---
_id: '12233'
abstract:
- lang: eng
text: A novel recursive list decoding (RLD) algorithm for Reed-Muller (RM) codes
based on successive permutations (SP) of the codeword is presented. A low-complexity
SP scheme applied to a subset of the symmetry group of RM codes is first proposed
to carefully select a good codeword permutation on the fly. Then, the proposed
SP technique is integrated into an improved RLD algorithm that initializes different
decoding paths with random codeword permutations, which are sampled from the full
symmetry group of RM codes. Finally, efficient latency and complexity reduction
schemes are introduced that virtually preserve the error-correction performance
of the proposed decoder. Simulation results demonstrate that at the target frame
error rate of 10−3 for the RM code of length 256 with 163 information bits, the
proposed decoder reduces 6% of the computational complexity and 22% of the decoding
latency of the state-of-the-art semi-parallel simplified successive-cancellation
decoder with fast Hadamard transform (SSC-FHT) that uses 96 permutations from
the full symmetry group of RM codes, while relatively maintaining the error-correction
performance and memory consumption of the semi-parallel permuted SSC-FHT decoder.
article_processing_charge: No
article_type: original
arxiv: 1
author:
- first_name: Nghia
full_name: Doan, Nghia
last_name: Doan
- 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: Warren J.
full_name: Gross, Warren J.
last_name: Gross
citation:
ama: Doan N, Hashemi SA, Mondelli M, Gross WJ. Decoding Reed-Muller codes with successive
codeword permutations. IEEE Transactions on Communications. 2022;70(11):7134-7145.
doi:10.1109/tcomm.2022.3211101
apa: Doan, N., Hashemi, S. A., Mondelli, M., & Gross, W. J. (2022). Decoding
Reed-Muller codes with successive codeword permutations. IEEE Transactions
on Communications. Institute of Electrical and Electronics Engineers. https://doi.org/10.1109/tcomm.2022.3211101
chicago: Doan, Nghia, Seyyed Ali Hashemi, Marco Mondelli, and Warren J. Gross. “Decoding
Reed-Muller Codes with Successive Codeword Permutations.” IEEE Transactions
on Communications. Institute of Electrical and Electronics Engineers, 2022.
https://doi.org/10.1109/tcomm.2022.3211101.
ieee: N. Doan, S. A. Hashemi, M. Mondelli, and W. J. Gross, “Decoding Reed-Muller
codes with successive codeword permutations,” IEEE Transactions on Communications,
vol. 70, no. 11. Institute of Electrical and Electronics Engineers, pp. 7134–7145,
2022.
ista: Doan N, Hashemi SA, Mondelli M, Gross WJ. 2022. Decoding Reed-Muller codes
with successive codeword permutations. IEEE Transactions on Communications. 70(11),
7134–7145.
mla: Doan, Nghia, et al. “Decoding Reed-Muller Codes with Successive Codeword Permutations.”
IEEE Transactions on Communications, vol. 70, no. 11, Institute of Electrical
and Electronics Engineers, 2022, pp. 7134–45, doi:10.1109/tcomm.2022.3211101.
short: N. Doan, S.A. Hashemi, M. Mondelli, W.J. Gross, IEEE Transactions on Communications
70 (2022) 7134–7145.
date_created: 2023-01-16T09:50:38Z
date_published: 2022-11-01T00:00:00Z
date_updated: 2023-08-04T09:34:43Z
day: '01'
department:
- _id: MaMo
doi: 10.1109/tcomm.2022.3211101
external_id:
arxiv:
- '2109.02122'
isi:
- '000937284600006'
intvolume: ' 70'
isi: 1
issue: '11'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: ' https://doi.org/10.48550/arXiv.2109.02122'
month: '11'
oa: 1
oa_version: Preprint
page: 7134-7145
publication: IEEE Transactions on Communications
publication_identifier:
eissn:
- 1558-0857
issn:
- 0090-6778
publication_status: published
publisher: Institute of Electrical and Electronics Engineers
quality_controlled: '1'
scopus_import: '1'
status: public
title: Decoding Reed-Muller codes with successive codeword permutations
type: journal_article
user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
volume: 70
year: '2022'
...
---
_id: '12234'
abstract:
- lang: eng
text: Hybrid speciation—the origin of new species resulting from the hybridization
of genetically divergent lineages—was once considered rare, but genomic data suggest
that it may occur more often than once thought. In this study, Noguerales and
Ortego found genomic evidence supporting the hybrid origin of a grasshopper that
is able to exploit a broader range of host plants than either of its putative
parents.
article_processing_charge: Yes (via OA deal)
article_type: original
author:
- first_name: Sean
full_name: Stankowski, Sean
id: 43161670-5719-11EA-8025-FABC3DDC885E
last_name: Stankowski
citation:
ama: 'Stankowski S. Digest: On the origin of a possible hybrid species. Evolution.
2022;76(11):2784-2785. doi:10.1111/evo.14632'
apa: 'Stankowski, S. (2022). Digest: On the origin of a possible hybrid species.
Evolution. Wiley. https://doi.org/10.1111/evo.14632'
chicago: 'Stankowski, Sean. “Digest: On the Origin of a Possible Hybrid Species.”
Evolution. Wiley, 2022. https://doi.org/10.1111/evo.14632.'
ieee: 'S. Stankowski, “Digest: On the origin of a possible hybrid species,” Evolution,
vol. 76, no. 11. Wiley, pp. 2784–2785, 2022.'
ista: 'Stankowski S. 2022. Digest: On the origin of a possible hybrid species. Evolution.
76(11), 2784–2785.'
mla: 'Stankowski, Sean. “Digest: On the Origin of a Possible Hybrid Species.” Evolution,
vol. 76, no. 11, Wiley, 2022, pp. 2784–85, doi:10.1111/evo.14632.'
short: S. Stankowski, Evolution 76 (2022) 2784–2785.
corr_author: '1'
date_created: 2023-01-16T09:50:48Z
date_published: 2022-11-01T00:00:00Z
date_updated: 2025-06-11T13:40:40Z
day: '01'
ddc:
- '570'
department:
- _id: NiBa
doi: 10.1111/evo.14632
external_id:
isi:
- '000855751600001'
pmid:
- '36112597'
file:
- access_level: open_access
checksum: 4c0f05083b414ac0323a1b9ee1abc275
content_type: application/pdf
creator: dernst
date_created: 2023-01-27T11:28:38Z
date_updated: 2023-01-27T11:28:38Z
file_id: '12425'
file_name: 2022_Evolution_Stankowski.pdf
file_size: 287282
relation: main_file
success: 1
file_date_updated: 2023-01-27T11:28:38Z
has_accepted_license: '1'
intvolume: ' 76'
isi: 1
issue: '11'
keyword:
- General Agricultural and Biological Sciences
- Genetics
- Ecology
- Evolution
- Behavior and Systematics
language:
- iso: eng
license: https://creativecommons.org/licenses/by-nc-nd/4.0/
month: '11'
oa: 1
oa_version: Published Version
page: 2784-2785
pmid: 1
publication: Evolution
publication_identifier:
eissn:
- 1558-5646
issn:
- 0014-3820
publication_status: published
publisher: Wiley
quality_controlled: '1'
scopus_import: '1'
status: public
title: 'Digest: On the origin of a possible hybrid species'
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: 76
year: '2022'
...
---
_id: '12235'
abstract:
- lang: eng
text: "Background: About 800 women die every day worldwide from pregnancy-related
complications, including excessive blood loss, infections and high-blood pressure
(World Health Organization, 2019). To improve screening for high-risk pregnancies,
we set out to identify patterns of maternal hematological changes associated with
future pregnancy complications.\r\n\r\nMethods: Using mixed effects models, we
established changes in 14 complete blood count (CBC) parameters for 1710 healthy
pregnancies and compared them to measurements from 98 pregnancy-induced hypertension,
106 gestational diabetes and 339 postpartum hemorrhage cases.\r\n\r\nResults:
Results show interindividual variations, but good individual repeatability in
CBC values during physiological pregnancies, allowing the identification of specific
alterations in women with obstetric complications. For example, in women with
uncomplicated pregnancies, haemoglobin count decreases of 0.12 g/L (95% CI −0.16,
−0.09) significantly per gestation week (p value <.001). Interestingly, this decrease
is three times more pronounced in women who will develop pregnancy-induced hypertension,
with an additional decrease of 0.39 g/L (95% CI −0.51, −0.26). We also confirm
that obstetric complications and white CBC predict the likelihood of giving birth
earlier during pregnancy.\r\n\r\nConclusion: We provide a comprehensive description
of the associations between haematological changes through pregnancy and three
major obstetric complications to support strategies for prevention, early-diagnosis
and maternal care."
acknowledgement: This project was funded by an SNSF Eccellenza Grant to MRR (PCEGP3-181181),
and by core funding from the Institute of Science and Technology Austria. We would
like to thank the participants of the study and all the midwives and doctors involved
for the computerized obstetrical data from the CHUV Maternity Hospital. Open access
funding provided by Universite de Lausanne.
article_processing_charge: No
article_type: original
author:
- first_name: Marion
full_name: Patxot, Marion
last_name: Patxot
- first_name: Miloš
full_name: Stojanov, Miloš
last_name: Stojanov
- first_name: Sven Erik
full_name: Ojavee, Sven Erik
last_name: Ojavee
- first_name: Rosanna Pescini
full_name: Gobert, Rosanna Pescini
last_name: Gobert
- first_name: Zoltán
full_name: Kutalik, Zoltán
last_name: Kutalik
- first_name: Mathilde
full_name: Gavillet, Mathilde
last_name: Gavillet
- first_name: David
full_name: Baud, David
last_name: Baud
- first_name: Matthew Richard
full_name: Robinson, Matthew Richard
id: E5D42276-F5DA-11E9-8E24-6303E6697425
last_name: Robinson
orcid: 0000-0001-8982-8813
citation:
ama: 'Patxot M, Stojanov M, Ojavee SE, et al. Haematological changes from conception
to childbirth: An indicator of major pregnancy complications. European Journal
of Haematology. 2022;109(5):566-575. doi:10.1111/ejh.13844'
apa: 'Patxot, M., Stojanov, M., Ojavee, S. E., Gobert, R. P., Kutalik, Z., Gavillet,
M., … Robinson, M. R. (2022). Haematological changes from conception to childbirth:
An indicator of major pregnancy complications. European Journal of Haematology.
Wiley. https://doi.org/10.1111/ejh.13844'
chicago: 'Patxot, Marion, Miloš Stojanov, Sven Erik Ojavee, Rosanna Pescini Gobert,
Zoltán Kutalik, Mathilde Gavillet, David Baud, and Matthew Richard Robinson. “Haematological
Changes from Conception to Childbirth: An Indicator of Major Pregnancy Complications.”
European Journal of Haematology. Wiley, 2022. https://doi.org/10.1111/ejh.13844.'
ieee: 'M. Patxot et al., “Haematological changes from conception to childbirth:
An indicator of major pregnancy complications,” European Journal of Haematology,
vol. 109, no. 5. Wiley, pp. 566–575, 2022.'
ista: 'Patxot M, Stojanov M, Ojavee SE, Gobert RP, Kutalik Z, Gavillet M, Baud D,
Robinson MR. 2022. Haematological changes from conception to childbirth: An indicator
of major pregnancy complications. European Journal of Haematology. 109(5), 566–575.'
mla: 'Patxot, Marion, et al. “Haematological Changes from Conception to Childbirth:
An Indicator of Major Pregnancy Complications.” European Journal of Haematology,
vol. 109, no. 5, Wiley, 2022, pp. 566–75, doi:10.1111/ejh.13844.'
short: M. Patxot, M. Stojanov, S.E. Ojavee, R.P. Gobert, Z. Kutalik, M. Gavillet,
D. Baud, M.R. Robinson, European Journal of Haematology 109 (2022) 566–575.
corr_author: '1'
date_created: 2023-01-16T09:50:58Z
date_published: 2022-11-01T00:00:00Z
date_updated: 2024-10-09T21:03:49Z
day: '01'
ddc:
- '570'
- '610'
department:
- _id: MaRo
doi: 10.1111/ejh.13844
external_id:
isi:
- '000849690500001'
pmid:
- '36059200'
file:
- access_level: open_access
checksum: a676d732f67c2990197e34f96b219370
content_type: application/pdf
creator: dernst
date_created: 2023-01-27T11:42:43Z
date_updated: 2023-01-27T11:42:43Z
file_id: '12426'
file_name: 2022_EuropJourHaematology_Patxot.pdf
file_size: 1225073
relation: main_file
success: 1
file_date_updated: 2023-01-27T11:42:43Z
has_accepted_license: '1'
intvolume: ' 109'
isi: 1
issue: '5'
keyword:
- Hematology
- General Medicine
language:
- iso: eng
month: '11'
oa: 1
oa_version: Published Version
page: 566-575
pmid: 1
publication: European Journal of Haematology
publication_identifier:
eissn:
- 1600-0609
issn:
- 0902-4441
publication_status: published
publisher: Wiley
quality_controlled: '1'
scopus_import: '1'
status: public
title: 'Haematological changes from conception to childbirth: An indicator of major
pregnancy complications'
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: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
volume: 109
year: '2022'
...
---
_id: '12236'
abstract:
- lang: eng
text: High-entropy materials offer numerous advantages as catalysts, including a
flexible composition to tune the catalytic activity and selectivity and a large
variety of adsorption/reaction sites for multistep or multiple reactions. Herein,
we report on the synthesis, properties, and electrocatalytic performance of an
amorphous high-entropy boride based on abundant transition metals, CoFeNiMnZnB.
This metal boride provides excellent performance toward the oxygen evolution reaction
(OER), including a low overpotential of 261 mV at 10 mA cm–2, a reduced Tafel
slope of 56.8 mV dec–1, and very high stability. The outstanding OER performance
of CoFeNiMnZnB is attributed to the synergistic interactions between the different
metals, the leaching of Zn ions, the generation of oxygen vacancies, and the in
situ formation of an amorphous oxyhydroxide at the CoFeNiMnZnB surface during
the OER.
acknowledgement: This work was supported by the Spanish MCIN project COMBENERGY (PID2019-105490RB-C32).
X.W. and L.Y. thank the China Scholarship Council (CSC) for the scholarship support.
article_processing_charge: No
article_type: original
author:
- first_name: Xiang
full_name: Wang, Xiang
last_name: Wang
- first_name: Yong
full_name: Zuo, Yong
last_name: Zuo
- first_name: Sharona
full_name: Horta, Sharona
id: 03a7e858-01b1-11ec-8b71-99ae6c4a05bc
last_name: Horta
- first_name: Ren
full_name: He, Ren
last_name: He
- first_name: Linlin
full_name: Yang, Linlin
last_name: Yang
- first_name: Ahmad
full_name: Ostovari Moghaddam, Ahmad
last_name: Ostovari Moghaddam
- first_name: Maria
full_name: Ibáñez, Maria
id: 43C61214-F248-11E8-B48F-1D18A9856A87
last_name: Ibáñez
orcid: 0000-0001-5013-2843
- first_name: Xueqiang
full_name: Qi, Xueqiang
last_name: Qi
- first_name: Andreu
full_name: Cabot, Andreu
last_name: Cabot
citation:
ama: Wang X, Zuo Y, Horta S, et al. CoFeNiMnZnB as a high-entropy metal boride to
boost the oxygen evolution reaction. ACS Applied Materials & Interfaces.
2022;14(42):48212-48219. doi:10.1021/acsami.2c11627
apa: Wang, X., Zuo, Y., Horta, S., He, R., Yang, L., Ostovari Moghaddam, A., … Cabot,
A. (2022). CoFeNiMnZnB as a high-entropy metal boride to boost the oxygen evolution
reaction. ACS Applied Materials & Interfaces. American Chemical Society.
https://doi.org/10.1021/acsami.2c11627
chicago: Wang, Xiang, Yong Zuo, Sharona Horta, Ren He, Linlin Yang, Ahmad Ostovari
Moghaddam, Maria Ibáñez, Xueqiang Qi, and Andreu Cabot. “CoFeNiMnZnB as a High-Entropy
Metal Boride to Boost the Oxygen Evolution Reaction.” ACS Applied Materials
& Interfaces. American Chemical Society, 2022. https://doi.org/10.1021/acsami.2c11627.
ieee: X. Wang et al., “CoFeNiMnZnB as a high-entropy metal boride to boost
the oxygen evolution reaction,” ACS Applied Materials & Interfaces,
vol. 14, no. 42. American Chemical Society, pp. 48212–48219, 2022.
ista: Wang X, Zuo Y, Horta S, He R, Yang L, Ostovari Moghaddam A, Ibáñez M, Qi X,
Cabot A. 2022. CoFeNiMnZnB as a high-entropy metal boride to boost the oxygen
evolution reaction. ACS Applied Materials & Interfaces. 14(42), 48212–48219.
mla: Wang, Xiang, et al. “CoFeNiMnZnB as a High-Entropy Metal Boride to Boost the
Oxygen Evolution Reaction.” ACS Applied Materials & Interfaces, vol.
14, no. 42, American Chemical Society, 2022, pp. 48212–19, doi:10.1021/acsami.2c11627.
short: X. Wang, Y. Zuo, S. Horta, R. He, L. Yang, A. Ostovari Moghaddam, M. Ibáñez,
X. Qi, A. Cabot, ACS Applied Materials & Interfaces 14 (2022) 48212–48219.
date_created: 2023-01-16T09:51:10Z
date_published: 2022-10-14T00:00:00Z
date_updated: 2023-10-04T08:28:14Z
day: '14'
department:
- _id: MaIb
doi: 10.1021/acsami.2c11627
external_id:
isi:
- '000873782700001'
pmid:
- '36239982'
intvolume: ' 14'
isi: 1
issue: '42'
keyword:
- General Materials Science
language:
- iso: eng
month: '10'
oa_version: None
page: 48212-48219
pmid: 1
publication: ACS Applied Materials & Interfaces
publication_identifier:
eissn:
- 1944-8252
issn:
- 1944-8244
publication_status: published
publisher: American Chemical Society
quality_controlled: '1'
scopus_import: '1'
status: public
title: CoFeNiMnZnB as a high-entropy metal boride to boost the oxygen evolution reaction
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 14
year: '2022'
...
---
OA_place: publisher
OA_type: free access
_id: '12238'
abstract:
- lang: eng
text: Upon the initiation of collective cell migration, the cells at the free edge
are specified as leader cells; however, the mechanism underlying the leader cell
specification remains elusive. Here, we show that lamellipodial extension after
the release from mechanical confinement causes sustained extracellular signal-regulated
kinase (ERK) activation and underlies the leader cell specification. Live-imaging
of Madin-Darby canine kidney (MDCK) cells and mouse epidermis through the use
of Förster resonance energy transfer (FRET)-based biosensors showed that leader
cells exhibit sustained ERK activation in a hepatocyte growth factor (HGF)-dependent
manner. Meanwhile, follower cells exhibit oscillatory ERK activation waves in
an epidermal growth factor (EGF) signaling-dependent manner. Lamellipodial extension
at the free edge increases the cellular sensitivity to HGF. The HGF-dependent
ERK activation, in turn, promotes lamellipodial extension, thereby forming a positive
feedback loop between cell extension and ERK activation and specifying the cells
at the free edge as the leader cells. Our findings show that the integration of
physical and biochemical cues underlies the leader cell specification during collective
cell migration.
acknowledgement: We thank the members of the Matsuda Laboratory for their helpful
discussion and encouragement, and we thank K. Hirano and K. Takakura for their technical
assistance. This work was supported by the Kyoto University Live Imaging Center.
Financial support was provided in the form of JSPS KAKENHI grants (nos. 17J02107
and 20K22653 to N.H., and 20H05898 and 19H00993 to M.M.), a JST CREST grant (no.
JPMJCR1654 to M.M.), a Moonshot R&D grant (no. JPMJPS2022-11 to M.M.), Generalitat
de Catalunya and the CERCA Programme (no. SGR-2017-01602 to X.T.), MICCINN/FEDER
(no. PGC2018-099645-B-I00 to X.T.), and European Research Council (no. Adv-883739
to X.T.). IBEC is a recipient of a Severo Ochoa Award of Excellence from the MINECO.
This work was partly supported by an Extramural Collaborative Research Grant of
Cancer Research Institute, Kanazawa University.
article_processing_charge: No
article_type: original
author:
- first_name: Naoya
full_name: Hino, Naoya
id: 5299a9ce-7679-11eb-a7bc-d1e62b936307
last_name: Hino
- first_name: Kimiya
full_name: Matsuda, Kimiya
last_name: Matsuda
- first_name: Yuya
full_name: Jikko, Yuya
last_name: Jikko
- first_name: Gembu
full_name: Maryu, Gembu
last_name: Maryu
- first_name: Katsuya
full_name: Sakai, Katsuya
last_name: Sakai
- first_name: Ryu
full_name: Imamura, Ryu
last_name: Imamura
- first_name: Shinya
full_name: Tsukiji, Shinya
last_name: Tsukiji
- first_name: Kazuhiro
full_name: Aoki, Kazuhiro
last_name: Aoki
- first_name: Kenta
full_name: Terai, Kenta
last_name: Terai
- first_name: Tsuyoshi
full_name: Hirashima, Tsuyoshi
last_name: Hirashima
- first_name: Xavier
full_name: Trepat, Xavier
last_name: Trepat
- first_name: Michiyuki
full_name: Matsuda, Michiyuki
last_name: Matsuda
citation:
ama: Hino N, Matsuda K, Jikko Y, et al. A feedback loop between lamellipodial extension
and HGF-ERK signaling specifies leader cells during collective cell migration.
Developmental Cell. 2022;57(19):2290-2304.e7. doi:10.1016/j.devcel.2022.09.003
apa: Hino, N., Matsuda, K., Jikko, Y., Maryu, G., Sakai, K., Imamura, R., … Matsuda,
M. (2022). A feedback loop between lamellipodial extension and HGF-ERK signaling
specifies leader cells during collective cell migration. Developmental Cell.
Elsevier. https://doi.org/10.1016/j.devcel.2022.09.003
chicago: Hino, Naoya, Kimiya Matsuda, Yuya Jikko, Gembu Maryu, Katsuya Sakai, Ryu
Imamura, Shinya Tsukiji, et al. “A Feedback Loop between Lamellipodial Extension
and HGF-ERK Signaling Specifies Leader Cells during Collective Cell Migration.”
Developmental Cell. Elsevier, 2022. https://doi.org/10.1016/j.devcel.2022.09.003.
ieee: N. Hino et al., “A feedback loop between lamellipodial extension and
HGF-ERK signaling specifies leader cells during collective cell migration,” Developmental
Cell, vol. 57, no. 19. Elsevier, p. 2290–2304.e7, 2022.
ista: Hino N, Matsuda K, Jikko Y, Maryu G, Sakai K, Imamura R, Tsukiji S, Aoki K,
Terai K, Hirashima T, Trepat X, Matsuda M. 2022. A feedback loop between lamellipodial
extension and HGF-ERK signaling specifies leader cells during collective cell
migration. Developmental Cell. 57(19), 2290–2304.e7.
mla: Hino, Naoya, et al. “A Feedback Loop between Lamellipodial Extension and HGF-ERK
Signaling Specifies Leader Cells during Collective Cell Migration.” Developmental
Cell, vol. 57, no. 19, Elsevier, 2022, p. 2290–2304.e7, doi:10.1016/j.devcel.2022.09.003.
short: N. Hino, K. Matsuda, Y. Jikko, G. Maryu, K. Sakai, R. Imamura, S. Tsukiji,
K. Aoki, K. Terai, T. Hirashima, X. Trepat, M. Matsuda, Developmental Cell 57
(2022) 2290–2304.e7.
corr_author: '1'
date_created: 2023-01-16T09:51:39Z
date_published: 2022-10-01T00:00:00Z
date_updated: 2025-06-25T07:35:27Z
day: '01'
department:
- _id: CaHe
doi: 10.1016/j.devcel.2022.09.003
external_id:
isi:
- '000898428700006'
pmid:
- '36174555'
intvolume: ' 57'
isi: 1
issue: '19'
keyword:
- Developmental Biology
- Cell Biology
- General Biochemistry
- Genetics and Molecular Biology
- Molecular Biology
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.1016/j.devcel.2022.09.003
month: '10'
oa: 1
oa_version: Published Version
page: 2290-2304.e7
pmid: 1
publication: Developmental Cell
publication_identifier:
issn:
- 1534-5807
publication_status: published
publisher: Elsevier
quality_controlled: '1'
scopus_import: '1'
status: public
title: A feedback loop between lamellipodial extension and HGF-ERK signaling specifies
leader cells during collective cell migration
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 57
year: '2022'
...
---
_id: '12239'
abstract:
- lang: eng
text: Biological systems are the sum of their dynamic three-dimensional (3D) parts.
Therefore, it is critical to study biological structures in 3D and at high resolution
to gain insights into their physiological functions. Electron microscopy of metal
replicas of unroofed cells and isolated organelles has been a key technique to
visualize intracellular structures at nanometer resolution. However, many of these
methods require specialized equipment and personnel to complete them. Here, we
present novel accessible methods to analyze biological structures in unroofed
cells and biochemically isolated organelles in 3D and at nanometer resolution,
focusing on Arabidopsis clathrin-coated vesicles (CCVs). While CCVs are essential
trafficking organelles, their detailed structural information is lacking due to
their poor preservation when observed via classical electron microscopy protocols
experiments. First, we establish a method to visualize CCVs in unroofed cells
using scanning transmission electron microscopy tomography, providing sufficient
resolution to define the clathrin coat arrangements. Critically, the samples are
prepared directly on electron microscopy grids, removing the requirement to use
extremely corrosive acids, thereby enabling the use of this method in any electron
microscopy lab. Secondly, we demonstrate that this standardized sample preparation
allows the direct comparison of isolated CCV samples with those visualized in
cells. Finally, to facilitate the high-throughput and robust screening of metal
replicated samples, we provide a deep learning analysis method to screen the “pseudo
3D” morphologies of CCVs imaged with 2D modalities. Collectively, our work establishes
accessible ways to examine the 3D structure of biological samples and provide
novel insights into the structure of plant CCVs.
acknowledged_ssus:
- _id: EM-Fac
- _id: LifeSc
- _id: Bio
acknowledgement: A.J. is supported by funding from the Austrian Science Fund I3630B25
(to J.F.). This research was supported by the Scientific Service Units of Institute
of Science and Technology Austria (ISTA) through resources provided by the Electron
Microscopy Facility, Lab Support Facility, and the Imaging and Optics Facility.
We acknowledge Prof. David Robinson (Heidelberg) and Prof. Jan Traas (Lyon) for
making us aware of previously published classical on-grid preparation methods. No
conflict of interest declared.
article_processing_charge: Yes (via OA deal)
article_type: original
author:
- first_name: Alexander J
full_name: Johnson, Alexander J
id: 46A62C3A-F248-11E8-B48F-1D18A9856A87
last_name: Johnson
orcid: 0000-0002-2739-8843
- first_name: Walter
full_name: Kaufmann, Walter
id: 3F99E422-F248-11E8-B48F-1D18A9856A87
last_name: Kaufmann
orcid: 0000-0001-9735-5315
- first_name: Christoph M
full_name: Sommer, Christoph M
id: 4DF26D8C-F248-11E8-B48F-1D18A9856A87
last_name: Sommer
orcid: 0000-0003-1216-9105
- first_name: Tommaso
full_name: Costanzo, Tommaso
id: D93824F4-D9BA-11E9-BB12-F207E6697425
last_name: Costanzo
orcid: 0000-0001-9732-3815
- first_name: Dana A.
full_name: Dahhan, Dana A.
last_name: Dahhan
- first_name: Sebastian Y.
full_name: Bednarek, Sebastian Y.
last_name: Bednarek
- first_name: Jiří
full_name: Friml, Jiří
id: 4159519E-F248-11E8-B48F-1D18A9856A87
last_name: Friml
orcid: 0000-0002-8302-7596
citation:
ama: Johnson AJ, Kaufmann W, Sommer CM, et al. Three-dimensional visualization of
planta clathrin-coated vesicles at ultrastructural resolution. Molecular Plant.
2022;15(10):1533-1542. doi:10.1016/j.molp.2022.09.003
apa: Johnson, A. J., Kaufmann, W., Sommer, C. M., Costanzo, T., Dahhan, D. A., Bednarek,
S. Y., & Friml, J. (2022). Three-dimensional visualization of planta clathrin-coated
vesicles at ultrastructural resolution. Molecular Plant. Elsevier. https://doi.org/10.1016/j.molp.2022.09.003
chicago: Johnson, Alexander J, Walter Kaufmann, Christoph M Sommer, Tommaso Costanzo,
Dana A. Dahhan, Sebastian Y. Bednarek, and Jiří Friml. “Three-Dimensional Visualization
of Planta Clathrin-Coated Vesicles at Ultrastructural Resolution.” Molecular
Plant. Elsevier, 2022. https://doi.org/10.1016/j.molp.2022.09.003.
ieee: A. J. Johnson et al., “Three-dimensional visualization of planta clathrin-coated
vesicles at ultrastructural resolution,” Molecular Plant, vol. 15, no.
10. Elsevier, pp. 1533–1542, 2022.
ista: Johnson AJ, Kaufmann W, Sommer CM, Costanzo T, Dahhan DA, Bednarek SY, Friml
J. 2022. Three-dimensional visualization of planta clathrin-coated vesicles at
ultrastructural resolution. Molecular Plant. 15(10), 1533–1542.
mla: Johnson, Alexander J., et al. “Three-Dimensional Visualization of Planta Clathrin-Coated
Vesicles at Ultrastructural Resolution.” Molecular Plant, vol. 15, no.
10, Elsevier, 2022, pp. 1533–42, doi:10.1016/j.molp.2022.09.003.
short: A.J. Johnson, W. Kaufmann, C.M. Sommer, T. Costanzo, D.A. Dahhan, S.Y. Bednarek,
J. Friml, Molecular Plant 15 (2022) 1533–1542.
corr_author: '1'
date_created: 2023-01-16T09:51:49Z
date_published: 2022-10-03T00:00:00Z
date_updated: 2025-04-15T07:32:09Z
day: '03'
ddc:
- '580'
department:
- _id: JiFr
- _id: EM-Fac
- _id: Bio
doi: 10.1016/j.molp.2022.09.003
external_id:
isi:
- '000882769800009'
pmid:
- '36081349'
file:
- access_level: open_access
checksum: 04d5c12490052d03e4dc4412338a43dd
content_type: application/pdf
creator: dernst
date_created: 2023-01-30T07:46:51Z
date_updated: 2023-01-30T07:46:51Z
file_id: '12435'
file_name: 2022_MolecularPlant_Johnson.pdf
file_size: 2307251
relation: main_file
success: 1
file_date_updated: 2023-01-30T07:46:51Z
has_accepted_license: '1'
intvolume: ' 15'
isi: 1
issue: '10'
keyword:
- Plant Science
- Molecular Biology
language:
- iso: eng
license: https://creativecommons.org/licenses/by/4.0/
month: '10'
oa: 1
oa_version: Published Version
page: 1533-1542
pmid: 1
project:
- _id: 26538374-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: I03630
name: Molecular mechanisms of endocytic cargo recognition in plants
publication: Molecular Plant
publication_identifier:
issn:
- 1674-2052
publication_status: published
publisher: Elsevier
quality_controlled: '1'
scopus_import: '1'
status: public
title: Three-dimensional visualization of planta clathrin-coated vesicles at ultrastructural
resolution
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: journal_article
user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
volume: 15
year: '2022'
...
---
_id: '12243'
abstract:
- lang: eng
text: 'We consider the eigenvalues of a large dimensional real or complex Ginibre
matrix in the region of the complex plane where their real parts reach their maximum
value. This maximum follows the Gumbel distribution and that these extreme eigenvalues
form a Poisson point process as the dimension asymptotically tends to infinity.
In the complex case, these facts have already been established by Bender [Probab.
Theory Relat. Fields 147, 241 (2010)] and in the real case by Akemann and Phillips
[J. Stat. Phys. 155, 421 (2014)] even for the more general elliptic ensemble with
a sophisticated saddle point analysis. The purpose of this article is to give
a very short direct proof in the Ginibre case with an effective error term. Moreover,
our estimates on the correlation kernel in this regime serve as a key input for
accurately locating [Formula: see text] for any large matrix X with i.i.d. entries
in the companion paper [G. Cipolloni et al., arXiv:2206.04448 (2022)]. '
acknowledgement: "The authors are grateful to G. Akemann for bringing Refs. 19 and
24–26 to their attention. Discussions with Guillaume Dubach on a preliminary version
of this project are acknowledged.\r\nL.E. and Y.X. were supported by the ERC Advanced
Grant “RMTBeyond” under Grant No. 101020331. D.S. was supported by Dr. Max Rössler,
the Walter Haefner Foundation, and the ETH Zürich Foundation."
article_number: '103303'
article_processing_charge: Yes (via OA deal)
article_type: original
arxiv: 1
author:
- first_name: Giorgio
full_name: Cipolloni, Giorgio
id: 42198EFA-F248-11E8-B48F-1D18A9856A87
last_name: Cipolloni
orcid: 0000-0002-4901-7992
- first_name: László
full_name: Erdös, László
id: 4DBD5372-F248-11E8-B48F-1D18A9856A87
last_name: Erdös
orcid: 0000-0001-5366-9603
- first_name: Dominik J
full_name: Schröder, Dominik J
id: 408ED176-F248-11E8-B48F-1D18A9856A87
last_name: Schröder
orcid: 0000-0002-2904-1856
- first_name: Yuanyuan
full_name: Xu, Yuanyuan
id: 7902bdb1-a2a4-11eb-a164-c9216f71aea3
last_name: Xu
orcid: 0000-0003-1559-1205
citation:
ama: Cipolloni G, Erdös L, Schröder DJ, Xu Y. Directional extremal statistics for
Ginibre eigenvalues. Journal of Mathematical Physics. 2022;63(10). doi:10.1063/5.0104290
apa: Cipolloni, G., Erdös, L., Schröder, D. J., & Xu, Y. (2022). Directional
extremal statistics for Ginibre eigenvalues. Journal of Mathematical Physics.
AIP Publishing. https://doi.org/10.1063/5.0104290
chicago: Cipolloni, Giorgio, László Erdös, Dominik J Schröder, and Yuanyuan Xu.
“Directional Extremal Statistics for Ginibre Eigenvalues.” Journal of Mathematical
Physics. AIP Publishing, 2022. https://doi.org/10.1063/5.0104290.
ieee: G. Cipolloni, L. Erdös, D. J. Schröder, and Y. Xu, “Directional extremal statistics
for Ginibre eigenvalues,” Journal of Mathematical Physics, vol. 63, no.
10. AIP Publishing, 2022.
ista: Cipolloni G, Erdös L, Schröder DJ, Xu Y. 2022. Directional extremal statistics
for Ginibre eigenvalues. Journal of Mathematical Physics. 63(10), 103303.
mla: Cipolloni, Giorgio, et al. “Directional Extremal Statistics for Ginibre Eigenvalues.”
Journal of Mathematical Physics, vol. 63, no. 10, 103303, AIP Publishing,
2022, doi:10.1063/5.0104290.
short: G. Cipolloni, L. Erdös, D.J. Schröder, Y. Xu, Journal of Mathematical Physics
63 (2022).
date_created: 2023-01-16T09:52:58Z
date_published: 2022-10-14T00:00:00Z
date_updated: 2025-04-14T07:57:18Z
day: '14'
ddc:
- '510'
- '530'
department:
- _id: LaEr
doi: 10.1063/5.0104290
ec_funded: 1
external_id:
arxiv:
- '2206.04443'
isi:
- '000869715800001'
file:
- access_level: open_access
checksum: 2db278ae5b07f345a7e3fec1f92b5c33
content_type: application/pdf
creator: dernst
date_created: 2023-01-30T08:01:10Z
date_updated: 2023-01-30T08:01:10Z
file_id: '12436'
file_name: 2022_JourMathPhysics_Cipolloni2.pdf
file_size: 7356807
relation: main_file
success: 1
file_date_updated: 2023-01-30T08:01:10Z
has_accepted_license: '1'
intvolume: ' 63'
isi: 1
issue: '10'
keyword:
- Mathematical Physics
- Statistical and Nonlinear Physics
language:
- iso: eng
month: '10'
oa: 1
oa_version: Published Version
project:
- _id: 62796744-2b32-11ec-9570-940b20777f1d
call_identifier: H2020
grant_number: '101020331'
name: Random matrices beyond Wigner-Dyson-Mehta
publication: Journal of Mathematical Physics
publication_identifier:
eissn:
- 1089-7658
issn:
- 0022-2488
publication_status: published
publisher: AIP Publishing
quality_controlled: '1'
scopus_import: '1'
status: public
title: Directional extremal statistics for Ginibre eigenvalues
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: journal_article
user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
volume: 63
year: '2022'
...
---
_id: '12245'
abstract:
- lang: eng
text: MicroRNAs (miRs) have an important role in tuning dynamic gene expression.
However, the mechanism by which they are quantitatively controlled is unknown.
We show that the amount of mature miR-9, a key regulator of neuronal development,
increases during zebrafish neurogenesis in a sharp stepwise manner. We characterize
the spatiotemporal profile of seven distinct microRNA primary transcripts (pri-mir)-9s
that produce the same mature miR-9 and show that they are sequentially expressed
during hindbrain neurogenesis. Expression of late-onset pri-mir-9-1 is added on
to, rather than replacing, the expression of early onset pri-mir-9-4 and -9-5
in single cells. CRISPR/Cas9 mutation of the late-onset pri-mir-9-1 prevents the
developmental increase of mature miR-9, reduces late neuronal differentiation
and fails to downregulate Her6 at late stages. Mathematical modelling shows that
an adaptive network containing Her6 is insensitive to linear increases in miR-9
but responds to stepwise increases of miR-9. We suggest that a sharp stepwise
increase of mature miR-9 is created by sequential and additive temporal activation
of distinct loci. This may be a strategy to overcome adaptation and facilitate
a transition of Her6 to a new dynamic regime or steady state.
acknowledgement: "We are grateful to Dr Tom Pettini for the advice on smiFISH technique
and Dr Laure Bally-Cuif for sharing plasmids. The authors also thank the Biological
Services Facility, Bioimaging and Systems Microscopy Facilities of the University
of Manchester for technical support.\r\nThis work was supported by a Wellcome Trust
Senior Research Fellowship (090868/Z/09/Z) and a Wellcome Trust Investigator Award
(224394/Z/21/Z) to N.P. and a Medical Research Council Career Development Award
to C.S.M. (MR/V032534/1). J.B. was supported by a Wellcome Trust Four-Year PhD Studentship
in Basic Science (219992/Z/19/Z). Open Access funding provided by The University
of Manchester. Deposited in PMC for immediate release."
article_number: dev200474
article_processing_charge: No
article_type: original
author:
- first_name: Ximena
full_name: Soto, Ximena
last_name: Soto
- first_name: Joshua
full_name: Burton, Joshua
last_name: Burton
- first_name: Cerys S.
full_name: Manning, Cerys S.
last_name: Manning
- first_name: Thomas
full_name: Minchington, Thomas
id: 7d1648cb-19e9-11eb-8e7a-f8c037fb3e3f
last_name: Minchington
- first_name: Robert
full_name: Lea, Robert
last_name: Lea
- first_name: Jessica
full_name: Lee, Jessica
last_name: Lee
- first_name: Jochen
full_name: Kursawe, Jochen
last_name: Kursawe
- first_name: Magnus
full_name: Rattray, Magnus
last_name: Rattray
- first_name: Nancy
full_name: Papalopulu, Nancy
last_name: Papalopulu
citation:
ama: Soto X, Burton J, Manning CS, et al. Sequential and additive expression of
miR-9 precursors control timing of neurogenesis. Development. 2022;149(19).
doi:10.1242/dev.200474
apa: Soto, X., Burton, J., Manning, C. S., Minchington, T., Lea, R., Lee, J., …
Papalopulu, N. (2022). Sequential and additive expression of miR-9 precursors
control timing of neurogenesis. Development. The Company of Biologists.
https://doi.org/10.1242/dev.200474
chicago: Soto, Ximena, Joshua Burton, Cerys S. Manning, Thomas Minchington, Robert
Lea, Jessica Lee, Jochen Kursawe, Magnus Rattray, and Nancy Papalopulu. “Sequential
and Additive Expression of MiR-9 Precursors Control Timing of Neurogenesis.” Development.
The Company of Biologists, 2022. https://doi.org/10.1242/dev.200474.
ieee: X. Soto et al., “Sequential and additive expression of miR-9 precursors
control timing of neurogenesis,” Development, vol. 149, no. 19. The Company
of Biologists, 2022.
ista: Soto X, Burton J, Manning CS, Minchington T, Lea R, Lee J, Kursawe J, Rattray
M, Papalopulu N. 2022. Sequential and additive expression of miR-9 precursors
control timing of neurogenesis. Development. 149(19), dev200474.
mla: Soto, Ximena, et al. “Sequential and Additive Expression of MiR-9 Precursors
Control Timing of Neurogenesis.” Development, vol. 149, no. 19, dev200474,
The Company of Biologists, 2022, doi:10.1242/dev.200474.
short: X. Soto, J. Burton, C.S. Manning, T. Minchington, R. Lea, J. Lee, J. Kursawe,
M. Rattray, N. Papalopulu, Development 149 (2022).
date_created: 2023-01-16T09:53:17Z
date_published: 2022-10-01T00:00:00Z
date_updated: 2023-08-04T09:41:08Z
day: '01'
ddc:
- '570'
department:
- _id: AnKi
doi: 10.1242/dev.200474
external_id:
isi:
- '000918161000003'
pmid:
- '36189829'
file:
- access_level: open_access
checksum: d7c29b74e9e4032308228cc704a30e88
content_type: application/pdf
creator: dernst
date_created: 2023-01-30T08:35:44Z
date_updated: 2023-01-30T08:35:44Z
file_id: '12438'
file_name: 2022_Development_Soto.pdf
file_size: 9348839
relation: main_file
success: 1
file_date_updated: 2023-01-30T08:35:44Z
has_accepted_license: '1'
intvolume: ' 149'
isi: 1
issue: '19'
keyword:
- Developmental Biology
- Molecular Biology
language:
- iso: eng
month: '10'
oa: 1
oa_version: Published Version
pmid: 1
publication: Development
publication_identifier:
eissn:
- 1477-9129
issn:
- 0950-1991
publication_status: published
publisher: The Company of Biologists
quality_controlled: '1'
related_material:
link:
- relation: software
url: ' https://github.com/burtonjosh/StepwiseMir9'
scopus_import: '1'
status: public
title: Sequential and additive expression of miR-9 precursors control timing of neurogenesis
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: journal_article
user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
volume: 149
year: '2022'
...
---
_id: '12246'
abstract:
- lang: eng
text: The Lieb–Oxford inequality provides a lower bound on the Coulomb energy of
a classical system of N identical charges only in terms of their one-particle
density. We prove here a new estimate on the best constant in this inequality.
Numerical evaluation provides the value 1.58, which is a significant improvement
to the previously known value 1.64. The best constant has recently been shown
to be larger than 1.44. In a second part, we prove that the constant can be reduced
to 1.25 when the inequality is restricted to Hartree–Fock states. This is the
first proof that the exchange term is always much lower than the full indirect
Coulomb energy.
acknowledgement: We would like to thank David Gontier for useful advice on the numerical
simulations. This project has received funding from the European Research Council
(ERC) under the European Union’s Horizon 2020 research and innovation program (Grant
Agreements MDFT No. 725528 of M.L. and AQUAMS No. 694227 of R.S.). We are thankful
for the hospitality of the Institut Henri Poincaré in Paris, where part of this
work was done.
article_number: '92'
article_processing_charge: No
article_type: original
arxiv: 1
author:
- first_name: Mathieu
full_name: Lewin, Mathieu
last_name: Lewin
- first_name: Elliott H.
full_name: Lieb, Elliott H.
last_name: Lieb
- first_name: Robert
full_name: Seiringer, Robert
id: 4AFD0470-F248-11E8-B48F-1D18A9856A87
last_name: Seiringer
orcid: 0000-0002-6781-0521
citation:
ama: Lewin M, Lieb EH, Seiringer R. Improved Lieb–Oxford bound on the indirect and
exchange energies. Letters in Mathematical Physics. 2022;112(5). doi:10.1007/s11005-022-01584-5
apa: Lewin, M., Lieb, E. H., & Seiringer, R. (2022). Improved Lieb–Oxford bound
on the indirect and exchange energies. Letters in Mathematical Physics.
Springer Nature. https://doi.org/10.1007/s11005-022-01584-5
chicago: Lewin, Mathieu, Elliott H. Lieb, and Robert Seiringer. “Improved Lieb–Oxford
Bound on the Indirect and Exchange Energies.” Letters in Mathematical Physics.
Springer Nature, 2022. https://doi.org/10.1007/s11005-022-01584-5.
ieee: M. Lewin, E. H. Lieb, and R. Seiringer, “Improved Lieb–Oxford bound on the
indirect and exchange energies,” Letters in Mathematical Physics, vol.
112, no. 5. Springer Nature, 2022.
ista: Lewin M, Lieb EH, Seiringer R. 2022. Improved Lieb–Oxford bound on the indirect
and exchange energies. Letters in Mathematical Physics. 112(5), 92.
mla: Lewin, Mathieu, et al. “Improved Lieb–Oxford Bound on the Indirect and Exchange
Energies.” Letters in Mathematical Physics, vol. 112, no. 5, 92, Springer
Nature, 2022, doi:10.1007/s11005-022-01584-5.
short: M. Lewin, E.H. Lieb, R. Seiringer, Letters in Mathematical Physics 112 (2022).
date_created: 2023-01-16T09:53:54Z
date_published: 2022-09-15T00:00:00Z
date_updated: 2025-04-14T07:26:59Z
day: '15'
department:
- _id: RoSe
doi: 10.1007/s11005-022-01584-5
ec_funded: 1
external_id:
arxiv:
- '2203.12473'
isi:
- '000854762600001'
intvolume: ' 112'
isi: 1
issue: '5'
keyword:
- Mathematical Physics
- Statistical and Nonlinear Physics
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.48550/arXiv.2203.12473
month: '09'
oa: 1
oa_version: Preprint
project:
- _id: 25C6DC12-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '694227'
name: Analysis of quantum many-body systems
publication: Letters in Mathematical Physics
publication_identifier:
eissn:
- 1573-0530
issn:
- 0377-9017
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
scopus_import: '1'
status: public
title: Improved Lieb–Oxford bound on the indirect and exchange energies
type: journal_article
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
volume: 112
year: '2022'
...
---
_id: '12247'
abstract:
- lang: eng
text: Chromosomal inversions have been shown to play a major role in a local adaptation
by suppressing recombination between alternative arrangements and maintaining
beneficial allele combinations. However, so far, their importance relative to
the remaining genome remains largely unknown. Understanding the genetic architecture
of adaptation requires better estimates of how loci of different effect sizes
contribute to phenotypic variation. Here, we used three Swedish islands where
the marine snail Littorina saxatilis has repeatedly evolved into two distinct
ecotypes along a habitat transition. We estimated the contribution of inversion
polymorphisms to phenotypic divergence while controlling for polygenic effects
in the remaining genome using a quantitative genetics framework. We confirmed
the importance of inversions but showed that contributions of loci outside inversions
are of similar magnitude, with variable proportions dependent on the trait and
the population. Some inversions showed consistent effects across all sites, whereas
others exhibited site-specific effects, indicating that the genomic basis for
replicated phenotypic divergence is only partly shared. The contributions of sexual
dimorphism as well as environmental factors to phenotypic variation were significant
but minor compared to inversions and polygenic background. Overall, this integrated
approach provides insight into the multiple mechanisms contributing to parallel
phenotypic divergence.
acknowledgement: We thank everyone who helped with fieldwork, snail processing, and
DNA extractions, particularly Laura Brettell, Mårten Duvetorp, Juan Galindo, Anne-Lise
Liabot, Irena Senčić, and Zuzanna Zagrodzka. We also thank Rui Faria and Jenny Larsson
for their contributions, with inversions and shell shape respectively. KJ was funded
by the Swedish research council Vetenskapsrådet, grant number 2017-03798. R.K.B.
and E.K. were funded by the European Research Council (ERC-2015-AdG-693030-BARRIERS).
R.K.B. was also funded by the Natural Environment Research Council and the Swedish
Research Council Vetenskapsrådet.
article_processing_charge: No
article_type: original
author:
- first_name: Eva L.
full_name: Koch, Eva L.
last_name: Koch
- first_name: Mark
full_name: Ravinet, Mark
last_name: Ravinet
- first_name: Anja M
full_name: Westram, Anja M
id: 3C147470-F248-11E8-B48F-1D18A9856A87
last_name: Westram
orcid: 0000-0003-1050-4969
- first_name: Kerstin
full_name: Johannesson, Kerstin
last_name: Johannesson
- first_name: Roger K.
full_name: Butlin, Roger K.
last_name: Butlin
citation:
ama: Koch EL, Ravinet M, Westram AM, Johannesson K, Butlin RK. Genetic architecture
of repeated phenotypic divergence in Littorina saxatilis evolution. Evolution.
2022;76(10):2332-2346. doi:10.1111/evo.14602
apa: Koch, E. L., Ravinet, M., Westram, A. M., Johannesson, K., & Butlin, R.
K. (2022). Genetic architecture of repeated phenotypic divergence in Littorina
saxatilis evolution. Evolution. Wiley. https://doi.org/10.1111/evo.14602
chicago: Koch, Eva L., Mark Ravinet, Anja M Westram, Kerstin Johannesson, and Roger
K. Butlin. “Genetic Architecture of Repeated Phenotypic Divergence in Littorina
Saxatilis Evolution.” Evolution. Wiley, 2022. https://doi.org/10.1111/evo.14602.
ieee: E. L. Koch, M. Ravinet, A. M. Westram, K. Johannesson, and R. K. Butlin, “Genetic
architecture of repeated phenotypic divergence in Littorina saxatilis evolution,”
Evolution, vol. 76, no. 10. Wiley, pp. 2332–2346, 2022.
ista: Koch EL, Ravinet M, Westram AM, Johannesson K, Butlin RK. 2022. Genetic architecture
of repeated phenotypic divergence in Littorina saxatilis evolution. Evolution.
76(10), 2332–2346.
mla: Koch, Eva L., et al. “Genetic Architecture of Repeated Phenotypic Divergence
in Littorina Saxatilis Evolution.” Evolution, vol. 76, no. 10, Wiley, 2022,
pp. 2332–46, doi:10.1111/evo.14602.
short: E.L. Koch, M. Ravinet, A.M. Westram, K. Johannesson, R.K. Butlin, Evolution
76 (2022) 2332–2346.
date_created: 2023-01-16T09:54:15Z
date_published: 2022-10-01T00:00:00Z
date_updated: 2023-08-04T09:42:11Z
day: '01'
ddc:
- '570'
department:
- _id: NiBa
doi: 10.1111/evo.14602
external_id:
isi:
- '000848449100001'
pmid:
- '35994296'
file:
- access_level: open_access
checksum: defd8a4bea61cf00a3c88d4a30e2728c
content_type: application/pdf
creator: dernst
date_created: 2023-01-30T08:45:35Z
date_updated: 2023-01-30T08:45:35Z
file_id: '12439'
file_name: 2022_Evolution_Koch.pdf
file_size: 2990581
relation: main_file
success: 1
file_date_updated: 2023-01-30T08:45:35Z
has_accepted_license: '1'
intvolume: ' 76'
isi: 1
issue: '10'
keyword:
- General Agricultural and Biological Sciences
- Genetics
- Ecology
- Evolution
- Behavior and Systematics
language:
- iso: eng
month: '10'
oa: 1
oa_version: Published Version
page: 2332-2346
pmid: 1
publication: Evolution
publication_identifier:
eissn:
- 1558-5646
issn:
- 0014-3820
publication_status: published
publisher: Wiley
quality_controlled: '1'
related_material:
record:
- id: '13066'
relation: research_data
status: public
scopus_import: '1'
status: public
title: Genetic architecture of repeated phenotypic divergence in Littorina saxatilis
evolution
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: journal_article
user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
volume: 76
year: '2022'
...
---
_id: '12249'
abstract:
- lang: eng
text: 'The chemical potential of a component in a solution is defined as the free
energy change as the amount of that component changes. Computing this fundamental
thermodynamic property from atomistic simulations is notoriously difficult because
of the convergence issues involved in free energy methods and finite size effects.
This Communication presents the so-called S0 method, which can be used to obtain
chemical potentials from static structure factors computed from equilibrium molecular
dynamics simulations under the isothermal–isobaric ensemble. This new method is
demonstrated on the systems of binary Lennard-Jones particles, urea–water mixtures,
a NaCl aqueous solution, and a high-pressure carbon–hydrogen mixture. '
acknowledgement: I thank Daan Frenkel for providing feedback on an early draft and
for stimulating discussions, Debashish Mukherji and Robinson Cortes-Huerto for sharing
the trajectories for urea–water mixtures, and Aleks Reinhardt for useful suggestions
on the manuscript.
article_number: '121101'
article_processing_charge: No
article_type: original
author:
- first_name: Bingqing
full_name: Cheng, Bingqing
id: cbe3cda4-d82c-11eb-8dc7-8ff94289fcc9
last_name: Cheng
orcid: 0000-0002-3584-9632
citation:
ama: Cheng B. Computing chemical potentials of solutions from structure factors.
The Journal of Chemical Physics. 2022;157(12). doi:10.1063/5.0107059
apa: Cheng, B. (2022). Computing chemical potentials of solutions from structure
factors. The Journal of Chemical Physics. AIP Publishing. https://doi.org/10.1063/5.0107059
chicago: Cheng, Bingqing. “Computing Chemical Potentials of Solutions from Structure
Factors.” The Journal of Chemical Physics. AIP Publishing, 2022. https://doi.org/10.1063/5.0107059.
ieee: B. Cheng, “Computing chemical potentials of solutions from structure factors,”
The Journal of Chemical Physics, vol. 157, no. 12. AIP Publishing, 2022.
ista: Cheng B. 2022. Computing chemical potentials of solutions from structure factors.
The Journal of Chemical Physics. 157(12), 121101.
mla: Cheng, Bingqing. “Computing Chemical Potentials of Solutions from Structure
Factors.” The Journal of Chemical Physics, vol. 157, no. 12, 121101, AIP
Publishing, 2022, doi:10.1063/5.0107059.
short: B. Cheng, The Journal of Chemical Physics 157 (2022).
corr_author: '1'
date_created: 2023-01-16T09:56:20Z
date_published: 2022-09-30T00:00:00Z
date_updated: 2025-06-11T13:41:59Z
day: '30'
ddc:
- '530'
- '540'
department:
- _id: BiCh
doi: 10.1063/5.0107059
external_id:
isi:
- '000862856000003'
pmid:
- '36182422'
file:
- access_level: open_access
checksum: b0915b706568a663a9a372fca24adf35
content_type: application/pdf
creator: dernst
date_created: 2023-01-30T09:07:00Z
date_updated: 2023-01-30T09:07:00Z
file_id: '12441'
file_name: 2022_JourChemPhysics_Cheng.pdf
file_size: 4402384
relation: main_file
success: 1
file_date_updated: 2023-01-30T09:07:00Z
has_accepted_license: '1'
intvolume: ' 157'
isi: 1
issue: '12'
keyword:
- Physical and Theoretical Chemistry
- General Physics and Astronomy
language:
- iso: eng
month: '09'
oa: 1
oa_version: Published Version
pmid: 1
publication: The Journal of Chemical Physics
publication_identifier:
eissn:
- 1089-7690
issn:
- 0021-9606
publication_status: published
publisher: AIP Publishing
quality_controlled: '1'
related_material:
link:
- relation: software
url: https://github.com/ BingqingCheng/S0
scopus_import: '1'
status: public
title: Computing chemical potentials of solutions from structure factors
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: 157
year: '2022'
...
---
_id: '12251'
abstract:
- lang: eng
text: Amyloid formation is linked to devastating neurodegenerative diseases, motivating
detailed studies of the mechanisms of amyloid formation. For Aβ, the peptide associated
with Alzheimer’s disease, the mechanism and rate of aggregation have been established
for a range of variants and conditions in vitro and
in bodily fluids. A key outstanding question is how the relative stabilities of
monomers, fibrils and intermediates affect each step in the fibril formation process.
By monitoring the kinetics of aggregation of Aβ42, in the presence of urea or
guanidinium hydrochloride (GuHCl), we here determine the rates of the underlying
microscopic steps and establish the importance of changes in relative stability
induced by the presence of denaturant for each individual step. Denaturants shift
the equilibrium towards the unfolded state of each species. We find that a non-ionic
denaturant, urea, reduces the overall aggregation rate, and that the effect on
nucleation is stronger than the effect on elongation. Urea reduces the rate of
secondary nucleation by decreasing the coverage of fibril surfaces and the rate
of nucleus formation. It also reduces the rate of primary nucleation, increasing
its reaction order. The ionic denaturant, GuHCl, accelerates the aggregation at
low denaturant concentrations and decelerates the aggregation at high denaturant
concentrations. Below approximately 0.25 M GuHCl, the screening of repulsive electrostatic
interactions between peptides by the charged denaturant dominates, leading to
an increased aggregation rate. At higher GuHCl concentrations, the electrostatic
repulsion is completely screened, and the denaturing effect dominates. The results
illustrate how the differential effects of denaturants on stability of monomer,
oligomer and fibril translate to differential effects on microscopic steps, with
the rate of nucleation being most strongly reduced.
acknowledgement: This work was supported by grants from the Swedish Research Council
(grant no. 2015-00143) and the European Research Council (grant no. 340890).
article_number: '943355'
article_processing_charge: No
article_type: original
author:
- first_name: Tanja
full_name: Weiffert, Tanja
last_name: Weiffert
- first_name: Georg
full_name: Meisl, Georg
last_name: Meisl
- first_name: Samo
full_name: Curk, Samo
last_name: Curk
- first_name: Risto
full_name: Cukalevski, Risto
last_name: Cukalevski
- first_name: Anđela
full_name: Šarić, Anđela
id: bf63d406-f056-11eb-b41d-f263a6566d8b
last_name: Šarić
orcid: 0000-0002-7854-2139
- first_name: Tuomas P. J.
full_name: Knowles, Tuomas P. J.
last_name: Knowles
- first_name: Sara
full_name: Linse, Sara
last_name: Linse
citation:
ama: Weiffert T, Meisl G, Curk S, et al. Influence of denaturants on amyloid β42
aggregation kinetics. Frontiers in Neuroscience. 2022;16. doi:10.3389/fnins.2022.943355
apa: Weiffert, T., Meisl, G., Curk, S., Cukalevski, R., Šarić, A., Knowles, T. P.
J., & Linse, S. (2022). Influence of denaturants on amyloid β42 aggregation
kinetics. Frontiers in Neuroscience. Frontiers Media. https://doi.org/10.3389/fnins.2022.943355
chicago: Weiffert, Tanja, Georg Meisl, Samo Curk, Risto Cukalevski, Anđela Šarić,
Tuomas P. J. Knowles, and Sara Linse. “Influence of Denaturants on Amyloid Β42
Aggregation Kinetics.” Frontiers in Neuroscience. Frontiers Media, 2022.
https://doi.org/10.3389/fnins.2022.943355.
ieee: T. Weiffert et al., “Influence of denaturants on amyloid β42 aggregation
kinetics,” Frontiers in Neuroscience, vol. 16. Frontiers Media, 2022.
ista: Weiffert T, Meisl G, Curk S, Cukalevski R, Šarić A, Knowles TPJ, Linse S.
2022. Influence of denaturants on amyloid β42 aggregation kinetics. Frontiers
in Neuroscience. 16, 943355.
mla: Weiffert, Tanja, et al. “Influence of Denaturants on Amyloid Β42 Aggregation
Kinetics.” Frontiers in Neuroscience, vol. 16, 943355, Frontiers Media,
2022, doi:10.3389/fnins.2022.943355.
short: T. Weiffert, G. Meisl, S. Curk, R. Cukalevski, A. Šarić, T.P.J. Knowles,
S. Linse, Frontiers in Neuroscience 16 (2022).
date_created: 2023-01-16T09:56:43Z
date_published: 2022-09-20T00:00:00Z
date_updated: 2023-08-04T09:48:56Z
day: '20'
ddc:
- '570'
department:
- _id: AnSa
doi: 10.3389/fnins.2022.943355
external_id:
isi:
- '000866287100001'
file:
- access_level: open_access
checksum: e67d16113ffb4fb4fa38a183d169f210
content_type: application/pdf
creator: dernst
date_created: 2023-01-30T09:15:13Z
date_updated: 2023-01-30T09:15:13Z
file_id: '12442'
file_name: 2022_FrontiersNeuroscience_Weiffert2.pdf
file_size: 19798610
relation: main_file
success: 1
file_date_updated: 2023-01-30T09:15:13Z
has_accepted_license: '1'
intvolume: ' 16'
isi: 1
keyword:
- General Neuroscience
language:
- iso: eng
month: '09'
oa: 1
oa_version: Published Version
publication: Frontiers in Neuroscience
publication_identifier:
issn:
- 1662-453X
publication_status: published
publisher: Frontiers Media
quality_controlled: '1'
scopus_import: '1'
status: public
title: Influence of denaturants on amyloid β42 aggregation kinetics
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: journal_article
user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
volume: 16
year: '2022'
...
---
_id: '12252'
abstract:
- lang: eng
text: The COVID−19 pandemic not only resulted in a global crisis, but also accelerated
vaccine development and antibody discovery. Herein we report a synthetic humanized
VHH library development pipeline for nanomolar-range affinity VHH binders to SARS-CoV-2
variants of concern (VoC) receptor binding domains (RBD) isolation. Trinucleotide-based
randomization of CDRs by Kunkel mutagenesis with the subsequent rolling-cycle
amplification resulted in more than 1011 diverse phage display
library in a manageable for a single person number of electroporation reactions.
We identified a number of nanomolar-range affinity VHH binders to SARS-CoV-2 variants
of concern (VoC) receptor binding domains (RBD) by screening a novel synthetic
humanized antibody library. In order to explore the most robust and fast method
for affinity improvement, we performed affinity maturation by CDR1 and CDR2 shuffling
and avidity engineering by multivalent trimeric VHH fusion protein construction.
As a result, H7-Fc and G12x3-Fc binders were developed with the affinities in
nM and pM range respectively. Importantly, these affinities are weakly influenced
by most of SARS-CoV-2 VoC mutations and they retain moderate binding to BA.4\5.
The plaque reduction neutralization test (PRNT) resulted in IC50 = 100 ng\ml and
9.6 ng\ml for H7-Fc and G12x3-Fc antibodies, respectively, for the emerging Omicron
BA.1 variant. Therefore, these VHH could expand the present landscape of SARS-CoV-2
neutralization binders with the therapeutic potential for present and future SARS-CoV-2
variants.
acknowledgement: The authors declare that this study received funding from Immunofusion.
The funder was not involved in the study design, collection, analysis, interpretation
of data, the writing of this article or the decision to submit it for publication.
article_number: '965446'
article_processing_charge: No
article_type: original
author:
- first_name: Dmitri
full_name: Dormeshkin, Dmitri
last_name: Dormeshkin
- first_name: Michail
full_name: Shapira, Michail
last_name: Shapira
- first_name: Simon
full_name: Dubovik, Simon
last_name: Dubovik
- first_name: Anton
full_name: Kavaleuski, Anton
id: 4968f7ad-eb97-11eb-a6c2-8ed382e8912c
last_name: Kavaleuski
orcid: 0000-0003-2091-526X
- first_name: Mikalai
full_name: Katsin, Mikalai
last_name: Katsin
- first_name: Alexandr
full_name: Migas, Alexandr
last_name: Migas
- first_name: Alexander
full_name: Meleshko, Alexander
last_name: Meleshko
- first_name: Sergei
full_name: Semyonov, Sergei
last_name: Semyonov
citation:
ama: Dormeshkin D, Shapira M, Dubovik S, et al. Isolation of an escape-resistant
SARS-CoV-2 neutralizing nanobody from a novel synthetic nanobody library. Frontiers
in Immunology. 2022;13. doi:10.3389/fimmu.2022.965446
apa: Dormeshkin, D., Shapira, M., Dubovik, S., Kavaleuski, A., Katsin, M., Migas,
A., … Semyonov, S. (2022). Isolation of an escape-resistant SARS-CoV-2 neutralizing
nanobody from a novel synthetic nanobody library. Frontiers in Immunology.
Frontiers Media. https://doi.org/10.3389/fimmu.2022.965446
chicago: Dormeshkin, Dmitri, Michail Shapira, Simon Dubovik, Anton Kavaleuski, Mikalai
Katsin, Alexandr Migas, Alexander Meleshko, and Sergei Semyonov. “Isolation of
an Escape-Resistant SARS-CoV-2 Neutralizing Nanobody from a Novel Synthetic Nanobody
Library.” Frontiers in Immunology. Frontiers Media, 2022. https://doi.org/10.3389/fimmu.2022.965446.
ieee: D. Dormeshkin et al., “Isolation of an escape-resistant SARS-CoV-2
neutralizing nanobody from a novel synthetic nanobody library,” Frontiers in
Immunology, vol. 13. Frontiers Media, 2022.
ista: Dormeshkin D, Shapira M, Dubovik S, Kavaleuski A, Katsin M, Migas A, Meleshko
A, Semyonov S. 2022. Isolation of an escape-resistant SARS-CoV-2 neutralizing
nanobody from a novel synthetic nanobody library. Frontiers in Immunology. 13,
965446.
mla: Dormeshkin, Dmitri, et al. “Isolation of an Escape-Resistant SARS-CoV-2 Neutralizing
Nanobody from a Novel Synthetic Nanobody Library.” Frontiers in Immunology,
vol. 13, 965446, Frontiers Media, 2022, doi:10.3389/fimmu.2022.965446.
short: D. Dormeshkin, M. Shapira, S. Dubovik, A. Kavaleuski, M. Katsin, A. Migas,
A. Meleshko, S. Semyonov, Frontiers in Immunology 13 (2022).
date_created: 2023-01-16T09:56:57Z
date_published: 2022-09-16T00:00:00Z
date_updated: 2025-06-11T13:42:26Z
day: '16'
ddc:
- '570'
department:
- _id: LeSa
doi: 10.3389/fimmu.2022.965446
external_id:
isi:
- '000862479100001'
pmid:
- '36189235'
file:
- access_level: open_access
checksum: f8f5d8110710033d0532e7e08bf9dad4
content_type: application/pdf
creator: dernst
date_created: 2023-01-30T09:22:26Z
date_updated: 2023-01-30T09:22:26Z
file_id: '12443'
file_name: 2022_FrontiersImmunology_Dormeshkin.pdf
file_size: 5695892
relation: main_file
success: 1
file_date_updated: 2023-01-30T09:22:26Z
has_accepted_license: '1'
intvolume: ' 13'
isi: 1
keyword:
- Immunology
- Immunology and Allergy
- COVID-19
- SARS-CoV-2
- synthetic library
- RBD
- neutralization nanobody
- VHH
language:
- iso: eng
month: '09'
oa: 1
oa_version: Published Version
pmid: 1
publication: Frontiers in Immunology
publication_identifier:
issn:
- 1664-3224
publication_status: published
publisher: Frontiers Media
quality_controlled: '1'
scopus_import: '1'
status: public
title: Isolation of an escape-resistant SARS-CoV-2 neutralizing nanobody from a novel
synthetic nanobody library
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 13
year: '2022'
...
---
_id: '12253'
abstract:
- lang: eng
text: The sculpting of germ layers during gastrulation relies on the coordinated
migration of progenitor cells, yet the cues controlling these long-range directed
movements remain largely unknown. While directional migration often relies on
a chemokine gradient generated from a localized source, we find that zebrafish
ventrolateral mesoderm is guided by a self-generated gradient of the initially
uniformly expressed and secreted protein Toddler/ELABELA/Apela. We show that the
Apelin receptor, which is specifically expressed in mesodermal cells, has a dual
role during gastrulation, acting as a scavenger receptor to generate a Toddler
gradient, and as a chemokine receptor to sense this guidance cue. Thus, we uncover
a single receptor–based self-generated gradient as the enigmatic guidance cue
that can robustly steer the directional migration of mesoderm through the complex
and continuously changing environment of the gastrulating embryo.
acknowledgement: 'We thank K. Aumayer and the team of the biooptics facility at the
Vienna Biocenter, particularly P. Pasierbek and T. Müller, for support with microscopy;
K. Panser, C. Pribitzer, and the animal facility personnel for taking care of zebrafish;
M. Binner and A. Bandura for help with genotyping; M. Codina Tobias for help with
establishing the conditions for the Toddler overexpression compensation experiment;
T. Lubiana Alves for sharing the code for scRNA-Seq analyses; the Heisenberg laboratory,
particularly D. Pinheiro, for joint laboratory meetings, discussions on the project,
and providing the tg(gsc:CAAX-GFP) fish line; the Raz laboratory for providing the
Lifeact-GFP plasmid; A. Andersen, A. Schier, C.-P. Heisenberg, and E. Tanaka for
comments on the manuscript; and the entire Pauli laboratory, particularly K. Gert
and V. Deneke, for valuable discussions and feedback on the manuscript. Funding:
Work in A.P.’s laboratory has been supported by the IMP, which receives institutional
funding from Boehringer Ingelheim and the Austrian Research Promotion Agency (Headquarter
grant FFG-852936), as well as the FWF START program (Y 1031-B28 to A.P.), the Human
Frontier Science Program (HFSP) Career Development Award (CDA00066/2015 to A.P.)
and Young Investigator Grant (RGY0079/2020 to A.P.), the SFB RNA-Deco (project number
F 80 to A.P.), a Whitman Center Fellowship from the Marine Biological Laboratory
(to A.P.), and EMBO-YIP funds (to A.P.). This work was supported by the European
Union (European Research Council Starting Grant 851288 to E.H.). For the purpose
of Open Access, the authors have applied a CC BY public copyright license to any
Author Accepted Manuscript (AAM) version arising from this submission.'
article_number: eadd2488
article_processing_charge: No
article_type: original
author:
- first_name: Jessica
full_name: Stock, Jessica
last_name: Stock
- first_name: Tomas
full_name: Kazmar, Tomas
last_name: Kazmar
- first_name: Friederike
full_name: Schlumm, Friederike
last_name: Schlumm
- first_name: Edouard B
full_name: Hannezo, Edouard B
id: 3A9DB764-F248-11E8-B48F-1D18A9856A87
last_name: Hannezo
orcid: 0000-0001-6005-1561
- first_name: Andrea
full_name: Pauli, Andrea
last_name: Pauli
citation:
ama: Stock J, Kazmar T, Schlumm F, Hannezo EB, Pauli A. A self-generated Toddler
gradient guides mesodermal cell migration. Science Advances. 2022;8(37).
doi:10.1126/sciadv.add2488
apa: Stock, J., Kazmar, T., Schlumm, F., Hannezo, E. B., & Pauli, A. (2022).
A self-generated Toddler gradient guides mesodermal cell migration. Science
Advances. American Association for the Advancement of Science. https://doi.org/10.1126/sciadv.add2488
chicago: Stock, Jessica, Tomas Kazmar, Friederike Schlumm, Edouard B Hannezo, and
Andrea Pauli. “A Self-Generated Toddler Gradient Guides Mesodermal Cell Migration.”
Science Advances. American Association for the Advancement of Science,
2022. https://doi.org/10.1126/sciadv.add2488.
ieee: J. Stock, T. Kazmar, F. Schlumm, E. B. Hannezo, and A. Pauli, “A self-generated
Toddler gradient guides mesodermal cell migration,” Science Advances, vol.
8, no. 37. American Association for the Advancement of Science, 2022.
ista: Stock J, Kazmar T, Schlumm F, Hannezo EB, Pauli A. 2022. A self-generated
Toddler gradient guides mesodermal cell migration. Science Advances. 8(37), eadd2488.
mla: Stock, Jessica, et al. “A Self-Generated Toddler Gradient Guides Mesodermal
Cell Migration.” Science Advances, vol. 8, no. 37, eadd2488, American Association
for the Advancement of Science, 2022, doi:10.1126/sciadv.add2488.
short: J. Stock, T. Kazmar, F. Schlumm, E.B. Hannezo, A. Pauli, Science Advances
8 (2022).
date_created: 2023-01-16T09:57:10Z
date_published: 2022-09-14T00:00:00Z
date_updated: 2025-04-14T07:52:27Z
day: '14'
ddc:
- '570'
department:
- _id: EdHa
doi: 10.1126/sciadv.add2488
ec_funded: 1
external_id:
isi:
- '000888875000009'
pmid:
- '36103529'
file:
- access_level: open_access
checksum: f59cdb824e5d4221045def81f46f6c65
content_type: application/pdf
creator: dernst
date_created: 2023-01-30T09:27:49Z
date_updated: 2023-01-30T09:27:49Z
file_id: '12444'
file_name: 2022_ScienceAdvances_Stock.pdf
file_size: 1636732
relation: main_file
success: 1
file_date_updated: 2023-01-30T09:27:49Z
has_accepted_license: '1'
intvolume: ' 8'
isi: 1
issue: '37'
language:
- iso: eng
month: '09'
oa: 1
oa_version: Published Version
pmid: 1
project:
- _id: 05943252-7A3F-11EA-A408-12923DDC885E
call_identifier: H2020
grant_number: '851288'
name: Design Principles of Branching Morphogenesis
publication: Science Advances
publication_identifier:
issn:
- 2375-2548
publication_status: published
publisher: American Association for the Advancement of Science
quality_controlled: '1'
scopus_import: '1'
status: public
title: A self-generated Toddler gradient guides mesodermal cell migration
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: journal_article
user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
volume: 8
year: '2022'
...
---
_id: '12259'
abstract:
- lang: eng
text: 'Theoretical foundations of chaos have been predominantly laid out for finite-dimensional
dynamical systems, such as the three-body problem in classical mechanics and the
Lorenz model in dissipative systems. In contrast, many real-world chaotic phenomena,
e.g., weather, arise in systems with many (formally infinite) degrees of freedom,
which limits direct quantitative analysis of such systems using chaos theory.
In the present work, we demonstrate that the hydrodynamic pilot-wave systems offer
a bridge between low- and high-dimensional chaotic phenomena by allowing for a
systematic study of how the former connects to the latter. Specifically, we present
experimental results, which show the formation of low-dimensional chaotic attractors
upon destabilization of regular dynamics and a final transition to high-dimensional
chaos via the merging of distinct chaotic regions through a crisis bifurcation.
Moreover, we show that the post-crisis dynamics of the system can be rationalized
as consecutive scatterings from the nonattracting chaotic sets with lifetimes
following exponential distributions. '
acknowledgement: 'This work was partially funded by the Institute of Science and Technology
Austria Interdisciplinary Project Committee Grant “Pilot-Wave Hydrodynamics: Chaos
and Quantum Analogies.”'
article_number: '093138'
article_processing_charge: No
article_type: original
arxiv: 1
author:
- first_name: George H
full_name: Choueiri, George H
id: 448BD5BC-F248-11E8-B48F-1D18A9856A87
last_name: Choueiri
- first_name: Balachandra
full_name: Suri, Balachandra
id: 47A5E706-F248-11E8-B48F-1D18A9856A87
last_name: Suri
- first_name: Jack
full_name: Merrin, Jack
id: 4515C308-F248-11E8-B48F-1D18A9856A87
last_name: Merrin
orcid: 0000-0001-5145-4609
- first_name: Maksym
full_name: Serbyn, Maksym
id: 47809E7E-F248-11E8-B48F-1D18A9856A87
last_name: Serbyn
orcid: 0000-0002-2399-5827
- first_name: Björn
full_name: Hof, Björn
id: 3A374330-F248-11E8-B48F-1D18A9856A87
last_name: Hof
orcid: 0000-0003-2057-2754
- first_name: Nazmi B
full_name: Budanur, Nazmi B
id: 3EA1010E-F248-11E8-B48F-1D18A9856A87
last_name: Budanur
orcid: 0000-0003-0423-5010
citation:
ama: 'Choueiri GH, Suri B, Merrin J, Serbyn M, Hof B, Budanur NB. Crises and chaotic
scattering in hydrodynamic pilot-wave experiments. Chaos: An Interdisciplinary
Journal of Nonlinear Science. 2022;32(9). doi:10.1063/5.0102904'
apa: 'Choueiri, G. H., Suri, B., Merrin, J., Serbyn, M., Hof, B., & Budanur,
N. B. (2022). Crises and chaotic scattering in hydrodynamic pilot-wave experiments.
Chaos: An Interdisciplinary Journal of Nonlinear Science. AIP Publishing.
https://doi.org/10.1063/5.0102904'
chicago: 'Choueiri, George H, Balachandra Suri, Jack Merrin, Maksym Serbyn, Björn
Hof, and Nazmi B Budanur. “Crises and Chaotic Scattering in Hydrodynamic Pilot-Wave
Experiments.” Chaos: An Interdisciplinary Journal of Nonlinear Science.
AIP Publishing, 2022. https://doi.org/10.1063/5.0102904.'
ieee: 'G. H. Choueiri, B. Suri, J. Merrin, M. Serbyn, B. Hof, and N. B. Budanur,
“Crises and chaotic scattering in hydrodynamic pilot-wave experiments,” Chaos:
An Interdisciplinary Journal of Nonlinear Science, vol. 32, no. 9. AIP Publishing,
2022.'
ista: 'Choueiri GH, Suri B, Merrin J, Serbyn M, Hof B, Budanur NB. 2022. Crises
and chaotic scattering in hydrodynamic pilot-wave experiments. Chaos: An Interdisciplinary
Journal of Nonlinear Science. 32(9), 093138.'
mla: 'Choueiri, George H., et al. “Crises and Chaotic Scattering in Hydrodynamic
Pilot-Wave Experiments.” Chaos: An Interdisciplinary Journal of Nonlinear Science,
vol. 32, no. 9, 093138, AIP Publishing, 2022, doi:10.1063/5.0102904.'
short: 'G.H. Choueiri, B. Suri, J. Merrin, M. Serbyn, B. Hof, N.B. Budanur, Chaos:
An Interdisciplinary Journal of Nonlinear Science 32 (2022).'
date_created: 2023-01-16T09:58:16Z
date_published: 2022-09-26T00:00:00Z
date_updated: 2025-06-11T13:41:34Z
day: '26'
ddc:
- '530'
department:
- _id: MaSe
- _id: BjHo
- _id: NanoFab
doi: 10.1063/5.0102904
external_id:
arxiv:
- '2206.01531'
isi:
- '000861009600005'
pmid:
- '36182399'
file:
- access_level: open_access
checksum: 17881eff8b21969359a2dd64620120ba
content_type: application/pdf
creator: dernst
date_created: 2023-01-30T09:41:12Z
date_updated: 2023-01-30T09:41:12Z
file_id: '12445'
file_name: 2022_Chaos_Choueiri.pdf
file_size: 3209644
relation: main_file
success: 1
file_date_updated: 2023-01-30T09:41:12Z
has_accepted_license: '1'
intvolume: ' 32'
isi: 1
issue: '9'
keyword:
- Applied Mathematics
- General Physics and Astronomy
- Mathematical Physics
- Statistical and Nonlinear Physics
language:
- iso: eng
month: '09'
oa: 1
oa_version: Published Version
pmid: 1
publication: 'Chaos: An Interdisciplinary Journal of Nonlinear Science'
publication_identifier:
eissn:
- 1089-7682
issn:
- 1054-1500
publication_status: published
publisher: AIP Publishing
quality_controlled: '1'
scopus_import: '1'
status: public
title: Crises and chaotic scattering in hydrodynamic pilot-wave experiments
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: 32
year: '2022'
...
---
_id: '14093'
abstract:
- lang: eng
text: ' We propose a stochastic conditional gradient method (CGM) for minimizing
convex finite-sum objectives formed as a sum of smooth and non-smooth terms. Existing
CGM variants for this template either suffer from slow convergence rates, or require
carefully increasing the batch size over the course of the algorithm’s execution,
which leads to computing full gradients. In contrast, the proposed method, equipped
with a stochastic average gradient (SAG) estimator, requires only one sample per
iteration. Nevertheless, it guarantees fast convergence rates on par with more
sophisticated variance reduction techniques. In applications we put special emphasis
on problems with a large number of separable constraints. Such problems are prevalent
among semidefinite programming (SDP) formulations arising in machine learning
and theoretical computer science. We provide numerical experiments on matrix completion,
unsupervised clustering, and sparsest-cut SDPs. '
alternative_title:
- PMLR
article_processing_charge: No
arxiv: 1
author:
- first_name: Gideon
full_name: Dresdner, Gideon
last_name: Dresdner
- first_name: Maria-Luiza
full_name: Vladarean, Maria-Luiza
last_name: Vladarean
- first_name: Gunnar
full_name: Rätsch, Gunnar
last_name: Rätsch
- first_name: Francesco
full_name: Locatello, Francesco
id: 26cfd52f-2483-11ee-8040-88983bcc06d4
last_name: Locatello
orcid: 0000-0002-4850-0683
- first_name: Volkan
full_name: Cevher, Volkan
last_name: Cevher
- first_name: Alp
full_name: Yurtsever, Alp
last_name: Yurtsever
citation:
ama: 'Dresdner G, Vladarean M-L, Rätsch G, Locatello F, Cevher V, Yurtsever A. Faster
one-sample stochastic conditional gradient method for composite convex minimization.
In: Proceedings of the 25th International Conference on Artificial Intelligence
and Statistics. Vol 151. ML Research Press; 2022:8439-8457.'
apa: 'Dresdner, G., Vladarean, M.-L., Rätsch, G., Locatello, F., Cevher, V., &
Yurtsever, A. (2022). Faster one-sample stochastic conditional gradient method
for composite convex minimization. In Proceedings of the 25th International
Conference on Artificial Intelligence and Statistics (Vol. 151, pp. 8439–8457).
Virtual: ML Research Press.'
chicago: Dresdner, Gideon, Maria-Luiza Vladarean, Gunnar Rätsch, Francesco Locatello,
Volkan Cevher, and Alp Yurtsever. “ Faster One-Sample Stochastic Conditional Gradient
Method for Composite Convex Minimization.” In Proceedings of the 25th International
Conference on Artificial Intelligence and Statistics, 151:8439–57. ML Research
Press, 2022.
ieee: G. Dresdner, M.-L. Vladarean, G. Rätsch, F. Locatello, V. Cevher, and A. Yurtsever,
“ Faster one-sample stochastic conditional gradient method for composite convex
minimization,” in Proceedings of the 25th International Conference on Artificial
Intelligence and Statistics, Virtual, 2022, vol. 151, pp. 8439–8457.
ista: 'Dresdner G, Vladarean M-L, Rätsch G, Locatello F, Cevher V, Yurtsever A.
2022. Faster one-sample stochastic conditional gradient method for composite
convex minimization. Proceedings of the 25th International Conference on Artificial
Intelligence and Statistics. AISTATS: Conference on Artificial Intelligence and
Statistics, PMLR, vol. 151, 8439–8457.'
mla: Dresdner, Gideon, et al. “ Faster One-Sample Stochastic Conditional Gradient
Method for Composite Convex Minimization.” Proceedings of the 25th International
Conference on Artificial Intelligence and Statistics, vol. 151, ML Research
Press, 2022, pp. 8439–57.
short: G. Dresdner, M.-L. Vladarean, G. Rätsch, F. Locatello, V. Cevher, A. Yurtsever,
in:, Proceedings of the 25th International Conference on Artificial Intelligence
and Statistics, ML Research Press, 2022, pp. 8439–8457.
conference:
end_date: 2022-03-30
location: Virtual
name: 'AISTATS: Conference on Artificial Intelligence and Statistics'
start_date: 2022-03-28
date_created: 2023-08-21T09:27:43Z
date_published: 2022-04-01T00:00:00Z
date_updated: 2023-09-06T10:28:17Z
day: '01'
department:
- _id: FrLo
extern: '1'
external_id:
arxiv:
- '2202.13212'
intvolume: ' 151'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/2202.13212
month: '04'
oa: 1
oa_version: Preprint
page: 8439-8457
publication: Proceedings of the 25th International Conference on Artificial Intelligence
and Statistics
publication_identifier:
issn:
- 2640-3498
publication_status: published
publisher: ML Research Press
quality_controlled: '1'
scopus_import: '1'
status: public
title: ' Faster one-sample stochastic conditional gradient method for composite convex
minimization'
type: conference
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 151
year: '2022'
...
---
_id: '14106'
abstract:
- lang: eng
text: "We show that deep networks trained to satisfy demographic parity often do
so\r\nthrough a form of race or gender awareness, and that the more we force a
network\r\nto be fair, the more accurately we can recover race or gender from
the internal state\r\nof the network. Based on this observation, we investigate
an alternative fairness\r\napproach: we add a second classification head to the
network to explicitly predict\r\nthe protected attribute (such as race or gender)
alongside the original task. After\r\ntraining the two-headed network, we enforce
demographic parity by merging the\r\ntwo heads, creating a network with the same
architecture as the original network.\r\nWe establish a close relationship between
existing approaches and our approach\r\nby showing (1) that the decisions of a
fair classifier are well-approximated by our\r\napproach, and (2) that an unfair
and optimally accurate classifier can be recovered\r\nfrom a fair classifier and
our second head predicting the protected attribute. We use\r\nour explicit formulation
to argue that the existing fairness approaches, just as ours,\r\ndemonstrate disparate
treatment and that they are likely to be unlawful in a wide\r\nrange of scenarios
under US law."
alternative_title:
- Advances in Neural Information Processing Systems
article_processing_charge: No
arxiv: 1
author:
- first_name: Michael
full_name: Lohaus, Michael
last_name: Lohaus
- first_name: Matthäus
full_name: Kleindessner, Matthäus
last_name: Kleindessner
- first_name: Krishnaram
full_name: Kenthapadi, Krishnaram
last_name: Kenthapadi
- first_name: Francesco
full_name: Locatello, Francesco
id: 26cfd52f-2483-11ee-8040-88983bcc06d4
last_name: Locatello
orcid: 0000-0002-4850-0683
- first_name: Chris
full_name: Russell, Chris
last_name: Russell
citation:
ama: 'Lohaus M, Kleindessner M, Kenthapadi K, Locatello F, Russell C. Are two heads
the same as one? Identifying disparate treatment in fair neural networks. In:
36th Conference on Neural Information Processing Systems. Vol 35. Neural
Information Processing Systems Foundation; 2022:16548-16562.'
apa: 'Lohaus, M., Kleindessner, M., Kenthapadi, K., Locatello, F., & Russell,
C. (2022). Are two heads the same as one? Identifying disparate treatment in fair
neural networks. In 36th Conference on Neural Information Processing Systems
(Vol. 35, pp. 16548–16562). New Orleans, LA, United States: Neural Information
Processing Systems Foundation.'
chicago: Lohaus, Michael, Matthäus Kleindessner, Krishnaram Kenthapadi, Francesco
Locatello, and Chris Russell. “Are Two Heads the Same as One? Identifying Disparate
Treatment in Fair Neural Networks.” In 36th Conference on Neural Information
Processing Systems, 35:16548–62. Neural Information Processing Systems Foundation,
2022.
ieee: M. Lohaus, M. Kleindessner, K. Kenthapadi, F. Locatello, and C. Russell, “Are
two heads the same as one? Identifying disparate treatment in fair neural networks,”
in 36th Conference on Neural Information Processing Systems, New Orleans,
LA, United States, 2022, vol. 35, pp. 16548–16562.
ista: 'Lohaus M, Kleindessner M, Kenthapadi K, Locatello F, Russell C. 2022. Are
two heads the same as one? Identifying disparate treatment in fair neural networks.
36th Conference on Neural Information Processing Systems. NeurIPS: Neural Information
Processing Systems, Advances in Neural Information Processing Systems, vol. 35,
16548–16562.'
mla: Lohaus, Michael, et al. “Are Two Heads the Same as One? Identifying Disparate
Treatment in Fair Neural Networks.” 36th Conference on Neural Information Processing
Systems, vol. 35, Neural Information Processing Systems Foundation, 2022,
pp. 16548–62.
short: M. Lohaus, M. Kleindessner, K. Kenthapadi, F. Locatello, C. Russell, in:,
36th Conference on Neural Information Processing Systems, Neural Information Processing
Systems Foundation, 2022, pp. 16548–16562.
conference:
end_date: 2022-12-09
location: New Orleans, LA, United States
name: 'NeurIPS: Neural Information Processing Systems'
start_date: 2022-11-28
date_created: 2023-08-21T12:12:42Z
date_published: 2022-12-15T00:00:00Z
date_updated: 2024-10-14T12:27:01Z
day: '15'
department:
- _id: FrLo
extern: '1'
external_id:
arxiv:
- '2204.04440'
intvolume: ' 35'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/2204.04440
month: '12'
oa: 1
oa_version: Preprint
page: 16548-16562
publication: 36th Conference on Neural Information Processing Systems
publication_identifier:
isbn:
- '9781713871088'
publication_status: published
publisher: Neural Information Processing Systems Foundation
quality_controlled: '1'
scopus_import: '1'
status: public
title: Are two heads the same as one? Identifying disparate treatment in fair neural
networks
type: conference
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 35
year: '2022'
...
---
_id: '14107'
abstract:
- lang: eng
text: "Amodal perception requires inferring the full shape of an object that is
partially occluded. This task is particularly challenging on two levels: (1) it
requires more information than what is contained in the instant retina or imaging
sensor, (2) it is difficult to obtain enough well-annotated amodal labels for
supervision. To this end, this paper develops a new framework of\r\nSelf-supervised
amodal Video object segmentation (SaVos). Our method efficiently leverages the
visual information of video temporal sequences to infer the amodal mask of objects.
The key intuition is that the occluded part of an object can be explained away
if that part is visible in other frames, possibly deformed as long as the deformation
can be reasonably learned.\r\nAccordingly, we derive a novel self-supervised learning
paradigm that efficiently utilizes the visible object parts as the supervision
to guide the training on videos. In addition to learning type prior to complete
masks for known types, SaVos also learns the spatiotemporal prior, which is also
useful for the amodal task and could generalize to unseen types. The proposed\r\nframework
achieves the state-of-the-art performance on the synthetic amodal segmentation
benchmark FISHBOWL and the real world benchmark KINS-Video-Car. Further, it lends
itself well to being transferred to novel distributions using test-time adaptation,
outperforming existing models even after the transfer to a new distribution."
article_processing_charge: No
arxiv: 1
author:
- first_name: Jian
full_name: Yao, Jian
last_name: Yao
- first_name: Yuxin
full_name: Hong, Yuxin
last_name: Hong
- first_name: Chiyu
full_name: Wang, Chiyu
last_name: Wang
- first_name: Tianjun
full_name: Xiao, Tianjun
last_name: Xiao
- first_name: Tong
full_name: He, Tong
last_name: He
- first_name: Francesco
full_name: Locatello, Francesco
id: 26cfd52f-2483-11ee-8040-88983bcc06d4
last_name: Locatello
orcid: 0000-0002-4850-0683
- first_name: David
full_name: Wipf, David
last_name: Wipf
- first_name: Yanwei
full_name: Fu, Yanwei
last_name: Fu
- first_name: Zheng
full_name: Zhang, Zheng
last_name: Zhang
citation:
ama: 'Yao J, Hong Y, Wang C, et al. Self-supervised amodal video object segmentation.
In: 36th Conference on Neural Information Processing Systems. ; 2022. doi:10.48550/arXiv.2210.12733'
apa: Yao, J., Hong, Y., Wang, C., Xiao, T., He, T., Locatello, F., … Zhang, Z. (2022).
Self-supervised amodal video object segmentation. In 36th Conference on Neural
Information Processing Systems. New Orleans, LA, United States. https://doi.org/10.48550/arXiv.2210.12733
chicago: Yao, Jian, Yuxin Hong, Chiyu Wang, Tianjun Xiao, Tong He, Francesco Locatello,
David Wipf, Yanwei Fu, and Zheng Zhang. “Self-Supervised Amodal Video Object Segmentation.”
In 36th Conference on Neural Information Processing Systems, 2022. https://doi.org/10.48550/arXiv.2210.12733.
ieee: J. Yao et al., “Self-supervised amodal video object segmentation,”
in 36th Conference on Neural Information Processing Systems, New Orleans,
LA, United States, 2022.
ista: 'Yao J, Hong Y, Wang C, Xiao T, He T, Locatello F, Wipf D, Fu Y, Zhang Z.
2022. Self-supervised amodal video object segmentation. 36th Conference on Neural
Information Processing Systems. NeurIPS: Neural Information Processing Systems.'
mla: Yao, Jian, et al. “Self-Supervised Amodal Video Object Segmentation.” 36th
Conference on Neural Information Processing Systems, 2022, doi:10.48550/arXiv.2210.12733.
short: J. Yao, Y. Hong, C. Wang, T. Xiao, T. He, F. Locatello, D. Wipf, Y. Fu, Z.
Zhang, in:, 36th Conference on Neural Information Processing Systems, 2022.
conference:
end_date: 2022-12-01
location: New Orleans, LA, United States
name: 'NeurIPS: Neural Information Processing Systems'
start_date: 2022-11-28
date_created: 2023-08-21T12:13:25Z
date_published: 2022-10-23T00:00:00Z
date_updated: 2023-09-11T09:34:17Z
day: '23'
department:
- _id: FrLo
doi: 10.48550/arXiv.2210.12733
extern: '1'
external_id:
arxiv:
- '2210.12733'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.48550/arXiv.2210.12733
month: '10'
oa: 1
oa_version: Preprint
publication: 36th Conference on Neural Information Processing Systems
publication_status: published
status: public
title: Self-supervised amodal video object segmentation
type: conference
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
year: '2022'
...
---
_id: '14114'
abstract:
- lang: eng
text: Algorithmic fairness is frequently motivated in terms of a trade-off in which
overall performance is decreased so as to improve performance on disadvantaged
groups where the algorithm would otherwise be less accurate. Contrary to this,
we find that applying existing fairness approaches to computer vision improve
fairness by degrading the performance of classifiers across all groups (with increased
degradation on the best performing groups). Extending the bias-variance decomposition
for classification to fairness, we theoretically explain why the majority of fairness
methods designed for low capacity models should not be used in settings involving
high-capacity models, a scenario common to computer vision. We corroborate this
analysis with extensive experimental support that shows that many of the fairness
heuristics used in computer vision also degrade performance on the most disadvantaged
groups. Building on these insights, we propose an adaptive augmentation strategy
that, uniquely, of all methods tested, improves performance for the disadvantaged
groups.
article_processing_charge: No
arxiv: 1
author:
- first_name: Dominik
full_name: Zietlow, Dominik
last_name: Zietlow
- first_name: Michael
full_name: Lohaus, Michael
last_name: Lohaus
- first_name: Guha
full_name: Balakrishnan, Guha
last_name: Balakrishnan
- first_name: Matthaus
full_name: Kleindessner, Matthaus
last_name: Kleindessner
- first_name: Francesco
full_name: Locatello, Francesco
id: 26cfd52f-2483-11ee-8040-88983bcc06d4
last_name: Locatello
orcid: 0000-0002-4850-0683
- first_name: Bernhard
full_name: Scholkopf, Bernhard
last_name: Scholkopf
- first_name: Chris
full_name: Russell, Chris
last_name: Russell
citation:
ama: 'Zietlow D, Lohaus M, Balakrishnan G, et al. Leveling down in computer vision:
Pareto inefficiencies in fair deep classifiers. In: 2022 IEEE/CVF Conference
on Computer Vision and Pattern Recognition. Institute of Electrical and Electronics
Engineers; 2022:10400-10411. doi:10.1109/cvpr52688.2022.01016'
apa: 'Zietlow, D., Lohaus, M., Balakrishnan, G., Kleindessner, M., Locatello, F.,
Scholkopf, B., & Russell, C. (2022). Leveling down in computer vision: Pareto
inefficiencies in fair deep classifiers. In 2022 IEEE/CVF Conference on Computer
Vision and Pattern Recognition (pp. 10400–10411). New Orleans, LA, United
States: Institute of Electrical and Electronics Engineers. https://doi.org/10.1109/cvpr52688.2022.01016'
chicago: 'Zietlow, Dominik, Michael Lohaus, Guha Balakrishnan, Matthaus Kleindessner,
Francesco Locatello, Bernhard Scholkopf, and Chris Russell. “Leveling down in
Computer Vision: Pareto Inefficiencies in Fair Deep Classifiers.” In 2022 IEEE/CVF
Conference on Computer Vision and Pattern Recognition, 10400–411. Institute
of Electrical and Electronics Engineers, 2022. https://doi.org/10.1109/cvpr52688.2022.01016.'
ieee: 'D. Zietlow et al., “Leveling down in computer vision: Pareto inefficiencies
in fair deep classifiers,” in 2022 IEEE/CVF Conference on Computer Vision and
Pattern Recognition, New Orleans, LA, United States, 2022, pp. 10400–10411.'
ista: 'Zietlow D, Lohaus M, Balakrishnan G, Kleindessner M, Locatello F, Scholkopf
B, Russell C. 2022. Leveling down in computer vision: Pareto inefficiencies in
fair deep classifiers. 2022 IEEE/CVF Conference on Computer Vision and Pattern
Recognition. CVPR: Conference on Computer Vision and Pattern Recognition, 10400–10411.'
mla: 'Zietlow, Dominik, et al. “Leveling down in Computer Vision: Pareto Inefficiencies
in Fair Deep Classifiers.” 2022 IEEE/CVF Conference on Computer Vision and
Pattern Recognition, Institute of Electrical and Electronics Engineers, 2022,
pp. 10400–11, doi:10.1109/cvpr52688.2022.01016.'
short: D. Zietlow, M. Lohaus, G. Balakrishnan, M. Kleindessner, F. Locatello, B.
Scholkopf, C. Russell, in:, 2022 IEEE/CVF Conference on Computer Vision and Pattern
Recognition, Institute of Electrical and Electronics Engineers, 2022, pp. 10400–10411.
conference:
end_date: 2022-06-24
location: New Orleans, LA, United States
name: 'CVPR: Conference on Computer Vision and Pattern Recognition'
start_date: 2022-06-18
date_created: 2023-08-21T12:18:00Z
date_published: 2022-07-01T00:00:00Z
date_updated: 2023-09-11T09:19:14Z
day: '01'
department:
- _id: FrLo
doi: 10.1109/cvpr52688.2022.01016
extern: '1'
external_id:
arxiv:
- '2203.04913'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/2203.04913
month: '07'
oa: 1
oa_version: Preprint
page: 10400-10411
publication: 2022 IEEE/CVF Conference on Computer Vision and Pattern Recognition
publication_identifier:
eissn:
- 2575-7075
isbn:
- '9781665469470'
issn:
- 1063-6919
publication_status: published
publisher: Institute of Electrical and Electronics Engineers
quality_controlled: '1'
scopus_import: '1'
status: public
title: 'Leveling down in computer vision: Pareto inefficiencies in fair deep classifiers'
type: conference
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
year: '2022'
...
---
_id: '14168'
abstract:
- lang: eng
text: "Recent work has seen the development of general purpose neural architectures\r\nthat
can be trained to perform tasks across diverse data modalities. General\r\npurpose
models typically make few assumptions about the underlying\r\ndata-structure and
are known to perform well in the large-data regime. At the\r\nsame time, there
has been growing interest in modular neural architectures that\r\nrepresent the
data using sparsely interacting modules. These models can be more\r\nrobust out-of-distribution,
computationally efficient, and capable of\r\nsample-efficient adaptation to new
data. However, they tend to make\r\ndomain-specific assumptions about the data,
and present challenges in how\r\nmodule behavior (i.e., parameterization) and
connectivity (i.e., their layout)\r\ncan be jointly learned. In this work, we
introduce a general purpose, yet\r\nmodular neural architecture called Neural
Attentive Circuits (NACs) that\r\njointly learns the parameterization and a sparse
connectivity of neural modules\r\nwithout using domain knowledge. NACs are best
understood as the combination of\r\ntwo systems that are jointly trained end-to-end:
one that determines the module\r\nconfiguration and the other that executes it
on an input. We demonstrate\r\nqualitatively that NACs learn diverse and meaningful
module configurations on\r\nthe NLVR2 dataset without additional supervision.
Quantitatively, we show that\r\nby incorporating modularity in this way, NACs
improve upon a strong non-modular\r\nbaseline in terms of low-shot adaptation
on CIFAR and CUBs dataset by about\r\n10%, and OOD robustness on Tiny ImageNet-R
by about 2.5%. Further, we find that\r\nNACs can achieve an 8x speedup at inference
time while losing less than 3%\r\nperformance. Finally, we find NACs to yield
competitive results on diverse data\r\nmodalities spanning point-cloud classification,
symbolic processing and\r\ntext-classification from ASCII bytes, thereby confirming
its general purpose\r\nnature."
alternative_title:
- ' Advances in Neural Information Processing Systems'
article_processing_charge: No
arxiv: 1
author:
- first_name: Nasim
full_name: Rahaman, Nasim
last_name: Rahaman
- first_name: Martin
full_name: Weiss, Martin
last_name: Weiss
- first_name: Francesco
full_name: Locatello, Francesco
id: 26cfd52f-2483-11ee-8040-88983bcc06d4
last_name: Locatello
orcid: 0000-0002-4850-0683
- first_name: Chris
full_name: Pal, Chris
last_name: Pal
- first_name: Yoshua
full_name: Bengio, Yoshua
last_name: Bengio
- first_name: Bernhard
full_name: Schölkopf, Bernhard
last_name: Schölkopf
- first_name: Li Erran
full_name: Li, Li Erran
last_name: Li
- first_name: Nicolas
full_name: Ballas, Nicolas
last_name: Ballas
citation:
ama: 'Rahaman N, Weiss M, Locatello F, et al. Neural attentive circuits. In: 36th
Conference on Neural Information Processing Systems. Vol 35. ; 2022.'
apa: Rahaman, N., Weiss, M., Locatello, F., Pal, C., Bengio, Y., Schölkopf, B.,
… Ballas, N. (2022). Neural attentive circuits. In 36th Conference on Neural
Information Processing Systems (Vol. 35). New Orleans, United States.
chicago: Rahaman, Nasim, Martin Weiss, Francesco Locatello, Chris Pal, Yoshua Bengio,
Bernhard Schölkopf, Li Erran Li, and Nicolas Ballas. “Neural Attentive Circuits.”
In 36th Conference on Neural Information Processing Systems, Vol. 35, 2022.
ieee: N. Rahaman et al., “Neural attentive circuits,” in 36th Conference
on Neural Information Processing Systems, New Orleans, United States, 2022,
vol. 35.
ista: 'Rahaman N, Weiss M, Locatello F, Pal C, Bengio Y, Schölkopf B, Li LE, Ballas
N. 2022. Neural attentive circuits. 36th Conference on Neural Information Processing
Systems. NeurIPS: Neural Information Processing Systems, Advances in Neural Information
Processing Systems, vol. 35.'
mla: Rahaman, Nasim, et al. “Neural Attentive Circuits.” 36th Conference on Neural
Information Processing Systems, vol. 35, 2022.
short: N. Rahaman, M. Weiss, F. Locatello, C. Pal, Y. Bengio, B. Schölkopf, L.E.
Li, N. Ballas, in:, 36th Conference on Neural Information Processing Systems,
2022.
conference:
end_date: 2022-12-01
location: New Orleans, United States
name: 'NeurIPS: Neural Information Processing Systems'
start_date: 2022-11-29
date_created: 2023-08-22T13:57:27Z
date_published: 2022-10-14T00:00:00Z
date_updated: 2023-09-11T09:29:09Z
day: '14'
department:
- _id: FrLo
extern: '1'
external_id:
arxiv:
- '2210.08031'
intvolume: ' 35'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.48550/arXiv.2210.08031
month: '10'
oa: 1
oa_version: Preprint
publication: 36th Conference on Neural Information Processing Systems
publication_status: published
status: public
title: Neural attentive circuits
type: conference
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 35
year: '2022'
...