---
_id: '10364'
abstract:
- lang: eng
text: 'This paper characterizes the latency of the simplified successive-cancellation
(SSC) decoding scheme for polar codes under hardware resource constraints. In
particular, when the number of processing elements P that can perform SSC decoding
operations in parallel is limited, as is the case in practice, the latency of
SSC decoding is O(N1-1/μ + N/P log2 log2 N/P), where N is the block length of
the code and μ is the scaling exponent of the channel. Three direct consequences
of this bound are presented. First, in a fully-parallel implementation where P
= N/2, the latency of SSC decoding is O(N1-1/μ), which is sublinear in the block
length. This recovers a result from our earlier work. Second, in a fully-serial
implementation where P = 1, the latency of SSC decoding scales as O(N log2 log2
N). The multiplicative constant is also calculated: we show that the latency of
SSC decoding when P = 1 is given by (2 + o(1))N log2 log2 N. Third, in a semi-parallel
implementation, the smallest P that gives the same latency as that of the fully-parallel
implementation is P = N1/μ. The tightness of our bound on SSC decoding latency
and the applicability of the foregoing results is validated through extensive
simulations.'
acknowledgement: "S. A. Hashemi is supported by a Postdoctoral Fellowship from the
Natural Sciences and\r\nEngineering Research Council of Canada (NSERC) and by Huawei.
M. Mondelli is partially\r\nsupported by the 2019 Lopez-Loreta Prize. A. Fazeli
and A. Vardy were supported in part by\r\nthe National Science Foundation under
Grant CCF-1764104."
article_processing_charge: No
article_type: original
arxiv: 1
author:
- first_name: Seyyed Ali
full_name: Hashemi, Seyyed Ali
last_name: Hashemi
- first_name: Marco
full_name: Mondelli, Marco
id: 27EB676C-8706-11E9-9510-7717E6697425
last_name: Mondelli
orcid: 0000-0002-3242-7020
- first_name: Arman
full_name: Fazeli, Arman
last_name: Fazeli
- first_name: Alexander
full_name: Vardy, Alexander
last_name: Vardy
- first_name: John
full_name: Cioffi, John
last_name: Cioffi
- first_name: Andrea
full_name: Goldsmith, Andrea
last_name: Goldsmith
citation:
ama: Hashemi SA, Mondelli M, Fazeli A, Vardy A, Cioffi J, Goldsmith A. Parallelism
versus latency in simplified successive-cancellation decoding of polar codes.
IEEE Transactions on Wireless Communications. 2022;21(6):3909-3920. doi:10.1109/TWC.2021.3125626
apa: Hashemi, S. A., Mondelli, M., Fazeli, A., Vardy, A., Cioffi, J., & Goldsmith,
A. (2022). Parallelism versus latency in simplified successive-cancellation decoding
of polar codes. IEEE Transactions on Wireless Communications. Institute
of Electrical and Electronics Engineers. https://doi.org/10.1109/TWC.2021.3125626
chicago: Hashemi, Seyyed Ali, Marco Mondelli, Arman Fazeli, Alexander Vardy, John
Cioffi, and Andrea Goldsmith. “Parallelism versus Latency in Simplified Successive-Cancellation
Decoding of Polar Codes.” IEEE Transactions on Wireless Communications.
Institute of Electrical and Electronics Engineers, 2022. https://doi.org/10.1109/TWC.2021.3125626.
ieee: S. A. Hashemi, M. Mondelli, A. Fazeli, A. Vardy, J. Cioffi, and A. Goldsmith,
“Parallelism versus latency in simplified successive-cancellation decoding of
polar codes,” IEEE Transactions on Wireless Communications, vol. 21, no.
6. Institute of Electrical and Electronics Engineers, pp. 3909–3920, 2022.
ista: Hashemi SA, Mondelli M, Fazeli A, Vardy A, Cioffi J, Goldsmith A. 2022. Parallelism
versus latency in simplified successive-cancellation decoding of polar codes.
IEEE Transactions on Wireless Communications. 21(6), 3909–3920.
mla: Hashemi, Seyyed Ali, et al. “Parallelism versus Latency in Simplified Successive-Cancellation
Decoding of Polar Codes.” IEEE Transactions on Wireless Communications,
vol. 21, no. 6, Institute of Electrical and Electronics Engineers, 2022, pp. 3909–20,
doi:10.1109/TWC.2021.3125626.
short: S.A. Hashemi, M. Mondelli, A. Fazeli, A. Vardy, J. Cioffi, A. Goldsmith,
IEEE Transactions on Wireless Communications 21 (2022) 3909–3920.
date_created: 2021-11-28T23:01:29Z
date_published: 2022-06-01T00:00:00Z
date_updated: 2025-04-15T07:50:11Z
day: '01'
department:
- _id: MaMo
doi: 10.1109/TWC.2021.3125626
external_id:
arxiv:
- '2012.13378'
isi:
- '000809406400028'
intvolume: ' 21'
isi: 1
issue: '6'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/2012.13378
month: '06'
oa: 1
oa_version: Preprint
page: 3909-3920
project:
- _id: 059876FA-7A3F-11EA-A408-12923DDC885E
name: Prix Lopez-Loretta 2019 - Marco Mondelli
publication: IEEE Transactions on Wireless Communications
publication_identifier:
eissn:
- 1558-2248
issn:
- 1536-1276
publication_status: published
publisher: Institute of Electrical and Electronics Engineers
quality_controlled: '1'
related_material:
record:
- id: '10053'
relation: earlier_version
status: public
scopus_import: '1'
status: public
title: Parallelism versus latency in simplified successive-cancellation decoding of
polar codes
type: journal_article
user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
volume: 21
year: '2022'
...
---
_id: '10413'
abstract:
- lang: eng
text: Motivated by the recent introduction of the intrinsic semilattice entropy,
we study generalized quasi-metric semilattices and their categories. We investigate
the relationship between these objects and generalized semivaluations, extending
Nakamura and Schellekens' approach. Finally, we use this correspondence to compare
the intrinsic semilattice entropy and the semigroup entropy induced in particular
situations, like sets, torsion abelian groups and vector spaces.
acknowledgement: Dedicated to the memory of Hans-Peter Künzi.
article_number: '107916'
article_processing_charge: No
article_type: original
author:
- first_name: Dikran
full_name: Dikranjan, Dikran
last_name: Dikranjan
- first_name: Anna
full_name: Giordano Bruno, Anna
last_name: Giordano Bruno
- first_name: Hans Peter
full_name: Künzi, Hans Peter
last_name: Künzi
- first_name: Nicolò
full_name: Zava, Nicolò
id: c8b3499c-7a77-11eb-b046-aa368cbbf2ad
last_name: Zava
orcid: 0000-0001-8686-1888
- first_name: Daniele
full_name: Toller, Daniele
last_name: Toller
citation:
ama: Dikranjan D, Giordano Bruno A, Künzi HP, Zava N, Toller D. Generalized quasi-metric
semilattices. Topology and its Applications. 2022;309. doi:10.1016/j.topol.2021.107916
apa: Dikranjan, D., Giordano Bruno, A., Künzi, H. P., Zava, N., & Toller, D.
(2022). Generalized quasi-metric semilattices. Topology and Its Applications.
Elsevier. https://doi.org/10.1016/j.topol.2021.107916
chicago: Dikranjan, Dikran, Anna Giordano Bruno, Hans Peter Künzi, Nicolò Zava,
and Daniele Toller. “Generalized Quasi-Metric Semilattices.” Topology and Its
Applications. Elsevier, 2022. https://doi.org/10.1016/j.topol.2021.107916.
ieee: D. Dikranjan, A. Giordano Bruno, H. P. Künzi, N. Zava, and D. Toller, “Generalized
quasi-metric semilattices,” Topology and its Applications, vol. 309. Elsevier,
2022.
ista: Dikranjan D, Giordano Bruno A, Künzi HP, Zava N, Toller D. 2022. Generalized
quasi-metric semilattices. Topology and its Applications. 309, 107916.
mla: Dikranjan, Dikran, et al. “Generalized Quasi-Metric Semilattices.” Topology
and Its Applications, vol. 309, 107916, Elsevier, 2022, doi:10.1016/j.topol.2021.107916.
short: D. Dikranjan, A. Giordano Bruno, H.P. Künzi, N. Zava, D. Toller, Topology
and Its Applications 309 (2022).
corr_author: '1'
date_created: 2021-12-05T23:01:44Z
date_published: 2022-03-15T00:00:00Z
date_updated: 2024-10-09T21:01:16Z
day: '15'
department:
- _id: HeEd
doi: 10.1016/j.topol.2021.107916
external_id:
isi:
- '000791838800012'
intvolume: ' 309'
isi: 1
language:
- iso: eng
month: '03'
oa_version: None
publication: Topology and its Applications
publication_identifier:
issn:
- 0166-8641
publication_status: published
publisher: Elsevier
quality_controlled: '1'
scopus_import: '1'
status: public
title: Generalized quasi-metric semilattices
type: journal_article
user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
volume: 309
year: '2022'
...
---
_id: '10530'
abstract:
- lang: eng
text: "Cell dispersion from a confined area is fundamental in a number of biological
processes,\r\nincluding cancer metastasis. To date, a quantitative understanding
of the interplay of single\r\ncell motility, cell proliferation, and intercellular
contacts remains elusive. In particular, the role\r\nof E- and N-Cadherin junctions,
central components of intercellular contacts, is still\r\ncontroversial. Combining
theoretical modeling with in vitro observations, we investigate the\r\ncollective
spreading behavior of colonies of human cancer cells (T24). The spreading of these\r\ncolonies
is driven by stochastic single-cell migration with frequent transient cell-cell
contacts.\r\nWe find that inhibition of E- and N-Cadherin junctions decreases
colony spreading and average\r\nspreading velocities, without affecting the strength
of correlations in spreading velocities of\r\nneighboring cells. Based on a biophysical
simulation model for cell migration, we show that the\r\nbehavioral changes upon
disruption of these junctions can be explained by reduced repulsive\r\nexcluded
volume interactions between cells. This suggests that in cancer cell migration,\r\ncadherin-based
intercellular contacts sharpen cell boundaries leading to repulsive rather than\r\ncohesive
interactions between cells, thereby promoting efficient cell spreading during
collective\r\nmigration.\r\n"
acknowledgement: Funded by the Deutsche Forschungsgemeinschaft (DFG, German Research
Foundation) - Project-ID 201269156 - SFB 1032 (Projects B8 and B12). D.B.B. is supported
in part by a DFG fellowship within the Graduate School of Quantitative Biosciences
Munich (QBM) and by the Joachim Herz Stiftung.
article_processing_charge: No
article_type: original
author:
- first_name: Themistoklis
full_name: Zisis, Themistoklis
last_name: Zisis
- first_name: David
full_name: Brückner, David
id: e1e86031-6537-11eb-953a-f7ab92be508d
last_name: Brückner
orcid: 0000-0001-7205-2975
- first_name: Tom
full_name: Brandstätter, Tom
last_name: Brandstätter
- first_name: Wei Xiong
full_name: Siow, Wei Xiong
last_name: Siow
- first_name: Joseph
full_name: d’Alessandro, Joseph
last_name: d’Alessandro
- first_name: Angelika M.
full_name: Vollmar, Angelika M.
last_name: Vollmar
- first_name: Chase P.
full_name: Broedersz, Chase P.
last_name: Broedersz
- first_name: Stefan
full_name: Zahler, Stefan
last_name: Zahler
citation:
ama: Zisis T, Brückner D, Brandstätter T, et al. Disentangling cadherin-mediated
cell-cell interactions in collective cancer cell migration. Biophysical Journal.
2022;121(1):P44-60. doi:10.1016/j.bpj.2021.12.006
apa: Zisis, T., Brückner, D., Brandstätter, T., Siow, W. X., d’Alessandro, J., Vollmar,
A. M., … Zahler, S. (2022). Disentangling cadherin-mediated cell-cell interactions
in collective cancer cell migration. Biophysical Journal. Elsevier. https://doi.org/10.1016/j.bpj.2021.12.006
chicago: Zisis, Themistoklis, David Brückner, Tom Brandstätter, Wei Xiong Siow,
Joseph d’Alessandro, Angelika M. Vollmar, Chase P. Broedersz, and Stefan Zahler.
“Disentangling Cadherin-Mediated Cell-Cell Interactions in Collective Cancer Cell
Migration.” Biophysical Journal. Elsevier, 2022. https://doi.org/10.1016/j.bpj.2021.12.006.
ieee: T. Zisis et al., “Disentangling cadherin-mediated cell-cell interactions
in collective cancer cell migration,” Biophysical Journal, vol. 121, no.
1. Elsevier, pp. P44-60, 2022.
ista: Zisis T, Brückner D, Brandstätter T, Siow WX, d’Alessandro J, Vollmar AM,
Broedersz CP, Zahler S. 2022. Disentangling cadherin-mediated cell-cell interactions
in collective cancer cell migration. Biophysical Journal. 121(1), P44-60.
mla: Zisis, Themistoklis, et al. “Disentangling Cadherin-Mediated Cell-Cell Interactions
in Collective Cancer Cell Migration.” Biophysical Journal, vol. 121, no.
1, Elsevier, 2022, pp. P44-60, doi:10.1016/j.bpj.2021.12.006.
short: T. Zisis, D. Brückner, T. Brandstätter, W.X. Siow, J. d’Alessandro, A.M.
Vollmar, C.P. Broedersz, S. Zahler, Biophysical Journal 121 (2022) P44-60.
date_created: 2021-12-10T09:48:19Z
date_published: 2022-01-04T00:00:00Z
date_updated: 2025-06-11T13:59:29Z
day: '04'
ddc:
- '570'
department:
- _id: EdHa
- _id: GaTk
doi: 10.1016/j.bpj.2021.12.006
external_id:
isi:
- '000740815400007'
pmid:
- '34890578'
file:
- access_level: open_access
checksum: 1aa7c3478e0c8256b973b632efd1f6b4
content_type: application/pdf
creator: dernst
date_created: 2022-07-29T10:17:10Z
date_updated: 2022-07-29T10:17:10Z
file_id: '11697'
file_name: 2022_BiophysicalJour_Zisis.pdf
file_size: 4475504
relation: main_file
success: 1
file_date_updated: 2022-07-29T10:17:10Z
has_accepted_license: '1'
intvolume: ' 121'
isi: 1
issue: '1'
keyword:
- Biophysics
language:
- iso: eng
month: '01'
oa: 1
oa_version: Published Version
page: P44-60
pmid: 1
project:
- _id: 9B861AAC-BA93-11EA-9121-9846C619BF3A
name: NOMIS Fellowship Program
publication: Biophysical Journal
publication_identifier:
issn:
- 0006-3495
publication_status: published
publisher: Elsevier
quality_controlled: '1'
scopus_import: '1'
status: public
title: Disentangling cadherin-mediated cell-cell interactions in collective cancer
cell migration
tmp:
image: /images/cc_by_nc_nd.png
legal_code_url: https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode
name: Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International
(CC BY-NC-ND 4.0)
short: CC BY-NC-ND (4.0)
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 121
year: '2022'
...
---
_id: '10537'
abstract:
- lang: eng
text: We consider the quantum many-body evolution of a homogeneous Fermi gas in
three dimensions in the coupled semiclassical and mean-field scaling regime. We
study a class of initial data describing collective particle–hole pair excitations
on the Fermi ball. Using a rigorous version of approximate bosonization, we prove
that the many-body evolution can be approximated in Fock space norm by a quasi-free
bosonic evolution of the collective particle–hole excitations.
acknowledgement: NB was supported by Gruppo Nazionale per la Fisica Matematica (GNFM).
RS was supported by the European Research Council (ERC) under the European Union’s
Horizon 2020 research and innovation program (Grant Agreement No. 694227). PTN was
supported by the Deutsche Forschungsgemeinschaft (DFG, German Research Foundation)
under Germany’s Excellence Strategy (EXC-2111-390814868). MP was supported by the
European Research Council (ERC) under the European Union’s Horizon 2020 research
and innovation program (ERC StG MaMBoQ, Grant Agreement No. 802901). BS was supported
by the NCCR SwissMAP, the Swiss National Science Foundation through the Grant “Dynamical
and energetic properties of Bose-Einstein condensates,” and the European Research
Council (ERC) under the European Union’s Horizon 2020 research and innovation program
through the ERC-AdG CLaQS (Grant Agreement No. 834782).
article_processing_charge: No
article_type: original
arxiv: 1
author:
- first_name: Niels P
full_name: Benedikter, Niels P
id: 3DE6C32A-F248-11E8-B48F-1D18A9856A87
last_name: Benedikter
orcid: 0000-0002-1071-6091
- first_name: Phan Thành
full_name: Nam, Phan Thành
last_name: Nam
- first_name: Marcello
full_name: Porta, Marcello
last_name: Porta
- first_name: Benjamin
full_name: Schlein, Benjamin
last_name: Schlein
- first_name: Robert
full_name: Seiringer, Robert
id: 4AFD0470-F248-11E8-B48F-1D18A9856A87
last_name: Seiringer
orcid: 0000-0002-6781-0521
citation:
ama: Benedikter NP, Nam PT, Porta M, Schlein B, Seiringer R. Bosonization of fermionic
many-body dynamics. Annales Henri Poincaré. 2022;23(5):1725-1764. doi:10.1007/s00023-021-01136-y
apa: Benedikter, N. P., Nam, P. T., Porta, M., Schlein, B., & Seiringer, R.
(2022). Bosonization of fermionic many-body dynamics. Annales Henri Poincaré.
Springer Nature. https://doi.org/10.1007/s00023-021-01136-y
chicago: Benedikter, Niels P, Phan Thành Nam, Marcello Porta, Benjamin Schlein,
and Robert Seiringer. “Bosonization of Fermionic Many-Body Dynamics.” Annales
Henri Poincaré. Springer Nature, 2022. https://doi.org/10.1007/s00023-021-01136-y.
ieee: N. P. Benedikter, P. T. Nam, M. Porta, B. Schlein, and R. Seiringer, “Bosonization
of fermionic many-body dynamics,” Annales Henri Poincaré, vol. 23, no.
5. Springer Nature, pp. 1725–1764, 2022.
ista: Benedikter NP, Nam PT, Porta M, Schlein B, Seiringer R. 2022. Bosonization
of fermionic many-body dynamics. Annales Henri Poincaré. 23(5), 1725–1764.
mla: Benedikter, Niels P., et al. “Bosonization of Fermionic Many-Body Dynamics.”
Annales Henri Poincaré, vol. 23, no. 5, Springer Nature, 2022, pp. 1725–64,
doi:10.1007/s00023-021-01136-y.
short: N.P. Benedikter, P.T. Nam, M. Porta, B. Schlein, R. Seiringer, Annales Henri
Poincaré 23 (2022) 1725–1764.
date_created: 2021-12-12T23:01:28Z
date_published: 2022-05-01T00:00:00Z
date_updated: 2025-04-14T07:26:53Z
day: '01'
department:
- _id: RoSe
doi: 10.1007/s00023-021-01136-y
ec_funded: 1
external_id:
arxiv:
- '2103.08224'
isi:
- '000725405700001'
intvolume: ' 23'
isi: 1
issue: '5'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/2103.08224
month: '05'
oa: 1
oa_version: Preprint
page: 1725-1764
project:
- _id: 25C6DC12-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '694227'
name: Analysis of quantum many-body systems
publication: Annales Henri Poincaré
publication_identifier:
issn:
- 1424-0637
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
scopus_import: '1'
status: public
title: Bosonization of fermionic many-body dynamics
type: journal_article
user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87
volume: 23
year: '2022'
...
---
_id: '10547'
abstract:
- lang: eng
text: "We establish global-in-time existence results for thermodynamically consistent
reaction-(cross-)diffusion systems coupled to an equation describing heat transfer.
Our main interest is to model species-dependent diffusivities,\r\nwhile at the
same time ensuring thermodynamic consistency. A key difficulty of the non-isothermal
case lies in the intrinsic presence of cross-diffusion type phenomena like the
Soret and the Dufour effect: due to the temperature/energy dependence of the thermodynamic
equilibria, a nonvanishing temperature gradient may drive a concentration flux
even in a situation with constant concentrations; likewise, a nonvanishing concentration
gradient may drive a heat flux even in a case of spatially constant temperature.
We use time discretisation and regularisation techniques and derive a priori estimates
based on a suitable entropy and the associated entropy production. Renormalised
solutions are used in cases where non-integrable diffusion fluxes or reaction
terms appear."
acknowledgement: M.K. gratefully acknowledges the hospitality of WIAS Berlin, where
a major part of the project was carried out. The research stay of M.K. at WIAS Berlin
was funded by the Austrian Federal Ministry of Education, Science and Research through
a research fellowship for graduates of a promotio sub auspiciis. The research of
A.M. has been partially supported by Deutsche Forschungsgemeinschaft (DFG) through
the Collaborative Research Center SFB 1114 “Scaling Cascades in Complex Systems”
(Project no. 235221301), Subproject C05 “Effective models for materials and interfaces
with multiple scales”. J.F. and A.M. are grateful for the hospitality of the Erwin
Schrödinger Institute in Vienna, where some ideas for this work have been developed.
The authors are grateful to two anonymous referees for several helpful comments,
in particular for the short proof of estimate (2.7).
article_processing_charge: No
article_type: original
arxiv: 1
author:
- first_name: Julian L
full_name: Fischer, Julian L
id: 2C12A0B0-F248-11E8-B48F-1D18A9856A87
last_name: Fischer
orcid: 0000-0002-0479-558X
- first_name: Katharina
full_name: Hopf, Katharina
last_name: Hopf
- first_name: Michael
full_name: Kniely, Michael
id: 2CA2C08C-F248-11E8-B48F-1D18A9856A87
last_name: Kniely
orcid: 0000-0001-5645-4333
- first_name: Alexander
full_name: Mielke, Alexander
last_name: Mielke
citation:
ama: Fischer JL, Hopf K, Kniely M, Mielke A. Global existence analysis of energy-reaction-diffusion
systems. SIAM Journal on Mathematical Analysis. 2022;54(1):220-267. doi:10.1137/20M1387237
apa: Fischer, J. L., Hopf, K., Kniely, M., & Mielke, A. (2022). Global existence
analysis of energy-reaction-diffusion systems. SIAM Journal on Mathematical
Analysis. Society for Industrial and Applied Mathematics. https://doi.org/10.1137/20M1387237
chicago: Fischer, Julian L, Katharina Hopf, Michael Kniely, and Alexander Mielke.
“Global Existence Analysis of Energy-Reaction-Diffusion Systems.” SIAM Journal
on Mathematical Analysis. Society for Industrial and Applied Mathematics,
2022. https://doi.org/10.1137/20M1387237.
ieee: J. L. Fischer, K. Hopf, M. Kniely, and A. Mielke, “Global existence analysis
of energy-reaction-diffusion systems,” SIAM Journal on Mathematical Analysis,
vol. 54, no. 1. Society for Industrial and Applied Mathematics, pp. 220–267, 2022.
ista: Fischer JL, Hopf K, Kniely M, Mielke A. 2022. Global existence analysis of
energy-reaction-diffusion systems. SIAM Journal on Mathematical Analysis. 54(1),
220–267.
mla: Fischer, Julian L., et al. “Global Existence Analysis of Energy-Reaction-Diffusion
Systems.” SIAM Journal on Mathematical Analysis, vol. 54, no. 1, Society
for Industrial and Applied Mathematics, 2022, pp. 220–67, doi:10.1137/20M1387237.
short: J.L. Fischer, K. Hopf, M. Kniely, A. Mielke, SIAM Journal on Mathematical
Analysis 54 (2022) 220–267.
date_created: 2021-12-16T12:08:56Z
date_published: 2022-01-04T00:00:00Z
date_updated: 2023-08-02T13:37:03Z
day: '04'
department:
- _id: JuFi
doi: 10.1137/20M1387237
external_id:
arxiv:
- '2012.03792 '
isi:
- '000762768000006'
intvolume: ' 54'
isi: 1
issue: '1'
keyword:
- Energy-Reaction-Diffusion Systems
- Cross Diffusion
- Global-In-Time Existence of Weak/Renormalised Solutions
- Entropy Method
- Onsager System
- Soret/Dufour Effect
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/2012.03792
month: '01'
oa: 1
oa_version: Preprint
page: 220-267
publication: SIAM Journal on Mathematical Analysis
publication_identifier:
issn:
- 0036-1410
publication_status: published
publisher: Society for Industrial and Applied Mathematics
quality_controlled: '1'
scopus_import: '1'
status: public
title: Global existence analysis of energy-reaction-diffusion systems
type: journal_article
user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
volume: 54
year: '2022'
...
---
_id: '10548'
abstract:
- lang: eng
text: "Consider a linear elliptic partial differential equation in divergence form
with a random coefficient field. The solution operator displays fluctuations around
its expectation. The recently developed pathwise theory of fluctuations in stochastic
homogenization reduces the characterization of these fluctuations to those of
the so-called standard homogenization commutator. In this contribution, we investigate
the scaling limit of this key quantity: starting\r\nfrom a Gaussian-like coefficient
field with possibly strong correlations, we establish the convergence of the rescaled
commutator to a fractional Gaussian field, depending on the decay of correlations
of the coefficient field, and we\r\ninvestigate the (non)degeneracy of the limit.
This extends to general dimension $d\\ge1$ previous results so far limited to
dimension $d=1$, and to the continuum setting with strong correlations recent
results in the discrete iid case."
acknowledgement: The authors thank Ivan Nourdin and Felix Otto for inspiring discussions.
The work of MD is financially supported by the CNRS-Momentum program. Financial
support of AG is acknowledged from the European Research Council under the European
Community’s Seventh Framework Programme (FP7/2014-2019 Grant Agreement QUANTHOM
335410).
article_processing_charge: No
article_type: original
arxiv: 1
author:
- first_name: Mitia
full_name: Duerinckx, Mitia
last_name: Duerinckx
- first_name: Julian L
full_name: Fischer, Julian L
id: 2C12A0B0-F248-11E8-B48F-1D18A9856A87
last_name: Fischer
orcid: 0000-0002-0479-558X
- first_name: Antoine
full_name: Gloria, Antoine
last_name: Gloria
citation:
ama: Duerinckx M, Fischer JL, Gloria A. Scaling limit of the homogenization commutator
for Gaussian coefficient fields. Annals of applied probability. 2022;32(2):1179-1209.
doi:10.1214/21-AAP1705
apa: Duerinckx, M., Fischer, J. L., & Gloria, A. (2022). Scaling limit of the
homogenization commutator for Gaussian coefficient fields. Annals of Applied
Probability. Institute of Mathematical Statistics. https://doi.org/10.1214/21-AAP1705
chicago: Duerinckx, Mitia, Julian L Fischer, and Antoine Gloria. “Scaling Limit
of the Homogenization Commutator for Gaussian Coefficient Fields.” Annals
of Applied Probability. Institute of Mathematical Statistics, 2022. https://doi.org/10.1214/21-AAP1705.
ieee: M. Duerinckx, J. L. Fischer, and A. Gloria, “Scaling limit of the homogenization
commutator for Gaussian coefficient fields,” Annals of applied probability,
vol. 32, no. 2. Institute of Mathematical Statistics, pp. 1179–1209, 2022.
ista: Duerinckx M, Fischer JL, Gloria A. 2022. Scaling limit of the homogenization
commutator for Gaussian coefficient fields. Annals of applied probability. 32(2),
1179–1209.
mla: Duerinckx, Mitia, et al. “Scaling Limit of the Homogenization Commutator for
Gaussian Coefficient Fields.” Annals of Applied Probability, vol. 32,
no. 2, Institute of Mathematical Statistics, 2022, pp. 1179–209, doi:10.1214/21-AAP1705.
short: M. Duerinckx, J.L. Fischer, A. Gloria, Annals of Applied Probability 32 (2022)
1179–1209.
corr_author: '1'
date_created: 2021-12-16T12:10:16Z
date_published: 2022-04-28T00:00:00Z
date_updated: 2024-10-09T21:01:17Z
day: '28'
department:
- _id: JuFi
doi: 10.1214/21-AAP1705
external_id:
arxiv:
- '1910.04088'
isi:
- '000791003700011'
intvolume: ' 32'
isi: 1
issue: '2'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/1910.04088
month: '04'
oa: 1
oa_version: Preprint
page: 1179-1209
publication: Annals of applied probability
publication_identifier:
issn:
- 1050-5164
publication_status: published
publisher: Institute of Mathematical Statistics
quality_controlled: '1'
scopus_import: '1'
status: public
title: Scaling limit of the homogenization commutator for Gaussian coefficient fields
type: journal_article
user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
volume: 32
year: '2022'
...
---
_id: '17057'
abstract:
- lang: eng
text: Martin Loose studied chemistry at the University of Heidelberg, Germany. He
then joined Petra Schwille's group at the Max Planck Institute of Molecular Cell
Biology and Genetics in Dresden, where he obtained his PhD degree in 2010 for
work on self-organization and pattern formation in the bacterial Min protein system.
He then moved to Tim Mitchison's lab at Harvard Medical School, Boston, USA for
his postdoc, funded by Human Frontier Science Program (HSFP) and European Molecular
Biology Organization (EMBO) long-term fellowships; there, he discovered that the
bacterial cell division proteins FtsA and FtsZ self-organize into dynamic cytoskeletal
patterns. Martin established his independent research group at the Institute of
Science and Technology (IST) Austria in 2015, supported by an European Research
Council (ERC) starting grant and HFSP Young Investigator Grant. His lab studies
the self-organization of bacterial cell division and small GTPase networks.
article_number: jcs259715
article_processing_charge: No
author:
- first_name: Martin
full_name: Loose, Martin
id: 462D4284-F248-11E8-B48F-1D18A9856A87
last_name: Loose
orcid: 0000-0001-7309-9724
citation:
ama: Loose M. Cell Scientist to Watch – Martin Loose. Vol 135. The Company
of Biologists; 2022. doi:10.1242/jcs.259715
apa: Loose, M. (2022). Cell scientist to watch – Martin Loose. Journal
of Cell Science (Vol. 135). The Company of Biologists. https://doi.org/10.1242/jcs.259715
chicago: Loose, Martin. Cell Scientist to Watch – Martin Loose. Journal
of Cell Science. Vol. 135. The Company of Biologists, 2022. https://doi.org/10.1242/jcs.259715.
ieee: M. Loose, Cell scientist to watch – Martin Loose, vol. 135, no. 2.
The Company of Biologists, 2022.
ista: Loose M. 2022. Cell scientist to watch – Martin Loose, The Company of Biologists,p.
mla: Loose, Martin. “Cell Scientist to Watch – Martin Loose.” Journal of Cell
Science, vol. 135, no. 2, jcs259715, The Company of Biologists, 2022, doi:10.1242/jcs.259715.
short: M. Loose, Cell Scientist to Watch – Martin Loose, The Company of Biologists,
2022.
date_created: 2024-05-28T13:28:30Z
date_published: 2022-01-19T00:00:00Z
date_updated: 2024-06-04T09:51:20Z
day: '19'
department:
- _id: MaLo
doi: 10.1242/jcs.259715
external_id:
isi:
- '000762665200015'
intvolume: ' 135'
isi: 1
issue: '2'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.1242/jcs.259715
month: '01'
oa: 1
oa_version: Published Version
publication: Journal of Cell Science
publication_identifier:
eissn:
- 1477-9137
issn:
- 0021-9533
publication_status: published
publisher: The Company of Biologists
quality_controlled: '1'
status: public
title: Cell scientist to watch – Martin Loose
type: other_academic_publication
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 135
year: '2022'
...
---
_id: '17058'
abstract:
- lang: eng
text: We compare the Manin-type conjecture for Campana points recently formulated
by Pieropan, Smeets, Tanimoto and Várilly-Alvarado with an alternative prediction
of Browning and Van Valckenborgh in the special case of the orbifold (P1,D), where
D=1/2[0]+1/2[1]+1/2[∞]. We find that the two predicted leading constants do not
agree, and we discuss whether thin sets could explain this discrepancy. Motivated
by this, we provide a counterexample to the Manin-type conjecture for Campana
points, by considering orbifolds corresponding to squareful values of binary quadratic
forms.
article_processing_charge: No
article_type: original
arxiv: 1
author:
- first_name: Alec L
full_name: Shute, Alec L
id: 440EB050-F248-11E8-B48F-1D18A9856A87
last_name: Shute
orcid: 0000-0002-1812-2810
citation:
ama: Shute AL. On the leading constant in the Manin-type conjecture for Campana
points. Acta Arithmetica. 2022;204(4):317-346. doi:10.4064/aa210430-1-7
apa: Shute, A. L. (2022). On the leading constant in the Manin-type conjecture for
Campana points. Acta Arithmetica. Institute of Mathematics. https://doi.org/10.4064/aa210430-1-7
chicago: Shute, Alec L. “On the Leading Constant in the Manin-Type Conjecture for
Campana Points.” Acta Arithmetica. Institute of Mathematics, 2022. https://doi.org/10.4064/aa210430-1-7.
ieee: A. L. Shute, “On the leading constant in the Manin-type conjecture for Campana
points,” Acta Arithmetica, vol. 204, no. 4. Institute of Mathematics, pp.
317–346, 2022.
ista: Shute AL. 2022. On the leading constant in the Manin-type conjecture for Campana
points. Acta Arithmetica. 204(4), 317–346.
mla: Shute, Alec L. “On the Leading Constant in the Manin-Type Conjecture for Campana
Points.” Acta Arithmetica, vol. 204, no. 4, Institute of Mathematics, 2022,
pp. 317–46, doi:10.4064/aa210430-1-7.
short: A.L. Shute, Acta Arithmetica 204 (2022) 317–346.
corr_author: '1'
date_created: 2024-05-28T13:39:26Z
date_published: 2022-08-22T00:00:00Z
date_updated: 2025-09-10T09:57:03Z
day: '22'
department:
- _id: TiBr
doi: 10.4064/aa210430-1-7
external_id:
arxiv:
- '2104.14946'
isi:
- '000844789100001'
intvolume: ' 204'
isi: 1
issue: '4'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.48550/arXiv.2104.14946
month: '08'
oa: 1
oa_version: Preprint
page: 317-346
publication: Acta Arithmetica
publication_identifier:
eissn:
- 1730-6264
issn:
- 0065-1036
publication_status: published
publisher: Institute of Mathematics
quality_controlled: '1'
related_material:
record:
- id: '12077'
relation: earlier_version
status: public
scopus_import: '1'
status: public
title: On the leading constant in the Manin-type conjecture for Campana points
type: journal_article
user_id: 317138e5-6ab7-11ef-aa6d-ffef3953e345
volume: 204
year: '2022'
...
---
_id: '17059'
abstract:
- lang: eng
text: The recent focus on the efficiency of deep neural networks (DNNs) has led
to significant work on model compression approaches, of which weight pruning is
one of the most popular. At the same time, there is rapidly-growing computational
support for efficiently executing the unstructured-sparse models obtained via
pruning. Yet, most existing pruning methods minimize just the number of remaining
weights, i.e. the size of the model, rather than optimizing for inference time.
We address this gap by introducing SPDY, a new compression method which automatically
determines layer-wise sparsity targets achieving a desired inference speedup on
a given system, while minimizing accuracy loss. SPDY is the composition of two
new techniques. The first is an efficient and general dynamic programming algorithm
for solving constrained layer-wise compression problems, given a set of layer-wise
error scores. The second technique is a local search procedure for automatically
determining such scores in an accurate and robust manner. Experiments across popular
vision and language models show that SPDY guarantees speedups while recovering
higher accuracy relative to existing strategies, both for one-shot and gradual
pruning scenarios, and is compatible with most existing pruning approaches. We
also extend our approach to the recently-proposed task of pruning with very little
data, where we achieve the best known accuracy recovery when pruning to the GPU-supported
2:4 sparsity pattern.
acknowledgement: "We gratefully acknowledge funding from the European Research Council
(ERC) under the European Union’s Horizon 2020 programme (grant agreement No 805223
ScaleML),\r\nas well as computational support from AWS EC2. We thank Eldar Kurtic
for code and hyper-parameters for BERT pruning, and the Neural Magic Team, notably
Michael Goin and\r\nMark Kurtz, for support with their software."
alternative_title:
- PMLR
article_processing_charge: Yes
author:
- first_name: Elias
full_name: Frantar, Elias
id: 09a8f98d-ec99-11ea-ae11-c063a7b7fe5f
last_name: Frantar
- first_name: Dan-Adrian
full_name: Alistarh, Dan-Adrian
id: 4A899BFC-F248-11E8-B48F-1D18A9856A87
last_name: Alistarh
orcid: 0000-0003-3650-940X
citation:
ama: 'Frantar E, Alistarh D-A. SPDY: Accurate pruning with speedup guarantees. In:
39th International Conference on Machine Learning. Vol 162. ML Research
Press; 2022:6726-6743.'
apa: 'Frantar, E., & Alistarh, D.-A. (2022). SPDY: Accurate pruning with speedup
guarantees. In 39th International Conference on Machine Learning (Vol.
162, pp. 6726–6743). Baltimore, MD, United States: ML Research Press.'
chicago: 'Frantar, Elias, and Dan-Adrian Alistarh. “SPDY: Accurate Pruning with
Speedup Guarantees.” In 39th International Conference on Machine Learning,
162:6726–43. ML Research Press, 2022.'
ieee: 'E. Frantar and D.-A. Alistarh, “SPDY: Accurate pruning with speedup guarantees,”
in 39th International Conference on Machine Learning, Baltimore, MD, United
States, 2022, vol. 162, pp. 6726–6743.'
ista: 'Frantar E, Alistarh D-A. 2022. SPDY: Accurate pruning with speedup guarantees.
39th International Conference on Machine Learning. ICML: International Conference
on Machine Learning, PMLR, vol. 162, 6726–6743.'
mla: 'Frantar, Elias, and Dan-Adrian Alistarh. “SPDY: Accurate Pruning with Speedup
Guarantees.” 39th International Conference on Machine Learning, vol. 162,
ML Research Press, 2022, pp. 6726–43.'
short: E. Frantar, D.-A. Alistarh, in:, 39th International Conference on Machine
Learning, ML Research Press, 2022, pp. 6726–6743.
conference:
end_date: 2022-07-23
location: Baltimore, MD, United States
name: 'ICML: International Conference on Machine Learning'
start_date: 2022-07-17
corr_author: '1'
date_created: 2024-05-28T13:45:20Z
date_published: 2022-07-20T00:00:00Z
date_updated: 2025-04-14T07:49:14Z
day: '20'
ddc:
- '000'
department:
- _id: DaAl
ec_funded: 1
external_id:
isi:
- '000922378801029'
file:
- access_level: open_access
checksum: 5179a1e4dfc0fbfab6674907299e414a
content_type: application/pdf
creator: dernst
date_created: 2024-08-19T06:54:41Z
date_updated: 2024-08-19T06:54:41Z
file_id: '17440'
file_name: 2022_PMLR_Frantar.pdf
file_size: 615916
relation: main_file
success: 1
file_date_updated: 2024-08-19T06:54:41Z
has_accepted_license: '1'
intvolume: ' 162'
isi: 1
language:
- iso: eng
month: '07'
oa: 1
oa_version: Published Version
page: 6726-6743
project:
- _id: 268A44D6-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '805223'
name: Elastic Coordination for Scalable Machine Learning
publication: 39th International Conference on Machine Learning
publication_status: published
publisher: ML Research Press
quality_controlled: '1'
scopus_import: '1'
status: public
title: 'SPDY: Accurate pruning with speedup guarantees'
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: conference
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 162
year: '2022'
...
---
_id: '17060'
abstract:
- lang: eng
text: "Payment channel networks (PCNs) are one of the most prominent solutions to
the limited transaction throughput of blockchains. Nevertheless, PCNs suffer themselves
from a throughput limitation due to the capital constraints of their channels.
A similar dependence on high capital is also found in inter-bank payment settlements,
where the so-called netting technique is used to mitigate liquidity demands.\r\nIn
this work, we alleviate this limitation by introducing the notion of transaction
aggregation: instead of executing transactions sequentially through a PCN, we
enable senders to aggregate multiple transactions and execute them simultaneously
to benefit from several amounts that may \"cancel out\". Two direct advantages
of our proposal is the decrease in intermediary fees paid by senders as well as
the obfuscation of the transaction data from the intermediaries.\r\nWe formulate
the transaction aggregation as a computational problem, a generalization of the
Bank Clearing Problem. We present a generic framework for the transaction aggregation
execution, and thereafter we propose Wiser as an implementation of this framework
in a specific hub-based setting. To overcome the NP-hardness of the transaction
aggregation problem, in Wiser we propose a fixed-parameter linear algorithm for
a special case of transaction aggregation as well as the Bank Clearing Problem.
Wiser can also be seen as a modern variant of the Hawala money transfer system,
as well as a decentralized implementation of the overseas remittance service of
Wise."
acknowledgement: "This work was supported partially by ERC Starting Grant QIP–805241,
by the Vienna business agency (Wirtschaftsagentur) through the Vienna Cybersecurity
and Privacy Research Center\r\n(ViSP) and by the Austrian Science Fund (FWF) project
I 4800-N (ADVISE).\r\nThe first author would like to thank Daniel Dadush for suggesting
the use of discrepancy techniques to solve the transaction aggregation problem."
article_processing_charge: Yes (in subscription journal)
arxiv: 1
author:
- first_name: Samarth
full_name: Tiwari, Samarth
last_name: Tiwari
- first_name: Michelle X
full_name: Yeo, Michelle X
id: 2D82B818-F248-11E8-B48F-1D18A9856A87
last_name: Yeo
orcid: 0009-0001-3676-4809
- first_name: Zeta
full_name: Avarikioti, Zeta
last_name: Avarikioti
- first_name: Iosif
full_name: Salem, Iosif
last_name: Salem
- first_name: Krzysztof Z
full_name: Pietrzak, Krzysztof Z
id: 3E04A7AA-F248-11E8-B48F-1D18A9856A87
last_name: Pietrzak
orcid: 0000-0002-9139-1654
- first_name: Stefan
full_name: Schmid, Stefan
last_name: Schmid
citation:
ama: 'Tiwari S, Yeo MX, Avarikioti Z, Salem I, Pietrzak KZ, Schmid S. Wiser: Increasing
throughput in payment channel networks with transaction aggregation. In: Proceedings
of the 4th ACM Conference on Advances in Financial Technologies. Association
for Computing Machinery; 2022:217-231. doi:10.1145/3558535.3559775'
apa: 'Tiwari, S., Yeo, M. X., Avarikioti, Z., Salem, I., Pietrzak, K. Z., &
Schmid, S. (2022). Wiser: Increasing throughput in payment channel networks with
transaction aggregation. In Proceedings of the 4th ACM Conference on Advances
in Financial Technologies (pp. 217–231). Cambridge, MA, United States: Association
for Computing Machinery. https://doi.org/10.1145/3558535.3559775'
chicago: 'Tiwari, Samarth, Michelle X Yeo, Zeta Avarikioti, Iosif Salem, Krzysztof
Z Pietrzak, and Stefan Schmid. “Wiser: Increasing Throughput in Payment Channel
Networks with Transaction Aggregation.” In Proceedings of the 4th ACM Conference
on Advances in Financial Technologies, 217–31. Association for Computing Machinery,
2022. https://doi.org/10.1145/3558535.3559775.'
ieee: 'S. Tiwari, M. X. Yeo, Z. Avarikioti, I. Salem, K. Z. Pietrzak, and S. Schmid,
“Wiser: Increasing throughput in payment channel networks with transaction aggregation,”
in Proceedings of the 4th ACM Conference on Advances in Financial Technologies,
Cambridge, MA, United States, 2022, pp. 217–231.'
ista: 'Tiwari S, Yeo MX, Avarikioti Z, Salem I, Pietrzak KZ, Schmid S. 2022. Wiser:
Increasing throughput in payment channel networks with transaction aggregation.
Proceedings of the 4th ACM Conference on Advances in Financial Technologies. AFT:
Conference on Advances in Financial Technologies, 217–231.'
mla: 'Tiwari, Samarth, et al. “Wiser: Increasing Throughput in Payment Channel Networks
with Transaction Aggregation.” Proceedings of the 4th ACM Conference on Advances
in Financial Technologies, Association for Computing Machinery, 2022, pp.
217–31, doi:10.1145/3558535.3559775.'
short: S. Tiwari, M.X. Yeo, Z. Avarikioti, I. Salem, K.Z. Pietrzak, S. Schmid, in:,
Proceedings of the 4th ACM Conference on Advances in Financial Technologies, Association
for Computing Machinery, 2022, pp. 217–231.
conference:
end_date: 2022-09-21
location: Cambridge, MA, United States
name: 'AFT: Conference on Advances in Financial Technologies'
start_date: 2022-09-19
date_created: 2024-05-28T13:58:35Z
date_published: 2022-09-19T00:00:00Z
date_updated: 2025-09-10T09:57:48Z
day: '19'
ddc:
- '000'
department:
- _id: KrPi
doi: 10.1145/3558535.3559775
external_id:
arxiv:
- '2205.11597'
isi:
- '001041852800015'
file:
- access_level: open_access
checksum: 54a7d405f8e57dba24728599ca63818c
content_type: application/pdf
creator: dernst
date_created: 2024-08-19T06:45:21Z
date_updated: 2024-08-19T06:45:21Z
file_id: '17439'
file_name: 2022_AFT_Tiwari.pdf
file_size: 574728
relation: main_file
success: 1
file_date_updated: 2024-08-19T06:45:21Z
has_accepted_license: '1'
isi: 1
language:
- iso: eng
month: '09'
oa: 1
oa_version: Published Version
page: 217-231
publication: Proceedings of the 4th ACM Conference on Advances in Financial Technologies
publication_identifier:
isbn:
- '9781450398619'
publication_status: published
publisher: Association for Computing Machinery
quality_controlled: '1'
scopus_import: '1'
status: public
title: 'Wiser: Increasing throughput in payment channel networks with transaction
aggregation'
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
year: '2022'
...
---
_id: '17061'
abstract:
- lang: eng
text: Across many domains of interaction, both natural and artificial, individuals
use past experience to shape future behaviors. The results of such learning processes
depend on what individuals wish to maximize. A natural objective is one’s own
success. However, when two such “selfish” learners interact with each other, the
outcome can be detrimental to both, especially when there are conflicts of interest.
Here, we explore how a learner can align incentives with a selfish opponent. Moreover,
we consider the dynamics that arise when learning rules themselves are subject
to evolutionary pressure. By combining extensive simulations and analytical techniques,
we demonstrate that selfish learning is unstable in most classical two-player
repeated games. If evolution operates on the level of long-run payoffs, selection
instead favors learning rules that incorporate social (other-regarding) preferences.
To further corroborate these results, we analyze data from a repeated prisoner’s
dilemma experiment. We find that selfish learning is insufficient to explain human
behavior when there is a trade-off between payoff maximization and fairness.
acknowledgement: The authors are grateful to Jörg Oechssler for many helpful comments.
A.M. was supported by a Simons Postdoctoral Fellowship (Math+X) at the University
of Pennsylvania; K.C. was supported by the European Research Council Consolidator
Grant 863818 (ForM-SMArt); and C.H. was supported by the European Research Council
Starting Grant 850529 (E-DIRECT).
article_number: pgac141
article_processing_charge: Yes
article_type: original
arxiv: 1
author:
- first_name: Alex
full_name: McAvoy, Alex
last_name: McAvoy
- first_name: Julian
full_name: Kates-Harbeck, Julian
last_name: Kates-Harbeck
- first_name: Krishnendu
full_name: Chatterjee, Krishnendu
id: 2E5DCA20-F248-11E8-B48F-1D18A9856A87
last_name: Chatterjee
orcid: 0000-0002-4561-241X
- first_name: Christian
full_name: Hilbe, Christian
id: 2FDF8F3C-F248-11E8-B48F-1D18A9856A87
last_name: Hilbe
orcid: 0000-0001-5116-955X
citation:
ama: McAvoy A, Kates-Harbeck J, Chatterjee K, Hilbe C. Evolutionary instability
of selfish learning in repeated games. PNAS Nexus. 2022;1(4). doi:10.1093/pnasnexus/pgac141
apa: McAvoy, A., Kates-Harbeck, J., Chatterjee, K., & Hilbe, C. (2022). Evolutionary
instability of selfish learning in repeated games. PNAS Nexus. Oxford University
Press. https://doi.org/10.1093/pnasnexus/pgac141
chicago: McAvoy, Alex, Julian Kates-Harbeck, Krishnendu Chatterjee, and Christian
Hilbe. “Evolutionary Instability of Selfish Learning in Repeated Games.” PNAS
Nexus. Oxford University Press, 2022. https://doi.org/10.1093/pnasnexus/pgac141.
ieee: A. McAvoy, J. Kates-Harbeck, K. Chatterjee, and C. Hilbe, “Evolutionary instability
of selfish learning in repeated games,” PNAS Nexus, vol. 1, no. 4. Oxford
University Press, 2022.
ista: McAvoy A, Kates-Harbeck J, Chatterjee K, Hilbe C. 2022. Evolutionary instability
of selfish learning in repeated games. PNAS Nexus. 1(4), pgac141.
mla: McAvoy, Alex, et al. “Evolutionary Instability of Selfish Learning in Repeated
Games.” PNAS Nexus, vol. 1, no. 4, pgac141, Oxford University Press, 2022,
doi:10.1093/pnasnexus/pgac141.
short: A. McAvoy, J. Kates-Harbeck, K. Chatterjee, C. Hilbe, PNAS Nexus 1 (2022).
date_created: 2024-05-28T14:23:12Z
date_published: 2022-09-01T00:00:00Z
date_updated: 2025-06-11T13:54:20Z
day: '01'
ddc:
- '000'
department:
- _id: KrCh
doi: 10.1093/pnasnexus/pgac141
ec_funded: 1
external_id:
arxiv:
- '2105.06199'
pmid:
- '36714856'
file:
- access_level: open_access
checksum: 79a8e3e4be7e8a2b407b4efddd65f3f3
content_type: application/pdf
creator: dernst
date_created: 2024-08-06T07:33:30Z
date_updated: 2024-08-06T07:33:30Z
file_id: '17400'
file_name: 2022_PNASNexus_McAvoy.pdf
file_size: 2410962
relation: main_file
success: 1
file_date_updated: 2024-08-06T07:33:30Z
has_accepted_license: '1'
intvolume: ' 1'
issue: '4'
language:
- iso: eng
month: '09'
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'
publication: PNAS Nexus
publication_identifier:
issn:
- 2752-6542
publication_status: published
publisher: Oxford University Press
quality_controlled: '1'
related_material:
link:
- relation: software
url: https://github.com/alexmcavoy/fmtl/
scopus_import: '1'
status: public
title: Evolutionary instability of selfish learning in repeated games
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 1
year: '2022'
...
---
_id: '17062'
acknowledgement: "Werner Siemens Foundation\r\nEuropean Union's Horizon 2020\r\nFWF
“Lise Meitner Fellowship”"
article_number: '159'
article_processing_charge: No
author:
- first_name: Maria
full_name: Ibáñez, Maria
id: 43C61214-F248-11E8-B48F-1D18A9856A87
last_name: Ibáñez
orcid: 0000-0001-5013-2843
- first_name: Yu
full_name: Liu, Yu
id: 2A70014E-F248-11E8-B48F-1D18A9856A87
last_name: Liu
orcid: 0000-0001-7313-6740
- first_name: Mariano
full_name: Calcabrini, Mariano
id: 45D7531A-F248-11E8-B48F-1D18A9856A87
last_name: Calcabrini
orcid: 0000-0003-4566-5877
citation:
ama: 'Ibáñez M, Liu Y, Calcabrini M. The importance of surface adsorbates in solution-processed
thermoelectric materials. In: Proceedings of the NanoGe Spring Meeting 2022.
Fundació Scito; 2022. doi:10.29363/nanoge.nsm.2022.159'
apa: 'Ibáñez, M., Liu, Y., & Calcabrini, M. (2022). The importance of surface
adsorbates in solution-processed thermoelectric materials. In Proceedings of
the nanoGe Spring Meeting 2022. Spain/Virtual: Fundació Scito. https://doi.org/10.29363/nanoge.nsm.2022.159'
chicago: Ibáñez, Maria, Yu Liu, and Mariano Calcabrini. “The Importance of Surface
Adsorbates in Solution-Processed Thermoelectric Materials.” In Proceedings
of the NanoGe Spring Meeting 2022. Fundació Scito, 2022. https://doi.org/10.29363/nanoge.nsm.2022.159.
ieee: M. Ibáñez, Y. Liu, and M. Calcabrini, “The importance of surface adsorbates
in solution-processed thermoelectric materials,” in Proceedings of the nanoGe
Spring Meeting 2022, Spain/Virtual, 2022.
ista: 'Ibáñez M, Liu Y, Calcabrini M. 2022. The importance of surface adsorbates
in solution-processed thermoelectric materials. Proceedings of the nanoGe Spring
Meeting 2022. SNI: Semiconductor Nanocrystals, 159.'
mla: Ibáñez, Maria, et al. “The Importance of Surface Adsorbates in Solution-Processed
Thermoelectric Materials.” Proceedings of the NanoGe Spring Meeting 2022,
159, Fundació Scito, 2022, doi:10.29363/nanoge.nsm.2022.159.
short: M. Ibáñez, Y. Liu, M. Calcabrini, in:, Proceedings of the NanoGe Spring Meeting
2022, Fundació Scito, 2022.
conference:
end_date: 2022-03-11
location: Spain/Virtual
name: 'SNI: Semiconductor Nanocrystals'
start_date: 2022-03-07
corr_author: '1'
date_created: 2024-05-29T05:38:47Z
date_published: 2022-02-07T00:00:00Z
date_updated: 2025-04-15T06:54:34Z
day: '07'
department:
- _id: MaIb
doi: 10.29363/nanoge.nsm.2022.159
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.29363/nanoge.nsm.2022.159
month: '02'
oa: 1
oa_version: Published Version
project:
- _id: 9B8F7476-BA93-11EA-9121-9846C619BF3A
name: 'HighTE: The Werner Siemens Laboratory for the High Throughput Discovery of
Semiconductors for Waste Heat Recovery'
publication: Proceedings of the nanoGe Spring Meeting 2022
publication_status: published
publisher: Fundació Scito
quality_controlled: '1'
related_material:
record:
- id: '10123'
relation: earlier_version
status: public
status: public
title: The importance of surface adsorbates in solution-processed thermoelectric materials
type: conference_abstract
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
year: '2022'
...
---
_id: '17063'
abstract:
- lang: eng
text: This workshop continued a biannual series of workshops at Oberwolfach on dynamical
systems that started with a meeting organized by Moser and Zehnder in 1981. Workshops
in this series focus on new results and developments in dynamical systems and
related areas of mathematics, with symplectic geometry playing an important role
in recent years in connection with Hamiltonian dynamics. In this year special
emphasis was placed on various kinds of spectra (in contact geometry, in Riemannian
geometry, in dynamical systems and in symplectic topology) and their applications
to dynamics.
article_processing_charge: No
article_type: original
author:
- first_name: Marie-Claude
full_name: Arnaud, Marie-Claude
last_name: Arnaud
- first_name: Helmut W.
full_name: Hofer, Helmut W.
last_name: Hofer
- first_name: Michael
full_name: Hutchings, Michael
last_name: Hutchings
- first_name: Vadim
full_name: Kaloshin, Vadim
id: FE553552-CDE8-11E9-B324-C0EBE5697425
last_name: Kaloshin
orcid: 0000-0002-6051-2628
citation:
ama: Arnaud M-C, Hofer HW, Hutchings M, Kaloshin V. Dynamische Systeme. Oberwolfach
Reports. 2022;18(3):1735-1803. doi:10.4171/owr/2021/33
apa: Arnaud, M.-C., Hofer, H. W., Hutchings, M., & Kaloshin, V. (2022). Dynamische
Systeme. Oberwolfach Reports. European Mathematical Society. https://doi.org/10.4171/owr/2021/33
chicago: Arnaud, Marie-Claude, Helmut W. Hofer, Michael Hutchings, and Vadim Kaloshin.
“Dynamische Systeme.” Oberwolfach Reports. European Mathematical Society,
2022. https://doi.org/10.4171/owr/2021/33.
ieee: M.-C. Arnaud, H. W. Hofer, M. Hutchings, and V. Kaloshin, “Dynamische Systeme,”
Oberwolfach Reports, vol. 18, no. 3. European Mathematical Society, pp.
1735–1803, 2022.
ista: Arnaud M-C, Hofer HW, Hutchings M, Kaloshin V. 2022. Dynamische Systeme. Oberwolfach
Reports. 18(3), 1735–1803.
mla: Arnaud, Marie-Claude, et al. “Dynamische Systeme.” Oberwolfach Reports,
vol. 18, no. 3, European Mathematical Society, 2022, pp. 1735–803, doi:10.4171/owr/2021/33.
short: M.-C. Arnaud, H.W. Hofer, M. Hutchings, V. Kaloshin, Oberwolfach Reports
18 (2022) 1735–1803.
corr_author: '1'
date_created: 2024-05-29T06:01:19Z
date_published: 2022-11-26T00:00:00Z
date_updated: 2024-08-06T07:28:50Z
day: '26'
department:
- _id: VaKa
doi: 10.4171/owr/2021/33
intvolume: ' 18'
issue: '3'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://www.doi.org/10.4171/OWR/2021/33
month: '11'
oa: 1
oa_version: Published Version
page: 1735-1803
publication: Oberwolfach Reports
publication_identifier:
eissn:
- 1660-8941
issn:
- 1660-8933
publication_status: published
publisher: European Mathematical Society
quality_controlled: '1'
scopus_import: '1'
status: public
title: Dynamische Systeme
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 18
year: '2022'
...
---
_id: '17065'
abstract:
- lang: eng
text: Past work on optimizing fabrication plans given a carpentry design can provide
Pareto-optimal plans trading off between material waste, fabrication time, precision,
and other considerations. However, when developing fabrication plans, experts
rarely restrict to a single design, instead considering families of design variations,
sometimes adjusting designs to simplify fabrication. Jointly exploring the design
and fabrication plan spaces for each design is intractable using current techniques.
We present a new approach to jointly optimize design and fabrication plans for
carpentered objects. To make this bi-level optimization tractable, we adapt recent
work from program synthesis based on equality graphs (e-graphs), which encode
sets of equivalent programs. Our insight is that subproblems within our bi-level
problem share significant substructures. By representing both designs and fabrication
plans in a new bag of parts (BOP) e-graph, we amortize the cost of optimizing
design components shared among multiple candidates. Even using BOP e-graphs, the
optimization space grows quickly in practice. Hence, we also show how a feedback-guided
search strategy dubbed Iterative Contraction and Expansion on E-graphs (ICEE)
can keep the size of the e-graph manageable and direct the search towards promising
candidates. We illustrate the advantages of our pipeline through examples from
the carpentry domain.
acknowledgement: The authors would like to thank anonymous reviewers for their helpful
feedback; Haomiao Wu for her contribution to the algorithm development in the early
stage of the project; Elias Baldwin, David Tsay, Alexander Lefort, and Qiyang Tan
for helping the experiments.
article_number: '32'
article_processing_charge: No
article_type: original
arxiv: 1
author:
- first_name: Haisen
full_name: Zhao, Haisen
id: fb7f793a-80d1-11eb-8869-d56e5b2a8ff4
last_name: Zhao
orcid: 0000-0002-6389-1045
- first_name: Max
full_name: Willsey, Max
last_name: Willsey
- first_name: Amy
full_name: Zhu, Amy
last_name: Zhu
- first_name: Chandrakana
full_name: Nandi, Chandrakana
last_name: Nandi
- first_name: Zachary
full_name: Tatlock, Zachary
last_name: Tatlock
- first_name: Justin
full_name: Solomon, Justin
last_name: Solomon
- first_name: Adriana
full_name: Schulz, Adriana
last_name: Schulz
citation:
ama: Zhao H, Willsey M, Zhu A, et al. Co-optimization of design and fabrication
plans for carpentry. ACM Transactions on Graphics. 2022;41(3). doi:10.1145/3508499
apa: Zhao, H., Willsey, M., Zhu, A., Nandi, C., Tatlock, Z., Solomon, J., &
Schulz, A. (2022). Co-optimization of design and fabrication plans for carpentry.
ACM Transactions on Graphics. Association for Computing Machinery. https://doi.org/10.1145/3508499
chicago: Zhao, Haisen, Max Willsey, Amy Zhu, Chandrakana Nandi, Zachary Tatlock,
Justin Solomon, and Adriana Schulz. “Co-Optimization of Design and Fabrication
Plans for Carpentry.” ACM Transactions on Graphics. Association for Computing
Machinery, 2022. https://doi.org/10.1145/3508499.
ieee: H. Zhao et al., “Co-optimization of design and fabrication plans for
carpentry,” ACM Transactions on Graphics, vol. 41, no. 3. Association for
Computing Machinery, 2022.
ista: Zhao H, Willsey M, Zhu A, Nandi C, Tatlock Z, Solomon J, Schulz A. 2022. Co-optimization
of design and fabrication plans for carpentry. ACM Transactions on Graphics. 41(3),
32.
mla: Zhao, Haisen, et al. “Co-Optimization of Design and Fabrication Plans for Carpentry.”
ACM Transactions on Graphics, vol. 41, no. 3, 32, Association for Computing
Machinery, 2022, doi:10.1145/3508499.
short: H. Zhao, M. Willsey, A. Zhu, C. Nandi, Z. Tatlock, J. Solomon, A. Schulz,
ACM Transactions on Graphics 41 (2022).
date_created: 2024-05-29T06:09:23Z
date_published: 2022-03-09T00:00:00Z
date_updated: 2024-08-06T07:03:14Z
day: '09'
department:
- _id: BeBi
doi: 10.1145/3508499
external_id:
arxiv:
- '2107.12265'
intvolume: ' 41'
issue: '3'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.48550/arXiv.2107.12265
month: '03'
oa: 1
oa_version: Preprint
publication: ACM Transactions on Graphics
publication_identifier:
eissn:
- 1557-7368
issn:
- 0730-0301
publication_status: published
publisher: Association for Computing Machinery
quality_controlled: '1'
scopus_import: '1'
status: public
title: Co-optimization of design and fabrication plans for carpentry
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 41
year: '2022'
...
---
_id: '17066'
abstract:
- lang: eng
text: A cell’s size affects the likelihood that it will die. But how is cell size
controlled in this context and how does cell size impact commitment to the cell
death fate? We present evidence that the caspase CED-3 interacts with the RhoGEF
ECT-2 in Caenorhabditis elegans neuroblasts that generate “unwanted” cells. We
propose that this interaction promotes polar actomyosin contractility, which leads
to unequal neuroblast division and the generation of a daughter cell that is below
the critical “lethal” size threshold. Furthermore, we find that hyperactivation
of ECT-2 RhoGEF reduces the sizes of unwanted cells. Importantly, this suppresses
the “cell death abnormal” phenotype caused by the partial loss of ced-3 caspase
and therefore increases the likelihood that unwanted cells die. A putative null
mutation of ced-3 caspase, however, is not suppressed, which indicates that cell
size affects CED-3 caspase activation and/or activity. Therefore, we have uncovered
novel sequential and reciprocal interactions between the apoptosis pathway and
cell size that impact a cell’s commitment to the cell death fate.
acknowledgement: "We thank members of the Conradt, Lambie, and Hajnal labs for discussions
and comments on the manuscript. We thank M. Bauer, L. Jocham, N. Lebedeva, and L.
McGuinness for excellent technical support; A. Hajnal and T. Kohlbrenner (University
of Zurich, Switzerland) for allele zh135; and H.R. Horvitz (Massachusetts of Technology,
USA) for plasmid pET-CED-3.\r\nSome strains were provided by the Caenorhabditis
Genetics Center (CGC), which is funded by NIH Office of Research Infrastructure
Programs (https://orip.nih.gov/) (P40 OD010440). This work was supported by UCL
(Capital Equipment Fund, CEF2), a predoctoral fellowship from the China Scholarship
Council (https://www.csc.edu.cn/) to HW, a predoctoral fellowship from the Studienstiftung
des Deutschen Volkes (https://www.studienstiftung.de/) to NM, a Wolfson Fellowship
from the Royal Society (https://royalsociety.org/) to BC (RSWF\\R1\\180008), the
Deutsche Forschungsgemeinschaft (https://www.dfg.de/en/index.jsp) (ZA619/3-1 and
ZA619/3-2 to EZ; C0204/10-1 and EXC114 to BC), and the Biotechnology and Biological
Sciences Research Council (https://bbsrc.ukri.org/) (BB/V007572/1 to BC). "
article_number: e3001786
article_processing_charge: Yes
article_type: original
author:
- first_name: Aditya
full_name: Sethi, Aditya
last_name: Sethi
- first_name: Hai
full_name: Wei, Hai
last_name: Wei
- first_name: Nikhil
full_name: Mishra, Nikhil
id: C4D70E82-1081-11EA-B3ED-9A4C3DDC885E
last_name: Mishra
orcid: 0000-0002-6425-5788
- first_name: Ioannis
full_name: Segos, Ioannis
last_name: Segos
- first_name: Eric J.
full_name: Lambie, Eric J.
last_name: Lambie
- first_name: Esther
full_name: Zanin, Esther
last_name: Zanin
- first_name: Barbara
full_name: Conradt, Barbara
last_name: Conradt
citation:
ama: Sethi A, Wei H, Mishra N, et al. A caspase–RhoGEF axis contributes to the cell
size threshold for apoptotic death in developing Caenorhabditis elegans. PLOS
Biology. 2022;20(10). doi:10.1371/journal.pbio.3001786
apa: Sethi, A., Wei, H., Mishra, N., Segos, I., Lambie, E. J., Zanin, E., &
Conradt, B. (2022). A caspase–RhoGEF axis contributes to the cell size threshold
for apoptotic death in developing Caenorhabditis elegans. PLOS Biology.
Public Library of Science. https://doi.org/10.1371/journal.pbio.3001786
chicago: Sethi, Aditya, Hai Wei, Nikhil Mishra, Ioannis Segos, Eric J. Lambie, Esther
Zanin, and Barbara Conradt. “A Caspase–RhoGEF Axis Contributes to the Cell Size
Threshold for Apoptotic Death in Developing Caenorhabditis Elegans.” PLOS Biology.
Public Library of Science, 2022. https://doi.org/10.1371/journal.pbio.3001786.
ieee: A. Sethi et al., “A caspase–RhoGEF axis contributes to the cell size
threshold for apoptotic death in developing Caenorhabditis elegans,” PLOS Biology,
vol. 20, no. 10. Public Library of Science, 2022.
ista: Sethi A, Wei H, Mishra N, Segos I, Lambie EJ, Zanin E, Conradt B. 2022. A
caspase–RhoGEF axis contributes to the cell size threshold for apoptotic death
in developing Caenorhabditis elegans. PLOS Biology. 20(10), e3001786.
mla: Sethi, Aditya, et al. “A Caspase–RhoGEF Axis Contributes to the Cell Size Threshold
for Apoptotic Death in Developing Caenorhabditis Elegans.” PLOS Biology,
vol. 20, no. 10, e3001786, Public Library of Science, 2022, doi:10.1371/journal.pbio.3001786.
short: A. Sethi, H. Wei, N. Mishra, I. Segos, E.J. Lambie, E. Zanin, B. Conradt,
PLOS Biology 20 (2022).
date_created: 2024-05-29T06:09:34Z
date_published: 2022-10-06T00:00:00Z
date_updated: 2024-08-06T07:08:54Z
day: '06'
ddc:
- '570'
department:
- _id: CaHe
doi: 10.1371/journal.pbio.3001786
external_id:
pmid:
- '36201522'
file:
- access_level: open_access
checksum: a7b46460b7819c196028481cc18a7c85
content_type: application/pdf
creator: dernst
date_created: 2024-08-06T07:07:52Z
date_updated: 2024-08-06T07:07:52Z
file_id: '17399'
file_name: 2022_PlosBio_Sethi.pdf
file_size: 2515388
relation: main_file
success: 1
file_date_updated: 2024-08-06T07:07:52Z
has_accepted_license: '1'
intvolume: ' 20'
issue: '10'
language:
- iso: eng
month: '10'
oa: 1
oa_version: Published Version
pmid: 1
publication: PLOS Biology
publication_identifier:
issn:
- 1545-7885
publication_status: published
publisher: Public Library of Science
quality_controlled: '1'
scopus_import: '1'
status: public
title: A caspase–RhoGEF axis contributes to the cell size threshold for apoptotic
death in developing Caenorhabditis elegans
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: 20
year: '2022'
...
---
_id: '17067'
abstract:
- lang: eng
text: 'Human doublecortin (DCX) mutations are associated with severe brain malformations
leading to aberrant neuron positioning (heterotopia), intellectual disability
and epilepsy. DCX is a microtubule-associated protein which plays a key role during
neurodevelopment in neuronal migration and differentiation. Dcx knockout (KO)
mice show disorganized hippocampal pyramidal neurons. The CA2/CA3 pyramidal cell
layer is present as two abnormal layers and disorganized CA3 KO pyramidal neurons
are also more excitable than wild-type (WT) cells. To further identify abnormalities,
we characterized Dcx KO hippocampal neurons at subcellular, molecular and ultrastructural
levels. Severe defects were observed in mitochondria, affecting number and distribution.
Also, the Golgi apparatus was visibly abnormal, increased in volume and abnormally
organized. Transcriptome analyses from laser microdissected hippocampal tissue
at postnatal day 60 (P60) highlighted organelle abnormalities. Ultrastructural
studies of CA3 cells performed in P60 (young adult) and > 9 months (mature) tissue
showed that organelle defects are persistent throughout life. Locomotor activity
and fear memory of young and mature adults were also abnormal: Dcx KO mice consistently
performed less well than WT littermates, with defects becoming more severe with
age. Thus, we show that disruption of a neurodevelopmentally-regulated gene can
lead to permanent organelle anomalies contributing to abnormal adult behavior.'
acknowledgement: "We thank Sylvie Dumont for initial aid with laser microdissection
and G. Martinez-Lorenzana for experimental help with electron microscopy. We thank
the animal experimentation facility and cellular and tissue imaging platforms at
the Institut du Fer à Moulin, supported also by the Région Ile de France and the
FRC Rotary. The Francis lab was associated with the BioPsy Labex project and the
Ecole des Neurosciences de Paris Ile-de-France (ENP) network. Our salaries and lab
were supported by Inserm, the Centre national de la recherche scientifique (CNRS)
and Sorbonne University. The Francis group obtained the following funding contributing
to this project: the European Union (EU- HEALTH-2013, DESIRE, N° 60253), the JTC
2015 Neurodevelopmental Disorders affiliated with the French Agence National de
la Recherche (for \r\nNEURON8-Full- 815-006 STEM-MCD, to FF), E-Rare-3, the ERA-Net
for Research on Rare Diseases affiliated with the French ANR (ERARE18-049), the
European Cooperation on Science and Technology (COST Action CA16118)."
article_number: '105702'
article_processing_charge: Yes
article_type: original
author:
- first_name: Melissa A
full_name: Stouffer, Melissa A
id: 4C9372C4-F248-11E8-B48F-1D18A9856A87
last_name: Stouffer
- first_name: R.
full_name: Khalaf-Nazzal, R.
last_name: Khalaf-Nazzal
- first_name: C.
full_name: Cifuentes-Diaz, C.
last_name: Cifuentes-Diaz
- first_name: G.
full_name: Albertini, G.
last_name: Albertini
- first_name: E.
full_name: Bandet, E.
last_name: Bandet
- first_name: G.
full_name: Grannec, G.
last_name: Grannec
- first_name: V.
full_name: Lavilla, V.
last_name: Lavilla
- first_name: J.-F.
full_name: Deleuze, J.-F.
last_name: Deleuze
- first_name: R.
full_name: Olaso, R.
last_name: Olaso
- first_name: M.
full_name: Nosten-Bertrand, M.
last_name: Nosten-Bertrand
- first_name: F.
full_name: Francis, F.
last_name: Francis
citation:
ama: Stouffer MA, Khalaf-Nazzal R, Cifuentes-Diaz C, et al. Doublecortin mutation
leads to persistent defects in the Golgi apparatus and mitochondria in adult hippocampal
pyramidal cells. Neurobiology of Disease. 2022;168. doi:10.1016/j.nbd.2022.105702
apa: Stouffer, M. A., Khalaf-Nazzal, R., Cifuentes-Diaz, C., Albertini, G., Bandet,
E., Grannec, G., … Francis, F. (2022). Doublecortin mutation leads to persistent
defects in the Golgi apparatus and mitochondria in adult hippocampal pyramidal
cells. Neurobiology of Disease. Elsevier. https://doi.org/10.1016/j.nbd.2022.105702
chicago: Stouffer, Melissa A, R. Khalaf-Nazzal, C. Cifuentes-Diaz, G. Albertini,
E. Bandet, G. Grannec, V. Lavilla, et al. “Doublecortin Mutation Leads to Persistent
Defects in the Golgi Apparatus and Mitochondria in Adult Hippocampal Pyramidal
Cells.” Neurobiology of Disease. Elsevier, 2022. https://doi.org/10.1016/j.nbd.2022.105702.
ieee: M. A. Stouffer et al., “Doublecortin mutation leads to persistent defects
in the Golgi apparatus and mitochondria in adult hippocampal pyramidal cells,”
Neurobiology of Disease, vol. 168. Elsevier, 2022.
ista: Stouffer MA, Khalaf-Nazzal R, Cifuentes-Diaz C, Albertini G, Bandet E, Grannec
G, Lavilla V, Deleuze J-F, Olaso R, Nosten-Bertrand M, Francis F. 2022. Doublecortin
mutation leads to persistent defects in the Golgi apparatus and mitochondria in
adult hippocampal pyramidal cells. Neurobiology of Disease. 168, 105702.
mla: Stouffer, Melissa A., et al. “Doublecortin Mutation Leads to Persistent Defects
in the Golgi Apparatus and Mitochondria in Adult Hippocampal Pyramidal Cells.”
Neurobiology of Disease, vol. 168, 105702, Elsevier, 2022, doi:10.1016/j.nbd.2022.105702.
short: M.A. Stouffer, R. Khalaf-Nazzal, C. Cifuentes-Diaz, G. Albertini, E. Bandet,
G. Grannec, V. Lavilla, J.-F. Deleuze, R. Olaso, M. Nosten-Bertrand, F. Francis,
Neurobiology of Disease 168 (2022).
date_created: 2024-05-29T06:10:05Z
date_published: 2022-06-15T00:00:00Z
date_updated: 2024-08-06T06:57:39Z
day: '15'
ddc:
- '570'
department:
- _id: SiHi
doi: 10.1016/j.nbd.2022.105702
external_id:
pmid:
- '35339680'
file:
- access_level: open_access
checksum: b705d3d23d0b424ba29920be7ab64c23
content_type: application/pdf
creator: dernst
date_created: 2024-08-06T06:54:24Z
date_updated: 2024-08-06T06:54:24Z
file_id: '17398'
file_name: 2022_NeurobioDisease_Stouffer.pdf
file_size: 8890818
relation: main_file
success: 1
file_date_updated: 2024-08-06T06:54:24Z
has_accepted_license: '1'
intvolume: ' 168'
language:
- iso: eng
month: '06'
oa: 1
oa_version: Published Version
pmid: 1
publication: Neurobiology of Disease
publication_identifier:
issn:
- 0969-9961
publication_status: published
publisher: Elsevier
quality_controlled: '1'
scopus_import: '1'
status: public
title: Doublecortin mutation leads to persistent defects in the Golgi apparatus and
mitochondria in adult hippocampal pyramidal cells
tmp:
image: /images/cc_by_nc_nd.png
legal_code_url: https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode
name: Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International
(CC BY-NC-ND 4.0)
short: CC BY-NC-ND (4.0)
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 168
year: '2022'
...
---
_id: '17068'
abstract:
- lang: eng
text: In plants, the antagonism between growth and defense is hardwired by hormonal
signaling. The perception of pathogen-associated molecular patterns (PAMPs) from
invading microorganisms inhibits auxin signaling and plant growth. Conversely,
pathogens manipulate auxin signaling to promote disease, but how this hormone
inhibits immunity is not fully understood. Ustilago maydis is a maize pathogen
that induces auxin signaling in its host. We characterized a U. maydis effector
protein, Naked1 (Nkd1), that is translocated into the host nucleus. Through its
native ethylene-responsive element binding factor-associated amphiphilic repression
(EAR) motif, Nkd1 binds to the transcriptional co-repressors TOPLESS/TOPLESS-related
(TPL/TPRs) and prevents the recruitment of a transcriptional repressor involved
in hormonal signaling, leading to the de-repression of auxin and jasmonate signaling
and thereby promoting susceptibility to (hemi)biotrophic pathogens. A moderate
upregulation of auxin signaling inhibits the PAMP-triggered reactive oxygen species
(ROS) burst, an early defense response. Thus, our findings establish a clear mechanism
for auxin-induced pathogen susceptibility. Engineered Nkd1 variants with increased
expression or increased EAR-mediated TPL/TPR binding trigger typical salicylic-acid-mediated
defense reactions, leading to pathogen resistance. This implies that moderate
binding of Nkd1 to TPL is a result of a balancing evolutionary selection process
to enable TPL manipulation while avoiding host recognition.
acknowledgement: "The research leading to these results received funding from the
European Research Council under the European Union Seventh Framework Programme ERC-2013-STG
grant agreement \r\n335691; the Austrian Science Fund (FWF) P27818-B22,I 3033-B22;
the Austrian Academy of Sciences (OEAW); and the Deutsche Forschungsgemeinschaft
(DFG, German Research Foundation) under Germany’s Excellence Strategy - EXC 2070-390732324.\r\nWe
would like to thank the GMI/IMBA/IMP core facilities for excellent technical support,
especially the BioOptics and Molecular Biology Services. We thank the Plant Sciences
and Next Generation Sequencing Facilities at the Vienna BioCenter Core Facilities
GmbH (VBCF). We are grateful to the Jirí Friml and Jürgen Kleine-Vehn laboratories
for providing useful A. thaliana lines. We thank Mathias Madalinski for peptide
synthesis and Dr. J. Matthew Watson for proofreading and valuable feedback on the
manuscript. The authors declare no competing interests."
article_number: '100269'
article_processing_charge: Yes
article_type: original
author:
- first_name: Fernando
full_name: Navarrete, Fernando
last_name: Navarrete
- first_name: Michelle C
full_name: Gallei, Michelle C
id: 35A03822-F248-11E8-B48F-1D18A9856A87
last_name: Gallei
orcid: 0000-0003-1286-7368
- first_name: Aleksandra E.
full_name: Kornienko, Aleksandra E.
last_name: Kornienko
- first_name: Indira
full_name: Saado, Indira
last_name: Saado
- first_name: Mamoona
full_name: Khan, Mamoona
last_name: Khan
- first_name: Khong-Sam
full_name: Chia, Khong-Sam
last_name: Chia
- first_name: Martin A.
full_name: Darino, Martin A.
last_name: Darino
- first_name: Janos
full_name: Bindics, Janos
last_name: Bindics
- first_name: Armin
full_name: Djamei, Armin
last_name: Djamei
citation:
ama: Navarrete F, Gallei MC, Kornienko AE, et al. TOPLESS promotes plant immunity
by repressing auxin signaling and is targeted by the fungal effector Naked1. Plant
Communications. 2022;3(2). doi:10.1016/j.xplc.2021.100269
apa: Navarrete, F., Gallei, M. C., Kornienko, A. E., Saado, I., Khan, M., Chia,
K.-S., … Djamei, A. (2022). TOPLESS promotes plant immunity by repressing auxin
signaling and is targeted by the fungal effector Naked1. Plant Communications.
Elsevier. https://doi.org/10.1016/j.xplc.2021.100269
chicago: Navarrete, Fernando, Michelle C Gallei, Aleksandra E. Kornienko, Indira
Saado, Mamoona Khan, Khong-Sam Chia, Martin A. Darino, Janos Bindics, and Armin
Djamei. “TOPLESS Promotes Plant Immunity by Repressing Auxin Signaling and Is
Targeted by the Fungal Effector Naked1.” Plant Communications. Elsevier,
2022. https://doi.org/10.1016/j.xplc.2021.100269.
ieee: F. Navarrete et al., “TOPLESS promotes plant immunity by repressing
auxin signaling and is targeted by the fungal effector Naked1,” Plant Communications,
vol. 3, no. 2. Elsevier, 2022.
ista: Navarrete F, Gallei MC, Kornienko AE, Saado I, Khan M, Chia K-S, Darino MA,
Bindics J, Djamei A. 2022. TOPLESS promotes plant immunity by repressing auxin
signaling and is targeted by the fungal effector Naked1. Plant Communications.
3(2), 100269.
mla: Navarrete, Fernando, et al. “TOPLESS Promotes Plant Immunity by Repressing
Auxin Signaling and Is Targeted by the Fungal Effector Naked1.” Plant Communications,
vol. 3, no. 2, 100269, Elsevier, 2022, doi:10.1016/j.xplc.2021.100269.
short: F. Navarrete, M.C. Gallei, A.E. Kornienko, I. Saado, M. Khan, K.-S. Chia,
M.A. Darino, J. Bindics, A. Djamei, Plant Communications 3 (2022).
date_created: 2024-05-29T06:10:22Z
date_published: 2022-03-14T00:00:00Z
date_updated: 2024-08-05T10:27:03Z
day: '14'
ddc:
- '580'
department:
- _id: JiFr
doi: 10.1016/j.xplc.2021.100269
external_id:
pmid:
- '35529945'
file:
- access_level: open_access
checksum: 1eeb6ee65419e4aa34627fea6857f343
content_type: application/pdf
creator: dernst
date_created: 2024-08-05T10:26:29Z
date_updated: 2024-08-05T10:26:29Z
file_id: '17393'
file_name: 2022_PlantComm_Navarrete.pdf
file_size: 3216686
relation: main_file
success: 1
file_date_updated: 2024-08-05T10:26:29Z
has_accepted_license: '1'
intvolume: ' 3'
issue: '2'
language:
- iso: eng
month: '03'
oa: 1
oa_version: Published Version
pmid: 1
publication: Plant Communications
publication_identifier:
issn:
- 2590-3462
publication_status: published
publisher: Elsevier
quality_controlled: '1'
scopus_import: '1'
status: public
title: TOPLESS promotes plant immunity by repressing auxin signaling and is targeted
by the fungal effector Naked1
tmp:
image: /images/cc_by_nc_nd.png
legal_code_url: https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode
name: Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International
(CC BY-NC-ND 4.0)
short: CC BY-NC-ND (4.0)
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 3
year: '2022'
...
---
OA_place: repository
OA_type: green
_id: '17069'
abstract:
- lang: eng
text: Fertilization of an egg by multiple sperm (polyspermy) leads to lethal genome
imbalance and chromosome segregation defects. In Arabidopsis thaliana, the block
to polyspermy is facilitated by a mechanism that prevents polytubey (the arrival
of multiple pollen tubes to one ovule). We show here that FERONIA, ANJEA, and
HERCULES RECEPTOR KINASE 1 receptor-like kinases located at the septum interact
with pollen tube–specific RALF6, 7, 16, 36, and 37 peptide ligands to establish
this polytubey block. The same combination of RALF (rapid alkalinization factor)
peptides and receptor complexes controls pollen tube reception and rupture inside
the targeted ovule. Pollen tube rupture releases the polytubey block at the septum,
which allows the emergence of secondary pollen tubes upon fertilization failure.
Thus, orchestrated steps in the fertilization process in Arabidopsis are coordinated
by the same signaling components to guarantee and optimize reproductive success.
acknowledgement: "We thank D. Ye for providing fer-4 and myb97 myb101 myb120 mutant
seeds; L. Smith for sharing anj, herk1, anj herk1, and fer anj herk1 mutant seeds;
J. F. Harper for providing aca9 mutant seeds; and C. Li and Q. Duan for sharing
fer+/− mutant seeds.\r\nL.-J.Q. was funded by the National Natural Science Foundation
of China (grant nos. 31991202, 31830004, 31620103903, and 31621001), S.Z. was supported
by the Young Elite Scientists Sponsorship Program by the China Association of Science
and Technology (2019QNRC001), Z.G. was supported by a NSFC Young Scientists Fund
(31900161), A.Y.C. was funded by the US Natural Science Foundation (IOS-1645854,
MCB-1715764, and MCB-0955910), J.D. was funded by the National Institute of Health
(R01GM109080), and T.D. was supported by the German Research Foundation DFG (SFB924)."
article_processing_charge: No
article_type: original
author:
- first_name: Sheng
full_name: Zhong, Sheng
last_name: Zhong
- first_name: Ling
full_name: Li, Ling
last_name: Li
- first_name: Zhijuan
full_name: Wang, Zhijuan
last_name: Wang
- first_name: Zengxiang
full_name: Ge, Zengxiang
id: f43371a3-09ff-11eb-8013-bd0c6a2f6de8
last_name: Ge
orcid: 0000-0001-9381-3577
- first_name: Qiyun
full_name: Li, Qiyun
last_name: Li
- first_name: Andrea
full_name: Bleckmann, Andrea
last_name: Bleckmann
- first_name: Jizong
full_name: Wang, Jizong
last_name: Wang
- first_name: Zihan
full_name: Song, Zihan
last_name: Song
- first_name: Yihao
full_name: Shi, Yihao
last_name: Shi
- first_name: Tianxu
full_name: Liu, Tianxu
last_name: Liu
- first_name: Luhan
full_name: Li, Luhan
last_name: Li
- first_name: Huabin
full_name: Zhou, Huabin
last_name: Zhou
- first_name: Yanyan
full_name: Wang, Yanyan
last_name: Wang
- first_name: Li
full_name: Zhang, Li
last_name: Zhang
- first_name: Hen-Ming
full_name: Wu, Hen-Ming
last_name: Wu
- first_name: Luhua
full_name: Lai, Luhua
last_name: Lai
- first_name: Hongya
full_name: Gu, Hongya
last_name: Gu
- first_name: Juan
full_name: Dong, Juan
last_name: Dong
- first_name: Alice Y.
full_name: Cheung, Alice Y.
last_name: Cheung
- first_name: Thomas
full_name: Dresselhaus, Thomas
last_name: Dresselhaus
- first_name: Li-Jia
full_name: Qu, Li-Jia
last_name: Qu
citation:
ama: Zhong S, Li L, Wang Z, et al. RALF peptide signaling controls the polytubey
block in Arabidopsis. Science. 2022;375(6578):290-296. doi:10.1126/science.abl4683
apa: Zhong, S., Li, L., Wang, Z., Ge, Z., Li, Q., Bleckmann, A., … Qu, L.-J. (2022).
RALF peptide signaling controls the polytubey block in Arabidopsis. Science.
American Association for the Advancement of Science. https://doi.org/10.1126/science.abl4683
chicago: Zhong, Sheng, Ling Li, Zhijuan Wang, Zengxiang Ge, Qiyun Li, Andrea Bleckmann,
Jizong Wang, et al. “RALF Peptide Signaling Controls the Polytubey Block in Arabidopsis.”
Science. American Association for the Advancement of Science, 2022. https://doi.org/10.1126/science.abl4683.
ieee: S. Zhong et al., “RALF peptide signaling controls the polytubey block
in Arabidopsis,” Science, vol. 375, no. 6578. American Association for
the Advancement of Science, pp. 290–296, 2022.
ista: Zhong S, Li L, Wang Z, Ge Z, Li Q, Bleckmann A, Wang J, Song Z, Shi Y, Liu
T, Li L, Zhou H, Wang Y, Zhang L, Wu H-M, Lai L, Gu H, Dong J, Cheung AY, Dresselhaus
T, Qu L-J. 2022. RALF peptide signaling controls the polytubey block in Arabidopsis.
Science. 375(6578), 290–296.
mla: Zhong, Sheng, et al. “RALF Peptide Signaling Controls the Polytubey Block in
Arabidopsis.” Science, vol. 375, no. 6578, American Association for the
Advancement of Science, 2022, pp. 290–96, doi:10.1126/science.abl4683.
short: S. Zhong, L. Li, Z. Wang, Z. Ge, Q. Li, A. Bleckmann, J. Wang, Z. Song, Y.
Shi, T. Liu, L. Li, H. Zhou, Y. Wang, L. Zhang, H.-M. Wu, L. Lai, H. Gu, J. Dong,
A.Y. Cheung, T. Dresselhaus, L.-J. Qu, Science 375 (2022) 290–296.
date_created: 2024-05-29T06:11:10Z
date_published: 2022-01-20T00:00:00Z
date_updated: 2025-04-24T11:39:46Z
day: '20'
department:
- _id: JiFr
doi: 10.1126/science.abl4683
external_id:
pmid:
- '35050671'
intvolume: ' 375'
issue: '6578'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9040003
month: '01'
oa: 1
oa_version: Submitted Version
page: 290-296
pmid: 1
publication: Science
publication_identifier:
eissn:
- 1095-9203
issn:
- 0036-8075
publication_status: published
publisher: American Association for the Advancement of Science
quality_controlled: '1'
scopus_import: '1'
status: public
title: RALF peptide signaling controls the polytubey block in Arabidopsis
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 375
year: '2022'
...
---
_id: '17070'
abstract:
- lang: eng
text: We investigate the formation of magnetic Bose polaron, an impurity atom dressed
by spin-wave excitations, in a one-dimensional spinor Bose gas. Within an effective
potential model, the impurity is strongly confined by the host excitations which
can even overcome the impurity-medium repulsion leading to a self-localized quasi-particle
state. The phase diagram of the attractive and self-bound repulsive magnetic polaron,
repulsive non-magnetic (Fröhlich-type) polaron and impurity-medium phase-separation
regimes is explored with respect to the Rabi-coupling between the spin components,
spin–spin interactions and impurity-medium coupling. The residue of such magnetic
polarons decreases substantially in both strong attractive and repulsive branches
with strong impurity-spin interactions, illustrating significant dressing of the
impurity. The impurity can be used to probe and maneuver the spin polarization
of the magnetic medium while suppressing ferromagnetic spin–spin correlations.
It is shown that mean-field theory fails as the spinor gas approaches immiscibility
since the generated spin-wave excitations are prominent. Our findings illustrate
that impurities can be utilized to generate controllable spin–spin correlations
and magnetic polaron states which can be realized with current cold atom setups.
article_number: '083030'
article_processing_charge: Yes
article_type: original
arxiv: 1
author:
- first_name: S I
full_name: Mistakidis, S I
last_name: Mistakidis
- first_name: Georgios
full_name: Koutentakis, Georgios
id: d7b23d3a-9e21-11ec-b482-f76739596b95
last_name: Koutentakis
- first_name: F
full_name: Grusdt, F
last_name: Grusdt
- first_name: P
full_name: Schmelcher, P
last_name: Schmelcher
- first_name: H R
full_name: Sadeghpour, H R
last_name: Sadeghpour
citation:
ama: 'Mistakidis SI, Koutentakis G, Grusdt F, Schmelcher P, Sadeghpour HR. Inducing
spin-order with an impurity: phase diagram of the magnetic Bose polaron. New
Journal of Physics. 2022;24(8). doi:10.1088/1367-2630/ac836c'
apa: 'Mistakidis, S. I., Koutentakis, G., Grusdt, F., Schmelcher, P., & Sadeghpour,
H. R. (2022). Inducing spin-order with an impurity: phase diagram of the magnetic
Bose polaron. New Journal of Physics. IOP Publishing. https://doi.org/10.1088/1367-2630/ac836c'
chicago: 'Mistakidis, S I, Georgios Koutentakis, F Grusdt, P Schmelcher, and H R
Sadeghpour. “Inducing Spin-Order with an Impurity: Phase Diagram of the Magnetic
Bose Polaron.” New Journal of Physics. IOP Publishing, 2022. https://doi.org/10.1088/1367-2630/ac836c.'
ieee: 'S. I. Mistakidis, G. Koutentakis, F. Grusdt, P. Schmelcher, and H. R. Sadeghpour,
“Inducing spin-order with an impurity: phase diagram of the magnetic Bose polaron,”
New Journal of Physics, vol. 24, no. 8. IOP Publishing, 2022.'
ista: 'Mistakidis SI, Koutentakis G, Grusdt F, Schmelcher P, Sadeghpour HR. 2022.
Inducing spin-order with an impurity: phase diagram of the magnetic Bose polaron.
New Journal of Physics. 24(8), 083030.'
mla: 'Mistakidis, S. I., et al. “Inducing Spin-Order with an Impurity: Phase Diagram
of the Magnetic Bose Polaron.” New Journal of Physics, vol. 24, no. 8,
083030, IOP Publishing, 2022, doi:10.1088/1367-2630/ac836c.'
short: S.I. Mistakidis, G. Koutentakis, F. Grusdt, P. Schmelcher, H.R. Sadeghpour,
New Journal of Physics 24 (2022).
date_created: 2024-05-29T06:11:35Z
date_published: 2022-09-08T00:00:00Z
date_updated: 2024-07-31T12:14:55Z
day: '08'
ddc:
- '530'
department:
- _id: MiLe
doi: 10.1088/1367-2630/ac836c
external_id:
arxiv:
- '2204.10960'
file:
- access_level: open_access
checksum: 85776a9d3abe163b33b322c8e346752a
content_type: application/pdf
creator: dernst
date_created: 2024-07-31T12:13:16Z
date_updated: 2024-07-31T12:13:16Z
file_id: '17358'
file_name: 2022_NewJournPhysics_Mistakidis.pdf
file_size: 4201283
relation: main_file
success: 1
file_date_updated: 2024-07-31T12:13:16Z
has_accepted_license: '1'
intvolume: ' 24'
issue: '8'
language:
- iso: eng
month: '09'
oa: 1
oa_version: Published Version
publication: New Journal of Physics
publication_identifier:
issn:
- 1367-2630
publication_status: published
publisher: IOP Publishing
quality_controlled: '1'
scopus_import: '1'
status: public
title: 'Inducing spin-order with an impurity: phase diagram of the magnetic Bose polaron'
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: 24
year: '2022'
...
---
_id: '17071'
abstract:
- lang: eng
text: "The eukaryotic nucleus protects the genome and is enclosed by the two membranes
of the nuclear envelope. Nuclear pore complexes (NPCs) perforate the nuclear envelope
to facilitate nucleocytoplasmic transport. With a molecular weight of ∼120 MDa,
the human NPC is one of the largest protein complexes. Its ~1000 proteins are
taken in multiple copies from a set of about 30 distinct nucleoporins (NUPs).
They can be roughly categorized into two classes. Scaffold NUPs contain folded
domains and form a cylindrical scaffold architecture around a central channel.
Intrinsically disordered NUPs line the scaffold and extend into the central channel,
where they interact with cargo complexes. The NPC architecture is highly dynamic.
It responds to changes in nuclear envelope tension with conformational breathing
that manifests in dilation and constriction movements. Elucidating the scaffold
architecture, ultimately at atomic resolution, will be important for gaining a
more precise understanding of NPC function and dynamics but imposes a substantial
challenge for structural biologists.\r\nConsiderable progress has been made toward
this goal by a joint effort in the field. A synergistic combination of complementary
approaches has turned out to be critical. In situ structural biology techniques
were used to reveal the overall layout of the NPC scaffold that defines the spatial
reference for molecular modeling. High-resolution structures of many NUPs were
determined in vitro. Proteomic analysis and extensive biochemical work unraveled
the interaction network of NUPs. Integrative modeling has been used to combine
the different types of data, resulting in a rough outline of the NPC scaffold.
Previous structural models of the human NPC, however, were patchy and limited
in accuracy owing to several challenges: (i) Many of the high-resolution structures
of individual NUPs have been solved from distantly related species and, consequently,
do not comprehensively cover their human counterparts. (ii) The scaffold is interconnected
by a set of intrinsically disordered linker NUPs that are not straightforwardly
accessible to common structural biology techniques. (iii) The NPC scaffold intimately
embraces the fused inner and outer nuclear membranes in a distinctive topology
and cannot be studied in isolation. (iv) The conformational dynamics of scaffold
NUPs limits the resolution achievable in structure determination.\r\nIn this study,
we used artificial intelligence (AI)–based prediction to generate an extensive
repertoire of structural models of human NUPs and their subcomplexes. The resulting
models cover various domains and interfaces that so far remained structurally
uncharacterized. Benchmarking against previous and unpublished x-ray and cryo–electron
microscopy structures revealed unprecedented accuracy. We obtained well-resolved
cryo–electron tomographic maps of both the constricted and dilated conformational
states of the human NPC. Using integrative modeling, we fitted the structural
models of individual NUPs into the cryo–electron microscopy maps. We explicitly
included several linker NUPs and traced their trajectory through the NPC scaffold.
We elucidated in great detail how membrane-associated and transmembrane NUPs
are distributed across the fusion topology of both nuclear membranes. The resulting
architectural model increases the structural coverage of the human NPC scaffold
by about twofold. We extensively validated our model against both earlier and
new experimental data. The completeness of our model has enabled microsecond-long
coarse-grained molecular dynamics simulations of the NPC scaffold within an explicit
membrane environment and solvent. These simulations reveal that the NPC scaffold
prevents the constriction of the otherwise stable double-membrane fusion pore
to small diameters in the absence of membrane tension\r\nOur 70-MDa atomically
resolved model covers >90% of the human NPC scaffold. It captures conformational
changes that occur during dilation and constriction. It also reveals the precise
anchoring sites for intrinsically disordered NUPs, the identification of which
is a prerequisite for a complete and dynamic model of the NPC. Our study exemplifies
how AI-based structure prediction may accelerate the elucidation of subcellular
architecture at atomic resolution."
acknowledgement: "We acknowledge support from the Electron Microscopy Core Facility
(EMCF) and IT services of European Molecular Biology Laboratory (EMBL) Heidelberg.
We thank S. Welsch at the Central Electron Microscopy Facility of the Max Planck
Institute of Biophysics for technical expertise. We thank T. Hoffman and R. Alves
for help with the AlphaFold installation.\r\nFunding: M.B. acknowledges funding
by EMBL, the Max Planck Society, and the European Research Council (ComplexAssembly
724349). J.K. acknowledges funding from the Federal Ministry of Education and Research
of Germany (FKZ 031L0100). The work by M.S. and G.H. on computer simulations was
supported by the Max Planck Society. M.S. was supported by the EMBL Interdisciplinary
Postdoc Programme under Marie Curie COFUND actions. M.S. and G.H. were supported
by the Landes-Offensive zur Entwicklung Wissenschaftlich-ökonomischer Exzellenz
(LOEWE) DynaMem program of the State of Hessen."
article_number: abm9506
article_processing_charge: No
article_type: original
author:
- first_name: Shyamal
full_name: Mosalaganti, Shyamal
last_name: Mosalaganti
- first_name: Agnieszka
full_name: Obarska-Kosinska, Agnieszka
last_name: Obarska-Kosinska
- first_name: Marc
full_name: Siggel, Marc
last_name: Siggel
- first_name: Reiya
full_name: Taniguchi, Reiya
last_name: Taniguchi
- first_name: Beata
full_name: Turoňová, Beata
last_name: Turoňová
- first_name: Christian E.
full_name: Zimmerli, Christian E.
last_name: Zimmerli
- first_name: Katarzyna
full_name: Buczak, Katarzyna
last_name: Buczak
- first_name: Florian
full_name: Schmidt, Florian
id: A2EF226A-AF19-11E9-924C-0525E6697425
last_name: Schmidt
- first_name: Erica
full_name: Margiotta, Erica
last_name: Margiotta
- first_name: Marie-Therese
full_name: Mackmull, Marie-Therese
last_name: Mackmull
- first_name: Wim J. H.
full_name: Hagen, Wim J. H.
last_name: Hagen
- first_name: Gerhard
full_name: Hummer, Gerhard
last_name: Hummer
- first_name: Jan
full_name: Kosinski, Jan
last_name: Kosinski
- first_name: Martin
full_name: Beck, Martin
last_name: Beck
citation:
ama: Mosalaganti S, Obarska-Kosinska A, Siggel M, et al. AI-based structure prediction
empowers integrative structural analysis of human nuclear pores. Science.
2022;376(6598). doi:10.1126/science.abm9506
apa: Mosalaganti, S., Obarska-Kosinska, A., Siggel, M., Taniguchi, R., Turoňová,
B., Zimmerli, C. E., … Beck, M. (2022). AI-based structure prediction empowers
integrative structural analysis of human nuclear pores. Science. American
Association for the Advancement of Science. https://doi.org/10.1126/science.abm9506
chicago: Mosalaganti, Shyamal, Agnieszka Obarska-Kosinska, Marc Siggel, Reiya Taniguchi,
Beata Turoňová, Christian E. Zimmerli, Katarzyna Buczak, et al. “AI-Based Structure
Prediction Empowers Integrative Structural Analysis of Human Nuclear Pores.” Science.
American Association for the Advancement of Science, 2022. https://doi.org/10.1126/science.abm9506.
ieee: S. Mosalaganti et al., “AI-based structure prediction empowers integrative
structural analysis of human nuclear pores,” Science, vol. 376, no. 6598.
American Association for the Advancement of Science, 2022.
ista: Mosalaganti S, Obarska-Kosinska A, Siggel M, Taniguchi R, Turoňová B, Zimmerli
CE, Buczak K, Schmidt F, Margiotta E, Mackmull M-T, Hagen WJH, Hummer G, Kosinski
J, Beck M. 2022. AI-based structure prediction empowers integrative structural
analysis of human nuclear pores. Science. 376(6598), abm9506.
mla: Mosalaganti, Shyamal, et al. “AI-Based Structure Prediction Empowers Integrative
Structural Analysis of Human Nuclear Pores.” Science, vol. 376, no. 6598,
abm9506, American Association for the Advancement of Science, 2022, doi:10.1126/science.abm9506.
short: S. Mosalaganti, A. Obarska-Kosinska, M. Siggel, R. Taniguchi, B. Turoňová,
C.E. Zimmerli, K. Buczak, F. Schmidt, E. Margiotta, M.-T. Mackmull, W.J.H. Hagen,
G. Hummer, J. Kosinski, M. Beck, Science 376 (2022).
date_created: 2024-05-29T06:12:02Z
date_published: 2022-06-10T00:00:00Z
date_updated: 2024-07-31T12:10:32Z
day: '10'
department:
- _id: MaJö
doi: 10.1126/science.abm9506
external_id:
pmid:
- '35679397'
intvolume: ' 376'
issue: '6598'
language:
- iso: eng
month: '06'
oa_version: None
pmid: 1
publication: Science
publication_identifier:
eissn:
- 1095-9203
issn:
- 0036-8075
publication_status: published
publisher: American Association for the Advancement of Science
quality_controlled: '1'
scopus_import: '1'
status: public
title: AI-based structure prediction empowers integrative structural analysis of human
nuclear pores
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 376
year: '2022'
...