Ministry of Economy and
Competitiveness of Spain through the “Severo Ochoa” program for Centers of Excellence
in R&D (SE5-0522), Fundació Privada Cellex, Fundació Privada Mir-Puig, the Generalitat
de Catalunya through the CERCA program, funding from the European Research Council
(ERC) under the European Union’s Horizon 2020 research and innovation program (grant
agreement no. 852927)” and the La Caixa Foundation. K.T.L. acknowledges the support
of the Ministry of Science and Technology of China and the HKRGC through grants
MOST20SC04, C6025-19G, 16310219, 16309718, and 16310520. J.D.M. acknowledges support
from the INPhINIT ‘la Caixa’ Foundation (ID 100010434) fellowship program (LCF/BQ/DI19/11730021).
Y.M.X. acknowledges the support of HKRGC through Grant No. PDFS2223-6S01.
article_number: '2396'
article_processing_charge: No
article_type: original
author:
- first_name: J.
full_name: Díez-Mérida, J.
last_name: Díez-Mérida
- first_name: A.
full_name: Díez-Carlón, A.
last_name: Díez-Carlón
- first_name: S. Y.
full_name: Yang, S. Y.
last_name: Yang
- first_name: Y. M.
full_name: Xie, Y. M.
last_name: Xie
- first_name: X. J.
full_name: Gao, X. J.
last_name: Gao
- first_name: Jorden L
full_name: Senior, Jorden L
id: 5479D234-2D30-11EA-89CC-40953DDC885E
last_name: Senior
- first_name: K.
full_name: Watanabe, K.
last_name: Watanabe
- first_name: T.
full_name: Taniguchi, T.
last_name: Taniguchi
- first_name: X.
full_name: Lu, X.
last_name: Lu
- first_name: Andrew P
full_name: Higginbotham, Andrew P
id: 4AD6785A-F248-11E8-B48F-1D18A9856A87
last_name: Higginbotham
orcid: 0000-0003-2607-2363
- first_name: K. T.
full_name: Law, K. T.
last_name: Law
- first_name: Dmitri K.
full_name: Efetov, Dmitri K.
last_name: Efetov
citation:
ama: Díez-Mérida J, Díez-Carlón A, Yang SY, et al. Symmetry-broken Josephson junctions
and superconducting diodes in magic-angle twisted bilayer graphene. Nature
Communications. 2023;14. doi:10.1038/s41467-023-38005-7
apa: Díez-Mérida, J., Díez-Carlón, A., Yang, S. Y., Xie, Y. M., Gao, X. J., Senior,
J. L., … Efetov, D. K. (2023). Symmetry-broken Josephson junctions and superconducting
diodes in magic-angle twisted bilayer graphene. Nature Communications.
Springer Nature. https://doi.org/10.1038/s41467-023-38005-7
chicago: Díez-Mérida, J., A. Díez-Carlón, S. Y. Yang, Y. M. Xie, X. J. Gao, Jorden
L Senior, K. Watanabe, et al. “Symmetry-Broken Josephson Junctions and Superconducting
Diodes in Magic-Angle Twisted Bilayer Graphene.” Nature Communications.
Springer Nature, 2023. https://doi.org/10.1038/s41467-023-38005-7.
ieee: J. Díez-Mérida et al., “Symmetry-broken Josephson junctions and superconducting
diodes in magic-angle twisted bilayer graphene,” Nature Communications,
vol. 14. Springer Nature, 2023.
ista: Díez-Mérida J, Díez-Carlón A, Yang SY, Xie YM, Gao XJ, Senior JL, Watanabe
K, Taniguchi T, Lu X, Higginbotham AP, Law KT, Efetov DK. 2023. Symmetry-broken
Josephson junctions and superconducting diodes in magic-angle twisted bilayer
graphene. Nature Communications. 14, 2396.
mla: Díez-Mérida, J., et al. “Symmetry-Broken Josephson Junctions and Superconducting
Diodes in Magic-Angle Twisted Bilayer Graphene.” Nature Communications,
vol. 14, 2396, Springer Nature, 2023, doi:10.1038/s41467-023-38005-7.
short: J. Díez-Mérida, A. Díez-Carlón, S.Y. Yang, Y.M. Xie, X.J. Gao, J.L. Senior,
K. Watanabe, T. Taniguchi, X. Lu, A.P. Higginbotham, K.T. Law, D.K. Efetov, Nature
Communications 14 (2023).
date_created: 2023-05-07T22:01:03Z
date_published: 2023-04-26T00:00:00Z
date_updated: 2023-08-01T14:34:00Z
day: '26'
ddc:
- '530'
department:
- _id: AnHi
doi: 10.1038/s41467-023-38005-7
external_id:
isi:
- '000979744000004'
pmid:
- '37100775'
file:
- access_level: open_access
checksum: a778105665c10beb2354c92d2b295115
content_type: application/pdf
creator: dernst
date_created: 2023-05-08T07:26:40Z
date_updated: 2023-05-08T07:26:40Z
file_id: '12917'
file_name: 2023_NatureComm_DiezMerida.pdf
file_size: 1405588
relation: main_file
success: 1
file_date_updated: 2023-05-08T07:26:40Z
has_accepted_license: '1'
intvolume: ' 14'
isi: 1
language:
- iso: eng
month: '04'
oa: 1
oa_version: Published Version
pmid: 1
publication: Nature Communications
publication_identifier:
eissn:
- 2041-1723
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
scopus_import: '1'
status: public
title: Symmetry-broken Josephson junctions and superconducting diodes in magic-angle
twisted bilayer graphene
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: journal_article
user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
volume: 14
year: '2023'
...
---
_id: '12914'
abstract:
- lang: eng
text: We numerically study two methods of measuring tunneling times using a quantum
clock. In the conventional method using the Larmor clock, we show that the Larmor
tunneling time can be shorter for higher tunneling barriers. In the second method,
we study the probability of a spin-flip of a particle when it is transmitted through
a potential barrier including a spatially rotating field interacting with its
spin. According to the adiabatic theorem, the probability depends on the velocity
of the particle inside the barrier. It is numerically observed that the probability
increases for higher barriers, which is consistent with the result obtained by
the Larmor clock. By comparing outcomes for different initial spin states, we
suggest that one of the main causes of the apparent decrease in the tunneling
time can be the filtering effect occurring at the end of the barrier.
acknowledgement: We thank W. H. Zurek, N. Sinitsyn, M. O. Scully, M. Arndt, and C.
H. Marrows for helpful discussions. F.S. acknowledges support from the Los Alamos
National Laboratory LDRD program under Project No. 20230049DR and the Center for
Nonlinear Studies. F.S. also thanks the European Union’s Horizon 2020 research and
innovation program under the Marie Skłodowska-Curie Grant No. 754411 for support.
W.G.U. thanks the Natural Science and Engineering Research Council of Canada, the
Hagler Institute of Texas A&M University, the Helmholz Inst HZDR, Germany for support
while this work was being done.
article_number: '042216'
article_processing_charge: No
article_type: original
arxiv: 1
author:
- first_name: Fumika
full_name: Suzuki, Fumika
id: 650C99FC-1079-11EA-A3C0-73AE3DDC885E
last_name: Suzuki
orcid: 0000-0003-4982-5970
- first_name: William G.
full_name: Unruh, William G.
last_name: Unruh
citation:
ama: Suzuki F, Unruh WG. Numerical quantum clock simulations for measuring tunneling
times. Physical Review A. 2023;107(4). doi:10.1103/PhysRevA.107.042216
apa: Suzuki, F., & Unruh, W. G. (2023). Numerical quantum clock simulations
for measuring tunneling times. Physical Review A. American Physical Society.
https://doi.org/10.1103/PhysRevA.107.042216
chicago: Suzuki, Fumika, and William G. Unruh. “Numerical Quantum Clock Simulations
for Measuring Tunneling Times.” Physical Review A. American Physical Society,
2023. https://doi.org/10.1103/PhysRevA.107.042216.
ieee: F. Suzuki and W. G. Unruh, “Numerical quantum clock simulations for measuring
tunneling times,” Physical Review A, vol. 107, no. 4. American Physical
Society, 2023.
ista: Suzuki F, Unruh WG. 2023. Numerical quantum clock simulations for measuring
tunneling times. Physical Review A. 107(4), 042216.
mla: Suzuki, Fumika, and William G. Unruh. “Numerical Quantum Clock Simulations
for Measuring Tunneling Times.” Physical Review A, vol. 107, no. 4, 042216,
American Physical Society, 2023, doi:10.1103/PhysRevA.107.042216.
short: F. Suzuki, W.G. Unruh, Physical Review A 107 (2023).
corr_author: '1'
date_created: 2023-05-07T22:01:03Z
date_published: 2023-04-20T00:00:00Z
date_updated: 2025-04-14T07:44:01Z
day: '20'
department:
- _id: MiLe
doi: 10.1103/PhysRevA.107.042216
ec_funded: 1
external_id:
arxiv:
- '2207.13130'
isi:
- '000975799300006'
intvolume: ' 107'
isi: 1
issue: '4'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.48550/arXiv.2207.13130
month: '04'
oa: 1
oa_version: Preprint
project:
- _id: 260C2330-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '754411'
name: ISTplus - Postdoctoral Fellowships
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: Numerical quantum clock simulations for measuring tunneling times
type: journal_article
user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
volume: 107
year: '2023'
...
---
OA_place: repository
OA_type: green
_id: '12915'
abstract:
- lang: eng
text: Cu2–xS and Cu2–xSe have recently been reported as promising thermoelectric
(TE) materials for medium-temperature applications. In contrast, Cu2–xTe, another
member of the copper chalcogenide family, typically exhibits low Seebeck coefficients
that limit its potential to achieve a superior thermoelectric figure of merit,
zT, particularly in the low-temperature range where this material could be effective.
To address this, we investigated the TE performance of Cu1.5–xTe–Cu2Se nanocomposites
by consolidating surface-engineered Cu1.5Te nanocrystals. This surface engineering
strategy allows for precise adjustment of Cu/Te ratios and results in a reversible
phase transition at around 600 K in Cu1.5–xTe–Cu2Se nanocomposites, as systematically
confirmed by in situ high-temperature X-ray diffraction combined with differential
scanning calorimetry analysis. The phase transition leads to a conversion from
metallic-like to semiconducting-like TE properties. Additionally, a layer of Cu2Se
generated around Cu1.5–xTe nanoparticles effectively inhibits Cu1.5–xTe grain
growth, minimizing thermal conductivity and decreasing hole concentration. These
properties indicate that copper telluride based compounds have a promising thermoelectric
potential, translated into a high dimensionless zT of 1.3 at 560 K.
acknowledgement: 'The authors acknowledge support from the projects ENE2016-77798-C4-3-R
and NANOGEN (PID2020-116093RB-C43) funded by MCIN/AEI/10.13039/501100011033/and
by “ERDF A way of making Europe”, and by the “European Union”. K.X. and B.N. thank
the China Scholarship Council (CSC) for scholarship support. The authors acknowledge
funding from Generalitat de Catalunya 2017 SGR 327 and 2017 SGR 1246. ICN2 is supported
by the Severo Ochoa program from the Spanish MCIN/AEI (Grant No.: CEX2021-001214-S).
IREC and ICN2 are funded by the CERCA Programme/Generalitat de Catalunya. J.L. acknowledges
support from the Natural Science Foundation of Sichuan province (2022NSFSC1229).
Part of the present work was performed in the frameworks of Universitat de Barcelona
Nanoscience Ph.D. program and Universitat Autònoma de Barcelona Materials Science
Ph.D. program. Y.L. acknowledges funding from the National Natural Science Foundation
of China (Grant No. 22209034) and the Innovation and Entrepreneurship Project of
Overseas Returnees in Anhui Province (Grants No. 2022LCX002). K.H.L. acknowledges
the financial support of the National Natural Science Foundation of China (Grant
No. 22208293).'
article_processing_charge: No
article_type: original
author:
- first_name: Congcong
full_name: Xing, Congcong
last_name: Xing
- first_name: Yu
full_name: Zhang, Yu
last_name: Zhang
- first_name: Ke
full_name: Xiao, Ke
last_name: Xiao
- first_name: Xu
full_name: Han, Xu
last_name: Han
- first_name: Yu
full_name: Liu, Yu
id: 2A70014E-F248-11E8-B48F-1D18A9856A87
last_name: Liu
orcid: 0000-0001-7313-6740
- first_name: Bingfei
full_name: Nan, Bingfei
last_name: 'Nan'
- first_name: Maria Garcia
full_name: Ramon, Maria Garcia
id: 1ffff7cd-ed76-11ed-8d5f-be5e7c364eb9
last_name: Ramon
- first_name: Khak Ho
full_name: Lim, Khak Ho
last_name: Lim
- first_name: Junshan
full_name: Li, Junshan
last_name: Li
- first_name: Jordi
full_name: Arbiol, Jordi
last_name: Arbiol
- first_name: Bed
full_name: Poudel, Bed
last_name: Poudel
- first_name: Amin
full_name: Nozariasbmarz, Amin
last_name: Nozariasbmarz
- first_name: Wenjie
full_name: Li, Wenjie
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: Andreu
full_name: Cabot, Andreu
last_name: Cabot
citation:
ama: Xing C, Zhang Y, Xiao K, et al. Thermoelectric performance of surface-engineered
Cu1.5–xTe–Cu2Se nanocomposites. ACS Nano. 2023;17(9):8442-8452. doi:10.1021/acsnano.3c00495
apa: Xing, C., Zhang, Y., Xiao, K., Han, X., Liu, Y., Nan, B., … Cabot, A. (2023).
Thermoelectric performance of surface-engineered Cu1.5–xTe–Cu2Se nanocomposites.
ACS Nano. American Chemical Society. https://doi.org/10.1021/acsnano.3c00495
chicago: Xing, Congcong, Yu Zhang, Ke Xiao, Xu Han, Yu Liu, Bingfei Nan, Maria Garcia
Ramon, et al. “Thermoelectric Performance of Surface-Engineered Cu1.5–XTe–Cu2Se
Nanocomposites.” ACS Nano. American Chemical Society, 2023. https://doi.org/10.1021/acsnano.3c00495.
ieee: C. Xing et al., “Thermoelectric performance of surface-engineered Cu1.5–xTe–Cu2Se
nanocomposites,” ACS Nano, vol. 17, no. 9. American Chemical Society, pp.
8442–8452, 2023.
ista: Xing C, Zhang Y, Xiao K, Han X, Liu Y, Nan B, Ramon MG, Lim KH, Li J, Arbiol
J, Poudel B, Nozariasbmarz A, Li W, Ibáñez M, Cabot A. 2023. Thermoelectric performance
of surface-engineered Cu1.5–xTe–Cu2Se nanocomposites. ACS Nano. 17(9), 8442–8452.
mla: Xing, Congcong, et al. “Thermoelectric Performance of Surface-Engineered Cu1.5–XTe–Cu2Se
Nanocomposites.” ACS Nano, vol. 17, no. 9, American Chemical Society, 2023,
pp. 8442–52, doi:10.1021/acsnano.3c00495.
short: C. Xing, Y. Zhang, K. Xiao, X. Han, Y. Liu, B. Nan, M.G. Ramon, K.H. Lim,
J. Li, J. Arbiol, B. Poudel, A. Nozariasbmarz, W. Li, M. Ibáñez, A. Cabot, ACS
Nano 17 (2023) 8442–8452.
corr_author: '1'
date_created: 2023-05-07T22:01:04Z
date_published: 2023-05-09T00:00:00Z
date_updated: 2025-06-25T06:01:54Z
day: '09'
department:
- _id: MaIb
doi: 10.1021/acsnano.3c00495
external_id:
isi:
- '000976063200001'
pmid:
- '37071412'
intvolume: ' 17'
isi: 1
issue: '9'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://ddd.uab.cat/pub/artpub/2023/zlnqprw07rek/acsnan_a2023_Pre.pdf
month: '05'
oa: 1
oa_version: Submitted Version
page: 8442-8452
pmid: 1
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: Thermoelectric performance of surface-engineered Cu1.5–xTe–Cu2Se nanocomposites
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 17
year: '2023'
...
---
_id: '12916'
abstract:
- lang: eng
text: "We apply a variant of the square-sieve to produce an upper bound for the
number of rational points of bounded height on a family of surfaces that admit
a fibration over P1 whose general fibre is a hyperelliptic curve. The implied
constant does not depend on the coefficients of the polynomial defining the surface.\r\n"
article_processing_charge: No
article_type: original
arxiv: 1
author:
- first_name: Dante
full_name: Bonolis, Dante
id: 6A459894-5FDD-11E9-AF35-BB24E6697425
last_name: Bonolis
- first_name: Timothy D
full_name: Browning, Timothy D
id: 35827D50-F248-11E8-B48F-1D18A9856A87
last_name: Browning
orcid: 0000-0002-8314-0177
citation:
ama: Bonolis D, Browning TD. Uniform bounds for rational points on hyperelliptic
fibrations. Annali della Scuola Normale Superiore di Pisa - Classe di Scienze.
2023;24(1):173-204. doi:10.2422/2036-2145.202010_018
apa: Bonolis, D., & Browning, T. D. (2023). Uniform bounds for rational points
on hyperelliptic fibrations. Annali Della Scuola Normale Superiore Di Pisa
- Classe Di Scienze. Scuola Normale Superiore - Edizioni della Normale. https://doi.org/10.2422/2036-2145.202010_018
chicago: Bonolis, Dante, and Timothy D Browning. “Uniform Bounds for Rational Points
on Hyperelliptic Fibrations.” Annali Della Scuola Normale Superiore Di Pisa
- Classe Di Scienze. Scuola Normale Superiore - Edizioni della Normale, 2023.
https://doi.org/10.2422/2036-2145.202010_018.
ieee: D. Bonolis and T. D. Browning, “Uniform bounds for rational points on hyperelliptic
fibrations,” Annali della Scuola Normale Superiore di Pisa - Classe di Scienze,
vol. 24, no. 1. Scuola Normale Superiore - Edizioni della Normale, pp. 173–204,
2023.
ista: Bonolis D, Browning TD. 2023. Uniform bounds for rational points on hyperelliptic
fibrations. Annali della Scuola Normale Superiore di Pisa - Classe di Scienze.
24(1), 173–204.
mla: Bonolis, Dante, and Timothy D. Browning. “Uniform Bounds for Rational Points
on Hyperelliptic Fibrations.” Annali Della Scuola Normale Superiore Di Pisa
- Classe Di Scienze, vol. 24, no. 1, Scuola Normale Superiore - Edizioni della
Normale, 2023, pp. 173–204, doi:10.2422/2036-2145.202010_018.
short: D. Bonolis, T.D. Browning, Annali Della Scuola Normale Superiore Di Pisa
- Classe Di Scienze 24 (2023) 173–204.
corr_author: '1'
date_created: 2023-05-07T22:01:04Z
date_published: 2023-02-16T00:00:00Z
date_updated: 2024-10-09T21:05:05Z
day: '16'
department:
- _id: TiBr
doi: 10.2422/2036-2145.202010_018
external_id:
arxiv:
- '2007.14182'
intvolume: ' 24'
issue: '1'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.48550/arXiv.2007.14182
month: '02'
oa: 1
oa_version: Preprint
page: 173-204
publication: Annali della Scuola Normale Superiore di Pisa - Classe di Scienze
publication_identifier:
eissn:
- 2036-2145
issn:
- 0391-173X
publication_status: published
publisher: Scuola Normale Superiore - Edizioni della Normale
quality_controlled: '1'
scopus_import: '1'
status: public
title: Uniform bounds for rational points on hyperelliptic fibrations
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 24
year: '2023'
...
---
_id: '12945'
abstract:
- lang: eng
text: "basic data for use in code for experimental data analysis for manuscript
under revision: \r\nDynamic pathogen detection and social feedback shape collective
hygiene in ants\r\nCasillas-Pérez B, Boďová K, Grasse AV, Tkačik G, Cremer S"
acknowledged_ssus:
- _id: LifeSc
acknowledgement: This project has received funding from the European Research Council
(ERC) under the European Union’s Horizon 2020 research and innovation programme
(Grant No. 771402; EPIDEMICSonCHIP) to SC, from the Scientific Grant Agency of the
Slovak Republic (Grant No. 1/0521/20) to KB, and the Human Frontier Science Program
(Grant No. RGP0065/2012) to GT.
article_processing_charge: No
author:
- first_name: Sylvia
full_name: Cremer, Sylvia
id: 2F64EC8C-F248-11E8-B48F-1D18A9856A87
last_name: Cremer
orcid: 0000-0002-2193-3868
citation:
ama: 'Cremer S. Data from: “Dynamic pathogen detection and social feedback shape
collective hygiene in ants” . 2023. doi:10.15479/AT:ISTA:12945'
apa: 'Cremer, S. (2023). Data from: “Dynamic pathogen detection and social feedback
shape collective hygiene in ants” . Institute of Science and Technology Austria.
https://doi.org/10.15479/AT:ISTA:12945'
chicago: 'Cremer, Sylvia. “Data from: ‘Dynamic Pathogen Detection and Social Feedback
Shape Collective Hygiene in Ants’ .” Institute of Science and Technology Austria,
2023. https://doi.org/10.15479/AT:ISTA:12945.'
ieee: 'S. Cremer, “Data from: ‘Dynamic pathogen detection and social feedback shape
collective hygiene in ants’ .” Institute of Science and Technology Austria, 2023.'
ista: 'Cremer S. 2023. Data from: ‘Dynamic pathogen detection and social feedback
shape collective hygiene in ants’ , Institute of Science and Technology Austria,
10.15479/AT:ISTA:12945.'
mla: 'Cremer, Sylvia. Data from: “Dynamic Pathogen Detection and Social Feedback
Shape Collective Hygiene in Ants” . Institute of Science and Technology Austria,
2023, doi:10.15479/AT:ISTA:12945.'
short: S. Cremer, (2023).
contributor:
- contributor_type: data_collector
first_name: Barbara E
id: 351ED2AA-F248-11E8-B48F-1D18A9856A87
last_name: Casillas Perez
- contributor_type: data_collector
first_name: Anna V
id: 406F989C-F248-11E8-B48F-1D18A9856A87
last_name: Grasse
- contributor_type: researcher
first_name: Katarina
last_name: Bodova
- contributor_type: supervisor
first_name: Gašper
id: 3D494DCA-F248-11E8-B48F-1D18A9856A87
last_name: Tkačik
orcid: 0000-0002-6699-1455
corr_author: '1'
date_created: 2023-05-11T21:35:17Z
date_published: 2023-05-12T00:00:00Z
date_updated: 2025-04-15T06:44:30Z
day: '12'
ddc:
- '570'
department:
- _id: SyCr
doi: 10.15479/AT:ISTA:12945
file:
- access_level: open_access
checksum: 3eadf17fd59ad8c98bf10bf63061863c
content_type: application/zip
creator: scremer
date_created: 2023-05-12T08:04:04Z
date_updated: 2023-05-12T08:04:04Z
file_id: '12947'
file_name: Experimental_data.zip
file_size: 3414674
relation: main_file
success: 1
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checksum: 1b5e8e01a0989154a76b44e6d8d68f89
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creator: scremer
date_created: 2023-05-12T08:04:08Z
date_updated: 2023-05-12T08:04:08Z
file_id: '12948'
file_name: README_Experimental_Data.md
file_size: 2113
relation: main_file
success: 1
file_date_updated: 2023-05-12T08:04:08Z
has_accepted_license: '1'
keyword:
- collective behavior
- host-pathogen interactions
- social immunity
- epidemiology
- social insects
- probabilistic modeling
month: '05'
oa: 1
oa_version: None
publisher: Institute of Science and Technology Austria
related_material:
record:
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relation: used_in_publication
status: public
status: public
title: 'Data from: "Dynamic pathogen detection and social feedback shape collective
hygiene in ants" '
tmp:
image: /images/cc_by_nc.png
legal_code_url: https://creativecommons.org/licenses/by-nc/4.0/legalcode
name: Creative Commons Attribution-NonCommercial 4.0 International (CC BY-NC 4.0)
short: CC BY-NC (4.0)
type: research_data
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
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...