---
_id: '11144'
abstract:
- lang: eng
text: Thermoelectric materials allow for direct conversion between heat and electricity,
offering the potential for power generation. The average dimensionless figure
of merit ZTave determines device efficiency. N-type tin selenide crystals exhibit
outstanding three-dimensional charge and two-dimensional phonon transport along
the out-of-plane direction, contributing to a high maximum figure of merit Zmax
of ~3.6 × 10−3 per kelvin but a moderate ZTave of ~1.1. We found an attractive
high Zmax of ~4.1 × 10−3 per kelvin at 748 kelvin and a ZTave of ~1.7 at 300 to
773 kelvin in chlorine-doped and lead-alloyed tin selenide crystals by phonon-electron
decoupling. The chlorine-induced low deformation potential improved the carrier
mobility. The lead-induced mass and strain fluctuations reduced the lattice thermal
conductivity. Phonon-electron decoupling plays a critical role to achieve high-performance
thermoelectrics.
acknowledgement: This work was supported by the Basic Science Center Project of the
National Natural Science Foundation of China (51788104), the National Key Research
and Development Program of China (2018YFA0702100), the National Science Fund for
Distinguished Young Scholars (51925101), the 111 Project (B17002), the Lise Meitner
Project (M2889-N), and the National Key Research and Development Program of China
(2018YFB0703600). This work is also supported by the National Postdoctoral Program
for Innovative Talents (BX20200028). L.-D.Z. is thankful for the high-performance
computing resources at Beihang University.
article_processing_charge: No
article_type: original
author:
- first_name: Lizhong
full_name: Su, Lizhong
last_name: Su
- first_name: Dongyang
full_name: Wang, Dongyang
last_name: Wang
- first_name: Sining
full_name: Wang, Sining
last_name: Wang
- first_name: Bingchao
full_name: Qin, Bingchao
last_name: Qin
- first_name: Yuping
full_name: Wang, Yuping
last_name: Wang
- first_name: Yongxin
full_name: Qin, Yongxin
last_name: Qin
- first_name: Yang
full_name: Jin, Yang
last_name: Jin
- first_name: Cheng
full_name: Chang, Cheng
id: 9E331C2E-9F27-11E9-AE48-5033E6697425
last_name: Chang
orcid: 0000-0002-9515-4277
- first_name: Li Dong
full_name: Zhao, Li Dong
last_name: Zhao
citation:
ama: Su L, Wang D, Wang S, et al. High thermoelectric performance realized through
manipulating layered phonon-electron decoupling. Science. 2022;375(6587):1385-1389.
doi:10.1126/science.abn8997
apa: Su, L., Wang, D., Wang, S., Qin, B., Wang, Y., Qin, Y., … Zhao, L. D. (2022).
High thermoelectric performance realized through manipulating layered phonon-electron
decoupling. Science. American Association for the Advancement of Science.
https://doi.org/10.1126/science.abn8997
chicago: Su, Lizhong, Dongyang Wang, Sining Wang, Bingchao Qin, Yuping Wang, Yongxin
Qin, Yang Jin, Cheng Chang, and Li Dong Zhao. “High Thermoelectric Performance
Realized through Manipulating Layered Phonon-Electron Decoupling.” Science.
American Association for the Advancement of Science, 2022. https://doi.org/10.1126/science.abn8997.
ieee: L. Su et al., “High thermoelectric performance realized through manipulating
layered phonon-electron decoupling,” Science, vol. 375, no. 6587. American
Association for the Advancement of Science, pp. 1385–1389, 2022.
ista: Su L, Wang D, Wang S, Qin B, Wang Y, Qin Y, Jin Y, Chang C, Zhao LD. 2022.
High thermoelectric performance realized through manipulating layered phonon-electron
decoupling. Science. 375(6587), 1385–1389.
mla: Su, Lizhong, et al. “High Thermoelectric Performance Realized through Manipulating
Layered Phonon-Electron Decoupling.” Science, vol. 375, no. 6587, American
Association for the Advancement of Science, 2022, pp. 1385–89, doi:10.1126/science.abn8997.
short: L. Su, D. Wang, S. Wang, B. Qin, Y. Wang, Y. Qin, Y. Jin, C. Chang, L.D.
Zhao, Science 375 (2022) 1385–1389.
date_created: 2022-04-10T22:01:40Z
date_published: 2022-03-25T00:00:00Z
date_updated: 2023-10-16T09:10:36Z
day: '25'
department:
- _id: MaIb
doi: 10.1126/science.abn8997
external_id:
isi:
- '000778894800038'
pmid:
- '35324303'
intvolume: ' 375'
isi: 1
issue: '6587'
language:
- iso: eng
month: '03'
oa_version: None
page: 1385-1389
pmid: 1
project:
- _id: 9B8804FC-BA93-11EA-9121-9846C619BF3A
grant_number: M02889
name: Bottom-up Engineering for Thermoelectric Applications
publication: Science
publication_identifier:
eissn:
- 1095-9203
publication_status: published
publisher: American Association for the Advancement of Science
quality_controlled: '1'
scopus_import: '1'
status: public
title: High thermoelectric performance realized through manipulating layered phonon-electron
decoupling
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 375
year: '2022'
...
---
_id: '11145'
abstract:
- lang: eng
text: List-decodability of Reed-Solomon codes has re-ceived a lot of attention,
but the best-possible dependence between the parameters is still not well-understood.
In this work, we focus on the case where the list-decoding radius is of the form
r=1−ε for ε tending to zero. Our main result states that there exist Reed-Solomon
codes with rate Ω(ε) which are (1−ε,O(1/ε) -list-decodable, meaning that any Hamming
ball of radius 1−ε contains at most O(1/ε) codewords. This trade-off between rate
and list-decoding radius is best-possible for any code with list size less than
exponential in the block length. By achieving this trade-off between rate and
list-decoding radius we improve a recent result of Guo, Li, Shangguan, Tamo, and
Wootters, and resolve the main motivating question of their work. Moreover, while
their result requires the field to be exponentially large in the block length,
we only need the field size to be polynomially large (and in fact, almost-linear
suffices). We deduce our main result from a more general theorem, in which we
prove good list-decodability properties of random puncturings of any given code
with very large distance.
article_processing_charge: No
arxiv: 1
author:
- first_name: Asaf
full_name: Ferber, Asaf
last_name: Ferber
- first_name: Matthew Alan
full_name: Kwan, Matthew Alan
id: 5fca0887-a1db-11eb-95d1-ca9d5e0453b3
last_name: Kwan
orcid: 0000-0002-4003-7567
- first_name: Lisa
full_name: Sauermann, Lisa
last_name: Sauermann
citation:
ama: 'Ferber A, Kwan MA, Sauermann L. List-decodability with large radius for Reed-Solomon
codes. In: 62nd Annual IEEE Symposium on Foundations of Computer Science.
Vol 2022. IEEE; 2022:720-726. doi:10.1109/FOCS52979.2021.00075'
apa: 'Ferber, A., Kwan, M. A., & Sauermann, L. (2022). List-decodability with
large radius for Reed-Solomon codes. In 62nd Annual IEEE Symposium on Foundations
of Computer Science (Vol. 2022, pp. 720–726). Denver, CO, United States: IEEE.
https://doi.org/10.1109/FOCS52979.2021.00075'
chicago: Ferber, Asaf, Matthew Alan Kwan, and Lisa Sauermann. “List-Decodability
with Large Radius for Reed-Solomon Codes.” In 62nd Annual IEEE Symposium on
Foundations of Computer Science, 2022:720–26. IEEE, 2022. https://doi.org/10.1109/FOCS52979.2021.00075.
ieee: A. Ferber, M. A. Kwan, and L. Sauermann, “List-decodability with large radius
for Reed-Solomon codes,” in 62nd Annual IEEE Symposium on Foundations of Computer
Science, Denver, CO, United States, 2022, vol. 2022, pp. 720–726.
ista: 'Ferber A, Kwan MA, Sauermann L. 2022. List-decodability with large radius
for Reed-Solomon codes. 62nd Annual IEEE Symposium on Foundations of Computer
Science. FOCS: Symposium on Foundations of Computer Science vol. 2022, 720–726.'
mla: Ferber, Asaf, et al. “List-Decodability with Large Radius for Reed-Solomon
Codes.” 62nd Annual IEEE Symposium on Foundations of Computer Science,
vol. 2022, IEEE, 2022, pp. 720–26, doi:10.1109/FOCS52979.2021.00075.
short: A. Ferber, M.A. Kwan, L. Sauermann, in:, 62nd Annual IEEE Symposium on Foundations
of Computer Science, IEEE, 2022, pp. 720–726.
conference:
end_date: 2022-02-10
location: Denver, CO, United States
name: 'FOCS: Symposium on Foundations of Computer Science'
start_date: 2022-02-07
date_created: 2022-04-10T22:01:40Z
date_published: 2022-02-01T00:00:00Z
date_updated: 2023-08-03T06:57:02Z
day: '01'
department:
- _id: MaKw
doi: 10.1109/FOCS52979.2021.00075
external_id:
arxiv:
- '2012.10584'
isi:
- '000802209600065'
intvolume: ' 2022'
isi: 1
language:
- iso: eng
main_file_link:
- open_access: '1'
url: ' https://doi.org/10.48550/arXiv.2012.10584'
month: '02'
oa: 1
oa_version: Preprint
page: 720-726
publication: 62nd Annual IEEE Symposium on Foundations of Computer Science
publication_identifier:
isbn:
- '9781665420556'
issn:
- 0272-5428
publication_status: published
publisher: IEEE
quality_controlled: '1'
related_material:
record:
- id: '10775'
relation: later_version
status: public
scopus_import: '1'
status: public
title: List-decodability with large radius for Reed-Solomon codes
type: conference
user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
volume: 2022
year: '2022'
...
---
_id: '11155'
abstract:
- lang: eng
text: The potential of energy filtering and direct electron detection for cryo-electron
microscopy (cryo-EM) has been well documented. Here, we assess the performance
of recently introduced hardware for cryo-electron tomography (cryo-ET) and subtomogram
averaging (STA), an increasingly popular structural determination method for complex
3D specimens. We acquired cryo-ET datasets of EIAV virus-like particles (VLPs)
on two contemporary cryo-EM systems equipped with different energy filters and
direct electron detectors (DED), specifically a Krios G4, equipped with a cold
field emission gun (CFEG), Thermo Fisher Scientific Selectris X energy filter,
and a Falcon 4 DED; and a Krios G3i, with a Schottky field emission gun (XFEG),
a Gatan Bioquantum energy filter, and a K3 DED. We performed constrained cross-correlation-based
STA on equally sized datasets acquired on the respective systems. The resulting
EIAV CA hexamer reconstructions show that both systems perform comparably in the
4–6 Å resolution range based on Fourier-Shell correlation (FSC). In addition,
by employing a recently introduced multiparticle refinement approach, we obtained
a reconstruction of the EIAV CA hexamer at 2.9 Å. Our results demonstrate the
potential of the new generation of energy filters and DEDs for STA, and the effects
of using different processing pipelines on their STA outcomes.
acknowledged_ssus:
- _id: LifeSc
- _id: ScienComp
- _id: EM-Fac
acknowledgement: This work was funded by the Austrian Science Fund (FWF) grant P31445
to F.K.M.S and the National Institute of Allergy and Infectious Diseases under awards
R01AI147890 to R.A.D. This research was also supported by the Scientific Service
Units (SSUs) of IST Austria through resources provided by Scientific Computing (SciComp),
the Life Science Facility (LSF), and the Electron Microscopy Facility (EMF). We
thank Dustin Morado for providing the software SubTOM for data processing. We also
thank William Wan for critical reading of the manuscript and valuable feedback.
article_number: '107852'
article_processing_charge: Yes (via OA deal)
article_type: original
author:
- first_name: Martin
full_name: Obr, Martin
id: 4741CA5A-F248-11E8-B48F-1D18A9856A87
last_name: Obr
- first_name: Wim J.H.
full_name: Hagen, Wim J.H.
last_name: Hagen
- first_name: Robert A.
full_name: Dick, Robert A.
last_name: Dick
- first_name: Lingbo
full_name: Yu, Lingbo
last_name: Yu
- first_name: Abhay
full_name: Kotecha, Abhay
last_name: Kotecha
- first_name: Florian KM
full_name: Schur, Florian KM
id: 48AD8942-F248-11E8-B48F-1D18A9856A87
last_name: Schur
orcid: 0000-0003-4790-8078
citation:
ama: Obr M, Hagen WJH, Dick RA, Yu L, Kotecha A, Schur FK. Exploring high-resolution
cryo-ET and subtomogram averaging capabilities of contemporary DEDs. Journal
of Structural Biology. 2022;214(2). doi:10.1016/j.jsb.2022.107852
apa: Obr, M., Hagen, W. J. H., Dick, R. A., Yu, L., Kotecha, A., & Schur, F.
K. (2022). Exploring high-resolution cryo-ET and subtomogram averaging capabilities
of contemporary DEDs. Journal of Structural Biology. Elsevier. https://doi.org/10.1016/j.jsb.2022.107852
chicago: Obr, Martin, Wim J.H. Hagen, Robert A. Dick, Lingbo Yu, Abhay Kotecha,
and Florian KM Schur. “Exploring High-Resolution Cryo-ET and Subtomogram Averaging
Capabilities of Contemporary DEDs.” Journal of Structural Biology. Elsevier,
2022. https://doi.org/10.1016/j.jsb.2022.107852.
ieee: M. Obr, W. J. H. Hagen, R. A. Dick, L. Yu, A. Kotecha, and F. K. Schur, “Exploring
high-resolution cryo-ET and subtomogram averaging capabilities of contemporary
DEDs,” Journal of Structural Biology, vol. 214, no. 2. Elsevier, 2022.
ista: Obr M, Hagen WJH, Dick RA, Yu L, Kotecha A, Schur FK. 2022. Exploring high-resolution
cryo-ET and subtomogram averaging capabilities of contemporary DEDs. Journal of
Structural Biology. 214(2), 107852.
mla: Obr, Martin, et al. “Exploring High-Resolution Cryo-ET and Subtomogram Averaging
Capabilities of Contemporary DEDs.” Journal of Structural Biology, vol.
214, no. 2, 107852, Elsevier, 2022, doi:10.1016/j.jsb.2022.107852.
short: M. Obr, W.J.H. Hagen, R.A. Dick, L. Yu, A. Kotecha, F.K. Schur, Journal of
Structural Biology 214 (2022).
date_created: 2022-04-15T07:10:26Z
date_published: 2022-06-01T00:00:00Z
date_updated: 2023-08-03T06:25:23Z
day: '01'
ddc:
- '570'
department:
- _id: FlSc
doi: 10.1016/j.jsb.2022.107852
external_id:
isi:
- '000790733600001'
pmid:
- '35351542'
file:
- access_level: open_access
checksum: 0b1eb53447aae8e95ae4c12d193b0b00
content_type: application/pdf
creator: dernst
date_created: 2022-08-02T11:07:58Z
date_updated: 2022-08-02T11:07:58Z
file_id: '11722'
file_name: 2022_JourStructuralBiology_Obr.pdf
file_size: 7080863
relation: main_file
success: 1
file_date_updated: 2022-08-02T11:07:58Z
has_accepted_license: '1'
intvolume: ' 214'
isi: 1
issue: '2'
keyword:
- Structural Biology
language:
- iso: eng
month: '06'
oa: 1
oa_version: Published Version
pmid: 1
project:
- _id: 26736D6A-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: P31445
name: Structural conservation and diversity in retroviral capsid
publication: Journal of Structural Biology
publication_identifier:
issn:
- 1047-8477
publication_status: published
publisher: Elsevier
quality_controlled: '1'
scopus_import: '1'
status: public
title: Exploring high-resolution cryo-ET and subtomogram averaging capabilities of
contemporary DEDs
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: journal_article
user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
volume: 214
year: '2022'
...
---
_id: '11160'
abstract:
- lang: eng
text: Mutations in the chromodomain helicase DNA-binding 8 (CHD8) gene are a frequent
cause of autism spectrum disorder (ASD). While its phenotypic spectrum often encompasses
macrocephaly, implicating cortical abnormalities, how CHD8 haploinsufficiency
affects neurodevelopmental is unclear. Here, employing human cerebral organoids,
we find that CHD8 haploinsufficiency disrupted neurodevelopmental trajectories
with an accelerated and delayed generation of, respectively, inhibitory and excitatory
neurons that yields, at days 60 and 120, symmetrically opposite expansions in
their proportions. This imbalance is consistent with an enlargement of cerebral
organoids as an in vitro correlate of patients’ macrocephaly. Through an isogenic
design of patient-specific mutations and mosaic organoids, we define genotype-phenotype
relationships and uncover their cell-autonomous nature. Our results define cell-type-specific
CHD8-dependent molecular defects related to an abnormal program of proliferation
and alternative splicing. By identifying cell-type-specific effects of CHD8 mutations,
our study uncovers reproducible developmental alterations that may be employed
for neurodevelopmental disease modeling.
acknowledged_ssus:
- _id: Bio
- _id: LifeSc
acknowledgement: We thank Farnaz Freeman for technical assistance. This research was
supported by the Scientific Service Units (SSU) of IST Austria through resources
provided by the Bioimaging Facility (BIF) and the Life Science Facility (LSF). This
work supported by the European Union’s Horizon 2020 research and innovation program
(ERC) grant 715508 to G.N. (REVERSEAUTISM) and grant 825759 to G.T. (ENDpoiNTs);
the Fondazione Cariplo 2017-0886 to A.L.T.; E-Rare-3 JTC 2018 IMPACT to M. Gabriele;
and the Austrian Science Fund FWF I 4205-B to G.N. Graphical abstract and figures
were created using BioRender.com.
article_number: '110615'
article_processing_charge: Yes
article_type: original
author:
- first_name: Carlo Emanuele
full_name: Villa, Carlo Emanuele
last_name: Villa
- first_name: Cristina
full_name: Cheroni, Cristina
last_name: Cheroni
- first_name: Christoph
full_name: Dotter, Christoph
id: 4C66542E-F248-11E8-B48F-1D18A9856A87
last_name: Dotter
orcid: 0000-0002-9033-9096
- first_name: Alejandro
full_name: López-Tóbon, Alejandro
last_name: López-Tóbon
- first_name: Bárbara
full_name: Oliveira, Bárbara
id: 3B03AA1A-F248-11E8-B48F-1D18A9856A87
last_name: Oliveira
- first_name: Roberto
full_name: Sacco, Roberto
id: 42C9F57E-F248-11E8-B48F-1D18A9856A87
last_name: Sacco
- first_name: Aysan Çerağ
full_name: Yahya, Aysan Çerağ
id: 365A65F8-F248-11E8-B48F-1D18A9856A87
last_name: Yahya
- first_name: Jasmin
full_name: Morandell, Jasmin
id: 4739D480-F248-11E8-B48F-1D18A9856A87
last_name: Morandell
- first_name: Michele
full_name: Gabriele, Michele
last_name: Gabriele
- first_name: Mojtaba
full_name: Tavakoli, Mojtaba
id: 3A0A06F4-F248-11E8-B48F-1D18A9856A87
last_name: Tavakoli
orcid: 0000-0002-7667-6854
- first_name: Julia
full_name: Lyudchik, Julia
id: 46E28B80-F248-11E8-B48F-1D18A9856A87
last_name: Lyudchik
- 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: Mariano
full_name: Gabitto, Mariano
last_name: Gabitto
- first_name: Johann G
full_name: Danzl, Johann G
id: 42EFD3B6-F248-11E8-B48F-1D18A9856A87
last_name: Danzl
orcid: 0000-0001-8559-3973
- first_name: Giuseppe
full_name: Testa, Giuseppe
last_name: Testa
- first_name: Gaia
full_name: Novarino, Gaia
id: 3E57A680-F248-11E8-B48F-1D18A9856A87
last_name: Novarino
orcid: 0000-0002-7673-7178
citation:
ama: Villa CE, Cheroni C, Dotter C, et al. CHD8 haploinsufficiency links autism
to transient alterations in excitatory and inhibitory trajectories. Cell Reports.
2022;39(1). doi:10.1016/j.celrep.2022.110615
apa: Villa, C. E., Cheroni, C., Dotter, C., López-Tóbon, A., Oliveira, B., Sacco,
R., … Novarino, G. (2022). CHD8 haploinsufficiency links autism to transient alterations
in excitatory and inhibitory trajectories. Cell Reports. Elsevier. https://doi.org/10.1016/j.celrep.2022.110615
chicago: Villa, Carlo Emanuele, Cristina Cheroni, Christoph Dotter, Alejandro López-Tóbon,
Bárbara Oliveira, Roberto Sacco, Aysan Çerağ Yahya, et al. “CHD8 Haploinsufficiency
Links Autism to Transient Alterations in Excitatory and Inhibitory Trajectories.”
Cell Reports. Elsevier, 2022. https://doi.org/10.1016/j.celrep.2022.110615.
ieee: C. E. Villa et al., “CHD8 haploinsufficiency links autism to transient
alterations in excitatory and inhibitory trajectories,” Cell Reports, vol.
39, no. 1. Elsevier, 2022.
ista: Villa CE, Cheroni C, Dotter C, López-Tóbon A, Oliveira B, Sacco R, Yahya AÇ,
Morandell J, Gabriele M, Tavakoli M, Lyudchik J, Sommer CM, Gabitto M, Danzl JG,
Testa G, Novarino G. 2022. CHD8 haploinsufficiency links autism to transient alterations
in excitatory and inhibitory trajectories. Cell Reports. 39(1), 110615.
mla: Villa, Carlo Emanuele, et al. “CHD8 Haploinsufficiency Links Autism to Transient
Alterations in Excitatory and Inhibitory Trajectories.” Cell Reports, vol.
39, no. 1, 110615, Elsevier, 2022, doi:10.1016/j.celrep.2022.110615.
short: C.E. Villa, C. Cheroni, C. Dotter, A. López-Tóbon, B. Oliveira, R. Sacco,
A.Ç. Yahya, J. Morandell, M. Gabriele, M. Tavakoli, J. Lyudchik, C.M. Sommer,
M. Gabitto, J.G. Danzl, G. Testa, G. Novarino, Cell Reports 39 (2022).
date_created: 2022-04-15T09:03:10Z
date_published: 2022-04-05T00:00:00Z
date_updated: 2024-03-25T23:30:25Z
day: '05'
ddc:
- '570'
department:
- _id: JoDa
- _id: GaNo
doi: 10.1016/j.celrep.2022.110615
ec_funded: 1
external_id:
isi:
- '000785983900003'
pmid:
- '35385734'
file:
- access_level: open_access
checksum: b4e8d68f0268dec499af333e6fd5d8e1
content_type: application/pdf
creator: dernst
date_created: 2022-04-15T09:06:25Z
date_updated: 2022-04-15T09:06:25Z
file_id: '11164'
file_name: 2022_CellReports_Villa.pdf
file_size: '7808644'
relation: main_file
success: 1
file_date_updated: 2022-04-15T09:06:25Z
has_accepted_license: '1'
intvolume: ' 39'
isi: 1
issue: '1'
keyword:
- General Biochemistry
- Genetics and Molecular Biology
language:
- iso: eng
month: '04'
oa: 1
oa_version: Published Version
pmid: 1
project:
- _id: 25444568-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '715508'
name: Probing the Reversibility of Autism Spectrum Disorders by Employing in vivo
and in vitro Models
- _id: 2690FEAC-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: I04205
name: Identification of converging Molecular Pathways Across Chromatinopathies as
Targets for Therapy
publication: Cell Reports
publication_identifier:
issn:
- 2211-1247
publication_status: published
publisher: Elsevier
quality_controlled: '1'
related_material:
record:
- id: '12364'
relation: dissertation_contains
status: public
status: public
title: CHD8 haploinsufficiency links autism to transient alterations in excitatory
and inhibitory trajectories
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: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87
volume: 39
year: '2022'
...
---
_id: '11167'
abstract:
- lang: eng
text: Complex I is one of the major respiratory complexes, conserved from bacteria
to mammals. It oxidises NADH, reduces quinone and pumps protons across the membrane,
thus playing a central role in the oxidative energy metabolism. In this review
we discuss our current state of understanding the structure of complex I from
various species of mammals, plants, fungi, and bacteria, as well as of several
complex I-related proteins. By comparing the structural evidence from these systems
in different redox states and data from mutagenesis and molecular simulations,
we formulate the mechanisms of electron transfer and proton pumping and explain
how they are conformationally and electrostatically coupled. Finally, we discuss
the structural basis of the deactivation phenomenon in mammalian complex I.
article_number: '102350'
article_processing_charge: Yes (via OA deal)
article_type: original
author:
- first_name: Domen
full_name: Kampjut, Domen
id: 37233050-F248-11E8-B48F-1D18A9856A87
last_name: Kampjut
- first_name: Leonid A
full_name: Sazanov, Leonid A
id: 338D39FE-F248-11E8-B48F-1D18A9856A87
last_name: Sazanov
orcid: 0000-0002-0977-7989
citation:
ama: Kampjut D, Sazanov LA. Structure of respiratory complex I – An emerging blueprint
for the mechanism. Current Opinion in Structural Biology. 2022;74. doi:10.1016/j.sbi.2022.102350
apa: Kampjut, D., & Sazanov, L. A. (2022). Structure of respiratory complex
I – An emerging blueprint for the mechanism. Current Opinion in Structural
Biology. Elsevier. https://doi.org/10.1016/j.sbi.2022.102350
chicago: Kampjut, Domen, and Leonid A Sazanov. “Structure of Respiratory Complex
I – An Emerging Blueprint for the Mechanism.” Current Opinion in Structural
Biology. Elsevier, 2022. https://doi.org/10.1016/j.sbi.2022.102350.
ieee: D. Kampjut and L. A. Sazanov, “Structure of respiratory complex I – An emerging
blueprint for the mechanism,” Current Opinion in Structural Biology, vol.
74. Elsevier, 2022.
ista: Kampjut D, Sazanov LA. 2022. Structure of respiratory complex I – An emerging
blueprint for the mechanism. Current Opinion in Structural Biology. 74, 102350.
mla: Kampjut, Domen, and Leonid A. Sazanov. “Structure of Respiratory Complex I
– An Emerging Blueprint for the Mechanism.” Current Opinion in Structural Biology,
vol. 74, 102350, Elsevier, 2022, doi:10.1016/j.sbi.2022.102350.
short: D. Kampjut, L.A. Sazanov, Current Opinion in Structural Biology 74 (2022).
date_created: 2022-04-15T09:32:35Z
date_published: 2022-06-01T00:00:00Z
date_updated: 2023-08-03T06:31:06Z
day: '01'
ddc:
- '570'
department:
- _id: LeSa
doi: 10.1016/j.sbi.2022.102350
external_id:
isi:
- '000829029500020'
pmid:
- '35316665'
file:
- access_level: open_access
checksum: 72bdde48853643a32d42b75f54965c44
content_type: application/pdf
creator: dernst
date_created: 2022-08-05T05:56:03Z
date_updated: 2022-08-05T05:56:03Z
file_id: '11725'
file_name: 2022_CurrentOpStructBiology_Kampjut.pdf
file_size: 815607
relation: main_file
success: 1
file_date_updated: 2022-08-05T05:56:03Z
has_accepted_license: '1'
intvolume: ' 74'
isi: 1
keyword:
- Molecular Biology
- Structural Biology
language:
- iso: eng
month: '06'
oa: 1
oa_version: Published Version
pmid: 1
publication: Current Opinion in Structural Biology
publication_identifier:
issn:
- 0959-440X
publication_status: published
publisher: Elsevier
quality_controlled: '1'
scopus_import: '1'
status: public
title: Structure of respiratory complex I – An emerging blueprint for the mechanism
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: journal_article
user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
volume: 74
year: '2022'
...
---
_id: '11179'
abstract:
- lang: eng
text: Large oligomeric enzymes control a myriad of cellular processes, from protein
synthesis and degradation to metabolism. The 0.5 MDa large TET2 aminopeptidase,
a prototypical protease important for cellular homeostasis, degrades peptides
within a ca. 60 Å wide tetrahedral chamber with four lateral openings. The mechanisms
of substrate trafficking and processing remain debated. Here, we integrate magic-angle
spinning (MAS) NMR, mutagenesis, co-evolution analysis and molecular dynamics
simulations and reveal that a loop in the catalytic chamber is a key element for
enzymatic function. The loop is able to stabilize ligands in the active site and
may additionally have a direct role in activating the catalytic water molecule
whereby a conserved histidine plays a key role. Our data provide a strong case
for the functional importance of highly dynamic - and often overlooked - parts
of an enzyme, and the potential of MAS NMR to investigate their dynamics at atomic
resolution.
acknowledgement: "We are grateful to Bernhard Brutscher, Alicia Vallet, and Adrien
Favier for excellent NMR\r\nplatform operation and management. The plasmid coding
for TET2 was kindly provided\r\nby Bruno Franzetti and Jerome Boisbouvier (IBS Grenoble).
We thank Anne-Marie Villard\r\nand the RoBioMol platform for preparing the loop
deletion construct. The RoBioMol\r\nplatform is part of the Grenoble Instruct-ERIC
center (ISBG; UAR 3518 CNRS-CEAUGA-EMBL) within the Grenoble Partnership for Structural
Biology (PSB), supported by FRISBI (ANR-10-INBS-0005-02) and GRAL (ANR-10-LABX-49-01),
financed within the University Grenoble Alpes graduate school (Ecoles Universitaires
de Recherche) CBHEUR-GS (ANR-17-EURE-0003). This work was supported by the European
Research Council (StG-2012-311318-ProtDyn2Function to P. S.) and the French Agence
Nationale de la Recherche (ANR), under grant ANR-14-ACHN-0016 (M.P. and A.B.)."
article_number: '1927'
article_processing_charge: No
article_type: original
author:
- first_name: Diego F.
full_name: Gauto, Diego F.
last_name: Gauto
- first_name: Pavel
full_name: Macek, Pavel
last_name: Macek
- first_name: Duccio
full_name: Malinverni, Duccio
last_name: Malinverni
- first_name: Hugo
full_name: Fraga, Hugo
last_name: Fraga
- first_name: Matteo
full_name: Paloni, Matteo
last_name: Paloni
- first_name: Iva
full_name: Sučec, Iva
last_name: Sučec
- first_name: Audrey
full_name: Hessel, Audrey
last_name: Hessel
- first_name: Juan Pablo
full_name: Bustamante, Juan Pablo
last_name: Bustamante
- first_name: Alessandro
full_name: Barducci, Alessandro
last_name: Barducci
- first_name: Paul
full_name: Schanda, Paul
id: 7B541462-FAF6-11E9-A490-E8DFE5697425
last_name: Schanda
orcid: 0000-0002-9350-7606
citation:
ama: Gauto DF, Macek P, Malinverni D, et al. Functional control of a 0.5 MDa TET
aminopeptidase by a flexible loop revealed by MAS NMR. Nature Communications.
2022;13. doi:10.1038/s41467-022-29423-0
apa: Gauto, D. F., Macek, P., Malinverni, D., Fraga, H., Paloni, M., Sučec, I.,
… Schanda, P. (2022). Functional control of a 0.5 MDa TET aminopeptidase by a
flexible loop revealed by MAS NMR. Nature Communications. Springer Nature.
https://doi.org/10.1038/s41467-022-29423-0
chicago: Gauto, Diego F., Pavel Macek, Duccio Malinverni, Hugo Fraga, Matteo Paloni,
Iva Sučec, Audrey Hessel, Juan Pablo Bustamante, Alessandro Barducci, and Paul
Schanda. “Functional Control of a 0.5 MDa TET Aminopeptidase by a Flexible Loop
Revealed by MAS NMR.” Nature Communications. Springer Nature, 2022. https://doi.org/10.1038/s41467-022-29423-0.
ieee: D. F. Gauto et al., “Functional control of a 0.5 MDa TET aminopeptidase
by a flexible loop revealed by MAS NMR,” Nature Communications, vol. 13.
Springer Nature, 2022.
ista: Gauto DF, Macek P, Malinverni D, Fraga H, Paloni M, Sučec I, Hessel A, Bustamante
JP, Barducci A, Schanda P. 2022. Functional control of a 0.5 MDa TET aminopeptidase
by a flexible loop revealed by MAS NMR. Nature Communications. 13, 1927.
mla: Gauto, Diego F., et al. “Functional Control of a 0.5 MDa TET Aminopeptidase
by a Flexible Loop Revealed by MAS NMR.” Nature Communications, vol. 13,
1927, Springer Nature, 2022, doi:10.1038/s41467-022-29423-0.
short: D.F. Gauto, P. Macek, D. Malinverni, H. Fraga, M. Paloni, I. Sučec, A. Hessel,
J.P. Bustamante, A. Barducci, P. Schanda, Nature Communications 13 (2022).
date_created: 2022-04-17T22:01:45Z
date_published: 2022-04-08T00:00:00Z
date_updated: 2023-08-03T06:54:56Z
day: '08'
ddc:
- '570'
department:
- _id: PaSc
doi: 10.1038/s41467-022-29423-0
external_id:
isi:
- '000781498700009'
file:
- access_level: open_access
checksum: db61d5534e988743d6266d3675d77b08
content_type: application/pdf
creator: dernst
date_created: 2022-05-02T08:48:00Z
date_updated: 2022-05-02T08:48:00Z
file_id: '11348'
file_name: 2022_NatureCommunications_Gauto.pdf
file_size: 2637590
relation: main_file
success: 1
file_date_updated: 2022-05-02T08:48:00Z
has_accepted_license: '1'
intvolume: ' 13'
isi: 1
language:
- iso: eng
month: '04'
oa: 1
oa_version: Published Version
publication: Nature Communications
publication_identifier:
eissn:
- 2041-1723
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
related_material:
link:
- relation: erratum
url: https://doi.org/10.1038/s41467-022-31243-1
scopus_import: '1'
status: public
title: Functional control of a 0.5 MDa TET aminopeptidase by a flexible loop revealed
by MAS NMR
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: journal_article
user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
volume: 13
year: '2022'
...
---
_id: '11180'
abstract:
- lang: eng
text: "Designing and implementing efficient parallel priority schedulers is an active
research area. An intriguing proposed design is the Multi-Queue: given n threads
and m ≥ n distinct priority queues, task insertions are performed uniformly at
random, while, to delete, a thread picks two queues uniformly at random, and removes
the observed task of higher priority. This approach scales well, and has probabilistic
rank guarantees: roughly, the rank of each task removed, relative to remaining
tasks in all other queues, is O (m) in expectation. Yet, the performance of this
pattern is below that of well-engineered schedulers, which eschew theoretical
guarantees for practical efficiency.\r\n\r\nWe investigate whether it is possible
to design and implement a Multi-Queue-based task scheduler that is both highly-efficient
and has analytical guarantees. We propose a new variant called the Stealing Multi-Queue
(SMQ), a cache-efficient variant of the Multi-Queue, which leverages both queue
affinity---each thread has a local queue, from which tasks are usually removed;
but, with some probability, threads also attempt to steal higher-priority tasks
from the other queues---and task batching, that is, the processing of several
tasks in a single insert / remove step. These ideas are well-known for task scheduling
without priorities; our theoretical contribution is showing that, despite relaxations,
this design can still provide rank guarantees, which in turn implies bounds on
total work performed. We provide a general SMQ implementation which can surpass
state-of-the-art schedulers such as OBIM and PMOD in terms of performance on popular
graph-processing benchmarks. Notably, the performance improvement comes mainly
from the superior rank guarantees provided by our scheduler, confirming that analytically-reasoned
approaches can still provide performance improvements for priority task scheduling."
acknowledgement: We would like to thank the anonymous reviewers for their useful comments.
This project has received funding from the European Research Council (ERC) under
the European Union’s Horizon 2020 research and innovation programme (grant agreement
No 805223 ScaleML).
article_processing_charge: No
arxiv: 1
author:
- first_name: Anastasiia
full_name: Postnikova, Anastasiia
last_name: Postnikova
- first_name: Nikita
full_name: Koval, Nikita
id: 2F4DB10C-F248-11E8-B48F-1D18A9856A87
last_name: Koval
- first_name: Giorgi
full_name: Nadiradze, Giorgi
id: 3279A00C-F248-11E8-B48F-1D18A9856A87
last_name: Nadiradze
- first_name: Dan-Adrian
full_name: Alistarh, Dan-Adrian
id: 4A899BFC-F248-11E8-B48F-1D18A9856A87
last_name: Alistarh
orcid: 0000-0003-3650-940X
citation:
ama: 'Postnikova A, Koval N, Nadiradze G, Alistarh D-A. Multi-queues can be state-of-the-art
priority schedulers. In: Proceedings of the 27th ACM SIGPLAN Symposium on Principles
and Practice of Parallel Programming. Association for Computing Machinery;
2022:353-367. doi:10.1145/3503221.3508432'
apa: 'Postnikova, A., Koval, N., Nadiradze, G., & Alistarh, D.-A. (2022). Multi-queues
can be state-of-the-art priority schedulers. In Proceedings of the 27th ACM
SIGPLAN Symposium on Principles and Practice of Parallel Programming (pp.
353–367). Seoul, Republic of Korea: Association for Computing Machinery. https://doi.org/10.1145/3503221.3508432'
chicago: Postnikova, Anastasiia, Nikita Koval, Giorgi Nadiradze, and Dan-Adrian
Alistarh. “Multi-Queues Can Be State-of-the-Art Priority Schedulers.” In Proceedings
of the 27th ACM SIGPLAN Symposium on Principles and Practice of Parallel Programming,
353–67. Association for Computing Machinery, 2022. https://doi.org/10.1145/3503221.3508432.
ieee: A. Postnikova, N. Koval, G. Nadiradze, and D.-A. Alistarh, “Multi-queues can
be state-of-the-art priority schedulers,” in Proceedings of the 27th ACM SIGPLAN
Symposium on Principles and Practice of Parallel Programming, Seoul, Republic
of Korea, 2022, pp. 353–367.
ista: 'Postnikova A, Koval N, Nadiradze G, Alistarh D-A. 2022. Multi-queues can
be state-of-the-art priority schedulers. Proceedings of the 27th ACM SIGPLAN Symposium
on Principles and Practice of Parallel Programming. PPoPP: Sympopsium on Principles
and Practice of Parallel Programming, 353–367.'
mla: Postnikova, Anastasiia, et al. “Multi-Queues Can Be State-of-the-Art Priority
Schedulers.” Proceedings of the 27th ACM SIGPLAN Symposium on Principles and
Practice of Parallel Programming, Association for Computing Machinery, 2022,
pp. 353–67, doi:10.1145/3503221.3508432.
short: A. Postnikova, N. Koval, G. Nadiradze, D.-A. Alistarh, in:, Proceedings of
the 27th ACM SIGPLAN Symposium on Principles and Practice of Parallel Programming,
Association for Computing Machinery, 2022, pp. 353–367.
conference:
end_date: 2022-04-06
location: Seoul, Republic of Korea
name: 'PPoPP: Sympopsium on Principles and Practice of Parallel Programming'
start_date: 2022-04-02
date_created: 2022-04-17T22:01:46Z
date_published: 2022-04-02T00:00:00Z
date_updated: 2023-08-03T06:48:35Z
day: '02'
department:
- _id: DaAl
doi: 10.1145/3503221.3508432
ec_funded: 1
external_id:
arxiv:
- '2109.00657'
isi:
- '000883318200025'
isi: 1
language:
- iso: eng
main_file_link:
- open_access: '1'
url: ' https://doi.org/10.48550/arXiv.2109.00657'
month: '04'
oa: 1
oa_version: Preprint
page: 353-367
project:
- _id: 268A44D6-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '805223'
name: Elastic Coordination for Scalable Machine Learning
publication: Proceedings of the 27th ACM SIGPLAN Symposium on Principles and Practice
of Parallel Programming
publication_identifier:
isbn:
- '9781450392044'
publication_status: published
publisher: Association for Computing Machinery
quality_controlled: '1'
related_material:
record:
- id: '13076'
relation: research_data
status: public
scopus_import: '1'
status: public
title: Multi-queues can be state-of-the-art priority schedulers
type: conference
user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
year: '2022'
...
---
_id: '11181'
abstract:
- lang: eng
text: 'To maximize the performance of concurrent data structures, researchers have
often turned to highly complex fine-grained techniques, resulting in efficient
and elegant algorithms, which can however be often difficult to understand and
prove correct. While simpler techniques exist, such as transactional memory, they
can have limited performance or portability relative to their fine-grained counterparts.
Approaches at both ends of this complexity-performance spectrum have been extensively
explored, but relatively less is known about the middle ground: approaches that
are willing to sacrifice some performance for simplicity, while remaining competitive
with state-of-the-art handcrafted designs. In this paper, we explore this middle
ground, and present PathCAS, a primitive that combines ideas from multi-word CAS
(KCAS) and transactional memory approaches, while carefully avoiding overhead.
We show how PathCAS can be used to implement efficient search data structures
relatively simply, using an internal binary search tree as an example, then extending
this to an AVL tree. Our best implementations outperform many handcrafted search
trees: in search-heavy workloads, it rivals the BCCO tree [5], the fastest known
concurrent binary tree in terms of search performance [3]. Our results suggest
that PathCAS can yield concurrent data structures that are relatively easy to
build and prove correct, while offering surprisingly high performance.'
acknowledgement: "This work was supported by: the Natural Sciences and Engineering
Research Council of Canada (NSERC) Collaborative Research and Development grant:
CRDPJ 539431-19, the\r\nCanada Foundation for Innovation John R. Evans Leaders Fund
with equal support from the Ontario Research Fund CFI Leaders Opportunity Fund:
38512, Waterloo Huawei Joint Innovation Lab project “Scalable Infrastructure for
Next Generation Data Management Systems”, NSERC Discovery Launch Supplement: DGECR-2019-00048,
NSERC Discovery\r\nProgram under the grants: RGPIN-2019-04227 and RGPIN04512-2018,
and the University of Waterloo. We would also like to thank the reviewers for their
insightful comments."
article_processing_charge: No
author:
- first_name: Trevor A
full_name: Brown, Trevor A
id: 3569F0A0-F248-11E8-B48F-1D18A9856A87
last_name: Brown
- first_name: William
full_name: Sigouin, William
last_name: Sigouin
- first_name: Dan-Adrian
full_name: Alistarh, Dan-Adrian
id: 4A899BFC-F248-11E8-B48F-1D18A9856A87
last_name: Alistarh
orcid: 0000-0003-3650-940X
citation:
ama: 'Brown TA, Sigouin W, Alistarh D-A. PathCAS: An efficient middle ground for
concurrent search data structures. In: Proceedings of the 27th ACM SIGPLAN
Symposium on Principles and Practice of Parallel Programming. Association
for Computing Machinery; 2022:385-399. doi:10.1145/3503221.3508410'
apa: 'Brown, T. A., Sigouin, W., & Alistarh, D.-A. (2022). PathCAS: An efficient
middle ground for concurrent search data structures. In Proceedings of the
27th ACM SIGPLAN Symposium on Principles and Practice of Parallel Programming
(pp. 385–399). Seoul, Republic of Korea: Association for Computing Machinery.
https://doi.org/10.1145/3503221.3508410'
chicago: 'Brown, Trevor A, William Sigouin, and Dan-Adrian Alistarh. “PathCAS: An
Efficient Middle Ground for Concurrent Search Data Structures.” In Proceedings
of the 27th ACM SIGPLAN Symposium on Principles and Practice of Parallel Programming,
385–99. Association for Computing Machinery, 2022. https://doi.org/10.1145/3503221.3508410.'
ieee: 'T. A. Brown, W. Sigouin, and D.-A. Alistarh, “PathCAS: An efficient middle
ground for concurrent search data structures,” in Proceedings of the 27th ACM
SIGPLAN Symposium on Principles and Practice of Parallel Programming, Seoul,
Republic of Korea, 2022, pp. 385–399.'
ista: 'Brown TA, Sigouin W, Alistarh D-A. 2022. PathCAS: An efficient middle ground
for concurrent search data structures. Proceedings of the 27th ACM SIGPLAN Symposium
on Principles and Practice of Parallel Programming. PPoPP: Sympopsium on Principles
and Practice of Parallel Programming, 385–399.'
mla: 'Brown, Trevor A., et al. “PathCAS: An Efficient Middle Ground for Concurrent
Search Data Structures.” Proceedings of the 27th ACM SIGPLAN Symposium on Principles
and Practice of Parallel Programming, Association for Computing Machinery,
2022, pp. 385–99, doi:10.1145/3503221.3508410.'
short: T.A. Brown, W. Sigouin, D.-A. Alistarh, in:, Proceedings of the 27th ACM
SIGPLAN Symposium on Principles and Practice of Parallel Programming, Association
for Computing Machinery, 2022, pp. 385–399.
conference:
end_date: 2022-04-06
location: Seoul, Republic of Korea
name: 'PPoPP: Sympopsium on Principles and Practice of Parallel Programming'
start_date: 2022-04-02
date_created: 2022-04-17T22:01:46Z
date_published: 2022-04-02T00:00:00Z
date_updated: 2023-08-03T06:49:20Z
day: '02'
ddc:
- '000'
department:
- _id: DaAl
doi: 10.1145/3503221.3508410
external_id:
isi:
- '000883318200027'
file:
- access_level: open_access
checksum: 8ceea411fa133795cd4903529498eb6b
content_type: application/pdf
creator: dernst
date_created: 2022-08-05T09:19:29Z
date_updated: 2022-08-05T09:19:29Z
file_id: '11731'
file_name: 2022_PPoPP_Brown.pdf
file_size: 1128343
relation: main_file
success: 1
file_date_updated: 2022-08-05T09:19:29Z
has_accepted_license: '1'
isi: 1
language:
- iso: eng
month: '04'
oa: 1
oa_version: Published Version
page: 385-399
publication: Proceedings of the 27th ACM SIGPLAN Symposium on Principles and Practice
of Parallel Programming
publication_identifier:
isbn:
- '9781450392044'
publication_status: published
publisher: Association for Computing Machinery
quality_controlled: '1'
scopus_import: '1'
status: public
title: 'PathCAS: An efficient middle ground for concurrent search data structures'
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: conference
user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
year: '2022'
...
---
_id: '11182'
abstract:
- lang: eng
text: Immune cells are constantly on the move through multicellular organisms to
explore and respond to pathogens and other harmful insults. While moving, immune
cells efficiently traverse microenvironments composed of tissue cells and extracellular
fibers, which together form complex environments of various porosity, stiffness,
topography, and chemical composition. In this protocol we describe experimental
procedures to investigate immune cell migration through microenvironments of heterogeneous
porosity. In particular, we describe micro-channels, micro-pillars, and collagen
networks as cell migration paths with alternative pore size choices. Employing
micro-channels or micro-pillars that divide at junctions into alternative paths
with initially differentially sized pores allows us to precisely (1) measure the
cellular translocation time through these porous path junctions, (2) quantify
the cellular preference for individual pore sizes, and (3) image cellular components
like the nucleus and the cytoskeleton. This reductionistic experimental setup
thus can elucidate how immune cells perform decisions in complex microenvironments
of various porosity like the interstitium. The setup further allows investigation
of the underlying forces of cellular squeezing and the consequences of cellular
deformation on the integrity of the cell and its organelles. As a complementary
approach that does not require any micro-engineering expertise, we describe the
usage of three-dimensional collagen networks with different pore sizes. Whereas
we here focus on dendritic cells as a model for motile immune cells, the described
protocols are versatile as they are also applicable for other immune cell types
like neutrophils and non-immune cell types such as mesenchymal and cancer cells.
In summary, we here describe protocols to identify the mechanisms and principles
of cellular probing, decision making, and squeezing during cellular movement through
microenvironments of heterogeneous porosity.
acknowledgement: "We thank Kasia Stefanowski for excellent technical assistance, and
the Core Facility Bioimaging of the Biomedical Center (BMC) of the Ludwig-Maximilian
University for excellent support. We gratefully acknowledge financial support from
the Peter Hans Hofschneider Professorship of the Stiftung Experimentelle Biomedizin
(to J.R), from the DFG (Collaborative Research Center SFB914, project A12; and Priority
Programme SPP2332, project 492014049; both to J.R) and from the LMU Institutional
Strategy LMU-Excellent within the framework of the German Excellence Initiative
(to J.R).\r\nOpen access funding enabled and organized by Projekt DEAL."
article_number: e407
article_processing_charge: No
article_type: original
author:
- first_name: Janina
full_name: Kroll, Janina
last_name: Kroll
- first_name: Mauricio J.A.
full_name: Ruiz-Fernandez, Mauricio J.A.
last_name: Ruiz-Fernandez
- first_name: Malte B.
full_name: Braun, Malte B.
last_name: Braun
- first_name: Jack
full_name: Merrin, Jack
id: 4515C308-F248-11E8-B48F-1D18A9856A87
last_name: Merrin
orcid: 0000-0001-5145-4609
- first_name: Jörg
full_name: Renkawitz, Jörg
id: 3F0587C8-F248-11E8-B48F-1D18A9856A87
last_name: Renkawitz
orcid: 0000-0003-2856-3369
citation:
ama: Kroll J, Ruiz-Fernandez MJA, Braun MB, Merrin J, Renkawitz J. Quantifying the
probing and selection of microenvironmental pores by motile immune cells. Current
Protocols. 2022;2(4). doi:10.1002/cpz1.407
apa: Kroll, J., Ruiz-Fernandez, M. J. A., Braun, M. B., Merrin, J., & Renkawitz,
J. (2022). Quantifying the probing and selection of microenvironmental pores by
motile immune cells. Current Protocols. Wiley. https://doi.org/10.1002/cpz1.407
chicago: Kroll, Janina, Mauricio J.A. Ruiz-Fernandez, Malte B. Braun, Jack Merrin,
and Jörg Renkawitz. “Quantifying the Probing and Selection of Microenvironmental
Pores by Motile Immune Cells.” Current Protocols. Wiley, 2022. https://doi.org/10.1002/cpz1.407.
ieee: J. Kroll, M. J. A. Ruiz-Fernandez, M. B. Braun, J. Merrin, and J. Renkawitz,
“Quantifying the probing and selection of microenvironmental pores by motile immune
cells,” Current Protocols, vol. 2, no. 4. Wiley, 2022.
ista: Kroll J, Ruiz-Fernandez MJA, Braun MB, Merrin J, Renkawitz J. 2022. Quantifying
the probing and selection of microenvironmental pores by motile immune cells.
Current Protocols. 2(4), e407.
mla: Kroll, Janina, et al. “Quantifying the Probing and Selection of Microenvironmental
Pores by Motile Immune Cells.” Current Protocols, vol. 2, no. 4, e407,
Wiley, 2022, doi:10.1002/cpz1.407.
short: J. Kroll, M.J.A. Ruiz-Fernandez, M.B. Braun, J. Merrin, J. Renkawitz, Current
Protocols 2 (2022).
date_created: 2022-04-17T22:01:46Z
date_published: 2022-04-05T00:00:00Z
date_updated: 2022-05-02T08:18:00Z
day: '05'
ddc:
- '570'
department:
- _id: NanoFab
doi: 10.1002/cpz1.407
external_id:
pmid:
- '35384410'
file:
- access_level: open_access
checksum: 72152d005c367777f6cf2f6a477f0d52
content_type: application/pdf
creator: dernst
date_created: 2022-05-02T08:16:10Z
date_updated: 2022-05-02T08:16:10Z
file_id: '11347'
file_name: 2022_CurrentProtocols_Kroll.pdf
file_size: 2142703
relation: main_file
success: 1
file_date_updated: 2022-05-02T08:16:10Z
has_accepted_license: '1'
intvolume: ' 2'
issue: '4'
language:
- iso: eng
month: '04'
oa: 1
oa_version: Published Version
pmid: 1
publication: Current Protocols
publication_identifier:
eissn:
- 2691-1299
publication_status: published
publisher: Wiley
quality_controlled: '1'
scopus_import: '1'
status: public
title: Quantifying the probing and selection of microenvironmental pores by motile
immune cells
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 2
year: '2022'
...
---
_id: '11183'
abstract:
- lang: eng
text: "Subgraph detection has recently been one of the most studied problems in
the CONGEST model of distributed computing. In this work, we study the distributed
complexity of problems closely related to subgraph detection, mainly focusing
on induced subgraph detection. The main line of this work presents lower bounds
and parameterized algorithms w.r.t structural parameters of the input graph:\r\n-
On general graphs, we give unconditional lower bounds for induced detection of
cycles and patterns of treewidth 2 in CONGEST. Moreover, by adapting reductions
from centralized parameterized complexity, we prove lower bounds in CONGEST for
detecting patterns with a 4-clique, and for induced path detection conditional
on the hardness of triangle detection in the congested clique.\r\n- On graphs
of bounded degeneracy, we show that induced paths can be detected fast in CONGEST
using techniques from parameterized algorithms, while detecting cycles and patterns
of treewidth 2 is hard.\r\n- On graphs of bounded vertex cover number, we show
that induced subgraph detection is easy in CONGEST for any pattern graph. More
specifically, we adapt a centralized parameterized algorithm for a more general
maximum common induced subgraph detection problem to the distributed setting.
In addition to these induced subgraph detection results, we study various related
problems in the CONGEST and congested clique models, including for multicolored
versions of subgraph-detection-like problems."
acknowledgement: "Amir Nikabadi: Supported by the LABEX MILYON (ANR-10-LABX-0070)
of Université de Lyon, within the program “Investissements d’Avenir” (ANR-11-IDEX-0007)
operated by the French National Research Agency (ANR). Janne H. Korhonen: Supported
by the European Research Council (ERC) under the European Union’s Horizon 2020 research
and innovation programme (grant agreement No 805223 ScaleML).\r\nWe thank François
Le Gall and Masayuki Miyamoto for sharing their work on lower bounds for induced
subgraph detection [36]."
alternative_title:
- LIPIcs
article_number: '15'
article_processing_charge: No
author:
- first_name: Amir
full_name: Nikabadi, Amir
last_name: Nikabadi
- first_name: Janne
full_name: Korhonen, Janne
id: C5402D42-15BC-11E9-A202-CA2BE6697425
last_name: Korhonen
citation:
ama: 'Nikabadi A, Korhonen J. Beyond distributed subgraph detection: Induced subgraphs,
multicolored problems and graph parameters. In: Bramas Q, Gramoli V, Milani A,
eds. 25th International Conference on Principles of Distributed Systems.
Vol 217. Schloss Dagstuhl - Leibniz-Zentrum für Informatik; 2022. doi:10.4230/LIPIcs.OPODIS.2021.15'
apa: 'Nikabadi, A., & Korhonen, J. (2022). Beyond distributed subgraph detection:
Induced subgraphs, multicolored problems and graph parameters. In Q. Bramas, V.
Gramoli, & A. Milani (Eds.), 25th International Conference on Principles
of Distributed Systems (Vol. 217). Strasbourg, France: Schloss Dagstuhl -
Leibniz-Zentrum für Informatik. https://doi.org/10.4230/LIPIcs.OPODIS.2021.15'
chicago: 'Nikabadi, Amir, and Janne Korhonen. “Beyond Distributed Subgraph Detection:
Induced Subgraphs, Multicolored Problems and Graph Parameters.” In 25th International
Conference on Principles of Distributed Systems, edited by Quentin Bramas,
Vincent Gramoli, and Alessia Milani, Vol. 217. Schloss Dagstuhl - Leibniz-Zentrum
für Informatik, 2022. https://doi.org/10.4230/LIPIcs.OPODIS.2021.15.'
ieee: 'A. Nikabadi and J. Korhonen, “Beyond distributed subgraph detection: Induced
subgraphs, multicolored problems and graph parameters,” in 25th International
Conference on Principles of Distributed Systems, Strasbourg, France, 2022,
vol. 217.'
ista: 'Nikabadi A, Korhonen J. 2022. Beyond distributed subgraph detection: Induced
subgraphs, multicolored problems and graph parameters. 25th International Conference
on Principles of Distributed Systems. OPODIS, LIPIcs, vol. 217, 15.'
mla: 'Nikabadi, Amir, and Janne Korhonen. “Beyond Distributed Subgraph Detection:
Induced Subgraphs, Multicolored Problems and Graph Parameters.” 25th International
Conference on Principles of Distributed Systems, edited by Quentin Bramas
et al., vol. 217, 15, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2022,
doi:10.4230/LIPIcs.OPODIS.2021.15.'
short: A. Nikabadi, J. Korhonen, in:, Q. Bramas, V. Gramoli, A. Milani (Eds.), 25th
International Conference on Principles of Distributed Systems, Schloss Dagstuhl
- Leibniz-Zentrum für Informatik, 2022.
conference:
end_date: 2021-12-15
location: Strasbourg, France
name: OPODIS
start_date: 2021-12-13
date_created: 2022-04-17T22:01:47Z
date_published: 2022-02-01T00:00:00Z
date_updated: 2022-05-02T07:56:35Z
day: '01'
ddc:
- '510'
department:
- _id: DaAl
doi: 10.4230/LIPIcs.OPODIS.2021.15
ec_funded: 1
editor:
- first_name: Quentin
full_name: Bramas, Quentin
last_name: Bramas
- first_name: Vincent
full_name: Gramoli, Vincent
last_name: Gramoli
- first_name: Alessia
full_name: Milani, Alessia
last_name: Milani
file:
- access_level: open_access
checksum: 626551c14de5d4091573200ed0535752
content_type: application/pdf
creator: dernst
date_created: 2022-05-02T07:53:00Z
date_updated: 2022-05-02T07:53:00Z
file_id: '11345'
file_name: 2022_LIPICs_Nikabadi.pdf
file_size: 790396
relation: main_file
success: 1
file_date_updated: 2022-05-02T07:53:00Z
has_accepted_license: '1'
intvolume: ' 217'
language:
- iso: eng
month: '02'
oa: 1
oa_version: Published Version
project:
- _id: 268A44D6-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '805223'
name: Elastic Coordination for Scalable Machine Learning
publication: 25th International Conference on Principles of Distributed Systems
publication_identifier:
isbn:
- '9783959772198'
issn:
- 1868-8969
publication_status: published
publisher: Schloss Dagstuhl - Leibniz-Zentrum für Informatik
quality_controlled: '1'
scopus_import: '1'
status: public
title: 'Beyond distributed subgraph detection: Induced subgraphs, multicolored problems
and graph parameters'
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: conference
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 217
year: '2022'
...
---
_id: '11184'
abstract:
- lang: eng
text: "Let G be a graph on n nodes. In the stochastic population protocol model,
a collection of n indistinguishable, resource-limited nodes collectively solve
tasks via pairwise interactions. In each interaction, two randomly chosen neighbors
first read each other’s states, and then update their local states. A rich line
of research has established tight upper and lower bounds on the complexity of
fundamental tasks, such as majority and leader election, in this model, when G
is a clique. Specifically, in the clique, these tasks can be solved fast, i.e.,
in n polylog n pairwise interactions, with high probability, using at most polylog
n states per node.\r\nIn this work, we consider the more general setting where
G is an arbitrary regular graph, and present a technique for simulating protocols
designed for fully-connected networks in any connected regular graph. Our main
result is a simulation that is efficient on many interesting graph families: roughly,
the simulation overhead is polylogarithmic in the number of nodes, and quadratic
in the conductance of the graph. As a sample application, we show that, in any
regular graph with conductance φ, both leader election and exact majority can
be solved in φ^{-2} ⋅ n polylog n pairwise interactions, with high probability,
using at most φ^{-2} ⋅ polylog n states per node. This shows that there are fast
and space-efficient population protocols for leader election and exact majority
on graphs with good expansion properties. We believe our results will prove generally
useful, as they allow efficient technology transfer between the well-mixed (clique)
case, and the under-explored spatial setting."
acknowledgement: "Dan Alistarh: This project has received funding from the European
Research Council (ERC)\r\nunder the European Union’s Horizon 2020 research and innovation
programme (grant agreement No.805223 ScaleML).\r\nJoel Rybicki: This project has
received from the European Union’s Horizon 2020 research and\r\ninnovation programme
under the Marie Skłodowska-Curie grant agreement No. 840605.\r\nAcknowledgements
We grateful to Giorgi Nadiradze for pointing out a generalisation of the phase clock
construction to non-regular graphs. We also thank anonymous reviewers for their
useful comments on earlier versions of this manuscript."
alternative_title:
- LIPIcs
article_number: '14'
article_processing_charge: No
arxiv: 1
author:
- first_name: Dan-Adrian
full_name: Alistarh, Dan-Adrian
id: 4A899BFC-F248-11E8-B48F-1D18A9856A87
last_name: Alistarh
orcid: 0000-0003-3650-940X
- first_name: Rati
full_name: Gelashvili, Rati
last_name: Gelashvili
- first_name: Joel
full_name: Rybicki, Joel
id: 334EFD2E-F248-11E8-B48F-1D18A9856A87
last_name: Rybicki
orcid: 0000-0002-6432-6646
citation:
ama: 'Alistarh D-A, Gelashvili R, Rybicki J. Fast graphical population protocols.
In: Bramas Q, Gramoli V, Milani A, eds. 25th International Conference on Principles
of Distributed Systems. Vol 217. Schloss Dagstuhl - Leibniz-Zentrum für Informatik;
2022. doi:10.4230/LIPIcs.OPODIS.2021.14'
apa: 'Alistarh, D.-A., Gelashvili, R., & Rybicki, J. (2022). Fast graphical
population protocols. In Q. Bramas, V. Gramoli, & A. Milani (Eds.), 25th
International Conference on Principles of Distributed Systems (Vol. 217).
Strasbourg, France: Schloss Dagstuhl - Leibniz-Zentrum für Informatik. https://doi.org/10.4230/LIPIcs.OPODIS.2021.14'
chicago: Alistarh, Dan-Adrian, Rati Gelashvili, and Joel Rybicki. “Fast Graphical
Population Protocols.” In 25th International Conference on Principles of Distributed
Systems, edited by Quentin Bramas, Vincent Gramoli, and Alessia Milani, Vol.
217. Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2022. https://doi.org/10.4230/LIPIcs.OPODIS.2021.14.
ieee: D.-A. Alistarh, R. Gelashvili, and J. Rybicki, “Fast graphical population
protocols,” in 25th International Conference on Principles of Distributed Systems,
Strasbourg, France, 2022, vol. 217.
ista: Alistarh D-A, Gelashvili R, Rybicki J. 2022. Fast graphical population protocols.
25th International Conference on Principles of Distributed Systems. OPODIS, LIPIcs,
vol. 217, 14.
mla: Alistarh, Dan-Adrian, et al. “Fast Graphical Population Protocols.” 25th
International Conference on Principles of Distributed Systems, edited by Quentin
Bramas et al., vol. 217, 14, Schloss Dagstuhl - Leibniz-Zentrum für Informatik,
2022, doi:10.4230/LIPIcs.OPODIS.2021.14.
short: D.-A. Alistarh, R. Gelashvili, J. Rybicki, in:, Q. Bramas, V. Gramoli, A.
Milani (Eds.), 25th International Conference on Principles of Distributed Systems,
Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2022.
conference:
end_date: 2021-12-15
location: Strasbourg, France
name: OPODIS
start_date: 2021-12-13
date_created: 2022-04-17T22:01:47Z
date_published: 2022-02-01T00:00:00Z
date_updated: 2022-05-02T08:09:39Z
day: '01'
ddc:
- '510'
department:
- _id: DaAl
doi: 10.4230/LIPIcs.OPODIS.2021.14
ec_funded: 1
editor:
- first_name: Quentin
full_name: Bramas, Quentin
last_name: Bramas
- first_name: Vincent
full_name: Gramoli, Vincent
last_name: Gramoli
- first_name: Alessia
full_name: Milani, Alessia
last_name: Milani
external_id:
arxiv:
- '2102.08808'
file:
- access_level: open_access
checksum: 2c7c982174c6f98c4ca6e92539d15086
content_type: application/pdf
creator: dernst
date_created: 2022-05-02T08:06:33Z
date_updated: 2022-05-02T08:06:33Z
file_id: '11346'
file_name: 2022_LIPICs_Alistarh.pdf
file_size: 959406
relation: main_file
success: 1
file_date_updated: 2022-05-02T08:06:33Z
has_accepted_license: '1'
intvolume: ' 217'
language:
- iso: eng
month: '02'
oa: 1
oa_version: Published Version
project:
- _id: 268A44D6-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '805223'
name: Elastic Coordination for Scalable Machine Learning
- _id: 26A5D39A-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '840605'
name: Coordination in constrained and natural distributed systems
publication: 25th International Conference on Principles of Distributed Systems
publication_identifier:
isbn:
- '9783959772198'
issn:
- 1868-8969
publication_status: published
publisher: Schloss Dagstuhl - Leibniz-Zentrum für Informatik
quality_controlled: '1'
scopus_import: '1'
status: public
title: Fast graphical population protocols
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: conference
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 217
year: '2022'
...
---
_id: '11185'
abstract:
- lang: eng
text: Bundling crossings is a strategy which can enhance the readability of graph
drawings. In this paper we consider bundlings for families of pseudosegments,
i.e., simple curves such that any two have share at most one point at which they
cross. Our main result is that there is a polynomial-time algorithm to compute
an 8-approximation of the bundled crossing number of such instances (up to adding
a term depending on the facial structure). This 8-approximation also holds for
bundlings of good drawings of graphs. In the special case of circular drawings
the approximation factor is 8 (no extra term), this improves upon the 10-approximation
of Fink et al. [6]. We also show how to compute a 92-approximation when the intersection
graph of the pseudosegments is bipartite.
acknowledgement: This work was initiated during the Workshop on Geometric Graphs in
November 2019 in Strobl, Austria. We would like to thank Oswin Aichholzer, Fabian
Klute, Man-Kwun Chiu, Martin Balko, Pavel Valtr for their avid discussions during
the workshop. The first author has received funding from the European Union’s Horizon
2020 research and innovation programme under the Marie Sklodowska Curie grant agreement
No 754411. The second author has been supported by the German Research Foundation
DFG Project FE 340/12-1.
article_processing_charge: No
arxiv: 1
author:
- first_name: Alan M
full_name: Arroyo Guevara, Alan M
id: 3207FDC6-F248-11E8-B48F-1D18A9856A87
last_name: Arroyo Guevara
orcid: 0000-0003-2401-8670
- first_name: Stefan
full_name: Felsner, Stefan
last_name: Felsner
citation:
ama: 'Arroyo Guevara AM, Felsner S. Approximating the bundled crossing number. In:
WALCOM 2022: Algorithms and Computation. Vol 13174. LNCS. Springer Nature;
2022:383-395. doi:10.1007/978-3-030-96731-4_31'
apa: 'Arroyo Guevara, A. M., & Felsner, S. (2022). Approximating the bundled
crossing number. In WALCOM 2022: Algorithms and Computation (Vol. 13174,
pp. 383–395). Jember, Indonesia: Springer Nature. https://doi.org/10.1007/978-3-030-96731-4_31'
chicago: 'Arroyo Guevara, Alan M, and Stefan Felsner. “Approximating the Bundled
Crossing Number.” In WALCOM 2022: Algorithms and Computation, 13174:383–95.
LNCS. Springer Nature, 2022. https://doi.org/10.1007/978-3-030-96731-4_31.'
ieee: 'A. M. Arroyo Guevara and S. Felsner, “Approximating the bundled crossing
number,” in WALCOM 2022: Algorithms and Computation, Jember, Indonesia,
2022, vol. 13174, pp. 383–395.'
ista: 'Arroyo Guevara AM, Felsner S. 2022. Approximating the bundled crossing number.
WALCOM 2022: Algorithms and Computation. WALCOM: Algorithms and ComputationLNCS
vol. 13174, 383–395.'
mla: 'Arroyo Guevara, Alan M., and Stefan Felsner. “Approximating the Bundled Crossing
Number.” WALCOM 2022: Algorithms and Computation, vol. 13174, Springer
Nature, 2022, pp. 383–95, doi:10.1007/978-3-030-96731-4_31.'
short: 'A.M. Arroyo Guevara, S. Felsner, in:, WALCOM 2022: Algorithms and Computation,
Springer Nature, 2022, pp. 383–395.'
conference:
end_date: 2022-03-26
location: Jember, Indonesia
name: 'WALCOM: Algorithms and Computation'
start_date: 2022-03-24
date_created: 2022-04-17T22:01:47Z
date_published: 2022-03-16T00:00:00Z
date_updated: 2023-09-25T10:56:10Z
day: '16'
department:
- _id: UlWa
doi: 10.1007/978-3-030-96731-4_31
ec_funded: 1
external_id:
arxiv:
- '2109.14892'
intvolume: ' 13174'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: ' https://doi.org/10.48550/arXiv.2109.14892'
month: '03'
oa: 1
oa_version: Preprint
page: 383-395
project:
- _id: 260C2330-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '754411'
name: ISTplus - Postdoctoral Fellowships
publication: 'WALCOM 2022: Algorithms and Computation'
publication_identifier:
eissn:
- 1611-3349
isbn:
- '9783030967307'
issn:
- 0302-9743
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
related_material:
record:
- id: '13969'
relation: later_version
status: public
scopus_import: '1'
series_title: LNCS
status: public
title: Approximating the bundled crossing number
type: conference
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 13174
year: '2022'
...
---
_id: '11186'
abstract:
- lang: eng
text: "In this note, we study large deviations of the number \U0001D40D of intercalates
( 2×2 combinatorial subsquares which are themselves Latin squares) in a random
\ \U0001D45B×\U0001D45B Latin square. In particular, for constant \U0001D6FF>0
\ we prove that exp(−\U0001D442(\U0001D45B2log\U0001D45B))⩽Pr(\U0001D40D⩽(1−\U0001D6FF)\U0001D45B2/4)⩽exp(−Ω(\U0001D45B2))
\ and exp(−\U0001D442(\U0001D45B4/3(log\U0001D45B)))⩽Pr(\U0001D40D⩾(1+\U0001D6FF)\U0001D45B2/4)⩽exp(−Ω(\U0001D45B4/3(log\U0001D45B)2/3))
. As a consequence, we deduce that a typical order- \U0001D45B Latin square has
\ (1+\U0001D45C(1))\U0001D45B2/4 intercalates, matching a lower bound due to
Kwan and Sudakov and resolving an old conjecture of McKay and Wanless."
acknowledgement: "We thank Zach Hunter for pointing out some important typographical
errors. We also thank the referee for several remarks which helped improve the paper
substantially.\r\nKwan was supported by NSF grant DMS-1953990. Sah and Sawhney were
supported by NSF Graduate Research Fellowship Program DGE-1745302."
article_processing_charge: No
article_type: original
arxiv: 1
author:
- first_name: Matthew Alan
full_name: Kwan, Matthew Alan
id: 5fca0887-a1db-11eb-95d1-ca9d5e0453b3
last_name: Kwan
orcid: 0000-0002-4003-7567
- first_name: Ashwin
full_name: Sah, Ashwin
last_name: Sah
- first_name: Mehtaab
full_name: Sawhney, Mehtaab
last_name: Sawhney
citation:
ama: Kwan MA, Sah A, Sawhney M. Large deviations in random latin squares. Bulletin
of the London Mathematical Society. 2022;54(4):1420-1438. doi:10.1112/blms.12638
apa: Kwan, M. A., Sah, A., & Sawhney, M. (2022). Large deviations in random
latin squares. Bulletin of the London Mathematical Society. Wiley. https://doi.org/10.1112/blms.12638
chicago: Kwan, Matthew Alan, Ashwin Sah, and Mehtaab Sawhney. “Large Deviations
in Random Latin Squares.” Bulletin of the London Mathematical Society.
Wiley, 2022. https://doi.org/10.1112/blms.12638.
ieee: M. A. Kwan, A. Sah, and M. Sawhney, “Large deviations in random latin squares,”
Bulletin of the London Mathematical Society, vol. 54, no. 4. Wiley, pp.
1420–1438, 2022.
ista: Kwan MA, Sah A, Sawhney M. 2022. Large deviations in random latin squares.
Bulletin of the London Mathematical Society. 54(4), 1420–1438.
mla: Kwan, Matthew Alan, et al. “Large Deviations in Random Latin Squares.” Bulletin
of the London Mathematical Society, vol. 54, no. 4, Wiley, 2022, pp. 1420–38,
doi:10.1112/blms.12638.
short: M.A. Kwan, A. Sah, M. Sawhney, Bulletin of the London Mathematical Society
54 (2022) 1420–1438.
date_created: 2022-04-17T22:01:48Z
date_published: 2022-08-01T00:00:00Z
date_updated: 2023-08-03T06:47:29Z
day: '01'
ddc:
- '510'
department:
- _id: MaKw
doi: 10.1112/blms.12638
external_id:
arxiv:
- '2106.11932'
isi:
- '000779920900001'
file:
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checksum: 02d74e7ae955ba3c808e2a8aebe6ef98
content_type: application/pdf
creator: dernst
date_created: 2023-02-03T09:43:38Z
date_updated: 2023-02-03T09:43:38Z
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file_size: 233758
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intvolume: ' 54'
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issue: '4'
language:
- iso: eng
license: https://creativecommons.org/licenses/by-nc/4.0/
month: '08'
oa: 1
oa_version: Published Version
page: 1420-1438
publication: Bulletin of the London Mathematical Society
publication_identifier:
eissn:
- 1469-2120
issn:
- 0024-6093
publication_status: published
publisher: Wiley
quality_controlled: '1'
scopus_import: '1'
status: public
title: Large deviations in random latin squares
tmp:
image: /images/cc_by_nc.png
legal_code_url: https://creativecommons.org/licenses/by-nc/4.0/legalcode
name: Creative Commons Attribution-NonCommercial 4.0 International (CC BY-NC 4.0)
short: CC BY-NC (4.0)
type: journal_article
user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
volume: 54
year: '2022'
...
---
_id: '11187'
abstract:
- lang: eng
text: During the COVID-19 pandemic, genomics and bioinformatics have emerged as
essential public health tools. The genomic data acquired using these methods have
supported the global health response, facilitated the development of testing methods
and allowed the timely tracking of novel SARS-CoV-2 variants. Yet the virtually
unlimited potential for rapid generation and analysis of genomic data is also
coupled with unique technical, scientific and organizational challenges. Here,
we discuss the application of genomic and computational methods for efficient
data-driven COVID-19 response, the advantages of the democratization of viral
sequencing around the world and the challenges associated with viral genome data
collection and processing.
acknowledgement: 'Our paper is dedicated to all freedom-loving people around the world,
and to the people of Ukraine who fight for our freedom. We thank William M. Switzer
and Ellsworth M. Campbell from the Division of HIV/AIDS Prevention, Centers for
Disease Control and Prevention (CDC), Atlanta, GA, USA, for discussions and suggestions.
We thank Jason Ladner from the Pathogen and Microbiome Institute, Northern Arizona
University, Flagstaff, AZ, for providing suggestions and feedback. S.M. was partially
supported by National Science Foundation grants 2041984. T.L. is supported by the
NSFC Excellent Young Scientists Fund (Hong Kong and Macau; 31922087), Research Grants
Council (RGC) Collaborative Research Fund (C7144-20GF), RGC Research Impact Fund
(R7021-20), Innovation and Technology Commission’s InnoHK funding (D24H) and Health
and Medical Research Fund (COVID190223). P.S. was supported by US National Institutes
of Health (NIH) grant 1R01EB025022 and National Science Foundation (NSF) grant 2047828.
M.A. acknowledges King Abdulaziz City for Science and Technology and the Saudi Human
Genome Project for technical and financial support (https://shgp.kacst.edu.sa) N.W.
was supported by US NIH grants R00 AI139445, DP2 AT011966 and R01 AI167910. A.S.
acknowledge funding from NSF grant no. 2029025. A.Z. has been partially supported
by NIH grants 1R01EB025022-01 and 1R21CA241044-01A1. S. Knyazev has been partly
supported by Molecular Basis of Disease at Georgia State University and NIH awards
R01 HG009120, R01 MH115676, R01 AI153827 and U01 HG011715. A.W. has been supported
by the CAMS Innovation Fund for Medical Sciences (2021-I2M-1-061). R.K. was supported
by NSF project 2038509, RAPID: Improving QIIME 2 and UniFrac for Viruses to Respond
to COVID-19, CDC project 30055281 with Scripps led by Kristian Andersen, Genomic
sequencing of SARS-CoV-2 to investigate local and cross-border emergence and spread.
J.O.W. was supported by NIH–National Institute of Allergy and Infectious Diseases
(NIAID) R01 AI135992 and receives funding from the CDC unrelated to this work. T.I.V.
is supported by the Branco Weiss Fellowship. Y.P. was supported by the Ministry
of Science and Higher Education of the Russian Federation within the framework of
state support for the creation and development of World-Class Research Centers “Digital
biodesign and personalized healthcare” N◦075-15-2020-926. E.B. was supported by
a US National Institute of General Medical Sciences IDeA Alaska INBRE (P20GM103395)
and NIAID CEIRR (75N93019R00028). C.E.M. thanks Testing for America (501c3), OpenCovidScreen
Foundation, Igor Tulchinsky and the WorldQuant Foundation, Bill Ackman and Olivia
Flatto and the Pershing Square Foundation, Ken Griffin and Citadel, the US National
Institutes of Health (R01AI125416, R01AI151059, R21AI129851, U01DA053941), and the
Alfred P. Sloan Foundation (G-2015-13964). C.Y.C. is supported by US CDC Epidemiology
and Laboratory Capacity (ELC) for Infectious Diseases grant 6NU50CK000539 to the
California Department of Public Health, the Innovative Genomics Institute (IGI)
at the University of California, Berkeley, and University of California, San Francisco,
NIH grant R33AI12945 and US CDC contract 75D30121C10991. A.K. was partly supported
by RFBR grant 20-515-80017. P.L. acknowledges support from the European Research
Council (ERC) under the European Union’s Horizon 2020 research and innovation program
(grant agreement no. ~725422 - ReservoirDOCS), the Wellcome Trust through project
206298/Z/17/Z (Artic Network) and NIH grants R01 AI153044 and U19 AI135995. K.C.
acknowledges support from the US NSF award EEID-IOS-2109688. F.K.’s work was supported
by an ERC Consolidator grant to F.K. (771209–CharFL).'
article_processing_charge: No
article_type: letter_note
author:
- first_name: Sergey
full_name: Knyazev, Sergey
last_name: Knyazev
- first_name: Karishma
full_name: Chhugani, Karishma
last_name: Chhugani
- first_name: Varuni
full_name: Sarwal, Varuni
last_name: Sarwal
- first_name: Ram
full_name: Ayyala, Ram
last_name: Ayyala
- first_name: Harman
full_name: Singh, Harman
last_name: Singh
- first_name: Smruthi
full_name: Karthikeyan, Smruthi
last_name: Karthikeyan
- first_name: Dhrithi
full_name: Deshpande, Dhrithi
last_name: Deshpande
- first_name: Pelin Icer
full_name: Baykal, Pelin Icer
last_name: Baykal
- first_name: Zoia
full_name: Comarova, Zoia
last_name: Comarova
- first_name: Angela
full_name: Lu, Angela
last_name: Lu
- first_name: Yuri
full_name: Porozov, Yuri
last_name: Porozov
- first_name: Tetyana I.
full_name: Vasylyeva, Tetyana I.
last_name: Vasylyeva
- first_name: Joel O.
full_name: Wertheim, Joel O.
last_name: Wertheim
- first_name: Braden T.
full_name: Tierney, Braden T.
last_name: Tierney
- first_name: Charles Y.
full_name: Chiu, Charles Y.
last_name: Chiu
- first_name: Ren
full_name: Sun, Ren
last_name: Sun
- first_name: Aiping
full_name: Wu, Aiping
last_name: Wu
- first_name: Malak S.
full_name: Abedalthagafi, Malak S.
last_name: Abedalthagafi
- first_name: Victoria M.
full_name: Pak, Victoria M.
last_name: Pak
- first_name: Shivashankar H.
full_name: Nagaraj, Shivashankar H.
last_name: Nagaraj
- first_name: Adam L.
full_name: Smith, Adam L.
last_name: Smith
- first_name: Pavel
full_name: Skums, Pavel
last_name: Skums
- first_name: Bogdan
full_name: Pasaniuc, Bogdan
last_name: Pasaniuc
- first_name: Andrey
full_name: Komissarov, Andrey
last_name: Komissarov
- first_name: Christopher E.
full_name: Mason, Christopher E.
last_name: Mason
- first_name: Eric
full_name: Bortz, Eric
last_name: Bortz
- first_name: Philippe
full_name: Lemey, Philippe
last_name: Lemey
- first_name: Fyodor
full_name: Kondrashov, Fyodor
id: 44FDEF62-F248-11E8-B48F-1D18A9856A87
last_name: Kondrashov
orcid: 0000-0001-8243-4694
- first_name: Niko
full_name: Beerenwinkel, Niko
last_name: Beerenwinkel
- first_name: Tommy Tsan Yuk
full_name: Lam, Tommy Tsan Yuk
last_name: Lam
- first_name: Nicholas C.
full_name: Wu, Nicholas C.
last_name: Wu
- first_name: Alex
full_name: Zelikovsky, Alex
last_name: Zelikovsky
- first_name: Rob
full_name: Knight, Rob
last_name: Knight
- first_name: Keith A.
full_name: Crandall, Keith A.
last_name: Crandall
- first_name: Serghei
full_name: Mangul, Serghei
last_name: Mangul
citation:
ama: Knyazev S, Chhugani K, Sarwal V, et al. Unlocking capacities of genomics for
the COVID-19 response and future pandemics. Nature Methods. 2022;19(4):374-380.
doi:10.1038/s41592-022-01444-z
apa: Knyazev, S., Chhugani, K., Sarwal, V., Ayyala, R., Singh, H., Karthikeyan,
S., … Mangul, S. (2022). Unlocking capacities of genomics for the COVID-19 response
and future pandemics. Nature Methods. Springer Nature. https://doi.org/10.1038/s41592-022-01444-z
chicago: Knyazev, Sergey, Karishma Chhugani, Varuni Sarwal, Ram Ayyala, Harman Singh,
Smruthi Karthikeyan, Dhrithi Deshpande, et al. “Unlocking Capacities of Genomics
for the COVID-19 Response and Future Pandemics.” Nature Methods. Springer
Nature, 2022. https://doi.org/10.1038/s41592-022-01444-z.
ieee: S. Knyazev et al., “Unlocking capacities of genomics for the COVID-19
response and future pandemics,” Nature Methods, vol. 19, no. 4. Springer
Nature, pp. 374–380, 2022.
ista: Knyazev S, Chhugani K, Sarwal V, Ayyala R, Singh H, Karthikeyan S, Deshpande
D, Baykal PI, Comarova Z, Lu A, Porozov Y, Vasylyeva TI, Wertheim JO, Tierney
BT, Chiu CY, Sun R, Wu A, Abedalthagafi MS, Pak VM, Nagaraj SH, Smith AL, Skums
P, Pasaniuc B, Komissarov A, Mason CE, Bortz E, Lemey P, Kondrashov F, Beerenwinkel
N, Lam TTY, Wu NC, Zelikovsky A, Knight R, Crandall KA, Mangul S. 2022. Unlocking
capacities of genomics for the COVID-19 response and future pandemics. Nature
Methods. 19(4), 374–380.
mla: Knyazev, Sergey, et al. “Unlocking Capacities of Genomics for the COVID-19
Response and Future Pandemics.” Nature Methods, vol. 19, no. 4, Springer
Nature, 2022, pp. 374–80, doi:10.1038/s41592-022-01444-z.
short: S. Knyazev, K. Chhugani, V. Sarwal, R. Ayyala, H. Singh, S. Karthikeyan,
D. Deshpande, P.I. Baykal, Z. Comarova, A. Lu, Y. Porozov, T.I. Vasylyeva, J.O.
Wertheim, B.T. Tierney, C.Y. Chiu, R. Sun, A. Wu, M.S. Abedalthagafi, V.M. Pak,
S.H. Nagaraj, A.L. Smith, P. Skums, B. Pasaniuc, A. Komissarov, C.E. Mason, E.
Bortz, P. Lemey, F. Kondrashov, N. Beerenwinkel, T.T.Y. Lam, N.C. Wu, A. Zelikovsky,
R. Knight, K.A. Crandall, S. Mangul, Nature Methods 19 (2022) 374–380.
date_created: 2022-04-17T22:01:48Z
date_published: 2022-04-08T00:00:00Z
date_updated: 2023-08-03T06:46:09Z
day: '08'
department:
- _id: FyKo
doi: 10.1038/s41592-022-01444-z
ec_funded: 1
external_id:
isi:
- '000781199600011'
pmid:
- '35396471'
intvolume: ' 19'
isi: 1
issue: '4'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.1038/s41592-022-01444-z
month: '04'
oa: 1
oa_version: Published Version
page: 374-380
pmid: 1
project:
- _id: 26580278-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '771209'
name: Characterizing the fitness landscape on population and global scales
publication: Nature Methods
publication_identifier:
eissn:
- 1548-7105
issn:
- 1548-7091
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
scopus_import: '1'
status: public
title: Unlocking capacities of genomics for the COVID-19 response and future pandemics
type: journal_article
user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
volume: 19
year: '2022'
...
---
_id: '11193'
abstract:
- lang: eng
text: "The infiltration of immune cells into tissues underlies the establishment
of tissue-resident\r\nmacrophages and responses to infections and tumors. However,
the mechanisms immune\r\ncells utilize to collectively migrate through tissue
barriers in vivo are not yet well understood.\r\nIn this thesis, I describe two
mechanisms that Drosophila immune cells (hemocytes) use to\r\novercome the tissue
barrier of the germband in the embryo. One strategy is the strengthening\r\nof
the actin cortex through developmentally controlled transcriptional regulation
induced by\r\nthe Drosophila proto-oncogene family member Dfos, which I show in
Chapter 2. Dfos induces\r\nexpression of the tetraspanin TM4SF and the filamin
Cher leading to higher levels of the\r\nactivated formin Dia at the cortex and
increased cortical F-actin. This enhanced cortical\r\nstrength allows hemocytes
to overcome the physical resistance of the surrounding tissue and\r\ntranslocate
their nucleus to move forward. This mechanism affects the speed of migration\r\nwhen
hemocytes face a confined environment in vivo.\r\nAnother aspect of the invasion
process is the initial step of the leading hemocytes entering\r\nthe tissue, which
potentially guides the follower cells. In Chapter 3, I describe a novel\r\nsubpopulation
of hemocytes activated by BMP signaling prior to tissue invasion that leads\r\npenetration
into the germband. Hemocytes that are deficient in BMP signaling activation\r\nshow
impaired persistence at the tissue entry, while their migration speed remains\r\nunaffected.\r\nThis
suggests that there might be different mechanisms controlling immune cell migration\r\nwithin
the confined environment in vivo, one of these being the general ability to overcome\r\nthe
resistance of the surrounding tissue and another affecting the order of hemocytes
that\r\ncollectively invade the tissue in a stream of individual cells.\r\nTogether,
my findings provide deeper insights into transcriptional changes in immune\r\ncells
that enable efficient tissue invasion and pave the way for future studies investigating
the\r\nearly colonization of tissues by macrophages in higher organisms. Moreover,
they extend the\r\ncurrent view of Drosophila immune cell heterogeneity and point
toward a potentially\r\nconserved role for canonical BMP signaling in specifying
immune cells that lead the migration\r\nof tissue resident macrophages during
embryogenesis."
acknowledged_ssus:
- _id: LifeSc
alternative_title:
- ISTA Thesis
article_processing_charge: No
author:
- first_name: Stephanie
full_name: Wachner, Stephanie
id: 2A95E7B0-F248-11E8-B48F-1D18A9856A87
last_name: Wachner
citation:
ama: Wachner S. Transcriptional regulation by Dfos and BMP-signaling support tissue
invasion of Drosophila immune cells. 2022. doi:10.15479/at:ista:11193
apa: Wachner, S. (2022). Transcriptional regulation by Dfos and BMP-signaling
support tissue invasion of Drosophila immune cells. Institute of Science and
Technology Austria. https://doi.org/10.15479/at:ista:11193
chicago: Wachner, Stephanie. “Transcriptional Regulation by Dfos and BMP-Signaling
Support Tissue Invasion of Drosophila Immune Cells.” Institute of Science and
Technology Austria, 2022. https://doi.org/10.15479/at:ista:11193.
ieee: S. Wachner, “Transcriptional regulation by Dfos and BMP-signaling support
tissue invasion of Drosophila immune cells,” Institute of Science and Technology
Austria, 2022.
ista: Wachner S. 2022. Transcriptional regulation by Dfos and BMP-signaling support
tissue invasion of Drosophila immune cells. Institute of Science and Technology
Austria.
mla: Wachner, Stephanie. Transcriptional Regulation by Dfos and BMP-Signaling
Support Tissue Invasion of Drosophila Immune Cells. Institute of Science and
Technology Austria, 2022, doi:10.15479/at:ista:11193.
short: S. Wachner, Transcriptional Regulation by Dfos and BMP-Signaling Support
Tissue Invasion of Drosophila Immune Cells, Institute of Science and Technology
Austria, 2022.
date_created: 2022-04-20T08:59:07Z
date_published: 2022-04-20T00:00:00Z
date_updated: 2023-09-19T10:15:54Z
day: '20'
ddc:
- '570'
degree_awarded: PhD
department:
- _id: GradSch
- _id: DaSi
doi: 10.15479/at:ista:11193
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project:
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grant_number: '24800'
name: Tissue barrier penetration is crucial for immunity and metastasis
publication_identifier:
issn:
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publication_status: published
publisher: Institute of Science and Technology Austria
related_material:
record:
- id: '10614'
relation: part_of_dissertation
status: public
- id: '544'
relation: part_of_dissertation
status: public
status: public
supervisor:
- first_name: Daria E
full_name: Siekhaus, Daria E
id: 3D224B9E-F248-11E8-B48F-1D18A9856A87
last_name: Siekhaus
orcid: 0000-0001-8323-8353
title: Transcriptional regulation by Dfos and BMP-signaling support tissue invasion
of Drosophila immune cells
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: dissertation
user_id: 8b945eb4-e2f2-11eb-945a-df72226e66a9
year: '2022'
...
---
_id: '11196'
abstract:
- lang: eng
text: "One of the fundamental questions in Neuroscience is how the structure of
synapses and their physiological properties are related. While synaptic transmission
remains a dynamic process, electron microscopy provides images with comparably
low temporal resolution (Studer et al., 2014). The current work overcomes this
challenge and describes an improved “Flash and Freeze” technique (Watanabe et
al., 2013a; Watanabe et al., 2013b) to study synaptic transmission at the hippocampal
mossy fiber-CA3 pyramidal neuron synapses, using mouse acute brain slices and
organotypic slices culture. The improved method allowed for selective stimulation
of presynaptic mossy fiber boutons and the observation of synaptic vesicle pool
dynamics at the active zones. Our results uncovered several intriguing morphological
features of mossy fiber boutons. First, the docked vesicle pool was largely depleted
(more than 70%) after stimulation, implying that the docked synaptic vesicles
pool and readily releasable pool are vastly overlapping in mossy fiber boutons.
Second, the synaptic vesicles are skewed towards larger diameters, displaying
a wide range of sizes. An increase in the mean diameter of synaptic vesicles,
after single and repetitive stimulation, suggests that smaller vesicles have a
higher release probability. Third, we observed putative endocytotic structures
after moderate light stimulation, matching the timing of previously described
ultrafast endocytosis (Watanabe et al., 2013a; Delvendahl et al., 2016). \r\n\tIn
addition, synaptic transmission depends on a sophisticated system of protein machinery
and calcium channels (Südhof, 2013b), which amplifies the challenge in studying
synaptic communication as these interactions can be potentially modified during
synaptic plasticity. And although recent study elucidated the potential correlation
between physiological and morphological properties of synapses during synaptic
plasticity (Vandael et al., 2020), the molecular underpinning of it remains unknown.
Thus, the presented work tries to overcome this challenge and aims to pinpoint
changes in the molecular architecture at hippocampal mossy fiber bouton synapses
during short- and long-term potentiation (STP and LTP), we combined chemical potentiation,
with the application of a cyclic adenosine monophosphate agonist (i.e. forskolin)
and freeze-fracture replica immunolabelling. This method allowed the localization
of membrane-bound proteins with nanometer precision within the active zone, in
particular, P/Q-type calcium channels and synaptic vesicle priming proteins Munc13-1/2.
First, we found that the number of clusters of Munc13-1 in the mossy fiber bouton
active zone increased significantly during STP, but decreased to lower than the
control value during LTP. Secondly, although the distance between the calcium
channels and Munc13-1s did not change after induction of STP, it shortened during
the LTP phase. Additionally, forskolin did not affect Munc13-2 distribution during
STP and LTP. These results indicate the existence of two distinct mechanisms that
govern STP and LTP at mossy fiber bouton synapses: an increase in the readily
realizable pool in the case of STP and a potential increase in release probability
during LTP. “Flash and freeze” and functional electron microscopy, are versatile
methods that can be successfully applied to intact brain circuits to study synaptic
transmission even at the molecular level.\r\n"
acknowledged_ssus:
- _id: EM-Fac
- _id: PreCl
alternative_title:
- ISTA Thesis
article_processing_charge: No
author:
- first_name: Olena
full_name: Kim, Olena
id: 3F8ABDDA-F248-11E8-B48F-1D18A9856A87
last_name: Kim
citation:
ama: Kim O. Nanoarchitecture of hippocampal mossy fiber-CA3 pyramidal neuron synapses.
2022. doi:10.15479/at:ista:11196
apa: Kim, O. (2022). Nanoarchitecture of hippocampal mossy fiber-CA3 pyramidal
neuron synapses. Institute of Science and Technology Austria. https://doi.org/10.15479/at:ista:11196
chicago: Kim, Olena. “Nanoarchitecture of Hippocampal Mossy Fiber-CA3 Pyramidal
Neuron Synapses.” Institute of Science and Technology Austria, 2022. https://doi.org/10.15479/at:ista:11196.
ieee: O. Kim, “Nanoarchitecture of hippocampal mossy fiber-CA3 pyramidal neuron
synapses,” Institute of Science and Technology Austria, 2022.
ista: Kim O. 2022. Nanoarchitecture of hippocampal mossy fiber-CA3 pyramidal neuron
synapses. Institute of Science and Technology Austria.
mla: Kim, Olena. Nanoarchitecture of Hippocampal Mossy Fiber-CA3 Pyramidal Neuron
Synapses. Institute of Science and Technology Austria, 2022, doi:10.15479/at:ista:11196.
short: O. Kim, Nanoarchitecture of Hippocampal Mossy Fiber-CA3 Pyramidal Neuron
Synapses, Institute of Science and Technology Austria, 2022.
date_created: 2022-04-20T09:47:12Z
date_published: 2022-04-20T00:00:00Z
date_updated: 2023-08-18T06:31:52Z
day: '20'
ddc:
- '570'
degree_awarded: PhD
department:
- _id: PeJo
- _id: GradSch
doi: 10.15479/at:ista:11196
ec_funded: 1
file:
- access_level: open_access
checksum: 1616a8bf6f13a57c892dac873dcd0936
content_type: application/pdf
creator: okim
date_created: 2022-04-20T14:21:56Z
date_updated: 2023-04-20T22:30:03Z
embargo: 2023-04-19
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file_size: 21273537
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date_created: 2022-04-20T14:22:56Z
date_updated: 2023-04-20T22:30:03Z
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file_size: 59248569
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file_date_updated: 2023-04-20T22:30:03Z
has_accepted_license: '1'
language:
- iso: eng
month: '04'
oa: 1
oa_version: Published Version
page: '132'
project:
- _id: 25BAF7B2-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '708497'
name: Presynaptic calcium channels distribution and impact on coupling at the hippocampal
mossy fiber synapse
- _id: 25B7EB9E-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '692692'
name: Biophysics and circuit function of a giant cortical glumatergic synapse
- _id: 25C3DBB6-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: W01205
name: Zellkommunikation in Gesundheit und Krankheit
- _id: 25C5A090-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: Z00312
name: The Wittgenstein Prize
publication_identifier:
issn:
- 2663-337X
publication_status: published
publisher: Institute of Science and Technology Austria
related_material:
record:
- id: '11222'
relation: part_of_dissertation
status: public
- id: '7473'
relation: part_of_dissertation
status: public
status: public
supervisor:
- first_name: Peter M
full_name: Jonas, Peter M
id: 353C1B58-F248-11E8-B48F-1D18A9856A87
last_name: Jonas
orcid: 0000-0001-5001-4804
title: Nanoarchitecture of hippocampal mossy fiber-CA3 pyramidal neuron synapses
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: dissertation
user_id: 8b945eb4-e2f2-11eb-945a-df72226e66a9
year: '2022'
...
---
_id: '11321'
abstract:
- lang: eng
text: 'Here are the research data underlying the publication "Effects of fine-scale
population structure on the distribution of heterozygosity in a long-term study
of Antirrhinum majus" Further information are summed up in the README document. '
article_processing_charge: No
author:
- first_name: Parvathy
full_name: Surendranadh, Parvathy
id: 455235B8-F248-11E8-B48F-1D18A9856A87
last_name: Surendranadh
- first_name: Louise S
full_name: Arathoon, Louise S
id: 2CFCFF98-F248-11E8-B48F-1D18A9856A87
last_name: Arathoon
orcid: 0000-0003-1771-714X
- first_name: Carina
full_name: Baskett, Carina
id: 3B4A7CE2-F248-11E8-B48F-1D18A9856A87
last_name: Baskett
orcid: 0000-0002-7354-8574
- first_name: David
full_name: Field, David
id: 419049E2-F248-11E8-B48F-1D18A9856A87
last_name: Field
orcid: 0000-0002-4014-8478
- first_name: Melinda
full_name: Pickup, Melinda
id: 2C78037E-F248-11E8-B48F-1D18A9856A87
last_name: Pickup
orcid: 0000-0001-6118-0541
- first_name: Nicholas H
full_name: Barton, Nicholas H
id: 4880FE40-F248-11E8-B48F-1D18A9856A87
last_name: Barton
orcid: 0000-0002-8548-5240
citation:
ama: Surendranadh P, Arathoon LS, Baskett C, Field D, Pickup M, Barton NH. Effects
of fine-scale population structure on the distribution of heterozygosity in a
long-term study of Antirrhinum majus. 2022. doi:10.15479/at:ista:11321
apa: Surendranadh, P., Arathoon, L. S., Baskett, C., Field, D., Pickup, M., &
Barton, N. H. (2022). Effects of fine-scale population structure on the distribution
of heterozygosity in a long-term study of Antirrhinum majus. Institute of Science
and Technology Austria. https://doi.org/10.15479/at:ista:11321
chicago: Surendranadh, Parvathy, Louise S Arathoon, Carina Baskett, David Field,
Melinda Pickup, and Nicholas H Barton. “Effects of Fine-Scale Population Structure
on the Distribution of Heterozygosity in a Long-Term Study of Antirrhinum Majus.”
Institute of Science and Technology Austria, 2022. https://doi.org/10.15479/at:ista:11321.
ieee: P. Surendranadh, L. S. Arathoon, C. Baskett, D. Field, M. Pickup, and N. H.
Barton, “Effects of fine-scale population structure on the distribution of heterozygosity
in a long-term study of Antirrhinum majus.” Institute of Science and Technology
Austria, 2022.
ista: Surendranadh P, Arathoon LS, Baskett C, Field D, Pickup M, Barton NH. 2022.
Effects of fine-scale population structure on the distribution of heterozygosity
in a long-term study of Antirrhinum majus, Institute of Science and Technology
Austria, 10.15479/at:ista:11321.
mla: Surendranadh, Parvathy, et al. Effects of Fine-Scale Population Structure
on the Distribution of Heterozygosity in a Long-Term Study of Antirrhinum Majus.
Institute of Science and Technology Austria, 2022, doi:10.15479/at:ista:11321.
short: P. Surendranadh, L.S. Arathoon, C. Baskett, D. Field, M. Pickup, N.H. Barton,
(2022).
contributor:
- contributor_type: project_member
first_name: Louise S
id: 2CFCFF98-F248-11E8-B48F-1D18A9856A87
last_name: Arathoon
- contributor_type: project_member
first_name: Carina
id: 3B4A7CE2-F248-11E8-B48F-1D18A9856A87
last_name: Baskett
orcid: 0000-0002-7354-8574
- contributor_type: project_member
first_name: David
id: 419049E2-F248-11E8-B48F-1D18A9856A87
last_name: Field
orcid: 0000-0002-4014-8478
- contributor_type: project_member
first_name: Melinda
id: 2C78037E-F248-11E8-B48F-1D18A9856A87
last_name: Pickup
orcid: 0000-0001-6118-0541
- contributor_type: project_member
first_name: Nicholas H
id: 4880FE40-F248-11E8-B48F-1D18A9856A87
last_name: Barton
orcid: 0000-0002-8548-5240
date_created: 2022-04-22T09:42:24Z
date_published: 2022-04-28T00:00:00Z
date_updated: 2024-02-21T12:41:09Z
day: '28'
ddc:
- '570'
department:
- _id: GradSch
- _id: NiBa
doi: 10.15479/at:ista:11321
file:
- access_level: open_access
checksum: 96c1b86cdf25481f2a52972fcc45ca7f
content_type: application/x-zip-compressed
creator: larathoo
date_created: 2022-04-22T09:39:03Z
date_updated: 2022-04-22T09:39:03Z
file_id: '11326'
file_name: Data_Code.zip
file_size: 13260571
relation: main_file
success: 1
file_date_updated: 2022-04-22T09:39:03Z
has_accepted_license: '1'
month: '04'
oa: 1
oa_version: Published Version
publisher: Institute of Science and Technology Austria
related_material:
record:
- id: '11411'
relation: used_in_publication
status: public
- id: '9192'
relation: earlier_version
status: public
- id: '8254'
relation: earlier_version
status: public
status: public
title: Effects of fine-scale population structure on the distribution of heterozygosity
in a long-term study of Antirrhinum majus
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: research_data
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
year: '2022'
...
---
_id: '11330'
abstract:
- lang: eng
text: In this article we study the noncommutative transport distance introduced
by Carlen and Maas and its entropic regularization defined by Becker and Li. We
prove a duality formula that can be understood as a quantum version of the dual
Benamou–Brenier formulation of the Wasserstein distance in terms of subsolutions
of a Hamilton–Jacobi–Bellmann equation.
acknowledgement: "The author wants to thank Jan Maas for helpful comments. He also
acknowledges financial support from the Austrian Science Fund (FWF) through Grant
Number F65 and from the European Research Council (ERC) under the European Union’s
Horizon 2020 Research and Innovation Programme (Grant Agreement No. 716117).\r\nOpen
access funding provided by Institute of Science and Technology (IST Austria)."
article_number: '19'
article_processing_charge: Yes (via OA deal)
article_type: original
author:
- first_name: Melchior
full_name: Wirth, Melchior
id: 88644358-0A0E-11EA-8FA5-49A33DDC885E
last_name: Wirth
orcid: 0000-0002-0519-4241
citation:
ama: Wirth M. A dual formula for the noncommutative transport distance. Journal
of Statistical Physics. 2022;187(2). doi:10.1007/s10955-022-02911-9
apa: Wirth, M. (2022). A dual formula for the noncommutative transport distance.
Journal of Statistical Physics. Springer Nature. https://doi.org/10.1007/s10955-022-02911-9
chicago: Wirth, Melchior. “A Dual Formula for the Noncommutative Transport Distance.”
Journal of Statistical Physics. Springer Nature, 2022. https://doi.org/10.1007/s10955-022-02911-9.
ieee: M. Wirth, “A dual formula for the noncommutative transport distance,” Journal
of Statistical Physics, vol. 187, no. 2. Springer Nature, 2022.
ista: Wirth M. 2022. A dual formula for the noncommutative transport distance. Journal
of Statistical Physics. 187(2), 19.
mla: Wirth, Melchior. “A Dual Formula for the Noncommutative Transport Distance.”
Journal of Statistical Physics, vol. 187, no. 2, 19, Springer Nature, 2022,
doi:10.1007/s10955-022-02911-9.
short: M. Wirth, Journal of Statistical Physics 187 (2022).
date_created: 2022-04-24T22:01:43Z
date_published: 2022-04-08T00:00:00Z
date_updated: 2023-08-03T06:37:49Z
day: '08'
ddc:
- '510'
- '530'
department:
- _id: JaMa
doi: 10.1007/s10955-022-02911-9
ec_funded: 1
external_id:
isi:
- '000780305000001'
file:
- access_level: open_access
checksum: f3e0b00884b7dde31347a3756788b473
content_type: application/pdf
creator: dernst
date_created: 2022-04-29T11:24:23Z
date_updated: 2022-04-29T11:24:23Z
file_id: '11338'
file_name: 2022_JourStatisticalPhysics_Wirth.pdf
file_size: 362119
relation: main_file
success: 1
file_date_updated: 2022-04-29T11:24:23Z
has_accepted_license: '1'
intvolume: ' 187'
isi: 1
issue: '2'
language:
- iso: eng
month: '04'
oa: 1
oa_version: Published Version
project:
- _id: fc31cba2-9c52-11eb-aca3-ff467d239cd2
grant_number: F6504
name: Taming Complexity in Partial Differential Systems
- _id: 256E75B8-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '716117'
name: Optimal Transport and Stochastic Dynamics
publication: Journal of Statistical Physics
publication_identifier:
eissn:
- '15729613'
issn:
- '00224715'
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
scopus_import: '1'
status: public
title: A dual formula for the noncommutative transport distance
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: 187
year: '2022'
...
---
_id: '11331'
abstract:
- lang: eng
text: "We propose separating the task of reliable transaction dissemination from
transaction ordering, to enable high-performance Byzantine fault-tolerant quorum-based
consensus. We design and evaluate a mempool protocol, Narwhal, specializing in
high-throughput reliable dissemination and storage of causal histories of transactions.
Narwhal tolerates an asynchronous network and maintains high performance despite
failures. Narwhal is designed to easily scale-out using multiple workers at each
validator, and we demonstrate that there is no foreseeable limit to the throughput
we can achieve.\r\nComposing Narwhal with a partially synchronous consensus protocol
(Narwhal-HotStuff) yields significantly better throughput even in the presence
of faults or intermittent loss of liveness due to asynchrony. However, loss of
liveness can result in higher latency. To achieve overall good performance when
faults occur we design Tusk, a zero-message overhead asynchronous consensus protocol,
to work with Narwhal. We demonstrate its high performance under a variety of configurations
and faults.\r\nAs a summary of results, on a WAN, Narwhal-Hotstuff achieves over
130,000 tx/sec at less than 2-sec latency compared with 1,800 tx/sec at 1-sec
latency for Hotstuff. Additional workers increase throughput linearly to 600,000
tx/sec without any latency increase. Tusk achieves 160,000 tx/sec with about 3
seconds latency. Under faults, both protocols maintain high throughput, but Narwhal-HotStuff
suffers from increased latency."
article_processing_charge: No
arxiv: 1
author:
- first_name: George
full_name: Danezis, George
last_name: Danezis
- first_name: Eleftherios
full_name: Kokoris Kogias, Eleftherios
id: f5983044-d7ef-11ea-ac6d-fd1430a26d30
last_name: Kokoris Kogias
- first_name: Alberto
full_name: Sonnino, Alberto
last_name: Sonnino
- first_name: Alexander
full_name: Spiegelman, Alexander
last_name: Spiegelman
citation:
ama: 'Danezis G, Kokoris Kogias E, Sonnino A, Spiegelman A. Narwhal and Tusk: A
DAG-based mempool and efficient BFT consensus. In: Proceedings of the 17th
European Conference on Computer Systems. Association for Computing Machinery;
2022:34-50. doi:10.1145/3492321.3519594'
apa: 'Danezis, G., Kokoris Kogias, E., Sonnino, A., & Spiegelman, A. (2022).
Narwhal and Tusk: A DAG-based mempool and efficient BFT consensus. In Proceedings
of the 17th European Conference on Computer Systems (pp. 34–50). Rennes, France:
Association for Computing Machinery. https://doi.org/10.1145/3492321.3519594'
chicago: 'Danezis, George, Eleftherios Kokoris Kogias, Alberto Sonnino, and Alexander
Spiegelman. “Narwhal and Tusk: A DAG-Based Mempool and Efficient BFT Consensus.”
In Proceedings of the 17th European Conference on Computer Systems, 34–50.
Association for Computing Machinery, 2022. https://doi.org/10.1145/3492321.3519594.'
ieee: 'G. Danezis, E. Kokoris Kogias, A. Sonnino, and A. Spiegelman, “Narwhal and
Tusk: A DAG-based mempool and efficient BFT consensus,” in Proceedings of the
17th European Conference on Computer Systems, Rennes, France, 2022, pp. 34–50.'
ista: 'Danezis G, Kokoris Kogias E, Sonnino A, Spiegelman A. 2022. Narwhal and Tusk:
A DAG-based mempool and efficient BFT consensus. Proceedings of the 17th European
Conference on Computer Systems. EuroSys: European Conference on Computer Systems,
34–50.'
mla: 'Danezis, George, et al. “Narwhal and Tusk: A DAG-Based Mempool and Efficient
BFT Consensus.” Proceedings of the 17th European Conference on Computer Systems,
Association for Computing Machinery, 2022, pp. 34–50, doi:10.1145/3492321.3519594.'
short: G. Danezis, E. Kokoris Kogias, A. Sonnino, A. Spiegelman, in:, Proceedings
of the 17th European Conference on Computer Systems, Association for Computing
Machinery, 2022, pp. 34–50.
conference:
end_date: 2022-04-08
location: Rennes, France
name: 'EuroSys: European Conference on Computer Systems'
start_date: 2022-04-05
date_created: 2022-04-24T22:01:43Z
date_published: 2022-03-28T00:00:00Z
date_updated: 2023-08-03T06:38:40Z
day: '28'
department:
- _id: ElKo
doi: 10.1145/3492321.3519594
external_id:
arxiv:
- '2105.11827'
isi:
- '000926506800003'
isi: 1
language:
- iso: eng
main_file_link:
- open_access: '1'
url: ' https://doi.org/10.48550/arXiv.2105.11827'
month: '03'
oa: 1
oa_version: Preprint
page: 34-50
publication: Proceedings of the 17th European Conference on Computer Systems
publication_identifier:
isbn:
- '9781450391627'
publication_status: published
publisher: Association for Computing Machinery
quality_controlled: '1'
scopus_import: '1'
status: public
title: 'Narwhal and Tusk: A DAG-based mempool and efficient BFT consensus'
type: conference
user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
year: '2022'
...
---
_id: '11332'
abstract:
- lang: eng
text: We show that the fluctuations of the largest eigenvalue of a real symmetric
or complex Hermitian Wigner matrix of size N converge to the Tracy–Widom laws
at a rate O(N^{-1/3+\omega }), as N tends to infinity. For Wigner matrices this
improves the previous rate O(N^{-2/9+\omega }) obtained by Bourgade (J Eur Math
Soc, 2021) for generalized Wigner matrices. Our result follows from a Green function
comparison theorem, originally introduced by Erdős et al. (Adv Math 229(3):1435–1515,
2012) to prove edge universality, on a finer spectral parameter scale with improved
error estimates. The proof relies on the continuous Green function flow induced
by a matrix-valued Ornstein–Uhlenbeck process. Precise estimates on leading contributions
from the third and fourth order moments of the matrix entries are obtained using
iterative cumulant expansions and recursive comparisons for correlation functions,
along with uniform convergence estimates for correlation kernels of the Gaussian
invariant ensembles.
acknowledgement: Kevin Schnelli is supported in parts by the Swedish Research Council
Grant VR-2017-05195, and the Knut and Alice Wallenberg Foundation. Yuanyuan Xu is
supported by the Swedish Research Council Grant VR-2017-05195 and the ERC Advanced
Grant “RMTBeyond” No. 101020331.
article_processing_charge: No
article_type: original
arxiv: 1
author:
- first_name: Kevin
full_name: Schnelli, Kevin
id: 434AD0AE-F248-11E8-B48F-1D18A9856A87
last_name: Schnelli
orcid: 0000-0003-0954-3231
- first_name: Yuanyuan
full_name: Xu, Yuanyuan
id: 7902bdb1-a2a4-11eb-a164-c9216f71aea3
last_name: Xu
citation:
ama: Schnelli K, Xu Y. Convergence rate to the Tracy–Widom laws for the largest
Eigenvalue of Wigner matrices. Communications in Mathematical Physics.
2022;393:839-907. doi:10.1007/s00220-022-04377-y
apa: Schnelli, K., & Xu, Y. (2022). Convergence rate to the Tracy–Widom laws
for the largest Eigenvalue of Wigner matrices. Communications in Mathematical
Physics. Springer Nature. https://doi.org/10.1007/s00220-022-04377-y
chicago: Schnelli, Kevin, and Yuanyuan Xu. “Convergence Rate to the Tracy–Widom
Laws for the Largest Eigenvalue of Wigner Matrices.” Communications in Mathematical
Physics. Springer Nature, 2022. https://doi.org/10.1007/s00220-022-04377-y.
ieee: K. Schnelli and Y. Xu, “Convergence rate to the Tracy–Widom laws for the largest
Eigenvalue of Wigner matrices,” Communications in Mathematical Physics,
vol. 393. Springer Nature, pp. 839–907, 2022.
ista: Schnelli K, Xu Y. 2022. Convergence rate to the Tracy–Widom laws for the largest
Eigenvalue of Wigner matrices. Communications in Mathematical Physics. 393, 839–907.
mla: Schnelli, Kevin, and Yuanyuan Xu. “Convergence Rate to the Tracy–Widom Laws
for the Largest Eigenvalue of Wigner Matrices.” Communications in Mathematical
Physics, vol. 393, Springer Nature, 2022, pp. 839–907, doi:10.1007/s00220-022-04377-y.
short: K. Schnelli, Y. Xu, Communications in Mathematical Physics 393 (2022) 839–907.
date_created: 2022-04-24T22:01:44Z
date_published: 2022-07-01T00:00:00Z
date_updated: 2023-08-03T06:34:24Z
day: '01'
ddc:
- '510'
department:
- _id: LaEr
doi: 10.1007/s00220-022-04377-y
ec_funded: 1
external_id:
arxiv:
- '2102.04330'
isi:
- '000782737200001'
file:
- access_level: open_access
checksum: bee0278c5efa9a33d9a2dc8d354a6c51
content_type: application/pdf
creator: dernst
date_created: 2022-08-05T06:01:13Z
date_updated: 2022-08-05T06:01:13Z
file_id: '11726'
file_name: 2022_CommunMathPhys_Schnelli.pdf
file_size: 1141462
relation: main_file
success: 1
file_date_updated: 2022-08-05T06:01:13Z
has_accepted_license: '1'
intvolume: ' 393'
isi: 1
language:
- iso: eng
month: '07'
oa: 1
oa_version: Published Version
page: 839-907
project:
- _id: 62796744-2b32-11ec-9570-940b20777f1d
call_identifier: H2020
grant_number: '101020331'
name: Random matrices beyond Wigner-Dyson-Mehta
publication: Communications in Mathematical Physics
publication_identifier:
eissn:
- 1432-0916
issn:
- 0010-3616
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
scopus_import: '1'
status: public
title: Convergence rate to the Tracy–Widom laws for the largest Eigenvalue of Wigner
matrices
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: 393
year: '2022'
...