---
_id: '9327'
abstract:
- lang: eng
text: "This archive contains the missing sweater mesh animations and displacement
models for the code of \"Mechanics-Aware Deformation of Yarn Pattern Geometry\"\r\n\r\nCode
Repository: https://git.ist.ac.at/gsperl/MADYPG"
author:
- first_name: Georg
full_name: Sperl, Georg
id: 4DD40360-F248-11E8-B48F-1D18A9856A87
last_name: Sperl
- first_name: Rahul
full_name: Narain, Rahul
last_name: Narain
- first_name: Christopher J
full_name: Wojtan, Christopher J
id: 3C61F1D2-F248-11E8-B48F-1D18A9856A87
last_name: Wojtan
orcid: 0000-0001-6646-5546
citation:
ama: Sperl G, Narain R, Wojtan C. Mechanics-Aware Deformation of Yarn Pattern Geometry
(Additional Animation/Model Data). 2021. doi:10.15479/AT:ISTA:9327
apa: Sperl, G., Narain, R., & Wojtan, C. (2021). Mechanics-Aware Deformation
of Yarn Pattern Geometry (Additional Animation/Model Data). IST Austria. https://doi.org/10.15479/AT:ISTA:9327
chicago: Sperl, Georg, Rahul Narain, and Chris Wojtan. “Mechanics-Aware Deformation
of Yarn Pattern Geometry (Additional Animation/Model Data).” IST Austria, 2021.
https://doi.org/10.15479/AT:ISTA:9327.
ieee: G. Sperl, R. Narain, and C. Wojtan, “Mechanics-Aware Deformation of Yarn Pattern
Geometry (Additional Animation/Model Data).” IST Austria, 2021.
ista: Sperl G, Narain R, Wojtan C. 2021. Mechanics-Aware Deformation of Yarn Pattern
Geometry (Additional Animation/Model Data), IST Austria, 10.15479/AT:ISTA:9327.
mla: Sperl, Georg, et al. Mechanics-Aware Deformation of Yarn Pattern Geometry
(Additional Animation/Model Data). IST Austria, 2021, doi:10.15479/AT:ISTA:9327.
short: G. Sperl, R. Narain, C. Wojtan, (2021).
date_created: 2021-04-16T14:26:19Z
date_published: 2021-05-01T00:00:00Z
date_updated: 2023-08-10T14:24:36Z
ddc:
- '005'
department:
- _id: GradSch
- _id: ChWo
doi: 10.15479/AT:ISTA:9327
file:
- access_level: open_access
checksum: 0324cb519273371708743f3282e7c081
content_type: application/zip
creator: gsperl
date_created: 2021-04-16T14:15:12Z
date_updated: 2021-04-16T14:15:12Z
file_id: '9328'
file_name: MADYPG_extra_data.zip
file_size: 802586232
relation: main_file
success: 1
- access_level: open_access
checksum: 4c224551adf852b136ec21a4e13f0c1b
content_type: application/gzip
creator: pub-gitlab-bot
date_created: 2021-04-26T09:33:44Z
date_updated: 2021-04-26T09:33:44Z
file_id: '9353'
file_name: MADYPG.zip
file_size: 64962865
relation: main_file
file_date_updated: 2021-04-26T09:33:44Z
gitlab_commit_id: 6a77e7e22769230ae5f5edaa090fb4b828e57573
gitlab_url: https://git.ist.ac.at/gsperl/MADYPG
has_accepted_license: '1'
license: https://opensource.org/licenses/MIT
month: '05'
oa: 1
publisher: IST Austria
related_material:
record:
- id: '9818'
relation: used_for_analysis_in
status: public
status: public
title: Mechanics-Aware Deformation of Yarn Pattern Geometry (Additional Animation/Model
Data)
tmp:
legal_code_url: https://opensource.org/licenses/MIT
name: The MIT License
short: MIT
type: software
user_id: 8b945eb4-e2f2-11eb-945a-df72226e66a9
year: '2021'
...
---
_id: '9770'
abstract:
- lang: eng
text: We study an effective one-dimensional quantum model that includes friction
and spin-orbit coupling (SOC), and show that the model exhibits spin polarization
when both terms are finite. Most important, strong spin polarization can be observed
even for moderate SOC, provided that the friction is strong. Our findings might
help to explain the pronounced effect of chirality on spin distribution and transport
in chiral molecules. In particular, our model implies static magnetic properties
of a chiral molecule, which lead to Shiba-like states when a molecule is placed
on a superconductor, in accordance with recent experimental data.
acknowledgement: "We thank Rafael Barfknecht for useful discussions. This work has
received funding from the European Union’s Horizon 2020 research and innovation
programme under the Marie Skłodowska-Curie Grant Agreement No. 754411 (A.G.\r\nand
A.G.V.). M.L. acknowledges support by the European Research Council (ERC) Starting
Grant No. 801770 (ANGULON). Y.P. and O.M. acknowledge funding from the Nidersachsen
Ministry of Science and Culture, and from the\r\nAcademia Sinica Research Program.
O.M. is thankful for support through the Harry de Jur Chair in Applied Science."
article_number: '024430'
article_processing_charge: No
article_type: original
author:
- first_name: Artem
full_name: Volosniev, Artem
id: 37D278BC-F248-11E8-B48F-1D18A9856A87
last_name: Volosniev
orcid: 0000-0003-0393-5525
- first_name: Hen
full_name: Alpern, Hen
last_name: Alpern
- first_name: Yossi
full_name: Paltiel, Yossi
last_name: Paltiel
- first_name: Oded
full_name: Millo, Oded
last_name: Millo
- first_name: Mikhail
full_name: Lemeshko, Mikhail
id: 37CB05FA-F248-11E8-B48F-1D18A9856A87
last_name: Lemeshko
orcid: 0000-0002-6990-7802
- first_name: Areg
full_name: Ghazaryan, Areg
id: 4AF46FD6-F248-11E8-B48F-1D18A9856A87
last_name: Ghazaryan
orcid: 0000-0001-9666-3543
citation:
ama: Volosniev A, Alpern H, Paltiel Y, Millo O, Lemeshko M, Ghazaryan A. Interplay
between friction and spin-orbit coupling as a source of spin polarization. Physical
Review B. 2021;104(2). doi:10.1103/physrevb.104.024430
apa: Volosniev, A., Alpern, H., Paltiel, Y., Millo, O., Lemeshko, M., & Ghazaryan,
A. (2021). Interplay between friction and spin-orbit coupling as a source of spin
polarization. Physical Review B. American Physical Society. https://doi.org/10.1103/physrevb.104.024430
chicago: Volosniev, Artem, Hen Alpern, Yossi Paltiel, Oded Millo, Mikhail Lemeshko,
and Areg Ghazaryan. “Interplay between Friction and Spin-Orbit Coupling as a Source
of Spin Polarization.” Physical Review B. American Physical Society, 2021.
https://doi.org/10.1103/physrevb.104.024430.
ieee: A. Volosniev, H. Alpern, Y. Paltiel, O. Millo, M. Lemeshko, and A. Ghazaryan,
“Interplay between friction and spin-orbit coupling as a source of spin polarization,”
Physical Review B, vol. 104, no. 2. American Physical Society, 2021.
ista: Volosniev A, Alpern H, Paltiel Y, Millo O, Lemeshko M, Ghazaryan A. 2021.
Interplay between friction and spin-orbit coupling as a source of spin polarization.
Physical Review B. 104(2), 024430.
mla: Volosniev, Artem, et al. “Interplay between Friction and Spin-Orbit Coupling
as a Source of Spin Polarization.” Physical Review B, vol. 104, no. 2,
024430, American Physical Society, 2021, doi:10.1103/physrevb.104.024430.
short: A. Volosniev, H. Alpern, Y. Paltiel, O. Millo, M. Lemeshko, A. Ghazaryan,
Physical Review B 104 (2021).
date_created: 2021-08-04T15:05:32Z
date_published: 2021-07-01T00:00:00Z
date_updated: 2023-08-10T14:27:07Z
day: '01'
department:
- _id: MiLe
doi: 10.1103/physrevb.104.024430
ec_funded: 1
external_id:
arxiv:
- '2101.05173'
isi:
- '000678780800003'
intvolume: ' 104'
isi: 1
issue: '2'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/2101.05173
month: '07'
oa: 1
oa_version: Preprint
project:
- _id: 260C2330-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '754411'
name: ISTplus - Postdoctoral Fellowships
- _id: 2688CF98-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '801770'
name: 'Angulon: physics and applications of a new quasiparticle'
publication: Physical Review B
publication_identifier:
eissn:
- 2469-9969
issn:
- 2469-9950
publication_status: published
publisher: American Physical Society
quality_controlled: '1'
scopus_import: '1'
status: public
title: Interplay between friction and spin-orbit coupling as a source of spin polarization
type: journal_article
user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
volume: 104
year: '2021'
...
---
_id: '9827'
abstract:
- lang: eng
text: 'The Nearest neighbour search (NNS) is a fundamental problem in many application
domains dealing with multidimensional data. In a concurrent setting, where dynamic
modifications are allowed, a linearizable implementation of the NNS is highly
desirable.This paper introduces the LockFree-kD-tree (LFkD-tree ): a lock-free
concurrent kD-tree, which implements an abstract data type (ADT) that provides
the operations Add, Remove, Contains, and NNS. Our implementation is linearizable.
The operations in the LFkD-tree use single-word read and compare-and-swap (Image
1 ) atomic primitives, which are readily supported on available multi-core processors.
We experimentally evaluate the LFkD-tree using several benchmarks comprising real-world
and synthetic datasets. The experiments show that the presented design is scalable
and achieves significant speed-up compared to the implementations of an existing
sequential kD-tree and a recently proposed multidimensional indexing structure,
PH-tree.'
article_processing_charge: No
article_type: original
author:
- first_name: Bapi
full_name: Chatterjee, Bapi
id: 3C41A08A-F248-11E8-B48F-1D18A9856A87
last_name: Chatterjee
orcid: 0000-0002-2742-4028
- first_name: Ivan
full_name: Walulya, Ivan
last_name: Walulya
- first_name: Philippas
full_name: Tsigas, Philippas
last_name: Tsigas
citation:
ama: Chatterjee B, Walulya I, Tsigas P. Concurrent linearizable nearest neighbour
search in LockFree-kD-tree. Theoretical Computer Science. 2021;886:27-48.
doi:10.1016/j.tcs.2021.06.041
apa: Chatterjee, B., Walulya, I., & Tsigas, P. (2021). Concurrent linearizable
nearest neighbour search in LockFree-kD-tree. Theoretical Computer Science.
Elsevier. https://doi.org/10.1016/j.tcs.2021.06.041
chicago: Chatterjee, Bapi, Ivan Walulya, and Philippas Tsigas. “Concurrent Linearizable
Nearest Neighbour Search in LockFree-KD-Tree.” Theoretical Computer Science.
Elsevier, 2021. https://doi.org/10.1016/j.tcs.2021.06.041.
ieee: B. Chatterjee, I. Walulya, and P. Tsigas, “Concurrent linearizable nearest
neighbour search in LockFree-kD-tree,” Theoretical Computer Science, vol.
886. Elsevier, pp. 27–48, 2021.
ista: Chatterjee B, Walulya I, Tsigas P. 2021. Concurrent linearizable nearest neighbour
search in LockFree-kD-tree. Theoretical Computer Science. 886, 27–48.
mla: Chatterjee, Bapi, et al. “Concurrent Linearizable Nearest Neighbour Search
in LockFree-KD-Tree.” Theoretical Computer Science, vol. 886, Elsevier,
2021, pp. 27–48, doi:10.1016/j.tcs.2021.06.041.
short: B. Chatterjee, I. Walulya, P. Tsigas, Theoretical Computer Science 886 (2021)
27–48.
date_created: 2021-08-08T22:01:31Z
date_published: 2021-09-13T00:00:00Z
date_updated: 2023-08-10T14:27:43Z
day: '13'
department:
- _id: DaAl
doi: 10.1016/j.tcs.2021.06.041
external_id:
isi:
- '000694718900004'
intvolume: ' 886'
isi: 1
keyword:
- Concurrent data structure
- kD-tree
- Nearest neighbor search
- Similarity search
- Lock-free
- Linearizability
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://publications.lib.chalmers.se/records/fulltext/232185/232185.pdf
month: '09'
oa: 1
oa_version: Submitted Version
page: 27-48
publication: Theoretical Computer Science
publication_identifier:
issn:
- 0304-3975
publication_status: published
publisher: Elsevier
quality_controlled: '1'
scopus_import: '1'
status: public
title: Concurrent linearizable nearest neighbour search in LockFree-kD-tree
type: journal_article
user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
volume: 886
year: '2021'
...
---
_id: '9877'
abstract:
- lang: eng
text: 'Parent-of-origin–dependent gene expression in mammals and flowering plants
results from differing chromatin imprints (genomic imprinting) between maternally
and paternally inherited alleles. Imprinted gene expression in the endosperm of
seeds is associated with localized hypomethylation of maternally but not paternally
inherited DNA, with certain small RNAs also displaying parent-of-origin–specific
expression. To understand the evolution of imprinting mechanisms in Oryza sativa
(rice), we analyzed imprinting divergence among four cultivars that span both
japonica and indica subspecies: Nipponbare, Kitaake, 93-11, and IR64. Most imprinted
genes are imprinted across cultivars and enriched for functions in chromatin and
transcriptional regulation, development, and signaling. However, 4 to 11% of imprinted
genes display divergent imprinting. Analyses of DNA methylation and small RNAs
revealed that endosperm-specific 24-nt small RNA–producing loci show weak RNA-directed
DNA methylation, frequently overlap genes, and are imprinted four times more often
than genes. However, imprinting divergence most often correlated with local DNA
methylation epimutations (9 of 17 assessable loci), which were largely stable
within subspecies. Small insertion/deletion events and transposable element insertions
accompanied 4 of the 9 locally epimutated loci and associated with imprinting
divergence at another 4 of the remaining 8 loci. Correlating epigenetic and genetic
variation occurred at key regulatory regions—the promoter and transcription start
site of maternally biased genes, and the promoter and gene body of paternally
biased genes. Our results reinforce models for the role of maternal-specific DNA
hypomethylation in imprinting of both maternally and paternally biased genes,
and highlight the role of transposition and epimutation in rice imprinting evolution.'
acknowledgement: We thank W. Schackwitz, M. Joel, and the Joint Genome Institute sequencing
team for generating the IR64 genome sequence and initial analysis; L. Bartley and
E. Marvinney for genomic DNA preparation for IR64 resequencing; and the University
of California (UC), Berkeley Sanger sequencing team for technical advice and service.
This work was partially funded by NSF Grant IOS-1025890 (to R.L.F. and D.Z.), NIH
Grant GM69415 (to R.L.F. and D.Z.), NIH Grant GM122968 (to P.C.R.), a Young Investigator
Grant from the Arnold and Mabel Beckman Foundation (to D.Z.), an International Fulbright
Science and Technology Award (to J.A.R.), and a Taiwan Ministry of Education Studying
Abroad Scholarship (to P.-H.H.). This work used the Vincent J. Coates Genomics Sequencing
Laboratory at UC Berkeley, supported by NIH Instrumentation Grant S10 OD018174.
article_number: e2104445118
article_processing_charge: Yes (in subscription journal)
article_type: original
author:
- first_name: Jessica A.
full_name: Rodrigues, Jessica A.
last_name: Rodrigues
- first_name: Ping-Hung
full_name: Hsieh, Ping-Hung
last_name: Hsieh
- first_name: Deling
full_name: Ruan, Deling
last_name: Ruan
- first_name: Toshiro
full_name: Nishimura, Toshiro
last_name: Nishimura
- first_name: Manoj K.
full_name: Sharma, Manoj K.
last_name: Sharma
- first_name: Rita
full_name: Sharma, Rita
last_name: Sharma
- first_name: XinYi
full_name: Ye, XinYi
last_name: Ye
- first_name: Nicholas D.
full_name: Nguyen, Nicholas D.
last_name: Nguyen
- first_name: Sukhranjan
full_name: Nijjar, Sukhranjan
last_name: Nijjar
- first_name: Pamela C.
full_name: Ronald, Pamela C.
last_name: Ronald
- first_name: Robert L.
full_name: Fischer, Robert L.
last_name: Fischer
- first_name: Daniel
full_name: Zilberman, Daniel
id: 6973db13-dd5f-11ea-814e-b3e5455e9ed1
last_name: Zilberman
orcid: 0000-0002-0123-8649
citation:
ama: Rodrigues JA, Hsieh P-H, Ruan D, et al. Divergence among rice cultivars reveals
roles for transposition and epimutation in ongoing evolution of genomic imprinting.
Proceedings of the National Academy of Sciences. 2021;118(29). doi:10.1073/pnas.2104445118
apa: Rodrigues, J. A., Hsieh, P.-H., Ruan, D., Nishimura, T., Sharma, M. K., Sharma,
R., … Zilberman, D. (2021). Divergence among rice cultivars reveals roles for
transposition and epimutation in ongoing evolution of genomic imprinting. Proceedings
of the National Academy of Sciences. National Academy of Sciences. https://doi.org/10.1073/pnas.2104445118
chicago: Rodrigues, Jessica A., Ping-Hung Hsieh, Deling Ruan, Toshiro Nishimura,
Manoj K. Sharma, Rita Sharma, XinYi Ye, et al. “Divergence among Rice Cultivars
Reveals Roles for Transposition and Epimutation in Ongoing Evolution of Genomic
Imprinting.” Proceedings of the National Academy of Sciences. National
Academy of Sciences, 2021. https://doi.org/10.1073/pnas.2104445118.
ieee: J. A. Rodrigues et al., “Divergence among rice cultivars reveals roles
for transposition and epimutation in ongoing evolution of genomic imprinting,”
Proceedings of the National Academy of Sciences, vol. 118, no. 29. National
Academy of Sciences, 2021.
ista: Rodrigues JA, Hsieh P-H, Ruan D, Nishimura T, Sharma MK, Sharma R, Ye X, Nguyen
ND, Nijjar S, Ronald PC, Fischer RL, Zilberman D. 2021. Divergence among rice
cultivars reveals roles for transposition and epimutation in ongoing evolution
of genomic imprinting. Proceedings of the National Academy of Sciences. 118(29),
e2104445118.
mla: Rodrigues, Jessica A., et al. “Divergence among Rice Cultivars Reveals Roles
for Transposition and Epimutation in Ongoing Evolution of Genomic Imprinting.”
Proceedings of the National Academy of Sciences, vol. 118, no. 29, e2104445118,
National Academy of Sciences, 2021, doi:10.1073/pnas.2104445118.
short: J.A. Rodrigues, P.-H. Hsieh, D. Ruan, T. Nishimura, M.K. Sharma, R. Sharma,
X. Ye, N.D. Nguyen, S. Nijjar, P.C. Ronald, R.L. Fischer, D. Zilberman, Proceedings
of the National Academy of Sciences 118 (2021).
date_created: 2021-08-10T19:30:41Z
date_published: 2021-07-16T00:00:00Z
date_updated: 2023-08-11T10:28:10Z
day: '16'
ddc:
- '580'
- '570'
department:
- _id: DaZi
doi: 10.1073/pnas.2104445118
external_id:
isi:
- '000685037700012'
pmid:
- '34272287'
file:
- access_level: open_access
checksum: 19e84ad8c03c60222744ee8e16cd6998
content_type: application/pdf
creator: asandaue
date_created: 2021-08-11T09:31:41Z
date_updated: 2021-08-11T09:31:41Z
file_id: '9879'
file_name: 2021_ProceedingsOfTheNationalAcademyOfSciences_Rodrigues.pdf
file_size: 1898360
relation: main_file
success: 1
file_date_updated: 2021-08-11T09:31:41Z
has_accepted_license: '1'
intvolume: ' 118'
isi: 1
issue: '29'
language:
- iso: eng
month: '07'
oa: 1
oa_version: Published Version
pmid: 1
publication: Proceedings of the National Academy of Sciences
publication_identifier:
eissn:
- 1091-6490
issn:
- 0027-8424
publication_status: published
publisher: National Academy of Sciences
quality_controlled: '1'
scopus_import: '1'
status: public
title: Divergence among rice cultivars reveals roles for transposition and epimutation
in ongoing evolution of genomic imprinting
tmp:
image: /images/cc_by_nc_nd.png
legal_code_url: https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode
name: Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International
(CC BY-NC-ND 4.0)
short: CC BY-NC-ND (4.0)
type: journal_article
user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
volume: 118
year: '2021'
...
---
_id: '9874'
abstract:
- lang: eng
text: Myocardial regeneration is restricted to early postnatal life, when mammalian
cardiomyocytes still retain the ability to proliferate. The molecular cues that
induce cell cycle arrest of neonatal cardiomyocytes towards terminally differentiated
adult heart muscle cells remain obscure. Here we report that the miR-106b~25 cluster
is higher expressed in the early postnatal myocardium and decreases in expression
towards adulthood, especially under conditions of overload, and orchestrates the
transition of cardiomyocyte hyperplasia towards cell cycle arrest and hypertrophy
by virtue of its targetome. In line, gene delivery of miR-106b~25 to the mouse
heart provokes cardiomyocyte proliferation by targeting a network of negative
cell cycle regulators including E2f5, Cdkn1c, Ccne1 and Wee1. Conversely, gene-targeted
miR-106b~25 null mice display spontaneous hypertrophic remodeling and exaggerated
remodeling to overload by derepression of the prohypertrophic transcription factors
Hand2 and Mef2d. Taking advantage of the regulatory function of miR-106b~25 on
cardiomyocyte hyperplasia and hypertrophy, viral gene delivery of miR-106b~25
provokes nearly complete regeneration of the adult myocardium after ischemic injury.
Our data demonstrate that exploitation of conserved molecular programs can enhance
the regenerative capacity of the injured heart.
acknowledgement: E.D. is supported by a VENI award 916-150-16 from the Netherlands
Organization for Health Research and Development (ZonMW), an EMBO Long-term Fellowship
(EMBO ALTF 848-2013) and a FP7 Marie Curie Intra-European Fellowship (Project number
627539). V.S.P. was funded by a fellowship from the FCT/ Ministério da Ciência,
Tecnologia e Inovação SFRH/BD/111799/2015. P.D.C.M. is an Established Investigator
of the Dutch Heart Foundation. L.D.W. acknowledges support from the Dutch CardioVascular
Alliance (ARENA-PRIME). L.D.W. was further supported by grant 311549 from the European
Research Council (ERC), a VICI award 918-156-47 from the Dutch Research Council
and Marie Sklodowska-Curie grant agreement no. 813716 (TRAIN-HEART).
article_number: '4808'
article_processing_charge: Yes
article_type: original
author:
- first_name: Andrea
full_name: Raso, Andrea
last_name: Raso
- first_name: Ellen
full_name: Dirkx, Ellen
last_name: Dirkx
- first_name: Vasco
full_name: Sampaio-Pinto, Vasco
last_name: Sampaio-Pinto
- first_name: Hamid
full_name: el Azzouzi, Hamid
last_name: el Azzouzi
- first_name: Ryan J
full_name: Cubero, Ryan J
id: 850B2E12-9CD4-11E9-837F-E719E6697425
last_name: Cubero
orcid: 0000-0003-0002-1867
- first_name: Daniel W.
full_name: Sorensen, Daniel W.
last_name: Sorensen
- first_name: Lara
full_name: Ottaviani, Lara
last_name: Ottaviani
- first_name: Servé
full_name: Olieslagers, Servé
last_name: Olieslagers
- first_name: Manon M.
full_name: Huibers, Manon M.
last_name: Huibers
- first_name: Roel
full_name: de Weger, Roel
last_name: de Weger
- first_name: Sailay
full_name: Siddiqi, Sailay
last_name: Siddiqi
- first_name: Silvia
full_name: Moimas, Silvia
last_name: Moimas
- first_name: Consuelo
full_name: Torrini, Consuelo
last_name: Torrini
- first_name: Lorena
full_name: Zentillin, Lorena
last_name: Zentillin
- first_name: Luca
full_name: Braga, Luca
last_name: Braga
- first_name: Diana S.
full_name: Nascimento, Diana S.
last_name: Nascimento
- first_name: Paula A.
full_name: da Costa Martins, Paula A.
last_name: da Costa Martins
- first_name: Jop H.
full_name: van Berlo, Jop H.
last_name: van Berlo
- first_name: Serena
full_name: Zacchigna, Serena
last_name: Zacchigna
- first_name: Mauro
full_name: Giacca, Mauro
last_name: Giacca
- first_name: Leon J.
full_name: De Windt, Leon J.
last_name: De Windt
citation:
ama: Raso A, Dirkx E, Sampaio-Pinto V, et al. A microRNA program regulates the balance
between cardiomyocyte hyperplasia and hypertrophy and stimulates cardiac regeneration.
Nature Communications. 2021;12. doi:10.1038/s41467-021-25211-4
apa: Raso, A., Dirkx, E., Sampaio-Pinto, V., el Azzouzi, H., Cubero, R. J., Sorensen,
D. W., … De Windt, L. J. (2021). A microRNA program regulates the balance between
cardiomyocyte hyperplasia and hypertrophy and stimulates cardiac regeneration.
Nature Communications. Springer Nature. https://doi.org/10.1038/s41467-021-25211-4
chicago: Raso, Andrea, Ellen Dirkx, Vasco Sampaio-Pinto, Hamid el Azzouzi, Ryan
J Cubero, Daniel W. Sorensen, Lara Ottaviani, et al. “A MicroRNA Program Regulates
the Balance between Cardiomyocyte Hyperplasia and Hypertrophy and Stimulates Cardiac
Regeneration.” Nature Communications. Springer Nature, 2021. https://doi.org/10.1038/s41467-021-25211-4.
ieee: A. Raso et al., “A microRNA program regulates the balance between cardiomyocyte
hyperplasia and hypertrophy and stimulates cardiac regeneration,” Nature Communications,
vol. 12. Springer Nature, 2021.
ista: Raso A, Dirkx E, Sampaio-Pinto V, el Azzouzi H, Cubero RJ, Sorensen DW, Ottaviani
L, Olieslagers S, Huibers MM, de Weger R, Siddiqi S, Moimas S, Torrini C, Zentillin
L, Braga L, Nascimento DS, da Costa Martins PA, van Berlo JH, Zacchigna S, Giacca
M, De Windt LJ. 2021. A microRNA program regulates the balance between cardiomyocyte
hyperplasia and hypertrophy and stimulates cardiac regeneration. Nature Communications.
12, 4808.
mla: Raso, Andrea, et al. “A MicroRNA Program Regulates the Balance between Cardiomyocyte
Hyperplasia and Hypertrophy and Stimulates Cardiac Regeneration.” Nature Communications,
vol. 12, 4808, Springer Nature, 2021, doi:10.1038/s41467-021-25211-4.
short: A. Raso, E. Dirkx, V. Sampaio-Pinto, H. el Azzouzi, R.J. Cubero, D.W. Sorensen,
L. Ottaviani, S. Olieslagers, M.M. Huibers, R. de Weger, S. Siddiqi, S. Moimas,
C. Torrini, L. Zentillin, L. Braga, D.S. Nascimento, P.A. da Costa Martins, J.H.
van Berlo, S. Zacchigna, M. Giacca, L.J. De Windt, Nature Communications 12 (2021).
date_created: 2021-08-10T11:49:20Z
date_published: 2021-08-10T00:00:00Z
date_updated: 2023-08-11T10:27:03Z
day: '10'
ddc:
- '610'
- '570'
department:
- _id: SaSi
doi: 10.1038/s41467-021-25211-4
external_id:
isi:
- '000683910200042'
pmid:
- '34376683'
file:
- access_level: open_access
checksum: 48d8562e8229e4282f3f354b329722c5
content_type: application/pdf
creator: asandaue
date_created: 2021-08-10T12:29:59Z
date_updated: 2021-08-10T12:29:59Z
file_id: '9876'
file_name: 2021_NatureCommunications_Raso.pdf
file_size: 4364333
relation: main_file
success: 1
file_date_updated: 2021-08-10T12:29:59Z
genbank:
- GSE178867
has_accepted_license: '1'
intvolume: ' 12'
isi: 1
language:
- iso: eng
month: '08'
oa: 1
oa_version: Published Version
pmid: 1
publication: Nature Communications
publication_identifier:
eissn:
- 2041-1723
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
related_material:
link:
- relation: erratum
url: https://doi.org/10.1038/s41467-022-32785-0
scopus_import: '1'
status: public
title: A microRNA program regulates the balance between cardiomyocyte hyperplasia
and hypertrophy and stimulates cardiac regeneration
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: 12
year: '2021'
...
---
_id: '9769'
abstract:
- lang: eng
text: A few years ago, flow equations were introduced as a technique for calculating
the ground-state energies of cold Bose gases with and without impurities. In this
paper, we extend this approach to compute observables other than the energy. As
an example, we calculate the densities, and phase fluctuations of one-dimensional
Bose gases with one and two impurities. For a single mobile impurity, we use flow
equations to validate the mean-field results obtained upon the Lee-Low-Pines transformation.
We show that the mean-field approximation is accurate for all values of the boson-impurity
interaction strength as long as the phase coherence length is much larger than
the healing length of the condensate. For two static impurities, we calculate
impurity-impurity interactions induced by the Bose gas. We find that leading order
perturbation theory fails when boson-impurity interactions are stronger than boson-boson
interactions. The mean-field approximation reproduces the flow equation results
for all values of the boson-impurity interaction strength as long as boson-boson
interactions are weak.
acknowledgement: We thank Matthias Heinz and Volker Karle for helpful comments on
the manuscript; Zoran Ristivojevic for useful correspondence regarding mean-field
calculations of induced impurity-impurity interactions; Fabian Grusdt for sharing
with us the data for the densities presented in Ref. [14]. This work has received
funding from the DFG Project No. 413495248 [VO 2437/1-1] (F. B., H.-W. H., A. G.
V.) and European Union’s Horizon 2020 research and innovation programme under the
Marie Skłodowska-Curie Grant Agreement No. 754411 (A. G. V.). M. L. acknowledges
support by the European Research Council (ERC) Starting Grant No. 801770 (ANGULON).
H.-W.H. thanks the ECT* for hospitality during the workshop “Universal physics in
Many-Body Quantum Systems – From Atoms to Quarks". This infrastructure is part of
a project that has received funding from the European Union’s Horizon 2020 research
and innovation programme under grant agreement No 824093. H.-W.H. was supported
by the Deutsche Forschungsgemeinschaft (DFG, German Research Foundation) - Project-ID
279384907 - SFB 1245.
article_number: '008'
article_processing_charge: Yes
article_type: original
author:
- first_name: Fabian
full_name: Brauneis, Fabian
last_name: Brauneis
- first_name: Hans-Werner
full_name: Hammer, Hans-Werner
last_name: Hammer
- first_name: Mikhail
full_name: Lemeshko, Mikhail
id: 37CB05FA-F248-11E8-B48F-1D18A9856A87
last_name: Lemeshko
orcid: 0000-0002-6990-7802
- first_name: Artem
full_name: Volosniev, Artem
id: 37D278BC-F248-11E8-B48F-1D18A9856A87
last_name: Volosniev
orcid: 0000-0003-0393-5525
citation:
ama: 'Brauneis F, Hammer H-W, Lemeshko M, Volosniev A. Impurities in a one-dimensional
Bose gas: The flow equation approach. SciPost Physics. 2021;11(1). doi:10.21468/scipostphys.11.1.008'
apa: 'Brauneis, F., Hammer, H.-W., Lemeshko, M., & Volosniev, A. (2021). Impurities
in a one-dimensional Bose gas: The flow equation approach. SciPost Physics.
SciPost. https://doi.org/10.21468/scipostphys.11.1.008'
chicago: 'Brauneis, Fabian, Hans-Werner Hammer, Mikhail Lemeshko, and Artem Volosniev.
“Impurities in a One-Dimensional Bose Gas: The Flow Equation Approach.” SciPost
Physics. SciPost, 2021. https://doi.org/10.21468/scipostphys.11.1.008.'
ieee: 'F. Brauneis, H.-W. Hammer, M. Lemeshko, and A. Volosniev, “Impurities in
a one-dimensional Bose gas: The flow equation approach,” SciPost Physics,
vol. 11, no. 1. SciPost, 2021.'
ista: 'Brauneis F, Hammer H-W, Lemeshko M, Volosniev A. 2021. Impurities in a one-dimensional
Bose gas: The flow equation approach. SciPost Physics. 11(1), 008.'
mla: 'Brauneis, Fabian, et al. “Impurities in a One-Dimensional Bose Gas: The Flow
Equation Approach.” SciPost Physics, vol. 11, no. 1, 008, SciPost, 2021,
doi:10.21468/scipostphys.11.1.008.'
short: F. Brauneis, H.-W. Hammer, M. Lemeshko, A. Volosniev, SciPost Physics 11
(2021).
date_created: 2021-08-04T15:00:55Z
date_published: 2021-07-13T00:00:00Z
date_updated: 2023-08-11T10:25:44Z
day: '13'
ddc:
- '530'
department:
- _id: MiLe
doi: 10.21468/scipostphys.11.1.008
ec_funded: 1
external_id:
arxiv:
- '2101.10958'
isi:
- '000680039500013'
file:
- access_level: open_access
checksum: eaa847346b1a023d97bbb291779610ed
content_type: application/pdf
creator: asandaue
date_created: 2021-08-10T11:44:59Z
date_updated: 2021-08-10T11:44:59Z
file_id: '9875'
file_name: 2021_SciPostPhysics_Brauneis.pdf
file_size: 1085300
relation: main_file
success: 1
file_date_updated: 2021-08-10T11:44:59Z
has_accepted_license: '1'
intvolume: ' 11'
isi: 1
issue: '1'
language:
- iso: eng
month: '07'
oa: 1
oa_version: Published Version
project:
- _id: 260C2330-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '754411'
name: ISTplus - Postdoctoral Fellowships
- _id: 2688CF98-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '801770'
name: 'Angulon: physics and applications of a new quasiparticle'
publication: SciPost Physics
publication_identifier:
eissn:
- 2542-4653
publication_status: published
publisher: SciPost
quality_controlled: '1'
scopus_import: '1'
status: public
title: 'Impurities in a one-dimensional Bose gas: The flow equation approach'
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: journal_article
user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
volume: 11
year: '2021'
...
---
_id: '9746'
abstract:
- lang: eng
text: Evolutionary adaptation is a major source of antibiotic resistance in bacterial
pathogens. Evolution-informed therapy aims to constrain resistance by accounting
for bacterial evolvability. Sequential treatments with antibiotics that target
different bacterial processes were previously shown to limit adaptation through
genetic resistance trade-offs and negative hysteresis. Treatment with homogeneous
sets of antibiotics is generally viewed to be disadvantageous, as it should rapidly
lead to cross-resistance. We here challenged this assumption by determining the
evolutionary response of Pseudomonas aeruginosa to experimental sequential treatments
involving both heterogenous and homogeneous antibiotic sets. To our surprise,
we found that fast switching between only β-lactam antibiotics resulted in increased
extinction of bacterial populations. We demonstrate that extinction is favored
by low rates of spontaneous resistance emergence and low levels of spontaneous
cross-resistance among the antibiotics in sequence. The uncovered principles may
help to guide the optimized use of available antibiotics in highly potent, evolution-informed
treatment designs.
acknowledgement: We would like to thank Leif Tueffers and João Botelho for discussions
and suggestions as well as Kira Haas and Julia Bunk for technical support. We acknowledge
financial support from the German Science Foundation (grant SCHU 1415/12-2 to HS,
and funding under Germany’s Excellence Strategy EXC 2167–390884018 as well as the
Research Training Group 2501 TransEvo to HS and SN), the Max Planck Society (IMPRS
scholarship to AB; Max-Planck fellowship to HS), and the Leibniz Science Campus
Evolutionary Medicine of the Lung (EvoLUNG, to HS and SN). This work was further
supported by the German Science Foundation Research Infrastructure NGS_CC (project
407495230) as part of the Next Generation Sequencing Competence Network (project
423957469). NGS analyses were carried out at the Competence Centre for Genomic Analysis
Kiel (CCGA Kiel).
article_number: e68876
article_processing_charge: No
article_type: original
author:
- first_name: Aditi
full_name: Batra, Aditi
last_name: Batra
- first_name: Roderich
full_name: Römhild, Roderich
id: 68E56E44-62B0-11EA-B963-444F3DDC885E
last_name: Römhild
orcid: 0000-0001-9480-5261
- first_name: Emilie
full_name: Rousseau, Emilie
last_name: Rousseau
- first_name: Sören
full_name: Franzenburg, Sören
last_name: Franzenburg
- first_name: Stefan
full_name: Niemann, Stefan
last_name: Niemann
- first_name: Hinrich
full_name: Schulenburg, Hinrich
last_name: Schulenburg
citation:
ama: Batra A, Römhild R, Rousseau E, Franzenburg S, Niemann S, Schulenburg H. High
potency of sequential therapy with only beta-lactam antibiotics. eLife.
2021;10. doi:10.7554/elife.68876
apa: Batra, A., Römhild, R., Rousseau, E., Franzenburg, S., Niemann, S., & Schulenburg,
H. (2021). High potency of sequential therapy with only beta-lactam antibiotics.
ELife. eLife Sciences Publications. https://doi.org/10.7554/elife.68876
chicago: Batra, Aditi, Roderich Römhild, Emilie Rousseau, Sören Franzenburg, Stefan
Niemann, and Hinrich Schulenburg. “High Potency of Sequential Therapy with Only
Beta-Lactam Antibiotics.” ELife. eLife Sciences Publications, 2021. https://doi.org/10.7554/elife.68876.
ieee: A. Batra, R. Römhild, E. Rousseau, S. Franzenburg, S. Niemann, and H. Schulenburg,
“High potency of sequential therapy with only beta-lactam antibiotics,” eLife,
vol. 10. eLife Sciences Publications, 2021.
ista: Batra A, Römhild R, Rousseau E, Franzenburg S, Niemann S, Schulenburg H. 2021.
High potency of sequential therapy with only beta-lactam antibiotics. eLife. 10,
e68876.
mla: Batra, Aditi, et al. “High Potency of Sequential Therapy with Only Beta-Lactam
Antibiotics.” ELife, vol. 10, e68876, eLife Sciences Publications, 2021,
doi:10.7554/elife.68876.
short: A. Batra, R. Römhild, E. Rousseau, S. Franzenburg, S. Niemann, H. Schulenburg,
ELife 10 (2021).
date_created: 2021-07-28T13:36:57Z
date_published: 2021-07-28T00:00:00Z
date_updated: 2023-08-11T10:26:29Z
day: '28'
department:
- _id: CaGu
doi: 10.7554/elife.68876
external_id:
isi:
- '000692027800001'
pmid:
- '34318749'
intvolume: ' 10'
isi: 1
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.7554/eLife.68876
month: '07'
oa: 1
oa_version: Published Version
pmid: 1
publication: eLife
publication_identifier:
eissn:
- 2050-084X
publication_status: published
publisher: eLife Sciences Publications
quality_controlled: '1'
scopus_import: '1'
status: public
title: High potency of sequential therapy with only beta-lactam antibiotics
type: journal_article
user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
volume: 10
year: '2021'
...
---
_id: '9911'
abstract:
- lang: eng
text: A modern day light microscope has evolved from a tool devoted to making primarily
empirical observations to what is now a sophisticated , quantitative device that
is an integral part of both physical and life science research. Nowadays, microscopes
are found in nearly every experimental laboratory. However, despite their prevalent
use in capturing and quantifying scientific phenomena, neither a thorough understanding
of the principles underlying quantitative imaging techniques nor appropriate knowledge
of how to calibrate, operate and maintain microscopes can be taken for granted.
This is clearly demonstrated by the well-documented and widespread difficulties
that are routinely encountered in evaluating acquired data and reproducing scientific
experiments. Indeed, studies have shown that more than 70% of researchers have
tried and failed to repeat another scientist's experiments, while more than half
have even failed to reproduce their own experiments. One factor behind the reproducibility
crisis of experiments published in scientific journals is the frequent underreporting
of imaging methods caused by a lack of awareness and/or a lack of knowledge of
the applied technique. Whereas quality control procedures for some methods used
in biomedical research, such as genomics (e.g. DNA sequencing, RNA-seq) or cytometry,
have been introduced (e.g. ENCODE), this issue has not been tackled for optical
microscopy instrumentation and images. Although many calibration standards and
protocols have been published, there is a lack of awareness and agreement on common
standards and guidelines for quality assessment and reproducibility. In April
2020, the QUality Assessment and REProducibility for instruments and images in
Light Microscopy (QUAREP-LiMi) initiative was formed. This initiative comprises
imaging scientists from academia and industry who share a common interest in achieving
a better understanding of the performance and limitations of microscopes and improved
quality control (QC) in light microscopy. The ultimate goal of the QUAREP-LiMi
initiative is to establish a set of common QC standards, guidelines, metadata
models and tools, including detailed protocols, with the ultimate aim of improving
reproducible advances in scientific research. This White Paper (1) summarizes
the major obstacles identified in the field that motivated the launch of the QUAREP-LiMi
initiative; (2) identifies the urgent need to address these obstacles in a grassroots
manner, through a community of stakeholders including, researchers, imaging scientists,
bioimage analysts, bioimage informatics developers, corporate partners, funding
agencies, standards organizations, scientific publishers and observers of such;
(3) outlines the current actions of the QUAREP-LiMi initiative and (4) proposes
future steps that can be taken to improve the dissemination and acceptance of
the proposed guidelines to manage QC. To summarize, the principal goal of the
QUAREP-LiMi initiative is to improve the overall quality and reproducibility of
light microscope image data by introducing broadly accepted standard practices
and accurately captured image data metrics.
acknowledgement: We thank https://www.somersault1824.com/somersault18:24 BV (Leuven,
Belgium) for help with Figure 1. E. C.-S. was supported by the project PPBI-POCI-01-0145-FEDER-022122,
in the scope of Fundação para a Ciência e Tecnologia, Portugal (FCT) National Roadmap
of Research Infrastructures. R.N. was funded by the Deutsche Forschungsgemeinschaft
(DFG, German Research Foundation) Grant number Ni 451/9-1 - MIAP-Freiburg.
article_processing_charge: Yes
article_type: original
author:
- first_name: Glyn
full_name: Nelson, Glyn
last_name: Nelson
- first_name: Ulrike
full_name: Boehm, Ulrike
last_name: Boehm
- first_name: Steve
full_name: Bagley, Steve
last_name: Bagley
- first_name: Peter
full_name: Bajcsy, Peter
last_name: Bajcsy
- first_name: Johanna
full_name: Bischof, Johanna
last_name: Bischof
- first_name: Claire M.
full_name: Brown, Claire M.
last_name: Brown
- first_name: Aurélien
full_name: Dauphin, Aurélien
last_name: Dauphin
- first_name: Ian M.
full_name: Dobbie, Ian M.
last_name: Dobbie
- first_name: John E.
full_name: Eriksson, John E.
last_name: Eriksson
- first_name: Orestis
full_name: Faklaris, Orestis
last_name: Faklaris
- first_name: Julia
full_name: Fernandez-Rodriguez, Julia
last_name: Fernandez-Rodriguez
- first_name: Alexia
full_name: Ferrand, Alexia
last_name: Ferrand
- first_name: Laurent
full_name: Gelman, Laurent
last_name: Gelman
- first_name: Ali
full_name: Gheisari, Ali
last_name: Gheisari
- first_name: Hella
full_name: Hartmann, Hella
last_name: Hartmann
- first_name: Christian
full_name: Kukat, Christian
last_name: Kukat
- first_name: Alex
full_name: Laude, Alex
last_name: Laude
- first_name: Miso
full_name: Mitkovski, Miso
last_name: Mitkovski
- first_name: Sebastian
full_name: Munck, Sebastian
last_name: Munck
- first_name: Alison J.
full_name: North, Alison J.
last_name: North
- first_name: Tobias M.
full_name: Rasse, Tobias M.
last_name: Rasse
- first_name: Ute
full_name: Resch-Genger, Ute
last_name: Resch-Genger
- first_name: Lucas C.
full_name: Schuetz, Lucas C.
last_name: Schuetz
- first_name: Arne
full_name: Seitz, Arne
last_name: Seitz
- first_name: Caterina
full_name: Strambio-De-Castillia, Caterina
last_name: Strambio-De-Castillia
- first_name: Jason R.
full_name: Swedlow, Jason R.
last_name: Swedlow
- first_name: Ioannis
full_name: Alexopoulos, Ioannis
last_name: Alexopoulos
- first_name: Karin
full_name: Aumayr, Karin
last_name: Aumayr
- first_name: Sergiy
full_name: Avilov, Sergiy
last_name: Avilov
- first_name: Gert Jan
full_name: Bakker, Gert Jan
last_name: Bakker
- first_name: Rodrigo R.
full_name: Bammann, Rodrigo R.
last_name: Bammann
- first_name: Andrea
full_name: Bassi, Andrea
last_name: Bassi
- first_name: Hannes
full_name: Beckert, Hannes
last_name: Beckert
- first_name: Sebastian
full_name: Beer, Sebastian
last_name: Beer
- first_name: Yury
full_name: Belyaev, Yury
last_name: Belyaev
- first_name: Jakob
full_name: Bierwagen, Jakob
last_name: Bierwagen
- first_name: Konstantin A.
full_name: Birngruber, Konstantin A.
last_name: Birngruber
- first_name: Manel
full_name: Bosch, Manel
last_name: Bosch
- first_name: Juergen
full_name: Breitlow, Juergen
last_name: Breitlow
- first_name: Lisa A.
full_name: Cameron, Lisa A.
last_name: Cameron
- first_name: Joe
full_name: Chalfoun, Joe
last_name: Chalfoun
- first_name: James J.
full_name: Chambers, James J.
last_name: Chambers
- first_name: Chieh Li
full_name: Chen, Chieh Li
last_name: Chen
- first_name: Eduardo
full_name: Conde-Sousa, Eduardo
last_name: Conde-Sousa
- first_name: Alexander D.
full_name: Corbett, Alexander D.
last_name: Corbett
- first_name: Fabrice P.
full_name: Cordelieres, Fabrice P.
last_name: Cordelieres
- first_name: Elaine Del
full_name: Nery, Elaine Del
last_name: Nery
- first_name: Ralf
full_name: Dietzel, Ralf
last_name: Dietzel
- first_name: Frank
full_name: Eismann, Frank
last_name: Eismann
- first_name: Elnaz
full_name: Fazeli, Elnaz
last_name: Fazeli
- first_name: Andreas
full_name: Felscher, Andreas
last_name: Felscher
- first_name: Hans
full_name: Fried, Hans
last_name: Fried
- first_name: Nathalie
full_name: Gaudreault, Nathalie
last_name: Gaudreault
- first_name: Wah Ing
full_name: Goh, Wah Ing
last_name: Goh
- first_name: Thomas
full_name: Guilbert, Thomas
last_name: Guilbert
- first_name: Roland
full_name: Hadleigh, Roland
last_name: Hadleigh
- first_name: Peter
full_name: Hemmerich, Peter
last_name: Hemmerich
- first_name: Gerhard A.
full_name: Holst, Gerhard A.
last_name: Holst
- first_name: Michelle S.
full_name: Itano, Michelle S.
last_name: Itano
- first_name: Claudia B.
full_name: Jaffe, Claudia B.
last_name: Jaffe
- first_name: Helena K.
full_name: Jambor, Helena K.
last_name: Jambor
- first_name: Stuart C.
full_name: Jarvis, Stuart C.
last_name: Jarvis
- first_name: Antje
full_name: Keppler, Antje
last_name: Keppler
- first_name: David
full_name: Kirchenbuechler, David
last_name: Kirchenbuechler
- first_name: Marcel
full_name: Kirchner, Marcel
last_name: Kirchner
- first_name: Norio
full_name: Kobayashi, Norio
last_name: Kobayashi
- first_name: Gabriel
full_name: Krens, Gabriel
id: 2B819732-F248-11E8-B48F-1D18A9856A87
last_name: Krens
orcid: 0000-0003-4761-5996
- first_name: Susanne
full_name: Kunis, Susanne
last_name: Kunis
- first_name: Judith
full_name: Lacoste, Judith
last_name: Lacoste
- first_name: Marco
full_name: Marcello, Marco
last_name: Marcello
- first_name: Gabriel G.
full_name: Martins, Gabriel G.
last_name: Martins
- first_name: Daniel J.
full_name: Metcalf, Daniel J.
last_name: Metcalf
- first_name: Claire A.
full_name: Mitchell, Claire A.
last_name: Mitchell
- first_name: Joshua
full_name: Moore, Joshua
last_name: Moore
- first_name: Tobias
full_name: Mueller, Tobias
last_name: Mueller
- first_name: Michael S.
full_name: Nelson, Michael S.
last_name: Nelson
- first_name: Stephen
full_name: Ogg, Stephen
last_name: Ogg
- first_name: Shuichi
full_name: Onami, Shuichi
last_name: Onami
- first_name: Alexandra L.
full_name: Palmer, Alexandra L.
last_name: Palmer
- first_name: Perrine
full_name: Paul-Gilloteaux, Perrine
last_name: Paul-Gilloteaux
- first_name: Jaime A.
full_name: Pimentel, Jaime A.
last_name: Pimentel
- first_name: Laure
full_name: Plantard, Laure
last_name: Plantard
- first_name: Santosh
full_name: Podder, Santosh
last_name: Podder
- first_name: Elton
full_name: Rexhepaj, Elton
last_name: Rexhepaj
- first_name: Arnaud
full_name: Royon, Arnaud
last_name: Royon
- first_name: Markku A.
full_name: Saari, Markku A.
last_name: Saari
- first_name: Damien
full_name: Schapman, Damien
last_name: Schapman
- first_name: Vincent
full_name: Schoonderwoert, Vincent
last_name: Schoonderwoert
- first_name: Britta
full_name: Schroth-Diez, Britta
last_name: Schroth-Diez
- first_name: Stanley
full_name: Schwartz, Stanley
last_name: Schwartz
- first_name: Michael
full_name: Shaw, Michael
last_name: Shaw
- first_name: Martin
full_name: Spitaler, Martin
last_name: Spitaler
- first_name: Martin T.
full_name: Stoeckl, Martin T.
last_name: Stoeckl
- first_name: Damir
full_name: Sudar, Damir
last_name: Sudar
- first_name: Jeremie
full_name: Teillon, Jeremie
last_name: Teillon
- first_name: Stefan
full_name: Terjung, Stefan
last_name: Terjung
- first_name: Roland
full_name: Thuenauer, Roland
last_name: Thuenauer
- first_name: Christian D.
full_name: Wilms, Christian D.
last_name: Wilms
- first_name: Graham D.
full_name: Wright, Graham D.
last_name: Wright
- first_name: Roland
full_name: Nitschke, Roland
last_name: Nitschke
citation:
ama: 'Nelson G, Boehm U, Bagley S, et al. QUAREP-LiMi: A community-driven initiative
to establish guidelines for quality assessment and reproducibility for instruments
and images in light microscopy. Journal of Microscopy. 2021;284(1):56-73.
doi:10.1111/jmi.13041'
apa: 'Nelson, G., Boehm, U., Bagley, S., Bajcsy, P., Bischof, J., Brown, C. M.,
… Nitschke, R. (2021). QUAREP-LiMi: A community-driven initiative to establish
guidelines for quality assessment and reproducibility for instruments and images
in light microscopy. Journal of Microscopy. Wiley. https://doi.org/10.1111/jmi.13041'
chicago: 'Nelson, Glyn, Ulrike Boehm, Steve Bagley, Peter Bajcsy, Johanna Bischof,
Claire M. Brown, Aurélien Dauphin, et al. “QUAREP-LiMi: A Community-Driven Initiative
to Establish Guidelines for Quality Assessment and Reproducibility for Instruments
and Images in Light Microscopy.” Journal of Microscopy. Wiley, 2021. https://doi.org/10.1111/jmi.13041.'
ieee: 'G. Nelson et al., “QUAREP-LiMi: A community-driven initiative to establish
guidelines for quality assessment and reproducibility for instruments and images
in light microscopy,” Journal of Microscopy, vol. 284, no. 1. Wiley, pp.
56–73, 2021.'
ista: 'Nelson G et al. 2021. QUAREP-LiMi: A community-driven initiative to establish
guidelines for quality assessment and reproducibility for instruments and images
in light microscopy. Journal of Microscopy. 284(1), 56–73.'
mla: 'Nelson, Glyn, et al. “QUAREP-LiMi: A Community-Driven Initiative to Establish
Guidelines for Quality Assessment and Reproducibility for Instruments and Images
in Light Microscopy.” Journal of Microscopy, vol. 284, no. 1, Wiley, 2021,
pp. 56–73, doi:10.1111/jmi.13041.'
short: G. Nelson, U. Boehm, S. Bagley, P. Bajcsy, J. Bischof, C.M. Brown, A. Dauphin,
I.M. Dobbie, J.E. Eriksson, O. Faklaris, J. Fernandez-Rodriguez, A. Ferrand, L.
Gelman, A. Gheisari, H. Hartmann, C. Kukat, A. Laude, M. Mitkovski, S. Munck,
A.J. North, T.M. Rasse, U. Resch-Genger, L.C. Schuetz, A. Seitz, C. Strambio-De-Castillia,
J.R. Swedlow, I. Alexopoulos, K. Aumayr, S. Avilov, G.J. Bakker, R.R. Bammann,
A. Bassi, H. Beckert, S. Beer, Y. Belyaev, J. Bierwagen, K.A. Birngruber, M. Bosch,
J. Breitlow, L.A. Cameron, J. Chalfoun, J.J. Chambers, C.L. Chen, E. Conde-Sousa,
A.D. Corbett, F.P. Cordelieres, E.D. Nery, R. Dietzel, F. Eismann, E. Fazeli,
A. Felscher, H. Fried, N. Gaudreault, W.I. Goh, T. Guilbert, R. Hadleigh, P. Hemmerich,
G.A. Holst, M.S. Itano, C.B. Jaffe, H.K. Jambor, S.C. Jarvis, A. Keppler, D. Kirchenbuechler,
M. Kirchner, N. Kobayashi, G. Krens, S. Kunis, J. Lacoste, M. Marcello, G.G. Martins,
D.J. Metcalf, C.A. Mitchell, J. Moore, T. Mueller, M.S. Nelson, S. Ogg, S. Onami,
A.L. Palmer, P. Paul-Gilloteaux, J.A. Pimentel, L. Plantard, S. Podder, E. Rexhepaj,
A. Royon, M.A. Saari, D. Schapman, V. Schoonderwoert, B. Schroth-Diez, S. Schwartz,
M. Shaw, M. Spitaler, M.T. Stoeckl, D. Sudar, J. Teillon, S. Terjung, R. Thuenauer,
C.D. Wilms, G.D. Wright, R. Nitschke, Journal of Microscopy 284 (2021) 56–73.
date_created: 2021-08-15T22:01:29Z
date_published: 2021-08-11T00:00:00Z
date_updated: 2023-08-11T10:30:40Z
day: '11'
department:
- _id: Bio
doi: 10.1111/jmi.13041
external_id:
isi:
- '000683702700001'
intvolume: ' 284'
isi: 1
issue: '1'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.1111/jmi.13041
month: '08'
oa: 1
oa_version: Published Version
page: 56-73
publication: Journal of Microscopy
publication_identifier:
eissn:
- 1365-2818
issn:
- 0022-2720
publication_status: published
publisher: Wiley
quality_controlled: '1'
scopus_import: '1'
status: public
title: 'QUAREP-LiMi: A community-driven initiative to establish guidelines for quality
assessment and reproducibility for instruments and images in light microscopy'
type: journal_article
user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
volume: 284
year: '2021'
...
---
_id: '9906'
abstract:
- lang: eng
text: Endometriosis is a common gynecological disorder characterized by ectopic
growth of endometrium outside the uterus and is associated with chronic pain and
infertility. We investigated the role of the long intergenic noncoding RNA 01133
(LINC01133) in endometriosis, an lncRNA that has been implicated in several types
of cancer. We found that LINC01133 is upregulated in ectopic endometriotic lesions.
As expression appeared higher in the epithelial endometrial layer, we performed
a siRNA knockdown of LINC01133 in an endometriosis epithelial cell line. Phenotypic
assays indicated that LINC01133 may promote proliferation and suppress cellular
migration, and affect the cytoskeleton and morphology of the cells. Gene ontology
analysis of differentially expressed genes indicated that cell proliferation and
migration pathways were affected in line with the observed phenotype. We validated
upregulation of p21 and downregulation of Cyclin A at the protein level, which
together with the quantification of the DNA content using fluorescence-activated
cell sorting (FACS) analysis indicated that the observed effects on cellular proliferation
may be due to changes in cell cycle. Further, we found testis-specific protein
kinase 1 (TESK1) kinase upregulation corresponding with phosphorylation and inactivation
of actin severing protein Cofilin, which could explain changes in the cytoskeleton
and cellular migration. These results indicate that endometriosis is associated
with LINC01133 upregulation, which may affect pathogenesis via the cellular proliferation
and migration pathways.
acknowledgement: "Open access funding provided by Medical University of Vienna. The
authors would like to thank all the participants and health professionals involved
in the present study. We want to thank our technical assistants Barbara Widmar and
Matthias Witzmann-Stern for their diligent work and constant assistance. We would
like to thank Simon Hippenmeyer for access to\r\nbioinformatic infrastructure and
resources."
article_number: '8385'
article_processing_charge: Yes
article_type: original
author:
- first_name: Iveta
full_name: Yotova, Iveta
last_name: Yotova
- first_name: Quanah J.
full_name: Hudson, Quanah J.
last_name: Hudson
- first_name: Florian
full_name: Pauler, Florian
id: 48EA0138-F248-11E8-B48F-1D18A9856A87
last_name: Pauler
orcid: 0000-0002-7462-0048
- first_name: Katharina
full_name: Proestling, Katharina
last_name: Proestling
- first_name: Isabella
full_name: Haslinger, Isabella
last_name: Haslinger
- first_name: Lorenz
full_name: Kuessel, Lorenz
last_name: Kuessel
- first_name: Alexandra
full_name: Perricos, Alexandra
last_name: Perricos
- first_name: Heinrich
full_name: Husslein, Heinrich
last_name: Husslein
- first_name: René
full_name: Wenzl, René
last_name: Wenzl
citation:
ama: Yotova I, Hudson QJ, Pauler F, et al. LINC01133 inhibits invasion and promotes
proliferation in an endometriosis epithelial cell line. International Journal
of Molecular Sciences. 2021;22(16). doi:10.3390/ijms22168385
apa: Yotova, I., Hudson, Q. J., Pauler, F., Proestling, K., Haslinger, I., Kuessel,
L., … Wenzl, R. (2021). LINC01133 inhibits invasion and promotes proliferation
in an endometriosis epithelial cell line. International Journal of Molecular
Sciences. MDPI. https://doi.org/10.3390/ijms22168385
chicago: Yotova, Iveta, Quanah J. Hudson, Florian Pauler, Katharina Proestling,
Isabella Haslinger, Lorenz Kuessel, Alexandra Perricos, Heinrich Husslein, and
René Wenzl. “LINC01133 Inhibits Invasion and Promotes Proliferation in an Endometriosis
Epithelial Cell Line.” International Journal of Molecular Sciences. MDPI,
2021. https://doi.org/10.3390/ijms22168385.
ieee: I. Yotova et al., “LINC01133 inhibits invasion and promotes proliferation
in an endometriosis epithelial cell line,” International Journal of Molecular
Sciences, vol. 22, no. 16. MDPI, 2021.
ista: Yotova I, Hudson QJ, Pauler F, Proestling K, Haslinger I, Kuessel L, Perricos
A, Husslein H, Wenzl R. 2021. LINC01133 inhibits invasion and promotes proliferation
in an endometriosis epithelial cell line. International Journal of Molecular Sciences.
22(16), 8385.
mla: Yotova, Iveta, et al. “LINC01133 Inhibits Invasion and Promotes Proliferation
in an Endometriosis Epithelial Cell Line.” International Journal of Molecular
Sciences, vol. 22, no. 16, 8385, MDPI, 2021, doi:10.3390/ijms22168385.
short: I. Yotova, Q.J. Hudson, F. Pauler, K. Proestling, I. Haslinger, L. Kuessel,
A. Perricos, H. Husslein, R. Wenzl, International Journal of Molecular Sciences
22 (2021).
date_created: 2021-08-15T22:01:27Z
date_published: 2021-08-04T00:00:00Z
date_updated: 2023-08-11T10:34:13Z
day: '04'
ddc:
- '570'
department:
- _id: SiHi
doi: 10.3390/ijms22168385
external_id:
isi:
- '000689147400001'
file:
- access_level: open_access
checksum: be7f0042607ca60549cb27513c19c6af
content_type: application/pdf
creator: asandaue
date_created: 2021-08-16T09:29:17Z
date_updated: 2021-08-16T09:29:17Z
file_id: '9922'
file_name: 2021_InternationalJournalOfMolecularSciences_Yotova.pdf
file_size: 2646018
relation: main_file
success: 1
file_date_updated: 2021-08-16T09:29:17Z
has_accepted_license: '1'
intvolume: ' 22'
isi: 1
issue: '16'
language:
- iso: eng
month: '08'
oa: 1
oa_version: Published Version
publication: International Journal of Molecular Sciences
publication_identifier:
eissn:
- '14220067'
issn:
- '16616596'
publication_status: published
publisher: MDPI
quality_controlled: '1'
scopus_import: '1'
status: public
title: LINC01133 inhibits invasion and promotes proliferation in an endometriosis
epithelial cell line
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: 22
year: '2021'
...
---
_id: '9910'
abstract:
- lang: eng
text: Adult height inspired the first biometrical and quantitative genetic studies
and is a test-case trait for understanding heritability. The studies of height
led to formulation of the classical polygenic model, that has a profound influence
on the way we view and analyse complex traits. An essential part of the classical
model is an assumption of additivity of effects and normality of the distribution
of the residuals. However, it may be expected that the normal approximation will
become insufficient in bigger studies. Here, we demonstrate that when the height
of hundreds of thousands of individuals is analysed, the model complexity needs
to be increased to include non-additive interactions between sex, environment
and genes. Alternatively, the use of log-normal approximation allowed us to still
use the additive effects model. These findings are important for future genetic
and methodologic studies that make use of adult height as an exemplar trait.
acknowledgement: "We are grateful to Marianna Bevova and Pavel Borodin for fruitful
discussion and help with conceptualising our findings and to Lennart C. Karssen
for help with handling the UK Biobank data.\r\n\r\nFunding\r\nThis research has
been conducted using the UK Biobank Resource (project # 41601, “Non-additive effects
in control of complex human traits”). The work of SAS, IAK, and TIS were supported
by Russian Ministry of Science and Education under the 5–100 Excellence Programme.
The work of YSA and TIA was supported by the Ministry of Education and Science of
the RF via the Institute of Cytology and Genetics SB RAS (project number 0324-2019-0040-C-01/AAAA-A17-117092070032-4).
FAK is supported by the ERC Consolidator Grant (ChrFL: 771209)."
article_processing_charge: Yes (in subscription journal)
article_type: original
author:
- first_name: Sergei A.
full_name: Slavskii, Sergei A.
last_name: Slavskii
- first_name: Ivan A.
full_name: Kuznetsov, Ivan A.
last_name: Kuznetsov
- first_name: Tatiana I.
full_name: Shashkova, Tatiana I.
last_name: Shashkova
- first_name: Georgii A.
full_name: Bazykin, Georgii A.
last_name: Bazykin
- first_name: Tatiana I.
full_name: Axenovich, Tatiana I.
last_name: Axenovich
- first_name: Fyodor
full_name: Kondrashov, Fyodor
id: 44FDEF62-F248-11E8-B48F-1D18A9856A87
last_name: Kondrashov
orcid: 0000-0001-8243-4694
- first_name: Yurii S.
full_name: Aulchenko, Yurii S.
last_name: Aulchenko
citation:
ama: Slavskii SA, Kuznetsov IA, Shashkova TI, et al. The limits of normal approximation
for adult height. European Journal of Human Genetics. 2021;29(7):1082-1091.
doi:10.1038/s41431-021-00836-7
apa: Slavskii, S. A., Kuznetsov, I. A., Shashkova, T. I., Bazykin, G. A., Axenovich,
T. I., Kondrashov, F., & Aulchenko, Y. S. (2021). The limits of normal approximation
for adult height. European Journal of Human Genetics. Springer Nature.
https://doi.org/10.1038/s41431-021-00836-7
chicago: Slavskii, Sergei A., Ivan A. Kuznetsov, Tatiana I. Shashkova, Georgii A.
Bazykin, Tatiana I. Axenovich, Fyodor Kondrashov, and Yurii S. Aulchenko. “The
Limits of Normal Approximation for Adult Height.” European Journal of Human
Genetics. Springer Nature, 2021. https://doi.org/10.1038/s41431-021-00836-7.
ieee: S. A. Slavskii et al., “The limits of normal approximation for adult
height,” European Journal of Human Genetics, vol. 29, no. 7. Springer Nature,
pp. 1082–1091, 2021.
ista: Slavskii SA, Kuznetsov IA, Shashkova TI, Bazykin GA, Axenovich TI, Kondrashov
F, Aulchenko YS. 2021. The limits of normal approximation for adult height. European
Journal of Human Genetics. 29(7), 1082–1091.
mla: Slavskii, Sergei A., et al. “The Limits of Normal Approximation for Adult Height.”
European Journal of Human Genetics, vol. 29, no. 7, Springer Nature, 2021,
pp. 1082–91, doi:10.1038/s41431-021-00836-7.
short: S.A. Slavskii, I.A. Kuznetsov, T.I. Shashkova, G.A. Bazykin, T.I. Axenovich,
F. Kondrashov, Y.S. Aulchenko, European Journal of Human Genetics 29 (2021) 1082–1091.
date_created: 2021-08-15T22:01:28Z
date_published: 2021-07-01T00:00:00Z
date_updated: 2023-08-11T10:33:42Z
day: '01'
ddc:
- '576'
department:
- _id: FyKo
doi: 10.1038/s41431-021-00836-7
ec_funded: 1
external_id:
isi:
- '000625853200001'
pmid:
- '33664501'
file:
- access_level: open_access
checksum: a676d76f91b0dbe0504c63e469129c2a
content_type: application/pdf
creator: asandaue
date_created: 2021-08-16T09:14:36Z
date_updated: 2021-08-16T09:14:36Z
file_id: '9921'
file_name: 2021_EuropeanJournalOfHumanGenetics_Slavskii.pdf
file_size: 1079395
relation: main_file
success: 1
file_date_updated: 2021-08-16T09:14:36Z
has_accepted_license: '1'
intvolume: ' 29'
isi: 1
issue: '7'
language:
- iso: eng
month: '07'
oa: 1
oa_version: Published Version
page: 1082-1091
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: European Journal of Human Genetics
publication_identifier:
eissn:
- '14765438'
issn:
- '10184813'
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
scopus_import: '1'
status: public
title: The limits of normal approximation for adult height
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: 29
year: '2021'
...
---
_id: '9912'
abstract:
- lang: eng
text: "In the customary random matrix model for transport in quantum dots with M
internal degrees of freedom coupled to a chaotic environment via \U0001D441≪\U0001D440
channels, the density \U0001D70C of transmission eigenvalues is computed from
a specific invariant ensemble for which explicit formula for the joint probability
density of all eigenvalues is available. We revisit this problem in the large
N regime allowing for (i) arbitrary ratio \U0001D719:=\U0001D441/\U0001D440≤1;
and (ii) general distributions for the matrix elements of the Hamiltonian of the
quantum dot. In the limit \U0001D719→0, we recover the formula for the density
\U0001D70C that Beenakker (Rev Mod Phys 69:731–808, 1997) has derived for a special
matrix ensemble. We also prove that the inverse square root singularity of the
density at zero and full transmission in Beenakker’s formula persists for any
\U0001D719<1 but in the borderline case \U0001D719=1 an anomalous \U0001D706−2/3
singularity arises at zero. To access this level of generality, we develop the
theory of global and local laws on the spectral density of a large class of noncommutative
rational expressions in large random matrices with i.i.d. entries."
acknowledgement: The authors are very grateful to Yan Fyodorov for discussions on
the physical background and for providing references, and to the anonymous referee
for numerous valuable remarks.
article_processing_charge: Yes (in subscription journal)
article_type: original
author:
- first_name: László
full_name: Erdös, László
id: 4DBD5372-F248-11E8-B48F-1D18A9856A87
last_name: Erdös
orcid: 0000-0001-5366-9603
- first_name: Torben H
full_name: Krüger, Torben H
id: 3020C786-F248-11E8-B48F-1D18A9856A87
last_name: Krüger
orcid: 0000-0002-4821-3297
- first_name: Yuriy
full_name: Nemish, Yuriy
id: 4D902E6A-F248-11E8-B48F-1D18A9856A87
last_name: Nemish
orcid: 0000-0002-7327-856X
citation:
ama: Erdös L, Krüger TH, Nemish Y. Scattering in quantum dots via noncommutative
rational functions. Annales Henri Poincaré . 2021;22:4205–4269. doi:10.1007/s00023-021-01085-6
apa: Erdös, L., Krüger, T. H., & Nemish, Y. (2021). Scattering in quantum dots
via noncommutative rational functions. Annales Henri Poincaré . Springer
Nature. https://doi.org/10.1007/s00023-021-01085-6
chicago: Erdös, László, Torben H Krüger, and Yuriy Nemish. “Scattering in Quantum
Dots via Noncommutative Rational Functions.” Annales Henri Poincaré . Springer
Nature, 2021. https://doi.org/10.1007/s00023-021-01085-6.
ieee: L. Erdös, T. H. Krüger, and Y. Nemish, “Scattering in quantum dots via noncommutative
rational functions,” Annales Henri Poincaré , vol. 22. Springer Nature,
pp. 4205–4269, 2021.
ista: Erdös L, Krüger TH, Nemish Y. 2021. Scattering in quantum dots via noncommutative
rational functions. Annales Henri Poincaré . 22, 4205–4269.
mla: Erdös, László, et al. “Scattering in Quantum Dots via Noncommutative Rational
Functions.” Annales Henri Poincaré , vol. 22, Springer Nature, 2021, pp.
4205–4269, doi:10.1007/s00023-021-01085-6.
short: L. Erdös, T.H. Krüger, Y. Nemish, Annales Henri Poincaré 22 (2021) 4205–4269.
date_created: 2021-08-15T22:01:29Z
date_published: 2021-12-01T00:00:00Z
date_updated: 2023-08-11T10:31:48Z
day: '01'
ddc:
- '510'
department:
- _id: LaEr
doi: 10.1007/s00023-021-01085-6
ec_funded: 1
external_id:
arxiv:
- '1911.05112'
isi:
- '000681531500001'
file:
- access_level: open_access
checksum: 8d6bac0e2b0a28539608b0538a8e3b38
content_type: application/pdf
creator: dernst
date_created: 2022-05-12T12:50:27Z
date_updated: 2022-05-12T12:50:27Z
file_id: '11365'
file_name: 2021_AnnHenriPoincare_Erdoes.pdf
file_size: 1162454
relation: main_file
success: 1
file_date_updated: 2022-05-12T12:50:27Z
has_accepted_license: '1'
intvolume: ' 22'
isi: 1
language:
- iso: eng
month: '12'
oa: 1
oa_version: Published Version
page: 4205–4269
project:
- _id: 258DCDE6-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '338804'
name: Random matrices, universality and disordered quantum systems
publication: 'Annales Henri Poincaré '
publication_identifier:
eissn:
- 1424-0661
issn:
- 1424-0637
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
scopus_import: '1'
status: public
title: Scattering in quantum dots via noncommutative rational functions
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: 22
year: '2021'
...
---
_id: '9891'
abstract:
- lang: eng
text: 'Extending on ideas of Lewin, Lieb, and Seiringer [Phys. Rev. B 100, 035127
(2019)], we present a modified “floating crystal” trial state for jellium (also
known as the classical homogeneous electron gas) with density equal to a characteristic
function. This allows us to show that three definitions of the jellium energy
coincide in dimensions d ≥ 2, thus extending the result of Cotar and Petrache
[“Equality of the Jellium and uniform electron gas next-order asymptotic terms
for Coulomb and Riesz potentials,” arXiv: 1707.07664 (2019)] and Lewin, Lieb,
and Seiringer [Phys. Rev. B 100, 035127 (2019)] that the three definitions coincide
in dimension d ≥ 3. We show that the jellium energy is also equivalent to a “renormalized
energy” studied in a series of papers by Serfaty and others, and thus, by the
work of Bétermin and Sandier [Constr. Approximation 47, 39–74 (2018)], we relate
the jellium energy to the order n term in the logarithmic energy of n points on
the unit 2-sphere. We improve upon known lower bounds for this renormalized energy.
Additionally, we derive formulas for the jellium energy of periodic configurations.'
acknowledgement: The author would like to thank Robert Seiringer for guidance and
many helpful comments on this project. The author would also like to thank Mathieu
Lewin for his comments on the manuscript and Lorenzo Portinale for providing his
lecture notes for the course “Mathematics of quantum many-body systems” in spring
2020, taught by Robert Seiringer. The Proof of Theorem III.1 is inspired by these
lecture notes.
article_number: '083305'
article_processing_charge: No
article_type: original
author:
- first_name: Asbjørn Bækgaard
full_name: Lauritsen, Asbjørn Bækgaard
id: e1a2682f-dc8d-11ea-abe3-81da9ac728f1
last_name: Lauritsen
orcid: 0000-0003-4476-2288
citation:
ama: Lauritsen AB. Floating Wigner crystal and periodic jellium configurations.
Journal of Mathematical Physics. 2021;62(8). doi:10.1063/5.0053494
apa: Lauritsen, A. B. (2021). Floating Wigner crystal and periodic jellium configurations.
Journal of Mathematical Physics. AIP Publishing. https://doi.org/10.1063/5.0053494
chicago: Lauritsen, Asbjørn Bækgaard. “Floating Wigner Crystal and Periodic Jellium
Configurations.” Journal of Mathematical Physics. AIP Publishing, 2021.
https://doi.org/10.1063/5.0053494.
ieee: A. B. Lauritsen, “Floating Wigner crystal and periodic jellium configurations,”
Journal of Mathematical Physics, vol. 62, no. 8. AIP Publishing, 2021.
ista: Lauritsen AB. 2021. Floating Wigner crystal and periodic jellium configurations.
Journal of Mathematical Physics. 62(8), 083305.
mla: Lauritsen, Asbjørn Bækgaard. “Floating Wigner Crystal and Periodic Jellium
Configurations.” Journal of Mathematical Physics, vol. 62, no. 8, 083305,
AIP Publishing, 2021, doi:10.1063/5.0053494.
short: A.B. Lauritsen, Journal of Mathematical Physics 62 (2021).
date_created: 2021-08-12T07:08:36Z
date_published: 2021-08-01T00:00:00Z
date_updated: 2023-08-11T10:29:48Z
day: '01'
ddc:
- '530'
department:
- _id: GradSch
- _id: RoSe
doi: 10.1063/5.0053494
external_id:
arxiv:
- '2103.07975'
isi:
- '000683960800003'
file:
- access_level: open_access
checksum: d035be2b894c4d50d90ac5ce252e27cd
content_type: application/pdf
creator: cziletti
date_created: 2021-10-27T12:57:06Z
date_updated: 2021-10-27T12:57:06Z
file_id: '10188'
file_name: 2021_JMathPhy_Lauritsen.pdf
file_size: 4352640
relation: main_file
success: 1
file_date_updated: 2021-10-27T12:57:06Z
has_accepted_license: '1'
intvolume: ' 62'
isi: 1
issue: '8'
keyword:
- Mathematical Physics
- Statistical and Nonlinear Physics
language:
- iso: eng
month: '08'
oa: 1
oa_version: Published Version
publication: Journal of Mathematical Physics
publication_identifier:
eissn:
- 1089-7658
issn:
- 0022-2488
publication_status: published
publisher: AIP Publishing
quality_controlled: '1'
scopus_import: '1'
status: public
title: Floating Wigner crystal and periodic jellium configurations
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: 62
year: '2021'
...
---
_id: '9909'
abstract:
- lang: eng
text: Roots are composed of different root types and, in the dicotyledonous Arabidopsis,
typically consist of a primary root that branches into lateral roots. Adventitious
roots emerge from non-root tissue and are formed upon wounding or other types
of abiotic stress. Here, we investigated adventitious root (AR) formation in Arabidopsis
hypocotyls under conditions of altered abscisic acid (ABA) signaling. Exogenously
applied ABA suppressed AR formation at 0.25 µM or higher doses. AR formation was
less sensitive to the synthetic ABA analog pyrabactin (PB). However, PB was a
more potent inhibitor at concentrations above 1 µM, suggesting that it was more
selective in triggering a root inhibition response. Analysis of a series of phosphonamide
and phosphonate pyrabactin analogs suggested that adventitious root formation
and lateral root branching are differentially regulated by ABA signaling. ABA
biosynthesis and signaling mutants affirmed a general inhibitory role of ABA and
point to PYL1 and PYL2 as candidate ABA receptors that regulate AR inhibition.
acknowledgement: We thank S. Cutler (Riverside, USA) for providing the ABA biosynthesis
mutants and ABA signaling mutants.
article_number: '1141'
article_processing_charge: Yes
article_type: original
author:
- first_name: Yinwei
full_name: Zeng, Yinwei
last_name: Zeng
- first_name: Inge
full_name: Verstraeten, Inge
id: 362BF7FE-F248-11E8-B48F-1D18A9856A87
last_name: Verstraeten
orcid: 0000-0001-7241-2328
- first_name: Hoang Khai
full_name: Trinh, Hoang Khai
last_name: Trinh
- first_name: Thomas
full_name: Heugebaert, Thomas
last_name: Heugebaert
- first_name: Christian V.
full_name: Stevens, Christian V.
last_name: Stevens
- first_name: Irene
full_name: Garcia-Maquilon, Irene
last_name: Garcia-Maquilon
- first_name: Pedro L.
full_name: Rodriguez, Pedro L.
last_name: Rodriguez
- first_name: Steffen
full_name: Vanneste, Steffen
last_name: Vanneste
- first_name: Danny
full_name: Geelen, Danny
last_name: Geelen
citation:
ama: Zeng Y, Verstraeten I, Trinh HK, et al. Arabidopsis hypocotyl adventitious
root formation is suppressed by ABA signaling. Genes. 2021;12(8). doi:10.3390/genes12081141
apa: Zeng, Y., Verstraeten, I., Trinh, H. K., Heugebaert, T., Stevens, C. V., Garcia-Maquilon,
I., … Geelen, D. (2021). Arabidopsis hypocotyl adventitious root formation is
suppressed by ABA signaling. Genes. MDPI. https://doi.org/10.3390/genes12081141
chicago: Zeng, Yinwei, Inge Verstraeten, Hoang Khai Trinh, Thomas Heugebaert, Christian
V. Stevens, Irene Garcia-Maquilon, Pedro L. Rodriguez, Steffen Vanneste, and Danny
Geelen. “Arabidopsis Hypocotyl Adventitious Root Formation Is Suppressed by ABA
Signaling.” Genes. MDPI, 2021. https://doi.org/10.3390/genes12081141.
ieee: Y. Zeng et al., “Arabidopsis hypocotyl adventitious root formation
is suppressed by ABA signaling,” Genes, vol. 12, no. 8. MDPI, 2021.
ista: Zeng Y, Verstraeten I, Trinh HK, Heugebaert T, Stevens CV, Garcia-Maquilon
I, Rodriguez PL, Vanneste S, Geelen D. 2021. Arabidopsis hypocotyl adventitious
root formation is suppressed by ABA signaling. Genes. 12(8), 1141.
mla: Zeng, Yinwei, et al. “Arabidopsis Hypocotyl Adventitious Root Formation Is
Suppressed by ABA Signaling.” Genes, vol. 12, no. 8, 1141, MDPI, 2021,
doi:10.3390/genes12081141.
short: Y. Zeng, I. Verstraeten, H.K. Trinh, T. Heugebaert, C.V. Stevens, I. Garcia-Maquilon,
P.L. Rodriguez, S. Vanneste, D. Geelen, Genes 12 (2021).
date_created: 2021-08-15T22:01:28Z
date_published: 2021-07-27T00:00:00Z
date_updated: 2023-08-11T10:32:21Z
day: '27'
ddc:
- '580'
- '570'
department:
- _id: JiFr
doi: 10.3390/genes12081141
external_id:
isi:
- '000690558000001'
file:
- access_level: open_access
checksum: 3d99535618cf9a5b14d264408fa52e97
content_type: application/pdf
creator: asandaue
date_created: 2021-08-16T09:02:40Z
date_updated: 2021-08-16T09:02:40Z
file_id: '9919'
file_name: 2021_Genes_Zeng.pdf
file_size: 1340305
relation: main_file
success: 1
file_date_updated: 2021-08-16T09:02:40Z
has_accepted_license: '1'
intvolume: ' 12'
isi: 1
issue: '8'
language:
- iso: eng
month: '07'
oa: 1
oa_version: Published Version
publication: Genes
publication_identifier:
eissn:
- '20734425'
publication_status: published
publisher: MDPI
quality_controlled: '1'
scopus_import: '1'
status: public
title: Arabidopsis hypocotyl adventitious root formation is suppressed by ABA signaling
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: 12
year: '2021'
...
---
_id: '9907'
abstract:
- lang: eng
text: 'DivIVA is a protein initially identified as a spatial regulator of cell division
in the model organism Bacillus subtilis, but its homologues are present in many
other Gram-positive bacteria, including Clostridia species. Besides its role as
topological regulator of the Min system during bacterial cell division, DivIVA
is involved in chromosome segregation during sporulation, genetic competence,
and cell wall synthesis. DivIVA localizes to regions of high membrane curvature,
such as the cell poles and cell division site, where it recruits distinct binding
partners. Previously, it was suggested that negative curvature sensing is the
main mechanism by which DivIVA binds to these specific regions. Here, we show
that Clostridioides difficile DivIVA binds preferably to membranes containing
negatively charged phospholipids, especially cardiolipin. Strikingly, we observed
that upon binding, DivIVA modifies the lipid distribution and induces changes
to lipid bilayers containing cardiolipin. Our observations indicate that DivIVA
might play a more complex and so far unknown active role during the formation
of the cell division septal membrane. '
acknowledged_ssus:
- _id: Bio
- _id: LifeSc
acknowledgement: "We thank Daniela Krajˇcíkova, Katarína Muchová, Zuzana Chromíkova
and other members of Barák’s laboratory for useful discussions, suggestions and
help. Special thanks also to Emília Chovancová for technical support. We are grateful
to Juraj Labaj for drawing the model and for help with graphics. Many thanks to
all members of Loose’s laboratory: Maria del Mar\r\nLópez, Paulo Caldas, Philipp
Radler, and other members of the Loose’s laboratory for sharing their knowledge
of SLB preparation and TIRF experiment chambers, for sharing coverslips and for
help with the TIRF microscope and data analysis. We also thank the members of the
Dept. of Biochemistry of Biomembranes at the Institute of Animal Biochemistry and
Genetics, CBs SAS for their help with preparing the lipid mixtures. We thank J.
Bauer for critically reading the manuscript."
article_number: '8350'
article_processing_charge: Yes
article_type: original
author:
- first_name: Naďa
full_name: Labajová, Naďa
last_name: Labajová
- first_name: Natalia S.
full_name: Baranova, Natalia S.
id: 38661662-F248-11E8-B48F-1D18A9856A87
last_name: Baranova
orcid: 0000-0002-3086-9124
- first_name: Miroslav
full_name: Jurásek, Miroslav
last_name: Jurásek
- first_name: Robert
full_name: Vácha, Robert
last_name: Vácha
- first_name: Martin
full_name: Loose, Martin
id: 462D4284-F248-11E8-B48F-1D18A9856A87
last_name: Loose
orcid: 0000-0001-7309-9724
- first_name: Imrich
full_name: Barák, Imrich
last_name: Barák
citation:
ama: Labajová N, Baranova NS, Jurásek M, Vácha R, Loose M, Barák I. Cardiolipin-containing
lipid membranes attract the bacterial cell division protein diviva. International
Journal of Molecular Sciences. 2021;22(15). doi:10.3390/ijms22158350
apa: Labajová, N., Baranova, N. S., Jurásek, M., Vácha, R., Loose, M., & Barák,
I. (2021). Cardiolipin-containing lipid membranes attract the bacterial cell division
protein diviva. International Journal of Molecular Sciences. MDPI. https://doi.org/10.3390/ijms22158350
chicago: Labajová, Naďa, Natalia S. Baranova, Miroslav Jurásek, Robert Vácha, Martin
Loose, and Imrich Barák. “Cardiolipin-Containing Lipid Membranes Attract the Bacterial
Cell Division Protein Diviva.” International Journal of Molecular Sciences.
MDPI, 2021. https://doi.org/10.3390/ijms22158350.
ieee: N. Labajová, N. S. Baranova, M. Jurásek, R. Vácha, M. Loose, and I. Barák,
“Cardiolipin-containing lipid membranes attract the bacterial cell division protein
diviva,” International Journal of Molecular Sciences, vol. 22, no. 15.
MDPI, 2021.
ista: Labajová N, Baranova NS, Jurásek M, Vácha R, Loose M, Barák I. 2021. Cardiolipin-containing
lipid membranes attract the bacterial cell division protein diviva. International
Journal of Molecular Sciences. 22(15), 8350.
mla: Labajová, Naďa, et al. “Cardiolipin-Containing Lipid Membranes Attract the
Bacterial Cell Division Protein Diviva.” International Journal of Molecular
Sciences, vol. 22, no. 15, 8350, MDPI, 2021, doi:10.3390/ijms22158350.
short: N. Labajová, N.S. Baranova, M. Jurásek, R. Vácha, M. Loose, I. Barák, International
Journal of Molecular Sciences 22 (2021).
date_created: 2021-08-15T22:01:27Z
date_published: 2021-08-01T00:00:00Z
date_updated: 2023-08-11T10:34:44Z
day: '01'
ddc:
- '570'
department:
- _id: MaLo
doi: 10.3390/ijms22158350
ec_funded: 1
external_id:
isi:
- '000681815400001'
pmid:
- '34361115'
file:
- access_level: open_access
checksum: a4bc06e9a2c803ceff5a91f10b174054
content_type: application/pdf
creator: asandaue
date_created: 2021-08-16T09:35:56Z
date_updated: 2021-08-16T09:35:56Z
file_id: '9923'
file_name: 2021_InternationalJournalOfMolecularSciences_Labajová .pdf
file_size: 6132410
relation: main_file
success: 1
file_date_updated: 2021-08-16T09:35:56Z
has_accepted_license: '1'
intvolume: ' 22'
isi: 1
issue: '15'
language:
- iso: eng
month: '08'
oa: 1
oa_version: Published Version
pmid: 1
project:
- _id: 2595697A-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '679239'
name: Self-Organization of the Bacterial Cell
publication: International Journal of Molecular Sciences
publication_identifier:
eissn:
- '14220067'
issn:
- '16616596'
publication_status: published
publisher: MDPI
quality_controlled: '1'
scopus_import: '1'
status: public
title: Cardiolipin-containing lipid membranes attract the bacterial cell division
protein diviva
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: 22
year: '2021'
...
---
_id: '9905'
abstract:
- lang: eng
text: Vaccines are thought to be the best available solution for controlling the
ongoing SARS-CoV-2 pandemic. However, the emergence of vaccine-resistant strains
may come too rapidly for current vaccine developments to alleviate the health,
economic and social consequences of the pandemic. To quantify and characterize
the risk of such a scenario, we created a SIR-derived model with initial stochastic
dynamics of the vaccine-resistant strain to study the probability of its emergence
and establishment. Using parameters realistically resembling SARS-CoV-2 transmission,
we model a wave-like pattern of the pandemic and consider the impact of the rate
of vaccination and the strength of non-pharmaceutical intervention measures on
the probability of emergence of a resistant strain. As expected, we found that
a fast rate of vaccination decreases the probability of emergence of a resistant
strain. Counterintuitively, when a relaxation of non-pharmaceutical interventions
happened at a time when most individuals of the population have already been vaccinated
the probability of emergence of a resistant strain was greatly increased. Consequently,
we show that a period of transmission reduction close to the end of the vaccination
campaign can substantially reduce the probability of resistant strain establishment.
Our results suggest that policymakers and individuals should consider maintaining
non-pharmaceutical interventions and transmission-reducing behaviours throughout
the entire vaccination period.
acknowledgement: We thank Alexey Kondrashov, Nick Machnik, Raimundo Julian Saona Urmeneta,
Gasper Tkacik and Nick Barton for fruitful discussions. We also thank participants
of EvoLunch seminar at IST Austria and the internal seminar at the Banco de España
for useful comments. The opinions expressed in this document are exclusively of
the authors and, therefore, do not necessarily coincide with those of the Banco
de España or the Eurosystem. ETD is supported by the Swiss National Science and
Louis Jeantet Foundation. The work of FAK was in part supported by the ERC Consolidator
Grant (771209-CharFL).
article_number: '15729'
article_processing_charge: Yes
article_type: original
author:
- first_name: Simon
full_name: Rella, Simon
id: B4765ACA-AA38-11E9-AC9A-0930E6697425
last_name: Rella
- first_name: Yuliya A.
full_name: Kulikova, Yuliya A.
last_name: Kulikova
- first_name: Emmanouil T.
full_name: Dermitzakis, Emmanouil T.
last_name: Dermitzakis
- first_name: Fyodor
full_name: Kondrashov, Fyodor
id: 44FDEF62-F248-11E8-B48F-1D18A9856A87
last_name: Kondrashov
orcid: 0000-0001-8243-4694
citation:
ama: Rella S, Kulikova YA, Dermitzakis ET, Kondrashov F. Rates of SARS-CoV-2 transmission
and vaccination impact the fate of vaccine-resistant strains. Scientific Reports.
2021;11(1). doi:10.1038/s41598-021-95025-3
apa: Rella, S., Kulikova, Y. A., Dermitzakis, E. T., & Kondrashov, F. (2021).
Rates of SARS-CoV-2 transmission and vaccination impact the fate of vaccine-resistant
strains. Scientific Reports. Springer Nature. https://doi.org/10.1038/s41598-021-95025-3
chicago: Rella, Simon, Yuliya A. Kulikova, Emmanouil T. Dermitzakis, and Fyodor
Kondrashov. “Rates of SARS-CoV-2 Transmission and Vaccination Impact the Fate
of Vaccine-Resistant Strains.” Scientific Reports. Springer Nature, 2021.
https://doi.org/10.1038/s41598-021-95025-3.
ieee: S. Rella, Y. A. Kulikova, E. T. Dermitzakis, and F. Kondrashov, “Rates of
SARS-CoV-2 transmission and vaccination impact the fate of vaccine-resistant strains,”
Scientific Reports, vol. 11, no. 1. Springer Nature, 2021.
ista: Rella S, Kulikova YA, Dermitzakis ET, Kondrashov F. 2021. Rates of SARS-CoV-2
transmission and vaccination impact the fate of vaccine-resistant strains. Scientific
Reports. 11(1), 15729.
mla: Rella, Simon, et al. “Rates of SARS-CoV-2 Transmission and Vaccination Impact
the Fate of Vaccine-Resistant Strains.” Scientific Reports, vol. 11, no.
1, 15729, Springer Nature, 2021, doi:10.1038/s41598-021-95025-3.
short: S. Rella, Y.A. Kulikova, E.T. Dermitzakis, F. Kondrashov, Scientific Reports
11 (2021).
date_created: 2021-08-15T22:01:26Z
date_published: 2021-07-30T00:00:00Z
date_updated: 2023-08-11T10:42:58Z
day: '30'
ddc:
- '570'
- '610'
department:
- _id: FyKo
doi: 10.1038/s41598-021-95025-3
ec_funded: 1
external_id:
isi:
- '000683329100001'
pmid:
- '34330988'
file:
- access_level: open_access
checksum: ac86892ed17e6724c7251844da5cef5c
content_type: application/pdf
creator: asandaue
date_created: 2021-08-16T11:36:49Z
date_updated: 2021-08-16T11:36:49Z
file_id: '9927'
file_name: 2021_ScientificReports_Rella.pdf
file_size: 3432001
relation: main_file
success: 1
file_date_updated: 2021-08-16T11:36:49Z
has_accepted_license: '1'
intvolume: ' 11'
isi: 1
issue: '1'
language:
- iso: eng
month: '07'
oa: 1
oa_version: Published Version
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: Scientific Reports
publication_identifier:
eissn:
- '20452322'
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
related_material:
link:
- description: News on IST Website
relation: press_release
url: https://ist.ac.at/en/news/counterintuitive-dynamics-threaten-the-end-of-the-pandemic/
scopus_import: '1'
status: public
title: Rates of SARS-CoV-2 transmission and vaccination impact the fate of vaccine-resistant
strains
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: journal_article
user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
volume: 11
year: '2021'
...
---
_id: '9903'
abstract:
- lang: eng
text: Eigenstate thermalization in quantum many-body systems implies that eigenstates
at high energy are similar to random vectors. Identifying systems where at least
some eigenstates are nonthermal is an outstanding question. In this Letter we
show that interacting quantum models that have a nullspace—a degenerate subspace
of eigenstates at zero energy (zero modes), which corresponds to infinite temperature,
provide a route to nonthermal eigenstates. We analytically show the existence
of a zero mode which can be represented as a matrix product state for a certain
class of local Hamiltonians. In the more general case we use a subspace disentangling
algorithm to generate an orthogonal basis of zero modes characterized by increasing
entanglement entropy. We show evidence for an area-law entanglement scaling of
the least-entangled zero mode in the broad parameter regime, leading to a conjecture
that all local Hamiltonians with the nullspace feature zero modes with area-law
entanglement scaling and, as such, break the strong thermalization hypothesis.
Finally, we find zero modes in constrained models and propose a setup for observing
their experimental signatures.
acknowledgement: "We acknowledge useful discussions with V. Gritsev and A. Garkun
and suggestions on implementation of the\r\nPPXPP model by D. Bluvstein. A. M. and
M. S. were supported by the European Research Council (ERC) under\r\nthe European
Union’s Horizon 2020 research and innovation program (Grant Agreement No. 850899)"
article_number: '060602'
article_processing_charge: Yes (in subscription journal)
article_type: letter_note
author:
- first_name: Volker
full_name: Karle, Volker
id: D7C012AE-D7ED-11E9-95E8-1EC5E5697425
last_name: Karle
orcid: 0000-0002-6963-0129
- first_name: Maksym
full_name: Serbyn, Maksym
id: 47809E7E-F248-11E8-B48F-1D18A9856A87
last_name: Serbyn
orcid: 0000-0002-2399-5827
- first_name: Alexios
full_name: Michailidis, Alexios
id: 36EBAD38-F248-11E8-B48F-1D18A9856A87
last_name: Michailidis
orcid: 0000-0002-8443-1064
citation:
ama: Karle V, Serbyn M, Michailidis A. Area-law entangled eigenstates from nullspaces
of local Hamiltonians. Physical Review Letters. 2021;127(6). doi:10.1103/physrevlett.127.060602
apa: Karle, V., Serbyn, M., & Michailidis, A. (2021). Area-law entangled eigenstates
from nullspaces of local Hamiltonians. Physical Review Letters. American
Physical Society. https://doi.org/10.1103/physrevlett.127.060602
chicago: Karle, Volker, Maksym Serbyn, and Alexios Michailidis. “Area-Law Entangled
Eigenstates from Nullspaces of Local Hamiltonians.” Physical Review Letters.
American Physical Society, 2021. https://doi.org/10.1103/physrevlett.127.060602.
ieee: V. Karle, M. Serbyn, and A. Michailidis, “Area-law entangled eigenstates from
nullspaces of local Hamiltonians,” Physical Review Letters, vol. 127, no.
6. American Physical Society, 2021.
ista: Karle V, Serbyn M, Michailidis A. 2021. Area-law entangled eigenstates from
nullspaces of local Hamiltonians. Physical Review Letters. 127(6), 060602.
mla: Karle, Volker, et al. “Area-Law Entangled Eigenstates from Nullspaces of Local
Hamiltonians.” Physical Review Letters, vol. 127, no. 6, 060602, American
Physical Society, 2021, doi:10.1103/physrevlett.127.060602.
short: V. Karle, M. Serbyn, A. Michailidis, Physical Review Letters 127 (2021).
date_created: 2021-08-13T09:27:39Z
date_published: 2021-08-06T00:00:00Z
date_updated: 2023-08-11T10:43:27Z
day: '06'
ddc:
- '539'
department:
- _id: MaSe
- _id: GradSch
- _id: MiLe
doi: 10.1103/physrevlett.127.060602
ec_funded: 1
external_id:
arxiv:
- '2102.13633'
isi:
- '000684276000002'
file:
- access_level: open_access
checksum: 51218f302dcef99d90d1209809fcc874
content_type: application/pdf
creator: mserbyn
date_created: 2021-08-13T09:28:08Z
date_updated: 2021-08-13T09:28:08Z
file_id: '9904'
file_name: PhysRevLett.127.060602_SOM.pdf
file_size: 5064231
relation: main_file
success: 1
file_date_updated: 2021-08-13T09:28:08Z
has_accepted_license: '1'
intvolume: ' 127'
isi: 1
issue: '6'
language:
- iso: eng
month: '08'
oa: 1
oa_version: Published Version
project:
- _id: 23841C26-32DE-11EA-91FC-C7463DDC885E
call_identifier: H2020
grant_number: '850899'
name: 'Non-Ergodic Quantum Matter: Universality, Dynamics and Control'
publication: Physical Review Letters
publication_identifier:
eissn:
- 1079-7114
issn:
- 0031-9007
publication_status: published
publisher: American Physical Society
quality_controlled: '1'
status: public
title: Area-law entangled eigenstates from nullspaces of local Hamiltonians
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: 127
year: '2021'
...
---
_id: '9952'
abstract:
- lang: eng
text: Proper control of division orientation and symmetry, largely determined by
spindle positioning, is essential to development and homeostasis. Spindle positioning
has been extensively studied in cells dividing in two-dimensional (2D) environments
and in epithelial tissues, where proteins such as NuMA (also known as NUMA1) orient
division along the interphase long axis of the cell. However, little is known
about how cells control spindle positioning in three-dimensional (3D) environments,
such as early mammalian embryos and a variety of adult tissues. Here, we use mouse
embryonic stem cells (ESCs), which grow in 3D colonies, as a model to investigate
division in 3D. We observe that, at the periphery of 3D colonies, ESCs display
high spindle mobility and divide asymmetrically. Our data suggest that enhanced
spindle movements are due to unequal distribution of the cell–cell junction protein
E-cadherin between future daughter cells. Interestingly, when cells progress towards
differentiation, division becomes more symmetric, with more elongated shapes in
metaphase and enhanced cortical NuMA recruitment in anaphase. Altogether, this
study suggests that in 3D contexts, the geometry of the cell and its contacts
with neighbors control division orientation and symmetry.
acknowledgement: We would like to thank the entire Paluch and Baum laboratories at
the MRC-LMCB and the Chalut lab at the Cambridge SCI for discussions and feedback
throughout the project, and the MRC-LMCB microscopy platform, in particular Andrew
Vaughan, for technical support.
article_number: jcs255018
article_processing_charge: Yes (in subscription journal)
article_type: original
author:
- first_name: Agathe
full_name: Chaigne, Agathe
last_name: Chaigne
- first_name: Matthew B.
full_name: Smith, Matthew B.
last_name: Smith
- first_name: R. L.
full_name: Cavestany, R. L.
last_name: Cavestany
- first_name: Edouard B
full_name: Hannezo, Edouard B
id: 3A9DB764-F248-11E8-B48F-1D18A9856A87
last_name: Hannezo
orcid: 0000-0001-6005-1561
- first_name: Kevin J.
full_name: Chalut, Kevin J.
last_name: Chalut
- first_name: Ewa K.
full_name: Paluch, Ewa K.
last_name: Paluch
citation:
ama: Chaigne A, Smith MB, Cavestany RL, Hannezo EB, Chalut KJ, Paluch EK. Three-dimensional
geometry controls division symmetry in stem cell colonies. Journal of Cell
Science. 2021;134(14). doi:10.1242/jcs.255018
apa: Chaigne, A., Smith, M. B., Cavestany, R. L., Hannezo, E. B., Chalut, K. J.,
& Paluch, E. K. (2021). Three-dimensional geometry controls division symmetry
in stem cell colonies. Journal of Cell Science. The Company of Biologists.
https://doi.org/10.1242/jcs.255018
chicago: Chaigne, Agathe, Matthew B. Smith, R. L. Cavestany, Edouard B Hannezo,
Kevin J. Chalut, and Ewa K. Paluch. “Three-Dimensional Geometry Controls Division
Symmetry in Stem Cell Colonies.” Journal of Cell Science. The Company of
Biologists, 2021. https://doi.org/10.1242/jcs.255018.
ieee: A. Chaigne, M. B. Smith, R. L. Cavestany, E. B. Hannezo, K. J. Chalut, and
E. K. Paluch, “Three-dimensional geometry controls division symmetry in stem cell
colonies,” Journal of Cell Science, vol. 134, no. 14. The Company of Biologists,
2021.
ista: Chaigne A, Smith MB, Cavestany RL, Hannezo EB, Chalut KJ, Paluch EK. 2021.
Three-dimensional geometry controls division symmetry in stem cell colonies. Journal
of Cell Science. 134(14), jcs255018.
mla: Chaigne, Agathe, et al. “Three-Dimensional Geometry Controls Division Symmetry
in Stem Cell Colonies.” Journal of Cell Science, vol. 134, no. 14, jcs255018,
The Company of Biologists, 2021, doi:10.1242/jcs.255018.
short: A. Chaigne, M.B. Smith, R.L. Cavestany, E.B. Hannezo, K.J. Chalut, E.K. Paluch,
Journal of Cell Science 134 (2021).
date_created: 2021-08-22T22:01:20Z
date_published: 2021-07-01T00:00:00Z
date_updated: 2023-08-11T10:55:36Z
day: '01'
ddc:
- '570'
department:
- _id: EdHa
doi: 10.1242/jcs.255018
external_id:
isi:
- '000681395800008'
file:
- access_level: open_access
checksum: f086f9d7cb63b2474c01921cb060c513
content_type: application/pdf
creator: asandaue
date_created: 2021-08-23T07:32:20Z
date_updated: 2021-08-23T07:32:20Z
file_id: '9954'
file_name: 2021_JournalOfCellScience_Chaigne.pdf
file_size: 8651724
relation: main_file
success: 1
file_date_updated: 2021-08-23T07:32:20Z
has_accepted_license: '1'
intvolume: ' 134'
isi: 1
issue: '14'
language:
- iso: eng
month: '07'
oa: 1
oa_version: Published Version
publication: Journal of Cell Science
publication_identifier:
eissn:
- '14779137'
issn:
- '00219533'
publication_status: published
publisher: The Company of Biologists
quality_controlled: '1'
scopus_import: '1'
status: public
title: Three-dimensional geometry controls division symmetry in stem cell colonies
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: 134
year: '2021'
...
---
_id: '9908'
abstract:
- lang: eng
text: About eight million animal species are estimated to live on Earth, and all
except those belonging to one subphylum are invertebrates. Invertebrates are incredibly
diverse in their morphologies, life histories, and in the range of the ecological
niches that they occupy. A great variety of modes of reproduction and sex determination
systems is also observed among them, and their mosaic-distribution across the
phylogeny shows that transitions between them occur frequently and rapidly. Genetic
conflict in its various forms is a long-standing theory to explain what drives
those evolutionary transitions. Here, we review (1) the different modes of reproduction
among invertebrate species, highlighting sexual reproduction as the probable ancestral
state; (2) the paradoxical diversity of sex determination systems; (3) the different
types of genetic conflicts that could drive the evolution of such different systems.
article_number: '1136'
article_processing_charge: Yes
article_type: review
author:
- first_name: Marion A L
full_name: Picard, Marion A L
id: 2C921A7A-F248-11E8-B48F-1D18A9856A87
last_name: Picard
orcid: 0000-0002-8101-2518
- first_name: Beatriz
full_name: Vicoso, Beatriz
id: 49E1C5C6-F248-11E8-B48F-1D18A9856A87
last_name: Vicoso
orcid: 0000-0002-4579-8306
- first_name: Stéphanie
full_name: Bertrand, Stéphanie
last_name: Bertrand
- first_name: Hector
full_name: Escriva, Hector
last_name: Escriva
citation:
ama: Picard MAL, Vicoso B, Bertrand S, Escriva H. Diversity of modes of reproduction
and sex determination systems in invertebrates, and the putative contribution
of genetic conflict. Genes. 2021;12(8). doi:10.3390/genes12081136
apa: Picard, M. A. L., Vicoso, B., Bertrand, S., & Escriva, H. (2021). Diversity
of modes of reproduction and sex determination systems in invertebrates, and the
putative contribution of genetic conflict. Genes. MDPI. https://doi.org/10.3390/genes12081136
chicago: Picard, Marion A L, Beatriz Vicoso, Stéphanie Bertrand, and Hector Escriva.
“Diversity of Modes of Reproduction and Sex Determination Systems in Invertebrates,
and the Putative Contribution of Genetic Conflict.” Genes. MDPI, 2021.
https://doi.org/10.3390/genes12081136.
ieee: M. A. L. Picard, B. Vicoso, S. Bertrand, and H. Escriva, “Diversity of modes
of reproduction and sex determination systems in invertebrates, and the putative
contribution of genetic conflict,” Genes, vol. 12, no. 8. MDPI, 2021.
ista: Picard MAL, Vicoso B, Bertrand S, Escriva H. 2021. Diversity of modes of reproduction
and sex determination systems in invertebrates, and the putative contribution
of genetic conflict. Genes. 12(8), 1136.
mla: Picard, Marion A. L., et al. “Diversity of Modes of Reproduction and Sex Determination
Systems in Invertebrates, and the Putative Contribution of Genetic Conflict.”
Genes, vol. 12, no. 8, 1136, MDPI, 2021, doi:10.3390/genes12081136.
short: M.A.L. Picard, B. Vicoso, S. Bertrand, H. Escriva, Genes 12 (2021).
date_created: 2021-08-15T22:01:27Z
date_published: 2021-08-01T00:00:00Z
date_updated: 2023-08-11T10:42:32Z
day: '01'
ddc:
- '570'
department:
- _id: BeVi
doi: 10.3390/genes12081136
ec_funded: 1
external_id:
isi:
- '000690475900001'
file:
- access_level: open_access
checksum: 744e60e56d290a96da3c91a9779f886f
content_type: application/pdf
creator: asandaue
date_created: 2021-08-16T09:49:35Z
date_updated: 2021-08-16T09:49:35Z
file_id: '9926'
file_name: 2021_Genes_Picard.pdf
file_size: 2297655
relation: main_file
success: 1
file_date_updated: 2021-08-16T09:49:35Z
has_accepted_license: '1'
intvolume: ' 12'
isi: 1
issue: '8'
language:
- iso: eng
month: '08'
oa: 1
oa_version: Published Version
project:
- _id: 250BDE62-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '715257'
name: Prevalence and Influence of Sexual Antagonism on Genome Evolution
publication: Genes
publication_identifier:
eissn:
- '20734425'
publication_status: published
publisher: MDPI
quality_controlled: '1'
scopus_import: '1'
status: public
title: Diversity of modes of reproduction and sex determination systems in invertebrates,
and the putative contribution of genetic conflict
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: 12
year: '2021'
...
---
_id: '9829'
abstract:
- lang: eng
text: In 2020, many in-person scientific events were canceled due to the COVID-19
pandemic, creating a vacuum in networking and knowledge exchange between scientists.
To fill this void in scientific communication, a group of early career nanocrystal
enthusiasts launched the virtual seminar series, News in Nanocrystals, in the
summer of 2020. By the end of the year, the series had attracted over 850 participants
from 46 countries. In this Nano Focus, we describe the process of organizing the
News in Nanocrystals seminar series; discuss its growth, emphasizing what the
organizers have learned in terms of diversity and accessibility; and provide an
outlook for the next steps and future opportunities. This summary and analysis
of experiences and learned lessons are intended to inform the broader scientific
community, especially those who are looking for avenues to continue fostering
discussion and scientific engagement virtually, both during the pandemic and after.
acknowledgement: K. E. Shulenberger, M. D. Klein, T. Šverko, and H. R. Keller would
like to thank Professors Moungi Bawendi (MIT) and Gordana Dukovic (CU Boulder) for
their feedback and support of the News in Nanocrystals initiative. The authors thank
Madison Jilek (CU Boulder) and Dhananjeya Kumaar (ETH Zurich) for their help in
the organization of the seminar, and Professors Brandi Cossairt (University of Washington)
and Gordana Dukovic for their feedback on an earlier version of this manuscript.
The authors thank all the seminar speakers and attendees for their interest and
continuing participation in the seminar series.
article_processing_charge: No
article_type: original
author:
- first_name: Dmitry
full_name: Baranov, Dmitry
last_name: Baranov
- first_name: Tara
full_name: Šverko, Tara
last_name: Šverko
- first_name: Taylor
full_name: Moot, Taylor
last_name: Moot
- first_name: Helena R.
full_name: Keller, Helena R.
last_name: Keller
- first_name: Megan D.
full_name: Klein, Megan D.
last_name: Klein
- first_name: E. K.
full_name: Vishnu, E. K.
last_name: Vishnu
- first_name: Daniel
full_name: Balazs, Daniel
id: 302BADF6-85FC-11EA-9E3B-B9493DDC885E
last_name: Balazs
orcid: 0000-0001-7597-043X
- first_name: Katherine E.
full_name: Shulenberger, Katherine E.
last_name: Shulenberger
citation:
ama: 'Baranov D, Šverko T, Moot T, et al. News in Nanocrystals seminar: Self-assembly
of early career researchers toward globally accessible nanoscience. ACS Nano.
2021;15(7):10743–10747. doi:10.1021/acsnano.1c03276'
apa: 'Baranov, D., Šverko, T., Moot, T., Keller, H. R., Klein, M. D., Vishnu, E.
K., … Shulenberger, K. E. (2021). News in Nanocrystals seminar: Self-assembly
of early career researchers toward globally accessible nanoscience. ACS Nano.
American Chemical Society. https://doi.org/10.1021/acsnano.1c03276'
chicago: 'Baranov, Dmitry, Tara Šverko, Taylor Moot, Helena R. Keller, Megan D.
Klein, E. K. Vishnu, Daniel Balazs, and Katherine E. Shulenberger. “News in Nanocrystals
Seminar: Self-Assembly of Early Career Researchers toward Globally Accessible
Nanoscience.” ACS Nano. American Chemical Society, 2021. https://doi.org/10.1021/acsnano.1c03276.'
ieee: 'D. Baranov et al., “News in Nanocrystals seminar: Self-assembly of
early career researchers toward globally accessible nanoscience,” ACS Nano,
vol. 15, no. 7. American Chemical Society, pp. 10743–10747, 2021.'
ista: 'Baranov D, Šverko T, Moot T, Keller HR, Klein MD, Vishnu EK, Balazs D, Shulenberger
KE. 2021. News in Nanocrystals seminar: Self-assembly of early career researchers
toward globally accessible nanoscience. ACS Nano. 15(7), 10743–10747.'
mla: 'Baranov, Dmitry, et al. “News in Nanocrystals Seminar: Self-Assembly of Early
Career Researchers toward Globally Accessible Nanoscience.” ACS Nano, vol.
15, no. 7, American Chemical Society, 2021, pp. 10743–10747, doi:10.1021/acsnano.1c03276.'
short: D. Baranov, T. Šverko, T. Moot, H.R. Keller, M.D. Klein, E.K. Vishnu, D.
Balazs, K.E. Shulenberger, ACS Nano 15 (2021) 10743–10747.
date_created: 2021-08-08T22:01:31Z
date_published: 2021-07-06T00:00:00Z
date_updated: 2023-08-11T10:55:08Z
day: '06'
department:
- _id: MaIb
doi: 10.1021/acsnano.1c03276
external_id:
isi:
- '000679406500002'
pmid:
- '34228432'
intvolume: ' 15'
isi: 1
issue: '7'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.1021/acsnano.1c03276
month: '07'
oa: 1
oa_version: Published Version
page: 10743–10747
pmid: 1
publication: ACS Nano
publication_identifier:
eissn:
- 1936086X
issn:
- '19360851'
publication_status: published
publisher: American Chemical Society
quality_controlled: '1'
scopus_import: '1'
status: public
title: 'News in Nanocrystals seminar: Self-assembly of early career researchers toward
globally accessible nanoscience'
type: journal_article
user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
volume: 15
year: '2021'
...
---
_id: '13057'
abstract:
- lang: eng
text: 'This dataset comprises all data shown in the figures of the submitted article
"Geometric superinductance qubits: Controlling phase delocalization across a single
Josephson junction". Additional raw data are available from the corresponding
author on reasonable request.'
article_processing_charge: No
author:
- first_name: Matilda
full_name: Peruzzo, Matilda
id: 3F920B30-F248-11E8-B48F-1D18A9856A87
last_name: Peruzzo
orcid: 0000-0002-3415-4628
- first_name: Farid
full_name: Hassani, Farid
id: 2AED110C-F248-11E8-B48F-1D18A9856A87
last_name: Hassani
orcid: 0000-0001-6937-5773
- first_name: Grisha
full_name: Szep, Grisha
last_name: Szep
- first_name: Andrea
full_name: Trioni, Andrea
id: 42F71B44-F248-11E8-B48F-1D18A9856A87
last_name: Trioni
- first_name: Elena
full_name: Redchenko, Elena
id: 2C21D6E8-F248-11E8-B48F-1D18A9856A87
last_name: Redchenko
- first_name: Martin
full_name: Zemlicka, Martin
id: 2DCF8DE6-F248-11E8-B48F-1D18A9856A87
last_name: Zemlicka
- first_name: Johannes M
full_name: Fink, Johannes M
id: 4B591CBA-F248-11E8-B48F-1D18A9856A87
last_name: Fink
orcid: 0000-0001-8112-028X
citation:
ama: 'Peruzzo M, Hassani F, Szep G, et al. Geometric superinductance qubits: Controlling
phase delocalization across a single Josephson junction. 2021. doi:10.5281/ZENODO.5592103'
apa: 'Peruzzo, M., Hassani, F., Szep, G., Trioni, A., Redchenko, E., Zemlicka, M.,
& Fink, J. M. (2021). Geometric superinductance qubits: Controlling phase
delocalization across a single Josephson junction. Zenodo. https://doi.org/10.5281/ZENODO.5592103'
chicago: 'Peruzzo, Matilda, Farid Hassani, Grisha Szep, Andrea Trioni, Elena Redchenko,
Martin Zemlicka, and Johannes M Fink. “Geometric Superinductance Qubits: Controlling
Phase Delocalization across a Single Josephson Junction.” Zenodo, 2021. https://doi.org/10.5281/ZENODO.5592103.'
ieee: 'M. Peruzzo et al., “Geometric superinductance qubits: Controlling
phase delocalization across a single Josephson junction.” Zenodo, 2021.'
ista: 'Peruzzo M, Hassani F, Szep G, Trioni A, Redchenko E, Zemlicka M, Fink JM.
2021. Geometric superinductance qubits: Controlling phase delocalization across
a single Josephson junction, Zenodo, 10.5281/ZENODO.5592103.'
mla: 'Peruzzo, Matilda, et al. Geometric Superinductance Qubits: Controlling
Phase Delocalization across a Single Josephson Junction. Zenodo, 2021, doi:10.5281/ZENODO.5592103.'
short: M. Peruzzo, F. Hassani, G. Szep, A. Trioni, E. Redchenko, M. Zemlicka, J.M.
Fink, (2021).
date_created: 2023-05-23T13:42:27Z
date_published: 2021-10-22T00:00:00Z
date_updated: 2023-08-11T10:44:21Z
day: '22'
ddc:
- '530'
department:
- _id: JoFi
doi: 10.5281/ZENODO.5592103
main_file_link:
- open_access: '1'
url: https://doi.org/10.5281/zenodo.5592104
month: '10'
oa: 1
oa_version: Published Version
publisher: Zenodo
related_material:
record:
- id: '9928'
relation: used_in_publication
status: public
status: public
title: 'Geometric superinductance qubits: Controlling phase delocalization across
a single Josephson junction'
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_reference
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
year: '2021'
...
---
_id: '9985'
abstract:
- lang: eng
text: AMPA receptor (AMPAR) abundance and positioning at excitatory synapses regulates
the strength of transmission. Changes in AMPAR localisation can enact synaptic
plasticity, allowing long-term information storage, and is therefore tightly controlled.
Multiple mechanisms regulating AMPAR synaptic anchoring have been described, but
with limited coherence or comparison between reports, our understanding of this
process is unclear. Here, combining synaptic recordings from mouse hippocampal
slices and super-resolution imaging in dissociated cultures, we compare the contributions
of three AMPAR interaction domains controlling transmission at hippocampal CA1
synapses. We show that the AMPAR C-termini play only a modulatory role, whereas
the extracellular N-terminal domain (NTD) and PDZ interactions of the auxiliary
subunit TARP γ8 are both crucial, and each is sufficient to maintain transmission.
Our data support a model in which γ8 accumulates AMPARs at the postsynaptic density,
where the NTD further tunes their positioning. This interplay between cytosolic
(TARP γ8) and synaptic cleft (NTD) interactions provides versatility to regulate
synaptic transmission and plasticity.
acknowledgement: The authors are very grateful to Andrew Penn for advice and discussions
on surface receptor labelling in slice tissue, dissociated culture transfection,
and for providing tdTomato and BirAER expression plasmids. This work would not have
been possible without support from the Biological Services teams at both the Laboratory
of Molecular Biology and Ares facilities. We are also very grateful to Nick Barry
and Jerome Boulanger of the LMB Light Microscopy facility for support with confocal
and STORM imaging and analysis, Junichi Takagi for providing scFv-Clasp expression
constructs, Veronica Chang for assistance with scFv-Clasp protein production, and
Nejc Kejzar for assistance with cluster analysis. We would like to thank Teru Nakagawa
and Ole Paulsen for critical reading of the manuscript and constructive feedback.
This work was supported by grants from the Medical Research Council (MC_U105174197)
and BBSRC (BB/N002113/1).
article_number: '5083'
article_processing_charge: Yes
article_type: original
author:
- first_name: Jake
full_name: Watson, Jake
id: 63836096-4690-11EA-BD4E-32803DDC885E
last_name: Watson
orcid: 0000-0002-8698-3823
- first_name: Alexandra
full_name: Pinggera, Alexandra
last_name: Pinggera
- first_name: Hinze
full_name: Ho, Hinze
last_name: Ho
- first_name: Ingo H.
full_name: Greger, Ingo H.
last_name: Greger
citation:
ama: Watson J, Pinggera A, Ho H, Greger IH. AMPA receptor anchoring at CA1 synapses
is determined by N-terminal domain and TARP γ8 interactions. Nature Communications.
2021;12(1). doi:10.1038/s41467-021-25281-4
apa: Watson, J., Pinggera, A., Ho, H., & Greger, I. H. (2021). AMPA receptor
anchoring at CA1 synapses is determined by N-terminal domain and TARP γ8 interactions.
Nature Communications. Nature Publishing Group. https://doi.org/10.1038/s41467-021-25281-4
chicago: Watson, Jake, Alexandra Pinggera, Hinze Ho, and Ingo H. Greger. “AMPA Receptor
Anchoring at CA1 Synapses Is Determined by N-Terminal Domain and TARP Γ8 Interactions.”
Nature Communications. Nature Publishing Group, 2021. https://doi.org/10.1038/s41467-021-25281-4.
ieee: J. Watson, A. Pinggera, H. Ho, and I. H. Greger, “AMPA receptor anchoring
at CA1 synapses is determined by N-terminal domain and TARP γ8 interactions,”
Nature Communications, vol. 12, no. 1. Nature Publishing Group, 2021.
ista: Watson J, Pinggera A, Ho H, Greger IH. 2021. AMPA receptor anchoring at CA1
synapses is determined by N-terminal domain and TARP γ8 interactions. Nature Communications.
12(1), 5083.
mla: Watson, Jake, et al. “AMPA Receptor Anchoring at CA1 Synapses Is Determined
by N-Terminal Domain and TARP Γ8 Interactions.” Nature Communications,
vol. 12, no. 1, 5083, Nature Publishing Group, 2021, doi:10.1038/s41467-021-25281-4.
short: J. Watson, A. Pinggera, H. Ho, I.H. Greger, Nature Communications 12 (2021).
date_created: 2021-09-05T22:01:23Z
date_published: 2021-08-23T00:00:00Z
date_updated: 2023-08-11T11:07:51Z
day: '23'
ddc:
- '612'
department:
- _id: PeJo
doi: 10.1038/s41467-021-25281-4
external_id:
isi:
- '000687672000006'
pmid:
- '34426577 '
file:
- access_level: open_access
checksum: 1bf4f6a561f96bc426d754de9cb57710
content_type: application/pdf
creator: cchlebak
date_created: 2021-09-08T12:57:06Z
date_updated: 2021-09-08T12:57:06Z
file_id: '9991'
file_name: 2021_NatureCommunications_Watson.pdf
file_size: 18310502
relation: main_file
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file_date_updated: 2021-09-08T12:57:06Z
has_accepted_license: '1'
intvolume: ' 12'
isi: 1
issue: '1'
language:
- iso: eng
month: '08'
oa: 1
oa_version: Published Version
pmid: 1
publication: Nature Communications
publication_identifier:
eissn:
- 2041-1723
publication_status: published
publisher: Nature Publishing Group
quality_controlled: '1'
scopus_import: '1'
status: public
title: AMPA receptor anchoring at CA1 synapses is determined by N-terminal domain
and TARP γ8 interactions
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: 12
year: '2021'
...
---
_id: '9981'
abstract:
- lang: eng
text: "The numerical simulation of dynamical phenomena in interacting quantum systems
is a notoriously hard problem. Although a number of promising numerical methods
exist, they often have limited applicability due to the growth of entanglement
or the presence of the so-called sign problem. In this work, we develop an importance
sampling scheme for the simulation of quantum spin dynamics, building on a recent
approach mapping quantum spin systems to classical stochastic processes. The importance
sampling scheme is based on identifying the classical trajectory that yields the
largest contribution to a given quantum observable. An exact transformation is
then carried out to preferentially sample trajectories that are close to the dominant
one. We demonstrate that this approach is capable of reducing the temporal growth
of fluctuations in the stochastic quantities, thus extending the range of accessible
times and system sizes compared to direct sampling. We discuss advantages and
limitations of the proposed approach, outlining directions\r\nfor further developments."
article_number: '048'
article_processing_charge: No
article_type: original
author:
- first_name: Stefano
full_name: De Nicola, Stefano
id: 42832B76-F248-11E8-B48F-1D18A9856A87
last_name: De Nicola
orcid: 0000-0002-4842-6671
citation:
ama: De Nicola S. Importance sampling scheme for the stochastic simulation of quantum
spin dynamics. SciPost Physics. 2021;11(3). doi:10.21468/scipostphys.11.3.048
apa: De Nicola, S. (2021). Importance sampling scheme for the stochastic simulation
of quantum spin dynamics. SciPost Physics. SciPost. https://doi.org/10.21468/scipostphys.11.3.048
chicago: De Nicola, Stefano. “Importance Sampling Scheme for the Stochastic Simulation
of Quantum Spin Dynamics.” SciPost Physics. SciPost, 2021. https://doi.org/10.21468/scipostphys.11.3.048.
ieee: S. De Nicola, “Importance sampling scheme for the stochastic simulation of
quantum spin dynamics,” SciPost Physics, vol. 11, no. 3. SciPost, 2021.
ista: De Nicola S. 2021. Importance sampling scheme for the stochastic simulation
of quantum spin dynamics. SciPost Physics. 11(3), 048.
mla: De Nicola, Stefano. “Importance Sampling Scheme for the Stochastic Simulation
of Quantum Spin Dynamics.” SciPost Physics, vol. 11, no. 3, 048, SciPost,
2021, doi:10.21468/scipostphys.11.3.048.
short: S. De Nicola, SciPost Physics 11 (2021).
date_created: 2021-09-02T11:49:47Z
date_published: 2021-09-02T00:00:00Z
date_updated: 2023-08-11T10:59:29Z
day: '02'
ddc:
- '519'
department:
- _id: MaSe
doi: 10.21468/scipostphys.11.3.048
ec_funded: 1
external_id:
arxiv:
- '2103.16468'
isi:
- '000692534200001'
file:
- access_level: open_access
checksum: e4ec69d893e31811efc6093cb6ea8eb7
content_type: application/pdf
creator: cchlebak
date_created: 2021-09-02T14:05:43Z
date_updated: 2021-09-02T14:05:43Z
file_id: '9984'
file_name: 2021_SciPostPhys_DeNicola.pdf
file_size: 373833
relation: main_file
success: 1
file_date_updated: 2021-09-02T14:05:43Z
has_accepted_license: '1'
intvolume: ' 11'
isi: 1
issue: '3'
keyword:
- General Physics and Astronomy
language:
- iso: eng
month: '09'
oa: 1
oa_version: Published Version
project:
- _id: 260C2330-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '754411'
name: ISTplus - Postdoctoral Fellowships
publication: SciPost Physics
publication_identifier:
eissn:
- 2666-9366
issn:
- 2542-4653
publication_status: published
publisher: SciPost
quality_controlled: '1'
status: public
title: Importance sampling scheme for the stochastic simulation of quantum spin dynamics
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: journal_article
user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
volume: 11
year: '2021'
...
---
_id: '9960'
abstract:
- lang: eng
text: The control of many-body quantum dynamics in complex systems is a key challenge
in the quest to reliably produce and manipulate large-scale quantum entangled
states. Recently, quench experiments in Rydberg atom arrays [Bluvstein et al.
Science 371, 1355 (2021)] demonstrated that coherent revivals associated with
quantum many-body scars can be stabilized by periodic driving, generating stable
subharmonic responses over a wide parameter regime. We analyze a simple, related
model where these phenomena originate from spatiotemporal ordering in an effective
Floquet unitary, corresponding to discrete time-crystalline behavior in a prethermal
regime. Unlike conventional discrete time crystals, the subharmonic response exists
only for Néel-like initial states, associated with quantum scars. We predict robustness
to perturbations and identify emergent timescales that could be observed in future
experiments. Our results suggest a route to controlling entanglement in interacting
quantum systems by combining periodic driving with many-body scars.
acknowledgement: We thank Dmitry Abanin, Ehud Altman, Iris Cong, Sepehr Ebadi, Alex
Keesling, Harry Levine, Ahmed Omran, Hannes Pichler, Rhine Samajdar, Guilia Semeghini,
Tout Wang, Norman Yao, and Harry Zhou or stimulating discussions. We acknowledge
support from the Center for Ultracold Atoms, the National Science Foundation, the
Vannevar Bush Faculty Fellowship, the U.S. Department of Energy, the Army Research
Office MURI, and the DARPA ONISQ program (M. L., N. M, W. W. H., D. B.); the European
Research Council (ERC) under the European Union’s Horizon 2020 Research and Innovation
Programme Grant Agreement No. 850899 (A. M. and M. S.); the Department of Energy
Computational Science Graduate Fellowship under Awards No. DESC0021110 (N. M.);
the Moore Foundation EPiQS initiative Grant No. GBMF4306, the National University
of Singapore (NUS) Development Grant AY2019/2020 and the Stanford Institute for
Theoretical Physics (W. W. H.); the NSF Graduate Research Fellowship Program (Grant
No. DGE1745303) and The Fannie and John Hertz Foundation (D. B.); the Miller Institute
for Basic Research in Science (S. C.); DOE Quantum Systems Accelerator – Contract
No. 7568717; and DOE Programmable Quantum Simulators for Lattice Gauge Theories
and Gauge-Gravity Correspondence – Grant No. DE-SC0021013.
article_number: '090602'
article_processing_charge: No
article_type: letter_note
author:
- first_name: N.
full_name: Maskara, N.
last_name: Maskara
- first_name: Alexios
full_name: Michailidis, Alexios
id: 36EBAD38-F248-11E8-B48F-1D18A9856A87
last_name: Michailidis
orcid: 0000-0002-8443-1064
- first_name: W. W.
full_name: Ho, W. W.
last_name: Ho
- first_name: D.
full_name: Bluvstein, D.
last_name: Bluvstein
- first_name: S.
full_name: Choi, S.
last_name: Choi
- first_name: M. D.
full_name: Lukin, M. D.
last_name: Lukin
- first_name: Maksym
full_name: Serbyn, Maksym
id: 47809E7E-F248-11E8-B48F-1D18A9856A87
last_name: Serbyn
orcid: 0000-0002-2399-5827
citation:
ama: 'Maskara N, Michailidis A, Ho WW, et al. Discrete time-crystalline order enabled
by quantum many-body scars: Entanglement steering via periodic driving. Physical
Review Letters. 2021;127(9). doi:10.1103/PhysRevLett.127.090602'
apa: 'Maskara, N., Michailidis, A., Ho, W. W., Bluvstein, D., Choi, S., Lukin, M.
D., & Serbyn, M. (2021). Discrete time-crystalline order enabled by quantum
many-body scars: Entanglement steering via periodic driving. Physical Review
Letters. American Physical Society. https://doi.org/10.1103/PhysRevLett.127.090602'
chicago: 'Maskara, N., Alexios Michailidis, W. W. Ho, D. Bluvstein, S. Choi, M.
D. Lukin, and Maksym Serbyn. “Discrete Time-Crystalline Order Enabled by Quantum
Many-Body Scars: Entanglement Steering via Periodic Driving.” Physical Review
Letters. American Physical Society, 2021. https://doi.org/10.1103/PhysRevLett.127.090602.'
ieee: 'N. Maskara et al., “Discrete time-crystalline order enabled by quantum
many-body scars: Entanglement steering via periodic driving,” Physical Review
Letters, vol. 127, no. 9. American Physical Society, 2021.'
ista: 'Maskara N, Michailidis A, Ho WW, Bluvstein D, Choi S, Lukin MD, Serbyn M.
2021. Discrete time-crystalline order enabled by quantum many-body scars: Entanglement
steering via periodic driving. Physical Review Letters. 127(9), 090602.'
mla: 'Maskara, N., et al. “Discrete Time-Crystalline Order Enabled by Quantum Many-Body
Scars: Entanglement Steering via Periodic Driving.” Physical Review Letters,
vol. 127, no. 9, 090602, American Physical Society, 2021, doi:10.1103/PhysRevLett.127.090602.'
short: N. Maskara, A. Michailidis, W.W. Ho, D. Bluvstein, S. Choi, M.D. Lukin, M.
Serbyn, Physical Review Letters 127 (2021).
date_created: 2021-08-28T08:08:58Z
date_published: 2021-08-27T00:00:00Z
date_updated: 2023-08-11T10:57:51Z
day: '27'
department:
- _id: MaSe
doi: 10.1103/PhysRevLett.127.090602
ec_funded: 1
external_id:
arxiv:
- '2102.13160'
isi:
- '000692200100002'
intvolume: ' 127'
isi: 1
issue: '9'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/2102.13160
month: '08'
oa: 1
oa_version: Submitted Version
project:
- _id: 23841C26-32DE-11EA-91FC-C7463DDC885E
call_identifier: H2020
grant_number: '850899'
name: 'Non-Ergodic Quantum Matter: Universality, Dynamics and Control'
publication: Physical Review Letters
publication_identifier:
eissn:
- 1079-7114
issn:
- 0031-9007
publication_status: published
publisher: American Physical Society
quality_controlled: '1'
status: public
title: 'Discrete time-crystalline order enabled by quantum many-body scars: Entanglement
steering via periodic driving'
type: journal_article
user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
volume: 127
year: '2021'
...
---
_id: '9961'
abstract:
- lang: eng
text: The notion of Thouless energy plays a central role in the theory of Anderson
localization. We investigate and compare the scaling of Thouless energy across
the many-body localization (MBL) transition in a Floquet model. We use a combination
of methods that are reliable on the ergodic side of the transition (e.g., spectral
form factor) and methods that work on the MBL side (e.g., typical matrix elements
of local operators) to obtain a complete picture of the Thouless energy behavior
across the transition. On the ergodic side, Thouless energy decreases slowly with
the system size, while at the transition it becomes comparable to the level spacing.
Different probes yield consistent estimates of Thouless energy in their overlapping
regime of applicability, giving the location of the transition point nearly free
of finite-size drift. This work establishes a connection between different definitions
of Thouless energy in a many-body setting and yields insights into the MBL transition
in Floquet systems.
acknowledgement: "We thank S. Garratt for useful comments on the manuscript. This
work was supported by the Swiss National Science Foundation (M. Sonner and D.A.A.)
and by the European Research Council (ERC) under the European Union’s Horizon 2020
research and innovation program (M. Serbyn, Grant Agreement No. 850899, and D.A.A.,
Grant Agreement No. 864597). Z.P. acknowledges support from EPSRC Grant No. EP/R020612/1
and from Leverhulme Trust Research Leadership Award No. RL-2019-015. The computations
were performed on the Baobab cluster of the University\r\nof Geneva."
article_number: L081112
article_processing_charge: No
article_type: letter_note
author:
- first_name: Michael
full_name: Sonner, Michael
last_name: Sonner
- first_name: Maksym
full_name: Serbyn, Maksym
id: 47809E7E-F248-11E8-B48F-1D18A9856A87
last_name: Serbyn
orcid: 0000-0002-2399-5827
- first_name: Zlatko
full_name: Papić, Zlatko
last_name: Papić
- first_name: Dmitry A.
full_name: Abanin, Dmitry A.
last_name: Abanin
citation:
ama: Sonner M, Serbyn M, Papić Z, Abanin DA. Thouless energy across the many-body
localization transition in Floquet systems. Physical Review B. 2021;104(8).
doi:10.1103/PhysRevB.104.L081112
apa: Sonner, M., Serbyn, M., Papić, Z., & Abanin, D. A. (2021). Thouless energy
across the many-body localization transition in Floquet systems. Physical Review
B. American Physical Society. https://doi.org/10.1103/PhysRevB.104.L081112
chicago: Sonner, Michael, Maksym Serbyn, Zlatko Papić, and Dmitry A. Abanin. “Thouless
Energy across the Many-Body Localization Transition in Floquet Systems.” Physical
Review B. American Physical Society, 2021. https://doi.org/10.1103/PhysRevB.104.L081112.
ieee: M. Sonner, M. Serbyn, Z. Papić, and D. A. Abanin, “Thouless energy across
the many-body localization transition in Floquet systems,” Physical Review
B, vol. 104, no. 8. American Physical Society, 2021.
ista: Sonner M, Serbyn M, Papić Z, Abanin DA. 2021. Thouless energy across the many-body
localization transition in Floquet systems. Physical Review B. 104(8), L081112.
mla: Sonner, Michael, et al. “Thouless Energy across the Many-Body Localization
Transition in Floquet Systems.” Physical Review B, vol. 104, no. 8, L081112,
American Physical Society, 2021, doi:10.1103/PhysRevB.104.L081112.
short: M. Sonner, M. Serbyn, Z. Papić, D.A. Abanin, Physical Review B 104 (2021).
date_created: 2021-08-28T16:44:55Z
date_published: 2021-08-15T00:00:00Z
date_updated: 2023-08-11T10:57:09Z
day: '15'
department:
- _id: MaSe
doi: 10.1103/PhysRevB.104.L081112
ec_funded: 1
external_id:
arxiv:
- '2012.15676'
isi:
- '000689734500009'
intvolume: ' 104'
isi: 1
issue: '8'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/2012.15676
month: '08'
oa: 1
oa_version: Submitted Version
project:
- _id: 23841C26-32DE-11EA-91FC-C7463DDC885E
call_identifier: H2020
grant_number: '850899'
name: 'Non-Ergodic Quantum Matter: Universality, Dynamics and Control'
publication: Physical Review B
publication_identifier:
eissn:
- 2469-9969
issn:
- 2469-9950
publication_status: published
publisher: American Physical Society
quality_controlled: '1'
status: public
title: Thouless energy across the many-body localization transition in Floquet systems
type: journal_article
user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
volume: 104
year: '2021'
...
---
_id: '9957'
abstract:
- lang: eng
text: The reflectance field of a face describes the reflectance properties responsible
for complex lighting effects including diffuse, specular, inter-reflection and
self shadowing. Most existing methods for estimating the face reflectance from
a monocular image assume faces to be diffuse with very few approaches adding a
specular component. This still leaves out important perceptual aspects of reflectance
as higher-order global illumination effects and self-shadowing are not modeled.
We present a new neural representation for face reflectance where we can estimate
all components of the reflectance responsible for the final appearance from a
single monocular image. Instead of modeling each component of the reflectance
separately using parametric models, our neural representation allows us to generate
a basis set of faces in a geometric deformation-invariant space, parameterized
by the input light direction, viewpoint and face geometry. We learn to reconstruct
this reflectance field of a face just from a monocular image, which can be used
to render the face from any viewpoint in any light condition. Our method is trained
on a light-stage training dataset, which captures 300 people illuminated with
150 light conditions from 8 viewpoints. We show that our method outperforms existing
monocular reflectance reconstruction methods, in terms of photorealism due to
better capturing of physical premitives, such as sub-surface scattering, specularities,
self-shadows and other higher-order effects.
acknowledgement: "We thank Tarun Yenamandra and Duarte David for helping us with the
comparisons. This work was supported by the\r\nERC Consolidator Grant 4DReply (770784).
We also acknowledge support from InterDigital."
article_processing_charge: No
author:
- first_name: Mallikarjun
full_name: B R, Mallikarjun
last_name: B R
- first_name: Ayush
full_name: Tewari, Ayush
last_name: Tewari
- first_name: Tae-Hyun
full_name: Oh, Tae-Hyun
last_name: Oh
- first_name: Tim
full_name: Weyrich, Tim
last_name: Weyrich
- first_name: Bernd
full_name: Bickel, Bernd
id: 49876194-F248-11E8-B48F-1D18A9856A87
last_name: Bickel
orcid: 0000-0001-6511-9385
- first_name: Hans-Peter
full_name: Seidel, Hans-Peter
last_name: Seidel
- first_name: Hanspeter
full_name: Pfister, Hanspeter
last_name: Pfister
- first_name: Wojciech
full_name: Matusik, Wojciech
last_name: Matusik
- first_name: Mohamed
full_name: Elgharib, Mohamed
last_name: Elgharib
- first_name: Christian
full_name: Theobalt, Christian
last_name: Theobalt
citation:
ama: 'B R M, Tewari A, Oh T-H, et al. Monocular reconstruction of neural face reflectance
fields. In: Proceedings of the IEEE Computer Society Conference on Computer
Vision and Pattern Recognition. IEEE; 2021:4791-4800. doi:10.1109/CVPR46437.2021.00476'
apa: 'B R, M., Tewari, A., Oh, T.-H., Weyrich, T., Bickel, B., Seidel, H.-P., …
Theobalt, C. (2021). Monocular reconstruction of neural face reflectance fields.
In Proceedings of the IEEE Computer Society Conference on Computer Vision and
Pattern Recognition (pp. 4791–4800). Nashville, TN, United States; Virtual:
IEEE. https://doi.org/10.1109/CVPR46437.2021.00476'
chicago: B R, Mallikarjun, Ayush Tewari, Tae-Hyun Oh, Tim Weyrich, Bernd Bickel,
Hans-Peter Seidel, Hanspeter Pfister, Wojciech Matusik, Mohamed Elgharib, and
Christian Theobalt. “Monocular Reconstruction of Neural Face Reflectance Fields.”
In Proceedings of the IEEE Computer Society Conference on Computer Vision and
Pattern Recognition, 4791–4800. IEEE, 2021. https://doi.org/10.1109/CVPR46437.2021.00476.
ieee: M. B R et al., “Monocular reconstruction of neural face reflectance
fields,” in Proceedings of the IEEE Computer Society Conference on Computer
Vision and Pattern Recognition, Nashville, TN, United States; Virtual, 2021,
pp. 4791–4800.
ista: 'B R M, Tewari A, Oh T-H, Weyrich T, Bickel B, Seidel H-P, Pfister H, Matusik
W, Elgharib M, Theobalt C. 2021. Monocular reconstruction of neural face reflectance
fields. Proceedings of the IEEE Computer Society Conference on Computer Vision
and Pattern Recognition. CVPR: Conference on Computer Vision and Pattern Recognition,
4791–4800.'
mla: B R, Mallikarjun, et al. “Monocular Reconstruction of Neural Face Reflectance
Fields.” Proceedings of the IEEE Computer Society Conference on Computer Vision
and Pattern Recognition, IEEE, 2021, pp. 4791–800, doi:10.1109/CVPR46437.2021.00476.
short: M. B R, A. Tewari, T.-H. Oh, T. Weyrich, B. Bickel, H.-P. Seidel, H. Pfister,
W. Matusik, M. Elgharib, C. Theobalt, in:, Proceedings of the IEEE Computer Society
Conference on Computer Vision and Pattern Recognition, IEEE, 2021, pp. 4791–4800.
conference:
end_date: 2021-06-25
location: Nashville, TN, United States; Virtual
name: 'CVPR: Conference on Computer Vision and Pattern Recognition'
start_date: 2021-06-20
date_created: 2021-08-24T06:03:00Z
date_published: 2021-09-01T00:00:00Z
date_updated: 2023-08-11T11:08:35Z
day: '01'
ddc:
- '000'
department:
- _id: BeBi
doi: 10.1109/CVPR46437.2021.00476
external_id:
arxiv:
- '2008.10247'
isi:
- '000739917304096'
file:
- access_level: open_access
checksum: 961db0bde76dd87cf833930080bb9f38
content_type: application/pdf
creator: bbickel
date_created: 2021-08-24T06:02:15Z
date_updated: 2021-08-24T06:02:15Z
file_id: '9958'
file_name: R_Monocular_Reconstruction_of_Neural_Face_Reflectance_Fields_CVPR_2021_paper[1].pdf
file_size: 4746649
relation: main_file
file_date_updated: 2021-08-24T06:02:15Z
has_accepted_license: '1'
isi: 1
language:
- iso: eng
month: '09'
oa: 1
oa_version: Preprint
page: 4791-4800
publication: Proceedings of the IEEE Computer Society Conference on Computer Vision
and Pattern Recognition
publication_identifier:
isbn:
- 978-166544509-2
issn:
- 1063-6919
publication_status: published
publisher: IEEE
quality_controlled: '1'
scopus_import: '1'
status: public
title: Monocular reconstruction of neural face reflectance fields
type: conference
user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
year: '2021'
...
---
_id: '9973'
abstract:
- lang: eng
text: In this article we introduce a complete gradient estimate for symmetric quantum
Markov semigroups on von Neumann algebras equipped with a normal faithful tracial
state, which implies semi-convexity of the entropy with respect to the recently
introduced noncommutative 2-Wasserstein distance. We show that this complete gradient
estimate is stable under tensor products and free products and establish its validity
for a number of examples. As an application we prove a complete modified logarithmic
Sobolev inequality with optimal constant for Poisson-type semigroups on free group
factors.
acknowledgement: Both authors would like to thank Jan Maas for fruitful discussions
and helpful comments.
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
- first_name: Haonan
full_name: Zhang, Haonan
id: D8F41E38-9E66-11E9-A9E2-65C2E5697425
last_name: Zhang
citation:
ama: Wirth M, Zhang H. Complete gradient estimates of quantum Markov semigroups.
Communications in Mathematical Physics. 2021;387:761–791. doi:10.1007/s00220-021-04199-4
apa: Wirth, M., & Zhang, H. (2021). Complete gradient estimates of quantum Markov
semigroups. Communications in Mathematical Physics. Springer Nature. https://doi.org/10.1007/s00220-021-04199-4
chicago: Wirth, Melchior, and Haonan Zhang. “Complete Gradient Estimates of Quantum
Markov Semigroups.” Communications in Mathematical Physics. Springer Nature,
2021. https://doi.org/10.1007/s00220-021-04199-4.
ieee: M. Wirth and H. Zhang, “Complete gradient estimates of quantum Markov semigroups,”
Communications in Mathematical Physics, vol. 387. Springer Nature, pp.
761–791, 2021.
ista: Wirth M, Zhang H. 2021. Complete gradient estimates of quantum Markov semigroups.
Communications in Mathematical Physics. 387, 761–791.
mla: Wirth, Melchior, and Haonan Zhang. “Complete Gradient Estimates of Quantum
Markov Semigroups.” Communications in Mathematical Physics, vol. 387, Springer
Nature, 2021, pp. 761–791, doi:10.1007/s00220-021-04199-4.
short: M. Wirth, H. Zhang, Communications in Mathematical Physics 387 (2021) 761–791.
date_created: 2021-08-30T10:07:44Z
date_published: 2021-08-30T00:00:00Z
date_updated: 2023-08-11T11:09:07Z
day: '30'
ddc:
- '621'
department:
- _id: JaMa
doi: 10.1007/s00220-021-04199-4
ec_funded: 1
external_id:
arxiv:
- '2007.13506'
isi:
- '000691214200001'
file:
- access_level: open_access
checksum: 8a602f916b1c2b0dc1159708b7cb204b
content_type: application/pdf
creator: cchlebak
date_created: 2021-09-08T07:34:24Z
date_updated: 2021-09-08T09:46:34Z
file_id: '9990'
file_name: 2021_CommunMathPhys_Wirth.pdf
file_size: 505971
relation: main_file
file_date_updated: 2021-09-08T09:46:34Z
has_accepted_license: '1'
intvolume: ' 387'
isi: 1
keyword:
- Mathematical Physics
- Statistical and Nonlinear Physics
language:
- iso: eng
month: '08'
oa: 1
oa_version: Published Version
page: 761–791
project:
- _id: B67AFEDC-15C9-11EA-A837-991A96BB2854
name: IST Austria Open Access Fund
- _id: 260C2330-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '754411'
name: ISTplus - Postdoctoral Fellowships
- _id: fc31cba2-9c52-11eb-aca3-ff467d239cd2
grant_number: F6504
name: Taming Complexity in Partial Differential Systems
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: Complete gradient estimates of quantum Markov semigroups
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: 387
year: '2021'
...
---
_id: '10000'
abstract:
- lang: eng
text: Inhibition or targeted deletion of histone deacetylase 3 (HDAC3) is neuroprotective
in a variety neurodegenerative conditions, including retinal ganglion cells (RGCs)
after acute optic nerve damage. Consistent with this, induced HDAC3 expression
in cultured cells shows selective toxicity to neurons. Despite an established
role for HDAC3 in neuronal pathology, little is known regarding the mechanism
of this pathology.
acknowledgement: 'The authors thank Joel Dietz for maintaining the mice used in this
study, Satoshi Kinoshita and the Translational Research Initiative in Pathology
Laboratory at the University of Wisconsin-Madison for cutting retinal sections analyzed
in this study, and Mark Banghart for statistical review of the data analysis. Supported
by National Eye Institute Grants R01 EY012223 (RWN), R01 EY030123 (RWN), R01 EY029809
(LWG), R01 EY029809 (LWG) and a Vision Research CORE grant P30 EY016665, NRSA grant
T32 GM081061, by an unrestricted research grant from Research to Prevent Blindness,
Inc., and by a University of Wisconsin-Madison Vilas Life Cycle award and the Frederick
A. Davis Research Chair (RWN). '
article_number: '14'
article_processing_charge: Yes
article_type: original
author:
- first_name: Heather M.
full_name: Schmitt, Heather M.
last_name: Schmitt
- first_name: Rachel L.
full_name: Fehrman, Rachel L.
last_name: Fehrman
- first_name: Margaret E
full_name: Maes, Margaret E
id: 3838F452-F248-11E8-B48F-1D18A9856A87
last_name: Maes
orcid: 0000-0001-9642-1085
- first_name: Huan
full_name: Yang, Huan
last_name: Yang
- first_name: Lian Wang
full_name: Guo, Lian Wang
last_name: Guo
- first_name: Cassandra L.
full_name: Schlamp, Cassandra L.
last_name: Schlamp
- first_name: Heather R.
full_name: Pelzel, Heather R.
last_name: Pelzel
- first_name: Robert W.
full_name: Nickells, Robert W.
last_name: Nickells
citation:
ama: Schmitt HM, Fehrman RL, Maes ME, et al. Increased susceptibility and intrinsic
apoptotic signaling in neurons by induced HDAC3 expression. Investigative Ophthalmology
and Visual Science. 2021;62(10). doi:10.1167/IOVS.62.10.14
apa: Schmitt, H. M., Fehrman, R. L., Maes, M. E., Yang, H., Guo, L. W., Schlamp,
C. L., … Nickells, R. W. (2021). Increased susceptibility and intrinsic apoptotic
signaling in neurons by induced HDAC3 expression. Investigative Ophthalmology
and Visual Science. Association for Research in Vision and Ophthalmology.
https://doi.org/10.1167/IOVS.62.10.14
chicago: Schmitt, Heather M., Rachel L. Fehrman, Margaret E Maes, Huan Yang, Lian
Wang Guo, Cassandra L. Schlamp, Heather R. Pelzel, and Robert W. Nickells. “Increased
Susceptibility and Intrinsic Apoptotic Signaling in Neurons by Induced HDAC3 Expression.”
Investigative Ophthalmology and Visual Science. Association for Research
in Vision and Ophthalmology, 2021. https://doi.org/10.1167/IOVS.62.10.14.
ieee: H. M. Schmitt et al., “Increased susceptibility and intrinsic apoptotic
signaling in neurons by induced HDAC3 expression,” Investigative Ophthalmology
and Visual Science, vol. 62, no. 10. Association for Research in Vision and
Ophthalmology, 2021.
ista: Schmitt HM, Fehrman RL, Maes ME, Yang H, Guo LW, Schlamp CL, Pelzel HR, Nickells
RW. 2021. Increased susceptibility and intrinsic apoptotic signaling in neurons
by induced HDAC3 expression. Investigative Ophthalmology and Visual Science. 62(10),
14.
mla: Schmitt, Heather M., et al. “Increased Susceptibility and Intrinsic Apoptotic
Signaling in Neurons by Induced HDAC3 Expression.” Investigative Ophthalmology
and Visual Science, vol. 62, no. 10, 14, Association for Research in Vision
and Ophthalmology, 2021, doi:10.1167/IOVS.62.10.14.
short: H.M. Schmitt, R.L. Fehrman, M.E. Maes, H. Yang, L.W. Guo, C.L. Schlamp, H.R.
Pelzel, R.W. Nickells, Investigative Ophthalmology and Visual Science 62 (2021).
date_created: 2021-09-12T22:01:23Z
date_published: 2021-08-16T00:00:00Z
date_updated: 2023-08-14T06:35:17Z
day: '16'
ddc:
- '570'
department:
- _id: SaSi
doi: 10.1167/IOVS.62.10.14
external_id:
isi:
- '000695230000014'
pmid:
- '34398198'
file:
- access_level: open_access
checksum: c430967746f653aa1ae84ee617f62b73
content_type: application/pdf
creator: dernst
date_created: 2022-05-13T07:40:15Z
date_updated: 2022-05-13T07:40:15Z
file_id: '11369'
file_name: 2021_IOVS_Schmitt.pdf
file_size: 19707796
relation: main_file
success: 1
file_date_updated: 2022-05-13T07:40:15Z
has_accepted_license: '1'
intvolume: ' 62'
isi: 1
issue: '10'
language:
- iso: eng
month: '08'
oa: 1
oa_version: Published Version
pmid: 1
publication: Investigative Ophthalmology and Visual Science
publication_identifier:
eissn:
- 1552-5783
issn:
- 0146-0404
publication_status: published
publisher: Association for Research in Vision and Ophthalmology
quality_controlled: '1'
scopus_import: '1'
status: public
title: Increased susceptibility and intrinsic apoptotic signaling in neurons by induced
HDAC3 expression
tmp:
image: /images/cc_by_nc_nd.png
legal_code_url: https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode
name: Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International
(CC BY-NC-ND 4.0)
short: CC BY-NC-ND (4.0)
type: journal_article
user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
volume: 62
year: '2021'
...
---
_id: '9998'
abstract:
- lang: eng
text: We define quantum equivariant K-theory of Nakajima quiver varieties. We discuss
type A in detail as well as its connections with quantum XXZ spin chains and trigonometric
Ruijsenaars-Schneider models. Finally we study a limit which produces a K-theoretic
version of results of Givental and Kim, connecting quantum geometry of flag varieties
and Toda lattice.
acknowledgement: 'First of all we would like to thank Andrei Okounkov for invaluable
discussions, advises and sharing with us his fantastic viewpoint on modern quantum
geometry. We are also grateful to D. Korb and Z. Zhou for their interest and comments.
The work of A. Smirnov was supported in part by RFBR Grants under Numbers 15-02-04175
and 15-01-04217 and in part by NSF Grant DMS–2054527. The work of P. Koroteev, A.M.
Zeitlin and A. Smirnov is supported in part by AMS Simons travel Grant. A. M. Zeitlin
is partially supported by Simons Collaboration Grant, Award ID: 578501. Open access
funding provided by Institute of Science and Technology (IST Austria).'
article_number: '87'
article_processing_charge: Yes (via OA deal)
article_type: original
author:
- first_name: Peter
full_name: Koroteev, Peter
last_name: Koroteev
- first_name: Petr
full_name: Pushkar, Petr
id: 151DCEB6-9EC3-11E9-8480-ABECE5697425
last_name: Pushkar
- first_name: Andrey V.
full_name: Smirnov, Andrey V.
last_name: Smirnov
- first_name: Anton M.
full_name: Zeitlin, Anton M.
last_name: Zeitlin
citation:
ama: Koroteev P, Pushkar P, Smirnov AV, Zeitlin AM. Quantum K-theory of quiver varieties
and many-body systems. Selecta Mathematica. 2021;27(5). doi:10.1007/s00029-021-00698-3
apa: Koroteev, P., Pushkar, P., Smirnov, A. V., & Zeitlin, A. M. (2021). Quantum
K-theory of quiver varieties and many-body systems. Selecta Mathematica.
Springer Nature. https://doi.org/10.1007/s00029-021-00698-3
chicago: Koroteev, Peter, Petr Pushkar, Andrey V. Smirnov, and Anton M. Zeitlin.
“Quantum K-Theory of Quiver Varieties and Many-Body Systems.” Selecta Mathematica.
Springer Nature, 2021. https://doi.org/10.1007/s00029-021-00698-3.
ieee: P. Koroteev, P. Pushkar, A. V. Smirnov, and A. M. Zeitlin, “Quantum K-theory
of quiver varieties and many-body systems,” Selecta Mathematica, vol. 27,
no. 5. Springer Nature, 2021.
ista: Koroteev P, Pushkar P, Smirnov AV, Zeitlin AM. 2021. Quantum K-theory of quiver
varieties and many-body systems. Selecta Mathematica. 27(5), 87.
mla: Koroteev, Peter, et al. “Quantum K-Theory of Quiver Varieties and Many-Body
Systems.” Selecta Mathematica, vol. 27, no. 5, 87, Springer Nature, 2021,
doi:10.1007/s00029-021-00698-3.
short: P. Koroteev, P. Pushkar, A.V. Smirnov, A.M. Zeitlin, Selecta Mathematica
27 (2021).
date_created: 2021-09-12T22:01:22Z
date_published: 2021-08-30T00:00:00Z
date_updated: 2023-08-14T06:34:14Z
day: '30'
ddc:
- '530'
department:
- _id: TaHa
doi: 10.1007/s00029-021-00698-3
external_id:
isi:
- '000692795200001'
file:
- access_level: open_access
checksum: beadc5a722ffb48190e1e63ee2dbfee5
content_type: application/pdf
creator: cchlebak
date_created: 2021-09-13T11:31:34Z
date_updated: 2021-09-13T11:31:34Z
file_id: '10010'
file_name: 2021_SelectaMath_Koroteev.pdf
file_size: 584648
relation: main_file
success: 1
file_date_updated: 2021-09-13T11:31:34Z
has_accepted_license: '1'
intvolume: ' 27'
isi: 1
issue: '5'
language:
- iso: eng
month: '08'
oa: 1
oa_version: Published Version
project:
- _id: B67AFEDC-15C9-11EA-A837-991A96BB2854
name: IST Austria Open Access Fund
publication: Selecta Mathematica
publication_identifier:
eissn:
- 1420-9020
issn:
- 1022-1824
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
scopus_import: '1'
status: public
title: Quantum K-theory of quiver varieties and many-body systems
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: 27
year: '2021'
...
---
_id: '9999'
abstract:
- lang: eng
text: 'The developmental strategies used by progenitor cells to endure a safe journey
from their induction place towards the site of terminal differentiation are still
poorly understood. Here we uncovered a progenitor cell allocation mechanism that
stems from an incomplete process of epithelial delamination that allows progenitors
to coordinate their movement with adjacent extra-embryonic tissues. Progenitors
of the zebrafish laterality organ originate from the surface epithelial enveloping
layer by an apical constriction process of cell delamination. During this process,
progenitors retain long-term apical contacts that enable the epithelial layer
to pull a subset of progenitors along their way towards the vegetal pole. The
remaining delaminated progenitors follow apically-attached progenitors’ movement
by a co-attraction mechanism, avoiding sequestration by the adjacent endoderm,
ensuring their fate and collective allocation at the differentiation site. Thus,
we reveal that incomplete delamination serves as a cellular platform for coordinated
tissue movements during development. Impact Statement: Incomplete delamination
serves as a cellular platform for coordinated tissue movements during development,
guiding newly formed progenitor cell groups to the differentiation site.'
article_number: e66483
article_processing_charge: Yes
article_type: original
author:
- first_name: Eduardo
full_name: Pulgar, Eduardo
last_name: Pulgar
- first_name: Cornelia
full_name: Schwayer, Cornelia
id: 3436488C-F248-11E8-B48F-1D18A9856A87
last_name: Schwayer
orcid: 0000-0001-5130-2226
- first_name: Néstor
full_name: Guerrero, Néstor
last_name: Guerrero
- first_name: Loreto
full_name: López, Loreto
last_name: López
- first_name: Susana
full_name: Márquez, Susana
last_name: Márquez
- first_name: Steffen
full_name: Härtel, Steffen
last_name: Härtel
- first_name: Rodrigo
full_name: Soto, Rodrigo
last_name: Soto
- first_name: Carl Philipp
full_name: Heisenberg, Carl Philipp
last_name: Heisenberg
- first_name: Miguel L.
full_name: Concha, Miguel L.
last_name: Concha
citation:
ama: Pulgar E, Schwayer C, Guerrero N, et al. Apical contacts stemming from incomplete
delamination guide progenitor cell allocation through a dragging mechanism. eLife.
2021;10. doi:10.7554/eLife.66483
apa: Pulgar, E., Schwayer, C., Guerrero, N., López, L., Márquez, S., Härtel, S.,
… Concha, M. L. (2021). Apical contacts stemming from incomplete delamination
guide progenitor cell allocation through a dragging mechanism. ELife. eLife
Sciences Publications. https://doi.org/10.7554/eLife.66483
chicago: Pulgar, Eduardo, Cornelia Schwayer, Néstor Guerrero, Loreto López, Susana
Márquez, Steffen Härtel, Rodrigo Soto, Carl Philipp Heisenberg, and Miguel L.
Concha. “Apical Contacts Stemming from Incomplete Delamination Guide Progenitor
Cell Allocation through a Dragging Mechanism.” ELife. eLife Sciences Publications,
2021. https://doi.org/10.7554/eLife.66483.
ieee: E. Pulgar et al., “Apical contacts stemming from incomplete delamination
guide progenitor cell allocation through a dragging mechanism,” eLife,
vol. 10. eLife Sciences Publications, 2021.
ista: Pulgar E, Schwayer C, Guerrero N, López L, Márquez S, Härtel S, Soto R, Heisenberg
CP, Concha ML. 2021. Apical contacts stemming from incomplete delamination guide
progenitor cell allocation through a dragging mechanism. eLife. 10, e66483.
mla: Pulgar, Eduardo, et al. “Apical Contacts Stemming from Incomplete Delamination
Guide Progenitor Cell Allocation through a Dragging Mechanism.” ELife,
vol. 10, e66483, eLife Sciences Publications, 2021, doi:10.7554/eLife.66483.
short: E. Pulgar, C. Schwayer, N. Guerrero, L. López, S. Márquez, S. Härtel, R.
Soto, C.P. Heisenberg, M.L. Concha, ELife 10 (2021).
date_created: 2021-09-12T22:01:23Z
date_published: 2021-08-27T00:00:00Z
date_updated: 2023-08-14T06:53:33Z
day: '27'
ddc:
- '570'
department:
- _id: CaHe
doi: 10.7554/eLife.66483
ec_funded: 1
external_id:
isi:
- '000700428500001'
pmid:
- '34448451'
file:
- access_level: open_access
checksum: a3f82b0499cc822ac1eab48a01f3f57e
content_type: application/pdf
creator: dernst
date_created: 2022-05-13T08:03:37Z
date_updated: 2022-05-13T08:03:37Z
file_id: '11371'
file_name: 2021_eLife_Pulgar.pdf
file_size: 9010446
relation: main_file
success: 1
file_date_updated: 2022-05-13T08:03:37Z
has_accepted_license: '1'
intvolume: ' 10'
isi: 1
keyword:
- cell delamination
- apical constriction
- dragging
- mechanical forces
- collective 18 locomotion
- dorsal forerunner cells
- zebrafish
language:
- iso: eng
month: '08'
oa: 1
oa_version: Published Version
pmid: 1
project:
- _id: 260F1432-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '742573'
name: Interaction and feedback between cell mechanics and fate specification in
vertebrate gastrulation
publication: eLife
publication_identifier:
eissn:
- 2050-084X
publication_status: published
publisher: eLife Sciences Publications
quality_controlled: '1'
scopus_import: '1'
status: public
title: Apical contacts stemming from incomplete delamination guide progenitor cell
allocation through a dragging 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: 10
year: '2021'
...
---
_id: '10002'
abstract:
- lang: eng
text: 'We present a faster symbolic algorithm for the following central problem
in probabilistic verification: Compute the maximal end-component (MEC) decomposition
of Markov decision processes (MDPs). This problem generalizes the SCC decomposition
problem of graphs and closed recurrent sets of Markov chains. The model of symbolic
algorithms is widely used in formal verification and model-checking, where access
to the input model is restricted to only symbolic operations (e.g., basic set
operations and computation of one-step neighborhood). For an input MDP with n vertices
and m edges, the classical symbolic algorithm from the 1990s for the MEC decomposition
requires O(n2) symbolic operations and O(1) symbolic space. The only other
symbolic algorithm for the MEC decomposition requires O(nm−−√) symbolic operations
and O(m−−√) symbolic space. A main open question is whether the worst-case O(n2) bound
for symbolic operations can be beaten. We present a symbolic algorithm that requires O˜(n1.5) symbolic
operations and O˜(n−−√) symbolic space. Moreover, the parametrization of our
algorithm provides a trade-off between symbolic operations and symbolic space:
for all 0<ϵ≤1/2 the symbolic algorithm requires O˜(n2−ϵ) symbolic operations
and O˜(nϵ) symbolic space ( O˜ hides poly-logarithmic factors). Using our techniques
we present faster algorithms for computing the almost-sure winning regions of ω
-regular objectives for MDPs. We consider the canonical parity objectives for ω
-regular objectives, and for parity objectives with d -priorities we present
an algorithm that computes the almost-sure winning region with O˜(n2−ϵ) symbolic
operations and O˜(nϵ) symbolic space, for all 0<ϵ≤1/2 .'
acknowledgement: The authors are grateful to the anonymous referees for their valuable
comments. A. S. is fully supported by the Vienna Science and Technology Fund (WWTF)
through project ICT15–003. K. C. is supported by the Austrian Science Fund (FWF)
NFN Grant No S11407-N23 (RiSE/SHiNE) and by the ERC CoG 863818 (ForM-SMArt). For
M. H. the research leading to these results has received funding from the European
Research Council under the European Unions Seventh Framework Programme (FP/2007–2013)
/ ERC Grant Agreement no. 340506.
article_processing_charge: No
author:
- first_name: Krishnendu
full_name: Chatterjee, Krishnendu
id: 2E5DCA20-F248-11E8-B48F-1D18A9856A87
last_name: Chatterjee
orcid: 0000-0002-4561-241X
- first_name: Wolfgang
full_name: Dvorak, Wolfgang
last_name: Dvorak
- first_name: Monika H
full_name: Henzinger, Monika H
id: 540c9bbd-f2de-11ec-812d-d04a5be85630
last_name: Henzinger
orcid: 0000-0002-5008-6530
- first_name: Alexander
full_name: Svozil, Alexander
last_name: Svozil
citation:
ama: 'Chatterjee K, Dvorak W, Henzinger MH, Svozil A. Symbolic time and space tradeoffs
for probabilistic verification. In: Proceedings of the 36th Annual ACM/IEEE
Symposium on Logic in Computer Science. Institute of Electrical and Electronics
Engineers; 2021:1-13. doi:10.1109/LICS52264.2021.9470739'
apa: 'Chatterjee, K., Dvorak, W., Henzinger, M. H., & Svozil, A. (2021). Symbolic
time and space tradeoffs for probabilistic verification. In Proceedings of
the 36th Annual ACM/IEEE Symposium on Logic in Computer Science (pp. 1–13).
Rome, Italy: Institute of Electrical and Electronics Engineers. https://doi.org/10.1109/LICS52264.2021.9470739'
chicago: Chatterjee, Krishnendu, Wolfgang Dvorak, Monika H Henzinger, and Alexander
Svozil. “Symbolic Time and Space Tradeoffs for Probabilistic Verification.” In
Proceedings of the 36th Annual ACM/IEEE Symposium on Logic in Computer Science,
1–13. Institute of Electrical and Electronics Engineers, 2021. https://doi.org/10.1109/LICS52264.2021.9470739.
ieee: K. Chatterjee, W. Dvorak, M. H. Henzinger, and A. Svozil, “Symbolic time and
space tradeoffs for probabilistic verification,” in Proceedings of the 36th
Annual ACM/IEEE Symposium on Logic in Computer Science, Rome, Italy, 2021,
pp. 1–13.
ista: 'Chatterjee K, Dvorak W, Henzinger MH, Svozil A. 2021. Symbolic time and space
tradeoffs for probabilistic verification. Proceedings of the 36th Annual ACM/IEEE
Symposium on Logic in Computer Science. LICS: Symposium on Logic in Computer Science,
1–13.'
mla: Chatterjee, Krishnendu, et al. “Symbolic Time and Space Tradeoffs for Probabilistic
Verification.” Proceedings of the 36th Annual ACM/IEEE Symposium on Logic in
Computer Science, Institute of Electrical and Electronics Engineers, 2021,
pp. 1–13, doi:10.1109/LICS52264.2021.9470739.
short: K. Chatterjee, W. Dvorak, M.H. Henzinger, A. Svozil, in:, Proceedings of
the 36th Annual ACM/IEEE Symposium on Logic in Computer Science, Institute of
Electrical and Electronics Engineers, 2021, pp. 1–13.
conference:
end_date: 2021-07-02
location: Rome, Italy
name: 'LICS: Symposium on Logic in Computer Science'
start_date: 2021-06-29
date_created: 2021-09-12T22:01:24Z
date_published: 2021-07-07T00:00:00Z
date_updated: 2023-08-14T06:51:33Z
day: '07'
department:
- _id: KrCh
doi: 10.1109/LICS52264.2021.9470739
ec_funded: 1
external_id:
arxiv:
- '2104.07466'
isi:
- '000947350400089'
isi: 1
keyword:
- Computer science
- Computational modeling
- Markov processes
- Probabilistic logic
- Formal verification
- Game Theory
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/2104.07466
month: '07'
oa: 1
oa_version: Preprint
page: 1-13
project:
- _id: 25863FF4-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: S11407
name: Game Theory
- _id: 0599E47C-7A3F-11EA-A408-12923DDC885E
call_identifier: H2020
grant_number: '863818'
name: 'Formal Methods for Stochastic Models: Algorithms and Applications'
publication: Proceedings of the 36th Annual ACM/IEEE Symposium on Logic in Computer
Science
publication_identifier:
eisbn:
- 978-1-6654-4895-6
isbn:
- 978-1-6654-4896-3
issn:
- 1043-6871
publication_status: published
publisher: Institute of Electrical and Electronics Engineers
quality_controlled: '1'
scopus_import: '1'
status: public
title: Symbolic time and space tradeoffs for probabilistic verification
type: conference
user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
year: '2021'
...
---
_id: '10024'
abstract:
- lang: eng
text: In this paper, we introduce a random environment for the exclusion process
in obtained by assigning a maximal occupancy to each site. This maximal occupancy
is allowed to randomly vary among sites, and partial exclusion occurs. Under the
assumption of ergodicity under translation and uniform ellipticity of the environment,
we derive a quenched hydrodynamic limit in path space by strengthening the mild
solution approach initiated in Nagy (2002) and Faggionato (2007). To this purpose,
we prove, employing the technology developed for the random conductance model,
a homogenization result in the form of an arbitrary starting point quenched invariance
principle for a single particle in the same environment, which is a result of
independent interest. The self-duality property of the partial exclusion process
allows us to transfer this homogenization result to the particle system and, then,
apply the tightness criterion in Redig et al. (2020).
acknowledgement: The authors would like to thank Marek Biskup and Alberto Chiarini
for useful suggestions and Cristian Giardina, Frank den Hollander and Shubhamoy Nandan for inspiring discussions. S.F. acknowledges Simona Villa for her help in creating the picture. Furthermore,
the authors thank two anonymous referees for the careful reading of the manuscript. S.F.
acknowledges financial support from NWO, The Netherlands via the grant TOP1.17.019.
F.S. acknowledges financial support from NWO via the TOP1 grant 613.001.552 as well as
funding from the European Union’s Horizon 2020 research and innovation programme
under the Marie-Skłodowska-Curie grant agreement No. 754411.
article_processing_charge: Yes
article_type: original
author:
- first_name: Simone
full_name: Floreani, Simone
last_name: Floreani
- first_name: Frank
full_name: Redig, Frank
last_name: Redig
- first_name: Federico
full_name: Sau, Federico
id: E1836206-9F16-11E9-8814-AEFDE5697425
last_name: Sau
citation:
ama: Floreani S, Redig F, Sau F. Hydrodynamics for the partial exclusion process
in random environment. Stochastic Processes and their Applications. 2021;142:124-158.
doi:10.1016/j.spa.2021.08.006
apa: Floreani, S., Redig, F., & Sau, F. (2021). Hydrodynamics for the partial
exclusion process in random environment. Stochastic Processes and Their Applications.
Elsevier. https://doi.org/10.1016/j.spa.2021.08.006
chicago: Floreani, Simone, Frank Redig, and Federico Sau. “Hydrodynamics for the
Partial Exclusion Process in Random Environment.” Stochastic Processes and
Their Applications. Elsevier, 2021. https://doi.org/10.1016/j.spa.2021.08.006.
ieee: S. Floreani, F. Redig, and F. Sau, “Hydrodynamics for the partial exclusion
process in random environment,” Stochastic Processes and their Applications,
vol. 142. Elsevier, pp. 124–158, 2021.
ista: Floreani S, Redig F, Sau F. 2021. Hydrodynamics for the partial exclusion
process in random environment. Stochastic Processes and their Applications. 142,
124–158.
mla: Floreani, Simone, et al. “Hydrodynamics for the Partial Exclusion Process in
Random Environment.” Stochastic Processes and Their Applications, vol.
142, Elsevier, 2021, pp. 124–58, doi:10.1016/j.spa.2021.08.006.
short: S. Floreani, F. Redig, F. Sau, Stochastic Processes and Their Applications
142 (2021) 124–158.
date_created: 2021-09-19T22:01:25Z
date_published: 2021-08-27T00:00:00Z
date_updated: 2023-08-14T06:52:43Z
day: '27'
ddc:
- '519'
department:
- _id: JaMa
doi: 10.1016/j.spa.2021.08.006
ec_funded: 1
external_id:
arxiv:
- '1911.12564'
isi:
- '000697748500005'
file:
- access_level: open_access
checksum: 56768c553d7218ee5714902ffec90ec4
content_type: application/pdf
creator: dernst
date_created: 2022-05-13T07:55:50Z
date_updated: 2022-05-13T07:55:50Z
file_id: '11370'
file_name: 2021_StochasticProcessesAppl_Floreani.pdf
file_size: 2115791
relation: main_file
success: 1
file_date_updated: 2022-05-13T07:55:50Z
has_accepted_license: '1'
intvolume: ' 142'
isi: 1
keyword:
- hydrodynamic limit
- random environment
- random conductance model
- arbitrary starting point quenched invariance principle
- duality
- mild solution
language:
- iso: eng
month: '08'
oa: 1
oa_version: Published Version
page: 124-158
project:
- _id: 260C2330-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '754411'
name: ISTplus - Postdoctoral Fellowships
publication: Stochastic Processes and their Applications
publication_identifier:
issn:
- 0304-4149
publication_status: published
publisher: Elsevier
quality_controlled: '1'
scopus_import: '1'
status: public
title: Hydrodynamics for the partial exclusion process in random environment
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: 142
year: '2021'
...
---
_id: '10004'
abstract:
- lang: eng
text: 'Markov chains are the de facto finite-state model for stochastic dynamical
systems, and Markov decision processes (MDPs) extend Markov chains by incorporating
non-deterministic behaviors. Given an MDP and rewards on states, a classical optimization
criterion is the maximal expected total reward where the MDP stops after T steps,
which can be computed by a simple dynamic programming algorithm. We consider a
natural generalization of the problem where the stopping times can be chosen according
to a probability distribution, such that the expected stopping time is T, to optimize
the expected total reward. Quite surprisingly we establish inter-reducibility
of the expected stopping-time problem for Markov chains with the Positivity problem
(which is related to the well-known Skolem problem), for which establishing either
decidability or undecidability would be a major breakthrough. Given the hardness
of the exact problem, we consider the approximate version of the problem: we show
that it can be solved in exponential time for Markov chains and in exponential
space for MDPs.'
acknowledgement: We are grateful to the anonymous reviewers of LICS 2021 and of a
previous version of this paper for insightful comments that helped improving the
presentation. This research was partially supported by the grant ERC CoG 863818
(ForM-SMArt).
article_processing_charge: No
author:
- first_name: Krishnendu
full_name: Chatterjee, Krishnendu
id: 2E5DCA20-F248-11E8-B48F-1D18A9856A87
last_name: Chatterjee
orcid: 0000-0002-4561-241X
- first_name: Laurent
full_name: Doyen, Laurent
last_name: Doyen
citation:
ama: 'Chatterjee K, Doyen L. Stochastic processes with expected stopping time. In:
Proceedings of the 36th Annual ACM/IEEE Symposium on Logic in Computer Science.
Institute of Electrical and Electronics Engineers; 2021:1-13. doi:10.1109/LICS52264.2021.9470595'
apa: 'Chatterjee, K., & Doyen, L. (2021). Stochastic processes with expected
stopping time. In Proceedings of the 36th Annual ACM/IEEE Symposium on Logic
in Computer Science (pp. 1–13). Rome, Italy: Institute of Electrical and Electronics
Engineers. https://doi.org/10.1109/LICS52264.2021.9470595'
chicago: Chatterjee, Krishnendu, and Laurent Doyen. “Stochastic Processes with Expected
Stopping Time.” In Proceedings of the 36th Annual ACM/IEEE Symposium on Logic
in Computer Science, 1–13. Institute of Electrical and Electronics Engineers,
2021. https://doi.org/10.1109/LICS52264.2021.9470595.
ieee: K. Chatterjee and L. Doyen, “Stochastic processes with expected stopping time,”
in Proceedings of the 36th Annual ACM/IEEE Symposium on Logic in Computer Science,
Rome, Italy, 2021, pp. 1–13.
ista: 'Chatterjee K, Doyen L. 2021. Stochastic processes with expected stopping
time. Proceedings of the 36th Annual ACM/IEEE Symposium on Logic in Computer Science.
LICS: Symposium on Logic in Computer Science, 1–13.'
mla: Chatterjee, Krishnendu, and Laurent Doyen. “Stochastic Processes with Expected
Stopping Time.” Proceedings of the 36th Annual ACM/IEEE Symposium on Logic
in Computer Science, Institute of Electrical and Electronics Engineers, 2021,
pp. 1–13, doi:10.1109/LICS52264.2021.9470595.
short: K. Chatterjee, L. Doyen, in:, Proceedings of the 36th Annual ACM/IEEE Symposium
on Logic in Computer Science, Institute of Electrical and Electronics Engineers,
2021, pp. 1–13.
conference:
end_date: 2021-07-02
location: Rome, Italy
name: 'LICS: Symposium on Logic in Computer Science'
start_date: 2021-06-29
date_created: 2021-09-12T22:01:25Z
date_published: 2021-07-07T00:00:00Z
date_updated: 2023-08-14T06:52:07Z
day: '07'
department:
- _id: KrCh
doi: 10.1109/LICS52264.2021.9470595
ec_funded: 1
external_id:
arxiv:
- '2104.07278'
isi:
- '000947350400036'
isi: 1
keyword:
- Computer science
- Heuristic algorithms
- Memory management
- Automata
- Markov processes
- Probability distribution
- Complexity theory
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/2104.07278
month: '07'
oa: 1
oa_version: Preprint
page: 1-13
project:
- _id: 0599E47C-7A3F-11EA-A408-12923DDC885E
call_identifier: H2020
grant_number: '863818'
name: 'Formal Methods for Stochastic Models: Algorithms and Applications'
publication: Proceedings of the 36th Annual ACM/IEEE Symposium on Logic in Computer
Science
publication_identifier:
eisbn:
- 978-1-6654-4895-6
isbn:
- 978-1-6654-4896-3
issn:
- 1043-6871
publication_status: published
publisher: Institute of Electrical and Electronics Engineers
quality_controlled: '1'
scopus_import: '1'
status: public
title: Stochastic processes with expected stopping time
type: conference
user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
year: '2021'
...
---
_id: '10053'
abstract:
- lang: eng
text: 'This paper characterizes the latency of the simplified successive-cancellation
(SSC) decoding scheme for polar codes under hardware resource constraints. In
particular, when the number of processing elements P that can perform SSC decoding
operations in parallel is limited, as is the case in practice, the latency of
SSC decoding is O(N1−1 μ+NPlog2log2NP), where N is the block length of the code
and μ is the scaling exponent of polar codes for the channel. Three direct consequences
of this bound are presented. First, in a fully-parallel implementation where P=N2
, the latency of SSC decoding is O(N1−1/μ) , which is sublinear in the block length.
This recovers a result from an earlier work. Second, in a fully-serial implementation
where P=1 , the latency of SSC decoding scales as O(Nlog2log2N) . The multiplicative
constant is also calculated: we show that the latency of SSC decoding when P=1
is given by (2+o(1))Nlog2log2N . Third, in a semi-parallel implementation, the
smallest P that gives the same latency as that of the fully-parallel implementation
is P=N1/μ . The tightness of our bound on SSC decoding latency and the applicability
of the foregoing results is validated through extensive simulations.'
acknowledgement: "S. A. Hashemi is supported by a Postdoctoral Fellowship from the
Natural Sciences and Engineering Research Council\r\nof Canada (NSERC) and by Huawei.
M. Mondelli is partially supported by the 2019 Lopez-Loreta Prize. A. Fazeli and
A. Vardy were supported in part by the National Science Foundation under Grant CCF-1764104."
article_processing_charge: No
author:
- first_name: Seyyed Ali
full_name: Hashemi, Seyyed Ali
last_name: Hashemi
- first_name: Marco
full_name: Mondelli, Marco
id: 27EB676C-8706-11E9-9510-7717E6697425
last_name: Mondelli
orcid: 0000-0002-3242-7020
- first_name: Arman
full_name: Fazeli, Arman
last_name: Fazeli
- first_name: Alexander
full_name: Vardy, Alexander
last_name: Vardy
- first_name: John
full_name: Cioffi, John
last_name: Cioffi
- first_name: Andrea
full_name: Goldsmith, Andrea
last_name: Goldsmith
citation:
ama: 'Hashemi SA, Mondelli M, Fazeli A, Vardy A, Cioffi J, Goldsmith A. Parallelism
versus latency in simplified successive-cancellation decoding of polar codes.
In: 2021 IEEE International Symposium on Information Theory. Institute
of Electrical and Electronics Engineers; 2021:2369-2374. doi:10.1109/ISIT45174.2021.9518153'
apa: 'Hashemi, S. A., Mondelli, M., Fazeli, A., Vardy, A., Cioffi, J., & Goldsmith,
A. (2021). Parallelism versus latency in simplified successive-cancellation decoding
of polar codes. In 2021 IEEE International Symposium on Information Theory
(pp. 2369–2374). Melbourne, Australia: Institute of Electrical and Electronics
Engineers. https://doi.org/10.1109/ISIT45174.2021.9518153'
chicago: Hashemi, Seyyed Ali, Marco Mondelli, Arman Fazeli, Alexander Vardy, John
Cioffi, and Andrea Goldsmith. “Parallelism versus Latency in Simplified Successive-Cancellation
Decoding of Polar Codes.” In 2021 IEEE International Symposium on Information
Theory, 2369–74. Institute of Electrical and Electronics Engineers, 2021.
https://doi.org/10.1109/ISIT45174.2021.9518153.
ieee: S. A. Hashemi, M. Mondelli, A. Fazeli, A. Vardy, J. Cioffi, and A. Goldsmith,
“Parallelism versus latency in simplified successive-cancellation decoding of
polar codes,” in 2021 IEEE International Symposium on Information Theory,
Melbourne, Australia, 2021, pp. 2369–2374.
ista: 'Hashemi SA, Mondelli M, Fazeli A, Vardy A, Cioffi J, Goldsmith A. 2021. Parallelism
versus latency in simplified successive-cancellation decoding of polar codes.
2021 IEEE International Symposium on Information Theory. ISIT: International Symposium
on Information Theory, 2369–2374.'
mla: Hashemi, Seyyed Ali, et al. “Parallelism versus Latency in Simplified Successive-Cancellation
Decoding of Polar Codes.” 2021 IEEE International Symposium on Information
Theory, Institute of Electrical and Electronics Engineers, 2021, pp. 2369–74,
doi:10.1109/ISIT45174.2021.9518153.
short: S.A. Hashemi, M. Mondelli, A. Fazeli, A. Vardy, J. Cioffi, A. Goldsmith,
in:, 2021 IEEE International Symposium on Information Theory, Institute of Electrical
and Electronics Engineers, 2021, pp. 2369–2374.
conference:
end_date: 2021-07-20
location: Melbourne, Australia
name: 'ISIT: International Symposium on Information Theory'
start_date: 2021-07-12
date_created: 2021-09-27T14:33:14Z
date_published: 2021-09-01T00:00:00Z
date_updated: 2023-08-14T06:55:58Z
day: '01'
department:
- _id: MaMo
doi: 10.1109/ISIT45174.2021.9518153
external_id:
arxiv:
- '2012.13378'
isi:
- '000701502202078'
isi: 1
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/2012.13378
month: '09'
oa: 1
oa_version: Preprint
page: 2369-2374
project:
- _id: 059876FA-7A3F-11EA-A408-12923DDC885E
name: Prix Lopez-Loretta 2019 - Marco Mondelli
publication: 2021 IEEE International Symposium on Information Theory
publication_identifier:
eisbn:
- 978-1-5386-8209-8
isbn:
- 978-1-5386-8210-4
issn:
- 2157-8095
publication_status: published
publisher: Institute of Electrical and Electronics Engineers
quality_controlled: '1'
related_material:
record:
- id: '10364'
relation: later_version
status: public
scopus_import: '1'
status: public
title: Parallelism versus latency in simplified successive-cancellation decoding of
polar codes
type: conference
user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
year: '2021'
...
---
_id: '10033'
abstract:
- lang: eng
text: The ⊗*-monoidal structure on the category of sheaves on the Ran space is not
pro-nilpotent in the sense of [3]. However, under some connectivity assumptions,
we prove that Koszul duality induces an equivalence of categories and that this
equivalence behaves nicely with respect to Verdier duality on the Ran space and
integrating along the Ran space, i.e. taking factorization homology. Based on
ideas sketched in [4], we show that these results also offer a simpler alternative
to one of the two main steps in the proof of the Atiyah-Bott formula given in
[7] and [5].
acknowledgement: 'The author would like to express his gratitude to D. Gaitsgory,
without whose tireless guidance and encouragement in pursuing this problem, this
work would not have been possible. The author is grateful to his advisor B.C. Ngô
for many years of patient guidance and support. This paper is revised while the
author is a postdoc in Hausel group at IST Austria. We thank him and the group for
providing a wonderful research environment. The author also gratefully acknowledges
the support of the Lise Meitner fellowship “Algebro-Geometric Applications of Factorization
Homology,” Austrian Science Fund (FWF): M 2751.'
article_number: '107992'
article_processing_charge: Yes (via OA deal)
article_type: original
author:
- first_name: Quoc P
full_name: Ho, Quoc P
id: 3DD82E3C-F248-11E8-B48F-1D18A9856A87
last_name: Ho
orcid: 0000-0001-6889-1418
citation:
ama: Ho QP. The Atiyah-Bott formula and connectivity in chiral Koszul duality. Advances
in Mathematics. 2021;392. doi:10.1016/j.aim.2021.107992
apa: Ho, Q. P. (2021). The Atiyah-Bott formula and connectivity in chiral Koszul
duality. Advances in Mathematics. Elsevier. https://doi.org/10.1016/j.aim.2021.107992
chicago: Ho, Quoc P. “The Atiyah-Bott Formula and Connectivity in Chiral Koszul
Duality.” Advances in Mathematics. Elsevier, 2021. https://doi.org/10.1016/j.aim.2021.107992.
ieee: Q. P. Ho, “The Atiyah-Bott formula and connectivity in chiral Koszul duality,”
Advances in Mathematics, vol. 392. Elsevier, 2021.
ista: Ho QP. 2021. The Atiyah-Bott formula and connectivity in chiral Koszul duality.
Advances in Mathematics. 392, 107992.
mla: Ho, Quoc P. “The Atiyah-Bott Formula and Connectivity in Chiral Koszul Duality.”
Advances in Mathematics, vol. 392, 107992, Elsevier, 2021, doi:10.1016/j.aim.2021.107992.
short: Q.P. Ho, Advances in Mathematics 392 (2021).
date_created: 2021-09-21T15:58:59Z
date_published: 2021-09-21T00:00:00Z
date_updated: 2023-08-14T06:54:35Z
day: '21'
ddc:
- '514'
department:
- _id: TaHa
doi: 10.1016/j.aim.2021.107992
external_id:
arxiv:
- '1610.00212'
isi:
- '000707040300031'
file:
- access_level: open_access
checksum: f3c0086d41af11db31c00014efb38072
content_type: application/pdf
creator: qho
date_created: 2021-09-21T15:58:52Z
date_updated: 2021-09-21T15:58:52Z
file_id: '10034'
file_name: 1-s2.0-S000187082100431X-main.pdf
file_size: 840635
relation: main_file
file_date_updated: 2021-09-21T15:58:52Z
has_accepted_license: '1'
intvolume: ' 392'
isi: 1
keyword:
- Chiral algebras
- Chiral homology
- Factorization algebras
- Koszul duality
- Ran space
language:
- iso: eng
month: '09'
oa: 1
oa_version: Published Version
project:
- _id: 26B96266-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: M02751
name: Algebro-Geometric Applications of Factorization Homology
publication: Advances in Mathematics
publication_identifier:
eissn:
- 1090-2082
issn:
- 0001-8708
publication_status: published
publisher: Elsevier
quality_controlled: '1'
scopus_import: '1'
status: public
title: The Atiyah-Bott formula and connectivity in chiral Koszul duality
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: 392
year: '2021'
...
---
_id: '10051'
abstract:
- lang: eng
text: 'Rab-interacting molecule (RIM)-binding protein 2 (BP2) is a multidomain protein
of the presynaptic active zone (AZ). By binding to RIM, bassoon (Bsn), and voltage-gated
Ca2+ channels (CaV), it is considered to be a central organizer of the topography
of CaV and release sites of synaptic vesicles (SVs) at the AZ. Here, we used RIM-BP2
knock-out (KO) mice and their wild-type (WT) littermates of either sex to investigate
the role of RIM-BP2 at the endbulb of Held synapse of auditory nerve fibers (ANFs)
with bushy cells (BCs) of the cochlear nucleus, a fast relay of the auditory pathway
with high release probability. Disruption of RIM-BP2 lowered release probability
altering short-term plasticity and reduced evoked EPSCs. Analysis of SV pool dynamics
during high-frequency train stimulation indicated a reduction of SVs with high
release probability but an overall normal size of the readily releasable SV pool
(RRP). The Ca2+-dependent fast component of SV replenishment after RRP depletion
was slowed. Ultrastructural analysis by superresolution light and electron microscopy
revealed an impaired topography of presynaptic CaV and a reduction of docked and
membrane-proximal SVs at the AZ. We conclude that RIM-BP2 organizes the topography
of CaV, and promotes SV tethering and docking. This way RIM-BP2 is critical for
establishing a high initial release probability as required to reliably signal
sound onset information that we found to be degraded in BCs of RIM-BP2-deficient
mice in vivo. SIGNIFICANCE STATEMENT: Rab-interacting molecule (RIM)-binding proteins
(BPs) are key organizers of the active zone (AZ). Using a multidisciplinary approach
to the calyceal endbulb of Held synapse that transmits auditory information at
rates of up to hundreds of Hertz with submillisecond precision we demonstrate
a requirement for RIM-BP2 for normal auditory signaling. Endbulb synapses lacking
RIM-BP2 show a reduced release probability despite normal whole-terminal Ca2+
influx and abundance of the key priming protein Munc13-1, a reduced rate of SV
replenishment, as well as an altered topography of voltage-gated (CaV)2.1 Ca2+
channels, and fewer docked and membrane proximal synaptic vesicles (SVs). This
hampers transmission of sound onset information likely affecting downstream neural
computations such as of sound localization.'
acknowledgement: This work was supported by the Deutsche Forschungsgemeinschaft (DFG,
German Research Foundation) through the Collaborative Sensory Research Center 1286
[to C.W. (A4) and T.M. (B5)] and under Germany’s Excellence Strategy Grant EXC 2067/1-390729940.
We thank S. Gerke, A.J. Goldak, and C. Senger-Freitag for expert technical assistance;
G. Hoch for developing image analysis routines; and S. Chepurwar and N. Strenzke
for technical support and discussion regarding in vivo experiments. We also thank
Dr. Christian Rosenmund, Dr. Katharina Grauel, and Dr. Stephan Sigrist for providing
RIM-BP2 KO mice and Dr. Masahiko Watanabe for providing the anti-neurexin-antibody,
and Dr. Toshihisa Ohtsuka for the anti-ELKS-antibody. J. Neef for help with the
STED imaging and image analysis; E. Neher and S. Rizzoli for discussion and comments
on the manuscript; K. Eguchi for help with the statistical analysis; and C. H. Huang
and J. Neef for constant support and scientific discussion.
article_processing_charge: No
article_type: original
author:
- first_name: Tanvi
full_name: Butola, Tanvi
last_name: Butola
- first_name: Theocharis
full_name: Alvanos, Theocharis
last_name: Alvanos
- first_name: Anika
full_name: Hintze, Anika
last_name: Hintze
- first_name: Peter
full_name: Koppensteiner, Peter
id: 3B8B25A8-F248-11E8-B48F-1D18A9856A87
last_name: Koppensteiner
orcid: 0000-0002-3509-1948
- first_name: David
full_name: Kleindienst, David
id: 42E121A4-F248-11E8-B48F-1D18A9856A87
last_name: Kleindienst
- first_name: Ryuichi
full_name: Shigemoto, Ryuichi
id: 499F3ABC-F248-11E8-B48F-1D18A9856A87
last_name: Shigemoto
orcid: 0000-0001-8761-9444
- first_name: Carolin
full_name: Wichmann, Carolin
last_name: Wichmann
- first_name: Tobias
full_name: Moser, Tobias
last_name: Moser
citation:
ama: Butola T, Alvanos T, Hintze A, et al. RIM-binding protein 2 organizes Ca21
channel topography and regulates release probability and vesicle replenishment
at a fast central synapse. Journal of Neuroscience. 2021;41(37):7742-7767.
doi:10.1523/JNEUROSCI.0586-21.2021
apa: Butola, T., Alvanos, T., Hintze, A., Koppensteiner, P., Kleindienst, D., Shigemoto,
R., … Moser, T. (2021). RIM-binding protein 2 organizes Ca21 channel
topography and regulates release probability and vesicle replenishment at a fast
central synapse. Journal of Neuroscience. Society for Neuroscience. https://doi.org/10.1523/JNEUROSCI.0586-21.2021
chicago: Butola, Tanvi, Theocharis Alvanos, Anika Hintze, Peter Koppensteiner, David
Kleindienst, Ryuichi Shigemoto, Carolin Wichmann, and Tobias Moser. “RIM-Binding
Protein 2 Organizes Ca21 Channel Topography and Regulates Release Probability
and Vesicle Replenishment at a Fast Central Synapse.” Journal of Neuroscience.
Society for Neuroscience, 2021. https://doi.org/10.1523/JNEUROSCI.0586-21.2021.
ieee: T. Butola et al., “RIM-binding protein 2 organizes Ca21
channel topography and regulates release probability and vesicle replenishment
at a fast central synapse,” Journal of Neuroscience, vol. 41, no. 37. Society
for Neuroscience, pp. 7742–7767, 2021.
ista: Butola T, Alvanos T, Hintze A, Koppensteiner P, Kleindienst D, Shigemoto R,
Wichmann C, Moser T. 2021. RIM-binding protein 2 organizes Ca21 channel
topography and regulates release probability and vesicle replenishment at a fast
central synapse. Journal of Neuroscience. 41(37), 7742–7767.
mla: Butola, Tanvi, et al. “RIM-Binding Protein 2 Organizes Ca21 Channel
Topography and Regulates Release Probability and Vesicle Replenishment at a Fast
Central Synapse.” Journal of Neuroscience, vol. 41, no. 37, Society for
Neuroscience, 2021, pp. 7742–67, doi:10.1523/JNEUROSCI.0586-21.2021.
short: T. Butola, T. Alvanos, A. Hintze, P. Koppensteiner, D. Kleindienst, R. Shigemoto,
C. Wichmann, T. Moser, Journal of Neuroscience 41 (2021) 7742–7767.
date_created: 2021-09-27T14:33:13Z
date_published: 2021-09-15T00:00:00Z
date_updated: 2023-08-14T06:56:30Z
day: '15'
ddc:
- '570'
department:
- _id: RySh
doi: 10.1523/JNEUROSCI.0586-21.2021
external_id:
isi:
- '000752287700005'
pmid:
- '34353898'
file:
- access_level: open_access
checksum: 769ab627c7355a50ccfd445e43a5f351
content_type: application/pdf
creator: dernst
date_created: 2022-05-31T09:10:15Z
date_updated: 2022-05-31T09:10:15Z
file_id: '11423'
file_name: 2021_JourNeuroscience_Butola.pdf
file_size: 11571961
relation: main_file
success: 1
file_date_updated: 2022-05-31T09:10:15Z
has_accepted_license: '1'
intvolume: ' 41'
isi: 1
issue: '37'
language:
- iso: eng
month: '09'
oa: 1
oa_version: Published Version
page: 7742-7767
pmid: 1
publication: Journal of Neuroscience
publication_identifier:
eissn:
- 1529-2401
issn:
- 0270-6474
publication_status: published
publisher: Society for Neuroscience
quality_controlled: '1'
scopus_import: '1'
status: public
title: RIM-binding protein 2 organizes Ca21 channel topography and regulates
release probability and vesicle replenishment at a fast central synapse
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: 41
year: '2021'
...
---
_id: '10055'
abstract:
- lang: eng
text: "Repeated idempotent elements are commonly used to characterise iterable behaviours
in abstract models of computation. Therefore, given a monoid M, it is natural
to ask how long a sequence of elements of M needs to be to ensure the presence
of consecutive idempotent factors. This question is formalised through the notion
of the Ramsey function R_M associated to M, obtained by mapping every k ∈ ℕ to
the minimal integer R_M(k) such that every word u ∈ M^* of length R_M(k) contains
k consecutive non-empty factors that correspond to the same idempotent element
of M. In this work, we study the behaviour of the Ramsey function R_M by investigating
the regular \U0001D49F-length of M, defined as the largest size L(M) of a submonoid
of M isomorphic to the set of natural numbers {1,2, …, L(M)} equipped with the
max operation. We show that the regular \U0001D49F-length of M determines the
degree of R_M, by proving that k^L(M) ≤ R_M(k) ≤ (k|M|⁴)^L(M). To allow applications
of this result, we provide the value of the regular \U0001D49F-length of diverse
monoids. In particular, we prove that the full monoid of n × n Boolean matrices,
which is used to express transition monoids of non-deterministic automata, has
a regular \U0001D49F-length of (n²+n+2)/2."
acknowledgement: This project has received funding from the European Union’s Horizon
2020 research and innovation programme under the Marie Skłodowska-Curie Grant Agreement
No. 754411. I wish to thank Michaël Cadilhac, Emmanuel Filiot and Charles Paperman
for their valuable insights concerning Green’s relations.
alternative_title:
- LIPIcs
article_number: '44'
article_processing_charge: No
author:
- first_name: Ismael R
full_name: Jecker, Ismael R
id: 85D7C63E-7D5D-11E9-9C0F-98C4E5697425
last_name: Jecker
citation:
ama: 'Jecker IR. A Ramsey theorem for finite monoids. In: 38th International
Symposium on Theoretical Aspects of Computer Science. Vol 187. Schloss Dagstuhl
- Leibniz Zentrum für Informatik; 2021. doi:10.4230/LIPIcs.STACS.2021.44'
apa: 'Jecker, I. R. (2021). A Ramsey theorem for finite monoids. In 38th International
Symposium on Theoretical Aspects of Computer Science (Vol. 187). Saarbrücken,
Germany: Schloss Dagstuhl - Leibniz Zentrum für Informatik. https://doi.org/10.4230/LIPIcs.STACS.2021.44'
chicago: Jecker, Ismael R. “A Ramsey Theorem for Finite Monoids.” In 38th International
Symposium on Theoretical Aspects of Computer Science, Vol. 187. Schloss Dagstuhl
- Leibniz Zentrum für Informatik, 2021. https://doi.org/10.4230/LIPIcs.STACS.2021.44.
ieee: I. R. Jecker, “A Ramsey theorem for finite monoids,” in 38th International
Symposium on Theoretical Aspects of Computer Science, Saarbrücken, Germany,
2021, vol. 187.
ista: 'Jecker IR. 2021. A Ramsey theorem for finite monoids. 38th International
Symposium on Theoretical Aspects of Computer Science. STACS: Symposium on Theoretical
Aspects of Computer Science, LIPIcs, vol. 187, 44.'
mla: Jecker, Ismael R. “A Ramsey Theorem for Finite Monoids.” 38th International
Symposium on Theoretical Aspects of Computer Science, vol. 187, 44, Schloss
Dagstuhl - Leibniz Zentrum für Informatik, 2021, doi:10.4230/LIPIcs.STACS.2021.44.
short: I.R. Jecker, in:, 38th International Symposium on Theoretical Aspects of
Computer Science, Schloss Dagstuhl - Leibniz Zentrum für Informatik, 2021.
conference:
end_date: 2021-03-19
location: Saarbrücken, Germany
name: 'STACS: Symposium on Theoretical Aspects of Computer Science'
start_date: 2021-03-16
date_created: 2021-09-27T14:33:15Z
date_published: 2021-03-10T00:00:00Z
date_updated: 2023-08-14T07:03:23Z
day: '10'
ddc:
- '000'
department:
- _id: KrCh
doi: 10.4230/LIPIcs.STACS.2021.44
ec_funded: 1
external_id:
isi:
- '000635691700044'
file:
- access_level: open_access
checksum: 17432a05733f408de300e17e390a90e4
content_type: application/pdf
creator: cchlebak
date_created: 2021-10-01T09:55:00Z
date_updated: 2021-10-01T09:55:00Z
file_id: '10063'
file_name: 2021_LIPIcs_Jecker.pdf
file_size: 720250
relation: main_file
success: 1
file_date_updated: 2021-10-01T09:55:00Z
has_accepted_license: '1'
intvolume: ' 187'
isi: 1
language:
- iso: eng
month: '03'
oa: 1
oa_version: Published Version
project:
- _id: 260C2330-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '754411'
name: ISTplus - Postdoctoral Fellowships
publication: 38th International Symposium on Theoretical Aspects of Computer Science
publication_identifier:
isbn:
- 978-3-9597-7180-1
issn:
- 1868-8969
publication_status: published
publisher: Schloss Dagstuhl - Leibniz Zentrum für Informatik
quality_controlled: '1'
scopus_import: '1'
status: public
title: A Ramsey theorem for finite monoids
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
volume: 187
year: '2021'
...
---
_id: '10069'
abstract:
- lang: eng
text: 'The extent to which women differ in the course of blood cell counts throughout
pregnancy, and the importance of these changes to pregnancy outcomes has not been
well defined. Here, we develop a series of statistical analyses of repeated measures
data to reveal the degree to which women differ in the course of pregnancy, predict
the changes that occur, and determine the importance of these changes for post-partum
hemorrhage (PPH) which is one of the leading causes of maternal mortality. We
present a prospective cohort of 4082 births recorded at the University Hospital,
Lausanne, Switzerland between 2009 and 2014 where full labour records could be
obtained, along with complete blood count data taken at hospital admission. We
find significant differences, at a [Formula: see text] level, among women in how
blood count values change through pregnancy for mean corpuscular hemoglobin, mean
corpuscular volume, mean platelet volume, platelet count and red cell distribution
width. We find evidence that almost all complete blood count values show trimester-specific
associations with PPH. For example, high platelet count (OR 1.20, 95% CI 1.01-1.53),
high mean platelet volume (OR 1.58, 95% CI 1.04-2.08), and high erythrocyte levels
(OR 1.36, 95% CI 1.01-1.57) in trimester 1 increased PPH, but high values in trimester
3 decreased PPH risk (OR 0.85, 0.79, 0.67 respectively). We show that differences
among women in the course of blood cell counts throughout pregnancy have an important
role in shaping pregnancy outcome and tracking blood count value changes through
pregnancy improves identification of women at increased risk of postpartum hemorrhage.
This study provides greater understanding of the complex changes in blood count
values that occur through pregnancy and provides indicators to guide the stratification
of patients into risk groups.'
acknowledgement: This project was funded by an SNSF Eccellenza Grant to MRR (PCEGP3-181181),
and by core funding from the Institute of Science and Technology Austria. We would
like to thank the participants of the study and all the midwives and doctors for
the computerized obstetrical data.
article_number: '19238'
article_processing_charge: Yes
article_type: original
author:
- first_name: Matthew Richard
full_name: Robinson, Matthew Richard
id: E5D42276-F5DA-11E9-8E24-6303E6697425
last_name: Robinson
orcid: 0000-0001-8982-8813
- first_name: Marion
full_name: Patxot, Marion
last_name: Patxot
- first_name: Miloš
full_name: Stojanov, Miloš
last_name: Stojanov
- first_name: Sabine
full_name: Blum, Sabine
last_name: Blum
- first_name: David
full_name: Baud, David
last_name: Baud
citation:
ama: Robinson MR, Patxot M, Stojanov M, Blum S, Baud D. Postpartum hemorrhage risk
is driven by changes in blood composition through pregnancy. Scientific Reports.
2021;11. doi:10.1038/s41598-021-98411-z
apa: Robinson, M. R., Patxot, M., Stojanov, M., Blum, S., & Baud, D. (2021).
Postpartum hemorrhage risk is driven by changes in blood composition through pregnancy.
Scientific Reports. Springer Nature. https://doi.org/10.1038/s41598-021-98411-z
chicago: Robinson, Matthew Richard, Marion Patxot, Miloš Stojanov, Sabine Blum,
and David Baud. “Postpartum Hemorrhage Risk Is Driven by Changes in Blood Composition
through Pregnancy.” Scientific Reports. Springer Nature, 2021. https://doi.org/10.1038/s41598-021-98411-z.
ieee: M. R. Robinson, M. Patxot, M. Stojanov, S. Blum, and D. Baud, “Postpartum
hemorrhage risk is driven by changes in blood composition through pregnancy,”
Scientific Reports, vol. 11. Springer Nature, 2021.
ista: Robinson MR, Patxot M, Stojanov M, Blum S, Baud D. 2021. Postpartum hemorrhage
risk is driven by changes in blood composition through pregnancy. Scientific Reports.
11, 19238.
mla: Robinson, Matthew Richard, et al. “Postpartum Hemorrhage Risk Is Driven by
Changes in Blood Composition through Pregnancy.” Scientific Reports, vol.
11, 19238, Springer Nature, 2021, doi:10.1038/s41598-021-98411-z.
short: M.R. Robinson, M. Patxot, M. Stojanov, S. Blum, D. Baud, Scientific Reports
11 (2021).
date_created: 2021-10-03T22:01:21Z
date_published: 2021-09-28T00:00:00Z
date_updated: 2023-08-14T07:05:15Z
day: '28'
ddc:
- '618'
department:
- _id: MaRo
doi: 10.1038/s41598-021-98411-z
external_id:
isi:
- '000701575500083'
pmid:
- '34584125'
file:
- access_level: open_access
checksum: f002ec22f609f58e1263b79e7f79601e
content_type: application/pdf
creator: cchlebak
date_created: 2021-10-05T14:56:48Z
date_updated: 2021-10-05T14:56:48Z
file_id: '10091'
file_name: 2021_ScientificReports_Robinson.pdf
file_size: 6970368
relation: main_file
success: 1
file_date_updated: 2021-10-05T14:56:48Z
has_accepted_license: '1'
intvolume: ' 11'
isi: 1
language:
- iso: eng
month: '09'
oa: 1
oa_version: Published Version
pmid: 1
publication: Scientific Reports
publication_identifier:
eissn:
- 2045-2322
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
scopus_import: '1'
status: public
title: Postpartum hemorrhage risk is driven by changes in blood composition through
pregnancy
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: journal_article
user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
volume: 11
year: '2021'
...
---
_id: '10025'
abstract:
- lang: eng
text: Ferromagnetism is most common in transition metal compounds but may also arise
in low-density two-dimensional electron systems, with signatures observed in silicon,
III-V semiconductor systems, and graphene moiré heterostructures. Here we show
that gate-tuned van Hove singularities in rhombohedral trilayer graphene drive
the spontaneous ferromagnetic polarization of the electron system into one or
more spin- and valley flavors. Using capacitance measurements on graphite-gated
van der Waals heterostructures, we find a cascade of density- and electronic displacement
field tuned phase transitions marked by negative electronic compressibility. The
transitions define the boundaries between phases where quantum oscillations have
either four-fold, two-fold, or one-fold degeneracy, associated with a spin and
valley degenerate normal metal, spin-polarized `half-metal', and spin and valley
polarized `quarter metal', respectively. For electron doping, the salient features
are well captured by a phenomenological Stoner model with a valley-anisotropic
Hund's coupling, likely arising from interactions at the lattice scale. For hole
filling, we observe a richer phase diagram featuring a delicate interplay of broken
symmetries and transitions in the Fermi surface topology. Finally, by rotational
alignment of a hexagonal boron nitride substrate to induce a moiré superlattice,
we find that the superlattice perturbs the preexisting isospin order only weakly,
leaving the basic phase diagram intact while catalyzing the formation of topologically
nontrivial gapped states whenever itinerant half- or quarter metal states occur
at half- or quarter superlattice band filling. Our results show that rhombohedral
trilayer graphene is an ideal platform for well-controlled tests of many-body
theory and reveal magnetism in moiré materials to be fundamentally itinerant in
nature.
acknowledgement: "The authors acknowledge discussions with A. Macdonald, L. Fu, F.
Wang and M. Zaletel. AFY acknowledges support of the National Science Foundation
under DMR1654186, and the Gordon and Betty Moore Foundation under award GBMF9471.
The authors acknowledge the use of the research facilities within the California
NanoSystems Institute, supported by the University of California, Santa Barbara
and the University of California, Office of the President.\r\nK.W. and T.T. acknowledge
support from the Elemental Strategy Initiative conducted by the MEXT, Japan, Grant
Number JPMXP0112101001 and JSPS KAKENHI, Grant Number JP20H00354. EB and TH were
supported by the European Research Council (ERC) under grant HQMAT (Grant Agreement
No. 817799). A.G. acknowledges support by the European Unions Horizon 2020 research
and innovation program under the Marie Sklodowska-Curie Grant Agreement\r\nNo. 754411.\r\n"
article_processing_charge: No
article_type: original
author:
- first_name: Haoxin
full_name: Zhou, Haoxin
last_name: Zhou
- first_name: Tian
full_name: Xie, Tian
last_name: Xie
- first_name: Areg
full_name: Ghazaryan, Areg
id: 4AF46FD6-F248-11E8-B48F-1D18A9856A87
last_name: Ghazaryan
orcid: 0000-0001-9666-3543
- first_name: Tobias
full_name: Holder, Tobias
last_name: Holder
- first_name: James R.
full_name: Ehrets, James R.
last_name: Ehrets
- first_name: Eric M.
full_name: Spanton, Eric M.
last_name: Spanton
- first_name: Takashi
full_name: Taniguchi, Takashi
last_name: Taniguchi
- first_name: Kenji
full_name: Watanabe, Kenji
last_name: Watanabe
- first_name: Erez
full_name: Berg, Erez
last_name: Berg
- first_name: Maksym
full_name: Serbyn, Maksym
id: 47809E7E-F248-11E8-B48F-1D18A9856A87
last_name: Serbyn
orcid: 0000-0002-2399-5827
- first_name: Andrea F.
full_name: Young, Andrea F.
last_name: Young
citation:
ama: Zhou H, Xie T, Ghazaryan A, et al. Half and quarter metals in rhombohedral
trilayer graphene. Nature. 2021. doi:10.1038/s41586-021-03938-w
apa: Zhou, H., Xie, T., Ghazaryan, A., Holder, T., Ehrets, J. R., Spanton, E. M.,
… Young, A. F. (2021). Half and quarter metals in rhombohedral trilayer graphene.
Nature. Springer Nature. https://doi.org/10.1038/s41586-021-03938-w
chicago: Zhou, Haoxin, Tian Xie, Areg Ghazaryan, Tobias Holder, James R. Ehrets,
Eric M. Spanton, Takashi Taniguchi, et al. “Half and Quarter Metals in Rhombohedral
Trilayer Graphene.” Nature. Springer Nature, 2021. https://doi.org/10.1038/s41586-021-03938-w.
ieee: H. Zhou et al., “Half and quarter metals in rhombohedral trilayer graphene,”
Nature. Springer Nature, 2021.
ista: Zhou H, Xie T, Ghazaryan A, Holder T, Ehrets JR, Spanton EM, Taniguchi T,
Watanabe K, Berg E, Serbyn M, Young AF. 2021. Half and quarter metals in rhombohedral
trilayer graphene. Nature.
mla: Zhou, Haoxin, et al. “Half and Quarter Metals in Rhombohedral Trilayer Graphene.”
Nature, Springer Nature, 2021, doi:10.1038/s41586-021-03938-w.
short: H. Zhou, T. Xie, A. Ghazaryan, T. Holder, J.R. Ehrets, E.M. Spanton, T. Taniguchi,
K. Watanabe, E. Berg, M. Serbyn, A.F. Young, Nature (2021).
date_created: 2021-09-19T22:01:25Z
date_published: 2021-09-01T00:00:00Z
date_updated: 2023-08-14T07:04:06Z
day: '01'
department:
- _id: MaSe
- _id: MiLe
doi: 10.1038/s41586-021-03938-w
ec_funded: 1
external_id:
arxiv:
- '2104.00653'
isi:
- '000706977400002'
isi: 1
keyword:
- condensed matter - mesoscale and nanoscale physics
- condensed matter - strongly correlated electrons
- multidisciplinary
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/2104.00653
month: '09'
oa: 1
oa_version: Preprint
project:
- _id: 260C2330-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '754411'
name: ISTplus - Postdoctoral Fellowships
publication: Nature
publication_identifier:
eissn:
- 1476-4687
issn:
- 0028-0836
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
related_material:
link:
- relation: erratum
url: https://doi.org/10.1038/s41586-021-04181-z
scopus_import: '1'
status: public
title: Half and quarter metals in rhombohedral trilayer graphene
type: journal_article
user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
year: '2021'
...
---
_id: '10076'
abstract:
- lang: eng
text: We present a novel approach for blockchain asset owners to reclaim their funds
in case of accidental private-key loss or transfer to a mistyped address. Our
solution can be deployed upon failure or absence of proactively implemented backup
mechanisms, such as secret sharing and cold storage. The main advantages against
previous proposals is it does not require any prior action from users and works
with both single-key and multi-sig accounts. We achieve this by a 3-phase Commit()→Reveal()→Claim()−or−Challenge() smart
contract that enables accessing funds of addresses for which the spending key
is not available. We provide an analysis of the threat and incentive models and
formalize the concept of reactive KEy-Loss Protection (KELP).
acknowledgement: The authors would like to thank all anonymous reviewers of FC21 WTSC
workshop for comments and suggestions that greatly improved the quality of this
paper.
alternative_title:
- LNCS
article_processing_charge: No
author:
- first_name: Sam
full_name: Blackshear, Sam
last_name: Blackshear
- first_name: Konstantinos
full_name: Chalkias, Konstantinos
last_name: Chalkias
- first_name: Panagiotis
full_name: Chatzigiannis, Panagiotis
last_name: Chatzigiannis
- first_name: Riyaz
full_name: Faizullabhoy, Riyaz
last_name: Faizullabhoy
- first_name: Irakliy
full_name: Khaburzaniya, Irakliy
last_name: Khaburzaniya
- first_name: Eleftherios
full_name: Kokoris Kogias, Eleftherios
id: f5983044-d7ef-11ea-ac6d-fd1430a26d30
last_name: Kokoris Kogias
- first_name: Joshua
full_name: Lind, Joshua
last_name: Lind
- first_name: David
full_name: Wong, David
last_name: Wong
- first_name: Tim
full_name: Zakian, Tim
last_name: Zakian
citation:
ama: 'Blackshear S, Chalkias K, Chatzigiannis P, et al. Reactive key-loss protection
in blockchains. In: FC 2021 Workshops. Vol 12676. Springer Nature; 2021:431-450.
doi:10.1007/978-3-662-63958-0_34'
apa: 'Blackshear, S., Chalkias, K., Chatzigiannis, P., Faizullabhoy, R., Khaburzaniya,
I., Kokoris Kogias, E., … Zakian, T. (2021). Reactive key-loss protection in blockchains.
In FC 2021 Workshops (Vol. 12676, pp. 431–450). Virtual: Springer Nature.
https://doi.org/10.1007/978-3-662-63958-0_34'
chicago: Blackshear, Sam, Konstantinos Chalkias, Panagiotis Chatzigiannis, Riyaz
Faizullabhoy, Irakliy Khaburzaniya, Eleftherios Kokoris Kogias, Joshua Lind, David
Wong, and Tim Zakian. “Reactive Key-Loss Protection in Blockchains.” In FC
2021 Workshops, 12676:431–50. Springer Nature, 2021. https://doi.org/10.1007/978-3-662-63958-0_34.
ieee: S. Blackshear et al., “Reactive key-loss protection in blockchains,”
in FC 2021 Workshops, Virtual, 2021, vol. 12676, pp. 431–450.
ista: 'Blackshear S, Chalkias K, Chatzigiannis P, Faizullabhoy R, Khaburzaniya I,
Kokoris Kogias E, Lind J, Wong D, Zakian T. 2021. Reactive key-loss protection
in blockchains. FC 2021 Workshops. FC: International Conference on Financial Cryptography
and Data Security, LNCS, vol. 12676, 431–450.'
mla: Blackshear, Sam, et al. “Reactive Key-Loss Protection in Blockchains.” FC
2021 Workshops, vol. 12676, Springer Nature, 2021, pp. 431–50, doi:10.1007/978-3-662-63958-0_34.
short: S. Blackshear, K. Chalkias, P. Chatzigiannis, R. Faizullabhoy, I. Khaburzaniya,
E. Kokoris Kogias, J. Lind, D. Wong, T. Zakian, in:, FC 2021 Workshops, Springer
Nature, 2021, pp. 431–450.
conference:
end_date: 2021-03-05
location: Virtual
name: 'FC: International Conference on Financial Cryptography and Data Security'
start_date: 2021-03-01
date_created: 2021-10-03T22:01:24Z
date_published: 2021-09-17T00:00:00Z
date_updated: 2023-08-14T07:06:16Z
day: '17'
department:
- _id: ElKo
doi: 10.1007/978-3-662-63958-0_34
external_id:
isi:
- '000713005000034'
isi: 1
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://research.fb.com/publications/reactive-key-loss-protection-in-blockchains/
month: '09'
oa: 1
oa_version: Preprint
page: 431-450
publication: FC 2021 Workshops
publication_identifier:
eisbn:
- 978-3-662-63958-0
eissn:
- 1611-3349
isbn:
- 978-3-6626-3957-3
issn:
- 0302-9743
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
scopus_import: '1'
status: public
title: Reactive key-loss protection in blockchains
type: conference
user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
volume: '12676 '
year: '2021'
...
---
_id: '10070'
abstract:
- lang: eng
text: We extensively discuss the Rademacher and Sobolev-to-Lipschitz properties
for generalized intrinsic distances on strongly local Dirichlet spaces possibly
without square field operator. We present many non-smooth and infinite-dimensional
examples. As an application, we prove the integral Varadhan short-time asymptotic
with respect to a given distance function for a large class of strongly local
Dirichlet forms.
acknowledgement: 'The authors are grateful to Professor Kazuhiro Kuwae for kindly
providing a copy of [49]. They are also grateful to Dr. Bang-Xian Han for helpful
discussions on the Sobolev-to-Lipschitz property on metric measure spaces. They
wish to express their deepest gratitude to an anonymous Reviewer, whose punctual
remarks and comments greatly improved the accessibility and overall quality of the
initial submission. This work was completed while L.D.S. was a member of the Institut
für Angewandte Mathematik of the University of Bonn. He acknowledges funding of
his position at that time by the Deutsche Forschungsgemeinschaft (DFG, German Research
Foundation) through the Sonderforschungsbereich (Sfb, Collaborative Research Center)
1060 - project number 211504053. He also acknowledges funding of his current position
by the Austrian Science Fund (FWF) grant F65, and by the European Research Council
(ERC, grant No. 716117, awarded to Prof. Dr. Jan Maas). K.S. gratefully acknowledges
funding by: the JSPS Overseas Research Fellowships, Grant Nr. 290142; World Premier
International Research Center Initiative (WPI), MEXT, Japan; and JSPS Grant-in-Aid
for Scientific Research on Innovative Areas “Discrete Geometric Analysis for Materials
Design”, Grant Number 17H06465.'
article_number: '109234'
article_processing_charge: No
article_type: original
author:
- first_name: Lorenzo
full_name: Dello Schiavo, Lorenzo
id: ECEBF480-9E4F-11EA-B557-B0823DDC885E
last_name: Dello Schiavo
orcid: 0000-0002-9881-6870
- first_name: Kohei
full_name: Suzuki, Kohei
last_name: Suzuki
citation:
ama: Dello Schiavo L, Suzuki K. Rademacher-type theorems and Sobolev-to-Lipschitz
properties for strongly local Dirichlet spaces. Journal of Functional Analysis.
2021;281(11). doi:10.1016/j.jfa.2021.109234
apa: Dello Schiavo, L., & Suzuki, K. (2021). Rademacher-type theorems and Sobolev-to-Lipschitz
properties for strongly local Dirichlet spaces. Journal of Functional Analysis.
Elsevier. https://doi.org/10.1016/j.jfa.2021.109234
chicago: Dello Schiavo, Lorenzo, and Kohei Suzuki. “Rademacher-Type Theorems and
Sobolev-to-Lipschitz Properties for Strongly Local Dirichlet Spaces.” Journal
of Functional Analysis. Elsevier, 2021. https://doi.org/10.1016/j.jfa.2021.109234.
ieee: L. Dello Schiavo and K. Suzuki, “Rademacher-type theorems and Sobolev-to-Lipschitz
properties for strongly local Dirichlet spaces,” Journal of Functional Analysis,
vol. 281, no. 11. Elsevier, 2021.
ista: Dello Schiavo L, Suzuki K. 2021. Rademacher-type theorems and Sobolev-to-Lipschitz
properties for strongly local Dirichlet spaces. Journal of Functional Analysis.
281(11), 109234.
mla: Dello Schiavo, Lorenzo, and Kohei Suzuki. “Rademacher-Type Theorems and Sobolev-to-Lipschitz
Properties for Strongly Local Dirichlet Spaces.” Journal of Functional Analysis,
vol. 281, no. 11, 109234, Elsevier, 2021, doi:10.1016/j.jfa.2021.109234.
short: L. Dello Schiavo, K. Suzuki, Journal of Functional Analysis 281 (2021).
date_created: 2021-10-03T22:01:21Z
date_published: 2021-09-15T00:00:00Z
date_updated: 2023-08-14T07:05:44Z
day: '15'
department:
- _id: JaMa
doi: 10.1016/j.jfa.2021.109234
ec_funded: 1
external_id:
arxiv:
- '2008.01492'
isi:
- '000703896600005'
intvolume: ' 281'
isi: 1
issue: '11'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.48550/arXiv.2008.01492
month: '09'
oa: 1
oa_version: Preprint
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 Functional Analysis
publication_identifier:
eissn:
- 1096-0783
issn:
- 0022-1236
publication_status: published
publisher: Elsevier
quality_controlled: '1'
scopus_import: '1'
status: public
title: Rademacher-type theorems and Sobolev-to-Lipschitz properties for strongly local
Dirichlet spaces
type: journal_article
user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
volume: 281
year: '2021'
...
---
_id: '10123'
abstract:
- lang: eng
text: Solution synthesis of particles emerged as an alternative to prepare thermoelectric
materials with less demanding processing conditions than conventional solid-state
synthetic methods. However, solution synthesis generally involves the presence
of additional molecules or ions belonging to the precursors or added to enable
solubility and/or regulate nucleation and growth. These molecules or ions can
end up in the particles as surface adsorbates and interfere in the material properties.
This work demonstrates that ionic adsorbates, in particular Na⁺ ions, are electrostatically
adsorbed in SnSe particles synthesized in water and play a crucial role not only
in directing the material nano/microstructure but also in determining the transport
properties of the consolidated material. In dense pellets prepared by sintering
SnSe particles, Na remains within the crystal lattice as dopant, in dislocations,
precipitates, and forming grain boundary complexions. These results highlight
the importance of considering all the possible unintentional impurities to establish
proper structure-property relationships and control material properties in solution-processed
thermoelectric materials.
acknowledged_ssus:
- _id: EM-Fac
- _id: NanoFab
acknowledgement: 'Y.L. and M.C. contributed equally to this work. This research was
supported by the Scientific Service Units (SSU) of IST Austria through resources
provided by Electron Microscopy Facility (EMF) and the Nanofabrication Facility
(NNF). This work was financially supported by IST Austria and the Werner Siemens
Foundation. Y.L. acknowledges funding from the European Union''s Horizon 2020 research
and innovation program under the Marie Sklodowska-Curie grant agreement No. 754411.
M.C. has received funding from the European Union''s Horizon 2020 research and innovation
program under the Marie Skłodowska-Curie Grant Agreement No. 665385. Y.Y. and O.C.-M.
acknowledge the financial support from DFG within the project SFB 917: Nanoswitches.
J.L. is a Serra Húnter Fellow and is grateful to ICREA Academia program. C.C. acknowledges
funding from the FWF “Lise Meitner Fellowship” grant agreement M 2889-N.'
article_number: '2106858'
article_processing_charge: Yes (via OA deal)
article_type: original
author:
- first_name: Yu
full_name: Liu, Yu
id: 2A70014E-F248-11E8-B48F-1D18A9856A87
last_name: Liu
orcid: 0000-0001-7313-6740
- first_name: Mariano
full_name: Calcabrini, Mariano
id: 45D7531A-F248-11E8-B48F-1D18A9856A87
last_name: Calcabrini
orcid: 0000-0003-4566-5877
- first_name: Yuan
full_name: Yu, Yuan
last_name: Yu
- first_name: Aziz
full_name: Genç, Aziz
last_name: Genç
- first_name: Cheng
full_name: Chang, Cheng
id: 9E331C2E-9F27-11E9-AE48-5033E6697425
last_name: Chang
orcid: 0000-0002-9515-4277
- first_name: Tommaso
full_name: Costanzo, Tommaso
id: D93824F4-D9BA-11E9-BB12-F207E6697425
last_name: Costanzo
orcid: 0000-0001-9732-3815
- first_name: Tobias
full_name: Kleinhanns, Tobias
id: 8BD9DE16-AB3C-11E9-9C8C-2A03E6697425
last_name: Kleinhanns
- first_name: Seungho
full_name: Lee, Seungho
id: BB243B88-D767-11E9-B658-BC13E6697425
last_name: Lee
orcid: 0000-0002-6962-8598
- first_name: Jordi
full_name: Llorca, Jordi
last_name: Llorca
- first_name: Oana
full_name: Cojocaru‐Mirédin, Oana
last_name: Cojocaru‐Mirédin
- first_name: Maria
full_name: Ibáñez, Maria
id: 43C61214-F248-11E8-B48F-1D18A9856A87
last_name: Ibáñez
orcid: 0000-0001-5013-2843
citation:
ama: 'Liu Y, Calcabrini M, Yu Y, et al. The importance of surface adsorbates in
solution‐processed thermoelectric materials: The case of SnSe. Advanced Materials.
2021;33(52). doi:10.1002/adma.202106858'
apa: 'Liu, Y., Calcabrini, M., Yu, Y., Genç, A., Chang, C., Costanzo, T., … Ibáñez,
M. (2021). The importance of surface adsorbates in solution‐processed thermoelectric
materials: The case of SnSe. Advanced Materials. Wiley. https://doi.org/10.1002/adma.202106858'
chicago: 'Liu, Yu, Mariano Calcabrini, Yuan Yu, Aziz Genç, Cheng Chang, Tommaso
Costanzo, Tobias Kleinhanns, et al. “The Importance of Surface Adsorbates in Solution‐processed
Thermoelectric Materials: The Case of SnSe.” Advanced Materials. Wiley,
2021. https://doi.org/10.1002/adma.202106858.'
ieee: 'Y. Liu et al., “The importance of surface adsorbates in solution‐processed
thermoelectric materials: The case of SnSe,” Advanced Materials, vol. 33,
no. 52. Wiley, 2021.'
ista: 'Liu Y, Calcabrini M, Yu Y, Genç A, Chang C, Costanzo T, Kleinhanns T, Lee
S, Llorca J, Cojocaru‐Mirédin O, Ibáñez M. 2021. The importance of surface adsorbates
in solution‐processed thermoelectric materials: The case of SnSe. Advanced Materials.
33(52), 2106858.'
mla: 'Liu, Yu, et al. “The Importance of Surface Adsorbates in Solution‐processed
Thermoelectric Materials: The Case of SnSe.” Advanced Materials, vol. 33,
no. 52, 2106858, Wiley, 2021, doi:10.1002/adma.202106858.'
short: Y. Liu, M. Calcabrini, Y. Yu, A. Genç, C. Chang, T. Costanzo, T. Kleinhanns,
S. Lee, J. Llorca, O. Cojocaru‐Mirédin, M. Ibáñez, Advanced Materials 33 (2021).
date_created: 2021-10-11T20:07:24Z
date_published: 2021-12-29T00:00:00Z
date_updated: 2023-08-14T07:25:27Z
day: '29'
ddc:
- '620'
department:
- _id: EM-Fac
- _id: MaIb
doi: 10.1002/adma.202106858
ec_funded: 1
external_id:
isi:
- '000709899300001'
pmid:
- '34626034'
file:
- access_level: open_access
checksum: 990bccc527c64d85cf1c97885110b5f4
content_type: application/pdf
creator: cchlebak
date_created: 2022-02-03T13:16:14Z
date_updated: 2022-02-03T13:16:14Z
file_id: '10720'
file_name: 2021_AdvancedMaterials_Liu.pdf
file_size: 5595666
relation: main_file
success: 1
file_date_updated: 2022-02-03T13:16:14Z
has_accepted_license: '1'
intvolume: ' 33'
isi: 1
issue: '52'
keyword:
- mechanical engineering
- mechanics of materials
- general materials science
language:
- iso: eng
month: '12'
oa: 1
oa_version: Published Version
pmid: 1
project:
- _id: 2564DBCA-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '665385'
name: International IST Doctoral Program
- _id: 260C2330-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '754411'
name: ISTplus - Postdoctoral Fellowships
- _id: 9B8804FC-BA93-11EA-9121-9846C619BF3A
grant_number: M02889
name: Bottom-up Engineering for Thermoelectric Applications
- _id: 9B8F7476-BA93-11EA-9121-9846C619BF3A
name: 'HighTE: The Werner Siemens Laboratory for the High Throughput Discovery of
Semiconductors for Waste Heat Recovery'
publication: Advanced Materials
publication_identifier:
eissn:
- 1521-4095
issn:
- 0935-9648
publication_status: published
publisher: Wiley
quality_controlled: '1'
related_material:
record:
- id: '12885'
relation: dissertation_contains
status: public
scopus_import: '1'
status: public
title: 'The importance of surface adsorbates in solution‐processed thermoelectric
materials: The case of SnSe'
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: 33
year: '2021'
...
---
_id: '10117'
abstract:
- lang: eng
text: Proximity labeling provides a powerful in vivo tool to characterize the proteome
of subcellular structures and the interactome of specific proteins. The nematode
Caenorhabditis elegans is one of the most intensely studied organisms in biology,
offering many advantages for biochemistry. Using the highly active biotin ligase
TurboID, we optimize here a proximity labeling protocol for C. elegans. An advantage
of TurboID is that biotin's high affinity for streptavidin means biotin-labeled
proteins can be affinity-purified under harsh denaturing conditions. By combining
extensive sonication with aggressive denaturation using SDS and urea, we achieved
near-complete solubilization of worm proteins. We then used this protocol to characterize
the proteomes of the worm gut, muscle, skin, and nervous system. Neurons are among
the smallest C. elegans cells. To probe the method's sensitivity, we expressed
TurboID exclusively in the two AFD neurons and showed that the protocol could
identify known and previously unknown proteins expressed selectively in AFD. The
active zones of synapses are composed of a protein matrix that is difficult to
solubilize and purify. To test if our protocol could solubilize active zone proteins,
we knocked TurboID into the endogenous elks-1 gene, which encodes a presynaptic
active zone protein. We identified many known ELKS-1-interacting active zone proteins,
as well as previously uncharacterized synaptic proteins. Versatile vectors and
the inherent advantages of using C. elegans, including fast growth and the ability
to rapidly make and functionally test knock-ins, make proximity labeling a valuable
addition to the armory of this model organism.
acknowledgement: We thank de Bono lab members for helpful comments on the manuscript,
IST Austria and University of Vienna Mass Spec Facilities for invaluable discussions
and comments for the optimization of mass spec analyses of worm samples. The biotin
auxotropic E. coli strain MG1655bioB:kan was gift from John Cronan (University of
Illinois) and was kindly sent to us by Jessica Feldman and Ariana Sanchez (Stanford
University). dg398 pEntryslot2_mNeongreen::3XFLAG::stop and dg397 pEntryslot3_mNeongreen::3XFLAG::stop::unc-54
3′UTR entry vector were kindly shared by Dr Dominique Glauser (University of Fribourg).
Codon-optimized mScarlet vector was a generous gift from Dr Manuel Zimmer (University
of Vienna).
article_number: '101094'
article_processing_charge: Yes
article_type: original
author:
- first_name: Murat
full_name: Artan, Murat
id: C407B586-6052-11E9-B3AE-7006E6697425
last_name: Artan
orcid: 0000-0001-8945-6992
- first_name: Stephen
full_name: Barratt, Stephen
id: 57740d2b-2a88-11ec-97cf-d9e6d1b39677
last_name: Barratt
- first_name: Sean M.
full_name: Flynn, Sean M.
last_name: Flynn
- first_name: Farida
full_name: Begum, Farida
last_name: Begum
- first_name: Mark
full_name: Skehel, Mark
last_name: Skehel
- first_name: Armel
full_name: Nicolas, Armel
id: 2A103192-F248-11E8-B48F-1D18A9856A87
last_name: Nicolas
- first_name: Mario
full_name: De Bono, Mario
id: 4E3FF80E-F248-11E8-B48F-1D18A9856A87
last_name: De Bono
orcid: 0000-0001-8347-0443
citation:
ama: Artan M, Barratt S, Flynn SM, et al. Interactome analysis of Caenorhabditis
elegans synapses by TurboID-based proximity labeling. Journal of Biological
Chemistry. 2021;297(3). doi:10.1016/J.JBC.2021.101094
apa: Artan, M., Barratt, S., Flynn, S. M., Begum, F., Skehel, M., Nicolas, A., &
de Bono, M. (2021). Interactome analysis of Caenorhabditis elegans synapses by
TurboID-based proximity labeling. Journal of Biological Chemistry. Elsevier.
https://doi.org/10.1016/J.JBC.2021.101094
chicago: Artan, Murat, Stephen Barratt, Sean M. Flynn, Farida Begum, Mark Skehel,
Armel Nicolas, and Mario de Bono. “Interactome Analysis of Caenorhabditis Elegans
Synapses by TurboID-Based Proximity Labeling.” Journal of Biological Chemistry.
Elsevier, 2021. https://doi.org/10.1016/J.JBC.2021.101094.
ieee: M. Artan et al., “Interactome analysis of Caenorhabditis elegans synapses
by TurboID-based proximity labeling,” Journal of Biological Chemistry,
vol. 297, no. 3. Elsevier, 2021.
ista: Artan M, Barratt S, Flynn SM, Begum F, Skehel M, Nicolas A, de Bono M. 2021.
Interactome analysis of Caenorhabditis elegans synapses by TurboID-based proximity
labeling. Journal of Biological Chemistry. 297(3), 101094.
mla: Artan, Murat, et al. “Interactome Analysis of Caenorhabditis Elegans Synapses
by TurboID-Based Proximity Labeling.” Journal of Biological Chemistry,
vol. 297, no. 3, 101094, Elsevier, 2021, doi:10.1016/J.JBC.2021.101094.
short: M. Artan, S. Barratt, S.M. Flynn, F. Begum, M. Skehel, A. Nicolas, M. de
Bono, Journal of Biological Chemistry 297 (2021).
date_created: 2021-10-10T22:01:23Z
date_published: 2021-09-01T00:00:00Z
date_updated: 2023-08-14T07:24:09Z
day: '01'
ddc:
- '612'
department:
- _id: MaDe
- _id: LifeSc
doi: 10.1016/J.JBC.2021.101094
ec_funded: 1
external_id:
isi:
- '000706409200006'
file:
- access_level: open_access
checksum: 19e39d36c5b9387c6dc0e89c9ae856ab
content_type: application/pdf
creator: cchlebak
date_created: 2021-10-11T12:20:58Z
date_updated: 2021-10-11T12:20:58Z
file_id: '10121'
file_name: 2021_JBC_Artan.pdf
file_size: 1680010
relation: main_file
success: 1
file_date_updated: 2021-10-11T12:20:58Z
has_accepted_license: '1'
intvolume: ' 297'
isi: 1
issue: '3'
language:
- iso: eng
month: '09'
oa: 1
oa_version: Published Version
project:
- _id: 260C2330-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '754411'
name: ISTplus - Postdoctoral Fellowships
publication: Journal of Biological Chemistry
publication_identifier:
eissn:
- 1083-351X
issn:
- 0021-9258
publication_status: published
publisher: Elsevier
quality_controlled: '1'
scopus_import: '1'
status: public
title: Interactome analysis of Caenorhabditis elegans synapses by TurboID-based proximity
labeling
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: 297
year: '2021'
...
---
_id: '10108'
abstract:
- lang: eng
text: We argue that the time is ripe to investigate differential monitoring, in
which the specification of a program's behavior is implicitly given by a second
program implementing the same informal specification. Similar ideas have been
proposed before, and are currently implemented in restricted form for testing
and specialized run-time analyses, aspects of which we combine. We discuss the
challenges of implementing differential monitoring as a general-purpose, black-box
run-time monitoring framework, and present promising results of a preliminary
implementation, showing low monitoring overheads for diverse programs.
acknowledgement: The authors would like to thank Borzoo Bonakdarpour, Derek Dreyer,
Adrian Francalanza, Owolabi Legunsen, Mae Milano, Manuel Rigger, Cesar Sanchez,
and the members of the IST Verification Seminar for their helpful comments and insights
on various stages of this work, as well as the reviewers of RV’21 for their helpful
suggestions on the actual paper.
alternative_title:
- LNCS
article_processing_charge: No
author:
- first_name: Fabian
full_name: Mühlböck, Fabian
id: 6395C5F6-89DF-11E9-9C97-6BDFE5697425
last_name: Mühlböck
orcid: 0000-0003-1548-0177
- first_name: Thomas A
full_name: Henzinger, Thomas A
id: 40876CD8-F248-11E8-B48F-1D18A9856A87
last_name: Henzinger
orcid: 0000-0002-2985-7724
citation:
ama: 'Mühlböck F, Henzinger TA. Differential monitoring. In: International Conference
on Runtime Verification. Vol 12974. Cham: Springer Nature; 2021:231-243. doi:10.1007/978-3-030-88494-9_12'
apa: 'Mühlböck, F., & Henzinger, T. A. (2021). Differential monitoring. In International
Conference on Runtime Verification (Vol. 12974, pp. 231–243). Cham: Springer
Nature. https://doi.org/10.1007/978-3-030-88494-9_12'
chicago: 'Mühlböck, Fabian, and Thomas A Henzinger. “Differential Monitoring.” In
International Conference on Runtime Verification, 12974:231–43. Cham: Springer
Nature, 2021. https://doi.org/10.1007/978-3-030-88494-9_12.'
ieee: F. Mühlböck and T. A. Henzinger, “Differential monitoring,” in International
Conference on Runtime Verification, Virtual, 2021, vol. 12974, pp. 231–243.
ista: 'Mühlböck F, Henzinger TA. 2021. Differential monitoring. International Conference
on Runtime Verification. RV: Runtime Verification, LNCS, vol. 12974, 231–243.'
mla: Mühlböck, Fabian, and Thomas A. Henzinger. “Differential Monitoring.” International
Conference on Runtime Verification, vol. 12974, Springer Nature, 2021, pp.
231–43, doi:10.1007/978-3-030-88494-9_12.
short: F. Mühlböck, T.A. Henzinger, in:, International Conference on Runtime Verification,
Springer Nature, Cham, 2021, pp. 231–243.
conference:
end_date: 2021-10-14
location: Virtual
name: 'RV: Runtime Verification'
start_date: 2021-10-11
date_created: 2021-10-07T23:30:10Z
date_published: 2021-10-06T00:00:00Z
date_updated: 2023-08-14T07:20:30Z
day: '06'
ddc:
- '005'
department:
- _id: ToHe
doi: 10.1007/978-3-030-88494-9_12
external_id:
isi:
- '000719383800012'
file:
- access_level: open_access
checksum: 554c7fdb259eda703a8b6328a6dad55a
content_type: application/pdf
creator: fmuehlbo
date_created: 2021-10-07T23:32:18Z
date_updated: 2021-10-07T23:32:18Z
file_id: '10109'
file_name: differentialmonitoring-cameraready-openaccess.pdf
file_size: 350632
relation: main_file
success: 1
file_date_updated: 2021-10-07T23:32:18Z
has_accepted_license: '1'
intvolume: ' 12974'
isi: 1
keyword:
- run-time verification
- software engineering
- implicit specification
language:
- iso: eng
month: '10'
oa: 1
oa_version: Preprint
page: 231-243
place: Cham
project:
- _id: 25F42A32-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: Z211
name: The Wittgenstein Prize
publication: International Conference on Runtime Verification
publication_identifier:
eisbn:
- 978-3-030-88494-9
eissn:
- 1611-3349
isbn:
- 978-3-030-88493-2
issn:
- 0302-9743
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
related_material:
record:
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relation: extended_version
status: public
scopus_import: '1'
status: public
title: Differential monitoring
type: conference
user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
volume: 12974
year: '2021'
...
---
_id: '10116'
abstract:
- lang: eng
text: The ubiquitous Ca2+ sensor calmodulin (CaM) binds and regulates many proteins,
including ion channels, CaM kinases, and calcineurin, according to Ca2+-CaM levels.
What regulates neuronal CaM levels, is, however, unclear. CaM-binding transcription
activators (CAMTAs) are ancient proteins expressed broadly in nervous systems
and whose loss confers pleiotropic behavioral defects in flies, mice, and humans.
Using Caenorhabditis elegans and Drosophila, we show that CAMTAs control neuronal
CaM levels. The behavioral and neuronal Ca2+ signaling defects in mutants lacking
camt-1, the sole C. elegans CAMTA, can be rescued by supplementing neuronal CaM.
CAMT-1 binds multiple sites in the CaM promoter and deleting these sites phenocopies
camt-1. Our data suggest CAMTAs mediate a conserved and general mechanism that
controls neuronal CaM levels, thereby regulating Ca2+ signaling, physiology, and
behavior.
acknowledgement: The authors thank the MRC-LMB Flow Cytometry facility and Imaging
Service for support, the Cancer Research UK Cambridge Institute Genomics Core for
Next Generation Sequencing, Julie Ahringer and Alex Appert for advice and technical
help for ChIP-seq experiments, Paula Freire-Pritchett, Tim Stevens, and Gurpreet
Ghattaoraya for RNA-seq and ChIP-seq analyses, Nikos Chronis for the TN-XL plasmid,
Hong-Sheng Li and Daisuke Yamamoto for generously sending the tes2 and cro mutants,
Daria Siekhaus for hosting the fly work, Michaela Misova for technical assistance.
The authors are very grateful to Salihah Ece Sönmez for teaching us how to dissect,
mount and stain Drosophila retinae. This work was supported by an Advanced ERC grant
(269058 ACMO) and a Wellcome Investigator Award (209504/Z/17/Z) to MdB, and an IST
Plus Fellowship to TV-B (Marie Sklodowska-Curie Agreement no 754411).
article_number: e68238
article_processing_charge: No
article_type: original
author:
- first_name: Thanh
full_name: Vuong-Brender, Thanh
id: D389312E-10C4-11EA-ABF4-A4B43DDC885E
last_name: Vuong-Brender
- first_name: Sean
full_name: Flynn, Sean
last_name: Flynn
- first_name: Yvonne
full_name: Vallis, Yvonne
id: 05A2795C-31B5-11EA-83A7-7DA23DDC885E
last_name: Vallis
- first_name: Mario
full_name: De Bono, Mario
id: 4E3FF80E-F248-11E8-B48F-1D18A9856A87
last_name: De Bono
orcid: 0000-0001-8347-0443
citation:
ama: Vuong-Brender T, Flynn S, Vallis Y, de Bono M. Neuronal calmodulin levels are
controlled by CAMTA transcription factors. eLife. 2021;10. doi:10.7554/eLife.68238
apa: Vuong-Brender, T., Flynn, S., Vallis, Y., & de Bono, M. (2021). Neuronal
calmodulin levels are controlled by CAMTA transcription factors. ELife.
eLife Sciences Publications. https://doi.org/10.7554/eLife.68238
chicago: Vuong-Brender, Thanh, Sean Flynn, Yvonne Vallis, and Mario de Bono. “Neuronal
Calmodulin Levels Are Controlled by CAMTA Transcription Factors.” ELife.
eLife Sciences Publications, 2021. https://doi.org/10.7554/eLife.68238.
ieee: T. Vuong-Brender, S. Flynn, Y. Vallis, and M. de Bono, “Neuronal calmodulin
levels are controlled by CAMTA transcription factors,” eLife, vol. 10.
eLife Sciences Publications, 2021.
ista: Vuong-Brender T, Flynn S, Vallis Y, de Bono M. 2021. Neuronal calmodulin levels
are controlled by CAMTA transcription factors. eLife. 10, e68238.
mla: Vuong-Brender, Thanh, et al. “Neuronal Calmodulin Levels Are Controlled by
CAMTA Transcription Factors.” ELife, vol. 10, e68238, eLife Sciences Publications,
2021, doi:10.7554/eLife.68238.
short: T. Vuong-Brender, S. Flynn, Y. Vallis, M. de Bono, ELife 10 (2021).
date_created: 2021-10-10T22:01:22Z
date_published: 2021-09-17T00:00:00Z
date_updated: 2023-08-14T07:23:39Z
day: '17'
ddc:
- '610'
department:
- _id: MaDe
doi: 10.7554/eLife.68238
ec_funded: 1
external_id:
isi:
- '000695716100001'
pmid:
- '34499028'
file:
- access_level: open_access
checksum: b465e172d2b1f57aa26a2571a085d052
content_type: application/pdf
creator: cchlebak
date_created: 2021-10-11T14:15:07Z
date_updated: 2021-10-11T14:15:07Z
file_id: '10122'
file_name: 2021_eLife_VuongBrender.pdf
file_size: 1774624
relation: main_file
success: 1
file_date_updated: 2021-10-11T14:15:07Z
has_accepted_license: '1'
intvolume: ' 10'
isi: 1
language:
- iso: eng
month: '09'
oa: 1
oa_version: Published Version
pmid: 1
project:
- _id: 260C2330-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '754411'
name: ISTplus - Postdoctoral Fellowships
publication: eLife
publication_identifier:
eissn:
- 2050-084X
publication_status: published
publisher: eLife Sciences Publications
quality_controlled: '1'
scopus_import: '1'
status: public
title: Neuronal calmodulin levels are controlled by CAMTA transcription factors
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: journal_article
user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
volume: 10
year: '2021'
...
---
_id: '10103'
abstract:
- lang: eng
text: The small cellular molecule inositol hexakisphosphate (IP6) has been known
for ~20 years to promote the in vitro assembly of HIV-1 into immature virus-like
particles. However, the molecular details underlying this effect have been determined
only recently, with the identification of the IP6 binding site in the immature
Gag lattice. IP6 also promotes formation of the mature capsid protein (CA) lattice
via a second IP6 binding site, and enhances core stability, creating a favorable
environment for reverse transcription. IP6 also enhances assembly of other retroviruses,
from both the Lentivirus and the Alpharetrovirus genera. These findings suggest
that IP6 may have a conserved function throughout the family Retroviridae. Here,
we discuss the different steps in the viral life cycle that are influenced by
IP6, and describe in detail how IP6 interacts with the immature and mature lattices
of different retroviruses.
acknowledgement: We thank Volker M. Vogt for his critical comments in preparation
of the review.
article_number: '1853'
article_processing_charge: Yes
article_type: original
author:
- first_name: Martin
full_name: Obr, Martin
id: 4741CA5A-F248-11E8-B48F-1D18A9856A87
last_name: Obr
orcid: 0000-0003-1756-6564
- first_name: Florian KM
full_name: Schur, Florian KM
id: 48AD8942-F248-11E8-B48F-1D18A9856A87
last_name: Schur
orcid: 0000-0003-4790-8078
- first_name: Robert A.
full_name: Dick, Robert A.
last_name: Dick
citation:
ama: Obr M, Schur FK, Dick RA. A structural perspective of the role of IP6 in immature
and mature retroviral assembly. Viruses. 2021;13(9). doi:10.3390/v13091853
apa: Obr, M., Schur, F. K., & Dick, R. A. (2021). A structural perspective of
the role of IP6 in immature and mature retroviral assembly. Viruses. MDPI.
https://doi.org/10.3390/v13091853
chicago: Obr, Martin, Florian KM Schur, and Robert A. Dick. “A Structural Perspective
of the Role of IP6 in Immature and Mature Retroviral Assembly.” Viruses.
MDPI, 2021. https://doi.org/10.3390/v13091853.
ieee: M. Obr, F. K. Schur, and R. A. Dick, “A structural perspective of the role
of IP6 in immature and mature retroviral assembly,” Viruses, vol. 13, no.
9. MDPI, 2021.
ista: Obr M, Schur FK, Dick RA. 2021. A structural perspective of the role of IP6
in immature and mature retroviral assembly. Viruses. 13(9), 1853.
mla: Obr, Martin, et al. “A Structural Perspective of the Role of IP6 in Immature
and Mature Retroviral Assembly.” Viruses, vol. 13, no. 9, 1853, MDPI, 2021,
doi:10.3390/v13091853.
short: M. Obr, F.K. Schur, R.A. Dick, Viruses 13 (2021).
date_created: 2021-10-07T09:13:29Z
date_published: 2021-09-17T00:00:00Z
date_updated: 2023-08-14T07:21:51Z
day: '17'
ddc:
- '616'
department:
- _id: FlSc
doi: 10.3390/v13091853
external_id:
isi:
- '000699841100001'
pmid:
- '34578434'
file:
- access_level: open_access
checksum: bcfd72a12977d48e22df3d0cc55aacf1
content_type: application/pdf
creator: cchlebak
date_created: 2021-10-08T10:38:15Z
date_updated: 2021-10-08T10:38:15Z
file_id: '10115'
file_name: 2021_Viruses_Obr.pdf
file_size: 4146796
relation: main_file
success: 1
file_date_updated: 2021-10-08T10:38:15Z
has_accepted_license: '1'
intvolume: ' 13'
isi: 1
issue: '9'
keyword:
- virology
- infectious diseases
language:
- iso: eng
month: '09'
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: Viruses
publication_identifier:
issn:
- 1999-4915
publication_status: published
publisher: MDPI
quality_controlled: '1'
status: public
title: A structural perspective of the role of IP6 in immature and mature retroviral
assembly
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: '2021'
...
---
_id: '10067'
abstract:
- lang: eng
text: The search for novel entangled phases of matter has lead to the recent discovery
of a new class of “entanglement transitions,” exemplified by random tensor networks
and monitored quantum circuits. Most known examples can be understood as some
classical ordering transitions in an underlying statistical mechanics model, where
entanglement maps onto the free-energy cost of inserting a domain wall. In this
paper we study the possibility of entanglement transitions driven by physics beyond
such statistical mechanics mappings. Motivated by recent applications of neural-network-inspired
variational Ansätze, we investigate under what conditions on the variational parameters
these Ansätze can capture an entanglement transition. We study the entanglement
scaling of short-range restricted Boltzmann machine (RBM) quantum states with
random phases. For uncorrelated random phases, we analytically demonstrate the
absence of an entanglement transition and reveal subtle finite-size effects in
finite-size numerical simulations. Introducing phases with correlations decaying
as 1/r^α in real space, we observe three regions with a different scaling of entanglement
entropy depending on the exponent α. We study the nature of the transition between
these regions, finding numerical evidence for critical behavior. Our work establishes
the presence of long-range correlated phases in RBM-based wave functions as a
required ingredient for entanglement transitions.
acknowledgement: We would like to thank S. De Nicola, P. Brighi, and V. Karle for
fruitful discussions and valuable feedback on the manuscript. R.M. and M.S. acknowledge
support by the European Research Council (ERC) under the European Union's Horizon
2020 research and innovation program (Grant Agreement No. 850899). R.V. acknowledges
support from the US Department of Energy, Office of Science, Basic Energy Sciences,
under Early Career Award No. DE-SC0019168, and the Alfred P. Sloan Foundation through
a Sloan Research Fellowship.
article_number: '104205'
article_processing_charge: No
article_type: original
author:
- first_name: Raimel A
full_name: Medina Ramos, Raimel A
id: CE680B90-D85A-11E9-B684-C920E6697425
last_name: Medina Ramos
orcid: 0000-0002-5383-2869
- first_name: Romain
full_name: Vasseur, Romain
last_name: Vasseur
- first_name: Maksym
full_name: Serbyn, Maksym
id: 47809E7E-F248-11E8-B48F-1D18A9856A87
last_name: Serbyn
orcid: 0000-0002-2399-5827
citation:
ama: Medina Ramos RA, Vasseur R, Serbyn M. Entanglement transitions from restricted
Boltzmann machines. Physical Review B. 2021;104(10). doi:10.1103/physrevb.104.104205
apa: Medina Ramos, R. A., Vasseur, R., & Serbyn, M. (2021). Entanglement transitions
from restricted Boltzmann machines. Physical Review B. American Physical
Society. https://doi.org/10.1103/physrevb.104.104205
chicago: Medina Ramos, Raimel A, Romain Vasseur, and Maksym Serbyn. “Entanglement
Transitions from Restricted Boltzmann Machines.” Physical Review B. American
Physical Society, 2021. https://doi.org/10.1103/physrevb.104.104205.
ieee: R. A. Medina Ramos, R. Vasseur, and M. Serbyn, “Entanglement transitions from
restricted Boltzmann machines,” Physical Review B, vol. 104, no. 10. American
Physical Society, 2021.
ista: Medina Ramos RA, Vasseur R, Serbyn M. 2021. Entanglement transitions from
restricted Boltzmann machines. Physical Review B. 104(10), 104205.
mla: Medina Ramos, Raimel A., et al. “Entanglement Transitions from Restricted Boltzmann
Machines.” Physical Review B, vol. 104, no. 10, 104205, American Physical
Society, 2021, doi:10.1103/physrevb.104.104205.
short: R.A. Medina Ramos, R. Vasseur, M. Serbyn, Physical Review B 104 (2021).
date_created: 2021-10-02T09:03:42Z
date_published: 2021-09-30T00:00:00Z
date_updated: 2023-08-14T07:24:47Z
day: '30'
department:
- _id: MaSe
doi: 10.1103/physrevb.104.104205
ec_funded: 1
external_id:
arxiv:
- '2107.05735'
isi:
- '000704414400002'
intvolume: ' 104'
isi: 1
issue: '10'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/2107.05735
month: '09'
oa: 1
oa_version: Preprint
project:
- _id: 23841C26-32DE-11EA-91FC-C7463DDC885E
call_identifier: H2020
grant_number: '850899'
name: 'Non-Ergodic Quantum Matter: Universality, Dynamics and Control'
publication: Physical Review B
publication_identifier:
eissn:
- 2469-9969
issn:
- 2469-9950
publication_status: published
publisher: American Physical Society
quality_controlled: '1'
status: public
title: Entanglement transitions from restricted Boltzmann machines
type: journal_article
user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
volume: 104
year: '2021'
...
---
_id: '9946'
abstract:
- lang: eng
text: We argue that the time is ripe to investigate differential monitoring, in
which the specification of a program's behavior is implicitly given by a second
program implementing the same informal specification. Similar ideas have been
proposed before, and are currently implemented in restricted form for testing
and specialized run-time analyses, aspects of which we combine. We discuss the
challenges of implementing differential monitoring as a general-purpose, black-box
run-time monitoring framework, and present promising results of a preliminary
implementation, showing low monitoring overheads for diverse programs.
acknowledgement: The authors would like to thank Borzoo Bonakdarpour, Derek Dreyer,
Adrian Francalanza, Owolabi Legunsen, Matthew Milano, Manuel Rigger, Cesar Sanchez,
and the members of the IST Verification Seminar for their helpful comments and insights
on various stages of this work, as well as the reviewers of RV’21 for their helpful
suggestions on the actual paper.
alternative_title:
- IST Austria Technical Report
article_processing_charge: No
author:
- first_name: Fabian
full_name: Mühlböck, Fabian
id: 6395C5F6-89DF-11E9-9C97-6BDFE5697425
last_name: Mühlböck
orcid: 0000-0003-1548-0177
- first_name: Thomas A
full_name: Henzinger, Thomas A
id: 40876CD8-F248-11E8-B48F-1D18A9856A87
last_name: Henzinger
orcid: 0000-0002-2985-7724
citation:
ama: Mühlböck F, Henzinger TA. Differential Monitoring. IST Austria; 2021.
doi:10.15479/AT:ISTA:9946
apa: Mühlböck, F., & Henzinger, T. A. (2021). Differential monitoring.
IST Austria. https://doi.org/10.15479/AT:ISTA:9946
chicago: Mühlböck, Fabian, and Thomas A Henzinger. Differential Monitoring.
IST Austria, 2021. https://doi.org/10.15479/AT:ISTA:9946.
ieee: F. Mühlböck and T. A. Henzinger, Differential monitoring. IST Austria,
2021.
ista: Mühlböck F, Henzinger TA. 2021. Differential monitoring, IST Austria, 17p.
mla: Mühlböck, Fabian, and Thomas A. Henzinger. Differential Monitoring.
IST Austria, 2021, doi:10.15479/AT:ISTA:9946.
short: F. Mühlböck, T.A. Henzinger, Differential Monitoring, IST Austria, 2021.
date_created: 2021-08-20T20:00:37Z
date_published: 2021-09-01T00:00:00Z
date_updated: 2023-08-14T07:20:29Z
day: '01'
ddc:
- '005'
department:
- _id: ToHe
doi: 10.15479/AT:ISTA:9946
file:
- access_level: open_access
checksum: 0f9aafd59444cb6bdca6925d163ab946
content_type: application/pdf
creator: fmuehlbo
date_created: 2021-08-20T19:59:44Z
date_updated: 2021-09-03T12:34:28Z
file_id: '9948'
file_name: differentialmonitoring-techreport.pdf
file_size: '320453'
relation: main_file
file_date_updated: 2021-09-03T12:34:28Z
has_accepted_license: '1'
keyword:
- run-time verification
- software engineering
- implicit specification
language:
- iso: eng
month: '09'
oa: 1
oa_version: Published Version
page: '17'
project:
- _id: 25F42A32-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: Z211
name: The Wittgenstein Prize
publication_identifier:
issn:
- 2664-1690
publication_status: published
publisher: IST Austria
related_material:
record:
- id: '9281'
relation: other
status: public
- id: '10108'
relation: shorter_version
status: public
status: public
title: Differential monitoring
type: technical_report
user_id: 8b945eb4-e2f2-11eb-945a-df72226e66a9
year: '2021'
...
---
_id: '10073'
abstract:
- lang: eng
text: Thermoelectric materials enable the direct conversion between heat and electricity.
SnTe is a promising candidate due to its high charge transport performance. Here,
we prepared SnTe nanocomposites by employing an aqueous method to synthetize SnTe
nanoparticles (NP), followed by a unique surface treatment prior NP consolidation.
This synthetic approach allowed optimizing the charge and phonon transport synergistically.
The novelty of this strategy was the use of a soluble PbS molecular complex prepared
using a thiol-amine solvent mixture that upon blending is adsorbed on the SnTe
NP surface. Upon consolidation with spark plasma sintering, SnTe-PbS nanocomposite
is formed. The presence of PbS complexes significantly compensates for the Sn
vacancy and increases the average grain size of the nanocomposite, thus improving
the carrier mobility. Moreover, lattice thermal conductivity is also reduced by
the Pb and S-induced mass and strain fluctuation. As a result, an enhanced ZT
of ca. 0.8 is reached at 873 K. Our finding provides a novel strategy to conduct
rational surface treatment on NP-based thermoelectrics.
acknowledged_ssus:
- _id: EM-Fac
acknowledgement: "The authors thank the EMF facility in IST Austria for providing
SEM and EDX measurements.\r\n"
article_number: '5416'
article_processing_charge: Yes
article_type: original
author:
- first_name: Cheng
full_name: Chang, Cheng
id: 9E331C2E-9F27-11E9-AE48-5033E6697425
last_name: Chang
orcid: 0000-0002-9515-4277
- first_name: Maria
full_name: Ibáñez, Maria
id: 43C61214-F248-11E8-B48F-1D18A9856A87
last_name: Ibáñez
orcid: 0000-0001-5013-2843
citation:
ama: Chang C, Ibáñez M. Enhanced thermoelectric performance by surface engineering
in SnTe-PbS nanocomposites. Materials. 2021;14(18). doi:10.3390/ma14185416
apa: Chang, C., & Ibáñez, M. (2021). Enhanced thermoelectric performance by
surface engineering in SnTe-PbS nanocomposites. Materials. MDPI. https://doi.org/10.3390/ma14185416
chicago: Chang, Cheng, and Maria Ibáñez. “Enhanced Thermoelectric Performance by
Surface Engineering in SnTe-PbS Nanocomposites.” Materials. MDPI, 2021.
https://doi.org/10.3390/ma14185416.
ieee: C. Chang and M. Ibáñez, “Enhanced thermoelectric performance by surface engineering
in SnTe-PbS nanocomposites,” Materials, vol. 14, no. 18. MDPI, 2021.
ista: Chang C, Ibáñez M. 2021. Enhanced thermoelectric performance by surface engineering
in SnTe-PbS nanocomposites. Materials. 14(18), 5416.
mla: Chang, Cheng, and Maria Ibáñez. “Enhanced Thermoelectric Performance by Surface
Engineering in SnTe-PbS Nanocomposites.” Materials, vol. 14, no. 18, 5416,
MDPI, 2021, doi:10.3390/ma14185416.
short: C. Chang, M. Ibáñez, Materials 14 (2021).
date_created: 2021-10-03T22:01:23Z
date_published: 2021-09-19T00:00:00Z
date_updated: 2023-08-14T08:00:01Z
day: '19'
ddc:
- '540'
department:
- _id: MaIb
doi: 10.3390/ma14185416
external_id:
isi:
- '000700689400001'
pmid:
- '34576640'
file:
- access_level: open_access
checksum: 4929dfc673a3ae77c010b6174279cc1d
content_type: application/pdf
creator: cchlebak
date_created: 2021-10-14T11:56:39Z
date_updated: 2021-10-14T11:56:39Z
file_id: '10140'
file_name: 2021_Materials_Chang.pdf
file_size: 4404141
relation: main_file
success: 1
file_date_updated: 2021-10-14T11:56:39Z
has_accepted_license: '1'
intvolume: ' 14'
isi: 1
issue: '18'
language:
- iso: eng
month: '09'
oa: 1
oa_version: Published Version
pmid: 1
project:
- _id: 9B8804FC-BA93-11EA-9121-9846C619BF3A
grant_number: M02889
name: Bottom-up Engineering for Thermoelectric Applications
publication: Materials
publication_identifier:
eissn:
- 1996-1944
publication_status: published
publisher: MDPI
quality_controlled: '1'
scopus_import: '1'
status: public
title: Enhanced thermoelectric performance by surface engineering in SnTe-PbS nanocomposites
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: journal_article
user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
volume: 14
year: '2021'
...
---
_id: '10167'
abstract:
- lang: eng
text: Schistosomes, the human parasites responsible for snail fever, are female-heterogametic.
Different parts of their ZW sex chromosomes have stopped recombining in distinct
lineages, creating “evolutionary strata” of various ages. Although the Z-chromosome
is well characterized at the genomic and molecular level, the W-chromosome has
remained largely unstudied from an evolutionary perspective, as only a few W-linked
genes have been detected outside of the model species Schistosoma mansoni. Here,
we characterize the gene content and evolution of the W-chromosomes of S. mansoni
and of the divergent species S. japonicum. We use a combined RNA/DNA k-mer based
pipeline to assemble around 100 candidate W-specific transcripts in each of the
species. About half of them map to known protein coding genes, the majority homologous
to S. mansoni Z-linked genes. We perform an extended analysis of the evolutionary
strata present in the two species (including characterizing a previously undetected
young stratum in S. japonicum) to infer patterns of sequence and expression evolution
of W-linked genes at different time points after recombination was lost. W-linked
genes show evidence of degeneration, including high rates of protein evolution
and reduced expression. Most are found in young lineage-specific strata, with
only a few high expression ancestral W-genes remaining, consistent with the progressive
erosion of nonrecombining regions. Among these, the splicing factor u2af2 stands
out as a promising candidate for primary sex determination, opening new avenues
for understanding the molecular basis of the reproductive biology of this group.
acknowledged_ssus:
- _id: ScienComp
acknowledgement: The authors thank IT support at IST Austria for providing an optimal
environment for bioinformatic analyses. This work was supported by an Austrian Science
Foundation FWF grant (Project P28842) to B.V.
article_processing_charge: No
article_type: original
author:
- first_name: Marwan N
full_name: Elkrewi, Marwan N
id: 0B46FACA-A8E1-11E9-9BD3-79D1E5697425
last_name: Elkrewi
orcid: 0000-0002-5328-7231
- first_name: Mikhail A.
full_name: Moldovan, Mikhail A.
id: c8bb7f32-3315-11ec-b58b-e5950e6c14a0
last_name: Moldovan
orcid: 0000-0002-8876-6494
- first_name: Marion A L
full_name: Picard, Marion A L
id: 2C921A7A-F248-11E8-B48F-1D18A9856A87
last_name: Picard
orcid: 0000-0002-8101-2518
- first_name: Beatriz
full_name: Vicoso, Beatriz
id: 49E1C5C6-F248-11E8-B48F-1D18A9856A87
last_name: Vicoso
orcid: 0000-0002-4579-8306
citation:
ama: Elkrewi MN, Moldovan MA, Picard MAL, Vicoso B. Schistosome W-Linked genes inform
temporal dynamics of sex chromosome evolution and suggest candidate for sex determination.
Molecular Biology and Evolution. 2021. doi:10.1093/molbev/msab178
apa: Elkrewi, M. N., Moldovan, M. A., Picard, M. A. L., & Vicoso, B. (2021).
Schistosome W-Linked genes inform temporal dynamics of sex chromosome evolution
and suggest candidate for sex determination. Molecular Biology and Evolution.
Oxford University Press . https://doi.org/10.1093/molbev/msab178
chicago: Elkrewi, Marwan N, Mikhail A. Moldovan, Marion A L Picard, and Beatriz
Vicoso. “Schistosome W-Linked Genes Inform Temporal Dynamics of Sex Chromosome
Evolution and Suggest Candidate for Sex Determination.” Molecular Biology and
Evolution. Oxford University Press , 2021. https://doi.org/10.1093/molbev/msab178.
ieee: M. N. Elkrewi, M. A. Moldovan, M. A. L. Picard, and B. Vicoso, “Schistosome
W-Linked genes inform temporal dynamics of sex chromosome evolution and suggest
candidate for sex determination,” Molecular Biology and Evolution. Oxford
University Press , 2021.
ista: Elkrewi MN, Moldovan MA, Picard MAL, Vicoso B. 2021. Schistosome W-Linked
genes inform temporal dynamics of sex chromosome evolution and suggest candidate
for sex determination. Molecular Biology and Evolution.
mla: Elkrewi, Marwan N., et al. “Schistosome W-Linked Genes Inform Temporal Dynamics
of Sex Chromosome Evolution and Suggest Candidate for Sex Determination.” Molecular
Biology and Evolution, Oxford University Press , 2021, doi:10.1093/molbev/msab178.
short: M.N. Elkrewi, M.A. Moldovan, M.A.L. Picard, B. Vicoso, Molecular Biology
and Evolution (2021).
date_created: 2021-10-21T07:49:12Z
date_published: 2021-06-19T00:00:00Z
date_updated: 2023-08-14T08:03:06Z
day: '19'
ddc:
- '610'
department:
- _id: BeVi
doi: 10.1093/molbev/msab178
external_id:
isi:
- '000741368600009'
pmid:
- '34146097'
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checksum: 1b096702fb356d9c0eb88e1b3fcff5f8
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creator: dernst
date_created: 2022-05-06T09:47:18Z
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file_size: 1008594
relation: main_file
success: 1
file_date_updated: 2022-05-06T09:47:18Z
has_accepted_license: '1'
isi: 1
keyword:
- sex chromosomes
- evolutionary strata
- W-linked gene
- sex determining gene
- schistosome parasites
language:
- iso: eng
month: '06'
oa: 1
oa_version: Published Version
pmid: 1
project:
- _id: 250ED89C-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: P28842-B22
name: Sex chromosome evolution under male- and female- heterogamety
publication: Molecular Biology and Evolution
publication_identifier:
eissn:
- 1537-1719
issn:
- 0737-4038
publication_status: published
publisher: 'Oxford University Press '
quality_controlled: '1'
scopus_import: '1'
status: public
title: Schistosome W-Linked genes inform temporal dynamics of sex chromosome evolution
and suggest candidate for sex determination
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
year: '2021'
...
---
_id: '10163'
abstract:
- lang: eng
text: The C-terminal domain (CTD) of the largest subunit of RNA polymerase II (Pol
II) is a regulatory hub for transcription and RNA processing. Here, we identify
PHD-finger protein 3 (PHF3) as a regulator of transcription and mRNA stability
that docks onto Pol II CTD through its SPOC domain. We characterize SPOC as a
CTD reader domain that preferentially binds two phosphorylated Serine-2 marks
in adjacent CTD repeats. PHF3 drives liquid-liquid phase separation of phosphorylated
Pol II, colocalizes with Pol II clusters and tracks with Pol II across the length
of genes. PHF3 knock-out or SPOC deletion in human cells results in increased
Pol II stalling, reduced elongation rate and an increase in mRNA stability, with
marked derepression of neuronal genes. Key neuronal genes are aberrantly expressed
in Phf3 knock-out mouse embryonic stem cells, resulting in impaired neuronal differentiation.
Our data suggest that PHF3 acts as a prominent effector of neuronal gene regulation
by bridging transcription with mRNA decay.
acknowledgement: 'D.S. thanks Claudine Kraft, Renée Schroeder, Verena Jantsch, Franz
Klein and Peter Schlögelhofer for support. We thank Anita Testa Salmazo for help
with purifying Pol II; Matthias Geyer and Robert Düster for sharing DYRK1A kinase;
Felix Hartmann and Clemens Plaschka for help with mass photometry; Goran Kokic for
design of the arrest assay sequences; Petra van der Lelij for help with generating
mESC KO; Maximilian Freilinger for help with the purification of mEGFP-CTD; Stefan
Ameres, Nina Fasching and Brian Reichholf for advice on SLAM-seq and for sharing
reagents; Laura Gallego Valle for advice regarding LLPS assays; Krzysztof Chylinski
for advice regarding CRISPR/Cas9 methodology; VBCF Protein Technologies facility
for purifying PHF3 and providing gRNAs and Cas9; VBCF NGS facility for sequencing;
Monoclonal antibody facility at the Helmholtz center for Pol II antibodies; Friedrich
Propst and Elzbieta Kowalska for advice and for sharing materials; Egon Ogris for
sharing materials; Martin Eilers for recommending a ChIP-grade TFIIS antibody; Susanne
Opravil, Otto Hudecz, Markus Hartl and Natascha Hartl for mass spectrometry analysis;
staff of the X-ray beamlines at the ESRF in Grenoble for their excellent support;
Christa Bücker, Anton Meinhart, Clemens Plaschka and members of the Slade lab for
critical comments on the manuscript; Life Science Editors for editing assistance.
M.B. and D.S. acknowledge support by the FWF-funded DK ‘Chromosome Dynamics’. T.K.
is a recipient of the DOC fellowship from the Austrian Academy of Sciences. U.S.
is supported by the L’Oreal for Women in Science Austria Fellowship and the Austrian
Science Fund (FWF T 795-B30). M.L is supported by the Vienna Science and Technology
Fund (WWTF, VRG14-006). R.S. is supported by the Czech Science Foundation (15-17670 S
and 21-24460 S), Ministry of Education, Youths and Sports of the Czech Republic
(CEITEC 2020 project (LQ1601)), and the European Research Council (ERC) under the
European Union’s Horizon 2020 research and innovation programme (Grant agreement
no. 649030); this publication reflects only the author’s view and the Research Executive
Agency is not responsible for any use that may be made of the information it contains.
M.S. is supported by the Czech Science Foundation (GJ20-21581Y). K.D.C. research
is supported by the Austrian Science Fund (FWF) Projects I525 and I1593, P22276,
P19060, and W1221, Federal Ministry of Economy, Family and Youth through the initiative
‘Laura Bassi Centres of Expertise’, funding from the Centre of Optimized Structural
Studies No. 253275, the Wellcome Trust Collaborative Award (201543/Z/16), COST action
BM1405 Non-globular proteins - from sequence to structure, function and application
in molecular physiopathology (NGP-NET), the Vienna Science and Technology Fund (WWTF
LS17-008), and by the University of Vienna. This project was funded by the MFPL
start-up grant, the Vienna Science and Technology Fund (WWTF LS14-001), and the
Austrian Science Fund (P31546-B28 and W1258 “DK: Integrative Structural Biology”)
to D.S.'
article_number: '6078'
article_processing_charge: No
article_type: original
author:
- first_name: Lisa-Marie
full_name: Appel, Lisa-Marie
last_name: Appel
- first_name: Vedran
full_name: Franke, Vedran
last_name: Franke
- first_name: Melania
full_name: Bruno, Melania
last_name: Bruno
- first_name: Irina
full_name: Grishkovskaya, Irina
last_name: Grishkovskaya
- first_name: Aiste
full_name: Kasiliauskaite, Aiste
last_name: Kasiliauskaite
- first_name: Tanja
full_name: Kaufmann, Tanja
last_name: Kaufmann
- first_name: Ursula E.
full_name: Schoeberl, Ursula E.
last_name: Schoeberl
- first_name: Martin G.
full_name: Puchinger, Martin G.
last_name: Puchinger
- first_name: Sebastian
full_name: Kostrhon, Sebastian
last_name: Kostrhon
- first_name: Carmen
full_name: Ebenwaldner, Carmen
last_name: Ebenwaldner
- first_name: Marek
full_name: Sebesta, Marek
last_name: Sebesta
- first_name: Etienne
full_name: Beltzung, Etienne
last_name: Beltzung
- first_name: Karl
full_name: Mechtler, Karl
last_name: Mechtler
- first_name: Gen
full_name: Lin, Gen
last_name: Lin
- first_name: Anna
full_name: Vlasova, Anna
last_name: Vlasova
- first_name: Martin
full_name: Leeb, Martin
last_name: Leeb
- first_name: Rushad
full_name: Pavri, Rushad
last_name: Pavri
- first_name: Alexander
full_name: Stark, Alexander
last_name: Stark
- first_name: Altuna
full_name: Akalin, Altuna
last_name: Akalin
- first_name: Richard
full_name: Stefl, Richard
last_name: Stefl
- first_name: Carrie A
full_name: Bernecky, Carrie A
id: 2CB9DFE2-F248-11E8-B48F-1D18A9856A87
last_name: Bernecky
orcid: 0000-0003-0893-7036
- first_name: Kristina
full_name: Djinovic-Carugo, Kristina
last_name: Djinovic-Carugo
- first_name: Dea
full_name: Slade, Dea
last_name: Slade
citation:
ama: Appel L-M, Franke V, Bruno M, et al. PHF3 regulates neuronal gene expression
through the Pol II CTD reader domain SPOC. Nature Communications. 2021;12(1).
doi:10.1038/s41467-021-26360-2
apa: Appel, L.-M., Franke, V., Bruno, M., Grishkovskaya, I., Kasiliauskaite, A.,
Kaufmann, T., … Slade, D. (2021). PHF3 regulates neuronal gene expression through
the Pol II CTD reader domain SPOC. Nature Communications. Springer Nature.
https://doi.org/10.1038/s41467-021-26360-2
chicago: Appel, Lisa-Marie, Vedran Franke, Melania Bruno, Irina Grishkovskaya, Aiste
Kasiliauskaite, Tanja Kaufmann, Ursula E. Schoeberl, et al. “PHF3 Regulates Neuronal
Gene Expression through the Pol II CTD Reader Domain SPOC.” Nature Communications.
Springer Nature, 2021. https://doi.org/10.1038/s41467-021-26360-2.
ieee: L.-M. Appel et al., “PHF3 regulates neuronal gene expression through
the Pol II CTD reader domain SPOC,” Nature Communications, vol. 12, no.
1. Springer Nature, 2021.
ista: Appel L-M, Franke V, Bruno M, Grishkovskaya I, Kasiliauskaite A, Kaufmann
T, Schoeberl UE, Puchinger MG, Kostrhon S, Ebenwaldner C, Sebesta M, Beltzung
E, Mechtler K, Lin G, Vlasova A, Leeb M, Pavri R, Stark A, Akalin A, Stefl R,
Bernecky C, Djinovic-Carugo K, Slade D. 2021. PHF3 regulates neuronal gene expression
through the Pol II CTD reader domain SPOC. Nature Communications. 12(1), 6078.
mla: Appel, Lisa-Marie, et al. “PHF3 Regulates Neuronal Gene Expression through
the Pol II CTD Reader Domain SPOC.” Nature Communications, vol. 12, no.
1, 6078, Springer Nature, 2021, doi:10.1038/s41467-021-26360-2.
short: L.-M. Appel, V. Franke, M. Bruno, I. Grishkovskaya, A. Kasiliauskaite, T.
Kaufmann, U.E. Schoeberl, M.G. Puchinger, S. Kostrhon, C. Ebenwaldner, M. Sebesta,
E. Beltzung, K. Mechtler, G. Lin, A. Vlasova, M. Leeb, R. Pavri, A. Stark, A.
Akalin, R. Stefl, C. Bernecky, K. Djinovic-Carugo, D. Slade, Nature Communications
12 (2021).
date_created: 2021-10-20T14:40:32Z
date_published: 2021-10-19T00:00:00Z
date_updated: 2023-08-14T08:02:31Z
day: '19'
ddc:
- '610'
department:
- _id: CaBe
doi: 10.1038/s41467-021-26360-2
external_id:
isi:
- '000709050300001'
file:
- access_level: open_access
checksum: d99fcd51aebde19c21314e3de0148007
content_type: application/pdf
creator: cchlebak
date_created: 2021-10-21T13:51:49Z
date_updated: 2021-10-21T13:51:49Z
file_id: '10169'
file_name: 2021_NatComm_Appel.pdf
file_size: 5111706
relation: main_file
success: 1
file_date_updated: 2021-10-21T13:51:49Z
has_accepted_license: '1'
intvolume: ' 12'
isi: 1
issue: '1'
keyword:
- general physics and astronomy
- general biochemistry
- genetics and molecular biology
- general chemistry
language:
- iso: eng
month: '10'
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:
- description: 'Preprint '
relation: earlier_version
url: https://www.biorxiv.org/content/10.1101/2020.02.11.943159
status: public
title: PHF3 regulates neuronal gene expression through the Pol II CTD reader domain
SPOC
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: 12
year: '2021'
...